Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga13g02578.F2
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: 2027
ACGTcount: A:0.28, C:0.40, G:0.09, T:0.23
Found at i:364 original size:66 final size:66
Alignment explanation
Indices: 263--400 Score: 204
Period size: 66 Copynumber: 2.1 Consensus size: 66
253 AAGGAGTCCT
* * **
263 CCACCACCACCACCACGTCCAAAAACACCTCCGCCAATTTCACATCCACCTTTGAGGGCGTCTCC
1 CCACCGCCACCACCACGTCCAAAAACACCTCCGCCAATCTCACATCCACCTTTGAGGGCACCTCC
328 A
66 A
* * * *
329 CCACCGCCACCATCACGTCCAAATACACCTCCGCCAGTCTCACTTCCACCTTTGAGGGCACCTCC
1 CCACCGCCACCACCACGTCCAAAAACACCTCCGCCAATCTCACATCCACCTTTGAGGGCACCTCC
394 A
66 A
395 CCACCG
1 CCACCG
401 TCACTGTCAC
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.25, C:0.47, G:0.12, T:0.17
Consensus pattern (66 bp):
CCACCGCCACCACCACGTCCAAAAACACCTCCGCCAATCTCACATCCACCTTTGAGGGCACCTCC
A
Found at i:516 original size:78 final size:77
Alignment explanation
Indices: 408--728 Score: 508
Period size: 78 Copynumber: 4.2 Consensus size: 77
398 CCGTCACTGT
408 CACCACCATCA-C-CACCACCACCACCACGTCCAAACACACCTCCACCAGTCTCACTTCCACCTT
1 CACCACCATCACCACACCACCACCACCACGTCCAAACACACCTCCACCAGTCTCACTTCCACCTT
471 TGAGGACGCCTC
66 TGAGGACGCCTC
* *
483 CACCACCATCACCATCACCACCACCACCACGTCCAAACATACCTCCGCCAGTCTCACTTCCACCT
1 CACCACCATCACCA-CACCACCACCACCACGTCCAAACACACCTCCACCAGTCTCACTTCCACCT
**
548 TTGAGGGTGCCTC
65 TTGAGGACGCCTC
*
561 CACCACCATCACCACCACCACCACCACCACGTCCAAACACACCTCCGCCAGTCTCACTTCCACCT
1 CACCACCATCACCA-CACCACCACCACCACGTCCAAACACACCTCCACCAGTCTCACTTCCACCT
626 TTGAGGACGCCTC
65 TTGAGGACGCCTC
* *
639 CACCACTATCA-C-CACCGCCACCACCACGTCCAAACACACCTCCACCAGTCTCACTTCCACCTT
1 CACCACCATCACCACACCACCACCACCACGTCCAAACACACCTCCACCAGTCTCACTTCCACCTT
702 TGAGTG-CGCCTC
66 TGAG-GACGCCTC
*
714 CACCACCACCACCAC
1 CACCACCATCACCAC
729 GCTCAAACAC
Statistics
Matches: 227, Mismatches: 13, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
75 79 0.35
76 3 0.01
77 2 0.01
78 143 0.63
ACGTcount: A:0.26, C:0.50, G:0.09, T:0.15
Consensus pattern (77 bp):
CACCACCATCACCACACCACCACCACCACGTCCAAACACACCTCCACCAGTCTCACTTCCACCTT
TGAGGACGCCTC
Found at i:568 original size:3 final size:3
Alignment explanation
Indices: 560--590 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
550 GAGGGTGCCT
*
560 CCA CCA CCA TCA CCA CCA CCA CCA CCA CCA C
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA C
591 GTCCAAACAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.65, G:0.00, T:0.03
Consensus pattern (3 bp):
CCA
Found at i:720 original size:156 final size:158
Alignment explanation
Indices: 263--728 Score: 591
Period size: 156 Copynumber: 3.0 Consensus size: 158
253 AAGGAGTCCT
* * * * *
263 CCACCACCACCACCACGTCCAAAAACACCTCCGCCAATTTCACATCCACCTTTGAGG--GCGT--
1 CCACCACCACCACCACGTCCAAACACACCTCCGCCAGTCTCACTTCCACCTTTGAGGACGCCTCC
* * *
