Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_41 ID=scaffold_41-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: 39383
ACGTcount: A:0.22, C:0.10, G:0.11, T:0.23
Warning! 13410 characters in sequence are not A, C, G, or T
Found at i:3286 original size:15 final size:15
Alignment explanation
Indices: 3266--3295 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3256 TTCCCAATTC
3266 ACTAACCCAATTTTT
1 ACTAACCCAATTTTT
3281 ACTAACCCAATTTTT
1 ACTAACCCAATTTTT
3296 GGGATATGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.40
Consensus pattern (15 bp):
ACTAACCCAATTTTT
Found at i:3915 original size:54 final size:54
Alignment explanation
Indices: 3847--3953 Score: 180
Period size: 54 Copynumber: 2.0 Consensus size: 54
3837 AATTATGTGA
*
3847 ACATGAATTGAGTTGTTAATTTTGCAAAA-TGGGCATGGTATGAATGATTGTATC
1 ACATGAATTAAGTTGTTAATTTTG-AAAACTGGGCATGGTATGAATGATTGTATC
*
3901 ACATGAATTAAGTTGTTAATTTTGAAAACTGGGCATGGTTTGAATGATTGTAT
1 ACATGAATTAAGTTGTTAATTTTGAAAACTGGGCATGGTATGAATGATTGTAT
3954 ATGATATGGT
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
53 4 0.08
54 46 0.92
ACGTcount: A:0.32, C:0.07, G:0.23, T:0.38
Consensus pattern (54 bp):
ACATGAATTAAGTTGTTAATTTTGAAAACTGGGCATGGTATGAATGATTGTATC
Found at i:13670 original size:168 final size:168
Alignment explanation
Indices: 13392--13819 Score: 784
Period size: 168 Copynumber: 2.5 Consensus size: 168
13382 NNNNNNNNNN
13392 GTACTCGGGTATTTTCGGATATTCGACTTCATGTTTCTCGTGCTCTTTGGGCTTTTCCCCTTTGG
1 GTACTCGGGTATTTTCGGATATTCGACTTCATGTTTCTCGTGCTCTTTGGGCTTTTCCCCTTTGG
13457 GGAAATTGGGTTTTTCTTTCTCGTACTCTTCGTGCTCCTTCGATTCGTGTGACTCGTGGCACTCC
66 GGAAATTGGGTTTTTCTTTCTCGTACTCTTCGTGCTCCTTCGATTCGTGTGACTCGTGGCACTCC
*
13522 TCATGTTTATGTTCCTTACCCTCATCTTGTTTTTCCTT
131 TCATGTTTATGTTCCTTACCCTCATCTTGCTTTTCCTT
13560 GTACTCGGGTATTTTCGGATATTCGACTTCATGTTTCTCGTGCTCTTTGGGCTTTTCCCCTTTGG
1 GTACTCGGGTATTTTCGGATATTCGACTTCATGTTTCTCGTGCTCTTTGGGCTTTTCCCCTTTGG
13625 GGAAATTGGGTTTTTCTTTCTCGTACTCTTCGTGCTCCTTCGATTCGTGTGACTCGTGGCACTCC
66 GGAAATTGGGTTTTTCTTTCTCGTACTCTTCGTGCTCCTTCGATTCGTGTGACTCGTGGCACTCC
13690 TCATGTTTATGTTCCTTACCCTCATCTTGCTTTTCCTT
131 TCATGTTTATGTTCCTTACCCTCATCTTGCTTTTCCTT
* * * **
13728 GTACTCGGGTATTTCCGGATATTCGACTTCGTGTTTCTCGTGCTCTTTAGGCTTTTCCAATTTGG
1 GTACTCGGGTATTTTCGGATATTCGACTTCATGTTTCTCGTGCTCTTTGGGCTTTTCCCCTTTGG
* *
13793 GGAACTCGGGTTTTTCTTTCTCGTACT
66 GGAAATTGGGTTTTTCTTTCTCGTACT
13820 NNNNNNNNNN
Statistics
Matches: 252, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
168 252 1.00
ACGTcount: A:0.11, C:0.25, G:0.20, T:0.45
Consensus pattern (168 bp):
GTACTCGGGTATTTTCGGATATTCGACTTCATGTTTCTCGTGCTCTTTGGGCTTTTCCCCTTTGG
GGAAATTGGGTTTTTCTTTCTCGTACTCTTCGTGCTCCTTCGATTCGTGTGACTCGTGGCACTCC
TCATGTTTATGTTCCTTACCCTCATCTTGCTTTTCCTT
