Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008027.1 Hibiscus syriacus cultivar Beakdansim tig00110503_pilon, whole genome shotgun sequence
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: 7662336
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 38
Found at i:3645386 original size:14 final size:14
Alignment explanation
Indices: 3645310--3645386 Score: 58
Period size: 14 Copynumber: 5.9 Consensus size: 14
3645300 TCGTAATAAT
*
3645310 TATTAAATCATTAA
1 TATTAAATCATTAC
* *
3645324 TATTAAATTATTAT
1 TATTAAATCATTAC
*
3645338 TATAAAATCATTAC
1 TATTAAATCATTAC
*
3645352 ---TAAATAATTAC
1 TATTAAATCATTAC
*
3645363 ---TAAATAATTAC
1 TATTAAATCATTAC
3645374 TATTAAATCATTA
1 TATTAAATCATTA
3645387 TTATCATTAC
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
11 20 0.38
14 32 0.62
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (14 bp):
TATTAAATCATTAC
Found at i:3645388 original size:11 final size:11
Alignment explanation
Indices: 3645308--3645687 Score: 121
Period size: 11 Copynumber: 31.3 Consensus size: 11
3645298 ATTCGTAATA
3645308 ATTATTAAATC
1 ATTATTAAATC
*
3645319 ATTAATATTAAATT
1 A-T--TATTAAATC
3645333 ATTATTATAAAATC
1 ATTA-T-T-AAATC
* *
3645347 ATTACTAAATA
1 ATTATTAAATC
* *
3645358 ATTACTAAATA
1 ATTATTAAATC
3645369 ATTACTATTAAATC
1 A-T--TATTAAATC
*
3645383 ATTATTATCATTAC
1 ATTATTA--AAT-C
3645397 TATTATTAAATC
1 -ATTATTAAATC
* *
3645409 ATTATTATCATT
1 ATTATTA-AATC
3645421 ATTATTAAATC
1 ATTATTAAATC
*
3645432 ATTATTATAATG
1 ATTATTA-AATC
3645444 ATTATTAATAAAATC
1 ATTA-T--T-AAATC
*
3645459 ATTATTATAATG
1 ATTATTA-AATC
3645471 ATTATTATCAAATC
1 ATTA-T-T-AAATC
3645485 ATTATTAAATC
1 ATTATTAAATC
*
3645496 ---ATCAAATC
1 ATTATTAAATC
*
3645504 ATTACTAAATC
1 ATTATTAAATC
3645515 ATCAAATCATTAAAT-
1 AT----T-ATTAAATC
3645530 A-T-TTAAATC
1 ATTATTAAATC
*
3645539 ATTATTAAATT
1 ATTATTAAATC
*
3645550 ATTATTATAATA
1 ATTATTA-AATC
3645562 ATTATTACTAAATC
1 ATTA-T--TAAATC
*
3645576 ATTATTATAATG
1 ATTATTA-AATC
3645588 ATTATTATCAAATC
1 ATTA-T-T-AAATC
*
3645602 ATTACTATAATGATT
1 ATTA-T-TAA--ATC
*
3645617 ATTATCAAATC
1 ATTATTAAATC
*
3645628 ATTACTAAATC
1 ATTATTAAATC
3645639 A-TA--AAATC
1 ATTATTAAATC
3645647 ATTAAATATTAAATTC
1 A-T---TATTAAA-TC
*
3645663 ATTATTAAATT
1 ATTATTAAATC
3645674 ATTATTAAATC
1 ATTATTAAATC
3645685 ATT
1 ATT
3645688 TTTATGGTTA
Statistics
Matches: 284, Mismatches: 33, Indels: 104
0.67 0.08 0.25
Matches are distributed among these distances:
8 19 0.07
9 1 0.00
10 4 0.01
11 95 0.33
12 51 0.18
13 19 0.07
14 54 0.19
15 31 0.11
16 10 0.04
ACGTcount: A:0.46, C:0.09, G:0.01, T:0.44
Consensus pattern (11 bp):
ATTATTAAATC
Found at i:3645394 original size:9 final size:9
Alignment explanation
Indices: 3645380--3645425 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
3645370 TTACTATTAA
3645380 ATCATTATT
1 ATCATTATT
*
3645389 ATCATTACT
1 ATCATTATT
* *
3645398 ATTATTA-A
1 ATCATTATT
3645406 ATCATTATT
1 ATCATTATT
3645415 ATCATTATT
1 ATCATTATT
3645424 AT
1 AT
3645426 TAAATCATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
8 6 0.19
9 25 0.81
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (9 bp):
ATCATTATT
Found at i:3645399 original size:23 final size:23
Alignment explanation
Indices: 3645369--3645439 Score: 106
Period size: 23 Copynumber: 3.0 Consensus size: 23
3645359 TTACTAAATA
3645369 ATTACTATTAAATCATTATTATC
1 ATTACTATTAAATCATTATTATC
3645392 ATTACTATTATTAAATCATTATTATC
1 ATTAC---TATTAAATCATTATTATC
*
3645418 ATTATTATTAAATCATTATTAT
1 ATTACTATTAAATCATTATTAT
3645440 AATGATTATT
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
23 22 0.50
26 22 0.50
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (23 bp):
ATTACTATTAAATCATTATTATC
Found at i:3645409 original size:26 final size:26
Alignment explanation
Indices: 3645308--3645491 Score: 173
Period size: 25 Copynumber: 7.3 Consensus size: 26
3645298 ATTCGTAATA
* * *
3645308 ATTATTA-AATCATTAATATTAAATT
1 ATTATTATAATGATTATTATTAAATC
* * * *
3645333 ATTATTATAA-AATCATTACTAAATA
1 ATTATTATAATGATTATTATTAAATC
* * *
3645358 ATTACTA-AATAATTACTATTAAATC
1 ATTATTATAATGATTATTATTAAATC
* * *
3645383 ATTATTATCATTACTATTATTAAATC
1 ATTATTATAATGATTATTATTAAATC
*
3645409 ATTA-T-T-ATCATTATTATTAAATC
1 ATTATTATAATGATTATTATTAAATC
*
3645432 ATTATTATAATGATTATTAATAAAATC
1 ATTATTATAATGATTATT-ATTAAATC
*
3645459 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATTAAATC
3645485 ATTATTA
1 ATTATTA
3645492 AATCATCAAA
Statistics
Matches: 132, Mismatches: 20, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
23 19 0.14
24 4 0.03
25 42 0.32
26 42 0.32
27 25 0.19
ACGTcount: A:0.45, C:0.08, G:0.01, T:0.46
Consensus pattern (26 bp):
ATTATTATAATGATTATTATTAAATC
Found at i:3645507 original size:16 final size:16
Alignment explanation
Indices: 3645488--3645542 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 16
3645478 TCAAATCATT
3645488 ATTAAATCATCAAATC
1 ATTAAATCATCAAATC
3645504 ATTACTAAATCATCAAATC
1 A-T--TAAATCATCAAATC
*
3645523 ATTAAAT-ATTTAAATC
1 ATTAAATCA-TCAAATC
3645539 ATTA
1 ATTA
3645543 TTAAATTATT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
15 1 0.03
16 16 0.47
17 1 0.03
18 1 0.03
19 15 0.44
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (16 bp):
ATTAAATCATCAAATC
Found at i:3645548 original size:19 final size:19
Alignment explanation
Indices: 3645477--3645526 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
3645467 AATGATTATT
3645477 ATCAAATCATTATTAAATC
1 ATCAAATCATTATTAAATC
*
3645496 ATCAAATCATTACTAAATC
1 ATCAAATCATTATTAAATC
3645515 ATCAAATCATTA
1 ATCAAATCATTA
3645527 AATATTTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.34
Consensus pattern (19 bp):
ATCAAATCATTATTAAATC
Found at i:3645579 original size:26 final size:26
Alignment explanation
Indices: 3645539--3645631 Score: 134
Period size: 26 Copynumber: 3.6 Consensus size: 26
3645529 TATTTAAATC
* * *
3645539 ATTATTAAATTATTATTATAATAATT
1 ATTATCAAATCATTATTATAATGATT
3645565 ATTA-CTAAATCATTATTATAATGATT
1 ATTATC-AAATCATTATTATAATGATT
*
3645591 ATTATCAAATCATTACTATAATGATT
1 ATTATCAAATCATTATTATAATGATT
3645617 ATTATCAAATCATTA
1 ATTATCAAATCATTA
3645632 CTAAATCATA
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
26 60 0.98
27 1 0.02
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (26 bp):
ATTATCAAATCATTATTATAATGATT
Found at i:3645665 original size:124 final size:118
Alignment explanation
Indices: 3645421--3645680 Score: 389
Period size: 124 Copynumber: 2.2 Consensus size: 118
3645411 TATTATCATT
* *
3645421 ATTATTAAATCATTATTATAATGATTATTAATAAAATCATTATTATAATGATTATTATCAAATCA
1 ATTATTAAATTATTATTATAATAATTATTAATAAAATCATTATTATAATGATTATTATCAAATCA
*
3645486 TTATTAAATCATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATC
66 TTATTAAATCATCAAATCATTACTAAATCATAAAATCATTAAATATTTAAATC
*
3645539 ATTATTAAATTATTATTATAATAATTATTACT-AAATCATTATTATAATGATTATTATCAAATCA
1 ATTATTAAATTATTATTATAATAATTATTAATAAAATCATTATTATAATGATTATTATCAAATCA
*
3645603 TTACTATAATGATTATTATCAAATCATTACTAAATCATAAAATCATTAAATA-TTAAATTC
66 TTA-T-T-A--A--ATCATCAAATCATTACTAAATCATAAAATCATTAAATATTTAAA-TC
3645663 ATTATTAAATTATTATTA
1 ATTATTAAATTATTATTA
3645681 AATCATTTTT
Statistics
Matches: 129, Mismatches: 5, Indels: 10
0.90 0.03 0.07
Matches are distributed among these distances:
117 35 0.27
118 30 0.23
119 1 0.01
120 1 0.01
122 1 0.01
123 5 0.04
124 56 0.43
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.43
Consensus pattern (118 bp):
ATTATTAAATTATTATTATAATAATTATTAATAAAATCATTATTATAATGATTATTATCAAATCA
TTATTAAATCATCAAATCATTACTAAATCATAAAATCATTAAATATTTAAATC
Found at i:3645883 original size:17 final size:18
Alignment explanation
Indices: 3645861--3645895 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
3645851 TATGAGTAAA
3645861 TCATTATTATT-ATAATT
1 TCATTATTATTAATAATT
3645878 TCATTATTATTAATAATT
1 TCATTATTATTAATAATT
3645896 ATTTATCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (18 bp):
TCATTATTATTAATAATT
Found at i:3645906 original size:20 final size:20
Alignment explanation
Indices: 3645860--3645906 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
3645850 CTATGAGTAA
*
3645860 ATCATTATTATTATAATTTC
1 ATCATTATTATAATAATTTC
* *
3645880 ATTATTATTAATAATTATTT-
1 ATCATTATT-ATAATAATTTC
3645900 ATCATTA
1 ATCATTA
3645907 CTATCAAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.55
Consensus pattern (20 bp):
ATCATTATTATAATAATTTC
Found at i:3645960 original size:49 final size:49
Alignment explanation
Indices: 3645900--3646080 Score: 335
Period size: 49 Copynumber: 3.7 Consensus size: 49
3645890 ATAATTATTT
*
3645900 ATCATTACTATCAAATAATTAAATATTAATAATAATTTTATTATTACTA
1 ATCATTACTATCAAATCATTAAATATTAATAATAATTTTATTATTACTA
*
3645949 ATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTA
1 ATCATTACTATCAAATCATTAAATATTAATAATAATTTTATTATTACTA
3645998 ATCATTACTATCAAATCATTAAATATTAATAATAATTTTATTATTACTA
1 ATCATTACTATCAAATCATTAAATATTAATAATAATTTTATTATTACTA
*
3646047 ATCGTTACTATCAAATCATTAAATATTAATAATA
1 ATCATTACTATCAAATCATTAAATATTAATAATA
3646081 GACGGGTGCC
Statistics
Matches: 128, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 128 1.00
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.43
Consensus pattern (49 bp):
ATCATTACTATCAAATCATTAAATATTAATAATAATTTTATTATTACTA
Found at i:3650131 original size:20 final size:20
Alignment explanation
Indices: 3650071--3650131 Score: 50
Period size: 20 Copynumber: 2.9 Consensus size: 20
3650061 TCCCCTGTGG
* *
3650071 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATT-CCC-TC-AT
* *
3650094 GGGGGAATCGGTTTCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
3650114 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
3650132 TGCACCAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
20 16 0.48
21 2 0.06
22 2 0.06
23 13 0.39
ACGTcount: A:0.16, C:0.25, G:0.34, T:0.25
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:3658600 original size:26 final size:24
Alignment explanation
Indices: 3658541--3658600 Score: 57
Period size: 26 Copynumber: 2.3 Consensus size: 24
3658531 ACTAATATTG
*
3658541 TTAATAATGATTTAATAATTATTA
1 TTAATAATGATTTAATAATTATGA
* *
