Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 159 of 230
Found at i:47124159 original size:39 final size:39
Alignment explanation
Indices: 47124116--47124248 Score: 223
Period size: 39 Copynumber: 3.4 Consensus size: 39
47124106 AGTTTATCCA
47124116 CCACCCAAGTCACCAAGCAAGCCGCCAACTTACGCTCCT
1 CCACCCAAGTCACCAAGCAAGCCGCCAACTTACGCTCCT
*
47124155 CCACCCAAGTCACCCAGCAAGCCGCCAACTTACGCTCCT
1 CCACCCAAGTCACCAAGCAAGCCGCCAACTTACGCTCCT
*
47124194 CCACCCAAGTCACCCAGCAAGCCGCCAACTTACGCTCCT
1 CCACCCAAGTCACCAAGCAAGCCGCCAACTTACGCTCCT
*
47124233 CCGA-CCAAGCCACCAA
1 CC-ACCCAAGTCACCAA
47124249 CTTACGCCCC
Statistics
Matches: 90, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
39 89 0.99
40 1 0.01
ACGTcount: A:0.28, C:0.48, G:0.13, T:0.11
Consensus pattern (39 bp):
CCACCCAAGTCACCAAGCAAGCCGCCAACTTACGCTCCT
Found at i:47124249 original size:27 final size:27
Alignment explanation
Indices: 47124211--47124274 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
47124201 AGTCACCCAG
* *
47124211 CAAGCCGCCAACTTACGCTCCTCCGA-C
1 CAAGCCACCAACTTACGCCCCTCC-ACC
47124238 CAAGCCACCAACTTACGCCCCTCCACC
1 CAAGCCACCAACTTACGCCCCTCCACC
47124265 CAAGCCACCA
1 CAAGCCACCA
47124275 GTTTATCCTC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 1 0.03
27 33 0.97
ACGTcount: A:0.27, C:0.52, G:0.11, T:0.11
Consensus pattern (27 bp):
CAAGCCACCAACTTACGCCCCTCCACC
Found at i:47124711 original size:2 final size:2
Alignment explanation
Indices: 47124704--47124736 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
47124694 ATTTGAGTTC
47124704 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
47124737 AATGGTTTCT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:47126522 original size:24 final size:24
Alignment explanation
Indices: 47126488--47126535 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
47126478 TTCATTAAAT
*
47126488 ATTAATGGAAGATAGAAGTTTATA
1 ATTAATGGAAGATAGAAATTTATA
* *
47126512 ATTAATTGAAGATGGAAATTTATA
1 ATTAATGGAAGATAGAAATTTATA
47126536 GATTTCACTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.00, G:0.19, T:0.35
Consensus pattern (24 bp):
ATTAATGGAAGATAGAAATTTATA
Found at i:47129310 original size:59 final size:58
Alignment explanation
Indices: 47129247--47129391 Score: 148
Period size: 59 Copynumber: 2.5 Consensus size: 58
47129237 TTTGATTTAT
* **
47129247 GTTTAGGGTTTTTGAGTTTGGGGATTTAGGGTTTTAAGTTGTTGAA-TTTGGGGATTTTG
1 GTTTAGGGTTTTTGAATTTGGGGATTTAGGGTTAGAAGTT-TT-AATTTTGGGGATTTTG
* * ** ** *
47129306 GTTTATGGTTGTTGAATTTGGGGATTTTTGGTTAGCGGTTTTAATTTTGGGGATTTTT
1 GTTTAGGGTTTTTGAATTTGGGGATTTAGGGTTAGAAGTTTTAATTTTGGGGATTTTG
* *
47129364 GTTTAGGGTTTTTTAATATTAGGGATTT
1 GTTTAGGGTTTTTGAAT-TTGGGGATTT
47129392 TTGTTTAGGG
Statistics
Matches: 70, Mismatches: 14, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
57 2 0.03
58 28 0.40
59 40 0.57
ACGTcount: A:0.16, C:0.01, G:0.32, T:0.52
Consensus pattern (58 bp):
GTTTAGGGTTTTTGAATTTGGGGATTTAGGGTTAGAAGTTTTAATTTTGGGGATTTTG
Found at i:47129318 original size:29 final size:29
Alignment explanation
Indices: 47129247--47129421 Score: 160
Period size: 30 Copynumber: 6.0 Consensus size: 29
47129237 TTTGATTTAT
* *
47129247 GTTTAGGGTTTTTGAGTTTGGGGATTTAGG
1 GTTTAGGGTTTTTGAATTTGGGGATTT-TG
* *
47129277 GTTTTA-AGTTGTTGAATTTGGGGATTTTG
1 G-TTTAGGGTTTTTGAATTTGGGGATTTTG
* *
47129306 GTTTATGGTTGTTGAATTTGGGGATTTTTG
1 GTTTAGGGTTTTTGAATTTGGGGA-TTTTG
*
47129336 G-TTAGCGG-TTTT-AATTTTGGGGATTTTT
1 GTTTAG-GGTTTTTGAA-TTTGGGGATTTTG
* * *
47129364 GTTTAGGGTTTTTTAATATTAGGGATTTTT
1 GTTTAGGGTTTTTGAAT-TTGGGGATTTTG
* *
47129394 GTTTAGGGTTTTTAAATTTTGGGATTTT
1 GTTTAGGGTTTTTGAATTTGGGGATTTT
47129422 TTTGTTTTCG
Statistics
Matches: 125, Mismatches: 11, Indels: 19
0.81 0.07 0.12
Matches are distributed among these distances:
28 13 0.10
29 52 0.42
30 56 0.45
31 4 0.03
ACGTcount: A:0.16, C:0.01, G:0.30, T:0.53
Consensus pattern (29 bp):
GTTTAGGGTTTTTGAATTTGGGGATTTTG
Found at i:47129337 original size:30 final size:30
Alignment explanation
Indices: 47129247--47129422 Score: 168
Period size: 29 Copynumber: 6.0 Consensus size: 30
47129237 TTTGATTTAT
* **
47129247 GTTTAGGGTTTTTGAGTTTGGGGATTTAGG
1 GTTTAGGGTTTTTGAATTTGGGGATTTTTG
* *
47129277 GTTTTA-AGTTGTTGAATTTGGGGA-TTTTG
1 G-TTTAGGGTTTTTGAATTTGGGGATTTTTG
* *
47129306 GTTTATGGTTGTTGAATTTGGGGATTTTTG
1 GTTTAGGGTTTTTGAATTTGGGGATTTTTG
47129336 G-TTAGCGG-TTTT-AATTTTGGGGATTTTT-
1 GTTTAG-GGTTTTTGAA-TTTGGGGATTTTTG
* *
47129364 GTTTAGGGTTTTTTAATATTAGGGATTTTT-
1 GTTTAGGGTTTTTGAAT-TTGGGGATTTTTG
* *
47129394 GTTTAGGGTTTTTAAATTTTGGGATTTTT
1 GTTTAGGGTTTTTGAATTTGGGGATTTTT
47129423 TTGTTTTCGA
Statistics
Matches: 126, Mismatches: 11, Indels: 19
0.81 0.07 0.12
Matches are distributed among these distances:
28 9 0.07
29 60 0.48
30 53 0.42
31 4 0.03
ACGTcount: A:0.16, C:0.01, G:0.30, T:0.53
Consensus pattern (30 bp):
GTTTAGGGTTTTTGAATTTGGGGATTTTTG
Found at i:47129401 original size:14 final size:14
Alignment explanation
Indices: 47129355--47129406 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
47129345 TTTAATTTTG
47129355 GGGATTTTTGTTTA
1 GGGATTTTTGTTTA
* *
47129369 GGGTTTTTTAATATTA
1 GGGATTTTT-GT-TTA
47129385 GGGATTTTTGTTTA
1 GGGATTTTTGTTTA
47129399 GGG-TTTTT
1 GGGATTTTT
47129407 AAATTTTGGG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
13 5 0.16
14 14 0.44
15 2 0.06
16 11 0.34
ACGTcount: A:0.15, C:0.00, G:0.27, T:0.58
Consensus pattern (14 bp):
GGGATTTTTGTTTA
Found at i:47129407 original size:59 final size:59
Alignment explanation
Indices: 47129293--47129422 Score: 167
Period size: 59 Copynumber: 2.2 Consensus size: 59
47129283 AGTTGTTGAA
* * *
47129293 TTTGGGGATTTTGGTTTATGGTTGTTGAATTTGGGGATTTTTGGTTAGCGGTTTT-AAT
1 TTTGGGGATTTTTGTTTAGGGTTGTTGAATTTAGGGATTTTTGGTTAGCGGTTTTAAAT
* * *
47129351 TTTGGGGATTTTTGTTTAGGGTTTTTTAATATTAGGGATTTTTGTTTAG-GGTTTTTAAAT
1 TTTGGGGATTTTTGTTTAGGGTTGTTGAAT-TTAGGGATTTTTGGTTAGCGG-TTTTAAAT
47129411 TTT-GGGATTTTT
1 TTTGGGGATTTTT
47129423 TTGTTTTCGA
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
58 28 0.44
59 29 0.46
60 6 0.10
ACGTcount: A:0.15, C:0.01, G:0.28, T:0.55
Consensus pattern (59 bp):
TTTGGGGATTTTTGTTTAGGGTTGTTGAATTTAGGGATTTTTGGTTAGCGGTTTTAAAT
Found at i:47129891 original size:14 final size:15
Alignment explanation
Indices: 47129855--47129895 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
47129845 ATATTAATAT
*
47129855 TTTGTTTGTCTATAC
1 TTTGTTTGTCTACAC
*
47129870 TTTTTTTG-CTACAC
1 TTTGTTTGTCTACAC
47129884 TTTGTTTGTCTA
1 TTTGTTTGTCTA
47129896 TTATTATGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.12, C:0.15, G:0.12, T:0.61
Consensus pattern (15 bp):
TTTGTTTGTCTACAC
Found at i:47130406 original size:48 final size:48
Alignment explanation
Indices: 47130339--47130454 Score: 151
Period size: 48 Copynumber: 2.4 Consensus size: 48
47130329 GTTTTTGTGG
* * **
47130339 TGGTAATAAATGTGTTGAGGGTTTAAATGGGGAGGGTGTTAAGGTTGT
1 TGGTAATAAAGGTGATGAGGGTTTAAATAAGGAGGGTGTTAAGGTTGT
* *
47130387 TGGTAGTAAAGGTGATGAGGGTTTAAATAAGGAGGGTGTTGAGGTTGT
1 TGGTAATAAAGGTGATGAGGGTTTAAATAAGGAGGGTGTTAAGGTTGT
* * *
47130435 TGGCAATAAAAGTGGTGAGG
1 TGGTAATAAAGGTGATGAGG
47130455 TTGAGGGTGG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 58 1.00
ACGTcount: A:0.28, C:0.01, G:0.41, T:0.31
Consensus pattern (48 bp):
TGGTAATAAAGGTGATGAGGGTTTAAATAAGGAGGGTGTTAAGGTTGT
Found at i:47130512 original size:81 final size:81
Alignment explanation
Indices: 47130406--47130555 Score: 230
Period size: 81 Copynumber: 1.9 Consensus size: 81
47130396 AGGTGATGAG
* *
47130406 GGTTTAAATAAGGAGGGTGTTGAGGTTGTTGGCAATAAAAGTGGTGAGGTTGAGGGTGGTGAAGA
1 GGTTTAAATAAGGAGGGTATGGAGGTTGTTGGCAATAAAAGTGGTGAGGTTGAGGGTGGTGAAGA
47130471 TGGTGAGAGTGTTGAA
66 TGGTGAGAGTGTTGAA
* * *
47130487 GGTTTAAAT-AGGTAGGGTATGGAGGTTGTTGGCAGTTAAGGTGGTGAGGTTGAGGGTGGTGAAG
1 GGTTTAAATAAGG-AGGGTATGGAGGTTGTTGGCAATAAAAGTGGTGAGGTTGAGGGTGGTGAAG
*
47130551 GTGGT
65 ATGGT
47130556 AAGGGTATTA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
80 3 0.05
81 59 0.95
ACGTcount: A:0.24, C:0.01, G:0.45, T:0.29
Consensus pattern (81 bp):
GGTTTAAATAAGGAGGGTATGGAGGTTGTTGGCAATAAAAGTGGTGAGGTTGAGGGTGGTGAAGA
TGGTGAGAGTGTTGAA
Found at i:47130551 original size:24 final size:24
Alignment explanation
Indices: 47130524--47130627 Score: 68
Period size: 24 Copynumber: 4.2 Consensus size: 24
47130514 GTTGGCAGTT
*
47130524 AAGGTGGTGAGGTTGAGGGTGGTG
1 AAGGTGGTGAGGTTAAGGGTGGTG
* * *
47130548 AAGGTGGTAAGGGTATTAAGGTTGCTG
1 AAGGTGGTGA-GG--TTAAGGGTGGTG
* * *
47130575 TCA-GTCAGTGTGG-TAAGGGTGGTG
1 -AAGGT-GGTGAGGTTAAGGGTGGTG
* *
47130599 AAGGTGGTGAGGTTGAGGGTGTTG
1 AAGGTGGTGAGGTTAAGGGTGGTG
47130623 AAGGT
1 AAGGT
47130628 TTAAATGGGG
Statistics
Matches: 58, Mismatches: 15, Indels: 14
0.67 0.17 0.16
Matches are distributed among these distances:
23 6 0.10
24 34 0.59
25 2 0.03
27 13 0.22
28 3 0.05
ACGTcount: A:0.20, C:0.03, G:0.49, T:0.28
Consensus pattern (24 bp):
AAGGTGGTGAGGTTAAGGGTGGTG
Found at i:47133202 original size:158 final size:157
Alignment explanation
Indices: 47132946--47133257 Score: 444
Period size: 158 Copynumber: 2.0 Consensus size: 157
47132936 GGTGAGGGTC
* * * *
47132946 ACAACAGAAGATCATGCATTCAACCTAACACAACTGGATCACAAGTATATCGTAAACACTTTTTC
1 ACAACAAAAGATCATGCAATCAACCTAACACAACTAGATCACAAGTATATCATAAACACTTTTTC
* * * **
47133011 ATTGTCAAGTTCCAACATATTTAAATATAATTTGGGGTTTTGTATTTTTTTCTCAATCTGATATG
66 ATTCTCAAGTTCCAAAATATTTAAATATAATTTGGGGTTGTG-ATTTTTTTCTCAATCTGATACA
*
47133076 AGTATAAGAACTAGAAGCCAAAAAAAGA
130 AGTACAAGAACTAGAAGCCAAAAAAAGA
* * *
47133104 ACAACAAAATATCATGCAATCAACCTAACACAACTAGATCACAGGTATATCATAAACACTTTTTT
1 ACAACAAAAGATCATGCAATCAACCTAACACAACTAGATCACAAGTATATCATAAACACTTTTTC
* * ** * *
47133169 ATTCTCAAGTTCCAAAATATTTAAATTTAATTTGGGGTTGTGATTTTTTTGTCTGTTTGGTACAA
66 ATTCTCAAGTTCCAAAATATTTAAATATAATTTGGGGTTGTGATTTTTTTCTCAATCTGATACAA
47133234 GTACAAGAACTAGAAGCCAAAAAA
131 GTACAAGAACTAGAAGCCAAAAAA
47133258 GGAGGGTATA
Statistics
Matches: 135, Mismatches: 19, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
157 39 0.29
158 96 0.71
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (157 bp):
ACAACAAAAGATCATGCAATCAACCTAACACAACTAGATCACAAGTATATCATAAACACTTTTTC
ATTCTCAAGTTCCAAAATATTTAAATATAATTTGGGGTTGTGATTTTTTTCTCAATCTGATACAA
GTACAAGAACTAGAAGCCAAAAAAAGA
Found at i:47135190 original size:18 final size:18
Alignment explanation
Indices: 47135169--47135203 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
47135159 CCTATATAAA
* *
47135169 CTCATTTTTTTTATTTTT
1 CTCATATTTTTCATTTTT
47135187 CTCATATTTTTCATTTT
1 CTCATATTTTTCATTTT
47135204 ATTCAATTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (18 bp):
CTCATATTTTTCATTTTT
Found at i:47136881 original size:16 final size:16
Alignment explanation
Indices: 47136856--47136890 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
47136846 TAAAAGGAGC
47136856 TTTACAAAACA-AAGT
1 TTTACAAAACATAAGT
47136871 TTTATCAAAACATAAGT
1 TTTA-CAAAACATAAGT
47136888 TTT
1 TTT
47136891 TTATACAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 7 0.39
17 7 0.39
ACGTcount: A:0.46, C:0.11, G:0.06, T:0.37
Consensus pattern (16 bp):
TTTACAAAACATAAGT
Found at i:47139312 original size:5 final size:5
Alignment explanation
Indices: 47139302--47139424 Score: 230
Period size: 5 Copynumber: 24.8 Consensus size: 5
47139292 TCATCACAAA
47139302 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
47139352 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATATC
*
47139402 TTATC ATATC ATATC ATA-C ATAT
1 ATATC ATATC ATATC ATATC ATAT
47139425 TAGAAGCAAA
Statistics
Matches: 115, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
4 4 0.03
5 111 0.97
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.41
Consensus pattern (5 bp):
ATATC
Found at i:47141002 original size:41 final size:41
Alignment explanation
Indices: 47140940--47141020 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
47140930 TTAAACAGAT
* *
