Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_261 ID=scaffold_261-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: 8955
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.28
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:3440 original size:26 final size:27
Alignment explanation
Indices: 3385--3433 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
3375 ATAAAATACA
*
3385 TCTTTGCATTCCTTTTTGAGCTAATAT
1 TCTTTGCATTCCTTTTTGAGATAATAT
3412 TCTTT-CATT-CTTTTTGA-ATAAT
1 TCTTTGCATTCCTTTTTGAGATAAT
3434 TATTTCTGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
25 8 0.38
26 4 0.19
27 5 0.24
ACGTcount: A:0.20, C:0.16, G:0.08, T:0.55
Consensus pattern (27 bp):
TCTTTGCATTCCTTTTTGAGATAATAT
Found at i:5119 original size:7 final size:7
Alignment explanation
Indices: 5107--5221 Score: 175
Period size: 7 Copynumber: 17.0 Consensus size: 7
5097 TCTAAGTCAA
5107 AAAAATG
1 AAAAATG
5114 AAAAATG
1 AAAAATG
5121 AAAAATG
1 AAAAATG
*
5128 -AGAATG
1 AAAAATG
5134 AAAAATG
1 AAAAATG
5141 AAAAATG
1 AAAAATG
5148 AAAAATG
1 AAAAATG
*
5155 -AGAATG
1 AAAAATG
5161 AAAAATG
1 AAAAATG
5168 AAAAATG
1 AAAAATG
*
5175 -AGAATG
1 AAAAATG
5181 AAAAATG
1 AAAAATG
5188 AAAAATG
1 AAAAATG
5195 AAAAATG
1 AAAAATG
5202 AAAAATG
1 AAAAATG
5209 -AAAATG
1 AAAAATG
5215 AAAAATG
1 AAAAATG
5222 GAGAGGCTAA
Statistics
Matches: 98, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
6 21 0.21
7 77 0.79
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (7 bp):
AAAAATG
Found at i:5135 original size:20 final size:21
Alignment explanation
Indices: 5107--5221 Score: 175
Period size: 20 Copynumber: 5.7 Consensus size: 21
5097 TCTAAGTCAA
5107 AAAAATGAAAAATGAAAAATG
1 AAAAATGAAAAATGAAAAATG
*
5128 -AGAATGAAAAATGAAAAATG
1 AAAAATGAAAAATGAAAAATG
*
5148 AAAAATG-AGAATGAAAAATG
1 AAAAATGAAAAATGAAAAATG
*
5168 AAAAATG-AGAATGAAAAATG
1 AAAAATGAAAAATGAAAAATG
5188 AAAAATGAAAAATGAAAAATG
1 AAAAATGAAAAATGAAAAATG
5209 -AAAATGAAAAATG
1 AAAAATGAAAAATG
5222 GAGAGGCTAA
Statistics
Matches: 88, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
20 71 0.81
21 17 0.19
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (21 bp):
AAAAATGAAAAATGAAAAATG
Found at i:5145 original size:27 final size:27
Alignment explanation
Indices: 5107--5221 Score: 187
Period size: 27 Copynumber: 4.3 Consensus size: 27
5097 TCTAAGTCAA
*
5107 AAAAATGAAAAATGAAAAATGAGAATG
1 AAAAATGAAAAATGAAAAATGAAAATG
*
5134 AAAAATGAAAAATGAAAAATGAGAATG
1 AAAAATGAAAAATGAAAAATGAAAATG
*
5161 AAAAATGAAAAATG-AGAATGAAAAATG
1 AAAAATGAAAAATGAAAAATG-AAAATG
5188 AAAAATGAAAAATGAAAAATGAAAATG
1 AAAAATGAAAAATGAAAAATGAAAATG
5215 AAAAATG
1 AAAAATG
5222 GAGAGGCTAA
Statistics
Matches: 83, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
26 5 0.06
27 73 0.88
28 5 0.06
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (27 bp):
AAAAATGAAAAATGAAAAATGAAAATG
Found at i:6677 original size:44 final size:44
Alignment explanation
Indices: 6629--6854 Score: 153
Period size: 43 Copynumber: 5.1 Consensus size: 44
6619 GACACAAACT
*
6629 TTGCCTCTCTTGGTTGTGATGGAGCTGGTTGCAGACAAAAGATC
1 TTGCCTCTCTTGGTTGTGATGGAGCTGGTTGAAGACAAAAGATC
* * ** * * *
6673 TTGCCT-TCCT-GTAT-TGACAGCGAAGCAAGTCGAAGACACAA-ACC
1 TTGCCTCTCTTGGT-TGTGA-TG-G-AGCTGGTTGAAGACAAAAGATC
* *
6717 TTGCCTCTCTCGTTTGTGATGGAGCTGGTTGAAGACAAAAGATC
1 TTGCCTCTCTTGGTTGTGATGGAGCTGGTTGAAGACAAAAGATC
* ** * * * *
6761 TTGCCT-TCCTGCAT-TGACAGCGAAGCAGGTCGAAGACACAA-A-C
