Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013734.1 Corchorus capsularis cultivar CVL-1 contig13755, 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: 27752
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:6444 original size:2 final size:2
Alignment explanation
Indices: 6432--6473 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
6422 TTATTCTTGT
6432 TC TC T- TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
6473 T
1 T
6474 TTCTTTTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:7770 original size:25 final size:25
Alignment explanation
Indices: 7719--7772 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
7709 AGTATTTTAC
*
7719 ATTTCATTCATGTAGCTCAAAAGTA
1 ATTTCATTCATGTAGCTCAAAACTA
*
7744 ATTTCATTCATGTAGCTCAAATCTA
1 ATTTCATTCATGTAGCTCAAAACTA
7769 ATTT
1 ATTT
7773 AGTTAACTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (25 bp):
ATTTCATTCATGTAGCTCAAAACTA
Found at i:11527 original size:27 final size:27
Alignment explanation
Indices: 11497--11587 Score: 76
Period size: 27 Copynumber: 3.3 Consensus size: 27
11487 AGTAGATAAT
11497 AGTAATTAGTAGATTAGTTTAATTCAG
1 AGTAATTAGTAGATTAGTTTAATTCAG
* ** * ***
11524 AGTAATTAAGCTAAAAGAG-TAAAAGGAGG
1 AGTAATT-AG-TAGATTAGTTTAATTCA-G
*
11553 AGTAATTAGTAGATTAGTTTAATTCGG
1 AGTAATTAGTAGATTAGTTTAATTCAG
11580 AGTAATTA
1 AGTAATTA
11588 AGCTAAAAAG
Statistics
Matches: 45, Mismatches: 15, Indels: 8
0.66 0.22 0.12
Matches are distributed among these distances:
27 21 0.47
28 11 0.24
29 13 0.29
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (27 bp):
AGTAATTAGTAGATTAGTTTAATTCAG
Found at i:11583 original size:56 final size:55
Alignment explanation
Indices: 11462--12171 Score: 912
Period size: 54 Copynumber: 12.9 Consensus size: 55
11452 GTCAAGAACC
* * *
11462 TAATTCAGAGTAATTAAGTTAAAAGAGT---AGATAATAGTAATTAGTAGATTAGTT
1 TAATTCAGAGTAATTAAGCTAAAA-AGTAAAAGA-AAGAGTAATCAGTAGATTAGTT
* * *
11516 TAATTCAGAGTAATTAAGCTAAAAGAGTAAAAGGAGGAGTAATTAGTAGATTAGTT
1 TAATTCAGAGTAATTAAGCTAAAA-AGTAAAAGAAAGAGTAATCAGTAGATTAGTT
* * * *
11572 TAATTCGGAGTAATTAAGCTAAAAAGTAAAGGAAAGAGAAATCAGTA-ACTAGTT
1 TAATTCAGAGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAGATTAGTT
* * *
11626 TAATTCAGAGTAATTAAGCTAAAACGTAAAGGAAAAGAGTAATCAGTAGATAAGTT
1 TAATTCAGAGTAATTAAGCTAAAAAGTAAAAG-AAAGAGTAATCAGTAGATTAGTT
* *
11682 TAATTCAGAATAATTAAACTAAAAGAGTAAAAGAAAGAGTAATCAGTAGA-TAGTT
