Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021154.1 Corchorus olitorius cultivar O-4 contig21187, 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: 11163
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:842 original size:16 final size:15
Alignment explanation
Indices: 802--845 Score: 56
Period size: 13 Copynumber: 3.0 Consensus size: 15
792 GAACTTAATT
802 TATTTATCTATACTA
1 TATTTATCTATACTA
*
817 T-TTT-TTTATACATA
1 TATTTATCTATAC-TA
831 TATTTATCTATACTA
1 TATTTATCTATACTA
846 GTCTTAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
13 6 0.25
14 6 0.25
15 6 0.25
16 6 0.25
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (15 bp):
TATTTATCTATACTA
Found at i:1923 original size:91 final size:92
Alignment explanation
Indices: 1767--1935 Score: 295
Period size: 91 Copynumber: 1.8 Consensus size: 92
1757 ATCAGTTCGA
* ** *
1767 TCCTCTTTCCTTTTTTTTTTTTTAAAGAAAGTATATAATCAATAAAGTTAGGAATTGATATTAGG
1 TCCTCTTTCCTCTTTTTTTTTCAAAAGAAAATATATAATCAATAAAGTTAGGAATTGATATTAGG
1832 GATGGGTGAGTGTACCGGGCAGTGCGG
66 GATGGGTGAGTGTACCGGGCAGTGCGG
1859 TCCTCTTTCC-CTTTTTTTTTCAAAAGAAAATATATAATCAATAAAGTTAGGAATTGATATTAGG
1 TCCTCTTTCCTCTTTTTTTTTCAAAAGAAAATATATAATCAATAAAGTTAGGAATTGATATTAGG
1923 GATGGGTGAGTGT
66 GATGGGTGAGTGT
1936 TATTCTTTAA
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
91 63 0.86
92 10 0.14
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (92 bp):
TCCTCTTTCCTCTTTTTTTTTCAAAAGAAAATATATAATCAATAAAGTTAGGAATTGATATTAGG
GATGGGTGAGTGTACCGGGCAGTGCGG
Found at i:2367 original size:15 final size:15
Alignment explanation
Indices: 2347--2383 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
2337 CACAATTATT
2347 TAATTATTTTCTATA
1 TAATTATTTTCTATA
2362 TAATTATTTTCTATA
1 TAATTATTTTCTATA
*
2377 AAATTAT
1 TAATTAT
2384 ATTTTGTAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (15 bp):
TAATTATTTTCTATA
Found at i:2402 original size:21 final size:20
Alignment explanation
Indices: 2378--2427 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
2368 TTTTCTATAA
* *
2378 AATTATATTTTGTAGGAAAAT
1 AATTATATTTTATA-AAAAAT
2399 AATTATAATTTTATAAAAAAT
1 AATTAT-ATTTTATAAAAAAT
2420 AATTATAT
1 AATTATAT
2428 AGAAAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 2 0.08
21 17 0.65
22 7 0.27
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (20 bp):
AATTATATTTTATAAAAAAT
Found at i:2423 original size:15 final size:15
Alignment explanation
Indices: 2403--2436 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2393 GAAAATAATT
*
2403 ATAATTTTATAAAAA
1 ATAATTATATAAAAA
*
2418 ATAATTATATAGAAA
1 ATAATTATATAAAAA
2433 ATAA
1 ATAA
2437 AACCCAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (15 bp):
ATAATTATATAAAAA
Found at i:3378 original size:2 final size:2
Alignment explanation
Indices: 3371--3424 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
3361 AGTATAGATT
3371 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3413 TG TG TG TG TG TG
1 TG TG TG TG TG TG
3425 ATTACTTAAC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:8997 original size:32 final size:32
Alignment explanation
Indices: 8961--9035 Score: 80
Period size: 32 Copynumber: 2.3 Consensus size: 32
8951 CATCATTCCG
* *
8961 TTGTAAATTTGGCATT-TTTTGCAATTAATGGA
1 TTGTAAATTTGGC-TTGATTTACAATTAATGGA
* * * *
