Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006767.1 Corchorus capsularis cultivar CVL-1 contig06788, 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: 64976
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:579 original size:19 final size:18
Alignment explanation
Indices: 555--590 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
545 TGAAGATTTC
555 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
574 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
591 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:3327 original size:19 final size:18
Alignment explanation
Indices: 3295--3330 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3285 TTGAATTAAT
*
3295 TCTTCAATTGTCTTCAAA
1 TCTTCAATTATCTTCAAA
3313 TCTTCAAATTATCTTCAA
1 TCTTC-AATTATCTTCAA
3331 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.31, C:0.22, G:0.03, T:0.44
Consensus pattern (18 bp):
TCTTCAATTATCTTCAAA
Found at i:6215 original size:24 final size:24
Alignment explanation
Indices: 6196--6250 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
6186 CCATTCAACG
*
6196 GCAGAAGCCAACCACTATTCTACC
1 GCAGAAGCCAACCACAATTCTACC
*
6220 GCAGAAGCCAACTACAATTCTACC
1 GCAGAAGCCAACCACAATTCTACC
6244 GCAGAAG
1 GCAGAAG
6251 TCAGTTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.36, C:0.33, G:0.16, T:0.15
Consensus pattern (24 bp):
GCAGAAGCCAACCACAATTCTACC
Found at i:11799 original size:27 final size:26
Alignment explanation
Indices: 11743--11831 Score: 128
Period size: 27 Copynumber: 3.4 Consensus size: 26
11733 GGTGGCGTTG
11743 GCATGAGTCCCATA-TG-GGAGCTTCA
1 GCATGAGTCCCA-ACTGCGGAGCTTCA
11768 GCATGAGTCCCAACTGCGGAAGCTTCA
1 GCATGAGTCCCAACTGCGG-AGCTTCA
*
11795 GCATGAGTCCCAACTGCGGGAGCTTCG
1 GCATGAGTCCCAACTGC-GGAGCTTCA
11822 GCATGAGTCC
1 GCATGAGTCC
11832 TTCAGCATAA
Statistics
Matches: 59, Mismatches: 1, Indels: 6
0.89 0.02 0.09
Matches are distributed among these distances:
24 1 0.02
25 14 0.24
26 2 0.03
27 40 0.68
28 2 0.03
ACGTcount: A:0.22, C:0.28, G:0.29, T:0.20
Consensus pattern (26 bp):
GCATGAGTCCCAACTGCGGAGCTTCA
Found at i:11847 original size:41 final size:41
Alignment explanation
Indices: 11790--11872 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 41
11780 ACTGCGGAAG
* *
11790 CTTCAGCATGAGTCCCAACTGCGG-GAGCTTCGGCATGAGTC
1 CTTCAGCATAAGTCCCAACTACGGAG-GCTTCGGCATGAGTC
*
11831 CTTCAGCATAAGTCCCAACTACGGAGGCTTTGGCATGAGTC
1 CTTCAGCATAAGTCCCAACTACGGAGGCTTCGGCATGAGTC
11872 C
1 C
11873 CAACCGCGGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 37 0.97
42 1 0.03
ACGTcount: A:0.22, C:0.29, G:0.27, T:0.23
Consensus pattern (41 bp):
CTTCAGCATAAGTCCCAACTACGGAGGCTTCGGCATGAGTC
Found at i:11874 original size:27 final size:27
Alignment explanation
Indices: 11836--11935 Score: 94
Period size: 27 Copynumber: 3.7 Consensus size: 27
11826 GAGTCCTTCA
* *
11836 GCATAAGTCCCAACTACGGAGGCTTTG
1 GCATGAGTCCCAACTGCGGAGGCTTTG
* * **
11863 GCATGAGTCCCAACCGCGG-GAGCCTCA
1 GCATGAGTCCCAACTGCGGAG-GCTTTG
* *
11890 ACATGAGTGCCAACTGCGGAGGCTTTG
1 GCATGAGTCCCAACTGCGGAGGCTTTG
* *
11917 GCGTGAGTCTCAACTGCGG
