Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023332.1 Corchorus olitorius cultivar O-4 contig23365, 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: 59417
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:7972 original size:14 final size:14
Alignment explanation
Indices: 7953--7982 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
7943 CCTGTGCATG
*
7953 GGTATGTTGTAAAT
1 GGTATGTGGTAAAT
7967 GGTATGTGGTAAAT
1 GGTATGTGGTAAAT
7981 GG
1 GG
7983 CCTTTTCGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.37, T:0.37
Consensus pattern (14 bp):
GGTATGTGGTAAAT
Found at i:9165 original size:226 final size:226
Alignment explanation
Indices: 8796--9231 Score: 845
Period size: 226 Copynumber: 1.9 Consensus size: 226
8786 TATCCTATAT
8796 GACTTTCAATCCTACCTTTTCAGTGCACATCCAAAATGGGATAACATGAGATATGCTGTCCATCT
1 GACTTTCAATCCTACCTTTTCAGTGCACATCCAAAATGGGATAACATGAGATATGCTGTCCATCT
* *
8861 TCTTGTGTGTTAAATGCACTCTTTATGTTCTCGAATGTTATGTTAGAATTTGCTGTCGGACTTGG
66 TCTTGTGTGTTAAATGCACTCTTTATGTCCTCGAATGTGATGTTAGAATTTGCTGTCGGACTTGG
8926 TGCTATCTTCTGTCATTTTTCCAGAAAATTTATTTCAGGAAACAACTTCTAAATCTTTACAAGCA
131 TGCTATCTTCTGTCATTTTTCCAGAAAATTTATTTCAGGAAACAACTTCTAAATCTTTACAAGCA
8991 ACTTTTTACAGGATTCTAACACACAAAATGG
196 ACTTTTTACAGGATTCTAACACACAAAATGG
9022 GACTTTCAATCCTACCTTTTCAGTGCACATCCAAAATGGGATAACATGAGATATGCTGTCCATCT
1 GACTTTCAATCCTACCTTTTCAGTGCACATCCAAAATGGGATAACATGAGATATGCTGTCCATCT
*
9087 TCTTGTGTGTTAAATGCACTCTTTATGTCCTCGAATGTGATGTTAGAATTTGCTGTTGGACTTGG
66 TCTTGTGTGTTAAATGCACTCTTTATGTCCTCGAATGTGATGTTAGAATTTGCTGTCGGACTTGG
9152 TGCTATCTTCTGTCATTTTTCCAGAAAATTTATTTCAGGAAACAACTTCTAAATCTTTACAAGCA
131 TGCTATCTTCTGTCATTTTTCCAGAAAATTTATTTCAGGAAACAACTTCTAAATCTTTACAAGCA
9217 ACTTTTTACAGGATT
196 ACTTTTTACAGGATT
9232 GTGGATACTT
Statistics
Matches: 207, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
226 207 1.00
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (226 bp):
GACTTTCAATCCTACCTTTTCAGTGCACATCCAAAATGGGATAACATGAGATATGCTGTCCATCT
TCTTGTGTGTTAAATGCACTCTTTATGTCCTCGAATGTGATGTTAGAATTTGCTGTCGGACTTGG
TGCTATCTTCTGTCATTTTTCCAGAAAATTTATTTCAGGAAACAACTTCTAAATCTTTACAAGCA
ACTTTTTACAGGATTCTAACACACAAAATGG
Found at i:10851 original size:85 final size:85
Alignment explanation
Indices: 10717--10971 Score: 483
Period size: 85 Copynumber: 3.0 Consensus size: 85
10707 ATGCTATAAA
*
10717 AAGCAATATTTTGATGGCTGATTTGTGTAGTAGTAATAGCTAATCAATCATAGTAAACATTTTAT
1 AAGCAATATTTTGATGGATGATTTGTGTAGTAGTAATAGCTAATCAATCATAGTAAACATTTTAT
10782 TATAAAGAAACATAAAGGAC
66 TATAAAGAAACATAAAGGAC
10802 AAGCAATATTTTGATGGATGATTTGTGTAGTAGTAATAGCTAATCAATCATAGTAAACATTTTAT
1 AAGCAATATTTTGATGGATGATTTGTGTAGTAGTAATAGCTAATCAATCATAGTAAACATTTTAT
10867 TATAAAGAAACATAAAGGAC
66 TATAAAGAAACATAAAGGAC
*
10887 AAGCAATATTTTGATGGATGATTTGTGTAGTAGTAATAGCTAATCAATCATTGTAAACATTTTAT
1 AAGCAATATTTTGATGGATGATTTGTGTAGTAGTAATAGCTAATCAATCATAGTAAACATTTTAT
10952 TATAAAGAAACATAATAGGA
66 TATAAAGAAACATAA-AGGA
10972 GGAAGTGAAA
Statistics
Matches: 167, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
85 163 0.98
86 4 0.02
ACGTcount: A:0.42, C:0.08, G:0.16, T:0.34
Consensus pattern (85 bp):
AAGCAATATTTTGATGGATGATTTGTGTAGTAGTAATAGCTAATCAATCATAGTAAACATTTTAT
