Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020565.1 Corchorus olitorius cultivar O-4 contig20598, 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: 5278
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:1394 original size:14 final size:13
Alignment explanation
Indices: 1370--1434 Score: 87
Period size: 14 Copynumber: 4.8 Consensus size: 13
1360 TAAAGGACGT
1370 TTTTCAAAAATGA
1 TTTTCAAAAATGA
1383 TTTTCAAGAAATTG-
1 TTTTCAA-AAA-TGA
1397 TTTTCAAGAAATGA
1 TTTTCAA-AAATGA
1411 TTTTCAAAAATGA
1 TTTTCAAAAATGA
1424 GTTTTCAAAAA
1 -TTTTCAAAAA
1435 GGTTTTGAGT
Statistics
Matches: 48, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
13 15 0.31
14 31 0.65
15 2 0.04
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (13 bp):
TTTTCAAAAATGA
Found at i:2104 original size:28 final size:27
Alignment explanation
Indices: 2060--2122 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
2050 GAAGCAATCT
*
2060 AAAGAAAAAAAGAAAAAAA-AGAGAAAG
1 AAAG-AAAAAAGAAAAAAAGAAAGAAAG
*
2087 CAAAGAAAAAAGTGAAAAAAGAAAGAAAG
1 -AAAGAAAAAAG-AAAAAAAGAAAGAAAG
2116 AAAGAAA
1 AAAGAAA
2123 GAAATAAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 7 0.23
28 17 0.55
29 7 0.23
ACGTcount: A:0.78, C:0.02, G:0.19, T:0.02
Consensus pattern (27 bp):
AAAGAAAAAAGAAAAAAAGAAAGAAAG
Found at i:2113 original size:4 final size:4
Alignment explanation
Indices: 2060--2137 Score: 67
Period size: 4 Copynumber: 19.8 Consensus size: 4
2050 GAAGCAATCT
*
2060 AAAG AAAA AAAG AAA- AAA- AAGAG AAAG CAAAG AAA- AAAGTG AAA-
1 AAAG AAAG AAAG AAAG AAAG AA-AG AAAG -AAAG AAAG AAA--G AAAG
*
2104 AAAG AAAG AAAG AAAG AAAG AAAT AAAG -AAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
2138 ATCAAAAGGA
Statistics
Matches: 62, Mismatches: 4, Indels: 16
0.76 0.05 0.20
Matches are distributed among these distances:
3 14 0.23
4 39 0.63
5 6 0.10
6 3 0.05
ACGTcount: A:0.77, C:0.01, G:0.19, T:0.03
Consensus pattern (4 bp):
AAAG
Found at i:3287 original size:37 final size:35
Alignment explanation
Indices: 3246--3658 Score: 301
Period size: 37 Copynumber: 11.2 Consensus size: 35
3236 AGATTTCTGA
3246 TTAGGTTACTTATCAAATCCTTATTTAAGGTCCTTGT
1 TTAGGTT-CTTATCAAATCCTTATTTAAGGTCC-TGT
* * * * * * *
3283 TTAGGTGTCTCATCAAAACCTTGTTCAAGATTTCTGA
1 TTAGGT-TCTTATCAAATCCTTATTTAAG-GTCCTGT
3320 TTAGGTTACTTATCAAATCCTTATTTAAGGTCCCTGT
1 TTAGGTT-CTTATCAAATCCTTATTTAAGGT-CCTGT
* * * *
3357 TTAGGTGTCTCATCAAAAT-CTTGTTCAAGATTCCTGT
1 TTAGGT-TCTTATC-AAATCCTTATTTAAG-GTCCTGT
* * *
3394 TTAGGTTTCTTATTAAATCTTTATTTAAGGTCCCTAT
1 TTAGG-TTCTTATCAAATCCTTATTTAAGGT-CCTGT
* * * * *
3431 TTAGGTGTCTCATTAAAAT-CTTGTTTAAGATCTCGGT
1 TTAGGT-TCTTA-TCAAATCCTTATTTAAGGTC-CTGT
3468 TTAGGTTTCTTATCAAATCCTTATTTAAGGTCCCTGT
1 TTAGG-TTCTTATCAAATCCTTATTTAAGGT-CCTGT
** * *
3505 TTAGGTGTCTTATCAAATTTTTGTTTAAGATCCTTGT
1 TTAGGT-TCTTATCAAATCCTTATTTAAGGTCC-TGT
*
3542 TTAGGTTTCTTATCAAATTCTTATTTAAGGTCACTGT
1 TTAGG-TTCTTATCAAATCCTTATTTAAGGTC-CTGT
* * * ** *
