Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr5
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: 43060996
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2186021 characters in sequence are not A, C, G, or T
File 11 of 128
Found at i:3269962 original size:7 final size:7
Alignment explanation
Indices: 3269950--3269976 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
3269940 AACCCTGAAT
3269950 CATAAAA
1 CATAAAA
3269957 CATAAAA
1 CATAAAA
3269964 CATAAAA
1 CATAAAA
3269971 CATAAA
1 CATAAA
3269977 CCCTAAACCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.70, C:0.15, G:0.00, T:0.15
Consensus pattern (7 bp):
CATAAAA
Found at i:3270113 original size:14 final size:14
Alignment explanation
Indices: 3269952--3270128 Score: 63
Period size: 14 Copynumber: 12.4 Consensus size: 14
3269942 CCCTGAATCA
* * *
3269952 TAAAACATAAAACA
1 TAAACCATAAACCC
*
3269966 TAAAACATAAACCC
1 TAAACCATAAACCC
* *
3269980 TAAACCCCTAACCCC
1 TAAA-CCATAAACCC
*
3269995 TAAACCTTAAATCCC
1 TAAACCATAAA-CCC
* * **
3270010 -AACCCTTAAACAA
1 TAAACCATAAACCC
**
3270023 TAAAACCATAAACTG
1 T-AAACCATAAACCC
* *
3270038 TAATCCCTAAACCC
1 TAAACCATAAACCC
* **
3270052 ATAATCCATAAACTT
1 -TAAACCATAAACCC
*
3270067 TAAA--ATAGTAACTCT
1 TAAACCATA--AAC-CC
* *
3270082 TAAACCTTAAACCT
1 TAAACCATAAACCC
*
3270096 TAAACCATATACCC
1 TAAACCATAAACCC
*
3270110 TAAATCATAAACCC
1 TAAACCATAAACCC
3270124 TAAAC
1 TAAAC
3270129 TAAAATCATA
Statistics
Matches: 123, Mismatches: 30, Indels: 20
0.71 0.17 0.12
Matches are distributed among these distances:
12 3 0.02
13 1 0.01
14 74 0.60
15 43 0.35
17 2 0.02
ACGTcount: A:0.48, C:0.29, G:0.01, T:0.22
Consensus pattern (14 bp):
TAAACCATAAACCC
Found at i:3270276 original size:15 final size:14
Alignment explanation
Indices: 3270258--3270314 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 14
3270248 ACCCTTGAAT
3270258 CCCTAAACCTTAAAC
1 CCCTAAACCTT-AAC
3270273 CCCT-AACTCTTAAC
1 CCCTAAAC-CTTAAC
*
3270287 CCC-ATAACGTCTAAC
1 CCCTA-AACCT-TAAC
3270302 CCCTAAACCTTAA
1 CCCTAAACCTTAA
3270315 ATCTCAACCC
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
14 13 0.37
15 21 0.60
16 1 0.03
ACGTcount: A:0.35, C:0.40, G:0.02, T:0.23
Consensus pattern (14 bp):
CCCTAAACCTTAAC
Found at i:3270359 original size:15 final size:15
Alignment explanation
Indices: 3270336--3270372 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
3270326 TAAACCAGAA
3270336 TCCCT-AATCCATAC
1 TCCCTAAATCCATAC
3270350 TCCCTAAATCCATAC
1 TCCCTAAATCCATAC
3270365 TCCCTAAA
1 TCCCTAAA
3270373 CCTTAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 5 0.23
15 17 0.77
ACGTcount: A:0.32, C:0.41, G:0.00, T:0.27
Consensus pattern (15 bp):
TCCCTAAATCCATAC
Found at i:3270815 original size:41 final size:41
Alignment explanation
Indices: 3270728--3270960 Score: 306
Period size: 41 Copynumber: 5.7 Consensus size: 41
3270718 TTTTTAACGG
* *
3270728 CGCTTTTTCAAAAACGCCGCTAAAGCCCCT-GCATTAGTGG
1 CGCTTTTTCAAAAACGCCGCTAAAGCCCCTAGCATTAGCGA
* *
3270768 CGCTTTTTCAGAAACGCCGCTAAAGCCTCTAGCATTAGCGA
1 CGCTTTTTCAAAAACGCCGCTAAAGCCCCTAGCATTAGCGA
*
3270809 CGCTTTTTCAAAAACGCCGCTAAAGCCACTAGCATTAGCGA
1 CGCTTTTTCAAAAACGCCGCTAAAGCCCCTAGCATTAGCGA
* * * * *
3270850 CGCTTTTTCAAAAACGCTGCTAAATCCCCGAGAATTAGCGG
1 CGCTTTTTCAAAAACGCCGCTAAAGCCCCTAGCATTAGCGA
* * * * *
3270891 CGCTTTTTGAAAAATGCCGCCAAAGCCCCAACCATTAGCGA
1 CGCTTTTTCAAAAACGCCGCTAAAGCCCCTAGCATTAGCGA
* *
3270932 CGTTTTTTGAAAAACGCCGCTAAAGCCCC
1 CGCTTTTTCAAAAACGCCGCTAAAGCCCC
3270961 GAAAGGTCAG
Statistics
Matches: 168, Mismatches: 24, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
40 28 0.17
41 140 0.83
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (41 bp):
CGCTTTTTCAAAAACGCCGCTAAAGCCCCTAGCATTAGCGA
Found at i:3271102 original size:41 final size:39
Alignment explanation
Indices: 3271002--3271106 Score: 131
Period size: 39 Copynumber: 2.6 Consensus size: 39
3270992 GGTTTTTTGG
*
3271002 GGCATTTTTTGAAAAACTCCGCTAATGCTCATTTTTAGC
1 GGCATTTTTTGAAAAACGCCGCTAATGCTCATTTTTAGC
* *
3271041 GACGTTTTTTGAAAAACGCCGCTAATGCTCGATTTTT-GTC
1 GGCATTTTTTGAAAAACGCCGCTAATGCTC-ATTTTTAG-C
**
3271081 GGCATTTTTTGTCCAAACGCCGCTAA
1 GGCATTTTTTG-AAAAACGCCGCTAA
3271107 AAGCCTGTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
39 28 0.50
40 16 0.29
41 12 0.21
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (39 bp):
GGCATTTTTTGAAAAACGCCGCTAATGCTCATTTTTAGC
Found at i:3271277 original size:27 final size:27
Alignment explanation
Indices: 3271247--3271301 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
3271237 GGACAGTCCA
3271247 CCAACATTCTCACACATAGACAATCTG
1 CCAACATTCTCACACATAGACAATCTG
* * *
3271274 CCAACATTCTTACAGATGGACAATCTG
1 CCAACATTCTCACACATAGACAATCTG
3271301 C
1 C
3271302 AAGCCTCCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.35, C:0.31, G:0.11, T:0.24
Consensus pattern (27 bp):
CCAACATTCTCACACATAGACAATCTG
Found at i:3273472 original size:41 final size:42
Alignment explanation
Indices: 3273411--3273608 Score: 224
Period size: 41 Copynumber: 4.7 Consensus size: 42
3273401 CTATGAATGA
*
3273411 AAGG-GGTTGCTATGTGCTGATTCC-CCGTATCATTGATTAT
1 AAGGTGGTTGCTAAGTGCTGATTCCACCGTATCATTGATTAT
* *
3273451 AAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTGT
1 AAGGTGGTTGCTAAGTGCTGATTCCACCGTATCATTGATTAT
* *
3273493 GAAAGG-GGTTGCTATGTGCTGATTAC-CCGTATCATTGATTAT
1 --AAGGTGGTTGCTAAGTGCTGATTCCACCGTATCATTGATTAT
* * * **
3273535 AAGGTGGTTGCTAAGTGCTCATTCCACCGGGATCCTTTGAACAT
1 AAGGTGGTTGCTAAGTGCTGATTCCACC-GTAT-CATTGATTAT
* *
3273579 GAGGTGGTTGTTAAGTGCTGATTCCACCGT
1 AAGGTGGTTGCTAAGTGCTGATTCCACCGT
3273609 GTAACGGTTA
Statistics
Matches: 132, Mismatches: 18, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
40 8 0.06
41 36 0.27
42 30 0.23
43 22 0.17
44 36 0.27
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.34
Consensus pattern (42 bp):
AAGGTGGTTGCTAAGTGCTGATTCCACCGTATCATTGATTAT
Found at i:3273549 original size:84 final size:84
Alignment explanation
Indices: 3273408--3273563 Score: 294
Period size: 84 Copynumber: 1.9 Consensus size: 84
3273398 ATTCTATGAA
* *
3273408 TGAAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGAT
1 TGAAAGGGGTTGCTATGTGCTGATTACCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTCAT
3273473 TCCACCGTATCCTTGATTG
66 TCCACCGTATCCTTGATTG
3273492 TGAAAGGGGTTGCTATGTGCTGATTACCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTCAT
1 TGAAAGGGGTTGCTATGTGCTGATTACCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTCAT
3273557 TCCACCG
66 TCCACCG
3273564 GGATCCTTTG
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 70 1.00
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (84 bp):
TGAAAGGGGTTGCTATGTGCTGATTACCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTCAT
TCCACCGTATCCTTGATTG
Found at i:3279875 original size:12 final size:12
Alignment explanation
Indices: 3279839--3279876 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
3279829 CGAGCAAACT
3279839 AATAAGAAGATA
1 AATAAGAAGATA
*
3279851 AAT--GAAAATA
1 AATAAGAAGATA
3279861 AATAAGAAGATA
1 AATAAGAAGATA
3279873 AATA
1 AATA
3279877 GATTATAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 9 0.41
12 13 0.59
ACGTcount: A:0.68, C:0.00, G:0.13, T:0.18
Consensus pattern (12 bp):
AATAAGAAGATA
Found at i:3279946 original size:6 final size:6
Alignment explanation
Indices: 3279935--3280015 Score: 64
Period size: 6 Copynumber: 14.0 Consensus size: 6
3279925 GAAAGTTCAG
* * *
3279935 AATAAA AAT-AA AAT-AA AATAAG ACTCACA AAT-AA AATAAA AATACAA
1 AATAAA AATAAA AATAAA AATAAA AAT-AAA AATAAA AATAAA AATA-AA
* *
3279982 CA-AAA AATAAA AATAAA AAT-AA AATTAA AATAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
3280016 TAAACAAAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
5 22 0.37
6 32 0.53
7 6 0.10
ACGTcount: A:0.75, C:0.06, G:0.01, T:0.17
Consensus pattern (6 bp):
AATAAA
Found at i:3279988 original size:18 final size:17
Alignment explanation
Indices: 3279935--3280015 Score: 85
Period size: 18 Copynumber: 4.7 Consensus size: 17
3279925 GAAAGTTCAG
3279935 AATAAAAAT-AAAATAA
1 AATAAAAATAAAAATAA
* * *
3279951 AATAAGACTCACAAATAA
1 AATAAAAAT-AAAAATAA
3279969 AATAAAAATACAACAA-AA
1 AATAAAAATA-AA-AATAA
3279987 AATAAAAATAAAAATAA
1 AATAAAAATAAAAATAA
*
3280004 AATTAAAATAAA
1 AATAAAAATAAA
3280016 TAAACAAAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
16 9 0.17
17 16 0.30
18 26 0.49
19 2 0.04
ACGTcount: A:0.75, C:0.06, G:0.01, T:0.17
Consensus pattern (17 bp):
AATAAAAATAAAAATAA
Found at i:3279989 original size:23 final size:24
Alignment explanation
Indices: 3279938--3280003 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
3279928 AGTTCAGAAT
*
3279938 AAAAATAAAAT-AAAATAAGACTC
1 AAAAATAAAATAAAAATAAGACTA
*
3279961 ACAAATAAAATAAAAATACA-AC-A
1 AAAAATAAAATAAAAATA-AGACTA
3279984 AAAAATAAAAATAAAAATAA
1 AAAAAT-AAAATAAAAATAA
3280004 AATTAAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
23 16 0.43
24 20 0.54
25 1 0.03
ACGTcount: A:0.76, C:0.08, G:0.02, T:0.15
Consensus pattern (24 bp):
AAAAATAAAATAAAAATAAGACTA
Found at i:3280797 original size:14 final size:15
Alignment explanation
Indices: 3280767--3280802 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
3280757 AAAAGTAACA
3280767 ATAATAAAAATATAT
1 ATAATAAAAATATAT
*
3280782 ATAATAAAACTA-AT
1 ATAATAAAAATATAT
3280796 ATAATAA
1 ATAATAA
3280803 TAAACAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (15 bp):
ATAATAAAAATATAT
Found at i:3280807 original size:16 final size:15
Alignment explanation
