Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_353 ID=scaffold_353-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: 9016
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.25
Warning! 1039 characters in sequence are not A, C, G, or T
Found at i:5976 original size:21 final size:20
Alignment explanation
Indices: 5952--5991 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
5942 AAGTGATGTG
*
5952 AAAAATGAAAAGATGAAAATC
1 AAAAATGAAAA-AAGAAAATC
5973 AAAAATGAAAAAAGAAAAT
1 AAAAATGAAAAAAGAAAAT
5992 GGAGAGGCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.72, C:0.03, G:0.12, T:0.12
Consensus pattern (20 bp):
AAAAATGAAAAAAGAAAATC
Found at i:7407 original size:100 final size:100
Alignment explanation
Indices: 7233--7501 Score: 441
Period size: 100 Copynumber: 2.7 Consensus size: 100
7223 ACCATAGATT
*
7233 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGACGGATCTGGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
*
7298 TGCACTTAAAAAGATTGAAGCCACAACGGCGGATC
66 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
7333 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
7398 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
66 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
* * * * * * *
7433 TTACTTCCCT-GAAGGTGCGGTGGAACAGATTGAAGCTACGACAGCGAATCTGGTTTCCCCGACA
1 TTACTTCCTTAGCA-GTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATA
7497 TTGCA
65 TTGCA
7502 GTTGAACAAA
Statistics
Matches: 159, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
99 2 0.01
100 157 0.99
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (100 bp):
TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATAT
TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
Found at i:7491 original size:50 final size:50
Alignment explanation
Indices: 7246--7517 Score: 233
Period size: 50 Copynumber: 5.4 Consensus size: 50
7236 CTTCCTTAGC
*
7246 AGTGCAGTGGAACAGATTGAAGCTACGACGACGGATCTGGTTTCCCTGAT
1 AGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGAT
* * ** * * * *** * *
7296 ATTGCACTTAAAAAGATTGAAGCCACAACGGCGGATCTTACTT-CCTTAGC
1 AGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGA-T
7346 AGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGAT
1 AGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGAT
* * ** * * * ***
7396 ATTGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGA-
1 AGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGAT
* * * * *
7445 AGGTGCGGTGGAACAGATTGAAGCTACGACAGCGAATCTGGTTTCCCCGAC
1 A-GTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGAT
* * *
7496 ATTGCAGTTGAACAAATTGAAG
1 AGTGCAGTGGAACAGATTGAAG
7518 ATTATAGATC
Statistics
Matches: 165, Mismatches: 53, Indels: 8
0.73 0.23 0.04
Matches are distributed among these distances:
49 5 0.03
50 155 0.94
51 5 0.03
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (50 bp):
AGTGCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGAT
Found at i:7682 original size:132 final size:132
Alignment explanation
Indices: 7511--8460 Score: 1107
Period size: 132 Copynumber: 7.2 Consensus size: 132
7501 AGTTGAACAA
