Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2966
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: 71954
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:3619 original size:40 final size:39
Alignment explanation
Indices: 3508--3605 Score: 110
Period size: 39 Copynumber: 2.5 Consensus size: 39
3498 TATAGTTAAT
* * *
3508 CTCGCACAAATGCCTTTC-AGGACTTAACCCAGATTTAGTAA
1 CTCGCACAAATGCC-TTCGA-G-CTTATCCCGGAATTAGTAA
*
3549 CTCGCACAAATGCCTTCGAGCTTATCCCGGAATTAGTAT
1 CTCGCACAAATGCCTTCGAGCTTATCCCGGAATTAGTAA
3588 CTCGCCACAAAT-CCTTCG
1 CTCG-CACAAATGCCTTCG
3606 GATCTTAGTC
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
39 25 0.49
40 11 0.22
41 15 0.29
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.27
Consensus pattern (39 bp):
CTCGCACAAATGCCTTCGAGCTTATCCCGGAATTAGTAA
Found at i:14275 original size:38 final size:37
Alignment explanation
Indices: 14174--14377 Score: 178
Period size: 35 Copynumber: 5.6 Consensus size: 37
14164 AAGTGAATAT
* * *
14174 ACCGGATTAAGATCCGAA-GC-TTTGTGCGAGATACTAA
1 ACCGG-TTAAG-TCCGAAGGCATTCGTGCGAGTTATTAA
*
14211 ATCCGG-TAAGTCC-AAAGCATTCGTGCGAGTTATTAA
1 A-CCGGTTAAGTCCGAAGGCATTCGTGCGAGTTATTAA
14247 ACCGGTTAAGTCCGAAGGCATTTCGTGCGAGTTATTAA
1 ACCGGTTAAGTCCGAAGGCA-TTCGTGCGAGTTATTAA
*
14285 ATTCGGGTTAAGTCCGAAGGCA-TCGTGCGAGTGTA--AA
1 A--CCGGTTAAGTCCGAAGGCATTCGTGCGAGT-TATTAA
* * *
14322 TCCGGTTATGTCCGAAGGCATT-GT--GAGTTACTAAA
1 ACCGGTTAAGTCCGAAGGCATTCGTGCGAGTTA-TTAA
*
14357 ACCGG-TATGTCCGAAGGCATT
1 ACCGGTTAAGTCCGAAGGCATT
14378 TCGAGAAAGT
Statistics
Matches: 145, Mismatches: 9, Indels: 29
0.79 0.05 0.16
Matches are distributed among these distances:
32 2 0.01
33 4 0.03
34 18 0.12
35 34 0.23
36 27 0.19
37 8 0.06
38 32 0.22
39 2 0.01
40 18 0.12
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (37 bp):
ACCGGTTAAGTCCGAAGGCATTCGTGCGAGTTATTAA
Found at i:14340 original size:75 final size:72
Alignment explanation
Indices: 14174--14377 Score: 188
Period size: 75 Copynumber: 2.8 Consensus size: 72
14164 AAGTGAATAT
14174 ACCGGATTAAGATCCGAA-GC-TTTGTGCGAGATACTAAATCCGGTAAGTCCAAAGCATTCGTGC
1 ACCGG-TTAAG-TCCGAAGGCATTTGTGCGAGATACTAAATCCGGTAAGTCCAAAGCATTCGTGC
14237 GAGTTATTAA
64 GAGTTA-TAA
* * * *
14247 ACCGGTTAAGTCCGAAGGCATTTCGTGCGAGTTATTAAATTCGGGTTAAGTCCGAAGGCA-TCGT
1 ACCGGTTAAGTCCGAAGGCATTT-GTGCGAGATACTAAA-TCCGG-TAAGTCC-AAAGCATTCGT
14311 GCGAGTGTA-AA
62 GCGAGT-TATAA
* * * * * *
14322 TCCGGTTATGTCCGAAGGCA-TTGT--GAGTTACTAAAACCGGTATGTCCGAAGGCATT
1 ACCGGTTAAGTCCGAAGGCATTTGTGCGAGATACTAAATCCGGTAAGTCC-AAAGCATT
14378 TCGAGAAAGT
Statistics
Matches: 113, Mismatches: 10, Indels: 19
0.80 0.07 0.13
Matches are distributed among these distances:
69 13 0.12
