Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010410.1 Corchorus capsularis cultivar CVL-1 contig10431, 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: 55897
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:863 original size:31 final size:30
Alignment explanation
Indices: 763--867 Score: 95
Period size: 31 Copynumber: 3.4 Consensus size: 30
753 TTTGATCAAT
* *
763 ATGCTCAAATAAGGGCCCAGCGTTTGT-GAAA
1 ATGCTCAAATAAGGGTCCAAC-TTT-TAGAAA
* ***** *
794 ATGCTTAAATAAGGGTCCAAAGAAAAAAAA
1 ATGCTCAAATAAGGGTCCAACTTTTAGAAA
824 ATGCTCAAATAAGGGTCCAACTTTTAGAAA
1 ATGCTCAAATAAGGGTCCAACTTTTAGAAA
854 ATTGCTCAAATAAG
1 A-TGCTCAAATAAG
868 TCTCTGCCAT
Statistics
Matches: 56, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
30 27 0.48
31 29 0.52
ACGTcount: A:0.43, C:0.15, G:0.19, T:0.23
Consensus pattern (30 bp):
ATGCTCAAATAAGGGTCCAACTTTTAGAAA
Found at i:977 original size:22 final size:21
Alignment explanation
Indices: 885--977 Score: 82
Period size: 22 Copynumber: 4.2 Consensus size: 21
875 CATCATTGTG
*
885 TGGTTATCAAAATTCCATAATA
1 TGGTTATCAAAATTTCAT-ATA
* *
907 AGATTATCAAAATTTCATA-A
1 TGGTTATCAAAATTTCATATA
*
927 GGGTGTCATCAAAATTTCATATGGA
1 TGGT-T-ATCAAAATTTCATAT--A
952 -GGTTATCAAAATTTCATTATA
1 TGGTTATCAAAATTTCA-TATA
973 TGGTT
1 TGGTT
978 TTGCAAATAT
Statistics
Matches: 59, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
20 3 0.05
21 3 0.05
22 45 0.76
23 4 0.07
24 3 0.05
25 1 0.02
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (21 bp):
TGGTTATCAAAATTTCATATA
Found at i:1176 original size:6 final size:6
Alignment explanation
Indices: 1165--1208 Score: 79
Period size: 6 Copynumber: 7.3 Consensus size: 6
1155 CAAGGCATAT
*
1165 AAATAC AAATAC AAATAC AAATAC AAATAC AGATAC AAATAC AA
1 AAATAC AAATAC AAATAC AAATAC AAATAC AAATAC AAATAC AA
1209 TGAAGTATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.66, C:0.16, G:0.02, T:0.16
Consensus pattern (6 bp):
AAATAC
Found at i:3867 original size:43 final size:44
Alignment explanation
Indices: 3819--3919 Score: 118
Period size: 44 Copynumber: 2.3 Consensus size: 44
3809 TGACAATTAA
* *
3819 ACCAAAATTACATAGA-AAGATTATC-AAA-TTTCATAGTATAGTT
1 ACCAAAATTTCATAGAGAAG-TCATCAAAACTTT-ATAGTATAGTT
* *
3862 ACCAAAATTTCATATAGAAGTCATCAAAACTTTATAGTGTAGTT
1 ACCAAAATTTCATAGAGAAGTCATCAAAACTTTATAGTATAGTT
*
3906 ATCAAAATTTCATA
1 ACCAAAATTTCATA
3920 CAGAGGTTAC
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
43 18 0.36
44 29 0.58
45 3 0.06
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.34
Consensus pattern (44 bp):
ACCAAAATTTCATAGAGAAGTCATCAAAACTTTATAGTATAGTT
Found at i:3872 original size:22 final size:22
Alignment explanation
Indices: 3819--4009 Score: 90
Period size: 22 Copynumber: 8.7 Consensus size: 22
3809 TGACAATTAA
*
3819 ACCAAAATTACATAG-AAAGATT
1 ACCAAAATTTCATAGTAAAG-TT
* *
3841 ATC-AAATTTCATAGTATAGTT
1 ACCAAAATTTCATAGTAAAGTT
*
3862 ACCAAAATTTCATA-TAGAAGTC
1 ACCAAAATTTCATAGTA-AAGTT
* **
3884 ATCAAAACTTT-ATAGTGTAGTT
1 ACCAAAA-TTTCATAGTAAAGTT
* * *
3906 ATCAAAATTTCATA-CAGAGGTT
1 ACCAAAATTTCATAGTA-AAGTT
**
3928 ACCAAAATTTCA-AAAAAAGATT
1 ACCAAAATTTCATAGTAAAG-TT
* * **
3950 ACCAAAATTTCTTAGGGATTGTT
1 ACCAAAATTTCATA-GTAAAGTT
***
3973 AATGAAATTTCATACG-AAAGTT
