Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 67 of 193
Found at i:21531343 original size:20 final size:20
Alignment explanation
Indices: 21531318--21531356 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
21531308 ATTTTGTGAG
*
21531318 TAATGAATACCCTGTTCTGT
1 TAATGAATACCCAGTTCTGT
21531338 TAATGAATACCCAGTTCTG
1 TAATGAATACCCAGTTCTG
21531357 CTCTTCATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (20 bp):
TAATGAATACCCAGTTCTGT
Found at i:21540931 original size:9 final size:9
Alignment explanation
Indices: 21540917--21540942 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
21540907 CAATTTCAAG
21540917 AATCAAGAA
1 AATCAAGAA
21540926 AATCAAGAA
1 AATCAAGAA
21540935 AATCAAGA
1 AATCAAGA
21540943 TTTCAAATTT
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:0.65, C:0.12, G:0.12, T:0.12
Consensus pattern (9 bp):
AATCAAGAA
Found at i:21541285 original size:5 final size:5
Alignment explanation
Indices: 21541275--21541299 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
21541265 ATACTTAGAA
21541275 TTATT TTATT TTATT TTATT TTATT
1 TTATT TTATT TTATT TTATT TTATT
21541300 AGTTGTCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTATT
Found at i:21548668 original size:29 final size:29
Alignment explanation
Indices: 21548636--21548710 Score: 123
Period size: 29 Copynumber: 2.6 Consensus size: 29
21548626 TTATATACTA
21548636 TAGATTCTGAAAACTATTATGTGAAACTT
1 TAGATTCTGAAAACTATTATGTGAAACTT
* * *
21548665 TAGATTATGAAAACTTTTATGTGAGACTT
1 TAGATTCTGAAAACTATTATGTGAAACTT
21548694 TAGATTCTGAAAACTAT
1 TAGATTCTGAAAACTAT
21548711 ATTGCGAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (29 bp):
TAGATTCTGAAAACTATTATGTGAAACTT
Found at i:21555201 original size:50 final size:50
Alignment explanation
Indices: 21555070--21555201 Score: 124
Period size: 50 Copynumber: 2.6 Consensus size: 50
21555060 TATCTGGAAG
* * * * *
21555070 TAAATCTGTAATTATCTGGTGGC-ATGTCCACATATTTCTGTATCTGGCAG
1 TAAATCTGCAATTATCTGGTGGCTA-GTCCATATAATTCTGTATCTAGCAA
* ** ** *
21555120 TAAATCTGCAAATATCTGGTGATTAAACCATACTAATTC-GTTTCTAGCAA
1 TAAATCTGCAATTATCTGGTGGCTAGTCCATA-TAATTCTGTATCTAGCAA
*
21555170 TAAATATGCAATTATCTGGTGGCTAGTCCATA
1 TAAATCTGCAATTATCTGGTGGCTAGTCCATA
21555202 ATTATTTGGT
Statistics
Matches: 63, Mismatches: 17, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
50 57 0.90
51 6 0.10
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (50 bp):
TAAATCTGCAATTATCTGGTGGCTAGTCCATATAATTCTGTATCTAGCAA
Found at i:21566816 original size:16 final size:16
Alignment explanation
Indices: 21566795--21566844 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 16
21566785 TGCTAAATTA
21566795 TATAAAAGAATTTAAG
1 TATAAAAGAATTTAAG
* *
21566811 TAT-AAA-AA-TCAAA
1 TATAAAAGAATTTAAG
21566824 T-TAAAAGAATTTAAG
1 TATAAAAGAATTTAAG
21566839 TATAAA
1 TATAAA
21566845 GATTGGAATC
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
12 1 0.04
13 7 0.27
14 4 0.15
15 7 0.27
16 7 0.27
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.30
Consensus pattern (16 bp):
TATAAAAGAATTTAAG
Found at i:21569483 original size:117 final size:114
Alignment explanation
Indices: 21569335--21569689 Score: 394
Period size: 114 Copynumber: 3.1 Consensus size: 114
21569325 GAAAAATTGG
* *
21569335 ATTTTTTGGTATTGGCCATCAAATGGTCGACACCCTCTTTTCTCGAAAAAAAATTAG-ATTTTTG
1 ATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCTCTTTTCT--AAAAAAAA-T-GCATTTTTG
** *
21569399 GGTGTTGGTTATTGCATGGACAACATCCCTTTT-TTGAGAAAAAAAAATTTAAA
62 GGTGTTGGCCATTGCATGGCCAACATCCCTTTTCTTGAG-AAAAAAAATTTAAA
* *
21569452 ATTTTTTGGTGTTGGCCATCAAAAGGCCGACACCCTCTTTTCTAAAAAAAATGCATTTTTAGGTG
1 ATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCTCTTTTCTAAAAAAAATGCATTTTTGGGTG
*** * * *
21569517 TTGGCCATCAAATGGCCGACACCTCCCTTTTCTCGAGAAAAAAATTTTAAA
66 TTGGCCATTGCATGGCC-A-ACATCCCTTTTCTTGAGAAAAAAAATTTAAA
* *** * *
21569568 TTTTTTTGGTGTTAATCATCAAATGGCTGACA-CCTCCTATT-TAAAAAAAATGCATTTTTGGGT
1 ATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCT-CTTTTCTAAAAAAAATGCATTTTTGGGT
* * *
21569631 GTTGGCCATTGCATGGCCGACACCCCCTTTTCTTGAGAAAAAAAATTCAAA
65 GTTGGCCATTGCATGGCCAACA-TCCCTTTTCTTGAGAAAAAAAATTTAAA
*
21569682 TTTTTTTG
1 ATTTTTTG
21569690 TGTCCCTTTT
Statistics
Matches: 202, Mismatches: 30, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
113 3 0.01
114 54 0.27
115 48 0.24
116 53 0.26
117 44 0.22
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (114 bp):
ATTTTTTGGTGTTGGCCATCAAATGGCCGACACCCTCTTTTCTAAAAAAAATGCATTTTTGGGTG
TTGGCCATTGCATGGCCAACATCCCTTTTCTTGAGAAAAAAAATTTAAA
Found at i:21569564 original size:54 final size:51
Alignment explanation
Indices: 21569449--21569564 Score: 142
Period size: 54 Copynumber: 2.2 Consensus size: 51
21569439 AAAAAAATTT
* *
21569449 AAAATTTTTTGGTGTTGGCCATCAAAAGGCCGACACCCTCTTTTCTAAAAA
1 AAAATTTTTAGGTGTTGGCCATCAAAAGGCCGACACCCCCTTTTCTAAAAA
* *
21569500 AAATGCATTTTTAGGTGTTGGCCATCAAATGGCCGACACCTCCCTTTTCTCGAGAAA
1 AAA---ATTTTTAGGTGTTGGCCATCAAAAGGCCGACACC-CCCTTTTCT--AAAAA
21569557 AAAATTTT
1 AAAATTTT
21569565 AAATTTTTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
51 3 0.05
54 37 0.67
55 8 0.15
57 7 0.13
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (51 bp):
AAAATTTTTAGGTGTTGGCCATCAAAAGGCCGACACCCCCTTTTCTAAAAA
Found at i:21569580 original size:62 final size:60
Alignment explanation
Indices: 21569336--21569689 Score: 226
Period size: 57 Copynumber: 6.1 Consensus size: 60
21569326 AAAAATTGGA
* * * *
21569336 TTTTTTGGTATTGGCCATCAAATGGTCGACACC-CTCTTTTCTCGA-AAAAAAA-TTAGA-
1 TTTTTTGGTGTTGGCCATCAAATGGCCGACACCTCCCTTTTCT-GAGAAAAAAATTTAAAT
* ** *** * * * *
21569393 TTTTTGGGTGTTGGTTATTGCATGGAC-A-ACATCCCTTTTTTGAGAAAAAAAAATTTAAAA
1 TTTTTTGGTGTTGGCCATCAAATGGCCGACACCTCCCTTTTCTGAG--AAAAAAATTTAAAT
* * **
21569453 TTTTTTGGTGTTGGCCATCAAAAGGCCGACACC-CTCTTTTCT-A-AAAAAAA--TGCA-
1 TTTTTTGGTGTTGGCCATCAAATGGCCGACACCTCCCTTTTCTGAGAAAAAAATTTAAAT
*
21569507 TTTTTAGGTGTTGGCCATCAAATGGCCGACACCTCCCTTTTCTCGAGAAAAAAATTTTAAAT
1 TTTTTTGGTGTTGGCCATCAAATGGCCGACACCTCCCTTTTCT-GAGAAAAAAA-TTTAAAT
*** * * **
21569569 TTTTTTGGTGTTAATCATCAAATGGCTGACACCT-CCTATT-T-A-AAAAAAA--TGCA-
1 TTTTTTGGTGTTGGCCATCAAATGGCCGACACCTCCCTTTTCTGAGAAAAAAATTTAAAT
* *** *
21569622 TTTTTGGGTGTTGGCCATTGCATGGCCGACACC-CCCTTTTCTTGAGAAAAAAAATTCAAAT
1 TTTTTTGGTGTTGGCCATCAAATGGCCGACACCTCCCTTTTC-TGAG-AAAAAAATTTAAAT
21569683 TTTTTTG
1 TTTTTTG
21569690 TGTCCCTTTT
Statistics
Matches: 221, Mismatches: 51, Indels: 46
0.69 0.16 0.14
Matches are distributed among these distances:
53 30 0.14
54 33 0.15
55 15 0.07
56 9 0.04
57 34 0.15
58 22 0.10
59 4 0.02
60 22 0.10
61 21 0.10
62 31 0.14
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.36
Consensus pattern (60 bp):
TTTTTTGGTGTTGGCCATCAAATGGCCGACACCTCCCTTTTCTGAGAAAAAAATTTAAAT
Found at i:21569590 original size:116 final size:115
Alignment explanation
Indices: 21569424--21569689 Score: 358
Period size: 116 Copynumber: 2.3 Consensus size: 115
21569414 ATGGACAACA
* **
21569424 TCCCTTTT-TTGAGAAAAAAAAATTTAAAATTTTTTGGTGTTGGCCATCAAAAGGCCGACACC-C
1 TCCCTTTTCTTGAG-AAAAAAAATTTAAATTTTTTTGGTGTTAACCATCAAAAGGCCGACACCTC
*
21569487 TCTTTTCTAAAAAAAATGCATTTTTAGGTGTTGGCCATCAAATGGCCGACACC
65 -CTATT-TAAAAAAAATGCATTTTTAGGTGTTGGCCATCAAATGGCCGACACC
* * * * *
21569540 TCCCTTTTCTCGAGAAAAAAATTTTAAATTTTTTTGGTGTTAATCATCAAATGGCTGACACCTCC
1 TCCCTTTTCTTGAGAAAAAAAATTTAAATTTTTTTGGTGTTAACCATCAAAAGGCCGACACCTCC
* ***
21569605 TATTTAAAAAAAATGCATTTTTGGGTGTTGGCCATTGCATGGCCGACACC
66 TATTTAAAAAAAATGCATTTTTAGGTGTTGGCCATCAAATGGCCGACACC
*
21569655 -CCCTTTTCTTGAGAAAAAAAATTCAAATTTTTTTG
1 TCCCTTTTCTTGAGAAAAAAAATTTAAATTTTTTTG
21569690 TGTCCCTTTT
Statistics
Matches: 132, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
114 32 0.24
115 42 0.32
116 53 0.40
117 5 0.04
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (115 bp):
TCCCTTTTCTTGAGAAAAAAAATTTAAATTTTTTTGGTGTTAACCATCAAAAGGCCGACACCTCC
TATTTAAAAAAAATGCATTTTTAGGTGTTGGCCATCAAATGGCCGACACC
Found at i:21569711 original size:38 final size:39
Alignment explanation
Indices: 21569655--21569728 Score: 107
Period size: 38 Copynumber: 1.9 Consensus size: 39
21569645 GGCCGACACC
*
21569655 CCCTTTTCTTGAGAAAAAAAATT-CAAATTTTTTTGTGT
1 CCCTTTTCTCGAGAAAAAAAATTGCAAATTTTTTTGTGT
*
21569693 CCCTTTTCTCG-GATAAAAAAATTGTAAATTTTTTTG
1 CCCTTTTCTCGAGA-AAAAAAATTGCAAATTTTTTTG
21569729 ATGTTAACCA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
37 2 0.06
38 19 0.59
39 11 0.34
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.45
Consensus pattern (39 bp):
CCCTTTTCTCGAGAAAAAAAATTGCAAATTTTTTTGTGT
Found at i:21572052 original size:14 final size:15
Alignment explanation
Indices: 21572020--21572052 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
21572010 TCTGAAAAAT
21572020 TAAAAAATAATTAGA
1 TAAAAAATAATTAGA
21572035 -AAAAAATAATTA-A
1 TAAAAAATAATTAGA
21572048 TAAAA
1 TAAAA
21572053 TTTAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 1 0.06
14 16 0.94
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (15 bp):
TAAAAAATAATTAGA
Found at i:21572908 original size:20 final size:21
Alignment explanation
Indices: 21572869--21572908 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
21572859 CATAATATGA
*
21572869 TGGACGAAACTCGGTCAACGG
1 TGGACGAAACTCGATCAACGG
*
21572890 TGGAC-AAAGTCGATCAACG
1 TGGACGAAACTCGATCAACG
21572909 ACGGTCAACG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.33, C:0.23, G:0.30, T:0.15
Consensus pattern (21 bp):
TGGACGAAACTCGATCAACGG
Found at i:21572994 original size:22 final size:21
Alignment explanation
Indices: 21572946--21573000 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
21572936 CAGGACATTG
* * *
21572946 GTGAGCTGGAATTTTGGTTTT
1 GTGAGATGGAATATTGGTTTA
21572967 GCTGAGATGGAATATTGGTTTAA
1 G-TGAGATGGAATATTGGTTT-A
*
21572990 GTGAGGTGGAA
1 GTGAGATGGAA
21573001 AGTGGGTGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 1 0.04
22 26 0.93
23 1 0.04
ACGTcount: A:0.24, C:0.04, G:0.36, T:0.36
Consensus pattern (21 bp):
GTGAGATGGAATATTGGTTTA
