Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1161
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: 2549
ACGTcount: A:0.21, C:0.19, G:0.15, T:0.25
Warning! 503 characters in sequence are not A, C, G, or T
Found at i:243 original size:132 final size:132
Alignment explanation
Indices: 6--1081 Score: 1292
Period size: 132 Copynumber: 8.2 Consensus size: 132
1 CTGCA
* * * * * * *
6 GCTTAGGGAGATTGGACTAATTGCTTAAATCTGCTTTTCCACTATCTTGGGAGGATAAGATTCAC
1 GCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCAC
* * *
71 CATCTTCGATCCGCTCCAC-AACTGCTTAGGGTAACAGAATCTGCAATC-TCTAACCTACTCCAC
66 CATCTTCGATCTGCTCCACTATC-GCTTAGGGTGACAGAATCTGCAATCTTC-AACCTACTCCAC
134 TACT
129 TACT
138 GCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCAC
1 GCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCAC
* *
203 AATCTTCGATCTGCTCCACTATCGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACCA
66 CATCTTCGATCTGCTCCACTATCGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTA
*
268 GT
131 CT
* * * * *
270 GCTTAGGGTGGTAGGACTAATGACTTAAATATACTTCTCCACTGTATTGGGAAGATAAGATTCAT
1 GCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCAC
* * *
335 CATCTTCGATCTGCTGCACTACATC-C-TAGGGTGACAGAATTTGCAATCTTCAGCCTACTCCAC
66 CATCTTCGATCTGCTCCACT--ATCGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCAC
398 TACT
129 TACT
* * * * *
402 GCTGAGGGAGATAAGACTAAGGGCTTAAATCTGCTTCTCCACTGCATTGGGAAGATAAGATTCAC
1 GCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCAC
* * * * **
467 CATCTTCGATCTCCTCCACTATTGCTTAGGCTTACAGAATCTATAATCTTCAACCTACTCCACTA
66 CATCTTCGATCTGCTCCACTATCGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTA
532 CT
131 CT
* * * *
534 GCTGAGGGTGATGGGACTAATTGCTTAAATCTGCTTCTCCACTGTATTGGTAAGATAAGATTCAC
1 GCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCAC
* * * * * * * *
599 CATCTTCGATCTCCTCCACTATTGCTTAGGCTTACAGAATCTGTAATCTTCAGCCTTCTCTACTA
66 CATCTTCGATCTGCTCCACTATCGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTA
664 CT
131 CT
* * * *
666 GCTGAGGGTGATGGGACTAATTGCTTAAATCTGCTTCTCCACTGTATTGGTAAGATAAGATTCAC
1 GCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCAC
* * * * * *
731 CATCTTCGATCTCCTCCACTATTGCTTAGGCT---A-AATCAGCATTCTTTAACCTACTCCACTA
66 CATCTTCGATCTGCTCCACTATCGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTA
792 CT
131 CT
* * ** * *
794 GCTCT-GGGAGATTGGACTAATGGCTTAAATCTATTTCTCTACTGTATTCGGAAGATAAGATTCA
1 GCT-TAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCA
* * * * *
858 CCATATTTGATCTACTCTACTA-CTGCTTAGTGTGACAGAATCTGCAATCTTCAACCTACTCCAC
65 CCATCTTCGATCTGCTCCACTATC-GCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCAC
*
922 TACA
129 TACT
* * * * * * * *
926 GCTTAGGGAGATTGGACTAATGGCTTAAATCTACTTCTTCACTATTTTGAGAAGATAAGATCCAC
1 GCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCAC
* * * * * *
991 CATCTTCGATCCGCTCTAC-AACTGCTTAGGGTAACAGAATTTGCAGTCTTCAACCTACTCCACT
66 CATCTTCGATCTGCTCCACTATC-GCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACT
1055 ACT
130 ACT
1058 GCTTAGGGTGATAGGACTAATGGC
1 GCTTAGGGTGATAGGACTAATGGC
1082 NNNNNNNNNN
Statistics
Matches: 830, Mismatches: 100, Indels: 28
0.87 0.10 0.03
Matches are distributed among these distances:
128 102 0.12
129 1 0.00
130 2 0.00
131 4 0.00
132 713 0.86
133 5 0.01
