Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_251 ID=scaffold_251-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: 9116
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.31
Warning! 184 characters in sequence are not A, C, G, or T
Found at i:824 original size:21 final size:19
Alignment explanation
Indices: 787--861 Score: 123
Period size: 19 Copynumber: 3.8 Consensus size: 19
777 AATCATATCT
787 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
806 TCCAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
827 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
846 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
862 CTTGAAGATT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
19 34 0.65
21 18 0.35
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:1739 original size:100 final size:100
Alignment explanation
Indices: 1566--1758 Score: 260
Period size: 100 Copynumber: 1.9 Consensus size: 100
1556 ATTTTCCATC
* * ** * * *
1566 TGCAATGTCGTGGAAACTAGATTTGCCGTCGTGGCTTCAATCTGCTCCGCTACAATGCCAGGGAA
1 TGCAATGTCGAGGAAACAAGATTCACCGTCGTAGCTTCAATCTGCTCCACTACAACGCCAGGGAA
*
1631 GTAAGATTTGCTGTTGCGGCTTCAATCTTTTAAAT
66 GTAAGATTTGCCGTTGCGGCTTCAATCTTTTAAAT
* * * * *
1666 TGCAATGTTGAGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCATTACACCGCCAGGGGA
1 TGCAATGTCGAGGAAACAAGATTCACCGTCGTAGCTTCAATCTGCTCCACTACAACGCCAGGGAA
*
1731 GTAAGATTTGCCGTTGCGGCTTTAATCT
66 GTAAGATTTGCCGTTGCGGCTTCAATCT
1759 GCTCCACTAT
Statistics
Matches: 79, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
100 79 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.31
Consensus pattern (100 bp):
TGCAATGTCGAGGAAACAAGATTCACCGTCGTAGCTTCAATCTGCTCCACTACAACGCCAGGGAA
GTAAGATTTGCCGTTGCGGCTTCAATCTTTTAAAT
Found at i:2028 original size:44 final size:44
Alignment explanation
Indices: 1957--2121 Score: 199
Period size: 44 Copynumber: 3.8 Consensus size: 44
1947 ATCTGCTATT
* * *
1957 TTCAACCTACTCCACTGTTG-CTCAGGGAGATAGTATTCACAATC
1 TTCAACCTATTCCACTGCTGAC-CAGGGAGATAGAATTCACAATC
* * *
2001 TTCAACCTATTCCACTGCTGACTAGGGAGATAGGA-CCTACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGAATTC-ACAATC
* * * *
2045 TTCAATCTATTCCACTGCGGCCCAGGGAGATAGAATTCTCAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGAATTCACAATC
*
2089 CTCAACCTATTCCACTGCTGACCAGGGAGATAG
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAG
2122 GGCTGGGGTC
Statistics
Matches: 102, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
43 1 0.01
44 99 0.97
45 2 0.02
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (44 bp):
TTCAACCTATTCCACTGCTGACCAGGGAGATAGAATTCACAATC
Found at i:2184 original size:88 final size:87
Alignment explanation
Indices: 2122--2585 Score: 667
Period size: 88 Copynumber: 5.3 Consensus size: 87
2112 AGGGAGATAG
* * * *
2122 GGCTGGGGTCATCGATCTGCTTCGCTGACGGTGCATGAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
* *
2187 TCCGCTACAACCTAGAGAGGCAA
66 TCCGCTGCAACC-AGGGAGGCAA
* *
2210 GGCTGGTGTTTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCCGCTATTTTTTAACCTG
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTA-TTTTTAACCTG
2275 CTCCGCTGCAACCCAGGGAGGCAA
65 CTCCGCTGCAA-CCAGGGAGGCAA
* * *
2299 GGCTGGTGTCTTCGATCTGCTTTGCTGTCGGTGTAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
* *
2364 TCCGCTGCAACCCAAGGAGGTAA
66 TCCGCTGCAA-CCAGGGAGGCAA
* * *
2387 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGTTATTTTTAGCCTAC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
*
2452 TCCGCTGCGACTCAGGGAGGCAA
66 TCCGCTGCAAC-CAGGGAGGCAA
* * *
2475 GGCTGGTGTCTTCGATCTGCTTCGCTATCAGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
* *