Found at i:21573247 original size:86 final size:86
Alignment explanation
Indices: 21573116--21573306 Score: 355
Period size: 86 Copynumber: 2.2 Consensus size: 86
21573106 AATTGTAATA
21573116 TAATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAATGTATTGTCAAATCA
1 TAAT-ATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAATGTATTGTCAAATCA
*
21573181 ACACATTATATGATAAAAATTG
65 ACACATTATATGATAAAAACTG
*
21573203 TAATATAATAATAATAATTTTTATTTAAATATATAAAATTAATAAATAATGTATTGTCAAATCAA
1 TAATATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAATGTATTGTCAAATCAA
21573268 CACATTATATGATAAAAACTG
66 CACATTATATGATAAAAACTG
21573289 TAATATAATAATAATAAT
1 TAATATAATAATAATAAT
21573307 AATTTTCAAA
Statistics
Matches: 102, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
86 98 0.96
87 4 0.04
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (86 bp):
TAATATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAATAATGTATTGTCAAATCAA
CACATTATATGATAAAAACTG
Found at i:21573307 original size:92 final size:91
Alignment explanation
Indices: 21573096--21573309 Score: 348
Period size: 86 Copynumber: 2.4 Consensus size: 91
21573086 TAAATTTAAA
*
21573096 ATATGACAAAAATTGTAATATAATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATA
1 ATATGATAAAAA-TGTAATATAATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATA
21573161 AATAATGTATTGTCAAATCAACACATT
65 AATAATGTATTGTCAAATCAACACATT
* *
21573188 ATATGATAAAAA--T--TGTAAT-ATAATAATAATAATTTTTATTTAAATATATAAAATTAATAA
1 ATATGATAAAAATGTAATATAATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAA
21573248 ATAATGTATTGTCAAATCAACACATT
66 ATAATGTATTGTCAAATCAACACATT
21573274 ATATGATAAAAACTGTAATATAATAATAATAATAAT
1 ATATGATAAAAA-TGTAATATAATAATAATAATAAT
21573310 TTTCAAATTA
Statistics
Matches: 112, Mismatches: 4, Indels: 12
0.88 0.03 0.09
Matches are distributed among these distances:
86 78 0.70
87 5 0.04
89 2 0.02
91 5 0.04
92 22 0.20
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (91 bp):
ATATGATAAAAATGTAATATAATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAA
ATAATGTATTGTCAAATCAACACATT
Found at i:21576573 original size:16 final size:15
Alignment explanation
Indices: 21576535--21576574 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
21576525 AAATATAAGT
21576535 ATTTATTTAAAAATG
1 ATTTATTTAAAAATG
*
21576550 ATTTATTTAAATATG
1 ATTTATTTAAAAATG
21576565 ATGTTATTTA
1 AT-TTATTTA
21576575 TTTAATTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (15 bp):
ATTTATTTAAAAATG
Found at i:21583371 original size:22 final size:22
Alignment explanation
Indices: 21583346--21583409 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 22
21583336 TAAAAATAAT
*
21583346 AAAATTTTAATTTATTTCTTTA
1 AAAATTATAATTTATTTCTTTA
* *
21583368 AAAATTATACTTTTACTAT-TTTA
1 AAAATTATA-ATTTA-TTTCTTTA
21583391 AAAATTATAATTTAATTTC
1 AAAATTATAATTT-ATTTC
21583410 GACCTTTTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
22 13 0.39
23 18 0.55
24 2 0.06
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (22 bp):
AAAATTATAATTTATTTCTTTA
Found at i:21588703 original size:16 final size:16
Alignment explanation
Indices: 21588682--21588712 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21588672 ATAATGTCAA
21588682 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
21588698 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
21588713 GGATCCATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:21589625 original size:37 final size:37
Alignment explanation
Indices: 21589575--21589646 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
21589565 ACAGCGAGGG
*
21589575 TGCAATTGAAGAATACTTATGCAGCGATAGTCTTGGA
1 TGCAATTGAAGAATACTTATGCAGCGACAGTCTTGGA
*
21589612 TGCAATTGAAGAATATTTATGCAGCGACAGTCTTG
1 TGCAATTGAAGAATACTTATGCAGCGACAGTCTTG
21589647 TGTACATTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.31
Consensus pattern (37 bp):
TGCAATTGAAGAATACTTATGCAGCGACAGTCTTGGA
Found at i:21589720 original size:37 final size:37
Alignment explanation
Indices: 21589665--21589751 Score: 120
Period size: 37 Copynumber: 2.4 Consensus size: 37
21589655 CTGAAAATAT
* * *
21589665 TCATGTGGGGACAATTTTGGGTGAAATCTGGAAGTGC
1 TCATGTGGCGACAATTTTGGGCGAAATCTAGAAGTGC
* *
21589702 TCATGTGGCGACAGTTTTGGGCGCAATCTAGAAGTGC
1 TCATGTGGCGACAATTTTGGGCGAAATCTAGAAGTGC
*
21589739 TCATGTAGCGACA
1 TCATGTGGCGACA
21589752 TTAGTAGTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.24, C:0.16, G:0.32, T:0.28
Consensus pattern (37 bp):
TCATGTGGCGACAATTTTGGGCGAAATCTAGAAGTGC
Found at i:21590840 original size:17 final size:17
Alignment explanation
Indices: 21590785--21590841 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
21590775 AAGATATATG
*
21590785 GAAATGCAATGACAAGA
1 GAAATGCAATGACAAAA
* * *
21590802 TAGATGCAGTGACAATAA
1 GAAATGCAATGACAA-AA
21590820 -AAATGCAATGACAAAA
1 GAAATGCAATGACAAAA
21590836 GAAATG
1 GAAATG
21590842 TGATGATATA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
16 2 0.06
17 29 0.91
18 1 0.03
ACGTcount: A:0.53, C:0.11, G:0.21, T:0.16
Consensus pattern (17 bp):
GAAATGCAATGACAAAA
Found at i:21593159 original size:16 final size:16
Alignment explanation
Indices: 21593138--21593168 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21593128 ATAATGTGAA
21593138 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
21593154 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
21593169 GGATCCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:21594082 original size:37 final size:37
Alignment explanation
Indices: 21594019--21594096 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
21594009 GTAGCGAGGG
* *
21594019 TGCAATTGAAGAATACTTATGCAGCGATAGTCCTAGA
1 TGCAATTGAAGAATAATTATGCAGCGACAGTCCTAGA
* * *
21594056 TGCAATTGAAGAA-AATTCATGTAGCGACAGTCTTAGG
1 TGCAATTGAAGAATAATT-ATGCAGCGACAGTCCTAGA
21594093 TGCA
1 TGCA
21594097 TTCCGAAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
36 3 0.09
37 32 0.91
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (37 bp):
TGCAATTGAAGAATAATTATGCAGCGACAGTCCTAGA
Found at i:21594155 original size:37 final size:37
Alignment explanation
Indices: 21594109--21594186 Score: 111
Period size: 37 Copynumber: 2.1 Consensus size: 37
21594099 CCGAAAATAT
* * *
21594109 TCATGCGGCGATAGTTTTAGGTGCAATATGGAAGTGC
1 TCATACGGCGACAGTTTTAGGTGCAATATAGAAGTGC
* *
21594146 TCATACGGCGACAGTTTTGGGTGCAATTTAGAAGTGC
1 TCATACGGCGACAGTTTTAGGTGCAATATAGAAGTGC
21594183 TCAT
1 TCAT
21594187 GTAGCGACAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.24, C:0.15, G:0.29, T:0.31
Consensus pattern (37 bp):
TCATACGGCGACAGTTTTAGGTGCAATATAGAAGTGC
Found at i:21594194 original size:37 final size:37
Alignment explanation
Indices: 21594116--21594195 Score: 97
Period size: 37 Copynumber: 2.2 Consensus size: 37
21594106 TATTCATGCG
* * *
21594116 GCGATAGTTTTAGGTGCAATATGGAAGTGCTCATACG
1 GCGACAGTTTTAGGTGCAATATAGAAGTGCTCATACA
* * **
21594153 GCGACAGTTTTGGGTGCAATTTAGAAGTGCTCATGTA
1 GCGACAGTTTTAGGTGCAATATAGAAGTGCTCATACA
21594190 GCGACA
1 GCGACA
21594196 TTAGTAGTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.29
Consensus pattern (37 bp):
GCGACAGTTTTAGGTGCAATATAGAAGTGCTCATACA
Found at i:21596020 original size:24 final size:24
Alignment explanation
Indices: 21595988--21596074 Score: 156
Period size: 24 Copynumber: 3.6 Consensus size: 24
21595978 TATATTTAAA
21595988 CACGCGTTTACGCTCACCACCTTG
1 CACGCGTTTACGCTCACCACCTTG
21596012 CACGCGTTTACGCTCACCACCTTG
1 CACGCGTTTACGCTCACCACCTTG
21596036 CACGCGTTTACGCTCACCACCTTG
1 CACGCGTTTACGCTCACCACCTTG
* *
21596060 CACACGTTTATGCTC
1 CACGCGTTTACGCTC
21596075 GTCAGGTTAT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.17, C:0.40, G:0.16, T:0.26
Consensus pattern (24 bp):
CACGCGTTTACGCTCACCACCTTG
Found at i:21596112 original size:52 final size:52
Alignment explanation
Indices: 21596039--21596162 Score: 158
Period size: 52 Copynumber: 2.4 Consensus size: 52
21596029 CACCTTGCAC
* * * * *
21596039 GCGTTTACGCTCACCACCTTGCACACGTTTATGCTCGTCAGGTTATACTTAT
1 GCGTTTACGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCTTATACATAT
* * * *
21596091 GTGTTTACGCTCGCAAGCTTGCACACGTTTACGCTTGTTAGCTTATACATAT
1 GCGTTTACGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCTTATACATAT
*
21596143 GCGTTTACGTTCGCCAGCTT
1 GCGTTTACGCTCGCCAGCTT
21596163 ATACATATGC
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
52 60 1.00
ACGTcount: A:0.19, C:0.27, G:0.19, T:0.35
Consensus pattern (52 bp):
GCGTTTACGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCTTATACATAT
Found at i:21596228 original size:131 final size:131
Alignment explanation
Indices: 21596047--21596302 Score: 368
Period size: 131 Copynumber: 2.0 Consensus size: 131
21596037 ACGCGTTTAC
* * ***
21596047 GCTCACCACCTTGCACACGTTTATGCTCGTCAGGTTATACTTATGTGTTTACGCTCGCAAGCTTG
1 GCTCACCACCTTGCACACGTTTATGCTCATCAGGTTATACATACACGTTTACGCTCGCAAGCTTG
* * * * *
21596112 CACACGTTTACGCTTGTTAGCTTATACATATGCGTTTACGTTCGCCAGCTTATACATATGCATTA
66 CACACGTTTACGCTCGTCAGCTTAAACATATGCGTTTACGCTCGCCAGCTTACACATATGCATTA
21596177 T
131 T
* * * * *
21596178 GCTCGCCAGCTTGCACACGTTTATGCTCATCAGTTTATACATACACGTTTATGCTCGCCAGCTTG
1 GCTCACCACCTTGCACACGTTTATGCTCATCAGGTTATACATACACGTTTACGCTCGCAAGCTTG
*
21596243 CACACGTTTACGCTCGTCAGCTTAAACATATGCGTTTACGCTCGCCAGCTTGCACATATG
66 CACACGTTTACGCTCGTCAGCTTAAACATATGCGTTTACGCTCGCCAGCTTACACATATG
21596303 TATTTTATAT
Statistics
Matches: 109, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
131 109 1.00
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.33
Consensus pattern (131 bp):
GCTCACCACCTTGCACACGTTTATGCTCATCAGGTTATACATACACGTTTACGCTCGCAAGCTTG
CACACGTTTACGCTCGTCAGCTTAAACATATGCGTTTACGCTCGCCAGCTTACACATATGCATTA
T
Found at i:21596240 original size:52 final size:52
Alignment explanation
Indices: 21596174--21596298 Score: 187
Period size: 52 Copynumber: 2.4 Consensus size: 52
21596164 TACATATGCA
* * *
21596174 TTATGCTCGCCAGCTTGCACACGTTTATGCTCATCAGTTTATACATACACGT
1 TTATGCTCGCCAGCTTGCACACGTTTACGCTCATCAGCTTAAACATACACGT
* **
