Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_363 ID=scaffold_363-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: 7891
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.31
Found at i:1908 original size:50 final size:50
Alignment explanation
Indices: 1655--2536 Score: 425
Period size: 50 Copynumber: 17.7 Consensus size: 50
1645 ACTGCAACCT
* *
1655 CAGGGAAGTAAGATTCGCCGTTGCAGCTTCAATCT-TTTAAATTGCAAT-G
1 CAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTCTTT-AATTGCAATAC
** * * ** ** * *
1704 TTGAGGAAGCAAGATTTGCCGTCATAGCTTCAATCTGC-TCCACTGCACCT-C
1 CAG-GGAAGTAAGATTCGCCGTTGTAGCTTCAATCT-CTTTAATTGCA-ATAC
* * * **
1755 CAGGGAAAGTAAGATTCGCCGTTATGGCTTCGATCTCTTTAATTGCAATGT
1 CAGGG-AAGTAAGATTCGCCGTTGTAGCTTCAATCTCTTTAATTGCAATAC
* * * * ** ** * * *
1806 CGGGGAA-CAAGATTCACCATTGTAGCTTCAATCTGATCCACTAC-ATCGC
1 CAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTCTTTAATTGCAAT-AC
* **
1855 CAGGAAAGTAAGATTCGCCGTTGCGGCTTCAATC-CTTTTAATTGCAATAC
1 CAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTC-TTTAATTGCAATAC
* * * * * * * **
1905 CAGGGAAGCAAGATTCGCCGTCGTAGCTTTAATCTACTCT-ACTGTACTGT
1 CAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCT-CTTTAATTGCAATAC
* * * **
1955 CAGGGAAGTGAGATTCACCGTTGTGGCTTCAATCTCTTTAATTGCAATGT
1 CAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTCTTTAATTGCAATAC
* * ** ** * *
2005 CGGGGAA-CAAGATTCGCCGTTGTAGCTTCAATCTGATCCACTAC-ATCAC
1 CAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTCTTTAATTGCAAT-AC
* * ** *
2054 CAGGAAAGTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATAC
1 CAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTCTTTAATTGCAATAC
* * ** * * * *
2104 CAGGGAAGCAAGATTCGCCGTTGTAGCTTTAATCTGC-TCCACTGTACTGC
1 CAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCT-CTTTAATTGCAATAC
* * * * **
2154 CAGGGAAGTGAGAATT-ACCGTTGTTGCTTCAATATCTTTAATTGCAATGT
1 CAGGGAAGTAAG-ATTCGCCGTTGTAGCTTCAATCTCTTTAATTGCAATAC
* * * ** ** * *
2204 CGGGGAA-CAAGATTCGTCGTTGTAGCTTCAATCTGATCCACTAC-AT-C
1 CAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTCTTTAATTGCAATAC
* * ** *
2251 GCTAGGAAAGTAAGATTCGCCATTGCGGCTTCAATCTTTTTAATTGCAATAC
1 -C-AGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTCTTTAATTGCAATAC
* * * * ** * * *
2303 CAGGGAAGTAAGATTCGCCGTCGTAGCTTTAATTTGCTCT-GCTGTACTGC
1 CAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCT-CTTTAATTGCAATAC
* * * * **
2353 CAGGGAAGTGAGATTCGCCGTTGTGGCTTCAATCTCTGTAATTGAAATGT
1 CAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTCTTTAATTGCAATAC
* ** ** * *
2403 C-GGTGAA-CAAGATTCGCCGTTGTAGCTTCAATCTGATCCACTAC-ATCAC
1 CAGG-GAAGTAAGATTCGCCGTTGTAGCTTCAATCTCTTTAATTGCAAT-AC
* * * ** *
2452 TAGGAAAGTAAGATTCGTCGTTGCGGCTTCAATCTTTTTAATTGCAATAC
1 CAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTCTTTAATTGCAATAC
* * * *
2502 CAGGGAAGCAAGATTCACCGTCGTAGCTTTAATCT
1 CAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCT
2537 GCTCCGTTGC
Statistics
Matches: 590, Mismatches: 210, Indels: 65
0.68 0.24 0.08
Matches are distributed among these distances:
48 12 0.02