1 TAATTCAGAGTAATTAAGCTAAAA-AGTAAAAGAAAGAGTAATCAGTAGATTAGTT
*
11737 TAATTCAGAGTAATTAAGCTAAAAAAGT-AAAGAAAGAGTAAGCAGT-GATTAGTT
1 TAATTCAGAGTAATTAAGCT-AAAAAGTAAAAGAAAGAGTAATCAGTAGATTAGTT
*
11791 TAATTCAGAGTAATTAAGCTAAAGAAGT-AAAGAAAGAGTAA-CATTAGA-TAGTT
1 TAATTCAGAGTAATTAAGCTAAA-AAGTAAAAGAAAGAGTAATCAGTAGATTAGTT
* *
11844 TAATTCAAGAGTAATTAAGCTAAGAAGT-AAAGAAAGAGTAAGCAGTA-ATTAGTT
1 TAATTC-AGAGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAGATTAGTT
* * *
11898 TAATTCAAGAGTAATTAAGCTAAGAAGT-AAAGGAAGAGTAAGCAGTAGA-TAGTT
1 TAATTC-AGAGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAGATTAGTT
* *
11952 TAATTCAGAGTAATTAAGCTAAAAAGTAAGAGAAAGAGTAATCAGTAAATTAGTT
1 TAATTCAGAGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAGATTAGTT
* * * *
12007 TAATTCAAGAGTAATTAAACTTAAAAGAGTAACAGAAAGAGTAATTAGTAAATTAGTT
1 TAATTC-AGAGTAATTAAGC-TAAAA-AGTAAAAGAAAGAGTAATCAGTAGATTAGTT
*
12065 TAATTCAGAGTAATTAAGCTGAAAAGAGTAAAAGAAAGAGTAATCAATA-ATTAGTT
1 TAATTCAGAGTAATTAAGCT-AAAA-AGTAAAAGAAAGAGTAATCAGTAGATTAGTT
*
12121 TAATTCTGAGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTA-ATTA
1 TAATTCAGAGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAGATTA
12172 AAAAGTAAAA
Statistics
Matches: 594, Mismatches: 42, Indels: 40
0.88 0.06 0.06
Matches are distributed among these distances:
53 57 0.10
54 249 0.42
55 73 0.12
56 130 0.22
57 50 0.08
58 35 0.06
ACGTcount: A:0.48, C:0.05, G:0.19, T:0.27
Consensus pattern (55 bp):
TAATTCAGAGTAATTAAGCTAAAAAGTAAAAGAAAGAGTAATCAGTAGATTAGTT
Found at i:11883 original size:27 final size:27
Alignment explanation
Indices: 11797--11938 Score: 78
Period size: 27 Copynumber: 5.3 Consensus size: 27
11787 AGTTTAATTC
11797 AGAGTAATTAAGCTAAAGAAGTAAAGAA
1 AGAGTAATTAAGCT-AAGAAGTAAAGAA
* ** ***
11825 AGAGTAACATT-AGAT-AG-TTTAATTCA
1 AGAGT-A-ATTAAGCTAAGAAGTAAAGAA
11851 AGAGTAATTAAGCTAAGAAGTAAAGAA
1 AGAGTAATTAAGCTAAGAAGTAAAGAA
** ** ***
11878 AGAGTAA-GCAG-TAATTAGTTTAATTCA
1 AGAGTAATTAAGCTAAGAAG--TAAAGAA
*
11905 AGAGTAATTAAGCTAAGAAGTAAAGGA
1 AGAGTAATTAAGCTAAGAAGTAAAGAA
11932 AGAGTAA
1 AGAGTAA
11939 GCAGTAGATA
Statistics
Matches: 79, Mismatches: 26, Indels: 19
0.64 0.21 0.15
Matches are distributed among these distances:
24 3 0.04
25 9 0.11
26 13 0.16
27 35 0.44
28 7 0.09
29 9 0.11
30 3 0.04
ACGTcount: A:0.50, C:0.05, G:0.21, T:0.24
Consensus pattern (27 bp):
AGAGTAATTAAGCTAAGAAGTAAAGAA
Found at i:12107 original size:30 final size:29