324 ----CT-CCACCACCGCCACCATCACGTCCAAATACACCTCCGCCAGTCTCACTTCCACCTTTGA
66 ACCACTATCACCACCGCCACCACCACGTCCAAACACACCTCCGCCAGTCTCACTTCCACCTTTGA
*
384 GGGCACCTCCACCACCGTCACTGTCACCACCATCA
131 GGGCGCCTCCACCA-C--CAC---CACCACCA-CA
*
419 CCACCACCACCACCACGTCCAAACACACCTCCACCAGTCTCACTTCCACCTTTGAGGACGCCTCC
1 CCACCACCACCACCACGTCCAAACACACCTCCGCCAGTCTCACTTCCACCTTTGAGGACGCCTCC
* * *
484 ACCACCATCACCATCACCACCACCACCACGTCCAAACATACCTCCGCCAGTCTCACTTCCACCTT
66 ACCACTATCA-C--CACCGCCACCACCACGTCCAAACACACCTCCGCCAGTCTCACTTCCACCTT
* *
549 TGAGGGTGCCT---CCACCACCATCA-C-CA
128 TGAGGGCGCCTCCACCACCACCACCACCACA
575 CCACCACCACCACCACGTCCAAACACACCTCCGCCAGTCTCACTTCCACCTTTGAGGACGCCTCC
1 CCACCACCACCACCACGTCCAAACACACCTCCGCCAGTCTCACTTCCACCTTTGAGGACGCCTCC
*
640 ACCACTATCACCACCGCCACCACCACGTCCAAACACACCTCCACCAGTCTCACTTCCACCTTTGA
66 ACCACTATCACCACCGCCACCACCACGTCCAAACACACCTCCGCCAGTCTCACTTCCACCTTTGA
*
705 GTGCGCCTCCACCACCACCACCAC
131 GGGCGCCTCCACCACCACCACCAC
729 GCTCAAACAC
Statistics
Matches: 271, Mismatches: 23, Indels: 31
0.83 0.07 0.10
Matches are distributed among these distances:
153 57 0.21
155 1 0.00
156 138 0.51
158 4 0.01
159 4 0.01
162 3 0.01
164 2 0.01
165 5 0.02
166 1 0.00
168 56 0.21
ACGTcount: A:0.25, C:0.49, G:0.10, T:0.16
Consensus pattern (158 bp):
CCACCACCACCACCACGTCCAAACACACCTCCGCCAGTCTCACTTCCACCTTTGAGGACGCCTCC
ACCACTATCACCACCGCCACCACCACGTCCAAACACACCTCCGCCAGTCTCACTTCCACCTTTGA
GGGCGCCTCCACCACCACCACCACCACA
Found at i:729 original size:63 final size:63
Alignment explanation
Indices: 650--783 Score: 207
Period size: 63 Copynumber: 2.1 Consensus size: 63
640 ACCACTATCA
* * *
650 CCACCGCCACCACCACG-TCCAAACACACCTCCACCAGTCTCACTTCCACCTTTGAGTGCGCCT
1 CCACCACCACCACCACGCT-CAAACACACCTCCACCAGTCTCACTTCCACCTTTGAGGGCACCT
*
713 CCACCACCACCACCACGCTCAAACACACCTCCGCCAGTCTCACTTCCACCTTTGAGGGCACCT
1 CCACCACCACCACCACGCTCAAACACACCTCCACCAGTCTCACTTCCACCTTTGAGGGCACCT
*
776 TCACCACC
1 CCACCACC
784 TCCAATTCCC
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
63 64 0.98
64 1 0.02
ACGTcount: A:0.23, C:0.50, G:0.10, T:0.16
Consensus pattern (63 bp):
CCACCACCACCACCACGCTCAAACACACCTCCACCAGTCTCACTTCCACCTTTGAGGGCACCT
Found at i:930 original size:36 final size:36
Alignment explanation
Indices: 795--1312 Score: 455
Period size: 36 Copynumber: 14.8 Consensus size: 36
785 CCAATTCCCC
* * *
795 CACCTTCAATGAACCAACCTTTACCTCCACCTCTGT
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
* * *
831 CACCTCCAATGAACCAACCATCACTTCCACCTTTCT
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
* * *
867 CACCTCCAACGAACCAACCTTTACCTCCACCTCTGT
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
* * *
903 CACCTCCAGTGAACCAACCGTCTCCTCCA---C-CT
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
* * ** *
935 -A-ATTCAAT-AA-C-ACCTTCACCT--TTCTCAC-
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
*
963 C---TCCAATGAACCAACCTTCACCTCTACCTCTGC-
