Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2605
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: 84278
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:4819 original size:39 final size:38
Alignment explanation
Indices: 4776--4860 Score: 98
Period size: 39 Copynumber: 2.2 Consensus size: 38
4766 GATTTGACAT
* * *
4776 ATTATCCTCAAAGGCATTCATTTGAGGCTGCAAGTGCTG
1 ATTATCCT-AAAGGCATTCAATTGAGACTGCAACTGCTG
* * *
4815 ATTATCAGTAACGGCGTTCAATTGAGACTGCAACTGCTG
1 ATTATC-CTAAAGGCATTCAATTGAGACTGCAACTGCTG
4854 ATTATCC
1 ATTATCC
4861 CCAATGAAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
39 37 0.97
40 1 0.03
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (38 bp):
ATTATCCTAAAGGCATTCAATTGAGACTGCAACTGCTG
Found at i:7728 original size:81 final size:77
Alignment explanation
Indices: 7573--7744 Score: 272
Period size: 81 Copynumber: 2.2 Consensus size: 77
7563 GTACAAAACC
*
7573 AAGAGAAAATTTGGGGTTTTTTATCTTTTTGATTTTTTTTTTTTTTGAGAAGAAGAGAACAGAGA
1 AAGAGAAAGTTTGGGGTTTTTTATCTTTTTGATTTTTTTTTTTTTTGAGAAGAAGAGAACAGAGA
7638 GAATTGCAGTCA
66 GAATTGCAGTCA
* *
7650 AAGAGAAAGTTTGGGGTTTTTTTTCTTTTTGGATTTTTTTTTTTTTTTTTGCGAAGAAGAGAACA
1 AAGAGAAAGTTTGGGGTTTTTTATCTTTTT-GA---TTTTTTTTTTTTTTGAGAAGAAGAGAACA
7715 GAGAGAATTGCAGTCA
62 GAGAGAATTGCAGTCA
7731 AAGATGAAAGTTTG
1 AAGA-GAAAGTTTG
7745 CGAAAGAACC
Statistics
Matches: 87, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
77 28 0.32
78 2 0.02
81 48 0.55
82 9 0.10
ACGTcount: A:0.30, C:0.05, G:0.23, T:0.42
Consensus pattern (77 bp):
AAGAGAAAGTTTGGGGTTTTTTATCTTTTTGATTTTTTTTTTTTTTGAGAAGAAGAGAACAGAGA
GAATTGCAGTCA
Found at i:8014 original size:10 final size:10
Alignment explanation
Indices: 8001--8077 Score: 57
Period size: 10 Copynumber: 7.3 Consensus size: 10
7991 ATATTTACAA
8001 ATAATTAAAT
1 ATAATTAAAT
8011 ATAATTAAAT
1 ATAATTAAAT
**
8021 ATGCTATAATTAT
1 ATAAT-TAA--AT
*
8034 ATAATATATAT
1 ATAAT-TAAAT
*
8045 ATAA-TAAAA
1 ATAATTAAAT
8054 ATAATTAAAAT
1 ATAATT-AAAT
*
8065 ATAATAAAAT
1 ATAATTAAAT
8075 ATA
1 ATA
8078 TAATAAAATA
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
9 7 0.13
10 21 0.40
11 17 0.32
13 8 0.15
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (10 bp):
ATAATTAAAT
Found at i:8057 original size:20 final size:20
Alignment explanation
Indices: 8043--8090 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 20
8033 TATAATATAT
8043 ATATAATAAAAATAATTAAA
1 ATATAATAAAAATAATTAAA
*
8063 ATATAATAAAATATATAATAAA
1 ATATAATAAAA-ATA-ATTAAA
8085 ATATAA
1 ATATAA
8091 AAATTATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 11 0.44
21 3 0.12
22 11 0.44
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
ATATAATAAAAATAATTAAA
Found at i:8104 original size:22 final size:22
Alignment explanation
Indices: 8043--8110 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
8033 TATAATATAT
*
8043 ATATAATAAAA-AT-AATTAAA
1 ATATAATAAAATATAAAATAAA
*
8063 ATATAATAAAATATATAATAAA
1 ATATAATAAAATATAAAATAAA
* *
8085 ATATAA-AAATTATAAAAATAAT
1 ATATAATAAAATAT-AAAATAAA
8107 ATAT
1 ATAT
8111 GTATATATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
20 11 0.28
21 8 0.20
22 21 0.52
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
ATATAATAAAATATAAAATAAA
Found at i:8730 original size:132 final size:134
Alignment explanation
Indices: 8580--8848 Score: 384
Period size: 132 Copynumber: 2.0 Consensus size: 134
8570 ATATGTAACT
* * *
8580 TTATGTTTAATATTAAAATTTTATAAATA-ATAAGTTTTTATAATATAAACATTTTATATTGTAT
1 TTATGTTTAATATAAAAATTTTATAAACATATAAG-TTTTATAATAT-AACATTTTATATTATAT
* * *
8644 TAT-AATCGTAATAAAATTTATTTCA-TTTTATGTATGATTTAGTGTTATAAATATTAATAG-AA
64 CATAAATAGTAATAAAATTTATTTCATTTTTATGTATGATTTAGTATTATAAATATTAATAGAAA
8706 TTATCA
129 TTATCA
*
8712 TTATGTTTAATATAAAAATTTTATAAACATATAAGTTTTATAATATAATATTTTATATTATATCA
1 TTATGTTTAATATAAAAATTTTATAAACATATAAGTTTTATAATATAACATTTTATATTATATCA
* * * * *
8777 TAAATAGTAATTAGATTTATTTTATTTTTATTTATGATTTTGTATTATAAATATTAATAGAAATT
66 TAAATAGTAATAAAATTTATTTCATTTTTATGTATGATTTAGTATTATAAATATTAATAGAAATT
8842 ATCA
131 ATCA
8846 TTA
1 TTA
8849 AAATTTTCAC
Statistics
Matches: 121, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
131 17 0.14
132 56 0.46
133 37 0.31
134 11 0.09
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (134 bp):
TTATGTTTAATATAAAAATTTTATAAACATATAAGTTTTATAATATAACATTTTATATTATATCA
TAAATAGTAATAAAATTTATTTCATTTTTATGTATGATTTAGTATTATAAATATTAATAGAAATT
ATCA
Found at i:9785 original size:23 final size:24
Alignment explanation
Indices: 9754--9804 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
9744 ATAAATTTTA
*
9754 ATATGTTAAAATTTATAT-TATAT
1 ATATGTTAAAATATATATGTATAT
* *
9777 ATATTTTAAAATATCTATGTATAT
1 ATATGTTAAAATATATATGTATAT
9801 ATAT
1 ATAT
9805 CGTACTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (24 bp):
ATATGTTAAAATATATATGTATAT
Found at i:10089 original size:3 final size:3
Alignment explanation
Indices: 10081--10111 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
10071 TATAATCTTT
10081 TAA TAA TAA TAA TAA TAA TAA TAA TAGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
10112 AAATTCAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:12551 original size:2 final size:2
Alignment explanation
Indices: 12544--12571 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12534 GTTACTCACA
12544 AT 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 AT
12572 TCTTTTGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13650 original size:2 final size:2
Alignment explanation
Indices: 13640--13673 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
13630 TTTTTTATTG
13640 TA TA T- TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13674 CACGTATAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:13660 original size:15 final size:15
Alignment explanation
Indices: 13640--13673 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
13630 TTTTTTATTG
13640 TATATTATATATATA
1 TATATTATATATATA
13655 TATATTATATATATA
1 TATATTATATATATA
13670 TATA
1 TATA
13674 CACGTATAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATTATATATATA
Found at i:13663 original size:13 final size:13
Alignment explanation
Indices: 13647--13672 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13637 TTGTATATTA
13647 TATATATATATAT
1 TATATATATATAT
13660 TATATATATATAT
1 TATATATATATAT
13673 ACACGTATAA
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TATATATATATAT
Found at i:14063 original size:29 final size:29
Alignment explanation
Indices: 14027--14083 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
14017 TATTTAAAAA
*
14027 TTTTATTTAATTCTTTAGATTCTAAGATT
1 TTTTATTTAATTCTTTAGATTCCAAGATT
14056 TTTTATTTAATTCTTTAGATTCCAAGAT
1 TTTTATTTAATTCTTTAGATTCCAAGAT
14084 CTAAAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.28, C:0.09, G:0.07, T:0.56
Consensus pattern (29 bp):
TTTTATTTAATTCTTTAGATTCCAAGATT
Found at i:15071 original size:37 final size:36
Alignment explanation
Indices: 15025--15104 Score: 85
Period size: 37 Copynumber: 2.2 Consensus size: 36
15015 AGATTTCTCA
*
15025 ATATAAATTAATTA-AATTTA-AAAATTTAATAAATAAT
1 ATATTAATT-ATTATAATTTACAAAA-TTAA-AAATAAT
**
15062 ATATTAATTATTATTTTTTACAAAATTAAAAATAAT
1 ATATTAATTATTATAATTTACAAAATTAAAAATAAT
15098 AT-TTAAT
1 ATATTAAT