70 4 0.04
71 16 0.14
72 7 0.06
73 10 0.09
74 15 0.13
75 24 0.21
76 17 0.15
77 7 0.06
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (72 bp):
ACCGGTTAAGTCCGAAGGCATTTGTGCGAGATACTAAATCCGGTAAGTCCAAAGCATTCGTGCGA
GTTATAA
Found at i:20848 original size:40 final size:40
Alignment explanation
Indices: 20811--20942 Score: 142
Period size: 40 Copynumber: 3.3 Consensus size: 40
20801 GCTACTCGTT
* * *
20811 CAAATGCCTTCGGGACATAGCTC-GGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCAGATT-TAGTAACTCGCA
* *
20851 CAAATGCCTTCAGGACTTAACCCAGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCAGATTTAGTAACTCGCA
* * * * * *
20891 CAAATGCCTTCGAG-CTTATCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCAGATTTAGTAACTCGCA
20930 CAAATGCCTTCGG
1 CAAATGCCTTCGG
20943 ATCTTAGTCC
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
39 33 0.42
40 43 0.54
41 3 0.04
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCAGATTTAGTAACTCGCA
Found at i:20932 original size:39 final size:41
Alignment explanation
Indices: 20839--20941 Score: 149
Period size: 39 Copynumber: 2.6 Consensus size: 41
20829 AGCTCGGTTA
*
20839 TAGTAACTCGCACAAATGCCTTC-AGGACTTAACCCAGATT
1 TAGTAACTCGCACAAATGCCTTCGAGGACTTAACCCAGAAT
* *
20879 TAGTAACTCGCACAAATGCCTTCGA-G-CTTATCCCGGAAT
1 TAGTAACTCGCACAAATGCCTTCGAGGACTTAACCCAGAAT
*
20918 TAGTATCTCGCACAAATGCCTTCG
1 TAGTAACTCGCACAAATGCCTTCG
20942 GATCTTAGTC
Statistics
Matches: 58, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
39 33 0.57
40 24 0.41
41 1 0.02
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (41 bp):
TAGTAACTCGCACAAATGCCTTCGAGGACTTAACCCAGAAT
Found at i:20979 original size:79 final size:80
Alignment explanation
Indices: 20811--20995 Score: 189
Period size: 79 Copynumber: 2.3 Consensus size: 80
20801 GCTACTCGTT
* * * *
20811 CAAATGCCTTCGGGACATAGCTCGG-TTATAGTAACTCGCACAAATGCCTTCAGGACTTAACCCA
1 CAAATGCCTTCGAGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCAGGACTTAACCCA
* *
20875 GATTTAGTAACTCGCA
65 GATATAGTAACTAGCA
* * ** *
20891 CAAATGCCTTCGAG-CTTATCCCGGAATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCG
1 CAAATGCCTTCGAGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCAGGA-CTTAACCCA
* *
20954 GATATGGTCACTTAGCA
65 GATATAGTAAC-TAGCA
*
20971 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGAGACTTAGCCCGGA
20996 CATCATTCAA
Statistics
Matches: 86, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
78 3 0.03
79 51 0.59
80 32 0.37
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGAGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCAGGACTTAACCCAG
ATATAGTAACTAGCA
Found at i:26572 original size:19 final size:17
Alignment explanation
