Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014097.1 Corchorus olitorius cultivar O-4 contig14130, 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: 58648
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2724 original size:22 final size:22
Alignment explanation
Indices: 2696--2739 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2686 CTATAAGCTA
*
2696 TACTAAATGCCAAAATTGAATT
1 TACTAAATGCCAAAAGTGAATT
2718 TACTAAATGCCAAAAGTGAATT
1 TACTAAATGCCAAAAGTGAATT
2740 AGAAAATGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (22 bp):
TACTAAATGCCAAAAGTGAATT
Found at i:3091 original size:46 final size:46
Alignment explanation
Indices: 3036--3124 Score: 153
Period size: 46 Copynumber: 1.9 Consensus size: 46
3026 GATCCACTGG
*
3036 ATCAAACTTTGAAGGAA-TATTGCACCGCATTAACTTGATTCACTAA
1 ATCAAACTTTGAA-GAACTATTGCACCGCAGTAACTTGATTCACTAA
3082 ATCAAACTTTGAAGAACTATTGCACCGCAGTAACTTGATTCAC
1 ATCAAACTTTGAAGAACTATTGCACCGCAGTAACTTGATTCAC
3125 CGAATCATCC
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
45 3 0.07
46 38 0.93
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.29
Consensus pattern (46 bp):
ATCAAACTTTGAAGAACTATTGCACCGCAGTAACTTGATTCACTAA
Found at i:3220 original size:79 final size:79
Alignment explanation
Indices: 3089--3288 Score: 355
Period size: 79 Copynumber: 2.5 Consensus size: 79
3079 TAAATCAAAC
* * *
3089 TTTGAAGAACTATTGCACCGCAGTAACTTGATTCACCGAATCATCCTGAATATGCTGCACCGAGC
1 TTTGAAGAAATAATGCACCGCATTAACTTGATTCACCGAATCATCCTGAATATGCTGCACCGAGC
3154 TCACCGAATCCAAT
66 TCACCGAATCCAAT
*
3168 TTTGAGGAAATAATGCACCGCATTAACTTGATTCACCGAATCATCCTGAATATGCTGCACCGAGC
1 TTTGAAGAAATAATGCACCGCATTAACTTGATTCACCGAATCATCCTGAATATGCTGCACCGAGC
*
3233 TCACTGAATCCAAT
66 TCACCGAATCCAAT
3247 TTTGAAGAAATAATGCACCGCATTAACTTGATTCACCGAATC
1 TTTGAAGAAATAATGCACCGCATTAACTTGATTCACCGAATC
3289 CCCTGAACTG
Statistics
Matches: 115, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
79 115 1.00
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.27
Consensus pattern (79 bp):
TTTGAAGAAATAATGCACCGCATTAACTTGATTCACCGAATCATCCTGAATATGCTGCACCGAGC
TCACCGAATCCAAT
Found at i:3444 original size:54 final size:53
Alignment explanation
Indices: 3344--3828 Score: 534
Period size: 54 Copynumber: 9.1 Consensus size: 53
3334 CAAATCATCG
** * * * * * *
3344 GAAGATAAACCCAAATCACTGAAAACTTCCTTAACTGACCGTACTGGATCACTT
1 GAAGATAAACTTAAACCACTGTAAACTTTCTTGATTGACCGCACTGGATCA-TT
* ** ** *
3398 GAAGATAAATTTAAGACCACTGGCAACTTTC-TGAACGATCGCACTGGATCACTT
1 GAAGATAAACTTAA-ACCACTGTAAACTTTCTTGATTGACCGCACTGGATCA-TT
* * *
3452 GAAGATAAACCTAAACCACTATAAACTTTCTTGATTGACCGCTCTGGATCATTT
1 GAAGATAAACTTAAACCACTGTAAACTTTCTTGATTGACCGCACTGGATCA-TT
** * * *
3506 GATCATAAGCTTAAACCATTGGAAACTTTCTTGATTGACCGCACTGGATCGATT
1 GAAGATAAACTTAAACCACTGTAAACTTTCTTGATTGACCGCACTGGATC-ATT
**
3560 GATCATAAACTTAAACCACTGTAAACTTTCTTGATTGACCGCACTGGATCGATT
1 GAAGATAAACTTAAACCACTGTAAACTTTCTTGATTGACCGCACTGGATC-ATT
*
3614 GAAGATAAACTTAAACCACTGTAAACTTTCTTGATTCACCGCACTGGATCGATT
1 GAAGATAAACTTAAACCACTGTAAACTTTCTTGATTGACCGCACTGGATC-ATT
3668 GAAGATAAACTTAAACCACTGTAAACTTTCTTGATTGACCGCACTGGATCACTT
1 GAAGATAAACTTAAACCACTGTAAACTTTCTTGATTGACCGCACTGGATCA-TT
* * *
3722 GAAGTTAGACTTAAACCACTGTAAA----CTTGATTGATCGCACTGGATCACTTT
1 GAAGATAAACTTAAACCACTGTAAACTTTCTTGATTGACCGCACTGGATCA--TT
* * * *
3773 GAAGATAAACTTAAGCCACT-TGAAAGTTT-TTAACTGACCGCACTGGATCATT
1 GAAGATAAACTTAAACCACTGT-AAACTTTCTTGATTGACCGCACTGGATCATT
3825 GAAG
1 GAAG
3829 CATTGGAGAA
Statistics
