Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020445.1 Corchorus olitorius cultivar O-4 contig20478, 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: 60717
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:301 original size:17 final size:16
Alignment explanation
Indices: 261--310 Score: 64
Period size: 17 Copynumber: 3.0 Consensus size: 16
251 CATGTAATCT
*
261 TTGATCACCGGTGATC
1 TTGATCACTGGTGATC
277 TTGCATCACTGGTGATC
1 TTG-ATCACTGGTGATC
*
294 TTAGATCACTAGTGATC
1 TT-GATCACTGGTGATC
311 CGGGGGGTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
16 3 0.10
17 26 0.87
18 1 0.03
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:4251 original size:451 final size:435
Alignment explanation
Indices: 3229--4268 Score: 1241
Period size: 438 Copynumber: 2.3 Consensus size: 435
3219 TTTATCCTAT
* * *
3229 TAAGGTGATTCAAGTGTCTATTAAAAGGTAATTTCATGATGTACAATTTTCATG-AAGAACTCAA
1 TAAGGTGATTCATGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATGAAAG-ACTCAA
* * * *
3293 GAGCCAATTTTGATGTTTTAATTCAAAAAAATGCTTCCGAAATTTTGTGGTTTTGATTGTCGGTC
65 AAGCAAATTTTGATGTTTTAATTCAAAAAAATGCTTCTGAAATTTTGT-GTTTCGATTGT-GGTC
* * * * * * * *
3358 AATTTACTATCGTATAATTTTTTGTCCACATGTCCGATTGAAGTTATTGAAGTGTCGAACAAAAG
128 TATTTAATACCATATAATTTTTCGTCAACATGTCCGATTAAAGTTATTCAAGTGTCGAACAAAAG
* * *
3423 GTTATTGCATGATTTACGACTTTCATGAAGGACCCAAAAGCTAAATTTGATCTACGAGTTTCATG
193 GTTACTGCATGATGTACGACTTTCATGAAGAACCCAAAAGCTAAATTTGATCTACGAGTTTCATG
* * *
3488 AAGGGTTCAAAAGGGAGTTTTTATGCTTCAAGATCTCCATTAACAAACATTTTCTTATTTGGATT
258 AAGGGTTCAAAAGGGAATTTTTATGCTTCAAGATATCCATTAACAAACATTTTCTTATTTGAATT
* *
3553 ATTTATCAAATGACCCTCATATTTTTCTATTTTATACTACTTAGTCCTTTACAAATTCTATCTTA
323 AATTATCAAATGACCCTCATATTTTTATATTTTATACTACTTAGTCCTTTACAAATTCTATCTTA
*
3618 ATCTAACGTTTAAGATTCATTTTTTAATTCTTTGTTCTATTTGTCCAAT
388 ATCT-ACGTTTAAGATTCATTTTTTAATTCTTTGTTCTATTTGTCCAAC
* *
3667 TAAGTTGATTCATGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATGAAGGACTCAAA
1 TAAGGTGATTCATGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATGAAAGACTCAAA
*
3732 AGCAAATTTTGATGTTTTAATTCAAAAAAATGCTTCCT-AAATTTGGTCGTTTCGATTGTTGGTC
66 AGCAAATTTTGATGTTTTAATTCAAAAAAATGCTT-CTGAAATTTTGT-GTTTCGATTG-TGGTC
* ***
3796 TATTTAATACCATATAA-TTTTCGATTAACATGTCCGATTAAAGTTATTCAAGTG-CTGGTTAAA
128 TATTTAATACCATATAATTTTTCG-TCAACATGTCCGATTAAAGTTATTCAAGTGTC-GAACAAA
* * * * *
3859 AGGTTACTGTATGATGTACGACTTTCATGAATAACCCGAAAG-TTAATTTGATCTACGAGTTTTA
191 AGGTTACTGCATGATGTACGACTTTCATGAAGAACCCAAAAGCTAAATTTGATCTACGAGTTTCA
* * *
3923 TGAAGGGTTCAAAAGGGAATTTTTATGTTTCAAGATATCCATTAAGAAATATTTTCTTATTTGAA
256 TGAAGGGTTCAAAAGGGAATTTTTATGCTTCAAGATATCCATTAACAAACATTTTCTTATTTGAA
3988 TTAATTATCAAATGACCCTCATACTTTTCTATTTATATTTTATATTTTATGCTACTTAGTCCTTT
321 TTAATTATCAAATGACCCTCATA----T-T-TTTATA-TTT-TA---TA--CTACTTAGTCCTTT
* * *
4053 ACAAATTTTATCTT-A-CT-CGATTTAACGCTTCATTTTTTCTATTTTCTTTGTTCTATTTGTCC
