Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012587.1 Corchorus olitorius cultivar O-4 contig12620, 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: 81195
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:5862 original size:15 final size:15
Alignment explanation
Indices: 5832--5873 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
5822 TTACTTTGCT
5832 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
5848 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
5863 TTGTTTTCTGT
1 TTGTTTTCTGT
5874 CAATCTCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:11273 original size:15 final size:15
Alignment explanation
Indices: 11243--11284 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
11233 TTACTTTGCT
11243 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
11259 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
11274 TTGTTTTCTGT
1 TTGTTTTCTGT
11285 CAATCTCTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 17 0.65
16 9 0.35
ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:13707 original size:125 final size:125
Alignment explanation
Indices: 13485--13740 Score: 469
Period size: 125 Copynumber: 2.0 Consensus size: 125
13475 TTGGATTGTG
*
13485 GTTTTTATTAGCCTACAATCTTTAAGGATTCTTATGAGTTTTGCAAGGATTGCCCACGATGTCAG
1 GTTTTCATTAGCCTACAATCTTTAAGGATTCTTATGAGTTTTGCAAGGATTGCCCACGATGTCAG
13550 AAAGTTGGAAGCATATAAAAAAGGAATCAAATGATTCAATCTCCTATACTTGTTGTTGAA
66 AAAGTTGGAAGCATATAAAAAAGGAATCAAATGATTCAATCTCCTATACTTGTTGTTGAA
*
13610 GTTTTCATTGGCCTACAATCTTTAAGGATTCTTATGAGTTTTGCAA-GACTTGCCCACGATGTCA
1 GTTTTCATTAGCCTACAATCTTTAAGGATTCTTATGAGTTTTGCAAGGA-TTGCCCACGATGTCA
*
13674 GAAAGTTGGAAGCATATCAAAAAGGAATCAAATGATTCAATCTCCTATACTTGTTGTTGAA
65 GAAAGTTGGAAGCATATAAAAAAGGAATCAAATGATTCAATCTCCTATACTTGTTGTTGAA
13735 GTTTTC
1 GTTTTC
13741 GATATATGGG
Statistics
Matches: 127, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
124 2 0.02
125 125 0.98
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (125 bp):
GTTTTCATTAGCCTACAATCTTTAAGGATTCTTATGAGTTTTGCAAGGATTGCCCACGATGTCAG
AAAGTTGGAAGCATATAAAAAAGGAATCAAATGATTCAATCTCCTATACTTGTTGTTGAA
Found at i:18017 original size:22 final size:21
Alignment explanation
Indices: 17991--18044 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
17981 GAAACTTGTG
17991 TTTGAAGACTTATTGAAGATAA
1 TTTGAAGA-TTATTGAAGATAA
*
18013 TTTGAAGA-T-TTGAAGATCA
1 TTTGAAGATTATTGAAGATAA
18032 -TTGAAGAATTATT
1 TTTGAAG-ATTATT
18045 TCAAGAAGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 10 0.36
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39
Consensus pattern (21 bp):
TTTGAAGATTATTGAAGATAA
Found at i:21774 original size:30 final size:32
Alignment explanation
Indices: 21706--21775 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 32
21696 TTTTTCGCCA
*
21706 TCAATTT-AAGTCTAAACCTTTCAAAAGTTGC
1 TCAATTTGAAGTCTAAACCTTTCAAAAGTGGC
21737 TCAATTTGAAG-CTAAACCTTTCAAAAG-GGAC
1 TCAATTTGAAGTCTAAACCTTTCAAAAGTGG-C
21768 -CAATTTGA
1 TCAATTTGA
21776 GCCATTTGAC
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
30 9 0.25
31 24 0.67
32 3 0.08
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (32 bp):
TCAATTTGAAGTCTAAACCTTTCAAAAGTGGC
Found at i:21898 original size:12 final size:12
Alignment explanation
Indices: 21881--21911 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
