Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2058
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: 25731
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2174 original size:16 final size:16
Alignment explanation
Indices: 2149--2182 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2139 ATCTCATTAG
2149 TTATTAATAATAAAAA
1 TTATTAATAATAAAAA
* *
2165 TTATTTATAATAATAA
1 TTATTAATAATAAAAA
2181 TT
1 TT
2183 TAAAAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTATTAATAATAAAAA
Found at i:2417 original size:28 final size:29
Alignment explanation
Indices: 2380--2434 Score: 71
Period size: 28 Copynumber: 1.9 Consensus size: 29
2370 TATTTATAAA
2380 AAATATTAAATATT-TT-TTTAATTAAATTT
1 AAATATTAAA-ATTATTATTT-ATTAAATTT
2409 AAATA-TAAAATTATTATTTATTAAAT
1 AAATATTAAAATTATTATTTATTAAAT
2435 AAACAACAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
27 3 0.12
28 13 0.54
29 8 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
AAATATTAAAATTATTATTTATTAAATTT
Found at i:2661 original size:14 final size:15
Alignment explanation
Indices: 2642--2674 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
2632 ATAACTTTTA
*
2642 TTTTTGGTGGAA-AT
1 TTTTTGGTGAAACAT
2656 TTTTTGGTGAAACAT
1 TTTTTGGTGAAACAT
2671 TTTT
1 TTTT
2675 ATTTTTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.21, C:0.03, G:0.21, T:0.55
Consensus pattern (15 bp):
TTTTTGGTGAAACAT
Found at i:3518 original size:48 final size:49
Alignment explanation
Indices: 3458--3551 Score: 136
Period size: 48 Copynumber: 1.9 Consensus size: 49
3448 ATATATCTTT
* *
3458 TTTAATAAGCACAAATTTAGATTTTC-CTTTTTCTTTCTTTAATATATA
1 TTTAATAAGCACAAACTTAAATTTTCTCTTTTTCTTTCTTTAATATATA
* *
3506 TTTAATAAGCACAAACTTAAATTTTCTTCTTTTTTTTTTTTTAATA
1 TTTAATAAGCACAAACTTAAATTTTC-TCTTTTTCTTTCTTTAATA
3552 ATTTGTGAGT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 24 0.60
50 16 0.40
ACGTcount: A:0.31, C:0.12, G:0.03, T:0.54
Consensus pattern (49 bp):
TTTAATAAGCACAAACTTAAATTTTCTCTTTTTCTTTCTTTAATATATA
Found at i:3781 original size:32 final size:33
Alignment explanation
Indices: 3739--3815 Score: 122
Period size: 32 Copynumber: 2.4 Consensus size: 33
3729 ACTTATCAAT
* *
3739 TTAAATTTGAAACTGCCTTAAACTC-AAATAAC
1 TTAAACTTGAAAATGCCTTAAACTCAAAATAAC
3771 TTAAACTTGAAAATGCCTTAAACTCAAAATAAC
1 TTAAACTTGAAAATGCCTTAAACTCAAAATAAC
3804 TTAAAC-TGAAAA
1 TTAAACTTGAAAA
3816 GACTCAAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
32 29 0.69
33 13 0.31
ACGTcount: A:0.48, C:0.17, G:0.06, T:0.29
Consensus pattern (33 bp):
TTAAACTTGAAAATGCCTTAAACTCAAAATAAC
Found at i:3806 original size:16 final size:16
Alignment explanation
Indices: 3755--3815 Score: 70
Period size: 16 Copynumber: 3.8 Consensus size: 16
3745 TTGAAACTGC
3755 CTTAAACTC-AAATAA
1 CTTAAACTCAAAATAA
* **
3770 CTTAAACTTGAAAATGC
1 CTTAAAC-TCAAAATAA
3787 CTTAAACTCAAAATAA
1 CTTAAACTCAAAATAA
*
