Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold695
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: 55369
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Found at i:7197 original size:40 final size:39
Alignment explanation
Indices: 7094--7273 Score: 249
Period size: 40 Copynumber: 4.6 Consensus size: 39
7084 TATTCGAATG
7094 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGT-CCGAAGGCATTTGTGCTAGTGACT
7134 ATAT-CGGGCTAAGTCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCGAAGGCATTTGTGCTAGTGACT
*
7172 ATATCCGGGCCTAAGTCCGAAGGCATTTGTGCTATTGACT
1 ATATCCGGG-CTAAGTCCGAAGGCATTTGTGCTAGTGACT
* * *
7212 ATATCCGGGCTAAGACCCAAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAG-TCCGAAGGCATTTGTGCTAG-TGACT
*
7252 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGT-CCGAAGG
7274 TACTTGGGTT
Statistics
Matches: 127, Mismatches: 8, Indels: 11
0.87 0.05 0.08
Matches are distributed among these distances:
38 28 0.22
39 31 0.24
40 66 0.52
41 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (39 bp):
ATATCCGGGCTAAGTCCGAAGGCATTTGTGCTAGTGACT
Found at i:14668 original size:40 final size:40
Alignment explanation
Indices: 14613--14791 Score: 281
Period size: 40 Copynumber: 4.5 Consensus size: 40
14603 TATTCGAATG
14613 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
14653 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
14693 ATATCCGGGCCAAGTCCCGAAGGCATTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* * *
14733 ATATCCGGGCTAAGACCCGAAGGCATTTGTCCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
14773 ATATCC-GGCTAAATCCCGA
1 ATATCCGGGCTAAGTCCCGA
14792 TGGTACTTGG
Statistics
Matches: 129, Mismatches: 9, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
39 11 0.09
40 116 0.90
41 2 0.02
ACGTcount: A:0.23, C:0.25, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:24928 original size:150 final size:150
Alignment explanation
Indices: 24656--25238 Score: 506
Period size: 150 Copynumber: 3.9 Consensus size: 150
24646 TTTGTGCCCC
* *
24656 GCACTAATCAGATAAACCAACAAATATAATGATGTTG-CTAGCACTAGTAAGATAAACTGATGAA
1 GCACTAGTCAGATAAACCAA-AAATATAATGATGTTGCCTAACACTAGTAAGATAAACTGATGAA
* * * * * ***
24720 AGTTACGCCTAGCGATAGTCAGATATACCGACAAATATAATGGTGTGCCCAGTGCTAGTAAGATA
65 AGTTGCGCCAAGCGCTAGTCAGATAAACCAACAAATATAATGGTGTGCCCAACACTAGTAAGATA
**
24785 AATTGATGAAAGTTGCACTTG
130 AATTGATGAAAGTTGCACTCA
* * * *
24806 GCACTAGTCAGATAAACCAAAAACTACAATGGTG-TGCCTAGCACTAGTCAA-ATAAAGTGATGA
1 GCACTAGTCAGATAAACCAAAAA-TATAATGATGTTGCCTAACACTAGT-AAGATAAACTGATGA
* * *
24869 AAGTTGCGCCAAGTGCTAGT-TGTATAAACCAACAAATATAATGGTGTGCCCAACACTAGT-TGA
64 AAGTTGCGCCAAGCGCTAGTCAG-ATAAACCAACAAATATAATGGTGTGCCCAACACTAGTAAG-
* ** *
24932 ATAAA-TCAACAAAGGTTTGCACCCA
127 ATAAATTGATGAAA-G-TTGCACTCA
** ** ** *
24957 GTGCTAGTTGGATAAAATGACAAATATAATGATGTTGCC-AACACTAGTAAGATAAACTGATGAA
1 GCACTAGTCAGAT-AAACCAAAAATATAATGATGTTGCCTAACACTAGTAAGATAAACTGATGAA
* * * * * * * *
25021 AGTTGTGACTAGCACTTGTCAGATAAACCGAA-AAATATAATGGTGTGCCTAGCATTAGTAAGAT
65 AGTTGCGCCAAGCGCTAGTCAGATAAACC-AACAAATATAATGGTGTGCCCAACACTAGTAAGAT
**
25085 AAATTGATGAAAGTTG-TGTCCA
129 AAATTGATGAAAGTTGCACT-CA
* * * * *
25107 ACACTAGTCAGATAAACCAAAAACTATAAT-A-GTGTACCCAACACTAGTCAGATAAAGTGATGA
1 GCACTAGTCAGATAAACCAAAAA-TATAATGATGT-TGCCTAACACTAGTAAGATAAACTGATGA
* * * * * *
