Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr7
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: 47983841
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869652 characters in sequence are not A, C, G, or T
File 88 of 153
Found at i:27725087 original size:18 final size:18
Alignment explanation
Indices: 27725064--27725107 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
27725054 TCCTCTCTTA
27725064 TCCCTCTCATCGCATCCT
1 TCCCTCTCATCGCATCCT
27725082 TCCCTCTCATCGCATCCT
1 TCCCTCTCATCGCATCCT
27725100 TCCCTCTC
1 TCCCTCTC
27725108 CATTATCCGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.09, C:0.52, G:0.05, T:0.34
Consensus pattern (18 bp):
TCCCTCTCATCGCATCCT
Found at i:27725386 original size:16 final size:15
Alignment explanation
Indices: 27725325--27725374 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
27725315 TTTGTTATTA
*
27725325 TTATTATTATTAT-T
1 TTATTGTTATTATAT
*
27725339 TTATT-TTCATTTTTAT
1 TTATTGTT-A-TTATAT
27725355 TTATTGTTATTATAT
1 TTATTGTTATTATAT
27725370 TTATT
1 TTATT
27725375 TGTTTTACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
13 2 0.07
14 6 0.20
15 13 0.43
16 7 0.23
17 2 0.07
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (15 bp):
TTATTGTTATTATAT
Found at i:27727105 original size:6 final size:6
Alignment explanation
Indices: 27727072--27727147 Score: 57
Period size: 6 Copynumber: 12.3 Consensus size: 6
27727062 AGATCATTGA
* * * *
27727072 TTTTAT TTCTCT TTTT-T TTTTCAA TTTTAT TTTTAT CTTTA- TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTT-AT TTTTAT TTTTAT TTTTAT TTTTAT
*
27727119 TTTTGT TTTTAGT TGTTTCAT TTTTAT TT
1 TTTTAT TTTTA-T T-TTT-AT TTTTAT TT
27727148 CTTAGACTTC
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
5 9 0.16
6 31 0.56
7 9 0.16
8 5 0.09
9 1 0.02
ACGTcount: A:0.13, C:0.07, G:0.04, T:0.76
Consensus pattern (6 bp):
TTTTAT
Found at i:27743908 original size:51 final size:51
Alignment explanation
Indices: 27743832--27744013 Score: 319
Period size: 51 Copynumber: 3.6 Consensus size: 51
27743822 TTTGAGTATT
* *
27743832 TCTGATCAGTGTCAAGTGACAAGTGATAAGTAGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
27743883 TCTGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
27743934 TCTGATCAGTGACAAGTAACAAGTGATAAATGGTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
27743985 TCTGATCAGGGACAAGTGACAAGTGATAA
1 TCTGATCAGTGACAAGTGACAAGTGATAA
27744014 ATGTGATCCG
Statistics
Matches: 125, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 125 1.00
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.29
Consensus pattern (51 bp):
TCTGATCAGTGACAAGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:27748518 original size:31 final size:29
Alignment explanation
Indices: 27748480--27748556 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
27748470 TTAACGGCTC
* *
27748480 AGTGACTAAAATGTTACATCATGATAACATA
1 AGTGACTAAAATGTAACAT-ATCA-AACATA
* *
27748511 AGTGACTAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACATATCAAACATA
27748540 AGTGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
27748557 CTGAACCAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
29 22 0.54
30 2 0.05
31 17 0.41
ACGTcount: A:0.47, C:0.14, G:0.13, T:0.26
Consensus pattern (29 bp):
AGTGACTAAAATGTAACATATCAAACATA
Found at i:27750023 original size:15 final size:15
Alignment explanation
Indices: 27749998--27750032 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
27749988 GACTCTATTT
*
27749998 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
27750012 TAATTAATATTAAGA
1 TAATTAATATTAAGA
27750027 TAATTA
1 TAATTA
27750033 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:27753996 original size:12 final size:11
Alignment explanation
Indices: 27753944--27753999 Score: 51
Period size: 12 Copynumber: 4.9 Consensus size: 11
27753934 AGGCAACCCA
27753944 ATTTTTATTTT
1 ATTTTTATTTT
* *
27753955 TTTCTTTACTTT
1 ATT-TTTATTTT
*
27753967 ATTTATTACTTT
1 ATTT-TTATTTT
27753979 A-TTTTATTTT
1 ATTTTTATTTT
27753989 ATTATTTATTT
1 ATT-TTTATTT
27754000 GGATATTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
10 7 0.19
11 6 0.16
12 24 0.65
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (11 bp):
ATTTTTATTTT
Found at i:27753996 original size:17 final size:17
Alignment explanation
Indices: 27753946--27753999 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
27753936 GCAACCCAAT
* *
27753946 TTTTATTTTTTTCTTTA
1 TTTTATTTTATTATTTA
*
27753963 CTTTA-TTTATTACTTTA
1 TTTTATTTTATTA-TTTA
27753980 TTTTATTTTATTATTTA
1 TTTTATTTTATTATTTA
27753997 TTT
1 TTT
27754000 GGATATTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
16 5 0.16
17 19 0.61
18 7 0.23
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTATTTTATTATTTA
Found at i:27755635 original size:15 final size:15
Alignment explanation
Indices: 27755610--27755644 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
27755600 CAGACTATTT
*
27755610 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
27755624 TAATTAATATTAAGA
1 TAATTAATATTAAGA
27755639 TAATTA
1 TAATTA
27755645 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:27755934 original size:15 final size:15
Alignment explanation
Indices: 27755909--27755943 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
27755899 CAGACTATTT
*
27755909 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
27755923 TAATTAATATTAAGA
1 TAATTAATATTAAGA
27755938 TAATTA
1 TAATTA
27755944 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:27756023 original size:299 final size:298
Alignment explanation
Indices: 27755480--27756081 Score: 1161
Period size: 299 Copynumber: 2.0 Consensus size: 298
27755470 AATTAAGGGC
27755480 CAAAA-GTGTGAATTTAGAGATAAAATGAGCCAATACGCAACACAAGGAAAAGTTGGTGCCAAAA
1 CAAAAGGTGTGAATTTAGAGATAAAATGAGCCAATACGCAACACAAGGAAAAGTTGGTGCCAAAA
27755544 GTGCAAGCATAGAGGACACAAGGGTTGAAATGCAAAAATAAGATATTTTATTCTATCAGACTATT
66 GTGCAAGCATAGAGGACACAAGGGTTGAAATGCAAAAATAAGATATTTTATTCTATCAGACTATT
27755609 TTAATTATATTAGGATAATTAATATTAAGATAATTATTAAGGATTATTTAATTTTAGGATTTAAT
131 TTAATTATATTAGGATAATTAATATTAAGATAATTATTAAGGATTATTTAATTTTAGGATTTAAT
27755674 TTTATTTATCTTTATTCATCTTCAATTAAATGTATTTACCTTTTGGGAATTTAAGTAGGATTAGA
196 TTTATTTATCTTTATTCATCTTCAATTAAATGTATTTACCTTTTGGGAATTTAAGTAGGATTAGA
* *
27755739 CTATCTCCCCTGGCACTATAAATAGGGGGTGAAGTGACT
261 CTATCTCCCCTAGCACTATAAATA-AGGGTGAAGTGACT
27755778 CAAAAGGTGTGAATTTAGAGATAAAATGAGCCAATACGCAACACAAGGAAAAGTTGGTGCCAAAA
1 CAAAAGGTGTGAATTTAGAGATAAAATGAGCCAATACGCAACACAAGGAAAAGTTGGTGCCAAAA
27755843 GTGCAAGCATAGAGGACACAAGGGTTGAAATGCAAAAATAAGATATTTTATTCTATCAGACTATT
66 GTGCAAGCATAGAGGACACAAGGGTTGAAATGCAAAAATAAGATATTTTATTCTATCAGACTATT
27755908 TTAATTATATTAGGATAATTAATATTAAGATAATTATTAAGGATTATTTAATTTTAGGATTTAAT
131 TTAATTATATTAGGATAATTAATATTAAGATAATTATTAAGGATTATTTAATTTTAGGATTTAAT
*
27755973 TTTATTTATCTTTATTCATCTTCAATTAAATGTATTTATCTTTTGGGAATTTAAGTAGGATTAGA
196 TTTATTTATCTTTATTCATCTTCAATTAAATGTATTTACCTTTTGGGAATTTAAGTAGGATTAGA
27756038 CTATCTCCCCTAGCACTATAAATAAGGGTGAAGTGACT
261 CTATCTCCCCTAGCACTATAAATAAGGGTGAAGTGACT
27756076 CAAAAG
1 CAAAAG
27756082 CTATCTCCCC
Statistics
Matches: 300, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
298 24 0.08
299 276 0.92
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (298 bp):
CAAAAGGTGTGAATTTAGAGATAAAATGAGCCAATACGCAACACAAGGAAAAGTTGGTGCCAAAA
GTGCAAGCATAGAGGACACAAGGGTTGAAATGCAAAAATAAGATATTTTATTCTATCAGACTATT
TTAATTATATTAGGATAATTAATATTAAGATAATTATTAAGGATTATTTAATTTTAGGATTTAAT
TTTATTTATCTTTATTCATCTTCAATTAAATGTATTTACCTTTTGGGAATTTAAGTAGGATTAGA
CTATCTCCCCTAGCACTATAAATAAGGGTGAAGTGACT
Found at i:27756101 original size:44 final size:45
Alignment explanation
Indices: 27756038--27756126 Score: 153
Period size: 44 Copynumber: 2.0 Consensus size: 45
27756028 TAGGATTAGA
27756038 CTATCTCCCCTAGCACTATAAATA-AGGGTGAAGTGACTCAAAAG
1 CTATCTCCCCTAGCACTATAAATAGAGGGTGAAGTGACTCAAAAG
* *
27756082 CTATCTCCCCTGGCACTATAAATAGGGGGTGAAGTGACTCAAAAG
1 CTATCTCCCCTAGCACTATAAATAGAGGGTGAAGTGACTCAAAAG
27756127 AGAGGCATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
44 23 0.55
45 19 0.45
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.22
Consensus pattern (45 bp):
CTATCTCCCCTAGCACTATAAATAGAGGGTGAAGTGACTCAAAAG
Found at i:27759840 original size:26 final size:25
Alignment explanation
Indices: 27759798--27759848 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
27759788 GGCCATGGGA
*
27759798 TTGTCTGTATGTGGGAGTTGGGATT
1 TTGTCTGTATGTGGGAGTGGGGATT
27759823 TTGTCATGTAATGT-GGAGTGGGGATT
1 TTGTC-TGT-ATGTGGGAGTGGGGATT
27759849 ATAAGCCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 5 0.22
26 14 0.61
27 4 0.17
ACGTcount: A:0.16, C:0.04, G:0.39, T:0.41
Consensus pattern (25 bp):
TTGTCTGTATGTGGGAGTGGGGATT
Found at i:27766164 original size:14 final size:14
Alignment explanation
Indices: 27766147--27766175 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
27766137 TTTTTATTAC
27766147 ATTATCTTTCCTGG
1 ATTATCTTTCCTGG
27766161 ATTATCTTTCCTGG
1 ATTATCTTTCCTGG
27766175 A
1 A
27766176 CATATAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.21, G:0.14, T:0.48
Consensus pattern (14 bp):
ATTATCTTTCCTGG
Found at i:27769347 original size:12 final size:12
Alignment explanation
Indices: 27769330--27769354 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27769320 TACTGATAAC
27769330 GTATTATAAAAT
1 GTATTATAAAAT
27769342 GTATTATAAAAT
1 GTATTATAAAAT
27769354 G
1 G
27769355 ATAATAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (12 bp):
GTATTATAAAAT
Found at i:27769436 original size:36 final size:36
Alignment explanation
Indices: 27769360--27769436 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
27769350 AAATGATAAT
** *
27769360 AATAATAATGCAAAAAACACAAGAATGTTATAAAAT
1 AATAATAATGCAAAAAACACAAGAATAATATAAAAG
* * **
27769396 AATAATAATGCAAAGAACATAAGAATAATATATCAG
1 AATAATAATGCAAAAAACACAAGAATAATATAAAAG
27769432 AATAA
1 AATAA
27769437 AAAGGGATTT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.61, C:0.08, G:0.09, T:0.22
Consensus pattern (36 bp):
AATAATAATGCAAAAAACACAAGAATAATATAAAAG
Found at i:27771126 original size:13 final size:14
Alignment explanation
Indices: 27771102--27771130 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
27771092 GATATCATAT
27771102 TAATTATTAATTTA
1 TAATTATTAATTTA
27771116 TAATT-TTAATTTA
1 TAATTATTAATTTA
27771129 TA
1 TA
