Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold133
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: 2564099
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 17052 characters in sequence are not A, C, G, or T
File 15 of 17
Found at i:2076326 original size:10 final size:11
Alignment explanation
Indices: 2076305--2076345 Score: 50
Period size: 10 Copynumber: 3.9 Consensus size: 11
2076295 CCCTAACAAT
2076305 TTTTCATCAAA
1 TTTTCATCAAA
2076316 TTTTC-TCAAA
1 TTTTCATCAAA
*
2076326 TTTTC-TTAAA
1 TTTTCATCAAA
*
2076336 ATTTCATCAA
1 TTTTCATCAA
2076346 TTCTACATCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
10 18 0.69
11 8 0.31
ACGTcount: A:0.34, C:0.17, G:0.00, T:0.49
Consensus pattern (11 bp):
TTTTCATCAAA
Found at i:2077755 original size:33 final size:33
Alignment explanation
Indices: 2077689--2077755 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
2077679 CGAGAGTTGA
* *
2077689 TCACTTCACTTTCGCAGCACATGAGTGAGCACT
1 TCACTTCACTCTCGCAGCACATGAGTGAACACT
* *
2077722 TCACTTCACTCTCGTAGCGCATTGA-TGAACACT
1 TCACTTCACTCTCGCAGCACA-TGAGTGAACACT
2077755 T
1 T
2077756 TAGTGCACTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 26 0.90
34 3 0.10
ACGTcount: A:0.24, C:0.30, G:0.16, T:0.30
Consensus pattern (33 bp):
TCACTTCACTCTCGCAGCACATGAGTGAACACT
Found at i:2082679 original size:20 final size:21
Alignment explanation
Indices: 2082654--2082704 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 21
2082644 CAAGGTCTAG
2082654 TATCGATACATTCACTT-ATA
1 TATCGATACATTCACTTGATA
* *
2082674 TATCGATACATTCACTTGTTG
1 TATCGATACATTCACTTGATA
2082695 TATCGATACA
1 TATCGATACA
2082705 AATTGTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (21 bp):
TATCGATACATTCACTTGATA
Found at i:2090696 original size:2 final size:2
Alignment explanation
Indices: 2090689--2090753 Score: 94
Period size: 2 Copynumber: 32.5 Consensus size: 2
2090679 ATAATCTAAG
* * *
2090689 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT GT CT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2090731 AT AT AT CT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
2090754 AATTAATCAA
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2091028 original size:22 final size:23
Alignment explanation
Indices: 2090990--2091037 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
2090980 TTATTAATAA
*
2090990 TAAAAATATTAATAATAGTAATT
1 TAAAAATATTAATAATAATAATT
*
2091013 TAAAAAATAATAAATAATAATAATT
1 T-AAAAAT-ATTAATAATAATAATT
2091038 ATTTTTACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 6 0.29
25 14 0.67
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (23 bp):
TAAAAATATTAATAATAATAATT
Found at i:2091084 original size:2 final size:2
Alignment explanation
Indices: 2091077--2091142 Score: 71
Period size: 2 Copynumber: 33.0 Consensus size: 2
2091067 TTTGTACTTT
* *
2091077 TA TA TA TA TA TA TA TA TA TCA TA AA TA TA TA TA TA TA TA TG TA
1 TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA
* * *
2091120 TA TG T- TA TG CA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
2091143 ATCATTTAAG
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
1 1 0.02
2 50 0.94
3 2 0.04
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2094351 original size:17 final size:17
Alignment explanation
Indices: 2094329--2094393 Score: 62
Period size: 17 Copynumber: 3.8 Consensus size: 17
2094319 TCTTCCGTCA
2094329 AAATAAAT-TTATTTAAT
1 AAATAAATATT-TTTAAT
2094346 AAATAAATATTTTTAAT
1 AAATAAATATTTTTAAT
* *
2094363 AAA-AAATAAATTTTGAT
1 AAATAAAT-ATTTTTAAT
* *
2094380 GAATAAAAATTTTT
1 AAATAAATATTTTT
2094394 GATGATTAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
16 4 0.10
17 31 0.77
18 5 0.12
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATAAATATTTTTAAT
Found at i:2094656 original size:18 final size:17
Alignment explanation
Indices: 2094621--2094654 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
2094611 TTTATGAAAT
2094621 ATTTTATATATTTTATA
1 ATTTTATATATTTTATA
2094638 ATTTT-TATA-TTTATA
1 ATTTTATATATTTTATA
2094653 AT
1 AT
2094655 AAATATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 4 0.24
17 5 0.29
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTTTATATATTTTATA
Found at i:2095660 original size:2 final size:2
Alignment explanation
Indices: 2095653--2095685 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2095643 AATGTTGCAT
2095653 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2095686 GTTTCGGCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2096883 original size:16 final size:16
Alignment explanation
Indices: 2096862--2096914 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
2096852 CACACCCAAA
2096862 TAAAAAATAATTTAAT
1 TAAAAAATAATTTAAT
2096878 TAAAAATATATATTT--T
1 TAAAAA-ATA-ATTTAAT
* *
2096894 TAAAAAATTATTTAAA
1 TAAAAAATAATTTAAT
2096910 TAAAA
1 TAAAA
2096915 TTTAACGTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
14 4 0.13
15 2 0.06
16 18 0.58
17 3 0.10
18 4 0.13
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TAAAAAATAATTTAAT
Found at i:2097367 original size:18 final size:19
Alignment explanation
Indices: 2097314--2097367 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 19
2097304 TATTATTATA
2097314 AAAATATATTATAAAAA-ATT
1 AAAATATA--ATAAAAATATT
*
2097334 AAAATATAAAAAAAATATT
1 AAAATATAATAAAAATATT
*
2097353 TAAA-ATAATAAAAAT
1 AAAATATAATAAAAAT
2097368 TTAGAGATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 16 0.53
19 6 0.20
20 8 0.27
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAATATAATAAAAATATT
Found at i:2099154 original size:25 final size:24
Alignment explanation
Indices: 2099119--2099197 Score: 67
Period size: 24 Copynumber: 3.4 Consensus size: 24
2099109 TTATTTAATA
2099119 ATTT-TAATAATTTTTATTTTTAT
1 ATTTATAATAATTTTTATTTTTAT
* *
2099142 ATTTATAATTAATATTTA-TTATA-
1 ATTTATAA-TAATTTTTATTTTTAT
* **
2099165 ATTAATAATAA-TAATATTTATTAT
1 ATTTATAATAATTTTTATTT-TTAT
2099189 ATTTATAAT
1 ATTTATAAT
2099198 TATAATAAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
21 2 0.05
22 5 0.12
23 13 0.30
24 15 0.35
25 8 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
ATTTATAATAATTTTTATTTTTAT
Found at i:2099172 original size:53 final size:51
Alignment explanation
Indices: 2099106--2099209 Score: 129
Period size: 53 Copynumber: 2.0 Consensus size: 51
2099096 AATCCTAGGA
** * * *
2099106 TTATTATTTAATAATTTTAATAATTT-TTATTTTTATATTTATAATTAATAT
1 TTATTATTTAATAATAATAAT-ATTTATTATATTTATAATTATAATAAATAT
2099157 TTATTATAATTAATAATAATAATATTTATTATATTTATAATTATAATAAATAT
1 TTATTAT--TTAATAATAATAATATTTATTATATTTATAATTATAATAAATAT
2099210 GACATTATAA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
51 7 0.16
52 4 0.09
53 34 0.76
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (51 bp):
TTATTATTTAATAATAATAATATTTATTATATTTATAATTATAATAAATAT
Found at i:2104411 original size:29 final size:29
Alignment explanation
Indices: 2104285--2104419 Score: 80
Period size: 29 Copynumber: 4.7 Consensus size: 29
2104275 AATGTTATCC
* * *
2104285 CATGCATTTTTGAAGATTACTATATAATTT
1 CATGCATTTTAG-AGATTATTATGTAATTT
* ** * *
2104315 CATGCATCTTAGTTATTATTATGCAGTTT
1 CATGCATTTTAGAGATTATTATGTAATTT
* * *
2104344 CATGCATTTTAAAG-TTATTTTGGTTATTT
1 CATGCATTTTAGAGATTATTAT-GTAATTT
* *
2104373 --TTCATGTTTAGGGATTATTATGTAATTT
1 CATGCAT-TTTAGAGATTATTATGTAATTT
* *
2104401 TATGCATTTTA-ATATTATT
1 CATGCATTTTAGAGATTATT
2104420 TTACTCAATT
Statistics
Matches: 76, Mismatches: 24, Indels: 12
0.68 0.21 0.11
Matches are distributed among these distances:
27 4 0.05
28 23 0.30
29 35 0.46
30 14 0.18
ACGTcount: A:0.27, C:0.08, G:0.13, T:0.52
Consensus pattern (29 bp):
CATGCATTTTAGAGATTATTATGTAATTT
Found at i:2104546 original size:58 final size:58
Alignment explanation
Indices: 2104484--2104615 Score: 140
Period size: 58 Copynumber: 2.3 Consensus size: 58
2104474 CATTTAAATC
* * *
2104484 ATTTTCCATAACTTCGAGATTTTTATATAATTTCATGCATTTTAATGGT-ATTTTAGTA
1 ATTTTCCATAACTTAGAGACTTTTATATAATTTCATGCACTTTAAT-GTCATTTTAGTA
* * * ** *
2104542 ATTTTTCATGACTTAGAGACTTTTATGTCGTTTTATGCACTTTAATGTCATTTTAGTA
1 ATTTTCCATAACTTAGAGACTTTTATATAATTTCATGCACTTTAATGTCATTTTAGTA
* * *
2104600 AGTTCCCATGACTTAG
1 ATTTTCCATAACTTAG