15105 AAAATTTTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
35 5 0.13
36 13 0.34
37 16 0.42
38 4 0.11
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (36 bp):
ATATTAATTATTATAATTTACAAAATTAAAAATAAT
Found at i:15396 original size:36 final size:36
Alignment explanation
Indices: 15344--15479 Score: 125
Period size: 36 Copynumber: 3.6 Consensus size: 36
15334 AGAAAAAATT
*
15344 TATTGTACATGTATTATTTTTATTAAAATTAATTAA
1 TATTATACATGTATTATTTTTATTAAAATTAATTAA
* *
15380 TATTATACATGTATTATTACTTTTTATTTATAATTTATTTATA
1 TATTATACATG---TATTA-TTTTTA-TTA-AAATTAATTA-A
* *
15423 AATTATACCA--T-TTATTTTTATTAAAATTAAATAA
1 TATTATA-CATGTATTATTTTTATTAAAATTAATTAA
*
15457 TATTGTACATGTATTATTTTTAT
1 TATTATACATGTATTATTTTTAT
15480 AATTGATAGA
Statistics
Matches: 80, Mismatches: 9, Indels: 22
0.72 0.08 0.20
Matches are distributed among these distances:
33 2 0.03
34 6 0.08
35 8 0.10
36 23 0.29
37 6 0.08
38 3 0.04
39 6 0.08
40 6 0.08
41 3 0.04
42 8 0.10
43 7 0.09
44 2 0.03
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (36 bp):
TATTATACATGTATTATTTTTATTAAAATTAATTAA
Found at i:15792 original size:274 final size:280
Alignment explanation
Indices: 15282--15900 Score: 908
Period size: 274 Copynumber: 2.2 Consensus size: 280
15272 TACATGTATT
* * * *
15282 ATTTTTCGGTAACGACTTAAATACGAACTTTTCTTTATCTGTAAAATTACTAAGAAAAAATTTAT
1 ATTTTTCGGTAACGACTTAAATACGAGCTTTCCTTTATCTGTAAAATGAC-CA-AAAAAATTTAT
*
15347 TGTACATGTATTATTTTTATTAAAATTAATTAATATTATACATGTATTATTACTTTTTATTTATA
64 TGTACATGTATTATTTCTATTAAAATTAATTAATATTATACATGTATTATTACTTTTTATTTATA
*
15412 ATTTATTTATAAATTATACCATTTATTTTTATTAAAATTAAATAATATTGTACATGTATTATTTT
129 A--TATTTAT-AATCATA-CATTTATTTTTATTAAAATTAAATAATATTGTACATGTATTATTTT
* * ** *
15477 TATAATTGATAGAACTTAAATTTATGTTAGCTAATAATAAATTACTTTTTTTTATAATGACTTAT
190 TATAATTGATAGAACTTAAATTTATGTTAGCCAACAATAAATTACTTTTTTCGATAACGACTTAT
* *
15542 TTCATATTTACAGATACACACATTTC
255 TTCAGATTTACAGACACACACATTTC
*
15568 ATTTTTCGATAACGACTTAAATACGAGCTTTCCTTTATCTGTAAAATGACCAAAAAAATTTATTG
1 ATTTTTCGGTAACGACTTAAATACGAGCTTTCCTTTATCTGTAAAATGACCAAAAAAATTTATTG
* * *
15633 TACATGTATTATTTCTATTAAAATTAATTAATATTGTGCATGTATTATTACTTTTTATTTCTAA-
66 TACATGTATTATTTCTATTAAAATTAATTAATATTATACATGTATTATTACTTTTTATTTATAAT
*
15697 A-TTAT-A-CA-A-ATTTATTTTTATTAAAATTAATTAATATTGTACATGTATTATTTTTATAAT
131 ATTTATAATCATACATTTATTTTTATTAAAATTAAATAATATTGTACATGTATTATTTTTATAAT
* *
15757 TGATAGAACTTAAATTTCTGTTAGCCAACAATAAATTACTTTTTTCGATAACGACTTATTTCGGA
196 TGATAGAACTTAAATTTATGTTAGCCAACAATAAATTACTTTTTTCGATAACGACTTATTTCAGA
* *
15822 TTTACAGACGCACACATTTT
261 TTTACAGACACACACATTTC
** *
15842 ATTTTTCGGTAACGACTTAAATATAAGCTTTCATTTATCTGTAAAATGACCAAGAAAAA
1 ATTTTTCGGTAACGACTTAAATACGAGCTTTCCTTTATCTGTAAAATGACCAA-AAAAA
15901 ATTTTCCTCA
Statistics
Matches: 306, Mismatches: 26, Indels: 13
0.89 0.08 0.04
Matches are distributed among these distances:
274 173 0.57
275 5 0.02
276 1 0.00
277 1 0.00
278 1 0.00
280 4 0.01
281 1 0.00
284 73 0.24
285 1 0.00
286 46 0.15
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (280 bp):
ATTTTTCGGTAACGACTTAAATACGAGCTTTCCTTTATCTGTAAAATGACCAAAAAAATTTATTG
TACATGTATTATTTCTATTAAAATTAATTAATATTATACATGTATTATTACTTTTTATTTATAAT
ATTTATAATCATACATTTATTTTTATTAAAATTAAATAATATTGTACATGTATTATTTTTATAAT
TGATAGAACTTAAATTTATGTTAGCCAACAATAAATTACTTTTTTCGATAACGACTTATTTCAGA
TTTACAGACACACACATTTC
Found at i:19378 original size:78 final size:78
Alignment explanation
Indices: 19274--19428 Score: 310
Period size: 78 Copynumber: 2.0 Consensus size: 78
19264 TAAGAATGAG
19274 AATGAAAATAACAATGATGAACTCTTATTTATAATGAAATATGAGATTATAAAAAAAAAATTTAT
1 AATGAAAATAACAATGATGAACTCTTATTTATAATGAAATATGAGATTATAAAAAAAAAATTTAT
19339 TCTTATTCAAGAT
66 TCTTATTCAAGAT
19352 AATGAAAATAACAATGATGAACTCTTATTTATAATGAAATATGAGATTATAAAAAAAAAATTTAT
1 AATGAAAATAACAATGATGAACTCTTATTTATAATGAAATATGAGATTATAAAAAAAAAATTTAT
19417 TCTTATTCAAGA
66 TCTTATTCAAGA
19429 CATCTGCATT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.34
Consensus pattern (78 bp):
AATGAAAATAACAATGATGAACTCTTATTTATAATGAAATATGAGATTATAAAAAAAAAATTTAT
TCTTATTCAAGAT
Found at i:19783 original size:93 final size:92
Alignment explanation
Indices: 19637--20400 Score: 826
Period size: 92 Copynumber: 8.4 Consensus size: 92
19627 CCTTGCAGTC
* * *
19637 TTTC-TTTTTTCTGTAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATTCC-T
1 TTTCTTTTTTTCTATAAAAAAGAATCCGATTCTCAGATATAATTCATGCATTAGTCTAA-TCCTT
* * *
19700 GCAGTCTGACATTTATAATCAATTAGTT
65 GCAGTCTGACATTTACAATCAATCAATT
* * * *
19728 TTTCTTTTTTTTCTATAAAAAA-AAGTCTGATTCTCAAATATAATTCATGCCTTAGTGTAATCCT
1 TTTC-TTTTTTTCTATAAAAAAGAA-TCCGATTCTCAGATATAATTCATGCATTAGTCTAATCCT
* * *
19792 TACAGTTTGACATTTACAATCAGTCAATT
64 TGCAGTCTGACATTTACAATCAATCAATT
* * * *
19821 TTTCTTTTCTTCTATAAAAAAGAATCTGATTCTCAAATATAATTCATGTATTAGTCTAATCCTTG
1 TTTCTTTTTTTCTATAAAAAAGAATCCGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTG
* * *
19886 CAGTCTAACATTTATAATCAATCAATC
66 CAGTCTGACATTTACAATCAATCAATT
* *
19913 TTTCTTTTTTTAATATAAAAAAGAATCCGATTCTCAGATATAATTCATGCATTAGTCTAATCTTT
1 TTTCTTTTTTT-CTATAAAAAAGAATCCGATTCTCAGATATAATTCATGCATTAGTCTAATCCTT
* * *
19978 GTAGTCTGATATTTAC-A--AA-C-AGT
65 GCAGTCTGACATTTACAATCAATCAATT
** * * * *
20001 TGACTTTTTTTCTATAAAAAAAAATCCGATTCGCAGATATAATTCATGCATTGGTCTAATCCTTA
1 TTTCTTTTTTTCTATAAAAAAGAATCCGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTG
* *
20066 CAATCTGACATTTACAATCAGTCAA--
66 CAGTCTGACATTTACAATCAATCAATT
* *
20091 ---CATTTTTTTCTATAAAAAATAATCCGATTCTCAGATATAATTCATGCATCAGTCTAATCCTT
1 TTTC-TTTTTTTCTATAAAAAAGAATCCGATTCTCAGATATAATTCATGCATTAGTCTAATCCTT
* * *
20153 GTAGTCTGGCATTTACAATCAATCAACT
65 GCAGTCTGACATTTACAATCAATCAATT
* * * * * *** * *
20181 TTTCATTTTTTCTATTAAAAA-AATTCGATTTTCAAATATAATTCATATGTTAGTCTAATTCTTA
1 TTTCTTTTTTTCTATAAAAAAGAATCCGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTG
*
20245 CAGTCTGACATTTACAATCAATCAACT
66 CAGTCTGACATTTACAATCAATCAATT
* * * * * *
20272 TTTCTTGTTTTCCATAAAAAAGAATCCAATTCTCAGATATAATTCATGCATTAATTTAATCTTTG
1 TTTCTTTTTTTCTATAAAAAAGAATCCGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTG
* * *
20337 CAGTTTGATATTTACAATCAATTAATT
66 CAGTCTGACATTTACAATCAATCAATT
*
20364 TTTC--TTTTTCTATAAAAAAG--TCTGATTCTCAGATATA
1 TTTCTTTTTTTCTATAAAAAAGAATCCGATTCTCAGATATA
20401 GTCATATTTA
Statistics
Matches: 566, Mismatches: 89, Indels: 39
0.82 0.13 0.06
Matches are distributed among these distances:
87 61 0.11
88 103 0.18
89 1 0.00
90 17 0.03
91 81 0.14
92 165 0.29
93 138 0.24
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.41
Consensus pattern (92 bp):
TTTCTTTTTTTCTATAAAAAAGAATCCGATTCTCAGATATAATTCATGCATTAGTCTAATCCTTG
CAGTCTGACATTTACAATCAATCAATT
Found at i:19962 original size:185 final size:182
Alignment explanation
Indices: 19637--20400 Score: 847
Period size: 185 Copynumber: 4.2 Consensus size: 182
19627 CCTTGCAGTC
* *
19637 TTTCTTTTTTCTGTAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATTCC-TG
1 TTTCTTTTTTCTATAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAA-TCCTTA
* * ** * *
19701 CAGTCTGACATTTATAATCAATTAGTTTTTCTTTTTTTTCTATAAAAAA-AAGTCTGATTCTCAA
65 CAGTCTGACATTTACAATCAATCA-ACTTTC-TTTTTTTCTATAAAAAAGAA-TCCGATTCTCAG
* * * * *
19765 ATATAATTCATGCCTTAGTGTAATCCTTACAGTTTGACATTTACAATCAGTCAATT
127 ATATAATTCATGCATTAGTCTAATCCTTGCAGTCTGACATTTACAATCAATCAATT
* *
