Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022704.1 Corchorus olitorius cultivar O-4 contig22737, 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: 73336
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:718 original size:24 final size:24
Alignment explanation
Indices: 668--722 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
658 TGACCCAAAT
*
668 GAAATAAAAAAAAAGAAAAAGGAG
1 GAAATAAAAAAAAAGAAAAAGAAG
692 GAAA-AAAAAAGAAAGAAGAAA-AAG
1 GAAATAAAAAA-AAAGAA-AAAGAAG
716 GAAATAA
1 GAAATAA
723 GGAAATTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 6 0.22
24 16 0.59
25 5 0.19
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (24 bp):
GAAATAAAAAAAAAGAAAAAGAAG
Found at i:5486 original size:2 final size:2
Alignment explanation
Indices: 5479--5516 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
5469 TGCATACTAA
*
5479 AT AT AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5517 CAATCCATTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:21335 original size:15 final size:16
Alignment explanation
Indices: 21315--21344 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21305 TGTAAGTTTA
21315 TCAAAA-ATCAATTTT
1 TCAAAAGATCAATTTT
21330 TCAAAAGATCAATTT
1 TCAAAAGATCAATTT
21345 GAATTCACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.13, G:0.03, T:0.37
Consensus pattern (16 bp):
TCAAAAGATCAATTTT
Found at i:22268 original size:11 final size:11
Alignment explanation
Indices: 22252--22276 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
22242 GGGGAATAAT
22252 CAATCCAAAAA
1 CAATCCAAAAA
22263 CAATCCAAAAA
1 CAATCCAAAAA
22274 CAA
1 CAA
22277 ACAATTTTCT
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:0.64, C:0.28, G:0.00, T:0.08
Consensus pattern (11 bp):
CAATCCAAAAA
Found at i:32648 original size:19 final size:18
Alignment explanation
Indices: 32624--32659 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
32614 TGAAGACTTA
32624 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
32643 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
32660 ATTATTTCCA
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:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:40816 original size:53 final size:53
Alignment explanation
Indices: 40758--40972 Score: 283
Period size: 53 Copynumber: 4.1 Consensus size: 53
40748 TCAAGTCTTC
*
40758 AAAGTATTCAATTTAGCTCTTTTTCAAGTCGGAAAGGTTCCCATCAGTTTTCA
1 AAAGTATTCAATTTAGCTCTTTTTCAAATCGGAAAGGTTCCCATCAGTTTTCA
* * *
40811 AAAGTATTCCATTTAGCTCTTTTTCAAGTCGGGAAGGTTCCCATCAGTTTTCA
1 AAAGTATTCAATTTAGCTCTTTTTCAAATCGGAAAGGTTCCCATCAGTTTTCA
* * *
40864 AAAGTATTCCATTTAGCCCTTTTTCAAATCGGGAAA-GTTCCCATCAATTTTC-
1 AAAGTATTCAATTTAGCTCTTTTTCAAATC-GGAAAGGTTCCCATCAGTTTTCA
* * * *
40916 AAAGTATTCAATTTAGC-CAGTCTTCAAATTGGGAAGGTTCCCATCTAGTTTTCA
1 AAAGTATTCAATTTAGCTC-TTTTTCAAATCGGAAAGGTTCCCATC-AGTTTTCA
40970 AAA
1 AAA
40973 TTGTCAAATT
Statistics
Matches: 145, Mismatches: 12, Indels: 9
0.87 0.07 0.05
Matches are distributed among these distances:
