Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2723
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: 19116
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Found at i:3881 original size:70 final size:66
Alignment explanation
Indices: 3773--3902 Score: 199
Period size: 71 Copynumber: 1.9 Consensus size: 66
3763 CGTCCAGAAA
3773 ACCCGAAGTTTCTTAATCGCCTGATCATCTTAAATTTCTTC-ATGACTAATGAAAAGATTCCGAA
1 ACCCGAAGTTTCTTAATCGCCTGATCATCTTAAATTTCTTCGATGACTAATGAAAAGATTCCGAA
3837 G
66 G
*
3838 ACCCGAAGTATTCTTAGATCGGCCTGAGTCATCTCTAAATTTCTTCGATGACTGATGAAAAGATT
1 ACCCGAAGT-TTCTTA-ATC-GCCTGA-TCATCT-TAAATTTCTTCGATGACTAATGAAAAGATT
3903 TTCCCGAAGA
Statistics
Matches: 58, Mismatches: 1, Indels: 6
0.89 0.02 0.09
Matches are distributed among these distances:
65 9 0.16
66 6 0.10
67 3 0.05
68 6 0.10
69 6 0.10
70 11 0.19
71 17 0.29
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (66 bp):
ACCCGAAGTTTCTTAATCGCCTGATCATCTTAAATTTCTTCGATGACTAATGAAAAGATTCCGAA
G
Found at i:5765 original size:45 final size:44
Alignment explanation
Indices: 5688--5805 Score: 173
Period size: 45 Copynumber: 2.6 Consensus size: 44
5678 CCGACATTTT
* * **
5688 GCCTGCTAGGCTCGAGGCCCGAAAAATATCTCACTGGCATTATA
1 GCCTGCTAGGCTCAAGGCCCGAATAATATCTCACCAGCATTATA
*
5732 GCCTGCTAGGCTCAAAGGCCCGAATAATGTCTCACCAGCATTATA
1 GCCTGCTAGGCTC-AAGGCCCGAATAATATCTCACCAGCATTATA
5777 GCCTGCTAGGCTCCAAGGCCCGAATAATA
1 GCCTGCTAGGCT-CAAGGCCCGAATAATA
5806 CTGTACAACA
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
44 13 0.20
45 52 0.79
46 1 0.02
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (44 bp):
GCCTGCTAGGCTCAAGGCCCGAATAATATCTCACCAGCATTATA
Found at i:9353 original size:71 final size:71
Alignment explanation
Indices: 9237--9379 Score: 268
Period size: 71 Copynumber: 2.0 Consensus size: 71
9227 TAACACCCTG
9237 AATTTGGGCCTAGAAGTTTTGGGCCTTGAGCATGGGAGCGGTTGAAGGCAGCTTATAATATTCTA
1 AATTTGGGCCTAGAAGTTTTGGGCCTTGAGCATGGGAGCGGTTGAAGGCAGCTTATAATATTCTA
9302 TTGTGC
66 TTGTGC
* *
9308 AATTTGGGCTTAGAAGTTTTGGGCCTTGAGCATGGGAGCGGTTGAAGGCAGCTTATAATATTCTG
1 AATTTGGGCCTAGAAGTTTTGGGCCTTGAGCATGGGAGCGGTTGAAGGCAGCTTATAATATTCTA
9373 TTGTGC
66 TTGTGC
9379 A
1 A
9380 TGTAAATTTC
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 70 1.00
ACGTcount: A:0.22, C:0.13, G:0.31, T:0.33
Consensus pattern (71 bp):
AATTTGGGCCTAGAAGTTTTGGGCCTTGAGCATGGGAGCGGTTGAAGGCAGCTTATAATATTCTA
TTGTGC
Found at i:10207 original size:27 final size:27
Alignment explanation
Indices: 10177--10335 Score: 237
Period size: 27 Copynumber: 5.9 Consensus size: 27
10167 AATACCAAAG
10177 TACCCTCGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* *
10204 TACCCTCGATTTATAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACTGTTT
10231 TACCCTCGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* *
10258 TACCCTCGATTTACAAAATTACCGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* * **
10285 TACCCTTGATTTATAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
10312 TACCCTCGATTTACAAAATTACTG
1 TACCCTCGATTTACAGAATTACTG
10336 AAATACCCTT
Statistics
Matches: 117, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 117 1.00
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACTGTTT
Found at i:10266 original size:81 final size:81
Alignment explanation
Indices: 10177--10335 Score: 273
Period size: 81 Copynumber: 2.0 Consensus size: 81
10167 AATACCAAAG
* * *
10177 TACCCTCGATTTACAGAATTACTGTTTTACCCTCGATTTATAGAATTACTATTTTACCCTCGATT
1 TACCCTCGATTTACAAAATTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATT
*
10242 TACAGAATTACTGTTT
66 TACAAAATTACTGTTT
*
10258 TACCCTCGATTTACAAAATTACCGTTTTACCCTTGATTTATAGAATTACCATTTTACCCTCGATT
1 TACCCTCGATTTACAAAATTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATT
10323 TACAAAATTACTG
66 TACAAAATTACTG
10336 AAATACCCTT
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 73 1.00
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (81 bp):
TACCCTCGATTTACAAAATTACCGTTTTACCCTCGATTTATAGAATTACCATTTTACCCTCGATT
TACAAAATTACTGTTT
Found at i:10356 original size:54 final size:54
Alignment explanation
Indices: 10245--10362 Score: 130
Period size: 54 Copynumber: 2.2 Consensus size: 54
10235 CTCGATTTAC
** *** **
10245 AGAATTACTGTTTTACCCTCGATTTACAAAATTACCGTTTTACCCTTGATTTAT
1 AGAATTACCATTTTACCCTCGATTTACAAAATTACCGAAATACCCTTGATGGAT
* *
10299 AGAATTACCATTTTACCCTCGATTTACAAAATTACTGAAATACCCTT-ATAGGGT
1 AGAATTACCATTTTACCCTCGATTTACAAAATTACCGAAATACCCTTGAT-GGAT
*
10353 AGAAATACCA
1 AGAATTACCA
10363 AATACCCTTG
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
53 2 0.04
54 51 0.96
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.36
Consensus pattern (54 bp):
AGAATTACCATTTTACCCTCGATTTACAAAATTACCGAAATACCCTTGATGGAT
Found at i:10367 original size:26 final size:26
Alignment explanation
Indices: 10336--10557 Score: 176
Period size: 27 Copynumber: 8.0 Consensus size: 26
10326 AAAATTACTG
* *
10336 AAATACCCTTATAGGGTAGAAATACC
1 AAATACCCCTGTAGGGTAGAAATACC
*
10362 AAATACCCTTGTAGGGTAGAAATACCGAAATACC
1 AAATACCCCTGTA-GG--G---TA--GAAATACC
* * *
10396 GAAATACCCCTATAGGGTAGAATTACTA
1 -AAATACCCCTGTAGGGTAGAAATAC-C
*
10424 AAATACCCCTGTAGGGTAGAATTACC
1 AAATACCCCTGTAGGGTAGAAATACC
* *
10450 GAAATACCCTTGTAGGGTAGAAATACTG
1 -AAATACCCCTGTAGGGTAGAAATAC-C
* *
10478 AAATACCCCTGTAGGGTAGAATTACT
1 AAATACCCCTGTAGGGTAGAAATACC
*
10504 AAATACCCCTGTAGGGTAGAATTACC
1 AAATACCCCTGTAGGGTAGAAATACC
* * *
10530 GAGATACCCTTGTGGGGTA-AAATTACC
1 -AAATACCCCTGTAGGGTAGAAA-TACC
10557 A
1 A
10558 TTTTACCCCT
Statistics
