Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015924.1 Corchorus olitorius cultivar O-4 contig15957, 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: 51330
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Found at i:8520 original size:43 final size:43
Alignment explanation
Indices: 8468--8795 Score: 454
Period size: 43 Copynumber: 7.8 Consensus size: 43
8458 TAAGGAGAAG
* *
8468 TGCCTCTGTGTTGTATATGTGTTTGAGGACTTTGTAATAGAGA
1 TGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGA
*
8511 TGCCCCTGTGTTATATATGTGTTT-AGGGACTTTGTAAT--AGT
1 TGCCCCTGTGTTATATATGTGTTTGA-GGACTTTGTAATAGAGA
* *
8552 TGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGG
1 TGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGA
8595 TGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAAT--AGA
1 TGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGA
* * * *
8636 TGCCTCTGTCTTATATATGTGTTTGAGGACTTTGGAATAGAGG
1 TGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGA
* * *
8679 TGCCCCTGTGTTATATATGTGTTTGGGGAC-TTG-AATATAGG
1 TGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGA
* *
8720 TGCCTCTGTGTTATATATGTGTTTGAGGACTTTGCAATAGAGA
1 TGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGA
* *
8763 TGCCCATGTGTTATATATGTGTTTGGGGACTTT
1 TGCCCCTGTGTTATATATGTGTTTGAGGACTTT
8796 TGGTTATTGG
Statistics
Matches: 255, Mismatches: 22, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
41 109 0.43
42 8 0.03
43 138 0.54
ACGTcount: A:0.20, C:0.11, G:0.27, T:0.41
Consensus pattern (43 bp):
TGCCCCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGA
Found at i:8579 original size:84 final size:84
Alignment explanation
Indices: 8468--8795 Score: 532
Period size: 84 Copynumber: 3.9 Consensus size: 84
8458 TAAGGAGAAG
*
8468 TGCCTCTGTGTTGTATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATGTGT
1 TGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATGTGT
* *
8533 TTAGGGACTTTGTAATAGT
66 TTGGGGACTTTGTAATAGA
*
8552 TGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGGTGCCCCTGTGTTATATATGTGT
1 TGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATGTGT
*
8617 TTGAGGACTTTGTAATAGA
66 TTGGGGACTTTGTAATAGA
* * *
8636 TGCCTCTGTCTTATATATGTGTTTGAGGACTTTGGAATAGAGGTGCCCCTGTGTTATATATGTGT
1 TGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATGTGT
* *
8701 TTGGGGAC-TTGAATATAGG
66 TTGGGGACTTTGTA-ATAGA
* *
8720 TGCCTCTGTGTTATATATGTGTTTGAGGACTTTGCAATAGAGATGCCCATGTGTTATATATGTGT
1 TGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATGTGT
8785 TTGGGGACTTT
66 TTGGGGACTTT
8796 TGGTTATTGG
Statistics
Matches: 228, Mismatches: 14, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
83 4 0.02
84 222 0.97
85 2 0.01
ACGTcount: A:0.20, C:0.11, G:0.27, T:0.41
Consensus pattern (84 bp):
TGCCTCTGTGTTATATATGTGTTTGAGGACTTTGTAATAGAGATGCCCCTGTGTTATATATGTGT
TTGGGGACTTTGTAATAGA
Found at i:9379 original size:13 final size:12
Alignment explanation
Indices: 9342--9389 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 12
