Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1722
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: 53135
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Found at i:6765 original size:80 final size:80
Alignment explanation
Indices: 6666--6817 Score: 227
Period size: 80 Copynumber: 1.9 Consensus size: 80
6656 AAATTGTACA
* *
6666 CACTAAGTGTGCGATTTGACTATGT-GCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTGT
1 CACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAAATG-ATACGTA-GCACTAAGTGT
6729 GCGAATTGACCATGCCG
64 GCGAATTGACCATGCCG
**
6746 CACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGATTTGATACGTAGCACTAAGTGTGC
1 CACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAAATGATACGTAGCACTAAGTGTGC
*
6811 GAGTTGA
66 GAATTGA
6818 TTATTATAGC
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
80 47 0.72
81 18 0.28
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (80 bp):
CACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAAATGATACGTAGCACTAAGTGTGC
GAATTGACCATGCCG
Found at i:6818 original size:26 final size:27
Alignment explanation
Indices: 6666--6839 Score: 192
Period size: 27 Copynumber: 6.5 Consensus size: 27
6656 AAATTGTACA
*
6666 CACTAAGTGTGCGATTTGACTATGT-G
1 CACTAAGTGTGCGAATTGACTATGTAG
* *
6692 CACTAAGTGTGCGAAATGAATATG-ATG
1 CACTAAGTGTGCGAATTGACTATGTA-G
* **
6719 CACTAAGTGTGCGAATTGACCATGCCG
1 CACTAAGTGTGCGAATTGACTATGTAG
*
6746 CACTAAGTGTGCGAGTTGACTATGTAG
1 CACTAAGTGTGCGAATTGACTATGTAG
* *
6773 CACTAAGTGTGCGATTTGA-TACGTAG
1 CACTAAGTGTGCGAATTGACTATGTAG
* * *
6799 CACTAAGTGTGCGAGTTGATTATTATAG
1 CACTAAGTGTGCGAATTGACTA-TGTAG
*
6827 CACTGAGTGTGCG
1 CACTAAGTGTGCG
6840 GACTCAATAT
Statistics
Matches: 126, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
26 45 0.36
27 66 0.52
28 15 0.12
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (27 bp):
CACTAAGTGTGCGAATTGACTATGTAG
Found at i:12625 original size:13 final size:13
Alignment explanation
Indices: 12607--12631 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12597 TTTTCTTTGC
12607 TTTTTATTTTTAA
1 TTTTTATTTTTAA
12620 TTTTTATTTTTA
1 TTTTTATTTTTA
12632 GCATAAGCAC
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTATTTTTAA
Found at i:15873 original size:26 final size:26
Alignment explanation
Indices: 15844--15925 Score: 128
Period size: 26 Copynumber: 3.2 Consensus size: 26
15834 TGGTACAAAT
*
15844 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
*
15870 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
* *
15896 TGATAATGGTTTGGGTAAATGTTCCA
1 TGATAATGGATTAGGTAAATGTTCCA
15922 TGAT
1 TGAT
15926 GGGCATTTCA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 51 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGATTAGGTAAATGTTCCA
Found at i:17303 original size:26 final size:26
Alignment explanation
Indices: 17274--17381 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
17264 TGGTACAAAT
*
17274 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
*
17300 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
17326 TGATAATGGGTTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
* * *
17352 TGATAATGGTTTGGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
17378 TGAT
1 TGAT
17382 GGGCATTTCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATATTCCA
Found at i:18759 original size:26 final size:26
Alignment explanation
Indices: 18730--18837 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
18720 TGGTACAAAT
*
18730 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
*
18756 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
18782 TGATAATGGGTTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
* * *
18808 TGATAATGGTTTGGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
18834 TGAT
1 TGAT
18838 GGGCATTTCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATATTCCA
Found at i:20218 original size:26 final size:26
Alignment explanation
Indices: 20189--20296 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
20179 TGGTACAAAT
*
20189 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
*