21596226 TTATGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCTTAAACATATGCGT
1 TTATGCTCGCCAGCTTGCACACGTTTACGCTCATCAGCTTAAACATACACGT
*
21596278 TTACGCTCGCCAGCTTGCACA
1 TTATGCTCGCCAGCTTGCACA
21596299 TATGTATTTT
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.22, C:0.30, G:0.18, T:0.31
Consensus pattern (52 bp):
TTATGCTCGCCAGCTTGCACACGTTTACGCTCATCAGCTTAAACATACACGT
Found at i:21596291 original size:28 final size:28
Alignment explanation
Indices: 21596064--21596302 Score: 126
Period size: 28 Copynumber: 9.0 Consensus size: 28
21596054 ACCTTGCACA
* * * *
21596064 CGTTTATGCTCGTCAGGTTATACTTATG
1 CGTTTACGCTCGCCAGCTTATACATATG
* * * *
21596092 TGTTTACGCTCGCAAGC-T-TGCACA--
1 CGTTTACGCTCGCCAGCTTATACATATG
* **
21596116 CGTTTACGCTTGTTAGCTTATACATATG
1 CGTTTACGCTCGCCAGCTTATACATATG
*
21596144 CGTTTACGTTCGCCAGCTTATACATATG
1 CGTTTACGCTCGCCAGCTTATACATATG
* * * *
21596172 C-ATTATGCTCGCCAGC-T-TGCACA--
1 CGTTTACGCTCGCCAGCTTATACATATG
* ** * **
21596195 CGTTTATGCTCATCAGTTTATACATACA
1 CGTTTACGCTCGCCAGCTTATACATATG
* * *
21596223 CGTTTATGCTCGCCAGC-T-TGCACA--
1 CGTTTACGCTCGCCAGCTTATACATATG
* *
21596247 CGTTTACGCTCGTCAGCTTAAACATATG
1 CGTTTACGCTCGCCAGCTTATACATATG
**
21596275 CGTTTACGCTCGCCAGCTTGCACATATG
1 CGTTTACGCTCGCCAGCTTATACATATG
21596303 TATTTTATAT
Statistics
Matches: 156, Mismatches: 42, Indels: 26
0.70 0.19 0.12
Matches are distributed among these distances:
23 1 0.01
24 39 0.25
25 7 0.04
26 19 0.12
27 14 0.09
28 76 0.49
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.34
Consensus pattern (28 bp):
CGTTTACGCTCGCCAGCTTATACATATG
Found at i:21599152 original size:31 final size:31
Alignment explanation
Indices: 21599106--21599164 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
21599096 ACTTTTGCGT
*
21599106 TTACTCTCGCCAGCTTGCACACATTTACACA
1 TTACGCTCGCCAGCTTGCACACATTTACACA
*
21599137 TTACGCTCGCTAGCTTGCACACATTTAC
1 TTACGCTCGCCAGCTTGCACACATTTAC
21599165 GCTCATTAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.24, C:0.34, G:0.12, T:0.31
Consensus pattern (31 bp):
TTACGCTCGCCAGCTTGCACACATTTACACA
Found at i:21599167 original size:24 final size:23
Alignment explanation
Indices: 21599132--21599206 Score: 71
Period size: 24 Copynumber: 3.1 Consensus size: 23
21599122 GCACACATTT
21599132 ACACA-TTACGCTCGCTAGCTTGC
1 ACACATTTACGCTCG-TAGCTTGC
* **
21599155 ACACATTTACGCTCATTAGCTTAT
1 ACACATTTACGCTC-GTAGCTTGC
*
21599179 ACATATTTTACGCTCGTCAGCTTGC
1 ACACA-TTTACGCTCGT-AGCTTGC
21599204 ACA
1 ACA
21599207 TGTTTATGCT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
23 5 0.12
24 19 0.46
25 17 0.41
ACGTcount: A:0.25, C:0.29, G:0.13, T:0.32
Consensus pattern (23 bp):
ACACATTTACGCTCGTAGCTTGC
Found at i:21599200 original size:25 final size:25
Alignment explanation
Indices: 21599160--21599233 Score: 87
Period size: 24 Copynumber: 3.0 Consensus size: 25
21599150 CTTGCACACA
*
21599160 TTTACGCTCATTAGCTTATACATAT
1 TTTACGCTCATCAGCTTATACATAT
* ** *
21599185 TTTACGCTCGTCAGCTTGCACAT-G
1 TTTACGCTCATCAGCTTATACATAT
*
21599209 TTTATGCTCATCAGCTTATACATAT
1 TTTACGCTCATCAGCTTATACATAT
21599234 GCGTTTATGC
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
24 19 0.50
25 19 0.50
ACGTcount: A:0.24, C:0.23, G:0.12, T:0.41
Consensus pattern (25 bp):
TTTACGCTCATCAGCTTATACATAT
Found at i:21599218 original size:49 final size:49
Alignment explanation
Indices: 21599137--21599233 Score: 142
Period size: 49 Copynumber: 2.0 Consensus size: 49
21599127 CATTTACACA
*
21599137 TTACGCTCGCTAGCTTGCACACATTTACGCTCATTAGCTTATACATATT
1 TTACGCTCGCTAGCTTGCACACATTTACGCTCATCAGCTTATACATATT
** *
21599186 TTACGCTCG-TCAGCTTGCACATGTTTATGCTCATCAGCTTATACATAT
1 TTACGCTCGCT-AGCTTGCACACATTTACGCTCATCAGCTTATACATAT
21599234 GCGTTTATGC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
48 1 0.02
49 42 0.98
ACGTcount: A:0.24, C:0.26, G:0.13, T:0.37
Consensus pattern (49 bp):
TTACGCTCGCTAGCTTGCACACATTTACGCTCATCAGCTTATACATATT
Found at i:21599269 original size:80 final size:77
Alignment explanation
Indices: 21599174--21599329 Score: 231
Period size: 80 Copynumber: 2.0 Consensus size: 77
21599164 CGCTCATTAG
* * * *
21599174 CTTATACATATTTTACGCTCGTCAGCTTGCACATGTTTATGCTCATCAGCTTATACATATGCGTT
1 CTTATACATATTTTACACTCGCCAGCTTGCACACGTTTATGCTCATCAGCTTATACATACGCGTT
*
21599239 TATGCTTGCCAC
66 TATGCTCGCCAC
*
21599251 CTTATACATATGCGTTTACACTCGCCAGCTTGCACACGTTTATGCTCGTCAGCTTATACATACGC
1 CTTATACATAT---TTTACACTCGCCAGCTTGCACACGTTTATGCTCATCAGCTTATACATACGC
21599316 GTTTATGCTCGCCA
63 GTTTATGCTCGCCA
21599330 GCTTGCACAC
Statistics
Matches: 70, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
77 11 0.16
80 59 0.84
ACGTcount: A:0.22, C:0.27, G:0.15, T:0.36
Consensus pattern (77 bp):
CTTATACATATTTTACACTCGCCAGCTTGCACACGTTTATGCTCATCAGCTTATACATACGCGTT
TATGCTCGCCAC
Found at i:21599307 original size:52 final size:52
Alignment explanation
Indices: 21599235--21599390 Score: 249
Period size: 52 Copynumber: 3.0 Consensus size: 52
21599225 TATACATATG
* * * *
21599235 CGTTTATGCTTGCCACCTTATACATATGCGTTTACACTCGCCAGCTTGCACA
1 CGTTTATGCTCGTCAGCTTATACATATGCGTTTACGCTCGCCAGCTTGCACA
* *
21599287 CGTTTATGCTCGTCAGCTTATACATACGCGTTTATGCTCGCCAGCTTGCACA
1 CGTTTATGCTCGTCAGCTTATACATATGCGTTTACGCTCGCCAGCTTGCACA
*
21599339 CGTTTATGCTCATCAGCTTATACATATGCGTTTACGCTCGCCAGCTTGCACA
1 CGTTTATGCTCGTCAGCTTATACATATGCGTTTACGCTCGCCAGCTTGCACA
21599391 TATGTATTGT
Statistics
Matches: 95, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 95 1.00
ACGTcount: A:0.21, C:0.29, G:0.17, T:0.33
Consensus pattern (52 bp):
CGTTTATGCTCGTCAGCTTATACATATGCGTTTACGCTCGCCAGCTTGCACA
Found at i:21599391 original size:28 final size:28
Alignment explanation
Indices: 21599208--21599394 Score: 156
Period size: 28 Copynumber: 7.0 Consensus size: 28
21599198 GCTTGCACAT
** *
21599208 GTTTATGCTCATCAGCTTATACATATGC
1 GTTTATGCTCGCCAGCTTACACATATGC
* * *
21599236 GTTTATGCTTGCCACCTTATACATATGC
1 GTTTATGCTCGCCAGCTTACACATATGC
** *
21599264 GTTTACACTCGCCAGCTTGCAC--A--C
1 GTTTATGCTCGCCAGCTTACACATATGC
* * *
21599288 GTTTATGCTCGTCAGCTTATACATACGC
1 GTTTATGCTCGCCAGCTTACACATATGC
*
21599316 GTTTATGCTCGCCAGCTTGCAC--A--C
1 GTTTATGCTCGCCAGCTTACACATATGC
** *
21599340 GTTTATGCTCATCAGCTTATACATATGC
1 GTTTATGCTCGCCAGCTTACACATATGC
* *
21599368 GTTTACGCTCGCCAGCTTGCACATATG
1 GTTTATGCTCGCCAGCTTACACATATG
21599395 TATTGTATAT
Statistics
Matches: 124, Mismatches: 27, Indels: 16
0.74 0.16 0.10
Matches are distributed among these distances:
24 37 0.30
26 4 0.03
28 83 0.67
ACGTcount: A:0.21, C:0.27, G:0.17, T:0.34
Consensus pattern (28 bp):
GTTTATGCTCGCCAGCTTACACATATGC
Found at i:21599392 original size:132 final size:132
Alignment explanation
Indices: 21599046--21599394 Score: 418
Period size: 132 Copynumber: 2.7 Consensus size: 132
21599036 ATATATTTAA
* * * * *
21599046 ACAT-GCGTTTACGCTCCCCAACTTGCACACGTTTATGCTCGTCAGCTTATACTTTTGCGTTTAC
1 ACATAGCGTTTACGCTCGCCAGCTTGCACACGTTTATGCTCATCAGCTTATACATATGCGTTTAC
* * * * * *
21599110 TCTCGCCAGCTTGCACACATTTACACATTACGCTCGCTAGCTTGCACACATTTACGCTCATTAGC
66 GCTCGCCAGCTTG--CACATATGCACATTACACTCGCCAGCTTGCACACATTTACGCTCATCAGC
21599175 TTAT
129 TTAT
* * * *
21599179 ACATA--TTTTACGCTCGTCAGCTTGCACATGTTTATGCTCATCAGCTTATACATATGCGTTTAT
1 ACATAGCGTTTACGCTCGCCAGCTTGCACACGTTTATGCTCATCAGCTTATACATATGCGTTTAC
* * ** ** * * *
21599242 GCTTGCCACCTTATACATATGC-GTTTACACTCGCCAGCTTGCACACGTTTATGCTCGTCAGCTT
66 GCTCGCCAGCTTGCACATATGCACATTACACTCGCCAGCTTGCACACATTTACGCTCATCAGCTT
21599306 AT
131 AT
*
21599308 ACATACGCGTTTATGCTCGCCAGCTTGCACACGTTTATGCTCATCAGCTTATACATATGCGTTTA
1 ACATA-GCGTTTACGCTCGCCAGCTTGCACACGTTTATGCTCATCAGCTTATACATATGCGTTTA
21599373 CGCTCGCCAGCTTGCACATATG
65 CGCTCGCCAGCTTGCACATATG
21599395 TATTGTATAT
Statistics
Matches: 179, Mismatches: 33, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
129 41 0.23
130 6 0.03
132 128 0.72
133 4 0.02
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.34
Consensus pattern (132 bp):
ACATAGCGTTTACGCTCGCCAGCTTGCACACGTTTATGCTCATCAGCTTATACATATGCGTTTAC
GCTCGCCAGCTTGCACATATGCACATTACACTCGCCAGCTTGCACACATTTACGCTCATCAGCTT
AT
Found at i:21605201 original size:25 final size:24
Alignment explanation
Indices: 21605165--21605211 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
21605155 AGTTAATAAT
21605165 AATTCTCTTTGAGTTTTTCTTTAAG
1 AATTCTCTTTGAGTTTTT-TTTAAG
21605190 AATTGCTC-TTGAGTTTTTTTTA
1 AATT-CTCTTTGAGTTTTTTTTA
21605212 GAAGTTGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 4 0.19
25 14 0.67
26 3 0.14
ACGTcount: A:0.19, C:0.11, G:0.13, T:0.57
Consensus pattern (24 bp):
AATTCTCTTTGAGTTTTTTTTAAG
Found at i:21609219 original size:23 final size:23
Alignment explanation
Indices: 21609193--21609245 Score: 63
Period size: 25 Copynumber: 2.3 Consensus size: 23
21609183 GATCTCGAAG
21609193 TCAAATAATATCTTTAATATTTT
1 TCAAATAATATCTTTAATATTTT
* *
21609216 TCAAAAAAAATATCTTTAATCTTTT
1 TC--AAATAATATCTTTAATATTTT
21609241 T-AAAT
1 TCAAAT
21609246 GAAATTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
22 3 0.12
23 2 0.08
25 20 0.80
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.47
Consensus pattern (23 bp):
TCAAATAATATCTTTAATATTTT
Found at i:21613154 original size:21 final size:21
Alignment explanation
Indices: 21613116--21613155 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
21613106 GCATATAACA
*
21613116 TTTAAATATCAATTTAATTTC
1 TTTAAATATCAATATAATTTC
21613137 TTTAAAT-TCAAATATAATT
1 TTTAAATATC-AATATAATT
21613156 CGAAATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTAAATATCAATATAATTTC
Found at i:21618719 original size:30 final size:30
Alignment explanation
Indices: 21618683--21618785 Score: 102
Period size: 30 Copynumber: 3.4 Consensus size: 30
21618673 GTGTCTTCGT
*
21618683 AACATGAGTGCTCGCAGCTCTAGTGTTCGC
1 AACATGAGTGCTCGCAGCTCTAGTGTTCAC
* * * *
21618713 AACATGATTGTTCGCTTTG-TGT-GTGTTCAC
1 AACATGAGTGCTCGC--AGCTCTAGTGTTCAC
* *
21618743 AACATGAGTGTTCGCAGCTCCAGTGTTCAC
1 AACATGAGTGCTCGCAGCTCTAGTGTTCAC
*
21618773 AACATGAGGGCTC
1 AACATGAGTGCTC
21618786 ACAACACTAT
Statistics
Matches: 58, Mismatches: 11, Indels: 8
0.75 0.14 0.10
