Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018537.1 Corchorus olitorius cultivar O-4 contig18570, 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: 20698
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:2906 original size:4 final size:4
Alignment explanation
Indices: 2897--2923 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2887 CTTTGAAAAA
2897 AATT AATT AATT AATT AATT AATT AAT
1 AATT AATT AATT AATT AATT AATT AAT
2924 AAAAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:6150 original size:210 final size:211
Alignment explanation
Indices: 5583--6545 Score: 1442
Period size: 210 Copynumber: 4.5 Consensus size: 211
5573 GACTCGATCA
*
5583 ATTTTCCTCCTAATTAATTGAATAAACCCAGTCCGTATGAATTTTGTGCCATCTAATAATTAAAC
1 ATTTTCCTCCTAATTAATTGAATAAACCCAGTCCATATGAATTTTGTGCCATCTAATAATTAAAC
*
5648 AAAATGCAATATCCAGTATCCCCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCCCC
66 AAAATGCAATATTCAGTATCCCCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCCCC
* *
5713 AAATAATTATAAGCATCGTACCCAAAATTCATTAGAGATTGAATAAAACCCAAAATTGGCTAT-A
131 AAATAATTATAAGCACCGTACCCAAAATTCATTAGAGATTGAATAAAACCCAAAATTGGCTTTAA
5777 ACGTGTTTTAATCCAT
196 ACGTGTTTTAATCCAT
* * *
5793 ATTTTCCT-C--ATTAATTGAATAAACCTC-GTCCATATGAATTTTGGGCAATCTAATAATCAAA
1 ATTTTCCTCCTAATTAATTGAATAAACC-CAGTCCATATGAATTTTGTGCCATCTAATAATTAAA
*
5854 CAAAATGCAATATTCAGTATCCCTAAACTGATATACTTTATACCCAAATCATTTCTCATCATCCC
65 CAAAATGCAATATTCAGTATCCCCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCCC
*
5919 TAAATAATTATAAGCACCGTACCCAAAATTCATTAGAGATTGAATAAAACCCAAAATTGGCTTTA
130 CAAATAATTATAAGCACCGTACCCAAAATTCATTAGAGATTGAATAAAACCCAAAATTGGCTTTA
5984 AACGTGTTTTAATCCAT
195 AACGTGTTTTAATCCAT
* *
6001 ATTTTCCTCCTAATTAATTGAATAAACCCAATCCATATGAATTTTGTGCCATCTATTAATTAAAC
1 ATTTTCCTCCTAATTAATTGAATAAACCCAGTCCATATGAATTTTGTGCCATCTAATAATTAAAC
*
6066 AAAATGCAATATTCAGTATCCCCAAA-TGATATACTTTAAACCCAAATCATTTCTCATCATCCCC
66 AAAATGCAATATTCAGTATCCCCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCCCC
6130 AAATAATTATAAGCACCGTACCCAAAATTCATTAGAGATTGAATAAAACCCAAAATTGGCTTTAA
131 AAATAATTATAAGCACCGTACCCAAAATTCATTAGAGATTGAATAAAACCCAAAATTGGCTTTAA
6195 ACGTGTTTTAATCCAT
196 ACGTGTTTTAATCCAT
*
6211 ATTTTCCTCTTAATTAATTGAATAAACCCAGTCCATATGAATTTTGTGCCATCTAATAATTAAAC
1 ATTTTCCTCCTAATTAATTGAATAAACCCAGTCCATATGAATTTTGTGCCATCTAATAATTAAAC
* *
6276 AAAATGCAATATTCAGTAT-CCCAAACTGATATACTTTAAACCCTAATCATTTCTCATCATCCCC
66 AAAATGCAATATTCAGTATCCCCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCCCC
*
6340 AAATAATTATAAGCACCGTACCCAAAATTCATTAGAGATTGACATTTTTTCTTATATACCCAAAA
131 AAATAATTATAAGCACCGTACCCAAAATTCATTAGAGATTGA-A--------TA-AAACCCAAAA
* * *
6405 TTGGTTTTAAAAAGTGCTTTAATCCAT
186 TTGGCTTT-AAACGTGTTTTAATCCAT
* * * * * * * *
6432 ATTTTCATCCTGATTAATTGAATAAACCCTTAAT--ATATTAGTTTAGCGTCC-TCTAATAATGA
1 ATTTTCCTCCTAATTAATTGAATAAACCC--AGTCCATATGAATTTTGTG-CCATCTAATAATTA
** * *
6494 AACAAAACCCAAAATTTAGTATCCCCAAACTGATATACTTTATACCCAAATC
63 AACAAAATGCAATATTCAGTATCCCCAAACTGATATACTTTATACCCAAATC
6546 TTGTGATTCC
Statistics
Matches: 691, Mismatches: 40, Indels: 32
0.91 0.05 0.04
