Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011968.1 Corchorus olitorius cultivar O-4 contig12001, 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: 63826
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:13 original size:2 final size:2
Alignment explanation
Indices: 7--73 Score: 116
Period size: 2 Copynumber: 33.5 Consensus size: 2
1 TACTTA
7 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* *
49 TC TC TC TC TC TC TC AC TC AC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
74 GTTCATTCTG
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.03, C:0.49, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:3367 original size:21 final size:21
Alignment explanation
Indices: 3343--3383 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3333 TGGAACCCTT
3343 TTGGATTCAAGTGGTACAAAA
1 TTGGATTCAAGTGGTACAAAA
* *
3364 TTGGATTTAAGTGGTTCAAA
1 TTGGATTCAAGTGGTACAAA
3384 TTAGGGTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.34
Consensus pattern (21 bp):
TTGGATTCAAGTGGTACAAAA
Found at i:8779 original size:38 final size:40
Alignment explanation
Indices: 8676--8791 Score: 168
Period size: 39 Copynumber: 3.0 Consensus size: 40
8666 GCTTAATGAA
*
8676 TTTTATTAATTTCCAAAATCTTCTTTTGGGA-TATCTTAAAC
1 TTTTATT--TTTCCAAAATCTTCTTTTGGAATTATCTTAAAC
*
8717 TTTTATTTTTCCAAAATCTGCTTTTGGAATTATC-TAAAC
1 TTTTATTTTTCCAAAATCTTCTTTTGGAATTATCTTAAAC
8756 TTTTA-TTTTCCAAAATCTTCTTTTGGAATTA-CTTAA
1 TTTTATTTTTCCAAAATCTTCTTTTGGAATTATCTTAA
8792 TTAAAAACAC
Statistics
Matches: 70, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
37 1 0.01
38 28 0.40
39 30 0.43
40 4 0.06
41 7 0.10
ACGTcount: A:0.28, C:0.15, G:0.07, T:0.50
Consensus pattern (40 bp):
TTTTATTTTTCCAAAATCTTCTTTTGGAATTATCTTAAAC
Found at i:13248 original size:5 final size:5
Alignment explanation
Indices: 13238--13267 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
13228 TATGATTAAG
13238 AAATA AAATA AAATA AAATA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA AAATA
13268 GCGTAGCTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:15004 original size:108 final size:105
Alignment explanation
Indices: 14805--15008 Score: 268
Period size: 108 Copynumber: 1.9 Consensus size: 105
14795 TTAGCTGATT
* * * *
14805 GGAAAATGATTGTTGAGCTAGAAGAGTAAGTGGTCATATGATTTTGATTTTGTTTTCTCTGTGTG
1 GGAAAAGGATTGTTGAGCTAGAAGACTAAGTGATCATAAGATTTTGATTTTGTTTTCTCTGTGTG
* * *
14870 GTTATCAAAATTTTATATTGAGATTATCAAACTTTCAGGA
66 GTTATCAAAATTTAATAGTGAAATTATCAAACTTTCAGGA
* *
14910 GGAAAAGGATTGTTGAGCTAGAAAAGTGACTAAGTGATCCTAAGA-TTTGATTTTGTTCTT-TTT
1 GGAAAAGGATTGTTGAGCTAG--AA--GACTAAGTGATCATAAGATTTTGATTTTGTT-TTCTCT
14973 GTGTGGTTATCAAAATTTAATAGTGAAATTATCAAA
61 GTGTGGTTATCAAAATTTAATAGTGAAATTATCAAA
15009 AGTTTACAAG
Statistics
Matches: 85, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
105 20 0.24
107 2 0.02
108 47 0.55
109 16 0.19
ACGTcount: A:0.32, C:0.07, G:0.22, T:0.39
Consensus pattern (105 bp):
GGAAAAGGATTGTTGAGCTAGAAGACTAAGTGATCATAAGATTTTGATTTTGTTTTCTCTGTGTG
GTTATCAAAATTTAATAGTGAAATTATCAAACTTTCAGGA
Found at i:15041 original size:22 final size:21
Alignment explanation
Indices: 15016--15219 Score: 86
Period size: 22 Copynumber: 9.7 Consensus size: 21
15006 AAAAGTTTAC
15016 AAGGAGGTTATCATAATTTCAT
1 AAGGAGGTTATCA-AATTTCAT
*
15038 -A--AGGTTATTTAAATTTCAT
1 AAGGAGGTTA-TCAAATTTCAT
*
15057 -AGTGTGG---TCAAATTTCAT
1 AAG-GAGGTTATCAAATTTCAT
*
15075 AAGGAGGTTATCACAATTTTAT
1 AAGGAGGTTATCA-AATTTCAT
