Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021586.1 Corchorus olitorius cultivar O-4 contig21619, 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: 41886
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Found at i:1910 original size:22 final size:22
Alignment explanation
Indices: 1652--1947 Score: 117
Period size: 22 Copynumber: 13.3 Consensus size: 22
1642 ACAATCAAAC
* *
1652 CAAAATTACATAGGAAAGTTAT
1 CAAAATTTCATAGGAAGGTTAT
* * *
1674 TAAAATTTCATACTGTAA--TTAC
1 CAAAATTTCATA--GGAAGGTTAT
* *
1696 CAAAACTTCATATGG-AGGTGAT
1 CAAAATTTCATA-GGAAGGTTAT
* * *
1718 CAAAACTTCATAATGTA-GTTAT
1 CAAAATTTCAT-AGGAAGGTTAT
* *
1740 CAAAATTTCATA-CAGAGGTTAC
1 CAAAATTTCATAGGA-AGGTTAT
* ** *
1762 CAAATTTTCATAAAAATGTTAT
1 CAAAATTTCATAGGAAGGTTAT
*
1784 CAAAATTTCATACGAAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
** * * *
1806 TGAAATTTTATAGTG-TGATTAT
1 CAAAATTTCATAG-GAAGGTTAT
* * *
1828 CAAAA-TTAATTA-GAACGTTAA
1 CAAAATTTCA-TAGGAAGGTTAT
*
1849 CAAAATTTCACAGGGAGAGAGGTTAT
1 CAAAATTTCATA--G-GA-AGGTTAT
** * *
1875 CAAAAAATCCTAGGAAGGTTAA
1 CAAAATTTCATAGGAAGGTTAT
*
1897 CAAAATTTCATAGGGAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
*
1919 GAAAATGTT-AT-GGAGAGGTTAT
1 CAAAAT-TTCATAGGA-AGGTTAT
1941 CAAAATT
1 CAAAATT
1948 ACTTATAGAG
Statistics
Matches: 201, Mismatches: 53, Indels: 41
0.68 0.18 0.14
Matches are distributed among these distances:
20 2 0.01
21 19 0.09
22 153 0.76
23 8 0.04
24 4 0.02
25 2 0.01
26 13 0.06
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (22 bp):
CAAAATTTCATAGGAAGGTTAT
Found at i:2018 original size:22 final size:22
Alignment explanation
Indices: 1993--2043 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
1983 GAAGTTAGCG
*
1993 AAATTTTATG-GTGTGGTTATCA
1 AAATTTTATGAG-GAGGTTATCA
2015 AAATTTTATGAGGAGGTTATCA
1 AAATTTTATGAGGAGGTTATCA
2037 AAATTTT
1 AAATTTT
2044 CAGAGCGCGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 26 0.96
23 1 0.04
ACGTcount: A:0.33, C:0.04, G:0.20, T:0.43
Consensus pattern (22 bp):
AAATTTTATGAGGAGGTTATCA
Found at i:2099 original size:22 final size:22
Alignment explanation
Indices: 2074--2240 Score: 147
Period size: 22 Copynumber: 7.6 Consensus size: 22
2064 TTTAATGTTA
* *
2074 TTATCAAAATTTCACACTGAGG
1 TTATCAAAATTTCACAGTGTGG
* **
2096 TTATCAAAACTTCATTGTGTGG
1 TTATCAAAATTTCACAGTGTGG
* *
2118 TTATCAGAATTTCACAGTGTGT
1 TTATCAAAATTTCACAGTGTGG
* *
2140 TTATCAAAATTTCTCACTGTGG
1 TTATCAAAATTTCACAGTGTGG
* * *
2162 TTATCAAATTTTCATAAG-GAGG
