Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2047
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: 22829
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Found at i:7928 original size:28 final size:28
Alignment explanation
Indices: 7847--7928 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
7837 TTTTGGAGAT
*
7847 AATAACGAGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-AT-CCTCGATGA
* * *
7875 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCTCGATGA
7903 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCTCGAT
7929 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 40 0.89
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:8071 original size:51 final size:51
Alignment explanation
Indices: 7911--8081 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
7901 GAAATAACGA
* * *
7911 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
7963 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
8016 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
8067 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
8082 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 39 0.40
52 16 0.16
53 32 0.33
54 10 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:8127 original size:27 final size:28
Alignment explanation
Indices: 8064--8139 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
8054 AAAATAAAGT
*
8064 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
8092 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
8119 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
8140 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:10629 original size:13 final size:13
Alignment explanation
Indices: 10611--10636 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10601 ACAAAGATCC
10611 ATGTATCGATACA
1 ATGTATCGATACA
10624 ATGTATCGATACA
1 ATGTATCGATACA
10637 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:10632 original size:33 final size:33
Alignment explanation
Indices: 10590--10656 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
10580 AAAATTTCCA
***
10590 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
10623 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
10656 A
1 A
10657 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:10700 original size:19 final size:18
Alignment explanation
Indices: 10676--10743 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
10666 CAGTAGCTAA
10676 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
10695 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
10710 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
10727 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
10744 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:10716 original size:13 final size:13
Alignment explanation
Indices: 10698--10722 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10688 ACAATACTTA
10698 TGTATCGATACAT
1 TGTATCGATACAT
10711 TGTATCGATACA
1 TGTATCGATACA
10723 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:10720 original size:32 final size:32
Alignment explanation
Indices: 10679--10741 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
10669 TAGCTAATTA
*
10679 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
10711 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
10742 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:10824 original size:21 final size:21
Alignment explanation
Indices: 10800--10855 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
10790 CATTTGTAGG
10800 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
10821 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
10842 ATGTATCGATACAT
1 ATGTATCGATACAT
10856 GTAAATGTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.32
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:10892 original size:17 final size:17