47140940 TCACTGGCACTTAGCCTGCTAGGCTTGA-AGCTTGATTCAGG
1 TCACCGGCACTTAGCCTGCTAGGCTT-ATAGCCTGATTCAGG
47140981 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAG
1 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAG
47141021 TTCTAGCTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 1 0.03
41 36 0.97
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.28
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGG
Found at i:47146968 original size:25 final size:25
Alignment explanation
Indices: 47146940--47146988 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
47146930 TATAGTCTAT
* *
47146940 CTATAGTAGTCTCAGTATATACTAC
1 CTATAGCAGTCTCAGGATATACTAC
*
47146965 CTATAGCAGTTTCAGGATATACTA
1 CTATAGCAGTCTCAGGATATACTA
47146989 TCAAACACAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (25 bp):
CTATAGCAGTCTCAGGATATACTAC
Found at i:47152744 original size:50 final size:50
Alignment explanation
Indices: 47152476--47152809 Score: 287
Period size: 51 Copynumber: 6.6 Consensus size: 50
47152466 TATCGATGAA
* * * * * *
47152476 CACGCGTGTAGTATTGTGTGAAGGCTACTACGTGTATCGATAAATA-ATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAA-ACTTGGT
* * * * * *
47152527 CACGTGTGTATTACTAAGTGAAGGCTACAATGTGTACCG-AGAAGCCTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTA-AA-ACTTGGT
* * * * ****
47152578 CACATGTGTAGTACTGTGAGAAGGCTACTACGTGAATCGATAAATGAGGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGGT
* * * * * * *
47152629 CACATGTGTAGTACCAAGTGATGGCTACTATGTGTACC-AAAAACCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAA-C-TTGGT
* * *
47152680 TACGTGTGTAGTACTATGTGAAGGCTACGACGTGAACCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGGT
* * *
47152730 CACGTGTGTAGTACTATGTGAAGACTACTACGTAAACCGTAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGGT
47152780 CACGTGTGTAGTACTATGTGAAGGCTACTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTA
47152810 TGTGTATCGA
Statistics
Matches: 224, Mismatches: 52, Indels: 15
0.77 0.18 0.05
Matches are distributed among these distances:
49 4 0.02
50 81 0.36
51 132 0.59
52 6 0.03
53 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.28
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGGT
Found at i:47166891 original size:75 final size:75
Alignment explanation
Indices: 47166715--47166987 Score: 390
Period size: 75 Copynumber: 3.6 Consensus size: 75
47166705 TGGATTTAGC
* * * * * *
47166715 ACTTAGTAACC-CCAGTGATTCGGGGAATCATCACTTAGCAACCCCTTTCACATTCAAAAATACG
1 ACTTAGCAACCACCAATAATTCGGGGAATCAACACTTAGCAACCCCTTTCAGATT-TAAAATACG
* *
47166779 GTGGAATCAGC-
65 ATGGGATCA-CA
*
47166790 ACTTAGCAACCACCAGTGAA-TCGGGGAATCAACACTTAGCAACCCCTTTCAGATTTAAAATACG
1 ACTTAGCAACCACCAAT-AATTCGGGGAATCAACACTTAGCAACCCCTTTCAGATTTAAAATACG
47166854 ATGGGATCACA
65 ATGGGATCACA
*
47166865 ACTTAGCAACCACCAATAATTCGGGGAATCAGCACTTAGCAACCCCTTTCAGATTTAAAATACGA
1 ACTTAGCAACCACCAATAATTCGGGGAATCAACACTTAGCAACCCCTTTCAGATTTAAAATACGA
47166930 TGGGATCACA
66 TGGGATCACA
* *
47166940 ACTTAGCAACCACCAATGATTCGAGGAATCAACACTTAGCAACCCCTT
1 ACTTAGCAACCACCAATAATTCGGGGAATCAACACTTAGCAACCCCTT
47166988 GGGGGAATCA
Statistics
Matches: 182, Mismatches: 12, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
74 3 0.02
75 140 0.77
76 38 0.21
77 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (75 bp):
ACTTAGCAACCACCAATAATTCGGGGAATCAACACTTAGCAACCCCTTTCAGATTTAAAATACGA
TGGGATCACA
Found at i:47169019 original size:26 final size:26
Alignment explanation
Indices: 47168952--47169023 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 26
47168942 TCTCATCTCA
* * *
47168952 ATTTTA-CTTCAGTAAAATTTTGACT
1 ATTTTACCTTAAGTAAAATTTTAACG
*
47168977 ATTTTACCTTAACTAAAATTTTAACG
1 ATTTTACCTTAAGTAAAATTTTAACG
*
47169003 ATTTTACCCTT-GGTAAAATTT
1 ATTTTA-CCTTAAGTAAAATTT
47169024 CGAGAAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
25 6 0.15
26 29 0.74
27 4 0.10
ACGTcount: A:0.33, C:0.14, G:0.07, T:0.46
Consensus pattern (26 bp):
ATTTTACCTTAAGTAAAATTTTAACG
Found at i:47170625 original size:11 final size:11
Alignment explanation
Indices: 47170609--47170634 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
47170599 TAGAAGAGAC
47170609 GAAACAGGGGA
1 GAAACAGGGGA
47170620 GAAACAGGGGA
1 GAAACAGGGGA
47170631 GAAA
1 GAAA
47170635 GAAGAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.08, G:0.42, T:0.00
Consensus pattern (11 bp):
GAAACAGGGGA
Found at i:47178196 original size:138 final size:136
Alignment explanation
Indices: 47177894--47178312 Score: 626
Period size: 138 Copynumber: 3.1 Consensus size: 136
47177884 AAGAAAAAGG
*
47177894 AATTATATTCTTTCCAAAAGAATATTAATTTCCATATCTTTTATATTTTGATCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGATCGAAATTAATTAA
* * *
47177959 TATAACTATTTATATTAAAAAATTTGGTAATATATATA-ATTAATATTTTGTATGAATCAAATTC
66 TATAACTGTTTATATTAATAAA-TTGGTAAAATATATACATTAATATTTTGTATGAATCAAATTC
*
47178023 GTATATT
130 ATATATT
* * * * * *
47178030 AATTATATTATTTCCAAAAGAAAATTAATTTTCACGTATTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGATCGAAATTAATTAA
* **
47178095 TATAACTGTTTATATTAATAAAGTTGGTAAAATATTTACCATTAATATTTTAAATGAATCAAATT
66 TATAACTGTTTATATTAATAAA-TTGGTAAAATATATA-CATTAATATTTTGTATGAATCAAATT
47178160 CATATATT
129 CATATATT
*
47178168 AATTATATTCTTTCTAAAAGAATATTAATTTCCATGTCTTTTATATTTTGATCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGATCGAAATTAATTAA
* *
47178233 TATAATTG-TTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
66 TATAACTGTTTATATTAATAAATT-GGTAAAATATATAC-ATTAATATTTTGTATGAATCAAATT
47178297 CATATATT
129 CATATATT
47178305 AATTATAT
1 AATTATAT
47178313 CTACGATTAA
Statistics
Matches: 252, Mismatches: 27, Indels: 7
0.88 0.09 0.02
Matches are distributed among these distances:
136 94 0.37
137 63 0.25
138 95 0.38
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.45
Consensus pattern (136 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGATCGAAATTAATTAA
TATAACTGTTTATATTAATAAATTGGTAAAATATATACATTAATATTTTGTATGAATCAAATTCA
TATATT
Found at i:47188833 original size:23 final size:23
Alignment explanation
Indices: 47188807--47188853 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
47188797 CTGATATTAA
47188807 GCATGTATGATATATGCATTTTG
1 GCATGTATGATATATGCATTTTG
* * *
47188830 GCATTTGTTATATATGCATTTTG
1 GCATGTATGATATATGCATTTTG
47188853 G
1 G
47188854 ATGAGATTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.23, C:0.09, G:0.21, T:0.47
Consensus pattern (23 bp):
GCATGTATGATATATGCATTTTG
Found at i:47188866 original size:23 final size:23
Alignment explanation
Indices: 47188816--47188867 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
47188806 AGCATGTATG
**
47188816 ATATATGCATTTTGGCATTTGTT
1 ATATATGCATTTTGGCATGAGTT
47188839 ATATATGCATTTTGG-ATGAGATT
1 ATATATGCATTTTGGCATGAG-TT
*
47188862 GTATAT
1 ATATAT
47188868 ATGGAGGAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 3 0.12
23 22 0.88
ACGTcount: A:0.27, C:0.06, G:0.19, T:0.48
Consensus pattern (23 bp):
ATATATGCATTTTGGCATGAGTT
Found at i:47196763 original size:38 final size:38
Alignment explanation
Indices: 47196700--47196912 Score: 255
Period size: 38 Copynumber: 5.6 Consensus size: 38
47196690 ACACTGGCAA
* * *
47196700 TAAGCCTACTAGGCACTAAGCCTGAATAACACCAACAC
1 TAAGCCTACTAGGCACAAAGCCTGAACAACACCGACAC
* * *
47196738 TAAGCCTACTAGGGACAAAGTCTGAATAACACCGACAC
1 TAAGCCTACTAGGCACAAAGCCTGAACAACACCGACAC
* *
47196776 TAAGCCTGCTAGGCACAAAGCCTAAACAACACCGACAC
1 TAAGCCTACTAGGCACAAAGCCTGAACAACACCGACAC
* * * *
47196814 TAAGCCTGCTAGGAACAAAGCCTGAACAACATCGGCAC
1 TAAGCCTACTAGGCACAAAGCCTGAACAACACCGACAC
* * * *
47196852 TATGCCTACTAGGCACAAAGCCTAAACTACACCGGCAC
1 TAAGCCTACTAGGCACAAAGCCTGAACAACACCGACAC
** *
47196890 TGTGCCTGCTAGGCACAAAGCCT
1 TAAGCCTACTAGGCACAAAGCCT
47196913 AAATAAGGGT
Statistics
Matches: 154, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 154 1.00
ACGTcount: A:0.36, C:0.31, G:0.18, T:0.15
Consensus pattern (38 bp):
TAAGCCTACTAGGCACAAAGCCTGAACAACACCGACAC
Found at i:47196900 original size:114 final size:114
Alignment explanation
Indices: 47196700--47196915 Score: 290
Period size: 114 Copynumber: 1.9 Consensus size: 114
47196690 ACACTGGCAA
* * * * * *
47196700 TAAGCCTACTAGGCACTAAGCCTGAATAACACCAACACTAAGCCTACTAGGGACAAAGTCTGAAT
1 TAAGCCTACTAGGAACAAAGCCTGAACAACACCAACACTAAGCCTACTAGGCACAAAGCCTAAAT
47196765 AACACCGACACTAAGCCTGCTAGGCACAAAGCCTAAACAACACCGACAC
66 AACACCGACACTAAGCCTGCTAGGCACAAAGCCTAAACAACACCGACAC
* * ** *
47196814 TAAGCCTGCTAGGAACAAAGCCTGAACAACATCGGCACTATGCCTACTAGGCACAAAGCCTAAAC
1 TAAGCCTACTAGGAACAAAGCCTGAACAACACCAACACTAAGCCTACTAGGCACAAAGCCTAAA-
* **
47196879 T-ACACCGGCACTGTGCCTGCTAGGCACAAAGCCTAAA
65 TAACACCGACACTAAGCCTGCTAGGCACAAAGCCTAAA
47196916 TAAGGGTATA
Statistics
Matches: 87, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
114 86 0.99
115 1 0.01
ACGTcount: A:0.37, C:0.31, G:0.18, T:0.15
Consensus pattern (114 bp):
TAAGCCTACTAGGAACAAAGCCTGAACAACACCAACACTAAGCCTACTAGGCACAAAGCCTAAAT
AACACCGACACTAAGCCTGCTAGGCACAAAGCCTAAACAACACCGACAC
Found at i:47203905 original size:38 final size:38
Alignment explanation
Indices: 47203859--47203975 Score: 171
Period size: 38 Copynumber: 3.1 Consensus size: 38
47203849 AACTTTAATT
* * * *
47203859 ACACCGGCAATAAGCCTACTAGGCACTAAGCCTGAATA
1 ACACCGGCACTAAGCCTGCTAGGCACAAAGCCTAAATA
*
47203897 ACATCGGCACTAAGCCTGCTAGGCACAAAGCCTAAATA
1 ACACCGGCACTAAGCCTGCTAGGCACAAAGCCTAAATA
* *
47203935 ACACCGACACTAAGCCTGCTAGGCACAAAACCTAAATA
1 ACACCGGCACTAAGCCTGCTAGGCACAAAGCCTAAATA
47203973 ACA
1 ACA
47203976 GTGTAACTCA
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 71 1.00
ACGTcount: A:0.39, C:0.30, G:0.16, T:0.15
Consensus pattern (38 bp):
ACACCGGCACTAAGCCTGCTAGGCACAAAGCCTAAATA
Found at i:47208201 original size:3 final size:3
Alignment explanation
Indices: 47208193--47208221 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
47208183 CACCCTTTTG
47208193 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
47208222 GCTTAGCCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:47209888 original size:19 final size:20
Alignment explanation
Indices: 47209864--47209957 Score: 83
Period size: 18 Copynumber: 5.0 Consensus size: 20
47209854 TAAATTTTGG
* *
47209864 AATTTTTATAAA-TATTTTT
1 AATTTTTAAAAATTATTTTA
47209883 AA-TTTTAAAAATTATTTTA
1 AATTTTTAAAAATTATTTTA
*
47209902 AA--TTTAAAAATTATTTTG
1 AATTTTTAAAAATTATTTTA
* *
47209920 AA--TTTAAAATTTATTTTG
1 AATTTTTAAAAATTATTTTA
* *
47209938 AATTTTTGAAAATTTTTTTA
1 AATTTTTAAAAATTATTTTA
47209958 TTTTATTGTA
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
18 42 0.66
19 10 0.16
20 12 0.19
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.56
Consensus pattern (20 bp):
AATTTTTAAAAATTATTTTA
Found at i:47209926 original size:36 final size:36
Alignment explanation
Indices: 47209868--47209942 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 36
47209858 TTTTGGAATT
* *
47209868 TTTATAAATATTTTTAATTTTAAAAATTATTTTAAA
1 TTTAAAAATATTTTGAATTTTAAAAATTATTTTAAA
* *
47209904 TTTAAAAATTATTTTGAA-TTTAAAATTTATTTTGAA
1 TTTAAAAA-TATTTTGAATTTTAAAAATTATTTTAAA
47209940 TTT
1 TTT
47209943 TTGAAAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 26 0.76
37 8 0.24
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (36 bp):
TTTAAAAATATTTTGAATTTTAAAAATTATTTTAAA
Found at i:47210657 original size:32 final size:32
Alignment explanation
Indices: 47210591--47210657 Score: 75
Period size: 32 Copynumber: 2.1 Consensus size: 32
47210581 TTAGGTTTTG
** *
47210591 ATTTCTAAATTTATTGCATTTCATTTGAATAT
1 ATTTCTAAATTTATTGCATTAAATTTGAAAAT
47210623 ATTTCTAAATTTATTTGCA-TAAATATT-AAAAT
1 ATTTCTAAATTTA-TTGCATTAAAT-TTGAAAAT
47210655 ATT
1 ATT
47210658 GTAATTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
32 23 0.77
33 7 0.23
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.51
Consensus pattern (32 bp):
ATTTCTAAATTTATTGCATTAAATTTGAAAAT
Found at i:47211690 original size:29 final size:28
Alignment explanation
