Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024396.1 Corchorus olitorius cultivar O-4 contig24429, 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: 17205
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:3606 original size:28 final size:27
Alignment explanation
Indices: 3573--3660 Score: 74
Period size: 28 Copynumber: 3.3 Consensus size: 27
3563 TTTTTTTCAA
3573 AATTTTCAAATTGGGAAAGTTCCCATC
1 AATTTTCAAATTGGGAAAGTTCCCATC
* *** * **
3600 AATTTTTCAAAGTGTTCAATTTAGC-TC
1 AA-TTTTCAAATTGGGAAAGTTCCCATC
3627 --TTTTCAAATTGGGAAAGTTCCCATC
1 AATTTTCAAATTGGGAAAGTTCCCATC
3652 AAGTTTTCA
1 AA-TTTTCA
3661 TAGTATTCAA
Statistics
Matches: 42, Mismatches: 14, Indels: 9
0.65 0.22 0.14
Matches are distributed among these distances:
24 15 0.36
25 2 0.05
27 4 0.10
28 21 0.50
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.39
Consensus pattern (27 bp):
AATTTTCAAATTGGGAAAGTTCCCATC
Found at i:3632 original size:52 final size:52
Alignment explanation
Indices: 3575--3722 Score: 251
Period size: 52 Copynumber: 2.8 Consensus size: 52
3565 TTTTTCAAAA
* *
3575 TTTTCAAATTGGGAAAGTTCCCATCAATTTTTCAAAGTGTTCAATTTAGCTC
1 TTTTCAAATTGGGAAAGTTCCCATCAAGTTTTCAAAGTATTCAATTTAGCTC
*
3627 TTTTCAAATTGGGAAAGTTCCCATCAAGTTTTCATAGTATTCAATTTAGCTC
1 TTTTCAAATTGGGAAAGTTCCCATCAAGTTTTCAAAGTATTCAATTTAGCTC
* *
3679 TTTTCAAATTGAGAAAGTTCCCATCAAGTTTTCAAAGTTTTCAA
1 TTTTCAAATTGGGAAAGTTCCCATCAAGTTTTCAAAGTATTCAA
3723 ATCGGGAAAG
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 90 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (52 bp):
TTTTCAAATTGGGAAAGTTCCCATCAAGTTTTCAAAGTATTCAATTTAGCTC
Found at i:3720 original size:37 final size:37
Alignment explanation
Indices: 3679--3863 Score: 169
Period size: 37 Copynumber: 4.9 Consensus size: 37
3669 AATTTAGCTC
*
3679 TTTTCAAATTGAGAAAGTTCCCATCAAGTTTTCAAAG
1 TTTTCAAATTGGGAAAGTTCCCATCAAGTTTTCAAAG
* *
3716 TTTTCAAATCGGGAAAGTTCCCATCAAGTTTTTTTCAAAA
1 TTTTCAAATTGGGAAAGTTCCCATCAAG---TTTTCAAAG
* * * ***
3756 TTTTCAATTTAGGGAAAGTTCCCGT-TAGTGTTGATTTTAG
1 TTTTCAAATT-GGGAAAGTTCCCATCAAGT-TT--TCAAAG
* *
3796 TTTTCAAGA-TAGGAAAGTTCCCATCAAGTTTTGAAAG
1 TTTTCAA-ATTGGGAAAGTTCCCATCAAGTTTTCAAAG
*
3833 TTATCAAATTGGGAAAGTTCCCATC-AGTTTT
1 TTTTCAAATTGGGAAAGTTCCCATCAAGTTTT
3864 TAGTTTTCTT
Statistics
Matches: 118, Mismatches: 20, Indels: 21
0.74 0.13 0.13
Matches are distributed among these distances:
36 7 0.06
37 51 0.43
38 2 0.02
39 14 0.12
40 31 0.26
41 13 0.11
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.38
