Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A08
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: 123748673
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5630000 characters in sequence are not A, C, G, or T
File 89 of 373
Found at i:28502676 original size:54 final size:54
Alignment explanation
Indices: 28502612--28502722 Score: 168
Period size: 54 Copynumber: 2.1 Consensus size: 54
28502602 TGCTACAATA
* * * *
28502612 TAGTCTTTAAAGCGTTATACCTCGGAGGTATGTAACTCGGAATCGAATTCTTAC
1 TAGTCCTTAAAGCATTATACCTCGGAGGTATGTAACTCGAAATCAAATTCTTAC
* *
28502666 TAGTCCTTAAAGCATTATACCTTGGAGGTATGTAACTTGAAATCAAATTCTTAC
1 TAGTCCTTAAAGCATTATACCTCGGAGGTATGTAACTCGAAATCAAATTCTTAC
28502720 TAG
1 TAG
28502723 CTAAGGTGAA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (54 bp):
TAGTCCTTAAAGCATTATACCTCGGAGGTATGTAACTCGAAATCAAATTCTTAC
Found at i:28517907 original size:27 final size:27
Alignment explanation
Indices: 28517877--28518054 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
28517867 ATATTGAGTC
* * * *
28517877 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
28517904 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28517931 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
28517959 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
28517986 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
28518013 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28518040 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28518055 GTACAATTCA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:28518016 original size:82 final size:81
Alignment explanation
Indices: 28517898--28518053 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
28517888 TGCTATATAA
* *
28517898 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
28517963 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
28517980 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
28518044 CACTTAGTGC
65 CACTTAGTGC
28518054 TGTACAATTC
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:28518066 original size:82 final size:83
Alignment explanation
Indices: 28517877--28518066 Score: 221
Period size: 82 Copynumber: 2.3 Consensus size: 83
28517867 ATATTGAGTC
* * * * *
28517877 CGCACACTCAGTGCTATATAA-TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTA
1 CGCACACTTAGTGCTGTACAATTCAATTCGCACACTTAGTGCTACATAATCAAATCGCACACTTA
*
28517941 GTGCTACATAGTCAAACT
66 GTGCAACATAGTCAAACT
* * **
28517959 CGCACACTTAGTGCCG--C-ATGGTCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACAC
1 CGCACACTTAGTGCTGTACAAT--TCAATTCGCACACTTAGTGCTA-CATAATCAAATCGCACAC
28518020 TTAGTGCAACATAGTCAAA-T
63 TTAGTGCAACATAGTCAAACT
28518040 CGCACACTTAGTGCTGTACAATTCAAT
1 CGCACACTTAGTGCTGTACAATTCAAT
28518067 CCCGCGCACT
Statistics
Matches: 90, Mismatches: 11, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
79 1 0.01
81 17 0.19
82 69 0.77
83 1 0.01
84 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (83 bp):
CGCACACTTAGTGCTGTACAATTCAATTCGCACACTTAGTGCTACATAATCAAATCGCACACTTA
GTGCAACATAGTCAAACT
Found at i:28526855 original size:15 final size:15