1 ACCAAAATTTCATA-GTAAAGTT
*
3995 AACAAAATTTCATAG
1 ACCAAAATTTCATAG
4010 AGAGGGAGGT
Statistics
Matches: 127, Mismatches: 31, Indels: 23
0.70 0.17 0.13
Matches are distributed among these distances:
21 23 0.18
22 84 0.66
23 18 0.14
24 2 0.02
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.32
Consensus pattern (22 bp):
ACCAAAATTTCATAGTAAAGTT
Found at i:3934 original size:44 final size:44
Alignment explanation
Indices: 3851--3934 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 44
3841 ATCAAATTTC
* *
3851 ATAGTATAGTTACCAAAATTTCATATAGAAGTCATCAAAACTTT
1 ATAGTATAGTTACCAAAATTTCATACAGAAGTCACCAAAACTTT
* * * *
3895 ATAGTGTAGTTATCAAAATTTCATACAGAGGTTACCAAAA
1 ATAGTATAGTTACCAAAATTTCATACAGAAGTCACCAAAA
3935 TTTCAAAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 34 1.00
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (44 bp):
ATAGTATAGTTACCAAAATTTCATACAGAAGTCACCAAAACTTT
Found at i:4103 original size:22 final size:22
Alignment explanation
Indices: 4035--4109 Score: 80
Period size: 22 Copynumber: 3.4 Consensus size: 22
4025 AAATTTGTGC
** *
4035 TTATCAAAATTTCCTATGGAGG
1 TTATCAAAATTTTATAGGGAGG
*
4057 TTAACAAAATTTTATAGGGAGG
1 TTATCAAAATTTTATAGGGAGG
* *
4079 TTATGAAAATTTTAT-GGAGATG
1 TTATCAAAATTTTATAGG-GAGG
4101 TTATCAAAA
1 TTATCAAAA
4110 ATACATAGAG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
21 2 0.05
22 42 0.95
ACGTcount: A:0.39, C:0.07, G:0.19, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTTATAGGGAGG
Found at i:4195 original size:19 final size:21
Alignment explanation
Indices: 4148--4199 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 21
4138 TCTCATATGA
*
4148 AGGTTATCGAAATTTCATGGTG
1 AGGTTATCAAAATTT-ATGGTG
*
4170 TGGTTATCAAAATTT-T-GTG
1 AGGTTATCAAAATTTATGGTG
4189 AGGTTATCAAA
1 AGGTTATCAAA
4200 TTAGATGTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 13 0.48
20 1 0.04
22 13 0.48
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (21 bp):
AGGTTATCAAAATTTATGGTG
Found at i:7734 original size:16 final size:17
Alignment explanation
Indices: 7702--7737 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
7692 CCGGTTAACG
7702 TTGCTATTTCTGTTACA
1 TTGCTATTTCTGTTACA
7719 TTGCTATTTC-GTTACA
1 TTGCTATTTCTGTTACA
7735 TTG
1 TTG
7738 GCTTCCGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.17, C:0.17, G:0.14, T:0.53
Consensus pattern (17 bp):
TTGCTATTTCTGTTACA
Found at i:8117 original size:6 final size:6
Alignment explanation
Indices: 8106--8146 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
8096 CTTCTTAGGC
* * *
8106 ATCAGA ATCAGA ATCAGA ATCATA ATCATA ATCAAA ATCAG
1 ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAG
8147 GCAGAGGGGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.51, C:0.17, G:0.10, T:0.22
Consensus pattern (6 bp):
ATCAGA
Found at i:8604 original size:1 final size:1
Alignment explanation
Indices: 8600--8625 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
8590 CCATGTATCC
8600 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
8626 AAATTTATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:9253 original size:1 final size:1
Alignment explanation
Indices: 9247--9290 Score: 88
Period size: 1 Copynumber: 44.0 Consensus size: 1
9237 ATATATAGTC
