Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold5515.1
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: 22157
ACGTcount: A:0.23, C:0.13, G:0.14, T:0.25
Warning! 5594 characters in sequence are not A, C, G, or T
Found at i:7021 original size:11 final size:12
Alignment explanation
Indices: 6991--7024 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
6981 TAGTTTCTTC
6991 AAAAAAAATTCA
1 AAAAAAAATTCA
*
7003 AAAAAAAATTAA
1 AAAAAAAATTCA
7015 AAAAAAAATT
1 AAAAAAAATT
7025 TGGTTTCCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:7083 original size:16 final size:17
Alignment explanation
Indices: 7062--7103 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
7052 GATATCAAGT
7062 TGAAAAAAAA-AATTCG
1 TGAAAAAAAATAATTCG
**
7078 TGAAAAAAAATTTTTCG
1 TGAAAAAAAATAATTCG
7095 TGAAAAAAA
1 TGAAAAAAA
7104 GAAGAAGAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.60, C:0.05, G:0.12, T:0.24
Consensus pattern (17 bp):
TGAAAAAAAATAATTCG
Found at i:18132 original size:24 final size:22
Alignment explanation
Indices: 18080--18134 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 22
18070 TTCGGCTACT
*
18080 GATGTGTTCACACAACAATTAAA
1 GATG-GTTCACACAAAAATTAAA
*
18103 -AGGGTTCACACTAAAACATTAAA
1 GATGGTTCACAC-AAAA-ATTAAA
18126 GATGGTTCA
1 GATGGTTCA
18135 TGAATTCGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 8 0.31
22 5 0.19
23 6 0.23
24 7 0.27
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.25
Consensus pattern (22 bp):
GATGGTTCACACAAAAATTAAA
Found at i:18832 original size:27 final size:27
Alignment explanation
Indices: 18791--18842 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
18781 TCATTGAAGC
* *
18791 ATCTTCATTGTTGTCCATGCATGTATT
1 ATCTTCAATGCTGTCCATGCATGTATT
18818 ATCTTCAATGCTGTCCATGCATGTA
1 ATCTTCAATGCTGTCCATGCATGTA
18843 CCTACAAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.42
Consensus pattern (27 bp):
ATCTTCAATGCTGTCCATGCATGTATT
Found at i:19387 original size:165 final size:165
Alignment explanation
Indices: 19115--19444 Score: 642
Period size: 165 Copynumber: 2.0 Consensus size: 165
19105 TGAGCTGAAA
19115 CTATATTAACTAACTTAATTTAAAGCATGAAATTTATTCCAGCAAGTAAATCAAATAAAATAAAA
1 CTATATTAACTAACTTAATTTAAAGCATGAAATTTATTCCAGCAAGTAAATCAAATAAAATAAAA
19180 AGATGGAAAACGAGTTCATTGAGCTAGAATCGAGCTTATTTAAGCTCAACGAGCTAAATTTGAGC
66 AGATGGAAAACGAGTTCATTGAGCTAGAATCGAGCTTATTTAAGCTCAACGAGCTAAATTTGAGC
19245 TAGGTCAGCTTGCAAAAGACGACAAGCCTCGCTTG
131 TAGGTCAGCTTGCAAAAGACGACAAGCCTCGCTTG
19280 CTATATTAACTAACTTAATTTAAAGCATGAAATTTATTCCAGCAAGTAAATCAAATAAAATAAAA
1 CTATATTAACTAACTTAATTTAAAGCATGAAATTTATTCCAGCAAGTAAATCAAATAAAATAAAA
19345 AGATGGAAAACGAGTTCATTGAGCTAGAATCGAGCTTATTTAAGCTCAACGAGCTAAATTTGAGC
66 AGATGGAAAACGAGTTCATTGAGCTAGAATCGAGCTTATTTAAGCTCAACGAGCTAAATTTGAGC
* *
19410 TAGGTCAGCTTGCAAAAGATGACAAGCCTTGCTTG
131 TAGGTCAGCTTGCAAAAGACGACAAGCCTCGCTTG
19445 GGAAGCTTAT
Statistics