2540 TCCGTTGCAACCCAGGAAGGCAA
66 TCCGCTGCAA-CCAGGGAGGCAA
*
2563 GGCTGGTGTCTTCGATCTACTTC
1 GGCTGGTGTCTTCGATCTGCTTC
2586 ACGCCAATAC
Statistics
Matches: 342, Mismatches: 30, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
87 1 0.00
88 259 0.76
89 80 0.23
90 2 0.01
ACGTcount: A:0.19, C:0.25, G:0.29, T:0.28
Consensus pattern (87 bp):
GGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
TCCGCTGCAACCAGGGAGGCAA
Found at i:2657 original size:132 final size:131
Alignment explanation
Indices: 2571--3084 Score: 799
Period size: 132 Copynumber: 3.9 Consensus size: 131
2561 AAGGCTGGTG
* *
2571 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTATTCGATCTACTTCGCCACC
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCTTCGATCTACTTCACCACC
*
2636 AGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGATAGGATCTA
66 AGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTC-CTACCAATATAGGAAGACAGGA-CTA
*
2701 CCA
129 CTA
* * * *
2704 TCTTCGATCTACTTCACGCCAATATATGAAGACAAGATTTGCTTTCTTCGATC-GC--CACCA--
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCTTCGATCTACTTCACCACC
2764 A-TATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACCTAC
66 AGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGA-CTAC
2828 TA
130 TA
* *
2830 TCTTCGATCTACTTCACGCCAATACATGAAGACAATATCTGA-TTTCTTCGATCTATTTCACCAC
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCT-ACTTTCTTCGATCTACTTCACCAC
*
2894 CAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAATACAGGACCTA
65 CAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGA-CTA
2959 CTA
129 CTA
* *
2962 TCTTCGATCTACTTCACGCCAATACATGAAGACAATATCTGCTTTCTTCGATCTACTTCACCACC
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCTTCGATCTACTTCACCACC
*
3027 AGTATGGGAAGATAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACA
66 AGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTC-CTACCAATATAGGAAGACA
3085 TAATCTGCTA
Statistics
Matches: 352, Mismatches: 20, Indels: 18
0.90 0.05 0.05
Matches are distributed among these distances:
126 74 0.21
127 36 0.10
128 1 0.00
129 5 0.01
130 4 0.01
131 1 0.00
132 164 0.47
133 67 0.19
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (131 bp):
TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCTTCGATCTACTTCACCACC
AGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACTACT
A
Found at i:2665 original size:44 final size:43
Alignment explanation
Indices: 2571--3099 Score: 415
Period size: 44 Copynumber: 12.1 Consensus size: 43
2561 AAGGCTGGTG
* * * * * *
2571 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTACTT
1 TCTTCGATCTACTTCCCACCAATATAGGAAGACAAGATCTGC-A
* * *
2615 TATTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCA
1 TCTTCGATCTACTTC-CCACCAATATAGGAAGACAAGATCTGCA
* * * * *
2659 TCTTCGATCCACTTCGCTACCAATATAGGAAGATAGGATCTACCA
1 TCTTCGATCTACTTC-CCACCAATATAGGAAGACAAGATCT-GCA
* * * * *
2704 TCTTCGATCTACTTCACGCCAATATATGAAGACAAGATTTGCTT
1 TCTTCGATCTACTTCCCACCAATATAGGAAGACAAGATCTGC-A
* *
2748 TCTTCGA--T-C--GCCACCAATATGGGAAGACAAGATCTGCA
1 TCTTCGATCTACTTCCCACCAATATAGGAAGACAAGATCTGCA
* * * * *
2786 TCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACCTACTA
1 TCTTCGATCTACTTCCCACCAATATAGGAAGACAAGATCTGC-A
* * * * *
2830 TCTTCGATCTACTTCACGCCAATACATGAAGACAATATCTG-A
1 TCTTCGATCTACTTCCCACCAATATAGGAAGACAAGATCTGCA
* * *
2872 TTTCTTCGATCTATTTCACCACCAGTATGGGAAGACAAGATCTGCA
1 --TCTTCGATCTACTTC-CCACCAATATAGGAAGACAAGATCTGCA
* * * * * *
2918 TCTTCGATCCACTTCCTACCAATATAGGAATACAGGACCTACTA
1 TCTTCGATCTACTTCCCACCAATATAGGAAGACAAGATCTGC-A
* * * * * *
2962 TCTTCGATCTACTTCACGCCAATACATGAAGACAATATCTGCTT
1 TCTTCGATCTACTTCCCACCAATATAGGAAGACAAGATCTGC-A
