Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015793.1 Corchorus olitorius cultivar O-4 contig15826, 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: 6904
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Found at i:739 original size:29 final size:28
Alignment explanation
Indices: 693--764 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
683 CCCATACCTG
*
693 TAAGTACAGGGACTAAATTGATCATTTCT
1 TAAGTACAGGGACCAAATTGA-CATTTCT
* * *
722 TAAGTAGAGGGGCCAAATTGACTTTTCTT
1 TAAGTACAGGGACCAAATTGACATTTC-T
751 GTAAGTACAGGGAC
1 -TAAGTACAGGGAC
765 GTGCCGGGTA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
28 5 0.14
29 19 0.54
30 11 0.31
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.31
Consensus pattern (28 bp):
TAAGTACAGGGACCAAATTGACATTTCT
Found at i:1598 original size:25 final size:25
Alignment explanation
Indices: 1549--1599 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 25
1539 GGCTCTAAAA
*
1549 TTTCAACAAACTAAAATTAATTTTT
1 TTTCAAAAAACTAAAATTAATTTTT
1574 TTTCAAAAAGACTAAAATTAATTTTT
1 TTTCAAAAA-ACTAAAATTAATTTTT
1600 GGATGATTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (25 bp):
TTTCAAAAAACTAAAATTAATTTTT
Found at i:4047 original size:22 final size:22
Alignment explanation
Indices: 4020--4072 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
4010 TCTTATGAGG
* *
4020 TTTTGATAACAATCCTTTGTCA
1 TTTTGATAACAATCCTTCGTAA
*
4042 TTTTGATAACTATCCTTCGTAA
1 TTTTGATAACAATCCTTCGTAA
*
4064 TTTTTATAA
1 TTTTGATAA
4073 ACACTTTATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.28, C:0.15, G:0.08, T:0.49
Consensus pattern (22 bp):
TTTTGATAACAATCCTTCGTAA
Found at i:4308 original size:65 final size:66
Alignment explanation
Indices: 4204--4472 Score: 202
Period size: 65 Copynumber: 4.1 Consensus size: 66
4194 CAAACGGTAA
* * * *
4204 TTATCAAAATT-TCATAGGACAGTTGTCAAAATTTCAATCGAAG-TTATTAAAATTATAAAGGAT
1 TTATCATAATTAT-ATAGGACAATTGTCAAAATTTCAATCGAAGATTATTAAAATTACAAAGGGT
4267 GG
65 GG
* *
4269 TTATCATAATTATATACGACAATTGTCAAAA-TTCTAATCG-AGATTATCAAAATCT-CAAAGGG
1 TTATCATAATTATATAGGACAATTGTCAAAATTTC-AATCGAAGATTATTAAAAT-TACAAAGGG
**
4331 CAG
64 TGG
* * * * * *
4334 TTATCA-ACAATATA-AGG-CGATTATCAAAATTTGATAT-GACGTTTGATTATCAAGATTACAA
1 TTATCATA-ATTATATAGGACAATTGTCAAAATTTCA-ATCGAAGATT-ATTA--AA-ATTACAA
4395 AGGGTGG
60 AGGGTGG
*
4402 TTATCATAATTATATAGGACAATTGTCAAAA-TTCTAATCG-AGATTATCAAAATCT-CAAAGGG
1 TTATCATAATTATATAGGACAATTGTCAAAATTTC-AATCGAAGATTATTAAAAT-TACAAAGGG
**
4464 CAG
64 TGG
4467 TTATCA
1 TTATCA
4473 ACAATATAGG
Statistics
Matches: 158, Mismatches: 27, Indels: 38
0.71 0.12 0.17
Matches are distributed among these distances:
63 12 0.08
64 15 0.09
65 76 0.48
66 5 0.03
67 3 0.02
68 24 0.15
69 11 0.07
70 12 0.08
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (66 bp):