134 3 0.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.32
Consensus pattern (132 bp):
GCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCAC
CATCTTCGATCTGCTCCACTATCGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTA
CT
Found at i:1829 original size:132 final size:132
Alignment explanation
Indices: 1585--2549 Score: 1157
Period size: 132 Copynumber: 7.3 Consensus size: 132
1575 NNNNNNNNNN
* * *
1585 ACTACTGCTGAGGGTGATGGGACTAATTGCTTAAATCTGCTTCTCCACTGTATTGGTAAGATAAG
1 ACTACTGCTGAGGGAGATAGGACTAATTGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAG
* * * * * * *
1650 ATTCACCATCTTCGATCTCCTCCACTATTGCTTAGGCTTACAGAATCTGTAATCTTCAGCCTTCT
66 ATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACT
*
1715 CT
131 CC
* *
1717 ACTACTGCTGAGGGTGATGGGACTAATTGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAG
1 ACTACTGCTGAGGGAGATAGGACTAATTGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAG
* * * * * *
1782 ATTCATCA-CAGTCGATCTGCACCACTACTG-TTCAGGGTGACAAAATCTGCAATTTTTAACCTA
66 ATTCACCATC-TTCGATCTGCTCCACTACTGCTT-AGGGTGACAGAATCTGCAATCTTCAACCTA
1845 CTCC
129 CTCC
* * * * * * * *
1849 ACTACTACTCAAGGAGATTGGACTAATCGCTTAAATCTACTTCTCCACAGTATTTGGAAGATAAG
1 ACTACTGCTGAGGGAGATAGGACTAATTGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAG
* * * ** * * *
1914 TTTCACCATCTTCAATCTACTCCACTACTGCTTTTGGTGATAGGATCTGCAATCGTCAACCTACT
66 ATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACT
1979 CC
131 CC
* * * * * * * *
1981 ACTGCAGCTTAGGGAGATTGGACTAATTGCTTAAATCTGCTTCTCCACTATCTTGAGAGGATAAG
1 ACTACTGCTGAGGGAGATAGGACTAATTGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAG
* * * * *
2046 ATTCACCATCTTCGATCCGCTCCACAACTGCTTAGGGTAATAGAATCTGCAATCTCCAACCTACT
66 ATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACT
2111 CC
131 CC
* *
2113 ACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAG
1 ACTACTGCTGAGGGAGATAGGACTAATTGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAG
*
2178 ATTCACAATCTTCGATCTGCTCCACTA-TCGCTTAGGGTGACAGAATCTGCAATCTTCAACCTAC
66 ATTCACCATCTTCGATCTGCTCCACTACT-GCTTAGGGTGACAGAATCTGCAATCTTCAACCTAC
2242 TCC
130 TCC
* * * * * * * * *
2245 ACCAGTGCTTAGGGTGGTAGGACTAA-TGACTTAATTATACTTCTCCACTGTATTGGGAATATAA
1 ACTACTGCTGAGGGAGATAGGACTAATTG-CTTAAATCTGCTTCTCCACTGTATTGGGAAGATAA
* * * *
2309 GATTCATCATCTTCGATCTGCTGCACTACAT-CCTAGGGTGACAGAATCTGCAATCTTCAGCCTA
65 GATTCACCATCTTCGATCTGCTCCACTAC-TGCTTAGGGTGACAGAATCTGCAATCTTCAACCTA
2373 CTCC
129 CTCC
** *
2377 ACTACTGCTGAGGGAGATAGGACTAAGGGCTTAAATCTGCTTCTCCACTGCATTGGGAAGATAAG
1 ACTACTGCTGAGGGAGATAGGACTAATTGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAG
* * * * * * *
2442 ATTCACCATCTTCGATCTCCTCCACTATTGCTTAGGCTTACAGAATCTGTAATCTTCAGCCTTCT
66 ATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACT
*
2507 CT
131 CC
* *
2509 ACTACTGCTGAGGGTGATGGGACTAATTGCTTAAATCTGCT
1 ACTACTGCTGAGGGAGATAGGACTAATTGCTTAAATCTGCT
Statistics
Matches: 708, Mismatches: 115, Indels: 20
0.84 0.14 0.02
Matches are distributed among these distances:
131 6 0.01
132 697 0.98
133 4 0.01
134 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.31
Consensus pattern (132 bp):
ACTACTGCTGAGGGAGATAGGACTAATTGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAG
ATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACT
CC
Done.