Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023185.1 Corchorus olitorius cultivar O-4 contig23218, 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: 21050
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35
Found at i:1675 original size:11 final size:12
Alignment explanation
Indices: 1655--1679 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1645 GAAACTCATG
1655 TTTTATTTTTTT
1 TTTTATTTTTTT
1667 TTTTATTTTTTT
1 TTTTATTTTTTT
1679 T
1 T
1680 ATGGGTCCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTTATTTTTTT
Found at i:2984 original size:40 final size:40
Alignment explanation
Indices: 2923--3048 Score: 136
Period size: 40 Copynumber: 3.2 Consensus size: 40
2913 ATTTATTCAC
*
2923 TATTTATTT-TTTTTAACTATTATCTATTTATTTACTATT
1 TATTTTTTTATTTTTAACTATTATCTATTTATTTACTATT
*
2962 TATTTTTTTATTTTTAATTATTATCTATTTATTTACT-TT
1 TATTTTTTTATTTTTAACTATTATCTATTTATTTACTATT
* * * * * *
3001 T-TTTTATTA-ATTTAGCTATTATTTATTTAATTATTA-T
1 TATTTTTTTATTTTTAACTATTATCTATTTATTTACTATT
3038 TATTATTTTTA
1 TATT-TTTTTA
3049 GTTACATATT
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
37 22 0.30
38 9 0.12
39 16 0.22
40 26 0.36
ACGTcount: A:0.26, C:0.05, G:0.01, T:0.68
Consensus pattern (40 bp):
TATTTTTTTATTTTTAACTATTATCTATTTATTTACTATT
Found at i:2995 original size:33 final size:33
Alignment explanation
Indices: 2958--3048 Score: 92
Period size: 37 Copynumber: 2.6 Consensus size: 33
2948 ATTTATTTAC
*
2958 TATTTATTTTTTTATTTTTAATTATTATCTATT
1 TATTTATTTTTTTATTTTTAACTATTATCTATT
* *
2991 TATTTACTTTTTTTTATTAATTTAGCTATTATTTATT
1 TATTTA--TTTTTTTATT--TTTAACTATTATCTATT
* *
3028 TAATTATTATTATTATTTTTA
1 TATTTATT-TTTTTATTTTTA
3049 GTTACATATT
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
33 6 0.12
34 4 0.08
35 12 0.25
36 7 0.15
37 19 0.40
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.69
Consensus pattern (33 bp):
TATTTATTTTTTTATTTTTAACTATTATCTATT
Found at i:3007 original size:25 final size:25
Alignment explanation
Indices: 2949--3048 Score: 70
Period size: 25 Copynumber: 4.2 Consensus size: 25
2939 CTATTATCTA
* * *
2949 TTTATTTACTATTTATTTTTTTATT
1 TTTATTTATTATCTATTTATTTATT
*
2974 TTTAATTATTATCTATTTATTTACTT
1 TTTATTTATTATCTATTTATTTA-TT
**
3000 TTT-TTTATTA---ATTTAGCTATT
1 TTTATTTATTATCTATTTATTTATT
3021 ATTTATTTAATTAT-TA-TTA-TTATT
1 -TTTATTT-ATTATCTATTTATTTATT
3045 TTTA
1 TTTA
3049 GTTACATATT
Statistics
Matches: 61, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
21 2 0.03
22 10 0.16
23 7 0.11
24 8 0.13
25 28 0.46
26 6 0.10
ACGTcount: A:0.26, C:0.04, G:0.01, T:0.69
Consensus pattern (25 bp):
TTTATTTATTATCTATTTATTTATT
Found at i:3022 original size:29 final size:33
Alignment explanation
Indices: 2958--3044 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 33
2948 ATTTATTTAC
* * *
2958 TATTTATTTTTTTATTTTTAATTATTATCTATT
1 TATTTACTTTTTTATTATTAATTATTAGCTATT
