Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015315.1 Corchorus olitorius cultivar O-4 contig15348, 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: 20198
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Found at i:1244 original size:8 final size:8
Alignment explanation
Indices: 1231--1501 Score: 84
Period size: 8 Copynumber: 34.9 Consensus size: 8
1221 ATTTATTCAT
1231 TATTTATC
1 TATTTATC
*
1239 TATTTATT
1 TATTTATC
*
1247 TATTTTTAAC
1 TA--TTTATC
1257 TA-TTATC
1 TATTTATC
1264 TATTTATTTAC
1 TATTTA--T-C
1275 TATTTATC
1 TATTTATC
* *
1283 TTTTTATT
1 TATTTATC
1291 TATTT-TC
1 TATTTATC
*
1298 -AATTAT-
1 TATTTATC
* *
1304 TATCTATT
1 TATTTATC
1312 TATTTA-C
1 TATTTATC
*
1319 TATATATC
1 TATTTATC
1327 TATTTA-C
1 TATTTATC
*
1334 TATATATC
1 TATTTATC
*
1342 TATTTATT
1 TATTTATC
*
1350 TATTTTTAAC
1 TA--TTTATC
1360 TA-TTATC
1 TATTTATC
1367 TATTT-T-
1 TATTTATC
1373 T-TTTA-C
1 TATTTATC
1379 TATTTATC
1 TATTTATC
1387 --TTT-T-
1 TATTTATC
1391 TATTTAT-
1 TATTTATC
*
1398 TAATTTAGC
1 T-ATTTATC
1407 TA-TTA-C
1 TATTTATC
*
1413 ATATTTATT
1 -TATTTATC
1422 TA-TTAT-
1 TATTTATC
1428 TA-TTATCC
1 TATTTAT-C
1436 T-TTTAGTTACC
1 TATTTA--T--C
1447 TATTTATC
1 TATTTATC
1455 TA-TTATTC
1 TATTTA-TC
* *
1463 TCTGTATC
1 TATTTATC
1471 TATTTATC
1 TATTTATC
1479 TATTTATC
1 TATTTATC
* * *
1487 TCTATACC
1 TATTTATC
1495 TATTTAT
1 TATTTAT
1502 TTTTTTTATT
Statistics
Matches: 195, Mismatches: 33, Indels: 70
0.65 0.11 0.23
Matches are distributed among these distances:
5 4 0.02
6 18 0.09
7 48 0.25
8 92 0.47
9 4 0.02
10 15 0.08
11 10 0.05
12 4 0.02
ACGTcount: A:0.26, C:0.11, G:0.01, T:0.62
Consensus pattern (8 bp):
TATTTATC
Found at i:1279 original size:44 final size:44
Alignment explanation
Indices: 1216--1332 Score: 173
Period size: 44 Copynumber: 2.7 Consensus size: 44
1206 AAGATTTTTT
* * *
1216 TTAT-TATTTATTCATTATTTATCTATTTATTTATTTTTAACTA
1 TTATCTATTTATTTACTATTTATCTATTTATTTATTTTCAACTA
* *
1259 TTATCTATTTATTTACTATTTATCTTTTTATTTATTTTCAATTA
1 TTATCTATTTATTTACTATTTATCTATTTATTTATTTTCAACTA
*
1303 TTATCTATTTATTTACTATATATCTATTTA
1 TTATCTATTTATTTACTATTTATCTATTTA
1333 CTATATATCT
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
43 4 0.06
44 62 0.94
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (44 bp):
TTATCTATTTATTTACTATTTATCTATTTATTTATTTTCAACTA
Found at i:1348 original size:59 final size:60
Alignment explanation
Indices: 1268--1392 Score: 180
Period size: 59 Copynumber: 2.1 Consensus size: 60
1258 ATTATCTATT
* * *
1268 TATTTACTATTTATCTTTTTATTTATTTTCAATTATTATCTA-TTTATTTACTATATATC
1 TATTTACTATATATCTATTTATTTATTTTCAACTATTATCTATTTTATTTACTATATATC
* * *
1327 TATTTACTATATATCTATTTATTTATTTTTAACTATTATCTATTTTTTTTACTATTTATC
1 TATTTACTATATATCTATTTATTTATTTTCAACTATTATCTATTTTATTTACTATATATC
*
1387 TTTTTA
1 TATTTA
1393 TTTATTAATT
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
59 38 0.66
60 20 0.34
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (60 bp):
TATTTACTATATATCTATTTATTTATTTTCAACTATTATCTATTTTATTTACTATATATC
Found at i:1424 original size:4 final size:4
Alignment explanation
Indices: 1215--1354 Score: 62
Period size: 4 Copynumber: 35.8 Consensus size: 4
1205 AAAGATTTTT
* * *
1215 TTTA -TTA TTTA TTCA -TTA TTTA TCTA TTTA TTTA TTT- TTAA CTATTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -T-TTA
* * * *
1262 TCTA TTTA TTTA -CTA TTTA TCTT- TTTA TTTA TTTTCA ATTA -TTA TCTA
1 TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA -TTT-A TTTA TTTA TTTA
* * * * * *
1310 TTTA TTTA -CTA TATA TCTA TTTA -CTA TATA TCTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1355 TTAACTATTA
Statistics
Matches: 102, Mismatches: 21, Indels: 26
0.68 0.14 0.17
Matches are distributed among these distances:
3 18 0.18
4 72 0.71
5 9 0.09
6 3 0.03
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (4 bp):
TTTA
Found at i:1537 original size:17 final size:17
Alignment explanation
Indices: 1497--1539 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1487 TCTATACCTA
*
1497 TTTATTTTTTTTATTAT
1 TTTATTTTATTTATTAT
** *
1514 TCGATTTTATTTATTTT
1 TTTATTTTATTTATTAT
1531 TTTATTTTA
1 TTTATTTTA
1540 AACTTATTTT
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (17 bp):
TTTATTTTATTTATTAT
Found at i:2611 original size:28 final size:28
Alignment explanation
Indices: 2580--2637 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
2570 TTTATGCATG
2580 AAAAATTCAAAAAGGTTTTG-AGAAAATC
1 AAAAATTCAAAAA-GTTTTGTAGAAAATC
* * * *
2608 AAAATTTTAAAAATTTTTGTCGAAAATC
1 AAAAATTCAAAAAGTTTTGTAGAAAATC
2636 AA
1 AA
2638 TTTTAAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
27 5 0.20
28 20 0.80
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (28 bp):
AAAAATTCAAAAAGTTTTGTAGAAAATC
Found at i:4674 original size:22 final size:22
Alignment explanation
Indices: 4649--4690 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
4639 TCGCGGGGCA
4649 TGGCCAAGTCATGACCGGGCTG
1 TGGCCAAGTCATGACCGGGCTG
** *
4671 TGGCCTGGTCATGTCCGGGC
1 TGGCCAAGTCATGACCGGGC
4691 GCCATCGAGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.12, C:0.29, G:0.38, T:0.21
Consensus pattern (22 bp):
TGGCCAAGTCATGACCGGGCTG
Found at i:14243 original size:11 final size:11
Alignment explanation
Indices: 14227--14252 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
14217 AGATAATTTC
14227 TTTTCTTCTAG
1 TTTTCTTCTAG
14238 TTTTCTTCTAG
1 TTTTCTTCTAG
14249 TTTT
1 TTTT
14253 TAGGCAAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Done.