Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018576.1 Corchorus olitorius cultivar O-4 contig18609, 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: 11722
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.28
Found at i:374 original size:15 final size:15
Alignment explanation
Indices: 318--374 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
308 TCTGAACCGT
*
318 ATGACCCGAAACCGAAA
1 ATGACCCG-AACC-CAA
335 ATGACCC-AACCCAAA
1 ATGACCCGAACCC-AA
*
350 ATTTACCCGAACCCAA
1 A-TGACCCGAACCCAA
366 ATGACCCGA
1 ATGACCCGA
375 CATTTGAACG
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
15 14 0.41
16 8 0.24
17 12 0.35
ACGTcount: A:0.42, C:0.35, G:0.12, T:0.11
Consensus pattern (15 bp):
ATGACCCGAACCCAA
Found at i:886 original size:22 final size:22
Alignment explanation
Indices: 854--895 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
844 TTTCTTTATT
854 CTTGTTGGGCCTTG-ATTGTTA
1 CTTGTTGGGCCTTGTATTGTTA
875 CTTGATTGGGCCTTGTATTGT
1 CTTG-TTGGGCCTTGTATTGT
896 GAGTTATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 4 0.21
22 10 0.53
23 5 0.26
ACGTcount: A:0.10, C:0.14, G:0.29, T:0.48
Consensus pattern (22 bp):
CTTGTTGGGCCTTGTATTGTTA
Found at i:1557 original size:38 final size:38
Alignment explanation
Indices: 1510--1586 Score: 111
Period size: 38 Copynumber: 2.0 Consensus size: 38
1500 TTTCATCAAG
* * *
1510 TTTTTTTAATTGGGAATGTTCCCA-CCAGTTTTAAGTTT
1 TTTTTTTAATTGGAAAAGTTCCCATCAAGTTTTAA-TTT
1548 TTTTTTTAATTGGAAAAGTTCCCATCAAGTTTTAATTT
1 TTTTTTTAATTGGAAAAGTTCCCATCAAGTTTTAATTT
1586 T
1 T
1587 CAATTGGGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
38 26 0.74
39 9 0.26
ACGTcount: A:0.25, C:0.12, G:0.13, T:0.51
Consensus pattern (38 bp):
TTTTTTTAATTGGAAAAGTTCCCATCAAGTTTTAATTT
Found at i:1601 original size:33 final size:33
Alignment explanation
Indices: 1542--1638 Score: 115
Period size: 33 Copynumber: 2.9 Consensus size: 33
1532 CACCAGTTTT
* * * *
1542 AAGTTTT-TTTTTTAATTGGAAAAGTTCCCATC
1 AAGTTTTAATTTTCAATTGGGAAAGTTCCCACC
*
1574 AAGTTTTAATTTTCAATTGGGATAGTTCCCACC
1 AAGTTTTAATTTTCAATTGGGAAAGTTCCCACC
*
1607 AAGTTTTAGTTTTCAATTTAGGGAAAGTTCCC
1 AAGTTTTAATTTTCAA-TT-GGGAAAGTTCCC
1639 GTCATTTTCG
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
32 7 0.13
33 35 0.64
34 2 0.04
35 11 0.20
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.42
Consensus pattern (33 bp):
AAGTTTTAATTTTCAATTGGGAAAGTTCCCACC
Found at i:10462 original size:31 final size:31
Alignment explanation
Indices: 10418--11325 Score: 819
Period size: 31 Copynumber: 29.1 Consensus size: 31
10408 TTCTAAGTTC
*
10418 TAATTGCGACCTCAGACAGGTCTTTATCTTT
1 TAATTTCGACCTCAGACAGGTCTTTATCTTT
* * * *
10449 TAATTCCGGCCTCAGACAAGTCTTTCTCAGTTT
1 TAATTTCGACCTCAGACAGGTCTTTATC--TTT
* *
10482 T-ATTTCGGCCTCAGACATGTCTTTATC---
1 TAATTTCGACCTCAGACAGGTCTTTATCTTT
10509 ---TTT-GACCTCAGACAGGTC-TT-TC--T
1 TAATTTCGACCTCAGACAGGTCTTTATCTTT
*