Indices: 47211658--47211734 Score: 82
Period size: 30 Copynumber: 2.6 Consensus size: 28
47211648 AATAAAAACC
47211658 AATAAAAATTATAAAAATTATTAAACTTT
1 AATAAAAATTATAAAAATT-TTAAACTTT
* *
47211687 AATAAAATATATATAAAAAATTTAAATTTT
1 AATAAAA-AT-TATAAAAATTTTAAACTTT
** *
47211717 ACCAAAAATTAGAAAAAT
1 AATAAAAATTATAAAAAT
47211735 ATAAAATGCA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
28 7 0.17
29 9 0.22
30 15 0.38
31 9 0.22
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.34
Consensus pattern (28 bp):
AATAAAAATTATAAAAATTTTAAACTTT
Found at i:47212050 original size:10 final size:9
Alignment explanation
Indices: 47212029--47212140 Score: 62
Period size: 9 Copynumber: 11.7 Consensus size: 9
47212019 TTTCTATACA
47212029 TTTTATAAT
1 TTTTATAAT
*
47212038 TTTTATGAT
1 TTTTATAAT
47212047 TTTTATAATT
1 TTTTATAA-T
*
47212057 TTTTCTAAT
1 TTTTATAAT
*
47212066 TTTTAATAAA
1 TTTT-ATAAT
** *
47212076 AATTAAATAT
1 TTTTATA-AT
*
47212086 TTCTTATATT
1 TT-TTATAAT
*
47212096 TTTTATTAAAA
1 TTTTA-T-AAT
*
47212107 TTTAATAAT
1 TTTTATAAT
*
47212116 TTTTATAAC
1 TTTTATAAT
*
47212125 TTTTATTTAT
1 TTTTA-TAAT
47212135 TTTTAT
1 TTTTAT
47212141 TTTTATCATT
Statistics
Matches: 75, Mismatches: 21, Indels: 14
0.68 0.19 0.13
Matches are distributed among these distances:
9 40 0.53
10 26 0.35
11 9 0.12
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (9 bp):
TTTTATAAT
Found at i:47212097 original size:29 final size:29
Alignment explanation
Indices: 47212064--47212122 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
47212054 ATTTTTTCTA
47212064 ATTTTTAATAAAAATTAAAT-ATTTCTTAT
1 ATTTTTAATAAAAATTAAATAATTT-TTAT
* * *
47212093 ATTTTTTATTAAAATTTAATAATTTTTAT
1 ATTTTTAATAAAAATTAAATAATTTTTAT
47212122 A
1 A
47212123 ACTTTTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (29 bp):
ATTTTTAATAAAAATTAAATAATTTTTAT
Found at i:47214058 original size:13 final size:14
Alignment explanation
Indices: 47214042--47214071 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
47214032 CCATTTTTCG
47214042 TATTTTATTT-TTT
1 TATTTTATTTATTT
47214055 TATTTTATTTATTT
1 TATTTTATTTATTT
47214069 TAT
1 TAT
47214072 ATATATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (14 bp):
TATTTTATTTATTT
Found at i:47214240 original size:6 final size:6
Alignment explanation
Indices: 47214193--47214233 Score: 75
Period size: 6 Copynumber: 7.0 Consensus size: 6
47214183 GCTTTAGCCC
47214193 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT A-TTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
47214234 TTGTTTTCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.15
6 29 0.85
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:47214883 original size:16 final size:15
Alignment explanation
Indices: 47214862--47214892 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
47214852 AATAGCAGCT
47214862 AGAAAGAAAGAAGAGA
1 AGAAAGAAA-AAGAGA
47214878 AGAAAGAAAAAGAGA
1 AGAAAGAAAAAGAGA
47214893 GAGAGGAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (15 bp):
AGAAAGAAAAAGAGA
Found at i:47215013 original size:13 final size:12
Alignment explanation
Indices: 47214989--47215076 Score: 95
Period size: 13 Copynumber: 6.8 Consensus size: 12
47214979 CCCGAAGAAG
47214989 AAGAAGAAAAAGA
1 AAGAA-AAAAAGA
47215002 AAGGAAAAAAAGA
1 AA-GAAAAAAAGA
47215015 GAAGAAAAAAGAGA
1 -AAGAAAAAA-AGA
*
47215029 GAAGAAAAAGAGA
1 -AAGAAAAAAAGA
*
47215042 AAGAAAAAAGAAA
1 AAGAAAAAA-AGA
*
47215055 AAGGAAAAAAGA
1 AAGAAAAAAAGA
47215067 AAGAAAAAAA
1 AAGAAAAAAA
47215077 TATCTTACAC
Statistics
Matches: 65, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
12 19 0.29
13 29 0.45
14 17 0.26
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (12 bp):
AAGAAAAAAAGA
Found at i:47215023 original size:25 final size:25
Alignment explanation
Indices: 47214990--47215075 Score: 99
Period size: 25 Copynumber: 3.4 Consensus size: 25
47214980 CCGAAGAAGA
47214990 AGAAG-AAAAAGAAAGGAAAAAAAG
1 AGAAGAAAAAAGAAAGGAAAAAAAG
*
47215014 AGAAGAAAAAAGAGA-GAAGAAAAAG
1 AGAAGAAAAAAGAAAGGAA-AAAAAG
47215039 AGAAAGAAAAAAGAAAAAGG-AAAAAAG
1 AG-AAGAAAAAAG--AAAGGAAAAAAAG
47215066 A-AAGAAAAAA
1 AGAAGAAAAAA
47215076 ATATCTTACA
Statistics
Matches: 54, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
24 8 0.15
25 25 0.46
26 10 0.19
27 7 0.13
28 3 0.06
29 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (25 bp):
AGAAGAAAAAAGAAAGGAAAAAAAG
Found at i:47215051 original size:7 final size:7
Alignment explanation
Indices: 47215016--47215068 Score: 56
Period size: 7 Copynumber: 7.9 Consensus size: 7
47215006 AAAAAAAGAG
47215016 AAGAAAA
1 AAGAAAA
* *
47215023 AAGAGAG
1 AAGAAAA
47215030 AAG-AAA
1 AAGAAAA
*
47215036 AAG-AGA
1 AAGAAAA
47215042 AAGAAAA
1 AAGAAAA
47215049 AAGAAAA
1 AAGAAAA
*
47215056 AGGAAAA
1 AAGAAAA
47215063 AAGAAA
1 AAGAAA
47215069 GAAAAAAATA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
6 9 0.24
7 28 0.76
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:47215056 original size:44 final size:44
Alignment explanation
Indices: 47214984--47215070 Score: 106
Period size: 44 Copynumber: 2.0 Consensus size: 44
47214974 TCGGCCCCGA
* * *
47214984 AGAAGAAGAAGAAAAAGAAAGGAAAAAAAGAGAAGAAA-AAAGAG
1 AGAAGAAAAAGAAAAAGAAAGAAAAAAAAG-GAAAAAAGAAAGAG
*
47215028 AGAAGAAAAAGAGAAAGAAA-AAAGAAAAAGGAAAAAAGAAAGA
1 AGAAGAAAAAGAAAAAGAAAGAAA-AAAAAGGAAAAAAGAAAGA
47215071 AAAAAATATC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
43 8 0.22
44 29 0.78
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (44 bp):
AGAAGAAAAAGAAAAAGAAAGAAAAAAAAGGAAAAAAGAAAGAG
Found at i:47215432 original size:13 final size:12
Alignment explanation
Indices: 47215404--47215442 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 12
47215394 AACCCCCAGC
47215404 AAAAAAAAAAGAG
1 AAAAAAAAAAG-G
47215417 AAAGAAAAAAAGG
1 AAA-AAAAAAAGG
47215430 AAAAAAGAAAAGG
1 AAAAAA-AAAAGG
47215443 GCCCACAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.12
13 13 0.54
14 8 0.33
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGG
Found at i:47215920 original size:17 final size:19
Alignment explanation
Indices: 47215886--47215934 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
47215876 AAATAAACAA
47215886 TCGTGTTTCAAAAGTTTTC
1 TCGTGTTTCAAAAGTTTTC
47215905 AT-GT-TTTCAAAA-TTTTC
1 -TCGTGTTTCAAAAGTTTTC
47215922 TCGTGTTTCAAAA
1 TCGTGTTTCAAAA
47215935 AAATAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 1 0.04
17 7 0.26
18 16 0.59
19 2 0.07
20 1 0.04
ACGTcount: A:0.27, C:0.14, G:0.12, T:0.47
Consensus pattern (19 bp):
TCGTGTTTCAAAAGTTTTC
Found at i:47216011 original size:15 final size:15
Alignment explanation
Indices: 47215993--47216043 Score: 66
Period size: 15 Copynumber: 3.1 Consensus size: 15
47215983 TTAAAAAAAC
47215993 AATTTTCGTGTTTCA
1 AATTTTCGTGTTTCA
47216008 AATTTTCGTGTTTTCAAA
1 AATTTTCGTG-TTTC--A
47216026 AATTTCTCGTGTTTCA
1 AATTT-TCGTGTTTCA
47216042 AA
1 AA
47216044 AATTTTCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
15 10 0.31
16 7 0.22
18 10 0.31
19 5 0.16
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.49
Consensus pattern (15 bp):
AATTTTCGTGTTTCA
Found at i:47216030 original size:18 final size:18
Alignment explanation
Indices: 47215993--47216398 Score: 139
Period size: 18 Copynumber: 24.1 Consensus size: 18
47215983 TTAAAAAAAC
47215993 AATTTTCGTG-TTTC--A
1 AATTTTCGTGTTTTCAAA
47216008 AATTTTCGTGTTTTCAAA
1 AATTTTCGTGTTTTCAAA
47216026 AATTTCTCGTG-TTTCAAA
1 AATTT-TCGTGTTTTCAAA
47216044 AA--------TTTTC--A
1 AATTTTCGTGTTTTCAAA
47216052 AATTTTCGTGTTTTCAAA
1 AATTTTCGTGTTTTCAAA
* *
47216070 AATTTTCTTCTTTTCAAAAAA
1 AATTTTCGTGTTTTC---AAA
*
47216091 AATTATCGTG-TTT-AAA
1 AATTTTCGTGTTTTCAAA
47216107 AATTTTCGCT-TTTTCAAA
1 AATTTTCG-TGTTTTCAAA
*
47216125 AATTTTCGTATTTTCAAA
1 AATTTTCGTGTTTTCAAA
* * *
47216143 AA-TTCCCTGTGTCTCAAA
1 AATTTTCGTGT-TTTCAAA
** * * *
47216161 AGCTTCCTTGTTTTTAAA
1 AATTTTCGTGTTTTCAAA
*
47216179 ATTTTTCGTG-TTTCAAA
1 AATTTTCGTGTTTTCAAA
** **
47216196 AATCCTCGTGTTTTCAGC
1 AATTTTCGTGTTTTCAAA
* *
47216214 AATTCTAGTG-TTTCAAA
1 AATTTTCGTGTTTTCAAA
*****
47216231 AA----AAAAATTT-AAA
1 AATTTTCGTGTTTTCAAA
*
47216244 ATTTTTCGTG-TTTCAAA
1 AATTTTCGTGTTTTCAAA
** *
47216261 AA-TTTCG-GTGCATCATA
1 AATTTTCGTGT-TTTCAAA
47216278 AATTTTCGTG-TTTCAAAA
1 AATTTTCGTGTTTTC-AAA
** *
47216296 AAAATTCGTGTTTCCAAA
1 AATTTTCGTGTTTTCAAA
* *
47216314 GATTCTCGTG-TTTC-AA
1 AATTTTCGTGTTTTCAAA
* *
47216330 AATTTTC--ATTTTAAAA
1 AATTTTCGTGTTTTCAAA
*
47216346 AATTTT-GTG-TTTCTAA
1 AATTTTCGTGTTTTCAAA
*
47216362 ACTTCTT-GTGTTTT-AAA
1 AATT-TTCGTGTTTTCAAA
47216379 AATTTTCGTGTTTTCAAA
1 AATTTTCGTGTTTTCAAA
47216397 AA
1 AA
47216399 ATAATTGTTT
Statistics
Matches: 285, Mismatches: 61, Indels: 87
0.66 0.14 0.20
Matches are distributed among these distances:
8 3 0.01
10 4 0.01
13 5 0.02
14 3 0.01
15 14 0.05
16 52 0.18
17 62 0.22
18 113 0.40
19 16 0.06
20 3 0.01
21 10 0.04
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.46
Consensus pattern (18 bp):
AATTTTCGTGTTTTCAAA
Found at i:47216054 original size:26 final size:26
Alignment explanation
Indices: 47216025--47216076 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
47216015 GTGTTTTCAA
47216025 AAATTTCTCGTG-TTTCAAAAATTTTC
1 AAATTT-TCGTGTTTTCAAAAATTTTC
47216051 AAATTTTCGTGTTTTCAAAAATTTTC
1 AAATTTTCGTGTTTTCAAAAATTTTC
47216077 TTCTTTTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.31, C:0.13, G:0.08, T:0.48
Consensus pattern (26 bp):
AAATTTTCGTGTTTTCAAAAATTTTC
Found at i:47216085 original size:44 final size:44
Alignment explanation
Indices: 47216003--47216131 Score: 150
Period size: 44 Copynumber: 3.1 Consensus size: 44
47215993 AATTTTCGTG
47216003 TTTCAAATTTTCGTGTTTTCAAAAA-TTTCTCGTGTTTCAAAAAT
1 TTTCAAATTTTCGTGTTTTCAAAAATTTTCTCGT-TTTCAAAAAT
47216047 TTTCAAATTTTCGTGTTTTCAAAAATTTTCTTC-TTTTCAAAAA-
1 TTTCAAATTTTCGTGTTTTCAAAAATTTTC-TCGTTTTCAAAAAT
* * *
47216090 ----AAATTATCGTG-TTT-AAAAATTTTCGCTTTTTCAAAAAT
1 TTTCAAATTTTCGTGTTTTCAAAAATTTTCTCGTTTTCAAAAAT
47216128 TTTC
1 TTTC
47216132 GTATTTTCAA
Statistics
Matches: 75, Mismatches: 2, Indels: 18
0.79 0.02 0.19
Matches are distributed among these distances:
36 1 0.01
37 20 0.27
38 3 0.04
39 10 0.13
44 34 0.45
45 5 0.07
46 2 0.03
ACGTcount: A:0.31, C:0.13, G:0.07, T:0.49
Consensus pattern (44 bp):
TTTCAAATTTTCGTGTTTTCAAAAATTTTCTCGTTTTCAAAAAT
Found at i:47216109 original size:16 final size:17
Alignment explanation
Indices: 47216088--47216430 Score: 145
Period size: 18 Copynumber: 20.3 Consensus size: 17
47216078 TCTTTTCAAA
*
47216088 AAAAATTATCGTGTTT-
1 AAAAATTTTCGTGTTTC
*
47216104 AAAAATTTTCGCTTTTTC
1 AAAAATTTTCG-TGTTTC
*
47216122 AAAAATTTTCGTATTTTC
1 AAAAATTTTCGT-GTTTC
** *
47216140 AAAAATTCCCTGTGTCTC
1 AAAAATTTTC-GTGTTTC
** * * *
47216158 AAAAGCTTCCTTGTTTTT
1 AAAAATTTTCGTG-TTTC
*
47216176 AAAATTTTTCGTGTTTC
1 AAAAATTTTCGTGTTTC
**
47216193 AAAAATCCTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
** * *
47216211 AGCAATTCTAGTGTTTC
1 AAAAATTTTCGTGTTTC
*****
47216228 AAAAA---AAAAATTT-
1 AAAAATTTTCGTGTTTC
*
47216241 AAAATTTTTCGTGTTTC
1 AAAAATTTTCGTGTTTC
**
47216258 AAAAA-TTTCGGTGCATC
1 AAAAATTTTC-GTGTTTC
*
47216275 ATAAATTTTCGTGTTTC
1 AAAAATTTTCGTGTTTC
**
47216292 AAAAAAAATTCGTGTTTCC
1 -AAAAATTTTCGTGTTT-C
* *
47216311 AAAGATTCTCGTGTTTC
1 AAAAATTTTCGTGTTTC
* *
47216328 -AAAATTTTCAT-TTTA
1 AAAAATTTTCGTGTTTC
47216343 AAAAATTTT-GTGTTTC
1 AAAAATTTTCGTGTTTC
* * *
47216359 TAAACTTCTT-GTGTTTT
1 AAAAATT-TTCGTGTTTC
47216376 AAAAATTTTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
**
47216394 AAAAAATAAT--TGTTTC
1 -AAAAATTTTCGTGTTTC
*
47216410 AAAAATCTTCGTGTTT-
1 AAAAATTTTCGTGTTTC
47216426 AAAAA
1 AAAAA
47216431 AAATTATCGT
Statistics
Matches: 240, Mismatches: 65, Indels: 44
0.69 0.19 0.13
Matches are distributed among these distances:
13 4 0.02
14 4 0.02
15 11 0.05
16 52 0.22
17 69 0.29
18 90 0.38
19 10 0.04
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (17 bp):
AAAAATTTTCGTGTTTC
