Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009719.1 Corchorus olitorius cultivar O-4 contig09751, 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: 3888
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Found at i:788 original size:19 final size:22
Alignment explanation
Indices: 736--786 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
726 TAACATCTAA
736 TGATAATGATAAGTAATTTTGG
1 TGATAATGATAAGTAATTTTGG
758 TGATAATGATAAGTAATTTTGG
1 TGATAATGATAAGTAATTTTGG
*
780 TAATAAT
1 TGATAAT
787 AAATGTAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.39, C:0.00, G:0.20, T:0.41
Consensus pattern (22 bp):
TGATAATGATAAGTAATTTTGG
Found at i:1847 original size:22 final size:22
Alignment explanation
Indices: 1817--1915 Score: 73
Period size: 22 Copynumber: 4.5 Consensus size: 22
1807 TCCAACGTAG
*
1817 AAATATTGATAACCACTCTGTGA
1 AAAT-TTGATAACCACTCTATGA
1840 AAATTTGATAATCTCA-T-TATG-
1 AAATTTGATAA-C-CACTCTATGA
* *
1861 AAATTTCGATAATCTCTCTATGA
1 AAATTT-GATAACCACTCTATGA
* *
1884 AAATTT-ATAACCACACTGT-A
1 AAATTTGATAACCACTCTATGA
1904 AAATTTTGATAA
1 AAA-TTTGATAA
1916 TCATAATCAT
Statistics
Matches: 61, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
20 5 0.08
21 19 0.31
22 23 0.38
23 12 0.20
24 2 0.03
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.36
Consensus pattern (22 bp):
AAATTTGATAACCACTCTATGA
Found at i:1866 original size:21 final size:22
Alignment explanation
Indices: 1817--1893 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 22
1807 TCCAACGTAG
* * *
1817 AAATATTGATAACCACTCTGTGA
1 AAAT-TTGATAATCTCTCTATGA
1840 AAATTTGATAATCTCAT-TATG-
1 AAATTTGATAATCTC-TCTATGA
1861 AAATTTCGATAATCTCTCTATGA
1 AAATTT-GATAATCTCTCTATGA
1884 AAATTT-ATAA
1 AAATTTGATAA
1894 CCACACTGTA
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
21 11 0.23
22 25 0.53
23 11 0.23
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (22 bp):
AAATTTGATAATCTCTCTATGA
Found at i:2104 original size:43 final size:43
Alignment explanation
Indices: 2000--2164 Score: 140
Period size: 43 Copynumber: 3.8 Consensus size: 43
1990 GATAATCATT
* * *
2000 CTATGAAATTTTGATAACCTTCATATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCTCCTTATGAAAATTTGGTAACC-CA
* * * * *
2044 GTATG-GATTTCTTATAACCTCCCTAT-AAAATTTGGTAACCGGA
1 CTATGAAATTT-TGATAACCTCCTTATGAAAATTTGGTAACC-CA
* *
2087 CTATGAAATTTTGATAACCTCCTTATGAAATTTTTGATAACCTC-
1 CTATGAAATTTTGATAACCTCCTTATGAAA-ATTTGGTAACC-CA
* *
2131 CTTATGAAATTTTGATAATCTCATTAT-AAAATTT
1 C-TATGAAATTTTGATAACCTCCTTATGAAAATTT
2165 TGATTACCAA
Statistics
Matches: 97, Mismatches: 19, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