TATAAAGAAACATAAAGGAC
Found at i:13589 original size:241 final size:241
Alignment explanation
Indices: 13151--13605 Score: 630
Period size: 241 Copynumber: 1.9 Consensus size: 241
13141 TGGACCGAAA
* *
13151 ATTATACAATATTAAATAGAACGACAATCGAAACCACACAATTTTGAAAGCAATTTTTAGAATCA
1 ATTATACAATATTAAATAGAACGACAATCGAAACCACAAAATTTAGAAAGCAATTTTTAGAATCA
*
13216 AAAAATTAAAATTGGCTTCTGAGTTATTCATGAAAGTTGTACATCATGAAATCACATTTTAATAG
66 AAAAATTAAAATTGGCTTCTGAGTTATTCATGAAAGTTGTACATCATGAAATCACATTTAAATAG
* **
13281 ACACTTGAATCACTTTAATCGGACAAATAGAACAAAAAAATACAAAAATAAAAACCGAAGTGTTA
131 ACACTTGAATCACCTTAATCGGACAAATAGAACAAAAAAATACAAAAATAAAAACCGAAACGTTA
* *
13346 AATTGTCCAACCCATAATTGTATTAGGTAATATCATCCTATCCTAT
196 AATCGTCCAACCCAGAATTGTATTAGGTAATATCATCCTATCCTAT
* * * * *
13392 ATTATACAATATTAGATAGACCGACAATCGAGACCACAAAATTTCAG-AAGCATTTTTTAGAATT
1 ATTATACAATATTAAATAGAACGACAATCGAAACCACAAAATTT-AGAAAGCAATTTTTAGAATC
* * * * * * *
13456 GAAACATTAAAATTGGCTTTTGAG-TACTTCATGAAAGTTTTAGATCATTAAA-CTACCTTTAAA
65 AAAAAATTAAAATTGGCTTCTGAGTTA-TTCATGAAAGTTGTACATCATGAAATC-ACATTTAAA
* * * *
13519 TAGACACTTGAATCACCTTGATCGGACAAATAGAACAAAAAAATA-AAAGAATTAAAGCTGAAAC
128 TAGACACTTGAATCACCTTAATCGGACAAATAGAACAAAAAAATACAAA-AATAAAAACCGAAAC
13583 GTTAAATCGTCCAACCCAGAATT
192 GTTAAATCGTCCAACCCAGAATT
13606 TGTGCGGGAT
Statistics
Matches: 186, Mismatches: 24, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
240 6 0.03
241 179 0.96
242 1 0.01
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.29
Consensus pattern (241 bp):
ATTATACAATATTAAATAGAACGACAATCGAAACCACAAAATTTAGAAAGCAATTTTTAGAATCA
AAAAATTAAAATTGGCTTCTGAGTTATTCATGAAAGTTGTACATCATGAAATCACATTTAAATAG
ACACTTGAATCACCTTAATCGGACAAATAGAACAAAAAAATACAAAAATAAAAACCGAAACGTTA
AATCGTCCAACCCAGAATTGTATTAGGTAATATCATCCTATCCTAT
Found at i:16460 original size:30 final size:31
Alignment explanation
Indices: 16398--16457 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
16388 TTTCGTTGAA
* *
16398 TTTTTTTTCTTTTTGACTCCTTAAAATAAAT
1 TTTTTTTTCTTTTAGACTCCTCAAAATAAAT
*
16429 TTTTTTTTCTTATTAG-CTTCTCAAAATAA
1 TTTTTTTTCTT-TTAGACTCCTCAAAATAA
16458 TTTATCTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 22 0.88
32 3 0.12
ACGTcount: A:0.27, C:0.13, G:0.03, T:0.57
Consensus pattern (31 bp):
TTTTTTTTCTTTTAGACTCCTCAAAATAAAT
Found at i:17193 original size:22 final size:24
Alignment explanation
Indices: 17158--17211 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 24
17148 ATAAATGTTG
* *
17158 CTGATAA-TCTTCTC-TTTTATCT
1 CTGATAATTCTTCTCAATTTATCA
17180 CTGATAATTC-TCTCAATTTATCA
1 CTGATAATTCTTCTCAATTTATCA
17203 CTTGATAAT
1 C-TGATAAT
17212 ATCTACACAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 11 0.41
23 9 0.33
24 7 0.26
ACGTcount: A:0.26, C:0.20, G:0.06, T:0.48
Consensus pattern (24 bp):
CTGATAATTCTTCTCAATTTATCA
Found at i:19335 original size:16 final size:15
Alignment explanation
Indices: 19297--19338 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
19287 ACAGAGATTG
*
19297 ACAAAAAGCAATTAA
1 ACAAAAAACAATTAA
*
19312 ACAGAAAACAATTAA
1 ACAAAAAACAATTAA
19327 ACTAAAAAACAA
1 AC-AAAAAACAA
19339 AGCAAAGTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.69, C:0.14, G:0.05, T:0.12
