Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1982
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: 34914
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Found at i:2743 original size:93 final size:93
Alignment explanation
Indices: 2628--2798 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
2618 GCCCGTAAGT
* *
2628 GAACTCGGACTCAACTCAACGAGCTT-GGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAG-TTCGGACATTCGCATCCATAAGTGAACTCGGAATCAACTCA
2692 ACAAGTTCGGATGCCTAGTTACATTTCAC
65 ACAAGTTCGGATGCCTAGTTACATTTCAC
*
2721 GAACTCGGAGTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGAATCAACTCAA
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGAATCAACTCAA
**
2786 TGAGTTCGGATGC
66 CAAGTTCGGATGC
2799 TCAACCATCC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 2 0.03
93 70 0.97
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGAATCAACTCAA
CAAGTTCGGATGCCTAGTTACATTTCAC
Found at i:2792 original size:46 final size:46
Alignment explanation
Indices: 2623--2795 Score: 176
Period size: 46 Copynumber: 3.7 Consensus size: 46
2613 AACCCGCCCG
*
2623 TAAGTGAACTCGGACTCAACTCAACGAGCTT-GGGCATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAG-TTCGGACATTCGCATCCA
* * *
2669 TAAGTGAACTCGGACTCAACTCAACAAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* * *
2717 TCA-CGAACTCGGAGTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* *
2762 TAAGTGAACTCGGAATCAACTCAATGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
2796 TGCTCAACCA
Statistics
Matches: 103, Mismatches: 14, Indels: 20
0.75 0.10 0.15
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 4 0.04
46 56 0.54
47 27 0.26
48 2 0.02
49 1 0.01
50 4 0.04
51 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:3251 original size:30 final size:30
Alignment explanation
Indices: 3217--3276 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
3207 ATTTAATACG
*
3217 AACTTTGGAAAAATTACACTTTTTCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
3247 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
3277 GGCTCGGAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.38
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:4969 original size:49 final size:49
Alignment explanation
Indices: 4912--5035 Score: 167
Period size: 55 Copynumber: 2.4 Consensus size: 49
4902 GTCAATGTTG
4912 TGTCCCAGATAGGTATTACATTGACTTTCATATATGAAGGCTGATGCCA
1 TGTCCCAGATAGGTATTACATTGACTTTCATATATGAAGGCTGATGCCA
*
4961 TGTCCCAGACAGGTCTTGGTATTACATTGACTTTCATATATGAAGGCTGATGCCA
1 TGTCCCAG--A----TAGGTATTACATTGACTTTCATATATGAAGGCTGATGCCA
* *
5016 TGTCCCAGACAGGTCTTACA
1 TGTCCCAGATAGGTATTACA
5036 CTGCCTCACA
Statistics
Matches: 65, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
49 16 0.25
51 1 0.02
53 1 0.02
55 47 0.72
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (49 bp):
TGTCCCAGATAGGTATTACATTGACTTTCATATATGAAGGCTGATGCCA
Found at i:5007 original size:55 final size:55
Alignment explanation
Indices: 4923--5032 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
4913 GTCCCAGATA
4923 GGTATTACATTGACTTTCATATATGAAGGCTGATGCCATGTCCCAGACAGGTCTT
1 GGTATTACATTGACTTTCATATATGAAGGCTGATGCCATGTCCCAGACAGGTCTT
4978 GGTATTACATTGACTTTCATATATGAAGGCTGATGCCATGTCCCAGACAGGTCTT
1 GGTATTACATTGACTTTCATATATGAAGGCTGATGCCATGTCCCAGACAGGTCTT
5033 ACACTGCCTC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (55 bp):
GGTATTACATTGACTTTCATATATGAAGGCTGATGCCATGTCCCAGACAGGTCTT
Found at i:5208 original size:46 final size:48
Alignment explanation
Indices: 5092--5215 Score: 135
Period size: 46 Copynumber: 2.6 Consensus size: 48
5082 GACACAACAA
