Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Tc09v2_t019170.1
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: 1792
ACGTcount: A:0.27, C:0.39, G:0.08, T:0.26
Found at i:442 original size:30 final size:30
Alignment explanation
Indices: 408--470 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
398 CACATCTCCT
* * *
408 CCTCCATATGTAGATAAGTCTCCTCCACCA
1 CCTCCATATGTAGACAAATCTCCACCACCA
*
438 CCTCCATATGTATACAAATCTCCACCACCA
1 CCTCCATATGTAGACAAATCTCCACCACCA
468 CCT
1 CCT
471 GTTCACTCAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.29, C:0.40, G:0.06, T:0.25
Consensus pattern (30 bp):
CCTCCATATGTAGACAAATCTCCACCACCA
Found at i:513 original size:30 final size:30
Alignment explanation
Indices: 486--577 Score: 121
Period size: 30 Copynumber: 3.1 Consensus size: 30
476 CTCACCACTT
* *
486 CCTCCTTACGTATACAAATCCCCACCACCA
1 CCTCCTTACATATACAAGTCCCCACCACCA
* *
516 CCTCCTTATATATACAAGTCCCCATCACCA
1 CCTCCTTACATATACAAGTCCCCACCACCA
* * *
546 CCTACTTACCTATACAAGTCCCCTCCACCA
1 CCTCCTTACATATACAAGTCCCCACCACCA
576 CC
1 CC
578 AGTCCACTCT
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.28, C:0.46, G:0.03, T:0.23
Consensus pattern (30 bp):
CCTCCTTACATATACAAGTCCCCACCACCA
Found at i:548 original size:108 final size:105
Alignment explanation
Indices: 423--652 Score: 235
Period size: 108 Copynumber: 2.2 Consensus size: 105
413 ATATGTAGAT
* * * ** * * * *
423 AAGTCTCCTCCACCACCTCCATATGTATACAAATCTCCACCACCACCTGTTCACTCACCACTTCC
1 AAGTCCCCACCACCACCTACATACCTATACAAATCCCCACCACCACCAGTCCACTCACCACCTCC
488 TCCTTACGTATACAAATCCCCACCACCACCTCCTTATATATAC
66 TCCTTACGTATACAAAT--CC-CCACCACCTCCTTATATATAC
* * * * * *
531 AAGTCCCCATCACCACCTACTTACCTATACAAGTCCCCTCCACCACCAGTCCACTCTCCTCCTCC
1 AAGTCCCCACCACCACCTACATACCTATACAAATCCCCACCACCACCAGTCCACTCACCACCTCC
* * * * * * *
596 TCCTTATGTGTACAAGTCCCCACTACCTCCTTATCTCTAT
66 TCCTTACGTATACAAATCCCCACCACCTCCTTATATATAC
636 AAGTCCCCACCACCACC
1 AAGTCCCCACCACCACC
653 AATACATTCA
Statistics
Matches: 99, Mismatches: 23, Indels: 3
0.79 0.18 0.02
Matches are distributed among these distances:
105 33 0.33
106 2 0.02
108 64 0.65
ACGTcount: A:0.25, C:0.45, G:0.05, T:0.25
Consensus pattern (105 bp):
AAGTCCCCACCACCACCTACATACCTATACAAATCCCCACCACCACCAGTCCACTCACCACCTCC
TCCTTACGTATACAAATCCCCACCACCTCCTTATATATAC
Found at i:624 original size:27 final size:27
Alignment explanation
Indices: 594--645 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
584 CTCTCCTCCT
* *
594 CCTCCTTATGTGTACAAGTCCCCACTA
1 CCTCCTTATCTCTACAAGTCCCCACTA
*
621 CCTCCTTATCTCTATAAGTCCCCAC
1 CCTCCTTATCTCTACAAGTCCCCAC
646 CACCACCAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.21, C:0.40, G:0.08, T:0.31
Consensus pattern (27 bp):
CCTCCTTATCTCTACAAGTCCCCACTA
Found at i:651 original size:75 final size:74
Alignment explanation
Indices: 511--772 Score: 238
Period size: 75 Copynumber: 3.4 Consensus size: 74
501 AAATCCCCAC
* * * *
511 CACCACCTCCTTATATATACAAGTCCCCATCACCACCTACTTACCTATACAAGTCCCCTCCACCA