Matches: 374, Mismatches: 47, Indels: 22
0.84 0.11 0.05
Matches are distributed among these distances:
50 22 0.06
51 22 0.06
52 6 0.02
53 14 0.04
54 297 0.79
55 13 0.03
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (53 bp):
GAAGATAAACTTAAACCACTGTAAACTTTCTTGATTGACCGCACTGGATCATT
Found at i:3864 original size:24 final size:24
Alignment explanation
Indices: 3837--4012 Score: 151
Period size: 24 Copynumber: 7.4 Consensus size: 24
3827 AGCATTGGAG
* *
3837 AATTGAAGTTTTGAATACTTGAAA
1 AATTGAAGCTTTGAATAATTGAAA
* * * *
3861 AATTGAAACTCTGAGTACTTGAAA
1 AATTGAAGCTTTGAATAATTGAAA
* * *
3885 AATTGAAG-TTGTAAAGAATTGAAG
1 AATTGAAGCTT-TGAATAATTGAAA
* **
3909 AATTGAAGTTTTGAAGGATTG--A
1 AATTGAAGCTTTGAATAATTGAAA
*
3931 AATTGAAGCATTGAATAATTGAAA
1 AATTGAAGCTTTGAATAATTGAAA
* *
3955 AGTTTGAAGCTTTGAATAATTGAAG
1 A-ATTGAAGCTTTGAATAATTGAAA
* *
3980 AACTGAAGCTTTGAATAATTGAAG
1 AATTGAAGCTTTGAATAATTGAAA
*
4004 AACTGAAGC
1 AATTGAAGC
4013 ATTGCAATTG
Statistics
Matches: 124, Mismatches: 23, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
22 17 0.14
23 1 0.01
24 83 0.67
25 23 0.19
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.31
Consensus pattern (24 bp):
AATTGAAGCTTTGAATAATTGAAA
Found at i:3909 original size:8 final size:8
Alignment explanation
Indices: 3898--4040 Score: 75
Period size: 8 Copynumber: 18.5 Consensus size: 8
3888 TGAAGTTGTA
3898 AAGAATTG
1 AAGAATTG
3906 AAGAATTG
1 AAGAATTG
**
3914 AAGTTTTG
1 AAGAATTG
*
3922 AAGGATTG
1 AAGAATTG
3930 -A-AATTG
1 AAGAATTG
*
3936 AAGCATTG
1 AAGAATTG
*
3944 AATAATTG
1 AAGAATTG
3952 AA-AAGTTTG
1 AAGAA--TTG
**
3961 AAGCTTTG
1 AAGAATTG
*
3969 AATAATTG
1 AAGAATTG
*
3977 AAGAACTG
1 AAGAATTG
**
3985 AAGCTTTG
1 AAGAATTG
*
3993 AATAATTG
1 AAGAATTG
*
4001 AAGAACTG
1 AAGAATTG
*
4009 AAGCATTG
1 AAGAATTG
*
4017 --CAATTG
1 AAGAATTG
*
4023 AAGTATTG
1 AAGAATTG
4031 -A-AATTG
1 AAGAATTG
4037 AAGA
1 AAGA
4041 TAGGCCACCC
Statistics
Matches: 96, Mismatches: 30, Indels: 18
0.67 0.21 0.12
Matches are distributed among these distances:
6 12 0.12
7 6 0.06
8 73 0.76
9 5 0.05
ACGTcount: A:0.43, C:0.05, G:0.22, T:0.30
Consensus pattern (8 bp):
AAGAATTG
Found at i:4161 original size:96 final size:96
Alignment explanation
Indices: 4071--4479 Score: 471
Period size: 96 Copynumber: 4.2 Consensus size: 96
4061 TGAAATAAAT
* * * * *
4071 TGAAGAAAAACCACCCTAGGTCAATTTGAAGAAAGATCGCTCTGGATCAACTGAAGTAAACCGAA
1 TGAAGAAAGACCGCCCTGGGTCAACTTGAAGAAAGATCGCTCTGGATCAACTGAAGTAAACTGAA
*
4136 GAATGATCACCCTGGATCAATTGAAACTAAC
66 GAATGATCGCCCTGGATCAATTGAAACTAAC
* * * * * * * * * *
4167 TGAAGAAAGACCGCCCTGGGTCAACTTGAAGCAGGATTGCTGTAGATCGATTAAAGCAAATTGAA
1 TGAAGAAAGACCGCCCTGGGTCAACTTGAAGAAAGATCGCTCTGGATCAACTGAAGTAAACTGAA
* * * *
4232 GAATGATTGCCCTAGATCGACTGAAACTAAC
66 GAATGATCGCCCTGGATCAATTGAAACTAAC
* * * * *
4263 TGAAGAAAAGACCGCCCTGGGCCAACTTGAAGCAACATCGCTCTGGATCGATTGAAGTAAACTGA
1 TGAAG-AAAGACCGCCCTGGGTCAACTTGAAGAAAGATCGCTCTGGATCAACTGAAGTAAACTGA
4328 AGAATGATCGCCCTGGATCAATTGAAACTAAC
65 AGAATGATCGCCCTGGATCAATTGAAACTAAC
* * * * * * *
4360 TGAAGAAAGACCGCCCTAGGTCAAC-TGAAGAACGACCACCCTCGATCAACTGAAATAAACTGAA
1 TGAAGAAAGACCGCCCTGGGTCAACTTGAAGAAAGATCGCTCTGGATCAACTGAAGTAAACTGAA
* *
4424 GAATGATGGCCCTGGATCAACTTAAAAAC-AAC
66 GAATGATCGCCCTGGATCAA-TT-GAAACTAAC
4456 TGAAGAAAGACCGCCCTGGGTCAA
1 TGAAGAAAGACCGCCCTGGGTCAA
4480 TATGAAACTA
Statistics
Matches: 262, Mismatches: 48, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
95 48 0.18
96 127 0.48
97 87 0.33
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.19