2104616 GATCATTTTA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
57 2 0.03
58 59 0.97
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.48
Consensus pattern (58 bp):
ATTTTCCATAACTTAGAGACTTTTATATAATTTCATGCACTTTAATGTCATTTTAGTA
Found at i:2104721 original size:58 final size:59
Alignment explanation
Indices: 2104621--2104761 Score: 140
Period size: 58 Copynumber: 2.4 Consensus size: 59
2104611 CTTAGGATCA
* * * *** *
2104621 TTTTATGCATTTTTATGTATTTTAGGGTTATTCTAGTAATTTTTCATATTT-TAGAGGC
1 TTTTATGCAATTTCATGCATTTTAGGACCATTCTAGTAATTTTTCATATTTAAAGAGGC
* * * * *
2104679 TTTTATGCAATTTCATGCATTTTAGGACCATTTTAGTCATTTTTTATGTTTAAAAGGGGC
1 TTTTATGCAATTTCATGCATTTTAGGACCATTCTAGTAATTTTTCATATTT-AAAGAGGC
* *
2104739 TATTATGCAATTTCTTGCATTTT
1 TTTTATGCAATTTCATGCATTTT
2104762 TAGCCTATTT
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
58 41 0.61
60 26 0.39
ACGTcount: A:0.23, C:0.10, G:0.15, T:0.52
Consensus pattern (59 bp):
TTTTATGCAATTTCATGCATTTTAGGACCATTCTAGTAATTTTTCATATTTAAAGAGGC
Found at i:2104834 original size:57 final size:57
Alignment explanation
Indices: 2104773--2104905 Score: 187
Period size: 58 Copynumber: 2.3 Consensus size: 57
2104763 AGCCTATTTA
* *
2104773 GGTCATTTAGGTCATTTTCATGGTC-AAGGGATTTTTATGTAATTTTATGTATGTTGG
1 GGTCATTTAGGTCATTTTCATGGTCTAAGGGA-TTTTATGTAATTTGATATATGTTGG
* * *
2104830 GGTCATTTAGGTCATATTCCATGTTCTTAGGGATTTTATGTAATTTGATATATGTTGG
1 GGTCATTTAGGTCAT-TTTCATGGTCTAAGGGATTTTATGTAATTTGATATATGTTGG
*
2104888 GGTCATTTAGGTTATTTT
1 GGTCATTTAGGTCATTTT
2104906 TTGTGATCTA
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
57 17 0.25
58 45 0.67
59 5 0.07
ACGTcount: A:0.21, C:0.08, G:0.23, T:0.48
Consensus pattern (57 bp):
GGTCATTTAGGTCATTTTCATGGTCTAAGGGATTTTATGTAATTTGATATATGTTGG
Found at i:2105456 original size:29 final size:27
Alignment explanation
Indices: 2105414--2105490 Score: 86
Period size: 27 Copynumber: 2.8 Consensus size: 27
2105404 CTTTGAATTA
*
2105414 AAAAAAT-AACATTAATTTTAAATATC
1 AAAAAATGAAAATTAATTTTAAATATC
*
2105440 ACAAAATATGAAAATT-ATAATTAAATATC
1 A-AAAA-ATGAAAATTAAT-TTTAAATATC
*
2105469 AAAAAATTAAAATTAATTTTAA
1 AAAAAATGAAAATTAATTTTAA
2105491 TCGAGATTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
26 1 0.02
27 16 0.38
28 10 0.24
29 15 0.36
ACGTcount: A:0.60, C:0.05, G:0.01, T:0.34
Consensus pattern (27 bp):
AAAAAATGAAAATTAATTTTAAATATC
Found at i:2111806 original size:2 final size:2
Alignment explanation
Indices: 2111799--2111831 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2111789 GCAAAAAGGA
2111799 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2111832 ATACATTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2112382 original size:2 final size:2
Alignment explanation
Indices: 2112375--2112416 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
2112365 TGCTTGATAC
*
2112375 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2112417 CTTCACAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2113397 original size:19 final size:20
Alignment explanation
Indices: 2113369--2113410 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
2113359 AATTAAGATG
2113369 TATTTAATTATTATAT-ATT
1 TATTTAATTATTATATAATT
* *
2113388 TATTTTATTATTTTATAATT
1 TATTTAATTATTATATAATT
2113408 TAT
1 TAT
2113411 ATTTGAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TATTTAATTATTATATAATT
Found at i:2113750 original size:3 final size:3
Alignment explanation
Indices: 2113737--2113783 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
2113727 TGAATTTTTA
2113737 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2113784 AAAATACATA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2138225 original size:2 final size:2
Alignment explanation
Indices: 2138218--2138271 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
2138208 GTTCCTTTAC
2138218 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2138260 AT AT AT AT AT AT
1 AT AT AT AT AT AT
2138272 CAACCTTCCC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2138368 original size:11 final size:10
Alignment explanation
Indices: 2138352--2138406 Score: 58
Period size: 11 Copynumber: 5.3 Consensus size: 10
2138342 AGGGTGATTG
2138352 AAAAGAAGGAA
1 AAAAGAA-GAA
2138363 AAAAGAAAGAA
1 AAAAG-AAGAA
*
2138374 AAGAGAAGAA
1 AAAAGAAGAA
*
2138384 AAGAGAAG-A
1 AAAAGAAGAA
2138393 AAAAGAGAGAA
1 AAAAGA-AGAA
2138404 AAA
1 AAA
2138407 GAACAGCATA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
9 6 0.15
10 15 0.38
11 16 0.41
12 2 0.05
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (10 bp):
AAAAGAAGAA
Found at i:2138375 original size:10 final size:10
Alignment explanation
Indices: 2138352--2138409 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
2138342 AGGGTGATTG
*
2138352 AAAAGAAGGAA
1 AAAAGAAAG-A
2138363 AAAAGAAAG-
1 AAAAGAAAGA
2138372 AAAAGAGAAG-
1 AAAAGA-AAGA
2138382 AAAAGAGAAGA
1 AAAAGA-AAGA
*
2138393 AAAAGAGAGA
1 AAAAGAAAGA
2138403 AAAAGAA
1 AAAAGAA
2138410 CAGCATACAT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
9 6 0.14
10 22 0.52
11 14 0.33
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (10 bp):
AAAAGAAAGA
Found at i:2138376 original size:20 final size:20
Alignment explanation
Indices: 2138363--2138409 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
2138353 AAAGAAGGAA
2138363 AAAAGA-AAGAAAAGAGAAG
1 AAAAGAGAAGAAAAGAGAAG
2138382 AAAAGAGAAGAAAA-AGAGAG
1 AAAAGAGAAGAAAAGAGA-AG
2138402 AAAA-AGAA
1 AAAAGAGAA
2138410 CAGCATACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (20 bp):
AAAAGAGAAGAAAAGAGAAG
Found at i:2138390 original size:21 final size:20
Alignment explanation
Indices: 2138362--2138409 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
2138352 AAAAGAAGGA
2138362 AAAAAGAAAGAAAAGAGAAG
1 AAAAAGAAAGAAAAGAGAAG
2138382 -AAAAGAGAAGAAAA-AGAGAG
1 AAAAAGA-AAGAAAAGAGA-AG
2138402 AAAAAGAA
1 AAAAAGAA
2138410 CAGCATACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 9 0.36
20 10 0.40
21 6 0.24
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (20 bp):
AAAAAGAAAGAAAAGAGAAG
Found at i:2139950 original size:15 final size:15
Alignment explanation
Indices: 2139930--2139959 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2139920 AGAATATAAA
2139930 ATTTAAATATTTATT
1 ATTTAAATATTTATT
*
2139945 ATTTAAATTTTTATT
1 ATTTAAATATTTATT
2139960 GTAATTCAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTTAAATATTTATT
Found at i:2140143 original size:22 final size:21
Alignment explanation
Indices: 2140117--2140157 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
2140107 AATAAATAAT
2140117 AATAAATTTAAATTTTAAATTA
1 AATAAATTTAAA-TTTAAATTA
2140139 AATAAATTTAAATTTAAAT
1 AATAAATTTAAATTTAAAT
2140158 ATTTAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AATAAATTTAAATTTAAATTA
Found at i:2140150 original size:15 final size:17
Alignment explanation
Indices: 2140125--2140158 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
2140115 ATAATAAATT
2140125 TAAATTTTAAA-TTAAA
1 TAAATTTTAAATTTAAA
2140141 TAAA-TTTAAATTTAAA
1 TAAATTTTAAATTTAAA
2140157 TA
1 TA
2140159 TTTAAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTTTAAATTTAAA
Found at i:2140287 original size:16 final size:15
Alignment explanation
Indices: 2140266--2140406 Score: 90
Period size: 16 Copynumber: 8.8 Consensus size: 15
2140256 TCTTTTATTG
2140266 ATAATTTTAAATAAAA
1 ATAA-TTTAAATAAAA
*
2140282 ATAA-TTAAATAAAT
1 ATAATTTAAATAAAA
*
2140296 ATAATATAATATAAAA
1 ATAATTTAA-ATAAAA
2140312 ATAATTTAAATATAAA
1 ATAATTTAAATA-AAA
*
2140328 ATAAATATAAA-AAATA
1 AT-AATTTAAATAAA-A
*
2140344 TCATAATTTATATAATAA
1 --ATAATTTAAATAA-AA
*
2140362 AT-ATTAACATATAAAA
1 ATAATTTA-A-ATAAAA
* *
2140378 ATATATATAAATATATA
1 ATA-ATTTAAATA-AAA
2140395 ATAATTTAAATA
1 ATAATTTAAATA
2140407 TAATGATGAT
Statistics
Matches: 98, Mismatches: 13, Indels: 28
0.71 0.09 0.20
Matches are distributed among these distances:
14 13 0.13
15 12 0.12
16 41 0.42
17 23 0.23
18 8 0.08
19 1 0.01
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (15 bp):
ATAATTTAAATAAAA
Found at i:2140300 original size:30 final size:31
Alignment explanation
Indices: 2140276--2140340 Score: 93
Period size: 28 Copynumber: 2.2 Consensus size: 31
2140266 ATAATTTTAA
