Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021356.1 Corchorus olitorius cultivar O-4 contig21389, 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: 19333
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Found at i:584 original size:13 final size:13
Alignment explanation
Indices: 566--591 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
556 AGCCCAATGG
566 AAGGTAAGAAACA
1 AAGGTAAGAAACA
579 AAGGTAAGAAACA
1 AAGGTAAGAAACA
592 GAGAGTGGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.23, T:0.08
Consensus pattern (13 bp):
AAGGTAAGAAACA
Found at i:1320 original size:22 final size:22
Alignment explanation
Indices: 1260--1911 Score: 192
Period size: 22 Copynumber: 29.8 Consensus size: 22
1250 CCTAATAGGG
* *
1260 GGTTATCAAAAATTCATAATGT
1 GGTTATCAAAATTTCATAGTGT
* *
1282 AGTTATCAAAATCTCATAGTGT
1 GGTTATCAAAATTTCATAGTGT
*
1304 GGTTATCAAATTTTCATAGTGT
1 GGTTATCAAAATTTCATAGTGT
* *
1326 -GTAGATCAAAATTTAATAGT-T
1 GGT-TATCAAAATTTCATAGTGT
* * * *
1347 TGTAGATCAACATTTCATAG-GAAG
1 GGT-TATCAAAATTTCATAGTG--T
*
1371 GGTTATCAAAATTTCATAATGAT
1 GGTTATCAAAATTTCATAGTG-T
* ** * *
1394 -GTTATAAAAAAAATCATAGGGA
1 GGTTAT-CAAAATTTCATAGTGT
* * *
1416 GGTTATTAAAATTTCATAGGGA
1 GGTTATCAAAATTTCATAGTGT
*** * * *
1438 AAATATCAAAATTTTATAGGGAC
1 GGTTATCAAAATTTCATAGTG-T
*
1461 GTTTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAGTGT
* *
1483 GGTCATCAAAATTTCATAAG-GA
1 GGTTATCAAAATTTCAT-AGTGT
* *
1505 CGTTATCACAATTTCATAGTGT
1 GGTTATCAAAATTTCATAGTGT
* *
1527 GGTTATCAAAATTTTACAGTGT
1 GGTTATCAAAATTTCATAGTGT
* * *
1549 GATTACCAACA-TT--T--T-T
1 GGTTATCAAAATTTCATAGTGT
* ** * * ***
1565 AGAAATTAACATGTT--TAGGAA
1 GGTTATCAAAAT-TTCATAGTGT
**
1586 GGTTATCAATTTTTCATAGTGT
1 GGTTATCAAAATTTCATAGTGT
* * * *
1608 GTGCTTACCAACATTTCACA-TAGA
1 G-G-TTATCAAAATTTCATAGT-GT
* * *
1632 GATTATCTAAATTTCATACTGT
1 GGTTATCAAAATTTCATAGTGT
* * * *
1654 GCTTCTCAAAATTTTATAG-GAA
1 GGTTATCAAAATTTCATAGTG-T
*
1676 GGTTATCAAAATTTCAT-GATGA
1 GGTTATCAAAATTTCATAG-TGT
* *
1698 AGTTATCAAAATTCCATAGTGT
1 GGTTATCAAAATTTCATAGTGT
* * * *
1720 AGTTATCAAAATTTCATTGGGA
1 GGTTATCAAAATTTCATAGTGT
* ** * *
1742 GGCTAAAAAAATTTCA-ATGGGA
1 GGTTATCAAAATTTCATA-GTGT
* * *
1764 GGTTCTCGAAATTCCATAGTGT
1 GGTTATCAAAATTTCATAGTGT
** * *
1786 CATTATCAAAATTT--TAGAGA
1 GGTTATCAAAATTTCATAGTGT
* *
1806 GTTTATCAAAATTTCATAG-GAA
1 GGTTATCAAAATTTCATAGTG-T
* * * *
1828 GATTATCTAGATTTCATAATGT
1 GGTTATCAAAATTTCATAGTGT
* * ***
1850 GATTTTCAAAATTTCATAGCCA
1 GGTTATCAAAATTTCATAGTGT
* * **
1872 GGTAATCACAATTTCATAGTAC
1 GGTTATCAAAATTTCATAGTGT
*
1894 GATTATCAAAATTTCATA
1 GGTTATCAAAATTTCATA
1912 AGGATGTTTA
Statistics
Matches: 456, Mismatches: 142, Indels: 64
0.69 0.21 0.10
Matches are distributed among these distances:
16 6 0.01
17 1 0.00
18 3 0.01
20 18 0.04
21 16 0.04
22 341 0.75
23 54 0.12
24 17 0.04
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGTGT
Found at i:1472 original size:45 final size:44
Alignment explanation
Indices: 1407--1523 Score: 128
Period size: 45 Copynumber: 2.6 Consensus size: 44
1397 ATAAAAAAAA
* *
1407 TCATAGGGAGGTTATTAAAATTTCATAGGGAAAAT-ATCAAAATT
