Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_4026
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: 16328
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.32
Found at i:1033 original size:13 final size:13
Alignment explanation
Indices: 1001--1034 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
991 GGATTCAGCT
1001 ATGGAGAAAGAAG
1 ATGGAGAAAGAAG
*
1014 A-GGAGAAAGCAG
1 ATGGAGAAAGAAG
1026 ATGGAGAAA
1 ATGGAGAAA
1035 AAAAGAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.53, C:0.03, G:0.38, T:0.06
Consensus pattern (13 bp):
ATGGAGAAAGAAG
Found at i:3974 original size:56 final size:56
Alignment explanation
Indices: 3906--4308 Score: 514
Period size: 56 Copynumber: 7.3 Consensus size: 56
3896 TTTTTAGTTC
* ** *
3906 GCATCGATATGTGATTCTGAAATATGTGTACGAGTAAGACCATGTTTAATACATTG
1 GCATCGATATGTGATTCTGAAATATGTGTGCGAGTAAGACCACATTTAATACGTTG
* ** * * ** *
3962 GCATCAATATGTGATTCCAAAATATGT-TGTGAGTAAGACTATGTTTAATATGTTG
1 GCATCGATATGTGATTCTGAAATATGTGTGCGAGTAAGACCACATTTAATACGTTG
* *
4017 GCATCAATATGTGATTCTGAAATATGTGTGCGAGTAAGACCA-ATTTTAATACATTG
1 GCATCGATATGTGATTCTGAAATATGTGTGCGAGTAAGACCACA-TTTAATACGTTG
4073 GCATCGATATGTGATTCTGAAATA--TGTGCGAGTAAGACCACATTTAATACGTTG
1 GCATCGATATGTGATTCTGAAATATGTGTGCGAGTAAGACCACATTTAATACGTTG
* * * * * *
4127 GCATCAATAAGTAATT-TCGAAATATGTGTGCGATTAAGA-CACGTTTAATATGTTG
1 GCATCGATATGTGATTCT-GAAATATGTGTGCGAGTAAGACCACATTTAATACGTTG
*
4182 GCATCGATATGTGATTCCGAAATATGTGTGCGAGTAAGACCACATTTAATACGTTG
1 GCATCGATATGTGATTCTGAAATATGTGTGCGAGTAAGACCACATTTAATACGTTG
* * * *
4238 GCATCGATATGTGAATCCGAAATATGTATGCGACTAAGACCACATTTAATACGTT-
1 GCATCGATATGTGATTCTGAAATATGTGTGCGAGTAAGACCACATTTAATACGTTG
4293 GCATCGATATGTGATT
1 GCATCGATATGTGATT
4309 TTGATATGTG
Statistics
Matches: 305, Mismatches: 34, Indels: 17
0.86 0.10 0.05
Matches are distributed among these distances:
53 1 0.00
54 46 0.15
55 111 0.36
56 147 0.48
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (56 bp):
GCATCGATATGTGATTCTGAAATATGTGTGCGAGTAAGACCACATTTAATACGTTG
Found at i:4180 original size:165 final size:165
Alignment explanation
Indices: 3906--4297 Score: 565
Period size: 165 Copynumber: 2.4 Consensus size: 165
3896 TTTTTAGTTC
** *
3906 GCATCGATATGTGATTCTGAAATATGTGTACGAGTAAGACCATGTTTAATACATTGGCATCAATA
1 GCATCGATATGTGATTCTGAAATATGTG--CGAGTAAGACCACATTTAATACGTTGGCATCAATA
* * * * *
3971 TGTGATTCCAAAATATGTTGTGAGTAAGACTATGTTTAATATGTTGGCATCAATATGTGATTCTG
64 AGTAATTCCAAAATATGTTGCGAGTAAGACTACGTTTAATATGTTGGCATCAATATGTGATTCCG