Alignment explanation
Indices: 28526835--28526881 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
28526825 TTGTCTCGTA
28526835 TTATGTTTTAGTCAC
1 TTATGTTTTAGTCAC
* *
28526850 TTATGTTTGGAAT-A-
1 TTATGTTT-TAGTCAC
28526864 TTATGTTTTAGTCAC
1 TTATGTTTTAGTCAC
28526879 TTA
1 TTA
28526882 CATTATCATG
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
13 2 0.08
14 9 0.36
15 12 0.48
16 2 0.08
ACGTcount: A:0.23, C:0.09, G:0.15, T:0.53
Consensus pattern (15 bp):
TTATGTTTTAGTCAC
Found at i:28531255 original size:19 final size:19
Alignment explanation
Indices: 28531217--28531255 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
28531207 AAATAGCGAG
*
28531217 AATTTATTTTCTAAGTATA
1 AATTTATTTTCTAAGAATA
28531236 AATTCTATTTTCT-AGAATA
1 AATT-TATTTTCTAAGAATA
28531255 A
1 A
28531256 CAATTCTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (19 bp):
AATTTATTTTCTAAGAATA
Found at i:28533741 original size:26 final size:25
Alignment explanation
Indices: 28533685--28533741 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
28533675 TATTTTTAAT
* *
28533685 TATTATTCATTTTAAATTTTATATA
1 TATTATTCATTTTAAATCTTATACA
** *
28533710 CGTTATTGATTTTAAACTCTTATACA
1 TATTATTCATTTTAAA-TCTTATACA
28533736 TATTAT
1 TATTAT
28533742 ATATTTTGAA
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
25 13 0.54
26 11 0.46
ACGTcount: A:0.33, C:0.09, G:0.04, T:0.54
Consensus pattern (25 bp):
TATTATTCATTTTAAATCTTATACA
Found at i:28534047 original size:26 final size:28
Alignment explanation
Indices: 28533999--28534051 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
28533989 TGTTTTTGTA
*
28533999 TATTATTTATTTTAAATTTCTCTTTTACT
1 TATTATTTATTTTAAA-TGCTCTTTTACT
28534028 TATTATTTATTTT-AA-GCTCTTTTA
1 TATTATTTATTTTAAATGCTCTTTTA
28534052 TATGTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 8 0.35
28 2 0.09
29 13 0.57
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (28 bp):
TATTATTTATTTTAAATGCTCTTTTACT
Found at i:28534288 original size:26 final size:23
Alignment explanation
Indices: 28534239--28534288 Score: 55
Period size: 23 Copynumber: 2.0 Consensus size: 23
28534229 TGTTATCTAT
*
28534239 TTTAAATTTTTTATCTTGTTTAC
1 TTTAAATTTTTTATCTTGTATAC
*
28534262 TTTAAATTGCTTTTTTCTTCGTATAC
1 TTTAAATT--TTTTATCTT-GTATAC
28534288 T
1 T
28534289 ATTTTACTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 8 0.36
25 8 0.36
26 6 0.27
ACGTcount: A:0.20, C:0.12, G:0.06, T:0.62
Consensus pattern (23 bp):
TTTAAATTTTTTATCTTGTATAC
Found at i:28539911 original size:28 final size:28
Alignment explanation
Indices: 28539869--28539968 Score: 101
Period size: 28 Copynumber: 3.6 Consensus size: 28
28539859 CGATGTCTAG
* * *
28539869 CACACTATGTACCATACTCGATACCTCA
1 CACACTAAGTGCCATTCTCGATACCTCA
* * * **
28539897 CACGCTAAGTTCCATTCTCGATACTTTT
1 CACACTAAGTGCCATTCTCGATACCTCA
* **
28539925 CACACTAAGTGCCATTCTCGATACTTTG
1 CACACTAAGTGCCATTCTCGATACCTCA
28539953 CACACTAAGTGCCATT
1 CACACTAAGTGCCATT
28539969 TATATATAGA
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 62 1.00
ACGTcount: A:0.27, C:0.31, G:0.11, T:0.31
Consensus pattern (28 bp):