9332 TTCAATCTTT
9342 TTATATATTA-A
1 TTATATATTATA
* *
9353 TAATAATGTTATA
1 TTAT-ATATTATA
9366 TTATATTATTATA
1 TTATA-TATTATA
9379 TTATATATTAT
1 TTATATATTAT
9390 CAATAAACTT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
11 3 0.10
12 12 0.40
13 15 0.50
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (12 bp):
TTATATATTATA
Found at i:9546 original size:17 final size:17
Alignment explanation
Indices: 9524--9556 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
9514 TCGAAATCAA
9524 ACCCGAG-CCTGAACCCT
1 ACCCGAGACC-GAACCCT
9541 ACCCGAGACCGAACCC
1 ACCCGAGACCGAACCC
9557 AAAAATACCC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.27, C:0.48, G:0.18, T:0.06
Consensus pattern (17 bp):
ACCCGAGACCGAACCCT
Found at i:9623 original size:16 final size:17
Alignment explanation
Indices: 9549--9623 Score: 59
Period size: 16 Copynumber: 4.6 Consensus size: 17
9539 CTACCCGAGA
*
9549 CCGAACCCAAAAAT-AC
1 CCGAACCCGAAAATAAC
*
9565 CCGAACCCG-ACATAAC
1 CCGAACCCGAAAATAAC
** **
9581 CCGAGTCCG-ACTTAAC
1 CCGAACCCGAAAATAAC
*
9597 CCGAGCCCGAAAAT-AC
1 CCGAACCCGAAAATAAC
9613 CCGAACCCGAA
1 CCGAACCCGAA
9624 CCCGCCCGAG
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
15 3 0.06
16 43 0.90
17 2 0.04
ACGTcount: A:0.37, C:0.40, G:0.15, T:0.08
Consensus pattern (17 bp):
CCGAACCCGAAAATAAC
Found at i:18215 original size:39 final size:39
Alignment explanation
Indices: 18125--18224 Score: 121
Period size: 39 Copynumber: 2.6 Consensus size: 39
18115 TTTTCCATTC
* * *
18125 GATTCAACGATGTATTTATTTTATTTTTTCCTACTTACC
1 GATTCAACGATGTATATATTTTAGTTTTTCCTACTTACA
* * *
18164 GGTTTAACGATGTATCTATTTTAGTTTTTCCTA-TCTACA
1 GATTCAACGATGTATATATTTTAGTTTTTCCTACT-TACA
*
18203 GATTCAATGATGTATATATTTT
1 GATTCAACGATGTATATATTTT
18225 GTTGTTTTCT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
38 1 0.02
39 50 0.98
ACGTcount: A:0.25, C:0.14, G:0.11, T:0.50
Consensus pattern (39 bp):
GATTCAACGATGTATATATTTTAGTTTTTCCTACTTACA
Found at i:18266 original size:32 final size:32
Alignment explanation
Indices: 18219--18345 Score: 87
Period size: 40 Copynumber: 3.7 Consensus size: 32
18209 ATGATGTATA
* *
18219 TATTTTGTTGTTTTCTTACCGAACAATATATC
1 TATTCTGTTTTTTTCTTACCGAACAATATATC
* *
18251 TATTCTGTTTTTTTCTTAACTACCGATTCAATGATGTATA
1 TATTCTGTTTTTTTC-T---TACCGA-ACAAT-A--TATC
* *
18291 TATTCCGTTTTTTTCCCTTACCGAACAATGTATC
1 TATTCTGTTTTTTT--CTTACCGAACAATATATC
18325 TATGT-TG-TTTTTTCTTACCGA
1 TAT-TCTGTTTTTTTCTTACCGA
18346 TTCAACGATG
Statistics
Matches: 75, Mismatches: 9, Indels: 23
0.70 0.08 0.21
Matches are distributed among these distances:
31 8 0.11
32 13 0.17
33 7 0.09
34 7 0.09
35 1 0.01
36 6 0.08
37 8 0.11
38 7 0.09
40 16 0.21
41 1 0.01
42 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.10, T:0.50
Consensus pattern (32 bp):
TATTCTGTTTTTTTCTTACCGAACAATATATC
Found at i:18287 original size:72 final size:72
Alignment explanation
Indices: 18188--18363 Score: 204
Period size: 72 Copynumber: 2.5 Consensus size: 72