Alignment explanation
Indices: 11958--12108 Score: 87
Period size: 30 Copynumber: 5.3 Consensus size: 29
11948 AGTTTAATTC
*
11958 AGAGTAATTAAGCTAAAA-AGTAAGAGAA
1 AGAGTAATTAAGCTAAAAGAGTAAAAGAA
* ** * ***
11986 AGAGTAA-TCAG-TAAATTAGTTTAATTCA
1 AGAGTAATTAAGCTAAAAGAG-TAAAAGAA
* *
12014 AGAGTAATTAAACTTAAAAGAGTAACAGAA
1 AGAGTAATTAAGC-TAAAAGAGTAAAAGAA
** ** ***
12044 AGAGTAATT-AG-TAAATTAGTTTAATTC
1 AGAGTAATTAAGCTAAAAGAGTAAAAGAA
12071 AGAGTAATTAAGCTGAAAAGAGTAAAAGAA
1 AGAGTAATTAAGCT-AAAAGAGTAAAAGAA
12101 AGAGTAAT
1 AGAGTAAT
12109 CAATAATTAG
Statistics
Matches: 83, Mismatches: 32, Indels: 14
0.64 0.25 0.11
Matches are distributed among these distances:
26 4 0.05
27 22 0.27
28 19 0.23
29 4 0.05
30 28 0.34
31 6 0.07
ACGTcount: A:0.51, C:0.05, G:0.19, T:0.26
Consensus pattern (29 bp):
AGAGTAATTAAGCTAAAAGAGTAAAAGAA
Found at i:12189 original size:28 final size:30
Alignment explanation
Indices: 12140--12199 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 30
12130 GTAATTAAGC
12140 TAAAAAGTAAAAGAAAGAGTAATCAGTAAT
1 TAAAAAGTAAAAGAAAGAGTAATCAGTAAT
* *
12170 TAAAAAGTAAAA-AATG-GTAATCCGTAAT
1 TAAAAAGTAAAAGAAAGAGTAATCAGTAAT
12198 TA
1 TA
12200 GCTTAATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 13 0.46
29 3 0.11
30 12 0.43
ACGTcount: A:0.57, C:0.05, G:0.15, T:0.23
Consensus pattern (30 bp):
TAAAAAGTAAAAGAAAGAGTAATCAGTAAT
Found at i:12254 original size:39 final size:39
Alignment explanation
Indices: 12211--12380 Score: 110
Period size: 39 Copynumber: 4.4 Consensus size: 39
12201 CTTAATTTAA
12211 AGTAATTAAGTTAATCAAGAAGTAA-AAGGAGTAATCAGT
1 AGTAATTAAGTTAATCAAGAAGTAATAA-GAGTAATCAGT
* *
12250 AGTAATT-AGCTTAATTC-AG-AGTAATTAAG-TTAATCAAGA
1 AGTAATTAAG-TTAA-TCAAGAAGTAA-TAAGAGTAATC-AGT
* * * *
12289 AGTAA--AAGGAGTAATCAA-TAGTAATTA-ACTCAATTCAG-
1 AGTAATTAA-G-TTAATCAAGAAGTAATAAGAGT-AA-TCAGT
12327 AGTAATTAAGTTAATCAAGAAGTAA-AAGGAGTAATCAGT
1 AGTAATTAAGTTAATCAAGAAGTAATAA-GAGTAATCAGT
*
12366 AGTAATTAACTTAAT
1 AGTAATTAAGTTAAT
12381 TCTAAGAAAT
Statistics
Matches: 102, Mismatches: 11, Indels: 36
0.68 0.07 0.24
Matches are distributed among these distances:
38 35 0.34
39 57 0.56
40 10 0.10
ACGTcount: A:0.47, C:0.07, G:0.17, T:0.29
Consensus pattern (39 bp):
AGTAATTAAGTTAATCAAGAAGTAATAAGAGTAATCAGT
Found at i:12262 original size:58 final size:58
Alignment explanation
Indices: 12193--12418 Score: 362
Period size: 58 Copynumber: 3.9 Consensus size: 58