43 38 0.39
44 27 0.28
45 32 0.33
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (43 bp):
CTATGAAATTTTGATAACCTCCTTATGAAAATTTGGTAACCCA
Found at i:2125 original size:23 final size:22
Alignment explanation
Indices: 1943--2168 Score: 156
Period size: 22 Copynumber: 10.2 Consensus size: 22
1933 CTAAAAAAAA
1943 TTGATAACCTTCCTT-TGAAATT
1 TTGATAACC-TCCTTATGAAATT
* ** * *
1965 TTAATAACCTAATAAATGTAATT
1 TTGATAACCTCCT-TATGAAATT
* *
1988 TTGATAATCATTC-TATGAAATT
1 TTGATAA-CCTCCTTATGAAATT
* *
2010 TTGATAACCTTCATATGAAATT
1 TTGATAACCTCCTTATGAAATT
* * ** *
2032 TTGGTAACCACAGTATG-GATT
1 TTGATAACCTCCTTATGAAATT
* * *
2053 TCTTATAACCTCCCTAT-AAAAT
1 T-TGATAACCTCCTTATGAAATT
* **
2075 TTGGTAACCGGAC-TATGAAATT
1 TTGATAACC-TCCTTATGAAATT
2097 TTGATAACCTCCTTATGAAATTT
1 TTGATAACCTCCTTATGAAA-TT
2120 TTGATAACCTCCTTATGAAATT
1 TTGATAACCTCCTTATGAAATT
* * *
2142 TTGATAATCTCATTATAAAATT
1 TTGATAACCTCCTTATGAAATT
2164 TTGAT
1 TTGAT
2169 TACCAAACAA
Statistics
Matches: 158, Mismatches: 36, Indels: 20
0.74 0.17 0.09
Matches are distributed among these distances:
21 20 0.13
22 102 0.65
23 34 0.22
24 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.41
Consensus pattern (22 bp):
TTGATAACCTCCTTATGAAATT
Found at i:2142 original size:45 final size:43
Alignment explanation
Indices: 1943--2168 Score: 159
Period size: 45 Copynumber: 5.1 Consensus size: 43
1933 CTAAAAAAAA
* * ** * *
1943 TTGATAACCTTCCTTTGAAATTTTAATAACCTAATAAATGTAATT
1 TTGATAACC-TCCTATGAAATTTTGATAACCTCCT-TATGAAATT
* * * *
1988 TTGATAATCATTCTATGAAATTTTGATAACCTTCATATGAAATT
1 TTGATAA-CCTCCTATGAAATTTTGATAACCTCCTTATGAAATT
* * * * * * *
2032 TTGGTAACCACAGTATG-GATTTCTTATAACCTCCCTAT-AAAAT
1 TTGATAACCTC-CTATGAAATTT-TGATAACCTCCTTATGAAATT
* **
2075 TTGGTAACCGGACTATGAAATTTTGATAACCTCCTTATGAAATTT
1 TTGATAACC-TCCTATGAAATTTTGATAACCTCCTTATGAAA-TT
* * *
2120 TTGATAACCTCCTTATGAAATTTTGATAATCTCATTATAAAATT
1 TTGATAACCTCC-TATGAAATTTTGATAACCTCCTTATGAAATT
2164 TTGAT
1 TTGAT
2169 TACCAAACAA
Statistics
Matches: 141, Mismatches: 32, Indels: 17
0.74 0.17 0.09
Matches are distributed among these distances:
43 35 0.25
44 44 0.31
45 61 0.43
46 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.41
Consensus pattern (43 bp):
TTGATAACCTCCTATGAAATTTTGATAACCTCCTTATGAAATT
Found at i:2291 original size:22 final size:22
Alignment explanation
Indices: 2242--2284 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2232 TAATTTTCCT
2242 ATGAAAGCTTGATAATCTCACC
1 ATGAAAGCTTGATAATCTCACC
*
2264 ATGAAAGTTTGATAATCTCAC
1 ATGAAAGCTTGATAATCTCAC
2285 TGAGAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (22 bp):
ATGAAAGCTTGATAATCTCACC
