Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold7143.1
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: 8080
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.32
Warning! 65 characters in sequence are not A, C, G, or T
Found at i:144 original size:46 final size:46
Alignment explanation
Indices: 77--251 Score: 176
Period size: 46 Copynumber: 3.8 Consensus size: 46
67 TGTAACCCGC
* *
77 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTTGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCATTTGCAT
* * * *
123 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCAGATGCCTAGTTACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC-G--GGC-ATTTGCAT
* * * *
173 --TTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCATTTGCAT
* * *
216 CCATAAGTGAAATCGGACTCAACTCAAAGAGTTCGG
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG
252 ATGCTCAACC
Statistics
Matches: 104, Mismatches: 18, Indels: 14
0.76 0.13 0.10
Matches are distributed among these distances:
43 5 0.05
44 2 0.02
45 2 0.02
46 59 0.57
47 27 0.26
48 2 0.02
49 2 0.02
50 5 0.05
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCATTTGCAT
Found at i:192 original size:93 final size:93
Alignment explanation
Indices: 84--255 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
74 CGCCCATAAG
* * * *
84 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAAATCGGACTCAACTCA
*
149 ACGAGTTCAGATGCCTAGTTACATTTCA
66 AAGAGTTCAGATGCCTAGTTACATTTCA
*
177 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAAATCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAAATCGGACTCAACTCA
*
242 AAGAGTTCGGATGC
66 AAGAGTTCAGATGC
256 TCAACCATCC
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAAATCGGACTCAACTCA
AAGAGTTCAGATGCCTAGTTACATTTCA
Found at i:879 original size:74 final size:75
Alignment explanation
Indices: 761--912 Score: 225
Period size: 74 Copynumber: 2.0 Consensus size: 75
751 TCCTTATTCT
* * * * *
761 TATGTTTTACAACATGCTGATCACTTTTCTCTTCTATGGCAACATCAAATTCTCACTCTAACATG
1 TATGTTTTACAACATGATGAGCACTTTTCCCTTCTATGGAAACATCAAATTCTCACTCTAACATA
826 TACTTATGAC
66 TACTTATGAC
* *
836 TATG-TTTATAACATGATGAGCACTTTTCCCTTCTATGGAAACATCAAATTCTCTCTCTAACATA
1 TATGTTTTACAACATGATGAGCACTTTTCCCTTCTATGGAAACATCAAATTCTCACTCTAACATA
*
900 TACTTGTGAC
66 TACTTATGAC
910 TAT
1 TAT
913 TAGGTATTTT
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
74 65 0.94
75 4 0.06
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (75 bp):
TATGTTTTACAACATGATGAGCACTTTTCCCTTCTATGGAAACATCAAATTCTCACTCTAACATA
TACTTATGAC
Found at i:2800 original size:33 final size:33
Alignment explanation
Indices: 2697--2803 Score: 112
Period size: 33 Copynumber: 3.2 Consensus size: 33
2687 ACCACAAAGA
2697 CAGAATAAGTTGGCCTTAGCCCAGAACAGATGT
1 CAGAATAAGTTGGCCTTAGCCCAGAACAGATGT
* * * * *
2730 CAGAATAA---AGCACTTAGGGCCGGAACAGANAGA
1 CAGAATAAGTTGGC-CTTA-GCCCAGAACAGA-TGT
*
2763 CAGAATAAGTTGGCCTTAGCCCAGAACAGATTT
1 CAGAATAAGTTGGCCTTAGCCCAGAACAGATGT
2796 CAGAATAA
1 CAGAATAA
2804 AGCCCTTAGG
Statistics
Matches: 57, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
30 2 0.04
31 4 0.07
32 10 0.18
33 25 0.44
34 10 0.18
35 4 0.07
36 2 0.04
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.18
Consensus pattern (33 bp):
CAGAATAAGTTGGCCTTAGCCCAGAACAGATGT
Found at i:2800 original size:66 final size:65
Alignment explanation
Indices: 2693--2824 Score: 228
Period size: 66 Copynumber: 2.0 Consensus size: 65
2683 TCAAACCACA
*
2693 AAGACAGAATAAGTTGGCCTTAGCCCAGAACAGATGTCAGAATAAAGCACTTAGGGCCGGAACAG
1 AAGACAGAATAAGTTGGCCTTAGCCCAGAACAGATGTCAGAATAAAGCACTTAGGCCCGGAACAG
* *
2758 ANAGACAGAATAAGTTGGCCTTAGCCCAGAACAGATTTCAGAATAAAGCCCTTAGGCCCGGAACA
1 A-AGACAGAATAAGTTGGCCTTAGCCCAGAACAGATGTCAGAATAAAGCACTTAGGCCCGGAACA
2823 G
65 G
2824 A
1 A
2825 TCAGAACAGA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
