Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022723.1 Corchorus olitorius cultivar O-4 contig22756, 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: 44745
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3121 original size:65 final size:62
Alignment explanation
Indices: 3001--3452 Score: 327
Period size: 60 Copynumber: 7.4 Consensus size: 62
2991 TTTGAAAGGT
* * *
3001 AAAATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCA-AGTGTCTATTGG
1 AAAATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACAACTT-ATGGTGTCAATTGG
* * *
3063 AAATTTATCATGACAACTTATGGTGTCAATTGAATAAAATTATGACAGCTTATGGTGTCAATTGC
1 AAA---ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACAACTTATGGTGTCAATTGG
* * * * * * * *
3128 AAGATCATGACAGCTTTTGGTGTCAATTG--CAACATCATGACAACTTTTGGTGTCAATTGC
1 AAAATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACAACTTATGGTGTCAATTGG
* * **** * *
3188 AAAATCATGACAGCTTCTGGTGTCAATTG--CAAGGCCATGACAACTTCTGGTGTCAATTGC
1 AAAATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACAACTTATGGTGTCAATTGG
*** * * * * * *
3248 AAGGCCATGACAACTTCTGGTGTCATTTGCAA-GACA--ATGACAACTTCTGGTGTCATTTGC
1 AAAATCATGACAACTTCTGGTGTCAATTG-AATAAAATTATGACAACTTATGGTGTCAATTGG
* * * * ** *
3308 AAGACCATGACAACTTCTGGTGTCAATTG--CAAGACCATGACAACTTATGGTGTCAATTGC
1 AAAATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACAACTTATGGTGTCAATTGG
* * * * * * * * *
3368 AAGACCATGGCAACTTCTGGTGTC-ATCTG--CAAGATCATGACAACTTCTGGTGTCGATTGT
1 AAAATCATGACAACTTCTGGTGTCAAT-TGAATAAAATTATGACAACTTATGGTGTCAATTGG
*
3428 AAAACCATGACAACTTCTGGTGTCA
1 AAAATCATGACAACTTCTGGTGTCA
3453 TTTAGAGAGT
Statistics
Matches: 337, Mismatches: 41, Indels: 25
0.84 0.10 0.06
Matches are distributed among these distances:
58 2 0.01
59 2 0.01
60 250 0.74
62 28 0.08
64 1 0.00
65 54 0.16
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (62 bp):
AAAATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACAACTTATGGTGTCAATTGG
Found at i:3140 original size:30 final size:30
Alignment explanation
Indices: 3071--3452 Score: 487
Period size: 30 Copynumber: 12.7 Consensus size: 30
3061 GGAAATTTAT
* * * *
3071 CATGACAACTTATGGTGTCAATTGAATAAAAT
1 CATGACAACTTCTGGTGTCAATTG--CAAGAC
* * * *
3103 TATGACAGCTTATGGTGTCAATTGCAAGAT
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
* * * *
3133 CATGACAGCTTTTGGTGTCAATTGCAACAT
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
* * *
3163 CATGACAACTTTTGGTGTCAATTGCAAAAT
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
* *
3193 CATGACAGCTTCTGGTGTCAATTGCAAGGC
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
*
3223 CATGACAACTTCTGGTGTCAATTGCAAGGC
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
*
3253 CATGACAACTTCTGGTGTCATTTGCAAGAC
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
* *
3283 AATGACAACTTCTGGTGTCATTTGCAAGAC
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
3313 CATGACAACTTCTGGTGTCAATTGCAAGAC
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
*
3343 CATGACAACTTATGGTGTCAATTGCAAGAC
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
* *
3373 CATGGCAACTTCTGGTGTC-ATCTGCAAGAT
1 CATGACAACTTCTGGTGTCAAT-TGCAAGAC
