Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A03
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: 105315579
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1369460 characters in sequence are not A, C, G, or T
File 5 of 325
Found at i:1319201 original size:2 final size:2
Alignment explanation
Indices: 1319196--1319222 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1319186 ATTAACAAAT
1319196 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1319223 TATACCAAAA
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1327879 original size:50 final size:50
Alignment explanation
Indices: 1327804--1327980 Score: 248
Period size: 50 Copynumber: 3.5 Consensus size: 50
1327794 CCATGGAAAC
1327804 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * * *
1327854 AAGTGATAAGTAATAACTTCGGCTACACTTATCTGATTAAGGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1327904 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGG-CAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAA-GGACAAATGA
* * * * *
1327954 CAACTGAAAAGTGGTAGTTTCAGCTAC
1 -AAGTGATAAGTGATAGCTTCGGCTAC
1327981 CTGATCAGTG
Statistics
Matches: 112, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
50 89 0.79
51 23 0.21
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:1328135 original size:31 final size:31
Alignment explanation
Indices: 1327958--1328135 Score: 257
Period size: 31 Copynumber: 5.7 Consensus size: 31
1327948 AAATGACAAC
* *
1327958 TGAAAAGTGGTAGTTTCAGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG
* *
1327989 TGAAAAGTGGTAGCTTCTGCTACCTAATCAG
1 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG
1328020 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG
*
1328051 TGAAAAGTGGTAGCTCCGGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG
* ** *
1328082 TGAAAAATGGTAGCACCAGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG
* *
1328113 TGAATAGTGGTAGCTTTGGCTAC
1 TGAAAAGTGGTAGCTTCGGCTAC
1328136 AAGTGACAAG
Statistics
Matches: 132, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 132 1.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.26
Consensus pattern (31 bp):
TGAAAAGTGGTAGCTTCGGCTACCTGATCAG
Found at i:1335565 original size:17 final size:17
Alignment explanation
Indices: 1335543--1335600 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
1335533 ATTAGATTAA
1335543 ATTATATTTTATGTATC
1 ATTATATTTTATGTATC
**
1335560 ATTATATTAAAT-TAT-
1 ATTATATTTTATGTATC
1335575 -TTATATATTTCATGTATC
1 ATTATAT-TTT-ATGTATC
1335593 ATTATATT
1 ATTATATT
1335601 AAATTATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
14 6 0.19
15 1 0.03
16 5 0.16
17 13 0.41
18 1 0.03
19 6 0.19
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.57
Consensus pattern (17 bp):
ATTATATTTTATGTATC
Found at i:1335582 original size:33 final size:33
Alignment explanation
Indices: 1335545--1335615 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1335535 TAGATTAAAT
*
1335545 TATATTTTATGTATCATTATATTAAATTATTTA
1 TATATTTCATGTATCATTATATTAAATTATTTA
1335578 TATATTTCATGTATCATTATATTAAATTATTTA
1 TATATTTCATGTATCATTATATTAAATTATTTA
*
1335611 AATAT
1 TATAT
1335616 CATATAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.55
Consensus pattern (33 bp):
TATATTTCATGTATCATTATATTAAATTATTTA
Found at i:1360112 original size:49 final size:49
Alignment explanation
Indices: 1360038--1360135 Score: 142
Period size: 49 Copynumber: 2.0 Consensus size: 49
1360028 TAATTGCAAA
* * * *
1360038 AGATACCTAACGGAGGGTTGCTTGCATGTTGTCCCCCACAAAGGGTCAT
1 AGATACCTAACGGAGGGTCGCTTGCAGGCTATCCCCCACAAAGGGTCAT
* *
1360087 AGATACCTAACGGAGGGTCGTTTGCAGGCTATCTCCCACAAAGGGTCAT
1 AGATACCTAACGGAGGGTCGCTTGCAGGCTATCCCCCACAAAGGGTCAT
1360136 TGGCAAGTAG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (49 bp):
AGATACCTAACGGAGGGTCGCTTGCAGGCTATCCCCCACAAAGGGTCAT
Found at i:1360855 original size:42 final size:42
Alignment explanation
Indices: 1360808--1360889 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
1360798 ATTCAAACTC
* *
1360808 CCAAATTCATGATTTTTCTTCAAAAACCCT-TAAATTAAATAT
1 CCAAATCCATGATTCTTCTTC-AAAACCCTCTAAATTAAATAT
** *
1360850 CCAAATCCATTCTTCTTCTTCAAAACTCTCTAAATTAAAT
1 CCAAATCCATGATTCTTCTTCAAAACCCTCTAAATTAAAT
1360890 CCTCCATTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 7 0.21
42 27 0.79
ACGTcount: A:0.38, C:0.23, G:0.01, T:0.38
Consensus pattern (42 bp):
CCAAATCCATGATTCTTCTTCAAAACCCTCTAAATTAAATAT
Found at i:1362621 original size:20 final size:22
Alignment explanation
Indices: 1362588--1362632 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
1362578 TTTATTTTTC
*
1362588 ATAATAAATTACATAATAT-AT
1 ATAATAAATAACATAATATAAT
1362609 ATAA-AAATAACATAATATAAT
1 ATAATAAATAACATAATATAAT
1362630 ATA
1 ATA
1362633 TTAGGAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (22 bp):
ATAATAAATAACATAATATAAT
Found at i:1368763 original size:25 final size:27
Alignment explanation
Indices: 1368715--1368766 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1368705 TAAATAAAAA
* *
1368715 ATTTTAAAAATATAATAAATCAAATAT
1 ATTTAAAAAACATAATAAATCAAATAT
1368742 ATTTAAAAAACATAA-AAA-CAAATAT
1 ATTTAAAAAACATAATAAATCAAATAT
1368767 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 7 0.30
26 3 0.13
27 13 0.57
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (27 bp):
ATTTAAAAAACATAATAAATCAAATAT
Found at i:1368778 original size:22 final size:22
Alignment explanation
Indices: 1368744--1368795 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
1368734 TCAAATATAT
1368744 TTAAAA-AACATAAAAACAAATA
1 TTAAAACAACATAAAAA-AAATA
*
1368766 TTAAAACAA-ATAAAAATAATA
1 TTAAAACAACATAAAAAAAATA
*
1368787 CTAAAACAA
1 TTAAAACAA
1368796 TTTTTAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 12 0.44
22 13 0.48
23 2 0.07
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.19
Consensus pattern (22 bp):
TTAAAACAACATAAAAAAAATA
Found at i:1368780 original size:21 final size:20
Alignment explanation
Indices: 1368748--1368795 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
1368738 ATATATTTAA
* *
1368748 AAAACATAAAAACA-AATATT
1 AAAACA-AAAAAAATAATACT
1368768 AAAACAAATAAAAATAATACT
1 AAAACAAA-AAAAATAATACT
1368789 AAAACAA
1 AAAACAA
1368796 TTTTTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 10 0.42
21 12 0.50
ACGTcount: A:0.73, C:0.10, G:0.00, T:0.17
Consensus pattern (20 bp):
AAAACAAAAAAAATAATACT
Found at i:1369742 original size:76 final size:77
Alignment explanation
Indices: 1369596--1369759 Score: 249
Period size: 76 Copynumber: 2.1 Consensus size: 77
1369586 TCTCACTTAC
* *
1369596 ACCATCGAGATTCAAACACAAAACCATCACACATAAATACAAACTGTCTGTATCTTCAGCTCATA
1 ACCATTGAGATTCAAACACAAAACCAT-ACACATAAACACAAACTGTCTGTATCTTCAGCTCATA
1369661 AACATCCCAATAA
65 AACATCCCAATAA
* * * *
1369674 ACCATTGAGATTCAAACACAAAACCAT-CACATAAACACATACTGTTTGTATCTTCAGTTCATCA
1 ACCATTGAGATTCAAACACAAAACCATACACATAAACACAAACTGTCTGTATCTTCAGCTCATAA
*
1369738 ACATCTCAATAA
66 ACATCCCAATAA
1369750 ACCATTGAGA
1 ACCATTGAGA
1369760 ATGTATTTCA
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
76 53 0.67
78 26 0.33
ACGTcount: A:0.42, C:0.26, G:0.07, T:0.24
Consensus pattern (77 bp):
ACCATTGAGATTCAAACACAAAACCATACACATAAACACAAACTGTCTGTATCTTCAGCTCATAA
ACATCCCAATAA
Found at i:1369873 original size:42 final size:42
Alignment explanation
Indices: 1369816--1369949 Score: 180
Period size: 42 Copynumber: 3.2 Consensus size: 42
1369806 ACGTTTGTAG
* * * *
1369816 CTTCAGTAGGTTTTCTTCTAACTCAGCTTTGTCCTTCTCCAG
1 CTTCAGTTGGTTTTCTTTTAACTCAGCTTTGCCCTTCTCCAC
* *
1369858 CTTCAGTTGGTTTTCTTTTAACTCAGCTTCGCCCTGCTCCAC
1 CTTCAGTTGGTTTTCTTTTAACTCAGCTTTGCCCTTCTCCAC
* *
1369900 CTTCAGTTTGTTTTCTTTTAAATCAGCTTCT-CCCTTCTCCAC
1 CTTCAGTTGGTTTTCTTTTAACTCAGCTT-TGCCCTTCTCCAC
1369942 CTTCAGTT
1 CTTCAGTT
1369950 CGCCTTTCCT
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
42 81 1.00
ACGTcount: A:0.13, C:0.31, G:0.12, T:0.44
Consensus pattern (42 bp):
CTTCAGTTGGTTTTCTTTTAACTCAGCTTTGCCCTTCTCCAC
Found at i:1377664 original size:18 final size:18
Alignment explanation
Indices: 1377641--1377821 Score: 130
Period size: 18 Copynumber: 9.4 Consensus size: 18
1377631 ACATCGTGAT
*
1377641 CTGAAGCCCGAAGTCTAG
1 CTGAAGCCCGAAGTCTAA
*
1377659 CTGAAGCACGCAAGTGCTAAA
1 CTGAAGCCCG-AAGT-CT-AA
* *
1377680 CGGAAGCCCGAAGGCTAA
1 CTGAAGCCCGAAGTCTAA
*
1377698 CTGAAGCACGCAAGTGCTAAA
1 CTGAAGCCCG-AAGT-CT-AA
* *
1377719 CGGAAGCCCGAAGGCTAA
1 CTGAAGCCCGAAGTCTAA
*
1377737 CTGAAGCACGCAAGTGCTATA
1 CTGAAGCCCG-AAGT-CTA-A
* *
1377758 CGGAAGCCCGAAGGCTAA
1 CTGAAGCCCGAAGTCTAA
1377776 CTGAAGCACAC-AAGTACTAA
1 CTGAAGC-C-CGAAGT-CTAA
* *
1377796 ATGGAAGCCCGAAGGCTAA
1 CT-GAAGCCCGAAGTCTAA
1377815 CTGAAGC
1 CTGAAGC
1377822 TCATCAGAGC
Statistics
Matches: 127, Mismatches: 22, Indels: 28
0.72 0.12 0.16
Matches are distributed among these distances:
18 41 0.32
19 27 0.21
20 26 0.20
21 33 0.26
ACGTcount: A:0.35, C:0.25, G:0.27, T:0.12
Consensus pattern (18 bp):
CTGAAGCCCGAAGTCTAA
Found at i:1377702 original size:39 final size:39
Alignment explanation
Indices: 1377643--1377821 Score: 304
Period size: 39 Copynumber: 4.6 Consensus size: 39
1377633 ATCGTGATCT
* *
1377643 GAAGCCCGAAGTCTAGCTGAAGCACGCAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACGCAAGTGCTAAACG
1377682 GAAGCCCGAAGGCTAACTGAAGCACGCAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACGCAAGTGCTAAACG
*
1377721 GAAGCCCGAAGGCTAACTGAAGCACGCAAGTGCTATACG
1 GAAGCCCGAAGGCTAACTGAAGCACGCAAGTGCTAAACG
* * *
1377760 GAAGCCCGAAGGCTAACTGAAGCACACAAGTACTAAATG
1 GAAGCCCGAAGGCTAACTGAAGCACGCAAGTGCTAAACG
1377799 GAAGCCCGAAGGCTAACTGAAGC
1 GAAGCCCGAAGGCTAACTGAAGC
1377822 TCATCAGAGC
Statistics
Matches: 133, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 133 1.00
ACGTcount: A:0.36, C:0.25, G:0.27, T:0.12
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTGAAGCACGCAAGTGCTAAACG
Found at i:1380956 original size:23 final size:23
Alignment explanation
Indices: 1380893--1380963 Score: 67
Period size: 22 Copynumber: 3.1 Consensus size: 23
1380883 ATTTCTTAAA
*
1380893 TAATTAGTTTACAA-AAATAATTT
1 TAATTATTTTA-AATAAATAATTT
*
1380916 TAATTATTTTAAAT-AATATTTT
1 TAATTATTTTAAATAAATAATTT
* *
1380938 CTAA-TATTTTAAGTAAATAAATT
1 -TAATTATTTTAAATAAATAATTT
1380961 TAA
1 TAA
1380964 AATTAATATT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
22 21 0.52
23 19 0.47
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (23 bp):
TAATTATTTTAAATAAATAATTT
Found at i:1381136 original size:14 final size:14
Alignment explanation
Indices: 1381117--1381144 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1381107 ATTAAGTTGT
1381117 AATTAATTCAAATA
1 AATTAATTCAAATA
1381131 AATTAATTCAAATA
1 AATTAATTCAAATA
1381145 TAAACTTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (14 bp):
AATTAATTCAAATA
Found at i:1381334 original size:16 final size:16
Alignment explanation
Indices: 1381301--1381345 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
1381291 TATTACGAGG
*
1381301 TTTTTGT-TTTTTGT-
1 TTTTTGTATTTTTATC
*
1381315 TTTTTTTATTTTTATC