Found at i:14846 original size:10 final size:10
Alignment explanation
Indices: 14831--14858 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
14821 AATTTCCATA
14831 AAATTATGAT
1 AAATTATGAT
14841 AAATTATGAT
1 AAATTATGAT
14851 AAATTATG
1 AAATTATG
14859 TANNNNNNNN
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (10 bp):
AAATTATGAT
Found at i:21044 original size:2 final size:2
Alignment explanation
Indices: 21037--21084 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
21027 AACAAAACAA
21037 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21079 AT AT AT
1 AT AT AT
21085 GGATCAATTC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21319 original size:66 final size:66
Alignment explanation
Indices: 21213--21345 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
21203 TCAAGTATAC
21213 ACAATGAAATTTCTTTAAAAAGACAAATGCAACAAAACAAGACTGCATTGATGGCAAATACCATA
1 ACAATGAAATTTCTTTAAAAAGACAAATGCAACAAAACAAGACTGCATTGATGGCAAATACCATA
21278 A
66 A
21279 ACAATGAAATTTCTTTAAAAAGACAAATGCAACAAAACAAGACTGCATTGATGGCAAATACCATA
1 ACAATGAAATTTCTTTAAAAAGACAAATGCAACAAAACAAGACTGCATTGATGGCAAATACCATA
21344 A
66 A
21345 A
1 A
21346 ATCTGCCACA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (66 bp):
ACAATGAAATTTCTTTAAAAAGACAAATGCAACAAAACAAGACTGCATTGATGGCAAATACCATA
A
Found at i:21337 original size:31 final size:31
Alignment explanation
Indices: 21236--21337 Score: 73
Period size: 31 Copynumber: 3.2 Consensus size: 31
21226 TTTAAAAAGA
21236 CAAATGCAACAAAACAAGACTGCATTGATGG
1 CAAATGCAACAAAACAAGACTGCATTGATGG
* * * * * * *
21267 CAAAT--ACCATAAACAATGAAATTTCTTTAAAAAGA
1 CAAATGCAACA-AAACAA-G--ACTGCATT--GATGG
21302 CAAATGCAACAAAACAAGACTGCATTGATGG
1 CAAATGCAACAAAACAAGACTGCATTGATGG
21333 CAAAT
1 CAAAT
21338 ACCATAAAAT
Statistics
Matches: 49, Mismatches: 14, Indels: 16
0.62 0.18 0.20
Matches are distributed among these distances:
29 3 0.06
30 6 0.12
31 13 0.27
33 10 0.20
35 8 0.16
36 6 0.12
37 3 0.06
ACGTcount: A:0.49, C:0.18, G:0.14, T:0.20
Consensus pattern (31 bp):
CAAATGCAACAAAACAAGACTGCATTGATGG
Found at i:22760 original size:17 final size:17
Alignment explanation
Indices: 22710--22761 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
22700 AATTAGTAAC
22710 AAAAATGAAAG-ACGAA
1 AAAAATGAAAGAACGAA
* * *
22726 GAAAA-GAAACAAAGGAA
1 AAAAATGAAA-GAACGAA
22743 AAAAATGAAAGAACGAA
1 AAAAATGAAAGAACGAA
22760 AA
1 AA
22762 CAAAATAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 5
0.71 0.16 0.13
Matches are distributed among these distances:
15 4 0.15
16 4 0.15
17 15 0.56
18 4 0.15
ACGTcount: A:0.71, C:0.06, G:0.19, T:0.04
Consensus pattern (17 bp):
AAAAATGAAAGAACGAA
Found at i:29881 original size:168 final size:168
Alignment explanation
