Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011964.1 Corchorus olitorius cultivar O-4 contig11997, 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: 37491
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Found at i:2864 original size:15 final size:16
Alignment explanation
Indices: 2844--2879 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
2834 TGTCGACTTA
2844 AAGGATC-AAGTCGAT
1 AAGGATCAAAGTCGAT
2859 AAGGATCAAAGTCGAT
1 AAGGATCAAAGTCGAT
2875 AAGGA
1 AAGGA
2880 GCAGGTGTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.44, C:0.11, G:0.28, T:0.17
Consensus pattern (16 bp):
AAGGATCAAAGTCGAT
Found at i:2926 original size:21 final size:23
Alignment explanation
Indices: 2897--2950 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
2887 TCGACTAGGG
2897 AATTGTCGAC-CAA-AGGAAGCA
1 AATTGTCGACTCAAGAGGAAGCA
*
2918 AATTTTCGACTCAAGAGGAAGCA
1 AATTGTCGACTCAAGAGGAAGCA
*
2941 AATCGTCGAC
1 AATTGTCGAC
2951 AAGAAGGCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 9 0.32
22 3 0.11
23 16 0.57
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.19
Consensus pattern (23 bp):
AATTGTCGACTCAAGAGGAAGCA
Found at i:2940 original size:23 final size:21
Alignment explanation
Indices: 2897--2964 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 21
2887 TCGACTAGGG
2897 AATTGTCGACCAAAGGAAGCA
1 AATTGTCGACCAAAGGAAGCA
*
2918 AATTTTCGACTCAAGAGGAAGCA
1 AATTGTCGAC-CAA-AGGAAGCA
* *
2941 AATCGTCGACAAGAAGGCAAGCA
1 AATTGTCGACCA-AAGG-AAGCA
2964 A
1 A
2965 GGAATTTCGA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
21 9 0.23
22 7 0.18
23 23 0.59
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.15
Consensus pattern (21 bp):
AATTGTCGACCAAAGGAAGCA
Found at i:5498 original size:22 final size:21
Alignment explanation
Indices: 5473--5526 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
5463 GAAGTTCGTG
5473 TTTGAAGACTTATTGAAGATAA
1 TTTGAAGA-TTATTGAAGATAA
*
5495 TTTGAAGA-T-TTGAAGATCA
1 TTTGAAGATTATTGAAGATAA
5514 -TTGAAGAATTATT
1 TTTGAAG-ATTATT
5527 TCCAAGAAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 10 0.36
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39
Consensus pattern (21 bp):
TTTGAAGATTATTGAAGATAA
Found at i:8393 original size:119 final size:119
Alignment explanation
Indices: 8182--8420 Score: 442
Period size: 119 Copynumber: 2.0 Consensus size: 119
8172 ATTACTGTCA
* *
8182 TTTCCTTGATTGATGCGGGATTTCGATTATTTTTCTCTCAAGTCAGTACTCGGTTTCCTTTAATT
1 TTTCCTTGATTGATGCAGGATTTCGATTATTTTTCTCTCAAGTCAATACTCGGTTTCCTTTAATT
8247 TGTTGGAGGTTCGGACTCATGATTGCTTAATTGGACTGGCCCCTCCTTATTAAC
66 TGTTGGAGGTTCGGACTCATGATTGCTTAATTGGACTGGCCCCTCCTTATTAAC
* *
8301 TTTCCTTGATTGATGCAGGATTTGGATTATTTTTCTCTCAAGTCAATACTCGGTTTCTTTTAATT
1 TTTCCTTGATTGATGCAGGATTTCGATTATTTTTCTCTCAAGTCAATACTCGGTTTCCTTTAATT
8366 TGTTGGAGGTTCGGACTCATGATTGCTTAATTGGACTGGCCCCTCCTTATTAAC
66 TGTTGGAGGTTCGGACTCATGATTGCTTAATTGGACTGGCCCCTCCTTATTAAC
8420 T
1 T
8421 ATGCGCCTAT
Statistics
Matches: 116, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
119 116 1.00
ACGTcount: A:0.18, C:0.19, G:0.20, T:0.43
Consensus pattern (119 bp):
TTTCCTTGATTGATGCAGGATTTCGATTATTTTTCTCTCAAGTCAATACTCGGTTTCCTTTAATT
TGTTGGAGGTTCGGACTCATGATTGCTTAATTGGACTGGCCCCTCCTTATTAAC
Found at i:12139 original size:53 final size:53
Alignment explanation
Indices: 12005--12152 Score: 167
Period size: 54 Copynumber: 2.8 Consensus size: 53