18178 TCTATTTTAG
* * **
18188 TTTTTCCTATCTACAGATTCAATGATGTATATATTTTGTTGTTTT-CTTACCGAACAATATATCT
1 TTTTTCTTAACTACAGATTCAATGATGTATATATTCCGTTGTTTTCCTTACCGAACAATATATCT
18252 AT-TCTGTT
66 ATGT-TG-T
* * *
18260 TTTTTCTTAACTACCGATTCAATGATGTATATATTCCGTTTTTTTCCCTTACCGAACAATGTATC
1 TTTTTCTTAACTACAGATTCAATGATGTATATATTCCGTTGTTTT-CCTTACCGAACAATATATC
18325 TATGTTGT
65 TATGTTGT
*
18333 TTTTTCTT-AC--C-GATTCAACGATGTAT-TATTC
1 TTTTTCTTAACTACAGATTCAATGATGTATATATTC
18364 TAAATTTATT
Statistics
Matches: 93, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
68 5 0.05
69 14 0.15
70 1 0.01
72 41 0.44
73 9 0.10
74 22 0.24
75 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.10, T:0.48
Consensus pattern (72 bp):
TTTTTCTTAACTACAGATTCAATGATGTATATATTCCGTTGTTTTCCTTACCGAACAATATATCT
ATGTTGT
Found at i:21271 original size:8 final size:8
Alignment explanation
Indices: 21258--21283 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
21248 ATTCAATAAC
21258 ATACATAT
1 ATACATAT
21266 ATACATAT
1 ATACATAT
21274 ATACATAT
1 ATACATAT
21282 AT
1 AT
21284 GTTTCAGTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (8 bp):
ATACATAT
Found at i:23687 original size:133 final size:133
Alignment explanation
Indices: 23528--23795 Score: 527
Period size: 133 Copynumber: 2.0 Consensus size: 133
23518 CCTTCATTAA
23528 AAAAATTCAAAACAGCTAAGAAATCAGGAAAAGAGATTTGAGAGAGGGCAAGCGGGTATTTAGGT
1 AAAAATTCAAAACAGCTAAGAAATCAGGAAAAGAGATTTGAGAGAGGGCAAGCGGGTATTTAGGT
*
23593 GTTTACAGATTATAAGTGTTTAGATATTGAATGAGATCATGATGCACCTATATATTTTTTTGGTA
66 GTTTACAGATTATAAGTGTTTAGATATTGAATGAGATCATGATGCACCCATATATTTTTTTGGTA
23658 CAT
131 CAT
23661 AAAAATTCAAAACAGCTAAGAAATCAGGAAAAGAGATTTGAGAGAGGGCAAGCGGGTATTTAGGT
1 AAAAATTCAAAACAGCTAAGAAATCAGGAAAAGAGATTTGAGAGAGGGCAAGCGGGTATTTAGGT
23726 GTTTACAGATTATAAGTGTTTAGATATTGAATGAGATCATGATGCACCCATATATTTTTTTGGTA
66 GTTTACAGATTATAAGTGTTTAGATATTGAATGAGATCATGATGCACCCATATATTTTTTTGGTA
23791 CAT
131 CAT
23794 AA
1 AA
23796 GAAAACTAAA
Statistics
Matches: 134, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
133 134 1.00
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.30
Consensus pattern (133 bp):
AAAAATTCAAAACAGCTAAGAAATCAGGAAAAGAGATTTGAGAGAGGGCAAGCGGGTATTTAGGT
GTTTACAGATTATAAGTGTTTAGATATTGAATGAGATCATGATGCACCCATATATTTTTTTGGTA
CAT
Found at i:24123 original size:30 final size:29
Alignment explanation
Indices: 24065--24123 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
24055 TTGCCAATTG
**
24065 AACTTCAATTTTGGACATTTTGTTCCCTC
1 AACTTCAATTTTGGACATTTTGCCCCCTC
*
24094 AACTCTCAATTTTGGACGTTTTGCCCCCTC
1 AACT-TCAATTTTGGACATTTTGCCCCCTC
24124 TCAAACAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.19, C:0.29, G:0.12, T:0.41
Consensus pattern (29 bp):
AACTTCAATTTTGGACATTTTGCCCCCTC
Found at i:24454 original size:16 final size:17
Alignment explanation
Indices: 24433--24467 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
24423 TACTTTTGCC
24433 TTTATCTATAT-CTATA