* * *
3006 TCTTCGATCTACTTCACCACCAGTATGGGAAGATAAGATCTGCA
1 TCTTCGATCTACTTC-CCACCAATATAGGAAGACAAGATCTGCA
* *
3050 TCTTCGATCCACTTCGCTACCAATATAGGAAGACATA-ATCTGCTA
1 TCTTCGATCTACTTC-CCACCAATATAGGAAGACA-AGATCTGC-A
3095 TCTTC
1 TCTTC
3100 ATAGATCTGC
Statistics
Matches: 373, Mismatches: 95, Indels: 33
0.74 0.19 0.07
Matches are distributed among these distances:
38 7 0.02
39 22 0.06
41 2 0.01
42 2 0.01
43 43 0.12
44 215 0.58
45 81 0.22
46 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (43 bp):
TCTTCGATCTACTTCCCACCAATATAGGAAGACAAGATCTGCA
Found at i:2665 original size:176 final size:176
Alignment explanation
Indices: 2133--2677 Score: 474
Period size: 176 Copynumber: 3.1 Consensus size: 176
2123 GCTGGGGTCA
* * * *
2133 TCGATCTGCTTCGCTGA-CGGTGCATGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAA
1 TCGATCTGCTTCGCT-ATCAGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGCTCCGCTGCAA
* * * * * ** * * **
2197 -CCTAGAGAGGCAAGGCTGGTGTTTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCCGC
65 CCCAAG-GAGGCAAGGCTGGTGTCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTAC
* * * ** * * * **
2261 TATTTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCT
129 TA-TTATTAGCCTACTCCGCCACCACTCAGGGAGACAAGGCTGGCATCT
* * * *
2310 TCGATCTGCTTTGCTGTCGGTGTAGGAAGGCAAGATCTGCTATTTTTAGCCTGCTCCGCTGCAAC
1 TCGATCTGCTTCGCTATCAGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGCTCCGCTGCAAC
* * * * ** * * **
2375 CCAAGGAGGTAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGTTA
66 CCAAGGAGGCAAGGCTGGTGTCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTACTA
* ** * * **
2440 TTTTTAGCCTACTCCGCTGCGACTCAGGGAGGCAAGGCTGGTGTCT
131 TTATTAGCCTACTCCGCCACCACTCAGGGAGACAAGGCTGGCATCT
*
2486 TCGATCTGCTTCGCTATCAGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGCTCCGTTGCAAC
1 TCGATCTGCTTCGCTATCAGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGCTCCGCTGCAAC
*
2551 CC-AGGAAGGCAAGGCTGGTGTCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGATCTACT
66 CCAAGG-AGGCAAGGCTGGTGTCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTACT
* * * * *
2614 -TTATTCGATCTACTTCGCCACCAGT-ATGGGAAGACAAGATCT-GCATCT
130 ATTATTAG-CCTACTCCGCCACCACTCA-GGG-AGACAAG-GCTGGCATCT
**
2662 TCGATCCACTTCGCTA
1 TCGATCTGCTTCGCTA
2678 CCAATATAGG
Statistics
Matches: 316, Mismatches: 45, Indels: 15
0.84 0.12 0.04
Matches are distributed among these distances:
174 6 0.02
175 35 0.11
176 156 0.49
177 115 0.36
178 4 0.01
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (176 bp):
TCGATCTGCTTCGCTATCAGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGCTCCGCTGCAAC
CCAAGGAGGCAAGGCTGGTGTCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTACTA
TTATTAGCCTACTCCGCCACCACTCAGGGAGACAAGGCTGGCATCT
Found at i:4407 original size:14 final size:15
Alignment explanation
Indices: 4384--4416 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
4374 TTCGACGCTT
4384 TTCCAAATAAGG-CC
1 TTCCAAATAAGGTCC
*
4398 TTCCACATAAGGTCC
1 TTCCAAATAAGGTCC
4413 TTCC
1 TTCC
4417 TCGCTTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.33, G:0.12, T:0.27
Consensus pattern (15 bp):
TTCCAAATAAGGTCC
Found at i:5289 original size:25 final size:26
Alignment explanation
Indices: 5235--5289 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
5225 AAGAAAATCC
* ** *
5235 AAAAGAATGAAAGAATAATTATTTCG
1 AAAAGAATGAAAAAATAATTAGCTCA
5261 AAAAGAATGAAAAAAT-ATTAGCTCA
1 AAAAGAATGAAAAAATAATTAGCTCA
5286 AAAA
1 AAAA
5290 TAAATGCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 10 0.40
26 15 0.60
ACGTcount: A:0.60, C:0.05, G:0.13, T:0.22
Consensus pattern (26 bp):
AAAAGAATGAAAAAATAATTAGCTCA
Done.