Matches: 164, Mismatches: 18, Indels: 28
0.78 0.09 0.13
Matches are distributed among these distances:
26 40 0.24
27 97 0.59
29 3 0.02
32 3 0.02
34 10 0.06
35 11 0.07
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (26 bp):
AAATACCCCTGTAGGGTAGAAATACC
Found at i:10428 original size:35 final size:34
Alignment explanation
Indices: 10355--10430 Score: 98
Period size: 35 Copynumber: 2.2 Consensus size: 34
10345 TATAGGGTAG
* * *
10355 AAATACCAAATACCCTTGTAGGGTAGAAATACCG
1 AAATACCAAATACCCCTATAGGGTAGAAATACCA
* *
10389 AAATACCGAAATACCCCTATAGGGTAGAATTACTA
1 AAATACC-AAATACCCCTATAGGGTAGAAATACCA
10424 AAATACC
1 AAATACC
10431 CCTGTAGGGT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
34 7 0.19
35 29 0.81
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.21
Consensus pattern (34 bp):
AAATACCAAATACCCCTATAGGGTAGAAATACCA
Found at i:10450 original size:62 final size:61
Alignment explanation
Indices: 10335--10457 Score: 192
Period size: 62 Copynumber: 2.0 Consensus size: 61
10325 CAAAATTACT
* * *
10335 GAAATACCCTTATAGGGTAGAAATACCAAATACCCTTGTAGGGTAGAAATACCGAAATACC
1 GAAATACCCCTATAGGGTAGAAATACAAAATACCCCTGTAGGGTAGAAATACCGAAATACC
* *
10396 GAAATACCCCTATAGGGTAGAATTACTAAAATACCCCTGTAGGGTAGAATTACCGAAATACC
1 GAAATACCCCTATAGGGTAGAAATAC-AAAATACCCCTGTAGGGTAGAAATACCGAAATACC
10458 CTTGTAGGGT
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
61 24 0.43
62 32 0.57
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22
Consensus pattern (61 bp):
GAAATACCCCTATAGGGTAGAAATACAAAATACCCCTGTAGGGTAGAAATACCGAAATACC
Found at i:10540 original size:80 final size:81
Alignment explanation
Indices: 10388--10552 Score: 280
Period size: 80 Copynumber: 2.1 Consensus size: 81
10378 TAGAAATACC
10388 GAAATACCGAAATACCCCTATAGGGTAGAATTACTAAAATACCCCTGTAGGGTAGAATTACCGAA
1 GAAATACCGAAATACCCCTATAGGGTAGAATTACTAAAATACCCCTGTAGGGTAGAATTACCGAA
10453 ATACCCTTGTAGGGTA
66 ATACCCTTGTAGGGTA
* * *
10469 GAAATACTGAAATACCCCTGTAGGGTAGAATTACT-AAATACCCCTGTAGGGTAGAATTACCGAG
1 GAAATACCGAAATACCCCTATAGGGTAGAATTACTAAAATACCCCTGTAGGGTAGAATTACCGAA
*
10533 ATACCCTTGTGGGGTA
66 ATACCCTTGTAGGGTA
10549 -AAAT
1 GAAAT
10553 TACCATTTTA
Statistics
Matches: 80, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
79 4 0.05
80 43 0.54
81 33 0.41
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (81 bp):
GAAATACCGAAATACCCCTATAGGGTAGAATTACTAAAATACCCCTGTAGGGTAGAATTACCGAA
ATACCCTTGTAGGGTA
Found at i:10556 original size:27 final size:27
Alignment explanation
Indices: 10392--10556 Score: 224
Period size: 27 Copynumber: 6.1 Consensus size: 27
10382 AATACCGAAA
*
10392 TACCGAAATACCCCTATAGGGTAGAAT
1 TACCGAAATACCCCTGTAGGGTAGAAT
**
10419 TACTAAAATACCCCTGTAGGGTAGAAT
1 TACCGAAATACCCCTGTAGGGTAGAAT
* *
10446 TACCGAAATACCCTTGTAGGGTAGAAA
