Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022531.1 Corchorus olitorius cultivar O-4 contig22564, 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: 233895
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2551 original size:21 final size:22
Alignment explanation
Indices: 2527--2567 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2517 GTTTATAATA
*
2527 TTCTTGGGTCA-TCGGGTTATC
1 TTCTCGGGTCATTCGGGTTATC
*
2548 TTCTCGGGTTATTCGGGTTA
1 TTCTCGGGTCATTCGGGTTA
2568 CGAGTTTGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.10, C:0.17, G:0.29, T:0.44
Consensus pattern (22 bp):
TTCTCGGGTCATTCGGGTTATC
Found at i:2974 original size:105 final size:102
Alignment explanation
Indices: 2865--3065 Score: 314
Period size: 105 Copynumber: 1.9 Consensus size: 102
2855 CTTAAATTTT
*
2865 TATAGTTTTACTCAACTAAAAACTCTATTTTTATTTGATTAAATCTAATATCCTTATAAGTACTA
1 TATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTAT-A--ACTA
2930 TTTTATTTTTACCATTTTACT-ATTTTAATTAAAATGCTTA
63 TTTTATTTTTACCATTTTACTAATTTT-ATTAAAATGCTTA
* * *
2970 TATAGTTTTACTCAACTAAAAACTTTATTTTTATTTAATTAAATCTAGTATCCTTATACCTATTT
1 TATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTATTT
*
3035 TATTTTTATCATTTTACTAATTTTATTAAAA
66 TATTTTTACCATTTTACTAATTTTATTAAAA
3066 AACTTAGATA
Statistics
Matches: 90, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
102 30 0.33
103 5 0.06
104 1 0.01
105 54 0.60
ACGTcount: A:0.34, C:0.12, G:0.03, T:0.51
Consensus pattern (102 bp):
TATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTATTT
TATTTTTACCATTTTACTAATTTTATTAAAATGCTTA
Found at i:3044 original size:23 final size:23
Alignment explanation
Indices: 3018--3061 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
3008 TTAAATCTAG
*
3018 TATCCTTATACCT-ATTTTATTTT
1 TATCATTATA-CTAATTTTATTTT
*
3041 TATCATTTTACTAATTTTATT
1 TATCATTATACTAATTTTATT
3062 AAAAAACTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 16 0.89
ACGTcount: A:0.25, C:0.14, G:0.00, T:0.61
Consensus pattern (23 bp):
TATCATTATACTAATTTTATTTT
Found at i:4899 original size:42 final size:42
Alignment explanation
Indices: 4840--4922 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
4830 AGCAACAATT
*
4840 AATATTAGCTTTATTTTGATGAATTATCTAGAGATGAAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGAAGTAG
* *
4882 AATATTAGCTTTATTTTGATGAATTACCTAGATATGGAGTA
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGAAGTA
4923 CTAGAATTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.35, C:0.06, G:0.18, T:0.41
Consensus pattern (42 bp):
AATATTAGCTTTATTTTGATGAATTACCTAGAGATGAAGTAG
Found at i:15042 original size:6 final size:6
Alignment explanation
Indices: 15031--15062 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
15021 GGTCTTCCTG
15031 ACATAC ACATAC ACATAC ACATAC ACATAC AC
1 ACATAC ACATAC ACATAC ACATAC ACATAC AC
15063 TAGTGTGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.34, G:0.00, T:0.16
Consensus pattern (6 bp):
ACATAC
Found at i:15185 original size:60 final size:60
Alignment explanation
Indices: 15106--15226 Score: 233
Period size: 60 Copynumber: 2.0 Consensus size: 60
15096 ACTAAAAAAG
15106 AGCAACAAAATTTACAATGAAAAAAAGCATATCTATATCTAAACTGCTAAAATCCCAACC
1 AGCAACAAAATTTACAATGAAAAAAAGCATATCTATATCTAAACTGCTAAAATCCCAACC
*
15166 AGCAACAAAATTTACAATGAAAAAGAGCATATCTATATCTAAACTGCTAAAATCCCAACC
1 AGCAACAAAATTTACAATGAAAAAAAGCATATCTATATCTAAACTGCTAAAATCCCAACC
15226 A
1 A
15227 AGTTTTGGGT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.50, C:0.21, G:0.07, T:0.21
Consensus pattern (60 bp):
AGCAACAAAATTTACAATGAAAAAAAGCATATCTATATCTAAACTGCTAAAATCCCAACC
