Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006247.1 Corchorus capsularis cultivar CVL-1 contig06266, 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: 55554
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:9543 original size:58 final size:58
Alignment explanation
Indices: 9438--9551 Score: 160
Period size: 58 Copynumber: 2.0 Consensus size: 58
9428 ATTAATCAAA
*
9438 TATCAAGTGACATGTATTTTATTAGATGCATAAAAAAAGACGGTTTAGGACCGAGGCT
1 TATCAAGTGACATGTATTTTATTAGATGCATAAAAAAAGACGGTTTAGGAACGAGGCT
* * *
9496 TATCGAGTGACATGT-TCTTTATTAGATGCCTAAAAACAA-ACGTTTTAGGAACGAGG
1 TATCAAGTGACATGTAT-TTTATTAGATGCATAAAAA-AAGACGGTTTAGGAACGAGG
9552 GATGATGCTA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
57 1 0.02
58 47 0.94
59 2 0.04
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (58 bp):
TATCAAGTGACATGTATTTTATTAGATGCATAAAAAAAGACGGTTTAGGAACGAGGCT
Found at i:12222 original size:32 final size:32
Alignment explanation
Indices: 12156--12220 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
12146 GTAGAGGGAG
*
12156 TTACCGAATGGTATTTGCTAGAGTTAATTTTT
1 TTACCGAATAGTATTTGCTAGAGTTAATTTTT
12188 TTACCGAATAGTATTTGC-AGAGTTAATTTTT
1 TTACCGAATAGTATTTGCTAGAGTTAATTTTT
12219 TT
1 TT
12221 TAGATATTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 15 0.47
32 17 0.53
ACGTcount: A:0.26, C:0.09, G:0.17, T:0.48
Consensus pattern (32 bp):
TTACCGAATAGTATTTGCTAGAGTTAATTTTT
Found at i:12481 original size:2 final size:2
Alignment explanation
Indices: 12476--12506 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
12466 AAAAAAAACC
*
12476 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12507 TTCATTACGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:15251 original size:2 final size:2
Alignment explanation
Indices: 15238--15279 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
15228 AAGTTACAAC
* * *
15238 AT AT AT AA AT AT AT AT AT AT AT AT AT AA AT AC AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15279 A
1 A
15280 CTAGCTAATG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:15253 original size:10 final size:10
Alignment explanation
Indices: 15238--15274 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
15228 AAGTTACAAC
15238 ATATATAAAT
1 ATATATAAAT
*
15248 ATATATATAT
1 ATATATAAAT
15258 ATATATAAAT
1 ATATATAAAT
*
15268 ACATATA
1 ATATATA
15275 TTATACTAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (10 bp):
ATATATAAAT
Found at i:18109 original size:19 final size:18
Alignment explanation
Indices: 18076--18112 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
18066 TTGAAATGAT
18076 TCTTCAATAATCTTCAAG
1 TCTTCAATAATCTTCAAG
*
18094 TCTTCAAATTATCTTCAAG
1 TCTTC-AATAATCTTCAAG
18113 AAATCTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (18 bp):
TCTTCAATAATCTTCAAG
Found at i:24355 original size:19 final size:18
Alignment explanation
Indices: 24321--24356 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
24311 AGTTTATTAA
*
24321 TTAAATTATTTATATATC
1 TTAAATTATATATATATC
24339 TTAAATATATATATATAT
1 TTAAAT-TATATATATAT
24357 ATACATAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
TTAAATTATATATATATC
Found at i:25431 original size:3 final size:3
Alignment explanation
Indices: 25425--25454 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
25415 GGTAGTAGGT
25425 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
25455 TATGATATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:27322 original size:3 final size:3
Alignment explanation
Indices: 27316--27345 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
27306 AGTAGTAGGT
27316 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
27346 TATGATATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:28433 original size:17 final size:17
Alignment explanation
Indices: 28390--28434 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
28380 AATAGTAAGA
*
28390 TTAGATAGTTTGTTACT
1 TTAGATATTTTGTTACT
*
28407 TT-GTTAATTTTGTTACT
1 TTAGAT-ATTTTGTTACT
28424 TTAGATATTTT
1 TTAGATATTTT