Matches are distributed among these distances:
28 1 0.02
29 1 0.02
30 53 0.91
31 2 0.03
32 1 0.02
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.30
Consensus pattern (30 bp):
AACATGAGTGCTCGCAGCTCTAGTGTTCAC
Found at i:21618747 original size:60 final size:60
Alignment explanation
Indices: 21618649--21618780 Score: 183
Period size: 60 Copynumber: 2.2 Consensus size: 60
21618639 TCATCCATGC
* ** *
21618649 TCACAACATCAGTGTTCGCGTTGTGTGTCTTCGTAACATGAGTGCTCGCAGCTCTAGTGT
1 TCACAACATGAGTGTTCGCGTTGTGTGTCTTCACAACATGAGTGCTCGCAGCTCCAGTGT
* * * * *
21618709 TCGCAACATGATTGTTCGCTTTGTGTGTGTTCACAACATGAGTGTTCGCAGCTCCAGTGT
1 TCACAACATGAGTGTTCGCGTTGTGTGTCTTCACAACATGAGTGCTCGCAGCTCCAGTGT
21618769 TCACAACATGAG
1 TCACAACATGAG
21618781 GGCTCACAAC
Statistics
Matches: 61, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.20, C:0.23, G:0.24, T:0.33
Consensus pattern (60 bp):
TCACAACATGAGTGTTCGCGTTGTGTGTCTTCACAACATGAGTGCTCGCAGCTCCAGTGT
Found at i:21618753 original size:15 final size:15
Alignment explanation
Indices: 21618735--21618791 Score: 53
Period size: 15 Copynumber: 3.8 Consensus size: 15
21618725 CGCTTTGTGT
21618735 GTGTTCACAACATGA
1 GTGTTCACAACATGA
* * *
21618750 GTGTTCGCAGC-TCCA
1 GTGTTCACAACAT-GA
21618765 GTGTTCACAACATGA
1 GTGTTCACAACATGA
* *
21618780 GGGCTCACAACA
1 GTGTTCACAACA
21618792 CTATTGCTCA
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
14 1 0.03
15 30 0.94
16 1 0.03
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (15 bp):
GTGTTCACAACATGA
Found at i:21628648 original size:42 final size:42
Alignment explanation
Indices: 21628585--21628959 Score: 448
Period size: 42 Copynumber: 8.9 Consensus size: 42
21628575 GAAAAATAAA
* ** * *
21628585 TAAATGGACCTCTATGCTTGGGCCTCTAAAGGGAATGAAAAG
1 TAAATGGACCTCCACACTTGGGCCTCTAAATGCAATGAAAAG
* * ** *
21628627 TAAATGGACCTCCACAGTTGGGCCTCTAAATGCATTGGTAAT
1 TAAATGGACCTCCACACTTGGGCCTCTAAATGCAATGAAAAG
* * * *
21628669 TAAATGGACCTTCACA-TATGGGCATCTAAATACAATGGAAAG
1 TAAATGGACCTCCACACT-TGGGCCTCTAAATGCAATGAAAAG
21628711 TAAATGGACCTCCACACTTGGGCCTCTAAATGCAATGAAAAG
1 TAAATGGACCTCCACACTTGGGCCTCTAAATGCAATGAAAAG
* * * **
21628753 TAAATGGACCTCCGCACCTAGGCCTCTAAATGTGATGAAAAG
1 TAAATGGACCTCCACACTTGGGCCTCTAAATGCAATGAAAAG
* *
21628795 TAAATAGACCTCAACAGC-TGGGCCTCTAAATGCAATGAAAAG
1 TAAATGGACCTCCACA-CTTGGGCCTCTAAATGCAATGAAAAG
* ** * * * *
21628837 TAAATAGACCTCCATGCCTAGGCCTCTAAATGCGATGAAAAA
1 TAAATGGACCTCCACACTTGGGCCTCTAAATGCAATGAAAAG
* *
21628879 TAAATGGACCTCCACACTTGAGCTTCTAAATGCAATGAAAAG
1 TAAATGGACCTCCACACTTGGGCCTCTAAATGCAATGAAAAG
21628921 TAAATGGACCTCCACACTTGGGCCTCTAAATGCAATGAA
1 TAAATGGACCTCCACACTTGGGCCTCTAAATGCAATGAA
21628960 TGCTTTCCTT
Statistics
Matches: 281, Mismatches: 48, Indels: 8
0.83 0.14 0.02
Matches are distributed among these distances:
41 2 0.01
42 277 0.99
43 2 0.01
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.23
Consensus pattern (42 bp):
TAAATGGACCTCCACACTTGGGCCTCTAAATGCAATGAAAAG
Found at i:21629397 original size:21 final size:21
Alignment explanation
Indices: 21629366--21629412 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
21629356 TCTCTCTATT
*
21629366 TTTTTCTTC-TTCTTTTGTTG
1 TTTTTCTTCTTTCTTTTGTGG
*
21629386 TTTTTCTCTCTTTTTTTTGTGG
1 TTTTTCT-TCTTTCTTTTGTGG
21629408 TTTTT
1 TTTTT
21629413 TTATTTTAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 7 0.30
21 2 0.09
22 14 0.61
ACGTcount: A:0.00, C:0.13, G:0.11, T:0.77
Consensus pattern (21 bp):
TTTTTCTTCTTTCTTTTGTGG
Found at i:21634732 original size:17 final size:17
Alignment explanation
Indices: 21634678--21634732 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
21634668 GACAAATGGA
* *
21634678 AATGCAATGACAATGCG
1 AATGCAATGATAATGAG
* * *
21634695 AATGCAGTGATAATTAA
1 AATGCAATGATAATGAG
*
21634712 AATGCAATAATAATGAG
1 AATGCAATGATAATGAG
21634729 AATG
1 AATG
21634733 TGATGACAAT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.47, C:0.09, G:0.20, T:0.24
Consensus pattern (17 bp):
AATGCAATGATAATGAG
Found at i:21641531 original size:21 final size:22
Alignment explanation
Indices: 21641505--21641557 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
21641495 ACAGCAAGCT
21641505 GAAGAAGAAGAA-GACCCTAAA
1 GAAGAAGAAGAAGGACCCTAAA
* *
21641526 GAAGAAGAA-AAGGATCCTAAG
1 GAAGAAGAAGAAGGACCCTAAA
21641547 GAAGAAGAAGA
1 GAAGAAGAAGA
21641558 TCCTGTAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 2 0.07
21 25 0.89
22 1 0.04
ACGTcount: A:0.57, C:0.09, G:0.28, T:0.06
Consensus pattern (22 bp):
GAAGAAGAAGAAGGACCCTAAA
Found at i:21641559 original size:18 final size:18
Alignment explanation
Indices: 21641506--21641561 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 18
21641496 CAGCAAGCTG
*
21641506 AAGAAGAAGAAGACCCTA
1 AAGAAGAAGAAGATCCTA
21641524 AAGAAGAAGAAAAGGATCCTA
1 AAGAAGAAG--AA-GATCCTA
*
21641545 AGGAAGAAGAAGATCCT
1 AAGAAGAAGAAGATCCT
21641562 GTAAAGATTG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 15 0.45
19 2 0.06
20 2 0.06
21 14 0.42
ACGTcount: A:0.54, C:0.12, G:0.25, T:0.09
Consensus pattern (18 bp):
AAGAAGAAGAAGATCCTA
Found at i:21643494 original size:16 final size:17
Alignment explanation
Indices: 21643467--21643499 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
21643457 ATTAATGTCG
*
21643467 ATAAATATAATTTATTT
1 ATAAATATAATTAATTT
21643484 ATAAA-ATAATTAATTT
1 ATAAATATAATTAATTT
21643500 GTGCTAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATAAATATAATTAATTT
Found at i:21647538 original size:17 final size:17
Alignment explanation
Indices: 21647512--21647544 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
21647502 AAGAAACAGA
*
21647512 TAAAAGAAGAAATAAAG
1 TAAAACAAGAAATAAAG
21647529 TAAAACAAGAAATAAA
1 TAAAACAAGAAATAAA
21647545 CATAAATGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.73, C:0.03, G:0.12, T:0.12
Consensus pattern (17 bp):
TAAAACAAGAAATAAAG
Found at i:21655399 original size:20 final size:19
Alignment explanation
Indices: 21655365--21655402 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
21655355 TTTTTTTTTC
21655365 TGCTTTTTCTCTTCTTCTT
1 TGCTTTTTCTCTTCTTCTT
*
21655384 TGCTTTCTTTTCTTCTTCT
1 TGCTTT-TTCTCTTCTTCT
21655403 CTAATTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.00, C:0.26, G:0.05, T:0.68
Consensus pattern (19 bp):
TGCTTTTTCTCTTCTTCTT
Found at i:21657553 original size:16 final size:17
Alignment explanation
Indices: 21657516--21657553 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
21657506 ACTAACAAGC
21657516 AAAATGCAAAGACAACT
1 AAAATGCAAAGACAACT
*
21657533 AAAATGCAATGACAA-T
1 AAAATGCAAAGACAACT
21657549 AAAAT
1 AAAAT
21657554 AAGATGCATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.61, C:0.13, G:0.11, T:0.16
Consensus pattern (17 bp):
AAAATGCAAAGACAACT
Found at i:21657969 original size:27 final size:27
Alignment explanation
Indices: 21657934--21657986 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
21657924 GGCATCTACA
* *
21657934 TCCTCTTCA-TTCTTCTTCTTTTCCTCC
1 TCCTCTTCAGTTCCT-TTCTCTTCCTCC
21657961 TCCTCTTCAGTTCCTTTCTCTTCCTC
1 TCCTCTTCAGTTCCTTTCTCTTCCTC
21657987 AGGGTTTTCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.04, C:0.42, G:0.02, T:0.53
Consensus pattern (27 bp):
TCCTCTTCAGTTCCTTTCTCTTCCTCC
Found at i:21660897 original size:40 final size:40
Alignment explanation
Indices: 21660842--21660917 Score: 152
Period size: 40 Copynumber: 1.9 Consensus size: 40
21660832 ACATTTACCC
21660842 CACCTTCCAGTGTTGGCAATGCCTTGCACTCAAGAAACCT
1 CACCTTCCAGTGTTGGCAATGCCTTGCACTCAAGAAACCT
21660882 CACCTTCCAGTGTTGGCAATGCCTTGCACTCAAGAA
1 CACCTTCCAGTGTTGGCAATGCCTTGCACTCAAGAA
21660918 CAAGTGACTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (40 bp):
CACCTTCCAGTGTTGGCAATGCCTTGCACTCAAGAAACCT
Found at i:21662192 original size:25 final size:24
Alignment explanation
Indices: 21662151--21662197 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
21662141 AACATATATT
*
21662151 TCTTTTTTCTTCTTTTCTCTTTTCC
1 TCTTCTTTCTTCTTTTC-CTTTTCC
21662176 TCTTCTTTCTT-TCTTTCCTTTT
1 TCTTCTTTCTTCT-TTTCCTTTT
21662198 TTTATAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (24 bp):
TCTTCTTTCTTCTTTTCCTTTTCC
Found at i:21662198 original size:25 final size:25
Alignment explanation
Indices: 21662151--21662199 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
21662141 AACATATATT
* *
21662151 TCTTTTTTCTTCTTTTCTCTTTTCC
1 TCTTCTTTCTTCTTTCCTCTTTTCC
*
21662176 TCTTCTTTCTTTCTTTCCTTTTTT
1 TCTTCTTTC-TTCTTTCCTCTTTT
21662200 TATAAATGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 8 0.40
26 12 0.60
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (25 bp):
TCTTCTTTCTTCTTTCCTCTTTTCC
Found at i:21666267 original size:18 final size:18
Alignment explanation
Indices: 21666244--21666290 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
21666234 AAGATTTGGC
21666244 TGCATCGACATGGGTAGT
1 TGCATCGACATGGGTAGT
21666262 TGCATCGACATGGGTAGT
1 TGCATCGACATGGGTAGT
21666280 TGCATCGACAT
1 TGCATCGACAT
21666291 CTATTTTGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (18 bp):
TGCATCGACATGGGTAGT
Found at i:21671291 original size:47 final size:47
Alignment explanation
Indices: 21671233--21671383 Score: 161
Period size: 47 Copynumber: 3.3 Consensus size: 47
21671223 GTGATAACAG
21671233 TTGTCGAAGCAATGGACAAATAAATGCAATAAAATTGTGAGGTTAAT
1 TTGTCGAAGCAATGGACAAATAAATGCAATAAAATTGTGAGGTTAAT
* ** ** * *
21671280 TTGTCGAAGCAATAATGTTAAATTAAA-G--ATAAAA-TGCAATGAT-A-
1 TTGTCGAAGCAAT--GGACAAA-TAAATGCAATAAAATTGTGAGGTTAAT
*
21671324 TTGTCGAAGCAATGGACAAATAAATGCAATAAAATTGTGTGGTTAAT
1 TTGTCGAAGCAATGGACAAATAAATGCAATAAAATTGTGAGGTTAAT
21671371 TTGTCGAAGCAAT
1 TTGTCGAAGCAAT
21671384 AATGTAAAAT
Statistics
Matches: 80, Mismatches: 15, Indels: 18
0.71 0.13 0.16
Matches are distributed among these distances:
41 4 0.05
42 5 0.06
44 19 0.24
45 5 0.06
46 6 0.08
47 32 0.40
49 5 0.06
50 4 0.05
ACGTcount: A:0.42, C:0.09, G:0.20, T:0.29
Consensus pattern (47 bp):
TTGTCGAAGCAATGGACAAATAAATGCAATAAAATTGTGAGGTTAAT
Found at i:21671341 original size:91 final size:91
