Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2793
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: 75405
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:3429 original size:40 final size:40
Alignment explanation
Indices: 3374--3587 Score: 326
Period size: 40 Copynumber: 5.4 Consensus size: 40
3364 TGATAACCGA
* *
3374 GCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCCGG
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCCGG
3414 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGG
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGG
*
3454 GCTGAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGG
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGG
* *
3494 GCTAGGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGG
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGG
*
3534 GCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATATCC-G
1 GCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGG
*
3573 GCTAAATCCCGAAGG
1 GCTAAGTCCCGAAGG
3588 TACTTGGTTT
Statistics
Matches: 162, Mismatches: 10, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
39 17 0.10
40 144 0.89
41 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (40 bp):
GCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGG
Found at i:12622 original size:21 final size:20
Alignment explanation
Indices: 12596--12635 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
12586 GCATTACGGT
12596 AAGTTGGGCCTCAAGGGGCTG
1 AAGTTGGGCC-CAAGGGGCTG
*
12617 AAGTTGGGCCCAATGGGCT
1 AAGTTGGGCCCAAGGGGCT
12636 TTCGGGCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.20, C:0.20, G:0.40, T:0.20
Consensus pattern (20 bp):
AAGTTGGGCCCAAGGGGCTG
Found at i:13021 original size:20 final size:20
Alignment explanation
Indices: 12980--13054 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
12970 ATACGTGGGA
12980 TATGATAT--ACATGAT-TG
1 TATGATATGCACATGATATG
*
12997 ATATGATATGCACATGCTATG
1 -TATGATATGCACATGATATG
13018 TATGATATGCACATGATATG
1 TATGATATGCACATGATATG
*
13038 TATGAAATGCACATGAT
1 TATGATATGCACATGAT
13055 GAATTCATAA
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
18 8 0.16
20 41 0.80
21 2 0.04
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.35
Consensus pattern (20 bp):
TATGATATGCACATGATATG
Found at i:13133 original size:26 final size:26
Alignment explanation
Indices: 13104--13165 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
13094 GAGGAAGTGC
**
13104 AAAAGGGCTTATGCCCCAATTTATTG
1 AAAAGGGCTTATGCCCCAATTTACCG
*
13130 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAATTTACCG
13156 AAAAGGGCTT
1 AAAAGGGCTT
13166 TACCCCAGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.26
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAATTTACCG
Found at i:21754 original size:40 final size:39
Alignment explanation
Indices: 21710--21842 Score: 167
Period size: 40 Copynumber: 3.3 Consensus size: 39
21700 AACCCAATTA
* ** * *
21710 CCTTCGGGATTTAGCCTGGATGTAACAACCAGCACAAATT
1 CCTTCGGGACTTA-CCTGGAAATAACAACCAGCACGAATG
* *
21750 CCTTCGGGACTTAACTCGGAAATAGCAACCAGCACGAATG
1 CCTTCGGGACTTACCT-GGAAATAACAACCAGCACGAATG
*
21790 CCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATG
1 CCTTCGGGACTT-ACCTGGAAATAACAACCAGCACGAATG
21830 CCTTCGGGACTTA
1 CCTTCGGGACTTA
21843 ACCCGGATAA
Statistics
Matches: 81, Mismatches: 10, Indels: 5
0.84 0.10 0.05
Matches are distributed among these distances:
39 3 0.04
40 76 0.94
41 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.20
Consensus pattern (39 bp):
CCTTCGGGACTTACCTGGAAATAACAACCAGCACGAATG
Found at i:21843 original size:40 final size:40
Alignment explanation
Indices: 21732--21849 Score: 200
Period size: 40 Copynumber: 3.0 Consensus size: 40
21722 AGCCTGGATG
* * *
21732 TAACAACCAGCACAAATTCCTTCGGGACTTAACTCGGAAA
1 TAACAACCAGCACGAATGCCTTCGGGACTTAACCCGGAAA
*
21772 TAGCAACCAGCACGAATGCCTTCGGGACTTAACCCGGAAA
1 TAACAACCAGCACGAATGCCTTCGGGACTTAACCCGGAAA
21812 TAACAACCAGCACGAATGCCTTCGGGACTTAACCCGGA
1 TAACAACCAGCACGAATGCCTTCGGGACTTAACCCGGA
21850 TAAAATCCTC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 73 1.00
ACGTcount: A:0.34, C:0.30, G:0.19, T:0.17
Consensus pattern (40 bp):
TAACAACCAGCACGAATGCCTTCGGGACTTAACCCGGAAA
Found at i:27266 original size:41 final size:41
Alignment explanation
Indices: 27209--27354 Score: 195
Period size: 41 Copynumber: 3.6 Consensus size: 41
27199 GGTTTAAATT
27209 CGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCATAATC
1 CGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCATAATC
*
27250 CGAGCTTGGTCTCGAAGGGCTTTTGAGCCCGTGTCATAA-C
1 CGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCATAATC
* * * * * * * * *
27290 CGAACCTAGTTTCGAAAGGCCTTCGGGCCAATGTCATAATC
1 CGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCATAATC
27331 CGAGCTTGGTCTCGAAGGGCTTTT
1 CGAGCTTGGTCTCGAAGGGCTTTT
27355 TGAGTCAGCG
Statistics
Matches: 86, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
40 30 0.35
41 56 0.65
ACGTcount: A:0.20, C:0.24, G:0.28, T:0.28
Consensus pattern (41 bp):
CGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGTGTCATAATC
Found at i:41587 original size:43 final size:42
Alignment explanation
Indices: 41539--41629 Score: 121
Period size: 42 Copynumber: 2.1 Consensus size: 42
41529 CCCGGACGTA
* **
41539 GTCTTACATGTAATTCA-ATATCGATGCCTCTGTCCCAGACAGG
1 GTCTTACATG-AAATCAGATAT-GATGCCGATGTCCCAGACAGG
*
41582 GTCTTACATGAAATCAGATATGATGCCGATGTCCCAGACATG
1 GTCTTACATGAAATCAGATATGATGCCGATGTCCCAGACAGG
41624 GTCTTA
1 GTCTTA
41630 TACGTAAATC
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
42 29 0.67
43 14 0.33
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (42 bp):
GTCTTACATGAAATCAGATATGATGCCGATGTCCCAGACAGG
Found at i:41617 original size:42 final size:43
Alignment explanation
Indices: 41539--41674 Score: 125
Period size: 43 Copynumber: 3.2 Consensus size: 43
41529 CCCGGACGTA
* **
41539 GTCTTACATGTAATTCAATATCGATGCCTCTGTCCCAGACAGG
1 GTCTTACATGTAAATCAATATCGATGCCGATGTCCCAGACAGG
*
41582 GTCTTACATG-AAATCAGATAT-GATGCCGATGTCCCAGACATG
1 GTCTTACATGTAAATCA-ATATCGATGCCGATGTCCCAGACAGG
* * * * * * *
41624 GTCTTATACGTAAATCTCA-ATCGAGGCCTATGTCCCAAACACG
1 GTCTTACATGTAAATC-AATATCGATGCCGATGTCCCAGACAGG
*
41667 TTCTTACA
1 GTCTTACA
41675 CGATGTCTCT
Statistics
Matches: 76, Mismatches: 13, Indels: 8
0.78 0.13 0.08
Matches are distributed among these distances:
42 33 0.43