20215 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
20241 TGATAATGGGTTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
* * *
20267 TGATAATGGTTTGGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
20293 TGAT
1 TGAT
20297 GGGCATTTCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATATTCCA
Found at i:21676 original size:26 final size:26
Alignment explanation
Indices: 21647--21754 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
21637 TGGTACAAAT
*
21647 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
*
21673 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
21699 TGATAATGGGTTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
* * *
21725 TGATAATGGTTTGGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATATTCCA
21751 TGAT
1 TGAT
21755 GGGCATTTCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATATTCCA
Found at i:23134 original size:26 final size:26
Alignment explanation
Indices: 23105--23212 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
23095 TGGTACAAAT
23105 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
23131 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
23157 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
23183 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
23209 TGAT
1 TGAT
23213 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:24594 original size:26 final size:26
Alignment explanation
Indices: 24565--24620 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
24555 TGGTACAAAT
24565 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
24591 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
24617 TGAT
1 TGAT
24621 GGGCATTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:26002 original size:26 final size:26
Alignment explanation
Indices: 25973--26080 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
25963 TGGTACAAAT
*
25973 TGATAATGGGTTAGGTAAATGTTCAA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
25999 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
26025 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
26051 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
26077 TGAT
1 TGAT
26081 GGGCATTTCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:27699 original size:27 final size:28
Alignment explanation
Indices: 27659--27786 Score: 160
Period size: 27 Copynumber: 4.7 Consensus size: 28
27649 GGAAGCGTCT
*
27659 TGGTGGCTATGCCACAAT-TATCTGATC
1 TGGTGGCTCTGCCACAATATATCTGATC
*
27686 TAGTGGCTCTGCCAC-ATATATCTG-TCC
1 TGGTGGCTCTGCCACAATATATCTGAT-C
*
27713 TGGTGGCTATGCCACAAT-TATCTGATC
1 TGGTGGCTCTGCCACAATATATCTGATC
*
27740 TGGTGGCTCTGCCAC-GTATATCT-ATTC
1 TGGTGGCTCTGCCACAATATATCTGA-TC
27767 TGGTGGCTCTGCCACAATAT
1 TGGTGGCTCTGCCACAATAT
27787 TTGTATCTCG
Statistics
Matches: 87, Mismatches: 7, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
26 5 0.06
27 76 0.87
28 6 0.07
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.34
Consensus pattern (28 bp):
TGGTGGCTCTGCCACAATATATCTGATC
Found at i:27746 original size:54 final size:54
Alignment explanation
Indices: 27659--27784 Score: 207
Period size: 54 Copynumber: 2.3 Consensus size: 54
27649 GGAAGCGTCT
*
27659 TGGTGGCTATGCCACAATTATCTGATCTAGTGGCTCTGCCACATATATCTGTCC
1 TGGTGGCTATGCCACAATTATCTGATCTAGTGGCTCTGCCACATATATCTATCC
* * *
27713 TGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACGTATATCTATTC
1 TGGTGGCTATGCCACAATTATCTGATCTAGTGGCTCTGCCACATATATCTATCC
*
27767 TGGTGGCTCTGCCACAAT
1 TGGTGGCTATGCCACAAT
27785 ATTTGTATCT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 67 1.00
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.33
Consensus pattern (54 bp):
TGGTGGCTATGCCACAATTATCTGATCTAGTGGCTCTGCCACATATATCTATCC
Found at i:35809 original size:47 final size:47
Alignment explanation
Indices: 35755--35948 Score: 280
Period size: 47 Copynumber: 4.1 Consensus size: 47
35745 TAGGATTTTC
** * *
35755 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
35802 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
35849 ATGTGATGAATGTGAGCATGCATATGTGTCATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * *
35896 ATGTGGTGAATATGAACATGCATATATGTGGTAAAGCCGAATGGCTA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
35943 ATGTGA
1 ATGTGA
35949 AATATATATA
Statistics
Matches: 131, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 131 1.00
ACGTcount: A:0.33, C:0.11, G:0.29, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:35855 original size:22 final size:22
Alignment explanation
Indices: 35784--35855 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
35774 GTATATATGA
35784 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCCGAATGGCCAATGT
* * *
35806 GATGAATG-TGAACAT-GCATATATGT
1 GAT-AAGGCCG-A-ATGGC-CA-ATGT
35831 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCCGAATGGCCAATGT
35853 GAT
1 GAT
35856 GAATGTGAGC
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
22 11 0.30
23 9 0.24
24 9 0.24
25 8 0.22
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (22 bp):
GATAAGGCCGAATGGCCAATGT
Found at i:36260 original size:37 final size:37
Alignment explanation
Indices: 36152--36260 Score: 164
Period size: 37 Copynumber: 2.9 Consensus size: 37
36142 GGAAATATAT
*
36152 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATA
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTA
*
36189 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTA
* * * *
36226 TCCGGGTAAGACCTGATAACTTCATGTGGAGATTT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTT
36261 CGCCTGAGCT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 66 1.00
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTA
Found at i:38622 original size:43 final size:42
Alignment explanation
Indices: 38542--38691 Score: 169
Period size: 42 Copynumber: 3.6 Consensus size: 42
38532 ATACCAATGC
* * * *
38542 CATATCCCAGATATGGTCTTACATG-GGATCTCGTATCGATGG
1 CATATCCTAGATATGGTCTTACACGAAG-TCTCATATCGATGG
* * * *
38584 CAATAGCCTAGCTATGGTCTTACACGAAGTCTCTTATCGATGT
1 C-ATATCCTAGATATGGTCTTACACGAAGTCTCATATCGATGG
* * *
38627 CATATCCCAGATATGGTCTTACACGAAGCCTCATATAGAT-G
1 CATATCCTAGATATGGTCTTACACGAAGTCTCATATCGATGG
38668 CATATCCTAGATATGGTCTTACAC
1 CATATCCTAGATATGGTCTTACAC
38692 ATAATTTTAG
Statistics
Matches: 91, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
41 23 0.25
42 34 0.37
43 33 0.36
44 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (42 bp):
CATATCCTAGATATGGTCTTACACGAAGTCTCATATCGATGG
Found at i:43041 original size:38 final size:38
Alignment explanation
Indices: 42990--43137 Score: 154
Period size: 38 Copynumber: 3.8 Consensus size: 38
42980 GTTTAAGTAA
*
42990 TTAATTATGTCATAATTTAAACATCATTAATATGAGTT
1 TTAATTATGTCATAATTTAAACATCTTTAATATGAGTT
* * *
43028 TTAATTATGTCATAATCTGAACATCTTTAATAAGAGATT
1 TTAATTATGTCATAATTTAAACATCTTTAATATGAG-TT
* * *
43067 TTAATTATGTCATAGTTTAGGACATCTTAAATAT-ATGTT
1 TTAATTATGTCATAATTTA-AACATCTTTAATATGA-GTT
* * * * *
43106 TTAAATGTGTCCTAGTTTAGACATCTTTAATA
1 TTAATTATGTCATAATTTAAACATCTTTAATA
43138 CATGTCTTTA
Statistics
Matches: 93, Mismatches: 14, Indels: 6
0.82 0.12 0.05
Matches are distributed among these distances:
38 44 0.47
39 37 0.40
40 12 0.13
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.44
Consensus pattern (38 bp):
TTAATTATGTCATAATTTAAACATCTTTAATATGAGTT
Found at i:45150 original size:8 final size:8
Alignment explanation
Indices: 45137--45165 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
45127 CACTAGAGAC
45137 CAGTGTTA
1 CAGTGTTA
45145 CAGTGTTA
1 CAGTGTTA
45153 CAGTGTTA
1 CAGTGTTA
45161 CAGTG
1 CAGTG
45166 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:45312 original size:22 final size:23
Alignment explanation
Indices: 45253--45327 Score: 125
Period size: 23 Copynumber: 3.3 Consensus size: 23
45243 AGTGTTATTG
45253 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
45276 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
45299 ATCA-TGTTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
45321 ATCAGTG
1 ATCAGTG
45328 TGGCACTTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
22 21 0.44
23 27 0.56
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.33
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Done.