Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020622.1 Corchorus olitorius cultivar O-4 contig20655, 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: 4525
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Found at i:2614 original size:48 final size:48
Alignment explanation
Indices: 2550--3747 Score: 1734
Period size: 48 Copynumber: 25.1 Consensus size: 48
2540 TTTGAAGACA
* *
2550 GGAA-AAAATATTGAAAACAACACCTTCCGACTGGGAAGGGCAAAACG
1 GGAATAAAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACG
* *
2597 GGAATAAAATATCGAAAACAACACCTTCCGACCGGGAAGGGCAAAACG
1 GGAATAAAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACG
* * **
2645 GGAATAAAACATTGAAGACAACACCTTCC-ATCCAGGAAGGGCAAAAAA
1 GGAATAAAATATTGAAGACAACACCTTCCGA-CCGGGAAGGGCAAAACG
2693 GGAATAAAATATTGGAA-ACAACACCTTCCGACCGGGAAGGGCAAAACG
1 GGAATAAAATATT-GAAGACAACACCTTCCGACCGGGAAGGGCAAAACG
* * *
2741 GGAATAAAACATTGAAGACAACACCTTCCGACCAGGAAGGGCAAAACA
1 GGAATAAAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACG
* * * *
2789 AGAATAAAATATTGAAAACAACACCTTCCGGCCGGGAAGGGCAAAACA
1 GGAATAAAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACG
*
2837 GGAATAAAATATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACG
1 GGAATAAAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACG
*
2885 GGAATAAAATATCGAAGACAACACCTTCCGACCGGGAAGGGCAAAACG
1 GGAATAAAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACG
* *
2933 GGAATAAAATATCGAAGACAACACCTTCCGTCCGGGAAGGGCAAAACG
1 GGAATAAAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACG
* **
2981 GGAATAAAATATTGAAGACAATACCTTCTAACCGGGAAGGGCAAAACG
1 GGAATAAAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACG
*
3029 GGAATAAAATATCGAAGACAACACCTTCCGACCGGGAAGGGCAAAACG
1 GGAATAAAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACG
* * *
3077 GGAATAAAACATTGAAGACAACACCTTCCAACCGGGAAGGGCAAAACA
1 GGAATAAAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACG
* **
3125 GGAATAAAATATTGGAA-ACAACACCTTCCAACCGGGAAGGATAAAACG
1 GGAATAAAATATT-GAAGACAACACCTTCCGACCGGGAAGGGCAAAACG
* * *
3173 GGAATAAAACATTGAAGACAATACCTTCTGACCGGGAAGGGCAAAACG
1 GGAATAAAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACG
* * *
3221 GGAATAAAATATCGAACACAACACCTTCCGACCTGGAAGGGCAAAACG
1 GGAATAAAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACG
* *
3269 GGAATAAAACATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACA
1 GGAATAAAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACG
* * *
3317 GGAATAAAATATTGAAAACAACACCTTCCGACCGAGAAGGGCAAAATG
1 GGAATAAAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACG
* *
3365 GGAATAAAACATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACA
1 GGAATAAAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACG
*
3413 GGAATAAAATATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACG
1 GGAATAAAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACG
* * * *
3461 GGAATAAAACATTGAAGACGACACCTTCCGACCGAGAAGGGCAAAACA
1 GGAATAAAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACG
*
3509 GGAATAAAATATTGAAAACAACACCTTCCGACCGGGAAGGGCAAAACG
1 GGAATAAAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACG
* * **
3557 GGAATAAAACATTGAAGACAACACCTTCCGACCGCGAAGGGCAAAATA
1 GGAATAAAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACG
* *
3605 GGAATAAAATATTGAAAATAACACCTTCCGACCGGGAAGGGCAAAACG
1 GGAATAAAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACG
* * * *
3653 GGAATAAAACATTGAAGACAACAGCATCCGACTGGGAAGGG-AAAACG
1 GGAATAAAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACG
* * *
3700 AGAAT---A-A-TGATGACAACACCTTCCGATCGGGAAGGGC-AAACTG
1 GGAATAAAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAAC-G
3743 GGAAT
1 GGAAT
3748 GTAAACAACA
Statistics
Matches: 1035, Mismatches: 107, Indels: 22
0.89 0.09 0.02
Matches are distributed among these distances:
42 28 0.03
43 6 0.01
44 1 0.00
47 21 0.02
48 972 0.94
49 7 0.01
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (48 bp):
GGAATAAAATATTGAAGACAACACCTTCCGACCGGGAAGGGCAAAACG
Found at i:3810 original size:41 final size:40
Alignment explanation
Indices: 3712--3829 Score: 166
Period size: 41 Copynumber: 2.9 Consensus size: 40
3702 AATAATGATG
*
3712 ACAACACCTTCCGATCG-GGAAGGGCAAACTGGGAATGTAA
1 ACAACACCTTCCGAT-GAGGAAGGGCAAACTGGGAATTTAA
**
3752 ACAACACCTTCTTATGAGGAAGGGCAAACTGGGAATTTAAA
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTT-AA
* *
3793 ACAACACCTTCCGATGAGGAAGGCCAAACTAGGAATT
1 ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATT
3830 ATCGAAGGAA
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
39 1 0.01
40 33 0.48
41 35 0.51
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.18
Consensus pattern (40 bp):
ACAACACCTTCCGATGAGGAAGGGCAAACTGGGAATTTAA
Found at i:3901 original size:44 final size:41
Alignment explanation
Indices: 3845--4144 Score: 228
Period size: 44 Copynumber: 6.8 Consensus size: 41
3835 AGGAAAACTG
*
3845 GGACCTTCCGACTAGGAAGGGGCATTTTTTGGAAATGGAAAAAA
1 GGACCTTCCGACCAGGAAGGGGCA-TTTTTGG-AAT-GAAAAAA
* ** *
3889 GGACCTTACGACTGGGAAGGGGCATTTTTAGAATGAGATATCCAAAA
1 GGACCTTCCGACCAGGAAGGGGCATTTTTGGAAT--GA-A---AAAA
*
3936 CTGGGATCTTCCGACC-GAGAAGGGGCATTTTTTGGAAATGAAAATAA
1 ---GGACCTTCCGACCAG-GAAGGGGCA-TTTTTGG-AATGAAAA-AA
*
3983 GGACCTTCCAACCAGGAAGGGGCA-TTTTGGTAATGAAAACAA
1 GGACCTTCCGACCAGGAAGGGGCATTTTTGG-AATGAAAA-AA
* * *
4025 AGACCTCCCAACCAGGAAGGGGCATTTTTGGAATGAAAGAAAA
1 GGACCTTCCGACCAGGAAGGGGCATTTTTGGAATG-AA-AAAA
** **
4068 CTGTGACCTTCCGACTGGGAAGGGGCATTTTTGGAAT-AAAACG
1 --G-GACCTTCCGACCAGGAAGGGGCATTTTTGGAATGAAAAAA
*
4111 GAGACCTTCCAACCAGGAAGGGGCATTTTTGGAA
1 G-GACCTTCCGACCAGGAAGGGGCATTTTTGGAA
4145 AGAGATAAGA
Statistics
Matches: 212, Mismatches: 25, Indels: 41
0.76 0.09 0.15
Matches are distributed among these distances:
41 30 0.14
42 45 0.21
43 20 0.09
44 47 0.22
45 1 0.00
46 31 0.15
47 6 0.03
49 2 0.01
50 21 0.10
51 6 0.03
52 3 0.01
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.22
Consensus pattern (41 bp):
GGACCTTCCGACCAGGAAGGGGCATTTTTGGAATGAAAAAA
Found at i:4018 original size:94 final size:94
Alignment explanation
Indices: 3838--4010 Score: 260
Period size: 94 Copynumber: 1.8 Consensus size: 94
3828 TTATCGAAGG
* * **
3838 AAAACTGGGACCTTCCGACTAGGAAGGGGCATTTTTTGGAAATGGAAAAAAGGACCTTACGACTG
1 AAAACTGGGACCTTCCGACGAGGAAGGGGCATTTTTTGGAAATGGAAAAAAGGACCTTACAACCA
3903 GGAAGGGGCATTTTTAGAATGAGATATCC
66 GGAAGGGGCATTTTTAGAATGAGATATCC
* *
3932 AAAACTGGGATCTTCCGACCGA-GAAGGGGCATTTTTTGGAAAT-GAAAATAAGGACCTTCCAAC
1 AAAACTGGGACCTTCCGA-CGAGGAAGGGGCATTTTTTGGAAATGGAAAA-AAGGACCTTACAAC