19821 TTTCTTTTCTTCTATAAAAAAGAATCTGATTCTCAAATATAATTCATGTATTAGTCTAATCCTTG
1 TTTCTTTT-TTCTATAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCCTTA
* * *
19886 CAGTCTAACATTTATAATCAATCAATCTTTCTTTTTTTAATATAAAAAAGAATCCGATTCTCAGA
65 CAGTCTGACATTTACAATCAATCAA-CTTTCTTTTTTT-CTATAAAAAAGAATCCGATTCTCAGA
* * * *
19951 TATAATTCATGCATTAGTCTAATCTTTGTAGTCTGATATTTAC-A--AA-C-AGT
128 TATAATTCATGCATTAGTCTAATCCTTGCAGTCTGACATTTACAATCAATCAATT
** * * * * *
20001 TGACTTTTTTTCTATAAAAAAAAATCCGATTCGCAGATATAATTCATGCATTGGTCTAATCCTTA
1 TTTC-TTTTTTCTATAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCCTTA
* * * *
20066 CAATCTGACATTTACAATCAGTCAAC---ATTTTTTTCTATAAAAAATAATCCGATTCTCAGATA
65 CAGTCTGACATTTACAATCAATCAACTTTCTTTTTTTCTATAAAAAAGAATCCGATTCTCAGATA
* * * *
20128 TAATTCATGCATCAGTCTAATCCTTGTAGTCTGGCATTTACAATCAATCAACT
130 TAATTCATGCATTAGTCTAATCCTTGCAGTCTGACATTTACAATCAATCAATT
* * *** *
20181 TTTCATTTTTTCTATTAAAAA-AAT-TCGATTTTCAAATATAATTCATATGTTAGTCTAATTCTT
1 TTTC-TTTTTTCTATAAAAAAGAATCT-GATTCTCAAATATAATTCATGCATTAGTCTAATCCTT
* * *
20244 ACAGTCTGACATTTACAATCAATCAACTTTTCTTGTTTTCCATAAAAAAGAATCCAATTCTCAGA
64 ACAGTCTGACATTTACAATCAATCAAC-TTTCTTTTTTTCTATAAAAAAGAATCCGATTCTCAGA
* * * * * *
20309 TATAATTCATGCATTAATTTAATCTTTGCAGTTTGATATTTACAATCAATTAATT
128 TATAATTCATGCATTAGTCTAATCCTTGCAGTCTGACATTTACAATCAATCAATT
*
20364 TTTC-TTTTTCTATAAAAAAG--TCTGATTCTCAGATATA
1 TTTCTTTTTTCTATAAAAAAGAATCTGATTCTCAAATATA
20401 GTCATATTTA
Statistics
Matches: 490, Mismatches: 72, Indels: 40
0.81 0.12 0.07
Matches are distributed among these distances:
175 63 0.13
176 8 0.02
178 2 0.00
179 59 0.12
180 106 0.22
181 20 0.04
182 1 0.00
183 78 0.16
184 19 0.04
185 132 0.27
186 2 0.00
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.41
Consensus pattern (182 bp):
TTTCTTTTTTCTATAAAAAAGAATCTGATTCTCAAATATAATTCATGCATTAGTCTAATCCTTAC
AGTCTGACATTTACAATCAATCAACTTTCTTTTTTTCTATAAAAAAGAATCCGATTCTCAGATAT
AATTCATGCATTAGTCTAATCCTTGCAGTCTGACATTTACAATCAATCAATT
Found at i:21206 original size:124 final size:123
Alignment explanation
Indices: 20908--21250 Score: 419
Period size: 125 Copynumber: 2.8 Consensus size: 123
20898 TATTTTTAAT
* * *
20908 AAAAATAATATTTAATTAACTTTAAAAAATTATATTATCAAATTAAAATATTAATTATT-TTTTA
1 AAAAATAATATTTAATTAAGTTTAAAAAATTACATTAACAAATTAAAATATTAATTATTATTTT-
** * * ** *
20972 AAAATAAAAAAAATTAAATA-AAAAATAAAAAAGATTTATATTATTATTTTTGAATAAAATT
65 -TTATAAAAATAA--AAATATTAAAATAAAAAAGATTTATATTAGAATTTTTGAATAAAATA
*
21033 AAAAATAATATTTAATTAAGTTTAAAAAATTACATTAGCAAATTAAAATATTAATTATTATATTT
1 AAAAATAATATTTAATTAAGTTTAAAAAATTACATTAACAAATTAAAATATTAATTATTAT-TTT
* * *
21098 TTATAAAAATAAAAATATTAAAATAAAAAGGTTTTTTATTAGAATTTTT-AATAAAATA
65 TTATAAAAATAAAAATATTAAAATAAAAAAGATTTATATTAGAATTTTTGAATAAAATA
21156 AAAAATAA-ATTTTAATTAAGTTTAAAAAATTTACATTAACAAATTAAAATATTAATTATTATGT
1 AAAAATAATA-TTTAATTAAGTTTAAAAAA-TTACATTAACAAATTAAAATATTAATTATTAT-T
* *
21220 TTTT-T-AAAATAAAAAATTTTAAATTAAAAAA
63 TTTTATAAAAAT-AAAAATATTAAAATAAAAAA
21251 AATTATTATA
Statistics
Matches: 194, Mismatches: 18, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
122 6 0.03
123 58 0.30
124 61 0.31
125 65 0.34
126 1 0.01
127 3 0.02
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (123 bp):
AAAAATAATATTTAATTAAGTTTAAAAAATTACATTAACAAATTAAAATATTAATTATTATTTTT
TATAAAAATAAAAATATTAAAATAAAAAAGATTTATATTAGAATTTTTGAATAAAATA
Found at i:21248 original size:14 final size:15
Alignment explanation
Indices: 21221--21250 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
21211 TTATTATGTT
21221 TTTTAAAATAAAAAA
1 TTTTAAAATAAAAAA
*
21236 TTTTAAATTAAAAAA
1 TTTTAAAATAAAAAA
21251 AATTATTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TTTTAAAATAAAAAA
Found at i:21587 original size:46 final size:46
Alignment explanation
Indices: 21536--21637 Score: 118
Period size: 46 Copynumber: 2.2 Consensus size: 46
21526 CATAGAGAGA
* * * *
21536 TTTTTATTTGAATAATG-ATAATTTTTTTTAA-TTATTTAAATATTAT
1 TTTTTATTTG-ATAATGTA-AATGTTTTTAAATTTAATTAAATATCAT
*
21582 TTTTTAATTTGGTAATGTAAATGTTTTTAAATTTAATTAAATATCAT
1 TTTTT-ATTTGATAATGTAAATGTTTTTAAATTTAATTAAATATCAT
21629 TTTTTATTT
1 TTTTTATTT
21638 TATTAAAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
46 24 0.50
47 24 0.50
ACGTcount: A:0.33, C:0.01, G:0.06, T:0.60
Consensus pattern (46 bp):
TTTTTATTTGATAATGTAAATGTTTTTAAATTTAATTAAATATCAT
Found at i:21668 original size:34 final size:32
Alignment explanation
Indices: 21629--21759 Score: 108
Period size: 33 Copynumber: 4.0 Consensus size: 32
21619 TAAATATCAT
21629 TTTTTATTTTATTAAAAAAAATAATAATAAATA
1 TTTTTATTTTATTAAAAAAAATAATAAT-AATA
* *
21662 CTTTTTA-TTT-TTATAAAAACATAATAATTATA
1 -TTTTTATTTTATTA-AAAAAAATAATAATAATA
* ** * *
21694 -TTTTAGTTTGTTTTAAAATTAATTA-AATATTA
1 TTTTTA-TTT-TATTAAAAAAAATAATAATAATA
21726 TTTTTAATTTTATTAAAAAATAATAATAATAATA
1 TTTTT-ATTTTATTAAAAAA-AATAATAATAATA
21760 AACTTTTTTT
Statistics
Matches: 75, Mismatches: 13, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
30 5 0.07
32 20 0.27
33 34 0.45
34 16 0.21
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (32 bp):
TTTTTATTTTATTAAAAAAAATAATAATAATA
Found at i:21742 original size:32 final size:32
Alignment explanation
Indices: 21615--21749 Score: 96
Period size: 33 Copynumber: 4.1 Consensus size: 32
21605 TTTTTAAATT
* *
21615 TAATTAAATATCATTTTTTATTTTATTAAAAA
1 TAATTAAATATTATTTTTAATTTTATTAAAAA
* * * * *
21647 AAATAATAATAAATACTTTTTATTTTTATAAAAACA
1 TAATTA-AAT-ATTA-TTTTTAATTTTATTAAAA-A
* * * *
21683 TAA-TAATTA-TA-TTTTAGTTTGTTTTAAAAT
1 TAATTAAATATTATTTTTAATTT-TATTAAAAA
21713 TAATTAAATATTATTTTTAATTTTATTAAAAAA
1 TAATTAAATATTATTTTTAATTTTATT-AAAAA
21746 TAAT
1 TAAT
21750 AATAATAATA
Statistics
Matches: 76, Mismatches: 18, Indels: 17
0.68 0.16 0.15
Matches are distributed among these distances:
30 11 0.14
31 11 0.14
32 11 0.14
33 20 0.26
34 4 0.05
35 16 0.21
36 3 0.04
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.50
Consensus pattern (32 bp):
TAATTAAATATTATTTTTAATTTTATTAAAAA
Found at i:21855 original size:67 final size:64
Alignment explanation
Indices: 21770--21901 Score: 167
Period size: 67 Copynumber: 2.0 Consensus size: 64
21760 AACTTTTTTT
*
21770 TATTTTTTTTTTAAAA-AATAATTAATATTTTAATTTATTAATATAAATTTTTTAAAGTTAATTA
1 TATTTTTTTTTTAAAATAATAATTAATATATT-A-TTATTAAT-TAAATTTTTTAAAGTTAATTA
21834 AA
63 AA
* * *
21836 TATTATTTTTTATTAAAAATAATAATTAATATATTATTATTTATTATATTTTTTAAATTTAATTA
1 TATT-TTTTTT-TT-AAAATAATAATTAATATATTATTATTAATTAAATTTTTTAAAGTTAATTA
21901 A
63 A
21902 TTTATAAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
66 4 0.07
67 26 0.45
68 9 0.16
69 5 0.09
70 14 0.24
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (64 bp):
TATTTTTTTTTTAAAATAATAATTAATATATTATTATTAATTAAATTTTTTAAAGTTAATTAAA
Found at i:22522 original size:9 final size:9
Alignment explanation
Indices: 22484--22525 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
22474 TTAAACTATT
22484 AATTAAAAA
1 AATTAAAAA
22493 AA-TAAAAA
1 AATTAAAAA
* *
22501 TATATATAAA
1 AAT-TAAAAA
22511 AATTAAAAA
1 AATTAAAAA
22520 AATTAA
1 AATTAA
22526 TTAAACTCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
8 7 0.26
9 13 0.48
10 7 0.26
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (9 bp):
AATTAAAAA
Found at i:23442 original size:31 final size:30
Alignment explanation