9247 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
9291 CCTGCCTGAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:14767 original size:72 final size:72
Alignment explanation
Indices: 14671--14888 Score: 355
Period size: 72 Copynumber: 3.0 Consensus size: 72
14661 ATAGCGTTAG
* * * *
14671 CCACCGCCCCTCCCCGTAGCAGTTGGCTATCAACATGATCAAGAAACGCCGCTGGCCTTGAATCA
1 CCACCACCCCTCCCCGTAGAAGTTGGCTATCAACATGACCAAGAAACGCCGCTGGCCTTGAATCC
14736 ACAGACC
66 ACAGACC
* *
14743 CCACCACCCTTCCCCGTAGAAGTTGGCTGTCAACATGACCAAGAAACGCCGCTGGCCTTGAATCC
1 CCACCACCCCTCCCCGTAGAAGTTGGCTATCAACATGACCAAGAAACGCCGCTGGCCTTGAATCC
14808 ACAGACC
66 ACAGACC
* * *
14815 CCATCACCCCTCCCCGTAGAAGTTGGCTATCAACATGACCAAGTAACGCCCCTGGCCTTGAATCC
1 CCACCACCCCTCCCCGTAGAAGTTGGCTATCAACATGACCAAGAAACGCCGCTGGCCTTGAATCC
14880 ACAGACC
66 ACAGACC
14887 CC
1 CC
14889 GCCGCCGTCA
Statistics
Matches: 135, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 135 1.00
ACGTcount: A:0.26, C:0.39, G:0.18, T:0.17
Consensus pattern (72 bp):
CCACCACCCCTCCCCGTAGAAGTTGGCTATCAACATGACCAAGAAACGCCGCTGGCCTTGAATCC
ACAGACC
Found at i:16629 original size:25 final size:25
Alignment explanation
Indices: 16600--16665 Score: 132
Period size: 25 Copynumber: 2.6 Consensus size: 25
16590 GATAATGGAT
16600 AATTAAAAAGGAACAATGACTGAAC
1 AATTAAAAAGGAACAATGACTGAAC
16625 AATTAAAAAGGAACAATGACTGAAC
1 AATTAAAAAGGAACAATGACTGAAC
16650 AATTAAAAAGGAACAA
1 AATTAAAAAGGAACAA
16666 AGGAGTATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.59, C:0.11, G:0.15, T:0.15
Consensus pattern (25 bp):
AATTAAAAAGGAACAATGACTGAAC
Found at i:21056 original size:156 final size:154
Alignment explanation
Indices: 20668--21062 Score: 440
Period size: 156 Copynumber: 2.5 Consensus size: 154
20658 ATTTCAAATG
*
20668 GACTTA-AGATGAAAAACTTATGCACGTTTTTCATTTAAGGACAGTTTGGGGTGTGAAACCAACT
1 GACTTAGA-ATGAAAAACTTATGCACGTTTTTCATTTAAGGACAGTTTGGGGTGTGAAACCAAGT
* * * ** * * *
20732 TCACTATGATAGG-GAGTTTGGTTTTACTTATAATTTTTTCCATAGTTTTATGGGAATAATCTAA
65 TCACCACGA-AGGAGAGCTCAGTTTTACTTAGAATTTTTTCCATAGTCTTATGGGAATAATATAA
**
20796 GGCTACTGGTGGAAAATCAGCTTCATTG
129 GGC-ACT-GTGGAAAATCAGCTTCATCA
* * * *
20824 GACTTAGAATGAAAAACTTATGCACGTTTTTCATTTAAGGACAATTTAGGGAGAGAAACCAAGTT
1 GACTTAGAATGAAAAACTTATGCACGTTTTTCATTTAAGGACAGTTTGGGGTGTGAAACCAAGTT
* * *
20889 CACCACTAAGGAGAGCTCAGTTTTACTTGGAATTTTTTCCATAGTCTTGT-GGAGATAATATAAG
66 CACCACGAAGGAGAGCTCAGTTTTACTTAGAATTTTTTCCATAGTCTTATGGGA-ATAATATAAG
* *
20953 TGC-CT-TGGAAAAGTTTCATCTTGATCA
130 -GCACTGTGGAAAA---TCAGCTTCATCA
* ** *
20980 GACTTAGAATGAATAACTTATGCTTGTTTTTCATTTAAGGACAGTTTGGGGTGTGAAACCTAGTT
1 GACTTAGAATGAAAAACTTATGCACGTTTTTCATTTAAGGACAGTTTGGGGTGTGAAACCAAGTT
* *
21045 CACCAGGAAGGAGGGCTC
66 CACCACGAAGGAGAGCTC
21063 GAACCAAGCC
Statistics
Matches: 201, Mismatches: 31, Indels: 14
0.82 0.13 0.06
Matches are distributed among these distances:
153 7 0.03
155 8 0.04
156 183 0.91
157 3 0.01
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (154 bp):
GACTTAGAATGAAAAACTTATGCACGTTTTTCATTTAAGGACAGTTTGGGGTGTGAAACCAAGTT
CACCACGAAGGAGAGCTCAGTTTTACTTAGAATTTTTTCCATAGTCTTATGGGAATAATATAAGG
CACTGTGGAAAATCAGCTTCATCA
Found at i:34124 original size:156 final size:158
Alignment explanation
Indices: 33706--34125 Score: 441