* * * *
5092 GCTGATGCCATGTCCCAGACAGGTCTTACACTAGCTTGTATATCTCGAG
1 GCTGATG-CATGTCCCAGACATGTCTTACACTAGCTTCTACATCTCAAG
* *** * *
5141 GCCGATGCATGTTGTAGACATGTCTTACACTAGC-TCT-CGTCTCAAT
1 GCTGATGCATGTCCCAGACATGTCTTACACTAGCTTCTACATCTCAAG
5187 GCTGATGCATGTCCCAGACATGTCTTACA
1 GCTGATGCATGTCCCAGACATGTCTTACA
5216 TTGGATTTTA
Statistics
Matches: 61, Mismatches: 14, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
46 30 0.49
47 2 0.03
48 23 0.38
49 6 0.10
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.30
Consensus pattern (48 bp):
GCTGATGCATGTCCCAGACATGTCTTACACTAGCTTCTACATCTCAAG
Found at i:5254 original size:92 final size:95
Alignment explanation
Indices: 5092--5268 Score: 243
Period size: 92 Copynumber: 1.9 Consensus size: 95
5082 GACACAACAA
* * **
5092 GCTGATGCCATGTCCCAGACAGGTCTTACACTAGCTTGTATATCTCGAGGCCGATGCATGTTGTA
1 GCTGATGCCATGTCCCAGACAGGTCTTACACTAGATTGTATATATCGAGGCCGATGCATGTCCTA
5157 GACATGTCTTACACTAGCTCTCGTCTCAAT
66 GACATGTCTTACACTAGCTCTCGTCTCAAT
* * * * *
5187 GCTGATG-CATGTCCCAGACATGTCTTACATTGGATTTTATA-AT-GTGGCCGATGCATGTCCTA
1 GCTGATGCCATGTCCCAGACAGGTCTTACACTAGATTGTATATATCGAGGCCGATGCATGTCCTA
*
5249 GACATGTCTTACACTGGCTC
66 GACATGTCTTACACTAGCTC
5269 ACATACCACC
Statistics
Matches: 72, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
92 35 0.49
93 1 0.01
94 29 0.40
95 7 0.10
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (95 bp):
GCTGATGCCATGTCCCAGACAGGTCTTACACTAGATTGTATATATCGAGGCCGATGCATGTCCTA
GACATGTCTTACACTAGCTCTCGTCTCAAT
Found at i:6522 original size:42 final size:43
Alignment explanation
Indices: 6441--6590 Score: 125
Period size: 42 Copynumber: 3.6 Consensus size: 43
6431 TTTCAGATGT
* *
6441 GGTCTTACATGTAATCAAATATCGATGCCACTGTCCCAGATAG
1 GGTCTTACACGAAATCAAATATCGATGCCACTGTCCCAGATAG
* *
6484 GGTCTTACACGAAATCAAATA-CGATGCTGA-TGTCCCAGA-AA
1 GGTCTTACACGAAATCAAATATCGATGC-CACTGTCCCAGATAG
* * * *
6525 TGTCTTACAC-ATAATCGAAGT-T-GATGCCAAC-ATCCCAGATAT
1 GGTCTTACACGA-AATC-AAATATCGATGCC-ACTGTCCCAGATAG
* *
6567 GGTCTTACACGAAAACACATATCG
1 GGTCTTACACGAAATCAAATATCG
6591 GATCCTTTGT
Statistics
Matches: 84, Mismatches: 13, Indels: 20
0.72 0.11 0.17
Matches are distributed among these distances:
40 1 0.01
41 29 0.35
42 32 0.38
43 22 0.26
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.25
Consensus pattern (43 bp):
GGTCTTACACGAAATCAAATATCGATGCCACTGTCCCAGATAG
Found at i:13413 original size:29 final size:29
Alignment explanation
Indices: 13379--13452 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
13369 TAATCAACCA
*
13379 CGCACACTTAGTGCCATGTACTTT-AAACT
1 CGCACACTTAGTGCCATGCA-TTTCAAACT
**
13408 CGCACACTTAGTGCCATGCATTTCAAGTT
1 CGCACACTTAGTGCCATGCATTTCAAACT
*
13437 CGCACACCTAGTGCCA
1 CGCACACTTAGTGCCA
13453 ATCTCACAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 3 0.08
29 37 0.93
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCATTTCAAACT
Found at i:21164 original size:29 final size:29
Alignment explanation
Indices: 21130--21203 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
21120 TAATCAACCA
*
21130 CGCACACTTAGTGCCATGTACTTT-AAACT
1 CGCACACTTAGTGCCATGCA-TTTCAAACT
**
21159 CGCACACTTAGTGCCATGCATTTCAAGTT
1 CGCACACTTAGTGCCATGCATTTCAAACT
*
21188 CGCACACCTAGTGCCA
1 CGCACACTTAGTGCCA
21204 ATCTCACAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 3 0.08
29 37 0.93
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCATTTCAAACT
Found at i:25344 original size:40 final size:39
Alignment explanation
Indices: 25289--25476 Score: 218
Period size: 40 Copynumber: 4.7 Consensus size: 39
25279 ATGATAACTA
* * *