Found at i:47216121 original size:37 final size:39
Alignment explanation
Indices: 47216007--47216146 Score: 107
Period size: 44 Copynumber: 3.6 Consensus size: 39
47215997 TTCGTGTTTC
*
47216007 AAATTTTCGTGTTTTCAAAAA-TTT-CTCGTGTTTCAAAAA
1 AAATTATCGTGTTTTCAAAAATTTTCCTC-T-TTTCAAAAA
* *
47216046 TTTTCAAATTTTCGTGTTTTCAAAAATTTTCTTCTTTTCAAAAA
1 -----AAATTATCGTGTTTTCAAAAATTTTCCTCTTTTCAAAAA
47216090 AAATTATCGTG-TTT-AAAAATTTTCGCT-TTTTC---AA
1 AAATTATCGTGTTTTCAAAAATTTTC-CTCTTTTCAAAAA
* *
47216124 AAATTTTCGTATTTTCAAAAATT
1 AAATTATCGTGTTTTCAAAAATT
47216147 CCCTGTGTCT
Statistics
Matches: 86, Mismatches: 5, Indels: 18
0.79 0.05 0.17
Matches are distributed among these distances:
34 11 0.13
35 3 0.03
36 7 0.08
37 15 0.17
38 4 0.05
39 10 0.12
44 30 0.35
45 4 0.05
46 2 0.02
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.48
Consensus pattern (39 bp):
AAATTATCGTGTTTTCAAAAATTTTCCTCTTTTCAAAAA
Found at i:47216297 original size:65 final size:65
Alignment explanation
Indices: 47216173--47216299 Score: 168
Period size: 64 Copynumber: 2.0 Consensus size: 65
47216163 CTTCCTTGTT
** *
47216173 TTTAAAATTTTTCGTGTTTCAAAAATCCTCGTGTTTTCAGCAATTCTAGTGTTTCAAAAAAAAAA
1 TTTAAAATTTTTCGTGTTTCAAAAATCCTCGTGTCATCAGAAATTCTAGTGTTTCAAAAAAAAAA
* * * *
47216238 TTTAAAATTTTTCGTGTTTCAAAAAT-TTCG-GTGCATCATAAATTTTCGTGTTTCAAAAAAAA
1 TTTAAAATTTTTCGTGTTTCAAAAATCCTCGTGT-CATCAGAAATTCTAGTGTTTCAAAAAAAA
47216300 TTCGTGTTTC
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
63 2 0.04
64 26 0.48
65 26 0.48
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (65 bp):
TTTAAAATTTTTCGTGTTTCAAAAATCCTCGTGTCATCAGAAATTCTAGTGTTTCAAAAAAAAAA
Found at i:47216431 original size:17 final size:17
Alignment explanation
Indices: 47216241--47216431 Score: 90
Period size: 17 Copynumber: 11.3 Consensus size: 17
47216231 AAAAAAATTT
* *
47216241 AAAATTTTTCGTGTTTC
1 AAAAATTTTCGTGTTTA
** *
47216258 AAAAA-TTTCGGTGCATC
1 AAAAATTTTC-GTGTTTA
*
47216275 ATAAATTTTCGTGTTTCA
1 AAAAATTTTCGTGTTT-A
** *
47216293 AAAAAAATTCGTGTTTCC
1 AAAAATTTTCGTGTTT-A
* *
47216311 AAAGATTCTCGTGTTT-
1 AAAAATTTTCGTGTTTA
* *
47216327 CAAAATTTTCAT-TTTA
1 AAAAATTTTCGTGTTTA
*
47216343 AAAAATTTT-GTGTTTC
1 AAAAATTTTCGTGTTTA
* * *
47216359 TAAACTTCTT-GTGTTTT
1 AAAAATT-TTCGTGTTTA
47216376 AAAAATTTTCGTGTTTTCA
1 AAAAATTTTCGTG-TTT-A
** *
47216395 AAAAATAAT--TGTTTC
1 AAAAATTTTCGTGTTTA
*
47216410 AAAAATCTTCGTGTTTA
1 AAAAATTTTCGTGTTTA
47216427 AAAAA
1 AAAAA
47216432 AATTATCGTA
Statistics
Matches: 129, Mismatches: 34, Indels: 22
0.70 0.18 0.12
Matches are distributed among these distances:
15 11 0.09
16 33 0.26
17 45 0.35
18 33 0.26
19 7 0.05
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.44
Consensus pattern (17 bp):
AAAAATTTTCGTGTTTA
Found at i:47227402 original size:11 final size:10
Alignment explanation
Indices: 47227381--47227414 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
47227371 TATTATGCCT
47227381 AAAAAACAAA
1 AAAAAACAAA
47227391 AAAAAACAAA
1 AAAAAACAAA
*
47227401 AAAAAAGAAA
1 AAAAAACAAA
47227411 AAAA
1 AAAA
47227415 TCAATATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.91, C:0.06, G:0.03, T:0.00
Consensus pattern (10 bp):
AAAAAACAAA
Found at i:47228633 original size:81 final size:77
Alignment explanation
Indices: 47228267--47228763 Score: 642
Period size: 74 Copynumber: 6.5 Consensus size: 77
47228257 TCAATTTTTG
* * *
47228267 TTTTTCAAAAATCAACTCATAATACGAAAGGTGAGTTAAGCCTCGGGTCACGCTGAGGTATTTTT
1 TTTTTAAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA-TTTT
47228332 TAATTTCTG---T
65 TAATTTCTGTCTT
* *
47228342 TTTTTCAAAAATCAACTCATAATACAAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTT
1 TTTTTAAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTT
*
47228407 AATTTATGT-TT
66 AATTTCTGTCTT
*
47228418 TTTTT--AAAGTCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTT
1 TTTTTAAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTT
* *
47228481 AATTTTTGTCCT
66 AATTTCTGTCTT
*
47228493 TTTTT---AAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAAGTATTTTT
1 TTTTTAAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTT
47228555 AATTTCTGTCTTT
66 AATTTCTGTC-TT
47228568 TTTTTAAAAAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
1 TTTTT---AAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
47228633 TTTAATTTCTGTCTT
63 TTTAATTTCTGTCTT
* * * * *
47228648 TTTTTAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCTGGTCACACGTCGAGGTATTT
1 TTTTTAAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGC-T-GAGGTATTT
*
47228713 TTCAA--T-T-TCTA
64 TT-AATTTCTGTCTT
* * * * *
47228724 TTCTTCAAAAGTCAAATCATAATCCGAGAGGTGAGTTGAG
1 TTTTTAAAAAATCAACTCATAATACGAGAGGTGAGTTGAG
47228764 TTTCGGATCG
Statistics
Matches: 383, Mismatches: 26, Indels: 25
0.88 0.06 0.06
Matches are distributed among these distances:
74 140 0.37
75 69 0.18
76 42 0.11
77 44 0.11
78 2 0.01
79 11 0.03
80 9 0.02
81 66 0.17
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (77 bp):
TTTTTAAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTT
AATTTCTGTCTT
Found at i:47229120 original size:6 final size:6
Alignment explanation
Indices: 47229067--47229113 Score: 87
Period size: 6 Copynumber: 8.0 Consensus size: 6
47229057 GCTTTAGCCC
47229067 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT A-TTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
47229114 TTGTTTTCAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 5 0.12
6 35 0.88
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:47229233 original size:30 final size:29
Alignment explanation
Indices: 47229181--47229319 Score: 115
Period size: 30 Copynumber: 4.7 Consensus size: 29
47229171 TACAAAAAAA
* *
47229181 TATAAATTATATTTTG-GCCCTAAACTTT
1 TATAAATTACATTTTGACCCCTAAACTTT
47229209 T-TCAAATTTACATTTTGACCCCT-AACATTT
1 TAT-AAA-TTACATTTTGACCCCTAAAC-TTT
* * *
47229239 TCTAAATTTTCATCTTGACCCCTAATA-TTT
1 TATAAA-TTACATTTTGACCCCTAA-ACTTT
* * *
47229269 TGTAAATTACATTTGGGCCCCTAAACTTT
1 TATAAATTACATTTTGACCCCTAAACTTT
*
47229298 ATATAAATTACATTTTGGCCCC
1 -TATAAATTACATTTTGACCCC
47229320 ATATTTTTCT
Statistics
Matches: 91, Mismatches: 11, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
27 1 0.01
28 5 0.05
29 29 0.32
30 53 0.58
31 2 0.02
32 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.42
Consensus pattern (29 bp):
TATAAATTACATTTTGACCCCTAAACTTT
Found at i:47229893 original size:13 final size:12
Alignment explanation
Indices: 47229869--47229963 Score: 90
Period size: 13 Copynumber: 7.8 Consensus size: 12
47229859 CCCGAAGAAG
47229869 AAGAAGAAAAAGA
1 AAGAA-AAAAAGA
47229882 AAGGAAAAAAAGA
1 AA-GAAAAAAAGA
47229895 GAAGAAAAAAGAGA
1 -AAGAAAAAA-AGA
*
47229909 GAAGAAAAAGAGA
1 -AAGAAAAAAAGA
47229922 AAG-AAAAAAG-
1 AAGAAAAAAAGA
*
47229932 AA-AAAAGAA-A
1 AAGAAAAAAAGA
*
47229942 AAGGAAAAAAGA
1 AAGAAAAAAAGA
47229954 AAGAAAAAAA
1 AAGAAAAAAA
47229964 TATCTTACAC
Statistics
Matches: 69, Mismatches: 6, Indels: 15
0.77 0.07 0.17
Matches are distributed among these distances:
10 9 0.13
11 11 0.16
12 13 0.19
13 19 0.28
14 17 0.25
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (12 bp):
AAGAAAAAAAGA
Found at i:47229903 original size:14 final size:14
Alignment explanation
Indices: 47229867--47229963 Score: 76
Period size: 14 Copynumber: 6.9 Consensus size: 14
47229857 ACCCCGAAGA
*
47229867 AGAAGAAGAAAAAG
1 AGAAGAAAAAAAAG
*
47229881 A-AAGGAAAAAAAG
1 AGAAGAAAAAAAAG
*
47229894 AGAAGAAAAAAGAG
1 AGAAGAAAAAAAAG
47229908 AGAAGAAAAAGAGAA-
1 AGAAGAAAAA-A-AAG
*
47229923 AGAA-AAAAGAAAAA
1 AGAAGAAAA-AAAAG
*
47229937 AGAAAAAGGAAAAAAG
1 AGAAGAA--AAAAAAG
47229953 A-AAGAAAAAAA
1 AGAAGAAAAAAA
47229964 TATCTTACAC
Statistics
Matches: 68, Mismatches: 7, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
13 18 0.26
14 30 0.44
15 12 0.18
16 6 0.09
17 2 0.03
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (14 bp):
AGAAGAAAAAAAAG
Found at i:47229903 original size:25 final size:24
Alignment explanation
Indices: 47229870--47229963 Score: 108
Period size: 25 Copynumber: 4.0 Consensus size: 24
47229860 CCGAAGAAGA
47229870 AGAAG-AAAAAGAAAGGAAAAAAAG
1 AGAAGAAAAAAGAAA-GAAAAAAAG
*
47229894 AGAAGAAAAAAGAGAGAAGAAAAAG
1 AGAAGAAAAAAGAAAGAA-AAAAAG
47229919 AGAAAGAAAAAAGAAA-AAAGAAAA-
1 AG-AAGAAAAAAGAAAGAAA-AAAAG
47229943 AG--GAAAAAAGAAAGAAAAAAA
1 AGAAGAAAAAAGAAAGAAAAAAA
47229964 TATCTTACAC
Statistics
Matches: 63, Mismatches: 2, Indels: 13
0.81 0.03 0.17
Matches are distributed among these distances:
21 15 0.24
22 3 0.05
24 11 0.17
25 22 0.35
26 12 0.19
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (24 bp):
AGAAGAAAAAAGAAAGAAAAAAAG
Found at i:47229931 original size:7 final size:7
Alignment explanation
Indices: 47229896--47229955 Score: 70
Period size: 7 Copynumber: 8.9 Consensus size: 7
47229886 AAAAAAAGAG
47229896 AAGAAAA
1 AAGAAAA
* *
47229903 AAGAGAG
1 AAGAAAA
47229910 AAG-AAA
1 AAGAAAA
*
47229916 AAG-AGA
1 AAGAAAA
47229922 AAGAAAA
1 AAGAAAA
47229929 AAGAAAA
1 AAGAAAA
47229936 AAGAAAA
1 AAGAAAA
*
47229943 AGGAAAA
1 AAGAAAA
47229950 AAGAAA
1 AAGAAA
47229956 GAAAAAAATA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
6 9 0.20
7 35 0.80
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:47229936 original size:32 final size:32
Alignment explanation
Indices: 47229896--47229962 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
47229886 AAAAAAAGAG
*
47229896 AAGAAAAAAGAGAGAA-GAAAAAGAGAAAGAAAA
1 AAGAAAAAAGA-AAAAGGAAAAA-AGAAAGAAAA
47229929 AAGAAAAAAGAAAAAGGAAAAAAGAAAGAAAA
1 AAGAAAAAAGAAAAAGGAAAAAAGAAAGAAAA
47229961 AA
1 AA
47229963 ATATCTTACA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 15 0.47
33 17 0.53
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (32 bp):
AAGAAAAAAGAAAAAGGAAAAAAGAAAGAAAA
Found at i:47230774 original size:20 final size:20
Alignment explanation
Indices: 47230749--47230799 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
47230739 TACTTTTTTT
47230749 AAAAAAAATAATCGTGTTTC
1 AAAAAAAATAATCGTGTTTC
** **
47230769 AAAAAATTTTCTCGTGTTTC
1 AAAAAAAATAATCGTGTTTC
47230789 -AAAAAAATAAT
1 AAAAAAAATAAT
47230800 AAAAAATTTC
Statistics
Matches: 23, Mismatches: 8, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.49, C:0.10, G:0.08, T:0.33
Consensus pattern (20 bp):
AAAAAAAATAATCGTGTTTC
Found at i:47230817 original size:30 final size:31
Alignment explanation
Indices: 47230769--47230827 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
47230759 ATCGTGTTTC
* *
47230769 AAAAAATTTTCTCGTGTTTCAAAAAAATAAT
1 AAAAAATTTTCCCATGTTTCAAAAAAATAAT
47230800 AAAAAA-TTTCCCATGTTTCAAAAAAATA
1 AAAAAATTTTCCCATGTTTCAAAAAAATA
47230828 TATTCGTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.51, C:0.12, G:0.05, T:0.32
Consensus pattern (31 bp):
AAAAAATTTTCCCATGTTTCAAAAAAATAAT
Found at i:47230887 original size:18 final size:18
Alignment explanation
Indices: 47230864--47231255 Score: 175
Period size: 18 Copynumber: 23.2 Consensus size: 18
47230854 TCCGTGTTTC
47230864 AAATTTTCGTGTTTTCAA
1 AAATTTTCGTGTTTTCAA
47230882 AAATTTCTCGTG-TTTC-A
1 AAATTT-TCGTGTTTTCAA
47230899 AAA-------GTTTTC--
1 AAATTTTCGTGTTTTCAA
47230908 AAATTTTCGTGTTTTCAA
1 AAATTTTCGTGTTTTCAA
* *
47230926 AAATTTTCTTCTTTTCAAAAA
1 AAATTTTCGTGTTTTC---AA
47230947 AAATTTCTCGTG-TTT-AA
1 AAATTT-TCGTGTTTTCAA
47230964 AAATTTTCGTGTTTTCAA
1 AAATTTTCGTGTTTTCAA
* *
47230982 AAATTTTCATATTTTCAA
1 AAATTTTCGTGTTTTCAA
**
47231000 AAATTCCCCGTG-TTTCAA
1 AAATT-TTCGTGTTTTCAA
** * * *
47231018 AAGCTTCCTTGTTTTTAA
1 AAATTTTCGTGTTTTCAA
*
47231036 AATTTTTCGTG-TTTCAA
1 AAATTTTCGTGTTTTCAA
**
47231053 AAATCCTCGTGTTTTCAA
1 AAATTTTCGTGTTTTCAA
* * ** *
47231071 CAATTCT-G-GAGTTCTA
1 AAATTTTCGTGTTTTCAA
*
47231087 AAATTTT--T-TTTT-TA
1 AAATTTTCGTGTTTTCAA
*
47231101 AATTTTTCGTG-TTTCAA
1 AAATTTTCGTGTTTTCAA
* ** *
47231118 AAATTTCCGTG-CATCAT
1 AAATTTTCGTGTTTTCAA
*
47231135 AAATTTCCGTG-TTTCAA
1 AAATTTTCGTGTTTTCAA
** *
47231152 AAAAATTCGTGTTTCCAA
