Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2912
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: 66074
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:3196 original size:7 final size:8
Alignment explanation
Indices: 3181--3211 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
3171 ATTGTATCAA
3181 TATTTTTT
1 TATTTTTT
3189 TATTTTTT
1 TATTTTTT
3197 TATTTTTT
1 TATTTTTT
3205 TATTTTT
1 TATTTTT
3212 AATAAACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (8 bp):
TATTTTTT
Found at i:3915 original size:17 final size:17
Alignment explanation
Indices: 3893--3963 Score: 63
Period size: 17 Copynumber: 3.9 Consensus size: 17
3883 TATTTCCTAC
3893 ATTATATAATAACATAA
1 ATTATATAATAACATAA
3910 ATTATATAATAAACTACATAA
1 ATTATATAAT--A--ACATAA
* *
3931 ACTATATAATAATA-AA
1 ATTATATAATAACATAA
*
3947 CATTATATAATATCATA
1 -ATTATATAATAACATA
3964 TTTCCCACAA
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
16 2 0.05
17 23 0.53
18 1 0.02
19 2 0.05
21 15 0.35
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.35
Consensus pattern (17 bp):
ATTATATAATAACATAA
Found at i:3949 original size:21 final size:21
Alignment explanation
Indices: 3898--3949 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
3888 CCTACATTAT
*
3898 ATAAT-AACATAAATTATATA
1 ATAATAAACATAAACTATATA
*
3918 ATAA-ACTACATAAACTATATA
1 ATAATA-AACATAAACTATATA
3939 ATAATAAACAT
1 ATAATAAACAT
3950 TATATAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 4 0.15
21 21 0.81
22 1 0.04
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAATAAACATAAACTATATA
Found at i:4132 original size:113 final size:113
Alignment explanation
Indices: 3975--4324 Score: 357
Period size: 114 Copynumber: 3.1 Consensus size: 113
3965 TTCCCACAAC
* * * *
3975 GCGCCGCTAATAATATGTTTTAGCGGCG-TTTAACCATAAGCGCCAC-AACTGCTAGTATACATC
1 GCGCCACTAATACTATGCTTTAGCGGCGTTTTAA-CATAAGCGCCACTAA-TGCTAATATACATC
*
4038 AAGACCAAAGCGCTGCGTTTTGGTTAATATTTTGCGGCGCTTTACAATAA
64 AAGACCAAAGCACTGCGTTTTGGTTAATATTTTGCGGCGCTTTACAATAA
* * * * * *
4088 GCGCCGCTAATACTTTGCTTTAGCGGCGTTTTCAA-ATAAACGCCACTAATCCTAATGTACCTCA
1 GCGCCACTAATACTATGCTTTAGCGGCGTTTT-AACATAAGCGCCACTAATGCTAATATACATCA
* * * * * * * * *
4152 AGACCAAA-CTCTGCATTTTTGTTAAGAAATATTGGGGCGCTTTTCAGTAC
65 AGACCAAAGCACTGCGTTTTGGTT-A-ATATTTTGCGGCGCTTTACAATAA
* * * * * *
4202 TCGCCACTAATACTATACTTTAGCGGCATTTTAATATAAGCGCCACTAATGCTACTATACATTAA
1 GCGCCACTAATACTATGCTTTAGCGGCGTTTTAACATAAGCGCCACTAATGCTAATATACATCAA
* ** *
4267 GACCAAAGCACTGCGTTTTGGTTAATCTTTTGCGGCATTTTCCAATAA
66 GACCAAAGCACTGCGTTTTGGTTAATATTTTGCGGCGCTTTACAATAA
4315 GCGCCACTAA
1 GCGCCACTAA
4325 GCCTAATATA
Statistics
Matches: 189, Mismatches: 41, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
112 12 0.06
113 81 0.43
114 82 0.43
115 14 0.07
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (113 bp):
GCGCCACTAATACTATGCTTTAGCGGCGTTTTAACATAAGCGCCACTAATGCTAATATACATCAA
GACCAAAGCACTGCGTTTTGGTTAATATTTTGCGGCGCTTTACAATAA
