Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020042.1 Corchorus olitorius cultivar O-4 contig20075, 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: 55597
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1923 original size:19 final size:18
Alignment explanation
Indices: 1890--1925 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1880 TGAAAATAAT
1890 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
1908 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
1926 TAAGTCTTCA
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:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:4314 original size:2 final size:2
Alignment explanation
Indices: 4302--4391 Score: 68
Period size: 2 Copynumber: 47.5 Consensus size: 2
4292 TATTATTATC
* *
4302 TA TA TA AA TA TA TA TA TA TA TCA TA TA TA T- TA T- TA -A TT TA
1 TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA
* * *
4342 CTA TA TA T- TA TA -A TA TA TA AA TA TA TA T- TA AA AA TA T- TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4381 TA TA TA TA TA T
1 TA TA TA TA TA T
4392 TTTAGGCGTT
Statistics
Matches: 71, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
1 7 0.10
2 60 0.85
3 4 0.06
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:4366 original size:20 final size:19
Alignment explanation
Indices: 4302--4387 Score: 76
Period size: 18 Copynumber: 4.7 Consensus size: 19
4292 TATTATTATC
4302 TATATAA-ATATA-TAT-A
1 TATATAATATATATTATAA
*
4318 TATATCATATATATTATTAA
1 TATATAATATATATTA-TAA
*
4338 T-T-TACTATATATTATAA
1 TATATAATATATATTATAA
4355 TATATAAATATATATTA-AA
1 TATAT-AATATATATTATAA
* *
4374 AATATTATATATAT
1 TATATAATATATAT
4388 ATATTTTAGG
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
16 6 0.11
17 9 0.16
18 21 0.37
19 9 0.16
20 12 0.21
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
TATATAATATATATTATAA
Found at i:12310 original size:46 final size:46
Alignment explanation
Indices: 12258--12386 Score: 235
Period size: 44 Copynumber: 2.8 Consensus size: 46
12248 GGGTTGTCTT
12258 CACTATTAGTTATTTTGGGTTTTGTCAAATTTCAGGATACCAATAG
1 CACTATTAGTTATTTTGGGTTTTGTCAAATTTCAGGATACCAATAG
12304 CACTATTAGTTATTTTGGGTTTTGTCAAATTTCAGG--ACCAATAG
1 CACTATTAGTTATTTTGGGTTTTGTCAAATTTCAGGATACCAATAG
*
12348 CACTATTAGTTATTTTGGGTTTTGTCAAATTTGAGGATA
1 CACTATTAGTTATTTTGGGTTTTGTCAAATTTCAGGATA
12387 TACCCGGTTG
Statistics
Matches: 80, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
44 43 0.54
46 37 0.46
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.43
Consensus pattern (46 bp):
CACTATTAGTTATTTTGGGTTTTGTCAAATTTCAGGATACCAATAG
Found at i:22226 original size:119 final size:118
Alignment explanation
Indices: 22039--22272 Score: 396
Period size: 119 Copynumber: 2.0 Consensus size: 118
22029 GCGCTTGCCC
22039 CAACAGAAATGAAGTTTCTGCTCTCCATTGTGAAGACCAGAGAGTTCCAACAAACATTTCATTCT
1 CAACAGAAATGAAGTTTCTGCTCTCCATTGTGAAGACCAGAGAGTTCCAACAAACATTTCATTCT
22104 TGGGTGATGGGGCATCTCTCTGCCCATAATGCTAGACAATTGCAGAGATGGGG
66 TGGGTGATGGGGCATCTCTCTGCCCATAATGCTAGACAATTGCAGAGATGGGG
* * * *
22157 CAACATAAATGAAGTTTCTGTTCTCCATTGTGAAAGACTAGAGAGTTCCAACAAACATTTCATTG
1 CAACAGAAATGAAGTTTCTGCTCTCCATTGTG-AAGACCAGAGAGTTCCAACAAACATTTCATTC
* * *
22222 TTGGGTGATGGTGCATCTCTCTGCTCATAATGCTAGATAATTGCAGAGATG
