Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_206 ID=scaffold_206-JGI_221_v2.0
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: 9508
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.30
Warning! 151 characters in sequence are not A, C, G, or T
Found at i:1801 original size:13 final size:13
Alignment explanation
Indices: 1783--1808 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1773 AAAGTGATTT
1783 GTTTTCTAGTAAA
1 GTTTTCTAGTAAA
1796 GTTTTCTAGTAAA
1 GTTTTCTAGTAAA
1809 AAATTGAACA
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:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
GTTTTCTAGTAAA
Found at i:4778 original size:21 final size:19
Alignment explanation
Indices: 4754--4793 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
4744 AAATGATGTG
*
4754 AAAAAGTGAAAAGATGAAAAT
1 AAAAACTGAAAA-AT-AAAAT
4775 AAAAACTGAAAAATAAAAT
1 AAAAACTGAAAAATAAAAT
4794 GGAGAGGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 2 0.11
21 11 0.61
ACGTcount: A:0.70, C:0.03, G:0.12, T:0.15
Consensus pattern (19 bp):
AAAAACTGAAAAATAAAAT
Found at i:6166 original size:44 final size:44
Alignment explanation
Indices: 6118--6566 Score: 166
Period size: 44 Copynumber: 10.2 Consensus size: 44
6108 CCAGTAATTC
*
6118 TATCTCCCTGGGCAACAGTGGAATAGACTGAAGATTACAGATCT
1 TATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTACAGATCT
** * ** ** **** *
6162 TATCTCCCTAAG-AAGTAGTGGAGCAGATCAAAGATGGTGGATTT
1 TATCTCCCTGGGCAA-CAGTGGAATAGATTGAAGATTACAGATCT
* * * * * * *
6206 TACCTCCCCGAGGCTACAGTGGAGTATATTGAAGCCAGTA-A-TTC-
1 TATCTCCCTG-GGCAACAGTGGAATAGATTGAAG--ATTACAGATCT
*
6250 TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCT
1 TATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTACAGATCT
** ** * * ** *
6294 TATCTCCCTAAGCAGTAGTGGAACAGA-TCAAGGATGGCAGATTT
1 TATCTCCCTGGGCAACAGTGGAATAGATTGAA-GATTACAGATCT
* ** * * * *
6338 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTA-A-TTC-
1 TATCTCCCTG-GGCAACAGTGGAATAGATTGAAG--ATTACAGATCT
* *
6382 TATCTCCCTGGGCAGCAGTGGAATACATTGAAGATTACAGATCT
1 TATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTACAGATCT
** * ** * ** *
6426 TATCTCCCTAAGCAATAGTGGAGCAGATCGAAGATGGC-GAATTT
1 TATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTACAG-ATCT
* * ** * * * * *
6470 TACCTCCCTGAAGTTACAATGGAGTACATTGAAGCCAGTA-A-TTC-
1 TATCTCCCTG-GGCAACAGTGGAATAGATTGAAG--ATTACAGATCT
* * *
6514 TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGACTACAAATCT
1 TATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTACAGATCT
6558 TATCTCCCT
1 TATCTCCCT
6567 AAGTAGTAGT
Statistics
Matches: 278, Mismatches: 103, Indels: 48
0.65 0.24 0.11
Matches are distributed among these distances:
41 9 0.03
42 3 0.01
43 66 0.24
44 149 0.54
45 43 0.15
46 5 0.02
47 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (44 bp):
TATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTACAGATCT
Found at i:6653 original size:44 final size:43
Alignment explanation
Indices: 6341--6655 Score: 138
Period size: 44 Copynumber: 7.2 Consensus size: 43
6331 CAGATTTTAC
6341 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTAT
1 CTCCCTGAGG-TACAGTGGAGTACATTGAAGCCAGTAATTCTAT
* * * *
6385 CTCCCTG-GGCAGCAGTGGAATACATTGAAG--ATTACAGATCTTAT
1 CTCCCTGAGGTA-CAGTGGAGTACATTGAAGCCAGTA-A-TTC-TAT
* ** * * * * *** * * *
6429 CTCCCTAAGCAATAGTGGAGCAGATCGAAGATGGCGAATTTTAC
1 CTCCCTGAGGTACAGTGGAGTACATTGAAGCCAG-TAATTCTAT
* *
6473 CTCCCTGAAGTTACAATGGAGTACATTGAAGCCAGTAATTCTAT
1 CTCCCTG-AGGTACAGTGGAGTACATTGAAGCCAGTAATTCTAT
* * * * * *
6517 CTCCCTG-GGCAGCAGTGGAATAGATTGAAGACTA-CAAATCTTAT
1 CTCCCTGAGGTA-CAGTGGAGTACATTGAAG-CCAGTAATTC-TAT
* * * * ** *** * * *