1 TTGCCTCTCTTGGTTGTGA-TG-G-AGCTGGTTGAAGACAAAAGATC
*
6804 TTTGCCTCTCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATC
1 -TTGCCTCTCTTGGTTGTGATGGAGCTGGTTGAAGACAAAAGATC
*
6849 ATGCCT
1 TTGCCT
6855 TCCTGTACTG
Statistics
Matches: 132, Mismatches: 34, Indels: 32
0.67 0.17 0.16
Matches are distributed among these distances:
42 8 0.06
43 40 0.30
44 39 0.30
45 38 0.29
46 7 0.05
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (44 bp):
TTGCCTCTCTTGGTTGTGATGGAGCTGGTTGAAGACAAAAGATC
Found at i:6689 original size:88 final size:88
Alignment explanation
Indices: 6494--6859 Score: 519
Period size: 88 Copynumber: 4.2 Consensus size: 88
6484 TAAAGATAGC
* * * *
6494 AGATCTTGCCTTCCTCCGTTAACAGCGAAGC-GGATCGAA-A-ACAAAGCCTTGCCT-TCATTGG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGG-TCGAAGACACAAA-CCTTGCCTCTC-TCGG
* **
6555 TTGT-AGTGGAGCTGGTTAAAGA-AGC
63 TTGTGA-TGGAGCTGGTTGAAGACAAA
* *
6580 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACTTTGCCTCTCTTGGTTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
*
6645 TGATGGAGCTGGTTGCAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
* * *
6668 AGATCTTGCCTTCCTGTATTGACAGCGAAGCAAGTCGAAGACACAAACCTTGCCTCTCTCGTTTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
6733 TGATGGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
*
6756 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACTTTGCCTCTCTCGGTTG
1 AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
6821 TGATGGAGCTGGTTGAAGACAAA
66 TGATGGAGCTGGTTGAAGACAAA
*
6844 AGATCATGCCTTCCTG
1 AGATCTTGCCTTCCTG
6860 TACTGGTAGT
Statistics
Matches: 255, Mismatches: 19, Indels: 10
0.90 0.07 0.04
Matches are distributed among these distances:
86 33 0.13
87 32 0.13
88 190 0.75
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (88 bp):
AGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTG
TGATGGAGCTGGTTGAAGACAAA
Found at i:6973 original size:45 final size:45
Alignment explanation
Indices: 6835--6978 Score: 130
Period size: 45 Copynumber: 3.2 Consensus size: 45
6825 GGAGCTGGTT
** * ** * * *
6835 GAAGACAAAAGATCATGCCTTCCTGTACTGGTAGTGAAGTAAATC
1 GAAGACACCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATC
* ** *
6880 GAAGACACCAG-CCTTGTTTTCCTGTACTGACAGCGGAGCAGAAT-
1 GAAGACACCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAG-ATC
* *
6924 GAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATC
1 GAAGACACCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATC
*
6969 GAAGAAACCA
1 GAAGACACCA
6979 TAGTTTGCAA
Statistics
Matches: 76, Mismatches: 20, Indels: 6
0.75 0.20 0.06
Matches are distributed among these distances:
44 31 0.41
45 45 0.59
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.22
Consensus pattern (45 bp):
GAAGACACCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATC
Found at i:7058 original size:50 final size:50
Alignment explanation
Indices: 6995--7558 Score: 471
Period size: 50 Copynumber: 11.5 Consensus size: 50
6985 GCAATTAAAA
*
6995 AGATTGAAGCTACAATAGCGGATCTTACTTTCCTAGCATTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTGGAAC
* * * *
7045 AGATTGAAGCTACAACAGCGGATCTTACTTCCCT-GACATTGCAAT-TAAGA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAG-CATTGCAGTGGAA-C
* *
7095 AGATTGAAGCTACAATAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTGGAAC
* * * ** *