2991 TATTTACTTTTTT-TTATTAA-T-TTAGCTA-T
1 TATTTACTTTTTTATTATTAATTATTAGCTATT
*
3020 TATTTA-TTTAATTATTATT-ATTATT
1 TATTTACTTT-TTTATTATTAATTATT
3045 TTTAGTTACA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
28 3 0.07
29 10 0.22
30 12 0.26
31 3 0.07
32 6 0.13
33 12 0.26
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.69
Consensus pattern (33 bp):
TATTTACTTTTTTATTATTAATTATTAGCTATT
Found at i:3067 original size:58 final size:58
Alignment explanation
Indices: 2942--3067 Score: 134
Period size: 58 Copynumber: 2.2 Consensus size: 58
2932 TTTTTAACTA
* * * *
2942 TTATCTATTTATTTACTATTTATTTTTTTATTTTTAATTATTATCTATTTATTTACTT
1 TTATCTATTAATTTACTATTTATTTTTTAATTATTAATTATTATCTATTTAGTTACTT
* *
3000 TTTTTTATTAATTTAGCTA-TTATTTATTTAATTATT-ATTATTAT-T-TTTAGTTACATAT
1 TTATCTATTAATTTA-CTATTTATTT-TTTAATTATTAATTATTATCTATTTAGTTAC-T-T
3058 TTATCTATTA
1 TTATCTATTA
3068 TTCTCTGTAG
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
56 8 0.14
57 2 0.04
58 35 0.62
59 11 0.20
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.66
Consensus pattern (58 bp):
TTATCTATTAATTTACTATTTATTTTTTAATTATTAATTATTATCTATTTAGTTACTT
Found at i:3082 original size:24 final size:24
Alignment explanation
Indices: 3055--3111 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
3045 TTTAGTTACA
* *
3055 TATTTATCTA-TTATTCTCTGTAGC
1 TATTTATCTATTTA-TCTCTATACC
3079 TATTTATCTATTTATCTCTATACC
1 TATTTATCTATTTATCTCTATACC
3103 TATTTATCT
1 TATTTATCT
3112 TTTTTTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 27 0.90
25 3 0.10
ACGTcount: A:0.23, C:0.18, G:0.04, T:0.56
Consensus pattern (24 bp):
TATTTATCTATTTATCTCTATACC
Found at i:12386 original size:14 final size:13
Alignment explanation
Indices: 12353--12435 Score: 69
Period size: 12 Copynumber: 7.2 Consensus size: 13
12343 AACCGTTTAA
12353 TAATTATATATAT
1 TAATTATATATAT
*
12366 T-ATTATATAT-G
1 TAATTATATATAT
12377 TAATTATATATAT
1 TAATTATATATAT
*
12390 T--TAATAT-TAT
1 TAATTATATATAT
12400 T--TTATATATA-
1 TAATTATATATAT
12410 TAA-TATATAT-T
1 TAATTATATATAT
*
12421 TAATTATAAATAT
1 TAATTATATATAT
12434 TA
1 TA
12436 CTAAACGGTC
Statistics
Matches: 57, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
10 10 0.18
11 18 0.32
12 24 0.42
13 5 0.09
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (13 bp):
TAATTATATATAT
Found at i:12407 original size:19 final size:20
Alignment explanation
Indices: 12352--12433 Score: 68
Period size: 19 Copynumber: 4.3 Consensus size: 20
12342 AAACCGTTTA
*
12352 ATAATTATATATATTAT-TAT
1 ATAA-TATATATTTTATATAT
* *
12372 AT-ATGTA-ATTATATATAT
1 ATAATATATATTTTATATAT
*
12390 TTAATAT-TATTTTATATAT
1 ATAATATATATTTTATATAT
*
12409 ATAATATATATTTAAT-TAT
1 ATAATATATATTTTATATAT
12428 A-AATAT
1 ATAATAT
12434 TACTAAACGG
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
17 5 0.10
18 12 0.24
19 24 0.48
20 9 0.18
