Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008815.1 Corchorus capsularis cultivar CVL-1 contig08836, 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: 61479
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Found at i:4726 original size:38 final size:37
Alignment explanation
Indices: 4657--4769 Score: 136
Period size: 38 Copynumber: 3.0 Consensus size: 37
4647 AATCAGAGTT
* * *
4657 GACTGGAAACAGGTCATCTTTCAGCAGTTATCAAGATC
1 GACTAGAAACAAGTCGTCTTTCAGCA-TTATCAAGATC
* * *
4695 GACTAGAGACATGTCGTCTTTCAGCACTTATCAAGTTC
1 GACTAGAAACAAGTCGTCTTTCAGCA-TTATCAAGATC
* *
4733 GACTAGAAACAAGTCGTCTTTCAACAGTATCAAGATC
1 GACTAGAAACAAGTCGTCTTTCAGCATTATCAAGATC
4770 ATCTTTCAAC
Statistics
Matches: 64, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
37 9 0.14
38 55 0.86
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (37 bp):
GACTAGAAACAAGTCGTCTTTCAGCATTATCAAGATC
Found at i:4897 original size:43 final size:43
Alignment explanation
Indices: 4778--4998 Score: 334
Period size: 43 Copynumber: 5.0 Consensus size: 43
4768 TCATCTTTCA
*
4778 ACAGTTTTTTCAGCTGCTCCAAGGAGGGGGCATTCCAACAACTTT
1 ACAG-TTTTT-AGTTGCTCCAAGGAGGGGGCATTCCAACAACTTT
* * *
4823 ACAGATTTTCAGCTGCTCCAAGGAGGGGGCATTCCAACACCTTT
1 ACAG-TTTTTAGTTGCTCCAAGGAGGGGGCATTCCAACAACTTT
4867 ACAGTTTTTAGTTGCTCCAAGGAGGGGGCATTCCAACAACTTT
1 ACAGTTTTTAGTTGCTCCAAGGAGGGGGCATTCCAACAACTTT
* *
4910 ACAGTTTTTACTTGCTCCAAGCAGGGGGCATTCCAACAACTTT
1 ACAGTTTTTAGTTGCTCCAAGGAGGGGGCATTCCAACAACTTT
* *
4953 ACATTTTTTCAATTGCTCCAAGGAGGGGGCATTCCAACAACTTT
1 ACAGTTTTT-AGTTGCTCCAAGGAGGGGGCATTCCAACAACTTT
4997 AC
1 AC
4999 TGATGCGCCA
Statistics
Matches: 164, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
43 85 0.52
44 71 0.43
45 8 0.05
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (43 bp):
ACAGTTTTTAGTTGCTCCAAGGAGGGGGCATTCCAACAACTTT
Found at i:4969 original size:87 final size:88
Alignment explanation
Indices: 4782--4998 Score: 350
Period size: 87 Copynumber: 2.5 Consensus size: 88
4772 CTTTCAACAG
* *
4782 TTTTTTCAGCTGCTCCAAGGAGGGGGCATTCCAACAACTTTACAGATTTTCAGCTGCTCCAAGGA
1 TTTTTTCAGTTGCTCCAAGGAGGGGGCATTCCAACAACTTTACAGATTTTCAGCTGCTCCAAGCA
*
4847 GGGGGCATTCCAACACCTTTACA
66 GGGGGCATTCCAACAACTTTACA
* *
4870 GTTTTT-AGTTGCTCCAAGGAGGGGGCATTCCAACAACTTTACAG-TTTTTA-CTTGCTCCAAGC
1 TTTTTTCAGTTGCTCCAAGGAGGGGGCATTCCAACAACTTTACAGATTTTCAGC-TGCTCCAAGC
4932 AGGGGGCATTCCAACAACTTTACA
65 AGGGGGCATTCCAACAACTTTACA
*
4956 TTTTTTCAATTGCTCCAAGGAGGGGGCATTCCAACAACTTTAC
1 TTTTTTCAGTTGCTCCAAGGAGGGGGCATTCCAACAACTTTAC
4999 TGATGCGCCA
Statistics
Matches: 120, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
85 1 0.01
86 42 0.35
87 72 0.60
88 5 0.04
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.29
Consensus pattern (88 bp):
TTTTTTCAGTTGCTCCAAGGAGGGGGCATTCCAACAACTTTACAGATTTTCAGCTGCTCCAAGCA
GGGGGCATTCCAACAACTTTACA
Found at i:5156 original size:12 final size:12
Alignment explanation
