Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019215.1 Corchorus olitorius cultivar O-4 contig19248, 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: 4861
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Found at i:1677 original size:66 final size:65
Alignment explanation
Indices: 1512--2560 Score: 1367
Period size: 66 Copynumber: 15.8 Consensus size: 65
1502 TGAACTTTAT
* *
1512 AAGTCTCAGTGGACTGCAAATTATGCATCCATTTCAAACATCTTAAGCCACAAAACCGACATTTG
1 AAGTCTCAGTGGACTGC-AATTATGCATCAATTTCAAACCTCTTAAGCCACAAAACCGACATTTG
1577 CC
65 -C
*
1579 AAGTCTCAGTGGACTGCAATTTATGCATCAATTTCAAACCTCTTAAGCCACAAAACCGACATTTA
1 AAGTCTCAGTGGACTGCAA-TTATGCATCAATTTCAAACCTCTTAAGCCACAAAACCGACATTTG
1644 C
65 C
* *
1645 AAGTCTCAGTGGACTACAATTTATGCATCAATTTCAAACCTCTTAGGCCACAAAACCGACATTTG
1 AAGTCTCAGTGGACTGCAA-TTATGCATCAATTTCAAACCTCTTAAGCCACAAAACCGACATTTG
1710 C
65 C
**
1711 AAGTCGT-AACGGACTGCAGATTATGCATCAA-TTCAAACCTCTTAAGCCACAAAACCGACATTT
1 AAGTC-TCAGTGGACTGCA-ATTATGCATCAATTTCAAACCTCTTAAGCCACAAAACCGACATTT
1774 GC
64 GC
* * * * *
1776 AAGTCCCAGTGGACTACAATTTATGCATCAATTTCAAACCTCTTAGGCCACAAAGCCGACACTTG
1 AAGTCTCAGTGGACTGCAA-TTATGCATCAATTTCAAACCTCTTAAGCCACAAAACCGACATTTG
1841 C
65 C
* * * **
1842 AAGT-TATAATGGACTGCAGATTATGCATCAATTTCAAACCTCTTAAGCCACAGAACCGATTTTT
1 AAGTCT-CAGTGGACTGCA-ATTATGCATCAATTTCAAACCTCTTAAGCCACAAAACCGACATTT
1906 GC
64 GC
* * * * *
1908 AAGTCTTAATGGTCTGCAGATTATGCATCCATTTCAAACCTCTTAAGCCACAAAGCCGACATTTG
1 AAGTCTCAGTGGACTGCA-ATTATGCATCAATTTCAAACCTCTTAAGCCACAAAACCGACATTTG
1973 C
65 C
* * * *
1974 AAGTCTCAGTGGATTGCAGATTATGCATCTATTTCAAACCCCTTAAGCCAC-AAACCCACATTTG
1 AAGTCTCAGTGGACTGCA-ATTATGCATCAATTTCAAACCTCTTAAGCCACAAAACCGACATTTG
2038 C
65 C
* *
2039 AAGTCTCAGTGGACTGCAGATTATGCATCAATTTCAAACCTCTTAAGCCACAAAACTGACATTTA
1 AAGTCTCAGTGGACTGCA-ATTATGCATCAATTTCAAACCTCTTAAGCCACAAAACCGACATTTG
2104 C
65 C
* *
2105 AAGTCTAAGTGGACTACAGATTATGCATCAATTTCAAACCTCTTAAGCCACAAAACCGACATTTG
1 AAGTCTCAGTGGACTGCA-ATTATGCATCAATTTCAAACCTCTTAAGCCACAAAACCGACATTTG
2170 C
65 C
* * *
2171 AAGTCACTGTGGACTGCAAATTATGCATCAATTTCAAACCCCTTAAGCCACAAAACCGA-ATTTT
1 AAGTCTCAGTGGACTGC-AATTATGCATCAATTTCAAACCTCTTAAGCCACAAAACCGACA-TTT
2235 GC
64 GC
* * * *
2237 AAGTCTTAGTGGACTGCAAATTATGCATCAATTTCAAACCCCTTAAGCCACAAAACCGGCAATTG
1 AAGTCTCAGTGGACTGC-AATTATGCATCAATTTCAAACCTCTTAAGCCACAAAACCGACATTTG
2302 C
65 C
*
2303 AAAAAGTCTCAGTGGACTGCAAATTATGCATCCATTTCAAACCTCTTAAGCCACAAAACCGA-AT
1 ---AAGTCTCAGTGGACTGC-AATTATGCATCAATTTCAAACCTCTTAAGCCACAAAACCGACA-
*
2367 TTTGT
61 TTTGC
* * * *
2372 AAGCCTTAGTGGATTGCAGATTATGCAT-ATATTTCAAATCC-CTTAAGCCACAAAATCGACATT
1 AAGTCTCAGTGGACTGCA-ATTATGCATCA-ATTTCAAA-CCTCTTAAGCCACAAAACCGACATT
2435 TGC
63 TGC
* *
2438 AAGTCTCAATGGACTGCAAAGTATGCATCAATTTCAAACCTCTTTAAGCCACAAAACCGACATTT
1 AAGTCTCAGTGGACTGC-AATTATGCATCAATTTCAAACCTC-TTAAGCCACAAAACCGACATTT
