Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023180.1 Corchorus olitorius cultivar O-4 contig23213, 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: 14719
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Found at i:5463 original size:28 final size:28
Alignment explanation
Indices: 5423--5479 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
5413 GAAAGCTAAC
5423 TCCGAGAGATACAACTTTCGTGTTTCGG
1 TCCGAGAGATACAACTTTCGTGTTTCGG
5451 TCCGAGAGATACAACTTTCGTGTTTCGG
1 TCCGAGAGATACAACTTTCGTGTTTCGG
5479 T
1 T
5480 GGAAACCCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (28 bp):
TCCGAGAGATACAACTTTCGTGTTTCGG
Found at i:7062 original size:41 final size:41
Alignment explanation
Indices: 7005--7088 Score: 150
Period size: 41 Copynumber: 2.0 Consensus size: 41
6995 GGAAATAAAG
*
7005 ACATAATTAAACAAGGATTGGATTTAGTCAAACAAGGCCCA
1 ACATAATTAAACAAGGATTGGACTTAGTCAAACAAGGCCCA
*
7046 ACATAATTAAACAAGGATTGGACTTAGTCAAAGAAGGCCCA
1 ACATAATTAAACAAGGATTGGACTTAGTCAAACAAGGCCCA
7087 AC
1 AC
7089 CCAAATAACA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.44, C:0.18, G:0.18, T:0.20
Consensus pattern (41 bp):
ACATAATTAAACAAGGATTGGACTTAGTCAAACAAGGCCCA
Found at i:9290 original size:33 final size:31
Alignment explanation
Indices: 9217--9387 Score: 126
Period size: 33 Copynumber: 5.2 Consensus size: 31
9207 GCTATGATCA
** *
9217 ACCAAAACAGATTTGTTTTCATCACAATTAGC
1 ACCAAAACAGATTTG-TTTCATCACAAACAAC
9249 ATCCAAAACAGAATTTGTTTCATCACAAACAAC
1 A-CCAAAACAG-ATTTGTTTCATCACAAACAAC
*
9282 ACCTAAAACAGATTTAGTGTCATCACAAACAAC
1 ACC-AAAACAGATTT-GTTTCATCACAAACAAC
** * * **
9315 ACTCAAATTAGTTTTAGTATCATTGCAAACAAC
1 AC-CAAAACAGATTT-GTTTCATCACAAACAAC
* * **
9348 ATCTAAAACAGATTTCGTGTCATTGCAAACAAC
1 A-CCAAAACAGATTT-GTTTCATCACAAACAAC
9381 ACTCAAA
1 AC-CAAA
9388 TTAGGTTTAG
Statistics
Matches: 115, Mismatches: 17, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
32 8 0.07
33 100 0.87
34 7 0.06
ACGTcount: A:0.42, C:0.22, G:0.09, T:0.27
Consensus pattern (31 bp):
ACCAAAACAGATTTGTTTCATCACAAACAAC
Found at i:9344 original size:66 final size:66
Alignment explanation
Indices: 9274--9397 Score: 203
Period size: 66 Copynumber: 1.9 Consensus size: 66
9264 TGTTTCATCA
*
9274 CAAACAACACCTAAAACAGATTTAGTGTCATCACAAACAACACTCAAATTAGTTTTAGTATCATT
1 CAAACAACACCTAAAACAGATTTAGTGTCATCACAAACAACACTCAAATTAGGTTTAGTATCATT
9339 G
66 G
* * **
9340 CAAACAACATCTAAAACAGATTTCGTGTCATTGCAAACAACACTCAAATTAGGTTTAG
1 CAAACAACACCTAAAACAGATTTAGTGTCATCACAAACAACACTCAAATTAGGTTTAG
9398 AATTACTCTT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 53 1.00
ACGTcount: A:0.42, C:0.21, G:0.10, T:0.27
Consensus pattern (66 bp):
CAAACAACACCTAAAACAGATTTAGTGTCATCACAAACAACACTCAAATTAGGTTTAGTATCATT
G
Found at i:11854 original size:21 final size:21
Alignment explanation
Indices: 11828--11869 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
11818 GCAACTTAGG
11828 CAACTCCGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
*
11849 CAACTCTGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
11870 TTCTTCCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21
Consensus pattern (21 bp):
CAACTCCGATGAGCTTGAAAC
Found at i:13481 original size:154 final size:153
Alignment explanation
Indices: 13201--14718 Score: 2376
Period size: 154 Copynumber: 9.9 Consensus size: 153
13191 TGGCGCATCA
*
13201 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAATGCATTGAGGTTTGCCAA
1 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
* * * **
13266 ATTGAAGACGATTCAAAACGGAACTAATGTGG-CCCGATATGCCCAAAATAACAAAAGTTCCAAA
66 ATCGAAGACGATTCAAAAC-GAACTAATG-GGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAA
13330 TGAGTTAAAAACTTCACAGTGGACT
129 TGAGTTAAAAACTTCACAGTGGACT
