Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011267.1 Corchorus olitorius cultivar O-4 contig11300, 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: 23456
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Found at i:312 original size:19 final size:18
Alignment explanation
Indices: 279--314 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
269 TTGAAATTAT
279 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
297 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
315 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:6044 original size:11 final size:11
Alignment explanation
Indices: 6028--6057 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
6018 TTCAAGAAAA
*
6028 TAATTATTAAT
1 TAATTAATAAT
6039 TAATTAATAAT
1 TAATTAATAAT
6050 TAATTAAT
1 TAATTAAT
6058 TTCAGCCCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TAATTAATAAT
Found at i:6051 original size:15 final size:15
Alignment explanation
Indices: 6028--6058 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6018 TTCAAGAAAA
*
6028 TAATTATTAATTAAT
1 TAATAATTAATTAAT
6043 TAATAATTAATTAAT
1 TAATAATTAATTAAT
6058 T
1 T
6059 TCAGCCCTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TAATAATTAATTAAT
Found at i:16934 original size:305 final size:305
Alignment explanation
Indices: 16413--16962 Score: 850
Period size: 305 Copynumber: 1.8 Consensus size: 305
16403 GGTTCACAAT
* ** * **
16413 GTCATCCATGGTCCTGACCAATAAGATCGTGACATGTCAGATTTTTTCATGTAATTTCTAAAACC
1 GTCATCCATGGTCCCGACCAATAAGATCGTGACAAATCAGATTCTTTCATACAATTTCTAAAACC
* * *
16478 CTAGCAAATTAATGTCCTAAATTCTGGGACTTACCTTGTAAATCTCATCTAGTTAAACTTGGGGC
66 CTAGCAAATTAATGTCCTAAATTCTGGGACTTACCCTGTAAATCTCATCTAGTGAAACTAGGGGC
* * * * *
16543 TAAATCTGATGCTAAATTTGTGTCTAAATTTTAGGAAGAAATTTGACTTGTCACAATATTATTGG
131 TAAACCTGATGCTAAATTCGTGCCTAAATTTTAGGAAGAAATCTGACTTGTCAAAATATTATTGG
* * * *
16608 TCGGGACCATGGATGACGTGGTGGAGCTGGTCCATCTAATAATTTCTCCTAAACGCCGAACCAAA
196 TCGGGACCACGGATGACGTGGTGGACCCGGTCCACCTAATAATTTCTCCTAAACGCCGAACCAAA
16673 AGTAGCTTTTAGCTAAGAAATTATTAGGTGGACCGGGTCCACCAC
261 AGTAGCTTTTAGCTAAGAAATTATTAGGTGGACCGGGTCCACCAC
* ** *
16718 GTCATCCGTGGTCCCGACCAATAAGATTTTGACAAATCAGATTCTTTCCTACAATTTCTAAAACC
1 GTCATCCATGGTCCCGACCAATAAGATCGTGACAAATCAGATTCTTTCATACAATTTCTAAAACC
* *
16783 CTAGCCAATTAATGTCCTAAATT-TAGGGACTTACCCTGTAAATCTCATCTGGTGAAACTAGGGG
66 CTAGCAAATTAATGTCCTAAATTCT-GGGACTTACCCTGTAAATCTCATCTAGTGAAACTAGGGG
* *
16847 CTAAACCTGATGCTAAATTCGTGCCTAAATTTTAGGAAGGAATCTGACTTGTCAAAATCTTATTG
130 CTAAACCTGATGCTAAATTCGTGCCTAAATTTTAGGAAGAAATCTGACTTGTCAAAATATTATTG
16912 GTCGGGACCACGGATGACGTGGTGGACCCGGTCCACCTAATAATTTCTCCT
195 GTCGGGACCACGGATGACGTGGTGGACCCGGTCCACCTAATAATTTCTCCT
16963 TTTAGCTACA
Statistics
Matches: 218, Mismatches: 26, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
304 1 0.00
305 217 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (305 bp):
GTCATCCATGGTCCCGACCAATAAGATCGTGACAAATCAGATTCTTTCATACAATTTCTAAAACC
CTAGCAAATTAATGTCCTAAATTCTGGGACTTACCCTGTAAATCTCATCTAGTGAAACTAGGGGC
TAAACCTGATGCTAAATTCGTGCCTAAATTTTAGGAAGAAATCTGACTTGTCAAAATATTATTGG
