Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2325
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: 64552
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:10336 original size:67 final size:68
Alignment explanation
Indices: 10258--10434 Score: 159
Period size: 67 Copynumber: 2.6 Consensus size: 68
10248 ATCATGTGTT
* * ** * *
10258 CAAGAAAGCTACGAGATACTATGTAGTAGCTAGGTCGCAT-GTGTGATACGGA-TGTA-TC-CCA
1 CAAGAGAGCTACGAGATA-TA--AAGTAGCTAGGTCGCATGGTGTGATACCAAGTGAAGGCACCA
10319 TGTAGA
63 TGTAGA
* *
10325 CAAGAGAGCTACGGAAGATGATAAATTAGCTAGGTCGCATGGTGTGATTCCAAGTGAAGGCACCA
1 CAAGAGAGCTAC-G-AGAT-ATAAAGTAGCTAGGTCGCATGGTGTGATACCAAGTGAAGGCACCA
10390 TGTAGA
63 TGTAGA
* * *
10396 CAAGAGAGCTACGAG--ATAAATTGGCTAGGTCACATGGTG
1 CAAGAGAGCTACGAGATATAAAGTAGCTAGGTCGCATGGTG
10435 GTACTAAGTG
Statistics
Matches: 93, Mismatches: 10, Indels: 15
0.79 0.08 0.13
Matches are distributed among these distances:
66 22 0.24
67 26 0.28
68 10 0.11
69 11 0.12
70 3 0.03
71 21 0.23
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.23
Consensus pattern (68 bp):
CAAGAGAGCTACGAGATATAAAGTAGCTAGGTCGCATGGTGTGATACCAAGTGAAGGCACCATGT
AGA
Found at i:16797 original size:68 final size:68
Alignment explanation
Indices: 16725--16900 Score: 175
Period size: 68 Copynumber: 2.6 Consensus size: 68
16715 CATCATGTGT
** * * *
16725 ACAAGAGAGCTACGAGATACTATGTAGTAGCTAGGTCACATGTGTGA-T-ACGGGATGTATC-CC
1 ACAAGAGAGCTACGAGATA-TAAAT-GTAGCTAGGTCACATGTGTGATTCAAGGGAAGGA-CACC
16787 ATGTAG
63 ATGTAG
* * *
16793 ACAAGAGAGCTACGGGAGAGATAAATGTAGCTAGGTCGCATGTGTGATTCCAAGTGAAGGACACC
1 ACAAGAGAGCTAC--GAGATATAAATGTAGCTAGGTCACATGTGTGATT-CAAGGGAAGGACACC
16858 ATGTAG
63 ATGTAG
*
16864 ACAAGAGAGCTACGAG--ATAAAT-TGGCTAGGTCACATG
1 ACAAGAGAGCTACGAGATATAAATGTAGCTAGGTCACATG
16901 GGTGGTACTA
Statistics
Matches: 92, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
66 13 0.14
67 6 0.07
68 33 0.36
69 7 0.08
70 6 0.07
71 27 0.29
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.22
Consensus pattern (68 bp):
ACAAGAGAGCTACGAGATATAAATGTAGCTAGGTCACATGTGTGATTCAAGGGAAGGACACCATG
TAG
Found at i:26769 original size:13 final size:13
Alignment explanation
Indices: 26753--26789 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
26743 ATAAGGGACA
26753 CATGGCCGTGTCG
1 CATGGCCGTGTCG
26766 CATGGCCGTGTCG
1 CATGGCCGTGTCG
*
26779 CATGGCTGTGT
1 CATGGCCGTGT
26790 GTCACACATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.08, C:0.27, G:0.38, T:0.27
Consensus pattern (13 bp):
CATGGCCGTGTCG
Found at i:46391 original size:23 final size:23
Alignment explanation
Indices: 46335--46381 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
46325 TCGCTGAAAC
46335 CACATGACCAAGAAATCCGACTT
1 CACATGACCAAGAAATCCGACTT
46358 CACATGACCAAGAAATCCGACTT
1 CACATGACCAAGAAATCCGACTT
46381 C
1 C
46382 TTTGAGCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.32, G:0.13, T:0.17
Consensus pattern (23 bp):
CACATGACCAAGAAATCCGACTT
Found at i:50267 original size:19 final size:20
Alignment explanation
Indices: 50225--50267 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
50215 TCATGCTTTC
* *
50225 TATTCACATTTTCATATTCA
1 TATTCAAATTTTCATAATCA
50245 -ATTCAAATTTTCA-AATCA
1 TATTCAAATTTTCATAATCA
50263 TATTC
1 TATTC
50268 CACATTCACG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.47
Consensus pattern (20 bp):
TATTCAAATTTTCATAATCA
Found at i:50693 original size:31 final size:32
Alignment explanation
Indices: 50628--50696 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 32
50618 ATCCATTTTC
*
50628 TCAATTCAATATCACTTTCAATTCATTTACAAA
1 TCAATTCAATATCACTTT-AATTCATATACAAA
*
50661 TCAATTCAATTTCACTTT-A-TCAATATACAAA
1 TCAATTCAATATCACTTTAATTC-ATATACAAA
50692 TCAAT
1 TCAAT
50697 ATTAATACTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 2 0.06
31 14 0.42
33 17 0.52
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (32 bp):
TCAATTCAATATCACTTTAATTCATATACAAA
Found at i:51439 original size:16 final size:15
Alignment explanation
Indices: 51409--51447 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
51399 CCCCTTTCCT
