Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018188.1 Corchorus olitorius cultivar O-4 contig18221, 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: 79703
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:1542 original size:333 final size:332
Alignment explanation
Indices: 79--1664 Score: 2277
Period size: 331 Copynumber: 4.7 Consensus size: 332
69 TCAGATCAGT
* * * * *
79 TTTTAGTCGAAATCGTGTATTAACCATCACGGTTTTTGGGCTAAAAACGCGTTTCCT--GGCTCC
1 TTTTAGTCGAAATCGTGTACTAACCATCACAGTTTTT--GCCAAAAACGC-ATT-CTGGGGCCCC
* * * * * *
142 GGCTCAGTTTTGCATGATTTTTGTCTGAAAGACTCCATGAAATATCTTTATTCATCTAACCAAAT
62 GGATCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTCAAATATCTATATTCATCTAACCAAAT
* * * * * * *
207 CTCAGCCACATTGGATTTAAAGATTTGTTTTTACGAGCTTATAAATCTTGTTTCGATTTAATTAG
127 CTCATCCACATTGGATTTAAGGATTTATTTTTACAAGATTTTGAATCTTGTTTCGATTTAATTAG
* * *
272 AAATAAATTCGGGAAAAATGGAAAAAAATGATATTAGAAGCGTCAAAAACCCTTTAATTTTTTTG
192 TAATAAATTCGGGAAAAATGGAAAAAAACGATATTAGAAGCGTGAAAAACCCTTTAATTTTTTTG
* * *
337 CGTTGAATTATACATTATTTCTGAGTATTGTGGCAAAGATTTGAGGAAAAAAATTTTCGGGTCAG
257 CGTTGAATTATACATTATTTCTGAGTATTGTGGCAAAGAATTAAGGAAAAAAAATTTCGGGTCAG
402 TTTTGGAAAAA
322 TTTTGGAAAAA
*
413 TTTTAGTCGAAATCGTGTATTAACCATCACAGTTTTTGCCAAAAACGCATTCTGGGG-CCCGGAT
1 TTTTAGTCGAAATCGTGTACTAACCATCACAGTTTTTGCCAAAAACGCATTCTGGGGCCCCGGAT
* *
477 CAGTTTCGCATGATTTTTGGCAAAAAGACTCCTTCAAATATCTATATTCATCTAACCAAATCTCA
66 CAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTCAAATATCTATATTCATCTAACCAAATCTCA
* * ** * *
542 TCCACATTGAATTGAACTATTTATTTTTATAAGATTTTGAATCTTGATTCGATTTAATTAGTAAT
131 TCCACATTGGATTTAAGGATTTATTTTTACAAGATTTTGAATCTTGTTTCGATTTAATTAGTAAT
** *
607 AAATTCGGGAAAAATTTTTTTTAAAAAAAACGATATTAGCAGCGTGAAAAACCCTTTAATTTTTT
196 AAATTCGGGAAAAA------TGGAAAAAAACGATATTAGAAGCGTGAAAAACCCTTTAATTTTTT
* * * * * *
672 T-TGATGAATTATAC-TTTTTTCTGAGTATTGAGGCAAATAATTGAGGAAAAAAAATTTCGGGTC
255 TGCGTTGAATTATACATTATTTCTGAGTATTGTGGCAAAGAATTAAGGAAAAAAAATTTCGGGTC
735 AGTTTTGGAAAAA
320 AGTTTTGGAAAAA
*
748 TTTTAGTCGAAATCGTGTACTAACAACCATCACAGTTTTTGCAAAAAACGCATTCTGGGGCCCCG
1 TTTTAGTCGAAATCGTGTACT---AACCATCACAGTTTTTGCCAAAAACGCATTCTGGGGCCCCG
813 GATCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTCAAATATCTATATTCATCTAACCAAATC
63 GATCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTCAAATATCTATATTCATCTAACCAAATC
* * * * *
878 TCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCTTATGAATCTTGTTTCGATTTAATTAGT
128 TCATCCACATTGGATTTAAGGATTTATTTTTACAAGATTTTGAATCTTGTTTCGATTTAATTAGT
* *
943 AATAAATTCGGGAAAAATGG-AAAAAACGATATTAGAAGCATGAAAAACCCTTTAAATTTTTTGC
193 AATAAATTCGGGAAAAATGGAAAAAAACGATATTAGAAGCGTGAAAAACCCTTTAATTTTTTTGC
* * *
1007 GTTGAATTATACATTATTTCTGAGTATTTTGGCAAAGAATTGAGGGAAAAAAATTTCGGGTCAGT
258 GTTGAATTATACATTATTTCTGAGTATTGTGGCAAAGAATTAAGGAAAAAAAATTTCGGGTCAGT
*
1072 TTTGGCAAAA
323 TTTGGAAAAA
* * * * *
1082 TTTTGGTCGAAATCATGTACTAATCATCACAGTTTTTGCCAAAAACGCATTTTGGGGCCCTGGAT
1 TTTTAGTCGAAATCGTGTACTAACCATCACAGTTTTTGCCAAAAACGCATTCTGGGGCCCCGGAT
