Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013034.1 Corchorus olitorius cultivar O-4 contig13067, 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: 11843
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Found at i:793 original size:22 final size:22
Alignment explanation
Indices: 765--1211 Score: 121
Period size: 22 Copynumber: 20.1 Consensus size: 22
755 ACGATTATCA
* *
765 AAAATTTCGTAGTGTGGTTACC
1 AAAATTTCATAGTGAGGTTACC
* *
787 AAAATTTCATA-TAGAGATTATC
1 AAAATTTCATAGT-GAGGTTACC
* *
809 AAAACTTCATAGTGTA-GTTATC
1 AAAATTTCATAGTG-AGGTTACC
**
831 AAAATTTCATACAGAGGTTACC
1 AAAATTTCATAGTGAGGTTACC
*
853 AAAATTTCATAGGGAGGGAGGTTACC
1 AAAATTTCAT----AGTGAGGTTACC
* *
879 AAAA-TT--T-GT--GCTTATC
1 AAAATTTCATAGTGAGGTTACC
* * *
895 AAAATTTCCTAGAGAGGTTAAC
1 AAAATTTCATAGTGAGGTTACC
* * **
917 AAAATTTTATAGGGAGGTTATG
1 AAAATTTCATAGTGAGGTTACC
* * * *
939 AAAATTTTATGGAGAGGTTATCG
1 AAAATTTCATAGTGAGGTTA-CC
* * *
962 AAAA-TACATAGAGAGGATATCAC
1 AAAATTTCATAGTGAGGTTA-C-C
** * *
985 AGTTTCATTCTCATAGGGAGGTTATC
1 A---AAATT-TCATAGTGAGGTTACC
* * * *
1011 GAAATTTCATGGTGTGGTTATC
1 AAAATTTCATAGTGAGGTTACC
*
1033 AAAATTTTCATAGTGCGGTTACC
1 AAAA-TTTCATAGTGAGGTTACC
* * * **
1056 --AATTTTATTTAGTGTGATTATT
1 AAAATTTCA--TAGTGAGGTTACC
* * *
1078 AAAATTTTATAG-GCAGATTATC
1 AAAATTTCATAGTG-AGGTTACC
* * * *
1100 AAAATTTCACACTGAGATTATC
1 AAAATTTCATAGTGAGGTTACC
* *
1122 GAAATTTCATAGTGTGGTTACC
1 AAAATTTCATAGTGAGGTTACC
* * *
1144 CAAATTTCATAGTGTGGTTATC
1 AAAATTTCATAGTGAGGTTACC
* * *
1166 GAATTTTCATAAG-GAGGTTATC
1 AAAATTTCAT-AGTGAGGTTACC
* * *
1188 GAAATTTCATA-TTAGGTTATC
1 AAAATTTCATAGTGAGGTTACC
1209 AAA
1 AAA
1212 TTTGCAAAAT
Statistics
Matches: 324, Mismatches: 71, Indels: 61
0.71 0.16 0.13
Matches are distributed among these distances:
16 9 0.03
17 2 0.01
18 1 0.00
19 1 0.00
20 5 0.02
21 16 0.05
22 223 0.69
23 30 0.09
24 7 0.02
25 2 0.01
26 16 0.05
27 1 0.00
28 11 0.03
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (22 bp):
AAAATTTCATAGTGAGGTTACC
Found at i:837 original size:44 final size:44
Alignment explanation
Indices: 739--864 Score: 146
Period size: 44 Copynumber: 2.8 Consensus size: 44
729 TGACAATCAA
* * * *
739 ACCAAAATTACATAGA-ACGATTATCAAAAATTTCGTAGTGTGGTT
1 ACCAAAATTTCATACAGA-GATTATC-AAAATTTCATAGTGTAGTT
* *
784 ACCAAAATTTCATATAGAGATTATCAAAACTTCATAGTGTAGTT
1 ACCAAAATTTCATACAGAGATTATCAAAATTTCATAGTGTAGTT
* * *
828 ATCAAAATTTCATACAGAGGTTACCAAAATTTCATAG
1 ACCAAAATTTCATACAGAGATTATCAAAATTTCATAG
865 GGAGGGAGGT
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
44 48 0.69
45 21 0.30