21871 AAATTGATTT
21881 TCAATAAATCAA
1 TCAATAAATCAA
21893 TCAATAAATCAA
1 TCAATAAATCAA
21905 TCAATAA
1 TCAATAA
21912 GCAACAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.26
Consensus pattern (12 bp):
TCAATAAATCAA
Found at i:30651 original size:19 final size:19
Alignment explanation
Indices: 30627--30666 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
30617 GGAAATACAA
30627 GGCATTTGATTTACAAATT
1 GGCATTTGATTTACAAATT
*
30646 GGCATTTGATTTGCAAATT
1 GGCATTTGATTTACAAATT
30665 GG
1 GG
30667 TGCTCTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.10, G:0.23, T:0.40
Consensus pattern (19 bp):
GGCATTTGATTTACAAATT
Found at i:32829 original size:20 final size:20
Alignment explanation
Indices: 32791--32829 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
32781 AACTCGTGGA
*
32791 AGAAGAAGAAGAAACAAGGC
1 AGAAGAAGAAGAAAAAAGGC
32811 AGAAG-AGAAGAAAGAAAGG
1 AGAAGAAGAAGAAA-AAAGG
32830 GCTCGCTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.62, C:0.05, G:0.33, T:0.00
Consensus pattern (20 bp):
AGAAGAAGAAGAAAAAAGGC
Found at i:34808 original size:38 final size:38
Alignment explanation
Indices: 34749--34852 Score: 138
Period size: 39 Copynumber: 2.7 Consensus size: 38
34739 TTTTTAATTG
*
34749 AGTAATTCCAAAAGAAAATTTTGGAAAATAAAAGTTTA
1 AGTAATTCCAAAAGAAGATTTTGGAAAATAAAAGTTTA
* * *
34787 GGTAATTCCAATAGTAGATTTTGGAAAAATAAAAGTTTA
1 AGTAATTCCAAAAGAAGATTTTGG-AAAATAAAAGTTTA
*
34826 AG-ATATCCCAAAAGAAGATTTTGGAAA
1 AGTA-ATTCCAAAAGAAGATTTTGGAAA
34853 TTAGTAAAAT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
38 24 0.43
39 32 0.57
ACGTcount: A:0.48, C:0.07, G:0.16, T:0.29
Consensus pattern (38 bp):
AGTAATTCCAAAAGAAGATTTTGGAAAATAAAAGTTTA
Found at i:35811 original size:105 final size:104
Alignment explanation
Indices: 35665--35862 Score: 297
Period size: 105 Copynumber: 1.9 Consensus size: 104
35655 AAAATGTTGT
* * * **
35665 TTGAACGCCTTGAAAACCTGACGGGAACTTTCCCACTTTGAAAGGAACTAAATTGAACACTTTTG
1 TTGAACACCTTGAAAACCTGACGGGAACTTTCCCACATTGAAAAGAACTAAATCAAACAC-TTTG
35730 AAAACTTGATGGGAACTTTCCCACTTTGAGAAGACCTAAA
65 AAAACTTGATGGGAACTTTCCCACTTTGAGAAGACCTAAA
* * * * *
35770 TTGAACACTTTGAAAACTTGATGGGAACTTTCCCACATTGAAAAGACCTAAATCAAATACTTTGA
1 TTGAACACCTTGAAAACCTGACGGGAACTTTCCCACATTGAAAAGAACTAAATCAAACACTTTGA
35835 AAACTTGATGGGAACTTTCCCACTTTGA
66 AAACTTGATGGGAACTTTCCCACTTTGA
35863 AAACTTTGAA
Statistics
Matches: 83, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
104 33 0.40
105 50 0.60
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (104 bp):
TTGAACACCTTGAAAACCTGACGGGAACTTTCCCACATTGAAAAGAACTAAATCAAACACTTTGA
AAACTTGATGGGAACTTTCCCACTTTGAGAAGACCTAAA
Found at i:35865 original size:52 final size:52
Alignment explanation
Indices: 35665--35865 Score: 294
Period size: 52 Copynumber: 3.8 Consensus size: 52
35655 AAAATGTTGT
* * * * * *
35665 TTGAACGCCTTGAAAACCTGACGGGAACTTTCCCACTTTGAAAGGAACTAAA
1 TTGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAA
*
35717 TTGAACACTTTTGAAAACTTGATGGGAACTTTCCCACTTTGAGAAGACCTAAA
1 TTGAACAC-TTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAA
*
35770 TTGAACACTTTGAAAACTTGATGGGAACTTTCCCACATTGAAAAGACCTAAA
1 TTGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAA
** *
35822 TCAAATACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAA
1 TTGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAA
35866 CTTTGAAGGA
Statistics
Matches: 135, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
52 89 0.66
53 46 0.34
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (52 bp):
TTGAACACTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAA
Found at i:36617 original size:25 final size:26
Alignment explanation
Indices: 36559--36618 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
36549 TAAAACAATC
36559 AAAGCCCAAATTTATAACTAAAAGCT
1 AAAGCCCAAATTTATAACTAAAAGCT
* *
36585 AAAGCCCAAATCTTATCA-TAACA-CT
1 AAAGCCCAAAT-TTATAACTAAAAGCT
36610 AAAGCCCAA
1 AAAGCCCAA
36619 TCCCACCAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
25 11 0.35
26 15 0.48
27 5 0.16
ACGTcount: A:0.48, C:0.25, G:0.07, T:0.20
Consensus pattern (26 bp):
AAAGCCCAAATTTATAACTAAAAGCT
Found at i:40228 original size:2 final size:2
Alignment explanation
Indices: 40221--40279 Score: 50
Period size: 2 Copynumber: 29.0 Consensus size: 2
40211 AAATAGCCCT
* *
40221 TA TA TA TA TA TA TA TA TA TA -A GTCA CGA -A AA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -T-A -TA TA TA TA TA TA TA TA
*
40262 TA TA TA TT TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
40280 AGTCACGAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
1 2 0.04
2 44 0.92
3 1 0.02
4 1 0.02
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.44
Consensus pattern (2 bp):
TA
Found at i:41159 original size:31 final size:33
Alignment explanation
Indices: 41103--41165 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
41093 TCTTTACATA
*
41103 AAACCTATCACTTGCTTCTTTACATCATCATCT
1 AAACCTATCAATTGCTTCTTTACATCATCATCT
*
41136 AAACCTATCAATTGC-T-TTTACATCCTCATC
1 AAACCTATCAATTGCTTCTTTACATCATCATC
41166 GAATTCATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 13 0.46
32 1 0.04
33 14 0.50
ACGTcount: A:0.29, C:0.30, G:0.03, T:0.38
Consensus pattern (33 bp):
AAACCTATCAATTGCTTCTTTACATCATCATCT
Found at i:51136 original size:19 final size:18
Alignment explanation
Indices: 51112--51147 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
51102 TGAAAACTCA
51112 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
51131 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
51148 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:61083 original size:19 final size:18
Alignment explanation
Indices: 61059--61094 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
61049 TGAAAACTCA
61059 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
61078 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
61095 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:67084 original size:21 final size:21
Alignment explanation
Indices: 67058--67120 Score: 108
Period size: 21 Copynumber: 3.0 Consensus size: 21
67048 TGGATTTTTA
67058 ATGTTGATTGTTTGTGGATTT
1 ATGTTGATTGTTTGTGGATTT
67079 ATGTTGATTGTTTGTGGATTT
1 ATGTTGATTGTTTGTGGATTT
* *
67100 CTGTTGAATGTTTGTGGATTT
1 ATGTTGATTGTTTGTGGATTT
67121 TTTATGTTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.14, C:0.02, G:0.29, T:0.56
Consensus pattern (21 bp):
ATGTTGATTGTTTGTGGATTT
Found at i:67125 original size:45 final size:42
Alignment explanation
Indices: 67059--67149 Score: 112
Period size: 45 Copynumber: 2.1 Consensus size: 42