Indices: 5139--5262 Score: 56
Period size: 10 Copynumber: 11.1 Consensus size: 12
5129 GCTGCGCAAC
*
5139 ACCGGCTACATG
1 ACCGGCCACATG
5151 ACCGGCCACATG
1 ACCGGCCACATG
* *
5163 ACTTGG--AGATG
1 AC-CGGCCACATG
* *
5174 CCCGGCCAC--C
1 ACCGGCCACATG
5184 ACCGGCCACATG
1 ACCGGCCACATG
5196 ACTCGG-C-CATG
1 AC-CGGCCACATG
*
5207 CCCGGCCACA--
1 ACCGGCCACATG
*
5217 ACCGGCTACATG
1 ACCGGCCACATG
*
5229 ACTC-GAC-CATG
1 AC-CGGCCACATG
*
5240 CCCGGCCACA--
1 ACCGGCCACATG
5250 ACCGGCCACATG
1 ACCGGCCACATG
5262 A
1 A
5263 TCCTTTAACT
Statistics
Matches: 80, Mismatches: 17, Indels: 30
0.63 0.13 0.24
Matches are distributed among these distances:
10 31 0.39
11 18 0.22
12 25 0.31
13 6 0.08
ACGTcount: A:0.23, C:0.41, G:0.24, T:0.11
Consensus pattern (12 bp):
ACCGGCCACATG
Found at i:5188 original size:33 final size:33
Alignment explanation
Indices: 5151--5262 Score: 154
Period size: 33 Copynumber: 3.4 Consensus size: 33
5141 CGGCTACATG
* *
5151 ACCGGCCACATGACTTGGAGATGCCCGGCCACC
1 ACCGGCCACATGACTTGGACATGCCCGGCCACA
* *
5184 ACCGGCCACATGACTCGGCCATGCCCGGCCACA
1 ACCGGCCACATGACTTGGACATGCCCGGCCACA
* *
5217 ACCGGCTACATGAC-TCGACCATGCCCGGCCACA
1 ACCGGCCACATGACTTGGA-CATGCCCGGCCACA
5250 ACCGGCCACATGA
1 ACCGGCCACATGA
5263 TCCTTTAACT
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
32 1 0.01
33 68 0.99
ACGTcount: A:0.23, C:0.42, G:0.24, T:0.11
Consensus pattern (33 bp):
ACCGGCCACATGACTTGGACATGCCCGGCCACA
Found at i:9275 original size:33 final size:33
Alignment explanation
Indices: 9235--9298 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
9225 AGCACAAGTG
* * *
9235 ACCGGCCATGCGACTTGGAGATGCCCGGCCAAC
1 ACCGGCCACGCGACATGGACATGCCCGGCCAAC
*
9268 ACCGGCCACGCGACATGGTCATGCCCGGCCA
1 ACCGGCCACGCGACATGGACATGCCCGGCCA
9299 CAACCAGCCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.20, C:0.39, G:0.30, T:0.11
Consensus pattern (33 bp):
ACCGGCCACGCGACATGGACATGCCCGGCCAAC
Found at i:15799 original size:33 final size:33
Alignment explanation
Indices: 15759--15855 Score: 149
Period size: 33 Copynumber: 2.9 Consensus size: 33
15749 AGCAGAAGTG
15759 ACCGGCCATGCGACTTGGAGATGCCCGGCCAAC
1 ACCGGCCATGCGACTTGGAGATGCCCGGCCAAC
*
15792 ACCGGCCATGCGACTTGGAGATGCCCGGCCATC
1 ACCGGCCATGCGACTTGGAGATGCCCGGCCAAC
* * **
15825 ACCGGCCACGCGACATGGTCATGCCCGGCCA
1 ACCGGCCATGCGACTTGGAGATGCCCGGCCA
15856 CAACCAGCCA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.20, C:0.38, G:0.30, T:0.12
Consensus pattern (33 bp):
ACCGGCCATGCGACTTGGAGATGCCCGGCCAAC
Found at i:15866 original size:33 final size:32
Alignment explanation
Indices: 15759--15899 Score: 133
Period size: 33 Copynumber: 4.3 Consensus size: 32
15749 AGCAGAAGTG
* *
15759 ACCGGCCATGCGACTTGGAGATGCCCGGCCA-A
1 ACCGGCCACGCGAC-TGGACATGCCCGGCCACA
* *
15791 CACCGGCCATGCGACTTGGAGATGCCCGGCCATC-
1 -ACCGGCCACGCGAC-TGGACATGCCCGGCCA-CA
*
15825 ACCGGCCACGCGACATGGTCATGCCCGGCCACA
1 ACCGGCCACGCGAC-TGGACATGCCCGGCCACA
* ** *