25170 AAGTTGTGCCAAGCGCTAGTCATATAAACCGACAAATATAATGGTGAGTCCAATACTAGTTAA-A
64 AAGTTGCGCCAAGCGCTAGTCAGATAAACCAACAAATATAATGGTGTGCCCAACACTAG-TAAGA
25234 TAAAT
128 TAAAT
25239 CAACAAAGGT
Statistics
Matches: 341, Mismatches: 72, Indels: 40
0.75 0.16 0.09
Matches are distributed among these distances:
148 2 0.01
149 24 0.07
150 197 0.58
151 98 0.29
152 20 0.06
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (150 bp):
GCACTAGTCAGATAAACCAAAAATATAATGATGTTGCCTAACACTAGTAAGATAAACTGATGAAA
GTTGCGCCAAGCGCTAGTCAGATAAACCAACAAATATAATGGTGTGCCCAACACTAGTAAGATAA
ATTGATGAAAGTTGCACTCA
Found at i:25228 original size:75 final size:75
Alignment explanation
Indices: 24663--25237 Score: 443
Period size: 75 Copynumber: 7.7 Consensus size: 75
24653 CCCGCACTAA
* * * * **
24663 TCAGATAAACCAACAAATATAATGATGTTG-CTAGCACTAGTAAGATAAACTGATGAAAGTTACG
1 TCAGATAAACCGACAAATATAATGGTG-TGCCCAACACTAGTAAGATAAACTGATGAAAGTTGTG
* *
24727 CCTAGCGATAG
65 CCAAGCGCTAG
* *** * **
24738 TCAGATATACCGACAAATATAATGGTGTGCCCAGTGCTAGTAAGATAAATTGATGAAAGTTGCAC
1 TCAGATAAACCGACAAATATAATGGTGTGCCCAACACTAGTAAGATAAACTGATGAAAGTTGTGC
*** *
24803 TTGGCACTAG
66 CAAGCGCTAG
* * * * * *
24813 TCAGATAAACC-AAAAACTACAATGGTGTGCCTAGCACTAGTCAA-ATAAAGTGATGAAAGTTGC
1 TCAGATAAACCGACAAA-TATAATGGTGTGCCCAACACTAGT-AAGATAAACTGATGAAAGTTGT
*
24876 GCCAAGTGCTAG
64 GCCAAGCGCTAG
* * * * **
24888 T-TGTATAAACCAACAAATATAATGGTGTGCCCAACACTAGT-TGAATAAA-TCAACAAAGGTT-
1 TCAG-ATAAACCGACAAATATAATGGTGTGCCCAACACTAGTAAG-ATAAACTGATGAAA-GTTG
* *
24949 TGCACCCAGTGCTAG
63 TG--CCAAGCGCTAG
** ** *
24964 TTGGATAAAATGACAAATATAATGATGTTG-CCAACACTAGTAAGATAAACTGATGAAAGTTGTG
1 TCAGATAAACCGACAAATATAATGGTG-TGCCCAACACTAGTAAGATAAACTGATGAAAGTTGTG
* * * *
25028 ACTAGCACTTG
65 CCAAGCGCTAG
* * * * *
25039 TCAGATAAACCGAAAAATATAATGGTGTGCCTAGCATTAGTAAGATAAATTGATGAAAGTTGTGT
1 TCAGATAAACCGACAAATATAATGGTGTGCCCAACACTAGTAAGATAAACTGATGAAAGTTGTG-
*
25104 CCAA-CACTAG
65 CCAAGCGCTAG
* * * * *
25114 TCAGATAAACC-AAAAACTATAATAGTGTACCCAACACTAGTCAGATAAAGTGATGAAAGTTGTG
1 TCAGATAAACCGACAAA-TATAATGGTGTGCCCAACACTAGTAAGATAAACTGATGAAAGTTGTG
25178 CCAAGCGCTAG
65 CCAAGCGCTAG
* * * *
25189 TCATATAAACCGACAAATATAATGGTGAGTCCAATACTAGTTAA-ATAAA
1 TCAGATAAACCGACAAATATAATGGTGTGCCCAACACTAG-TAAGATAAA
25238 TCAACAAAGG
Statistics
Matches: 399, Mismatches: 80, Indels: 42
0.77 0.15 0.08
Matches are distributed among these distances:
74 24 0.06
75 301 0.75
76 63 0.16
77 11 0.03
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (75 bp):
TCAGATAAACCGACAAATATAATGGTGTGCCCAACACTAGTAAGATAAACTGATGAAAGTTGTGC
CAAGCGCTAG
Found at i:25230 original size:301 final size:301
Alignment explanation
Indices: 24675--25249 Score: 830
Period size: 301 Copynumber: 1.9 Consensus size: 301
24665 AGATAAACCA
* * *
24675 ACAAATATAATGATGTTGCTAGCACTAGTAAGATAAACTGATGAAAGTTACGCCTAGCGATAGTC
1 ACAAATATAATGATGTTGCCAACACTAGTAAGATAAACTGATGAAAGTTACGACTAGCGATAGTC
* * ** *
24740 AGATATACCGACAAATATAATGGTGTGCCCAGTGCTAGTAAGATAAATTGATGAAAGTTGCACTT
66 AGATAAACCGAAAAATATAATGGTGTGCCCAGCACTAGTAAGATAAATTGATGAAAGTTGCACTC
** * * * *
24805 GGCACTAGTCAGATAAACCAAAAACTACAATGGTGTGCCTAGCACTAGTCAAATAAAGTGATGAA
131 AACACTAGTCAGATAAACCAAAAACTACAATAGTGTACCCAACACTAGTCAAATAAAGTGATGAA
* ** * *
24870 AGTTGCGCCAAGTGCTAGTTGTATAAACCAACAAATATAATGGTGTGCCCAACACTAGTTGAATA
196 AGTTGCGCCAAGCGCTAGTCATATAAACCAACAAATATAATGGTGAGCCCAACACTAGTTAAATA
24935 AATCAACAAAGGTTTGCACCCAGTGCTAGTTGGATAAAATG
