Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017419.1 Corchorus olitorius cultivar O-4 contig17452, 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: 24389
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:8727 original size:8 final size:8
Alignment explanation
Indices: 8714--8790 Score: 109
Period size: 8 Copynumber: 9.6 Consensus size: 8
8704 TGAAGCACCA
8714 AAGAATTG
1 AAGAATTG
8722 AAGAATTG
1 AAGAATTG
8730 AAGAATTG
1 AAGAATTG
*
8738 AAGTATTG
1 AAGAATTG
*
8746 AATAATTG
1 AAGAATTG
*
8754 AAAAATTG
1 AAGAATTG
*
8762 AAGCATTG
1 AAGAATTG
*
8770 AATAATTG
1 AAGAATTG
8778 AAGAATTG
1 AAGAATTG
8786 AAGAA
1 AAGAA
8791 AGACCACCCT
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
8 60 1.00
ACGTcount: A:0.51, C:0.01, G:0.21, T:0.27
Consensus pattern (8 bp):
AAGAATTG
Found at i:8819 original size:34 final size:34
Alignment explanation
Indices: 8780--8880 Score: 96
Period size: 34 Copynumber: 3.3 Consensus size: 34
8770 AATAATTGAA
8780 GAATTGAAGAAAGACCACCCTGGATCATTGAAAT
1 GAATTGAAGAAAGACCACCCTGGATCATTGAAAT
* *
8814 GAATT---G-AAG--CA--TTGGATAATTGAAA-
1 GAATTGAAGAAAGACCACCCTGGATCATTGAAAT
*
8839 -AATTGAAGAAAGACCACCCTGGATCATTGAAGT
1 GAATTGAAGAAAGACCACCCTGGATCATTGAAAT
*
8872 AAATTGAAG
1 GAATTGAAG
8881 CATTGAATAG
Statistics
Matches: 52, Mismatches: 5, Indels: 20
0.68 0.06 0.26
Matches are distributed among these distances:
24 4 0.08
26 12 0.23
27 1 0.02
28 5 0.10
30 5 0.10
31 1 0.02
32 11 0.21
34 13 0.25
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.23
Consensus pattern (34 bp):
GAATTGAAGAAAGACCACCCTGGATCATTGAAAT
Found at i:8843 original size:58 final size:58
Alignment explanation
Indices: 8756--8971 Score: 254
Period size: 58 Copynumber: 3.6 Consensus size: 58
8746 AATAATTGAA
*
8756 AAATTGAAGCATTGAATAATTGAAGAATTGAAGAAAGACCACCCTGGATCATTGAAAT
1 AAATTGAAGCATTGAATAATTGAAAAATTGAAGAAAGACCACCCTGGATCATTGAAAT
* * *
8814 GAATTGAAGCATTGGATAATTGAAAAATTGAAGAAAGACCACCCTGGATCATTGAAGT
1 AAATTGAAGCATTGAATAATTGAAAAATTGAAGAAAGACCACCCTGGATCATTGAAAT
* * * * *
8872 AAATTGAAGCATTGAATAGTTGAAGATTTGAATAATTGAAGAAAGACCATCATGGATCGTTGAAG
1 AAATTGAAGCATTG-A-A--T--A-A-TTGAAAAATTGAAGAAAGACCACCCTGGATCATTGAAA
8937 T
58 T
* *
8938 AAATTGATGCATTGAATCATTG-AAAATTGAAGAA
1 AAATTGAAGCATTGAATAATTGAAAAATTGAAGAA
8972 TTGAAGTATT
Statistics
Matches: 137, Mismatches: 13, Indels: 17
0.82 0.08 0.10
Matches are distributed among these distances:
57 11 0.08
58 70 0.51
59 1 0.01
60 1 0.01
62 2 0.01
64 2 0.01
65 2 0.01
66 48 0.35
ACGTcount: A:0.43, C:0.10, G:0.21, T:0.26
Consensus pattern (58 bp):