CACACTAAGTGCCATTCTCGATACCTCA
Found at i:28540043 original size:40 final size:39
Alignment explanation
Indices: 28539979--28540064 Score: 118
Period size: 40 Copynumber: 2.2 Consensus size: 39
28539969 TATATATAGA
* *
28539979 TAGCCGAAGCTATCTCGAATTGCACACCAAGTGCCACTTT
1 TAGCCGAAGCTATCTCCAACTGCACACCAAGTGCCA-TTT
* * *
28540019 TAGCTGAAGCTATTTCCAACTGCACACTAAGTGCCATTT
1 TAGCCGAAGCTATCTCCAACTGCACACCAAGTGCCATTT
28540058 TAGCCGA
1 TAGCCGA
28540065 TAAGTCGTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 9 0.22
40 31 0.77
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (39 bp):
TAGCCGAAGCTATCTCCAACTGCACACCAAGTGCCATTT
Found at i:28541878 original size:20 final size:20
Alignment explanation
Indices: 28541840--28541887 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
28541830 TAAAATCTAA
* **
28541840 AAAGATAAATACATTTAATT
1 AAAGATAAATAAAGATAATT
28541860 AAAGATAAATAAAGATAATT
1 AAAGATAAATAAAGATAATT
28541880 AAA-ATAAA
1 AAAGATAAA
28541888 ATCCTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (20 bp):
AAAGATAAATAAAGATAATT
Found at i:28541912 original size:27 final size:26
Alignment explanation
Indices: 28541882--28541944 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
28541872 AGATAATTAA
28541882 AATAAAATCCTAAAATTAAATAATCCT
1 AATAAAATCCTAAAATT-AATAATCCT
* * * *
28541909 AATAATTATCTTAATATTAATTATCCT
1 AATAA-AATCCTAAAATTAATAATCCT
28541936 AATATAAAT
1 AATA-AAAT
28541945 AAAATGGAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
27 19 0.66
28 10 0.34
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (26 bp):
AATAAAATCCTAAAATTAATAATCCT
Found at i:28541931 original size:15 final size:15
Alignment explanation
Indices: 28541911--28541940 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28541901 ATAATCCTAA
*
28541911 TAATTATCTTAATAT
1 TAATTATCCTAATAT
28541926 TAATTATCCTAATAT
1 TAATTATCCTAATAT
28541941 AAATAAAATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTATCCTAATAT
Found at i:28546881 original size:28 final size:28
Alignment explanation
Indices: 28546818--28546915 Score: 162
Period size: 28 Copynumber: 3.5 Consensus size: 28
28546808 ATATTAAGTC
*
28546818 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
28546845 TGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
28546873 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
28546901 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28546916 GTACAATTTA
Statistics
Matches: 66, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
27 21 0.32
28 45 0.68
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:28550171 original size:8 final size:9
Alignment explanation
Indices: 28550149--28550183 Score: 70
Period size: 9 Copynumber: 3.9 Consensus size: 9
28550139 TTTGGTGTTA
28550149 GTTTTTGAT
1 GTTTTTGAT
28550158 GTTTTTGAT
1 GTTTTTGAT
28550167 GTTTTTGAT
1 GTTTTTGAT
28550176 GTTTTTGA
1 GTTTTTGA
28550184 GATCCTCGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.11, C:0.00, G:0.23, T:0.66
Consensus pattern (9 bp):
GTTTTTGAT
Found at i:28556243 original size:43 final size:43
Alignment explanation
