Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2374
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: 53785
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:1042 original size:16 final size:16
Alignment explanation
Indices: 1008--1063 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
998 CTAGCTCTTC
**
1008 TTTTTTTC-ACGAAAA
1 TTTTTTTCAACGAATT
1023 TTTTTTTCAACGAATT
1 TTTTTTTCAACGAATT
1039 TTTTTTT-ATACGAAATCT
1 TTTTTTTCA-ACG-AAT-T
1057 TTTTTTT
1 TTTTTTT
1064 GGCAAACTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
15 9 0.26
16 15 0.43
17 3 0.09
18 8 0.23
ACGTcount: A:0.25, C:0.11, G:0.05, T:0.59
Consensus pattern (16 bp):
TTTTTTTCAACGAATT
Found at i:1128 original size:13 final size:13
Alignment explanation
Indices: 1110--1137 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1100 TGGAAACGCA
1110 AATTTTTTTTTTG
1 AATTTTTTTTTTG
1123 AATTTTTTTTTTG
1 AATTTTTTTTTTG
1136 AA
1 AA
1138 AATTTTGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.71
Consensus pattern (13 bp):
AATTTTTTTTTTG
Found at i:9907 original size:21 final size:21
Alignment explanation
Indices: 9862--9924 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
9852 TTTGAACCAT
* *
9862 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
9884 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
9905 TACCATTTCG-AGCCAATTCC
1 TACCATTTCGTA-CCAATTCC
9925 CAAATACCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 1 0.03
21 24 0.63
22 13 0.34
ACGTcount: A:0.32, C:0.33, G:0.06, T:0.29
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:10304 original size:16 final size:16
Alignment explanation
Indices: 10283--10350 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
10273 TTTGGTTCGC
10283 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
10299 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
10315 TGTAATGGATTAGAGG
1 TGTATTGGATTAGAGG
10331 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
10347 TGTA
1 TGTA
10351 ATAGCAAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.26, C:0.00, G:0.37, T:0.37
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:10604 original size:16 final size:16
Alignment explanation
Indices: 10567--10608 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
10557 TTAATCATAT
*
10567 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
10583 TT-AAATATATTATAA
1 TTAAAATATATTATAA
10598 TTAAAATATAT
1 TTAAAATATAT
10609 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:10615 original size:14 final size:15
Alignment explanation
Indices: 10576--10617 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
10566 TTTAAACATA
*
10576 ATTATTATTAAATAT
1 ATTATAATTAAATAT
10591 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
10605 A-TATAATTTAATA
1 ATTATAATTAAATA
10618 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:10735 original size:14 final size:15
Alignment explanation
Indices: 10686--10737 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
10676 ATAAAATATA
10686 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
10701 TATTAAATATATTAT
1 AATTAAATATATTAT
10716 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
10729 AATTTAATA
1 AATTAAATA
10738 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:10805 original size:119 final size:120
Alignment explanation
Indices: 10570--11009 Score: 841
Period size: 119 Copynumber: 3.7 Consensus size: 120
10560 ATCATATTTA
10570 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
10635 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
10690 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAA-AATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
10754 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
10809 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAA-AATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
10873 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
* *
10928 AACATAATTATTATTAAATATATTATAACTAAAATATATAATTTAATAAAATTATTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
10993 TATTCTTATAT-AATTTA
66 TATTCTTATATGAATTTA
11010 ATAAAACAAT
Statistics
Matches: 317, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
119 242 0.76
120 75 0.24