261 AATCAACAAAGGTTTGCACCCAGTGCTAGTTGGATAAAATG
** *
24976 ACAAATATAATGATGTTGCCAACACTAGTAAGATAAACTGATGAAAGTTGTGACTAGC-ACTTGT
1 ACAAATATAATGATGTTGCCAACACTAGTAAGATAAACTGATGAAAGTTACGACTAGCGA-TAGT
* * **
25040 CAGATAAACCGAAAAATATAATGGTGTGCCTAGCATTAGTAAGATAAATTGATGAAAGTTG-TGT
65 CAGATAAACCGAAAAATATAATGGTGTGCCCAGCACTAGTAAGATAAATTGATGAAAGTTGCACT
* *
25104 CCAACACTAGTCAGATAAACCAAAAACTATAATAGTGTACCCAACACTAGTCAGATAAAGTGATG
130 -CAACACTAGTCAGATAAACCAAAAACTACAATAGTGTACCCAACACTAGTCAAATAAAGTGATG
* * * *
25169 AAAGTTGTGCCAAGCGCTAGTCATATAAACCGACAAATATAATGGTGAGTCCAATACTAGTTAAA
194 AAAGTTGCGCCAAGCGCTAGTCATATAAACCAACAAATATAATGGTGAGCCCAACACTAGTTAAA
25234 TAAATCAACAAAGGTT
259 TAAATCAACAAAGGTT
25250 GGGTGCCCAG
Statistics
Matches: 240, Mismatches: 32, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
300 2 0.01
301 238 0.99
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (301 bp):
ACAAATATAATGATGTTGCCAACACTAGTAAGATAAACTGATGAAAGTTACGACTAGCGATAGTC
AGATAAACCGAAAAATATAATGGTGTGCCCAGCACTAGTAAGATAAATTGATGAAAGTTGCACTC
AACACTAGTCAGATAAACCAAAAACTACAATAGTGTACCCAACACTAGTCAAATAAAGTGATGAA
AGTTGCGCCAAGCGCTAGTCATATAAACCAACAAATATAATGGTGAGCCCAACACTAGTTAAATA
AATCAACAAAGGTTTGCACCCAGTGCTAGTTGGATAAAATG
Found at i:27957 original size:21 final size:22
Alignment explanation
Indices: 27933--27979 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
27923 GAAAAACTAT
**
27933 AAAAATTTTAAA-TGTTATAAA
1 AAAAATTTTAAACAATTATAAA
*
27954 AAAACTTTTAAACAATTATAAA
1 AAAAATTTTAAACAATTATAAA
27976 AAAA
1 AAAA
27980 TTAAATTAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (22 bp):
AAAAATTTTAAACAATTATAAA
Found at i:28773 original size:11 final size:11
Alignment explanation
Indices: 28757--28781 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28747 TAAATTGAAC
28757 ATTTTAAAGGT
1 ATTTTAAAGGT
28768 ATTTTAAAGGT
1 ATTTTAAAGGT
28779 ATT
1 ATT
28782 CAATCATAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (11 bp):
ATTTTAAAGGT
Found at i:37364 original size:15 final size:15
Alignment explanation
Indices: 37338--37393 Score: 87
Period size: 15 Copynumber: 3.7 Consensus size: 15
37328 CAAGGAAACC
37338 GAATAAAGAAATCCA
1 GAATAAAGAAATCCA
*
37353 -AGATAGAGAAATCCA
1 GA-ATAAAGAAATCCA
37368 GAATAAAGAAATCCA
1 GAATAAAGAAATCCA
37383 GAATAAAGAAA
1 GAATAAAGAAA
37394 CCCAAGATAC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
14 1 0.03
15 35 0.95
16 1 0.03
ACGTcount: A:0.61, C:0.11, G:0.16, T:0.12
Consensus pattern (15 bp):
GAATAAAGAAATCCA
Found at i:40466 original size:93 final size:93
Alignment explanation
Indices: 40354--40524 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
40344 GCCCATAAGT
* *
40354 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40419 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* *
40447 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCTATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
* *
40512 TGAGTTCGGATGC
66 CGAGCTCGGATGC
40525 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:40521 original size:46 final size:46
Alignment explanation
Indices: 40348--40521 Score: 194
Period size: 46 Copynumber: 3.8 Consensus size: 46
40338 TAACCCGCCC
* * *
40348 ATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCC
1 ATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCT
*
