Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010768.1 Corchorus olitorius cultivar O-4 contig10800, 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: 21531
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:976 original size:4 final size:4
Alignment explanation
Indices: 960--1020 Score: 52
Period size: 4 Copynumber: 15.5 Consensus size: 4
950 TCAAAAATAC
* * * * * *
960 ATAT ATAT GTAT ATAT ATAT ATAT ATAT GTAT GTAT GTAT GTAT GTAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
*
1008 ATGT ATA- ATAT AT
1 ATAT ATAT ATAT AT
1021 TTAGCCAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
3 3 0.06
4 47 0.94
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.49
Consensus pattern (4 bp):
ATAT
Found at i:977 original size:12 final size:12
Alignment explanation
Indices: 960--1014 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 12
950 TCAAAAATAC
960 ATATATATGTAT
1 ATATATATGTAT
*
972 ATATATATATAT
1 ATATATATGTAT
*
984 ATATGTATGTAT
1 ATATATATGTAT
* *
996 GTATGTATGTAT
1 ATATATATGTAT
*
1008 ATGTATA
1 ATATATA
1015 ATATATTTAG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (12 bp):
ATATATATGTAT
Found at i:2997 original size:15 final size:15
Alignment explanation
Indices: 2977--3007 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2967 TTTCTTTTCT
2977 TCAATTCAGGAGAAG
1 TCAATTCAGGAGAAG
2992 TCAATTCAGGAGAAG
1 TCAATTCAGGAGAAG
3007 T
1 T
3008 ATATCATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.23
Consensus pattern (15 bp):
TCAATTCAGGAGAAG
Found at i:3470 original size:22 final size:23
Alignment explanation
Indices: 3445--3494 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
3435 AATGCTATAA
* **
3445 ATAAATTCTTTATTTGTTTT-AT
1 ATAAATACTTTATTCATTTTAAT
*
3467 ATAACTACTTTATTCATTTTAAT
1 ATAAATACTTTATTCATTTTAAT
3490 ATAAA
1 ATAAA
3495 GTTTCTGTTA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.36, C:0.08, G:0.02, T:0.54
Consensus pattern (23 bp):
ATAAATACTTTATTCATTTTAAT
Found at i:3625 original size:70 final size:70
Alignment explanation
Indices: 3542--3679 Score: 258
Period size: 70 Copynumber: 2.0 Consensus size: 70
3532 GCATATTTTG
* *
3542 AAACTATATGTAGAAAATGGGATTATACATACATACATTAGTCTACATATATATATGTATGTATA
1 AAACTATATGTAGAAAATGGGATTATACATACATACATTAGTCTACATATATATATATATATATA
3607 TATAT
66 TATAT
3612 AAACTATATGTAGAAAATGGGATTATACATACATACATTAGTCTACATATATATATATATATATA
1 AAACTATATGTAGAAAATGGGATTATACATACATACATTAGTCTACATATATATATATATATATA
3677 TAT
66 TAT
3680 GTATGTTAAT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 66 1.00
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.37
Consensus pattern (70 bp):
AAACTATATGTAGAAAATGGGATTATACATACATACATTAGTCTACATATATATATATATATATA
TATAT
Found at i:11768 original size:24 final size:23
Alignment explanation
Indices: 11724--11768 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
11714 GCAAATAAAG
*
11724 AACTAAGAAAGAAAAGTAGAGAA
1 AACTAAGAAAGAAAAGGAGAGAA
11747 AACTATAGAGAAG-AAAGGAGAG
1 AACTA-AGA-AAGAAAAGGAGAG
11769 GGGGGAGACG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 11 0.58
25 3 0.16
ACGTcount: A:0.60, C:0.04, G:0.27, T:0.09
Consensus pattern (23 bp):
AACTAAGAAAGAAAAGGAGAGAA
Found at i:11893 original size:25 final size:24
Alignment explanation
Indices: 11843--11906 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 24
11833 TCATAAGAAT
11843 ATATATTTATATAATTCATTAATAC
1 ATATA-TTATATAATTCATTAATAC
* **
11868 ATATATTCATATAATTTATTTTTAC
1 ATATATT-ATATAATTCATTAATAC
*
11893 AAATA-TATATAATT
1 ATATATTATATAATT
11907 ACTACTTAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
23 8 0.24
24 3 0.09
25 23 0.68
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (24 bp):
ATATATTATATAATTCATTAATAC
Found at i:12240 original size:24 final size:24
Alignment explanation
Indices: 12213--12262 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
12203 TTCTGAGTAC
*
12213 TTTGCAACGGAATCAAAAACGGAA
1 TTTGCAACAGAATCAAAAACGGAA
*
12237 TTTGCAATAGAATCAAAAACGGAA
1 TTTGCAACAGAATCAAAAACGGAA
12261 TT
1 TT
