Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2072
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: 40451
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Found at i:56 original size:13 final size:13
Alignment explanation
Indices: 38--63 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28 CACAGCCAGA
38 TGTATCGATACAT
1 TGTATCGATACAT
51 TGTATCGATACAT
1 TGTATCGATACAT
64 GTTCAATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:166 original size:13 final size:13
Alignment explanation
Indices: 145--175 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
135 CAATACATGG
*
145 TACAATGTATCGA
1 TACATTGTATCGA
158 TACATTGTATCGA
1 TACATTGTATCGA
171 TACAT
1 TACAT
176 GAAGAAATGT
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:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:174 original size:33 final size:32
Alignment explanation
Indices: 129--195 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 32
119 CTATCACTAT
129 TTGTATCAATACATG-GTACAATGTATCGATACA
1 TTGTATCAATACATGAG-A-AATGTATCGATACA
*
162 TTGTATCGATACATGAAGAAATGTATCGATACA
1 TTGTATCAATACATG-AGAAATGTATCGATACA
195 T
1 T
196 AGCTTGTAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 29 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.33
Consensus pattern (32 bp):
TTGTATCAATACATGAGAAATGTATCGATACA
Found at i:3678 original size:20 final size:21
Alignment explanation
Indices: 3638--3690 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 21
3628 TTCTAAAATT
*
3638 TGTATCGATACAATTAGTGAA
1 TGTATCGATACAATAAGTGAA
*
3659 TGTATCGATAC-CTAAGTGAA
1 TGTATCGATACAATAAGTGAA
3679 TGTATCGATACA
1 TGTATCGATACA
3691 TGTCTCAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 18 0.62
21 11 0.38
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (21 bp):
TGTATCGATACAATAAGTGAA
Found at i:3789 original size:20 final size:21
Alignment explanation
Indices: 3736--3794 Score: 84
Period size: 22 Copynumber: 2.8 Consensus size: 21
3726 ACTACCAGGA
3736 AATGTATCGATACATGCTTAC
1 AATGTATCGATACATGCTTAC
*
3757 AATTGTATCGATACATTCTT-C
1 AA-TGTATCGATACATGCTTAC
*
3778 AATGTATTGATACATGC
1 AATGTATCGATACATGC
3795 AGGCAAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 13 0.38
21 5 0.15
22 16 0.47
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATGCTTAC
Found at i:10916 original size:17 final size:17
Alignment explanation
Indices: 10894--10926 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
10884 AAAGTTCCCT
*
10894 TCAAAATGACAAAAAAG
1 TCAAAAGGACAAAAAAG
10911 TCAAAAGGACAAAAAA
1 TCAAAAGGACAAAAAA
10927 AACAAAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.12, G:0.12, T:0.09
Consensus pattern (17 bp):
TCAAAAGGACAAAAAAG
Found at i:10932 original size:17 final size:17
Alignment explanation
Indices: 10895--10933 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
10885 AAGTTCCCTT
* **
10895 CAAAATGACAAAAAAGT
1 CAAAAGGACAAAAAAAA
10912 CAAAAGGACAAAAAAAA
1 CAAAAGGACAAAAAAAA
10929 CAAAA
1 CAAAA
10934 AGAAGAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.72, C:0.13, G:0.10, T:0.05
Consensus pattern (17 bp):
CAAAAGGACAAAAAAAA
Found at i:12506 original size:42 final size:41
Alignment explanation
Indices: 12423--12782 Score: 250
Period size: 42 Copynumber: 8.7 Consensus size: 41
12413 CATTTTCTTC
* **
12423 TTTTTCCTTTGTCCTCAAGGAATAGGACCTATTTCATTTTCCT
1 TTTTTCCTTTGTCCTCAAAGAGCAGGACC-ATTTCA-TTTCCT
* *
12466 TTTTTCCTCTGTCCTCAAAGAGCAGGACCTATTTTATTTCCT
1 TTTTTCCTTTGTCCTCAAAGAGCAGGACC-ATTTCATTTCCT
* * * *
12508 TTTCTCCTTTATCCTTAAAGTGCAGGACGCATTTCATTTCCT
1 TTTTTCCTTTGTCCTCAAAGAGCAGGAC-CATTTCATTTCCT
* * *
12550 TTTTTCCTTTGTCCTTAAAGAGCAGGATGCATTTTATTCTCC-
1 TTTTTCCTTTGTCCTCAAAGAGCAGGA-CCATTTCATT-TCCT
* * * * *
12592 TTTTTCCTTCGTCTTCGAAGGGCAGGA-CA--T-A-TACC-
1 TTTTTCCTTTGTCCTCAAAGAGCAGGACCATTTCATTTCCT
* * * * * *
12627 TTTTCCCTTTGTCCTCAAAGAGTAGGATGCTTTTCTTTTTCCC
1 TTTTTCCTTTGTCCTCAAAGAGCAGGA-CCATTTC-ATTTCCT
* * * **
12670 TTTTTCTTTTGTCCTCAAGGAGTAGGACCCACCTCATTTCCTT
1 TTTTTCCTTTGTCCTCAAAGAGCAGGA-CCATTTCATTTCC-T
** * * *
12713 TTTTTTATTTGTCCTCAAGGAGTAGGATGCATTTCATTATCC-
1 TTTTTCCTTTGTCCTCAAAGAGCAGGA-CCATTTCATT-TCCT
*
12755 TTTTTCCTTTGCCCTCAAAGAGCAGGAC
1 TTTTTCCTTTGTCCTCAAAGAGCAGGAC
12783 ATGCCCTCAT
Statistics
Matches: 251, Mismatches: 53, Indels: 28
0.76 0.16 0.08
Matches are distributed among these distances:
35 23 0.09
36 1 0.00
37 2 0.01
38 1 0.00
39 1 0.00
40 2 0.01
42 124 0.49
43 94 0.37
44 3 0.01
ACGTcount: A:0.19, C:0.24, G:0.14, T:0.42
