Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010099.1 Corchorus capsularis cultivar CVL-1 contig10120, 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: 33293
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:2527 original size:24 final size:27
Alignment explanation
Indices: 2500--2566 Score: 68
Period size: 29 Copynumber: 2.5 Consensus size: 27
2490 AAAAAAAACT
2500 AAAACAGAAAGTTAA-AAC-AAA-TAA
1 AAAACAGAAAGTTAATAACTAAAGTAA
* *
2524 AAAAAAGAACAGGTAAATAACTAAAGTAA
1 AAAACAGAA-A-GTTAATAACTAAAGTAA
*
2553 TAAACAGAAAGTTA
1 AAAACAGAAAGTTA
2567 TAATTTCTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
24 8 0.24
25 1 0.03
26 4 0.12
27 6 0.18
28 4 0.12
29 10 0.30
ACGTcount: A:0.66, C:0.07, G:0.12, T:0.15
Consensus pattern (27 bp):
AAAACAGAAAGTTAATAACTAAAGTAA
Found at i:2768 original size:18 final size:19
Alignment explanation
Indices: 2733--2770 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
2723 TATGTTTTGT
2733 ATTTTTGAGGAAAGAATGA
1 ATTTTTGAGGAAAGAATGA
* *
2752 ATTTTTTAGGTAA-AATGA
1 ATTTTTGAGGAAAGAATGA
2770 A
1 A
2771 CTATTGAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.37
Consensus pattern (19 bp):
ATTTTTGAGGAAAGAATGA
Found at i:3975 original size:193 final size:196
Alignment explanation
Indices: 3638--4024 Score: 690
Period size: 193 Copynumber: 2.0 Consensus size: 196
3628 TGAAATTTGA
*
3638 AAAAAAAAAGGCTATGAGAGACAAAAAAATTGACATGACATGAAATTTAAACCCTAAGTGAGATA
1 AAAAAAAAAGGCTATGAGAGACAAAAAAATTGACATGACATGAAATCTAAACCCTAAGTGAGATA
* *
3703 AAAATACATGATATATAAACCCTAAGTGAGAGAAAGAAATGCTCCAAAACTATATTAAACCCTAA
66 AAAATACATGATATATAAACCCTAAGTGAGAGAAAGAAATGCCCCAAAACAATATTAAACCCTAA
3768 GTGAGATAGTCTAAATTTCAACATTTTATGTCATAAAAAATGGTGGAAGAGTCAAAATTTGAAAT
131 GTGAGATAGTCTAAATTTCAACATTTTATGTCATAAAAAATGGTGGAAGAGTCAAAATTTGAAAT
3833 T
196 T
* *
3834 AAAAAAAATGGCTATGAGAGAC-AAAAAA-TGACATGACATGAAATCTATACCCTAAGTGAGAT-
1 AAAAAAAAAGGCTATGAGAGACAAAAAAATTGACATGACATGAAATCTAAACCCTAAGTGAGATA
*
3896 AAAATACATGATATATAAACCCTAAGTGAGATAAAGAAATGCCCCAAAACAATATTAAACCCTAA
66 AAAATACATGATATATAAACCCTAAGTGAGAGAAAGAAATGCCCCAAAACAATATTAAACCCTAA
*
3961 GTGAGATGGTCTAAATTTCAACATTTTATGTCATAAAAAATGGTGGAAGAGTCAAAATTTGAAA
131 GTGAGATAGTCTAAATTTCAACATTTTATGTCATAAAAAATGGTGGAAGAGTCAAAATTTGAAA
4025 AGTTGTGACA
Statistics
Matches: 184, Mismatches: 7, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
193 125 0.68
194 32 0.17
195 6 0.03
196 21 0.11
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.24