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (20 bp):
ATAATATATATTTTATATAT
Found at i:12426 original size:28 final size:29
Alignment explanation
Indices: 12350--12427 Score: 81
Period size: 30 Copynumber: 2.7 Consensus size: 29
12340 TTAAACCGTT
* *
12350 TAATAAT-TATATAT-ATTATTATATATG
1 TAATAATATATATTTAATTATTATATATA
* *
12377 TAATTATATATATTTAA-TATTATTTTATA
1 TAATAATATATATTTAATTATTA-TATATA
12406 TATATAATATATATTTAATTAT
1 TA-ATAATATATATTTAATTAT
12428 AAATATTACT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
27 6 0.15
28 11 0.27
29 7 0.17
30 14 0.34
31 3 0.07
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (29 bp):
TAATAATATATATTTAATTATTATATATA
Found at i:17725 original size:22 final size:22
Alignment explanation
Indices: 17616--17737 Score: 86
Period size: 22 Copynumber: 5.5 Consensus size: 22
17606 TGAAAACATT
*
17616 ACTATAAAATTTTGATAATCTAC
1 ACTATGAAATTTTGATAATC-AC
* * * *
17639 A-TGTGAAATGTTGGTAAGCAC
1 ACTATGAAATTTTGATAATCAC
* * * *
17660 ACTATGATACTTTTTATAACCTC
1 ACTATGA-AATTTTGATAATCAC
* * *
17683 CCTATGAAATCTT-AGTGATCAC
1 ACTATGAAATTTTGA-TAATCAC
*
17705 ACTGTGAAATTTTGATAATCAC
1 ACTATGAAATTTTGATAATCAC
17727 ACTATGAAATT
1 ACTATGAAATT
17738 GTAATGACCT
Statistics
Matches: 72, Mismatches: 23, Indels: 9
0.69 0.22 0.09
Matches are distributed among these distances:
21 4 0.06
22 51 0.71
23 17 0.24
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (22 bp):
ACTATGAAATTTTGATAATCAC
Found at i:17789 original size:23 final size:23
Alignment explanation
Indices: 17751--17834 Score: 107
Period size: 23 Copynumber: 3.7 Consensus size: 23
17741 ATGACCTCGG
* * * * *
17751 TATAAAAGTTTCATAAACATTCA
1 TATAAAATTTTGATAAACCTCCT
*
17774 TATAAGATTTTGATAAACCTCCT
1 TATAAAATTTTGATAAACCTCCT
17797 TATAAAATTTTGAT-AACCTCCT
1 TATAAAATTTTGATAAACCTCCT
17819 TATAAAATTTTGATAA
1 TATAAAATTTTGATAA
17835 TCACAAATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
22 22 0.42
23 31 0.58
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.39
Consensus pattern (23 bp):
TATAAAATTTTGATAAACCTCCT
Found at i:17817 original size:22 final size:22
Alignment explanation
Indices: 17780--18556 Score: 260
Period size: 22 Copynumber: 35.5 Consensus size: 22
17770 TTCATATAAG
*
17780 ATTTTGATAAACCTCCTTATAAA
1 ATTTTGAT-AACCTCCTTATGAA
*
17803 ATTTTGATAACCTCCTTATAAA
1 ATTTTGATAACCTCCTTATGAA
*
17825 ATTTTGATAA--T-C--A-CAA
1 ATTTTGATAACCTCCTTATGAA
* * *
17841 ATTTCGATAACCTCCCTATGAT
1 ATTTTGATAACCTCCTTATGAA
* * *
17863 TTTTTGATAACTTCATTATGAA
1 ATTTTGATAACCTCCTTATGAA
* *
17885 ATTTTGTTAACCTCCCTATGAA
1 ATTTTGATAACCTCCTTATGAA
*
17907 ATTTTGATAA-C-CC-TATAAA
1 ATTTTGATAACCTCCTTATGAA
* *
17926 ATTTTGA-AAACTAAAC-TATGAA
1 ATTTTGATAACCT--CCTTATGAA
* *
17948 ATTTTGATATCCTCCCTATGAA
1 ATTTTGATAACCTCCTTATGAA
17970 ATTTTGATAATCC-CCATT-TGAA
1 ATTTTGATAA-CCTCC-TTATGAA
* * * *