*
1147 CAGTTTTGCATGATTTTTGGCAAAAAGACTCCTTCAAATATCTATATTCATCTAACCAAATCTCA
66 CAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTCAAATATCTATATTCATCTAACCAAATCTCA
* *
1212 TCCACATTGAATTTAAGGATTTATTTTTACAAGATTTTGAATCTTGTTTCGATTTAATTGGTAAT
131 TCCACATTGGATTTAAGGATTTATTTTTACAAGATTTTGAATCTTGTTTCGATTTAATTAGTAAT
1277 AAATTCGGGAAAAATGGAAAAAAACGATATTAGAAGCGTGAAAAACCCTTTAATTTTTTTCGCGT
196 AAATTCGGGAAAAATGGAAAAAAACGATATTAGAAGCGTGAAAAACCCTTTAATTTTTTT-GCGT
* *
1342 TGAATTATACATTATTTCTAAGTATTGTGGCAAAGAATTAAGG-AAAAAACTTTCGGGTCAGTTT
260 TGAATTATACATTATTTCTGAGTATTGTGGCAAAGAATTAAGGAAAAAAAATTTCGGGTCAGTTT
*
1406 TGGCAAAA
325 TGGAAAAA
* *
1414 TTTTAGTCGAAATCGTGTACTAACCATCACAGTTTTTTGCTAAATACGCATTCTGGGGCCCCGGA
1 TTTTAGTCGAAATCGTGTACTAACCATCACAG-TTTTTGCCAAAAACGCATTCTGGGGCCCCGGA
* * *
1479 TCAGTATTGCATGATTTATGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTC
65 TCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTCAAATATCTATATTCATCTAACCAAATCTC
* *
1544 ATCCACAATGGATTTAAGGATTTATTTTTACAAGATTTTGAATCTTGTTTCGATTTAATTGGTAA
130 ATCCACATTGGATTTAAGGATTTATTTTTACAAGATTTTGAATCTTGTTTCGATTTAATTAGTAA
* *
1609 TAAATTCGGGAAAAATGAAAAAAAAAAAACCGATATTAGAAGCATGAAAAACCCTT
195 TAAATTCGGGAAAAATG----GAAAAAAA-CGATATTAGAAGCGTGAAAAACCCTT
1665 GAAATATCTA
Statistics
Matches: 1130, Mismatches: 100, Indels: 40
0.89 0.08 0.03
Matches are distributed among these distances:
330 2 0.00
331 310 0.27
332 148 0.13
333 225 0.20
334 111 0.10
335 77 0.07
336 11 0.01
337 48 0.04
338 60 0.05
339 138 0.12
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (332 bp):
TTTTAGTCGAAATCGTGTACTAACCATCACAGTTTTTGCCAAAAACGCATTCTGGGGCCCCGGAT
CAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTCAAATATCTATATTCATCTAACCAAATCTCA
TCCACATTGGATTTAAGGATTTATTTTTACAAGATTTTGAATCTTGTTTCGATTTAATTAGTAAT
AAATTCGGGAAAAATGGAAAAAAACGATATTAGAAGCGTGAAAAACCCTTTAATTTTTTTGCGTT
GAATTATACATTATTTCTGAGTATTGTGGCAAAGAATTAAGGAAAAAAAATTTCGGGTCAGTTTT
GGAAAAA
Found at i:18076 original size:1 final size:1
Alignment explanation
Indices: 18070--18094 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
18060 AATAAATTTG
18070 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
18095 GGTTATAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:23203 original size:3 final size:3
Alignment explanation
Indices: 23197--23231 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
23187 AACTTTTCTC
23197 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
23232 GAGGGGATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:23625 original size:3 final size:3
Alignment explanation
Indices: 23619--23646 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
23609 ATCCCTCCTC
23619 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
23647 TATCTAATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:23938 original size:55 final size:55
Alignment explanation
Indices: 23854--23961 Score: 207
Period size: 55 Copynumber: 2.0 Consensus size: 55
23844 GTCTCAAATG
*