2140276 ATAAAAATAA-TTAAATAAATATAATATAAT
1 ATAAAAATAATTTAAATAAATATAATATAAT
*
2140306 ATAAAAATAATTTAAAT--ATAAAATA-AAT
1 ATAAAAATAATTTAAATAAATATAATATAAT
2140334 ATAAAAA
1 ATAAAAA
2140341 ATATCATAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
28 10 0.30
29 7 0.21
30 10 0.30
31 6 0.18
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (31 bp):
ATAAAAATAATTTAAATAAATATAATATAAT
Found at i:2140315 original size:11 final size:11
Alignment explanation
Indices: 2140276--2140392 Score: 68
Period size: 11 Copynumber: 10.8 Consensus size: 11
2140266 ATAATTTTAA
*
2140276 ATAAAAATAAT
1 ATAAATATAAT
2140287 -TAAATA-AAT
1 ATAAATATAAT
2140296 AT-AATATAAT
1 ATAAATATAAT
*
2140306 ATAAAAATAAT
1 ATAAATATAAT
* *
2140317 TTAAATATAAA
1 ATAAATATAAT
2140328 ATAAATATAA-
1 ATAAATATAAT
*
2140338 A-AAATATCAT
1 ATAAATATAAT
**
2140348 A-ATTTAT-AT
1 ATAAATATAAT
2140357 AATAAATATTAACAT
1 -ATAAATA-T-A-AT
*
2140372 ATAAAAATATAT
1 ATAAATATA-AT
2140384 ATAAATATA
1 ATAAATATA
2140393 TAATAATTTA
Statistics
Matches: 82, Mismatches: 14, Indels: 19
0.71 0.12 0.17
Matches are distributed among these distances:
9 16 0.20
10 18 0.22
11 27 0.33
12 12 0.15
13 1 0.01
14 6 0.07
15 2 0.02
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (11 bp):
ATAAATATAAT
Found at i:2140350 original size:34 final size:38
Alignment explanation
Indices: 2140312--2140387 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 38
2140302 TAATATAAAA
2140312 ATAATTTAAAT-ATAAA-A-TAA-ATATAAAAA-ATAT
1 ATAATTTAAATAATAAATATTAACATATAAAAATATAT
*
2140345 CATAATTTATATAATAAATATTAACATATAAAAATATAT
1 -ATAATTTAAATAATAAATATTAACATATAAAAATATAT
2140384 ATAA
1 ATAA
2140388 ATATATAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
34 10 0.28
35 5 0.14
36 1 0.03
37 3 0.08
38 13 0.36
39 4 0.11
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (38 bp):
ATAATTTAAATAATAAATATTAACATATAAAAATATAT
Found at i:2140377 original size:49 final size:49
Alignment explanation
Indices: 2140266--2140402 Score: 128
Period size: 49 Copynumber: 2.9 Consensus size: 49
2140256 TCTTTTATTG
* *
2140266 ATAATTTTAAATA-AAAATAAT-TA-AATAAATATAAT-A-TAATATAAAA
1 ATAA-TTTAAATATAAAAAAATATATAA-AAATATAATAATTTATATAAAA
*
2140312 ATAATTTAAATATAAAATAAATATA-AAAAATATCATAATTTATATAATAA
1 ATAATTTAAATATAAAA-AAATATATAAAAATATAATAATTTATATAA-AA
* *
2140362 AT-A-TTAACATATAAAAATATATATAAATATATAATAATTTA
1 ATAATTTAA-ATATAAAAAAATATATAAAAATATAATAATTTA
2140403 AATATAATGA
Statistics
Matches: 77, Mismatches: 6, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
45 8 0.10
46 8 0.10
47 11 0.14
48 15 0.19
49 31 0.40
50 4 0.05
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (49 bp):
ATAATTTAAATATAAAAAAATATATAAAAATATAATAATTTATATAAAA
Found at i:2140381 original size:8 final size:9
Alignment explanation
Indices: 2140289--2140392 Score: 65
Period size: 9 Copynumber: 11.1 Consensus size: 9
2140279 AAAATAATTA
2140289 AATAAATAT
1 AATAAATAT
2140298 AATATAATAT
1 AATA-AATAT
2140308 AA-AAATA-
1 AATAAATAT
*
2140315 ATTTAAATAT
1 A-ATAAATAT
2140325 AAAATAAATAT
1 --AATAAATAT
*
2140336 AAAAAATAT
1 AATAAATAT
*
2140345 CATAATTTATAT
1 AATAA---ATAT
2140357 AATAAATAT
1 AATAAATAT
2140366 --TAACATAT
1 AATAA-ATAT
2140374 AA-AAATAT
1 AATAAATAT
2140382 ATATAAATAT
1 A-ATAAATAT
2140392 A
1 A
2140393 TAATAATTTA
Statistics
Matches: 75, Mismatches: 6, Indels: 27
0.69 0.06 0.25
Matches are distributed among these distances:
7 4 0.05
8 13 0.17
9 28 0.37
10 14 0.19
11 7 0.09
12 9 0.12
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (9 bp):
AATAAATAT
Found at i:2140389 original size:10 final size:10
Alignment explanation
Indices: 2140287--2140394 Score: 57
Period size: 10 Copynumber: 11.0 Consensus size: 10
2140277 TAAAAATAAT
*
2140287 TAAATAAATA
1 TAAATATATA
2140297 T-AATATAATA
1 TAAATAT-ATA
* *
2140307 TAAAAATAATT
1 TAAATAT-ATA
*
2140318 TAAATATAAAA
1 TAAATAT-ATA
2140329 TAAATATA-A
1 TAAATATATA
2140338 -AAA-ATATCA
1 TAAATATAT-A
*
2140347 T-AATTTATA
1 TAAATATATA
*
2140356 T-AATAAATA
1 TAAATATATA
* *
2140365 TTAACATATA
1 TAAATATATA
*
2140375 AAAATATATA
1 TAAATATATA
2140385 TAAATATATA
1 TAAATATATA
2140395 ATAATTTAAA
Statistics
Matches: 76, Mismatches: 15, Indels: 14
0.72 0.14 0.13
Matches are distributed among these distances:
7 3 0.04
8 3 0.04
9 17 0.22
10 31 0.41
11 22 0.29
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (10 bp):
TAAATATATA
Found at i:2140830 original size:23 final size:20
Alignment explanation
Indices: 2140804--2140851 Score: 53
Period size: 23 Copynumber: 2.3 Consensus size: 20
2140794 TTTTTTAAAA
2140804 AATATAAAAATTAATGAAAATTT
1 AATATAAAAA-TAAT--AAATTT
*
2140827 AATATATAAATAATAAATTT
1 AATATAAAAATAATAAATTT
2140847 -ATATA
1 AATATA
2140852 TTAAATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 5 0.21
20 6 0.25
22 4 0.17
23 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
AATATAAAAATAATAAATTT
Found at i:2141517 original size:29 final size:30
Alignment explanation
Indices: 2141450--2141522 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 30
2141440 TTATTTTTTA
* *
2141450 ATCAAAGTATTATTGTTAATTAAATTAACT
1 ATCAAAATATTATTATTAATTAAATTAACT
* **
2141480 ATCACAATATTATTATT-ATTAAATTATTT
1 ATCAAAATATTATTATTAATTAAATTAACT
*
2141509 ATTAAAATATTATT
1 ATCAAAATATTATT
2141523 TTTTATCTAT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 22 0.61
30 14 0.39
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (30 bp):
ATCAAAATATTATTATTAATTAAATTAACT
Found at i:2141815 original size:18 final size:19
Alignment explanation
Indices: 2141788--2141834 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
2141778 TTATTCTATG
*
2141788 TATATTAAAAAATTT-TAA-
1 TATA-TAAAAAATTTAAAAT
2141806 TATAT-AAAAATTTAAAAT
1 TATATAAAAAATTTAAAAT
2141824 TATATAAAAAA
1 TATATAAAAAA
2141835 ATAACACATA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 8 0.32
17 3 0.12
18 9 0.36
19 5 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TATATAAAAAATTTAAAAT
Found at i:2142302 original size:32 final size:32
Alignment explanation
Indices: 2142266--2142336 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 32
2142256 AAGGCGCCAT
*
2142266 TTGAAAGC-TCCAATACTCTTGGAGCTTTTA-A
1 TTGAAAGCATCC-AGACTCTTGGAGCTTTTATA
*
2142297 CTTGAAAGCATCCAGAGTCTTGGAGCTTTTATA
1 -TTGAAAGCATCCAGACTCTTGGAGCTTTTATA
2142330 TTGAAAG
1 TTGAAAG
2142337 AGTCAAAAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 31 0.89
33 4 0.11
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.34
Consensus pattern (32 bp):
TTGAAAGCATCCAGACTCTTGGAGCTTTTATA
Found at i:2143249 original size:19 final size:19
Alignment explanation
Indices: 2143220--2143259 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
2143210 TATTCGATAT
2143220 AAAATATTATAATAAGTAAA
1 AAAATATTATAATAA-TAAA
2143240 AAAATA-TATAATAATAAA
1 AAAATATTATAATAATAAA
2143258 AA
1 AA
2143260 CAAAAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 6 0.30
19 8 0.40
20 6 0.30
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (19 bp):
AAAATATTATAATAATAAA
Found at i:2143792 original size:16 final size:16
Alignment explanation
Indices: 2143768--2143804 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
2143758 GAGAAACGCA
*
2143768 TGAAACATGCAGCACG
1 TGAAGCATGCAGCACG
2143784 TGAAGCATGCAGCACG
1 TGAAGCATGCAGCACG
2143800 TGAAG
1 TGAAG
2143805 TGCTGAAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.35, C:0.22, G:0.30, T:0.14
Consensus pattern (16 bp):
TGAAGCATGCAGCACG
Found at i:2144186 original size:60 final size:57
Alignment explanation
Indices: 2144122--2144339 Score: 208
Period size: 60 Copynumber: 3.7 Consensus size: 57
2144112 CAGCATCTTC
* *
2144122 CACGATAGCAACAACAACAGCTCCAACAAGCACGGCAACAATAACTTTAGCTCCAACAAG
1 CACGACAGCAGCAACAACAGCTCCAACAAGCACGGCAACAATAAC---AGCTCCAACAAG
* *
2144182 CACGACAGCAGCAACAGCAGCTCCAACAAGCACGGTAGCAACAATAGCAGCTCCAACAAG
1 CACGACAGCAGCAACAACAGCTCCAACAAGCAC-G--GCAACAATAACAGCTCCAACAAG
* * *
2144242 CATGACAGCAGCAACAACAGCTCCAACAAGCA-GGCAAGCACGAACAACAGC-CAAACAACAG
1 CACGACAGCAGCAACAACAGCTCCAACAAGCACGGC-A--AC-AATAACAGCTCCAAC-A-AG
* * * *
2144303 CACGGCAACAGCAACAGCAGCTCCAATAAGCA-GGCAA
1 CACGACAGCAGCAACAACAGCTCCAACAAGCACGGCAA
2144340 ACACGAACAG
Statistics
