Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2669
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: 30352
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:5071 original size:12 final size:12
Alignment explanation
Indices: 5051--5086 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
5041 TGGGCTATGC
*
5051 AATGTATGAATG
1 AATGCATGAATG
5063 AATGCATGAATG
1 AATGCATGAATG
5075 AATGCATGAATG
1 AATGCATGAATG
5087 TCAAATGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.28
Consensus pattern (12 bp):
AATGCATGAATG
Found at i:8273 original size:7 final size:7
Alignment explanation
Indices: 8261--8286 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
8251 TTTTAATTTC
8261 ATATTGA
1 ATATTGA
8268 ATATTGA
1 ATATTGA
8275 ATATTGA
1 ATATTGA
8282 ATATT
1 ATATT
8287 TAAAATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (7 bp):
ATATTGA
Found at i:8734 original size:10 final size:10
Alignment explanation
Indices: 8719--8765 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
8709 TGACTTCTTC
8719 TTTTCTTTAT
1 TTTTCTTTAT
8729 TTTTCTTTAT
1 TTTTCTTTAT
**
8739 TTGGCTTTAT
1 TTTTCTTTAT
*
8749 CTTTCTTT-T
1 TTTTCTTTAT
8758 TTTT-TTTA
1 TTTTCTTTA
8766 CTTATTTGTT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
8 3 0.10
9 4 0.13
10 23 0.77
ACGTcount: A:0.09, C:0.11, G:0.04, T:0.77
Consensus pattern (10 bp):
TTTTCTTTAT
Found at i:8867 original size:27 final size:25
Alignment explanation
Indices: 8818--8867 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
8808 TAAGACAACA
* *
8818 TATTATAATATATTTTAACTTTAAT
1 TATTATAATATATTATAAATTTAAT
8843 TATTATAATATATATAATAAATTTA
1 TATTATAATATAT-T-ATAAATTTA
8868 CACATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 13 0.62
26 1 0.05
27 7 0.33
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (25 bp):
TATTATAATATATTATAAATTTAAT
Found at i:9728 original size:30 final size:31
Alignment explanation
Indices: 9669--9738 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 31
9659 AACTAAAAAA
9669 AGTTTAAGTACCAACTTAAGAAAAAAATGGTAT
1 AGTTTAAGTACCAACTTAAG--AAAAATGGTAT
*
9702 AGTTTAAGTACCAATTTAAG-AAAATGGTAT
1 AGTTTAAGTACCAACTTAAGAAAAATGGTAT
*
9732 AATTTAA
1 AGTTTAA
9739 AAACTATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
30 16 0.46
33 19 0.54
ACGTcount: A:0.47, C:0.07, G:0.14, T:0.31
Consensus pattern (31 bp):
AGTTTAAGTACCAACTTAAGAAAAATGGTAT
Found at i:13637 original size:43 final size:40
Alignment explanation
Indices: 13574--13666 Score: 125
Period size: 43 Copynumber: 2.3 Consensus size: 40
13564 GGATTTTAGT
*
13574 GTTTAGGG-TTAGTGTTAGGGTTTTTGAAAAATTAAATTAAG
1 GTTTAGGGTTTAGGGTTAGGGTTTTTGAAAAA--AAATTAAG
* *
13615 GCTTTATGGTTTAGGGTTAGGGTTTTTGGAAAAAAATTAAG
1 G-TTTAGGGTTTAGGGTTAGGGTTTTTGAAAAAAAATTAAG
13656 GTTTAGGGTTT
1 GTTTAGGGTTT
13667 TAAAAAAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
40 9 0.20
41 10 0.22
42 6 0.13
43 21 0.46
ACGTcount: A:0.28, C:0.01, G:0.29, T:0.42
Consensus pattern (40 bp):
