Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2081
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: 42756
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:440 original size:13 final size:14
Alignment explanation
Indices: 422--450 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
412 TCTATTTACT
422 AATTTTTT-TCTAG
1 AATTTTTTGTCTAG
435 AATTTTTTGTCTAG
1 AATTTTTTGTCTAG
449 AA
1 AA
451 AATTAGTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.28, C:0.07, G:0.10, T:0.55
Consensus pattern (14 bp):
AATTTTTTGTCTAG
Found at i:1656 original size:46 final size:46
Alignment explanation
Indices: 1482--1656 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
1472 CATGTAACCC
* *
1482 CCATAAGTGAACTC-GACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
1527 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** *
1573 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
1620 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
1657 TGCCCAAACA
Statistics
Matches: 110, Mismatches: 12, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 14 0.13
46 55 0.50
47 32 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:1656 original size:93 final size:92
Alignment explanation
Indices: 1490--1660 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 92
1480 CCCCATAAGT
* *
1490 GAACTCGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 GAACTCGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1555 GAGCTCGGATGCCTAGTTACATCTCTC
66 GAGCTCGGATGCCTAGTTACATCTCTC
*
1582 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTC-GACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
1647 CGAGTTCGGATGCC
65 CGAGCTCGGATGCC
1661 CAAACATCCT
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
92 6 0.08
93 68 0.92
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.21
Consensus pattern (92 bp):
GAACTCGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGCTCGGATGCCTAGTTACATCTCTC
Found at i:1675 original size:46 final size:46
Alignment explanation
Indices: 1532--1675 Score: 143
Period size: 46 Copynumber: 3.1 Consensus size: 46
1522 CGCATCCATA
* *
1532 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA--TACATC-CT
* * * * *
1581 --CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT--A
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCCCATACATCCT
*
1625 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAACATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCATACATCCT
1671 AGTGA
1 AGTGA
1676 CATGTCACTT
Statistics
Matches: 76, Mismatches: 13, Indels: 15
0.73 0.12 0.14
Matches are distributed among these distances:
44 8 0.11
46 33 0.43
47 31 0.41
49 4 0.05
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (46 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCATACATCCT
Found at i:7048 original size:45 final size:45
Alignment explanation
Indices: 6984--7157 Score: 217
Period size: 45 Copynumber: 3.8 Consensus size: 45
6974 CATGTAACGC
*
6984 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCAT
*
7029 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG-ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGCATTCGC-A--T
* *** *
7075 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCAT
*
7122 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
7158 ATGCCCAAAC
Statistics
Matches: 110, Mismatches: 12, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 36 0.33
46 33 0.30
47 32 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCAT
Found at i:7150 original size:93 final size:92
Alignment explanation
Indices: 6992--7162 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 92
6982 GCCCATAAGT
*
6992 GAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
7057 GAGCTCGGATGCCTAGTTACATCTCTC
66 GAGCTCGGATGCCTAGTTACATCTCTC
*
7084 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
7149 CGAGTTCGGATGCC
65 CGAGCTCGGATGCC
7163 CAAACATCCT
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
92 27 0.36
93 48 0.64
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.21
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGCTCGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGCTCGGATGCCTAGTTACATCTCTC
Found at i:7177 original size:46 final size:46
Alignment explanation
Indices: 6989--7177 Score: 156
Period size: 46 Copynumber: 4.1 Consensus size: 46
6979 AACGCCCATA
* * * * *
6989 AGTGAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCATCCAT--A
1 AGTGAACTCGGACTCAACTCAACGAGCTCGG-ATGCCCATACATCCT
*
7034 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTCT
1 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCCA--TACATC-CT
* * * * * *
7083 --CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCAT--A
1 AGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGCCCATACATCCT
* *
7127 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAACATCCT
1 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCCATACATCCT
7173 AGTGA
1 AGTGA
7178 CATGTCACTT
Statistics
Matches: 114, Mismatches: 19, Indels: 21
0.74 0.12 0.14
Matches are distributed among these distances:
44 11 0.10
45 31 0.27
46 37 0.32
47 31 0.27
49 4 0.04
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCCATACATCCT
Found at i:16103 original size:46 final size:46
Alignment explanation
Indices: 16050--16172 Score: 160
Period size: 46 Copynumber: 2.6 Consensus size: 46
16040 ATTGTGAGCT
16050 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGACG-TAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGG-CTACGAGACGAT-AGCC