1 AAATTTTCGTGTTTTCAA
* *
47231170 AGATTCTCGTG-TTTC-A
1 AAATTTTCGTGTTTTCAA
*
47231186 AAATTTTC--ATTTT-AA
1 AAATTTTCGTGTTTTCAA
*
47231201 AATATTTT-GTG-TTTCTA
1 AA-ATTTTCGTGTTTTCAA
*
47231218 AACTTCTT-GTGTTTT-AA
1 AAATT-TTCGTGTTTTCAA
47231235 AAATTTTCGTGTTTTCAA
1 AAATTTTCGTGTTTTCAA
47231253 AAA
1 AAA
47231256 ATAATTGTTT
Statistics
Matches: 279, Mismatches: 59, Indels: 72
0.68 0.14 0.18
Matches are distributed among these distances:
9 4 0.01
10 4 0.01
14 8 0.03
15 8 0.03
16 44 0.16
17 91 0.33
18 99 0.35
19 7 0.03
21 11 0.04
22 3 0.01
ACGTcount: A:0.29, C:0.14, G:0.10, T:0.47
Consensus pattern (18 bp):
AAATTTTCGTGTTTTCAA
Found at i:47230901 original size:17 final size:17
Alignment explanation
Indices: 47230850--47231254 Score: 109
Period size: 17 Copynumber: 24.1 Consensus size: 17
47230840 TAAAAAAAAC
47230850 AATTTC-CGTGTTTC-A
1 AATTTCTCGTGTTTCAA
47230865 AATTT-TCGTGTTTTCAAA
1 AATTTCTCGTG-TTTC-AA
47230883 AATTTCTCGTGTTTCAA
1 AATTTCTCGTGTTTCAA
47230900 AA------GT-TTTC-A
1 AATTTCTCGTGTTTCAA
47230909 AATTT-TCGTGTTTTCAAA
1 AATTTCTCGTG-TTTC-AA
47230927 AATTTTCTTC-T-TTTCAAAAAA
1 AA-TTTC-TCGTGTTTC----AA
*
47230948 AATTTCTCGTGTTTAAA
1 AATTTCTCGTGTTTCAA
47230965 AATTT-TCGTGTTTTCAAA
1 AATTTCTCGTG-TTTC-AA
* *
47230983 AATTT-TCATATTTTCAAA
1 AATTTCTCGT-GTTTC-AA
* *
47231001 AATTCCCCGTGTTTCAA
1 AATTTCTCGTGTTTCAA
* * *
47231018 AAGCTTC-CTTGTTTTTAA
1 AA-TTTCTCGTG-TTTCAA
*
47231036 AATTTTTCGTGTTTCAA
1 AATTTCTCGTGTTTCAA
* *
47231053 AAATCCTCGTGTTTTCAA
1 AATTTCTCGTG-TTTCAA
* *
47231071 CAA-TTCTGGAG-TTCTAA
1 -AATTTCTCGTGTTTC-AA
**
47231088 AATTT-T--T-TTTTTA
1 AATTTCTCGTGTTTCAA
*
47231101 AATTTTTCGTGTTTCAAA
1 AATTTCTCGTGTTTC-AA
**
47231119 AATTTC-CGTGCATCATA
1 AATTTCTCGTGTTTCA-A
47231136 AATTTC-CGTGTTTCAAA
1 AATTTCTCGTGTTTC-AA
**
47231153 AAAAT-TCGTGTTTCCAA
1 AATTTCTCGTGTTT-CAA
47231170 AGA-TTCTCGTGTTTCAA
1 A-ATTTCTCGTGTTTCAA
*
47231187 AATTT-TCAT-TTT-AA
1 AATTTCTCGTGTTTCAA
* *
47231201 AATATT-TTGTGTTTCTA
1 AAT-TTCTCGTGTTTCAA
* * *
47231218 AACTTCTTGTGTTTTAAA
1 AATTTCTCGTG-TTTCAA
47231236 AATTT-TCGTGTTTTCAA
1 AATTTCTCGTG-TTTCAA
47231253 AA
1 AA
47231255 AATAATTGTT
Statistics
Matches: 294, Mismatches: 45, Indels: 100
0.67 0.10 0.23
Matches are distributed among these distances:
9 3 0.01
10 4 0.01
11 2 0.01
13 6 0.02
14 10 0.03
15 16 0.05
16 30 0.10
17 103 0.35
18 90 0.31
19 14 0.05
20 6 0.02
21 10 0.03
ACGTcount: A:0.28, C:0.14, G:0.10, T:0.47
Consensus pattern (17 bp):
AATTTCTCGTGTTTCAA
Found at i:47230911 original size:26 final size:26
Alignment explanation
Indices: 47230882--47230933 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
47230872 GTGTTTTCAA
*
47230882 AAATTTCTCGTG-TTTCAAAAGTTTTC
1 AAATTT-TCGTGTTTTCAAAAATTTTC
47230908 AAATTTTCGTGTTTTCAAAAATTTTC
1 AAATTTTCGTGTTTTCAAAAATTTTC
47230934 TTCTTTTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.29, C:0.13, G:0.10, T:0.48
Consensus pattern (26 bp):
AAATTTTCGTGTTTTCAAAAATTTTC
Found at i:47230969 original size:38 final size:39
Alignment explanation
Indices: 47230864--47231004 Score: 123
Period size: 44 Copynumber: 3.6 Consensus size: 39
47230854 TCCGTGTTTC
* *
47230864 AAATTTTCGTGTTTTCAAAAATTTCTCGT-GTTTCAAAAGTTTTC
1 AAATTTTCGTGTTTTCAAAAATTT-TCGTCTTTTCAAAA-----A
*
47230908 AAATTTTCGTGTTTTCAAAAATTTTCTTCTTTTCAAAAA
1 AAATTTTCGTGTTTTCAAAAATTTTCGTCTTTTCAAAAA
*
47230947 AAATTTCTCGTG-TTT-AAAAATTTTCGTGTTTTC---AA
1 AAATTT-TCGTGTTTTCAAAAATTTTCGTCTTTTCAAAAA
* *
47230982 AAATTTTCATATTTTCAAAAATT
1 AAATTTTCGTGTTTTCAAAAATT
47231005 CCCCGTGTTT
Statistics
Matches: 86, Mismatches: 7, Indels: 16
0.79 0.06 0.15
Matches are distributed among these distances:
34 3 0.03
35 11 0.13
36 7 0.08
38 16 0.19
39 9 0.10
40 5 0.06
43 3 0.03
44 32 0.37
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (39 bp):
AAATTTTCGTGTTTTCAAAAATTTTCGTCTTTTCAAAAA
Found at i:47231119 original size:100 final size:100
Alignment explanation
Indices: 47231008--47231256 Score: 233
Period size: 99 Copynumber: 2.5 Consensus size: 100
47230998 AAAAATTCCC
** *
47231008 CGTGTTTCAAAAGCTTCCTTGTTTTTAAAATTTTTCGTGTTTCAAAAATCCTCGTGTTTTCAACA
1 CGTGTTTCAAAA-CTTCCTTGTTTTTAAAA-TTTTCGTGTTTCAAAAAAACTCGTGTTTCCAA-A
* * *
47231073 -ATTCTGGAG-TTCTAAAATTTT-TTTTTTAAAT-TTTT
63 GATTCTCGAGTTTC-AAAATTTTCATTTTAAAATATTTT
* * ** * * *
47231108 CGTGTTTCAAAAATTTCCGTG-CATCATAAATTTCCGTGTTTCAAAAAAATTCGTGTTTCCAAAG
1 CGTGTTTC-AAAACTTCCTTGTTTTTA-AAATTTTCGTGTTTCAAAAAAACTCGTGTTTCCAAAG
*
47231172 ATTCTCGTGTTTCAAAATTTTCATTTTAAAATATTTT
64 ATTCTCGAGTTTCAAAATTTTCATTTTAAAATATTTT
*
47231209 -GTGTTTCTAAACTT-CTTGTGTTTTAAAAATTTTCGTGTTTTCAAAAAA
1 CGTGTTTCAAAACTTCCTTGT-TTTT-AAAATTTTCGTG-TTTCAAAAAA
47231257 TAATTGTTTC
Statistics
Matches: 118, Mismatches: 21, Indels: 19
0.75 0.13 0.12
Matches are distributed among these distances:
98 4 0.03
99 49 0.42
100 46 0.39
101 19 0.16
ACGTcount: A:0.28, C:0.14, G:0.11, T:0.47
Consensus pattern (100 bp):
CGTGTTTCAAAACTTCCTTGTTTTTAAAATTTTCGTGTTTCAAAAAAACTCGTGTTTCCAAAGAT
TCTCGAGTTTCAAAATTTTCATTTTAAAATATTTT
Found at i:47231265 original size:34 final size:34
Alignment explanation
Indices: 47231227--47231291 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
47231217 AAACTTCTTG
* * * **
47231227 TGTTTTAAAAATTTTCGTGTTTTCAAAAAATAAT
1 TGTTTCAAAAATCTTCATGTTTAAAAAAAATAAT
47231261 TGTTTCAAAAATCTTCATGTTTAAAAAAAAT
1 TGTTTCAAAAATCTTCATGTTTAAAAAAAAT
47231292 TCTCGTATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.43
Consensus pattern (34 bp):
TGTTTCAAAAATCTTCATGTTTAAAAAAAATAAT
Found at i:47236165 original size:16 final size:17
Alignment explanation
Indices: 47236134--47236166 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
47236124 CGAGAATGTA
*
47236134 TTCACACTTGAAAAGTG
1 TTCACACATGAAAAGTG
47236151 TTCACACAT-AAAAGTG
1 TTCACACATGAAAAGTG
47236167 GATGTCTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.27
Consensus pattern (17 bp):
TTCACACATGAAAAGTG
Found at i:47237386 original size:21 final size:22
Alignment explanation
Indices: 47237362--47237403 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
47237352 TTTAAACTTC
*
47237362 TATATTAAATC-CTTAATTTAG
1 TATAATAAATCACTTAATTTAG
47237383 TATAATAAATCAACTTAATTT
1 TATAATAAATC-ACTTAATTT
47237404 TATTTTGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
23 8 0.44
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (22 bp):
TATAATAAATCACTTAATTTAG
Found at i:47239602 original size:22 final size:21
Alignment explanation
Indices: 47239577--47239621 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
47239567 GTATTTTAGG
*
47239577 ATTTTTAGTCTAGTTTTATTTT
1 ATTTTTAGTCTAGTGTT-TTTT
*
47239599 ATTTTTAGTTTAGTGTTTTTT
1 ATTTTTAGTCTAGTGTTTTTT
47239620 AT
1 AT
47239622 ACTTTTTGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.18, C:0.02, G:0.11, T:0.69
Consensus pattern (21 bp):
ATTTTTAGTCTAGTGTTTTTT
Found at i:47240241 original size:16 final size:16
Alignment explanation
Indices: 47240201--47240241 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
47240191 GTTTATTTTC
* *
47240201 AATTTTTAAATTAGTT
1 AATTTTTAGATTAATT
*
47240217 AATTTTTAGTTTAATT
1 AATTTTTAGATTAATT
47240233 AATTTTTAG
1 AATTTTTAG
47240242 GTTGATTAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (16 bp):
AATTTTTAGATTAATT
Found at i:47240249 original size:16 final size:16
Alignment explanation
Indices: 47240201--47240249 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
47240191 GTTTATTTTC
** *
47240201 AATTTTTAAATTAGTT
1 AATTTTTAGGTTAATT
*
47240217 AATTTTTAGTTTAATT
1 AATTTTTAGGTTAATT
*
47240233 AATTTTTAGGTTGATT
1 AATTTTTAGGTTAATT
47240249 A
1 A
47240250 GATAAATTGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (16 bp):
AATTTTTAGGTTAATT
Found at i:47246468 original size:12 final size:12
Alignment explanation
Indices: 47246451--47246475 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
47246441 CATATCCTTT
47246451 TATATTTATATA
1 TATATTTATATA
47246463 TATATTTATATA
1 TATATTTATATA
47246475 T
1 T
47246476 TATGTTTACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TATATTTATATA
Found at i:47249134 original size:20 final size:22
Alignment explanation
Indices: 47249104--47249144 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
47249094 CAGGAAAAAG
47249104 GAAAAATAAAAGAAC-AATGGC
1 GAAAAATAAAAGAACGAATGGC
47249125 GAAAAA-AAAAGAACGAATGG
1 GAAAAATAAAAGAACGAATGG
47249145 AAGATGACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.63, C:0.07, G:0.22, T:0.07
Consensus pattern (22 bp):
GAAAAATAAAAGAACGAATGGC
Found at i:47260722 original size:39 final size:40
Alignment explanation
Indices: 47260518--47260740 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
47260508 TTGAATGCTG
* * * * * *
47260518 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAA
** * * *
47260558 TCCGGACTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAA
*
47260598 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
**
47260638 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
47260678 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * *
47260717 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
47260741 TGAACGAGGA
Statistics
Matches: 161, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
39 35 0.22
40 118 0.73
41 8 0.05
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Found at i:47260760 original size:79 final size:80
Alignment explanation
Indices: 47260593--47260775 Score: 226
Period size: 79 Copynumber: 2.3 Consensus size: 80
47260583 GTGCGAGATA
* * *
47260593 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
47260658 CATTCGTGCGAGTTG
66 CATTCGAACGAGGAG
* * * *
47260673 TTAAATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
*
47260737 CATTTGAACGAGGAG
66 CATTCGAACGAGGAG
* *
47260752 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
47260776 TACGTGATTT
Statistics
Matches: 87, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 14 0.16
79 46 0.53
80 27 0.31
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:47277237 original size:40 final size:40
Alignment explanation
Indices: 47277207--47277375 Score: 207
Period size: 40 Copynumber: 4.3 Consensus size: 40
47277197 GGACTAAGAT
* *
47277207 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* *
47277247 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* ** *
47277287 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGT-
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
* * * * *
47277326 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
47277365 CCGAAGGCATT
1 CCGAAGGCATT
47277376 TGAACGAGGA
Statistics
Matches: 117, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
38 22 0.19
39 22 0.19
40 73 0.62
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
Found at i:47277291 original size:80 final size:79
Alignment explanation
Indices: 47277154--47277377 Score: 245
Period size: 80 Copynumber: 2.8 Consensus size: 79
47277144 TTGAATGCTG
* * * * * * *
47277154 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCCTT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTAATAAATCCGGGCTAAG-TCCCGAAGGCATT
47277218 TGTGCGAGATACTAAA
64 TGTGCGAGATACTAAA
* * *
47277234 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTAATAAATCCGGGCTAAGTCCCGAAGGCATTT
* **
47277299 GTGCGAGTTGTTAAA
65 GTGCGAGATACTAAA
* * * * *
47277314 TCCGGGTTATGT-CCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTAATAAATCCGGGCTAAGTCCCGAAGGCATTTG
47277378 AACGAGGAGC
Statistics
Matches: 122, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
78 35 0.29
79 12 0.10
80 71 0.58
81 4 0.03
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTAATAAATCCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGATACTAAA
Found at i:47277395 original size:78 final size:80
Alignment explanation
Indices: 47277229--47277410 Score: 217
Period size: 78 Copynumber: 2.3 Consensus size: 80
47277219 GTGCGAGATA
* * *