Consensus pattern (15 bp):
ACAAAAAACAATTAA
Found at i:20112 original size:11 final size:11
Alignment explanation
Indices: 20096--20121 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
20086 CCTTTGCCTA
20096 AAAACTAGAAG
1 AAAACTAGAAG
20107 AAAACTAGAAG
1 AAAACTAGAAG
20118 AAAA
1 AAAA
20122 GAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:22531 original size:5 final size:5
Alignment explanation
Indices: 22521--22548 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
22511 TGGAGGTTTT
22521 TAGTC TAGTC TAGTC TAGTC TAGTC TAG
1 TAGTC TAGTC TAGTC TAGTC TAGTC TAG
22549 GATTGATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.39
Consensus pattern (5 bp):
TAGTC
Found at i:23274 original size:36 final size:36
Alignment explanation
Indices: 23234--23358 Score: 209
Period size: 36 Copynumber: 3.5 Consensus size: 36
23224 AATTTAGCTC
23234 TTTTCAAATTGGGAAAGTTCCCATCAAGTTTTTAAG
1 TTTTCAAATTGGGAAAGTTCCCATCAAGTTTTTAAG
*
23270 TTTTCAAATTGGGAAAGTTCCCATCAAGTTCTTAAG
1 TTTTCAAATTGGGAAAGTTCCCATCAAGTTTTTAAG
23306 TTTTCAAATTGGGAAAGTTCCCATCAAG-TTTT-AG
1 TTTTCAAATTGGGAAAGTTCCCATCAAGTTTTTAAG
*
23340 TTTTCAATTTAGGGAAAGT
1 TTTTCAAATT-GGGAAAGT
23359 ACCCGTCATT
Statistics
Matches: 85, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
34 11 0.13
35 11 0.13
36 63 0.74
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (36 bp):
TTTTCAAATTGGGAAAGTTCCCATCAAGTTTTTAAG
Found at i:27182 original size:21 final size:21
Alignment explanation
Indices: 27158--27224 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
27148 AATTCTCTGT
27158 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * **
27179 AAATCATAGATAATTCTC-TGT-
1 AAATTA-AGA-AATACTCAACTC
27200 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
27221 AAAT
1 AAAT
27225 CATGATCCTT
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
19 6 0.18
20 4 0.12
21 14 0.41
22 4 0.12
23 6 0.18
ACGTcount: A:0.49, C:0.16, G:0.06, T:0.28
Consensus pattern (21 bp):
AAATTAAGAAATACTCAACTC
Found at i:27207 original size:42 final size:42
Alignment explanation
Indices: 27148--27227 Score: 160
Period size: 42 Copynumber: 1.9 Consensus size: 42
27138 AAGTCTTGAA
27148 AATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATAGAT
1 AATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATAGAT
27190 AATTCTCTGTAAATTAAGAAATACTCAACTCAAATCAT
1 AATTCTCTGTAAATTAAGAAATACTCAACTCAAATCAT
27228 GATCCTTAGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.45, C:0.17, G:0.06, T:0.31
Consensus pattern (42 bp):
AATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATAGAT
Found at i:27386 original size:55 final size:56
Alignment explanation
Indices: 27291--27395 Score: 185
Period size: 55 Copynumber: 1.9 Consensus size: 56
27281 TTTATTTTAT
* *
27291 AGAATAATTAAGTATAGATATTGGGGATAGGATTTATTATAACATTTATTGTGTGA
1 AGAATAATTAAGTAGAGATATGGGGGATAGGATTTATTATAACATTTATTGTGTGA
27347 AGAATAATTAAGTAGAGATA-GGGGGATAGGATTTATTATAACATTTATT
1 AGAATAATTAAGTAGAGATATGGGGGATAGGATTTATTATAACATTTATT
27396 TATTGTGTGA
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
55 28 0.60
56 19 0.40
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.37