Found at i:2967 original size:25 final size:22
Alignment explanation
Indices: 2914--3418 Score: 166
Period size: 22 Copynumber: 22.7 Consensus size: 22
2904 TTTCACAATG
* * *
2914 AGGTAATCAAAATTTCACAGTA
1 AGGTTATCAAAATTTCATAGGA
* *
2936 TGGTTATCAACATTTCATATGGA
1 AGGTTATCAAAATTTCATA-GGA
*
2959 TTAGGTTATTAAAATTTCATAGGA
1 --AGGTTATCAAAATTTCATAGGA
*
2983 AAGTTATCAAAATTTCATAGTG-
1 AGGTTATCAAAATTTCATAG-GA
* **
3005 TGGTTATCAAAATTTTTTAAGG-
1 AGGTTATCAAAATTTCAT-AGGA
3027 AGGTTATCAAAGATTTCATAGTG-
1 AGGTTATCAAA-ATTTCATAG-GA
* * *
3050 TGGTTACCAAAATTTCATAGTA
1 AGGTTATCAAAATTTCATAGGA
* * *
3072 ATGTTAGAAAAATCTAAATTTCATATGA
1 AGGTT------ATCAAAATTTCATAGGA
* *
3100 AGATTATCAAAATTT--TA--T
1 AGGTTATCAAAATTTCATAGGA
* *
3118 A-GTAATCAAAATTTCATCGGGA
1 AGGTTATCAAAATTTCAT-AGGA
** * *
3140 A-GCAATCAAAATTTCAGA-GT
1 AGGTTATCAAAATTTCATAGGA
* *
3160 A-GTTATAAAAAATTCATAGAGA
1 AGGTTATCAAAATTTCATAG-GA
* * *
3182 TCAGATTACCAAAATTTCATAGAA
1 --AGGTTATCAAAATTTCATAGGA
* * *
3206 ATGTTAT-AAAAATTCATAATG-
1 AGGTTATCAAAATTTCAT-AGGA
* * *
3227 TGGTTATCGAAATTTCATAGAA
1 AGGTTATCAAAATTTCATAGGA
* * *
3249 AAGTTATCAAAATTTTAAAGCG-
1 AGGTTATCAAAATTTCATAG-GA
**
3271 AGGTTATCAAAATTTCCCAGTGA
1 AGGTTATCAAAATTTCATAG-GA
* **
3294 A-GTTATGAAAAAATTTACATATTA
1 AGGTTAT--CAAAATTT-CATAGGA
* * *
3318 TGGTTATTAAAGTTTCATATGG-
1 AGGTTATCAAAATTTCATA-GGA
* *
3340 AGATT-TC-AAATTTCATAGTA
1 AGGTTATCAAAATTTCATAGGA
* *
3360 TGATTATCAAAATTTCATA-GA
1 AGGTTATCAAAATTTCATAGGA
* * * *
3381 GCGGTTAGCAATATTTCATTGGA
1 -AGGTTATCAAAATTTCATAGGA
3404 AGGTTATCAAAATTT
1 AGGTTATCAAAATTT
3419 TATAATGTTA
Statistics
Matches: 347, Mismatches: 97, Indels: 78
0.66 0.19 0.15
Matches are distributed among these distances:
17 11 0.03
18 1 0.00
19 2 0.01
20 29 0.08
21 19 0.05
22 190 0.55
23 29 0.08
24 13 0.04
25 37 0.11
28 16 0.05
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.36
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATAGGA
Found at i:3355 original size:20 final size:22
Alignment explanation
Indices: 3303--3440 Score: 63
Period size: 22 Copynumber: 6.3 Consensus size: 22
3293 AAGTTATGAA
** * *
3303 AAAATTTACATATTATGGTTATT
1 AAAATTT-CATAGGATGATTATC
*
3326 AAAGTTTCATATGGA-GATT-TC
1 AAAATTTCATA-GGATGATTATC
*
3347 -AAATTTCATAGTATGATTATC
1 AAAATTTCATAGGATGATTATC
* * *
3368 AAAATTTCATA-GAGCGGTTAGC
1 AAAATTTCATAGGA-TGATTATC
* * * *
3390 AATATTTCATTGGAAGGTTATC
1 AAAATTTCATAGGATGATTATC
*
3412 AAAATTTTATA--ATGTTATTATC
1 AAAATTTCATAGGATG--ATTATC
3434 AAAATTT
1 AAAATTT
3441 TAGAGTGTGG
Statistics
Matches: 87, Mismatches: 20, Indels: 17
0.70 0.16 0.14
Matches are distributed among these distances:
19 2 0.02