15858 ACCAGCCACATGACTCGGCCATGCCCGGCCACA
1 ACCGGCCACGCGACT-GGACATGCCCGGCCACA
15891 ACCGGCCAC
1 ACCGGCCAC
15900 ATGATCCTTT
Statistics
Matches: 95, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
32 2 0.02
33 93 0.98
ACGTcount: A:0.21, C:0.41, G:0.27, T:0.11
Consensus pattern (32 bp):
ACCGGCCACGCGACTGGACATGCCCGGCCACA
Found at i:19331 original size:33 final size:32
Alignment explanation
Indices: 19294--19402 Score: 121
Period size: 33 Copynumber: 3.3 Consensus size: 32
19284 CTACATGACT
*
19294 GGCCACATGACTTCGAGATGCCCGGCCACCACC
1 GGCCACATGAC-TCGAGATGCCCGGCCACAACC
* *
19327 GGCCACATGACTCG-GCCATGGCCGGCCACAAGC
1 GGCCACATGACTCGAG--ATGCCCGGCCACAACC
* *
19360 GGCTACATGACTCGACTATGCCCGGCCACAACC
1 GGCCACATGACTCGA-GATGCCCGGCCACAACC
*
19393 AGCCACATGA
1 GGCCACATGA
19403 TCCTTTAACT
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
31 1 0.02
32 3 0.05
33 59 0.94
ACGTcount: A:0.24, C:0.39, G:0.25, T:0.12
Consensus pattern (32 bp):
GGCCACATGACTCGAGATGCCCGGCCACAACC
Found at i:22698 original size:15 final size:15
Alignment explanation
Indices: 22678--22706 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
22668 CTTTTGCTTG
22678 TTATTGTAAACAGGT
1 TTATTGTAAACAGGT
22693 TTATTGTAAACAGG
1 TTATTGTAAACAGG
22707 GGTATATTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.07, G:0.21, T:0.38
Consensus pattern (15 bp):
TTATTGTAAACAGGT
Found at i:27227 original size:1 final size:1
Alignment explanation
Indices: 27221--27254 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
27211 AAGAAAGGGG
27221 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
27255 CAATTCCCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:28133 original size:1 final size:1
Alignment explanation
Indices: 28129--28154 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
28119 TAAAAAGATT
28129 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
28155 CCCTGAGGTC
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:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:30674 original size:29 final size:28
Alignment explanation
Indices: 30627--30703 Score: 109
Period size: 29 Copynumber: 2.6 Consensus size: 28
30617 CTTAGCTGAG
30627 GGGGCAAAACGTCCCAAAATTGAAGTTCA
1 GGGGCAAAACGT-CCAAAATTGAAGTTCA
*
30656 GGGAGCAAAATGTCCAAAATTGAAGTTCA
1 GGG-GCAAAACGTCCAAAATTGAAGTTCA
*
30685 TGGGGCAAAACATCCAAAA
1 -GGGGCAAAACGTCCAAAA
30704 GCTACAAGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
29 32 0.74
30 11 0.26
ACGTcount: A:0.42, C:0.18, G:0.23, T:0.17
Consensus pattern (28 bp):
GGGGCAAAACGTCCAAAATTGAAGTTCA
Found at i:34732 original size:22 final size:22
Alignment explanation
Indices: 34706--34752 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
34696 ATTTATTCAT
34706 TATTAATTAACTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
*
34728 TATTAATTAGCTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
34750 TAT
1 TAT