** * * *
15097 ATTGTGATTATCAAAATTCAT
1 AAGGAGGTTATCAAATTTCAT
*
15118 -AGTGTGGTTATCAGAATTTC-T
1 AAG-GAGGTTATCA-AATTTCAT
* *
15139 TAGGAACGTTATCAGAATTTCAT
1 AAGG-AGGTTATCA-AATTTCAT
* *
15162 AGAGTA-TTTATCAAAATTTCAT
1 A-AGGAGGTTATC-AAATTTCAT
** *
15184 AAAAAAGTTATCAAAATTTCAT
1 AAGGAGGTTATC-AAATTTCAT
*
15206 AGGGAGGTTATCAA
1 AAGGAGGTTATCAA
15220 CGAGTTTATC
Statistics
Matches: 138, Mismatches: 27, Indels: 35
0.69 0.14 0.17
Matches are distributed among these distances:
18 13 0.09
19 17 0.12
20 2 0.01
21 25 0.18
22 76 0.55
23 3 0.02
24 2 0.01
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (21 bp):
AAGGAGGTTATCAAATTTCAT
Found at i:15128 original size:21 final size:21
Alignment explanation
Indices: 15052--15135 Score: 59
Period size: 21 Copynumber: 4.1 Consensus size: 21
15042 TTATTTAAAT
*
15052 TTCATAGTGTGG---TCAAAT
1 TTCATAGTGTGGTTATCAAAA
* *
15070 TTCATAAG-GAGGTTATCACAAT
1 TTCAT-AGTGTGGTTATCA-AAA
* * *
15092 TTTATATTGTGATTATCAAAA
1 TTCATAGTGTGGTTATCAAAA
*
15113 TTCATAGTGTGGTTATCAGAA
1 TTCATAGTGTGGTTATCAAAA
15134 TT
1 TT
15136 TCTTAGGAAC
Statistics
Matches: 50, Mismatches: 10, Indels: 9
0.72 0.14 0.13
Matches are distributed among these distances:
18 8 0.16
19 2 0.04
21 25 0.50
22 15 0.30
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (21 bp):
TTCATAGTGTGGTTATCAAAA
Found at i:15217 original size:44 final size:44
Alignment explanation
Indices: 15104--15219 Score: 119
Period size: 44 Copynumber: 2.7 Consensus size: 44
15094 TATATTGTGA
* * * * ** *
15104 TTATCAAAA-TTCATAGTGTGGTTATCAGAATTTCTTAGGAACG
1 TTATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAAAAAAG
* * *
15147 TTATCAGAATTTCATAGAGTA-TTTATCAAAATTTCATAAAAAAG
1 TTATCAAAATTTCATAG-GGAGGTTATCAAAATTTCATAAAAAAG
15191 TTATCAAAATTTCATAGGGAGGTTATCAA
1 TTATCAAAATTTCATAGGGAGGTTATCAA
15220 CGAGTTTATC
Statistics
Matches: 57, Mismatches: 13, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
43 10 0.18
44 47 0.82
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (44 bp):
TTATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAAAAAAG
Found at i:15250 original size:22 final size:22
Alignment explanation
Indices: 15225--15277 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
15215 ATCAACGAGT
15225 TTATCAAAATTTTATAGTGAGG
1 TTATCAAAATTTTATAGTGAGG
* * *
15247 TTATCAGAATTTTATGGTGTGG
1 TTATCAAAATTTTATAGTGAGG
15269 TTATCAAAA
1 TTATCAAAA
15278 ATTTCATCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.34, C:0.06, G:0.19, T:0.42
Consensus pattern (22 bp):
TTATCAAAATTTTATAGTGAGG
Found at i:15290 original size:23 final size:23
Alignment explanation
Indices: 15264--15307 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
15254 AATTTTATGG
15264 TGTGG-TTATCAAAAATTTCATCA
1 TGTGGTTTA-CAAAAATTTCATCA
*
15287 TGTGGTTTACCAAAATTTCAT
1 TGTGGTTTACAAAAATTTCAT
15308 AGGAAGGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (23 bp):
TGTGGTTTACAAAAATTTCATCA
Found at i:15352 original size:22 final size:23
Alignment explanation
Indices: 15327--15383 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
15317 AGAAAAACCT
15327 AAATTTCATAAG-G-ATCTTATCA
1 AAATTTCATAAGTGTA-CTTATCA
* *
15349 AAATTTTAT-AGTGTAGTTATCA
1 AAATTTCATAAGTGTACTTATCA
15371 AAATTTCATAAGT
1 AAATTTCATAAGT
15384 AAGTAATCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 2 0.07
22 23 0.79
23 4 0.14
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (23 bp):
AAATTTCATAAGTGTACTTATCA
Found at i:15392 original size:22 final size:22