1 TTTATCTATATACTATA
*
24449 TTTATCTATCTACTATA
1 TTTATCTATATACTATA
24466 TT
1 TT
24468 AAAAAGTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.29, C:0.14, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTATCTATATACTATA
Found at i:24767 original size:19 final size:19
Alignment explanation
Indices: 24743--24779 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
24733 CGTGTTAACT
24743 GCTGACGTGTAATTTTTTA
1 GCTGACGTGTAATTTTTTA
24762 GCTGACGTGTAATTTTTT
1 GCTGACGTGTAATTTTTT
24780 GTATGGGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.19, C:0.11, G:0.22, T:0.49
Consensus pattern (19 bp):
GCTGACGTGTAATTTTTTA
Found at i:30312 original size:10 final size:10
Alignment explanation
Indices: 30297--30332 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
30287 CAGAGACAAC
30297 TTTTTTTATA
1 TTTTTTTATA
30307 TTTTTTTATA
1 TTTTTTTATA
*
30317 -TTTTTTACA
1 TTTTTTTATA
30326 TTTTTTT
1 TTTTTTT
30333 CTTCAGCTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 8 0.33
10 16 0.67
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTTTTATA
Found at i:30320 original size:8 final size:9
Alignment explanation
Indices: 30298--30331 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
30288 AGAGACAACT
30298 TTTTTTATA
1 TTTTTTATA
30307 TTTTTTTATA
1 -TTTTTTATA
*
30317 TTTTTTACA
1 TTTTTTATA
30326 TTTTTT
1 TTTTTT
30332 TCTTCAGCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTTATA
Found at i:31281 original size:45 final size:45
Alignment explanation
Indices: 31197--31369 Score: 223
Period size: 45 Copynumber: 4.0 Consensus size: 45
31187 ATCGATTTTA
*
31197 TTAA-TTTCCAAAATCTTCTTTTGG-ATTTCTT--A-A-AAAACT
1 TTAATTTTCCAAAATCTTCTTTTGGAATTACTTAAATAGAAAACT
*
31236 TTAATTTTCCAAAATCTTCTTTTGGAATTACTTACATAGAAAACT
1 TTAATTTTCCAAAATCTTCTTTTGGAATTACTTAAATAGAAAACT
* * *
31281 TTTATTTTCCAAAATCTTCTTTTGGAATTACTTAAATGGGAAACT
1 TTAATTTTCCAAAATCTTCTTTTGGAATTACTTAAATAGAAAACT
* * * *
31326 TTTATTTTCCAAAATCTTCTTTAGGAGTTACTTAAATAAAAAAC
1 TTAATTTTCCAAAATCTTCTTTTGGAATTACTTAAATAGAAAAC
31370 ATTCTTTTTG
Statistics
Matches: 118, Mismatches: 10, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
39 4 0.03
40 20 0.17
41 6 0.05
43 1 0.01
44 1 0.01
45 86 0.73
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (45 bp):
TTAATTTTCCAAAATCTTCTTTTGGAATTACTTAAATAGAAAACT
Found at i:32081 original size:2 final size:2
Alignment explanation
Indices: 32074--32116 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
32064 AGCCCAAACC
*
32074 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
32115 TA
1 TA
32117 GAATCTGAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:32151 original size:14 final size:14
Alignment explanation
Indices: 32132--32158 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
32122 TGAGGATACC
32132 AGAGTTGGAAGCTT
1 AGAGTTGGAAGCTT
32146 AGAGTTGGAAGCT
1 AGAGTTGGAAGCT
32159 AATTGGTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.07, G:0.37, T:0.26
Consensus pattern (14 bp):