* * * * *
7511 ATTGAAGATTATAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAAATCAAAGATGGTGGATTTTAC
1 ATTGAAGATAACAGATCTTGTCTTCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTAGATTTTAC
* *
7576 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAATAATTCTA-TCTCCCTGGGCAGCAGTGGAA
66 CTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACT-TCCCTGGGCAGCAGTGGAA
7640 TAG
130 TAG
* * * *
7643 ATTAAAGATAACATATCTTATCTTCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTAC
1 ATTGAAGATAACAGATCTTGTCTTCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTAGATTTTAC
* *
7708 CT-CCTCATGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAG-AGCGGAA
66 CTCCCT-GTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAA
*
7771 TGG
130 TAG
* * * * * * *
7774 ATTGAAGATAGCAGATCTTGCCTTCCTACA-TAGATAGCGAAGCAGATCGAAGATGGCAGATTTT
1 ATTGAAGATAACAGATCTTGTCTTCCTA-AGCAG-TAGTGGAGCAGATCAAAGATGGTAGATTTT
* * * *
7838 ACCT-CCTCGTGGTTACAATGGAGTACATTGAAGCTAGTAATTCTACTTCCCTGGGCAACAGCGG
64 ACCTCCCT-GTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGG
7902 AATAG
128 AATAG
* * * * *
7907 ATTGAAGATAGCAGATCTTGCCTTCCT--GCA-TAGACATCGAAGCAGATCGAAGATGGCAGATT
1 ATTGAAGATAACAGATCTTGTCTTCCTAAGCAGTAG---T-GGAGCAGATCAAAGATGGTAGATT
* * * *
7969 TTACCT-CCTCGTGGTTACAGTGGAGTACATTGAAGCCAGCAATTCTACTTCCCTAGACAACAGT
62 TTACCTCCCT-GTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGT
*
8033 AGAATAG
126 GGAATAG
** * *
8040 ATTGAAGATTTCAAATCTTGTCTTCCTAAGCAGTAGTGGGGCAGATCAAAGATGGT-GAATTTTA
1 ATTGAAGATAACAGATCTTGTCTTCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTAG-ATTTTA
* * *
8104 CCTCCCTGTGGTTACAGTGGAGTACATTGAAACCGGTAATTTTACTTCCCTGGGCAGCAGTGGAA
65 CCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAA
8169 TAG
130 TAG
** * * * *
8172 ATTGAAGATTTCAGATCTTATCTCCCCAAGCAGTAATGGAGCAGATCAAAGATGGT-GAATTTTA
1 ATTGAAGATAACAGATCTTGTCTTCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTAG-ATTTTA
*
8236 CCTCCCTGTGGTTACAGTGGAGTACATTGAAACCAGTAATTCTACTTCCCTGGGCAGCAGTGGAA
65 CCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAA
8301 TAG
130 TAG
* * * * *
8304 ATTGAAGATTACAGGTCTTATCTCCCTAAGCAGTAGTGGAACAGATCAAAGATGGTAGATTTTAC
1 ATTGAAGATAACAGATCTTGTCTTCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTAGATTTTAC
* * * * ** *
8369 CTCCCTGAGGTTGCAGTGGAGTATATTGAAGCCAGTAATTCTA-TTCCCCCGATCGGCAGTGGAA
66 CTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTT-CCCTGGGCAGCAGTGGAA
*
8433 TCG
130 TAG
* *
8436 ATCGAAGA-AAGTAGATCTTGTCTTC
1 ATTGAAGATAA-CAGATCTTGTCTTC
8461 ATGTATTGGC
Statistics
Matches: 719, Mismatches: 81, Indels: 36
0.86 0.10 0.04
Matches are distributed among these distances:
129 3 0.00
131 41 0.06
132 516 0.72
133 153 0.21
135 3 0.00
136 3 0.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.28
Consensus pattern (132 bp):
ATTGAAGATAACAGATCTTGTCTTCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTAGATTTTAC
CTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAAT
AG
Found at i:8303 original size:397 final size:395
Alignment explanation
Indices: 7511--8416 Score: 1129
