Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018664.1 Corchorus olitorius cultivar O-4 contig18697, 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: 10089
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:2223 original size:22 final size:22
Alignment explanation
Indices: 2197--2245 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
2187 GAATTTCGAG
* *
2197 AACCTTTTTAT-AAATTTTTTTT
1 AACCTTCTTATGAAA-TTTTGTT
2219 AACCTTCTTATGAAATTTTGTT
1 AACCTTCTTATGAAATTTTGTT
2241 AACCT
1 AACCT
2246 CCCTAAGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.29, C:0.14, G:0.04, T:0.53
Consensus pattern (22 bp):
AACCTTCTTATGAAATTTTGTT
Found at i:2420 original size:22 final size:22
Alignment explanation
Indices: 2382--2441 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
2372 AAAACCTCCA
*
2382 TATG-AATTGTTAGTAATCACAC
1 TATGAAATTGTGA-TAATCACAC
* * *
2404 TCTGAAATTTTGATAATTACAC
1 TATGAAATTGTGATAATCACAC
2426 TATGAAATTGTGATAA
1 TATGAAATTGTGATAA
2442 CCTCGCTATA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
22 25 0.81
23 6 0.19
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (22 bp):
TATGAAATTGTGATAATCACAC
Found at i:2450 original size:22 final size:22
Alignment explanation
Indices: 2425--2515 Score: 114
Period size: 23 Copynumber: 4.1 Consensus size: 22
2415 GATAATTACA
* *
2425 CTATGAAATTGTGAT-AACCTC
1 CTATAAAATTTTGATAAACCTC
2446 GCTATAAAATTTTGATAAACCTTC
1 -CTATAAAATTTTGATAAACC-TC
*
2470 CTATAAAATTTTGATAAAGCTCC
1 CTATAAAATTTTGATAAACCT-C
2493 CTATAAAATTTTGAT-AACCTC
1 CTATAAAATTTTGATAAACCTC
2514 CT
1 CT
2516 TATGTAATAT
Statistics
Matches: 62, Mismatches: 4, Indels: 7
0.85 0.05 0.10
Matches are distributed among these distances:
21 3 0.05
22 18 0.29
23 39 0.63
24 2 0.03
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (22 bp):
CTATAAAATTTTGATAAACCTC
Found at i:2512 original size:45 final size:46
Alignment explanation
Indices: 2408--2512 Score: 128
Period size: 46 Copynumber: 2.3 Consensus size: 46
2398 TCACACTCTG
* *
2408 AAATTTTGATAA--TTACACTATGAAATTGTGATAACCTCGCTATA
1 AAATTTTGATAACCTTACACTATAAAATTGTGATAACCTCCCTATA
* *
2452 AAATTTTGATAAACCTT-C-CTATAAAATTTTGATAAAGCTCCCTATA
1 AAATTTTGAT-AACCTTACACTATAAAATTGTGAT-AACCTCCCTATA
2498 AAATTTTGATAACCT
1 AAATTTTGATAACCT
2513 CCTTATGTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
44 10 0.19
45 20 0.38
46 21 0.40
47 2 0.04
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (46 bp):
AAATTTTGATAACCTTACACTATAAAATTGTGATAACCTCCCTATA
Found at i:2580 original size:22 final size:23
Alignment explanation
Indices: 2539--2582 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
2529 TAACTACAAA
*
2539 TTTTGATAACCTCGCCTTATGATT
1 TTTTGATAACCTC-CATTATGATT
2563 TTTTGATAACCT-CATTATGA
1 TTTTGATAACCTCCATTATGA
2583 AAATTTGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
24 12 0.63
ACGTcount: A:0.25, C:0.18, G:0.11, T:0.45
Consensus pattern (23 bp):
TTTTGATAACCTCCATTATGATT
Found at i:2589 original size:22 final size:22
Alignment explanation
Indices: 2564--2657 Score: 57
Period size: 22 Copynumber: 4.1 Consensus size: 22
2554 CTTATGATTT
2564 TTTGATAACCTCATTATGAAAA
1 TTTGATAACCTCATTATGAAAA