3579 TTAGGTGTCTCATCAAAAT-CTTGTTCAAAATTCCTAT
1 TTAGGT-TCTTATC-AAATCCTTATT-TAAGGTCCTGT
*
3616 TTAGGTTTCTTATTAAATCCTTATTTAAGGTACCTGT
1 TTAGG-TTCTTATCAAATCCTTATTTAAGGT-CCTGT
3653 TTAGGT
1 TTAGGT
3659 GTCTCTTCAA
Statistics
Matches: 293, Mismatches: 57, Indels: 53
0.73 0.14 0.13
Matches are distributed among these distances:
36 26 0.09
37 239 0.82
38 28 0.10
ACGTcount: A:0.24, C:0.16, G:0.15, T:0.45
Consensus pattern (35 bp):
TTAGGTTCTTATCAAATCCTTATTTAAGGTCCTGT
Found at i:3305 original size:74 final size:74
Alignment explanation
Indices: 3215--3672 Score: 634
Period size: 74 Copynumber: 6.2 Consensus size: 74
3205 ACAAAATTTA
* * * *
3215 GTCTCATCAAAACCTTGTTCAAGATTTCTGATTAGGTTACTTATCAAATCCTTATTTAAGGTCCT
1 GTCTCATCAAAATCTTGTTCAAGATTCCTGATTAGGTTTCTTATCAAATCCTTATTTAAGGTCCC
3280 TGTTTAGGT
66 TGTTTAGGT
* * *
3289 GTCTCATCAAAACCTTGTTCAAGATTTCTGATTAGGTTACTTATCAAATCCTTATTTAAGGTCCC
1 GTCTCATCAAAATCTTGTTCAAGATTCCTGATTAGGTTTCTTATCAAATCCTTATTTAAGGTCCC
3354 TGTTTAGGT
66 TGTTTAGGT
* * *
3363 GTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAGGTTTCTTATTAAATCTTTATTTAAGGTCCC
1 GTCTCATCAAAATCTTGTTCAAGATTCCTGATTAGGTTTCTTATCAAATCCTTATTTAAGGTCCC
*
3428 TATTTAGGT
66 TGTTTAGGT
* * * *
3437 GTCTCATTAAAATCTTGTTTAAGA-TCTCGGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCC
1 GTCTCATCAAAATCTTGTTCAAGATTC-CTGATTAGGTTTCTTATCAAATCCTTATTTAAGGTCC
3501 CTGTTTAGGT
65 CTGTTTAGGT
* * * * * * *
3511 GTCTTATCAAATTTTTGTTTAAGA-TCCTTGTTTAGGTTTCTTATCAAATTCTTATTTAAGGTCA
1 GTCTCATCAAAATCTTGTTCAAGATTCC-TGATTAGGTTTCTTATCAAATCCTTATTTAAGGTCC
3575 CTGTTTAGGT
65 CTGTTTAGGT
* * *
3585 GTCTCATCAAAATCTTGTTCAAAATTCCT-ATTTAGGTTTCTTATTAAATCCTTATTTAAGGTAC
1 GTCTCATCAAAATCTTGTTCAAGATTCCTGA-TTAGGTTTCTTATCAAATCCTTATTTAAGGTCC
3649 CTGTTTAGGT
65 CTGTTTAGGT
*
3659 GTCTCTTCAAAATC
1 GTCTCATCAAAATC
3673 CCAGTTTAGG
Statistics
Matches: 348, Mismatches: 32, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
73 3 0.01
74 342 0.98
75 3 0.01
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.44
Consensus pattern (74 bp):
GTCTCATCAAAATCTTGTTCAAGATTCCTGATTAGGTTTCTTATCAAATCCTTATTTAAGGTCCC
TGTTTAGGT
Found at i:3735 original size:18 final size:18
Alignment explanation
Indices: 3696--3737 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
3686 CTTATCAAAA
*
3696 TTTTGTTCAAAATCCATT
1 TTTTGTTCAAAATCCATG
3714 TTTTGTTCAAAATTCC-TG
1 TTTTGTTCAAAA-TCCATG
3732 TTTTGT
1 TTTTGT
3738 GTTTAAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.21, C:0.14, G:0.10, T:0.55
Consensus pattern (18 bp):
TTTTGTTCAAAATCCATG
Found at i:3884 original size:54 final size:53
Alignment explanation
Indices: 3768--3939 Score: 152
Period size: 54 Copynumber: 3.2 Consensus size: 53
3758 GTCTCTCTAG
* * **
3768 AAAGTTGATCTTCAGATGACCCTGTGTGGTC-TTCCATAGAAGTTTTCAAAAATC
1 AAAGTTGATCTTAAGATGACCCAGTGTGGTCATTCCA-AGAAG-TTTCAATGATC
* * *
3822 TAAA-TTGATCTTAAGTTGATCCAGTGTGGTCATTCCAAGAAGTTTACGATGATC
1 -AAAGTTGATCTTAAGATGACCCAGTGTGGTCATTCCAAGAAGTTT-CAATGATC