Indices: 28556153--28556265 Score: 124
Period size: 43 Copynumber: 2.7 Consensus size: 43
28556143 TGATTACATG
* * * *
28556153 TAAGGCCATGTCTGGGACATTGGCATTGTATTGAGATTATGTG
1 TAAGACCATGTCTGGGACATTGGCATCGTAATGAGATTATGTA
*
28556196 TAAGACCATGTCTGGGACATTGGCATCGTTAAT-CGATT-TCGTA
1 TAAGACCATGTCTGGGACATTGGCATCG-TAATGAGATTAT-GTA
* *
28556239 TAAGACCCTGTCTGGGACAGT-GCATCG
1 TAAGACCATGTCTGGGACATTGGCATCG
28556266 ATATGTGATA
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
42 7 0.11
43 51 0.84
44 3 0.05
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (43 bp):
TAAGACCATGTCTGGGACATTGGCATCGTAATGAGATTATGTA
Found at i:28556414 original size:33 final size:33
Alignment explanation
Indices: 28556377--28556443 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
28556367 ATAAGTCAAG
28556377 AAAGAATGTGTTAATGAGTTAAACGACTCAGGT
1 AAAGAATGTGTTAATGAGTTAAACGACTCAGGT
28556410 AAAGAATGTGTTAATGAGTTAAACGACTCAGGT
1 AAAGAATGTGTTAATGAGTTAAACGACTCAGGT
28556443 A
1 A
28556444 CGTACGAGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.40, C:0.09, G:0.24, T:0.27
Consensus pattern (33 bp):
AAAGAATGTGTTAATGAGTTAAACGACTCAGGT
Found at i:28558149 original size:27 final size:27
Alignment explanation
Indices: 28558047--28558151 Score: 95
Period size: 27 Copynumber: 3.9 Consensus size: 27
28558037 AATACTTTAG
* *
28558047 TTTACCAAATTACTGAAATACCCTCGA
1 TTTACAAAATTACCGAAATACCCTCGA
* ** *
28558074 CTTGTAAAATTACC-AAAGTACCCCCGA
1 TTTACAAAATTACCGAAA-TACCCTCGA
* * ***
28558101 TTTACAGAATTATCGTTTTACCCTCGA
1 TTTACAAAATTACCGAAATACCCTCGA
28558128 TTTACAAAATTACCGAAATACCCT
1 TTTACAAAATTACCGAAATACCCT
28558152 TGTAGGGTAG
Statistics
Matches: 56, Mismatches: 20, Indels: 4
0.70 0.25 0.05
Matches are distributed among these distances:
26 3 0.05
27 53 0.95
ACGTcount: A:0.35, C:0.26, G:0.09, T:0.30
Consensus pattern (27 bp):
TTTACAAAATTACCGAAATACCCTCGA
Found at i:28558171 original size:27 final size:26
Alignment explanation
Indices: 28558133--28558221 Score: 101
Period size: 27 Copynumber: 3.3 Consensus size: 26
28558123 CTCGATTTAC
28558133 AAAATTACCGAAATACCCTTGTAGGGT
1 AAAATTA-CGAAATACCCTTGTAGGGT
28558160 AGAAA-TATCGAAATACCCCTT-TAGGGT
1 A-AAATTA-CGAAATA-CCCTTGTAGGGT
* *
28558187 AAAATTACTGAGATACCCTTGTGGGGT
1 AAAATTAC-GAAATACCCTTGTAGGGT
28558214 AAAATTAC
1 AAAATTAC
28558222 CATTTTGCCC
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
26 9 0.17
27 37 0.69
28 8 0.15
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (26 bp):
AAAATTACGAAATACCCTTGTAGGGT
Found at i:28558887 original size:19 final size:19
Alignment explanation
Indices: 28558865--28558913 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
28558855 CTGATACTAG
*
28558865 TTCTAATTCTGTCACCTAA
1 TTCTGATTCTGTCACCTAA
*
28558884 TTCTGATTCTGTCACCTGA
1 TTCTGATTCTGTCACCTAA
28558903 TTCTGATTCTG
1 TTCTGATTCTG
28558914 ATTCTCATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.18, C:0.24, G:0.12, T:0.45
Consensus pattern (19 bp):
TTCTGATTCTGTCACCTAA
Found at i:28558893 original size:25 final size:25
Alignment explanation
Indices: 28558833--28558893 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