Period size: 162 Copynumber: 2.6 Consensus size: 158
33696 TGTATACCAT
* * *
33706 CTTGGCTAAGTTTCATCTCAAACGGACTTA-AGATGAAAAATTTATGCACGTTTTTCATTTAAGG
1 CTTGGCAAAGTTTCATCTC-ATCGGACTTAGA-ATGAAAAACTTATGCACGTTTTTCATTTAAGG
*
33770 ACAATTTGGGGTGTGAAA-CTAGCTTCACTATGATAGGGAGTTCGGTTTTACTTAGAATTTTTTC
64 ACAATTTGGGGTGTGAAACCTAG-TTCACCATGA-A-GGAGTTCGGTTTTACTTAGAATTTTTTC
* *
33834 CATAGTTTTATGGGAATGGGAATAATCTAAGGCTA
126 CATAGTCTTATGGGAA--GGAATAATATAAGGCTA
* * *
33869 CTAGTGG-AAA-ATT-AGCTTCATTGGACTTAGAATGAAAAACTTATGCACGTTTTTCATTTAAG
1 CT--TGGCAAAGTTTCATC-TCATCGGACTTAGAATGAAAAACTTATGCACGTTTTTCATTTAAG
* * * * *
33931 GACAATTTAGGGAGAGAAACCAAGTTCACCACT-AAGGA-TTGCTTGGTTTTACTTGGAATTTTT
63 GACAATTTGGGGTGTGAAACCTAGTTCACCA-TGAAGGAGTT-C--GGTTTTACTTAGAATTTTT
* * *
33994 TCCATAGTCTTGT-GG-A-G-ATAATATAAGTC-C
124 TCCATAGTCTTATGGGAAGGAATAATATAAGGCTA
* **
34024 CTTGGCAAAGTTTCATCTCGATCAGACTTAGAATGAAAAACTTATGCTTGTTTTTCATTTAAGGA
1 CTTGGCAAAGTTTCATCTC-ATCGGACTTAGAATGAAAAACTTATGCACGTTTTTCATTTAAGGA
34089 CAATTTGGGGTGTGAAACCTAGTTCACCATGAAGGAG
65 CAATTTGGGGTGTGAAACCTAGTTCACCATGAAGGAG
34126 GGCTCGAACC
Statistics
Matches: 215, Mismatches: 27, Indels: 36
0.77 0.10 0.13
Matches are distributed among these distances:
153 3 0.01
154 3 0.01
155 7 0.03
156 83 0.39
157 1 0.00
159 2 0.01
160 5 0.02
161 3 0.01
162 92 0.43
163 11 0.05
164 2 0.01
165 3 0.01
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (158 bp):
CTTGGCAAAGTTTCATCTCATCGGACTTAGAATGAAAAACTTATGCACGTTTTTCATTTAAGGAC
AATTTGGGGTGTGAAACCTAGTTCACCATGAAGGAGTTCGGTTTTACTTAGAATTTTTTCCATAG
TCTTATGGGAAGGAATAATATAAGGCTA
Found at i:36723 original size:78 final size:76
Alignment explanation
Indices: 36572--36800 Score: 326
Period size: 78 Copynumber: 3.1 Consensus size: 76
36562 TTTTATATAG
* * * *
36572 TTTTACTTAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAAC---TATTTT-
1 TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTTATATTTTA
36633 --ATTTTACTA
66 CCATTTTACTA
*
36642 TTTTACTCAACTAAAAACTGTATTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTT
1 TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAAC--TTATATTT
*
36707 TATCATTTTACTA
64 TACCATTTTACTA
* *
36720 TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATTTAATATCCTTATTACTTATATTTTA
1 TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTTATATTTTA
36785 CCATTTTACTA
66 CCATTTTACTA
36796 TTTTA
1 TTTTA
36801 ATTAAAAAAC
Statistics
Matches: 142, Mismatches: 9, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
70 50 0.35
75 6 0.04
76 25 0.18
78 61 0.43
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.51
Consensus pattern (76 bp):
TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTTATATTTTA
CCATTTTACTA
Found at i:42212 original size:2 final size:2
Alignment explanation
Indices: 42207--42271 Score: 66
Period size: 2 Copynumber: 33.5 Consensus size: 2
42197 CCATTCTTCA
* *
42207 AT AT AT AT AT AT AT AT AT AT AT A- AT ACC AT -T CT -T CA- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT -AT AT AT
42247 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
42272 ATACCAACAA
Statistics
Matches: 55, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
1 4 0.07
2 50 0.91
3 1 0.02