27771131 TGTAATGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TAATTATTAATTTA
Found at i:27771901 original size:29 final size:29
Alignment explanation
Indices: 27771853--27771910 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
27771843 ACTGCTCTGC
*
27771853 GTCACACGACCGTGTAGTAGGCTGTGTGG
1 GTCACACGACCATGTAGTAGGCTGTGTGG
* * *
27771882 GTCACATGACCATGTGGTAGGTTGTGTGG
1 GTCACACGACCATGTAGTAGGCTGTGTGG
27771911 TAAACCGTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.17, C:0.17, G:0.38, T:0.28
Consensus pattern (29 bp):
GTCACACGACCATGTAGTAGGCTGTGTGG
Found at i:27773093 original size:25 final size:24
Alignment explanation
Indices: 27773046--27773092 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
27773036 TAATTATATA
27773046 GTTTCTTTTAAAAAGAAAAAAAAC
1 GTTTCTTTTAAAAAGAAAAAAAAC
27773070 GTTTCTTTTAAAAAGAAAAAAAA
1 GTTTCTTTTAAAAAGAAAAAAAA
27773093 AATTTGTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.55, C:0.06, G:0.09, T:0.30
Consensus pattern (24 bp):
GTTTCTTTTAAAAAGAAAAAAAAC
Found at i:27777790 original size:13 final size:13
Alignment explanation
Indices: 27777765--27777854 Score: 51
Period size: 13 Copynumber: 6.5 Consensus size: 13
27777755 AACAAAACTA
27777765 AAATAAAGT-AAAT
1 AAATAAA-TAAAAT
27777778 AAATAAATAAAATT
1 AAATAAATAAAA-T
27777792 CAAA-ATAATAAAAAT
1 -AAATA-AAT-AAAAT
*
27777807 TAATATAATAATAA-
1 AAATA-AATAA-AAT
*
27777821 AAATAATATATAAT
1 AAATAA-ATAAAAT
* *
27777835 AAATATATATAAT
1 AAATAAATAAAAT
27777848 AAATAAA
1 AAATAAA
27777855 AGGAACAAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
12 1 0.02
13 26 0.41
14 18 0.29
15 14 0.22
16 4 0.06
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.29
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:27777831 original size:19 final size:18
Alignment explanation
Indices: 27777795--27777855 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 18
27777785 TAAAATTCAA
*
27777795 AATAATAAAAATTAATAT
1 AATAATAAAAATAAATAT
27777813 AATAATAAAAAT-AATAT
1 AATAATAAAAATAAATAT
*
27777830 -ATAAT--AAATATATAT
1 AATAATAAAAATAAATAT
27777845 AATAAATAAAA
1 AAT-AATAAAA
27777856 GGAACAAAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
14 4 0.11
15 4 0.11
16 7 0.19
17 8 0.22
18 12 0.32
19 2 0.05
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AATAATAAAAATAAATAT
Found at i:27777853 original size:27 final size:27
Alignment explanation
Indices: 27777793--27777850 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 27
27777783 AATAAAATTC
*
27777793 AAAATAATAAAAATTAATATAATAATA
1 AAAATAATAAAAATAAATATAATAATA
*
27777820 AAAATAATATATAATAAATATATATAATA
1 AAAATAATA-AAAATAAATATA-ATAATA
27777849 AA
1 AA
27777851 TAAAAGGAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 9 0.33
28 10 0.37
29 8 0.30
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (27 bp):
AAAATAATAAAAATAAATATAATAATA
Found at i:27778394 original size:6 final size:7
Alignment explanation
Indices: 27778364--27778402 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
27778354 AGAAGGAAGG
27778364 AAAATAA
1 AAAATAA
27778371 TAAAATAA
1 -AAAATAA
27778379 AAGAA-AA
1 AA-AATAA
27778386 AAAATAA
1 AAAATAA
27778393 AAAATAA
1 AAAATAA
27778400 AAA
1 AAA
27778403 GAAAGAAACC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
6 2 0.07
7 18 0.62
8 9 0.31
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.13
Consensus pattern (7 bp):
AAAATAA
Found at i:27778396 original size:21 final size:23
Alignment explanation
Indices: 27778364--27778406 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
27778354 AGAAGGAAGG
27778364 AAAATAATAAAAT-AAAAGAAAA
1 AAAATAATAAAATAAAAAGAAAA
27778386 AAAATAA-AAAATAAAAAGAAA
1 AAAATAATAAAATAAAAAGAAA
27778407 GAAACCCTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.12
Consensus pattern (23 bp):
AAAATAATAAAATAAAAAGAAAA
Found at i:27779564 original size:6 final size:7
Alignment explanation
Indices: 27779534--27779572 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
27779524 AGAAGGAAGG
27779534 AAAATAA
1 AAAATAA
27779541 TAAAATAA
1 -AAAATAA
27779549 AAGAA-AA
1 AA-AATAA
27779556 AAAATAA
1 AAAATAA
27779563 AAAATAA
1 AAAATAA
27779570 AAA
1 AAA
27779573 GAAAGAAACC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
6 2 0.07
7 18 0.62
8 9 0.31
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.13
Consensus pattern (7 bp):
AAAATAA
Found at i:27779566 original size:21 final size:23
Alignment explanation
Indices: 27779534--27779576 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
27779524 AGAAGGAAGG
27779534 AAAATAATAAAAT-AAAAGAAAA
1 AAAATAATAAAATAAAAAGAAAA
27779556 AAAATAA-AAAATAAAAAGAAA
1 AAAATAATAAAATAAAAAGAAA
27779577 GAAACCCTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.12
Consensus pattern (23 bp):
AAAATAATAAAATAAAAAGAAAA
Found at i:27781610 original size:6 final size:6
Alignment explanation
Indices: 27781599--27781645 Score: 76
Period size: 6 Copynumber: 7.5 Consensus size: 6
27781589 TGTAAAAATT
27781599 AAATAA AAATAA AAATAA AAATAA AAATAA AAATATTA AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATA--A AAATAA AAA
27781646 ATGGATAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
6 33 0.85
8 6 0.15
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
AAATAA
Found at i:27781620 original size:18 final size:19
Alignment explanation
Indices: 27781591--27781645 Score: 80
Period size: 18 Copynumber: 3.0 Consensus size: 19
27781581 AATTAGAATG
27781591 TAAAAAT-T-AAATAAAAA
1 TAAAAATATAAAATAAAAA
27781608 TAAAAATA-AAAATAAAAA
1 TAAAAATATAAAATAAAAA
27781626 TAAAAATATTAAAATAAAAA
1 TAAAAATA-TAAAATAAAAA
27781646 ATGGATAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.21
18 17 0.50
20 10 0.29
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (19 bp):
TAAAAATATAAAATAAAAA
Found at i:27788691 original size:16 final size:17
Alignment explanation
Indices: 27788670--27788705 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
27788660 ACGAGAAAAT
*
27788670 TTTAATTATA-ATTTTC
1 TTTAATTATATAGTTTC
27788686 TTTAATTATATAGTTTC
1 TTTAATTATATAGTTTC
27788703 TTT
1 TTT
27788706 TAAAAAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.64
Consensus pattern (17 bp):
TTTAATTATATAGTTTC
Found at i:27790203 original size:21 final size:23
Alignment explanation
Indices: 27790140--27790203 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 23
27790130 GGTAGGAAAA
27790140 TACATCTG-ATTCTGAT-CTGTTC
1 TACATCTGTATT-TGATACTGTTC
27790162 TACATCTGTATTTGATA-TGTTC
1 TACATCTGTATTTGATACTGTTC
27790184 TTA-ATCT-TATTTGA-ACTGTT
1 -TACATCTGTATTTGATACTGTT
27790204 ACAACATTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
20 1 0.03
21 11 0.29
22 21 0.55
23 5 0.13
ACGTcount: A:0.22, C:0.16, G:0.12, T:0.50
Consensus pattern (23 bp):
TACATCTGTATTTGATACTGTTC
Found at i:27791664 original size:46 final size:46
Alignment explanation
Indices: 27791597--27791734 Score: 224
Period size: 46 Copynumber: 3.0 Consensus size: 46
27791587 AAATTGCTAT
* *
27791597 AACTCAGTATGGTTTTTTTCACGGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTATTCACTGAAATACCATACCTACTTTTCAC
* *
27791643 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTATTCACTGAAATACCATACCTACTTTTCAC
*
27791689 -ACTCAGTATGGTTTTATTCACTGAAATACCATACCTACGTTTCAC
1 AACTCAGTATGGTTTTATTCACTGAAATACCATACCTACTTTTCAC
27791734 A
1 A
27791735 CTTTGCCATG
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
45 42 0.49
46 43 0.51
ACGTcount: A:0.29, C:0.25, G:0.10, T:0.36
Consensus pattern (46 bp):
AACTCAGTATGGTTTTATTCACTGAAATACCATACCTACTTTTCAC
Found at i:27791709 original size:45 final size:45
Alignment explanation
Indices: 27791598--27791736 Score: 224
Period size: 45 Copynumber: 3.1 Consensus size: 45
27791588 AATTGCTATA
* *
27791598 ACTCAGTATGGTTTTTTTCACGGAAATACCATACCTACTTTTCAC
1 ACTCAGTATGGTTTTATTCACTGAAATACCATACCTACTTTTCAC
* *
27791643 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 -ACTCAGTATGGTTTTATTCACTGAAATACCATACCTACTTTTCAC
*
27791689 ACTCAGTATGGTTTTATTCACTGAAATACCATACCTACGTTTCAC
1 ACTCAGTATGGTTTTATTCACTGAAATACCATACCTACTTTTCAC
27791734 ACT
1 ACT
27791737 TTGCCATGGA
Statistics
Matches: 87, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
45 45 0.52
46 42 0.48
ACGTcount: A:0.28, C:0.26, G:0.10, T:0.36
Consensus pattern (45 bp):
ACTCAGTATGGTTTTATTCACTGAAATACCATACCTACTTTTCAC
Found at i:27792503 original size:17 final size:17
Alignment explanation
Indices: 27792481--27792513 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
27792471 AAATTCTTTT
27792481 TAAATCACAAAATTCAA
1 TAAATCACAAAATTCAA
27792498 TAAATCACAAAATTCA
1 TAAATCACAAAATTCA
27792514 CTAATTCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.58, C:0.18, G:0.00, T:0.24
Consensus pattern (17 bp):
TAAATCACAAAATTCAA
Found at i:27795118 original size:23 final size:24
Alignment explanation
Indices: 27795073--27795119 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
27795063 TTTATAAAAA
* *
27795073 AATATTTTAATTTTCTATCTTTTT
1 AATATTTTAAATTTATATCTTTTT
27795097 AATA-TTTAAATTTATAT-TTTTT
1 AATATTTTAAATTTATATCTTTTT
27795119 A
1 A
27795120 TCAAACTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 6 0.29
23 11 0.52
24 4 0.19
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (24 bp):
AATATTTTAAATTTATATCTTTTT
Found at i:27795241 original size:31 final size:29
Alignment explanation
Indices: 27795206--27795267 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
27795196 AATTAATTTT
*
27795206 TTTTTAAAATTTTAAAATATTATAAAAATTA
1 TTTTTAAAAATTT-AAA-ATTATAAAAATTA
* *
27795237 TTTTTAAAAATTTAGAATTATTAAAATTA
1 TTTTTAAAAATTTAAAATTATAAAAATTA
27795266 TT
1 TT
27795268 AAAAGGTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 14 0.50
30 2 0.07
31 12 0.43
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (29 bp):
TTTTTAAAAATTTAAAATTATAAAAATTA
Found at i:27799686 original size:21 final size:21
Alignment explanation
Indices: 27799656--27799697 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
27799646 TTTTCCAAAG
* *
27799656 ATGTGTATTGGATTGAATTGA
1 ATGTGAATTGGATTAAATTGA
*
27799677 ATGTGAATTGTATTAAATTGA
1 ATGTGAATTGGATTAAATTGA
27799698 GTTAAATTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.43
Consensus pattern (21 bp):
ATGTGAATTGGATTAAATTGA
Found at i:27800158 original size:27 final size:26
Alignment explanation
Indices: 27800062--27800160 Score: 105