Alignment explanation
Indices: 15327--15422 Score: 65
Period size: 22 Copynumber: 4.5 Consensus size: 22
15317 AGAAAAACCT
* * *
15327 AAATTTCATAAGGATCTTATCA
1 AAATTTCATAAGTAACTAATCA
* * * *
15349 AAATTTTAT-AGTGTAGTTATCA
1 AAATTTCATAAGT-AACTAATCA
*
15371 AAATTTCATAAGTAAGTAATCA
1 AAATTTCATAAGTAACTAATCA
* *
15393 AAATCTCAT-AG--ACTAATTA
1 AAATTTCATAAGTAACTAATCA
15412 AAATTTCATAA
1 AAATTTCATAA
15423 AAATCATATT
Statistics
Matches: 59, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
19 14 0.24
20 1 0.02
21 4 0.07
22 37 0.63
23 3 0.05
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.36
Consensus pattern (22 bp):
AAATTTCATAAGTAACTAATCA
Found at i:16950 original size:15 final size:16
Alignment explanation
Indices: 16918--16955 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
16908 GGTATTAAAT
16918 AAAACAATTAAAAAGA
1 AAAACAATTAAAAAGA
*
16934 AAAACAATT-AAACGA
1 AAAACAATTAAAAAGA
16949 AAAACAA
1 AAAACAA
16956 AGCAAAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.74, C:0.11, G:0.05, T:0.11
Consensus pattern (16 bp):
AAAACAATTAAAAAGA
Found at i:18889 original size:20 final size:20
Alignment explanation
Indices: 18861--18978 Score: 102
Period size: 20 Copynumber: 5.8 Consensus size: 20
18851 TTCATGAGAA
18861 AGTTATCAAAATTTCAGTCT
1 AGTTATCAAAATTTCAGTCT
* *
18881 AGTTTTCAAAATTTCA-T-A
1 AGTTATCAAAATTTCAGTCT
18899 AGGGTTATCAAAATTTCAGTCT
1 A--GTTATCAAAATTTCAGTCT
* *
18921 AGTTTTCAAAATTTCA-T-A
1 AGTTATCAAAATTTCAGTCT
18939 AGGGTTATCAAAATTTCA-TACCGT
1 A--GTTATCAAAATTTCAGT--C-T
18963 AGTTATCAAAATTTCA
1 AGTTATCAAAATTTCA
18979 TAGGGAGGTT
Statistics
Matches: 80, Mismatches: 8, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
18 2 0.03
19 2 0.03
20 58 0.73
21 1 0.01
22 16 0.20
24 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (20 bp):
AGTTATCAAAATTTCAGTCT
Found at i:18913 original size:40 final size:40
Alignment explanation
Indices: 18844--18980 Score: 195
Period size: 40 Copynumber: 3.3 Consensus size: 40
18834 AGCGAGGTTA
**
18844 TCAAAATTTCATGAGAAAGTTATCAAAATTTCAGTCTAGTTT
1 TCAAAATTTCAT-A-AGGGTTATCAAAATTTCAGTCTAGTTT
18886 TCAAAATTTCATAAGGGTTATCAAAATTTCAGTCTAGTTT
1 TCAAAATTTCATAAGGGTTATCAAAATTTCAGTCTAGTTT
*
18926 TCAAAATTTCATAAGGGTTATCAAAATTTCA-TACCGTAGTTA
1 TCAAAATTTCATAAGGGTTATCAAAATTTCAGT--C-TAGTTT
18968 TCAAAATTTCATA
1 TCAAAATTTCATA
18981 GGGAGGTTAA
Statistics
Matches: 89, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
39 1 0.01
40 56 0.63
41 2 0.02
42 30 0.34
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (40 bp):
TCAAAATTTCATAAGGGTTATCAAAATTTCAGTCTAGTTT
Found at i:18980 original size:22 final size:21
Alignment explanation
Indices: 18710--19133 Score: 158
Period size: 22 Copynumber: 19.7 Consensus size: 21
18700 CACAGTGTGC
* *
18710 TTATCAAAATTTCATAAGAAGG
1 TTATCAAAATTTCATACGTA-G
* *
18732 TTA--GAAATTTCATA-TTATG
1 TTATCAAAATTTCATACGTA-G
* *
18751 ATTATCAAAATTTCATAAAAGCAG
1 -TTATCAAAATTTCAT--ACGTAG
* * *
18775 TTAACAAAATTTCATATGGTTG
1 TTATCAAAATTTCATA-CGTAG
* * * *
18797 TTACCAAAATTTTATATGAAGG
1 TTATCAAAATTTCATACGTA-G
* *
18819 TTATTAAAATTTCACAGCG-AGG
1 TTATCAAAATTTCATA-CGTA-G
*
18841 TTATCAAAATTTCATGA-GAAAG
1 TTATCAAAATTTCAT-ACG-TAG
18863 TTATCAAAATTTCAGT-C-TAG
1 TTATCAAAATTTCA-TACGTAG
* * *
18883 TTTTCAAAATTTCATAAG-GG
1 TTATCAAAATTTCATACGTAG
18903 TTATCAAAATTTCAGT-C-TAG
1 TTATCAAAATTTCA-TACGTAG
* * *
18923 TTTTCAAAATTTCATAAG-GG
1 TTATCAAAATTTCATACGTAG
18943 TTATCAAAATTTCATACCGTAG