1 CACCTCCTCCTTATAT-TACAAGT-CCC--CACCACCTCCTTATCTATACAAGTCCCCACCACCA
* *
576 CCAGTCCACTC-T
62 CCAATACACTCAT
* * * * *
588 CCTCCTCCTCCTTATGTGTACAAGTCCCCACTACCTCCTTATCTCTATAAGTCCCCACCACCACC
1 -CACCTCCTCCTTATAT-TACAAGTCCCCACCACCTCCTTATCTATACAAGTCCCCACCACCACC
*
653 AATACATTCAT
64 AATACACTCAT
* * * * *
664 CACCTCTTCCTTACCATTACAAGTCCCCACCACTTCCTTATGTATACAAGTCTCCACCACCACCA
1 CACCTCCTCCTTA-TATTACAAGTCCCCACCACCTCCTTATCTATACAAGTCCCCACCACCACCA
* * *
729 ACACATTCAC
65 ATACACTCAT
* * *
739 CACCTCATCCTTATCTATACAAGTCCCCTCCACC
1 CACCTCCTCCTTATAT-TACAAGTCCCCACCACC
773 ACCAGTCCAC
Statistics
Matches: 151, Mismatches: 30, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
74 1 0.01
75 125 0.83
76 2 0.01
77 3 0.02
78 20 0.13
ACGTcount: A:0.26, C:0.44, G:0.04, T:0.26
Consensus pattern (74 bp):
CACCTCCTCCTTATATTACAAGTCCCCACCACCTCCTTATCTATACAAGTCCCCACCACCACCAA
TACACTCAT
Found at i:742 original size:48 final size:48
Alignment explanation
Indices: 698--1463 Score: 572
Period size: 48 Copynumber: 15.8 Consensus size: 48
688 CCCCACCACT
* *
698 TCCTTATGTATACAAGTCTCCACCACCACCAACACATTCACCACCTCA
1 TCCTTATGTATACAAGTCCCCACCACCACCAACACATTCACCACCTCC
* * * * * *
746 TCCTTATCTATACAAGTCCCCTCCACCACCAGTC-CACTT-TCCTCCTCT
1 TCCTTATGTATACAAGTCCCCACCACCACCA-ACACA-TTCACCACCTCC
* * * * * *
794 TCCTTATGTCTATAAGTCCCCACCACCTCCAAAACACTCACCACCACC
1 TCCTTATGTATACAAGTCCCCACCACCACCAACACATTCACCACCTCC
* * *
842 TACTTATGTGTACAAGTCTCCACCACCACCAACACATTCACCACCTCC
1 TCCTTATGTATACAAGTCCCCACCACCACCAACACATTCACCACCTCC
* ** * * * * *
890 TACTTACCTATACAAGTCCCCTCCACCACCAATC-CACTCTCCTCTTCC
1 TCCTTATGTATACAAGTCCCCACCACCACCAA-CACATTCACCACCTCC
* * * * * * * * *
938 TCTTTATGTGTACAAGTTCCCACCACCTCCAAAATACTCACCGCCACC
1 TCCTTATGTATACAAGTCCCCACCACCACCAACACATTCACCACCTCC
**
986 TCCTTATGTATACAAGTCCCCACCACCACCAATGCATTCACCACCTCC
1 TCCTTATGTATACAAGTCCCCACCACCACCAACACATTCACCACCTCC
** * * * ** *
1034 TCCTTACATATACAAGTCACCTCCACCACCTATTCATTCACCGCCTCC
1 TCCTTATGTATACAAGTCCCCACCACCACCAACACATTCACCACCTCC
* * ** ** * *
1082 TCCTTACT-TATATAAGTCCCCTCCTTCACCGGTC-CACTCTCCTCCTCCTCCTTC
1 TCCTTA-TGTATACAAGTCCCCACCACCACC-AACACA-T-T-CACCACCT-C--C
* * * *
1136 TCCTTATGTTTACAAGTCCCCACCACCTCCAAAACATTCACCACCACC
1 TCCTTATGTATACAAGTCCCCACCACCACCAACACATTCACCACCTCC
* * **
1184 TCTTTATGTATACAAGTCTCCACCACCACCAGTACATTCACCACCTCC
1 TCCTTATGTATACAAGTCCCCACCACCACCAACACATTCACCACCTCC
* * * * * *
1232 TCCTTATCTATACAAGTCCCCTCCACCACCAGTC-CATTCTCCTCCTTC
1 TCCTTATGTATACAAGTCCCCACCACCACCA-ACACATTCACCACCTCC
* * * * * * *
1280 TCCTTATGTCTATAAGTCCCCACCGCCTCCAAAACACTCACCACCACC
1 TCCTTATGTATACAAGTCCCCACCACCACCAACACATTCACCACCTCC
* * *
1328 TCCTTATGTATACAAGTCTCCACCACCACCACCTATTTATTCACCACCTCC
1 TCCTTATGTATACAAGTCCCCACCACCACCAAC-A--CATTCACCACCTCC
** * * *
1379 TCCTTACCTATACAAGTCTCCACCACCACCAATACATTCACCACATCC
1 TCCTTATGTATACAAGTCCCCACCACCACCAACACATTCACCACCTCC
* * * * * *
1427 ACCTTATGTTTACAAATCTCCACCTCCACCATCACAT
1 TCCTTATGTATACAAGTCCCCACCACCACCAACACAT
1464 CCTAAGCCTC
Statistics