Period size: 27 Copynumber: 3.9 Consensus size: 26
27800052 GGATCTCACG
*
27800062 AGCTTCCCAATTAATGGCTCTCT-TA
1 AGCTTCCCGATTAATGGCTCTCTATA
* * *
27800087 AGCTTCCCG-TTTATGGCT-TGTATG
1 AGCTTCCCGATTAATGGCTCTCTATA
* * *
27800111 AGCTTCCCGATAAAAGACTCTCTCATA
1 AGCTTCCCGATTAATGGCTCTCT-ATA
27800138 AGCTTCCCGATTAATGGCTCTCT
1 AGCTTCCCGATTAATGGCTCTCT
27800161 GGAGCTACGC
Statistics
Matches: 57, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
23 2 0.04
24 18 0.32
25 13 0.23
26 2 0.04
27 22 0.39
ACGTcount: A:0.22, C:0.27, G:0.16, T:0.34
Consensus pattern (26 bp):
AGCTTCCCGATTAATGGCTCTCTATA
Found at i:27800207 original size:25 final size:25
Alignment explanation
Indices: 27800178--27800231 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
27800168 CGCGATATTA
27800178 GCTCACATGAGCTTCCCGTTACATG
1 GCTCACATGAGCTTCCCGTTACATG
* *
27800203 GCTCACATGAGCTTCCTGTTATATG
1 GCTCACATGAGCTTCCCGTTACATG
27800228 GCTC
1 GCTC
27800232 GAAAGAGCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.19, C:0.30, G:0.20, T:0.31
Consensus pattern (25 bp):
GCTCACATGAGCTTCCCGTTACATG
Found at i:27800239 original size:25 final size:25
Alignment explanation
Indices: 27800178--27800240 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
27800168 CGCGATATTA
*
27800178 GCTCACATGAGCTTCCCGTTACATG
1 GCTCACAAGAGCTTCCCGTTACATG
* * *
27800203 GCTCACATGAGCTTCCTGTTATATG
1 GCTCACAAGAGCTTCCCGTTACATG
27800228 GCTCGA-AAGAGCT
1 GCTC-ACAAGAGCT
27800241 ATTCGTTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
25 33 0.97
26 1 0.03
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (25 bp):
GCTCACAAGAGCTTCCCGTTACATG
Found at i:27800264 original size:25 final size:24
Alignment explanation
Indices: 27800178--27800264 Score: 72
Period size: 25 Copynumber: 3.5 Consensus size: 24
27800168 CGCGATATTA
*
27800178 GCTCACATGAGCTTCCCG-TTACATG
1 GCTCACATGAGCTT--CGTTTATATG
*
27800203 GCTCACATGAGCTTCCTGTTATATG
1 GCTCACATGAGCTTCGT-TTATATG
*
27800228 GCTCGA-AAGAGCTATTCGTTTATAT-
1 GCTC-ACATGAGC--TTCGTTTATATG
27800253 GCTCACATGAGC
1 GCTCACATGAGC
27800265 ATTCCTGAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
23 1 0.02
24 1 0.02
25 38 0.75
26 7 0.14
27 4 0.08
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (24 bp):
GCTCACATGAGCTTCGTTTATATG
Found at i:27806703 original size:29 final size:30
Alignment explanation
Indices: 27806657--27806718 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
27806647 ATTATTCATC
27806657 ATTGAAAAATTAAGAAAAGAAA-ATGATTAA
1 ATTGAAAAATTAAGAAAAGAAAGATGA-TAA
*
27806687 ATTGAAAAGA-TAA-AAAATAAAGATGATAA
1 ATTGAAAA-ATTAAGAAAAGAAAGATGATAA
27806716 ATT
1 ATT
27806719 AATTAAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 13 0.45
30 15 0.52
31 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.13, T:0.24
Consensus pattern (30 bp):
ATTGAAAAATTAAGAAAAGAAAGATGATAA
Found at i:27807710 original size:25 final size:25
Alignment explanation
Indices: 27807668--27807715 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
27807658 CTCGTATGAG
*
27807668 CTTCCCGATAATTAGCTCTCTGAAA
1 CTTCCCGATAATAAGCTCTCTGAAA
27807693 CTTCCCGATAA-AAGGCTCTCTGA
1 CTTCCCGATAATAA-GCTCTCTGA
27807716 TGAGTTTCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (25 bp):
CTTCCCGATAATAAGCTCTCTGAAA
Found at i:27807783 original size:25 final size:25
Alignment explanation
Indices: 27807728--27807819 Score: 71
Period size: 25 Copynumber: 3.7 Consensus size: 25
27807718 AGTTTCCCGA
** **
27807728 ATATGGCTCTTATGAGCTTCCCATT
1 ATATGGCTCACATGAGCTTCCTGTT
**
27807753 CCATGGCTCACATGAGCTTCCTGTT
1 ATATGGCTCACATGAGCTTCCTGTT
* *
27807778 ATATGGCTCGA-AAGAGCTACCTGTT
1 ATATGGCTC-ACATGAGCTTCCTGTT
*
27807803 -TATACGCTCACATGAGC
1 ATAT-GGCTCACATGAGC
27807820 ATTCTGGAAT
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
24 4 0.08
25 47 0.90
26 1 0.02
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.32
Consensus pattern (25 bp):
ATATGGCTCACATGAGCTTCCTGTT
Found at i:27820002 original size:35 final size:33
Alignment explanation
Indices: 27819948--27820012 Score: 94
Period size: 35 Copynumber: 1.9 Consensus size: 33
27819938 TCTAATACAT
*
27819948 ATTTCATTTCATGTCATTTGCTATTTCAATAGC
1 ATTTCATTTCATGTCATTTGCCATTTCAATAGC
*
27819981 ATTTCATCTTCAATTTCATTTGCCATTTCAAT
1 ATTTCAT-TTC-ATGTCATTTGCCATTTCAAT
27820013 TTCAATAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 7 0.25
34 3 0.11
35 18 0.64
ACGTcount: A:0.25, C:0.20, G:0.06, T:0.49
Consensus pattern (33 bp):
ATTTCATTTCATGTCATTTGCCATTTCAATAGC
Found at i:27820012 original size:18 final size:18
Alignment explanation
Indices: 27819952--27820016 Score: 64
Period size: 18 Copynumber: 3.7 Consensus size: 18
27819942 ATACATATTT
*
27819952 CATTTC-ATGTCATTTGC
1 CATTTCAATTTCATTTGC
* **
27819969 TATTTCAATAGCATTT--
1 CATTTCAATTTCATTTGC
27819985 CATCTTCAATTTCATTTGC
1 CAT-TTCAATTTCATTTGC
27820004 CATTTCAATTTCA
1 CATTTCAATTTCA
27820017 ATAATACAAG
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
16 2 0.05
17 16 0.42
18 17 0.45
19 3 0.08
ACGTcount: A:0.25, C:0.22, G:0.06, T:0.48
Consensus pattern (18 bp):
CATTTCAATTTCATTTGC
Found at i:27829657 original size:27 final size:27
Alignment explanation
Indices: 27829626--27829870 Score: 312
Period size: 27 Copynumber: 9.1 Consensus size: 27
27829616 TTACACTATT
*
27829626 ATGACCGAATTACCCCCATAGGATAAA
1 ATGACCGAATTACCCCCATAGGGTAAA
27829653 ATGACCGAATTACCCCCATAGGGTAAA
1 ATGACCGAATTACCCCCATAGGGTAAA
* *
27829680 ATAACCGAATTACCCCCATAAGGTAAA
1 ATGACCGAATTACCCCCATAGGGTAAA
* **
27829707 ATGACCGAATTAACCTTATAGGGTAAA
1 ATGACCGAATTACCCCCATAGGGTAAA
** *
27829734 ATGATTGAATTA-CCTCATAGGGTAAA
1 ATGACCGAATTACCCCCATAGGGTAAA
* *
27829760 ATGACCGAATTACCCCATATAGGGTAAG
1 ATGACCGAATTACCCC-CATAGGGTAAA
* *
27829788 ACGACTGAATTACCCCCATAGGGTAAA
1 ATGACCGAATTACCCCCATAGGGTAAA
*
27829815 ATGACCAAATTACCCCCATAGGGTAAA
1 ATGACCGAATTACCCCCATAGGGTAAA
* * **
27829842 ATGATCGAAATACCCCCATATTGTAAA
1 ATGACCGAATTACCCCCATAGGGTAAA
27829869 AT
1 AT
27829871 AACTGCTATA
Statistics
Matches: 188, Mismatches: 28, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
26 23 0.12
27 142 0.76
28 23 0.12
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (27 bp):
ATGACCGAATTACCCCCATAGGGTAAA
Found at i:27830276 original size:28 final size:28
Alignment explanation
Indices: 27830236--27830298 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 28
27830226 GCACTGTACC
* *
27830236 GTTATTGTATTGGGCTAAGGCCCACATT
1 GTTACTGTATTGGGCTAAGGCCCACACT
27830264 GTTACTGTATTGGGCTAAGGCCCACACT
1 GTTACTGTATTGGGCTAAGGCCCACACT
27830292 G-TACTGT
1 GTTACTGT
27830299 TACTAAATAG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
27 6 0.18
28 27 0.82
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (28 bp):
GTTACTGTATTGGGCTAAGGCCCACACT
Found at i:27830300 original size:33 final size:33
Alignment explanation
Indices: 27830227--27830331 Score: 103
Period size: 33 Copynumber: 3.3 Consensus size: 33
27830217 TGCATTATTG
* *
27830227 CACTGTACCGTTATTGTATTGGGCTAAGGCCCA
1 CACTGTACTGTTACTGTATTGGGCTAAGGCCCA
27830260 CA---T--TGTTACTGTATTGGGCTAAGGCCCA
1 CACTGTACTGTTACTGTATTGGGCTAAGGCCCA
** * *
27830288 CACTGTACTGTTACTAAATAGGGCTCAGGCCCA
1 CACTGTACTGTTACTGTATTGGGCTAAGGCCCA
*
27830321 GACTGTCACTG
1 CACTGT-ACTG
27830332 CTTGTTGTAT
Statistics
Matches: 59, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
28 25 0.42
30 1 0.02
31 1 0.02
33 28 0.47
34 4 0.07
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.29
Consensus pattern (33 bp):
CACTGTACTGTTACTGTATTGGGCTAAGGCCCA
Found at i:27833460 original size:42 final size:42
Alignment explanation
Indices: 27833369--27833465 Score: 108
Period size: 42 Copynumber: 2.3 Consensus size: 42
27833359 GTTTCAAGTT
** ** *
27833369 AGTGAGTTACACGGCCTGGCACACGACTGTGTGTGGCAACTT
1 AGTGAGTTACACGGCCTGGCACACGACCATGTGTACCAACTC
*
27833411 AGAGAGTTACACGGCCT-GCGACACGACCATGTG-ACCTAACTC
1 AGTGAGTTACACGGCCTGGC-ACACGACCATGTGTACC-AACTC
27833453 AGTGAGTTACACG
1 AGTGAGTTACACG
27833466 AGTGAGGACA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
41 3 0.07
42 43 0.93
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.21
Consensus pattern (42 bp):
AGTGAGTTACACGGCCTGGCACACGACCATGTGTACCAACTC
Found at i:27837526 original size:23 final size:23
Alignment explanation
Indices: 27837499--27837549 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
27837489 ATGAATAAAG
*
27837499 ATGAATAGGAAATATTCTTTGGC
1 ATGAATAGGAAATATTCTCTGGC
27837522 ATGAATAGGAAATATTCTCTGGC
1 ATGAATAGGAAATATTCTCTGGC
27837545 ATGAA
1 ATGAA
27837550 CAGTAGAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (23 bp):
ATGAATAGGAAATATTCTCTGGC
Found at i:27840543 original size:11 final size:11
Alignment explanation
Indices: 27840516--27840550 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
27840506 CATATTGTAC
27840516 TTGAAAAAAAA
1 TTGAAAAAAAA
*
27840527 GT-AAAAAAAA
1 TTGAAAAAAAA
27840537 TTGAAAAAAAA
1 TTGAAAAAAAA
27840548 TTG
1 TTG
27840551 CATAAAGTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.69, C:0.00, G:0.11, T:0.20
Consensus pattern (11 bp):
TTGAAAAAAAA
Found at i:27842742 original size:28 final size:27
Alignment explanation
Indices: 27842703--27842767 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
27842693 GTCTGTGGAA
* *
27842703 AAATTGAGAGAAACGAACAATGAAAAAG
1 AAATTGAAAGAAACGAA-AAAGAAAAAG
*
27842731 AAATTGAAAGAAATGAAAAAGAAAAAG
1 AAATTGAAAGAAACGAAAAAGAAAAAG
*
27842758 AAAGTGAAAG
1 AAATTGAAAG
27842768 TAAAAAAACA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
27 18 0.55
28 15 0.45
ACGTcount: A:0.65, C:0.03, G:0.22, T:0.11
Consensus pattern (27 bp):
AAATTGAAAGAAACGAAAAAGAAAAAG
Found at i:27842760 original size:21 final size:21
Alignment explanation
Indices: 27842721--27842761 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
27842711 AGAAACGAAC
**
27842721 AATGAAAAAGAAATTGAAAGA
1 AATGAAAAAGAAAAAGAAAGA
27842742 AATGAAAAAGAAAAAGAAAG
1 AATGAAAAAGAAAAAGAAAG
27842762 TGAAAGTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.20, T:0.10
Consensus pattern (21 bp):
AATGAAAAAGAAAAAGAAAGA
Found at i:27846360 original size:37 final size:37
Alignment explanation
Indices: 27846310--27846384 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
27846300 TTCTTGGAAA
27846310 TAGAATATTGTGGTGAAGAAGCAACTCTACTCTAAGT
1 TAGAATATTGTGGTGAAGAAGCAACTCTACTCTAAGT
27846347 TAGAATATTGTGGTGAAGAAGCAACTCTACTCTAAGT