67049 GGATTTTTAA
*
67059 TGTTGATTGTTTGTGGATTTATGTTGATTGT-TTGTGGATTTC
1 TGTTGAATGTTTGTGGATTTATGTTGATT-TCTTGTGGATTTC
**
67101 TGTTGAATGTTTGTGGATTTTTTATGTTGATTTCTTGTGTTTTTC
1 TGTTGAATGTTTGTGGA---TTTATGTTGATTTCTTGTGGATTTC
67146 TGTT
1 TGTT
67150 TTATGTTGAT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
42 16 0.38
44 1 0.02
45 25 0.60
ACGTcount: A:0.11, C:0.03, G:0.25, T:0.60
Consensus pattern (42 bp):
TGTTGAATGTTTGTGGATTTATGTTGATTTCTTGTGGATTTC
Found at i:76409 original size:13 final size:13
Alignment explanation
Indices: 76390--76427 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
76380 GATGGGCTAA
*
76390 CCTTTTTATTTTT
1 CCTTTTTCTTTTT
*
76403 TCTTTTTCTTTTT
1 CCTTTTTCTTTTT
76416 CCTTTTTCTTTT
1 CCTTTTTCTTTT
76428 GGCTAGGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (13 bp):
CCTTTTTCTTTTT
Found at i:76415 original size:19 final size:19
Alignment explanation
Indices: 76391--76427 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
76381 ATGGGCTAAC
*
76391 CTTTTTATTTTTTCTTTTT
1 CTTTTTACTTTTTCTTTTT
*
76410 CTTTTTCCTTTTTCTTTT
1 CTTTTTACTTTTTCTTTT
76428 GGCTAGGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (19 bp):
CTTTTTACTTTTTCTTTTT
Found at i:77004 original size:11 final size:11
Alignment explanation
Indices: 76988--77012 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
76978 AGACACAACC
76988 AAACAAAAAGA
1 AAACAAAAAGA
76999 AAACAAAAAGA
1 AAACAAAAAGA
77010 AAA
1 AAA
77013 TCAGGCATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.08, G:0.08, T:0.00
Consensus pattern (11 bp):
AAACAAAAAGA
Found at i:77073 original size:20 final size:20
Alignment explanation
Indices: 77048--77092 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
77038 AACCCTTCAG
*
77048 ACACTGGCAAACACAAACAC
1 ACACTGCCAAACACAAACAC
** *
77068 ACACTGCCACGCACCAACAC
1 ACACTGCCAAACACAAACAC
77088 ACACT
1 ACACT
77093 CTTACACAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.42, C:0.42, G:0.09, T:0.07
Consensus pattern (20 bp):
ACACTGCCAAACACAAACAC
Found at i:77683 original size:18 final size:17
Alignment explanation
Indices: 77644--77687 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
77634 AAACCCCAAC
* *
77644 CAAAACAGAAAAACATA
1 CAAAAAAGAAAAAAATA
*
77661 AAAAAAAGAAAGAAAATA
1 CAAAAAAGAAA-AAAATA
77679 CAAAAAAGA
1 CAAAAAAGA
77688 TGAAGAGGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.77, C:0.09, G:0.09, T:0.05
Consensus pattern (17 bp):
CAAAAAAGAAAAAAATA
Found at i:79481 original size:53 final size:53
Alignment explanation
Indices: 79418--79564 Score: 219
Period size: 53 Copynumber: 2.8 Consensus size: 53
79408 AATTTCATCT
*
79418 ATTTAGCTCTTTTTCAAATTGGGAAAGTTCCCATCAAGTTTTCAAAGTATTCA
1 ATTTAGCTCTTTTTCAAATTGGGAAAGTTCCCATCAAGTTTTCAAAGTATCCA
79471 ATTTAGCTCTTTTTCAAATTGGGAAAGTTCCCATC-AGTTTTCAAAGTATCCA
1 ATTTAGCTCTTTTTCAAATTGGGAAAGTTCCCATCAAGTTTTCAAAGTATCCA
* * *
79523 ATTTAGC-CAGTTTTT-AAATTAGGAAAGTTCCCGTCAGGTTTT
1 ATTTAGCTC--TTTTTCAAATTGGGAAAGTTCCCATCAAGTTTT
79565 AGTTTTCAAT
Statistics
Matches: 87, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
51 1 0.01
52 41 0.47
53 45 0.52
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (53 bp):
ATTTAGCTCTTTTTCAAATTGGGAAAGTTCCCATCAAGTTTTCAAAGTATCCA
Found at i:79603 original size:34 final size:34