11995 TACAATCAAA
* * * *
12005 AGTTTAAATCAGAGCAATTAAACTAAAGGGTAGAAGAAGAAGTAAACAAAGGCT
1 AGTTT-AATCAGAGCGATTAAACTAAAGAGTAAAAGAAGAAGTAAACAAAGACT
* * * *
12059 AGTTTAATTCTGGGTGATTAAACTAAAGAGTAAAAGAAGAAGTAAGCAGAA-AC-
1 AGTTTAA-TCAGAGCGATTAAACTAAAGAGTAAAAGAAGAAGTAAACA-AAGACT
12112 AGTTTCAATCAGAGCGATTAAACTAAAGAGTAAAAG-AGAAG
1 AGTTT-AATCAGAGCGATTAAACTAAAGAGTAAAAGAAGAAG
12153 AGGTTAGTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
52 5 0.06
53 32 0.40
54 41 0.51
55 2 0.03
ACGTcount: A:0.49, C:0.09, G:0.22, T:0.20
Consensus pattern (53 bp):
AGTTTAATCAGAGCGATTAAACTAAAGAGTAAAAGAAGAAGTAAACAAAGACT
Found at i:12208 original size:48 final size:47
Alignment explanation
Indices: 12128--12309 Score: 291
Period size: 48 Copynumber: 3.9 Consensus size: 47
12118 AATCAGAGCG
*
12128 ATTAAACTAAAGAGTAAAAG-AGAAGAGGTTAGTTTAATTCTGGGTA
1 ATTAAACTAAAAAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGTA
12174 ATTAAACTAAATAAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGTA
1 ATTAAACTAAA-AAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGTA
12222 ATTAAACTAAATAAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGTA
1 ATTAAACTAAA-AAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGTA
* *
12270 ATTAAACTAAAGAGT--AA-AAGAAGATGTTAGTTTAATTCTG
1 ATTAAACTAAAAAGTAAAAGAAGAAGAGGTTAGTTTAATTCTG
12310 AGCACGTGCA
Statistics
Matches: 131, Mismatches: 3, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
44 22 0.17
45 2 0.02
46 11 0.08
47 11 0.08
48 85 0.65
ACGTcount: A:0.45, C:0.04, G:0.21, T:0.30
Consensus pattern (47 bp):
ATTAAACTAAAAAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGTA
Found at i:14076 original size:53 final size:54
Alignment explanation
Indices: 13938--14086 Score: 178
Period size: 53 Copynumber: 2.8 Consensus size: 54
13928 TACAATCAAA
* * * *
13938 AGTTTAAATCAGAACAATTAAACTAAAGGGTAAAAGAAGAAGTTAACAAAGGCT
1 AGTTTAAATCAGAGCGATTAAACTAAAGAGTAAAAGAAGAAGTTAACAAAGACT
* * * * *
13992 AGTTTAATTCCGGGTGATTAAACTAACGAGTAAAAGAAGAAG-TAAGCAGAA-AC-
1 AGTTTAAATCAGAGCGATTAAACTAAAGAGTAAAAGAAGAAGTTAA-CA-AAGACT
14045 AGTTTAAATCAGAGCGATTAAACTAAAGAGTAAAAGAAGAAG
1 AGTTTAAATCAGAGCGATTAAACTAAAGAGTAAAAGAAGAAG
14087 AGGTTAGATT
Statistics
Matches: 79, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
53 40 0.51
54 37 0.47
55 2 0.03
ACGTcount: A:0.50, C:0.09, G:0.21, T:0.20
Consensus pattern (54 bp):
AGTTTAAATCAGAGCGATTAAACTAAAGAGTAAAAGAAGAAGTTAACAAAGACT
Found at i:14114 original size:47 final size:47
Alignment explanation
Indices: 14061--14536 Score: 502
Period size: 47 Copynumber: 9.5 Consensus size: 47
14051 AATCAGAGCG
* *
14061 ATTAAACTAAAGAGTAAAAGAAGAAGAGGTTAGATTAATTCTGGGTA
1 ATTAAACTAAATAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGTA
14108 ATTAAACTAAATAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGTA
1 ATTAAACTAAATAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGTA
* *
14155 ATTAAACTAAATAGTAAAAGAAGGAGTAAACAGTAATTAGTTTAATTCTGGGTA
1 ATTAAACTAAATAGTAAAAG-A--AG--AAGAG--GTTAGTTTAATTCTGGGTA
* *
14209 ATTACACTAAAGAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGTA
1 ATTAAACTAAATAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGTA
* *
14256 ATTAAACTAAAGAGTAAAAGAAGAAGAGGTTAGTTTAATTCTAGGTA
1 ATTAAACTAAATAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGTA
14303 ATTAAACTAAATAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGTA
1 ATTAAACTAAATAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGTA
* **
14350 ATTAAACTAAATAGTAAAAGAAGGAGTAAACAATAATTAGTTTAATTCTGGGTA
1 ATTAAACTAAATAGTAAAAG-A--AG--AA-GA-GGTTAGTTTAATTCTGGGTA
* * *
14404 ATTACACTAAAGAGCAAAATAAGAAGTAAACAGAGGTTAGTTTAATTCTGGGTA
1 ATTAAACTAAATAG--TAA-AAGAAG---A-AGAGGTTAGTTTAATTCTGGGTA
* * * **
14458 ATTAAAGTAAAAAAAGTTAAAGAAGAAGTAAACAATAATTAGTTTAATTCTGGGTA
1 ATTAAACT--AAATAG-T-AA-AAGAAG--AA-GA-GGTTAGTTTAATTCTGGGTA
*
14514 ATTAGACTAAATAGTAAAAGAAG
1 ATTAAACTAAATAGTAAAAGAAG
14537 GAGTAAACAG
Statistics
Matches: 370, Mismatches: 35, Indels: 44
0.82 0.08 0.10
Matches are distributed among these distances:
47 193 0.52
48 2 0.01
49 4 0.01
50 4 0.01
51 8 0.02
52 8 0.02
53 3 0.01
54 98 0.26
55 6 0.02
56 41 0.11
57 3 0.01
ACGTcount: A:0.47, C:0.05, G:0.20, T:0.28
Consensus pattern (47 bp):
ATTAAACTAAATAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGTA
Found at i:14247 original size:148 final size:147
Alignment explanation
Indices: 13991--14536 Score: 618
Period size: 148 Copynumber: 3.6 Consensus size: 147
13981 TAACAAAGGC
* * ** * ** * *
13991 TAGTTTAATTCCGGGTGATTAAACTAACGAGTAAAAGAAGAAGTAAGCAGAAACAGTTTAAATCA
1 TAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGAAGTAAACAGAATTAGTTTAATTCT
* ** * *
14056 GAGCGATTAAACTAAAGAGTAAAAGAAGAAGAGGTTAGATTAATTCTGGGTAATTAAACTAAATA
66 GGGTAATTAAACTAAAGAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGTAATTAAACTAAAGA
14121 GTAAAAGAAGAAGAGGT
131 GTAAAAGAAGAAGAGGT
*
14138 TAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGGAGTAAACAGTAATTAGTTTAATTC
1 TAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGAAGTAAACAG-AATTAGTTTAATTC
*
14203 TGGGTAATTACACTAAAGAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGTAATTAAACTAAAG
65 TGGGTAATTAAACTAAAGAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGTAATTAAACTAAAG
14268 AGTAAAAGAAGAAGAGGT
130 AGTAAAAGAAGAAGAGGT
* *
14286 TAGTTTAATTCTAGGTAATTAAACTAAATAGTAAAAGAAGAAG-----AG-GTTAGTTTAATTCT
1 TAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGAAGTAAACAGAATTAGTTTAATTCT
* * ** *
14345 GGGTAATTAAACTAAATAGTAAAAGAAGGAGTAAACAATAATTAGTTTAATTCTGGGTAATTACA
66 GGGTAATTAAACTAAAGAGTAAAAG-A--AG--AA-GA-GGTTAGTTTAATTCTGGGTAATTAAA
*
14410 CTAAAGAGCAAAATAAGAAGTAAACAGAGGT
124 CTAAAGAG--TAA-AAGAAG---A-AGAGGT
* * * *
14441 TAGTTTAATTCTGGGTAATTAAAGTAAAAAAAGTTAAAGAAGAAGTAAACAATAATTAGTTTAAT
1 TAGTTTAATTCTGGGTAATTAAACT--AAATAGTAAAAGAAGAAGTAAAC-AGAATTAGTTTAAT
* *
14506 TCTGGGTAATTAGACTAAATAGTAAAAGAAG
63 TCTGGGTAATTAAACTAAAGAGTAAAAGAAG
14537 GAGTAAACAG
Statistics
Matches: 342, Mismatches: 33, Indels: 34
0.84 0.08 0.08
Matches are distributed among these distances:
141 36 0.11
142 1 0.00
143 2 0.01
144 2 0.01
146 2 0.01
147 45 0.13
148 159 0.46
150 2 0.01
151 6 0.02
154 1 0.00
155 29 0.08
157 16 0.05
161 2 0.01
163 2 0.01
164 37 0.11
ACGTcount: A:0.46, C:0.06, G:0.20, T:0.27
Consensus pattern (147 bp):
TAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGAAGTAAACAGAATTAGTTTAATTCT
GGGTAATTAAACTAAAGAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGTAATTAAACTAAAGA
GTAAAAGAAGAAGAGGT
Found at i:14305 original size:195 final size:199
Alignment explanation
Indices: 14061--14536 Score: 726
Period size: 195 Copynumber: 2.4 Consensus size: 199
14051 AATCAGAGCG
*
14061 ATTAAACTAAAGAGTAAAAGAAGAAGAGGTTAGATTAATTCTGGGTAATTAAACTAAATAGTAAA
1 ATTAAACTAAAGAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAA
*
14126 AGAAGAAGAGGTTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGGAGTAAACAGTAA
66 AGAAGAAGAGGTTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGGAGTAAACAATAA
*
14191 TTAGTTTAATTCTGGGTAATTACACTAAAGAG-TAA-AAGAAG-A-AGAGGTTAGTTTAATTCTG
131 TTAGTTTAATTCTGGGTAATTACACTAAAGAGAAAATAAGAAGAACAGAGGTTAGTTTAATTCTG
14252 GGTA
196 GGTA
*
14256 ATTAAACTAAAGAGTAAAAGAAGAAGAGGTTAGTTTAATTCTAGGTAATTAAACTAAATAGTAAA
1 ATTAAACTAAAGAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAA
14321 AGAAGAAGAGGTTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGGAGTAAACAATAA
66 AGAAGAAGAGGTTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGGAGTAAACAATAA
14386 TTAGTTTAATTCTGGGTAATTACACTAAAGAGCAAAATAAGAAGTAAACAGAGGTTAGTTTAATT
131 TTAGTTTAATTCTGGGTAATTACACTAAAGAG-AAAATAAGAAG--AACAGAGGTTAGTTTAATT
14451 CTGGGTA
193 CTGGGTA
* * * ** *
14458 ATTAAAGTAAAAAAAGTTAAAGAAGAAGTAAACAATAATTAGTTTAATTCTGGGTAATTAGACTA
1 ATTAAACT--AAAGAG-T-AA-AAGAAG--AA-GA-GGTTAGTTTAATTCTGGGTAATTAAACTA
14523 AATAGTAAAAGAAG
57 AATAGTAAAAGAAG
14537 GAGTAAACAG
Statistics
Matches: 254, Mismatches: 11, Indels: 16
0.90 0.04 0.06
Matches are distributed among these distances:
195 159 0.63
197 2 0.01
198 6 0.02
201 1 0.00
202 30 0.12
204 5 0.02
205 1 0.00
206 2 0.01
207 6 0.02
209 2 0.01
210 1 0.00
211 39 0.15
ACGTcount: A:0.47, C:0.05, G:0.20, T:0.28
Consensus pattern (199 bp):
ATTAAACTAAAGAGTAAAAGAAGAAGAGGTTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAA
AGAAGAAGAGGTTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGGAGTAAACAATAA
TTAGTTTAATTCTGGGTAATTACACTAAAGAGAAAATAAGAAGAACAGAGGTTAGTTTAATTCTG
GGTA
Found at i:14507 original size:110 final size:108
Alignment explanation
Indices: 13953--14607 Score: 506
Period size: 94 Copynumber: 6.4 Consensus size: 108
13943 AAATCAGAAC
** * ** * * *
13953 AATTAAACTAAAGGGTAAAAGAAGAAGTTAACAA-AGGCTAGTTTAATTCCGGGTGATTAAACTA
1 AATTAAACTAAAAAGTAAAAGAAGAAGTAAACAATA-ATTAGTTTAATTCTGGGTAATTACACTA
* * * *** * * * *
14017 ACGAGTAAAAGAAGAAGTAAGCAGA-AACAGTTTAAATCAGAGC
65 AAGAGCAAAAGAAGAAGTAAACAGAGGTTAGTTTAATTCTGGGT
* * ** * *
14060 GATTAAACTAAAGAGTAAAAGAAGAAG------A-GGTTAGATTAATTCTGGGTAATTAAACTAA
1 AATTAAACTAAAAAGTAAAAGAAGAAGTAAACAATAATTAGTTTAATTCTGGGTAATTACACTAA
* *
14118 ATAG--TAA-AAGAAG---A-AGAGGTTAGTTTAATTCTGGGT
66 AGAGCAAAAGAAGAAGTAAACAGAGGTTAGTTTAATTCTGGGT
* * *
14154 AATTAAACTAAATAGTAAAAGAAGGAGTAAACAGTAATTAGTTTAATTCTGGGTAATTACACTAA
1 AATTAAACTAAAAAGTAAAAGAAGAAGTAAACAATAATTAGTTTAATTCTGGGTAATTACACTAA
*
14219 AGAG--TAA-AAGAAG---A-AGAGGTTAGTTTAATTCTGGGT
66 AGAGCAAAAGAAGAAGTAAACAGAGGTTAGTTTAATTCTGGGT
* ** * *
14255 AATTAAACTAAAGAGTAAAAGAAGAAG------A-GGTTAGTTTAATTCTAGGTAATTAAACTAA
1 AATTAAACTAAAAAGTAAAAGAAGAAGTAAACAATAATTAGTTTAATTCTGGGTAATTACACTAA
* *
14313 ATAG--TAA-AAGAAG---A-AGAGGTTAGTTTAATTCTGGGT
66 AGAGCAAAAGAAGAAGTAAACAGAGGTTAGTTTAATTCTGGGT
* *
14349 AATTAAACTAAATAGTAAAAGAAGGAGTAAACAATAATTAGTTTAATTCTGGGTAATTACACTAA
1 AATTAAACTAAAAAGTAAAAGAAGAAGTAAACAATAATTAGTTTAATTCTGGGTAATTACACTAA
*
14414 AGAGCAAAATAAGAAGTAAACAGAGGTTAGTTTAATTCTGGGT
66 AGAGCAAAAGAAGAAGTAAACAGAGGTTAGTTTAATTCTGGGT
* * *
14457 AATTAAAGTAAAAAAAGTTAAAGAAGAAGTAAACAATAATTAGTTTAATTCTGGGTAATTAGACT
1 AATTAAACT--AAAAAGTAAAAGAAGAAGTAAACAATAATTAGTTTAATTCTGGGTAATTACACT
* * * * * *
14522 AAATAGTAAAAGAAGGAGTAAACAGTA-ATTAGTTTAATTCTAGAT
64 AAAGAGCAAAAGAAGAAGTAAACAG-AGGTTAGTTTAATTCTGGGT