Alignment explanation
Indices: 10870--10902 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
10860 ATGTGTATTT
10870 AATTTTTTTTTTTTTTC
1 AATTTTTTTTTTTTTTC
10887 AATTTTTTTTTTTTTT
1 AATTTTTTTTTTTTTT
10903 TGTTCAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (17 bp):
AATTTTTTTTTTTTTTC
Found at i:12024 original size:30 final size:30
Alignment explanation
Indices: 11988--12051 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 30
11978 TCATTTGTGA
11988 TTTTTTGATACCAAATGTGTTCAG-GTTGAT
1 TTTTTTGATACCAAATGTG-TCAGAGTTGAT
* *
12018 TTTTTTGATACTAAATGTGTCCGAGTTGAT
1 TTTTTTGATACCAAATGTGTCAGAGTTGAT
12048 TTTT
1 TTTT
12052 CAAAGTTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 3 0.10
30 28 0.90
ACGTcount: A:0.22, C:0.09, G:0.19, T:0.50
Consensus pattern (30 bp):
TTTTTTGATACCAAATGTGTCAGAGTTGAT
Found at i:12752 original size:80 final size:79
Alignment explanation
Indices: 12483--12773 Score: 342
Period size: 80 Copynumber: 3.7 Consensus size: 79
12473 TAACATATCG
* * * *
12483 ATTTTCCACCATCGAGGATACTCC-ACCTTGTTATTTCGAGGGGATACTCCAA-CTCCAGTTATG
1 ATTTTCCACCATCGGGGATACTCCAACCTTGTTATTTCGAGAGGATACTCCAACCTCGA-TTTTG
* *
12546 TTTCTA-AAGCACCA
65 TTTCTACAAACACTA
* * *
12560 ATTTTTCACTATCGGGGATACT-CAACCTTGTTATTTCTGAGGGGATACTCCAACCTCGATTTTG
1 ATTTTCCACCATCGGGGATACTCCAACCTTGTTATTTC-GAGAGGATACTCCAACCTCGATTTTG
*
12624 TTTTTAC-AACA-TCA
65 TTTCTACAAACACT-A
* * * *
12638 ATTTTCCACCATCGGGGATATTCCAACCCTGTTATTTTCGAGAGGATACTCCAACCTTGATTTTA
1 ATTTTCCACCATCGGGGATACTCCAACCTTGTTA-TTTCGAGAGGATACTCCAACCTCGATTTTG
12703 TTTCTACAAACACTA
65 TTTCTACAAACACTA
* * *
12718 ATTTTTCACCATCGGGGATACTCCAACCTTGTTATTTCCGAAAAGATACTCCAACC
1 ATTTTCCACCATCGGGGATACTCCAACCTTGTTATTT-CGAGAGGATACTCCAACC
12774 CTAATTTTGC
Statistics
Matches: 183, Mismatches: 21, Indels: 17
0.83 0.10 0.08
Matches are distributed among these distances:
76 1 0.01
77 32 0.17
78 47 0.26
79 46 0.25
80 56 0.31
81 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.34
Consensus pattern (79 bp):
ATTTTCCACCATCGGGGATACTCCAACCTTGTTATTTCGAGAGGATACTCCAACCTCGATTTTGT
TTCTACAAACACTA
Found at i:12781 original size:80 final size:79
Alignment explanation
Indices: 12464--12824 Score: 356
Period size: 79 Copynumber: 4.6 Consensus size: 79
12454 TCATTGATGT
* * * * * * *
12464 TTTTATTTCTAACATATCGATTTTCCACCATCGAGGATACTCC-ACCTTGTTATTT-CGAGGGGA
1 TTTTGTTTCTAAAACATCAATTTTTCACCATCGGGGATACTCCAACCTTGTTATTTCCGAGAGGA
*
12527 TACTCCAACTCC-AG
66 TACTCCAAC-CCTAA
* * * * * *
12541 TTATGTTTCTAAAGCACCAATTTTTCACTATCGGGGATACT-CAACCTTGTTATTTCTGAGGGGA
1 TTTTGTTTCTAAAACATCAATTTTTCACCATCGGGGATACTCCAACCTTGTTATTTCCGAGAGGA
*
12605 TACTCCAA-CCTCGA
66 TACTCCAACCCT-AA
* * * * * *
12619 TTTTGTTTTTACAACATCAATTTTCCACCATCGGGGATATTCCAACCCTGTTATTTTCGAGAGGA
1 TTTTGTTTCTAAAACATCAATTTTTCACCATCGGGGATACTCCAACCTTGTTATTTCCGAGAGGA
* *
12684 TACTCCAACCTTGA
66 TACTCCAACCCTAA
* * *
12698 TTTTATTTCTACAAACA-CTAATTTTTCACCATCGGGGATACTCCAACCTTGTTATTTCCGAAAA
1 TTTTGTTTCTA-AAACATC-AATTTTTCACCATCGGGGATACTCCAACCTTGTTATTTCCGAGAG
12762 GATACTCCAACCCTAA
64 GATACTCCAACCCTAA
* * * * * *
12778 TTTTGCTTCCAAAATATCAACTTTTCACCATTGGGGATACTCTAACC
1 TTTTGTTTCTAAAACATCAATTTTTCACCATCGGGGATACTCCAACC
12825 CCATTTTTAT
Statistics
Matches: 231, Mismatches: 44, Indels: 16
0.79 0.15 0.05
Matches are distributed among these distances:
76 3 0.01
77 43 0.19
78 48 0.21
79 69 0.30
80 68 0.29
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (79 bp):
TTTTGTTTCTAAAACATCAATTTTTCACCATCGGGGATACTCCAACCTTGTTATTTCCGAGAGGA
TACTCCAACCCTAA
Found at i:12797 original size:159 final size:156
Alignment explanation
Indices: 12477--12825 Score: 400
Period size: 159 Copynumber: 2.2 Consensus size: 156
12467 TATTTCTAAC
* * * *
12477 ATATCGATTTTCCACCATCGAGGATACTCC-ACCTTGTTATTTCGAGGGGATACTCCAACTCCAG
1 ATATCAATTTTCCACCATCGGGGATACTCCAACCCTGTTATTTCGAGAGGATACTCCAACTCCAG