40394 ATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACATCT
1 ATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA---C-A-TTCGCATCT
* * *
40444 CT---CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCT
1 ATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCT
* *
40487 ATAAGTGAACTCGGACTCAACTCAATGAGTTCGGA
1 ATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
40522 TGCTCAACCA
Statistics
Matches: 108, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 7 0.06
44 1 0.01
46 62 0.57
47 28 0.26
49 1 0.01
50 5 0.05
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
ATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCT
Found at i:43527 original size:34 final size:33
Alignment explanation
Indices: 43470--43535 Score: 87
Period size: 34 Copynumber: 2.0 Consensus size: 33
43460 CGTAAAATAG
* *
43470 TGTGGGCCTTAGCCCAATACAGTAATAGTATCAA
1 TGTGAGCCTTAGCCCAATACAGT-ACAGTATCAA
* *
43504 TGTGAGCCTTAGCCCATTTCAGTACAGTATCA
1 TGTGAGCCTTAGCCCAATACAGTACAGTATCA
43536 GTAATGCACA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 8 0.29
34 20 0.71
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.29
Consensus pattern (33 bp):
TGTGAGCCTTAGCCCAATACAGTACAGTATCAA
Found at i:44475 original size:52 final size:52
Alignment explanation
Indices: 44414--44516 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
44404 CTTGTTCTAA
* *
44414 CCTACGTATTCTCCCCAACACTTAACCTTTACAAAAACGGTTAACCAAATCT
1 CCTACGTATTCTCCCCAACACTTAACCCTCACAAAAACGGTTAACCAAATCT
44466 CCTACGTATTCTCCCCAACACTTAACCCTCACAAAAACGGTTAACCAAATC
1 CCTACGTATTCTCCCCAACACTTAACCCTCACAAAAACGGTTAACCAAATC
44517 ATGAGAATCT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.35, C:0.35, G:0.06, T:0.24
Consensus pattern (52 bp):
CCTACGTATTCTCCCCAACACTTAACCCTCACAAAAACGGTTAACCAAATCT
Found at i:46641 original size:39 final size:39
Alignment explanation
Indices: 46553--46703 Score: 160
Period size: 39 Copynumber: 3.8 Consensus size: 39
46543 TGATGTGTAT
* *
46553 CCGGGCTTAAAGACCCGCAGGCTATATGCTGGAATTATAT
1 CCGGACTT-AAGACCCGCAGGCTATATGCTGGAATTATAA
* *
46593 CCGGGCTTAAAGACCCGCAGGCTATATGCT-GAATTATAC
1 CCGGACTT-AAGACCCGCAGGCTATATGCTGGAATTATAA
** * * *
46632 CCGGACTTAAGGTCCACAGGCTATGTACTGGAATTATAA
1 CCGGACTTAAGACCCGCAGGCTATATGCTGGAATTATAA
** **
46671 CCGGACTTAAGGTCCGCAGGCTACGTGCTGGAA
1 CCGGACTTAAGACCCGCAGGCTATATGCTGGAA
46704 ATATGTCCGA
Statistics
Matches: 99, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
38 16 0.16
39 53 0.54
40 30 0.30
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (39 bp):
CCGGACTTAAGACCCGCAGGCTATATGCTGGAATTATAA
Found at i:54467 original size:40 final size:40
Alignment explanation
Indices: 54412--54527 Score: 180
Period size: 40 Copynumber: 2.9 Consensus size: 40
54402 ATTTGATGTG
54412 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTGGAATTA
1 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTGGAATTA
54452 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTGGAATTA
1 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTGGAATTA
* * ** *
54492 TACCCGGACTT-AAGGTCCGCAGGCTATGTGCTGGAA
1 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTGGAA
54528 ATATGTCCTG
Statistics
Matches: 71, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
39 22 0.31
40 49 0.69
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
TATCCGGGCTTAAAGACCCGCAGGCTATATGCTGGAATTA
Done.