28435 TTTTTATCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 2 0.09
17 19 0.83
18 2 0.09
ACGTcount: A:0.22, C:0.04, G:0.13, T:0.60
Consensus pattern (17 bp):
TTAGATATTTTGTTACT
Found at i:29124 original size:54 final size:54
Alignment explanation
Indices: 29066--29175 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
29056 GGTCCCACTC
29066 TTTGCAAATTTTTTCTTATTTAATTGTAATAAATAATTTTATGATACTCTAAAG
1 TTTGCAAATTTTTTCTTATTTAATTGTAATAAATAATTTTATGATACTCTAAAG
29120 TTTGCAAATTTTTTCTTATTTAATTGTAATAAATAATTTTATGATACTCTAAAG
1 TTTGCAAATTTTTTCTTATTTAATTGTAATAAATAATTTTATGATACTCTAAAG
29174 TT
1 TT
29176 GTAAACCAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.51
Consensus pattern (54 bp):
TTTGCAAATTTTTTCTTATTTAATTGTAATAAATAATTTTATGATACTCTAAAG
Found at i:29157 original size:28 final size:28
Alignment explanation
Indices: 29072--29159 Score: 74
Period size: 28 Copynumber: 3.2 Consensus size: 28
29062 ACTCTTTGCA
29072 AATTTTTTCTTATTTAATTGTAATAAAT
1 AATTTTTTCTTATTTAATTGTAATAAAT
* ** * * * **
29100 AATTTTATGATACTCTAA-AGT-TTGCA-
1 AATTTTTTCTTA-TTTAATTGTAATAAAT
29126 AATTTTTTCTTATTTAATTGTAATAAAT
1 AATTTTTTCTTATTTAATTGTAATAAAT
29154 AATTTT
1 AATTTT
29160 ATGATACTCT
Statistics
Matches: 40, Mismatches: 16, Indels: 8
0.62 0.25 0.12
Matches are distributed among these distances:
25 4 0.10
26 11 0.28
27 4 0.10
28 17 0.43
29 4 0.10
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (28 bp):
AATTTTTTCTTATTTAATTGTAATAAAT
Found at i:32262 original size:45 final size:45
Alignment explanation
Indices: 32198--32292 Score: 181
Period size: 45 Copynumber: 2.1 Consensus size: 45
32188 TATAAACAGT
32198 GTAGACAAACAAGCTCTGATTTCTGTTAAATCGTAGCATGCAAAG
1 GTAGACAAACAAGCTCTGATTTCTGTTAAATCGTAGCATGCAAAG
*
32243 GTAGACAAACAAGTTCTGATTTCTGTTAAATCGTAGCATGCAAAG
1 GTAGACAAACAAGCTCTGATTTCTGTTAAATCGTAGCATGCAAAG
32288 GTAGA
1 GTAGA
32293 ATATGACATG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (45 bp):
GTAGACAAACAAGCTCTGATTTCTGTTAAATCGTAGCATGCAAAG
Found at i:32329 original size:19 final size:19
Alignment explanation
Indices: 32305--32361 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
32295 ATGACATGAT
32305 AAAAGGTACTATATATTAA
1 AAAAGGTACTATATATTAA
* * *
32324 AAAAGGTA-T-GACATGAA
1 AAAAGGTACTATATATTAA
32341 AAAAGGTACTATATATTAA
1 AAAAGGTACTATATATTAA
32360 AA
1 AA
32362 CTGAGAAGAT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
17 13 0.43
18 2 0.07
19 15 0.50
ACGTcount: A:0.54, C:0.05, G:0.14, T:0.26
Consensus pattern (19 bp):
AAAAGGTACTATATATTAA
Found at i:32342 original size:17 final size:17
Alignment explanation
Indices: 32294--32348 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
32284 AAAGGTAGAA
*
32294 TATGACATGATAAAAGG
1 TATGACATGAAAAAAGG
* * *
32311 TACTATATATTAAAAAAGG
1 TA-T-GACATGAAAAAAGG
32330 TATGACATGAAAAAAGG
1 TATGACATGAAAAAAGG
32347 TA
1 TA
32349 CTATATATTA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
17 15 0.52
18 2 0.07
19 12 0.41
ACGTcount: A:0.51, C:0.05, G:0.18, T:0.25
Consensus pattern (17 bp):
TATGACATGAAAAAAGG
Found at i:36003 original size:55 final size:55
Alignment explanation
Indices: 35937--36049 Score: 217
Period size: 55 Copynumber: 2.1 Consensus size: 55
35927 GGCTTAGCCC
*
35937 AAACATTGAAAATTTTAAAAAGCCCAAAATCTGAAGCCCAAAAATGGAAAATGAA
1 AAACATTGAAAATTTTAAAAAGCCCAAAATCTGAAGCCCAAAAAAGGAAAATGAA
35992 AAACATTGAAAATTTTAAAAAGCCCAAAATCTGAAGCCCAAAAAAGGAAAATGAA
1 AAACATTGAAAATTTTAAAAAGCCCAAAATCTGAAGCCCAAAAAAGGAAAATGAA
36047 AAA
1 AAA
36050 TAGAATGTTG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.57, C:0.14, G:0.12, T:0.17
Consensus pattern (55 bp):
AAACATTGAAAATTTTAAAAAGCCCAAAATCTGAAGCCCAAAAAAGGAAAATGAA
Found at i:37446 original size:5 final size:5
Alignment explanation
Indices: 37436--37462 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
37426 TAGTATTTAA
37436 TTCTT TTCTT TTCTT TTCTT TTCTT TT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TT
37463 TTTCTATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTCTT
Done.