34753 AGTATAATGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (22 bp):
TATTAATTAACTATTAATTAGA
Found at i:34748 original size:11 final size:11
Alignment explanation
Indices: 34706--34748 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
34696 ATTTATTCAT
*
34706 TATTAATTAAC
1 TATTAATTAGC
*
34717 TATTAATTAGA
1 TATTAATTAGC
34728 TATTAATTAGC
1 TATTAATTAGC
34739 TATTAATTAG
1 TATTAATTAG
34749 ATATAGTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (11 bp):
TATTAATTAGC
Found at i:34983 original size:11 final size:11
Alignment explanation
Indices: 34967--35008 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
34957 ATTTATTCAT
34967 TATTAATTAAC
1 TATTAATTAAC
34978 TATTAATTAGA-
1 TATTAATTA-AC
* *
34989 TATTAAATAGC
1 TATTAATTAAC
35000 TATTAATTA
1 TATTAATTA
35009 GATATAGTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 25 0.96
12 1 0.04
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (11 bp):
TATTAATTAAC
Found at i:34993 original size:22 final size:22
Alignment explanation
Indices: 34967--35013 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
34957 ATTTATTCAT
*
34967 TATTAATTAACTATTAATTAGA
1 TATTAAATAACTATTAATTAGA
*
34989 TATTAAATAGCTATTAATTAGA
1 TATTAAATAACTATTAATTAGA
35011 TAT
1 TAT
35014 AGTATAATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (22 bp):
TATTAAATAACTATTAATTAGA
Found at i:35094 original size:261 final size:260
Alignment explanation
Indices: 34625--35149 Score: 989
Period size: 261 Copynumber: 2.0 Consensus size: 260
34615 TCTTCTTGTG
*
34625 TAATCAAAAAAATGAGGATGAAGGGAATAATTAGGTATTAATTAGCTATTATTGCCTTTTAATCA
1 TAATCAAAAAAATGAGGATGAAGGGAATAATTAGGTATTAATTAGCTATTATTCCCTTTTAATCA
*
34690 TATTGAATTTATTCATTATTAATTAACTATTAATTAGATATTAATTAGCTATTAATTAGATATAG
66 TATTGAATTTATTCATTATTAATTAACTATTAATTAGATATTAAATAGCTATTAATTAGATATAG
34755 TATAATGGATGATTAAGGAGGGGCTTTAAATTAATATGTTAGATGTGAGAAATTACCAAAATGGG
131 TATAATGGATGATTAAGGAGGGGCTTTAAATTAATATGTTAGATGTGAGAAATTACCAAAATGGG
*
34820 GCGATAAGGTGGCACCAGGTTAAAAGTTGAAAGGG-CTTGTTAGTAATTTCCATAGGGGACAAAA
196 GCAATAAGGTGGCACCAGGTTAAAAGTTGAAAGGGTC-TGTTAGTAATTTCCATAGGGGACAAAA
34884 A
260 A
*
34885 TAATCTAAAAAAATGAGGTTGAAGGGAATAATTAGGTATTAATTAGCTATTATTCCCTTTTAATC
1 TAATC-AAAAAAATGAGGATGAAGGGAATAATTAGGTATTAATTAGCTATTATTCCCTTTTAATC
34950 ATATTGAATTTATTCATTATTAATTAACTATTAATTAGATATTAAATAGCTATTAATTAGATATA
65 ATATTGAATTTATTCATTATTAATTAACTATTAATTAGATATTAAATAGCTATTAATTAGATATA
35015 GTATAATGGATGATTAAGGAGGGGCTTTAAATTAATATGTTAGATGTGAGAAATTACCAAAATGG
130 GTATAATGGATGATTAAGGAGGGGCTTTAAATTAATATGTTAGATGTGAGAAATTACCAAAATGG
35080 GGCAATAAGGTGGCACCAGGTTAAAAGTTGAAAGGGTCTGTTAGTAATTTCCATAGGGGACAAAA
195 GGCAATAAGGTGGCACCAGGTTAAAAGTTGAAAGGGTCTGTTAGTAATTTCCATAGGGGACAAAA
35145 A
260 A
35146 TAAT
1 TAAT
35150 ATATAGTATA
Statistics
Matches: 259, Mismatches: 4, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
260 5 0.02
261 253 0.98
262 1 0.00
ACGTcount: A:0.39, C:0.07, G:0.19, T:0.34