1 TCATAGGGACGTTATCAAAATTTCATAGGG-AAATCATCAAAATT
* * ***
1451 TTATAGGGACGTTTATCAAAATTTCATAGTGTGGTCATCAAAATT
1 TCATAGGGACG-TTATCAAAATTTCATAGGGAAATCATCAAAATT
* *
1496 TCATAAGGACGTTATCACAATTTCATAG
1 TCATAGGGACGTTATCAAAATTTCATAG
1524 TGTGGTTATC
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
44 26 0.43
45 35 0.57
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (44 bp):
TCATAGGGACGTTATCAAAATTTCATAGGGAAATCATCAAAATT
Found at i:1710 original size:66 final size:65
Alignment explanation
Indices: 1631--1911 Score: 214
Period size: 66 Copynumber: 4.3 Consensus size: 65
1621 TTTCACATAG
* * * * *
1631 AGATTATCTAAATTTCATACTGTGCTTCTCAAAATTTTATAGGAAGGTTATCAAAATTTCATGAT
1 AGATTATCAAAATTTCATAGTGTGCTTATCAAAATTTCATAGG-AGGTTATCAAAATTTCAT-AG
1696 GA
64 GA
* * * **
1698 AG-TTATCAAAATTCCATAGTGTAG-TTATCAAAATTTCATTGGGAGGCTAAAAAAATTTCA-AT
1 AGATTATCAAAATTTCATAGTGT-GCTTATCAAAATTTCA-TAGGAGGTTATCAAAATTTCATA-
*
1760 GGG
63 GGA
* * * * *
1763 AGGTTCTCGAAATTCCATAGTGT-CATTATCAAAATTT--TAGAGAGTTTATCAAAATTTCATAG
1 AGATTATCAAAATTTCATAGTGTGC-TTATCAAAATTTCATAG-GAGGTTATCAAAATTTCATAG
1825 GA
64 GA
* * * * * * * * *
1827 AGATTATCTAGATTTCATAATGTGATTTTCAAAATTTCATAGCCAGGTAATCACAATTTCATAGT
1 AGATTATCAAAATTTCATAGTGTGCTTATCAAAATTTCATAG-GAGGTTATCAAAATTTCATAGG
1892 A
65 A
*
1893 CGATTATCAAAATTTCATA
1 AGATTATCAAAATTTCATA
1912 AGGATGTTTA
Statistics
Matches: 167, Mismatches: 36, Indels: 23
0.74 0.16 0.10
Matches are distributed among these distances:
63 2 0.01
64 45 0.27
65 4 0.02
66 110 0.66
67 6 0.04
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36
Consensus pattern (65 bp):
AGATTATCAAAATTTCATAGTGTGCTTATCAAAATTTCATAGGAGGTTATCAAAATTTCATAGGA
Found at i:3141 original size:36 final size:36
Alignment explanation
Indices: 3094--3163 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
3084 TTCAATAACC
* *
3094 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
3130 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
3164 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:3965 original size:203 final size:204
Alignment explanation
Indices: 3676--4087 Score: 747
Period size: 205 Copynumber: 2.0 Consensus size: 204
3666 GCTTAATAAC
3676 TTTATCAATGGTGAATGTTATTAATTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAG
1 TTTATCAATGGTGAATGTTATTAATTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAG
* *
3741 ATACAACACATTATTATTATATATA-A-AACTATACCTAAAAAAAATTAGTTGAACATTAGTGGT
66 ATACAACACATTACTATTATATATATAGAACTATACCAAAAAAAAATTAGTTGAACATTAGTGGT
3804 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGA
131 TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGA
3869 TCCGATTTA
196 TCCGATTTA
* * *
3878 TTTATCACTGGTGAATGTTATTAATTTTTTAAGTCTAAGGTTACTATCAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAA-TTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
3943 GATACAACACATTACTATTATATATATAGAACTATACCAAAAAAAAATTAGTTGAACATTAGTGG
65 GATACAACACATTACTATTATATATATAGAACTATACCAAAAAAAAATTAGTTGAACATTAGTGG
*
4008 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAT
130 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAG
4073 ATCCGATTTA
195 ATCCGATTTA