1 GCATGAGTCCCAACTGCGG
11936 GAATTTTAGT
Statistics
Matches: 55, Mismatches: 16, Indels: 4
0.73 0.21 0.05
Matches are distributed among these distances:
26 1 0.02
27 53 0.96
28 1 0.02
ACGTcount: A:0.22, C:0.28, G:0.31, T:0.19
Consensus pattern (27 bp):
GCATGAGTCCCAACTGCGGAGGCTTTG
Found at i:11895 original size:68 final size:68
Alignment explanation
Indices: 11763--11897 Score: 189
Period size: 68 Copynumber: 2.0 Consensus size: 68
11753 CATATGGGAG
* * * * **
11763 CTTCAGCATGAGTCCCAACTGCGGAAGCTTCAGCATGAGTCCCAACTGCGGGAGCTTCGGCATGA
1 CTTCAGCATAAGTCCCAACTACGGAAGCTTCAGCATGAGTCCCAACCGCGGGAGCCTCAACATGA
11828 GTC
66 GTC
* **
11831 CTTCAGCATAAGTCCCAACTACGGAGGCTTTGGCATGAGTCCCAACCGCGGGAGCCTCAACATGA
1 CTTCAGCATAAGTCCCAACTACGGAAGCTTCAGCATGAGTCCCAACCGCGGGAGCCTCAACATGA
11896 GT
66 GT
11898 GCCAACTGCG
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
68 58 1.00
ACGTcount: A:0.24, C:0.30, G:0.27, T:0.20
Consensus pattern (68 bp):
CTTCAGCATAAGTCCCAACTACGGAAGCTTCAGCATGAGTCCCAACCGCGGGAGCCTCAACATGA
GTC
Found at i:12741 original size:24 final size:24
Alignment explanation
Indices: 12696--12741 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
12686 ATTCAACGGC
*
12696 AGAAGCCAACCACTATTATACCGT
1 AGAAGCCAACCACAATTATACCGT
* *
12720 AGAAGCCAACTACAATTCTACC
1 AGAAGCCAACCACAATTATACC
12742 CCAGAAGTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.39, C:0.30, G:0.11, T:0.20
Consensus pattern (24 bp):
AGAAGCCAACCACAATTATACCGT
Found at i:12747 original size:24 final size:24
Alignment explanation
Indices: 12695--12748 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
12685 CATTCAACGG
* *
12695 CAGAAGCCAACCACTATTATACCG
1 CAGAAGCCAACCACAATTATACCC
* * *
12719 TAGAAGCCAACTACAATTCTACCC
1 CAGAAGCCAACCACAATTATACCC
12743 CAGAAG
1 CAGAAG
12749 TCAGTTTAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.39, C:0.31, G:0.13, T:0.17
Consensus pattern (24 bp):
CAGAAGCCAACCACAATTATACCC
Found at i:22493 original size:31 final size:30
Alignment explanation
Indices: 22457--22515 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
22447 ATATAAAATA
22457 AAAAACAGAAAAAG-AAAATATTTTTTTTAGG
1 AAAAAC-GAAAAAGCAAAA-ATTTTTTTTAGG
* *
22488 AAAAACGGAAAAGCAAAACTTTTTTTTA
1 AAAAACGAAAAAGCAAAAATTTTTTTTA
22516 AAAAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.53, C:0.07, G:0.12, T:0.29
Consensus pattern (30 bp):
AAAAACGAAAAAGCAAAAATTTTTTTTAGG
Found at i:24237 original size:19 final size:18
Alignment explanation
Indices: 24205--24241 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
24195 TTGAATTAAT
*
24205 TCTTCAATTGTCTTCAAA
1 TCTTCAATTATCTTCAAA
24223 TCTTCAAATTATCTTCAAA
1 TCTTC-AATTATCTTCAAA
24242 ACACGAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.32, C:0.22, G:0.03, T:0.43
Consensus pattern (18 bp):
TCTTCAATTATCTTCAAA
Found at i:32255 original size:21 final size:21
Alignment explanation
Indices: 32189--32255 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
32179 ATGTGCATAA
*
32189 CTTGGAATCGGTTGGAATATT
1 CTTGGAATCGATTGGAATATT
* * *
32210 CCTAGAATCGATTGTGAGA-A-G
1 CTTGGAATCGATTG-GA-ATATT