20 15 0.17
21 4 0.05
22 57 0.66
23 9 0.10
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (22 bp):
AAAATTTCATAGGATGATTATC
Found at i:3693 original size:60 final size:60
Alignment explanation
Indices: 3622--3734 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
3612 GGGATGTTAA
*
3622 CAAAATTTCATAATAAAGTTATCGAAAA-ATCATTGGGAGG-TTATCAAAATTTTTTATTAT
1 CAAAATTTCATAAGAAAGTTATC-AAAATATCATT-GGAGGTTTATCAAAATTTTTTATTAT
* * * *
3682 CAAAATTTCATAAGGAGGTTATCAAAATTTTATTGGAGGTTTATCAAAATTTT
1 CAAAATTTCATAAGAAAGTTATCAAAATATCATTGGAGGTTTATCAAAATTTT
3735 ATATGAATGT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 9 0.20
60 37 0.80
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (60 bp):
CAAAATTTCATAAGAAAGTTATCAAAATATCATTGGAGGTTTATCAAAATTTTTTATTAT
Found at i:3706 original size:22 final size:22
Alignment explanation
Indices: 3452--3760 Score: 144
Period size: 22 Copynumber: 14.4 Consensus size: 22
3442 AGAGTGTGGT
3452 ATTTCA-AAGGGAGGTTATCAAA
1 ATTTCATAA-GGAGGTTATCAAA
* ** * *
3474 ATTGCATTTGTGTGGTTACCAAA
1 ATTTCATAAG-GAGGTTATCAAA
* * * *
3497 ATTTCGTATGAAGATTATCAAA
1 ATTTCATAAGGAGGTTATCAAA
3519 ATTTCA-AAGG-GGATTATCAAA
1 ATTTCATAAGGAGG-TTATCAAA
* * *
3540 CTTTCATAGGGAGGATATCAAA
1 ATTTCATAAGGAGGTTATCAAA
* *
3562 ATTTCAT-AGTTTA-GTTTTCAAA
1 ATTTCATAAG--GAGGTTATCAAA
* *
3584 ATTTTAT-AGG-GGTTATCGAA
1 ATTTCATAAGGAGGTTATCAAA
* * *
3604 ATTTCATAGGGATGTTAACAAA
1 ATTTCATAAGGAGGTTATCAAA
** *
3626 ATTTCATAATAAAGTTATCGAAA
1 ATTTCATAAGGAGGTTATC-AAA
* **
3649 A-ATCATTGGGAGGTTATCAAA
1 ATTTCATAAGGAGGTTATCAAA
**
3670 ATTT--T--TTA--TTATCAAA
1 ATTTCATAAGGAGGTTATCAAA
3686 ATTTCATAAGGAGGTTATCAAA
1 ATTTCATAAGGAGGTTATCAAA
* *
3708 ATTTTAT-TGGAGGTTTATCAAA
1 ATTTCATAAGGAGG-TTATCAAA
* * * *
3730 ATTTTATATGAATGTTTATCAAA
1 ATTTCATAAGGA-GGTTATCAAA
3753 ATTTCATA
1 ATTTCATA
3761 CTGAGGTCAT
Statistics
Matches: 212, Mismatches: 54, Indels: 41
0.69 0.18 0.13
Matches are distributed among these distances:
16 12 0.06
18 2 0.01
20 16 0.08
21 27 0.13
22 112 0.53
23 42 0.20
24 1 0.00
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (22 bp):
ATTTCATAAGGAGGTTATCAAA
Found at i:3799 original size:22 final size:22
Alignment explanation
Indices: 3774--3827 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
3764 AGGTCATTAC
*
3774 AATTTCATAGTTTGATTA-TCAA
1 AATTTCATAGTGTGATTACT-AA
* *
3796 AATTTAACAGTGTGATTACTAA
1 AATTTCATAGTGTGATTACTAA
*
3818 GATTTCATAG
1 AATTTCATAG
3828 GGAGGTTATA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 24 0.96
23 1 0.04
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.41
Consensus pattern (22 bp):
AATTTCATAGTGTGATTACTAA
Done.