10532 CAA-TTCTGACCTCAGACAGGTCTTTATCTTT
1 TAATTTC-GACCTCAGACAGGTCTTTATCTTT
* *
10563 CAATTCCGACCTCAGACAGGTCTTTATCTTT
1 TAATTTCGACCTCAGACAGGTCTTTATCTTT
* * * *
10594 CAATTCCGGCCTCAGACAGGTCTTTCT-TAGTT
1 TAATTTCGACCTCAGACAGGTCTTTATCT--TT
* *
10626 TTATTTCGACCTCAGACATGTCTTTATCTTT
1 TAATTTCGACCTCAGACAGGTCTTTATCTTT
* * *
10657 CAATTCCGACCTCAGACAGGTCTTTCTCAGTTT
1 TAATTTCGACCTCAGACAGGTCTTTATC--TTT
10690 T-ATTTCGACCTCAGACAGGTCTTTATCTTT
1 TAATTTCGACCTCAGACAGGTCTTTATCTTT
* *
10720 CAATTTCGACCTCAGACAGGTCTTTCTCAGTTT
1 TAATTTCGACCTCAGACAGGTCTTTATC--TTT
10753 T-ATTTCGACCTCAGACAGGTCTTTATCTTT
1 TAATTTCGACCTCAGACAGGTCTTTATCTTT
* * *
10783 CAATTCCGACCTCAGACAGGTCTTTCTCAGTTT
1 TAATTTCGACCTCAGACAGGTCTTTATC--TTT
10816 T-ATTTCGACCTCAGACAGGTCTTTATCTTT
1 TAATTTCGACCTCAGACAGGTCTTTATCTTT
* * * * *
10846 CAATTCCGACCTCAGACACGTCTTTCTCAGTCT
1 TAATTTCGACCTCAGACAGGTCTTTATC--TTT
10879 T-ATTTCGACCTCAGACAGGTCTTTATCTTT
1 TAATTTCGACCTCAGACAGGTCTTTATCTTT
* *
10909 CT-A-TTCCAGCCTCAGACAGGTCTTTCTCAGTTT
1 -TAATTTCGA-CCTCAGACAGGTCTTTATC--TTT
*
10942 T-ATTTCGACCTCAGACAGGTCTTTCTCAGTTT
1 TAATTTCGACCTCAGACAGGTCTTTATC--TTT
10974 T-ATTTCGACCTCAGACAGGTCTTTATCTTT
1 TAATTTCGACCTCAGACAGGTCTTTATCTTT
* *
11004 CAATTCCGACCTCAGACAGGTCTTT-TCTTAGT
1 TAATTTCGACCTCAGACAGGTCTTTATCTT--T
*
11036 CTTATTTCGACCTCAGACAGGTCTTTATCTTT
1 -TAATTTCGACCTCAGACAGGTCTTTATCTTT
* * *
11068 CT-ATTTAGGCCTCAGACAGGTCTTTCTCAGTTT
1 -TAATTTCGACCTCAGACAGGTCTTTATC--TTT
*
11101 T-ATTTCGACCTCAGACAAGTCTTTATCTTT
1 TAATTTCGACCTCAGACAGGTCTTTATCTTT
* * * * * *
11131 CAACTCCAAGCCTCAGACAGGTATTTCTCGGCTTT
1 TAATTTCGA-CCTCAGACAGGTCTTTAT---CTTT
*
11166 TTATTTCGACCTCAGACAGGTCTTTATCTTT
1 TAATTTCGACCTCAGACAGGTCTTTATCTTT
* * * * *
11197 CAATTTCGGCCTCAAACAAGTCTTTCTCAGTTT
1 TAATTTCGACCTCAGACAGGTCTTTATC--TTT
*
11230 T-ATTTCGACCTCAAACAGGTC-TTATCTTT
1 TAATTTCGACCTCAGACAGGTCTTTATCTTT
* * *
11259 TAAATTCGACCTTAGACAGGTCTTTCTCAGTTT
1 TAATTTCGACCTCAGACAGGTCTTTATC--TTT
*
11292 T-ATTTCGACCTCAGACATGTCTTTATCTTT
1 TAATTTCGACCTCAGACAGGTCTTTATCTTT
11322 TAAT
1 TAAT
11326 AGCGTAAGAA
Statistics
Matches: 732, Mismatches: 94, Indels: 102
0.79 0.10 0.11
Matches are distributed among these distances:
22 2 0.00
23 2 0.00
24 13 0.02
25 5 0.01
27 15 0.02
28 2 0.00
29 6 0.01
30 47 0.06
31 279 0.38
32 278 0.38
33 55 0.08
34 20 0.03
35 8 0.01
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.39
Consensus pattern (31 bp):
TAATTTCGACCTCAGACAGGTCTTTATCTTT
Found at i:10505 original size:63 final size:62
Alignment explanation
Indices: 10392--11323 Score: 854
Period size: 63 Copynumber: 14.9 Consensus size: 62
10382 CGAAGTTCCA
* * * * * *
10392 GACCACAGACAAGTCTTTCTAAGTTCTAATTGCGACCTCAGACAGGTCTTTATCTTTTAATTCC
1 GACCTCAGACAGGTCTTTCTCAGTT-TTATTTCGACCTCAGACAGGTCTTTATCTTTT-ATTTC
* * * *
10456 GGCCTCAGACAAGTCTTTCTCAGTTTTATTTCGGCCTCAGACATGTCTTTATC-----TTT-
1 GACCTCAGACAGGTCTTTCTCAGTTTTATTTCGACCTCAGACAGGTCTTTATCTTTTATTTC
* *