12183 ATGGTAATCC
* *
12193 GTAATTAGCTTAATTTAAAGTAATTAAGTTAATCAAGAAGTAAAAGGAGTAATCAGTA
1 GTAATTAACTTAATTCAAAGTAATTAAGTTAATCAAGAAGTAAAAGGAGTAATCAGTA
* * *
12251 GTAATTAGCTTAATTCAGAGTAATTAAGTTAATCAAGAAGTAAAAGGAGTAATCAATA
1 GTAATTAACTTAATTCAAAGTAATTAAGTTAATCAAGAAGTAAAAGGAGTAATCAGTA
* *
12309 GTAATTAACTCAATTCAGAGTAATTAAGTTAATCAAGAAGTAAAAGGAGTAATCAGTA
1 GTAATTAACTTAATTCAAAGTAATTAAGTTAATCAAGAAGTAAAAGGAGTAATCAGTA
* * *
12367 GTAATTAACTTAATTCTAAGAAATTAAGTTAATCAAGAAGTAATAGGAGTAA
1 GTAATTAACTTAATTCAAAGTAATTAAGTTAATCAAGAAGTAAAAGGAGTAA
12419 ACAACTTAAT
Statistics
Matches: 157, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 157 1.00
ACGTcount: A:0.47, C:0.07, G:0.17, T:0.30
Consensus pattern (58 bp):
GTAATTAACTTAATTCAAAGTAATTAAGTTAATCAAGAAGTAAAAGGAGTAATCAGTA
Found at i:12264 original size:19 final size:18
Alignment explanation
Indices: 12242--12401 Score: 71
Period size: 19 Copynumber: 8.3 Consensus size: 18
12232 GTAAAAGGAG
12242 TAATCAGTAGTAATT-AGCT
1 TAATCAG-AGTAATTAAG-T
12261 TAATTCAGAGTAATTAAGT
1 TAA-TCAGAGTAATTAAGT
*
12280 TAATCAAGAAGTAA--AAGGAG
1 TAATC-AG-AGTAATTAA-G-T
* *
12300 TAATCAATAGTAATTAACT
1 TAATC-AGAGTAATTAAGT
*
12319 CAATTCAGAGTAATTAAGT
1 TAA-TCAGAGTAATTAAGT
*
12338 TAATCAAGAAGTAA--AAGGAG
1 TAATC-AG-AGTAATTAA-G-T
*
12358 TAATCAGTAGTAATTAACT
1 TAATCAG-AGTAATTAAGT
*
12377 TAATTCTA-AGAAATTAAGT
1 TAA-TC-AGAGTAATTAAGT
12396 TAATCA
1 TAATCA
12402 AGAAGTAATA
Statistics
Matches: 110, Mismatches: 14, Indels: 36
0.69 0.09 0.22
Matches are distributed among these distances:
17 1 0.01
18 10 0.09
19 62 0.56
20 32 0.29
21 5 0.05
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (18 bp):
TAATCAGAGTAATTAAGT
Found at i:12996 original size:5 final size:6
Alignment explanation
Indices: 12966--12996 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
12956 CTCACTAATA
12966 ATTTGC ATTTGC ATTTGC ATTTGC A-TTGC AT
1 ATTTGC ATTTGC ATTTGC ATTTGC ATTTGC AT
12997 GAGTTTACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.48
Consensus pattern (6 bp):
ATTTGC
Found at i:14223 original size:21 final size:20
Alignment explanation
Indices: 14175--14229 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
14165 AAGAAATGGT
* *
14175 GCGCCGGGATGAGGAAGAAA
1 GCGCCGGGACGAAGAAGAAA
* *
14195 GCACCGGGACGAAGAAGCAA
1 GCGCCGGGACGAAGAAGAAA
*
14215 GACGCCGGGAGGAAG
1 G-CGCCGGGACGAAG
14230 CAACAAATGC
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.35, C:0.20, G:0.44, T:0.02
