Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_756 ID=scaffold_756-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: 5358
ACGTcount: A:0.26, C:0.08, G:0.16, T:0.25
Warning! 1327 characters in sequence are not A, C, G, or T
Found at i:2526 original size:51 final size:50
Alignment explanation
Indices: 2462--2644 Score: 258
Period size: 51 Copynumber: 3.6 Consensus size: 50
2452 TATCGATGAA
*
2462 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTACCGATAAATAATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAT-ATGGT
* * * * * *
2513 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGAGAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAA-ATATGGT
*
2564 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTACCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAT-ATGGT
*
2615 CACGTATGTAGTACTATGTGAAGGCTACTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTA
2645 TGTGAAGGCT
Statistics
Matches: 114, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
50 1 0.01
51 112 0.98
52 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATGGT
Found at i:2638 original size:102 final size:102
Alignment explanation
Indices: 2462--2869 Score: 421
Period size: 102 Copynumber: 3.9 Consensus size: 102
2452 TATCGATGAA
* *
2462 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTACCGATAAATAATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATGATGGTCACATGTGTAGTAC
*
2527 TAAGTGAAGGCTACTATGTGTACCGAGAAGCTTTGGT
66 TAAGTGAAGGCTACTATGTGTACCGAGAAGCTTTGAT
* * *
2564 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTACCGATAAATGATGGTCACGTATGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATGATGGTCACATGTGTAGTAC
* ** *
2629 TATGTGAAGGCTACTATGTGAAGGCTACTACGTGAATCGTAAAATTTAAT
66 TAAGTGAAGGCTACTATGT----G-TAC--C--G-A--G-AAGCTTTGAT
* * *
2679 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCG--GAATGATGAGTCACATGTGTAGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATGATG-GTCACATGTGTAGTA
* * * *
2742 CTAGGTGCAGGCTACTATGCGTACC-AAATAGCTTTGAT
65 CTAAGTGAAGGCTACTATGTGTACCGAGA-AGCTTTGAT
* * *
2780 CACGTGTGTAATACTATGTGCAGGCTACTACGTGTATCGGATGAAA--ATGGTCACATGTGTAGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA-CCGAT-AAATGATGGTCACATGTGTAGT
* * *
2843 ACTACGTGCAGGCTACTATGTGAACCG
64 ACTAAGTGAAGGCTACTATGTGTACCG
2870 GTTACCATTG
Statistics
Matches: 258, Mismatches: 28, Indels: 39
0.79 0.09 0.12
Matches are distributed among these distances:
100 1 0.00
101 41 0.16
102 118 0.46
103 4 0.02
105 2 0.01
106 1 0.00
107 4 0.02
109 4 0.02
110 1 0.00
111 1 0.00
112 1 0.00
113 7 0.03
114 31 0.12
115 42 0.16
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.29
Consensus pattern (102 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATGATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACTATGTGTACCGAGAAGCTTTGAT
Found at i:2645 original size:14 final size:14
Alignment explanation
Indices: 2626--2664 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
2616 ACGTATGTAG
2626 TACTATGTGAAGGC
1 TACTATGTGAAGGC
2640 TACTATGTGAAGGC
1 TACTATGTGAAGGC
*
2654 TACTACGTGAA
1 TACTATGTGAA
2665 TCGTAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (14 bp):
TACTATGTGAAGGC
Found at i:2737 original size:50 final size:51
Alignment explanation
Indices: 2640--2860 Score: 204
Period size: 50 Copynumber: 4.4 Consensus size: 51
2630 ATGTGAAGGC
* * * * * *
2640 TACTATGTGAAGGCTACTACGTGAATCGTAA--AATTTAATCACGTGTGTAG
