Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022333.1 Corchorus olitorius cultivar O-4 contig22366, 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: 28633
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:492 original size:33 final size:32
Alignment explanation
Indices: 422--564 Score: 117
Period size: 33 Copynumber: 4.3 Consensus size: 32
412 ATGATCAACC
** *
422 AAAACAGATTTGTTTTCATCACAATTAGCATCC-
1 AAAACAGATTTG-TTTCATCACAAACAACA-CCT
455 AAAACAGAATTTGTTTCATCACAAACAACACCT
1 AAAACAG-ATTTGTTTCATCACAAACAACACCT
* *
488 AAAACAGATTTAGTGTCATCACAAACAACACTT
1 AAAACAGATTT-GTTTCATCACAAACAACACCT
** * ** * *
521 AAATTAGGTTTAGCATCATCACTAACAACATCT
1 AAAACAGATTT-GTTTCATCACAAACAACACCT
*
554 AAAACGGATTT
1 AAAACAGATTT
565 CATGTCATTG
Statistics
Matches: 90, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
32 6 0.07
33 79 0.88
34 5 0.06
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (32 bp):
AAAACAGATTTGTTTCATCACAAACAACACCT
Found at i:540 original size:66 final size:66
Alignment explanation
Indices: 470--596 Score: 175
Period size: 66 Copynumber: 1.9 Consensus size: 66
460 AGAATTTGTT
* *
470 TCATCACAAACAACACCTAAAACAGATTT-AGTGTCATCACAAACAACACTTAAATTAGGTTTAG
1 TCATCACAAACAACACCTAAAACAGATTTCA-TGTCATCACAAACAACACTCAAATCAGGTTTAG
534 CA
65 CA
* * * **
536 TCATCACTAACAACATCTAAAACGGATTTCATGTCATTGCAAACAACACTCAAATCAGGTT
1 TCATCACAAACAACACCTAAAACAGATTTCATGTCATCACAAACAACACTCAAATCAGGTT
597 CAGAATTACT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
66 52 0.98
67 1 0.02
ACGTcount: A:0.42, C:0.24, G:0.09, T:0.25
Consensus pattern (66 bp):
TCATCACAAACAACACCTAAAACAGATTTCATGTCATCACAAACAACACTCAAATCAGGTTTAGC
A
Found at i:5499 original size:55 final size:55
Alignment explanation
Indices: 5418--5540 Score: 246
Period size: 55 Copynumber: 2.2 Consensus size: 55
5408 AAATACTTAT
5418 AAAATAGGGTTAAATTCCACATAAAAATAGTAAAAAGCATTGGAAAATGATCATA
1 AAAATAGGGTTAAATTCCACATAAAAATAGTAAAAAGCATTGGAAAATGATCATA
5473 AAAATAGGGTTAAATTCCACATAAAAATAGTAAAAAGCATTGGAAAATGATCATA
1 AAAATAGGGTTAAATTCCACATAAAAATAGTAAAAAGCATTGGAAAATGATCATA
5528 AAAATAGGGTTAA
1 AAAATAGGGTTAA
5541 TTTTGGCTCG
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 68 1.00
ACGTcount: A:0.53, C:0.08, G:0.15, T:0.24
Consensus pattern (55 bp):
AAAATAGGGTTAAATTCCACATAAAAATAGTAAAAAGCATTGGAAAATGATCATA
Found at i:13345 original size:63 final size:65
Alignment explanation
Indices: 13244--13371 Score: 233
Period size: 63 Copynumber: 2.0 Consensus size: 65
13234 GTTTTTATAC
13244 GTGACATATTGTTTATGTCACGTATTGTATTAAATTATTTGTGACATAAAGTAATGTCACCAAAT
1 GTGACATATTGTTTATGTCACGTATTGTATTAAATTATTTGTGACATAAAGTAATGTCACCAAAT
*
13309 GTGACATATTG-TT-TGTCACGTATTGTATTAAATTATTTGTGACATAAAGTGATGTCACCAAAT
1 GTGACATATTGTTTATGTCACGTATTGTATTAAATTATTTGTGACATAAAGTAATGTCACCAAAT
13372 TTTTATACAC
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
63 49 0.79
64 2 0.03
65 11 0.18
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (65 bp):
GTGACATATTGTTTATGTCACGTATTGTATTAAATTATTTGTGACATAAAGTAATGTCACCAAAT
Found at i:21684 original size:120 final size:118
Alignment explanation
Indices: 21512--21890 Score: 550
Period size: 120 Copynumber: 3.2 Consensus size: 118