Indices: 26527--26576 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
26517 GATATAATTT
*
26527 TTGTCATAAAAAATTAAT
1 TTGT-ATAAAAAATTAAA
*
26545 TTTTATAAAATAATTAAA
1 TTGTATAAAA-AATTAAA
*
26563 TTGTATTAAAAATT
1 TTGTATAAAAAATT
26577 TGGACATGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 10 0.37
18 17 0.63
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (17 bp):
TTGTATAAAAAATTAAA
Found at i:27209 original size:14 final size:14
Alignment explanation
Indices: 27186--27215 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
27176 CATCCCTCAT
*
27186 TCACATCTCTTCTC
1 TCACAACTCTTCTC
27200 TCACAACTCTTCTC
1 TCACAACTCTTCTC
27214 TC
1 TC
27216 CTCTCTCAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.43, G:0.00, T:0.40
Consensus pattern (14 bp):
TCACAACTCTTCTC
Found at i:40694 original size:51 final size:55
Alignment explanation
Indices: 40563--40700 Score: 160
Period size: 56 Copynumber: 2.6 Consensus size: 55
40553 GGGATGAGAC
* *
40563 CCCATGTAAGACCATGTTTGGGACATGGCATTAGCATTATTGAGGTTACAAGAGGT
1 CCCACGTAAGACCATGTTTGGGACATGGCATTAGCATTATCGAGG-TACAAGAGGT
* * **
40619 CCCACGTAAGACCATGTCTAGGACATGGCATT-G-A-TATCGA-G-ATGAGAGGT
1 CCCACGTAAGACCATGTTTGGGACATGGCATTAGCATTATCGAGGTACAAGAGGT
*
40669 CCCCCCGTAAGACCATGTTTGGGACATGGCAT
1 -CCCACGTAAGACCATGTTTGGGACATGGCAT
40701 GGGCACCGAC
Statistics
Matches: 72, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
50 7 0.10
51 28 0.39
52 1 0.01
53 5 0.07
54 1 0.01
55 1 0.01
56 29 0.40
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.25
Consensus pattern (55 bp):
CCCACGTAAGACCATGTTTGGGACATGGCATTAGCATTATCGAGGTACAAGAGGT
Found at i:40715 original size:51 final size:50
Alignment explanation
Indices: 40613--40734 Score: 127
Period size: 51 Copynumber: 2.4 Consensus size: 50
40603 TGAGGTTACA
* * * *
40613 AGAGGTCCCACGTAAGACCATGTCTAGGACATGGCATTGATATCGAGATG
1 AGAGGTCCCACGTAAGACCATGTCTAGGACATGGCATGGACACCGACATG
* * * *
40663 AGAGGTCCCCCCGTAAGACCATGTTTGGGACATGGCATGGGCACCGACATG
1 AGAGGT-CCCACGTAAGACCATGTCTAGGACATGGCATGGACACCGACATG
** **
40714 AGAACTCTTACGTAAGACCAT
1 AGAGGTCCCACGTAAGACCAT
40735 ATCTGGTATA
Statistics
Matches: 58, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
50 18 0.31
51 40 0.69
ACGTcount: A:0.29, C:0.24, G:0.27, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCACGTAAGACCATGTCTAGGACATGGCATGGACACCGACATG
Found at i:41030 original size:20 final size:20
Alignment explanation
Indices: 41005--41043 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
40995 TAAGTTATTT
41005 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
41025 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