Indices: 23375--23443 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 30
23365 TATATTAATT
23375 AAATATATTTTCAATTTTTAATTCTATTAA
1 AAATATATTTTCAATTTTTAATTCTATTAA
** *
23405 ATAATATATTTTTTATTTTATATATTTTA-TAA
1 A-AATATATTTTCAATTTT-TA-ATTCTATTAA
23437 AAATATA
1 AAATATA
23444 ACCTAATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
30 1 0.03
31 21 0.64
32 6 0.18
33 5 0.15
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (30 bp):
AAATATATTTTCAATTTTTAATTCTATTAA
Found at i:26786 original size:17 final size:17
Alignment explanation
Indices: 26767--26800 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
26757 AAATATTAAT
26767 AAATAAATAATATAATTA
1 AAATAAA-AATATAATTA
26785 AAATAAAAATATAATT
1 AAATAAAAATATAATT
26801 GCATCTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAATAAAAATATAATTA
Found at i:28049 original size:14 final size:13
Alignment explanation
Indices: 28011--28092 Score: 58
Period size: 14 Copynumber: 6.0 Consensus size: 13
28001 TTGCAATTGA
28011 AAATTT-AAATTT
1 AAATTTAAAATTT
* *
28023 AGATTTTAAATTT
1 AAATTTAAAATTT
28036 AAATTTCAAAATTT
1 AAATTT-AAAATTT
**
28050 TTATTTAAAAATTAT
1 AAATTT-AAAATT-T
* *
28065 AAATTTTAAATTC
1 AAATTTAAAATTT
28078 ACGAATTTAAAATTT
1 A--AATTTAAAATTT
28093 TTTATTAAAA
Statistics
Matches: 53, Mismatches: 12, Indels: 7
0.74 0.17 0.10
Matches are distributed among these distances:
12 5 0.09
13 12 0.23
14 21 0.40
15 15 0.28
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (13 bp):
AAATTTAAAATTT
Found at i:28943 original size:2 final size:2
Alignment explanation
Indices: 28938--28970 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
28928 ACACTAACAC
*
28938 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28971 CACTCCAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29053 original size:2 final size:2
Alignment explanation
Indices: 29048--29086 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
29038 ACACACTAAC
* *
29048 AT AT AT AT AT AT AT AT AT AT GT AT AT AT GT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29087 CACTTCAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29110 original size:116 final size:113
Alignment explanation
Indices: 28917--29253 Score: 526
Period size: 116 Copynumber: 3.0 Consensus size: 113
28907 TCCTATGCGA
*
28917 AGCACAGGTACACACTAACACATATATATATATATATATATGTA--TATATATATACACTCCAAT
1 AGCACAGGTACACACTAACA-ATATATATATATATATATATATATGTATATATATACACTCCAAT
28980 TTTGCAGATAATTAATTGATTTTATTTTTACTTTTGTAAGATATTTAAT
65 TTTGCAGATAATTAATTGATTTTATTTTTACTTTTGTAAGATATTTAAT
*
29029 AGCACAGGTACACACTAACATATATATATATATATATATGTATATATGTATATATATACACTTCA
1 AGCACAGGTACACACTAACA-ATATATATATATATATA--TATATATGTATATATATACACTCCA
*
29094 ATTTTGCAGATGATTAATTGATTTTATTTTTACTTTTGTAAGATATTTAAT
63 ATTTTGCAGATAATTAATTGATTTTATTTTTACTTTTGTAAGATATTTAAT
*
29145 AGCACAGGTACACACTAAC---ATATATGTATATATATATATATGTATATATATACACTCCAAAT
1 AGCACAGGTACACACTAACAATATATATATATATATATATATATGTATATATATACACTCC-AAT
* *
29207 TTT-CAGATAATTAATTGATTTTACTTTTA-TTTTGCAAGATATTTAAT
65 TTTGCAGATAATTAATTGATTTTATTTTTACTTTTGTAAGATATTTAAT
29254 TAAATGGAGT
Statistics
Matches: 211, Mismatches: 9, Indels: 13
0.91 0.04 0.06
Matches are distributed among these distances:
109 17 0.08
110 47 0.22
111 6 0.03
112 51 0.24
114 5 0.02
116 85 0.40
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (113 bp):
AGCACAGGTACACACTAACAATATATATATATATATATATATATGTATATATATACACTCCAATT
TTGCAGATAATTAATTGATTTTATTTTTACTTTTGTAAGATATTTAAT
Found at i:29175 original size:8 final size:8
Alignment explanation
Indices: 29164--29193 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
29154 ACACACTAAC
29164 ATATATGT
1 ATATATGT
*
29172 ATATATAT
1 ATATATGT
29180 ATATATGT
1 ATATATGT
29188 ATATAT
1 ATATAT
29194 ATACACTCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (8 bp):
ATATATGT
Found at i:29185 original size:16 final size:16
Alignment explanation
Indices: 29164--29196 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
29154 ACACACTAAC
29164 ATATATGTATATATAT
1 ATATATGTATATATAT
29180 ATATATGTATATATAT
1 ATATATGTATATATAT
29196 A
1 A
29197 CACTCCAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (16 bp):
ATATATGTATATATAT
Found at i:29367 original size:32 final size:31
Alignment explanation
Indices: 29339--29401 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 31
29329 AATATTAATT
* *
29339 TTTATTATATT-TAAAAAT-TTATTTTATTA
1 TTTATTATGTTATTAAAATATTATTTTATTA
29368 TTTATTATGTTATTAAAATATTATTTTATATA
1 TTTATTATGTTATTAAAATATTATTTTAT-TA
29400 TT
1 TT
29402 AATATTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 10 0.34
30 6 0.21
31 9 0.31
32 4 0.14
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (31 bp):
TTTATTATGTTATTAAAATATTATTTTATTA
Found at i:29413 original size:16 final size:16
Alignment explanation
Indices: 29389--29426 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
29379 ATTAAAATAT
29389 TATTT-TATATATTAA
1 TATTTATATATATTAA
*
29404 TATTTATATATTTTAA
1 TATTTATATATATTAA
29420 TAATTTA
1 T-ATTTA
29427 ATTTAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 5 0.25
16 10 0.50
17 5 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTTATATATATTAA
Found at i:29430 original size:5 final size:5
Alignment explanation
Indices: 29420--29480 Score: 58
Period size: 5 Copynumber: 12.4 Consensus size: 5
29410 TATATTTTAA
*
29420 TAATT TAATT TAAATT TGA-T TAATT TAA-- TAATT TAATT TAAATT TAA-T
1 TAATT TAATT T-AATT TAATT TAATT TAATT TAATT TAATT T-AATT TAATT
29468 TAATT TAAATT TA
1 TAATT T-AATT TA
29481 TAATAATTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
3 3 0.06
4 7 0.15
5 22 0.47
6 15 0.32
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (5 bp):
TAATT
Found at i:29443 original size:20 final size:20
Alignment explanation
Indices: 29420--29504 Score: 68
Period size: 20 Copynumber: 4.0 Consensus size: 20
29410 TATATTTTAA
29420 TAATTTAATTTAAATTTGAT
1 TAATTTAATTTAAATTTGAT
* *
29440 TAATTTAATAATTTAATTTAAATT
1 TAATTTAAT--TTAAATTT-GA-T
29464 TAA-TTAATTTAAATTT-AT
1 TAATTTAATTTAAATTTGAT
29482 AATAATTT-ATTTAAGATTTGAT
1 --TAATTTAATTTAA-ATTTGAT
29504 T
1 T
29505 CGTATTAGCC
Statistics
Matches: 53, Mismatches: 3, Indels: 18
0.72 0.04 0.24
Matches are distributed among these distances:
18 1 0.02
19 1 0.02
20 19 0.36
21 13 0.25
22 9 0.17
23 6 0.11
24 4 0.08
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (20 bp):
TAATTTAATTTAAATTTGAT
Found at i:29444 original size:9 final size:9
Alignment explanation
Indices: 29415--29475 Score: 63
Period size: 8 Copynumber: 6.6 Consensus size: 9
29405 ATTTATATAT
29415 TTTAA-TAA
1 TTTAATTAA
29423 TTTAATTTAAA
1 TTTAA-TT-AA
*
29434 TTTGATTAA
1 TTTAATTAA
29443 TTTAA-TAA
1 TTTAATTAA
29451 TTTAATTTAAA
1 TTTAA-TT-AA
29462 TTTAATTAA
1 TTTAATTAA
29471 TTTAA
1 TTTAA
29476 ATTTATAATA
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
8 13 0.29
9 13 0.29
10 6 0.13
11 13 0.29
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (9 bp):
TTTAATTAA
Found at i:29444 original size:15 final size:15
Alignment explanation
Indices: 29424--29490 Score: 77
Period size: 15 Copynumber: 4.5 Consensus size: 15
29414 TTTTAATAAT
*
29424 TTAATTTAAATTTGA
1 TTAATTTAAATTTAA
29439 TTAATTT-AA--TAA
1 TTAATTTAAATTTAA
29451 TTTAATTTAAATTTAA
1 -TTAATTTAAATTTAA
29467 TTAATTTAAATTTATA