1 TTATCAAAATTTCA-CAGTGTGG
** * *
2184 TTATTGAAATTTCACAATGAGG
1 TTATCAAAATTTCACAGTGTGG
* *
2206 TTATCAAATTTTCGCAGTGTGG
1 TTATCAAAATTTCACAGTGTGG
*
2228 TTATCAATATTTC
1 TTATCAAAATTTC
2241 TACGTTGGAG
Statistics
Matches: 111, Mismatches: 32, Indels: 4
0.76 0.22 0.03
Matches are distributed among these distances:
21 1 0.01
22 109 0.98
23 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.40
Consensus pattern (22 bp):
TTATCAAAATTTCACAGTGTGG
Found at i:2176 original size:66 final size:66
Alignment explanation
Indices: 2074--2239 Score: 174
Period size: 66 Copynumber: 2.5 Consensus size: 66
2064 TTTAATGTTA
* ** * * *
2074 TTATCAAAATTTCACACTGAGGTTATCAAAACTTCAT-TGTGTGGTTATCAG-AATTTCACAGTG
1 TTATCAAAATTTCACACTGTGGTTATCAAATTTTCATAAG-GAGGTTAT-AGAAATTTCACAATG
* *
2137 TGT
64 AGG
* *
2140 TTATCAAAATTTCTCACTGTGGTTATCAAATTTTCATAAGGAGGTTATTGAAATTTCACAATGAG
1 TTATCAAAATTTCACACTGTGGTTATCAAATTTTCATAAGGAGGTTATAGAAATTTCACAATGAG
2205 G
66 G
* * *
2206 TTATCAAATTTTCGCAGTGTGGTTATCAATATTT
1 TTATCAAAATTTCACACTGTGGTTATCAA-ATTT
2240 CTACGTTGGA
Statistics
Matches: 84, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
65 1 0.01
66 78 0.93
67 5 0.06
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (66 bp):
TTATCAAAATTTCACACTGTGGTTATCAAATTTTCATAAGGAGGTTATAGAAATTTCACAATGAG
G
Found at i:4141 original size:9 final size:9
Alignment explanation
Indices: 4127--4151 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
4117 GAGGAAGCAG
4127 TACACCCTC
1 TACACCCTC
4136 TACACCCTC
1 TACACCCTC
4145 TACACCC
1 TACACCC
4152 CTAGGAGGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.56, G:0.00, T:0.20
Consensus pattern (9 bp):
TACACCCTC
Found at i:5381 original size:39 final size:39
Alignment explanation
Indices: 5327--5405 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
5317 TCACACAACT
*
5327 CACCATATGCTTAACTTCCAATGAGAAATTAACAATAAA
1 CACCAAATGCTTAACTTCCAATGAGAAATTAACAATAAA
*
5366 CACCAAATGTTTAACTTCCAATGAGAAATTAACAATAAA
1 CACCAAATGCTTAACTTCCAATGAGAAATTAACAATAAA
5405 C
1 C
5406 TATATTTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.47, C:0.20, G:0.08, T:0.25
Consensus pattern (39 bp):
CACCAAATGCTTAACTTCCAATGAGAAATTAACAATAAA
Found at i:5814 original size:73 final size:73
Alignment explanation
Indices: 5719--5864 Score: 256
Period size: 73 Copynumber: 2.0 Consensus size: 73
5709 TGAGCTAACC
* *
5719 TATGTGCCAAAAAATTGGCCTCCCTATTTATATGAGAAAAAGAGCACTCATCAAACAACAAGGCC
1 TATGTACCAAAAAATTGGCCTCCCTATTTATATGAGAAAAAGAGCACTCACCAAACAACAAGGCC