32231 CTTGGAATCGATTGGAATATT
1 CTTGGAATCGATTGGAATATT
32252 CTTG
1 CTTG
32256 CTCAAAACAT
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
19 1 0.03
20 3 0.09
21 27 0.77
22 3 0.09
23 1 0.03
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.34
Consensus pattern (21 bp):
CTTGGAATCGATTGGAATATT
Found at i:35805 original size:32 final size:32
Alignment explanation
Indices: 35769--35870 Score: 84
Period size: 32 Copynumber: 3.2 Consensus size: 32
35759 TCGGGTTTCA
*
35769 GGTCATACAGGTCTCGGATCACTCT-GGTTACT
1 GGTCATACAGGTCTCGGATCA-TCTGGGTTACG
* * * *
35801 GGTCATTCGGGTTTCGGGTCATCTGGGTTACG
1 GGTCATACAGGTCTCGGATCATCTGGGTTACG
* * *
35833 GGTCATTC-GAGTCTC-GAGTCTTCTGGGTTAAG
1 GGTCATACAG-GTCTCGGA-TCATCTGGGTTACG
35865 GGTCAT
1 GGTCAT
35871 TTGGGTAGCG
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
31 5 0.09
32 53 0.91
ACGTcount: A:0.15, C:0.21, G:0.31, T:0.33
Consensus pattern (32 bp):
GGTCATACAGGTCTCGGATCATCTGGGTTACG
Found at i:35820 original size:16 final size:16
Alignment explanation
Indices: 35750--35841 Score: 69
Period size: 16 Copynumber: 5.8 Consensus size: 16
35740 GGTTAATTTC
*
35750 TCGGGTTATTCGGGTT
1 TCGGGTCATTCGGGTT
* * * *
35766 TCAGGTCATACAGGTC
1 TCGGGTCATTCGGGTT
* * *
35782 TCGGATCACTCTGGTT
1 TCGGGTCATTCGGGTT
* *
35798 ACTGGTCATTCGGGTT
1 TCGGGTCATTCGGGTT
35814 TCGGGTCA-TCTGGGTT
1 TCGGGTCATTC-GGGTT
*
35830 ACGGGTCATTCG
1 TCGGGTCATTCG
35842 AGTCTCGAGT
Statistics
Matches: 55, Mismatches: 19, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
15 2 0.04
16 51 0.93
17 2 0.04
ACGTcount: A:0.13, C:0.21, G:0.32, T:0.35
Consensus pattern (16 bp):
TCGGGTCATTCGGGTT
Found at i:35871 original size:32 final size:32
Alignment explanation
Indices: 35801--35871 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
35791 TCTGGTTACT
* * * *
35801 GGTCATTCGGGTTTCGGGTCATCTGGGTTACG
1 GGTCATTCGAGTCTCGAGTCATCTGGGTTAAG
*
35833 GGTCATTCGAGTCTCGAGTCTTCTGGGTTAAG
1 GGTCATTCGAGTCTCGAGTCATCTGGGTTAAG
35865 GGTCATT
1 GGTCATT
35872 TGGGTAGCGA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.13, C:0.18, G:0.34, T:0.35
Consensus pattern (32 bp):
GGTCATTCGAGTCTCGAGTCATCTGGGTTAAG
Found at i:35883 original size:32 final size:32
Alignment explanation
Indices: 35822--35884 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
35812 TTTCGGGTCA
* **
35822 TCTGGGTTACGGGTCATTCGAGTCTCGAGTCT
1 TCTGGGTTAAGGGTCATTCGAGTAGCGAGTCT
* *
35854 TCTGGGTTAAGGGTCATTTGGGTAGCGAGTC
1 TCTGGGTTAAGGGTCATTCGAGTAGCGAGTC
35885 AGGCGGGTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.14, C:0.17, G:0.35, T:0.33
Consensus pattern (32 bp):
TCTGGGTTAAGGGTCATTCGAGTAGCGAGTCT
Found at i:36338 original size:18 final size:18
Alignment explanation
Indices: 36310--36371 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 18
36300 GCTGACGTGG
*
36310 AATTTAATATAT-TTAA-
1 AATTTAAAATATATTAAT
36326 AATTTAAAATATA-TAATT
1 AATTTAAAATATATTAA-T
36344 AATTTAAAATATA-TAATT
1 AATTTAAAATATATTAA-T
36362 AATTTAAAAT
1 AATTTAAAAT
36372 CTAAAAACTA
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
16 14 0.33
