Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012778.1 Corchorus olitorius cultivar O-4 contig12811, 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: 20498
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:333 original size:2 final size:2
Alignment explanation
Indices: 326--358 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
316 ACCTCAGGAA
326 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
359 CTAGTACTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1467 original size:166 final size:167
Alignment explanation
Indices: 1267--1617 Score: 370
Period size: 167 Copynumber: 2.1 Consensus size: 167
1257 ATGTTTCGCG
* * * * * * *
1267 CACAAACGCACAAAATTGTGAAGTTGATGTTTTAGGTTTTAAAGAACG-CTTTGTTTGGCAAGCC
1 CACAAACACGCAAAATCGTGAAGTTCAAGTTTTAGCTTTTAAAGAAAGTCTTTGTTTGGCAAGCC
* * *
1331 -AC-TTTCAAATGTGCTCTACTAACTCCGAAACACGACATATAG-GCATTGGTTACACAAATAAC
66 AACTTTTC-AATGAG-TCTACTAACTCCGAAACACAAAAT-TAGAGCATTGGTTACACAAATAAC
*
1393 GCATTTGAAATGAACACTTT-CTCAAGAACAACATTTTGCA
128 GCATTTGAAATGAAC-CTTTCCCCAAGAACAACATTTTGCA
* * * *
1433 CACAAACATGCAAAATCGTGAAGTTCAAGTTTTAGCTTTTGAAGAAAGTTTTTTTTTGGCAAGCC
1 CACAAACACGCAAAATCGTGAAGTTCAAGTTTTAGCTTTTAAAGAAAGTCTTTGTTTGGCAAGCC
* * * ** * * * * *
1498 AACTTTTCTATGAGTTTACTTACTTTGAAACACAAAATTTGAGCGTTGGTTTCACAAATAATGTA
66 AACTTTTCAATGAGTCTACTAACTCCGAAACACAAAATTAGAGCATTGGTTACACAAATAACGCA
* * *
1563 TTTGGAATGAGCGTTTCCCCAAGAACAACATTTTGCA
131 TTTGAAATGAACCTTTCCCCAAGAACAACATTTTGCA
*
1600 CACAAACACGCTAAATCG
1 CACAAACACGCAAAATCG
1618 GGAAATTGAG
Statistics
Matches: 150, Mismatches: 30, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
166 44 0.29
167 96 0.64
168 6 0.04
169 4 0.03
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (167 bp):
CACAAACACGCAAAATCGTGAAGTTCAAGTTTTAGCTTTTAAAGAAAGTCTTTGTTTGGCAAGCC
AACTTTTCAATGAGTCTACTAACTCCGAAACACAAAATTAGAGCATTGGTTACACAAATAACGCA
TTTGAAATGAACCTTTCCCCAAGAACAACATTTTGCA
Found at i:1822 original size:22 final size:22
Alignment explanation
Indices: 1797--1856 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
1787 AATCACACTG
1797 TGAAAATTTGATAACCT-CATTA
1 TGAAAATTTGATAACCTAC-TTA
* *
1819 TG-AAATCTGGATAAACTACTTA
1 TGAAAAT-TTGATAACCTACTTA
*
1841 TTAAAATTTGATAACC
1 TGAAAATTTGATAACC
1857 ACACTGTGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
21 4 0.13
22 21 0.70
23 5 0.17
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (22 bp):
TGAAAATTTGATAACCTACTTA