Matches: 135, Mismatches: 14, Indels: 20
0.80 0.08 0.12
Matches are distributed among these distances:
56 2 0.01
57 1 0.01
58 2 0.01
59 6 0.04
60 81 0.60
61 33 0.24
63 10 0.07
ACGTcount: A:0.43, C:0.33, G:0.18, T:0.07
Consensus pattern (57 bp):
CACGACAGCAGCAACAACAGCTCCAACAAGCACGGCAACAATAACAGCTCCAACAAG
Found at i:2144204 original size:30 final size:30
Alignment explanation
Indices: 2144128--2144338 Score: 187
Period size: 30 Copynumber: 7.0 Consensus size: 30
2144118 CTTCCACGAT
2144128 AGCAACAACAACAGCTCCAACAAGCACGGC
1 AGCAACAACAACAGCTCCAACAAGCACGGC
* * *** *
2144158 AACAATAACTTTAGCTCCAACAAGCACGAC
1 AGCAACAACAACAGCTCCAACAAGCACGGC
* * *
2144188 AGCAGCAACAGCAGCTCCAACAAGCACGGT
1 AGCAACAACAACAGCTCCAACAAGCACGGC
* * * *
2144218 AGCAACAATAGCAGCTCCAACAAGCATGAC
1 AGCAACAACAACAGCTCCAACAAGCACGGC
*
2144248 AGCAGCAACAACAGCTCCAACAAGCA-GGC
1 AGCAACAACAACAGCTCCAACAAGCACGGC
*
2144277 AAGC-ACGAACAACAGC-CAAACAACAGCACGGC
1 -AGCAAC-AACAACAGCTCCAAC-A-AGCACGGC
* * * *
2144309 AACAGCAACAGCAGCTCCAATAAGCA-GGC
1 AGCAACAACAACAGCTCCAACAAGCACGGC
2144338 A
1 A
2144339 AACACGAACA
Statistics
Matches: 144, Mismatches: 30, Indels: 15
0.76 0.16 0.08
Matches are distributed among these distances:
29 11 0.08
30 111 0.77
31 15 0.10
32 7 0.05
ACGTcount: A:0.43, C:0.33, G:0.18, T:0.07
Consensus pattern (30 bp):
AGCAACAACAACAGCTCCAACAAGCACGGC
Found at i:2144349 original size:30 final size:30
Alignment explanation
Indices: 2144254--2144348 Score: 88
Period size: 30 Copynumber: 3.1 Consensus size: 30
2144244 TGACAGCAGC
* *
2144254 AACAACAGCTCCAACAAGCAGGCAAGCACG
1 AACAACAGCTCCAAAAAGCAGGCAAACACG
*
2144284 AACAACAGC-CAAACAACAGCACGGC-AACA-G
1 AACAACAGCTCCAA-AA-AGCA-GGCAAACACG
* *
2144314 CAACAGCAGCTCCAATAAGCAGGCAAACACG
1 -AACAACAGCTCCAAAAAGCAGGCAAACACG
2144345 AACA
1 AACA
2144349 GTAATGAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
29 6 0.12
30 23 0.44
31 17 0.33
32 6 0.12
ACGTcount: A:0.46, C:0.33, G:0.18, T:0.03
Consensus pattern (30 bp):
AACAACAGCTCCAAAAAGCAGGCAAACACG
Found at i:2153132 original size:20 final size:19
Alignment explanation
Indices: 2153109--2153177 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 19
2153099 CACATCCAGA
*
2153109 TGTATCGATACAT-TATGCTT
1 TGTATCGATACATGT-T-CAT
2153129 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTTCAT
**
2153148 TGTATCGATACATACTCAAT
1 TGTATCGATACATGTTC-AT
2153168 TGTATCGATA
1 TGTATCGATA
2153178 TATGAAACTG
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
19 17 0.39
20 26 0.59
21 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (19 bp):
TGTATCGATACATGTTCAT
Found at i:2159956 original size:13 final size:13
Alignment explanation
Indices: 2159938--2159976 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
2159928 TACATTTTCT
2159938 TTGTATCGATACA
1 TTGTATCGATACA
2159951 TTGTATCGATACA
1 TTGTATCGATACA
*
2159964 CTGTATCGATACA
1 TTGTATCGATACA
2159977 GGGGGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2160140 original size:20 final size:20
Alignment explanation
Indices: 2160097--2160142 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
2160087 AAATCTTTTG
2160097 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
2160118 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
2160138 CAAAA
1 CAAAA
2160143 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:2160442 original size:20 final size:20
Alignment explanation
Indices: 2160417--2160491 Score: 123
Period size: 20 Copynumber: 3.8 Consensus size: 20
2160407 GGCAGCACCA
2160417 CCAGGTCGCGACCGGCATTC
1 CCAGGTCGCGACCGGCATTC
2160437 CCAGGTCGCGACCGGCATTC
1 CCAGGTCGCGACCGGCATTC
* *
2160457 CCAGGTCGCGACCGACACTC
1 CCAGGTCGCGACCGGCATTC
*
2160477 CCAGGTCGCAACCGG
1 CCAGGTCGCGACCGG
2160492 GCAGTCCCCA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.17, C:0.41, G:0.29, T:0.12
Consensus pattern (20 bp):
CCAGGTCGCGACCGGCATTC
Found at i:2162599 original size:13 final size:13
Alignment explanation
Indices: 2162581--2162606 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2162571 TACACCAAGT
2162581 ATGTATCGATACA
1 ATGTATCGATACA
2162594 ATGTATCGATACA
1 ATGTATCGATACA
2162607 CCAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2162625 original size:34 final size:32
Alignment explanation
Indices: 2162563--2162627 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
2162553 TAGCCAAACT
**
2162563 TGTATCGATACACCAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAATGTATCGATACAA
2162595 TGTATCGATACACCAAAAAATTGTATCGATACA
1 TGTATCGATACACC-AAAAA-TGTATCGATACA
2162628 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 14 0.48
33 3 0.10
34 12 0.41
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACCAAAAATGTATCGATACAA
Found at i:2165312 original size:19 final size:21
Alignment explanation
Indices: 2165274--2165315 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
2165264 TATAAGTGTG
*
2165274 GGGGCTGCCTGGTTGCGACCT
1 GGGGCTGCCTGGTCGCGACCT
2165295 GGGG-TGCC-GGTCGCGACCT
1 GGGGCTGCCTGGTCGCGACCT
2165314 GG
1 GG
2165316 TGAGTGCTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 12 0.60
20 4 0.20
21 4 0.20
ACGTcount: A:0.05, C:0.29, G:0.48, T:0.19
Consensus pattern (21 bp):
GGGGCTGCCTGGTCGCGACCT
Found at i:2166436 original size:13 final size:13
Alignment explanation
Indices: 2166418--2166443 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2166408 CAATTTTTTG
2166418 TGTATCGATACAT
1 TGTATCGATACAT
2166431 TGTATCGATACAT
1 TGTATCGATACAT
2166444 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2166458 original size:32 final size:33
Alignment explanation
Indices: 2166398--2166461 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
2166388 TACAAGCCAA
** *
2166398 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
2166431 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
2166462 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:2168854 original size:21 final size:21
Alignment explanation
Indices: 2168830--2168876 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
2168820 TTTGATGCTG
2168830 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
*
2168850 AATTTGAAGTGAAAAACAAGT
1 ATTTTGAAGTGAAAAACAAGT
2168871 ATTTTG
1 ATTTTG
2168877 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 5 0.22
21 10 0.43
22 8 0.35
ACGTcount: A:0.45, C:0.04, G:0.19, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:2169015 original size:13 final size:13
Alignment explanation
Indices: 2168997--2169034 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
2168987 ATAATCTCCT
2168997 TGTATCGATACAG
1 TGTATCGATACAG
*
2169010 TGTATCGATACAT
1 TGTATCGATACAG
*
2169023 TGTATCCATACA
1 TGTATCGATACA
2169035 AAGAAAATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:2171127 original size:15 final size:15
Alignment explanation
Indices: 2171107--2171137 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2171097 ATTTCGTTTG
*
2171107 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
2171122 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
2171137 G
1 G
2171138 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:2175233 original size:13 final size:13
Alignment explanation
Indices: 2175215--2175240 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2175205 CAATTTTTTG
2175215 TGTATCGATACAT
1 TGTATCGATACAT
2175228 TGTATCGATACAT
1 TGTATCGATACAT
2175241 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2175255 original size:32 final size:33
Alignment explanation
Indices: 2175195--2175258 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
2175185 TACAAGCCAA
** *
2175195 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
2175228 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
2175259 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:2182724 original size:33 final size:32
Alignment explanation
Indices: 2182687--2182748 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
2182677 TTCATGACAC
2182687 TTTTTTT-ATTTATAAAACTTTTTTGCATTTTCA
1 TTTTTTTCATTT-TAAAACTTTTTT-CATTTTCA
* *
2182720 TTTTTTTCATTTTTAATCTTTTTTCATTT
1 TTTTTTTCATTTTAAAACTTTTTTCATTT
2182749 ATTTTTATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 5 0.19
33 17 0.65
34 4 0.15
