Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 115 of 335
Found at i:35282350 original size:18 final size:17
Alignment explanation
Indices: 35282321--35282354 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
35282311 TATACTTATA
35282321 TTAATTATTAATTAAAC
1 TTAATTATTAATTAAAC
35282338 TTAATTAATTAATTAAA
1 TTAATT-ATTAATTAAA
35282355 ATTTTAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAATTATTAATTAAAC
Found at i:35284112 original size:44 final size:44
Alignment explanation
Indices: 35284049--35284135 Score: 165
Period size: 44 Copynumber: 2.0 Consensus size: 44
35284039 ATTTCGAAAG
*
35284049 TAAGCAACTAAGAACAATAATCACAACATTTATATTTTTAGTCA
1 TAAGCAACTAAAAACAATAATCACAACATTTATATTTTTAGTCA
35284093 TAAGCAACTAAAAACAATAATCACAACATTTATATTTTTAGTC
1 TAAGCAACTAAAAACAATAATCACAACATTTATATTTTTAGTC
35284136 CATTTTATAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.46, C:0.16, G:0.06, T:0.32
Consensus pattern (44 bp):
TAAGCAACTAAAAACAATAATCACAACATTTATATTTTTAGTCA
Found at i:35287673 original size:6 final size:6
Alignment explanation
Indices: 35287644--35287695 Score: 59
Period size: 6 Copynumber: 8.3 Consensus size: 6
35287634 AGAGGAGACG
* * *
35287644 GATTTA GATTTA GATCTTT GGATTTT GATTCT GATTTT GATTTT GATTTT
1 GATTTT GATTTT GAT-TTT -GATTTT GATTTT GATTTT GATTTT GATTTT
35287694 GA
1 GA
35287696 AATTGGAGAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
6 33 0.80
7 5 0.12
8 3 0.07
ACGTcount: A:0.21, C:0.04, G:0.19, T:0.56
Consensus pattern (6 bp):
GATTTT
Found at i:35292076 original size:17 final size:17
Alignment explanation
Indices: 35292034--35292082 Score: 66
Period size: 16 Copynumber: 3.0 Consensus size: 17
35292024 ATTTTTTTGA
*
35292034 TTTAATCTA-ATTATTT
1 TTTAATATATATTATTT
35292050 TTTAA-ATATATTATTT
1 TTTAATATATATTATTT
*
35292066 TTTAATTTATATTATTT
1 TTTAATATATATTATTT
35292083 GTAATCCCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 2 0.07
16 17 0.59
17 10 0.34
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTAATATATATTATTT
Found at i:35295658 original size:31 final size:31
Alignment explanation
Indices: 35295623--35295685 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
35295613 TACAATTTGG
* *
35295623 TCACTGAACTATTCAAAAGGTTTCT-TTTAAA
1 TCACTAAACTATTCAAAA-GCTTCTATTTAAA
35295654 TCACTAAACTATTCAAAAGCTTCTATTTAAA
1 TCACTAAACTATTCAAAAGCTTCTATTTAAA
35295685 T
1 T
35295686 AAAGTTCCAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 5 0.17
31 24 0.83
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.38
Consensus pattern (31 bp):
TCACTAAACTATTCAAAAGCTTCTATTTAAA
Found at i:35296366 original size:16 final size:17
Alignment explanation
Indices: 35296333--35296370 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
35296323 ATTAATAGAT
35296333 TTTTATGTAAAAAAATA
1 TTTTATGTAAAAAAATA
**
35296350 TTTTAT-TAAAATCATA
1 TTTTATGTAAAAAAATA
35296366 TTTTA
1 TTTTA
35296371 ACCAAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (17 bp):
TTTTATGTAAAAAAATA
Found at i:35297654 original size:5 final size:5
Alignment explanation
Indices: 35297644--35297684 Score: 73
Period size: 5 Copynumber: 8.0 Consensus size: 5
35297634 AATAATTAAG
35297644 TATAT TATAT TATAT TATAT TATAT TATAT TATTAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TA-TAT TATAT
35297685 ATAAAAGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 30 0.86
6 5 0.14
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:35297754 original size:31 final size:30
Alignment explanation
Indices: 35297719--35297779 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
35297709 GAAACAGAAT
*
35297719 GAAAGCAAACGAAAC-AGAGAAGAACAGGGGA
1 GAAAG-AAACGAAACAAGA-AAGAAAAGGGGA
* *
35297750 GAAAGAAAGGAAAGAAGAAAGAAAAGGGGA
1 GAAAGAAACGAAACAAGAAAGAAAAGGGGA
35297780 AATAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.59, C:0.07, G:0.34, T:0.00
Consensus pattern (30 bp):
GAAAGAAACGAAACAAGAAAGAAAAGGGGA
Found at i:35299352 original size:39 final size:39
Alignment explanation
Indices: 35299245--35299379 Score: 123
Period size: 39 Copynumber: 3.4 Consensus size: 39
35299235 GACCTCGAGT
* * *
35299245 CGATGAGACACTGGGTGTC-ACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCAAC--TATTACTTCGGCTAG-TC
** ** *
35299286 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
*
35299324 CGATGAGACACTGGGTGTCAACTATTACTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAACTATTACTTCG-GCTAGTC
*
35299363 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
35299380 CCATATTGGT
Statistics
Matches: 76, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
38 19 0.25
39 36 0.47
40 4 0.05
41 15 0.20
42 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
Found at i:35305441 original size:5 final size:5
Alignment explanation
Indices: 35305431--35305471 Score: 73
Period size: 5 Copynumber: 8.0 Consensus size: 5
35305421 AATAATTAAG
35305431 TATAT TATAT TATAT TATAT TATAT TATAT TATTAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TA-TAT TATAT
35305472 ATAAAAGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 30 0.86
6 5 0.14
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:35305541 original size:31 final size:30
Alignment explanation
Indices: 35305506--35305566 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
35305496 GAAACAGAAT
*
35305506 GAAAGCAAACGAAAC-AGAGAAGAACAGGGGA
1 GAAAG-AAACGAAACAAGA-AAGAAAAGGGGA
* *
35305537 GAAAGAAAGGAAAGAAGAAAGAAAAGGGGA
1 GAAAGAAACGAAACAAGAAAGAAAAGGGGA
35305567 AATAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.59, C:0.07, G:0.34, T:0.00
Consensus pattern (30 bp):
GAAAGAAACGAAACAAGAAAGAAAAGGGGA
Found at i:35307140 original size:39 final size:39
Alignment explanation
Indices: 35307033--35307167 Score: 123
Period size: 39 Copynumber: 3.4 Consensus size: 39
35307023 GACCTCGAGT
* * *
35307033 CGATGAGACACTGGGTGTC-ACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCAAC--TATTACTTCGGCTAG-TC
** ** *
35307074 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
*
35307112 CGATGAGACACTGGGTGTCAACTATTACTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAACTATTACTTCG-GCTAGTC
*
35307151 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
35307168 CCATATTGGT
Statistics
Matches: 76, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
38 19 0.25
39 36 0.47
40 4 0.05
41 15 0.20
42 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
Found at i:35308373 original size:34 final size:34
Alignment explanation
Indices: 35308330--35308397 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
35308320 ACGATTATAA
*
35308330 CGGTAACAAGGCATGAGGCAATCAAGAATCAAAC
1 CGGTAACAAGGCACGAGGCAATCAAGAATCAAAC
35308364 CGGTAACAAGGCACGAGGCAATCAAGAATCAAAC
1 CGGTAACAAGGCACGAGGCAATCAAGAATCAAAC
35308398 TCTTCCAACA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.10
Consensus pattern (34 bp):
CGGTAACAAGGCACGAGGCAATCAAGAATCAAAC
Found at i:35316687 original size:184 final size:184
Alignment explanation
Indices: 35316378--35316746 Score: 729
Period size: 184 Copynumber: 2.0 Consensus size: 184
35316368 ATCCCTTAAA
35316378 TATATTTAATTTTTTCATAAAAATTACAATCAACTTCAATTAGAATCAAGTATTTCAAATTTTTA
1 TATATTTAATTTTTTCATAAAAATTACAATCAACTTCAATTAGAATCAAGTATTTCAAATTTTTA
*
35316443 TATTTAATTTAGTAAGCTTGAGATTAGTTCATTAAAATATTTTTTGTGATCATTATTTAAAAGTT
66 TATTTAATTTAGTAAGCTTGAGATTAATTCATTAAAATATTTTTTGTGATCATTATTTAAAAGTT
35316508 GTTAATGAAAAAGGAGTAGAAAAATAAAGGGAGTAAATATAATTAAATTAAAAT
131 GTTAATGAAAAAGGAGTAGAAAAATAAAGGGAGTAAATATAATTAAATTAAAAT
35316562 TATATTTAATTTTTTCATAAAAATTACAATCAACTTCAATTAGAATCAAGTATTTCAAATTTTTA
1 TATATTTAATTTTTTCATAAAAATTACAATCAACTTCAATTAGAATCAAGTATTTCAAATTTTTA
35316627 TATTTAATTTAGTAAGCTTGAGATTAATTCATTAAAATATTTTTTGTGATCATTATTTAAAAGTT
66 TATTTAATTTAGTAAGCTTGAGATTAATTCATTAAAATATTTTTTGTGATCATTATTTAAAAGTT
35316692 GTTAATGAAAAAGGAGTAGAAAAATAAAGGGAGTAAATATAATTAAATTAAAAT
131 GTTAATGAAAAAGGAGTAGAAAAATAAAGGGAGTAAATATAATTAAATTAAAAT
35316746 T
1 T
35316747 TCAATATATA
Statistics
Matches: 184, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
184 184 1.00
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.40
Consensus pattern (184 bp):
TATATTTAATTTTTTCATAAAAATTACAATCAACTTCAATTAGAATCAAGTATTTCAAATTTTTA
TATTTAATTTAGTAAGCTTGAGATTAATTCATTAAAATATTTTTTGTGATCATTATTTAAAAGTT
GTTAATGAAAAAGGAGTAGAAAAATAAAGGGAGTAAATATAATTAAATTAAAAT
Found at i:35318709 original size:39 final size:39
Alignment explanation
Indices: 35318663--35318783 Score: 206
Period size: 39 Copynumber: 3.1 Consensus size: 39
35318653 GCTCTGATGA
* *
35318663 GCTTCAGTTAGCCTCCGGGCTTCTGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTCCGGGCTGCCGTTTAGCACTTATGT
*
35318702 GCTTCAGTTAGCCTCCGGGCTGCCATTTAGCACTTATGT
1 GCTTCAGTTAGCCTCCGGGCTGCCGTTTAGCACTTATGT
*
35318741 GCTTCAGTTAGCCTTCGGGCTGCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTCCGGGCTGCCGTTTAGCACTTATGT
35318780 GCTT
1 GCTT
35318784 AAGCTAGATT
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 77 1.00
ACGTcount: A:0.13, C:0.26, G:0.24, T:0.36
Consensus pattern (39 bp):
GCTTCAGTTAGCCTCCGGGCTGCCGTTTAGCACTTATGT
Found at i:35319819 original size:13 final size:13
Alignment explanation
Indices: 35319801--35319827 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35319791 CTCATTGGGC
35319801 AATTGGACTTGAA
1 AATTGGACTTGAA
35319814 AATTGGACTTGAA
1 AATTGGACTTGAA
35319827 A
1 A
35319828 TCATAAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.30
Consensus pattern (13 bp):
AATTGGACTTGAA
Found at i:35320203 original size:62 final size:59
Alignment explanation
Indices: 35320131--35320244 Score: 149
Period size: 62 Copynumber: 1.9 Consensus size: 59
35320121 AGTGATTATC
* * *
35320131 TTAATATTAAATTTAAT-TTAATGTTTATCTTGTAGATAAATATTCTATTAATTTAATAAGAT
1 TTAATATTAAATTTAATCTT-ATATTTA-CCT-TA-ATAAATATTATATTAATTTAATAAGAT
*
35320193 TTAATTTTAAATTTAATCTTATATTTACCTTAATAAATATTATATTAATTTA
1 TTAATATTAAATTTAATCTTATATTTACCTTAATAAATATTATATTAATTTA
35320245 CTATTAAAGT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
59 19 0.40
60 2 0.04