Consensus pattern (41 bp):
TTTTTCCTTTGTCCTCAAAGAGCAGGACCATTTCATTTCCT
Found at i:12617 original size:84 final size:83
Alignment explanation
Indices: 12395--12782 Score: 325
Period size: 84 Copynumber: 4.7 Consensus size: 83
12385 CACCTTTTAA
* * **
12395 TCCTCAAAGAGCATGATGCA--TT-TTCTTCTTTTTCCTTTGTCCTCAAGGAATAGGACCTATTT
1 TCCTCAAAGAGCAGGATGCATTTTATTCTCCTTTTTCCTTTGTCCTCAAGGAGCAGGACC-ATTT
*
12457 CATTTTCCTTTTTTCCTCTG
65 CA-TTTCCTTTTTTCCTTTG
* * * * *
12477 TCCTCAAAGAGCAGGA-CCTATTTTATT-TCCTTTTCTCCTTTATCCTTAAAGTGCAGGACGCAT
1 TCCTCAAAGAGCAGGATGC-ATTTTATTCTCCTTTT-TCCTTTGTCCTCAAGGAGCAGGAC-CAT
12540 TTCATTTCCTTTTTTCCTTTG
63 TTCATTTCCTTTTTTCCTTTG
* * *
12561 TCCTTAAAGAGCAGGATGCATTTTATTCTCCTTTTTCCTTCGTCTTCGAAGG-GCAGGA-CA--T
1 TCCTCAAAGAGCAGGATGCATTTTATTCTCCTTTTTCCTTTGTCCTC-AAGGAGCAGGACCATTT
* *
12622 -A-TACC-TTTTCCCTTTG
65 CATTTCCTTTTTTCCTTTG
* * * * * *
12638 TCCTCAAAGAGTAGGATGC-TTTTCTTTTTCCCTTTTTCTTTTGTCCTCAAGGAGTAGGACCCAC
1 TCCTCAAAGAGCAGGATGCATTTT-ATTCT-CCTTTTTCCTTTGTCCTCAAGGAGCAGGA-CCAT
* **
12702 CTCATTTCCTTTTTTTTATTTG
63 TTCATTTCC-TTTTTTCCTTTG
* * * * * *
12724 TCCTCAAGGAGTAGGATGCATTTCATTATCCTTTTTCCTTTGCCCTCAAAGAGCAGGAC
1 TCCTCAAAGAGCAGGATGCATTTTATTCTCCTTTTTCCTTTGTCCTCAAGGAGCAGGAC
12783 ATGCCCTCAT
Statistics
Matches: 246, Mismatches: 39, Indels: 40
0.76 0.12 0.12
Matches are distributed among these distances:
76 4 0.02
77 34 0.14
78 23 0.09
79 1 0.00
80 3 0.01
81 1 0.00
82 19 0.08
83 1 0.00
84 65 0.26
85 62 0.25
86 30 0.12
87 3 0.01
ACGTcount: A:0.19, C:0.24, G:0.14, T:0.42
Consensus pattern (83 bp):
TCCTCAAAGAGCAGGATGCATTTTATTCTCCTTTTTCCTTTGTCCTCAAGGAGCAGGACCATTTC
ATTTCCTTTTTTCCTTTG
Found at i:12791 original size:86 final size:87
Alignment explanation
Indices: 12634--12799 Score: 212
Period size: 86 Copynumber: 1.9 Consensus size: 87
12624 ACCTTTTCCC
* * * * * * *
12634 TTTGTCCTCAAAGAGTAGGATGCTTTTCTTTTTCCCTTTTTCTTTTGTCCTCAAGGAGTAGGACC
1 TTTGTCCTCAAAGAGTAGGATGCATTTCATTATCCCTTTTTCCTTTGCCCTCAAAGAGCAGGACC
12699 CACCTCA-TTTCCTTTTTTTTA
66 CACCTCATTTTCCTTTTTTTTA
*
12720 TTTGTCCTCAAGGAGTAGGATGCATTTCATTAT-CCTTTTTCCTTTGCCCTCAAAGAGCAGGACA
1 TTTGTCCTCAAAGAGTAGGATGCATTTCATTATCCCTTTTTCCTTTGCCCTCAAAGAGCAGGAC-
*
12784 TGC-CCTCATTTTCCTT
65 -CCACCTCATTTTCCTT
12800 CCCCTTTTAA
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
85 26 0.38
86 34 0.50
87 8 0.12
ACGTcount: A:0.18, C:0.25, G:0.15, T:0.42
Consensus pattern (87 bp):
TTTGTCCTCAAAGAGTAGGATGCATTTCATTATCCCTTTTTCCTTTGCCCTCAAAGAGCAGGACC
CACCTCATTTTCCTTTTTTTTA
Found at i:12843 original size:31 final size:31
Alignment explanation
Indices: 12808--12925 Score: 112
Period size: 31 Copynumber: 3.8 Consensus size: 31
12798 TTCCCCTTTT
*
12808 AAAGCCCACATGAGTTGGTGGCACCCTAGTC
1 AAAGCCCACACGAGTTGGTGGCACCCTAGTC
* * *
12839 AAAGCCTACACGAGTTGGTGGCAACCC-AATT
1 AAAGCCCACACGAGTTGGTGGC-ACCCTAGTC
*** * * *
12870 AAAGCTTGCACAAGTTAGCGGCACCCTAGTC
1 AAAGCCCACACGAGTTGGTGGCACCCTAGTC
* *
12901 AATGCCCACACAAGTTGGTGGCACC
1 AAAGCCCACACGAGTTGGTGGCACC
12926 TAAGTTTAAG
Statistics
Matches: 68, Mismatches: 17, Indels: 4
0.76 0.19 0.04
Matches are distributed among these distances:
30 4 0.06
31 60 0.88
32 4 0.06
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.19
Consensus pattern (31 bp):
AAAGCCCACACGAGTTGGTGGCACCCTAGTC
Found at i:13020 original size:31 final size:30
Alignment explanation
Indices: 12985--13074 Score: 90
Period size: 31 Copynumber: 2.9 Consensus size: 30
12975 GCCTTAGAAT
* * *
12985 GTCAAAGTCTACACGAGTTGGTGGCACCCTA
1 GTCAAAG-CTACACAAGTTGGTAGCACCCGA
** *
13016 GTCAAAGCCCGCACAAGTTGGCAGCACCCGA
1 GTCAAAG-CTACACAAGTTGGTAGCACCCGA
*
13047 GTCAAAGCTCACACAAGTTGGTTGCACC
1 GTCAAAGCT-ACACAAGTTGGTAGCACC
13075 TAAGTTTGAG
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
30 1 0.02
31 46 0.98
ACGTcount: A:0.28, C:0.30, G:0.24, T:0.18
Consensus pattern (30 bp):
GTCAAAGCTACACAAGTTGGTAGCACCCGA
Found at i:13320 original size:31 final size:31
Alignment explanation
Indices: 13282--13371 Score: 162
Period size: 31 Copynumber: 2.9 Consensus size: 31
13272 GCCTTAGAAT
*
13282 GTCAAAGCCCACATGAGTTGGTGGCACCCTA
1 GTCAAAGCCCACACGAGTTGGTGGCACCCTA
13313 GTCAAAGCCCACACGAGTTGGTGGCACCCTA
1 GTCAAAGCCCACACGAGTTGGTGGCACCCTA
*
13344 GTCAAAGCCCACACGATTTGGTGGCACC
1 GTCAAAGCCCACACGAGTTGGTGGCACC
13372 TAAGTTTAAG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 57 1.00
ACGTcount: A:0.26, C:0.31, G:0.26, T:0.18
Consensus pattern (31 bp):
GTCAAAGCCCACACGAGTTGGTGGCACCCTA
Found at i:13347 original size:148 final size:149