1 TTATCAAAATTTCATA-CGTAG
* *
18965 TTATCAAAATTTCATAGGGAGG
1 TTATCAAAATTTCATACGTA-G
* * *
18987 TTAACAAAATATCATA-ATGAGG
1 TTATCAAAATTTCATACGT-A-G
** * *
19009 TTATCAAAAAATCATAGGGAGG
1 TTATCAAAATTTCATACGTA-G
* * *
19031 TTATCAAAGTTTCATAAGGAGG
1 TTATCAAAATTTCATACGTA-G
* * *
19053 TTATCAAAATTTTATAGGAATG
1 TTATCAAAATTTCATACGTA-G
*
19075 TTTATCAGAATTTCATA-GTGAGG
1 -TTATCAAAATTTCATACGT-A-G
*
19098 TTATCACAAA-TTCATA-GTTTG
1 TTATCA-AAATTTCATACG-TAG
19119 ATTATCAAAATTTCA
1 -TTATCAAAATTTCA
19134 CAGGGTGATT
Statistics
Matches: 310, Mismatches: 61, Indels: 62
0.72 0.14 0.14
Matches are distributed among these distances:
19 4 0.01
20 72 0.23
21 11 0.04
22 183 0.59
23 37 0.12
24 2 0.01
25 1 0.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (21 bp):
TTATCAAAATTTCATACGTAG
Found at i:19142 original size:22 final size:21
Alignment explanation
Indices: 18774--19267 Score: 226
Period size: 22 Copynumber: 22.9 Consensus size: 21
18764 CATAAAAGCA
* *
18774 GTTAACAAAATTTCATATGGTT
1 GTTATCAAAATTTCATA-GGGT
* * *
18796 GTTACCAAAATTTTATATGAAG-
1 GTTATCAAAATTTCATA-G-GGT
* *
18818 GTTATTAAAATTTCACAGCGAG-
1 GTTATCAAAATTTCATAG-G-GT
***
18840 GTTATCAAAATTTCATGAGAAA
1 GTTATCAAAATTTCAT-AGGGT
**
18862 GTTATCAAAATTTC--AGTCT
1 GTTATCAAAATTTCATAGGGT
* *
18881 AGTTTTCAAAATTTCATAAGG-
1 -GTTATCAAAATTTCATAGGGT
**
18902 GTTATCAAAATTTC--AGTCT
1 GTTATCAAAATTTCATAGGGT
* *
18921 AGTTTTCAAAATTTCATAAGG-
1 -GTTATCAAAATTTCATAGGGT
**
18942 GTTATCAAAATTTCATACCGT
1 GTTATCAAAATTTCATAGGGT
*
18963 AGTTATCAAAATTTCATAGGGAG
1 -GTTATCAAAATTTCATAGGG-T
* * *
18986 GTTAACAAAATATCATAATGAG-
1 GTTATCAAAATTTCAT-A-GGGT
** *
19008 GTTATCAAAAAATCATAGGGAG
1 GTTATCAAAATTTCATAGGG-T
*
19030 GTTATCAAAGTTTCATAAGGAG-
1 GTTATCAAAATTTCAT-AGG-GT
* *
19052 GTTATCAAAATTTTATAGGAAT
1 GTTATCAAAATTTCATAGG-GT
*
19074 GTTTATCAGAATTTCATAGTGAG-
1 G-TTATCAAAATTTCATAG-G-GT
**
19097 GTTATCACAAA-TTCATAGTTT
1 GTTATCA-AAATTTCATAGGGT
*
19118 GATTATCAAAATTTCACAGGGT
1 G-TTATCAAAATTTCATAGGGT
* *
19140 GATTA-CTAACATTTTATAGGAG-
1 G-TTATC-AAAATTTCATAGG-GT
* *
19162 GTAATCAAAATTTCATAGTGTT
1 GTTATCAAAATTTCATAG-GGT
* * *
19184 CTTACCAACATTTCATAGGGAT
1 GTTATCAAAATTTCATAGGG-T
* *
19206 GTTATCAAAATTTTATAGTGT
1 GTTATCAAAATTTCATAGGGT
19227 GGTTATCAAAATTTCATTAGGAG-
1 -GTTATCAAAATTTCA-TAGG-GT
*
19250 GTTAGCAAAATTTCATAG
1 GTTATCAAAATTTCATAG
19268 TAAGATTTTC
Statistics
Matches: 360, Mismatches: 76, Indels: 73
0.71 0.15 0.14
Matches are distributed among these distances:
18 1 0.00
19 2 0.01
20 58 0.16
21 28 0.08
22 237 0.66
23 28 0.08
24 6 0.02
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (21 bp):
GTTATCAAAATTTCATAGGGT
Found at i:19263 original size:66 final size:65
Alignment explanation
Indices: 18648--19315 Score: 334
Period size: 66 Copynumber: 10.2 Consensus size: 65
18638 CTATTTAGCC
* * ** ** * * * *
18648 AAATTTCATATGGTGGTTATCTAAATTTCCCAATGAGGTTATCAAAATTTTTCACAGTGTGCTTA
1 AAATTTCATA-GGAGGTTATCAAAATTTCATAGGGATGTTATCAAAA--TTTCATAGTGAGGTTA
18713 TCA
63 TCA
* * ** **
18716 AAATTTCATAAGAAGGTTA--GAAATTTCATA-TTATGATTATCAAAATTTCATA-AAAGCAGTT
1 AAATTTCAT-AGGAGGTTATCAAAATTTCATAGGGATG-TTATCAAAATTTCATAGTGAG--GTT
*
18777 AACA
62 ATCA
** * * * * * * * *
18781 AAATTTCATATGGTTGTTACCAAAATTTTATATGAAGGTTATTAAAATTTCACAGCGAGGTTATC
1 AAATTTCATA-GGAGGTTATCAAAATTTCATAGGGATGTTATCAAAATTTCATAGTGAGGTTATC
18846 A
65 A
* * ** * *
18847 AAATTTCATGAGAAAGTTATCAAAATTTC--A-GTCTAGTTTTCAAAATTTCATA-AG-GGTTAT
1 AAATTTCAT-AGGAGGTTATCAAAATTTCATAGGGAT-GTTATCAAAATTTCATAGTGAGGTTAT
