Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019282.1 Corchorus olitorius cultivar O-4 contig19315, 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: 28742
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:446 original size:2 final size:2
Alignment explanation
Indices: 439--470 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
429 ATACATATGC
439 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
471 GACTTCAGTT
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:2484 original size:27 final size:27
Alignment explanation
Indices: 2454--2510 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
2444 AAAAGAAACA
*
2454 GAGGGTATGGGCTTATAATAAGGAACG
1 GAGGGTATGGACTTATAATAAGGAACG
2481 GAGGGTATGGACTTATAATAAGGAACG
1 GAGGGTATGGACTTATAATAAGGAACG
2508 GAG
1 GAG
2511 AAAGTAATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.35, C:0.07, G:0.37, T:0.21
Consensus pattern (27 bp):
GAGGGTATGGACTTATAATAAGGAACG
Found at i:3170 original size:45 final size:45
Alignment explanation
Indices: 3121--3207 Score: 122
Period size: 45 Copynumber: 1.9 Consensus size: 45
3111 TTTAATCATC
3121 AAACACTTAAATGCTTAA-TAAAAAAACACTTTTTTTAGAAATAAA
1 AAACACTTAAATGCTTAATTAAAAAAACACTTTTTTTA-AAATAAA
* * **
3166 AAACACTTACATGCTTAATTAAAAGAATTCTTTTTTTAAAAT
1 AAACACTTAAATGCTTAATTAAAAAAACACTTTTTTTAAAAT
3208 CATGTGACAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
45 21 0.57
46 16 0.43
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.36
Consensus pattern (45 bp):
AAACACTTAAATGCTTAATTAAAAAAACACTTTTTTTAAAATAAA
Found at i:6825 original size:22 final size:23
Alignment explanation
Indices: 6800--6850 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
6790 CTTCTTATTC
*
6800 TATATATTTTG-ATTCATATA-AT
1 TATATATTATGAATT-ATATATAT
6822 TATATA-TATGAATTATATATAT
1 TATATATTATGAATTATATATAT
6844 TATATAT
1 TATATAT
6851 ATACCTCAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 8 0.32
22 17 0.68
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (23 bp):
TATATATTATGAATTATATATAT
Found at i:6837 original size:13 final size:12
Alignment explanation
Indices: 6815--6853 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
6805 ATTTTGATTC
6815 ATATAATTATAT
1 ATATAATTATAT
6827 ATATGAATTATAT
1 ATAT-AATTATAT
*
6840 ATATTA-TATAT
1 ATATAATTATAT
6851 ATA
1 ATA
6854 CCTCAGGGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 8 0.32
12 5 0.20
13 12 0.48
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (12 bp):
ATATAATTATAT
Found at i:8433 original size:3 final size:3
Alignment explanation
Indices: 8425--8450 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
8415 AAATCACTGC
8425 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
8451 CTTATCTACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:13671 original size:436 final size:435
Alignment explanation
Indices: 12834--13693 Score: 1018
Period size: 434 Copynumber: 2.0 Consensus size: 435
12824 TTAAATCGAG
* * ** *
12834 TAAGATAGAATTTGTAAAGGACTAAGTAGCATAAAATAAAAAAGTATAAGGGTGATGTGATAACT
1 TAAGATAGAATTTGTAAAGAACTAAGGAGCATAAAATAAAAAAGTATAAGGGCCATGTGATAAAT
* *
12899 AATTCAAATAAGAAAATATTTGTTAATTAATGAAGATCTTGAAACATAAAAAAATTCCCTTTGGA
66 AATTCAAAGAAGAAAATATTTG---ATTAATGAAGATCTTGAAACAT-AAAAAATTCCATTTGGA
* * * * * * * *
12964 ATCATTCATGAAACTCGTAGATTAAATCAACTTTCGGGTTCTTCATGAAAGTCATAGATTATACA
127 ACCATTAACGAAACTCATAGATCAAATCAACTTTCGGGTCCTTCATGAAAGTCATAAATCATACA
* * * * * * *