18 28 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AATTTAAAATATATTAAT
Found at i:36474 original size:3 final size:3
Alignment explanation
Indices: 36466--36497 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
36456 GTCTTTTATT
36466 TTC TTC TTC TTC TTCC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TT-C TTC TTC TTC TTC TTC T
36498 CTACCCAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:39426 original size:3 final size:3
Alignment explanation
Indices: 39411--39441 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
39401 TATATATATA
39411 TAT TAT ATAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT
39442 ATACAAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:39567 original size:15 final size:16
Alignment explanation
Indices: 39533--39576 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
39523 TTCGAGCGGG
39533 TTCGGGTATTTTCAGA
1 TTCGGGTATTTTCAGA
*
39549 TTCGGGTATTTT-GGA
1 TTCGGGTATTTTCAGA
*
39564 TTCGCGTATTTTC
1 TTCGGGTATTTTC
39577 GGGTTTGACC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 13 0.52
16 12 0.48
ACGTcount: A:0.14, C:0.14, G:0.25, T:0.48
Consensus pattern (16 bp):
TTCGGGTATTTTCAGA
Found at i:40143 original size:31 final size:31
Alignment explanation
Indices: 40108--40179 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 31
40098 TAAATTGTAG
*
40108 CAAATTAAAACAAAT-TAAGTATTAGATTAAA
1 CAAATTAAAA-AAATGCAAGTATTAGATTAAA
* ** * *
40139 CAAATCATCAAAATGCAAGTCTTAGGTTAAA
1 CAAATTAAAAAAATGCAAGTATTAGATTAAA
40170 CAAATTAAAA
1 CAAATTAAAA
40180 GCTAATGTAC
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.54, C:0.11, G:0.08, T:0.26
Consensus pattern (31 bp):
CAAATTAAAAAAATGCAAGTATTAGATTAAA
Found at i:40409 original size:16 final size:16
Alignment explanation
Indices: 40364--40409 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
40354 CAGGTTCGGT
*
40364 TTCGGGTTCGGGTGGA
1 TTCGGGTTCGGGTTGA
*
40380 TTCGGGCTCGGGTTG-
1 TTCGGGTTCGGGTTGA
40395 TCTCGGGTTCGGGTT
1 T-TCGGGTTCGGGTT
40410 CGGACGGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 1 0.04
16 25 0.96
ACGTcount: A:0.02, C:0.17, G:0.46, T:0.35
Consensus pattern (16 bp):
TTCGGGTTCGGGTTGA
Found at i:40419 original size:38 final size:38
Alignment explanation
Indices: 40342--40419 Score: 95
Period size: 38 Copynumber: 2.0 Consensus size: 38
40332 TATTTTGATC
* **
40342 TCGGGCTCGGGTCAGGTTCGGTTTCGGGTTCGGGTGGAT
1 TCGGGCTCGGGT-AGGTTCGGGTTCGGGTTCGGACGGAT
*
40381 TCGGGCTCGGGT-TGTCTCGGGTTCGGGTTCGGACGGAT
1 TCGGGCTCGGGTAGGT-TCGGGTTCGGGTTCGGACGGAT
40419 T
1 T
40420 TAGGATGTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
37 2 0.06
38 20 0.59
39 12 0.35
ACGTcount: A:0.05, C:0.19, G:0.45, T:0.31
Consensus pattern (38 bp):
TCGGGCTCGGGTAGGTTCGGGTTCGGGTTCGGACGGAT
Found at i:42057 original size:16 final size:16
Alignment explanation
Indices: 42022--42063 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
42012 GGGTAATTCG
* * *
42022 GATTTCGGGTCATTTG
1 GATTTCGGGTTATCTA
42038 GATTTCGGGTTATCTA
1 GATTTCGGGTTATCTA
42054 GA-TTCGGGTT
1 GATTTCGGGTT
42064 TCGGGTCAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.14, C:0.12, G:0.31, T:0.43