1 TTTTTGTATTTTTATC
1381331 TTTTTGTATTTTTAT
1 TTTTTGTATTTTTAT
1381346 AAATAAACGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 6 0.23
15 6 0.23
16 14 0.54
ACGTcount: A:0.09, C:0.02, G:0.07, T:0.82
Consensus pattern (16 bp):
TTTTTGTATTTTTATC
Found at i:1382105 original size:20 final size:19
Alignment explanation
Indices: 1382080--1382122 Score: 68
Period size: 20 Copynumber: 2.2 Consensus size: 19
1382070 ATTTTTCATA
*
1382080 ATAAATTACATAATATATAT
1 ATAAATAACATAATATA-AT
1382100 ATAAATAACATAATATAAT
1 ATAAATAACATAATATAAT
1382119 ATAA
1 ATAA
1382123 TACATTAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
ATAAATAACATAATATAAT
Found at i:1387948 original size:76 final size:78
Alignment explanation
Indices: 1387801--1387965 Score: 253
Period size: 76 Copynumber: 2.1 Consensus size: 78
1387791 TATCACTTAG
* *
1387801 ACCATCGAGATTCAAACACAAAACCATCACGCATAAATACAAACTGTCTGTATCTTCAGCTCATA
1 ACCATTGAGATTCAAACACAAAACCATCAC-CATAAACACAAACTGTCTGTATCTTCAGCTCATA
1387866 AACATCC-CAATAA
65 AACATCCTCAATAA
* * * *
1387879 ACCATTGAGATTCAAACACAAAACCATCA-CATAAACACATACTGTTTGTATCTTCAGTTCATCA
1 ACCATTGAGATTCAAACACAAAACCATCACCATAAACACAAACTGTCTGTATCTTCAGCTCATAA
1387943 ACATCCTCAATAA
66 ACATCCTCAATAA
1387956 ACCATTGAGA
1 ACCATTGAGA
1387966 ATGTATTTCA
Statistics
Matches: 80, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
76 36 0.45
77 16 0.20
78 28 0.35
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.24
Consensus pattern (78 bp):
ACCATTGAGATTCAAACACAAAACCATCACCATAAACACAAACTGTCTGTATCTTCAGCTCATAA
ACATCCTCAATAA
Found at i:1388078 original size:42 final size:42
Alignment explanation
Indices: 1388022--1388155 Score: 180
Period size: 42 Copynumber: 3.2 Consensus size: 42
1388012 TCGTTTTCAG
* * * *
1388022 CTTCAGTAGGTTTTCTTCTAACTCAGCTTTGTCCTTCTCCAG
1 CTTCAGTTGGTTTTCTTTTAACTCAGCTTTGCCCTTCTCCAC
* *
1388064 CTTCACTTGGTTTTCTTTTAACTCAGCTTCGCCCTTCTCCAC
1 CTTCAGTTGGTTTTCTTTTAACTCAGCTTTGCCCTTCTCCAC
* *
1388106 CTTCAGTTTGTTTTCTTTTAAATCAGCTTCT-CCCTTCTCCAC
1 CTTCAGTTGGTTTTCTTTTAACTCAGCTT-TGCCCTTCTCCAC
1388148 CTTCAGTT
1 CTTCAGTT
1388156 CGTCTTTCCT
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
42 81 1.00
ACGTcount: A:0.13, C:0.31, G:0.10, T:0.45
Consensus pattern (42 bp):
CTTCAGTTGGTTTTCTTTTAACTCAGCTTTGCCCTTCTCCAC
Found at i:1388517 original size:24 final size:24
Alignment explanation
Indices: 1388487--1388539 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
1388477 ACAGCTTCAT
1388487 ATTGTCTTGATTTTCTCTGGCATC
1 ATTGTCTTGATTTTCTCTGGCATC
1388511 ATTGTCTTGATTTTCTCTGGCATC
1 ATTGTCTTGATTTTCTCTGGCATC
1388535 ATTGT
1 ATTGT
1388540 TTCCCAATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.13, C:0.19, G:0.17, T:0.51
Consensus pattern (24 bp):
ATTGTCTTGATTTTCTCTGGCATC
Found at i:1399381 original size:38 final size:39
Alignment explanation
Indices: 1399332--1399406 Score: 125
Period size: 38 Copynumber: 1.9 Consensus size: 39
1399322 TCCCTACTCA
* *
1399332 AATATTTTAGGAGATATTTACCTGTTACTTATAATTCAG
1 AATATTTTAGGAAATATTCACCTGTTACTTATAATTCAG
1399371 AATA-TTTAGGAAATATTCACCTGTTACTTATAATTC
1 AATATTTTAGGAAATATTCACCTGTTACTTATAATTC
1399407 GAGGAGTATC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 30 0.88
39 4 0.12
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.43
Consensus pattern (39 bp):
AATATTTTAGGAAATATTCACCTGTTACTTATAATTCAG
Found at i:1405498 original size:13 final size:13
Alignment explanation
Indices: 1405480--1405504 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1405470 TGTAGTTGTT
1405480 TTTTTATTTTTTA
1 TTTTTATTTTTTA
1405493 TTTTTATTTTTT
1 TTTTTATTTTTT
1405505 TTAATTTAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:1408230 original size:628 final size:626
Alignment explanation
Indices: 1406643--1409740 Score: 5328
Period size: 624 Copynumber: 4.9 Consensus size: 626
1406633 GGTAAGGTTT
* * *
1406643 GGCATATATATATATATATAGTTGAAGTTGCTTATTTTTTTGGATCAAGTCTGATTCTCTTCTTC
1 GGCATATATATATATATATAATTGAAGTTGCTTATTTTTTTGGATCAAATCTGATTCTCTTCTGC
* *
1406708 ATATAGGATCTTTCGTCACTGTGGTTCTTTGATGTGGAAAAATATGGTTTGGAAAACCATCATCT
66 ATATAGGATCTTTCGTCACTGTGGTTCTTTGATGTGGAAAAATATGATTTGGAAAACCGTCATCT
* **
1406773 GCCAGGTAGTGGCTGCAAGTTGATATTCTATTATGTCATTTTACAGAAATAATTTGGTCTCTACA
131 GCCAGGTAATGGCTGCAAGTTGATATTCTATTATGTCAACTTACAGAAATAATTTGGTCTCTACA
*
1406838 TTCTTAAACTGTGACTATAATAATCTTAATGGTTTTATACTTGTCAATTGTCAACATTAATATCC
196 TTCTTAAACTGTGACTATAATAATCTTAATGGTCTTATACTTGTCAATTGTCAACATTAATATCC
* * * * *
1406903 TTTAGATTTTGGACATCAATATCCGGATGAAGGCAGCAGTAAGGCAAGAGCAAATCAAGACAATA
261 TTTAGATTTTGGACATCAATATCCGGGTGAAGGCAGCAGTGATGCCAGAGCAAATCAAGAGAATA
* * *
1406968 TGAAGCTGTCAAATGAGAACATCTCTCCTGTCCAAGGGTATACAACATTTATGGACGCAATGTTA
326 TGAAGCTGTCACATGAGAACACCTCTCCTGTCCAAGGGTATACAACATTTATGGACGCAATGCTA
* *
1407033 ATGTGCTCACTGAGATATTTCAAAAGCACCCTCATACTGATAACAAGTTCTTCATTTAGGCATGC
391 ATGTGCTCACTGAGATATTTCAAAAGCACCCTCATACTGATAACAAGTTTTTTATTTAGGCATGC
* * *
1407098 AGATTTTCAGAACATCCTTACAAACTCTCTAACTGAAGCTGATCATAATATAGAAAGCAAACCAG
456 AGATTTTCAGAACATCCTTGCAAACTCTCTAACTGAAGCTGACCATAATATAGAAAGTAAACCAG
* *
1407163 AGAGGCTCGAGCTAAAAGACATCACAAATATAGAGGTAAGGGTGCAAAGCATAAAGAATAACTTG
521 AGAGGCTCGAGCTAAAAGACATCACAAATATAGAGGTAAGGGTGCAAAACATAAGGAATAACTTG
*
1407228 GAGAAGGCTCGTGAAAGGAAGAAATTGGAAGAAGAGATCAG
586 GAGAAGGCTCGTGAAAAGAAGAAATTGGAAGAAGAGATCAG
*
1407269 GGCATATATATATATATATATAAAATTGAAGTTGCTTATTTTTTTGGATCAATTCTGATTCTCTT
1 GGC--ATATATATATATATAT--AATTGAAGTTGCTTATTTTTTTGGATCAAATCTGATTCTCTT
* * **
1407334 CTGCATATAGGATCTTTTGTCACCGCAGTTCTTTGATGTGGAAAAATATGATTTGGAAAACCGTC
62 CTGCATATAGGATCTTTCGTCACTGTGGTTCTTTGATGTGGAAAAATATGATTTGGAAAACCGTC
*
1407399 ATCTGCCAGGTAATGGCTGCAAGTTGATATTCTATCATGTCAACTTACAGAAATAATTTGGTCTC
127 ATCTGCCAGGTAATGGCTGCAAGTTGATATTCTATTATGTCAACTTACAGAAATAATTTGGTCTC
1407464 TACATTCTTAAACTGTGACTATAATAATCTTAATGGTCTTATACTTGTCAATTGTCAACATTAAT
192 TACATTCTTAAACTGTGACTATAATAATCTTAATGGTCTTATACTTGTCAATTGTCAACATTAAT
1407529 ATCCTTTAGATTTTGGACATCAATATCCGGGTGAAGGCAGCAGTGATGCCAGAGCAAATCAAGAG
257 ATCCTTTAGATTTTGGACATCAATATCCGGGTGAAGGCAGCAGTGATGCCAGAGCAAATCAAGAG
* * *
1407594 AATATGAAGCTGTCATATGAGAACATCTCTCCTGTCCAAGGGTATACAACATTTATAGACGCAAT
322 AATATGAAGCTGTCACATGAGAACACCTCTCCTGTCCAAGGGTATACAACATTTATGGACGCAAT
1407659 GCTAATGTGCTCACTGAGATATTTCAAAAGCACCCTCATACTGATAACAAGTTTTTTATTTAGGC
387 GCTAATGTGCTCACTGAGATATTTCAAAAGCACCCTCATACTGATAACAAGTTTTTTATTTAGGC
*
1407724 ATGCAGATTTTCAGAACATCCTTGCAAACTCTCTAACTGAAGCTGACCATTATATAGAAAGTAAA
452 ATGCAGATTTTCAGAACATCCTTGCAAACTCTCTAACTGAAGCTGACCATAATATAGAAAGTAAA
* *
1407789 CCAGATAGGCTCGAGCTAAAAGACATCACAAATATAGAGGTAAGGGTGCAAAGCATAAGGAATAA
517 CCAGAGAGGCTCGAGCTAAAAGACATCACAAATATAGAGGTAAGGGTGCAAAACATAAGGAATAA
* *
1407854 CTTGGAGAATGCTCGTGAAAGGAAGAAATTGGAAGAAGAGATCAG
582 CTTGGAGAAGGCTCGTGAAAAGAAGAAATTGGAAGAAGAGATCAG
*
1407899 GGCACATATATATATATATATAATTGAAGTTGCTTATTTTTTTGGATCAATTCTGATTCTCTTCT
1 GG--CATATATATATATATATAATTGAAGTTGCTTATTTTTTTGGATCAAATCTGATTCTCTTCT
* * *
1407964 GCATATAGGATCTTTCGTCACTTTGGTTCTTTGATGTGGAAAAAAATGATTTGGAAAACCATCAT
64 GCATATAGGATCTTTCGTCACTGTGGTTCTTTGATGTGGAAAAATATGATTTGGAAAACCGTCAT
*
1408029 CTGCCAGGTAATGGCTGCAAGTTGATATTCTATTATGTCAATTTACAGAAATAATTTGGTCTCTA
129 CTGCCAGGTAATGGCTGCAAGTTGATATTCTATTATGTCAACTTACAGAAATAATTTGGTCTCTA
1408094 CATTCTTAAACTGTGACTATAATAATCTTAATGGTCTTATACTTGTCAATTGTCAACATTAATAT
194 CATTCTTAAACTGTGACTATAATAATCTTAATGGTCTTATACTTGTCAATTGTCAACATTAATAT
* *
1408159 CCTTTAGATTTTGGACATCAATATCCGGGTGAAGGCAGCAGTGATGCCAGAGCGAATCAAGAGAT
259 CCTTTAGATTTTGGACATCAATATCCGGGTGAAGGCAGCAGTGATGCCAGAGCAAATCAAGAGAA
1408224 TATGAAGCTGTCACATGAGAACACCTCTCCTGTCCAAGGGTATACAACATTTATGGACGCAATGC
324 TATGAAGCTGTCACATGAGAACACCTCTCCTGTCCAAGGGTATACAACATTTATGGACGCAATGC
**
1408289 TAATGTGCTCACTGAGATATTTTTAAAGCACCCTCATACTGATAACAAGTTTTTTATTTAGGCAT
389 TAATGTGCTCACTGAGATATTTCAAAAGCACCCTCATACTGATAACAAGTTTTTTATTTAGGCAT
*
1408354 GCAGATTTTCAGAACATCCTTGCAAACTCTCTAACTGAAGCTGACCATAATATAGAACGTAAACC
454 GCAGATTTTCAGAACATCCTTGCAAACTCTCTAACTGAAGCTGACCATAATATAGAAAGTAAACC
1408419 AGAGAGGCTCGAGCTAAAAGACATCACAAATATAGAGGTAAGGGTGCAAAACATAAGGAATAACT
519 AGAGAGGCTCGAGCTAAAAGACATCACAAATATAGAGGTAAGGGTGCAAAACATAAGGAATAACT
*
1408484 TGGAGAAGGCTCGTGAAAAGAAGAAATTGGAAGAAGAGATTAG
584 TGGAGAAGGCTCGTGAAAAGAAGAAATTGGAAGAAGAGATCAG
* *
1408527 GGC--ATATATATATATGTAATTGAAGTTGTTTATTTTTTTGGATCAAATCTGATTCTCTTCTGC
1 GGCATATATATATATATATAATTGAAGTTGCTTATTTTTTTGGATCAAATCTGATTCTCTTCTGC
* *
1408590 GTATAGGATCTTTCGTCACTGTGGTTTTTTGATGTGGAAAAATATGATTTGGAAAACCGTCATCT
66 ATATAGGATCTTTCGTCACTGTGGTTCTTTGATGTGGAAAAATATGATTTGGAAAACCGTCATCT
*
1408655 GCCAGGTAATGACTGCAAGTTGATATTCTATTATGTCAACTTACAGAAATAATTTGGTCTCTACA
131 GCCAGGTAATGGCTGCAAGTTGATATTCTATTATGTCAACTTACAGAAATAATTTGGTCTCTACA
*
1408720 TTCTTAAACT-TGGAGTATAATAATCTTAATGGTCTTATACTTGTCAATTGTCAACATTAATATC
196 TTCTTAAACTGT-GACTATAATAATCTTAATGGTCTTATACTTGTCAATTGTCAACATTAATATC
1408784 CTTTAGATTTTGGACATCAATATCCGGGTGAAGGCAGCAGTGATGCCAGAGCAAATCAAGAGAAT
260 CTTTAGATTTTGGACATCAATATCCGGGTGAAGGCAGCAGTGATGCCAGAGCAAATCAAGAGAAT
* * *
1408849 ATGAAGCTGTCATATGAGAACACCTCTCCTGTCCAAGGGTATACAACATTTATTGACGCAATGTT
325 ATGAAGCTGTCACATGAGAACACCTCTCCTGTCCAAGGGTATACAACATTTATGGACGCAATGCT
*
1408914 AATATGCTCACTGAGATATTTCAAAAGCACCCTCATACTGATAACAAGTTTTTTATTTAGGCATG
390 AATGTGCTCACTGAGATATTTCAAAAGCACCCTCATACTGATAACAAGTTTTTTATTTAGGCATG
*
1408979 CAGATTTTCAGAACATCCTTGCAAACTCTCTAACTGAAGCTGACCATAATGTAGAAAGTAAACCA
455 CAGATTTTCAGAACATCCTTGCAAACTCTCTAACTGAAGCTGACCATAATATAGAAAGTAAACCA
*
1409044 GAGAGGCTCGAGCTAAAAGACATCACAAATATAGAGGTAAGGGTGCAAAACATAAGGAACAACTT
520 GAGAGGCTCGAGCTAAAAGACATCACAAATATAGAGGTAAGGGTGCAAAACATAAGGAATAACTT
*
1409109 GGAGAAGGCTCGTGAAAAGAAGAAATTGGAAGAAGAGATTAG
585 GGAGAAGGCTCGTGAAAAGAAGAAATTGGAAGAAGAGATCAG
*
1409151 GGCATATATATATATATGTAATTGAAGTTGCTTATTTTTTTTGGATCAAATCTGATTCTCTTCTG
1 GGCATATATATATATATATAATTGAAGTTGCTTA-TTTTTTTGGATCAAATCTGATTCTCTTCTG
* *
1409216 CGTGTAGGATCTTTCGTCACTGTGGTTCTTTGATGTGGAAAAATATGATTTGGAAAACCGTCATC
65 CATATAGGATCTTTCGTCACTGTGGTTCTTTGATGTGGAAAAATATGATTTGGAAAACCGTCATC
*
1409281 TGCCAGGTAATGACTGCAAGTTGATATTCTATTATGTCAACTTACAGAAATAATTTGGTCTCTAC
130 TGCCAGGTAATGGCTGCAAGTTGATATTCTATTATGTCAACTTACAGAAATAATTTGGTCTCTAC
1409346 ATTCTTAAACTGTGACTATAATAATCTTAATGGTCTTATACTTGTCAATTGTCAACATTAATATC
195 ATTCTTAAACTGTGACTATAATAATCTTAATGGTCTTATACTTGTCAATTGTCAACATTAATATC
*
1409411 CTTTAGATTTTGGACATCAATATCCGGATGAAGGCAGCAGTGATGCCAGAGCAAATCAAGAGAAT
260 CTTTAGATTTTGGACATCAATATCCGGGTGAAGGCAGCAGTGATGCCAGAGCAAATCAAGAGAAT
* *
1409476 ATGAAGCTGTCACATGAGAACACCTCTCTTGTCCAAAGGTATACAACATTTATGGACGCAATGCT
325 ATGAAGCTGTCACATGAGAACACCTCTCCTGTCCAAGGGTATACAACATTTATGGACGCAATGCT
*
1409541 AATGTGCTCACTGAGATATTTCAAAAGCACCCTCATACTGATAACAATTTTTTTATTTAGGCATG
390 AATGTGCTCACTGAGATATTTCAAAAGCACCCTCATACTGATAACAAGTTTTTTATTTAGGCATG
* * * * * *
1409606 CATATTTTGAGAACATCCTTTCAAACTCTCTAGCAGAAGCTGACCAT-A-A-AGAAAGTAACCCA
455 CAGATTTTCAGAACATCCTTGCAAACTCTCTAACTGAAGCTGACCATAATATAGAAAGTAAACCA
* * * *
1409668 GAGAGGCTCGGGCTAAGAGACATCACAAATATGGAGGTAACGGTGCAAAACA-AGAGGAATAACT