GTTTAGGGTTTAGGGTTAGGGTTTTTGAAAAAAAATTAAG
Found at i:13682 original size:24 final size:25
Alignment explanation
Indices: 13626--13691 Score: 73
Period size: 24 Copynumber: 2.6 Consensus size: 25
13616 CTTTATGGTT
*
13626 TAGGG-TTAGGGTTTTTGGAAAAAAAT
1 TAGGGTTTAGGG-TTTT-GAAAAAAAA
*
13652 TAAGGTTTAGGGTTTT-AAAAAAAA
1 TAGGGTTTAGGGTTTTGAAAAAAAA
*
13676 TAGGGTTTAGGATTTT
1 TAGGGTTTAGGGTTTT
13692 TTTAATAGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
24 21 0.60
26 8 0.23
27 6 0.17
ACGTcount: A:0.35, C:0.00, G:0.27, T:0.38
Consensus pattern (25 bp):
TAGGGTTTAGGGTTTTGAAAAAAAA
Found at i:14202 original size:25 final size:25
Alignment explanation
Indices: 14169--14240 Score: 117
Period size: 25 Copynumber: 2.9 Consensus size: 25
14159 TTACAGCAAG
14169 AAAAATTGAAGAAGTTCAGAAGAAT
1 AAAAATTGAAGAAGTTCAGAAGAAT
*
14194 AAAAATTGAAGAAGTTTAGAAGAAT
1 AAAAATTGAAGAAGTTCAGAAGAAT
* *
14219 AAAAATTGAAGAAATTGAGAAG
1 AAAAATTGAAGAAGTTCAGAAG
14241 GTATAAGTTG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.57, C:0.01, G:0.21, T:0.21
Consensus pattern (25 bp):
AAAAATTGAAGAAGTTCAGAAGAAT
Found at i:17012 original size:30 final size:30
Alignment explanation
Indices: 16974--17072 Score: 171
Period size: 30 Copynumber: 3.3 Consensus size: 30
16964 CTAGCCTTTG
16974 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
*
17004 CTACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
* *
17034 CCACCACCTACTCCATTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
17064 CCACCACCA
1 CCACCACCA
17073 CTTATACCTA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 64 1.00
ACGTcount: A:0.26, C:0.49, G:0.06, T:0.18
Consensus pattern (30 bp):
CCACCACCAACTCCACTAGCCACACTTGCT
Found at i:17263 original size:17 final size:17
Alignment explanation
Indices: 17241--17275 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
17231 GTTATTGTAA
17241 AGGCTAGTTTTTTGGAG
1 AGGCTAGTTTTTTGGAG
*
17258 AGGCTATTTTTTTGGAG
1 AGGCTAGTTTTTTGGAG
17275 A
1 A
17276 TTAATCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.20, C:0.06, G:0.31, T:0.43
Consensus pattern (17 bp):
AGGCTAGTTTTTTGGAG
Found at i:17652 original size:25 final size:26
Alignment explanation
Indices: 17624--17683 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 26
17614 CTATATTACG
*
17624 TATATATATT-ATACTATTTTATGTA
1 TATATATATTAATACTATATTATGTA
* *
17649 TATATCT-TTAATACTATATTATTTA
1 TATATATATTAATACTATATTATGTA
17674 TATATATATT
1 TATATATATT
17684 TTTCTACATG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 2 0.07
25 25 0.86
26 2 0.07
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.57
Consensus pattern (26 bp):
TATATATATTAATACTATATTATGTA
Found at i:17707 original size:28 final size:28
Alignment explanation
Indices: 17641--17749 Score: 104
Period size: 28 Copynumber: 4.0 Consensus size: 28
17631 ATTATACTAT
17641 TTTATGTATATATCTTTAATACTATATTA
1 TTTATGTATATAT-TTTAATACTATATTA
* ** *
17670 TTTATATATATATTTTTCTAC-ATGTTA