Consensus pattern (196 bp):
AAAAAAAAAGGCTATGAGAGACAAAAAAATTGACATGACATGAAATCTAAACCCTAAGTGAGATA
AAAATACATGATATATAAACCCTAAGTGAGAGAAAGAAATGCCCCAAAACAATATTAAACCCTAA
GTGAGATAGTCTAAATTTCAACATTTTATGTCATAAAAAATGGTGGAAGAGTCAAAATTTGAAAT
T
Found at i:9032 original size:6 final size:6
Alignment explanation
Indices: 9016--9049 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
9006 CGTTAGGGTT
9016 TGGGAAA TGGGAA TGGGAA TGGGAA TGGGAA TGG
1 TGGG-AA TGGGAA TGGGAA TGGGAA TGGGAA TGG
9050 AGACATACAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 23 0.85
7 4 0.15
ACGTcount: A:0.32, C:0.00, G:0.50, T:0.18
Consensus pattern (6 bp):
TGGGAA
Found at i:22874 original size:17 final size:17
Alignment explanation
Indices: 22851--22891 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
22841 ATAAGAATTG
22851 AGTGATC-TTGCATCACT
1 AGTGATCTTTG-ATCACT
*
22868 GGTGATCTTTGATCACT
1 AGTGATCTTTGATCACT
22885 AGTGATC
1 AGTGATC
22892 CGGGGGGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (17 bp):
AGTGATCTTTGATCACT
Found at i:27718 original size:204 final size:206
Alignment explanation
Indices: 27361--27768 Score: 669
Period size: 204 Copynumber: 2.0 Consensus size: 206
27351 GATGATAACG
* * *
27361 ATTGTGACGAACATCTTGAAATTCAACTACCACATCTTTATGGTTTTGAAAAAAAAAAAAAACCG
1 ATTGGGACGAACATCTTGAAATTCAACTACCAAATCTTTATGGTTTTG-AAAAAAAAAAAAACAG
* *
27426 AAGGGTAAGATGAAGTTCTCTTTTTCTTACTAGCATAATTTTGTGGGATACTTACGGATTGTTAT
65 AAAGGTAAGATGAAGTTCTCTTTTTCTTACTAGCATAATTTGGTGGGATACTTACGGATTGTTAT
* * *
27491 GTTTGTAGGCTATCTACTTTGACAACTGATGTTTCAGAAAAAGAGATAGTTACGG-TGGTTACTC
130 GTTTGTAGGATATCTACTTTGACAACTGATATTTCAGAAAAAGAGATAGTTACGGCTAGTTACTC
27555 CACACGAGAATT
195 CACACGAGAATT
27567 ATTGGGACGAACATCTTGAAATTCAACTACCAAATCTTTATGGTTTTG-AAAAAAAAAAAACAGA
1 ATTGGGACGAACATCTTGAAATTCAACTACCAAATCTTTATGGTTTTGAAAAAAAAAAAAACAGA
27631 AAGGTAAGATGAAGTTCTCTTTTTCTTACTAGCATAATTTGGTGGGATACTTACGGATTGTTATG
66 AAGGTAAGATGAAGTTCTCTTTTTCTTACTAGCATAATTTGGTGGGATACTTACGGATTGTTATG
* **
27696 TTTAG-AGGATATCTACTTTGACAAGTGATATTTCAGAAACTGAGATAGTTACGGCTAGTTACTC
131 TTT-GTAGGATATCTACTTTGACAACTGATATTTCAGAAAAAGAGATAGTTACGGCTAGTTACTC
*
27760 CATACGAGA
195 CACACGAGA
27769 TCCAGCGGGG
Statistics
Matches: 188, Mismatches: 12, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
204 125 0.66
205 17 0.09
206 46 0.24
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (206 bp):
ATTGGGACGAACATCTTGAAATTCAACTACCAAATCTTTATGGTTTTGAAAAAAAAAAAAACAGA
