Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016703.1 Corchorus olitorius cultivar O-4 contig16736, 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: 58354
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:3226 original size:21 final size:22
Alignment explanation
Indices: 3188--3228 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3178 CCAAGCCACA
*
3188 ACCGGCCATTCACCGTGCCAAC
1 ACCGGCCATGCACCGTGCCAAC
3210 ACCGGCCATGC-CCGTGCCA
1 ACCGGCCATGCACCGTGCCA
3229 TCATTCAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.20, C:0.46, G:0.22, T:0.12
Consensus pattern (22 bp):
ACCGGCCATGCACCGTGCCAAC
Found at i:7334 original size:24 final size:24
Alignment explanation
Indices: 7307--7355 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
7297 CTTTCTGGCC
* *
7307 ATTTTGGTACCAATTGTTTGATAG
1 ATTTCGGTACCAACTGTTTGATAG
7331 ATTTCGGTACCAACTGTTTGATAG
1 ATTTCGGTACCAACTGTTTGATAG
7355 A
1 A
7356 AATTGAAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (24 bp):
ATTTCGGTACCAACTGTTTGATAG
Found at i:12485 original size:96 final size:96
Alignment explanation
Indices: 12356--12548 Score: 359
Period size: 96 Copynumber: 2.0 Consensus size: 96
12346 AGTGGGAGAA
12356 AATAATAATTTGGCTCGTGGAAATATTATACCCGGAACTGGTGGGCCAGTCTATCTTCATGTGGA
1 AATAATAATTTGGCTCGTGGAAATATTATACCCGGAACTGGTGGGCCAGTCTATCTTCATGTGGA
12421 GCGTATGGGTGAAAATTAAGCTCATAACTGT
66 GCGTATGGGTGAAAATTAAGCTCATAACTGT
* *
12452 AATAATAATTTGGCTCGTGGAAATGTTATACCCGGAACTGGTGGGCCAGTCTATGTTCATGTGGA
1 AATAATAATTTGGCTCGTGGAAATATTATACCCGGAACTGGTGGGCCAGTCTATCTTCATGTGGA
*
12517 GGGTATGGGTGAAAATTAAGCTCATAACTGT
66 GCGTATGGGTGAAAATTAAGCTCATAACTGT
12548 A
1 A
12549 TTCATGGAAG
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
96 94 1.00
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (96 bp):
AATAATAATTTGGCTCGTGGAAATATTATACCCGGAACTGGTGGGCCAGTCTATCTTCATGTGGA
GCGTATGGGTGAAAATTAAGCTCATAACTGT
Found at i:17394 original size:42 final size:43
Alignment explanation
Indices: 17343--17436 Score: 138
Period size: 45 Copynumber: 2.2 Consensus size: 43
17333 AGTACATTAT
*
17343 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
*
17384 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAT
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
17429 CTAATATT
1 CTAATATT
17437 AATTGTTGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 37 0.79
ACGTcount: A:0.38, C:0.22, G:0.04, T:0.35
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:18661 original size:15 final size:15
Alignment explanation
Indices: 18641--18672 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
18631 CTTATTTCAT
18641 GCACGTAGCAAGATC
1 GCACGTAGCAAGATC
18656 GCACGTAGCAAGATC
1 GCACGTAGCAAGATC
18671 GC
1 GC
18673 TTGTCAGCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.28, G:0.28, T:0.12
