Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01007184.1 Corchorus olitorius cultivar O-4 contig07209, 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, 825
Length: 1375
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.31
Found at i:415 original size:2 final size:2
Alignment explanation
Indices: 408--469 Score: 88
Period size: 2 Copynumber: 29.5 Consensus size: 2
398 AAACCACATA
*
408 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT AGAA GAT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT -G-T G-T GT GT GT
451 GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT G
470 AAGCTATGAA
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
2 52 0.93
3 4 0.07
ACGTcount: A:0.06, C:0.00, G:0.48, T:0.45
Consensus pattern (2 bp):
GT
Found at i:1002 original size:94 final size:94
Alignment explanation
Indices: 826--1002 Score: 225
Period size: 94 Copynumber: 1.9 Consensus size: 94
816 TTTCCTAAAA
*
826 AGGTTAACAAAATTTCATAGGGAGGTTATGAAAATTTTATGGAGAGGTTATCAAAATTATATAGA
1 AGGTTAACAAAATTTCATAGGGAGGTTATCAAAATTTTATGGAGAGGTTATCAAAATTATATAGA
***
891 GAAGATATCACGGTTTCATTCTCATAGGG
66 GAAGATATCAAAATTTCATTCTCATAGGG
* * * *
920 AGGTTATCTAAATTTCAT-GGTGTGGTTATCAAAATTTTAT-GAGGAGGTTATCAAAATTTTATA
1 AGGTTAACAAAATTTCATAGG-GAGGTTATCAAAATTTTATGGA-GAGGTTATCAAAATTATATA
*
983 G-GGAGATTATCAAAATTTCA
64 GAGAAGA-TATCAAAATTTCA
1003 CAATGAGGTT
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
93 8 0.11
94 63 0.89
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.35
Consensus pattern (94 bp):
AGGTTAACAAAATTTCATAGGGAGGTTATCAAAATTTTATGGAGAGGTTATCAAAATTATATAGA
GAAGATATCAAAATTTCATTCTCATAGGG
Found at i:1034 original size:22 final size:22
Alignment explanation
Indices: 630--1107 Score: 220
Period size: 22 Copynumber: 21.5 Consensus size: 22
620 TTACATGAGA
**
630 AGGTTATCAAAATTTCATACAG
1 AGGTTATCAAAATTTCATAGTG
* ***
652 AGGTTACCAAAATTTCATAAAA
1 AGGTTATCAAAATTTCATAGTG
* *
674 AGGTTATCAAAATTTCTTAGGG
1 AGGTTATCAAAATTTCATAGTG
* * ***
696 AGGTTAACAAAATATCATACAA
1 AGGTTATCAAAATTTCATAGTG
* *
718 AGGTTATCGAAATTTTATAGTG
1 AGGTTATCAAAATTTCATAGTG
* *
740 TA-GTTATCAAAATTTAATAAG-A
1 -AGGTTATCAAAATTTCAT-AGTG
* *
762 AGGTTAACAAAATTTCATAGGGAGG
1 AGGTTATCAAAATTTCATA--G-TG
787 AAGGTTATCAAAA-TT--T-GT-
1 -AGGTTATCAAAATTTCATAGTG
* * * ***
805 -GCTTATTAAAATTTCCTAAAA
1 AGGTTATCAAAATTTCATAGTG
* *
826 AGGTTAACAAAATTTCATAGGG
1 AGGTTATCAAAATTTCATAGTG
* * * *
848 AGGTTATGAAAATTTTATGGAG
1 AGGTTATCAAAATTTCATAGTG
*
870 AGGTTATCAAAATTAT-ATAGAG
1 AGGTTATCAAAATT-TCATAGTG
* * ** *
892 AAGATATCACGGTTTCATTCTCATAGGG
1 AGGTTATCA-----AAATT-TCATAGTG
* *
920 AGGTTATCTAAATTTCATGGTG
1 AGGTTATCAAAATTTCATAGTG