* * * * ***
12541 TTATGTTTCTAAAGCACCAATTTTTCACTATCGGGGATACTCAACCTTGTTATTTCTGAGGGGAT
66 TTATATTTCTAAAACACCAATTTTTCACCATCGGGGATACTCAACCTTGTTATTTCCGAAAAGAT
* * ** *
12606 ACTCCAACCTCGATTTTGTTTTTACA
131 ACTCCAACCTCAATTTTGCTTCCAAA
* * **
12632 ACATCAATTTTCCACCATCGGGGATATTCCAACCCTGTTATTTTCGAGAGGATACTCCAAC-CTT
1 ATATCAATTTTCCACCATCGGGGATACTCCAACCCTGTTA-TTTCGAGAGGATACTCCAACTCCA
* *
12696 GATTTTATTTCTACAAACACTAATTTTTCACCATCGGGGATACTCCAACCTTGTTATTTCCGAAA
65 G-TTATATTTCTA-AAACACCAATTTTTCACCATCGGGGATACT-CAACCTTGTTATTTCCGAAA
12761 AGATACTCCAACC-CTAATTTTGCTTCCAAA
127 AGATACTCCAACCTC-AATTTTGCTTCCAAA
* *
12791 ATATCAACTTTT-CACCATTGGGGATACTCTAACCC
1 ATATCAA-TTTTCCACCATCGGGGATACTCCAACCC
12826 CATTTTTATT
Statistics
Matches: 161, Mismatches: 26, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
155 26 0.16
156 10 0.06
157 28 0.17
158 28 0.17
159 65 0.40
160 4 0.02
ACGTcount: A:0.27, C:0.26, G:0.13, T:0.34
Consensus pattern (156 bp):
ATATCAATTTTCCACCATCGGGGATACTCCAACCCTGTTATTTCGAGAGGATACTCCAACTCCAG
TTATATTTCTAAAACACCAATTTTTCACCATCGGGGATACTCAACCTTGTTATTTCCGAAAAGAT
ACTCCAACCTCAATTTTGCTTCCAAA
Found at i:12825 original size:51 final size:51
Alignment explanation
Indices: 12762--12877 Score: 153
Period size: 51 Copynumber: 2.3 Consensus size: 51
12752 TTTCCGAAAA
* * *
12762 GATACTCCAACCCTAATTTTGCTTCCAAAATATCAACTTT-TCACCATTGGG
1 GATACTCCAACCCCAATTTTACTTCCAAAATATCAA-TTTCTCACCATCGGG
* * *
12813 GATACTCTAACCCCATTTTTATTTCCAAAATATCAATTTCTCACCATCGGG
1 GATACTCCAACCCCAATTTTACTTCCAAAATATCAATTTCTCACCATCGGG
*
12864 GATATTCCAACCCC
1 GATACTCCAACCCC
12878 GTTGTTTTTG
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
50 3 0.05
51 53 0.95
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (51 bp):
GATACTCCAACCCCAATTTTACTTCCAAAATATCAATTTCTCACCATCGGG
Found at i:14615 original size:51 final size:53
Alignment explanation
Indices: 14515--14616 Score: 136
Period size: 51 Copynumber: 2.0 Consensus size: 53
14505 CCCTAGAAAG
* *
14515 TATCGATACACATCCAAATGTATCGATACATTATGCTTTGTATCGATACATTA
1 TATCGATACACATCCAAATGTATCGATACATTATCCATTGTATCGATACATTA
** * *
14568 TATCGATACATGTCC-ATTGTATCGATACA-TGTCCATTGTATCGATACAT
1 TATCGATACACATCCAAATGTATCGATACATTATCCATTGTATCGATACAT
14617 ACTCAATTGT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
51 17 0.40
52 13 0.30
53 13 0.30
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (53 bp):
TATCGATACACATCCAAATGTATCGATACATTATCCATTGTATCGATACATTA
Found at i:14627 original size:20 final size:19
Alignment explanation
Indices: 14563--14637 Score: 114
Period size: 19 Copynumber: 3.9 Consensus size: 19
14553 TGTATCGATA
*
14563 CATTATATCGATACATGTC
1 CATTGTATCGATACATGTC
14582 CATTGTATCGATACATGTC
1 CATTGTATCGATACATGTC
*
14601 CATTGTATCGATACATACTC
1 CATTGTATCGATACAT-GTC
*
14621 AATTGTATCGATACATG
1 CATTGTATCGATACATG
14638 AAACTGGTAG
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 34 0.67
20 17 0.33
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (19 bp):
CATTGTATCGATACATGTC
Found at i:14632 original size:39 final size:38
Alignment explanation
Indices: 14563--14637 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 38
14553 TGTATCGATA
* *
14563 CATTATATCGATACATGTCCATTGTATCGATACATGTC
1 CATTATATCGATACATCTCAATTGTATCGATACATGTC
*
14601 CATTGTATCGATACATACTCAATTGTATCGATACATG
1 CATTATATCGATACAT-CTCAATTGTATCGATACATG
14638 AAACTGGTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 15 0.45
39 18 0.55
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (38 bp):
CATTATATCGATACATCTCAATTGTATCGATACATGTC
Found at i:14705 original size:13 final size:13
Alignment explanation
Indices: 14687--14711 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14677 CATGGCACAT
14687 TGTATCGATACAC
1 TGTATCGATACAC
14700 TGTATCGATACA
1 TGTATCGATACA
14712 TGAAGAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Done.