Consensus pattern (20 bp):
GCGCCGGGACGAAGAAGAAA
Found at i:15648 original size:18 final size:17
Alignment explanation
Indices: 15625--15672 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
15615 TTAGCATTTG
15625 TTGCTTCCTCCCGGCGTC
1 TTGCTTCCTCCCGGCG-C
15643 TTGCTTCTTCATCCCGGCGC
1 TTGCTTC--C-TCCCGGCGC
*
15663 TTACTTCCTC
1 TTGCTTCCTC
15673 ATCCCGGCGC
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
17 2 0.08
18 8 0.31
20 8 0.31
21 8 0.31
ACGTcount: A:0.04, C:0.42, G:0.17, T:0.38
Consensus pattern (17 bp):
TTGCTTCCTCCCGGCGC
Found at i:15657 original size:21 final size:20
Alignment explanation
Indices: 15628--15682 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
15618 GCATTTGTTG
* *
15628 CTTCCTCCCGGCGTCTTGCTT
1 CTTCATCCCGGCG-CTTACTT
15649 CTTCATCCCGGCGCTTACTT
1 CTTCATCCCGGCGCTTACTT
*
15669 CCTCATCCCGGCGC
1 CTTCATCCCGGCGC
15683 ACCATTTCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 19 0.61
21 12 0.39
ACGTcount: A:0.05, C:0.45, G:0.18, T:0.31
Consensus pattern (20 bp):
CTTCATCCCGGCGCTTACTT
Found at i:17600 original size:19 final size:19
Alignment explanation
Indices: 17578--17660 Score: 68
Period size: 19 Copynumber: 4.3 Consensus size: 19
17568 TTTACTTCTT
17578 AATTAACTTAATTACTCTG
1 AATTAACTTAATTACTCTG
17597 AATTAAGC-TAATTACTACTG
1 AATTAA-CTTAATTACT-CTG
*
17617 -ATT-ACTCCT-TTTACTTCTTG
1 AATTAACT--TAATTAC-TC-TG
17637 -ATTAACTTAATTACTCTG
1 AATTAACTTAATTACTCTG
17655 AATTAA
1 AATTAA
17661 GCTAATTGCG
Statistics
Matches: 52, Mismatches: 2, Indels: 20
0.70 0.03 0.27
Matches are distributed among these distances:
17 1 0.02
18 3 0.06
19 30 0.58
20 15 0.29
21 3 0.06
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.43
Consensus pattern (19 bp):
AATTAACTTAATTACTCTG
Found at i:17641 original size:58 final size:57
Alignment explanation
Indices: 17551--17667 Score: 198
Period size: 58 Copynumber: 2.0 Consensus size: 57
17541 ACCCAATGTC
* *
17551 TTACTATTGATTACCTTTTTACTTCTTAATTAACTTAATTACTCTGAATTAAGCTAA
1 TTACTACTGATTACCCTTTTACTTCTTAATTAACTTAATTACTCTGAATTAAGCTAA
*
17608 TTACTACTGATTACTCCTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAA
1 TTACTACTGATTAC-CCTTTTACTTCTTAATTAACTTAATTACTCTGAATTAAGCTAA
17666 TT
1 TT
17668 GCGGATTACC
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
57 13 0.23
58 43 0.77
ACGTcount: A:0.30, C:0.17, G:0.06, T:0.47
Consensus pattern (57 bp):
