Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01001339.1 Corchorus olitorius cultivar O-4 contig01339, 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, 942
Length: 1571
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:882 original size:32 final size:32
Alignment explanation
Indices: 826--952 Score: 121
Period size: 32 Copynumber: 3.9 Consensus size: 32
816 TTTTGAAAGG
* * **
826 TAAAATCATGACAACTTCTGGTGTCAATTGAA
1 TAAAATTATGACATCTTCAAGTGTCAATTGAA
* *
858 TAAAATTATGATATCTTCAAGTGTCTATTGGAA
1 TAAAATTATGACATCTTCAAGTGTCAATT-GAA
** * * **
891 -ATTTATCATGACAACTTCTGGTGTCAATTGAA
1 TA-AAATTATGACATCTTCAAGTGTCAATTGAA
923 TAAAATTATGACATCTTCAAGTGTCAATTG
1 TAAAATTATGACATCTTCAAGTGTCAATTG
953 CAAGATCATG
Statistics
Matches: 72, Mismatches: 20, Indels: 6
0.73 0.20 0.06
Matches are distributed among these distances:
32 49 0.68
33 23 0.32
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.36
Consensus pattern (32 bp):
TAAAATTATGACATCTTCAAGTGTCAATTGAA
Found at i:906 original size:65 final size:62
Alignment explanation
Indices: 830--982 Score: 234
Period size: 65 Copynumber: 2.4 Consensus size: 62
820 GAAAGGTAAA
* * *
830 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGATATCTTCAAGTGTCTATTGGAAATTT
1 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAGTGTCAATT-GAAA--G
*
895 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAGTGTCAATTGAAAG
*
957 ATCATGACAACTTATGGTGTCAATTG
1 ATCATGACAACTTCTGGTGTCAATTG
983 CAAGATCATG
Statistics
Matches: 83, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
62 25 0.30
64 3 0.04
65 55 0.66
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Consensus pattern (62 bp):
ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAGTGTCAATTGAAAG
Found at i:915 original size:33 final size:33
Alignment explanation
Indices: 797--1012 Score: 135
Period size: 30 Copynumber: 6.7 Consensus size: 33
787 AATAGTGCAT
* * *
797 ATGACAACTTCTTGTGTCATTTTGAAAGGTAAAATC
1 ATGACAACTTCTGGTGTCA-ATTGGAA--TAAAATC
*
833 ATGACAACTTCTGGTGTCAATT-GAATAAAATT
1 ATGACAACTTCTGGTGTCAATTGGAATAAAATC
* * ** * **
865 ATGATATCTTCAAGTGTCTATTGGAA-ATTTATC
1 ATGACAACTTCTGGTGTCAATTGGAATA-AAATC
*
898 ATGACAACTTCTGGTGTCAATT-GAATAAAATT
1 ATGACAACTTCTGGTGTCAATTGGAATAAAATC
* ** * *
930 ATGACATCTTCAAGTGTCAATT-G--CAAGATC
1 ATGACAACTTCTGGTGTCAATTGGAATAAAATC
* * *
960 ATGACAACTTATGGTGTCAATT-G--CAAGATC
1 ATGACAACTTCTGGTGTCAATTGGAATAAAATC
* *
990 ATGACAGCTTCTGGTATCAATTG
1 ATGACAACTTCTGGTGTCAATTG
1013 CAACATTATG
Statistics
Matches: 143, Mismatches: 33, Indels: 13
0.76 0.17 0.07
Matches are distributed among these distances:
30 49 0.34
32 49 0.34
33 23 0.16
34 2 0.01
35 2 0.01
36 18 0.13
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (33 bp):
ATGACAACTTCTGGTGTCAATTGGAATAAAATC
Found at i:1024 original size:60 final size:60