13029 ATAACCTTTTAACCGATACATGAATAACTTTAATTGGACATGTGGATCAAAAATTATATGGTATT
192 ATAACCTTTAAACCGACACATCAATAACTTCAATCGGACATGTGGATCAAAAATTATACGATATT
* ** * * * ** *
13094 AAATAGACCAACAATCGAAATGACCAAATTTAGGAAGCATTTTTTTGAATTGAGATAAAAATTTG
257 AAATAGACCAACAATCAAAACCACAAAATTTAGGAAGCAATTTTTAGAATAAACATAAAAATTTG
** *
13159 CTTTTGAGTCCTTCATGAAAGTTGTAGATCATGAAATTACCTTTTAATAGACACATGAATCAACT
322 CTTTTGAGTCCTAAATGAAAATTGTAGATCATGAAATTACCTTTTAATAGACACATGAATCAACT
* *
13224 TCATTGGACAAATAGAAAAAAGAATA-AAAAATAAAGCTTAAATGTTAGAT
387 TAATAGGACAAATAG-AAAAA-AATACAAAAATAAAGCTTAAATGTTAGAT
* * * * * *
13274 TAAGATAGAATTTGTAAAGAATTAAGGAGTATAAAGTAGAAAAGTATGAGGGCCATTTGATAAAT
1 TAAGATAGAATTTGTAAAGAACTAAGGAGCATAAAATAAAAAAGTATAAGGGCCATGTGATAAAT
* *
13339 AATTCAAAGAAGAAAATGTTTG-TTAATGGAGATCTTGAAACAT-AAAAATT-CATGTT-GAACC
66 AATTCAAAGAAGAAAATATTTGATTAATGAAGATCTTGAAACATAAAAAATTCCAT-TTGGAACC
* * * * *
13400 CTTAACGAAACTCATAGATCAAATTTAGCTTTCGGGTCCTTCATGAAAGTCGTAAATCATGCAAT
130 ATTAACGAAACTCATAGATCAAA-TCAACTTTCGGGTCCTTCATGAAAGTCATAAATCATACAAT
* *
13465 AACCTTTAAACCGACACTTCAATAACTTCAATCGGAGATGTGGA-CAAAAAATTATACGATATTA
194 AACCTTTAAACCGACACATCAATAACTTCAATCGGACATGTGGATC-AAAAATTATACGATATTA
** *
13529 AATTA-ACCGGCAATCAAAACCACAAAATTTCA-GAAGCAATTTTTAGAATCAAAACATTAAAA-
258 AA-TAGACCAACAATCAAAACCACAAAATTT-AGGAAGCAATTTTTAGAAT--AAACATAAAAAT
* *
13591 TTGACTTTTGAGTTCTAAATGAAAATTGTAGATCATGAAATTACCTTTTAATAGACACTTGAATC
319 TTG-CTTTTGAGTCCTAAATGAAAATTGTAGATCATGAAATTACCTTTTAATAGACACATGAATC
*
13656 ACCTTAATAGGACAAATAGAAAAAAATACAAAAATAAA
383 AACTTAATAGGACAAATAGAAAAAAATACAAAAATAAA
13694 AGTGAACGCG
Statistics
Matches: 354, Mismatches: 57, Indels: 23
0.82 0.13 0.05
Matches are distributed among these distances:
433 25 0.07
434 136 0.38
435 20 0.06
436 99 0.28
440 74 0.21
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.30
Consensus pattern (435 bp):
TAAGATAGAATTTGTAAAGAACTAAGGAGCATAAAATAAAAAAGTATAAGGGCCATGTGATAAAT
AATTCAAAGAAGAAAATATTTGATTAATGAAGATCTTGAAACATAAAAAATTCCATTTGGAACCA
TTAACGAAACTCATAGATCAAATCAACTTTCGGGTCCTTCATGAAAGTCATAAATCATACAATAA
CCTTTAAACCGACACATCAATAACTTCAATCGGACATGTGGATCAAAAATTATACGATATTAAAT
AGACCAACAATCAAAACCACAAAATTTAGGAAGCAATTTTTAGAATAAACATAAAAATTTGCTTT
TGAGTCCTAAATGAAAATTGTAGATCATGAAATTACCTTTTAATAGACACATGAATCAACTTAAT
AGGACAAATAGAAAAAAATACAAAAATAAAGCTTAAATGTTAGAT
Found at i:14519 original size:30 final size:30
Alignment explanation
Indices: 14483--14544 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
14473 GTTAATAAGC
14483 CATTAAAATTTGAGGGTATAAGAGAAAAGT
1 CATTAAAATTTGAGGGTATAAGAGAAAAGT
* *
14513 CATTAAATTTTGAGGGTATAAGAGGAAAGT
1 CATTAAAATTTGAGGGTATAAGAGAAAAGT
14543 CA
1 CA
14545 AGATAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.44, C:0.05, G:0.24, T:0.27
Consensus pattern (30 bp):
CATTAAAATTTGAGGGTATAAGAGAAAAGT
Found at i:17161 original size:3 final size:3
Alignment explanation
Indices: 17153--17186 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
17143 GAAATTTTCT
*
17153 TTC TTC TTC TTC TAC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
17187 GTAACCTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:17788 original size:15 final size:15
Alignment explanation
Indices: 17770--17803 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
17760 AAATCATGCC
*
17770 GCAGTAAATATTACT
1 GCAGCAAATATTACT
*
17785 GCAGCAAATATTGCT
1 GCAGCAAATATTACT
17800 GCAG
1 GCAG
17804 ACACTTGGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (15 bp):
GCAGCAAATATTACT
Done.