373 ACAAATTCTATCTTAATCTACG-TTTAA-GATTCA-TTTTT-TA-ATTCTTTGTTCTATTTGTCC
4115 AAC
433 AAC
* * * *
4118 TAAGGTAATTCATGTGTCTATTAAAAAGTAATTTTATGATCTACAACTTTCATGAAAGAGTCAAA
1 TAAGGTGATTCATGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATGAAAGACTCAAA
* * * * * * * **
4183 AGCTAATTTTCATGTTTTAATTCTAAAGAATACTTTTGAAATTTTATGATTTCGATTGATAATCT
66 AGCAAATTTTGATGTTTTAATTCAAAAAAATGCTTCTGAAATTTTGTG-TTTCGATTG-TGGTCT
** *
4248 ATTTAATTTCATATTATTTTT
129 ATTTAATACCATATAATTTTT
4269 TATCCATATA
Statistics
Matches: 513, Mismatches: 63, Indels: 38
0.84 0.10 0.06
Matches are distributed among these distances:
437 107 0.21
438 190 0.37
439 4 0.01
441 1 0.00
442 1 0.00
443 5 0.01
444 3 0.01
445 2 0.00
446 2 0.00
447 5 0.01
448 9 0.02
449 6 0.01
450 31 0.06
451 143 0.28
452 4 0.01
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (435 bp):
TAAGGTGATTCATGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATGAAAGACTCAAA
AGCAAATTTTGATGTTTTAATTCAAAAAAATGCTTCTGAAATTTTGTGTTTCGATTGTGGTCTAT
TTAATACCATATAATTTTTCGTCAACATGTCCGATTAAAGTTATTCAAGTGTCGAACAAAAGGTT
ACTGCATGATGTACGACTTTCATGAAGAACCCAAAAGCTAAATTTGATCTACGAGTTTCATGAAG
GGTTCAAAAGGGAATTTTTATGCTTCAAGATATCCATTAACAAACATTTTCTTATTTGAATTAAT
TATCAAATGACCCTCATATTTTTATATTTTATACTACTTAGTCCTTTACAAATTCTATCTTAATC
TACGTTTAAGATTCATTTTTTAATTCTTTGTTCTATTTGTCCAAC
Found at i:4603 original size:3 final size:3
Alignment explanation
Indices: 4595--4621 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
4585 TATAACGAGA
4595 AGC AGC AGC AGC AGC AGC AGC AGC AGC
1 AGC AGC AGC AGC AGC AGC AGC AGC AGC
4622 TTTTGGAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.33, T:0.00
Consensus pattern (3 bp):
AGC
Found at i:4677 original size:3 final size:3
Alignment explanation
Indices: 4669--4702 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
4659 AAAGTAGACC
*
4669 TAT TAT TAT TAT TAT TAT TAG TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
4703 GTGAGCCATG
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:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:9963 original size:3 final size:3
Alignment explanation
Indices: 9957--9983 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
9947 CCTTCTTCCA
9957 TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT
9984 ACTTGCTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:29653 original size:17 final size:16
Alignment explanation
Indices: 29626--29667 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
29616 GTCTTATATT
29626 AATTA-ATTAATAATG
1 AATTATATTAATAATG
*
29641 AATTATTATTAATAATT
1 AATTA-TATTAATAATG
29658 AATTATATTA
1 AATTATATTA
29668 TTTTCACGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 5 0.21
16 5 0.21
17 14 0.58
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
AATTATATTAATAATG
Found at i:35318 original size:18 final size:18
