Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_233 ID=scaffold_233-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: 9234
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:1068 original size:21 final size:22
Alignment explanation
Indices: 1044--1086 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
1034 CTATATATAA
1044 ACATGT-ATATTTATTTTTTAT
1 ACATGTAATATTTATTTTTTAT
1065 ACATGTACATATTTATTTTTTA
1 ACATGTA-ATATTTATTTTTTA
1087 ACTAATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 6 0.30
23 14 0.70
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.58
Consensus pattern (22 bp):
ACATGTAATATTTATTTTTTAT
Found at i:1641 original size:19 final size:20
Alignment explanation
Indices: 1600--1641 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
1590 ATTTCTATGC
* *
1600 CATTGTAATATTTATTATTG
1 CATTGTAATATTTAATATAG
*
1620 CATTGT-ATATTTAATGTAG
1 CATTGTAATATTTAATATAG
1639 CAT
1 CAT
1642 CACATCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (20 bp):
CATTGTAATATTTAATATAG
Found at i:7230 original size:88 final size:88
Alignment explanation
Indices: 6652--7204 Score: 777
Period size: 88 Copynumber: 6.3 Consensus size: 88
6642 AGAGATATTC
** * * *
6652 CCTTCCTGCACCGACAGTGAGGCAGATCGAAGACACCAGCCTTGCCTCCCTAGGTTGCAGTGGAG
1 CCTTCCTGCACCGACAACGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAG
*
6717 CAGGCTAAAAATAGTAGATCTTG
66 CAGGCTAAAAATAGCAGATCTTG
* * * * * *
6740 CCTTCCTACACCGACAACGGAGTAGATCGAAGTCACCAGCCTTGCCTCCCAGGGTTGCA-TGGAG
1 CCTTCCTGCACCGACAACGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAG
6804 CAGGCTAAAAATAGCAGATCTTG
66 CAGGCTAAAAATAGCAGATCTTG
*
6827 CCTTCCTGCACCGACAACGAAGTAGATC-AAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAG
1 CCTTCCTGCACCGACAACGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAG
*
6891 CAAGCTAAAAATAGCAGATCTTG
66 CAGGCTAAAAATAGCAGATCTTG
** ** * *
6914 CCTTCCTGCACAAACAATTAAACAGATCGAAGTCACCAGCCTTGCCTCCCTGGGTTGCAGCGGAG
1 CCTTCCTGCACCGACAACGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAG
6979 CAGGCTAAAAATAGCAGATCTTG
66 CAGGCTAAAAATAGCAGATCTTG
* * * * *
7002 CCTTCCTCCACCGACAAAGAAGCAGATCGAAGTCACCAGCCTTGCCTACCTGGGTTGCAGCAGAG
1 CCTTCCTGCACCGACAACGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAG
*
7067 TAGGCTAAAAATAGCAGATCTTG
66 CAGGCTAAAAATAGCAGATCTTG
* ** * *
7090 CCTTCCTGCACAGACAATTAAGCAGATCGAAGACACCAGCCTTGCCTTCCTGGGTTGCAACGGAG
1 CCTTCCTGCACCGACAACGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAG
* *
7155 CAGGTTAAAAATAGCAGATATTG
66 CAGGCTAAAAATAGCAGATCTTG
* *
7178 CCTTCTTGCACCGACAGCGAAGCAGAT
1 CCTTCCTGCACCGACAACGAAGCAGAT
7205 TGATGACCCC
Statistics
Matches: 414, Mismatches: 49, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
86 28 0.07
87 101 0.24
88 285 0.69
ACGTcount: A:0.29, C:0.28, G:0.23, T:0.20
Consensus pattern (88 bp):
CCTTCCTGCACCGACAACGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAG
CAGGCTAAAAATAGCAGATCTTG
Found at i:7281 original size:44 final size:44
Alignment explanation
Indices: 7218--7593 Score: 439
Period size: 44 Copynumber: 8.7 Consensus size: 44
7208 TGACCCCAAC
*
7218 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* *
7262 CCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAGATTGTGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* *
7306 CCTATCTCCCTGGTCGGCAGTGGAATAGGTTGAAGATTGAGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* * *
7350 CCTATCTCCTTGGGCAAG-AGTGGAATAGATT-AA-A----GAAT
1 CCTATCTCCCTGGTC-AGCAGTGGAATAGGTTGAAGATTGTGAAT
* * * * * *
7388 CCTATCTCCCTAGACAGTAGTGGAATGGGTTAAAGATTGTAAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
*
7432 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* * * *
7476 TCTATCTCCCTGGGT-AGCATTGGAATAGATTGAAGATTGT-AGGT
1 CCTATCTCCCT-GGTCAGCAGTGGAATAGGTTGAAGATTGTGA-AT
* *
7520 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATCGTGAAC
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* *