Consensus pattern (260 bp):
TAATCAAAAAAATGAGGATGAAGGGAATAATTAGGTATTAATTAGCTATTATTCCCTTTTAATCA
TATTGAATTTATTCATTATTAATTAACTATTAATTAGATATTAAATAGCTATTAATTAGATATAG
TATAATGGATGATTAAGGAGGGGCTTTAAATTAATATGTTAGATGTGAGAAATTACCAAAATGGG
GCAATAAGGTGGCACCAGGTTAAAAGTTGAAAGGGTCTGTTAGTAATTTCCATAGGGGACAAAAA
Found at i:37350 original size:33 final size:33
Alignment explanation
Indices: 37313--37396 Score: 132
Period size: 33 Copynumber: 2.5 Consensus size: 33
37303 TGGCCGGTTG
* * *
37313 TGGCCAAGTCATGTGGCCGGTTGTGGTCGGGCA
1 TGGCCGAGTCATGTGGCCGGTGGTGGCCGGGCA
37346 TGGCCGAGTCATGTGGCCGGTGGTGGCCGGGCA
1 TGGCCGAGTCATGTGGCCGGTGGTGGCCGGGCA
*
37379 TGGCTGAGTCATGTGGCC
1 TGGCCGAGTCATGTGGCC
37397 AGTGTTGCGC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.11, C:0.23, G:0.44, T:0.23
Consensus pattern (33 bp):
TGGCCGAGTCATGTGGCCGGTGGTGGCCGGGCA
Found at i:38179 original size:33 final size:33
Alignment explanation
Indices: 38142--38226 Score: 152
Period size: 33 Copynumber: 2.6 Consensus size: 33
38132 GAGAATTCAG
38142 AAAATTGTGCTACATCAAAGGCAATTATTGGAC
1 AAAATTGTGCTACATCAAAGGCAATTATTGGAC
*
38175 AAAATTGTGCTACATCAAAGGCAATTATTGGAG
1 AAAATTGTGCTACATCAAAGGCAATTATTGGAC
*
38208 AAAATTGTGCAACATCAAA
1 AAAATTGTGCTACATCAAA
38227 CGCAGTTTCC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (33 bp):
AAAATTGTGCTACATCAAAGGCAATTATTGGAC
Found at i:38245 original size:33 final size:33
Alignment explanation
Indices: 38142--38246 Score: 104
Period size: 33 Copynumber: 3.2 Consensus size: 33
38132 GAGAATTCAG
* * **
38142 AAAATTGTGCTACATCAAAGGCAATTATTGGAC
1 AAAATTGTGCAACATCAAACGCAATTATCAGAC
* * ** *
38175 AAAATTGTGCTACATCAAAGGCAATTATTGGAG
1 AAAATTGTGCAACATCAAACGCAATTATCAGAC
*
38208 AAAATTGTGCAACATCAAACGCAGTT-TCCAGAC
1 AAAATTGTGCAACATCAAACGCAATTAT-CAGAC
38241 AAAATT
1 AAAATT
38247 TGCGTGCTGA
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
32 1 0.02
33 63 0.98
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.26
Consensus pattern (33 bp):
AAAATTGTGCAACATCAAACGCAATTATCAGAC
Found at i:43527 original size:33 final size:33
Alignment explanation
Indices: 43477--43600 Score: 135
Period size: 33 Copynumber: 3.7 Consensus size: 33
43467 CCGCGCAACA
43477 CCGGCCACAAGACCGGCCACGCGACATGGACATGT
1 CCGGCCAC-A-ACCGGCCACGCGACATGGACATGT
43512 CCGGCCATC-ACCGGCCACGCGACATGGACATGT
1 CCGGCCA-CAACCGGCCACGCGACATGGACATGT
* * * ** * *
43545 ACGGCTACAATCGGCCAAACGAC-TCGGCCATGC
1 CCGGCCACAACCGGCCACGCGACAT-GGACATGT
43578 CCGGCCACAACCGGCCACGCGAC
1 CCGGCCACAACCGGCCACGCGAC
43601 CCTTTGTCTA
Statistics
Matches: 74, Mismatches: 12, Indels: 8
0.79 0.13 0.09
Matches are distributed among these distances:
32 2 0.03
33 64 0.86
35 7 0.09
36 1 0.01
ACGTcount: A:0.24, C:0.40, G:0.27, T:0.09
Consensus pattern (33 bp):
CCGGCCACAACCGGCCACGCGACATGGACATGT
Found at i:47129 original size:2 final size:2
Alignment explanation
Indices: 47122--47147 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
