Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_329 ID=scaffold_329-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: 8140
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Found at i:716 original size:44 final size:44
Alignment explanation
Indices: 644--1081 Score: 207
Period size: 44 Copynumber: 9.8 Consensus size: 44
634 ACCTGATGTG
* * * * * * *
644 ATCTACTCTACTGTAA-CTTCAGTGAGATAAGATCATTTGTTTTA
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCACTAGCTTCA
* * *
688 ATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCACTAGCTTCA
* ** * * *
732 ATCTGCTCCGCTGTAATCTCAGAAAGATAAGATCTGA-AATTCTTCG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATC--ACTA-GCTTCA
* * * * * *
778 GTCTGTTCCACTGTAATCTCAGGGAAATAAGA-C-CT-GGTGCG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCACTAGCTTCA
* * * * *
819 ATCTACTCTACTGTAA-CTTCAGAGAGATAAGATC-CTTAGTTTTA
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCAC-TAGCTTCA
* * * *
863 ATCCGCTCCACTGTAATATCAGGGAGATAAGATTACTAGCTTTA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCACTAGCTTCA
* ** *
907 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCACTAGCTTCA
* * ** *
951 ATCTGATGCGATCTACTCTGCTGTAA-CTTCAGAGAGATAAGATCTTTTA-TTTCA
1 ATC---T--G--CT-C-C-ACTGTAATC-TCAGGGAGATAAGATC-ACTAGCTTCA
* * *
1005 ATCCGCTCCACTGTAA-CTTCAGGGAGATAGGAT-AGT-GTCTTCA
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCACTAG-CTTCA
* *
1048 ATTTGCTCCGCTGTAATCTCAGGGAGATAAGATC
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATC
1082 TGAAATTCTT
Statistics
Matches: 299, Mismatches: 68, Indels: 54
0.71 0.16 0.13
Matches are distributed among these distances:
40 1 0.00
41 27 0.09
42 3 0.01
43 32 0.11
44 159 0.53
45 5 0.02
46 32 0.11
47 3 0.01
49 2 0.01
51 2 0.01
52 1 0.00
53 2 0.01
54 28 0.09
55 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (44 bp):
ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCACTAGCTTCA
Found at i:900 original size:175 final size:175
Alignment explanation
Indices: 609--939 Score: 527
Period size: 175 Copynumber: 1.9 Consensus size: 175
599 TTCAATGTAC
** * *
609 TCCACTGTAACCACAGGGAGGTAAAACCTGATGTGATCTACTCTACTGTAACTTCAGTGAGATAA
1 TCCACTGTAACCACAGGGAAATAAAACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAA
* * *
674 GATCATTTGTTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCT
66 GATCATTAGTTTTAATCCGCTCCACTGTAATATCAGGGAGATAAGATTACTAGCTTCAATCTGCT
739 CCGCTGTAATCTCAGAAAGATAAGATCTGAAATTCTTCGGTCTGT
131 CCGCTGTAATCTCAGAAAGATAAGATCTGAAATTCTTCGGTCTGT
* * * *
784 TCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTACTCTACTGTAACTTCAGAGAGATAA
1 TCCACTGTAACCACAGGGAAATAAAACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAA
* *
849 GATCCTTAGTTTTAATCCGCTCCACTGTAATATCAGGGAGATAAGATTACTAGCTTTAATCTGCT
66 GATCATTAGTTTTAATCCGCTCCACTGTAATATCAGGGAGATAAGATTACTAGCTTCAATCTGCT
**
914 CCGCTGTAATCTCAGGGAGATAAGAT
131 CCGCTGTAATCTCAGAAAGATAAGAT
940 TTCTGGCTTC
Statistics
