Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3184
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: 28366
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.32
Found at i:695 original size:27 final size:27
Alignment explanation
Indices: 657--745 Score: 117
Period size: 27 Copynumber: 3.2 Consensus size: 27
647 GTGACAGAGT
657 CACCAGATACAGATATTTGTGGCAGTGC
1 CACCAGA-ACAGATATTTGTGGCAGTGC
** *
685 CACCAGAACAGATATACGTGGCAGGGC
1 CACCAGAACAGATATTTGTGGCAGTGC
712 CACCAGAACAGATAATTTGTGGCA-TAGC
1 CACCAGAACAGAT-ATTTGTGGCAGT-GC
740 CACCAG
1 CACCAG
746 GACGCTTCCT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
27 30 0.57
28 23 0.43
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.18
Consensus pattern (27 bp):
CACCAGAACAGATATTTGTGGCAGTGC
Found at i:900 original size:28 final size:27
Alignment explanation
Indices: 851--913 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 27
841 AAATTAACCC
*
851 TAGGGGTA-AAGGTCATTTTGCATACA
1 TAGGGGTATAAGGTAATTTTGCATACA
877 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAA-GGTAATTTTGCATACA
905 TAGGGGTAT
1 TAGGGGTAT
914 TCTAGTACAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
26 8 0.24
27 2 0.06
28 24 0.71
ACGTcount: A:0.30, C:0.08, G:0.29, T:0.33
Consensus pattern (27 bp):
TAGGGGTATAAGGTAATTTTGCATACA
Found at i:8489 original size:28 final size:27
Alignment explanation
Indices: 8446--8535 Score: 90
Period size: 28 Copynumber: 3.2 Consensus size: 27
8436 GTGACAGAGT
* *
8446 CACCAGATACAGATATTTTGTGGTAGTGC
1 CACCAGA-ACAGATA-TTTGTGGCAGGGC
* **
8475 CATCAGAACAGATATACGTGGCAGGGC
1 CACCAGAACAGATATTTGTGGCAGGGC
**
8502 CACCAGAACAGATAATTTGTGGCATAGC
1 CACCAGAACAGAT-ATTTGTGGCAGGGC
8530 CACCAG
1 CACCAG
8536 GACGCTTCTT
Statistics
Matches: 50, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
27 21 0.42
28 23 0.46
29 6 0.12
ACGTcount: A:0.32, C:0.22, G:0.24, T:0.21
Consensus pattern (27 bp):
CACCAGAACAGATATTTGTGGCAGGGC
Found at i:8688 original size:28 final size:28
Alignment explanation
Indices: 8641--8705 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
8631 AAATTAACCC
* *
8641 TAGGGGTATAAAGGTCATTTTGTATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
*
8669 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
8697 TAGGGGTAT
1 TAGGGGTAT
8706 TCTAGTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.31, C:0.06, G:0.28, T:0.35
Consensus pattern (28 bp):
TAGGGGTATAAAGGTAATTTTGCATACA
Found at i:10534 original size:38 final size:38
Alignment explanation
Indices: 10438--10525 Score: 126
Period size: 38 Copynumber: 2.3 Consensus size: 38
10428 GGGGCGTTAC
* *
10438 ATATTACCAGCACGAAGCCTG-CGAGATTTAACCCGGAT
1 ATATTACCAGCACGAAGCCTGTAG-GATTTAACCCAGAT
10476 ATATTACCAGCACGAAGCCTGTAGGATTTAACCCAGAT
1 ATATTACCAGCACGAAGCCTGTAGGATTTAACCCAGAT
10514 ATAATT-CCAGCA
1 AT-ATTACCAGCA
10526 TATAGCCTGC
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