Found at i:16608 original size:21 final size:22
Alignment explanation
Indices: 16569--16609 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
16559 TCTGTTGGTT
* *
16569 GTTTTTTTGGTTTGGTTATTGA
1 GTTTTTTTGGATTGATTATTGA
16591 GTTTTTTTGGATT-ATTATT
1 GTTTTTTTGGATTGATTATT
16610 AAAGTGTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.12, C:0.00, G:0.22, T:0.66
Consensus pattern (22 bp):
GTTTTTTTGGATTGATTATTGA
Found at i:36970 original size:3 final size:3
Alignment explanation
Indices: 36962--37018 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
36952 GGTTGAAAGA
36962 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
37010 ATT ATT ATT
1 ATT ATT ATT
37019 TTCACTGCTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:41332 original size:26 final size:26
Alignment explanation
Indices: 41302--41385 Score: 84
Period size: 26 Copynumber: 3.2 Consensus size: 26
41292 TAGTAACGAA
41302 TTGTTCATTGGTTCCTTTATGTAAAT
1 TTGTTCATTGGTTCCTTTATGTAAAT
* * *
41328 TTGTTGAATTGCTGT-C-TTA-GTAACGAA
1 TTGTT-CATTGGT-TCCTTTATGTAA--AT
41355 TTGTTCATTGGTTCCTTTATGTAAAT
1 TTGTTCATTGGTTCCTTTATGTAAAT
41381 TTGTT
1 TTGTT
41386 GAATTGCTGT
Statistics
Matches: 45, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
25 5 0.11
26 20 0.44
27 15 0.33
28 5 0.11
ACGTcount: A:0.20, C:0.11, G:0.18, T:0.51
Consensus pattern (26 bp):
TTGTTCATTGGTTCCTTTATGTAAAT
Found at i:41359 original size:53 final size:53
Alignment explanation
Indices: 41292--41399 Score: 216
Period size: 53 Copynumber: 2.0 Consensus size: 53
41282 ATGAATTTTG
41292 TAGTAACGAATTGTTCATTGGTTCCTTTATGTAAATTTGTTGAATTGCTGTCT
1 TAGTAACGAATTGTTCATTGGTTCCTTTATGTAAATTTGTTGAATTGCTGTCT
41345 TAGTAACGAATTGTTCATTGGTTCCTTTATGTAAATTTGTTGAATTGCTGTCT
1 TAGTAACGAATTGTTCATTGGTTCCTTTATGTAAATTTGTTGAATTGCTGTCT
41398 TA
1 TA
41400 AAGTTGTGTC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.23, C:0.11, G:0.19, T:0.47
Consensus pattern (53 bp):
TAGTAACGAATTGTTCATTGGTTCCTTTATGTAAATTTGTTGAATTGCTGTCT
Found at i:53592 original size:6 final size:7
Alignment explanation
Indices: 53574--53598 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
53564 AAACGGAGAT
53574 GAAAAAA
1 GAAAAAA
53581 GAAAAAA
1 GAAAAAA
53588 GAAAAAA
1 GAAAAAA
53595 GAAA
1 GAAA
53599 GCACCTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:56414 original size:21 final size:21
Alignment explanation
Indices: 56385--56432 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
56375 ATACTCCCTA
*
56385 TCAA-CAAACTCA-GAACATTC
1 TCAATCAAAC-CATGAACAATC
*
56405 TGAATCAAACCATGAACAATC
1 TCAATCAAACCATGAACAATC
56426 TCAATCA
1 TCAATCA
56433 TCACCTTCCC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.46, C:0.27, G:0.06, T:0.21
Consensus pattern (21 bp):
TCAATCAAACCATGAACAATC
Found at i:71986 original size:14 final size:15
Alignment explanation
Indices: 71959--71991 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
71949 AAAATAAAAT
71959 TATAATATATAATAA
1 TATAATATATAATAA
71974 TATAATA-ATAATAA
1 TATAATATATAATAA
71988 TATA
1 TATA
71992 TAGCTAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TATAATATATAATAA
Found at i:88094 original size:19 final size:19
Alignment explanation
Indices: 88070--88107 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
88060 TAAAATTAAC
88070 ATTATAAGCTATGTTTCAT
1 ATTATAAGCTATGTTTCAT
88089 ATTATAAGCTATGTTTCAT
1 ATTATAAGCTATGTTTCAT
88108 TAAAATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (19 bp):
ATTATAAGCTATGTTTCAT
Found at i:88115 original size:23 final size:22
Alignment explanation
Indices: 88064--88117 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 22
88054 TCTATTTAAA