ACGTcount: A:0.19, C:0.10, G:0.02, T:0.69
Consensus pattern (32 bp):
TTTTTTTCATTTTAAAACTTTTTTCATTTTCA
Found at i:2182733 original size:16 final size:16
Alignment explanation
Indices: 2182705--2182748 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 16
2182695 TTTATAAAAC
* *
2182705 TTTTTTGCA-TTTTCA
1 TTTTTTTCATTTTTAA
2182720 TTTTTTTCATTTTTAA
1 TTTTTTTCATTTTTAA
2182736 TCTTTTTTCATTT
1 T-TTTTTTCATTT
2182749 ATTTTTATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 8 0.32
16 6 0.24
17 11 0.44
ACGTcount: A:0.14, C:0.11, G:0.02, T:0.73
Consensus pattern (16 bp):
TTTTTTTCATTTTTAA
Found at i:2182741 original size:17 final size:17
Alignment explanation
Indices: 2182704--2182748 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
2182694 ATTTATAAAA
*
2182704 CTTTTTTGCA-TTTTCAT
1 CTTTTTT-CATTTTTAAT
2182721 -TTTTTTCATTTTTAAT
1 CTTTTTTCATTTTTAAT
2182737 CTTTTTTCATTT
1 CTTTTTTCATTT
2182749 ATTTTTATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 2 0.08
16 12 0.48
17 11 0.44
ACGTcount: A:0.13, C:0.13, G:0.02, T:0.71
Consensus pattern (17 bp):
CTTTTTTCATTTTTAAT
Found at i:2184181 original size:22 final size:24
Alignment explanation
Indices: 2184151--2184195 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
2184141 CCTCTCAATC
*
2184151 TCTTCAAGA-ATTATACCCCAAAT
1 TCTTCAAGAGATTATAACCCAAAT
*
2184174 TCTT-AAGAGATTGTAACCCAAA
1 TCTTCAAGAGATTATAACCCAAA
2184196 GTTGAATGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.29
Consensus pattern (24 bp):
TCTTCAAGAGATTATAACCCAAAT
Found at i:2185296 original size:13 final size:13
Alignment explanation
Indices: 2185278--2185303 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2185268 AATTTTTTGG
2185278 TGTATCGATACAT
1 TGTATCGATACAT
2185291 TGTATCGATACAT
1 TGTATCGATACAT
2185304 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2187887 original size:13 final size:13
Alignment explanation
Indices: 2187869--2187907 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
2187859 ATAATCCCCC
* *
2187869 TGTATCGATATAG
1 TGTATCGATACAA
2187882 TGTATCGATACAA
1 TGTATCGATACAA
2187895 TGTATCGATACAA
1 TGTATCGATACAA
2187908 AGAAAAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2194094 original size:13 final size:13
Alignment explanation
Indices: 2194076--2194101 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2194066 AATTTTTTGG
2194076 TGTATCGATACAT
1 TGTATCGATACAT
2194089 TGTATCGATACAT
1 TGTATCGATACAT
2194102 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2194216 original size:20 final size:20
Alignment explanation
Indices: 2194193--2194246 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
2194183 CATTGCAACA
2194193 TGTATCGATACTTTGAATTG
1 TGTATCGATACTTTGAATTG
*
2194213 TGTATTGATACTTTGAATTG
1 TGTATCGATACTTTGAATTG
2194233 TGTATCGATACTTT
1 TGTATCGATACTTT
2194247 TAAGGGTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.24, C:0.09, G:0.19, T:0.48
Consensus pattern (20 bp):
TGTATCGATACTTTGAATTG
Found at i:2194629 original size:20 final size:21
Alignment explanation
Indices: 2194604--2194656 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
2194594 ATCGTTAAGT
*
2194604 TGTATCGATACATG-ACCA-AA
1 TGTATCGATACATGCA-AAGAA
*
2194624 TGTATCGATACTTGCAAAGAA
1 TGTATCGATACATGCAAAGAA
2194645 TGTATCGATACA
1 TGTATCGATACA
2194657 GGTGATTGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGCAAAGAA
Found at i:2205343 original size:20 final size:19
Alignment explanation
Indices: 2205318--2205390 Score: 74
Period size: 20 Copynumber: 3.7 Consensus size: 19
2205308 CTACCAGTTT
**
2205318 CATGTATCGATACAATTGTG
1 CATGTATCGATACAA-TGAA
2205338 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
* * *
2205357 CATGTTTCGATACAAAGCAT
1 CATGTATCGATACAATG-AA
*
2205377 GATGTATCGATACA
1 CATGTATCGATACA
2205391 TCTAGGTGTG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
19 17 0.38
20 28 0.62
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:2205366 original size:19 final size:20
Alignment explanation
Indices: 2205318--2205371 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
2205308 CTACCAGTTT
**
2205318 CATGTATCGATACAATTGTG
1 CATGTATCGATACAATTGAA
2205338 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
*
2205357 CATGTTTCGATACAA
1 CATGTATCGATACAA
2205372 AGCATGATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:2209511 original size:13 final size:13
Alignment explanation
Indices: 2209493--2209517 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2209483 CATTTTATGG
2209493 TGTATCGATACAA
1 TGTATCGATACAA
2209506 TGTATCGATACA
1 TGTATCGATACA
2209518 TACTGTGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2209616 original size:20 final size:20
Alignment explanation
Indices: 2209569--2209644 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
2209559 GCCAATGACC
**
2209569 TGTATCGATACATCTTTTTCA
1 TGTATCGATACAT-TTGATCA
* *
2209590 AGTATCGATACATTTGGTCA
1 TGTATCGATACATTTGATCA
* *
2209610 TGTATCGATAC-TGTGCAACA
1 TGTATCGATACATTTG-ATCA
2209630 TGTATCGATACATTT
1 TGTATCGATACATTT
2209645 AAATGTGTAT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 3 0.07
20 28 0.62
21 14 0.31
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATTTGATCA
Found at i:2212092 original size:13 final size:13
Alignment explanation
Indices: 2212074--2212111 Score: 60
Period size: 12 Copynumber: 3.0 Consensus size: 13
2212064 ATAAACCCCT
2212074 TGTATCGATACAG
1 TGTATCGATACAG
*
2212087 TGTATC-ATACAA
1 TGTATCGATACAG
2212099 TGTATCGATACAG
1 TGTATCGATACAG
2212112 AGAATGTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:2218324 original size:13 final size:13
Alignment explanation
Indices: 2218306--2218330 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2218296 CATTTTATGG
2218306 TGTATCGATACAA
1 TGTATCGATACAA
2218319 TGTATCGATACA
1 TGTATCGATACA
2218331 TACTGTGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2218346 original size:32 final size:33
Alignment explanation
Indices: 2218284--2218350 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
2218274 GTTACAAGCT
**
2218284 AATGTATCGATACATTTTATGGTGTATCGATAC
1 AATGTATCGATACATACTATGGTGTATCGATAC
*
2218317 AATGTATCGATACATACTGT-GTGTATCGATAC
1 AATGTATCGATACATACTATGGTGTATCGATAC
2218349 AA
1 AA
2218351 GTTTGGCTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
32 14 0.45
33 17 0.55
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (33 bp):
AATGTATCGATACATACTATGGTGTATCGATAC
Found at i:2218440 original size:13 final size:13
Alignment explanation
Indices: 2218422--2218446 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2218412 ACATTTGGTC
2218422 ATGTATCGATACA
1 ATGTATCGATACA
2218435 ATGTATCGATAC
1 ATGTATCGATAC
2218447 TGTGCAACAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2221194 original size:20 final size:20
Alignment explanation
Indices: 2221169--2221243 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 20
2221159 CAAAACCCTG
**
2221169 AAATGTATCGATACACCTTC
1 AAATGTATCGATACATATTC
2221189 AAATGTATCGATACATATTGC
1 AAATGTATCGATACATATT-C
* *
2221210 ACA-GTATCGATACATGA-CC
1 AAATGTATCGATACAT-ATTC
2221229 AAATGTATCGATACA
1 AAATGTATCGATACA
2221244 GGTCATTGGC
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
19 3 0.06
20 40 0.85
21 4 0.09
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28
Consensus pattern (20 bp):
AAATGTATCGATACATATTC
Found at i:2221317 original size:20 final size:20
Alignment explanation
Indices: 2221274--2221325 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
2221264 ATTAACTGTT
**
2221274 TGTATCGATACA-CACATTA
1 TGTATCGATACATCACAAAA
*
2221293 TGTATCGATACATCCCAAAA
1 TGTATCGATACATCACAAAA
2221313 TGTATCGATACAT
1 TGTATCGATACAT
2221326 TGGCTTGTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.31
Consensus pattern (20 bp):
TGTATCGATACATCACAAAA
Found at i:2223262 original size:13 final size:13
Alignment explanation
Indices: 2223244--2223268 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2223234 CATGGCACAT
2223244 TGTATCGATACAA
1 TGTATCGATACAA
2223257 TGTATCGATACA
1 TGTATCGATACA
2223269 TAATGAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2232645 original size:20 final size:20
Alignment explanation