1 TAGAATATTGTGGTGAAGAAGCAACTCTACTCTAAGT
27846384 T
1 T
27846385 TCTGTACTAA
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:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (37 bp):
TAGAATATTGTGGTGAAGAAGCAACTCTACTCTAAGT
Found at i:27861320 original size:26 final size:26
Alignment explanation
Indices: 27861291--27861459 Score: 81
Period size: 26 Copynumber: 6.8 Consensus size: 26
27861281 TCCTCTCTCA
*
27861291 AGCCATATAAT-AGGAGGCTCACAAAG
1 AGCCAT-TAATCAGGAAGCTCACAAAG
*
27861317 AGCCATTAATCGGGAAGCTCACAAAG
1 AGCCATTAATCAGGAAGCTCACAAAG
* * * *
27861343 AGCC--T-ATCAAGAAGGTTATC--TG
1 AGCCATTAATCAGGAAGCTCA-CAAAG
* * *
27861365 GGCTATATAA-CAGGAAGCTCA-TAAG
1 AGCCAT-TAATCAGGAAGCTCACAAAG
* *
27861390 AGCCA-TAATAAGGAAGTTCACAAAG
1 AGCCATTAATCAGGAAGCTCACAAAG
* * *
27861415 A-ACTTTCAATCAGGAAGCTCACGAAG
1 AGCCATT-AATCAGGAAGCTCACAAAG
* *
27861441 AGCCTTTAACCAGG-AGCTC
1 AGCCATTAATCAGGAAGCTC
27861460 CGGATAGCCA
Statistics
Matches: 105, Mismatches: 25, Indels: 27
0.67 0.16 0.17
Matches are distributed among these distances:
22 3 0.03
23 12 0.11
24 12 0.11
25 27 0.26
26 47 0.45
27 4 0.04
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.19
Consensus pattern (26 bp):
AGCCATTAATCAGGAAGCTCACAAAG
Found at i:27862209 original size:20 final size:20
Alignment explanation
Indices: 27862168--27862209 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
27862158 AGCCTATGTA
*
27862168 TTTCATAAAATTTAGAATTT
1 TTTCATAAAATTTACAATTT
*
27862188 TTTCATAAATTTTACATATTT
1 TTTCATAAAATTTACA-ATTT
27862209 T
1 T
27862210 CAATATAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (20 bp):
TTTCATAAAATTTACAATTT
Found at i:27862442 original size:14 final size:15
Alignment explanation
Indices: 27862423--27862452 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
27862413 GTTGGCTTGA
27862423 GGTTA-GGTTTCCAT
1 GGTTAGGGTTTCCAT
27862437 GGTTAGGGTTTCCAT
1 GGTTAGGGTTTCCAT
27862452 G
1 G
27862453 CTTTTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.13, C:0.13, G:0.33, T:0.40
Consensus pattern (15 bp):
GGTTAGGGTTTCCAT
Found at i:27868189 original size:25 final size:25
Alignment explanation
Indices: 27868160--27868254 Score: 86
Period size: 26 Copynumber: 3.8 Consensus size: 25
27868150 GGAAACTCAT
*
27868160 AAGAGCCATAATTAGGAAGTTCACA
1 AAGAGCCATAATTAGGAAGCTCACA
* * *
27868185 AAGAGCTCTTAATCAAGAAGCTCACA
1 AAGAGC-CATAATTAGGAAGCTCACA
*
27868211 AAGAGCCTTTAATTAGG-AGCTC-CA
1 AAGAGCC-ATAATTAGGAAGCTCACA
* *
27868235 GATAGCCATATATTAGGAAG
1 AAGAGCCATA-ATTAGGAAG
27868255 TTCAAGCGAG
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
23 2 0.04
24 13 0.23
25 14 0.25
26 28 0.49
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.22
Consensus pattern (25 bp):
AAGAGCCATAATTAGGAAGCTCACA
Found at i:27870145 original size:4 final size:4
Alignment explanation
Indices: 27870136--27870206 Score: 142
Period size: 4 Copynumber: 17.8 Consensus size: 4
27870126 TTTGAGAAGT
27870136 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
27870184 TGTA TGTA TGTA TGTA TGTA TGT
1 TGTA TGTA TGTA TGTA TGTA TGT
27870207 GCTCTCTGTG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 67 1.00
ACGTcount: A:0.24, C:0.00, G:0.25, T:0.51
Consensus pattern (4 bp):
TGTA
Found at i:27870832 original size:50 final size:50
Alignment explanation
Indices: 27870770--27870967 Score: 209
Period size: 50 Copynumber: 4.0 Consensus size: 50
27870760 CCTTTGTAGT
* * * *
27870770 AAATTGTTTGGGAAGCCTTTGTGACGAGTCATCTGGGAAGCCCTTATGGC
1 AAATTGTTTGGGAAACCTTTGTGGCGAGTCATCTGGAAAGCCCTTGTGGC
* * * * *
27870820 AAATTGTTTGGGAAATCTTTATGGTGAGTCATTTGTAAAGCCCTTGTGGC
1 AAATTGTTTGGGAAACCTTTGTGGCGAGTCATCTGGAAAGCCCTTGTGGC
* * * * * * *
27870870 AAATTATTTAGGAAACATTTGT-GCGATTCATCTGTAAAGCCTTTGTGGT
1 AAATTGTTTGGGAAACCTTTGTGGCGAGTCATCTGGAAAGCCCTTGTGGC
* * * *
27870919 GAATTGTTTGGGAAATCTTTGTGGCAAGTCATCTGGAAAGCCTTTGTGG
1 AAATTGTTTGGGAAACCTTTGTGGCGAGTCATCTGGAAAGCCCTTGTGG
27870968 GGAGTCATTT
Statistics
Matches: 120, Mismatches: 27, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
49 39 0.32
50 81 0.68
ACGTcount: A:0.24, C:0.14, G:0.27, T:0.35
Consensus pattern (50 bp):
AAATTGTTTGGGAAACCTTTGTGGCGAGTCATCTGGAAAGCCCTTGTGGC
Found at i:27870979 original size:50 final size:50
Alignment explanation
Indices: 27870757--27870982 Score: 186
Period size: 50 Copynumber: 4.5 Consensus size: 50
27870747 AAACCAAACT
* ** * ** * **
27870757 AAGCCTTTGTAGTAAATTGTTTGGGAAGCCTTTGTGACGAGTCATCTGGG
1 AAGCCTTTGTGGCGAATTATTTGGGAAATCTTTGTGGCGAGTCATCTGTA
* * * * * * *
27870807 AAGCCCTTATGGCAAATTGTTTGGGAAATCTTTATGGTGAGTCATTTGTA
1 AAGCCTTTGTGGCGAATTATTTGGGAAATCTTTGTGGCGAGTCATCTGTA
* * * *
27870857 AAGCCCTTGTGGCAAATTATTTAGGAAA-CATTTGT-GCGATTCATCTGTA
1 AAGCCTTTGTGGCGAATTATTTGGGAAATC-TTTGTGGCGAGTCATCTGTA
* * * *
27870906 AAGCCTTTGTGGTGAATTGTTTGGGAAATCTTTGTGGCAAGTCATCTGGA
1 AAGCCTTTGTGGCGAATTATTTGGGAAATCTTTGTGGCGAGTCATCTGTA
* * *
27870956 AAGCCTTTGTGGGGAGTCATTTGGGAA
1 AAGCCTTTGTGGCGAATTATTTGGGAA
27870983 GTTTGTAAGG
Statistics
Matches: 142, Mismatches: 31, Indels: 6
0.79 0.17 0.03
Matches are distributed among these distances:
49 40 0.28
50 102 0.72
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.35
Consensus pattern (50 bp):
AAGCCTTTGTGGCGAATTATTTGGGAAATCTTTGTGGCGAGTCATCTGTA
Found at i:27872715 original size:39 final size:39
Alignment explanation
Indices: 27872556--27872732 Score: 183
Period size: 39 Copynumber: 4.5 Consensus size: 39
27872546 ATTCACTTTT
** * * * **
27872556 AAGCATATATCATATTACACATATAATCACATAAAATTT
1 AAGCATATATCGCAATACTCATATAATCACATAACATCC
* * *
27872595 AAGCATATATCACAATACTCATATAATTACATAACTTCC
1 AAGCATATATCGCAATACTCATATAATCACATAACATCC
* * * * * * *
27872634 AAGCACATATCGCAATAATGACATAATAACATAGCATTC
1 AAGCATATATCGCAATACTCATATAATCACATAACATCC
27872673 AAGCATATATCGCAATACTCATATAATCACATAACATCC
1 AAGCATATATCGCAATACTCATATAATCACATAACATCC
* *
27872712 AAGCATATGTTGCAATACTCA
1 AAGCATATATCGCAATACTCA
27872733 AAAACATGTT
Statistics
Matches: 112, Mismatches: 26, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
39 112 1.00
ACGTcount: A:0.45, C:0.21, G:0.06, T:0.28
Consensus pattern (39 bp):
AAGCATATATCGCAATACTCATATAATCACATAACATCC
Found at i:27878803 original size:50 final size:50
Alignment explanation
Indices: 27878728--27878825 Score: 178
Period size: 50 Copynumber: 2.0 Consensus size: 50
27878718 GTAAACTCTG
*
27878728 CCATTTACTTTAAGTATAAATACCCCACTCATTCCCCATAACAAACATTT
1 CCATTTACTTCAAGTATAAATACCCCACTCATTCCCCATAACAAACATTT
*
27878778 CCATTTACTTCAAGTATAGATACCCCACTCATTCCCCATAACAAACAT
1 CCATTTACTTCAAGTATAAATACCCCACTCATTCCCCATAACAAACAT
27878826 CCTTCATCCC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.36, C:0.32, G:0.03, T:0.30
Consensus pattern (50 bp):
CCATTTACTTCAAGTATAAATACCCCACTCATTCCCCATAACAAACATTT
Found at i:27884333 original size:18 final size:18
Alignment explanation
Indices: 27884310--27884346 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
27884300 AAAAATAGAA
27884310 AGACCATTTCCTACTGCT
1 AGACCATTTCCTACTGCT
27884328 AGACCATTTCCTACTGCT
1 AGACCATTTCCTACTGCT
27884346 A
1 A
27884347 TTCTTTAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.32, G:0.11, T:0.32
Consensus pattern (18 bp):
AGACCATTTCCTACTGCT
Found at i:27884764 original size:11 final size:11
Alignment explanation
Indices: 27884701--27884764 Score: 51
Period size: 12 Copynumber: 5.7 Consensus size: 11
27884691 GTAAAACAAA
27884701 TTTAATTT--T
1 TTTAATTTCAT
*
27884710 TTTAATTTTAAT
1 TTTAA-TTTCAT
*
27884722 TTTAATTTTAAT
1 TTTAA-TTTCAT
*
27884734 TTTAATTTTAAT
1 TTTAA-TTTCAT
27884746 TTTAATTTCAT
1 TTTAATTTCAT
*
27884757 TTTTATTT
1 TTTAATTT
27884765 TTTCAATAAG
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
9 5 0.10
10 3 0.06
11 12 0.24
12 30 0.60
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTAATTTCAT
Found at i:27884766 original size:6 final size:6
Alignment explanation
Indices: 27884709--27884753 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
27884699 AATTTAATTT
27884709 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTT
27884754 CATTTTTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTTAA
Found at i:27886970 original size:25 final size:25
Alignment explanation
Indices: 27886936--27886994 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
27886926 GTCATTAGGG
* *
27886936 TTACCGATTCTCAACTCGTCTGAGC
1 TTACCGATTCTCAACTCATATGAGC
* *
27886961 TTACCGATTCTTAGCTCATATGAGC
1 TTACCGATTCTCAACTCATATGAGC
*
27886986 TTATCGATT
1 TTACCGATT
27886995 TACAATTTTG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.22, C:0.25, G:0.15, T:0.37
Consensus pattern (25 bp):
TTACCGATTCTCAACTCATATGAGC
Found at i:27896328 original size:19 final size:19
Alignment explanation
Indices: 27896304--27896340 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
27896294 TAGGTCAAAG
27896304 TGTAATAGTTAATTTAATA
1 TGTAATAGTTAATTTAATA
27896323 TGTAATAGTTAATTTAAT
1 TGTAATAGTTAATTTAAT
27896341 TTGATGTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.49
Consensus pattern (19 bp):
TGTAATAGTTAATTTAATA
Found at i:27898203 original size:30 final size:30
Alignment explanation
Indices: 27898165--27898280 Score: 94
Period size: 31 Copynumber: 4.2 Consensus size: 30
27898155 TAAAATTTTT
* *
27898165 TATTTTTTTT--ATTTTTTTACTTTTAAAA
1 TATTTTTTTTAAAATTTTTTAATTTTAAAA
27898193 TACTTTTTTTTAAAATTTTTTAATTTTAAAA
1 TA-TTTTTTTTAAAATTTTTTAATTTTAAAA
*
27898224 TA---TTTTTAAAA-----TATTTTTAAAA
1 TATTTTTTTTAAAATTTTTTAATTTTAAAA
* *
27898246 TA-CTTTTTT-AATTTTTTTAATTTTAAAA
1 TATTTTTTTTAAAATTTTTTAATTTTAAAA
27898274 TATTTTT
1 TATTTTT
27898281 AAAATACTTT
Statistics
Matches: 71, Mismatches: 6, Indels: 21
0.72 0.06 0.21
Matches are distributed among these distances:
22 12 0.17
23 2 0.03
24 5 0.07
27 9 0.13
28 14 0.20
29 11 0.15
31 18 0.25
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (30 bp):
TATTTTTTTTAAAATTTTTTAATTTTAAAA
Found at i:27898221 original size:16 final size:17
Alignment explanation
Indices: 27898178--27898232 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
27898168 TTTTTTTATT
*
27898178 TTTTTACTTTTAAAATA
1 TTTTTAATTTTAAAATA
*
27898195 CTTTT--TTTTAAAAT-
1 TTTTTAATTTTAAAATA
27898209 TTTTTAATTTTAAAATA
1 TTTTTAATTTTAAAATA
27898226 TTTTTAA
1 TTTTTAA
27898233 AATATTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 4 0.12
15 9 0.27
16 9 0.27
17 11 0.33