AAATTGAAGCATTGAATAATTGAAAAATTGAAGAAAGACCACCCTGGATCATTGAAAT
Found at i:8896 original size:16 final size:16
Alignment explanation
Indices: 8873--8913 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
8863 CATTGAAGTA
8873 AATTGAAGCA-TTGAAT
1 AATTGAAG-ATTTGAAT
*
8889 AGTTGAAGATTTGAAT
1 AATTGAAGATTTGAAT
8905 AATTGAAGA
1 AATTGAAGA
8914 AAGACCATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 1 0.05
16 21 0.95
ACGTcount: A:0.44, C:0.02, G:0.22, T:0.32
Consensus pattern (16 bp):
AATTGAAGATTTGAAT
Found at i:8958 original size:8 final size:7
Alignment explanation
Indices: 8956--9450 Score: 133
Period size: 8 Copynumber: 68.1 Consensus size: 7
8946 GCATTGAATC
*
8956 ATTGAAA
1 ATTGAAG
8963 ATTGAAG
1 ATTGAAG
8970 AATTGAAG
1 -ATTGAAG
8978 TATTGAA-
1 -ATTGAAG
*
8985 ATTGAAAC
1 ATTG-AAG
8993 ATTGAAGG
1 ATTGAA-G
9001 ATTGAA-
1 ATTGAAG
*
9007 TTTGAAG
1 ATTGAAG
9014 AATTGAA-
1 -ATTGAAG
9021 ATTG-AG
1 ATTGAAG
*
9027 CCATTGAAAT
1 --ATTG-AAG
9037 ATTGAA-
1 ATTGAAG
9043 ATTGAAG
1 ATTGAAG
9050 CATTGAAG
1 -ATTGAAG
9058 CATTGAAG
1 -ATTGAAG
9066 AATTG-A-
1 -ATTGAAG
9072 ATTGAA-
1 ATTGAAG
*
9078 ATCGAAG
1 ATTGAAG
*
9085 CATTGAAAT
1 -ATTG-AAG
9094 ATTGAA-
1 ATTGAAG
9100 ATTGAAG
1 ATTGAAG
9107 CATTGAAG
1 -ATTGAAG
9115 AATTGAA-
1 -ATTGAAG
*
9122 ATTGAAAC
1 ATTG-AAG
9130 ATTGAAGG
1 ATTGAA-G
9138 ATTGAA-
1 ATTGAAG
* *
9144 TTTAAAG
1 ATTGAAG
9151 AATTGAA-
1 -ATTGAAG
9158 ATTGAAG
1 ATTGAAG
*
9165 CATTGAAAT
1 -ATTG-AAG
9174 ATTGAA-
1 ATTGAAG
9180 ATTGAAG
1 ATTGAAG
9187 CATTGAAGG
1 -ATTGAA-G
*
9196 ATAG-A-
1 ATTGAAG
*
9201 ATCTGGAG
1 AT-TGAAG
*
9209 AATTGACAT
1 -ATTGA-AG
*
9218 ATTAAAG
1 ATTGAAG
*
9225 -TTGAAAC
1 ATTG-AAG
**
9232 ATTTTAG
1 ATTGAAG
9239 AATTGAA-
1 -ATTGAAG
*
9246 TTTGAAG
1 ATTGAAG
*
9253 AATGGAA-
1 -ATTGAAG
9260 ATTGAAG
1 ATTGAAG
*
9267 CATTGAAAT
1 -ATTG-AAG
9276 ATTGAA-
1 ATTGAAG
*
9282 ATTGAAAC
1 ATTG-AAG
9290 ATTGAAGG
1 ATTGAA-G
9298 ATTG-AG
1 ATTGAAG
*
9304 TTTGAAG
1 ATTGAAG
*
9311 CATTGAAT
1 -ATTGAAG
9319 ATTGAA-
1 ATTGAAG
9325 ATTGAAG
1 ATTGAAG
9332 CATTGAAG
1 -ATTGAAG
*
9340 AATTCAA-
1 -ATTGAAG
*
9347 ATTGAAAC
1 ATTG-AAG
*
9355 ATTGAAAA
1 ATTG-AAG
*
9363 ATTGTA-
1 ATTGAAG
9369 ATTGAAG
1 ATTGAAG
*
9376 CATTGAAAT
1 -ATTG-AAG
*
9385 ATTGGA-
1 ATTGAAG
*
9391 ATTGAATC
1 ATTGAA-G
9399 ATTGAAG
1 ATTGAAG
9406 AATTGAA-
1 -ATTGAAG
9413 ATTGAAG
1 ATTGAAG
*
9420 CATTGAATA
1 -ATTGAA-G
9429 ATTGAA-
1 ATTGAAG
9435 ATTGAAG
1 ATTGAAG
9442 CATTGAAG
1 -ATTGAAG
9450 A
1 A
9451 ATTAAAGAAA
Statistics
Matches: 375, Mismatches: 50, Indels: 126
0.68 0.09 0.23
Matches are distributed among these distances:
5 7 0.02
6 103 0.27