6561 CTCCCT-AAGTAGTAGTGGAGCAGATCCAAGATGGCAGATTTTAC
1 CTCCCTGAGGTA-CAGTGGAGTACATTGAAGCCAGTA-ATTCTAT
6605 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTAT
1 CTCCCTGAGG-TACAGTGGAGTACATTGAAGCCAGTAATTCTAT
6649 CTCCCTG
1 CTCCCTG
6656 GGCAGCAGTG
Statistics
Matches: 190, Mismatches: 64, Indels: 34
0.66 0.22 0.12
Matches are distributed among these distances:
41 3 0.02
42 4 0.02
43 41 0.22
44 99 0.52
45 39 0.21
46 3 0.02
47 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (43 bp):
CTCCCTGAGGTACAGTGGAGTACATTGAAGCCAGTAATTCTAT
Found at i:6674 original size:88 final size:88
Alignment explanation
Indices: 6294--6674 Score: 209
Period size: 88 Copynumber: 4.3 Consensus size: 88
6284 TTACAGATCT
** * *
6294 TATCTCCCTAAGCAGTAGTGGAACAGAT-CAAGGATGGCAGATTTTACCTCCCTGAGGTTACAGT
1 TATCTCCCTGGGCAGCAGTGGAATAGATCCAA-GATGGCAGATTTTACCTCCCTGAGGTTACAGT
6358 GGAGTACATTGAAGCCAGTAATTC
65 GGAGTACATTGAAGCCAGTAATTC
* ** ** * * * ** *
6382 TATCTCCCTGGGCAGCAGTGGAATACATTGAAGATTACAGATCTTATCTCCCT-AAGCAATAGTG
1 TATCTCCCTGGGCAGCAGTGGAATAGATCCAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTG
* * * *** * *
6446 GAGCAGATCGAAGATGGCGAATTT
66 GAGTACATTGAAGCCAG-TAATTC
* ** * * * ** *** * * * *
6470 TACCTCCCTGAAGTTA-CAATGGAGTACATTGAAGCCAGTA-ATTCTATCTCCCTG-GG-CAGCA
1 TATCTCCCTG--GGCAGCAGTGGAATAGATCCAAGATGGCAGATTTTACCTCCCTGAGGTTA-CA
* * * * *
6531 GTGGAATAGATTGAAGACTA-CAAATC
63 GTGGAGTACATTGAAG-CCAGTAATTC
** * * **
6557 TTATCTCCCTAAGTAGTAGTGGAGCAGATCCAAGATGGCAGATTTTACCTCCCTGAGGTTACAGT
1 -TATCTCCCTGGGCAGCAGTGGAATAGATCCAAGATGGCAGATTTTACCTCCCTGAGGTTACAGT
6622 GGAGTACATTGAAGCCAGTAATTC
65 GGAGTACATTGAAGCCAGTAATTC
6646 TATCTCCCTGGGCAGCAGTGGAATAGATC
1 TATCTCCCTGGGCAGCAGTGGAATAGATC
6675 AGAAAAAGCA
Statistics
Matches: 207, Mismatches: 73, Indels: 26
0.68 0.24 0.08
Matches are distributed among these distances:
86 2 0.01
87 36 0.17
88 124 0.60
89 42 0.20
90 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (88 bp):
TATCTCCCTGGGCAGCAGTGGAATAGATCCAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTG
GAGTACATTGAAGCCAGTAATTC
Found at i:6731 original size:132 final size:132
Alignment explanation
Indices: 6011--6724 Score: 1114
Period size: 132 Copynumber: 5.4 Consensus size: 132
6001 ACAGCGAAGC
* * **
6011 AGATCGAAGA-TACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGGATTTT
1 AGATTGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCAAAGATGGCAGATTTT
* * *
6075 ACCTCCCTGAGGTTACAGTGGACTATATTGAAGCCAGTAATTCTATCTCCCTGGGCAACAGTGGA
66 ACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGA
6140 AT
131 AT
* **
6142 AGACTGAAGATTACAGATCTTATCTCCCTAAG-AAGTAGTGGAGCAGATCAAAGATGGTGGATTT
1 AGATTGAAGATTACAGATCTTATCTCCCTAAGCAA-TAGTGGAGCAGATCAAAGATGGCAGATTT
* * *
6206 TACCTCCCCGAGGCTACAGTGGAGTATATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGG
65 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGG
6271 AAT
130 AAT
* * *
6274 AGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAACAGATCAAGGATGGCAGATTTT
1 AGATTGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCAAAGATGGCAGATTTT
6339 ACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGA
66 ACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGA
6404 AT
131 AT
* *
6406 ACATTGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGAAGATGGC-GAATTT
1 AGATTGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCAAAGATGGCAG-ATTT
* *
6470 TACCTCCCTGAAGTTACAATGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGG
65 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGG
6535 AAT
130 AAT
* * * * *
6538 AGATTGAAGACTACAAATCTTATCTCCCTAAGTAGTAGTGGAGCAGATCCAAGATGGCAGATTTT
1 AGATTGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCAAAGATGGCAGATTTT
6603 ACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGA
66 ACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGA
6668 AT
131 AT
* *
6670 AGATCAGAA-A-AAGCAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCAAAGAT
1 AGAT-TGAAGATTA-CAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCAAAGAT
6725 AACAGATCTT
Statistics
Matches: 539, Mismatches: 37, Indels: 13
0.92 0.06 0.02
Matches are distributed among these distances:
131 11 0.02
132 523 0.97
133 5 0.01
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (132 bp):
AGATTGAAGATTACAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCAAAGATGGCAGATTTT
ACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAGCAGTGGA
AT
Found at i:6793 original size:45 final size:44
Alignment explanation
Indices: 6714--6812 Score: 110
Period size: 45 Copynumber: 2.2 Consensus size: 44
6704 ATAGTGGAGC
* * *
6714 AGATCAAAGATAA-CAGATCTTGTCTTCCCATACTGGTGGCGAAGT
1 AGATCAAAGA-AAGTAGATCTTGTCTTCACATACTGG-CGCGAAGT
* ** *
6759 AGATCGAAGAAAGTAGATCTTGTCTTCATGTACTGGCGTGAAGT
1 AGATCAAAGAAAGTAGATCTTGTCTTCACATACTGGCGCGAAGT
6803 AGATCAAAGA
1 AGATCAAAGA
6813 TAACAGANNN
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
44 17 0.38
45 28 0.62
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.26
Consensus pattern (44 bp):
AGATCAAAGAAAGTAGATCTTGTCTTCACATACTGGCGCGAAGT
Found at i:7381 original size:89 final size:89
Alignment explanation
Indices: 6971--7391 Score: 657
Period size: 89 Copynumber: 4.7 Consensus size: 89
6961 NNNNNNNNNN
*
6971 GGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCTATACTGGTGGTGAAGTAGATCGAAGA
1 GGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGA
*
7036 AAACAGATCTTGTCTTCATGTACT
66 AAGCAGATCTTGTCTTCATGTACT
* **
7060 GGCGTGAAGTAGATCAAAGATAATAGATCTTGTCTTCCCATACTGGTGGCAAAGTAGATCGGAA-
1 GGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATC-GAAG
7124 AAAGCAGATCTTGTCTTCATGTACT
65 AAAGCAGATCTTGTCTTCATGTACT
* *
7149 GGCATGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGTGAAGCAGATCGAAGA
1 GGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGA
7214 AAGCAGATCTTGTCTTCATGTACT
66 AAGCAGATCTTGTCTTCATGTACT
* *
7238 GGCGTGAAGTAGATCAAAGATACCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGA
1 GGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGA
* **
7303 AAGTAGATCTTGTCTTCATACACT
66 AAGCAGATCTTGTCTTCATGTACT
* ** **
7327 GGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCTGTA-TAGGCAGTGAAGTAGATCGAAG
1 GGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACT-GGTGGTGAAGTAGATCGAAG
7391 A
65 A
7392 TACAAGTCTT
Statistics
Matches: 306, Mismatches: 23, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
88 4 0.01
89 299 0.98
90 3 0.01
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.27
Consensus pattern (89 bp):
GGCGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGA
AAGCAGATCTTGTCTTCATGTACT
Found at i:8152 original size:20 final size:20
Alignment explanation
Indices: 8127--8168 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
8117 GATAGTTTTG
*
8127 TTATTTTGGTTATTTTTATT
1 TTATTTTAGTTATTTTTATT
8147 TTATTTTAGTTATTTTTATT
1 TTATTTTAGTTATTTTTATT
8167 TT
1 TT
8169 TCTCTAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (20 bp):
TTATTTTAGTTATTTTTATT
Found at i:8944 original size:20 final size:19
Alignment explanation
Indices: 8904--8946 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
8894 TATACATACT
*
8904 CTTTCTATTTTTATTTTTA
1 CTTTCTATTTTTATTTATA
8923 CTTTCCTATTTTT-TTATATA
1 CTTT-CTATTTTTATT-TATA
8943 CTTT
1 CTTT
8947 ATACTTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.16, C:0.14, G:0.00, T:0.70
Consensus pattern (19 bp):
CTTTCTATTTTTATTTATA
Done.