65 TTGGGTGATGGGGCATCTCTCTGCCCATAATGCTAGACAATTGCAGAGATG
22273 AGAAGTGAAA
Statistics
Matches: 108, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
118 30 0.28
119 78 0.72
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.29
Consensus pattern (118 bp):
CAACAGAAATGAAGTTTCTGCTCTCCATTGTGAAGACCAGAGAGTTCCAACAAACATTTCATTCT
TGGGTGATGGGGCATCTCTCTGCCCATAATGCTAGACAATTGCAGAGATGGGG
Found at i:26249 original size:69 final size:66
Alignment explanation
Indices: 26121--26254 Score: 180
Period size: 66 Copynumber: 2.0 Consensus size: 66
26111 AGCCTCACAC
*
26121 GTAGATAGTAGGTATGCATCGTTCTCTTTGACATCATTCTTCAGCCATAAATAAATTTCTAAAAT
1 GTAGATAGTAGGTATGCATCGTTCTCTTTGACATCATTCTCCAGCCATAAATAAATTTCTAAAAT
26186 A
66 A
** * *
26187 GTAGATAGTAGGTATGCATCGTTCTCTTCTTTC-TCTTTATTCTCCAGCCATAAGTAAATTTCTC
1 GTAGATAGTAGGTATGCATCGTTCTCTT-TGACATC---ATTCTCCAGCCATAAATAAATTTCTA
26251 AAAT
62 AAAT
26255 CTATTTCCCA
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
66 30 0.51
67 2 0.03
69 27 0.46
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (66 bp):
GTAGATAGTAGGTATGCATCGTTCTCTTTGACATCATTCTCCAGCCATAAATAAATTTCTAAAAT
A
Found at i:30399 original size:106 final size:106
Alignment explanation
Indices: 30214--30427 Score: 428
Period size: 106 Copynumber: 2.0 Consensus size: 106
30204 TCGAAATTCC
30214 AGGTTAAAAGTTCAATCTAGTCCTAATTGTTTTATAAAATTTCCAATTTAAGTCTAAATGCAAGT
1 AGGTTAAAAGTTCAATCTAGTCCTAATTGTTTTATAAAATTTCCAATTTAAGTCTAAATGCAAGT
30279 CTTATTTGGATGAAAATAGACTCAATTCGGATTATTGTATT
66 CTTATTTGGATGAAAATAGACTCAATTCGGATTATTGTATT
30320 AGGTTAAAAGTTCAATCTAGTCCTAATTGTTTTATAAAATTTCCAATTTAAGTCTAAATGCAAGT
1 AGGTTAAAAGTTCAATCTAGTCCTAATTGTTTTATAAAATTTCCAATTTAAGTCTAAATGCAAGT
30385 CTTATTTGGATGAAAATAGACTCAATTCGGATTATTGTATT
66 CTTATTTGGATGAAAATAGACTCAATTCGGATTATTGTATT
30426 AG
1 AG
30428 AACTAGCTAC
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 108 1.00
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.39
Consensus pattern (106 bp):
AGGTTAAAAGTTCAATCTAGTCCTAATTGTTTTATAAAATTTCCAATTTAAGTCTAAATGCAAGT
CTTATTTGGATGAAAATAGACTCAATTCGGATTATTGTATT
Found at i:30553 original size:12 final size:12
Alignment explanation
Indices: 30536--30560 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30526 ATCAACCGTC
30536 CACTCTTTAACA
1 CACTCTTTAACA
30548 CACTCTTTAACA
1 CACTCTTTAACA
30560 C
1 C
30561 TTTTTAAATT
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:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (12 bp):
CACTCTTTAACA
Found at i:34502 original size:1 final size:1
Alignment explanation
Indices: 34496--34528 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
34486 TAAGTTATAG
34496 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
34529 AAGATAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:37068 original size:31 final size:31
Alignment explanation
Indices: 37030--37092 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
37020 ATATAAATTG
*
37030 TTTTTTTTT-ATATAAAAGTCTATTTTCACA
1 TTTTTTTTTGATACAAAAGTCTATTTTCACA
37060 TTTTTTTTTGATACAAAAGTCTATTTTCACA
1 TTTTTTTTTGATACAAAAGTCTATTTTCACA
37091 TT
1 TT
37093 AAATACATGA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 9 0.29
31 22 0.71
ACGTcount: A:0.29, C:0.11, G:0.05, T:0.56