Indices: 2232583--2232654 Score: 76
Period size: 19 Copynumber: 3.7 Consensus size: 20
2232573 AACCCTTATA
** * *
2232583 TGTATCGATACACACCCAAA
1 TGTATCGATACATGCACAAT
**
2232603 TGTATCGATACATGTTC-AT
1 TGTATCGATACATGCACAAT
2232622 TGTATCGATACATGCACAAT
1 TGTATCGATACATGCACAAT
2232642 TGTAT-GATACATG
1 TGTATCGATACATG
2232655 AAACTGGCAG
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
19 24 0.55
20 20 0.45
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.32
Consensus pattern (20 bp):
TGTATCGATACATGCACAAT
Found at i:2235563 original size:13 final size:13
Alignment explanation
Indices: 2235545--2235570 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2235535 ACATTTGGTC
2235545 ATGTATCGATACA
1 ATGTATCGATACA
2235558 ATGTATCGATACA
1 ATGTATCGATACA
2235571 TTTAAAGGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2244216 original size:13 final size:13
Alignment explanation
Indices: 2244198--2244223 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2244188 CATTTTGGGA
2244198 TGTATCGATACAT
1 TGTATCGATACAT
2244211 TGTATCGATACAT
1 TGTATCGATACAT
2244224 CTTGTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2244220 original size:33 final size:32
Alignment explanation
Indices: 2244178--2244241 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
2244168 TACAAGCCAA
*
2244178 TGTATCGATACATTTTGGGATGTATCGATACAT
1 TGTATCGATACATCTTGGG-TGTATCGATACAT
*
2244211 TGTATCGATACATCTTGTGTGTATCGATACA
1 TGTATCGATACATCTTGGGTGTATCGATACA
2244242 AACAGTTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATCTTGGGTGTATCGATACAT
Found at i:2244330 original size:13 final size:13
Alignment explanation
Indices: 2244312--2244336 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2244302 ACATTTGGTC
2244312 ATGTATCGATACA
1 ATGTATCGATACA
2244325 ATGTATCGATAC
1 ATGTATCGATAC
2244337 TATACAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2251655 original size:19 final size:20
Alignment explanation
Indices: 2251610--2251659 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
2251600 CACCTTCAGA
*
2251610 TGTATCGATACATAATGCAC
1 TGTATCGATACATAATCCAC
* *
2251630 AGTATCGATACATGA-CCAC
1 TGTATCGATACATAATCCAC
2251649 TGTATCGATAC
1 TGTATCGATAC
2251660 TTGCAAAGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (20 bp):
TGTATCGATACATAATCCAC
Found at i:2257942 original size:13 final size:13
Alignment explanation
Indices: 2257920--2257957 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
2257910 CAGCATTCTC
*
2257920 TGTATCGATACAT
1 TGTATCGATACAG
*
2257933 TGTATGGATACAG
1 TGTATCGATACAG
2257946 TGTATCGATACA
1 TGTATCGATACA
2257958 AGGGGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:2260464 original size:13 final size:13
Alignment explanation
Indices: 2260446--2260470 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2260436 ATAATGCACA
2260446 GTATCGATACATT
1 GTATCGATACATT
2260459 GTATCGATACAT
1 GTATCGATACAT
2260471 GACCACTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:2260467 original size:33 final size:32
Alignment explanation
Indices: 2260425--2260487 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
2260415 CACCTTCAGA
*
2260425 TGTATCGATACATAATGCACAGTATCGATACAT
1 TGTATCGATACATAA-CCACAGTATCGATACAT
* *
2260458 TGTATCGATACATGACCACTGTATCGATAC
1 TGTATCGATACATAACCACAGTATCGATAC
2260488 TTGGAAAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (32 bp):
TGTATCGATACATAACCACAGTATCGATACAT
Found at i:2263374 original size:20 final size:20
Alignment explanation
Indices: 2263349--2263386 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2263339 ATACATGTTT
2263349 ATTGTATCGATACATGAAGA
1 ATTGTATCGATACATGAAGA
2263369 ATTGTATCGATACATGAA
1 ATTGTATCGATACATGAA
2263387 ACTGGCAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (20 bp):
ATTGTATCGATACATGAAGA
Found at i:2272575 original size:13 final size:13
Alignment explanation
Indices: 2272557--2272582 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2272547 ACATTTGGTC
2272557 ATGTATCGATACA
1 ATGTATCGATACA
2272570 ATGTATCGATACA
1 ATGTATCGATACA
2272583 TCTTGTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2272577 original size:33 final size:32
Alignment explanation
Indices: 2272535--2272602 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 32
2272525 CGTTACAAGC
2272535 CAATGTATCGATACAT-TTGGTCATGTATCGATA
1 CAATGTATCGATACATCTT-GT-ATGTATCGATA
2272568 CAATGTATCGATACATCTTGTATGTATCGATA
1 CAATGTATCGATACATCTTGTATGTATCGATA
2272600 CAA
1 CAA
2272603 ACAATTAAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
32 14 0.41
33 18 0.53
34 2 0.06
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATCTTGTATGTATCGATA
Found at i:2275207 original size:13 final size:13
Alignment explanation
Indices: 2275189--2275225 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
2275179 ATAAACCCCT
*
2275189 TGTATCGATACAG
1 TGTATCGATACAA
2275202 TGTATCGATACAA
1 TGTATCGATACAA
2275215 TGTATCGATAC
1 TGTATCGATAC
2275226 TGAGAATGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2281331 original size:20 final size:21
Alignment explanation
Indices: 2281306--2281404 Score: 66
Period size: 20 Copynumber: 4.8 Consensus size: 21
2281296 ATCTCGTGTC
2281306 AATGTATCGATACAATTTG-G
1 AATGTATCGATACAATTTGAG
*
2281326 AATGTATCGATACATGCATTTGAA
1 AATGTATCGATACA---ATTTGAG
* * **
2281350 AATGTAGCCGTTACAA---GCC
1 AATGTA-TCGATACAATTTGAG
2281369 AATGTATCGATAC-ATTTG-G
1 AATGTATCGATACAATTTGAG
2281388 TAATGTATCGATACAAT
1 -AATGTATCGATACAAT
2281405 GTATCGATAC
Statistics
Matches: 61, Mismatches: 8, Indels: 19
0.69 0.09 0.22
Matches are distributed among these distances:
17 1 0.02
18 5 0.08
19 7 0.11
20 28 0.46
21 2 0.03
22 1 0.02
23 5 0.08
24 6 0.10
25 6 0.10
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.32
Consensus pattern (21 bp):
AATGTATCGATACAATTTGAG
Found at i:2281407 original size:13 final size:13
Alignment explanation
Indices: 2281389--2281415 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2281379 TACATTTGGT
2281389 AATGTATCGATAC
1 AATGTATCGATAC
2281402 AATGTATCGATAC
1 AATGTATCGATAC
2281415 A
1 A
2281416 TCTTGTATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:2281410 original size:33 final size:32
Alignment explanation
Indices: 2281368--2281435 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 32
2281358 CGTTACAAGC
*
2281368 CAATGTATCGATACAT-TTGGTAATGTATCGATA
1 CAATGTATCGATACATCTT-GT-ATGTATCAATA
2281401 CAATGTATCGATACATCTTGTATGTATCAATA
1 CAATGTATCGATACATCTTGTATGTATCAATA
2281433 CAA
1 CAA
2281436 ACAGTTAAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 13 0.39
33 18 0.55
34 2 0.06
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATCTTGTATGTATCAATA
Found at i:2283471 original size:13 final size:13
Alignment explanation
Indices: 2283453--2283490 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
2283443 AAGGATCATA
*
2283453 GTATCGATACATT
1 GTATCGATACAAT
*
2283466 GTATCGATATAAT
1 GTATCGATACAAT
2283479 GTATCGATACAA
1 GTATCGATACAA
2283491 AAAGGTACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (13 bp):
GTATCGATACAAT
Found at i:2285311 original size:19 final size:20
Alignment explanation
Indices: 2285283--2285332 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
2285273 GGGAAATATT
*
2285283 TTTTTTTTAAAAGGGA-AAA
1 TTTTTATTAAAAGGGAGAAA
*
2285302 TTTTTATTAAATGGGAGAAA
1 TTTTTATTAAAAGGGAGAAA
2285322 TATTTTATTAA
1 T-TTTTATTAA
2285333 GGGGGAGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 14 0.52
20 4 0.15
21 9 0.33
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (20 bp):
TTTTTATTAAAAGGGAGAAA
Found at i:2285338 original size:21 final size:20
Alignment explanation
Indices: 2285283--2285339 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
2285273 GGGAAATATT
* *
2285283 TTTTTTTTAAAAGGGA-AAA
1 TTTTTATTAAAGGGGAGAAA
*
2285302 TTTTTATTAAATGGGAGAAA
1 TTTTTATTAAAGGGGAGAAA
*
2285322 TATTTTATTAAGGGGGAG
1 T-TTTTATTAAAGGGGAG
2285340 TTATAAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 14 0.44
20 4 0.12
21 14 0.44
ACGTcount: A:0.37, C:0.00, G:0.23, T:0.40
Consensus pattern (20 bp):
TTTTTATTAAAGGGGAGAAA
Found at i:2285948 original size:20 final size:21
Alignment explanation