47277229 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
** **
47277294 CATTCGTGCGAGTTG
66 CATTCGAACGAGGAG
* * * *
47277309 TTAAATCCGGGTTATGT-CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
*
47277372 CATTTGAACGAGGAG
66 CATTCGAACGAGGAG
* *
47277387 CTATATCC-GGTTAAATCCCGAAGG
1 CTAAATCCGGGTTAAGTCCCGAAGG
47277411 TACGTGATTT
Statistics
Matches: 85, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
77 6 0.07
78 53 0.62
79 11 0.13
80 15 0.18
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
CTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGG
CATTCGAACGAGGAG
Found at i:47284514 original size:50 final size:50
Alignment explanation
Indices: 47284412--47284653 Score: 191
Period size: 50 Copynumber: 4.7 Consensus size: 50
47284402 GGTAATGAGA
* * * *
47284412 TCCCATGTAAGACTATGTTTGGGACATGGAATTGGCATCATTGAGGTTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGA-G--ATGAGAGG
47284468 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
** * * * * * **
47284518 TCCCCCGTAAGACCATGTCTAGGACGTGGCATGGGCACCGATATAAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * * * * * **
47284568 TCTCATGTAAGACCATATCTGGGATATGGCATTGGCA--GTATAAGAAACA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAGG
* * *
47284617 TCCCATGTAAAACCATTTCTGGGACATGGCTTTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
47284654 TGTTATTATC
Statistics
Matches: 154, Mismatches: 31, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
48 1 0.01
49 37 0.24
50 78 0.51
52 1 0.01
53 2 0.01
55 1 0.01
56 34 0.22
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:47294280 original size:30 final size:30
Alignment explanation
Indices: 47294246--47294343 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
47294236 TAAACTAAAA
*
47294246 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
47294276 TGAGCTGAGGCTAAACTCCTAAGCTGAAGAT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAG-T
47294307 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
47294336 ATGAGCTA
1 -TGAGCTA
47294344 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
29 1 0.02
30 28 0.55
31 22 0.43
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:47295135 original size:11 final size:11
Alignment explanation
Indices: 47295107--47295151 Score: 54
Period size: 11 Copynumber: 3.7 Consensus size: 11
47295097 ATAGGTACGT
47295107 AAAAAAAAGTTCG
1 AAAAAAAA-TT-G
47295120 AAAAAAAAATTG
1 -AAAAAAAATTG
47295132 AAAAAAAATTG
1 AAAAAAAATTG
47295143 AAAAGAAAA
1 AAAA-AAAA
47295152 AAAAATTGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 15 0.50
12 5 0.17
13 2 0.07
14 8 0.27
ACGTcount: A:0.73, C:0.02, G:0.11, T:0.13
Consensus pattern (11 bp):
AAAAAAAATTG
Found at i:47297387 original size:17 final size:16
Alignment explanation
Indices: 47297365--47297417 Score: 61
Period size: 17 Copynumber: 3.2 Consensus size: 16
47297355 AGAAAAGAGC
47297365 GAAAATACAAAAGAAAA
1 GAAAATACAAAA-AAAA
*
47297382 GAAAATGATAAAAAAAA
1 GAAAAT-ACAAAAAAAA
* *
47297399 GAAAATTCAAAAAAGA
1 GAAAATACAAAAAAAA
47297415 GAA
1 GAA
47297418 TGAAAAGAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
16 10 0.32
17 16 0.52
18 5 0.16
ACGTcount: A:0.74, C:0.04, G:0.13, T:0.09
Consensus pattern (16 bp):
GAAAATACAAAAAAAA
Found at i:47307885 original size:41 final size:40
Alignment explanation
Indices: 47307815--47308054 Score: 273
Period size: 41 Copynumber: 5.8 Consensus size: 40
47307805 TTTGTATCTT
* *
47307815 TCGGGGCTTTAGCGGCGTTTTTAAGAAAGCACCGCTAATGC
1 TCGGGGCTTTAGCGGCGTTTTTGA-AAAGCGCCGCTAATGC
* **
47307856 TCAGATCTTTAGCGGCGTTTTTGATAAAGCGCCGCTAATGC
1 TCGGGGCTTTAGCGGCGTTTTTGA-AAAGCGCCGCTAATGC
* ** *
47307897 TCAGATCTTTAGTGGCGTTTTTGATAAAGCGCCGCTAATGC
1 TCGGGGCTTTAGCGGCGTTTTTGA-AAAGCGCCGCTAATGC
* *
47307938 TCGGGGCTTTAGCGGCATTTTTCAAGAAGCGCCGCTAATGC
1 TCGGGGCTTTAGCGGCGTTTTTGAA-AAGCGCCGCTAATGC
* * * *
47307979 TCGGGGATTTAGTGGCGTTTTTCAAGAAGCCCCGCTAATGC
1 TCGGGGCTTTAGCGGCGTTTTTGAA-AAGCGCCGCTAATGC
* *
47308020 TCGGGGATTTAGAGGCGTTTTTGAAAAAGCGCCGC
1 TCGGGGCTTTAGCGGCGTTTTTG-AAAAGCGCCGC
47308055 CATAGCATTT
Statistics
Matches: 177, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
40 1 0.01
41 174 0.98
42 2 0.01
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.29
Consensus pattern (40 bp):
TCGGGGCTTTAGCGGCGTTTTTGAAAAGCGCCGCTAATGC
Found at i:47308037 original size:123 final size:123
Alignment explanation
Indices: 47307815--47308054 Score: 313
Period size: 123 Copynumber: 2.0 Consensus size: 123
47307805 TTTGTATCTT
* ** *
47307815 TCGGGGCTTTAGCGGCGTTTTTAAGAAAGCACCGCTAATGCTCAGATCTTTAGCGGCGTTTTTGA
1 TCGGGGCTTTAGCGGCATTTTTAAGAAAGCACCGCTAATGCTCAGAGATTTAGCGGCGTTTTTCA
* ** * *
47307880 TAAAGCGCCGCTAATGCTCAGATCTTTAGTGGCGTTTTTGATAAAGCGCCGCTAATGC
66 TAAAGCCCCGCTAATGCTCAGAGATTTAGAGGCGTTTTTGAAAAAGCGCCGCTAATGC
* * * *
47307938 TCGGGGCTTTAGCGGCATTTTTCAAG-AAGCGCCGCTAATGCTCGGGGATTTAGTGGCGTTTTTC
1 TCGGGGCTTTAGCGGCATTTTT-AAGAAAGCACCGCTAATGCTCAGAGATTTAGCGGCGTTTTTC
* *
47308002 A-AGAAGCCCCGCTAATGCTCGGGGATTTAGAGGCGTTTTTGAAAAAGCGCCGC
65 ATA-AAGCCCCGCTAATGCTCAGAGATTTAGAGGCGTTTTTGAAAAAGCGCCGC
47308055 CATAGCATTT
Statistics
Matches: 100, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
122 1 0.01
123 96 0.96
124 3 0.03
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.29
Consensus pattern (123 bp):
TCGGGGCTTTAGCGGCATTTTTAAGAAAGCACCGCTAATGCTCAGAGATTTAGCGGCGTTTTTCA
TAAAGCCCCGCTAATGCTCAGAGATTTAGAGGCGTTTTTGAAAAAGCGCCGCTAATGC
Found at i:47308196 original size:21 final size:20
Alignment explanation
Indices: 47308130--47308196 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 20
47308120 TTTTTAATTG
*
47308130 AATATTTGTTAAAAATGGAT
1 AATATTTGTTAAAAATGGAA
* *
47308150 AA-ATTTGAAATAAAAAATAGAAA
1 AATATTTG---TTAAAAAT-GGAA
47308173 AATATTTGTTAAAAATGGAGA
1 AATATTTGTTAAAAATGGA-A
47308194 AAT
1 AAT
47308197 TAAAATACTA
Statistics
Matches: 36, Mismatches: 5, Indels: 11
0.69 0.10 0.21
Matches are distributed among these distances:
19 5 0.14
20 4 0.11
21 11 0.31
22 7 0.19
23 4 0.11
24 5 0.14
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.31
Consensus pattern (20 bp):
AATATTTGTTAAAAATGGAA
Found at i:47308470 original size:13 final size:14
Alignment explanation
Indices: 47308441--47308470 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
47308431 AGAGTATGAA
47308441 ATTAGGGATTATTG
1 ATTAGGGATTATTG
47308455 ATTAGGGATT-TTG
1 ATTAGGGATTATTG
47308468 ATT
1 ATT
47308471 TAAGGGTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.47
Consensus pattern (14 bp):
ATTAGGGATTATTG
Found at i:47308541 original size:21 final size:21
Alignment explanation
Indices: 47308488--47308541 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
47308478 TGTGATTTAA
*
47308488 GATTTATGGGTTAGTGGTTAGG
1 GATTTA-GGGTTAGGGGTTAGG
*
47308510 G-GTTAGAGGTTAGGGGTTAGG
1 GATTTAG-GGTTAGGGGTTAGG
47308531 GATTTAGGGTT
1 GATTTAGGGTT
47308542 TATGGATTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
20 1 0.04
21 21 0.78
22 5 0.19
ACGTcount: A:0.19, C:0.00, G:0.44, T:0.37
Consensus pattern (21 bp):
GATTTAGGGTTAGGGGTTAGG
Found at i:47308543 original size:7 final size:7
Alignment explanation
Indices: 47308495--47308531 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
47308485 TAAGATTTAT
47308495 GGGTTAG
1 GGGTTAG
*
47308502 TGGTTAG
1 GGGTTAG
47308509 GGGTTAG
1 GGGTTAG
*
47308516 AGGTTAG
1 GGGTTAG
47308523 GGGTTAG
1 GGGTTAG
47308530 GG
1 GG
47308532 ATTTAGGGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.16, C:0.00, G:0.54, T:0.30
Consensus pattern (7 bp):
GGGTTAG
Found at i:47308731 original size:14 final size:14
Alignment explanation
Indices: 47308706--47308752 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
47308696 TATTAAATAA
*
47308706 GGTTTAGGGGTTAGT
1 GGTTT-GGGGTTAGG
*
47308721 GGTTTGGGGTTTGG
1 GGTTTGGGGTTAGG
*
47308735 GGTTTGGGGTTTGG
1 GGTTTGGGGTTAGG
47308749 GGTT
1 GGTT
47308753 AAGAGTTAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
14 25 0.83
15 5 0.17
ACGTcount: A:0.04, C:0.00, G:0.53, T:0.43
Consensus pattern (14 bp):
GGTTTGGGGTTAGG
Found at i:47308737 original size:21 final size:22
Alignment explanation
Indices: 47308706--47308752 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
47308696 TATTAAATAA
*
47308706 GGTTTAGGGGTTAGTGGTTTGG
1 GGTTTAGGGGTTAGGGGTTTGG
*
47308728 GGTTT-GGGGTTTGGGGTTTGG
1 GGTTTAGGGGTTAGGGGTTTGG
47308749 GGTT
1 GGTT
47308753 AAGAGTTAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.04, C:0.00, G:0.53, T:0.43
Consensus pattern (22 bp):
GGTTTAGGGGTTAGGGGTTTGG
Found at i:47309889 original size:22 final size:22
Alignment explanation
Indices: 47309856--47309920 Score: 73
Period size: 21 Copynumber: 3.0 Consensus size: 22
47309846 TAAAATCCCC
47309856 TCCCCCC-GAAATCCCCAACTT
1 TCCCCCCTGAAATCCCCAACTT
* *
47309877 TCCCCCCTAAAATCCCTAA--T
1 TCCCCCCTGAAATCCCCAACTT
*
47309897 TCCCCCCTTGAAACCCCCAACTT
1 TCCCCCC-TGAAATCCCCAACTT
47309920 T
1 T
47309921 ACAAACATAC
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
20 8 0.23
21 16 0.46
22 9 0.26
23 2 0.06
ACGTcount: A:0.25, C:0.49, G:0.03, T:0.23
Consensus pattern (22 bp):
TCCCCCCTGAAATCCCCAACTT
Found at i:47315401 original size:43 final size:43
Alignment explanation
Indices: 47315348--47315664 Score: 361
Period size: 43 Copynumber: 7.4 Consensus size: 43
47315338 GCTAAAAGTC
* * * * * *
47315348 ATCTTATAGTGGCATTTGTGGTATAAGTGTCACTAAAGGTCGTG
1 ATCTT-TAGCGGCGTTTGTGGTAGAAGCGCCACTAAAGGTCATG
* * *
47315392 TTCTTTAGTGGCG-TTGTGGTAGAAGCGCCTCTAAAGGTCATG
1 ATCTTTAGCGGCGTTTGTGGTAGAAGCGCCACTAAAGGTCATG
*
47315434 ATCTTTAGCGGCGTTTGTGGTAGAAGCGCCGCTAAAGGTCATG
1 ATCTTTAGCGGCGTTTGTGGTAGAAGCGCCACTAAAGGTCATG
*
47315477 ATCTTTAGCGGCGTTTGTGGTAGAAGCGCCGCTAAAGGTCATG
1 ATCTTTAGCGGCGTTTGTGGTAGAAGCGCCACTAAAGGTCATG
* * *
47315520 ATCTTTAGCGGTGTTTGTGGTAGAAGCGCCACTAACGGTCTTG
1 ATCTTTAGCGGCGTTTGTGGTAGAAGCGCCACTAAAGGTCATG
* ** *
47315563 TTCTTTAGCGGCGTTTGTGAG-AGAAGCGCTGCTAAAGATCATG
1 ATCTTTAGCGGCGTTTGTG-GTAGAAGCGCCACTAAAGGTCATG
* * * * * *
47315606 ATCTATAGCAGCTTTTGTGGGATAAGCGCCGCTAAAGGTCATG
1 ATCTTTAGCGGCGTTTGTGGTAGAAGCGCCACTAAAGGTCATG
*
47315649 A-CTTTTAGTGGCGTTT
1 ATC-TTTAGCGGCGTTT
47315665 ATTTTTAAAA
Statistics
Matches: 237, Mismatches: 32, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
42 37 0.16
43 195 0.82
44 5 0.02
ACGTcount: A:0.21, C:0.17, G:0.30, T:0.32
Consensus pattern (43 bp):
ATCTTTAGCGGCGTTTGTGGTAGAAGCGCCACTAAAGGTCATG
Found at i:47315568 original size:129 final size:127
Alignment explanation
Indices: 47315304--47315663 Score: 406
Period size: 129 Copynumber: 2.8 Consensus size: 127
47315294 TTTTTAAAAA
** * * * *
47315304 GTCATGTT-TTTAGCGGCGTTTGTCAAAAAGCGTCGCTAAAAGTC---ATCTTATAGTGGCATTT
1 GTCATGTTCTTTAGCGGCGTTTGTGGAGAAGCGCCGCTAAAGGTCATGATCTT-TAGCGGCATTT
* * * * * * *
47315365 GTGGTATAAGTGTCACTAAAGGTCGTGTTCTTTAGTGGCGTTGTGGTAGAAGCGCCTCTAAAG
65 GTGGTATAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTGTGGTAGAAGCGCCACTAAAG
* *
47315428 GTCATGATCTTTAGCGGCGTTTGTGGTAGAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTT
1 GTCATGTTCTTTAGCGGCGTTTGTGG-AGAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCATTT
* * *
47315493 GTGGTAGAAGCGCCGCTAAAGGTCATGATCTTTAGCGGTGTTTGTGGTAGAAGCGCCACTAACG
65 GTGGTATAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCG-TTGTGGTAGAAGCGCCACTAAAG
* * * * * *
47315557 GTCTTGTTCTTTAGCGGCGTTTGTGAGAGAAGCGCTGCTAAAGATCATGATCTATAGCAGCTTTT
1 GTCATGTTCTTTAGCGGCGTTTGTG-GAGAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCATTT
* *
47315622 GTGGGATAAGCGCCGCTAAAGGTCATGA-CTTTTAGTGGCGTT
65 GTGGTATAAGCGCCGCTAAAGGTCATGATC-TTTAGCGGCGTT
47315664 TATTTTTAAA
Statistics
Matches: 199, Mismatches: 29, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
124 7 0.04
125 15 0.08
126 16 0.08
128 44 0.22
129 116 0.58
130 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.29, T:0.32
Consensus pattern (127 bp):
GTCATGTTCTTTAGCGGCGTTTGTGGAGAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCATTTG
TGGTATAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTGTGGTAGAAGCGCCACTAAAG
Found at i:47317659 original size:26 final size:27
Alignment explanation
Indices: 47317595--47317686 Score: 91
Period size: 26 Copynumber: 3.5 Consensus size: 27
47317585 GCGGATACTC
* * *
47317595 CACAGCTCGTGTGAGCAGGCCCTTTTT
1 CACAACTCGTGTGAGCAGACCCTGTTT
*
47317622 CACAACTTGTGTGAGCAGACCC-GTTT
1 CACAACTCGTGTGAGCAGACCCTGTTT
* *
47317648 CATAACTCGTGTGAGCGGACCCAT-TTT
1 CACAACTCGTGTGAGCAGACCC-TGTTT
*
47317675 -ACAGCTCGTGTG
1 CACAACTCGTGTG
47317687 CTCAACCATG
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
26 32 0.59
27 22 0.41
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.28
Consensus pattern (27 bp):
CACAACTCGTGTGAGCAGACCCTGTTT
Found at i:47328059 original size:51 final size:51
Alignment explanation
Indices: 47327997--47328187 Score: 203
Period size: 51 Copynumber: 3.8 Consensus size: 51
47327987 CCAGTTCACA
* * *
47327997 TAGTAGTCTGCACATAGTACTACACATGTGACCATCACTATCCTATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCTGTACACG
* ** * *
47328048 TAGTAGCCTGCACATAGTACTACACACGTGATCGA--AGCTATCAGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTATCCTGTACACG
* *
47328099 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-T-CTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTATCCT-GTACACG
* *
47328149 TAGTAGCCTACACATAGTACTACACACGTGACCAACACT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
47328188 TTCACTTTCA
Statistics
Matches: 114, Mismatches: 19, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
49 3 0.03
50 39 0.34
51 69 0.61
52 2 0.02
53 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCTGTACACG
Found at i:47328164 original size:101 final size:102
Alignment explanation
Indices: 47327995--47328179 Score: 295
Period size: 101 Copynumber: 1.8 Consensus size: 102
47327985 TACCAGTTCA
* * *
47327995 CATAGTAGTCTGCACATAGTACTACACATGTGACCATCACTATCCTATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCTATACACGTAGTAGCCTACA
47328060 CATAGTACTACACACGTGATCGAAGCTATCAGGTACG
66 CATAGTACTACACACGTGATCGAAGCTATCAGGTACG
*
47328097 CATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-T-CTGGTACACGTAGTAGCCTA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACC-ATCACTATCCT-ATACACGTAGTAGCCTA
47328159 CACATAGTACTACACACGTGA
64 CACATAGTACTACACACGTGA
47328180 CCAACACTTT
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
100 2 0.03
101 37 0.48
102 34 0.44
103 4 0.05
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.24
Consensus pattern (102 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCTATACACGTAGTAGCCTACA
CATAGTACTACACACGTGATCGAAGCTATCAGGTACG
Found at i:47328202 original size:101 final size:102
Alignment explanation
Indices: 47327990--47328213 Score: 276
Period size: 101 Copynumber: 2.2 Consensus size: 102
47327980 AATGATACCA
* *
47327990 GTTCACATAGTAGTCTGCACATAGTACTACACATGTGACCATCACTATCCTATACACGTAGTAGC
1 GTTCACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCTATACACGTAGTAGC
* * * *
47328055 CTGCACATAGTACTACACACGTGATCGAAGCTATCAG
66 CTACACATAGTACTACACACGTGATCCAAACTATCAC
* * *
47328092 GTACGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-T-CTGGTACACGTAGTA
1 GTTCACATAGTAGCCTGCACATAGTACTACACATGCGACC-ATCACTATCCT-ATACACGTAGTA
*
47328154 GCCTACACATAGTACTACACACGTGA-CCAACACTTTCAC
64 GCCTACACATAGTACTACACACGTGATCCAA-ACTATCAC
* * *
47328193 TTTCACATAGTGGCCTACACA
1 GTTCACATAGTAGCCTGCACA
47328214 CAGTTCATGC
Statistics
Matches: 104, Mismatches: 15, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
100 5 0.05
101 58 0.56
102 37 0.36
103 4 0.04
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (102 bp):
GTTCACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCTATACACGTAGTAGC
CTACACATAGTACTACACACGTGATCCAAACTATCAC
Found at i:47330968 original size:58 final size:58
Alignment explanation
Indices: 47330906--47331022 Score: 135
Period size: 58 Copynumber: 2.0 Consensus size: 58
47330896 GGCAGAATTA
* * * * * *
47330906 AAATTCTGAAACAAAATCAAAATCAATTTTGTTAAATGACATGATTAAATCCCAAAAC
1 AAATTATGAAACAAAATCAAAATAAATTCTGTTAAACGACAGGAATAAATCCCAAAAC
* ** **
47330964 AAATTATGTAATTAAATCAAAATAAATTCTGTTAAACGGTAGGAATAAATCCCAAAAC
1 AAATTATGAAACAAAATCAAAATAAATTCTGTTAAACGACAGGAATAAATCCCAAAAC
47331022 A
1 A
47331023 GAATCATTTG
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
58 48 1.00
ACGTcount: A:0.50, C:0.14, G:0.09, T:0.27
Consensus pattern (58 bp):
AAATTATGAAACAAAATCAAAATAAATTCTGTTAAACGACAGGAATAAATCCCAAAAC
Found at i:47331698 original size:446 final size:442
Alignment explanation
Indices: 47330826--47332193 Score: 2011
Period size: 446 Copynumber: 3.0 Consensus size: 442
47330816 TTGATAATTT
* *
47330826 TTTTTAATTCAAAATTTCAAGCCACAATTAGG--CAAAAAAAACAGAAAATTTCCCTTTGGTTTT
1 TTTTTAATTCACAATTTCAAGCCACAATTAGGCACAAAAAAAACAGAAAATTTCCCTTTGATTTT
*
47330889 GTTAAACGGCAGAATTAAAATTCTGAAACAAAATCAAAATCAATTTTGTTAAATGACATGATTAA
66 GTTAAACGGCAGAATTAAAATTCTGAAACAAAAACAAAATCAATTTTGTTAAATGACATGATTAA
*
47330954 ATCCCAAAACAAATTATGTAATTAAATCAAAATAAATTCTGTTAAACGGTAGGAATAAATCCCAA
131 ATCCCGAAACAAATTATGTAATTAAATCAAAATAAATTCTGTTAAACGGTAGGAATAAATCCCAA
47331019 AACAGAATCATTTGATTAAGTCTTCGTTTAGAAACAAATCAATATCGAATAAAATCTTGTTAAAC
196 AACAGAATCATTTGATTAAGTCTTCGTTTAGAAACAAATCAATATCGAATAAAATCTTGTTAAAC
47331084 GGCGGGAATAAATCCCGAAATAGATTTTATTTAATTTAAGATAAATGTCCTTATATAAATAGATT
261 GGCGGGAATAAATCCCGAAATAGATTTTATTTAATTTAAGATAAATGTCCTTATATAAATAGATT
* *
47331149 ATATTTGCTAAGGAAAAATAATTTCGTGTTGGGCTGAAATATGAGGTGGTGCACTCGGCACGCTT
326 ATGTCTGCTAAGGAAAAATAATTTCGTGTTGGGCTGAAATATGAGGTGGTGCACTCGGCACGCTT
47331214 AAATACCAATTCTTCCAAAGAACCAATCCTAGACATGCATTCTCATATTGTC
391 AAATACCAATTCTTCCAAAGAACCAATCCTAGACATGCATTCTCATATTGTC
*
47331266 TTTTTAATTCACAATTTCAAGCCACAATTAGGCACAAAAAAAACCCAGAAAATTTTCCTTTGATT
1 TTTTTAATTCACAATTTCAAGCCACAATTAGGCACAAAAAAAA--CAGAAAATTTCCCTTTGATT
* * * * ** *
47331331 TTGTTAAACGTCAGAATTAAAATTCTAAAATAAAAACAAAATCAATTTTGTTAAACGGTAGGATT
64 TTGTTAAACGGCAGAATTAAAATTCTGAAACAAAAACAAAATCAATTTTGTTAAATGACATGATT
* * * * **
47331396 AAATTCTGAAACAAAATTATGTAATTAAATCAAAATAAATTCTATTAAATGGGGGGGAATAAATC
129 AAATCCCGAAAC-AAATTATGTAATTAAATCAAAATAAATTCTGTTAAA-CGGTAGGAATAAATC
*** * * *
47331461 TTGAAACAAAATTATTTGATTAAGTCTACGTTTAGAAACAAATCAATATCGAATAAAATCTTGTT
192 CCAAAACAGAATCATTTGATTAAGTCTTCGTTTAGAAACAAATCAATATCGAATAAAATCTTGTT
** * *
47331526 AAACGGCGGGGGTTAATCCCGAAATAGATTTTATTTAATTTAAGATAAATGTTCTTATATAAATA
257 AAACGGCGGGAATAAATCCCGAAATAGATTTTATTTAATTTAAGATAAATGTCCTTATATAAATA
* *
47331591 GATTATGCCTGCTAAGGAAAAATAATTTCGTGTTGGGCTGAAATATGAGGTTGTGCACTCGGCAC
322 GATTATGTCTGCTAAGGAAAAATAATTTCGTGTTGGGCTGAAATATGAGGTGGTGCACTCGGCAC
* * * * ** *
47331656 GCTTAAATACTAAGTCTTTCAAATAACCAATTTTAAACATGCATTCTCATATTGTC
387 GCTTAAATACCAATTCTTCCAAAGAACCAATCCTAGACATGCATTCTCATATTGTC
*
47331712 TTTTTAATTCACTATTGATAAATTTCTTTTTTAATTCAAAATTTCAAGCCACAATTAGGCAAAAA
1 --------T---T-TT--T-AA-TTC-------A--C--AATTTCAAGCCACAATTAGGC-ACAA
*
47331777 AAAAAACAGAAAATTTCCCTTTGATTTTGTTAAACGGCAGAATTAAAATTCTGAAACAAAAGCAA
38 AAAAAACAGAAAATTTCCCTTTGATTTTGTTAAACGGCAGAATTAAAATTCTGAAACAAAAACAA
*
47331842 AATCAATTTTGTTAAATGACATGTTTAAATCCCGAAACAAATTATGTAATTAAATCAAAATAAAT
103 AATCAATTTTGTTAAATGACATGATTAAATCCCGAAACAAATTATGTAATTAAATCAAAATAAAT
47331907 TCTGTTAAACGGTAGGAATAAATCCCAAAACAGAATCATTTGATTAAGTCTTCGTTTAGAAACAA
168 TCTGTTAAACGGTAGGAATAAATCCCAAAACAGAATCATTTGATTAAGTCTTCGTTTAGAAACAA
* * *
47331972 ATCAATATCGAATAAAATCTTGTTAAACGACGGGAATAAATCCCCAATTAGATTTTATTTAATTT
233 ATCAATATCGAATAAAATCTTGTTAAACGGCGGGAATAAATCCCGAAATAGATTTTATTTAATTT
47332037 AAGATAAATGTCCTTATATAAATAGATTATGTCTGCTAAGGAAAAATAATTTCGTGTTGGGCTGA
298 AAGATAAATGTCCTTATATAAATAGATTATGTCTGCTAAGGAAAAATAATTTCGTGTTGGGCTGA
* *
47332102 AATATGAAGTGGTGCACTCAGCACGCTTAAATACCAATTCTTCCAAAGAACCAATCCTAGACATG
363 AATATGAGGTGGTGCACTCGGCACGCTTAAATACCAATTCTTCCAAAGAACCAATCCTAGACATG
47332167 CATTCTCATATTGTC
428 CATTCTCATATTGTC
47332182 TTTTTAATTCAC
1 TTTTTAATTCAC
47332194 CATTGATAAA
Statistics
Matches: 814, Mismatches: 80, Indels: 63
0.85 0.08 0.07
Matches are distributed among these distances:
440 31 0.04
442 9 0.01
444 84 0.10
445 36 0.04
446 242 0.30
447 1 0.00
454 4 0.00
455 2 0.00
456 1 0.00
457 1 0.00
458 4 0.00
459 1 0.00
460 1 0.00
461 2 0.00
462 4 0.00
469 1 0.00
470 239 0.29
471 36 0.04
472 85 0.10
473 21 0.03
474 9 0.01
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.32
Consensus pattern (442 bp):
TTTTTAATTCACAATTTCAAGCCACAATTAGGCACAAAAAAAACAGAAAATTTCCCTTTGATTTT
GTTAAACGGCAGAATTAAAATTCTGAAACAAAAACAAAATCAATTTTGTTAAATGACATGATTAA
ATCCCGAAACAAATTATGTAATTAAATCAAAATAAATTCTGTTAAACGGTAGGAATAAATCCCAA
AACAGAATCATTTGATTAAGTCTTCGTTTAGAAACAAATCAATATCGAATAAAATCTTGTTAAAC
GGCGGGAATAAATCCCGAAATAGATTTTATTTAATTTAAGATAAATGTCCTTATATAAATAGATT
ATGTCTGCTAAGGAAAAATAATTTCGTGTTGGGCTGAAATATGAGGTGGTGCACTCGGCACGCTT
AAATACCAATTCTTCCAAAGAACCAATCCTAGACATGCATTCTCATATTGTC
Found at i:47332156 original size:470 final size:471
Alignment explanation
Indices: 47331264--47332309 Score: 1576
Period size: 470 Copynumber: 2.2 Consensus size: 471
47331254 TCTCATATTG
**
47331264 TCTTTTTAATTCACAATTTCAAGCCACAATTAGGCACAAAAAAAACCCAGAAAATTTTCCTTTGA
1 TCTTTTTAATTCACAATTTCAAGCCACAATTAGGCA-AAAAAAAAAACAGAAAATTTTCCTTTGA
* * **
47331329 TTTTGTTAAACGTCAGAATTAAAATTCTAAAATAAAAACAAAATCAATTTTGTTAAACGGTAGGA
65 TTTTGTTAAACGACAGAATTAAAATTCTGAAATAAAAACAAAATCAATTTTGTTAAACGACAGGA
* * * *
47331394 TTAAATTCTGAAACAAAATTATGTAATTAAATCAAAATAAATTCTATTAAATGGGGGGGAATAAA
130 TTAAATCCCGAAACAAAATTATGTAATTAAATCAAAATAAATTCTATTAAATCGGGAGGAATAAA
*** *
47331459 TCTTGAAACAAAATTATTTGATTAAGTCTACGTTTAGAAACAAATCAATATCGAATAAAATCTTG
195 TCCCAAAACAAAATCATTTGATTAAGTCTACGTTTAGAAACAAATCAATATCGAATAAAATCTTG
* ** * * *
47331524 TTAAACGGCGGGGGTTAATCCCGAAATAGATTTTATTTAATTTAAGATAAATGTTCTTATATAAA
260 TTAAACGACGGGAATAAATCCCCAAATAGATTTTATTTAATTTAAGATAAATGTCCTTATATAAA
* * *
47331589 TAGATTATGCCTGCTAAGGAAAAATAATTTCGTGTTGGGCTGAAATATGAGGTTGTGCACTCGGC
325 TAGATTATGCCTGCTAAGGAAAAATAATTTCGTGTTGGGCTGAAATATGAAGTGGTGCACTCAGC
* * * **
47331654 ACGCTTAAATACTAAGTCTTTCAAATAACCAATTTTAAACATGCATTCTCATATTGTCTTTTTAA
390 ACGCTTAAATACCAAGTCTTCCAAAGAACCAATCCTAAACATGCATTCTCATATTGTCTTTTTAA
*
47331719 TTCACTATTGATAAATT
455 TTCACCATTGATAAATT
* *
47331736 TCTTTTTTAATTCAAAATTTCAAGCCACAATTAGGCAAAAAAAAAAACAGAAAATTTCCCTTTGA
1 TC-TTTTTAATTCACAATTTCAAGCCACAATTAGGCAAAAAAAAAAACAGAAAATTTTCCTTTGA
* * * * * *
47331801 TTTTGTTAAACGGCAGAATTAAAATTCTGAAACAAAAGCAAAATCAATTTTGTTAAATGACATGT
65 TTTTGTTAAACGACAGAATTAAAATTCTGAAATAAAAACAAAATCAATTTTGTTAAACGACAGGA
* *
47331866 TTAAATCCCGAAAC-AAATTATGTAATTAAATCAAAATAAATTCTGTTAAA-CGGTAGGAATAAA
130 TTAAATCCCGAAACAAAATTATGTAATTAAATCAAAATAAATTCTATTAAATCGGGAGGAATAAA
* *
47331929 TCCCAAAACAGAATCATTTGATTAAGTCTTCGTTTAGAAACAAATCAATATCGAATAAAATCTTG
195 TCCCAAAACAAAATCATTTGATTAAGTCTACGTTTAGAAACAAATCAATATCGAATAAAATCTTG
*
47331994 TTAAACGACGGGAATAAATCCCCAATTAGATTTTATTTAATTTAAGATAAATGTCCTTATATAAA
260 TTAAACGACGGGAATAAATCCCCAAATAGATTTTATTTAATTTAAGATAAATGTCCTTATATAAA
*
47332059 TAGATTATGTCTGCTAAGGAAAAATAATTTCGTGTTGGGCTGAAATATGAAGTGGTGCACTCAGC
325 TAGATTATGCCTGCTAAGGAAAAATAATTTCGTGTTGGGCTGAAATATGAAGTGGTGCACTCAGC
* *
47332124 ACGCTTAAATACCAATTCTTCCAAAGAACCAATCCTAGACATGCATTCTCATATTGTCTTTTTAA
390 ACGCTTAAATACCAAGTCTTCCAAAGAACCAATCCTAAACATGCATTCTCATATTGTCTTTTTAA
47332189 TTCACCATTGATAAATT
455 TTCACCATTGATAAATT
* *
47332206 TCTTTTTAATTCACAATTTCAAGCCACAATTAGGAAAAAAGAAAAAGAAAAAGAAAATTTTCCTT
1 TCTTTTTAATTCACAATTTCAAGCCACAATTAGG--CAAA-AAAAA-AAACAGAAAATTTTCCTT
* *
47332271 TGATTTTGTTAAACGACAGGATT-AAATTATGAAATAAAA
62 TGATTTTGTTAAACGACAGAATTAAAATTCTGAAATAAAA
47332310 TTATGTAATT
Statistics
Matches: 517, Mismatches: 52, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
469 31 0.06
470 264 0.51
471 38 0.07
472 114 0.22
473 70 0.14
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.33
Consensus pattern (471 bp):