Alignment explanation
Indices: 21671233--21671414 Score: 346
Period size: 91 Copynumber: 2.0 Consensus size: 91
21671223 GTGATAACAG
21671233 TTGTCGAAGCAATGGACAAATAAATGCAATAAAATTGTGAGGTTAATTTGTCGAAGCAATAATGT
1 TTGTCGAAGCAATGGACAAATAAATGCAATAAAATTGTGAGGTTAATTTGTCGAAGCAATAATGT
*
21671298 TAAATTAAAGATAAAATGCAATGATA
66 AAAATTAAAGATAAAATGCAATGATA
*
21671324 TTGTCGAAGCAATGGACAAATAAATGCAATAAAATTGTGTGGTTAATTTGTCGAAGCAATAATGT
1 TTGTCGAAGCAATGGACAAATAAATGCAATAAAATTGTGAGGTTAATTTGTCGAAGCAATAATGT
21671389 AAAATTAAAGATAAAATGCAATGATA
66 AAAATTAAAGATAAAATGCAATGATA
21671415 ATGAGATGGG
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 89 1.00
ACGTcount: A:0.45, C:0.08, G:0.19, T:0.29
Consensus pattern (91 bp):
TTGTCGAAGCAATGGACAAATAAATGCAATAAAATTGTGAGGTTAATTTGTCGAAGCAATAATGT
AAAATTAAAGATAAAATGCAATGATA
Found at i:21671403 original size:47 final size:47
Alignment explanation
Indices: 21671261--21671405 Score: 135
Period size: 47 Copynumber: 3.1 Consensus size: 47
21671251 AATAAATGCA
* *
21671261 ATAAAATTGTGAGGTTAATTTGTCGAAGCAATAATGTTAAATTAAAG
1 ATAAAATTGTGTGGTTAATTTGTCGAAGCAATAATGTAAAATTAAAG
** * *
21671308 ATAAAA-TGCAAT-GAT-A-TTGTCGAAGC---AATGGACAAA-TAAATG
1 ATAAAATTG-TGTGGTTAATTTGTCGAAGCAATAATGTA-AAATTAAA-G
21671350 CAATAAAATTGTGTGGTTAATTTGTCGAAGCAATAATGTAAAATTAAAG
1 --ATAAAATTGTGTGGTTAATTTGTCGAAGCAATAATGTAAAATTAAAG
21671399 ATAAAAT
1 ATAAAAT
21671406 GCAATGATAA
Statistics
Matches: 75, Mismatches: 10, Indels: 26
0.68 0.09 0.23
Matches are distributed among these distances:
41 8 0.11
42 4 0.05
44 17 0.23
45 5 0.07
46 5 0.07
47 23 0.31
49 4 0.05
50 9 0.12
ACGTcount: A:0.46, C:0.06, G:0.18, T:0.30
Consensus pattern (47 bp):
ATAAAATTGTGTGGTTAATTTGTCGAAGCAATAATGTAAAATTAAAG
Found at i:21674882 original size:24 final size:24
Alignment explanation
Indices: 21674850--21674905 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
21674840 ACAGCAAGTT
21674850 GAAGAAGAAGAAGACCCTGAA-GAA
1 GAAGAAGAAGAAGACCCT-AAGGAA
* *
21674874 GAAGAAGAAGAGGATCCTAAGGAA
1 GAAGAAGAAGAAGACCCTAAGGAA
21674898 GAAGAAGA
1 GAAGAAGA
21674906 TCCTGTGGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 2 0.07
24 27 0.93
ACGTcount: A:0.54, C:0.09, G:0.32, T:0.05
Consensus pattern (24 bp):
GAAGAAGAAGAAGACCCTAAGGAA
Found at i:21675587 original size:18 final size:18
Alignment explanation
Indices: 21675564--21675599 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
21675554 GTACAGTATT
*
21675564 TGTTCACTTTTATTTTTA
1 TGTTCACTATTATTTTTA
*
21675582 TGTTCACTATTGTTTTTA
1 TGTTCACTATTATTTTTA
21675600 ACAATGAGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.11, G:0.08, T:0.64
Consensus pattern (18 bp):
TGTTCACTATTATTTTTA
Found at i:21679106 original size:101 final size:101
Alignment explanation
Indices: 21678977--21679160 Score: 271
Period size: 101 Copynumber: 1.8 Consensus size: 101
21678967 CCGTATATAA
* * *
21678977 ATTCATATACGCACGATGACATTGAGTCATATAACCTTTAATTCGTAATGGATTCATTTACTCAC
1 ATTCATATACGCACGATGACATTGAGTCATAGAACCTTTAATCCGTAAAGGATTCATTTACTCAC
* *
21679042 GATGACACTTAGTCATCGTACCTTTATCCGTAAAGG
66 GATGACACTAAATCATCGTACCTTTATCCGTAAAGG
* * * *
21679078 ATTCATTTACTCACGATGACACTT-AGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCA
1 ATTCATATACGCACGATGACA-TTGAGTCATAGAACCTTTAATCCGTAAAGGATTCATTTACTCA
21679142 CGATGACACTAAATCATCG
65 CGATGACACTAAATCATCG
21679161 GACTCTTTCA
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
101 71 0.97
102 2 0.03
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (101 bp):
ATTCATATACGCACGATGACATTGAGTCATAGAACCTTTAATCCGTAAAGGATTCATTTACTCAC
GATGACACTAAATCATCGTACCTTTATCCGTAAAGG
Found at i:21679159 original size:51 final size:51
Alignment explanation
Indices: 21678977--21679168 Score: 262
Period size: 51 Copynumber: 3.8 Consensus size: 51
21678967 CCGTATATAA
* * *** * *
21678977 ATTCATATACGCACGATGACA-TTGAGTCATATAACCTTTAATTCGTAATGG
1 ATTCATTTACTCACGATGACACTT-AGTCATCGGACCTTTAATCCGTAAAGG
*
21679028 ATTCATTTACTCACGATGACACTTAGTCATCGTACCTTT-ATCCGTAAAGG
1 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGG
21679078 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGG
1 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGG
* *
21679129 ATTCATTTACTCACGATGACACTAAATCATCGGACTCTTT
1 ATTCATTTACTCACGATGACACTTAGTCATCGGAC-CTTT
21679169 CATTTATAGC
Statistics
Matches: 128, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
50 47 0.37
51 75 0.59
52 6 0.05
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.33
Consensus pattern (51 bp):
ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGG
Found at i:21687145 original size:21 final size:22
Alignment explanation
Indices: 21687098--21687157 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
21687088 AACTGTGTAG
***
21687098 ATTTCTACCGATACCTTTACTA
1 ATTTCTACCGATACAAGTACTA
21687120 A-TTCTACCGATACAAGTA-TA
1 ATTTCTACCGATACAAGTACTA
*
21687140 ATTTCTACTGATACAAGT
1 ATTTCTACCGATACAAGT
21687158 CATTCAATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 3 0.09
21 29 0.88
22 1 0.03
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (22 bp):
ATTTCTACCGATACAAGTACTA
Found at i:21687998 original size:51 final size:51
Alignment explanation
Indices: 21687919--21688266 Score: 538
Period size: 51 Copynumber: 6.8 Consensus size: 51
21687909 CCGTATAGAA
* ** *
21687919 ATTCATATACTCACGATGAC-CTTAAGTCATCGGACCTTTAATTTGTAATGG
1 ATTCATTTACTCACGATGACACTT-AGTCATCGGACCTTTAATCCGTAAAGG
* *
21687970 ATTTATTTACTCACGATGACACTTAGTCATCGTACCTTTAATCCGTAAAGG
1 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGG
*
21688021 ATTCATTTGCTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGG
1 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGG
21688072 ATTCATTTACTCACGATGACACTTAGTCA-CTGGACCTTTAATCCGTAAAGG
1 ATTCATTTACTCACGATGACACTTAGTCATC-GGACCTTTAATCCGTAAAGG
* * *
21688123 ATTCATTTACTCAAGATGACACTTAGTCATCGGTCCTTTAATCTGTAAAGG
1 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGG
*
21688174 ATTCATTTACTCACGATGACACTTAGTCATCGGGGACCTTTAATCCTTAAAGG
1 ATTCATTTACTCACGATGACACTTAGTCATC--GGACCTTTAATCCGTAAAGG
21688227 ATTCATTTACTCACGATGACACTTAGTCATCGGACTCTTT
1 ATTCATTTACTCACGATGACACTTAGTCATCGGAC-CTTT
21688267 CGTTTATAGC
Statistics
Matches: 274, Mismatches: 17, Indels: 11
0.91 0.06 0.04
Matches are distributed among these distances:
50 1 0.00
51 217 0.79
52 8 0.03
53 48 0.18
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (51 bp):
ATTCATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGG
Found at i:21695886 original size:23 final size:23
Alignment explanation
Indices: 21695848--21695904 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
21695838 TATTAACGCT
* *
21695848 AACAAATATGAAAGAAACAACTAAC
1 AACAAAGAT-AAAGAAACAA-GAAC
21695873 -ACAAAGATAAAGAAACAAGAAC
1 AACAAAGATAAAGAAACAAGAAC
21695895 AACAAAGATA
1 AACAAAGATA
21695905 GGATTTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 3 0.10
23 19 0.66
24 7 0.24
ACGTcount: A:0.67, C:0.14, G:0.11, T:0.09
Consensus pattern (23 bp):
AACAAAGATAAAGAAACAAGAAC
Found at i:21697798 original size:94 final size:94
Alignment explanation
Indices: 21697682--21697902 Score: 379
Period size: 94 Copynumber: 2.4 Consensus size: 94
21697672 CAAATATTTT
* * *
21697682 ATACCATACAATTAACCCTTCTTCAATTCATTTATTCTTGTTCAATTTGACAAATATTTTTGTTC
1 ATACCATACAATCAATCATTCTTCAATTCATTTATTCTTGTTCAATTTGACAAATATTTTTGTTC
* *
21697747 TTTTCAAAATGTTCTCTTCATTCATAATC
66 TTGTCAAAATGCTCTCTTCATTCATAATC
21697776 ATACCATACAATCAATCATTCTTCAATTCATTTATTCTTGTTCAATTTGACAAATATTTTTGTTC
1 ATACCATACAATCAATCATTCTTCAATTCATTTATTCTTGTTCAATTTGACAAATATTTTTGTTC
21697841 TTGTCAAAATGCTCTCTTCATTCATAATC
66 TTGTCAAAATGCTCTCTTCATTCATAATC
* *
21697870 ATACCATACAATCAATCATTCTTAAAATCATTT
1 ATACCATACAATCAATCATTCTTCAATTCATTT
21697903 GTTTCTGTGA
Statistics
Matches: 120, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
94 120 1.00
ACGTcount: A:0.31, C:0.20, G:0.04, T:0.44
Consensus pattern (94 bp):
ATACCATACAATCAATCATTCTTCAATTCATTTATTCTTGTTCAATTTGACAAATATTTTTGTTC
TTGTCAAAATGCTCTCTTCATTCATAATC
Found at i:21702840 original size:78 final size:78
Alignment explanation
Indices: 21702294--21702843 Score: 780
Period size: 78 Copynumber: 7.0 Consensus size: 78
21702284 AAGCGAAGCT
* * *
21702294 ACACACCAATCTCTTACCCCCGATCATGGGGCAGATTGAAACATCCAATATTTTACCCTAATCTG
1 ACACACCAATCTCTTA-CCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAG
* * *
21702359 AGGGAAAATTAAAG
65 AGGGCAGATTGAAG
* * * *
21702373 ACACACCAATCTCTTACCCCCAATCATGGGGTAGATTGAAGCATCCAATCTTTCACCCAAATCAG
1 ACACACCAATCTCTTA-CCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAG
* *
21702438 AGGGCAAATTAAAG
65 AGGGCAGATTGAAG
* * * *
21702452 ACACACCAATCTCTTACCCTGACCATGGGGCAGATTGAAGCATCTAATCTTTCACCCTAATCAGA
1 ACACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGA
21702517 GGGCAGATTGAAG
66 GGGCAGATTGAAG
* * * *
21702530 ACACACCAATCTCTTACCCTGACCATGGGGCAGATTGAAGCATCTAATCTTTTACCCTAATCAAA
1 ACACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGA
21702595 GGGCAGATTGAAG
66 GGGCAGATTGAAG
* * *
21702608 ACACACCAATCTCTTACCCCGATCATGGGGCAGATTAAAGCATCTAATCTTTTACCCTAATTAGA
1 ACACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGA
*
21702673 GGGCAGATTGAAA
66 GGGCAGATTGAAG
*
21702686 ACACACCAATCT-TATACCCCGATCATGGGACAGATTGAAGCATCCAATCTTTTACCCTAATCAG
1 ACACACCAATCTCT-TACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAG
21702750 AGGGCA-ATTTGAAG
65 AGGGCAGA-TTGAAG
* * * *
21702764 ACACATCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCAACCAATCTTTTACCCTAATTAAA
1 ACACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGA
*
21702829 GGGTAGATTGAAG
66 GGGCAGATTGAAG
21702842 AC
1 AC
21702844 GCTATTCGAT
Statistics
Matches: 432, Mismatches: 35, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
77 2 0.00
78 341 0.79
79 89 0.21
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (78 bp):
ACACACCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGA
GGGCAGATTGAAG
Found at i:21710165 original size:23 final size:24
Alignment explanation