Indices: 2285918--2285956 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
2285908 AGGTCAAAAC
2285918 CCTAGAAAGTATCGATACAAG
1 CCTAGAAAGTATCGATACAAG
2285939 CCTA-AAAGTATCGATACA
1 CCTAGAAAGTATCGATACA
2285957 TGTTGCTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.21
Consensus pattern (21 bp):
CCTAGAAAGTATCGATACAAG
Found at i:2285969 original size:20 final size:20
Alignment explanation
Indices: 2285946--2286017 Score: 128
Period size: 20 Copynumber: 3.6 Consensus size: 20
2285936 AAGCCTAAAA
2285946 GTATCGATACATGTTGCTTT
1 GTATCGATACATGTTGCTTT
2285966 GTATCGATACATGTTGCTTT
1 GTATCGATACATGTTGCTTT
*
2285986 GTATCGATACATGTT-CATT
1 GTATCGATACATGTTGCTTT
2286005 GTATCGATACATG
1 GTATCGATACATG
2286018 AAGAATTGTG
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
19 16 0.31
20 35 0.69
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.42
Consensus pattern (20 bp):
GTATCGATACATGTTGCTTT
Found at i:2286035 original size:39 final size:40
Alignment explanation
Indices: 2285946--2286037 Score: 105
Period size: 39 Copynumber: 2.3 Consensus size: 40
2285936 AAGCCTAAAA
* * ** **
2285946 GTATCGATACATGTTGCTTTGTATCGATACATGTTGCTTT
1 GTATCAATACATGTTGCATTGTATCGATACATGAAGAATT
*
2285986 GTATCGATACATGTT-CATTGTATCGATACATGAAGAATT
1 GTATCAATACATGTTGCATTGTATCGATACATGAAGAATT
*
2286025 GTGTCAATACATG
1 GTATCAATACATG
2286038 AAACTGGCAG
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 30 0.67
40 15 0.33
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (40 bp):
GTATCAATACATGTTGCATTGTATCGATACATGAAGAATT
Found at i:2291580 original size:21 final size:18
Alignment explanation
Indices: 2291549--2291614 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 18
2291539 TCATTTTTTA
*
2291549 TTTTTTATTTTTTTACTTC
1 TTTTTT-TTTTTTTTCTTC
2291568 TTTTTGTCTTTTTTTTCTTTC
1 TTTTT-T-TTTTTTTTC-TTC
2291589 TTTTTTTTCTTTTTTTCTTC
1 -TTTTTTT-TTTTTTTCTTC
2291609 TTTTTT
1 TTTTTT
2291615 CTCTTATTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
19 11 0.27
20 13 0.32
21 12 0.29
22 5 0.12
ACGTcount: A:0.03, C:0.12, G:0.02, T:0.83
Consensus pattern (18 bp):
TTTTTTTTTTTTTTCTTC
Found at i:2291580 original size:33 final size:33
Alignment explanation
Indices: 2291542--2291624 Score: 89
Period size: 33 Copynumber: 2.5 Consensus size: 33
2291532 AGGTTTTTCA
*
2291542 TTTTTTATTTTTTATTTTTTTACTTCTTTTT-GTC
1 TTTTTT-TTCTTTATTTTTTTACTT-TTTTTCGTC
* * *
2291576 TTTTTTTTCTTTCTTTTTTTTCTTTTTTTCTTC
1 TTTTTTTTCTTTATTTTTTTACTTTTTTTCGTC
*
2291609 TTTTTTCTC-TTATTTT
1 TTTTTTTTCTTTATTTT
2291625 CTTTCCCTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
32 11 0.26
33 25 0.60
34 6 0.14
ACGTcount: A:0.05, C:0.12, G:0.01, T:0.82
Consensus pattern (33 bp):
TTTTTTTTCTTTATTTTTTTACTTTTTTTCGTC
Found at i:2291594 original size:41 final size:41
Alignment explanation
Indices: 2291549--2291629 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 41
2291539 TCATTTTTTA
* *
2291549 TTTTTTAT-TTTTTTACTTCTTTTTGTCT-TTTTTTTCTTTC
1 TTTTTTTTCTTTTTTACTTCTTTTT-TCTCTTATTTTCTTTC
*
2291589 TTTTTTTTCTTTTTTTCTTCTTTTTTCTCTTATTTTCTTTC
1 TTTTTTTTCTTTTTTACTTCTTTTTTCTCTTATTTTCTTTC
2291630 CCTAAATTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
40 10 0.28
41 26 0.72
ACGTcount: A:0.04, C:0.15, G:0.01, T:0.80
Consensus pattern (41 bp):
TTTTTTTTCTTTTTTACTTCTTTTTTCTCTTATTTTCTTTC
Found at i:2291603 original size:9 final size:9
Alignment explanation
Indices: 2291549--2291628 Score: 61
Period size: 10 Copynumber: 8.1 Consensus size: 9
2291539 TCATTTTTTA
*
2291549 TTTTTTATT
1 TTTTTTCTT
*
2291558 TTTTTACTT
1 TTTTTTCTT
2291567 CTTTTTGTCTT
1 -TTTTT-TCTT
2291578 TTTTTTCTTT
1 TTTTTTC-TT
*
2291588 CTTTTTTTTCT
1 -TTTTTTCT-T
2291599 TTTTTTCTT
1 TTTTTTCTT
2291608 CTTTTTTCTCT
1 -TTTTTTCT-T
*
2291619 TATTTTCTT
1 TTTTTTCTT
2291628 T
1 T
2291629 CCCTAAATTT
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
9 12 0.21
10 35 0.60
11 11 0.19
ACGTcount: A:0.04, C:0.14, G:0.01, T:0.81
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:2291605 original size:8 final size:8
Alignment explanation
Indices: 2291535--2291628 Score: 57
Period size: 8 Copynumber: 11.1 Consensus size: 8
2291525 CCACTTAAGG
*
2291535 TTTTTCAT
1 TTTTTCTT
*
2291543 TTTTTATT
1 TTTTTCTT
*
2291551 TTTTATTTT
1 TTTT-TCTT
2291560 TTTACTTCTT
1 TTT--TTCTT
*
2291570 TTTGTCTTT
1 TTTTTC-TT
2291579 TTTTTCTT
1 TTTTTCTT
2291587 TCTTTT-TT
1 T-TTTTCTT
2291595 TTCTTT-TT
1 TT-TTTCTT
*
2291603 TTCTTCTT
1 TTTTTCTT
2291611 TTTTCTCTT
1 TTTT-TCTT
*
2291620 ATTTTCTT
1 TTTTTCTT
2291628 T
1 T
2291629 CCCTAAATTT
Statistics
Matches: 68, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
7 3 0.04
8 34 0.50
9 24 0.35
10 6 0.09
11 1 0.01
ACGTcount: A:0.05, C:0.13, G:0.01, T:0.81
Consensus pattern (8 bp):
TTTTTCTT
Found at i:2291624 original size:21 final size:20
Alignment explanation
Indices: 2291556--2291627 Score: 92
Period size: 20 Copynumber: 3.5 Consensus size: 20
2291546 TTATTTTTTA
2291556 TTTTTTTACTTCTTTTTGTCT-
1 TTTTTTT-CTTCTTTTT-TCTC
*
2291577 TTTTTTTCTTTCTTTTTTTTC
1 TTTTTTTC-TTCTTTTTTCTC
2291598 TTTTTTTCTTCTTTTTTCTC
1 TTTTTTTCTTCTTTTTTCTC
*
2291618 TTATTTTCTT
1 TTTTTTTCTT
2291628 TCCCTAAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
20 23 0.50
21 23 0.50
ACGTcount: A:0.03, C:0.15, G:0.01, T:0.81
Consensus pattern (20 bp):
TTTTTTTCTTCTTTTTTCTC
Found at i:2305555 original size:20 final size:21
Alignment explanation
Indices: 2305513--2305563 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
2305503 TTCTACAATT
*
2305513 TGTATAGATATAACAAGTTAA
1 TGTATAGATATAACAAGTGAA
* *
2305534 TGTATCGATAT-AGAAGTGAA
1 TGTATAGATATAACAAGTGAA
*
2305554 TGTATTGATA
1 TGTATAGATA
2305564 CCAGACTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.41, C:0.04, G:0.20, T:0.35
Consensus pattern (21 bp):
TGTATAGATATAACAAGTGAA
Found at i:2307695 original size:79 final size:79
Alignment explanation
Indices: 2307560--2307842 Score: 318
Period size: 79 Copynumber: 3.6 Consensus size: 79
2307550 CTTAATCGAG
* * * ** * *
2307560 GGGATACTCCAACCTCAGTTTTATTTCCAAAACATCAATTTTTCACCATAGAGGATACCCCAACC
1 GGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATAGAGGATACTCTAACC
2307625 CTGTTATTTCTGAA
66 CTGTTATTTCTGAA
* * * * *
2307639 GGGATGCTCTAACCCCGGCTTTATTTCTAAAACATCGATTTTCCATAATCAG-GGATACTCTAAC
1 GGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAAT-AGAGGATACTCTAAC
*
2307703 CCCGTTATTTCT-AA
65 CCTGTTATTTCTGAA
* * * *
2307717 GGGGATACACCAACCCCGGTTTTATTTCTAAAACATCGATTTTTCATAATTGCGGATACTCTAAC
1 -GGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATAGAGGATACTCTAAC
** * *
2307782 TTTGTTATTTTTGAG
65 CCTGTTATTTCTGAA
* *
2307797 GGGATACTCCAACCCCGATTTTTATTTTTAAAACATCAATTTTTCA
1 GGGATACTCCAACCCCG-GTTTTATTTCTAAAACATCAATTTTTCA
2307843 CCATCGGGGA
Statistics
Matches: 171, Mismatches: 28, Indels: 9
0.82 0.13 0.04
Matches are distributed among these distances:
78 3 0.02
79 140 0.82
80 28 0.16
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.35
Consensus pattern (79 bp):
GGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATAGAGGATACTCTAACC
CTGTTATTTCTGAA
Found at i:2309092 original size:28 final size:27
Alignment explanation
Indices: 2309057--2309750 Score: 677
Period size: 28 Copynumber: 24.6 Consensus size: 27
2309047 TCAACACGAC
*
2309057 CCTTTCAAAGCCCACAAGTCAGTGACA
1 CCTTTCAAAGCCCACAAGTCAGTGGCA
* * * *
2309084 CCTTCTCAAAACCCACAAGTCAATAGTA
1 CCTT-TCAAAGCCCACAAGTCAGTGGCA
* * * *
2309112 TCATTTCAAAGCCCATAAGTTAGTGACA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCA
*
2309140 CCTTTTTCAAAGCCCACAAGTCAGTGGTA
1 CC--TTTCAAAGCCCACAAGTCAGTGGCA
* *
2309169 TCTTTTTTCAAAGCCCACAAGTCAGTGGTA
1 -C--CTTTCAAAGCCCACAAGTCAGTGGCA
* *
2309199 TTCTTTCAAAGCCCACAAGTCAGTGGTA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCA
*
2309227 TTCTTTCAAAGCCCACAAGTCAGTGGCA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCA
* ** *
2309255 CCTTTTCAAAGCTCACAAGTGTTGGTGGTA
1 CC-TTTCAAAGCCCACAA--GTCAGTGGCA
*
2309285 TCCTTTCAAAGCCCACAAGTTAGTGGCA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCA
*
2309313 CCTTCTCAAAGCCCACAAGTCAGTGGTA
1 CCTT-TCAAAGCCCACAAGTCAGTGGCA
** *
2309341 TTTTTTCAAAGCCCACAAGTTAGTGGCA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
