Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_23 ID=scaffold_23-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: 70483
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Warning! 609 characters in sequence are not A, C, G, or T
Found at i:7809 original size:21 final size:19
Alignment explanation
Indices: 7775--7813 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
7765 ATAATCCTCC
7775 GGAAAATGGCTTAGATAGA
1 GGAAAATGGCTTAGATAGA
7794 GGAAACATGGTCTTAGATAG
1 GGAAA-ATGG-CTTAGATAG
7814 GGAGGCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 4 0.22
21 9 0.50
ACGTcount: A:0.38, C:0.08, G:0.31, T:0.23
Consensus pattern (19 bp):
GGAAAATGGCTTAGATAGA
Found at i:11871 original size:20 final size:21
Alignment explanation
Indices: 11848--11890 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
11838 TTCAAGATTT
11848 AGGTTCAGGG-TTTGAGTTCA
1 AGGTTCAGGGTTTTGAGTTCA
* *
11868 AGGTTCGGGGTTTTGGGTTCA
1 AGGTTCAGGGTTTTGAGTTCA
11889 AG
1 AG
11891 ATAAAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.16, C:0.09, G:0.40, T:0.35
Consensus pattern (21 bp):
AGGTTCAGGGTTTTGAGTTCA
Found at i:18647 original size:37 final size:36
Alignment explanation
Indices: 18606--18714 Score: 146
Period size: 37 Copynumber: 2.9 Consensus size: 36
18596 ATTAATCATC
*
18606 AATAGAATGAGAAAACAAGCAAGAAAGGTATGTTCAA
1 AATAGAATGAGAAAACAA-CAAGAAAGGTATATTCAA
*
18643 AATAGAATGAGAAAACTAACAAGAAAGGTATATTCAT
1 AATAGAATGAGAAAAC-AACAAGAAAGGTATATTCAA
* * *
18680 AATCGAATGAGAATACAAACAAGAAAGCTATATTC
1 AATAGAATGAGAAAAC-AACAAGAAAGGTATATTC
18715 CTATGAATTA
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
37 63 0.97
38 2 0.03
ACGTcount: A:0.53, C:0.10, G:0.17, T:0.19
Consensus pattern (36 bp):
AATAGAATGAGAAAACAACAAGAAAGGTATATTCAA
Found at i:18851 original size:25 final size:25
Alignment explanation
Indices: 18797--18852 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
18787 TTCACTTATA
*
18797 AATTTGTATATATAATTTCATTTGT
1 AATTTATATATATAATTTCATTTGT
*
18822 TATTTATATATATAATTTCATCTT-T
1 AATTTATATATATAATTTCAT-TTGT
18847 AATTTA
1 AATTTA
18853 AAAGAATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 25 0.93
26 2 0.07
ACGTcount: A:0.34, C:0.05, G:0.04, T:0.57
Consensus pattern (25 bp):
AATTTATATATATAATTTCATTTGT
Found at i:27766 original size:23 final size:23
Alignment explanation
Indices: 27740--27834 Score: 127
Period size: 23 Copynumber: 4.1 Consensus size: 23
27730 AAGTTAGAAG
27740 AGTGAAGAGACTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
* * *
27763 AGTGAAAAAAACTTGAATATGAAT
1 AGTG-AAGAGACTTGAATATGAAA
*
27787 AGTGAAGAGACTTGAAGATGAAA
1 AGTGAAGAGACTTGAATATGAAA
* *
27810 AGTTAAGAGGCTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
27833 AG
1 AG
27835 ATACACACAT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
23 41 0.67