3658565 TTAATCTAATGATTTGATATTTAATGA
1 TTAA--TAATGATTTAATAATT-ATGA
3658592 TTTAATAAT
1 -TTAATAAT
3658601 AATATGATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
24 4 0.14
26 18 0.62
27 3 0.10
28 4 0.14
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.50
Consensus pattern (24 bp):
TTAATAATGATTTAATAATTATGA
Found at i:3659400 original size:28 final size:30
Alignment explanation
Indices: 3659360--3659422 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
3659350 ATTTTTTATA
3659360 TAATATAATATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
*
3659390 TAATAT-A-ATATAACTTAAACTAGCAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
3659418 TAATA
1 TAATA
3659423 ATTTATACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 25 0.78
29 1 0.03
30 6 0.19
ACGTcount: A:0.56, C:0.13, G:0.02, T:0.30
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:3659429 original size:28 final size:28
Alignment explanation
Indices: 3659364--3659429 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
3659354 TTTATATAAT
3659364 ATAATATATAACTTAAACTAACAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
*
3659392 AT-ATAATATAACTTAAACTAGCAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
3659420 ATAATTTATA
1 ATAATATATA
3659430 CTAACAAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 30 0.88
29 2 0.06
ACGTcount: A:0.55, C:0.12, G:0.02, T:0.32
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:3659432 original size:21 final size:21
Alignment explanation
Indices: 3659399--3659447 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
3659389 CTAATATAAT
*
3659399 ATAACTTAAACTAGCAAACTA
1 ATAACTTAAACTAACAAACTA
* *
3659420 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
3659441 ATTAACT
1 A-TAACT
3659448 AGATTTTAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.51, C:0.16, G:0.02, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:3660030 original size:40 final size:41
Alignment explanation
Indices: 3659975--3660056 Score: 157
Period size: 40 Copynumber: 2.0 Consensus size: 41
3659965 CAAAGAGAAT
3659975 CACGAGAATGATAAAGAACGTTGGACGCC-GGCGTGCATGG
1 CACGAGAATGATAAAGAACGTTGGACGCCGGGCGTGCATGG
3660015 CACGAGAATGATAAAGAACGTTGGACGCCGGGCGTGCATGG
1 CACGAGAATGATAAAGAACGTTGGACGCCGGGCGTGCATGG
3660056 C
1 C
3660057 GACCTATGCT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 29 0.71
41 12 0.29
ACGTcount: A:0.29, C:0.21, G:0.35, T:0.15
Consensus pattern (41 bp):
CACGAGAATGATAAAGAACGTTGGACGCCGGGCGTGCATGG
Found at i:3671997 original size:13 final size:13
Alignment explanation
Indices: 3671979--3672004 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3671969 TTAAAAATAA
3671979 TTTTAGGTAAATT
1 TTTTAGGTAAATT
3671992 TTTTAGGTAAATT
1 TTTTAGGTAAATT
3672005 ATATCACGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (13 bp):
TTTTAGGTAAATT
Found at i:3672590 original size:3 final size:3
Alignment explanation
Indices: 3672582--3672652 Score: 142
Period size: 3 Copynumber: 23.7 Consensus size: 3
3672572 ACCATTATCC
3672582 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3672630 AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
3672653 AAGCAAGTTA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3673451 original size:29 final size:29
Alignment explanation
Indices: 3673405--3673469 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
3673395 GGAAGAGAAG
*
3673405 GAAAGAAATGTTAAGCATCAAATTGAAAC
1 GAAATAAATGTTAAGCATCAAATTGAAAC
* * *
3673434 GAAATAAATGTTAGGCATTAAATTGGAAC
1 GAAATAAATGTTAAGCATCAAATTGAAAC
*
3673463 AAAATAA
1 GAAATAA
3673470 TTTCTTATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.52, C:0.08, G:0.17, T:0.23
Consensus pattern (29 bp):
GAAATAAATGTTAAGCATCAAATTGAAAC
Found at i:3676523 original size:225 final size:226
Alignment explanation
Indices: 3675870--3676757 Score: 1067
Period size: 225 Copynumber: 3.9 Consensus size: 226
3675860 GTTTTTTGCA
* *
3675870 TGCTTGTTTTGGTTCCATCAAGCTGTTGTATTTTCACACATCATCTCA-TCCTGGGACTGCACTG
1 TGCTTGTTTTGGTTCCATCAAGCTGTTGTTTTTTCACACTTCATCTCATTCCTGGGACTGCACTG
* * * * *
3675934 TTAGCCGTTAATCAATCAATGGTCCCAGGAACCAGGCCCCATTGTCTGCCAAGACCTTTTCCGAG
66 TTAG-CGTAAATCAACCAATGGTCCCAGGAATCAGGCCCCATAGTCTGCCAAGACCATTTCCGAG
* * * * *
3675999 TGCTCAATTAGTATTATTCACGTTCTCT-CTGTACTTGGATTTTGTTAATAAACATACTCTAT-C
130 TGCTCGAGTAGTATTATTCGCGTTCT-TGTTGTACTCGGATTTTGTTAATAAACATACTCTATCC
*
3676062 TCGAATTA--TGTGACTGTGGACTGATAATTTTT
194 T-GAATTATGTGTGATTGTGGACTGATAATTTTT
* * * *
3676094 TGCTTGTTTTGGTTCTATCAAGCTCTTGTTTTTTCACACTTCATCTCATTCCTGGG-GTCGCACC
1 TGCTTGTTTTGGTTCCATCAAGCTGTTGTTTTTTCACACTTCATCTCATTCCTGGGACT-GCACT
* * * ** *
3676158 GTTAGCTGTAAATCAATCAATAGT-CCA-G-----GG--CC--GGTCTGCTGAGACCATCTCCGA
65 GTTAGC-GTAAATCAACCAATGGTCCCAGGAATCAGGCCCCATAGTCTGCCAAGACCATTTCCGA
* * * *
3676212 GTGCTCGAGTAGTATTATTCGTGTTCTTGTTGTACACAGATTTTGTTAATAAA-ACTATTCTATC
129 GTGCTCGAGTAGTATTATTCGCGTTCTTGTTGTACTCGGATTTTGTTAATAAACA-TACTCTATC
*
3676276 TTGAATTATGTGTGATTGTGGACTGATAATTTTT
193 CTGAATTATGTGTGATTGTGGACTGATAATTTTT
*
3676310 TGCTTGTTTTGGTTCCATCAAGCTGTTGTTTTTTCACACTTCATCTCATTCCTTGGACTGCACTG
1 TGCTTGTTTTGGTTCCATCAAGCTGTTGTTTTTTCACACTTCATCTCATTCCTGGGACTGCACTG
* * *
3676375 TTAG-GTAAATCAACCAATGGTCCCAGGATTCAGGCCCCATAGTCTGCCCAGACCATTTTCGAGT
66 TTAGCGTAAATCAACCAATGGTCCCAGGAATCAGGCCCCATAGTCTGCCAAGACCATTTCCGAGT
* * * *
3676439 ACTCGAGTAGTATTATTCGTGTTCTTGTTGTACCCGGATTTTGTTAATAAACATACTCTATCCAG
131 GCTCGAGTAGTATTATTCGCGTTCTTGTTGTACTCGGATTTTGTTAATAAACATACTCTATCCTG
*
3676504 AATTTTGTGTGATTGTGGACTGATAATTTTT
196 AATTATGTGTGATTGTGGACTGATAATTTTT
* * *
3676535 TGCTTGTTTTGGTTACTTCAAGCTGTTGTTTCTTCACACTTCATCTCATTCCTGGGACTTCACTG
1 TGCTTGTTTTGGTTCCATCAAGCTGTTGTTTTTTCACACTTCATCTCATTCCTGGG-----ACTG
*
3676600 TTTCTCTGTTAGCTGTAAATCAACCAATGGTCCCAGGAATCAGGCCCCATAGTCTGCCAAGACCA
61 ---CACTGTTAGC-GTAAATCAACCAATGGTCCCAGGAATCAGGCCCCATAGTCTGCCAAGACCA
* * ** * *
3676665 TTTCCGAGTGCTCGAGTAGTATTATTCGCATTCTTCTTGTACTCTTATTATGTTAATCAACATAC
122 TTTCCGAGTGCTCGAGTAGTATTATTCGCGTTCTTGTTGTACTCGGATTTTGTTAATAAACATAC
* *
3676730 TATATCTTGAATTATGTGTGATTGTGGA
187 TCTATCCTGAATTATGTGTGATTGTGGA
3676758 TTCTGGATTG
Statistics
Matches: 569, Mismatches: 64, Indels: 51
0.83 0.09 0.07
Matches are distributed among these distances:
213 2 0.00
214 88 0.15
215 4 0.01
216 88 0.15
217 1 0.00
218 2 0.00
221 2 0.00
223 3 0.01
224 49 0.09
225 189 0.33
226 1 0.00
230 4 0.01
233 8 0.01
235 128 0.22
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.39
Consensus pattern (226 bp):
TGCTTGTTTTGGTTCCATCAAGCTGTTGTTTTTTCACACTTCATCTCATTCCTGGGACTGCACTG
TTAGCGTAAATCAACCAATGGTCCCAGGAATCAGGCCCCATAGTCTGCCAAGACCATTTCCGAGT
GCTCGAGTAGTATTATTCGCGTTCTTGTTGTACTCGGATTTTGTTAATAAACATACTCTATCCTG
AATTATGTGTGATTGTGGACTGATAATTTTT
Found at i:3677335 original size:2 final size:2
Alignment explanation
Indices: 3677328--3677365 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3677318 GGTGAAATTG
3677328 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3677366 TTGAAAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3677564 original size:2 final size:2
Alignment explanation
Indices: 3677557--3677583 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3677547 TAATAAACCC
3677557 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
3677584 TCAAATAGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3682513 original size:2 final size:2
Alignment explanation
Indices: 3682506--3682540 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3682496 TAATAAACCC
3682506 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3682541 TCAAATAGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3686541 original size:2 final size:2
Alignment explanation
Indices: 3686534--3686566 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
3686524 ATGAATTGTT
3686534 TA TA TA TA TA -A TA TGA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA T
3686567 TTAGTATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 26 0.90
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3686818 original size:13 final size:13
Alignment explanation
Indices: 3686802--3686840 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
3686792 GAACGTCGTT
3686802 AATGCGCGTCATA
1 AATGCGCGTCATA
* *
3686815 AATGTGTGTCATA
1 AATGCGCGTCATA
*
3686828 AATGCGCATCATA
1 AATGCGCGTCATA
3686841 GATTTATGAC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:3688563 original size:17 final size:17
Alignment explanation
Indices: 3688541--3688573 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3688531 GGATCTCAGA
*
3688541 ATCTCAAATGGTTATAC
1 ATCTCAAATGATTATAC
3688558 ATCTCAAATGATTATA
1 ATCTCAAATGATTATA
3688574 GGATCAGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.36
Consensus pattern (17 bp):
ATCTCAAATGATTATAC
Found at i:3688691 original size:52 final size:51
Alignment explanation
Indices: 3688628--3688738 Score: 204
Period size: 52 Copynumber: 2.2 Consensus size: 51
3688618 TCAAGCGATC
*
3688628 ATCATTTTTCTAATAGAAAATGACGAGTTTGGAAAATATCAATAGTCGGCTG
1 ATCATTTTTCTAATAGAAAATGACGAGTTTGGAAAATATCAATAGTC-ACTG
3688680 ATCATTTTTCTAATAGAAAATGACGAGTTTGGAAAATATCAATAGTCACTG
1 ATCATTTTTCTAATAGAAAATGACGAGTTTGGAAAATATCAATAGTCACTG
3688731 ATCATTTT
1 ATCATTTT
3688739 ATAACTTTTA
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
51 11 0.19
52 47 0.81
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (51 bp):
ATCATTTTTCTAATAGAAAATGACGAGTTTGGAAAATATCAATAGTCACTG
Found at i:3690755 original size:44 final size:44
Alignment explanation
Indices: 3690700--3690787 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 44
3690690 TGAAATATTA
** * *
3690700 ATTAATAATTTAGTATTTTTTATTGTTTATTAGAAAATTAATAG
1 ATTAATAATTTAGTACATTTTATTATCTATTAGAAAATTAATAG
* * *
3690744 ATTAGTAATTTATTACATTTTATTATCTATTAGTAAATTAATAG
1 ATTAATAATTTAGTACATTTTATTATCTATTAGAAAATTAATAG
3690788 TTTTTTGAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.39, C:0.02, G:0.08, T:0.51
Consensus pattern (44 bp):
ATTAATAATTTAGTACATTTTATTATCTATTAGAAAATTAATAG
Found at i:3693223 original size:63 final size:64
Alignment explanation
Indices: 3693151--3693279 Score: 179