10512 GACCTCAGACAGGTCTTTCTCA-----A-TTCTGACCTCAGACAGGTCTTTATCTTTCAATTCC
1 GACCTCAGACAGGTCTTTCTCAGTTTTATTTC-GACCTCAGACAGGTCTTTATCTTT-TATTTC
* * * * * *
10570 GACCTCAGACAGGTCTTTATC--TTTCAATTCCGGCCTCAGACAGGTCTTTCTTAGTTTTATTTC
1 GACCTCAGACAGGTCTTTCTCAGTTT-TATTTCGACCTCAGACAGGTCTTT-AT-CTTTTATTTC
* * * * *
10633 GACCTCAGACATGTCTTTATC--TTTCAATTCCGACCTCAGACAGGTCTTTCTCAGTTTTATTTC
1 GACCTCAGACAGGTCTTTCTCAGTTT-TATTTCGACCTCAGACAGGTCTTTATC--TTTTATTTC
* * *
10696 GACCTCAGACAGGTCTTTATC--TTTCAATTTCGACCTCAGACAGGTCTTTCTCAGTTTTATTTC
1 GACCTCAGACAGGTCTTTCTCAGTTT-TATTTCGACCTCAGACAGGTCTTTATC--TTTTATTTC
* * * *
10759 GACCTCAGACAGGTCTTTATC--TTTCAATTCCGACCTCAGACAGGTCTTTCTCAGTTTTATTTC
1 GACCTCAGACAGGTCTTTCTCAGTTT-TATTTCGACCTCAGACAGGTCTTTATC--TTTTATTTC
* * * * * *
10822 GACCTCAGACAGGTCTTTATC--TTTCAATTCCGACCTCAGACACGTCTTTCTCAGTCTTATTTC
1 GACCTCAGACAGGTCTTTCTCAGTTT-TATTTCGACCTCAGACAGGTCTTTATC--TTTTATTTC
* * *
10885 GACCTCAGACAGGTCTTTATC--TTTCTA-TTCCAGCCTCAGACAGGTCTTTCTCAGTTTTATTT
1 GACCTCAGACAGGTCTTTCTCAGTTT-TATTTCGA-CCTCAGACAGGTCTTTATC--TTTTATTT
10947 C
62 C
* *
10948 GACCTCAGACAGGTCTTTCTCAGTTTTATTTCGACCTCAGACAGGTCTTTATCTTTCAATTCC
1 GACCTCAGACAGGTCTTTCTCAGTTTTATTTCGACCTCAGACAGGTCTTTATCTTT-TATTTC
* * *
11011 GACCTCAGACAGGTCTTTTCTTAGTCTTATTTCGACCTCAGACAGGTCTTTATCTTTCTATTTA
1 GACCTCAGACAGGTC-TTTCTCAGTTTTATTTCGACCTCAGACAGGTCTTTATCTTT-TATTTC
* * * * *
11075 GGCCTCAGACAGGTCTTTCTCAGTTTTATTTCGACCTCAGACAAGTCTTTATCTTTCAACTCC
1 GACCTCAGACAGGTCTTTCTCAGTTTTATTTCGACCTCAGACAGGTCTTTATCTTT-TATTTC
* * * *
11138 AAGCCTCAGACAGGTATTTCTCGGCTTTTTATTTCGACCTCAGACAGGTCTTTATCTTTCAATTT
1 GA-CCTCAGACAGGTCTTTCTCAG--TTTTATTTCGACCTCAGACAGGTCTTTATCTTT-TATTT
11203 C
62 C
* * * * *
11204 GGCCTCAAACAAGTCTTTCTCAGTTTTATTTCGACCTCAAACAGGTC-TTATCTTTTAAATTC
1 GACCTCAGACAGGTCTTTCTCAGTTTTATTTCGACCTCAGACAGGTCTTTATCTTTT-ATTTC
* *
11266 GACCTTAGACAGGTCTTTCTCAGTTTTATTTCGACCTCAGACATGTCTTTATCTTTTA
1 GACCTCAGACAGGTCTTTCTCAGTTTTATTTCGACCTCAGACAGGTCTTTATCTTTTA
11324 ATAGCGTAAG
Statistics
Matches: 765, Mismatches: 74, Indels: 60
0.85 0.08 0.07
Matches are distributed among these distances:
50 3 0.00
51 20 0.03
56 20 0.03
57 4 0.01
58 20 0.03
62 79 0.10
63 437 0.57
64 121 0.16
65 24 0.03
66 37 0.05
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.39
Consensus pattern (62 bp):
GACCTCAGACAGGTCTTTCTCAGTTTTATTTCGACCTCAGACAGGTCTTTATCTTTTATTTC
Found at i:10518 original size:24 final size:24
Alignment explanation
Indices: 10490--10562 Score: 101
Period size: 27 Copynumber: 2.9 Consensus size: 24
10480 TTTATTTCGG
*
10490 CCTCAGACATGTCTTTATCTTTGA
1 CCTCAGACAGGTCTTTATCTTTGA
*
10514 CCTCAGACAGGTCTTTCTCAATTCTGA
1 CCTCAGACAGGTCTTTATC--TT-TGA
10541 CCTCAGACAGGTCTTTATCTTT
1 CCTCAGACAGGTCTTTATCTTT
10563 CAATTCCGAC
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
24 18 0.42
25 2 0.05
26 2 0.05
27 21 0.49
ACGTcount: A:0.21, C:0.27, G:0.14, T:0.38
Consensus pattern (24 bp):
CCTCAGACAGGTCTTTATCTTTGA
Done.