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: 38781
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32
Found at i:1390 original size:43 final size:43
Alignment explanation
Indices: 1330--1426 Score: 187
Period size: 43 Copynumber: 2.3 Consensus size: 43
1320 TACAAGTCCT
1330 ATGTAT-GATACAAAAAGTGATAAGGTAGCTACTGCTAGTTTC
1 ATGTATCGATACAAAAAGTGATAAGGTAGCTACTGCTAGTTTC
1372 ATGTATCGATACAAAAAGTGATAAGGTAGCTACTGCTAGTTTC
1 ATGTATCGATACAAAAAGTGATAAGGTAGCTACTGCTAGTTTC
1415 ATGTATCGATAC
1 ATGTATCGATAC
1427 CATTCTCATA
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 6 0.11
43 48 0.89
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (43 bp):
ATGTATCGATACAAAAAGTGATAAGGTAGCTACTGCTAGTTTC
Found at i:13810 original size:21 final size:21
Alignment explanation
Indices: 13777--13826 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
13767 TTGCAAGTTG
*
13777 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
13799 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
13820 AAATAAA
1 AAATAAA
13827 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:15646 original size:15 final size:15
Alignment explanation
Indices: 15626--15656 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
15616 TAAAAATGTC
*
15626 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
15641 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
15656 C
1 C
15657 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:17745 original size:13 final size:13
Alignment explanation
Indices: 17727--17752 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17717 TACATTTTCT
17727 TTGTATCGATACA
1 TTGTATCGATACA
17740 TTGTATCGATACA
1 TTGTATCGATACA
17753 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:17916 original size:20 final size:20
Alignment explanation
Indices: 17873--17919 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
17863 AAATCTTTTG
17873 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
17894 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
17914 CAAAAT
1 CAAAAT
17920 CAGCATCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.32, C:0.19, G:0.04, T:0.45
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:20304 original size:13 final size:13
Alignment explanation
Indices: 20286--20311 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20276 TACAGCAAGT
20286 ATGTATCGATACA
1 ATGTATCGATACA
20299 ATGTATCGATACA
1 ATGTATCGATACA
20312 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:23915 original size:19 final size:19
Alignment explanation
Indices: 23891--23991 Score: 124
Period size: 19 Copynumber: 5.6 Consensus size: 19
23881 TAGCTTACAT
*
23891 TGTATCGATACAAAACTTA
1 TGTATCGATACAACACTTA
*
23910 TGTATCGATACAACACTTG
1 TGTATCGATACAACACTTA
23929 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
*
23942 TGTATCGATACAACACTCA
1 TGTATCGATACAACACTTA
23961 TGTATCGATACAACACTTTA
1 TGTATCGATACAACAC-TTA
23981 TGTATCGATAC
1 TGTATCGATAC
23992 GAATCGTTGA
Statistics
Matches: 71, Mismatches: 4, Indels: 13
0.81 0.05 0.15
Matches are distributed among these distances:
13 9 0.13
14 1 0.01
16 6 0.08
19 42 0.59
20 13 0.18
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:23947 original size:13 final size:13
Alignment explanation
Indices: 23929--23953 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23919 ACAACACTTG
23929 TGTATCGATACAT
1 TGTATCGATACAT
23942 TGTATCGATACA
1 TGTATCGATACA
23954 ACACTCATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:23949 original size:51 final size:52
Alignment explanation
Indices: 23886--23991 Score: 178
Period size: 51 Copynumber: 2.1 Consensus size: 52
23876 GGCAGTAGCT
* *
23886 TACATTGTATCGATACAAAACTTATGTATCGATACAACAC-TTGTGTATCGA
1 TACATTGTATCGATACAAAACTCATGTATCGATACAACACTTTATGTATCGA
*
23937 TACATTGTATCGATACAACACTCATGTATCGATACAACACTTTATGTATCGA
1 TACATTGTATCGATACAAAACTCATGTATCGATACAACACTTTATGTATCGA
23989 TAC
1 TAC
23992 GAATCGTTGA
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
51 38 0.75
52 13 0.25
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (52 bp):
TACATTGTATCGATACAAAACTCATGTATCGATACAACACTTTATGTATCGA
Found at i:23951 original size:32 final size:32
Alignment explanation
Indices: 23910--23972 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