7 47 0.13
8 205 0.55
9 12 0.03
10 1 0.00
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.30
Consensus pattern (7 bp):
ATTGAAG
Found at i:8965 original size:23 final size:22
Alignment explanation
Indices: 8938--9194 Score: 137
Period size: 22 Copynumber: 11.8 Consensus size: 22
8928 TCGTTGAAGT
*
8938 AAATTGATGCATTGAA-TCATTG
1 AAATTGAAGCATTGAAGT-ATTG
*
8960 AAAATTGAAGAATTGAAGTATTG
1 -AAATTGAAGCATTGAAGTATTG
* *
8983 AAATTGAAACATTGAAGGATTG
1 AAATTGAAGCATTGAAGTATTG
* *
9005 AATTTGAAGAATTGAA--ATTG
1 AAATTGAAGCATTGAAGTATTG
* **
9025 AGCCATTGAAATATTGAA--ATTG
1 A--AATTGAAGCATTGAAGTATTG
*
9047 AAGCATTGAAGCATTGAAGAATTG
1 AA--ATTGAAGCATTGAAGTATTG
* *
9071 -AATTGAA--ATCGAAGCATTG
1 AAATTGAAGCATTGAAGTATTG
*
9090 AAATATTGAA--ATTGAAGCATTG
1 -AA-ATTGAAGCATTGAAGTATTG
**
9112 AAGAATTGAA--ATTGAAACATTG
1 -A-AATTGAAGCATTGAAGTATTG
* * *
9134 AAGGATTGAA--TTTAAAGAATTG
1 AA--ATTGAAGCATTGAAGTATTG
*
9156 AAATTGAAGCATTGAAATATTG
1 AAATTGAAGCATTGAAGTATTG
9178 AAATTGAAGCATTGAAG
1 AAATTGAAGCATTGAAG
9195 GATAGAATCT
Statistics
Matches: 191, Mismatches: 28, Indels: 31
0.76 0.11 0.12
Matches are distributed among these distances:
19 10 0.05
20 12 0.06
21 8 0.04
22 136 0.71
23 20 0.10
24 5 0.03
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.30
Consensus pattern (22 bp):
AAATTGAAGCATTGAAGTATTG
Found at i:8989 original size:14 final size:14
Alignment explanation
Indices: 8948--9448 Score: 140
Period size: 14 Copynumber: 36.0 Consensus size: 14
8938 AAATTGATGC
*
8948 ATTGAATCATTGAAA
1 ATTGAAGCATTG-AA
*
8963 ATTGAAGAATTGAA
1 ATTGAAGCATTGAA
8977 GTATTGAA--ATTGAAA
1 --ATTGAAGCATTG-AA
*
8992 CATTGAAGGATTGAA
1 -ATTGAAGCATTGAA
* *
9007 TTTGAAGAATTGAA
1 ATTGAAGCATTGAA
9021 ATTG-AGCCATTGAA
1 ATTGAAG-CATTGAA
9035 A-T-----ATTGAA
1 ATTGAAGCATTGAA
9043 ATTGAAGCATTGAA
1 ATTGAAGCATTGAA
*
9057 GCATTGAAGAATTG-A
1 --ATTGAAGCATTGAA
*
9072 ATTGAA--ATCGAA
1 ATTGAAGCATTGAA
**
9084 GCATTGAAATATTGAA
1 --ATTGAAGCATTGAA
9100 ATTGAAGCATTGAAGA
1 ATTGAAGCATTG-A-A
9116 ATTGAA--ATTGAAA
1 ATTGAAGCATTG-AA
*
9129 CATTGAAGGATTGAA
1 -ATTGAAGCATTGAA
* * *
9144 TTTAAAGAATTGAA
1 ATTGAAGCATTGAA
9158 ATTGAAGCATTGAAA
1 ATTGAAGCATTG-AA
9173 TATTGAA--ATTGAA
1 -ATTGAAGCATTGAA
* *
9186 GCATTGAAGGATAG-A
1 --ATTGAAGCATTGAA
* *
9201 ATCTGGAGAATTGACA
1 AT-TGAAGCATTGA-A
*
9217 TATTAAAG--TTGAAA
1 -ATTGAAGCATTG-AA
** *
9231 CATTTTAGAATTGAA
1 -ATTGAAGCATTGAA
* * *
9246 TTTGAAGAATGGAA
1 ATTGAAGCATTGAA
9260 ATTGAAGCATTGAAA
1 ATTGAAGCATTG-AA
9275 TATTGAA--ATTGAAA
1 -ATTGAAGCATTG-AA
* *
9289 CATTGAAGGATTGAG
1 -ATTGAAGCATTGAA
*
9304 TTTGAAGCATTGAA