49 126 0.21
50 396 0.67
51 54 0.09
52 2 0.00
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (50 bp):
CAGGGAAGTAAGATTCGCCGTTGTAGCTTCAATCTCTTTAATTGCAATAC
Found at i:2038 original size:199 final size:199
Alignment explanation
Indices: 1655--2541 Score: 1357
Period size: 199 Copynumber: 4.5 Consensus size: 199
1645 ACTGCAACCT
* * * ***
1655 CAGGGAAGTAAGATTCGCCGTTGCAGCTTCAATCTTTTAAATTGCAAT-GTTGAGGAAGCAAGAT
1 CAGGAAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATACCAG-GGAAGCAAGAT
* * * * * * *
1719 TTGCCGTCATAGCTTCAATCTGCTCCACTGCACCT-CCAGGGAAAGTAAGATTCGCCGTTATGGC
65 TCGCCGTCGTAGCTTTAATCTGCTCCACTGTA-CTGCCAGGG-AAGTGAGATTCACCGTTGTGGC
* * *
1783 TTCGATCTCTTTAATTGCAATGTCGGGGAACAAGATTCACCATTGTAGCTTCAATCTGATCCACT
128 TTCAATCTCTTTAATTGCAATGTCGGGGAACAAGATTCGCCGTTGTAGCTTCAATCTGATCCACT
*
1848 ACATCGC
193 ACATCAC
*
1855 CAGGAAAGTAAGATTCGCCGTTGCGGCTTCAATCCTTTTAATTGCAATACCAGGGAAGCAAGATT
1 CAGGAAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATACCAGGGAAGCAAGATT
* * *
1920 CGCCGTCGTAGCTTTAATCTACTCTACTGTACTGTCAGGGAAGTGAGATTCACCGTTGTGGCTTC
66 CGCCGTCGTAGCTTTAATCTGCTCCACTGTACTGCCAGGGAAGTGAGATTCACCGTTGTGGCTTC
1985 AATCTCTTTAATTGCAATGTCGGGGAACAAGATTCGCCGTTGTAGCTTCAATCTGATCCACTACA
131 AATCTCTTTAATTGCAATGTCGGGGAACAAGATTCGCCGTTGTAGCTTCAATCTGATCCACTACA
2050 TCAC
196 TCAC
*
2054 CAGGAAAGTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATACCAGGGAAGCAAGATT
1 CAGGAAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATACCAGGGAAGCAAGATT
* *
2119 CGCCGTTGTAGCTTTAATCTGCTCCACTGTACTGCCAGGGAAGTGAGAATT-ACCGTTGTTGCTT
66 CGCCGTCGTAGCTTTAATCTGCTCCACTGTACTGCCAGGGAAGTGAG-ATTCACCGTTGTGGCTT
* *
2183 CAATATCTTTAATTGCAATGTCGGGGAACAAGATTCGTCGTTGTAGCTTCAATCTGATCCACTAC
130 CAATCTCTTTAATTGCAATGTCGGGGAACAAGATTCGCCGTTGTAGCTTCAATCTGATCCACTAC
*
2248 ATCGC
195 ATCAC
* * *
2253 TAGGAAAGTAAGATTCGCCATTGCGGCTTCAATCTTTTTAATTGCAATACCAGGGAAGTAAGATT
1 CAGGAAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATACCAGGGAAGCAAGATT
* ** *
2318 CGCCGTCGTAGCTTTAATTTGCTCTGCTGTACTGCCAGGGAAGTGAGATTCGCCGTTGTGGCTTC
66 CGCCGTCGTAGCTTTAATCTGCTCCACTGTACTGCCAGGGAAGTGAGATTCACCGTTGTGGCTTC
* * *
2383 AATCTCTGTAATTGAAATGTCGGTGAACAAGATTCGCCGTTGTAGCTTCAATCTGATCCACTACA
131 AATCTCTTTAATTGCAATGTCGGGGAACAAGATTCGCCGTTGTAGCTTCAATCTGATCCACTACA
2448 TCAC
196 TCAC
* *
2452 TAGGAAAGTAAGATTCGTCGTTGCGGCTTCAATCTTTTTAATTGCAATACCAGGGAAGCAAGATT
1 CAGGAAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATACCAGGGAAGCAAGATT
*
2517 CACCGTCGTAGCTTTAATCTGCTCC
66 CGCCGTCGTAGCTTTAATCTGCTCC
2542 GTTGCATCGC
Statistics
Matches: 630, Mismatches: 53, Indels: 9
0.91 0.08 0.01
Matches are distributed among these distances:
198 3 0.00
199 537 0.85
200 89 0.14
201 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (199 bp):
CAGGAAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAATACCAGGGAAGCAAGATT
CGCCGTCGTAGCTTTAATCTGCTCCACTGTACTGCCAGGGAAGTGAGATTCACCGTTGTGGCTTC
AATCTCTTTAATTGCAATGTCGGGGAACAAGATTCGCCGTTGTAGCTTCAATCTGATCCACTACA
TCAC
Found at i:2671 original size:44 final size:44
Alignment explanation
Indices: 2613--3091 Score: 401
