Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012652.1 Corchorus olitorius cultivar O-4 contig12685, 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: 24194
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:2734 original size:11 final size:11
Alignment explanation
Indices: 2695--2734 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
2685 TTGACAGCGC
2695 AACAAAAACAA
1 AACAAAAACAA
*
2706 AACGAAAACAA
1 AACAAAAACAA
2717 AAC-AAAACAA
1 AACAAAAACAA
2727 AACAAAAA
1 AACAAAAA
2735 ACAGAAAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
10 10 0.37
11 17 0.63
ACGTcount: A:0.80, C:0.17, G:0.03, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:2752 original size:6 final size:5
Alignment explanation
Indices: 2699--2733 Score: 61
Period size: 5 Copynumber: 6.8 Consensus size: 5
2689 CAGCGCAACA
2699 AAAAC AAAAC GAAAAC AAAAC AAAAC AAAAC AAAA
1 AAAAC AAAAC -AAAAC AAAAC AAAAC AAAAC AAAA
2734 AACAGAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.80, C:0.17, G:0.03, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:5090 original size:10 final size:10
Alignment explanation
Indices: 5077--5101 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5067 ACATTAATAC
5077 TAATTGATTT
1 TAATTGATTT
5087 TAATTGATTT
1 TAATTGATTT
5097 TAATT
1 TAATT
5102 TGATCAATAT
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:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (10 bp):
TAATTGATTT
Found at i:5181 original size:60 final size:60
Alignment explanation
Indices: 5087--5314 Score: 334
Period size: 60 Copynumber: 3.8 Consensus size: 60
5077 TAATTGATTT
* *
5087 TAATTGATTTTAATTTGATC-A-ATATTCAAATCAATCAATCAATTTATATCATTAGTAC
1 TAATTGATTCTAATTGGATCAAGATATTCAAATCAATCAATCAATTTATATCATTAGTAC
* * * *
5145 TAATTGATTCTAATTGGGTTAAGATATTCAAATCAATCAATCAATCAATTTAATAGCATTGGTAC
1 TAATTGATTCTAATTGGATCAAGATATTC--A--AATCAATCAATCAATTT-ATATCATTAGTAC
*
5210 TAATTGATTCTAATTTGATCAAGATATTCAAATCAATCAATCAATTTATATCATTAGTAC
1 TAATTGATTCTAATTGGATCAAGATATTCAAATCAATCAATCAATTTATATCATTAGTAC
5270 TAATTGATTCTAATTGGATCAAGATATTCAAATCAATCAATCAAT
1 TAATTGATTCTAATTGGATCAAGATATTCAAATCAATCAATCAAT
5315 CAATCAATCA
Statistics
Matches: 151, Mismatches: 12, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
58 16 0.11
59 1 0.01
60 61 0.40
61 17 0.11
62 1 0.01
63 1 0.01
64 17 0.11
65 37 0.25
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.39
Consensus pattern (60 bp):
TAATTGATTCTAATTGGATCAAGATATTCAAATCAATCAATCAATTTATATCATTAGTAC
Found at i:5234 original size:65 final size:64
Alignment explanation
Indices: 5115--5391 Score: 346
Period size: 65 Copynumber: 4.2 Consensus size: 64
5105 TCAATATTCA
* *
5115 AATCAATCAATCAATTTATATCATTAGTACTAATTGATTCTAATTGGGTTAAGATATTCAAATC
1 AATCAATCAATCAATTTATATCATTAGTACTAATTGATTCTAATTGGATCAAGATATTCAAATC
* * *
5179 AATCAATCAATCAATTTAATAGCATTGGTACTAATTGATTCTAATTTGATCAAGATATTC--A--
1 AATCAATCAATCAATTT-ATATCATTAGTACTAATTGATTCTAATTGGATCAAGATATTCAAATC
5240 AATCAATCAATCAATTTATATCATTAGTACTAATTGATTCTAATTGGATCAAGATATTCAAATCA
1 AATCAATCAATCAATTTATATCATTAGTACTAATTGATTCTAATTGGATCAAGATA-T----TC-
5305 ATCAATC
60 A--AATC
*
5312 AATCAATCAATCAATTTAATATCATTTTAGTACTAATTGATTCTAATTGGATCAAAATATATTCA
1 AATCAATCAATCAATTT-ATATCA--TTAGTACTAATTGATTCTAATTGGATC--AAGATATTCA
5377 AATC
61 AATC
5381 AATCAATCAAT
1 AATCAATCAAT
5392 TTAATATATA