Period size: 64 Copynumber: 2.0 Consensus size: 64
3693141 ACGACTATTC
* * * * **
3693151 ATTATGTTCCAAGCTCATCTTTTTTT-GTTAAAAATTTAACGGCTGTCTGAGTTGTACTATCAT
1 ATTATGTTCCAAACTCATCTTTTTTTCATTAAAAATTTAACGACTGCCCAAGTTGTACTATCAT
* *
3693214 ATTATGTTCCAAACTCATCTTTTTTTCATTAAGAATTTAACGACTGCCCAAGTTGTACTATTAT
1 ATTATGTTCCAAACTCATCTTTTTTTCATTAAAAATTTAACGACTGCCCAAGTTGTACTATCAT
3693278 AT
1 AT
3693280 CTCAATCAAC
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
63 25 0.44
64 32 0.56
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.43
Consensus pattern (64 bp):
ATTATGTTCCAAACTCATCTTTTTTTCATTAAAAATTTAACGACTGCCCAAGTTGTACTATCAT
Found at i:3693688 original size:3 final size:3
Alignment explanation
Indices: 3693680--3693720 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
3693670 CATCTCGTTC
*
3693680 TTA TTA TTA TTA -TA TGTA TTA TTA TTA TTA TTA ATA TTA TT
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TT
3693721 TTACATATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:3693728 original size:12 final size:12
Alignment explanation
Indices: 3693680--3693729 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
3693670 CATCTCGTTC
*
3693680 TTATTATTATTA
1 TTATTATTAATA
*
3693692 -TATGTATTATTA
1 TTAT-TATTAATA
3693704 TTATTATTAATA
1 TTATTATTAATA
3693716 TTATT-TTACATA
1 TTATTATTA-ATA
3693728 TT
1 TT
3693730 TGGCAGGCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
11 6 0.18
12 25 0.74
13 3 0.09
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (12 bp):
TTATTATTAATA
Found at i:3706676 original size:27 final size:27
Alignment explanation
Indices: 3706634--3706696 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
3706624 GTATTTCGCT
3706634 TGAAAAAAAAATGAAAAAGACAA-AAAA
1 TGAAAAAAAAATGAAAAAGA-AAGAAAA
*
3706661 TGAAAAATAAAA-GAAAGAGAAAGAAAA
1 TGAAAAA-AAAATGAAAAAGAAAGAAAA
3706688 -GAAAAAAAA
1 TGAAAAAAAA
3706697 TAAAAGGAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
25 3 0.09
26 8 0.24
27 18 0.55
28 4 0.12
ACGTcount: A:0.78, C:0.02, G:0.14, T:0.06
Consensus pattern (27 bp):
TGAAAAAAAAATGAAAAAGAAAGAAAA
Found at i:3708058 original size:96 final size:92
Alignment explanation
Indices: 3707837--3708196 Score: 504
Period size: 96 Copynumber: 4.0 Consensus size: 92
3707827 ATCAACTCCC
*
3707837 CCAGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCT-CAAGATTTGATATTCCC
1 CCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCC
* *
3707901 TTCAGAGTAAGTGGAACAAGTC--T-G
66 TTCAGAGTAAGTGGAACAAATCTATCT
*
3707925 CCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAAAGATTTGATATTCCC
1 CCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCC
3707990 TTCAGAGTAAGTGGAACAAATCTATCTTCT
66 TTCAGAGTAAGTGGAACAAATCTA---TCT
*
3708020 CCAAGATCTGATATTTCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCC
1 CC-AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCC
*
3708085 CTTCAGAGTAAGTGGAACAAGTCTA---
65 CTTCAGAGTAAGTGGAACAAATCTATCT
* * * *
3708110 CCAGATCTGACATTCCCTTCAGAGTAAGTGGAACAGGTCTCT-TTTTCCATGATTTGATATTCCC
1 CCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCC
* *
3708174 TTCAGAAG-AAGCGGAACATATCT
66 TTCAG-AGTAAGTGGAACAAATCT
3708197 CTTTTTTCCA
Statistics
Matches: 248, Mismatches: 15, Indels: 18
0.88 0.05 0.06
Matches are distributed among these distances:
88 83 0.33
89 76 0.31
90 2 0.01
94 1 0.00
95 2 0.01
96 84 0.34
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.31
Consensus pattern (92 bp):
CCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCC
TTCAGAGTAAGTGGAACAAATCTATCT
Found at i:3708150 original size:185 final size:183
Alignment explanation
Indices: 3707839--3708196 Score: 592
Period size: 185 Copynumber: 1.9 Consensus size: 183
3707829 CAACTCCCCC
*
3707839 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCAAGATTTGATATTCCCTTC
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAAGATTTGATATTCCCTTC
* *
3707904 AGAGTAAGTGGAACAAGTCTGCCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCT
66 AGAGTAAGTGGAACAAGTCTACCAGATCTGACATTCCCTTCAGAGTAAGCGGAACAGGTCTCT-T
*
3707969 TCTCAAAGATTTGATATTCCCTTCAG-AGTAAGTGGAACAAATCTATCTTCTCCA
130 TCTCAAAGATTTGATATTCCCTTCAGAAG-AAGCGGAACAAATCTATCTTCTCCA
*
3708023 AGATCTGATATTTCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCCTT
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCT-CAAGATTTGATATTCCCTT
*
3708088 CAGAGTAAGTGGAACAAGTCTACCAGATCTGACATTCCCTTCAGAGTAAGTGGAACAGGTCTCTT
65 CAGAGTAAGTGGAACAAGTCTACCAGATCTGACATTCCCTTCAGAGTAAGCGGAACAGGTCTCTT
* * * *
3708153 TTTCCATGATTTGATATTCCCTTCAGAAGAAGCGGAACATATCT
130 TCTCAAAGATTTGATATTCCCTTCAGAAGAAGCGGAACAAATCT
3708197 CTTTTTTCCA
Statistics
Matches: 162, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
184 80 0.49
185 82 0.51
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (183 bp):
AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAAGATTTGATATTCCCTTC
AGAGTAAGTGGAACAAGTCTACCAGATCTGACATTCCCTTCAGAGTAAGCGGAACAGGTCTCTTT
CTCAAAGATTTGATATTCCCTTCAGAAGAAGCGGAACAAATCTATCTTCTCCA
Found at i:3708222 original size:48 final size:47
Alignment explanation
Indices: 3707839--3708222 Score: 346
Period size: 48 Copynumber: 8.3 Consensus size: 47
3707829 CAACTCCCCC
* * * *
3707839 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTC-TCTTCTCA
1 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAGATCTCTTTTTC-CA
* * *
3707886 AGATTTGATATTCCCTTCAGAGTAAGTGGAACA-A-GTC---TGCC-
1 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAGATCTCTTTTTCCA
* * * *
3707927 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAA
1 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAGATCTCT-TTTTCCA
* * * *
3707975 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATCTATCTTCTCCA
1 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAGATCTCT-TTTTCCA
* * * *
3708023 AGATCTGATATTTCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCA
1 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAGATCTCT-TTTTCCA
* * *
3708071 AGATTTGATATTCCCTTCAGAGTAAGTGGAACA-A-GTC---TACC-
1 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAGATCTCTTTTTCCA
* * * *
3708112 AGATCTGACATTCCCTTCAGAGTAAGTGGAACAGGTCTCTTTTTCCA
1 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAGATCTCTTTTTCCA
* *
3708159 TGATTTGATATTCCCTTCAGAAG-AAGCGGAACATATCTCTTTTTTCCA
1 AGATTTGATATTCCCTTCAG-AGTAAGCGGAACAGATCTC-TTTTTCCA
* *
3708207 AGGTTTGGTATTCCCT
1 AGATTTGATATTCCCT
3708223 GTGACAGCGG
Statistics
Matches: 278, Mismatches: 44, Indels: 29
0.79 0.13 0.08
Matches are distributed among these distances:
41 62 0.22
42 3 0.01
43 6 0.02
45 2 0.01
46 5 0.02
47 63 0.23
48 137 0.49
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.32
Consensus pattern (47 bp):
AGATTTGATATTCCCTTCAGAGTAAGCGGAACAGATCTCTTTTTCCA
Found at i:3708466 original size:3 final size:3
Alignment explanation
Indices: 3708458--3708495 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
3708448 CATCTCGTTC
*
3708458 TTA TTA TTA TTA -TA TGTA TTA TTA TTA TTA ATA TTA TT
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TT
3708496 TTACATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:3714442 original size:20 final size:20
Alignment explanation
Indices: 3714399--3714444 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
3714389 GAGTGTGGCG
* *
3714399 GCGGACGGCGGCAGCAGACG
1 GCGGGCGGCGGCAGCAGACA
* *
3714419 GCGGGCGGCGGCAGCGGCCA
1 GCGGGCGGCGGCAGCAGACA
3714439 GCGGGC
1 GCGGGC
3714445 AACAGACGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.13, C:0.33, G:0.54, T:0.00
Consensus pattern (20 bp):
GCGGGCGGCGGCAGCAGACA
Found at i:3722211 original size:29 final size:27
Alignment explanation
Indices: 3722158--3722213 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
3722148 AAAAAAAGAG
* *
3722158 AAAAAAGAAGAAAAGAGTTTCGAACTA
1 AAAAAAGAAGAAAAAACTTTCGAACTA
*
3722185 AAAAAATGAAAGAAAAAACTTTTGAACTA
1 AAAAAA-G-AAGAAAAAACTTTCGAACTA
3722214 GAGAGAACCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 6 0.25
28 1 0.04
29 17 0.71
ACGTcount: A:0.61, C:0.07, G:0.14, T:0.18
Consensus pattern (27 bp):
AAAAAAGAAGAAAAAACTTTCGAACTA
Found at i:3723283 original size:2 final size:2
Alignment explanation
Indices: 3723276--3723310 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3723266 AATTTGCATT
3723276 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3723311 GTCTCTAGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3728282 original size:36 final size:36
Alignment explanation
Indices: 3728183--3728291 Score: 121
Period size: 36 Copynumber: 3.0 Consensus size: 36
3728173 TTTGATATTG
* * * *
3728183 TTTCTCTCGAAACAAAGTGTCGTCTCACTAGAGACAA
1 TTTCTCTCAAAACAAA-TTTCGTCTCGCTTGAGACAA
* *
3728220 -TTCTTCTTAAAAACAAATTTCTTCTCGCTTGAGACAA
1 TTTC-TC-TCAAAACAAATTTCGTCTCGCTTGAGACAA
*
3728257 TTTCTCTCAAAATAAATTTCGTCTCGCTTGAGACA
1 TTTCTCTCAAAACAAATTTCGTCTCGCTTGAGACA
3728292 TTTTTCCTTT
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
36 29 0.48
37 20 0.33
38 11 0.18
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.34
Consensus pattern (36 bp):
TTTCTCTCAAAACAAATTTCGTCTCGCTTGAGACAA
Found at i:3728624 original size:103 final size:101
Alignment explanation
Indices: 3728517--3728708 Score: 233
Period size: 103 Copynumber: 1.9 Consensus size: 101
3728507 TTAATCTCAC
* * * * *
3728517 TTGAGTTTGTTTCT-TTCAAAACATATTTCGTCTCGCTTGAGACAATTTTTCTTCAAAATATAAA
1 TTGAGATTATTTCTCTT-AAAACAAATTTCGTCTCGCTTGAGACAATTTCTCTT-AAAACAT-AA
3728581 ATTTGGAAATTGTTTCACTTGAAACAAAATTGATAAACT
63 ATTTGGAAATTGTTTCACTTGAAACAAAATTGATAAACT
* * * * *
3728620 TTGAGATTATTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAATT
1 TTGAGATTATTTCTCTTAAAACAAATTTCGTCTCGCTTGAGACAATTTCTCTTAAAACATAAATT
* * *
3728685 TTGAGATTGTTTCTCTTGAAACAA
66 TGGAAATTGTTTCACTTGAAACAA
3728709 GTTTTTGTCT
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
101 26 0.35
102 5 0.07
103 42 0.56
104 2 0.03
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (101 bp):
TTGAGATTATTTCTCTTAAAACAAATTTCGTCTCGCTTGAGACAATTTCTCTTAAAACATAAATT
TGGAAATTGTTTCACTTGAAACAAAATTGATAAACT
Found at i:3728682 original size:65 final size:65
Alignment explanation