Consensus pattern (96 bp):
TGAAGAAAGACCGCCCTGGGTCAACTTGAAGAAAGATCGCTCTGGATCAACTGAAGTAAACTGAA
GAATGATCGCCCTGGATCAATTGAAACTAAC
Found at i:4172 original size:35 final size:36
Alignment explanation
Indices: 4097--4196 Score: 105
Period size: 35 Copynumber: 2.8 Consensus size: 36
4087 TAGGTCAATT
* * *
4097 TGAAGAAAGATCGCTCTGGATCAACTG-AAGTAAAC
1 TGAAGAAAGATCGCCCTGGATCAATTGAAACTAAAC
* * *
4132 CGAAGAATGATCACCCTGGATCAATTGAAACT-AAC
1 TGAAGAAAGATCGCCCTGGATCAATTGAAACTAAAC
* *
4167 TGAAGAAAGACCGCCCTGGGTCAACTTGAA
1 TGAAGAAAGATCGCCCTGGATCAA-TTGAA
4197 GCAGGATTGC
Statistics
Matches: 52, Mismatches: 11, Indels: 3
0.79 0.17 0.05
Matches are distributed among these distances:
35 44 0.85
36 8 0.15
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.19
Consensus pattern (36 bp):
TGAAGAAAGATCGCCCTGGATCAATTGAAACTAAAC
Found at i:4338 original size:35 final size:35
Alignment explanation
Indices: 4299--4489 Score: 95
Period size: 35 Copynumber: 5.7 Consensus size: 35
4289 TTGAAGCAAC
* * *
4299 ATCGCTCTGGATCGATTG-AAGTAAACTGAAGAATG
1 ATCGCCCTGGATCAATTGAAACT-AACTGAAGAATG
*
4334 ATCGCCCTGGATCAATTGAAACTAACTGAAGAAAG
1 ATCGCCCTGGATCAATTGAAACTAACTGAAGAATG
* *
4369 ACCGCCCTAGG------T----C-AACTGAAGAACG
1 ATCGCCCT-GGATCAATTGAAACTAACTGAAGAATG
* * * *
4394 ACCACCCTCGATCAACTGAAA-TAAACTGAAGAATG
1 ATCGCCCTGGATCAATTGAAACT-AACTGAAGAATG
* * *
4429 ATGGCCCTGGATCAACTTAAAAAC-AACTGAAGAAAG
1 ATCGCCCTGGATCAA-TT-GAAACTAACTGAAGAATG
* *
4465 ACCGCCCTGGGTCAATATGAAACTA
1 ATCGCCCTGGATCAAT-TGAAACTA
4490 TCTAACAGAC
Statistics
Matches: 117, Mismatches: 20, Indels: 37
0.67 0.11 0.21
Matches are distributed among these distances:
24 1 0.01
25 18 0.15
26 1 0.01
30 2 0.02
35 61 0.52
36 31 0.26
37 3 0.03
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (35 bp):
ATCGCCCTGGATCAATTGAAACTAACTGAAGAATG
Found at i:4391 original size:25 final size:25
Alignment explanation
Indices: 4357--4413 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
4347 AATTGAAACT
* *
4357 AACTGAAGAAAGACCGCCCTAGGTC
1 AACTGAAGAAAGACCACCCTAGATC
* *
4382 AACTGAAGAACGACCACCCTCGATC
1 AACTGAAGAAAGACCACCCTAGATC
4407 AACTGAA
1 AACTGAA
4414 ATAAACTGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.39, C:0.30, G:0.19, T:0.12
Consensus pattern (25 bp):
AACTGAAGAAAGACCACCCTAGATC
Found at i:4436 original size:60 final size:60
Alignment explanation
Indices: 4322--4445 Score: 144
Period size: 60 Copynumber: 2.1 Consensus size: 60
4312 GATTGAAGTA
* * * * *
4322 AACTGAAGAATGATCGCCCTGGATCAATTGAAACTAACTGAAGAAAGACCGCCCTAGG-TC
1 AACTGAAGAACGACCACCCTCGATCAACTGAAACTAACTGAAGAAAGACCGCCCT-GGATC
* **
4382 AACTGAAGAACGACCACCCTCGATCAACTGAAA-TAAACTGAAGAATGATGGCCCTGGATC
1 AACTGAAGAACGACCACCCTCGATCAACTGAAACT-AACTGAAGAAAGACCGCCCTGGATC
4442 AACT
1 AACT
4446 TAAAAACAAC
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
59 3 0.06
60 51 0.94
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (60 bp):
AACTGAAGAACGACCACCCTCGATCAACTGAAACTAACTGAAGAAAGACCGCCCTGGATC
Found at i:4459 original size:193 final size:193
Alignment explanation
Indices: 4071--4475 Score: 505
Period size: 193 Copynumber: 2.1 Consensus size: 193
4061 TGAAATAAAT
* * * * *
4071 TGAAGAAAA-ACCACCCTAGGTCAATTTGAAGAAAGATCGCTCTGGATCAACTGAAGTAAACCGA
1 TGAAGAAAAGACCGCCCTGGGCCAACTTGAAGAAACATCGCTCTGGATCAACTGAAGTAAACCGA
* *
4135 AGAATGATCACCCTGGATCAATTGAAACTAACTGAAGAAAGACCGCCCTGGGTCAACTTGAAGCA
66 AGAATGATCACCCTGGATCAATTGAAACTAACTGAAGAAAGACCGCCCTAGGTCAACTTGAAGAA
* *** ** * * * * * *