1 ATTGAAGCATTGAA
9318 TATTGAA--ATTGAA
1 -ATTGAAGCATTGAA
* *
9331 GCATTGAAGAATTCAA
1 --ATTGAAGCATTGAA
*
9347 ATTGAAACATTG-A
1 ATTGAAGCATTGAA
*
9360 A---AA--ATTGTA
1 ATTGAAGCATTGAA
9369 ATTGAAGCATTGAAA
1 ATTGAAGCATTG-AA
*
9384 TATTG--GAATTGAA
1 -ATTGAAGCATTGAA
*
9397 TCATTGAAGAATTGAA
1 --ATTGAAGCATTGAA
9413 ATTGAAGCATTG-A
1 ATTGAAGCATTGAA
9426 A-T--A--ATTGAA
1 ATTGAAGCATTGAA
9435 ATTGAAGCATTGAA
1 ATTGAAGCATTGAA
9449 GAATTAAAGA
Statistics
Matches: 375, Mismatches: 50, Indels: 123
0.68 0.09 0.22
Matches are distributed among these distances:
8 15 0.04
9 5 0.01
10 4 0.01
11 3 0.01
12 5 0.01
13 26 0.07
14 202 0.54
15 33 0.09
16 80 0.21
17 2 0.01
ACGTcount: A:0.44, C:0.05, G:0.20, T:0.31
Consensus pattern (14 bp):
ATTGAAGCATTGAA
Found at i:9019 original size:36 final size:36
Alignment explanation
Indices: 8948--9448 Score: 165
Period size: 36 Copynumber: 14.0 Consensus size: 36
8938 AAATTGATGC
* *
8948 ATTGAATCATTGAAA-ATTGAAGAATTGAAGTATTGAA
1 ATTGAAACATTGAAAGATTG-A-AATTGAAGAATTGAA
* *
8985 ATTGAAACATTGAAGGATTGAATTTGAAGAATTGAA
1 ATTGAAACATTGAAAGATTGAAATTGAAGAATTGAA
** * *
9021 ATTGAGCCATTGAAATATTGAAATTGAAGCATTGAA
1 ATTGAAACATTGAAAGATTGAAATTGAAGAATTGAA
* *
9057 GCATTGAAGA-ATTGAATTGAAATCGAAGCATTGAA-ATATTGAA
1 --ATTGAA-ACATTGAA---AGATTGAA--ATTGAAGA-ATTGAA
*
9100 ATTGAAGCATTG-AAGAATTGAAATTGAA-ACATTGAA
1 ATTGAAACATTGAAAG-ATTGAAATTGAAGA-ATTGAA
* *
9136 GGATTG--A-ATTTAAAGAATTGAAATTGAAGCATTGAAA
1 --ATTGAAACATTGAAAG-ATTGAAATTGAAGAATTG-AA
*
9173 TATTG-AA-ATTG-AAGCATTG-AA-GGATAGAATCTGGAGA
1 -ATTGAAACATTGAAAG-ATTGAAATTGA-AGAAT-T-GA-A
* * **
9210 ATTGACATATT-AAAG-TTGAAACATTTTAGAATTGAA
1 ATTGAAACATTGAAAGATTG-AA-ATTGAAGAATTGAA
* *
9246 TTTGAAGA-A-TGGAA-ATTGAAGCATTGAA-ATATTGAA
1 ATTGAA-ACATTGAAAGATTGAA--ATTGAAGA-ATTGAA
* ** *
9282 ATTGAAACATTGAAGGATTGAGTTTGAAGCATTGAA
1 ATTGAAACATTGAAAGATTGAAATTGAAGAATTGAA
* *
9318 TATTG-AA-ATTG--A-A--G-CATTGAAGAATTCAA
1 -ATTGAAACATTGAAAGATTGAAATTGAAGAATTGAA
* * *
9347 ATTGAAACATTGAAAAATTGTAATTGAAGCATTGAA
1 ATTGAAACATTGAAAGATTGAAATTGAAGAATTGAA
*
9383 A-T-----ATTG-GA-ATTGAATCATTGAAGAATTGAA
1 ATTGAAACATTGAAAGATTGAA--ATTGAAGAATTGAA
* *
9413 ATTGAAGCATTGAATA-ATTGAAATTGAAGCATTGAA
1 ATTGAAACATTGAA-AGATTGAAATTGAAGAATTGAA
9449 GAATTAAAGA
Statistics
Matches: 352, Mismatches: 55, Indels: 115
0.67 0.11 0.22
Matches are distributed among these distances:
28 9 0.03
29 14 0.04
30 23 0.07
31 1 0.00
32 2 0.01
33 1 0.00
34 2 0.01
35 20 0.06
36 167 0.47
37 34 0.10
38 44 0.12
39 6 0.02
40 1 0.00
41 16 0.05
43 12 0.03
ACGTcount: A:0.44, C:0.05, G:0.20, T:0.31
Consensus pattern (36 bp):