*** * *
14567 AATTAAACTAGGGAGTAAAAGAA-AGAGTAAGCAGTAATTAG
1 AATTAAACTAAAAAGTAAAAGAAGA-AGTAAACAATAATTAG
14608 CAACCAAAAA
Statistics
Matches: 460, Mismatches: 62, Indels: 51
0.80 0.11 0.09
Matches are distributed among these distances:
93 3 0.01
94 121 0.26
97 6 0.01
98 2 0.00
100 28 0.06
101 116 0.25
103 2 0.00
104 6 0.01
107 27 0.06
108 54 0.12
110 94 0.20
111 1 0.00
ACGTcount: A:0.47, C:0.06, G:0.20, T:0.27
Consensus pattern (108 bp):
AATTAAACTAAAAAGTAAAAGAAGAAGTAAACAATAATTAGTTTAATTCTGGGTAATTACACTAA
AGAGCAAAAGAAGAAGTAAACAGAGGTTAGTTTAATTCTGGGT
Found at i:14553 original size:54 final size:54
Alignment explanation
Indices: 14332--14607 Score: 338
Period size: 54 Copynumber: 5.1 Consensus size: 54
14322 GAAGAAGAGG
* *
14332 TTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAGAAGGAGTAAACAATAA
1 TTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGGAGTAAACAGTAA
* * * * *
14386 TTAGTTTAATTCTGGGTAATTACACTAAAGAGCAAAATAAGAAGTAAACAG-AGG
1 TTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGGAGTAAACAGTA-A
* * * * *
14440 TTAGTTTAATTCTGGGTAATTAAAGTAAAAAAAGTTAAAGAAGAAGTAAACAATAA
1 TTAGTTTAATTCTGGGTAATTAAACT--AAAGAGTAAAAGAAGGAGTAAACAGTAA
* *
14496 TTAGTTTAATTCTGGGTAATTAGACTAAATAGTAAAAGAAGGAGTAAACAGTAA
1 TTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGGAGTAAACAGTAA
* * ** * *
14550 TTAGTTTAATTCTAGATAATTAAACTAGGGAGTAAAAGAAAGAGTAAGCAGTAA
1 TTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGGAGTAAACAGTAA
14604 TTAG
1 TTAG
14608 CAACCAAAAA
Statistics
Matches: 189, Mismatches: 29, Indels: 8
0.84 0.13 0.04
Matches are distributed among these distances:
53 1 0.01
54 143 0.76
56 44 0.23
57 1 0.01
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.29
Consensus pattern (54 bp):
TTAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGGAGTAAACAGTAA
Found at i:17514 original size:28 final size:27
Alignment explanation
Indices: 17415--17514 Score: 119
Period size: 27 Copynumber: 3.7 Consensus size: 27
17405 GGTCACATAG
* * * * *
17415 GGGGCATGTTAGTCATTTACACGTCCA
1 GGGGCATTTTGGTCATTTGCACATTCA
*
17442 TGGGCATTTTGGTCATTTGCACATTCA
1 GGGGCATTTTGGTCATTTGCACATTCA
*
17469 TGGGCATTTTGGTCATTTGCACATTCA
1 GGGGCATTTTGGTCATTTGCACATTCA
*
17496 GGGGGGATTTTGGTCATTT
1 -GGGGCATTTTGGTCATTT
17515 TAAGTTCACT
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
27 48 0.75
28 16 0.25
ACGTcount: A:0.18, C:0.17, G:0.27, T:0.38
Consensus pattern (27 bp):
GGGGCATTTTGGTCATTTGCACATTCA
Found at i:20117 original size:41 final size:41
Alignment explanation
Indices: 20005--20107 Score: 188
Period size: 41 Copynumber: 2.5 Consensus size: 41
19995 TTTCAGATTT
*
20005 TATTTATTAATTGGTTCAATTATGTCCCTGATTAAGGGTAA
1 TATTTATTAATTGGTTCAATTATGTCCCTGATTTAGGGTAA
*
20046 TATTTATTAATTGGTTCAATTATGTCCCTGATTTAGGTTAA
1 TATTTATTAATTGGTTCAATTATGTCCCTGATTTAGGGTAA
20087 TATTTATTAATTGGTTCAATT
1 TATTTATTAATTGGTTCAATT
20108 TCATCCCTGA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.28, C:0.09, G:0.15, T:0.49
Consensus pattern (41 bp):
TATTTATTAATTGGTTCAATTATGTCCCTGATTTAGGGTAA
Found at i:20123 original size:41 final size:41
Alignment explanation
Indices: 20005--20123 Score: 179
Period size: 41 Copynumber: 2.9 Consensus size: 41
19995 TTTCAGATTT
20005 TATTTATTAATTGGTTCAATTATGTCCCTG-ATTAAGGGTAA
1 TATTTATTAATTGGTTCAATTATGTCCCTGAATT-AGGGTAA
* *
20046 TATTTATTAATTGGTTCAATTATGTCCCTGATTTAGGTTAA
1 TATTTATTAATTGGTTCAATTATGTCCCTGAATTAGGGTAA
