Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_365 ID=scaffold_365-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: 7984
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.32
Warning! 108 characters in sequence are not A, C, G, or T
Found at i:1287 original size:44 final size:44
Alignment explanation
Indices: 1239--1853 Score: 257
Period size: 44 Copynumber: 13.9 Consensus size: 44
1229 GTAAGACCTG
*
1239 TATCTTCGATCTACTTCA-CACTAGTATGGAAAGACATGATCTAC
1 TATCTTCGATCTACTTCATCACTAGTATGG-AAGACAAGATCTAC
* * * *
1283 TATC-TCTGATCTACTTCATGTCAATA-CAT-GAAGACAAGATCCAT
1 TATCTTC-GATCTACTTCA--TCACTAGTATGGAAGACAAGATCTAC
* * *
1327 TATCTTCGATCTACTTCACCACCAGTATAGGAAGACAAGATCT-G
1 TATCTTCGATCTACTTCATCACTAGTAT-GGAAGACAAGATCTAC
* * *
1371 TCATCTTCGATCTACTTCATGTCAATA-CAT-GAAGACAAGATCCAC
1 T-ATCTTCGATCTACTTCA--TCACTAGTATGGAAGACAAGATCTAC
* * *
1416 TATC-TCTGATCTACTTCATGTCAATA-CAT-GAAGACAAGAT-TCAT
1 TATCTTC-GATCTACTTCA--TCACTAGTATGGAAGACAAGATCT-AC
* * * **
1460 TATCTTCGATCTACTTCATGTCAATA-CAT-GTAGACAAGATCCGC
1 TATCTTCGATCTACTTCA--TCACTAGTATGGAAGACAAGATCTAC
* * **
1504 TATC-TCTGATCTACTTCATGTCAATA-CAT-GAAGACAAGATCCGC
1 TATCTTC-GATCTACTTCA--TCACTAGTATGGAAGACAAGATCTAC
* * *
1548 TATCTTCGATCTACTTCATGTCAATA-CAT-GAAGACAAGAT-TCAT
1 TATCTTCGATCTACTTCA--TCACTAGTATGGAAGACAAGATCT-AC
* * * *
1592 TATC-TCTGATCTACTTCATGTCAATA-CAT-GAAGACAAGATCCAT
1 TATCTTC-GATCTACTTCA--TCACTAGTATGGAAGACAAGATCTAC
* * * **
1636 TATCTTTGATCTACTTCACCACCAGTATGGGAAGACAAGATCCGC
1 TATCTTCGATCTACTTCATCACTAGTAT-GGAAGACAAGATCTAC
* * *
1681 TATCTTCGATCTACTTCATGTCAATA-CAT-GAAGACAAGATGC-AT
1 TATCTTCGATCTACTTCA--TCACTAGTATGGAAGACAAGAT-CTAC
* * * *
1725 TATC-TCTGATCTACTTCATGTCAAT-GCAT-GAATACAAGATCCA-
1 TATCTTC-GATCTACTTCA--TCACTAGTATGGAAGACAAGATCTAC
* * **
1768 TCATCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCCGC
1 T-ATCTTCGATCTACTTCATCACTAGTAT-GGAAGACAAGATCTAC
* * * *
1814 TAGCTTTGATTTACTTCATGTCAATA-TAT-GAAGACAAGAT
1 TATCTTCGATCTACTTCA--TCACTAGTATGGAAGACAAGAT
1854 TCGCTGCTTT
Statistics
Matches: 477, Mismatches: 55, Indels: 78
0.78 0.09 0.13
Matches are distributed among these distances:
42 8 0.02
43 19 0.04
44 330 0.69
45 97 0.20
46 10 0.02
47 13 0.03
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.31
Consensus pattern (44 bp):
TATCTTCGATCTACTTCATCACTAGTATGGAAGACAAGATCTAC
Found at i:1507 original size:88 final size:88
Alignment explanation
Indices: 1290--1853 Score: 643
Period size: 88 Copynumber: 6.4 Consensus size: 88
1280 TACTATCTCT
* *** *
1290 GATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCT-TCGATCTACTTCACCACCAGTA
1 GATCTACTTCATGTCAATACATGAAGACAAGATCCACTATCTCT-GATCTACTTCA-TGTCAATA
* * ** *
1354 TAGGAAGACAAGATCTGTCATCTTC
64 CATGAAGACAAGATCCATTATCTTC
1379 GATCTACTTCATGTCAATACATGAAGACAAGATCCACTATCTCTGATCTACTTCATGTCAATACA