Indices: 3280766--3280809 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 15
3280756 TAAAAGTAAC
3280766 AATAATAAA-AATAT
1 AATAATAAACAATAT
3280780 ATATAATAAAACTAATAT
1 A-ATAAT-AAAC-AATAT
3280798 AATAATAAACAA
1 AATAATAAACAA
3280810 ATATTCAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 1 0.04
15 7 0.27
16 7 0.27
17 5 0.19
18 6 0.23
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (15 bp):
AATAATAAACAATAT
Found at i:3280812 original size:16 final size:16
Alignment explanation
Indices: 3280766--3280813 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
3280756 TAAAAGTAAC
3280766 AATAAT-AA-AAATAT
1 AATAATAAACAAATAT
*
3280780 ATATAATAAAACTAATAT
1 A-ATAAT-AAACAAATAT
3280798 AATAATAAACAAATAT
1 AATAATAAACAAATAT
3280814 TCAAGGGGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
14 1 0.04
15 5 0.18
16 9 0.32
17 7 0.25
18 6 0.21
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (16 bp):
AATAATAAACAAATAT
Found at i:3281149 original size:11 final size:11
Alignment explanation
Indices: 3281133--3281172 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
3281123 TGAATGGAAA
3281133 TTTTTTAAAAT
1 TTTTTTAAAAT
*
3281144 TTTTTT-AATT
1 TTTTTTAAAAT
*
3281154 TTTTTTCAAAT
1 TTTTTTAAAAT
3281165 TTTTTTAA
1 TTTTTTAA
3281173 TAACATAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTTTTAAAAT
Found at i:3281157 original size:21 final size:21
Alignment explanation
Indices: 3281133--3281173 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
3281123 TGAATGGAAA
3281133 TTTTTTAAAATTTTTTTAATT
1 TTTTTTAAAATTTTTTTAATT
*
3281154 TTTTTTCAAATTTTTTTAAT
1 TTTTTTAAAATTTTTTTAAT
3281174 AACATAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTTTAAAATTTTTTTAATT
Found at i:3289300 original size:2 final size:2
Alignment explanation
Indices: 3289288--3289318 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3289278 TTTTGCACCT
*
3289288 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3289319 GAATACACGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3289649 original size:51 final size:53
Alignment explanation
Indices: 3289540--3289640 Score: 152
Period size: 51 Copynumber: 1.9 Consensus size: 53
3289530 GAAGACTATG
* * * *
3289540 CCAAAGAGGAGTGACGTGTTTTATGCGTGGTGTTTACTTGGCAAAGATTGAGA
1 CCAAAGAGGAGTGAAGCGTTTTATGCATGGTGTTCACTTGGCAAAGATTGAGA
3289593 CCAAAGAGG-GTGAAGCG-TTTATGCATGGTGTTCACTTGGCAAAGATTG
1 CCAAAGAGGAGTGAAGCGTTTTATGCATGGTGTTCACTTGGCAAAGATTG
3289641 GTAGCAAAGC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 29 0.66
52 6 0.14
53 9 0.20
ACGTcount: A:0.27, C:0.13, G:0.32, T:0.29
Consensus pattern (53 bp):
CCAAAGAGGAGTGAAGCGTTTTATGCATGGTGTTCACTTGGCAAAGATTGAGA
Found at i:3290995 original size:51 final size:53
Alignment explanation
Indices: 3290886--3290986 Score: 152
Period size: 51 Copynumber: 1.9 Consensus size: 53
3290876 GAAGACTATG
* * * *
3290886 CCAAAGAGGAGTGACGTGTTTTATGCGTGGTGTTTACTTGGCAAAGATTGAGA
1 CCAAAGAGGAGTGAAGCGTTTTATGCATGGTGTTCACTTGGCAAAGATTGAGA
3290939 CCAAAGAGG-GTGAAGCG-TTTATGCATGGTGTTCACTTGGCAAAGATTG
1 CCAAAGAGGAGTGAAGCGTTTTATGCATGGTGTTCACTTGGCAAAGATTG
3290987 GTAGCAAAGC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 29 0.66
52 6 0.14
53 9 0.20
ACGTcount: A:0.27, C:0.13, G:0.32, T:0.29
Consensus pattern (53 bp):
CCAAAGAGGAGTGAAGCGTTTTATGCATGGTGTTCACTTGGCAAAGATTGAGA
Found at i:3292262 original size:10 final size:10
Alignment explanation
Indices: 3292247--3292271 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3292237 AAAATTATTA
3292247 TTTTAGAAAT
1 TTTTAGAAAT
3292257 TTTTAGAAAT
1 TTTTAGAAAT
3292267 TTTTA
1 TTTTA
3292272 ACTTTTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (10 bp):
TTTTAGAAAT
Found at i:3292350 original size:16 final size:17
Alignment explanation
Indices: 3292288--3292350 Score: 56
Period size: 19 Copynumber: 3.6 Consensus size: 17
3292278 TATACTTTAG
* *
3292288 AATTTTTATTTTGTTTTA
1 AATTTTTATATT-TTGTA
3292306 GAATTTTTATAATTTTGTA
1 -AATTTTTAT-ATTTTGTA
* *
3292325 AATATATATATTTTG-A
1 AATTTTTATATTTTGTA
3292341 AATTTTTATA
1 AATTTTTATA
3292351 AATATTTGGA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
16 9 0.24
17 6 0.16
18 7 0.19
19 13 0.35
20 2 0.05
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.60
Consensus pattern (17 bp):
AATTTTTATATTTTGTA
Found at i:3292363 original size:19 final size:20
Alignment explanation
Indices: 3292336--3292402 Score: 63
Period size: 19 Copynumber: 3.5 Consensus size: 20
3292326 ATATATATAT
*
3292336 TTTGAAATTTTTATAAA-TA
1 TTTGGAATTTTTATAAATTA
3292355 TTTGGAA-TTTTA-AAATTTA
1 TTTGGAATTTTTATAAA-TTA
*
3292374 TTT-TAATTTTT-TAAATTA
1 TTTGGAATTTTTATAAATTA
*
3292392 TTTTGAATTTT
1 TTTGGAATTTT
3292403 CTTGTAAAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
17 3 0.08
18 13 0.32
19 24 0.60
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (20 bp):
TTTGGAATTTTTATAAATTA
Found at i:3293190 original size:14 final size:14
Alignment explanation
Indices: 3293171--3293197 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3293161 ATAGTAATAA
3293171 TTTTATTTATATTC
1 TTTTATTTATATTC
3293185 TTTTATTTATATT
1 TTTTATTTATATT
3293198 ATTAAATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTATTTATATTC
Found at i:3301370 original size:2 final size:2
Alignment explanation
Indices: 3301363--3301388 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3301353 CTAAGTCTTA
3301363 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3301389 GTCATAGTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3301783 original size:41 final size:41
Alignment explanation
Indices: 3301721--3301831 Score: 170
Period size: 41 Copynumber: 2.7 Consensus size: 41
3301711 TTCTAACCTT
*
3301721 TCGGGGCTTTAGTGGCGTTTTT-AAACAAGCGCCGCTAATGC
1 TCGGGGCTTTAGCGGCGTTTTTGAAA-AAGCGCCGCTAATGC
* *
3301762 TCGGGGCTTTAGCGGCTTTTTTGAAAAAGCGCTGCTAATGC
1 TCGGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
*
3301803 TCGGGGCTTTAGCAGCGTTTTTGAAAAAG
1 TCGGGGCTTTAGCGGCGTTTTTGAAAAAG
3301832 TGCCACAAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
41 61 0.95
42 3 0.05
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.31
Consensus pattern (41 bp):
TCGGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
Found at i:3302192 original size:14 final size:15
Alignment explanation
Indices: 3302164--3302196 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
3302154 AAGGTTTATA
3302164 GATTATGGAATTAGG
1 GATTATGGAATTAGG
3302179 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
3302193 GATT
1 GATT
3302197 CTAGTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:3302308 original size:7 final size:7
Alignment explanation
Indices: 3302296--3302335 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
3302286 TAAATAAGGT
*
3302296 TTAGGGG
1 TTAGGGA
3302303 TTAGGGA
1 TTAGGGA
3302310 TTAGGGA
1 TTAGGGA
3302317 TTAGGGA
1 TTAGGGA
*
3302324 TTCGGG-
1 TTAGGGA
3302330 TTAGGG
1 TTAGGG
3302336 TTTAAGGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
6 5 0.17
7 25 0.83
ACGTcount: A:0.20, C:0.03, G:0.47, T:0.30
Consensus pattern (7 bp):
TTAGGGA
Found at i:3302409 original size:7 final size:7
Alignment explanation
Indices: 3302386--3302465 Score: 70
Period size: 7 Copynumber: 11.4 Consensus size: 7
3302376 TAAATAAGGT
3302386 TTAGGGG
1 TTAGGGG
**
3302393 TTAGTAG
1 TTAGGGG
3302400 TTAGGGG
1 TTAGGGG
*
3302407 TTATGGG
1 TTAGGGG
**
3302414 TTTTGGG
1 TTAGGGG
3302421 TTAGGGG
1 TTAGGGG
* *
3302428 TTTGTGG
1 TTAGGGG
3302435 TTAGGGG
1 TTAGGGG
*
3302442 TTAGAGG
1 TTAGGGG
*
3302449 TTAGAGG
1 TTAGGGG
*
3302456 TTAGAGG
1 TTAGGGG
3302463 TTA
1 TTA
3302466 AGAGTTAGTG
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 60 1.00
ACGTcount: A:0.17, C:0.00, G:0.45, T:0.38
Consensus pattern (7 bp):
TTAGGGG
Found at i:3302472 original size:21 final size:21
Alignment explanation
Indices: 3302419--3302473 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
3302409 ATGGGTTTTG
* * * *
3302419 GGTTAGGGGTTTGTGGTTAGG
1 GGTTAGAGGTTAGAGGTTAGA
3302440 GGTTAGAGGTTAGAGGTTAGA
1 GGTTAGAGGTTAGAGGTTAGA
3302461 GGTTA-AGAGTTAG
1 GGTTAGAG-GTTAG
3302474 TGATTTAGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 2 0.07
21 27 0.93
ACGTcount: A:0.22, C:0.00, G:0.45, T:0.33
Consensus pattern (21 bp):
GGTTAGAGGTTAGAGGTTAGA
Found at i:3302746 original size:46 final size:46
Alignment explanation
Indices: 3302694--3302787 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
3302684 TTCTTATATA
*
3302694 ATTGTAAAAGAGATAATATTAATTTTAATATATTAAAATTATGATT
1 ATTGTAAAAGAGATAATATTAATTTTAATATAATAAAATTATGATT
*
3302740 ATTGTAAAAGAGATAATATTAATTTTAATATAATAAAATTATTATT
1 ATTGTAAAAGAGATAATATTAATTTTAATATAATAAAATTATGATT
3302786 AT
1 AT
3302788 AGTTTAAATT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (46 bp):
ATTGTAAAAGAGATAATATTAATTTTAATATAATAAAATTATGATT
Found at i:3302775 original size:20 final size:20
Alignment explanation
Indices: 3302706--3302780 Score: 51
Period size: 20 Copynumber: 3.5 Consensus size: 20
3302696 TGTAAAAGAG
*
3302706 ATAATATTAATTTTAATATA
1 ATAAAATTAATTTTAATATA
* * *
3302726 TTAAAATTATGATTATTGTAAAAGA
1 ATAAAATTA--A-T-TT-TAATATA
*
3302751 GATAATATTAATTTTAATATA
1 -ATAAAATTAATTTTAATATA
3302772 ATAAAATTA
1 ATAAAATTA
3302781 TTATTATAGT
Statistics
Matches: 40, Mismatches: 9, Indels: 12
0.66 0.15 0.20
Matches are distributed among these distances:
20 15 0.38
21 5 0.12
22 3 0.08
23 2 0.05
24 3 0.08
25 5 0.12
26 7 0.17
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (20 bp):
ATAAAATTAATTTTAATATA
Found at i:3305798 original size:17 final size:17