Indices: 3728613--3728808 Score: 259
Period size: 66 Copynumber: 3.0 Consensus size: 65
3728603 AACAAAATTG
*
3728613 ATAAACTTTGAGATTATTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
1 ATAAACTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
* * * * *
3728678 ATAAATTTTGAGATTGTTTCTCTTGAAACAAGTTTTTGTCTCTCTTGAGTA-GGTTTTTCTTTAA
1 ATAAACTTTGAGATTGTTTCTCTTGAAACAA-ATTTTGTCTCTCTTGAG-ACAGTTTCTCTTGAA
3728742 AC
64 AC
* * * * *
3728744 ATAAAACATTGAGATTGTTTCGCTTGAAACATATTTTGTCTCACTTGAGACCGTTTCTCTTGAAA
1 AT-AAACTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAA
3728809 TAAATTATCC
Statistics
Matches: 112, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
65 30 0.27
66 56 0.50
67 26 0.23
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (65 bp):
ATAAACTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
Found at i:3728976 original size:95 final size:95
Alignment explanation
Indices: 3728813--3728986 Score: 296
Period size: 95 Copynumber: 1.8 Consensus size: 95
3728803 TTGAAATAAA
* *
3728813 TTATCCCTAAAGATGGCCCATCGTCCTCATCAAGTAGGAACCGTGTCATCCACCGACCAGATCTC
1 TTATCCCTAAAGATGGCCCACCATCCTCATCAAGTAGGAACCGTGTCATCCACCGACCAGATCTC
3728878 CTCATCACGTAGGAACCGTGTTATCACTAT
66 CTCATCACGTAGGAACCGTGTTATCACTAT
* *
3728908 TTATCCCTAAAGATGG-CCAGCCATCCTCATCACGTAGGAACTGTGTCATCCACCGACCAGATCT
1 TTATCCCTAAAGATGGCCCA-CCATCCTCATCAAGTAGGAACCGTGTCATCCACCGACCAGATCT
3728972 CCTCATCACGTAGGA
65 CCTCATCACGTAGGA
3728987 GCCGCGTCAA
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
94 3 0.04
95 71 0.96
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.24
Consensus pattern (95 bp):
TTATCCCTAAAGATGGCCCACCATCCTCATCAAGTAGGAACCGTGTCATCCACCGACCAGATCTC
CTCATCACGTAGGAACCGTGTTATCACTAT
Found at i:3729116 original size:138 final size:134
Alignment explanation
Indices: 3728868--3729306 Score: 506
Period size: 138 Copynumber: 3.2 Consensus size: 134
3728858 TCATCCACCG
*
3728868 ACCAGATCTCCTCATCACGTAGGAACCGTGTTATCACTATTTATCCCTAAAGATGGCCAGCCATC
1 ACCAG-TCTCCTCATCACGTAGGAA-CGTGTTATCAC-ATTTATCCCTAAAGATGGCCAACCATC
* *
3728933 CTCATCACGTAGGAACTGTGTCATCCACCGACCAGATCTCCTCATCACGTAGGAGCCGCGTCAAC
63 CTCATCACGTAGGAACTGTGTCAT-CACCGACCATATCTCCTCATCACGTAGGAGCCGCGTCACC
3728998 CTTAGATA
127 CTTAGATA
*
3729006 ACCAGTCGTCCTCATCACGTTA-GAACTGTGTTATCACAATTTATCCCTAAAGATGGCCAACCGT
1 ACCAGTC-TCCTCATCACG-TAGGAAC-GTGTTATCAC-ATTTATCCCTAAAGATGGCCAACCAT
* * * * * ** *
3729070 CTTCATCATGTAGGATCTGTGTCATACACTGACCATATCTCCTCATCACATAGGAGTTGTGTCAC
62 CCTCATCACGTAGGAACTGTGTCAT-CACCGACCATATCTCCTCATCACGTAGGAGCCGCGTCAC
3729135 CCTTAGATA
126 CCTTAGATA
* * * * * *
3729144 ACCACTCATCCTCATAATGTAGGAAGCATATTATCTACA-TTATCCCTAAAGATGACCAA-CATT
1 ACCAGTC-TCCTCATCACGTAGGAA-CGTGTTATC-ACATTTATCCCTAAAGATGGCCAACCA-T
* * * *
3729207 CCTCATCACGTAGGAACCGTGTCATCAACCGACCATATCTACTCATCACGTAAGAGCCGCGTTAC
62 CCTCATCACGTAGGAACTGTGTCATC-ACCGACCATATCTCCTCATCACGTAGGAGCCGCGTCAC
3729272 CCTTAGATA
126 CCTTAGATA
* *
3729281 ACCAGACTTCTCCATCACGTAGGAAC
1 ACCAGTCTCCT-CATCACGTAGGAAC
3729307 CATGTTACCT
Statistics
Matches: 253, Mismatches: 39, Indels: 20
0.81 0.12 0.06
Matches are distributed among these distances:
136 6 0.02
137 101 0.40
138 141 0.56
139 5 0.02
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.26
Consensus pattern (134 bp):
ACCAGTCTCCTCATCACGTAGGAACGTGTTATCACATTTATCCCTAAAGATGGCCAACCATCCTC
ATCACGTAGGAACTGTGTCATCACCGACCATATCTCCTCATCACGTAGGAGCCGCGTCACCCTTA
GATA
Found at i:3729540 original size:20 final size:20
Alignment explanation
Indices: 3729502--3729545 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
3729492 TGTTCGGGTC
* *
3729502 TTTATTATTATTATTATTAT
1 TTTATTATTATTATAATTAG
3729522 TTTATT-TTATTAATAATTAG
1 TTTATTATTATT-ATAATTAG
3729542 TTTA
1 TTTA
3729546 CATTTTGTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTATTATTATTATAATTAG
Found at i:3737887 original size:20 final size:20
Alignment explanation
Indices: 3737862--3737899 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3737852 CCGTTGCAGC
*
3737862 CAGGGTGCATGGATGCACAA
1 CAGGGTGCATCGATGCACAA
3737882 CAGGGTGCATCGATGCAC
1 CAGGGTGCATCGATGCAC
3737900 TAATTGCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.24, G:0.34, T:0.16
Consensus pattern (20 bp):
CAGGGTGCATCGATGCACAA
Found at i:3737963 original size:20 final size:19
Alignment explanation
Indices: 3737919--3737972 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
3737909 TCGAAATGGA
* *
3737919 GTGCATGGATGCAATGCAT
1 GTGCATGGATGCACTGCAG
3737938 GTGCATGGATGCACTGCAGG
1 GTGCATGGATGCACTGCA-G
3737958 GTGCATGGATGCACT
1 GTGCATGGATGCACT
3737973 TTGACACCCT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.22, C:0.19, G:0.35, T:0.24
Consensus pattern (19 bp):
GTGCATGGATGCACTGCAG
Found at i:3740764 original size:20 final size:19
Alignment explanation
Indices: 3740739--3740827 Score: 105
Period size: 20 Copynumber: 4.8 Consensus size: 19
3740729 TCGAAATGGA
3740739 GTGCATGGATGCACTATACG
1 GTGCATGGATGCACTATA-G
*
3740759 GTGCATCGATGCAC---A-
1 GTGCATGGATGCACTATAG
*
3740774 GTGCATGGATGCACTACAG
1 GTGCATGGATGCACTATAG
*
3740793 GTGCATCGATGCACTATAAG
1 GTGCATGGATGCACTAT-AG
3740813 GTGCATGGATGCACT
1 GTGCATGGATGCACT
3740828 TTGACACCCT
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
15 13 0.22
17 1 0.02
18 1 0.02
19 15 0.25
20 29 0.49
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (19 bp):
GTGCATGGATGCACTATAG
Found at i:3740779 original size:15 final size:16
Alignment explanation
Indices: 3740758--3740806 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 16
3740748 TGCACTATAC
3740758 GGTGCATCGATGCACA
1 GGTGCATCGATGCACA
*
3740774 -GTGCATGGATGCACTACA
1 GGTGCATCGATG--C-ACA
3740792 GGTGCATCGATGCAC
1 GGTGCATCGATGCAC
3740807 TATAAGGTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
15 10 0.37
16 2 0.07
17 2 0.07
18 3 0.11
19 10 0.37
ACGTcount: A:0.24, C:0.24, G:0.31, T:0.20
Consensus pattern (16 bp):
GGTGCATCGATGCACA
Found at i:3740801 original size:34 final size:35
Alignment explanation
Indices: 3740738--3740806 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
3740728 TTCGAAATGG
*
3740738 AGTGCATGGATGCACTATACGGTGCATCGATGCAC
1 AGTGCATGGATGCACTACACGGTGCATCGATGCAC
3740773 AGTGCATGGATGCACTACA-GGTGCATCGATGCAC
1 AGTGCATGGATGCACTACACGGTGCATCGATGCAC
3740807 TATAAGGTGC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 15 0.45
35 18 0.55
ACGTcount: A:0.26, C:0.23, G:0.29, T:0.22
Consensus pattern (35 bp):
AGTGCATGGATGCACTACACGGTGCATCGATGCAC
Found at i:3740974 original size:16 final size:16
Alignment explanation
Indices: 3740953--3740985 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3740943 AATTTGTTAT
*
3740953 ATCGAAACATATTTCA
1 ATCGAAACATACTTCA
3740969 ATCGAAACATACTTCA
1 ATCGAAACATACTTCA
3740985 A
1 A
3740986 CATATTATCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.21, G:0.06, T:0.27
Consensus pattern (16 bp):
ATCGAAACATACTTCA
Found at i:3746643 original size:60 final size:60
Alignment explanation
Indices: 3746533--3746646 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
3746523 GTCGAGTGAT
* * * *
3746533 TATTTTATAACTTTTAATAGTCGAGAGATTTAATAAAATAACACTCTATAATCAGATGAC
1 TATTTTATAACTTTTAATAATCAAAAGATTTAATAAAATAACACTATATAATCAGATGAC
* *
3746593 TATTTTATAA-TTATTAATAATCAAAAGATTTAATAAAATAATATTATATAATCA
1 TATTTTATAACTT-TTAATAATCAAAAGATTTAATAAAATAACACTATATAATCA
3746647 AAGATCATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 2 0.04
60 45 0.96
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.39
Consensus pattern (60 bp):
TATTTTATAACTTTTAATAATCAAAAGATTTAATAAAATAACACTATATAATCAGATGAC
Found at i:3749443 original size:18 final size:19
Alignment explanation
Indices: 3749420--3749462 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
3749410 TTTGGTACTA
3749420 ATACTCAAGAA-AGTATCG
1 ATACTCAAGAAGAGTATCG
3749438 ATACTCAAGAAGGAGTATCG
1 ATACTCAAGAA-GAGTATCG
3749458 ATACT
1 ATACT
3749463 AGCCCTTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 11 0.48
20 12 0.52
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (19 bp):
ATACTCAAGAAGAGTATCG
Found at i:3749519 original size:20 final size:20
Alignment explanation
Indices: 3749493--3749543 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
3749483 AACAAGTTAG
3749493 CAGTATCGATACCCAAAGGT
1 CAGTATCGATACCCAAAGGT
* * *
3749513 TAGTATCGATACCTAGAGGT
1 CAGTATCGATACCCAAAGGT
3749533 CAGTATCGATA
1 CAGTATCGATA
3749544 TTGAGGAGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (20 bp):
CAGTATCGATACCCAAAGGT
Found at i:3750480 original size:59 final size:59
Alignment explanation
Indices: 3750389--3750555 Score: 178
Period size: 60 Copynumber: 2.8 Consensus size: 59
3750379 GTACATATGT
* * * *
3750389 ATAGTTTAGGATGAAATTGAAATGTTTAAAAGTTTGA-GACTAATTTAGAATGAAGA-TC
1 ATAGTTTAGGATGAAATTGAAATATTCAAAAGTTTAAGGACTAATTTAGAAT-AACATTC
* * *
3750447 ATAGTTTGAGGATGGAATTGATATATTCAAAAGTTTAAGGACTAATTTAGAATATCATTC
1 ATAGTTT-AGGATGAAATTGAAATATTCAAAAGTTTAAGGACTAATTTAGAATAACATTC
* * * *
3750507 ATAGTTTAAGGATGAAATTGGAAA-ATTTAAAATTTTAGGGACCAATTTA
1 ATAGTTT-AGGATGAAATT-GAAATATTCAAAAGTTTAAGGACTAATTTA
3750556 AAATGAGGAC
Statistics
Matches: 91, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
58 7 0.08
59 27 0.30
60 54 0.59
61 3 0.03
ACGTcount: A:0.41, C:0.05, G:0.19, T:0.35
Consensus pattern (59 bp):
ATAGTTTAGGATGAAATTGAAATATTCAAAAGTTTAAGGACTAATTTAGAATAACATTC
Found at i:3751043 original size:20 final size:20
Alignment explanation
Indices: 3750826--3751056 Score: 221
Period size: 20 Copynumber: 11.5 Consensus size: 20
3750816 TCAGTTTCCA
* * *
3750826 AAATCGCAACGCGATTCTTGA
1 AAATCGCAACGCGAATC-CGT
*
3750847 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATC-CGT
*
3750867 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
3750887 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATCCGT
* * *
3750907 ATATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* * *
3750927 AAATCGTAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
3750947 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
**
3750967 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
3750987 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