Matches are distributed among these distances:
207 170 0.25
208 26 0.04
209 8 0.01
210 286 0.41
211 72 0.10
219 2 0.00
220 16 0.02
221 80 0.12
222 29 0.04
223 2 0.00
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (211 bp):
ATTTTCCTCCTAATTAATTGAATAAACCCAGTCCATATGAATTTTGTGCCATCTAATAATTAAAC
AAAATGCAATATTCAGTATCCCCAAACTGATATACTTTATACCCAAATCATTTCTCATCATCCCC
AAATAATTATAAGCACCGTACCCAAAATTCATTAGAGATTGAATAAAACCCAAAATTGGCTTTAA
ACGTGTTTTAATCCAT
Found at i:12122 original size:28 final size:28
Alignment explanation
Indices: 12077--12132 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
12067 GGAGCGCTTG
*
12077 TTCAAGCTAGGGTTAAAGCTTGGTGTTGT
1 TTCAAGCTAGGGTGAAAGCTTGGT-TTGT
*
12106 TTCAAGCTTGGG-GAAAGCTTGGTTTGT
1 TTCAAGCTAGGGTGAAAGCTTGGTTTGT
12133 GTAAAGGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.16
28 10 0.40
29 11 0.44
ACGTcount: A:0.20, C:0.11, G:0.32, T:0.38
Consensus pattern (28 bp):
TTCAAGCTAGGGTGAAAGCTTGGTTTGT
Found at i:19841 original size:15 final size:15
Alignment explanation
Indices: 19803--19842 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
19793 AATAGTCCAA
*
19803 AATGCAAACATGACT
1 AATGCAAATATGACT
19818 AATGCAAATATGACT
1 AATGCAAATATGACT
*
19833 AATGTAAATA
1 AATGCAAATA
19843 GTACATGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.25
Consensus pattern (15 bp):
AATGCAAATATGACT
Found at i:20047 original size:29 final size:29
Alignment explanation
Indices: 19986--20128 Score: 160
Period size: 29 Copynumber: 4.9 Consensus size: 29
19976 GTTTAAAGTA
** * * **
19986 TGCAAAAACAACCAAAATGCCCCAGAACC
1 TGCAAAAATGACCAAAATGCCCCTGGAGG
*
20015 TGCAAAAATGACCAAAATGCCCCTGGATG
1 TGCAAAAATGACCAAAATGCCCCTGGAGG
*
20044 TGCACAAATGACCAAAATGCCCCTGGAGG
1 TGCAAAAATGACCAAAATGCCCCTGGAGG
* *
20073 TGCAAGAATGACCATAATGCCCCTGGAGG
1 TGCAAAAATGACCAAAATGCCCCTGGAGG
* * * *
20102 TGCGAAAATTATCATAATGCCCCTGGA
1 TGCAAAAATGACCAAAATGCCCCTGGA
20129 TGTGACCCTA
Statistics
Matches: 99, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 99 1.00
ACGTcount: A:0.37, C:0.27, G:0.20, T:0.16
Consensus pattern (29 bp):
TGCAAAAATGACCAAAATGCCCCTGGAGG
Found at i:20490 original size:30 final size:30
Alignment explanation
Indices: 20454--20698 Score: 382
Period size: 30 Copynumber: 8.1 Consensus size: 30
20444 ATTAACTGAC
** * **
20454 AAGCAACGATCCTGGACCAAGATCGAAATA
1 AAGCAACGATCCTCAACCAGGATTAAAATA
20484 AAGCAACGATCCTCAACCAGGATTAAAATA
1 AAGCAACGATCCTCAACCAGGATTAAAATA
*
20514 AAGCAATGATCCTCAACCAGGATTAAAATA
1 AAGCAACGATCCTCAACCAGGATTAAAATA
* *
20544 AAGCGATGATCCTCAACCAGGATTAAAATA
1 AAGCAACGATCCTCAACCAGGATTAAAATA
*
20574 AAGCAACGATACTCAACCAGGATTAAAATA
1 AAGCAACGATCCTCAACCAGGATTAAAATA
*
20604 AAGCAATGATCCTCAACCAGGATTAAAATA
1 AAGCAACGATCCTCAACCAGGATTAAAATA
20634 AAGCAACGATCCTCAACCAGGATTAAAATA
1 AAGCAACGATCCTCAACCAGGATTAAAATA
*
20664 AAGCAGATGATCCTCAACCAGGATTAAAATA
1 AAGCA-ACGATCCTCAACCAGGATTAAAATA
20695 AAGC
1 AAGC
Statistics
Matches: 200, Mismatches: 14, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
30 172 0.86
31 28 0.14
ACGTcount: A:0.46, C:0.21, G:0.15, T:0.18
Consensus pattern (30 bp):
AAGCAACGATCCTCAACCAGGATTAAAATA
Done.