1 GATCTACTTCATGTCAATACATGAAGACAAGATCCACTATCTCTGATCTACTTCATGTCAATACA
*
1444 TGAAGACAAGATTCATTATCTTC
66 TGAAGACAAGATCCATTATCTTC
* *
1467 GATCTACTTCATGTCAATACATGTAGACAAGATCCGCTATCTCTGATCTACTTCATGTCAATACA
1 GATCTACTTCATGTCAATACATGAAGACAAGATCCACTATCTCTGATCTACTTCATGTCAATACA
**
1532 TGAAGACAAGATCCGCTATCTTC
66 TGAAGACAAGATCCATTATCTTC
* *
1555 GATCTACTTCATGTCAATACATGAAGACAAGATTCATTATCTCTGATCTACTTCATGTCAATACA
1 GATCTACTTCATGTCAATACATGAAGACAAGATCCACTATCTCTGATCTACTTCATGTCAATACA
*
1620 TGAAGACAAGATCCATTATCTTT
66 TGAAGACAAGATCCATTATCTTC
*** * *** *
1643 GATCTACTTCACCACCAGTATGGGAAGACAAGATCCGCTATCT-TCGATCTACTTCATGTCAATA
1 GATCTACTTCA-TGTCAATACATGAAGACAAGATCCACTATCTCT-GATCTACTTCATGTCAATA
*
1707 CATGAAGACAAGATGCATTATC-TC
64 CATGAAGACAAGATCCATTATCTTC
* * *** *
1731 TGATCTACTTCATGTCAATGCATGAATACAAGATCCA-TCATCT-TCGATCTACTTCACCACCAG
1 -GATCTACTTCATGTCAATACATGAAGACAAGATCCACT-ATCTCT-GATCTACTTCA-TGTCAA
*** ** * *
1794 TATGGGAAGACAAGATCCGCTAGCTTT
62 TACATGAAGACAAGATCCATTATCTTC
* *
1821 GATTTACTTCATGTCAATATATGAAGACAAGAT
1 GATCTACTTCATGTCAATACATGAAGACAAGAT
1854 TCGCTGCTTT
Statistics
Matches: 407, Mismatches: 61, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
87 1 0.00
88 232 0.57
89 172 0.42
90 2 0.00
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (88 bp):
GATCTACTTCATGTCAATACATGAAGACAAGATCCACTATCTCTGATCTACTTCATGTCAATACA
TGAAGACAAGATCCATTATCTTC
Found at i:1743 original size:133 final size:132
Alignment explanation
Indices: 1239--1855 Score: 749
Period size: 133 Copynumber: 4.7 Consensus size: 132
1229 GTAAGACCTG
* * * **
1239 TATCTTCGATCTACTTCACACTAGTATGGAAAGACATGATCTACTATC-TCTGATCTACTTCATG
1 TATCTTCGATCTACTTCACACCAGTATGGGAAGACAAGATCCGCTATCTTC-GATCTACTTCATG
* *** * * *
1303 TCAATACATGAAGACAAGATCCATTATCTTCGATCTACTTCACCACCAGTATAGGAAGACAAGAT
65 TCAATACATGAAGACAAGATTCATTATCTTCGATCTACTTCA-TGTCAATACATGAAGACAAGAT
**
1368 CTGT
129 CCAT
* *** * *** *
1372 CATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATCCACTATC-TCTGATCTACTTCATG
1 TATCTTCGATCTACTTCACACCAGTATGGGAAGACAAGATCCGCTATCTTC-GATCTACTTCATG
*
1436 TCAATACATGAAGACAAGATTCATTATCTTCGATCTACTTCATGTCAATACATGTAGACAAGATC
65 TCAATACATGAAGACAAGATTCATTATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATC
**
1501 CGC
130 CAT
*** * ***
1504 TATC-TCTGATCTACTTCATGTCAATACATGAAGACAAGATCCGCTATCTTCGATCTACTTCATG
1 TATCTTC-GATCTACTTCACACCAGTATGGGAAGACAAGATCCGCTATCTTCGATCTACTTCATG
1568 TCAATACATGAAGACAAGATTCATTATC-TCTGATCTACTTCATGTCAATACATGAAGACAAGAT
65 TCAATACATGAAGACAAGATTCATTATCTTC-GATCTACTTCATGTCAATACATGAAGACAAGAT
1632 CCAT
129 CCAT
*
1636 TATCTTTGATCTACTTCACCACCAGTATGGGAAGACAAGATCCGCTATCTTCGATCTACTTCATG
1 TATCTTCGATCTACTTCA-CACCAGTATGGGAAGACAAGATCCGCTATCTTCGATCTACTTCATG
* * *