47112 CAACAACACA
47122 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
47148 GCACAATGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51107 original size:33 final size:34
Alignment explanation
Indices: 51069--51142 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 34
51059 GCCGAGTCAA
*
51069 ATGGCCGGGTG-TGACCGGACATGGCCATGTCGC
1 ATGGCCGGGTGATGACCGGACATCGCCATGTCGC
* * * *
51102 GTGGCC-GGTGATGGCCGGGCATCTCCATGTCGC
1 ATGGCCGGGTGATGACCGGACATCGCCATGTCGC
51135 ATGGCCGG
1 ATGGCCGG
51143 TGTTGCGCGG
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
32 4 0.12
33 28 0.85
34 1 0.03
ACGTcount: A:0.12, C:0.28, G:0.41, T:0.19
Consensus pattern (34 bp):
ATGGCCGGGTGATGACCGGACATCGCCATGTCGC
Found at i:51143 original size:33 final size:33
Alignment explanation
Indices: 51093--51176 Score: 125
Period size: 33 Copynumber: 2.5 Consensus size: 33
51083 CCGGACATGG
51093 CCATGTCGCGTGGCCGGTGATGGC-CGGGCATCT
1 CCATGTCGCGTGGCCGGTG-TGGCGCGGGCATCT
* *
51126 CCATGTCGCATGGCCGGTGTTGCGCGGGCATCT
1 CCATGTCGCGTGGCCGGTGTGGCGCGGGCATCT
*
51159 CCAAGTCGCGTGGCCGGT
1 CCATGTCGCGTGGCCGGT
51177 CACTCGCGCC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
32 3 0.07
33 43 0.93
ACGTcount: A:0.10, C:0.31, G:0.38, T:0.21
Consensus pattern (33 bp):
CCATGTCGCGTGGCCGGTGTGGCGCGGGCATCT
Found at i:55779 original size:9 final size:9
Alignment explanation
Indices: 55765--55799 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
55755 TCTGGTCGAA
55765 ATTTTTTTT
1 ATTTTTTTT
55774 ATTTTTTTT
1 ATTTTTTTT
*
55783 ATTTGTTTT
1 ATTTTTTTT
55792 ATATTTTT
1 AT-TTTTT
55800 CGATATAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 19 0.83
10 4 0.17
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:56873 original size:33 final size:34
Alignment explanation
Indices: 56836--56908 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 34
56826 CCGAGTCAAG
* * *
56836 TGGCCGGGTG-TGACCGGGCATGGCCATGTTGCA
1 TGGCCGGGTGATGACCGAGCATCGCCATGTCGCA
* *
56869 TGGCC-GGTGATGGCCGAGCATCTCCATGTCGCA
1 TGGCCGGGTGATGACCGAGCATCGCCATGTCGCA
56902 TGGCCGG
1 TGGCCGG
56909 TGTTGCGCGG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
32 4 0.12
33 28 0.85
34 1 0.03
ACGTcount: A:0.12, C:0.27, G:0.40, T:0.21
Consensus pattern (34 bp):
TGGCCGGGTGATGACCGAGCATCGCCATGTCGCA
Found at i:56909 original size:33 final size:33
Alignment explanation
Indices: 56859--56942 Score: 107
Period size: 33 Copynumber: 2.5 Consensus size: 33
56849 CCGGGCATGG
*
56859 CCATGTTGCATGGCCGGTGATGGC-CGAGCATCT
1 CCATGTCGCATGGCCGGTG-TGGCGCGAGCATCT
* *
56892 CCATGTCGCATGGCCGGTGTTGCGCGGGCATCT
1 CCATGTCGCATGGCCGGTGTGGCGCGAGCATCT
* *
56925 CCAAGTCGCGTGGCCGGT
1 CCATGTCGCATGGCCGGT
56943 CACTCGCGCC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
32 3 0.07
33 42 0.93
ACGTcount: A:0.12, C:0.30, G:0.36, T:0.23
Consensus pattern (33 bp):
CCATGTCGCATGGCCGGTGTGGCGCGAGCATCT