23854 ATGTGTCATGTGGAATCATCTCATGTTTTGTAGCAAAACTCCATTTAATTAGTAT
1 ATGTGTCATGTGGAATCATCTCATGTTTTGTAGCAAAACTCCATTTAAATAGTAT
23909 ATGTGTCATGTGGAATCATCTCATGTTTTGTAGCAAAACTCCATTTAAATAGT
1 ATGTGTCATGTGGAATCATCTCATGTTTTGTAGCAAAACTCCATTTAAATAGT
23962 GTTGGGACCA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.39
Consensus pattern (55 bp):
ATGTGTCATGTGGAATCATCTCATGTTTTGTAGCAAAACTCCATTTAAATAGTAT
Found at i:33292 original size:18 final size:18
Alignment explanation
Indices: 33266--33305 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
33256 TTATTTTTAT
*
33266 TGTCCATAAATGGGTATG
1 TGTCAATAAATGGGTATG
33284 TGTCAATAAATGGGTATG
1 TGTCAATAAATGGGTATG
33302 TGTC
1 TGTC
33306 CACTTCACAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.28, C:0.10, G:0.28, T:0.35
Consensus pattern (18 bp):
TGTCAATAAATGGGTATG
Found at i:44595 original size:15 final size:16
Alignment explanation
Indices: 44566--44599 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
44556 AGCCCCATCT
*
44566 AAGCAAAAGCCAGATG
1 AAGCAAAAGCAAGATG
44582 AAGC-AAAGCAAGATG
1 AAGCAAAAGCAAGATG
44597 AAG
1 AAG
44600 GCTCAGATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.53, C:0.15, G:0.26, T:0.06
Consensus pattern (16 bp):
AAGCAAAAGCAAGATG
Found at i:57970 original size:21 final size:21
Alignment explanation
Indices: 57945--58027 Score: 64
Period size: 22 Copynumber: 3.8 Consensus size: 21
57935 TATCTTAGAT
57945 ATAAT-ATATATTATTAAATAA
1 ATAATAATATATT-TTAAATAA
57966 ATAATAAATATATTTTAAAT-A
1 ATAAT-AATATATTTTAAATAA
* **
57987 ATAAATAATGA-GTTCAAAATAA
1 AT-AATAAT-ATATTTTAAATAA
58009 ATAAATAATATATATTTAA
1 AT-AATAATATAT-TTTAA
58028 TTACTAAACG
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
21 18 0.37
22 21 0.43
23 10 0.20
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (21 bp):
ATAATAATATATTTTAAATAA
Found at i:57978 original size:25 final size:25
Alignment explanation
Indices: 57947--57995 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
57937 TCTTAGATAT
*
57947 AATATATATT-ATTAAATAAATAATA
1 AATATATATTAAAT-AATAAATAATA
*
57972 AATATATTTTAAATAATAAATAAT
1 AATATATATTAAATAATAAATAAT
57996 GAGTTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AATATATATTAAATAATAAATAATA
Found at i:60689 original size:6 final size:6
Alignment explanation
Indices: 60680--60705 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
60670 ATATATATTT
60680 ATATGA ATATGA ATATGA ATATGA AT
1 ATATGA ATATGA ATATGA ATATGA AT
60706 TACTAATTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (6 bp):
ATATGA
Found at i:63262 original size:2 final size:2
Alignment explanation
Indices: 63220--63244 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
63210 CAACATATTT
63220 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
63245 TATGAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:66666 original size:3 final size:3
Alignment explanation
Indices: 66658--66696 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
66648 ACAAATCATA