Indices: 21710138--21710207 Score: 63
Period size: 27 Copynumber: 2.9 Consensus size: 24
21710128 ATATATATTT
* **
21710138 TAAATATTTTTAAGTAATTAAT-A
1 TAAATATATTTAAAAAATTAATGA
21710161 TAAAT-TATTTAAAAAATTAATGA
1 TAAATATATTTAAAAAATTAATGA
*
21710184 TAAATAAAATATTTAAAAATTTAA
1 TAAAT---ATATTTAAAAAATTAA
21710208 ATATTATATT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
22 13 0.34
23 11 0.29
27 14 0.37
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (24 bp):
TAAATATATTTAAAAAATTAATGA
Found at i:21710181 original size:26 final size:26
Alignment explanation
Indices: 21710152--21710207 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
21710142 TATTTTTAAG
*
21710152 TAAT-TAATATAAATTATTTAAAAAAT
1 TAATATAA-ATAAAATATTTAAAAAAT
*
21710178 TAATGATAAATAAAATATTTAAAAATT
1 TAAT-ATAAATAAAATATTTAAAAAAT
21710205 TAA
1 TAA
21710208 ATATTATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 4 0.15
27 19 0.73
28 3 0.12
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (26 bp):
TAATATAAATAAAATATTTAAAAAAT
Found at i:21710232 original size:13 final size:12
Alignment explanation
Indices: 21710204--21710248 Score: 63
Period size: 13 Copynumber: 3.6 Consensus size: 12
21710194 ATTTAAAAAT
21710204 TTAAATATTATA
1 TTAAATATTATA
*
21710216 TTAAATAATTCTA
1 TTAAAT-ATTATA
21710229 TTAAATATTATA
1 TTAAATATTATA
21710241 TTTAAATA
1 -TTAAATA
21710249 ACATAATCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (12 bp):
TTAAATATTATA
Found at i:21712115 original size:4 final size:4
Alignment explanation
Indices: 21712108--21712136 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
21712098 GTATATATAA
21712108 ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
21712137 TATATTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:21712855 original size:38 final size:38
Alignment explanation
Indices: 21712813--21712934 Score: 97
Period size: 38 Copynumber: 3.1 Consensus size: 38
21712803 TCAATTTTGA
21712813 AAAGATCATATTGTTTCAACATTTTTTGAAACTGTAAC
1 AAAGATCATATTGTTTCAACATTTTTTGAAACTGTAAC
** * * * * * *
21712851 AAAGAGAACATGGTTT--ATATTTATTCTAGAATCAATTTTGA-
1 AAAGATCATATTGTTTCAACATTT-TT-T-G-A--AACTGTAAC
21712892 AAAGATCATATTGTTTCAACATTTTTTGAAACTGTAAC
1 AAAGATCATATTGTTTCAACATTTTTTGAAACTGTAAC
21712930 AAAGA
1 AAAGA
21712935 GAACATGGTT
Statistics
Matches: 59, Mismatches: 16, Indels: 18
0.63 0.17 0.19
Matches are distributed among these distances:
36 5 0.08
37 7 0.12
38 18 0.31
39 2 0.03
40 2 0.03
41 13 0.22
42 7 0.12
43 5 0.08
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (38 bp):
AAAGATCATATTGTTTCAACATTTTTTGAAACTGTAAC
Found at i:21712928 original size:79 final size:79
Alignment explanation
Indices: 21712797--21712954 Score: 316
Period size: 79 Copynumber: 2.0 Consensus size: 79
21712787 TCACAAAAAA
21712797 CTAGAATCAATTTTGAAAAGATCATATTGTTTCAACATTTTTTGAAACTGTAACAAAGAGAACAT
1 CTAGAATCAATTTTGAAAAGATCATATTGTTTCAACATTTTTTGAAACTGTAACAAAGAGAACAT
21712862 GGTTTATATTTATT
66 GGTTTATATTTATT
21712876 CTAGAATCAATTTTGAAAAGATCATATTGTTTCAACATTTTTTGAAACTGTAACAAAGAGAACAT
1 CTAGAATCAATTTTGAAAAGATCATATTGTTTCAACATTTTTTGAAACTGTAACAAAGAGAACAT
21712941 GGTTTATATTTATT
66 GGTTTATATTTATT
21712955 TTCTGTTTGG
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 79 1.00
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (79 bp):
CTAGAATCAATTTTGAAAAGATCATATTGTTTCAACATTTTTTGAAACTGTAACAAAGAGAACAT
GGTTTATATTTATT
Found at i:21720632 original size:18 final size:18
Alignment explanation
Indices: 21720592--21720652 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
21720582 TGCTCTCTTT
** *
21720592 TTTTTAATATTTTGTTTTT
1 TTTTTAATATTTTG-AATA
*
21720611 TTTTTAATTTTTTGAATA
1 TTTTTAATATTTTGAATA
*
21720629 TTTTGAATATTTTGAATA
1 TTTTTAATATTTTGAATA
21720647 TTTTTA
1 TTTTTA
21720653 TAATTTTTAT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
18 22 0.63
19 13 0.37
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.69
Consensus pattern (18 bp):
TTTTTAATATTTTGAATA
Found at i:21725591 original size:15 final size:16
Alignment explanation
Indices: 21725554--21725588 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
21725544 AAAAAATATA
*
21725554 AAAATAAATAGACATG
1 AAAATAAATAAACATG
*
21725570 AAAATAAATAAAGATG
1 AAAATAAATAAACATG
21725586 AAA
1 AAA
21725589 TAAGAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.69, C:0.03, G:0.11, T:0.17
Consensus pattern (16 bp):
AAAATAAATAAACATG
Found at i:21725674 original size:25 final size:24
Alignment explanation
Indices: 21725629--21725675 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
21725619 ATAAATATAA
*
21725629 AACATTAAAATAAAATGCATAATT
1 AACATCAAAATAAAATGCATAATT
21725653 AACATCAAATATATAAA-GCATAA
1 AACATCAAA-ATA-AAATGCATAA
21725676 ATGCAAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 8 0.40
25 9 0.45
26 3 0.15
ACGTcount: A:0.60, C:0.11, G:0.04, T:0.26
Consensus pattern (24 bp):
AACATCAAAATAAAATGCATAATT
Found at i:21726236 original size:18 final size:19
Alignment explanation
Indices: 21726213--21726249 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
21726203 TTTGAAATGG
21726213 TAAAAAAATT-AACTTTTT
1 TAAAAAAATTAAACTTTTT
*
21726231 TAAAAAATTTAAACTTTTT
1 TAAAAAAATTAAACTTTTT
21726250 CCTTTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (19 bp):
TAAAAAAATTAAACTTTTT
Found at i:21738227 original size:18 final size:18
Alignment explanation
Indices: 21738204--21738238 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
21738194 AGGATGTTCT
*
21738204 TCAGGATCTTCTTCTTCC
1 TCAGGATCCTCTTCTTCC
21738222 TCAGGATCCTCTTCTTC
1 TCAGGATCCTCTTCTTC
21738239 TTATTTAGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.34, G:0.11, T:0.43
Consensus pattern (18 bp):
TCAGGATCCTCTTCTTCC
Found at i:21745589 original size:37 final size:37
Alignment explanation
Indices: 21745538--21745639 Score: 114
Period size: 37 Copynumber: 2.7 Consensus size: 37
21745528 TCCAAAATTG
** *
21745538 CGCCCAAACATGTCGTTGCATGAGCACTTCTAGATTA
1 CGCCCAAACATGTCGCCGCATGAGCACCTCTAGATTA
* * *
21745575 TGCCCAAACATGTCGCCGTATGAGCACCTCTAGATTG
1 CGCCCAAACATGTCGCCGCATGAGCACCTCTAGATTA
* * *
21745612 CGCCCAAAAACTGTAGCCACATGAGCAC
1 CGCCCAAACA-TGTCGCCGCATGAGCAC
21745640 TTCCAGCATG
Statistics
Matches: 53, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
37 39 0.74
38 14 0.26
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.22
Consensus pattern (37 bp):
CGCCCAAACATGTCGCCGCATGAGCACCTCTAGATTA
Found at i:21749900 original size:26 final size:26
Alignment explanation
Indices: 21749866--21749921 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
21749856 TAGTATTGCG
*
21749866 TCTTGAGATGTCAGTGTC-GGGATCTA
1 TCTTGAGATGTCAGTG-CAGAGATCTA
*
21749892 TCTTTAGATGTCAGTGCAGAGATCTA
1 TCTTGAGATGTCAGTGCAGAGATCTA
21749918 TCTT
1 TCTT
21749922 AAAAGATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 1 0.04
26 26 0.96
ACGTcount: A:0.21, C:0.16, G:0.25, T:0.38
Consensus pattern (26 bp):
TCTTGAGATGTCAGTGCAGAGATCTA
Found at i:21750077 original size:38 final size:37
Alignment explanation
Indices: 21749996--21750077 Score: 92
Period size: 37 Copynumber: 2.2 Consensus size: 37
21749986 ACATGCCGCT
* * *
21749996 ACATGAGCACTTCTAGATTACGCCCAAACATGTCGTC
1 ACATGAGCACCTCTAGATTACGCCCAAAAATGTCGCC
** **
21750033 GTATGAGCACCTCTAGATTGTGCCCAAAAACTGTCGCC
1 ACATGAGCACCTCTAGATTACGCCCAAAAA-TGTCGCC
21750071 ACATGAG
1 ACATGAG
21750078 TACTTCCAGA
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
37 24 0.69
38 11 0.31
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (37 bp):
ACATGAGCACCTCTAGATTACGCCCAAAAATGTCGCC
Found at i:21750204 original size:26 final size:26
Alignment explanation
Indices: 21750172--21750227 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
21750162 CACCTAGGAA
*
21750172 TGTCACTACATGAACATGTACAGAAT
1 TGTCACTACATGAACATGCACAGAAT
* * *
21750198 TGTCACTGCATGAACGTGCCCAGAAT
1 TGTCACTACATGAACATGCACAGAAT
21750224 TGTC
1 TGTC
21750228 GATGCATCTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (26 bp):
TGTCACTACATGAACATGCACAGAAT
Found at i:21759024 original size:21 final size:23
Alignment explanation
Indices: 21758974--21759024 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 23
21758964 TTTCCTAGAA
21758974 ATGGAGAAATAAGGAAGACGAGAG
1 ATGGAGAAATAAGGAAGA-GAGAG
* *
21758998 AAGGAGAAATAAGG-AG-GTGAG
1 ATGGAGAAATAAGGAAGAGAGAG
21759019 ATGGAG
1 ATGGAG
21759025 TGGGACGTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 9 0.38
23 2 0.08
24 13 0.54
ACGTcount: A:0.47, C:0.02, G:0.41, T:0.10
Consensus pattern (23 bp):
ATGGAGAAATAAGGAAGAGAGAG
Found at i:21760598 original size:12 final size:12
Alignment explanation
Indices: 21760581--21760615 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
21760571 AACGTTTTGC
*
21760581 TTTTATTTTCTA
1 TTTTATTTTATA
*
21760593 TTTTATTTTATC
1 TTTTATTTTATA
21760605 TTTTATTTTAT
1 TTTTATTTTAT
21760616 GCTATTTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTATTTTATA
Found at i:21760603 original size:17 final size:17
Alignment explanation
Indices: 21760581--21760615 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
21760571 AACGTTTTGC
21760581 TTTTAT-TTTCTATTTTA
1 TTTTATCTTT-TATTTTA
21760598 TTTTATCTTTTATTTTA
1 TTTTATCTTTTATTTTA
21760615 T
1 T
21760616 GCTATTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTATCTTTTATTTTA
Found at i:21763451 original size:29 final size:31
Alignment explanation
Indices: 21763391--21763452 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 31
21763381 CTACTTCCTT
* * *
21763391 AAAAATCAAAGCTTTTATTTTAAAATAGTTA
1 AAAAATCAAAGATTTTAGTTTAAAAAAGTTA
*
21763422 AAAAATCAAA-ATTTT-GTTTAAAAAATTTA
1 AAAAATCAAAGATTTTAGTTTAAAAAAGTTA
21763451 AA
1 AA
21763453 CATTTTCCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 13 0.48
30 4 0.15
31 10 0.37
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (31 bp):
AAAAATCAAAGATTTTAGTTTAAAAAAGTTA
Found at i:21763457 original size:22 final size:21
Alignment explanation
Indices: 21763419--21763467 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