Consensus pattern (56 bp):
AGAATAATTAAGTAGAGATATGGGGGATAGGATTTATTATAACATTTATTGTGTGA
Found at i:29342 original size:30 final size:30
Alignment explanation
Indices: 28895--29334 Score: 578
Period size: 30 Copynumber: 14.7 Consensus size: 30
28885 GGAAATTTAT
* *
28895 CATGACAACTTCT-G-GTCAATTGTAATAC
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
* * *
28923 CATTGACAACTTCTGATGTCAATTGTAAGAT
1 CA-TGACAACTTCTGGTGTCAATTGCAAGAC
* * * *
28954 CATGACAATTTCTGGTGTTAATTGCAATAT
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
*
28984 CATGACAACTTCTGGTGTCAATTGCAAGAG
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
*
29014 CATGACAACTTCTGGTGTCAATTGCAAGAG
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
* * *
29044 CAGGACAACTTCTGGTGTCAATTGCAAAAG
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
** *
29074 CATGACAACTTCAAGTGTCAATTGCAAGAG
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
* *
29104 CATGACAACTTCTGGTGTCAATTGCAGGAG
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
* * * *
29134 CATGACAAGTTCTAGTGTCAATTGAAAGAT
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
* * *
29164 CATGACAAGTTTTGGTGTCAATTGCAAGAT
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
29194 CATTGACAACTTCTGGTGTCAATTGCAAGAC
1 CA-TGACAACTTCTGGTGTCAATTGCAAGAC
*
29225 CATGACAACTTCTGGTGTCAATTGGAAGAC
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
29255 CATGACAACTTCTGGTGTCAATTGCAAGAC
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
* *
29285 CATGACAACTTCTGGTGTCATTTGTAAGAC
1 CATGACAACTTCTGGTGTCAATTGCAAGAC
*
29315 CATGACAATTTCTGGTGTCA
1 CATGACAACTTCTGGTGTCA
29335 TTTGTAAGTA
Statistics
Matches: 371, Mismatches: 37, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
28 2 0.01
29 11 0.03
30 317 0.85
31 41 0.11
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.30
Consensus pattern (30 bp):
CATGACAACTTCTGGTGTCAATTGCAAGAC
Found at i:30803 original size:41 final size:41
Alignment explanation
Indices: 30746--30827 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
30736 AATGGTATGG
*
30746 GAGGTGAGAAAAAATGATGATGAAAAAGGGGACGGAAATTT
1 GAGGTGAGAAAAAATGATGATGAAAAAGGGGACGAAAATTT
*
30787 GAGGTGAGAAAAAATGATGTTGAAAAAGGGGACGAAAATTT
1 GAGGTGAGAAAAAATGATGATGAAAAAGGGGACGAAAATTT
30828 TCAAAGCTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.46, C:0.02, G:0.33, T:0.18
Consensus pattern (41 bp):
GAGGTGAGAAAAAATGATGATGAAAAAGGGGACGAAAATTT
Found at i:32207 original size:27 final size:27
Alignment explanation
Indices: 32177--32228 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
32167 AAGTATACTC
*
32177 CTTTTGTTCTTTTTTAATTGTCCCTTT
1 CTTTTGTTCCTTTTTAATTGTCCCTTT
32204 CTTTTGTTCCTTTTTAATTGTCCCT
1 CTTTTGTTCCTTTTTAATTGTCCCT
32229 CATATTTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.08, C:0.21, G:0.08, T:0.63
Consensus pattern (27 bp):
CTTTTGTTCCTTTTTAATTGTCCCTTT
Found at i:32895 original size:12 final size:12
Alignment explanation
Indices: 32878--32916 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
32868 TGTAATGATC
*
32878 ATGAAGAAGCAG
1 ATGAAGAAGAAG
32890 ATGAAGAAGAAGG
1 ATGAAGAAGAA-G
32903 A-GAAGAAGAAG
1 ATGAAGAAGAAG