Found at i:4345 original size:74 final size:73
Alignment explanation
Indices: 4219--4364 Score: 188
Period size: 74 Copynumber: 2.0 Consensus size: 73
4209 TAATACTATA
* **
4219 CTTTAGCGGCATTTTAATATAAGCGCCACTAATGCTACTATACATTAAGACCAAAGCACTGCGTT
1 CTTTAGCGGCATTTTAATATAAGCGCCACTAATGCTAATATACAGCAAGACCAAA-CACTGCGTT
4284 TTGGTTAAT
65 TTGGTTAAT
* * * *
4293 CTTTTGCGGCATTTTCCA-ATAAGCGCCACTAA-GCCTAATATACCGCAAGACCAAACTCTGCGT
1 CTTTAGCGGCATTTT-AATATAAGCGCCACTAATG-CTAATATACAGCAAGACCAAACACTGCGT
4356 TTTGGTTAA
64 TTTGGTTAA
4365 GAAATCTTAC
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
73 17 0.27
74 45 0.71
75 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.31
Consensus pattern (73 bp):
CTTTAGCGGCATTTTAATATAAGCGCCACTAATGCTAATATACAGCAAGACCAAACACTGCGTTT
TGGTTAAT
Found at i:4451 original size:188 final size:188
Alignment explanation
Indices: 4105--4506 Score: 572
Period size: 188 Copynumber: 2.1 Consensus size: 188
4095 TAATACTTTG
* * * * * *
4105 CTTTAGCGGCGTTTTCAAATAAACGCCACTAATCCTAATGTACCTCAAGACCAAACTCTGCATTT
1 CTTTTGCGGCGTTTTCCAATAAGCGCCACTAAGCCTAATATACCGCAAGACCAAACTCTGCATTT
* ** * *
4170 TTGTTAAGAAATATTGGGGCGCTTTTCAGTACTCGCCACTAATACTATACTTTAGCGGCATTTTA
66 TGGTTAAGAAATATTACGGCGCTTTTCACTACTCGCCACTAATACTATACTTTAGCGACATTTTA
*
4235 ATATAAGCGCCACTAATGCTACTATACATTAAGACCAAAGCACTGCGTTTTGGTTAAT
131 ATATAAGCGCCACTAATGCTACTATACATCAAGACCAAAGCACTGCGTTTTGGTTAAT
* *
4293 CTTTTGCGGCATTTTCCAATAAGCGCCACTAAGCCTAATATACCGCAAGACCAAACTCTGCGTTT
1 CTTTTGCGGCGTTTTCCAATAAGCGCCACTAAGCCTAATATACCGCAAGACCAAACTCTGCATTT
* * *
4358 TGGTTAAGAAATCTTACGGCGCTTTTCACTACTCGCCGCTAATACTATGA-TTTAGCGACGTTTT
66 TGGTTAAGAAATATTACGGCGCTTTTCACTACTCGCCACTAATACTAT-ACTTTAGCGACATTTT
* * * *
4422 AATATAAGCGCCACTACTGGTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAAT
130 AATATAAGCGCCACTAATGCTACTATACATCAAGACCAAAGCACTGCGTTTTGGTTAAT
* * *
4481 ATTTTGCGGCGCTTTACAATAAGCGC
1 CTTTTGCGGCGTTTTCCAATAAGCGC
4507 TGCAAATACT
Statistics
Matches: 188, Mismatches: 25, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
188 187 0.99
189 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (188 bp):
CTTTTGCGGCGTTTTCCAATAAGCGCCACTAAGCCTAATATACCGCAAGACCAAACTCTGCATTT
TGGTTAAGAAATATTACGGCGCTTTTCACTACTCGCCACTAATACTATACTTTAGCGACATTTTA
ATATAAGCGCCACTAATGCTACTATACATCAAGACCAAAGCACTGCGTTTTGGTTAAT
Found at i:4607 original size:227 final size:228
Alignment explanation
Indices: 4293--4723 Score: 659
Period size: 227 Copynumber: 1.9 Consensus size: 228
4283 TTTGGTTAAT
*
4293 CTTTTGCGGCATTTTCCAATAAGCGCCACTAAGCCTAATATACCGCAAGACCAAACTCTGCGTTT
1 CTTTAGCGGCATTTTCCAATAAGCGCCACTAAGCCTAATATACCGCAAGACCAAACTCTGCGTTT
*
4358 TGGTTAAGAAATCTTACGGCGCTTTTCACTACTCGCCGCTAATACTATGATTTAGCGACGTTTTA
66 TGGTTAAGAAATATTACGGCGCTTTTCACTACTCGCCGCTAATACTATGATTTAGCGACGTTTTA
* * *
4423 ATATAAGCGCCACTACTGGTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAATAT-T-TT
131 ATATAAGCGCCACTAATGCTAGTATACATCAAGACCAAA-CGCTGCGTTTTGGTTAAGATGTATT
4486 GCGGCGCTTTACAATAAGCGCTGCAAATACTATG