TTACTACTGATTACCCTTTTACTTCTTAATTAACTTAATTACTCTGAATTAAGCTAA
Found at i:17695 original size:28 final size:29
Alignment explanation
Indices: 17663--17722 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
17653 TGAATTAAGC
*
17663 TAATTGCGGATTAC-CATTT-TTTACTTTT
1 TAATTACGGATTACTC-TTTATTTACTTTT
*
17691 TAATTACTGATTACTCTTTCATTTACTTTT
1 TAATTACGGATTACTCTTT-ATTTACTTTT
17721 TA
1 TA
17723 GCTTAATTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 15 0.56
29 1 0.04
30 11 0.41
ACGTcount: A:0.23, C:0.15, G:0.07, T:0.55
Consensus pattern (29 bp):
TAATTACGGATTACTCTTTATTTACTTTT
Found at i:17749 original size:54 final size:54
Alignment explanation
Indices: 17691--18399 Score: 884
Period size: 54 Copynumber: 12.9 Consensus size: 54
17681 TTTTACTTTT
* *
17691 TAATTACTGATTACTCTTTCATTTACTTTTTAGCTTAATTACTCAGAATTAAAC
1 TAATTACTGATTACTCTTTCTTTTACTTTTTAGCTTAATTACTCTGAATTAAAC
17745 TAATTACTGATTACTCTTTCTTTTACTCTTTTCAGCTTAATTACTCTGAATTAAAC
1 TAATTACTGATTACTCTTTCTTTTACT-TTTT-AGCTTAATTACTCTGAATTAAAC
* * * *
17801 TAATTTACTAATTACTCTTTCTGTTACTCTTTTAAGTTTAATTACTTTTGAATTAAAC
1 TAA-TTACTGATTACTCTTTCTTTTACT-TTTT-AGCTTAATTAC-TCTGAATTAAAC
17859 TAATTTACTGATTACTCTTTCTTTTACTTTTTAGCTTAATTACTCTGAATTAAAC
1 TAA-TTACTGATTACTCTTTCTTTTACTTTTTAGCTTAATTACTCTGAATTAAAC
* * *
17914 T-ATCTACTGCTTACTC-TTCCTTTACTTCTTAGCTTAATTACTCTTGAATTAAAC
1 TAAT-TACTGATTACTCTTTCTTTTACTTTTTAGCTTAATTACTC-TGAATTAAAC
* *
17968 TAATTACTGCTTACTCTTTC-TTTACTTCTTAGCTTAATTACTCTTGAATTAAAC
1 TAATTACTGATTACTCTTTCTTTTACTTTTTAGCTTAATTACTC-TGAATTAAAC
*
18022 T-ATCTAATG-TTACTCTTTC-TTTACTTCTTTAGCTTAATTACTCTGAATTAAAC
1 TAAT-TACTGATTACTCTTTCTTTTACTT-TTTAGCTTAATTACTCTGAATTAAAC
* * *
18075 TAATCACTGCTTACTCTTTC-ATTACCTTTTTAGCTTAATTACTCTGAATTAAAC
1 TAATTACTGATTACTCTTTCTTTTA-CTTTTTAGCTTAATTACTCTGAATTAAAC
* *
18129 T-ATCTACTGATTACTCTTTCTTTTACTCTTTTAGTTTAATTATTCTGAATTAAAC
1 TAAT-TACTGATTACTCTTTCTTTTACT-TTTTAGCTTAATTACTCTGAATTAAAC
* *
18184 TTATCTACTGATTACTCTTTTCCTTTACTTTTTAGCTTAATTACTCTGAATT-AAC
1 TAAT-TACTGATTACTC-TTTCTTTTACTTTTTAGCTTAATTACTCTGAATTAAAC
* * *
18239 TAGTTACTGATTTCTCTTTCCTTTACTTTTTAGCTTAATTACTCTGAATTAAAC
1 TAATTACTGATTACTCTTTCTTTTACTTTTTAGCTTAATTACTCTGAATTAAAC
* * *
18293 TAATCTACTAATTACTCCTCCTTTTACTCTTTTAGCTTAATTACTCTGAATTAAAC
1 TAAT-TACTGATTACTCTTTCTTTTACT-TTTTAGCTTAATTACTCTGAATTAAAC
* * *
18349 TAATCTACTAATTACTATTATC---TACTCTTTTAACTTAATTACTCTGAATTA
1 TAAT-TACTGATTACTCTT-TCTTTTACT-TTTTAGCTTAATTACTCTGAATTA