43 43 0.57
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.29
Consensus pattern (43 bp):
GTCTTACATGTAAATCAATATCGATGCCGATGTCCCAGACAGG
Found at i:61190 original size:34 final size:34
Alignment explanation
Indices: 61138--61214 Score: 102
Period size: 34 Copynumber: 2.3 Consensus size: 34
61128 AAATAGTCTA
* * *
61138 GCCTAAGCCCTTATCAGTAGCAATATCAGTGTGG
1 GCCTTAGCCCTTATCAGTAGCAATAGCAATGTGG
*
61172 GCCTTAGCCCATTA-CAGTAGCAGTAGCAATGTGG
1 GCCTTAGCCC-TTATCAGTAGCAATAGCAATGTGG
61206 GCCTTAGCC
1 GCCTTAGCC
61215 TAATTCAGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
34 35 0.92
35 3 0.08
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.25
Consensus pattern (34 bp):
GCCTTAGCCCTTATCAGTAGCAATAGCAATGTGG
Found at i:61224 original size:34 final size:33
Alignment explanation
Indices: 61151--61229 Score: 97
Period size: 34 Copynumber: 2.4 Consensus size: 33
61141 TAAGCCCTTA
* * * *
61151 TCAGTAGCAATATCAGTGTGGGCCTTAGCCCAT
1 TCAGTAGCAGTAGCAATGTGGGCCTTAGCCAAT
61184 TACAGTAGCAGTAGCAATGTGGGCCTTAGCCTAAT
1 T-CAGTAGCAGTAGCAATGTGGGCCTTAGCC-AAT
61219 TCAGTA-CAGTA
1 TCAGTAGCAGTA
61230 TTAGAGATGC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
33 6 0.15
34 31 0.77
35 3 0.08
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.27
Consensus pattern (33 bp):
TCAGTAGCAGTAGCAATGTGGGCCTTAGCCAAT
Found at i:64844 original size:16 final size:16
Alignment explanation
Indices: 64823--64853 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
64813 AACCCAACCC
*
64823 ATGCAACATGTCATGT
1 ATGCAAAATGTCATGT
64839 ATGCAAAATGTCATG
1 ATGCAAAATGTCATG
64854 CCCATATTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (16 bp):
ATGCAAAATGTCATGT
Found at i:65669 original size:27 final size:27
Alignment explanation
Indices: 65610--65694 Score: 75
Period size: 27 Copynumber: 3.1 Consensus size: 27
65600 CATATTCGTT
*
65610 ATTTTACCATACAGGGGTATTACGGTC
1 ATTTTACCATACAGGGGTATTACAGTC
* *
65637 ACTTTACCCTACAGGGGCT-TTACAGTC
1 ATTTTACCATACAGGGG-TATTACAGTC
* * **
65664 TTTTTACC-TATTAGGGGTATTTTAGTC
1 ATTTTACCATA-CAGGGGTATTACAGTC
65691 ATTT
1 ATTT
65695 CATCCTATAA
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
26 3 0.07
27 42 0.91
28 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (27 bp):
ATTTTACCATACAGGGGTATTACAGTC
Found at i:65755 original size:27 final size:27
Alignment explanation
Indices: 65725--65858 Score: 96
Period size: 27 Copynumber: 4.9 Consensus size: 27
65715 GTAAATCTAC
65725 AAACCAAGGGTATTTCAGTAATTTTGT
1 AAACCAAGGGTATTTCAGTAATTTTGT
* *
65752 AAACCAATGGTATTTTTA-TAATTTT-T
1 AAACCAAGGGTA-TTTCAGTAATTTTGT
* *
65778 AAAAAGTCAAGGGTATTTCTGTAATTTTGT
1 --AAA-CCAAGGGTATTTCAGTAATTTTGT
* * **
65808 AAATC-AGAGGTATTT-TGATAATTTTAC
1 AAACCAAG-GGTATTTCAG-TAATTTTGT
* *
65835 AAACTAAGGGTATTTCGGTAATTT
1 AAACCAAGGGTATTTCAGTAATTT
65859 CACAAACTAG
Statistics
Matches: 86, Mismatches: 11, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
26 5 0.06
27 50 0.58
28 16 0.19
29 14 0.16
30 1 0.01
ACGTcount: A:0.34, C:0.08, G:0.16, T:0.41
Consensus pattern (27 bp):
AAACCAAGGGTATTTCAGTAATTTTGT
Found at i:65863 original size:27 final size:27
Alignment explanation
Indices: 65813--65911 Score: 121