* * ** *
2586 TTTGTTAATCTCCCTATGAAAT
1 TTTGATAACCTCATTATGAAAA
* * *
2608 TTTGATCTACATACTATATATGAAAT
1 TTTGAT-AACCT-C-AT-TATGAAAA
2634 TTTGATAACCCTC-TTAT-AAAA
1 TTTGATAA-CCTCATTATGAAAA
2655 TTT
1 TTT
2658 CGAAAATTAA
Statistics
Matches: 53, Mismatches: 14, Indels: 11
0.68 0.18 0.14
Matches are distributed among these distances:
21 6 0.11
22 25 0.47
23 3 0.06
24 1 0.02
25 2 0.04
26 16 0.30
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.43
Consensus pattern (22 bp):
TTTGATAACCTCATTATGAAAA
Found at i:2843 original size:22 final size:22
Alignment explanation
Indices: 2811--2998 Score: 86
Period size: 22 Copynumber: 8.6 Consensus size: 22
2801 TCACATTTTG
2811 AAAA-TTTGATAACCTCTTTAT
1 AAAATTTTGATAACCTCTTTAT
* *
2832 AAAATTTTGATAAACTCTCTAT
1 AAAATTTTGATAACCTCTTTAT
* * * *
2854 AAAATTTTGTTGACC-C-CTCT
1 AAAATTTTGATAACCTCTTTAT
* * *
2874 AAAATTTTGATAATCACATTAT
1 AAAATTTTGATAACCTCTTTAT
** *
2896 GTAATTTTGATAACCTCGCTTT-G
1 AAAATTTTGATAACCT--CTTTAT
** **
2919 AAAA-TTTGATAACAACACTAT
1 AAAATTTTGATAACCTCTTTAT
*
2940 GAAATTTTGATAA--TCTTCCTAT
1 AAAATTTTGATAACCTCTT--TAT
2962 -AAATTTTGATAATCCGATCTTTAT
1 AAAATTTTGATAA-CC--TCTTTAT
* *
2986 GAAATTTCGATAA
1 AAAATTTTGATAA
2999 TCACTCTATG
Statistics
Matches: 123, Mismatches: 29, Indels: 26
0.69 0.16 0.15
Matches are distributed among these distances:
20 18 0.15
21 21 0.17
22 61 0.50
23 2 0.02
24 6 0.05
25 11 0.09
26 4 0.03
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (22 bp):
AAAATTTTGATAACCTCTTTAT
Found at i:2945 original size:86 final size:86
Alignment explanation
Indices: 2789--2948 Score: 191
Period size: 86 Copynumber: 1.9 Consensus size: 86
2779 TACCACTATG
* * * * * *
2789 AAATTTTGGTACTCACATTTTGAAAATTTGATAACCTCTTTATAAAATTTTGATAAACTCTCTAT
1 AAATTTTGATAATCACATTATGAAAATTTGATAACCTCTTTAGAAAATTTTGATAAACACACTAT
2854 AAAATTTTGTTGACCCCTCTA
66 AAAATTTTGTTGACCCCTCTA
* *
2875 AAATTTTGATAATCACATTATGTAATTTTGATAACCTCGCTTT-GAAAA-TTTGAT-AACAACAC
1 AAATTTTGATAATCACATTATGAAAATTTGATAACCT--CTTTAGAAAATTTTGATAAAC-ACAC
*
2937 TATGAAATTTTG
63 TATAAAATTTTG
2949 ATAATCTTCC
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
85 3 0.05
86 51 0.82
87 4 0.06
88 4 0.06
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (86 bp):
AAATTTTGATAATCACATTATGAAAATTTGATAACCTCTTTAGAAAATTTTGATAAACACACTAT
AAAATTTTGTTGACCCCTCTA
Found at i:2991 original size:25 final size:23
Alignment explanation
Indices: 2875--3000 Score: 88
Period size: 22 Copynumber: 5.6 Consensus size: 23
2865 GACCCCTCTA
2875 AAATTTTGATAATCACAT--TATG
1 AAATTTTGATAATC-CATCCTATG
* *
2897 TAATTTTGATAA-CC-TCGCTTTG
1 AAATTTTGATAATCCATC-CTATG
* *
2919 AAAATTTGATAA--CAACACTATG
1 AAATTTTGATAATCCATC-CTATG
*
2941 AAATTTTGATAAT-CTTCCTAT-
1 AAATTTTGATAATCCATCCTATG
*
2962 AAATTTTGATAATCCGATCTTTATG
1 AAATTTTGATAATCC-ATC-CTATG
*
2987 AAATTTCGATAATC
1 AAATTTTGATAATC
3001 ACTCTATGAG
Statistics
Matches: 82, Mismatches: 13, Indels: 15
0.75 0.12 0.14
Matches are distributed among these distances:
19 1 0.01
20 1 0.01
21 15 0.18
22 45 0.55
23 4 0.05
24 3 0.04
25 13 0.16
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (23 bp):
AAATTTTGATAATCCATCCTATG