4036 AAATATGTGTGCGAGTAAGACCA-ATTTTAATACATTG
129 AAATATGTGTGCGAGTAAGACCACA-TTTAATACATTG
4073 GCATCGATATGTGATTCTGAAATATGTGCGAGTAAGACCACATTTAATACGTTGGCATCAATAAG
1 GCATCGATATGTGATTCTGAAATATGTGCGAGTAAGACCACATTTAATACGTTGGCATCAATAAG
* * * *
4138 TAATTTCGAAATATGTGTGCGATTAAGAC-ACGTTTAATATGTTGGCATCGATATGTGATTCCGA
66 TAATTCCAAAATATGT-TGCGAGTAAGACTACGTTTAATATGTTGGCATCAATATGTGATTCCGA
*
4202 AATATGTGTGCGAGTAAGACCACATTTAATACGTTG
130 AATATGTGTGCGAGTAAGACCACATTTAATACATTG
* * *
4238 GCATCGATATGTGAATCCGAAATATGTATGCGACTAAGACCACATTTAATACGTT-GCATC
1 GCATCGATATGTGATTCTGAAATATG--TGCGAGTAAGACCACATTTAATACGTTGGCATC
4298 GATATGTGAT
Statistics
Matches: 205, Mismatches: 16, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
165 135 0.66
166 16 0.08
167 54 0.26
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.33
Consensus pattern (165 bp):
GCATCGATATGTGATTCTGAAATATGTGCGAGTAAGACCACATTTAATACGTTGGCATCAATAAG
TAATTCCAAAATATGTTGCGAGTAAGACTACGTTTAATATGTTGGCATCAATATGTGATTCCGAA
ATATGTGTGCGAGTAAGACCACATTTAATACATTG
Found at i:4259 original size:111 final size:112
Alignment explanation
Indices: 3906--4308 Score: 512
Period size: 111 Copynumber: 3.6 Consensus size: 112
3896 TTTTTAGTTC
* * * * * *
3906 GCATCGATATGTGATTCTGAAATATGTGTACGAGTAAGACCATGTTTAATACATTGGCATCAATA
1 GCATCAATATGTGAATCCGAAATATGTGTGCGAGTAAGACCACGTTTAATACATTGGCATCGATA
* * * ** *
3971 TGTGATTCCAAAATATGT-TGTGAGTAAGACTATGTTTAATATGTTG
66 TGTGATTCCGAAATATGTGTGCGAGTAAGACCACATTTAATACGTTG
* * **
4017 GCATCAATATGTGATTCTGAAATATGTGTGCGAGTAAGACCAATTTTAATACATTGGCATCGATA
1 GCATCAATATGTGAATCCGAAATATGTGTGCGAGTAAGACCACGTTTAATACATTGGCATCGATA
*
4082 TGTGATTCTGAAATA--TGTGCGAGTAAGACCACATTTAATACGTTG
66 TGTGATTCCGAAATATGTGTGCGAGTAAGACCACATTTAATACGTTG
* * * **
4127 GCATCAATAAGT-AATTTCGAAATATGTGTGCGATTAAGA-CACGTTTAATATGTTGGCATCGAT
1 GCATCAATATGTGAA-TCCGAAATATGTGTGCGAGTAAGACCACGTTTAATACATTGGCATCGAT
4190 ATGTGATTCCGAAATATGTGTGCGAGTAAGACCACATTTAATACGTTG
65 ATGTGATTCCGAAATATGTGTGCGAGTAAGACCACATTTAATACGTTG
* * * * *
4238 GCATCGATATGTGAATCCGAAATATGTATGCGACTAAGACCACATTTAATACGTT-GCATCGATA
1 GCATCAATATGTGAATCCGAAATATGTGTGCGAGTAAGACCACGTTTAATACATTGGCATCGATA
4302 TGTGATT
66 TGTGATT
4309 TTGATATGTG
Statistics
Matches: 257, Mismatches: 29, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
109 37 0.14
110 55 0.21
111 150 0.58
112 15 0.06
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (112 bp):
GCATCAATATGTGAATCCGAAATATGTGTGCGAGTAAGACCACGTTTAATACATTGGCATCGATA