2503 GC
64 GC
* * *
2505 AAGTCTCAGTGGACTGCAAATTATACATCCATTTCAAACCTCTTAGGCCACAAAAC
1 AAGTCTCAGTGGACTGC-AATTATGCATCAATTTCAAACCTCTTAAGCCACAAAAC
2561 AAACATAAAC
Statistics
Matches: 873, Mismatches: 84, Indels: 51
0.87 0.08 0.05
Matches are distributed among these distances:
64 1 0.00
65 121 0.14
66 561 0.64
67 131 0.15
68 1 0.00
69 58 0.07
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.27
Consensus pattern (65 bp):
AAGTCTCAGTGGACTGCAATTATGCATCAATTTCAAACCTCTTAAGCCACAAAACCGACATTTGC
Found at i:1994 original size:263 final size:263
Alignment explanation
Indices: 1512--2560 Score: 1430
Period size: 263 Copynumber: 4.0 Consensus size: 263
1502 TGAACTTTAT
* *
1512 AAGTCTCAGTGGACTGCAAATTATGCATCCATTTCAAACATCTTAAGCCACAAAACCGACATTTG
1 AAGTCTCAGTGGACTGCAAATTATGCATCAATTTCAAACCTCTTAAGCCACAAAACCGACATTTG
*
1577 CCAAGTCTCAGTGGACTGCA-ATTTATGCATCAATTTCAAACCTCTTAAGCCACAAAACCGACAT
66 -CAAGTCTTAGTGGACTGCAGA-TTATGCATCAATTTCAAACCTCTTAAGCCACAAAACCGACAT
* * * * *
1641 TTACAAGTCTCAGTGGACTACAATTTATGCATCAATTTCAAACCTCTTAGGCCACAAAACCGACA
129 TTGCAAGTCTCAATGGACTGCAAATTATGCATCAATTTCAAACCTCTTAAGCCACAAAACCGACA
** * *
1706 TTTGCAAGTCGT-AACGGACTGCAGATTATGCATCAATTCAAACCTCTTAAGCCACAAAACCGAC
194 TTTGCAAGTC-TCAGTGGACTGCAAATTATGCATCAATTCAAACCCCTTAAGCCACAAAACCGAC
1770 ATTTGC
258 ATTTGC
* * * * * *
1776 AAGTCCCAGTGGACTACAATTTATGCATCAATTTCAAACCTCTTAGGCCACAAAGCCGACACTTG
1 AAGTCTCAGTGGACTGCAAATTATGCATCAATTTCAAACCTCTTAAGCCACAAAACCGACATTTG
* * **
1841 CAAGT-TATAATGGACTGCAGATTATGCATCAATTTCAAACCTCTTAAGCCACAGAACCGATTTT
66 CAAGTCT-TAGTGGACTGCAGATTATGCATCAATTTCAAACCTCTTAAGCCACAAAACCGACATT
* * * * *
1905 TGCAAGTCTTAATGGTCTGCAGATTATGCATCCATTTCAAACCTCTTAAGCCACAAAGCCGACAT
130 TGCAAGTCTCAATGGACTGCAAATTATGCATCAATTTCAAACCTCTTAAGCCACAAAACCGACAT
* * * *
1970 TTGCAAGTCTCAGTGGATTGCAGATTATGCATCTATTTCAAACCCCTTAAGCCAC-AAACCCACA
195 TTGCAAGTCTCAGTGGACTGCAAATTATGCATC-AATTCAAACCCCTTAAGCCACAAAACCGACA
2034 TTTGC
259 TTTGC
* * *
2039 AAGTCTCAGTGGACTGCAGATTATGCATCAATTTCAAACCTCTTAAGCCACAAAACTGACATTTA
1 AAGTCTCAGTGGACTGCAAATTATGCATCAATTTCAAACCTCTTAAGCCACAAAACCGACATTTG
* *
2104 CAAGTCTAAGTGGACTACAGATTATGCATCAATTTCAAACCTCTTAAGCCACAAAACCGACATTT
66 CAAGTCTTAGTGGACTGCAGATTATGCATCAATTTCAAACCTCTTAAGCCACAAAACCGACATTT
* ** *
2169 GCAAGTCACTGTGGACTGCAAATTATGCATCAATTTCAAACCCCTTAAGCCACAAAACCGA-ATT
131 GCAAGTCTCAATGGACTGCAAATTATGCATCAATTTCAAACCTCTTAAGCCACAAAACCGACA-T
* *
2233 TTGCAAGTCTTAGTGGACTGCAAATTATGCATCAATTTCAAACCCCTTAAGCCACAAAACCGGCA
195 TTGCAAGTCTCAGTGGACTGCAAATTATGCATCAA-TTCAAACCCCTTAAGCCACAAAACCGACA
*
2298 ATTGC
259 TTTGC
*
2303 AAAAAGTCTCAGTGGACTGCAAATTATGCATCCATTTCAAACCTCTTAAGCCACAAAACCGA-AT
1 ---AAGTCTCAGTGGACTGCAAATTATGCATCAATTTCAAACCTCTTAAGCCACAAAACCGACA-
* * * *
2367 TTTGTAAGCCTTAGTGGATTGCAGATTATGCAT-ATATTTCAAATCC-CTTAAGCCACAAAATCG