24 20 0.33
ACGTcount: A:0.48, C:0.04, G:0.25, T:0.22
Consensus pattern (23 bp):
AGTGAAGAGACTTGAATATGAAA
Found at i:32340 original size:23 final size:23
Alignment explanation
Indices: 32314--32408 Score: 127
Period size: 23 Copynumber: 4.1 Consensus size: 23
32304 AAGTTAGAAG
32314 AGTGAAGAGACTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
* * *
32337 AGTGAAAAAAACTTGAATATGAAT
1 AGTG-AAGAGACTTGAATATGAAA
*
32361 AGTGAAGAGACTTGAAGATGAAA
1 AGTGAAGAGACTTGAATATGAAA
* *
32384 AGTTAAGAGGCTTGAATATGAAA
1 AGTGAAGAGACTTGAATATGAAA
32407 AG
1 AG
32409 ATACACACAT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
23 41 0.67
24 20 0.33
ACGTcount: A:0.48, C:0.04, G:0.25, T:0.22
Consensus pattern (23 bp):
AGTGAAGAGACTTGAATATGAAA
Found at i:37021 original size:190 final size:190
Alignment explanation
Indices: 36692--37065 Score: 581
Period size: 190 Copynumber: 2.0 Consensus size: 190
36682 AGCCACAGTA
*
36692 TTGGAGTATGATAGAAGGAACATCTTTGACTATGTAGAAATCTTCTCCTCATTTCTCCAATCTTT
1 TTGGAATATGATAGAAGGAACATCTTTGACTATGTAGAAATCTTCTCCTCATTTCTCCAATCTTT
* * * *
36757 CTTTGAATGCCTTTGGCATTGATTCAATCTTCAGTTCTTTGAGGGTTGTAATGGAGCTCAATCCC
66 CTTTGAATGCATCTGGCATTGATTCAATCTTCAGTTCTTTGAGGGTTGTAATGAACCTCAATCCC
* * *
36822 TCTGGAAGCATCTTCAAGCTTGGGCAATGCC-TGATATCCAATCGCTGAAGAGAACATGCG
131 TCTGGAAGCATCTTCAAGCCTAGGCAA-CCCTTGATATCCAATCGCTGAAGAGAACATGCG
* * *
36882 TTGGAATATGATAGAAGGAACATGTTTGACTTTGTAGAAATCTTCTCCTC-CTTCTTCCAATCTT
1 TTGGAATATGATAGAAGGAACATCTTTGACTATGTAGAAATCTTCTCCTCATTTC-TCCAATCTT
* *
36946 TTTTTGAATTCATCTGGCATTGATTCAATCTTCAGTTCTTTGAGGGTTGTAATGAACCTCAATCC
65 TCTTTGAATGCATCTGGCATTGATTCAATCTTCAGTTCTTTGAGGGTTGTAATGAACCTCAATCC
* *
37011 CTCTGGAAGCATCTTCAATCCTAGGCAACCCTTGATCTCCAATCGCTGAAGAGAA
130 CTCTGGAAGCATCTTCAAGCCTAGGCAACCCTTGATATCCAATCGCTGAAGAGAA
37066 GGCATGGCTC
Statistics
Matches: 167, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
189 5 0.03
190 162 0.97
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (190 bp):
TTGGAATATGATAGAAGGAACATCTTTGACTATGTAGAAATCTTCTCCTCATTTCTCCAATCTTT
CTTTGAATGCATCTGGCATTGATTCAATCTTCAGTTCTTTGAGGGTTGTAATGAACCTCAATCCC
TCTGGAAGCATCTTCAAGCCTAGGCAACCCTTGATATCCAATCGCTGAAGAGAACATGCG
Found at i:38489 original size:21 final size:19
Alignment explanation
Indices: 38455--38495 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 19
38445 ATAATCCTCT
38455 GGAAAATGGCTTAGATAGA
1 GGAAAATGGCTTAGATAGA
38474 GGAAACATGGTCTTAGATAGA
1 GGAAA-ATGG-CTTAGATAGA
38495 G
1 G
38496 AGGCAAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 5 0.25
20 4 0.20
21 11 0.55
ACGTcount: A:0.39, C:0.07, G:0.32, T:0.22
Consensus pattern (19 bp):
GGAAAATGGCTTAGATAGA
Found at i:48893 original size:37 final size:37
Alignment explanation
Indices: 48801--48953 Score: 198
Period size: 37 Copynumber: 4.1 Consensus size: 37