195 GCGGCGCTTTACAATAAGCGCTGCAAATACTATG
* * * * *
4520 CTTTAGCGGCGTTTTTCGATAAGCGCCACTAATCCTAATATACCTCAAGACCAAACTCTGCGTTT
1 CTTTAGCGGCATTTTCCAATAAGCGCCACTAAGCCTAATATACCGCAAGACCAAACTCTGCGTTT
* ** * *
4585 TGGTTAAGAAATATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATTCTTTAGCGGCGTTTTT
66 TGGTTAAGAAATATTACGGCGCTTTTCACTACTCGCCGCTAATACTATGATTTAGCGACGTTTTA
* * * * *
4650 GTATGAGCGCCACTAATGCTAGTGTACCTCAAGACCAAACTCTGCGTTTTGGTTAAGATGTATTG
131 ATATAAGCGCCACTAATGCTAGTATACATCAAGACCAAACGCTGCGTTTTGGTTAAGATGTATTG
4715 CGGCGCTTT
196 CGGCGCTTT
4724 TTGCGACTCG
Statistics
Matches: 182, Mismatches: 20, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
226 18 0.10
227 152 0.84
228 12 0.07
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (228 bp):
CTTTAGCGGCATTTTCCAATAAGCGCCACTAAGCCTAATATACCGCAAGACCAAACTCTGCGTTT
TGGTTAAGAAATATTACGGCGCTTTTCACTACTCGCCGCTAATACTATGATTTAGCGACGTTTTA
ATATAAGCGCCACTAATGCTAGTATACATCAAGACCAAACGCTGCGTTTTGGTTAAGATGTATTG
CGGCGCTTTACAATAAGCGCTGCAAATACTATG
Found at i:4647 original size:114 final size:114
Alignment explanation
Indices: 4310--4780 Score: 570
Period size: 114 Copynumber: 4.1 Consensus size: 114
4300 GGCATTTTCC
* * * *
4310 AATAAGCGCCACTAAGCCTAATATACCGCAAGACCAAACTCTGCGTTTTGGTTAAGAAATCTTAC
1 AATAAGCGCCACTAATCCTAATATACCTCAAGACCAAACTCTGCGTTTTGGTTAAGAAATATTGC
* *
4375 GGCGCTTTTCACTACTCGCCGCTAATACTATGATTTAGCGACG-TTTTA
66 GGCGCTTTTCACTACTCGCCGCTAATACTATGCTTTAGCGGCGTTTTTA
* ** * * * * *
4423 ATATAAGCGCCACTACTGGTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTT-A-ATATTTT
1 A-ATAAGCGCCACTAATCCTAATATACCTCAAGACCAAA-CTCTGCGTTTTGGTTAAGAAATATT
* * ** * * *
4486 GCGGCGCTTTACAATAAGCGCTGCAAATACTATGCTTTAGCGGCGTTTTTC
64 GCGGCGCTTTTCACTACTCGCCGCTAATACTATGCTTTAGCGGCGTTTTTA
*
4537 GATAAGCGCCACTAATCCTAATATACCTCAAGACCAAACTCTGCGTTTTGGTTAAGAAATATTGC
1 AATAAGCGCCACTAATCCTAATATACCTCAAGACCAAACTCTGCGTTTTGGTTAAGAAATATTGC
* *
4602 GGCGCTTTTCACTACTCGCCGCTAATACTATTCTTTAGCGGCGTTTTTG
66 GGCGCTTTTCACTACTCGCCGCTAATACTATGCTTTAGCGGCGTTTTTA
* * * * * **
4651 TATGAGCGCCACTAATGCTAGTGTACCTCAAGACCAAACTCTGCGTTTTGGTTAAGATGTATTGC
1 AATAAGCGCCACTAATCCTAATATACCTCAAGACCAAACTCTGCGTTTTGGTTAAGAAATATTGC
** * * * *
4716 GGCGCTTTTTGCGACTCGCCGCTAATTCTATGCTTTAGCGGTGATTTTA
66 GGCGCTTTTCACTACTCGCCGCTAATACTATGCTTTAGCGGCGTTTTTA
4765 AATAAGCGCCACTAAT
1 AATAAGCGCCACTAAT
4781 ACTTTCTTTA
Statistics
Matches: 299, Mismatches: 54, Indels: 9
0.83 0.15 0.02
Matches are distributed among these distances:
112 14 0.05
113 75 0.25
114 196 0.66
115 14 0.05
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.31
Consensus pattern (114 bp):
AATAAGCGCCACTAATCCTAATATACCTCAAGACCAAACTCTGCGTTTTGGTTAAGAAATATTGC
GGCGCTTTTCACTACTCGCCGCTAATACTATGCTTTAGCGGCGTTTTTA
Found at i:5660 original size:14 final size:13
Alignment explanation
Indices: 5634--5692 Score: 50
Period size: 13 Copynumber: 4.3 Consensus size: 13
5624 AGGCCAACAT
5634 TATATATTGCATA
1 TATATATTGCATA
5647 TATATATATGCATA
1 TATATAT-TGCATA
*
5661 TA-AAAGTGCTGC-TA