1 TTAATTTAAATTTA-A
*
29483 ATAATTTA
1 TTAATTTA
29491 TTTAAGATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
12 2 0.04
13 7 0.16
14 4 0.09
15 21 0.47
16 11 0.24
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (15 bp):
TTAATTTAAATTTAA
Found at i:29484 original size:33 final size:28
Alignment explanation
Indices: 29415--29475 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
29405 ATTTATATAT
*
29415 TTTAATAATTTAATTTAAATTTGATTAA
1 TTTAATAATTTAATTTAAATTTAATTAA
29443 TTTAATAATTTAATTTAAATTTAATTAA
1 TTTAATAATTTAATTTAAATTTAATTAA
29471 TTTAA
1 TTTAA
29476 ATTTATAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (28 bp):
TTTAATAATTTAATTTAAATTTAATTAA
Found at i:29784 original size:21 final size:22
Alignment explanation
Indices: 29758--29807 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
29748 ATTTTTAATA
*
29758 TTTAATGTAT-TCAAGTAAAAT
1 TTTAATGTATATCAACTAAAAT
* *
29779 TTTAATTTATACTTAACTAAAAT
1 TTTAATGTATA-TCAACTAAAAT
29802 TTTAAT
1 TTTAAT
29808 TTTTAATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 9 0.38
23 15 0.62
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (22 bp):
TTTAATGTATATCAACTAAAAT
Found at i:29912 original size:19 final size:19
Alignment explanation
Indices: 29890--29926 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
29880 AAATTTAGTT
29890 TATAA-TAAAAATATAAAAA
1 TATAATTAAAAAT-TAAAAA
29909 TATAATTAAAAATTAAAA
1 TATAATTAAAAATTAAAA
29927 TAATTAAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
TATAATTAAAAATTAAAAA
Found at i:31341 original size:2 final size:2
Alignment explanation
Indices: 31334--31361 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
31324 AGCTACCTTC
31334 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
31362 ATCTATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:34081 original size:27 final size:27
Alignment explanation
Indices: 34050--34103 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
34040 GTGGCAACAA
34050 TTAGGTCATTGTTGAATATGATGTTTT
1 TTAGGTCATTGTTGAATATGATGTTTT
34077 TTAGGTCATTGTTGAATATGATGTTTT
1 TTAGGTCATTGTTGAATATGATGTTTT
34104 AATCCAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.22, C:0.04, G:0.22, T:0.52
Consensus pattern (27 bp):
TTAGGTCATTGTTGAATATGATGTTTT
Found at i:35355 original size:93 final size:94
Alignment explanation
Indices: 35245--35434 Score: 328
Period size: 94 Copynumber: 2.0 Consensus size: 94
35235 TTACCATGCA
* *
35245 TTTGCTGGTCATGAAATAACATAAACAAATCTTTAACTATAAA-TAAAAGTTGTCTCAAAGTTTG
1 TTTGCTGGTCATAAAATAACATAAACAAATCTTTAACTATAAACAAAAAGTTGTCTCAAAGTTTG
* *
35309 AGACAACTCAATTTCAATTTTGAGTTCTC
66 AGACAACTCAATTTCAATTTTGAATTCCC
35338 TTTGCTGGTCATAAAATAACATAAACAAATCTTTAACTATAAACAAAAAGTTGTCTCAAAGTTTG
1 TTTGCTGGTCATAAAATAACATAAACAAATCTTTAACTATAAACAAAAAGTTGTCTCAAAGTTTG
*
35403 AGAGAACTCAATTTCAATTTTGAATTCCC
66 AGACAACTCAATTTCAATTTTGAATTCCC
35432 TTT
1 TTT
35435 CTTTGAGACA
Statistics
Matches: 91, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
93 42 0.46
94 49 0.54
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.35
Consensus pattern (94 bp):
TTTGCTGGTCATAAAATAACATAAACAAATCTTTAACTATAAACAAAAAGTTGTCTCAAAGTTTG
AGACAACTCAATTTCAATTTTGAATTCCC
Found at i:35517 original size:5 final size:5
Alignment explanation
Indices: 35507--35553 Score: 69
Period size: 5 Copynumber: 9.4 Consensus size: 5
35497 TTTTTGTAAG
*
35507 AAGAA AAGAA AAGAA AAGAA AAGAAA AAGAA AAAAA AAG-A AAGAA AA
1 AAGAA AAGAA AAGAA AAGAA AAG-AA AAGAA AAGAA AAGAA AAGAA AA
35554 AGGGAAAAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
4 4 0.11
5 29 0.76
6 5 0.13
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:35561 original size:21 final size:21
Alignment explanation
Indices: 35504--35562 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
35494 TGATTTTTGT
*
35504 AAGAAGAAAAGAAAAGAAAAGAA
1 AAGAA-AAAGGAAAA-AAAAGAA
*
35527 AAGAAAAAGAAAAAAAAAG-A
1 AAGAAAAAGGAAAAAAAAGAA
*
35547 AAGAAAAAGGGAAAAA
1 AAGAAAAAGGAAAAAA
35563 CAATTTTGTG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 15 0.47
21 5 0.16
22 7 0.22
23 5 0.16
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (21 bp):
AAGAAAAAGGAAAAAAAAGAA
Found at i:35562 original size:20 final size:21
Alignment explanation
Indices: 35510--35555 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
35500 TTGTAAGAAG
*
35510 AAAAGAAAAGAAAAGAAAAGA
1 AAAAGAAAAAAAAAGAAAAGA
35531 AAAAGAAAAAAAAAG-AAAGA
1 AAAAGAAAAAAAAAGAAAAGA
35551 AAAAG
1 AAAAG
35556 GGAAAAACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (21 bp):
AAAAGAAAAAAAAAGAAAAGA
Found at i:35851 original size:11 final size:11
Alignment explanation
Indices: 35837--35869 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
35827 TATTGTGTTA
35837 ATATTATTTTT
1 ATATTATTTTT
35848 ATATTATATTTT
1 ATATTAT-TTTT
35860 A-ATTATTTTT
1 ATATTATTTTT
35870 TTATGTTCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 4 0.19
11 12 0.57
12 5 0.24
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
ATATTATTTTT
Found at i:38246 original size:17 final size:17
Alignment explanation
Indices: 38224--38280 Score: 84
Period size: 17 Copynumber: 3.5 Consensus size: 17
38214 TTGCTTGTAT
*
38224 TTTTCTTGTATTTTCTC
1 TTTTCTTTTATTTTCTC
38241 TTTTCTTTTATTTTCTC
1 TTTTCTTTTATTTTCTC
38258 -TTTCTTTTA-TTTCTC
1 TTTTCTTTTATTTTCTC
38273 TTTT-TTTT
1 TTTTCTTTT
38281 CCTTTCCCTT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
15 10 0.26
16 12 0.32
17 16 0.42
ACGTcount: A:0.05, C:0.16, G:0.02, T:0.77
Consensus pattern (17 bp):
TTTTCTTTTATTTTCTC
Found at i:38280 original size:15 final size:16
Alignment explanation
Indices: 38232--38280 Score: 73
Period size: 15 Copynumber: 3.1 Consensus size: 16
38222 ATTTTTCTTG
38232 TATTTTCTCTTTTCTTT
1 TATTTTCTCTTTT-TTT
*
38249 TATTTTCTCTTTCTTT
1 TATTTTCTCTTTTTTT
38265 TA-TTTCTCTTTTTTT
1 TATTTTCTCTTTTTTT
38280 T
1 T
38281 CCTTTCCCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 13 0.43
16 5 0.17
17 12 0.40
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (16 bp):
TATTTTCTCTTTTTTT
Found at i:38292 original size:25 final size:25
Alignment explanation
Indices: 38244--38301 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
38234 TTTTCTCTTT
**
38244 TCTTTTATTTTCTCTTTCTTTTATTTC
1 TCTTTT-TTTTCTCTTTCCCTTA-TTC
38271 TCTTTTTTTTC-CTTTCCCTTATTC
1 TCTTTTTTTTCTCTTTCCCTTATTC
38295 T-TTTTTT
1 TCTTTTTT
38302 CCTTCTCTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 6 0.21
24 4 0.14
25 8 0.28
26 5 0.17
27 6 0.21
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (25 bp):
TCTTTTTTTTCTCTTTCCCTTATTC
Found at i:39495 original size:105 final size:104
Alignment explanation
Indices: 39302--39495 Score: 273
Period size: 105 Copynumber: 1.9 Consensus size: 104
39292 CACAAAAACT
* * *
39302 CTTTTTTTTAAAAAGAATCAAACTACCATGTCAAACAACATTAGGAATTTAATCAAAATTAATTA
1 CTTTTTTTTAAAAAGAAACAAACCACCATGTCAAACAACATTAGAAATTTAATCAAAATTAATTA
**
39367 AAAGTGTATAACATCTATGATCAAGTTGTAACACAAGAA
66 AAAGTGTATAACATCTAAAATCAAGTTGTAACACAAGAA
* * * *
39406 CTTTTTTTTAGAAAGAAACAAACCATCATGTCAAACAATC-TTAAGAAATTTGATCAAAGTTAAT
1 CTTTTTTTTAAAAAGAAACAAACCACCATGTCAAACAA-CATT-AGAAATTTAATCAAAATTAAT
*
39470 TAAAAGTGTATAATATCTAAAATCAA
64 TAAAAGTGTATAACATCTAAAATCAA
39496 AGTGTATAAA
Statistics
Matches: 78, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
