Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014680.1 Corchorus olitorius cultivar O-4 contig14713, 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: 6065
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Found at i:890 original size:22 final size:21
Alignment explanation
Indices: 865--1294 Score: 153
Period size: 22 Copynumber: 19.8 Consensus size: 21
855 AGTTTAGTTT
865 TCAAAATTTCATAAGAGGATTA
1 TCAAAATTTCATAAGAGG-TTA
* *
887 TCAAAATTTCAT-AGTATGTAGA
1 TCAAAATTTCATAAG-AGGT-TA
* *
909 TCAAAATTTCATAGGGAGATTA
1 TCAAAATTTCATA-AGAGGTTA
*
931 ACAAAATTTCATAATGAGGTTA
1 TCAAAATTTCATAA-GAGGTTA
** * *
953 TCAAAAAATCATAGGGAGGTGA
1 TCAAAATTTCATA-AGAGGTTA
**
975 TCAAAA-TT--T--GTTGTTA
1 TCAAAATTTCATAAGAGGTTA
*
991 TCAAGATTTCATAAGGAGGTTA
1 TCAAAATTTCATAA-GAGGTTA
* *
1013 TCAAAATTTTATAGGGAGGTTTA
1 TCAAAATTTCATA-AGAGG-TTA
* * *
1036 TTAAAATTTTAAAAGAAGGTTTA
1 TCAAAATTTCATAAG-AGG-TTA
*
1059 TCAAAATTTCATAGCGAGGTTA
1 TCAAAATTTCATA-AGAGGTTA
* * *
1081 TCACATTTTCAT-AGTGTGATTA
1 TCAAAATTTCATAAGAG-G-TTA
* *
1103 TCAAAATTTCA-GAGTGTGATTA
1 TCAAAATTTCATAAGAG-G-TTA
* *
1125 -CTAACAA-TTCATATGGAGGTTT
1 TC-AA-AATTTCATA-AGAGGTTA
* * *
1147 TTAAATTTTCATAACGTGGTTA
1 TCAAAATTTCATAA-GAGGTTA
* * *
1169 TCAATATATCATATGGAGGTTA
1 TCAAAATTTCATA-AGAGGTTA
* * * * *
1191 TTAACATCTCATAGTGTTGGTTA
1 TCAAAATTTCATA-AG-AGGTTA
** *
1214 TCAAAATTTCATTGGAAGTTA
1 TCAAAATTTCATAAGAGGTTA
* *
1235 TCAAAATTTCATAGTGATGTCT-
1 TCAAAATTTCATA-AGAGGT-TA
**
1257 TCAAAATTTTTTAGAGAGGTTA
1 TCAAAATTTCATA-AGAGGTTA
*
1279 ACAAAATTTCATAAGA
1 TCAAAATTTCATAAGA
1295 AAGTTTTTAA
Statistics
Matches: 302, Mismatches: 75, Indels: 63
0.69 0.17 0.14
Matches are distributed among these distances:
16 9 0.03
17 2 0.01
19 2 0.01
20 2 0.01
21 27 0.09
22 202 0.67
23 54 0.18
24 4 0.01
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.37
Consensus pattern (21 bp):
TCAAAATTTCATAAGAGGTTA
Found at i:956 original size:44 final size:44
Alignment explanation
Indices: 804--1291 Score: 258
Period size: 44 Copynumber: 11.3 Consensus size: 44
794 TTGTGGAGTA
* * * * *
804 ATCAAAATTTC--AGGGAGGATAGCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGAGGTT
* * *
846 ATC---A-TTCATAGTTTA-GTTTTCAAAATTTCATA-AGAGGATT
1 ATCAAAATTTCATAG-TGAGGTTATCAAAATTTCATAGGGAGG-TT
* * *
886 ATCAAAATTTCATAGT-ATGTAGATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGTGAGGT-TATCAAAATTTCATAGGGAGGTT
* * ** *
930 AACAAAATTTCATAATGAGGTTATCAAAAAATCATAGGGAGGTG
1 ATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGAGGTT
* * *
974 ATCAAAA-TT--T-GT--TGTTATCAAGATTTCATAAGGAGGTT
1 ATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGAGGTT
* * * * * * *
1012 ATCAAAATTTTATAGGGAGGTTTATTAAAATTTTAAAAGAAGGTTT
1 ATCAAAATTTCATAGTGAGG-TTATCAAAATTTCATAGGGAGG-TT
* * * * * *
1058 ATCAAAATTTCATAGCGAGGTTATCACATTTTCATAGTGTGATT
1 ATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGAGGTT
* * * *
1102 ATCAAAATTTCAGAGTGTGATTA-CTAACAA-TTCATATGGAGGTT
1 ATCAAAATTTCATAGTGAGGTTATC-AA-AATTTCATAGGGAGGTT
* * * ** * * * *
1146 TTTAAATTTTCATAACGTGGTTATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGAGGTT
* * * * * *
1190 ATTAACATCTCATAGTGTTGGTTATCAAAATTTCAT-TGGAAGTT
1 ATCAAAATTTCATAGTG-AGGTTATCAAAATTTCATAGGGAGGTT
* ** *
1234 ATCAAAATTTCATAGTGATGTCT-TCAAAATTTTTTAGAGAGGTT
1 ATCAAAATTTCATAGTGAGGT-TATCAAAATTTCATAGGGAGGTT
*
1278 AACAAAATTTCATA
1 ATCAAAATTTCATA
1292 AGAAAGTTTT
Statistics
Matches: 334, Mismatches: 85, Indels: 52