AGAGTTGGAAGCTT
Found at i:32430 original size:22 final size:22
Alignment explanation
Indices: 32386--32447 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
32376 TTGGAAACAT
* *
32386 CTTTGCAGAG-ATT-CTTTCTA
1 CTTTGCAGAGCATTATTTTCCA
32406 CTTTGCAGAGCATTATTTTCCA
1 CTTTGCAGAGCATTATTTTCCA
32428 CTTTGCAGAGCATTATTTTC
1 CTTTGCAGAGCATTATTTTC
32448 TTCAACTTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.26
21 3 0.08
22 25 0.66
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.44
Consensus pattern (22 bp):
CTTTGCAGAGCATTATTTTCCA
Found at i:34011 original size:22 final size:21
Alignment explanation
Indices: 33984--34057 Score: 102
Period size: 18 Copynumber: 3.7 Consensus size: 21
33974 GATTGAAGAA
33984 AATGCTCTGCAAAGTGGAAAAT
1 AATGCTCTGCAAAGTGG-AAAT
34006 AATGCTCTGCAAAGTGG---T
1 AATGCTCTGCAAAGTGGAAAT
*
34024 AATGCTCTGCAAAGTGGAAAG
1 AATGCTCTGCAAAGTGGAAAT
34045 AAT-CTCTGCAAAG
1 AATGCTCTGCAAAG
34058 ATGTTTCCAA
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
18 18 0.38
20 10 0.21
21 3 0.06
22 17 0.35
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.23
Consensus pattern (21 bp):
AATGCTCTGCAAAGTGGAAAT
Found at i:34384 original size:14 final size:14
Alignment explanation
Indices: 34365--34391 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
34355 AGTACCAATT
34365 AGCTTCCAACTCTA
1 AGCTTCCAACTCTA
34379 AGCTTCCAACTCT
1 AGCTTCCAACTCT
34392 GGTATATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.37, G:0.07, T:0.30
Consensus pattern (14 bp):
AGCTTCCAACTCTA
Found at i:34747 original size:33 final size:33
Alignment explanation
Indices: 34696--34779 Score: 109
Period size: 33 Copynumber: 2.6 Consensus size: 33
34686 CCGCCCTCGG
* *
34696 AGGGCGGCA-TAACCATGGCATGCCATCCTCCT
1 AGGGCGGCACGAACCATGGCATGCCACCCTCCT
**
34728 AGGGCGGCACGAACCATGGCATGCTGCCCTCCT
1 AGGGCGGCACGAACCATGGCATGCCACCCTCCT
34761 AGGGCGGCACTG-ACCATGG
1 AGGGCGGCAC-GAACCATGG
34780 TTAATTTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
32 9 0.20
33 36 0.78
34 1 0.02
ACGTcount: A:0.20, C:0.33, G:0.31, T:0.15
Consensus pattern (33 bp):
AGGGCGGCACGAACCATGGCATGCCACCCTCCT
Found at i:37802 original size:28 final size:28
Alignment explanation
Indices: 37769--37847 Score: 142
Period size: 28 Copynumber: 2.8 Consensus size: 28
37759 AGGCATCTTG
37769 TACATGTTAGAATTGTCAAATGT-AATT
1 TACATGTTAGAATTGTCAAATGTAAATT
37796 TGACATGTTAGAATTGTCAAATGTAAATT
1 T-ACATGTTAGAATTGTCAAATGTAAATT
37825 TACATGTTAGAATTGTCAAATGT
1 TACATGTTAGAATTGTCAAATGT
37848 TATATATTGT
Statistics
Matches: 50, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
27 1 0.02
28 44 0.88
29 5 0.10
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (28 bp):
TACATGTTAGAATTGTCAAATGTAAATT
Found at i:37838 original size:14 final size:15
Alignment explanation
Indices: 37770--37849 Score: 55
Period size: 16 Copynumber: 5.5 Consensus size: 15
37760 GGCATCTTGT
37770 ACATGTTAGAATTGTC
1 ACATGTTAGAATT-TC
* *
37786 AAATG-T--AATTTG
1 ACATGTTAGAATTTC
