Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012616.1 Corchorus olitorius cultivar O-4 contig12649, 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: 37777
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Found at i:2136 original size:24 final size:24
Alignment explanation
Indices: 2086--2136 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
2076 AACAATGTAT
**
2086 GTTATGGGTCTCCATTAATTCGGA
1 GTTATGGGTCTCCATTAATTCAAA
* * *
2110 GTTATTGGTCTCGATTAATTTAAA
1 GTTATGGGTCTCCATTAATTCAAA
2134 GTT
1 GTT
2137 GAGTTATCTC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.24, C:0.12, G:0.22, T:0.43
Consensus pattern (24 bp):
GTTATGGGTCTCCATTAATTCAAA
Found at i:14888 original size:15 final size:15
Alignment explanation
Indices: 14868--14937 Score: 122
Period size: 15 Copynumber: 4.6 Consensus size: 15
14858 AGAGGTTGAT
14868 AGAAAACAATTAAAC
1 AGAAAACAATTAAAC
*
14883 AGAAAATAATTAAAC
1 AGAAAACAATTAAAC
14898 AGAAAACAATTAAAC
1 AGAAAACAATTAAAC
14913 AGAAAACAATTAAAC
1 AGAAAACAATTAAAC
14928 TAGAAAACAA
1 -AGAAAACAA
14938 AGCAAAGTAA
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
15 43 0.83
16 9 0.17
ACGTcount: A:0.67, C:0.11, G:0.07, T:0.14
Consensus pattern (15 bp):
AGAAAACAATTAAAC
Found at i:15204 original size:10 final size:10
Alignment explanation
Indices: 15189--15214 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
15179 TTAAGCCTTA
15189 AAGATTTGCT
1 AAGATTTGCT
15199 AAGATTTGCT
1 AAGATTTGCT
15209 AAGATT
1 AAGATT
15215 CAAAGCATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (10 bp):
AAGATTTGCT
Found at i:23805 original size:21 final size:22
Alignment explanation
Indices: 23755--23805 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 22
23745 GTAAAAAACA
23755 AAAGAAAAAATTAGAAATTTTC
1 AAAGAAAAAATTAGAAATTTTC
23777 AATA-AAAAAA-TA-AAATTTTC
1 AA-AGAAAAAATTAGAAATTTTC
23797 ACAAGAAAA
1 A-AAGAAAA
23806 GAGATGAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
20 10 0.38
21 7 0.27
22 8 0.31
23 1 0.04
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (22 bp):
AAAGAAAAAATTAGAAATTTTC
Found at i:26457 original size:30 final size:30
Alignment explanation
Indices: 26423--26480 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
26413 AATTCTTGCT
* *
26423 TCTTGGAATAATTCTTCAAT-GATCTTCATA
1 TCTTGAAATAA-TCTTCAATAAATCTTCATA
*
26453 TCTTGAAATTATCTTCAATAAATCTTCA
1 TCTTGAAATAATCTTCAATAAATCTTCA
26481 ATCACGAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (30 bp):
TCTTGAAATAATCTTCAATAAATCTTCATA
Found at i:27305 original size:105 final size:108
Alignment explanation
Indices: 27124--27415 Score: 384
Period size: 107 Copynumber: 2.8 Consensus size: 108
27114 AATTTTTCTA
* ** *
27124 ACCCTTAAAATAAAATTTTAATTTTAATTT-GGGCTAAACTTAGTG-AATTAGTTATATATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTA
*
27187 TTTCTAAAACCCTATAACAAT-A-T-TATTAATTATGGAATTT
66 TTTCTAAAACCCTATAACAATAATTATATTAATTATGAAATTT
* *
27227 ACCCTTATAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTA
* * * *
27292 ATTCTAAAACCCTATAATAATAAATTACTATTAGTTTTGAAATTT
66 TTTCTAAAACCCTATAACAAT-AATTA-TATTAATTATGAAATTT
*
27337 ACCCTTAAAATAAAAATAAAA-TTTAA-TTGGGGCT-AACTTAGTGAAATTAGTTTTATATATTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTA
* *
27399 TTTCTAGAACTCTATAA
66 TTTCTAAAACCCTATAA
27416 TAAAAAACCT
Statistics
Matches: 165, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
103 26 0.16
104 15 0.09
105 35 0.21
107 41 0.25
108 9 0.05
109 5 0.03
110 34 0.21
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.41
Consensus pattern (108 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTA
TTTCTAAAACCCTATAACAATAATTATATTAATTATGAAATTT
Found at i:27448 original size:104 final size:104
Alignment explanation
Indices: 27124--27450 Score: 353
Period size: 107 Copynumber: 3.1 Consensus size: 104
27114 AATTTTTCTA
* * * * *
27124 ACCCTTAAAATAAAATTTTAATTTTAATTTGGGCTAAACTTAGTG-AATTAGTTATATATTTTAT
1 ACCCTTAAAATAAAA-ATAAAATTTAATTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTAT
* * *
27188 TTCTAAAACCCTAT-A-ACAATATTATTAA-TTATGGAATTT
65 TTCTAAAACCCTATAATAAAAAACTATTAATTTAT--AATTT