3751007 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
3751027 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
*
3751047 AAATCACAAC
1 AAATCGCAAC
3751057 ACTGAAATTT
Statistics
Matches: 182, Mismatches: 27, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
20 167 0.92
21 15 0.08
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (20 bp):
AAATCGCAACGCGAATCCGT
Found at i:3751778 original size:24 final size:24
Alignment explanation
Indices: 3751739--3751785 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3751729 AAATTTGGTC
3751739 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
3751763 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
3751786 GATGTTTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:3754318 original size:33 final size:34
Alignment explanation
Indices: 3754267--3754476 Score: 215
Period size: 33 Copynumber: 6.2 Consensus size: 34
3754257 CGGAAATTAC
*
3754267 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGCGAAATGAA
*
3754300 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGC-GAAATGAA
*
3754334 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGCGAAATGAA
*
3754367 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAG
1 AATCGCAA--CG--ATGAAAATCGCAATGCGAAATGAA
3754400 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATG-A
1 AATCGCAA--CG--ATGAAAATCGCAATGCGAAATGAA
* *
3754437 AATCGCAACGA-GAGAATCGCAATGCGAAATTAA
1 AATCGCAACGATGAAAATCGCAATGCGAAATGAA
3754470 AATCGCA
1 AATCGCA
3754477 TTGCGATTCT
Statistics
Matches: 154, Mismatches: 9, Indels: 28
0.81 0.05 0.15
Matches are distributed among these distances:
32 19 0.12
33 75 0.49
34 30 0.19
35 7 0.05
36 2 0.01
37 10 0.06
38 11 0.07
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (34 bp):
AATCGCAACGATGAAAATCGCAATGCGAAATGAA
Found at i:3754372 original size:19 final size:19
Alignment explanation
Indices: 3754281--3754482 Score: 194
Period size: 19 Copynumber: 11.7 Consensus size: 19
3754271 GCAACGAGAG
3754281 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3754300 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
3754314 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
3754334 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
3754348 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3754367 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3754386 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
3754400 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
3754419 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
*
3754437 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
3754451 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
3754470 AATCGCATTGCGA
1 AATCGCAATGCGA
3754483 TTCTCCCGTT
Statistics
Matches: 151, Mismatches: 10, Indels: 44
0.74 0.05 0.21
Matches are distributed among these distances:
13 1 0.01
14 41 0.27
15 2 0.01
16 9 0.06
17 4 0.03
18 13 0.09
19 68 0.45
20 13 0.09
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:3754394 original size:52 final size:52
Alignment explanation
Indices: 3754309--3754482 Score: 314
Period size: 52 Copynumber: 3.3 Consensus size: 52
3754299 AAATCCCAAC
3754309 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
3754362 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
3754414 ATGAAAATCGCAATGCGAAATG-AAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
3754465 ATTAAAATCGCATTGCGA
1 ATGAAAATCGCAATGCGA
3754483 TTCTCCCGTT
Statistics
Matches: 119, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
51 45 0.38
52 58 0.49
53 16 0.13
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:3754531 original size:19 final size:19
Alignment explanation
Indices: 3754491--3754588 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
3754481 GATTCTCCCG
3754491 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
3754511 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3754530 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
3754544 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3754563 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3754582 TTGCGAT
1 TTGCGAT
3754589 AGTCAATTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:3754585 original size:52 final size:53
Alignment explanation
Indices: 3754472--3754588 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
3754462 GAAATTAAAA
3754472 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
*
3754525 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
3754577 TCGCATTGCGAT
1 TCGCATTGCGAT
3754589 AGTCAATTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 30 0.48
53 33 0.52
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:3754714 original size:14 final size:14
Alignment explanation
Indices: 3754695--3754731 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3754685 CATCAATTAC
3754695 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3754709 ACAAATCATCTTTT
1 ACAAATCAACTTTT
3754723 ACAAATCAA
1 ACAAATCAA
3754732 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3756730 original size:14 final size:14
Alignment explanation
Indices: 3756711--3756766 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
3756701 GCGAAATGAA
*
3756711 AATCGCAACGACAG
1 AATCGCAACGAAAG
3756725 AATCGCAACGCGAAATG
1 AATCGCAA--CGAAA-G
3756742 AAATCGCAACGAAAG
1 -AATCGCAACGAAAG
3756757 AATCGCAACG
1 AATCGCAACG
3756767 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 18 0.49
15 1 0.03
16 9 0.24
17 1 0.03
18 8 0.22
ACGTcount: A:0.45, C:0.25, G:0.21, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:3756751 original size:32 final size:33
Alignment explanation
Indices: 3756692--3756783 Score: 168
Period size: 32 Copynumber: 2.8 Consensus size: 33
3756682 GCGAAACCAA
*
3756692 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
3756725 AATCGCAACGCGAAATG-AAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
3756757 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
3756784 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.54
33 26 0.46
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:3756781 original size:19 final size:19
Alignment explanation
Indices: 3756655--3756788 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
3756645 TAGTTTACTT
* *
3756655 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
3756675 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
3756694 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
3756713 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
3756727 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
3756745 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
3756759 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
3756778 TCGCAATGCGA
1 TCGCAACGCGA
3756789 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 19
0.78 0.06 0.15
Matches are distributed among these distances:
14 16 0.16
15 1 0.01
16 15 0.15
17 6 0.06
18 8 0.08
19 39 0.40
20 12 0.12
ACGTcount: A:0.46, C:0.25, G:0.19, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:3756806 original size:19 final size:19
Alignment explanation
Indices: 3756784--3756912 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
3756774 AAAATCGCAA
3756784 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
3756803 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
3756817 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
3756836 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
3756850 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
3756869 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
3756888 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
3756908 TGCGA
1 TGCGA
3756913 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:3756826 original size:33 final size:33
Alignment explanation
Indices: 3756784--3756875 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
3756774 AAAATCGCAA
3756784 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
3756817 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
3756850 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
3756876 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:3757076 original size:93 final size:93
Alignment explanation
Indices: 3756960--3757428 Score: 913
Period size: 93 Copynumber: 5.1 Consensus size: 93
3756950 ATGGATTGCA
3756960 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
3757024 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
3757052 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
3757117 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
3757145 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
3757210 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
3757238 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
3757303 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
3757331 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCATAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
3757396 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
3757424 TTACT
1 TTACT
3757429 AAGCAATCTA
Statistics
Matches: 374, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 4 0.01
93 370 0.99
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:3759152 original size:14 final size:14
Alignment explanation
Indices: 3759133--3759222 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
3759123 TTGAAATGAA
3759133 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
3759147 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
3759166 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
3759180 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
3759199 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3759213 AATCGCAACG
1 AATCGCAACG
3759223 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 20 0.32
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:3759165 original size:33 final size:33
Alignment explanation
Indices: 3759125--3759238 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
3759115 TCTTTTGGTT