46 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.32
Consensus pattern (44 bp):
ACCAAAATTTCATACAGAGATTATCAAAATTTCATAGTGTAGTT
Found at i:1165 original size:66 final size:65
Alignment explanation
Indices: 1095--1238 Score: 157
Period size: 66 Copynumber: 2.2 Consensus size: 65
1085 TATAGGCAGA
** * *
1095 TTATCAAAATTTCACACTGAGATTATCGAAATTTCATAGTGT-GGTTACCCAAATTT-CATAGTG
1 TTATCAAAATTTCACAAGGAGATTATCGAAATTTCATA-T-TAGGTTA-CCAAATTTGCAAAATG
1158 TGG
63 TGG
* * * * *
1161 TTATCGAATTTTCATAAGGAGGTTATCGAAATTTCATATTAGGTTATCAAATTTGCAAAATGTGG
1 TTATCAAAATTTCACAAGGAGATTATCGAAATTTCATATTAGGTTACCAAATTTGCAAAATGTGG
*
1226 TTATCAATATTTC
1 TTATCAAAATTTC
1239 TACATTGGAG
Statistics
Matches: 64, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
64 8 0.12
65 24 0.38
66 32 0.50
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.39
Consensus pattern (65 bp):
TTATCAAAATTTCACAAGGAGATTATCGAAATTTCATATTAGGTTACCAAATTTGCAAAATGTGG
Found at i:1185 original size:44 final size:43
Alignment explanation
Indices: 995--1214 Score: 155
Period size: 44 Copynumber: 5.0 Consensus size: 43
985 AGTTTCATTC
* *
995 TCATAGGGAGGTTATCGAAATTTCATGGTGTGGTTATCAAAATTT
1 TCATA-GGAGGTTATCCAAATTTCATAGTGTGGTTATC-AAATTT
* * * *
1040 TCATAGTGCGGTTA-CC-AATTTTATTTAGTGTGATTATTAAAATTT
1 TCATAG-GAGGTTATCCAAATTTCA--TAGTGTGGTTA-TCAAATTT
* * * * * *
1085 T-ATAGGCAGATTATCAAAATTTCACACTGAGATTATCGAAA-TT
1 TCATAGG-AGGTTATCCAAATTTCATAGTGTGGTTATC-AAATTT
* * *
1128 TCATAGTGTGGTTACCCAAATTTCATAGTGTGGTTATCGAATTT
1 TCATAG-GAGGTTATCCAAATTTCATAGTGTGGTTATCAAATTT
*
1172 TCATAAGGAGGTTATCGAAATTTCATA-T-TAGGTTATCAAATTT
1 TCAT-AGGAGGTTATCCAAATTTCATAGTGT-GGTTATCAAATTT
1215 GCAAAATGTG
Statistics
Matches: 135, Mismatches: 27, Indels: 28
0.71 0.14 0.15
Matches are distributed among these distances:
42 1 0.01
43 26 0.19
44 70 0.52
45 31 0.23
46 7 0.05
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (43 bp):
TCATAGGAGGTTATCCAAATTTCATAGTGTGGTTATCAAATTT
Found at i:1228 original size:43 final size:42
Alignment explanation
Indices: 1004--1238 Score: 118
Period size: 44 Copynumber: 5.3 Consensus size: 42
994 CTCATAGGGA
* * *
1004 GGTTATCGAAATTTCATGGTGTGGTTATCAAAATTTTCATAGTGC
1 GGTTATC-AAATTTCATAGTGTGGTTATC-AAA-TTTCATAATGT
* * * * * * *
1049 GGTTA-CCAATTTTATTTAGTGTGATTATTAAAATTTTAT-AGGCA
1 GGTTATCAAATTTCA--TAGTGTGGTTA-TCAAATTTCATAATG-T
* * * * * *
1093 GATTATCAAAATTTCACACTGAGATTATCGAAATTTCATAGTGT
1 GGTTATC-AAATTTCATAGTGTGGTTATC-AAATTTCATAATGT
* * * *
1137 GGTTACCCAAATTTCATAGTGTGGTTATCGAATTTTCATAAGGA
1 GGTTA-TCAAATTTCATAGTGTGGTTATC-AAATTTCATAATGT