12263 CTATCTATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.14, G:0.18, T:0.22
Consensus pattern (24 bp):
TTTGCAACAGAATCAAAAACGGAA
Found at i:13825 original size:3 final size:3
Alignment explanation
Indices: 13810--13886 Score: 57
Period size: 3 Copynumber: 25.7 Consensus size: 3
13800 CTCCTCATGG
* * * ** *
13810 TCA TCA CCA TCA TCA TCA TCG TCC TCA TTG TCA TC- TCCG TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T-CA TCA TCA
* * *
13855 TCA TCA TCA TCC TCG TCA TCA TCC TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
13887 GCCATCAACT
Statistics
Matches: 57, Mismatches: 15, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
2 1 0.02
3 55 0.96
4 1 0.02
ACGTcount: A:0.22, C:0.39, G:0.05, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:13837 original size:30 final size:29
Alignment explanation
Indices: 13801--13886 Score: 91
Period size: 30 Copynumber: 2.9 Consensus size: 29
13791 GAGCTAAATC
* *
13801 TCCTCATGGTCATCACCATCATCATCATCG
1 TCCTCATCGTCATCACC-TCATCATCATCA
* *
13831 TCCTCATTGTCATCTCCGTCATCATCATCA
1 TCCTCATCGTCATCACC-TCATCATCATCA
* *
13861 TCATCCTCGTCATCATCCTCATCATC
1 TCCTCATCGTCATCA-CCTCATCATC
13887 GCCATCAACT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
30 45 0.96
31 2 0.04
ACGTcount: A:0.21, C:0.38, G:0.07, T:0.34
Consensus pattern (29 bp):
TCCTCATCGTCATCACCTCATCATCATCA
Found at i:13843 original size:21 final size:20
Alignment explanation
Indices: 13809--13886 Score: 79
Period size: 21 Copynumber: 3.9 Consensus size: 20
13799 TCTCCTCATG
*
13809 GTCATCACCATCATCATCATC
1 GTCATCATCATCATCATC-TC
* **
13830 GTCCTCATTGTCATC-TC-C
1 GTCATCATCATCATCATCTC
13848 GTCATCATCATCATCATCCTC
1 GTCATCATCATCATCAT-CTC
*
13869 GTCATCATCCTCATCATC
1 GTCATCATCATCATCATC
13887 GCCATCAACT
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
18 13 0.28
19 1 0.02
20 4 0.09
21 28 0.61
ACGTcount: A:0.22, C:0.38, G:0.06, T:0.33
Consensus pattern (20 bp):
GTCATCATCATCATCATCTC
Found at i:16389 original size:12 final size:13
Alignment explanation
Indices: 16364--16392 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
16354 CATCTCAAAA
16364 TCCGTGTCTAAAT
1 TCCGTGTCTAAAT
16377 TCCGTGT-TAAAT
1 TCCGTGTCTAAAT
16389 TCCG
1 TCCG
16393 GGTTTAAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38
Consensus pattern (13 bp):
TCCGTGTCTAAAT
Found at i:19706 original size:2 final size:2
Alignment explanation
Indices: 19699--19730 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
19689 ATTATATGTA
19699 AT AT AT AT 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 AT
19731 GTAAATAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20543 original size:32 final size:33
Alignment explanation
Indices: 20502--20566 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
20492 GGAAAAGGAC
*
20502 ATTCGTGTCCTTGCT-GTTTGGAGCGCTATTTT
1 ATTCGTGTCCTTGCTGGCTTGGAGCGCTATTTT
*
20534 ATTCGTGTCCTTTCTGGCTTGGAGCGCTATTTT
1 ATTCGTGTCCTTGCTGGCTTGGAGCGCTATTTT
20567 CTTAGTCTCG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.47
33 16 0.53
ACGTcount: A:0.09, C:0.20, G:0.25, T:0.46
Consensus pattern (33 bp):
ATTCGTGTCCTTGCTGGCTTGGAGCGCTATTTT
Found at i:20772 original size:9 final size:9
Alignment explanation
Indices: 20750--20780 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
20740 AGCAGCCGCG
20750 ATAGCGGCAA
1 ATAGCGG-AA
20760 ATAGCGGAA
1 ATAGCGGAA
20769 ATAGCGGAA
1 ATAGCGGAA
20778 ATA
1 ATA
20781 ACGGGGTGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 14 0.67
10 7 0.33
ACGTcount: A:0.45, C:0.13, G:0.29, T:0.13
Consensus pattern (9 bp):
ATAGCGGAA
Found at i:21303 original size:17 final size:19
Alignment explanation
Indices: 21264--21310 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
21254 TTCCATCAAA
21264 TTTCAAACTTT-TCAATTC
1 TTTCAAACTTTCTCAATTC
*
21282 TTTCAAATTTTCTCAA-TC
1 TTTCAAACTTTCTCAATTC
21300 -TTCAAACTTTC
1 TTTCAAACTTTC
21311 AAAACTCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 10 0.38
18 12 0.46
19 4 0.15
ACGTcount: A:0.28, C:0.23, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTCAAACTTTCTCAATTC
Done.