18400 GGTTCTTGAC
Statistics
Matches: 593, Mismatches: 40, Indels: 44
0.88 0.06 0.06
Matches are distributed among these distances:
53 95 0.16
54 218 0.37
55 76 0.13
56 115 0.19
57 52 0.09
58 37 0.06
ACGTcount: A:0.27, C:0.19, G:0.05, T:0.49
Consensus pattern (54 bp):
TAATTACTGATTACTCTTTCTTTTACTTTTTAGCTTAATTACTCTGAATTAAAC
Found at i:18008 original size:27 final size:27
Alignment explanation
Indices: 17924--18065 Score: 78
Period size: 27 Copynumber: 5.3 Consensus size: 27
17914 TATCTACTGC
*
17924 TTACTCTTCCTTTACTTCTTAGCTTAA
1 TTACTCTTTCTTTACTTCTTAGCTTAA
** * ** **
17951 TTACTCTTGAATTAAACTAATTA-C-TGC
1 TTACTCTT-TCTT-TACTTCTTAGCTTAA
17978 TTACTCTTTCTTTACTTCTTAGCTTAA
1 TTACTCTTTCTTTACTTCTTAGCTTAA
*** ** *
18005 TTACTCTTGAATTA-AAC-TATC-TAA
1 TTACTCTTTCTTTACTTCTTAGCTTAA
18029 TGTTACTCTTTCTTTACTTCTTTAGCTTAA
1 --TTACTCTTTCTTTACTTC-TTAGCTTAA
18059 TTACTCT
1 TTACTCT
18066 GAATTAAACT
Statistics
Matches: 79, Mismatches: 26, Indels: 19
0.64 0.21 0.15
Matches are distributed among these distances:
24 3 0.04
25 9 0.11
26 15 0.19
27 30 0.38
28 10 0.13
29 9 0.11
30 3 0.04
ACGTcount: A:0.24, C:0.21, G:0.05, T:0.50
Consensus pattern (27 bp):
TTACTCTTTCTTTACTTCTTAGCTTAA
Found at i:18289 original size:109 final size:109
Alignment explanation
Indices: 17695--18399 Score: 900
Period size: 109 Copynumber: 6.4 Consensus size: 109
17685 ACTTTTTAAT
* *
17695 TACTGATTACTCTTTCATTTACTTTTTAGCTTAATTACTCAGAATTAAACTAAT-TACTGATTAC
1 TACTGATTACTCTTTCCTTTACTTTTTAGCTTAATTACTCTGAATTAAACTAATCTACTGATTAC
* *
17759 TCTTTCTTTTACTCTTTTCAGCTTAATTACTCTGAATTAAACTAATT
66 TCTTTCCTTTACT-TTTT-AGCTTAATTACTCTGAATTAAACT-ATC
* * * *
17806 TACTAATTACTCTTT-CTGTTACTCTTTTAAGTTTAATTACTTTTGAATTAAACTAATTTACTGA
1 TACTGATTACTCTTTCCT-TTACT-TTTT-AGCTTAATTAC-TCTGAATTAAACTAATCTACTGA
*
17870 TTACTCTTTCTTTTACTTTTTAGCTTAATTACTCTGAATTAAACTATC
62 TTACTCTTTCCTTTACTTTTTAGCTTAATTACTCTGAATTAAACTATC
* * *
17918 TACTGCTTACTC-TTCCTTTACTTCTTAGCTTAATTACTCTTGAATTAAACTAAT-TACTGCTTA
1 TACTGATTACTCTTTCCTTTACTTTTTAGCTTAATTACTC-TGAATTAAACTAATCTACTGATTA
*
17981 CTCTTT-CTTTACTTCTTAGCTTAATTACTCTTGAATTAAACTATC
65 CTCTTTCCTTTACTTTTTAGCTTAATTACTC-TGAATTAAACTATC
* *
18026 TAATG-TTACTCTTT-CTTTACTTCTTTAGCTTAATTACTCTGAATTAAACTAATC-ACTGCTTA
1 TACTGATTACTCTTTCCTTTACTT-TTTAGCTTAATTACTCTGAATTAAACTAATCTACTGATTA
*
18088 CTCTTT-CATTACCTTTTTAGCTTAATTACTCTGAATTAAACTATC
65 CTCTTTCCTTTA-CTTTTTAGCTTAATTACTCTGAATTAAACTATC