Statistics
Matches: 186, Mismatches: 9, Indels: 31
0.82 0.04 0.14
Matches are distributed among these distances:
60 36 0.19
61 18 0.10
63 1 0.01
64 17 0.09
65 39 0.21
69 15 0.08
70 1 0.01
71 1 0.01
72 19 0.10
73 6 0.03
75 27 0.15
76 1 0.01
77 5 0.03
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.38
Consensus pattern (64 bp):
AATCAATCAATCAATTTATATCATTAGTACTAATTGATTCTAATTGGATCAAGATATTCAAATC
Found at i:5259 original size:125 final size:129
Alignment explanation
Indices: 5087--5394 Score: 439
Period size: 125 Copynumber: 2.4 Consensus size: 129
5077 TAATTGATTT
*
5087 TAATTGATTTTAATTTGATC-AATATTCAAATCAATCAATCAATTTATATCATTAGTACTAATTG
1 TAATTGATTCTAATTTGATCAAATATTCAAATCAATCAATCAATTTATATCATTAGTACTAATTG
* * *
5151 ATTCTAATTGGGTTAAGATA-T-TC-A-AATCAATCAATCAATCAATTTAATAGCA-TTGGTAC
66 ATTCTAATTGGATCAAGATATTATCAACAATCAATCAATCAATCAATTTAATAGCATTTAGTAC
5210 TAATTGATTCTAATTTGATCAAGATATTCAAATCAATCAATCAATTTATATCATTAGTACTAATT
1 TAATTGATTCTAATTTGATCAA-ATATTCAAATCAATCAATCAATTTATATCATTAGTACTAATT
*
5275 GATTCTAATTGGATCAAGATATTCAAATCAATCAATCAATCAATCAATCAATTTAATATCATTTT
65 GATTCTAATTGGATCAAGATATT---ATCAA-CAATCAATCAATCAATCAATTTAATAGCA-TTT
5340 AGTAC
125 AGTAC
*
5345 TAATTGATTCTAATTGGATCAAAATATATTCAAATCAATCAATCAATTTA
1 TAATTGATTCTAATTTGATC--AA-ATATTCAAATCAATCAATCAATTTA
5395 ATATATATAT
Statistics
Matches: 164, Mismatches: 7, Indels: 14
0.89 0.04 0.08
Matches are distributed among these distances:
123 19 0.12
124 1 0.01
125 61 0.37
126 1 0.01
130 2 0.01
131 1 0.01
133 27 0.16
135 25 0.15
137 27 0.16
ACGTcount: A:0.41, C:0.13, G:0.07, T:0.39
Consensus pattern (129 bp):
TAATTGATTCTAATTTGATCAAATATTCAAATCAATCAATCAATTTATATCATTAGTACTAATTG
ATTCTAATTGGATCAAGATATTATCAACAATCAATCAATCAATCAATTTAATAGCATTTAGTAC
Found at i:5309 original size:4 final size:4
Alignment explanation
Indices: 5300--5326 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
5290 AAGATATTCA
5300 AATC AATC AATC AATC AATC AATC AAT
1 AATC AATC AATC AATC AATC AATC AAT
5327 TTAATATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
AATC
Found at i:5355 original size:75 final size:73
Alignment explanation
Indices: 5240--5391 Score: 252
Period size: 75 Copynumber: 2.0 Consensus size: 73
5230 AAGATATTCA
5240 AATCAATCAATCAATTTATATCATTAGTACTAATTGATTCTAATTGGATC-AAGATATTCAAATC
1 AATCAATCAATCAATTTATATCATTAGTACTAATTGATTCTAATTGGATCAAAGATATTCAAATC
5304 AATCAATC
66 AATCAATC
*
5312 AATCAATCAATCAATTTAATATCATTTTAGTACTAATTGATTCTAATTGGATCAAAATATATTCA
1 AATCAATCAATCAATTT-ATATCA--TTAGTACTAATTGATTCTAATTGGATC-AAAGATATTCA
5377 AATCAATCAATC
62 AATCAATCAATC
5389 AAT
1 AAT
5392 TTAATATATA
Statistics
Matches: 74, Mismatches: 1, Indels: 5
0.93 0.01 0.06
Matches are distributed among these distances:
72 17 0.23
73 6 0.08
75 27 0.36
77 24 0.32
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.37
Consensus pattern (73 bp):
AATCAATCAATCAATTTATATCATTAGTACTAATTGATTCTAATTGGATCAAAGATATTCAAATC
AATCAATC
Found at i:8104 original size:19 final size:19
Alignment explanation
Indices: 8080--8116 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
8070 CTTATCTGTA
*
8080 ATCGTTTCATCACCGTTTG
1 ATCGTTTCACCACCGTTTG
8099 ATCGTTTCACCACCGTTT
1 ATCGTTTCACCACCGTTT
8117 TGACACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.30, G:0.14, T:0.41
Consensus pattern (19 bp):
ATCGTTTCACCACCGTTTG
Done.