Period size: 44 Copynumber: 10.9 Consensus size: 44
2603 ATATCTGTTT
*
2613 TCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGC-A
1 TCTTCGATCTACTTC-CCACCAATATAGGAAGACAAGATCTGCTA
* * * * *
2657 TCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACCTACTA
1 TCTTCGATCTACTTCCCACCAATATAGGAAGACAAGATCTGCTA
* * * ** * *
2701 TTTTCGATCTACTTCACGCCAATGCATGAAGACAAAATCTGCT-
1 TCTTCGATCTACTTCCCACCAATATAGGAAGACAAGATCTGCTA
* * * *
2744 TCTTCGATCCACTTCGCCACCAGTATGGGAAGACAAGACCTGC-A
1 TCTTCGATCTACTTC-CCACCAATATAGGAAGACAAGATCTGCTA
* * * * * * *
2788 TCTTCGATCCACTTCCTACCAATATTGGGAGATAGGACCTGCTA
1 TCTTCGATCTACTTCCCACCAATATAGGAAGACAAGATCTGCTA
* * * * * *
2832 TCTTCGATCTACTTCACGCCAATACATGAATACAAGATATGCT-
1 TCTTCGATCTACTTCCCACCAATATAGGAAGACAAGATCTGCTA
* * * * *
2875 TCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACCTACTA
1 TCTTCGATCTACTTCCCACCAATATAGGAAGACAAGATCTGCTA
* * * * * * *
2919 TCTACGATCTACTTCACGCCAATACATGAAGACAAGATCTCCTT
1 TCTTCGATCTACTTCCCACCAATATAGGAAGACAAGATCTGCTA
* * * *
2963 TCTTCAATCTACTTCGCCACCAGTATGGGAAGACAAGATTTGC-A
1 TCTTCGATCTACTTC-CCACCAATATAGGAAGACAAGATCTGCTA
* * * * *
3007 TCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACCTACTA
1 TCTTCGATCTACTTCCCACCAATATAGGAAGACAAGATCTGCTA
* * * *
3051 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTG
1 TCTTCGATCTACTTCCCACCAATATAGGAAGACAAGATCTG
3092 ATTTAATGAC
Statistics
Matches: 329, Mismatches: 99, Indels: 14
0.74 0.22 0.03
Matches are distributed among these distances:
43 108 0.33
44 202 0.61
45 19 0.06
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (44 bp):
TCTTCGATCTACTTCCCACCAATATAGGAAGACAAGATCTGCTA
Found at i:2735 original size:87 final size:86
Alignment explanation
Indices: 2613--3091 Score: 340
Period size: 87 Copynumber: 5.5 Consensus size: 86
2603 ATATCTGTTT
* ***
2613 TCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTC-CTACC
1 TCTTCGATCTACTT--CCGCCAATACATGAAGACAAGATCTGCATCTTCGATCCACTTCAC-ACC
*
2677 AATATAGGAAGACAGGACCTACTA
63 AATATAGGAAGACAAGACCTACTA
* * * * *
2701 TTTTCGATCTACTTCACGCCAATGCATGAAGACAAAATCTGCTTCTTCGATCCACTTCGCCACCA
1 TCTTCGATCTACTTC-CGCCAATACATGAAGACAAGATCTGCATCTTCGATCCACTTC-ACACCA
* * *
2766 GTATGGGAAGACAAGACCTGC-A
64 ATATAGGAAGACAAGACCTACTA
* * * * * * * * *
2788 TCTTCGATCCACTTCCTACCAATA-TTGGGAGATAGGACCTGCTATCTTCGATCTACTTCACGCC
1 TCTTCGATCTACTTCC-GCCAATACAT-GAAGACAAGATCTGC-ATCTTCGATCCACTTCACACC
* * * ** *
2852 AATACATGAATACAAGATATGCT-
63 AATATAGGAAGACAAGACCTACTA
* * * * * * * * * *
2875 TCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACCTACTATCTACGATCTACTTCACGCCA
1 TCTTCGATCTACTTCC-GCCAATACATGAAGACAAGATCTGC-ATCTTCGATCCACTTCACACCA
* * * * *
2940 ATACATGAAGACAAGATCTCCTT
64 ATATAGGAAGACAAGACCTACTA
* *** *
2963 TCTTCAATCTACTT-CGCCACCAGTATGGGAAGACAAGATTTGCATCTTCGATCCACTTC-CTAC
1 TCTTCGATCTACTTCCGCCA--A-TACATGAAGACAAGATCTGCATCTTCGATCCACTTCAC-AC
*
3026 CAATATAGGAAGACAGGACCTACTA
62 CAATATAGGAAGACAAGACCTACTA
3051 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTG
1 TCTTCGATCTACTTC-CGCCAATACATGAAGACAAGATCTG
3092 ATTTAATGAC
Statistics