4200 GGATTGCTGTAGATCGATTAAAGCAAATTGAAGAATGATTGCCCTAGATCGACTGAAACTAAC
131 CGACCACCCTAGATCAATGAAAGCAAACTGAAGAATGATGGCCCTAGATCAACTAAAACTAAC
* * * *
4263 TGAAGAAAAGACCGCCCTGGGCCAACTTGAAGCAACATCGCTCTGGATCGATTGAAGTAAACTGA
1 TGAAGAAAAGACCGCCCTGGGCCAACTTGAAGAAACATCGCTCTGGATCAACTGAAGTAAACCGA
*
4328 AGAATGATCGCCCTGGATCAATTGAAACTAACTGAAGAAAGACCGCCCTAGGTCAAC-TGAAGAA
66 AGAATGATCACCCTGGATCAATTGAAACTAACTGAAGAAAGACCGCCCTAGGTCAACTTGAAGAA
* * *
4392 CGACCACCCTCGATCAACTGAAA-TAAACTGAAGAATGATGGCCCTGGATCAACTTAAAAAC-AA
131 CGACCACCCTAGATCAA-TGAAAGCAAACTGAAGAATGATGGCCCTAGATCAAC-T-AAAACTAA
4455 C
193 C
4456 TGAAG-AAAGACCGCCCTGGG
1 TGAAGAAAAGACCGCCCTGGG
4476 TCAATATGAA
Statistics
Matches: 182, Mismatches: 27, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
192 64 0.35
193 114 0.63
194 4 0.02
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.19
Consensus pattern (193 bp):
TGAAGAAAAGACCGCCCTGGGCCAACTTGAAGAAACATCGCTCTGGATCAACTGAAGTAAACCGA
AGAATGATCACCCTGGATCAATTGAAACTAACTGAAGAAAGACCGCCCTAGGTCAACTTGAAGAA
CGACCACCCTAGATCAATGAAAGCAAACTGAAGAATGATGGCCCTAGATCAACTAAAACTAAC
Found at i:4472 original size:36 final size:36
Alignment explanation
Indices: 4381--4479 Score: 110
Period size: 35 Copynumber: 2.8 Consensus size: 36
4371 CGCCCTAGGT
* * * *
4381 CAACTGAAGAACGACCACCCTCGATCAACTGAAATA
1 CAACTGAAGAAAGACCGCCCTGGATCAACTGAAAAA
* ** *
4417 -AACTGAAGAATGATGGCCCTGGATCAACTTAAAAA
1 CAACTGAAGAAAGACCGCCCTGGATCAACTGAAAAA
*
4452 CAACTGAAGAAAGACCGCCCTGGGTCAA
1 CAACTGAAGAAAGACCGCCCTGGATCAA
4480 TATGAAACTA
Statistics
Matches: 51, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
35 28 0.55
36 23 0.45
ACGTcount: A:0.40, C:0.25, G:0.19, T:0.15
Consensus pattern (36 bp):
CAACTGAAGAAAGACCGCCCTGGATCAACTGAAAAA
Found at i:5698 original size:11 final size:11
Alignment explanation
Indices: 5670--5702 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
5660 CCTAAAGCTT
5670 TTTCTTTTTC-
1 TTTCTTTTTCA
*
5680 TTTTTTTTTCA
1 TTTCTTTTTCA
5691 TTTCTTTTTCA
1 TTTCTTTTTCA
5702 T
1 T
5703 CTTTTATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTCTTTTTCA
Found at i:8932 original size:7 final size:7
Alignment explanation
Indices: 8912--8955 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
8902 ACTATATCTT
8912 TATTCATA
1 TATT-ATA
8920 TATTATA
1 TATTATA
8927 T-TT-TA
1 TATTATA
8932 TA-TATA
1 TATTATA
8938 TA-TATA
1 TATTATA
8944 TATTATA
1 TATTATA
8951 TATTA
1 TATTA
8956 ATGGTACAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
5 4 0.12
6 12 0.36
7 13 0.39
8 4 0.12
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (7 bp):
TATTATA
Found at i:8949 original size:17 final size:16
Alignment explanation
Indices: 8917--8953 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
8907 ATCTTTATTC
*
8917 ATATATTATATTTTAT
1 ATATATTATATATTAT
8933 ATATATATATATATTAT
1 ATATAT-TATATATTAT
8950 ATAT
1 ATAT
8954 TAATGGTACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATATATTATATATTAT
Found at i:10086 original size:18 final size:18
Alignment explanation
Indices: 10063--10101 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
10053 TGGGTATTTA
10063 TAGATGTCTTGGAGGAGT
1 TAGATGTCTTGGAGGAGT
10081 TAGATGTCTTGGAGGAGT
1 TAGATGTCTTGGAGGAGT
10099 TAG
1 TAG
10102 CTGCCTTGGG
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:0.23, C:0.05, G:0.38, T:0.33
Consensus pattern (18 bp):
TAGATGTCTTGGAGGAGT
Found at i:10109 original size:18 final size:18
Alignment explanation