1 TATATA-T--TGCATA
5675 TTATATATTGCATA
1 -TATATATTGCATA
5689 TATA
1 TATA
5693 CAATTGGCAC
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
13 16 0.43
14 13 0.35
15 6 0.16
16 2 0.05
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.42
Consensus pattern (13 bp):
TATATATTGCATA
Found at i:5959 original size:26 final size:25
Alignment explanation
Indices: 5930--5978 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
5920 TCACAAAAAA
5930 TTTTAAAATATCATTTAAACTTTTTT
1 TTTTAAAATATCA-TTAAACTTTTTT
* * *
5956 TTTTCAATTTTCATTAAACTTTT
1 TTTTAAAATATCATTAAACTTTT
5979 AAAATTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 10 0.50
26 10 0.50
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.59
Consensus pattern (25 bp):
TTTTAAAATATCATTAAACTTTTTT
Found at i:8137 original size:23 final size:23
Alignment explanation
Indices: 8049--8173 Score: 78
Period size: 24 Copynumber: 5.3 Consensus size: 23
8039 TACATAATAC
*
8049 ATTTAAAATAATAATAT-TGGATA
1 ATTTAAAATAATAGTATAT-GATA
* * *
8072 AGTTTTAAATTATAGTATACGATAA
1 A-TTTAAAATAATAGTATATGAT-A
* *
8097 ATTTTAAATTAT-GATATATGATA
1 ATTTAAAATAATAG-TATATGATA
* *
8120 ATTTAAAATGATAGTATATTA-A
1 ATTTAAAATAATAGTATATGATA
* *
8142 ATATTAAAATAACACTA-ATGATAA
1 AT-TTAAAATAATAGTATATGAT-A
8166 ATTTAAAA
1 ATTTAAAA
8174 CAATGTTAAG
Statistics
Matches: 82, Mismatches: 12, Indels: 16
0.75 0.11 0.15
Matches are distributed among these distances:
22 6 0.07
23 36 0.44
24 38 0.46
25 2 0.02
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.39
Consensus pattern (23 bp):
ATTTAAAATAATAGTATATGATA
Found at i:9634 original size:17 final size:17
Alignment explanation
Indices: 9612--9645 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
9602 TTACATACTT
* *
9612 TTTTAATATTTTTTTAA
1 TTTTAAAATATTTTTAA
9629 TTTTAAAATATTTTTAA
1 TTTTAAAATATTTTTAA
9646 AATACTTGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTAAAATATTTTTAA
Found at i:9643 original size:11 final size:11
Alignment explanation
Indices: 9629--9735 Score: 56
Period size: 11 Copynumber: 10.4 Consensus size: 11
9619 ATTTTTTTAA
9629 TTTTAAAATAT
1 TTTTAAAATAT
9640 TTTTAAAATACT
1 TTTTAAAATA-T
**
9652 TGTTTTTAAT-T
1 T-TTTAAAATAT
9663 TTTT---A-A-
1 TTTTAAAATAT
9669 TTTTAAAATAT
1 TTTTAAAATAT
9680 TTTTAAAATACT
1 TTTTAAAATA-T
**
9692 TTTTTTAAT-T
1 TTTTAAAATAT
*
9702 TTTT----TAA
1 TTTTAAAATAT
9709 TTTTAAAATAT
1 TTTTAAAATAT
9720 TTTTAAAATACT
1 TTTTAAAATA-T
9732 TTTT
1 TTTT
9736 TTTTAATTTT
Statistics
Matches: 75, Mismatches: 6, Indels: 29
0.68 0.05 0.26
Matches are distributed among these distances:
6 5 0.07
7 5 0.07
9 1 0.01
10 9 0.12
11 34 0.45
12 15 0.20
13 6 0.08
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.61
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:9677 original size:81 final size:81
Alignment explanation
Indices: 9578--9749 Score: 283
Period size: 81 Copynumber: 2.1 Consensus size: 81
9568 AAATATATTT
* *
9578 ATTTTTTAAATTTTAAAATATTTTTTACATACTTTTTTAATATTTTTTTAATTTTAAAATATTTT