3803 CTTAAACTGAAAA
1 CTTAAACTCAAAA
3816 GACTCAAATT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
15 7 0.19
16 19 0.51
17 11 0.30
ACGTcount: A:0.51, C:0.18, G:0.05, T:0.26
Consensus pattern (16 bp):
CTTAAACTCAAAATAA
Found at i:4056 original size:16 final size:16
Alignment explanation
Indices: 4031--4096 Score: 53
Period size: 16 Copynumber: 4.1 Consensus size: 16
4021 ATTTGAATTT
*
4031 AAAATGACTCAAAATA
1 AAAATAACTCAAAATA
* * *
4047 AAAATAACTCGAACTC
1 AAAATAACTCAAAATA
*
4063 AAAATAAC-CTAAAATC
1 AAAATAACTC-AAAATA
* *
4079 AAAATGATTCAAAATA
1 AAAATAACTCAAAATA
4095 AA
1 AA
4097 TAATTTAAAC
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
15 1 0.03
16 37 0.95
17 1 0.03
ACGTcount: A:0.61, C:0.15, G:0.05, T:0.20
Consensus pattern (16 bp):
AAAATAACTCAAAATA
Found at i:4122 original size:46 final size:47
Alignment explanation
Indices: 4031--4123 Score: 107
Period size: 46 Copynumber: 2.0 Consensus size: 47
4021 ATTTGAATTT
* * *
4031 AAAATGACTCAAAATAAAAATAACTCGAACTCAAAATAACCTAAAATC
1 AAAATGACTCAAAAT-AAAATAACTCAAACTAAAAATAACATAAAATC
* * * *
4079 AAAATGATTCAAAAT-AAATAATTTAAACTAAAAATAATATAAAAT
1 AAAATGACTCAAAATAAAATAACTCAAACTAAAAATAACATAAAAT
4124 TTAAAAACTT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
46 24 0.63
48 14 0.37
ACGTcount: A:0.61, C:0.12, G:0.03, T:0.24
Consensus pattern (47 bp):
AAAATGACTCAAAATAAAATAACTCAAACTAAAAATAACATAAAATC
Found at i:19717 original size:1 final size:1
Alignment explanation
Indices: 19711--19776 Score: 51
Period size: 1 Copynumber: 66.0 Consensus size: 1
19701 CTTCATACGC
* * * * * ** * *
19711 AAAAAAAACAAAAAATAGAAAAAAACAAAAAAAAAACAAAAAAAAAACCAAGAAAAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
19776 A
1 A
19777 TAGAAAGAGG
Statistics
Matches: 49, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.86, C:0.09, G:0.03, T:0.02
Consensus pattern (1 bp):
A
Found at i:19734 original size:17 final size:16
Alignment explanation
Indices: 19712--19782 Score: 65
Period size: 17 Copynumber: 4.2 Consensus size: 16
19702 TTCATACGCA
19712 AAAAAAACAAAAAATAG
1 AAAAAAA-AAAAAATAG
19729 AAAAAAACAAAAAA-A-
1 AAAAAAA-AAAAAATAG
*
19744 AAACAAAAAAAAAACCAAG
1 AAA-AAAAAAAAAA--TAG
19763 AAAAAAAACAAAAATAG
1 AAAAAAAA-AAAAATAG
19780 AAA
1 AAA
19783 GAGGTCCATA
Statistics
Matches: 47, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
15 9 0.19
16 5 0.11
17 19 0.40
18 6 0.13
19 8 0.17
ACGTcount: A:0.85, C:0.08, G:0.04, T:0.03
Consensus pattern (16 bp):
AAAAAAAAAAAAATAG
Found at i:20961 original size:20 final size:19
Alignment explanation
Indices: 20936--21006 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
20926 ACCCTGAAAA
20936 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
20956 GTATCGATACAAATTGCAT
1 GTATCGATACACATTAAAT
**
20975 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
20996 GTATCGATACA
1 GTATCGATACA