Matches: 163, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
165 163 1.00
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (165 bp):
CTATATTAACTAACTTAATTTAAAGCATGAAATTTATTCCAGCAAGTAAATCAAATAAAATAAAA
AGATGGAAAACGAGTTCATTGAGCTAGAATCGAGCTTATTTAAGCTCAACGAGCTAAATTTGAGC
TAGGTCAGCTTGCAAAAGACGACAAGCCTCGCTTG
Found at i:21011 original size:6 final size:6
Alignment explanation
Indices: 21002--21109 Score: 74
Period size: 6 Copynumber: 17.5 Consensus size: 6
20992 TTTTTCAACA
* * * * *
21002 TCTTTT TCTTTT TCAATTT TCTTTTCT TCATTT TCTTTT TCTCTC ACTTTT
1 TCTTTT TCTTTT TC-TTTT TC-TTT-T TCTTTT TCTTTT TCTTTT TCTTTT
** ** *
21053 TCAATT TCTTTT TCTTTT GT-AATT TCTTTT TCTTTT TCGTTT TCTTTT
1 TCTTTT TCTTTT TCTTTT -TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT
*
21101 TCATTT TCT
1 TCTTTT TCT
21110 CGCTCGCACT
Statistics
Matches: 75, Mismatches: 23, Indels: 8
0.71 0.22 0.08
Matches are distributed among these distances:
5 1 0.01
6 61 0.81
7 10 0.13
8 3 0.04
ACGTcount: A:0.08, C:0.19, G:0.02, T:0.71
Consensus pattern (6 bp):
TCTTTT
Found at i:21034 original size:14 final size:14
Alignment explanation
Indices: 21005--21041 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
20995 TTCAACATCT
21005 TTTTC-TTTTTCAA
1 TTTTCTTTTTTCAA
21018 TTTTCTTTTCTTC-A
1 TTTTCTTTT-TTCAA
21032 TTTTCTTTTT
1 TTTTCTTTTT
21042 CTCTCACTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 6 0.27
14 13 0.59
15 3 0.14
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTCTTTTTTCAA
Found at i:21090 original size:12 final size:12
Alignment explanation
Indices: 21005--21109 Score: 88
Period size: 12 Copynumber: 8.5 Consensus size: 12
20995 TTCAACATCT
21005 TTTTCTTTTTCAA
1 TTTTCTTTTTC-A
21018 TTTTCTTTTCTTCA
1 TTTTC-TTT-TTCA
21032 TTTTCTTTTTC-
1 TTTTCTTTTTCA
**
21043 TCTCACTTTTTCA
1 T-TTTCTTTTTCA
*
21056 ATTTCTTTTTC-
1 TTTTCTTTTTCA
* * *
21067 TTTTGTAATTTCT
1 TTTTCT-TTTTCA
*
21080 TTTTCTTTTTCG
1 TTTTCTTTTTCA
21092 TTTTCTTTTTCA
1 TTTTCTTTTTCA
21104 TTTTCT
1 TTTTCT
21110 CGCTCGCACT
Statistics
Matches: 74, Mismatches: 12, Indels: 13
0.75 0.12 0.13
Matches are distributed among these distances:
11 5 0.07
12 44 0.59
13 13 0.18
14 9 0.12
15 3 0.04
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (12 bp):
TTTTCTTTTTCA
Found at i:21101 original size:18 final size:18
Alignment explanation
Indices: 20988--21108 Score: 91
Period size: 18 Copynumber: 6.6 Consensus size: 18
20978 TTTCCTCTCG
***
20988 TTTCTTTTTCAACATCTT
1 TTTCTTTTTCATTTTCTT
21006 TTTCTTTTTCAATTTTCTTT
1 TTTCTTTTTC-ATTTTC-TT
* * *
21026 TCTTCATTTTCTTTTTCTC
1 T-TTCTTTTTCATTTTCTT
** *
21045 TCACTTTTTCAATTTCTT
1 TTTCTTTTTCATTTTCTT
*
21063 TTTCTTTTGT-AATTTCTT
1 TTTCTTTT-TCATTTTCTT
*
21081 TTTCTTTTTCGTTTTCTT
1 TTTCTTTTTCATTTTCTT
*
21099 TTTCATTTTC
1 TTTCTTTTTC
21109 TCGCTCGCAC
Statistics
Matches: 81, Mismatches: 17, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
17 1 0.01