*
20087 TATTTATTAATTGGTTCAATT-TCATCCCTGAATTAGG
1 TATTTATTAATTGGTTCAATTAT-GTCCCTGAATTAGG
20124 ATTTTATTTT
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
40 1 0.01
41 69 0.96
42 2 0.03
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.46
Consensus pattern (41 bp):
TATTTATTAATTGGTTCAATTATGTCCCTGAATTAGGGTAA
Found at i:20132 original size:41 final size:41
Alignment explanation
Indices: 20000--20132 Score: 164
Period size: 41 Copynumber: 3.2 Consensus size: 41
19990 CTTGATTTCA
*
20000 GATTTTATTTATTAATTGGTTCAATTATGTCCCTG-ATTAAG
1 GATTATATTTATTAATTGGTTCAATTATGTCCCTGAATT-AG
* * *
20041 GGTAATATTTATTAATTGGTTCAATTATGTCCCTGATTTAG
1 GATTATATTTATTAATTGGTTCAATTATGTCCCTGAATTAG
*
20082 G-TTAATATTTATTAATTGGTTCAATT-TCATCCCTGAATTAG
1 GATT-ATATTTATTAATTGGTTCAATTAT-GTCCCTGAATTAG
*
20123 GATTTTATTT
1 GATTATATTT
20133 TTGATTTATG
Statistics
Matches: 80, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
40 2 0.03
41 74 0.93
42 4 0.05
ACGTcount: A:0.27, C:0.10, G:0.14, T:0.49
Consensus pattern (41 bp):
GATTATATTTATTAATTGGTTCAATTATGTCCCTGAATTAG
Found at i:20788 original size:8 final size:8
Alignment explanation
Indices: 20767--20816 Score: 55
Period size: 8 Copynumber: 6.0 Consensus size: 8
20757 GTCAAAGTTG
20767 AAGAAAATA
1 AAGAAAA-A
20776 AAGAAAAA
1 AAGAAAAA
*
20784 AAGAAGAA
1 AAGAAAAA
*
20792 AGGAAAAA
1 AAGAAAAA
*
20800 ATGAAAAA
1 AAGAAAAA
20808 AAGGAAAAA
1 AA-GAAAAA
20817 CTAGAAAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
8 22 0.63
9 13 0.37
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (8 bp):
AAGAAAAA
Found at i:20810 original size:17 final size:17
Alignment explanation
Indices: 20767--20816 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
20757 GTCAAAGTTG
20767 AAGAAAATAAA-GAAAAA
1 AAGAAAA-AAAGGAAAAA
*
20784 AAG-AAGAAAGGAAAAA
1 AAGAAAAAAAGGAAAAA
*
20800 ATGAAAAAAAGGAAAAA
1 AAGAAAAAAAGGAAAAA
20817 CTAGAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 3 0.11
16 10 0.36
17 15 0.54
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (17 bp):
AAGAAAAAAAGGAAAAA
Found at i:20824 original size:17 final size:17
Alignment explanation
Indices: 20768--20824 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
20758 TCAAAGTTGA
*
20768 AGAAAATAAAGAAAAAA-
1 AGAAAA-AAGGAAAAAAT
*
20785 AGAAGAAAGGAAAAAAT
1 AGAAAAAAGGAAAAAAT
*
20802 -GAAAAAAAGGAAAAACT
1 AG-AAAAAAGGAAAAAAT
20819 AGAAAA
1 AGAAAA
20825 TTAAAAGATG
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
16 10 0.30
17 22 0.67
18 1 0.03
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.05
Consensus pattern (17 bp):
AGAAAAAAGGAAAAAAT
Found at i:25553 original size:7 final size:7
Alignment explanation
Indices: 25518--25618 Score: 57
Period size: 7 Copynumber: 13.7 Consensus size: 7
25508 AGAAATTCGA
25518 AAAAAAT
1 AAAAAAT
*
25525 AATAATAAC
1 AA-AA-AAT
25534 AAAAAAGT
1 AAAAAA-T
*
25542 CAAAAAT
1 AAAAAAT
25549 AAAAAAT
1 AAAAAAT
25556 AAAAACA-
1 AAAAA-AT
25563 AAAAAAT
1 AAAAAAT
25570 CGAATCAAAAT
1 --AA--AAAAT
*
25581 -CAAAAT
1 AAAAAAT
25587 AAAAAAT
1 AAAAAAT
25594 AAAAAA-
1 AAAAAAT
25600 AAAAACA-
1 AAAAA-AT
*
25607 AAAAAAC
1 AAAAAAT
25614 AAAAA
1 AAAAA
25619 GAAAAAAAAA
Statistics
Matches: 76, Mismatches: 6, Indels: 24
0.72 0.06 0.23
Matches are distributed among these distances:
6 12 0.16
7 43 0.57
8 10 0.13
9 6 0.08
11 5 0.07
ACGTcount: A:0.79, C:0.08, G:0.02, T:0.11