Matches: 141, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
175 141 1.00
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (175 bp):
TCCACTGTAACCACAGGGAAATAAAACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAA
GATCATTAGTTTTAATCCGCTCCACTGTAATATCAGGGAGATAAGATTACTAGCTTCAATCTGCT
CCGCTGTAATCTCAGAAAGATAAGATCTGAAATTCTTCGGTCTGT
Found at i:1251 original size:44 final size:44
Alignment explanation
Indices: 1127--2210 Score: 285
Period size: 44 Copynumber: 24.9 Consensus size: 44
1117 AGGTAAGGTT
* *
1127 TGTCTTCGACCTGCTTCGCTGTCAATGCAAGAAGGCAAGATCTTT
1 TGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGAT-TTG
* * * * * *
1172 TGTCTTCAACCAGC-TC-C-ATCACA-ACCGAGAGAGGCAAGGTTTG
1 TGTCTTCGACCTGCTTCGCTGTCA-ATGCAG-GA-AGGCAAGATTTG
* * *
1215 TATCTTCGACCTGCTTTGCTGTCAATGCAGGAAGGCAAGATCTG
1 TGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATTTG
* * * * * *
1259 CTGTCTTCAACCAGCTCCGCT-ACAA--CCGAGAGAGGCAAGTTTTG
1 -TGTCTTCGACCTGCTTCGCTGTCAATGCAG-GA-AGGCAAGATTTG
*
1303 TGTCTTCGACCTGCTTCACTGTCAATGCAGGAAGGCAAGATCAATTG
1 TGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGAT---TTG
* * * * *
1350 T-T-TTCAACCAGC-TC-C-ATCACA-ACCGAGAGAGGCAAGATTTG
1 TGTCTTCGACCTGCTTCGCTGTCA-ATGCAG-GA-AGGCAAGATTTG
*
1391 CGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTAT-
1 TGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGAT-T-TG
* * * * * *
1436 TGTCTTCAACCAGC-TC-C-ATCACA-ACCGAGAGAGGCAAGGTTTG
1 TGTCTTCGACCTGCTTCGCTGTCA-ATGCAG-GA-AGGCAAGATTTG
* *
1479 TGTCTTCGACCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTG
1 TGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATTTG
* * * ** * * **
1523 TTGTCTTCAACCAGC-TC-C-ATCACAACCGATGAAGGTAAGGCTTG
1 -TGTCTTCGACCTGCTTCGCTGTCA-ATGC-AGGAAGGCAAGATTTG
* * * ** * *
1567 T-T-TTCGATCTGCTTCGTTGTTAACACAGGAAGGAAAGATCTG
1 TGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATTTG
* * * *
1609 TTGTCTTCAACCAGCTTCGCT-ACAA--CCGAGAGAGGCAATG-TTTG
1 -TGTCTTCGACCTGCTTCGCTGTCAATGCAG-GA-AGGCAA-GATTTG
* *
1653 TGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTTT
1 TGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGAT-TTG
* * * * ** * *
1698 TGTCTTCAACCAGCTCCAC-CACAA--CCGAGAGAGGCAAGGTTTG
1 TGTCTTCGACCTGCTTCGCTGTCAATGCAG-GA-AGGCAAGATTTG
* *
1741 TGTCTTCGACCTGCTTCGTTGTCAATGCAGGAAGGCAAGATCTG
1 TGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATTTG
** * * * * * **
1785 CT-TCTTTTACCAGCTCCACTGT-AA-CCAATGAAGGCAAGGCTTG
1 -TGTCTTCGACCTGCTTCGCTGTCAATGC-AGGAAGGCAAGATTTG
* * * *
1828 T-T-TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTG
1 TGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATTTG
*** ** * * * * * *
1870 CCCCTTTAACCAGCTCCACTG-CAA-CCAATGAAGGCAAGGCTTTG
1 TGTCTTCGACCTGCTTCGCTGTCAATGC-AGGAAGGCAA-GATTTG
* * * *
1914 T-T-TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTG
1 TGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATTTG
** ** * * * * * *
1956 CCTCTTTAACCAGCTCCACTG-CAA-CCAATGAAGGTAAGACTTTG
1 TGTCTTCGACCTGCTTCGCTGTCAATGC-AGGAAGGCAAGA-TTTG