3759125 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3759158 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3759191 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3759224 GAAATG-AAATCGCAA
1 GAAATGAAAATCGCAA
3759239 TGCGATTTTG
Statistics
Matches: 81, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
32 9 0.11
33 72 0.89
ACGTcount: A:0.46, C:0.20, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:3759171 original size:19 final size:19
Alignment explanation
Indices: 3759147--3759243 Score: 90
Period size: 14 Copynumber: 5.7 Consensus size: 19
3759137 GCAACGAGAG
3759147 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
3759166 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
3759180 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
3759199 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
3759213 AATCGCAACGCGAAATG-A
1 AATCGCAACGCGAAATGAA
*
3759231 AATCGCAATGCGA
1 AATCGCAACGCGA
3759244 TTTTGGTTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 21
0.71 0.06 0.24
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 4 0.06
17 4 0.06
18 14 0.22
19 19 0.30
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:3759261 original size:19 final size:18
Alignment explanation
Indices: 3759239--3759297 Score: 54
Period size: 19 Copynumber: 3.4 Consensus size: 18
3759229 GAAATCGCAA
*
3759239 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-ATTTCGCGT
*
3759258 TGCGA--TTCTTT--CGT
1 TGCGATTTTATTTCGCGT
3759272 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-ATTTCGCGT
3759291 TGCGATT
1 TGCGATT
3759298 CTCTCGTTGC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 8 0.24
16 5 0.15
17 5 0.15
19 15 0.45
ACGTcount: A:0.08, C:0.19, G:0.25, T:0.47
Consensus pattern (18 bp):
TGCGATTTTATTTCGCGT
Found at i:3759274 original size:14 final size:14
Alignment explanation
Indices: 3759255--3759311 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3759245 TTTGGTTTCG
3759255 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
3759269 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
3759286 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTTT
3759302 CGTTGCGATT
1 CGTTGCGATT
3759312 TTCATTTCTC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:3759287 original size:33 final size:33
Alignment explanation
Indices: 3759239--3759319 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
3759229 GAAATCGCAA
** *
3759239 TGCGATTTTGGTTTCGCGTTGCGATTCTTTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
3759272 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
3759305 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
3759320 TCTCGTTGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.21, G:0.22, T:0.48
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:3759352 original size:41 final size:41
Alignment explanation
Indices: 3759295--3759372 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
3759285 TCGCGTTGCG
*
3759295 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
3759336 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
3759373 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:3759357 original size:20 final size:21
Alignment explanation
Indices: 3759296--3759371 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
3759286 CGCGTTGCGA
3759296 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
3759317 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
3759337 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
3759358 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
3759372 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:3759493 original size:33 final size:33
Alignment explanation
Indices: 3759451--3759521 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
3759441 AATACTAACT
*
3759451 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
3759484 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
3759517 TGAAA
1 TGAAA
3759522 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:3759755 original size:22 final size:22
Alignment explanation
Indices: 3759703--3759757 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
3759693 TGGTTGTGAG
**
3759703 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
3759725 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
3759747 GGATTTCTTCG
1 GGATTTCTTCG
3759758 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:3759929 original size:20 final size:20
Alignment explanation
Indices: 3759904--3760057 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
3759894 CTTTAAATAT
3759904 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
3759924 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
3759946 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3759965 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
3759985 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
3760005 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
3760025 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
3760045 CGCGTTGCGATTT
1 CGCGTTGCGATTT
3760058 TGGAAAATCG
Statistics
Matches: 113, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 94 0.83
21 15 0.13
22 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:3760031 original size:40 final size:40
Alignment explanation
Indices: 3759903--3760057 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
3759893 GCTTTAAATA
*
3759903 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGT
** * *
3759944 TATCGTTGCGATTTACGGATACGCGTTGCGATATACG-GAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
* *
3759984 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
* ** *
3760024 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTT
3760058 TGGAAAATCG
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
40 66 0.69
41 30 0.31
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.37
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
Found at i:3760074 original size:21 final size:21
Alignment explanation
Indices: 3760044--3760126 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
3760034 ATTTTCATAT
*
3760044 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
3760065 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
3760086 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
3760107 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
3760127 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:3760117 original size:42 final size:43
Alignment explanation
Indices: 3760024--3760122 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
3760014 ATTTATGTGT
* *
3760024 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
3760065 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
3760107 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
3760123 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:3761323 original size:16 final size:16
Alignment explanation
Indices: 3761302--3761341 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
3761292 TCGAGTCGAG
3761302 TCGAGCTCAGCAATAC
1 TCGAGCTCAGCAATAC
3761318 TCGAGCTCAGCAATAC
1 TCGAGCTCAGCAATAC
3761334 TCGAGCTC
1 TCGAGCTC
3761342 GACTCGGCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.28, C:0.33, G:0.20, T:0.20
Consensus pattern (16 bp):
TCGAGCTCAGCAATAC
Found at i:3767110 original size:10 final size:10
Alignment explanation
Indices: 3767095--3767130 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
3767085 TTAAAAAGCG
3767095 TAAAGCGCCC
1 TAAAGCGCCC
3767105 TAAAGCG---
1 TAAAGCGCCC
3767112 TAAAGCGCCC
1 TAAAGCGCCC
3767122 TAAAGCGCC
1 TAAAGCGCC
3767131 TAGGGTCCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
7 7 0.30
10 16 0.70
ACGTcount: A:0.33, C:0.33, G:0.22, T:0.11
Consensus pattern (10 bp):
TAAAGCGCCC
Found at i:3767111 original size:17 final size:17
Alignment explanation
Indices: 3767089--3767128 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
3767079 TTGGTTTTAA
3767089 AAAGCGTAAAGCGCCCT
1 AAAGCGTAAAGCGCCCT
3767106 AAAGCGTAAAGCGCCCT
1 AAAGCGTAAAGCGCCCT
3767123 AAAGCG
1 AAAGCG
3767129 CCTAGGGTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.38, C:0.28, G:0.25, T:0.10
Consensus pattern (17 bp):
AAAGCGTAAAGCGCCCT
Found at i:3770219 original size:18 final size:18
Alignment explanation
Indices: 3770196--3770232 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
3770186 ATTAAACATA
3770196 AAGTCAAACTAAAATAAC
1 AAGTCAAACTAAAATAAC
3770214 AAGTCAAACTAAAATAAC
1 AAGTCAAACTAAAATAAC
3770232 A
1 A
3770233 GAAAGCAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.62, C:0.16, G:0.05, T:0.16
Consensus pattern (18 bp):
AAGTCAAACTAAAATAAC
Found at i:3774206 original size:19 final size:20
Alignment explanation
Indices: 3774181--3774229 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
3774171 AAATAAATAG
3774181 AATTTATTT-TTTTAATATTT
1 AATTTATTTATTTT-ATATTT
*
3774201 -ATTTATTTATTTTATTTTT
1 AATTTATTTATTTTATATTT
3774220 AATTTATTTA
1 AATTTATTTA
3774230 AATTTGGCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
AATTTATTTATTTTATATTT
Found at i:3775200 original size:21 final size:23
Alignment explanation
Indices: 3775170--3775222 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
3775160 TTATATATTA
* *
3775170 TATATGTATT-TATATT-AAAAC
1 TATATATATTATAAATTCAAAAC
3775191 TATATATATTATAAATTCAAAAC
1 TATATATATTATAAATTCAAAAC
3775214 TATATATAT
1 TATATATAT
3775223 AAAGTATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 9 0.32
22 5 0.18
23 14 0.50
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (23 bp):
TATATATATTATAAATTCAAAAC
Found at i:3785106 original size:65 final size:64
Alignment explanation
Indices: 3785028--3785188 Score: 234
Period size: 65 Copynumber: 2.5 Consensus size: 64
3785018 AATTAAATTG
* * *
3785028 AACATCGAATGCATTTCATGTATCGATGCACTTACCATGCACCGATGCACTGGGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACTTACCATGCACCGATGCACTCGGGATATTT-TG-
3785092 A
64 A
* * *
3785093 AACATCGAATGCATTTGATGCATCGATGCACTTACCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCACTTACCATGCACCGATGCACTCGGGATATTTTGA
*
3785157 AACATCGAATGCACTTGATGCATCGATGCACT