51 5 0.03
52 33 0.23
53 100 0.69
54 7 0.05
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (53 bp):
AAAGTATTCAATTTAGCTCTTTTTCAAATCGGAAAGGTTCCCATCAGTTTTCA
Found at i:41027 original size:35 final size:35
Alignment explanation
Indices: 40938--41136 Score: 224
Period size: 35 Copynumber: 5.6 Consensus size: 35
40928 TTAGCCAGTC
* * * *
40938 TTCAAATTGGGAAGGTTCCCATCTAGTTTTCAAAATT
1 TTCAAATTGGGAAAGTTCCCA-CCAGTTTT-TAAGTT
* *
40975 GTCAAATTGGGAAAGTTCCCGCCAGTTTTTAAGTT
1 TTCAAATTGGGAAAGTTCCCACCAGTTTTTAAGTT
* *
41010 TTTAAATTGGGAGAGTTCCCACCAGTTTTTAAGTT
1 TTCAAATTGGGAAAGTTCCCACCAGTTTTTAAGTT
* *
41045 TTCAAATTGGGAAAGTTCCCATTCAGTTTTCAAAG-T
1 TTCAAATTGGGAAAGTTCCCA-CCAGTTTT-TAAGTT
41081 TTCTAAATTGGGAAAGTTCCCACCAAG-TTTT-AGTT
1 TTC-AAATTGGGAAAGTTCCCACC-AGTTTTTAAGTT
*
41116 TTCAAAGTGGGAAAGTTCCCA
1 TTCAAATTGGGAAAGTTCCCA
41137 TCAAAAGCGT
Statistics
Matches: 140, Mismatches: 17, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
34 19 0.14
35 58 0.41
36 22 0.16
37 41 0.29
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (35 bp):
TTCAAATTGGGAAAGTTCCCACCAGTTTTTAAGTT
Found at i:41055 original size:107 final size:106
Alignment explanation
Indices: 40938--41136 Score: 287
Period size: 107 Copynumber: 1.9 Consensus size: 106
40928 TTAGCCAGTC
* *
40938 TTCAAATTGGGAAGGTTCCCA-TCTAGTTTTCAAAATTGTC-AAATTGGGAAAGTTCCCGCC-AG
1 TTCAAATTGGGAAAGTTCCCATTC-AGTTTTCAAAATT-TCTAAATTGGGAAAGTTCCCACCAAG
* * *
41000 TTTTTAAGTTTTTAAATTGGGAGAGTTCCCACCAGTTTTTAAGTT
64 -TTTT-AGTTTTCAAAGTGGGAAAGTTCCCACCAGTTTTTAAGTT
*
41045 TTCAAATTGGGAAAGTTCCCATTCAGTTTTCAAAGTTTCTAAATTGGGAAAGTTCCCACCAAGTT
1 TTCAAATTGGGAAAGTTCCCATTCAGTTTTCAAAATTTCTAAATTGGGAAAGTTCCCACCAAGTT
41110 TTAGTTTTCAAAGTGGGAAAGTTCCCA
66 TTAGTTTTCAAAGTGGGAAAGTTCCCA
41137 TCAAAAGCGT
Statistics
Matches: 83, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
106 24 0.29
107 55 0.66
108 4 0.05
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (106 bp):
TTCAAATTGGGAAAGTTCCCATTCAGTTTTCAAAATTTCTAAATTGGGAAAGTTCCCACCAAGTT
TTAGTTTTCAAAGTGGGAAAGTTCCCACCAGTTTTTAAGTT
Found at i:41129 original size:71 final size:71
Alignment explanation
Indices: 40941--41138 Score: 240
Period size: 72 Copynumber: 2.8 Consensus size: 71
40931 GCCAGTCTTC
* * * * * * *
40941 AAATTGGGAAGGTTCCCATCTAGTTTTCAAAATTGTCAAATTGGGAAAGTTCCC-GCCAGTTTTT
1 AAATTGGGAAAGTTCCCA-CCAGTTTT-TAAGTTTTCAAATTGGGAAAGTTCCCATCCAGTTTTA
*
41005 AAGTTTTT
64 AAGTTTCT
* *
41013 AAATTGGGAGAGTTCCCACCAGTTTTTAAGTTTTCAAATTGGGAAAGTTCCCATTCAGTTTTCAA
1 AAATTGGGAAAGTTCCCACCAGTTTTTAAGTTTTCAAATTGGGAAAGTTCCCATCCAGTTTT-AA
41078 AGTTTCT
65 AGTTTCT
*
41085 AAATTGGGAAAGTTCCCACCAAG-TTTT-AGTTTTCAAAGTGGGAAAGTTCCCATC
1 AAATTGGGAAAGTTCCCACC-AGTTTTTAAGTTTTCAAATTGGGAAAGTTCCCATC
41139 AAAAGCGTTT
Statistics
Matches: 110, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
70 23 0.21
71 39 0.35
72 46 0.42
73 2 0.02
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (71 bp):
AAATTGGGAAAGTTCCCACCAGTTTTTAAGTTTTCAAATTGGGAAAGTTCCCATCCAGTTTTAAA