51409 TTCTTTCT-T-TTTC
1 TTCTTTCTCTGTTTC
51422 TTCTGTTCTCTGTTTC
1 TTCT-TTCTCTGTTTC
51438 TTCTTTCTCT
1 TTCTTTCTCT
51448 CTTTTGTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 4 0.17
14 4 0.17
15 7 0.30
16 8 0.35
ACGTcount: A:0.00, C:0.26, G:0.05, T:0.69
Consensus pattern (15 bp):
TTCTTTCTCTGTTTC
Found at i:52553 original size:21 final size:21
Alignment explanation
Indices: 52527--52571 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
52517 GTAATGTCAA
52527 CATATCACCTATTCAAACTAT
1 CATATCACCTATTCAAACTAT
52548 CATATCACCTATTCAAACTAT
1 CATATCACCTATTCAAACTAT
52569 CAT
1 CAT
52572 GCTTTCATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.29, G:0.00, T:0.33
Consensus pattern (21 bp):
CATATCACCTATTCAAACTAT
Found at i:53551 original size:20 final size:20
Alignment explanation
Indices: 53526--53595 Score: 68
Period size: 20 Copynumber: 3.3 Consensus size: 20
53516 GTAACATATA
53526 TCATGAACTCAGACCACAAC
1 TCATGAACTCAGACCACAAC
** * *
53546 TCATGAGTTCAGATGTCACATATA
1 TCATGAACTCAGA--CCACA-A-C
53570 TCATGAACTCAGACCACAAC
1 TCATGAACTCAGACCACAAC
53590 TCATGA
1 TCATGA
53596 GTTCAGATCA
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
20 17 0.45
21 1 0.03
22 8 0.21
23 1 0.03
24 11 0.29
ACGTcount: A:0.37, C:0.27, G:0.13, T:0.23
Consensus pattern (20 bp):
TCATGAACTCAGACCACAAC
Found at i:53582 original size:44 final size:44
Alignment explanation
Indices: 53519--53603 Score: 170
Period size: 44 Copynumber: 1.9 Consensus size: 44
53509 AACATGTGTA
53519 ACATATATCATGAACTCAGACCACAACTCATGAGTTCAGATGTC
1 ACATATATCATGAACTCAGACCACAACTCATGAGTTCAGATGTC
53563 ACATATATCATGAACTCAGACCACAACTCATGAGTTCAGAT
1 ACATATATCATGAACTCAGACCACAACTCATGAGTTCAGAT
53604 CACATAGTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.38, C:0.25, G:0.13, T:0.25
Consensus pattern (44 bp):
ACATATATCATGAACTCAGACCACAACTCATGAGTTCAGATGTC
Found at i:53601 original size:20 final size:20
Alignment explanation
Indices: 53534--53607 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
53524 TATCATGAAC
53534 TCAGACCACAACTCATGAGT
1 TCAGACCACAACTCATGAGT
* * **
53554 TCAGATGTCACATATATCATGAAC
1 TCAGA--CCACA-A-CTCATGAGT
53578 TCAGACCACAACTCATGAGT
1 TCAGACCACAACTCATGAGT
*
53598 TCAGATCACA
1 TCAGACCACA
53608 TAGTTCCTAG
Statistics
Matches: 41, Mismatches: 9, Indels: 8
0.71 0.16 0.14
Matches are distributed among these distances:
20 20 0.49
21 1 0.02
22 8 0.20
23 1 0.02
24 11 0.27
ACGTcount: A:0.36, C:0.27, G:0.14, T:0.23
Consensus pattern (20 bp):
TCAGACCACAACTCATGAGT
Found at i:54945 original size:25 final size:27
Alignment explanation
Indices: 54908--54960 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
54898 TCAAACATGC
54908 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
54934 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
54960 A
1 A
54961 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:56474 original size:32 final size:32
Alignment explanation
Indices: 56437--56501 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
56427 AATGCTTACC
56437 ATGCCCATCATCCATTAACTATTAAAATGCTA
1 ATGCCCATCATCCATTAACTATTAAAATGCTA
56469 ATGCCCATCATCCATTAACTATTAAAATGCTA
1 ATGCCCATCATCCATTAACTATTAAAATGCTA
56501 A
1 A
56502 AATGCATACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (32 bp):
ATGCCCATCATCCATTAACTATTAAAATGCTA
Found at i:61354 original size:12 final size:12
Alignment explanation
Indices: 61337--61367 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
61327 AGTACTACTT
61337 CGGCCTCGACCA
1 CGGCCTCGACCA
61349 CGGCCTCGACCA
1 CGGCCTCGACCA
61361 CGGCCTC
1 CGGCCTC
61368 TTCCCCGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.13, C:0.52, G:0.26, T:0.10
Consensus pattern (12 bp):
CGGCCTCGACCA
Found at i:62983 original size:25 final size:27
Alignment explanation
Indices: 62946--62995 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
62936 TCAAACATGC
62946 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
62972 ATTTCGGT-AATTTATCTCCTAGGG
1 ATTTAGGTCAATTTAACTCCTAGGG
62996 TAAAACTGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Done.