Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3460
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: 55664
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:3406 original size:40 final size:39
Alignment explanation
Indices: 3204--3426 Score: 267
Period size: 40 Copynumber: 5.7 Consensus size: 39
3194 TTGAATGATG
* * *
3204 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTA-A
* *
3244 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA
*
3283 TTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
3322 TTCC-GGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AA
*
3361 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-A
* *
3401 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
3427 AACGAGTAGC
Statistics
Matches: 164, Mismatches: 11, Indels: 16
0.86 0.06 0.08
Matches are distributed among these distances:
38 34 0.21
39 40 0.24
40 82 0.50
41 8 0.05
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAA
Found at i:8388 original size:29 final size:29
Alignment explanation
Indices: 8296--8391 Score: 122
Period size: 29 Copynumber: 3.3 Consensus size: 29
8286 TGTATCTGGA
* * *
8296 CCATTAAGCCC-AATCATATTCATATGGC
1 CCATTAGGCCCAAATCACATTTATATGGC
* * *
8324 CCATTACGCCCAAATCACCTATATATGGC
1 CCATTAGGCCCAAATCACATTTATATGGC
8353 CCATTAGGCCCAAATCACATTTATATGGC
1 CCATTAGGCCCAAATCACATTTATATGGC
*
8382 CCGTTAGGCC
1 CCATTAGGCC
8392 TAGTCACATT
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
28 10 0.17
29 48 0.83
ACGTcount: A:0.29, C:0.31, G:0.14, T:0.26
Consensus pattern (29 bp):
CCATTAGGCCCAAATCACATTTATATGGC
Found at i:12625 original size:27 final size:29
Alignment explanation
Indices: 12519--12632 Score: 110
Period size: 29 Copynumber: 4.0 Consensus size: 29
12509 TACCTGTATC
* * *
12519 TGGCCCATTAAGCCC-AATTATATTTATA
1 TGGCCCATTAGGCCCAAATCACATTTATA
12547 TGGCCCATTAGGCCCAAATCAC-TTATATA
1 TGGCCCATTAGGCCCAAATCACATT-TATA
*** *
12576 TAAACCATTAGGCCCAAACCACATTTATA
1 TGGCCCATTAGGCCCAAATCACATTTATA
* *
12605 TGGCCCATT-GGCCC-AGTCACATTCATA
1 TGGCCCATTAGGCCCAAATCACATTTATA
12632 T
1 T
12633 CATGCGTACA
Statistics
Matches: 70, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
27 11 0.16
28 21 0.30
29 36 0.51
30 2 0.03
ACGTcount: A:0.32, C:0.27, G:0.12, T:0.29
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTTATA
Found at i:17112 original size:29 final size:29
Alignment explanation
Indices: 17046--17156 Score: 111
Period size: 29 Copynumber: 3.9 Consensus size: 29
17036 AATTTCACAT
* * *
17046 ACCTTTATCTGGCCCATTAAGCCC-AATC
1 ACCTATATATGGCCCATTAGGCCCAAATC
17074 A--TATTCATATGGCCCATTAGGCCCAAATC
1 ACCTA-T-ATATGGCCCATTAGGCCCAAATC
*
17103 ACCTATATATGGTCCATTAGGCCCAAATC
1 ACCTATATATGGCCCATTAGGCCCAAATC
* * **
17132 ACATTTATATGGCCTGTTAGGCCCA
1 ACCTATATATGGCCCATTAGGCCCA
17157 GTCATATTCA
Statistics
Matches: 69, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
26 1 0.01
27 1 0.01
28 17 0.25
29 47 0.68
30 1 0.01
31 2 0.03
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (29 bp):
ACCTATATATGGCCCATTAGGCCCAAATC
Found at i:17409 original size:17 final size:17
Alignment explanation
Indices: 17380--17423 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
17370 GTAGGCAAAC
17380 TTTTAGC-TTTTCGACA
1 TTTTAGCTTTTTCGACA
*
17396 TTTTAGCTTTTTCGGCA
1 TTTTAGCTTTTTCGACA
*
17413 TTTCAGCTTTT
1 TTTTAGCTTTT
17424 GCCGATACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 7 0.28
17 18 0.72
ACGTcount: A:0.14, C:0.18, G:0.14, T:0.55
Consensus pattern (17 bp):
TTTTAGCTTTTTCGACA
Found at i:20730 original size:24 final size:23
Alignment explanation
Indices: 20701--20749 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
20691 TCAACTTCTT
20701 ATAATTACAATGAA-AATAACAATA
1 ATAATTACAAT-AATAATAAC-ATA
*
