Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013067.1 Corchorus capsularis cultivar CVL-1 contig13088, 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: 4576
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Found at i:833 original size:32 final size:31
Alignment explanation
Indices: 758--866 Score: 137
Period size: 32 Copynumber: 3.5 Consensus size: 31
748 GAACCCGTCC
*
758 GACCCGAGACCCGAATGACCCGCAACCCAGT
1 GACCCGAGACCCGAATGACCCGTAACCCAGT
* *
789 GACCCGAGACCCGAATGACCCGTAATCTAGAT
1 GACCCGAGACCCGAATGACCCGTAACCCAG-T
* *
821 GACCCGAAACCCGAATGACTCGTAACCCGAGT
1 GACCCGAGACCCGAATGACCCGTAACCC-AGT
* *
853 GGCCCGAAACCCGA
1 GACCCGAGACCCGA
867 GAAGTTAACC
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
31 27 0.40
32 39 0.57
33 2 0.03
ACGTcount: A:0.30, C:0.37, G:0.23, T:0.10
Consensus pattern (31 bp):
GACCCGAGACCCGAATGACCCGTAACCCAGT
Found at i:867 original size:16 final size:16
Alignment explanation
Indices: 758--867 Score: 89
Period size: 16 Copynumber: 6.9 Consensus size: 16
748 GAACCCGTCC
* *
758 GACCCGAGACCCGAAT
1 GACCCGAAACCCGAGT
*
774 GACCCGCAACCC-AGT
1 GACCCGAAACCCGAGT
* *
789 GACCCGAGACCCGAAT
1 GACCCGAAACCCGAGT
* * *
805 GACCCGTAA-TCTAGAT
1 GACCCGAAACCCGAG-T
*
821 GACCCGAAACCCGAAT
1 GACCCGAAACCCGAGT
* *
837 GACTCGTAACCCGAGT
1 GACCCGAAACCCGAGT
*
853 GGCCCGAAACCCGAG
1 GACCCGAAACCCGAG
868 AAGTTAACCT
Statistics
Matches: 70, Mismatches: 21, Indels: 6
0.72 0.22 0.06
Matches are distributed among these distances:
15 14 0.20
16 54 0.77
17 2 0.03
ACGTcount: A:0.30, C:0.36, G:0.24, T:0.10
Consensus pattern (16 bp):
GACCCGAAACCCGAGT
Found at i:1960 original size:16 final size:16
Alignment explanation
Indices: 1941--2066 Score: 94
Period size: 16 Copynumber: 7.5 Consensus size: 16
1931 TTGACCAAAT
*
1941 TGACCCGAAACCCGAG
1 TGACCCGAAACCCGAA
* *
1957 TGACCCGAGACCCG-G
1 TGACCCGAAACCCGAA
* *
1972 TAGACCTGAGACCCGAA
1 T-GACCCGAAACCCGAA
*
1989 TGACCCGGAACCCGTAA
1 TGACCCGAAACCCG-AA
*
2006 -GACCCGAGACCCGAA
1 TGACCCGAAACCCGAA
*
2021 TTACCCGAAACCCGAACCTAGA
1 TGACCCGAAACCCG-----A-A
2043 TGACCCGAAACCCGAA
1 TGACCCGAAACCCGAA
2059 TGACCCGA
1 TGACCCGA
2067 GAAAGCTGCC
Statistics
Matches: 89, Mismatches: 11, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
15 4 0.04
16 66 0.74
17 4 0.04
21 1 0.01
22 14 0.16
ACGTcount: A:0.32, C:0.37, G:0.23, T:0.09
Consensus pattern (16 bp):
TGACCCGAAACCCGAA
Found at i:1993 original size:9 final size:8
Alignment explanation
Indices: 1942--2066 Score: 61
Period size: 7 Copynumber: 15.9 Consensus size: 8
1932 TGACCAAATT
1942 GACCCGAA
1 GACCCGAA
*
1950 -ACCCGAGT
1 GACCCGA-A
1958 GACCCG-A
1 GACCCGAA
*
1965 GACCCGGTA
1 GACCC-GAA