1 TTTATGTATATATTTTAATACTATATTA
17697 TCTTATGTATATATTTTAAT--TATATTA
1 T-TTATGTATATATTTTAATACTATATTA
* *
17724 TGTATGTAT-T-TTTT-ACACTATATTA
1 TTTATGTATATATTTTAATACTATATTA
17749 T
1 T
17750 GTACATATTT
Statistics
Matches: 66, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
23 1 0.02
24 4 0.06
25 9 0.14
26 7 0.11
27 12 0.18
28 21 0.32
29 12 0.18
ACGTcount: A:0.31, C:0.06, G:0.05, T:0.58
Consensus pattern (28 bp):
TTTATGTATATATTTTAATACTATATTA
Found at i:17750 original size:25 final size:24
Alignment explanation
Indices: 17700--17762 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 24
17690 CATGTTATCT
*
17700 TATGTATATATTTTAATTATATTATG
1 TATGTAT-T-TTTTAACTATATTATG
17726 TATGTATTTTTTACACTATATTATG
1 TATGTATTTTTTA-ACTATATTATG
**
17751 TACATATTTTTT
1 TATGTATTTTTT
17763 TTATATCTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 5 0.15
25 21 0.64
26 7 0.21
ACGTcount: A:0.30, C:0.05, G:0.06, T:0.59
Consensus pattern (24 bp):
TATGTATTTTTTAACTATATTATG
Found at i:17800 original size:79 final size:78
Alignment explanation
Indices: 17626--17800 Score: 176
Period size: 79 Copynumber: 2.2 Consensus size: 78
17616 ATATTACGTA
* * * * *
17626 TATATATTATACTATTTTATGTATATATCTTTAATACTATATTATTTATATATATATTTTTCTAC
1 TATATATTATACTATATTATGTATATATCTTTAACACTATATTATGTACATATATATTTTTATAC
*
17691 ATGTTATCTTATG
66 ATGTTATCATATG
* * * * * *
17704 TATATATTTTAATTATATTATGTATGTATTTTTTACACTATATTATGTACATAT-TTTTTTTATA
1 TATATATTAT-ACTATATTATGTATATATCTTTAACACTATATTATGTACATATATATTTTTATA
17768 TCTAT-TTCATACATATG
65 -C-ATGTT-AT-CATATG
17785 TATATATTATA-TATAT
1 TATATATTATACTATAT
17801 CTTAACATTA
Statistics
Matches: 79, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
78 17 0.22
79 43 0.54
80 5 0.06
81 14 0.18
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.57
Consensus pattern (78 bp):
TATATATTATACTATATTATGTATATATCTTTAACACTATATTATGTACATATATATTTTTATAC
ATGTTATCATATG
Found at i:29786 original size:81 final size:80
Alignment explanation
Indices: 29663--29908 Score: 244
Period size: 93 Copynumber: 2.9 Consensus size: 80
29653 TATCTTTCAA
* ** *
29663 AAAAATCAACT-TATTGCGAGAGTGAGTTG-GCCTCAGTACACGCTGAGGATTTTCAATTCCGTT
1 AAAAATCAACTCAATTGCGAGAGTGAGTTGAGCCTC-GGGCACGCTGAGGATTTTCAATTCTGTT
29726 TTTTAATTATGTTTTC
65 TTTTAATTATGTTTTC
* * * *
29742 AAAAATCAACTCAATTGCGAGCAGTGAGCTGAGCCTCGGGCACGCCGAGTATTTTTAATTTCTGT
1 AAAAATCAACTCAATTGCGAG-AGTGAGTTGAGCCTCGGGCACGCTGAGGATTTTCAA-TTCTG-
*
29807 TTTTCATTCTACTTTTATTCTGTTTTC
63 -TTT--TT-TA-----ATTATGTTTTC
*
29834 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGCACGCTGAGGTATTTTCAATTCTG
1 AAAAATCAACTCA-ATTGCGAGA-GTGAGTTGAGCCTCGGGCACGCTGAGG-ATTTTCAATTCTG
29899 TTTTTTAATT
63 TTTTTTAATT
29909 TTTGCTTACA
Statistics
Matches: 136, Mismatches: 14, Indels: 30
0.76 0.08 0.17
Matches are distributed among these distances:
79 11 0.08
80 8 0.06
81 24 0.18
82 9 0.07
83 3 0.02
84 3 0.02
86 2 0.01
87 2 0.01
88 2 0.01
89 2 0.01
91 3 0.02
92 24 0.18
93 36 0.26
94 7 0.05
