Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016109.1 Corchorus olitorius cultivar O-4 contig16142, 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: 39618
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:6325 original size:41 final size:41
Alignment explanation
Indices: 6268--6508 Score: 290
Period size: 41 Copynumber: 5.9 Consensus size: 41
6258 TTTTCATTTG
6268 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
**
6309 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
*
6350 TTCAAGATTAAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
* * *
6391 TTCAAGAACAAGTCATCGAGACCCTTGGATCGAATTATTATCAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAAT-TAA--ATTATCAA
* * * * * * *
6435 TTCAAGACCAAGT-GTCAAGAACCTTGAATTAGATTGTTAA
1 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
* *
6475 TTCAAGACCAAGTCATTC--GACCCTTGAATCAAAT
1 TTCAAGATCAAGTCA-TCGAGACCCTTGAATTAAAT
6509 CAAATCAAAC
Statistics
Matches: 175, Mismatches: 20, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
40 32 0.18
41 106 0.61
42 5 0.03
43 12 0.07
44 20 0.11
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.29
Consensus pattern (41 bp):
TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
Found at i:7568 original size:21 final size:21
Alignment explanation
Indices: 7544--7586 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
7534 CATTGGATAT
7544 GTGCATCCAAGGCATGAACTG
1 GTGCATCCAAGGCATGAACTG
7565 GTGCATCCAAGGCATGAACTG
1 GTGCATCCAAGGCATGAACTG
7586 G
1 G
7587 ACCCTGCGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.23, G:0.30, T:0.19
Consensus pattern (21 bp):
GTGCATCCAAGGCATGAACTG
Found at i:8355 original size:62 final size:63
Alignment explanation
Indices: 8270--8398 Score: 161
Period size: 62 Copynumber: 2.1 Consensus size: 63
8260 AAAAAAAAGG
* * * *
8270 AAAAAAAAGGCTCGGTAACTTGAAAATCCTGTAAAGGATGGCTTAGGCAAAAGTTAGAGC-CA
1 AAAAAAAAGGCTCGCTAACTTGAAAATCCTGCAAAGGACGGCTTAGACAAAAGTTAGAGCACA
* * * * * *
8332 AAAAAAAAGTCTTGCTAAGTTGAAAATCCTGCAAAGGACGTCTTAGACAAAATTTTGAGCACA
1 AAAAAAAAGGCTCGCTAACTTGAAAATCCTGCAAAGGACGGCTTAGACAAAAGTTAGAGCACA
8395 AAAA
1 AAAA
8399 TAATGAACTA
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
62 50 0.89
63 6 0.11
ACGTcount: A:0.44, C:0.15, G:0.20, T:0.21
Consensus pattern (63 bp):
AAAAAAAAGGCTCGCTAACTTGAAAATCCTGCAAAGGACGGCTTAGACAAAAGTTAGAGCACA
Found at i:9240 original size:41 final size:41
Alignment explanation
Indices: 9183--9383 Score: 226
Period size: 41 Copynumber: 4.9 Consensus size: 41
9173 TTTTCGTTTG
*
9183 TTCAAGATCAAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCAAGACCCTTGAATTAAATTATCAA
** *
9224 TTCAAGATTGAGTCATCGAGACCCTTGAATTAAATTATCAA
1 TTCAAGATCAAGTCATCAAGACCCTTGAATTAAATTATCAA
* *
9265 TTCAAGAACAAGTCATCAAGACCCTTGAATCGAATTATTATCAA
1 TTCAAGATCAAGTCATCAAGACCCTTGAAT-TAA--ATTATCAA
* * * * * *
9309 ATCAAGACCAAGTCGTCAAGAACCTTGAATTAGATTGTCAA
1 TTCAAGATCAAGTCATCAAGACCCTTGAATTAAATTATCAA
* *
9350 TTCAAGACCAAGTCATTC--GACCCTTGAATCAAAT
1 TTCAAGATCAAGTCA-TCAAGACCCTTGAATTAAAT
9384 CAAATCAAAC
Statistics
Matches: 137, Mismatches: 19, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
40 13 0.09
41 85 0.62
42 4 0.03
43 1 0.01
44 34 0.25
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.28
Consensus pattern (41 bp):
TTCAAGATCAAGTCATCAAGACCCTTGAATTAAATTATCAA
Found at i:9353 original size:85 final size:82
Alignment explanation
Indices: 9183--9383 Score: 228
Period size: 85 Copynumber: 2.4 Consensus size: 82
9173 TTTTCGTTTG
* * * *** * *
9183 TTCAAGATCAAGTCATCGAGACCCTTGAAT-TAAATTATCAATTCAAGATTGAGTCATCGAGACC
1 TTCAAGAACAAGTCATC-AGACCCTTGAATCGAAATTATCAAATCAAGACCAAGTCATCAAGAAC
9247 CTTGAATTAAATTATCAA
65 CTTGAATTAAATTATCAA
*
9265 TTCAAGAACAAGTCATCAAGACCCTTGAATCGAATTATTATCAAATCAAGACCAAGTCGTCAAGA
1 TTCAAGAACAAGTCATC-AGACCCTTGAATCGAA--ATTATCAAATCAAGACCAAGTCATCAAGA
* *
9330 ACCTTGAATTAGATTGTCAA
63 ACCTTGAATTAAATTATCAA
*
9350 TTCAAGACCAAGTCATTC-GACCCTTGAATC-AAAT
1 TTCAAGAACAAGTCA-TCAGACCCTTGAATCGAAAT
9384 CAAATCAAAC
Statistics
Matches: 102, Mismatches: 13, Indels: 9
0.82 0.10 0.07
Matches are distributed among these distances:
81 2 0.02
82 28 0.27
83 4 0.04
84 12 0.12
85 54 0.53
86 2 0.02
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.28
Consensus pattern (82 bp):
TTCAAGAACAAGTCATCAGACCCTTGAATCGAAATTATCAAATCAAGACCAAGTCATCAAGAACC
TTGAATTAAATTATCAA
Found at i:9950 original size:27 final size:27