5784 AGTTCCCG
66 AGTTCCCG
* *
5792 TATGTACCAAAAAATTGGCCTCCCTATTTATATGAGCAAAAGAGCACTCACCAAACAACAAGGCT
1 TATGTACCAAAAAATTGGCCTCCCTATTTATATGAGAAAAAGAGCACTCACCAAACAACAAGGCC
5857 AGTTCCCG
66 AGTTCCCG
5865 AATCTCATAA
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 69 1.00
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.22
Consensus pattern (73 bp):
TATGTACCAAAAAATTGGCCTCCCTATTTATATGAGAAAAAGAGCACTCACCAAACAACAAGGCC
AGTTCCCG
Found at i:6981 original size:25 final size:25
Alignment explanation
Indices: 6949--6999 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
6939 CCACCTTGAC
6949 TCAAATTCCTTCATCAAAACTTAAT
1 TCAAATTCCTTCATCAAAACTTAAT
*
6974 TCAAATTCCTTCATCAAAGCTTAAT
1 TCAAATTCCTTCATCAAAACTTAAT
6999 T
1 T
7000 GCTCCACCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.37
Consensus pattern (25 bp):
TCAAATTCCTTCATCAAAACTTAAT
Found at i:10234 original size:20 final size:20
Alignment explanation
Indices: 10197--10235 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
10187 TTGCTATTAT
10197 TTTTGAATTTAATATTTTAC
1 TTTTGAATTTAATATTTTAC
*
10217 TTTT-AATTTCAATTTTTTA
1 TTTTGAATTT-AATATTTTA
10236 AATGTCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTGAATTTAATATTTTAC
Found at i:11764 original size:37 final size:37
Alignment explanation
Indices: 11722--11830 Score: 150
Period size: 36 Copynumber: 3.0 Consensus size: 37
11712 TCAACTTAAT
*
11722 TTTTCAAATTGGGAAAGTTTCCATCCAGTTTTCAAAA
1 TTTTCAAATTGGGAAAGTTCCCATCCAGTTTTCAAAA
* * *
11759 TTTTCAAAATGGGAAAGTTCCCA-CCAAGTTTT-TAAG
1 TTTTCAAATTGGGAAAGTTCCCATCC-AGTTTTCAAAA
*
11795 TTTTCAAATTGGGAAAGTTCCCATCCAGTCTTCAAA
1 TTTTCAAATTGGGAAAGTTCCCATCCAGTTTTCAAA
11831 GTATTAAATT
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
36 31 0.50
37 31 0.50
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (37 bp):
TTTTCAAATTGGGAAAGTTCCCATCCAGTTTTCAAAA
Found at i:11808 original size:36 final size:36
Alignment explanation
Indices: 11717--11823 Score: 144
Period size: 37 Copynumber: 2.9 Consensus size: 36
11707 ATATTTCAAC
* *
11717 TTAATTTTTCAAATTGGGAAAGTTTCCATCCAGTTT
1 TTAAATTTTCAAATTGGGAAAGTTCCCATCCAGTTT
* *
11753 TCAAAATTTTCAAAATGGGAAAGTTCCCA-CCAAGTTT
1 T-TAAATTTTCAAATTGGGAAAGTTCCCATCC-AGTTT
*
11790 TTAAGTTTTCAAATTGGGAAAGTTCCCATCCAGT
1 TTAAATTTTCAAATTGGGAAAGTTCCCATCCAGT
11824 CTTCAAAGTA
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
36 30 0.49
37 31 0.51
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (36 bp):