* * *
3403 CATGACAACTTCTGGTGTCGATTGTAAAAC
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
3433 CATGACAACTTCTGGTGTCA
1 CATGACAACTTCTGGTGTCA
3453 TTTAGAGAGT
Statistics
Matches: 319, Mismatches: 29, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
29 2 0.01
30 293 0.92
31 2 0.01
32 22 0.07
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (30 bp):
CATGACAACTTCTGGTGTCAATTGCAAGAC
Found at i:3690 original size:24 final size:23
Alignment explanation
Indices: 3658--3709 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 23
3648 TCAACTCCTC
3658 ACCAAACCAAGAAGATTCACAAAA
1 ACCAAACCAAGAAGATTCAC-AAA
3682 ACCAAACCAAGAAGATTCACAAA
1 ACCAAACCAAGAAGATTCACAAA
3705 ACCAA
1 ACCAA
3710 GGAGATAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 8 0.29
24 20 0.71
ACGTcount: A:0.58, C:0.27, G:0.08, T:0.08
Consensus pattern (23 bp):
ACCAAACCAAGAAGATTCACAAA
Found at i:11340 original size:6 final size:7
Alignment explanation
Indices: 11325--11353 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
11315 TAGCTTTCGT
11325 AAAACAA
1 AAAACAA
11332 AAAACAA
1 AAAACAA
11339 AAAAC-A
1 AAAACAA
11345 AAAACAA
1 AAAACAA
11352 AA
1 AA
11354 GTACGTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAACAA
Found at i:11347 original size:13 final size:14
Alignment explanation
Indices: 11325--11353 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
11315 TAGCTTTCGT
11325 AAAACAAAAAACAA
1 AAAACAAAAAACAA
11339 AAAAC-AAAAACAA
1 AAAACAAAAAACAA
11352 AA
1 AA
11354 GTACGTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAACAAAAAACAA
Found at i:12176 original size:22 final size:22
Alignment explanation
Indices: 12151--12598 Score: 121
Period size: 22 Copynumber: 20.2 Consensus size: 22
12141 GAACGATTAT
* *
12151 CAAAATTTCGTAGTGTGGTTAC
1 CAAAATTTCATAGTGAGGTTAC
*
12173 CAAAATTTCATA-TAGAGGTTAT
1 CAAAATTTCATAGT-GAGGTTAC
* *
12195 CAAAACTTCATAGTGTA-GTTAT
1 CAAAATTTCATAGTG-AGGTTAC
**
12217 CAAAATTTCATACAGAGGTTAC
1 CAAAATTTCATAGTGAGGTTAC
12239 CAAAATTTCATAGGGAGTGAGGTTAC
1 CAAAATTTCAT----AGTGAGGTTAC
* * *
12265 CGAAA-TT--T-GT--GCTTAT
1 CAAAATTTCATAGTGAGGTTAC
* * *
12281 CAAAATTTCCTAGAGAGGTTAA
1 CAAAATTTCATAGTGAGGTTAC
* * *
12303 CAAAATTTTATAGGGAGGTTAT
1 CAAAATTTCATAGTGAGGTTAC
* * * *
12325 GAAAATTTTATGGAGAGGTTATC
1 CAAAATTTCATAGTGAGGTTA-C
* * * *
12348 GAAAA-TACATAGAGAGGATATC
1 CAAAATTTCATAGTGAGGTTA-C
** * * *
12370 ACAGTTTCATTCTCGTAGGGAGGTTAT
1 -CA---AAATT-TCATAGTGAGGTTAC
* * * *
12397 CGAAATTTCATGGTGTGGTTAT
1 CAAAATTTCATAGTGAGGTTAC
*
12419 CAAAATTTTCATAGTGCGGTTAC
1 CAAAA-TTTCATAGTGAGGTTAC
* * * *
12442 C--AATTTTATTTAGTGTGATTAT
1 CAAAATTTCA--TAGTGAGGTTAC
* * * *
12464 TAAAATTTTATAG-GCAGATTAT
1 CAAAATTTCATAGTG-AGGTTAC
* * * *
12486 CAAAATTTCACACTGAGATTAT
1 CAAAATTTCATAGTGAGGTTAC
* *
12508 CGAAATTTCATAGTGTGGTTAC
1 CAAAATTTCATAGTGAGGTTAC
* * * *
12530 CCAAATTTCACAGTGTGGTTAT
1 CAAAATTTCATAGTGAGGTTAC
* * * *
12552 CGAATTTTCATAGGGAGGTTAT
1 CAAAATTTCATAGTGAGGTTAC
* * *
12574 CGAAATTTCATA-TTAGGTTAT
1 CAAAATTTCATAGTGAGGTTAC
12595 CAAA
1 CAAA
12599 TTTGCAAAAT
Statistics
Matches: 322, Mismatches: 76, Indels: 57
0.71 0.17 0.13
Matches are distributed among these distances:
16 8 0.02
17 2 0.01
18 2 0.01
19 1 0.00
20 5 0.02
21 15 0.05
22 226 0.70
23 28 0.09
24 7 0.02
25 2 0.01
26 15 0.05
27 1 0.00
28 10 0.03
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATAGTGAGGTTAC
Found at i:12195 original size:44 final size:44
Alignment explanation
Indices: 12147--12251 Score: 156
Period size: 44 Copynumber: 2.4 Consensus size: 44
12137 CATAGAACGA
* * *
12147 TTATCAAAATTTCGTAGTGTGGTTACCAAAATTTCATATAGAGG
1 TTATCAAAATTTCATAGTGTAGTTACCAAAATTTCATACAGAGG
* *
12191 TTATCAAAACTTCATAGTGTAGTTATCAAAATTTCATACAGAGG
1 TTATCAAAATTTCATAGTGTAGTTACCAAAATTTCATACAGAGG
*
12235 TTACCAAAATTTCATAG
1 TTATCAAAATTTCATAG
12252 GGAGTGAGGT
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 54 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.35
Consensus pattern (44 bp):
TTATCAAAATTTCATAGTGTAGTTACCAAAATTTCATACAGAGG
Found at i:13044 original size:169 final size:170
Alignment explanation
Indices: 12757--13068 Score: 389
Period size: 169 Copynumber: 1.8 Consensus size: 170
12747 AGCTTTCTAA
* * *
12757 AAAGCCTAAAACCTCAACTTCCCGATTTAGCACGTTTGAGCGCCAAACGTTGTTCTCAGGAAAAT
1 AAAGCCTAAAACCTAAACTTCACGATTTAGCACGCTTGAGCGCCAAACGTTGTTCTCAGGAAAAT
* * * * *
12822 GCTCATTCCAAGTACATTATTTGTGAAACCAATGCTCAAATGTTATGTTTCAGAGTGAGTA-AGC
66 GCTAATTCCAAGTACATTATTTGTGAAACCAATGCTCAAATGTCATATTTCAGAGTCAATAGAGC
12886 TAATTGGAAAGTGGGTTTGCAAAAAAAAAAAACTTTCTTC
131 TAATTGGAAAGTGGGTTTGCAAAAAAAAAAAACTTTCTTC
* * ** * **
12926 AAAGCCTAAAACTTAAACTTCACGATTTTGCGTGCTTGTGCG-CAGAACGTTGTTCTTGGGAAAA
1 AAAGCCTAAAACCTAAACTTCACGATTTAGCACGCTTGAGCGCCA-AACGTTGTTCTCAGGAAAA
* * * *
12990 TGTTAATTCCGAA-TGCATTATTTGTGTAACC-ATCGCTCATATGTCATATTTCAGAGTCAATAG
65 TGCTAATTCC-AAGTACATTATTTGTGAAACCAAT-GCTCAAATGTCATATTTCAGAGTCAATAG
*
13053 AGCTCATTGGAAAGTG
128 AGCTAATTGGAAAGTG
13069 ACTTGCCAAA
Statistics
Matches: 119, Mismatches: 20, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
168 4 0.03
169 98 0.82
170 17 0.14
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (170 bp):
AAAGCCTAAAACCTAAACTTCACGATTTAGCACGCTTGAGCGCCAAACGTTGTTCTCAGGAAAAT
GCTAATTCCAAGTACATTATTTGTGAAACCAATGCTCAAATGTCATATTTCAGAGTCAATAGAGC
TAATTGGAAAGTGGGTTTGCAAAAAAAAAAAACTTTCTTC
Found at i:14401 original size:22 final size:22
Alignment explanation
Indices: 14360--14922 Score: 210
Period size: 22 Copynumber: 25.4 Consensus size: 22
14350 ACAATCAAAC
* *
14360 CAAAATTACATAGTAAGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
* *
14382 TAAAATTTCATAGTGTGGTTA-
1 CAAAATTTCATAGTGAGGTTAT
14403 CAAAAATTTCATA-TGGAGGTTAT
1 C-AAAATTTCATAGT-GAGGTTAT
* * *
14426 CAAAACTTCGTAGTGTA-ATTAT
1 CAAAATTTCATAGTG-AGGTTAT
** *
14448 CAAAATTTCATACAGAGGTTAC
1 CAAAATTTCATAGTGAGGTTAT
***
14470 CAAAATTTCATAAAAAAAGGTTAT
1 CAAAATTTCAT--AGTGAGGTTAT
* * *
14494 CAAAATCTCTTA-TGGAGATTAT
1 CAAAATTTCATAGT-GAGGTTAT
*
14516 CAAAATTTCATACG-AAGGTTAT
1 CAAAATTTCATA-GTGAGGTTAT
** * * *
14538 TGAAATTTTATAGTGTGATTAT
1 CAAAATTTCATAGTGAGGTTAT
* * *
14560 CAAAA-TTAATTAG-AACGTTAT
1 CAAAATTTCA-TAGTGAGGTTAT
**
14581 CAAAA-TT--T-GT--TCTTAT
1 CAAAATTTCATAGTGAGGTTAT
* *
14597 CAAAATTTCCTAG-GATGGTTAA
1 CAAAATTTCATAGTGA-GGTTAT
* *