Period size: 27 Copynumber: 3.7 Consensus size: 27
65803 TTTGTAAATC
* *
65813 AGAGGTATTTTGATAATTTTACAAACT
1 AGAGGTATTTTGGTAATTTCACAAACT
*
65840 A-AGGGTATTTCGGTAATTTCACAAACT
1 AGA-GGTATTTTGGTAATTTCACAAACT
* *
65867 AGTGGTATTTTGGTAATTTTACAAACT
1 AGAGGTATTTTGGTAATTTCACAAACT
65894 AG-GGTTATTTTGGTAATT
1 AGAGG-TATTTTGGTAATT
65912 CTACCCTATA
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
26 3 0.05
27 60 0.95
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.41
Consensus pattern (27 bp):
AGAGGTATTTTGGTAATTTCACAAACT
Found at i:65874 original size:54 final size:54
Alignment explanation
Indices: 65722--65911 Score: 204
Period size: 54 Copynumber: 3.5 Consensus size: 54
65712 TTGGTAAATC
* * * * *
65722 TACAAACCAAGGGTATTTCAGTAATTTTGTAAACCAATGGTATTTTTATAATTTT
1 TACAAACTAAGGGTATTTCGGTAATTTTGTAAACTAGTGGTATTTTGATAA-TTT
* * * *
65777 TAAAAAGTCAAGGGTATTTCTGTAATTTTGTAAA-TCAGAGGTATTTTGATAATTT
1 TACAAACT-AAGGGTATTTCGGTAATTTTGTAAACT-AGTGGTATTTTGATAATTT
*** *
65832 TACAAACTAAGGGTATTTCGGTAATTTCACAAACTAGTGGTATTTTGGTAATTT
1 TACAAACTAAGGGTATTTCGGTAATTTTGTAAACTAGTGGTATTTTGATAATTT
*
65886 TACAAACT-AGGGTTATTTTGGTAATT
1 TACAAACTAAGGG-TATTTCGGTAATT
65912 CTACCCTATA
Statistics
Matches: 114, Mismatches: 17, Indels: 9
0.81 0.12 0.06
Matches are distributed among these distances:
53 4 0.04
54 58 0.51
55 15 0.13
56 37 0.32
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.41
Consensus pattern (54 bp):
TACAAACTAAGGGTATTTCGGTAATTTTGTAAACTAGTGGTATTTTGATAATTT
Found at i:68094 original size:31 final size:31
Alignment explanation
Indices: 68051--68114 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
68041 CCTTTTCATA
*
68051 TTTCGTATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
**
68082 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
68113 TT
1 TT
68115 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.22, C:0.23, G:0.17, T:0.38
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:68359 original size:23 final size:23
Alignment explanation
Indices: 68329--68400 Score: 144
Period size: 23 Copynumber: 3.1 Consensus size: 23
68319 CCTAGCCTCT
68329 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
68352 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
68375 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
68398 TTT
1 TTT
68401 TACACTTCCT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:68516 original size:20 final size:20
Alignment explanation
Indices: 68452--68510 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
68442 TATGATTACA
68452 TCATGTGCATATCATACATG
1 TCATGTGCATATCATACATG
68472 TCATGTGCATATCATACATG
1 TCATGTGCATATCATACATG
*
68492 TCATGCGCATATCATACAT
1 TCATGTGCATATCATACAT
68511 ACCATGTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.34
Consensus pattern (20 bp):
TCATGTGCATATCATACATG
Found at i:68586 original size:25 final size:25
Alignment explanation
Indices: 68554--68601 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
68544 ATACATAAAC
* * *
68554 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
68579 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
68602 CATGTTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Done.