1 ATTTTTT-AATTTTAAAATATTTTTAAAATACTTTTTTAA-ATTTTTTTAATTTTAAAATATTTT
9643 TAAAATAC-TTGTTTTTA
64 TAAAATACTTTGTTTTTA
*
9660 ATTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTAATTTTTTTAATTTTAAAATATTTTTA
1 ATTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAAATTTTTTTAATTTTAAAATATTTTTA
*
9725 AAATACTTTTTTTTTA
66 AAATACTTTGTTTTTA
9741 ATTTTTTAA
1 ATTTTTTAA
9750 AATTTTTAAA
Statistics
Matches: 85, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
80 32 0.38
81 46 0.54
82 7 0.08
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (81 bp):
ATTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAAATTTTTTTAATTTTAAAATATTTTTA
AAATACTTTGTTTTTA
Found at i:9737 original size:41 final size:40
Alignment explanation
Indices: 9578--9762 Score: 264
Period size: 40 Copynumber: 4.5 Consensus size: 40
9568 AAATATATTT
* * * *
9578 ATTTTTTAAATTTTAAAATATTTTTTACATACTTTTTTAA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
9618 TATTTTTTTAATTTTAAAATATTTTTAAAATACTTGTTTTTA
1 -ATTTTTTTAATTTTAAAATATTTTTAAAATACTT-TTTTTA
9660 A-TTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
9699 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTTTA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATAC--TTTTTTTA
*
9741 ATTTTTTAAAATTTTTAAAATA
1 ATTTTTT-TAA-TTTTAAAATA
9763 AAAATGGGCC
Statistics
Matches: 133, Mismatches: 5, Indels: 9
0.90 0.03 0.06
Matches are distributed among these distances:
39 7 0.05
40 62 0.47
41 32 0.24
42 20 0.15
43 2 0.02
44 10 0.08
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.61
Consensus pattern (40 bp):
ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
Found at i:9742 original size:33 final size:33
Alignment explanation
Indices: 9700--9762 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
9690 CTTTTTTTAA
9700 TTTTTTTAA-TTTTAAAATATTTTTAAAATACTT
1 TTTTTTTAATTTTTAAAA-ATTTTTAAAATACTT
*
9733 TTTTTTTAATTTTTTAAAATTTTTAAAATA
1 TTTTTTTAATTTTTAAAAATTTTTAAAATA
9763 AAAATGGGCC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
33 21 0.75
34 7 0.25
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (33 bp):
TTTTTTTAATTTTTAAAAATTTTTAAAATACTT
Found at i:15248 original size:14 final size:13
Alignment explanation
Indices: 15226--15375 Score: 53
Period size: 13 Copynumber: 11.2 Consensus size: 13
15216 AAGTGTTTTC
*
15226 TTTCTTCAAGTGTT
1 TTTCATCAAGT-TT
15240 TTTCATCAAGTTCT
1 TTTCATCAAGTT-T
15254 TTT-ATCAAGTTT
1 TTTCATCAAGTTT
* *
15266 TTAATTACCAAGGTTTTTT
1 TT--TCATCAA-G---TTT
* *
15285 TTGTTATTAAGT-T
1 TT-TCATCAAGTTT
*
15298 TTGCATCAAGTTCT
1 TTTCATCAAGTT-T
15312 TTT--T-AAGT-T
1 TTTCATCAAGTTT
*
15321 TTTCATCAAGTCT
1 TTTCATCAAGTTT
*
15334 TTTCATAAAG-TT
1 TTTCATCAAGTTT
*
15346 TTCCATCAAGTTT
1 TTTCATCAAGTTT
*
15359 TTAATCATTAAGTTT
1 TT--TCATCAAGTTT
15374 TT
1 TT
15376 CAATTAAGCT
Statistics
Matches: 104, Mismatches: 15, Indels: 33
0.68 0.10 0.22
Matches are distributed among these distances:
9 4 0.04
11 5 0.05
12 23 0.22