Consensus pattern (31 bp):
TTTTTTTTTGATACAAAAGTCTATTTTCACA
Found at i:39392 original size:31 final size:32
Alignment explanation
Indices: 39327--39401 Score: 100
Period size: 32 Copynumber: 2.4 Consensus size: 32
39317 TAGTATAATC
* * *
39327 GAGTCTAAAAGATTTTTTATGTTTTGGCCAAT
1 GAGTCTAGAAGATTTTTTATGTTTTGACAAAT
39359 GAGTCTAGAAGATTTTTT-T-TTTTGACAACAT
1 GAGTCTAGAAGATTTTTTATGTTTTGACAA-AT
39390 GAGTCTAGAAGA
1 GAGTCTAGAAGA
39402 ATTTAGGTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
30 7 0.18
31 15 0.38
32 17 0.44
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (32 bp):
GAGTCTAGAAGATTTTTTATGTTTTGACAAAT
Found at i:43166 original size:55 final size:53
Alignment explanation
Indices: 43106--43328 Score: 189
Period size: 54 Copynumber: 4.1 Consensus size: 53
43096 ACGGAAACCT
* * *
43106 TTCTTGGAATGATCGCACTGGATCAAATTGAAAATCAACTCTGATCATCAAAAAC
1 TTCTTGGAATGACCGCACTGGATC-AATAG-AGATCAACTCTGATCATCAAAAAC
* ** * * * ***
43161 GTCTTGGAATGACTACACTGTATCAATAGAAGATCAACTTTGATCATTGAAATTT
1 TTCTTGGAATGACCGCACTGGATCAATAG-AGATCAACTCTGATCA-TCAAAAAC
* * * * *
43216 TTTTTGGAAAGACCGCACTAGATC-ATCTGGGATCAACTCTGATC-TCTAAAAAC
1 TTCTTGGAATGACCGCACTGGATCAAT-AGAGATCAACTCTGATCATC-AAAAAC
* * *
43269 TTCTTGGAATGACCGCACTGGATCATCTAGGGATCAACTCTGATCATCGAAAAC
1 TTCTTGGAATGACCGCACTGGATCA-ATAGAGATCAACTCTGATCATCAAAAAC
43323 TTCTTG
1 TTCTTG
43329 AAAGGAGATC
Statistics
Matches: 130, Mismatches: 32, Indels: 13
0.74 0.18 0.07
Matches are distributed among these distances:
52 1 0.01
53 24 0.18
54 61 0.47
55 44 0.34
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (53 bp):
TTCTTGGAATGACCGCACTGGATCAATAGAGATCAACTCTGATCATCAAAAAC
Found at i:43346 original size:35 final size:35
Alignment explanation
Indices: 43300--43900 Score: 808
Period size: 35 Copynumber: 16.9 Consensus size: 35
43290 ATCATCTAGG
*
43300 GATCAACTCTGATCATCGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
**
43335 GATCAACTCTGATCATAAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCAT-CGAAAACTTCTTGAAACGA
* *
43371 GACCAACTCTGATCATCGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
* **
43406 GATAAACTCTGATCATAAAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCAT--CGAAAACTTCTTGAAACGA
* * **
43443 GATAAACTCTGATAAAAAGAAAAAAAAACTTCTTGAAACGA
1 GATCAACTCTGAT-CATCG-----AAAACTTCTTGAAACGA
* *
43484 GATCAATTCTGATCATCGAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
*
43519 GATCAACTCTGATCATCAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
* *
43554 GATCAACTCTGATCATCGAAAACTTATTGAAAGGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
**
43589 GATCAACTCTGATCATAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
* *
43624 GATAAACTCTGATCATCAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
43659 GATCAACTCTGATCATC-AAAACTTCTTGAAACGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
*
43693 GATCAACTCTGATCATCGAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
* * **
43728 GATCAACTTTGATCCTAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
* *
43763 GATCAACTCTGATCATCGAAAACTTCTTAAAATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
* *
43798 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
* *
43833 GATCAACTCTGATCATCGAAAACTTTCTCGAAATGA
1 GATCAACTCTGATCATCGAAAAC-TTCTTGAAACGA