23900 ACAAAACTTA
**
23910 TGTATCGATACAACACTTGTGTATCGATACAT
1 TGTATCGATACAACACTCATGTATCGATACAT
23942 TGTATCGATACAACACTCATGTATCGATACA
1 TGTATCGATACAACACTCATGTATCGATACA
23973 ACACTTTATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32
Consensus pattern (32 bp):
TGTATCGATACAACACTCATGTATCGATACAT
Found at i:24827 original size:155 final size:155
Alignment explanation
Indices: 24548--24824 Score: 364
Period size: 155 Copynumber: 1.8 Consensus size: 155
24538 CATTGGGTTC
* * *
24548 GCTTTTATGTCGAAGGTAGATATTTAGGATAGGTTCATCTCATCTATTATCCTTTTTAAATCTTT
1 GCTTTCATGTCGAAGGTAGATATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAATCTTT
* *
24613 TAAGGGTACCGGGTACTTTTACATCGAAGGTATCCCCTAGAGGCATTTTGGTAATTTTTTAGAAC
66 TAAGGGTACCAGGTACTTTTACATCGAAGGTATCCCCTAGAGGCATTTTCGTAATTTTTTAGAAC
24678 CGAATCCTAGGTTGTCACCAGGTCT
131 CGAATCCTAGGTTGTCACCAGGTCT
* * * * *
24703 GCTTTCATGTCGAAGGTAGGTATTTAGGATAGGTTCATCCCTTTTA-AAT-TTTTTTAAGTCTTT
1 GCTTTCATGTCGAAGGTAGATATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAATCTTT
* * * * * * *
24766 TAGGGGTA-TAGGTACTTTTACGTCGAAGTTATTCCTTA-AGAGTATTTTCGTAATTTTTT
66 TAAGGGTACCAGGTACTTTTACATCGAAGGTATCCCCTAGAG-GCATTTTCGTAATTTTTT
24825 TTTGAATTTA
Statistics
Matches: 104, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
151 2 0.02
152 40 0.38
153 19 0.18
154 2 0.02
155 41 0.39
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.42
Consensus pattern (155 bp):
GCTTTCATGTCGAAGGTAGATATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAATCTTT
TAAGGGTACCAGGTACTTTTACATCGAAGGTATCCCCTAGAGGCATTTTCGTAATTTTTTAGAAC
CGAATCCTAGGTTGTCACCAGGTCT
Found at i:27917 original size:10 final size:10
Alignment explanation
Indices: 27902--27936 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
27892 AAGAGAAGGA
*
27902 AAAAAAAAAC
1 AAAAAAAAAG
27912 AAAAAAAAAG
1 AAAAAAAAAG
*
27922 AAACAAAAAG
1 AAAAAAAAAG
27932 AAAAA
1 AAAAA
27937 GGAAATTCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.89, C:0.06, G:0.06, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:27918 original size:14 final size:14
Alignment explanation
Indices: 27901--27936 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
27891 AAAGAGAAGG
27901 AAAAAAAAAACAAA
1 AAAAAAAAAACAAA
*
27915 AAAAAAGAAACAAA
1 AAAAAAAAAACAAA
27929 AAGAAAAA
1 AA-AAAAA
27937 GGAAATTCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.89, C:0.06, G:0.06, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAACAAA
Found at i:28290 original size:17 final size:17
Alignment explanation
Indices: 28262--28308 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
28252 TCTCTAAATA
28262 AGAAAAATAAGAAAAAAG
1 AGAAAAA-AAGAAAAAAG
28280 AGAAAAAAAGAAAAAAG
1 AGAAAAAAAGAAAAAAG
*
28297 A-AAAAGAAGAAA
1 AGAAAAAAAGAAA
28309 GAAAAATCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
16 10 0.36
17 11 0.39
18 7 0.25
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (17 bp):
AGAAAAAAAGAAAAAAG
Found at i:28302 original size:13 final size:13
Alignment explanation
Indices: 28284--28314 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
28274 AAAAAGAGAA
28284 AAAAAGAAAAAAG
1 AAAAAGAAAAAAG
*
28297 AAAAAGAAGAAAG
1 AAAAAGAAAAAAG
28310 AAAAA
1 AAAAA
28315 TCATGAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAAG
Found at i:28334 original size:9 final size:8
Alignment explanation
Indices: 28261--28313 Score: 63
Period size: 9 Copynumber: 6.2 Consensus size: 8
28251 TTCTCTAAAT
28261 AAGAAAAA
1 AAGAAAAA
28269 TAAGAAAAA
1 -AAGAAAAA
28278 AGAGAAAAA
1 A-AGAAAAA
28287 AAG-AAAA
1 AAGAAAAA
28294 AAGAAAAA
1 AAGAAAAA
28302 GAAGAAAGAA
1 -AAGAAA-AA
28312 AA
1 AA
28314 ATCATGAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
7 7 0.17
8 7 0.17
9 24 0.60
10 2 0.05
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (8 bp):
AAGAAAAA
Found at i:29221 original size:10 final size:11
Alignment explanation
Indices: 29206--29234 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
29196 AGAGGCTTAC
29206 AAAAAAAA-CA
1 AAAAAAAACCA
29216 AAAAAAAACCA
1 AAAAAAAACCA
29227 AAAAAAAA
1 AAAAAAAA
29235 GAATACTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.44
11 10 0.56
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAACCA
Found at i:30636 original size:20 final size:20