Alignment explanation
Indices: 35295--35401 Score: 65
Period size: 18 Copynumber: 5.6 Consensus size: 18
35285 TTGCACTTTG
35295 GAAACCTTATTATTTGGA
1 GAAACCTTATTATTTGGA
*
35313 GAAACCCTA--ATCTTGAGA
1 GAAACCTTATTAT-TTG-GA
35331 GTGGAAACCTTATTATTTGGA
1 ---GAAACCTTATTATTTGGA
* * * *
35352 GAAACCCTAATCTTGGGA
1 GAAACCTTATTATTTGGA
*
35370 GTGGAAACCTTATTGTTTGGA
1 ---GAAACCTTATTATTTGGA
*
35391 GAAACCATATT
1 GAAACCTTATT
35402 CTTGGCAGTA
Statistics
Matches: 68, Mismatches: 11, Indels: 20
0.69 0.11 0.20
Matches are distributed among these distances:
16 2 0.03
17 3 0.04
18 34 0.50
21 24 0.35
22 3 0.04
23 2 0.03
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.32
Consensus pattern (18 bp):
GAAACCTTATTATTTGGA
Found at i:35391 original size:21 final size:21
Alignment explanation
Indices: 35293--35391 Score: 70
Period size: 21 Copynumber: 5.0 Consensus size: 21
35283 ATTTGCACTT
35293 TGGAAACCTTATTATTTGGA-
1 TGGAAACCTTATTATTTGGAG
*
35313 --GAAACCCTA--ATCTTGAGAG
1 TGGAAACCTTATTAT-TTG-GAG
35332 TGGAAACCTTATTATTTGGA-
1 TGGAAACCTTATTATTTGGAG
* * * *
35352 --GAAACCCTAATCTTGGGAG
1 TGGAAACCTTATTATTTGGAG
*
35371 TGGAAACCTTATTGTTTGGAG
1 TGGAAACCTTATTATTTGGAG
35392 AAACCATATT
Statistics
Matches: 59, Mismatches: 10, Indels: 19
0.67 0.11 0.22
Matches are distributed among these distances:
16 2 0.03
17 3 0.05
18 24 0.41
21 25 0.42
22 3 0.05
23 2 0.03
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.32
Consensus pattern (21 bp):
TGGAAACCTTATTATTTGGAG
Found at i:35406 original size:39 final size:39
Alignment explanation
Indices: 35293--35406 Score: 192
Period size: 39 Copynumber: 2.9 Consensus size: 39
35283 ATTTGCACTT
*
35293 TGGAAACCTTATTATTTGGAGAAACCCTAATCTTGAGAG
1 TGGAAACCTTATTATTTGGAGAAACCCTAATCTTGGGAG
35332 TGGAAACCTTATTATTTGGAGAAACCCTAATCTTGGGAG
1 TGGAAACCTTATTATTTGGAGAAACCCTAATCTTGGGAG
* * *
35371 TGGAAACCTTATTGTTTGGAGAAACCATATTCTTGG
1 TGGAAACCTTATTATTTGGAGAAACCCTAATCTTGG
35407 CAGTAGAATC
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 71 1.00
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (39 bp):
TGGAAACCTTATTATTTGGAGAAACCCTAATCTTGGGAG
Found at i:45197 original size:11 final size:11
Alignment explanation
Indices: 45154--45191 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
45144 TTCCTATATA
*
45154 AAATAAATTAT
1 AAATTAATTAT
45165 CAAA-TAATTAT
1 -AAATTAATTAT
45176 AAATTAATTAT
1 AAATTAATTAT
45187 AAATT
1 AAATT
45192 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:45829 original size:15 final size:15
Alignment explanation
Indices: 45809--45838 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
45799 GGCTAAATGT
45809 GTTTCGTGTCGTGTC
1 GTTTCGTGTCGTGTC
45824 GTTTCGTGTCGTGTC
1 GTTTCGTGTCGTGTC
45839 ATGACCTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.20, G:0.33, T:0.47
Consensus pattern (15 bp):
GTTTCGTGTCGTGTC
Done.