Alignment explanation
Indices: 3305776--3305814 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
3305766 TGAAACCATG
* *
3305776 AAAAAAGAAAGGAAAAC
1 AAAAAAAAAAAGAAAAC
3305793 AAAAAAAAAAAGAAAAC
1 AAAAAAAAAAAGAAAAC
3305810 AAAAA
1 AAAAA
3305815 TAATATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAGAAAAC
Found at i:3308390 original size:3 final size:3
Alignment explanation
Indices: 3308384--3308409 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3308374 AACATCCATT
3308384 ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC AT
3308410 TTATAACAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:3309723 original size:41 final size:41
Alignment explanation
Indices: 3309678--3309872 Score: 275
Period size: 41 Copynumber: 4.8 Consensus size: 41
3309668 TGATCGGGCT
* *
3309678 TTTAGCGGCGATTTTGAAAAAGCGCCGCTAATGCTCGGAGC
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAGC
* ** *
3309719 TTTAGTGGCGTTTTTGGGAAAGCACCGCTAATGCTCAGAGC
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAGC
* * *
3309760 TTTAGCAGCGTTTTTGAGAAAGCGCCGGTAATGCTCAG-GC
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAGC
* *
3309800 TTTTAGCGACGTTTTTGAAAAAGTGCCGCTAATGCTCAGAGC
1 -TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAGC
3309842 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAA
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAA
3309873 AACATTTTAT
Statistics
Matches: 134, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
40 2 0.01
41 130 0.97
42 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAGC
Found at i:3310421 original size:7 final size:7
Alignment explanation
Indices: 3310411--3310454 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
3310401 ATTTAGGGAC
*
3310411 TAGGGGT
1 TAGGGTT
*
3310418 TAGGGAT
1 TAGGGTT
*
3310425 TCGGG-T
1 TAGGGTT
3310431 TAGGGTT
1 TAGGGTT
3310438 TAGGGTT
1 TAGGGTT
3310445 TAGGGTT
1 TAGGGTT
3310452 TAG
1 TAG
3310455 AGTAATTAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
6 5 0.15
7 28 0.85
ACGTcount: A:0.16, C:0.02, G:0.45, T:0.36
Consensus pattern (7 bp):
TAGGGTT
Found at i:3310432 original size:13 final size:13
Alignment explanation
Indices: 3310403--3310454 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
3310393 TAAATAAGAT
*
3310403 TTAGGGACTAGGGG
1 TTAGGGATTA-GGG
*
3310417 TTAGGGATTCGGG
1 TTAGGGATTAGGG
*
3310430 TTAGGGTTTAGGG
1 TTAGGGATTAGGG
*
3310443 TTTAGGGTTTAG
1 -TTAGGGATTAG
3310455 AGTAATTAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
13 14 0.42
14 19 0.58
ACGTcount: A:0.17, C:0.04, G:0.44, T:0.35
Consensus pattern (13 bp):
TTAGGGATTAGGG
Found at i:3310450 original size:20 final size:20
Alignment explanation
Indices: 3310411--3310451 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3310401 ATTTAGGGAC
*
3310411 TAGGGGTTAGGGATTCGGGT
1 TAGGGGTTAGGGATTAGGGT
* *
3310431 TAGGGTTTAGGGTTTAGGGT
1 TAGGGGTTAGGGATTAGGGT
3310451 T
1 T
3310452 TAGAGTAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.02, G:0.46, T:0.37
Consensus pattern (20 bp):
TAGGGGTTAGGGATTAGGGT
Found at i:3310641 original size:7 final size:7
Alignment explanation
Indices: 3310629--3310701 Score: 80
Period size: 7 Copynumber: 10.6 Consensus size: 7
3310619 ATTGTAAAAG
*
3310629 AGGGGTT
1 AGGGATT
*
3310636 AGGGGTT
1 AGGGATT
3310643 AGAGG-TT
1 AG-GGATT
*
3310650 AAGGATT
1 AGGGATT
3310657 AGGGATT
1 AGGGATT
3310664 AGGGATT
1 AGGGATT
3310671 AGGGATT
1 AGGGATT
3310678 A-GGATT
1 AGGGATT
3310684 AGGGATT
1 AGGGATT
3310691 AGAGG-TT
1 AG-GGATT
3310698 AGGG
1 AGGG
3310702 GCTATGGATG
Statistics
Matches: 60, Mismatches: 2, Indels: 9
0.85 0.03 0.13
Matches are distributed among these distances:
6 10 0.17
7 46 0.77
8 4 0.07
ACGTcount: A:0.27, C:0.00, G:0.45, T:0.27
Consensus pattern (7 bp):
AGGGATT
Found at i:3310684 original size:13 final size:13
Alignment explanation
Indices: 3310651--3310692 Score: 75
Period size: 13 Copynumber: 3.2 Consensus size: 13
3310641 TTAGAGGTTA
3310651 AGGATTAGGGATT
1 AGGATTAGGGATT
3310664 AGGGATTAGGGATT
1 A-GGATTAGGGATT
3310678 AGGATTAGGGATT
1 AGGATTAGGGATT
3310691 AG
1 AG
3310693 AGGTTAGGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 15 0.54
14 13 0.46
ACGTcount: A:0.31, C:0.00, G:0.40, T:0.29
Consensus pattern (13 bp):
AGGATTAGGGATT
Found at i:3310688 original size:27 final size:26
Alignment explanation
Indices: 3310629--3310701 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 26
3310619 ATTGTAAAAG
*
3310629 AGGGGTTAGGGGTTAGAGGTTAAGGATT
1 AGGGATTA-GGGTTAG-GGTTAAGGATT
3310657 AGGGATTAGGGATTAGGGATT-AGGATT
1 AGGGATTAGGG-TTAGGG-TTAAGGATT
3310684 AGGGATTAGAGGTTAGGG
1 AGGGATTAG-GGTTAGGG
3310702 GCTATGGATG
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
27 26 0.63
28 15 0.37
ACGTcount: A:0.27, C:0.00, G:0.45, T:0.27
Consensus pattern (26 bp):
AGGGATTAGGGTTAGGGTTAAGGATT
Found at i:3310700 original size:20 final size:20
Alignment explanation
Indices: 3310652--3310692 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
3310642 TAGAGGTTAA
3310652 GGATTAGGGATTAGGGATTAG
1 GGATTA-GGATTAGGGATTAG
3310673 GGATTAGGATTAGGGATTAG
1 GGATTAGGATTAGGGATTAG
3310693 AGGTTAGGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.29, C:0.00, G:0.41, T:0.29
Consensus pattern (20 bp):
GGATTAGGATTAGGGATTAG
Found at i:3315111 original size:20 final size:20
Alignment explanation
Indices: 3315078--3315162 Score: 68
Period size: 21 Copynumber: 4.2 Consensus size: 20
3315068 TTGAGTTAAT
3315078 TTTTTTTGATAATTATGT-TTA
1 TTTTTTT-A-AATTATGTATTA
* *
3315099 TTTTCTTTAAATTAAGTGTTA
1 TTTT-TTTAAATTATGTATTA
*
3315120 TTTTTTTAATTTCATGTATTA
1 TTTTTTTAAATT-ATGTATTA
* *
3315141 TTTATTTAATTTAT-TATT-
1 TTTTTTTAAATTATGTATTA
3315159 TTTT
1 TTTT
3315163 ACATATACAT
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
18 3 0.05
19 4 0.07
20 16 0.29
21 29 0.53
22 3 0.05
ACGTcount: A:0.25, C:0.02, G:0.06, T:0.67
Consensus pattern (20 bp):
TTTTTTTAAATTATGTATTA
Found at i:3315120 original size:21 final size:19
Alignment explanation
Indices: 3315078--3315128 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
3315068 TTGAGTTAAT
*
3315078 TTTTTTTGATAATTATGTTTA
1 TTTTTTT-A-AATTAAGTTTA
3315099 TTTTCTTTAAATTAAGTGTTA
1 TTTT-TTTAAATTAAGT-TTA
3315120 TTTTTTTAA
1 TTTTTTTAA
3315129 TTTCATGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 12 0.44
21 12 0.44
22 3 0.11
ACGTcount: A:0.25, C:0.02, G:0.08, T:0.65
Consensus pattern (19 bp):
TTTTTTTAAATTAAGTTTA
Found at i:3316075 original size:30 final size:30
Alignment explanation
Indices: 3316041--3316100 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
3316031 CCTTTCTCTT
*
3316041 GTGCAATGAATATGTGGATTTTATGAACTA
1 GTGCAATGAAGATGTGGATTTTATGAACTA
3316071 GTGCAATGAAGATGTGGATTTTATGAACTA
1 GTGCAATGAAGATGTGGATTTTATGAACTA
3316101 ATCATGTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.33, C:0.07, G:0.25, T:0.35
Consensus pattern (30 bp):
GTGCAATGAAGATGTGGATTTTATGAACTA
Found at i:3316411 original size:43 final size:43
Alignment explanation
Indices: 3316345--3316478 Score: 196
Period size: 43 Copynumber: 3.1 Consensus size: 43
3316335 AGAAAATTTA
* **
3316345 CGTTAGTGACAAAAGTTCCGCTAAAGGTCATGTTCTTTAGCAG
1 CGTTTGTGACAAAAGCCCCGCTAAAGGTCATGTTCTTTAGCAG
* *
3316388 CGTTTGTGACAAAAGCGCCGCTAAAGGTCATGTTCTTTAACAG
1 CGTTTGTGACAAAAGCCCCGCTAAAGGTCATGTTCTTTAGCAG
* * *
3316431 CGTTTGTGATAAAAGCCCCGCTAAAGGTCATGATCTTTAGCGG
1 CGTTTGTGACAAAAGCCCCGCTAAAGGTCATGTTCTTTAGCAG
3316474 CGTTT
1 CGTTT
3316479 TTTACATAAA
Statistics
Matches: 82, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 82 1.00
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (43 bp):
CGTTTGTGACAAAAGCCCCGCTAAAGGTCATGTTCTTTAGCAG
Found at i:3317621 original size:122 final size:121
Alignment explanation
Indices: 3317467--3317707 Score: 383
Period size: 122 Copynumber: 2.0 Consensus size: 121
3317457 TAGTTTAAAG
* * *
3317467 TTTAAATTTCAAAAATAAAATAAAATAAAATATTTATGATAGAAATAAATATTATTTAATTAAAA
1 TTTAAATTTCAAAAACAAAACAAAATAAAATATTTATCATAGAAATAAATATTATTTAATTAAAA
* * *
3317532 TATTTTTTAAAAAGTTATGTTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAAAAGTT
66 TATTTTTT-AAAAGTCATGTTTTTAGCGGCGTTTGTCAAAAAGCGCCGCTAAAAGTT
* * *
3317589 TTTAAATTTCAAAAACAAAACATAATATAATATTTATCATAGAAATAAATATTTTTTAATTAAAA
1 TTTAAATTTCAAAAACAAAACAAAATAAAATATTTATCATAGAAATAAATATTATTTAATTAAAA
*
3317654 TATTTTTTAAAAGTCATGTTTTTAGCGGTGTTTGTCAAAAAGCGCCGCTAAAAG
66 TATTTTTTAAAAGTCATGTTTTTAGCGGCGTTTGTCAAAAAGCGCCGCTAAAAG
3317708 CCATCTTTAT
Statistics
Matches: 109, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
121 42 0.39
122 67 0.61
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.38
Consensus pattern (121 bp):
TTTAAATTTCAAAAACAAAACAAAATAAAATATTTATCATAGAAATAAATATTATTTAATTAAAA
TATTTTTTAAAAGTCATGTTTTTAGCGGCGTTTGTCAAAAAGCGCCGCTAAAAGTT
Found at i:3318137 original size:2 final size:2
Alignment explanation
Indices: 3318130--3318180 Score: 77
Period size: 2 Copynumber: 25.5 Consensus size: 2
3318120 AAAACCCAAC
*
3318130 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT CAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
3318173 A- AT AT AT A
1 AT AT AT AT A
3318181 CANNNNNNNN
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 1 0.02
2 42 0.93
3 2 0.04
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3324039 original size:19 final size:20
Alignment explanation
Indices: 3324011--3324048 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
3324001 AATTTATCCA
*
3324011 TTTTATTATTTTTATTTTAT