65 1 0.02
66 62 0.98
ACGTcount: A:0.38, C:0.21, G:0.24, T:0.16
Consensus pattern (65 bp):
AAGACAGAATAAGTTGGCCTTAGCCCAGAACAGATGTCAGAATAAAGCACTTAGGCCCGGAACAG
Found at i:2825 original size:32 final size:31
Alignment explanation
Indices: 2710--2825 Score: 106
Period size: 32 Copynumber: 3.6 Consensus size: 31
2700 AATAAGTTGG
2710 CCTTAGCCCAGAACAGATGTCAGAATAAAGC
1 CCTTAGCCCAGAACAGATGTCAGAATAAAGC
* * * * * * *
2741 ACTTAGGGCCGGAACAGANAGACAGAATAAGTTGG
1 CCTTA-GCCCAGAACAGA-TGTCAGAATAA--AGC
*
2776 CCTTAGCCCAGAACAGATTTCAGAATAAAGC
1 CCTTAGCCCAGAACAGATGTCAGAATAAAGC
*
2807 CCTTAGGCCCGGAACAGAT
1 CCTTA-GCCCAGAACAGAT
2826 CAGAACAGAT
Statistics
Matches: 64, Mismatches: 16, Indels: 9
0.72 0.18 0.10
Matches are distributed among these distances:
31 10 0.16
32 22 0.34
33 17 0.27
34 10 0.16
35 5 0.08
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.16
Consensus pattern (31 bp):
CCTTAGCCCAGAACAGATGTCAGAATAAAGC
Found at i:2854 original size:66 final size:65
Alignment explanation
Indices: 2694--2843 Score: 174
Period size: 66 Copynumber: 2.2 Consensus size: 65
2684 CAAACCACAA
** *
2694 AGACAGAATAAGTTGGCCTTAGCCCAGAACAGATGTCAGAATAAAGCACTTAGGGCCGGAACAGA
1 AGACAGAATAACATGGCCTTAG-CCAGAACAGATGTCAGAATAAAGCACTTAGGCCCGGAACAGA
*
2759 N
65 C
** * *
2760 AGACAGAATAAGTTGGCCTTAGCCCAGAACAGATTTCAGAATAAAGCCCTTAGGCCCGGAACAGA
1 AGACAGAATAACATGGCCTTAG-CCAGAACAGATGTCAGAATAAAGCACTTAGGCCCGGAACAGA
2825 TC
65 -C
*
2827 AGAACAGATATATCATG
1 AG-ACAGA-ATAACATG
2844 CTTATGCAGA
Statistics
Matches: 74, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
66 62 0.84
67 2 0.03
68 5 0.07
69 5 0.07
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.17
Consensus pattern (65 bp):
AGACAGAATAACATGGCCTTAGCCAGAACAGATGTCAGAATAAAGCACTTAGGCCCGGAACAGAC
Found at i:3099 original size:28 final size:28
Alignment explanation
Indices: 3052--3116 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
3042 AAATTAACCC
*
3052 TAGGGGTATAAAGGTCATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
* *
3080 TAGGGTTATAATGGTAATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
3108 TAGGGGTAT
1 TAGGGGTAT
3117 TCTAGTACAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.31, C:0.08, G:0.26, T:0.35
Consensus pattern (28 bp):
TAGGGGTATAAAGGTAATTTTGCATACA
Found at i:5248 original size:48 final size:48
Alignment explanation
Indices: 5183--5715 Score: 933
Period size: 48 Copynumber: 11.0 Consensus size: 48
5173 GCTGAAATTG
* *
5183 ATGTATAAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATATGAAAT
5231 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATATGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATATGAAAT
5279 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATATGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATATGAAAT
5327 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATATGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATATGAAAT
5375 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATATGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATATGAAAT
5423 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATATGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATATGAAAT
5471 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATATGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATATGAAAT
*
5519 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATATGAAAT
5567 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATATGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATATGAAAT
**
5615 ATGTATGAGATATGTATATGTGGTAAAGCC-AATGGCTAATGCAAAATATAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAAT--ATGA-A-AT
* * * * *
5666 ATATATGAGATATGTATATGTGGTAAAGCTGAATGGTTGATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATATGAAAT
5714 AT
1 AT
5716 ATATATGAGA
Statistics