104 36 0.46
105 42 0.54
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (104 bp):
CTTTTTTTTAAAAAGAAACAAACCACCATGTCAAACAACATTAGAAATTTAATCAAAATTAATTA
AAAGTGTATAACATCTAAAATCAAGTTGTAACACAAGAA
Found at i:39870 original size:15 final size:15
Alignment explanation
Indices: 39846--39876 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
39836 AGTTAGTTTC
39846 GGGTTAGGTCATTTT
1 GGGTTAGGTCATTTT
*
39861 GGGTTGGGTCATTTT
1 GGGTTAGGTCATTTT
39876 G
1 G
39877 AGTTTTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.10, C:0.06, G:0.39, T:0.45
Consensus pattern (15 bp):
GGGTTAGGTCATTTT
Found at i:39925 original size:16 final size:16
Alignment explanation
Indices: 39889--39966 Score: 75
Period size: 16 Copynumber: 4.8 Consensus size: 16
39879 TTTTAAAATT
* *
39889 TTCGGGTCTTTTTCGGG
1 TTCGGGTCATTTT-AGG
39906 TTCGGGTCATTTTAGG
1 TTCGGGTCATTTTAGG
* *
39922 TTCGGATTATTTTAGG
1 TTCGGGTCATTTTAGG
* * * *
39938 TTTGGATCATTCTGGG
1 TTCGGGTCATTTTAGG
39954 TTCGGGTCATTTT
1 TTCGGGTCATTTT
39967 GGATTCTGGT
Statistics
Matches: 50, Mismatches: 11, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
16 38 0.76
17 12 0.24
ACGTcount: A:0.10, C:0.13, G:0.29, T:0.47
Consensus pattern (16 bp):
TTCGGGTCATTTTAGG
Found at i:40811 original size:16 final size:16
Alignment explanation
Indices: 40790--40856 Score: 82
Period size: 16 Copynumber: 4.2 Consensus size: 16
40780 TAATTGTCCA
*
40790 GGTCATTTCGGGTTCG
1 GGTCATTTTGGGTTCG
*
40806 GGTCATTTTGAGTTCG
1 GGTCATTTTGGGTTCG
* *
40822 AGTCATTTTGGGTTCA
1 GGTCATTTTGGGTTCG
40838 GGTCA-TTTGGGTTTCG
1 GGTCATTTTGGG-TTCG
40854 GGT
1 GGT
40857 TGGTCAGTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
15 6 0.14
16 37 0.86
ACGTcount: A:0.10, C:0.13, G:0.34, T:0.42
Consensus pattern (16 bp):
GGTCATTTTGGGTTCG
Found at i:42229 original size:21 final size:21
Alignment explanation
Indices: 42203--42264 Score: 124
Period size: 21 Copynumber: 3.0 Consensus size: 21
42193 TACCTTTTCA
42203 TCTGCAAGAGTAGCAAAGCTG
1 TCTGCAAGAGTAGCAAAGCTG
42224 TCTGCAAGAGTAGCAAAGCTG
1 TCTGCAAGAGTAGCAAAGCTG
42245 TCTGCAAGAGTAGCAAAGCT
1 TCTGCAAGAGTAGCAAAGCT
42265 TTTTTAGCCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.34, C:0.19, G:0.27, T:0.19
Consensus pattern (21 bp):
TCTGCAAGAGTAGCAAAGCTG
Found at i:45681 original size:52 final size:52
Alignment explanation
Indices: 45532--45661 Score: 206
Period size: 53 Copynumber: 2.5 Consensus size: 52
45522 CGAAATATGA
*
45532 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCAATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* * *
45584 AAATTTTTCCTGTATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAA-TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
45637 AAATTTGCCTGCACGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
45662 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
52 22 0.31
53 48 0.69
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:45780 original size:32 final size:32
Alignment explanation
Indices: 45739--45809 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 32
45729 AGCTTCGTAG
*
45739 CGATACATTGTATCGATACAGA-ACTTATGTAT
1 CGATACATTGTATCGAAACA-ACACTTATGTAT
45771 CGATACATTGTATCGAAACAACACTTATGTAT
1 CGATACATTGTATCGAAACAACACTTATGTAT
45803 CGATACA
1 CGATACA
45810 AATCGTTGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
31 1 0.03
32 36 0.97
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (32 bp):
CGATACATTGTATCGAAACAACACTTATGTAT
Found at i:52155 original size:11 final size:12
Alignment explanation
Indices: 52139--52168 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
52129 AGCTAATTGG
52139 TAGCAAATTTAA
1 TAGCAAATTTAA
52151 T-GCAAATTTAA
1 TAGCAAATTTAA
52162 TAGCAAA
1 TAGCAAA
52169 AAGAGATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (12 bp):
TAGCAAATTTAA
Found at i:54452 original size:28 final size:28
Alignment explanation
Indices: 54412--54483 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
54402 GAAAAAAAAT
* ** *
54412 CGGGATTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
54440 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
54468 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
54484 TCGATTGTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:54535 original size:53 final size:52
Alignment explanation
Indices: 54472--54604 Score: 142
Period size: 53 Copynumber: 2.5 Consensus size: 52
54462 AAATAACGAG
* * * *
54472 GTTGGAGTATCCTCGATTGTGAAAAATCGGTATTTTTGGAAATAAAATCAGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATCGG-AGTTTTGAAAATAAAACCAGGA
** * * * *
54525 GTTGGAGTATCCCCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCGGGA
1 GTTGGAGTATCCCCGATT-GTGAAAAATCGGAGTTTTGAAAATAAAACCAGGA
54578 -TTGGAGTATCCCCGATTGTGGAAAAAT
1 GTTGGAGTATCCCCGATTGT-GAAAAAT
54605 TAGTGTTTTA
Statistics
Matches: 65, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
52 23 0.35
53 34 0.52
54 8 0.12
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.29
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGAAAAATCGGAGTTTTGAAAATAAAACCAGGA
Found at i:54604 original size:52 final size:52
Alignment explanation
Indices: 54473--54642 Score: 157
Period size: 52 Copynumber: 3.2 Consensus size: 52
54463 AATAACGAGG
* * * * * *
54473 TTGGAGTATCCTCGATTGT-GAAAAATCGGTATTTTTGGAAATAAAATCAGGA
1 TTGGAGTATCCCCGATTGTGGAAAAATTGG-AGTTTTGAAAATAAAACCGGGA
** *
54525 GTTGGAGTATCCCCGATTAAAGG-AAAATTGGCGTTTTGAAAATAAAACCGGGA
1 -TTGGAGTATCCCCGATT-GTGGAAAAATTGGAGTTTTGAAAATAAAACCGGGA
* * ** *
54578 TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT-AGCGATAAAACCGGGG
1 TTGGAGTATCCCCGATTGTGGAAAAATTGGAGTTTTGA-AAATAAAACCGGGA
54630 TTGGAGTATCCCC
1 TTGGAGTATCCCC
54643 TCGGAAATAA
Statistics
Matches: 97, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
51 3 0.03
52 53 0.55
53 33 0.34
54 7 0.07
55 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.29
Consensus pattern (52 bp):
TTGGAGTATCCCCGATTGTGGAAAAATTGGAGTTTTGAAAATAAAACCGGGA
Found at i:54688 original size:27 final size:28
Alignment explanation
Indices: 54625--54697 Score: 94
Period size: 27 Copynumber: 2.6 Consensus size: 28
54615 GCGATAAAAC
**
54625 CGGGGTTGGAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCAAGGAAATAA
* *
54653 CGGGGTTGGAGTATCCCCAATG-ATTAA
1 CGGGGTTGGAGTATCCCCAAGGAAATAA
*
54680 CGGGGTTGGAGAATCCCC
1 CGGGGTTGGAGTATCCCC
54698 GATTGTGAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 21 0.52
28 19 0.47
ACGTcount: A:0.23, C:0.22, G:0.33, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCAAGGAAATAA
Found at i:54748 original size:213 final size:212
Alignment explanation
Indices: 54407--54811 Score: 618
Period size: 213 Copynumber: 1.9 Consensus size: 212
54397 CAGAAGAAAA
* * *
54407 AAAATCGGGATTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAG
1 AAAACCGGGATTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATGAAATAACGAG
* * *
54472 GTTGGAGTATCCTCGATTGTGAAAAATCGGTATTTTTGGAAATAAAATCAGGAGTTGGAGTATCC
66 GTTGGAGAATCCCCGATTGTGAAAAATCGGTATTTTTGGAAATAAAATCAGGAGTTAGAGTATCC
* *
54537 CCGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCGG-GATTGGAGTATCCCCGATTGTGGAA
131 CCGATTAAA-GAAAATTAGCGTTTTGAAAATAAAACCGGAG-TTGGAATATCCCCGATTGTGGAA
54601 AAATTAGTGTTTTAGCGAT
194 AAATTAGTGTTTTAGCGAT