* * * *
18133 TACTGATTACTCTTTCTTTTACTCTTTTAGTTTAATTATTCTGAATTAAACTTATCTACTGATTA
1 TACTGATTACTCTTTCCTTTACT-TTTTAGCTTAATTACTCTGAATTAAACTAATCTACTGATTA
18198 CTCTTTTCCTTTACTTTTTAGCTTAATTACTCTGAATT-AACTAGT-
65 CTC-TTTCCTTTACTTTTTAGCTTAATTACTCTGAATTAAACTA-TC
* *
18243 TACTGATTTCTCTTTCCTTTACTTTTTAGCTTAATTACTCTGAATTAAACTAATCTACTAATTAC
1 TACTGATTACTCTTTCCTTTACTTTTTAGCTTAATTACTCTGAATTAAACTAATCTACTGATTAC
*
18308 TC-CTCCTTTTACTCTTTTAGCTTAATTACTCTGAATTAAACTAATC
66 TCTTTCC-TTTACT-TTTTAGCTTAATTACTCTGAATTAAACT-ATC
* * *
18354 TACTAATTACTATTAT-C--TACTCTTTTAACTTAATTACTCTGAATTA
1 TACTGATTACTCTT-TCCTTTACT-TTTTAGCTTAATTACTCTGAATTA
18400 GGTTCTTGAC
Statistics
Matches: 532, Mismatches: 36, Indels: 53
0.86 0.06 0.09
Matches are distributed among these distances:
107 89 0.17
108 83 0.16
109 125 0.23
110 69 0.13
111 68 0.13
112 23 0.04
113 34 0.06
114 18 0.03
115 23 0.04
ACGTcount: A:0.27, C:0.19, G:0.05, T:0.49
Consensus pattern (109 bp):
TACTGATTACTCTTTCCTTTACTTTTTAGCTTAATTACTCTGAATTAAACTAATCTACTGATTAC
TCTTTCCTTTACTTTTTAGCTTAATTACTCTGAATTAAACTATC
Found at i:18304 original size:27 final size:27
Alignment explanation
Indices: 18274--18364 Score: 85
Period size: 27 Copynumber: 3.3 Consensus size: 27
18264 CTTTTTAGCT
18274 TAATTACTCTGAATTAAACTAATCTAC
1 TAATTACTCTGAATTAAACTAATCTAC
** ** ** *
18301 TAATTACTCCT-CCTTTTACTCTTTTAGC
1 TAATTACT-CTGAATTAAACTAATCTA-C
18329 TTAATTACTCTGAATTAAACTAATCTAC
1 -TAATTACTCTGAATTAAACTAATCTAC
18357 TAATTACT
1 TAATTACT
18365 ATTATCTACT
Statistics
Matches: 46, Mismatches: 14, Indels: 8
0.68 0.21 0.12
Matches are distributed among these distances:
27 24 0.52
28 6 0.13
29 16 0.35
ACGTcount: A:0.33, C:0.21, G:0.03, T:0.43
Consensus pattern (27 bp):
TAATTACTCTGAATTAAACTAATCTAC
Found at i:26942 original size:2 final size:2
Alignment explanation
Indices: 26937--26978 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
26927 AAAGAAAGAA
26937 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A- AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
26978 A
1 A
26979 ACAAGAATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:27704 original size:2 final size:2
Alignment explanation
Indices: 27697--27752 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
27687 GAACTTTTGT
27697 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
27739 AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Done.