520 GAGAGGCTCGAGCTAAAAGACATCACAAATATAGAGGTAAGGGTGCAAAACATA-AGGAATAACT
1409732 TGGAAGAAG
584 TGG-AGAAG
1409741 AGACCAAGAA
Statistics
Matches: 2359, Mismatches: 100, Indels: 27
0.95 0.04 0.01
Matches are distributed among these distances:
623 2 0.00
624 672 0.28
625 5 0.00
626 33 0.01
627 449 0.19
628 603 0.26
630 594 0.25
632 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (626 bp):
GGCATATATATATATATATAATTGAAGTTGCTTATTTTTTTGGATCAAATCTGATTCTCTTCTGC
ATATAGGATCTTTCGTCACTGTGGTTCTTTGATGTGGAAAAATATGATTTGGAAAACCGTCATCT
GCCAGGTAATGGCTGCAAGTTGATATTCTATTATGTCAACTTACAGAAATAATTTGGTCTCTACA
TTCTTAAACTGTGACTATAATAATCTTAATGGTCTTATACTTGTCAATTGTCAACATTAATATCC
TTTAGATTTTGGACATCAATATCCGGGTGAAGGCAGCAGTGATGCCAGAGCAAATCAAGAGAATA
TGAAGCTGTCACATGAGAACACCTCTCCTGTCCAAGGGTATACAACATTTATGGACGCAATGCTA
ATGTGCTCACTGAGATATTTCAAAAGCACCCTCATACTGATAACAAGTTTTTTATTTAGGCATGC
AGATTTTCAGAACATCCTTGCAAACTCTCTAACTGAAGCTGACCATAATATAGAAAGTAAACCAG
AGAGGCTCGAGCTAAAAGACATCACAAATATAGAGGTAAGGGTGCAAAACATAAGGAATAACTTG
GAGAAGGCTCGTGAAAAGAAGAAATTGGAAGAAGAGATCAG
Found at i:1417865 original size:21 final size:21
Alignment explanation
Indices: 1417841--1417895 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
1417831 CCTACAGCCA
* *
1417841 CTGTTATTCCTGTTTTGGAAC
1 CTGTTTTTCCTATTTTGGAAC
1417862 CTGTTTTTCCTATTTTGGAAC
1 CTGTTTTTCCTATTTTGGAAC
1417883 CTGTTTTTCCTAT
1 CTGTTTTTCCTAT
1417896 CTCCACTGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.13, C:0.20, G:0.15, T:0.53
Consensus pattern (21 bp):
CTGTTTTTCCTATTTTGGAAC
Found at i:1420727 original size:47 final size:47
Alignment explanation
Indices: 1420597--1420767 Score: 166
Period size: 47 Copynumber: 3.6 Consensus size: 47
1420587 ATAGTAAAAC
* * * *
1420597 TATGGTCTTGCACA-TAGTCACATATCACATACCGAGGCCATAGCCCAGC
1 TATGGTCTTACACAGTAG-CACATATCAC--ACCGATGCCATATCCCAGA
* * * * *
1420646 CATGGTCTTACAC-GGATCACATATCACACTGATGCCATATCCTAGA
1 TATGGTCTTACACAGTAGCACATATCACACCGATGCCATATCCCAGA
* *
1420692 TATGGTCTTATACAGTAGCACATATCACACCGATGCCATATCCCGGA
1 TATGGTCTTACACAGTAGCACATATCACACCGATGCCATATCCCAGA
* * * *
1420739 TATGGTTTTATACGGAAGCACATATCACA
1 TATGGTCTTACACAGTAGCACATATCACA
1420768 TTTCTTCGAA
Statistics
Matches: 101, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
46 25 0.25
47 54 0.53
48 10 0.10
49 12 0.12
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (47 bp):
TATGGTCTTACACAGTAGCACATATCACACCGATGCCATATCCCAGA
Found at i:1427333 original size:24 final size:24
Alignment explanation
Indices: 1427301--1427521 Score: 187
Period size: 24 Copynumber: 9.2 Consensus size: 24
1427291 GCTAAATCGC
1427301 TTAGTGACCATCCATCCATGCATA
1 TTAGTGACCATCCATCCATGCATA
*
1427325 TTAGTGACCATCCATCCATCCAT-
1 TTAGTGACCATCCATCCATGCATA
**
1427348 CCA-T--CCATCCATCCATGCATA
1 TTAGTGACCATCCATCCATGCATA
*
1427369 TTAGTGACCATCCATTCATGCATA
1 TTAGTGACCATCCATCCATGCATA
1427393 TTAGTGACCATCCATCCAT-C---
1 TTAGTGACCATCCATCCATGCATA
*
1427413 -CA-T--CCATCCATCCATGCATA
1 TTAGTGACCATCCATCCATGCATA
1427433 TTAGTGACCATCCATCCATCGATGCATA
1 TTAGTGACCATCCAT-C--C-ATGCATA
1427461 TTAGTGACCATCCTTCTATCCATCCATGCATA
1 TTAGTG---A--C--C-ATCCATCCATGCATA
* *
1427493 TTAGTGACCATTCAACCATGCATA
1 TTAGTGACCATCCATCCATGCATA
1427517 TTAGT
1 TTAGT
1427522 TTCGTACACA
Statistics
Matches: 161, Mismatches: 12, Indels: 48
0.73 0.05 0.22
Matches are distributed among these distances:
16 12 0.07
17 1 0.01
18 1 0.01
19 1 0.01
20 15 0.09
21 2 0.01
22 3 0.02
23 2 0.01
24 82 0.51
25 2 0.01
27 2 0.01
28 13 0.08
29 1 0.01
31 1 0.01
32 13 0.08
33 2 0.01
35 2 0.01
36 6 0.04
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.30
Consensus pattern (24 bp):
TTAGTGACCATCCATCCATGCATA
Found at i:1427341 original size:4 final size:4
Alignment explanation
Indices: 1427332--1427363 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
1427322 ATATTAGTGA
1427332 CCAT CCAT CCAT CCAT CCAT CCAT CCAT CCAT
1 CCAT CCAT CCAT CCAT CCAT CCAT CCAT CCAT
1427364 GCATATTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.50, G:0.00, T:0.25
Consensus pattern (4 bp):
CCAT
Found at i:1427409 original size:4 final size:4
Alignment explanation
Indices: 1427400--1427427 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1427390 ATATTAGTGA
1427400 CCAT CCAT CCAT CCAT CCAT CCAT CCAT
1 CCAT CCAT CCAT CCAT CCAT CCAT CCAT
1427428 GCATATTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.50, G:0.00, T:0.25
Consensus pattern (4 bp):
CCAT
Found at i:1427410 original size:68 final size:68
Alignment explanation
Indices: 1427301--1427487 Score: 283
Period size: 64 Copynumber: 2.8 Consensus size: 68
1427291 GCTAAATCGC
*
1427301 TTAGTGACCATCCATCCATGCATATTAGTGACCATCCATCCATCCATCCATCCATCCATCCATGC
1 TTAGTGACCATCCATTCATGCATATTAGTGACCATCCATCCATCCATCCATCCATCCATCCATGC
1427366 ATA
66 ATA
1427369 TTAGTGACCATCCATTCATGCATATTAGTG---A-CCATCCATCCATCCATCCATCCATCCATGC
1 TTAGTGACCATCCATTCATGCATATTAGTGACCATCCATCCATCCATCCATCCATCCATCCATGC
1427430 ATA
66 ATA
* *
1427433 TTAGTGACCATCCATCCATCGATGCATATTAGTGACCATCCTTCTATCCATCCAT
1 TTAGTGACCATCCAT---TC-ATGCATATTAGTGACCATCCATCCATCCATCCAT
1427488 GCATATTAGT
Statistics
Matches: 108, Mismatches: 3, Indels: 12
0.88 0.02 0.10
Matches are distributed among these distances:
64 48 0.44
65 1 0.01
67 2 0.02
68 42 0.39
71 1 0.01
72 14 0.13
ACGTcount: A:0.27, C:0.33, G:0.10, T:0.30
Consensus pattern (68 bp):
TTAGTGACCATCCATTCATGCATATTAGTGACCATCCATCCATCCATCCATCCATCCATCCATGC
ATA
Found at i:1427420 original size:40 final size:40
Alignment explanation
Indices: 1427376--1427452 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
1427366 ATATTAGTGA
*
1427376 CCATCCATTCATGCATATTAGTGACCATCCATCCATCCAT
1 CCATCCATCCATGCATATTAGTGACCATCCATCCATCCAT
1427416 CCATCCATCCATGCATATTAGTGACCATCCATCCATC
1 CCATCCATCCATGCATATTAGTGACCATCCATCCATC
1427453 GATGCATATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.27, C:0.36, G:0.08, T:0.29
Consensus pattern (40 bp):
CCATCCATCCATGCATATTAGTGACCATCCATCCATCCAT
Found at i:1427452 original size:28 final size:28
Alignment explanation
Indices: 1427412--1427503 Score: 139
Period size: 28 Copynumber: 3.1 Consensus size: 28
1427402 ATCCATCCAT
1427412 CCATCCATCCATCCATGCATATTAGTGA
1 CCATCCATCCATCCATGCATATTAGTGA
*
1427440 CCATCCATCCATCGATGCATATTAGTGA
1 CCATCCATCCATCCATGCATATTAGTGA
1427468 CCATCCTTCTATCCATCCATGCATATTAGTGA
1 CCAT-C--C-ATCCATCCATGCATATTAGTGA
1427500 CCAT
1 CCAT
1427504 TCAACCATGC
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
28 31 0.53
29 1 0.02
31 1 0.02
32 25 0.43
ACGTcount: A:0.27, C:0.32, G:0.11, T:0.30
Consensus pattern (28 bp):
CCATCCATCCATCCATGCATATTAGTGA
Found at i:1427472 original size:60 final size:58
Alignment explanation
Indices: 1427341--1427521 Score: 213
Period size: 64 Copynumber: 3.0 Consensus size: 58
1427331 ACCATCCATC
1427341 CATCCATCCATCCATCCATCCATGCATATTAGTGACCATCCATTCATGCATATTAGTG
1 CATCCATCCATCCATCCATCCATGCATATTAGTGACCATCCATTCATGCATATTAGTG
1427399 ACCATCCATCCATCCATCCATCCATCCATGCATATTAGTGACCATCCATCCATCGATGCATATTA
1 ------CATCCATCCATCCATCCATCCATGCATATTAGTGACCATCCAT---TC-ATGCATATTA
1427464 GTG
56 GTG
* * * **
1427467 -A-CCATCCTTCTATCCATCCATGCATATTAGTGACCATTCAACCATGCATATTAGT
1 CATCCATCCATCCATCCATCCATGCATATTAGTGACCATCCATTCATGCATATTAGT
1427522 TTCGTACACA
Statistics
Matches: 108, Mismatches: 5, Indels: 16
0.84 0.04 0.12
Matches are distributed among these distances:
56 12 0.11
57 1 0.01
60 36 0.33
61 1 0.01
64 43 0.40
67 2 0.02
68 13 0.12
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.30
Consensus pattern (58 bp):
CATCCATCCATCCATCCATCCATGCATATTAGTGACCATCCATTCATGCATATTAGTG
Found at i:1432153 original size:40 final size:40
Alignment explanation
Indices: 1432109--1432190 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
1432099 AAAGTAAAAT
1432109 TATTTAGTTTTATATTAATGGAAAATATGAAAATAATTAA
1 TATTTAGTTTTATATTAATGGAAAATATGAAAATAATTAA
1432149 TATTTAGTTTTATATTAATGGAAAATATGAAAATAATTAA
1 TATTTAGTTTTATATTAATGGAAAATATGAAAATAATTAA
1432189 TA
1 TA
1432191 GAACTTAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.43
Consensus pattern (40 bp):
TATTTAGTTTTATATTAATGGAAAATATGAAAATAATTAA
Found at i:1437138 original size:24 final size:24
Alignment explanation
Indices: 1437103--1437160 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
1437093 GGCGCGACCC
1437103 ATTTTTTT--AATAATATAATTTT
1 ATTTTTTTAAAATAATATAATTTT
* *
1437125 ATTTTTTTAAAATATTATTATTTT
1 ATTTTTTTAAAATAATATAATTTT
1437149 ATTATATTTTAA
1 ATT-T-TTTTAA
1437161 TAATTTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 8 0.27
24 15 0.50
25 1 0.03
26 6 0.20
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
ATTTTTTTAAAATAATATAATTTT
Found at i:1437162 original size:24 final size:22
Alignment explanation
Indices: 1437103--1437164 Score: 72
Period size: 22 Copynumber: 2.6 Consensus size: 22
1437093 GGCGCGACCC
1437103 ATTTTTTTAATAATATAATTTT
1 ATTTTTTTAATAATATAATTTT
1437125 ATTTTTTTAA-AATATTATTATTTT
1 ATTTTTTTAATAATA-TA--ATTTT
1437149 ATTATATTTTAATAAT
1 ATT-T-TTTTAATAAT
1437165 TTTTAAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
21 4 0.12
22 12 0.35
24 8 0.24
25 1 0.03
26 6 0.18
27 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
ATTTTTTTAATAATATAATTTT
Found at i:1437402 original size:3 final size:3
Alignment explanation
Indices: 1437387--1437455 Score: 77
Period size: 3 Copynumber: 22.7 Consensus size: 3
1437377 TGCAGCAGCA
*
1437387 AAG AGAG AA- AAG AAG AAG AAG AAG AAG AAA AAG AAG AAG AAG AAG
1 AAG A-AG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
* * *
1437432 AAG GAG AAG GAG GAG AAAG AAG AA
1 AAG AAG AAG AAG AAG -AAG AAG AA
1437456 AAAATGTTAG
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.04
3 50 0.88
4 5 0.09
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1440157 original size:12 final size:12
Alignment explanation
Indices: 1440137--1440185 Score: 62
Period size: 12 Copynumber: 4.1 Consensus size: 12
1440127 TGCACCAACT
1440137 CCGGAGCCAGAG
1 CCGGAGCCAGAG
*
1440149 CCAGAGCCAGAG
1 CCGGAGCCAGAG
* *
1440161 CCGGAGGCAGTG
1 CCGGAGCCAGAG
*
1440173 CCGGACCCAGAG
1 CCGGAGCCAGAG
1440185 C
1 C
1440186 GGCGGCTAGA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.24, C:0.35, G:0.39, T:0.02
Consensus pattern (12 bp):
CCGGAGCCAGAG
Found at i:1443801 original size:17 final size:17
Alignment explanation
Indices: 1443765--1443805 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1443755 CTCCTCCTTG
* * *
1443765 TTTTCTTCTCCTTTTTT
1 TTTTCTTCTCCCTATCT
1443782 TTTTCTTCTCCCTATCT
1 TTTTCTTCTCCCTATCT
1443799 TTTTCTT
1 TTTTCTT
1443806 TCCGTTCAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTCTTCTCCCTATCT
Found at i:1444408 original size:23 final size:22
Alignment explanation
Indices: 1444367--1444425 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 22
1444357 ATTTAAAAAT
1444367 TATTAAAATATAATAAAATAATAA
1 TATTAAAA-A-AATAAAATAATAA
* *
1444391 TATTTAAAAAAATAAAATTATAT
1 TA-TTAAAAAAATAAAATAATAA
1444414 TATTAAAAAAAT
1 TATTAAAAAAAT
1444426 GGGCCGCGCC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 10 0.31