Consensus pattern (15 bp):
GCACGTAGCAAGATC
Found at i:24390 original size:43 final size:43
Alignment explanation
Indices: 24329--24427 Score: 180
Period size: 43 Copynumber: 2.3 Consensus size: 43
24319 TATCTAAATT
*
24329 TTAACGGTCCAAGGCTTCTTTCTTTTAACTTACTATATAAGTC
1 TTAACGGTCTAAGGCTTCTTTCTTTTAACTTACTATATAAGTC
24372 TTAACGGTCTAAGGCTTCTTTCTTTTAACTTACTATATAAGTC
1 TTAACGGTCTAAGGCTTCTTTCTTTTAACTTACTATATAAGTC
*
24415 TTAATGGTCTAAG
1 TTAACGGTCTAAG
24428 ACTTTTTTGT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.42
Consensus pattern (43 bp):
TTAACGGTCTAAGGCTTCTTTCTTTTAACTTACTATATAAGTC
Found at i:25488 original size:2 final size:2
Alignment explanation
Indices: 25481--25513 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
25471 ACTTTTATGT
25481 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25514 TATTGCCAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25597 original size:2 final size:2
Alignment explanation
Indices: 25590--25628 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
25580 TTACTCAAAC
25590 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25629 GTTATTTGGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29566 original size:22 final size:22
Alignment explanation
Indices: 29538--29591 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
29528 AAAGTTACTA
29538 AAAAAGT-TACAATGATTATTCT
1 AAAAAGTATA-AATGATTATTCT
*
29560 AAAAAGTATAAGTGATTATTCT
1 AAAAAGTATAAATGATTATTCT
*
29582 AAAAACTATA
1 AAAAAGTATA
29592 TTATTATCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 27 0.93
23 2 0.07
ACGTcount: A:0.50, C:0.07, G:0.09, T:0.33
Consensus pattern (22 bp):
AAAAAGTATAAATGATTATTCT
Found at i:29958 original size:19 final size:20
Alignment explanation
Indices: 29936--29980 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
29926 TTGATTACTA
*
29936 CAAAACAATTA-GAGGTTAT
1 CAAAACAATTACAAGGTTAT
29955 CAAAACAATTACAAGGTTAT
1 CAAAACAATTACAAGGTTAT
29975 CGAAAA
1 C-AAAA
29981 TTCAATAACC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.48
20 8 0.35
21 4 0.17
ACGTcount: A:0.51, C:0.13, G:0.13, T:0.22
Consensus pattern (20 bp):
CAAAACAATTACAAGGTTAT
Found at i:31527 original size:23 final size:24
Alignment explanation
Indices: 31480--31530 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 24
31470 CCACTAATAA
*
31480 TAATTATTATAATAATAAGAAGTT
1 TAATAATTATAATAATAAGAAGTT
*
31504 TAATAATTATAA-AATAAGATGTT
1 TAATAATTATAATAATAAGAAGTT
31527 TAAT
1 TAAT
31531 GTAAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (24 bp):
TAATAATTATAATAATAAGAAGTT
Found at i:31609 original size:84 final size:84
Alignment explanation
Indices: 31506--31662 Score: 262
Period size: 84 Copynumber: 1.9 Consensus size: 84
31496 AAGAAGTTTA
** * *
31506 ATAATTATAAAATAAGATGTTTAATGTAAAAAAATTTGTTATTATTTTAGACTTTTTTAGTATGT