Found at i:3484 original size:27 final size:27
Alignment explanation
Indices: 3444--3502 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
3434 CTCATTATAA
* * *
3444 GGGTAAAATCGTAATTTTATCAATCAG
1 GGGTAAAATAGTAAATTTATCAATCAC
* * *
3471 GGGTAATATAGTAAATTTGTCCATCAC
1 GGGTAAAATAGTAAATTTATCAATCAC
3498 GGGTA
1 GGGTA
3503 TTTTGGTAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (27 bp):
GGGTAAAATAGTAAATTTATCAATCAC
Found at i:5715 original size:22 final size:22
Alignment explanation
Indices: 5540--6075 Score: 168
Period size: 22 Copynumber: 24.0 Consensus size: 22
5530 CGATGTTATA
* *
5540 GAAAGTTTGATAA-CTACACTAT
1 GAAATTTTGATAACCT-CCCTAT
** *
5562 GAAATTTTGATAACCTCAGTGT
1 GAAATTTTGATAACCTCCCTAT
* *
5584 GAAATTGTGATAATCTCCCTAT
1 GAAATTTTGATAACCTCCCTAT
* * *
5606 -AAATTTTGATAATCACACTAT
1 GAAATTTTGATAACCTCCCTAT
* * * **
5627 -AAA-ATTGGTAACCGCATTAT
1 GAAATTTTGATAACCTCCCTAT
5647 GAAAATTTTGATAACCT-CCTCAT
1 G-AAATTTTGATAACCTCCCT-AT
* *
5670 AAAATTTTGATAACCACACC-AT
1 GAAATTTTGATAACCTC-CCTAT
*
5692 GAAATTTCGATAACCTCCCTAT
1 GAAATTTTGATAACCTCCCTAT
* **
5714 GAGAATGAAATTGTGATATCCTTTCTAT
1 GA-AAT----TT-TGATAACCTCCCTAT
* *
5742 GTAATTTTGATAACATCTCC-AT
1 GAAATTTTGATAACCTC-CCTAT
* * *
5764 AAAATTTTCATAATCTCCCTAT
1 GAAATTTTGATAACCTCCCTAT
** ** * *
5786 GGCATTTTTTTAACCTCTCTAG
1 GAAATTTTGATAACCTCCCTAT
*
5808 GAAATTTTGATAA----GC-A-
1 GAAATTTTGATAACCTCCCTAT
* *
5824 CAAATTTTGATAACATCCCTCCGTAT
1 GAAATTTTGAT-A-A--CCTCCCTAT
* ** *
5850 GAAATTTTGTTAATATCCTTAT
1 GAAATTTTGATAACCTCCCTAT
5872 GAAATTTTGATAACCATACACACTAT
1 GAAATTTTGATAACC-T-C-C-CTAT
* * ***
5898 -ATAATTTCGATAATCTTGGTAT
1 GA-AATTTTGATAACCTCCCTAT
* * * *
5920 GAAATTTTGTTAACATCTCTAA
1 GAAATTTTGATAACCTCCCTAT
***
5942 GAAATTTTGATAACCTTTTTTAT
1 GAAATTTTGATAACC-TCCCTAT
**
5965 GAAATTTTTG-TAACCTCTATAT
1 GAAA-TTTTGATAACCTCCCTAT
* * *
5987 AAAATATTGATAA-CTACACTAT
1 GAAATTTTGATAACCT-CCCTAT
* * **
6009 GAAGTTTTGATAATCTCTATAT
1 GAAATTTTGATAACCTCCCTAT
* * *
6031 GAAATTTTGGTAACCACACTAT
1 GAAATTTTGATAACCTCCCTAT
* *
6053 GAAATATTGATAACCTTCCTAT
1 GAAATTTTGATAACCTCCCTAT
6075 G
1 G
6076 TAAAGTTGGT
Statistics
Matches: 372, Mismatches: 105, Indels: 74
0.68 0.19 0.13
Matches are distributed among these distances:
16 10 0.03
17 2 0.01
18 2 0.01
20 12 0.03
21 31 0.08
22 226 0.61
23 35 0.09
24 9 0.02
25 5 0.01
26 23 0.06
27 5 0.01
28 12 0.03
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (22 bp):
GAAATTTTGATAACCTCCCTAT
Found at i:6860 original size:2 final size:2