AAGGTAAGATGAAGTTCTCTTTTTCTTACTAGCATAATTTGGTGGGATACTTACGGATTGTTATG
TTTGTAGGATATCTACTTTGACAACTGATATTTCAGAAAAAGAGATAGTTACGGCTAGTTACTCC
ACACGAGAATT
Found at i:29660 original size:200 final size:202
Alignment explanation
Indices: 29312--29707 Score: 589
Period size: 200 Copynumber: 2.0 Consensus size: 202
29302 TGATGAGAGC
* * *
29312 GATTGGGACGAACATCTTGAAATTCAACTACCACATTTTTATGGTTTTGAAAAAAAAAAAACCGA
1 GATTGGGACGAACATCTTGAAATTCAACTACCAAATCTTTATGGTTTT---AAAAAAAAAACAGA
* * *
29377 AGGGTAAGATGAAGTTCCCTTTTTCCTACTAGCATAATTTTGTGGGATACTTACGGATTGTTATG
63 AAGGTAAGACGAAGTTCCCTTTTTCCTACTAGCATAATTTGGTGGGATACTTACGGATTGTTATG
* * * * *
29442 TTTGTAGGCTATCTACTTTGACAACTGATGTTTCAGAAAAAGAGATAGTTACAGCTGGTTACTCC
128 TTTGGAAGATATCTACTTTGACAACTGATATTTCAGAAAAAGAGATAGTTACAGCTAGTTACTCC
29507 ACAAGAGAAT
193 ACAAGAGAAT
*
29517 GATTGGGACGAACATCTTGAAATTCAACTACCAAATCTTTCT-GTTTT-AAAAAAAAACAGAAAG
1 GATTGGGACGAACATCTTGAAATTCAACTACCAAATCTTTATGGTTTTAAAAAAAAAACAGAAAG
* *
29580 GTAAGACGAAGTTCTCTTTTTCTTACTAGCATAATTTGGTGGGATACTTACGGATTGTTATGTTT
66 GTAAGACGAAGTTCCCTTTTTCCTACTAGCATAATTTGGTGGGATACTTACGGATTGTTATGTTT
* * * *
29645 GGAAGATATCTACTTTGACAAGTGATATTTCAGAAACAGAGATAGTTACGGTTAGTTACTCCA
131 GGAAGATATCTACTTTGACAACTGATATTTCAGAAAAAGAGATAGTTACAGCTAGTTACTCCA
29708 TACGAGATCC
Statistics
Matches: 173, Mismatches: 18, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
200 129 0.75
204 5 0.03
205 39 0.23
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (202 bp):
GATTGGGACGAACATCTTGAAATTCAACTACCAAATCTTTATGGTTTTAAAAAAAAAACAGAAAG
GTAAGACGAAGTTCCCTTTTTCCTACTAGCATAATTTGGTGGGATACTTACGGATTGTTATGTTT
GGAAGATATCTACTTTGACAACTGATATTTCAGAAAAAGAGATAGTTACAGCTAGTTACTCCACA
AGAGAAT
Found at i:31241 original size:206 final size:205
Alignment explanation
Indices: 30880--31294 Score: 677
Period size: 206 Copynumber: 2.0 Consensus size: 205
30870 CAAGATTGAT
* *
30880 GAGAGTGATTGGGACGAACATCTTGAAATTCTACTACCAAATCTTTATGGTTTTGAAAAAAAAAA
1 GAGAATGATTGGGACGAACATCTTGAAATTCAACTACCAAATCTTTATGGTTTTGAAAAAAAAAA
* * *
30945 AACCGAAGGGTAAGATGAAGTTCTCTTTTTCTTACTAGCATAATTTTGTGGGATACTTACGGATT
66 AACAGAAAGGTAAGATGAAGTTCTCTTTTTCTTACTAGCATAATTTGGTGGGATACTTACGGATT
* * *
31010 GTTATGTTTGTAGGCTATCTACTTTGACAACTGATGTTTCAGAAAAAGAGATAGTTACGGCTGGT
131 GTTATGTTTGGAGGATATCTACTTTGACAACTGATATTTCAGAAAAAGAGATAGTTACGGCTGGT
31075 TACTCCACAC
196 TACTCCACAC
* *
31085 GAGAATGATTGGGCCGAACATCTTGAAATTCAACTACCACATCTTTATGGTTTTGAAAAAAAAAA
1 GAGAATGATTGGGACGAACATCTTGAAATTCAACTACCAAATCTTTATGGTTTTGAAAAAAAAAA