61 2 0.04
62 22 0.47
63 2 0.04
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (59 bp):
TTAATATTAAATTTAATCTTATATTTACCTTAATAAATATTATATTAATTTAATAAGAT
Found at i:35324329 original size:23 final size:23
Alignment explanation
Indices: 35324303--35324361 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
35324293 TTCATTTAAC
35324303 TTAATCGAACATGTTCACAAACA
1 TTAATCGAACATGTTCACAAACA
* * **
35324326 TTAAACAAACATGTTCATGAACA
1 TTAATCGAACATGTTCACAAACA
*
35324349 TATAATTGAACAT
1 T-TAATCGAACAT
35324362 ATCTGCGAAC
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
23 20 0.71
24 8 0.29
ACGTcount: A:0.46, C:0.17, G:0.08, T:0.29
Consensus pattern (23 bp):
TTAATCGAACATGTTCACAAACA
Found at i:35325921 original size:13 final size:14
Alignment explanation
Indices: 35325903--35325933 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
35325893 ATGTACGAAT
35325903 ATATACATATA-TA
1 ATATACATATATTA
35325916 ATATACATATATTA
1 ATATACATATATTA
35325930 ATAT
1 ATAT
35325934 TAGTATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (14 bp):
ATATACATATATTA
Found at i:35326761 original size:9 final size:8
Alignment explanation
Indices: 35326745--35326781 Score: 56
Period size: 9 Copynumber: 4.4 Consensus size: 8
35326735 ATTAGAGTCT
35326745 AGAAAAAA
1 AGAAAAAA
35326753 AGCAAAAAA
1 AG-AAAAAA
35326762 AGAAAAAAA
1 AG-AAAAAA
35326771 AGAAAAAA
1 AGAAAAAA
35326779 AGA
1 AGA
35326782 TTCGGCAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
8 11 0.41
9 16 0.59
ACGTcount: A:0.84, C:0.03, G:0.14, T:0.00
Consensus pattern (8 bp):
AGAAAAAA
Found at i:35326767 original size:17 final size:16
Alignment explanation
Indices: 35326745--35326781 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
35326735 ATTAGAGTCT
35326745 AGAAAAAAAGCAAAAAA
1 AGAAAAAAAG-AAAAAA
35326762 AGAAAAAAAAGAAAAAA
1 AG-AAAAAAAGAAAAAA
35326779 AGA
1 AGA
35326782 TTCGGCAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 1 0.05
17 10 0.53
18 8 0.42
ACGTcount: A:0.84, C:0.03, G:0.14, T:0.00
Consensus pattern (16 bp):
AGAAAAAAAGAAAAAA
Found at i:35328207 original size:37 final size:37
Alignment explanation
Indices: 35328166--35328240 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
35328156 AGGAATATGA
35328166 ATGTCTAAATGAAAGCAAACACAAACTTGTATGCCTG
1 ATGTCTAAATGAAAGCAAACACAAACTTGTATGCCTG
35328203 ATGTCTAAATGAAAGCAAACACAAACTTGTATGCCTG
1 ATGTCTAAATGAAAGCAAACACAAACTTGTATGCCTG
35328240 A
1 A
35328241 GTTTACATCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (37 bp):
ATGTCTAAATGAAAGCAAACACAAACTTGTATGCCTG
Found at i:35333600 original size:7 final size:6
Alignment explanation
Indices: 35333559--35333596 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
35333549 CCCTATAATT
*
35333559 AATTTA AATTT- AATCTTT AATTTA AATTTA AATTTA AA
1 AATTTA AATTTA AAT-TTA AATTTA AATTTA AATTTA AA
35333597 ATTTTAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
5 3 0.10
6 23 0.79
7 3 0.10
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (6 bp):
AATTTA
Found at i:35333623 original size:23 final size:23
Alignment explanation
Indices: 35333597--35333651 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
35333587 TAAATTTAAA
*
35333597 ATTTTAAAATATTTAGTGATAAT
1 ATTTTAAAATATTTAGTAATAAT
*
35333620 A-TTTAAGATTATTTAGTAATAAT
1 ATTTTAA-AATATTTAGTAATAAT
35333643 ATTTTAAAA
1 ATTTTAAAA
35333652 AAATCTAACT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 5 0.19
23 17 0.63
24 5 0.19
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (23 bp):
ATTTTAAAATATTTAGTAATAAT
Found at i:35333818 original size:12 final size:13
Alignment explanation
Indices: 35333796--35333827 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
35333786 ACTGCAAACT
35333796 TTTATTTTATTTA
1 TTTATTTTATTTA
35333809 TTTA-TTTATTTA
1 TTTATTTTATTTA
35333821 TTT-TTTT
1 TTTATTTT
35333828 TTACTTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 14 0.78
13 4 0.22
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:35337665 original size:21 final size:22
Alignment explanation
Indices: 35337639--35337679 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
35337629 TATTAATAGT
35337639 TCTCAAATTTA-AGATTTAGGG
1 TCTCAAATTTAGAGATTTAGGG
* *
35337660 TCTCAAGTTTAGAGTTTTAG
1 TCTCAAATTTAGAGATTTAG
35337680 CATTTAGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (22 bp):
TCTCAAATTTAGAGATTTAGGG
Found at i:35344259 original size:13 final size:13
Alignment explanation
Indices: 35344241--35344273 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
35344231 GATCACACGC
*
35344241 CCGTGTGTATAGG
1 CCGTGTGAATAGG
35344254 CCGTGTGAATAGG
1 CCGTGTGAATAGG
35344267 CCGTGTG
1 CCGTGTG
35344274 CCTCACACAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.15, C:0.18, G:0.39, T:0.27
Consensus pattern (13 bp):
CCGTGTGAATAGG
Found at i:35345186 original size:31 final size:31
Alignment explanation
Indices: 35345150--35345212 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
35345140 CACACAAAGT
35345150 AAGCTTTAAAATCTTAGTAAGCCATATACAA
1 AAGCTTTAAAATCTTAGTAAGCCATATACAA
35345181 AAGCTTTAAAATCTTAGTAAGCCATATACAA
1 AAGCTTTAAAATCTTAGTAAGCCATATACAA
35345212 A
1 A
35345213 TAAAATTACC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.46, C:0.16, G:0.10, T:0.29
Consensus pattern (31 bp):
AAGCTTTAAAATCTTAGTAAGCCATATACAA
Found at i:35345606 original size:43 final size:43
Alignment explanation
Indices: 35345452--35345610 Score: 162
Period size: 43 Copynumber: 3.7 Consensus size: 43
35345442 CAATTCCATA
* ** * *
35345452 TCCCAAATATGGTCTTACATGTTATCACAT-ATCGATGCCGATAG
1 TCCCAGATATGGTCTTACACATAATCACATAAT-GATGCCAAT-G
* * * *
35345496 -CCCAGCTATGGTCTTACACGA-AACCAAATAACGATGCCAATG
1 TCCCAGATATGGTCTTACAC-ATAATCACATAATGATGCCAATG
* *
35345538 TCCCAGATATGGTCTTATACGTAATCACATAATGATGCCAATG
1 TCCCAGATATGGTCTTACACATAATCACATAATGATGCCAATG
*
35345581 TCCCAGATATGATCTTACACATAATCACAT
1 TCCCAGATATGGTCTTACACATAATCACAT
35345611 CTCGTTAATC
Statistics
Matches: 93, Mismatches: 18, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
42 1 0.01
43 91 0.98
44 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (43 bp):
TCCCAGATATGGTCTTACACATAATCACATAATGATGCCAATG
Found at i:35346257 original size:19 final size:20
Alignment explanation
Indices: 35346235--35346273 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
35346225 TCAAGCATTC
35346235 ATCAATGA-AACTTCAAAAA
1 ATCAATGACAACTTCAAAAA
* *
35346254 ATCATTTACAACTTCAAAAA
1 ATCAATGACAACTTCAAAAA
35346274 TTAATGCATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.54, C:0.18, G:0.03, T:0.26
Consensus pattern (20 bp):
ATCAATGACAACTTCAAAAA
Found at i:35349001 original size:6 final size:6
Alignment explanation
Indices: 35348983--35349150 Score: 112
Period size: 6 Copynumber: 27.3 Consensus size: 6
35348973 AAGAAACATT
* * *
35348983 ATCAGA A-CAAGA ATCAGA ATCAGA ATTAGA ATCAGA ACCAGA GTCAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA
* * * * * *
35349031 ATTAG- GTGACAGA ATCAGA ATCAGA ATCAGT ATCAGA TAACCGA ATCAAA
1 ATCAGA AT--CAGA ATCAGA ATCAGA ATCAGA ATCAGA -ATCAGA ATCAGA
* *
35349081 ATCAGA ATCAGC ATCAGGTA A-CAGA ATCAAA ATCAGA ATCA-A TATCAAGTA
1 ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAGA -ATC-AG-A
*
35349132 A-CAGA ATCAAA ATCAGA AT
1 ATCAGA ATCAGA ATCAGA AT
35349151 GTGAATGCAA
Statistics
Matches: 124, Mismatches: 24, Indels: 28
0.70 0.14 0.16
Matches are distributed among these distances:
5 7 0.06
6 101 0.81
7 12 0.10
8 3 0.02
9 1 0.01
ACGTcount: A:0.49, C:0.17, G:0.16, T:0.18
Consensus pattern (6 bp):
ATCAGA
Found at i:35349031 original size:18 final size:18
Alignment explanation
Indices: 35348992--35349149 Score: 72
Period size: 19 Copynumber: 8.6 Consensus size: 18
35348982 TATCAGAACA
* *
35348992 AGAATCAGAATCAGAATT
1 AGAATCAGAACCAGAATC
*
35349010 AGAATCAGAACCAGAGTC
1 AGAATCAGAACCAGAATC
* *
35349028 AGAATTAGGTGA-CAGAATC
1 AGAATCA-G-AACCAGAATC
* *
35349047 AGAATCAGAATCAGTATC
1 AGAATCAGAACCAGAATC
* * * *
35349065 AGATAACCGAATCAAAATC
1 AGA-ATCAGAACCAGAATC
* *
35349084 AGAATCAGCATCAGGTAA-C
1 AGAATCAGAACCA-G-AATC
* *
35349103 AGAATCAAAATCAGAATC
1 AGAATCAGAACCAGAATC
35349121 A-ATATCAAGTAA-CAGAATC
1 AGA-ATC-AG-AACCAGAATC
*
35349140 AAAATCAGAA
1 AGAATCAGAA
35349150 TGTGAATGCA
Statistics
Matches: 109, Mismatches: 20, Indels: 23
0.72 0.13 0.15
Matches are distributed among these distances:
17 6 0.06
18 46 0.42
19 51 0.47
20 6 0.06
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.18
Consensus pattern (18 bp):
AGAATCAGAACCAGAATC
Found at i:35349077 original size:31 final size:31
Alignment explanation
Indices: 35349039--35349150 Score: 163
Period size: 31 Copynumber: 3.6 Consensus size: 31
35349029 GAATTAGGTG
*
35349039 ACAGAATCAGAATCAGAATCAGTATCAGATA
1 ACAGAATCAAAATCAGAATCAGTATCAGATA
* * *
35349070 ACCGAATCAAAATCAGAATCAGCATCAGGTA
1 ACAGAATCAAAATCAGAATCAGTATCAGATA
*
35349101 ACAGAATCAAAATCAGAATCAATATCA-AGTA
1 ACAGAATCAAAATCAGAATCAGTATCAGA-TA
35349132 ACAGAATCAAAATCAGAAT
1 ACAGAATCAAAATCAGAAT
35349151 GTGAATGCAA
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
31 72 1.00
ACGTcount: A:0.51, C:0.18, G:0.13, T:0.18
Consensus pattern (31 bp):
ACAGAATCAAAATCAGAATCAGTATCAGATA
Found at i:35349115 original size:62 final size:62
Alignment explanation
Indices: 35349010--35349150 Score: 185
Period size: 62 Copynumber: 2.3 Consensus size: 62
35349000 AATCAGAATT
* * * * * * *
35349010 AGAATCAGAACCAGAGTCAGAATTAGGTGACAGAATCAGAATCAGAATCAGTATC-AGATAAC
1 AGAATCAAAATCAGAATCAGAATCAGGTAACAGAATCAAAATCAGAATCAATATCAAG-TAAC
* *
35349072 CGAATCAAAATCAGAATCAGCATCAGGTAACAGAATCAAAATCAGAATCAATATCAAGTAAC
1 AGAATCAAAATCAGAATCAGAATCAGGTAACAGAATCAAAATCAGAATCAATATCAAGTAAC
35349134 AGAATCAAAATCAGAAT
1 AGAATCAAAATCAGAAT
35349151 GTGAATGCAA
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
62 66 0.97
63 2 0.03
ACGTcount: A:0.49, C:0.17, G:0.16, T:0.18
Consensus pattern (62 bp):
AGAATCAAAATCAGAATCAGAATCAGGTAACAGAATCAAAATCAGAATCAATATCAAGTAAC
Found at i:35349325 original size:27 final size:26
Alignment explanation