1 TTTTATTATTTTCATTTTAT
3324031 TTTTA-TATTTTCATTTTA
1 TTTTATTATTTTCATTTTA
3324049 GTTTAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTATTATTTTCATTTTAT
Found at i:3327107 original size:60 final size:60
Alignment explanation
Indices: 3326995--3327112 Score: 182
Period size: 60 Copynumber: 2.0 Consensus size: 60
3326985 CTAGCGACAT
* * * * * *
3326995 GGCCGTGTGAATATTGGAGTTAATTTTTGAATTTTACTTATAAGTTATTGAGTTACACAC
1 GGCCATGTGAATATTGGAGTTAATTTTTGAACTTTAATTACAAGTCAATGAGTTACACAC
3327055 GGCCATGTGAATATTGGAGTTAATTTTTGAACTTTAATTACAAGTCAATGAGTTACAC
1 GGCCATGTGAATATTGGAGTTAATTTTTGAACTTTAATTACAAGTCAATGAGTTACAC
3327113 GGGCCATAGA
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (60 bp):
GGCCATGTGAATATTGGAGTTAATTTTTGAACTTTAATTACAAGTCAATGAGTTACACAC
Found at i:3327724 original size:20 final size:21
Alignment explanation
Indices: 3327685--3327725 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
3327675 ACATTTCTTC
*
3327685 CCTCACAACCCCTTCTCCCCT
1 CCTCACAACCCCTTCCCCCCT
*
3327706 CCTCAC-ACCTCTTCCCCCCT
1 CCTCACAACCCCTTCCCCCCT
3327726 TTCCCCAGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.12, C:0.63, G:0.00, T:0.24
Consensus pattern (21 bp):
CCTCACAACCCCTTCCCCCCT
Found at i:3329038 original size:85 final size:85
Alignment explanation
Indices: 3328925--3329302 Score: 423
Period size: 85 Copynumber: 4.4 Consensus size: 85
3328915 CGCTTATAGG
* * *
3328925 AAAATACGCCGCTACAGAACATGTTCTTTAGCGGCGCTAATAAAACAAACG-CAGCTAAAGAACA
1 AAAAT-CGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAGAAAACAAACGTC-GCTAAAGAACA
3328989 TGTTCTTCAGCGGCGCTTGGAA
64 TGTTCTTCAGCGGCGCTTGGAA
* * *
3329011 AAAATCGCCACTAAAGATCATGTTCTTTAGCGGCGCTAAGAAAATAAACGCCGCTAAAGAACATG
1 AAAATCGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAGAAAACAAACGTCGCTAAAGAACATG
* *
3329076 TTCTTTAGCGGCGCTAAGGAA
66 TTCTTCAGCGGCGCT-TGGAA
* * * * *
3329097 ATAAA-CGCCGCTAAAGAACATATTCTTTAGCGGCACTTAGTAAAAC--ACGTCGCTAAAGATCA
1 A-AAATCGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAG-AAAACAAACGTCGCTAAAGAACA
3329159 TGTTCTTCAGCGGCGCTTGGAA
64 TGTTCTTCAGCGGCGCTTGGAA
* * * *
3329181 AAAATCGCCACTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAGA-AAACGTCGCTAAA-AATAA
1 AAAATCGCCGCTAAAGATCATGTTCTTTAGCGGCGC-TAAGAAAACAAACGTCGCTAAAGAA-CA
*
3329244 TGTTCTAT-AGCGGCGCTTGGTGA
64 TGTTCT-TCAGCGGCGCTTGG-AA
* *
3329267 AAAA-CGCCGCTAAA-ATTAGTGTTCTTTAGTGGCGCT
1 AAAATCGCCGCTAAAGATCA-TGTTCTTTAGCGGCGCT
3329303 TATTTCAAAA
Statistics
Matches: 250, Mismatches: 30, Indels: 26
0.82 0.10 0.08
Matches are distributed among these distances:
83 3 0.01
84 40 0.16
85 153 0.61
86 47 0.19
87 7 0.03
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.24
Consensus pattern (85 bp):
AAAATCGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAGAAAACAAACGTCGCTAAAGAACATG
TTCTTCAGCGGCGCTTGGAA
Found at i:3329043 original size:42 final size:41
Alignment explanation
Indices: 3328906--3329303 Score: 386
Period size: 43 Copynumber: 9.3 Consensus size: 41
3328896 ACGTCGCTAA
* * *
3328906 CTTTAGCGGCGCTTATAGGAAAATACGCCGCTACAGAACATGTT
1 CTTTAGCGGCGC-T-T-GGAAAAAACGCCGCTAAAGATCATGTT
* * *
3328950 CTTTAGCGGCGCTAAT-AAAACAAACGCAGCTAAAGAACATGTT
1 CTTTAGCGGCGCT--TGGAAA-AAACGCCGCTAAAGATCATGTT
* *
3328993 CTTCAGCGGCGCTTGGAAAAAATCGCCACTAAAGATCATGTT
1 CTTTAGCGGCGCTTGGAAAAAA-CGCCGCTAAAGATCATGTT
* * *
3329035 CTTTAGCGGCGCTAAGAAAATAAACGCCGCTAAAGAACATGTT
1 CTTTAGCGGCGCT-TGGAAA-AAACGCCGCTAAAGATCATGTT
* * *
3329078 CTTTAGCGGCGCTAAGGAAATAAACGCCGCTAAAGAACATATT
1 CTTTAGCGGCGCT-TGGAAA-AAACGCCGCTAAAGATCATGTT
* * * *
3329121 CTTTAGCGGCACTTAGTAAAACACGTCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTT-GGAAAAAACGCCGCTAAAGATCATGTT
* *
3329163 CTTCAGCGGCGCTTGGAAAAAATCGCCACTAAAGATCATGTT
1 CTTTAGCGGCGCTTGGAAAAAA-CGCCGCTAAAGATCATGTT
* * *
3329205 CTTTAGCGGCGCTTAGGAAGAAAACGTCGCTAAAAATAATGTT
1 CTTTAGCGGCGCTT-GGAA-AAAACGCCGCTAAAGATCATGTT
* * *
3329248 CTATAGCGGCGCTTGGTGAAAAACGCCGCTAAA-ATTAGTGTT
1 CTTTAGCGGCGCTTGG-AAAAAACGCCGCTAAAGATCA-TGTT
*
3329290 CTTTAGTGGCGCTT
1 CTTTAGCGGCGCTT
3329304 ATTTCAAAAA
Statistics
Matches: 302, Mismatches: 40, Indels: 26
0.82 0.11 0.07
Matches are distributed among these distances:
41 13 0.04
42 125 0.41
43 143 0.47
44 21 0.07
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (41 bp):
CTTTAGCGGCGCTTGGAAAAAACGCCGCTAAAGATCATGTT
Found at i:3329176 original size:170 final size:170
Alignment explanation
Indices: 3328906--3329280 Score: 521
Period size: 170 Copynumber: 2.2 Consensus size: 170
3328896 ACGTCGCTAA
* * * *
3328906 CTTTAGCGGCGCTTATAGGAAAATACGCCGCTACAGAACATGTTCTTTAGCGGCGCTAATAAAAC
1 CTTTAGCGGCGC-TATAGGAAAAAACGCCGCTAAAGAACATATTCTTTAGCGGCACTAATAAAAC
3328971 AAACGCAGCTAAAGAACATGTTCTTCAGCGGCGCTTGGAAAAAATCGCCACTAAAGATCATGTTC
65 -AACGCAGCTAAAGAACATGTTCTTCAGCGGCGCTTGGAAAAAATCGCCACTAAAGATCATGTTC
*
3329036 TTTAGCGGCGC-TAAGAAAATAAACGCCGCTAAAGAA-CATGTT
129 TTTAGCGGCGCTTAAGAAAA-AAACGCCGCTAAA-AATAATGTT
*
3329078 CTTTAGCGGCGCTA-AGGAAATAAACGCCGCTAAAGAACATATTCTTTAGCGGCACTTAGTAAAA
1 CTTTAGCGGCGCTATAGGAAA-AAACGCCGCTAAAGAACATATTCTTTAGCGGCAC-TAATAAAA
*
3329142 C-ACGTC-GCTAAAGATCATGTTCTTCAGCGGCGCTTGGAAAAAATCGCCACTAAAGATCATGTT
64 CAACG-CAGCTAAAGAACATGTTCTTCAGCGGCGCTTGGAAAAAATCGCCACTAAAGATCATGTT
* * *
3329205 CTTTAGCGGCGCTTAGGAAGAAAACGTCGCTAAAAATAATGTT
128 CTTTAGCGGCGCTTAAGAAAAAAACGCCGCTAAAAATAATGTT
* *
3329248 CTATAGCGGCGCT-T-GGTGAAAAACGCCGCTAAA
1 CTTTAGCGGCGCTATAGG-AAAAAACGCCGCTAAA
3329281 ATTAGTGTTC
Statistics
Matches: 184, Mismatches: 12, Indels: 17
0.86 0.06 0.08
Matches are distributed among these distances:
169 17 0.09
170 108 0.59
171 39 0.21
172 20 0.11
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.23
Consensus pattern (170 bp):
CTTTAGCGGCGCTATAGGAAAAAACGCCGCTAAAGAACATATTCTTTAGCGGCACTAATAAAACA
ACGCAGCTAAAGAACATGTTCTTCAGCGGCGCTTGGAAAAAATCGCCACTAAAGATCATGTTCTT
TAGCGGCGCTTAAGAAAAAAACGCCGCTAAAAATAATGTT
Found at i:3329775 original size:12 final size:12
Alignment explanation
Indices: 3329736--3329775 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
3329726 TTTTGAACCT
*
3329736 CTGCTTCTATCG
1 CTGCTTCTCTCG
*
3329748 CTACTTCTCTCG
1 CTGCTTCTCTCG
*
3329760 CTGCTTCTCTCA
1 CTGCTTCTCTCG
3329772 CTGC
1 CTGC
3329776 GGCCTCTGCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.07, C:0.40, G:0.12, T:0.40
Consensus pattern (12 bp):
CTGCTTCTCTCG
Found at i:3329786 original size:21 final size:21
Alignment explanation
Indices: 3329760--3329849 Score: 108
Period size: 21 Copynumber: 4.3 Consensus size: 21
3329750 ACTTCTCTCG
*
3329760 CTGCTTCTCTCACTGCGGCCT
1 CTGCTTCTCTCGCTGCGGCCT
*
3329781 CTGCTTCTCTTGCTGCGGCCT
1 CTGCTTCTCTCGCTGCGGCCT
* * * *
3329802 CTACTTCTCTTGTTGCAGCCT
1 CTGCTTCTCTCGCTGCGGCCT
* *
3329823 CTGCTTCCCTCGCTGCCGCCT
1 CTGCTTCTCTCGCTGCGGCCT
3329844 CTGCTT
1 CTGCTT
3329850 GAAGTTGTTG
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 59 1.00
ACGTcount: A:0.03, C:0.41, G:0.19, T:0.37
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCGGCCT
Found at i:3336403 original size:16 final size:16
Alignment explanation
Indices: 3336382--3336433 Score: 68
Period size: 16 Copynumber: 3.1 Consensus size: 16
3336372 TATAAATTTA
3336382 AATTATGTAAGTTATG
1 AATTATGTAAGTTATG
3336398 AATTATGTAAGTTATG
1 AATTATGTAAGTTATG
* *
3336414 TAAATTACGTAAGTTGTG
1 --AATTATGTAAGTTATG
3336432 AA
1 AA
3336434 ATTTGAACTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 18 0.56
18 14 0.44
ACGTcount: A:0.38, C:0.02, G:0.19, T:0.40
Consensus pattern (16 bp):
AATTATGTAAGTTATG
Found at i:3336412 original size:9 final size:9
Alignment explanation
Indices: 3336384--3336428 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
3336374 TAAATTTAAA
3336384 TTATGTAAG
1 TTATGTAAG
3336393 TTATG-AA-
1 TTATGTAAG
3336400 TTATGTAAG
1 TTATGTAAG
*
3336409 TTATGTAAA
1 TTATGTAAG
*
3336418 TTACGTAAG
1 TTATGTAAG
3336427 TT
1 TT
3336429 GTGAAATTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
7 5 0.16
8 4 0.13
9 22 0.71
ACGTcount: A:0.36, C:0.02, G:0.18, T:0.44
Consensus pattern (9 bp):
TTATGTAAG
Found at i:3336527 original size:35 final size:35
Alignment explanation
Indices: 3336443--3336530 Score: 135
Period size: 34 Copynumber: 2.6 Consensus size: 35
3336433 AATTTGAACT
* *
3336443 TTAAAA-AAAATTAAATATTTAAAAATATTCGTGA
1 TTAAAATAAAATAAAATATTTAAAAAAATTCGTGA
3336477 TTAAAATAAAA-AAAATATTTAAAAAAATTCGTGA
1 TTAAAATAAAATAAAATATTTAAAAAAATTCGTGA
*
3336511 TTAACATAAAATAAAATATT
1 TTAAAATAAAATAAAATATT
3336531 AATATAACTT
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
34 37 0.76
35 12 0.24
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (35 bp):
TTAAAATAAAATAAAATATTTAAAAAAATTCGTGA
Found at i:3339457 original size:15 final size:15
Alignment explanation
Indices: 3339427--3339466 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
3339417 TCTAAACCTC
3339427 AAACCCCAAA-TCTT
1 AAACCCCAAACTCTT
3339441 AAACCCCAAACTCTT
1 AAACCCCAAACTCTT
*
3339456 AAACCCTAAAC
1 AAACCCCAAAC
3339467 CCAAAACACC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.45, C:0.38, G:0.00, T:0.17
Consensus pattern (15 bp):
AAACCCCAAACTCTT
Found at i:3340027 original size:115 final size:114
Alignment explanation
Indices: 3339786--3340534 Score: 388
Period size: 115 Copynumber: 6.6 Consensus size: 114
3339776 ATGCATGGTT
* * * * * * * *
3339786 AAGACCAAAACTGTA-CGTTTTGGTAAAGATCTTTTGCGGCGCTTATAAAAAAGTGCCGCTAATA
1 AAGACCAAAAC-GCAGCGTTTTGGTTAACATATCTTGCGGCGCTTCTAATAAAGCGCCGCTAATA
* * * *** *
3339850 ATATGATTTAGCGGCGATTTCTTGTGAACGCCACTAATTCCAGTATACATC