1 AACATCGAATGCATTTGATGCATCGATGCACT
3785189 CTTAGTGCAG
Statistics
Matches: 88, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
64 32 0.36
65 53 0.60
66 3 0.03
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCGATGCACTTACCATGCACCGATGCACTCGGGATATTTTGA
Found at i:3785187 original size:17 final size:19
Alignment explanation
Indices: 3785159--3785207 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
3785149 TATTTTGAAA
3785159 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
3785177 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
3785196 CAGCGATGCACT
1 CATCGATGCACT
3785208 AAGGGTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:3793025 original size:57 final size:56
Alignment explanation
Indices: 3792954--3793062 Score: 130
Period size: 56 Copynumber: 1.9 Consensus size: 56
3792944 GATGAACTTA
* * *
3792954 CCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCAAATGCATTTGATGCACCAG
1 CCATGCACCAATGCACTCAGGATATTT-TG-AAACATCAAATGCACTTGATGCACCAG
* * * *
3793011 CCATGCATCAATGCACTCTGGCTATTTTGAAACATCGAATGCACTTGATGCA
1 CCATGCACCAATGCACTCAGGATATTTTGAAACATCAAATGCACTTGATGCA
3793063 TCGATGCACT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
56 21 0.48
57 20 0.45
58 3 0.07
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (56 bp):
CCATGCACCAATGCACTCAGGATATTTTGAAACATCAAATGCACTTGATGCACCAG
Found at i:3800200 original size:22 final size:23
Alignment explanation
Indices: 3800172--3800215 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3800162 CACGCAAAGC
**
3800172 TCGAAAAC-AAATTATACTCGAT
1 TCGAAAACGAAAAAATACTCGAT
3800194 TCGAAAACGAAAAAATACTCGA
1 TCGAAAACGAAAAAATACTCGA
3800216 AATACCTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.50, C:0.18, G:0.11, T:0.20
Consensus pattern (23 bp):
TCGAAAACGAAAAAATACTCGAT
Found at i:3800425 original size:17 final size:17
Alignment explanation
Indices: 3800403--3800476 Score: 104
Period size: 17 Copynumber: 4.6 Consensus size: 17
3800393 CGGTTGGTGT
3800403 AGAAATTGGTGGCTTGG
1 AGAAATTGGTGGCTTGG
3800420 AGAAATTGGTGGCTTGG
1 AGAAATTGGTGGCTTGG
3800437 AGAAATTGGT-G--T--
1 AGAAATTGGTGGCTTGG
3800449 AGAAATTGGTGGCTTGG
1 AGAAATTGGTGGCTTGG
*
3800466 AGAAATCGGTG
1 AGAAATTGGTG
3800477 ACAAAATCAT
Statistics
Matches: 51, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
12 10 0.20
13 1 0.02
14 1 0.02
15 1 0.02
16 1 0.02
17 37 0.73
ACGTcount: A:0.27, C:0.05, G:0.39, T:0.28
Consensus pattern (17 bp):
AGAAATTGGTGGCTTGG
Found at i:3800452 original size:29 final size:29
Alignment explanation
Indices: 3800420--3800476 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
3800410 GGTGGCTTGG
*
3800420 AGAAATTGGTGGCTTGGAGAAATTGGTGT
1 AGAAATTGGTGGCTTGGAGAAATCGGTGT
3800449 AGAAATTGGTGGCTTGGAGAAATCGGTG
1 AGAAATTGGTGGCTTGGAGAAATCGGTG
3800477 ACAAAATCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.28, C:0.05, G:0.39, T:0.28
Consensus pattern (29 bp):
AGAAATTGGTGGCTTGGAGAAATCGGTGT
Found at i:3801400 original size:88 final size:88
Alignment explanation
Indices: 3801308--3801723 Score: 558
Period size: 88 Copynumber: 4.7 Consensus size: 88
3801298 TGTTGATACA
3801308 CCTTCTTCTGTGATGGAATCGAACGAGATGTCT-GTGTTGATCTACCTACTTCTGTGATAGAATC
1 CCTTCTTCTGTGATGGAATCGAACGAGATGT-TGGTGTTGATCTACCT-CTTCTGTGATAGAATC
*
3801372 T-AGTGAAATGAAAATGTCAATCCC
64 TGAGTGAAATGAAAATGTCGATCCC
* * * *
3801396 CCTTCTTCTGTGATAGAATCGAACGAGATGTTGGTGTTGGTCTACCTCCTTCCGTGATAG-ATTT
1 CCTTCTTCTGTGATGGAATCGAACGAGATGTTGGTGTTGATCTACCT-CTTCTGTGATAGAATCT
3801460 GAGTGAAATGAAAATGTCGATCCC
65 GAGTGAAATGAAAATGTCGATCCC
* *
3801484 CC-TCATTCTGTGATGGAATCGAACAAGATGTTGGTGTTGATCTACCTCTTTTTGTGATAGAATC
1 CCTTC-TTCTGTGATGGAATCGAACGAGATGTTGGTGTTGATCTACCTC-TTCTGTGATAGAATC
*
3801548 -GAGTGAAATGAAAATATCGATCCC
64 TGAGTGAAATGAAAATGTCGATCCC
* * * * *
3801572 CCTTCTTCTGTGATGAAATCAAACGAGATGTTTGTGTTGATTTACCTCCTTCTGTGATAG-ATTT
1 CCTTCTTCTGTGATGGAATCGAACGAGATGTTGGTGTTGATCTACCT-CTTCTGTGATAGAATCT
3801636 GAGTGAAATGAAAATGTCGATCCC
65 GAGTGAAATGAAAATGTCGATCCC
* * * *
3801660 CCTCCTTCTGTAATAGG-ATCAAACGAGATGTTGGTGTTGATCTACCTCATTCTGTGATAAAATC
1 CCTTCTTCTGTGAT-GGAATCGAACGAGATGTTGGTGTTGATCTACCTC-TTCTGTGATAGAATC
3801724 GAGCAAAAAG
Statistics
Matches: 289, Mismatches: 28, Indels: 21
0.86 0.08 0.06
Matches are distributed among these distances:
87 10 0.03
88 271 0.94
89 8 0.03
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (88 bp):
CCTTCTTCTGTGATGGAATCGAACGAGATGTTGGTGTTGATCTACCTCTTCTGTGATAGAATCTG
AGTGAAATGAAAATGTCGATCCC
Found at i:3801497 original size:44 final size:44
Alignment explanation
Indices: 3801356--3801675 Score: 185
Period size: 44 Copynumber: 7.3 Consensus size: 44
3801346 GATCTACCTA
* * *
3801356 CTTCTGTGATAGAATCTAGTGAAATGAAAATGTCAATCCCCCTT
1 CTTCTGTGATAGAATCGAGTGAAATGAAAATGTCGATCCCCCTC
** * **** * * **
3801400 CTTCTGTGATAGAATCGAACGAGATGTTGGTGTTGGTCTACCTC
1 CTTCTGTGATAGAATCGAGTGAAATGAAAATGTCGATCCCCCTC
* * *
3801444 CTTCCGTGATAGATTTGAGTGAAATGAAAATGTCGATCCCCCTC
1 CTTCTGTGATAGAATCGAGTGAAATGAAAATGTCGATCCCCCTC
* * ** **** * **
3801488 ATTCTGTGATGGAATCGA-ACAAGATGTTGGTGTTGATCTACCTC
1 CTTCTGTGATAGAATCGAGTGAA-ATGAAAATGTCGATCCCCCTC
* * * *
3801532 TTTTTGTGATAGAATCGAGTGAAATGAAAATATCGATCCCCCTT
1 CTTCTGTGATAGAATCGAGTGAAATGAAAATGTCGATCCCCCTC
* ** * **** * ***
3801576 CTTCTGTGAT-GAAATCAAACGAGATGTTTGTGTTGATTTACCTC
1 CTTCTGTGATAG-AATCGAGTGAAATGAAAATGTCGATCCCCCTC
* *
3801620 CTTCTGTGATAGATTTGAGTGAAATGAAAATGTCGATCCCCCTC
1 CTTCTGTGATAGAATCGAGTGAAATGAAAATGTCGATCCCCCTC
*
3801664 CTTCTGTAATAG
1 CTTCTGTGATAG
3801676 GATCAAACGA
Statistics
Matches: 185, Mismatches: 87, Indels: 8
0.66 0.31 0.03
Matches are distributed among these distances:
43 3 0.02
44 179 0.97
45 3 0.02
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (44 bp):
CTTCTGTGATAGAATCGAGTGAAATGAAAATGTCGATCCCCCTC
Found at i:3801620 original size:176 final size:175
Alignment explanation
Indices: 3801313--3801726 Score: 627
Period size: 176 Copynumber: 2.3 Consensus size: 175
3801303 ATACACCTTC
*
3801313 TTCTGTGATGGAATCGAACGAGATGTCT-GTGTTGATCTACCTACTTCTGTGATAGAATCTAGTG
1 TTCTGTGATGGAATCGAACGAGATGT-TGGTGTTGATCTACCT-CTTCTGTGATAGAATCGAGTG
* * *
3801377 AAATGAAAATGTCAATCCCCCTTCTTCTGTGATAGAATCGAACGAGATGTTGGTGTTGGTCTACC
64 AAATGAAAATATCAATCCCCCTTCTTCTGTGATAGAATCAAACGAGATGTTGGTGTTGATCTACC
3801442 TCCTTCCGTGATAGATTTGAGTGAAATGAAAATGTCGATCCCCCTCA
129 TCCTTCCGTGATAGATTTGAGTGAAATGAAAATGTCGATCCCCCTCA
* *
3801489 TTCTGTGATGGAATCGAACAAGATGTTGGTGTTGATCTACCTCTTTTTGTGATAGAATCGAGTGA
1 TTCTGTGATGGAATCGAACGAGATGTTGGTGTTGATCTACCTC-TTCTGTGATAGAATCGAGTGA
* * *
3801554 AATGAAAATATCGATCCCCCTTCTTCTGTGAT-GAAATCAAACGAGATGTTTGTGTTGATTTACC
65 AATGAAAATATCAATCCCCCTTCTTCTGTGATAG-AATCAAACGAGATGTTGGTGTTGATCTACC
* *
3801618 TCCTTCTGTGATAGATTTGAGTGAAATGAAAATGTCGATCCCCCTCC
129 TCCTTCCGTGATAGATTTGAGTGAAATGAAAATGTCGATCCCCCTCA
* * *
3801665 TTCTGTAATAGG-ATCAAACGAGATGTTGGTGTTGATCTACCTCATTCTGTGATAAAATCGAG
1 TTCTGTGAT-GGAATCGAACGAGATGTTGGTGTTGATCTACCTC-TTCTGTGATAGAATCGAG
3801727 CAAAAAGTTA
Statistics
Matches: 217, Mismatches: 17, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
175 3 0.01
176 212 0.98
177 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.34
Consensus pattern (175 bp):
TTCTGTGATGGAATCGAACGAGATGTTGGTGTTGATCTACCTCTTCTGTGATAGAATCGAGTGAA
ATGAAAATATCAATCCCCCTTCTTCTGTGATAGAATCAAACGAGATGTTGGTGTTGATCTACCTC
CTTCCGTGATAGATTTGAGTGAAATGAAAATGTCGATCCCCCTCA
Found at i:3802377 original size:66 final size:66
Alignment explanation
Indices: 3802296--3802555 Score: 303
Period size: 66 Copynumber: 3.9 Consensus size: 66
3802286 CAACGTTTTT
* * * *
3802296 GTGTTTCAAGAGAAACTATCTCATGGGAGACAAAATTCATTTCAAGGGAAATGATCTCAAAGATC
1 GTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGGGAAATGATCTCAAAGATT
3802361 A
66 A
* * *
3802362 GTGTTTCAAGGGAAACTGTCTCAAGTGAGACAAAATTCGTTTCAAGGGAAATGATCCCAAAGATT
1 GTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGGGAAATGATCTCAAAGATT
*
3802427 T
66 A
* ** * *
3802428 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTTTTCAAGAGAAACAT-AT-TCAGAGA
1 GTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAG-GGAA-ATGATCTCAAAGA
3802491 TTTTA
64 --TTA
* * *
3802496 -TGTTTCAAGAGAAATTGTCTCAAGCGAGACAAAATTTGTTTCAAGGGAAAATG-TCTCAAA
1 GTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGGG-AAATGATCTCAAA
3802556 AGAGACAAAA
Statistics
Matches: 165, Mismatches: 22, Indels: 13
0.82 0.11 0.06
Matches are distributed among these distances:
66 108 0.65
67 53 0.32
68 4 0.02
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (66 bp):
GTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGGGAAATGATCTCAAAGATT
A
Found at i:3802621 original size:39 final size:39
Alignment explanation
Indices: 3802493--3802830 Score: 384
Period size: 39 Copynumber: 8.8 Consensus size: 39
3802483 TTCAGAGATT
* * * *
3802493 TTATGTTTCAAGAGAAATTGTCTCAAGCGAGACAAAA--
1 TTATATTTCAAGGGAAACTATCTCAAGCGAGACAAAATC
* * * **
3802530 TT-TGTTTCAAGGGAAAATGTCTCAAAAGAGACAAAA-C
1 TTATATTTCAAGGGAAACTATCTCAAGCGAGACAAAATC
* * * *
3802567 -T-CATTCCAAGGGAAACTGTCTCAAGCGAGACAAACTC
1 TTATATTTCAAGGGAAACTATCTCAAGCGAGACAAAATC
* *
3802604 TTCTATTTCGAA-GGAAACTATCTCAAGCGAGACAAGATC
1 TTATATTTC-AAGGGAAACTATCTCAAGCGAGACAAAATC
* *
3802643 TTCTATTTCAAGGGAAACTATCTCAAGCGAGACAAAATA
1 TTATATTTCAAGGGAAACTATCTCAAGCGAGACAAAATC
* * *
3802682 TTATGTTTCAATGGAAACTATCTCCAGCGAGACAAAATC
1 TTATATTTCAAGGGAAACTATCTCAAGCGAGACAAAATC
*
3802721 TTATATTTCAAGGGAAACTATCTCAAGCGAGATAAAATC
1 TTATATTTCAAGGGAAACTATCTCAAGCGAGACAAAATC
* *
3802760 TTATGTTTCAAGGGAAACTATCTCAAGCGAGACAAAATA
1 TTATATTTCAAGGGAAACTATCTCAAGCGAGACAAAATC
* * *
3802799 TTTTGTTTCAAGGAAAACTATCTCAAGCGAGA
1 TTATATTTCAAGGGAAACTATCTCAAGCGAGA
3802831 TACAATCCTC
Statistics
Matches: 263, Mismatches: 32, Indels: 10
0.86 0.10 0.03
Matches are distributed among these distances:
36 58 0.22
37 3 0.01
38 3 0.01
39 197 0.75
40 2 0.01
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (39 bp):
TTATATTTCAAGGGAAACTATCTCAAGCGAGACAAAATC
Found at i:3802956 original size:76 final size:75
Alignment explanation
Indices: 3802844--3803081 Score: 241
Period size: 76 Copynumber: 3.1 Consensus size: 75