*
1181 GGTTATCGAAATTTCATA-T-TAGGTTATCAAATTTGCAAAATGT
1 GGTTATC-AAATTTCATAGTGT-GGTTATCAAATTT-CATAATGT
1224 GGTTATCAATATTTC
1 GGTTATCAA-ATTTC
1239 TACATTGGAG
Statistics
Matches: 142, Mismatches: 35, Indels: 28
0.69 0.17 0.14
Matches are distributed among these distances:
42 8 0.06
43 34 0.24
44 73 0.51
45 20 0.14
46 7 0.05
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.40
Consensus pattern (42 bp):
GGTTATCAAATTTCATAGTGTGGTTATCAAATTTCATAATGT
Found at i:1229 original size:22 final size:21
Alignment explanation
Indices: 1117--1238 Score: 104
Period size: 22 Copynumber: 5.6 Consensus size: 21
1107 CACACTGAGA
*
1117 TTATCGAAATTTCATAGTGTGG
1 TTATC-AAATTTCATAATGTGG
* *
1139 TTACCCAAATTTCATAGTGTGG
1 TTA-TCAAATTTCATAATGTGG
* * *
1161 TTATCGAATTTTCATAAGGAGG
1 TTATC-AAATTTCATAATGTGG
1183 TTATCGAAATTTCAT-AT-TAGG
1 TTATC-AAATTTCATAATGT-GG
*
1204 TTATCAAATTTGCAAAATGTGG
1 TTATCAAATTT-CATAATGTGG
1226 TTATCAATATTTC
1 TTATCAA-ATTTC
1239 TACATTGGAG
Statistics
Matches: 83, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
20 6 0.07
21 11 0.13
22 60 0.72
23 6 0.07
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.40
Consensus pattern (21 bp):
TTATCAAATTTCATAATGTGG
Found at i:3031 original size:44 final size:42
Alignment explanation
Indices: 2983--3087 Score: 129
Period size: 44 Copynumber: 2.5 Consensus size: 42
2973 TTACATGGTA
* **
2983 AGGTTATTAAAATTTCATAGTGTGGTTACCAAAATTTCATATGG
1 AGGTTATCAAAATTTCATAGTGTAATTACCAAAATTTCATA--G
* * *
3027 AGGTTATCAAAACTTCGTAGTGTAATTATCAAAATTTCATAG
1 AGGTTATCAAAATTTCATAGTGTAATTACCAAAATTTCATAG
*
3069 AGGTTACCAAAATTTCATA
1 AGGTTATCAAAATTTCATA
3088 AAAAAAAGTT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 17 0.33
44 35 0.67
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.36
Consensus pattern (42 bp):
AGGTTATCAAAATTTCATAGTGTAATTACCAAAATTTCATAG
Found at i:3099 original size:66 final size:65
Alignment explanation
Indices: 2986--3142 Score: 158
Period size: 66 Copynumber: 2.4 Consensus size: 65
2976 CATGGTAAGG
* * * *** * *
2986 TTATTAAAATTTCATAGTGTGGTTACCAAAATTTCATATGGAGGTTATCAAAA-CTTCGTAGTGT
1 TTATCAAAATTTCATA-CGAGGTTACCAAAATTTCATAAAAAAGTTATCAAAATC-TCGTA-TGG
3050 A-A
63 AGA
*
3052 TTATCAAAATTTCATA-GAGGTTACCAAAATTTCATAAAAAAAAGTTATCAAAATCTCTTATGGA
1 TTATCAAAATTTCATACGAGGTTACCAAAATTTCAT--AAAAAAGTTATCAAAATCTCGTATGGA
3116 GA
64 GA
3118 TTATCAAAATTTCATACGAAGGTTA
1 TTATCAAAATTTCATACG-AGGTTA
3143 TTGAAATTTT
Statistics
Matches: 77, Mismatches: 8, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
64 18 0.23
65 3 0.04