38 42 0.91
39 4 0.09
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (38 bp):
ATATTACCAGCACGAAGCCTGTAGGATTTAACCCAGAT
Found at i:10888 original size:45 final size:43
Alignment explanation
Indices: 10822--10956 Score: 155
Period size: 43 Copynumber: 3.1 Consensus size: 43
10812 ACATAACATT
*
10822 TCATTTCACCGACATTATAGCCTGCTAGGCTCAAAGGCTCGAATAA
1 TCATTTCACCGGCATTATAGCCTGCTAGGCTCAAA-GC-CGAAT-A
* * * *
10868 T-ATTTCACCGGCATCATAGCCTACTAAGCTCAAAGCCGGATA
1 TCATTTCACCGGCATTATAGCCTGCTAGGCTCAAAGCCGAATA
* * *
10910 TCATTTCACCAGCATTATAGCCTGCTAGGCCCGAAGCCTGAATA
1 TCATTTCACCGGCATTATAGCCTGCTAGGCTCAAAGCC-GAATA
10954 TCA
1 TCA
10957 CAGTTCGATA
Statistics
Matches: 75, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
42 2 0.03
43 34 0.45
44 9 0.12
45 29 0.39
46 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (43 bp):
TCATTTCACCGGCATTATAGCCTGCTAGGCTCAAAGCCGAATA
Found at i:10930 original size:43 final size:45
Alignment explanation
Indices: 10822--10932 Score: 131
Period size: 45 Copynumber: 2.5 Consensus size: 45
10812 ACATAACATT
* *
10822 TCATTTCACCGACATTATAGCCTGCTAGGCTCAAAGGCTCGAATAA
1 TCATTTCACCG-CATTATAGCCTACTAAGCTCAAAGGCTCGAATAA
* *
10868 T-ATTTCACCGGCATCATAGCCTACTAAGCTCAAA-GC-CGGAT-A
1 TCATTTCACC-GCATTATAGCCTACTAAGCTCAAAGGCTCGAATAA
10910 TCATTTCACCAGCATTATAGCCT
1 TCATTTCACC-GCATTATAGCCT
10933 GCTAGGCCCG
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
42 2 0.04
43 23 0.40
44 2 0.04
45 28 0.49
46 2 0.04
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (45 bp):
TCATTTCACCGCATTATAGCCTACTAAGCTCAAAGGCTCGAATAA
Found at i:16303 original size:38 final size:38
Alignment explanation
Indices: 16255--16418 Score: 247
Period size: 38 Copynumber: 4.3 Consensus size: 38
16245 GGCTCAAAGG
* * *
16255 CCCGAATATAATACCAGCACTAGGCCTGCAGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCAGGATTTAA
* *
16293 CCCGGATATAATACCAGCACGAAGCCTGCGGGAATTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCAGGATTTAA
* *
16331 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCAGGATTTAA
* *
16369 CCCGGATATATTACAAGCACGAAGCCTGCAGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCAGGATTTAA
16407 CCCGGATATAAT
1 CCCGGATATAAT
16419 TCTAGCATAT
Statistics
Matches: 116, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 116 1.00
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.20
Consensus pattern (38 bp):
CCCGGATATAATACCAGCACGAAGCCTGCAGGATTTAA
Found at i:16847 original size:43 final size:44
Alignment explanation
Indices: 16722--16839 Score: 168
Period size: 45 Copynumber: 2.7 Consensus size: 44
16712 ACATAACATT
*
16722 TCATTTCACCGGCATTATAGCCTGCTAGGCTCAAAGGCTCGAATAA
1 TCATTTCACCGGCATTATAGCCTGCTAGGCTCAAA-GC-CCAATAA
* * *
16768 T-ATTTCACCGGCATCATAGCCTACTAAGCTCAAAGCCCAA-AA
1 TCATTTCACCGGCATTATAGCCTGCTAGGCTCAAAGCCCAATAA
16810 TCATTTCACCGGCATTATAGCCTGCTAGGC