TTATCATAATTATATAGGACAATTGTCAAAATTTCAATCGAAGATTATTAAAATTACAAAGGGTG
G
Found at i:4428 original size:133 final size:133
Alignment explanation
Indices: 4255--4538 Score: 514
Period size: 133 Copynumber: 2.1 Consensus size: 133
4245 AGTTATTAAA
*
4255 ATTATAAAGGATGGTTATCATAATTATATACGACAATTGTCAAAATTCTAATCGAGATTATCAAA
1 ATTACAAAGGATGGTTATCATAATTATATACGACAATTGTCAAAATTCTAATCGAGATTATCAAA
4320 ATCTCAAAGGGCAGTTATCAACAATATAAGGCGATTATCAAAATTTGATATGACGTTTGATTATC
66 ATCTCAAAGGGCAGTTATCAACAATATAAGGCGATTATCAAAATTTGATATGACGTTTGATTATC
4385 AAG
131 AAG
* *
4388 ATTACAAAGGGTGGTTATCATAATTATATAGGACAATTGTCAAAATTCTAATCGAGATTATCAAA
1 ATTACAAAGGATGGTTATCATAATTATATACGACAATTGTCAAAATTCTAATCGAGATTATCAAA
* *
4453 ATCTCAAAGGGCAGTTATCAACAATATAGGGCGATTATCAAAATTTGATATGGCGTTTGATTATC
66 ATCTCAAAGGGCAGTTATCAACAATATAAGGCGATTATCAAAATTTGATATGACGTTTGATTATC
4518 AAG
131 AAG
*
4521 ATTGCAAAGGATGGTTAT
1 ATTACAAAGGATGGTTAT
4539 AAAAAATACA
Statistics
Matches: 144, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
133 144 1.00
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (133 bp):
ATTACAAAGGATGGTTATCATAATTATATACGACAATTGTCAAAATTCTAATCGAGATTATCAAA
ATCTCAAAGGGCAGTTATCAACAATATAAGGCGATTATCAAAATTTGATATGACGTTTGATTATC
AAG
Found at i:4530 original size:68 final size:67
Alignment explanation
Indices: 4310--4519 Score: 236
Period size: 68 Copynumber: 3.1 Consensus size: 67
4300 TTCTAATCGA
*
4310 GATTATCAAAATCTCAAAGGGCAGTTATCAACAATATAAGGCGATTATCAAAATTTGATATGACG
1 GATTATCAAAATCTCAAAGGGCAGTTATCAACAATATAGGGCGATTATCAAAATTTGATATG-CG
4375 TTT
65 TTT
* ** * * *
4378 GATTATCAAGAT-TACAAAGGGTGGTTATCATA-ATTATATAGGACAATTGTCAAAATTCT-A-A
1 GATTATCAAAATCT-CAAAGGGCAGTTATCA-ACA--ATATAGGGCGATTATCAAAATT-TGATA
*
4439 T-CG--A
61 TGCGTTT
4443 GATTATCAAAATCTCAAAGGGCAGTTATCAACAATATAGGGCGATTATCAAAATTTGATATGGCG
1 GATTATCAAAATCTCAAAGGGCAGTTATCAACAATATAGGGCGATTATCAAAATTTGATAT-GCG
4508 TTT
65 TTT
4511 GATTATCAA
1 GATTATCAA
4520 GATTGCAAAG
Statistics
Matches: 114, Mismatches: 15, Indels: 26
0.74 0.10 0.17
Matches are distributed among these distances:
62 1 0.01
63 20 0.18
64 3 0.03
65 26 0.23
66 3 0.03
67 3 0.03
68 35 0.31
69 3 0.03
70 19 0.17
71 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.31
Consensus pattern (67 bp):
GATTATCAAAATCTCAAAGGGCAGTTATCAACAATATAGGGCGATTATCAAAATTTGATATGCGT
TT
Found at i:6703 original size:3 final size:3
Alignment explanation
Indices: 6695--6781 Score: 167
Period size: 3 Copynumber: 29.3 Consensus size: 3
6685 ATATCTACTA
6695 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
6743 TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
6782 TATGATTTAA
Statistics
Matches: 83, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.02
3 81 0.98
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Done.