Consensus pattern (37 bp):
TTTTCAAATTGGGAAAGTTCCCATCAAGTTTTCAAAG
Found at i:3831 original size:20 final size:20
Alignment explanation
Indices: 3808--3863 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 20
3798 TTCAAGATAG
3808 GAAAGTTCCCATCAAGTTTT
1 GAAAGTTCCCATCAAGTTTT
* **
3828 GAAAGTT---ATCAAATTGG
1 GAAAGTTCCCATCAAGTTTT
3845 GAAAGTTCCCATC-AGTTTT
1 GAAAGTTCCCATCAAGTTTT
3864 TAGTTTTCTT
Statistics
Matches: 27, Mismatches: 6, Indels: 7
0.68 0.15 0.17
Matches are distributed among these distances:
17 14 0.52
19 3 0.11
20 10 0.37
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (20 bp):
GAAAGTTCCCATCAAGTTTT
Found at i:3932 original size:115 final size:114
Alignment explanation
Indices: 3679--3937 Score: 301
Period size: 115 Copynumber: 2.2 Consensus size: 114
3669 AATTTAGCTC
* * *
3679 TTTTCAAATTGAGAAAGTTCCCATCAAGTTTTCAAAGTTTTCAAATCGGGAAAGTTCCCATCAAG
1 TTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTTATCAAATCGGGAAAGTTCCCATCAAG
* * * *
3744 TTTTTTTCAAAATTTTCAATTTAGGGAAAGTTCCCGTTAGTGTTGATTTTAG
66 TTTTTTT---AATTTTCAATTTAGGGAAAGCTCCCGTCAATGTCGATTTTAG
* * *
3796 TTTTC-AAGATAGGAAAGTTCCCATCAAGTTTTGAAAGTTATCAAATTGGGAAAGTTCCCATC-A
1 TTTTCAAAG-TGGGAAAGTTCCCATCAAGTTTTCAAAGTTATCAAATCGGGAAAGTTCCCATCAA
* *
3859 GTTTTTAGTT-TTCTTTCAATTTAGGGAAAGCTCCCGTCAAT-TCCGGTTTTAG
65 GTTTTT--TTAAT-TTTCAATTTAGGGAAAGCTCCCGTCAATGT-CGATTTTAG
*
3911 TTTTCAAAGTGGGAAAATTCCCATCAA
1 TTTTCAAAGTGGGAAAGTTCCCATCAA
3938 AAGCATTGTT
Statistics
Matches: 122, Mismatches: 14, Indels: 14
0.81 0.09 0.09
Matches are distributed among these distances:
114 2 0.02
115 53 0.43
116 12 0.10
117 53 0.43
118 2 0.02
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (114 bp):
TTTTCAAAGTGGGAAAGTTCCCATCAAGTTTTCAAAGTTATCAAATCGGGAAAGTTCCCATCAAG
TTTTTTTAATTTTCAATTTAGGGAAAGCTCCCGTCAATGTCGATTTTAG
Found at i:4610 original size:41 final size:41
Alignment explanation
Indices: 4515--4704 Score: 223
Period size: 41 Copynumber: 4.7 Consensus size: 41
4505 TTTAACAATA
*
4515 TCTCTCTTAGGGTTTAGCTT-GATTTTAGGGT-TTT--TTTA
1 TCTCTCTTAGGGTTTAGCTTAG-TTTTAGGGTGTTTAATTTC
* * *
4553 TTTCTCATAGGGTTTAGCTTAGTTTTAGGGTGTTGAATTTC
1 TCTCTCTTAGGGTTTAGCTTAGTTTTAGGGTGTTTAATTTC
* * *
4594 TCTCTCTTAGGGTTTAGCTT-GATTTT-GGGGGTTTATTTTG
1 TCTCTCTTAGGGTTTAGCTTAG-TTTTAGGGTGTTTAATTTC
*
4634 TCTCTCCTAGGGTTTAGCTTAGTTTTAGGGGTGTTTAATTTC
1 TCTCTCTTAGGGTTTAGCTTAGTTTTA-GGGTGTTTAATTTC
*
4676 TCTCT-TTAGGGTTTAGCTTATTTTTAGGG
1 TCTCTCTTAGGGTTTAGCTTAGTTTTAGGG