1 TACCGAAATACCCCTGTAGGGTAGAAT
*
10473 TACTGAAATACCCCTGTAGGGTAGAAT
1 TACCGAAATACCCCTGTAGGGTAGAAT
*
10500 TA-CTAAATACCCCTGTAGGGTAGAAT
1 TACCGAAATACCCCTGTAGGGTAGAAT
* * * *
10526 TACCGAGATACCCTTGTGGGGTAAAAT
1 TACCGAAATACCCCTGTAGGGTAGAAT
10553 TACC
1 TACC
10557 ATTTTACCCC
Statistics
Matches: 120, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
26 24 0.20
27 96 0.80
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.25
Consensus pattern (27 bp):
TACCGAAATACCCCTGTAGGGTAGAAT
Found at i:10916 original size:70 final size:67
Alignment explanation
Indices: 10781--10937 Score: 190
Period size: 70 Copynumber: 2.3 Consensus size: 67
10771 GAGGAAGTAT
* * * *
10781 TCTGGCAGCCTCGCTGCAATCTGGTGGCCTCGCTACATATATCTGTTCTGGTGACTTCGTCACAA
1 TCTGGCAGCCTCACTGCAATCTGGTGGCCTCGCTACATATATCTGTTCTGGTGACCTAGCCACAA
10846 TA
66 TA
* * *
10848 TCTGGCAGCCTCACTGTAATCTGGTGG-CTCGCCACATATATATATCTGTTCTGGTGGCCTAGCC
1 TCTGGCAGCCTCACTGCAATCTGGTGGCCTCG---C-TACATATATCTGTTCTGGTGACCTAGCC
10912 ACAATA
62 ACAATA
* *
10918 TCTGGTAGCCTCGCTGCAAT
1 TCTGGCAGCCTCACTGCAAT
10938 TTCTGTGGTG
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
66 4 0.05
67 25 0.33
69 1 0.01
70 46 0.61
ACGTcount: A:0.19, C:0.28, G:0.22, T:0.31
Consensus pattern (67 bp):
TCTGGCAGCCTCACTGCAATCTGGTGGCCTCGCTACATATATCTGTTCTGGTGACCTAGCCACAA
TA
Found at i:11049 original size:6 final size:6
Alignment explanation
Indices: 11040--11201 Score: 118
Period size: 6 Copynumber: 26.3 Consensus size: 6
11030 TTGCATTCAC
* *
11040 ATTCTG ATTCTG ATTCT- ATTACCTG ATACTG ATTCTG ATTCTG -TTACCTA
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATT--CTG
* * * *
11090 ATTTTG ATTCTG GTTTTG ATTCTG ATTCTG -TTACCTG ATACTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG
* * * *
11139 ATTTTG ATTCTG -TCACCTG ATTCTG ATTCTG ATTCTG ATTCTC ATTTTG
1 ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG
11188 ATTCT- AGTTCTG AT
1 ATTCTG A-TTCTG AT
11202 AATGTTTCTT
Statistics
Matches: 122, Mismatches: 20, Indels: 28
0.72 0.12 0.16
Matches are distributed among these distances:
5 9 0.07
6 96 0.79
7 11 0.09
8 6 0.05
ACGTcount: A:0.19, C:0.17, G:0.15, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:11075 original size:31 final size:31
Alignment explanation
Indices: 11040--11180 Score: 153
Period size: 31 Copynumber: 4.5 Consensus size: 31
11030 TTGCATTCAC
11040 ATTCTGATTCTGATTCTATTACCTGATACTG
1 ATTCTGATTCTGATTCTATTACCTGATACTG
* *
11071 ATTCTGATTCTG-TTACCTAATT--TTGATTCTG
1 ATTCTGATTCTGATT--CT-ATTACCTGATACTG
* * *
11102 GTTTTGATTCTGATTCTGTTACCTGATACTG
1 ATTCTGATTCTGATTCTATTACCTGATACTG
* * * *
11133 ATTCTGATTTTGATTCTGTCACCTGATTCTG
1 ATTCTGATTCTGATTCTATTACCTGATACTG
11164 ATTCTGATTCTGATTCT
1 ATTCTGATTCTGATTCT
11181 CATTTTGATT
Statistics