* * *
3876 AAAGTTGATCTCTAA-ACTGACCCGGTGCGGTCATTCCAAGAAATGTTTCCATGATC
1 AAAGTTGATCT-TAAGA-TGACCCAGTGTGGTCATTCCAAG-AA-GTTTCAATGATC
*
3932 AAGGTTGA
1 AAAGTTGA
3940 ATTCTTAATA
Statistics
Matches: 97, Mismatches: 13, Indels: 13
0.79 0.11 0.11
Matches are distributed among these distances:
53 6 0.06
54 40 0.41
55 31 0.32
56 16 0.16
57 4 0.04
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (53 bp):
AAAGTTGATCTTAAGATGACCCAGTGTGGTCATTCCAAGAAGTTTCAATGATC
Found at i:3959 original size:55 final size:55
Alignment explanation
Indices: 3840--3959 Score: 129
Period size: 55 Copynumber: 2.2 Consensus size: 55
3830 TCTTAAGTTG
* * *
3840 ATCCAGTGTGGTCATTCCAAGAAGTTTACGATGATCAAAGTTGATCTCTAAACTG
1 ATCCAGTGCGGTCATTCCAAGAAGTTTACCATGATCAAAGTTGATCTCTAAACTA
* * * *
3895 ACCCGGTGCGGTCATTCCAAGAAATGTTT-CCATGATCAAGGTTGAAT-TCTTAA-TA
1 ATCCAGTGCGGTCATTCCAAG-AA-GTTTACCATGATCAAAGTTG-ATCTCTAAACTA
3950 ATCCAGTGCG
1 ATCCAGTGCG
3960 ATTAATTAAG
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
55 27 0.51
56 20 0.38
57 6 0.11
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (55 bp):
ATCCAGTGCGGTCATTCCAAGAAGTTTACCATGATCAAAGTTGATCTCTAAACTA
Found at i:4012 original size:33 final size:33
Alignment explanation
Indices: 3970--4047 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 33
3960 ATTAATTAAG
* * * *
3970 AAGTTCAAAATTTGCAT-TCCATTTCAAAATTCA
1 AAGTTCAAAATCTACATAT-CATATCAAAACTCA
4003 AAGTTCAAAATCTACATATCATATCAAAACTCA
1 AAGTTCAAAATCTACATATCATATCAAAACTCA
4036 AAGTTCAAAATC
1 AAGTTCAAAATC
4048 CACAGATTCT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
33 39 0.98
34 1 0.03
ACGTcount: A:0.45, C:0.19, G:0.05, T:0.31
Consensus pattern (33 bp):
AAGTTCAAAATCTACATATCATATCAAAACTCA
Found at i:4199 original size:7 final size:7
Alignment explanation
Indices: 4187--4211 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
4177 ATTTCATAGC
4187 TTCAAAA
1 TTCAAAA
4194 TTCAAAA
1 TTCAAAA
4201 TTCAAAA
1 TTCAAAA
4208 TTCA
1 TTCA
4212 TGGCTCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (7 bp):
TTCAAAA
Found at i:4220 original size:28 final size:29
Alignment explanation
Indices: 4179--4235 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
4169 CTGTTTGCAT
*
4179 TTCATAGCTTCAAAATTCAAAATTCAAAA
1 TTCATAGCTTCAAAAATCAAAATTCAAAA
* *
4208 TTCATGGC-TCAAAAATCAAATTTCAAAA
1 TTCATAGCTTCAAAAATCAAAATTCAAAA
4236 CCTGCATTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.47, C:0.18, G:0.05, T:0.30
Consensus pattern (29 bp):
TTCATAGCTTCAAAAATCAAAATTCAAAA
Found at i:4301 original size:7 final size:7
Alignment explanation
Indices: 4260--4299 Score: 71
Period size: 7 Copynumber: 5.7 Consensus size: 7
4250 TTTCATTCTC
4260 CAAAAGT
1 CAAAAGT
4267 CAAAAGT
1 CAAAAGT
4274 CAAAAGT
1 CAAAAGT
4281 CAAAAGT
1 CAAAAGT
*
4288 CAAAATT
1 CAAAAGT
4295 CAAAA
1 CAAAA
4300 TTTGCATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.60, C:0.15, G:0.10, T:0.15
Consensus pattern (7 bp):
CAAAAGT
Done.