48791 GCAACATTAA
*
48801 TCATCAATAGAATAAGAATACAAACAAGAAAGGTATATAT
1 TCAT-AATAGAATGAGAATACAAACAAGAAAGG--TATAT
* * *
48841 TCATAATAGAATGAGAAAACAAGCAAGAAAGGTATGT
1 TCATAATAGAATGAGAATACAAACAAGAAAGGTATAT
* *
48878 TCAAAATAGAATGAGAATACTAACAAGAAAGGTATAT
1 TCATAATAGAATGAGAATACAAACAAGAAAGGTATAT
* * *
48915 TCATAATCGAATGAGAATAGAAACAAGAAAGCTATAT
1 TCATAATAGAATGAGAATACAAACAAGAAAGGTATAT
48952 TC
1 TC
48954 CTATGAATTA
Statistics
Matches: 99, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
37 70 0.71
39 25 0.25
40 4 0.04
ACGTcount: A:0.52, C:0.10, G:0.16, T:0.22
Consensus pattern (37 bp):
TCATAATAGAATGAGAATACAAACAAGAAAGGTATAT
Found at i:49057 original size:25 final size:25
Alignment explanation
Indices: 49027--49080 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
49017 TATAAATTTG
*
49027 TATATATAATTAATTTCATTTTTAATT
1 TATATAT-A-TAATTTCATCTTTAATT
49054 TATATATATAATTTCATCTTTAATT
1 TATATATATAATTTCATCTTTAATT
49079 TA
1 TA
49081 AAAGAATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 18 0.69
26 1 0.04
27 7 0.27
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (25 bp):
TATATATATAATTTCATCTTTAATT
Found at i:50044 original size:2 final size:2
Alignment explanation
Indices: 50039--50072 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
50029 GTCTCTCTTA
50039 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
50073 TTAGTAGGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50853 original size:156 final size:154
Alignment explanation
Indices: 50291--50832 Score: 611
Period size: 156 Copynumber: 3.5 Consensus size: 154
50281 CAGCAACGGT
* * * *
50291 AAAAAAGGA-ATAAAATGTAAGTCTTTGTTTATGGTTTCGGCTTGCTTATGTAGCAAGAAAAGTG
1 AAAAAAGGAGA-AAAAAGTATGCCTTTGTTTATGGTTTCGGCTTGCTTGTGTAGCAAGAAAAGTG
* *
50355 AATATAAACACATATAT-T-TAGT-AT-GGTTTCTTGAACTTGAATTGAACGAAGAATTTAAAAA
65 AATATAAACACATATATATATA-TAATAGGTTTCTTGAAATTGAATTGAATGAAGAATTT-AAAA
*
50416 ACAACAAAGAAACAAGAAAGCCATTT-
128 ACAACAAAGAAACAAGAAAACCATTTA
* * * * **
50442 AAAAAAGGAG-AAAATGTATGCCTTTATTTATGGTTTCAGCTTGCTTGTGTAGCAAAAAAAAACG
1 AAAAAAGGAGAAAAAAGTATGCCTTTGTTTATGGTTTCGGCTTGCTTGTGTAGC-AAGAAAAGTG
* *
50506 AATATAAATATATATATATATATAATATGGTTTCTT-AAACTTGAATTGAATGAAGAATTTTAAA
65 AATATAAACACATATATATATATAATA-GGTTTCTTGAAA-TTGAATTGAATGAAGAA-TTTAAA
* *
50570 AACAATAAAGAATCAAGAAAACCA-TTA
127 AACAACAAAGAAACAAGAAAACCATTTA
* * ** * * * *
50597 AAAAAAAGAAAAAAAAACATGCTTTTGTTTATGGTTTTGGCTTGCTTGTGTAGTAAGAAAAGTAA
1 AAAAAAGGAGAAAAAAGTATGCCTTTGTTTATGGTTTCGGCTTGCTTGTGTAGCAAGAAAAGTGA
* *
50662 ATATAAACATATATATATATTTAAATATGGTTTCTTGAAATTGAATTGAATGAAGAATTTAAAAA
66 ATATAAACACATATATATATAT-AATA-GGTTTCTTGAAATTGAATTGAATGAAGAATTTAAAAA
*
50727 GCGGA-AAAGAAACAAGAAAACCATTTA
129 -C-AACAAAGAAACAAGAAAACCATTTA
* * * *
50754 AAAAAAGGCGAAAAAAGTATTCCTTTGTTTATGGTTTCGGATTGCTTGTGGAGCAA-AAAAGTGA
