Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014732.1 Corchorus olitorius cultivar O-4 contig14765, 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: 50788
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:2778 original size:24 final size:24
Alignment explanation
Indices: 2751--2808 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
2741 GACCCTGCTT
* *
2751 CCACAACCACCACCACCACATCCC
1 CCACAACCACCACCACCACAGCCA
* *
2775 CCACATCCACCAGCACCACAGCCA
1 CCACAACCACCACCACCACAGCCA
2799 CCACAACCAC
1 CCACAACCAC
2809 TGCTGTTTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.34, C:0.59, G:0.03, T:0.03
Consensus pattern (24 bp):
CCACAACCACCACCACCACAGCCA
Found at i:2840 original size:76 final size:75
Alignment explanation
Indices: 2749--2914 Score: 262
Period size: 76 Copynumber: 2.2 Consensus size: 75
2739 CTGACCCTGC
*
2749 TTCCACAACCACCACCACCA-CATCCCCCACATCCACCAGCACCACAGCCACCACAACCACTGCT
1 TTCCACAACCACCACCA-CATCATCCACCACATCCACCAGCACCACAGCCACCACAACCACTGCT
2813 GTTTCACCATGA
65 G-TTCACCATGA
* * *
2825 TTCCACAACCTCCACCACATCCTCCACCACATCCGCCAGCACCACAGCCACCACAACCACTGCTG
1 TTCCACAACCACCACCACATCATCCACCACATCCACCAGCACCACAGCCACCACAACCACTGCTG
*
2890 TTCACCATGC
66 TTCACCATGA
2900 TTCCACAACCACCAC
1 TTCCACAACCACCAC
2915 ATCCGCCAGC
Statistics
Matches: 83, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
75 25 0.30
76 58 0.70
ACGTcount: A:0.29, C:0.51, G:0.07, T:0.14
Consensus pattern (75 bp):
TTCCACAACCACCACCACATCATCCACCACATCCACCAGCACCACAGCCACCACAACCACTGCTG
TTCACCATGA
Found at i:2848 original size:12 final size:12
Alignment explanation
Indices: 2827--2858 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
2817 CACCATGATT
*
2827 CCACAACCTCCA
1 CCACATCCTCCA
2839 CCACATCCTCCA
1 CCACATCCTCCA
2851 CCACATCC
1 CCACATCC
2859 GCCAGCACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.28, C:0.59, G:0.00, T:0.12
Consensus pattern (12 bp):
CCACATCCTCCA
Found at i:2906 original size:27 final size:27
Alignment explanation
Indices: 2875--2971 Score: 77
Period size: 27 Copynumber: 3.4 Consensus size: 27
2865 ACCACAGCCA
2875 CCACAACCACTGCTGTTCACCATGCTT
1 CCACAACCACTGCTGTTCACCATGCTT
** ** * **
2902 CCACAACCACCACATCCGCCAGCACCACAGCCA
1 CCACAACCACTGC-T--G--TTCACCA-TGCTT
2935 CCACAACCACTGCTGTTCACCATGCTT
1 CCACAACCACTGCTGTTCACCATGCTT
2962 CCACAACCAC
1 CCACAACCAC
2972 CACATCCGCC
Statistics
Matches: 50, Mismatches: 14, Indels: 12
0.66 0.18 0.16
Matches are distributed among these distances:
27 23 0.46
28 6 0.12
30 2 0.04
32 6 0.12
33 13 0.26
ACGTcount: A:0.28, C:0.47, G:0.09, T:0.15
Consensus pattern (27 bp):
CCACAACCACTGCTGTTCACCATGCTT
Found at i:2916 original size:60 final size:60
Alignment explanation
Indices: 2848--3081 Score: 432
Period size: 60 Copynumber: 3.9 Consensus size: 60
2838 ACCACATCCT
2848 CCACCACATCCGCCAGCACCACAGCCACCACAACCACTGCTGTTCACCATGCTTCCACAA
1 CCACCACATCCGCCAGCACCACAGCCACCACAACCACTGCTGTTCACCATGCTTCCACAA
2908 CCACCACATCCGCCAGCACCACAGCCACCACAACCACTGCTGTTCACCATGCTTCCACAA