Indices: 10063--10110 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
10053 TGGGTATTTA
*
10063 TAGATGTCTTGGAGGAGT
1 TAGATGCCTTGGAGGAGT
*
10081 TAGATGTCTTGGAGGAGT
1 TAGATGCCTTGGAGGAGT
*
10099 TAGCTGCCTTGG
1 TAGATGCCTTGG
10111 GCTAATTGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.19, C:0.10, G:0.38, T:0.33
Consensus pattern (18 bp):
TAGATGCCTTGGAGGAGT
Found at i:11668 original size:11 final size:11
Alignment explanation
Indices: 11638--11670 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
11628 ATATTTAACC
11638 TTTATATAT-A
1 TTTATATATAA
11648 -TTATATATAA
1 TTTATATATAA
11658 TTTATATATAA
1 TTTATATATAA
11669 TT
1 TT
11671 CCTAGAGATC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 8 0.38
10 1 0.05
11 12 0.57
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTATATATAA
Found at i:12044 original size:16 final size:15
Alignment explanation
Indices: 12019--12049 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
12009 ACTCTCATCA
12019 ATTTCTAACAACTTC
1 ATTTCTAACAACTTC
12034 ATTTCCTAACAACTTC
1 ATTT-CTAACAACTTC
12050 TTCAAACTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (15 bp):
ATTTCTAACAACTTC
Found at i:13777 original size:31 final size:30
Alignment explanation
Indices: 13715--13778 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
13705 AATTTTGGAC
* **
13715 AATTTTACCATTAAACTTTTTTTTTCTACA
1 AATTTTACCATTAAACTTTATTTTTAAACA
13745 AATTTTACCATTAAACTTTGATTTTTAAACA
1 AATTTTACCATTAAACTTT-ATTTTTAAACA
13776 AAT
1 AAT
13779 GACTCAATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 19 0.63
31 11 0.37
ACGTcount: A:0.36, C:0.14, G:0.02, T:0.48
Consensus pattern (30 bp):
AATTTTACCATTAAACTTTATTTTTAAACA
Found at i:16474 original size:29 final size:28
Alignment explanation
Indices: 16442--16512 Score: 94
Period size: 26 Copynumber: 2.6 Consensus size: 28
16432 TACTTGGCAG
16442 GTCCCTCTACTTACAAAA-AGGTCAATTTA
1 GTCCCTCTACTTACAAAATA--TCAATTTA
16471 GTCCCTCTA-TTA-AAAATATCAATTTA
1 GTCCCTCTACTTACAAAATATCAATTTA
*
16497 ATCCCTCTACTTACAA
1 GTCCCTCTACTTACAA
16513 GATTGGGTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
26 16 0.42
27 7 0.18
28 6 0.16
29 9 0.24
ACGTcount: A:0.35, C:0.25, G:0.06, T:0.34
Consensus pattern (28 bp):
GTCCCTCTACTTACAAAATATCAATTTA
Found at i:16581 original size:27 final size:27
Alignment explanation
Indices: 16551--16605 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
16541 TACAGAAGTC
16551 GTTAAGTTGCTGACGTGTCCGTTAACT
1 GTTAAGTTGCTGACGTGTCCGTTAACT
16578 GTTAAGTTGCTGACGTGTCCGTTAACT
1 GTTAAGTTGCTGACGTGTCCGTTAACT
16605 G
1 G
16606 ATGATATGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.36
Consensus pattern (27 bp):
GTTAAGTTGCTGACGTGTCCGTTAACT
Found at i:16992 original size:17 final size:17
Alignment explanation
Indices: 16970--17009 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
16960 TATTTCAATT
*
16970 AATCAAAGGCACAAATA
1 AATCAAAGACACAAATA
16987 AATCAAAGACACAAATA
1 AATCAAAGACACAAATA
17004 ATATCA
1 A-ATCA
17010 GAATTCATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.60, C:0.17, G:0.07, T:0.15
Consensus pattern (17 bp):
AATCAAAGACACAAATA
Found at i:17763 original size:29 final size:30
Alignment explanation
Indices: 17718--17787 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
17708 CCAAAATGCC
** *
17718 AAGTAGAGGGACTAAATTGATCATTTT-T-T
1 AAGTAGAGGGAAGAAATTGAT-ATTTTGTGA
17747 AAGTAGAGGGAAGAAATTGATATTTTGTGA
1 AAGTAGAGGGAAGAAATTGATATTTTGTGA
17777 AAGTAGAGGGA
1 AAGTAGAGGGA
