Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3122
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: 34183
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:3740 original size:71 final size:71
Alignment explanation
Indices: 3495--3776 Score: 433
Period size: 72 Copynumber: 3.9 Consensus size: 71
3485 CATAATAATG
* **
3495 AAACAGAAA-TGAAAATACCTCAATGTGTC-TGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1 AAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
3558 TTTTTTTGA
66 ---TTTTGA
* * * *
3567 CAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
1 AAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTG-
3632 ATTTTGA
65 ATTTTGA
3639 AAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
1 AAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
3704 TTTTGA
66 TTTTGA
* *
3710 AAACAGAAATTGAAATTACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
1 AAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
3775 TT
66 TT
3777 CTTTAAAAAC
Statistics
Matches: 195, Mismatches: 12, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
71 72 0.37
72 74 0.38
73 17 0.09
74 31 0.16
75 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (71 bp):
AAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA
TTTTGA
Found at i:3853 original size:87 final size:87
Alignment explanation
Indices: 3707--3946 Score: 292
Period size: 87 Copynumber: 2.8 Consensus size: 87
3697 GAGTTGATTT
* ** * **
3707 TGAAAACAGAAATTGAAATTACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGT
1 TGAAAACAGAAATTGAAAATACCTCGGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
3772 TGATTCTTT-AAAAACATAATAA
66 TGATTCTTTGAAAAACA-AATAA
* *
3794 TGAAAACAGAAATGGAAAATACCTCGGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGT
1 TGAAAACAGAAATTGAAAATACCTCGGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
* * *
3859 TGATTTTTTGAAAAAGAAATCA
66 TGATTCTTTGAAAAACAAATAA
* **
3881 --AAAGC-TTAATTG-AAATACCTCGGCGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TGAAAACAGAAATTGAAAATACCTC-G-GTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
3942 GTTGA
64 GTTGA
3947 AATTAAAACA
Statistics
Matches: 134, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
83 9 0.07
84 5 0.04
85 45 0.34
87 69 0.51
88 6 0.04
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (87 bp):
TGAAAACAGAAATTGAAAATACCTCGGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
TGATTCTTTGAAAAACAAATAA
Found at i:4094 original size:122 final size:122
Alignment explanation
Indices: 3917--4410 Score: 413
Period size: 122 Copynumber: 3.8 Consensus size: 122
3907 GTGTCCTGAG
** * *
3917 GCTCAACTCACCTCTCGCAATATGAGTTGAAATTAAAACAAAAATTGAAAATACCTCAGCGTGCC
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAACAGAAATTGAAAATACCTCAGCGTGAC
3982 CCGAGGCTCAACTCACCTCT-GCAATATGAGTTGATTTTGAAAAGTAGAAATTAAAAG-
66 CCGAGGCTCAACTCACCTCTCGCAATATGA-TTGATTTTGAAAA-TAGAAATTAAAAGA
* * * *
4039 GTTCAAC-CACCTCTCGCAATATGAGTTGATTTTGAAAACAGAAATTGAAATTACCTCATCGTGT
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTT-AAAACAGAAATTGAAAATACCTCAGCGTGA
* **** * * ****
4103 CCTGAGGCTCAACTCACCTCTCGCAATATGAATTGA-AAAAAAAATACCACAGTGTGTCTGA
65 CCCGAGGCTCAACTCACCTCTCGCAATATG-ATTGATTTTGAAAATA-GA-AAT-TAAAAGA
4164 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAACAGAAATTGAAAATACCTCAGCATG
1 GCTCAACTCACCTCTCGCAATATGAGTTGA-TTTT-AAAACAGAAATTGAAAATACCTCAGC--G
* ** *
4229 TGAACCGAGGCTCAACTCACCTCTCGCAATATGATTTTTTTTGAAAACAGAAATTGAAATACCTC
62 TGACCCGAGGCTCAACTCACCTCTCGCAATATGATTGATTTTGAAAATAGAAATT--AA-A----
4294 AGCGTGTCTGA
120 A--------GA
** *
4305 GGCTCAACTCATTTCTCGCAATAT-AGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAGCGT
1 -GCTCAACTCACCTCTCGCAATATGAGTTG-ATTTT-AAAACAGAAATTGAAAATACCTCAGCGT
* * **
4369 GTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
63 GACCCGAGGCTCAACTCACCTCTCGCAATATGA-TTGATTTT
4411 TTAACAACAG
Statistics
Matches: 293, Mismatches: 49, Indels: 42
0.76 0.13 0.11
Matches are distributed among these distances:
121 26 0.09
122 57 0.19
123 14 0.05
124 3 0.01
125 6 0.02
126 23 0.08
127 30 0.10
128 4 0.01
129 36 0.12
139 30 0.10
140 6 0.02
141 36 0.12
142 22 0.08
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.28
Consensus pattern (122 bp):
GCTCAACTCACCTCTCGCAATATGAGTTGATTTTAAAACAGAAATTGAAAATACCTCAGCGTGAC
CCGAGGCTCAACTCACCTCTCGCAATATGATTGATTTTGAAAATAGAAATTAAAAGA
Found at i:4393 original size:71 final size:72
Alignment explanation
Indices: 4147--4497 Score: 468
Period size: 73 Copynumber: 4.9 Consensus size: 72
4137 GAAAAAAAAA
* * *
4147 TACCACAGTGTGT-CTGA-GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAACAGAAA
1 TACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAA
*
4210 TTGAAAA
66 TTGAAAT
* *
4217 TACCTCAGCATGTGAACC-GAGGCTCAACTCACCTCTCGCAATATGA-TT-TTTTTTGAAAACAG