41044 GAAGAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:42458 original size:50 final size:49
Alignment explanation
Indices: 42397--42509 Score: 127
Period size: 50 Copynumber: 2.3 Consensus size: 49
42387 GTACATGTAT
* * ** *
42397 GCTCATACGAGCTATGAATCGGTATGCTCTCACAAGCTGTAAATTGGTAA
1 GCTCATACGAGCTA-GAATCGATAAGCTCTCACAAGCTACAAATCGGTAA
* * **
42447 GCTCAGACGAGCCGAGAATCGATAAGCTCTCATGAGCTACAAATCGGTAA
1 GCTCATACGAG-CTAGAATCGATAAGCTCTCACAAGCTACAAATCGGTAA
42497 GCTCATACGAGCT
1 GCTCATACGAGCT
42510 GTGGTGTGTC
Statistics
Matches: 51, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
49 1 0.02
50 48 0.94
51 2 0.04
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (49 bp):
GCTCATACGAGCTAGAATCGATAAGCTCTCACAAGCTACAAATCGGTAA
Found at i:42508 original size:25 final size:25
Alignment explanation
Indices: 42397--42509 Score: 72
Period size: 25 Copynumber: 4.5 Consensus size: 25
42387 GTACATGTAT
** *
42397 GCTCATACGAGCTATGAATCGGTAT
1 GCTCATACGAGCTACAAATCGGTAA
* ** *
42422 GCTC-TCACAAGCTGTAAATTGGTAA
1 GCTCAT-ACGAGCTACAAATCGGTAA
* *
42447 GCTCAGACGAGC--CGAGAATCGATAA
1 GCTCATACGAGCTAC-A-AATCGGTAA
*
42472 GCTC-TCATGAGCTACAAATCGGTAA
1 GCTCAT-ACGAGCTACAAATCGGTAA
42497 GCTCATACGAGCT
1 GCTCATACGAGCT
42510 GTGGTGTGTC
Statistics
Matches: 66, Mismatches: 14, Indels: 16
0.69 0.15 0.17
Matches are distributed among these distances:
24 2 0.03
25 61 0.92
26 2 0.03
27 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (25 bp):
GCTCATACGAGCTACAAATCGGTAA
Found at i:48468 original size:28 final size:28
Alignment explanation
Indices: 48428--48484 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
48418 TTGCTATAAG
*
48428 AAAACATGTTTTAAAATGACTAGGAGAT
1 AAAACATGTTTTAAAACGACTAGGAGAT
48456 AAAACATGTTTTAAAACGACTAGGAGAT
1 AAAACATGTTTTAAAACGACTAGGAGAT
48484 A
1 A
48485 TCATAGTATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.47, C:0.09, G:0.18, T:0.26
Consensus pattern (28 bp):
AAAACATGTTTTAAAACGACTAGGAGAT
Found at i:48946 original size:12 final size:12
Alignment explanation
Indices: 48929--48953 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
48919 CTCACACGCC
48929 CATGTGCTAGGT
1 CATGTGCTAGGT
48941 CATGTGCTAGGT
1 CATGTGCTAGGT
48953 C
1 C
48954 GTGTAACAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.20, G:0.32, T:0.32
Consensus pattern (12 bp):
CATGTGCTAGGT
Found at i:59905 original size:15 final size:15
Alignment explanation
Indices: 59861--59905 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
59851 TTGGTCGAAA
59861 AATTTTAATTATTATG
1 AATTTT-ATTATTATG
*
59877 AAATTTATTATTATG
1 AATTTTATTATTATG
59892 TAATTTTATT-TTAT
1 -AATTTTATTATTAT
59906 TTTTGTTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (15 bp):