ATTGAAACATTGAAAGATTGAAATTGAAGAATTGAA
Found at i:9106 original size:137 final size:138
Alignment explanation
Indices: 8946--9194 Score: 432
Period size: 137 Copynumber: 1.8 Consensus size: 138
8936 GTAAATTGAT
* *
8946 GCATTGAATCATTGAAAATTGAAGAATTGAAGTATTGAAATTGAAACATTGAAGGATTGAATTTG
1 GCATTGAATCATTGAAAATTGAAGAATTGAAGAATTGAAATTGAAACATTGAAGGATTGAATTTA
9011 AAGAATTGAAATTG-AGCCATTGAAATATTGAAATTGAAGCATTGAAGCATTGAAGAATTGAATT
66 AAGAATTGAAATTGAAG-CATTGAAATATTGAAATTGAAGCATTGAAGCATTGAAGAATTGAATT
9075 GAAATCGAA
130 GAAATCGAA
*
9084 GCATTGAAAT-ATTG-AAATTGAAGCATTGAAGAATTGAAATTGAAACATTGAAGGATTGAATTT
1 GCATTG-AATCATTGAAAATTGAAGAATTGAAGAATTGAAATTGAAACATTGAAGGATTGAATTT
9147 AAAGAATTGAAATTGAAGCATTGAAATATTGAAATTGAAGCATTGAAG
65 AAAGAATTGAAATTGAAGCATTGAAATATTGAAATTGAAGCATTGAAG
9195 GATAGAATCT
Statistics
Matches: 106, Mismatches: 3, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
137 91 0.86
138 12 0.11
139 3 0.03
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.30
Consensus pattern (138 bp):
GCATTGAATCATTGAAAATTGAAGAATTGAAGAATTGAAATTGAAACATTGAAGGATTGAATTTA
AAGAATTGAAATTGAAGCATTGAAATATTGAAATTGAAGCATTGAAGCATTGAAGAATTGAATTG
AAATCGAA
Found at i:9255 original size:44 final size:44
Alignment explanation
Indices: 9148--9453 Score: 201
Period size: 44 Copynumber: 7.2 Consensus size: 44
9138 ATTGAATTTA
* * *
9148 AAGAATTGAAATTGAAGCATTGAAATATTGAAATTGAAGCATTG
1 AAGAATTGAATTTGAAGAATTGAAATATTGAAATTGAAACATTG
* * * * * *
9192 AAGGATAGAATCTGGAGAATTGACATATT-AAAGTTGAAACATTT
1 AAGAATTGAATTTGAAGAATTGAAATATTGAAA-TTGAAACATTG
* *
9236 TAGAATTGAATTTGAAGAA-TG-------GAAATTGAAGCATTG
1 AAGAATTGAATTTGAAGAATTGAAATATTGAAATTGAAACATTG
* ** ** *
9272 AA-ATATTGAAATTGAA-ACATTGAAGGATTGAGTTTGAAGCATTG
1 AAGA-ATTGAATTTGAAGA-ATTGAAATATTGAAATTGAAACATTG
* * * *
9316 AA-TATTGAAATTGAAGCATTGAAGA-ATTCAAATTGAAACATTG
1 AAGAATTGAATTTGAAGAATTGAA-ATATTGAAATTGAAACATTG
* * * *
9359 AAAAATTGTAA-TTGAAGCATTGAAATATTGGAATTGAATCATTG
1 AAGAATTG-AATTTGAAGAATTGAAATATTGAAATTGAAACATTG
* * *
9403 AAGAATTGAAATTGAAGCATTG-AATAATTGAAATTGAAGCATTG
1 AAGAATTGAATTTGAAGAATTGAAAT-ATTGAAATTGAAACATTG
9447 AAGAATT
1 AAGAATT
9454 AAAGAAATAG
Statistics
Matches: 209, Mismatches: 34, Indels: 38
0.74 0.12 0.14
Matches are distributed among these distances:
35 2 0.01
36 22 0.11
37 5 0.02
43 45 0.22
44 133 0.64
45 2 0.01
ACGTcount: A:0.44, C:0.05, G:0.20, T:0.31
Consensus pattern (44 bp):
AAGAATTGAATTTGAAGAATTGAAATATTGAAATTGAAACATTG
Found at i:9272 original size:22 final size:22
Alignment explanation
Indices: 9247--9548 Score: 283
Period size: 22 Copynumber: 13.6 Consensus size: 22