Alignment explanation
Indices: 12836--13512 Score: 919
Period size: 148 Copynumber: 4.6 Consensus size: 149
12826 TGGCACCCTA
* * * *** * *
12836 GTCAAAGCCTACACGAGTTGGTGGCAACCC-AATTAAAGCTTGCACAAGTTAGCGGCACCCTAGT
1 GTCAAAGCCCACACGAGTTGGTGGC-ACCCTAGTCAAAGCCCACACAAGTTGGCGGCACCCGAGT
* *
12900 CAATGCCCACACAAGTTGGTGGCACCTAAGTTTAAGTCAAGTCCACATTAGTTGGCACCTGTCTA
65 CAAAGCCCACACAAGTTGGTGGCACCTAAGTTTAAGTCAAGTCCACATTAGTTGGCACTTGTCTA
** *
12965 AGGAGGTTGAGCCTTAGAAT
130 AAAAGGTTAAGCCTTAGAAT
* * * *
12985 GTCAAAGTCTACACGAGTTGGTGGCACCCTAGTCAAAGCCCGCACAAGTTGGCAGCACCCGAGTC
1 GTCAAAGCCCACACGAGTTGGTGGCACCCTAGTCAAAGCCCACACAAGTTGGCGGCACCCGAGTC
* * *
13050 AAAGCTCACACAAGTTGGTTGCACCTAAGTTTGAGTCAAGTCCACATTAGTTGGCACTTGTCTAA
66 AAAGCCCACACAAGTTGGTGGCACCTAAGTTTAAGTCAAGTCCACATTAGTTGGCACTTGTCTAA
**
13115 GGAGGTTAAGCCTTAGAAT
131 AAAGGTTAAGCCTTAGAAT
* * * * * * ** * *
13134 GTCAAAGCTCACAGGAGTTAGTGGCACCTTAATTAAAGCATACATAAGTTGGCAGCACCCGAGTC
1 GTCAAAGCCCACACGAGTTGGTGGCACCCTAGTCAAAGCCCACACAAGTTGGCGGCACCCGAGTC
* *
13199 AAAGCCCACACGATTTGGTGGCACCTAAGTTTAAGTCAAGTCCACATTAGTTGGC-CTTGTCTAA
66 AAAGCCCACACAAGTTGGTGGCACCTAAGTTTAAGTCAAGTCCACATTAGTTGGCACTTGTCTAA
13263 AAAGGTTAAGCCTTAGAAT
131 AAAGGTTAAGCCTTAGAAT
* * * *
13282 GTCAAAGCCCACATGAGTTGGTGGCACCCTAGTCAAAGCCCACACGAGTTGGTGGCACCCTAGTC
1 GTCAAAGCCCACACGAGTTGGTGGCACCCTAGTCAAAGCCCACACAAGTTGGCGGCACCCGAGTC
* *
13347 AAAGCCCACACGATTTGGTGGCACCTAAGTTTAAGTCAAGTCCACATTAGTTGGC-CTTGTCTAA
66 AAAGCCCACACAAGTTGGTGGCACCTAAGTTTAAGTCAAGTCCACATTAGTTGGCACTTGTCTAA
13411 AAAGGTTAAGCCTTAGAAT
131 AAAGGTTAAGCCTTAGAAT
* * * *
13430 GTCAAAGCCCACATGAGTTGGTGGCACCCTAGTCAAAGCCCACACGAGTTGGTGGCACCCCAGTC
1 GTCAAAGCCCACACGAGTTGGTGGCACCCTAGTCAAAGCCCACACAAGTTGGCGGCACCCGAGTC
*
13495 AAAGCCCGCACAAGTTGG
66 AAAGCCCACACAAGTTGG
13513 CGACACCCAA
Statistics
Matches: 477, Mismatches: 50, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
148 244 0.51
149 233 0.49
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (149 bp):
GTCAAAGCCCACACGAGTTGGTGGCACCCTAGTCAAAGCCCACACAAGTTGGCGGCACCCGAGTC
AAAGCCCACACAAGTTGGTGGCACCTAAGTTTAAGTCAAGTCCACATTAGTTGGCACTTGTCTAA
AAAGGTTAAGCCTTAGAAT
Found at i:13468 original size:31 final size:31
Alignment explanation
Indices: 13430--13555 Score: 153
Period size: 31 Copynumber: 4.1 Consensus size: 31
13420 GCCTTAGAAT
* *
13430 GTCAAAGCCCACATGAGTTGGTGGCACCCTA
1 GTCAAAGCCCACACGAGTTGGTGGCACCCAA
*
13461 GTCAAAGCCCACACGAGTTGGTGGCACCCCA
1 GTCAAAGCCCACACGAGTTGGTGGCACCCAA
* * * *
13492 GTCAAAGCCCGCACAAGTTGGCGACACCCAA
1 GTCAAAGCCCACACGAGTTGGTGGCACCCAA
* * * *
13523 CTTAAAGCCGACACGAGTTGGTGGCACCTAA
1 GTCAAAGCCCACACGAGTTGGTGGCACCCAA
13554 GT
1 GT
13556 TTGAGTCAAG
Statistics
Matches: 79, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 79 1.00
ACGTcount: A:0.28, C:0.31, G:0.25, T:0.16
Consensus pattern (31 bp):
GTCAAAGCCCACACGAGTTGGTGGCACCCAA
Found at i:13497 original size:179 final size:180
Alignment explanation
Indices: 13282--13637 Score: 509
Period size: 179 Copynumber: 2.0 Consensus size: 180
13272 GCCTTAGAAT
* * * * * * *
13282 GTCAAAGCCCACATGAGTTGGTGGCACCCTAGTCAAAGCCCACACGAGTTGGTGGCACCCTAGTC
1 GTCAAAGCCCACACGAGTTGGTGGCACCCCAGTCAAAGCCCACACAAGTTGGCGACACCCAACTC
* * *
13347 AAAGCCCACACGATTTGGTGGCACCTAAGTTTAAGTCAAGTCCACATTAGTTGGC-CTTGTCTAA
66 AAAGCCCACACGAGTTGGTGGCACCTAAGTTTAAGTCAAGTCCACATTAGTTAGCACCTGTC-AA
*
13411 AA-AGGTTAAGCCTTAGAATGTCAAAGCCCACATGAGTTGGTGGCACCCTA
130 AAGAGGTTAAGCCTTAGAATGTCAAAGCCCACACGAGTTGGTGGCACCCTA
* *
13461 GTCAAAGCCCACACGAGTTGGTGGCACCCCAGTCAAAGCCCGCACAAGTTGGCGACACCCAACTT
1 GTCAAAGCCCACACGAGTTGGTGGCACCCCAGTCAAAGCCCACACAAGTTGGCGACACCCAACTC
* * ** *
13526 AAAGCCGACACGAGTTGGTGGCACCTAAGTTTGAGTCAAGTTTATATTAGTTAGCACCTGTCAAA
66 AAAGCCCACACGAGTTGGTGGCACCTAAGTTTAAGTCAAGTCCACATTAGTTAGCACCTGTCAAA
* *
13591 AGAGGTTTAGCCTTAGAATGTCAAAGTCCACACGAGTTGGTGGCACC
131 AGAGGTTAAGCCTTAGAATGTCAAAGCCCACACGAGTTGGTGGCACC
13638 TAAGTCCGAA
Statistics
Matches: 155, Mismatches: 20, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
179 108 0.70
180 47 0.30
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (180 bp):
GTCAAAGCCCACACGAGTTGGTGGCACCCCAGTCAAAGCCCACACAAGTTGGCGACACCCAACTC
AAAGCCCACACGAGTTGGTGGCACCTAAGTTTAAGTCAAGTCCACATTAGTTAGCACCTGTCAAA
AGAGGTTAAGCCTTAGAATGTCAAAGCCCACACGAGTTGGTGGCACCCTA
Found at i:13683 original size:87 final size:87
Alignment explanation
Indices: 13533--13695 Score: 209
Period size: 87 Copynumber: 1.9 Consensus size: 87
13523 CTTAAAGCCG