* * *
54620 AAAACCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATG-ATTAACGGG
1 AAAACCGGGATTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATGAAATAACGAG
*
54684 GTTGGAGAATCCCCGATTGTGAAGAAATTGGTATTTTTTGGAAATAAAATC-GGAGTTAGAGTAT
66 GTTGGAGAATCCCCGATTGTGAA-AAATCGGTA-TTTTTGGAAATAAAATCAGGAGTTAGAGTAT
* * *
54748 CCCCGATTATAGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGA
129 CCCCGATTAAAGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGA
54812 GAATTGAGAA
Statistics
Matches: 174, Mismatches: 15, Indels: 7
0.89 0.08 0.04
Matches are distributed among these distances:
212 75 0.43
213 82 0.47
214 17 0.10
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (212 bp):
AAAACCGGGATTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATGAAATAACGAG
GTTGGAGAATCCCCGATTGTGAAAAATCGGTATTTTTGGAAATAAAATCAGGAGTTAGAGTATCC
CCGATTAAAGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAA
ATTAGTGTTTTAGCGAT
Found at i:57189 original size:33 final size:33
Alignment explanation
Indices: 57147--57211 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
57137 AAAATTTCCA
***
57147 AATGTATCGATACAAAGATCCATGTATCGATAT
1 AATGTATCGATACAAAGAAAAATGTATCGATAT
*
57180 AATGTATCGATACACAGAAAAATGTATCGATA
1 AATGTATCGATACAAAGAAAAATGTATCGATA
57212 CATTTCCTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAT
Found at i:57257 original size:19 final size:18
Alignment explanation
Indices: 57233--57300 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
57223 CAGTAGCTAA
57233 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
57252 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
57267 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
57284 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
57301 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:57273 original size:13 final size:13
Alignment explanation
Indices: 57255--57279 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57245 ACAATACTTA
57255 TGTATCGATACAT
1 TGTATCGATACAT
57268 TGTATCGATACA
1 TGTATCGATACA
57280 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:57277 original size:32 final size:32
Alignment explanation
Indices: 57236--57298 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
57226 TAGCTAATTA
*
57236 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
57268 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
57299 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:57365 original size:21 final size:21
Alignment explanation
Indices: 57336--57391 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
57326 GTTGGGACCC
*
57336 TGTAGCGATACATTCCACAAA
1 TGTATCGATACATTCCACAAA
*
57357 TGTATCGATACATTCTACAAA
1 TGTATCGATACATTCCACAAA
57378 TGTATCGATACATT
1 TGTATCGATACATT
57392 TGGATAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (21 bp):
TGTATCGATACATTCCACAAA
Found at i:58226 original size:55 final size:54
Alignment explanation
Indices: 58132--58432 Score: 426
Period size: 55 Copynumber: 5.5 Consensus size: 54
58122 AAGAGGACAA
* * * * * *
58132 TAAAGTGTCTCCTGCTCATTGAAGAGT-AAAAGTGCCACCAACTCGTGTGGGCTT
1 TAAAG-GTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
*
58186 TGAAAGGCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
1 T-AAAGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
*
58241 TAAGAGGTGTCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTT
1 TAA-AGGTGTCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTT
* *
58296 TAAAAGGTGTCCTGCTCTTTGGGGACTAAAAGGTGCCACCAACTTGTGTGGGCTT
1 T-AAAGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
*
58351 TAAAAGGTGTCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
1 T-AAAGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
58406 TAAGAGGTGTCCTGCTCTTTGAGGACT
1 TAA-AGGTGTCCTGCTCTTTGAGGACT
58433 AAAAAGCGGA
Statistics
Matches: 226, Mismatches: 14, Indels: 13
0.89 0.06 0.05
Matches are distributed among these distances:
54 24 0.11
55 196 0.87
56 6 0.03
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (54 bp):
TAAAGGTGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTT
Found at i:58382 original size:26 final size:26
Alignment explanation
Indices: 58296--58385 Score: 85
Period size: 26 Copynumber: 3.3 Consensus size: 26
58286 GTGTGGGCTT
58296 TAAAAGGTGTCCTGCTCTTTGGGGAC
1 TAAAAGGTGTCCTGCTCTTTGGGGAC
** *
58322 TAAAAGGTG-CCACCAACTTGTGTGGG-C
1 TAAAAGGTGTCCTGC-TCTT-TG-GGGAC
58349 TTTAAAAGGTGTCCTGCTCTTTGGGGAC
1 --TAAAAGGTGTCCTGCTCTTTGGGGAC
*
58377 TGAAAGGTG
1 TAAAAGGTG
58386 CCACCAACTT
Statistics
Matches: 50, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
25 3 0.06
26 20 0.40
27 6 0.12
28 6 0.12
29 12 0.24
30 3 0.06
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (26 bp):
TAAAAGGTGTCCTGCTCTTTGGGGAC
Found at i:59433 original size:14 final size:14
Alignment explanation
Indices: 59416--59466 Score: 68
Period size: 13 Copynumber: 3.6 Consensus size: 14
59406 CTTTTCTCTC
*
59416 TTTTCTTTGTTTTG
1 TTTTTTTTGTTTTG
59430 -TTTTTTTGTTTTG
1 TTTTTTTTGTTTTG
*
59443 TTTTTTTTCTTTTG
1 TTTTTTTTGTTTTG
59457 CTTTTTTTTG
1 -TTTTTTTTG
59467 AAGAGAATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
13 12 0.38
14 12 0.38
15 8 0.25
ACGTcount: A:0.00, C:0.06, G:0.12, T:0.82
Consensus pattern (14 bp):
TTTTTTTTGTTTTG
Found at i:59439 original size:13 final size:14
Alignment explanation
Indices: 59415--59464 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
59405 TCTTTTCTCT
59415 CTTTTCTTTGTTTTG
1 CTTTT-TTTGTTTTG
59430 -TTTTTTTGTTTTG
1 CTTTTTTTGTTTTG
* *
59443 TTTTTTTTCTTTTG
1 CTTTTTTTGTTTTG
59457 CTTTTTTT
1 CTTTTTTT
59465 TGAAGAGAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
13 9 0.28
14 23 0.72
ACGTcount: A:0.00, C:0.08, G:0.10, T:0.82
Consensus pattern (14 bp):
CTTTTTTTGTTTTG
Found at i:71978 original size:28 final size:28
Alignment explanation
Indices: 71938--72009 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
71928 GAAAAAAAAT
* ** *
71938 CGGGATTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
71966 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
71994 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
72010 TCGATTGTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:72129 original size:52 final size:51
Alignment explanation
Indices: 71999--72166 Score: 128
Period size: 52 Copynumber: 3.2 Consensus size: 51
71989 AATAACGAGG
* * * *
71999 TTGGAGTATCCTCGATTGT-GAAAAATCGGTATTTTTGGAAATAAAATC-GGA
1 TTGGAGTATCC-CGATTGTGGAAAAATTGG-AGTTTTGAAAATAAAACCGGGA
* ** *
72050 GTTTGAGTATCCCCGATTAAAGG-AAAATTGGCGTTTTGAAAATAAAACCGGGA
1 -TTGGAGTAT-CCCGATT-GTGGAAAAATTGGAGTTTTGAAAATAAAACCGGGA
* * ** *
72103 TTGGAGTATCTCCGATTGTGGAAAAATTAGTGTTTT-AGCGATAAAACCGGGG
1 TTGGAGTATC-CCGATTGTGGAAAAATTGGAGTTTTGA-AAATAAAACCGGGA
72155 TTGGAGTATCCC
1 TTGGAGTATCCC
72167 CTCGAAAATA
Statistics
Matches: 93, Mismatches: 16, Indels: 15
0.75 0.13 0.12
Matches are distributed among these distances:
51 6 0.06
52 74 0.80
53 12 0.13
54 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (51 bp):
TTGGAGTATCCCGATTGTGGAAAAATTGGAGTTTTGAAAATAAAACCGGGA
Found at i:72209 original size:28 final size:28
Alignment explanation
Indices: 72147--72222 Score: 88
Period size: 27 Copynumber: 2.8 Consensus size: 28
72137 TTAGCGATAA