65 ATAT-ATTTAGCGGCGTTTTGTTGTAAACGCCACTAATGATATTATACATC
*** * * *
3339901 AAGATTTAAACGCAGCGTTTCGGTTAATATATCTTGCGGCGCTTCTAATAAAGCGCCGCTAATAG
1 AAGACCAAAACGCAGCGTTTTGGTTAACATATCTTGCGGCGCTTCTAATAAAGCGCCGCTAATAA
*
3339966 TGATATTTAGCGGTGTTTTGTTGTAAACGCCACTAATGATATTATACATC
66 T-ATATTTAGCGGCGTTTTGTTGTAAACGCCACTAATGATATTATACATC
** * * * * * * * *
3340016 AAGACCAAAACGTTGAGTTTTGGTTAAGAAATATAGCGGCGCTTCTCCA-AACGTGCCGCTAATA
1 AAGACCAAAACGCAGCGTTTTGGTTAACATATCTTGCGGCGCTTCT-AATAAAGCGCCGCTAATA
* * * ** * *
3340080 ATACTCTTTAGCGGCG-CTT-CTCCAAACGCGCCACTAATTG-TAATATACCTC
65 ATA-TATTTAGCGGCGTTTTGTTGTAAA--CGCCACTAA-TGATATTATACATC
* * * *
3340131 AATACC-AAACCCTA-CGTTTTGGTGT-GCATATCTTGCGGCGC-T-TAATTGAAAGCGCCGCGA
1 AAGACCAAAACGC-AGCGTTTTGGT-TAACATATCTTGCGGCGCTTCTAA-T-AAAGCGCCGCTA
* * *
3340191 ATACTGATATTTAGCGGCGTTTTGTTGTAACCGCCACTAATTATATTATACATC
62 ATAAT-ATATTTAGCGGCGTTTTGTTGTAAACGCCACTAATGATATTATACATC
** * * * * * * * *
3340245 AAGACCAAAACGTTGAGTTTTGGTTAAGAAATATAGCGGCGCTTCTCCA-AACGCGCCACTAATA
1 AAGACCAAAACGCAGCGTTTTGGTTAACATATCTTGCGGCGCTTCT-AATAAAGCGCCGCTAATA
* * * ** ** * *
3340309 ATACTCTTTAGCGGCG-CTT-CTACAAACGCGCCACTAATCCTAATATACCTC
65 ATA-TATTTAGCGGCGTTTTGTTGTAAA--CGCCACTAATGATATTATACATC
* * * * * * * *
3340360 AAGACC-AAACTCTGCGTTTTGGTGT-GCATATCTTGCGGTGATTCTAAAAAACCGCCGCTAATT
1 AAGACCAAAACGCAGCGTTTTGGT-TAACATATCTTGCGGCGCTTCTAATAAAGCGCCGCTAATA
* * * *
3340423 TTATACTTTAGCGGTG-TTT-TTGCCT-AATGCCAGTAACTG-TATTATACATC
65 ATATA-TTTAGCGGCGTTTTGTTG--TAAACGCCACTAA-TGATATTATACATC
* * * * * * *
3340473 GAA-ACCAAACCGCTGCGTTTTGGTTAACATTTTTTGCGGCACTTCT-ATTAAGCGCCACTAAT
1 -AAGACCAAAACGCAGCGTTTTGGTTAACATATCTTGCGGCGCTTCTAATAAAGCGCCGCTAAT
3340535 TCTAATATAC
Statistics
Matches: 468, Mismatches: 132, Indels: 70
0.70 0.20 0.10
Matches are distributed among these distances:
111 1 0.00
112 1 0.00
113 43 0.09
114 163 0.35
115 249 0.53
116 9 0.02
117 1 0.00
118 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.31
Consensus pattern (114 bp):
AAGACCAAAACGCAGCGTTTTGGTTAACATATCTTGCGGCGCTTCTAATAAAGCGCCGCTAATAA
TATATTTAGCGGCGTTTTGTTGTAAACGCCACTAATGATATTATACATC
Found at i:3340206 original size:114 final size:114
Alignment explanation
Indices: 3340051--3340397 Score: 310
Period size: 114 Copynumber: 3.0 Consensus size: 114
3340041 AAGAAATATA
* * * * * *
3340051 GCGGCGCTTCTCCAAACGTGCCGCTAATAATACTCTTTAGCGGCGCTTCTCCAAACGCGCCACTA
1 GCGGCGCTTATCCAAACGCGCCACGAATAATACTATTTAGCGGCGCTTCTACAAACGCGCCACTA
* *
3340116 ATTGTAATATACCTCAATACCAAACCCTACGTTTTGGTGTGCATATCTT
66 ATTATAATATACCTCAAGACCAAACCCTACGTTTTGGTGTGCATATCTT
** * * * * ***
3340165 GCGGCGCTTAATTGAAA-GCGCCGCGAATACTGA-TATTTAGCGGCGTTTTGTTGTAAC-CGCCA
1 GCGGCGCTT-ATCCAAACGCGCCACGAATAAT-ACTATTTAGCGGCG-CTTCTACAAACGCGCCA
* * ** * * *
3340227 CTAATTATATTATACATCAAGACCAAAACGTTGA-GTTTTGGT-TAAG-AAATATA
63 CTAATTATAATATACCTCAAGACC-AAACCCT-ACGTTTTGGTGT--GCATATCTT
* * *
3340280 GCGGCGCTTCTCCAAACGCGCCACTAATAATACTCTTTAGCGGCGCTTCTACAAACGCGCCACTA
1 GCGGCGCTTATCCAAACGCGCCACGAATAATACTATTTAGCGGCGCTTCTACAAACGCGCCACTA
** * *
3340345 ATCCTAATATACCTCAAGACCAAACTCTGCGTTTTGGTGTGCATATCTT
66 ATTATAATATACCTCAAGACCAAACCCTACGTTTTGGTGTGCATATCTT
3340394 GCGG
1 GCGG
3340398 TGATTCTAAA
Statistics
Matches: 177, Mismatches: 43, Indels: 26
0.72 0.17 0.11
Matches are distributed among these distances:
113 1 0.01
114 89 0.50
115 85 0.48
116 2 0.01
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.29
Consensus pattern (114 bp):
GCGGCGCTTATCCAAACGCGCCACGAATAATACTATTTAGCGGCGCTTCTACAAACGCGCCACTA
ATTATAATATACCTCAAGACCAAACCCTACGTTTTGGTGTGCATATCTT
Found at i:3340239 original size:229 final size:229
Alignment explanation
Indices: 3339929--3340417 Score: 793
Period size: 229 Copynumber: 2.1 Consensus size: 229
3339919 TTCGGTTAAT
* * *
3339929 ATATCTTGCGGCGCTTCTAATAAAGCGCCGCTAATAGTGATATTTAGCGGTGTTTTGTTGTAAAC
1 ATATCTTGCGGCGCTTCTAATAAAGCGCCGCGAATACTGATATTTAGCGGCGTTTTGTTGTAAAC
3339994 GCCACTAATGATATTATACATCAAGACCAAAACGTTGAGTTTTGGTTAAGAAATATAGCGGCGCT
66 GCCACTAATGATATTATACATCAAGACCAAAACGTTGAGTTTTGGTTAAGAAATATAGCGGCGCT
* * * **
3340059 TCTCCAAACGTGCCGCTAATAATACTCTTTAGCGGCGCTTCTCCAAACGCGCCACTAATTGTAAT
131 TCTCCAAACGCGCCACTAATAATACTCTTTAGCGGCGCTTCTACAAACGCGCCACTAATCCTAAT
*
3340124 ATACCTCAATACCAAACCCTACGTTTTGGTGTGC
196 ATACCTCAAGACCAAACCCTACGTTTTGGTGTGC
3340158 ATATCTTGCGGCGC-T-TAATTGAAAGCGCCGCGAATACTGATATTTAGCGGCGTTTTGTTGTAA
1 ATATCTTGCGGCGCTTCTAA-T-AAAGCGCCGCGAATACTGATATTTAGCGGCGTTTTGTTGTAA
* *
3340221 CCGCCACTAATTATATTATACATCAAGACCAAAACGTTGAGTTTTGGTTAAGAAATATAGCGGCG
64 ACGCCACTAATGATATTATACATCAAGACCAAAACGTTGAGTTTTGGTTAAGAAATATAGCGGCG
3340286 CTTCTCCAAACGCGCCACTAATAATACTCTTTAGCGGCGCTTCTACAAACGCGCCACTAATCCTA
129 CTTCTCCAAACGCGCCACTAATAATACTCTTTAGCGGCGCTTCTACAAACGCGCCACTAATCCTA
* *
3340351 ATATACCTCAAGACCAAACTCTGCGTTTTGGTGTGC
194 ATATACCTCAAGACCAAACCCTACGTTTTGGTGTGC
* * * *
3340387 ATATCTTGCGGTGATTCTAAAAAACCGCCGC
1 ATATCTTGCGGCGCTTCTAATAAAGCGCCGC
3340418 TAATTTTATA
Statistics
Matches: 239, Mismatches: 17, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
227 3 0.01
228 2 0.01
229 230 0.96
230 1 0.00
231 3 0.01
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (229 bp):
ATATCTTGCGGCGCTTCTAATAAAGCGCCGCGAATACTGATATTTAGCGGCGTTTTGTTGTAAAC
GCCACTAATGATATTATACATCAAGACCAAAACGTTGAGTTTTGGTTAAGAAATATAGCGGCGCT
TCTCCAAACGCGCCACTAATAATACTCTTTAGCGGCGCTTCTACAAACGCGCCACTAATCCTAAT
ATACCTCAAGACCAAACCCTACGTTTTGGTGTGC
Found at i:3342121 original size:44 final size:43
Alignment explanation
Indices: 3342068--3342192 Score: 144
Period size: 44 Copynumber: 2.9 Consensus size: 43
3342058 GATTATCGAA
* *
3342068 TTCAATCTGCTCCACTGCAACCTCAGGGAGATAAGA-TTGGCTTT
1 TTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-G-TTT
* ** *
3342112 TTCAGTCTGCCCCACTGTGACTTCAGGGGGATAAGACTTGTTT
1 TTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTT
* *
3342155 TCTCAGTCTGCTCCGCTGCAACTTCAGAGAGATAAGAC
1 T-TCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGAC
3342193 CTGATGTGAT
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
43 4 0.06
44 61 0.91
45 2 0.03
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (43 bp):
TTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTTT
Found at i:3342602 original size:87 final size:87
Alignment explanation
Indices: 3342488--3342814 Score: 539
Period size: 87 Copynumber: 3.8 Consensus size: 87
3342478 TTAAGGATAT
*
3342488 AAGATCTG-TCATCTTTAACCAGCTCCACTGCAACCAATGGAGGCAAGGCTTTGTTTTCGATCTG
1 AAGATCTGCT-ATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTG
*
3342552 CTTCGCTGTTAATGCAGGAAGGC
65 CTTCGCTGTCAATGCAGGAAGGC
* * *
3342575 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAGGGTTTTGTTCTCGATCTGC
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
* * *
3342640 TTCGCTGTCAATGCAGAAAAGA
66 TTCGCTGTCAATGCAGGAAGGC
*
3342662 AAGATCTGCCATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
* *
3342727 TTCGCTGTCAATGTAGGAAGAC
66 TTCGCTGTCAATGCAGGAAGGC
3342749 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
1 AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
3342814 T
66 T
3342815 GATCTGTTCT
Statistics
Matches: 221, Mismatches: 18, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
87 220 1.00
88 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.28
Consensus pattern (87 bp):
AAGATCTGCTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTTCGATCTGC
TTCGCTGTCAATGCAGGAAGGC
Found at i:3345071 original size:36 final size:36
Alignment explanation
Indices: 3344990--3345073 Score: 93
Period size: 36 Copynumber: 2.4 Consensus size: 36
3344980 TCTCCTTTTC
*
3344990 TTTTATTT--TTTCTCTTTTTCATATTTTTATTTTGA
1 TTTTATTTGATTTCTCTTTTT-ATATTTTTACTTTGA
* * *
3345025 CTTTAATTGATTTCTCTTTTT-TGTTTTTGACTTTGA
1 TTTTATTTGATTTCTCTTTTTATATTTTT-ACTTTGA
3345061 TTTTATTTGATTT
1 TTTTATTTGATTT
3345074 TTTTTATTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
35 12 0.30
36 17 0.43
37 11 0.28
ACGTcount: A:0.14, C:0.08, G:0.07, T:0.70
Consensus pattern (36 bp):
TTTTATTTGATTTCTCTTTTTATATTTTTACTTTGA
Found at i:3350116 original size:27 final size:28
Alignment explanation
Indices: 3350086--3350152 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 28
3350076 GTATAGGATG
* *
3350086 ATTTTAAAATAATTATTATATAAAA-CA
1 ATTTTAAAATAATAACTATATAAAAGCA
** *
3350113 A-TTTGGAATAA-AACTATATAAAAGTA
1 ATTTTAAAATAATAACTATATAAAAGCA
3350139 ATTTTAAAATAATA
1 ATTTTAAAATAATA
3350153 TGTAGTAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
25 10 0.33
26 10 0.33
27 9 0.30
28 1 0.03
ACGTcount: A:0.55, C:0.03, G:0.04, T:0.37
Consensus pattern (28 bp):
ATTTTAAAATAATAACTATATAAAAGCA
Found at i:3351643 original size:21 final size:21
Alignment explanation
Indices: 3351614--3351680 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
3351604 ATGCTTAGTT
*
3351614 TTATTTTTATTTTATTTTTTA
1 TTATATTTATTTTATTTTTTA
* *
3351635 TTATATTTA-GTAATTTTATTA
1 TTATATTTATTTTATTTT-TTA
* *
3351656 TTTTATTT-TTATTATTGTTTA
1 TTATATTTATT-TTATTTTTTA
3351677 TTAT
1 TTAT
3351681 TATTCTTGCT
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
20 6 0.17
21 24 0.69
22 5 0.14
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (21 bp):
TTATATTTATTTTATTTTTTA
Found at i:3351778 original size:3 final size:3
Alignment explanation
Indices: 3351770--3351803 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
3351760 TCTGTTTATG
3351770 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3351804 GTTATTACTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3353250 original size:6 final size:6
Alignment explanation