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTTAATTTTAAAATA
Found at i:27898281 original size:39 final size:39
Alignment explanation
Indices: 27898168--27898301 Score: 146
Period size: 39 Copynumber: 3.4 Consensus size: 39
27898158 AATTTTTTAT
* * *
27898168 TTTTTTTATTTTTTTACTTTTAAAATACTTTTTTTTAAA-A-
1 TTTTTTAATTTTTTTAATTTTAAAATA---TTTTTAAAATAC
** *
27898208 TTTTTTAATTTTAAAATATTTTTAAAATATTTTTAAAATAC
1 TTTTTTAATTTT--TTTAATTTTAAAATATTTTTAAAATAC
27898249 TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATAC
*
27898288 TTTTTTAAATTTTT
1 TTTTTTAATTTTTT
27898302 AAAATAAATT
Statistics
Matches: 81, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
39 45 0.56
40 12 0.15
41 12 0.15
42 12 0.15
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (39 bp):
TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATAC
Found at i:27898313 original size:21 final size:21
Alignment explanation
Indices: 27898275--27898314 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
27898265 ATTTTAAAAT
**
27898275 ATTTTTAAAATACTTTTTTAA
1 ATTTTTAAAATAAATTTTTAA
27898296 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
27898315 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTAA
Found at i:27899157 original size:22 final size:22
Alignment explanation
Indices: 27899127--27899170 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
27899117 GAAAGTTTCA
* *
27899127 CCTTTGAAGAAAGTATTTTGGT
1 CCTTGGAAGAAAGTACTTTGGT
27899149 CCTTGGAAGAAAGTACTTTGGT
1 CCTTGGAAGAAAGTACTTTGGT
27899171 TTGACAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.27, C:0.11, G:0.25, T:0.36
Consensus pattern (22 bp):
CCTTGGAAGAAAGTACTTTGGT
Found at i:27901295 original size:50 final size:50
Alignment explanation
Indices: 27901240--27901339 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
27901230 ATTTGACCTG
27901240 ATAAGCTTTATCGTTTAATCGACGAATTTACTAAGCTTTATGTAAGCTTA
1 ATAAGCTTTATCGTTTAATCGACGAATTTACTAAGCTTTATGTAAGCTTA
27901290 ATAAGCTTTATCGTTTAATCGACGAATTTACTAAGCTTTATGTAAGCTTA
1 ATAAGCTTTATCGTTTAATCGACGAATTTACTAAGCTTTATGTAAGCTTA
27901340 CTTGTGTTCT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (50 bp):
ATAAGCTTTATCGTTTAATCGACGAATTTACTAAGCTTTATGTAAGCTTA
Found at i:27912033 original size:20 final size:21
Alignment explanation
Indices: 27911997--27912045 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
27911987 ATTATATTAA
**
27911997 TAAAT-TTAATAATTAAATTG
1 TAAATATTAATAATTAAAAAG
*
27912017 TAAATATTAATCA-TAAAAAG
1 TAAATATTAATAATTAAAAAG
27912037 TAAATATTA
1 TAAATATTA
27912046 TATTAATGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 19 0.76
21 6 0.24
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (21 bp):
TAAATATTAATAATTAAAAAG
Found at i:27914381 original size:27 final size:29
Alignment explanation
Indices: 27914350--27914409 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 29
27914340 GCAGGTTTTG
27914350 AATTTTGA-ATTTTGAATTTCGAGTTT-A
1 AATTTTGAGATTTTGAATTTCGAGTTTCA
**
27914377 AA-TTTGAGATTTTGGGTTTCGAGTTTCA
1 AATTTTGAGATTTTGAATTTCGAGTTTCA
27914405 AATTT
1 AATTT
27914410 CGAGTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 5 0.18
27 18 0.64
28 3 0.11
29 2 0.07
ACGTcount: A:0.27, C:0.05, G:0.18, T:0.50
Consensus pattern (29 bp):
AATTTTGAGATTTTGAATTTCGAGTTTCA
Found at i:27918287 original size:21 final size:22
Alignment explanation
Indices: 27918251--27918298 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
27918241 TAAAAATAGT
27918251 TTAATTAAAGAATAAATTAAGG-
1 TTAATTAAAGAATAAA-TAAGGA
*
27918273 TTAATT-AAGATTAAATAAGGA
1 TTAATTAAAGAATAAATAAGGA
27918294 TTAAT
1 TTAAT
27918299 ATTAGTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 5 0.21
21 13 0.54
22 6 0.25
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.35
Consensus pattern (22 bp):
TTAATTAAAGAATAAATAAGGA
Found at i:27919702 original size:20 final size:20
Alignment explanation
Indices: 27919662--27919703 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
27919652 TATTTAAATT
*
27919662 TTTTTGAAAATTATTTAGAA
1 TTTTTGAAAATAATTTAGAA
27919682 TTTTTGAAAATCAATTT-GAA
1 TTTTTGAAAAT-AATTTAGAA
27919702 TT
1 TT
27919704 ATTTTGTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.38, C:0.02, G:0.10, T:0.50
Consensus pattern (20 bp):
TTTTTGAAAATAATTTAGAA
Found at i:27920333 original size:288 final size:287
Alignment explanation
Indices: 27919779--27920347 Score: 766
Period size: 288 Copynumber: 2.0 Consensus size: 287
27919769 TATTTACACT
* * * *
27919779 AATCTGTTATTCGAATTATTCAAGTTAATCAAATTATAAAATTTAACTTGACTCAAACTCAAAAC
1 AATCCGTTATTCAAATTATTCAAGTTAATCAAATTACAAAATTTAACTCGACTCAAACTCAAAAC
** *
27919844 TTGAATTACTTATTCGAGTTTACTCAAATAACTCGATTGGATGAACTCAAAATTCGATTTTTTTT
66 TCAAATTACTTATCCGAGTTTACTCAAATAACTCGATTGGATGAACTCAAAATTCGATTTTTTTT
* **
27919909 CACTTTTTTTTAATCGAATTGAGTTTTTCTCACCCTAGTTGGCATGCCATAGGGTCAAGATATTG
131 CAATTTTTTCGAATCGAATTGAGTTTTTCTCACCCTAGTTGGCATGCCATAGGGTCAAGATATTG
* * * ** * * *
27919974 ATTAGAAATCATCATTTCTCAGGAACTCCGGGTGGTAGATTGTGCATATAAAGTCATCGTTGCTG
196 ATTAGAAACCATCATTTCTCAGGAACCCCAGGTAATAGATTGTACATATAAAGTCATCGTTACTA
*
27920039 TAACACCCCATACATGACCCGGTCGCC
261 TAACACCCCATACACGACCCGGTCGCC
* * * * * * *
27920066 AATCCGTTATTCAAATTA-TCGAGTTATTCGAATTACAAATTTTAACTCGACTCGAATTCGAAAC
1 AATCCGTTATTCAAATTATTCAAGTTAATCAAATTACAAAATTTAACTCGACTCAAACTCAAAAC
* ** * *
27920130 TCAAATTACTTATCCGAGTTTACTTAAATAACTTTATTGGATGAACTCAAATTTTGATTTTTTTT
66 TCAAATTACTTATCCGAGTTTACTCAAATAACTCGATTGGATGAACTCAAAATTCGATTTTTTTT
* * *
27920195 CTAATTTTTTCGAATTGAATTGAGTTTTTCTCACCCCTATTTGGCATGCCATATGGTCAAGATAT
131 C-AATTTTTTCGAATCGAATTGAGTTTTTCTCA-CCCTAGTTGGCATGCCATAGGGTCAAGATAT
*
27920260 TGATTAGAAACCATCAATTT-T-GGGCAACCCCAGGTAATAGATTGTACATATAAAGTCATCGTT
194 TGATTAGAAACCATC-ATTTCTCAGG-AACCCCAGGTAATAGATTGTACATATAAAGTCATCGTT
27920323 ACTATAACACCCCATACACGACCCG
257 ACTATAACACCCCATACACGACCCG
27920348 ATTGTTGGGT
Statistics
Matches: 243, Mismatches: 35, Indels: 7
0.85 0.12 0.02
Matches are distributed among these distances:
286 95 0.39
287 45 0.19
288 99 0.41
289 4 0.02
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (287 bp):
AATCCGTTATTCAAATTATTCAAGTTAATCAAATTACAAAATTTAACTCGACTCAAACTCAAAAC
TCAAATTACTTATCCGAGTTTACTCAAATAACTCGATTGGATGAACTCAAAATTCGATTTTTTTT
CAATTTTTTCGAATCGAATTGAGTTTTTCTCACCCTAGTTGGCATGCCATAGGGTCAAGATATTG
ATTAGAAACCATCATTTCTCAGGAACCCCAGGTAATAGATTGTACATATAAAGTCATCGTTACTA
TAACACCCCATACACGACCCGGTCGCC
Found at i:27921411 original size:14 final size:14
Alignment explanation
Indices: 27921367--27921414 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
27921357 TAGTTATTTG
27921367 TTTATTTTATTGTTTA
1 TTTATTTT-TTG-TTA
*
27921383 TTTA-TTTTAGTTA
1 TTTATTTTTTGTTA
*
27921396 TTTATTTTTTGATA
1 TTTATTTTTTGTTA
27921410 TTTAT
1 TTTAT
27921415 CTCTTTTATG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
13 7 0.25
14 14 0.50
15 3 0.11
16 4 0.14
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.73
Consensus pattern (14 bp):
TTTATTTTTTGTTA
Found at i:27924677 original size:44 final size:43
Alignment explanation
Indices: 27924605--27924687 Score: 105
Period size: 44 Copynumber: 1.9 Consensus size: 43
27924595 AAAATTTTTA
*
27924605 TTTAATCTTTTAAAAAATATAAACTCTTA-AAATGATATTACAT
1 TTTAATCTTATAAAAAATATAAACTCTTATAAAT-ATATTACAT
* **
27924648 TTTAATTCTTATAACAAATATAATTTCTTATAAATATATT
1 TTTAA-TCTTATAAAAAATATAAACTCTTATAAATATATT
27924688 CAAATAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
43 5 0.15
44 25 0.74
45 4 0.12
ACGTcount: A:0.45, C:0.08, G:0.01, T:0.46
Consensus pattern (43 bp):
TTTAATCTTATAAAAAATATAAACTCTTATAAATATATTACAT
Found at i:27925213 original size:20 final size:19
Alignment explanation
Indices: 27925188--27925227 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
27925178 TATTAATTTC
27925188 ATTAATAATATAATTGTAAA
1 ATTAATAATA-AATTGTAAA
* *
27925208 ATTAATACTAAATTTTAAA
1 ATTAATAATAAATTGTAAA
27925227 A
1 A
27925228 ACATGAATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (19 bp):
ATTAATAATAAATTGTAAA
Found at i:27928020 original size:40 final size:41
Alignment explanation
Indices: 27927976--27928067 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 41
27927966 TCCTTGAGAG
** *
27927976 CGCGATTTCCTTCCACGTCAGCAT-C-TCGCGCTGACGTGGA
1 CGCGATTTCCTGACACGT-ACCATACATCGCGCTGACGTGGA
* *
27928016 CGCGATTTCCTGACGCGTACCCTGACATCGCGCTGACGTGGA
1 CGCGATTTCCTGACACGTACCAT-ACATCGCGCTGACGTGGA
27928058 CGCGATTTCC
1 CGCGATTTCC
27928068 CGAAAAAAGG
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
39 3 0.07
40 15 0.34
41 1 0.02
42 25 0.57
ACGTcount: A:0.15, C:0.35, G:0.26, T:0.24
Consensus pattern (41 bp):
CGCGATTTCCTGACACGTACCATACATCGCGCTGACGTGGA
Found at i:27929743 original size:27 final size:27
Alignment explanation
Indices: 27929706--27929761 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
27929696 TGATACATTC
*
27929706 ATATAACTAAAATAAAAATT-AAATTAT
1 ATATAAATAAAATAAAAATTGAAA-TAT
* *
27929733 ATATAAATAAATTAATAATTGAAATAT
1 ATATAAATAAAATAAAAATTGAAATAT
27929760 AT
1 AT
27929762 TTGAATAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 22 0.88
28 3 0.12
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (27 bp):
ATATAAATAAAATAAAAATTGAAATAT
Found at i:27931393 original size:20 final size:20
Alignment explanation
Indices: 27931343--27931393 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 20
27931333 AATAGTTCTG
27931343 TCTCTTGATGAAC-ATATGTA
1 TCTCTTG-TGAACAATATGTA
27931363 TCT-TT-TGAACAAT-TGTA
1 TCTCTTGTGAACAATATGTA
27931380 TCTCTTGGTGAACA
1 TCTCTT-GTGAACA
27931394 GATTTATTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 12 0.44
18 4 0.15
19 2 0.07
20 9 0.33
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (20 bp):
TCTCTTGTGAACAATATGTA
Found at i:27942351 original size:42 final size:42
Alignment explanation
Indices: 27942217--27942356 Score: 144
Period size: 42 Copynumber: 3.3 Consensus size: 42
27942207 CTCGGTGGAT
* * *
27942217 TCAGCACTTAGCAACCACC-TTAAATTCAGTGATACGGGGAA
1 TCAGCACTTAGCAACCACCTTTAAAATCAATAATACGGGGAA
*
27942258 TCAGCACATT-GCAACC-CCTTTCACAATCAA-AGATACGGTGGAA
1 TCAGCAC-TTAGCAACCACCTTT-AAAATCAATA-ATACGG-GGAA
* * *
27942301 TCAGCACTTAGCAACCACCTTTAGAGTCAATAATTCGGGGAA
1 TCAGCACTTAGCAACCACCTTTAAAATCAATAATACGGGGAA
*
27942343 TCAACACTTAGCAA
1 TCAGCACTTAGCAA
27942357 ACCCTCGAGG
Statistics
Matches: 83, Mismatches: 8, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