28558823 TTGCATTCAC
* *
28558833 ATTCTGATTCTAATTCTGTTACCTG
1 ATTCTGATTCTAATTCTGTCACCTA
*
28558858 ATACT-AGTTCTAATTCTGTCACCTA
1 ATTCTGA-TTCTAATTCTGTCACCTA
28558883 ATTCTGATTCT
1 ATTCTGATTCT
28558894 GTCACCTGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
24 1 0.03
25 28 0.93
26 1 0.03
ACGTcount: A:0.23, C:0.21, G:0.10, T:0.46
Consensus pattern (25 bp):
ATTCTGATTCTAATTCTGTCACCTA
Found at i:28558911 original size:25 final size:24
Alignment explanation
Indices: 28558833--28558918 Score: 74
Period size: 25 Copynumber: 3.7 Consensus size: 24
28558823 TTGCATTCAC
*
28558833 ATTCTGATTCTAATTCTGTTACCTG
1 ATTCT-ATTCTAATTCTGTCACCTG
*
28558858 ATACTAGTTCTAATTCTGTCACCT-
1 ATTCTA-TTCTAATTCTGTCACCTG
*
28558882 A----ATTCTGATTCTGTCACCTG
1 ATTCTATTCTAATTCTGTCACCTG
*
28558902 ATTCTGATTCTGATTCT
1 ATTCT-ATTCTAATTCT
28558919 CATTTTGGTT
Statistics
Matches: 51, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
19 16 0.31
20 2 0.04
24 2 0.04
25 31 0.61
ACGTcount: A:0.21, C:0.22, G:0.12, T:0.45
Consensus pattern (24 bp):
ATTCTATTCTAATTCTGTCACCTG
Found at i:28564927 original size:17 final size:18
Alignment explanation
Indices: 28564879--28564928 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
28564869 GGTGACCAAA
*
28564879 TTTCATCTAATTTTGACT
1 TTTCAACTAATTTTGACT
28564897 TTTCAACTAATTTTGACT
1 TTTCAACTAATTTTGACT
28564915 TTTCAAC-AATTTTG
1 TTTCAACTAATTTTG
28564929 TCTCCCATGG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 7 0.23
18 24 0.77
ACGTcount: A:0.26, C:0.16, G:0.06, T:0.52
Consensus pattern (18 bp):
TTTCAACTAATTTTGACT
Found at i:28567437 original size:138 final size:139
Alignment explanation
Indices: 28567205--28567549 Score: 384
Period size: 138 Copynumber: 2.5 Consensus size: 139
28567195 GTCGATGCCG
*
28567205 TGTCCCAGACA-GGTCTTACACTGACACATATCAAGCCGATGCCATGTCCCAGACATGGTCTTAC
1 TGTCCCAGACATGGTCTTACACTGACACATATCAAGCCGATGACATGTCCCAGACATGGTCTTAC
* * **
28567269 ACTAGCTTTCACGATGTGGTTGATGCATGTCCCAGACATGTCTTACACTAGCACACATATCTGTG
66 ACTAGCTTTCACGATGAGGCTGATGCATGTCCCAGACATGTCTTACACTAGCACACATATCAATG
28567334 CCAACGCCA
131 CCAACGCCA
* * * * *
28567343 TGTCCCAAACATGGTCTTACACTGACACATCTCGTAGCTGAT-ACATGTCCTAGACAT-GTCTTA
1 TGTCCCAGACATGGTCTTACACTGACACATATC-AAGCCGATGACATGTCCCAGACATGGTCTTA
* * *
28567406 CACTAGC-TT-ACG-TCCCGAGGCTGATGCATGTCCCAGACATGTCTTACACTAGCACTCGTCTC
65 CACTAGCTTTCACGAT---GAGGCTGATGCATGTCCCAGACATGTCTTACACTAGCACACATATC
* *
28567468 AATGCCGATGCCA
127 AATGCCAACGCCA
* * * *
28567481 TGTTCCAGACATGGTCTTACACTGGCTCTTAT-AATGTGGCCGATG-CATGTCCCAGACAT-GTC
1 TGTCCCAGACATGGTCTTACACTGACACATATCAA----GCCGATGACATGTCCCAGACATGGTC
28567543 TTACACT
62 TTACACT
28567550 GGCGCACATA
Statistics
Matches: 173, Mismatches: 24, Indels: 18
0.80 0.11 0.08
Matches are distributed among these distances:
135 1 0.01
136 4 0.02
137 2 0.01
138 99 0.57
139 33 0.19
140 34 0.20
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (139 bp):
TGTCCCAGACATGGTCTTACACTGACACATATCAAGCCGATGACATGTCCCAGACATGGTCTTAC
ACTAGCTTTCACGATGAGGCTGATGCATGTCCCAGACATGTCTTACACTAGCACACATATCAATG
CCAACGCCA