17992 ATTTTAATAACCTTCATACGAA
1 ATTTTGATAACCTCCTTATGAA
* * **
18014 ATTTTGGTAACCGCACAAATGCAA
1 ATTTTGATAACCTC-CTTATG-AA
*
18038 TTTTTTGATAACCTCACTT-TGAA
1 -ATTTTGATAACCTC-CTTATGAA
**
18061 A---T-ACCACACT-C-TA--AA
1 ATTTTGATAAC-CTCCTTATGAA
* * *** *
18076 ATATGGATAATAACATTATGAA
1 ATTTTGATAACCTCCTTATGAA
* *
18098 ATTTCGATAACCTTCTTATGAA
1 ATTTTGATAACCTCCTTATGAA
* *
18120 ATTTCGATAACCTCCCTATGAA
1 ATTTTGATAACCTCCTTATGAA
*
18142 ATTTTGCTAACCTCAC-TATGAA
1 ATTTTGATAACCTC-CTTATGAA
** *
18164 ATTTTGATAATTATAC-TATGAA
1 ATTTTGATAA-CCTCCTTATGAA
*
18186 A-TTTGA-AACCTCCATATGAA
1 ATTTTGATAACCTCCTTATGAA
* * ** *
18206 ATTTTAATAACCACAATATAAAA
1 ATTTTGATAACCTCCTTAT-GAA
*
18229 ATTTTTCATAACCTCAC-TA-GAAA
1 A-TTTTGATAACCTC-CTTATG-AA
*
18252 ATTTTGATAACCTTCC-TATGGA
1 ATTTTGATAACC-TCCTTATGAA
* * *
18274 ATTTTGATAACCACATTA-GGA
1 ATTTTGATAACCTCCTTATGAA
* *
18295 ATTTTGATGACCTTCC-TATGCA
1 ATTTTGATAACC-TCCTTATGAA
* * *
18317 ATTTTGGTAATCTGATCTCTATGAA
1 ATTTTGATAACCT--CCT-TATGAA
* * *
18342 TTTTTGATAA-CTACTCTATGAG
1 ATTTTGATAACCTCCT-TATGAA
**** *
18364 ATTTTGATTGGTTCCTGATGAA
1 ATTTTGATAACCTCCTTATGAA
* *
18386 ATTTTGATAACCACAC-TATAAA
1 ATTTTGATAACCTC-CTTATGAA
** * *
18408 ATTTTGATAATATTCGTATGAA
1 ATTTTGATAACCTCCTTATGAA
* * *
18430 ATTTAGAATTTTATAACATTAC-TATGAA
1 A--T----TTTGATAAC-CTCCTTATGAA
*
18458 ATTTTGATAACCACAC-TATGAA
1 ATTTTGATAACCTC-CTTATGAA
* *
18480 ATCTTTAATAACCTCCTTATAAA
1 AT-TTTGATAACCTCCTTATGAA
** *
18503 ATTTAAATAACCACAC-TATGAA
1 ATTTTGATAACCTC-CTTATGAA
*
18525 ATTTTGATAACCTCGC-TATGGA
1 ATTTTGATAACCTC-CTTATGAA
18547 ATTTTGATAA
1 ATTTTGATAA
18557 TCTCTTTGAT
Statistics
Matches: 563, Mismatches: 130, Indels: 123
0.69 0.16 0.15
Matches are distributed among these distances:
15 3 0.01
16 12 0.02
17 2 0.00
18 6 0.01
19 22 0.04
20 14 0.02
21 34 0.06
22 353 0.63
23 54 0.10
24 20 0.04
25 26 0.05
26 1 0.00
28 14 0.02
29 2 0.00
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.38
Consensus pattern (22 bp):
ATTTTGATAACCTCCTTATGAA
Found at i:18252 original size:24 final size:22
Alignment explanation
Indices: 18204--18264 Score: 59
Period size: 24 Copynumber: 2.7 Consensus size: 22
18194 CCTCCATATG
* *
18204 AAATTTTAATAACCACAATATAA
1 AAATTTTAATAACCTCAATA-GA
* *
18227 AAATTTTTCATAACCTCACTAGA
1 AAA-TTTTAATAACCTCAATAGA
*
18250 AAATTTTGATAACCT
1 AAATTTTAATAACCT
18265 TCCTATGGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
22 11 0.34
23 7 0.22
24 14 0.44
ACGTcount: A:0.46, C:0.16, G:0.03, T:0.34
Consensus pattern (22 bp):
AAATTTTAATAACCTCAATAGA
Found at i:18455 original size:28 final size:29
Alignment explanation
Indices: 18407--18461 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
18397 CACACTATAA
*
18407 AATTTTGATAATATTCGTATGAAATTTAG
1 AATTTTGATAACATTCGTATGAAATTTAG
18436 AATTTT-ATAACATTAC-TATGAAATTT
1 AATTTTGATAACATT-CGTATGAAATTT