4705 GTTAGTTTTA
Statistics
Matches: 128, Mismatches: 16, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
38 27 0.21
39 3 0.02
40 37 0.29
41 45 0.35
42 16 0.12
ACGTcount: A:0.14, C:0.11, G:0.24, T:0.51
Consensus pattern (41 bp):
TCTCTCTTAGGGTTTAGCTTAGTTTTAGGGTGTTTAATTTC
Found at i:4647 original size:40 final size:40
Alignment explanation
Indices: 4513--4729 Score: 203
Period size: 40 Copynumber: 5.4 Consensus size: 40
4503 ATTTTAACAA
*
4513 TATCTCTCTTAGGGTTTAGCTT-GATTTT-AGGGTTT-TTT
1 TATCTCTCTTAGGGTTTAGCTTAG-TTTTGGGGGTTTATTT
* * * * *
4551 TATTTCTCATAGGGTTTAGCTTAGTTTTAGGGTGTTGAATT
1 TATCTCTCTTAGGGTTTAGCTTAGTTTT-GGGGGTTTATTT
*
4592 TCTCTCTCTTAGGGTTTAGCTT-GATTTTGGGGGTTTATTT
1 TATCTCTCTTAGGGTTTAGCTTAG-TTTTGGGGGTTTATTT
* * *
4632 TGTCTCTCCTAGGGTTTAGCTTAGTTTTAGGGGTGTTTAATT
1 TATCTCTCTTAGGGTTTAGCTTAGTTTT-GGGG-GTTTATTT
* * *
4674 TCTCTCT-TTAGGGTTTAGCTTATTTTTAGGGG-TTAGTTT
1 TATCTCTCTTAGGGTTTAGCTTAGTTTTGGGGGTTTA-TTT
* *
4713 TATCTTTCCTAGGGTTT
1 TATCTCTCTTAGGGTTT
4730 GGGCTTTGTT
Statistics
Matches: 146, Mismatches: 23, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
38 27 0.18
39 9 0.06
40 49 0.34
41 48 0.33
42 13 0.09
ACGTcount: A:0.14, C:0.11, G:0.24, T:0.52
Consensus pattern (40 bp):
TATCTCTCTTAGGGTTTAGCTTAGTTTTGGGGGTTTATTT
Found at i:4661 original size:81 final size:81
Alignment explanation
Indices: 4515--4729 Score: 305
Period size: 81 Copynumber: 2.7 Consensus size: 81
4505 TTTAACAATA
* * *
4515 TCTCTCTTAGGGTTTAGCTTGATTTTAGGGTTT-TTTTATTTCTCATAGGGTTTAGCTTAGTTTT
1 TCTCTCTTAGGGTTTAGCTTGATTTTGGGGTTTATTTTATCTCTCCTAGGGTTTAGCTTAGTTTT
4579 A-GGGTGTTGAATTTC
66 AGGGGTGTTGAATTTC
*
4594 TCTCTCTTAGGGTTTAGCTTGATTTTGGGGGTTTATTTTGTCTCTCCTAGGGTTTAGCTTAGTTT
1 TCTCTCTTAGGGTTTAGCTTGATTTT-GGGGTTTATTTTATCTCTCCTAGGGTTTAGCTTAGTTT
*
4659 TAGGGGTGTTTAATTTC
65 TAGGGGTGTTGAATTTC
*
4676 TCTCT-TTAGGGTTTAGCTT-ATTTTTAGGGG-TTAGTTTTATCTTTCCTAGGGTTT
1 TCTCTCTTAGGGTTTAGCTTGA-TTTT-GGGGTTTA-TTTTATCTCTCCTAGGGTTT
4730 GGGCTTTGTT
Statistics
Matches: 123, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
79 26 0.21
80 10 0.08
81 69 0.56
82 18 0.15
ACGTcount: A:0.13, C:0.11, G:0.24, T:0.52
Consensus pattern (81 bp):
TCTCTCTTAGGGTTTAGCTTGATTTTGGGGTTTATTTTATCTCTCCTAGGGTTTAGCTTAGTTTT
AGGGGTGTTGAATTTC
Found at i:5204 original size:32 final size:32
Alignment explanation
Indices: 5150--5234 Score: 100
Period size: 32 Copynumber: 2.7 Consensus size: 32
5140 TTCGGGTAAT
* *
5150 TCGGGTTCAGGTATTTTCGGGCTTGGATTA-A
