Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_334 ID=scaffold_334-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: 8091
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Found at i:1217 original size:17 final size:17
Alignment explanation
Indices: 1191--1226 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1181 GTGTGTTTTG
*
1191 TTTTGGCTGCATGACAT
1 TTTTGACTGCATGACAT
1208 TTTTGACTGCATGACAT
1 TTTTGACTGCATGACAT
1225 TT
1 TT
1227 CATCATAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.44
Consensus pattern (17 bp):
TTTTGACTGCATGACAT
Found at i:3623 original size:20 final size:20
Alignment explanation
Indices: 3598--3638 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
3588 AATGTTCTTT
3598 CATTCTTTAT-GATTTTTTTC
1 CATTCTTT-TGGATTTTTTTC
3618 CATTCTTTTGGATTTTTTTC
1 CATTCTTTTGGATTTTTTTC
3638 C
1 C
3639 TGCCAGACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 1 0.05
20 19 0.95
ACGTcount: A:0.12, C:0.17, G:0.07, T:0.63
Consensus pattern (20 bp):
CATTCTTTTGGATTTTTTTC
Found at i:4602 original size:21 final size:21
Alignment explanation
Indices: 4575--4619 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
4565 AAAAGTGATG
4575 TGAAAAACTGAAAAGAG-AAAAA
1 TGAAAAA-TGAAAA-AGTAAAAA
4597 TGAAAAATGAAAAAGTAAAAA
1 TGAAAAATGAAAAAGTAAAAA
4618 TG
1 TG
4620 GAGAGGCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 2 0.09
21 13 0.59
22 7 0.32
ACGTcount: A:0.67, C:0.02, G:0.18, T:0.13
Consensus pattern (21 bp):
TGAAAAATGAAAAAGTAAAAA
Found at i:6036 original size:89 final size:89
Alignment explanation
Indices: 5890--6607 Score: 906
Period size: 89 Copynumber: 8.1 Consensus size: 89
5880 TACTGGTGGC
* * * *
5890 GAAGTAGATCGAA-AAAACAGATCTTGTCTTCATATACTGGT-GTGAAGTAGATCAAAGATAACA
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCGAAGAAAACA
*** * *
5953 GATCTTGTCTTCCCATACTGGTGGC
66 GATCTTGTCTTCATGTACTGG-CGT
* * ** * * * *
5978 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGATAGCA
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCGAAGAAAACA
*** * *
6042 GATCTTGTCTTCCCATACTGGTGGC
66 GATCTTGTCTTCATGTACTGG-CGT
* * * ** * *
6067 GAAGTAGATCGAAGAAAGCAGATCTTATCTTCATGTATTAG-GGTGAAGTAGATCGAAGAAAACA
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCGAAGAAAACA
*
6131 GATCTTGTCTTCATGTACCGGCGT
66 GATCTTGTCTTCATGTACTGGCGT
* *
6155 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACA
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCGAAGAAAACA
*
6220 GATCTTGTCTTCATGTACCGGCGT
66 GATCTTGTCTTCATGTACTGGCGT
*
6244 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAACA
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCGAAGAAAACA
6309 GATCTTGTCTTCATGTACTGGCGT
66 GATCTTGTCTTCATGTACTGGCGT
* * * * *
6333 GAAGTTGATCAAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAATTAGATCGAAGAAAATA
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCGAAGAAAACA
6398 GATCTTGTCTTCATGTACTGGCGT
66 GATCTTGTCTTCATGTACTGGCGT
** * *
6422 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGAAAACA
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCGAAGAAAACA
6486 GATCTTGTCTTCATGTACTGGCGT
66 GATCTTGTCTTCATGTACTGGCGT
* * * * *
6510 GAAGTAGATCAAAGATAACAGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCGAAGAAAACA
1 GAAGTAGATCAAAGAAAACAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCGAAGAAAACA
* * * *
6575 GATATTGTCTTCGTGTATTGGCAT
66 GATCTTGTCTTCATGTACTGGCGT
*
6599 GGAGTAGAT
1 GAAGTAGAT
6608 TGAAGATTAC
Statistics
Matches: 572, Mismatches: 54, Indels: 7
0.90 0.09 0.01
Matches are distributed among these distances:
88 125 0.22
89 447 0.78
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (89 bp):
GAAGTAGATCAAAGAAAACAGATCTTGTCTTCACATACTGGTGGTGAAGTAGATCGAAGAAAACA
GATCTTGTCTTCATGTACTGGCGT
Found at i:6250 original size:222 final size:220
Alignment explanation
Indices: 5890--6586 Score: 959
Period size: 222 Copynumber: 3.1 Consensus size: 220
5880 TACTGGTGGC
* *
5890 GAAGTAGATCGAA-AAAACAGATCTTGTCTTCATATACTGGTGTGAAGTAGATCAAAGATAACAG