Indices: 35349283--35349355 Score: 83
Period size: 27 Copynumber: 2.8 Consensus size: 26
35349273 CTCAGTTATT
* *
35349283 AGATATTGTGACAGAGTCACCAGATAC
1 AGATATTGTGGCAGAGCCACCAGA-AC
* *
35349310 AGATATTGTGGTAGAGCCACCAGAAT
1 AGATATTGTGGCAGAGCCACCAGAAC
* *
35349336 AGATAATGTGGCAAAGCCAC
1 AGATATTGTGGCAGAGCCAC
35349356 TTAACAAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
26 18 0.46
27 21 0.54
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.21
Consensus pattern (26 bp):
AGATATTGTGGCAGAGCCACCAGAAC
Found at i:35349542 original size:22 final size:23
Alignment explanation
Indices: 35349514--35349575 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 23
35349504 GCAAATACGT
*
35349514 TTGGCACACAGCCATAAT-TAGG
1 TTGGCACAAAGCCATAATGTAGG
*
35349536 TTGGCACAGAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAATGTAGG
**
35349558 TTAACACAAAGCCATAAT
1 TTGGCACAAAGCCATAAT
35349576 CAGAAGGCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 2 0.06
22 30 0.88
23 2 0.06
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (23 bp):
TTGGCACAAAGCCATAATGTAGG
Found at i:35350062 original size:27 final size:27
Alignment explanation
Indices: 35350004--35350334 Score: 454
Period size: 27 Copynumber: 12.3 Consensus size: 27
35349994 AGGGGCAAAA
* * *
35350004 TGGTAATTTTACCCCACA-AGGTA-TC
1 TGGTAATTCTACCCTACAGGGGTATTC
* *
35350029 TCGGTAATTCCACCCTACAGGGGTATTT
1 T-GGTAATTCTACCCTACAGGGGTATTC
* *
35350057 TAGTAATTCTACCCTACAAGGGTATT-
1 TGGTAATTCTACCCTACAGGGGTATTC
35350083 TCGGTAATTCTACCCTACAGGGGTATTGC
1 T-GGTAATTCTACCCTACAGGGGTATT-C
*
35350112 -GGTAATTCTACCCTACAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTC
*
35350138 TGGTAATTCTACCCTACAAGGGTATTC
1 TGGTAATTCTACCCTACAGGGGTATTC
35350165 TGGTAATTCTACCCTACAGGGGTATTC
1 TGGTAATTCTACCCTACAGGGGTATTC
* *
35350192 CGGTAATTCTACTCTACAGGGGTATTC
1 TGGTAATTCTACCCTACAGGGGTATTC
35350219 TGGTAATTCTACCCTACAGGGGTATTC
1 TGGTAATTCTACCCTACAGGGGTATTC
* *
35350246 CGGTAATTCTACCCTACAGGGATATTC
1 TGGTAATTCTACCCTACAGGGGTATTC
* *
35350273 CGGTAATTCTACCTTACAGGGGTATTC
1 TGGTAATTCTACCCTACAGGGGTATTC
* *
35350300 TGGTAATTCTACCCTATAGGGGTATTT
1 TGGTAATTCTACCCTACAGGGGTATTC
35350327 TGGTAATT
1 TGGTAATT
35350335 TTGTAAATCG
Statistics
Matches: 273, Mismatches: 26, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
25 1 0.00
26 15 0.05
27 255 0.93
28 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (27 bp):
TGGTAATTCTACCCTACAGGGGTATTC
Found at i:35350512 original size:81 final size:78
Alignment explanation
Indices: 35350356--35350595 Score: 194
Period size: 81 Copynumber: 3.0 Consensus size: 78
35350346 GGGTAAAATG
* * * * * *
35350356 GTAATTCTGTAAATCAGGGGTACTTTGGTAATTCTACAAG-TCGAGGGTATTTCAATAATTTTAC
1 GTAATT-TATAAATCAGGGGTA-TTTTGTTATTTTACAAGCTAG-GGGTATTT-TATAATTTTAC
*** *
35350420 AGGTCAAGGGTATTTCA
62 AAACCAGGGGTATTTCA
*
35350437 GTAATTTCATAAATCAGGGATATTTTGTTACTTTTACAAGCTAGGGGTATTTTGATAATTTTACA
1 GTAATTT-ATAAATCAGGGGTATTTTGTTA-TTTTACAAGCTAGGGGTATTTT-ATAATTTTACA
**
35350502 AACCAGGGGTATTTTG
63 AACCAGGGGTATTTCA
* * * * * * * *
35350518 GTAATTTACAAACCAGGGGTATTTTGGTGATTTTATAAACCAAGGGTATTCTAGTAATTTTACAA
1 GTAATTTATAAATCAGGGGTATTTT-GTTATTTTACAAGCTAGGGGTATTTTA-TAATTTTACAA
*
35350583 ACCAGTGGTATTT
64 ACCAGGGGTATTT
35350596 TGGTAAACTA
Statistics
Matches: 130, Mismatches: 23, Indels: 13
0.78 0.14 0.08
Matches are distributed among these distances:
79 1 0.01
80 62 0.48
81 65 0.50
82 2 0.02
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.38
Consensus pattern (78 bp):
GTAATTTATAAATCAGGGGTATTTTGTTATTTTACAAGCTAGGGGTATTTTATAATTTTACAAAC
CAGGGGTATTTCA
Found at i:35350542 original size:53 final size:53
Alignment explanation
Indices: 35350451--35350597 Score: 168
Period size: 53 Copynumber: 2.7 Consensus size: 53
35350441 TTTCATAAAT
* * * * *
35350451 CAGGGATATTTTGTTACTTTTACAAGCTAGGGGTATTTTGATAATTTTACAAAC
1 CAGGGGTATTTTGGTA-ATTTACAAACCAGGGGTATTTTGATAATTTTACAAAC
* * *
35350505 CAGGGGTATTTTGGTAATTTACAAACCAGGGGTATTTTGGTGATTTTATAAAC
1 CAGGGGTATTTTGGTAATTTACAAACCAGGGGTATTTTGATAATTTTACAAAC
* * * *
35350558 CAAGGGTATTCTAGTAATTTTACAAACCAGTGGTATTTTG
1 CAGGGGTATTTTGGTAA-TTTACAAACCAGGGGTATTTTG
35350598 GTAAACTAAA
Statistics
Matches: 80, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
53 45 0.56
54 35 0.44
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (53 bp):
CAGGGGTATTTTGGTAATTTACAAACCAGGGGTATTTTGATAATTTTACAAAC
Found at i:35350584 original size:27 final size:27
Alignment explanation
Indices: 35350319--35350601 Score: 167
Period size: 27 Copynumber: 10.5 Consensus size: 27
35350309 TACCCTATAG
** * *
35350319 GGGTATTTTGGTAATTTTGTAAATCGA
1 GGGTATTTTGGTAATTTTACAAACCAA
*** * ** * *
35350346 GGGTAAAATGGTAATTCTGTAAATCAG
1 GGGTATTTTGGTAATTTTACAAACCAA
* * ** *
35350373 GGGTACTTTGGTAATTCTACAAGTCGA
1 GGGTATTTTGGTAATTTTACAAACCAA
*** ***
35350400 GGGTATTTCAATAATTTTACAGGTCAA
1 GGGTATTTTGGTAATTTTACAAACCAA
** * * *
35350427 GGGTATTTCAGTAATTTCATAAATC-A
1 GGGTATTTTGGTAATTTTACAAACCAA
* * * * *
35350453 GGGATATTTTGTTACTTTTACAAGCTAG
1 GGG-TATTTTGGTAATTTTACAAACCAA
* *
35350481 GGGTATTTTGATAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAA
*
35350508 GGGTATTTTGGTAA-TTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAA
* *
35350534 GGGTATTTTGGTGATTTTATAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCAA
* *
35350561 GGGTATTCTAGTAATTTTACAAACC-A
1 GGGTATTTTGGTAATTTTACAAACCAA
35350587 GTGGTATTTTGGTAA
1 G-GGTATTTTGGTAA
35350602 ACTAAAGTAT
Statistics
Matches: 202, Mismatches: 50, Indels: 8
0.78 0.19 0.03
Matches are distributed among these distances:
26 31 0.15
27 168 0.83
28 3 0.01
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.38
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACCAA
Found at i:35352566 original size:6 final size:6
Alignment explanation
Indices: 35352555--35352713 Score: 103
Period size: 6 Copynumber: 25.8 Consensus size: 6
35352545 TATCGGAACT
* * *
35352555 AGAATC AGAATC AGAATT AGAATC AGAA-C TAGAATC AGAATT AG-GTGAC
1 AGAATC AGAATC AGAATC AGAATC AGAATC -AGAATC AGAATC AGAAT--C
* * * *
35352604 AGAATC AGAATC AGAATC AGTATC AAGTAA-C CGAATC AAAATC AAAATC
1 AGAATC AGAATC AGAATC AGAATC -AG-AATC AGAATC AGAATC AGAATC
* * *
35352653 AGCATC AGGTAA-C AGAATC AAAATC AGAATC AGTATC AAGTAA-C AGAATC
1 AGAATC A-G-AATC AGAATC AGAATC AGAATC AGAATC -AG-AATC AGAATC
*
35352703 AAAATC AGAAT
1 AGAATC AGAAT
35352714 GTGAATGCAA
Statistics
Matches: 119, Mismatches: 20, Indels: 28
0.71 0.12 0.17
Matches are distributed among these distances:
5 8 0.07
6 95 0.80
7 12 0.10
8 4 0.03
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.19
Consensus pattern (6 bp):
AGAATC
Found at i:35352575 original size:18 final size:18
Alignment explanation
Indices: 35352555--35352713 Score: 103
Period size: 19 Copynumber: 8.6 Consensus size: 18
35352545 TATCGGAACT
*
35352555 AGAATCAGAATCAGAATT
1 AGAATCAGAATCAGAATC
35352573 AGAATCAGAA-CTAGAATC
1 AGAATCAGAATC-AGAATC
* *
35352591 AGAATTAG-GTGACAGAATC
1 AGAATCAGAAT--CAGAATC
*
35352610 AGAATCAGAATCAGTATC
1 AGAATCAGAATCAGAATC
* *
35352628 AAGTAA-CCGAATCAAAATC
1 -AG-AATCAGAATCAGAATC
* *
35352647 AAAATCAGCATCAGGTAA-C
1 AGAATCAGAATCA-G-AATC
*
35352666 AGAATCAAAATCAGAATC
1 AGAATCAGAATCAGAATC
*
35352684 AGTATCAAGTAA-CAGAATC
1 AGAATC-AG-AATCAGAATC
*
35352703 AAAATCAGAAT
1 AGAATCAGAAT
35352714 GTGAATGCAA
Statistics
Matches: 107, Mismatches: 20, Indels: 28
0.69 0.13 0.18
Matches are distributed among these distances:
17 7 0.07
18 44 0.41
19 48 0.45
20 8 0.07
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.19
Consensus pattern (18 bp):
AGAATCAGAATCAGAATC
Found at i:35352640 original size:31 final size:31
Alignment explanation
Indices: 35352602--35352713 Score: 179
Period size: 31 Copynumber: 3.6 Consensus size: 31
35352592 GAATTAGGTG
*
35352602 ACAGAATCAGAATCAGAATCAGTATCAAGTA
1 ACAGAATCAAAATCAGAATCAGTATCAAGTA
* * * *
35352633 ACCGAATCAAAATCAAAATCAGCATCAGGTA
1 ACAGAATCAAAATCAGAATCAGTATCAAGTA
35352664 ACAGAATCAAAATCAGAATCAGTATCAAGTA
1 ACAGAATCAAAATCAGAATCAGTATCAAGTA
35352695 ACAGAATCAAAATCAGAAT
1 ACAGAATCAAAATCAGAAT
35352714 GTGAATGCAA
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 72 1.00
ACGTcount: A:0.51, C:0.18, G:0.13, T:0.18
Consensus pattern (31 bp):
ACAGAATCAAAATCAGAATCAGTATCAAGTA
Found at i:35352653 original size:62 final size:62
Alignment explanation
Indices: 35352587--35352709 Score: 201
Period size: 62 Copynumber: 2.0 Consensus size: 62
35352577 TCAGAACTAG
* * * *
35352587 AATCAGAATTAGGTGACAGAATCAGAATCAGAATCAGTATCAAGTAACCGAATCAAAATCAA
1 AATCAGAATCAGGTAACAGAATCAAAATCAGAATCAGTATCAAGTAACAGAATCAAAATCAA
*
35352649 AATCAGCATCAGGTAACAGAATCAAAATCAGAATCAGTATCAAGTAACAGAATCAAAATCA
1 AATCAGAATCAGGTAACAGAATCAAAATCAGAATCAGTATCAAGTAACAGAATCAAAATCA
35352710 GAATGTGAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 56 1.00
ACGTcount: A:0.50, C:0.17, G:0.15, T:0.19
Consensus pattern (62 bp):
AATCAGAATCAGGTAACAGAATCAAAATCAGAATCAGTATCAAGTAACAGAATCAAAATCAA
Found at i:35352908 original size:26 final size:27
Alignment explanation
Indices: 35352844--35352917 Score: 96
Period size: 27 Copynumber: 2.8 Consensus size: 27
35352834 GCTCAGTTAT
* *
35352844 CAGATATTGTGACAGAGTCACCAGAAA
1 CAGATATTGTGGCAGAGCCACCAGAAA
*
35352871 TAGATATTGTGGCAGAGCCACCAG-AA
1 CAGATATTGTGGCAGAGCCACCAGAAA
* *
35352897 CAGATAATGTGGCAAAGCCAC
1 CAGATATTGTGGCAGAGCCAC
35352918 TTAACAGAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
26 20 0.49
27 21 0.51
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.18
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGAAA
Found at i:35353104 original size:22 final size:22
Alignment explanation
Indices: 35353076--35353140 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
35353066 GTAAATACAT
*
35353076 TTGGCACACAGCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
* *
35353098 TTGGCACAGAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
**
35353120 TTAACACAAAGCCATAATCAG
1 TTGGCACAAAGCCATAATCAG