21007 GGACATTGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.10
20 35 0.85
21 2 0.05
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:21091 original size:53 final size:54
Alignment explanation
Indices: 20976--21113 Score: 242
Period size: 54 Copynumber: 2.6 Consensus size: 54
20966 AAATTGCATA
20976 GTATCGATACACACAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTTT
1 GTATCGATACACAC-AATATGTATCGATACAGGACATTGGCAGTAGCCAAATTTT
*
21031 GTATCGATACACACAATATGTATCGATACAGGTCATTGGCAGTAGCCAAA-TTT
1 GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTTT
*
21084 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACACAATATGTATCGATACA
21114 TTGGAAGTAG
Statistics
Matches: 81, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
53 32 0.40
54 35 0.43
55 14 0.17
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (54 bp):
GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTTT
Found at i:22465 original size:28 final size:28
Alignment explanation
Indices: 22420--22715 Score: 301
Period size: 28 Copynumber: 10.8 Consensus size: 28
22410 CGTTCAGCTC
* * *
22420 TTCATAGCCCACAAGTCAGTAGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
22448 TTTAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* ** *
22476 TTTAAAGCCCACAAGTCAG-AACACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
22503 TTCAAAGCCCACAAGTTAGTGGTATCC-
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
22530 TTCAAAGCCCCACAAGTCAGTGGCATATCCTT
1 TTCAAAG-CCCACAAGTCAGTGGC--ATCC-T
*
22562 TTCAAAG-CC-CAAGT-AGTGGTATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
22587 TTC-AAG-CC-C-AGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
22611 TTCAAA--CCATAAGTCAGTGGGCACTCTT
1 TTCAAAGCCCACAAGTCAGT-GGCA-TCCT
22639 TTC-AAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
22666 TTCAAAGCCCACAAGTCAGTAGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
22694 TTCAAAGCCCACGAGCCAGTGG
1 TTCAAAGCCCACAAGTCAGTGG
22716 TAACTCTTTT
Statistics
Matches: 227, Mismatches: 26, Indels: 30
0.80 0.09 0.11
Matches are distributed among these distances:
23 3 0.01
24 21 0.09
25 6 0.03
26 11 0.05
27 41 0.18
28 116 0.51
29 16 0.07
30 6 0.03
32 7 0.03
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.23
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:22511 original size:55 final size:56
Alignment explanation
Indices: 22425--22705 Score: 262
Period size: 55 Copynumber: 5.1 Consensus size: 56
22415 AGCTCTTCAT
*
22425 AGCCCACAAGTCAGTAGCACCCTTTTAAAGCCCACAAGTCAGTGGCATCCTTTTAA
1 AGCCCACAAGTCAGTAGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTAA
* * * *
22481 AGCCCACAAGTCAG-AACACCCTTTCAAAGCCCACAAGTTAGTGGTATCC-TTCAA
1 AGCCCACAAGTCAGTAGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTAA
* * * *
22535 AGCCCCACAAGTCAGTGGCATATCCTTTTCAAAG-CC-CAAGT-AGTGGTATCC-TTTCA
1 AG-CCCACAAGTCAGTAGC--A-CCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTAA
* * * *
22591 AG-CC-C-AGTCAGTGGCATCCTTTCAAA--CCATAAGTCAGTGGGCA-CTCTTTTCA
1 AGCCCACAAGTCAGTAGCACCCTTTCAAAGCCCACAAGTCAGT-GGCATC-CTTTTAA
* * * * *
22643 AGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTAGCACCCTTTCAA
1 AGCCCACAAGTCAGTAGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTAA
22699 AGCCCAC
1 AGCCCAC
22706 GAGCCAGTGG
Statistics
Matches: 191, Mismatches: 18, Indels: 32
0.79 0.07 0.13
Matches are distributed among these distances:
48 2 0.01
49 12 0.06
50 5 0.03
51 4 0.02
52 17 0.09
53 3 0.02
54 9 0.05
55 64 0.34
56 45 0.24
57 17 0.09
58 3 0.02
59 10 0.05
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (56 bp):
AGCCCACAAGTCAGTAGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTTAA
Found at i:22698 original size:83 final size:83
Alignment explanation
Indices: 22420--22715 Score: 290
Period size: 83 Copynumber: 3.6 Consensus size: 83
22410 CGTTCAGCTC
* * *
22420 TTCATAGCCCACAAGTCAGTAGCACCCTTTTAAAGCCCACAAGTCAGTGGCATCCTTTTAAAGCC
1 TTCAAAGCCCACAAGTCAGTAGCACCCTTTCAAA-CCCACAAGTCAGTGGCATCCTTTTCAAGCC
** *
22485 CACAAGTCAG-AACACCCT
65 CACAAGTCAGTGGCATCCT
* * * *
22503 TTCAAAGCCCACAAGTTAGTGGTATCC-TTCAAAGCCCCACAAGTCAGTGGCATATCCTTTTCAA
1 TTCAAAGCCCACAAGTCAGTAGCACCCTTTCAAA--CCCACAAGTCAGTGGC--ATCCTTTTC-A
*
22567 AG-CC-CAAGT-AGTGGTATCCT
61 AGCCCACAAGTCAGTGGCATCCT
* * *
22587 TTC-AAG-CC-C-AGTCAGTGGCATCCTTTCAAA-CCATAAGTCAGTGGGCA-CTCTTTTCAAGC
1 TTCAAAGCCCACAAGTCAGTAGCACCCTTTCAAACCCACAAGTCAGT-GGCATC-CTTTTCAAGC
22646 CCACAAGTCAGTGGCATCCT
64 CCACAAGTCAGTGGCATCCT
* *
22666 TTCAAAGCCCACAAGTCAGTAGCACCCTTTCAAAGCCCACGAGCCAGTGG
1 TTCAAAGCCCACAAGTCAGTAGCACCCTTTCAAA-CCCACAAGTCAGTGG
22716 TAACTCTTTT
Statistics
Matches: 175, Mismatches: 21, Indels: 33
0.76 0.09 0.14
Matches are distributed among these distances:
76 4 0.02
77 9 0.05
78 16 0.09
79 16 0.09
80 15 0.09
81 9 0.05
82 8 0.05
83 62 0.35
84 14 0.08
85 19 0.11
86 3 0.02
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.23
Consensus pattern (83 bp):
TTCAAAGCCCACAAGTCAGTAGCACCCTTTCAAACCCACAAGTCAGTGGCATCCTTTTCAAGCCC
ACAAGTCAGTGGCATCCT
Found at i:22752 original size:32 final size:30
Alignment explanation
Indices: 22633--22764 Score: 103
Period size: 28 Copynumber: 4.5 Consensus size: 30
22623 GTCAGTGGGC
* * *
22633 ACTCTTTTC-AAGCCCACAAGTCAGTGG-C
1 ACTCTTTTCAAAGCCCACGAGCCAGTGGTA
* * * * *
22661 A-TCCTTTCAAAGCCCACAAGTCAGTAG-C
1 ACTCTTTTCAAAGCCCACGAGCCAGTGGTA
*
22689 AC-CCTTTCAAAGCCCACGAGCCAGTGGTA
1 ACTCTTTTCAAAGCCCACGAGCCAGTGGTA
* * *
22718 ACTCTTTTCAAAGCTCACACGAGTCGGTGTTA
1 ACTCTTTTCAAAGC-C-CACGAGCCAGTGGTA
22750 ACTCTTTTCAAAGCC
1 ACTCTTTTCAAAGCC
22765 TACACAAGTT
Statistics
Matches: 88, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
27 6 0.07
28 42 0.48
29 2 0.02
30 10 0.11
31 2 0.02
32 26 0.30
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (30 bp):
ACTCTTTTCAAAGCCCACGAGCCAGTGGTA
Done.