1 ATAATTATAAAATAAGATGTTTAACATAAAAAAATTTGTTATTATTTTAGACTTTTTTAATATGG
31571 AAA-AAAACGTAATGATAT
66 AAATAAAACGTAATGATAT
31589 ATAATTATAATAATAAGATGTTTAACATAAAAAAATTTGTTATTATTTTAGACTTTTTTAATATG
1 ATAATTATAA-AATAAGATGTTTAACATAAAAAAATTTGTTATTATTTTAGACTTTTTTAATATG
31654 GAAATAAAA
65 GAAATAAAA
31663 TCTGGTTGGA
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
83 10 0.15
84 54 0.79
85 4 0.06
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.42
Consensus pattern (84 bp):
ATAATTATAAAATAAGATGTTTAACATAAAAAAATTTGTTATTATTTTAGACTTTTTTAATATGG
AAATAAAACGTAATGATAT
Found at i:35502 original size:22 final size:22
Alignment explanation
Indices: 35453--35503 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
35443 AAATATTACC
* **
35453 ATAATTATTTTTGGCAGCCATA
1 ATAATTATTTTTGCCAGAAATA
35475 ATAATTATTTTTGCCAAGAAATA
1 ATAATTATTTTTGCC-AGAAATA
35498 A-AATTA
1 ATAATTA
35504 GGGAATAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 19 0.76
23 6 0.24
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (22 bp):
ATAATTATTTTTGCCAGAAATA
Found at i:40744 original size:27 final size:26
Alignment explanation
Indices: 40705--40786 Score: 92
Period size: 27 Copynumber: 3.0 Consensus size: 26
40695 TTAATTACCA
40705 AATTAACCAATTTCCTTTTACTCTTT
1 AATTAACCAATTTCCTTTTACTCTTT
* *
40731 AATTAACCAGATTTTCTCTTACTCTCTT
1 AATTAACCA-ATTTCCTTTTACTCT-TT
* *
40759 AACTAACCAAATTTTCTTTTTACTCTTT
1 AATTAACC-AA-TTTCCTTTTACTCTTT
40787 TACTCCTTAG
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
26 9 0.20
27 13 0.28
28 12 0.26
29 12 0.26
ACGTcount: A:0.27, C:0.23, G:0.01, T:0.49
Consensus pattern (26 bp):
AATTAACCAATTTCCTTTTACTCTTT
Found at i:40781 original size:29 final size:27
Alignment explanation
Indices: 40708--40786 Score: 97
Period size: 28 Copynumber: 2.9 Consensus size: 27
40698 ATTACCAAAT
* *
40708 TAACC-AATTTCCTTTTACTCTTTAAT
1 TAACCAAATTTTCTTTTACTCTTTAAC
* *
40734 TAACCAGATTTTCTCTTACTCTCTTAAC
1 TAACCAAATTTTCTTTTACTCT-TTAAC
40762 TAACCAAATTTTCTTTTTACTCTTT
1 TAACCAAATTTTC-TTTTACTCTTT
40787 TACTCCTTAG
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
26 5 0.11
27 13 0.30
28 18 0.41
29 8 0.18
ACGTcount: A:0.25, C:0.24, G:0.01, T:0.49
Consensus pattern (27 bp):
TAACCAAATTTTCTTTTACTCTTTAAC
Found at i:40887 original size:20 final size:21
Alignment explanation
Indices: 40862--40902 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
40852 CAAATTTCCA
*
40862 AATTCATTTTACTT-TTAATT
1 AATTCACTTTACTTCTTAATT
40882 AATTCACTTTACTTCTTAATT
1 AATTCACTTTACTTCTTAATT
40903 TGCAAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.29, C:0.15, G:0.00, T:0.56
Consensus pattern (21 bp):
AATTCACTTTACTTCTTAATT
Found at i:41005 original size:27 final size:26
Alignment explanation
Indices: 40974--41028 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
