Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015754.1 Corchorus capsularis cultivar CVL-1 contig15775, 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: 26416
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34
Found at i:3225 original size:26 final size:26
Alignment explanation
Indices: 3196--3259 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
3186 TAGTTTATTG
*
3196 GTTTATGTTTAATTGGTATCTAATTA
1 GTTTATGTTTAATTAGTATCTAATTA
*
3222 GTTTAT-TATTAATTAGTATTTAATTA
1 GTTTATGT-TTAATTAGTATCTAATTA
*
3248 GTTTATGATTAA
1 GTTTATGTTTAA
3260 AATGAAGGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 1 0.03
26 32 0.97
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.55
Consensus pattern (26 bp):
GTTTATGTTTAATTAGTATCTAATTA
Found at i:3236 original size:15 final size:15
Alignment explanation
Indices: 3216--3259 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
3206 AATTGGTATC
3216 TAATTAGTTTATTAT
1 TAATTAGTTTATTAT
3231 TAATTAG--TA-T-T
1 TAATTAGTTTATTAT
*
3242 TAATTAGTTTATGAT
1 TAATTAGTTTATTAT
3257 TAA
1 TAA
3260 AATGAAGGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 8
0.73 0.03 0.24
Matches are distributed among these distances:
11 8 0.33
12 1 0.04
13 4 0.17
15 11 0.46
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (15 bp):
TAATTAGTTTATTAT
Found at i:3307 original size:24 final size:25
Alignment explanation
Indices: 3268--3327 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
3258 AAAATGAAGG
*
3268 AAAATGAA-TTTGAAG-ATTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
3291 AAAATGAAGTTTGAAGAAGTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
*
3316 GAAATGAAGTTT
1 AAAATGAAGTTT
3328 AGGGTTTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
23 8 0.24
24 7 0.21
25 18 0.55
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (25 bp):
AAAATGAAGTTTGAAGAAGTTGTTA
Found at i:3595 original size:113 final size:113
Alignment explanation
Indices: 3469--3758 Score: 472
Period size: 113 Copynumber: 2.6 Consensus size: 113
3459 TTGGCAAAAG
3469 ACACCGCTAAATGGTGGCGTCTGAAGTACAAAACGCCGCCATATTTATTTTTTTCGGATAAATGT
1 ACACCGCTAAATGGTGGCGTCTGAAGTACAAAACGCCGCCATATTTATTTTTTTCGGATAAATGT
3534 AAATTGAGTAAAAATGAAGTCTAAAAAATAGCAGCATCTTGACCCTAA
66 AAATTGAGTAAAAATGAAGTCTAAAAAATAGCAGCATCTTGACCCTAA
*
3582 ACACCGCTAAATGGTGGCGTCTGAAGTACAAAACGCCGCCATATTTATTCTTTTCGGATAAATGT
1 ACACCGCTAAATGGTGGCGTCTGAAGTACAAAACGCCGCCATATTTATTTTTTTCGGATAAATGT
* * *
3647 AAATTGAGTAAAACTGAAGTCTAAAAAATAGCGGCGTCTTGACCCTAA
66 AAATTGAGTAAAAATGAAGTCTAAAAAATAGCAGCATCTTGACCCTAA
* * * * ** * *
3695 ACGCCGCTAAATGGTGGCGTCTGAGGCACGAAACGCCGCCATACGTAATTTTTTCGGAGAAATG
1 ACACCGCTAAATGGTGGCGTCTGAAGTACAAAACGCCGCCATATTTATTTTTTTCGGATAAATG
3759 CAATAAAACC
Statistics
Matches: 164, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
113 164 1.00
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.26
Consensus pattern (113 bp):
ACACCGCTAAATGGTGGCGTCTGAAGTACAAAACGCCGCCATATTTATTTTTTTCGGATAAATGT
AAATTGAGTAAAAATGAAGTCTAAAAAATAGCAGCATCTTGACCCTAA
Found at i:3868 original size:32 final size:33
Alignment explanation