Indices: 3353216--3353288 Score: 74
Period size: 6 Copynumber: 12.0 Consensus size: 6
3353206 ACTTATTTCC
* * * *
3353216 TTTTTA GTTTTA GTTTTA TTTTTA TTTTTA TTTTTTA TGTTTA TGTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA -TTTTTA TTTTTA TTTTTA
* * *
3353265 TGTTTA TGTTTA TGTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA
3353289 GTTGTTTTTG
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
6 56 0.90
7 6 0.10
ACGTcount: A:0.16, C:0.00, G:0.10, T:0.74
Consensus pattern (6 bp):
TTTTTA
Found at i:3368104 original size:59 final size:59
Alignment explanation
Indices: 3368010--3368127 Score: 227
Period size: 59 Copynumber: 2.0 Consensus size: 59
3368000 GTTCTTTAGG
*
3368010 TAGATTAATTTAGTAAATCTTAGTTTAAAATAATCACTCCAATTTGTCGGCTAAATAAT
1 TAGATTAATTTAGTAAATCTTAGTTTAAAACAATCACTCCAATTTGTCGGCTAAATAAT
3368069 TAGATTAATTTAGTAAATCTTAGTTTAAAACAATCACTCCAATTTGTCGGCTAAATAAT
1 TAGATTAATTTAGTAAATCTTAGTTTAAAACAATCACTCCAATTTGTCGGCTAAATAAT
3368128 AGGAAAACGG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (59 bp):
TAGATTAATTTAGTAAATCTTAGTTTAAAACAATCACTCCAATTTGTCGGCTAAATAAT
Found at i:3371338 original size:15 final size:16
Alignment explanation
Indices: 3371300--3371346 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 16
3371290 GACATGACTA
3371300 TGTGGCACACACGGCC
1 TGTGGCACACACGGCC
* *
3371316 TG-GACACACA-GGCG
1 TGTGGCACACACGGCC
*
3371330 TGTGGCACACACAGCC
1 TGTGGCACACACGGCC
3371346 T
1 T
3371347 AAACACACGG
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
14 5 0.21
15 14 0.58
16 5 0.21
ACGTcount: A:0.23, C:0.34, G:0.30, T:0.13
Consensus pattern (16 bp):
TGTGGCACACACGGCC
Found at i:3372120 original size:15 final size:16
Alignment explanation
Indices: 3372093--3372123 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
3372083 GGGAGAGAGC
3372093 TTAGAATCAAACTTTA
1 TTAGAATCAAACTTTA
3372109 TTAGAA-CAAACTTTA
1 TTAGAATCAAACTTTA
3372124 AGTTCTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.35
Consensus pattern (16 bp):
TTAGAATCAAACTTTA
Found at i:3375472 original size:13 final size:13
Alignment explanation
Indices: 3375435--3375475 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
3375425 TCCTAATTGG
3375435 TTTCTTGATTTA-
1 TTTCTTGATTTAT
3375447 TTTCATTTG-TTTAT
1 TTTC--TTGATTTAT
3375461 TTTCTTGATTTAT
1 TTTCTTGATTTAT
3375474 TT
1 TT
3375476 CTTTTCATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
12 7 0.28
13 11 0.44
14 7 0.28
ACGTcount: A:0.15, C:0.07, G:0.07, T:0.71
Consensus pattern (13 bp):
TTTCTTGATTTAT
Found at i:3380190 original size:22 final size:21
Alignment explanation
Indices: 3380164--3380208 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
3380154 GGTTCCGTTT
*
3380164 TTCTTTTCT-TTTTACTTTTTTG
1 TTCTTTT-TATTTT-CTTTCTTG
3380186 TTCTTTTTATTTTCTTTCTTG
1 TTCTTTTTATTTTCTTTCTTG
3380207 TT
1 TT
3380209 TTTAAAACGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.04, C:0.13, G:0.04, T:0.78
Consensus pattern (21 bp):
TTCTTTTTATTTTCTTTCTTG
Found at i:3380780 original size:3 final size:3
Alignment explanation
Indices: 3380766--3380795 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
3380756 TTTCAATAGC
*
3380766 ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3380796 TATTTTGGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:3381304 original size:22 final size:24
Alignment explanation
Indices: 3381279--3381334 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
3381269 ATATTCTACA
3381279 ATAATATATACA-TTT-ATATTTT
1 ATAATATATACATTTTCATATTTT
* *
3381301 ATAATATTTATATTTTCATATTTT
1 ATAATATATACATTTTCATATTTT
*
3381325 ATAATTTATA
1 ATAATATATA
3381335 TATGTTTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 10 0.36
23 3 0.11
24 15 0.54
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (24 bp):
ATAATATATACATTTTCATATTTT
Found at i:3381323 original size:14 final size:16
Alignment explanation
Indices: 3381290--3381344 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
3381280 TAATATATAC
3381290 ATTTATATTTTATAAT
1 ATTTATATTTTATAAT
3381306 ATTTATATTTTCAT-AT
1 ATTTATATTTT-ATAAT
*
3381322 -TTTATAATTTATATAT
1 ATTTATATTTTATA-AT
*
3381338 GTTTATA
1 ATTTATA
3381345 CATCCTTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 2 0.06
15 9 0.26
16 15 0.44
17 8 0.24
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (16 bp):
ATTTATATTTTATAAT
Found at i:3381344 original size:8 final size:7
Alignment explanation
Indices: 3381291--3381335 Score: 54
Period size: 7 Copynumber: 6.0 Consensus size: 7
3381281 AATATATACA
3381291 TTTATAT
1 TTTATAT
3381298 TTTATAAT
1 TTTAT-AT
3381306 ATTTATAT
1 -TTTATAT
3381314 TTTCATAT
1 TTT-ATAT
*
3381322 TTTATAA
1 TTTATAT
3381329 TTTATAT
1 TTTATAT
3381336 ATGTTTATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
7 17 0.52
8 11 0.33
9 5 0.15
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (7 bp):
TTTATAT
Found at i:3381505 original size:140 final size:146
Alignment explanation
Indices: 3381349--3381637 Score: 475
Period size: 149 Copynumber: 2.0 Consensus size: 146
3381339 TTTATACATC
*
3381349 CTTTATAATATATATATGTACTTTTTAGAATTATTATAAG-TTTTTTTGTTATTATTTTG-TTT-
1 CTTTATAATATATATATGTACTTTTTAGAATTATCATAAGTTTTTTTTGTTATTATTTTGTTTTG
3381411 G-GTATTTCATGTTTTTATATATGTATACTTA-A-ATATG-TCTGTTTTAATATATGCATATACA
66 GTGTATTTCATGTTTTTATATATGTATACTTATATATATGCT-TGTTTTAATATATGCATATACA
3381472 TGTTTTCAAAATTTATT
130 TGTTTTCAAAATTTATT
3381489 CTTTATAATATATATATGTACTTTTTAGAATTATCATAAGTTTTTTTTTTTGTTATTATTTTGTT
1 CTTTATAATATATATATGTACTTTTTAGAATTATCATAAG---TTTTTTTTGTTATTATTTTGTT
3381554 TTGGTGTATTTCATGTTTTTATATATGTATACTTATATATATGCTTGTTTTAATATATGCATATA
63 TTGGTGTATTTCATGTTTTTATATATGTATACTTATATATATGCTTGTTTTAATATATGCATATA
*
3381619 CATGTTTTCAAATTTTATT
128 CATGTTTTCAAAATTTATT
3381638 TATGTATTAT
Statistics
Matches: 137, Mismatches: 2, Indels: 11
0.91 0.01 0.07
Matches are distributed among these distances:
140 39 0.28
144 19 0.14
145 3 0.02
146 1 0.01
147 30 0.22
148 1 0.01
149 43 0.31
150 1 0.01
ACGTcount: A:0.28, C:0.06, G:0.09, T:0.57
Consensus pattern (146 bp):
CTTTATAATATATATATGTACTTTTTAGAATTATCATAAGTTTTTTTTGTTATTATTTTGTTTTG
GTGTATTTCATGTTTTTATATATGTATACTTATATATATGCTTGTTTTAATATATGCATATACAT
GTTTTCAAAATTTATT
Found at i:3383060 original size:11 final size:11
Alignment explanation
Indices: 3383044--3383069 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3383034 TAGAAGAGAC
3383044 GAAACAGGGGA
1 GAAACAGGGGA
3383055 GAAACAGGGGA
1 GAAACAGGGGA
3383066 GAAA
1 GAAA
3383070 GAAGAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.08, G:0.42, T:0.00
Consensus pattern (11 bp):
GAAACAGGGGA
Found at i:3383833 original size:39 final size:40
Alignment explanation
Indices: 3383790--3383877 Score: 110
Period size: 39 Copynumber: 2.2 Consensus size: 40
3383780 CGAATTATGG
*
3383790 AATACTGAATATTGTCT-TG-ATTACTG-AGTGAATTGTGAA
1 AATACTGAATATTGT-TATGCA-TAATGCAGTGAATTGTGAA
*
3383829 AATACTGAATATTGTTATGCATAATGCATTGAATTGTGAA
1 AATACTGAATATTGTTATGCATAATGCAGTGAATTGTGAA
*
3383869 ATTACTGAA
1 AATACTGAA
3383878 GTAAAGAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
38 1 0.02
39 21 0.49
40 21 0.49
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (40 bp):
AATACTGAATATTGTTATGCATAATGCAGTGAATTGTGAA
Found at i:3384443 original size:45 final size:45
Alignment explanation
Indices: 3384379--3384508 Score: 197
Period size: 45 Copynumber: 2.9 Consensus size: 45
3384369 NNNNNNNNNN
*
3384379 TCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTACTGAC
1 TCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTACAGAC
* **
3384424 TCGGCACTTTGTGTGTCGAATACTGTTACCGTTACTGTTACAGGT
1 TCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTACAGAC
** *
3384469 TCAACACTTTGTGTGTTGAATACTGTTACTGTTACTGTTA
1 TCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTA
3384509 TTGATTACTG
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 77 1.00
ACGTcount: A:0.19, C:0.18, G:0.22, T:0.41
Consensus pattern (45 bp):
TCGGCACTTTGTGTGTCGAATACTGTTACTGTTACTGTTACAGAC
Found at i:3388438 original size:6 final size:6
Alignment explanation
Indices: 3388427--3388488 Score: 106
Period size: 6 Copynumber: 10.3 Consensus size: 6
3388417 TCATGCACCG
* *
3388427 GAGCCA GAGCCA GAGCCA GAGCCA GAGCCA GAGCCA GAGCCG GAGCCG
1 GAGCCA GAGCCA GAGCCA GAGCCA GAGCCA GAGCCA GAGCCA GAGCCA
3388475 GAGCCA GAGCCA GA
1 GAGCCA GAGCCA GA
3388489 ACTACATTCT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 54 1.00
ACGTcount: A:0.31, C:0.32, G:0.37, T:0.00
Consensus pattern (6 bp):
GAGCCA
Found at i:3391782 original size:27 final size:27
Alignment explanation
Indices: 3391708--3391783 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 27
3391698 AAAATAATAG
* *
3391708 CATTGGCGCCTCTCAGA-ATGACACCAC
1 CATTGGCGCCTCCCAGATA-GGCACCAC
*
3391735 CATTGGCGCCTCCCAGGTAGGCACCAC
1 CATTGGCGCCTCCCAGATAGGCACCAC
3391762 CATTGGCGCCTCCCAGATAGGC
1 CATTGGCGCCTCCCAGATAGGC
3391784 GCCAATACTA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
27 43 0.98
28 1 0.02
ACGTcount: A:0.21, C:0.38, G:0.24, T:0.17
Consensus pattern (27 bp):
CATTGGCGCCTCCCAGATAGGCACCAC
Found at i:3394701 original size:6 final size:6
Alignment explanation
Indices: 3394690--3394719 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
3394680 GAACTGTAAG
3394690 CTTTTC CTTTTC CTTTTC CTTTTC CTTTTC
1 CTTTTC CTTTTC CTTTTC CTTTTC CTTTTC
3394720 ATTCTTTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (6 bp):
CTTTTC
Found at i:3398644 original size:94 final size:94
Alignment explanation