88064 ATTAACATTATAAGCTATGTTTC
1 ATTAA-ATTATAAGCTATGTTTC
88087 A-T--ATTATAAGCTATGTTTC
1 ATTAAATTATAAGCTATGTTTC
88106 ATTAAAATTATA
1 ATT-AAATTATA
88118 TCAGAAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
19 18 0.67
20 1 0.04
22 1 0.04
23 7 0.26
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.44
Consensus pattern (22 bp):
ATTAAATTATAAGCTATGTTTC
Found at i:90834 original size:34 final size:34
Alignment explanation
Indices: 90796--90868 Score: 78
Period size: 34 Copynumber: 2.1 Consensus size: 34
90786 TTTGAAAACT
*
90796 AAAACCGAAAA-TGACGGGAACTTTCCCTAAATTG
1 AAAACCGAAAACTGACGGGAAC-TTCCCCAAATTG
* * *
90830 AAAA-CTAAAACCTGATGGGAACTTCCCCAATTTG
1 AAAACCGAAAA-CTGACGGGAACTTCCCCAAATTG
90864 AAAAC
1 AAAAC
90869 TTGAAAAACT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
33 5 0.16
34 18 0.56
35 9 0.28
ACGTcount: A:0.42, C:0.22, G:0.15, T:0.21
Consensus pattern (34 bp):
AAAACCGAAAACTGACGGGAACTTCCCCAAATTG
Found at i:90886 original size:37 final size:35
Alignment explanation
Indices: 90811--90918 Score: 110
Period size: 37 Copynumber: 3.0 Consensus size: 35
90801 CGAAAATGAC
* * *
90811 GGGAACTTTCCCTAAATTGAAAACT-AAAACCTGAT
1 GGGAAC-TTCCCCAATTTGAAAACTGAAAACTTGAT
90846 GGGAACTTCCCCAATTTGAAAACTTGAAAAACTTGAT
1 GGGAACTTCCCCAATTTGAAAAC-TG-AAAACTTGAT
* * *
90883 GGGAAATTTCTCAATTTGAAAACTTTGAAAACTTGA
1 GGGAACTTCCCCAATTTGAAAAC--TGAAAACTTGA
90919 AAAACTTGAT
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
34 15 0.24
35 7 0.11
37 38 0.60
38 3 0.05
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.29
Consensus pattern (35 bp):
GGGAACTTCCCCAATTTGAAAACTGAAAACTTGAT
Found at i:90912 original size:46 final size:46
Alignment explanation
Indices: 90860--90950 Score: 164
Period size: 46 Copynumber: 2.0 Consensus size: 46
90850 ACTTCCCCAA
*
90860 TTTGAAAACTTGAAAAACTTGATGGGAAATTTCTCAATTTGAAAAC
1 TTTGAAAACTTGAAAAACTTGATGGGAAATTTCCCAATTTGAAAAC
*
90906 TTTGAAAACTTGAAAAACTTGATGGGAACTTTCCCAATTTGAAAA
1 TTTGAAAACTTGAAAAACTTGATGGGAAATTTCCCAATTTGAAAA
90951 GAGCTAAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (46 bp):
TTTGAAAACTTGAAAAACTTGATGGGAAATTTCCCAATTTGAAAAC
Found at i:90981 original size:52 final size:52
Alignment explanation
Indices: 90919--91026 Score: 162
Period size: 52 Copynumber: 2.1 Consensus size: 52
90909 GAAAACTTGA
* * * *
90919 AAAACTTGATGGGAACTTTCCCAATTTGAAAAGAGCTAAATAGAATACTTTG
1 AAAACCTGATGGGAACTTTCCCAACTTGAAAAGACCTAAATAGAACACTTTG
* *
90971 AAAACCTGATGGGAACTTTCCCACCTTGAAAAGACCTAAATTGAACACTTTG
1 AAAACCTGATGGGAACTTTCCCAACTTGAAAAGACCTAAATAGAACACTTTG
91023 AAAA
1 AAAA
91027 AAAAATAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.26
Consensus pattern (52 bp):
AAAACCTGATGGGAACTTTCCCAACTTGAAAAGACCTAAATAGAACACTTTG
Found at i:91389 original size:22 final size:23
Alignment explanation
Indices: 91349--91391 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
91339 ACTTGAAATG
*
91349 AACTTTTTTCCTTTGATTTTTGA
1 AACTTTTTTCCTTTCATTTTTGA
*
91372 AACTTTTTT-TTTTCATTTTT
1 AACTTTTTTCCTTTCATTTTT
91392 TCTTTTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.16, C:0.12, G:0.05, T:0.67
Consensus pattern (23 bp):
AACTTTTTTCCTTTCATTTTTGA
Found at i:91714 original size:18 final size:18
Alignment explanation
Indices: 91687--91724 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
91677 ACATTTAAAG
*
91687 AATATATAAAGAATTATA
1 AATATATAAAGAAATATA
*
91705 AATATTTAAAGAAATATA
1 AATATATAAAGAAATATA
91723 AA
1 AA
91725 CATGGATGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (18 bp):
AATATATAAAGAAATATA
Found at i:92800 original size:45 final size:42
Alignment explanation
Indices: 92736--92829 Score: 127