40 2 0.02
41 15 0.18
42 32 0.39
43 28 0.34
44 6 0.07
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (42 bp):
TCAGCACTTAGCAACCACCTTTAAAATCAATAATACGGGGAA
Found at i:27946981 original size:20 final size:20
Alignment explanation
Indices: 27946956--27946993 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
27946946 CAAATTAAAC
*
27946956 AATAGTTCTGTCTTTTGATG
1 AATAGTTCTATCTTTTGATG
*
27946976 AATAGTTGTATCTTTTGA
1 AATAGTTCTATCTTTTGA
27946994 ACAATTGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.08, G:0.18, T:0.50
Consensus pattern (20 bp):
AATAGTTCTATCTTTTGATG
Found at i:27949611 original size:38 final size:38
Alignment explanation
Indices: 27949568--27949643 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
27949558 AATACAAAAG
27949568 TTAGTGCATTTATACATAACTCTCTTTTGATTCATACA
1 TTAGTGCATTTATACATAACTCTCTTTTGATTCATACA
27949606 TTAGTGCATTTATACATAACTCTCTTTTGATTCATACA
1 TTAGTGCATTTATACATAACTCTCTTTTGATTCATACA
27949644 ACCTTTTCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.45
Consensus pattern (38 bp):
TTAGTGCATTTATACATAACTCTCTTTTGATTCATACA
Found at i:27952636 original size:37 final size:37
Alignment explanation
Indices: 27952513--27952637 Score: 135
Period size: 37 Copynumber: 3.3 Consensus size: 37
27952503 AGTTTGCTCA
* * *
27952513 ATTTAAGATTGCGACTGTTATTTTTAAGGTTCGCTAG
1 ATTTAAGATCGCGACTGTTATTTTTAAGGTTCGTTCG
* * *
27952550 ATTTAAGATCGCGATCT-TCGATATTCTAACAGTTCGTTCG
1 ATTTAAGATCGCGA-CTGT-TAT-TTTTAA-GGTTCGTTCG
* *
27952590 ATTTAAGATCGTGACTGTTATTTTTAAGGTTCTTTCG
1 ATTTAAGATCGCGACTGTTATTTTTAAGGTTCGTTCG
27952627 ATTTAAGATCG
1 ATTTAAGATCG
27952638 AGACCTTCGA
Statistics
Matches: 72, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
37 33 0.46
38 9 0.12
39 9 0.12
40 21 0.29
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.42
Consensus pattern (37 bp):
ATTTAAGATCGCGACTGTTATTTTTAAGGTTCGTTCG
Found at i:27952681 original size:77 final size:77
Alignment explanation
Indices: 27952370--27952677 Score: 379
Period size: 77 Copynumber: 4.0 Consensus size: 77
27952360 TTTAATATCA
* * * *
27952370 CGACTGTTATTTTTAAGGTT-TGCTCGATTTAAGATTGCGACCTTCGGTATTCTAACAGTTTGCT
1 CGACTGTTATTTTTAAGGTTCT-CTCGATTTAAGATCGAGACCTTCGATATTCTAACAGTTCGCT
*
27952434 CGATTGAAGATTG
65 CGATTTAAGATTG
* * * * * *
27952447 CGACTTTTATTTTTATGGTTCGCTTGATTTAATATC-ATGACCTTC-AGTATTCTAACAGTTTGC
1 CGACTGTTATTTTTAAGGTTCTCTCGATTTAAGATCGA-GACCTTCGA-TATTCTAACAGTTCGC
*
27952510 TCAATTTAAGATTG
64 TCGATTTAAGATTG
* * * * *
27952524 CGACTGTTATTTTTAAGGTTCGCTAGATTTAAGATCGCGATCTTCGATATTCTAACAGTTCGTTC
1 CGACTGTTATTTTTAAGGTTCTCTCGATTTAAGATCGAGACCTTCGATATTCTAACAGTTCGCTC
*
27952589 GATTTAAGATCG
66 GATTTAAGATTG
* * *
27952601 TGACTGTTATTTTTAAGGTTCTTTCGATTTAAGATCGAGACCTTCGATATTCTAACAGTTCACTC
1 CGACTGTTATTTTTAAGGTTCTCTCGATTTAAGATCGAGACCTTCGATATTCTAACAGTTCGCTC
27952666 GATTTAAGATTG
66 GATTTAAGATTG
27952678 TGACCTTCGG
Statistics
Matches: 197, Mismatches: 29, Indels: 10
0.83 0.12 0.04
Matches are distributed among these distances:
77 196 0.99
78 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.42
Consensus pattern (77 bp):
CGACTGTTATTTTTAAGGTTCTCTCGATTTAAGATCGAGACCTTCGATATTCTAACAGTTCGCTC
GATTTAAGATTG
Found at i:27952723 original size:194 final size:194
Alignment explanation
Indices: 27952484--27953349 Score: 534
Period size: 194 Copynumber: 4.5 Consensus size: 194
27952474 TTTAATATCA
** * *
27952484 TGACCTTCAGTATTCTAACAGTTTGCTCAATTTAAGATTGCGACTGTTATTTTTAAGGTTCGCT-
1 TGACCTTCAGTATTCTAACAGTTCACTCAATTTAAGATCGCGACTGTCATTTTTAAGGTTCGCTC
* * * **
27952548 AGATTTAAGATCGCGATCTTC-GATATTCTAACAGTTCGTTCGATTTAAGATCGTGACTGTTATT
66 A-ATTTAAGATCGCGACCTTCAG-TATTCTAACAGTTCGCTCGATTGAAGATCAAGACTGTTATT
*
27952612 TTTAAGGTTCT-TTCGATTTAAGATCGAGACCTTCGATATTCTAACAGTTCACTCGATTTAAGAT
129 TTTAAGGTT-TGCTCGATTTAAGATCGAGACCTTCGATATTCTAACAGTTCACTCGATTTAAGAT
27952676 TG
193 TG
* * * * *
27952678 TGACCTTCGGTATTCTAATAGTTCACTCGATTTAAGATCGCGACTGTCATTTTTATGGTTTGCTC
1 TGACCTTCAGTATTCTAACAGTTCACTCAATTTAAGATCGCGACTGTCATTTTTAAGGTTCGCTC
* * * * *
27952743 AATTTAATATCGTGACCTTCAGTATTCTAACAGTTTGCTCGATTGAATATTAAGACTGTTATTTT
66 AATTTAAGATCGCGACCTTCAGTATTCTAACAGTTCGCTCGATTGAAGATCAAGACTGTTATTTT
* * * * * **
27952808 TACGGTTTGCTCGATTTAAGATCGAGACTTTCGGTATTCTAATAGTTCACTCGATTTAATATCA
131 TAAGGTTTGCTCGATTTAAGATCGAGACCTTCGATATTCTAACAGTTCACTCGATTTAAGATTG
** * * * * * * ** * * *
27952872 TGAATTTCA-T-TT-TTA-GGTTCGCTCGATTTAAGATCGTGACCTTTTGTATTCTAATAGTTCA
1 TGACCTTCAGTATTCTAACAGTTCACTCAATTTAAGATCGCGA-CTGTCAT-TTTTAA-GGTTCG
* * * * * * * **
27952933 CTCGATTTAAGAT--TG-TCTGTCA-T-TTTTAA-GGTTCGCTTGATTTAAGATTGAGACCT-TC
63 CTCAATTTAAGATCGCGACCT-TCAGTATTCTAACAGTTCGCTCGATTGAAGATCAAGA-CTGT-
* * * * * * *
27952991 GATATTCTAATAGTTTGCTTGATTTAAGATC-ACGACTTTC-AT-TTGT-AC-GATTCGCTCGAT
125 TAT-TTTTAA-GGTTTGCTCGATTTAAGATCGA-GACCTTCGATATTCTAACAG-TTCACTCGAT
*
27953051 TTAAGATCG
186 TTAAGATTG
* * * * ** *
27953060 TGACCTTCGGTATTCTAATAGTTCATTCGATTTAAGATCGTAACTATCATTTTTACA-GTTCGCT
1 TGACCTTCAGTATTCTAACAGTTCACTCAATTTAAGATCGCGACTGTCATTTTTA-AGGTTCGCT
* * * * * * *
27953124 CAATTTAAGATAGTGACCTTCAGTATTCTAACAATTTC-CTTGATTTAATATCACA-ACTGTCAT
65 CAATTTAAGATCGCGACCTTCAGTATTCTAAC-AGTTCGCTCGATTGAAGATCA-AGACTGTTAT
* ** * * *
27953187 TTTTAAGGTTCGCTTAATTTAAGATCTCA-ACAGTT-GATATTCTAACAGTTCACTTGATTTAAG
128 TTTTAAGGTTTGCTCGATTTAAGATC-GAGAC-CTTCGATATTCTAACAGTTCACTCGATTTAAG
**
27953250 ATCA
191 ATTG
* * * ** * *
27953254 TG-TCTGTCA-T-TTCT-ACAGTTCGCTCAATTTAATATCATGACTTTCATTTTTACA-GTTCAC
1 TGACCT-TCAGTATTCTAACAGTTCACTCAATTTAAGATCGCGACTGTCATTTTTA-AGGTTCGC
* *
27953314 T-AATTTAAGGTCGCGACCTTCCA-TTTTCTAACAGTT
64 TCAATTTAAGATCGCGACCTT-CAGTATTCTAACAGTT
27953350 TGGTTGGTTT
Statistics
Matches: 526, Mismatches: 110, Indels: 77
0.74 0.15 0.11
Matches are distributed among these distances:
187 1 0.00
188 42 0.08
189 32 0.06
190 60 0.11
191 107 0.20
192 42 0.08
193 32 0.06
194 203 0.39
195 7 0.01
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.41
Consensus pattern (194 bp):
TGACCTTCAGTATTCTAACAGTTCACTCAATTTAAGATCGCGACTGTCATTTTTAAGGTTCGCTC
AATTTAAGATCGCGACCTTCAGTATTCTAACAGTTCGCTCGATTGAAGATCAAGACTGTTATTTT
TAAGGTTTGCTCGATTTAAGATCGAGACCTTCGATATTCTAACAGTTCACTCGATTTAAGATTG
Found at i:27952748 original size:77 final size:77
Alignment explanation
Indices: 27952658--27953294 Score: 602
Period size: 77 Copynumber: 8.3 Consensus size: 77
27952648 TATTCTAACA
* * *
27952658 GTTCACTCGATTTAAGATTGTGACCTTCGGTATTCTAATAGTTCACTCGATTTAAGATCGCGACT
1 GTTCGCTCGATTTAAGATCGTGACCTTCGGTATTCTAATAGTTCACTCGATTTAAGATCACGACT
*
27952723 GTCATTTTTATG
66 GTCATTTTTACG
* * * * * ** * * * *
27952735 GTTTGCTCAATTTAATATCGTGACCTTCAGTATTCTAACAGTTTGCTCGATTGAATATTAAGACT
1 GTTCGCTCGATTTAAGATCGTGACCTTCGGTATTCTAATAGTTCACTCGATTTAAGATCACGACT
*
27952800 GTTATTTTTACG
66 GTCATTTTTACG
* * * * * *
27952812 GTTTGCTCGATTTAAGATCGAGACTTTCGGTATTCTAATAGTTCACTCGATTTAATATCATGAAT
1 GTTCGCTCGATTTAAGATCGTGACCTTCGGTATTCTAATAGTTCACTCGATTTAAGATCACGACT
*
27952877 TTCATTTTTA-G
66 GTCATTTTTACG
** * *
27952888 GTTCGCTCGATTTAAGATCGTGACCTTTTGTATTCTAATAGTTCACTCGATTTAAGAT--TGTCT
1 GTTCGCTCGATTTAAGATCGTGACCTTCGGTATTCTAATAGTTCACTCGATTTAAGATCACGACT
*
27952951 GTCATTTTTAAG
66 GTCATTTTTACG
* * * * ** *
27952963 GTTCGCTTGATTTAAGATTGAGACCTTCGATATTCTAATAGTTTGCTTGATTTAAGATCACGACT
1 GTTCGCTCGATTTAAGATCGTGACCTTCGGTATTCTAATAGTTCACTCGATTTAAGATCACGACT
* *
27953028 TTCATTTGTACG
66 GTCATTTTTACG
* * ***
27953040 ATTCGCTCGATTTAAGATCGTGACCTTCGGTATTCTAATAGTTCATTCGATTTAAGATCGTAACT
1 GTTCGCTCGATTTAAGATCGTGACCTTCGGTATTCTAATAGTTCACTCGATTTAAGATCACGACT
* *
27953105 ATCATTTTTACA
66 GTCATTTTTACG
* * * * * * * *
27953117 GTTCGCTCAATTTAAGATAGTGACCTTCAGTATTCTAACAATTTC-CTTGATTTAATATCACAAC
1 GTTCGCTCGATTTAAGATCGTGACCTTCGGTATTCTAA-TAGTTCACTCGATTTAAGATCACGAC
*
27953181 TGTCATTTTTAAG
65 TGTCATTTTTACG
** * * * * * * *
27953194 GTTCGCTTAATTTAAGATC-TCAACAGTT-GATATTCTAACAGTTCACTTGATTTAAGATCATGT
1 GTTCGCTCGATTTAAGATCGT-GAC-CTTCGGTATTCTAATAGTTCACTCGATTTAAGATCACGA
* *
27953257 CTGTCATTTCTACA
64 CTGTCATTTTTACG
* * *
27953271 GTTCGCTCAATTTAATATCATGAC
1 GTTCGCTCGATTTAAGATCGTGAC
27953295 TTTCATTTTT
Statistics
Matches: 452, Mismatches: 100, Indels: 16
0.80 0.18 0.03
Matches are distributed among these distances:
74 12 0.03
75 50 0.11
76 58 0.13
77 325 0.72
78 7 0.02
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.41
Consensus pattern (77 bp):
GTTCGCTCGATTTAAGATCGTGACCTTCGGTATTCTAATAGTTCACTCGATTTAAGATCACGACT
GTCATTTTTACG
Found at i:27952999 original size:305 final size:306
Alignment explanation
Indices: 27952666--27953265 Score: 717
Period size: 305 Copynumber: 2.0 Consensus size: 306
27952656 CAGTTCACTC
* * * *
27952666 GATTTAAGATTGTGACCTTCGGTATTCTAATAGTTCACTCGATTTAAGATCGCGACTGTCATTTT
1 GATTTAAGATTGAGACCTTCGATATTCTAATAGTTCACTCGATTTAAGATCACGACTGTCATTTG
* * * * ** *
27952731 TATGGTTTGCTCAATTTAATATCGTGACCTTCAGTATTCTAACAGTTTGCTCGATTGAATAT-TA
66 TACGATTCGCTCAATTTAAGATCGTGACCTTCAGTATTCTAACAGTTCACTCGATTGAAGATCT-
* * * * * * * * *
27952795 AGACTGTTATTTTTACGGTTTGCTCGATTTAAGATCGAGACTTTCGGTATTCTAA-TAGTTCACT
130 A-ACTATCATTTTTACAGTTCGCTCAATTTAAGATAGAGACCTTCAGTATTCTAACAAGTTC-CT
* * * * * **
27952859 CGATTTAATATCATGAA-TTTCATTTTT-AGGTTCGCTCGATTTAAGATCGTGACCTTTTG-TAT
193 CGATTTAATATCA-CAACTGTCATTTTTAAGGTTCGCTCAATTTAAGATC-TCAACAGTTGATAT
*
27952921 TCTAATAGTTCACTCGATTTAAGAT-TGTCTGTCATTTTTAAGGTTCGCTT
256 TCTAACAGTTCACTCGATTTAAGATATGTCTGTCATTTTTAAGGTTCGCTT
** * *
27952971 GATTTAAGATTGAGACCTTCGATATTCTAATAGTTTGCTTGATTTAAGATCACGACTTTCATTTG
1 GATTTAAGATTGAGACCTTCGATATTCTAATAGTTCACTCGATTTAAGATCACGACTGTCATTTG
* * * * *
27953036 TACGATTCGCTCGATTTAAGATCGTGACCTTCGGTATTCTAATAGTTCATTCGATTTAAGATCGT
66 TACGATTCGCTCAATTTAAGATCGTGACCTTCAGTATTCTAACAGTTCACTCGATTGAAGATC-T
* * *
27953101 AACTATCATTTTTACAGTTCGCTCAATTTAAGATAGTGACCTTCAGTATTCTAACAATTTCCTTG
130 AACTATCATTTTTACAGTTCGCTCAATTTAAGATAGAGACCTTCAGTATTCTAACAAGTTCCTCG
*
27953166 ATTTAATATCACAACTGTCATTTTTAAGGTTCGCTTAATTTAAGATCTCAACAGTTGATATTCTA
195 ATTTAATATCACAACTGTCATTTTTAAGGTTCGCTCAATTTAAGATCTCAACAGTTGATATTCTA
*
27953231 ACAGTTCACTTGATTTAAGATCATGTCTGTCATTT
260 ACAGTTCACTCGATTTAAGAT-ATGTCTGTCATTT
27953266 CTACAGTTCG
Statistics
Matches: 245, Mismatches: 42, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
304 2 0.01
305 180 0.73
306 50 0.20
307 1 0.00
308 12 0.05
ACGTcount: A:0.26, C:0.16, G:0.16, T:0.42
Consensus pattern (306 bp):