18 58 0.72
19 6 0.07
20 8 0.10
21 8 0.10
ACGTcount: A:0.10, C:0.19, G:0.02, T:0.69
Consensus pattern (18 bp):
TTTCTTTTTCATTTTCTT
Found at i:21876 original size:45 final size:45
Alignment explanation
Indices: 21812--21903 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
21802 GCGGCTTAGA
21812 GGATCGGCTTCAAATGGGTGCAACGGATAACGTTAGGGTGTATAG
1 GGATCGGCTTCAAATGGGTGCAACGGATAACGTTAGGGTGTATAG
21857 GGATCGGCTTCAAATGGGTGCAACGGATAACGTTAGGGTGTATAG
1 GGATCGGCTTCAAATGGGTGCAACGGATAACGTTAGGGTGTATAG
21902 GG
1 GG
21904 TAGGCTGAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.26, C:0.13, G:0.37, T:0.24
Consensus pattern (45 bp):
GGATCGGCTTCAAATGGGTGCAACGGATAACGTTAGGGTGTATAG
Found at i:22074 original size:12 final size:11
Alignment explanation
Indices: 22053--22093 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 11
22043 TTTATACTTC
22053 GAATTTTTTTT
1 GAATTTTTTTT
22064 GAATCTTTTTTT
1 GAAT-TTTTTTT
22076 G-A-TTTTTTT
1 GAATTTTTTTT
22085 G-ATTTTTTT
1 GAATTTTTTT
22094 CGATTTTCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 9 0.32
10 6 0.21
11 5 0.18
12 8 0.29
ACGTcount: A:0.15, C:0.02, G:0.10, T:0.73
Consensus pattern (11 bp):
GAATTTTTTTT
Found at i:22083 original size:8 final size:9
Alignment explanation
Indices: 22069--22122 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
22059 TTTTTGAATC
22069 TTTTTTTGA
1 TTTTTTTGA
22078 TTTTTTTGA
1 TTTTTTTGA
22087 TTTTTTTCGA
1 TTTTTTT-GA
** *
22097 TTTTCCT-C
1 TTTTTTTGA
22105 TTTTTTTCGA
1 TTTTTTT-GA
22115 TTTTTTTG
1 TTTTTTTG
22123 TTCAATTACA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
8 5 0.14
9 17 0.47
10 14 0.39
ACGTcount: A:0.07, C:0.09, G:0.09, T:0.74
Consensus pattern (9 bp):
TTTTTTTGA
Found at i:22090 original size:18 final size:19
Alignment explanation
Indices: 22057--22122 Score: 71
Period size: 18 Copynumber: 3.4 Consensus size: 19
22047 TACTTCGAAT
*
22057 TTTTTTTGAATCTTTTTTTGA
1 TTTTTTTG-AT-TTTTTTCGA
22078 TTTTTTTGATTTTTTTCGA
1 TTTTTTTGATTTTTTTCGA
** *
22097 TTTTCCT-CTTTTTTTCGA
1 TTTTTTTGATTTTTTTCGA
22115 TTTTTTTG
1 TTTTTTTG
22123 TTCAATTACA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
18 15 0.39
19 13 0.34
20 2 0.05
21 8 0.21
ACGTcount: A:0.09, C:0.09, G:0.09, T:0.73
Consensus pattern (19 bp):
TTTTTTTGATTTTTTTCGA
Found at i:22118 original size:10 final size:10
Alignment explanation
Indices: 22050--22121 Score: 60
Period size: 10 Copynumber: 7.2 Consensus size: 10
22040 TTTTTTATAC
22050 TTCGAATTTTT
1 TTCG-ATTTTT
*
22061 TTTGAATCTTTT
1 TTCG-AT-TTTT
*
22073 TTTGATTTTT
1 TTCGATTTTT
22083 TT-GATTTTT
1 TTCGATTTTT
*
22092 TTCGATTTTC
1 TTCGATTTTT
*
22102 CTC--TTTTT
1 TTCGATTTTT
22110 TTCGATTTTT
1 TTCGATTTTT
22120 TT
1 TT
22122 GTTCAATTAC
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
8 6 0.12
9 9 0.17
10 21 0.40
11 8 0.15
12 8 0.15
ACGTcount: A:0.11, C:0.10, G:0.08, T:0.71
Consensus pattern (10 bp):
TTCGATTTTT
Done.