Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5458.1
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: 23470
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3295 original size:35 final size:35
Alignment explanation
Indices: 3249--3318 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
3239 CTGCCATCGT
3249 ATTTGCTTTAAAAATATGGCGACATTACTTATTTG
1 ATTTGCTTTAAAAATATGGCGACATTACTTATTTG
3284 ATTTGCTTTAAAAATATGGCGACATTACTTATTTG
1 ATTTGCTTTAAAAATATGGCGACATTACTTATTTG
3319 GTGAGAAGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.43
Consensus pattern (35 bp):
ATTTGCTTTAAAAATATGGCGACATTACTTATTTG
Found at i:6735 original size:40 final size:39
Alignment explanation
Indices: 6646--6829 Score: 173
Period size: 39 Copynumber: 4.6 Consensus size: 39
6636 TTGAATGATG
*
6646 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
6684 ATCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGATACTAAT
* * *
6725 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAT
*
6764 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGA-TACTAAT
* *
6803 AACCGGGCTATGTCCTGAAGGCATTTG
1 -TCCGGGCTAAGTCC-GAAGGCATTTG
6830 AACGAGGAGC
Statistics
Matches: 123, Mismatches: 13, Indels: 17
0.80 0.08 0.11
Matches are distributed among these distances:
39 56 0.46
40 55 0.45
41 11 0.09
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:6741 original size:39 final size:41
Alignment explanation
Indices: 6646--6829 Score: 199
Period size: 40 Copynumber: 4.6 Consensus size: 41
6636 TTGAATGATG
*
6646 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGT-ACTAATA
*
6685 TCCGGACTAAGAT-CCGAAGGCATTTGTGCG-AGATACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAAG-TACTAATA
6725 TCCGGGCTAAG-CCCGAAGGCATTTGTGCG-AGTTACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAG-TACTAATA
* *
6764 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATA
* * *
6804 ACCGGGCTATGTCCTGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
6830 AACGAGGAGC
Statistics
Matches: 125, Mismatches: 10, Indels: 19
0.81 0.06 0.12
Matches are distributed among these distances:
39 54 0.43
40 60 0.48
41 11 0.09
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTACTAATA
Found at i:6781 original size:79 final size:81
Alignment explanation
Indices: 6646--6829 Score: 213
Period size: 79 Copynumber: 2.3 Consensus size: 81
6636 TTGAATGATG
6646 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
6709 TGTGCGAGA-TACTA-A
66 TGTGCGA-ATTACTATA
* * **
6724 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAA-ATCCGGGTTAAG-TCCCGAAGGC
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGAC-AATATCCGGACTAAGAT-CCGAAGGC
6785 ATTTGTGCGAATTACTATA
63 ATTTGTGCGAATTACTATA
* * *
6804 ACCGGGCTATGTCCTGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
6830 AACGAGGAGC
Statistics
Matches: 91, Mismatches: 7, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
78 11 0.12
79 58 0.64
80 22 0.24
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACAATATCCGGACTAAGATCCGAAGGCATT
TGTGCGAATTACTATA
Found at i:6851 original size:79 final size:79
Alignment explanation
Indices: 6698--6862 Score: 185
Period size: 79 Copynumber: 2.1 Consensus size: 79
6688 GGACTAAGAT
* ** *
6698 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
*
6763 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
6777 CCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCTGAAGGCATTTGAACGAG-GAG
1 CCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTGA-
* *
6839 CTATATCC-GGTTAAATT
62 CTAAATCCGGGTTAAATC
6856 CCGAAGG
1 CCGAAGG
6863 TACGTGATTT
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
78 3 0.04
79 46 0.63
80 24 0.33
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTGACTAA
ATCCGGGTTAAATC
Found at i:13504 original size:14 final size:14
Alignment explanation
Indices: 13480--13525 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
13470 GCCTAAACTG
*
13480 ACCAATTCATTCAT
1 ACCACTTCATTCAT
*
13494 ACCCCTTCATTCAT
1 ACCACTTCATTCAT
* *
13508 ACCATTTCGTTCAT
1 ACCACTTCATTCAT
13522 ACCA
1 ACCA
13526 TTTCGACCAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.28, C:0.35, G:0.02, T:0.35
Consensus pattern (14 bp):
ACCACTTCATTCAT
Found at i:13526 original size:14 final size:14
Alignment explanation
Indices: 13489--13530 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
13479 GACCAATTCA
** *
13489 TTCATACCCCTTCA
1 TTCATACCATTTCG
13503 TTCATACCATTTCG
1 TTCATACCATTTCG
13517 TTCATACCATTTCG
1 TTCATACCATTTCG
13531 ACCATTCCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.21, C:0.33, G:0.05, T:0.40
Consensus pattern (14 bp):
TTCATACCATTTCG
Found at i:20945 original size:30 final size:30
Alignment explanation
Indices: 20911--21007 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
20901 TAAACTAAAA
20911 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
20941 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
20971 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
21001 TGAGCTA
1 TGAGCTA
21008 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:23202 original size:30 final size:31
Alignment explanation
Indices: 23122--23204 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 31
23112 CTTTTGTTTC
* * *
23122 AATTTCTTTTTCATCTTCTTTTTTACTCTCA
1 AATTTCTTTTTCATTTTCTTTTTCAATCTCA
* *
23153 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTCATTTTCTTTTTCAATCTCA
* *
23182 ATTTTCTTTTTAATTTTCTTTTT
1 AATTTCTTTTTCATTTTCTTTTT
23205 TCTTTTCAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
29 5 0.12
30 31 0.74
31 6 0.14
ACGTcount: A:0.14, C:0.19, G:0.01, T:0.65
Consensus pattern (31 bp):
AATTTCTTTTTCATTTTCTTTTTCAATCTCA
Found at i:23222 original size:12 final size:12
Alignment explanation
Indices: 23207--23237 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
23197 TTCTTTTTTC
23207 TTTTCAAAGGCT
1 TTTTCAAAGGCT
23219 TTTTCAAAGGCT
1 TTTTCAAAGGCT
23231 TTTTCAA
1 TTTTCAA
23238 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:23325 original size:15 final size:15
Alignment explanation
Indices: 23285--23326 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
23275 CTCTTGCCTC
*
23285 TCTTTTCTTTTTATT
1 TCTTTTCTTTTTACT
23300 TCATTTTCTTTTT-CT
1 TC-TTTTCTTTTTACT
23315 TCTTTTGCTTTT
1 TCTTTT-CTTTT
23327 GCTTTTTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 4 0.17
15 10 0.42
16 10 0.42
ACGTcount: A:0.05, C:0.17, G:0.02, T:0.76
Consensus pattern (15 bp):
TCTTTTCTTTTTACT
Found at i:23347 original size:21 final size:19
Alignment explanation
Indices: 23287--23349 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 19
23277 CTTGCCTCTC
23287 TTTTCTTTTTATTTCATTTTCT
1 TTTTC-TTTT-TTT-ATTTTCT
**
23309 TTTTCTTCTTTTGCTTTTGCT
1 TTTTCTT-TTTTTATTTT-CT
23330 TTTTCTTTTCTTTATTTTCT
1 TTTTCTTTT-TTTATTTTCT
23350 CTTTACAAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
20 8 0.24
21 19 0.56
22 7 0.21
ACGTcount: A:0.05, C:0.16, G:0.03, T:0.76
Consensus pattern (19 bp):
TTTTCTTTTTTTATTTTCT
Done.