13 26 0.25
14 19 0.18
15 15 0.14
16 1 0.01
17 1 0.01
18 5 0.05
19 5 0.05
ACGTcount: A:0.24, C:0.13, G:0.10, T:0.53
Consensus pattern (13 bp):
TTTCATCAAGTTT
Found at i:15317 original size:23 final size:23
Alignment explanation
Indices: 15291--15357 Score: 82
Period size: 23 Copynumber: 2.8 Consensus size: 23
15281 TTTTTTGTTA
*
15291 TTAAGTTTTGCATCAAGTTCTTT
1 TTAAGTTTTCCATCAAGTTCTTT
*
15314 TTAAGTTTTTCATCAAG-TCTTT
1 TTAAGTTTTCCATCAAGTTCTTT
15336 TCATAAAGTTTTCCATCAAGTT
1 T--T-AAGTTTTCCATCAAGTT
15358 TTTAATCATT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
22 6 0.16
23 16 0.42
24 1 0.03
25 14 0.37
26 1 0.03
ACGTcount: A:0.25, C:0.15, G:0.10, T:0.49
Consensus pattern (23 bp):
TTAAGTTTTCCATCAAGTTCTTT
Found at i:15358 original size:12 final size:12
Alignment explanation
Indices: 15293--15365 Score: 69
Period size: 12 Copynumber: 6.1 Consensus size: 12
15283 TTTTGTTATT
*
15293 AAGTTTTGCATC
1 AAGTTTTTCATC
*
15305 AAGTTCTTT--TT
1 AAGTT-TTTCATC
15316 AAGTTTTTCATC
1 AAGTTTTTCATC
*
15328 AAGTCTTTTCATA
1 AAGT-TTTTCATC
*
15341 AAGTTTTCCATC
1 AAGTTTTTCATC
*
15353 AAGTTTTTAATC
1 AAGTTTTTCATC
15365 A
1 A
15366 TTAAGTTTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
10 3 0.06
11 6 0.12
12 27 0.55
13 13 0.27
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48
Consensus pattern (12 bp):
AAGTTTTTCATC
Found at i:15383 original size:13 final size:12
Alignment explanation
Indices: 15290--15388 Score: 67
Period size: 12 Copynumber: 7.8 Consensus size: 12
15280 TTTTTTTGTT
*
15290 ATTAAGTTTTGC
1 ATTAAGTTTTTC
*
15302 ATCAAGTTCTTT-
1 ATTAAGTT-TTTC
15314 -TTAAGTTTTTC
1 ATTAAGTTTTTC
*
15325 ATCAAGTCTTTTC
1 ATTAAGT-TTTTC
* *
15338 ATAAAGTTTTCC
1 ATTAAGTTTTTC
*
15350 ATCAAGTTTTTAATC
1 ATTAAG-TTTT--TC
15365 ATTAAGTTTTTC
1 ATTAAGTTTTTC
15377 AATTAAGCTTTT
1 -ATTAAG-TTTT
15389 ATCTCTTGCA
Statistics
Matches: 69, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
10 3 0.04
11 6 0.09
12 23 0.33
13 23 0.33
14 8 0.12
15 6 0.09
ACGTcount: A:0.27, C:0.13, G:0.09, T:0.51
Consensus pattern (12 bp):
ATTAAGTTTTTC
Found at i:22167 original size:16 final size:16
Alignment explanation
Indices: 22146--22180 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
22136 AAAACGCACA
* *
22146 TTTTATTTTATTTTAT
1 TTTTATCTTATCTTAT
22162 TTTTATCTTATCTTAT
1 TTTTATCTTATCTTAT
22178 TTT
1 TTT
22181 GTAGTTAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTATCTTATCTTAT
Found at i:23594 original size:14 final size:13
Alignment explanation
Indices: 23572--23721 Score: 53
Period size: 13 Copynumber: 11.2 Consensus size: 13
23562 AAGTGTTTTC
*
23572 TTTCTTCAAGTGTT
1 TTTCATCAAGT-TT
23586 TTTCATCAAGTTCT
1 TTTCATCAAGTT-T
23600 TTT-ATCAAGTTT
1 TTTCATCAAGTTT
* *
23612 TTAATTACCAAGGTTTTTT
1 TT--TCATCAA-G---TTT
* *
23631 TTGTTATTAAGT-T
1 TT-TCATCAAGTTT
*
23644 TTGCATCAAGTTCT
1 TTTCATCAAGTT-T
23658 TTT--T-AAGT-T
1 TTTCATCAAGTTT
*
23667 TTTCATCAAGTCT
1 TTTCATCAAGTTT
*
23680 TTTCATAAAG-TT
1 TTTCATCAAGTTT
*
