Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2386
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: 42532
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Found at i:1502 original size:25 final size:27
Alignment explanation
Indices: 1456--1568 Score: 146
Period size: 25 Copynumber: 4.3 Consensus size: 27
1446 CAAATGGCTA
1456 AAATACCCTCGAAGGGTAAAATGACCG
1 AAATACCCTCGAAGGGTAAAATGACCG
1483 -AATACCCTCG-AGGGTAAAATGA-CG
1 AAATACCCTCGAAGGGTAAAATGACCG
* * *
1507 AAATACCC-CGAA-GCTAAAATGATCT
1 AAATACCCTCGAAGGGTAAAATGACCG
1532 ATAATACCCTCTGAAGGGTAAAATGACCG
1 A-AATACCCTC-GAAGGGTAAAATGACCG
1561 AAATACCC
1 AAATACCC
1569 CATAAGGCTA
Statistics
Matches: 74, Mismatches: 5, Indels: 13
0.80 0.05 0.14
Matches are distributed among these distances:
24 13 0.18
25 22 0.30
26 17 0.23
27 1 0.01
28 10 0.14
29 11 0.15
ACGTcount: A:0.41, C:0.23, G:0.19, T:0.18
Consensus pattern (27 bp):
AAATACCCTCGAAGGGTAAAATGACCG
Found at i:5003 original size:27 final size:27
Alignment explanation
Indices: 4966--5170 Score: 223
Period size: 27 Copynumber: 7.6 Consensus size: 27
4956 TAAATTGTAC
*
4966 AGCACTAAGTGTGCGATTTGGCTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
4993 AGCACTAAGTGTGCGATTTGACCATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** **
5020 TGCACTAAGTGTGCGAAATGAAAATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
5046 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
* *
5074 GGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
5101 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* * * *
5129 GGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
5156 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
5171 GACTTAATAT
Statistics
Matches: 152, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
27 128 0.84
28 24 0.16
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:5027 original size:54 final size:54
Alignment explanation
Indices: 4967--5170 Score: 257
Period size: 54 Copynumber: 3.8 Consensus size: 54
4957 AAATTGTACA
* * *
4967 GCACTAAGTGTGCGATTTGGCTATGTAGCACTAAGTGTGCGATTTGACCATGTT
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGATTTGACCATGTG
** ** * *
5021 GCACTAAGTGTGCGAAATGAAAATG-ATGCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAGTTGACTATGTA-GCACTAAGTGTGCGATTTGACCATGTG
**
5075 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGTG
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGA-TTTGACCATGTG
* * *
5130 GCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
5171 GACTTAATAT
Statistics
Matches: 128, Mismatches: 19, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
53 1 0.01
54 80 0.62
55 47 0.37
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGATTTGACCATGTG
Found at i:13160 original size:27 final size:27
Alignment explanation
Indices: 13123--13327 Score: 223
Period size: 27 Copynumber: 7.6 Consensus size: 27
13113 TAAATTGTAC
*
13123 AGCACTAAGTGTGCGATTTGGCTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
13150 AGCACTAAGTGTGCGATTTGACCATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** **
13177 TGCACTAAGTGTGCGAAATGAAAATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
13203 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
* *
13231 GGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
13258 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* * * *
13286 GGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
13313 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
13328 GACTTAATAT
Statistics
Matches: 152, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
27 128 0.84
28 24 0.16
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:13184 original size:54 final size:54
Alignment explanation
Indices: 13124--13327 Score: 257
Period size: 54 Copynumber: 3.8 Consensus size: 54
13114 AAATTGTACA
* * *
13124 GCACTAAGTGTGCGATTTGGCTATGTAGCACTAAGTGTGCGATTTGACCATGTT
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGATTTGACCATGTG
** ** * *
13178 GCACTAAGTGTGCGAAATGAAAATG-ATGCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAGTTGACTATGTA-GCACTAAGTGTGCGATTTGACCATGTG
