Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018931.1 Corchorus olitorius cultivar O-4 contig18964, 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: 16472
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.25
Found at i:60 original size:39 final size:39
Alignment explanation
Indices: 6--157 Score: 151
Period size: 39 Copynumber: 3.9 Consensus size: 39
1 CCTTA
6 CGAGCCCATCTACAAGCCCGAGGTCAAGCCCTACGTGCC
1 CGAGCCCATCTACAAGCCCGAGGTCAAGCCCTACGTGCC
* *** ***
45 CGAGCCCATATACAAGCATAAGGTCAAGCCCTACGTTTT
1 CGAGCCCATCTACAAGCCCGAGGTCAAGCCCTACGTGCC
** ** * *
84 CGAGCCTGTCTGGAAACCCGAGGTCAAGCCCTATGTGCC
1 CGAGCCCATCTACAAGCCCGAGGTCAAGCCCTACGTGCC
** * *
123 CGAGCCTGTCTATAAGCCCGAGGTCAAGCCTTACG
1 CGAGCCCATCTACAAGCCCGAGGTCAAGCCCTACG
158 AGCCGAAGAA
Statistics
Matches: 88, Mismatches: 25, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
39 88 1.00
ACGTcount: A:0.24, C:0.34, G:0.24, T:0.18
Consensus pattern (39 bp):
CGAGCCCATCTACAAGCCCGAGGTCAAGCCCTACGTGCC
Found at i:1262 original size:41 final size:43
Alignment explanation
Indices: 1162--1488 Score: 359
Period size: 41 Copynumber: 7.8 Consensus size: 43
1152 CCAATAACCA
* * *
1162 AAAGTCCCCAAACAC--ATATAACACAGGGGCATCTCTATTCC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATTAC
** *
1203 AAAAGTCTTCAAACACATATATAACACAGAGGCACCTATATT-C
1 -AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATTAC
* * *
1246 -AAGTCCCCAAACACATATATAACACAGGGGCACCTTTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATTAC
* *
1288 AAAGTCCTCAAACAC--ATATAACATAGAGGCATCTATA-T-C
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATTAC
* * * * *
1327 AAAGTCCCCAAACACATATATAATAGAGGGGCAACTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATTAC
* * *
1370 AAATTCCTCAAACACATATATAACACAGAGGCATTTATA-T-C
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATTAC
* *
1411 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATTAC
* *
1454 AAAAGTTCTCAAACACATATATAACACAGAGGCAT
1 -AAAGTCCCCAAACACATATATAACACAGAGGCAT
1489 TTCTCCTTAT
Statistics
Matches: 238, Mismatches: 36, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
39 15 0.06
40 1 0.00
41 106 0.45
42 17 0.07
43 47 0.20
44 52 0.22
ACGTcount: A:0.42, C:0.25, G:0.11, T:0.22
Consensus pattern (43 bp):
AAAGTCCCCAAACACATATATAACACAGAGGCATCTATATTAC
Found at i:1307 original size:84 final size:85
Alignment explanation
Indices: 1162--1488 Score: 488
Period size: 84 Copynumber: 3.9 Consensus size: 85
1152 CCAATAACCA
* *
1162 AAAGTCCCCAAACAC--ATATAACACAGGGGCATCTCTATTCCAAAAGTCTTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAAGTCCTCAAACACATATAT
*
1225 AACACAGAGGCACCTATATTC
66 AACACAGAGGCATCTATA-TC
* *
1246 -AAGTCCCCAAACACATATATAACACAGGGGCACCTTTATTAC-AAAGTCCTCAAACAC--ATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAAGTCCTCAAACACATATAT
*
1307 AACATAGAGGCATCTATATC
66 AACACAGAGGCATCTATATC
* * * *
1327 AAAGTCCCCAAACACATATATAATAGAGGGGCAACTCTATTAC-AAATTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAAGTCCTCAAACACATATAT
*
1391 AACACAGAGGCATTTATATC
66 AACACAGAGGCATCTATATC
*
1411 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAAGTTCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAAGTCCTCAAACACATATAT
1476 AACACAGAGGCAT
66 AACACAGAGGCAT
1489 TTCTCCTTAT
Statistics
Matches: 219, Mismatches: 18, Indels: 11
0.88 0.07 0.04
Matches are distributed among these distances:
81 2 0.01
82 72 0.33
83 14 0.06
84 76 0.35
85 55 0.25
ACGTcount: A:0.42, C:0.25, G:0.11, T:0.22
Consensus pattern (85 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAAGTCCTCAAACACATATAT
AACACAGAGGCATCTATATC
Found at i:1609 original size:2 final size:2
Alignment explanation
Indices: 1597--1634 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