1 TACTATGTGCAGGCTACTACGTGTATCGGAATGAA-TGAGTCACATGTGTAG
2690 TACTATGTGCAGGCTACTACGTGTATCGGAATG-ATGAGTCACATGTGTAG
1 TACTATGTGCAGGCTACTACGTGTATCGGAATGAATGAGTCACATGTGTAG
* * * ** ** * *
2740 TACTAGGTGCAGGCTACTATGCGTA-CCAAATAGCTTTGA-TCACGTGTGTAA
1 TACTATGTGCAGGCTACTACGTGTATCGGAAT-G-AATGAGTCACATGTGTAG
2791 TACTATGTGCAGGCTACTACGTGTATCGG-ATGAAAATG-GTCACATGTGTAG
1 TACTATGTGCAGGCTACTACGTGTATCGGAATG--AATGAGTCACATGTGTAG
*
2842 TACTACGTGCAGGCTACTA
1 TACTATGTGCAGGCTACTA
2861 TGTGAACCGG
Statistics
Matches: 138, Mismatches: 25, Indels: 15
0.78 0.14 0.08
Matches are distributed among these distances:
49 4 0.03
50 65 0.47
51 65 0.47
52 4 0.03
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (51 bp):
TACTATGTGCAGGCTACTACGTGTATCGGAATGAATGAGTCACATGTGTAG
Found at i:2786 original size:101 final size:100
Alignment explanation
Indices: 2677--2862 Score: 311
Period size: 101 Copynumber: 1.8 Consensus size: 100
2667 GTAAAATTTA
*
2677 ATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAATG-ATGAGTCACATGTGTAGT
1 ATCACGTGTGTAATACTATGTGCAGGCTACTACGTGTATCGG-ATGAATG-GTCACATGTGTAGT
*
2741 ACTAGGTGCAGGCTACTATGCGTACCAAATAGCTTTG
64 ACTACGTGCAGGCTACTATGCGTACCAAATAGCTTTG
2778 ATCACGTGTGTAATACTATGTGCAGGCTACTACGTGTATCGGATGAAAATGGTCACATGTGTAGT
1 ATCACGTGTGTAATACTATGTGCAGGCTACTACGTGTATCGGATG--AATGGTCACATGTGTAGT
2843 ACTACGTGCAGGCTACTATG
64 ACTACGTGCAGGCTACTATG
2863 TGAACCGGTT
Statistics
Matches: 80, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
100 3 0.04
101 41 0.51
102 33 0.41
103 3 0.04
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (100 bp):
ATCACGTGTGTAATACTATGTGCAGGCTACTACGTGTATCGGATGAATGGTCACATGTGTAGTAC
TACGTGCAGGCTACTATGCGTACCAAATAGCTTTG
Found at i:2801 original size:51 final size:49
Alignment explanation
Indices: 2677--2860 Score: 165
Period size: 51 Copynumber: 3.7 Consensus size: 49
2667 GTAAAATTTA
* **
2677 ATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAATGATG
1 ATCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTATCCAAATGATG
* * * *
2726 AGTCACATGTGTAGTACTAGGTGCAGGCTACTATGCGTA-CCAAATAGCTTTG
1 A-TCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTATCCAAAT-G--ATG
* * * *
2778 ATCACGTGTGTAATACTATGTGCAGGCTACTACGTGTATCGGATGAA-AATG
1 ATCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTATC-CA--AATGATG
* * *
2829 GTCACATGTGTAGTACTACGTGCAGGCTACTA
1 ATCACGTGTGTAGTACTATGTGCAGGCTACTA
2861 TGTGAACCGG
Statistics
Matches: 108, Mismatches: 19, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
49 5 0.05
50 34 0.31
51 62 0.57
52 4 0.04
53 1 0.01
55 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (49 bp):
ATCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTATCCAAATGATG
Found at i:2843 original size:216 final size:215
Alignment explanation
Indices: 2462--2866 Score: 573
Period size: 216 Copynumber: 1.9 Consensus size: 215
2452 TATCGATGAA
*
2462 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTACCGATAAATAATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGA-AAATAATGGTCACATGTGTAGTAC
* * * * *
2527 TAAGTGAAGGCTACTATGTGTACCGAGAAGCTTTGGTCACGTGTGTAGTACTGTGTGAAGGCTAC
65 TAAGTGAAGGCTACTATGCGTACCGAAAAGCTTTGATCACGTGTGTAATACTATGTGAAGGCTAC
* *
2592 TACGTGTACCGATAAATGATGGTCACGTATGTAGTACTATGTGAAGGCTACTATGTGAAGGCTAC
130 TACGTGTACCGATAAA-GATGGTCACATATGTAGTACTACGTGAAGGCTACTATGTGAAGGCTAC
2657 TACGTGAATCGTAAAATTTAAT
194 TACGTGAATCGTAAAATTTAAT