** * ** * *
13533 ACACGAGTTGGTGGCACCTAAGTTTGAGTCAAGTTTATATTAGTTAGCACCTGTCAAAAGAGGTT
1 ACACGAGTTGGTGGCACCTAAGTCCGAATCAAGTCCACATTAGTTAGCACCTATCAAAAGAGGTT
*
13598 TAGCCTTAGAATGTCAAAGTCC
66 AAGCCTTAGAATGTCAAAGTCC
* ** *
13620 ACACGAGTTGGTGGCACCTAAGTCCGAATCAAGTCCACATTAGTTGGCACCTATCTTAGGAGGTT
1 ACACGAGTTGGTGGCACCTAAGTCCGAATCAAGTCCACATTAGTTAGCACCTATCAAAAGAGGTT
*
13685 AAGCTTTAGAA
66 AAGCCTTAGAA
13696 AACCAAAACC
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
87 63 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.28
Consensus pattern (87 bp):
ACACGAGTTGGTGGCACCTAAGTCCGAATCAAGTCCACATTAGTTAGCACCTATCAAAAGAGGTT
AAGCCTTAGAATGTCAAAGTCC
Found at i:14231 original size:21 final size:21
Alignment explanation
Indices: 14207--14263 Score: 91
Period size: 20 Copynumber: 2.8 Consensus size: 21
14197 ACAATCTGTG
14207 AATGTATCGATACATGTC-TC
1 AATGTATCGATACATGTCTTC
14227 AAATGTATCGATACAT-TCTTC
1 -AATGTATCGATACATGTCTTC
14248 AATGTATCGATACATG
1 AATGTATCGATACATG
14264 CAAGCAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
21 17 0.50
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (21 bp):
AATGTATCGATACATGTCTTC
Found at i:14253 original size:20 final size:20
Alignment explanation
Indices: 14188--14262 Score: 89
Period size: 21 Copynumber: 3.6 Consensus size: 20
14178 TTGTATGATT
* * *
14188 TGTATCGACACAATCTGTGAA
1 TGTATCGATACATTCT-TCAA
14209 TGTATCGATACATGTC-TCAAA
1 TGTATCGATACAT-TCTTC-AA
14230 TGTATCGATACATTCTTCAA
1 TGTATCGATACATTCTTCAA
14250 TGTATCGATACAT
1 TGTATCGATACAT
14263 GCAAGCAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
20 18 0.38
21 28 0.58
22 2 0.04
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.35
Consensus pattern (20 bp):
TGTATCGATACATTCTTCAA
Found at i:20750 original size:20 final size:20
Alignment explanation
Indices: 20725--20762 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
20715 TTTTTACCTA
20725 GATGTATCGATACATTTTTC
1 GATGTATCGATACATTTTTC
*
20745 GATGTATTGATACATTTT
1 GATGTATCGATACATTTT
20763 ATTTTTTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.11, G:0.16, T:0.47
Consensus pattern (20 bp):
GATGTATCGATACATTTTTC
Found at i:20769 original size:51 final size:51
Alignment explanation
Indices: 20696--20810 Score: 151
Period size: 51 Copynumber: 2.3 Consensus size: 51
20686 TAAATAGTAC
* * * * *
20696 ATGTATCTATAGATTCTA-TTTTTTACCTAGATGTATCGATACATTTTTCG
1 ATGTATCGATACATTTTATTTTTTTACCCAGATGTATCGATACATTTTTCA
* * *
20746 ATGTATTGATACATTTTATTTTTTTACCCAGATGTATTGATACATTTTTTA
1 ATGTATCGATACATTTTATTTTTTTACCCAGATGTATCGATACATTTTTCA
20797 ATGTATCGATACAT
1 ATGTATCGATACAT
20811 CTGGTTAATT
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
50 14 0.25
51 41 0.75
ACGTcount: A:0.28, C:0.12, G:0.11, T:0.49
Consensus pattern (51 bp):
ATGTATCGATACATTTTATTTTTTTACCCAGATGTATCGATACATTTTTCA
Found at i:30980 original size:52 final size:51
Alignment explanation
Indices: 30895--31018 Score: 212
Period size: 52 Copynumber: 2.4 Consensus size: 51
30885 ATATGAAAAG
* *
30895 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAA
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
*
30946 TTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA
1 -TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
30998 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
31019 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 21 0.30
52 48 0.70
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
Found at i:31031 original size:51 final size:51
Alignment explanation
Indices: 30895--31038 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 51
30885 ATATGAAAAG
*
30895 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
30947 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA-
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
30998 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
31039 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
50 2 0.02
51 34 0.40
52 48 0.57
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:31045 original size:13 final size:13
Alignment explanation
Indices: 31027--31051 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31017 CAAAGATCAG
31027 TGTATCGATACAA
1 TGTATCGATACAA
31040 TGTATCGATACA
1 TGTATCGATACA
31052 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:31852 original size:49 final size:49
Alignment explanation
Indices: 31793--32132 Score: 407
Period size: 49 Copynumber: 7.1 Consensus size: 49
31783 ATATGCGGCT