23692 TTCCATCAAGTTT
1 TTTCATCAAGTTT
*
23705 TTAATCATTAAGTTT
1 TT--TCATCAAGTTT
23720 TT
1 TT
23722 CAATTAAGCT
Statistics
Matches: 104, Mismatches: 15, Indels: 33
0.68 0.10 0.22
Matches are distributed among these distances:
9 4 0.04
11 5 0.05
12 23 0.22
13 26 0.25
14 19 0.18
15 15 0.14
16 1 0.01
17 1 0.01
18 5 0.05
19 5 0.05
ACGTcount: A:0.24, C:0.13, G:0.10, T:0.53
Consensus pattern (13 bp):
TTTCATCAAGTTT
Found at i:23663 original size:23 final size:23
Alignment explanation
Indices: 23637--23703 Score: 82
Period size: 23 Copynumber: 2.8 Consensus size: 23
23627 TTTTTTGTTA
*
23637 TTAAGTTTTGCATCAAGTTCTTT
1 TTAAGTTTTCCATCAAGTTCTTT
*
23660 TTAAGTTTTTCATCAAG-TCTTT
1 TTAAGTTTTCCATCAAGTTCTTT
23682 TCATAAAGTTTTCCATCAAGTT
1 T--T-AAGTTTTCCATCAAGTT
23704 TTTAATCATT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
22 6 0.16
23 16 0.42
24 1 0.03
25 14 0.37
26 1 0.03
ACGTcount: A:0.25, C:0.15, G:0.10, T:0.49
Consensus pattern (23 bp):
TTAAGTTTTCCATCAAGTTCTTT
Found at i:23704 original size:12 final size:12
Alignment explanation
Indices: 23639--23711 Score: 69
Period size: 12 Copynumber: 6.1 Consensus size: 12
23629 TTTTGTTATT
*
23639 AAGTTTTGCATC
1 AAGTTTTTCATC
*
23651 AAGTTCTTT--TT
1 AAGTT-TTTCATC
23662 AAGTTTTTCATC
1 AAGTTTTTCATC
*
23674 AAGTCTTTTCATA
1 AAGT-TTTTCATC
*
23687 AAGTTTTCCATC
1 AAGTTTTTCATC
*
23699 AAGTTTTTAATC
1 AAGTTTTTCATC
23711 A
1 A
23712 TTAAGTTTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
10 3 0.06
11 6 0.12
12 27 0.55
13 13 0.27
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48
Consensus pattern (12 bp):
AAGTTTTTCATC
Found at i:23729 original size:13 final size:12
Alignment explanation
Indices: 23636--23734 Score: 67
Period size: 12 Copynumber: 7.8 Consensus size: 12
23626 TTTTTTTGTT
*
23636 ATTAAGTTTTGC
1 ATTAAGTTTTTC
*
23648 ATCAAGTTCTTT-
1 ATTAAGTT-TTTC
23660 -TTAAGTTTTTC
1 ATTAAGTTTTTC
*
23671 ATCAAGTCTTTTC
1 ATTAAGT-TTTTC
* *
23684 ATAAAGTTTTCC
1 ATTAAGTTTTTC
*
23696 ATCAAGTTTTTAATC
1 ATTAAG-TTTT--TC
23711 ATTAAGTTTTTC
1 ATTAAGTTTTTC
23723 AATTAAGCTTTT
1 -ATTAAG-TTTT
23735 ATCTCTTGCA
Statistics
Matches: 69, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
10 3 0.04
11 6 0.09
12 23 0.33
13 23 0.33
14 8 0.12
15 6 0.09
ACGTcount: A:0.27, C:0.13, G:0.09, T:0.51
Consensus pattern (12 bp):
ATTAAGTTTTTC
Found at i:30509 original size:16 final size:16
Alignment explanation
Indices: 30488--30522 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
30478 AAAACGCACA
* *
30488 TTTTATTTTATTTTAT
1 TTTTATCTTATCTTAT
30504 TTTTATCTTATCTTAT
1 TTTTATCTTATCTTAT
30520 TTT
1 TTT
30523 GCAGTTAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTATCTTATCTTAT
Found at i:31935 original size:14 final size:13
Alignment explanation
Indices: 31913--32062 Score: 53
Period size: 13 Copynumber: 11.2 Consensus size: 13
31903 AAGTGTTTTC
*
31913 TTTCTTCAAGTGTT
1 TTTCATCAAGT-TT
31927 TTTCATCAAGTTCT
1 TTTCATCAAGTT-T
31941 TTT-ATCAAGTTT
1 TTTCATCAAGTTT
* *
