Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010700.1 Corchorus olitorius cultivar O-4 contig10732, 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: 13047
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Found at i:441 original size:27 final size:26
Alignment explanation
Indices: 389--441 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
379 AATATACTTG
*
389 AAATGACCAAAATGCCCTGGACATGC
1 AAATGACCAAAATGCCCTGAACATGC
* *
415 AAATGACTAAAATGCCCCTGAATATGC
1 AAATGACCAAAATG-CCCTGAACATGC
442 CCTTAGTGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (26 bp):
AAATGACCAAAATGCCCTGAACATGC
Found at i:3055 original size:18 final size:19
Alignment explanation
Indices: 3027--3063 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
3017 CTCTTTTTCT
3027 TTTTCTCTTCTAGTTTTAG
1 TTTTCTCTTCTAGTTTTAG
3046 TTTT-TCTTCTAGTTTTAG
1 TTTTCTCTTCTAGTTTTAG
3064 GGCTAGGGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.11, C:0.14, G:0.11, T:0.65
Consensus pattern (19 bp):
TTTTCTCTTCTAGTTTTAG
Found at i:4608 original size:18 final size:17
Alignment explanation
Indices: 4571--4647 Score: 61
Period size: 18 Copynumber: 4.4 Consensus size: 17
4561 TTAAAAATTA
*
4571 ATAAATCAATAAATAATAG
1 ATAAAT-AATATA-AATAG
4590 ATAAATATATATAAATAG
1 ATAAATA-ATATAAATAG
* *
4608 AAAAATAAGTAAAAATA-
1 ATAAATAA-TATAAATAG
4625 ATAAATAA-ATGAAA-AG
1 ATAAATAATAT-AAATAG
4641 ATAAATA
1 ATAAATA
4648 GGTATATAGA
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
15 2 0.04
16 10 0.20
17 8 0.16
18 19 0.39
19 10 0.20
ACGTcount: A:0.68, C:0.01, G:0.06, T:0.25
Consensus pattern (17 bp):
ATAAATAATATAAATAG
Found at i:4613 original size:29 final size:28
Alignment explanation
Indices: 4562--4644 Score: 75
Period size: 29 Copynumber: 3.0 Consensus size: 28
4552 AGAAAATTAT
*
4562 TAAAAATTAATAAATCAAT-AAATAAT-AG
1 TAAAAA-TAATAAATAAATGAAA-AATAAG
* *
4590 -ATAAAT-ATATATAAATAGAAAAATAAG
1 TAAAAATAATAAATAAAT-GAAAAATAAG
4617 TAAAAATAATAAATAAATGAAAAGATAA
1 TAAAAATAATAAATAAATGAAAA-ATAA
4645 ATAGGTATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
25 8 0.18
26 4 0.09
27 9 0.20
28 10 0.23
29 13 0.30
ACGTcount: A:0.67, C:0.01, G:0.06, T:0.25
Consensus pattern (28 bp):
TAAAAATAATAAATAAATGAAAAATAAG
Found at i:4667 original size:24 final size:24
Alignment explanation
Indices: 4639--4684 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
4629 ATAAATGAAA
* * *
4639 AGATAAATAGGTATATAGATAATT
1 AGATAAAGAGGTAAAGAGATAATT
4663 AGATAAAGAGGTAAAGAGATAA
1 AGATAAAGAGGTAAAGAGATAA
4685 ATAGGTAGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.22, T:0.24
Consensus pattern (24 bp):
AGATAAAGAGGTAAAGAGATAATT
Found at i:4742 original size:19 final size:18
Alignment explanation
Indices: 4704--4773 Score: 62
Period size: 19 Copynumber: 4.1 Consensus size: 18
4694 TAAAAAAAAG
4704 TAGATAATAGTAAATAAA
1 TAGATAATAGTAAATAAA
4722 TAGATAATAGCTAAAT---
1 TAGATAATAG-TAAATAAA
4738 TA-ATAA-A-TAAATAAA
1 TAGATAATAGTAAATAAA
* *
4753 AAGAAAAATAGTAAATAAA
1 TAG-ATAATAGTAAATAAA
4772 TA
1 TA
4774 ATTGATAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 15
0.69 0.05 0.25
Matches are distributed among these distances:
12 5 0.12
14 1 0.02
15 5 0.12
16 2 0.05
17 3 0.07
18 11 0.27
19 14 0.34
ACGTcount: A:0.64, C:0.01, G:0.09, T:0.26
Consensus pattern (18 bp):
TAGATAATAGTAAATAAA
Found at i:4752 original size:31 final size:31
Alignment explanation
Indices: 4714--4774 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
4704 TAGATAATAG
* * *
4714 TAAATAAATAG-ATAATAGCTAAATTAATAAA
1 TAAATAAAAAGAAAAATAG-TAAATAAATAAA
4745 TAAATAAAAAGAAAAATAGTAAATAAATAA
1 TAAATAAAAAGAAAAATAGTAAATAAATAA
4775 TTGATAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 20 0.77
32 6 0.23
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.25
Consensus pattern (31 bp):
TAAATAAAAAGAAAAATAGTAAATAAATAAA
Found at i:6668 original size:64 final size:64
Alignment explanation
Indices: 6567--6758 Score: 375
Period size: 64 Copynumber: 3.0 Consensus size: 64
6557 CTTATCAACA
*
6567 GATAATCACATAGTTTTTTAAGATATTGAACATTGAGCAAAGCGATAGCCTAACCCACAAAACT
1 GATAATCACATAGTTTTTTAAGATATTGAACATTGAGCAAAGAGATAGCCTAACCCACAAAACT
6631 GATAATCACATAGTTTTTTAAGATATTGAACATTGAGCAAAGAGATAGCCTAACCCACAAAACT
1 GATAATCACATAGTTTTTTAAGATATTGAACATTGAGCAAAGAGATAGCCTAACCCACAAAACT
6695 GATAATCACATAGTTTTTTAAGATATTGAACATTGAGCAAAGAGATAGCCTAACCCACAAAACT
1 GATAATCACATAGTTTTTTAAGATATTGAACATTGAGCAAAGAGATAGCCTAACCCACAAAACT
6759 AATAGAGAAC
Statistics
Matches: 127, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
64 127 1.00
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.27
Consensus pattern (64 bp):
GATAATCACATAGTTTTTTAAGATATTGAACATTGAGCAAAGAGATAGCCTAACCCACAAAACT
Found at i:12084 original size:10 final size:10
Alignment explanation
Indices: 12069--12100 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
12059 ACCGCTACCA
12069 CCACCGTCGG
1 CCACCGTCGG
*
12079 CCACCGTTGG
1 CCACCGTCGG
12089 CCACCGTCGG
1 CCACCGTCGG
12099 CC
1 CC
12101 GCCGGAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.09, C:0.50, G:0.28, T:0.12
Consensus pattern (10 bp):
CCACCGTCGG
Found at i:12389 original size:10 final size:9
Alignment explanation
Indices: 12369--12395 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
12359 ACTAGCCGAA
12369 TTTTTTGTT
1 TTTTTTGTT
12378 TTTTTTGTT
1 TTTTTTGTT
12387 TTTTTTGTT
1 TTTTTTGTT
12396 ATTGGGTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (9 bp):
TTTTTTGTT
Found at i:12959 original size:3 final size:3
Alignment explanation
Indices: 12953--13046 Score: 188
Period size: 3 Copynumber: 31.3 Consensus size: 3
12943 ATTCTCTAAC
12953 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
13001 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
13047 G
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 91 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Done.