Period size: 45 Copynumber: 2.2 Consensus size: 42
92726 AACAACAATT
* * *
92736 AATATTAACTTTATTTTGATGAATTATCTAGAGATTGAGGAGTAG
1 AATATTAGCTTTATTTTGATGAACTACCTAGAGA-T--GGAGTAG
92781 AATATTAGCTTTATTTTGATGAACTACCTAGAGATGGAGTAG
1 AATATTAGCTTTATTTTGATGAACTACCTAGAGATGGAGTAG
92823 AAT-TTAG
1 AATATTAG
92830 GTAATACACT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 10 0.22
44 1 0.02
45 31 0.67
ACGTcount: A:0.35, C:0.06, G:0.20, T:0.38
Consensus pattern (42 bp):
AATATTAGCTTTATTTTGATGAACTACCTAGAGATGGAGTAG
Found at i:96052 original size:27 final size:27
Alignment explanation
Indices: 96022--96078 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
96012 TGCGTTTTTT
*
96022 TTTAAAAATTATTTTTGCGTTAAAAAA
1 TTTAAAAATTATTTCTGCGTTAAAAAA
****
96049 TTTATTTCTTATTTCTGCGTTAAAAAA
1 TTTAAAAATTATTTCTGCGTTAAAAAA
96076 TTT
1 TTT
96079 TATTTTCTGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.51
Consensus pattern (27 bp):
TTTAAAAATTATTTCTGCGTTAAAAAA
Found at i:96083 original size:28 final size:27
Alignment explanation
Indices: 96030--96083 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
96020 TTTTTAAAAA
*
96030 TTATTTTTGCGTTAAAAAATTTATTTC
1 TTATTTCTGCGTTAAAAAATTTATTTC
96057 TTATTTCTGCGTTAAAAAATTTTATTT
1 TTATTTCTGCGTTAAAAAA-TTTATTT
96084 TCTGTTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 18 0.72
28 7 0.28
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (27 bp):
TTATTTCTGCGTTAAAAAATTTATTTC
Found at i:101102 original size:14 final size:15
Alignment explanation
Indices: 101083--101113 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
101073 GTGTGAAAAA
101083 TTGTTCTTTA-TGAT
1 TTGTTCTTTAGTGAT
101097 TTGTTCTTTAGTGAT
1 TTGTTCTTTAGTGAT
101112 TT
1 TT
101114 TTAAGCCTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.13, C:0.06, G:0.16, T:0.65
Consensus pattern (15 bp):
TTGTTCTTTAGTGAT
Found at i:103759 original size:181 final size:178
Alignment explanation
Indices: 103447--103850 Score: 483
Period size: 181 Copynumber: 2.3 Consensus size: 178
103437 CAAAATTTCG
* ** *
103447 GTTGTAGATCATGGAATAGCCTTTTAAGAGACACTTGAATCATCC-CAATCAGACATATGGAGCA
1 GTTGTAGATCATGGAACAATCTTTTAAGAGACACTTGAATCA-CCTCAATCAGACATATGAAGCA
*
103511 AAAATTATGTAATATTAAGTAGACCGTACATTCCCGCTCACCGAAACAACTAATTCTTCGTAAGC
65 AAAATTATGTAATATTAAGTAGACCGTACATTCCCGCTAACCGAAACAACTAATTCTTCGTAAGC
* * * *
103576 ATTTTTTTTTATAATTTAAACATTAAAATTAGCTTTT-GAGTCGTTCATAAAA
130 A---TTTTTGATAACTGAAACATTAAAATTAG-TTTTCGAGTCCTTCATAAAA
* *
103628 GTTGTAGATCATGGAACAATCTTTTAAGAGACACTTGAATCACCTCAAT-TGAACATCTGAAGCA
1 GTTGTAGATCATGGAACAATCTTTTAAGAGACACTTGAATCACCTCAATCAG-ACATATGAAGCA
* * * * * * * *
103692 AAAGTTATGTAATATTAAGTGGACCGTCCATTCCCGTTAACCGAAATAATTAATATTTTTG-AAG
65 AAAATTATGTAATATTAAGTAGACCGTACATTCCCGCTAACCGAAACAACTAAT-TCTTCGTAAG
* * *
103756 CATTTTTGATACCTGAAACATTAAATTTAGTTTTCGAGTCCTTCATGAAA
129 CATTTTTGATAACTGAAACATTAAAATTAGTTTTCGAGTCCTTCATAAAA
* * * *
103806 GTTGTAGATCATGAAACAATCTTTTAATAAACACTTAAATCACCT
1 GTTGTAGATCATGGAACAATCTTTTAAGAGACACTTGAATCACCT
103851 TGATCGGATA
Statistics
Matches: 193, Mismatches: 26, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
177 4 0.02
178 77 0.40
180 3 0.02
181 105 0.54
182 4 0.02
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (178 bp):
GTTGTAGATCATGGAACAATCTTTTAAGAGACACTTGAATCACCTCAATCAGACATATGAAGCAA
AAATTATGTAATATTAAGTAGACCGTACATTCCCGCTAACCGAAACAACTAATTCTTCGTAAGCA
TTTTTGATAACTGAAACATTAAAATTAGTTTTCGAGTCCTTCATAAAA
Found at i:104223 original size:17 final size:16
Alignment explanation
Indices: 104176--104228 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
104166 CTAATACAGT
104176 ATAACCTCCATAAATTA