GATTTAAGATTGAGACCTTCGATATTCTAATAGTTCACTCGATTTAAGATCACGACTGTCATTTG
TACGATTCGCTCAATTTAAGATCGTGACCTTCAGTATTCTAACAGTTCACTCGATTGAAGATCTA
ACTATCATTTTTACAGTTCGCTCAATTTAAGATAGAGACCTTCAGTATTCTAACAAGTTCCTCGA
TTTAATATCACAACTGTCATTTTTAAGGTTCGCTCAATTTAAGATCTCAACAGTTGATATTCTAA
CAGTTCACTCGATTTAAGATATGTCTGTCATTTTTAAGGTTCGCTT
Found at i:27953099 original size:40 final size:40
Alignment explanation
Indices: 27952391--27953154 Score: 340
Period size: 40 Copynumber: 19.9 Consensus size: 40
27952381 TTTAAGGTTT
* * * *
27952391 GCTCGATTTAAGATTGCGACCTTCGGTATTCTAACAGTTT
1 GCTCGATTTAAGATCGTGACCTTCGGTATTCTAATAGTTC
* * * * * * *
27952431 GCTCGATTGAAGATTGCGA-CTT--TTATTTTTATGGTTC
1 GCTCGATTTAAGATCGTGACCTTCGGTATTCTAATAGTTC
* * * * * *
27952468 GCTTGATTTAATATCATGACCTTCAGTATTCTAACAGTTT
1 GCTCGATTTAAGATCGTGACCTTCGGTATTCTAATAGTTC
* * * * * *
27952508 GCTCAATTTAAGATTGCGA-C-T-GTTATTTTTAA-GGTTC
1 GCTCGATTTAAGATCGTGACCTTCGGTA-TTCTAATAGTTC
* * * * *
27952545 GCTAGATTTAAGATCGCGATCTTCGATATTCTAACAGTTC
1 GCTCGATTTAAGATCGTGACCTTCGGTATTCTAATAGTTC
* * * *
27952585 GTTCGATTTAAGATCGTGA-C-T-GTTATTTTTAA-GGTTC
1 GCTCGATTTAAGATCGTGACCTTCGGTA-TTCTAATAGTTC
** * * *
27952622 TTTCGATTTAAGATCGAGACCTTCGATATTCTAACAGTTC
1 GCTCGATTTAAGATCGTGACCTTCGGTATTCTAATAGTTC
* *
27952662 ACTCGATTTAAGATTGTGACCTTCGGTATTCTAATAGTTC
1 GCTCGATTTAAGATCGTGACCTTCGGTATTCTAATAGTTC
* * * * * *
27952702 ACTCGATTTAAGATCGCGA-C-T--GTCATTTTTATGGTTT
1 GCTCGATTTAAGATCGTGACCTTCGGT-ATTCTAATAGTTC
* * * * *
27952739 GCTCAATTTAATATCGTGACCTTCAGTATTCTAACAGTTT
1 GCTCGATTTAAGATCGTGACCTTCGGTATTCTAATAGTTC
* * *** * * * ** *
27952779 GCTCGATTGAATATTAAGA-C-T-GTTATTTTTACGGTTT
1 GCTCGATTTAAGATCGTGACCTTCGGTATTCTAATAGTTC
* *
27952816 GCTCGATTTAAGATCGAGACTTTCGGTATTCTAATAGTTC
1 GCTCGATTTAAGATCGTGACCTTCGGTATTCTAATAGTTC
* * * ** *
27952856 ACTCGATTTAATATCATGAATTTC---ATT-T-TTAGGTTC
1 GCTCGATTTAAGATCGTGACCTTCGGTATTCTAATA-GTTC
**
27952892 GCTCGATTTAAGATCGTGACCTTTTGTATTCTAATAGTTC
1 GCTCGATTTAAGATCGTGACCTTCGGTATTCTAATAGTTC
* * * * *
27952932 ACTCGATTTAAGAT--TG-TCTGTC-AT-TTTTAA-GGTTC
1 GCTCGATTTAAGATCGTGACCT-TCGGTATTCTAATAGTTC
* * * * *
27952967 GCTTGATTTAAGATTGAGACCTTCGATATTCTAATAGTTT
1 GCTCGATTTAAGATCGTGACCTTCGGTATTCTAATAGTTC
* ** * * * **
27953007 GCTTGATTTAAGATCACGACTTTC-AT-TTGTACGA-TTC
1 GCTCGATTTAAGATCGTGACCTTCGGTATTCTAATAGTTC
27953044 GCTCGATTTAAGATCGTGACCTTCGGTATTCTAATAGTTC
1 GCTCGATTTAAGATCGTGACCTTCGGTATTCTAATAGTTC
** * * * *
27953084 ATTCGATTTAAGATCGT-AACTATC---ATTTTTACAGTTC
1 GCTCGATTTAAGATCGTGACCT-TCGGTATTCTAATAGTTC
* * *
27953121 GCTCAATTTAAGATAGTGACCTTCAGTATTCTAA
1 GCTCGATTTAAGATCGTGACCTTCGGTATTCTAA
27953155 CAATTTCCTT
Statistics
Matches: 539, Mismatches: 143, Indels: 84
0.70 0.19 0.11
Matches are distributed among these distances:
35 18 0.03
36 30 0.06
37 173 0.32
38 36 0.07
39 39 0.07
40 239 0.44
41 4 0.01
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.41
Consensus pattern (40 bp):
GCTCGATTTAAGATCGTGACCTTCGGTATTCTAATAGTTC
Found at i:27953130 original size:37 final size:37
Alignment explanation
Indices: 27953089--27953322 Score: 113
Period size: 37 Copynumber: 6.2 Consensus size: 37
27953079 AGTTCATTCG
* *
27953089 ATTTAAGATCGTAACTATCATTTTTACAGTTCGCTCA
1 ATTTAAGATCATAACTATCATTTTTACAGTTCGCTTA
* * * *
27953126 ATTTAAGAT-AGTGACCT-TCAGTATTCTAACAATTTC-CTTG
1 ATTTAAGATCA-T-AACTATCA-T-TT-TTAC-AGTTCGCTTA
* * *
27953166 ATTTAATATCACAACTGTCATTTTTA-AGGTTCGCTTA
1 ATTTAAGATCATAACTATCATTTTTACA-GTTCGCTTA
* * * *
27953203 ATTTAAGATC-TCAACAGTTGAT-ATTCTAACAGTTCACTTG
1 ATTTAAGATCAT-AAC---T-ATCATTTTTACAGTTCGCTTA
** * * *
27953243 ATTTAAGATCATGTCTGTCATTTCTACAGTTCGCTCA
1 ATTTAAGATCATAACTATCATTTTTACAGTTCGCTTA
* * * *
27953280 ATTTAATATCATGACTTTCATTTTTACAGTTCAC-TA
1 ATTTAAGATCATAACTATCATTTTTACAGTTCGCTTA
27953316 ATTTAAG
1 ATTTAAG
27953323 GTCGCGACCT
Statistics
Matches: 144, Mismatches: 35, Indels: 37
0.67 0.16 0.17
Matches are distributed among these distances:
35 1 0.01
36 11 0.08
37 72 0.50
38 6 0.04
39 6 0.04
40 40 0.28
41 8 0.06
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.41
Consensus pattern (37 bp):
ATTTAAGATCATAACTATCATTTTTACAGTTCGCTTA
Found at i:27959908 original size:32 final size:33
Alignment explanation
Indices: 27959661--27959909 Score: 183
Period size: 32 Copynumber: 7.8 Consensus size: 33
27959651 TACAGCAATG
* * * * *
27959661 TGATTGGCCCAAAGCCATTAGTAGCAGTGA-TA
1 TGATCGGCACAAAGCCATCAGTAACGGTGACTA
* *
27959693 TGATCGGTACACAA-CCATCAGTAACGGTAAC-A
1 TGATCGGCACA-AAGCCATCAGTAACGGTGACTA
* * * * *
27959725 TGATCAGCACAAAGCCATTAGTAGCAGTGA-TT
1 TGATCGGCACAAAGCCATCAGTAACGGTGACTA
* * ** *
27959757 TGATCAGCACACAGCCATCAGTAACAATGA-AA
1 TGATCGGCACAAAGCCATCAGTAACGGTGACTA
* * * *
27959789 TGGTCGGCACACAA-CCATCGGTAATGGT-AATA
1 TGATCGGCACA-AAGCCATCAGTAACGGTGACTA
* * * *
27959821 TGATTGGTACAAAGCCATCAATAACGAT-ACTA
1 TGATCGGCACAAAGCCATCAGTAACGGTGACTA
27959853 TGATCGGCACAAAGCCATCAGTAACGGT-ACTA
1 TGATCGGCACAAAGCCATCAGTAACGGTGACTA
*
27959885 TGATCGGAACAAAGCCATCAGTAAC
1 TGATCGGCACAAAGCCATCAGTAAC
27959910 ATCGCAGCAA
Statistics
Matches: 169, Mismatches: 41, Indels: 14
0.75 0.18 0.06
Matches are distributed among these distances:
31 5 0.03
32 161 0.95
33 3 0.02
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (33 bp):
TGATCGGCACAAAGCCATCAGTAACGGTGACTA
Found at i:27959941 original size:26 final size:26
Alignment explanation
Indices: 27959910--27959963 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
27959900 CATCAGTAAC
27959910 ATCGCAGCAAAGCTGCTAGCAATAGT
1 ATCGCAGCAAAGCTGCTAGCAATAGT
* *
27959936 ATCGCAGCAAAGTTGCTAGTAATAGT
1 ATCGCAGCAAAGCTGCTAGCAATAGT
27959962 AT
1 AT
27959964 ACGTGGCCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (26 bp):
ATCGCAGCAAAGCTGCTAGCAATAGT
Found at i:27964594 original size:43 final size:42
Alignment explanation
Indices: 27964547--27964627 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 42
27964537 GGGTAACTCT
* * *
27964547 AACAACCC-ATGTTTATCTTCTCCTCTTTTTAAATTATTTTTTC
1 AACAACCCAATATTT-TCTTCTCCT-TTTTAAAACTATTTTTTC
27964590 AACAACCCAATATTTTCTTCTCCTTTTTAAAACTATTT
1 AACAACCCAATATTTTCTTCTCCTTTTTAAAACTATTT
27964628 ATTTTCTAGC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
42 12 0.35
43 17 0.50
44 5 0.15
ACGTcount: A:0.27, C:0.23, G:0.01, T:0.48
Consensus pattern (42 bp):
AACAACCCAATATTTTCTTCTCCTTTTTAAAACTATTTTTTC
Found at i:27967623 original size:18 final size:16
Alignment explanation
Indices: 27967589--27967620 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
27967579 CTCCTTTTAG
27967589 GTTGTGGAATTTTTTT
1 GTTGTGGAATTTTTTT
27967605 GTTGTGGAATTTTTTT
1 GTTGTGGAATTTTTTT
27967621 TTGGTAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.25, T:0.62
Consensus pattern (16 bp):
GTTGTGGAATTTTTTT
Found at i:27969260 original size:24 final size:25
Alignment explanation
Indices: 27969222--27969271 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
27969212 AATCTTTTAG
* *
27969222 AAACTAAATATAACTAAGTTAAATA
1 AAACTAAATAGAACTAAGTAAAATA
27969247 AAACT-AATAGAACTAAGTAAAATA
1 AAACTAAATAGAACTAAGTAAAATA
27969271 A
1 A
27969272 CAAAACCAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.62, C:0.08, G:0.06, T:0.24
Consensus pattern (25 bp):
AAACTAAATAGAACTAAGTAAAATA
Found at i:27982960 original size:20 final size:21
Alignment explanation
Indices: 27982935--27982974 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
27982925 GAGTTTTATT
27982935 TATTTTA-TGTACTAA-TTAGA
1 TATTTTAGTGT-CTAAGTTAGA
27982955 TATTTTAGTGTCTAAGTTAG
1 TATTTTAGTGTCTAAGTTAG
27982975 GACTGATCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.30, C:0.05, G:0.15, T:0.50
Consensus pattern (21 bp):
TATTTTAGTGTCTAAGTTAGA
Found at i:27989446 original size:14 final size:14
Alignment explanation
Indices: 27989422--27989457 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
27989412 AATCGAATAT
27989422 AATTA-GGTTACAC
1 AATTAGGGTTACAC
27989435 AATTAGGGTTACAC
1 AATTAGGGTTACAC
*
27989449 AATTTGGGT
1 AATTAGGGT
27989458 CGGGTCAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 5 0.24
14 16 0.76
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.33
Consensus pattern (14 bp):
AATTAGGGTTACAC
Found at i:27996967 original size:7 final size:6
Alignment explanation
Indices: 27996922--27996988 Score: 56
Period size: 6 Copynumber: 12.0 Consensus size: 6
27996912 GACCCATTTT
* *
27996922 ATTAAA A-T-AA A-TAAA ACTAAC ATTAAA ATTAAA ATTAAA GATT-AA
1 ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA ATTAAA -ATTAAA
*
27996967 ATTGAA ATT--A ATTAAA ATTAAA
1 ATTAAA ATTAAA ATTAAA ATTAAA
27996989 GACAAAGATA
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
4 8 0.15
5 7 0.13
6 34 0.65
7 3 0.06
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (6 bp):
ATTAAA
Found at i:28006031 original size:45 final size:45
Alignment explanation
Indices: 28005989--28006167 Score: 225
Period size: 45 Copynumber: 4.0 Consensus size: 45
28005979 ATTCACACTG
* * *
28005989 TATTATTAACTTTTATTTGCATCGAA-TAGTGGTTTATCCACACCA
1 TATTAGTAACTTTTATCTACATC-AAGTAGTGGTTTATCCACACCA
* * *
28006034 TATTAGCAACATTTATCTACACCAAGTAGTGGTTTATCCACACCA
1 TATTAGTAACTTTTATCTACATCAAGTAGTGGTTTATCCACACCA
* * * *
28006079 TATTTGTAACTTTTATCTACATCAAGTAGTGGTTTATCCATATCG
1 TATTAGTAACTTTTATCTACATCAAGTAGTGGTTTATCCACACCA
* * *
28006124 TATTAGTAGCTTTTATCTACATCAATTAGTGGTCTATCCACACC
1 TATTAGTAACTTTTATCTACATCAAGTAGTGGTTTATCCACACC
28006168 GTACTAGCAA
Statistics
Matches: 114, Mismatches: 19, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
44 2 0.02
45 112 0.98
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (45 bp):
TATTAGTAACTTTTATCTACATCAAGTAGTGGTTTATCCACACCA
Found at i:28006071 original size:21 final size:21
Alignment explanation
Indices: 28006045--28006116 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
28006035 ATTAGCAACA
28006045 TTTATCTACACCAAGTAGTGG
1 TTTATCTACACCAAGTAGTGG
* * * **
28006066 TTTATCCACACCATATTTGTAACT
1 TTTATCTACACCA-AGTAGT--GG
*
28006090 TTTATCTACATCAAGTAGTGG
1 TTTATCTACACCAAGTAGTGG
28006111 TTTATC
1 TTTATC
28006117 CATATCGTAT
Statistics
Matches: 37, Mismatches: 11, Indels: 6
0.69 0.20 0.11
Matches are distributed among these distances:
21 18 0.49
22 4 0.11
23 4 0.11
24 11 0.30
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.40
Consensus pattern (21 bp):
TTTATCTACACCAAGTAGTGG
Found at i:28007871 original size:5 final size:5
Alignment explanation