31150 AATCAGAAAGGTAAGATGAAGTTCTCTTTTTCTTACTAGCATAATTTGGTGGGATACTTACGGAT
66 AA-CAGAAAGGTAAGATGAAGTTCTCTTTTTCTTACTAGCATAATTTGGTGGGATACTTACGGAT
* * ** *
31215 TGTTATGTTTGGAGGATATTTACTTTGACAAGTGATATTTCAGAAACTGAGATAGTTACGGCTTG
130 TGTTATGTTTGGAGGATATCTACTTTGACAACTGATATTTCAGAAAAAGAGATAGTTACGGCTGG
*
31280 TTACTCCATAC
195 TTACTCCACAC
31291 GAGA
1 GAGA
31295 TCCAGCGGGG
Statistics
Matches: 193, Mismatches: 16, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
205 63 0.33
206 130 0.67
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.33
Consensus pattern (205 bp):
GAGAATGATTGGGACGAACATCTTGAAATTCAACTACCAAATCTTTATGGTTTTGAAAAAAAAAA
AACAGAAAGGTAAGATGAAGTTCTCTTTTTCTTACTAGCATAATTTGGTGGGATACTTACGGATT
GTTATGTTTGGAGGATATCTACTTTGACAACTGATATTTCAGAAAAAGAGATAGTTACGGCTGGT
TACTCCACAC
Found at i:33215 original size:203 final size:203
Alignment explanation
Indices: 32826--33237 Score: 630
Period size: 203 Copynumber: 2.0 Consensus size: 203
32816 CAAGATTGAT
* * *
32826 GAGAATGATTGGGTCGAACATCTTGAAATTCAACTACCACATTTTTATGGTTTTGAAAAAAAAAA
1 GAGAATGATTGGGACGAACATCTTGAAAATCAACTACCACATCTTTATGGTTTTG--AAAAAAAA
* * *
32891 AACCGAATGGTAAGATGAAGTTCTCTTTTTCTTACAAGCATAATTTTGTGGGATACTTACGGATT
64 AACAGAAAGGTAAGATGAAGTTCTCTTTTTCTTACAAGCATAATTTGGTGGGATACTTACGGATT
* * * *
32956 GTTATGTTTGTAGGCTATCTACTTTGACAACTGATGTTTCAGGAAAAGAGATAGTTACGGCT-GG
129 GCTATGTTTGCAGGATATCTACTTTGACAACTGATATTTCAGGAAAAGAGATAGTTACGGCTAGG
33020 TTACTCCACAC
194 -TACTCCACAC
33031 GAGAATGATTGGGACGAACATCTTGAAAATCAACTACCACATCTTTATGGTTTTG-AAAAAAAAA
1 GAGAATGATTGGGACGAACATCTTGAAAATCAACTACCACATCTTTATGGTTTTGAAAAAAAAAA
*
33095 CAGAAAGGTAAGATGAAGTTCTCTTTTTCTTACTAGCATAAATTTGGTGGGATACTTACGGATTG
66 CAGAAAGGTAAGATGAAGTTCTCTTTTTCTTACAAGCAT-AATTTGGTGGGATACTTACGGATTG
* * **
33160 CTATGTTTGCAGGATATCTACTTTGACAAGTGATATTTCAGTAACTGAGATAGTTACGGCTAGGT
130 CTATGTTTGCAGGATATCTACTTTGACAACTGATATTTCAGGAAAAGAGATAGTTACGGCTAGGT
*
33225 ACTCCATAC
195 ACTCCACAC
33234 GAGA
1 GAGA
33238 TCCAGCGGGG
Statistics
Matches: 189, Mismatches: 16, Indels: 6
0.90 0.08 0.03
Matches are distributed among these distances:
202 45 0.24
203 90 0.48
204 2 0.01
205 52 0.28
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33
Consensus pattern (203 bp):
GAGAATGATTGGGACGAACATCTTGAAAATCAACTACCACATCTTTATGGTTTTGAAAAAAAAAA
CAGAAAGGTAAGATGAAGTTCTCTTTTTCTTACAAGCATAATTTGGTGGGATACTTACGGATTGC
TATGTTTGCAGGATATCTACTTTGACAACTGATATTTCAGGAAAAGAGATAGTTACGGCTAGGTA
CTCCACAC
Done.