**
13232 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGTG
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGA-TTTGACCATGTG
* * *
13287 GCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
13328 GACTTAATAT
Statistics
Matches: 128, Mismatches: 19, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
53 1 0.01
54 80 0.62
55 47 0.37
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGATTTGACCATGTG
Found at i:16167 original size:30 final size:29
Alignment explanation
Indices: 16070--16168 Score: 137
Period size: 30 Copynumber: 3.4 Consensus size: 29
16060 ACTGTAATAT
*
16070 GCTAAGGCCCACA-CTATTACTGTATTGG
1 GCTAAGGCCCACACCTGTTACTGTATTGG
* *
16098 GCTAAGGCACACACACTGTTACCGTATTGG
1 GCTAAGGCCCACAC-CTGTTACTGTATTGG
*
16128 GCTAAGGCCCACACGCTGTTACTGTACTGG
1 GCTAAGGCCCACAC-CTGTTACTGTATTGG
16158 GCTAAGGCCCA
1 GCTAAGGCCCA
16169 TACTATACTG
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
28 12 0.19
30 50 0.81
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.23
Consensus pattern (29 bp):
GCTAAGGCCCACACCTGTTACTGTATTGG
Found at i:16826 original size:13 final size:13
Alignment explanation
Indices: 16804--16838 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
16794 TAATTTCGTG
16804 AAAATTTCGTT-C
1 AAAATTTCGTTCC
16816 AAAAGTTTCGTTCC
1 AAAA-TTTCGTTCC
16830 AAAATTTCG
1 AAAATTTCG
16839 ACGTTTGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.19
13 12 0.57
14 5 0.24
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.37
Consensus pattern (13 bp):
AAAATTTCGTTCC
Found at i:17883 original size:41 final size:40
Alignment explanation
Indices: 17838--18194 Score: 293
Period size: 41 Copynumber: 8.6 Consensus size: 40
17828 TTTTGAATGT
* * *
17838 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCATTGATCAGA
1 AAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGATTA-A
* * *
17879 AAGGGGTTGC-ATGTGTTGATTCCCCGTATCATTGATTAT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGATTAA
* * *
17918 AAGGTGGTTGCTAAGTGTTGATTCCACCGTATCCTTGATTGTGA
1 AAGG-GGTTGCTAAGTGCTGATTCC-CCGTATCATTGA-T-TAA
* * * * *
17962 AAGGGGTTGCTATGTTCTAATTCCTCGTATCATTGATTAT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGATTAA
* * * *
18002 AAGGTGGTTGTTAAGTGCTGATTCCACCATATCCTTGATTGTGA
1 AAGG-GGTTGCTAAGTGCTGATTCC-CCGTATCATTGA-T-TAA
* * * *
18046 AAGGGGTTGCTATGTGTTGATTCCCTGTATCATTGATTAT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGATTAA
* * * *
18086 AAGGTGGTTGCTAAGTACTGATTCCACCATATCCTTGATTGTGA
1 AAGG-GGTTGCTAAGTGCTGATTCC-CCGTATCATTGA-T-TAA
* * ** * *
18130 AAGGAGTTTCTATCTGCTGATTCACCGTATCATTGATTAT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGATTAA
18170 AAGGTGGTTGCTAAGTGCTGATTCC
1 AAGG-GGTTGCTAAGTGCTGATTCC
18195 ACCGGGATCC
Statistics
Matches: 244, Mismatches: 58, Indels: 28
0.74 0.18 0.08
Matches are distributed among these distances:
39 4 0.02
40 44 0.18
41 73 0.30
42 58 0.24
43 50 0.20
44 15 0.06
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.36
Consensus pattern (40 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGTATCATTGATTAA
Found at i:17999 original size:84 final size:83
Alignment explanation
Indices: 17837--18198 Score: 509
Period size: 84 Copynumber: 4.4 Consensus size: 83
17827 TTTTTGAATG
* * * **
17837 TAAGG-GGTTGCTAAGTGCAGATTCC-CCGAATCATTGA-TCAGAAAGGGGTTGC-ATGTGTTGA
1 TAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTGTGAAAGGGGTTGCTATGTGTTGA
17898 TTCCCCGTATCATTGATTA
66 TT-CCCGTATCATTGATTA
* *
17917 TAAGGTGGTTGCTAAGTGTTGATTCCACCGTATCCTTGATTGTGAAAGGGGTTGCTATGT-TCTA
1 TAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTGTGAAAGGGGTTGCTATGTGT-TG
17981 ATTCCTCGTATCATTGATTA
65 ATTCC-CGTATCATTGATTA
* *
18001 TAAGGTGGTTGTTAAGTGCTGATTCCACCATATCCTTGATTGTGAAAGGGGTTGCTATGTGTTGA
1 TAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTGTGAAAGGGGTTGCTATGTGTTGA
18066 TTCCCTGTATCATTGATTA
66 TTCCC-GTATCATTGATTA
* * * * * *
18085 TAAGGTGGTTGCTAAGTACTGATTCCACCATATCCTTGATTGTGAAAGGAGTTTCTATCTGCTGA
1 TAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTGTGAAAGGGGTTGCTATGTGTTGA