Indices: 28007861--28007891 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
28007851 GTGTATCTTG
28007861 TTATA TTATA TTATA TTATA TTATA TTATA T
1 TTATA TTATA TTATA TTATA TTATA TTATA T
28007892 AAAAAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTATA
Found at i:28012169 original size:28 final size:28
Alignment explanation
Indices: 28012136--28012229 Score: 122
Period size: 28 Copynumber: 3.4 Consensus size: 28
28012126 GTGTTTAGGA
28012136 TTAGGGTTTTTGAAAAAAAAATTAGAGT
1 TTAGGGTTTTTGAAAAAAAAATTAGAGT
*
28012164 TTAGGGTTTTTG-AAAAAAATTTA-AGGT
1 TTAGGGTTTTTGAAAAAAAAATTAGA-GT
* *
28012191 TTAGGG-TTTTAAAAAAATAAATTTGAGT
1 TTAGGGTTTTTGAAAAAA-AAATTAGAGT
28012219 TTAGGGTTTTT
1 TTAGGGTTTTT
28012230 AATTGGTAAG
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
26 5 0.09
27 23 0.40
28 24 0.42
29 5 0.09
ACGTcount: A:0.37, C:0.00, G:0.21, T:0.41
Consensus pattern (28 bp):
TTAGGGTTTTTGAAAAAAAAATTAGAGT
Found at i:28012257 original size:36 final size:37
Alignment explanation
Indices: 28012217--28012320 Score: 122
Period size: 36 Copynumber: 2.9 Consensus size: 37
28012207 ATAAATTTGA
28012217 GTTTAGGGTTTTTAATTGGTAAGTGATGTGTTTAG-G
1 GTTTAGGGTTTTTAATTGGTAAGTGATGTGTTTAGAG
**** * * *
28012253 GTTTAGGGTTTTTAAAAAATAAAT-TTGGGTTTAGAG
1 GTTTAGGGTTTTTAATTGGTAAGTGATGTGTTTAGAG
*
28012289 TTTTAGGGTTTTTAATTGGTAAGTGATGTGTT
1 GTTTAGGGTTTTTAATTGGTAAGTGATGTGTT
28012321 CTGAAAAAAT
Statistics
Matches: 51, Mismatches: 15, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
35 8 0.16
36 38 0.75
37 5 0.10
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (37 bp):
GTTTAGGGTTTTTAATTGGTAAGTGATGTGTTTAGAG
Found at i:28012990 original size:10 final size:9
Alignment explanation
Indices: 28012975--28013000 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
28012965 ACCTAAATAA
28012975 TTTTTTTTC
1 TTTTTTTTC
28012984 TTTTTTTTC
1 TTTTTTTTC
28012993 TTTTTTTT
1 TTTTTTTT
28013001 AACCTTAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:28015575 original size:14 final size:15
Alignment explanation
Indices: 28015556--28015584 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
28015546 TCACGAAACT
28015556 TTCACACAT-ATAAA
1 TTCACACATAATAAA
28015570 TTCACACATAATAAA
1 TTCACACATAATAAA
28015585 CACAGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:28015824 original size:86 final size:87
Alignment explanation
Indices: 28015722--28015896 Score: 271
Period size: 87 Copynumber: 2.0 Consensus size: 87
28015712 GCAAGATGCA
* * *
28015722 CTGTTAGCAAAAGTACTGAAAAAAGCTCCCAGCTGG-CGCTCTTTTTGTACAATAGTTTCTGAAA
1 CTGTCAGCAAAAGTACTAAAAAAAGCTCCCAACTGGACGCTCTTTTTGTACAATAGTTTCTGAAA
28015786 AAATAACTTTGAGAAGATGTTT
66 AAATAACTTTGAGAAGATGTTT
* * * *
28015808 CTGTCAGCAAAAGTACTAAAAAAATCTCCCAACTGGATGCTCTTTTTGTACAGTAGTTTCTGAAC
1 CTGTCAGCAAAAGTACTAAAAAAAGCTCCCAACTGGACGCTCTTTTTGTACAATAGTTTCTGAAA
*
28015873 AAATAATTTTGAGAAGATGTTT
66 AAATAACTTTGAGAAGATGTTT
28015895 CT
1 CT
28015897 AAAAGAATAG
Statistics
Matches: 80, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
86 32 0.40
87 48 0.60
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Consensus pattern (87 bp):
CTGTCAGCAAAAGTACTAAAAAAAGCTCCCAACTGGACGCTCTTTTTGTACAATAGTTTCTGAAA
AAATAACTTTGAGAAGATGTTT
Found at i:28015944 original size:126 final size:125
Alignment explanation
Indices: 28015808--28016114 Score: 452
Period size: 126 Copynumber: 2.4 Consensus size: 125
28015798 GAAGATGTTT
*
28015808 CTGTCAGCAAAAGTACTAAAAAAATCTCCCAACTGGATGCTCTTTTTGTACAGTAGTTTCTGAAC
1 CTGTCAGCAAAAGTACTAAAAAAA-CTCCCAACTGGATGCTCTTTTTGTACAGTAGTTTCTGAAA
*
28015873 AAATAATTTTGAGAAGATGTTTCTAAAAGAATAGGTAGAAAAACGCTTCAAACAGGATGCA
65 AAATAATTTTGAGAAGATGTTTCTAAAAAAATAGGTAGAAAAACGCTTCAAACAGGATGCA
* * * * * *
28015934 CTGTCAGCAAAAGTACTGAAATAAACTCCTAGCTTGAAGCTCTTTTTGTATAGTAGTTTCTGAAA
1 CTGTCAGCAAAAGTACT-AAAAAAACTCCCAACTGGATGCTCTTTTTGTACAGTAGTTTCTGAAA
* * **
28015999 AAATAATTTTGAGAAGATGTTTCTAAAAAAATAGGTTGAAAAATGCTTCAAGTAGGATGCA
65 AAATAATTTTGAGAAGATGTTTCTAAAAAAATAGGTAGAAAAACGCTTCAAACAGGATGCA
* * *
28016060 CTGTTAGCAAAAGTACTGAGAAAACCTCCCAACTGGATGCTCTTTTTGTACAGTA
1 CTGTCAGCAAAAGTACT-AAAAAAACTCCCAACTGGATGCTCTTTTTGTACAGTA
28016115 CATCCTACTT
Statistics
Matches: 159, Mismatches: 21, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
126 153 0.96
127 6 0.04
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (125 bp):
CTGTCAGCAAAAGTACTAAAAAAACTCCCAACTGGATGCTCTTTTTGTACAGTAGTTTCTGAAAA
AATAATTTTGAGAAGATGTTTCTAAAAAAATAGGTAGAAAAACGCTTCAAACAGGATGCA
Found at i:28019672 original size:39 final size:39
Alignment explanation
Indices: 28019615--28019693 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
28019605 TATTAAAGTC
*
28019615 TGTTTATTAAGGGTTGTGTAATAGCTTATAATATTTAGA
1 TGTTTATTAAGGGATGTGTAATAGCTTATAATATTTAGA
28019654 TGTTTATTAAGGGATGTGTAATAGCTTATAATATTTAGA
1 TGTTTATTAAGGGATGTGTAATAGCTTATAATATTTAGA
28019693 T
1 T
28019694 AAAGTGTTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.32, C:0.03, G:0.20, T:0.46
Consensus pattern (39 bp):
TGTTTATTAAGGGATGTGTAATAGCTTATAATATTTAGA
Found at i:28020238 original size:33 final size:32
Alignment explanation
Indices: 28020166--28020238 Score: 74
Period size: 33 Copynumber: 2.2 Consensus size: 32
28020156 ATTTTTAAAT
* * * *
28020166 GTAAGACCATAGCTGGGCTATGGCATTTTAAT
1 GTAAGACCATAACTGGGCTATGGCACTTGAAC
* *
28020198 GAAAAGACCATAACTGGGTTATGGCACCTTGAAC
1 G-TAAGACCATAACTGGGCTATGGCA-CTTGAAC
28020232 GTAAGAC
1 GTAAGAC
28020239 TATGGTTGGA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
32 1 0.03
33 26 0.81
34 5 0.16
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.25
Consensus pattern (32 bp):
GTAAGACCATAACTGGGCTATGGCACTTGAAC
Found at i:28026751 original size:33 final size:32
Alignment explanation
Indices: 28026679--28026755 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 32
28026669 TAGATACATG
* **
28026679 TGTAAGACCATAACTGGGCTATGACATTCTGA
1 TGTAAGACCATAACTGGGCTATGACATACAAA
*
28026711 TGATAAGACCATAACTGGGTTATGGA-ACTACAAA
1 TG-TAAGACCATAACTGGGCTAT-GACA-TACAAA
28026745 TGTAAGACCAT
1 TGTAAGACCAT
28026756 GGCAGGGCCA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
32 2 0.05
33 29 0.76
34 7 0.18
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (32 bp):
TGTAAGACCATAACTGGGCTATGACATACAAA
Found at i:28030906 original size:105 final size:105
Alignment explanation
Indices: 28030757--28030988 Score: 410
Period size: 105 Copynumber: 2.2 Consensus size: 105
28030747 TTTAAATGTT
* * *
28030757 AGACCATAGTTGGGCTAAGGCATTTTAATGAAAATACCATAACTGGGTTATGACACCTTGAACAT
1 AGACCATAGTTGGGCTATGGCATTCTAATGAAAAGACCATAACTGGGTTATGACACCTTGAACAT
28030822 AATACCATGGTTGGACCATGGTAGTATAGATACATGTGTA
66 AATACCATGGTTGGACCATGGTAGTATAGATACATGTGTA
* *
28030862 AGACCATAGTTGGGCTATGGCATTCTGATGATAAGACCATAACTGGGTTATGACACCTTGAACAT
1 AGACCATAGTTGGGCTATGGCATTCTAATGAAAAGACCATAACTGGGTTATGACACCTTGAACAT
28030927 AATACCATGGTTGGACCATGGTAGTATAGATACATGTGTA
66 AATACCATGGTTGGACCATGGTAGTATAGATACATGTGTA
*
28030967 AGACCATAGTTGGACTATGGCA
1 AGACCATAGTTGGGCTATGGCA
28030989 CAAAAAGAAT
Statistics
Matches: 121, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
105 121 1.00
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (105 bp):
AGACCATAGTTGGGCTATGGCATTCTAATGAAAAGACCATAACTGGGTTATGACACCTTGAACAT
AATACCATGGTTGGACCATGGTAGTATAGATACATGTGTA
Found at i:28037739 original size:8 final size:8
Alignment explanation
Indices: 28037728--28037858 Score: 52
Period size: 8 Copynumber: 14.8 Consensus size: 8
28037718 AATTAGAAAA
28037728 AAAATTAT
1 AAAATTAT
*
28037736 AAAA-AATT
1 AAAATTA-T
28037744 AAAATATAT
1 AAAAT-TAT
28037753 AAATATTATT
1 AAA-ATTA-T
*
28037763 AAATTTTAAT
1 AAA-ATT-AT
*
28037773 AAAAATTTT
1 -AAAATTAT
*
28037782 AAATATTAA
1 AAA-ATTAT
28037791 AAAATTGCA-
1 AAAATT--AT
*
28037800 AAAATTGT
1 AAAATTAT
28037808 AAAAAATTAT
1 -AA-AATTAT
28037818 AAAATTAT
1 AAAATTAT
28037826 AAAATATAT
1 AAAAT-TAT
28037835 AGAAA-TAT
1 A-AAATTAT
28037843 AAAATTTTAT
1 AAAA--TTAT
28037853 AAAATT
1 AAAATT
28037859 TTATAAAGTT
Statistics
Matches: 96, Mismatches: 9, Indels: 36
0.68 0.06 0.26
Matches are distributed among these distances:
7 4 0.04
8 32 0.33
9 27 0.28
10 29 0.30
11 4 0.04
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (8 bp):
AAAATTAT
Found at i:28037760 original size:16 final size:16
Alignment explanation
Indices: 28037728--28037829 Score: 53
Period size: 19 Copynumber: 5.8 Consensus size: 16
28037718 AATTAGAAAA
28037728 AAAATTATAAAAAATT
1 AAAATTATAAAAAATT
*
28037744 AAAATATATAAATATTATT
1 AAAAT-TATAAA-A-AATT
* *
28037763 AAATTTTAATAAAAATTT
1 AAA-ATT-ATAAAAAATT
*
28037781 TAAA-TATTAAAAAATT
1 AAAATTA-TAAAAAATT
*
28037797 GCAAAAATTGTAAAAAATTAT
1 ---AAAATTATAAAAAA-T-T
28037818 AAAATTATAAAA
1 AAAATTATAAAA
28037830 TATATAGAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 22
0.67 0.10 0.23
Matches are distributed among these distances:
15 1 0.02
16 14 0.22
17 6 0.09
18 16 0.25
19 18 0.28
20 8 0.12
21 1 0.02
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (16 bp):
AAAATTATAAAAAATT
Found at i:28037783 original size:19 final size:20
Alignment explanation
Indices: 28037751--28037794 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
28037741 ATTAAAATAT
* *
28037751 ATAAATATTATTAAATTTTA
1 ATAAAAATTATTAAATATTA
28037771 ATAAAAATT-TTAAATATTA
1 ATAAAAATTATTAAATATTA
28037790 A-AAAA
1 ATAAAA
28037795 TTGCAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 4 0.18
19 10 0.45
20 8 0.36
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATAAAAATTATTAAATATTA
Found at i:28037829 original size:17 final size:17
Alignment explanation
Indices: 28037728--28037858 Score: 74
Period size: 17 Copynumber: 7.4 Consensus size: 17
28037718 AATTAGAAAA
*
28037728 AAAATTATAAAAAAT-T
1 AAAATTATAAAAATTAT
*
28037744 AAAATATATAAATATTATT
1 AAAAT-TATAAAAATTA-T
* *
28037763 AAATTTTAATAAAAATTTT
1 AAA-ATT-ATAAAAATTAT
28037782 AAATATTA-AAAAATTGCA-
1 AAA-ATTATAAAAATT--AT
*
28037800 AAAATTGTAAAAAATTAT
1 AAAATTAT-AAAAATTAT
28037818 AAAATTAT-AAAATATAT
1 AAAATTATAAAAAT-TAT
*
28037835 AGAAA-TATAAAATTTTAT
1 A-AAATTATAAAA-ATTAT
28037853 AAAATT
1 AAAATT
28037859 TTATAAAGTT
Statistics
Matches: 90, Mismatches: 10, Indels: 28
0.70 0.08 0.22
Matches are distributed among these distances:
16 10 0.11
17 29 0.32
18 22 0.24
19 20 0.22
20 9 0.10
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (17 bp):
AAAATTATAAAAATTAT
Done.