Indices: 3398483--3398676 Score: 361
Period size: 94 Copynumber: 2.1 Consensus size: 94
3398473 AAGCTTGCAA
*
3398483 AACCTAATACCTAAATCTGTAATGAGTTATCTTTCTAGGGTGGAAAAAATGACCTATTTATAGGC
1 AACCTAATACCTAAATCTGTAATGAGTTATCTTTCTAAGGTGGAAAAAATGACCTATTTATAGGC
*
3398548 TAAATTCGTAAGTTAAATAATATTAAAAT
66 TAAATTCGCAAGTTAAATAATATTAAAAT
*
3398577 AACCTAATACCTAAATCTGTAATGAGTTATCTTTCTAAGGTGGAAAAAATTACCTATTTATAGGC
1 AACCTAATACCTAAATCTGTAATGAGTTATCTTTCTAAGGTGGAAAAAATGACCTATTTATAGGC
3398642 TAAATTCGCAAGTTAAATAATATTAAAAT
66 TAAATTCGCAAGTTAAATAATATTAAAAT
3398671 AACCTA
1 AACCTA
3398677 CACTAATCAG
Statistics
Matches: 97, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
94 97 1.00
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.34
Consensus pattern (94 bp):
AACCTAATACCTAAATCTGTAATGAGTTATCTTTCTAAGGTGGAAAAAATGACCTATTTATAGGC
TAAATTCGCAAGTTAAATAATATTAAAAT
Found at i:3400615 original size:44 final size:44
Alignment explanation
Indices: 3400550--3400640 Score: 128
Period size: 44 Copynumber: 2.1 Consensus size: 44
3400540 GTAGGTCAAG
* * * *
3400550 TAATATTAAAATAACATACACTAATCAGCGTTTAAATGTGAAAC
1 TAATATTAAAATAACACACACTAATAAGAGTTTAAATGGGAAAC
* *
3400594 TAATATTAAAATAACCCACACTAATAAGAGTTTAAGTGGGAAAC
1 TAATATTAAAATAACACACACTAATAAGAGTTTAAATGGGAAAC
3400638 TAA
1 TAA
3400641 GAAACAAAGT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.48, C:0.13, G:0.11, T:0.27
Consensus pattern (44 bp):
TAATATTAAAATAACACACACTAATAAGAGTTTAAATGGGAAAC
Found at i:3403228 original size:13 final size:13
Alignment explanation
Indices: 3403210--3403234 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3403200 TGGTCGGTTT
3403210 TATATTTTTATAA
1 TATATTTTTATAA
3403223 TATATTTTTATA
1 TATATTTTTATA
3403235 TATTATGTAG
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:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TATATTTTTATAA
Found at i:3403483 original size:92 final size:90
Alignment explanation
Indices: 3403321--3403505 Score: 235
Period size: 92 Copynumber: 2.0 Consensus size: 90
3403311 AATTAAGCTC
* * * *
3403321 CTCATTTTTTTACACTTAATTAAGCACTTGAACTTTCAAAATGCATTAAAAAGACCCTCAAACTT
1 CTCATTTTTTTACACTCAATTAAGCACTTAAACTTTCAAAATGCATCAAAAAGACCCTCAAAATT
*
3403386 CTTCAAAAAACAGCAATTAAGCCTCTG
66 CTTC-AAAAA-AGCAATTAAGCCCCTG
* ** * * *
3403413 CTCATTTTTTTTCACTCAATTGGGTACTTAAACTTTCAAAATGCATCAAAAATACTCTCAAAATT
1 CTCATTTTTTTACACTCAATTAAGCACTTAAACTTTCAAAATGCATCAAAAAGACCCTCAAAATT
* *
3403478 TTTCAAAAAAGCATTTAAGCCCCTG
66 CTTCAAAAAAGCAATTAAGCCCCTG
3403503 CTC
1 CTC
3403506 TTATTAAAAA
Statistics
Matches: 80, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
90 17 0.21
91 5 0.06
92 58 0.73
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.34
Consensus pattern (90 bp):
CTCATTTTTTTACACTCAATTAAGCACTTAAACTTTCAAAATGCATCAAAAAGACCCTCAAAATT
CTTCAAAAAAGCAATTAAGCCCCTG
Found at i:3404098 original size:91 final size:91
Alignment explanation
Indices: 3403941--3404121 Score: 258
Period size: 91 Copynumber: 2.0 Consensus size: 91
3403931 TTCCTAAGAT
* *
3403941 GGGGCTTAATTGCTTTTTTTTTGAAAAAGTTTGACGGTCTTTTTGATGCATTTTGAAAGTTTAAG
1 GGGGCTTAATTGC-TTTTCTTTGAAAAAGTTTAACGGTCTTTTTGATGCATTTTGAAAGTTTAAG
*
3404006 TACCCAATTGAGTGAAAGAAAAAAAGTA
65 TACCCAAATGAGTGAAA-AAAAAAAGTA
* *
3404034 GGGGCTTAATTG-TTTTCTTTGAAAAGGTTTAAGGGAT-TTTTTGATGCATTTTGAAAGTTTAAG
1 GGGGCTTAATTGCTTTTCTTTGAAAAAGTTTAACGG-TCTTTTTGATGCATTTTGAAAGTTTAAG
* *
3404097 TACTCAAATGAGTGCAAAAAAAAAG
65 TACCCAAATGAGTGAAAAAAAAAAG
3404122 AAGCAAGAAC
Statistics
Matches: 80, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
90 8 0.10
91 59 0.74
92 1 0.01
93 12 0.15
ACGTcount: A:0.33, C:0.08, G:0.22, T:0.37
Consensus pattern (91 bp):
GGGGCTTAATTGCTTTTCTTTGAAAAAGTTTAACGGTCTTTTTGATGCATTTTGAAAGTTTAAGT
ACCCAAATGAGTGAAAAAAAAAAGTA
Found at i:3405252 original size:14 final size:15
Alignment explanation
Indices: 3405219--3405256 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
3405209 TCGAGATTTT
3405219 TTTTATAAAAAAAAC
1 TTTTATAAAAAAAAC
* *
3405234 CTTTATAAAAAAGA-
1 TTTTATAAAAAAAAC
3405248 TTTTATAAA
1 TTTTATAAA
3405257 TTGTCCAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (15 bp):
TTTTATAAAAAAAAC
Found at i:3406106 original size:19 final size:19
Alignment explanation
Indices: 3406082--3406118 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3406072 TATTTTTTTG
*
3406082 TTATAACTTTATAAAATAC
1 TTATAAATTTATAAAATAC
*
3406101 TTATAAATTTTTAAAATA
1 TTATAAATTTATAAAATA
3406119 TATATTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (19 bp):
TTATAAATTTATAAAATAC
Found at i:3408170 original size:34 final size:34
Alignment explanation
Indices: 3408127--3408196 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
3408117 ACGTAACACA
3408127 TTAACCTATTAAATAACTAACAAGTGACATTTCT
1 TTAACCTATTAAATAACTAACAAGTGACATTTCT
3408161 TTAACCTATTAAATAACTAACAAGTGACATTTCT
1 TTAACCTATTAAATAACTAACAAGTGACATTTCT
3408195 TT
1 TT
3408197 TTACTTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.37
Consensus pattern (34 bp):
TTAACCTATTAAATAACTAACAAGTGACATTTCT
Found at i:3409936 original size:25 final size:25
Alignment explanation
Indices: 3409908--3409972 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
3409898 ATTAGCGATA
* *
3409908 AACGGTAAGCTCCTCCGAGCTGAAT
1 AACGGTAAGCTCATACGAGCTGAAT
*
3409933 AACGGTAAGCTCATACGAGCTGAGT
1 AACGGTAAGCTCATACGAGCTGAAT
* *
3409958 ATCTGTAAGCTCATA
1 AACGGTAAGCTCATA
3409973 AAAGCTAGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (25 bp):
AACGGTAAGCTCATACGAGCTGAAT
Found at i:3411729 original size:6 final size:6
Alignment explanation
Indices: 3411718--3411743 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3411708 TTTCAAACTG
3411718 TCACTT TCACTT TCACTT TCACTT TC
1 TCACTT TCACTT TCACTT TCACTT TC
3411744 TCTTCGATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.35, G:0.00, T:0.50
Consensus pattern (6 bp):
TCACTT
Found at i:3412996 original size:21 final size:21
Alignment explanation
Indices: 3412971--3413014 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
3412961 GCCTATCACT
*
3412971 TTGTCTTGTGTCGGATAATTC
1 TTGTCGTGTGTCGGATAATTC
3412992 TTGTCGTGTGTCGGATAATTC
1 TTGTCGTGTGTCGGATAATTC
3413013 TT
1 TT
3413015 CTTGTGCGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.25, T:0.48
Consensus pattern (21 bp):
TTGTCGTGTGTCGGATAATTC
Found at i:3415270 original size:25 final size:25
Alignment explanation
Indices: 3415236--3415283 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
3415226 ACAACCGATA
* *
3415236 AACGGGAAGCTCCTCCGAGCTGAAT
1 AACGGGAAGCTCATACGAGCTGAAT
*
3415261 AACGGTAAGCTCATACGAGCTGA
1 AACGGGAAGCTCATACGAGCTGA
3415284 GTATCAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.31, C:0.25, G:0.27, T:0.17
Consensus pattern (25 bp):
AACGGGAAGCTCATACGAGCTGAAT
Found at i:3419290 original size:4 final size:4
Alignment explanation
Indices: 3419273--3419309 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
3419263 TATATAATGC
* *
3419273 AAGA AAGA AGGA AAGA AAGA AAGA AAGA AGGA AAGA A
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA A
3419310 GATGGAAAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:3419884 original size:24 final size:22
Alignment explanation
Indices: 3419834--3419898 Score: 67
Period size: 24 Copynumber: 2.8 Consensus size: 22
3419824 ACAAATAAAG
*
3419834 AAATAAAAAGAAATAGAAAGAAAA
1 AAATGAAAA-AAA-AGAAAGAAAA
3419858 AAATGAAAAAAAAGAAAGAAACAA
1 AAATGAAAAAAAAGAAAG-AA-AA
* *
3419882 AAAGGAAAGAAAAGAAA
1 AAATGAAAAAAAAGAAA
3419899 AAGGGGAAGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 6 0.17
23 5 0.14
24 25 0.69
ACGTcount: A:0.78, C:0.02, G:0.15, T:0.05
Consensus pattern (22 bp):
AAATGAAAAAAAAGAAAGAAAA
Found at i:3419885 original size:10 final size:9
Alignment explanation
Indices: 3419830--3419874 Score: 54
Period size: 10 Copynumber: 4.8 Consensus size: 9
3419820 TAAAACAAAT
3419830 AAAGAAATAA
1 AAAGAAA-AA
*
3419840 AAAGAAATAG
1 AAAGAAA-AA
3419850 AAAGAAAAA
1 AAAGAAAAA
*
3419859 AATGAAAAA
1 AAAGAAAAA
3419868 AAAGAAA
1 AAAGAAA
3419875 GAAACAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
9 15 0.48
10 16 0.52
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (9 bp):
AAAGAAAAA
Found at i:3419885 original size:42 final size:42
Alignment explanation
Indices: 3419821--3419900 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
3419811 ATTATATAAT
* * *
3419821 AAAACAAATAAAGAAATAAAAAGAAATAG-AAAGAAAAAAATG
1 AAAAAAAAGAAAGAAACAAAAAGAAA-AGAAAAGAAAAAAATG
*
3419863 AAAAAAAAGAAAGAAACAAAAAGGAAAGAAAAGAAAAA
1 AAAAAAAAGAAAGAAACAAAAAGAAAAGAAAAGAAAAA
3419901 GGGGAAGGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 2 0.06
42 31 0.94
ACGTcount: A:0.79, C:0.03, G:0.14, T:0.05
Consensus pattern (42 bp):
AAAAAAAAGAAAGAAACAAAAAGAAAAGAAAAGAAAAAAATG
Found at i:3419899 original size:15 final size:13
Alignment explanation
Indices: 3419830--3419899 Score: 61
Period size: 15 Copynumber: 4.9 Consensus size: 13
3419820 TAAAACAAAT
3419830 AAAGAAATAAAAAG
1 AAAGAAA-AAAAAG
3419844 AAATAGAAAGAAAAA-
1 -AA-AGAAA-AAAAAG
*
3419859 AATGAAAAAAAAG
1 AAAGAAAAAAAAG
3419872 AAAGAAACAAAAAGG
1 AAAGAAA-AAAAA-G
3419887 AAAGAAAAGAAAA
1 AAAGAAAA-AAAA
3419900 AGGGGAAGGA
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
12 5 0.11
13 10 0.21
14 8 0.17
15 14 0.30
16 10 0.21
ACGTcount: A:0.79, C:0.01, G:0.16, T:0.04
Consensus pattern (13 bp):
AAAGAAAAAAAAG
Found at i:3419902 original size:16 final size:15
Alignment explanation
Indices: 3419830--3419893 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 15