* * *
13355 AATCTCACAAAAATGATTATAGTTAGGCCATAAATAATGGAAAGAAATGCATTGAGGTTTGCCAA
1 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
* *
13420 ATCAAAGACGATTCAAAACGACACTAATTGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAAT
66 ATCGAAGACGATTCAAAACGA-ACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAAT
13485 GAGTTAAAAACTTCACAGTGGACT
130 GAGTTAAAAACTTCACAGTGGACT
* *
13509 AATCTCACTAAAATGATTATAGTTAGGCCATAAACAACGGAAAGAAAAGCATTGAGGTTTGCCAA
1 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
* * * *
13574 ATTGAAGACGATTCAAAACGGAACTAATGTGCCCCGATATGCCCAAAATAACAAGTGTTCCAAAT
66 ATCGAAGACGATTCAAAAC-GAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAAT
13639 GAGTTAAAAACTTCACAGTGGACT
130 GAGTTAAAAACTTCACAGTGGACT
* *
13663 AATCTCACCAAAATGATTATAGTTAGGCGATAAACAATGAAAAGAAAAGCATTGAGGTTTGCCAA
1 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
* * * *
13728 ATCGAGGACAATTCAAAACGTCACTAATGGGCCTCGAAAGGCCCAAAATAACAAGTGTTCCAAAT
66 ATCGAAGACGATTCAAAACG-AACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAAT
13793 GAGTTAAAAACTTCACAGTGGACT
130 GAGTTAAAAACTTCACAGTGGACT
13817 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
1 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
* * *
13882 ATCGAAGACAATTCAAAACGAGACTAATGGGCCCTGAAAGGCCCAATATAACAAGTGTTCCAAAT
66 ATCGAAGACGATTCAAAACGA-ACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAAT
13947 GAGTTAAAAACTTCACAGTGGACT
130 GAGTTAAAAACTTCACAGTGGACT
* *
13971 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGAATTGAGGTTTGCAAA
1 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
* * *
14036 ATCAAAGACGATTCAAAACGGAACTAATGGGTCCCGAAAGGCCCAAAATAACAAGAGTTCCAAAT
66 ATCGAAGACGATTCAAAAC-GAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAAT
14101 GAGTTAAAAACTTCACAGTGGACT
130 GAGTTAAAAACTTCACAGTGGACT
*
14125 AATCTCACCAAAATGATTATAGTTAGGCGATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
1 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
* * * *
14190 ATCGAAGACGATTCAAAACGGAACTAATGTGCCCCGATATGCCGAAAATAACAAGTGTTCCAAAT
66 ATCGAAGACGATTCAAAAC-GAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAAT
*
14255 GAGTTAAAAACATCACAGTGGACT
130 GAGTTAAAAACTTCACAGTGGACT
* *
14279 AAGCTCACCAAAATGATTATAGTTAGGCCATAAACAACT-TAAAGAAAAGCATTGAGGTTTGCCA
1 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAA-TGGAAAGAAAAGCATTGAGGTTTGCCA
* *
14343 AATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGAAAGGCCCAAAATAGCAAGTGTTCCAAA
65 AATCGAAGACGATTCAAAACG-AACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAA
*
14408 TGAGTTAAAAACTTCACAGTGGACA
129 TGAGTTAAAAACTTCACAGTGGACT
* *
14433 AATCTCACCAAAATGATTATAGTTAGGCGATAAACAATGAAAAGAAAAGCATTGAGGTTTGCCAA
1 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
* * * * * *
14498 ATCGAAGACGATTCTAAACCGAACTAATGGGCCCTGAAGGGCCCAAAAGAACAAATGTTCAAAAT
66 ATCGAAGACGATTC-AAAACGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAAT
*
14563 GAGCTAAAAACTTCACAGTGGACT
130 GAGTTAAAAACTTCACAGTGGACT
* * * *
14587 AATCTTACCAAAATGATAATAGTTAGGCCATAAACAATGGAAAGAAAAGCCTTGTGGTTTGCCAA
1 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
* * * *
14652 ATCGAAGACGAGTCAAAACCGAACTAATGGGCCTCGAAAGGTCCAAAAT-ACAAGTGTTCAAAAT
66 ATCGAAGACGATTCAAAA-CGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAAT
14716 GAG
130 GAG
14719 C
Statistics
Matches: 1258, Mismatches: 95, Indels: 23
0.91 0.07 0.02
Matches are distributed among these distances:
153 27 0.02
154 1221 0.97
155 10 0.01
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (153 bp):
AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
ATCGAAGACGATTCAAAACGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATG
AGTTAAAAACTTCACAGTGGACT
Done.