*
1974 GACCTG-A
1 GACCCGAA
1981 GACCCGAA
1 GACCCGAA
*
1989 TGACCCGGA
1 -GACCCGAA
1998 -ACCCGTAA
1 GACCCG-AA
2006 GACCCG-A
1 GACCCGAA
2013 GACCCGAA
1 GACCCGAA
*
2021 TTACCCGAA
1 -GACCCGAA
2030 -ACCCG-A
1 GACCCGAA
* *
2036 -ACCTAGAT
1 GACC-CGAA
2044 GACCCGAA
1 GACCCGAA
2052 -ACCCGAA
1 GACCCGAA
2059 TGACCCGA
1 -GACCCGA
2067 GAAAGCTGCC
Statistics
Matches: 91, Mismatches: 11, Indels: 29
0.69 0.08 0.22
Matches are distributed among these distances:
6 4 0.04
7 42 0.46
8 7 0.08
9 38 0.42
ACGTcount: A:0.32, C:0.37, G:0.23, T:0.08
Consensus pattern (8 bp):
GACCCGAA
Found at i:1993 original size:32 final size:33
Alignment explanation
Indices: 1942--2068 Score: 116
Period size: 32 Copynumber: 3.8 Consensus size: 33
1932 TGACCAAATT
* *
1942 GACCCGAAACCCGAGTGACCCGAGACCCGGT-A
1 GACCCGAGACCCGAATGACCCGAGACCCGGTAA
*
1974 GACCTGAGACCCGAATGACCCG-GAACCC-GTAA
1 GACCCGAGACCCGAATGACCCGAG-ACCCGGTAA
* * *
2006 GACCCGAGACCCGAATTACCCGAAACCCGAACCTAGA
1 GACCCGAGACCCGAATGACCCGAGACCCG---GTA-A
*
2043 TGACCCGAAACCCGAATGACCCGAGA
1 -GACCCGAGACCCGAATGACCCGAGA
2069 AAGCTGCCTG
Statistics
Matches: 76, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
31 3 0.04
32 48 0.63
36 2 0.03
37 1 0.01
38 22 0.29
ACGTcount: A:0.32, C:0.36, G:0.24, T:0.08
Consensus pattern (33 bp):
GACCCGAGACCCGAATGACCCGAGACCCGGTAA
Found at i:2234 original size:31 final size:31
Alignment explanation
Indices: 2199--2257 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
2189 ATGTTTTCCG
**
2199 ATTGTACCCT-TATTTTTAAAACATATTTTCA
1 ATTGTACCCTCT-TTTAAAAAACATATTTTCA
2230 ATTGTACCCTCTTTTAAAAAACATATTT
1 ATTGTACCCTCTTTTAAAAAACATATTT
2258 CTAAATTGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 24 0.96
32 1 0.04
ACGTcount: A:0.34, C:0.17, G:0.03, T:0.46
Consensus pattern (31 bp):
ATTGTACCCTCTTTTAAAAAACATATTTTCA
Found at i:2448 original size:38 final size:37
Alignment explanation
Indices: 2384--2479 Score: 120
Period size: 38 Copynumber: 2.6 Consensus size: 37
2374 TTTGGATTTT
2384 TTTGTTTCCAACGTCCTATTTAATTTTACCTTTTGTA
1 TTTGTTTCCAACGTCCTATTTAATTTTACCTTTTGTA
** * * *
2421 TTTGTTTCCAATCGTTGTATTTAATTTTGCTTTTTGTC
1 TTTGTTTCCAA-CGTCCTATTTAATTTTACCTTTTGTA
* *
2459 TTCGTCTCCAACGTCCTATTT
1 TTTGTTTCCAACGTCCTATTT
2480 GGACATTGAT
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
37 19 0.39
38 30 0.61
ACGTcount: A:0.16, C:0.20, G:0.10, T:0.54
Consensus pattern (37 bp):
TTTGTTTCCAACGTCCTATTTAATTTTACCTTTTGTA
Found at i:2565 original size:22 final size:22
Alignment explanation
Indices: 2537--2659 Score: 92
Period size: 22 Copynumber: 5.6 Consensus size: 22
2527 TGGTTCAATT
*
2537 TCAAAATTTCAAAGCGAGGTTA
1 TCAAAATTTCAAAGAGAGGTTA