1 GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATATACTGGCGTGAAGTAGATCAAAGAAAACAG
*
5954 ATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTACTGG
66 ATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGG
* * *
6019 CGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAA
131 CGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAA
* *
6084 GCAGATCTTATCTTCATGTATTAGGGT
196 -CAGATCTTGTCTTCATGTACT-GGGT
* *
6111 GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACCGGCGTGAAGTAGATCAAAGAAAACAG
1 GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATATACTGGCGTGAAGTAGATCAAAGAAAACAG
*
6176 ATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACCGG
66 ATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGG
6241 CGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAA
131 CGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAG-AA
6306 ACAGATCTTGTCTTCATGTACTGGCGT
195 ACAGATCTTGTCTTCATGTACTGG-GT
* * ** * * * * *
6333 GAAGTTGATCAAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAATTAGATCGAAGAAAATA
1 GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATATACTGG-CGTGAAGTAGATCAAAGAAAACA
*** * * *
6398 GATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTG
65 GATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTG
*** * *
6462 GCGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCAAAGAT
130 GCGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGA-
* *** *
6526 AACAGATCTTGCCTTCCCATACTGGTGGC
194 AACAGATCTTGTCTTCATGTACT-G-GGT
* *
6555 GAAGCAGATCGAAGAAAACAGATATTGTCTTC
1 GAAGTAGATCGAAGAAAACAGATCTTGTCTTC
6587 GTGTATTGGC
Statistics
Matches: 426, Mismatches: 43, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
220 1 0.00
221 49 0.12
222 336 0.79
223 40 0.09
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (220 bp):
GAAGTAGATCGAAGAAAACAGATCTTGTCTTCATATACTGGCGTGAAGTAGATCAAAGAAAACAG
ATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACTGG
CGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAA
CAGATCTTGTCTTCATGTACTGGGT
Found at i:6607 original size:133 final size:132
Alignment explanation
Indices: 5864--6586 Score: 838
Period size: 133 Copynumber: 5.4 Consensus size: 132
5854 GAGTAGCAGT
* * * *
5864 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAA-AAAACAGATCTTGTCTTCATATACT
1 AGATCTTGTCTTCACATACTGG-CGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCATATACT
* * *** * *
5928 GGTGTGAAGTAGATCAAAGATAACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGA
65 GGCGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCGAAGA
*
5993 AAGC
129 AAAC
** * * **
5997 AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATAGCAGATCTTGTCTTCCCATACTG
1 AGATCTTGTCTTCACATACTGGCGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCATATACTG
* * * * * *
6062 GTGGCGAAGTAGATCGAAGAAAGCAGATCTTATCTTCATGTATTAGG-GTGAAGTAGATCGAAGA
66 G-CGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACT-GGCGTGAAGTAGATCGAAGA
6126 AAAC
129 AAAC
** * **
6130 AGATCTTGTCTTCATGTACCGGCGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCCCATACTG
1 AGATCTTGTCTTCACATACTGGCGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCATATACTG
* * * * *
6195 GTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACCGGCGTGAAGTAGATCAAAGAA
66 G-CGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAAGAA
6260 AAC
130 AAC
* * * *
6263 AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTACT
1 AGATCTTGTCTTCACATACTGG-CGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCATATACT
* *** * * *
6328 GGCGTGAAGTTGATCAAAGAAAACAGATCTTGTCTTCCCATACTGGTGGCGAATTAGATCGAAGA
65 GGCGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGG-CGTGAAGTAGATCGAAGA
*
6393 AAAT
129 AAAC
** *
6397 AGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTG
1 AGATCTTGTCTTCACATACTGGCGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCATATACTG
* *
6462 GCGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCAAAGATA
66 GCGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAAGAAA
6527 AC