32914 ATG
1 ATG
32917 CTGCTGCTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
11 2 0.08
12 20 0.83
13 2 0.08
ACGTcount: A:0.54, C:0.03, G:0.36, T:0.08
Consensus pattern (12 bp):
ATGAAGAAGAAG
Found at i:32900 original size:15 final size:15
Alignment explanation
Indices: 32880--32914 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
32870 TAATGATCAT
*
32880 GAAGAAGCAGATGAA
1 GAAGAAGCAGAAGAA
*
32895 GAAGAAGGAGAAGAA
1 GAAGAAGCAGAAGAA
32910 GAAGA
1 GAAGA
32915 TGCTGCTGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.57, C:0.03, G:0.37, T:0.03
Consensus pattern (15 bp):
GAAGAAGCAGAAGAA
Found at i:48833 original size:21 final size:22
Alignment explanation
Indices: 48809--48851 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
48799 ATGCTTCTCT
* *
48809 TATCCAAACAAATTC-TTTCTG
1 TATCAAAACAAATACATTTCTG
48830 TATCAAAACAAATACATTTCTG
1 TATCAAAACAAATACATTTCTG
48852 CCATTTGAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.35
Consensus pattern (22 bp):
TATCAAAACAAATACATTTCTG
Found at i:51319 original size:16 final size:16
Alignment explanation
Indices: 51298--51330 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
51288 ACAGATTGCC
51298 TATCAATAAGAATTTG
1 TATCAATAAGAATTTG
*
51314 TATCAATAGGAATTTG
1 TATCAATAAGAATTTG
51330 T
1 T
51331 GGAGTCTCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.15, T:0.39
Consensus pattern (16 bp):
TATCAATAAGAATTTG
Found at i:55472 original size:41 final size:41
Alignment explanation
Indices: 55427--55522 Score: 138
Period size: 41 Copynumber: 2.3 Consensus size: 41
55417 ATTAGGAACC
* *
55427 AAATTGAATTAAATAGTAACTAAAATCCTAAATCAGGGGCT
1 AAATTGAATCAAATAGTAACTAAAATCCTAAATCAGGGGCG
* * *
55468 AAATTGCATCAAGTAGTTACTAAAATCCTAAATCAGGGGCG
1 AAATTGAATCAAATAGTAACTAAAATCCTAAATCAGGGGCG
*
55509 AAATTGAATGAAAT
1 AAATTGAATCAAAT
55523 CACACAAATC
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.26
Consensus pattern (41 bp):
AAATTGAATCAAATAGTAACTAAAATCCTAAATCAGGGGCG
Found at i:57401 original size:16 final size:15
Alignment explanation
Indices: 57363--57404 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
57353 ACAGAGATTG
*
57363 ACAGAAAGCAATTAA
1 ACAGAAAACAATTAA
57378 ACAGAAAACAATTAA
1 ACAGAAAACAATTAA
57393 ACTAGAAAACAA
1 AC-AGAAAACAA
57405 AGCAGAGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.64, C:0.14, G:0.10, T:0.12
Consensus pattern (15 bp):
ACAGAAAACAATTAA
Found at i:58165 original size:11 final size:11
Alignment explanation
Indices: 58149--58174 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
58139 CCTTTCCCTA
58149 AAAACTAGAAG
1 AAAACTAGAAG
58160 AAAACTAGAAG
1 AAAACTAGAAG
58171 AAAA
1 AAAA
58175 AGAAATTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:58822 original size:29 final size:29
Alignment explanation
Indices: 58766--58823 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
58756 CTTGAAATAA
* *
58766 ATCTTCAATGGTCTTCAAGTCTCCAATTT
1 ATCTTCAATGGTCTTCAAGACACCAATTT
*
58795 ATCTTCAAATGGTCTTCAA-ACACGAATTT
1 ATCTTC-AATGGTCTTCAAGACACCAATTT
58824 CGAATCTCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.38
Consensus pattern (29 bp):
ATCTTCAATGGTCTTCAAGACACCAATTT
Done.