23 13 0.41
24 3 0.09
25 6 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
TATTAAAAAAATAAAATAATAA
Found at i:1447440 original size:17 final size:16
Alignment explanation
Indices: 1447417--1447458 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
1447407 ACGATAAAAA
1447417 TATAATTTTAT-TATT
1 TATAATTTTATATATT
1447432 TA-AATAATTTATATATT
1 TATAAT--TTTATATATT
1447449 TATAATTTTA
1 TATAATTTTA
1447459 AAAGGTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
14 3 0.13
15 2 0.09
16 9 0.39
17 6 0.26
18 3 0.13
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TATAATTTTATATATT
Found at i:1452412 original size:2 final size:2
Alignment explanation
Indices: 1452400--1452433 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
1452390 ATAGGTCTAA
1452400 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1452434 ATTGATAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1454951 original size:42 final size:42
Alignment explanation
Indices: 1454897--1455052 Score: 169
Period size: 42 Copynumber: 3.7 Consensus size: 42
1454887 AAATCAGACA
*
1454897 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACATGAAATCAATATCG
*
1454939 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGAAATCAAATAT-G
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACATGAAATC-AATATCG
* * *
1454981 ATGCCGATGTCCCAGACATGGTCTTATACAT-AAATCTCAA-ATCG
1 ATGCCAACGTCCCAGACGTGGTC-T-TACATGAAA--TCAATATCG
1455025 ATGCCAACGTCCCAGACGTGGTCTTACA
1 ATGCCAACGTCCCAGACGTGGTCTTACA
1455053 CGATAACATA
Statistics
Matches: 96, Mismatches: 8, Indels: 20
0.77 0.06 0.16
Matches are distributed among these distances:
41 2 0.02
42 51 0.53
43 14 0.15
44 27 0.28
45 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACGTGGTCTTACATGAAATCAATATCG
Found at i:1462278 original size:42 final size:42
Alignment explanation
Indices: 1462213--1462368 Score: 169
Period size: 42 Copynumber: 3.7 Consensus size: 42
1462203 AAATCGTACA
*
1462213 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACATGAAATCAATATCG
*
1462255 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGAAATCAAATAT-G
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACATGAAATC-AATATCG
* * *
1462297 ATGCCGATGTCCCAGACATGGTCTTATACAT-AAATCTCAA-ATCG
1 ATGCCAACGTCCCAGACGTGGTC-T-TACATGAAA--TCAATATCG
1462341 ATGCCAACGTCCCAGACGTGGTCTTACA
1 ATGCCAACGTCCCAGACGTGGTCTTACA
1462369 CGATAACATA
Statistics
Matches: 96, Mismatches: 8, Indels: 20
0.77 0.06 0.16
Matches are distributed among these distances:
41 2 0.02
42 51 0.53
43 14 0.15
44 27 0.28
45 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACGTGGTCTTACATGAAATCAATATCG
Found at i:1468199 original size:27 final size:27
Alignment explanation
Indices: 1468166--1468233 Score: 120
Period size: 26 Copynumber: 2.6 Consensus size: 27
1468156 ATAATGGCCC
1468166 GTTAGGTAAATGTTTCCATGACAATGG
1 GTTAGGTAAATGTTTCCATGACAATGG
*
1468193 GTTAGGTAAATG-TTCCATGATAATGG
1 GTTAGGTAAATGTTTCCATGACAATGG
1468219 GTTAGGTAAATGTTT
1 GTTAGGTAAATGTTT
1468234 ATGAATAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
26 25 0.64
27 14 0.36
ACGTcount: A:0.29, C:0.07, G:0.26, T:0.37
Consensus pattern (27 bp):
GTTAGGTAAATGTTTCCATGACAATGG
Found at i:1471136 original size:21 final size:21
Alignment explanation
Indices: 1471110--1471150 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1471100 ATCTGCTCAA
* *
1471110 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
1471131 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
1471151 TCGCTCGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:1474714 original size:129 final size:128
Alignment explanation
Indices: 1474464--1474792 Score: 480
Period size: 129 Copynumber: 2.6 Consensus size: 128
1474454 AAAAAGCCAA
* * * * * * *
1474464 AACCCAGCACGGTAGGGCACAATTTCTCGAATTTCCAAACATTGAACATTGCCTCGCTTT-AGCA
1 AACCCAGCACGATAGGGCACGATTCCCCGAATTTCCAAACATCGAACATTGCCTCGTTTTAAGAA
**
1474528 TTTAGAAAACATGAGTGAAATTCTAAAGGAATATTCGATTATTTCGAACAAACGGGAAATTGC
66 TTTTCAAAACATGAGTGAAATTCTAAAGGAATATTCGATTATTTCGAACAAACGGGAAATTGC
*
1474591 AACCCAGCATGATAGGGCACGATTCCCCGAATTTCCAAACATCGAACATTGCCTCGTTTTAAGGA
1 AACCCAGCACGATAGGGCACGATTCCCCGAATTTCCAAACATCGAACATTGCCTCGTTTTAA-GA
* * * *
1474656 ATTTTCAAAGCATGAGTGAAATTCTAAAGGAATATTTGATTATTTTGAACAAATGGGAAATTGC
65 ATTTTCAAAACATGAGTGAAATTCTAAAGGAATATTCGATTATTTCGAACAAACGGGAAATTGC
* *
1474720 AACCCAGCACGATAGGGCACGATTCCCCGAATTTCCAAACATCAAACATTGCCTTCATTTTAAAG
1 AACCCAGCACGATAGGGCACGATTCCCCGAATTTCCAAACATCGAACATTGCC-TCGTTTT-AAG
1474785 AATTTTCA
64 AATTTTCA
1474793 GACGAATAAT
Statistics
Matches: 181, Mismatches: 17, Indels: 5
0.89 0.08 0.02
Matches are distributed among these distances:
127 53 0.29
128 1 0.01
129 110 0.61
130 15 0.08
131 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (128 bp):
AACCCAGCACGATAGGGCACGATTCCCCGAATTTCCAAACATCGAACATTGCCTCGTTTTAAGAA
TTTTCAAAACATGAGTGAAATTCTAAAGGAATATTCGATTATTTCGAACAAACGGGAAATTGC
Found at i:1476714 original size:26 final size:26
Alignment explanation
Indices: 1476677--1476734 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
1476667 TGATACAAAT
1476677 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
1476703 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
1476729 TGATAA
1 TGATAA
1476735 GAATTTCATG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:1482749 original size:15 final size:15
Alignment explanation
Indices: 1482729--1482757 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1482719 AATCTCAGTC
1482729 TAAGTGAGAGAGAGG
1 TAAGTGAGAGAGAGG
1482744 TAAGTGAGAGAGAG
1 TAAGTGAGAGAGAG
1482758 ATGGGTGACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.45, T:0.14
Consensus pattern (15 bp):
TAAGTGAGAGAGAGG
Found at i:1485098 original size:8 final size:8
Alignment explanation
Indices: 1485064--1485123 Score: 68
Period size: 8 Copynumber: 7.5 Consensus size: 8
1485054 TAATGATGTG
*
1485064 AATAATAA
1 AATATTAA
1485072 AATATATAA
1 AATAT-TAA
1485081 AATA-TAA
1 AATATTAA
1485088 AATATTAA
1 AATATTAA
*
1485096 AATATCAA
1 AATATTAA
*
1485104 AATATCAA
1 AATATTAA
*
1485112 AATATTAG
1 AATATTAA
1485120 AATA
1 AATA
1485124 ATAATAATTA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
7 7 0.15
8 32 0.70
9 7 0.15
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (8 bp):
AATATTAA
Found at i:1485389 original size:23 final size:23
Alignment explanation
Indices: 1485363--1485488 Score: 59
Period size: 23 Copynumber: 5.5 Consensus size: 23
1485353 AAAAAAATAT
1485363 ATATAAATAATATAATATTAAAG
1 ATATAAATAATATAATATTAAAG
* * *
1485386 ATATATACATAAAATAGTA-TAATAT
1 ATATA-A-ATAATATAATATTAA-AG
**
1485411 ATATACGTAATATAGA-ATTTAAA-
1 ATATAAATAATATA-ATA-TTAAAG
** *
1485434 ATATACCT-A-AT-ATATTAAAA
1 ATATAAATAATATAATATTAAAG
*
1485454 ATATATATAATATAATATT-AAG
1 ATATAAATAATATAATATTAAAG
*
1485476 AAATATAATAATA
1 ATATA-AATAATA
1485489 ACAAAAAAGG
Statistics
Matches: 78, Mismatches: 13, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
19 6 0.08
20 7 0.09
21 3 0.04
22 9 0.12
23 30 0.38
24 5 0.06
25 18 0.23
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.36
Consensus pattern (23 bp):
ATATAAATAATATAATATTAAAG
Found at i:1485397 original size:25 final size:25
Alignment explanation
Indices: 1485271--1485488 Score: 88
Period size: 25 Copynumber: 9.0 Consensus size: 25
1485261 TAAATACGTG
* * *
1485271 ATAATACTAAAAATATGTACATAAT
1 ATAATATTAAAGATATATACATAAT
* * * *
1485296 ATAGTGTTAAAAATACATACATAAT
1 ATAATATTAAAGATATATACATAAT
* *
1485321 AT-A-GTT-AAGATATATACATAAG
1 ATAATATTAAAGATATATACATAAT
* * *
1485343 ATAACATGTAAAAAAAATATATATAAATAAT
1 ATAATAT-T-----AAAGATATATACATAAT
*
1485374 ATAATATTAAAGATATATACATAAA
1 ATAATATTAAAGATATATACATAAT
* * *
1485399 ATAGTA-T-AATATATATACGTAAT
1 ATAATATTAAAGATATATACATAAT
* *
1485422 ATAGA-ATTTAA-A-ATATACCT-A-
1 ATA-ATATTAAAGATATATACATAAT
*
1485443 AT-ATATTAAA-A-ATATATATAAT
1 ATAATATTAAAGATATATACATAAT
*
1485465 ATAATATT-AAGAAATATA-ATAAT
1 ATAATATTAAAGATATATACATAAT
1485488 A
1 A
1485489 ACAAAAAAGG
Statistics
Matches: 149, Mismatches: 26, Indels: 38
0.70 0.12 0.18
Matches are distributed among these distances:
19 1 0.01
20 12 0.08
21 3 0.02
22 20 0.13
23 40 0.27
24 9 0.06
25 44 0.30
30 1 0.01
31 19 0.13
ACGTcount: A:0.56, C:0.05, G:0.06, T:0.33
Consensus pattern (25 bp):
ATAATATTAAAGATATATACATAAT
Found at i:1485795 original size:17 final size:16
Alignment explanation
Indices: 1485759--1485791 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1485749 TTTGATTAAT
1485759 CTTCTCCAAAAACTAG
1 CTTCTCCAAAAACTAG
1485775 CTTCTCCAAAAACTAG
1 CTTCTCCAAAAACTAG
1485791 C
1 C
1485792 CTTCACAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.33, G:0.06, T:0.24
Consensus pattern (16 bp):
CTTCTCCAAAAACTAG
Found at i:1486013 original size:30 final size:30
Alignment explanation
Indices: 1485976--1486090 Score: 178
Period size: 30 Copynumber: 3.8 Consensus size: 30
1485966 TGGGTACAAG
* *
1485976 TGGTGGTGGAGCAA-GTGTGGTTAGTGGAGT
1 TGGTGGTGGA-AAAGGTGTGGCTAGTGGAGT
* *
1486006 AGGTGGTGGAAAAGGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1486036 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1486066 TGGTGGTGGAAAAGGTGTGGCTAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGT
1486091 TGAGAAAAGT
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
29 2 0.03
30 76 0.97
ACGTcount: A:0.21, C:0.03, G:0.50, T:0.26
Consensus pattern (30 bp):
TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
Found at i:1486855 original size:14 final size:14
Alignment explanation
Indices: 1486836--1486885 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
1486826 GAGTTGATTT
* *
1486836 TTGAAAAATATAAA
1 TTGAAAAACAGAAA
1486850 TTGAAAAAACAGAAA
1 TTG-AAAAACAGAAA
*
1486865 TTGAAAAGCAGAAA
1 TTGAAAAACAGAAA
1486879 TT-AAAAA
1 TTGAAAAA
1486886 GACCTCAGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
13 4 0.13
14 15 0.48
15 12 0.39
ACGTcount: A:0.64, C:0.04, G:0.12, T:0.20
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:1487065 original size:74 final size:74
Alignment explanation
Indices: 1486865--1487184 Score: 398
Period size: 74 Copynumber: 4.3 Consensus size: 74
1486855 AAAACAGAAA
*
1486865 TTGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAATTAAAAAGACCTCAGCA-GTGAGCCGAGGCTCAACTCACCTCTCGCAATAT
*
1486930 GAGTTAATTT
65 GAGTTGATTT
* ** * *
1486940 TTGACAAAA-AGAAATTGAAATTACCTCAGC-GTG-TCACGAGGCTCAACTCACCTTTCGCAATA
1 TTGA-AAAACAGAAATTAAAAAGACCTCAGCAGTGAGC-CGAGGCTCAACTCACCTCTCGCAATA
1487002 TGAGTTGATTT
64 TGAGTTGATTT
* *
1487013 TTGAAAAACAGAAATTTAAAAATACCTCAGC-GTG-TCCTGAGGCTCAACTCACCTCTCGCAATA
1 TTGAAAAACAGAAA-TTAAAAAGACCTCAGCAGTGAGCC-GAGGCTCAACTCACCTCTCGCAATA
1487076 TGAGTTGATTTTTT
64 TGAGTTGA---TTT
* ** *
1487090 TTTACGAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAATTAAAAAGACCTCAGCA-GTGAGCCGAGGCTCAACTCACCTCTCGCAATAT
1487155 GAGTTGATTT
65 GAGTTGATTT
*
1487165 TTGACAAACAGAAATTAAAA
1 TTGAAAAACAGAAATTAAAA
1487185 GGCTTAACTC
Statistics
Matches: 215, Mismatches: 19, Indels: 22
0.84 0.07 0.09