Indices: 3804--3881 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 33
3794 ACGTCTAGAC
*
3804 ATAGTGGCGTCT-A-GACACTAAACACCGTTAA
1 ATAGTGGCGTCTAAGGACACTAAACACCGCTAA
* *
3835 ATAGTGGCGTCTAAGGTC-CTAAACGCCGCTAA
1 ATAGTGGCGTCTAAGGACACTAAACACCGCTAA
* *
3867 ATGGTGGCATCTAAG
1 ATAGTGGCGTCTAAG
3882 TTTCAAGACA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
31 12 0.30
32 26 0.65
33 2 0.05
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.23
Consensus pattern (33 bp):
ATAGTGGCGTCTAAGGACACTAAACACCGCTAA
Found at i:5615 original size:27 final size:27
Alignment explanation
Indices: 5585--5662 Score: 111
Period size: 27 Copynumber: 2.9 Consensus size: 27
5575 ATTAGGGTCG
* * *
5585 CCCAAGGGTATTTTGGTCATTTTTTCA
1 CCCAGGGGCATTTTGGTCATTTTTGCA
5612 CCCAGGGGCATTTTGGTCATTTTTGCA
1 CCCAGGGGCATTTTGGTCATTTTTGCA
* *
5639 CTCAGGGGCATTTTAGTCATTTTT
1 CCCAGGGGCATTTTGGTCATTTTT
5663 AAGTTCACCT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (27 bp):
CCCAGGGGCATTTTGGTCATTTTTGCA
Found at i:7124 original size:61 final size:63
Alignment explanation
Indices: 7053--7172 Score: 199
Period size: 61 Copynumber: 1.9 Consensus size: 63
7043 GCATCCACAT
*
7053 TAAGCAACATTTAGTCACAGTCTCAATTCAATAAGAATC-A-ATACACTAGCACACACTATAC
1 TAAGCAACATTTAGTCACAGTCTCAATTCAATAAGAATCAACACACACTAGCACACACTATAC
**
7114 TAAGCAACATTTAGTCACAGTCTCAATTCAATAAGGGTCAACACACACTAGCACACACT
1 TAAGCAACATTTAGTCACAGTCTCAATTCAATAAGAATCAACACACACTAGCACACACT
7173 GCACCCAATC
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
61 37 0.69
62 1 0.02
63 16 0.30
ACGTcount: A:0.41, C:0.26, G:0.10, T:0.23
Consensus pattern (63 bp):
TAAGCAACATTTAGTCACAGTCTCAATTCAATAAGAATCAACACACACTAGCACACACTATAC
Found at i:9439 original size:38 final size:38
Alignment explanation
Indices: 9379--9660 Score: 223
Period size: 38 Copynumber: 7.3 Consensus size: 38
9369 ACCCCAATAA
*
9379 AATTAAGAGTCAAAGTAATAGTAATCAGTGAATTAAGT
1 AATTAAGAATCAAAGTAATAGTAATCAGTGAATTAAGT
* * * *
9417 AATTGAGAATCAAAGTAATAGTAATCAGTAAAATCAA-A
1 AATTAAGAATCAAAGTAATAGTAATCAGT-GAATTAAGT
*
9455 AATTAAGAGTCAAAGTAATAGTAATCAGTGAATTAAGT
1 AATTAAGAATCAAAGTAATAGTAATCAGTGAATTAAGT
* * * *
9493 AATTGAGAATCAAAGTAATAGTAATCAGTAAAAT-CGAT
1 AATTAAGAATCAAAGTAATAGTAATCAGTGAATTAAG-T
** * * * *
9531 AATTAAGGGTCAAAGTGATAGTAATCAGTAAAAT-CGAT
1 AATTAAGAATCAAAGTAATAGTAATCAGTGAATTAAG-T
* ** *
9569 AATCAAGGGTCAAAGTAATAGTAATCAGTAAAATTAA-T
1 AATTAAGAATCAAAGTAATAGTAATCAGT-GAATTAAGT
* * * * *
9607 AATGAAGAGTCAAGGTAAAAATAGTAATCAGTAAATCAA-T
1 AATTAAGAATCAAAGT---AATAGTAATCAGTGAATTAAGT
*
9647 AAATTAAGAGTCAA
1 -AATTAAGAATCAA
9661 GGGATTAATC
Statistics
Matches: 207, Mismatches: 28, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
37 6 0.03
38 160 0.77
39 9 0.04
40 7 0.03
41 25 0.12
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.26
Consensus pattern (38 bp):
AATTAAGAATCAAAGTAATAGTAATCAGTGAATTAAGT
Found at i:9503 original size:76 final size:76
Alignment explanation
Indices: 9377--9638 Score: 346
Period size: 76 Copynumber: 3.4 Consensus size: 76
9367 GTACCCCAAT
9377 AAAATTAAGAGTCAAAGTAATAGTAATCAGTGAATTAAGTAATTGAGAATCAAAGTAATAGTAAT
1 AAAATTAAGAGTCAAAGTAATAGTAATCAGTGAATTAAGTAATTGAGAATCAAAGTAATAGTAAT