9237 AGAATTGAAT
*
9247 TTGAAGAATGGAAATTGAAGCA
1 TTGAAGAATTGAAATTGAAGCA
*
9269 TTGAA-ATATTGAAATTGAAACA
1 TTGAAGA-ATTGAAATTGAAGCA
* **
9291 TTGAAGGATTGAGTTTGAAGCA
1 TTGAAGAATTGAAATTGAAGCA
*
9313 TTGAA-TATTGAAATTGAAGCA
1 TTGAAGAATTGAAATTGAAGCA
* *
9334 TTGAAGAATTCAAATTGAAACA
1 TTGAAGAATTGAAATTGAAGCA
* *
9356 TTGAAAAATTGTAATTGAAGCA
1 TTGAAGAATTGAAATTGAAGCA
* *
9378 TTGAA-ATATTGGAATTGAATCA
1 TTGAAGA-ATTGAAATTGAAGCA
9400 TTGAAGAATTGAAATTGAAGCA
1 TTGAAGAATTGAAATTGAAGCA
*
9422 TTGAATAATTGAAATTGAAGCA
1 TTGAAGAATTGAAATTGAAGCA
* *
9444 TTGAAGAATTAAAGAAATAG-ATCA
1 TTGAAGAATT---GAAATTGAAGCA
** *
9468 TT-CCGAAAT-AAATTGAAGCA
1 TTGAAGAATTGAAATTGAAGCA
*
9488 TTGAAGAATTGAAGATTTGAGGCA
1 TTGAAGAATTGAA-A-TTGAAGCA
* *
9512 TTGAATAATTGAAAGGTTGGAGCA
1 TTGAAGAATTGAAA--TTGAAGCA
*
9536 TTGAATAATTGAA
1 TTGAAGAATTGAA
9549 GAATTGGATA
Statistics
Matches: 229, Mismatches: 37, Indels: 26
0.78 0.13 0.09
Matches are distributed among these distances:
19 5 0.02
20 5 0.02
21 24 0.10
22 139 0.61
23 7 0.03
24 43 0.19
25 6 0.03
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.30
Consensus pattern (22 bp):
TTGAAGAATTGAAATTGAAGCA
Found at i:9492 original size:8 final size:8
Alignment explanation
Indices: 9478--9615 Score: 116
Period size: 8 Copynumber: 17.2 Consensus size: 8
9468 TTCCGAAATA
9478 AATTGAAG
1 AATTGAAG
*
9486 CATTGAAG
1 AATTGAAG
9494 AATTGAAG
1 AATTGAAG
* *
9502 ATTTGAGG
1 AATTGAAG
* *
9510 CATTGAAT
1 AATTGAAG
9518 AATTGAA-
1 AATTGAAG
* *
9525 AGGTTGGAG
1 A-ATTGAAG
* *
9534 CATTGAAT
1 AATTGAAG
9542 AATTGAAG
1 AATTGAAG
* *
9550 AATTGGAT
1 AATTGAAG
9558 AATTGAAG
1 AATTGAAG
*
9566 AGTTGAAG
1 AATTGAAG
* *
9574 CATTGAAT
1 AATTGAAG
*
9582 AATTGAAA
1 AATTGAAG
9590 AATTGAAG
1 AATTGAAG
*
9598 AATTGAAT
1 AATTGAAG
9606 AATTGAAG
1 AATTGAAG
9614 AA
1 AA
9616 AGAGATCATT
Statistics
Matches: 98, Mismatches: 30, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
7 1 0.01
8 97 0.99
ACGTcount: A:0.44, C:0.03, G:0.24, T:0.29
Consensus pattern (8 bp):
AATTGAAG
Found at i:10008 original size:22 final size:22
Alignment explanation
Indices: 9983--10024 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
9973 TGCAAGTTAA
*
9983 AAAATGCCTCATGATGCAATGC
1 AAAATGCATCATGATGCAATGC
*
10005 AAAATGCATGATGATGCAAT
1 AAAATGCATCATGATGCAAT
10025 ATGTATGACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (22 bp):
AAAATGCATCATGATGCAATGC
Found at i:10856 original size:1 final size:1
Alignment explanation
Indices: 10850--10876 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
10840 AGCGTTTTGC