66658 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
66697 AATAATGTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:70204 original size:32 final size:32
Alignment explanation
Indices: 70160--70225 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
70150 TTAAGAGGGG
70160 ATTTTGGACATTAAACCTTTACGTAAACCATC
1 ATTTTGGACATTAAACCTTTACGTAAACCATC
* *
70192 ATTTTGGGCATTAAGCCTTTACGTAAACCATC
1 ATTTTGGACATTAAACCTTTACGTAAACCATC
70224 AT
1 AT
70226 GTCATCTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (32 bp):
ATTTTGGACATTAAACCTTTACGTAAACCATC
Found at i:75075 original size:20 final size:21
Alignment explanation
Indices: 75044--75111 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 21
75034 TGAACTACCT
75044 ATAAACTAAACTCATACACAA
1 ATAAACTAAACTCATACACAA
*
75065 ATAAA-TAAA--C-TAC-C-T
1 ATAAACTAAACTCATACACAA
75080 ATAAACTAAACTCATACACAA
1 ATAAACTAAACTCATACACAA
75101 ATAAA-TAAACT
1 ATAAACTAAACT
75112 ACAAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 13
0.72 0.04 0.24
Matches are distributed among these distances:
15 5 0.13
16 5 0.13
17 3 0.08
18 2 0.05
19 3 0.08
20 11 0.28
21 10 0.26
ACGTcount: A:0.57, C:0.21, G:0.00, T:0.22
Consensus pattern (21 bp):
ATAAACTAAACTCATACACAA
Found at i:75083 original size:36 final size:36
Alignment explanation
Indices: 75036--75113 Score: 156
Period size: 36 Copynumber: 2.2 Consensus size: 36
75026 AAAAAGAATG
75036 AACTACCTATAAACTAAACTCATACACAAATAAATA
1 AACTACCTATAAACTAAACTCATACACAAATAAATA
75072 AACTACCTATAAACTAAACTCATACACAAATAAATA
1 AACTACCTATAAACTAAACTCATACACAAATAAATA
75108 AACTAC
1 AACTAC
75114 AAATTAAACT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.55, C:0.23, G:0.00, T:0.22
Consensus pattern (36 bp):
AACTACCTATAAACTAAACTCATACACAAATAAATA
Found at i:75122 original size:32 final size:34
Alignment explanation
Indices: 75036--75125 Score: 121
Period size: 36 Copynumber: 2.6 Consensus size: 34
75026 AAAAAGAATG
75036 AACTACCTATAAACTAAACTCATACACAAATAAATA
1 AACTACC--TAAACTAAACTCATACACAAATAAATA
75072 AACTACCTATAAACTAAACTCATACACAAATAAATA
1 AACTACC--TAAACTAAACTCATACACAAATAAATA
*
75108 AACTA-C-AAATTAAACTCA
1 AACTACCTAAACTAAACTCA
75126 CATTCCGTGA
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
32 11 0.21
35 1 0.02
36 41 0.77
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (34 bp):
AACTACCTAAACTAAACTCATACACAAATAAATA
Found at i:77033 original size:3 final size:3
Alignment explanation
Indices: 77007--77047 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
76997 AAATGAATTC
* *
77007 TAA TAA T-A TAA TAC TAA TAC TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
77048 AGCCACCCTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:77996 original size:2 final size:2
Alignment explanation
Indices: 77985--78023 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
77975 ATATGAGCAG
77985 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
78024 ATGGGAAATC
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Done.