18907 CA
64 CA
** * *
18909 AAATTTCAGT-CTA-GTTTTCAAAATTTCATAAGG--GTTATCAAAATTTCATACCGT-A-GTTA
1 AAATTTCA-TAGGAGGTTATCAAAATTTCATAGGGATGTTATCAAAATTTCATA--GTGAGGTTA
18968 TCA
63 TCA
* * ** * ** *
18971 AAATTTCATAGGGAGGTTAACAAAATATCATAATGAGGTTATCAAAAAATCATAGGGAGGTTATC
1 AAATTTCATA-GGAGGTTATCAAAATTTCATAGGGATGTTATCAAAATTTCATAGTGAGGTTATC
19036 A
65 A
* * * *
19037 AAGTTTCATAAGGAGGTTATCAAAATTTTATAGGAATGTTTATCAGAATTTCATAGTGAGGTTAT
1 AAATTTCAT-AGGAGGTTATCAAAATTTCATAGGGATG-TTATCAAAATTTCATAGTGAGGTTAT
19102 CA
64 CA
** * * * * *
19104 CAAA-TTCATAGTTTGATTATCAAAATTTCACAGGG-TGATTA-CTAACATTTTATAG-GAGGTA
1 -AAATTTCATAG-GAGGTTATCAAAATTTCATAGGGATG-TTATC-AAAATTTCATAGTGAGGTT
19165 ATCA
62 ATCA
*** * * * *
19169 AAATTTCATAGTGTTCTTACCAACATTTCATAGGGATGTTATCAAAATTTTATAGTGTGGTTATC
1 AAATTTCATAG-GAGGTTATCAAAATTTCATAGGGATGTTATCAAAATTTCATAGTGAGGTTATC
19234 A
65 A
* * * * * *
19235 AAATTTCATTAGGAGGTTAGCAAAATTTCATAGTAAGAT-TT-TCAAAATTCCATTGGGAAGTTA
1 AAATTTCA-TAGGAGGTTATCAAAATTTCATAG--GGATGTTATCAAAATTTCATAGTGAGGTTA
*
19298 ACA
63 TCA
19301 AAATTTCATAAGGAG
1 AAATTTCAT-AGGAG
19316 AATATTGAAA
Statistics
Matches: 462, Mismatches: 99, Indels: 80
0.72 0.15 0.12
Matches are distributed among these distances:
60 29 0.06
61 2 0.00
62 32 0.07
63 6 0.01
64 42 0.09
65 73 0.16
66 177 0.38
67 76 0.16
68 24 0.05
69 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (65 bp):
AAATTTCATAGGAGGTTATCAAAATTTCATAGGGATGTTATCAAAATTTCATAGTGAGGTTATCA
Found at i:19268 original size:44 final size:43
Alignment explanation
Indices: 18648--19310 Score: 409
Period size: 44 Copynumber: 15.2 Consensus size: 43
18638 CTATTTAGCC
* *
18648 AAATTTCATA-TGGTGGTTATCTAAATTTCCCA-ATGAGGTTATCA
1 AAATTTCATAGT-GTGGTTATCAAAATTT--CATAGGAGGTTATCA
* * * *
18692 AAATTTTTCACAGTGTGCTTATCAAAATTTCATAAGAAGGTTA--G
1 AAA--TTTCATAGTGTGGTTATCAAAATTTCAT-AGGAGGTTATCA
* * * ** *
18736 AAATTTCATATTATGATTATCAAAATTTCATAAAAGCAGTTAACA
1 AAATTTCATAGTGTGGTTATCAAAATTTCATAGGAG--GTTATCA
* * * * *
18781 AAATTTCATA-TGGTTGTTACCAAAATTTTATATGAAGGTTATTA
1 AAATTTCATAGT-GTGGTTATCAAAATTTCATA-GGAGGTTATCA
* * * * *
18825 AAATTTCACAGCGAGGTTATCAAAATTTCATGAGAAAGTTATCA
1 AAATTTCATAGTGTGGTTATCAAAATTTCAT-AGGAGGTTATCA
* * * *
18869 AAATTTC--AGTCTAGTTTTCAAAATTTCATAAG-GGTTATCA
1 AAATTTCATAGTGTGGTTATCAAAATTTCATAGGAGGTTATCA
* * * *
18909 AAATTTC--AGTCTAGTTTTCAAAATTTCATAAG-GGTTATCA
1 AAATTTCATAGTGTGGTTATCAAAATTTCATAGGAGGTTATCA
** * *
18949 AAATTTCATACCGTAGTTATCAAAATTTCATAGGGAGGTTAACA
1 AAATTTCATAGTGTGGTTATCAAAATTTCATA-GGAGGTTATCA
* * * **
18993 AAATATCATAATGAGGTTATCAAAAAATCATAGGGAGGTTATCA
1 AAATTTCATAGTGTGGTTATCAAAATTTCATA-GGAGGTTATCA
* * * *
19037 AAGTTTCATAAG-GAGGTTATCAAAATTTTATAGGAATGTTTATCA
1 AAATTTCAT-AGTGTGGTTATCAAAATTTCATAGG-A-GGTTATCA
* * ** *
19082 GAATTTCATAGTGAGGTTATCACAAA-TTCATAGTTTGATTATCA
1 AAATTTCATAGTGTGGTTATCA-AAATTTCATAG-GAGGTTATCA
* * * * * *
19126 AAATTTCACAGGGTGATTA-CTAACATTTTATAGGAGGTAATCA
1 AAATTTCATAGTGTGGTTATC-AAAATTTCATAGGAGGTTATCA
** * * *
19169 AAATTTCATAGTGTTCTTACCAACATTTCATAGGGATGTTATCA
1 AAATTTCATAGTGTGGTTATCAAAATTTCATA-GGAGGTTATCA
* *
19213 AAATTTTATAGTGTGGTTATCAAAATTTCATTAGGAGGTTAGCA
1 AAATTTCATAGTGTGGTTATCAAAATTTCA-TAGGAGGTTATCA
** * * * * * *
19257 AAATTTCATAGTAAGATTTTCAAAATTCCATTGGGAAGTTAACA
1 AAATTTCATAGTGTGGTTATCAAAATTTCA-TAGGAGGTTATCA
19301 AAATTTCATA
1 AAATTTCATA
19311 AGGAGAATAT
Statistics
Matches: 494, Mismatches: 97, Indels: 56
0.76 0.15 0.09
Matches are distributed among these distances:
40 54 0.11
41 5 0.01
42 60 0.12
43 41 0.08
44 241 0.49
45 59 0.12
46 33 0.07
47 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (43 bp):
AAATTTCATAGTGTGGTTATCAAAATTTCATAGGAGGTTATCA
Found at i:19561 original size:14 final size:16
Alignment explanation
Indices: 19531--19569 Score: 55
Period size: 14 Copynumber: 2.5 Consensus size: 16
19521 GTGTTGAATT
19531 AATTAAATTATTAAAA
1 AATTAAATTATTAAAA
19547 AATT-AATTA-TAAAA
1 AATTAAATTATTAAAA
19561 AATTTAAAT
1 AA-TTAAAT
19570 CCAAGTAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 7 0.33
15 7 0.33
16 7 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AATTAAATTATTAAAA
Found at i:28845 original size:13 final size:13
Alignment explanation
Indices: 28826--28861 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
28816 TTCAAATTTA
28826 ATAAAATTTTATT
1 ATAAAATTTTATT
* *
28839 TTAAAATTTAATT
1 ATAAAATTTTATT
28852 ATAAAATTTT
1 ATAAAATTTT
28862 TCAATTTAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
ATAAAATTTTATT
Found at i:29583 original size:22 final size:21
Alignment explanation
Indices: 29558--29813 Score: 108
Period size: 22 Copynumber: 11.7 Consensus size: 21
29548 TTGATAGTTT
29558 GGTTATCAAAATTGTATAGGGA
1 GGTTATCAAAATT-TATAGGGA
** * *
29580 GGTTATCGTAATTTCTCAGTGTA
1 GGTTATCAAAATTTAT-AG-GGA
*
29603 -GTTATCAAAATTTTATA-GTA
1 GGTTATCAAAA-TTTATAGGGA
*
29623 TGGTTTTCAAAATTTCATAGGGA
1 -GGTTATCAAAATTT-ATAGGGA
* * * *
29646 GATTAACAAAATTCTGTAAGGA
1 GGTTATCAAAATT-TATAGGGA
* *
29668 TGTTATCAAAAATTCATAGGGA
1 GGTTATC-AAAATTTATAGGGA
* * *
29690 GGATATAAAAATTTCACAGGGTA
1 GGTTATCAAAATTT-ATAGGG-A
* *
29713 -ATTATCAAAATTTCAT-GAGGT
1 GGTTATCAAAATTT-ATAG-GGA
* *
29734 GGTTATCGAAATTTCATGGGGA
1 GGTTATCAAAATTT-ATAGGGA
* **
29756 GATTATCAAAATTTCA-AAAGA
1 GGTTATCAAAATTT-ATAGGGA
**
29777 GGGTTATCAAAATTTTATAATGA
1 -GGTTATCAAAA-TTTATAGGGA
*
29800 GGTTATCACAATTT
1 GGTTATCAAAATTT
29814 GAGGAAAACC
Statistics
Matches: 176, Mismatches: 41, Indels: 35
0.70 0.16 0.14
Matches are distributed among these distances:
20 3 0.02
21 17 0.10
22 132 0.75
23 24 0.14
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (21 bp):
GGTTATCAAAATTTATAGGGA
Found at i:29601 original size:66 final size:66
Alignment explanation
Indices: 29493--29646 Score: 179
Period size: 66 Copynumber: 2.3 Consensus size: 66
29483 TAAGAGGGAT
* * *
29493 GTTATCAAAATTTCATTGTGG-GGTAATC-TAAATTTCTTAGTGTAGTTAAAAAAAATTGATAGT
1 GTTATCAAAATTTCATAG-GGAGGTTATCGT-AATTTCTCAGTGTAGTTAAAAAAAATTGATAGT
*
29556 TTG
64 ATG
** * *
29559 GTTATCAAAATTGT-ATAGGGAGGTTATCGTAATTTCTCAGTGTAGTTATCAAAATTTTATAGTA
1 GTTATCAAAATT-TCATAGGGAGGTTATCGTAATTTCTCAGTGTAGTTAAAAAAAATTGATAGTA
29623 TG
65 TG
*
29625 GTTTTCAAAATTTCATAGGGAG
1 GTTATCAAAATTTCATAGGGAG
29647 ATTAACAAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
65 3 0.04
66 70 0.93
67 2 0.03
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.40
Consensus pattern (66 bp):
GTTATCAAAATTTCATAGGGAGGTTATCGTAATTTCTCAGTGTAGTTAAAAAAAATTGATAGTAT
G
Found at i:29879 original size:44 final size:44
Alignment explanation
Indices: 29826--29920 Score: 172
Period size: 44 Copynumber: 2.2 Consensus size: 44
29816 GGAAAACCAA
29826 CAACATTTTATAGGAAGGTGATCAAAATTTCGTAGTGTGCTTAC
1 CAACATTTTATAGGAAGGTGATCAAAATTTCGTAGTGTGCTTAC
* *
29870 CAACATTTTATGGGATGGTGATCAAAATTTCGTAGTGTGCTTAC
1 CAACATTTTATAGGAAGGTGATCAAAATTTCGTAGTGTGCTTAC
29914 CAACATT
1 CAACATT
29921 CCACATGGAG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.35