Consensus pattern (16 bp):
GATTTCGGGTTATCTA
Found at i:42076 original size:16 final size:17
Alignment explanation
Indices: 42057--42097 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
42047 TTATCTAGAT
42057 TCGGGTTTCGGGTCA-A
1 TCGGGTTTCGGGTCATA
*
42073 TCGGGTCTCGGGTCATA
1 TCGGGTTTCGGGTCATA
42090 T-GGGTTTC
1 TCGGGTTTC
42098 TAGTCATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 20 0.91
17 2 0.09
ACGTcount: A:0.10, C:0.20, G:0.37, T:0.34
Consensus pattern (17 bp):
TCGGGTTTCGGGTCATA
Found at i:42950 original size:16 final size:16
Alignment explanation
Indices: 42929--42973 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
42919 TATAATATTC
42929 TCGGGTCATTCGGATT
1 TCGGGTCATTCGGATT
* *
42945 TCGGGTCATACGGGTT
1 TCGGGTCATTCGGATT
*
42961 TCGGGTCACTCGG
1 TCGGGTCATTCGG
42974 GTTACAAGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.11, C:0.22, G:0.36, T:0.31
Consensus pattern (16 bp):
TCGGGTCATTCGGATT
Found at i:43061 original size:16 final size:16
Alignment explanation
Indices: 43013--43063 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
43003 TGGGATACGA
*
43013 GTCATTCGGGTCTCAA
1 GTCATTCGGGTCTCAG
43029 GTCA-TCTGGGT-TGCAG
1 GTCATTC-GGGTCT-CAG
43045 GTCATTCGGGTCTCAG
1 GTCATTCGGGTCTCAG
43061 GTC
1 GTC
43064 GGGCAGGTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
15 3 0.10
16 24 0.80
17 3 0.10
ACGTcount: A:0.14, C:0.24, G:0.31, T:0.31
Consensus pattern (16 bp):
GTCATTCGGGTCTCAG
Found at i:44875 original size:87 final size:87
Alignment explanation
Indices: 44779--44999 Score: 356
Period size: 86 Copynumber: 2.6 Consensus size: 87
44769 AATATTTTCC
*
44779 AAATCTCCCACAATCTGGCAAGATTTAGAGAAATATTCTCATTACTATTCAATCTTTATTATTTA
1 AAATCTCCCACAATTTGGCAAGATTTAGAGAAATATTCTCATTACTATTCAATCTTTATTATTTA
44844 TTTATTTCTTAAAACATCTCCT
66 TTTATTTCTTAAAACATCTCCT
* * *
44866 AAATCTCCCACAATTTGGCAAGATTTAGA-AAATATGCTTATTACTATGCAATCTTTATTATTTA
1 AAATCTCCCACAATTTGGCAAGATTTAGAGAAATATTCTCATTACTATTCAATCTTTATTATTTA
* *
44930 TTTATTTCTTAAAATATCTCTT
66 TTTATTTCTTAAAACATCTCCT
* *
44952 AAATCTCCCACAATTTGGCAAGATTTAGAG-AATACTCTCATTATTATT
1 AAATCTCCCACAATTTGGCAAGATTTAGAGAAATATTCTCATTACTATT
45000 TTAATGATTT
Statistics
Matches: 122, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
86 94 0.77
87 28 0.23
ACGTcount: A:0.34, C:0.18, G:0.07, T:0.41
Consensus pattern (87 bp):
AAATCTCCCACAATTTGGCAAGATTTAGAGAAATATTCTCATTACTATTCAATCTTTATTATTTA
TTTATTTCTTAAAACATCTCCT
Found at i:46390 original size:35 final size:35
Alignment explanation
Indices: 46335--46450 Score: 119
Period size: 35 Copynumber: 3.3 Consensus size: 35
46325 ACTCCCCTGG
* * * *
46335 ATCAATTCTGATCATCGGAAATTTCTTG-AAATGAC
1 ATCAACTCTGATCGTTGGAAACTTC-TGAAAATGAC
* * *
46370 ATCACCTCTGATTGTTGGAAACTACTGAAAATG-C
1 ATCAACTCTGATCGTTGGAAACTTCTGAAAATGAC
* *
46404 GATCAATTCTGATCGTTGGAAACTTCTGAAAATGAG
1 -ATCAACTCTGATCGTTGGAAACTTCTGAAAATGAC
46440 ATCAACTCTGA
1 ATCAACTCTGA
46451 CCTCTGAACC
Statistics
Matches: 65, Mismatches: 13, Indels: 6
0.77 0.15 0.07
Matches are distributed among these distances:
34 3 0.05
35 62 0.95
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (35 bp):
ATCAACTCTGATCGTTGGAAACTTCTGAAAATGAC
Found at i:46456 original size:25 final size:25
Alignment explanation
Indices: 46428--46483 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
46418 GTTGGAAACT
46428 TCTGAAAATGAGATCAACTCTGACC
1 TCTGAAAATGAGATCAACTCTGACC
**
46453 TCTGAACCTGAGATCAACTCTGACC
1 TCTGAAAATGAGATCAACTCTGACC
46478 TCTGAA
1 TCTGAA
46484 CTTCTTGGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (25 bp):
TCTGAAAATGAGATCAACTCTGACC
Found at i:46484 original size:25 final size:25
Alignment explanation
Indices: 46436--46484 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
46426 CTTCTGAAAA
46436 TGAGATCAACTCTGACCTCTGAACC
1 TGAGATCAACTCTGACCTCTGAACC
46461 TGAGATCAACTCTGACCTCTGAAC
1 TGAGATCAACTCTGACCTCTGAAC
46485 TTCTTGGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.29, C:0.31, G:0.16, T:0.24
Consensus pattern (25 bp):
TGAGATCAACTCTGACCTCTGAACC
Found at i:46562 original size:35 final size:35
Alignment explanation
Indices: 46461--46872 Score: 657
Period size: 35 Copynumber: 11.8 Consensus size: 35
46451 CCTCTGAACC
*
46461 TGAGATCAACTCTGACCTCTG--AACTTCTTGGAA
1 TGAGATCAACTCTGACCTCTGAAAACTTCTTGAAA
46494 TGAGATCAACTCTGACCTCTGAAAAACTTCTTGAAA
1 TGAGATCAACTCTGACCTCTG-AAAACTTCTTGAAA
46530 TGAGATCAACTCTGACCTCTGAAAACTTCTTGAAA
1 TGAGATCAACTCTGACCTCTGAAAACTTCTTGAAA
* * *
46565 TGTGATCAACTCTGACCTCTAAAAACTACTTGAAA
1 TGAGATCAACTCTGACCTCTGAAAACTTCTTGAAA
* * *
46600 TGAGATAAACTCTGACCTCTGGAAACTACTTGAAA
1 TGAGATCAACTCTGACCTCTGAAAACTTCTTGAAA
*
46635 TGAGATCAACTCTGACCTCTGAAAACTACTTGAAA
1 TGAGATCAACTCTGACCTCTGAAAACTTCTTGAAA
46670 TGAGATCAACTCTGACCTCTGAAAACTTCTTGAAA
1 TGAGATCAACTCTGACCTCTGAAAACTTCTTGAAA
*
46705 TGAGATCAACTCTGACCTCTGAAAACTTCTTGGAA
1 TGAGATCAACTCTGACCTCTGAAAACTTCTTGAAA
*
46740 TGAGATCAACTCTGACCTCTGAAAACTTCTTGGAA
1 TGAGATCAACTCTGACCTCTGAAAACTTCTTGAAA
**
46775 TGAGATCAACTCTGACCTCTGAAAACTTCTTGGGA
1 TGAGATCAACTCTGACCTCTGAAAACTTCTTGAAA
* **
46810 TGAGATCAACTCTGACCTCTGACAACTTCTTGGGA
1 TGAGATCAACTCTGACCTCTGAAAACTTCTTGAAA
*
46845 TGAGATCAACTCTGACCTCTGGAAACTT
1 TGAGATCAACTCTGACCTCTGAAAACTT
46873 TTATGCAAGA
Statistics
Matches: 360, Mismatches: 16, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
33 21 0.06
35 307 0.85
36 32 0.09
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (35 bp):
TGAGATCAACTCTGACCTCTGAAAACTTCTTGAAA
Found at i:46954 original size:35 final size:35
Alignment explanation
Indices: 46879--47133 Score: 309
Period size: 35 Copynumber: 7.3 Consensus size: 35
46869 ACTTTTATGC
*
46879 AAGACCGCCCTGGGTCAACTG-AATAAACTGGAGA
1 AAGACCGCCCTGGGTCAACTGAAATAAACTGAAGA
* *
46913 ATGACCGCCCTGGGTCAACTGAAATAAGCTGAAGA
1 AAGACCGCCCTGGGTCAACTGAAATAAACTGAAGA
* * *
46948 AAGACCGCCTTGGGCCAACTTAAATAAACTGAAGA
1 AAGACCGCCCTGGGTCAACTGAAATAAACTGAAGA
* * * * *
46983 ATGATCGCCCTGGATCGAA-TCAAATATACTGAAGA
1 AAGACCGCCCTGGGTC-AACTGAAATAAACTGAAGA
* * *
47018 AAGACCACCCTGGGTTAACTGAAATAAACTTAAGA
1 AAGACCGCCCTGGGTCAACTGAAATAAACTGAAGA
* *
47053 ATGACCGCTCTGGGTCAACTG-AATAAACTGAAGA