35353141 AAGGCTTTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 2 0.06
22 31 0.89
23 2 0.06
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:35353624 original size:27 final size:27
Alignment explanation
Indices: 35353567--35353869 Score: 421
Period size: 27 Copynumber: 11.3 Consensus size: 27
35353557 GGGGCAAAAT
* * *
35353567 GGTAATTTTACCCCACA-AGGTA-TCTC
1 GGTAATTCTACCCTACAGGGGTATTC-C
* **
35353593 GGTAATTCCACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTCC
*
35353620 AGTAATTCTACCCTACAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTCC
35353647 GGTAATTCTACCCTACAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTCC
* **
35353674 GGTAATTCTACCCTATAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTCC
* * * *
35353701 GGTAATTCTACCCAACAAGGGTGTTCT
1 GGTAATTCTACCCTACAGGGGTATTCC
35353728 GGTAATTCTACCCTACAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTCC
* *
35353755 GGTAATTCTACCTTACAGGGATATTCC
1 GGTAATTCTACCCTACAGGGGTATTCC
35353782 GGTAATTCTACCCTACAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTCC
35353809 GGTAATTCTACCCTACAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTCC
**
35353836 GGTAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTCC
35353863 GGTAATT
1 GGTAATT
35353870 TTGTAAATCG
Statistics
Matches: 246, Mismatches: 29, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
26 14 0.06
27 231 0.94
28 1 0.00
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTCC
Found at i:35353884 original size:27 final size:27
Alignment explanation
Indices: 35353854--35353942 Score: 90
Period size: 27 Copynumber: 3.3 Consensus size: 27
35353844 TACCCTACAG
*
35353854 GGGTATTTTGGTAATTTTGTAAATCGA
1 GGGTATTTTGGTAATTCTGTAAATCGA
***
35353881 GGGTAAAATGGTAATTCTGTAAATC-A
1 GGGTATTTTGGTAATTCTGTAAATCGA
* ** *
35353907 GGGGTACTTTGGTAATTCTACAAGTCGA
1 -GGGTATTTTGGTAATTCTGTAAATCGA
35353935 GGGTATTT
1 GGGTATTT
35353943 CAATAATTTT
Statistics
Matches: 49, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
26 1 0.02
27 47 0.96
28 1 0.02
ACGTcount: A:0.28, C:0.08, G:0.27, T:0.37
Consensus pattern (27 bp):
GGGTATTTTGGTAATTCTGTAAATCGA
Found at i:35353978 original size:27 final size:27
Alignment explanation
Indices: 35353919--35354035 Score: 98
Period size: 27 Copynumber: 4.4 Consensus size: 27
35353909 GGTACTTTGG
*
35353919 TAATTCTACAAGTCGAGGGTATTTCAA
1 TAATTTTACAAGTCGAGGGTATTTCAA
* *
35353946 TAATTTTACAGGTCGAGGGTATTTCAC
1 TAATTTTACAAGTCGAGGGTATTTCAA
* * ***
35353973 TAATTTCACAAATC-AGGGATATTTTGG
1 TAATTTTACAAGTCGAGGG-TATTTCAA
* *
35354000 TAATTTTACAAG-CTAGGGGTA-TT-GA
1 TAATTTTACAAGTCGA-GGGTATTTCAA
35354025 TAATTTTACAA
1 TAATTTTACAA
35354036 ACCAGGGGTA
Statistics
Matches: 75, Mismatches: 12, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
25 12 0.16
26 7 0.09
27 53 0.71
28 3 0.04
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (27 bp):
TAATTTTACAAGTCGAGGGTATTTCAA
Found at i:35354049 original size:52 final size:54
Alignment explanation
Indices: 35353901--35354128 Score: 173
Period size: 54 Copynumber: 4.3 Consensus size: 54
35353891 GTAATTCTGT
* ** ***
35353901 AAATCAGGGGTACTTTG-GTAATTCTACAAGTC-GAGGGTATTTCAATAATTTTAC
1 AAATCAGGGGTA-TTTGAGTAATTTTACAAACCAG-GGGTATTTTGGTAATTTTAC
** * * * * *
35353955 AGGTC-GAGGGTATTTCACTAATTTCACAAATCAGGGATATTTTGGTAATTTTAC
1 AAATCAG-GGGTATTTGAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTAC
*
35354009 -AAGCTAGGGGTA-TTGA-TAATTTTACAAACCAGGGGTATTTTGGTAA-TTTAC
1 AAATC-AGGGGTATTTGAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTAC
* * * * * *
35354060 AAATCAGGGGTATTTTAGTGATTTTATAAACCAAGGGTATTCTAGTAATTTTAC
1 AAATCAGGGGTATTTGAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTAC
* *
35354114 AAACCAGTGGTATTT
1 AAATCAGGGGTATTT
35354129 TGGTAAACTA
Statistics
Matches: 138, Mismatches: 27, Indels: 18
0.75 0.15 0.10
Matches are distributed among these distances:
51 12 0.09
52 33 0.24
53 33 0.24
54 58 0.42
55 2 0.01
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (54 bp):
AAATCAGGGGTATTTGAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTAC
Found at i:35354098 original size:53 final size:53
Alignment explanation
Indices: 35353962--35354129 Score: 171
Period size: 53 Copynumber: 3.2 Consensus size: 53
35353952 TACAGGTCGA
* * * * *
35353962 GGGTATTTCACTAATTTCACAAATC-AGGGATATTTTGGTAATTTTACAAGCTAG
1 GGGTATTTTA-TAATTTTACAAACCAAGGG-TATTTTGGTAATTTTACAAACCAG
* * *
35354016 GGGTA-TTGATAATTTTACAAACCAGGGGTATTTTGGTAA-TTTACAAATCAG
1 GGGTATTTTATAATTTTACAAACCAAGGGTATTTTGGTAATTTTACAAACCAG
* * * *
35354067 GGGTATTTTAGTGATTTTATAAACCAAGGGTATTCTAGTAATTTTACAAACCAG
1 GGGTATTTTA-TAATTTTACAAACCAAGGGTATTTTGGTAATTTTACAAACCAG
*
35354121 TGGTATTTT
1 GGGTATTTT
35354130 GGTAAACTAA
Statistics
Matches: 95, Mismatches: 15, Indels: 8
0.81 0.13 0.07
Matches are distributed among these distances:
51 14 0.15
52 26 0.27
53 31 0.33
54 24 0.25
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.38
Consensus pattern (53 bp):
GGGTATTTTATAATTTTACAAACCAAGGGTATTTTGGTAATTTTACAAACCAG
Found at i:35354134 original size:27 final size:27
Alignment explanation
Indices: 35353973--35354134 Score: 177
Period size: 27 Copynumber: 6.1 Consensus size: 27
35353963 GGTATTTCAC
* * *
35353973 TAATTTCACAAATCAGGGATATTTTGG
1 TAATTTTACAAACCAGGGGTATTTTGG
* * *
35354000 TAATTTTACAAGCTAGGGGTA--TTGA
1 TAATTTTACAAACCAGGGGTATTTTGG
35354025 TAATTTTACAAACCAGGGGTATTTTGG
1 TAATTTTACAAACCAGGGGTATTTTGG
* *
35354052 TAA-TTTACAAATCAGGGGTATTTTAG
1 TAATTTTACAAACCAGGGGTATTTTGG
* * * * *
35354078 TGATTTTATAAACCAAGGGTATTCTAG
1 TAATTTTACAAACCAGGGGTATTTTGG
*
35354105 TAATTTTACAAACCAGTGGTATTTTGG
1 TAATTTTACAAACCAGGGGTATTTTGG
35354132 TAA
1 TAA
35354135 ACTAAAGTAT
Statistics
Matches: 110, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
25 22 0.20
26 23 0.21
27 65 0.59
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.38
Consensus pattern (27 bp):
TAATTTTACAAACCAGGGGTATTTTGG
Found at i:35365776 original size:21 final size:21
Alignment explanation
Indices: 35365748--35365833 Score: 100
Period size: 21 Copynumber: 4.1 Consensus size: 21
35365738 CCTGATCAGT
* *
35365748 ATACGACACATAAAGTGCCTA
1 ATACGACACACAAAGTGCCTG
* * *
35365769 AAACGACACACGAGGTGCCTG
1 ATACGACACACAAAGTGCCTG
* *
35365790 ATACGACACACGAGGTGCCTG
1 ATACGACACACAAAGTGCCTG
*
35365811 ATACGACACATAAAGTGCCTG
1 ATACGACACACAAAGTGCCTG
35365832 AT
1 AT
35365834 CGATAAAGCC
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.36, C:0.26, G:0.22, T:0.16
Consensus pattern (21 bp):
ATACGACACACAAAGTGCCTG
Found at i:35367299 original size:16 final size:17
Alignment explanation
Indices: 35367264--35367299 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
35367254 CCTAATTCTC
35367264 CCTT-TTTCTTTTCTTT
1 CCTTCTTTCTTTTCTTT
35367280 -CTTCTTTC-TTTCTTT
1 CCTTCTTTCTTTTCTTT
35367295 CCTTC
1 CCTTC
35367300 CCCTGCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (17 bp):
CCTTCTTTCTTTTCTTT
Found at i:35372357 original size:18 final size:17
Alignment explanation
Indices: 35372334--35372376 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
35372324 CGTAAGATTC
35372334 TTCTTCTCCAGTATGCAT
1 TTCTTCTCCAGTAT-CAT
35372352 TTCTTCAT-CAGTATCAT
1 TTCTTC-TCCAGTATCAT
*
35372369 TTATTCTC
1 TTCTTCTC
35372377 TCATCCGACA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
16 1 0.05
17 8 0.36
18 12 0.55
19 1 0.05
ACGTcount: A:0.19, C:0.26, G:0.07, T:0.49
Consensus pattern (17 bp):
TTCTTCTCCAGTATCAT
Found at i:35373662 original size:21 final size:21
Alignment explanation
Indices: 35373634--35373719 Score: 100
Period size: 21 Copynumber: 4.1 Consensus size: 21
35373624 CCTGATCAGT
* *
35373634 ATACGACACATAAAGTGCCTA
1 ATACGACACACAAAGTGCCTG
* * *
35373655 AAACGACACACGAGGTGCCTG
1 ATACGACACACAAAGTGCCTG
* *
35373676 ATACGACACACGAGGTGCCTG
1 ATACGACACACAAAGTGCCTG
*
35373697 ATACGACACATAAAGTGCCTG
1 ATACGACACACAAAGTGCCTG
35373718 AT
1 AT
35373720 CGATAAAGCC
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.36, C:0.26, G:0.22, T:0.16
Consensus pattern (21 bp):
ATACGACACACAAAGTGCCTG
Found at i:35375176 original size:16 final size:17
Alignment explanation
Indices: 35375141--35375176 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
35375131 CCTAATTCTC
35375141 CCTT-TTTCTTTTCTTT
1 CCTTCTTTCTTTTCTTT
35375157 -CTTCTTTC-TTTCTTT
1 CCTTCTTTCTTTTCTTT
35375172 CCTTC
1 CCTTC
35375177 CCCTGCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (17 bp):
CCTTCTTTCTTTTCTTT
Found at i:35381088 original size:159 final size:158
Alignment explanation
Indices: 35380842--35381608 Score: 1011
Period size: 159 Copynumber: 4.9 Consensus size: 158
35380832 TTTTTCCGTC
* * * *
35380842 TTTTGGGAAAACGGCAACGTTTTATAGTATATT-TAATAT-AGAATTCAAAGTAAGAAGTCAACG
1 TTTTGGGAAAACGGCAACGTTTTATATTAT-TTATAAAATCAGAATTCAGAGTAAGAAATCAACG
35380905 GCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGC
65 GCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGC
35380970 ATGGGCCAGTGAAAGCAACTTCCTCTAATT
130 ATGGGCCA-TGAAAGCAACTTCCTCTAATT
* ** *
35381000 TTTTGGGAAAACGGCAACGTTTAATATTATTTATAAAATCAGAACACAGAGAAAGAAATCAACGG
1 TTTTGGGAAAACGGCAACGTTTTATATTATTTATAAAATCAGAATTCAGAGTAAGAAATCAACGG
35381065 CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCA
66 CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCA
35381130 TGGGCCAATGAAAGCAACTTCCTCTAATT
131 TGGGCC-ATGAAAGCAACTTCCTCTAATT
* * *
35381159 TTTTGGGAAAACGGCAACGTTTTATATTATTTATAAAAACAGAACTCAGAGTCAGAAATCAACGG
1 TTTTGGGAAAACGGCAACGTTTTATATTATTTATAAAATCAGAATTCAGAGTAAGAAATCAACGG
*
35381224 CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCACAGGTTCGAGACCTGCA
66 CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCA
* *
35381289 TAGGCCACTAAAAGCAACTTCCTCTAATT
131 TGGGCCA-TGAAAGCAACTTCCTCTAATT
* ** * *
35381318 TTTTGGGAAAACGGCAACGTTTTATATTATCTATTAAAA-CAGAATTTTGAGTAAGAAGTCAATG
1 TTTTGGGAAAACGGCAACGTTTTATATTATTTA-TAAAATCAGAATTCAGAGTAAGAAATCAACG
35381382 GCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGC
65 GCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGC
* * * * *