* * * *
2679 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCG-GAATGATGAGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGAAAATAATG-GTCACATGTGTAGTAC
* * *
2743 TAGGTGCAGGCTACTATGCGTACC-AAATAGCTTTGATCACGTGTGTAATACTATGTGCAGGCTA
65 TAAGTGAAGGCTACTATGCGTACCGAAA-AGCTTTGATCACGTGTGTAATACTATGTGAAGGCTA
* * *
2807 CTACGTGTATCGGATGAAA-ATGGTCACATGTGTAGTACTACGTGCAGGCTACTATGTGAA
129 CTACGTGTA-CCGAT-AAAGATGGTCACATATGTAGTACTACGTGAAGGCTACTATGTGAA
2867 CCGGTTACCA
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
215 8 0.05
216 115 0.69
217 40 0.24
218 3 0.02
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (215 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGAAAATAATGGTCACATGTGTAGTACT
AAGTGAAGGCTACTATGCGTACCGAAAAGCTTTGATCACGTGTGTAATACTATGTGAAGGCTACT
ACGTGTACCGATAAAGATGGTCACATATGTAGTACTACGTGAAGGCTACTATGTGAAGGCTACTA
CGTGAATCGTAAAATTTAAT
Found at i:2971 original size:33 final size:33
Alignment explanation
Indices: 2933--3065 Score: 115
Period size: 33 Copynumber: 3.7 Consensus size: 33
2923 ATGTGAAAGG
*
2933 GGTTGCTAAGTGCTGATTCCTCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* *
2966 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAAG-
1 GGTTGCTAAGTGCTGATTCC-CCGAATC----AT-TG----GT
*
3008 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
*
3041 GGTTGCTAAGTGCTGAATCCACCGA
1 GGTTGCTAAGTGCTGATTCC-CCGA
3066 TAACGGATAG
Statistics
Matches: 81, Mismatches: 7, Indels: 23
0.73 0.06 0.21
Matches are distributed among these distances:
32 1 0.01
33 38 0.47
34 9 0.11
36 2 0.02
37 2 0.02
38 2 0.02
39 2 0.02
41 5 0.06
42 19 0.23
43 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
Found at i:3011 original size:75 final size:74
Alignment explanation
Indices: 2888--3064 Score: 266
Period size: 75 Copynumber: 2.4 Consensus size: 74
2878 TGACTATAAA
* * *
2888 GGTGGTTGCTACGTGCTAATTCCACCGTAATTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCC
1 GGTGGTTGCTAAGTGCTGA-TCCACCGTAATTTAAATGTGAAAAGGGTTGCTAAGTGCTGATTCC
*
2953 TCGAATCATT
65 CCGAATCATT
2963 GGTGGTTGCTAAGTGCTGATCCCACCGT-ATCTTAAATGTGAAAAGGGTTGCTAAGTGCTGATTC
1 GGTGGTTGCTAAGTGCTGAT-CCACCGTAAT-TTAAATGTGAAAAGGGTTGCTAAGTGCTGATTC
*
3027 CCCGATTCATT
64 CCCGAATCATT
3038 GGTGGTTGCTAAGTGCTGAATCCACCG
1 GGTGGTTGCTAAGTGCTG-ATCCACCG
3065 ATAACGGATA
Statistics
Matches: 94, Mismatches: 5, Indels: 6
0.90 0.05 0.06
Matches are distributed among these distances:
74 3 0.03
75 89 0.95
76 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.32
Consensus pattern (74 bp):
GGTGGTTGCTAAGTGCTGATCCACCGTAATTTAAATGTGAAAAGGGTTGCTAAGTGCTGATTCCC
CGAATCATT
Found at i:3963 original size:49 final size:49
Alignment explanation
Indices: 3901--4044 Score: 207
Period size: 49 Copynumber: 2.9 Consensus size: 49
3891 ATGTGAACAT
* *
3901 GTGATTATGTGATTCCGTATAAGACCATAGCTGGGTTATGGCATCGGTAA
1 GTGA-TATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* *
3951 GTGATATGTGATTCCGTGTAAGACCATAACTGGGCTATGGCATCGGTAT
1 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
* * * *
4000 GTGATTTGTGATTACGTGTAAGACCATAGTTGGACTATGGCATCG
1 GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCG
4045 AGAAAATGAA
Statistics
Matches: 85, Mismatches: 9, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
49 81 0.95
50 4 0.05
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.32
Consensus pattern (49 bp):
GTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
Done.