* *
942 TGGTTATCAAAATTTTATGAG-G
1 AGGTTATCAAAATTTCAT-AGTG
* *
964 AGGTTATCAAAATTTTATAGGG
1 AGGTTATCAAAATTTCATAGTG
* * *
986 AGATTATCAAAATTTCACAATG
1 AGGTTATCAAAATTTCATAGTG
1008 AGGTTATCAAAATTTCATAGTG
1 AGGTTATCAAAATTTCATAGTG
* * * **
1030 TGGTTATTAAGATTTCACCGTG
1 AGGTTATCAAAATTTCATAGTG
* * * *
1052 TGGTTATCAAATTTTCACAGGG
1 AGGTTATCAAAATTTCATAGTG
** * *
1074 AGGTTATCGACCATTTCATAATA
1 AGGTTATC-AAAATTTCATAGTG
1097 AGGTTATCAAA
1 AGGTTATCAAA
1108 TGTTCACAGT
Statistics
Matches: 339, Mismatches: 93, Indels: 48
0.71 0.19 0.10
Matches are distributed among these distances:
16 9 0.03
17 2 0.01
19 1 0.00
20 1 0.00
21 4 0.01
22 269 0.79
23 25 0.07
25 2 0.01
26 11 0.03
27 4 0.01
28 11 0.03
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGTG
Found at i:1045 original size:44 final size:44
Alignment explanation
Indices: 919--1135 Score: 166
Period size: 44 Copynumber: 4.9 Consensus size: 44
909 TTCTCATAGG
* * * ** *
919 GAGGTTATCTAAATTTCATGGTGTGGTTATCAAAATTTTATGAG
1 GAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCACAAT
* * * *
963 GAGGTTATCAAAATTTTATAGGGAGATTATCAAAATTTCACAAT
1 GAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCACAAT
* * **
1007 GAGGTTATCAAAATTTCATAGTGTGGTTATTAAGATTTCACCGT
1 GAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCACAAT
* * * * * ** *
1051 GTGGTTATCAAATTTTCACAGGGAGGTTATCGACCATTTCATAAT
1 GAGGTTATCAAAATTTCATAGTGTGGTTATC-AAAATTTCACAAT
* * * * *
1096 AAGGTTATC-AAATGTTCACAGTATTGTTATCAATATTTCA
1 GAGGTTATCAAAAT-TTCATAGTGTGGTTATCAAAATTTCA
1136 ACGTTGGAGC
Statistics
Matches: 133, Mismatches: 38, Indels: 4
0.76 0.22 0.02
Matches are distributed among these distances:
44 105 0.79
45 28 0.21
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (44 bp):
GAGGTTATCAAAATTTCATAGTGTGGTTATCAAAATTTCACAAT
Found at i:1125 original size:89 final size:88
Alignment explanation
Indices: 965--1135 Score: 202
Period size: 89 Copynumber: 1.9 Consensus size: 88
955 TTTATGAGGA
* * * *
965 GGTTATCAAAATTTTATAGGGAGATTATCAAAATTTCACAATGAGGTTATCAAAATTTCATAGTG
1 GGTTATCAAAATTTTACAGGGAGATTATCAAAATTTCACAATAAGGTTATCAAAATTTCACAGTA
*
1030 TGGTTATTAAGATTTCACCGTGT
66 TGGTTATCAAGATTTCACCGTGT
* ** *
1053 GGTTATC-AAATTTTCACAGGGAGGTTATCGACCATTTCATAATAAGGTTATC-AAATGTTCACA
1 GGTTATCAAAATTTT-ACAGGGAGATTATC-AAAATTTCACAATAAGGTTATCAAAAT-TTCACA
* *
1116 GTATTGTTATCAATATTTCA
63 GTATGGTTATCAAGATTTCA
1136 ACGTTGGAGC
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
87 7 0.10
88 23 0.33
89 39 0.57
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.37
Consensus pattern (88 bp):
GGTTATCAAAATTTTACAGGGAGATTATCAAAATTTCACAATAAGGTTATCAAAATTTCACAGTA
TGGTTATCAAGATTTCACCGTGT
Done.