Alignment explanation
Indices: 895--1089 Score: 246
Period size: 60 Copynumber: 3.2 Consensus size: 60
885 TTGGAAATTT
* * * * ** *
895 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAGTGTCAATTGCAAG
1 ATCATGACAACTTATGGTGTCAATTG--CAAAATCATGACAGCTTCTGGTGTCAATTGCAAC
* *
957 ATCATGACAACTTATGGTGTCAATTGCAAGATCATGACAGCTTCTGGTATCAATTGCAAC
1 ATCATGACAACTTATGGTGTCAATTGCAAAATCATGACAGCTTCTGGTGTCAATTGCAAC
* ** * *
1017 ATTATGACAGTTTATGGTGTCAATTGCAACATCATAACAGCTTCTGGTGTCAATTGCAAC
1 ATCATGACAACTTATGGTGTCAATTGCAAAATCATGACAGCTTCTGGTGTCAATTGCAAC
1077 ATCATGACAACTT
1 ATCATGACAACTT
1090 CTCATGACAA
Statistics
Matches: 115, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
60 90 0.78
62 25 0.22
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (60 bp):
ATCATGACAACTTATGGTGTCAATTGCAAAATCATGACAGCTTCTGGTGTCAATTGCAAC
Found at i:1051 original size:90 final size:91
Alignment explanation
Indices: 895--1553 Score: 393
Period size: 90 Copynumber: 7.2 Consensus size: 91
885 TTGGAAATTT
* * *
895 ATCATGACAACTTCTGGTGTCAATTGAATAAAATTATGACATCTTCAAGTGTCAATTGCAAGATC
1 ATCATGACAACTTCTGGTATCAATTG-ACAAAATTATGACATCTTCAAGTGTCAATTGCAACATC
* *
960 ATGACAACTTATGGTGTCAATTGCAAG
65 ATAACAACTTATGGTGTCAATTGCAAC
* * *
987 ATCATGACAGCTTCTGGTATCAATTG-CAACATTATGACAGT-TT-ATGGTGTCAATTGCAACAT
1 ATCATGACAACTTCTGGTATCAATTGACAAAATTATGACA-TCTTCA-AGTGTCAATTGCAACAT
* *
1049 CATAACAGCTTCTGGTGTCAATTGCAAC
64 CATAACAACTTATGGTGTCAATTGCAAC
** * * * **
1077 ATCATGACAACTTCTCATGA-CAACTTCTGGTCTCAATTGCAAGATCATGACAGCTTCTGGTGTC
1 ATCATGACAACTTCTGGT-ATCAA--T-T-G-----A---CAAAATTATGACATCTTCAAGTGTC
* * *
1141 AATTGCAACATCATGACAGCTTCTGGTGTCAATTGCAAC
53 AATTGCAACATCATAACAACTTATGGTGTCAATTGCAAC
* ** * * ** *
1180 ATCATGACAGCTTC-----TC-A-TGACAACTTCTGATGCCAAT-TGCAA-CATC-A-TGACAGC
1 ATCATGACAACTTCTGGTATCAATTGACAAAAT-T-ATGAC-ATCTTCAAGTGTCAATTG-CAAC
* * * * *
1234 TTCTCATGACGACTTCTGGTGTCAATTGCAAG
62 --ATCATAACAACTTATGGTGTCAATTGCAAC
* * * * ** * *
1266 ATCATGACAACTTCTGGTGTCATTTG-CAAGATCATGACGAT-TTCTGGTGTCATTTGCAAGATC
1 ATCATGACAACTTCTGGTATCAATTGACAAAATTATGAC-ATCTTCAAGTGTCAATTGCAACATC
* * * *
1329 ATGACAACTTCTGGTGTCATTTGCAAG
65 ATAACAACTTATGGTGTCAATTGCAAC
* * * * ** *
1356 ATCATGACAACTTCTGGTGTCAATTG-CAAGATCATGACAACTTCTGGTGTCAATTGCAAGATCA
1 ATCATGACAACTTCTGGTATCAATTGACAAAATTATGACATCTTCAAGTGTCAATTGCAACATCA
* * *
1420 TGACAACTTCTGGTGTCAATTGCAAG
66 TAACAACTTATGGTGTCAATTGCAAC
* * * * ** *
1446 ATCATGACAACTTCTGGTGTCAATTG-CAAGATCATGACAACTTCTGGTGTCAATTGCAAGATCA
1 ATCATGACAACTTCTGGTATCAATTGACAAAATTATGACATCTTCAAGTGTCAATTGCAACATCA
* * *
1510 TGACAACTTCTGGTGTCAATTGCAAG
66 TAACAACTTATGGTGTCAATTGCAAC
1536 ATCATGACAACTTCTGGT
1 ATCATGACAACTTCTGGT
1554 GTCATTTAGA
Statistics
Matches: 475, Mismatches: 56, Indels: 74
0.79 0.09 0.12
Matches are distributed among these distances:
83 2 0.00
84 8 0.02