17788 CCTCCCAGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 5 0.14
29 20 0.56
30 11 0.31
ACGTcount: A:0.39, C:0.03, G:0.29, T:0.30
Consensus pattern (30 bp):
AAGTAGAGGGAAGAAATTGATATTTTGTGA
Found at i:20904 original size:3 final size:3
Alignment explanation
Indices: 20896--20932 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
20886 TCTACTATAT
*
20896 ATA ATA AT- ATT ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
20933 TAGATCATGT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:27253 original size:40 final size:40
Alignment explanation
Indices: 27191--27706 Score: 314
Period size: 40 Copynumber: 12.1 Consensus size: 40
27181 AGGAAATAGG
* * * * *
27191 AACAACGCCTTCCGTTGAGGAAGGGCAGACTGAGAATTTA
1 AACAACACCTTCCGATGGGGAAGGGCAAACTGGGAATTTA
* * * *
27231 GACAACACCTTCTGGTGGGGAAGGGCAAACTGGGAA-ATA
1 AACAACACCTTCCGATGGGGAAGGGCAAACTGGGAATTTA
* *
27270 AACAACACCTTCCGGTGGGGAAGGGCAAACTGGGAATGTA
1 AACAACACCTTCCGATGGGGAAGGGCAAACTGGGAATTTA
** * ** * **
27310 AACAACAATTTCTGATTAGGAAGGGCAAACTGGTAAACTA
1 AACAACACCTTCCGATGGGGAAGGGCAAACTGGGAATTTA
* * *
27350 AACAACACCTTCCGATGGGGAATGGCAAATTGGTAAACTAAACTTA
1 AACAACACCTTCCGATGGGGAAGGGCAAACTGG-GAA-T----TTA
** *
27396 AACAACACCTTCTTATGAGGAAGGGCAAACTGGGAATTTA
1 AACAACACCTTCCGATGGGGAAGGGCAAACTGGGAATTTA
* * *
27436 GACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTAAAGTAGACTTA
1 AACAACACCTTCCGATGGGGAAGGGCAAACTGGG--AA-T----TTA
* * *
27483 AACAACACCTTCCGATGAGAAAGGGCAAACTGGGAATATA
1 AACAACACCTTCCGATGGGGAAGGGCAAACTGGGAATTTA
* * *
27523 AACAATACCTTCCGGTGGGGAAGGGCAAATTGGGTAAAGTACACTTA
1 AACAACACCTTCCGATGGGGAAGGGCAAACTGGG--AA-T----TTA
* * * * *
27570 GACAACACCTTCCGGTGAGGAAGGACAAACTGAGAAAGTAGACTTA
1 AACAACACCTTCCGATGGGGAAGGGCAAACTG-G---G-A-ATTTA
* * * * *
27616 GACAACACCTTCCGGTGGGGAAGGACAAATTGGTGCATTAAACTTA
1 AACAACACCTTCCGATGGGGAAGGGCAAACTGG-G-----AATTTA
* * *
27662 AACAACACCTTCCGGTGGGGAAGGACAAATTGGGAATTTA
1 AACAACACCTTCCGATGGGGAAGGGCAAACTGGGAATTTA
27702 AACAA
1 AACAA
27707 GGCAATGCTG
Statistics
Matches: 379, Mismatches: 67, Indels: 60
0.75 0.13 0.12
Matches are distributed among these distances:
39 36 0.09
40 160 0.42
41 2 0.01
42 4 0.01
43 3 0.01
44 2 0.01
45 6 0.02
46 100 0.26
47 62 0.16
48 1 0.00
50 1 0.00
51 2 0.01
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.19
Consensus pattern (40 bp):
AACAACACCTTCCGATGGGGAAGGGCAAACTGGGAATTTA
Found at i:27514 original size:87 final size:86
Alignment explanation
Indices: 27232--27706 Score: 496
Period size: 87 Copynumber: 5.5 Consensus size: 86
27222 GAGAATTTAG
* * * *
27232 ACAACACCTTCTGGTGGGGAAGGGCAAACTGGGAA-ATAAACAACACCTTCCGGTGGGGAAGGGC
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAGGGC
* * *
27296 AAACTGGGAATGTAAAC---A
66 AAATTGGTAAAGTAAACTTAA
* * * * ** * *
27314 AC-A-A-TTTCTGATTAGGAAGGGCAAACTGGTAAACTAAACAACACCTTCCGATGGGGAATGGC
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAGGGC
*
27376 AAATTGGTAAACTAAACTTAA
66 AAATTGGTAAAGTAAACTTAA
** *
27397 ACAACACCTTCTTATGAGGAAGGGCAAACTGGGAATTTAGACAACACCTTCCGGTGGGGAAGGGC
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAGGGC
*
27462 AAATTGGGTAAAGTAGACTTAA
66 AAATT-GGTAAAGTAAACTTAA
* * *
27484 ACAACACCTTCCGATGAGAAAGGGCAAACTGGGAATATAAACAATACCTTCCGGTGGGGAAGGGC
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAGGGC
* *
27549 AAATTGGGTAAAGTACACTTAG
66 AAATT-GGTAAAGTAAACTTAA
* * * *
27571 ACAACACCTTCCGGTGAGGAAGGACAAACTGAGAAAGTAGACTTAGACAACACCTTCCGGTGGGG
1 ACAACACCTTCCGATGAGGAAGGGCAAACTG-G---G-A-ATTTAAACAACACCTTCCGGTGGGG