Found at i:28567478 original size:46 final size:45
Alignment explanation
Indices: 28567205--28567549 Score: 204
Period size: 46 Copynumber: 7.5 Consensus size: 45
28567195 GTCGATGCCG
* * *
28567205 TGTCCCAGACAGGTCTTACACT-GACACATATCAA-GCCGATGCCA
1 TGTCCCAGACATGTCTTACACTAGACTCATCTCAATGCCGATG-CA
* * * **
28567249 TGTCCCAGACATGGTCTTACACTAG-CT-TTCACGATGTGGTTGATGCA
1 TGTCCCAGACAT-GTCTTACACTAGACTCATCTC-A-AT-GCCGATGCA
* * ** * *
28567296 TGTCCCAGACATGTCTTACACTAGCACACATATCTGTGCCAACGCCA
1 TGTCCCAGACATGTCTTACACTAG-ACTCATCTCAATGCCGATG-CA
* * * * *
28567343 TGTCCCAAACATGGTCTTACACT-GACACATCTC-GTAGCTGATACA
1 TGTCCCAGACAT-GTCTTACACTAGACTCATCTCAAT-GCCGATGCA
* * * * * *
28567388 TGTCCTAGACATGTCTTACACTAG-CTTACGTCCCGAGGCTGATGCA
1 TGTCCCAGACATGTCTTACACTAGAC-T-CATCTCAATGCCGATGCA
*
28567434 TGTCCCAGACATGTCTTACACTAGCACTCGTCTCAATGCCGATGCCA
1 TGTCCCAGACATGTCTTACACTAG-ACTCATCTCAATGCCGATG-CA
* * * *
28567481 TGTTCCAGACATGGTCTTACACT-GGCTCTTAT-AATGTGGCCGATGCA
1 TGTCCCAGACAT-GTCTTACACTAGACTCATCTCAA--T-GCCGATGCA
28567528 TGTCCCAGACATGTCTTACACT
1 TGTCCCAGACATGTCTTACACT
28567550 GGCGCACATA
Statistics
Matches: 237, Mismatches: 41, Indels: 44
0.74 0.13 0.14
Matches are distributed among these distances:
44 24 0.10
45 29 0.12
46 89 0.38
47 59 0.25
48 34 0.14
49 2 0.01
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (45 bp):
TGTCCCAGACATGTCTTACACTAGACTCATCTCAATGCCGATGCA
Found at i:28572352 original size:9 final size:9
Alignment explanation
Indices: 28572333--28572363 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
28572323 CCATACCTAG
28572333 AATTACATCA
1 AATT-CATCA
28572343 AATTCATCA
1 AATTCATCA
28572352 AATTCATCA
1 AATTCATCA
28572361 AAT
1 AAT
28572364 GACAATAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 17 0.81
10 4 0.19
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.32
Consensus pattern (9 bp):
AATTCATCA
Found at i:28577120 original size:58 final size:58
Alignment explanation
Indices: 28576980--28577126 Score: 174
Period size: 56 Copynumber: 2.6 Consensus size: 58
28576970 CCTCATAACA
* * ** * *
28576980 TATAACAGGATTACTAGTCCAGGCTAAATCCTTTTTGTAATATATGCTCAGAAGAGCT
1 TATATCAGGATTACCAGTCCAGGCTAAATCCTAATTGTAATATATACTCAGAAGAGAT
* * * *
28577038 TA-ATTAGGATTA-CAGTCCAAGCTAAATCCTAATTGTTATATATACTC-GAGAGGGAT
1 TATATCAGGATTACCAGTCCAGGCTAAATCCTAATTGTAATATATACTCAGA-AGAGAT
28577094 TATATCAGGATTACCAGTCCAGGCTAAATCCTA
1 TATATCAGGATTACCAGTCCAGGCTAAATCCTA
28577127 TCGGCAACAA
Statistics
Matches: 74, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
55 2 0.03
56 35 0.47
57 17 0.23
58 20 0.27
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (58 bp):
TATATCAGGATTACCAGTCCAGGCTAAATCCTAATTGTAATATATACTCAGAAGAGAT
Found at i:28583335 original size:31 final size:31
Alignment explanation
Indices: 28583297--28583445 Score: 244
Period size: 31 Copynumber: 4.8 Consensus size: 31
28583287 ATAAATGACA
*
28583297 AGTGAAAAGTGGTAGCTTCTGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
28583328 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
28583359 AATGAAAAGTGGTAGCTTCGGCTACCTAATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
