Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_572 ID=scaffold_572-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: 8172
ACGTcount: A:0.20, C:0.15, G:0.12, T:0.22
Warning! 2591 characters in sequence are not A, C, G, or T
Found at i:1221 original size:44 final size:44
Alignment explanation
Indices: 1158--1450 Score: 322
Period size: 44 Copynumber: 6.5 Consensus size: 44
1148 TCAGGGGGAT
* *
1158 AAGATTTG-TATCTTGGATCTACTTCACGCCAATACATGAAGAC
1 AAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGAC
* * * * ***
1201 AAGATCTGCTATCTTCGATCTACTTCGCCACCAGTATGGGAAGAC
1 AAGATCTGCTATCTTTGATCTACTTC-ACGCCAATACATGAAGAC
* *
1246 AAGATCTGCTATCTTTGATCTACTTCACGTCAATACATGAAGAT
1 AAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGAC
1290 AAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGAC
1 AAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGAC
* ** *
1334 AAGATCTGCTTTCTTCTTTTGATCTACTT--CGCCACCAGTATGGAAAGAC
1 AAGATCTGC--T-ATC-TTTGATCTACTTCACGCCAATA-CAT-G-AAGAC
* *
1383 AAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGAC
1 AAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGAC
* *
1427 AAGATCTGTTTTCTTTGATCTACT
1 AAGATCTGCTATCTTTGATCTACT
1451 CCACCACCAG
Statistics
Matches: 210, Mismatches: 29, Indels: 21
0.81 0.11 0.08
Matches are distributed among these distances:
43 7 0.03
44 105 0.50
45 50 0.24
46 11 0.05
47 11 0.05
48 13 0.06
49 13 0.06
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.33
Consensus pattern (44 bp):
AAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGAC
Found at i:1399 original size:93 final size:89
Alignment explanation
Indices: 1196--1476 Score: 298
Period size: 89 Copynumber: 3.1 Consensus size: 89
1186 CCAATACATG
* * * * *** * *
1196 AAGACAAGATCTGCTATCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTT
1 AAGACAAGATCTGCTATCTTTGATCTACTTC-ACGCCAATACATGAAGACAAGATCTGTTTTCTT
* ** *
1261 TGATCTACTTCACGTCAATA-CAT-G-
65 TGATCTACTCCAC--CACCAGTATGGA
*
1285 AAGATAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTC
1 AAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTG--TT-TTC
* *
1350 TTTTGATCTACTTCGCCACCAGTATGGA
63 -TTTGATCTACTCCACCACCAGTATGGA
* *
1378 AAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTT
1 AAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTT
*
1443 GATCTACTCCACCACCAGTATGGG
66 GATCTACTCCACCACCAGTATGGA
*
1467 GAGACAAGAT
1 AAGACAAGAT
1477 NNNNNNNNNN
Statistics
Matches: 164, Mismatches: 21, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
88 20 0.12
89 62 0.38
90 7 0.04
91 6 0.04
92 15 0.09
93 54 0.33
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (89 bp):
AAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTT
GATCTACTCCACCACCAGTATGGA
Found at i:1408 original size:137 final size:132
Alignment explanation
Indices: 1155--1450 Score: 457
Period size: 137 Copynumber: 2.2 Consensus size: 132
1145 ACTTCAGGGG
* *
1155 GATAAGATTTGTATCTTGGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTTCGAT
1 GATAAGATCTGTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTTCGAT
* *
1220 CTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTTGATCTACTTCACGTCAATACATG
66 CTACTTCGCCACCAGTATGGAAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATG
1285 AA
131 AA
*
1287 GATAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCTT
1 GATAAGATCTG-TATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTTC--
* *
1352 TTGATCTACTTCGCCACCAGTATGGAAAGACAAGATCTGTTATCTTTGATCTACTTCACGCCAGT
63 --GATCTACTTCGCCACCAGTATGGAAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAAT
1417 ACATGAA
126 ACATGAA
* *
1424 GACAAGATCTGTTTTCTTTGATCTACT
1 GATAAGATCTG-TATCTTTGATCTACT
1451 CCACCACCAG
Statistics
Matches: 149, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
132 10 0.07
133 49 0.33
137 90 0.60
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.33
Consensus pattern (132 bp):
GATAAGATCTGTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTATCTTCGAT
CTACTTCGCCACCAGTATGGAAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATG
AA
Found at i:1716 original size:45 final size:45
Alignment explanation
Indices: 1577--1941 Score: 393
Period size: 44 Copynumber: 8.3 Consensus size: 45
1567 NNNNNNNNNN
* * *