21763409 TTTAAAATAG
*
21763419 TTAAAAAATCAAAATTTT-GT
1 TTAAAAAATCAAAATTTTCCT
*
21763439 TTAAAAAATTTAAACATTTTCCT
1 TTAAAAAA-TCAAA-ATTTTCCT
21763462 TTAAAA
1 TTAAAA
21763468 TGACTAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 8 0.33
21 4 0.17
22 5 0.21
23 7 0.29
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (21 bp):
TTAAAAAATCAAAATTTTCCT
Found at i:21763510 original size:143 final size:141
Alignment explanation
Indices: 21763220--21763515 Score: 425
Period size: 143 Copynumber: 2.1 Consensus size: 141
21763210 AAGTTTTCTT
* * * *
21763220 TCTTTTTTAAACAAAATCACTATTTTTCTTAAAATTCAAAGCTTTTAATTCAAGATAGTTAAAAA
1 TCTTTTTTAAACAAAATCACTATCTTCCTTAAAAATCAAAGCTTTTAATTCAAAATAGTTAAAAA
*
21763285 ATAAAATTAGTTTAAAAAATTTAAAATTTTTCCTTTAAAATGAATAAAAAATATTTATTTTTAAA
66 ATAAAATTAGTTTAAAAAATTTAAAATTTTTCCTTTAAAATGAATAAAAAAAATTTATTTTTAAA
*
21763350 AATCTAAACTT
131 AATCTAAACTG
* * *
21763361 TCTTTTTCTAAAGAAAATCACTA-CTTCCTTAAAAATCAAAGCTTTTATTTTAAAATAGTTAAAA
1 TCTTTTT-TAAACAAAATCACTATCTTCCTTAAAAATCAAAGCTTTTAATTCAAAATAGTTAAAA
* *
21763425 AATCAAAATTTTGTTTAAAAAATTTAAACA-TTTTCCTTTAAAATGACTAAAAAAAATTTTATTT
65 AAT-AAAA-TTAGTTTAAAAAATTTAAA-ATTTTTCCTTTAAAATGAATAAAAAAAA-TTTATTT
21763489 TTAAAAATCTAAACTG
126 TTAAAAATCTAAACTG
*
21763505 TTTTTTTTAAA
1 TCTTTTTTAAA
21763516 ATCACTTATT
Statistics
Matches: 138, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
141 45 0.33
142 18 0.13
143 46 0.33
144 29 0.21
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (141 bp):
TCTTTTTTAAACAAAATCACTATCTTCCTTAAAAATCAAAGCTTTTAATTCAAAATAGTTAAAAA
ATAAAATTAGTTTAAAAAATTTAAAATTTTTCCTTTAAAATGAATAAAAAAAATTTATTTTTAAA
AATCTAAACTG
Found at i:21764540 original size:75 final size:75
Alignment explanation
Indices: 21764447--21764605 Score: 230
Period size: 75 Copynumber: 2.1 Consensus size: 75
21764437 CATATTAATA
* * * * *
21764447 AAAAGAAAATTAGGATTATTCCCTTATTAATAGAGAAGGCAAATAGAAAGTTCGAAAAATGAATT
1 AAAAGAATATTAGGATTATTCCCTAATTAATAGAGAAGACAAATAGAAAGTTAGAAAAAGGAATT
21764512 ATATTCTTTCC
66 ATATT-TTTCC
* *
21764523 AAAAGAATA-TAGGATTATTCTCTAATTAATAGAGAAGACAAATGGAAAGTTAGAAAAAGGAATT
1 AAAAGAATATTAGGATTATTCCCTAATTAATAGAGAAGACAAATAGAAAGTTAGAAAAAGGAATT
*
21764587 ATATTTTTTC
66 ATATTTTTCC
21764597 AAAAGAATA
1 AAAAGAATA
21764606 ATAATTTCCA
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
74 13 0.17
75 54 0.72
76 8 0.11
ACGTcount: A:0.48, C:0.08, G:0.15, T:0.30
Consensus pattern (75 bp):
AAAAGAATATTAGGATTATTCCCTAATTAATAGAGAAGACAAATAGAAAGTTAGAAAAAGGAATT
ATATTTTTCC
Found at i:21771865 original size:52 final size:52
Alignment explanation
Indices: 21771783--21772072 Score: 431
Period size: 52 Copynumber: 5.6 Consensus size: 52
21771773 CATGAAAAAT
21771783 GTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAG
1 GTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAG
* *
21771835 GTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATGAG
1 GTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAG
* **
21771887 GTCCGATAACTATGTGTCATCGTGAGTATATGAATCCTTTAAAGATTATGAG
1 GTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAG
*
21771939 GTCCGATGACTATGTGTCATCGTGAGTATTTGAATCCTTTACGGATTATGAG
1 GTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAG
* * * *
21771991 GTCTGATGACTATGTGTCATCGTGAGTATAT-AATTCCTAATACAGATTA-AAG
1 GTCCGATGACTATGTGTCATCGTGAGTATATGAA-TCCT-TTACGGATTATGAG
* * *
21772043 GTCCGATGACTCTGTGTTATCATGAGTATA
1 GTCCGATGACTATGTGTCATCGTGAGTATA
21772073 AAAAATGCAT
Statistics
Matches: 217, Mismatches: 19, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
51 2 0.01
52 207 0.95
53 8 0.04
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (52 bp):
GTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAG
Found at i:21782285 original size:27 final size:27
Alignment explanation
Indices: 21782238--21782290 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
21782228 GGAAAAACTT
*
21782238 GAGGAAGAGAAAGGAACTGAATAGGAG
1 GAGGAAGAGAAAGGAACTGAAGAGGAG
21782265 GAGGAAGAGGAGAAGG-A-TGAAGAGGA
1 GAGGAAGA-GA-AAGGAACTGAAGAGGA
21782291 TGTAGATGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 16 0.70
28 3 0.13
29 4 0.17
ACGTcount: A:0.47, C:0.02, G:0.45, T:0.06
Consensus pattern (27 bp):
GAGGAAGAGAAAGGAACTGAAGAGGAG
Found at i:21782711 original size:17 final size:17
Alignment explanation
Indices: 21782685--21782729 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
21782675 GCATGCATTT
21782685 ATTTTAATTGTCAT-TGC
1 ATTTTAATTGTC-TCTGC
*
21782702 ATTTTTATTGTCTCTGC
1 ATTTTAATTGTCTCTGC
*
21782719 ATTTTATTTGT
1 ATTTTAATTGT
21782730 TTAGCATTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 1 0.04
17 23 0.96
ACGTcount: A:0.18, C:0.11, G:0.11, T:0.60
Consensus pattern (17 bp):
ATTTTAATTGTCTCTGC
Found at i:21783333 original size:16 final size:16
Alignment explanation
Indices: 21783306--21783348 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
21783296 GTCACATAAG
*
21783306 AAAAAGAGAAAAA-TA
1 AAAAAAAGAAAAATTA
21783321 AAAAGAAAGAAAAATTA
1 AAAA-AAAGAAAAATTA
*
21783338 ACAAAAAGAAA
1 AAAAAAAGAAA
21783349 GAAGAAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 4 0.17
16 15 0.62
17 5 0.21
ACGTcount: A:0.79, C:0.02, G:0.12, T:0.07
Consensus pattern (16 bp):
AAAAAAAGAAAAATTA
Found at i:21785281 original size:83 final size:84
Alignment explanation
Indices: 21785141--21785308 Score: 329
Period size: 83 Copynumber: 2.0 Consensus size: 84
21785131 ATTTACAGGC
21785141 CGATGCCTGACTTAAAAAAAGATGAAACTAATGAGGTAAACAGCAATGTTCTGACTAATGACTCT
1 CGATGCCTGACTTAAAAAAAGATGAAACTAATGAGGTAAACAGCAATGTTCTGACTAATGACTCT
21785206 AGGGCTAGTCACAGTGCAT
66 AGGGCTAGTCACAGTGCAT
21785225 CGATGCCTGACTT-AAAAAAGATGAAACTAATGAGGTAAACAGCAATGTTCTGACTAATGACTCT
1 CGATGCCTGACTTAAAAAAAGATGAAACTAATGAGGTAAACAGCAATGTTCTGACTAATGACTCT
21785289 AGGGCTAGTCACAGTGCAT
66 AGGGCTAGTCACAGTGCAT
21785308 C
1 C
21785309 AATATTACCA
Statistics
Matches: 84, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
83 71 0.85
84 13 0.15
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.24
Consensus pattern (84 bp):
CGATGCCTGACTTAAAAAAAGATGAAACTAATGAGGTAAACAGCAATGTTCTGACTAATGACTCT
AGGGCTAGTCACAGTGCAT
Found at i:21791161 original size:52 final size:52
Alignment explanation
Indices: 21791083--21791325 Score: 360
Period size: 52 Copynumber: 4.6 Consensus size: 52
21791073 TAAATTAAAA
* * *
21791083 AGGTCCGATAACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATG
* * *
21791135 AGGTCCAATTACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATA
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATG
* *
21791187 AGATCCGATGACTATGTGTCATCCTGAGAGTATATGAATCCTTTACGAATTATG
1 AGGTCCGATGACTATGTGTCAT-C-GTGAGTATATGAATCCTTTACGAATTATG
* *
21791241 AGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATG
* *
21791293 AGGTCTGATGACTATGTGTCATTGTGAGTATAT
1 AGGTCCGATGACTATGTGTCATCGTGAGTATAT
21791326 AATTCCCAAT
Statistics
Matches: 172, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
52 123 0.72
53 2 0.01
54 47 0.27
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (52 bp):
AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATG
Found at i:21791269 original size:106 final size:104
Alignment explanation
Indices: 21791086--21791325 Score: 345
Period size: 106 Copynumber: 2.3 Consensus size: 104
21791076 ATTAAAAAGG
* * * * *
21791086 TCCGATAACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATGAGGTCCAATTACTATG
1 TCCGATGACTATGTGTCATCGAGAGTATATGAATCCTTTACGAATTATGAGGTCCAATGACTATG
21791151 TGTCATCGTGAGTATATGAATCCTTTACGAATTATAAGA
66 TGTCATCGTGAGTATATGAATCCTTTACGAATTATAAGA
* *
21791190 TCCGATGACTATGTGTCATCCTGAGAGTATATGAATCCTTTACGAATTATGAGGTTCGATGACTA
1 TCCGATGACTATGTGTCAT-C-GAGAGTATATGAATCCTTTACGAATTATGAGGTCCAATGACTA
* * *
21791255 TGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGG
64 TGTGTCATCGTGAGTATATGAATCCTTTACGAATTATAAGA
* * *
21791296 TCTGATGACTATGTGTCATTGTGAGTATAT
1 TCCGATGACTATGTGTCATCGAGAGTATAT
21791326 AATTCCCAAT
Statistics
Matches: 121, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
104 27 0.22
105 1 0.01
106 93 0.77
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.37
Consensus pattern (104 bp):
TCCGATGACTATGTGTCATCGAGAGTATATGAATCCTTTACGAATTATGAGGTCCAATGACTATG
TGTCATCGTGAGTATATGAATCCTTTACGAATTATAAGA
Found at i:21791349 original size:52 final size:52
Alignment explanation
Indices: 21791082--21791373 Score: 356
Period size: 52 Copynumber: 5.6 Consensus size: 52
21791072 GTAAATTAAA
* *
21791082 AAGGTCCGATAACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* * * *
21791134 GAGGTCCAATTACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* * *
21791186 AAGATCCGATGACTATGTGTCATCCTGAGAGTATATGAATCCTTTACGAATTAT
1 AAGGTCCGATGACTATGTGTCAT-C-GTGAGTATATGAATCCTTTACGGATTAT
* *
21791240 GAGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* * * **
21791292 GAGGTCTGATGACTATGTGTCATTGTGAGTATAT-AATTCCCAATACGGATTA-
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAA-T-CCTTTACGGATTAT
* * *
21791344 AAGGTCCGATGTCTCTGTGT-GTCGTGAGTA
1 AAGGTCCGATGACTATGTGTCATCGTGAGTA
21791374 AAAAAATGCA
Statistics
Matches: 210, Mismatches: 26, Indels: 9
0.86 0.11 0.04
Matches are distributed among these distances:
51 10 0.05
52 140 0.67
53 13 0.06
54 47 0.22
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (52 bp):
AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
Found at i:21791365 original size:106 final size:105
Alignment explanation
Indices: 21791086--21791373 Score: 316
Period size: 106 Copynumber: 2.8 Consensus size: 105
21791076 ATTAAAAAGG
* * ** * * * * *
21791086 TCCGATAACTATGTGTCATC-GTGAGTATATGAATCCTTTATGGATTATGAGGTCCAATTACTAT
1 TCCGATGACTATGTGTCATCTGAGAGTATATGAATCCAATACGAATTATAAGGTCCGATGACTAT
21791150 GTGTCATCGTGAGTATATGAATCCTTTACGAATTATAAGA
66 GTGTCATCGTGAGTATATGAATCCTTTACGAATTATAAGA
** * *
21791190 TCCGATGACTATGTGTCATCCTGAGAGTATATGAATCCTTTACGAATTATGAGGTTCGATGACTA
1 TCCGATGACTATGTGTCAT-CTGAGAGTATATGAATCCAATACGAATTATAAGGTCCGATGACTA
* * *