Period size: 397 Copynumber: 2.3 Consensus size: 395
7501 AGTTGAACAA
* ** * * *
7511 ATTGAAGATTATAGATCTTGTCTCCCTAAGCAGTAGT-GGAGCAAATCAAAGATGGTGGATTTTA
1 ATTGAAGATTACAGATCTTACCTCCCT-AGCAGTAGTCGAAGCAGATCAAAGATGGTAGATTTTA
* * * * *
7575 CCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAATAATTCTATCTCCCTGGGCAGCAGTGGAA
65 CCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTAT-TCCCTAGACAACAGTAGAA
*
7640 TAGATTAAAGATAACATATCTTATCTTCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTT
129 TAGATTAAAGATAACAAATCTTATCTTCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTT
*
7705 TACCTCCTCATGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGAGCGGA
194 TACCTCCTCATGGTTACAGTGGAGTACATTGAAACCAGTAATTCTACTTCCCTGGGCAGAGCGGA
* * * * *
7770 ATGGATTGAAGATAGCAGATCTTGCCTTCCTACATAGATAGCGAAGCAGATCGAAGATGGCAGAT
259 ATAGATTGAAGATAGCAGATCTTACCTCCCAACATAGATAGCGAAGCAGATCAAAGATGGCAGAT
* *
7835 TTTACCTCCTCGTGGTTACAATGGAGTACATTGAAGCTAGTAATTCTACTTCCCTGGGCAACAGC
324 TTTACCTCCTCGTGGTTACAATGGAGTACATTGAAACCAGTAATTCTACTTCCCTGGGCAACAGC
7900 GGAATAG
389 GGAATAG
* * * *
7907 ATTGAAGA-TAGCAGATCTTGCCTTCCT-GCA-TAGACATCGAAGCAGATCGAAGATGGCAGATT
1 ATTGAAGATTA-CAGATCTTACCTCCCTAGCAGTAG---TCGAAGCAGATCAAAGATGGTAGATT
* *
7969 TTACCT-CCTCGTGGTTACAGTGGAGTACATTGAAGCCAGCAATTCTACTTCCCTAGACAACAGT
62 TTACCTCCCT-GAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA-TTCCCTAGACAACAGT
* ** * * *
8033 AGAATAGATTGAAGATTTCAAATCTTGTCTTCCTAAGCAGTAGTGGGGCAGATCAAAGATGG-TG
125 AGAATAGATTAAAGATAACAAATCTTATCTTCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAG
* * *
8097 AATTTTACCTCC-CTGTGGTTACAGTGGAGTACATTGAAACCGGTAATTTTACTTCCCTGGGCAG
190 -ATTTTACCTCCTC-ATGGTTACAGTGGAGTACATTGAAACCAGTAATTCTACTTCCCTGGGCAG
* ** *
8161 CAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCCAAGCAGTA-AT-G-G-AGCAGATCAAA
253 -AGCGGAATAGATTGAAGATAGCAGATCTTACCT-CCCAA-CA-TAGATAGCGAAGCAGATCAAA
* *
8222 GATGG-TGAATTTTACCTCC-CTGTGGTTACAGTGGAGTACATTGAAACCAGTAATTCTACTTCC
314 GATGGCAG-ATTTTACCTCCTC-GTGGTTACAATGGAGTACATTGAAACCAGTAATTCTACTTCC
* *
8285 CTGGGCAGCAGTGGAATAG
377 CTGGGCAACAGCGGAATAG
* * *
8304 ATTGAAGATTACAGGTCTTATCTCCCTAAGCAGTAGTGGAA-CAGATCAAAGATGGTAGATTTTA
1 ATTGAAGATTACAGATCTTACCTCCCT-AGCAGTAGTCGAAGCAGATCAAAGATGGTAGATTTTA
* *
8368 CCTCCCTGAGGTTGCAGTGGAGTATATTGAAGCCAGTAATTCTATTCCC
65 CCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATTCCC
8417 CCGATCGGCA
Statistics
Matches: 438, Mismatches: 52, Indels: 41
0.82 0.10 0.08
Matches are distributed among these distances:
393 3 0.01
394 3 0.01
395 7 0.02
396 86 0.20
397 292 0.67
398 31 0.07
399 7 0.02
400 7 0.02
401 2 0.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (395 bp):
ATTGAAGATTACAGATCTTACCTCCCTAGCAGTAGTCGAAGCAGATCAAAGATGGTAGATTTTAC
CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATTCCCTAGACAACAGTAGAATA
GATTAAAGATAACAAATCTTATCTTCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCAGATTTTA
CCTCCTCATGGTTACAGTGGAGTACATTGAAACCAGTAATTCTACTTCCCTGGGCAGAGCGGAAT
AGATTGAAGATAGCAGATCTTACCTCCCAACATAGATAGCGAAGCAGATCAAAGATGGCAGATTT
TACCTCCTCGTGGTTACAATGGAGTACATTGAAACCAGTAATTCTACTTCCCTGGGCAACAGCGG
AATAG
Done.