72147 AACCGGGGTTGGAGTATCCCCTCGAAAAT
1 AACCGGGGTTGGAGTATCCCCTCG-AAAT
*
72176 AA-CGGGGTTGGAGTATCCCCAAT-G-ATT
1 AACCGGGGTTGGAGTATCCCC--TCGAAAT
72203 AACC-GGGTTGGAGTATCCCC
1 AACCGGGGTTGGAGTATCCCC
72223 GATTGTGAAG
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
27 20 0.47
28 19 0.44
29 3 0.07
30 1 0.02
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (28 bp):
AACCGGGGTTGGAGTATCCCCTCGAAAT
Found at i:72290 original size:212 final size:212
Alignment explanation
Indices: 71933--72336 Score: 609
Period size: 212 Copynumber: 1.9 Consensus size: 212
71923 CAGAAGAAAA
* * * *
71933 AAAATCGGGATTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAG
1 AAAACCGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATGAAATAACGAG
* *
71998 GTTGGAGTATCCTCGATTGTGAAAAATCGGTATTTTTGGAAATAAAATCGGAGTTTGAGTATCCC
66 GTTGGAGTATCCCCGATTGTGAAAAATCGGTATTTTTGGAAATAAAATCGGAGTTAGAGTATCCC
* * *
72063 CGATTAAAGGAAAATTGGCGTTTTGAAAATAAAACCGG-GATTGGAGTATCTCCGATTGTGGAAA
131 CGATTAAAGGAAAATTAGCGTTTTGAAAATAAAACCGGAG-TTGGAATATCCCCGATTGTGGAAA
72127 AATTAGTGTTTTAGCGAT
195 AATTAGTGTTTTAGCGAT
* *
72145 AAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATG-ATTAACCG-
1 AAAACCGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATGAAATAA-CGA
*
72208 GGTTGGAGTATCCCCGATTGTGAAGAAATTGGTATTTTTTGGAAATAAAATCGGAGTTAGAGTAT
65 GGTTGGAGTATCCCCGATTGTGAA-AAATCGGTA-TTTTTGGAAATAAAATCGGAGTTAGAGTAT
* * *
72273 CCCCGATTATA-GAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGA
128 CCCCGATTAAAGGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGA
72337 GAATTGAGAA
Statistics
Matches: 173, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
211 27 0.16
212 106 0.61
213 40 0.23
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (212 bp):
AAAACCGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATGAAATAACGAG
GTTGGAGTATCCCCGATTGTGAAAAATCGGTATTTTTGGAAATAAAATCGGAGTTAGAGTATCCC
CGATTAAAGGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAA
ATTAGTGTTTTAGCGAT
Found at i:74713 original size:33 final size:33
Alignment explanation
Indices: 74671--74735 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
74661 AAAATTTCCA
***
74671 AATGTATCGATACAAAGATCCATGTATCGATAT
1 AATGTATCGATACAAAGAAAAATGTATCGATAT
*
74704 AATGTATCGATACACAGAAAAATGTATCGATA
1 AATGTATCGATACAAAGAAAAATGTATCGATA
74736 CATTTCCTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAT
Found at i:74781 original size:19 final size:18
Alignment explanation
Indices: 74757--74824 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
74747 CAGTAGCTAA
74757 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
74776 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
74791 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
74808 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
74825 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:74797 original size:13 final size:13
Alignment explanation
Indices: 74779--74803 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
74769 ACAATACTTA
74779 TGTATCGATACAT
1 TGTATCGATACAT
74792 TGTATCGATACA
1 TGTATCGATACA
74804 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:74801 original size:32 final size:32
Alignment explanation
Indices: 74760--74822 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
74750 TAGCTAATTA
*
74760 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
74792 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
74823 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:76117 original size:7 final size:7
Alignment explanation
Indices: 76105--76139 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
76095 AATCTATTCA
76105 TGTATAT
1 TGTATAT
76112 TGTATAT
1 TGTATAT
*
76119 TGCATAT
1 TGTATAT
76126 TGTATAT
1 TGTATAT
76133 TGTATAT
1 TGTATAT
76140 AGTAATTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.29, C:0.03, G:0.14, T:0.54
Consensus pattern (7 bp):
TGTATAT
Found at i:76127 original size:14 final size:14
Alignment explanation
Indices: 76108--76152 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
76098 CTATTCATGT
76108 ATATTGTATATTGC
1 ATATTGTATATTGC
*
76122 ATATTGTATATTGT
1 ATATTGTATATTGC
* *
76136 ATATAGTA-ATTTC
1 ATATTGTATATTGC
76149 ATAT
1 ATAT
76153 GAATATATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
13 7 0.26
14 20 0.74
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.51
Consensus pattern (14 bp):
ATATTGTATATTGC
Found at i:76911 original size:7 final size:7
Alignment explanation
Indices: 76896--76929 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
76886 ATAGTAAAAC
76896 ATAGGCA
1 ATAGGCA
*
76903 ATCGGCA
1 ATAGGCA
76910 ATAGGCA
1 ATAGGCA
*
76917 ATGGGCA
1 ATAGGCA
76924 ATAGGC
1 ATAGGC
76930 TAGGTCCCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.35, C:0.18, G:0.32, T:0.15
Consensus pattern (7 bp):
ATAGGCA
Found at i:76915 original size:14 final size:14
Alignment explanation
Indices: 76896--76929 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
76886 ATAGTAAAAC
76896 ATAGGCAATCGGCA
1 ATAGGCAATCGGCA
*
76910 ATAGGCAATGGGCA
1 ATAGGCAATCGGCA
76924 ATAGGC
1 ATAGGC
76930 TAGGTCCCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.35, C:0.18, G:0.32, T:0.15
Consensus pattern (14 bp):
ATAGGCAATCGGCA
Found at i:77339 original size:15 final size:15
Alignment explanation
Indices: 77321--77350 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
77311 GCTGTTTGTT
77321 GCTGTGGTTTGGTGG
1 GCTGTGGTTTGGTGG
77336 GCTGTGGTTTGGTGG
1 GCTGTGGTTTGGTGG
77351 CTTAAGGCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.07, G:0.53, T:0.40
Consensus pattern (15 bp):
GCTGTGGTTTGGTGG
Found at i:78377 original size:24 final size:24
Alignment explanation
Indices: 78335--78384 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
78325 TTACCTTTAA
*
78335 CTTTTTTCTTTTTCGATTTTTTCT
1 CTTTTTTCTTTTTCGATTTTTCCT
*
78359 CTTTTTT-TTTTTCTTATTTTTCCT
1 CTTTTTTCTTTTTC-GATTTTTCCT
78383 CT
1 CT
78385 CAATCGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.76
Consensus pattern (24 bp):
CTTTTTTCTTTTTCGATTTTTCCT
Found at i:78775 original size:2 final size:2
Alignment explanation
Indices: 78762--78810 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
78752 AGGGATGCTT
*
78762 TC TC TG TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
78804 TA TC TC T
1 TC TC TC T
78811 TTTGTTGGAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.02, C:0.45, G:0.02, T:0.51
Consensus pattern (2 bp):
TC
Found at i:80140 original size:16 final size:16
Alignment explanation
Indices: 80119--80150 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
80109 TTATATTATA
*
80119 AAAATTAAAATTAATT
1 AAAATTAAAAGTAATT
80135 AAAATTAAAAGTAATT
1 AAAATTAAAAGTAATT
80151 TTGATTTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (16 bp):
AAAATTAAAAGTAATT
Found at i:80754 original size:22 final size:23
Alignment explanation
Indices: 80729--80774 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
80719 AATTTTATAC
*
80729 ATAAATTATTTTAA-TATATTTA
1 ATAAATTATATTAATTATATTTA
*
80751 ATAATTTATATTAATTTATATTTA
1 ATAAATTATATTAA-TTATATTTA
80775 CATTACTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 12 0.60
24 8 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
ATAAATTATATTAATTATATTTA
Done.