*
43869 GATCAACTCTGATCATTGAAAACTTCTTGAAA
1 GATCAACTCTGATCATCGAAAACTTCTTGAAA
43901 TGATCGCACT
Statistics
Matches: 503, Mismatches: 52, Indels: 22
0.87 0.09 0.04
Matches are distributed among these distances:
34 34 0.07
35 344 0.68
36 65 0.13
37 29 0.06
38 1 0.00
40 2 0.00
41 28 0.06
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.26
Consensus pattern (35 bp):
GATCAACTCTGATCATCGAAAACTTCTTGAAACGA
Found at i:43732 original size:209 final size:209
Alignment explanation
Indices: 43300--43900 Score: 842
Period size: 209 Copynumber: 2.8 Consensus size: 209
43290 ATCATCTAGG
* * **
43300 GATCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATCAACTCTGATCATAAAAAAACTTCTTG
1 GATCAACTCTGATCATCAAAAACTTCTTGAAACGAGATCAACTCTGATCAT-CGAAAACTTCTTG
* * * *
43365 AAACGAGACCAACTCTGATCATCGAAAACTTCTTGAAAGGAGATAAACTCTGATCATAAAAAAAA
65 AAACGAGATCAACTCTGATCATCAAAAACTTCTTGAAACGAGATAAACTCTGATCAT--CAAAAA
* * * *
43430 CTTCTTGAAACGAGATAAACTCTGATAAAAAGAAAAAAAAACTTCTTGAAACGAGATCAATTCTG
128 CTTCTTGAAACGAGATCAACTCTGAT-------CATAAAAACTTCTTGAAACGAGATCAACTCTG
43495 ATCATCGAAAACTTCTTGAAAGGA
186 ATCATCGAAAACTTCTTGAAAGGA
*
43519 GATCAACTCTGATCATCAAAAACTTCTTGAAACGAGATCAACTCTGATCATCGAAAACTTATTGA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAACGAGATCAACTCTGATCATCGAAAACTTCTTGA
* *
43584 AAGGAGATCAACTCTGATCATAAAAAACTTCTTGAAACGAGATAAACTCTGATCATCAAAAACTT
66 AACGAGATCAACTCTGATCATCAAAAACTTCTTGAAACGAGATAAACTCTGATCATCAAAAACTT
*
43649 CTTGAAACGAGATCAACTCTGATCATCAAAACTTCTTGAAACGAGATCAACTCTGATCATCGAAA
131 CTTGAAACGAGATCAACTCTGATCATAAAAACTTCTTGAAACGAGATCAACTCTGATCATCGAAA
*
43714 ACTTCTTGAAATGA
196 ACTTCTTGAAAGGA
* * * *
43728 GATCAACTTTGATCCTAAAAAACTTCTTGAAACGAGATCAACTCTGATCATCGAAAACTTCTTAA
1 GATCAACTCTGATCATCAAAAACTTCTTGAAACGAGATCAACTCTGATCATCGAAAACTTCTTGA
* * * *
43793 AATGAGATCAACTCTGATCATCAAAAACTTCTTGAAATGAGATCAACTCTGATCATCGAAAACTT
66 AACGAGATCAACTCTGATCATCAAAAACTTCTTGAAACGAGATAAACTCTGATCATCAAAAAC-T
* * *
43858 TCTCGAAATGAGATCAACTCTGATCATTGAAAACTTCTTGAAA
130 TCTTGAAACGAGATCAACTCTGATCA-TAAAAACTTCTTGAAA
43901 TGATCGCACT
Statistics
Matches: 350, Mismatches: 30, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
209 169 0.48
210 25 0.07
211 15 0.04
216 30 0.09
218 62 0.18
219 49 0.14
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.26
Consensus pattern (209 bp):
GATCAACTCTGATCATCAAAAACTTCTTGAAACGAGATCAACTCTGATCATCGAAAACTTCTTGA
AACGAGATCAACTCTGATCATCAAAAACTTCTTGAAACGAGATAAACTCTGATCATCAAAAACTT
CTTGAAACGAGATCAACTCTGATCATAAAAACTTCTTGAAACGAGATCAACTCTGATCATCGAAA
ACTTCTTGAAAGGA
Found at i:44037 original size:55 final size:54
Alignment explanation
Indices: 43869--44056 Score: 245
Period size: 54 Copynumber: 3.5 Consensus size: 54
43859 CTCGAAATGA
* * * *
43869 GATCAACTCTGATCATTGAAAACTTCTTGAAATGATCGCACTAGATCATTTTGG
1 GATCAACTCTGATCATTGAAAACTTCTTGAAATGACCGCACTGGATCATCTAGG
* * * * *
43923 GATCAACTTTGATCACTAAAAACTTCTTGAAATGACCGCACTGGATCAACTGGG
1 GATCAACTCTGATCATTGAAAACTTCTTGAAATGACCGCACTGGATCATCTAGG
*
43977 GATCAACTCTGATCATTGAAAACTTCTTTGGAATGACCGCACTGGATCATCTAGG
1 GATCAACTCTGATCATTGAAAACTTC-TTGAAATGACCGCACTGGATCATCTAGG
44032 GATCAACT-TAGATC-TCTGAAAACTT
1 GATCAACTCT-GATCAT-TGAAAACTT
44057 TAAAAGATCG
Statistics
Matches: 117, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