31953 TTAATTACCAAGGTTTTTT
1 TT--TCATCAA-G---TTT
* *
31972 TTGTTATTAAGT-T
1 TT-TCATCAAGTTT
*
31985 TTGCATCAAGTTCT
1 TTTCATCAAGTT-T
31999 TTT--T-AAGT-T
1 TTTCATCAAGTTT
*
32008 TTTCATCAAGTCT
1 TTTCATCAAGTTT
*
32021 TTTCATAAAG-TT
1 TTTCATCAAGTTT
*
32033 TTCCATCAAGTTT
1 TTTCATCAAGTTT
*
32046 TTAATCATTAAGTTT
1 TT--TCATCAAGTTT
32061 TT
1 TT
32063 CAATTAAGCT
Statistics
Matches: 104, Mismatches: 15, Indels: 33
0.68 0.10 0.22
Matches are distributed among these distances:
9 4 0.04
11 5 0.05
12 23 0.22
13 26 0.25
14 19 0.18
15 15 0.14
16 1 0.01
17 1 0.01
18 5 0.05
19 5 0.05
ACGTcount: A:0.24, C:0.13, G:0.10, T:0.53
Consensus pattern (13 bp):
TTTCATCAAGTTT
Found at i:32004 original size:23 final size:23
Alignment explanation
Indices: 31978--32044 Score: 82
Period size: 23 Copynumber: 2.8 Consensus size: 23
31968 TTTTTTGTTA
*
31978 TTAAGTTTTGCATCAAGTTCTTT
1 TTAAGTTTTCCATCAAGTTCTTT
*
32001 TTAAGTTTTTCATCAAG-TCTTT
1 TTAAGTTTTCCATCAAGTTCTTT
32023 TCATAAAGTTTTCCATCAAGTT
1 T--T-AAGTTTTCCATCAAGTT
32045 TTTAATCATT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
22 6 0.16
23 16 0.42
24 1 0.03
25 14 0.37
26 1 0.03
ACGTcount: A:0.25, C:0.15, G:0.10, T:0.49
Consensus pattern (23 bp):
TTAAGTTTTCCATCAAGTTCTTT
Found at i:32045 original size:12 final size:12
Alignment explanation
Indices: 31980--32052 Score: 69
Period size: 12 Copynumber: 6.1 Consensus size: 12
31970 TTTTGTTATT
*
31980 AAGTTTTGCATC
1 AAGTTTTTCATC
*
31992 AAGTTCTTT--TT
1 AAGTT-TTTCATC
32003 AAGTTTTTCATC
1 AAGTTTTTCATC
*
32015 AAGTCTTTTCATA
1 AAGT-TTTTCATC
*
32028 AAGTTTTCCATC
1 AAGTTTTTCATC
*
32040 AAGTTTTTAATC
1 AAGTTTTTCATC
32052 A
1 A
32053 TTAAGTTTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
10 3 0.06
11 6 0.12
12 27 0.55
13 13 0.27
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48
Consensus pattern (12 bp):
AAGTTTTTCATC
Found at i:32070 original size:13 final size:12
Alignment explanation
Indices: 31977--32075 Score: 67
Period size: 12 Copynumber: 7.8 Consensus size: 12
31967 TTTTTTTGTT
*
31977 ATTAAGTTTTGC
1 ATTAAGTTTTTC
*
31989 ATCAAGTTCTTT-
1 ATTAAGTT-TTTC
32001 -TTAAGTTTTTC
1 ATTAAGTTTTTC
*
32012 ATCAAGTCTTTTC
1 ATTAAGT-TTTTC
* *
32025 ATAAAGTTTTCC
1 ATTAAGTTTTTC
*
32037 ATCAAGTTTTTAATC
1 ATTAAG-TTTT--TC
32052 ATTAAGTTTTTC
1 ATTAAGTTTTTC
32064 AATTAAGCTTTT
1 -ATTAAG-TTTT
32076 ATCTCTTGCA
Statistics
Matches: 69, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
10 3 0.04
11 6 0.09
12 23 0.33
13 23 0.33
14 8 0.12
15 6 0.09
ACGTcount: A:0.27, C:0.13, G:0.09, T:0.51
Consensus pattern (12 bp):
ATTAAGTTTTTC
Found at i:45462 original size:15 final size:16
Alignment explanation
Indices: 45436--45465 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
45426 CAACACTGCT
45436 AACTTAGAAGATTGAG
1 AACTTAGAAGATTGAG
45452 AACTT-GAAGATTGA
1 AACTTAGAAGATTGA
45466 AAGAGGAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.43, C:0.07, G:0.23, T:0.27
Consensus pattern (16 bp):
AACTTAGAAGATTGAG
Done.