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.43
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
Found at i:10854 original size:14 final size:15
Alignment explanation
Indices: 10805--10856 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
10795 ATAAAATATA
10805 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
10820 TATTAAATATATTAT
1 AATTAAATATATTAT
10835 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
10848 AATTTAATA
1 AATTAAATA
10857 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:10982 original size:44 final size:43
Alignment explanation
Indices: 10663--10984 Score: 149
Period size: 44 Copynumber: 7.9 Consensus size: 43
10653 CTCAAATCAT
*
10663 AATATATGATACTATAAAATATAAATTAACATAATTATTATTA
1 AATATATGATACTATAAAATATAAATTAACAAAATTATTATTA
* * * *
10706 AATATATTATAAT-TAAAATATATAATTTAATAAAATTCTTA--A
1 AATATATGATACTATAAAATATA-AA-TTAACAAAATTATTATTA
* * * ** *
10748 AAT-TAAT-ATTCT-T---ATATGAATTTACTCAA--ATCA-T-
1 AATAT-ATGATACTATAAAATATAAATTAACAAAATTATTATTA
*
10782 AATATATGATACTATAAAATATAAATTAACATAATTATTATTA
1 AATATATGATACTATAAAATATAAATTAACAAAATTATTATTA
* * * *
10825 AATATATTATAAT-TAAAATATATAATTTAATAAAATTCTTA--A
1 AATATATGATACTATAAAATATA-AA-TTAACAAAATTATTATTA
* * * ** *
10867 AAT-TAAT-ATTCT-T---ATATGAATTTACTCAA--ATCA-T-
1 AATAT-ATGATACTATAAAATATAAATTAACAAAATTATTATTA
*
10901 AATATATGATACTATAAAATATAAATTAACATAATTATTATTA
1 AATATATGATACTATAAAATATAAATTAACAAAATTATTATTA
* * *
10944 AATATATTATAACTA-AAATATATAATTTAATAAAATTATTA
1 AATATATGAT-ACTATAAA-ATATAAATTAACAAAATTATTA
10985 ATAATTAATA
Statistics
Matches: 205, Mismatches: 44, Indels: 59
0.67 0.14 0.19
Matches are distributed among these distances:
34 14 0.07
35 10 0.05
36 12 0.06
37 4 0.02
38 8 0.04
39 24 0.12
41 16 0.08
42 32 0.16
43 38 0.19
44 47 0.23
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.42
Consensus pattern (43 bp):
AATATATGATACTATAAAATATAAATTAACAAAATTATTATTA
Found at i:13318 original size:12 final size:13
Alignment explanation
Indices: 13287--13320 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
13277 TGGAGAAAGC
13287 AAAGCAAAGGAAG
1 AAAGCAAAGGAAG
13300 AAAGCAAAGG-AG
1 AAAGCAAAGGAAG
*
13312 GAAGCAAAG
1 AAAGCAAAG
13321 CAAAGAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.59, C:0.09, G:0.32, T:0.00
Consensus pattern (13 bp):
AAAGCAAAGGAAG
Found at i:13389 original size:19 final size:19
Alignment explanation
Indices: 13365--13401 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
13355 AATCGGGCGA
13365 AACAGAAGAGGCAAAGGGG
1 AACAGAAGAGGCAAAGGGG
13384 AACAGAAGAGGCAAAGGG
1 AACAGAAGAGGCAAAGGG
13402 TAAAACAGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.11, G:0.41, T:0.00
Consensus pattern (19 bp):
AACAGAAGAGGCAAAGGGG
Found at i:22985 original size:12 final size:12
Alignment explanation
Indices: 22970--23000 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
22960 TTCTTTTTGC
22970 TTTTCAAAGGCT
1 TTTTCAAAGGCT
22982 TTTTCAAAGGCT
1 TTTTCAAAGGCT
22994 TTTTCAA
1 TTTTCAA
23001 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:35108 original size:20 final size:21
Alignment explanation
Indices: 35073--35111 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
35063 CAGCTCGTTG
35073 AGCTCAATTCAGCTCATTTCC
1 AGCTCAATTCAGCTCATTTCC
*
35094 AGCTC-ATTGAGCTCATTT
1 AGCTCAATTCAGCTCATTT
35112 GCTTGTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.36
Consensus pattern (21 bp):
AGCTCAATTCAGCTCATTTCC
Found at i:35519 original size:13 final size:13
Alignment explanation
Indices: 35501--35526 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35491 TGTGTCCTAA
35501 TATGAATTAAATT
1 TATGAATTAAATT
35514 TATGAATTAAATT
1 TATGAATTAAATT
35527 GCTTTCAGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TATGAATTAAATT
Found at i:39077 original size:20 final size:19
Alignment explanation
Indices: 39054--39118 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
39044 AAGCTCAAAC
39054 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
39074 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
39094 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
39114 GAGCT
1 GAGCT
39119 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:40930 original size:33 final size:33