TGTGATTCCGAAATATGTGTGCGAGTAAGACCACATTTAATACGTTG
Found at i:11958 original size:22 final size:23
Alignment explanation
Indices: 11930--12013 Score: 82
Period size: 23 Copynumber: 3.7 Consensus size: 23
11920 GGAGGAATAC
11930 AAAAGGGC-ATGCCCAGTTACCG
1 AAAAGGGCTATGCCCAGTTACCG
* *
11952 AAAAGGGCTTTGTCCAGTTACCG
1 AAAAGGGCTATGCCCAGTTACCG
* * *
11975 AAAAGGG-TTTGCCCCAGTTTATCA
1 AAAAGGGCTATG-CCCAG-TTACCG
*
11999 AAAAGGGCTTTGCCC
1 AAAAGGGCTATGCCC
12014 CATTATTAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
22 12 0.23
23 23 0.43
24 14 0.26
25 4 0.08
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.23
Consensus pattern (23 bp):
AAAAGGGCTATGCCCAGTTACCG
Found at i:11972 original size:23 final size:24
Alignment explanation
Indices: 11941--12015 Score: 100
Period size: 23 Copynumber: 3.2 Consensus size: 24
11931 AAAGGGCATG
11941 CCCAGTTACCGAAAAGGGCTTTG-
1 CCCAGTTACCGAAAAGGGCTTTGC
*
11964 TCCAGTTACCGAAAAGGG-TTTGC
1 CCCAGTTACCGAAAAGGGCTTTGC
* *
11987 CCCAGTTTATCAAAAAGGGCTTTGC
1 CCCAG-TTACCGAAAAGGGCTTTGC
12012 CCCA
1 CCCA
12016 TTATTAAAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
22 4 0.09
23 21 0.47
24 11 0.24
25 9 0.20
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.24
Consensus pattern (24 bp):
CCCAGTTACCGAAAAGGGCTTTGC
Found at i:12019 original size:23 final size:24
Alignment explanation
Indices: 11941--12024 Score: 84
Period size: 23 Copynumber: 3.6 Consensus size: 24
11931 AAAGGGCATG
* *
11941 CCCAGTTACCGAAAAGGGCTTTG-
1 CCCAGTTATCAAAAAGGGCTTTGC
* * *
11964 TCCAGTTACCGAAAAGGG-TTTGC
1 CCCAGTTATCAAAAAGGGCTTTGC
11987 CCCAGTTTATCAAAAAGGGCTTTGC
1 CCCAG-TTATCAAAAAGGGCTTTGC
*
12012 CCCA-TTATTAAAA
1 CCCAGTTATCAAAA
12025 GAGGCTAGCC
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
22 4 0.08
23 29 0.55
24 11 0.21
25 9 0.17
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (24 bp):
CCCAGTTATCAAAAAGGGCTTTGC
Found at i:12261 original size:28 final size:29
Alignment explanation
Indices: 12229--12300 Score: 94
Period size: 30 Copynumber: 2.5 Consensus size: 29
12219 TTACAGTAAG
*
12229 AGGCTTCGGCCAGTGATA-GAA-AATGAAA
1 AGGCTTCGGCCAGTGACATGAATAATG-AA
*
12257 AGGCTTCGGCCTAGTGACATGAATAATGCA
1 AGGCTTCGGCC-AGTGACATGAATAATGAA
12287 AGGCTTCGGCCAGT
1 AGGCTTCGGCCAGT
12301 ATATGTTGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
28 11 0.28
29 9 0.23
30 15 0.38
31 4 0.10
ACGTcount: A:0.31, C:0.19, G:0.29, T:0.21
Consensus pattern (29 bp):
AGGCTTCGGCCAGTGACATGAATAATGAA
Done.