54 71 0.61
55 46 0.39
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.30
Consensus pattern (54 bp):
GATCAACTCTGATCATTGAAAACTTCTTGAAATGACCGCACTGGATCATCTAGG
Found at i:45265 original size:38 final size:39
Alignment explanation
Indices: 45184--45265 Score: 94
Period size: 38 Copynumber: 2.1 Consensus size: 39
45174 TTGAAAAACT
** * * **
45184 TTTTTTCTCTTTTGAAAAGATTGCATTTTGAGGGGAAT-
1 TTTTTTCTCTTTTGAAAAGATCACACTTTGAAGAAAATC
*
45222 TTTTTTTTCTTTTGAAAAGATCACACTTTGAAGAAAATC
1 TTTTTTCTCTTTTGAAAAGATCACACTTTGAAGAAAATC
45261 TTTTT
1 TTTTT
45266 CTTTCCAATA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
38 31 0.86
39 5 0.14
ACGTcount: A:0.27, C:0.10, G:0.15, T:0.49
Consensus pattern (39 bp):
TTTTTTCTCTTTTGAAAAGATCACACTTTGAAGAAAATC
Found at i:48801 original size:5 final size:5
Alignment explanation
Indices: 48791--48818 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
48781 CCTAATTTGG
48791 ATTAA ATTAA ATTAA ATTAA ATTAA ATT
1 ATTAA ATTAA ATTAA ATTAA ATTAA ATT
48819 GTTAAGAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
ATTAA
Found at i:50928 original size:24 final size:24
Alignment explanation
Indices: 50884--50929 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
50874 TAGGTGGACC
* * *
50884 ATATGCTACCATTTTTTTAAGGAT
1 ATATGCTACCATGTATCTAAGGAT
50908 ATATGCTACCATGTATCTAAGG
1 ATATGCTACCATGTATCTAAGG
50930 CTTAATTTGG
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:0.30, C:0.15, G:0.15, T:0.39
Consensus pattern (24 bp):
ATATGCTACCATGTATCTAAGGAT
Found at i:50992 original size:13 final size:13
Alignment explanation
Indices: 50968--51003 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
50958 AAAAATTTGG
50968 TTTTGAAGAAGTGT
1 TTTTGAA-AAGTGT
50982 TTTTGAAAAGTGT
1 TTTTGAAAAGTGT
*
50995 TTTTTAAAA
1 TTTTGAAAA
51004 TGGGTAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 14 0.67
14 7 0.33
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.47
Consensus pattern (13 bp):
TTTTGAAAAGTGT
Found at i:54956 original size:22 final size:22
Alignment explanation
Indices: 54931--55005 Score: 89
Period size: 22 Copynumber: 3.4 Consensus size: 22
54921 TTGAATATTT
54931 TTATGAAATTTTGATAACTACC
1 TTATGAAATTTTGATAACTACC
* * *
54953 TTATTAAATTTTGATAACCACG
1 TTATGAAATTTTGATAACTACC
* *
54975 TTATGGAATTTTGATAATTTACC
1 TTATGAAATTTTGATAA-CTACC
54998 -TATGAAAT
1 TTATGAAAT
55006 ATGAAACTTT
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
22 41 0.95
23 2 0.05
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.43
Consensus pattern (22 bp):
TTATGAAATTTTGATAACTACC
Found at i:55109 original size:21 final size:22
Alignment explanation
Indices: 55005--55111 Score: 110
Period size: 23 Copynumber: 4.9 Consensus size: 22
54995 ACCTATGAAA
* **
55005 TATGAAACTTTGATAACCTAAC
1 TATGAAATTTTGATAACCTTCC
* *
55027 TATGAAATTTTAATAAATCTTCC
1 TATGAAATTTTGAT-AACCTTCC
*
55050 TATGAAATTTTAATAAACCTTCC
1 TATGAAATTTTGAT-AACCTTCC
*
55073 TATGAAATTTTG-TAACTTTCC
1 TATGAAATTTTGATAACCTTCC
*
55094 TATG-ATTTTTGATAACCT
1 TATGAAATTTTGATAACCT
55112 CTCTGTGAGA
Statistics
Matches: 73, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
20 6 0.08
21 16 0.22
22 13 0.18
23 38 0.52
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Done.