1 ATAACCTCC-TAAATTA
*
104193 AT-A-CTCGATAAATTA
1 ATAACCTC-CTAAATTA
104208 ATAACCTCTCTAAATTA
1 ATAACCTC-CTAAATTA
104225 ATAA
1 ATAA
104229 TTTTTCATGG
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 12 0.40
16 2 0.07
17 16 0.53
ACGTcount: A:0.47, C:0.19, G:0.02, T:0.32
Consensus pattern (16 bp):
ATAACCTCCTAAATTA
Found at i:112434 original size:25 final size:25
Alignment explanation
Indices: 112406--112461 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
112396 TGCGCTGGGT
* *
112406 AAACGCTCATGTGCTTGCGTTTGGA
1 AAACGCGCATGTGCTTGCGTTTGAA
* *
112431 AAACGAGCCTGTGCTTGCGTTTGAA
1 AAACGCGCATGTGCTTGCGTTTGAA
112456 AAACGC
1 AAACGC
112462 ATGGGCTGCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (25 bp):
AAACGCGCATGTGCTTGCGTTTGAA
Found at i:115613 original size:10 final size:10
Alignment explanation
Indices: 115598--115642 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
115588 GTCTAGAGTT
*
115598 TCAGAGTATC
1 TCAGAGTATA
115608 TCAGAGTATA
1 TCAGAGTATA
*
115618 TCCGAGTATA
1 TCAGAGTATA
* *
115628 TGAGAGTATC
1 TCAGAGTATA
115638 TCAGA
1 TCAGA
115643 TAAATGAGGG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (10 bp):
TCAGAGTATA
Found at i:124250 original size:17 final size:17
Alignment explanation
Indices: 124201--124250 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
124191 CCTCTCAATA
124201 ACTGGTCATCTGAGATG
1 ACTGGTCATCTGAGATG
* * * * *
124218 AATAGTTATATAAGATG
1 ACTGGTCATCTGAGATG
124235 ACTGGTCATCTGAGAT
1 ACTGGTCATCTGAGAT
124251 TACATGGTTG
Statistics
Matches: 23, Mismatches: 10, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (17 bp):
ACTGGTCATCTGAGATG
Found at i:136880 original size:2 final size:2
Alignment explanation
Indices: 136873--136902 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
136863 ACTTTTATGT
136873 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
136903 TATTATTGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:136906 original size:8 final size:9
Alignment explanation
Indices: 136872--136908 Score: 53
Period size: 8 Copynumber: 4.4 Consensus size: 9
136862 GACTTTTATG
136872 TTATATATA
1 TTATATATA
136881 -TATATATA
1 TTATATATA
136889 -TATATATA
1 TTATATATA
136897 TTATAT-TA
1 TTATATATA
136905 TTAT
1 TTAT
136909 TGGCCAACCC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 22 0.81
9 5 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
TTATATATA
Found at i:137409 original size:45 final size:45
Alignment explanation
Indices: 137344--137431 Score: 158
Period size: 45 Copynumber: 2.0 Consensus size: 45
137334 TTATCGAAGA
*
137344 AGTTGAATTTTTAAATGTATAATCATACTATAAGAACTAAACCTG
1 AGTTGAATTTTTAAACGTATAATCATACTATAAGAACTAAACCTG
*
137389 AGTTGAATTTTTAAACGTATAATCATACTATAAGAGCTAAACC
1 AGTTGAATTTTTAAACGTATAATCATACTATAAGAACTAAACC
137432 GGATTAGATT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.34
Consensus pattern (45 bp):
AGTTGAATTTTTAAACGTATAATCATACTATAAGAACTAAACCTG
Found at i:138850 original size:22 final size:22
Alignment explanation
Indices: 138733--139057 Score: 193
Period size: 22 Copynumber: 14.7 Consensus size: 22
138723 CATACTATAG
* *
138733 TATCAAAATAATT-ATAGGGAGAT
1 TATCAAAAT--TTCATAGGTAGGT
* * *
138756 TAACAAAATCTCATAGGGAGGT
1 TATCAAAATTTCATAGGTAGGT
* * *
138778 TATCAAAA-ATCATAGGAAGAT
1 TATCAAAATTTCATAGGTAGGT
* * *
138799 TA-CAGAATTTCATAAGAAGGTT
1 TATCAAAATTTCATAGGTAGG-T
* *
138821 TATTAAAATTTCATAGTTAGGT
1 TATCAAAATTTCATAGGTAGGT
*
138843 TATCAAAATTTCATATGG-AGTT
1 TATCAAAATTTCATA-GGTAGGT
* * *
138865 TATCACAATTTTATAGGTA-AT
1 TATCAAAATTTCATAGGTAGGT
*
138886 TATCAAAATTTCATATGG-AGTT
1 TATCAAAATTTCATA-GGTAGGT
** *
138908 TATCACATCAAAAATCATAGGAAGGT