18462 TGATAACCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.45
Consensus pattern (29 bp):
AATTTTGATAACATTCGTATGAAATTTAG
Found at i:18589 original size:22 final size:22
Alignment explanation
Indices: 18561--18907 Score: 137
Period size: 22 Copynumber: 15.4 Consensus size: 22
18551 TGATAATCTC
*
18561 TTTGATAGCCTCCCTATGAAAT
1 TTTGATAACCTCCCTATGAAAT
* *
18583 TTTGATAACCACACTATGAAAT
1 TTTGATAACCTCCCTATGAAAT
* *
18605 TTTGATAACTTTCCTATGAAAT
1 TTTGATAACCTCCCTATGAAAT
* *
18627 TTTAATAACCTAATCCATATGAAAT
1 TTTGATAACC---TCCCTATGAAAT
** * *
18652 TTTGATAACCTTTCAATAAAAT
1 TTTGATAACCTCCCTATGAAAT
* * ** *
18674 TTTAATAATCT-TTTGATGCCACAAAAAAA
1 TTTGATAACCTCCCT-ATG-------AAAT
* * *
18703 ATTGATAACCTTCCTTTGAAAT
1 TTTGATAACCTCCCTATGAAAT
* *
18725 TTTAATAACATAATCCCTAT-AAAT
1 TTTGATAAC---CTCCCTATGAAAT
* * *
18749 TTTGATAACCACTCAATGAAAT
1 TTTGATAACCTCCCTATGAAAT
* * *
18771 TTTGTTAACCTTCATATGAAAT
1 TTTGATAACCTCCCTATGAAAT
* * *
18793 TTTGGTAACCGCACTATGAAAT
1 TTTGATAACCTCCCTATGAAAT
* * * ** *
18815 TTGGGTAACCACAATATGAATT
1 TTTGATAACCTCCCTATGAAAT
* *
18837 TTTGATAATCTCCCTAT-AAAA
1 TTTGATAACCTCCCTATGAAAT
* ***
18858 TTTGTTAACCGGACTATGAAA-
1 TTTGATAACCTCCCTATGAAAT
* *
18879 TTTGATAAACTCCTTATGAAA-
1 TTTGATAACCTCCCTATGAAAT
18900 TTTGATAA
1 TTTGATAA
18908 TGTCATTAAG
Statistics
Matches: 234, Mismatches: 74, Indels: 35
0.68 0.22 0.10
Matches are distributed among these distances:
21 42 0.18
22 142 0.61
24 12 0.05
25 24 0.10
29 13 0.06
30 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (22 bp):
TTTGATAACCTCCCTATGAAAT
Found at i:18622 original size:78 final size:78
Alignment explanation
Indices: 18481--18634 Score: 211
Period size: 78 Copynumber: 2.0 Consensus size: 78
18471 CACTATGAAA
* *
18481 TCTTTAATAACCTCCTTATAAAATTTAAATAACCACACTATGAAATTTTGATAACCTCGCTATGG
1 TCTTTAATAACCTCCCTATAAAATTTAAATAACCACACTATGAAATTTTGATAACCTCGCTATGA
*
18546 AATTTTGATAATC
66 AATTTTAATAATC
* * * ** *
18559 TCTTTGATAGCCTCCCTATGAAATTTTGATAACCACACTATGAAATTTTGATAACTTTC-CTATG
1 TCTTTAATAACCTCCCTATAAAATTTAAATAACCACACTATGAAATTTTGATAAC-CTCGCTATG
18623 AAATTTTAATAA
65 AAATTTTAATAA
18635 CCTAATCCAT
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
78 64 0.97
79 2 0.03
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (78 bp):
TCTTTAATAACCTCCCTATAAAATTTAAATAACCACACTATGAAATTTTGATAACCTCGCTATGA
AATTTTAATAATC
Found at i:18686 original size:123 final size:122
Alignment explanation
Indices: 18451--18686 Score: 300
Period size: 123 Copynumber: 1.9 Consensus size: 122
18441 TATAACATTA
18451 CTATGAAATTTTGATAACCACACTATGAAATCTTTAATAACCTCCTTATAAAATTTAAATAACCA
1 CTATGAAATTTTGATAACCACACTATGAAATCTTTAATAACCTCCTTATAAAATTTAAATAACCA
* ** *
18516 CACTATGAAATTTTGATAACCTCGCTATGGAATTTTGATAATCTCTTTGATAGCCTCC
66 CACTATGAAATTTTGATAACCTCGCAATAAAATTTTAATAA-CTCTTTGATAGCCTCC
* * * *
18574 CTATGAAATTTTGATAACCACACTATGAAAT-TTTGATAACTTTCC-TATGAAATTTTAATAACC