40964 ATTTACCACT
* *
40974 TTACCCAATTTCATTTTACTTTTTTAA
1 TTACCCAATTACATTCTAC-TTTTTAA
*
41001 TTACCCGATTACATTCTACTTTTTAA
1 TTACCCAATTACATTCTACTTTTTAA
41027 TT
1 TT
41029 GTTAATTTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 9 0.36
27 16 0.64
ACGTcount: A:0.25, C:0.20, G:0.02, T:0.53
Consensus pattern (26 bp):
TTACCCAATTACATTCTACTTTTTAA
Found at i:41203 original size:19 final size:18
Alignment explanation
Indices: 41148--41206 Score: 75
Period size: 18 Copynumber: 3.2 Consensus size: 18
41138 CTTTTCATTC
41148 TTTAATTACCAAATTC-T
1 TTTAATTACCAAATTCTT
* *
41165 TTCACTTTACCAAATTCTT
1 TTTA-ATTACCAAATTCTT
41184 TTTAATTACCAAATTTCTT
1 TTTAATTACCAAA-TTCTT
41203 TTTA
1 TTTA
41207 CTTTACTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
17 3 0.09
18 19 0.54
19 13 0.37
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTAATTACCAAATTCTT
Found at i:41217 original size:19 final size:19
Alignment explanation
Indices: 41168--41218 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
41158 AAATTCTTTC
41168 ACTTTACCAAA-TTCTTTTT
1 ACTTTA-CAAATTTCTTTTT
*
41187 A-ATTACCAAATTTCTTTTT
1 ACTTTA-CAAATTTCTTTTT
*
41206 ACTTTACTAATTT
1 ACTTTACAAATTT
41219 GCCTTTACTC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 8 0.30
19 16 0.59
20 3 0.11
ACGTcount: A:0.29, C:0.18, G:0.00, T:0.53
Consensus pattern (19 bp):
ACTTTACAAATTTCTTTTT
Found at i:41267 original size:19 final size:20
Alignment explanation
Indices: 41222--41268 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
41212 CTAATTTGCC
* *
41222 TTTACTCTTTAATTATCAGA
1 TTTACTTTTTAATTACCAGA
*
41242 -TTCCTTTTTAATTACCA-A
1 TTTACTTTTTAATTACCAGA
41260 TTTACTTTT
1 TTTACTTTT
41269 ACTCTTTAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
18 1 0.05
19 21 0.95
ACGTcount: A:0.26, C:0.17, G:0.02, T:0.55
Consensus pattern (20 bp):
TTTACTTTTTAATTACCAGA
Found at i:41275 original size:44 final size:44
Alignment explanation
Indices: 41184--41433 Score: 293
Period size: 51 Copynumber: 5.3 Consensus size: 44
41174 CCAAATTCTT
* * * * *
41184 TTTAATTACCAAATTTCTTTTTACTTTACTAATTTGCCTTTACTC
1 TTTAATTACCAAATTCCTTTTTA-ATTACCAATTTACTTTTACTC
* *
41229 TTTAATTATCAGATTCCTTTTTAATTACCAATTTACTTTTACTC
1 TTTAATTACCAAATTCCTTTTTAATTACCAATTTACTTTTACTC
*
41273 TTTAATTACCAAATTCTTTGTACACTTTTAATTACCAATTTACTTTTACTC
1 TTTAATTACCAAATTC------C-TTTTTAATTACCAATTTACTTTTACTC
41324 TTTAATTACCAAATTCCTTTTTAATTACCAATTTACTTTTACTC
1 TTTAATTACCAAATTCCTTTTTAATTACCAATTTACTTTTACTC
41368 TTTAATTACCAAATTCTTTGTACTCTTTTAATTACCAATTTACTTTTACTC
1 TTTAATTACCAAATTC------CT-TTTTAATTACCAATTTACTTTTACTC
41419 TTTAATTACCAAATT
1 TTTAATTACCAAATT
41434 TTCTCTTTGT
Statistics
Matches: 180, Mismatches: 11, Indels: 22
0.85 0.05 0.10
Matches are distributed among these distances:
44 73 0.41
45 21 0.12
50 3 0.02
51 83 0.46