Indices: 29570--30113 Score: 964
Period size: 168 Copynumber: 3.2 Consensus size: 168
29560 NNNNNNCTTC
** * *
29570 GTGCTCCTTCGATT-ATGTGACTCGTGGCACTCCTCATGTTTATGTTCCTTACCCTCATCTTGCT
1 GTGCTCCTTCGATTCGCGTGACTCGTGGTACTCTTCATGTTTATGTTCCTTACCCTCATCTTGCT
*
29634 TTTCCTTGTACTCGGGTATTTCCGGATATTCGACTTCGTGTTTCTCGTGCTCTTTAGGCTTTTCC
66 TTTCCTTGTACTCGGGTATTTTCGGATATTCGACTTCGTGTTTCTCGTGCTCTTTAGGCTTTTCC
29699 AATTTGGGGAACTCGGGTTTTTCTTTCTCGTACTCTTT
131 AATTTGGGGAACTCGGGTTTTTCTTTCTCGTACTCTTT
*
29737 GTGCTCCTTCGATTCGCGTGATTCGTGGTACTCTTCATGTTTATGTTCCTTACCCTCATCTTGCT
1 GTGCTCCTTCGATTCGCGTGACTCGTGGTACTCTTCATGTTTATGTTCCTTACCCTCATCTTGCT
29802 TTTCCTTGTACTCGGGTATTTTCGGATATTCGACTTCGTGTTTCTCGTGCTCTTTAGGCTTTTCC
66 TTTCCTTGTACTCGGGTATTTTCGGATATTCGACTTCGTGTTTCTCGTGCTCTTTAGGCTTTTCC
29867 AATTTGGGGAACTCGGGTTTTTCTTTCTCGTACTCTTT
131 AATTTGGGGAACTCGGGTTTTTCTTTCTCGTACTCTTT
*
29905 GTGCTCCTTCGATTCGCGTGATTCGTGGTACTCTTCATGTTTATGTTCCTTACCCTCATCTTGCT
1 GTGCTCCTTCGATTCGCGTGACTCGTGGTACTCTTCATGTTTATGTTCCTTACCCTCATCTTGCT
29970 TTTCCTTGTACTCGGGTATTTTCGGATATTCGACTTCGTGTTTCTCGTGCTCTTTAGGCTTTTCC
66 TTTCCTTGTACTCGGGTATTTTCGGATATTCGACTTCGTGTTTCTCGTGCTCTTTAGGCTTTTCC
* * * *
30035 AACTTGGGGAACTCGGGTTTTTCTTTTTGGTACTCTTC
131 AATTTGGGGAACTCGGGTTTTTCTTTCTCGTACTCTTT
* *
30073 GTGCTCCTTCGATTTGTGTGACTCGTGGTACTCTTCATGTT
1 GTGCTCCTTCGATTCGCGTGACTCGTGGTACTCTTCATGTT
30114 GCTTGCAGGG
Statistics
Matches: 363, Mismatches: 13, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
167 14 0.04
168 349 0.96
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (168 bp):
GTGCTCCTTCGATTCGCGTGACTCGTGGTACTCTTCATGTTTATGTTCCTTACCCTCATCTTGCT
TTTCCTTGTACTCGGGTATTTTCGGATATTCGACTTCGTGTTTCTCGTGCTCTTTAGGCTTTTCC
AATTTGGGGAACTCGGGTTTTTCTTTCTCGTACTCTTT
Found at i:31660 original size:2 final size:2
Alignment explanation
Indices: 31653--31696 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
31643 AAACATAAAA
31653 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31695 AT
1 AT
31697 GGTCAATCTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33638 original size:15 final size:15
Alignment explanation
Indices: 33613--33647 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
33603 AACTCTATTT
*
33613 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
33627 TAATTAATATTAAGA
1 TAATTAATATTAAGA
33642 TAATTA
1 TAATTA
33648 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:33690 original size:10 final size:10
Alignment explanation
Indices: 33672--33719 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
33662 ATTTTAGTAT
33672 TTTAT-TTTA
1 TTTATCTTTA
33681 TTTATCTTTA
1 TTTATCTTTA
33691 TTTATCTTTA
1 TTTATCTTTA
* ** *
33701 ATTAAATGTA
1 TTTATCTTTA
33711 TTTATCTTT
1 TTTATCTTT
33720 TGGGAGTTTA