TTAAATTTTCAAATTGGGAAAGTTCCCATCCAGTTT
Found at i:11901 original size:52 final size:52
Alignment explanation
Indices: 11795--12140 Score: 460
Period size: 52 Copynumber: 6.6 Consensus size: 52
11785 AGTTTTTAAG
* * *
11795 TTTTCAAATTGGGAAAGTTCCCATCCAGTCTTCAAAGTATTAAATTTAGCTCT
1 TTTTCAAATCGGGAAAGTTCCCAT-CAGTTTTCAAAGTATTTAATTTAGCTCT
*
11848 TTTTCAAATCGGGAAAGTTCCCATCAGTTTTCAAAGTATTCAATTTAGCTCT
1 TTTTCAAATCGGGAAAGTTCCCATCAGTTTTCAAAGTATTTAATTTAGCTCT
* * * *
11900 TTTTCCAATTGGGAAGGTTCCCATCAATTTTCAAAGTATTTAATTTAGCTCT
1 TTTTCAAATCGGGAAAGTTCCCATCAGTTTTCAAAGTATTTAATTTAGCTCT
* * *
11952 TTTTCATATCGGGAAAGTTCCCATAAGTTTTCAAAGTATTTAATTTAGCTTTT
1 TTTTCAAATCGGGAAAGTTCCCATCAGTTTTCAAAGTATTTAATTTAGC-TCT
* * *
12005 TTTTCAAATCAGGAAAGTTCCCATCAAGTTTTCAAAGTATTTAATTTAACTTT
1 TTTTCAAATCGGGAAAGTTCCCATC-AGTTTTCAAAGTATTTAATTTAGCTCT
* * *
12058 TTTTCAAATTGGGAAAGTTCCCATCAGTTTTCAAAGTATTCAATTTAGC-CGG
1 TTTTCAAATCGGGAAAGTTCCCATCAGTTTTCAAAGTATTTAATTTAGCTC-T
* * *
12110 TTTTCAATTAAGGGAAAGTTCCCGTCAGTTT
1 TTTTCAAAT-CGGGAAAGTTCCCATCAGTTT
12141 CGGTTTCAGT
Statistics
Matches: 261, Mismatches: 28, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
52 146 0.56
53 92 0.35
54 23 0.09
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (52 bp):
TTTTCAAATCGGGAAAGTTCCCATCAGTTTTCAAAGTATTTAATTTAGCTCT
Found at i:13113 original size:22 final size:22
Alignment explanation
Indices: 13088--13298 Score: 173
Period size: 22 Copynumber: 9.5 Consensus size: 22
13078 TGTTTCTGTG
* *
13088 TGGTTATCAAAATTTCGTAAGA
1 TGGTTATCAAAATTTCATAGGA
* *
13110 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
*
13133 -GGTTATCAAATTTTCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
* *
13154 TGCTTACCAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA-GGA
*
13177 -AGTTATCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
* *
13198 AGGTTATTAAAATTTCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
*
13220 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
*
13242 TCAGGTTATTAAAATTTC-TCAGGA
1 T--GGTTATCAAAATTTCAT-AGGA
* **
13266 AGGTTATTGAAATTTCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
13288 TGGTTATCAAA
1 TGGTTATCAAA
13299 GAGATTATCA
Statistics
Matches: 151, Mismatches: 25, Indels: 26
0.75 0.12 0.13
Matches are distributed among these distances:
21 6 0.04
22 120 0.79
23 8 0.05
24 17 0.11
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:13138 original size:44 final size:43
Alignment explanation
Indices: 13089--14301 Score: 242