ACGTcount: A:0.28, C:0.19, G:0.02, T:0.51
Consensus pattern (44 bp):
TTTAATTACCAAATTCCTTTTTAATTACCAATTTACTTTTACTC
Found at i:41302 original size:26 final size:25
Alignment explanation
Indices: 41247--41490 Score: 229
Period size: 25 Copynumber: 9.6 Consensus size: 25
41237 TCAGATTCCT
*
41247 TTTTAATTACCAATTTACTTTTACTC
1 TTTTAATTACCAAATT-CTTTTACTC
*
41273 -TTTAATTACCAAATTCTTTGTACAC
1 TTTTAATTACCAAATTCTTT-TACTC
*
41298 TTTTAATTACCAATTTACTTTTACTC
1 TTTTAATTACCAAATT-CTTTTACTC
41324 -TTTAATTACCAAATTC-----CT-
1 TTTTAATTACCAAATTCTTTTACTC
*
41342 TTTTAATTACCAATTTACTTTTACTC
1 TTTTAATTACCAAATT-CTTTTACTC
41368 -TTTAATTACCAAATTCTTTGTACTC
1 TTTTAATTACCAAATTCTTT-TACTC
*
41393 TTTTAATTACCAATTTACTTTTACTC
1 TTTTAATTACCAAATT-CTTTTACTC
41419 -TTTAATTACCAAATTTTCTCTTTGTACTC
1 TTTTAATTACCAAA---T-TCTTT-TACTC
* **
41448 TTTTAATTACCAATTTCATAGTACTC
1 TTTTAATTACCAAATTC-TTTTACTC
41474 TTTTAATTACCCAAATT
1 TTTTAATTA-CCAAATT
41491 TACTAATTAC
Statistics
Matches: 183, Mismatches: 13, Indels: 43
0.77 0.05 0.18
Matches are distributed among these distances:
19 16 0.09
20 1 0.01
24 9 0.05
25 65 0.36
26 53 0.29
27 16 0.09
28 5 0.03
29 6 0.03
30 12 0.07
ACGTcount: A:0.29, C:0.20, G:0.02, T:0.50
Consensus pattern (25 bp):
TTTTAATTACCAAATTCTTTTACTC
Found at i:41303 original size:51 final size:51
Alignment explanation
Indices: 41247--41490 Score: 342
Period size: 51 Copynumber: 4.8 Consensus size: 51
41237 TCAGATTCCT
*
41247 TTTTAATTACCAATTTACTTTTACTCTTTAATTACCAAATTCTTTGTACAC
1 TTTTAATTACCAATTTACTTTTACTCTTTAATTACCAAATTCTTTGTACTC
41298 TTTTAATTACCAATTTACTTTTACTCTTTAATTACCAAATTC------CT-
1 TTTTAATTACCAATTTACTTTTACTCTTTAATTACCAAATTCTTTGTACTC
41342 TTTTAATTACCAATTTACTTTTACTCTTTAATTACCAAATTCTTTGTACTC
1 TTTTAATTACCAATTTACTTTTACTCTTTAATTACCAAATTCTTTGTACTC
41393 TTTTAATTACCAATTTACTTTTACTCTTTAATTACCAAATTTTCTCTTTGTACTC
1 TTTTAATTACCAATTTACTTTTACTCTTTAATTACCAAA---T-TCTTTGTACTC
**
41448 TTTTAATTACCAATTT-CATAGTACTCTTTTAATTACCCAAATT
1 TTTTAATTACCAATTTAC-TTTTACTC-TTTAATTA-CCAAATT
41491 TACTAATTAC
Statistics
Matches: 176, Mismatches: 3, Indels: 26
0.86 0.01 0.13
Matches are distributed among these distances:
44 42 0.24
45 1 0.01
50 2 0.01
51 81 0.46
53 1 0.01
54 3 0.02
55 33 0.19
56 8 0.05
57 5 0.03
ACGTcount: A:0.29, C:0.20, G:0.02, T:0.50
Consensus pattern (51 bp):
TTTTAATTACCAATTTACTTTTACTCTTTAATTACCAAATTCTTTGTACTC
Found at i:41313 original size:95 final size:95
Alignment explanation
Indices: 41222--41433 Score: 397
Period size: 95 Copynumber: 2.2 Consensus size: 95
41212 CTAATTTGCC
* *
41222 TTTACTCTTTAATTATCAGATTCCTTTTTAATTACCAATTTACTTTTACTCTTTAATTACCAAAT
1 TTTACTCTTTAATTACCAAATTCCTTTTTAATTACCAATTTACTTTTACTCTTTAATTACCAAAT
41287 TCTTTGTACACTTTTAATTACCAATTTACT
66 TCTTTGTACACTTTTAATTACCAATTTACT
41317 TTTACTCTTTAATTACCAAATTCCTTTTTAATTACCAATTTACTTTTACTCTTTAATTACCAAAT