GTTTCT
Found at i:43865 original size:14 final size:14
Alignment explanation
Indices: 43848--43905 Score: 59
Period size: 14 Copynumber: 4.3 Consensus size: 14
43838 CGAGAAGTAT
*
43848 TTTTCAAGAAAATG
1 TTTTCAAGAAAAGG
*
43862 TTTTCGAGAAAAGG
1 TTTTCAAGAAAAGG
*
43876 TTTTCAA-AAATGAG
1 TTTTCAAGAAAAG-G
43890 TTTTC-A-AAAAGG
1 TTTTCAAGAAAAGG
43902 TTTT
1 TTTT
43906 TGAGTTTTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
12 5 0.13
13 9 0.24
14 24 0.63
ACGTcount: A:0.38, C:0.07, G:0.17, T:0.38
Consensus pattern (14 bp):
TTTTCAAGAAAAGG
Found at i:46591 original size:53 final size:53
Alignment explanation
Indices: 46533--46737 Score: 227
Period size: 53 Copynumber: 4.1 Consensus size: 53
46523 TCAAGTCTTC
*
46533 AAAGTATTCAATTTAGCTCTTTTTCAAGTCGGGAAGGTTCCCATCAGTTTTCA
1 AAAGTATTCAATTTAGCTCTTTTTCAAATCGGGAAGGTTCCCATCAGTTTTCA
*
46586 AAAG---T--A--T---TCTTTTTCAAGTCGGGAAGGTTCCCATCAGTTTTCA
1 AAAGTATTCAATTTAGCTCTTTTTCAAATCGGGAAGGTTCCCATCAGTTTTCA
* * * *
46629 AAAGTATTCCATTTAGCCCTTTTTCAAATCGGGAAAGTTCCCATCAATTTTC-
1 AAAGTATTCAATTTAGCTCTTTTTCAAATCGGGAAGGTTCCCATCAGTTTTCA
* * *
46681 AAAGTATTCAATTTAGC-CAGTCTTCAAATTGGGAAGGTTCCCATCTAGTTTTCA
1 AAAGTATTCAATTTAGCTC-TTTTTCAAATCGGGAAGGTTCCCATC-AGTTTTCA
46735 AAA
1 AAA
46738 TTGTCAAATT
Statistics
Matches: 129, Mismatches: 10, Indels: 25
0.79 0.06 0.15
Matches are distributed among these distances:
43 40 0.31
46 2 0.02
48 2 0.02
50 2 0.02
51 1 0.01
52 38 0.29
53 41 0.32
54 3 0.02
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.36
Consensus pattern (53 bp):
AAAGTATTCAATTTAGCTCTTTTTCAAATCGGGAAGGTTCCCATCAGTTTTCA
Found at i:46600 original size:43 final size:43
Alignment explanation
Indices: 46550--46637 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
46540 TCAATTTAGC
46550 TCTTTTTCAAGTCGGGAAGGTTCCCATCAGTTTTCAAAAGTAT
1 TCTTTTTCAAGTCGGGAAGGTTCCCATCAGTTTTCAAAAGTAT
46593 TCTTTTTCAAGTCGGGAAGGTTCCCATCAGTTTTCAAAAGTAT
1 TCTTTTTCAAGTCGGGAAGGTTCCCATCAGTTTTCAAAAGTAT
46636 TC
1 TC
46638 CATTTAGCCC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (43 bp):
TCTTTTTCAAGTCGGGAAGGTTCCCATCAGTTTTCAAAAGTAT
Found at i:46707 original size:52 final size:52
Alignment explanation
Indices: 46598--46736 Score: 188
Period size: 52 Copynumber: 2.6 Consensus size: 52
46588 AGTATTCTTT
* * ** *
46598 TTCAAGTCGGGAAGGTTCCCATCAGTTTTCAAAAGTATTCCATTTAGCCCTTT
1 TTCAAATCGGGAAGGTTCCCATCAGTTTTC-AAAGTATTCAATTTAGCCAGTC
* *
46651 TTCAAATCGGGAAAGTTCCCATCAATTTTCAAAGTATTCAATTTAGCCAGTC
1 TTCAAATCGGGAAGGTTCCCATCAGTTTTCAAAGTATTCAATTTAGCCAGTC
*
46703 TTCAAATTGGGAAGGTTCCCATCTAGTTTTCAAA
1 TTCAAATCGGGAAGGTTCCCATC-AGTTTTCAAA
46737 ATTGTCAAAT
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
52 39 0.52
53 36 0.48
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.35
Consensus pattern (52 bp):
TTCAAATCGGGAAGGTTCCCATCAGTTTTCAAAGTATTCAATTTAGCCAGTC
Found at i:46792 original size:35 final size:35
Alignment explanation
Indices: 46703--46901 Score: 224
Period size: 35 Copynumber: 5.6 Consensus size: 35
