Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2504
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: 1293507
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.25
Warning! 302448 characters in sequence are not A, C, G, or T
File 7 of 7
Found at i:1279681 original size:36 final size:36
Alignment explanation
Indices: 1279625--1279739 Score: 130
Period size: 36 Copynumber: 3.3 Consensus size: 36
1279615 CCTTCTATTC
*
1279625 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
1 AAAGCCCACAACTTCGTGGCACTCTTTTTCCCTTTT
* * *
1279661 AAAGTCCACAACTTCATGGCAC-CTTGTT-CCTTTT
1 AAAGCCCACAACTTCGTGGCACTCTTTTTCCCTTTT
* **
1279695 -AAGTCCACAACTTCGTGGCA-TCTTTCACCCTTTTT
1 AAAGCCCACAACTTCGTGGCACTCTTTTTCCC-TTTT
1279730 AAAGCCCACA
1 AAAGCCCACA
1279740 CAAGTCGGTG
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
33 22 0.33
34 8 0.12
35 9 0.14
36 27 0.41
ACGTcount: A:0.23, C:0.33, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAGCCCACAACTTCGTGGCACTCTTTTTCCCTTTT
Found at i:1279704 original size:33 final size:36
Alignment explanation
Indices: 1279625--1279718 Score: 124
Period size: 33 Copynumber: 2.7 Consensus size: 36
1279615 CCTTCTATTC
* * *
1279625 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
1 AAAGTCCACAACTTCGTGGCACTCTTGTTCCCTTTT
*
1279661 AAAGTCCACAACTTCATGGCAC-CTTGTT-CCTTTT
1 AAAGTCCACAACTTCGTGGCACTCTTGTTCCCTTTT
1279695 -AAGTCCACAACTTCGTGGCA-TCTT
1 AAAGTCCACAACTTCGTGGCACTCTT
1279719 TCACCCTTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
33 22 0.42
34 6 0.12
35 5 0.10
36 19 0.37
ACGTcount: A:0.22, C:0.32, G:0.13, T:0.33
Consensus pattern (36 bp):
AAAGTCCACAACTTCGTGGCACTCTTGTTCCCTTTT
Found at i:1279766 original size:32 final size:32
Alignment explanation
Indices: 1279730--1279816 Score: 147
Period size: 32 Copynumber: 2.7 Consensus size: 32
1279720 CACCCTTTTT
*
1279730 AAAGCCCACACAAGTCGGTGGCAACCCCTCCC
1 AAAGCCCACACAAGTCGGTGGCAACCCCTCCA
*
1279762 AAAGCCCACACAAGTCGGTGGCAACCCTTCCA
1 AAAGCCCACACAAGTCGGTGGCAACCCCTCCA
*
1279794 AAAGCCCACACAAGTTGGTGGCA
1 AAAGCCCACACAAGTCGGTGGCA
1279817 TCTACCTTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.31, C:0.37, G:0.21, T:0.11
Consensus pattern (32 bp):
AAAGCCCACACAAGTCGGTGGCAACCCCTCCA
Found at i:1279880 original size:49 final size:49
Alignment explanation
Indices: 1279822--1280429 Score: 641
Period size: 43 Copynumber: 12.9 Consensus size: 49
1279812 TGGCATCTAC
*
1279822 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* * *
1279871 CTTTAAGTCCAATGTAGCTAGCCTTGAATCAGCACATTGGCA----C--
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
*
1279914 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* * *
1279963 CTTTAAGTCCAATGTAGCTAGCCTTGAATCAGCACATTGGCA----C--
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* *
1280006 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* *
1280055 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
**
1280098 CTTTAAGTCCAATACCGCTGGCCTTGAATCAGCATATTGGCACCTT-AT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* *
1280146 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* * *
1280189 CTTTAAGGCCAATATAGCTGGCCTTGAATTAGCATATTGGCACCTTCTT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* *
1280238 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
1280281 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CAT
* * *
1280333 CTTTAAGAT-CAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTCCTCAT
1 CTTTAAG-TCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC---T--TCAT
* * * * *
1280388 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA
1280430 TCTTTATCAC
Statistics
Matches: 471, Mismatches: 48, Indels: 74
0.79 0.08 0.12
Matches are distributed among these distances:
43 192 0.41
45 4 0.01
47 3 0.01
48 38 0.08
49 153 0.32
50 1 0.00
52 37 0.08
53 3 0.01
54 3 0.01
55 36 0.08
56 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (49 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
Found at i:1279977 original size:92 final size:92
Alignment explanation
Indices: 1279820--1280380 Score: 973
Period size: 92 Copynumber: 6.1 Consensus size: 92
1279810 GGTGGCATCT
1279820 ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