* *
2559 TCAAAATTACATAATGTGA--TTA
1 TCAAAATTTCA-AA-GAGAGGTTA
* * *
2581 TCAAAATTTCATAGAGGGGTCA
1 TCAAAATTTCAAAGAGAGGTTA
* *
2603 ACAAAAATTT-ATAGAGAGGTTA
1 TC-AAAATTTCAAAGAGAGGTTA
*
2625 TTAAAATTTCATAA-AGAGGTTA
1 TCAAAATTTCA-AAGAGAGGTTA
*
2647 TCAAATTTTCAAA
1 TCAAAATTTCAAA
2660 ATGTGATTAC
Statistics
Matches: 79, Mismatches: 15, Indels: 15
0.72 0.14 0.14
Matches are distributed among these distances:
20 2 0.03
21 10 0.13
22 54 0.68
23 10 0.13
24 3 0.04
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.32
Consensus pattern (22 bp):
TCAAAATTTCAAAGAGAGGTTA
Found at i:2608 original size:44 final size:43
Alignment explanation
Indices: 2537--3195 Score: 134
Period size: 44 Copynumber: 14.8 Consensus size: 43
2527 TGGTTCAATT
* *
2537 TCAAAATTTCAAAGCGAGGTTATCAAAATTACATAATGTGATTA
1 TCAAAATTTCATAGAGAGGTTATCAAAATT-CATAATGTGATTA
* * * * * *
2581 TCAAAATTTCATAGAGGGGTCAACAAAAATTTATAGA-GAGGTTA
1 TCAAAATTTCATAGAGAGGTTATC-AAAATTCATA-ATGTGATTA
* * * *
2625 TTAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGATTA
1 TCAAAATTTCATAGAGAGGTTATCAAA-ATTCATAATGTGATTA
* * *
2669 CCAAAATTTCATAGTGGTATTTCTGGGGAGGTTATCAAAATTTCATAATATGGTTA
1 TCAAAATTTCATA---G-A--------GAGGTTATCAAAA-TTCATAATGTGATTA
* * * * * * * *
2725 -CCAAA-TT-A-GGA-AGGTTATTAAACTTTTATTATG-AAGTAA
1 TCAAAATTTCATAGAGAGGTTATCAAA-ATTCATAATGTGA-TTA
* * * *
2764 TCAAAATTTC--AGGGATGATATCAAAATTTCAT-ATGAAGATTA
1 TCAAAATTTCATAGAGAGGTTATCAAAA-TTCATAATG-TGATTA
** * * *
2806 TCAAAATTTCATAGTTTA-GTTTTCAAAATTTCATAA-GAGGGTTA
1 TCAAAATTTCATAG-AGAGGTTATCAAAA-TTCATAATG-TGATTA
* * * * * *
2850 TCAAAATTCCATAGTG-TGTAGATCAAAATTTCATAAGGAGATTA
1 TCAAAATTTCATAGAGAGGT-TATCAAAA-TTCATAATGTGATTA
* * ** * *
2894 ACAAAATTTCATA-ATGAGGTTATCAAAAAATCATAGGGAGGTTA
1 TCAAAATTTCATAGA-GAGGTTATC-AAAATTCATAATGTGATTA
* ** *
2938 TCAAAATTTCATA-AGGAGGTTATCAAAATTTTATAGGGAGATTTA
1 TCAAAATTTCATAGA-GAGGTTATCAAAA-TTCATAATGTGA-TTA
* ** * *
2983 TCAAAATTTTATAG-GAAGGTTTATCAAAATTTCATAGCGAGGTTA
1 TCAAAATTTCATAGAG-AGG-TTATCAAAA-TTCATAATGTGATTA
* * * * * *
3028 TCACAATTTCATAGTGTGATTATCAAAATTTCAGAGTGTGATTAA
1 TCAAAATTTCATAGAGAGGTTATCAAAA-TTCATAATGTGATT-A
* * * * * *
3073 TGACAA-TTCATATG-GAGGTTTTTAAATTTTCATAATGTGGTTA
1 TCAAAATTTCATA-GAGAGGTTATCAAA-ATTCATAATGTGATTA
* * * * * *
3116 TCAATATATCATATG-GAGGTTATCAACATCTTATAGTGTTGGTTA
1 TCAAAATTTCATA-GAGAGGTTATCAAAAT-TCATAATG-TGATTA
* *
3161 TCAAAATTTCATTTG-GAAGTTATCAAAATTTCATA
1 TCAAAATTTCA-TAGAGAGGTTATCAAAA-TTCATA
3196 GTGAGGTCTT
Statistics
Matches: 458, Mismatches: 107, Indels: 99
0.69 0.16 0.15
Matches are distributed among these distances:
39 18 0.04
40 4 0.01
41 6 0.01
42 24 0.05
43 17 0.04
44 245 0.53
45 88 0.19
46 22 0.05