AATTTTATTATTATG
Found at i:71185 original size:389 final size:389
Alignment explanation
Indices: 70468--71250 Score: 1305
Period size: 389 Copynumber: 2.0 Consensus size: 389
70458 TTAATTATAG
* * *
70468 CACTACAGAGAAAGAATTTTTGGTTGTAGTCTTTGCTTTCCACAAGTTTCGTTCTTATCTTGTCG
1 CACTACAGAGAAAGAATTGTTGGCTGTAGTCTTTGCTTTCAACAAGTTTCGTTCTTATCTTGTCG
* * * *
70533 ACACAAAGTTTACCGTATTTACTGATCAATTGGCGTTGAGATATCTTTTTACGAAGAAGGATGCA
66 ACACAAAGGTTACCGTATTTACTAATCAATCGGCGTTGAGATATCTTTTTACAAAGAAGGATGCA
*
70598 AAACCAAGAATTCGACATTGAGATAAAAGATCTCAAGGGTTCAAAAAATCAGGTTGCAGACCATC
131 AAACCAAGAATTCGACATCGAGATAAAAGATCTCAAGGGTTCAAAAAATCAGGTTGCAGACCATC
* * *
70663 TATCTCGATTGGAAGTTGGCAGTGAAGATGGAAACATACTTCAAATTGTCTACGCATTCCCAGAT
196 TATCTCGATTGAAAGTTGGCAGCGAAGATGGAAACATACTTCAAATTGTCGACGCATTCCCAGAT
*
70728 GAGAAGTTATTTGCTATAGATGCAACCCCTTGGTATGCAGATTTGGTTAATTATCTAGTGTATGG
261 GAGAAGTTATTTGCTATAGATGCAACCCCTTAGTATGCAGATTTGGTTAATTATCTAGTGTATGG
*
70793 AAAACTCCCATTGGTTGTAACAGGCCATAAAAAAGAAAGATTTCTTCATGAAGTAGTGAAGTAC
326 AAAACTCCCATTGGGTGTAACAGGCCATAAAAAAGAAAGATTTCTTCATGAAGTAGTGAAGTAC
* *
70857 CACTACAGAGAAAGAATTGTTGGCTGTAGTCTTTGCTTTCAACAAGTTTTGTTCTTATCTTTTCG
1 CACTACAGAGAAAGAATTGTTGGCTGTAGTCTTTGCTTTCAACAAGTTTCGTTCTTATCTTGTCG
* * * *
70922 GCCCAAAGGTTACCGTATTTACTAATCACTCGTCGTTGAGATATCTTTTTACAAAGAAGGATGCA
66 ACACAAAGGTTACCGTATTTACTAATCAATCGGCGTTGAGATATCTTTTTACAAAGAAGGATGCA
*
70987 AAACCAAGAATTCGACATCGAGATAAAAGATCTCAAGGGTTCAGAAAATCAGGTTGCAGACCATC
131 AAACCAAGAATTCGACATCGAGATAAAAGATCTCAAGGGTTCAAAAAATCAGGTTGCAGACCATC
*
71052 TATCTCGATTGAAAGTTGGCAGCGAAGATGGAAACATACTTCAAATTGTCGATGCATTCCCAGAT
196 TATCTCGATTGAAAGTTGGCAGCGAAGATGGAAACATACTTCAAATTGTCGACGCATTCCCAGAT
* * * * * *
71117 GAGAAGTTATTTGCTGTAGGTGGAACCTCTTAGTATGCGGATTTGGTTAGTTATCTAGTGTATGG
261 GAGAAGTTATTTGCTATAGATGCAACCCCTTAGTATGCAGATTTGGTTAATTATCTAGTGTATGG
* *
71182 AAAACTCCCATTGGGTGTCACAGGCCATAAAAAAGAAAGATTTCTTCATGAAGTATTGAAGTAC
326 AAAACTCCCATTGGGTGTAACAGGCCATAAAAAAGAAAGATTTCTTCATGAAGTAGTGAAGTAC
71246 CACTA
1 CACTA
71251 GAACAAGCCG
Statistics
Matches: 365, Mismatches: 29, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
389 365 1.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.31
Consensus pattern (389 bp):
CACTACAGAGAAAGAATTGTTGGCTGTAGTCTTTGCTTTCAACAAGTTTCGTTCTTATCTTGTCG
ACACAAAGGTTACCGTATTTACTAATCAATCGGCGTTGAGATATCTTTTTACAAAGAAGGATGCA
AAACCAAGAATTCGACATCGAGATAAAAGATCTCAAGGGTTCAAAAAATCAGGTTGCAGACCATC
TATCTCGATTGAAAGTTGGCAGCGAAGATGGAAACATACTTCAAATTGTCGACGCATTCCCAGAT
GAGAAGTTATTTGCTATAGATGCAACCCCTTAGTATGCAGATTTGGTTAATTATCTAGTGTATGG
AAAACTCCCATTGGGTGTAACAGGCCATAAAAAAGAAAGATTTCTTCATGAAGTAGTGAAGTAC
Done.