37798 ACATGTTAGAATTGTC
1 ACATGTTAGAATT-TC
*
37814 AAATG-TA-AATTT-
1 ACATGTTAGAATTTC
37826 ACATGTTAGAATTGTC
1 ACATGTTAGAATT-TC
*
37842 AAATGTTA
1 ACATGTTA
37850 TATATTGTAC
Statistics
Matches: 49, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
12 9 0.18
13 8 0.16
14 8 0.16
15 8 0.16
16 16 0.33
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.39
Consensus pattern (15 bp):
ACATGTTAGAATTTC
Found at i:39619 original size:217 final size:217
Alignment explanation
Indices: 39244--39674 Score: 826
Period size: 217 Copynumber: 2.0 Consensus size: 217
39234 CTGGCGGCTT
* *
39244 GGGGCAATTGAGGCTTAGGACGATCACGTGGGGGGCGAAAGCATGGGAAGTACTCGTATATCCAT
1 GGGGCAATTGAGGCTCAAGACGATCACGTGGGGGGCGAAAGCATGGGAAGTACTCGTATATCCAT
*
39309 GCCTGCAGTAAGGTCATGCAACCAGCAATACCCTGACAATCTCCTCTACTTGCCACCCCTAGCTG
66 GCCTGCAGTAAGGTCATGCAACCAGCAATACCCTGACAATCTCCTCTACTCGCCACCCCTAGCTG
*
39374 ACGATATATATAGGCTAATGTAGCAGCTCCCCATGAATATCTGGGAACAGTCCCCAACCCGTCCT
131 ACGATATATATAGGCTAATGTAGCAGCTCCCCATGAATATCCGGGAACAGTCCCCAACCCGTCCT
39439 TCACCTCGTGCAGGCATGACTC
196 TCACCTCGTGCAGGCATGACTC
39461 GGGGCAATTGAGGCTCAAGACGATCACGTGGGGGGCGAAAGCATGGGAAGTACTCGTATATCCAT
1 GGGGCAATTGAGGCTCAAGACGATCACGTGGGGGGCGAAAGCATGGGAAGTACTCGTATATCCAT
39526 GCCTGCAGTAAGGTCATGCAACCAGCAATACCCTGACAATCTCCTCTACTCGCCACCCCTAGCTG
66 GCCTGCAGTAAGGTCATGCAACCAGCAATACCCTGACAATCTCCTCTACTCGCCACCCCTAGCTG
39591 ACGATATATATAGGCTAATGTAGCAGCTCCCCATGAATATCCGGGAACAGTCCCCAACCCGTCCT
131 ACGATATATATAGGCTAATGTAGCAGCTCCCCATGAATATCCGGGAACAGTCCCCAACCCGTCCT
39656 TCACCTCGTGCAGGCATGA
196 TCACCTCGTGCAGGCATGA
39675 AGGTCTAATC
Statistics
Matches: 210, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
217 210 1.00
ACGTcount: A:0.26, C:0.29, G:0.24, T:0.21
Consensus pattern (217 bp):
GGGGCAATTGAGGCTCAAGACGATCACGTGGGGGGCGAAAGCATGGGAAGTACTCGTATATCCAT
GCCTGCAGTAAGGTCATGCAACCAGCAATACCCTGACAATCTCCTCTACTCGCCACCCCTAGCTG
ACGATATATATAGGCTAATGTAGCAGCTCCCCATGAATATCCGGGAACAGTCCCCAACCCGTCCT
TCACCTCGTGCAGGCATGACTC
Found at i:41235 original size:36 final size:35
Alignment explanation
Indices: 41182--41260 Score: 101
Period size: 36 Copynumber: 2.3 Consensus size: 35
41172 TTGAGGATTT
41182 GTTG-AAG-AAATTGAAGGTTGAACAAGTTTGAAGAA
1 GTTGTAAGAAAATTGAAGGTTGAACAAGTTTG-AG-A
*
41217 GTTGTAAGAAAATT-AAGGTTGAAGAAGTTTGAGA
1 GTTGTAAGAAAATTGAAGGTTGAACAAGTTTGAGA
*
41251 GTTTTAAGAA
1 GTTGTAAGAA
41261 GTTGTTAGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
34 10 0.25
35 6 0.15
36 19 0.47
37 5 0.12
ACGTcount: A:0.42, C:0.01, G:0.28, T:0.29
Consensus pattern (35 bp):
GTTGTAAGAAAATTGAAGGTTGAACAAGTTTGAGA
Found at i:42627 original size:18 final size:18
Alignment explanation
Indices: 42604--42638 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42594 AAACCAGAAA
*
42604 AAATGAAGTAGAAAAAGC
1 AAATGAAATAGAAAAAGC
*
42622 AAATGAAATTGAAAAAG
1 AAATGAAATAGAAAAAG
42639 ATGAAGTTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.03, G:0.20, T:0.14
Consensus pattern (18 bp):
AAATGAAATAGAAAAAGC