1701 TCAATACATGAAGACAAGATGCATTATC-TCTGATCTACTTCATGTCAATGCATGAATACAAGAT
65 TCAATACATGAAGACAAGATTCATTATCTTC-GATCTACTTCATGTCAATACATGAAGACAAGAT
1765 CCAT
129 CCAT
* * * *
1769 CATCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCCGCTAGCTTTGATTTACTTCATG
1 TATCTTCGATCTACTTCA-CACCAGTATGGGAAGACAAGATCCGCTATCTTCGATCTACTTCATG
*
1834 TCAATATATGAAGACAAGATTC
65 TCAATACATGAAGACAAGATTC
1856 GCTGCTTTTC
Statistics
Matches: 434, Mismatches: 45, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
131 4 0.01
132 150 0.35
133 280 0.65
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.31
Consensus pattern (132 bp):
TATCTTCGATCTACTTCACACCAGTATGGGAAGACAAGATCCGCTATCTTCGATCTACTTCATGT
CAATACATGAAGACAAGATTCATTATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATCC
AT
Found at i:3154 original size:7 final size:7
Alignment explanation
Indices: 3144--3204 Score: 72
Period size: 7 Copynumber: 8.7 Consensus size: 7
3134 TCTATTTTAC
3144 TTTTTCA
1 TTTTTCA
3151 TTTTTCA
1 TTTTTCA
3158 TTTTTC-
1 TTTTTCA
*
3164 CTTTTCA
1 TTTTTCA
3171 CTTTTTCA
1 -TTTTTCA
3179 TTTTTC-
1 TTTTTCA
*
3185 CTTTTCA
1 TTTTTCA
3192 CTTTTTCA
1 -TTTTTCA
3200 TTTTT
1 TTTTT
3205 TTTCATTTCA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
6 10 0.22
7 24 0.52
8 12 0.26
ACGTcount: A:0.10, C:0.20, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTTTCA
Found at i:3167 original size:21 final size:21
Alignment explanation
Indices: 3145--3204 Score: 113
Period size: 21 Copynumber: 2.9 Consensus size: 21
3135 CTATTTTACT
3145 TTTTCA-TTTTTCATTTTTCC
1 TTTTCACTTTTTCATTTTTCC
3165 TTTTCACTTTTTCATTTTTCC
1 TTTTCACTTTTTCATTTTTCC
3186 TTTTCACTTTTTCATTTTT
1 TTTTCACTTTTTCATTTTT
3205 TTTCATTTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
20 6 0.15
21 33 0.85
ACGTcount: A:0.10, C:0.20, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTCACTTTTTCATTTTTCC
Found at i:3195 original size:28 final size:29
Alignment explanation
Indices: 3145--3205 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 29
3135 CTATTTTACT
*
3145 TTTTCATTTTTCATTTTTCC-TTTTCACT
1 TTTTCATTTTTCACTTTTCCTTTTTCACT
*
3173 TTTTCATTTTTC-CTTTTCACTTTTTCATT
1 TTTTCATTTTTCACTTTTC-CTTTTTCACT
3202 TTTT
1 TTTT
3206 TTCATTTCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 5 0.17
28 13 0.45
29 11 0.38
ACGTcount: A:0.10, C:0.20, G:0.00, T:0.70
Consensus pattern (29 bp):
TTTTCATTTTTCACTTTTCCTTTTTCACT
Found at i:6582 original size:17 final size:17
Alignment explanation
Indices: 6560--6595 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
6550 TTCTATGATG
*
6560 AAATGTCATGCAGTCAA
1 AAATGTCATGCAGCCAA
6577 AAATGTCATGCAGCCAA
1 AAATGTCATGCAGCCAA
6594 AA
1 AA
6596 CAAAACACAC
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:0.44, C:0.19, G:0.17, T:0.19
Consensus pattern (17 bp):
AAATGTCATGCAGCCAA
Done.