Matches are distributed among these distances:
72 5 0.02
73 48 0.22
74 51 0.24
75 42 0.20
76 17 0.08
77 14 0.07
78 36 0.17
79 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (74 bp):
TTGAAAAACAGAAATTAAAAAGACCTCAGCAGTGAGCCGAGGCTCAACTCACCTCTCGCAATATG
AGTTGATTT
Found at i:1487165 original size:152 final size:147
Alignment explanation
Indices: 1486865--1487184 Score: 437
Period size: 152 Copynumber: 2.1 Consensus size: 147
1486855 AAAACAGAAA
*
1486865 TTGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAATTAAAAAGACCTCAGCA-GTGAGCCGAGGCTCAACTCACCTCTCGCAATAT
** * *
1486930 GAGTTAATTTTTGACAAAAAGAAATTGAAATTACCTCAGCGTGTCACGAGGCTCAACTCACCTTT
65 GAGTTAATTTTTGACAAAAAGAAATTGAAAAGACCTCAGCATGTCACGAGGCTCAACTCACCTCT
1486995 CGCAATATGAGTTGATTT
130 CGCAATATGAGTTGATTT
* *
1487013 TTGAAAAACAGAAATTTAAAAATACCTCAGC-GTG-TCCTGAGGCTCAACTCACCTCTCGCAATA
1 TTGAAAAACAGAAA-TTAAAAAGACCTCAGCAGTGAGCC-GAGGCTCAACTCACCTCTCGCAATA
* * * * *
1487076 TGAGTTGATTTTTTTTTACGAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTC
64 TGAGTT-A--ATTTTTGACAAAAAGAAATTGAAAAGACCTCAGCATGTCA--CGAGGCTCAACTC
1487141 ACCTCTCGCAATATGAGTTGATTT
124 ACCTCTCGCAATATGAGTTGATTT
*
1487165 TTGACAAACAGAAATTAAAA
1 TTGAAAAACAGAAATTAAAA
1487185 GGCTTAACTC
Statistics
Matches: 152, Mismatches: 13, Indels: 11
0.86 0.07 0.06
Matches are distributed among these distances:
146 2 0.01
147 34 0.22
148 14 0.09
149 15 0.10
150 32 0.21
151 6 0.04
152 49 0.32
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (147 bp):
TTGAAAAACAGAAATTAAAAAGACCTCAGCAGTGAGCCGAGGCTCAACTCACCTCTCGCAATATG
AGTTAATTTTTGACAAAAAGAAATTGAAAAGACCTCAGCATGTCACGAGGCTCAACTCACCTCTC
GCAATATGAGTTGATTT
Found at i:1487212 original size:54 final size:55
Alignment explanation
Indices: 1487130--1487237 Score: 164
Period size: 54 Copynumber: 2.0 Consensus size: 55
1487120 ATGTGAGCCG
* * *
1487130 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACA-AACAGAAATTAAA
1 AGGCTCAACTCACCTCTCGCAACATGAGTTGATTTTTGAAACAACAAAAATTAAA
* *
1487184 AGGCTTAACTCACTTCTCGCAACATGAGTTGATTTTTGAAACAACAAAAATTAA
1 AGGCTCAACTCACCTCTCGCAACATGAGTTGATTTTTGAAACAACAAAAATTAA
1487238 GAATACCTCA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
54 37 0.77
55 11 0.23
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (55 bp):
AGGCTCAACTCACCTCTCGCAACATGAGTTGATTTTTGAAACAACAAAAATTAAA
Found at i:1487291 original size:128 final size:128
Alignment explanation
Indices: 1487052--1487441 Score: 484
Period size: 128 Copynumber: 3.0 Consensus size: 128
1487042 GCGTGTCCTG
* *** *
1487052 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTACGAACAGAAATTGAAAAGACCTC
1 AGGCTTAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAC-AACAGAAATTGAAAATACCTC
*
1487117 AGCATGTGAGCC-GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATT
64 AGC--GTGA-CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT
1487181 AAA
126 AAA
* * *
1487184 AGGCTTAACTCACTTCTCGCAACATGAGTTGATTTTTGAAACAACAAAAATT-AAGAATACCTCA
1 AGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTGAAACAACAGAAATTGAA-AATACCTCA
* * *
1487248 GCGTGACCTGAGGCTCAACTCACCTCTCGCAATATAAGCTGA-TTTTGAAAAAGTAGAAATTAAA
65 GCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA-CAGAAATTAAA
* * * *
1487312 AGG-TTCAACCCACCTCTCGCAATATGAGTTGATTCTTGACA-AACAGAAATTGAAATTACCTCA
1 AGGCTT-AACTCACCTCTCGCAATATGAGTTGATTTTTGAAACAACAGAAATTGAAAATACCTCA
* * *
1487375 TCGTGTCCTGAGGCTCAACTCATCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTTAA
65 GCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAA-TTAA
1487440 A
128 A
1487441 A
1 A
1487442 ATACCTCAGC
Statistics
Matches: 225, Mismatches: 25, Indels: 19
0.84 0.09 0.07
Matches are distributed among these distances:
127 67 0.30
128 85 0.38
129 18 0.08
130 19 0.08
131 7 0.03
132 29 0.13
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (128 bp):
AGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTGAAACAACAGAAATTGAAAATACCTCAG
CGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAA
Found at i:1487466 original size:75 final size:75
Alignment explanation
Indices: 1487316--1487734 Score: 404
Period size: 73 Copynumber: 5.5 Consensus size: 75
1487306 ATTAAAAGGT
* * * * *
1487316 TCAACCCACCTCTCGCAATATGAGTTGA-TTCTTGACAAACAGAAA-TTGAAATTACCTCATCGT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGACAAACAGAAATTTAAAAATACCTCAGCGT
1487379 GTCCTGAGGC
66 GTCCTGAGGC
* *
1487389 TCAACTCATCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGACAAACAGAAATTTAAAAATACCTCAGCGT
1487454 GTCCTGAGGC
66 GTCCTGAGGC
* * * * **
1487464 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTACGAACAGAAATTGAAGAACAGAAATTGA
1 TCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGACAAACAGAAATTTAA-AA-A-TACCT--
* * * *
1487529 AAAGACCTCAG-CATGTGAGC
60 -CAG-CGT--GTCCTGAG-GC
* * * * *
1487549 -CGAGGCTCAACTCACCTATCGCAATATGAGTT-AATTTTTGACAAACAGAAA-TTGAAATTACC
1 TC-A-ACT-----CACCTCTCGCAATATGAGTTGATTTTTTGACAAACAGAAATTTAAAAATACC
*
1487611 TCAGCGTGTCCCGAGGC
59 TCAGCGTGTCCTGAGGC
*
1487628 TCAACTCACCTTTCGCAATATGAGTTGA-TTTTTGA-AAACAGAAATTTAAAAATACCTCAGCGT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGACAAACAGAAATTTAAAAATACCTCAGCGT
1487691 GTCCTGAGGC
66 GTCCTGAGGC
1487701 TCAACTCACCTCTCGCAATATGAGTTGATTTTTT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTT
1487735 TTACGATCAG
Statistics
Matches: 280, Mismatches: 41, Indels: 49
0.76 0.11 0.13
Matches are distributed among these distances:
72 9 0.03
73 104 0.37
74 21 0.08
75 52 0.19
76 19 0.07
77 2 0.01
78 3 0.01
79 6 0.02
80 4 0.01
81 2 0.01
82 4 0.01
83 2 0.01
84 5 0.02
85 6 0.02
86 2 0.01
87 2 0.01
88 2 0.01
89 15 0.05
90 1 0.00
91 19 0.07
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (75 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTTTGACAAACAGAAATTTAAAAATACCTCAGCGT
GTCCTGAGGC
Found at i:1487521 original size:14 final size:14
Alignment explanation
Indices: 1487502--1487529 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1487492 TTTTTTTTAC
1487502 GAACAGAAATTGAA
1 GAACAGAAATTGAA
1487516 GAACAGAAATTGAA
1 GAACAGAAATTGAA
1487530 AAGACCTCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.21, T:0.14
Consensus pattern (14 bp):
GAACAGAAATTGAA
Found at i:1487575 original size:91 final size:88
Alignment explanation
Indices: 1487421--1487605 Score: 239
Period size: 89 Copynumber: 2.1 Consensus size: 88
1487411 AGTTGATTTT
* * *
1487421 TTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAATTTAAAAAGACCTCAGCGTGGCCTGAGGCTCAACTCACCTATCGCAATATG
* * *
1487486 AGTTGATTTTTTTTACGAACAGAAA
66 AGTT-A-ATTTTTGACAAACAGAAA
* *
1487511 TTGAAGAACAGAAA-TTGAAAAGACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTATCGCAAT
1 TTGAAAAACAGAAATTTAAAAAGACCTCAGC--GTG-GCCTGAGGCTCAACTCACCTATCGCAAT
1487574 ATGAGTTAATTTTTGACAAACAGAAA
63 ATGAGTTAATTTTTGACAAACAGAAA
1487600 TTGAAA
1 TTGAAA
1487606 TTACCTCAGC
Statistics
Matches: 83, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
89 34 0.41
90 14 0.17
91 33 0.40
92 2 0.02
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (88 bp):
TTGAAAAACAGAAATTTAAAAAGACCTCAGCGTGGCCTGAGGCTCAACTCACCTATCGCAATATG
AGTTAATTTTTGACAAACAGAAA
Found at i:1487629 original size:164 final size:154
Alignment explanation
Indices: 1487352--1487969 Score: 574
Period size: 164 Copynumber: 3.9 Consensus size: 154
1487342 GATTCTTGAC
* *
1487352 AAACAGAAATTGAAATTACCTCATCGTGTCCTGAGGCTCAACTCATCTCTCGCAATATGAGTTGA
1 AAACAGAAATTGAAA--ACCTCAGCGTGTCC-GAGGCTCAACTCACCTCTCGCAATATGAGTTGA
* * * *
1487417 TTTTTTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAA
63 ATTTTTGACAAACAGAAA-TTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAA
1487482 TATGAGTTGATTTTTTTTACGAACAGAAATT
127 TATGAGTTGA--TTTTTTA-GAACAGAAATT
* *
1487513 GAAGAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTATCGCAATATGA
1 --A-AACAGAAATTG-AAA-ACCTCAGC--GTG-TCCGAGGCTCAACTCACCTCTCGCAATATGA
* *
1487578 GTT-AATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTTTC
58 GTTGAATTTTTGACAAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTC
* *
1487642 GCAATATGAGTTGATTTTTGAAAACAGAAATT
123 GCAATATGAGTTGATTTTTTAGAACAGAAATT
*
1487674 -TA-A-AAA-T----ACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
1 AAACAGAAATTGAAAACCTCAGCGTGTCC-GAGGCTCAACTCACCTCTCGCAATATGAGTTGA--
* * **
1487731 TTTTTTACGATCAGAAATTGAAGAACAGAAATTGAAAAGACCTCAGCAAGTGAGCCGAGGCTCAA
63 ATTTTT--GA-C---------A-AACAGAAATTGAAAATACCTCAGC--GTGTCCCGAGGCTCAA
1487796 CTCACCTCTCGCAATATGAGTTGA-TTTTT-G-AC-------
113 CTCACCTCTCGCAATATGAGTTGATTTTTTAGAACAGAAATT
* *
1487828 AAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCACCTTTCGCAATATGAGTTG-
1 AAACAGAAATTGAAA--ACCTCAGCGTGTC-CGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
* * *
1487892 ATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAAT
63 ATTTTTGACAAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAAT
1487957 ATGAGTTGATTTT
128 ATGAGTTGATTTT
1487970 GAAAAAAAAA
Statistics
Matches: 385, Mismatches: 34, Indels: 88
0.76 0.07 0.17
Matches are distributed among these distances:
145 2 0.01
146 69 0.18
147 4 0.01
148 30 0.08
149 6 0.02
151 2 0.01
152 1 0.00
154 1 0.00
155 4 0.01
156 2 0.01
157 4 0.01
158 2 0.01
159 2 0.01
161 18 0.05
162 28 0.07
163 5 0.01
164 151 0.39
165 20 0.05
166 32 0.08
167 2 0.01
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (154 bp):
AAACAGAAATTGAAAACCTCAGCGTGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATT
TTTGACAAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATG
AGTTGATTTTTTAGAACAGAAATT
Found at i:1487748 original size:237 final size:237
Alignment explanation
Indices: 1487316--1487969 Score: 1148
Period size: 237 Copynumber: 2.8 Consensus size: 237
1487306 ATTAAAAGGT
* * *
1487316 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGACAAACAGAAATTGAAATTACCTCATCGTGT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGT
* *
1487381 CCTGAGGCTCAACTCATCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAATTTAAAAATAC
66 CCTGAGGCTCAACTCACCTTTCGCAATATGAGTTGA-TTTTTG-AAAACAGAAATTTAAAAATAC
1487446 CTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTACGAACAGAAA
129 CTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTACGAACAGAAA
*
1487511 TTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGC
194 TTGAAGAACAGAAATTGAAAAGACCTCAGCAAGTGAGCCGAGGC
* *
1487555 TCAACTCACCTATCGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGT
*
1487620 CCCGAGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTGAAAACAGAAATTTAAAAATACCT
66 CCTGAGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTGAAAACAGAAATTTAAAAATACCT
*
1487685 CAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTACGATCAGAAATT
131 CAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTACGAACAGAAATT
1487750 GAAGAACAGAAATTGAAAAGACCTCAGCAAGTGAGCCGAGGC
196 GAAGAACAGAAATTGAAAAGACCTCAGCAAGTGAGCCGAGGC
1487792 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGT
1 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGT
* * *
1487857 CTTGAGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTGACAAACAGAAA-TTGAAATTACC