1 ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
*
1279885 TAGCTAGCCTTGAATCAGCACATTGGC
66 TAGCTGGCCTTGAATCAGCACATTGGC
1279912 ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
1 ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
*
1279977 TAGCTAGCCTTGAATCAGCACATTGGC
66 TAGCTGGCCTTGAATCAGCACATTGGC
*
1280004 ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATG
1 ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
1280069 TAGCTGGCCTTGAATCAGCACATTGGC
66 TAGCTGGCCTTGAATCAGCACATTGGC
*
1280096 ACCTTTAAGTCCAATACCGCTGGCCTTGAATCAGCATATTGGCACCTT-ATCTTTAAGTCCAATG
1 ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
1280160 TAGCTGGCCTTGAATCAGCACATTGGC
66 TAGCTGGCCTTGAATCAGCACATTGGC
* * * *
1280187 ACCTTTAAGGCCAATATAGCTGGCCTTGAATTAGCATATTGGCACCTTCTTCTTTAAGTCCAATG
1 ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
1280252 TAGCTGGCCTTGAATCAGCACATTGGC
66 TAGCTGGCCTTGAATCAGCACATTGGC
*
1280279 ACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGAT-C
1 ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTTTAAG-TCC
*
1280343 AATGTAGCTGGCCTTGAATCAGCACATTGAC
62 AATGTAGCTGGCCTTGAATCAGCACATTGGC
1280374 ATCCTTT
1 A-CCTTT
1280381 TCCTCATCTT
Statistics
Matches: 450, Mismatches: 13, Indels: 8
0.96 0.03 0.02
Matches are distributed among these distances:
91 87 0.19
92 314 0.70
94 2 0.00
95 41 0.09
96 6 0.01
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (92 bp):
ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
TAGCTGGCCTTGAATCAGCACATTGGC
Found at i:1280312 original size:275 final size:278
Alignment explanation
Indices: 1279820--1280380 Score: 977
Period size: 275 Copynumber: 2.0 Consensus size: 278
1279810 GGTGGCATCT
*
1279820 ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
1 ACCTTTAAGTCCAATACCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
* *
1279885 TAGCTAGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATA
66 TAGCTAGCCTTGAATCAGCACATTGGCACCTTTAAGGCCAATATAGCTGGCCTTGAATCAGCATA
1279950 TTGGCACCTTCATCTTTAAGTCCAATGTAGCTAGCCTTGAATCAGCACATTGGCACCTTTAAGTC
131 TTGGCACCTTCATCTTTAAGTCCAATGTAGCTAGCCTTGAATCAGCACATTGGCACCTTTAAGTC
*
1280015 CAATATCGCTGGCCTTGAATCAGCATATTGGCA-TCTT-CATCTTTAAG-TCCAATGTAGCTGGC
196 CAATATAGCTGGCCTTGAATCAGCATATTGGCACTCTTCCATCTTTAAGAT-CAATGTAGCTGGC
*
1280077 CTTGAATCAGCACATTGGC
260 CTTGAATCAGCACATTGAC
1280096 ACCTTTAAGTCCAATACCGCTGGCCTTGAATCAGCATATTGGCACCTT-ATCTTTAAGTCCAATG
1 ACCTTTAAGTCCAATACCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
* *
1280160 TAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGGCCAATATAGCTGGCCTTGAATTAGCATA
66 TAGCTAGCCTTGAATCAGCACATTGGCACCTTTAAGGCCAATATAGCTGGCCTTGAATCAGCATA
* *
1280225 TTGGCACCTTCTTCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTC
131 TTGGCACCTTCATCTTTAAGTCCAATGTAGCTAGCCTTGAATCAGCACATTGGCACCTTTAAGTC
*
1280290 CAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGATCAATGTAGCTGGC
196 CAATATAGCTGGCCTTGAATCAGCATATTGGCA-CTCTTCCATCTTTAAGATCAATGTAGCTGGC
1280355 CTTGAATCAGCACATTGAC
260 CTTGAATCAGCACATTGAC
1280374 ATCCTTT
1 A-CCTTT
1280381 TCCTCATCTT
Statistics
Matches: 270, Mismatches: 10, Indels: 7
0.94 0.03 0.02
Matches are distributed among these distances:
275 172 0.64
276 47 0.17
277 3 0.01
278 42 0.16
279 6 0.02
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (278 bp):
ACCTTTAAGTCCAATACCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
TAGCTAGCCTTGAATCAGCACATTGGCACCTTTAAGGCCAATATAGCTGGCCTTGAATCAGCATA
TTGGCACCTTCATCTTTAAGTCCAATGTAGCTAGCCTTGAATCAGCACATTGGCACCTTTAAGTC
CAATATAGCTGGCCTTGAATCAGCATATTGGCACTCTTCCATCTTTAAGATCAATGTAGCTGGCC
TTGAATCAGCACATTGAC
Found at i:1280359 original size:52 final size:53
Alignment explanation
Indices: 1280281--1280434 Score: 177
Period size: 52 Copynumber: 2.9 Consensus size: 53
1280271 ACATTGGCAC
1280281 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTT-C-CAT
1 CTTTAAGT-CAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCTCAT
* * *
1280333 CTTTAAGATCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTCCTCAT
1 CTTTAAG-TCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CCTTTTCCTCAT
* * * * * *
1280388 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTT
1 CTTTAAG-TCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTT
1280435 ATCACTTTTC
Statistics
Matches: 85, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
52 37 0.44
53 7 0.08
54 5 0.06
55 36 0.42
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (53 bp):
CTTTAAGTCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCTCAT
Found at i:1281254 original size:13 final size:13
Alignment explanation
Indices: 1281236--1281260 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1281226 CATAAAGTGT
1281236 TGTATCGATACAA
1 TGTATCGATACAA
1281249 TGTATCGATACA
1 TGTATCGATACA
1281261 TAGGTTTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1281276 original size:32 final size:33
Alignment explanation
Indices: 1281216--1281281 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 33
1281206 TTCAACGATT
1281216 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
* *
1281249 TGTATCGATACAT-AGGTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
1281281 T
1 T
1281282 TTAAGCTACT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.58
33 13 0.42
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.36
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:1281319 original size:13 final size:13
Alignment explanation
Indices: 1281301--1281325 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1281291 TGCCAAAAAA
1281301 TGTATCGATACAT
1 TGTATCGATACAT
1281314 TGTATCGATACA
1 TGTATCGATACA
1281326 CTAATCTTTG
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:1281375 original size:32 final size:32
Alignment explanation
Indices: 1281334--1281409 Score: 143
Period size: 32 Copynumber: 2.4 Consensus size: 32
1281324 CACTAATCTT
*
1281334 TGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACATGCAAGCAAATTTGCCCAGA
1281366 TGTATCGATACATGCAAGCAAATTTGCCCAGA
1 TGTATCGATACATGCAAGCAAATTTGCCCAGA
1281398 TGTATCGATACA
1 TGTATCGATACA
1281410 CTATGAAATG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (32 bp):
TGTATCGATACATGCAAGCAAATTTGCCCAGA
Found at i:1288000 original size:90 final size:89
Alignment explanation
Indices: 1287835--1288123 Score: 380
Period size: 90 Copynumber: 3.2 Consensus size: 89
1287825 GGTGTCTACA
* * * *
1287835 GATATGATTGGGAATGTGTGGGTTGCACCTTGCCCTAAGAAAATTAGGCTTGGTGATGCATCAAT
1 GATATGATTGGAAATGTGTTGGCTGCACCTTGCCCTAAGGAAATTAGGCTTGGTGATGCATCAAT
**
1287900 ATTATCTAGTGGTTGGATGAAAGG
66 ACCATCTAGTGGTTGGATGAAAGG
* * *
1287924 GATATGATTTGGAAATGTGTTGACTGCACCTTGCCCTAAGGAAATTAGGCTTGGTGATGCATTAG
1 GATATGA-TTGGAAATGTGTTGGCTGCACCTTGCCCTAAGGAAATTAGGCTTGGTGATGCATCAA
*
1287989 TACCATCTAGTGGTTGGATGAAGGG
65 TACCATCTAGTGGTTGGATGAAAGG
* * * * * * * *
1288014 GATATGATTGGGAATGTGTAGGCTACACCTTACCCTAAGGAAATTAGGTTTAGTGATACACCAAT
1 GATATGATTGGAAATGTGTTGGCTGCACCTTGCCCTAAGGAAATTAGGCTTGGTGATGCATCAAT
*
1288079 ACCATCTAGTGGTTGGATGAACGG
66 ACCATCTAGTGGTTGGATGAAAGG
*
1288103 GATATAATTAGGAAATGTGTT
1 GATATGATT-GGAAATGTGTT
1288124 TTCCTTGAAG
Statistics
Matches: 173, Mismatches: 25, Indels: 3
0.86 0.12 0.01
Matches are distributed among these distances:
89 85 0.49
90 88 0.51
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.31
Consensus pattern (89 bp):
GATATGATTGGAAATGTGTTGGCTGCACCTTGCCCTAAGGAAATTAGGCTTGGTGATGCATCAAT
ACCATCTAGTGGTTGGATGAAAGG
Found at i:1289412 original size:20 final size:21
Alignment explanation
Indices: 1289361--1289412 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
1289351 AAAGCTTCAC
1289361 TTTTTCCATTT-TTTGTCTCT
1 TTTTTCCATTTCTTTGTCTCT
* *
1289381 TTTTTCCTTTTCTTT-TCTTT
1 TTTTTCCATTTCTTTGTCTCT
*
1289401 TTTTTTCATTTC
1 TTTTTCCATTTC
1289413 AACATGTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 24 0.89
21 3 0.11
ACGTcount: A:0.04, C:0.19, G:0.02, T:0.75
Consensus pattern (21 bp):
TTTTTCCATTTCTTTGTCTCT
Found at i:1291694 original size:3 final size:3
Alignment explanation
Indices: 1291679--1291712 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
1291669 AACCATCAAA
* *
1291679 GAT GAT GAA GAT GAT GGT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1291713 TTGACTCAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.32, C:0.00, G:0.38, T:0.29
Consensus pattern (3 bp):
GAT
Done.