18150 TTCACCGTATCATTGATTA
66 TTC-CCGTATCATTGATTA
18169 TAAGGTGGTTGCTAAGTGCTGATTCCACCG
1 TAAGGTGGTTGCTAAGTGCTGATTCCACCG
18199 GGATCCTTTG
Statistics
Matches: 254, Mismatches: 19, Indels: 14
0.89 0.07 0.05
Matches are distributed among these distances:
80 5 0.02
81 18 0.07
82 10 0.04
83 17 0.07
84 201 0.79
85 3 0.01
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (83 bp):
TAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTGTGAAAGGGGTTGCTATGTGTTGA
TTCCCGTATCATTGATTA
Found at i:22797 original size:13 final size:13
Alignment explanation
Indices: 22781--22813 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
22771 TGATTTCATG
22781 AAAATTTCGTTCC
1 AAAATTTCGTTCC
22794 AAAATTTCGTTCC
1 AAAATTTCGTTCC
22807 AAAATTT
1 AAAATTT
22814 TGACATTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.36, C:0.18, G:0.06, T:0.39
Consensus pattern (13 bp):
AAAATTTCGTTCC
Found at i:23944 original size:42 final size:41
Alignment explanation
Indices: 23825--24182 Score: 318
Period size: 42 Copynumber: 8.6 Consensus size: 41
23815 TCTTTGTATG
* * * *
23825 TAAGG-GGTTGCTAAGTGCAGATTCCCCGAATCATTGATCA
1 TAAGGTGGTTTCTAAGTGCTGATTCCCCGTATCATTGATTA
* * * *
23865 GAAAGG-GGTTGC-ATGTGTTGATTCCCCGTATCATTGATTA
1 -TAAGGTGGTTTCTAAGTGCTGATTCCCCGTATCATTGATTA
* *
23905 TAAGGTGGTTTCTAAGTGCTGATTCCACCGTATCCTTGATTG
1 TAAGGTGGTTTCTAAGTGCTGATTCC-CCGTATCATTGATTA
*
23947 TGAAAGG-GGTTTCTATA-TGCTGATTACCCGTATCATTGATTA
1 T--AAGGTGGTTTCTA-AGTGCTGATTCCCCGTATCATTGATTA
* * * *
23989 TAAGGTGGTTGCTAAGTGCTGATTCCAGCGTATCCTTGATTG
1 TAAGGTGGTTTCTAAGTGCTGATTCC-CCGTATCATTGATTA
* * * *
24031 TGAAAGG-GGTTGCTATGTGATGATTCCCCGTATCATTGACTA
1 T--AAGGTGGTTTCTAAGTGCTGATTCCCCGTATCATTGATTA
* ** * *
24073 TAAGTTGGTTGATAAGTGCTGATTCCACCGTATCCTTAATTA
1 TAAGGTGGTTTCTAAGTGCTGATTCC-CCGTATCATTGATTA
*
24115 TGAAAGG-GGTTTCTATGTGCTGATTCCCCGTATCATTGATTA
1 T--AAGGTGGTTTCTAAGTGCTGATTCCCCGTATCATTGATTA
*
24157 TAAGGTGGTTGT-TAAGTGGTGATTCC
1 TAAGGTGGTT-TCTAAGTGCTGATTCC
24183 GTTGGGATCC
Statistics
Matches: 259, Mismatches: 41, Indels: 34
0.78 0.12 0.10
Matches are distributed among these distances:
39 4 0.02
40 40 0.15
41 70 0.27
42 81 0.31
43 52 0.20
44 12 0.05
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (41 bp):
TAAGGTGGTTTCTAAGTGCTGATTCCCCGTATCATTGATTA
Found at i:23981 original size:84 final size:84
Alignment explanation
Indices: 23825--24182 Score: 508
Period size: 84 Copynumber: 4.3 Consensus size: 84
23815 TCTTTGTATG
* * * ** *
23825 TAAGG-GGTTGCTAAGTGCAGATTCC-CCGAATCATTGA-TCAGAAAGGGGTTGC-ATGTGTTGA
1 TAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTGTGAAAGGGGTTGCTATGTGCTGA
23886 TTCCCCGTATCATTGATTA
66 TTCCCCGTATCATTGATTA
* * *
23905 TAAGGTGGTTTCTAAGTGCTGATTCCACCGTATCCTTGATTGTGAAAGGGGTTTCTATATGCTGA
1 TAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTGTGAAAGGGGTTGCTATGTGCTGA
*
23970 TTACCCGTATCATTGATTA
66 TTCCCCGTATCATTGATTA
* *
23989 TAAGGTGGTTGCTAAGTGCTGATTCCAGCGTATCCTTGATTGTGAAAGGGGTTGCTATGTGATGA
1 TAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTGTGAAAGGGGTTGCTATGTGCTGA
*
24054 TTCCCCGTATCATTGACTA
66 TTCCCCGTATCATTGATTA
* * * * *
24073 TAAGTTGGTTGATAAGTGCTGATTCCACCGTATCCTTAATTATGAAAGGGGTTTCTATGTGCTGA
1 TAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTGTGAAAGGGGTTGCTATGTGCTGA
24138 TTCCCCGTATCATTGATTA
66 TTCCCCGTATCATTGATTA
* *
24157 TAAGGTGGTTGTTAAGTGGTGATTCC
1 TAAGGTGGTTGCTAAGTGCTGATTCC
24183 GTTGGGATCC
Statistics
Matches: 246, Mismatches: 28, Indels: 4
0.88 0.10 0.01
Matches are distributed among these distances:
80 5 0.02
81 18 0.07
82 10 0.04
83 12 0.05
84 201 0.82
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (84 bp):
TAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTGTGAAAGGGGTTGCTATGTGCTGA
TTCCCCGTATCATTGATTA
Found at i:31743 original size:17 final size:17
Alignment explanation
Indices: 31723--31757 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
31713 TTAAGTCATC
31723 TATTTATCTTTC-TTATT
1 TATTTAT-TTTCATTATT
31740 TATTTATTTTCATTATT
1 TATTTATTTTCATTATT
31757 T
1 T
31758 TTCTTCTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTTATTTTCATTATT
Done.