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCT-CT
* * * * *
996 CACCTTCGATAAACCAACCGTCACCTCCACCTTTCT
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
1032 CACCTCCAATGAACCAACCTTCACCTCCACC-CT-T
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
* *
1066 GCCACCACCAATGAACCAACCTTCACCTCCACCTTTCT
1 --CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
* * * *
1104 CACCACCAATGAACGAA-CTATCACCTCCACCCCTAT
1 CACCTCCAATGAACCAACCT-TCACCTCCACCTCTCT
* *
1140 CACCTCCAATGAACCAACCTACACCTCCACCTTTCT
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
* *
1176 TACCTCCAATGAACCAACCTTCACCTCCACCTTTCT
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
* * * * *
1212 CACCACCAATGAACGAACCATCACCTCCACCCCTGT
1 CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
* *
1248 CACCTCCAATGAAACAACCTTCATCTCCACCAT-TCT
1 CACCTCCAATGAACCAACCTTCACCTCCACC-TCTCT
* ** *
1284 CACCACCAATGAATGAACCATCACCTCCA
1 CACCTCCAATGAACCAACCTTCACCTCCA
1313 ATGAACCAAC
Statistics
Matches: 388, Mismatches: 72, Indels: 44
0.77 0.14 0.09
Matches are distributed among these distances:
27 13 0.03
28 4 0.01
29 4 0.01
30 14 0.04
31 1 0.00
32 4 0.01
33 3 0.01
34 1 0.00
35 4 0.01
36 336 0.87
37 3 0.01
38 1 0.00
ACGTcount: A:0.28, C:0.45, G:0.05, T:0.22
Consensus pattern (36 bp):
CACCTCCAATGAACCAACCTTCACCTCCACCTCTCT
Found at i:963 original size:93 final size:93
Alignment explanation
Indices: 858--1027 Score: 261
Period size: 93 Copynumber: 1.8 Consensus size: 93
848 CCATCACTTC
* * *
858 CACCTTTCTCACCTCCAACGAACCAACCTTTACCTCCACCTCTGTCACCTCC-AGTGAACCAACC
1 CACCTTTCTCACCTCCAACGAACCAACCTTCACCTCCACCTCTGCCACCTCCGA-TAAACCAACC
*
922 GTCTCCTCCACCTAATTCAATAACACCTT
65 GTCACCTCCACCTAATTCAATAACACCTT
* * *
951 CACCTTTCTCACCTCCAATGAACCAACCTTCACCTCTACCTCTGCCACCTTCGATAAACCAACCG
1 CACCTTTCTCACCTCCAACGAACCAACCTTCACCTCCACCTCTGCCACCTCCGATAAACCAACCG
1016 TCACCTCCACCT
66 TCACCTCCACCT
1028 TTCTCACCTC
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
93 68 0.99
94 1 0.01
ACGTcount: A:0.25, C:0.45, G:0.05, T:0.24
Consensus pattern (93 bp):
CACCTTTCTCACCTCCAACGAACCAACCTTCACCTCCACCTCTGCCACCTCCGATAAACCAACCG
TCACCTCCACCTAATTCAATAACACCTT
Found at i:1314 original size:57 final size:57
Alignment explanation
Indices: 1247--1369 Score: 192
Period size: 57 Copynumber: 2.2 Consensus size: 57
1237 TCCACCCCTG
* *
1247 TCACCTCCAATGAAACAACCTTCATCTCCACCATTCTCACCACCAATGAATGAACCA
1 TCACCTCCAATGAAACAACCTTCACCTCCACCATTCTCACCACCAATGAACGAACCA
* * *
1304 TCACCTCCAATGAACCAACCTTCACCTCCACCTTTTTCACCACCAATGAACGAACCA
1 TCACCTCCAATGAAACAACCTTCACCTCCACCATTCTCACCACCAATGAACGAACCA
*
1361 TCACATCCA
1 TCACCTCCA
1370 CCCCTGTCAC
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.33, C:0.41, G:0.05, T:0.21
Consensus pattern (57 bp):
TCACCTCCAATGAAACAACCTTCACCTCCACCATTCTCACCACCAATGAACGAACCA