46693 TTAGCCAGTC
* * * *
46703 TTCAAATTGGGAAGGTTCCCATCTAGTTTTCAAAATT
1 TTCAAATTGGGAAAGTTCCCA-CCAGTTTT-TAAGTT
* *
46740 GTCAAATTGGGAAAGTTCCCGCCAGTTTTTAAGTT
1 TTCAAATTGGGAAAGTTCCCACCAGTTTTTAAGTT
* *
46775 TTTAAATTGGGAGAGTTCCCACCAGTTTTTAAGTT
1 TTCAAATTGGGAAAGTTCCCACCAGTTTTTAAGTT
* *
46810 TTCAAATTGGGAAAGTTCCCATTCAGTTTTCAAAG-T
1 TTCAAATTGGGAAAGTTCCCA-CCAGTTTT-TAAGTT
46846 TTCTAAATTGGGAAAGTTCCCACCAAG-TTTT-AGTT
1 TTC-AAATTGGGAAAGTTCCCACC-AGTTTTTAAGTT
*
46881 TTCAAAGTGGGAAAGTTCCCA
1 TTCAAATTGGGAAAGTTCCCA
46902 TCAAAAGCGT
Statistics
Matches: 140, Mismatches: 17, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
34 19 0.14
35 58 0.41
36 22 0.16
37 41 0.29
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (35 bp):
TTCAAATTGGGAAAGTTCCCACCAGTTTTTAAGTT
Found at i:46820 original size:107 final size:106
Alignment explanation
Indices: 46703--46901 Score: 287
Period size: 107 Copynumber: 1.9 Consensus size: 106
46693 TTAGCCAGTC
* *
46703 TTCAAATTGGGAAGGTTCCCA-TCTAGTTTTCAAAATTGTC-AAATTGGGAAAGTTCCCGCC-AG
1 TTCAAATTGGGAAAGTTCCCATTC-AGTTTTCAAAATT-TCTAAATTGGGAAAGTTCCCACCAAG
* * *
46765 TTTTTAAGTTTTTAAATTGGGAGAGTTCCCACCAGTTTTTAAGTT
64 -TTTT-AGTTTTCAAAGTGGGAAAGTTCCCACCAGTTTTTAAGTT
*
46810 TTCAAATTGGGAAAGTTCCCATTCAGTTTTCAAAGTTTCTAAATTGGGAAAGTTCCCACCAAGTT
1 TTCAAATTGGGAAAGTTCCCATTCAGTTTTCAAAATTTCTAAATTGGGAAAGTTCCCACCAAGTT
46875 TTAGTTTTCAAAGTGGGAAAGTTCCCA
66 TTAGTTTTCAAAGTGGGAAAGTTCCCA
46902 TCAAAAGCGT
Statistics
Matches: 83, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
106 24 0.29
107 55 0.66
108 4 0.05
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (106 bp):
TTCAAATTGGGAAAGTTCCCATTCAGTTTTCAAAATTTCTAAATTGGGAAAGTTCCCACCAAGTT
TTAGTTTTCAAAGTGGGAAAGTTCCCACCAGTTTTTAAGTT
Found at i:46894 original size:71 final size:71
Alignment explanation
Indices: 46706--46903 Score: 240
Period size: 72 Copynumber: 2.8 Consensus size: 71
46696 GCCAGTCTTC
* * * * * * *
46706 AAATTGGGAAGGTTCCCATCTAGTTTTCAAAATTGTCAAATTGGGAAAGTTCCC-GCCAGTTTTT
1 AAATTGGGAAAGTTCCCA-CCAGTTTT-TAAGTTTTCAAATTGGGAAAGTTCCCATCCAGTTTTA
*
46770 AAGTTTTT
64 AAGTTTCT
* *
46778 AAATTGGGAGAGTTCCCACCAGTTTTTAAGTTTTCAAATTGGGAAAGTTCCCATTCAGTTTTCAA
1 AAATTGGGAAAGTTCCCACCAGTTTTTAAGTTTTCAAATTGGGAAAGTTCCCATCCAGTTTT-AA
46843 AGTTTCT
65 AGTTTCT
*
46850 AAATTGGGAAAGTTCCCACCAAG-TTTT-AGTTTTCAAAGTGGGAAAGTTCCCATC
1 AAATTGGGAAAGTTCCCACC-AGTTTTTAAGTTTTCAAATTGGGAAAGTTCCCATC
46904 AAAAGCGTTT
Statistics
Matches: 110, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
70 23 0.21
71 39 0.35
72 46 0.42
73 2 0.02
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (71 bp):
AAATTGGGAAAGTTCCCACCAGTTTTTAAGTTTTCAAATTGGGAAAGTTCCCATCCAGTTTTAAA
GTTTCT
Found at i:54792 original size:78 final size:75
Alignment explanation
Indices: 54648--55067 Score: 487
Period size: 74 Copynumber: 5.5 Consensus size: 75
54638 TTTTTATTTA
* * * *
54648 TGATGAAACGGACT-AAGGGGAGACGTTCGTTTCATTTGTT-TTATACGGGGACACCAACTTTGG
1 TGATGAAACGGTCTCAA-TGGAGACGGTCGTTTCATTTATTCTTATACGGGGACACCAA--TTGG