1 AAGACCGCCCTGGGTCAACTGAAATAAACTGAAGA
* * *
47087 AAGACCACCCTGGGTCAACTGAAATAAACTAAAGC
1 AAGACCGCCCTGGGTCAACTGAAATAAACTGAAGA
47122 AAGACCGCCCTG
1 AAGACCGCCCTG
47134 TACTTGACTC
Statistics
Matches: 183, Mismatches: 34, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
34 52 0.28
35 129 0.70
36 2 0.01
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.18
Consensus pattern (35 bp):
AAGACCGCCCTGGGTCAACTGAAATAAACTGAAGA
Found at i:48142 original size:15 final size:14
Alignment explanation
Indices: 48112--48167 Score: 76
Period size: 15 Copynumber: 3.9 Consensus size: 14
48102 AGCCTTATCA
*
48112 TTTCTTTTTTTTTT
1 TTTCTTTTTTTCTT
48126 TTTCTTTCTTTTCTT
1 TTTCTTT-TTTTCTT
*
48141 TTTCTTTCTTTTTTT
1 TTTCTTT-TTTTCTT
48156 TTTCTTTTTTTC
1 TTTCTTTTTTTC
48168 GTCATGCATT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
14 11 0.29
15 27 0.71
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTCTTTTTTTCTT
Found at i:48144 original size:29 final size:29
Alignment explanation
Indices: 48112--48167 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 29
48102 AGCCTTATCA
48112 TTTCTTT-TTTTTTTTTTCTTTCTTTTCTT
1 TTTCTTTCTTTTTTTTTTCTTT-TTTTCTT
48141 TTTCTTTCTTTTTTTTTTCTTTTTTTC
1 TTTCTTTCTTTTTTTTTTCTTTTTTTC
48168 GTCATGCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 12 0.46
30 14 0.54
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (29 bp):
TTTCTTTCTTTTTTTTTTCTTTTTTTCTT
Found at i:48165 original size:11 final size:11
Alignment explanation
Indices: 48112--48166 Score: 69
Period size: 11 Copynumber: 5.0 Consensus size: 11
48102 AGCCTTATCA
48112 TTTCTTTTTTT
1 TTTCTTTTTTT
48123 TTT-TTTCTTTCT
1 TTTCTTT-TTT-T
*
48135 TTTC-TTTTTC
1 TTTCTTTTTTT
48145 TTTCTTTTTTT
1 TTTCTTTTTTT
48156 TTTCTTTTTTT
1 TTTCTTTTTTT
48167 CGTCATGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
10 7 0.18
11 25 0.66
12 6 0.16
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:48527 original size:21 final size:22
Alignment explanation
Indices: 48481--48523 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
48471 CTTTCCTCCA
48481 TCTTTTGCTTTTTCAACTTCTT
1 TCTTTTGCTTTTTCAACTTCTT
48503 TCTTTT-CTTTTTCAA-TTCTT
1 TCTTTTGCTTTTTCAACTTCTT
48523 T
1 T
48524 TCTTCATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.29
21 9 0.43
22 6 0.29
ACGTcount: A:0.09, C:0.21, G:0.02, T:0.67
Consensus pattern (22 bp):
TCTTTTGCTTTTTCAACTTCTT
Found at i:48533 original size:20 final size:21
Alignment explanation
Indices: 48488--48534 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
48478 CCATCTTTTG
*
48488 CTTTTTCAACTTCTTTCTTTT
1 CTTTTTCAACTTCTTTCTCTT
48509 CTTTTTCAA-TTCTTT-TCTT
1 CTTTTTCAACTTCTTTCTCTT
48528 CATTTTT
1 C-TTTTT
48535 TTCTTCTCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 4 0.17
20 11 0.46
21 9 0.38
ACGTcount: A:0.11, C:0.21, G:0.00, T:0.68
Consensus pattern (21 bp):
CTTTTTCAACTTCTTTCTCTT
Found at i:48534 original size:21 final size:21
Alignment explanation
Indices: 48488--48537 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
48478 CCATCTTTTG
*
48488 CTTTTTCAACTTCTTTCTTTT
1 CTTTTTCAACTTCTTTCTTAT