Found at i:1314 original size:93 final size:93
Alignment explanation
Indices: 1211--1405 Score: 223
Period size: 93 Copynumber: 2.1 Consensus size: 93
1201 TCCACCTTTC
* * * *
1211 TCACCACCAATGAACGAACCATCACCTCCACCCCTGTCACCTCCAATGAAAC-AACCTTCATC-T
1 TCACCTCCAATGAACCAACCATCACCTCCACCCCTGTCACCACCAATG-AACGAACCATCA-CAT
* **
1274 CCACCATTCTCACCACCAATGAATGAACCA
64 CCACCACTCTCACCACCAATGAACCAACCA
* ** *
1304 TCACCTCCAATGAACCAACCTTCACCTCCACCTTTTTCACCACCAATGAACGAACCATCACATCC
1 TCACCTCCAATGAACCAACCATCACCTCCACCCCTGTCACCACCAATGAACGAACCATCACATCC
* * * *
1369 ACCCCTGTCACCTCCAATGAACCAACCT
66 ACCACTCTCACCACCAATGAACCAACCA
1397 TCACCTCCA
1 TCACCTCCA
1406 CCTTACTCAC
Statistics
Matches: 85, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
92 4 0.05
93 81 0.95
ACGTcount: A:0.31, C:0.44, G:0.06, T:0.19
Consensus pattern (93 bp):
TCACCTCCAATGAACCAACCATCACCTCCACCCCTGTCACCACCAATGAACGAACCATCACATCC
ACCACTCTCACCACCAATGAACCAACCA
Found at i:1323 original size:21 final size:21
Alignment explanation
Indices: 1283--1333 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
1273 TCCACCATTC
* **
1283 TCACCACCAATGAATGAACCA
1 TCACCTCCAATGAACCAACCA
*
1304 TCACCTCCAATGAACCAACCT
1 TCACCTCCAATGAACCAACCA
1325 TCACCTCCA
1 TCACCTCCA
1334 CCTTTTTCAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.41, G:0.06, T:0.18
Consensus pattern (21 bp):
TCACCTCCAATGAACCAACCA
Found at i:1323 original size:129 final size:129
Alignment explanation
Indices: 1177--1439 Score: 465
Period size: 129 Copynumber: 2.0 Consensus size: 129
1167 CACCTTTCTT
*
1177 ACCTCCAATGAACCAACCTTCACCTCCACCTTTCTCACCACCAATGAACGAACCATCACCTCCAC
1 ACCTCCAATGAACCAACCTTCACCTCCACCTTTCTCACCACCAATGAACGAACCATCACATCCAC
* *
1242 CCCTGTCACCTCCAATGAAACAACCTTCATCTCCACCATT-CTCACCACCAATGAATGAACCATC
66 CCCTGTCACCTCCAATGAAACAACCTTCACCTCCACC-TTACTCACCACCAATGAACGAACCATC
*
1306 ACCTCCAATGAACCAACCTTCACCTCCACCTTTTTCACCACCAATGAACGAACCATCACATCCAC
1 ACCTCCAATGAACCAACCTTCACCTCCACCTTTCTCACCACCAATGAACGAACCATCACATCCAC
*
1371 CCCTGTCACCTCCAATGAACCAACCTTCACCTCCACCTTACTCACCACCAATGAACGAACCATC
66 CCCTGTCACCTCCAATGAAACAACCTTCACCTCCACCTTACTCACCACCAATGAACGAACCATC
1435 ACCTC
1 ACCTC
1440 AACCTTTCTC
Statistics
Matches: 128, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
128 2 0.02
129 126 0.98
ACGTcount: A:0.31, C:0.44, G:0.05, T:0.20
Consensus pattern (129 bp):
ACCTCCAATGAACCAACCTTCACCTCCACCTTTCTCACCACCAATGAACGAACCATCACATCCAC
CCCTGTCACCTCCAATGAAACAACCTTCACCTCCACCTTACTCACCACCAATGAACGAACCATC
Found at i:1344 original size:36 final size:36
Alignment explanation
Indices: 1304--1588 Score: 347
Period size: 36 Copynumber: 7.9 Consensus size: 36
1294 GAATGAACCA
*
1304 TCACCTCCAATGAACCAACCTTCACCTCCACCTTTT
1 TCACCTCCAATGAACCAACCTTCACCTCCACCTTTC
* * * * ** *
1340 TCACCACCAATGAACGAACCATCACATCCACCCCTG
1 TCACCTCCAATGAACCAACCTTCACCTCCACCTTTC
*