62 TTTGCAAGTCTTAGTGGACTGCAGATTATGCATCA-ATTTCAAA-CCTCTTAAGCCACAAAACCG
*
2430 ACATTTGCAAGTCTCAATGGACTGCAAAGTATGCATCAATTTCAAACCTCTTTAAGCCACAAAAC
125 ACATTTGCAAGTCTCAATGGACTGCAAATTATGCATCAATTTCAAACCTC-TTAAGCCACAAAAC
* * * *
2495 CGACATTTGCAAGTCTCAGTGGACTGCAAATTATACATCCATTTCAAACCTCTTAGGCCACAAAA
189 CGACATTTGCAAGTCTCAGTGGACTGCAAATTATGCAT-CAATTCAAACCCCTTAAGCCACAAAA
2560 C
253 C
2561 AAACATAAAC
Statistics
Matches: 688, Mismatches: 80, Indels: 30
0.86 0.10 0.04
Matches are distributed among these distances:
262 4 0.01
263 366 0.53
264 89 0.13
266 2 0.00
267 152 0.22
268 72 0.10
269 3 0.00
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.27
Consensus pattern (263 bp):
AAGTCTCAGTGGACTGCAAATTATGCATCAATTTCAAACCTCTTAAGCCACAAAACCGACATTTG
CAAGTCTTAGTGGACTGCAGATTATGCATCAATTTCAAACCTCTTAAGCCACAAAACCGACATTT
GCAAGTCTCAATGGACTGCAAATTATGCATCAATTTCAAACCTCTTAAGCCACAAAACCGACATT
TGCAAGTCTCAGTGGACTGCAAATTATGCATCAATTCAAACCCCTTAAGCCACAAAACCGACATT
TGC
Found at i:3063 original size:70 final size:71
Alignment explanation
Indices: 2980--3133 Score: 231
Period size: 72 Copynumber: 2.2 Consensus size: 71
2970 GATGTTATAA
* * * *
2980 AAAAAATATATTCAAGAAAAGATAAAAGAAA-AACAACGGAAGAAAAC-ACCACAAAGAAGAAAA
1 AAAAAAGAAATTCAAGAAAAGATAAAAGAAAGAAAAACAGAAGAAAACAACC-CAAAGAAGAAAA
3043 TATGTTT
65 TATGTTT
*
3050 AAAAAAGAAATTCAAGAAAAGATAAAAGAAATGAAAAACAGAAGAAAACAACCCAAAGAAGAAGA
1 AAAAAAGAAATTCAAGAAAAGATAAAAGAAA-GAAAAACAGAAGAAAACAACCCAAAGAAGAAAA
3115 TATGTTT
65 TATGTTT
3122 AAAAAAGAAATT
1 AAAAAAGAAATT
3134 ACATAACAGG
Statistics
Matches: 76, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
70 29 0.38
72 44 0.58
73 3 0.04
ACGTcount: A:0.64, C:0.08, G:0.14, T:0.14
Consensus pattern (71 bp):
AAAAAAGAAATTCAAGAAAAGATAAAAGAAAGAAAAACAGAAGAAAACAACCCAAAGAAGAAAAT
ATGTTT
Found at i:4111 original size:66 final size:66
Alignment explanation
Indices: 3926--4128 Score: 228
Period size: 66 Copynumber: 3.1 Consensus size: 66
3916 AAGTGGATTA
* * * * *
3926 CAAATTACGCATCAATTTTAAACCTTTTCAGCCACAAAACCGACATTTGC-AGCACTAAATGAAC
1 CAAATTATGCATCAATTTCAAACCTTTTAAGCCACAAAACCGACATTTGCAAG-TCTAAGTGAAC
*
3990 CG
65 TG
* ** * * * **
3992 CAAATTGTGCATCAATTTCAAACCTCGTAGGCCACAAAACCGACATTTCCAAGTCTTAGTTTACT
1 CAAATTATGCATCAATTTCAAACCTTTTAAGCCACAAAACCGACATTTGCAAGTCTAAGTGAACT
4057 G
66 G
* * * *
4058 CAAATTATGCATCAATTTCAAAACTTTTAAGCCATAAAACCGACATTTGCAAGTCTCAGTGGACT
1 CAAATTATGCATCAATTTCAAACCTTTTAAGCCACAAAACCGACATTTGCAAGTCTAAGTGAACT
4123 G
66 G
4124 CAAAT
1 CAAAT
4129 AGACAGAAGA
Statistics
Matches: 112, Mismatches: 24, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
66 110 0.98
67 2 0.02
ACGTcount: A:0.36, C:0.25, G:0.12, T:0.27
Consensus pattern (66 bp):
CAAATTATGCATCAATTTCAAACCTTTTAAGCCACAAAACCGACATTTGCAAGTCTAAGTGAACT
G
Done.