7145 AGATTGAAGCTTCAACAGCGGATCTTACTTCCCT-GACATTGCATTTAAAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAG-CATTGCAGTGGAAC
* *
7195 AGATTGAAGCTACAACAGCAGATCTTACTTTCCTAGCGTTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTGGAAC
* ** ** *
7245 AGATTGAAGCTACAACAGCGGATCTTGC-TTCC---C-CGGCAGTTAAAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTGGAAC
* *
7290 AGATTGAAGCTACAACAGCAGATCTTACTTTCCTAGCGTTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTGGAAC
* * ** ** *
7340 AGATTGAAGCTACAACAACGGATCTTGC-TTCCCCG-A---CAGTTAAAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTGGAAC
* * * * *
7385 AGATTGAAGCCACAACGGCGAATCTTACTTTCCAAGCGA-TGCAGCGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGC-ATTGCAGTGGAAC
* * * * * * * * *
7435 AGATTGAAGCTACAACGGTGAATCTTGCTTCTCCGA-CATTACAAT-TAAA
1 AGATTGAAGCTACAACAGCGGATCTTACTT-TCCTAGCATTGCAGTGGAAC
* ** * * *
7484 AGATTGAAGCCACAA-AGGCAAATCTTAC-TTCCCAGGCATTGCAGCGAAAC
1 AGATTGAAGCTACAACA-GCGGATCTTACTTTCCTA-GCATTGCAGTGGAAC
* *
7534 AGATTGAAGCTACGACAGCGAATCT
1 AGATTGAAGCTACAACAGCGGATCT
7559 CGCTTCCCCG
Statistics
Matches: 407, Mismatches: 84, Indels: 46
0.76 0.16 0.09
Matches are distributed among these distances:
45 62 0.15
46 10 0.02
47 4 0.01
48 2 0.00
49 45 0.11
50 275 0.68
51 9 0.02
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.25
Consensus pattern (50 bp):
AGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCATTGCAGTGGAAC
Found at i:7565 original size:50 final size:50
Alignment explanation
Indices: 6995--7666 Score: 440
Period size: 50 Copynumber: 13.7 Consensus size: 50
6985 GCAATTAAAA
* * * *
6995 AGATTGAAGCTACAATAGCGGATCTTACTTTCCTA-GCATTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGAATCTTAC-TTCCCAGGCATTGCAGTGAAAC
* * * * *
7045 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATTAAGA-
1 AGATTGAAGCTACAACAGCGAATCTTACTTCCCAGGCATTGCAGTGAA-AC
* * * * *
7095 AGATTGAAGCTACAATAGCGGATCTTACTTTCCTA-GCGTTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGAATCTTAC-TTCCCAGGCATTGCAGTGAAAC
* * * * * * *
7145 AGATTGAAGCTTCAACAGCGGATCTTACTTCCCTGACATTGCATTTAAAA
1 AGATTGAAGCTACAACAGCGAATCTTACTTCCCAGGCATTGCAGTGAAAC
* * *
7195 AGATTGAAGCTACAACAGC-AGATCTTACTTTCCTA-GCGTTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGA-ATCTTAC-TTCCCAGGCATTGCAGTGAAAC
* * *
7245 AGATTGAAGCTACAACAGCGGATCTTGCTTCCCCGGCAGTT--A---AAA-
1 AGATTGAAGCTACAACAGCGAATCTTACTTCCCAGGCA-TTGCAGTGAAAC
* * *
7290 AGATTGAAGCTACAACAGC-AGATCTTACTTTCCTA-GCGTTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGA-ATCTTAC-TTCCCAGGCATTGCAGTGAAAC
* * * * * *
7340 AGATTGAAGCTACAACAACGGATCTTGCTTCCC-CG-A---CAGTTAAAA
1 AGATTGAAGCTACAACAGCGAATCTTACTTCCCAGGCATTGCAGTGAAAC
* * * * * *
7385 AGATTGAAGCCACAACGGCGAATCTTACTTTCCAAGCGA-TGCAGCGGAAC
1 AGATTGAAGCTACAACAGCGAATCTTACTTCCCAGGC-ATTGCAGTGAAAC
* * * * * * *
7435 AGATTGAAGCTACAACGGTGAATCTTGCTTCTCC-GACATTACAATTAAA-
1 AGATTGAAGCTACAACAGCGAATCTTACTTC-CCAGGCATTGCAGTGAAAC
* * *
7484 AGATTGAAGCCACAA-AGGCAAATCTTACTTCCCAGGCATTGCAGCGAAAC
1 AGATTGAAGCTACAACA-GCGAATCTTACTTCCCAGGCATTGCAGTGAAAC
* ** * * * *
7534 AGATTGAAGCTACGACAGCGAATCTCGCTTCCCCGACATTGCAATTAAA-
1 AGATTGAAGCTACAACAGCGAATCTTACTTCCCAGGCATTGCAGTGAAAC
* * * * * *
7583 AGATTGATGCCACAACGGCGAATCTTACTTTCCCAGGCAATGCAGCAGAGTA-
1 AGATTGAAGCTACAACAGCGAATCTTAC-TTCCCAGGCATTGCAG-TGA-AAC
* *
7635 A-ATTGAAGCTACAGCAGCGAATTTTACTTCCC
1 AGATTGAAGCTACAACAGCGAATCTTACTTCCC
7667 CGATATTACA
Statistics
Matches: 473, Mismatches: 115, Indels: 68