1 TACCTCAGC--GTG-TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAG
4279 AAATTGAAA-
63 AAATTGAAAT
** *
4288 TACCTCAGCGTGT-CTGAGGCTCAACTCATTTCTCGCAATAT-AGTTGAATTTTGAAAACAGAAA
1 TACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAA
4351 TTGAAAT
66 TTGAAAT
** *
4358 TACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTAACAACAGAA
1 TACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAA-AACAGAA
4423 ATTGAAAT
65 ATTGAAAT
* *
4431 TACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGA-TTTTGAAAAACAAAA
1 TACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAACAGAA
4495 ATT
65 ATT
4498 AAAAGGCTTA
Statistics
Matches: 251, Mismatches: 17, Indels: 24
0.86 0.06 0.08
Matches are distributed among these distances:
67 2 0.01
68 26 0.10
69 24 0.10
70 20 0.08
71 37 0.15
72 49 0.20
73 67 0.27
74 26 0.10
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (72 bp):
TACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAA
TTGAAAT
Found at i:4411 original size:141 final size:142
Alignment explanation
Indices: 4144--4501 Score: 478
Period size: 141 Copynumber: 2.5 Consensus size: 142
4134 ATTGAAAAAA
* * * *
4144 AAATACCACAGTGTGTCTGA-GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTAAAAACAGA
1 AAATACCTCAGCGTGTCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGA
*
4208 AATTGAAAATACCTCAGCATGTGAACCGAGGCTCAACTCACCTCTCGCAATATGATTTTTTTTGA
66 AATTGAAAATACCTCAGCA-GTGAACCGAGGCTCAACTCACCTCTCGCAATATGATTATTTTTGA
4273 A-AACAGAAATTG
130 ACAACAGAAATTG
**
4285 AAATACCTCAGCGTGTCTGAGGCTCAACTCATTTCTCGCAATAT-AGTTGAATTTTGAAAACAGA
1 AAATACCTCAGCGTGTCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGA
* * **
4349 AATTGAAATTACCTCAGC-GTG-TCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTT
66 AATTGAAAATACCTCAGCAGTGAACC-GAGGCTCAACTCACCTCTCGCAATATGA-TT-ATTTTT
*
4412 TAACAACAGAAATTG
128 GAACAACAGAAATTG
*
4427 AAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTG-ATTTTGAAAAAC
1 AAA-TACCTCAGCGTGT-CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTG-AAAAC
*
4491 AAAAATT-AAAA
63 AGAAATTGAAAA
4502 GGCTTAACTC
Statistics
Matches: 191, Mismatches: 17, Indels: 15
0.86 0.08 0.07
Matches are distributed among these distances:
138 2 0.01
139 29 0.15
140 2 0.01
141 60 0.31
142 35 0.18
143 13 0.07
144 34 0.18
145 16 0.08
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.29
Consensus pattern (142 bp):
AAATACCTCAGCGTGTCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGA
AATTGAAAATACCTCAGCAGTGAACCGAGGCTCAACTCACCTCTCGCAATATGATTATTTTTGAA
CAACAGAAATTG
Found at i:4646 original size:68 final size:70
Alignment explanation
Indices: 4501--4673 Score: 219
Period size: 68 Copynumber: 2.5 Consensus size: 70
4491 AAAAATTAAA
* * * * **
4501 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTTAAAACATAAACTAAAAATACCTCGGCGTG
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACATAAACTAAAAATACCTCAACGTG
4565 CCCCG
66 CCCCG
*
4570 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAA-A-AAATTAAAAATACCTCAACGTG
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACATAAACTAAAAATACCTCAACGTG
* **
4633 TCTTG
66 CCCCG
4638 AGGCTCAACTCA-TCTCTCGCAATATGAGTTGATTTT
1 AGGCTCAACTCACT-TCTCGCAATATGAGTTGATTTT
4674 CCTTGGAAAG
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
67 1 0.01
68 55 0.60
69 27 0.29
70 9 0.10
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (70 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACATAAACTAAAAATACCTCAACGTG
CCCCG
Found at i:17965 original size:22 final size:22
Alignment explanation
Indices: 17935--17997 Score: 99
Period size: 22 Copynumber: 2.9 Consensus size: 22
17925 TACGAGGGCT
*
17935 GTGGAGGTATGGGACTGCTGTA
1 GTGGAGGTATGGGGCTGCTGTA
* *
17957 GTGGGGGTATGGGGCCGCTGTA
1 GTGGAGGTATGGGGCTGCTGTA
17979 GTGGAGGTATGGGGCTGCT
1 GTGGAGGTATGGGGCTGCT
17998 TCATGGTTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.13, C:0.11, G:0.51, T:0.25
Consensus pattern (22 bp):
GTGGAGGTATGGGGCTGCTGTA
Found at i:22777 original size:31 final size:30
Alignment explanation
Indices: 22719--22785 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 30
22709 CAATTTAAGA
* *
22719 AAAAAGTGTCAAGTTTAGGTACTAAATTAGG
1 AAAAAGTGACAAGTTTAGGCACTAAATT-GG
*
22750 AAAAAGTGACAAGTTTGGGCA-TCAAATTGG
1 AAAAAGTGACAAGTTTAGGCACT-AAATTGG
22780 ACAAAA
1 A-AAAA
22786 AAAGTTTAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.45, C:0.09, G:0.22, T:0.24
Consensus pattern (30 bp):
AAAAAGTGACAAGTTTAGGCACTAAATTGG
Found at i:29766 original size:13 final size:13
Alignment explanation
Indices: 29748--29776 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
29738 TTTAGTTTAA
29748 TTAGTTAATTAGT
1 TTAGTTAATTAGT
29761 TTAGTTAATTAGT
1 TTAGTTAATTAGT
29774 TTA
1 TTA
29777 ATAAACAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (13 bp):
TTAGTTAATTAGT
Done.