85 2 0.00
86 45 0.09
87 2 0.00
89 2 0.00
90 297 0.63
91 6 0.01
92 32 0.07
93 6 0.01
94 1 0.00
97 1 0.00
98 1 0.00
103 70 0.15
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (91 bp):
ATCATGACAACTTCTGGTATCAATTGACAAAATTATGACATCTTCAAGTGTCAATTGCAACATCA
TAACAACTTATGGTGTCAATTGCAAC
Found at i:1091 original size:30 final size:30
Alignment explanation
Indices: 895--1091 Score: 223
Period size: 30 Copynumber: 6.5 Consensus size: 30
885 TTGGAAATTT
* *
895 ATCATGACAACTTCTGGTGTCAATTGAATAAA
1 ATCATGACAACTTCTGGTGTCAATTG--CAAC
* * ** *
927 ATTATGACATCTTCAAGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAC
* *
957 ATCATGACAACTTATGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAC
* *
987 ATCATGACAGCTTCTGGTATCAATTGCAAC
1 ATCATGACAACTTCTGGTGTCAATTGCAAC
* ** *
1017 ATTATGACAGTTTATGGTGTCAATTGCAAC
1 ATCATGACAACTTCTGGTGTCAATTGCAAC
* *
1047 ATCATAACAGCTTCTGGTGTCAATTGCAAC
1 ATCATGACAACTTCTGGTGTCAATTGCAAC
1077 ATCATGACAACTTCT
1 ATCATGACAACTTCT
1092 CATGACAACT
Statistics
Matches: 140, Mismatches: 25, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
30 118 0.84
32 22 0.16
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (30 bp):
ATCATGACAACTTCTGGTGTCAATTGCAAC
Found at i:1096 original size:13 final size:13
Alignment explanation
Indices: 1078--1104 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1068 AATTGCAACA
1078 TCATGACAACTTC
1 TCATGACAACTTC
1091 TCATGACAACTTC
1 TCATGACAACTTC
1104 T
1 T
1105 GGTCTCAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.30, G:0.07, T:0.33
Consensus pattern (13 bp):
TCATGACAACTTC
Found at i:1118 original size:43 final size:43
Alignment explanation
Indices: 1048--1134 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 43
1038 AATTGCAACA
* *
1048 TCATAACAGCTTCTGGTGTCAATTGCAACATCATGACAACTTC
1 TCATAACAACTTCTGGTCTCAATTGCAACATCATGACAACTTC
* * *
1091 TCATGACAACTTCTGGTCTCAATTGCAAGATCATGACAGCTTC
1 TCATAACAACTTCTGGTCTCAATTGCAACATCATGACAACTTC
1134 T
1 T
1135 GGTGTCAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (43 bp):
TCATAACAACTTCTGGTCTCAATTGCAACATCATGACAACTTC
Found at i:1127 original size:30 final size:30
Alignment explanation
Indices: 1091--1557 Score: 630
Period size: 30 Copynumber: 15.7 Consensus size: 30
1081 TGACAACTTC
*
1091 TCATGACAACTTCTGGTCTCAATTGCAAGA
1 TCATGACAACTTCTGGTGTCAATTGCAAGA
* *
1121 TCATGACAGCTTCTGGTGTCAATTGCAACA
1 TCATGACAACTTCTGGTGTCAATTGCAAGA
* *
1151 TCATGACAGCTTCTGGTGTCAATTGCAACA
1 TCATGACAACTTCTGGTGTCAATTGCAAGA
* ** * *
1181 TCATGACAGCTTCTCATGACAACTT-C-TGA
1 TCATGACAACTTCTGGTGTCAA-TTGCAAGA
* * * *
1210 TGCCAATTG-CAACATC--ATGACAGCTT-C----
1 T--C-A-TGACAACTTCTGGTGTCA-ATTGCAAGA
*
1237 TCATGACGACTTCTGGTGTCAATTGCAAGA
1 TCATGACAACTTCTGGTGTCAATTGCAAGA
*
1267 TCATGACAACTTCTGGTGTCATTTGCAAGA
1 TCATGACAACTTCTGGTGTCAATTGCAAGA
* * *
1297 TCATGACGATTTCTGGTGTCATTTGCAAGA