Period size: 44 Copynumber: 28.3 Consensus size: 43
13079 GTTTCTGTGT
* *
13089 GGTTATCAAAATTTCGTAAGATGGTTATTATAATTTCATGAGGA
1 GGTTATCAAAATTTCATAAGATGGTTATTAAAATTTCAT-AGGA
* **
13133 GGTTATCAAATTTTCAT-AG-TGTGCTTACCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATAAGATG-G-TTATTAAAATTTCATA-GGA
* * * *
13177 AGTTATCAAAATTTCATAGGAAGGTTATTAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAAGATGGTTATTAAAATTTCATAG-GA
* *
13221 GGTTACCAAAATTTCATAGGATCAGGTTATTAAAATTTC-TCAGGAA
1 GGTTATCAAAATTTCATAAGAT--GGTTATTAAAATTTCAT-AGG-A
** ** *
13267 GGTTATTGAAATTTCAT-AG-T-GTGGTT---A--TCA-AAGA
1 GGTTATCAAAATTTCATAAGATGGTTATTAAAATTTCATAGGA
* * *
13301 GATTATCAAAATGTCATAACGA-GGTTA-TAAGAATTTCATA--T
1 GGTTATCAAAATTTCATAA-GATGGTTATTAA-AATTTCATAGGA
* * * * *
13342 GGTTAACAAAATTTCATAAGAAGGTTACTAATATTTCATTGGGA
1 GGTTATCAAAATTTCATAAGATGGTTATTAAAATTTCA-TAGGA
* ** * *
13386 GGTTATCAAAATTTCATATGAAAGTTATAAAAGTCTCAATTTCGTAAGGA
1 GGTTATCAAAATTTCATAAGATGGTTAT-TAA-----AATTTCAT-AGGA
* * * * *
13436 -G-TACCAAAATTTGAT-AGAAGGTTA-TCAAATCTCATA-GA
1 GGTTATCAAAATTTCATAAGATGGTTATTAAAATTTCATAGGA
* * *
13474 GTGATTATC-GAA--TCACAGAGATCGGATTATCAAAATTT-ATAGGAA
1 G-G-TTATCAAAATTTCATA-AGAT-GG-TTATTAAAATTTCATAGG-A
* * * *
13519 GATTATCAAAATTTCAT-AGAGTTGTTATCAAAATTTCAAAGCGA
1 GGTTATCAAAATTTCATAAGA-TGGTTATTAAAATTTCATAG-GA
* * *
13563 GGTTATCAAAATTACAT-AG-TGTGATTATCAAAATTTCATAGAGG
1 GGTTATCAAAATTTCATAAGATG-G-TTATTAAAATTTCATAG-GA
* * * * *
13607 GGTCAACAAAATTTTATAGAGA-GGTTATCAAAATTTCATAAAGA
1 GGTTATCAAAATTTCATA-AGATGGTTATTAAAATTTCAT-AGGA
* ** *
13651 GGTTATCAAATTTTCA-AA-ATGTGATTACCAAAATTTCATA-GT
1 GGTTATCAAAATTTCATAAGATG-G-TTATTAAAATTTCATAGGA
* * *
13693 GG---T----ATTTC-TGGAGA-GGTTATCAAAATTTCATAGTA
1 GGTTATCAAAATTTCAT-AAGATGGTTATTAAAATTTCATAGGA
* * * * *
13728 TGGTTA-CCAAA--T--TAGGAAGGTTATTAAACTTTTATTATGGA
1 -GGTTATCAAAATTTCATAAGATGGTTATTAAAATTTCA-TA-GGA
* * * ** *
13769 -GTAATCAAAATTTCAT-GGA-GGATAACAAAATTTCATATGAA
1 GGTTATCAAAATTTCATAAGATGGTTATTAAAATTTCATA-GGA
* * *
13810 GGTTATCAAAATTTCAT-AGTTTAGTT-TTCAAAATTTCATAAGA
1 GGTTATCAAAATTTCATAAG-ATGGTTATT-AAAATTTCATAGGA
* *
13853 GGGTTATCAAAATTTCAT-AGTAT-GTAGATAAAAATTTCATAGGGAGA
1 -GGTTATCAAAATTTCATAAG-ATGGT-TATTAAAATTTCATA--G-GA
* * *
13900 GGTTATCAAAA-TT--T--G-TAGTTATCAAGATTTCATAAGGA
1 GGTTATCAAAATTTCATAAGATGGTTATTAAAATTTCAT-AGGA
* * * * *
13938 GATTATCAAAATTTTATAGGGA-GGTT-TGTCAAAATTTTATAAGAA
1 GGTTATCAAAATTTCATA-AGATGGTTAT-T-AAAATTTCAT-AGGA
*
13983 GGTTTATCAAAATTTCATAACGA-GGTTA-TAACAATTTCATAGTGT