35381447 ATGGGCCATTATTAGTTC-A-TT-CTTTTA-C
130 ATGGGCCATGA-AAG--CAACTTCCTCTAATT
* ** * * ** * * *
35381475 TTTTGGGAAAACGG-AGATG-TTT-T-TGCTTTAGAGAAGAAGAATTTA-A-AAATTGAAAACAA
1 TTTTGGGAAAACGGCA-ACGTTTTATATTATTTATAAAATCAGAATTCAGAGTAA--GAAATCAA
* * *
35381534 GGGCCTATTAGCTCAGTTGTTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCT
63 CGGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCT
35381599 GCATGGGCCA
128 GCATGGGCCA
35381609 CTTATGATAT
Statistics
Matches: 553, Mismatches: 44, Indels: 28
0.88 0.07 0.04
Matches are distributed among these distances:
152 2 0.00
153 4 0.01
154 89 0.16
155 1 0.00
156 4 0.01
157 18 0.03
158 40 0.07
159 387 0.70
160 7 0.01
161 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.27
Consensus pattern (158 bp):
TTTTGGGAAAACGGCAACGTTTTATATTATTTATAAAATCAGAATTCAGAGTAAGAAATCAACGG
CCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCA
TGGGCCATGAAAGCAACTTCCTCTAATT
Found at i:35382316 original size:42 final size:42
Alignment explanation
Indices: 35382257--35382342 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 42
35382247 ACGGTATTTG
** *
35382257 ATCGGCAAACCTTGATAAGGATGTCAGCCAGGCATTGTAAAA
1 ATCGGCAAACCTTGATAAGGAAATCAGCCAGGCATTATAAAA
35382299 ATCGGCAAACCTTGATAAGGAAATCAGCCAGGCATTATAAAA
1 ATCGGCAAACCTTGATAAGGAAATCAGCCAGGCATTATAAAA
35382341 AT
1 AT
35382343 TAAATTCATT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.21
Consensus pattern (42 bp):
ATCGGCAAACCTTGATAAGGAAATCAGCCAGGCATTATAAAA
Found at i:35383165 original size:6 final size:6
Alignment explanation
Indices: 35383154--35383192 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
35383144 GGTTTTCTCC
*
35383154 AAAATG AAAATG AAAATG AAAATG AAAACG AAAAATG AA
1 AAAATG AAAATG AAAATG AAAATG AAAATG -AAAATG AA
35383193 TTTATTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 25 0.83
7 5 0.17
ACGTcount: A:0.69, C:0.03, G:0.15, T:0.13
Consensus pattern (6 bp):
AAAATG
Found at i:35385933 original size:3 final size:3
Alignment explanation
Indices: 35385925--35385965 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
35385915 TACTATAGCG
35385925 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
35385966 ATTTATTAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:35385993 original size:16 final size:16
Alignment explanation
Indices: 35385955--35385996 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
35385945 TTATTATTAT
35385955 TATT-ATTATTAATTTA
1 TATTAATTA-TAATTTA
*
35385971 T-TAAATTATAATTTA
1 TATTAATTATAATTTA
35385986 TATTAATTATA
1 TATTAATTATA
35385997 TTATGAGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTAATTATAATTTA
Found at i:35385995 original size:9 final size:10
Alignment explanation
Indices: 35385925--35385999 Score: 64
Period size: 9 Copynumber: 8.5 Consensus size: 10
35385915 TACTATAGCG
35385925 TATT-ATTAT
1 TATTAATTAT
35385934 TATT-ATTAT
1 TATTAATTAT
35385943 TATT-ATTAT
1 TATTAATTAT
35385952 TATT-ATTAT
1 TATTAATTAT
35385961 TATTAA-T-T
1 TATTAATTAT
35385969 TATTAA--AT
1 TATTAATTAT
35385977 TA-TAATT-T
1 TATTAATTAT
35385985 ATATTAATTA-
1 -TATTAATTAT
35385995 TATTA
1 TATTA
35386000 TGAGATTTTT
Statistics
Matches: 59, Mismatches: 0, Indels: 14
0.81 0.00 0.19
Matches are distributed among these distances:
7 3 0.05
8 11 0.19
9 39 0.66
10 6 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
TATTAATTAT
Found at i:35387263 original size:17 final size:18
Alignment explanation
Indices: 35387241--35387276 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
35387231 TAAATGAGTT
35387241 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
35387258 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
35387276 A
1 A
35387277 TAGAAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:35387596 original size:18 final size:18
Alignment explanation
Indices: 35387573--35387609 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
35387563 TTTGTGATCA
*
35387573 AAATTGAAGGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
*
35387591 AAATTGAAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
35387609 A
1 A
35387610 CAGGAATTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:35389533 original size:198 final size:198
Alignment explanation
Indices: 35389185--35389581 Score: 704
Period size: 198 Copynumber: 2.0 Consensus size: 198
35389175 ACTAGTCACA
*
35389185 GCATTTTACTCGGTGAGATTGTTCCAATATAACTCATTTGTGGTGCATGATACAATAGGTGTTGA
1 GCATGTTACTCGGTGAGATTGTTCCAATATAACTCATTTGTGGTGCATGATACAATAGGTGTTGA
*
35389250 GTTGATGGTTATACACTCAAGATCTTTTAGTTAAATAACTCCCCAAGGAGTTATGCTTAAGTTAG
66 GTTGATGGTTATACACTCAAGATCTTTTAGTTAAATAACTCCCCAAAGAGTTATGCTTAAGTTAG
* *
35389315 AAAGATGGTCAAACGTTACACAATTATTAGTACATGCGAATGCCTAAGGAATTAGGCTCGTCTAA
131 AAAGATCGTCAAACGTTACACAATTATTAGTACATGCGAATGCCTAAGGAATTAAGCTCGTCTAA
35389380 TTG
196 TTG
*
35389383 GCATGTTACTCGGTGAGATTGTTCCAATATAACTCATTTGTGGTGCATGATACGATAGGTGTTGA
1 GCATGTTACTCGGTGAGATTGTTCCAATATAACTCATTTGTGGTGCATGATACAATAGGTGTTGA
*
35389448 GTTGATGGTTATACACTCAAGATCTTTTAGTTAAATAACTTCCCAAAGAGTTATGCTTAAGTTAG
66 GTTGATGGTTATACACTCAAGATCTTTTAGTTAAATAACTCCCCAAAGAGTTATGCTTAAGTTAG
* * * *
35389513 AAAGATCGTCAAATGTTACACGATTATTAGTACGTGCGAATGCCTAAGGAATTAAGTTCGTCTAA
131 AAAGATCGTCAAACGTTACACAATTATTAGTACATGCGAATGCCTAAGGAATTAAGCTCGTCTAA
35389578 TTG
196 TTG
35389581 G
1 G
35389582 ATGAAATTAT
Statistics
Matches: 189, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
198 189 1.00
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (198 bp):
GCATGTTACTCGGTGAGATTGTTCCAATATAACTCATTTGTGGTGCATGATACAATAGGTGTTGA
GTTGATGGTTATACACTCAAGATCTTTTAGTTAAATAACTCCCCAAAGAGTTATGCTTAAGTTAG
AAAGATCGTCAAACGTTACACAATTATTAGTACATGCGAATGCCTAAGGAATTAAGCTCGTCTAA
TTG
Found at i:35391386 original size:13 final size:13
Alignment explanation
Indices: 35391364--35391402 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
35391354 AGTCTACCCG
*
35391364 TATTAATTTTTTA
1 TATTATTTTTTTA
35391377 TATTATTTTTTTA
1 TATTATTTTTTTA
35391390 TATTATTTTTTTA
1 TATTATTTTTTTA
35391403 AGAATATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TATTATTTTTTTA
Found at i:35395615 original size:25 final size:25
Alignment explanation
Indices: 35395587--35395637 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
35395577 AAATTGCTCC
35395587 CTAACTCAAAGTATCAATGCTTATA
1 CTAACTCAAAGTATCAATGCTTATA
*
35395612 CTAACTCAAAGTGTCAATGCTTATA
1 CTAACTCAAAGTATCAATGCTTATA
35395637 C
1 C
35395638 CAAGAATCGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.31
Consensus pattern (25 bp):
CTAACTCAAAGTATCAATGCTTATA
Found at i:35396742 original size:3 final size:3
Alignment explanation
Indices: 35396734--35396782 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
35396724 AGAACAAATA
*
35396734 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAA AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
35396781 AA
1 AA
35396783 ATAAATAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:35403578 original size:11 final size:11
Alignment explanation
Indices: 35403562--35403588 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
35403552 ACCTATCTCT
35403562 TAATATTTACA
1 TAATATTTACA
35403573 TAATATTTACA
1 TAATATTTACA
35403584 TAATA
1 TAATA
35403589 AACTAAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (11 bp):
TAATATTTACA
Found at i:35404002 original size:15 final size:16
Alignment explanation
Indices: 35403978--35404016 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
35403968 TAATTCATGC
*
35403978 AAAATAATAA-TATTT
1 AAAATAATAATTAATT
*
35403993 AAAATGATAATTAATT
1 AAAATAATAATTAATT
35404009 AAAATAAT
1 AAAATAAT
35404017 TAAAATATAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
AAAATAATAATTAATT
Found at i:35408675 original size:11 final size:11
Alignment explanation
Indices: 35408659--35408701 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
35408649 TAATAACGTG
35408659 TTTAATTAGGC
1 TTTAATTAGGC
*
35408670 TTTAATTAAGTGA
1 TTTAATT-AG-GC
*
35408683 ATTAATTAGGC
1 TTTAATTAGGC
35408694 TTTAATTA
1 TTTAATTA
35408702 AGTGAACTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 15 0.58
12 4 0.15
13 7 0.27
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.47
Consensus pattern (11 bp):
TTTAATTAGGC
Found at i:35408687 original size:24 final size:24
Alignment explanation
Indices: 35408660--35408707 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
35408650 AATAACGTGT
35408660 TTAATTAGGCTTTAATTAAGTGAA
1 TTAATTAGGCTTTAATTAAGTGAA
35408684 TTAATTAGGCTTTAATTAAGTGAA
1 TTAATTAGGCTTTAATTAAGTGAA
35408708 CTTAGCTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.17, T:0.42
Consensus pattern (24 bp):
TTAATTAGGCTTTAATTAAGTGAA
Found at i:35409724 original size:14 final size:13
Alignment explanation
Indices: 35409701--35409734 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
35409691 AAAATATAAA
*
35409701 CAAAATAAAAAAG
1 CAAAAAAAAAAAG
35409714 CAAAAAAAAAAAG
1 CAAAAAAAAAAAG
*
35409727 GAAAAAAA
1 CAAAAAAA
35409735 TCGAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.82, C:0.06, G:0.09, T:0.03
Consensus pattern (13 bp):
CAAAAAAAAAAAG
Found at i:35409878 original size:18 final size:16
Alignment explanation
Indices: 35409841--35409870 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35409831 TCCCTCTCCT
35409841 TCTCCCCTCTCTCTTC
1 TCTCCCCTCTCTCTTC
35409857 TCTCCCCTC-CTCTT
1 TCTCCCCTCTCTCTT
35409871 TTTCTCTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (16 bp):
TCTCCCCTCTCTCTTC
Found at i:35414929 original size:8 final size:8
Alignment explanation
Indices: 35414916--35414964 Score: 55
Period size: 8 Copynumber: 5.9 Consensus size: 8
35414906 AGTCATGAAA
35414916 AAAAAAAC
1 AAAAAAAC
35414924 AAAAAAAC
1 AAAAAAAC
35414932 AAAAAGAA-
1 AAAAA-AAC
*
35414940 AAAAGACAAG
1 AAAA-A-AAC
35414950 AAAAAAAC
1 AAAAAAAC
35414958 AAAAAAA
1 AAAAAAA
35414965 AAATCAAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
8 26 0.72
9 6 0.17
10 4 0.11
ACGTcount: A:0.86, C:0.08, G:0.06, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:35414930 original size:12 final size:12