1 TCATGACAACTTCTGGTGTCAATTGCAAGA
*
1327 TCATGACAACTTCTGGTGTCATTTGCAAGA
1 TCATGACAACTTCTGGTGTCAATTGCAAGA
1357 TCATGACAACTTCTGGTGTCAATTGCAAGA
1 TCATGACAACTTCTGGTGTCAATTGCAAGA
1387 TCATGACAACTTCTGGTGTCAATTGCAAGA
1 TCATGACAACTTCTGGTGTCAATTGCAAGA
1417 TCATGACAACTTCTGGTGTCAATTGCAAGA
1 TCATGACAACTTCTGGTGTCAATTGCAAGA
1447 TCATGACAACTTCTGGTGTCAATTGCAAGA
1 TCATGACAACTTCTGGTGTCAATTGCAAGA
1477 TCATGACAACTTCTGGTGTCAATTGCAAGA
1 TCATGACAACTTCTGGTGTCAATTGCAAGA
1507 TCATGACAACTTCTGGTGTCAATTGCAAGA
1 TCATGACAACTTCTGGTGTCAATTGCAAGA
1537 TCATGACAACTTCTGGTGTCA
1 TCATGACAACTTCTGGTGTCA
1558 TTTAGAGAGT
Statistics
Matches: 400, Mismatches: 23, Indels: 28
0.89 0.05 0.06
Matches are distributed among these distances:
23 2 0.00
24 6 0.01
25 3 0.01
26 5 0.01
27 1 0.00
29 2 0.00
30 370 0.93
31 3 0.01
32 6 0.01
33 2 0.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (30 bp):
TCATGACAACTTCTGGTGTCAATTGCAAGA
Found at i:1139 original size:73 final size:73
Alignment explanation
Indices: 1031--1303 Score: 288
Period size: 73 Copynumber: 3.7 Consensus size: 73
1021 TGACAGTTTA
* * * * *
1031 TGGTGTCAATTGCAACATCATAACAGCTTCTGGTGTCAATTGCAACATCATGACAACTTCTCATG
1 TGGTCTCAATTGCAAGATCATGACAACTTCTGGTGTCAATTGCAACATCATGACAGCTTCTCATG
1096 ACAACTTC
66 ACAACTTC
* **
1104 TGGTCTCAATTGCAAGATCATGACAGCTTCTGGTGTCAATTGCAACATCATGACAGCTTCTGGTG
1 TGGTCTCAATTGCAAGATCATGACAACTTCTGGTGTCAATTGCAACATCATGACAGCTTCTCATG
*
1169 TCAA--T-
66 ACAACTTC
** * * *
1174 TGCAACATC-A-TG-ACAGCTTCTCATGACAACTTCTGATGCCAATTGCAACATCATGACAGCTT
1 TG-GTC-TCAATTGCA-AG---ATCATGACAACTTCTGGTGTCAATTGCAACATCATGACAGCTT
*
1236 CTCATGACGACTTC
60 CTCATGACAACTTC
* * *
1250 TGGTGTCAATTGCAAGATCATGACAACTTCTGGTGTCATTTGCAAGATCATGAC
1 TGGTCTCAATTGCAAGATCATGACAACTTCTGGTGTCAATTGCAACATCATGAC
1304 GATTTCTGGT
Statistics
Matches: 163, Mismatches: 25, Indels: 24
0.77 0.12 0.11
Matches are distributed among these distances:
69 1 0.01
70 6 0.04
71 3 0.02
72 2 0.01
73 140 0.86
74 2 0.01
75 2 0.01
76 6 0.04
77 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (73 bp):
TGGTCTCAATTGCAAGATCATGACAACTTCTGGTGTCAATTGCAACATCATGACAGCTTCTCATG
ACAACTTC
Found at i:1217 original size:43 final size:43
Alignment explanation
Indices: 1151--1280 Score: 206
Period size: 43 Copynumber: 3.0 Consensus size: 43
1141 AATTGCAACA
*
1151 TCATGACAGCTTCTGGTGTCAATTGCAACATCATGACAGCTTC
1 TCATGACAACTTCTGGTGTCAATTGCAACATCATGACAGCTTC
* *
1194 TCATGACAACTTCTGATGCCAATTGCAACATCATGACAGCTTC
1 TCATGACAACTTCTGGTGTCAATTGCAACATCATGACAGCTTC
* * *
1237 TCATGACGACTTCTGGTGTCAATTGCAAGATCATGACAACTTC
1 TCATGACAACTTCTGGTGTCAATTGCAACATCATGACAGCTTC
1280 T
1 T
1281 GGTGTCATTT
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 79 1.00
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (43 bp):
TCATGACAACTTCTGGTGTCAATTGCAACATCATGACAGCTTC
Done.