1577 AGACAAGATTTGTTTTCTTTGATCTACTCCACCACCAGTATGGGG
1 AGACAAGATCTGTTTTCTTTGATCTACTTCACCACCAGTATGGGA
* * ***
1622 AGACAAGATTTG-TTTCTTTGATCTACTTCA-CGCCAGTACATGA
1 AGACAAGATCTGTTTTCTTTGATCTACTTCACCACCAGTATGGGA
* * * *
1665 AGACAAGATCTGCTATCTTTGATCTACTCCACCACCAGTATGGGG
1 AGACAAGATCTGTTTTCTTTGATCTACTTCACCACCAGTATGGGA
** ***
1710 AGACAAGATCTG-TTTCTTTGATCTACTTCA-TGCCAGTACATGA
1 AGACAAGATCTGTTTTCTTTGATCTACTTCACCACCAGTATGGGA
* *
1753 AGACAAGATCTGTTTTCTTTGATCTACTCCACCACCAGTATGGGG
1 AGACAAGATCTGTTTTCTTTGATCTACTTCACCACCAGTATGGGA
* * ***
1798 AGACAAGATCTG-TTTCTTTGATCTACTTCA-CGCTAGTACATGA
1 AGACAAGATCTGTTTTCTTTGATCTACTTCACCACCAGTATGGGA
* *
1841 AGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGTATGGGA
1 AGACAAGATCTGTTTTCTTTGATCTACTTCACCACCAGTATGGGA
* * * ***
1886 AGACAAGATATGTTATCTTTGATCTACTTCA-CGCCAGTACATGA
1 AGACAAGATCTGTTTTCTTTGATCTACTTCACCACCAGTATGGGA
1930 AGACAAGATCTG
1 AGACAAGATCTG
1942 CTGCTTTTCA
Statistics
Matches: 262, Mismatches: 52, Indels: 13
0.80 0.16 0.04
Matches are distributed among these distances:
43 57 0.22
44 119 0.45
45 86 0.33
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.32
Consensus pattern (45 bp):
AGACAAGATCTGTTTTCTTTGATCTACTTCACCACCAGTATGGGA
Found at i:1726 original size:88 final size:88
Alignment explanation
Indices: 1577--1941 Score: 622
Period size: 88 Copynumber: 4.1 Consensus size: 88
1567 NNNNNNNNNN
* *
1577 AGACAAGATTTGTTTTCTTTGATCTACTCCACCACCAGTATGGGGAGACAAGATTTGTTTCTTTG
1 AGACAAGATCTGTTTTCTTTGATCTACTCCACCACCAGTATGGGGAGACAAGATCTGTTTCTTTG
1642 ATCTACTTCACGCCAGTACATGA
66 ATCTACTTCACGCCAGTACATGA
* *
1665 AGACAAGATCTGCTATCTTTGATCTACTCCACCACCAGTATGGGGAGACAAGATCTGTTTCTTTG
1 AGACAAGATCTGTTTTCTTTGATCTACTCCACCACCAGTATGGGGAGACAAGATCTGTTTCTTTG
*
1730 ATCTACTTCATGCCAGTACATGA
66 ATCTACTTCACGCCAGTACATGA
1753 AGACAAGATCTGTTTTCTTTGATCTACTCCACCACCAGTATGGGGAGACAAGATCTGTTTCTTTG
1 AGACAAGATCTGTTTTCTTTGATCTACTCCACCACCAGTATGGGGAGACAAGATCTGTTTCTTTG
*
1818 ATCTACTTCACGCTAGTACATGA
66 ATCTACTTCACGCCAGTACATGA
* * * * *
1841 AGACAAGATCTGTTTTCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATATGTTATCTTT
1 AGACAAGATCTGTTTTCTTTGATCTACTCCACCACCAGTATGGGGAGACAAGATCTGTT-TCTTT
1906 GATCTACTTCACGCCAGTACATGA
65 GATCTACTTCACGCCAGTACATGA
1930 AGACAAGATCTG
1 AGACAAGATCTG
1942 CTGCTTTTCA
Statistics
Matches: 261, Mismatches: 15, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
88 221 0.85
89 40 0.15
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.32
Consensus pattern (88 bp):
AGACAAGATCTGTTTTCTTTGATCTACTCCACCACCAGTATGGGGAGACAAGATCTGTTTCTTTG
ATCTACTTCACGCCAGTACATGA
Found at i:3214 original size:7 final size:7
Alignment explanation
Indices: 3198--3250 Score: 72
Period size: 7 Copynumber: 7.6 Consensus size: 7
3188 AGCCTCTCCA
*
3198 TTTTCTT
1 TTTTCAT
3205 TTTTCAT
1 TTTTCAT
3212 TTTTCAT
1 TTTTCAT
3219 TTTTCAT
1 TTTTCAT
*
3226 TTTTC-C
1 TTTTCAT
3232 TTTTCACT
1 TTTTCA-T
3240 TTTTCAT
1 TTTTCAT
3247 TTTT
1 TTTT
3251 TCACTTCATC
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
6 5 0.12
7 30 0.73
8 6 0.15
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTCAT
Found at i:3258 original size:21 final size:20
Alignment explanation
Indices: 3214--3259 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
3204 TTTTTCATTT
**
3214 TTCATTTTTCATTTTTCCTT
1 TTCATTTTTCATTTTTCCAC
*
3234 TTCACTTTTTCATTTTTTCAC
1 TTCA-TTTTTCATTTTTCCAC
3255 TTCAT
1 TTCAT
3260 CATTTTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.13, C:0.22, G:0.00, T:0.65
Consensus pattern (20 bp):
TTCATTTTTCATTTTTCCAC
Found at i:4223 original size:46 final size:46
Alignment explanation
Indices: 4153--4286 Score: 243
Period size: 46 Copynumber: 2.9 Consensus size: 46
4143 AATAATATGA
*
4153 ATGAATGAATGAATGGTTTGGCAGAAAAAAAAATCAAAGGAATAAT
1 ATGAATGAATGAATGGTTTGGCAGAAAAAAAAATCAAAAGAATAAT
*
4199 ATGAATGAATGAATGGTTTTGCAGAAAAAAAAATCAAAAGAATAAT
1 ATGAATGAATGAATGGTTTGGCAGAAAAAAAAATCAAAAGAATAAT
4245 ATGAATGAATGAATGGTTTGGCAG-AAAAAAAATCAAAAGAAT
1 ATGAATGAATGAATGGTTTGGCAGAAAAAAAAATCAAAAGAAT
4287 GAAAAAAATC
Statistics
Matches: 85, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
45 18 0.21
46 67 0.79
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (46 bp):
ATGAATGAATGAATGGTTTGGCAGAAAAAAAAATCAAAAGAATAAT
Done.