20725 ATAATTCCAATAATAATAACATA
1 ATAATTACAATAATAATAACATA
20748 AT
1 AT
20750 GAAACCTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.59, C:0.10, G:0.02, T:0.29
Consensus pattern (23 bp):
ATAATTACAATAATAATAACATA
Found at i:21669 original size:29 final size:29
Alignment explanation
Indices: 21603--21713 Score: 111
Period size: 29 Copynumber: 3.9 Consensus size: 29
21593 AATTTCACAT
* * *
21603 ACCTTTATCTGGCCCATTAAGCCC-AATC
1 ACCTATATATGGCCCATTAGGCCCAAATC
21631 A--TATTCATATGGCCCATTAGGCCCAAATC
1 ACCTA-T-ATATGGCCCATTAGGCCCAAATC
*
21660 ACCTATATATGGTCCATTAGGCCCAAATC
1 ACCTATATATGGCCCATTAGGCCCAAATC
* * **
21689 ACATTTATATGGCCTGTTAGGCCCA
1 ACCTATATATGGCCCATTAGGCCCA
21714 GTCATATTCA
Statistics
Matches: 69, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
26 1 0.01
27 1 0.01
28 17 0.25
29 47 0.68
30 1 0.01
31 2 0.03
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (29 bp):
ACCTATATATGGCCCATTAGGCCCAAATC
Found at i:21966 original size:17 final size:17
Alignment explanation
Indices: 21944--21980 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
21934 AACTTTTAGC
21944 TTTTCGACATTTCAGCT
1 TTTTCGACATTTCAGCT
*
21961 TTTTCGGCATTTCAGCT
1 TTTTCGACATTTCAGCT
21978 TTT
1 TTT
21981 GCTGATACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.14, C:0.22, G:0.14, T:0.51
Consensus pattern (17 bp):
TTTTCGACATTTCAGCT
Found at i:26218 original size:28 final size:29
Alignment explanation
Indices: 26176--26289 Score: 126
Period size: 29 Copynumber: 4.0 Consensus size: 29
26166 TACCTTTATC
* *
26176 TGGCCCATTAAGCCC-AATCATATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
*
26204 TGGCCCATTAGGCCCAAATCACCTGT-ATA
1 TGGCCCATTAGGCCCAAATCACAT-TCATA
* *
26233 TGGTCCATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
* * *
26262 TGGCCCGTTAGG-CCTAGTCACATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
26290 ATCATGCTCA
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
28 28 0.38
29 44 0.60
30 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTCATA
Found at i:26233 original size:29 final size:29
Alignment explanation
Indices: 26170--26275 Score: 133
Period size: 29 Copynumber: 3.7 Consensus size: 29
26160 TTCACATACC
* * *
26170 TTTATCTGGCCCATTAAGCCC-AATCATA
1 TTTATATGGCCCATTAGGCCCAAATCACA
* *
26198 TTCATATGGCCCATTAGGCCCAAATCACC
1 TTTATATGGCCCATTAGGCCCAAATCACA
* *
26227 TGTATATGGTCCATTAGGCCCAAATCACA
1 TTTATATGGCCCATTAGGCCCAAATCACA
*
26256 TTTATATGGCCCGTTAGGCC
1 TTTATATGGCCCATTAGGCC
26276 TAGTCACATT
Statistics
Matches: 65, Mismatches: 12, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
28 18 0.28
29 47 0.72
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.29
Consensus pattern (29 bp):
TTTATATGGCCCATTAGGCCCAAATCACA
Found at i:31940 original size:51 final size:51
Alignment explanation
Indices: 31853--31952 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 51
31843 TGGATGTGTG
* *
31853 CATCCGAGTTCGTTGAGTGGTCTGAGTTCATAATGGATGCGATACATGTAA
1 CATCCGAGCTCGTTGAGTGGTCCGAGTTCATAATGGATGCGATACATGTAA
* * * *
31904 CATCTGAGCTCGTTGA-TAGGTCCGAGTTCATTATGGATGTGTTACATGT
1 CATCCGAGCTCGTTGAGT-GGTCCGAGTTCATAATGGATGCGATACATGT
31953 TATAAGGTAG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 1 0.02
51 41 0.98
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (51 bp):
CATCCGAGCTCGTTGAGTGGTCCGAGTTCATAATGGATGCGATACATGTAA
Found at i:34789 original size:22 final size:20
Alignment explanation
Indices: 34760--34800 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
34750 TATTTTTATC
34760 TTTTTTTTAAAACTACTTTTT
1 TTTTTTTTAAAACTA-TTTTT
*
34781 TTTTCTTTTAATACTATTTT
1 TTTT-TTTTAAAACTATTTT
34801 ATCTTGAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.22, C:0.10, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTTTTTAAAACTATTTTT
Found at i:36678 original size:13 final size:14
Alignment explanation
Indices: 36660--36700 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
36650 CTAGACTTCC
*
36660 TCACACGA-GTGTG
1 TCACACGAGGAGTG
36673 TCACAC-AGGAGTG
1 TCACACGAGGAGTG
36686 TCACACG-GGAGTG
1 TCACACGAGGAGTG
36699 TC
1 TC
36701 CCTTTGGCAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 1 0.04
13 24 0.96
ACGTcount: A:0.24, C:0.24, G:0.32, T:0.20
Consensus pattern (14 bp):
TCACACGAGGAGTG
Found at i:43194 original size:13 final size:13
Alignment explanation
Indices: 43176--43200 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43166 AAAGAAGCAA
43176 GACACGGCCGTGC
1 GACACGGCCGTGC
43189 GACACGGCCGTG
1 GACACGGCCGTG
43201 TGCACCCACA
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:0.36, G:0.40, T:0.08
Consensus pattern (13 bp):
GACACGGCCGTGC
Found at i:49913 original size:19 final size:18
Alignment explanation
Indices: 49887--49927 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
49877 TTTATTTACG
*
49887 TTTTTATATTTTAGCTTA
1 TTTTTATATTTTAGCTGA
49905 TTTTATATATTTTAGCTGA
1 TTTT-TATATTTTAGCTGA
49924 TTTT
1 TTTT
49928 GAACCATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.22, C:0.05, G:0.07, T:0.66
Consensus pattern (18 bp):
TTTTTATATTTTAGCTGA
Found at i:50134 original size:68 final size:68
Alignment explanation
Indices: 50062--50244 Score: 298
Period size: 68 Copynumber: 2.7 Consensus size: 68
50052 CATCATGTGT
50062 ACAAGAGAGCTACGAGGTACTATATGGTAGCTAGGTCACATGTGTGATACAGGATGTATACCATG
1 ACAAGAGAGCTACGAGGTACTATATGGTAGCTAGGTCACATGTGTGATACAGGATGTATACCATG
50127 TAG
66 TAG
*
50130 ACAAGAGAGCTACGAGGTACTATATGGTAGCTAGGTCACATGTGTGATACGGGATGTATACCATG
1 ACAAGAGAGCTACGAGGTACTATATGGTAGCTAGGTCACATGTGTGATACAGGATGTATACCATG
50195 TAG
66 TAG
* *
50198 ACAAGAGAGCTACGGGAGAGGA-TAAAT-GTAGCTAGGTCACATGTGTG
1 ACAAGAGAGCTAC--GAG-GTACTATATGGTAGCTAGGTCACATGTGTG
50245 GTTCCAAGTG
Statistics
Matches: 109, Mismatches: 3, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
68 80 0.73
69 20 0.18
70 7 0.06
71 2 0.02
ACGTcount: A:0.32, C:0.14, G:0.30, T:0.23
Consensus pattern (68 bp):
ACAAGAGAGCTACGAGGTACTATATGGTAGCTAGGTCACATGTGTGATACAGGATGTATACCATG
TAG
Found at i:52650 original size:132 final size:132
Alignment explanation
Indices: 52489--52756 Score: 527
Period size: 132 Copynumber: 2.0 Consensus size: 132
52479 TTTTTCCAAA
52489 GTTTGAGTTAAGGACTGTTTTGAATAGTACATTAATTAAATAAGTAAAATATGATGTTTTAGATC
1 GTTTGAGTTAAGGACTGTTTTGAATAGTACATTAATTAAATAAGTAAAATATGATGTTTTAGATC
*
52554 CCGGAAAATGATATTTGAACCTAGAATGAGAGAAAAATCGAAAATTGGGAAAGTTGGTAAAATGA
66 CCGGAAAATGATATTTGAACCTAGAATGAGAGAAAAATCAAAAATTGGGAAAGTTGGTAAAATGA
52619 TC
131 TC
52621 GTTTGAGTTAAGGACTGTTTTGAATAGTACATTAATTAAATAAGTAAAATATGATGTTTTAGATC
1 GTTTGAGTTAAGGACTGTTTTGAATAGTACATTAATTAAATAAGTAAAATATGATGTTTTAGATC
52686 CCGGAAAATGATATTTGAACCTAGAATGAGAGAAAAATCAAAAATTGGGAAAGTTGGTAAAATGA
66 CCGGAAAATGATATTTGAACCTAGAATGAGAGAAAAATCAAAAATTGGGAAAGTTGGTAAAATGA
52751 TC
131 TC
52753 GTTT
1 GTTT
52757 TAGTATCGAG
Statistics
Matches: 135, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
132 135 1.00
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.32
Consensus pattern (132 bp):
GTTTGAGTTAAGGACTGTTTTGAATAGTACATTAATTAAATAAGTAAAATATGATGTTTTAGATC
CCGGAAAATGATATTTGAACCTAGAATGAGAGAAAAATCAAAAATTGGGAAAGTTGGTAAAATGA
TC
Found at i:54504 original size:16 final size:16
Alignment explanation
Indices: 54483--54513 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54473 ACTATGGTAT
*
54483 ATGAAATATTGATATA
1 ATGAAATAATGATATA
54499 ATGAAATAATGATAT
1 ATGAAATAATGATAT
54514 GTGTTTATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.13, T:0.35
Consensus pattern (16 bp):
ATGAAATAATGATATA
Done.