2309369 CTTTTTCAAAGCCCACAAGTTAGTGGTA
1 C-CTTTCAAAGCCCACAAGTCAGTGGCA
* *
2309397 TCCTTTTAAAGCCCACAAGTCAGTGGTA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
2309425 CCTACTCAAAGCCCACAAGTTAGTGGTA
1 CCT-TTCAAAGCCCACAAGTCAGTGGCA
*
2309453 CCTTTTCAAAACCCACAAGTCAGTGGCA
1 CC-TTTCAAAGCCCACAAGTCAGTGGCA
2309481 TCCTTTCAAAGCCCACAAGTCAGTGGCA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCA
*
2309509 TCCTTTCAAAGCCCACAAGTCAATGGCA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCA
* * *
2309537 CCTTCTCAATGCCCATAAGTTAGTGGCA
1 CCTT-TCAAAGCCCACAAGTCAGTGGCA
** * * *
2309565 TATTTTCAAAGCCCATAAGTTAGTGTCA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCA
*
2309593 CCTTTTTCAAAGCCCACAAGTCAATGGCA
1 CC--TTTCAAAGCCCACAAGTCAGTGGCA
*
2309622 TCCTTTCAAAGCCCACAAGTCAGTGGTA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCA
*
2309650 CCTTCTCAAAGCCCACAAGTCAGTGGTA
1 CCTT-TCAAAGCCCACAAGTCAGTGGCA
* * *
2309678 TCCTTTCAAAGCCCACAAGTTAATGGAA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCA
2309706 CCTTCTCAAAGCCCACAAGTCAGTGGCA
1 CCTT-TCAAAGCCCACAAGTCAGTGGCA
*
2309734 TCTTTACAAAGCCCACA
1 CCTTT-CAAAGCCCACA
2309751 CAAATTGGTG
Statistics
Matches: 567, Mismatches: 73, Indels: 53
0.82 0.11 0.08
Matches are distributed among these distances:
27 26 0.05
28 432 0.76
29 57 0.10
30 50 0.09
31 2 0.00
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (27 bp):
CCTTTCAAAGCCCACAAGTCAGTGGCA
Found at i:2309121 original size:56 final size:56
Alignment explanation
Indices: 2309057--2309750 Score: 838
Period size: 56 Copynumber: 12.3 Consensus size: 56
2309047 TCAACACGAC
* * * *
2309057 CCTTTCAAAGCCCACAAGTCAGTGACACCTTCTCAAAACCCACAAGTCAATAGTAT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACCTTCTCAAAGCCCACAAGTCAGTGGTAT
* * * * *
2309113 CATTTCAAAGCCCATAAGTTAGTGACACCTTTTTCAAAGCCCACAAGTCAGTGGTAT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACC-TTCTCAAAGCCCACAAGTCAGTGGTAT
* * *
2309170 CTTTTTTCAAAGCCCACAAGTCAGTGGTATTCTT-TCAAAGCCCACAAGTCAGTGGTAT
1 C--CTTTCAAAGCCCACAAGTCAGTGGCA-CCTTCTCAAAGCCCACAAGTCAGTGGTAT
* * * **
2309228 TCTTTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCTCACAAGTGTTGGTGGTAT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACCTTCTCAAAGCCCACAA--GTCAGTGGTAT
*
2309286 CCTTTCAAAGCCCACAAGTTAGTGGCACCTTCTCAAAGCCCACAAGTCAGTGGTAT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACCTTCTCAAAGCCCACAAGTCAGTGGTAT
** * * * *
2309342 TTTTTCAAAGCCCACAAGTTAGTGGCACTTTTTCAAAGCCCACAAGTTAGTGGTAT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACCTTCTCAAAGCCCACAAGTCAGTGGTAT
* * * *
2309398 CCTTTTAAAGCCCACAAGTCAGTGGTACCTACTCAAAGCCCACAAGTTAGTGGTA-
1 CCTTTCAAAGCCCACAAGTCAGTGGCACCTTCTCAAAGCCCACAAGTCAGTGGTAT
* *
2309453 CCTTTTCAAAACCCACAAGTCAGTGGCATCCTT-TCAAAGCCCACAAGTCAGTGGCAT
1 CC-TTTCAAAGCCCACAAGTCAGTGGCA-CCTTCTCAAAGCCCACAAGTCAGTGGTAT
* * * * *
2309510 CCTTTCAAAGCCCACAAGTCAATGGCACCTTCTCAATGCCCATAAGTTAGTGGCAT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACCTTCTCAAAGCCCACAAGTCAGTGGTAT
** * * * * * *
2309566 ATTTTCAAAGCCCATAAGTTAGTGTCACCTTTTTCAAAGCCCACAAGTCAATGGCAT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACC-TTCTCAAAGCCCACAAGTCAGTGGTAT
*
2309623 CCTTTCAAAGCCCACAAGTCAGTGGTACCTTCTCAAAGCCCACAAGTCAGTGGTAT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACCTTCTCAAAGCCCACAAGTCAGTGGTAT
* * * *
2309679 CCTTTCAAAGCCCACAAGTTAATGGAACCTTCTCAAAGCCCACAAGTCAGTGGCAT
1 CCTTTCAAAGCCCACAAGTCAGTGGCACCTTCTCAAAGCCCACAAGTCAGTGGTAT
2309735 -CTTTACAAAGCCCACA
1 CCTTT-CAAAGCCCACA
2309751 CAAATTGGTG
Statistics
Matches: 551, Mismatches: 74, Indels: 26
0.85 0.11 0.04
Matches are distributed among these distances:
55 13 0.02
56 366 0.66
57 74 0.13
58 74 0.13
59 23 0.04
60 1 0.00
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (56 bp):
CCTTTCAAAGCCCACAAGTCAGTGGCACCTTCTCAAAGCCCACAAGTCAGTGGTAT
Found at i:2310775 original size:51 final size:48
Alignment explanation
Indices: 2310673--2310783 Score: 125
Period size: 51 Copynumber: 2.2 Consensus size: 48
2310663 TAAACAGTAC
* ****
2310673 ATGTATCGATACATTCTTTTTTACCTATATGTATCGATATATTTTTCA
1 ATGTATCGATACATTCTTTTTTACCTATATGTATCGATACATTAAAAA
*
2310721 ATGTATCGATACATTCTATTTTTTTACCT-TGATGTATTGATACATTAAAAA
1 ATGTATCGATACATTC---TTTTTTACCTAT-ATGTATCGATACATTAAAAA
2310772 ATGTATCGATAC
1 ATGTATCGATAC
2310784 GTCTAGTTTA
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
48 16 0.30
50 1 0.02
51 36 0.68
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.46
Consensus pattern (48 bp):
ATGTATCGATACATTCTTTTTTACCTATATGTATCGATACATTAAAAA
Found at i:2312874 original size:20 final size:22
Alignment explanation
Indices: 2312849--2312903 Score: 82
Period size: 20 Copynumber: 2.7 Consensus size: 22
2312839 CTGCCAAGGA
2312849 AATGTATCGATACATT-AT-TT
1 AATGTATCGATACATTGATCTT
2312869 AATGTATCGATACATTGATCTT
1 AATGTATCGATACATTGATCTT
2312891 --TGTATCGATACAT
1 AATGTATCGATACAT
2312904 CTGGGAATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 29 0.88
21 2 0.06
22 2 0.06
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.42
Consensus pattern (22 bp):
AATGTATCGATACATTGATCTT
Found at i:2313848 original size:20 final size:20
Alignment explanation
Indices: 2313803--2313848 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
2313793 GTTAACAGCC
*
2313803 CATGATTCATGCATTTTAAG
1 CATGTTTCATGCATTTTAAG
2313823 CTATGTTTCATGCA-TTTACAG
1 C-ATGTTTCATGCATTTTA-AG
2313844 CATGT
1 CATGT
2313849 CCAGCACCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.41
Consensus pattern (20 bp):
CATGTTTCATGCATTTTAAG
Found at i:2314402 original size:21 final size:20
Alignment explanation
Indices: 2314364--2314402 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2314354 ATTGCATGTT
2314364 TAAAAATTATTTTAAAATAC
1 TAAAAATTATTTTAAAATAC
2314384 TAAAAGATT-TTTCTAAAAT
1 TAAAA-ATTATTT-TAAAAT
2314403 GTTTTAGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (20 bp):
TAAAAATTATTTTAAAATAC
Found at i:2318370 original size:28 final size:27
Alignment explanation
Indices: 2318297--2318375 Score: 81
Period size: 26 Copynumber: 2.9 Consensus size: 27
2318287 TTATCAAAAG
*
2318297 AAAGGCCACACTAGCTAGCACCTAAGT
1 AAAGCCCACACTAGCTAGCACCTAAGT
* * *
2318324 AAA-CCTACACTAGCAAGCACAC-GAGT
1 AAAGCCCACACTAGCTAGCAC-CTAAGT
*
2318350 CAAAGCCCACACTTGCTAGCACCTAA
1 -AAAGCCCACACTAGCTAGCACCTAA
2318376 TAAGAGATTA
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
26 17 0.43
27 8 0.20
28 15 0.38
ACGTcount: A:0.38, C:0.33, G:0.15, T:0.14
Consensus pattern (27 bp):
AAAGCCCACACTAGCTAGCACCTAAGT
Found at i:2318434 original size:28 final size:28
Alignment explanation
Indices: 2318402--2318476 Score: 96
Period size: 28 Copynumber: 2.7 Consensus size: 28
2318392 TATAGAGTCA
* *
2318402 AAGCCTATATTACTTGGCACATGAATCG
1 AAGCCCATATTAATTGGCACATGAATCG
** *
2318430 AAGCCCATATTAATTGGCTTATGAATTG
1 AAGCCCATATTAATTGGCACATGAATCG
*
2318458 AAGCCCATATTAGTTGGCA
1 AAGCCCATATTAATTGGCA
2318477 TCTAAGTCTA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Consensus pattern (28 bp):
AAGCCCATATTAATTGGCACATGAATCG
Found at i:2318520 original size:26 final size:26
Alignment explanation
Indices: 2318485--2318546 Score: 115
Period size: 26 Copynumber: 2.4 Consensus size: 26
2318475 CATCTAAGTC
2318485 TAAGCCCACACTAGCTAGCACCTAAG
1 TAAGCCCACACTAGCTAGCACCTAAG
*
2318511 TAAGCCCACACTAGGTAGCACCTAAG
1 TAAGCCCACACTAGCTAGCACCTAAG
2318537 TAAGCCCACA
1 TAAGCCCACA
2318547 TTGGTTGGCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.35, C:0.34, G:0.16, T:0.15
Consensus pattern (26 bp):
TAAGCCCACACTAGCTAGCACCTAAG
Found at i:2318557 original size:26 final size:26
Alignment explanation
Indices: 2318458--2318557 Score: 101
Period size: 26 Copynumber: 3.8 Consensus size: 26
2318448 TTATGAATTG
* * *
2318458 AAGCCCATATTAGTTGGCATCTAAGTCT
1 AAGCCCACATTAGTTAGCACCTAAG--T
* *
2318486 AAGCCCACACTAGCTAGCACCTAAGT
1 AAGCCCACATTAGTTAGCACCTAAGT
* *
2318512 AAGCCCACACTAGGTAGCACCTAAGT
1 AAGCCCACATTAGTTAGCACCTAAGT
* *
2318538 AAGCCCACATTGGTTGGCAC
1 AAGCCCACATTAGTTAGCAC
2318558 TTAAATCGAG
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
26 42 0.68
28 20 0.32
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (26 bp):
AAGCCCACATTAGTTAGCACCTAAGT
Done.