Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_426 ID=scaffold_426-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: 8335
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.24
Warning! 1185 characters in sequence are not A, C, G, or T
Found at i:6331 original size:44 final size:44
Alignment explanation
Indices: 6268--7038 Score: 440
Period size: 44 Copynumber: 17.8 Consensus size: 44
6258 GTAGTCGATA
*
6268 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAAATCACAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAATCACAG
* * ***
6312 ATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-TCGCA-C-CTAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAATCAC-AG
*
6353 -TCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAGTAAGT-A-AG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAA--AA-TCACAG
* * *
6397 -TCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGACAA
1 ATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAAATCACAG
* * ** *
6441 ATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCA-ATA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAATCACA-G
* * *
6485 ATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAATCACAG
* * * *** *
6529 ATCTTATCTCTCTGAAGTTGCAG-AGAGCAG-GTCGCATC-TAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAATCACAG
* *
6570 -TCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAGTAAGCA-AG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAA--AATCACAG
* * * ** *
6614 -TCTTATC-CTCCTAAAGTTCCAGT-GAGGCAGACTGAAGATGGCAA
1 ATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAAATCACAG
* * * ** *
6658 ATCTTACCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCCGATA-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAATC-ACAG
* * * *
6702 ATCCTATC-CCCTTGAAGTTGCAGGGGAGCGGATTAAAATCACAG
1 ATCTTATCTCCC-TGAAGTTGCAGTGGAGCAGACTAAAATCACAG
* * * *** *
6746 ATCTTATCTCTCTGAAGTTGCAG-AGAGTAGA-TTGCATC-TAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAATCACAG
* *
6787 -TCTTATCTCCCTGAAGTTGCAATGGAGCAGACTAAGTAAGCA-AG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAA--AATCACAG
* ** *
6831 -TCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGCAA
1 ATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAAATCACAG
* * * **
6875 ATCTTATCTTCCTGAAGTTGCACTGGAGCAGATTAAAGCCGACA-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAATC-ACAG
* * * *
6919 ATCCTATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAATCACAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAATCACAG
* * * * *** *
6963 ATCTTATCTCTCTAAAGTTGGAG-AGAGCAGA-TTGCATC-TAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAATCACAG
* *
7004 -TCTTATCTCCCTGAAGTTACAATGGAGCAGACTAA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAA
7039 GTAGGCAAAT
Statistics
Matches: 550, Mismatches: 127, Indels: 102
0.71 0.16 0.13
Matches are distributed among these distances:
40 80 0.15
41 34 0.06
42 19 0.03
43 44 0.08
44 278 0.51
45 87 0.16
46 8 0.01
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (44 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAATCACAG
Found at i:6411 original size:84 final size:85
Alignment explanation
Indices: 6269--6427 Score: 220
Period size: 84 Copynumber: 1.9 Consensus size: 85
6259 TAGTCGATAA
6269 TCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAAATCACAGATCTTATCTCTCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAAATCACAGATCTTATCTCTCTGAAGTTGCA
6334 GAGA-GCAGATCGCACCTAG
66 GAGAGGCAGATCGCACCTAG
**
6353 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAGTAAGT-A-AG-TCTTATC-CTCCTGAAGT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAA--AA-TCACAGATCTTATCTCT-CTGAAGT
*
6414 TGCAGTGAGGCAGA
62 TGCAGAGAGGCAGA
6428 CTGAAGATGA
Statistics
Matches: 67, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