14619 CAAAATTTCATAGGGAGCTTAT
1 CAAAATTTCATAGTGAGGTTAT
* * *
14641 GAAAATATT-ATGGAGAGGTTAT
1 CAAAAT-TTCATAGTGAGGTTAT
* **
14663 CAAAATTACATA-TAGAGAATAT
1 CAAAATTTCATAGT-GAGGTTAT
* * *
14685 CACAATTTCATTCTTATAGGGAAGTTAT
1 CA-AA----ATT-TCATAGTGAGGTTAT
* * *
14713 CGAAATTTCATGGTGTGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
* *
14735 CAAAATTTTCATAGTGCGATTA-
1 CAAAA-TTTCATAGTGAGGTTAT
* * * * *
14757 C-CAATTTTATAATGTGATTAT
1 CAAAATTTCATAGTGAGGTTAT
14778 CAAAATTTCATAGACAATGAGGTTAT
1 CAAAATTTCATAG----TGAGGTTAT
* *
14804 CAAAACTTCATTGT-ATGGTTAT
1 CAAAATTTCATAGTGA-GGTTAT
* * *
14826 CAGAATTTCACAGTGTGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
* * *
14848 CAAAATTTCACATTGTGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
* *
14870 CAAATTTTCATAGGGAGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
* * *
14892 CGAAATTTCACAATGAGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
*
14914 CAAATTTTC
1 CAAAATTTC
14923 GCGGTGTGGT
Statistics
Matches: 396, Mismatches: 104, Indels: 82
0.68 0.18 0.14
Matches are distributed among these distances:
16 9 0.02
17 3 0.01
18 1 0.00
19 1 0.00
20 14 0.04
21 22 0.06
22 272 0.69
23 25 0.06
24 17 0.04
26 18 0.05
27 5 0.01
28 9 0.02
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.36
Consensus pattern (22 bp):
CAAAATTTCATAGTGAGGTTAT
Found at i:14867 original size:44 final size:44
Alignment explanation
Indices: 14798--14944 Score: 156
Period size: 44 Copynumber: 3.3 Consensus size: 44
14788 TAGACAATGA
*
14798 GGTTATCAAAACTT--CATTGTATGGTTATCAGAA-TTTCACAGTGT
1 GGTTATCAAAATTTCACATTG--TGGTTATCA-AATTTTCACAGTGT
* * *
14842 GGTTATCAAAATTTCACATTGTGGTTATCAAATTTTCATAGGGA
1 GGTTATCAAAATTTCACATTGTGGTTATCAAATTTTCACAGTGT
* * * * *
14886 GGTTATCGAAATTTCACAATGAGGTTATCAAATTTTCGCGGTGT
1 GGTTATCAAAATTTCACATTGTGGTTATCAAATTTTCACAGTGT
*
14930 GGTTATCAATATTTC
1 GGTTATCAAAATTTC
14945 TACGTTGGAG
Statistics
Matches: 86, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
43 2 0.02
44 79 0.92
46 5 0.06
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (44 bp):
GGTTATCAAAATTTCACATTGTGGTTATCAAATTTTCACAGTGT
Found at i:14933 original size:22 final size:22
Alignment explanation
Indices: 14819--14943 Score: 128
Period size: 22 Copynumber: 5.6 Consensus size: 22
14809 CTTCATTGTA
14819 TGGTTATCAGAA-TTTCACAGTG
1 TGGTTATCA-AATTTTCACAGTG
* *
14841 TGGTTATCAAAATTTCACATTG
1 TGGTTATCAAATTTTCACAGTG
* *
14863 TGGTTATCAAATTTTCATAGGG
1 TGGTTATCAAATTTTCACAGTG
* *
14885 AGGTTATCGAAA-TTTCACAATG
1 TGGTTATC-AAATTTTCACAGTG
* * *
14907 AGGTTATCAAATTTTCGCGGTG
1 TGGTTATCAAATTTTCACAGTG
14929 TGGTTATCAATATTT
1 TGGTTATCAA-ATTT
14944 CTACGTTGGA
Statistics
Matches: 86, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
21 5 0.06
22 74 0.86
23 7 0.08
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (22 bp):
TGGTTATCAAATTTTCACAGTG
Found at i:16427 original size:19 final size:19
Alignment explanation
Indices: 16403--16442 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
16393 ATTCTAATGT
16403 CTATTCAAATAATTATCTA
1 CTATTCAAATAATTATCTA
16422 CTATTCAAATAATTATCTA
1 CTATTCAAATAATTATCTA
16441 CT
1 CT