3995 CAGGAAGGGGCATTTT
64 CAGGAAGGGGCATTTT
4011 GGTAATGAAA
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
93 5 0.07
94 64 0.90
95 2 0.03
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (94 bp):
AAAACTGGGACCTTCCGACGAGGAAGGGGCATTTTTTGGAAATGGAAAAAAGGACCTTACAACCA
GGAAGGGGCATTTTTAGAATGAGATATCC
Found at i:4030 original size:42 final size:42
Alignment explanation
Indices: 3954--4144 Score: 217
Period size: 42 Copynumber: 4.4 Consensus size: 42
3944 TTCCGACCGA
* *
3954 GAAGGGGCATTTTTTGGAAATGAAAATAAGGACCTTCCAACCAG
1 GAAGGGGCA-TTTTTGG-AATGAAAACAAAGACCTTCCAACCAG
*
3998 GAAGGGGCA-TTTTGGTAATGAAAACAAAGACCTCCCAACCAG
1 GAAGGGGCATTTTTGG-AATGAAAACAAAGACCTTCCAACCAG
* **
4040 GAAGGGGCATTTTTGGAATGAAAGA-AAACTGTGACCTTCCGACTGG
1 GAAGGGGCATTTTTGGAATGAAA-ACAAA----GACCTTCCAACCAG
**
4086 GAAGGGGCATTTTTGGAAT-AAAACGGAGACCTTCCAACCAG
1 GAAGGGGCATTTTTGGAATGAAAACAAAGACCTTCCAACCAG
4127 GAAGGGGCATTTTTGGAA
1 GAAGGGGCATTTTTGGAA
4145 AGAGATAAGA
Statistics
Matches: 127, Mismatches: 13, Indels: 17
0.81 0.08 0.11
Matches are distributed among these distances:
41 29 0.23
42 48 0.38
43 7 0.06
44 10 0.08
45 4 0.03
46 29 0.23
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.21
Consensus pattern (42 bp):
GAAGGGGCATTTTTGGAATGAAAACAAAGACCTTCCAACCAG
Found at i:4130 original size:41 final size:42
Alignment explanation
Indices: 3954--4144 Score: 192
Period size: 41 Copynumber: 4.4 Consensus size: 42
3944 TTCCGACCGA
3954 GAAGGGGCATTTTTTGGAAATGAAAATA-AG-GACCTTCCAACCAG
1 GAAGGGGCA-TTTTTGG-AAT-AAAA-ACAGAGACCTTCCAACCAG
* * *
3998 GAAGGGGCA-TTTTGGTAATGAAAACAAAGACCTCCCAACCAG
1 GAAGGGGCATTTTTGG-AATAAAAACAGAGACCTTCCAACCAG
* * * **
4040 GAAGGGGCATTTTTGGAATGAAAGAAAACTGTGACCTTCCGACTGG
1 GAAGGGGCATTTTTGGAAT---A-AAAACAGAGACCTTCCAACCAG
*
4086 GAAGGGGCATTTTTGGAAT-AAAACGGAGACCTTCCAACCAG
1 GAAGGGGCATTTTTGGAATAAAAACAGAGACCTTCCAACCAG
4127 GAAGGGGCATTTTTGGAA
1 GAAGGGGCATTTTTGGAA
4145 AGAGATAAGA
Statistics
Matches: 123, Mismatches: 17, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
40 1 0.01
41 39 0.32
42 34 0.28
43 6 0.05
44 9 0.07
46 34 0.28
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.21
Consensus pattern (42 bp):
GAAGGGGCATTTTTGGAATAAAAACAGAGACCTTCCAACCAG
Found at i:4134 original size:87 final size:84
Alignment explanation
Indices: 3954--4144 Score: 242
Period size: 87 Copynumber: 2.2 Consensus size: 84
3944 TTCCGACCGA
*
3954 GAAGGGGCATTTTTTGGAAATGAAAATAAGGACCTTCCAACCAGGAAGGGGCATTTTGGTAATGA
1 GAAGGGGCA-TTTTTGG-AATGAAAAAAAGGACCTTCCAACCAGGAAGGGGCATTTTGGTAATGA
4019 AAACAAAGACCTCCCAACCAG
64 AAACAAAGACCTCCCAACCAG
* **
4040 GAAGGGGCATTTTTGGAATGAAAGAAAACTGTGACCTTCCGACTGGGAAGGGGCATTTTTGG-AA
1 GAAGGGGCATTTTTGGAATGAAA-AAAA--G-GACCTTCCAACCAGGAAGGGGCA-TTTTGGTAA
** *
4104 T-AAAACGGAGACCTTCCAACCAG
61 TGAAAACAAAGACCTCCCAACCAG
4127 GAAGGGGCATTTTTGGAA
1 GAAGGGGCATTTTTGGAA
4145 AGAGATAAGA
Statistics
Matches: 93, Mismatches: 7, Indels: 9
0.85 0.06 0.08
Matches are distributed among these distances:
84 7 0.08
85 10 0.11
86 9 0.10
87 38 0.41
88 23 0.25
89 6 0.06
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.21
Consensus pattern (84 bp):
GAAGGGGCATTTTTGGAATGAAAAAAAGGACCTTCCAACCAGGAAGGGGCATTTTGGTAATGAAA
ACAAAGACCTCCCAACCAG
Done.