Alignment explanation
Indices: 6849--6877 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
6839 AAATTTCCCA
6849 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6878 TTGTTAGTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:7380 original size:233 final size:234
Alignment explanation
Indices: 6973--7434 Score: 872
Period size: 233 Copynumber: 2.0 Consensus size: 234
6963 CTCGAGTTGC
6973 AAGCTCAGTTGGTATGCGTATCGTACATGTATCATGATTATGTGTTCAAGTCCCACTGCATGTAA
1 AAGCTCAGTTGGTATGCGTATCGTACATGTATCATGATTATGTGTTCAAGTCCCACTGCATGTAA
*
7038 ATTGTATGCGATTTTTGTCCGATTTTATATGGACTTTGTGCTCCTTTACATGGCCTCGCTTAGTG
66 ATTGTATGCGAGTTTTGTCCGATTTTATATGGACTTTGTGCTCCTTTACATGGCCTCGCTTAGTG
7103 TGTTACCTTTATTAATGTAATAGACGTAGTTTGTAGTTGTGATTTCTCCTTGAATTGTTTGAGCA
131 TGTTACCTTTATTAATGTAATAGACGTAGTTTGTAGTTGTGATTTCTCCTTGAATTGTTTGAGCA
7168 TAAAGAG-ATTTGATTGTGATATAGAAGTACTTAGTTAA
196 TAAAGAGAATTTGATTGTGATATAGAAGTACTTAGTTAA
*
7206 AAGCTCAGTTGGTATGTGTATCGTACATGTATCATGATTATGTGTTCAAGTCCCACTGCATGTAA
1 AAGCTCAGTTGGTATGCGTATCGTACATGTATCATGATTATGTGTTCAAGTCCCACTGCATGTAA
7271 ATTGTATGCGAGTTTTGTCCGATTTTATATGGACTTTGTGCTCCTTTACATGGCCTCGCTTAGTG
66 ATTGTATGCGAGTTTTGTCCGATTTTATATGGACTTTGTGCTCCTTTACATGGCCTCGCTTAGTG
*
7336 TGTTACCTTTATTAATGTAATAGACGTAGTTTGTAGTTGTGATTTTTCCTTGAATTGTTTGAGCA
131 TGTTACCTTTATTAATGTAATAGACGTAGTTTGTAGTTGTGATTTCTCCTTGAATTGTTTGAGCA
*
7401 TAAAGAGATATTTTATTGTGATATAGAAGTACTT
196 TAAAGAGA-ATTTGATTGTGATATAGAAGTACTT
7435 CTGATTATTT
Statistics
Matches: 223, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
233 199 0.89
235 24 0.11
ACGTcount: A:0.24, C:0.13, G:0.21, T:0.41
Consensus pattern (234 bp):
AAGCTCAGTTGGTATGCGTATCGTACATGTATCATGATTATGTGTTCAAGTCCCACTGCATGTAA
ATTGTATGCGAGTTTTGTCCGATTTTATATGGACTTTGTGCTCCTTTACATGGCCTCGCTTAGTG
TGTTACCTTTATTAATGTAATAGACGTAGTTTGTAGTTGTGATTTCTCCTTGAATTGTTTGAGCA
TAAAGAGAATTTGATTGTGATATAGAAGTACTTAGTTAA
Found at i:16431 original size:39 final size:39
Alignment explanation
Indices: 16377--16458 Score: 155
Period size: 39 Copynumber: 2.1 Consensus size: 39
16367 TCGGATGAGC
16377 CTGCCCAATCACTATCAACATAACCATGAAGCTTCAACT
1 CTGCCCAATCACTATCAACATAACCATGAAGCTTCAACT
*
16416 CTGCCCAATCACTATCAACATAAGCATGAAGCTTCAACT
1 CTGCCCAATCACTATCAACATAACCATGAAGCTTCAACT
16455 CTGC
1 CTGC
16459 TGACTTCTTG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.34, C:0.33, G:0.10, T:0.23
Consensus pattern (39 bp):
CTGCCCAATCACTATCAACATAACCATGAAGCTTCAACT
Done.