Consensus pattern (7 bp):
AAAAAAT
Found at i:25591 original size:12 final size:13
Alignment explanation
Indices: 25576--25628 Score: 56
Period size: 12 Copynumber: 4.2 Consensus size: 13
25566 AAATCGAATC
*
25576 AAAATCAAAATAA
1 AAAATCAAAAAAA
25589 AAAAT-AAAAAAA
1 AAAATCAAAAAAA
25601 AAAA-CAAAAAAA
1 AAAATCAAAAAAA
**
25613 CAAAAAGAAAAAAA
1 -AAAATCAAAAAAA
25627 AA
1 AA
25629 GGAGAATTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
12 17 0.49
13 11 0.31
14 7 0.20
ACGTcount: A:0.87, C:0.06, G:0.02, T:0.06
Consensus pattern (13 bp):
AAAATCAAAAAAA
Found at i:25617 original size:38 final size:38
Alignment explanation
Indices: 25544--25617 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
25534 AAAAAAGTCA
*** *
25544 AAAATAAAAAATAAAAACAAAAAAATCGAATCAAAATC
1 AAAATAAAAAATAAAAACAAAAAAAAAAAAACAAAATC
25582 AAAATAAAAAATAAAAA-AAAAAACAAAAAAACAAAA
1 AAAATAAAAAATAAAAACAAAAAA-AAAAAAACAAAA
25618 AGAAAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 6 0.19
38 25 0.81
ACGTcount: A:0.81, C:0.08, G:0.01, T:0.09
Consensus pattern (38 bp):
AAAATAAAAAATAAAAACAAAAAAAAAAAAACAAAATC
Found at i:27354 original size:69 final size:69
Alignment explanation
Indices: 27262--27550 Score: 321
Period size: 69 Copynumber: 4.2 Consensus size: 69
27252 AATGTTTTGA
* * * * *
27262 CTTTTCCATAAGTCAAGCTCGTTTCCA-AGCGAGTCAATTTTAGCTTTGGTTCCATCCAAACAGC
1 CTTTTCCATAAGCCAAACTCGTTTCCATA-CGAGTCAGTTTAAACTTTGGTTCCATCCAAACAGC
27326 ATAGG
65 ATAGG
* * * *
27331 TTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTTGAACTTTGGTTCCATCCAAGCCA-C
1 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAACTTTGGTTCCATCCAA-ACAGC
27395 ATAGG
65 ATAGG
* * * * * * * * *
27400 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGACAGTTCAAGCCTTGGTTACATCCAAGCCGTA
1 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAACTTTGGTTCCATCCAAACAGCA
*
27465 TAGA
66 TAGG
* * * * *
27469 CTTTTCCATAAGTCAAACTCGCTTCCATGCGAGTCAGTTTAAACATTGGTTCCATCCATACAGCA
1 CTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAACTTTGGTTCCATCCAAACAGCA
*
27534 GAGG
66 TAGG
27538 CTTTTCCATAAGC
1 CTTTTCCATAAGC
27551 TAAGTTTAAT
Statistics
Matches: 182, Mismatches: 35, Indels: 6
0.82 0.16 0.03
Matches are distributed among these distances:
68 1 0.01
69 178 0.98
70 3 0.02
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (69 bp):
CTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCAGTTTAAACTTTGGTTCCATCCAAACAGCA
TAGG
Found at i:27927 original size:169 final size:169
Alignment explanation
Indices: 27645--27960 Score: 483
Period size: 169 Copynumber: 1.9 Consensus size: 169
27635 TCTATACAAG
* * *
27645 TTAAGTTTAAAATCCTTGGTCAAGGTCTCTTTTCAGAGTTTACATTGGTAAGTCCTCCGGGCACA
1 TTAAGTTTAAAATCCTTGGTCAAGGTCTCATTTCAAAGTTTACACTGGTAAGTCCTCCGGGCACA
* * * * *
27710 AATTCAGAAACCTCCGAGTATTAATTCTGATAAGTCCTCCGGGCAATTGGTAAAGCCTCCGGGTA
66 AATTCAGAAACCTCCGAGTATTAATCCTAATAAGTCCTCCGAGCAATTGATAAAACCTCCGGGTA
27775 CCATTTAATTTCATAAAGTTTTTCATCAAAGATTCATGT
131 CCATTTAATTTCATAAAGTTTTTCATCAAAGATTCATGT
* * *
27814 TTAAGTTTAAAATCCTTGTTCAAGGTCTCATTTCAAAGTTTGA-ACTGGTAAGTCCTTCGGGCAT
1 TTAAGTTTAAAATCCTTGGTCAAGGTCTCATTTCAAAGTTT-ACACTGGTAAGTCCTCCGGGCAC
*
27878 AATTTCAGAAACCTCC-AGGTATTAATCCTAATAAGTCCTCCGAGCAATTGATAAAACCTCCGGG
65 AAATTCAGAAACCTCCGA-GTATTAATCCTAATAAGTCCTCCGAGCAATTGATAAAACCTCCGGG
*
27942 TACCATTTGATTTCATAAA
129 TACCATTTAATTTCATAAA
27961 AAATTCATGT
Statistics