* * * *
2000 T-T-TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTG
1 TGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATTTG
** * * * * * *
2042 CT-TCTTTAACCAGCTCCACTG-CAA-CCAATGAAGGCAATGCTTTG
1 -TGTCTTCGACCTGCTTCGCTGTCAATGC-AGGAAGGCAA-GATTTG
* * * *
2086 T-T-TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTG
1 TGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATTTG
** * * * * * *
2128 CT-TCTTTAACCAGCTCCACTG-CAA-CCAATGAAGGCAAGGCTTTG
1 -TGTCTTCGACCTGCTTCGCTGTCAATGC-AGGAAGGCAA-GATTTG
* *
2172 T-T-TTCGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGAT
1 TGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGAT
2211 CTTTCTTCTT
Statistics
Matches: 721, Mismatches: 233, Indels: 173
0.64 0.21 0.15
Matches are distributed among these distances:
41 22 0.03
42 117 0.16
43 223 0.31
44 226 0.31
45 107 0.15
46 22 0.03
47 4 0.01
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (44 bp):
TGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATTTG
Found at i:1252 original size:88 final size:86
Alignment explanation
Indices: 1088--2308 Score: 1326
Period size: 88 Copynumber: 14.1 Consensus size: 86
1078 GATCTGAAAT
* * *
1088 TCTTCAACCAGCTCCACTACAACCGA-GAGAGGTAAGGTTTGTCTTCGACCTGCTTCGCTGTCAA
1 TCTTCAACCAGCTCCACTACAACCGATGA-AGGCAAGGTTTGTTTTCGATCTGCTTCGCTGTCAA
* *
1152 TGCAAGAAGGCAAGATCTTTTG
65 TGCAGGAAGGCAAGATCTGTTG
* *
1174 TCTTCAACCAGCTCCA-TCACAACCGA-GAGAGGCAAGGTTTGTATCTTCGACCTGCTTTGCTGT
1 TCTTCAACCAGCTCCACT-ACAACCGATGA-AGGCAAGGTTTGT-T-TTCGATCTGCTTCGCTGT
*
1237 CAATGCAGGAAGGCAAGATCTGCTG
62 CAATGCAGGAAGGCAAGATCTGTTG
* * * *
1262 TCTTCAACCAGCTCCGCTACAACCGA-GAGAGGCAAGTTTTGTGTCTTCGACCTGCTTCACTGTC
1 TCTTCAACCAGCTCCACTACAACCGATGA-AGGCAAGGTTTGT-T-TTCGATCTGCTTCGCTGTC
**
1326 AATGCAGGAAGGCAAGATCAATTG
63 AATGCAGGAAGGCAAGATCTGTTG
* * * *
1350 TTTTCAACCAGCTCCA-TCACAACCGA-GAGAGGCAAGATTTGCGTCTTCGACCTGCTTCGCTGT
1 TCTTCAACCAGCTCCACT-ACAACCGATGA-AGGCAAGGTTT--GTTTTCGATCTGCTTCGCTGT
*
1413 CAATGCAGGAAGGCAAGATCTATTG
62 CAATGCAGGAAGGCAAGATCTGTTG
*
1438 TCTTCAACCAGCTCCA-TCACAACCGA-GAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGT
1 TCTTCAACCAGCTCCACT-ACAACCGATGA-AGGCAAGGTTTGT-T-TTCGATCTGCTTCGCTGT
*
1501 CAATGTAGGAAGGCAAGATCTGTTG
62 CAATGCAGGAAGGCAAGATCTGTTG
* * * *
1526 TCTTCAACCAGCTCCA-TCACAACCGATGAAGGTAAGGCTTGTTTTCGATCTGCTTCGTTGTTAA
1 TCTTCAACCAGCTCCACT-ACAACCGATGAAGGCAAGGTTTGTTTTCGATCTGCTTCGCTGTCAA
** *
1590 CACAGGAAGGAAAGATCTGTTG
65 TGCAGGAAGGCAAGATCTGTTG
* * *
1612 TCTTCAACCAGCTTCGCTACAACCGA-GAGAGGCAATGTTTGTGTCTTCGATCTGCTTCGCTGTC
1 TCTTCAACCAGCTCCACTACAACCGATGA-AGGCAAGGTTTGT-T-TTCGATCTGCTTCGCTGTC
*
1676 AATGCAGGAAGGCAAGATCTTTTG
63 AATGCAGGAAGGCAAGATCTGTTG
* * *
1700 TCTTCAACCAGCTCCACCACAACCGA-GAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGTTGTC
1 TCTTCAACCAGCTCCACTACAACCGATGA-AGGCAAGGTTTGT-T-TTCGATCTGCTTCGCTGTC
*
1764 AATGCAGGAAGGCAAGATCTGCT-
63 AATGCAGGAAGGCAAGATCTGTTG
** ** * * * *
1787 TCTTTTACCAGCTCCACTGTAACCAATGAAGGCAAGGCTTGTTTTCGATCTGCTTCGCTGTTAAC