9442 CAGTAAAATCA
66 CAGTAAAATCA
9453 AAAATTAAGAGTCAAAGTAATAGTAATCAGTGAATTAAGTAATTGAGAATCAAAGTAATAGTAAT
1 AAAATTAAGAGTCAAAGTAATAGTAATCAGTGAATTAAGTAATTGAGAATCAAAGTAATAGTAAT
*
9518 CAGTAAAATCG
66 CAGTAAAATCA
* * * * * * ** **
9529 ATAATTAAGGGTCAAAGTGATAGTAATCAGTAAAAT-CGATAATCAAGGGTCAAAGTAATAGTAA
1 AAAATTAAGAGTCAAAGTAATAGTAATCAGTGAATTAAG-TAATTGAGAATCAAAGTAATAGTAA
*
9593 TCAGTAAAATTA
65 TCAGTAAAATCA
* * *
9605 ATAATGAAGAGTCAAGGTAAAAATAGTAATCAGT
1 AAAATTAAGAGTCAAAGT---AATAGTAATCAGT
9639 AAATCAATAA
Statistics
Matches: 165, Mismatches: 17, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
75 1 0.01
76 152 0.92
79 12 0.07
ACGTcount: A:0.50, C:0.07, G:0.18, T:0.26
Consensus pattern (76 bp):
AAAATTAAGAGTCAAAGTAATAGTAATCAGTGAATTAAGTAATTGAGAATCAAAGTAATAGTAAT
CAGTAAAATCA
Found at i:9569 original size:19 final size:19
Alignment explanation
Indices: 9510--9569 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
9500 AATCAAAGTA
9510 ATAGTAATCAGTAAAATCG
1 ATAGTAATCAGTAAAATCG
* ** *
9529 ATAATTAA-GGGTCAAAGT-G
1 AT-AGTAATCAGT-AAAATCG
9548 ATAGTAATCAGTAAAATCG
1 ATAGTAATCAGTAAAATCG
9567 ATA
1 ATA
9570 ATCAAGGGTC
Statistics
Matches: 29, Mismatches: 8, Indels: 8
0.64 0.18 0.18
Matches are distributed among these distances:
18 8 0.28
19 13 0.45
20 8 0.28
ACGTcount: A:0.47, C:0.08, G:0.18, T:0.27
Consensus pattern (19 bp):
ATAGTAATCAGTAAAATCG
Found at i:9588 original size:114 final size:113
Alignment explanation
Indices: 9379--9676 Score: 345
Period size: 114 Copynumber: 2.6 Consensus size: 113
9369 ACCCCAATAA
* * * * * *
9379 AATTAAGAGTCAAAGTAATAGTAATCAGTGAATTAAGTAATTGAGAATCAAAGTAATAGTAATCA
1 AATTGAGAGTCAAAGTAATAGTAATCAGTAAATCAA-TAATTAAGAGTCAAAGTGATAGTAATCA
* *
9444 GTAAAATCAAAAATTAAGAGTCAAAGTAATAGTAATCAGT-GAATTAAGT
65 GTAAAATCAAAAATCAAGAGTCAAAGTAATAGTAATCAGTAAAATTAA-T
* * *
9493 AATTGAGAATCAAAGTAATAGTAATCAGTAAAATCGATAATTAAGGGTCAAAGTGATAGTAATCA
1 AATTGAGAGTCAAAGTAATAGTAATCAGT-AAATCAATAATTAAGAGTCAAAGTGATAGTAATCA
* * *
9558 GTAAAATCGATAATCAAGGGTCAAAGTAATAGTAATCAGTAAAATTAAT
65 GTAAAATCAAAAATCAAGAGTCAAAGTAATAGTAATCAGTAAAATTAAT
* *
9607 AA-TGAAGAGTCAAGGTAAAAATAGTAATCAGTAAATCAATAAATTAAGAGTC-AAGGGAT--TA
1 AATTG-AGAGTCAAAGT---AATAGTAATCAGTAAATCAAT-AATTAAGAGTCAAAGTGATAGTA
9668 ATCAGTAAA
61 ATCAGTAAA
9677 TTGGTACTTA
Statistics
Matches: 158, Mismatches: 19, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
113 2 0.01
114 110 0.70
115 10 0.06
116 13 0.08
117 23 0.15
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.26
Consensus pattern (113 bp):
AATTGAGAGTCAAAGTAATAGTAATCAGTAAATCAATAATTAAGAGTCAAAGTGATAGTAATCAG
TAAAATCAAAAATCAAGAGTCAAAGTAATAGTAATCAGTAAAATTAAT
Found at i:9640 original size:41 final size:41
Alignment explanation
Indices: 9585--9662 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
9575 GGGTCAAAGT
*
9585 AATAGTAATCAGTAAAATTAAT-AATGAAGAGTCAAGGTAAA
1 AATAGTAATCAGT-AAATCAATAAATGAAGAGTCAAGGTAAA
*
9626 AATAGTAATCAGTAAATCAATAAATTAAGAGTCAAGG
1 AATAGTAATCAGTAAATCAATAAATGAAGAGTCAAGG
9663 GATTAATCAG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 7 0.21
41 27 0.79
ACGTcount: A:0.53, C:0.06, G:0.17, T:0.24