1 TAT--CA--AAATTTCATAGGTAGGT
* * *
138934 TA-CAGAATTTCATAAGAAGGTT
1 TATCAAAATTTCATAGGTAGG-T
* *
138956 TATTAAAATTTCATAGTTAGGT
1 TATCAAAATTTCATAGGTAGGT
*
138978 TATCAAAATTTCATATGG-AGTT
1 TATCAAAATTTCATA-GGTAGGT
* * *
139000 TATCACAATTTTATAGGTA-AT
1 TATCAAAATTTCATAGGTAGGT
*
139021 TATCAAAATTTCATAGCGT-GAT
1 TATCAAAATTTCATAG-GTAGGT
139043 TATCAAAATTTCATA
1 TATCAAAATTTCATA
139058 AAATATTCAA
Statistics
Matches: 238, Mismatches: 45, Indels: 39
0.74 0.14 0.12
Matches are distributed among these distances:
20 4 0.02
21 68 0.29
22 111 0.47
23 38 0.16
24 2 0.01
25 2 0.01
26 13 0.05
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATAGGTAGGT
Found at i:138895 original size:43 final size:43
Alignment explanation
Indices: 138754--139057 Score: 213
Period size: 43 Copynumber: 6.9 Consensus size: 43
138744 TTATAGGGAG
* * * * ** *
138754 ATTAACAAAATCTCATAGGGAGGTTATCA-AAAATCATAGGAA
1 ATTATCAAAATTTCATATGGAGTTTATCACAATTTCATAGGTA
* * * * * *
138796 GATTA-CAGAATTTCATAAGAAGGTTTATTAAAATTTCATAGTTA
1 -ATTATCAAAATTTCATATGGA-GTTTATCACAATTTCATAGGTA
* *
138840 GGTTATCAAAATTTCATATGGAGTTTATCACAATTTTATAGGTA
1 -ATTATCAAAATTTCATATGGAGTTTATCACAATTTCATAGGTA
**
138884 ATTATCAAAATTTCATATGGAGTTTATCACATCAAAAATCATAGG-A
1 ATTATCAAAATTTCATATGGAGTTTAT--CA-C-AATTTCATAGGTA
* * * * * *
138930 AGGTTA-CAGAATTTCATAAGAAGGTTTATTAAAATTTCATAGTTA
1 A--TTATCAAAATTTCATATGGA-GTTTATCACAATTTCATAGGTA
* *
138975 GGTTATCAAAATTTCATATGGAGTTTATCACAATTTTATAGGTA
1 -ATTATCAAAATTTCATATGGAGTTTATCACAATTTCATAGGTA
* * *
139019 ATTATCAAAATTTCATA-GCGTGATTATCAAAATTTCATA
1 ATTATCAAAATTTCATATG-GAGTTTATCACAATTTCATA
139058 AAATATTCAA
Statistics
Matches: 204, Mismatches: 43, Indels: 28
0.74 0.16 0.10
Matches are distributed among these distances:
42 13 0.06
43 68 0.33
44 60 0.29
45 29 0.14
46 4 0.02
47 21 0.10
48 9 0.04
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (43 bp):
ATTATCAAAATTTCATATGGAGTTTATCACAATTTCATAGGTA
Found at i:138955 original size:135 final size:135
Alignment explanation
Indices: 138779--139035 Score: 505
Period size: 135 Copynumber: 1.9 Consensus size: 135
138769 TAGGGAGGTT
138779 ATCAAAAATCATAGGAAGATTACAGAATTTCATAAGAAGGTTTATTAAAATTTCATAGTTAGGTT
1 ATCAAAAATCATAGGAAGATTACAGAATTTCATAAGAAGGTTTATTAAAATTTCATAGTTAGGTT
138844 ATCAAAATTTCATATGGAGTTTATCACAATTTTATAGGTAATTATCAAAATTTCATATGGAGTTT
66 ATCAAAATTTCATATGGAGTTTATCACAATTTTATAGGTAATTATCAAAATTTCATATGGAGTTT
138909 ATCAC
131 ATCAC
*
138914 ATCAAAAATCATAGGAAGGTTACAGAATTTCATAAGAAGGTTTATTAAAATTTCATAGTTAGGTT
1 ATCAAAAATCATAGGAAGATTACAGAATTTCATAAGAAGGTTTATTAAAATTTCATAGTTAGGTT
138979 ATCAAAATTTCATATGGAGTTTATCACAATTTTATAGGTAATTATCAAAATTTCATA
66 ATCAAAATTTCATATGGAGTTTATCACAATTTTATAGGTAATTATCAAAATTTCATA
139036 GCGTGATTAT
Statistics
Matches: 121, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
135 121 1.00
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.37
Consensus pattern (135 bp):
ATCAAAAATCATAGGAAGATTACAGAATTTCATAAGAAGGTTTATTAAAATTTCATAGTTAGGTT
ATCAAAATTTCATATGGAGTTTATCACAATTTTATAGGTAATTATCAAAATTTCATATGGAGTTT
ATCAC
Found at i:139228 original size:106 final size:106
Alignment explanation
Indices: 139043--139250 Score: 398
Period size: 106 Copynumber: 2.0 Consensus size: 106
139033 ATAGCGTGAT
139043 TATCAAAATTTCATAAAATATTCAATCGAAGCATGTTGGGTCACGTGCAACGCACGTGAAAGGTA
1 TATCAAAATTTCATAAAATATTCAATCGAAGCATGTTGGGTCACGTGCAACGCACGTGAAAGGTA
*
139108 AAACTAGTATTATTAAAAATATATAGGTGCTCATTTAAGAA
66 AAACTAGTATTATTAAAAATATATAGCTGCTCATTTAAGAA
*
139149 TATCAAAATTTCATAAAATATTCAATCGAAGCATGTTGGGTCACGTGCGACGCACGTGAAAGGTA
1 TATCAAAATTTCATAAAATATTCAATCGAAGCATGTTGGGTCACGTGCAACGCACGTGAAAGGTA