Found at i:42648 original size:15 final size:15
Alignment explanation
Indices: 42600--42652 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
42590 TGTAAAACCA
*
42600 GAAAAA-ATGAAGTA
1 GAAAAAGATGAAGTT
*
42614 GAAAAAGCAAATGAAATT
1 GAAAAAG---ATGAAGTT
42632 GAAAAAGATGAAGTT
1 GAAAAAGATGAAGTT
42647 GAAAAA
1 GAAAAA
42653 TGGGTGTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
14 6 0.19
15 13 0.41
18 13 0.41
ACGTcount: A:0.62, C:0.02, G:0.21, T:0.15
Consensus pattern (15 bp):
GAAAAAGATGAAGTT
Found at i:43353 original size:10 final size:10
Alignment explanation
Indices: 43338--43363 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
43328 AGAGAGGAAA
43338 AGACCCAATC
1 AGACCCAATC
43348 AGACCCAATC
1 AGACCCAATC
43358 AGACCC
1 AGACCC
43364 CACCTCGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.38, C:0.42, G:0.12, T:0.08
Consensus pattern (10 bp):
AGACCCAATC
Found at i:44740 original size:18 final size:19
Alignment explanation
Indices: 44713--44750 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
44703 AAAAGCAAAT
*
44713 AGAAAGCAAT-TAAAATAA
1 AGAAAACAATGTAAAATAA
*
44731 AGAAAACAATGTATAATAA
1 AGAAAACAATGTAAAATAA
44750 A
1 A
44751 CATCTTGCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.66, C:0.05, G:0.11, T:0.18
Consensus pattern (19 bp):
AGAAAACAATGTAAAATAA
Found at i:45805 original size:21 final size:21
Alignment explanation
Indices: 45779--45870 Score: 150
Period size: 21 Copynumber: 4.4 Consensus size: 21
45769 TGCTAGGAGA
45779 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
*
45800 TCATTGGAGAAGATTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
45821 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
45842 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
45863 TCATTGGA
1 TCATTGGA
45871 ATTGCCTAAG
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
20 2 0.03
21 65 0.97
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.26
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:46475 original size:31 final size:31
Alignment explanation
Indices: 46440--46533 Score: 188
Period size: 31 Copynumber: 3.0 Consensus size: 31
46430 GTTTGAGCAA
46440 AACTTAGGGTTCTTCAATCTTGTAGAGTCCT
1 AACTTAGGGTTCTTCAATCTTGTAGAGTCCT
46471 AACTTAGGGTTCTTCAATCTTGTAGAGTCCT
1 AACTTAGGGTTCTTCAATCTTGTAGAGTCCT
46502 AACTTAGGGTTCTTCAATCTTGTAGAGTCCT
1 AACTTAGGGTTCTTCAATCTTGTAGAGTCCT
46533 A
1 A
46534 GCAAACAATT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (31 bp):
AACTTAGGGTTCTTCAATCTTGTAGAGTCCT
Found at i:46838 original size:25 final size:24
Alignment explanation
Indices: 46802--46848 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
46792 TCCTTCTATT
46802 CATCTATCATC-AAGTTTTTCATC
1 CATCTATCATCAAAGTTTTTCATC
46825 CATCTCATCCATCAAAGTTTTTCA
1 CATCT-AT-CATCAAAGTTTTTCA
46849 AATTTTCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 4 0.19
26 10 0.48
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (24 bp):
CATCTATCATCAAAGTTTTTCATC
Done.