Consensus pattern (41 bp):
AATAGTAATCAGTAAATCAATAAATGAAGAGTCAAGGTAAA
Found at i:9804 original size:14 final size:15
Alignment explanation
Indices: 9787--9826 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
9777 AATGGTAAAG
9787 AGTAAAGAA-TAATC
1 AGTAAAGAAGTAATC
*
9801 AGT-AAGAAGTAATT
1 AGTAAAGAAGTAATC
9815 AGTAAAG-AGTAA
1 AGTAAAGAAGTAA
9827 AATGATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 5 0.22
14 15 0.65
15 3 0.13
ACGTcount: A:0.55, C:0.03, G:0.20, T:0.23
Consensus pattern (15 bp):
AGTAAAGAAGTAATC
Found at i:9855 original size:20 final size:20
Alignment explanation
Indices: 9827--9864 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
9817 TAAAGAGTAA
9827 AATGATAAAAAGTAAAGAAT
1 AATGATAAAAAGTAAAGAAT
*
9847 AATGGTAAAAAGTAAAGA
1 AATGATAAAAAGTAAAGA
9865 GTAAAATAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.18, T:0.18
Consensus pattern (20 bp):
AATGATAAAAAGTAAAGAAT
Found at i:9876 original size:50 final size:50
Alignment explanation
Indices: 9775--9878 Score: 129
Period size: 50 Copynumber: 2.1 Consensus size: 50
9765 AGTAAAAGGA
* * * **
9775 AAAATGGTAAAGAGTAAAGAATAATCAGTAAGAAGTAATTAGTAAAGAGT
1 AAAATGATAAAAAGTAAAGAATAATCAGTAAAAAGTAAAGAGTAAAGAGT
* *
9825 AAAATGATAAAAAGTAAAGAATAAT-GGTAAAAAGTAAAGAGTAAAATAGT
1 AAAATGATAAAAAGTAAAGAATAATCAGTAAAAAGTAAAGAGT-AAAGAGT
9875 AAAA
1 AAAA
9879 GGTAATCAGT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
49 13 0.28
50 33 0.72
ACGTcount: A:0.60, C:0.01, G:0.19, T:0.20
Consensus pattern (50 bp):
AAAATGATAAAAAGTAAAGAATAATCAGTAAAAAGTAAAGAGTAAAGAGT
Found at i:9883 original size:22 final size:21
Alignment explanation
Indices: 9815--9892 Score: 79
Period size: 22 Copynumber: 3.7 Consensus size: 21
9805 AGAAGTAATT
9815 AGTAAAGAGTAAAATGATAAAA
1 AGTAAAGAGTAAAATG-TAAAA
*
9837 AGTAAAGA--ATAATGGTAAAA
1 AGTAAAGAGTAAAAT-GTAAAA
9857 AGTAAAGAGTAAAATAGTAAAA
1 AGTAAAGAGTAAAAT-GTAAAA
* **
9879 GGTAATCAGTAAAA
1 AGTAAAGAGTAAAA
9893 AAAGGGGTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
20 17 0.36
21 1 0.02
22 29 0.62
ACGTcount: A:0.60, C:0.01, G:0.19, T:0.19
Consensus pattern (21 bp):
AGTAAAGAGTAAAATGTAAAA
Found at i:9955 original size:36 final size:37
Alignment explanation
Indices: 9913--10016 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 37
9903 AAGGTAATGA
*
9913 TAATCAGTAAAGAGTAAAATAGTAACCA-TTAAAAGG
1 TAATCAGTAAAGAGTAAAATAGTAACCAGTAAAAAGG
*
9949 TAATCAGTAAAGAGTAAAATAGTAATCAGTAAAAAGG
1 TAATCAGTAAAGAGTAAAATAGTAACCAGTAAAAAGG
*
9986 TAATCAGT-AAGAGTAAAATAGTGACCAGTAA
1 TAATCAGTAAAGAGTAAAATAGTAACCAGTAA
10017 GAGCAAAATG
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
36 48 0.76
37 15 0.24
ACGTcount: A:0.52, C:0.08, G:0.18, T:0.22
Consensus pattern (37 bp):
TAATCAGTAAAGAGTAAAATAGTAACCAGTAAAAAGG
Found at i:9979 original size:15 final size:15
Alignment explanation
Indices: 9961--9995 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
9951 ATCAGTAAAG
9961 AGTAAAATA-GTAATC
1 AGTAAAA-AGGTAATC
9976 AGTAAAAAGGTAATC
1 AGTAAAAAGGTAATC
9991 AGTAA
1 AGTAA
9996 GAGTAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 1 0.05
15 18 0.95