16443 GGATCACTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.42
Consensus pattern (19 bp):
CTATTCAAATAATTATCTA
Found at i:37972 original size:31 final size:31
Alignment explanation
Indices: 37936--38009 Score: 121
Period size: 31 Copynumber: 2.4 Consensus size: 31
37926 CTATTCCTTA
* *
37936 CTTCCCTGGCAAAAACCTGGAGAAAGTTTTC
1 CTTCCCCGGCAAAAACCAGGAGAAAGTTTTC
37967 CTTCCCCGGCAAAAACCAGGAGAAAGTTTTC
1 CTTCCCCGGCAAAAACCAGGAGAAAGTTTTC
*
37998 CTTCCCCAGCAA
1 CTTCCCCGGCAA
38010 CGGCGCCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.30, C:0.31, G:0.18, T:0.22
Consensus pattern (31 bp):
CTTCCCCGGCAAAAACCAGGAGAAAGTTTTC
Found at i:40101 original size:15 final size:16
Alignment explanation
Indices: 40079--40116 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
40069 CGCTCAAATG
40079 TCGGGTC-ATTTGGGT
1 TCGGGTCAATTTGGGT
* *
40094 TTGGGTCAATTTTGGT
1 TCGGGTCAATTTGGGT
40110 TCGGGTC
1 TCGGGTC
40117 TTTTTTTTCG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.08, C:0.13, G:0.37, T:0.42
Consensus pattern (16 bp):
TCGGGTCAATTTGGGT
Found at i:43707 original size:134 final size:132
Alignment explanation
Indices: 43457--43709 Score: 316
Period size: 134 Copynumber: 1.9 Consensus size: 132
43447 TCCGGTACAA
* *
43457 ACGCCGCTAAATTAGAATAATTGGTGGGAAAATTCCCCCAAAATAATTCAAGAAAAAGTTAAAAG
1 ACGCCGCTAAATTAGAAAAATTGGTGGGAAAATTCCCCCAAAATAATTAAAGAAAAAGTTAAAAG
* * * *
43522 ATAAACTAAACCATTTAACGGCTTTTGGTATTGGAAACGCCACTATTTAGTGGCGTATCATATAA
66 ATAAACTAAACCATTTAACGGCGTTTGGTATTAGAAACGCCACAAATTAGTGGCGTATCATATAA
43587 AG
131 AG
* *
43589 ACGCCGCT-ATTTAGAAAAATTGGTGGGAAAAATTTTCCCCCCAAAATAATTAAAGGAAAAGTTA
1 ACGCCGCTAAATTAGAAAAATTGGTGGG-AAAA--TT-CCCCCAAAATAATTAAAGAAAAAGTTA
* * * *
43653 GAAG-TAAAGTAAGA-CATTTAGCGGCGTTT-GTAGTTAGAAATGCCACAAATTAGTGGC
62 AAAGATAAACTAA-ACCATTTAACGGCGTTTGGTA-TTAGAAACGCCACAAATTAGTGGC
43710 ATTTTACTTG
Statistics
Matches: 103, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
131 17 0.17
132 12 0.12
133 3 0.03
134 42 0.41
135 29 0.28
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (132 bp):
ACGCCGCTAAATTAGAAAAATTGGTGGGAAAATTCCCCCAAAATAATTAAAGAAAAAGTTAAAAG
ATAAACTAAACCATTTAACGGCGTTTGGTATTAGAAACGCCACAAATTAGTGGCGTATCATATAA
AG
Found at i:43729 original size:32 final size:32
Alignment explanation
Indices: 43688--43750 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
43678 GTTTGTAGTT
43688 AGAAATGCCACAAATTAGTGGCATTTTACTTG
1 AGAAATGCCACAAATTAGTGGCATTTTACTTG
* *
43720 AGAAATGCCACTAATTAGTGGCGTTTTACTT
1 AGAAATGCCACAAATTAGTGGCATTTTACTT
43751 TAAAAACGCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (32 bp):
AGAAATGCCACAAATTAGTGGCATTTTACTTG
Found at i:43762 original size:32 final size:32
Alignment explanation
Indices: 43694--43764 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
43684 AGTTAGAAAT
* * *
43694 GCCACAAATTAGTGGCATTTTACTTGAGAAAT
1 GCCACTAATTAGTGGCATTTTACTTGAAAAAC
* *
43726 GCCACTAATTAGTGGCGTTTTACTTTAAAAAC
1 GCCACTAATTAGTGGCATTTTACTTGAAAAAC
43758 GCCACTA
1 GCCACTA
43765 TTATATTAGT
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:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (32 bp):
GCCACTAATTAGTGGCATTTTACTTGAAAAAC
Done.