Matches: 555, Mismatches: 142, Indels: 42
0.75 0.19 0.06
Matches are distributed among these distances:
47 1 0.00
48 465 0.84
49 6 0.01
50 3 0.01
51 51 0.09
52 2 0.00
53 2 0.00
54 25 0.05
ACGTcount: A:0.26, C:0.43, G:0.05, T:0.26
Consensus pattern (48 bp):
TCCTTATGTATACAAGTCCCCACCACCACCAACACATTCACCACCTCC
Found at i:1332 original size:198 final size:193
Alignment explanation
Indices: 794--1433 Score: 572
Period size: 198 Copynumber: 3.3 Consensus size: 193
784 TTCCTCCTCT
* * * * * * * * * *
794 TCCTTATGTCTATAAGTCCCCACCACCTCCAAAACACTCACCACCACCTACTTAT-GTGTACAAG
1 TCCTTATGTATACAAGTCTCCACCACCACCAATACATTCACCACCTCCTCCTTATCATATACAAG
* * * * * * * * *
858 TCTCCACCACCACC-AACACATTCACCACCTCCTACTTACCTATACAAGTCCCCTCCACCACCAA
66 TCACCTCCACCACCTATC-CATTCACCGCCTCCTCCTTACTTATATAAGTCCCCACCGCCACCAA
** * * ** * * * * *
922 TCCACTCTCCTCTTCCTCTTTATGTGTACAAGTTCCCACCACCTCCAAAATACTCACCGCCACC
130 AACACTCACCACCACCTCCTTATGTATACAAGTCCCCACCACCTCCAAAATATTCACCACCACC
* *
986 TCCTTATGTATACAAGTCCCCACCACCACCAATGCATTCACCACCTCCTCCTTA-CATATACAAG
1 TCCTTATGTATACAAGTCTCCACCACCACCAATACATTCACCACCTCCTCCTTATCATATACAAG
* * ** *
1050 TCACCTCCACCACCTATTCATTCACCGCCTCCTCCTTACTTATATAAGTCCCCTCCTTCACCGGT
66 TCACCTCCACCACCTATCCATTCACCGCCTCCTCCTTACTTATATAAGTCCCCACCGCCACC--A
** * * * * * *
1115 CCACTCTCCTCCTCCTCCTTCTCCTTATGTTTACAAGTCCCCACCACCTCCAAAACATTCACCAC
129 AAACACT-CACCACC-AC--CTCCTTATGTATACAAGTCCCCACCACCTCCAAAATATTCACCAC
1180 CACC
190 CACC
* *
1184 TCTTTATGTATACAAGTCTCCACCACCACCAGTACATTCACCACCTCCTCCTTATC-TATACAAG
1 TCCTTATGTATACAAGTCTCCACCACCACCAATACATTCACCACCTCCTCCTTATCATATACAAG
* * * * * *
1248 TCCCCTCCACCACC-AGTCCATTCTCCTCCTTCTCCTTA-TGTCTATAAGTCCCCACCGCCTCCA
66 TCACCTCCACCACCTA-TCCATTCACCGCCTCCTCCTTACT-TATATAAGTCCCCACCGCCACCA
* * **
1311 AAACACTCACCACCACCTCCTTATGTATACAAGTCTCCACCACCACCACCTATTTATTCACCACC
129 AAACACTCACCACCACCTCCTTATGTATACAAG--TCC-CCACCACCTCCAAAATATTCACCACC
*
1376 TCC
191 ACC
** * *
1379 TCCTTACCTATACAAGTCTCCACCACCACCAATACATTCACCACATCCACCTTAT
1 TCCTTATGTATACAAGTCTCCACCACCACCAATACATTCACCACCTCCTCCTTAT
1434 GTTTACAAAT
Statistics
Matches: 367, Mismatches: 67, Indels: 25
0.80 0.15 0.05
Matches are distributed among these distances:
192 119 0.32
193 1 0.00
194 7 0.02
195 83 0.23
196 5 0.01
197 2 0.01
198 149 0.41
199 1 0.00
ACGTcount: A:0.25, C:0.44, G:0.05, T:0.26
Consensus pattern (193 bp):
TCCTTATGTATACAAGTCTCCACCACCACCAATACATTCACCACCTCCTCCTTATCATATACAAG
TCACCTCCACCACCTATCCATTCACCGCCTCCTCCTTACTTATATAAGTCCCCACCGCCACCAAA
ACACTCACCACCACCTCCTTATGTATACAAGTCCCCACCACCTCCAAAATATTCACCACCACC
Found at i:1506 original size:21 final size:22
Alignment explanation
Indices: 1482--1525 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
1472 TCATCCCTCT
*
1482 CATCCCCCTCATCCTAA-ACCC
1 CATCCCCCGCATCCTAAGACCC
1503 CATCCCCCGCATCCTAAGACCC
1 CATCCCCCGCATCCTAAGACCC
1525 C
1 C
1526 TTCAACGCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.23, C:0.57, G:0.05, T:0.16
Consensus pattern (22 bp):
CATCCCCCGCATCCTAAGACCC
Done.