3419820 TAAAACAAAT
* *
3419830 AAAGAAATAAAAAGA
1 AAAGAAACAAAAAGG
*
3419845 AATAGAAAGAAAAA--
1 AA-AGAAACAAAAAGG
*
3419859 AATGAAA-AAAAA-G
1 AAAGAAACAAAAAGG
3419872 AAAGAAACAAAAAGG
1 AAAGAAACAAAAAGG
3419887 AAAGAAA
1 AAAGAAA
3419894 AGAAAAAGGG
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
12 5 0.12
13 10 0.24
14 7 0.17
15 10 0.24
16 10 0.24
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.05
Consensus pattern (15 bp):
AAAGAAACAAAAAGG
Found at i:3420899 original size:37 final size:37
Alignment explanation
Indices: 3420785--3420903 Score: 112
Period size: 37 Copynumber: 3.1 Consensus size: 37
3420775 TTAGGGACTT
*
3420785 CTTCGGCTTTGAGTCGATGAGACAGTGGGTGTCAAATTATTA
1 CTTCGG-TTT-AGTCGATGAGACACTGGGTGTC-AA-T-TTA
* * * * * * *
3420827 CTTCAGATATATTCGATGGGGCACTAGGTGCCAATTTA
1 CTTC-GGTTTAGTCGATGAGACACTGGGTGTCAATTTA
3420865 CTTCGGTTTAGTCGATGAGACACTGGGTGTCAATTTA
1 CTTCGGTTTAGTCGATGAGACACTGGGTGTCAATTTA
3420902 CT
1 CT
3420904 ACTTTGAATT
Statistics
Matches: 61, Mismatches: 15, Indels: 7
0.73 0.18 0.08
Matches are distributed among these distances:
37 28 0.46
38 7 0.11
39 1 0.02
40 2 0.03
41 16 0.26
42 6 0.10
43 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.34
Consensus pattern (37 bp):
CTTCGGTTTAGTCGATGAGACACTGGGTGTCAATTTA
Found at i:3428690 original size:16 final size:16
Alignment explanation
Indices: 3428669--3428728 Score: 111
Period size: 16 Copynumber: 3.8 Consensus size: 16
3428659 NNNNNNNNNN
3428669 TAATCCAATACACCTC
1 TAATCCAATACACCTC
*
3428685 TAATCCAATACACCTT
1 TAATCCAATACACCTC
3428701 TAATCCAATACACCTC
1 TAATCCAATACACCTC
3428717 TAATCCAATACA
1 TAATCCAATACA
3428729 GCGAACCAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.40, C:0.33, G:0.00, T:0.27
Consensus pattern (16 bp):
TAATCCAATACACCTC
Found at i:3434309 original size:33 final size:33
Alignment explanation
Indices: 3434267--3434336 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 33
3434257 TCGGTACACA
3434267 GATTCTCCCACGGAAATAGAGCACCCCTTCGCT
1 GATTCTCCCACGGAAATAGAGCACCCCTTCGCT
3434300 GATTCTCCCACGGAAATAGAGCACCCCTTCGCT
1 GATTCTCCCACGGAAATAGAGCACCCCTTCGCT
3434333 -ATTC
1 GATTC
3434337 AGGTTAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 4 0.11
33 33 0.89
ACGTcount: A:0.24, C:0.36, G:0.17, T:0.23
Consensus pattern (33 bp):
GATTCTCCCACGGAAATAGAGCACCCCTTCGCT
Found at i:3435437 original size:12 final size:12
Alignment explanation
Indices: 3435420--3435445 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3435410 TAACGAGTCC
3435420 TAAATGTCGTCT
1 TAAATGTCGTCT
3435432 TAAATGTCGTCT
1 TAAATGTCGTCT
3435444 TA
1 TA
3435446 TGTACATCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (12 bp):
TAAATGTCGTCT
Found at i:3440490 original size:3 final size:3
Alignment explanation
Indices: 3440476--3440577 Score: 186
Period size: 3 Copynumber: 33.7 Consensus size: 3
3440466 AAAGTGTAAA
*
3440476 AAG AAG AGG AAG AAG AAAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG -AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
3440522 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
3440570 AAG AAG AA
1 AAG AAG AA
3440578 ATAGCAAAAC
Statistics
Matches: 96, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
3 93 0.97
4 3 0.03
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:3442582 original size:13 final size:13
Alignment explanation
Indices: 3442561--3442593 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3442551 ATTTATAAAT
3442561 TTATT-ATATATA
1 TTATTAATATATA
3442573 TTATTAATATATA
1 TTATTAATATATA
*
3442586 TTCTTAAT
1 TTATTAAT
3442594 GATTAAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (13 bp):
TTATTAATATATA
Found at i:3442667 original size:31 final size:31
Alignment explanation
Indices: 3442632--3442693 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
3442622 CATATAATAA
*
3442632 AACAAATAAAGAAAGAA-AAAGAAATAGAAAG
1 AACAAATAAAGAAA-AAGAAAGAAACAGAAAG
* *
3442663 AACAAATGAATAAAAAGAAAGAAACAGAAAG
1 AACAAATAAAGAAAAAGAAAGAAACAGAAAG
3442694 GAAAGAAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 2 0.07
31 25 0.93
ACGTcount: A:0.73, C:0.05, G:0.16, T:0.06
Consensus pattern (31 bp):
AACAAATAAAGAAAAAGAAAGAAACAGAAAG
Found at i:3443733 original size:40 final size:38
Alignment explanation
Indices: 3443613--3443746 Score: 110
Period size: 40 Copynumber: 3.4 Consensus size: 38
3443603 ACTTTGAGTC
3443613 GATGAGACACTGGGTGTCAAATTATTACTTCGAATATAT-T
1 GATGAGACACTGGGTGTC-AATTA-TACTTCGAAT-TATCT
** * * ** *
3443653 CGATGAGGTACTAGGTGCCAATT-TACTTCGGTTTAGCT
1 -GATGAGACACTGGGTGTCAATTATACTTCGAATTATCT
*
3443691 GATGAGACATTGGGTGTCAATTTACTACTTCGAATTATCT
1 GATGAGACACTGGGTGTCAA-TTA-TACTTCGAATTATCT
* *
3443731 GATGAGGCACTAGGTG
1 GATGAGACACTGGGTG
3443747 CCAAACTGGT
Statistics
Matches: 71, Mismatches: 18, Indels: 9
0.72 0.18 0.09
Matches are distributed among these distances:
37 17 0.24
38 11 0.15
40 29 0.41
41 14 0.20
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.34
Consensus pattern (38 bp):
GATGAGACACTGGGTGTCAATTATACTTCGAATTATCT
Found at i:3449497 original size:4 final size:4
Alignment explanation
Indices: 3449483--3449516 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
3449473 TGCTCCATTC
3449483 AGAA A-AA AGAA AGAA AGAA AGAA AGAA AGAA AGA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGA
3449517 GAGACATGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:3450892 original size:33 final size:33
Alignment explanation
Indices: 3450834--3450899 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
3450824 AACTTTTTGA
* *
3450834 AAAAATATTTATATTATTTTTAATTTTATATTT
1 AAAAATATTTATATTATTTTAAATTTTAAATTT
3450867 AAAAAT-TTTATATT-TGTTTCAAATTTTAAATTT
1 AAAAATATTTATATTAT-TTT-AAATTTTAAATTT
3450900 TACATAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 1 0.03
32 11 0.38
33 17 0.59
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (33 bp):
AAAAATATTTATATTATTTTAAATTTTAAATTT
Found at i:3452858 original size:27 final size:27
Alignment explanation
Indices: 3452750--3452986 Score: 176
Period size: 27 Copynumber: 8.8 Consensus size: 27
3452740 AGTCTGTCGA
***
3452750 GACAGTAAACACGGGTTAGTTTGTCGG
1 GACAGTAAACACGGGTTAGTCCATCGG
* * * * * **
3452777 GATATTAAACACGGATTAGTCTAGCAA
1 GACAGTAAACACGGGTTAGTCCATCGG
* *
3452804 GACAGTAAACACAGGTTAGTCCACCGG
1 GACAGTAAACACGGGTTAGTCCATCGG
3452831 GACAGTAAACACGGGTTAGTCCATCGG
1 GACAGTAAACACGGGTTAGTCCATCGG
* *
3452858 GACATTAAACATGGGTTAGT-C-TGCTGG
1 GACAGTAAACACGGGTTAGTCCAT-C-GG
** * * **
3452885 GACAGTAAACACGAATTAGACTATTAG
1 GACAGTAAACACGGGTTAGTCCATCGG
* * *
3452912 GACATTAAACACAGGTTAGTCCATTGG
1 GACAGTAAACACGGGTTAGTCCATCGG
* *
3452939 GATAGTAAACACGGGGTAGTTCGC-T-GG
1 GACAGTAAACACGGGTTAG-TC-CATCGG
*
3452966 GACAGTAAACACGGGGTAGTC
1 GACAGTAAACACGGGTTAGTC
3452987 AGCCAAGATG
Statistics
Matches: 164, Mismatches: 40, Indels: 13
0.76 0.18 0.06
Matches are distributed among these distances:
25 1 0.01
26 4 0.02
27 154 0.94
28 3 0.02
29 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.22
Consensus pattern (27 bp):
GACAGTAAACACGGGTTAGTCCATCGG
Found at i:3452915 original size:81 final size:83
Alignment explanation
Indices: 3452750--3452978 Score: 243
Period size: 81 Copynumber: 2.8 Consensus size: 83
3452740 AGTCTGTCGA
*** * **
3452750 GACAGTAAACACGGGTTAGTTTGTCGGGATATTAAACACGGATTAGTCTAGC-AAGACAGTAAAC
1 GACAGTAAACACGGGTTAGTCCATCGGGATATTAAACACGGGTTAGTCTAGCTGGGACAGTAAAC
* * *
3452814 AC-AGGTTAGTCCACCGG
66 ACGAGATTAGACCACCAG
* *
3452831 GACAGTAAACACGGGTTAGTCCATCGGGACATTAAACATGGGTTAGTCT-GCTGGGACAGTAAAC
1 GACAGTAAACACGGGTTAGTCCATCGGGATATTAAACACGGGTTAGTCTAGCTGGGACAGTAAAC
* **
3452895 ACGA-ATTAGACTATTAG
66 ACGAGATTAGACCACCAG
* * * * * *
3452912 GACATTAAACACAGGTTAGTCCATTGGGATAGTAAACACGGGGTAGT-TCGCTGGGACAGTAAAC
1 GACAGTAAACACGGGTTAGTCCATCGGGATATTAAACACGGGTTAGTCTAGCTGGGACAGTAAAC
3452976 ACG
66 ACG
3452979 GGGTAGTCAG
Statistics
Matches: 124, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
80 3 0.02
81 120 0.97
82 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.22
Consensus pattern (83 bp):
GACAGTAAACACGGGTTAGTCCATCGGGATATTAAACACGGGTTAGTCTAGCTGGGACAGTAAAC
ACGAGATTAGACCACCAG
Found at i:3456232 original size:13 final size:13
Alignment explanation
Indices: 3456214--3456269 Score: 73
Period size: 13 Copynumber: 4.5 Consensus size: 13
3456204 TAATTTTTTC
3456214 CTAAATATTATCA
1 CTAAATATTATCA
3456227 CTAAATA--ATC-
1 CTAAATATTATCA
*
3456237 CTAAATATTGTCA
1 CTAAATATTATCA
*
3456250 TTAAATATTATCA
1 CTAAATATTATCA
3456263 CTAAATA
1 CTAAATA
3456270 ATTCAAAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
10 7 0.19
11 3 0.08
12 2 0.06
13 24 0.67
ACGTcount: A:0.46, C:0.14, G:0.02, T:0.38
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:3456239 original size:23 final size:23
Alignment explanation
Indices: 3456212--3456256 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3456202 GCTAATTTTT
3456212 TCCTAAATATTATCACTAAATAA
1 TCCTAAATATTATCACTAAATAA
* *
3456235 TCCTAAATATTGTCATTAAATA
1 TCCTAAATATTATCACTAAATA
3456257 TTATCACTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.44, C:0.16, G:0.02, T:0.38
Consensus pattern (23 bp):
TCCTAAATATTATCACTAAATAA
Found at i:3466171 original size:3 final size:3
Alignment explanation
Indices: 3466163--3466193 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
3466153 AGGAATTGAA
*
3466163 AAG AAG AAG AAG AAG AAT AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
3466194 GGAAAATGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (3 bp):
AAG
Done.