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (80 bp):
AAAAATCAACTCAATTGCGAGAGTGAGTTGAGCCTCGGGCACGCTGAGGATTTTCAATTCTGTTT
TTTAATTATGTTTTC
Found at i:29955 original size:95 final size:90
Alignment explanation
Indices: 29730--30071 Score: 359
Period size: 95 Copynumber: 3.8 Consensus size: 90
29720 TCCGTTTTTT
* * * *
29730 AATTATGTTTTCAAAAATCAACTCA-ATTGCGAGCAGTGAGCTGAGCCTCGGGCACGCCGA-GTA
1 AATTCTGTTTTC--AAATCAACTCATATTGCGAG-AGTGAGTTGAGCCTCAGGCACGCTGAGGTA
* * * * *
29793 TTTTTAATTTCTGTTTTTCATTCTACTTT
63 TTTTCAA-TTCTGTTTTTAATTTTTCTTA
*
29822 TATTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGCACGCTGAGGTA
1 AATTCTGTTTTC--AAATCAACTCATATTGCGAGA-GTGAGTTGAGCCTCAGGCACGCTGAGGTA
29887 TTTTCAATTCTGTTTTTTAATTTTTGCTTA
63 TTTTCAATTCTG-TTTTTAATTTTT-CTTA
29917 CAATTCTGCTTTTCAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGT
1 -AATTCTG-TTTTCAAATCAACTCATATTGCGAGA-GTGAGTTGAGCCTCAGG-CACGCTGAGGT
29982 ATTTTCAA------TTTTAATTTTT-TTA
62 ATTTTCAATTCTGTTTTTAATTTTTCTTA
* *
30004 AATTTTG-TTTCAAAATCAACTCATATTGCGAGAGTGAGTT--GCCTCAGACACGCTGAGGTA-T
1 AATTCTGTTTTC-AAATCAACTCATATTGCGAGAGTGAGTTGAGCCTCAGGCACGCTGAGGTATT
30065 TTCAATT
65 TTCAATT
30072 TTCGTTTGTC
Statistics
Matches: 226, Mismatches: 13, Indels: 32
0.83 0.05 0.12
Matches are distributed among these distances:
80 6 0.03
81 12 0.05
82 7 0.03
84 11 0.05
85 21 0.09
86 6 0.03
87 3 0.01
89 11 0.05
92 24 0.11
93 35 0.15
94 18 0.08
95 42 0.19
96 25 0.11
97 5 0.02
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (90 bp):
AATTCTGTTTTCAAATCAACTCATATTGCGAGAGTGAGTTGAGCCTCAGGCACGCTGAGGTATTT
TCAATTCTGTTTTTAATTTTTCTTA
Found at i:30118 original size:69 final size:70
Alignment explanation
Indices: 30015--30349 Score: 396
Period size: 69 Copynumber: 4.9 Consensus size: 70
30005 ATTTTGTTTC
30015 AAAATCAACTCATATTGCGAGA-GTGAGTT--GCCTCAGACACGCTGAGGTATTTCAATTTTCGT
1 AAAATCAACTCATATTGCGAGAGGTGA-TTGAGCCTCAGACACGCTGAGGTATTTCAATTTT-GT
30077 TTGTCAA
64 TTGTCAA
*
30084 AAAATCAACTCATATTG-TAGA-GTGATTGAGCCTCAGGACACGCTGAGGT-TTTCAATTTTGTT
1 AAAATCAACTCATATTGCGAGAGGTGATTGAGCCTCA-GACACGCTGAGGTATTTCAATTTTG-T
30146 TTGTC--
64 TTGTCAA
*
30151 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAA-TTTG
1 AAAATCAACTCATATTGCGAGAGGTGA-TTGAGCCTC-AGACACGCTGAGGTA-TTTCAATTTTG
30215 TTTGTCAA
63 TTTGTCAA
* *
30223 AAAATC-ACTCATATTGC--GAGGTGGTTG-GCCTCAAGACAC-TTGAGGTATTTCAATTTCTGT
1 AAAATCAACTCATATTGCGAGAGGTGATTGAGCCTC-AGACACGCTGAGGTATTTCAATTT-TGT
*
30283 TTTTCAA
64 TTGTCAA
* * *
30290 AAAA-AAACTCATATTGCGAGAGGTGATTGAACCTCAAACACG-TGAGGTATTTTCAATTTT
1 AAAATCAACTCATATTGCGAGAGGTGATTGAGCCTCAGACACGCTGAGGTA-TTTCAATTTT
30350 TGT
Statistics
Matches: 237, Mismatches: 9, Indels: 40
0.83 0.03 0.14
Matches are distributed among these distances:
65 6 0.03
66 10 0.04
67 55 0.23
68 14 0.06
69 71 0.30
70 53 0.22
71 16 0.07
72 12 0.05
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (70 bp):
AAAATCAACTCATATTGCGAGAGGTGATTGAGCCTCAGACACGCTGAGGTATTTCAATTTTGTTT
GTCAA
Done.