1 GG-TTATCAAAATTTCATAA-GATGGTTATTAA-AATTTCATAG-GA
* * * * * *
14028 GATTATCAAAATTTCAGAGGGTGATTACTAACAA-TTCATATGGA
1 GGTTATCAAAATTTCATAAGATGGTTATTAA-AATTTCATA-GGA
* * * * * * * *
14072 GGTTTTTAAATTTTCATAATATGGTTATCAATATATCATATGTA
1 GGTTATCAAAATTTCATAAGATGGTTATTAAAATTTCATA-GGA
* * * * * *
14116 AGTTATCAACATCTCAT-AGATTAGTTATCAAAATTTCATTGGGA
1 GGTTATCAAAATTTCATAAGA-TGGTTATTAAAATTTCA-TAGGA
* * * * ** *
14160 GATCT-TTAAAATTTCTTAGGGA-GGTTAACAAAATTTCATAAGAA
1 GGT-TATCAAAATTTCATA-AGATGGTTATTAAAATTTCAT-AGGA
** * * ** * *
14204 GGTTAAAAAAAATTT-ATAA-AAGGTTCTCGAAATTCCATAGTA
1 GGTT-ATCAAAATTTCATAAGATGGTTATTAAAATTTCATAGGA
* * * * *
14246 TCGTTATGAAAATTTCATAGGAAGGTTATCAAAATTTCATAAGGA
1 -GGTTATCAAAATTTCATAAGATGGTTATTAAAATTTCAT-AGGA
*
14291 GGTCATCAAAA
1 GGTTATCAAAA
14302 ATAGTGTAAT
Statistics
Matches: 852, Mismatches: 194, Indels: 246
0.66 0.15 0.19
Matches are distributed among these distances:
34 29 0.03
35 8 0.01
36 8 0.01
37 3 0.00
38 17 0.02
39 24 0.03
40 29 0.03
41 48 0.06
42 62 0.07
43 66 0.08
44 397 0.47
45 58 0.07
46 72 0.08
47 9 0.01
48 12 0.01
49 2 0.00
50 8 0.01
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.35
Consensus pattern (43 bp):
GGTTATCAAAATTTCATAAGATGGTTATTAAAATTTCATAGGA
Found at i:13399 original size:22 final size:21
Alignment explanation
Indices: 13342--13417 Score: 62
Period size: 22 Copynumber: 3.5 Consensus size: 21
13332 AATTTCATAT
13342 GGTTAACAAAATTTCATAAGAA
1 GGTT-ACAAAATTTCATAAGAA
* ** *
13364 GGTTACTAATATTTCATTGGGA
1 GGTTAC-AAAATTTCATAAGAA
*
13386 GGTTATCAAAATTTCATATGAA
1 GGTTA-CAAAATTTCATAAGAA
* *
13408 AGTTATAAAA
1 GGTTACAAAA
13418 GTCTCAATTT
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
21 6 0.14
22 35 0.83
23 1 0.02
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.34
Consensus pattern (21 bp):
GGTTACAAAATTTCATAAGAA
Found at i:13546 original size:22 final size:22
Alignment explanation
Indices: 13440--14301 Score: 202
Period size: 22 Copynumber: 39.2 Consensus size: 22
13430 TAAGGAGTAC
*
13440 CAAAATTTGATAGA-AGGTTAT
1 CAAAATTTCATAGAGAGGTTAT
* * *
13461 C-AAATCTCATAGAGTGATTAT
1 CAAAATTTCATAGAGAGGTTAT
* *
13482 C-GAA--TCACAGAGATCGGATTAT
1 CAAAATTTCATAGAGA--GG-TTAT
*
13504 CAAAATTT-ATAG-GAAGATTAT
1 CAAAATTTCATAGAG-AGGTTAT
**
13525 CAAAATTTCATAGAGTTGTTAT
1 CAAAATTTCATAGAGAGGTTAT
* *
13547 CAAAATTTCAAAGCGAGGTTAT
1 CAAAATTTCATAGAGAGGTTAT
* * * *
13569 CAAAATTACATAGTGTGATTAT
1 CAAAATTTCATAGAGAGGTTAT
* * *
13591 CAAAATTTCATAGAGGGGTCAA