131 AC
* * * * * * *
6529 AGATCTTGCCTTCCCATACTGGTGGCGAAGCAGATCGAAGAAAACAGATATTGTCTTC
1 AGATCTTGTCTTCACATACTGG-CGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTC
6587 GTGTATTGGC
Statistics
Matches: 507, Mismatches: 76, Indels: 14
0.85 0.13 0.02
Matches are distributed among these distances:
132 49 0.10
133 349 0.69
134 107 0.21
135 2 0.00
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (132 bp):
AGATCTTGTCTTCACATACTGGCGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCATATACTG
GCGTGAAGTAGATCAAAGAAAACAGATCTTGTCTTCATGTACTGGCGTGAAGTAGATCGAAGAAA
AC
Found at i:6646 original size:44 final size:44
Alignment explanation
Indices: 6598--6808 Score: 144
Period size: 44 Copynumber: 4.8 Consensus size: 44
6588 TGTATTGGCA
6598 TGGAGTAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAG
1 TGGAGTAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAG
* ** **** * * *
6642 TGGAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAG--GTTACAG
1 TGGAGTAGATTGAAGATTACAGATCTTATCTCCCTAAGCAG-T--AG
* * * ** *
6687 TGGAGTACATTGAAGCCAGTA-A-TTC-TATCTCCCTGGGCAATAG
1 TGGAGTAGATTGAAG--ATTACAGATCTTATCTCCCTAAGCAGTAG
*
6730 TGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAG
1 TGGAGTAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAG
* * * * *
6774 TGGAGCAGATCGAAGATGACAGATTTTACCTCCCT
1 TGGAGTAGATTGAAGATTACAGATCTTATCTCCCT
6809 GAGGTTACAG
Statistics
Matches: 121, Mismatches: 36, Indels: 20
0.68 0.20 0.11
Matches are distributed among these distances:
41 3 0.02
42 2 0.02
43 18 0.15
44 82 0.68
45 15 0.12
47 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (44 bp):
TGGAGTAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAG
Found at i:6847 original size:132 final size:132
Alignment explanation
Indices: 6598--6850 Score: 445
Period size: 132 Copynumber: 1.9 Consensus size: 132
6588 TGTATTGGCA
* ***
6598 TGGAGTAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTG
1 TGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGACA
6663 GATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAAT
66 GATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAAT
6728 AG
131 AG
*
6730 TGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGACA
1 TGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGACA
6795 GATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGT-ATTCCTATCTCC
66 GATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATT-CTATCTCC
6851 TTGAAGTTAC
Statistics
Matches: 115, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
131 3 0.03
132 112 0.97
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (132 bp):
TGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGACA
GATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAAT
AG
Found at i:6884 original size:132 final size:132
Alignment explanation
Indices: 6597--6893 Score: 382
Period size: 132 Copynumber: 2.2 Consensus size: 132
6587 GTGTATTGGC
* * ** **
6597 ATGGAGTAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGT
1 ATGGAATAGATTGAAAACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGAC
* *
6662 GGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAA
66 AGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGAGCAA
*
6727 TA
131 CA
* * ** *
6729 GTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGAC
1 ATGGAATAGATTGAAAACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGAC
* *
6794 AGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGT-ATTCCTATCTCCTTGAAGT
66 AGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATT-CTATCTCCCTG-AGC
*
6858 TACA
129 AACA
* * *
6862 ATGGAGTGGATT-AAAACCACAGATCTCATCTC
1 ATGGAATAGATTGAAAACCACAGATCTTATCTC
6894 TCTGAAGTTG
Statistics
Matches: 145, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
131 3 0.02
132 130 0.90
133 12 0.08
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (132 bp):
ATGGAATAGATTGAAAACCACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGAC
AGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGAGCAA
CA
Done.