TCTTTTTAATTCACAATTTCAAGCCACAATTAGGCAAAAAAAAAAACAGAAAATTTTCCTTTGAT
TTTGTTAAACGACAGAATTAAAATTCTGAAATAAAAACAAAATCAATTTTGTTAAACGACAGGAT
TAAATCCCGAAACAAAATTATGTAATTAAATCAAAATAAATTCTATTAAATCGGGAGGAATAAAT
CCCAAAACAAAATCATTTGATTAAGTCTACGTTTAGAAACAAATCAATATCGAATAAAATCTTGT
TAAACGACGGGAATAAATCCCCAAATAGATTTTATTTAATTTAAGATAAATGTCCTTATATAAAT
AGATTATGCCTGCTAAGGAAAAATAATTTCGTGTTGGGCTGAAATATGAAGTGGTGCACTCAGCA
CGCTTAAATACCAAGTCTTCCAAAGAACCAATCCTAAACATGCATTCTCATATTGTCTTTTTAAT
TCACCATTGATAAATT
Found at i:47332681 original size:427 final size:427
Alignment explanation
Indices: 47331880--47332737 Score: 1414
Period size: 427 Copynumber: 2.0 Consensus size: 427
47331870 ATCCCGAAAC
* * *
47331880 AAATTATGTAATTAAATCAAAATAAATTCTGTTAAACGGTAGGAATAAATCCCAAAACAGAATCA
1 AAATTATGTAATTAAATCAAAATAAATTCTATTAAACGGCAGGAATAAATCCCAAAACAAAATCA
47331945 TTTGATTAAGTCTTCGTTTAGAAACAAATCAATATCGAATAAAATCTTGTTAAACGACGGGAATA
66 TTTGATTAAGTCTTCGTTTAGAAACAAATCAATATCGAATAAAATCTTGTTAAACGACGGGAATA
** *
47332010 AATCCCCAATTAGATTTTATTTAATTTAAGATAAATGTCCTTATATAAATAGATTATGTCTGCTA
131 AATCCCCAAACAGATTTTATTTAATTTAAGATAAATGTCCTTATATAAATAAATTATGTCTGCTA
* *
47332075 AGGAAAAATAATTTCGTGTTGGGCTGAAATATGAAGTGGTGCACTCAGCACGCTTAAATACCAAT
196 AAGAAAAATAATTTCGTGTTGGGCTGAAATATGAAGTGGTGCACTCAGCACGCTTAAATACCAAG
*
47332140 TCTTCCAAAGAACCAATCCTAGACATGCATTCTCATATTGTCTTTTTAATTCACCATTGATAAAT
261 TCTTCCAAAGAACCAATACTAGACATGCATTCTCATATTGTCTTTTTAATTCACCATTGATAAAT
*
47332205 TTCTTTTTAATTCACAATTTCAAGCCACAATTAGGAAAAAAGAAAAAGAAAAAGAAAATTTTCCT
326 TTCTTTTTAATTCACAATTTCAAGCCACAATTAGGAAAAAAGAAAAAG-AAAAGAAAATTTCCCT
* *
47332270 TTGATTTTGTTAAACGACAGGATT-AAATTATGAAATA
390 TTGATTTTGTAAAACGACAGAATTAAAATTATGAAATA
* * * *
47332307 AAATTATGTAATTAAATCAAAATAAATTCTATTAAATGGCGGGAATAAATCCCGAAACAAAATTA
1 AAATTATGTAATTAAATCAAAATAAATTCTATTAAACGGCAGGAATAAATCCCAAAACAAAATCA
* * *
47332372 TTTGATTAAGTTTTCGTTTAGAAACAAATCAATATTGAATAAAATCTTGTTAAACGGCGGGAATA
66 TTTGATTAAGTCTTCGTTTAGAAACAAATCAATATCGAATAAAATCTTGTTAAACGACGGGAATA
* *
47332437 AATCCCGAAACAGATTTTATTTAATTTAATATAAATGTCCTTATATAAATAAATTATGTCTGCTA
131 AATCCCCAAACAGATTTTATTTAATTTAAGATAAATGTCCTTATATAAATAAATTATGTCTGCTA
* *
47332502 AAGAAAAATAATTTCGTGTTGGGCTGAAATATGAGGTGGTGCACTCGGCACGCTTAAATACCAAG
196 AAGAAAAATAATTTCGTGTTGGGCTGAAATATGAAGTGGTGCACTCAGCACGCTTAAATACCAAG
* * *
47332567 TCTTTCAAAGAACCAATACTAGACATGCATTCTTATATTGTCTTTTTAATTCACCGTTGATAAAT
261 TCTTCCAAAGAACCAATACTAGACATGCATTCTCATATTGTCTTTTTAATTCACCATTGATAAAT
* *
47332632 TTTTTTTTAATTCCCAATTTCAAGCCACAATTAGGCAAAAAAG-AAAAGAAAAGAAAATTTCCCT
326 TTCTTTTTAATTCACAATTTCAAGCCACAATTAGG-AAAAAAGAAAAAGAAAAGAAAATTTCCCT
* *
47332696 TTGATTTTGTAAAACTACAGAATTAAAATTCTGAAATA
390 TTGATTTTGTAAAACGACAGAATTAAAATTATGAAATA
47332734 AAAT
1 AAAT
47332738 CAAAACCAAT
Statistics
Matches: 399, Mismatches: 30, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
426 36 0.09
427 356 0.89
428 7 0.02
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.33
Consensus pattern (427 bp):
AAATTATGTAATTAAATCAAAATAAATTCTATTAAACGGCAGGAATAAATCCCAAAACAAAATCA
TTTGATTAAGTCTTCGTTTAGAAACAAATCAATATCGAATAAAATCTTGTTAAACGACGGGAATA
AATCCCCAAACAGATTTTATTTAATTTAAGATAAATGTCCTTATATAAATAAATTATGTCTGCTA
AAGAAAAATAATTTCGTGTTGGGCTGAAATATGAAGTGGTGCACTCAGCACGCTTAAATACCAAG
TCTTCCAAAGAACCAATACTAGACATGCATTCTCATATTGTCTTTTTAATTCACCATTGATAAAT
TTCTTTTTAATTCACAATTTCAAGCCACAATTAGGAAAAAAGAAAAAGAAAAGAAAATTTCCCTT
TGATTTTGTAAAACGACAGAATTAAAATTATGAAATA
Found at i:47334934 original size:11 final size:10
Alignment explanation
Indices: 47334917--47334941 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
47334907 TCTTTACCTC
47334917 CTTTTTTTTT
1 CTTTTTTTTT
47334927 CTTTTTTTTT
1 CTTTTTTTTT
47334937 CTTTT
1 CTTTT
47334942 CCTTTTCTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:47343692 original size:39 final size:39
Alignment explanation
Indices: 47343572--47343693 Score: 124
Period size: 39 Copynumber: 3.1 Consensus size: 39
47343562 CTTTGAGTCA
* *
47343572 ATGAGACACTAGGTGTCAATATATTACTTAGAATTAATTCG
1 ATGAGACACTAGGTGTCAAT-TATTACTTCGAATT-ATCCG
* * ** * *
47343613 ATGAGACACTGGGTGCCAA-T-TTACTTCGGTTTAGCTG
1 ATGAGACACTAGGTGTCAATTATTACTTCGAATTATCCG
47343650 ATGAGACACT-GGTGTCAACTTATTACTTCGAATTATCCG
1 ATGAGACACTAGGTGTCAA-TTATTACTTCGAATTATCCG
47343689 ATGAG
1 ATGAG
47343694 GTACTGGGTA
Statistics
Matches: 65, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
36 7 0.11
37 12 0.18
38 10 0.15
39 19 0.29
41 17 0.26
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (39 bp):
ATGAGACACTAGGTGTCAATTATTACTTCGAATTATCCG
Found at i:47346453 original size:35 final size:32
Alignment explanation
Indices: 47346404--47346467 Score: 83
Period size: 35 Copynumber: 1.9 Consensus size: 32
47346394 AAAAAAATCT
47346404 AAAGTTAAAATATATTATTATAATAATATTATTTA
1 AAAGTTAAAATATA-TATTAT-AT-ATATTATTTA
**
47346439 AAAGTTAAGTTATATATTATATATATTAT
1 AAAGTTAAAATATATATTATATATATTAT
47346468 ATTATATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 7 0.26
33 2 0.07
34 6 0.22
35 12 0.44
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (32 bp):
AAAGTTAAAATATATATTATATATATTATTTA
Found at i:47346459 original size:5 final size:5
Alignment explanation
Indices: 47346451--47346491 Score: 75
Period size: 5 Copynumber: 8.4 Consensus size: 5
47346441 AGTTAAGTTA
47346451 TATAT TATA- TATAT TATAT TATAT TATAT TATAT TATAT TA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TA
47346492 AATAAAAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 4 0.11
5 31 0.89
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:47347481 original size:25 final size:25
Alignment explanation
Indices: 47347453--47347556 Score: 85
Period size: 25 Copynumber: 4.4 Consensus size: 25
47347443 GAACTTTAGC
* **
47347453 GTGCTCTCTGATTATTAGCACGTTG
1 GTGCTCTCTGATTACTAGCACGTCA
*
47347478 GTGCTCTCTGATTACTAGTACGTCA
1 GTGCTCTCTGATTACTAGCACGTCA
* * *
47347503 GTGCTCTCTGTTTA-GAGCA--TCT
1 GTGCTCTCTGATTACTAGCACGTCA
* *
47347525 GTGCTCTCTG--TA-TAGCACTTTA
1 GTGCTCTCTGATTACTAGCACGTCA
47347547 GTGCTCTCTG
1 GTGCTCTCTG
47347557 TTCATTAGTG
Statistics
Matches: 66, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
20 6 0.09
22 23 0.35
24 3 0.05
25 34 0.52
ACGTcount: A:0.15, C:0.23, G:0.22, T:0.39
Consensus pattern (25 bp):
GTGCTCTCTGATTACTAGCACGTCA
Found at i:47347541 original size:20 final size:22
Alignment explanation
Indices: 47347502--47347557 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
47347492 CTAGTACGTC
47347502 AGTGCTCTCTGTTTAGAGCA-TCT
1 AGTGCTCTCTG--TAGAGCACTCT
* *
47347525 -GTGCTCTCTGTATAGCACTTT
1 AGTGCTCTCTGTAGAGCACTCT
47347546 AGTGCTCTCTGT
1 AGTGCTCTCTGT
47347558 TCATTAGTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 6 0.21
21 2 0.07
22 21 0.72
ACGTcount: A:0.14, C:0.23, G:0.21, T:0.41
Consensus pattern (22 bp):
AGTGCTCTCTGTAGAGCACTCT
Found at i:47351185 original size:35 final size:33
Alignment explanation
Indices: 47351136--47351200 Score: 85
Period size: 35 Copynumber: 1.9 Consensus size: 33
47351126 AAAAAAATCT
47351136 AAAGTTAAAATATATTATTATAATAATATTATTTA
1 AAAGTTAAAATATA-TATTAT-ATAATATTATTTA
** *
47351171 AAAGTTAAGTTATATATTATATTATATTAT
1 AAAGTTAAAATATATATTATATAATATTAT
47351201 ATTATATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 9 0.33
34 6 0.22
35 12 0.44
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (33 bp):
AAAGTTAAAATATATATTATATAATATTATTTA
Found at i:47351191 original size:5 final size:5
Alignment explanation
Indices: 47351183--47351244 Score: 124
Period size: 5 Copynumber: 12.4 Consensus size: 5
47351173 AGTTAAGTTA
47351183 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
47351233 TATAT TATAT TA
1 TATAT TATAT TA
47351245 AATAAAAGAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 57 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:47352234 original size:25 final size:25
Alignment explanation
Indices: 47352206--47352290 Score: 125
Period size: 25 Copynumber: 3.4 Consensus size: 25
47352196 GAACTTTAGC
*
47352206 GTGCTCTCTAATTATTAGCACGTTG
1 GTGCTCTCTGATTATTAGCACGTTG
47352231 GTGCTCTCTGATTATTAGCACGTTG
1 GTGCTCTCTGATTATTAGCACGTTG
* * **
47352256 GTGCTATCTGATTACTAGCACGTCA
1 GTGCTCTCTGATTATTAGCACGTTG
47352281 GTGCTCTCTG
1 GTGCTCTCTG
47352291 TTTAGCACAT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 54 1.00
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (25 bp):
GTGCTCTCTGATTATTAGCACGTTG
Found at i:47354304 original size:13 final size:13
Alignment explanation
Indices: 47354288--47354313 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
47354278 TTAGACTCGT
47354288 AAATATTTATTAA
1 AAATATTTATTAA
47354301 AAATATTTATTAA
1 AAATATTTATTAA
47354314 GCTAGCTGTG
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAATATTTATTAA
Found at i:47354568 original size:5 final size:5
Alignment explanation
Indices: 47354516--47354626 Score: 140
Period size: 5 Copynumber: 22.6 Consensus size: 5
47354506 AAGTTAATAA
* * * *
47354516 ATATT ATAAT ATTATA ATATT ATATCT -TAAT -TATT A-AGT ATA-T ATATT
1 ATATT ATATT A-TATT ATATT ATAT-T ATATT ATATT ATATT ATATT ATATT
47354564 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
47354614 ATATT ATATT ATA
1 ATATT ATATT ATA
47354627 ATGATAAAAT
Statistics
Matches: 94, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
4 11 0.12
5 79 0.84
6 4 0.04
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (5 bp):
ATATT
Found at i:47360585 original size:17 final size:17
Alignment explanation
Indices: 47360563--47360629 Score: 57
Period size: 17 Copynumber: 3.7 Consensus size: 17
47360553 TTGAATGTTA
47360563 TGTGATTATATGAGTAT
1 TGTGATTATATGAGTAT
*
47360580 TGTGATATATGCTTGAATGT-T
1 TGTGAT-TAT--ATG-A-GTAT
47360601 ATGTGATTATATGAGTAT
1 -TGTGATTATATGAGTAT
47360619 TGTGA-TATATG
1 TGTGATTATATG
47360630 CTTAAATGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 15
0.71 0.03 0.26
Matches are distributed among these distances:
16 6 0.15
17 13 0.32
18 5 0.12
19 2 0.05
20 2 0.05
21 5 0.12
22 8 0.20
ACGTcount: A:0.28, C:0.01, G:0.24, T:0.46
Consensus pattern (17 bp):
TGTGATTATATGAGTAT
Found at i:47360590 original size:39 final size:39
Alignment explanation
Indices: 47360534--47360669 Score: 186
Period size: 39 Copynumber: 3.5 Consensus size: 39
47360524 AACATGTTTT
* * *
47360534 TGAGTATTATGACATATGATTGAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
47360573 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
* *
47360612 TGAGTATTGTGATATATGCTTAAATGTTATGTG--CATA
1 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
* * *
47360649 TGTGTAATGTGATAGATGCTT
1 TGAGTATTGTGATATATGCTT
47360670 AAAAGTGAAT
Statistics
Matches: 89, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
37 21 0.24
39 68 0.76
ACGTcount: A:0.29, C:0.04, G:0.23, T:0.44
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTGAATGTTATGTGATTATA
Found at i:47363087 original size:17 final size:17
Alignment explanation
Indices: 47363053--47363104 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 17
47363043 AATATATAAA
47363053 ATATAAAATTATTCAAAAT
1 ATATAAAA--ATTCAAAAT
47363072 ATTATAAAAATT-AAAAT
1 A-TATAAAAATTCAAAAT
*
47363089 ATGTAAAAATTCAAAA
1 ATATAAAAATTCAAAA
47363105 AAATTGTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
16 9 0.30
17 10 0.33
18 3 0.10
19 1 0.03
20 7 0.23
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.33
Consensus pattern (17 bp):
ATATAAAAATTCAAAAT
Found at i:47363097 original size:27 final size:26
Alignment explanation
Indices: 47363040--47363098 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 26
47363030 AAAACTATAA
47363040 AAAAATATATAAAATATAAAATTATT
1 AAAAATATATAAAATATAAAATTATT
*
47363066 CAAAATATTATAAAA-ATTAAAA-TATGT
1 AAAAATA-TATAAAATA-TAAAATTAT-T
47363093 AAAAAT
1 AAAAAT
47363099 TCAAAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
26 10 0.36
27 18 0.64
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (26 bp):
AAAAATATATAAAATATAAAATTATT
Done.