1 CAAAATTTCATAGAGAGGTTAT
*
13613 CAAAATTTTATAGAGAGGTTAT
1 CAAAATTTCATAGAGAGGTTAT
*
13635 CAAAATTTCATAAAGAGGTTAT
1 CAAAATTTCATAGAGAGGTTAT
* * * * *
13657 CAAATTTTCA-AAATGTGATTAC
1 CAAAATTTCATAGA-GAGGTTAT
* *
13679 CAAAATTTCAT--AGTGGTATTT
1 CAAAATTTCATAGAGAGGT-TAT
**
13700 CTGGAGAGGTTATCA-A-A-A--TT-T
1 C---A-AAATT-TCATAGAGAGGTTAT
*
13721 CATAGTATGGTTACCAAATTAG-GAAGGTTAT
1 CA-A-AAT--TT--C--A-TAGAG-AGGTTAT
* * * *
13752 TAAACTTTTATTATG-GA-GTAAT
1 CAAAATTTCA-TA-GAGAGGTTAT
* *
13774 CAAAATTTCAT-G-GAGGATAA
1 CAAAATTTCATAGAGAGGTTAT
13794 CAAAATTTCATATGA-AGGTTAT
1 CAAAATTTCATA-GAGAGGTTAT
** *
13816 CAAAATTTCATAGTTTA-GTTTT
1 CAAAATTTCATAG-AGAGGTTAT
13838 CAAAATTTCATA-AGAGGGTTAT
1 CAAAATTTCATAGAGA-GGTTAT
* * *
13860 CAAAATTTCATAG-TATGTAGAT
1 CAAAATTTCATAGAGAGGT-TAT
*
13882 AAAAATTTCATAGGGAGAGGTTAT
1 CAAAATTTCATA--GAGAGGTTAT
*
13906 CAAAA-TT--T-G-TA-GTTAT
1 CAAAATTTCATAGAGAGGTTAT
* *
13922 CAAGATTTCATA-AGGAGATTAT
1 CAAAATTTCATAGA-GAGGTTAT
* * *
13944 CAAAATTTTATAGGGAGGTTTGT
1 CAAAATTTCATAGAGAGG-TTAT
*
13967 CAAAATTTTATA-AGAAGGTTTAT
1 CAAAATTTCATAGAG-AGG-TTAT
13990 CAAAATTTCATA-ACGAGGTTAT
1 CAAAATTTCATAGA-GAGGTTAT
* * *
14012 -AACAATTTCATAGTGTGATTAT
1 CAA-AATTTCATAGAGAGGTTAT
* * * *
14034 CAAAATTTCAGAGGGTGATTA-
1 CAAAATTTCATAGAGAGGTTAT
*
14055 CTAACAA-TTCATATG-GAGGTTTT
1 C-AA-AATTTCATA-GAGAGGTTAT
* * *
14078 TAAATTTTCATA-ATATGGTTAT
1 CAAAATTTCATAGAGA-GGTTAT
* *
14100 CAATATATCATATGTA-A-GTTAT
1 CAAAATTTCATA-G-AGAGGTTAT
* * *
14122 CAACATCTCATAGATTA-GTTAT
1 CAAAATTTCATAGA-GAGGTTAT
* * *
14144 CAAAATTTCATTGGGAGATCT-T
1 CAAAATTTCATAGAGAGGT-TAT
* * * *
14166 TAAAATTTCTTAGGGAGGTTAA
1 CAAAATTTCATAGAGAGGTTAT
*
14188 CAAAATTTCATA-AGAAGGTTAAA
1 CAAAATTTCATAGAG-AGGTT-AT
* * *
14211 AAAAATTT-ATA-AAAGGTTCT
1 CAAAATTTCATAGAGAGGTTAT
* * **
14231 CGAAATTCCATAGTA-TCGTTAT
1 CAAAATTTCATAG-AGAGGTTAT
*
14253 GAAAATTTCATAG-GAAGGTTAT
1 CAAAATTTCATAGAG-AGGTTAT
*
14275 CAAAATTTCATA-AGGAGGTCAT
1 CAAAATTTCATAGA-GAGGTTAT
14297 CAAAA
1 CAAAA
14302 ATAGTGTAAT
Statistics
Matches: 618, Mismatches: 137, Indels: 171
0.67 0.15 0.18
Matches are distributed among these distances:
16 9 0.01
17 3 0.00
18 3 0.00
19 12 0.02
20 35 0.06
21 54 0.09
22 396 0.64
23 67 0.11
24 17 0.03
25 8 0.01
26 5 0.01
27 2 0.00
28 1 0.00
29 1 0.00
30 3 0.00
31 2 0.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATAGAGAGGTTAT
Found at i:14008 original size:23 final size:23
Alignment explanation
Indices: 13918--14023 Score: 110