25289 GGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCTG
1 GGCTAAGTCCCGAAGGCA-TTGTGCGAGTTACTAATTCCG
25329 GGCTAAGTCCCGAAGGCATTGTTGCGAGTTACTAATTCCG
1 GGCTAAGTCCCGAAGGCATTG-TGCGAGTTACTAATTCCG
*
25369 GGCTAAGTCTCGAAGGCATTGTGCGAGTTACT-ATATCCG
1 GGCTAAGTCCCGAAGGCATTGTGCGAGTTACTAAT-TCCG
* * **
25408 GGCTAAGTCCCAAAGGCATTTGTGGGAACTACT-ATATCCG
1 GGCTAAGTCCCGAAGGCA-TTGTGCGAGTTACTAAT-TCCG
* *
25448 GGCTAAGTCCTGAAGGCATTCGAGCGAGT
1 GGCTAAGTCCCGAAGGCATT-GTGCGAGT
25477 GGCTATATCC
Statistics
Matches: 129, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
38 2 0.02
39 36 0.28
40 91 0.71
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (39 bp):
GGCTAAGTCCCGAAGGCATTGTGCGAGTTACTAATTCCG
Found at i:25424 original size:79 final size:78
Alignment explanation
Indices: 25289--25488 Score: 226
Period size: 79 Copynumber: 2.5 Consensus size: 78
25279 ATGATAACTA
* * *
25289 GGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCTGGGCTAAGTCCCGAAGGCA-TTGTT
1 GGCTAAGT-CCGAAGGCA-TTGTGCGAGTGACTATA-TCCGGGCTAAGTCCCAAAGGCATTTG-T
**
25352 GCGAGTTACTA-ATTCCG
62 GCGAACTACTATA-TCCG
* *
25369 GGCTAAGTCTCGAAGGCATTGTGCGAGTTACTATATCCGGGCTAAGTCCCAAAGGCATTTGTGGG
1 GGCTAAGTC-CGAAGGCATTGTGCGAGTGACTATATCCGGGCTAAGTCCCAAAGGCATTTGTGCG
25434 AACTACTATATCCG
65 AACTACTATATCCG
* *
25448 GGCTAAGTCCTGAAGGCATTCGAGCGAGTGGCTATATCCGG
1 GGCTAAGTCC-GAAGGCATT-GTGCGAGTGACTATATCCGG
25489 TTAAATCCTG
Statistics
Matches: 104, Mismatches: 10, Indels: 12
0.83 0.08 0.10
Matches are distributed among these distances:
78 1 0.01
79 65 0.62
80 38 0.37
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.27
Consensus pattern (78 bp):
GGCTAAGTCCGAAGGCATTGTGCGAGTGACTATATCCGGGCTAAGTCCCAAAGGCATTTGTGCGA
ACTACTATATCCG
Found at i:33351 original size:40 final size:40
Alignment explanation
Indices: 33296--33511 Score: 305
Period size: 40 Copynumber: 5.5 Consensus size: 40
33286 CGGATGATAA
* *
33296 CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TC
33336 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-ATTC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TC
33376 CGGGCTAAGTCCCGAAGGCA-TTGTGCGAGTTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
**
33415 CGGGCTAAGTCCCGAAGGCATTTGTGCGAACTACTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
* **
33455 CGGGCTAAGTCCCGAAGGCATTTGAGCGAGTGGCTATATC
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
* *
33495 C-GGTTAAATCCCGAAGG
1 CGGGCTAAGTCCCGAAGG
33512 TACTTGGTTT
Statistics
Matches: 163, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
39 51 0.31
40 112 0.69
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATC
Found at i:33428 original size:79 final size:80
Alignment explanation
Indices: 33296--33511 Score: 314
Period size: 79 Copynumber: 2.7 Consensus size: 80
33286 CGGATGATAA
*
33296 CGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAGTCCCGAAGGCATTTG
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATA-TCCGGGCTAAGTCCCGAAGGCATTTG
**
33360 TGCGAGTTACTA-ATTC
65 TGCGAACTACTATA-TC
*
33376 CGGGCTAAGTCCCGAAGGCA-TTGTGCGAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTGT
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTTGT
33440 GCGAACTACTATATC
66 GCGAACTACTATATC
* * * *
33455 CGGGCTAAGTCCCGAAGGCATTTGAGCGAGTGGCTATATCC-GGTTAAATCCCGAAGG
1 CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTCCCGAAGG
33512 TACTTGGTTT
Statistics
Matches: 124, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
79 85 0.69
80 39 0.31
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (80 bp):
CGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTTGT
GCGAACTACTATATC
Done.