Matches: 467, Mismatches: 13, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
47 10 0.02
48 414 0.89
49 3 0.01
50 2 0.00
51 30 0.06
52 8 0.02
ACGTcount: A:0.37, C:0.06, G:0.25, T:0.32
Consensus pattern (48 bp):
ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATATGAAAT
Found at i:5785 original size:48 final size:48
Alignment explanation
Indices: 5729--5986 Score: 498
Period size: 48 Copynumber: 5.4 Consensus size: 48
5719 TATGAGATCT
5729 GCTAATATGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATG
1 GCTAATATGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATG
5777 GCTAATATGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATG
1 GCTAATATGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATG
5825 GCTAATATGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATG
1 GCTAATATGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATG
5873 GCTAATATGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATG
1 GCTAATATGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATG
5921 GCTAATATGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATG
1 GCTAATATGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATG
* *
5969 GCTAGTGTGAAATATGTA
1 GCTAATATGAAATATGTA
5987 GGCGATGTGT
Statistics
Matches: 208, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
48 208 1.00
ACGTcount: A:0.37, C:0.06, G:0.25, T:0.31
Consensus pattern (48 bp):
GCTAATATGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATG
Found at i:6187 original size:37 final size:37
Alignment explanation
Indices: 6137--6239 Score: 172
Period size: 37 Copynumber: 2.8 Consensus size: 37
6127 ATATATTCCA
6137 GGTAAGACCCGATGACTACGTGTGGAGATTATGTCCG
1 GGTAAGACCCGATGACTACGTGTGGAGATTATGTCCG
*
6174 GGTAAGACCCGATGACTACGTGTGGAGATTTTGTCCG
1 GGTAAGACCCGATGACTACGTGTGGAGATTATGTCCG
* *
6211 GGTAAGACCCGATAACTTCGT-TGGAGATT
1 GGTAAGACCCGATGACTACGTGTGGAGATT
6240 TCATCTCAGC
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
36 8 0.13
37 55 0.87
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.26
Consensus pattern (37 bp):
GGTAAGACCCGATGACTACGTGTGGAGATTATGTCCG
Found at i:7550 original size:40 final size:40
Alignment explanation
Indices: 7495--8080 Score: 938
Period size: 40 Copynumber: 14.7 Consensus size: 40
7485 CGAGAGTTAT
7495 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
*
7535 ATATATCCGGGCTAAGTCCCAAAGAGCATTCGTGCTAGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
*
7575 ATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
*
7615 ATATATCCGGGCTAAGTCCCAAAGAGCATTCGTGCTAGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
*
7655 ATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
*
7695 ATATATCCGGGCTAAGTCCCAAAGAGCATTCGTGCTAGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
*
7735 ATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
*
7775 ATATATCCGGGCTAAGTCCCAAAGAGCATTCGTGCTAGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
*
7815 ATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
*
7855 ATATATCCGGGCTAAGTCCCAAAGAGCATTCGTGCTAGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
* * *
7895 ATGTATCCGGGCTAAGTCCCGAAGAGCATTTGTGCTGGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
* * *
7935 TTATATCCGGGCTAAGTCCCGAAGAGCATTTGTGCTGGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
* * * * *
7975 TTATATCCGGGCTAAGTCTCAAAGAGCATTTGTGCTAGAG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
* * * **
8015 TTATATCAGGGCGAAGTCCCGAAGAGCATTCGTGCCGGTG
1 ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
*
8055 TTATATCCGGGCTAAGTCCCGAAGAG
1 ATATATCCGGGCTAAGTCCCGAAGAG
Statistics
Matches: 509, Mismatches: 37, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 509 1.00
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
ATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTG
Done.