TCGGGACCACGGATGACGTGGTGGACCCGGTCCACCTAATAATTTCTCCTAAACGCCGAACCAAA
AGTAGCTTTTAGCTAAGAAATTATTAGGTGGACCGGGTCCACCAC
Found at i:17882 original size:11 final size:11
Alignment explanation
Indices: 17868--17905 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
17858 ATTCATAACA
17868 AATTTATAATT
1 AATTTATAATT
17879 AATTTATAATT
1 AATTTATAATT
17890 -ATTTGATAATT
1 AATTT-ATAATT
*
17901 TATTT
1 AATTT
17906 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:21943 original size:6 final size:6
Alignment explanation
Indices: 21929--21963 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
21919 TACTTCATTC
*
21929 ATATAT ATATCT ATATCT ATATCT ATATACT ATAT
1 ATATCT ATATCT ATATCT ATATCT ATAT-CT ATAT
21964 AAGTCTAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (6 bp):
ATATCT
Found at i:22243 original size:21 final size:21
Alignment explanation
Indices: 22219--22285 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
22209 GTAACATAAA
22219 TAATAACTAAAATACTTACAT
1 TAATAACTAAAATACTTACAT
* ** *
22240 TAATTAAATGTAATA-ATAC-T
1 TAA-TAACTAAAATACTTACAT
*
22260 ATAATAACTAAAACACTTACAT
1 -TAATAACTAAAATACTTACAT
22282 TAAT
1 TAAT
22286 TAAATTCTTA
Statistics
Matches: 33, Mismatches: 9, Indels: 8
0.66 0.18 0.16
Matches are distributed among these distances:
20 8 0.24
21 16 0.48
22 9 0.27
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.34
Consensus pattern (21 bp):
TAATAACTAAAATACTTACAT
Found at i:22649 original size:203 final size:203
Alignment explanation
Indices: 22400--22813 Score: 681
Period size: 203 Copynumber: 2.0 Consensus size: 203
22390 TTCCTTATTA
*
22400 ATAAATAAATCGGATCTTAATATTTTTAATTTATAATTTTGAAATTTTGTTTGACATTGATCTAA
1 ATAAATAAATCGGATCTTAATA-TTCT-ATTTATAATTTTGAAATTTTGTTTGACATTGATCTAA
*
22465 TTTAATTTAATAAATCAACCACTAATGTTCAACTA-ATTTTTTTGGTATAGTTCTATGTATATAA
64 TTTAATTTAATAAATCAACCACTAATGTTCAACTACATTTTTTTGGTATAG-T-TATATATATAA
* *
22529 TAGTAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGATTTAAAAAATTAATAA
127 TAATAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAA
*
22594 CATTCACCATTG
192 CATTCACCATTC
22606 ATAAATAAATCGGATCTTTAATA-TCT-TTTATAATTTTGAAATTTTGTTTGACATTGATCTAAT
1 ATAAATAAATCGGATC-TTAATATTCTATTTATAATTTTGAAATTTTGTTTGACATTGATCTAAT
* *
22669 TTAATTTAATAAATCAACCACTAATGTTCAACTACTTTTTTTTTGTTATAGTTATATATATAATA
65 TTAATTTAATAAATCAACCACTAATGTTCAACTAC-ATTTTTTTGGTATAGTTATATATATAATA
*
22734 ATAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAACAATTAATAACA
129 ATAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACA
22799 TTCACCATTC
194 TTCACCATTC
22809 ATAAA
1 ATAAA
22814 GTTATTAAGC
Statistics
Matches: 197, Mismatches: 8, Indels: 9
0.92 0.04 0.04
Matches are distributed among these distances:
203 159 0.81
204 1 0.01
205 15 0.08
206 16 0.08
207 6 0.03
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.44
Consensus pattern (203 bp):
ATAAATAAATCGGATCTTAATATTCTATTTATAATTTTGAAATTTTGTTTGACATTGATCTAATT
TAATTTAATAAATCAACCACTAATGTTCAACTACATTTTTTTGGTATAGTTATATATATAATAAT
AATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATT
CACCATTC
Done.