Alignment explanation
Indices: 35414913--35414972 Score: 61
Period size: 12 Copynumber: 5.2 Consensus size: 12
35414903 GACAGTCATG
35414913 AAAAAAAAAACA
1 AAAAAAAAAACA
*
35414925 AAAAAACAAA-A
1 AAAAAAAAAACA
* *
35414936 AGAAAAAAGAC-
1 AAAAAAAAAACA
*
35414947 AAGAAAAAAACA
1 AAAAAAAAAACA
*
35414959 AAAAAAAAATCA
1 AAAAAAAAAACA
35414971 AA
1 AA
35414973 TGCCAGAAAG
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
11 16 0.43
12 21 0.57
ACGTcount: A:0.85, C:0.08, G:0.05, T:0.02
Consensus pattern (12 bp):
AAAAAAAAAACA
Found at i:35416836 original size:18 final size:18
Alignment explanation
Indices: 35416784--35416824 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
35416774 TACAAGAGCC
*
35416784 TCAAGGCAAGGACAAAGT
1 TCAACGCAAGGACAAAGT
35416802 TCAACGCAAGGACAAAGT
1 TCAACGCAAGGACAAAGT
35416820 TCAAC
1 TCAAC
35416825 CAGGGGCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (18 bp):
TCAACGCAAGGACAAAGT
Found at i:35417573 original size:55 final size:55
Alignment explanation
Indices: 35417496--35417655 Score: 266
Period size: 55 Copynumber: 2.9 Consensus size: 55
35417486 GTTTTCATTA
* *
35417496 TTATGTTTTTGAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTCAAT
1 TTATGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTCAAT
* *
35417551 TTATATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAAT
1 TTATGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTCAAT
*
35417606 TTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 TTATGTTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
35417656 CAGGGCACGC
Statistics
Matches: 98, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
55 60 0.61
56 38 0.39
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (55 bp):
TTATGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTCAAT
Found at i:35417692 original size:14 final size:14
Alignment explanation
Indices: 35417673--35417707 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
35417663 CGCTGAGGTA
35417673 TTTTCAATTTCTGC
1 TTTTCAATTTCTGC
35417687 TTTTCAATTTCTGC
1 TTTTCAATTTCTGC
35417701 TTTTCAA
1 TTTTCAA
35417708 AAAAATCAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.17, C:0.20, G:0.06, T:0.57
Consensus pattern (14 bp):
TTTTCAATTTCTGC
Found at i:35417758 original size:89 final size:88
Alignment explanation
Indices: 35417598--35417771 Score: 294
Period size: 89 Copynumber: 2.0 Consensus size: 88
35417588 TGAGTTGAGC
* * *
35417598 CTTTTAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCA
1 CTTTTAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCACGACA
* *
35417663 CGCTGAGGTATTTTCAATTTCTG
66 CACTGAGGTAATTTCAATTTCTG
35417686 CTTTTCAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCACGAC
1 CTTTT-AATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCACGAC
35417751 ACACTGAGGTAATTTCAATTT
65 ACACTGAGGTAATTTCAATTT
35417772 ATGTTTGTCA
Statistics
Matches: 80, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
88 5 0.06
89 75 0.94
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Consensus pattern (88 bp):
CTTTTAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCACGACA
CACTGAGGTAATTTCAATTTCTG
Found at i:35417811 original size:75 final size:75
Alignment explanation
Indices: 35417688--35418102 Score: 422
Period size: 75 Copynumber: 5.3 Consensus size: 75
35417678 AATTTCTGCT
* *
35417688 TTTCAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCACGACAC
1 TTTCAATTTCTGCTTTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
*
35417753 ACTGAGGTAA
66 GCTGAGGTAA
* *
35417763 TTTCAATTTATG-TTTGTCAAAAAAATCAGCTCATATGGCGAGAGGTGAGTTGAGCCTCAGGACA
1 TTTCAATTTCTGCTTT-TCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
*
35417827 TGCTGAGGTAA
65 CGCTGAGGTAA
* *
35417838 TTTCAATTTCTGATTTCTTCAATTTATGTTTTTCAAAAATCAGTTCATATTGCGAGAGGTGAGTT
1 TTTCAATTTCTG-CTT-TTC-A---A--------AAAAATCAGCTCATATTGCGAGAGGTGAGTT
* *
35417903 GAGCCTCAGGGCACGCTGAGGTAT
52 GAGCCTCAGGACACGCTGAGGTAA
* * * *
35417927 TTTCAATTTCTGCTTTTCAAAAACATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGAAAC
1 TTTCAATTTCTGCTTTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
35417992 GCTGAGGTAA
66 GCTGAGGTAA
* * * *
35418002 TTTCAATTTATG-TTTGTAAAAAAAAAAAAAAATCAGCTCATATCGCGAGATGTGAGTTGAGCCT
1 TTTCAATTTCTGCTTT-T-------CAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCT
* *
35418066 CAGGTCACGCTGAGGTAT
58 CAGGACACGCTGAGGTAA
35418084 TTTCAATTTCTG-TTTTCAA
1 TTTCAATTTCTGCTTTTCAA
35418103 TTTATGTTGT
Statistics
Matches: 284, Mismatches: 32, Indels: 49
0.78 0.09 0.13
Matches are distributed among these distances:
74 8 0.03
75 136 0.48
77 4 0.01
78 2 0.01
81 2 0.01
82 63 0.22
83 1 0.00
86 1 0.00
87 3 0.01
88 2 0.01
89 62 0.22
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (75 bp):
TTTCAATTTCTGCTTTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
GCTGAGGTAA
Found at i:35417811 original size:164 final size:162
Alignment explanation
Indices: 35417603--35418010 Score: 586
Period size: 164 Copynumber: 2.5 Consensus size: 162
35417593 TGAGCCTTTT
*
35417603 AATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTG
1 AATTTCTG-TTTTCAAAAAAATCAACTCATA-TGCGAGAGGTGAGTTGAGCCTCAGGACACGCTG
* *
35417668 AGGTATTTTCAATTTCTG-CTT-TTCAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGA
64 AGGTAATTTCAATTTCTGACTTCTTCAATTTATGCTTTTC--AAAAATCAACTCATATTGCGAGA
35417731 GGTGAGTTGAGCCTCACGACACACTGAGGTAATTTC
127 GGTGAGTTGAGCCTCACGACACACTGAGGTAATTTC
* * *
35417767 AATTTATGTTTGTCAAAAAAATCAGCTCATATGGCGAGAGGTGAGTTGAGCCTCAGGACATGCTG
1 AATTTCTGTTT-TCAAAAAAATCAACTCATAT-GCGAGAGGTGAGTTGAGCCTCAGGACACGCTG
* * **
35417832 AGGTAATTTCAATTTCTGATTTCTTCAATTTATGTTTTTCAAAAATCAGTTCATATTGCGAGAGG
64 AGGTAATTTCAATTTCTGACTTCTTCAATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAGG
* * * *
35417897 TGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTC
129 TGAGTTGAGCCTCACGACACACTGAGGTAATTTC
* *
35417931 AATTTCTGCTTTTCAAAAACATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGAAACGCTG
1 AATTTCTG-TTTTCAAAAAAATCAACTCAT-ATGCGAGAGGTGAGTTGAGCCTCAGGACACGCTG
35417996 AGGTAATTTCAATTT
64 AGGTAATTTCAATTT
35418011 ATGTTTGTAA
Statistics
Matches: 219, Mismatches: 19, Indels: 12
0.88 0.08 0.05
Matches are distributed among these distances:
163 4 0.02
164 193 0.88
165 7 0.03
166 15 0.07
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (162 bp):
AATTTCTGTTTTCAAAAAAATCAACTCATATGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
GTAATTTCAATTTCTGACTTCTTCAATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTG
AGTTGAGCCTCACGACACACTGAGGTAATTTC
Found at i:35417921 original size:89 final size:90
Alignment explanation
Indices: 35417764--35417938 Score: 280
Period size: 89 Copynumber: 1.9 Consensus size: 90
35417754 CTGAGGTAAT
*
35417764 TTCAATTTATGTTTGTCAAAAAAATCAGCTCATATGGCGAGAGGTGAGTTGAGCCTCAGGACATG
1 TTCAATTTATGTTTGTC-AAAAAATCAGCTCATATGGCGAGAGGTGAGTTGAGCCTCAGGACACG
35417829 CTGAGGTAATTTCAATTTCTGATTTC
65 CTGAGGTAATTTCAATTTCTGATTTC
* * * *
35417855 TTCAATTTATGTTTTTC-AAAAATCAGTTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGC
1 TTCAATTTATGTTTGTCAAAAAATCAGCTCATATGGCGAGAGGTGAGTTGAGCCTCAGGACACGC
*
35417919 TGAGGTATTTTCAATTTCTG
66 TGAGGTAATTTCAATTTCTG
35417939 CTTTTCAAAA
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
89 62 0.79
91 16 0.21
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.35
Consensus pattern (90 bp):
TTCAATTTATGTTTGTCAAAAAATCAGCTCATATGGCGAGAGGTGAGTTGAGCCTCAGGACACGC
TGAGGTAATTTCAATTTCTGATTTC
Found at i:35418026 original size:239 final size:237
Alignment explanation
Indices: 35417687--35418147 Score: 681
Period size: 239 Copynumber: 1.9 Consensus size: 237
35417677 CAATTTCTGC
* *
35417687 TTTTCAATTTCTGCTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCACGACA
1 TTTTCAATTTCTGCTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCACGAAA
* *
35417752 CACTGAGGTAATTTCAATTTATGTTTGT-CAAAAAAATCAGCTCATATGGCGAGAGGTGAGTTGA
66 CACTGAGGTAATTTCAATTTATGTTTGTAAAAAAAAATCAGCTCATATCGCGAGAGGTGAGTTGA
* * * *
35417816 GCCTCAGGACATGCTGAGGTAATTTCAATTTCTGATTTCTTCAATTTATGTTTTTCAAAAATCAG
131 GCCTCAGGACACGCTGAGGTAATTTCAATTTCTG--TT-TTCAATTTATGTTGTTCAAAAACCAA
*
35417881 TTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTA
193 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTA
* *
35417926 TTTTCAATTTCTGCTTTTCAAAAACATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGAAA
1 TTTTCAATTTCTGCTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCACGAAA
* *
35417991 CGCTGAGGTAATTTCAATTTATGTTTGTAAAAAAAAAAAAAAATCAGCTCATATCGCGAGATGTG
66 CACTGAGGTAATTTCAATTTATGTTTGT------AAAAAAAAATCAGCTCATATCGCGAGAGGTG
* * *
35418056 AGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGTTTTCAATTTATGTTGTTCAAGAAC
125 AGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTTCAATTTATGTTGTTCAAAAAC
*
35418121 CAACTCATATTGCGAGAGGTGGGTTGA
190 CAACTCATATTGCGAGAGGTGAGTTGA
35418148 ACCTTTTAAT
Statistics
Matches: 198, Mismatches: 17, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
239 88 0.44
243 44 0.22
244 2 0.01
246 64 0.32
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (237 bp):
TTTTCAATTTCTGCTTTTCAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCACGAAA
CACTGAGGTAATTTCAATTTATGTTTGTAAAAAAAAATCAGCTCATATCGCGAGAGGTGAGTTGA
GCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTTCAATTTATGTTGTTCAAAAACCAACTC
ATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTA
Found at i:35418082 original size:82 final size:82
Alignment explanation
Indices: 35417945--35418098 Score: 229
Period size: 82 Copynumber: 1.9 Consensus size: 82
35417935 TCTGCTTTTC
*
35417945 AAAAACATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGAAACGCTGAGGTAATTTCAATT
1 AAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGAAACGCTGAGGTAATTTCAATT
35418010 TATGTTTGTAAAAAAAA
66 TATGTTTGTAAAAAAAA
* * ** *
35418027 AAAAAAATCAGCTCAT-ATCGCGAGATGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAAT
1 AAAAAAATCAACTCATAAT-GCGAGAGGTGAGTTGAGCCTCAGGAAACGCTGAGGTAATTTCAAT