139214 AAACTAGTATTATTAAAAATATATAGCTGCTCATTTA
66 AAACTAGTATTATTAAAAATATATAGCTGCTCATTTA
139251 GGCTCGCGAG
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
106 100 1.00
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (106 bp):
TATCAAAATTTCATAAAATATTCAATCGAAGCATGTTGGGTCACGTGCAACGCACGTGAAAGGTA
AAACTAGTATTATTAAAAATATATAGCTGCTCATTTAAGAA
Found at i:143328 original size:24 final size:24
Alignment explanation
Indices: 143301--143386 Score: 118
Period size: 24 Copynumber: 3.6 Consensus size: 24
143291 TATGCCATAG
*
143301 AACAGAATCAACATTATTACAAGC
1 AACAGAATCAACATCATTACAAGC
* *
143325 AACAGGATCAACATCATTACAATC
1 AACAGAATCAACATCATTACAAGC
* *
143349 AACAGAATCATCATCATTACAAGG
1 AACAGAATCAACATCATTACAAGC
*
143373 AACAAAATCAACAT
1 AACAGAATCAACAT
143387 TTGTACAAGA
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.50, C:0.22, G:0.08, T:0.20
Consensus pattern (24 bp):
AACAGAATCAACATCATTACAAGC
Found at i:161870 original size:15 final size:16
Alignment explanation
Indices: 161850--161882 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
161840 GGCTTGTAGA
161850 TTCTTCCTCTT-TTTT
1 TTCTTCCTCTTCTTTT
*
161865 TTCTTCTTCTTCTTTT
1 TTCTTCCTCTTCTTTT
161881 TT
1 TT
161883 TTTTGTTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (16 bp):
TTCTTCCTCTTCTTTT
Found at i:161873 original size:18 final size:18
Alignment explanation
Indices: 161850--161884 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
161840 GGCTTGTAGA
161850 TTCTTCCTCTTTTTTTTC
1 TTCTTCCTCTTTTTTTTC
*
161868 TTCTTCTTCTTTTTTTT
1 TTCTTCCTCTTTTTTTT
161885 TTGTTTTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (18 bp):
TTCTTCCTCTTTTTTTTC
Found at i:165573 original size:2 final size:2
Alignment explanation
Indices: 165566--165609 Score: 79
Period size: 2 Copynumber: 21.5 Consensus size: 2
165556 GAGAAGTAGA
165566 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
165609 A
1 A
165610 AATTATTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 39 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:177965 original size:22 final size:23
Alignment explanation
Indices: 177896--177965 Score: 58
Period size: 22 Copynumber: 3.0 Consensus size: 23
177886 AGAGAATTTT
*
177896 ATTATATTTCCATTTTTTGATATAAA
1 ATTATATTT--ATTTTTTCATAT-AA
*
177922 ATT-T-TCTATGTTTTTCAT-TAA
1 ATTATATTTAT-TTTTTCATATAA
177943 ATTATATTTATTTTTT-ATATAA
1 ATTATATTTATTTTTTCATATAA
177965 A
1 A
177966 CTTAGTACTA
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
21 7 0.19
22 13 0.35
23 11 0.30
24 2 0.05
25 1 0.03
26 3 0.08
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.59
Consensus pattern (23 bp):
ATTATATTTATTTTTTCATATAA
Found at i:178185 original size:24 final size:24
Alignment explanation
Indices: 178153--178200 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
178143 CCCAAGACTC
*
178153 ATATAAGGTGTATATAGAGCTAAG
1 ATATAAGGTGCATATAGAGCTAAG
178177 ATATAAGGTGCATATAGAGCTAAG
1 ATATAAGGTGCATATAGAGCTAAG
178201 GTATGTCTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.27
Consensus pattern (24 bp):
ATATAAGGTGCATATAGAGCTAAG
Found at i:202817 original size:7 final size:7
Alignment explanation
Indices: 202805--202843 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
202795 CTGCAATTCT
202805 TTTTTTC
1 TTTTTTC
202812 TTTTTTC
1 TTTTTTC
202819 TTTTTTC
1 TTTTTTC
202826 TTTTTTC
1 TTTTTTC
202833 TTTTTTC
1 TTTTTTC
202840 TTTT
1 TTTT
202844 GTGGGACAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTTC
Found at i:207339 original size:22 final size:22
Alignment explanation
Indices: 207296--207340 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
207286 TAGCTTCGGG
*