28583390 AGTGAAAAATGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
28583421 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
28583446 AAGTGACAAG
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 108 1.00
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:28583537 original size:47 final size:46
Alignment explanation
Indices: 28583467--28583676 Score: 180
Period size: 47 Copynumber: 4.6 Consensus size: 46
28583457 GATTTCCGTA
* *
28583467 TAAGACCA-AATCTGGGATATGGCATCGGTGTGATATATGCTAC-TG
1 TAAGACCATAA-CTGGGATATGGCATCGGTGTGATATGTGATACGTG
* * *
28583512 TAGAAGACCATAACTGGGATATGGCATCAGTGAGATATGTGATTCGTG
1 T--AAGACCATAACTGGGATATGGCATCGGTGTGATATGTGATACGTG
* * *
28583560 TAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTACGTG
1 TAAGACCATAACTGGGATATGGCATCG--GTGTGATATGTGA-TACGTG
* * * * *
28583609 TAAGACCATAACTGGGCTATGGGATC-G-AT-ATATG-AATATGTG
1 TAAGACCATAACTGGGATATGGCATCGGTGTGATATGTGATACGTG
* * *
28583651 TAAGACTATAGCTGGGCTATGGCATC
1 TAAGACCATAACTGGGATATGGCATC
28583677 ATGATGTGAA
Statistics
Matches: 138, Mismatches: 20, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
42 28 0.20
43 1 0.01
44 5 0.04
45 2 0.01
46 23 0.17
47 34 0.25
48 16 0.12
49 29 0.21
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.29
Consensus pattern (46 bp):
TAAGACCATAACTGGGATATGGCATCGGTGTGATATGTGATACGTG
Found at i:28583618 original size:49 final size:47
Alignment explanation
Indices: 28583515--28583685 Score: 185
Period size: 49 Copynumber: 3.7 Consensus size: 47
28583505 GCTACTGTAG
* * *
28583515 AAGACCATAACTGGGATATGGCATCA-GTGAGATATGTGATTCGTGT
1 AAGACCATAACTGGGCTATGGCATCATATGTGATATGTGATTCGTGT
*
28583561 AAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTACGTGT
1 AAGACCATAACTGGGCTATGGCATC-ATATGTGATATGTGATT-CGTGT
* *
28583610 AAGACCATAACTGGGCTATGGGATCGATATATGA-A--T-A-T-GTGT
1 AAGACCATAACTGGGCTATGGCATC-ATATGTGATATGTGATTCGTGT
* *
28583652 AAGACTATAGCTGGGCTATGGCATCATGATGTGA
1 AAGACCATAACTGGGCTATGGCATCAT-ATGTGA
28583686 AGATGTGTAA
Statistics
Matches: 110, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
41 2 0.02
42 31 0.28
44 1 0.01
45 1 0.01
46 24 0.22
47 1 0.01
48 14 0.13
49 36 0.33
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.29
Consensus pattern (47 bp):
AAGACCATAACTGGGCTATGGCATCATATGTGATATGTGATTCGTGT
Found at i:28583652 original size:42 final size:42
Alignment explanation
Indices: 28583515--28583702 Score: 148
Period size: 42 Copynumber: 4.2 Consensus size: 42
28583505 GCTACTGTAG
* *
28583515 AAGACCATAACTGGGATATGGCATCAGTGAGATATG-TGATTCGTGT
1 AAGACCATAACTGGGCTATGGCATCA-T--GATATGAAGA-T-GTGT
* *
28583561 AAGACCATAGCTGGGCTATGGCATCGATATGTGATATG-TGATTACGTGT
1 AAGACCATAACTGGGCTATGGCATC---A--TGATATGAAGA-T--GTGT
* *
28583610 AAGACCATAACTGGGCTATGGGATCGAT-ATATGAATATGTGT
1 AAGACCATAACTGGGCTATGGCATC-ATGATATGAAGATGTGT
* * *
28583652 AAGACTATAGCTGGGCTATGGCATCATGATGTGAAGATGTGT
1 AAGACCATAACTGGGCTATGGCATCATGATATGAAGATGTGT
28583694 AAGACCATA
1 AAGACCATA
28583703 GTTAAACTAT
Statistics
Matches: 122, Mismatches: 13, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