1376 TCACCTCCAATGAACCAACCTTCACCTCCACCTTAC
1 TCACCTCCAATGAACCAACCTTCACCTCCACCTTTC
* * * *
1412 TCACCACCAATGAACGAACCATCACCTCAACCTTTC
1 TCACCTCCAATGAACCAACCTTCACCTCCACCTTTC
* * *
1448 TCATCTCCAATGGACCAACCTTTACCTCCACCTTTC
1 TCACCTCCAATGAACCAACCTTCACCTCCACCTTTC
*
1484 TCACCTCCAAT-AGACCAACCTTCACCTCCATCTTTC
1 TCACCTCCAATGA-ACCAACCTTCACCTCCACCTTTC
* * * * * *
1520 TCACCACCAAAGAACGAACCATCACCTCCACCCTTG
1 TCACCTCCAATGAACCAACCTTCACCTCCACCTTTC
1556 TCACCTCCAATGAACCAACCTTCACCTCCACCT
1 TCACCTCCAATGAACCAACCTTCACCTCCACCT
1589 CCACCTTCAG
Statistics
Matches: 204, Mismatches: 43, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
36 203 1.00
37 1 0.00
ACGTcount: A:0.28, C:0.45, G:0.05, T:0.22
Consensus pattern (36 bp):
TCACCTCCAATGAACCAACCTTCACCTCCACCTTTC
Found at i:1641 original size:45 final size:45
Alignment explanation
Indices: 1586--1809 Score: 340
Period size: 45 Copynumber: 4.8 Consensus size: 45
1576 TTCACCTCCA
*
1586 CCTCCACCTTCAGCTCTATCACCAAGGAGGACACCACCCCCACCG
1 CCTCCACCTTCAGCTCCATCACCAAGGAGGACACCACCCCCACCG
*
1631 CCTCCGCCTTCAGCTCCATCACCAAGGAGGACACCACCCCCACCG
1 CCTCCACCTTCAGCTCCATCACCAAGGAGGACACCACCCCCACCG
* *
1676 CCTCCACCTTCAGCTCCATCACCAAGAAGGACACCACCACCACCACCACCA
1 CCTCCACCTTCAGCTCCATCACCAAGGAGG--A-CACCA-C-CC-CCACCG
*
1727 CCTCCACCTTCAGCTCCATCACCAAGGAGGACACCACCACCACCG
1 CCTCCACCTTCAGCTCCATCACCAAGGAGGACACCACCCCCACCG
*
1772 CCTCCACCTTCAACTCCATCACCAAGGAGGACACCACC
1 CCTCCACCTTCAGCTCCATCACCAAGGAGGACACCACC
1810 ACCTCCACCA
Statistics
Matches: 164, Mismatches: 9, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
45 113 0.69
46 1 0.01
47 2 0.01
48 10 0.06
49 2 0.01
50 2 0.01
51 34 0.21
ACGTcount: A:0.27, C:0.50, G:0.12, T:0.12
Consensus pattern (45 bp):
CCTCCACCTTCAGCTCCATCACCAAGGAGGACACCACCCCCACCG
Found at i:1744 original size:96 final size:95
Alignment explanation
Indices: 1586--1822 Score: 367
Period size: 96 Copynumber: 2.5 Consensus size: 95
1576 TTCACCTCCA
* * *
1586 CCTCCACCTTCAGCTCTATCACCAAGGAGG--A-CACCA-CCC-CCACCGCCTCCGCCTTCAGCT
1 CCTCCACCTTCAGCTCCATCACCAAGGAGGACACCACCACCCCACCACCACCTCCACCTTCAGCT
*
1646 CCATCACCAAGGAGGACACCACCCCCACCG
66 CCATCACCAAGGAGGACACCACCACCACCG
*
1676 CCTCCACCTTCAGCTCCATCACCAAGAAGGACACCACCACCACCACCACCACCTCCACCTTCAGC
1 CCTCCACCTTCAGCTCCATCACCAAGGAGGACACCACCACC-CCACCACCACCTCCACCTTCAGC
1741 TCCATCACCAAGGAGGACACCACCACCACCG
65 TCCATCACCAAGGAGGACACCACCACCACCG
*
1772 CCTCCACCTTCAACTCCATCACCAAGGAGGACACCACCACCTCCACCACCA
1 CCTCCACCTTCAGCTCCATCACCAAGGAGGACACCACCACC-CCACCACCA
1823 AGGACACATT
Statistics
Matches: 133, Mismatches: 8, Indels: 6
0.90 0.05 0.04
Matches are distributed among these distances:
90 28 0.21
92 1 0.01
93 5 0.04
94 1 0.01
95 2 0.02
96 96 0.72
ACGTcount: A:0.27, C:0.50, G:0.11, T:0.11
Consensus pattern (95 bp):
CCTCCACCTTCAGCTCCATCACCAAGGAGGACACCACCACCCCACCACCACCTCCACCTTCAGCT
CCATCACCAAGGAGGACACCACCACCACCG
Done.