48 2 0.00
49 1 0.00
53 1 0.00
54 2 0.00
55 4 0.01
56 24 0.05
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (43 bp):
TCAAAATTTCATAGAGAGGTTATCAAAATTCATAATGTGATTA
Found at i:2810 original size:22 final size:22
Alignment explanation
Indices: 2782--3239 Score: 279
Period size: 22 Copynumber: 20.7 Consensus size: 22
2772 TCAGGGATGA
* *
2782 TATCAAAATTTCATATGAAGAT
1 TATCAAAATTTCATATGGAGGT
**
2804 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGGAGGT
* *
2826 TTTCAAAATTTCATA-AGAGGGT
1 TATCAAAATTTCATATGGA-GGT
*
2848 TATCAAAATTCCATAGTGTGTA-G-
1 TATCAAAATTTCATA-TG-G-AGGT
* *
2871 -ATCAAAATTTCATAAGGAGAT
1 TATCAAAATTTCATATGGAGGT
*
2892 TAACAAAATTTCATAAT-GAGGT
1 TATCAAAATTTCAT-ATGGAGGT
** *
2914 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATATGGAGGT
*
2936 TATCAAAATTTCATAAGGAGGT
1 TATCAAAATTTCATATGGAGGT
* * *
2958 TATCAAAATTTTATAGGGAGATT
1 TATCAAAATTTCATATGGAG-GT
*
2981 TATCAAAATTTTATA-GGAAGGTT
1 TATCAAAATTTCATATGG-AGG-T
3004 TATCAAAATTTCATA-GCGAGGT
1 TATCAAAATTTCATATG-GAGGT
*
3026 TATCACAATTTCATAGTGTGA--T
1 TATCAAAATTTCATA-TG-GAGGT
*
3048 TATCAAAATTTCAGAGTGTGA--T
1 TATCAAAATTTCATA-TG-GAGGT
* *
3070 TAATGACAA-TTCATATGGAGGT
1 T-ATCAAAATTTCATATGGAGGT
* * * *
3092 TTTTAAATTTTCATAAT-GTGGT
1 TATCAAAATTTCAT-ATGGAGGT
* *
3114 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATATGGAGGT
* **
3136 TATCAACATCTT-ATAGTGTTGGT
1 TATCAAAAT-TTCATA-TGGAGGT
* *
3159 TATCAAAATTTCATTTGGAAGT
1 TATCAAAATTTCATATGGAGGT
3181 TATCAAAATTTCATA-GTGAGGT
1 TATCAAAATTTCATATG-GAGGT
*
3203 CT-TCAAAA-TTCTTTATGGAGGT
1 -TATCAAAATTTC-ATATGGAGGT
3225 TAAT-AAAATTTCATA
1 T-ATCAAAATTTCATA
3240 AGAAGATTAA
Statistics
Matches: 344, Mismatches: 58, Indels: 68
0.73 0.12 0.14
Matches are distributed among these distances:
19 1 0.00
20 4 0.01
21 14 0.04
22 249 0.72
23 69 0.20
24 5 0.01
25 1 0.00
26 1 0.00
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATATGGAGGT
Found at i:3350 original size:62 final size:62
Alignment explanation
Indices: 3298--3449 Score: 232
Period size: 62 Copynumber: 2.5 Consensus size: 62
3288 TCGTTATTGA
*
3298 AATTTTATAGGAAGGTTATCAAAATTTCATAAAGACGTCATAAAAAATAGTGTAGTTATCAT
1 AATTTAATAGGAAGGTTATCAAAATTTCATAAAGACGTCATAAAAAATAGTGTAGTTATCAT
* * * * *
3360 AATTTCATAGGAAGGTTATCAAAATTCCATAAGGACGTCATCAAAAATAGTGTAATTATCAT
1 AATTTAATAGGAAGGTTATCAAAATTTCATAAAGACGTCATAAAAAATAGTGTAGTTATCAT
* *
3422 AATTTAATAGGAATGTTATCATAATTTC
1 AATTTAATAGGAAGGTTATCAAAATTTC
3450 GTATGAATAT
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
62 81 1.00
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (62 bp):
AATTTAATAGGAAGGTTATCAAAATTTCATAAAGACGTCATAAAAAATAGTGTAGTTATCAT
Done.