0.72 0.18 0.10
Matches are distributed among these distances:
44 2 0.00
45 60 0.13
46 8 0.02
48 3 0.01
49 79 0.17
50 283 0.60
51 36 0.08
52 2 0.00
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (50 bp):
AGATTGAAGCTACAACAGCGAATCTTACTTCCCAGGCATTGCAGTGAAAC
Found at i:7669 original size:100 final size:100
Alignment explanation
Indices: 6983--7615 Score: 794
Period size: 100 Copynumber: 6.5 Consensus size: 100
6973 AAACCATAGT
* * *
6983 TTGCAATTAAAAAGATTGAAGCTACAATAGCGGATCTTACTTTCCTAGCATTGCAGTGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGAATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
* *
7048 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
66 TTGAAGCTACAACAGCGGATCTTGCTTCCCCGACA
* * *
7083 TTGCAATTAAGAAGATTGAAGCTACAATAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGAATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
* * *
7148 TTGAAGCTTCAACAGCGGATCTTACTTCCCTGACA
66 TTGAAGCTACAACAGCGGATCTTGCTTCCCCGACA
*
7183 TTGCATTTAAAAAGATTGAAGCTACAACAGC-AGATCTTACTTTCCTAGCGTTGCAGTGGAACAG
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGA-ATCTTACTTTCCTAGCGTTGCAGTGGAACAG
7247 ATTGAAGCTACAACAGCGGATCTTGCTTCCCCG---
65 ATTGAAGCTACAACAGCGGATCTTGCTTCCCCGACA
*
7280 --GCAGTTAAAAAGATTGAAGCTACAACAGC-AGATCTTACTTTCCTAGCGTTGCAGTGGAACAG
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGA-ATCTTACTTTCCTAGCGTTGCAGTGGAACAG
*
7342 ATTGAAGCTACAACAACGGATCTTGCTTCCCCGACA
65 ATTGAAGCTACAACAGCGGATCTTGCTTCCCCGACA
* * * * *
7378 --G---TTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTTCCAAGCGATGCAGCGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGAATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
* * * *
7438 TTGAAGCTACAACGGTGAATCTTGCTTCTCCGACA
66 TTGAAGCTACAACAGCGGATCTTGCTTCCCCGACA
* * * * * * *
7473 TTACAATT-AAAAGATTGAAGCCACAA-AGGCAAATCTTAC-TTCCCAGGCATTGCAGCGAAACA
1 TTGCAATTAAAAAGATTGAAGCTACAACA-GCGAATCTTACTTTCCTA-GCGTTGCAGTGGAACA
* * *
7535 GATTGAAGCTACGACAGCGAATCTCGCTTCCCCGACA
64 GATTGAAGCTACAACAGCGGATCTTGCTTCCCCGACA
* * *
7572 TTGCAATT-AAAAGATTGATGCCACAACGGCGAATCTTACTTTCC
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGAATCTTACTTTCC
7616 CAGGCAATGC
Statistics
Matches: 481, Mismatches: 38, Indels: 28
0.88 0.07 0.05
Matches are distributed among these distances:
95 175 0.36
96 1 0.00
98 6 0.01
99 107 0.22
100 192 0.40
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (100 bp):
TTGCAATTAAAAAGATTGAAGCTACAACAGCGAATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
TTGAAGCTACAACAGCGGATCTTGCTTCCCCGACA
Found at i:8013 original size:85 final size:85
Alignment explanation
Indices: 7883--8039 Score: 201
Period size: 85 Copynumber: 1.8 Consensus size: 85
7873 TAGCCAATCC
** *
7883 TATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAACTACAGATCTTATCTCTCTAAAGTTACAGTA
1 TATCTCCCTGAAGTCATAGTGGAGCAGATTAAAACTACAGATCTTATCTCCCTAAAGTTACAGTA
7948 GAGCAGATCGCATCCAGTCT
66 GAGCAGATCGCATCCAGTCT
* * * * *
7968 TATCTCCCTGAAGTCATAGTGGAGCAGGTTGAAGC-ATCA-AGTCTTATCTCCCTGATGTTACAG
1 TATCTCCCTGAAGTCATAGTGGAGCAGATTAAAACTA-CAGA-TCTTATCTCCCTAAAGTTACAG
*
8031 TGGAGCAGA
64 TAGAGCAGA
8040 CTAAAATCAC
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
84 2 0.03
85 59 0.97
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.29
Consensus pattern (85 bp):
TATCTCCCTGAAGTCATAGTGGAGCAGATTAAAACTACAGATCTTATCTCCCTAAAGTTACAGTA
GAGCAGATCGCATCCAGTCT
Done.