66 CCTGAGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTGA-AAACAGAAATTTAAAAATACC
*
1487921 TCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTT
130 TCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1487970 GAAAAAAAAA
Statistics
Matches: 397, Mismatches: 17, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
237 289 0.73
238 15 0.04
239 93 0.23
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (237 bp):
TCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGT
CCTGAGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTGAAAACAGAAATTTAAAAATACCT
CAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTACGAACAGAAATT
GAAGAACAGAAATTGAAAAGACCTCAGCAAGTGAGCCGAGGC
Found at i:1487812 original size:91 final size:89
Alignment explanation
Indices: 1487659--1487824 Score: 255
Period size: 91 Copynumber: 1.8 Consensus size: 89
1487649 GAGTTGATTT
* *
1487659 TTGAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAACAGAAATTTAAAAAGACCTCAGCGTGGCCTGAGGCTCAACTCACCTCTCGCAATATGA
1487724 GTTGATTTTTTTTACGATCAGAAA
66 GTTGATTTTTTTTACGATCAGAAA
*
1487748 TTGAAGAACAGAAA-TTGAAAAGACCTCAGCAAGTGAGCC-GAGGCTCAACTCACCTCTCGCAAT
1 TTGAA-AACAGAAATTTAAAAAGACCTCAGC--GTG-GCCTGAGGCTCAACTCACCTCTCGCAAT
1487811 ATGAGTTGATTTTT
62 ATGAGTTGATTTTT
1487825 GACAAACAGA
Statistics
Matches: 70, Mismatches: 3, Indels: 6
0.89 0.04 0.08
Matches are distributed among these distances:
89 19 0.27
90 8 0.11
91 41 0.59
92 2 0.03
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (89 bp):
TTGAAAACAGAAATTTAAAAAGACCTCAGCGTGGCCTGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTTTTTTTACGATCAGAAA
Found at i:1488025 original size:143 final size:147
Alignment explanation
Indices: 1487754--1488039 Score: 420
Period size: 143 Copynumber: 2.0 Consensus size: 147
1487744 GAAATTGAAG
*
1487754 AACAGAAATTGAAAAGACCTCAGCAAGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
1 AACAGAAATTGAAAAGACCTCAGC-AGTGAGCCGAGGCTCAACTCACCTCTAGCAATATGAGTTG
* * * * *
1487819 ATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCACCTTTCGCAAT
65 ATTTTTGACAAACAAAAATTAAAAGTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAAT
1487884 ATGAGTTGATTTTTGACA
130 ATGAGTTGATTTTTGACA
** *
1487902 AACAGAAATTGAAATTACCTCAGC-GTG-TCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTG
1 AACAGAAATTGAAAAGACCTCAGCAGTGAGCC-GAGGCTCAACTCACCTCTAGCAATATGAGTTG
* *
1487965 A-TTTTGA-AAA-AAAAATTAAAAGTATCTCAACGTGTCTTGAGGCTCAACTCATCTCTCGCAAT
65 ATTTTTGACAAACAAAAATTAAAAGTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAAT
1488027 ATGAGTTGATTTT
130 ATGAGTTGATTTT
1488040 CCTTGAAAAG
Statistics
Matches: 126, Mismatches: 11, Indels: 7
0.88 0.08 0.05
Matches are distributed among these distances:
143 58 0.46
144 3 0.02
145 8 0.06
146 35 0.28
148 22 0.17
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.29
Consensus pattern (147 bp):
AACAGAAATTGAAAAGACCTCAGCAGTGAGCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGA
TTTTTGACAAACAAAAATTAAAAGTACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATA
TGAGTTGATTTTTGACA
Found at i:1488026 original size:70 final size:73
Alignment explanation
Indices: 1487787--1488039 Score: 404
Period size: 73 Copynumber: 3.5 Consensus size: 73
1487777 CAAGTGAGCC
1487787 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAATTACCTCAG
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAATTACCTCAG
1487852 CGTGTCTT
66 CGTGTCTT
*
1487860 GAGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAATTACCTCAG
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAATTACCTCAG
*
1487925 CGTGTCCT
66 CGTGTCTT
* * * * * *
1487933 GAGGCTCAACTCACCTCTAGCAATATGAGTTGA-TTTTGA-AAA-AAAAATTAAAAGTATCTCAA
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAATTACCTCAG
1487995 CGTGTCTT
66 CGTGTCTT
*
1488003 GAGGCTCAACTCATCTCTCGCAATATGAGTTGATTTT
1 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1488040 CCTTGAAAAG
Statistics
Matches: 167, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
70 53 0.32
71 6 0.04
72 6 0.04
73 102 0.61
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (73 bp):
GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACAGAAATTGAAATTACCTCAG
CGTGTCTT
Found at i:1496356 original size:12 final size:12
Alignment explanation
Indices: 1496334--1496388 Score: 57
Period size: 12 Copynumber: 5.0 Consensus size: 12
1496324 TGGGATATGC
*
1496334 AATGAATGAATG
1 AATGCATGAATG
*
1496346 GATGCATGAATG
1 AATGCATGAATG
1496358 AATGCATGAATG
1 AATGCATGAATG
1496370 --T-CA--AATG
1 AATGCATGAATG
1496377 AATGCATGAATG
1 AATGCATGAATG
1496389 TCAAATGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
7 4 0.11
9 3 0.09
10 3 0.09
12 25 0.71
ACGTcount: A:0.42, C:0.07, G:0.25, T:0.25
Consensus pattern (12 bp):
AATGCATGAATG
Found at i:1496356 original size:16 final size:17
Alignment explanation
Indices: 1496330--1496361 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1496320 AGTATGGGAT
1496330 ATGCAATGAATGAATGG
1 ATGCAATGAATGAATGG
1496347 ATGC-ATGAATGAATG
1 ATGCAATGAATGAATG
1496362 CATGAATGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.41, C:0.06, G:0.28, T:0.25
Consensus pattern (17 bp):
ATGCAATGAATGAATGG
Found at i:1496378 original size:19 final size:19
Alignment explanation
Indices: 1496354--1496399 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
1496344 TGGATGCATG
1496354 AATGAATGCATGAATGTCA
1 AATGAATGCATGAATGTCA
1496373 AATGAATGCATGAATGTCA
1 AATGAATGCATGAATGTCA
1496392 AATGAATG
1 AATGAATG
1496400 TCAGTCATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.43, C:0.09, G:0.22, T:0.26
Consensus pattern (19 bp):
AATGAATGCATGAATGTCA
Found at i:1496379 original size:11 final size:11
Alignment explanation
Indices: 1496363--1496402 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
1496353 GAATGAATGC
1496363 ATGAATGTCAA
1 ATGAATGTCAA
1496374 ATGAATG-C--
1 ATGAATGTCAA
1496382 ATGAATGTCAA
1 ATGAATGTCAA
1496393 ATGAATGTCA
1 ATGAATGTCA
1496403 GTCATGAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
8 7 0.27
9 1 0.04
10 1 0.04
11 17 0.65
ACGTcount: A:0.42, C:0.10, G:0.20, T:0.28
Consensus pattern (11 bp):
ATGAATGTCAA
Found at i:1498203 original size:25 final size:25
Alignment explanation
Indices: 1498175--1498223 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
1498165 CGTGATAATA
**
1498175 TTAAAAATATGTACATAATATAGTG
1 TTAAAAATACATACATAATATAGTG
*
1498200 TTAAAATTACATACATAATATAGT
1 TTAAAAATACATACATAATATAGT
1498224 TAAGATATAT
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:0.49, C:0.06, G:0.08, T:0.37
Consensus pattern (25 bp):
TTAAAAATACATACATAATATAGTG
Found at i:1498238 original size:22 final size:23
Alignment explanation
Indices: 1498178--1498366 Score: 73
Period size: 23 Copynumber: 7.8 Consensus size: 23
1498168 GATAATATTA
*
1498178 AAAATATGTACATAATATAGTGTT
1 AAAATATATACATAATATAG-GTT
*
1498202 AAAATTACATACATAATATA-GTT
1 AAAA-TATATACATAATATAGGTT
* * * *
1498225 AAGATATATACATAAGATAACATGTAAA
1 AAAATATATACAT-A-AT-ATAGGT--T
* **
1498253 AAATATATATAAATAATATAATATT
1 AAA-ATATATACATAATAT-AGGTT
*
1498278 AAAGATATATACATAAAATA-GTAT
1 AAA-ATATATACATAATATAGGT-T
* * *
1498302 AATATATATACGTAATATAGAATT
1 AAAATATATACATAATATAG-GTT
* *
1498326 TAAA-ATATACCTAATATA--TT
1 AAAATATATACATAATATAGGTT
*
1498346 AAAAAATATATATATAATATA
1 --AAAATATATACATAATATA
1498367 ATATTAAGAA
Statistics
Matches: 125, Mismatches: 25, Indels: 31
0.69 0.14 0.17
Matches are distributed among these distances:
20 2 0.02
22 11 0.09
23 47 0.38
24 13 0.10
25 32 0.26
26 3 0.02
27 5 0.04
28 3 0.02
29 9 0.07
ACGTcount: A:0.55, C:0.05, G:0.06, T:0.34
Consensus pattern (23 bp):
AAAATATATACATAATATAGGTT
Found at i:1498285 original size:23 final size:23
Alignment explanation
Indices: 1498259--1498387 Score: 59
Period size: 23 Copynumber: 5.5 Consensus size: 23
1498249 TAAAAAATAT
1498259 ATATAAATAATATAATATTAAAG
1 ATATAAATAATATAATATTAAAG
* * *
1498282 ATATATACATAAAATAGTA-TAATAT
1 ATATA-A-ATAATATAATATTAA-AG
**
1498307 ATATACGTAATATAGA-ATTTAAA-
1 ATATAAATAATATA-ATA-TTAAAG
** * ** *
1498330 ATATACCTAATATATTAAAAAAT
1 ATATAAATAATATAATATTAAAG
*
1498353 ATATATATAATATAATATT-AAG
1 ATATAAATAATATAATATTAAAG
*
1498375 AAATATAATAATA
1 ATATA-AATAATA
1498388 ACAAAAAAGG
Statistics
Matches: 78, Mismatches: 19, Indels: 18
0.68 0.17 0.16
Matches are distributed among these distances:
22 9 0.12
23 46 0.59
24 5 0.06
25 18 0.23
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.36
Consensus pattern (23 bp):
ATATAAATAATATAATATTAAAG
Found at i:1498287 original size:29 final size:29
Alignment explanation
Indices: 1498228--1498306 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 29
1498218 TATAGTTAAG
* * *
1498228 ATATATACATAAGATAACATGTAAAAAAT
1 ATATATAAATAATATAATATGTAAAAAAT
*
1498257 ATATATAAATAATATAATAT-TAAAGATAT
1 ATATATAAATAATATAATATGTAAA-AAAT
* *
1498286 ATACATAAAATAGTATAATAT
1 ATATAT-AAATAATATAATAT
1498307 ATATACGTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
28 4 0.10
29 25 0.60
30 13 0.31
ACGTcount: A:0.58, C:0.04, G:0.05, T:0.33
Consensus pattern (29 bp):
ATATATAAATAATATAATATGTAAAAAAT
Found at i:1498387 original size:46 final size:47
Alignment explanation
Indices: 1498169--1498387 Score: 144
Period size: 46 Copynumber: 4.5 Consensus size: 47
1498159 TAAATACGTG
* * * *
1498169 ATAATATTAA-AAATATGTACATAATATAGTGTTAAAATTACATACATAAT
1 ATAATATTAAGAAATA--TACATAATATA--GTAAAAAATATATATATAAT
* * *
1498219 AT-A-GTTAAGATATATACATAAGATAACATGTAAAAAATATATATAAATAAT
1 ATAATATTAAGAAATATACAT-A-AT-ATA-GTAAAAAATATATAT--ATAAT
* * * * **
1498270 ATAATATTAAAGATATATACATAAAATAGTATAATATATATACGTAAT
1 ATAATATT-AAGAAATATACATAATATAGTAAAAAATATATATATAAT
* * *
1498318 ATAGA-ATTTA-AAATATACCTAATATATTAAAAAATATATATATAAT
1 ATA-ATATTAAGAAATATACATAATATAGTAAAAAATATATATATAAT
1498364 ATAATATTAAGAAATATA-ATAATA
1 ATAATATTAAGAAATATACATAATA
1498388 ACAAAAAAGG
Statistics
Matches: 132, Mismatches: 25, Indels: 28
0.71 0.14 0.15
Matches are distributed among these distances:
45 1 0.01
46 40 0.30
47 13 0.10
48 15 0.11
49 20 0.15
50 16 0.12
51 9 0.07
52 2 0.02
53 3 0.02
54 13 0.10
ACGTcount: A:0.56, C:0.04, G:0.05, T:0.35
Consensus pattern (47 bp):
ATAATATTAAGAAATATACATAATATAGTAAAAAATATATATATAAT
Found at i:1498694 original size:17 final size:16
Alignment explanation
Indices: 1498658--1498690 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1498648 TTTGATTAAT
1498658 CTTCTCCAAAAACTAG
1 CTTCTCCAAAAACTAG
1498674 CTTCTCCAAAAACTAG
1 CTTCTCCAAAAACTAG
1498690 C
1 C
1498691 CTTCACAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.33, G:0.06, T:0.24
Consensus pattern (16 bp):
CTTCTCCAAAAACTAG
Found at i:1498933 original size:30 final size:30
Alignment explanation
Indices: 1498899--1498959 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
1498889 GTGTGGTTAA
1498899 TGGAGTAGGTGGTGGAAAAGGAGTGGCTAG
1 TGGAGTAGGTGGTGGAAAAGGAGTGGCTAG
* *
1498929 TGGAGTTGGTGGTGGAAAAGGTGTGGCTAG
1 TGGAGTAGGTGGTGGAAAAGGAGTGGCTAG
1498959 T
1 T