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
9 5 0.17
10 25 0.83
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (10 bp):
TTTATCTTTA
Found at i:35865 original size:168 final size:168
Alignment explanation
Indices: 35571--36249 Score: 1045
Period size: 168 Copynumber: 4.0 Consensus size: 168
35561 CTTTGGGAAC
* * *
35571 TCATGCTTATGTTCCTTACCCTCATCTTGTTTTTCCTTGTACTCGGGTATTTTTGGATATTCGAC
1 TCATGTTTATGTTCCTTACCCTCATCTTGCTTTTCCTTGTACTCGGGTATTTTCGGATATTCGAC
** * **
35636 TTCGTGTTTCTCGTGCTCTTTAGGCTTTTCCCCTTTGGGGAAATTAGGTTTTTCTTTCTCGTACG
66 TTCGTGTTTCTCGTGCTCTTTAGGCTTTTCCAATTTGGGGAACTCGGGTTTTTCTTTCTCGTAC-
* *
35701 T-TTCGTGCTCCTTCGATTCGTGTGACTCGTGGCACTCC
130 TCTTCGTGCTCCTTCGATTCGTGTGACTCGTGGTACTCT
* * * * *
35739 TCATGTTTATGATCCCTACCCTCATCTTGCTTTTCCTTATACTCGGTTATTTTCAGATATTCGAC
1 TCATGTTTATGTTCCTTACCCTCATCTTGCTTTTCCTTGTACTCGGGTATTTTCGGATATTCGAC
* * * *
35804 TTCGTGTTACTCATGATCTTTAGGCTTTTCCAATTTGAGGAACTCGGGTTTTTCTTTCTCGTACT
66 TTCGTGTTTCTCGTGCTCTTTAGGCTTTTCCAATTTGGGGAACTCGGGTTTTTCTTTCTCGTACT
* *
35869 CTTCATGCTCCTTCAATTCGTGTGACTCGTGGTACTCT
131 CTTCGTGCTCCTTCGATTCGTGTGACTCGTGGTACTCT
*
35907 TCATGTTTATGTTCCTTACCCTCATCTTGCTTTTCCTTGTACTCGGGTATTTCCGGATATTCGAC
1 TCATGTTTATGTTCCTTACCCTCATCTTGCTTTTCCTTGTACTCGGGTATTTTCGGATATTCGAC
*
35972 TTCGTGTTTCTCGTGCTCTTTAGGCTTTTCCAATTTGGGGAACTCGGGCTTTTCTTTCTCGTACT
66 TTCGTGTTTCTCGTGCTCTTTAGGCTTTTCCAATTTGGGGAACTCGGGTTTTTCTTTCTCGTACT
* * *
36037 TTTCGTGCTCCTTCGATTCGCGTGATTCGTGGTACTCT
131 CTTCGTGCTCCTTCGATTCGTGTGACTCGTGGTACTCT
* *
36075 TCATGTTTATGTTCCTTACCCTCATCTTGGTTTTCCTTGTACTCGGGTATTTTTGGATATTCGAC
1 TCATGTTTATGTTCCTTACCCTCATCTTGCTTTTCCTTGTACTCGGGTATTTTCGGATATTCGAC
* * *
36140 TTCGTGTTTTTCGTGCTCTTTAGGCTTTTCCAATTTGGGGAACTCGGGTTTTTCTTTTTGGTACT
66 TTCGTGTTTCTCGTGCTCTTTAGGCTTTTCCAATTTGGGGAACTCGGGTTTTTCTTTCTCGTACT
* *
36205 CTTCCTGCTCCTTCGATTTGTGTGACTCGTGGTACTCT
131 CTTCGTGCTCCTTCGATTCGTGTGACTCGTGGTACTCT
36243 TCATGTT
1 TCATGTT
36250 GCTTGCAGGG
Statistics
Matches: 461, Mismatches: 49, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
167 1 0.00
168 460 1.00
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.46
Consensus pattern (168 bp):
TCATGTTTATGTTCCTTACCCTCATCTTGCTTTTCCTTGTACTCGGGTATTTTCGGATATTCGAC
TTCGTGTTTCTCGTGCTCTTTAGGCTTTTCCAATTTGGGGAACTCGGGTTTTTCTTTCTCGTACT
CTTCGTGCTCCTTCGATTCGTGTGACTCGTGGTACTCT
Found at i:38571 original size:24 final size:24
Alignment explanation
Indices: 38539--38588 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
38529 AATAAGATTG
*
38539 AACTTTCACCTTGGGGTCAAAGGC
1 AACTTTCACCTCGGGGTCAAAGGC
38563 AACTTTCACCTCGGGGTCAAAGGC
1 AACTTTCACCTCGGGGTCAAAGGC
38587 AA
1 AA
38589 TTGCTATGGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (24 bp):
AACTTTCACCTCGGGGTCAAAGGC
Done.