3802834 AATCCTCTTT
* * * * * *
3802844 AAAAACAATCTTCAGTGAAATGAAATGTCTTTTTTCGAGTAAAAATCATCTCAATCGAGATAAAT
1 AAAAATAATCTTGAGTGAAATGAAATATCTTCTTTCGAGTAAAAATCGTCTCAATCGAGACAAAT
3802909 CTTGTTTTAAG
66 -TTGTTTTAAG
* * * * *
3802920 AAAAATAATCTTGAGTGAAAT-AAATCTTCTTGTTTCGAGTAAAAA-CTGTCCCAAGCGATACAA
1 AAAAATAATCTTGAGTGAAATGAAAT-ATCTTCTTTCGAGTAAAAATC-GTCTCAATCGAGACAA
*
3802983 ATATTATTTTAAG
64 AT-TTGTTTTAAG
* * * * *
3802996 AAAAAAAATCTTGAGTCAAGTGAAATATCTTCTTTTGAGTAAAACT-GTCTCAAGT-GAGACAAA
1 AAAAATAATCTTGAGTGAAATGAAATATCTTCTTTCGAGTAAAAATCGTCTCAA-TCGAGACAAA
3803059 GTTTGTTTTAAG
65 -TTTGTTTTAAG
3803071 AAAAATAATCT
1 AAAAATAATCT
3803082 CAAGTGAGAT
Statistics
Matches: 133, Mismatches: 23, Indels: 13
0.79 0.14 0.08
Matches are distributed among these distances:
75 37 0.28
76 92 0.69
77 4 0.03
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (75 bp):
AAAAATAATCTTGAGTGAAATGAAATATCTTCTTTCGAGTAAAAATCGTCTCAATCGAGACAAAT
TTGTTTTAAG
Found at i:3806174 original size:23 final size:23
Alignment explanation
Indices: 3806143--3806233 Score: 110
Period size: 23 Copynumber: 4.0 Consensus size: 23
3806133 CACCACAGCT
* * *
3806143 CGTATAAATGTACTGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* * *
3806166 CGTAGAAATGCACGGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCG
*
3806189 CGTAGAATTGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
*
3806212 CGTAGAAATGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
3806234 ATATAATATC
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.29, C:0.23, G:0.29, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:3808119 original size:19 final size:19
Alignment explanation
Indices: 3808097--3808141 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
3808087 CAACTTTGTT
3808097 ATAAATCCTTTCTAACTTC
1 ATAAATCCTTTCTAACTTC
3808116 ATAAATCCTTTCTAACTTC
1 ATAAATCCTTTCTAACTTC
3808135 ATAAATC
1 ATAAATC
3808142 TCTTATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.40
Consensus pattern (19 bp):
ATAAATCCTTTCTAACTTC
Found at i:3808450 original size:2 final size:2
Alignment explanation
Indices: 3808445--3808472 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3808435 ATCCTTATCC
3808445 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3808473 CATTATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3810192 original size:22 final size:23
Alignment explanation
Indices: 3810164--3810207 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3810154 CACGCAAAGC
**
3810164 TCGAAAAC-AAATTATACTCGAT
1 TCGAAAACGAAAAAATACTCGAT
3810186 TCGAAAACGAAAAAATACTCGA
1 TCGAAAACGAAAAAATACTCGA
3810208 AATACCTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.50, C:0.18, G:0.11, T:0.20
Consensus pattern (23 bp):
TCGAAAACGAAAAAATACTCGAT
Found at i:3811397 original size:24 final size:24
Alignment explanation
Indices: 3811370--3811418 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
3811360 TATATCAAAA
*
3811370 ATCAAAACATAAATCAGGTCAAGT
1 ATCAAAACAGAAATCAGGTCAAGT
* *
3811394 ATCATATCAGAAATCAGGTCAAGT
1 ATCAAAACAGAAATCAGGTCAAGT
3811418 A
1 A
3811419 ACAGATCAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.47, C:0.16, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAAATCAGGTCAAGT
Found at i:3811426 original size:24 final size:24
Alignment explanation
Indices: 3811384--3811502 Score: 134
Period size: 24 Copynumber: 5.0 Consensus size: 24
3811374 AAACATAAAT
*
3811384 CAGGTCAAGTATCATATCAGAAAT-
1 CAGGTCAAGTATCAGATCAG-AATC
*
3811408 CAGGTCAAGTAACAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
**
3811432 CAACTCAAGTATCAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
**
3811456 CTTGTC-AGATATCAGATCAGAATC
1 CAGGTCAAG-TATCAGATCAGAATC
* *
3811480 CATGTCAAGTAACAGATCAGAAT
1 CAGGTCAAGTATCAGATCAGAAT
3811503 TCAAATCGAA
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
23 5 0.06
24 75 0.91
25 2 0.02
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (24 bp):
CAGGTCAAGTATCAGATCAGAATC
Found at i:3811518 original size:48 final size:48
Alignment explanation
Indices: 3811420--3811520 Score: 114
Period size: 48 Copynumber: 2.1 Consensus size: 48
3811410 GGTCAAGTAA
* *** *
3811420 CAGATCAGAATCCAACTCAAGTATCAGATCAGAATCCTTGTCAGATAT
1 CAGATCAGAATCCAACTCAAGTAACAGATCAGAATCCAAATCAGAAAT
** *
3811468 CAGATCAGAATCCATGTCAAGTAACAGATCAGAATTCAAATC-GAAAAT
1 CAGATCAGAATCCAACTCAAGTAACAGATCAGAATCCAAATCAG-AAAT
3811516 CAGAT
1 CAGAT
3811521 AAAATATTCA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
47 1 0.02
48 43 0.98
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.23
Consensus pattern (48 bp):
CAGATCAGAATCCAACTCAAGTAACAGATCAGAATCCAAATCAGAAAT
Found at i:3816101 original size:24 final size:24
Alignment explanation
Indices: 3816074--3816125 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
3816064 AACGGATATA
*
3816074 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAAAAATCAGG
** * *
3816098 TCAAGTATCATATCAAAAATCAGG
1 TCAAAAATCAAAACAAAAATCAGG
3816122 TCAA
1 TCAA
3816126 GTAACAGATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.52, C:0.17, G:0.10, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAAAAATCAGG
Found at i:3816136 original size:24 final size:24
Alignment explanation
Indices: 3816090--3816136 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
3816080 ATCAAAACAT
* *
3816090 AAATCAGGTCAAGTATCATATCAA
1 AAATCAGGTCAAGTAACAGATCAA
3816114 AAATCAGGTCAAGTAACAGATCA
1 AAATCAGGTCAAGTAACAGATCA
3816137 GAATCCAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.21
Consensus pattern (24 bp):
AAATCAGGTCAAGTAACAGATCAA
Found at i:3816151 original size:24 final size:23
Alignment explanation
Indices: 3816124--3816208 Score: 116
Period size: 24 Copynumber: 3.6 Consensus size: 23
3816114 AAATCAGGTC
* *
3816124 AAGTAACAGATCAGAATCCAAGT
1 AAGTATCAGATCAGAATCCATGT
3816147 AAAGTATCAGATCAGAATCCATGT
1 -AAGTATCAGATCAGAATCCATGT
*
3816171 CAGATATCAGATCAGAATCCATGT
1 AAG-TATCAGATCAGAATCCATGT
3816195 CAAGTATCAGATCA
1 -AAGTATCAGATCA
3816209 TAATTCAAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
23 2 0.04
24 51 0.93
25 2 0.04
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.22
Consensus pattern (23 bp):
AAGTATCAGATCAGAATCCATGT
Found at i:3816228 original size:48 final size:48
Alignment explanation
Indices: 3816130--3816230 Score: 123
Period size: 48 Copynumber: 2.1 Consensus size: 48
3816120 GGTCAAGTAA
** *
3816130 CAGATCAGAATCCAAGTAAAGTATCAGATCAGAATCCATGTCAGATAT
1 CAGATCAGAATCCAAGTAAAGTATCAGATCAGAATCCAAATCAGAAAT
* * * *
3816178 CAGATCAGAATCCATGTCAAGTATCAGATCATAATTCAAATC-GAAAAT
1 CAGATCAGAATCCAAGTAAAGTATCAGATCAGAATCCAAATCAG-AAAT
3816226 CAGAT
1 CAGAT
3816231 AAAATATTCA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
47 1 0.02
48 44 0.98
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.24
Consensus pattern (48 bp):
CAGATCAGAATCCAAGTAAAGTATCAGATCAGAATCCAAATCAGAAAT
Found at i:3818698 original size:20 final size:18
Alignment explanation
Indices: 3818673--3818720 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 18
3818663 GTCAAAGTTT
3818673 TGGTCAACAGTGGTCAACGC
1 TGGTCAAC-G-GGTCAACGC
3818693 TGGTCAACGGGTCAA--C
1 TGGTCAACGGGTCAACGC
3818709 -GGTCAACGGGTC
1 TGGTCAACGGGTC
3818721 GGGTCGGGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 12 0.43
16 1 0.04
18 6 0.21
19 1 0.04
20 8 0.29
ACGTcount: A:0.23, C:0.25, G:0.33, T:0.19
Consensus pattern (18 bp):
TGGTCAACGGGTCAACGC
Found at i:3818707 original size:8 final size:8
Alignment explanation
Indices: 3818674--3818720 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 8
3818664 TCAAAGTTTT
3818674 GGTCAACAG
1 GGTCAAC-G
3818683 TGGTCAACG
1 -GGTCAACG
3818692 CTGGTCAACG
1 --GGTCAACG
3818702 GGTCAAC-
1 GGTCAACG
3818709 GGTCAACG
1 GGTCAACG
3818717 GGTC
1 GGTC
3818721 GGGTCGGGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
7 7 0.20
8 11 0.31
9 1 0.03
10 16 0.46
ACGTcount: A:0.23, C:0.26, G:0.34, T:0.17
Consensus pattern (8 bp):
GGTCAACG
Found at i:3821790 original size:24 final size:24
Alignment explanation
Indices: 3821741--3821790 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
3821731 GAGCCCTAAC
* * *
3821741 ATAATCAGGACTTGGTCGCCTGCG
1 ATAAGCAGGACTTGGTAGCCTCCG
3821765 ATAAGCAGGACTTGG-AGACCTCCG
1 ATAAGCAGGACTTGGTAG-CCTCCG
3821789 AT
1 AT
3821791 GTGGACTATC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.22
Consensus pattern (24 bp):
ATAAGCAGGACTTGGTAGCCTCCG
Found at i:3825149 original size:31 final size:31
Alignment explanation
Indices: 3825114--3825191 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
3825104 TTAAAAAATA
* *
3825114 TAAGTTTTGGTCACTTATATTATCAATTTAT
1 TAAGTTTTAGTCACTTACATTATCAATTTAT
** * * **
3825145 TAAGTTTTTTTCGCTTACGTTATCGTTTTAT
1 TAAGTTTTAGTCACTTACATTATCAATTTAT
3825176 TAAGTTTTAGTCACTT
1 TAAGTTTTAGTCACTT
3825192 GGGCGTTGAA
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.54
Consensus pattern (31 bp):
TAAGTTTTAGTCACTTACATTATCAATTTAT
Found at i:3826547 original size:25 final size:27
Alignment explanation
Indices: 3826487--3826540 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
3826477 TCGTATAAAT
* *
3826487 TGCACCGAAGTGCCGCGTAG-AGTTTT
1 TGCACCGAAGTGCCGCGTAGAAATTTG
3826513 TGCACCGAAGTGCCGCGTAGAAATTTG
1 TGCACCGAAGTGCCGCGTAGAAATTTG
3826540 T
1 T
3826541 CCGGAAGGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 20 0.80
27 5 0.20
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.26
Consensus pattern (27 bp):
TGCACCGAAGTGCCGCGTAGAAATTTG
Found at i:3826572 original size:24 final size:24
Alignment explanation
Indices: 3826491--3826575 Score: 75
Period size: 26 Copynumber: 3.4 Consensus size: 24
3826481 ATAAATTGCA
*
3826491 CCGAAGTG-CCGCGTAGAGTTTTTGC
1 CCGAAG-GACCGCGTAGAATTTTT-C
*
3826516 ACCGAAGTG-CCGCGTAGAAATTTGTC
1 -CCGAAG-GACCGCGTAG-AATTTTTC
*
3826542 CGGAAGGACCGCGTAGAATTTTTC
1 CCGAAGGACCGCGTAGAATTTTTC
*
3826566 CCAAAGGACC
1 CCGAAGGACC
3826576 ACATATAAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
24 16 0.31
25 13 0.25
26 17 0.33
27 5 0.10
ACGTcount: A:0.25, C:0.25, G:0.28, T:0.22
Consensus pattern (24 bp):
CCGAAGGACCGCGTAGAATTTTTC
Done.