Alignment explanation
Indices: 79530--79604 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 34
79520 CCAATTTAGC
* * *
79530 CAGTTTTTAAATTAGGAAAGTTCCCGTCAGGTTTT
1 CAGTTTTCAAATTAGGAAAGGTCCCATCA-GTTTT
*
79565 -AGTTTTCAATTTAGGGAAAGGTCCCATCA-TTTT
1 CAGTTTTCAAATTA-GGAAAGGTCCCATCAGTTTT
79598 CAGTTTT
1 CAGTTTT
79605 AGTTTTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
33 4 0.12
34 17 0.50
35 13 0.38
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (34 bp):
CAGTTTTCAAATTAGGAAAGGTCCCATCAGTTTT
Found at i:80174 original size:38 final size:39
Alignment explanation
Indices: 80119--80214 Score: 124
Period size: 38 Copynumber: 2.5 Consensus size: 39
80109 ACGTTACGAC
* * **
80119 ATAATCCTAAATCAGGATTGGAATAAGACTGAT-AAGGG
1 ATAATCCTAAATCAGGATTGGAATAAAAATGATAAAGCA
80157 ATAATCCTAAA-CTAGGATTGGAATAAAAATGATAAAGCA
1 ATAATCCTAAATC-AGGATTGGAATAAAAATGATAAAGCA
*
80196 ATAATCCTAAATCAAGATT
1 ATAATCCTAAATCAGGATT
80215 AAAAATAAAG
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
37 1 0.02
38 29 0.58
39 19 0.38
40 1 0.02
ACGTcount: A:0.47, C:0.11, G:0.17, T:0.25
Consensus pattern (39 bp):
ATAATCCTAAATCAGGATTGGAATAAAAATGATAAAGCA
Found at i:80258 original size:30 final size:31
Alignment explanation
Indices: 80188--80260 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
80178 AATAAAAATG
* * * *
80188 ATAAAGCAATAATCCTAAATCAAGATTAAAA
1 ATAAAGCAATGACCCTAAACCAAGATCAAAA
80219 ATAAAGCAATGACCCTAAACCAAGATCAAAA
1 ATAAAGCAATGACCCTAAACCAAGATCAAAA
*
80250 CT-AAGCAATGA
1 ATAAAGCAATGA
80261 TTCTAACTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 9 0.24
31 28 0.76
ACGTcount: A:0.55, C:0.18, G:0.10, T:0.18
Consensus pattern (31 bp):
ATAAAGCAATGACCCTAAACCAAGATCAAAA
Found at i:80318 original size:61 final size:62
Alignment explanation
Indices: 80191--80599 Score: 326
Period size: 61 Copynumber: 7.0 Consensus size: 62
80181 AAAAATGATA
* * * * * * * * * * *
80191 AAGCAATAATCCTAAATCAAGATTAAAAATAAAGCAATGACCCTAAACCAAGATCAAAACT-
1 AAGCAATGATCCTCAACCAGGATTTAAAATGAAGCAATGATCCTCAACCAGGATTAAAAATG
* * * *
80252 AAGCAATGATTCT-AACTCAGGATTTAAAATGAAG-AGGTGATCCTTAACCAGGATT-AAGATG
1 AAGCAATGATCCTCAAC-CAGGATTTAAAATGAAGCA-ATGATCCTCAACCAGGATTAAAAATG
* * * *
80313 GAGCAAAGATCCTCAACCAGGATTTAAAATAAAGCAATGATCCTCAACCGGGATTAAAAATG
1 AAGCAATGATCCTCAACCAGGATTTAAAATGAAGCAATGATCCTCAACCAGGATTAAAAATG
* * * *
80375 AAGCAATGATCCTCAAACAGGATATAAAATGAAGCAATGGTCCTCAAACAGGATT--AAA--
1 AAGCAATGATCCTCAACCAGGATTTAAAATGAAGCAATGATCCTCAACCAGGATTAAAAATG
*
80433 AA-C---GATCCTCAACCAGGA-TT-AAA--AA-C---GATCCTCAACCAGGATT-AAAATA
1 AAGCAATGATCCTCAACCAGGATTTAAAATGAAGCAATGATCCTCAACCAGGATTAAAAATG
* * * *
80482 AAGCTATGATCCTCAACCAGGA-TTAAAATAAAGCTATGATCCTCAACCAGGATT-AAAATA
1 AAGCAATGATCCTCAACCAGGATTTAAAATGAAGCAATGATCCTCAACCAGGATTAAAAATG
* * * * * *
80542 AAGCAATGATCCTCAAACAAGA-TTAAAGTAAAGCAACGATCCTCAACCAAGATTAAAA
1 AAGCAATGATCCTCAACCAGGATTTAAAATGAAGCAATGATCCTCAACCAGGATTAAAA
80600 TAAAGCTGAT
Statistics
Matches: 287, Mismatches: 40, Indels: 42
0.78 0.11 0.11
Matches are distributed among these distances:
46 15 0.05
47 3 0.01
49 3 0.01
50 3 0.01
52 3 0.01
53 18 0.06
54 17 0.06
56 2 0.01
57 2 0.01
58 2 0.01
60 79 0.28
61 84 0.29
62 56 0.20
ACGTcount: A:0.46, C:0.19, G:0.15, T:0.20
Consensus pattern (62 bp):
AAGCAATGATCCTCAACCAGGATTTAAAATGAAGCAATGATCCTCAACCAGGATTAAAAATG