7564 CCTATCTCCCTGAG-CAGTAGTGGAGTAGGT
1 CCTATCTCCCTG-GTCAGCAGTGGAATAGGT
7594 GGCAAATAGC
Statistics
Matches: 284, Mismatches: 35, Indels: 26
0.82 0.10 0.08
Matches are distributed among these distances:
37 2 0.01
38 27 0.10
39 2 0.01
40 1 0.00
42 1 0.00
43 6 0.02
44 239 0.84
45 6 0.02
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.28
Consensus pattern (44 bp):
CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
Found at i:7410 original size:38 final size:38
Alignment explanation
Indices: 7345--7423 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 38
7335 TTGAAGATTG
* * *
7345 AGAATCCTATCTCCTTGGGCAAGAGTGGAATAGATTAA
1 AGAATCCTATCTCCCTAGACAAGAGTGGAATAGATTAA
* *
7383 AGAATCCTATCTCCCTAGAC-AGTAGTGGAATGGGTTAA
1 AGAATCCTATCTCCCTAGACAAG-AGTGGAATAGATTAA
7421 AGA
1 AGA
7424 TTGTAAATCC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
37 2 0.06
38 33 0.94
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.25
Consensus pattern (38 bp):
AGAATCCTATCTCCCTAGACAAGAGTGGAATAGATTAA
Found at i:7420 original size:126 final size:129
Alignment explanation
Indices: 7218--7593 Score: 465
Period size: 126 Copynumber: 2.9 Consensus size: 129
7208 TGACCCCAAC
** * *
7218 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGACAGCAGT
1 CCTATCTCCCTGGGAAGCAGTGGAATAGATTGAAGA---TGAATCCTATCTCCCTGGACAGCAGT
*
7283 GGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCGGCAGTGGAATAGGTTGAAGATTGAGA
63 GGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGA
7348 AT
128 AT
* * *
7350 CCTATCTCCTTGGGCAAG-AGTGGAATAGATT-AA-A-GAATCCTATCTCCCTAGACAGTAGTGG
1 CCTATCTCCCTGGG-AAGCAGTGGAATAGATTGAAGATGAATCCTATCTCCCTGGACAGCAGTGG
* *
7411 AATGGGTTAAAGATTGTAAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAAT
65 AATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAAT
* * * * *
7476 TCTATCTCCCTGGGTAGCATTGGAATAGATTGAAGATTGTAGGTCCTATCTCCCTGGTCAGCAGT
1 CCTATCTCCCTGGGAAGCAGTGGAATAGATTGAAGA-TG-A-ATCCTATCTCCCTGGACAGCAGT
* * * * *
7541 GGAATAGGTTGAAGATCGTGAACCCTATCTCCCTGAG-CAGTAGTGGAGTAGGT
63 GGAATAGGTTAAAGATTGTGAATCCTATCTCCCTG-GTCAGCAGTGGAATAGGT
7594 GGCAAATAGC
Statistics
Matches: 211, Mismatches: 24, Indels: 18
0.83 0.09 0.07
Matches are distributed among these distances:
125 2 0.01
126 111 0.53
127 2 0.01
128 1 0.00
130 2 0.01
131 3 0.01
132 87 0.41
133 3 0.01
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.28
Consensus pattern (129 bp):
CCTATCTCCCTGGGAAGCAGTGGAATAGATTGAAGATGAATCCTATCTCCCTGGACAGCAGTGGA
ATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGAGAAT
Found at i:7502 original size:170 final size:170
Alignment explanation
Indices: 7218--7547 Score: 477
Period size: 170 Copynumber: 1.9 Consensus size: 170
7208 TGACCCCAAC
* * *
7218 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGACAGCAGT
1 CCTATCTCCCTAGACAGCAGTGGAATAGGTTAAAGATTGTAAATCCTATCTCCCTGGACAGCAGT
* * *
7283 GGAATAGGTTAAAGATTGTGAATCCTATCTCCCTGGTCGGCAGTGGAATAGGTTGAAGATTG-AG
66 GGAATAGGTTAAAGATTGAGAATCCTATCTCCCTGGTCAGCAGTGGAATAGATTGAAGATTGTAG
*
7347 AATCCTATCTCCTTGGGCAAG-AGTGGAATAGATTAAAGAAT
131 -ATCCTATCTCCCTGGGC-AGCAGTGGAATAGATTAAAGAAT
* * *
7388 CCTATCTCCCTAGACAGTAGTGGAATGGGTTAAAGATTGTAAATCCTATCTCCCTGGTCAGCAGT
1 CCTATCTCCCTAGACAGCAGTGGAATAGGTTAAAGATTGTAAATCCTATCTCCCTGGACAGCAGT
* * *
7453 GGAATAGGTTGAAGATTGAGAATTCTATCTCCCTGGGT-AGCATTGGAATAGATTGAAGATTGTA
66 GGAATAGGTTAAAGATTGAGAATCCTATCTCCCT-GGTCAGCAGTGGAATAGATTGAAGATTGTA
* *
7517 GGTCCTATCTCCCTGGTCAGCAGTGGAATAG
130 GATCCTATCTCCCTGGGCAGCAGTGGAATAG
7548 GTTGAAGATC
Statistics
Matches: 142, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
169 2 0.01
170 135 0.95
171 5 0.04
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (170 bp):
CCTATCTCCCTAGACAGCAGTGGAATAGGTTAAAGATTGTAAATCCTATCTCCCTGGACAGCAGT
GGAATAGGTTAAAGATTGAGAATCCTATCTCCCTGGTCAGCAGTGGAATAGATTGAAGATTGTAG
ATCCTATCTCCCTGGGCAGCAGTGGAATAGATTAAAGAAT
Done.