Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2408
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: 26953
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.36
Found at i:3193 original size:3 final size:3
Alignment explanation
Indices: 3185--3211 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3175 AAATAAAGAA
3185 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
3212 GATCCCACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:7380 original size:7 final size:8
Alignment explanation
Indices: 7351--7380 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
7341 AATATATTTA
7351 GTTTAATC
1 GTTTAATC
7359 GTTTAATC
1 GTTTAATC
7367 GTTTAATC
1 GTTTAATC
7375 -TTTAAT
1 GTTTAAT
7381 ATAAAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.53
Consensus pattern (8 bp):
GTTTAATC
Found at i:14649 original size:13 final size:13
Alignment explanation
Indices: 14631--14661 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
14621 ACAATTCATC
*
14631 ATGTATTGATACA
1 ATGTATCGATACA
14644 ATGTATCGATACA
1 ATGTATCGATACA
14657 ATGTA
1 ATGTA
14662 CCATGTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:14651 original size:33 final size:33
Alignment explanation
Indices: 14609--14677 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
14599 CCATTAGAAG
* *
14609 CAATGTATCGATACAAT-TCATCATGTATTGATA
1 CAATGTATCGATACAATGT-ACCATGTATTAATA
14642 CAATGTATCGATACAATGTACCATGTATTAATA
1 CAATGTATCGATACAATGTACCATGTATTAATA
14675 CAA
1 CAA
14678 ACAGTGGTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (33 bp):
CAATGTATCGATACAATGTACCATGTATTAATA
Found at i:14744 original size:12 final size:12
Alignment explanation
Indices: 14727--14766 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
14717 ATAATGTATC
14727 AATACAAAGCAT
1 AATACAAAGCAT
* *
14739 AATACAATGTAT
1 AATACAAAGCAT
14751 CAATACAAAGCAT
1 -AATACAAAGCAT
14764 AAT
1 AAT
14767 GTATCGATAC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.55, C:0.15, G:0.07, T:0.23
Consensus pattern (12 bp):
AATACAAAGCAT
Found at i:14753 original size:25 final size:25
Alignment explanation
Indices: 14719--14766 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
14709 ATATCGATAT
14719 AATGTATCAATACAAAGCATAATAC
1 AATGTATCAATACAAAGCATAATAC
14744 AATGTATCAATACAAAGCATAAT
1 AATGTATCAATACAAAGCATAAT
14767 GTATCGATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.52, C:0.15, G:0.08, T:0.25
Consensus pattern (25 bp):
AATGTATCAATACAAAGCATAATAC
Found at i:14757 original size:13 final size:13
Alignment explanation
Indices: 14719--14758 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
14709 ATATCGATAT
14719 AATGTATCAATAC
1 AATGTATCAATAC
* *
14732 AAAGCAT-AATAC
1 AATGTATCAATAC
14744 AATGTATCAATAC
1 AATGTATCAATAC
14757 AA
1 AA
14759 AGCATAATGT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.53, C:0.15, G:0.07, T:0.25
Consensus pattern (13 bp):
AATGTATCAATAC
Found at i:14769 original size:20 final size:21
Alignment explanation
Indices: 14717--14777 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 21
14707 ATATATCGAT
14717 ATAATGTATCAATACAAAGCATA
1 ATAATGTATCAATACAAAGC--A
14740 ATACAATGTATCAATACAAAGC-
1 AT--AATGTATCAATACAAAGCA
*
14762 ATAATGTATCGATACA
1 ATAATGTATCAATACA
14778 TCTGGGTGTG
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
20 13 0.37
22 2 0.06
23 2 0.06
25 18 0.51
ACGTcount: A:0.49, C:0.15, G:0.10, T:0.26
Consensus pattern (21 bp):
ATAATGTATCAATACAAAGCA
Found at i:22100 original size:110 final size:114
Alignment explanation
Indices: 21892--22105 Score: 298
Period size: 112 Copynumber: 1.9 Consensus size: 114
21882 ACAAAAAACT
*
21892 AATCATTATATAGTAAAATTGAAAACTAAAAAAATATTATTTAATTAACTTATTAATTTTAAGTT
1 AATCATTATATAATAAAATTGAAAACTAAAAAAATATTATTTAATTAACTTATTAATTTTAAGTT
21957 TAGAAGAAAGATATAAAATATAATTTTATAAATTAGTTATGAAATAAAA
66 TAGAAGAAAGATATAAAATATAATTTTATAAATTAGTTATGAAATAAAA
* * *
22006 AATCATTATTTAATAGAATTGAAAACT-AAAAATTATT-TTTAATTAA-TATATT-ATTTATAAG
1 AATCATTATATAATAAAATTGAAAACTAAAAAAATATTATTTAATTAACT-TATTAATTT-TAAG
* *
22067 -TTATGAATAAGGAT-T-AAATATAATTTTATAAATTAGTTA
64 TTTA-GAAGAAAGATATAAAATATAATTTTATAAATTAGTTA
22106 AATTATTGTT
Statistics
Matches: 91, Mismatches: 6, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
110 24 0.26
111 9 0.10
112 25 0.27
113 9 0.10
114 24 0.26
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (114 bp):
AATCATTATATAATAAAATTGAAAACTAAAAAAATATTATTTAATTAACTTATTAATTTTAAGTT
TAGAAGAAAGATATAAAATATAATTTTATAAATTAGTTATGAAATAAAA
Found at i:22576 original size:48 final size:47
Alignment explanation
Indices: 22514--22656 Score: 180
Period size: 48 Copynumber: 3.0 Consensus size: 47
22504 CTCAACAAAT
* *
22514 TAATTTGCTGCATGTATAGGAGAGAGGTGATGAATACATTTAATAAAG
1 TAATTTGGTTCATGTATAGGAGAGAGG-GATGAATACATTTAATAAAG
* * *
22562 TAATTTGGTTCATGTATAGGAGAGAAGAGATGAATATATTTAATAAAT
1 TAATTTGGTTCATGTATAGGAGAG-AGGGATGAATACATTTAATAAAG
* *
22610 TAATTTGGTTCATGTAT-GAGAGAGAGGGAATGTATACATATAATAAA
1 TAATTTGGTTCATGTATAG-GAGAGAGGG-ATGAATACATTTAATAAA
22657 TTATTTTAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
47 4 0.05
48 77 0.93
49 2 0.02
ACGTcount: A:0.40, C:0.04, G:0.23, T:0.33
Consensus pattern (47 bp):
TAATTTGGTTCATGTATAGGAGAGAGGGATGAATACATTTAATAAAG
Found at i:23483 original size:3 final size:3
Alignment explanation
Indices: 23475--23504 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
23465 AAATAAAGAA
23475 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
23505 GATCCCACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Done.