Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2867
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: 52400
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1832 original size:29 final size:29
Alignment explanation
Indices: 1793--1848 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
1783 GGGGTAGTAT
1793 TAATAAAACTAATATGAAAGGAACCTTAG
1 TAATAAAACTAATATGAAAGGAACCTTAG
*
1822 TAATAAAACTAATATGAAATGAACCTT
1 TAATAAAACTAATATGAAAGGAACCTT
1849 GCCTAAGTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.52, C:0.11, G:0.11, T:0.27
Consensus pattern (29 bp):
TAATAAAACTAATATGAAAGGAACCTTAG
Found at i:14975 original size:20 final size:21
Alignment explanation
Indices: 14932--14979 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
14922 ATTTCCTAAC
*
14932 AAAATTTTAATACCATATTAAT
1 AAAA-TTTAATACAATATTAAT
*
14954 AAAATTTAATA-AATATTTAT
1 AAAATTTAATACAATATTAAT
14974 AAAATT
1 AAAATT
14980 ATTTTTGACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 13 0.54
21 7 0.29
22 4 0.17
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (21 bp):
AAAATTTAATACAATATTAAT
Found at i:30340 original size:14 final size:15
Alignment explanation
Indices: 30315--30343 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
30305 GCCGTGAGTA
30315 GAAAAGAAAAAGAAG
1 GAAAAGAAAAAGAAG
30330 GAAAA-AAAAAGAAG
1 GAAAAGAAAAAGAAG
30344 CTCAAGACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (15 bp):
GAAAAGAAAAAGAAG
Found at i:32919 original size:47 final size:47
Alignment explanation
Indices: 32868--32972 Score: 192
Period size: 47 Copynumber: 2.2 Consensus size: 47
32858 TAGTATTAAT
*
32868 TATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAAAGTGTATA
1 TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATA
32915 TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATA
1 TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATA
*
32962 AATGTGATAAG
1 TATGTGATAAG
32973 TCTCGAAGGG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 56 1.00
ACGTcount: A:0.34, C:0.08, G:0.30, T:0.28
Consensus pattern (47 bp):
TATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATA
Found at i:39951 original size:29 final size:28
Alignment explanation
Indices: 39918--39977 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 28
39908 AGCCTGGTTA
39918 TAGTAACTCGCACAAATGCCTTCGGGGCT
1 TAGTAACTCGCACAAATGCCTTC-GGGCT
*
39947 TAGTAACTCGCACCAATGCCTTCGGGCT
1 TAGTAACTCGCACAAATGCCTTCGGGCT
39975 TAG
1 TAG
39978 CCTGGAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 8 0.27
29 22 0.73
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.25
Consensus pattern (28 bp):
TAGTAACTCGCACAAATGCCTTCGGGCT
Found at i:43092 original size:39 final size:39
Alignment explanation
Indices: 42922--43145 Score: 222
Period size: 40 Copynumber: 5.7 Consensus size: 39
42912 TTGAATGCTG
* * *
42922 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGT-ACTAAA
* *
42962 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAGT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAG-TACTAA-A
* * *
43002 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTAAA
* * *
43042 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTATTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTAAA
* *
43081 TCCGGGTTAAGTCCCGAAGGCA-TTGTGTGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTAAA
* *
43120 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
43146 AACGAGGAGC
Statistics
Matches: 156, Mismatches: 20, Indels: 16
0.81 0.10 0.08
Matches are distributed among these distances:
38 7 0.04
39 54 0.35
40 84 0.54
41 11 0.07
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTAAA
Found at i:43167 original size:78 final size:79
Alignment explanation
Indices: 43002--43178 Score: 205
Period size: 78 Copynumber: 2.3 Consensus size: 79
42992 AGATACAAGT
* * * *
43002 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
43067 GTGCGAGTATTAAA
66 GAACGAGGACTAAA
* * * *
43081 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
43145 GAACGAGGAGCTATA
66 GAACGAGGA-CTAAA
*
43160 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
43179 TACGTGATTT
Statistics
Matches: 83, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
78 58 0.70
79 25 0.30
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGGACTAAA
Found at i:50967 original size:77 final size:77
Alignment explanation
Indices: 50830--51050 Score: 248
Period size: 77 Copynumber: 2.8 Consensus size: 77
50820 TTGAATGCTG
* * * * *
50830 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGC-GAGT-ACTAAATCCGGGCTAAG-TCCCGAAGGCATT
*
50894 TGTGCGAGATACAAT
63 TGTGCGAGATACAAA
* *
50909 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGTACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
1 TCCGGGTTAAGTCCCGAAGG-CTTTGTGCGAGTACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
* **
50973 TGCGAGTTTTAAA
65 TGCGAGATACAAA
* * * *
50986 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAG-TACTAAATCCGGGCTAAGTCCCGAAGGCATTTG
51051 AACGAGGAGC
Statistics
Matches: 121, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
76 1 0.01
77 54 0.45
78 48 0.40
79 18 0.15
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (77 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCGAGTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGT
GCGAGATACAAA
Found at i:50976 original size:39 final size:39
Alignment explanation
Indices: 50830--51083 Score: 232
Period size: 39 Copynumber: 6.5 Consensus size: 39
50820 TTGAATGCTG
* * * *
50830 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGT-ACTAAA
** *
50870 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAT
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAG-TACTAAA
*
50909 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTACTAAA
* **
50947 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTACTAAA
*
50986 TCCGGGTTAAGTCCCGAAGGCA-TTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAG-TACTAAA
* * * ** * *
51025 ACCGGGCTATGTCCCGAAGGCATTTGAACGAGGAGCTATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTA-CTAAA
*
51065 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
51084 TACGTGATTT
Statistics
Matches: 176, Mismatches: 29, Indels: 19
0.79 0.13 0.08
Matches are distributed among these distances:
37 3 0.02
38 38 0.22
39 93 0.53
40 33 0.19
41 9 0.05
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTACTAAA
Done.