1498960 TGAGAAAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.23, C:0.03, G:0.49, T:0.25
Consensus pattern (30 bp):
TGGAGTAGGTGGTGGAAAAGGAGTGGCTAG
Found at i:1500185 original size:24 final size:24
Alignment explanation
Indices: 1500134--1500185 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1500124 TTTAGTATTT
* *
1500134 ATTAGTATAATATATTTATCATTT
1 ATTAGCATAATATATTTATCATTA
1500158 ATTAGCATAATATATTTGA-CATTA
1 ATTAGCATAATATATTT-ATCATTA
1500182 ATTA
1 ATTA
1500186 TAATTAGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (24 bp):
ATTAGCATAATATATTTATCATTA
Found at i:1502091 original size:28 final size:28
Alignment explanation
Indices: 1502047--1502114 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
1502037 ATAAAAATTT
* *
1502047 CACTAAGTGTGCGAGTTTGGTTAACGAG
1 CACTAAGTGTGCAAGTTTGATTAACGAG
*
1502075 CACTAAGTGTGCAAGTTTGATTATCGAG
1 CACTAAGTGTGCAAGTTTGATTAACGAG
*
1502103 CACTAGGTGTGC
1 CACTAAGTGTGC
1502115 GAAGGAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.29
Consensus pattern (28 bp):
CACTAAGTGTGCAAGTTTGATTAACGAG
Found at i:1504275 original size:18 final size:19
Alignment explanation
Indices: 1504246--1504281 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
1504236 CAGTATCATT
1504246 TTGTGCGTGATATTATTGC
1 TTGTGCGTGATATTATTGC
1504265 TTGTG-GTGATATTATTG
1 TTGTGCGTGATATTATTG
1504282 TAAGCAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.17, C:0.06, G:0.28, T:0.50
Consensus pattern (19 bp):
TTGTGCGTGATATTATTGC
Found at i:1504472 original size:29 final size:29
Alignment explanation
Indices: 1504415--1504473 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
1504405 TCGTGGAAAA
* *
1504415 GGTGAAGAACTTGTTTGTTGAGAGCTCGT
1 GGTGAAGAACTTGTTCGTTGAGAACTCGT
*
1504444 GGTGAAGAACTTGTTCGTTGAGAATTCGT
1 GGTGAAGAACTTGTTCGTTGAGAACTCGT
1504473 G
1 G
1504474 TTAAGGTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.22, C:0.10, G:0.34, T:0.34
Consensus pattern (29 bp):
GGTGAAGAACTTGTTCGTTGAGAACTCGT
Found at i:1504615 original size:24 final size:24
Alignment explanation
Indices: 1504558--1504609 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
1504548 TTTCTAAAAG
* * *
1504558 ATTTAGTATTTATCAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
1504582 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
1504606 ATTT
1 ATTT
1504610 GACATTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.06, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:1504620 original size:24 final size:24
Alignment explanation
Indices: 1504575--1504621 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1504565 ATTTATCAGT
*
1504575 ATAATATATTTAGCATTTATTAGC
1 ATAATATATTTAGCATTGATTAGC
1504599 ATAATATATTT-GACATTGATTAG
1 ATAATATATTTAG-CATTGATTAG
1504622 AATTAGGCTT
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:0.38, C:0.06, G:0.11, T:0.45
Consensus pattern (24 bp):
ATAATATATTTAGCATTGATTAGC
Found at i:1505351 original size:110 final size:109
Alignment explanation
Indices: 1505167--1505369 Score: 370
Period size: 110 Copynumber: 1.9 Consensus size: 109
1505157 TTTTTAATAA
*
1505167 AAATGTTGAGCACCAAACGCACGATACGTATTAACAAGCTCAATGGTCTAAAGACTTAGACCGTA
1 AAATGTTGAGCACCAAACGCACGATACATATTAACAAGCTCAATGGTCTAAAGACTTAGACCGTA
1505232 AGCAAGACTCCAAAATGAAAAGTAATTGAAACGCATTTTCTAAT
66 AGCAAGACTCCAAAATGAAAAGTAATTGAAACGCATTTTCTAAT
1505276 AAATGTTGAGACACCAAACGCACGATACATATTAACAAGCTCAATGGTCTAAAGACTTAGACCGT
1 AAATGTTGAG-CACCAAACGCACGATACATATTAACAAGCTCAATGGTCTAAAGACTTAGACCGT
* *
1505341 AAGTATGACTCCAAAATGAAAAGTAATTG
65 AAGCAAGACTCCAAAATGAAAAGTAATTG
1505370 TGACCATTTC
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
109 10 0.11
110 80 0.89
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.23
Consensus pattern (109 bp):
AAATGTTGAGCACCAAACGCACGATACATATTAACAAGCTCAATGGTCTAAAGACTTAGACCGTA
AGCAAGACTCCAAAATGAAAAGTAATTGAAACGCATTTTCTAAT
Found at i:1507360 original size:20 final size:19
Alignment explanation
Indices: 1507324--1507361 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1507314 ATGTATAGAT
*
1507324 GCATTTTTTAGTTAATTTA
1 GCATTTTTTAGTAAATTTA
1507343 GCATTTTTTAGTCAAATTT
1 GCATTTTTTAGT-AAATTT
1507362 CACTGAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (19 bp):
GCATTTTTTAGTAAATTTA
Found at i:1521548 original size:4 final size:4
Alignment explanation
Indices: 1521539--1521567 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
1521529 ACAGTGACTC
1521539 AGTG AGTG AGTG AGTG AGTG AGTG AGTG A
1 AGTG AGTG AGTG AGTG AGTG AGTG AGTG A
1521568 CACAAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.48, T:0.24
Consensus pattern (4 bp):
AGTG
Found at i:1533441 original size:20 final size:18
Alignment explanation
Indices: 1533415--1533463 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 18
1533405 GTTATTATTA
1533415 ATTATTTTTAAATTATAT
1 ATTATTTTTAAATTATAT
1533433 ATTTTATTTTT--ATTATAT
1 A--TTATTTTTAAATTATAT
1533451 ATTATTTTTAAAT
1 ATTATTTTTAAAT
1533464 ACATACACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
16 8 0.30
18 11 0.41
20 8 0.30
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTATTTTTAAATTATAT
Found at i:1533447 original size:18 final size:19
Alignment explanation
Indices: 1533416--1533461 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 19
1533406 TTATTATTAA
1533416 TTATTTTTAAATTATATATT
1 TTATTTTT-AATTATATATT
1533436 TTATTTTT-ATTATATA--
1 TTATTTTTAATTATATATT
1533452 TTATTTTTAA
1 TTATTTTTAA
1533462 ATACATACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 8 0.32
17 1 0.04
18 8 0.32
20 8 0.32
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATTTTTAATTATATATT
Found at i:1539197 original size:15 final size:16
Alignment explanation
Indices: 1539177--1539206 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1539167 GTGAATCTTC
1539177 TATTTTTTT-ATTTTT
1 TATTTTTTTCATTTTT
1539192 TATTTTTTTCATTTT
1 TATTTTTTTCATTTT
1539207 ATTTTCGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.83
Consensus pattern (16 bp):
TATTTTTTTCATTTTT
Found at i:1539899 original size:22 final size:23
Alignment explanation
Indices: 1539860--1539908 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 23
1539850 AGTATTTTCG
*
1539860 TTATTTTATTTCACTTT-AAATA
1 TTATTTGATTTCACTTTAAAATA
1539882 TTATTTGATTATCA-TTTACAAATA
1 TTATTTGATT-TCACTTTA-AAATA
1539906 TTA
1 TTA
1539909 GTGTATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 12 0.52
23 3 0.13
24 8 0.35
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.55
Consensus pattern (23 bp):
TTATTTGATTTCACTTTAAAATA
Found at i:1540073 original size:3 final size:3
Alignment explanation
Indices: 1540052--1540115 Score: 56
Period size: 3 Copynumber: 20.7 Consensus size: 3
1540042 TTTTCTTTTG
* ** * *
1540052 TAT TTT TAT TAT TGC TAT TAT TGT TGT TAT TAT TAT TAT TAT TAT TATT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
*
1540101 TAT ATAA TAT TAT TA
1 TAT -TAT TAT TAT TA
1540116 ATAGGTACTT
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
3 44 0.90
4 5 0.10
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1540380 original size:24 final size:22
Alignment explanation
Indices: 1540353--1540410 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
1540343 TAGTGTGTTT
1540353 TATTATATGTATATATACTCTCAA
1 TATTATAT-TAT-TATACTCTCAA
* *
1540377 TATTATATTCTTATACTCTTAA
1 TATTATATTATTATACTCTCAA
**
1540399 TACCATATTATT
1 TATTATATTATT
1540411 CTTATTATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
22 19 0.66
23 2 0.07
24 8 0.28
ACGTcount: A:0.34, C:0.14, G:0.02, T:0.50
Consensus pattern (22 bp):
TATTATATTATTATACTCTCAA
Found at i:1540851 original size:30 final size:31
Alignment explanation
Indices: 1540817--1540894 Score: 88
Period size: 30 Copynumber: 2.5 Consensus size: 31
1540807 ATGTAAATAT
1540817 TATGTATATAT-TT-TTAAATACTATATTGTA
1 TATGTATATATATTCTT-AATACTATATTGTA
*
1540847 TATGTATATATATTCTTAGTACTATATTATGTA
1 TATGTATATATATTCTTAATACTATA-T-TGTA
*
1540880 TATATTATATATATT
1 TAT-GTATATATATT
1540895 TATTTTTACC
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
30 11 0.27
31 10 0.24
32 3 0.07
33 7 0.17
34 10 0.24
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.54
Consensus pattern (31 bp):
TATGTATATATATTCTTAATACTATATTGTA
Found at i:1540889 original size:32 final size:32
Alignment explanation
Indices: 1540821--1540894 Score: 87
Period size: 32 Copynumber: 2.2 Consensus size: 32
1540811 AAATATTATG
* *
1540821 TATATATTTTTAAATACTATATTGTATATGTA
1 TATATATTCTTAAATACTATATTGTATATATA
*
1540853 TATATATTCTT-AGTACTATATTATGTATATATTA
1 TATATATTCTTAAATACTATA-T-TGTATATA-TA
1540887 TATATATT
1 TATATATT
1540895 TATTTTTACC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 8 0.22
32 11 0.31
33 7 0.19
34 10 0.28
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.54
Consensus pattern (32 bp):
TATATATTCTTAAATACTATATTGTATATATA
Found at i:1540889 original size:34 final size:35
Alignment explanation
Indices: 1540800--1540894 Score: 99
Period size: 34 Copynumber: 2.7 Consensus size: 35
1540790 ATATTTATTT
* *
1540800 TATATATATGTAAATATTATGTATATATTTTTAAATAC
1 TATAT-TATGTATATATTA--TATATATTCTTAAATAC
* *
1540838 TATA-T-TGTATAT-GTATATATATTCTT-AGTAC
1 TATATTATGTATATATTATATATATTCTTAAATAC
1540869 TATATTATGTATATATTATATATATT
1 TATATTATGTATATATTATATATATT
1540895 TATTTTTACC
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
31 8 0.16
32 11 0.22
33 7 0.14
34 12 0.24
35 6 0.12
36 1 0.02
38 4 0.08
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (35 bp):
TATATTATGTATATATTATATATATTCTTAAATAC
Found at i:1546332 original size:31 final size:33
Alignment explanation
Indices: 1546297--1546367 Score: 85
Period size: 31 Copynumber: 2.2 Consensus size: 33
1546287 GCTGTTTTTG
1546297 AAATTAATAACTAGAATTTAT-CATCA-TAAAT
1 AAATTAATAACTAGAATTTATACATCATTAAAT
* * * *
1546328 AAATTAATCATTTGAATTTATATATCATTAAAT
1 AAATTAATAACTAGAATTTATACATCATTAAAT
1546361 -AATTAAT
1 AAATTAAT
1546368 TAAATTATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 18 0.53
32 11 0.32
33 5 0.15
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (33 bp):
AAATTAATAACTAGAATTTATACATCATTAAAT
Found at i:1553304 original size:5 final size:5
Alignment explanation
Indices: 1553294--1553319 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1553284 ACTGTCGAAC
1553294 TAATT TAATT TAATT TAATT TAATT T
1 TAATT TAATT TAATT TAATT TAATT T
1553320 GCGTCGTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TAATT
Found at i:1555972 original size:3 final size:3
Alignment explanation
Indices: 1555966--1555993 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1555956 GTCGTCGTCC
1555966 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1555994 TTAATGGCGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:1559522 original size:17 final size:16
Alignment explanation
Indices: 1559494--1559543 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
1559484 TCTAGTTCGA
1559494 TCATTTTGGGTTTGGG
1 TCATTTTGGGTTTGGG
* *
1559510 TCAATTTTAGGTTCT-AG
1 TC-ATTTTGGGTT-TGGG
1559527 TCATTTTGGGTTTGGG