0.71 0.18 0.11
Matches are distributed among these distances:
38 30 0.09
39 6 0.02
40 22 0.07
41 3 0.01
42 5 0.01
43 20 0.06
44 175 0.52
45 53 0.16
46 20 0.06
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (44 bp):
ATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGGAGGTT
Found at i:1374 original size:22 final size:22
Alignment explanation
Indices: 804--1388 Score: 150
Period size: 22 Copynumber: 27.0 Consensus size: 22
794 TTGTGGAGTA
* *
804 ATCAAAATTTC--AGGGAGGAT
1 ATCAAAATTTCATAGGAAGGTT
* *
824 AGCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATAGGAAGGTT
**
846 ATC---A-TTCATAGTTTA-GTT
1 ATCAAAATTTCATAG-GAAGGTT
* *
864 TTCAAAATTTCATAAG-AGGATT
1 ATCAAAATTTCATAGGAAGG-TT
* * *
886 ATCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATAGGAAGGT-T
* *
908 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGGAAGGTT
* *
930 AACAAAATTTCATAATG-AGGTT
1 ATCAAAATTTCAT-AGGAAGGTT
** * *
952 ATCAAAAAATCATAGGGAGGTG
1 ATCAAAATTTCATAGGAAGGTT
**
974 ATCAAAA-TT--T--G-TTGTT
1 ATCAAAATTTCATAGGAAGGTT
*
990 ATCAAGATTTCATAAGG-AGGTT
1 ATCAAAATTTCAT-AGGAAGGTT
* *
1012 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAGGAAGG-TT
* * * *
1035 ATTAAAATTTTAAAAGAAGGTTT
1 ATCAAAATTTCATAGGAAGG-TT
1058 ATCAAAATTTCATAGCG-AGGTT
1 ATCAAAATTTCATAG-GAAGGTT
* * * *
1080 ATCACATTTTCATAGTG-TGATT
1 ATCAAAATTTCATAG-GAAGGTT
* * *
1102 ATCAAAATTTCAGAGTG-TGATT
1 ATCAAAATTTCATAG-GAAGGTT
1124 A-CTAACAA-TTCATATGG-AGGTT
1 ATC-AA-AATTTCATA-GGAAGGTT
* * * * *
1146 TTTAAATTTTCATAACG-TGGTT
1 ATCAAAATTTCAT-AGGAAGGTT
* *
1168 ATCAATATATCATATGG-AGGTT
1 ATCAAAATTTCATA-GGAAGGTT
* * * **
1190 ATTAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAG-GAAGGTT
*
1213 ATCAAAATTTCATTGGAA-GTT
1 ATCAAAATTTCATAGGAAGGTT
*
1234 ATCAAAATTTCATAGTG-ATGTCT
1 ATCAAAATTTCATAG-GAAGGT-T
**
1257 -TCAAAATTTTTTA-GAGAGGTT
1 ATCAAAATTTCATAGGA-AGGTT
* * *
1278 AACAAAATTTCATAAGAAAGTTTTT
1 ATCAAAATTTCAT-AGGAAG--GTT
** **
1303 AAAAAAATTT-ATAAAAAGGTT
1 ATCAAAATTTCATAGGAAGGTT
* * * * **
1324 CTCGAAATTCCATAGTATCGTT
1 ATCAAAATTTCATAGGAAGGTT
*
1346 ATTAAAATTTCATAGGAAGGTT
1 ATCAAAATTTCATAGGAAGGTT
* * *
1368 CTCAAAATTTTATAAGAAGGT
1 ATCAAAATTTCATAGGAAGGT
1389 CATAAAAAAT
Statistics
Matches: 414, Mismatches: 108, Indels: 84
0.68 0.18 0.14
Matches are distributed among these distances:
16 8 0.02
17 3 0.01
18 11 0.03
19 4 0.01
20 12 0.03
21 40 0.10
22 253 0.61
23 68 0.16
24 4 0.01
25 11 0.03
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAGGAAGGTT
Found at i:1396 original size:22 final size:22
Alignment explanation
Indices: 1349--1396 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
1339 TATCGTTATT
* *
1349 AAAATTTCATAGGAAGGTTCTC
1 AAAATTTCATAAGAAGGTTCTA
*
1371 AAAATTTTATAAGAAGG-TCATA
1 AAAATTTCATAAGAAGGTTC-TA
1393 AAAA
1 AAAA
1397 ATCGTGTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.48, C:0.08, G:0.15, T:0.29
Consensus pattern (22 bp):
AAAATTTCATAAGAAGGTTCTA
Found at i:4393 original size:26 final size:26
Alignment explanation
Indices: 4357--4412 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
4347 CTAGAGAAGC
*
4357 AAAAGTTTAAAAAGCAAAAA-T-TTTTG
1 AAAAATTTAAAAA--AAAAATTGTTTTG
4383 AAAAATTTAAAAAAAAAATTGTTTTG
1 AAAAATTTAAAAAAAAAATTGTTTTG
4409 AAAA
1 AAAA
4413 GCCTTCTCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 5 0.19
25 1 0.04
26 21 0.78
ACGTcount: A:0.59, C:0.02, G:0.09, T:0.30
Consensus pattern (26 bp):
AAAAATTTAAAAAAAAAATTGTTTTG
Done.