83 2 0.03
84 54 0.81
85 7 0.10
86 3 0.04
87 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (85 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAAATCACAGATCTTATCTCTCTGAAGTTGCA
GAGAGGCAGATCGCACCTAG
Found at i:6465 original size:89 final size:88
Alignment explanation
Indices: 6353--7078 Score: 382
Period size: 89 Copynumber: 8.4 Consensus size: 88
6343 TCGCACCTAG
*
6353 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAGTAAGTAAGTCTTATC-CTCCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGTAAGTCTTATCTC-CCTGAAGTTGC
6417 AGT-GAGGCAGACTGAAGATGACAAA
64 AGTGGA-GCAGACTGAAGATGACAAA
* * *
6442 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAA-TAA-TCCTATCTCCCTGAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAG--AAGTAAGTCTTATCTCCCTGAAGTTG
* * * * *
6505 CAGTGGAGCGGA-TTAAAATCACAGA
63 CAGTGGAGCAGACTGAAGATGACAAA
* * * * * *
6530 TCTTATCTCTCTGAAGTTGCAG-AGAGCAG-GT-CGCA-TCTAGTCTTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGT-AAGTCTTATCTCCCTGAAGTTGCA
* * *
6591 GTGGAGCAGGCT-AAG-TAAGCAAG
65 GTGGAGCAGACTGAAGATGA-CAAA
* * * * * *
6614 TCTTATC-CTCCTAAAGTTCCAGT-GAGGCAGACTGAAGATGGCAAATCTTACCTCCCTGAAGTT
1 TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AGTAAGTCTTATCTCCCTGAAGTT
* * * ** *
6677 GCAGTGGAGTAGATTAAAGCCGA-TAA
62 GCAGTGGAGCAGACTGAAGATGACAAA
* * * * *
6703 TCCTATC-CCCTTGAAGTTGCAGGGGAGCGGATTAA-AA-TCACAGATCTTATCTCTCTGAAGTT
1 TCTTATCTCCC-TGAAGTTGCAGTGGAGCAGACTAAGAAGT-A-AG-TCTTATCTCCCTGAAGTT
* * * * * *
6765 GCAG-AGAGTAGATTG--CAT--CTAG
62 GCAGTGGAGCAGACTGAAGATGACAAA
* *
6787 TCTTATCTCCCTGAAGTTGCAATGGAGCAGACTAAGTAAGCAAGTCTTATC-CTCCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGTAAGTCTTATCTC-CCTGAAGTTGC
*
6851 AGT-GAGGCAGACTGAAGATGGCAAA
64 AGTGGA-GCAGACTGAAGATGACAAA
* * * ** * * *
6876 TCTTATCTTCCTGAAGTTGCACTGGAGCAGATTAAAGCCG-ACAATCCTATCTCCTTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGAAGTA-AGTCTTATCTCCCTGAAGTTGC
* * * * *
6940 AGTGGAGCGGA-TTAAAATCACAGA
64 AGTGGAGCAGACTGAAGATGACAAA
* * * * * * * *
6964 TCTTATCTCTCTAAAGTTGGAG-AGAGCAGA-T-TGCA-TCTAGTCTTATCTCCCTGAAGTTACA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGT-AAGTCTTATCTCCCTGAAGTTGCA
* *
7025 ATGGAGCAGACT-AAG-TAGGCAAA
65 GTGGAGCAGACTGAAGAT-GACAAA
* * * *
7048 TCTTATCTTCTTGAAGTTGCAATAGAGCAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
7079 TTAAAGCTGA
Statistics
Matches: 483, Mismatches: 110, Indels: 92
0.71 0.16 0.13
Matches are distributed among these distances:
82 2 0.00
83 6 0.01
84 151 0.31
85 25 0.05
86 7 0.01
87 26 0.05
88 80 0.17
89 163 0.34
90 20 0.04
91 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.27
Consensus pattern (88 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGTAAGTCTTATCTCCCTGAAGTTGCAG
TGGAGCAGACTGAAGATGACAAA
Found at i:6647 original size:217 final size:217
Alignment explanation
Indices: 6263--7068 Score: 1299
Period size: 217 Copynumber: 3.7 Consensus size: 217
6253 AATCCGTAGT
* ** *
6263 CGATAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAAATCACAGATCTTATCTCTCTGAA
1 CGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAA
* * *
6328 GTTGCAGAGAGCAGATCGCACCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAGTAAG
66 GTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTAAGTAAG
* * *
6393 TAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGACAAATCTTATCTCCCTAAAG
131 CAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAG
6458 TTGCAGTGGAGCAGATTAAAGC
196 TTGCAGTGGAGCAGATTAAAGC
*
6480 CAATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAA
1 CGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAA
* * *
6545 GTTGCAGAGAGCAGGTCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAGTAAG
66 GTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTAAGTAAG
* * *
6610 CAAGTCTTATCCTCCTAAAGTTCCAGTGAGGCAGACTGAAGATGGCAAATCTTACCTCCCTGAAG