10850 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
10877 GACTGTTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:11176 original size:25 final size:25
Alignment explanation
Indices: 11131--11181 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
11121 TTAATTTTTG
* * *
11131 TTTTCATTTTTTTTATTTTTTTATT
1 TTTTCATTTTTTTGATCTTTTGATT
11156 TTTTCATTTTTATTGA-CTTTTGATT
1 TTTTCATTTTT-TTGATCTTTTGATT
11181 T
1 T
11182 GAATTTCTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.14, C:0.06, G:0.04, T:0.76
Consensus pattern (25 bp):
TTTTCATTTTTTTGATCTTTTGATT
Found at i:11498 original size:16 final size:15
Alignment explanation
Indices: 11477--11510 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
11467 TTTGAAACCA
*
11477 TTTTTGAGAAATCATT
1 TTTTTGAAAAATC-TT
11493 TTTTTGAAAAATCTT
1 TTTTTGAAAAATCTT
11508 TTT
1 TTT
11511 AAAAAATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.29, C:0.06, G:0.09, T:0.56
Consensus pattern (15 bp):
TTTTTGAAAAATCTT
Found at i:12548 original size:20 final size:20
Alignment explanation
Indices: 12523--12564 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
12513 ATTGTTCCTT
12523 AGTTGTCATACTAACTCCCC
1 AGTTGTCATACTAACTCCCC
12543 AGTTGTCATACTAACTCCCC
1 AGTTGTCATACTAACTCCCC
12563 AG
1 AG
12565 GCTGGCTTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.33, G:0.12, T:0.29
Consensus pattern (20 bp):
AGTTGTCATACTAACTCCCC
Found at i:13995 original size:15 final size:16
Alignment explanation
Indices: 13971--14010 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
13961 AGAGGTTGAA
*
13971 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
13986 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
14002 AGAAAACAA
1 AGAAAACAA
14011 AGCAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:17313 original size:22 final size:22
Alignment explanation
Indices: 17277--17318 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
17267 TGGCACGGGC
**
17277 ATGGCCGGTGGTGGCATGGTGT
1 ATGGCCGGTAATGGCATGGTGT
*
17299 ATGGCCGGTAATGGCTTGGT
1 ATGGCCGGTAATGGCATGGT
17319 AGTGGCGCGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.12, C:0.14, G:0.45, T:0.29
Consensus pattern (22 bp):
ATGGCCGGTAATGGCATGGTGT
Found at i:21009 original size:15 final size:16
Alignment explanation
Indices: 20985--21024 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
20975 AGAGGTTGAA
*
20985 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
21000 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
21016 AGAAAACAA
1 AGAAAACAA
21025 AGCAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Done.