Alignment explanation
Indices: 30594--30644 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
30584 GTTGGGCATA
*
30594 ATGTATTGATACAATTCTTC
1 ATGTATTGATACAATTCTCC
30614 ATGTATTGATACAATGTC-CC
1 ATGTATTGATACAAT-TCTCC
*
30634 ATGTATCGATA
1 ATGTATTGATA
30645 TATTTCACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 26 0.93
21 2 0.07
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (20 bp):
ATGTATTGATACAATTCTCC
Found at i:30723 original size:19 final size:20
Alignment explanation
Indices: 30675--30727 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
30665 CTGCCAGTTT
*
30675 CATGTATCAATACAATTGAG
1 CATGTATCGATACAATTGAG
** *
30695 TGTGTCTCGATACAA-TGAG
1 CATGTATCGATACAATTGAG
30714 CATGTATCGATACA
1 CATGTATCGATACA
30728 TTATATCGAT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATTGAG
Found at i:31453 original size:17 final size:17
Alignment explanation
Indices: 31431--31464 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
31421 GTTTAAAACA
*
31431 ATTTTCTCCCCCTTTGT
1 ATTTTCTCCCCCATTGT
31448 ATTTTCTCCCCCATTGT
1 ATTTTCTCCCCCATTGT
31465 CAAATGTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.09, C:0.35, G:0.06, T:0.50
Consensus pattern (17 bp):
ATTTTCTCCCCCATTGT
Found at i:33678 original size:20 final size:20
Alignment explanation
Indices: 33653--33705 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
33643 ATTGGGCATA
*
33653 ATGTATCGATACAAT-TCTT
1 ATGTATCGATACAATGTCCT
33672 CATGTATCGATACAATGTCCT
1 -ATGTATCGATACAATGTCCT
33693 ATGTATCGATACA
1 ATGTATCGATACA
33706 TTTCACTTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 28 0.90
21 3 0.10
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACAATGTCCT
Found at i:33777 original size:19 final size:20
Alignment explanation
Indices: 33734--33786 Score: 90
Period size: 19 Copynumber: 2.7 Consensus size: 20
33724 CTGCCAGTTT
33734 CATGTATCGATACAATTGAG
1 CATGTATCGATACAATTGAG
*
33754 TATGTATCGATACAA-TGAG
1 CATGTATCGATACAATTGAG
33773 CATGTATCGATACA
1 CATGTATCGATACA
33787 TTGTATCAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATTGAG
Found at i:34258 original size:81 final size:82
Alignment explanation
Indices: 34123--34285 Score: 247
Period size: 81 Copynumber: 2.0 Consensus size: 82
34113 GTGTTGATGC
* * *
34123 ATCACCAAGCCTAATTTCCTTGAGGCAAGGTGCAGCCCACACATTCTCAATCATATCCCCTTCAT
1 ATCACCAAGCCTAATTTCCTTGAGGCAAGGTGCAACCCACACATTCCCAATCATATCCCCTTCAC
*
34188 CCAACCA-TTGATGGTA
66 CCAACCACTAGATGGTA
* * * *
34204 ATCACTAAGCCTAATTTCCTTGAGGCAAGTTGCAACTCACACATTCCCAATCATATTCCCTTCAC
1 ATCACCAAGCCTAATTTCCTTGAGGCAAGGTGCAACCCACACATTCCCAATCATATCCCCTTCAC
34269 CCAACCACTAGATGGTA
66 CCAACCACTAGATGGTA
34286 CTGATACATC
Statistics
Matches: 73, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
81 65 0.89
82 8 0.11
ACGTcount: A:0.29, C:0.32, G:0.12, T:0.26
Consensus pattern (82 bp):
ATCACCAAGCCTAATTTCCTTGAGGCAAGGTGCAACCCACACATTCCCAATCATATCCCCTTCAC
CCAACCACTAGATGGTA
Found at i:35066 original size:20 final size:20
Alignment explanation
Indices: 35043--35115 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
35033 ACAATTCAAA
35043 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
35063 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
35084 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
35104 GTATCGATACAT
1 GTATCGATACAT
35116 AAAAAAAGAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:35094 original size:41 final size:42
Alignment explanation
Indices: 35043--35137 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 42
35033 ACAATTCAAA
*
35043 GTATCGATACATGTTGCAATGTATCGATACAT-GAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
35084 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
35126 GTATCGATACAT
1 GTATCGATACAT
35138 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 32 0.62
42 20 0.38
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (42 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
Found at i:35194 original size:13 final size:13
Alignment explanation
Indices: 35176--35201 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35166 TACAGCAAGT
35176 ATGTATCGATACA
1 ATGTATCGATACA
35189 ATGTATCGATACA
1 ATGTATCGATACA
35202 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Done.