1587 ACCAAATTCC
*
1597 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1635 GTGACAAAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:7416 original size:19 final size:18
Alignment explanation
Indices: 7383--7418 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
7373 TGGAAATTAT
7383 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
7401 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
7419 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:9047 original size:63 final size:63
Alignment explanation
Indices: 8974--9103 Score: 251
Period size: 63 Copynumber: 2.1 Consensus size: 63
8964 ACGCTGTATC
8974 GAAAAAGAGGAGGCGGAGCTCGTCCTCAAAGAGACTCATGAGAAGTCTTGTGGCATAGCTCCT
1 GAAAAAGAGGAGGCGGAGCTCGTCCTCAAAGAGACTCATGAGAAGTCTTGTGGCATAGCTCCT
*
9037 GAAAAAGAGGAGGCGGAGCTTGTCCTCAAAGAGACTCATGAGAAGTCTTGTGGCATAGCTCCT
1 GAAAAAGAGGAGGCGGAGCTCGTCCTCAAAGAGACTCATGAGAAGTCTTGTGGCATAGCTCCT
9100 GAAA
1 GAAA
9104 TTAGCCTCTA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 66 1.00
ACGTcount: A:0.32, C:0.19, G:0.30, T:0.19
Consensus pattern (63 bp):
GAAAAAGAGGAGGCGGAGCTCGTCCTCAAAGAGACTCATGAGAAGTCTTGTGGCATAGCTCCT
Found at i:15716 original size:43 final size:43
Alignment explanation
Indices: 15582--15912 Score: 433
Period size: 41 Copynumber: 7.8 Consensus size: 43
15572 CCAATAACCA
* *
15582 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
* * * *
15625 AAAAGTCCTCAAACACATATATAACACAGAGACACCTATATT-C
1 -AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
* * *
15668 -AAGTCCCCAAACACATATATAACACAGGGGCACCTTTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
* * *
15710 AAAGTCCTCAAACACATATATAACATAGAGGCATCTATA-T-C
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
* *
15751 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
* *
15794 AAAGTCCTCAAACACATATATAACACAGAGGCA--T-TAATATC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTA-C
*
15835 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTAC
1 AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
15878 AAAAGTCCCCAAACACATATATAACACAGAGGCAT
1 -AAAGTCCCCAAACACATATATAACACAGAGGCAT
15913 TTCTCCTTAT
Statistics
Matches: 252, Mismatches: 26, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
40 4 0.02
41 104 0.41
42 3 0.01
43 68 0.27
44 73 0.29
ACGTcount: A:0.43, C:0.26, G:0.11, T:0.21
Consensus pattern (43 bp):
AAAGTCCCCAAACACATATATAACACAGAGGCATCTCTATTAC
Found at i:15756 original size:84 final size:85
Alignment explanation
Indices: 15582--15912 Score: 544
Period size: 84 Copynumber: 3.9 Consensus size: 85
15572 CCAATAACCA
*
15582 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTCCAAAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAAGTCCTCAAACACATATAT
* *
15647 AACACAGAGACACCTATATTC
66 AACACAGAGGCATCTATA-TC
* *
15668 -AAGTCCCCAAACACATATATAACACAGGGGCACCTTTATTAC-AAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAAGTCCTCAAACACATATAT
*
15731 AACATAGAGGCATCTATATC
66 AACACAGAGGCATCTATATC
*
15751 AAAGTCCCCAAACACATATATAACACAGGGGCAACTCTATTAC-AAAGTCCTCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAAGTCCTCAAACACATATAT
15815 AACACAGAGGCAT-TAATATC
66 AACACAGAGGCATCT-ATATC
*
15835 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAAGTCCCCAAACACATATAT
1 AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAAGTCCTCAAACACATATAT
15900 AACACAGAGGCAT
66 AACACAGAGGCAT
15913 TTCTCCTTAT
Statistics
Matches: 231, Mismatches: 11, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
83 3 0.01
84 156 0.68
85 72 0.31
ACGTcount: A:0.43, C:0.26, G:0.11, T:0.21
Consensus pattern (85 bp):
AAAGTCCCCAAACACATATATAACACAGGGGCATCTCTATTACAAAAGTCCTCAAACACATATAT
AACACAGAGGCATCTATATC
Done.