1 AAAAAAGGAGAAAAAAGTATGCCTTTGTTTATGGTTTCGGCTTGCTTGTGTAGCAAGAAAAGTGA
50818 ATATAAACAGCATAT
66 ATATAAACA-CATAT
50833 GTGATTCCTC
Statistics
Matches: 328, Mismatches: 46, Indels: 28
0.82 0.11 0.07
Matches are distributed among these distances:
150 38 0.12
151 31 0.09
152 2 0.01
153 4 0.01
154 4 0.01
155 91 0.28
156 102 0.31
157 56 0.17
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.31
Consensus pattern (154 bp):
AAAAAAGGAGAAAAAAGTATGCCTTTGTTTATGGTTTCGGCTTGCTTGTGTAGCAAGAAAAGTGA
ATATAAACACATATATATATATAATAGGTTTCTTGAAATTGAATTGAATGAAGAATTTAAAAACA
ACAAAGAAACAAGAAAACCATTTA
Found at i:62567 original size:21 final size:21
Alignment explanation
Indices: 62524--62569 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
62514 TAATTTTTTT
* *
62524 ACCCTGAATCCAGAATCTTAA
1 ACCCTGAATCCAGAAACTAAA
62545 ACCCTGAATCCA-AAACATAAA
1 ACCCTGAATCCAGAAAC-TAAA
62566 ACCC
1 ACCC
62570 CAAACTCGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.43, C:0.33, G:0.07, T:0.17
Consensus pattern (21 bp):
ACCCTGAATCCAGAAACTAAA
Found at i:62671 original size:20 final size:19
Alignment explanation
Indices: 62633--62671 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
62623 ACCCTTGAAC
*
62633 TTTAAACTTGAACCTCGAA
1 TTTAAACTTAAACCTCGAA
*
62652 TTTAAACTTTAAATCTCGAA
1 TTTAAAC-TTAAACCTCGAA
62672 ACCAAACCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (19 bp):
TTTAAACTTAAACCTCGAA
Found at i:62932 original size:17 final size:18
Alignment explanation
Indices: 62910--62943 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
62900 TTGTTTGTAA
62910 TTTAAA-AAATTAATTAT
1 TTTAAATAAATTAATTAT
*
62927 TTTAAATAATTTAATTA
1 TTTAAATAAATTAATTA
62944 AAGTTAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTAAATAAATTAATTAT
Found at i:65467 original size:21 final size:21
Alignment explanation
Indices: 65443--65495 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
65433 CAGTAAATTA
65443 CGTCCACGTCAGCACTATTTG
1 CGTCCACGTCAGCACTATTTG
65464 CGTCCACGTCAGCACTATTTG
1 CGTCCACGTCAGCACTATTTG
*
65485 TGTCCACGTCA
1 CGTCCACGTCA
65496 ACATAGCGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.19, C:0.34, G:0.19, T:0.28
Consensus pattern (21 bp):
CGTCCACGTCAGCACTATTTG
Found at i:66041 original size:58 final size:58
Alignment explanation
Indices: 65951--66063 Score: 199
Period size: 58 Copynumber: 1.9 Consensus size: 58
65941 GTTCCTTGAG
*
65951 GGAATTCTATTGAATCTTTTATCGTCGCAAGTTAAGCTGACTTAGGCGTTTTTGGAGT
1 GGAATTCTATTGAATCCTTTATCGTCGCAAGTTAAGCTGACTTAGGCGTTTTTGGAGT
* *
66009 GGAATTCTGTTGAATCCTTTATCGTCGCAAGTTAGGCTGACTTAGGCGTTTTTGG
1 GGAATTCTATTGAATCCTTTATCGTCGCAAGTTAAGCTGACTTAGGCGTTTTTGG
66064 GAGCAAAGAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.20, C:0.15, G:0.26, T:0.39
Consensus pattern (58 bp):
GGAATTCTATTGAATCCTTTATCGTCGCAAGTTAAGCTGACTTAGGCGTTTTTGGAGT
Done.