8993 TTGTAATTTTGTCTTGATTTACATTTAATGGC
1 TTGTAAATTTGGCTTGATTTACAATTAATGGA
9025 TTGTAAATTTG
1 TTGTAAATTTG
9036 TCACCTTTTG
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
31 2 0.06
32 33 0.94
ACGTcount: A:0.25, C:0.07, G:0.17, T:0.51
Consensus pattern (32 bp):
TTGTAAATTTGGCTTGATTTACAATTAATGGA
Found at i:9029 original size:64 final size:64
Alignment explanation
Indices: 8961--9086 Score: 157
Period size: 64 Copynumber: 2.0 Consensus size: 64
8951 CATCATTCCG
** * * *
8961 TTGTAAATTTGGCATTTTTTGCAATT-AAT-GGATTGTAATTTTGTCTTGATTTACATTTAATGG
1 TTGTAAATTTGGCACCTTTTGC-ATTAAATCAG-TTGTAATTCTGGCTTGATTTACATTTAATGG
9024 C
64 C
* *
9025 TTGTAAATTTGTCACCTTTTGCATTAAATCAGTTGTAATTCTGGCTTGATTTGCATTTAATG
1 TTGTAAATTTGGCACCTTTTGCATTAAATCAGTTGTAATTCTGGCTTGATTTACATTTAATG
9087 AGTTGAAATT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
63 3 0.06
64 49 0.92
65 1 0.02
ACGTcount: A:0.25, C:0.10, G:0.17, T:0.48
Consensus pattern (64 bp):
TTGTAAATTTGGCACCTTTTGCATTAAATCAGTTGTAATTCTGGCTTGATTTACATTTAATGGC
Found at i:9370 original size:9 final size:9
Alignment explanation
Indices: 9345--9373 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
9335 CCCGTTCTTG
9345 GATGGGTTT
1 GATGGGTTT
9354 GA-GGGTTT
1 GATGGGTTT
9362 GATGGGTTT
1 GATGGGTTT
9371 GAT
1 GAT
9374 TTGATTTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.14, C:0.00, G:0.45, T:0.41
Consensus pattern (9 bp):
GATGGGTTT
Found at i:10058 original size:31 final size:31
Alignment explanation
Indices: 10017--10105 Score: 126
Period size: 31 Copynumber: 2.9 Consensus size: 31
10007 TAATATGTAA
10017 CCCAAA-AAAAACATAAGGGATTTTTTTGTC
1 CCCAAAGAAAAACATAAGGGATTTTTTTGTC
***
10047 TTTAAAGAAAAACATAAGGGATTTTTTTGTC
1 CCCAAAGAAAAACATAAGGGATTTTTTTGTC
* *
10078 CCCAAAGAAAAGCATAATGGATTTTTTT
1 CCCAAAGAAAAACATAAGGGATTTTTTT
10106 AGTATTTAGT
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
30 3 0.06
31 47 0.94
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (31 bp):
CCCAAAGAAAAACATAAGGGATTTTTTTGTC
Found at i:10452 original size:154 final size:153
Alignment explanation
Indices: 10254--10560 Score: 422
Period size: 154 Copynumber: 2.0 Consensus size: 153
10244 TAATTCCCTA
* **
10254 AAAATGTAAAGACAAAATAGTTATAAAAACATTGAATTTAATTAAATAAAAATAGAATT-TTTGG
1 AAAATGTAAAAACAAAATAGTTATAAAAACATTGAATTTAATTAAATAAAAATAGAATTCTTAAG
* *
10318 TGAAATAAAACTGTAAAAGTTTAAATAATGTCATTTAAGAAATATATTTAAAAAAATTCTAATAT
66 TG-AATAAAACTGTAAAAGTTTAAATAATGACATTAAAGAAATATATTT-AAAAAATTCTAATAT
*
10383 ATCTAA-CTTTTTAATTAAAGTAGT
129 ATCTAAGCTTTTTAATTAAAATAGT
* * * * *
10407 AAAATGGTAAAAATAAAATAGTTATAAATATATT-AGATTTGATTAAATAAAAATAGAGTTCTTA
1 AAAAT-GTAAAAACAAAATAGTTATAAAAACATTGA-ATTTAATTAAATAAAAATAGAATTCTTA
* * *
10471 ATTGAGTAAAATTGTAAAAGTTTAAATAATGACATTAAAGAAATATATTTAAAAAATTCTAATAT
64 AGTGAATAAAACTGTAAAAGTTTAAATAATGACATTAAAGAAATATATTTAAAAAATTCTAATAT
*
10536 ATCTAAGTTTTTTAATTAAAATAGT
129 ATCTAAGCTTTTTAATTAAAATAGT
10561 GTCGCAACGT
Statistics
Matches: 135, Mismatches: 15, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
153 27 0.20
154 104 0.77
155 4 0.03
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (153 bp):
AAAATGTAAAAACAAAATAGTTATAAAAACATTGAATTTAATTAAATAAAAATAGAATTCTTAAG
TGAATAAAACTGTAAAAGTTTAAATAATGACATTAAAGAAATATATTTAAAAAATTCTAATATAT
CTAAGCTTTTTAATTAAAATAGT
Done.