31793 AGCGATATTGGACTTAAAGATAAAGGTGCCAATGTGCTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATAAAGGTGCCAATGTGCTGATTCAAGGCC
*
31842 AGCGACATTGGACTT----A-AAA-GTGCCAATGTGCTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATAAAGGTGCCAATGTGCTGATTCAAGGCC
* * * *
31885 AGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCC
1 AGCGATATTGGACTTAAAGATAAAGGTGCCAATGTGCTGATTCAAGGCC
* * * *
31934 AGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTAAAGGCC
1 AGCGATATTGGACTTAAAGATAAAGGTGCCAATGTGCTGATTCAAGGCC
* * *
31983 AGCTATATTGGACTTAAAGATAAAGGTGCCAATATGGTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATAAAGGTGCCAATGTGCTGATTCAAGGCC
* * *
32032 AACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAATGTGCTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGAT-----AAAGG-TGCCAATGTGCTGATTCAAGGCC
32087 AGCGATATTGGACTT----A-AAA-GTGCCAATGTGCTGATTCAAGGCC
1 AGCGATATTGGACTTAAAGATAAAGGTGCCAATGTGCTGATTCAAGGCC
32130 AGC
1 AGC
32133 TAATATGCTG
Statistics
Matches: 259, Mismatches: 20, Indels: 30
0.84 0.06 0.10
Matches are distributed among these distances:
43 63 0.24
44 4 0.02
45 4 0.02
47 1 0.00
48 2 0.01
49 146 0.56
51 1 0.00
54 5 0.02
55 33 0.13
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (49 bp):
AGCGATATTGGACTTAAAGATAAAGGTGCCAATGTGCTGATTCAAGGCC
Found at i:32178 original size:66 final size:66
Alignment explanation
Indices: 32072--32200 Score: 258
Period size: 66 Copynumber: 2.0 Consensus size: 66
32062 GATGTCAATG
32072 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAAGTGCCAATGTGCTGATTCAAGGCCAGCTAAT
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAAGTGCCAATGTGCTGATTCAAGGCCAGCTAAT
32137 A
66 A
32138 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAAGTGCCAATGTGCTGATTCAAGGCCAGCTA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAAGTGCCAATGTGCTGATTCAAGGCCAGCTA
32201 CATTGGACTT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (66 bp):
TGCTGATTCAAGGCCAGCGATATTGGACTTAAAAGTGCCAATGTGCTGATTCAAGGCCAGCTAAT
A
Found at i:32244 original size:49 final size:43
Alignment explanation
Indices: 32138--32292 Score: 229
Period size: 43 Copynumber: 3.5 Consensus size: 43
32128 CCAGCTAATA
* *
32138 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAAGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAAGTGCCAATG
32181 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTT--A-A--AA-GTGCCAATG
*
32230 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAAGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAAGTGCCAATG
32273 TGCTGATTCAAGGCCAGCTA
1 TGCTGATTCAAGGCCAGCTA
32293 ATATGCTGAT
Statistics
Matches: 102, Mismatches: 4, Indels: 12
0.86 0.03 0.10
Matches are distributed among these distances:
43 56 0.55
44 2 0.02
45 1 0.01
46 2 0.02
47 1 0.01
48 2 0.02
49 38 0.37
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.25
Consensus pattern (43 bp):
TGCTGATTCAAGGCCAGCTACATTGGACTTAAAAGTGCCAATG
Found at i:32302 original size:115 final size:113
Alignment explanation
Indices: 32181--32407 Score: 318
Period size: 115 Copynumber: 2.0 Consensus size: 113
32171 AGTGCCAATG
*
32181 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCA
1 TGCTGATTCAAGGCCAGCGACATTGGACTT--A-A--AA-GTGCCAATGTGCTGAGTCAAGGCCA
*
32246 GCTACATTGGACTT-A-A-AA-GTGCCAATGTGCTGATTCAAGGCCAGCTAATA
60 GCTACATTGGACTTAAGAGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTAATA
* *
32296 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAAGTGCCAATGTGCTGATTCAAGGCCAGCTACA
1 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAAGTGCCAATGTGCTGAGTCAAGGCCAGCTACA
32361 TTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTA
66 TTGGACTT-AAGA-GAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTA
32408 CATTGGACTT
Statistics
Matches: 102, Mismatches: 4, Indels: 12
0.86 0.03 0.10
Matches are distributed among these distances:
109 38 0.37
110 2 0.02
111 1 0.01
112 2 0.02
113 1 0.01
114 2 0.02
115 56 0.55
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (113 bp):
TGCTGATTCAAGGCCAGCGACATTGGACTTAAAAGTGCCAATGTGCTGAGTCAAGGCCAGCTACA
TTGGACTTAAGAGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTAATA
Found at i:32302 original size:158 final size:158
Alignment explanation
Indices: 31964--32456 Score: 707
Period size: 158 Copynumber: 3.0 Consensus size: 158
31954 TAAAGGTGCC
* * * *
31964 AATATGCTGATTAAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGCCAATATGGTGATTCAAG
1 AATATGCTGATTCAAGGCCAGCGATATTGGACTT----A-AAA-GTGCCAATGTGCTGATTCAAG
* * * * * * * *