21502 TAATGAAAAA
*
21512 TTTCCTCATATTTTGTGACAATCAACAATTGTAAGTGACGTTATATTTTAGTATTTTGTGACACA
1 TTTCCTCAT-TTTTGTGACAATCAACAATTGTTAGTGACGTTATATTTTAGTATTTTGTGACACA
21577 CATTCCGTCACCTATACATGTGACGTTCCACTTTTCGTCACAAATAATGGAACAT
65 -ATTCCGTCACCTATACATGTGACGTTCCACTTTTCGTCACAAATAATGGAACAT
* *
21632 TTTCATCATTTTTCGTGACAATCAACAATTGTTAGTGACGTTATATTGTAGTATTTTGTGACACA
1 TTTCCTCATTTTT-GTGACAATCAACAATTGTTAGTGACGTTATATTTTAGTATTTTGTGACAC-
*
21697 AATTCCGTCACCTATACATGTGACGTTCCAATTTTCGTCACAAATAATGGAACAT
64 AATTCCGTCACCTATACATGTGACGTTCCACTTTTCGTCACAAATAATGGAACAT
* *
21752 TTTCCTCATTTTTTGTGACAATCAACAATTGTTAGTGACGTTATATTTTAATATTTTATGACGA-
1 TTTCCTCA-TTTTTGTGACAATCAACAATTGTTAGTGACGTTATATTTTAGTATTTTGTGAC-AC
**
21816 AATGGGCGTCACCTATACATGTGACGTT-CACATTTTCGTCACAAATAACT--AAGCAT
64 AAT-TCCGTCACCTATACATGTGACGTTCCAC-TTTTCGTCACAAATAA-TGGAA-CAT
*
21872 TTTCCTCATATTTGGTGAC
1 TTTCCTCAT-TTTTGTGAC
21891 GACCCATGAT
Statistics
Matches: 238, Mismatches: 12, Indels: 18
0.89 0.04 0.07
Matches are distributed among these distances:
119 12 0.05
120 218 0.92
121 8 0.03
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (118 bp):
TTTCCTCATTTTTGTGACAATCAACAATTGTTAGTGACGTTATATTTTAGTATTTTGTGACACAA
TTCCGTCACCTATACATGTGACGTTCCACTTTTCGTCACAAATAATGGAACAT
Found at i:21910 original size:120 final size:116
Alignment explanation
Indices: 21463--21890 Score: 536
Period size: 120 Copynumber: 3.6 Consensus size: 116
21453 ACTAAACTTA
* * * ** ** * *
21463 CGTCACCTATTCTTGTGACGTTCTGAAATTCGTCAGGAATAATGAAAAATTTCCTCATATTTT-G
1 CGTCACCTATACATGTGACGTTC-CATTTTCGTCACAAATAATGAACATTTTCCTCAT-TTTTCG
*
21527 TGACAATCAACAATTGTAAGTGACGTTATATTTTAGTATTTTGTGACACACATTC
64 TGACAATCAACAATTGTTAGTGACGTTATATTTTAGTATTTTGTGACA-A-ATTC
*
21582 CGTCACCTATACATGTGACGTTCCACTTTTCGTCACAAATAATGGAACATTTTCATCATTTTTCG
1 CGTCACCTATACATGTGACGTTCCA-TTTTCGTCACAAATAAT-GAACATTTTCCTCATTTTTCG
*
21647 TGACAATCAACAATTGTTAGTGACGTTATATTGTAGTATTTTGTGACACAAATTC
64 TGACAATCAACAATTGTTAGTGACGTTATATTTTAGTATTTTGTG--ACAAATTC
*
21702 CGTCACCTATACATGTGACGTTCCAATTTTCGTCACAAATAATGGAACATTTTCCTCATTTTTTG
1 CGTCACCTATACATGTGACGTTCC-ATTTTCGTCACAAATAAT-GAACATTTTCCTCATTTTTCG
* * **
21767 TGACAATCAACAATTGTTAGTGACGTTATATTTTAATATTTTATGACGAAATGGG
64 TGACAATCAACAATTGTTAGTGACGTTATATTTTAGTATTTTGTGAC-AAAT-TC
* *
21822 CGTCACCTATACATGTGACGTTCACATTTTCGTCACAAATAACT-AAGCATTTTCCTCATATTTG
1 CGTCACCTATACATGTGACGTTC-CATTTTCGTCACAAATAA-TGAA-CATTTTCCTCATTTTTC
21886 GTGAC
63 GTGAC
21891 GACCCATGAT
Statistics
Matches: 277, Mismatches: 21, Indels: 21
0.87 0.07 0.07
Matches are distributed among these distances:
118 3 0.01
119 44 0.16
120 223 0.81
121 4 0.01
122 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.37
Consensus pattern (116 bp):
CGTCACCTATACATGTGACGTTCCATTTTCGTCACAAATAATGAACATTTTCCTCATTTTTCGTG
ACAATCAACAATTGTTAGTGACGTTATATTTTAGTATTTTGTGACAAATTC
Found at i:25414 original size:11 final size:11
Alignment explanation
Indices: 25400--25425 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
25390 GAAAAATATC
25400 AAAAAAAATAA
1 AAAAAAAATAA
25411 AAAAAAAATAA
1 AAAAAAAATAA
25422 AAAA
1 AAAA
25426 TTTCGACCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAAAAAATAA
Done.