*
35418091 TTCTGTTT
65 TTATGTTT
35418099 TCAATTTATG
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
81 2 0.03
82 62 0.97
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (82 bp):
AAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGAAACGCTGAGGTAATTTCAATT
TATGTTTGTAAAAAAAA
Found at i:35418101 original size:13 final size:13
Alignment explanation
Indices: 35418083--35418116 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
35418073 CGCTGAGGTA
*
35418083 TTTTCAATTTCTG
1 TTTTCAATTTATG
35418096 TTTTCAATTTATG
1 TTTTCAATTTATG
35418109 TTGTTCAA
1 TT-TTCAA
35418117 GAACCAACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.59
Consensus pattern (13 bp):
TTTTCAATTTATG
Found at i:35418244 original size:53 final size:52
Alignment explanation
Indices: 35418112--35418310 Score: 254
Period size: 53 Copynumber: 3.7 Consensus size: 52
35418102 ATTTATGTTG
* * * *
35418112 TTCAAGAACCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACATT
1 TTCAA-AATCAACTCATATTGCGAGAGGTGAGTTGAGCC-TTTAATTTCTA-TTT
* * *
35418167 TTCAAAATCAGCTCATATCGCGAGAGGTGAGTTGAGCCTTTAATTTCTGTTT
1 TTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTAATTTCTATTT
* *
35418219 TTCAAAAGTCAACTCGTATTGCGAGAGGTGAGTTGAGCTTTTAATTTCTATTT
1 TTCAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTAATTTCTATTT
* *
35418272 TTCAAAAATCAACTCATATTGCAAAAGGTGAGTTGAGCC
1 TTC-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
35418311 CCAGGTCACA
Statistics
Matches: 126, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
52 9 0.07
53 80 0.63
54 32 0.25
55 5 0.04
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.35
Consensus pattern (52 bp):
TTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTAATTTCTATTT
Found at i:35419621 original size:14 final size:13
Alignment explanation
Indices: 35419598--35419631 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
35419588 AAAATATAAA
*
35419598 CAAAATAAAAAAG
1 CAAAAAAAAAAAG
35419611 CAAAAAAAAAAAG
1 CAAAAAAAAAAAG
*
35419624 GAAAAAAA
1 CAAAAAAA
35419632 TCGAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.82, C:0.06, G:0.09, T:0.03
Consensus pattern (13 bp):
CAAAAAAAAAAAG
Found at i:35419786 original size:18 final size:16
Alignment explanation
Indices: 35419749--35419778 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35419739 TCCCTCTCCT
35419749 TCTCCCCTCTCTCTTC
1 TCTCCCCTCTCTCTTC
35419765 TCTCCCCTC-CTCTT
1 TCTCCCCTCTCTCTT
35419779 TTTCTCTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (16 bp):
TCTCCCCTCTCTCTTC
Found at i:35422313 original size:51 final size:51
Alignment explanation
Indices: 35422237--35422359 Score: 185
Period size: 51 Copynumber: 2.4 Consensus size: 51
35422227 AGAACTAAGT
* *
35422237 TATCCGGATGAAATATGAAGTTCTTGTTGAAACTAGAGCAATAAAGTAATA
1 TATCCGGATGAAATATGAAGTTCTTGTTGAAACCAGAACAATAAAGTAATA
* *
35422288 TATCCGGATGAAATATGAAGTTCTTGTTGAAGCCAGAACAATAAAGTAGTA
1 TATCCGGATGAAATATGAAGTTCTTGTTGAAACCAGAACAATAAAGTAATA
*
35422339 -AGTCCGGATGAAGTATGAAGT
1 TA-TCCGGATGAAATATGAAGT
35422360 AAGTTTGGGA
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
50 1 0.02
51 65 0.98
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.28
Consensus pattern (51 bp):
TATCCGGATGAAATATGAAGTTCTTGTTGAAACCAGAACAATAAAGTAATA
Found at i:35422986 original size:23 final size:23
Alignment explanation
Indices: 35422959--35423017 Score: 109
Period size: 23 Copynumber: 2.6 Consensus size: 23
35422949 TAATATTTCG
*
35422959 GGTGTGTTTGGGTTGGATATTCT
1 GGTGTGTTTGGGTTGGACATTCT
35422982 GGTGTGTTTGGGTTGGACATTCT
1 GGTGTGTTTGGGTTGGACATTCT
35423005 GGTGTGTTTGGGT
1 GGTGTGTTTGGGT
35423018 GGAATCCGCG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.07, C:0.05, G:0.42, T:0.46
Consensus pattern (23 bp):
GGTGTGTTTGGGTTGGACATTCT
Found at i:35427603 original size:20 final size:20
Alignment explanation
Indices: 35427578--35427629 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
35427568 AGGGGCACAC
35427578 GCCCGTGTGGCCTAGG-ACAT
1 GCCCGTGTGGCCT-GGAACAT
35427598 GCCCGTGTGGCCTGGAACAT
1 GCCCGTGTGGCCTGGAACAT
* *
35427618 GGCCGTGGGGCC
1 GCCCGTGTGGCC
35427630 AGGCCGCGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 2 0.07
20 27 0.93
ACGTcount: A:0.12, C:0.31, G:0.40, T:0.17
Consensus pattern (20 bp):
GCCCGTGTGGCCTGGAACAT
Found at i:35427640 original size:13 final size:13
Alignment explanation
Indices: 35427618--35427647 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
35427608 CCTGGAACAT
*
35427618 GGCCGTGGGGCCA
1 GGCCGCGGGGCCA
35427631 GGCCGCGGGGCCA
1 GGCCGCGGGGCCA
35427644 GGCC
1 GGCC
35427648 ATGGGCAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.37, G:0.53, T:0.03
Consensus pattern (13 bp):
GGCCGCGGGGCCA
Found at i:35428492 original size:12 final size:12
Alignment explanation
Indices: 35428462--35428508 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
35428452 AAATTAAATT
35428462 TATTTAAA-ATA
1 TATTTAAATATA
35428473 TGAGTTTAAAT-TGA
1 T-A-TTTAAATAT-A
35428487 TATTTAAATATA
1 TATTTAAATATA
35428499 TATTTAAATA
1 TATTTAAATA
35428509 CAAACTAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
11 1 0.03
12 19 0.61
13 9 0.29
14 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (12 bp):
TATTTAAATATA
Found at i:35428504 original size:24 final size:23
Alignment explanation
Indices: 35428455--35428507 Score: 65
Period size: 25 Copynumber: 2.3 Consensus size: 23
35428445 TAACAAAAAA
35428455 TTAAATTTATTTAAAATATGAGT
1 TTAAATTTATTTAAAATATGAGT
35428478 TTAAATTGATATTTAAATATAT-A-T
1 TTAAATT--TATTTAAA-ATATGAGT
35428502 TTAAAT
1 TTAAAT
35428508 ACAAACTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
23 7 0.26
24 7 0.26
25 9 0.33
26 4 0.15
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (23 bp):
TTAAATTTATTTAAAATATGAGT
Found at i:35429324 original size:19 final size:19
Alignment explanation
Indices: 35429290--35429338 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
35429280 AAATGAAATT
*
35429290 TTAAAA-GAAAATAAAACA-
1 TTAAAATGAAAA-AAAAAAG
35429308 TTAAAATGAAAAAAAAAAG
1 TTAAAATGAAAAAAAAAAG
35429327 TT-AAATGAAAAA
1 TTAAAATGAAAAA
35429339 TTAAAAGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 21 0.75
19 7 0.25
ACGTcount: A:0.71, C:0.02, G:0.08, T:0.18
Consensus pattern (19 bp):
TTAAAATGAAAAAAAAAAG
Found at i:35429337 original size:12 final size:12
Alignment explanation
Indices: 35429274--35429355 Score: 53
Period size: 13 Copynumber: 6.8 Consensus size: 12
35429264 TATTTGACAT
35429274 AAATTAAAATGAA
1 AAATTAAAA-GAA
**
35429287 ATTTTAAAAG-A
1 AAATTAAAAGAA
*
35429298 AAA-TAAAACATTA
1 AAATTAAAAGA--A
* *
35429311 AAATGAAAAAAA
1 AAATTAAAAGAA
*
35429323 AAAGTTAAATGAA
1 AAA-TTAAAAGAA
35429336 AAATTAAAAGAA
1 AAATTAAAAGAA
35429348 AAA-TAAAA
1 AAATTAAAA
35429356 CATCGTCGTG
Statistics
Matches: 53, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
10 5 0.09
11 7 0.13
12 16 0.30
13 20 0.38
14 5 0.09
ACGTcount: A:0.71, C:0.01, G:0.07, T:0.21
Consensus pattern (12 bp):
AAATTAAAAGAA
Found at i:35429342 original size:31 final size:30
Alignment explanation
Indices: 35429298--35429355 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
35429288 TTTTAAAAGA
35429298 AAATAAAACATTAAAATGAAAAAAAAAAGTT
1 AAATAAAACATTAAAA-GAAAAAAAAAAGTT
*
35429329 AAATGAAAA-ATTAAAAGAAAAATAAAA
1 AAAT-AAAACATTAAAAGAAAAAAAAAA
35429356 CATCGTCGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 10 0.40
31 11 0.44
32 4 0.16
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.17
Consensus pattern (30 bp):
AAATAAAACATTAAAAGAAAAAAAAAAGTT
Found at i:35429355 original size:18 final size:19
Alignment explanation
Indices: 35429290--35429345 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 19
35429280 AAATGAAATT
35429290 TTAAAAG-AAAATAAAACA-
1 TTAAAAGAAAAATAAAA-AG
35429308 TTAAAATGAAAAA-AAAAAG
1 TTAAAA-GAAAAATAAAAAG
* *
35429327 TTAAATGAAAAATTAAAAG
1 TTAAAAGAAAAATAAAAAG
35429346 AAAAATAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
18 13 0.41
19 15 0.47
20 4 0.12
ACGTcount: A:0.70, C:0.02, G:0.09, T:0.20
Consensus pattern (19 bp):
TTAAAAGAAAAATAAAAAG
Found at i:35433740 original size:11 final size:11
Alignment explanation
Indices: 35433714--35433769 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
35433704 ATTAAAGAGG
*
35433714 AAAGAAAATAGA
1 AAAGAAAA-ATA
*
35433726 AAAGAAAAATC
1 AAAGAAAAATA
35433737 AAAGTAAAAGA-A
1 AAAG-AAAA-ATA
*
35433749 AAAGAAAAAAA
1 AAAGAAAAATA
35433760 AAAGAAAAAT
1 AAAGAAAAAT
35433770 TCAAAGAAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
10 1 0.03
11 19 0.51
12 16 0.43
13 1 0.03
ACGTcount: A:0.79, C:0.02, G:0.12, T:0.07
Consensus pattern (11 bp):
AAAGAAAAATA
Found at i:35433747 original size:17 final size:17
Alignment explanation
Indices: 35433725--35433778 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
35433715 AAGAAAATAG
*
35433725 AAAAGAAAAATCAAAGT
1 AAAAGAAAAATCAAAGA
** *
35433742 AAAAGAAAAAGAAAAAA
1 AAAAGAAAAATCAAAGA
35433759 AAAAGAAAAATTCAAAGA
1 AAAAGAAAAA-TCAAAGA
35433777 AA
1 AA
35433779 GTATATACTA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
17 23 0.79
18 6 0.21
ACGTcount: A:0.78, C:0.04, G:0.11, T:0.07
Consensus pattern (17 bp):
AAAAGAAAAATCAAAGA
Found at i:35433768 original size:6 final size:6
Alignment explanation
Indices: 35433714--35433768 Score: 53
Period size: 6 Copynumber: 9.5 Consensus size: 6
35433704 ATTAAAGAGG
** *
35433714 AAAGAA AATAG-A AAAGAA AAA-TC AAAGTA AAAGAA AAAGAA AAA-AA
1 AAAGAA AA-AGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
35433760 AAAGAA AAA
1 AAAGAA AAA
35433769 TTCAAAGAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 10 0.24
6 29 0.71
7 2 0.05
ACGTcount: A:0.80, C:0.02, G:0.13, T:0.05
Consensus pattern (6 bp):
AAAGAA
Found at i:35435938 original size:15 final size:16
Alignment explanation
Indices: 35435918--35435951 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
35435908 AATTTTTTAA
35435918 AAATTATTAAAAT-AT
1 AAATTATTAAAATAAT
35435933 AAATTATTAAAATAAT