1 CCACCACATCCGCCAGCACCACAGCCACCACAACCACTGCTGTTCACCATGCTTCCACAA
*
2968 CCACCACATCCGCCAGCACCACAGCCACCACAACCACTGCTGTTCACCATGATTCCACAA
1 CCACCACATCCGCCAGCACCACAGCCACCACAACCACTGCTGTTCACCATGCTTCCACAA
3028 CCTCCACCACATCCGCCAGCACCACAGCCACCACAACCACTGCTGTTCACCATG
1 ---CCACCACATCCGCCAGCACCACAGCCACCACAACCACTGCTGTTCACCATG
3082 ACATTAGTAC
Statistics
Matches: 170, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
60 119 0.70
63 51 0.30
ACGTcount: A:0.28, C:0.48, G:0.10, T:0.13
Consensus pattern (60 bp):
CCACCACATCCGCCAGCACCACAGCCACCACAACCACTGCTGTTCACCATGCTTCCACAA
Found at i:16242 original size:9 final size:9
Alignment explanation
Indices: 16228--16257 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
16218 GAAAACATTC
16228 TTCTCTGTT
1 TTCTCTGTT
16237 TTCTCTGTT
1 TTCTCTGTT
*
16246 TCCTCTGTT
1 TTCTCTGTT
16255 TTC
1 TTC
16258 CCCTGTTTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.00, C:0.27, G:0.10, T:0.63
Consensus pattern (9 bp):
TTCTCTGTT
Found at i:16265 original size:19 final size:18
Alignment explanation
Indices: 16230--16272 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
16220 AAACATTCTT
*
16230 CTCTGTTTTCTCTGTTTC
1 CTCTGTTTTCCCTGTTTC
16248 CTCTGTTTTCCCCTGTTTC
1 CTCTGTTTT-CCCTGTTTC
*
16267 CCCTGT
1 CTCTGT
16273 CTATGCCATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.00, C:0.35, G:0.12, T:0.53
Consensus pattern (18 bp):
CTCTGTTTTCCCTGTTTC
Found at i:29284 original size:23 final size:23
Alignment explanation
Indices: 29254--29297 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
29244 GAGTCGGATC
29254 CGGATTAATCAGGGTTAAGCCCT
1 CGGATTAATCAGGGTTAAGCCCT
29277 CGGATTAATCAGGGTTAAGCC
1 CGGATTAATCAGGGTTAAGCC
29298 TGGATATCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.25
Consensus pattern (23 bp):
CGGATTAATCAGGGTTAAGCCCT
Found at i:35726 original size:97 final size:97
Alignment explanation
Indices: 35533--35712 Score: 351
Period size: 97 Copynumber: 1.9 Consensus size: 97
35523 ACTAACTTAA
35533 GTAGTTATTCTAGCATTTAATTAAGCCGCCATGACAGGAAGGGAATAAAAACTCCCAATTTATAT
1 GTAGTTATTCTAGCATTTAATTAAGCCGCCATGACAGGAAGGGAATAAAAACTCCCAATTTATAT
*
35598 GATAGATAGATAGATAAATAAACAACGTTACT
66 GATAGATAGATAAATAAATAAACAACGTTACT
35630 GTAGTTATTCTAGCATTTAATTAAGCCGCCATGACAGGAAGGGAATAAAAACTCCCAATTTATAT
1 GTAGTTATTCTAGCATTTAATTAAGCCGCCATGACAGGAAGGGAATAAAAACTCCCAATTTATAT
35695 GATAGATAGATAAATAAA
66 GATAGATAGATAAATAAA
35713 CAACGTTACT
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
97 82 1.00
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.28
Consensus pattern (97 bp):
GTAGTTATTCTAGCATTTAATTAAGCCGCCATGACAGGAAGGGAATAAAAACTCCCAATTTATAT
GATAGATAGATAAATAAATAAACAACGTTACT
Found at i:46340 original size:3 final size:3
Alignment explanation
Indices: 46334--46365 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
46324 CTAATAATAA
*
46334 AAG AAG AAG AAG AAG AAG AAG GAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
46366 AGAAATTCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AAG
Done.