* ** *
27636 AAGGACAAATTGGTGCATTAAACTTAA
60 AAGGGCAAATTGGTAAAGTAAACTTAA
* * * *
27663 ACAACACCTTCCGGTGGGGAAGGACAAATTGGGAATTTAAACAA
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTTAAACAA
27707 GGCAATGCTG
Statistics
Matches: 331, Mismatches: 48, Indels: 24
0.82 0.12 0.06
Matches are distributed among these distances:
79 23 0.07
80 40 0.12
81 1 0.00
82 2 0.01
83 3 0.01
84 1 0.00
85 1 0.00
86 62 0.19
87 122 0.37
88 2 0.01
91 2 0.01
92 41 0.12
93 31 0.09
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.19
Consensus pattern (86 bp):
ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTTAAACAACACCTTCCGGTGGGGAAGGGC
AAATTGGTAAAGTAAACTTAA
Found at i:27704 original size:46 final size:46
Alignment explanation
Indices: 27342--27697 Score: 335
Period size: 46 Copynumber: 8.0 Consensus size: 46
27332 GGGCAAACTG
* * *
27342 GTAAAC-TAAACAACACCTTCCGATGGGGAATGGCAAATTGGTAAA
1 GTAAACTTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGGAAA
* *** * *
27387 CTAAACTTAAACAACACCTTCTTATGAGGAAGGGCAAACTGGG-AA
1 GTAAACTTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGGAAA
*
27432 -T----TTAGACAACACCTTCCGGTGGGGAAGGGCAAATTGGGTAAA
1 GTAAACTTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGG-AAA
* * * * *
27474 GTAGACTTAAACAACACCTTCCGATGAGAAAGGGCAAACTGGG-AA
1 GTAAACTTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGGAAA
*
27519 -T--A--TAAACAATACCTTCCGGTGGGGAAGGGCAAATTGGGTAAA
1 GTAAACTTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGG-AAA
* * * * * *
27561 GTACACTTAGACAACACCTTCCGGTGAGGAAGGACAAACTGAGAAA
1 GTAAACTTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGGAAA
* * * *
27607 GTAGACTTAGACAACACCTTCCGGTGGGGAAGGACAAATTGGTG-CA
1 GTAAACTTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGG-GAAA
* *
27653 TTAAACTTAAACAACACCTTCCGGTGGGGAAGGACAAATTGGGAA
1 GTAAACTTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGGAA
27698 TTTAAACAAG
Statistics
Matches: 256, Mismatches: 38, Indels: 33
0.78 0.12 0.10
Matches are distributed among these distances:
40 62 0.24
42 5 0.02
43 2 0.01
44 2 0.01
45 11 0.04
46 111 0.43
47 63 0.25
ACGTcount: A:0.37, C:0.19, G:0.26, T:0.19
Consensus pattern (46 bp):
GTAAACTTAAACAACACCTTCCGGTGGGGAAGGGCAAATTGGGAAA
Found at i:30768 original size:11 final size:11
Alignment explanation
Indices: 30736--30768 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
30726 GTATGGCAGT
*
30736 GCTTGATGATA
1 GCTTGATGATG
30747 GCTTGATGATG
1 GCTTGATGATG
30758 GCTTGATGATG
1 GCTTGATGATG
30769 CCTGCCATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.21, C:0.09, G:0.33, T:0.36
Consensus pattern (11 bp):
GCTTGATGATG
Found at i:31064 original size:18 final size:21
Alignment explanation
Indices: 31025--31065 Score: 61
Period size: 18 Copynumber: 2.1 Consensus size: 21
31015 TTTTCAAGTC
31025 TGTGCAATGTTTGATATTTGA
1 TGTGCAATGTTTGATATTTGA
31046 TGTGC-ATG-TTGAT-TTTGA
1 TGTGCAATGTTTGATATTTGA
31064 TG
1 TG
31066 ACAGGTAGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
19 5 0.25
20 3 0.15
21 5 0.25
ACGTcount: A:0.20, C:0.05, G:0.27, T:0.49
Consensus pattern (21 bp):
TGTGCAATGTTTGATATTTGA
Found at i:31805 original size:42 final size:42
Alignment explanation
Indices: 31713--31805 Score: 104
Period size: 42 Copynumber: 2.3 Consensus size: 42
31703 AAAACATGTC
* *
31713 AATTACAAAA-CCAAACGAAATAAACTATAGAATCATATAGA
1 AATTACAAAACCCAAAAGAAATAAACAATAGAATCATATAGA
* *
31754 AA--ACGAAAACCCCAAAAGAAATAAACAATTGAATCATTTA-A
1 AATTAC-AAAA-CCCAAAAGAAATAAACAATAGAATCATATAGA