131 CAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAG
*
6675 TTGCAGTGGAGTAGATTAAAGC
196 TTGCAGTGGAGCAGATTAAAGC
*
6697 CGATAATCCTATC-CCCTTGAAGTTGCAGGGGAGCGGATTAAAATCACAGATCTTATCTCTCTGA
1 CGATAATCCTATCTCCC-TGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGA
* *
6761 AGTTGCAGAGAGTAGATTGCATCTAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTAAGTAA
65 AGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTAAGTAA
*
6826 GCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTTCCTGAA
130 GCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAA
*
6891 GTTGCACTGGAGCAGATTAAAGC
195 GTTGCAGTGGAGCAGATTAAAGC
* * *
6914 CGACAATCCTATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTAAA
1 CGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAA
* * * *
6979 GTTGGAGAGAGCAGATTGCATCTAGTCTTATCTCCCTGAAGTTACAATGGAGCAGACTAAGTAGG
66 GTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTAAGTAAG
* * *
7044 CAAATCTTATCTTCTTGAAGTTGCA
131 CAAGTCTTATCCTCCTGAAGTTGCA
7069 ATAGAGCAGA
Statistics
Matches: 549, Mismatches: 38, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
216 3 0.01
217 544 0.99
218 2 0.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (217 bp):
CGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAA
GTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTAAGTAAG
CAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAG
TTGCAGTGGAGCAGATTAAAGC
Found at i:6835 original size:84 final size:84
Alignment explanation
Indices: 6269--6952 Score: 333
Period size: 89 Copynumber: 7.9 Consensus size: 84
6259 TAGTCGATAA
* *
6269 TCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAA-AATCACAGATCTTATCTCTCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA-AG-TCTTATCTCTCTGAAGTTGC
* * *
6333 AG-AGAGCAGATCGCACCTAG
64 AGTGGAGCAGATTGCATCTAG
* *
6353 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTAAGTAAGTAAGTCTTATC-CTCCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAGTCTTATCTCT-CTGAAGTTGC
* * * *
6417 AGT-GAGGCAGACTGAAGATGACAAA
64 AGTGGA-GCAGATTG--CAT--CTAG
* * * * *
6442 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGA-TTA-AAGCCAATAATCCTATCTCCCTGAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A-AGTCTTATCTCTCTGAAGTTG
* ** *
6505 CAGTGGAGCGGATTAAAATCACAG
63 CAGTGGAGCAGATT-GCATC-TAG
* * * * * * * *
6529 ATCTTATCTCTCTGAAGTTGCAG-AGAGCAG-GT-CGCATCTAGTCTTATCTCCCTGAAGTTGCA
1 -TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCTTATCTCTCTGAAGTTGCA
* * * * *
6591 GTGGAGCAGGCTAAGTAAGCAAG
65 GTGGAGCA-GAT-TG-CATCTAG
* * * * * *
6614 TCTTATC-CTCCTAAAGTTCCAGT-GAGGCAGACTGAAGATGGCAAATCTTACCTCCCTGAAGTT
1 TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AGCAAGTCTTATCTCTCTGAAGTT
* *** *
6677 GCAGTGGAGTAGATTAAAGCCGATAA
62 GCAGTGGAGCAGATT---GCATCTAG
* * * * *
6703 TCCTATC-CCCTTGAAGTTGCAGGGGAGCGGATTAA-AATCACAGATCTTATCTCTCTGAAGTTG
1 TCTTATCTCCC-TGAAGTTGCAGTGGAGCAGACTAAGAAGCA-AG-TCTTATCTCTCTGAAGTTG
* *
6766 CAG-AGAGTAGATTGCATCTAG
63 CAGTGGAGCAGATTGCATCTAG
*
6787 TCTTATCTCCCTGAAGTTGCAATGGAGCAGACTAAGTAAGCAAGTCTTATC-CTCCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAGTCTTATCTCT-CTGAAGTTGC
* * * *
6851 AGT-GAGGCAGACTGAAGATGGCAAA
64 AGTGGA-GCAGATTG--CAT--CTAG
* * * ** *
6876 TCTTATCTTCCTGAAGTTGCACTGGAGCAGATTAAAGCCGACAA-TCCTATCTC-CTTGAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGAAG-CAAGTCTTATCTCTC-TGAAGTTG
*
6939 CAGTGGAGCGGATT
63 CAGTGGAGCAGATT
6953 AAAATCACAG
Statistics
Matches: 457, Mismatches: 92, Indels: 97
0.71 0.14 0.15
Matches are distributed among these distances:
83 5 0.01
84 152 0.33
85 27 0.06
86 18 0.04
87 23 0.05
88 53 0.12
89 164 0.36
90 15 0.03
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (84 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCTTATCTCTCTGAAGTTGCAG
TGGAGCAGATTGCATCTAG
Done.