Period size: 23 Copynumber: 4.7 Consensus size: 23
13908 AAATTTGTAG
* *
13918 TTATCAAGATTTCATAAGGA-GA
1 TTATCAAAATTTCATAAGGAGGT
* *
13940 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTCATAAGGAGGT
* * *
13963 TTGTCAAAATTTTATAAGAAGGT
1 TTATCAAAATTTCATAAGGAGGT
*
13986 TTATCAAAATTTCATAACGAGG-
1 TTATCAAAATTTCATAAGGAGGT
14008 TTAT-AACAATTTCATA
1 TTATCAA-AATTTCATA
14024 GTGTGATTAT
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
21 2 0.03
22 30 0.42
23 39 0.55
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (23 bp):
TTATCAAAATTTCATAAGGAGGT
Found at i:23821 original size:29 final size:30
Alignment explanation
Indices: 23763--23840 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 30
23753 ATCGTTTGAG
23763 AGGGGACAAAAAGTCCAAAATTGAGAGTTC
1 AGGGGACAAAAAGTCCAAAATTGAGAGTTC
* *
23793 AGGGGACAAAATGTTCAAAATTGA-AGTTC
1 AGGGGACAAAAAGTCCAAAATTGAGAGTTC
* *
23822 A-AGGAGCAAAACGTCCAAA
1 AGGGGA-CAAAAAGTCCAAA
23841 CGCTACAAGT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
28 3 0.07
29 17 0.40
30 22 0.52
ACGTcount: A:0.45, C:0.14, G:0.24, T:0.17
Consensus pattern (30 bp):
AGGGGACAAAAAGTCCAAAATTGAGAGTTC
Found at i:30461 original size:21 final size:21
Alignment explanation
Indices: 30432--30478 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
30422 GTTGCGTGCT
*
30432 TCTCAATTGGCACTTCAACAA
1 TCTCTATTGGCACTTCAACAA
30453 TCTCTATTGGCACTTCAACAA
1 TCTCTATTGGCACTTCAACAA
30474 TCTCT
1 TCTCT
30479 GGAAACCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.34
Consensus pattern (21 bp):
TCTCTATTGGCACTTCAACAA
Found at i:32099 original size:18 final size:17
Alignment explanation
Indices: 32076--32109 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
32066 TTAGGAAAAT
32076 CTAGAAGAAAAACTAGAA
1 CTAGAAGAAAAA-TAGAA
32094 CTAGAAGAAAAATAGA
1 CTAGAAGAAAAATAGA
32110 TGAAGAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.62, C:0.09, G:0.18, T:0.12
Consensus pattern (17 bp):
CTAGAAGAAAAATAGAA
Found at i:32742 original size:30 final size:30
Alignment explanation
Indices: 32685--32745 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
32675 CAATTCTTGC
**
32685 TTCTTGAAATAATTCTTCATTGGTCTTCAA
1 TTCTTGAAATAATTCTTCATTAATCTTCAA
*
32715 TTCTTGAAATTA-TCTTCAATTAATCTTCAA
1 TTCTTGAAATAATTCTTC-ATTAATCTTCAA
32745 T
1 T
32746 CACGAACTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 5 0.19
30 22 0.81
ACGTcount: A:0.30, C:0.16, G:0.07, T:0.48
Consensus pattern (30 bp):
TTCTTGAAATAATTCTTCATTAATCTTCAA
Done.