207296 ACCTCAAAAATGTTTTTCTTTT
1 ACCTCAAAAATGTTTGTCTTTT
*
207318 ACCTCAAAAATGGTTTGTTTTTT
1 ACCTCAAAAAT-GTTTGTCTTTT
207341 TGGCAGTCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.49
Consensus pattern (22 bp):
ACCTCAAAAATGTTTGTCTTTT
Found at i:212074 original size:4 final size:4
Alignment explanation
Indices: 212065--212124 Score: 54
Period size: 4 Copynumber: 15.0 Consensus size: 4
212055 CTAATAATTC
* *
212065 ACAT ACAT ACAT AC-- ACAT ACAT ATAT ACAT -CGT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
212110 GACAT GACAT GACAT
1 -ACAT -ACAT -ACAT
212125 TTCTTTTGGT
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
2 2 0.04
3 2 0.04
4 30 0.62
5 14 0.29
ACGTcount: A:0.45, C:0.23, G:0.07, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:220592 original size:31 final size:31
Alignment explanation
Indices: 220555--220692 Score: 141
Period size: 31 Copynumber: 4.5 Consensus size: 31
220545 ACGGTGTCCG
**
220555 ACGTGGCATGCCACGTGTACCAAAAAACGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
* * * *
220586 ATGTGGCACGCCACGTGTATCAAAAAGTGAT
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
* ** * *
220617 ATGTATCACGCCATGTGTACCAAAAAGTGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
* * **
220648 ACGTGGCATACCATGTGTTTCAAAAAGTGAC
1 ACGTGGCATGCCACGTGTACCAAAAAGTGAC
220679 ACGTGGCATGCCAC
1 ACGTGGCATGCCAC
220693 ATGCACAAAA
Statistics
Matches: 87, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 87 1.00
ACGTcount: A:0.33, C:0.24, G:0.23, T:0.20
Consensus pattern (31 bp):
ACGTGGCATGCCACGTGTACCAAAAAGTGAC
Found at i:221276 original size:33 final size:33
Alignment explanation
Indices: 221232--221296 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
221222 TCCCTAGGAC
*
221232 TTGTAACATTCGTGG-GGCTCTCCCAAACTCTGG
1 TTGTAACATTCG-GGAGACTCTCCCAAACTCTGG
*
221265 TTGTAATATTCGGGAGACTCTCCCAAACTCTG
1 TTGTAACATTCGGGAGACTCTCCCAAACTCTG
221297 ATGTCATTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 2 0.07
33 27 0.93
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.31
Consensus pattern (33 bp):
TTGTAACATTCGGGAGACTCTCCCAAACTCTGG
Found at i:221925 original size:31 final size:31
Alignment explanation
Indices: 221890--221948 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
221880 AAAAAGATGA
221890 TTAATTTAG-TCATTATACTCATAAGATTAGG
1 TTAATTTAGTTCATT-TACTCATAAGATTAGG
221921 TTAATTTAGTTCATTTACTCATAAGATT
1 TTAATTTAGTTCATTTACTCATAAGATT
221949 GAACCAATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
31 22 0.81
32 5 0.19
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (31 bp):
TTAATTTAGTTCATTTACTCATAAGATTAGG
Found at i:223993 original size:25 final size:25
Alignment explanation
Indices: 223965--224014 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
223955 TGAATTTAAA
*
223965 CTGTTCGCTTGATCAATTTAGTAAT
1 CTGTTCGCTTGATCAATCTAGTAAT
223990 CTGTTCGCTTGATCAATCTAGTAAT
1 CTGTTCGCTTGATCAATCTAGTAAT
224015 TTAGTAGCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (25 bp):
CTGTTCGCTTGATCAATCTAGTAAT
Found at i:225032 original size:26 final size:29
Alignment explanation
Indices: 224997--225069 Score: 116
Period size: 26 Copynumber: 2.6 Consensus size: 29
224987 ACACAGAGAC
224997 AAAATAGATAGCTTTTATTGGTA-C-AAA
1 AAAATAGATAGCTTTTATTGGTACCAAAA
225024 AAAAT-GATAGCTTTTATTGGTACCATAAA
1 AAAATAGATAGCTTTTATTGGTACCA-AAA
225053 AAAATAGATAGCTTTTA
1 AAAATAGATAGCTTTTA
225070 GTGTATTTCT
Statistics
Matches: 42, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
26 17 0.40
27 6 0.14
29 8 0.19
30 11 0.26
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (29 bp):
AAAATAGATAGCTTTTATTGGTACCAAAA
Done.