31795 AATTACAAAAC
1 AATTACAAAAC
31806 GGGATTGCCT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
39 2 0.05
40 4 0.09
41 6 0.14
42 29 0.67
43 2 0.05
ACGTcount: A:0.59, C:0.16, G:0.06, T:0.18
Consensus pattern (42 bp):
AATTACAAAACCCAAAAGAAATAAACAATAGAATCATATAGA
Found at i:41512 original size:19 final size:19
Alignment explanation
Indices: 41488--41524 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
41478 ATATAGTACC
41488 TAATCTAATCTGTACAGTG
1 TAATCTAATCTGTACAGTG
*
41507 TAATCTCATCTGTACAGT
1 TAATCTAATCTGTACAGT
41525 TGCTAAACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (19 bp):
TAATCTAATCTGTACAGTG
Found at i:42433 original size:15 final size:15
Alignment explanation
Indices: 42415--42446 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
42405 ATCATATAAT
42415 AATTTACAATATATC
1 AATTTACAATATATC
42430 AATTTACAATATATC
1 AATTTACAATATATC
42445 AA
1 AA
42447 ACAACTAAGC
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:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (15 bp):
AATTTACAATATATC
Found at i:52095 original size:23 final size:22
Alignment explanation
Indices: 52049--52091 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
52039 AAAATTGGGG
*
52049 AAAATGAGATTAATCCAAAAAC
1 AAAATAAGATTAATCCAAAAAC
52071 AAAATAAGATTAATCCAAAAA
1 AAAATAAGATTAATCCAAAAA
52092 ACAATCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.63, C:0.12, G:0.07, T:0.19
Consensus pattern (22 bp):
AAAATAAGATTAATCCAAAAAC
Found at i:55565 original size:36 final size:37
Alignment explanation
Indices: 55524--55593 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
55514 AGAACTTTAG
55524 TTGAATATTT-TTATATGTATTTTGAACTTAATTACA
1 TTGAATATTTATTATATGTATTTTGAACTTAATTACA
*
55560 TTGAATATTTATTATATTTATTTTGAACTTAATT
1 TTGAATATTTATTATATGTATTTTGAACTTAATT
55594 TATGTTCATG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 10 0.31
37 22 0.69
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.56
Consensus pattern (37 bp):
TTGAATATTTATTATATGTATTTTGAACTTAATTACA
Found at i:57092 original size:32 final size:32
Alignment explanation
Indices: 57056--57171 Score: 142
Period size: 32 Copynumber: 3.6 Consensus size: 32
57046 AATTGAATGA
*
57056 GGACAAATTTCCAATGCATTAATTACAAATAG
1 GGACAAATTTGCAATGCATTAATTACAAATAG
* ** *
57088 GGACAAATTTACAATGCATTAATTGTAAATGG
1 GGACAAATTTGCAATGCATTAATTACAAATAG
* *
57120 GGACAAATTTGCAATGCATTAATTTCGAATAG
1 GGACAAATTTGCAATGCATTAATTACAAATAG
* * *
57152 AGACAATTTTGCAATTCATT
1 GGACAAATTTGCAATGCATT
57172 TAAGTATATG
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 72 1.00
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.32
Consensus pattern (32 bp):
GGACAAATTTGCAATGCATTAATTACAAATAG
Found at i:57157 original size:64 final size:64
Alignment explanation
Indices: 57051--57192 Score: 171
Period size: 64 Copynumber: 2.2 Consensus size: 64
57041 TATTAAATTG
*
57051 AATGAGGACAAATTTCCAATGCATTAATTACAAATAGGGACAAATTTACAATGCATTAATTGTA
1 AATGAGGACAAATTTCCAATGCATTAATTACAAATAGAGACAAATTTACAATGCATTAATTGTA
* * * * * * *
57115 AATGGGGACAAATTTGCAATGCATTAATTTCGAATAGAGACAATTTTGCAATTCATTTAA--GTA
1 AATGAGGACAAATTTCCAATGCATTAATTACAAATAGAGACAAATTTACAATGCA-TTAATTGTA
* *
57178 TATGAAGACAAATTT
1 AATGAGGACAAATTT
57193 ACAAACTAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
63 15 0.23
64 47 0.71
65 4 0.06
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (64 bp):
AATGAGGACAAATTTCCAATGCATTAATTACAAATAGAGACAAATTTACAATGCATTAATTGTA
Done.