21791255 TGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGG
65 TGTGTCATCGTGAGTATATGAATCCTTTACGAATTATAAGA
* * * *
21791296 TCTGATGACTATGTGTCAT-TGTGAGTATAT-AATTCCCAATACGGATTA-AAGGTCCGATGTCT
1 TCCGATGACTATGTGTCATCTGAGAGTATATGAA-T-CCAATACGAATTATAAGGTCCGATGACT
* *
21791358 CTGTGT-GTCGTGAGTA
64 ATGTGTCATCGTGAGTA
21791374 AAAAAATGCA
Statistics
Matches: 160, Mismatches: 20, Indels: 9
0.85 0.11 0.05
Matches are distributed among these distances:
103 11 0.07
104 45 0.28
105 11 0.07
106 93 0.58
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.36
Consensus pattern (105 bp):
TCCGATGACTATGTGTCATCTGAGAGTATATGAATCCAATACGAATTATAAGGTCCGATGACTAT
GTGTCATCGTGAGTATATGAATCCTTTACGAATTATAAGA
Found at i:21795505 original size:6 final size:6
Alignment explanation
Indices: 21795494--21795531 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
21795484 AGGCAACCCA
21795494 ATTTTT ATTTTT ATTTTT ATTTATT -TTATTT ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTT-TT ATT-TTT ATTTTT A
21795532 GTTTAGTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
6 24 0.83
7 5 0.17
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (6 bp):
ATTTTT
Found at i:21795553 original size:25 final size:25
Alignment explanation
Indices: 21795497--21795554 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
21795487 CAACCCAATT
*
21795497 TTTATTTTTATTTTTATTTATTTTA
1 TTTATTTTTATGTTTATTTATTTTA
*
21795522 TTTATTTTTA-GTTTAGTTT-TTTTC
1 TTTATTTTTATGTTTA-TTTATTTTA
21795546 TTTCATTTT
1 TTT-ATTTT
21795555 AATAAATTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 11 0.38
25 18 0.62
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.78
Consensus pattern (25 bp):
TTTATTTTTATGTTTATTTATTTTA
Found at i:21797096 original size:11 final size:11
Alignment explanation
Indices: 21797082--21797112 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
21797072 AGGATATTGT
21797082 TTATATTTAAA
1 TTATATTTAAA
*
21797093 TTATATTTAAT
1 TTATATTTAAA
21797104 TTATATTTA
1 TTATATTTA
21797113 TCTTTTAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTATATTTAAA
Found at i:21801283 original size:3 final size:3
Alignment explanation
Indices: 21801275--21801308 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
21801265 GAAGATTCCA
21801275 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
21801309 GAGATGGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:21808482 original size:31 final size:31
Alignment explanation
Indices: 21808447--21808536 Score: 110
Period size: 31 Copynumber: 2.9 Consensus size: 31
21808437 TCGACATATT
*
21808447 TGTTATTAGTGGTAGTTTAT-TTGCAAATAAA
1 TGTTATTAGTGGCAGTTTATCTT-CAAATAAA
* *
21808478 TGTTATTAATTGCAGTTTATCTTCAAATAAA
1 TGTTATTAGTGGCAGTTTATCTTCAAATAAA
* * *
21808509 TGTTGTCAGTGGCAGTTTATCTACAAAT
1 TGTTATTAGTGGCAGTTTATCTTCAAAT
21808537 CAGTGGTGGC
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
31 48 0.96
32 2 0.04
ACGTcount: A:0.31, C:0.09, G:0.17, T:0.43
Consensus pattern (31 bp):
TGTTATTAGTGGCAGTTTATCTTCAAATAAA
Found at i:21810056 original size:38 final size:37
Alignment explanation
Indices: 21810006--21810103 Score: 115
Period size: 38 Copynumber: 2.5 Consensus size: 37
21809996 AAATAAATAT
*
21810006 CCCGATGAACACCAGCACGATGGCCTACTAGGCATAAAA
1 CCCGAT-AACACC-GCACGAAGGCCTACTAGGCATAAAA
* * *
21810045 CCCGATAACACCGACACGAAGGCTTGCTAGGCATAAAG
1 CCCGATAACACCG-CACGAAGGCCTACTAGGCATAAAA
*
21810083 CCCAATAACACCGGCACGAAG
1 CCCGATAACACC-GCACGAAG
21810104 AACTGCTAGG
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
37 1 0.02
38 44 0.85
39 7 0.13
ACGTcount: A:0.36, C:0.32, G:0.21, T:0.11
Consensus pattern (37 bp):
CCCGATAACACCGCACGAAGGCCTACTAGGCATAAAA
Found at i:21810111 original size:38 final size:38
Alignment explanation
Indices: 21810033--21810127 Score: 120
Period size: 38 Copynumber: 2.5 Consensus size: 38
21810023 CGATGGCCTA
* * *
21810033 CTAGGCATAAAACCCGATAACACCGACACGAAGGCTTG
1 CTAGGCATAAAGCCCAATAACACCGACACGAAGACTTG
*
21810071 CTAGGCATAAAGCCCAATAACACCGGCACGAAGAAC-TG
1 CTAGGCATAAAGCCCAATAACACCGACACGAAG-ACTTG
* *
21810109 CTAGGCATGAAGCCTAATA
1 CTAGGCATAAAGCCCAATA
21810128 TACCAGCACA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
38 49 0.98
39 1 0.02
ACGTcount: A:0.38, C:0.27, G:0.21, T:0.14
Consensus pattern (38 bp):
CTAGGCATAAAGCCCAATAACACCGACACGAAGACTTG
Found at i:21810219 original size:37 final size:37
Alignment explanation
Indices: 21810169--21810277 Score: 146
Period size: 37 Copynumber: 2.9 Consensus size: 37
21810159 TCGATACATC
* * *
21810169 GGCATGAAGGCCTGCTAGGCGCATAACTCAATTACACT
1 GGCACGAA-GCCTGCTAGGCACATAACCCAATTACACT
*
21810207 GGCACGAAGCCTGCTAGGCACATAGCCCAATTACACT
1 GGCACGAAGCCTGCTAGGCACATAACCCAATTACACT
* * *
21810244 GGCACGAAGCCTGTTAGGCACATACCCCGATTAC
1 GGCACGAAGCCTGCTAGGCACATAACCCAATTAC
21810278 TTAAATGCAA
Statistics
Matches: 64, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
37 57 0.89
38 7 0.11
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.18
Consensus pattern (37 bp):
GGCACGAAGCCTGCTAGGCACATAACCCAATTACACT
Found at i:21814081 original size:21 final size:20
Alignment explanation
Indices: 21814053--21814091 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
21814043 TCGATAGTAC
*
21814053 CCATACTTGTATTGGTAGAA
1 CCATACTTGTATCGGTAGAA
*
21814073 CCATCACTTTTATCGGTAG
1 CCAT-ACTTGTATCGGTAG
21814092 GAAATTGTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.36
Consensus pattern (20 bp):
CCATACTTGTATCGGTAGAA
Found at i:21825964 original size:21 final size:21
Alignment explanation
Indices: 21825939--21825980 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
21825929 CCTAAATTAT
21825939 CTCCAAATCCCTAATTGACAG
1 CTCCAAATCCCTAATTGACAG
* *
21825960 CTCCAAATCTCTTATTGACAG
1 CTCCAAATCCCTAATTGACAG
21825981 ATTATATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.31, G:0.10, T:0.29
Consensus pattern (21 bp):
CTCCAAATCCCTAATTGACAG
Found at i:21830320 original size:20 final size:22
Alignment explanation
Indices: 21830279--21830324 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
21830269 ATTCTCTTAT
*
21830279 AAAAAATTATAAAATTATGTTA
1 AAAAAATTATAAAACTATGTTA
21830301 AAAAAATTAT-AAACTA-GTTA
1 AAAAAATTATAAAACTATGTTA
21830321 AAAA
1 AAAA
21830325 CTTTTATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.35
21 5 0.22
22 10 0.43
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.30
Consensus pattern (22 bp):
AAAAAATTATAAAACTATGTTA
Found at i:21840183 original size:21 final size:21
Alignment explanation
Indices: 21840159--21840198 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
21840149 TGTGTAAAGA
21840159 GGATTGGAGCCCTATATGTCT
1 GGATTGGAGCCCTATATGTCT
21840180 GGATTGGAGCCCTATATGT
1 GGATTGGAGCCCTATATGT
21840199 ATTTCTCGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.17, G:0.30, T:0.33
Consensus pattern (21 bp):
GGATTGGAGCCCTATATGTCT
Found at i:21844634 original size:8 final size:8
Alignment explanation
Indices: 21844621--21844653 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
21844611 AAATAGCGGA
21844621 AGAAATTG
1 AGAAATTG
21844629 AGAAATTG
1 AGAAATTG
21844637 AGAAATTG
1 AGAAATTG
21844645 AGAAATTG
1 AGAAATTG
21844653 A
1 A
21844654 ACACACAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (8 bp):
AGAAATTG
Found at i:21847750 original size:22 final size:22
Alignment explanation
Indices: 21847724--21847766 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
21847714 CAAATGAACC
*
21847724 TAAATTTTAAA-ATTATGAAGAT
1 TAAATTCTAAACA-TATGAAGAT
21847746 TAAATTCTAAACATATGAAGA
1 TAAATTCTAAACATATGAAGA
21847767 ATACAAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.51, C:0.05, G:0.09, T:0.35
Consensus pattern (22 bp):
TAAATTCTAAACATATGAAGAT
Found at i:21848139 original size:18 final size:18
Alignment explanation
Indices: 21848116--21848154 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
21848106 AAAAATATTA
21848116 TTTTTGCATATTAATA-AT
1 TTTTTG-ATATTAATATAT
*
21848134 TTTTTGGTATTAATATAT
1 TTTTTGATATTAATATAT
21848152 TTT
1 TTT
21848155 GTCCCAAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.28, C:0.03, G:0.08, T:0.62
Consensus pattern (18 bp):
TTTTTGATATTAATATAT
Found at i:21850536 original size:75 final size:75
Alignment explanation
Indices: 21850404--21850554 Score: 239
Period size: 75 Copynumber: 2.0 Consensus size: 75
21850394 TTTTTTGGGG
* * *
21850404 AGGCATCAATTGAGGGATCGGGTCATGTGGCTGATATTCTAAGGGAGTATGAACTCTGTTCTGGT
1 AGGCATCAATTGAGGGATCGGGTCACGTGGCTGATATTCTAAGGGAGAATGAACTCTGTTCTAGT
21850469 TAGAAGATTA
66 TAGAAGATTA
* * * *
21850479 AGGCATTAGTTGAGGGATTGGGTCACGTGGCTGATATTCTAAGGGAGAATGAGCTCTGTTCTAGT
1 AGGCATCAATTGAGGGATCGGGTCACGTGGCTGATATTCTAAGGGAGAATGAACTCTGTTCTAGT
21850544 TAGAAGATTA
66 TAGAAGATTA
21850554 A
1 A
21850555 CTTTGCGACG
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 69 1.00
ACGTcount: A:0.27, C:0.11, G:0.31, T:0.30
Consensus pattern (75 bp):
AGGCATCAATTGAGGGATCGGGTCACGTGGCTGATATTCTAAGGGAGAATGAACTCTGTTCTAGT
TAGAAGATTA
Found at i:21854607 original size:20 final size:20
Alignment explanation
Indices: 21854563--21854608 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
21854553 CTGTTCAAAA
*
21854563 AATAATATTATTTTAATAGTT
1 AATAATATTAATTTAATA-TT
21854584 -ATAATATTAAATTTAAT-TT
1 AATAATATT-AATTTAATATT
21854603 AATAAT
1 AATAAT
21854609 TATCTTGTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 2 0.09
20 13 0.59
21 7 0.32
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
AATAATATTAATTTAATATT
Found at i:21861391 original size:9 final size:9
Alignment explanation
Indices: 21861377--21861422 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
21861367 GAATATGAAT
21861377 ATATAAAAA
1 ATATAAAAA
21861386 ATATAAAAA
1 ATATAAAAA
*
21861395 ATGAT--AGA
1 AT-ATAAAAA
21861403 ATATAAAAA
1 ATATAAAAA
21861412 ATA-AAAAA
1 ATATAAAAA
21861420 ATA
1 ATA
21861423 ATAAGAGGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
7 2 0.06
8 12 0.38
9 16 0.50
10 2 0.06
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (9 bp):
ATATAAAAA
Done.