1 CTATGAAATTTTGATAACCACACTATGAAATCTTTAATAAC-CTCCTTATAAAATTTAAATAACC
**
18637 TA-ATCCATATGAAATTTTGATAACCTTTCAATAAAATTTTAATAA-TCTTT
65 -ACA--C-TATGAAATTTTGATAACCTCGCAATAAAATTTTAATAACTCTTT
18687 TGATGCCACA
Statistics
Matches: 98, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
122 25 0.26
123 40 0.41
124 1 0.01
125 32 0.33
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.38
Consensus pattern (122 bp):
CTATGAAATTTTGATAACCACACTATGAAATCTTTAATAACCTCCTTATAAAATTTAAATAACCA
CACTATGAAATTTTGATAACCTCGCAATAAAATTTTAATAACTCTTTGATAGCCTCC
Found at i:18920 original size:21 final size:21
Alignment explanation
Indices: 18875--18923 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
18865 ACCGGACTAT
* *
18875 GAAATTTGATAAACTCCTTAT
1 GAAATTTGATAAACTCATTAA
**
18896 GAAATTTGATAATGTCATTAA
1 GAAATTTGATAAACTCATTAA
18917 GAAATTT
1 GAAATTT
18924 TGATTACCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (21 bp):
GAAATTTGATAAACTCATTAA
Found at i:19054 original size:21 final size:22
Alignment explanation
Indices: 19005--19046 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
18995 TAATTTTCCT
19005 CATGAAAGCTTGATAATCTCAC
1 CATGAAAGCTTGATAATCTCAC
19027 CATGAAAG-TTGATAATCTCA
1 CATGAAAGCTTGATAATCTCA
19047 TTATGAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (22 bp):
CATGAAAGCTTGATAATCTCAC
Found at i:19709 original size:22 final size:22
Alignment explanation
Indices: 19679--19800 Score: 79
Period size: 22 Copynumber: 5.7 Consensus size: 22
19669 TAGTGTCCGA
*
19679 GGTTTTCAAAATTTCACAGTGT
1 GGTTATCAAAATTTCACAGTGT
*
19701 GGTTATCAAAATTT--CATTGT
1 GGTTATCAAAATTTCACAGTGT
* * * * *
19721 AGTTATCAAATTTTCATAGGGA
1 GGTTATCAAAATTTCACAGTGT
* * * * *
19743 GGTTATCGAAATTTTATAATGA
1 GGTTATCAAAATTTCACAGTGT
* * *
19765 GATTATC-AATTTTCACAGTAT
1 GGTTATCAAAATTTCACAGTGT
*
19786 GGTTATCAATATTTC
1 GGTTATCAAAATTTC
19801 TACATTTGAG
Statistics
Matches: 73, Mismatches: 24, Indels: 6
0.71 0.23 0.06
Matches are distributed among these distances:
20 17 0.23
21 14 0.19
22 42 0.58
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.42
Consensus pattern (22 bp):
GGTTATCAAAATTTCACAGTGT
Found at i:19790 original size:43 final size:42
Alignment explanation
Indices: 19684--19800 Score: 114
Period size: 42 Copynumber: 2.8 Consensus size: 42
19674 TCCGAGGTTT
* *
19684 TCAAAATTTCACAGTGTGGTTATCAAAATTTCATTGTAGTTA
1 TCAAATTTTCACAGTATGGTTATCAAAATTTCATTGTAGTTA
* * * *
19726 TCAAATTTTCATAGGGA-GGTTATCGAAATTTTATAATG-AGATTA
1 TCAAATTTTCACA-GTATGGTTATCAAAATTTCAT--TGTAG-TTA
*
19770 TC-AATTTTCACAGTATGGTTATCAATATTTC
1 TCAAATTTTCACAGTATGGTTATCAAAATTTC
19801 TACATTTGAG
Statistics
Matches: 59, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
42 28 0.47
43 24 0.41
44 7 0.12
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (42 bp):
TCAAATTTTCACAGTATGGTTATCAAAATTTCATTGTAGTTA
Done.