Alignment explanation
Indices: 40892--40954 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
40882 GATTACTCAC
40892 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
40925 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
40955 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:41044 original size:17 final size:17
Alignment explanation
Indices: 41024--41080 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
41014 TTCTCTCACT
41024 TTTTCGATTTCTTTTTC
1 TTTTCGATTTCTTTTTC
*
41041 TTTTGCAATTTC-TTTTC
1 TTTT-CGATTTCTTTTTC
* *
41058 TTTTTCGTTTTCTTTTTG
1 -TTTTCGATTTCTTTTTC
41076 TTTTC
1 TTTTC
41081 TTTCAATTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
17 19 0.58
18 14 0.42
ACGTcount: A:0.05, C:0.16, G:0.07, T:0.72
Consensus pattern (17 bp):
TTTTCGATTTCTTTTTC
Found at i:41096 original size:6 final size:6
Alignment explanation
Indices: 40969--41083 Score: 63
Period size: 6 Copynumber: 18.7 Consensus size: 6
40959 TCTTTTTTCG
* * * **
40969 CTTTTT CTTTTT CAATTTTTT TTTTTT CTTTTCTT CATTTT CTTTTT CTCTCA
1 CTTTTT CTTTTT C---TTTTT CTTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT
** * ** *
41022 CTTTTT CGATTT CTTTTT CTTTTG CAATTT C-TTTT CTTTTT CGTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
41069 CTTTTT -GTTTT CTTT
1 CTTTTT CTTTTT CTTT
41084 CAATTTCTTT
Statistics
Matches: 79, Mismatches: 23, Indels: 14
0.68 0.20 0.12
Matches are distributed among these distances:
5 8 0.10
6 58 0.73
7 5 0.06
8 3 0.04
9 5 0.06
ACGTcount: A:0.06, C:0.17, G:0.03, T:0.73
Consensus pattern (6 bp):
CTTTTT
Found at i:42173 original size:11 final size:11
Alignment explanation
Indices: 42158--42226 Score: 50
Period size: 11 Copynumber: 5.8 Consensus size: 11
42148 TTTTTGCTCG
42158 ATTTTTTTTCA
1 ATTTTTTTTCA
* *
42169 CTTTTTTTTGA
1 ATTTTTTTTCA
42180 ATTTTTTTTTCAATCA
1 A--TTTTTTT---TCA
42196 ATTTTTTTTCGA
1 ATTTTTTTTC-A
*
42208 ATTTTTTTT-T
1 ATTTTTTTTCA
42218 ATTTTTTTT
1 ATTTTTTTT
42227 GTTACTCCAA
Statistics
Matches: 47, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
10 9 0.19
11 11 0.23
12 10 0.21
13 7 0.15
14 7 0.15
16 3 0.06
ACGTcount: A:0.16, C:0.07, G:0.03, T:0.74
Consensus pattern (11 bp):
ATTTTTTTTCA
Found at i:42174 original size:12 final size:12
Alignment explanation
Indices: 42159--42226 Score: 61
Period size: 12 Copynumber: 5.6 Consensus size: 12
42149 TTTTGCTCGA
*
42159 TTTTTTTTC-AC
1 TTTTTTTTCAAT
*
42170 TTTTTTTTGAAT
1 TTTTTTTTCAAT
42182 TTTTTTTTCAAT
1 TTTTTTTTCAAT
42194 CAATTTTTTTTCGAAT
1 ---TTTTTTTTC-AAT
42210 TTTTTTTT--AT
1 TTTTTTTTCAAT
42220 TTTTTTT
1 TTTTTTT
42227 GTTACTCCAA
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
10 9 0.18
11 8 0.16
12 12 0.24
13 8 0.16
15 9 0.18
16 3 0.06
ACGTcount: A:0.15, C:0.07, G:0.03, T:0.75
Consensus pattern (12 bp):
TTTTTTTTCAAT
Found at i:42177 original size:29 final size:28
Alignment explanation
Indices: 42096--42177 Score: 78
Period size: 30 Copynumber: 2.8 Consensus size: 28
42086 GCAAGACTTT
**
42096 TCACTTTTTTTTTAACTTGATTTTTTTTGC
1 TCAC-TTTTTTTT-ACTTTTTTTTTTTTGC
42126 TCACCTTTTTTTT-CTTTTCTTTTTTTTGC
1 TCA-CTTTTTTTTACTTTT-TTTTTTTTGC
42155 TCGA-TTTTTTTTCACTTTTTTTT
1 TC-ACTTTTTTTT-ACTTTTTTTT
42178 GAATTTTTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
28 11 0.24
29 16 0.36
30 17 0.38
31 1 0.02
ACGTcount: A:0.09, C:0.16, G:0.05, T:0.71
Consensus pattern (28 bp):
TCACTTTTTTTTACTTTTTTTTTTTTGC
Found at i:43822 original size:20 final size:19
Alignment explanation
Indices: 43799--43863 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
43789 AAGCTCAAAC
43799 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
43819 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
43839 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
43859 GAGCT
1 GAGCT
43864 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:47094 original size:14 final size:14
Alignment explanation
Indices: 47075--47108 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
47065 GGACGAAAGC
47075 TCTAAACGAACAGA
1 TCTAAACGAACAGA
47089 TCTAAACGAACAGA
1 TCTAAACGAACAGA
47103 TCTAAA
1 TCTAAA
47109 AATTAAAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.50, C:0.21, G:0.12, T:0.18
Consensus pattern (14 bp):
TCTAAACGAACAGA
Done.