1 TCGGGTTCGGGTATTTTCGGGCTCGGATTATA
* * *
5181 GTCGGATTCGGGTATTTTTGGGCTCGGGTTATA
1 -TCGGGTTCGGGTATTTTCGGGCTCGGATTATA
*
5214 TCGGGTTCGGGTATATTCGGG
1 TCGGGTTCGGGTATTTTCGGG
5235 TTTGGTCGCG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
32 43 0.98
33 1 0.02
ACGTcount: A:0.13, C:0.13, G:0.36, T:0.38
Consensus pattern (32 bp):
TCGGGTTCGGGTATTTTCGGGCTCGGATTATA
Found at i:5223 original size:16 final size:16
Alignment explanation
Indices: 5138--5236 Score: 71
Period size: 16 Copynumber: 6.2 Consensus size: 16
5128 TGCTAGGGCA
5138 GGTTCGGGTA-ATTCG
1 GGTTCGGGTATATTCG
* *
5153 GGTTCAGGTATTTTCG
1 GGTTCGGGTATATTCG
* *
5169 GGCTT-GGAT-TAAGTCG
1 GG-TTCGGGTAT-ATTCG
* * *
5185 GATTCGGGTATTTTTG
1 GGTTCGGGTATATTCG
*
5201 GGCTCGGGT-TATATCG
1 GGTTCGGGTATAT-TCG
5217 GGTTCGGGTATATTCG
1 GGTTCGGGTATATTCG
5233 GGTT
1 GGTT
5237 TGGTCGCGGG
Statistics
Matches: 61, Mismatches: 16, Indels: 13
0.68 0.18 0.14
Matches are distributed among these distances:
15 14 0.23
16 41 0.67
17 6 0.10
ACGTcount: A:0.13, C:0.12, G:0.36, T:0.38
Consensus pattern (16 bp):
GGTTCGGGTATATTCG
Found at i:10269 original size:33 final size:33
Alignment explanation
Indices: 10232--10298 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
10222 TCTCCCTAGT
10232 TCTTTGTTTGCTCCTCCTCCTTGACTAGTATTG
1 TCTTTGTTTGCTCCTCCTCCTTGACTAGTATTG
*
10265 TCTTTGTTTGCTCCTCCTCCTTGGCTAGTATTG
1 TCTTTGTTTGCTCCTCCTCCTTGACTAGTATTG
10298 T
1 T
10299 TAAGGGGGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.07, C:0.27, G:0.16, T:0.49
Consensus pattern (33 bp):
TCTTTGTTTGCTCCTCCTCCTTGACTAGTATTG
Found at i:10431 original size:15 final size:15
Alignment explanation
Indices: 10411--10445 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
10401 GATCTTGGAT
*
10411 GTTTGAGTCAGTTTA
1 GTTTGAGTCAGTTGA
10426 GTTTGAGTCAGTTGA
1 GTTTGAGTCAGTTGA
10441 GTTTG
1 GTTTG
10446 TCGAGTTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.17, C:0.06, G:0.31, T:0.46
Consensus pattern (15 bp):
GTTTGAGTCAGTTGA
Found at i:17032 original size:31 final size:28
Alignment explanation
Indices: 16995--17053 Score: 91
Period size: 31 Copynumber: 2.0 Consensus size: 28
16985 TAATAGTGTG
16995 TTCTTAATTTAAAAGCTGATCATCTTGGAGT
1 TTCTTAATTTAAAAGC---TCATCTTGGAGT
17026 TTCTTAATTTAAAAGCTCATCTTGGAGT
1 TTCTTAATTTAAAAGCTCATCTTGGAGT
17054 GGTGTTATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 12 0.43
31 16 0.57
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (28 bp):
TTCTTAATTTAAAAGCTCATCTTGGAGT
Done.