32029 GCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAATGTGCTGATTCAAGGCCAGCGATA
60 GCCAGCTACATTGGACTTAAAGAT--G---AAGG-TGCCAATGTGCTGAGTCAAGGCCAGCTACA
32094 TTGGACTTAAAAGTGCCAATGTGCTGATTCAAGGCCAGCT
119 TTGGACTTAAAAGTGCCAATGTGCTGATTCAAGGCCAGCT
32134 AATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAGTGCCAATGTGCTGATTCAAGGCCAGC
1 AATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAGTGCCAATGTGCTGATTCAAGGCCAGC
32199 TACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAA
66 TACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAA
32264 GTGCCAATGTGCTGATTCAAGGCCAGCT
131 GTGCCAATGTGCTGATTCAAGGCCAGCT
32292 AATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAGTGCCAATGTGCTGATTCAAGGCCAGC
1 AATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAGTGCCAATGTGCTGATTCAAGGCCAGC
32357 TACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAG
66 TACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTT----
*
32422 ATAAAGGTGCCAATATGCTGATTCAAGGCCAGCT
127 A-AAA-GTGCCAATGTGCTGATTCAAGGCCAGCT
32456 A
1 A
32457 TATTGGATTT
Statistics
Matches: 304, Mismatches: 13, Indels: 18
0.91 0.04 0.05
Matches are distributed among these distances:
158 192 0.63
159 4 0.01
162 2 0.01
163 3 0.01
164 67 0.22
165 3 0.01
166 1 0.00
170 32 0.11
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (158 bp):
AATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAGTGCCAATGTGCTGATTCAAGGCCAGC
TACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAA
GTGCCAATGTGCTGATTCAAGGCCAGCT
Found at i:32336 original size:66 final size:66
Alignment explanation
Indices: 32230--32358 Score: 231
Period size: 66 Copynumber: 2.0 Consensus size: 66
32220 GGTGCCAATG
*
32230 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAAGTGCCAATGTGCTGATTCAAGGCCAGCTAAT
1 TGCTGAGTCAAGGCCAGCGACATTGGACTTAAAAGTGCCAATGTGCTGATTCAAGGCCAGCTAAT
32295 A
66 A
* *
32296 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAAGTGCCAATGTGCTGATTCAAGGCCAGCTA
1 TGCTGAGTCAAGGCCAGCGACATTGGACTTAAAAGTGCCAATGTGCTGATTCAAGGCCAGCTA
32359 CATTGGACTT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (66 bp):
TGCTGAGTCAAGGCCAGCGACATTGGACTTAAAAGTGCCAATGTGCTGATTCAAGGCCAGCTAAT
A
Found at i:32402 original size:49 final size:49
Alignment explanation
Indices: 32292--32516 Score: 309
Period size: 49 Copynumber: 4.7 Consensus size: 49
32282 AAGGCCAGCT
* *
32292 AATATGCTGATTCAAGGCCAGCGATATTGGACTT----A-AAA-GTGCC
1 AATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCC
* *
32335 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCC
1 AATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCC
* *
32384 AATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCC
1 AATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCC
* *
32433 AATATGCTGATTCAAGGCCAGCTATATTGGATTTAAAGATAAAGGTGCC
1 AATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCC
* * *
32482 AATATGGTGATTCAAGGCCAGCTATATTGGGCTTA
1 AATATGCTGATTCAAGGCCAGCTACATTGGACTTA
32517 GAAGGGTTGC
Statistics
Matches: 163, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
43 31 0.19
47 1 0.01
48 2 0.01
49 129 0.79
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (49 bp):
AATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCC
Found at i:32560 original size:33 final size:35
Alignment explanation
Indices: 32516--32585 Score: 126
Period size: 33 Copynumber: 2.1 Consensus size: 35
32506 TATTGGGCTT
32516 AGAAGGGTTGCCACCGACTTGTGTGGGCTTT-GGA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGA
32550 AGAA-GGTTGCCACCGACTTGTGTGGGCTTTAGGA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGA
32584 AG
1 AG
32586 GGAGAAAGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 26 0.74
34 9 0.26
ACGTcount: A:0.20, C:0.17, G:0.37, T:0.26
Consensus pattern (35 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGGA
Found at i:32700 original size:70 final size:70
Alignment explanation
Indices: 32570--32965 Score: 464
Period size: 70 Copynumber: 5.7 Consensus size: 70
32560 CACCGACTTG
* * * *
32570 TGTGGGCTTTAGGAAGGGAGAAAGATGCCACGGAGTTGTGGAC-TTAAAAGGGAAAAAGAGTGCC
1 TGTGGGCTTT-GAAAAGGAAAAAG-TGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCC
32634 ACGGAGT
64 ACGGAGT
32641 TGTGGGCTTT-AAAAGGAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCA
1 TGTGGGCTTTGAAAAGGAAAAAGTGCCACGGAGTTGTGGGCTTT-AAAAGGGAAAAAGAGTGCCA
32705 CGGAGT
65 CGGAGT
* *
32711 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAA--GTAAAA-AGTGC
1 TGTGGGCTTTGAAAA-GG-AAAA-AGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGC
32773 CACGGAGT
63 CACGGAGT
*
32781 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAATGAGTG
1 TGTGGGCTTTGAAAA-GG-AAAA-AGTGCCACGGAGTTGTGGGCTTT-AAAAGGGAAAAAGAGTG
32846 CCACGGAGT
62 CCACGGAGT
32855 TGTGGGCTTT-AAACA-GAAAAAGGTGCCACGGAGTTGTGGGCTTT--------AAAAGAGTGCC
1 TGTGGGCTTTGAAA-AGGAAAAA-GTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCC
*
32910 ATGGAGT
64 ACGGAGT
* *
32917 TATGGGCTTTGAAAA-GAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAA
1 TGTGGGCTTTGAAAAGGAA-AAAGTGCCACGGAGTTGTGGGCTTT-AAAA
32966 AGATGCCACT
Statistics
Matches: 293, Mismatches: 13, Indels: 42
0.84 0.04 0.12
Matches are distributed among these distances:
62 51 0.17
63 5 0.02
68 17 0.06
69 11 0.04
70 96 0.33
71 49 0.17
72 3 0.01
73 15 0.05
74 46 0.16
ACGTcount: A:0.32, C:0.11, G:0.36, T:0.21
Consensus pattern (70 bp):
TGTGGGCTTTGAAAAGGAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCAC
GGAGT
Found at i:32711 original size:37 final size:36
Alignment explanation
Indices: 32570--32965 Score: 485
Period size: 37 Copynumber: 11.4 Consensus size: 36
32560 CACCGACTTG
* *
32570 TGTGGGCTTTAGGAAGGGAGAAAGA-TGCCACGGAGT
1 TGTGGGCTTTA-AAAGGGAAAAAGAGTGCCACGGAGT
*
32606 TGTGGAC-TTAAAAGGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
32641 TGTGGGCTTTAAAA-GG-AAAA-AGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
32674 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGGAGT
*
32711 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACAGAGT
1 TGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGGAGT
*
32748 TGTGGGCTTTAAAA--GTAAAA-AGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
32781 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGGAGT
*
32818 TGTGGGCTTTGAAAAGGGAAAATGAGTGCCACGGAGT
1 TGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGGAGT
32855 TGTGGGCTTTAAACA--GAAAAAG-GTGCCACGGAGT
1 TGTGGGCTTTAAA-AGGGAAAAAGAGTGCCACGGAGT
*
32889 TGTGGGCTTT--------AAAAGAGTGCCATGGAGT
1 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
* *
32917 TATGGGCTTTGAAAA--GAAGAAG-GTGCCACGGAGT
1 TGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGGAGT
32951 TGTGGGCTTTGAAAA
1 TGTGGGCTTT-AAAA
32966 AGATGCCACT
Statistics
Matches: 326, Mismatches: 15, Indels: 40
0.86 0.04 0.10
Matches are distributed among these distances:
27 5 0.02
28 20 0.06
33 45 0.14
34 75 0.23
35 34 0.10
36 28 0.09
37 119 0.37
ACGTcount: A:0.32, C:0.11, G:0.36, T:0.21
Consensus pattern (36 bp):
TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
Found at i:32753 original size:107 final size:106
Alignment explanation
Indices: 32570--32992 Score: 562
Period size: 107 Copynumber: 4.1 Consensus size: 106
32560 CACCGACTTG
* * *
32570 TGTGGGCTTT-AGGAAGGGAGAAAGA-TGCCACGGAGTTGTGGAC-TT-AAAAGGGAAAAAGAGT
1 TGTGGGCTTTGA-AAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGT
32631 GCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGTGCCACGGAGT
65 GCCACGGAGTTGTGGGCTTTAAAA-GAAAAAGTGCCACGGAGT
32674 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTG
1 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTG
*
32739 CCACAGAGTTGTGGGCTTTAAAAGTAAAAAGTGCCACGGAGT
66 CCACGGAGTTGTGGGCTTTAAAAG-AAAAAGTGCCACGGAGT
*
32781 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAATGAGTG
1 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTG
32846 CCACGGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGT
66 CCACGGAGTTGTGGGCTTTAAA-AGAAAAA-GTGCCACGGAGT
* * *
32889 TGTGGGCTTT---------AAAAGAGTGCCATGGAGTTATGGGCTTTGAAAA--GAAGAAG-GTG
1 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTG
* *
32942 CCACGGAGTTGTGGGCTTT----GAAAAAGATGCCACTGACT
66 CCACGGAGTTGTGGGCTTTAAAAGAAAAAG-TGCCACGGAGT
32980 TGTGGGCTTTGAA
1 TGTGGGCTTTGAA
32993 GGGTAAAGAA
Statistics
Matches: 296, Mismatches: 12, Indels: 32
0.87 0.04 0.09
Matches are distributed among these distances:
90 1 0.00
91 25 0.08
96 22 0.07
97 5 0.02
99 31 0.10
104 21 0.07
105 18 0.06
106 3 0.01
107 146 0.49
108 24 0.08
ACGTcount: A:0.31, C:0.12, G:0.35, T:0.22
Consensus pattern (106 bp):
TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTG
CCACGGAGTTGTGGGCTTTAAAAGAAAAAGTGCCACGGAGT
Found at i:32940 original size:62 final size:64
Alignment explanation
Indices: 32835--32992 Score: 218
Period size: 62 Copynumber: 2.5 Consensus size: 64
32825 TTTGAAAAGG
*
32835 GAAAATGAGTGCCACGGAGTTGTGGGCTTT-AAACAGAAAAAGGTGCCACGGAGTTGTGGGCTTT
1 GAAAA-GAGTGCCATGGAGTTGTGGGCTTTGAAACAGAAAAAGGTGCCACGGAGTTGTGGGCTTT