Consensus pattern (44 bp):
CAACATTTTATAGGAAGGTGATCAAAATTTCGTAGTGTGCTTAC
Found at i:29967 original size:21 final size:21
Alignment explanation
Indices: 29938--29990 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
29928 GAGGTTAATG
* *
29938 AAATATCATAGTGTGCTTATC-
1 AAATTTCATAG-GAGCTTATCA
*
29959 AAATTTCATAAGGAGGTTATCA
1 AAATTTCAT-AGGAGCTTATCA
29981 AAATTTCATA
1 AAATTTCATA
29991 AACAACTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 16 0.59
22 11 0.41
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (21 bp):
AAATTTCATAGGAGCTTATCA
Found at i:30000 original size:22 final size:21
Alignment explanation
Indices: 29953--30007 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 21
29943 TCATAGTGTG
** *
29953 CTTATCAAATTTCATAAGGAG
1 CTTATCAAATTTCATAAACAA
*
29974 GTTATCAAAATTTCATAAACAA
1 CTTATC-AAATTTCATAAACAA
*
29996 CTTATTAAATTT
1 CTTATCAAATTT
30008 TTCATAGTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
21 11 0.41
22 16 0.59
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.38
Consensus pattern (21 bp):
CTTATCAAATTTCATAAACAA
Found at i:30089 original size:22 final size:22
Alignment explanation
Indices: 30043--30090 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
30033 GTTTCATTGG
* *
30043 GAGGTTATCAAAATTTCATATT
1 GAGGTTATCAAAATTTCAGAGT
* *
30065 GAGGTTTTCAAAATTTTAGAGT
1 GAGGTTATCAAAATTTCAGAGT
30087 GAGG
1 GAGG
30091 CTAACTAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.38
Consensus pattern (22 bp):
GAGGTTATCAAAATTTCAGAGT
Found at i:30139 original size:21 final size:21
Alignment explanation
Indices: 30041--30143 Score: 75
Period size: 21 Copynumber: 4.9 Consensus size: 21
30031 TTGTTTCATT
30041 GGGAGGTTATCAAAATTTCATA
1 GGGAGGTTATCAAAATTT-ATA
** *
30063 TTGAGGTTTTCAAAATTT-TA
1 GGGAGGTTATCAAAATTTATA
* * * *
30083 GAGTGAGGCTAAC-TAATTCATA
1 G-G-GAGGTTATCAAAATTTATA
* *
30105 GGGAAGTTAACAAAATTTATA
1 GGGAGGTTATCAAAATTTATA
*
30126 GGGAGGTTCTCAAAATTT
1 GGGAGGTTATCAAAATTT
30144 TGATGTCGTT
Statistics
Matches: 60, Mismatches: 17, Indels: 9
0.70 0.20 0.10
Matches are distributed among these distances:
20 9 0.15
21 27 0.45
22 24 0.40
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.34
Consensus pattern (21 bp):
GGGAGGTTATCAAAATTTATA
Found at i:30204 original size:22 final size:22
Alignment explanation
Indices: 30152--30229 Score: 70
Period size: 22 Copynumber: 3.5 Consensus size: 22
30142 TTTGATGTCG
*
30152 TTATTAGAATTTCATAATGTGA
1 TTATTAAAATTTCATAATGTGA
*
30174 TTATCAAAATTTCAT-ATG-GA
1 TTATTAAAATTTCATAATGTGA
* **
30194 TGTCATTAAAATTTTATGGTGTGA
1 T-T-ATTAAAATTTCATAATGTGA
*
30218 TTATCAAAATTT
1 TTATTAAAATTT
30230 AATATAAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
20 3 0.07
21 4 0.09
22 33 0.72
23 3 0.07
24 3 0.07
ACGTcount: A:0.36, C:0.06, G:0.13, T:0.45
Consensus pattern (22 bp):
TTATTAAAATTTCATAATGTGA
Found at i:36095 original size:5 final size:5
Alignment explanation
Indices: 36085--36135 Score: 75
Period size: 5 Copynumber: 9.8 Consensus size: 5
36075 AATAAAAAAG
*
36085 TTGTT TTGTT TTGTT TTGTT TTGTT TTGTT TTGTTTT TTGTT TTTTT TTGT
1 TTGTT TTGTT TTGTT TTGTT TTGTT TTGTT TTG--TT TTGTT TTGTT TTGT
36136 CTTCTTTTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
5 37 0.88
7 5 0.12
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (5 bp):
TTGTT
Found at i:36143 original size:12 final size:10
Alignment explanation
Indices: 36088--36145 Score: 62