* *
27227 ACCCTTATAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAA-TTTAA-TTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTA
* *
27292 ATTCTAAAACCCTATAATAATAAATTACTATTAGTTT-TGAAATTT
64 TTTCTAAAACCCTATAATAA-AAA--ACTATTAATTTAT--AATTT
*
27337 ACCCTTAAAATAAAAATAAAATTTAATTGGGGCT-AACTTAGTGAAATTAGTTTTATATATTATT
1 ACCCTTAAAATAAAAATAAAATTTAATTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATT
* *
27401 TCTAGAACTCTATAATAAAAAACCT-TTAATTTCATAATTT
66 TCTAAAACCCTATAATAAAAAA-CTATTAATTT-ATAATTT
*
27441 ACTCTTAAAA
1 ACCCTTAAAA
27451 ATTAAATTTC
Statistics
Matches: 191, Mismatches: 21, Indels: 23
0.81 0.09 0.10
Matches are distributed among these distances:
102 3 0.02
103 19 0.10
104 38 0.20
105 32 0.17
106 5 0.03
107 44 0.23
108 10 0.05
109 5 0.03
110 33 0.17
111 2 0.01
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (104 bp):
ACCCTTAAAATAAAAATAAAATTTAATTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATT
TCTAAAACCCTATAATAAAAAACTATTAATTTATAATTT
Found at i:29486 original size:62 final size:63
Alignment explanation
Indices: 29389--29547 Score: 293
Period size: 63 Copynumber: 2.5 Consensus size: 63
29379 TATCAATTGT
*
29389 TTTTTAGAAGAAAAATAGATAGCAAGAAACAATCAAACAAATA-AAGGGTGAAATCAAATTAA
1 TTTTTAGAAGAAAAATGGATAGCAAGAAACAATCAAACAAATACAAGGGTGAAATCAAATTAA
29451 TTTTTAGAAGAAAAATGGATAGCAAGAAACAATCAAACAAATACAAGGGTGAAATCAAATTAA
1 TTTTTAGAAGAAAAATGGATAGCAAGAAACAATCAAACAAATACAAGGGTGAAATCAAATTAA
*
29514 TTTTTAGAAGAAAAATGGATAGCAAAAAACAATC
1 TTTTTAGAAGAAAAATGGATAGCAAGAAACAATC
29548 GTTAAATCAA
Statistics
Matches: 94, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
62 42 0.45
63 52 0.55
ACGTcount: A:0.55, C:0.09, G:0.15, T:0.21
Consensus pattern (63 bp):
TTTTTAGAAGAAAAATGGATAGCAAGAAACAATCAAACAAATACAAGGGTGAAATCAAATTAA
Found at i:30656 original size:21 final size:21
Alignment explanation
Indices: 30629--30677 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
30619 GCACGGTGGC
30629 AATGAGATTA-ATTACTGTACA
1 AATGAGATTAGA-TACTGTACA
*
30650 TATGAGATTAGATACTGTACA
1 AATGAGATTAGATACTGTACA
30671 AATGAGA
1 AATGAGA
30678 ATGTAATCAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.43, C:0.08, G:0.18, T:0.31
Consensus pattern (21 bp):
AATGAGATTAGATACTGTACA
Found at i:30893 original size:2 final size:2
Alignment explanation
Indices: 30886--30915 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
30876 TTTTGCACAA
30886 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
30916 TCTAACCTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31267 original size:2 final size:2
Alignment explanation
Indices: 31262--31302 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
31252 ACTTATTATC
31262 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31303 AATCATCAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:34386 original size:27 final size:27
Alignment explanation
Indices: 34338--34398 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
34328 ATTACCAAAA
* * *
34338 TACCCGTGATGGACAAATTTACTATAT
1 TACCCCTGATGGACAAAATTACGATAT
* * *
34365 TACCCCTGATTGATAAAATTACGATTT
1 TACCCCTGATGGACAAAATTACGATAT
34392 TACCCCT
1 TACCCCT
34399 ATAATGAGGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.34
Consensus pattern (27 bp):
TACCCCTGATGGACAAAATTACGATAT
Found at i:36304 original size:32 final size:32
Alignment explanation
Indices: 36257--36402 Score: 215
Period size: 32 Copynumber: 4.5 Consensus size: 32
36247 TAAAAGCAGT
*
36257 TAAATATAGCGGCGTTTTGTTCTAAAGACGCCGC
1 TAAATA-AG-GGCGTTTTGTTCTTAAGACGCCGC
*
36291 TAAATAAGGGCGTTTTGTTCTCT-AGACGCCGT
1 TAAATAAGGGCGTTTTGTTCT-TAAGACGCCGC
*
36323 TAAATAAGGGCGTTTTGTTCTTTAGACGCCGC
1 TAAATAAGGGCGTTTTGTTCTTAAGACGCCGC
36355 TAAATAAGGGCGTTTTGTTCTTTAA-ACGCCGC
1 TAAATAAGGGCGTTTTGTTC-TTAAGACGCCGC
36387 TAAATAAGGGCGTTTT
1 TAAATAAGGGCGTTTT
36403 CTTTCCACAC
Statistics
Matches: 105, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
31 1 0.01
32 93 0.89
33 5 0.05
34 6 0.06
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.34
Consensus pattern (32 bp):
TAAATAAGGGCGTTTTGTTCTTAAGACGCCGC
Done.