* *
32899 -AAAAGAGTGCCATGGAGTTATGGGCTTTGAAA-AGAAGAAGGTGCCACGGAGTTGTGGGCTTT
1 GAAAAGAGTGCCATGGAGTTGTGGGCTTTGAAACAGAAAAAGGTGCCACGGAGTTGTGGGCTTT
*
32961 GAAAA-AGATGCCACT-GACTTGTGGGCTTTGAA
1 GAAAAGAG-TGCCA-TGGAGTTGTGGGCTTTGAA
32993 GGGTAAAGAA
Statistics
Matches: 85, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
62 53 0.62
63 31 0.36
64 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.34, T:0.24
Consensus pattern (64 bp):
GAAAAGAGTGCCATGGAGTTGTGGGCTTTGAAACAGAAAAAGGTGCCACGGAGTTGTGGGCTTT
Found at i:34435 original size:1 final size:1
Alignment explanation
Indices: 34431--34563 Score: 86
Period size: 1 Copynumber: 133.0 Consensus size: 1
34421 CGGACCCCCC
* * * * * ** *
34431 TTTTTTTGTTTGTTTTTTTTATTGTTTTTTGTTTTTTTTTTCCTTTTGTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
** ** ** ** ** **
34496 TTTGGTTTTCATTTTTTCGTTTTTTTTTTTTGGTTTTTCATTTTTTTTCGTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
34561 TTT
1 TTT
34564 GGAGGACGCC
Statistics
Matches: 102, Mismatches: 30, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 102 1.00
ACGTcount: A:0.02, C:0.05, G:0.08, T:0.85
Consensus pattern (1 bp):
T
Found at i:34448 original size:12 final size:11
Alignment explanation
Indices: 34431--34563 Score: 105
Period size: 11 Copynumber: 11.7 Consensus size: 11
34421 CGGACCCCCC
34431 TTTTTTTGTTTG
1 TTTTTTT-TTTG
34443 TTTTTTTTATTG
1 TTTTTTTT-TTG
34455 TTTTTTGTTTT-
1 TTTTTT-TTTTG
34466 TTTTTTCCTTTTG
1 TTTTTT--TTTTG
34479 TTTTTTTTTT-
1 TTTTTTTTTTG
34489 TTTTTTTTTTGG
1 TTTTTTTTTT-G
34501 TTTTCATTTTTTCG
1 TTTT--TTTTTT-G
34515 -TTTTTTTTT-
1 TTTTTTTTTTG
** *
34524 TTTGGTTTTTC
1 TTTTTTTTTTG
* *
34535 ATTTTTTTTCG
1 TTTTTTTTTTG
34546 TTTTTTTTTT-
1 TTTTTTTTTTG
34556 TTTTTTTT
1 TTTTTTTT
34564 GGAGGACGCC
Statistics
Matches: 100, Mismatches: 11, Indels: 22
0.75 0.08 0.17
Matches are distributed among these distances:
10 25 0.25
11 31 0.31
12 26 0.26
13 11 0.11
14 7 0.07
ACGTcount: A:0.02, C:0.05, G:0.08, T:0.85
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:34455 original size:16 final size:15
Alignment explanation
Indices: 34431--34563 Score: 100
Period size: 15 Copynumber: 8.9 Consensus size: 15
34421 CGGACCCCCC
34431 TTTTTTTGTTTGTTT-
1 TTTTTTTGTTT-TTTG
34446 TTTTTATTGTTTTTTG
1 TTTTT-TTGTTTTTTG
*
34462 TTTTTTTTTTCCTTTTG
1 TTTTTTTGTT--TTTTG
34479 TTTTTTT-TTTTTT-
1 TTTTTTTGTTTTTTG
* **
34492 TTTTTTTGGTTTTCA
1 TTTTTTTGTTTTTTG
*
34507 TTTTTTCGTTTTTT-
1 TTTTTTTGTTTTTTG
*
34521 TTTTTTGGTTTTTCAT-
1 TTTTTTTGTTTTT--TG
34537 TTTTTTTCGTTTTTT-
1 TTTTTTT-GTTTTTTG
34552 TTTTTTT-TTTTT
1 TTTTTTTGTTTTT
34564 GGAGGACGCC
Statistics
Matches: 101, Mismatches: 8, Indels: 20
0.78 0.06 0.16
Matches are distributed among these distances:
13 12 0.12
14 20 0.20
15 31 0.31
16 20 0.20
17 18 0.18
ACGTcount: A:0.02, C:0.05, G:0.08, T:0.85
Consensus pattern (15 bp):
TTTTTTTGTTTTTTG
Found at i:34458 original size:23 final size:22
Alignment explanation
Indices: 34432--34563 Score: 126
Period size: 23 Copynumber: 5.9 Consensus size: 22
34422 GGACCCCCCT
*
34432 TTTTTTGTTTGTTTTTTTTATTG
1 TTTTTTGTTT-TTTTTTTTTTTG
34455 TTTTTTGTTTTTTTTTTCCTTTTG
1 TTTTTTGTTTTTTTTTT--TTTTG
34479 TTTTTT-TTTTTTTTTTTTTTG
1 TTTTTTGTTTTTTTTTTTTTTG
* ** *
34500 GTTTTCATTTTTTCGTTTTTTT-
1 TTTTTTGTTTTTT-TTTTTTTTG
* *
34522 TTTTTGGTTTTTCATTTTTTTTCG
1 TTTTTTGTTTTT--TTTTTTTTTG
34546 TTTTTT-TTTTTTTTTTTT
1 TTTTTTGTTTTTTTTTTTT
34564 GGAGGACGCC
Statistics
Matches: 92, Mismatches: 10, Indels: 16
0.78 0.08 0.14
Matches are distributed among these distances:
21 16 0.17
22 22 0.24
23 38 0.41
24 16 0.17
ACGTcount: A:0.02, C:0.05, G:0.08, T:0.85
Consensus pattern (22 bp):
TTTTTTGTTTTTTTTTTTTTTG
Found at i:34486 original size:28 final size:26
Alignment explanation
Indices: 34431--34563 Score: 99
Period size: 28 Copynumber: 4.9 Consensus size: 26
34421 CGGACCCCCC
* *
34431 TTTTTTTGTTTGTTTTTTTTATTGTTTTT
1 TTTTTTTTTTTG-GTTTTTT-TT-TTTTT
**
34460 TGTTTTTTTTTTCCTTTTGTTTTTTTTT
1 T-TTTTTTTTTTGGTTTT-TTTTTTTTT
**
34488 TTTTTTTTTTTGGTTTTCATTTTTTCGT
1 TTTTTTTTTTTGGTTTT--TTTTTTTTT
**
34516 TTTTTTTTTTTGGTTTTTCATTTTTT
1 TTTTTTTTTTTGGTTTTTTTTTTTTT
**
34542 TTCGTTTTTTT--TTTTTTTTTTT
1 TTTTTTTTTTTGGTTTTTTTTTTT
34564 GGAGGACGCC
Statistics
Matches: 85, Mismatches: 16, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
24 9 0.11
26 14 0.16
27 14 0.16
28 30 0.35
29 7 0.08
30 11 0.13
ACGTcount: A:0.02, C:0.05, G:0.08, T:0.85
Consensus pattern (26 bp):
TTTTTTTTTTTGGTTTTTTTTTTTTT
Done.