Found at i:80331 original size:30 final size:30
Alignment explanation
Indices: 80188--80605 Score: 384
Period size: 30 Copynumber: 14.2 Consensus size: 30
80178 AATAAAAATG
* * * *
80188 ATAAAGCAATAATCCTAAATCAAGATTAAAA
1 ATAAAGCAATGATCCTCAACCAGGATT-AAA
* * * *
80219 ATAAAGCAATGACCCTAAACCAAGATCAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
*
80249 ACT-AAGCAATGATTCT-AACTCAGGATTTAAA
1 A-TAAAGCAATGATCCTCAAC-CAGGA-TTAAA
* * * *
80280 ATGAAG-AGGTGATCCTTAACCAGGATTAAG
1 ATAAAGCA-ATGATCCTCAACCAGGATTAAA
** *
80310 ATGGAGCAAAGATCCTCAACCAGGATTTAAA
1 ATAAAGCAATGATCCTCAACCAGGA-TTAAA
*
80341 ATAAAGCAATGATCCTCAACCGGGATTAAAA
1 ATAAAGCAATGATCCTCAACCAGGATT-AAA
* *
80372 ATGAAGCAATGATCCTCAAACAGGATATAAA
1 ATAAAGCAATGATCCTCAACCAGGAT-TAAA
* * *
80403 ATGAAGCAATGGTCCTCAAACAGGATT--A
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
80431 A-AAA-C---GATCCTCAACCAGGATT--A
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
80454 A-AAA-C---GATCCTCAACCAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
*
80479 ATAAAGCTATGATCCTCAACCAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
*
80509 ATAAAGCTATGATCCTCAACCAGGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* *
80539 ATAAAGCAATGATCCTCAAACAAGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
* * *
80569 GTAAAGCAACGATCCTCAACCAAGATTAAA
1 ATAAAGCAATGATCCTCAACCAGGATTAAA
80599 ATAAAGC
1 ATAAAGC
80606 TGATAAAGCA
Statistics
Matches: 336, Mismatches: 34, Indels: 35
0.83 0.08 0.09
Matches are distributed among these distances:
23 38 0.11
25 2 0.01
26 4 0.01
27 3 0.01
28 2 0.01
29 3 0.01
30 157 0.47
31 123 0.37
32 4 0.01
ACGTcount: A:0.46, C:0.19, G:0.15, T:0.20
Consensus pattern (30 bp):
ATAAAGCAATGATCCTCAACCAGGATTAAA
Found at i:80449 original size:23 final size:23
Alignment explanation
Indices: 80415--80479 Score: 121
Period size: 23 Copynumber: 2.8 Consensus size: 23
80405 GAAGCAATGG
*
80415 TCCTCAAACAGGATTAAAAACGA
1 TCCTCAACCAGGATTAAAAACGA
80438 TCCTCAACCAGGATTAAAAACGA
1 TCCTCAACCAGGATTAAAAACGA
80461 TCCTCAACCAGGATTAAAA
1 TCCTCAACCAGGATTAAAA
80480 TAAAGCTATG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.45, C:0.25, G:0.12, T:0.18
Consensus pattern (23 bp):
TCCTCAACCAGGATTAAAAACGA
Found at i:81002 original size:36 final size:36
Alignment explanation
Indices: 80945--81195 Score: 348
Period size: 36 Copynumber: 7.1 Consensus size: 36
80935 GGATCAATTA
* *
80945 AAGAAAAGATCACCCTCGATCAACTGAAATAAACTG
1 AAGAAAAGATCGCCCTGGATCAACTGAAATAAACTG
* * *
80981 AAGAAAAGATTGCCCCGGATCAATTGAAATAAACTG
1 AAGAAAAGATCGCCCTGGATCAACTGAAATAAACTG
*
81017 AAGAAAAGATCGCCCTGGATCAACTGAAATAAACTA
1 AAGAAAAGATCGCCCTGGATCAACTGAAATAAACTG
*
81053 AAGAAAAGATCGCCCTGGATCAATTGAAATAAACTG
1 AAGAAAAGATCGCCCTGGATCAACTGAAATAAACTG
*
81089 AAG-AAAGACCGCCCTGGATCAACTGAAATAAACTG
1 AAGAAAAGATCGCCCTGGATCAACTGAAATAAACTG
* *
81124 AAG-AAAGACCG-CCTGGGTCAACTGAAATAAACTG
1 AAGAAAAGATCGCCCTGGATCAACTGAAATAAACTG
* ** *
81158 AAG-AAAGACCGCCCTGCCTCAATTGAAATAAACTG
1 AAGAAAAGATCGCCCTGGATCAACTGAAATAAACTG
81193 AAG
1 AAG
Statistics
Matches: 197, Mismatches: 17, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
34 33 0.17
35 64 0.32
36 100 0.51
ACGTcount: A:0.44, C:0.20, G:0.19, T:0.17
Consensus pattern (36 bp):
AAGAAAAGATCGCCCTGGATCAACTGAAATAAACTG
Done.