Matches: 91, Mismatches: 13, Indels: 12
0.78 0.11 0.10
Matches are distributed among these distances:
29 2 0.02
30 4 0.04
31 78 0.86
32 4 0.04
33 3 0.03
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.49
Consensus pattern (31 bp):
ATTCTGATTCTGATTCTATTACCTGATACTG
Found at i:11097 original size:25 final size:25
Alignment explanation
Indices: 11043--11101 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
11033 CATTCACATT
*
11043 CTGATTCTGATTCTATTACCTGATA
1 CTGATTCTGATTCTATTACCTAATA
* *
11068 CTGATTCTGATTCTGTTACCTAATT
1 CTGATTCTGATTCTATTACCTAATA
*
11093 TTGATTCTG
1 CTGATTCTG
11102 GTTTTGATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.20, C:0.19, G:0.14, T:0.47
Consensus pattern (25 bp):
CTGATTCTGATTCTATTACCTAATA
Found at i:11110 original size:37 final size:37
Alignment explanation
Indices: 11069--11150 Score: 128
Period size: 37 Copynumber: 2.2 Consensus size: 37
11059 TACCTGATAC
** *
11069 TGATTCTGATTCTGTTACCTAATTTTGATTCTGGTTT
1 TGATTCTGATTCTGTTACCTAATACTGATTCTGATTT
*
11106 TGATTCTGATTCTGTTACCTGATACTGATTCTGATTT
1 TGATTCTGATTCTGTTACCTAATACTGATTCTGATTT
11143 TGATTCTG
1 TGATTCTG
11151 TCACCTGATT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.17, C:0.15, G:0.17, T:0.51
Consensus pattern (37 bp):
TGATTCTGATTCTGTTACCTAATACTGATTCTGATTT
Found at i:11133 original size:19 final size:19
Alignment explanation
Indices: 11068--11169 Score: 87
Period size: 19 Copynumber: 5.8 Consensus size: 19
11058 TTACCTGATA
11068 CTGATTCTGATTCTGTTAC
1 CTGATTCTGATTCTGTTAC
* *
11087 CTAATTTTGATTCTGGTT--
1 CTGATTCTGATTCT-GTTAC
*
11105 TTGATTCTGATTCTGTTAC
1 CTGATTCTGATTCTGTTAC
*
11124 CTGATACTGATTCTG--A-
1 CTGATTCTGATTCTGTTAC
*
11140 -T--TT-TGATTCTGTCAC
1 CTGATTCTGATTCTGTTAC
11155 CTGATTCTGATTCTG
1 CTGATTCTGATTCTG
11170 ATTCTGATTC
Statistics
Matches: 65, Mismatches: 8, Indels: 20
0.70 0.09 0.22
Matches are distributed among these distances:
12 8 0.12
13 1 0.02
14 1 0.02
15 1 0.02
16 1 0.02
17 4 0.06
18 13 0.20
19 33 0.51
20 3 0.05
ACGTcount: A:0.17, C:0.18, G:0.17, T:0.49
Consensus pattern (19 bp):
CTGATTCTGATTCTGTTAC
Found at i:15492 original size:33 final size:33
Alignment explanation
Indices: 15407--15503 Score: 88
Period size: 33 Copynumber: 2.9 Consensus size: 33
15397 ATGGATCCTA
* * *
15407 TTTGTGTTTATTGTCCCAACGGACTATCTCTGT
1 TTTGTATTTACTGTCCCAACGGACTATCTCTAT
* * * * *
15440 TCTGTACTTACTATTCCAAC-GAGCTATTTCTAT
1 TTTGTATTTACTGTCCCAACGGA-CTATCTCTAT
**
15473 TTTGTATTTACTGTCCCAACAAACTATCTCT
1 TTTGTATTTACTGTCCCAACGGACTATCTCT
15504 GTGGATGCCA
Statistics
Matches: 48, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
32 2 0.04
33 45 0.94
34 1 0.02
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.43
Consensus pattern (33 bp):
TTTGTATTTACTGTCCCAACGGACTATCTCTAT
Done.