48509 CTTTTTCAA-TTCTTTTCTTCAT
1 CTTTTTCAACTTC-TTTCTT-AT
*
48531 TTTTTTC
1 CTTTTTC
48538 TTCTCCTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 3 0.12
21 15 0.60
22 7 0.28
ACGTcount: A:0.10, C:0.22, G:0.00, T:0.68
Consensus pattern (21 bp):
CTTTTTCAACTTCTTTCTTAT
Found at i:49014 original size:9 final size:9
Alignment explanation
Indices: 49000--49036 Score: 56
Period size: 10 Copynumber: 3.9 Consensus size: 9
48990 TTCTTTCACA
49000 TTTTTTTCT
1 TTTTTTTCT
49009 TTTTTTTCCT
1 TTTTTTT-CT
49019 TTTTTTCTCT
1 TTTTTT-TCT
49029 TTTTTTTC
1 TTTTTTTC
49037 ACTTGATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 9 0.35
10 16 0.62
11 1 0.04
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:49049 original size:20 final size:19
Alignment explanation
Indices: 49003--49053 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
48993 TTTCACATTT
**
49003 TTTTCTTTTTTTTCCTTTT
1 TTTTCTTTTTTTTCCTTGA
49022 TTTCTCTTTTTTTTCACTTGA
1 TTT-TCTTTTTTTTC-CTTGA
49043 TTTTCTTTTTT
1 TTTTCTTTTTT
49054 CTTTTGCTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 3 0.11
20 19 0.68
21 6 0.21
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.78
Consensus pattern (19 bp):
TTTTCTTTTTTTTCCTTGA
Found at i:52756 original size:86 final size:86
Alignment explanation
Indices: 52617--52837 Score: 388
Period size: 86 Copynumber: 2.6 Consensus size: 86
52607 AATATTTTCC
*
52617 AAATCTCCCACAATCTGGCAAGATTTAGAGAAATATTCTCATTACTATTCAATCTTTATTATTTA
1 AAATCTCCCACAATTTGGCAAGATTTAGAG-AATATTCTCATTACTATTCAATCTTTATTATTTA
52682 TTTATTTCTTAAAATATCTCCT
65 TTTATTTCTTAAAATATCTCCT
*
52704 AAATCTCCCACAATTTGGCAAGATTTAGAGAATATTCTTATTACTATTCAATCTTTATTATTTAT
1 AAATCTCCCACAATTTGGCAAGATTTAGAGAATATTCTCATTACTATTCAATCTTTATTATTTAT
*
52769 TTATTTCTTAAAATATCTCTT
66 TTATTTCTTAAAATATCTCCT
* *
52790 AAATCTCCCACAATTTGGCAAGATTTAGAGAATACTCTCATTATTATT
1 AAATCTCCCACAATTTGGCAAGATTTAGAGAATATTCTCATTACTATT
52838 TTAATGATTT
Statistics
Matches: 128, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
86 99 0.77
87 29 0.23
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (86 bp):
AAATCTCCCACAATTTGGCAAGATTTAGAGAATATTCTCATTACTATTCAATCTTTATTATTTAT
TTATTTCTTAAAATATCTCCT
Found at i:53024 original size:16 final size:17
Alignment explanation
Indices: 53005--53038 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
52995 TATTTGGAAA
53005 TCTTTTAT-TTTGATTT
1 TCTTTTATATTTGATTT
*
53021 TCTTTTATATTTTATTT
1 TCTTTTATATTTGATTT
53038 T
1 T
53039 AATCAATTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.15, C:0.06, G:0.03, T:0.76
Consensus pattern (17 bp):
TCTTTTATATTTGATTT
Found at i:60309 original size:21 final size:21
Alignment explanation
Indices: 60256--60315 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
60246 CTTGGAGCAA
*
60256 GAATATTCCAATCGATTCTAT
1 GAATATTCCAATCGATTCTAG
** * * *
60277 GTCTACTACAATCGATTTTAG
1 GAATATTCCAATCGATTCTAG
60298 GAATATTCCAATCGATTC
1 GAATATTCCAATCGATTC
60316 CAAGTTATGC
Statistics
Matches: 28, Mismatches: 11, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.37
Consensus pattern (21 bp):
GAATATTCCAATCGATTCTAG
Done.