Period size: 10 Copynumber: 5.5 Consensus size: 10
36078 AAAAAAGTTG
*
36088 TTTTGTTTTG
1 TTTTGTTTTT
*
36098 TTTTGTTTTG
1 TTTTGTTTTT
36108 TTTTGTTTTGTT
1 TTTTG-TTT-TT
36120 TTTTGTTTTT
1 TTTTGTTTTT
*
36130 TTTTGTCTTCT
1 TTTTGT-TTTT
36141 TTTTG
1 TTTTG
36146 GAAGCCCTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
10 23 0.53
11 14 0.33
12 6 0.14
ACGTcount: A:0.00, C:0.03, G:0.16, T:0.81
Consensus pattern (10 bp):
TTTTGTTTTT
Found at i:47347 original size:128 final size:128
Alignment explanation
Indices: 47215--47450 Score: 429
Period size: 128 Copynumber: 1.8 Consensus size: 128
47205 GATTGAGCCA
*
47215 AATTAA-TTCTTATAATTATTGGTTTGTTTTTTTATCTTAATATTAAATATCAATGATAATAAAT
1 AATTAATTTC-TATAATTATTGGTTTGTTTTTTTATCTTAATATCAAATATCAATGATAATAAAT
47279 GACAATAATTATTGTAATTTCCGTTATACTTTATATATGACTATATATATGGATTCACTTCTAT
65 GACAATAATTATTGTAATTTCCGTTATACTTTATATATGACTATATATATGGATTCACTTCTAT
*
47343 AATTAATTTCTATAATTATTGGTTTGTTTTTTTATCTTAATATCAAATATCAATGATACTAAATG
1 AATTAATTTCTATAATTATTGGTTTGTTTTTTTATCTTAATATCAAATATCAATGATAATAAATG
*
47408 ACGATAATTATTGTAATTTCCGTTATACTTTATATATGACTAT
66 ACAATAATTATTGTAATTTCCGTTATACTTTATATATGACTAT
47451 GGATTCACCT
Statistics
Matches: 104, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
128 101 0.97
129 3 0.03
ACGTcount: A:0.35, C:0.09, G:0.08, T:0.48
Consensus pattern (128 bp):
AATTAATTTCTATAATTATTGGTTTGTTTTTTTATCTTAATATCAAATATCAATGATAATAAATG
ACAATAATTATTGTAATTTCCGTTATACTTTATATATGACTATATATATGGATTCACTTCTAT
Found at i:50575 original size:19 final size:18
Alignment explanation
Indices: 50542--50577 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
50532 TTGAAATAAT
50542 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
50560 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
50578 TGAGTCTTCA
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:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:50585 original size:11 final size:10
Alignment explanation
Indices: 50542--50588 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
50532 TTGAAATAAT
50542 TCTTCAATGA
1 TCTTCAATGA
50552 TCTTCAA--A
1 TCTTCAATGA
*
50560 TCTTCAAATTA
1 TCTTC-AATGA
50571 TCTTCAATGA
1 TCTTCAATGA
50581 GTCTTCAA
1 -TCTTCAA
50589 ACACAAACTC
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
8 6 0.19
9 2 0.06
10 11 0.34
11 13 0.41
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.40
Consensus pattern (10 bp):
TCTTCAATGA
Found at i:60462 original size:19 final size:19
Alignment explanation
Indices: 60412--60462 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
60402 TGTGGGATTT
60412 TTAATAA-TAATTATTCAA
1 TTAATAATTAATTATTCAA
*
60430 -TAA-AATTATTATTATTTAA
1 TTAATAATTA--ATTATTCAA
60449 TTAATAATTAATTA
1 TTAATAATTAATTA
60463 ATTTCAGCCC
Statistics
Matches: 27, Mismatches: 1, Indels: 9
0.73 0.03 0.24
Matches are distributed among these distances:
16 2 0.07
17 5 0.19
19 12 0.44
20 3 0.11
21 5 0.19
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
TTAATAATTAATTATTCAA
Found at i:62397 original size:22 final size:22
Alignment explanation
Indices: 62348--62398 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
62338 AAATATTACC
* **
62348 ATAATTATTTTTGGCAGCCATA
1 ATAATTATTTTTGCCAGAAATA
62370 ATAATTATTTTTGCCAAGAAATA
1 ATAATTATTTTTGCC-AGAAATA
62393 A-AATTA
1 ATAATTA
62399 GGGAATAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 19 0.76
23 6 0.24
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (22 bp):
ATAATTATTTTTGCCAGAAATA
Done.