1 TTTACTCTTTAATTACCAAATTCCTTTTTAATTACCAATTTACTTTTACTCTTTAATTACCAAAT
*
41382 TCTTTGTACTCTTTTAATTACCAATTTACT
66 TCTTTGTACACTTTTAATTACCAATTTACT
41412 TTTACTCTTTAATTACCAAATT
1 TTTACTCTTTAATTACCAAATT
41434 TTCTCTTTGT
Statistics
Matches: 114, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
95 114 1.00
ACGTcount: A:0.29, C:0.19, G:0.01, T:0.50
Consensus pattern (95 bp):
TTTACTCTTTAATTACCAAATTCCTTTTTAATTACCAATTTACTTTTACTCTTTAATTACCAAAT
TCTTTGTACACTTTTAATTACCAATTTACT
Found at i:41362 original size:19 final size:19
Alignment explanation
Indices: 41317--41363 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
41307 CCAATTTACT
*
41317 TTTACTCTTTAATTACCAA
1 TTTACTTTTTAATTACCAA
* *
41336 ATTCCTTTTTAATTACCAA
1 TTTACTTTTTAATTACCAA
41355 TTTACTTTT
1 TTTACTTTT
41364 ACTCTTTAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.28, C:0.19, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTACTTTTTAATTACCAA
Found at i:49417 original size:24 final size:24
Alignment explanation
Indices: 49385--49447 Score: 110
Period size: 24 Copynumber: 2.7 Consensus size: 24
49375 ATGGCCCAAC
49385 GCTGG-CCAGGCGCGCGGGCCTGA
1 GCTGGCCCAGGCGCGCGGGCCTGA
*
49408 GCTGGCCCAGGCGCACGGGCCTGA
1 GCTGGCCCAGGCGCGCGGGCCTGA
49432 GCTGGCCCAGGCGCGC
1 GCTGGCCCAGGCGCGC
49448 CAGGCCCTGG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
23 5 0.14
24 32 0.86
ACGTcount: A:0.10, C:0.38, G:0.44, T:0.08
Consensus pattern (24 bp):
GCTGGCCCAGGCGCGCGGGCCTGA
Found at i:50673 original size:18 final size:17
Alignment explanation
Indices: 50646--50679 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
50636 TTGATTGATT
50646 ATCTTGGTTTTACTTTG
1 ATCTTGGTTTTACTTTG
*
50663 ATCTATGGTTTTGCTTT
1 ATCT-TGGTTTTACTTT
50680 TAATTGTTTT
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:0.12, C:0.12, G:0.18, T:0.59
Consensus pattern (17 bp):
ATCTTGGTTTTACTTTG
Found at i:50878 original size:37 final size:37
Alignment explanation
Indices: 50828--50912 Score: 143
Period size: 37 Copynumber: 2.3 Consensus size: 37
50818 CCCGTTGAGG
* *
50828 AAAATGTTTTATTACTGTTTTTATTTAAATGCTTTAT
1 AAAATGTTTTATTACTGATTTTATTTAAATGCTTAAT
50865 AAAATGTTTTATTACTGATTTTATTTAAATGCTTAAT
1 AAAATGTTTTATTACTGATTTTATTTAAATGCTTAAT
*
50902 AAAATATTTTA
1 AAAATGTTTTA
50913 ATAAATTATT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.35, C:0.05, G:0.07, T:0.53
Consensus pattern (37 bp):
AAAATGTTTTATTACTGATTTTATTTAAATGCTTAAT
Found at i:57860 original size:19 final size:18
Alignment explanation
Indices: 57821--57859 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
57811 TTGCAATTAG
57821 AAATCATTTACATTAAAA
1 AAATCATTTACATTAAAA
57839 AAATCATTTACATTAAAA
1 AAATCATTTACATTAAAA
57857 AAA
1 AAA
57860 ACTGTTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.31
Consensus pattern (18 bp):
AAATCATTTACATTAAAA
Done.