Alignment explanation
Indices: 9906--9958 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
9896 GAAGACAAGA
* *
9906 AAAAGAAATAAAGCAAAAATAAAAAGG
1 AAAAGAAATAAAACAAAAACAAAAAGG
9933 AAAAGAAA-AAAACAAAAAACAAAAAG
1 AAAAGAAATAAAAC-AAAAACAAAAAG
9959 AAATATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.79, C:0.06, G:0.11, T:0.04
Consensus pattern (27 bp):
AAAAGAAATAAAACAAAAACAAAAAGG
Found at i:15750 original size:28 final size:29
Alignment explanation
Indices: 15689--15793 Score: 122
Period size: 29 Copynumber: 3.6 Consensus size: 29
15679 GATCACCTAG
*** * * *
15689 GGGCATTTTGGTCATTTTCAAAAATCCAG
1 GGGCATTTTGGTCATTTTTGCACATTCAA
*
15718 GGGCATTTTGGTC-TTTTTTCACATTCAA
1 GGGCATTTTGGTCATTTTTGCACATTCAA
*
15746 GGGCATTATGGTCATTTTTGCACATTCAA
1 GGGCATTTTGGTCATTTTTGCACATTCAA
15775 GGGCATTTTGGGTCATTTT
1 GGGCATTTT-GGTCATTTT
15794 AAGTTCGCTT
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
28 21 0.32
29 35 0.54
30 9 0.14
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.41
Consensus pattern (29 bp):
GGGCATTTTGGTCATTTTTGCACATTCAA
Found at i:24051 original size:2 final size:2
Alignment explanation
Indices: 24044--24104 Score: 80
Period size: 2 Copynumber: 33.5 Consensus size: 2
24034 CTACTCGTTA
24044 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT -T AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24083 AT AT -T AT AT AT -T AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
24105 CTAAATAGTA
Statistics
Matches: 53, Mismatches: 0, Indels: 12
0.82 0.00 0.18
Matches are distributed among these distances:
1 6 0.11
2 47 0.89
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:24066 original size:19 final size:19
Alignment explanation
Indices: 24042--24104 Score: 87
Period size: 17 Copynumber: 3.5 Consensus size: 19
24032 CACTACTCGT
24042 TAATATATATATATATATA
1 TAATATATATATATATATA
24061 TAATATATATATAT-TATA
1 TAATATATATATATATATA
*
24079 TTATATAT-TATATAT-TA
1 TAATATATATATATATATA
*
24096 TTATATATA
1 TAATATATA
24105 CTAAATAGTA
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
17 15 0.37
18 12 0.29
19 14 0.34
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TAATATATATATATATATA
Found at i:24429 original size:10 final size:10
Alignment explanation
Indices: 24416--24440 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
24406 TTTAATTTAA
24416 TTTAATCGGT
1 TTTAATCGGT
24426 TTTAATCGGT
1 TTTAATCGGT
24436 TTTAA
1 TTTAA
24441 AATAGGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.52
Consensus pattern (10 bp):
TTTAATCGGT
Found at i:25350 original size:55 final size:55
Alignment explanation
Indices: 25278--25388 Score: 206
Period size: 54 Copynumber: 2.0 Consensus size: 55
25268 TGTGTTTCCT
25278 TTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATTC
1 TTTCACACAATAAATGTTATAATAAATCCTAT-CCCCTATCTCTACTTAATTATTC
25334 TTTCACAC-ATAAATGTTATAATAAATCCTATCCCCTATCTCTACTTAATTATTC
1 TTTCACACAATAAATGTTATAATAAATCCTATCCCCTATCTCTACTTAATTATTC
25388 T
1 T
25389 ACAAAATAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
54 24 0.44
55 23 0.42
56 8 0.15
ACGTcount: A:0.33, C:0.24, G:0.02, T:0.41
Consensus pattern (55 bp):
TTTCACACAATAAATGTTATAATAAATCCTATCCCCTATCTCTACTTAATTATTC
Found at i:25511 original size:42 final size:42
Alignment explanation
Indices: 25452--25534 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
25442 ACTAAGGATC
25452 ATGATTTGAGTTGAGTATTTCTTAATTAACAAAGAATTTTCT
1 ATGATTTGAGTTGAGTATTTCTTAATTAACAAAGAATTTTCT
* * *
25494 ATGATTTGAGTTGAGTATTTTTTAATTTACAGAGAATTTTC
1 ATGATTTGAGTTGAGTATTTCTTAATTAACAAAGAATTTTC
25535 AAGACTTAGG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.31, C:0.06, G:0.16, T:0.47
Consensus pattern (42 bp):
ATGATTTGAGTTGAGTATTTCTTAATTAACAAAGAATTTTCT
Found at i:30451 original size:2 final size:2
Alignment explanation
Indices: 30444--30475 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
30434 AATCACATGG
30444 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
30476 TGTAGTGGCC
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:31460 original size:13 final size:13
Alignment explanation
Indices: 31436--31460 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31426 ATTGTTTTTA
31436 TAAATGATTTTGT
1 TAAATGATTTTGT
31449 TAAATGATTTTG
1 TAAATGATTTTG
31461 GGTGCATGAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (13 bp):
TAAATGATTTTGT
Done.