*
54711 TGTTCTACCGTTG
63 TGTTCGACCGTTG
* * *
54724 TGATGAAACGGTCTCGATGGAGACAGTCGTTTCATCTAGTTCTTATACGGGGACACCAATTTTGG
1 TGATGAAACGGTCTCAATGGAGACGGTCGTTTCATTTA-TTCTTATACGGGGACACCAA--TTGG
54789 TGTTCGACCGTTG
63 TGTTCGACCGTTG
* *
54802 TGATGAAACGGTCTCAATGGAGACGGTCGTTTCATTTATTTTTATACGGGGGCACCAA-TGGTGT
1 TGATGAAACGGTCTCAATGGAGACGGTCGTTTCATTTATTCTTATACGGGGACACCAATTGGTGT
*
54866 TCGACCATTG
66 TCGACCGTTG
*
54876 TGACGAAACGGTCTCAATGGAGACGGTCGTTTCATTTATT-TCTATACGGGGACACCAA-TGGTG
1 TGATGAAACGGTCTCAATGGAGACGGTCGTTTCATTTATTCT-TATACGGGGACACCAATTGGTG
*
54939 TTCGGCCGTTG
65 TTCGACCGTTG
* * *
54950 TGACGAAACGGTCTCAATGGAGATGGTCGTTTCATTTATTTTTATACGGGGGACACCAATGTTGG
1 TGATGAAACGGTCTCAATGGAGACGGTCGTTTCATTTATTCTTATAC-GGGGACACCAA--TTGG
*
55015 TGTTCGGCCGTTG
63 TGTTCGACCGTTG
* * *
55028 T-AGTAAAACGGTCTC--TGGGAAGACGTTCGTTTTATTTATT
1 TGA-TGAAACGGTCTCAAT-GG-AGACGGTCGTTTCATTTATT
55068 TCAGAATTTC
Statistics
Matches: 307, Mismatches: 25, Indels: 22
0.87 0.07 0.06
Matches are distributed among these distances:
73 1 0.00
74 127 0.41
75 12 0.04
76 30 0.10
77 24 0.08
78 113 0.37
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (75 bp):
TGATGAAACGGTCTCAATGGAGACGGTCGTTTCATTTATTCTTATACGGGGACACCAATTGGTGT
TCGACCGTTG
Found at i:56992 original size:16 final size:15
Alignment explanation
Indices: 56954--56995 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
56944 ACAGAGGTTG
56954 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
56969 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
56984 ACTAGAAAACAA
1 AC-AGAAAACAA
56996 AACAAAGTAA
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:0.67, C:0.14, G:0.07, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:68164 original size:23 final size:23
Alignment explanation
Indices: 68120--68165 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
68110 ATAGACAAAG
**
68120 CTCTCACAAAGGAGTACCAAAAA
1 CTCTCACAAAGGAGTAAAAAAAA
68143 CTCTCACAAAGGAGTAAAAAAAA
1 CTCTCACAAAGGAGTAAAAAAAA
68166 AAAAAAGATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.52, C:0.22, G:0.13, T:0.13
Consensus pattern (23 bp):
CTCTCACAAAGGAGTAAAAAAAA
Found at i:72386 original size:49 final size:47
Alignment explanation
Indices: 72285--72426 Score: 160
Period size: 49 Copynumber: 3.0 Consensus size: 47
72275 GAGCGTGCCA
* * * **
72285 ATCAATTTTGTCAAAAAATTGATAAAAAGTGCGATGAAATTTAAAAG
1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAG
72332 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAA-GTAAAAATAAAAG
1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGCAATG-AAAAATAAAAG
* * * *
72381 TTCAATTTTGTGGTAAAAATTGAGAAAAAGTGCAGTGAAAAGTAAA
1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAATGAAAAATAAA
72427 TGATTGCTTG
Statistics
Matches: 81, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
47 12 0.15
48 28 0.35
49 41 0.51
ACGTcount: A:0.49, C:0.06, G:0.17, T:0.28
Consensus pattern (47 bp):
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAATGAAAAATAAAAG
Done.