Found at i:3290 original size:22 final size:22
Alignment explanation
Indices: 3194--3394 Score: 144
Period size: 22 Copynumber: 9.0 Consensus size: 22
3184 GATAACAATT
* * *
3194 CTATAAAATTATGATAATCACA
1 CTATGAAATTTTGATAACCACA
** *
3216 CTATGAAATTTCAATAACCTTC-
1 CTATGAAATTTTGATAACC-ACA
* *
3238 CTAAGAAATTTTAATAACCTGATC-
1 CTATGAAATTTTGATAACC--A-CA
*
3262 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
3284 CTATGAAATTTTGATAACTTC-CA
1 CTATGAAATTTTGATAAC--CACA
* *
3307 -TATGAACTTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
* *
3328 CAATGAAATTTTGATAACCTC-
1 CTATGAAATTTTGATAACCACA
* *
3349 CTCATGAAATTATAATAACCATC-
1 CT-ATGAAATTTTGATAACCA-CA
*
3372 TTATGAAATTTTGATAACCACA
1 CTATGAAATTTTGATAACCACA
3394 C
1 C
3395 AGAGACAAGA
Statistics
Matches: 140, Mismatches: 28, Indels: 22
0.74 0.15 0.12
Matches are distributed among these distances:
20 1 0.01
21 5 0.04
22 111 0.79
23 5 0.04
24 18 0.13
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.34
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:3325 original size:44 final size:43
Alignment explanation
Indices: 3242--3390 Score: 165
Period size: 44 Copynumber: 3.3 Consensus size: 43
3232 ACCTTCCTAA
*
3242 GAAATTTTAATAACCTGATCCTATGAAATTTTGGTAACCACACTAT
1 GAAATTTTGATAACC---TCCTATGAAATTTTGGTAACCACACTAT
* * *
3288 GAAATTTTGATAACTTCCATATGAACTTTTGGTAACCACACAAT
1 GAAATTTTGATAACCTCC-TATGAAATTTTGGTAACCACACTAT
* ** *
3332 GAAATTTTGATAACCTCCTCATGAAATTATAATAACCATC-TTAT
1 GAAATTTTGATAACCTCCT-ATGAAATTTTGGTAACCA-CACTAT
3376 GAAATTTTGATAACC
1 GAAATTTTGATAACC
3391 ACACAGAGAC
Statistics
Matches: 89, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
43 4 0.04
44 71 0.80
45 1 0.01
46 13 0.15
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (43 bp):
GAAATTTTGATAACCTCCTATGAAATTTTGGTAACCACACTAT
Found at i:3367 original size:66 final size:66
Alignment explanation
Indices: 3199--3395 Score: 177
Period size: 66 Copynumber: 3.0 Consensus size: 66
3189 CAATTCTATA
* * * * * *
3199 AAATTATGATAATCACACTATGAAATT-TCAATAACCTTCCTAAGAAATTTTAATAACCTGATC-
1 AAATTTTGATAACCACACTATGAAATTAT-AATAACCATCATATGAAATTTTGATAACC--A-CA
*
3262 CTATG
62 CAATG
* * * * * *
3267 AAATTTTGGTAACCACACTATGAAATTTTGATAA-CTTCCATATGAACTTTTGGTAACCACACAA
1 AAATTTTGATAACCACACTATGAAATTATAATAACCAT-CATATGAAATTTTGATAACCACACAA
3331 TG
65 TG
* *
3333 AAATTTTGATAACCTC-CTCATGAAATTATAATAACCATCTTATGAAATTTTGATAACCACACA
1 AAATTTTGATAACCACACT-ATGAAATTATAATAACCATCATATGAAATTTTGATAACCACACA
3396 GAGACAAGAA
Statistics
Matches: 106, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
65 3 0.03
66 54 0.51
67 5 0.05
68 43 0.41
69 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.34
Consensus pattern (66 bp):
AAATTTTGATAACCACACTATGAAATTATAATAACCATCATATGAAATTTTGATAACCACACAAT
G
Found at i:9417 original size:25 final size:27
Alignment explanation
Indices: 9381--9430 Score: 86
Period size: 25 Copynumber: 1.9 Consensus size: 27
9371 TCCATCCGAT
9381 TATAATTATCCATTATATT-TTTAAAA
1 TATAATTATCCATTATATTATTTAAAA
9407 TATAA-TATCCATTATATTATTTAA
1 TATAATTATCCATTATATTATTTAA
9431 TTATCTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (27 bp):
TATAATTATCCATTATATTATTTAAAA
Done.