66 48 0.62
67 2 0.03
68 6 0.08
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.35
Consensus pattern (65 bp):
TTATCAAAATTTCATACGAGGTTACCAAAATTTCATAAAAAAGTTATCAAAATCTCGTATGGAGA
Found at i:3143 original size:22 final size:22
Alignment explanation
Indices: 2982--3143 Score: 109
Period size: 22 Copynumber: 7.4 Consensus size: 22
2972 ATTACATGGT
*
2982 AAGGTTATTAAAATTTCATAGTG
1 AAGGTTATCAAAATTTCATA-TG
* *
3005 -TGGTTACCAAAATTTCATATG
1 AAGGTTATCAAAATTTCATATG
* * *
3026 GAGGTTATCAAAACTTCGTAGTG
1 AAGGTTATCAAAATTTCATA-TG
3049 TAA--TTATCAAAATTTCATA-G
1 -AAGGTTATCAAAATTTCATATG
* **
3069 -AGGTTACCAAAATTTCATAAAAA
1 AAGGTTATCAAAATTTCAT--ATG
* * *
3092 AAAGTTATCAAAATCTCTTATG
1 AAGGTTATCAAAATTTCATATG
* * *
3114 GAGATTATCAAAATTTCATACG
1 AAGGTTATCAAAATTTCATATG
3136 AAGGTTAT
1 AAGGTTAT
3144 TGAAATTTTA
Statistics
Matches: 104, Mismatches: 26, Indels: 19
0.70 0.17 0.13
Matches are distributed among these distances:
18 1 0.01
20 15 0.14
21 2 0.02
22 69 0.66
23 2 0.02
24 15 0.14
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (22 bp):
AAGGTTATCAAAATTTCATATG
Found at i:3346 original size:22 final size:22
Alignment explanation
Indices: 3314--3550 Score: 163
Period size: 22 Copynumber: 10.6 Consensus size: 22
3304 TTATAGGTAA
* *
3314 GTTATCGAAATTTCATGGTGTG
1 GTTATCAAAATTTCATAGTGTG
*
3336 GTTATCAAAATTTTCATAGTGCG
1 GTTATCAAAA-TTTCATAGTGTG
* * * * *
3359 ATTA-C-CAGTTTTATAATGTG
1 GTTATCAAAATTTCATAGTGTG
* *
3379 ATTATCAAAATTTCATAGACAATGAG
1 GTTATCAAAATTTCATAG----TGTG
* * *
3405 ATTATCAAAACTTCATTGTGTG
1 GTTATCAAAATTTCATAGTGTG
* *
3427 GTTATCAGAATTTCACAGTGTG
1 GTTATCAAAATTTCATAGTGTG
*
3449 GTTATCAAAATTTCACAGTGTG
1 GTTATCAAAATTTCATAGTGTG
* * *
3471 GTTATCAAATTTTCATAGGGAG
1 GTTATCAAAATTTCATAGTGTG
* * * *
3493 GTTATCGAAATTTCACAATGAG
1 GTTATCAAAATTTCATAGTGTG
* ***
3515 GTTATCAAATTTTCGCGGTGTG
1 GTTATCAAAATTTCATAGTGTG
*
3537 GTTATCAATATTTC
1 GTTATCAAAATTTC
3551 TATGTTGGAG
Statistics
Matches: 168, Mismatches: 40, Indels: 14
0.76 0.18 0.06
Matches are distributed among these distances:
20 13 0.08
21 2 0.01
22 121 0.72
23 13 0.08
26 19 0.11
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGTGTG
Found at i:5039 original size:19 final size:19
Alignment explanation
Indices: 5015--5054 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
5005 ATTCTAATGT
5015 CTATTCAAATAATTATCTA
1 CTATTCAAATAATTATCTA
5034 CTATTCAAATAATTATCTA
1 CTATTCAAATAATTATCTA
5053 CT
1 CT
5055 GGATCCCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.42
Consensus pattern (19 bp):
CTATTCAAATAATTATCTA
Done.