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:42226 original size:36 final size:36
Alignment explanation
Indices: 42179--42265 Score: 174
Period size: 36 Copynumber: 2.4 Consensus size: 36
42169 GTATAATGTA
42179 ATATATATATATATAATACCATTCTTCAATATATAT
1 ATATATATATATATAATACCATTCTTCAATATATAT
42215 ATATATATATATATAATACCATTCTTCAATATATAT
1 ATATATATATATATAATACCATTCTTCAATATATAT
42251 ATATATATATATATA
1 ATATATATATATATA
42266 TATATAATAC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.45
Consensus pattern (36 bp):
ATATATATATATATAATACCATTCTTCAATATATAT
Found at i:44791 original size:6 final size:6
Alignment explanation
Indices: 44745--44791 Score: 62
Period size: 6 Copynumber: 7.8 Consensus size: 6
44735 TCTTGGTGCG
44745 AAAA-A AAAA-A AAAACA AAAACA AAAACA AAAACCAA AAAACA AAAAC
1 AAAACA AAAACA AAAACA AAAACA AAAACA AAAA-C-A AAAACA AAAAC
44792 CTTACATCCC
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
5 9 0.23
6 23 0.59
7 2 0.05
8 5 0.13
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:44792 original size:14 final size:14
Alignment explanation
Indices: 44753--44792 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
44743 CGAAAAAAAA
44753 AAAAAACAAAAA-C
1 AAAAAACAAAAACC
44766 -AAAAACAAAAACC
1 AAAAAACAAAAACC
44779 AAAAAACAAAAACC
1 AAAAAACAAAAACC
44793 TTACATCCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 11 0.44
13 1 0.04
14 13 0.52
ACGTcount: A:0.80, C:0.20, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAACAAAAACC
Found at i:45813 original size:29 final size:29
Alignment explanation
Indices: 45775--45836 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
45765 TCAACAAATT
45775 TAGTAACCTTACACTCTTAGTAAATTTAG
1 TAGTAACCTTACACTCTTAGTAAATTTAG
45804 TAGTAACCTTACACTCTTAGTAAATTTAG
1 TAGTAACCTTACACTCTTAGTAAATTTAG
45833 TAGT
1 TAGT
45837 CTTTTATCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (29 bp):
TAGTAACCTTACACTCTTAGTAAATTTAG
Found at i:46890 original size:13 final size:13
Alignment explanation
Indices: 46856--46881 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
46846 TGACCTTTTA
46856 TTAATGATTAAGG
1 TTAATGATTAAGG
46869 TTAATGATTAAGG
1 TTAATGATTAAGG
46882 GTTTTGATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (13 bp):
TTAATGATTAAGG
Found at i:53345 original size:23 final size:23
Alignment explanation
Indices: 53304--53349 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
53294 CAAACAATCT
* *
53304 TGAGCACTCTTGCTCGGTCTCTA
1 TGAGCACTCTCGATCGGTCTCTA
*
53327 TGAGCACTCTCGATTGGTCTCTA
1 TGAGCACTCTCGATCGGTCTCTA
53350 ACAAACTAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.15, C:0.28, G:0.22, T:0.35
Consensus pattern (23 bp):
TGAGCACTCTCGATCGGTCTCTA
Found at i:55247 original size:1 final size:1
Alignment explanation
Indices: 55241--55265 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
55231 CAAGTGAATG
55241 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
55266 GTTGGTTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:55872 original size:2 final size:2
Alignment explanation
Indices: 55865--55896 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
55855 GGACTAACCT
55865 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
55897 C
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.