Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2011
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: 12109
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Found at i:2837 original size:10 final size:11
Alignment explanation
Indices: 2804--2838 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
2794 TCAACCTTTT
2804 TTTTATCTTGA
1 TTTTATCTTGA
2815 TTTTATCTTGA
1 TTTTATCTTGA
2826 TTTTAT-TTGA
1 TTTTATCTTGA
2836 TTT
1 TTT
2839 CAATATCTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 7 0.29
11 17 0.71
ACGTcount: A:0.17, C:0.06, G:0.09, T:0.69
Consensus pattern (11 bp):
TTTTATCTTGA
Found at i:3526 original size:40 final size:40
Alignment explanation
Indices: 3481--3792 Score: 292
Period size: 40 Copynumber: 7.7 Consensus size: 40
3471 GTTTTAGTCT
*
3481 GCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCT
1 GCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCC
* * * *
3521 ACTCCACTACTGCTTAGGG-GAATAAGATCTGTGGTTCTG-TCT
1 GCTCCACTACTGCTTAGGGAG-ATAAGA-CT-T-GATGTGATCC
* * * * *
3563 GCTCCACTATTGCTTGGGGAGATAAGACTTGAAGCGATCT
1 GCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCC
* * *
3603 GCTCCACTATTGCTTAGGGAGATAAGATCTGTGGTTTTG-TCC
1 GCTCCACTACTGCTTAGGGAGATAAGA-CT-T-GATGTGATCC
* *
3645 GCTCCGCTACTGCTTAGGGAGATAAGACTTGATGCGATCC
1 GCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCC
* * *
3685 GCTCCACTATTGCTTAGGGA-ATAAGATCTGTGGTTTTG-TCC
1 GCTCCACTACTGCTTAGGGAGATAAGA-CT-T-GATGTGATCC
* * **
3726 GCTCCGCTACTACTTAGGGAGATAAGACTTGATACGATCC
1 GCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCC
*
3766 GCTCCACTATTGCTTAGGGAGATAAGA
1 GCTCCACTACTGCTTAGGGAGATAAGA
3793 TCTGTGGTTT
Statistics
Matches: 222, Mismatches: 35, Indels: 30
0.77 0.12 0.10
Matches are distributed among these distances:
39 15 0.07
40 106 0.48
41 31 0.14
42 63 0.28
43 7 0.03
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.30
Consensus pattern (40 bp):
GCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCC
Found at i:3565 original size:82 final size:82
Alignment explanation
Indices: 3462--3803 Score: 508
Period size: 82 Copynumber: 4.2 Consensus size: 82
3452 CCATGGGATG
* * * **
3462 AGATTTGTGGTTTTAGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCTACTCCA
1 AGATCTGTGGTTTT-GTCCGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCCGCTCCA
*
3527 CTACTGCTTAGGG-GAATA
65 CTATTGCTTAGGGAG-ATA
* * * * * *
3545 AGATCTGTGGTTCTGTCTGCTCCACTATTGCTTGGGGAGATAAGACTTGAAGCGATCTGCTCCAC
1 AGATCTGTGGTTTTGTCCGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCCGCTCCAC
3610 TATTGCTTAGGGAGATA
66 TATTGCTTAGGGAGATA
*
3627 AGATCTGTGGTTTTGTCCGCTCCGCTACTGCTTAGGGAGATAAGACTTGATGCGATCCGCTCCAC
1 AGATCTGTGGTTTTGTCCGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCCGCTCCAC
3692 TATTGCTTAGGGA-ATA
66 TATTGCTTAGGGAGATA
* * *
3708 AGATCTGTGGTTTTGTCCGCTCCGCTACTACTTAGGGAGATAAGACTTGATACGATCCGCTCCAC
1 AGATCTGTGGTTTTGTCCGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCCGCTCCAC
3773 TATTGCTTAGGGAGATA
66 TATTGCTTAGGGAGATA
3790 AGATCTGTGGTTTT
1 AGATCTGTGGTTTT
3804 CACTCTATTC
Statistics
Matches: 240, Mismatches: 17, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
81 79 0.33
82 148 0.62
83 13 0.05
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.32
Consensus pattern (82 bp):
AGATCTGTGGTTTTGTCCGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCCGCTCCAC
TATTGCTTAGGGAGATA
Found at i:3775 original size:163 final size:165
Alignment explanation
Indices: 3462--3803 Score: 528
Period size: 163 Copynumber: 2.1 Consensus size: 165
3452 CCATGGGATG
* * * *
3462 AGATTTGTGGTTTTAGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTGATCTACTCCA
1 AGATCTGTGGTTTTAGTCCGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCCACTCCA
* * * *
3527 CTACTGCTTAGGGGAATAAGATCTGTGGTTCTGTCTGCTCCACTATTGCTTGGGGAGATAAGACT
66 CTACTGCTTAGGGGAATAAGATCTGTGGTTCTGTCCGCTCCACTACTACTTAGGGAGATAAGACT
*
3592 TGAAGCGATCTGCTCCACTATTGCTTAGGGAGATA
131 TGAAGCGATCCGCTCCACTATTGCTTAGGGAGATA
* *
3627 AGATCTGTGGTTTT-GTCCGCTCCGCTACTGCTTAGGGAGATAAGACTTGATGCGATCCGCTCCA
1 AGATCTGTGGTTTTAGTCCGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCCACTCCA
* * *
3691 CTATTGCTTA-GGGAATAAGATCTGTGGTTTTGTCCGCTCCGCTACTACTTAGGGAGATAAGACT
66 CTACTGCTTAGGGGAATAAGATCTGTGGTTCTGTCCGCTCCACTACTACTTAGGGAGATAAGACT
3755 TGATA-CGATCCGCTCCACTATTGCTTAGGGAGATA
131 TGA-AGCGATCCGCTCCACTATTGCTTAGGGAGATA
3790 AGATCTGTGGTTTT
1 AGATCTGTGGTTTT
3804 CACTCTATTC
Statistics
Matches: 162, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
163 94 0.58
164 55 0.34
165 13 0.08
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.32
Consensus pattern (165 bp):
AGATCTGTGGTTTTAGTCCGCTCCACTACTGCTTAGGGAGATAAGACTTGATGCGATCCACTCCA
CTACTGCTTAGGGGAATAAGATCTGTGGTTCTGTCCGCTCCACTACTACTTAGGGAGATAAGACT
TGAAGCGATCCGCTCCACTATTGCTTAGGGAGATA
Found at i:4107 original size:44 final size:45
Alignment explanation
Indices: 3959--4464 Score: 473
Period size: 44 Copynumber: 11.6 Consensus size: 45
3949 TGTCAAATAC
* * * *
3959 GACAA-ATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAA
1 GACAAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAA
* * * *
4003 GACAAGATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAA
1 GACAAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAA
* * *
4048 GACAAGATCTG-TATCTTGGATCCACTTC-CTATCAATATAGGAA
1 GACAAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAA
* * * * * *
4091 GATAGGACCTGCTATCTTCGATCTACTTCAC-GCCAATACATGAA
1 GACAAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAA
* * * * *
4135 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAA
1 GACAAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAA
* *
4180 GACAAGATCTGC-ATCGTCGATCCACTTC-CTACCAATATAGG-A
1 GACAAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAA
** * * * *
4222 -ACCGGACCTGCTATCTTCGATCTACTTCAC-GCCAATACATGAA
1 GACAAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAA
* * * *
4265 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAA-AT-GGAA
1 GACAAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAA
*
4308 GACAAGATCTGC-ATCTTCGATCCACTTC-CTACCAATATAGGAA
1 GACAAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAA
* * * * * *
4351 GATAGGATCTGCTACCTTCGATCTACTTCAC-GCCAATACATGAA
1 GACAAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAA
* * * * * *
4395 GATAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAA
1 GACAAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAA
* *
4440 GACAAGATCTGCAATCTTCAATCTA
1 GACAAGATCTGCTATCTTCGATCTA
4465 TTCCACTGCC
Statistics
Matches: 374, Mismatches: 74, Indels: 27
0.79 0.16 0.06
Matches are distributed among these distances:
41 14 0.04
42 38 0.10
43 61 0.16
44 155 0.41
45 106 0.28
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (45 bp):
GACAAGATCTGCTATCTTCGATCTACTTCACTACCAATATAGGAA
Found at i:4284 original size:130 final size:132
Alignment explanation
Indices: 3966--4458 Score: 778
Period size: 130 Copynumber: 3.8 Consensus size: 132
3956 TACGACAAAT
* * * *** *
3966 CTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTTTCTTCGATCTACTT
1 CTGCTATCTTCGATCTACTTCA-CGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTT
* * * * *
4031 CACCACCAGTATGGGAAGACAAGATCTGTATCTTGGATCCACTTCCTATCAATATAGGAAGATAG
65 CGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAG
4096 GAC
130 GAC
4099 CTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
1 CTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
* **
4164 GCCACCAATATGGGAAGACAAGATCTGCATCGTCGATCCACTTCCTACCAATATAGG-A-ACCGG
66 GCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGG
4227 AC
131 AC
4229 CTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
1 CTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
4294 GCCACCAA-AT-GGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGG
66 GCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGG
*
4357 AT
131 AC
* *
4359 CTGCTACCTTCGATCTACTTCACGCCAATACATGAAGATAAGATCTGCTTTCTGCGATCTACTTC
1 CTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
4424 GCCACCAATATGGGAAGACAAGATCTGCAATCTTC
66 GCCACCAATATGGGAAGACAAGATCTGC-ATCTTC
4459 AATCTATTCC
Statistics
Matches: 334, Mismatches: 21, Indels: 10
0.92 0.06 0.03
Matches are distributed among these distances:
128 44 0.13
129 3 0.01
130 153 0.46
131 3 0.01
132 104 0.31