1 TCATTTCACCGGCATTATAGCCTGCTAGGC
16840 CTGAAGCCTG
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
42 3 0.05
43 28 0.44
44 2 0.03
45 30 0.47
46 1 0.02
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (44 bp):
TCATTTCACCGGCATTATAGCCTGCTAGGCTCAAAGCCCAATAA
Found at i:25085 original size:68 final size:64
Alignment explanation
Indices: 24868--25120 Score: 210
Period size: 68 Copynumber: 3.8 Consensus size: 64
24858 ATATAGTTCG
* * * *
24868 GCTCTCTTGTAC-ACATGGTGAACACTCAGTACCACCCATGTGACCTAGCCA-ATTTA-TCTCGT
1 GCTCTCTTGT-CTACATGGTGTACACT-AGTACCACCCATGCGACCTAGCTACATATATTCTCGT
24930 A
64 A
* * * * *
24931 GCTCTCTTGTCTACATGGTGTCCTTCACCTGGAACCACGCATGCGACCTAGCTACATATA-TCCC
1 GCTCTCTTGTCTACATGGTG---TACA-CTAGTACCACCCATGCGACCTAGCTACATATATTCTC
24995 GTA
62 GTA
* *
24998 GCTCTCTTGTCTACATGGTGTACACATAGTATCACCCATGCGACCTAGCTACATCATAATGTCTT
1 GCTCTCTTGTCTACATGGTGTACAC-TAGTACCACCCATGCGACCTAGCTACAT-AT-AT-TCTC
25063 GTA
62 GTA
* ** ** *
25066 GCTCTCTTGTAC-ACATGGTGTGCACTCAGCCCCATACATGTGACCTAGCTACATA
1 GCTCTCTTGT-CTACATGGTGTACACT-AGTACCACCCATGCGACCTAGCTACATA
25121 CTATCTGTAT
Statistics
Matches: 154, Mismatches: 23, Indels: 22
0.77 0.12 0.11
Matches are distributed among these distances:
62 1 0.01
63 19 0.12
64 27 0.18
65 2 0.01
66 22 0.14
67 34 0.22
68 48 0.31
69 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (64 bp):
GCTCTCTTGTCTACATGGTGTACACTAGTACCACCCATGCGACCTAGCTACATATATTCTCGTA
Found at i:25100 original size:64 final size:62
Alignment explanation
Indices: 24868--25086 Score: 158
Period size: 67 Copynumber: 3.3 Consensus size: 62
24858 ATATAGTTCG
* * * * *
24868 GCTCTCTTGTAC-ACATGGTGAACAC-TCAGTACCACCCATGTGACCTAGCCA-ATTTATCTCGT
1 GCTCTCTTGT-CTACATGGTGTACACAT-AGT--CACCCATGCGACCTAGCTACATATATCCCGT
24930 A
62 A
* * ** *
24931 GCTCTCTTGTCTACATGGTGTCCTTCACCTGGAACCACGCATGCGACCTAGCTACATATATCCCG
1 GCTCTCTTGTCTACATGGTG---TACACAT--AGTCACCCATGCGACCTAGCTACATATATCCCG
24996 TA
61 TA
**
24998 GCTCTCTTGTCTACATGGTGTACACATAGTATCACCCATGCGACCTAGCTACATCATAATGTCTT
1 GCTCTCTTGTCTACATGGTGTACACATAG--TCACCCATGCGACCTAGCTACAT-AT-A--TCCC
25063 GTA
60 GTA
25066 GCTCTCTTGTAC-ACATGGTGT
1 GCTCTCTTGT-CTACATGGTGT
25087 GCACTCAGCC
Statistics
Matches: 125, Mismatches: 17, Indels: 23
0.76 0.10 0.14
Matches are distributed among these distances:
62 2 0.02
63 18 0.14
64 26 0.21
65 2 0.02
66 20 0.16
67 31 0.25
68 25 0.20
69 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.31
Consensus pattern (62 bp):
GCTCTCTTGTCTACATGGTGTACACATAGTCACCCATGCGACCTAGCTACATATATCCCGTA
Found at i:25817 original size:30 final size:30
Alignment explanation
Indices: 25783--25843 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
25773 TCCTTAACTC
25783 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
25813 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
25843 A
1 A
25844 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Done.