Matches: 312, Mismatches: 64, Indels: 31
0.77 0.16 0.08
Matches are distributed among these distances:
86 6 0.02
87 176 0.56
88 109 0.35
89 16 0.05
90 5 0.02
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (86 bp):
TCTTCGATCTACTTCCGCCAATACATGAAGACAAGATCTGCATCTTCGATCCACTTCACACCAAT
ATAGGAAGACAAGACCTACTA
Found at i:2846 original size:131 final size:131
Alignment explanation
Indices: 2612--3065 Score: 491
Period size: 131 Copynumber: 3.5 Consensus size: 131
2602 AATATCTGTT
* *
2612 TTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACC
1 TTCTTCGATCCACTTCGCCACCAATATGGGAAGACAAGACCTGCATCTTCGATCCACTTCCTACC
* * *
2677 AATATAGGAAGACAGGACCTACTATTTTCGATCTACTTCACGCCAATGCATGAAGACAAAATCTG
66 AATATAGGAAGACAGGACCTACTATCTTCGATCTACTTCACGCCAATACATGAAGACAAAATATG
2742 C
131 C
*
2743 TTCTTCGATCCACTTCGCCACCAGTATGGGAAGACAAGACCTGCATCTTCGATCCACTTCCTACC
1 TTCTTCGATCCACTTCGCCACCAATATGGGAAGACAAGACCTGCATCTTCGATCCACTTCCTACC
* * * * * *
2808 AATATTGGGAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAATACAAGATATG
66 AATATAGGAAGACAGGACCTACTATCTTCGATCTACTTCACGCCAATACATGAAGACAAAATATG
2873 C
131 C
* * * * * * *
2874 TTCTTCGATCCACTTC-CTACCAATATAGGAAGACAGGACCTACTATCTACGATCTACTTCAC-G
1 TTCTTCGATCCACTTCGCCACCAATATGGGAAGACAAGACCTGC-ATCTTCGATCCACTTC-CTA
* * * * * * * * * * *** *
2937 CCAATACATGAAGACAAGATCTCCTTTCTTCAATCTACTTCGCCACCAGTATGGGAAGACAAGAT
64 CCAATATAGGAAGACAGGACCTACTATCTTCGATCTACTTC-ACGCCAATACATGAAGACAAAAT
*
3002 TTGC
128 ATGC
* * * * * *
3006 ATCTTCGATCCACTTC-CTACCAATATAGGAAGACAGGACCTACTATCTTCGATCTACTTC
1 TTCTTCGATCCACTTCGCCACCAATATGGGAAGACAAGACCTGC-ATCTTCGATCCACTTC
3066 ACGCCAATAC
Statistics
Matches: 280, Mismatches: 40, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
130 22 0.08
131 180 0.64
132 78 0.28
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (131 bp):
TTCTTCGATCCACTTCGCCACCAATATGGGAAGACAAGACCTGCATCTTCGATCCACTTCCTACC
AATATAGGAAGACAGGACCTACTATCTTCGATCTACTTCACGCCAATACATGAAGACAAAATATG
C
Found at i:7754 original size:127 final size:129
Alignment explanation
Indices: 7522--7764 Score: 300
Period size: 127 Copynumber: 1.9 Consensus size: 129
7512 TCATTTCAAT
*
7522 TTTAAAAGGATATTCAGTTATTTAGGTTCAATACGAGAAAAATCGAAACCCAGTAAGTTAGGGCA
1 TTTAAAAGGATATTCAGCTATTTAGGTTCAATACGAGAAAAATCGAAACCCAGTAAGTTAGGGCA
* * * *
7587 CGATTTCTCGAATTTTCTAAATATAGAATATTACCTTTATTTTTGAAATTTTATGCGTTTGGAAA
66 CAATTTCTCGAATTTCCTAAATAGAGAATATTACCTTTA-TTTTAAAATTTTATGCGTTTGGAAA
** * * *
7652 TTTAAAAGGATATTTTGCTATTTAGGTT-TA-ACGAG-AAAATCGAGACCCAGTAAGTTAGGGTA
1 TTTAAAAGGATATTCAGCTATTTAGGTTCAATACGAGAAAAATCGAAACCCAGTAAGTTAGGGCA
* *
7714 CAA-TTCTTCGAATTTCCTAAA-ACGCGAGATATTGCC-TTATTTTAAAATTTT
66 CAATTTC-TCGAATTTCCTAAATA-GAGA-ATATTACCTTTATTTTAAAATTTT
7765 TCTTTTTGAA
Statistics
Matches: 98, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
126 15 0.15
127 45 0.46
128 12 0.12
129 1 0.01
130 25 0.26
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (129 bp):
TTTAAAAGGATATTCAGCTATTTAGGTTCAATACGAGAAAAATCGAAACCCAGTAAGTTAGGGCA
CAATTTCTCGAATTTCCTAAATAGAGAATATTACCTTTATTTTAAAATTTTATGCGTTTGGAAA
Done.