Matches: 132, Mismatches: 13, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
168 1 0.01
169 130 0.98
170 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (169 bp):
TTAAGTTTAAAATCCTTGGTCAAGGTCTCATTTCAAAGTTTACACTGGTAAGTCCTCCGGGCACA
AATTCAGAAACCTCCGAGTATTAATCCTAATAAGTCCTCCGAGCAATTGATAAAACCTCCGGGTA
CCATTTAATTTCATAAAGTTTTTCATCAAAGATTCATGT
Found at i:28094 original size:20 final size:20
Alignment explanation
Indices: 28057--28097 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
28047 GTATTAATTC
* **
28057 TGATAAGTCCTCTGGGCATT
1 TGATAAGACCTCCAGGCATT
28077 TGATAAGACCTCCAGGCATT
1 TGATAAGACCTCCAGGCATT
28097 T
1 T
28098 CATATTTTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (20 bp):
TGATAAGACCTCCAGGCATT
Found at i:28210 original size:30 final size:30
Alignment explanation
Indices: 28171--28293 Score: 174
Period size: 30 Copynumber: 4.1 Consensus size: 30
28161 GCTTTATCAG
28171 TTTACTTTTAATCCTGGTTTAGGATCATTGC
1 TTTA-TTTTAATCCTGGTTTAGGATCATTGC
* **
28202 TTTATTTTAATCCTGGTTGAGGATCATTAT
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
*
28232 TTTATTTTAATCCTGGTTTTGGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
* * *
28262 TTCATTTCAATCCTGATTTAGGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
28292 TT
1 TT
28294 CATCAGTTAA
Statistics
Matches: 81, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
30 77 0.95
31 4 0.05
ACGTcount: A:0.20, C:0.15, G:0.15, T:0.50
Consensus pattern (30 bp):
TTTATTTTAATCCTGGTTTAGGATCATTGC
Found at i:28323 original size:32 final size:30
Alignment explanation
Indices: 28249--28336 Score: 83
Period size: 32 Copynumber: 2.8 Consensus size: 30
28239 TAATCCTGGT
*
28249 TTTGGATCATTGCTTCAT--TTCAATCCTGA
1 TTTGGATCATTGCTTCATAGTT-AATCCCGA
28278 TTTAGGATCATTGCTTCATCAGTTAATCCCGA
1 TTT-GGATCATTGCTTCAT-AGTTAATCCCGA
*
28310 TGTTGGATTATTGCATT-ATGAGTTAAT
1 T-TTGGATCATTGC-TTCAT-AGTTAAT
28337 TTTAATCCTG
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
29 3 0.06
30 15 0.30
32 26 0.52
33 6 0.12
ACGTcount: A:0.24, C:0.16, G:0.17, T:0.43
Consensus pattern (30 bp):
TTTGGATCATTGCTTCATAGTTAATCCCGA
Found at i:28836 original size:27 final size:27
Alignment explanation
Indices: 28806--28904 Score: 135
Period size: 27 Copynumber: 3.7 Consensus size: 27
28796 GGTCACATAG
* * * * *
28806 GGGGCATGTTAGTCATTTACACGTCCA
1 GGGGCATTTTGGTCATTTGCACATTCA
28833 GGGGCATTTTGGTCATTTGCACATTCA
1 GGGGCATTTTGGTCATTTGCACATTCA
* *
28860 GGGCCATTTTGGTCATTTGCATATTCA
1 GGGGCATTTTGGTCATTTGCACATTCA
28887 GGGGCATTTTGGTCATTT
1 GGGGCATTTTGGTCATTT
28905 TAAGTTCACT
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 64 1.00
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.37
Consensus pattern (27 bp):
GGGGCATTTTGGTCATTTGCACATTCA
Found at i:31444 original size:41 final size:41
Alignment explanation
Indices: 31334--31445 Score: 163
Period size: 41 Copynumber: 2.7 Consensus size: 41
31324 TTTCGGATTT
* *
31334 TATTTATTAATTAGTTCAATTACGTCCCTGATTGAGGGTAA
1 TATTTATTAATTGGTTCAATTTCGTCCCTGATTGAGGGTAA
* *
31375 TATTTATTAATTGGTTCAA-TTCTGTCCCTGATTTAGGTTAA
1 TATTTATTAATTGGTTCAATTTC-GTCCCTGATTGAGGGTAA
*
31416 TATTTATTAATTGGTTCAATTTCATCCCTG
1 TATTTATTAATTGGTTCAATTTCGTCCCTG
31446 GAGGATTTTA
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
40 2 0.03
41 59 0.92
42 3 0.05
ACGTcount: A:0.26, C:0.13, G:0.14, T:0.46
Consensus pattern (41 bp):
TATTTATTAATTGGTTCAATTTCGTCCCTGATTGAGGGTAA
Done.