* * * *
16096 AGTGTAAGACATGTCTGGGACATGTATCGGCTACGAGATGATGGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGACGATAGCC
16142 AGTGTAAGACCATGTCTGGGACATTGCATCG
1 AGTGTAAGA-CATGTCTGGGACA-TGCATCG
16173 ACTTGAGATA
Statistics
Matches: 68, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
45 2 0.03
46 46 0.68
47 14 0.21
48 6 0.09
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGACGATAGCC
Found at i:16181 original size:47 final size:44
Alignment explanation
Indices: 16050--16219 Score: 153
Period size: 46 Copynumber: 3.7 Consensus size: 44
16040 ATTGTGAGCT
* * * *
16050 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATC-GACTCGAGATG-ATGGC
* *
16096 AGTGTAAGACATGTCTGGGACATGTATCGGCTACGAGATGATGGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGACT-CGAGATGATGG-C
*
16142 AGTGTAAGACCATGTCTGGGACATTGCATCGACTTGAGAT-ATGAGC
1 AGTGTAAGA-CATGTCTGGGACA-TGCATCGACTCGAGATGATG-GC
* * *
16188 TTGTGTAAAACCTTGTCTGGGACATGGCATCG
1 -AGTGTAAGA-CATGTCTGGGACAT-GCATCG
16220 GCACCTTACC
Statistics
Matches: 106, Mismatches: 11, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
45 5 0.05
46 48 0.45
47 45 0.42
48 8 0.08
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACATGCATCGACTCGAGATGATGGC
Found at i:19317 original size:13 final size:13
Alignment explanation
Indices: 19299--19323 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19289 TTTTAAAATC
19299 ATTTTCATTTTTT
1 ATTTTCATTTTTT
19312 ATTTTCATTTTT
1 ATTTTCATTTTT
19324 GAGAAAACGA
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:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (13 bp):
ATTTTCATTTTTT
Found at i:27291 original size:15 final size:15
Alignment explanation
Indices: 27271--27335 Score: 73
Period size: 15 Copynumber: 4.4 Consensus size: 15
27261 GTATCTTGGG
27271 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
27286 TTTCTTTATTCTGGG
1 TTTCTTTATTCTGGA
27301 TTT-TTCTA-TCTTGGA
1 TTTCTT-TATTC-TGGA
*
27316 TTTCTTTATT-TGGT
1 TTTCTTTATTCTGGA
27330 TTTCTT
1 TTTCTT
27336 GTTATCTTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
14 13 0.30
15 27 0.63
16 3 0.07
ACGTcount: A:0.09, C:0.12, G:0.14, T:0.65
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:27302 original size:30 final size:30
Alignment explanation
Indices: 27266--27335 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
27256 GTATCGTATC
27266 TTGGGTTTCTT-TAT-TCTGGATTTCTTTAT
1 TTGGGTTTCTTCTATCT-TGGATTTCTTTAT
27295 TCTGGGTTT-TTCTATCTTGGATTTCTTTAT
1 T-TGGGTTTCTTCTATCTTGGATTTCTTTAT
*
27325 TTGGTTTTCTT
1 TTGGGTTTCTT
27336 GTTATCTTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
29 9 0.25
30 26 0.72
31 1 0.03
ACGTcount: A:0.09, C:0.11, G:0.17, T:0.63
Consensus pattern (30 bp):
TTGGGTTTCTTCTATCTTGGATTTCTTTAT
Found at i:32978 original size:40 final size:40
Alignment explanation
Indices: 32901--33157 Score: 387
Period size: 40 Copynumber: 6.5 Consensus size: 40
32891 AAACCGAGTA
* *
32901 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
32940 CCTTCGGGACTTAGCCTGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
32980 CCTTTGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
33020 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
33060 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * *
33100 CCTTCGGGGCTTAGCCC-GAAATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
33140 CCTTC-GGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
33158 TTATCATCCG
Statistics
Matches: 201, Mismatches: 13, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
39 27 0.13
40 174 0.87
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:39498 original size:78 final size:79
Alignment explanation
Indices: 39349--39532 Score: 268
Period size: 77 Copynumber: 2.4 Consensus size: 79
39339 ATTCGGATTG
** *
39349 ATAACC-GGCTAAGTCCCGAAGGCA-TTCGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTCGTGCGAGTTACTATAA-CGCACTAAGTCCCAAAGGC
39412 ATTTGTGCGAGTTATT
65 ATTTGTGCGAGTTA-T
* *
39428 TTATCCGGGCTAAGTCCCGAAGGCATTTCGTGCGAGTTACTATAA-GCACT-AGTCCCAAAGGCA
1 ATAACCGGGCTAAGTCCCGAAGGCATTTCGTGCGAGTTACTATAACGCACTAAGTCCCAAAGGCA
39491 TTTGTGCGAGTTAT
66 TTTGTGCGAGTTAT
*
39505 ATAACCGGGCTAAGTCTCGAAGGCATTT
1 ATAACCGGGCTAAGTCCCGAAGGCATTT
39533 GAGCTAGTAG
Statistics
Matches: 95, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
77 26 0.27
78 25 0.26
79 7 0.07
80 18 0.19
81 19 0.20
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.27
Consensus pattern (79 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTCGTGCGAGTTACTATAACGCACTAAGTCCCAAAGGCA
TTTGTGCGAGTTAT
Found at i:39556 original size:39 final size:40
Alignment explanation
Indices: 39349--39533 Score: 254
Period size: 40 Copynumber: 4.7 Consensus size: 40
39339 ATTCGGATTG
*
39349 ATAACC-GGCTAAGTCCCGAAGGCATTCGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
39388 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
39428 TTATCCGGGCTAAGTCCCGAAGGCATTTCGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTT-GTGCGAGTTACT
** *
39469 ATAA--GCACT-AGTCCCAAAGGCATTTGTGCGAGTTA-T
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
39505 ATAACCGGGCTAAGTCTCGAAGGCATTTG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTG
39534 AGCTAGTAGC
Statistics
Matches: 127, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
36 5 0.04
37 10 0.08
38 18 0.14
39 24 0.19
40 57 0.45
41 13 0.10
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.26
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Done.