133 27 0.08
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (132 bp):
CTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTC
GCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGG
AC
Found at i:4579 original size:131 final size:133
Alignment explanation
Indices: 4436--4724 Score: 455
Period size: 131 Copynumber: 2.2 Consensus size: 133
4426 CACCAATATG
*
4436 GGAAGACAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATACA-GGAGATAGAGTTATC-GC
1 GGAAGGCAAGATCTGCAATCTTCAATCTA-TCCACTGCCAAATACAGGGAGATAGAGTTATCGGC
4499 TTCAATCTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCC-T-TTCGATCTGCTTCGCTG-CA
65 TTCAATCTACTCCACTGTAGT--CAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCA
4561 AATACA
128 AATACA
*
4567 GGAAGGCAAGATCTGCAATCTTCAATCTATCCACTGCCAGATACAGGGAGATAGAGTTATCGGCT
1 GGAAGGCAAGATCTGCAATCTTCAATCTATCCACTGCCAAATACAGGGAGATAGAGTTATCGGCT
* *
4632 TCAATGTACTCCACTGTTGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAAT
66 TCAATCTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAAT
4697 ACA
131 ACA
*
4700 GGAAAGCAAGATCTG-ATATCTTCAA
1 GGAAGGCAAGATCTGCA-ATCTTCAA
4725 CCAGCTCTGC
Statistics
Matches: 147, Mismatches: 5, Indels: 10
0.91 0.03 0.06
Matches are distributed among these distances:
130 34 0.23
131 44 0.30
132 39 0.27
133 30 0.20
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (133 bp):
GGAAGGCAAGATCTGCAATCTTCAATCTATCCACTGCCAAATACAGGGAGATAGAGTTATCGGCT
TCAATCTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAAT
ACA
Found at i:4876 original size:42 final size:42
Alignment explanation
Indices: 4830--4963 Score: 105
Period size: 42 Copynumber: 3.1 Consensus size: 42
4820 CAAACGAGAT
4830 GGCAAGGTTTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAA
1 GGCAAGGTTTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAA
* * * * * * * * *
4872 GGCAAGATCTGCTATCTTCAACCAGC-TCTACT-ACAA-AC-GAGAGT
1 GGCAAGGT-T--TGTCTTCGATCTGCTTC-GCTGTCAATGCAG-GA-A
4916 GGCAAGGTTTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAA
1 GGCAAGGTTTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAA
4958 GGCAAG
1 GGCAAG
4964 ATCTGATAAC
Statistics
Matches: 64, Mismatches: 18, Indels: 20
0.63 0.18 0.20
Matches are distributed among these distances:
41 12 0.19
42 19 0.30
43 8 0.12
44 13 0.20
45 12 0.19
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (42 bp):
GGCAAGGTTTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAA
Found at i:4955 original size:86 final size:86
Alignment explanation
Indices: 4672--5017 Score: 529
Period size: 86 Copynumber: 4.1 Consensus size: 86
4662 AAATCTGCCA
* * * *
4672 TCTTCGATCTGCTTCGCTGCCAAATACAGGAAAGCAAGATCTGATATCTTCAACCAGCTCTGCTA
1 TCTTCGATCTGCTTCGCTGTC-AATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTACTA
*
4737 CAAACGAG-G-AGCAAGGTTTG
65 CAAACGAGAGTGGCAAGGTTTG
* *
4757 TCTTCGATCTGCTTCGCTGTCAGTGCAGGAA-GCAAGATCTGCTATCTTCAACCAGCTCTACTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTACTAC
4821 AAACGAGA-TGGCAAGGTTTG
66 AAACGAGAGTGGCAAGGTTTG
*
4841 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCTACTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTACTAC
4906 AAACGAGAGTGGCAAGGTTTG
66 AAACGAGAGTGGCAAGGTTTG
* *
4927 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATAACTTCAACCAGCTCTGCTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTACTAC
* * * *
4992 GACCGAGAGAGGCAAGGTTTA
66 AAACGAGAGTGGCAAGGTTTG
5013 TCTTC
1 TCTTC
5018 AATTTTTACT
Statistics
Matches: 243, Mismatches: 14, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
83 38 0.16
84 48 0.20
85 61 0.25
86 96 0.40
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (86 bp):
TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTACTAC
AAACGAGAGTGGCAAGGTTTG
Found at i:9085 original size:19 final size:20
Alignment explanation
Indices: 9061--9104 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
9051 CGTGAAAGTC
* *
9061 TAATGCATATG-ATGCAATG
1 TAATGCAAATGCATGAAATG
9080 TAATGCAAATGCATGAAATG
1 TAATGCAAATGCATGAAATG
9100 -AATGC
1 TAATGC
9105 CAAAAGAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.27
Consensus pattern (20 bp):
TAATGCAAATGCATGAAATG
Done.