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (15 bp):
AGTAAAAAGGTAATC
Found at i:10002 original size:21 final size:21
Alignment explanation
Indices: 9976--10037 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
9966 AATAGTAATC
9976 AGTAAAAAGGTAATCAGTAAG
1 AGTAAAAAGGTAATCAGTAAG
* *
9997 AGTAAAATA-GTGACCAGTAAG
1 AGTAAAA-AGGTAATCAGTAAG
* * *
10018 AGCAAAATGGTAATTAGTAA
1 AGTAAAAAGGTAATCAGTAA
10038 AAGTGCAATA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
21 31 0.97
22 1 0.03
ACGTcount: A:0.50, C:0.06, G:0.23, T:0.21
Consensus pattern (21 bp):
AGTAAAAAGGTAATCAGTAAG
Found at i:10077 original size:28 final size:28
Alignment explanation
Indices: 10033--10088 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
10023 AATGGTAATT
10033 AGTAAAAGTGCAATAGTAA-TCAATAAAG
1 AGTAAAAGTGCAATAGTAATTCAA-AAAG
*
10061 AGTAAAAG-GCGATTAGTAATTCAAAAAG
1 AGTAAAAGTGC-AATAGTAATTCAAAAAG
10089 TAAAATGGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 2 0.08
28 19 0.76
29 4 0.16
ACGTcount: A:0.52, C:0.07, G:0.20, T:0.21
Consensus pattern (28 bp):
AGTAAAAGTGCAATAGTAATTCAAAAAG
Found at i:10158 original size:13 final size:13
Alignment explanation
Indices: 10142--10188 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
10132 GTGATAAAAA
10142 AAAAGAGAGTAAG
1 AAAAGAGAGTAAG
* *
10155 AAAAGAGTAATTAG
1 AAAAGAG-AGTAAG
10169 TAAAA-AGAGTAAG
1 -AAAAGAGAGTAAG
10182 AAAAGAG
1 AAAAGAG
10189 TAAAAATGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 4 0.15
13 13 0.48
14 6 0.22
15 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.26, T:0.13
Consensus pattern (13 bp):
AAAAGAGAGTAAG
Found at i:11501 original size:24 final size:24
Alignment explanation
Indices: 11466--11550 Score: 134
Period size: 24 Copynumber: 3.5 Consensus size: 24
11456 ACACTTTAAT
*
11466 ATAGCGGCGTCTAGACGCCTCTAA
1 ATAGCAGCGTCTAGACGCCTCTAA
*
11490 ATAGCAGTGTCTAGACGCCTCTAA
1 ATAGCAGCGTCTAGACGCCTCTAA
*
11514 ATAGCAGCGTCTAGACACCTCTAA
1 ATAGCAGCGTCTAGACGCCTCTAA
*
11538 ATAGCGGCGTCTA
1 ATAGCAGCGTCTA
11551 AACGTTGCTA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 56 1.00
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.22
Consensus pattern (24 bp):
ATAGCAGCGTCTAGACGCCTCTAA
Found at i:21636 original size:18 final size:18
Alignment explanation
Indices: 21613--21648 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
21603 ATTCATTCAT
21613 TCAATTAATTAATAACAA
1 TCAATTAATTAATAACAA
21631 TCAATTAATTAATAACAA
1 TCAATTAATTAATAACAA
21649 ATTAGCCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (18 bp):
TCAATTAATTAATAACAA
Found at i:25281 original size:40 final size:40
Alignment explanation
Indices: 25237--25314 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
25227 TTTTTGGCAG
* * *
25237 AACAATGCTTTAAC-CTTTTTAGAAGTTTTAAATTACTATT
1 AACAATGCTTGAACTCGTTTTAGAAG-TTTAAATGACTATT
*
25277 AACAATGCTTGAACTCGTTTTGGAAGTTTAAATGACTA
1 AACAATGCTTGAACTCGTTTTAGAAGTTTAAATGACTA
25315 CGATTTAATC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 24 0.73
41 9 0.27
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (40 bp):
AACAATGCTTGAACTCGTTTTAGAAGTTTAAATGACTATT
Done.