1 AAATTATTAAAATAAT
35435949 AAA
1 AAA
35435952 ATTACAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATTATTAAAATAAT
Found at i:35436289 original size:47 final size:47
Alignment explanation
Indices: 35436220--35436310 Score: 182
Period size: 47 Copynumber: 1.9 Consensus size: 47
35436210 TAATTGGTTA
35436220 AATTCTTCTATTAGTCTCTATACTTTATAAATGTTATGAATTTAACC
1 AATTCTTCTATTAGTCTCTATACTTTATAAATGTTATGAATTTAACC
35436267 AATTCTTCTATTAGTCTCTATACTTTATAAATGTTATGAATTTA
1 AATTCTTCTATTAGTCTCTATACTTTATAAATGTTATGAATTTA
35436311 GTCCATGTAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.32, C:0.13, G:0.07, T:0.48
Consensus pattern (47 bp):
AATTCTTCTATTAGTCTCTATACTTTATAAATGTTATGAATTTAACC
Found at i:35436368 original size:31 final size:31
Alignment explanation
Indices: 35436331--35436389 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
35436321 TTTAATTTGA
*
35436331 TCAATTTTACTTC-TTCTACTTTTTGAATCGG
1 TCAATTTTA-GTCATTCTACTTTTTGAATCGG
*
35436362 TCAATTTTAGTCATTGTACTTTTTGAAT
1 TCAATTTTAGTCATTCTACTTTTTGAAT
35436390 TTTGAAGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 2 0.08
31 23 0.92
ACGTcount: A:0.22, C:0.15, G:0.10, T:0.53
Consensus pattern (31 bp):
TCAATTTTAGTCATTCTACTTTTTGAATCGG
Found at i:35436957 original size:3 final size:3
Alignment explanation
Indices: 35436949--35437006 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
35436939 ATCCATCACA
35436949 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
35436997 AAT AAT AAT A
1 AAT AAT AAT A
35437007 CAATTTCCTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:35438052 original size:15 final size:15
Alignment explanation
Indices: 35438032--35438085 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
35438022 ATACTATAAA
35438032 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
35438047 ATATTTATAATTGTAAT
1 ATATTTATTA-T-TAAT
*
35438064 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
35438081 ATATT
1 ATATT
35438086 AATATTGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 14 0.44
16 1 0.03
17 7 0.22
18 1 0.03
19 9 0.28
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:35438719 original size:44 final size:44
Alignment explanation
Indices: 35438668--35438757 Score: 162
Period size: 44 Copynumber: 2.0 Consensus size: 44
35438658 TTTGTAAGCA
* *
35438668 ATGTCACCAGAATCTCATCAAAAGTTGTTGAAATTTGACAAACT
1 ATGTCACCAGAATCTCATCAAAAATGGTTGAAATTTGACAAACT
35438712 ATGTCACCAGAATCTCATCAAAAATGGTTGAAATTTGACAAACT
1 ATGTCACCAGAATCTCATCAAAAATGGTTGAAATTTGACAAACT
35438756 AT
1 AT
35438758 AAAACTAACC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29
Consensus pattern (44 bp):
ATGTCACCAGAATCTCATCAAAAATGGTTGAAATTTGACAAACT
Found at i:35447112 original size:164 final size:163
Alignment explanation
Indices: 35446776--35447482 Score: 887
Period size: 164 Copynumber: 4.5 Consensus size: 163
35446766 ATTTGAACCT
* * * * * *
35446776 TGCAGGACTCGAAACTG-G-CCTTCGCGTTATTAGCACGACGATCTAACCAGCAGACCTAATAAG
1 TGCAGGTCTCGAACCTGCGACCTTCGCGTTATTAGCACGACGCTCTAACCAGCTGAGCTAATAGG
* * * * * * *
35446839 CCGCTATGTTGTT---GTCTAAATTCTATTTTATTAACTAATGTAAAACGCTGCCGTTTTCCA-A
66 CCG-T-TGGTGTTCACG-CCAAATTCTGTTTTACTAAATACTGTAAAACGTTGCCGTTTTCCAGA
* * *
35446900 AAA-AAAAACGAAAAGAAAATAGCGCATAATGGCCCA
128 AAACAAAAACG-AAAGAAAAAAGCACTTAATGGCCCA
*
35446936 TGCAGGTCTCGAACCTGCGACCTTCGCGTTATTAGCACGACACTCTAACCAGCTGAGCTAATAGG
1 TGCAGGTCTCGAACCTGCGACCTTCGCGTTATTAGCACGACGCTCTAACCAGCTGAGCTAATAGG
*
35447001 CCGTTGGTGTTCACGACCAAATTCTGTTTTACTAAATACTGTAAAACTTTGCCGTTTTCCAGAAA
66 CCGTTGGTGTTCACG-CCAAATTCTGTTTTACTAAATACTGTAAAACGTTGCCGTTTTCCAGAAA
35447066 ACAAAAACGAAAGAAAAAAGCACTTAATGGCCCA
130 ACAAAAACGAAAGAAAAAAGCACTTAATGGCCCA
35447100 TGCAGGTCTCGAACCTGCGACCTTCGCGTTATTAGCACGACGCTCTAACCAGCTGAGCTAATAGG
1 TGCAGGTCTCGAACCTGCGACCTTCGCGTTATTAGCACGACGCTCTAACCAGCTGAGCTAATAGG
** * *
35447165 CCACTGGTGTTCACGCCCAAATTCTGTTCTT-CTAAATAGTGTAAAACGGTGCCGTTTTCCAGAA
66 CCGTTGGTGTTCACG-CCAAATTCTGTT-TTACTAAATACTGTAAAACGTTGCCGTTTTCCAGAA
*
35447229 AACAAAAACGAAAGTAAAAAGCACTTAAT-G----
129 AACAAAAACGAAAGAAAAAAGCACTTAATGGCCCA
35447259 -GC----C-C--ACCTGCGACCTTCGCGTTATTAGCACGACGCTCTAACCAGCTGAGCTAATAGG
1 TGCAGGTCTCGAACCTGCGACCTTCGCGTTATTAGCACGACGCTCTAACCAGCTGAGCTAATAGG
* * * *
35447316 CCATTGGTGTTCACGCTCAAATTCAGTTTTAATAAATACTATAAAACGTTGCCG-------G-AA
66 CCGTTGGTGTTCACGC-CAAATTCTGTTTTACTAAATACTGTAAAACGTTGCCGTTTTCCAGAAA
*
35447373 ACAAAAACGAAAGAAAAAAGCACTGAATGGCCCA
130 ACAAAAACGAAAGAAAAAAGCACTTAATGGCCCA
35447407 TGCAGGTCTCGAACCTGCGACCTTCGCGTTATTAGCACGACGCTCTAACCAGCTGAGCTAATAGG
1 TGCAGGTCTCGAACCTGCGACCTTCGCGTTATTAGCACGACGCTCTAACCAGCTGAGCTAATAGG
35447472 CCGTTGGTGTT
66 CCGTTGGTGTT
35447483 ATGGCCCAAA
Statistics
Matches: 488, Mismatches: 36, Indels: 50
0.85 0.06 0.09
Matches are distributed among these distances:
143 28 0.06
144 2 0.00
149 2 0.00
150 3 0.01
151 96 0.20
153 2 0.00
154 2 0.00
156 63 0.13
158 2 0.00
160 21 0.04
161 2 0.00
162 43 0.09
163 40 0.08
164 173 0.35
165 9 0.02
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (163 bp):
TGCAGGTCTCGAACCTGCGACCTTCGCGTTATTAGCACGACGCTCTAACCAGCTGAGCTAATAGG
CCGTTGGTGTTCACGCCAAATTCTGTTTTACTAAATACTGTAAAACGTTGCCGTTTTCCAGAAAA
CAAAAACGAAAGAAAAAAGCACTTAATGGCCCA
Found at i:35453187 original size:58 final size:58
Alignment explanation
Indices: 35453115--35453240 Score: 225
Period size: 58 Copynumber: 2.2 Consensus size: 58
35453105 CATACTCTCT
* *
35453115 TTTTTGTTATCTAGATTTTCTTTTTGCAAATTAAAGTGAAAATAATAATTTGTATTTTA
1 TTTTT-TTCTCTAGATTTTCTTTTTGCAAATAAAAGTGAAAATAATAATTTGTATTTTA
35453174 TTTTTTTCTCTAGATTTTCTTTTTGCAAATAAAAGTGAAAATAATAATTTGTATTTTA
1 TTTTTTTCTCTAGATTTTCTTTTTGCAAATAAAAGTGAAAATAATAATTTGTATTTTA
35453232 TTTTTTTCT
1 TTTTTTTCT
35453241 ATCAAATACA
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
58 60 0.92
59 5 0.08
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (58 bp):
TTTTTTTCTCTAGATTTTCTTTTTGCAAATAAAAGTGAAAATAATAATTTGTATTTTA
Found at i:35455731 original size:8 final size:8
Alignment explanation
Indices: 35455718--35455743 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
35455708 ATCCTCAAAA
35455718 AGAGTGAG
1 AGAGTGAG
35455726 AGAGTGAG
1 AGAGTGAG
35455734 AGAGTGAG
1 AGAGTGAG
35455742 AG
1 AG
35455744 CGAACGCAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.50, T:0.12
Consensus pattern (8 bp):
AGAGTGAG
Found at i:35457759 original size:21 final size:21
Alignment explanation
Indices: 35457733--35457772 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
35457723 CAAAATGATG
35457733 TAGTTTTG-CATTTTAACTTAA
1 TAGTTTTGAC-TTTTAACTTAA
35457754 TAGTTTTGACTTTTAACTT
1 TAGTTTTGACTTTTAACTT
35457773 TGTAAAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.55
Consensus pattern (21 bp):
TAGTTTTGACTTTTAACTTAA
Found at i:35458116 original size:7 final size:7
Alignment explanation
Indices: 35458106--35458134 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
35458096 TATACTTTTT
35458106 AAATTTA
1 AAATTTA
35458113 AAATTTA
1 AAATTTA
35458120 AAATTTA
1 AAATTTA
35458127 AAATTTA
1 AAATTTA
35458134 A
1 A
35458135 TTGTTAAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
AAATTTA
Found at i:35482502 original size:14 final size:14
Alignment explanation
Indices: 35482461--35482502 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
35482451 TTTCAATTTG
35482461 ATTTT-TTTTTTAA
1 ATTTTATTTTTTAA
* *
35482474 ATTTTATTATATAA
1 ATTTTATTTTTTAA
35482488 ATTTTATTTTTTAA
1 ATTTTATTTTTTAA
35482502 A
1 A
35482503 AAAAAATTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 5 0.21
14 19 0.79
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTTTATTTTTTAA
Found at i:35483116 original size:22 final size:22
Alignment explanation
Indices: 35483088--35483131 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
35483078 ATTAGTGAAT
*
35483088 CAAATATATAAATATAAATAAA
1 CAAATATATAAATAAAAATAAA
* *
35483110 CAAATATTTATATAAAAATAAA
1 CAAATATATAAATAAAAATAAA
35483132 ATATAAATAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (22 bp):
CAAATATATAAATAAAAATAAA
Found at i:35486931 original size:20 final size:21
Alignment explanation
Indices: 35486906--35486962 Score: 75
Period size: 20 Copynumber: 2.8 Consensus size: 21
35486896 TTGATTTAAT
35486906 TTCATTT-TTT-TATTTATTTG
1 TTCATTTCTTTCTATTT-TTTG
35486926 TTCATTTCTTTCTATTTTTTG
1 TTCATTTCTTTCTATTTTTTG
*
35486947 TT-ATTTCTTACTATTT
1 TTCATTTCTTTCTATTT
35486963 CGTTTTAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
20 20 0.59
21 9 0.26
22 5 0.15
ACGTcount: A:0.14, C:0.11, G:0.04, T:0.72
Consensus pattern (21 bp):
TTCATTTCTTTCTATTTTTTG
Found at i:35489647 original size:19 final size:19
Alignment explanation
Indices: 35489623--35489668 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
35489613 CCTTTTTTTT
35489623 TTTGCATT-CATTCCATGCA
1 TTTGCATTGCATTCCAT-CA
*
35489642 TTTGCATTGCATTGCATCA
1 TTTGCATTGCATTCCATCA
35489661 TTTGCATT
1 TTTGCATT
35489669 AAACTTTCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.20, C:0.22, G:0.13, T:0.46
Consensus pattern (19 bp):
TTTGCATTGCATTCCATCA
Found at i:35491224 original size:23 final size:23
Alignment explanation
Indices: 35491194--35491241 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
35491184 TTAAGGATGG
35491194 TAGAGTAAGATGAAAACAAATCT
1 TAGAGTAAGATGAAAACAAATCT
*
35491217 TAGAGTAAGATGAAAACAGATCT
1 TAGAGTAAGATGAAAACAAATCT
35491240 TA
1 TA
35491242 CCTTACAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.19, T:0.23
Consensus pattern (23 bp):
TAGAGTAAGATGAAAACAAATCT
Found at i:35513800 original size:17 final size:17
Alignment explanation
Indices: 35513755--35513806 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 17
35513745 ATTTGACAAA
*
35513755 GCCCGATAAATGATAAT
1 GCCCAATAAATGATAAT
*
35513772 GCCTGAAATAAATGATAAT
1 GCC--CAATAAATGATAAT
*
35513791 GCCCAATAAACGATAA
1 GCCCAATAAATGATAA
35513807 ATGATAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 14 0.48
19 15 0.52
ACGTcount: A:0.46, C:0.17, G:0.15, T:0.21
Consensus pattern (17 bp):
GCCCAATAAATGATAAT
Done.