1 TCTTCAACCAGCTCCACTACAACCGATGAAGGCAAGGTTTGTTTTCGATCTGCTTCGCTGTCAAT
**
1852 GCAGGAAGGCAAGATCTG-CC
66 GCAGGAAGGCAAGATCTGTTG
* * * * *
1872 CCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAA
1 TCTTCAACCAGCTCCACTACAACCGATGAAGGCAAGG-TTTGTTTTCGATCTGCTTCGCTGTCAA
* **
1937 CGCAGGAAGGCAAGATCTG-CC
65 TGCAGGAAGGCAAGATCTGTTG
* * * * * *
1958 TCTTTAACCAGCTCCACTGCAACCAATGAAGGTAAGACTTTGTTTTCGATCTGCTTCGCTGTTAA
1 TCTTCAACCAGCTCCACTACAACCGATGAAGGCAAG-GTTTGTTTTCGATCTGCTTCGCTGTCAA
* *
2023 CGCAGGAAGGCAAGATCTGCT-
65 TGCAGGAAGGCAAGATCTGTTG
* * * * *
2044 TCTTTAACCAGCTCCACTGCAACCAATGAAGGCAATGCTTTGTTTTCGATCTGCTTCGCTGTTAA
1 TCTTCAACCAGCTCCACTACAACCGATGAAGGCAA-GGTTTGTTTTCGATCTGCTTCGCTGTCAA
* *
2109 CGCAGGAAGGCAAGATCTGCT-
65 TGCAGGAAGGCAAGATCTGTTG
* * * *
2130 TCTTTAACCAGCTCCACTGCAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAA
1 TCTTCAACCAGCTCCACTACAACCGATGAAGGCAAGG-TTTGTTTTCGATCTGCTTCGCTGTCAA
*
2195 TGCAGGAAGGCAAGATCT-TTCT
65 TGCAGGAAGGCAAGATCTGTT-G
* ** * *
2217 TCTTTAACCAGCTCCACTGTAACCAATGAAGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAA
1 TCTTCAACCAGCTCCACTACAACCGATGAAGGCAAGG-TTTGTTTTCGATCTGCTTCGCTGTCAA
* *
2282 CGCAGGAAGGCAAGATCTGCT-
65 TGCAGGAAGGCAAGATCTGTTG
2303 TCTTCA
1 TCTTCA
2309 CTGATTTATT
Statistics
Matches: 1030, Mismatches: 81, Indels: 48
0.89 0.07 0.04
Matches are distributed among these distances:
85 75 0.07
86 404 0.39
87 118 0.11
88 428 0.42
89 3 0.00
90 2 0.00
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.27
Consensus pattern (86 bp):
TCTTCAACCAGCTCCACTACAACCGATGAAGGCAAGGTTTGTTTTCGATCTGCTTCGCTGTCAAT
GCAGGAAGGCAAGATCTGTTG
Found at i:4544 original size:6 final size:6
Alignment explanation
Indices: 4518--4633 Score: 57
Period size: 6 Copynumber: 19.8 Consensus size: 6
4508 TCTTTTTCTC
* * * *
4518 ATTTTC ATTTTG ATCTTG ATTTTG ATTTT- -TTCTT- ATTTTTTC TTTTTG
1 ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATT-TTG A--TTTTG ATTTTG
* * * * *
4566 -TTTTG TTTTTTT ATTTTG ATTTTG A-TTT- -TTTTC ATTTTC ATTTTC
1 ATTTTG -ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG ATTTTG
*
4611 ATTTTG ACTTTG ATTTTG ATTTT
1 ATTTTG ATTTTG ATTTTG ATTTT
4634 TCTTTTTCTT
Statistics
Matches: 89, Mismatches: 11, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
4 5 0.06
5 10 0.11
6 66 0.74
7 6 0.07
8 2 0.02
ACGTcount: A:0.13, C:0.07, G:0.09, T:0.72
Consensus pattern (6 bp):
ATTTTG
Found at i:4577 original size:19 final size:21
Alignment explanation
Indices: 4553--4615 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
4543 TTTTTTCTTA
4553 TTTTTTCTTTTTG-TTTTG-T
1 TTTTTTCTTTTTGATTTTGAT
*
4572 TTTTTT-ATTTTGATTTTGAT
1 TTTTTTCTTTTTGATTTTGAT
* * *
4592 TTTTTTCATTTTCATTTTCAT
1 TTTTTTCTTTTTGATTTTGAT
4613 TTT
1 TTT
4616 GACTTTGATT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 5 0.13
19 11 0.29
20 7 0.18
21 15 0.39
ACGTcount: A:0.10, C:0.06, G:0.06, T:0.78
Consensus pattern (21 bp):
TTTTTTCTTTTTGATTTTGAT
Done.