1 TCATTTTGGGTTTGGG
1559543 T
1 T
1559544 TTGAGTTTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
15 1 0.04
16 13 0.48
17 12 0.44
18 1 0.04
ACGTcount: A:0.12, C:0.08, G:0.30, T:0.50
Consensus pattern (16 bp):
TCATTTTGGGTTTGGG
Found at i:1559534 original size:33 final size:32
Alignment explanation
Indices: 1559459--1559543 Score: 102
Period size: 32 Copynumber: 2.6 Consensus size: 32
1559449 TAAAATTTAC
* *
1559459 CGATCATTTT-GATTCTGTGTCAATTTCTAGTT
1 CGATCATTTTGGGTT-TGGGTCAATTTCTAGTT
1559491 CGATCATTTTGGGTTTGGGTCAATTT-TAGGTT
1 CGATCATTTTGGGTTTGGGTCAATTTCTA-GTT
*
1559523 CTAGTCATTTTGGGTTTGGGT
1 CGA-TCATTTTGGGTTTGGGT
1559544 TTGAGTTTGA
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
31 2 0.04
32 25 0.53
33 20 0.43
ACGTcount: A:0.15, C:0.12, G:0.25, T:0.48
Consensus pattern (32 bp):
CGATCATTTTGGGTTTGGGTCAATTTCTAGTT
Found at i:1559538 original size:16 final size:16
Alignment explanation
Indices: 1559494--1559540 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
1559484 TCTAGTTCGA
*
1559494 TCATTTTGGGTTTGGG
1 TCATTTTGGGTTTGAG
*
1559510 TCAATTTTAGGTTCT-AG
1 TC-ATTTTGGGTT-TGAG
1559527 TCATTTTGGGTTTG
1 TCATTTTGGGTTTG
1559541 GGTTTGAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
15 1 0.04
16 11 0.44
17 12 0.48
18 1 0.04
ACGTcount: A:0.13, C:0.09, G:0.28, T:0.51
Consensus pattern (16 bp):
TCATTTTGGGTTTGAG
Found at i:1561248 original size:22 final size:23
Alignment explanation
Indices: 1561209--1561251 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
1561199 GTAACCTAAT
1561209 TTAAAATTAATAAAAATTAAACC
1 TTAAAATTAATAAAAATTAAACC
*
1561232 TTAAAGTTAA-AAAAATTAAA
1 TTAAAATTAATAAAAATTAAA
1561252 AGAAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (23 bp):
TTAAAATTAATAAAAATTAAACC
Found at i:1561601 original size:32 final size:34
Alignment explanation
Indices: 1561537--1561602 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
1561527 CTTCACCTCA
1561537 TAATCTCAATGAAAAGTGGAAACAACTATGTTAT
1 TAATCTCAATGAAAAGTGGAAACAACTATGTTAT
1561571 TAATCTCAATGAAAAGTGG-AA-AACTATGTTAT
1 TAATCTCAATGAAAAGTGGAAACAACTATGTTAT
1561603 CAATTTAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 11 0.34
33 2 0.06
34 19 0.59
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.30
Consensus pattern (34 bp):
TAATCTCAATGAAAAGTGGAAACAACTATGTTAT
Found at i:1572420 original size:13 final size:13
Alignment explanation
Indices: 1572402--1572433 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1572392 TTTCCAGCAA
1572402 TTATGAATTTATT
1 TTATGAATTTATT
1572415 TTATGAATTTATT
1 TTATGAATTTATT
*
1572428 TGATGA
1 TTATGA
1572434 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:1572699 original size:50 final size:51
Alignment explanation
Indices: 1572528--1572775 Score: 297
Period size: 50 Copynumber: 4.8 Consensus size: 51
1572518 ATTTGGGTAA
* *
1572528 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC----GATCACG
* *
1572584 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCA-TGGCACCGA-GACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATCACG
* * *
1572633 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGA-GATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATCACG
* * *
1572683 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATCACG
** *
1572733 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
1572776 TGTTATTATC
Statistics
Matches: 170, Mismatches: 19, Indels: 11
0.85 0.09 0.05
Matches are distributed among these distances:
49 37 0.22
50 58 0.34
51 34 0.20
54 2 0.01
55 5 0.03
56 34 0.20
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (51 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATCACG
Found at i:1572716 original size:99 final size:103
Alignment explanation
Indices: 1572528--1572776 Score: 355
Period size: 99 Copynumber: 2.4 Consensus size: 103
1572518 ATTTGGGTAA
1572528 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
1572593 CTGTAAGACCATGTCTGGGACATGGCAT-GGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
1572633 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
1572695 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
1572733 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
1572777 GTTATTATCA
Statistics
Matches: 132, Mismatches: 8, Indels: 11
0.87 0.05 0.07
Matches are distributed among these distances:
99 40 0.30
100 13 0.10
101 37 0.28
104 2 0.02
105 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:1572735 original size:105 final size:99
Alignment explanation
Indices: 1572527--1572776 Score: 310
Period size: 105 Copynumber: 2.4 Consensus size: 99
1572517 CATTTGGGTA
1572527 AAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCC
1 AAGAG-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCC
*
1572592 CCTGTAAGACCATGTCTGGGACATGGCATGGCACCGAG
62 CCTATAAGACCATGTCTGGGACATGGCATGGCACCGAG
* *
1572630 ACGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCC
1 A--AGA-GTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCC
1572692 CTATAAGACCATGTCTGGGACATGGCATGGGCACCATCACGAG
63 CTATAAGACCATGTCTGGGACATGGCAT-GG---CA-C-CGAG
* *
1572735 AACA-TCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AAGAGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
1572777 GTTATTATCA
Statistics
Matches: 132, Mismatches: 5, Indels: 21
0.84 0.03 0.13
Matches are distributed among these distances:
99 39 0.30
100 4 0.03
101 36 0.27
103 5 0.04
104 3 0.02
105 44 0.33
106 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (99 bp):
AAGAGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGCACCGAG
Found at i:1579786 original size:29 final size:30
Alignment explanation
Indices: 1579727--1579784 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1579717 TCCGAGCCTT
*
1579727 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
1579757 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
1579785 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:1580014 original size:13 final size:13
Alignment explanation
Indices: 1579996--1580027 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1579986 TTTCCAGCAA
1579996 TTATGAATTTATT
1 TTATGAATTTATT
1580009 TTATGAATTTATT
1 TTATGAATTTATT
*
1580022 TGATGA
1 TTATGA
1580028 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:1580235 original size:50 final size:50
Alignment explanation
Indices: 1580122--1580363 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
1580112 ATTTGGGTAA
* * *
1580122 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
1580178 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
1580228 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
1580278 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
1580328 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
1580364 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:1580311 original size:100 final size:103
Alignment explanation
Indices: 1580122--1580371 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
1580112 ATTTGGGTAA
1580122 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
1580187 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
1580228 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
1580290 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
1580328 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
1580372 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:1592939 original size:13 final size:13
Alignment explanation
Indices: 1592923--1592950 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1592913 TTCACAACTT
1592923 AACGTAAGATACA
1 AACGTAAGATACA
1592936 AACGTAAGATACA
1 AACGTAAGATACA
1592949 AA
1 AA
1592951 AACTAATAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.14
Consensus pattern (13 bp):
AACGTAAGATACA
Found at i:1599223 original size:2 final size:2
Alignment explanation
Indices: 1599216--1599247 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1599206 ATACAGCTAC
1599216 AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1599248 GAATAGACTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1602201 original size:20 final size:20
Alignment explanation
Indices: 1602172--1602215 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
1602162 GAAGAGCTTT
1602172 ACCT-TTGCTTAGATTTCTA
1 ACCTATTGCTTAGATTTCTA
1602191 ACCTATTGCTTAGATTTCTA
1 ACCTATTGCTTAGATTTCTA
1602211 ACCTA
1 ACCTA
1602216 ACTCTCTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.25, C:0.23, G:0.09, T:0.43
Consensus pattern (20 bp):
ACCTATTGCTTAGATTTCTA
Found at i:1603385 original size:30 final size:30
Alignment explanation
Indices: 1603353--1603455 Score: 170
Period size: 30 Copynumber: 3.4 Consensus size: 30
1603343 AGCCACATTG
*
1603353 CCTCCCACTTGCACCTACTCTAACACCTTG
1 CCTCCCACTTGCACCTACTCTAACACCTTA
1603383 CCTCCCACTTGCACCTACTCTAACACCTTA
1 CCTCCCACTTGCACCTACTCTAACACCTTA
* *
1603413 CCTCCCACTTGCACCTACTCCACCACCTTA
1 CCTCCCACTTGCACCTACTCTAACACCTTA
*
1603443 TCTCCCACTTGCA
1 CCTCCCACTTGCA
1603456 TTTACACCAT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 69 1.00
ACGTcount: A:0.20, C:0.49, G:0.05, T:0.26
Consensus pattern (30 bp):
CCTCCCACTTGCACCTACTCTAACACCTTA
Found at i:1603963 original size:3 final size:3
Alignment explanation
Indices: 1603952--1604031 Score: 53
Period size: 3 Copynumber: 26.3 Consensus size: 3
1603942 TTTATTTTTT
* *
1603952 TTA TT- TTA TTA TTT TTA CTA TTA TT- TATA TTA TTA TTA TT- TCTCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA T-T-A
1603997 TGTA TATA TTA TTA TT- TATA TTA TTA TTA -TA TTA T
1 T-TA T-TA TTA TTA TTA T-TA TTA TTA TTA TTA TTA T
1604032 ATATACCCTC
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
2 7 0.11
3 46 0.74
4 7 0.11
5 2 0.03
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1603968 original size:9 final size:9
Alignment explanation
Indices: 1603943--1604031 Score: 56
Period size: 9 Copynumber: 9.4 Consensus size: 9
1603933 GAGCTTTGTT
*
1603943 TTATTTTTT
1 TTATTTTTA
1603952 TTA-TTTTA
1 TTATTTTTA
1603960 TTATTTTTA
1 TTATTTTTA
*
1603969 CTATTATTTA
1 TTATT-TTTA
*
1603979 -TATTATTA
1 TTATTTTTA
*
1603987 TTATTTCTCA
1 TTATTT-TTA
*
1603997 TGTATATATTA
1 T-TAT-TTTTA
*
1604008 TTATTTATA
1 TTATTTTTA
1604017 TTATTATTATA
1 TTATT-TT-TA
1604028 TTAT
1 TTAT
1604032 ATATACCCTC
Statistics
Matches: 62, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
8 10 0.16
9 28 0.45
10 11 0.18
11 12 0.19
12 1 0.02
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.67
Consensus pattern (9 bp):
TTATTTTTA
Found at i:1603973 original size:17 final size:14
Alignment explanation
Indices: 1603941--1603992 Score: 50
Period size: 15 Copynumber: 3.6 Consensus size: 14
1603931 GAGAGCTTTG
1603941 TTTTATTTTTTTTA
1 TTTTATTTTTTTTA
*
1603955 TTTTATTATTTTTA
1 TTTTATTTTTTTTA
* * *
1603969 CTATTATTTATATTA
1 -TTTTATTTTTTTTA
1603984 TTATTATTT
1 TT-TTATTT
1603993 CTCATGTATA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
14 14 0.47
15 16 0.53
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTATTTTTTTTA
Done.