Found at i:57173 original size:33 final size:32
Alignment explanation
Indices: 57099--57174 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 32
57089 CGCCAAGCGA
* *
57099 TGGCCGGTTGTGGCCGGACATGTCCATGTTGCG
1 TGGCCGG-TGTGGCCGGACATCTCCATGTCGCG
*
57132 TGGCCGGTGATGGCCGGGCATCTCCGA-GTCGCG
1 TGGCCGGTG-TGGCCGGACATCTCC-ATGTCGCG
57165 TGGCCGGTGT
1 TGGCCGGTGT
57175 TAGCCGGTCT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
32 3 0.08
33 34 0.89
34 1 0.03
ACGTcount: A:0.08, C:0.26, G:0.42, T:0.24
Consensus pattern (32 bp):
TGGCCGGTGTGGCCGGACATCTCCATGTCGCG
Found at i:57195 original size:33 final size:33
Alignment explanation
Indices: 57111--57196 Score: 82
Period size: 33 Copynumber: 2.6 Consensus size: 33
57101 GCCGGTTGTG
* * * * *
57111 GCCGGACATGTCCATGTTGCGTGGCCGGTGATG
1 GCCGGGCATCTCCAAGTCGCGTGGCCGGTGATA
* *
57144 GCCGGGCATCTCCGAGTCGCGTGGCCGGTGTTA
1 GCCGGGCATCTCCAAGTCGCGTGGCCGGTGATA
* * *
57177 GCCGGTCTTCTCTAAGTCGC
1 GCCGGGCATCTCCAAGTCGC
57197 ATGGTCGATC
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.10, C:0.29, G:0.36, T:0.24
Consensus pattern (33 bp):
GCCGGGCATCTCCAAGTCGCGTGGCCGGTGATA
Found at i:57273 original size:263 final size:263
Alignment explanation
Indices: 56836--57315 Score: 757
Period size: 263 Copynumber: 1.8 Consensus size: 263
56826 CCGAGTCAAG
*
56836 TGGCCGGGTGTGACCGGGCATGGCCATGTTGCATGGCCGGTGATGGCCGAGCATCTCCATGTCGC
1 TGGCCGGGTGTGACCGGACATGGCCATGTTGCATGGCCGGTGATGGCCGAGCATCTCCATGTCGC
* * *
56901 ATGGCCGGTGTTGCGCGGGCATCTCCAAGTCGCGTGGCCGGTCACTCGCGCCTCCATCCCCATGC
66 ATGGCCGGTGTTGCGCGGGCATCTCCAAGTCGCATGGCCGATCACTCGCGCCTCCAACCCCATGC
*
56966 TCCTCCAAGCTAGCATCGATGACATCTCCATGATCTTCATTGGCTCCAATGTGTCTTTCTAAGCC
131 TCCTCCAAGCTAGCATCGATGACATCTCCATGATCTTCATTGGCTCCAATGTGTCCTTCTAAGCC
57031 ATGATAAGCCCTTGGCGCATCAATGGCCCTATCGATGTCCGGTTGTGGCCGGTTGGTGCGCCAAG
196 ATGATAAGCCCTTGGCGCATCAATGGCCCTATCGATGTCCGGTTGTGGCCGGTTGGTGCGCCAAG
57096 CGA
261 CGA
* * * * *
57099 TGGCCGGTTGTGGCCGGACATGTCCATGTTGCGTGGCCGGTGATGGCCGGGCATCTCCGA-GTCG
1 TGGCCGGGTGTGACCGGACATGGCCATGTTGCATGGCCGGTGATGGCCGAGCATCTCC-ATGTCG
* * * * * *
57163 CGTGGCCGGTGTTAGC-CGGTCTTCTCTAAGTCGCATGGTCGATCACTCGCGCCTCCAACTCCAT
65 CATGGCCGGTGTT-GCGCGGGCATCTCCAAGTCGCATGGCCGATCACTCGCGCCTCCAACCCCAT
* * *
57227 GCTCCTTCAAGCTAGCATCGATGGCATCTCCTTGATCTTCATTGGCTCCAATGTGTCCTTCTAAG
129 GCTCCTCCAAGCTAGCATCGATGACATCTCCATGATCTTCATTGGCTCCAATGTGTCCTTCTAAG
57292 CCATGATAAGCCCTTGGCGCATCA
194 CCATGATAAGCCCTTGGCGCATCA
57316 TCCCCTCTCC
Statistics
Matches: 196, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
263 193 0.98
264 3 0.02
ACGTcount: A:0.15, C:0.31, G:0.28, T:0.26
Consensus pattern (263 bp):
TGGCCGGGTGTGACCGGACATGGCCATGTTGCATGGCCGGTGATGGCCGAGCATCTCCATGTCGC
ATGGCCGGTGTTGCGCGGGCATCTCCAAGTCGCATGGCCGATCACTCGCGCCTCCAACCCCATGC
TCCTCCAAGCTAGCATCGATGACATCTCCATGATCTTCATTGGCTCCAATGTGTCCTTCTAAGCC
ATGATAAGCCCTTGGCGCATCAATGGCCCTATCGATGTCCGGTTGTGGCCGGTTGGTGCGCCAAG
CGA
Done.