4083 TTTAT
1 TTTAT
4088 TATTAAGGAA
Statistics
Matches: 201, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
202 23 0.11
203 63 0.31
204 1 0.00
205 114 0.57
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (204 bp):
TTTATCAATGGTGAATGTTATTAATTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAG
ATACAACACATTACTATTATATATATAGAACTATACCAAAAAAAAATTAGTTGAACATTAGTGGT
TGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGA
TCCGATTTA
Found at i:5344 original size:10 final size:11
Alignment explanation
Indices: 5310--5348 Score: 55
Period size: 10 Copynumber: 3.7 Consensus size: 11
5300 CAAGGCTAGG
5310 CCCGGCCCGAA
1 CCCGGCCCGAA
5321 CCCGG-CCGAA
1 CCCGGCCCGAA
*
5331 CCCGGCCCG-G
1 CCCGGCCCGAA
5341 CCCGGCCC
1 CCCGGCCC
5349 ATGAATAGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 18 0.69
11 8 0.31
ACGTcount: A:0.10, C:0.59, G:0.31, T:0.00
Consensus pattern (11 bp):
CCCGGCCCGAA
Found at i:5505 original size:25 final size:25
Alignment explanation
Indices: 5471--5523 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
5461 TCTCACCGAA
5471 TGTGAGTTTAGTTTATTTATTTGTT
1 TGTGAGTTTAGTTTATTTATTTGTT
*
5496 TGTGAGTTTAGTTTATTTGTTTGTT
1 TGTGAGTTTAGTTTATTTATTTGTT
5521 TGT
1 TGT
5524 TTGGTAGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.13, C:0.00, G:0.23, T:0.64
Consensus pattern (25 bp):
TGTGAGTTTAGTTTATTTATTTGTT
Found at i:5512 original size:21 final size:20
Alignment explanation
Indices: 5480--5519 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
5470 ATGTGAGTTT
5480 AGTTTATTTATTTGTTTGTG
1 AGTTTATTTATTTGTTTGTG
5500 AGTTTAGTTTATTTGTTTGT
1 AGTTTA-TTTATTTGTTTGT
5520 TTGTTTGGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.15, C:0.00, G:0.20, T:0.65
Consensus pattern (20 bp):
AGTTTATTTATTTGTTTGTG
Found at i:5525 original size:21 final size:20
Alignment explanation
Indices: 5476--5525 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
5466 CCGAATGTGA
5476 GTTTAGTTTATTTATTTGTTT
1 GTTT-GTTTATTTATTTGTTT
**
5497 GTGAGTTTAGTTTATTTGTTT
1 GTTTGTTTA-TTTATTTGTTT
5518 GTTTGTTT
1 GTTTGTTT
5526 GGTAGTTTGG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 5 0.21
21 19 0.79
ACGTcount: A:0.12, C:0.00, G:0.20, T:0.68
Consensus pattern (20 bp):
GTTTGTTTATTTATTTGTTT
Found at i:15312 original size:16 final size:16
Alignment explanation
Indices: 15291--15325 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
15281 ATGGTTTTTA
15291 AAACGACAATGATGCG
1 AAACGACAATGATGCG
15307 AAACGACAATGATGCG
1 AAACGACAATGATGCG
15323 AAA
1 AAA
15326 GTATTTAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.49, C:0.17, G:0.23, T:0.11
Consensus pattern (16 bp):
AAACGACAATGATGCG
Found at i:19273 original size:23 final size:23
Alignment explanation
Indices: 19243--19291 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
19233 TCGTGCATCA
19243 CAATTCACAACCATTAAATTGAG
1 CAATTCACAACCATTAAATTGAG
19266 CAATTCACAACCATTAAATTGAG
1 CAATTCACAACCATTAAATTGAG
19289 CAA
1 CAA
19292 ATTTCCTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.45, C:0.22, G:0.08, T:0.24
Consensus pattern (23 bp):
CAATTCACAACCATTAAATTGAG
Done.