41 2 0.02
42 46 0.38
44 6 0.05
45 2 0.02
46 23 0.19
47 1 0.01
48 11 0.09
49 29 0.24
50 2 0.02
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.28
Consensus pattern (42 bp):
AAGACCATAACTGGGCTATGGCATCATGATATGAAGATGTGT
Found at i:28584854 original size:10 final size:10
Alignment explanation
Indices: 28584839--28584863 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
28584829 GGGCACTTTT
28584839 CAGATCTTAC
1 CAGATCTTAC
28584849 CAGATCTTAC
1 CAGATCTTAC
28584859 CAGAT
1 CAGAT
28584864 GATATATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.28, G:0.12, T:0.28
Consensus pattern (10 bp):
CAGATCTTAC
Found at i:28585941 original size:19 final size:18
Alignment explanation
Indices: 28585917--28585990 Score: 54
Period size: 19 Copynumber: 4.4 Consensus size: 18
28585907 CCCTGTTTAA
28585917 GAGTAGACTTAGTGTAATT
1 GAGTAGACTTAGTGTAA-T
*
28585936 GAGTAGAGTTAG-G-AAT
1 GAGTAGACTTAGTGTAAT
* *
28585952 -AG-A-CCCT-GTGTAA-
1 GAGTAGACTTAGTGTAAT
28585965 GAGTAGACTTAGTGTAATT
1 GAGTAGACTTAGTGTAA-T
28585984 GAGTAGA
1 GAGTAGA
28585991 GTTACATGCA
Statistics
Matches: 41, Mismatches: 6, Indels: 16
0.65 0.10 0.25
Matches are distributed among these distances:
12 1 0.02
13 2 0.05
14 5 0.12
15 3 0.07
16 3 0.07
17 8 0.20
18 1 0.02
19 18 0.44
ACGTcount: A:0.34, C:0.07, G:0.30, T:0.30
Consensus pattern (18 bp):
GAGTAGACTTAGTGTAAT
Found at i:28585969 original size:48 final size:48
Alignment explanation
Indices: 28585898--28585994 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
28585888 AAATCAAAGG
*
28585898 AGGAATAGACCCTGTTTAAGAGTAGACTTAGTGTAATTGAGTAGAGTT
1 AGGAATAGACCCTGTGTAAGAGTAGACTTAGTGTAATTGAGTAGAGTT
28585946 AGGAATAGACCCTGTGTAAGAGTAGACTTAGTGTAATTGAGTAGAGTT
1 AGGAATAGACCCTGTGTAAGAGTAGACTTAGTGTAATTGAGTAGAGTT
28585994 A
1 A
28585995 CATGCAATCT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.34, C:0.08, G:0.28, T:0.30
Consensus pattern (48 bp):
AGGAATAGACCCTGTGTAAGAGTAGACTTAGTGTAATTGAGTAGAGTT
Found at i:28591673 original size:28 final size:28
Alignment explanation
Indices: 28591627--28591740 Score: 156
Period size: 28 Copynumber: 4.1 Consensus size: 28
28591617 AATACCGTTG
* *
28591627 CATACTCAATGTCTTGCACACTAAGTGC
1 CATACTCAATATCTCGCACACTAAGTGC
*
28591655 CATAATCAATATCTCGCACACTAAGTGC
1 CATACTCAATATCTCGCACACTAAGTGC
* * * *
28591683 CATTCTCAATGTTTCGCACACTAACTGC
1 CATACTCAATATCTCGCACACTAAGTGC
*
28591711 CATACTCGATATCTCGCACACTAAGTGC
1 CATACTCAATATCTCGCACACTAAGTGC
28591739 CA
1 CA
28591741 AATTTAGCTA
Statistics
Matches: 73, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 73 1.00
ACGTcount: A:0.30, C:0.31, G:0.12, T:0.27
Consensus pattern (28 bp):
CATACTCAATATCTCGCACACTAAGTGC
Found at i:28591723 original size:56 final size:56
Alignment explanation
Indices: 28591631--28591740 Score: 177
Period size: 56 Copynumber: 2.0 Consensus size: 56
28591621 CCGTTGCATA
*
28591631 CTCAATGTCTTGCACACTAAGTGCCATAATCAATATCTCGCACACTAAGTGCCATT
1 CTCAATGTCTTGCACACTAACTGCCATAATCAATATCTCGCACACTAAGTGCCATT
* *
28591687 CTCAATGT-TTCGCACACTAACTGCCATACTCGATATCTCGCACACTAAGTGCCA
1 CTCAATGTCTT-GCACACTAACTGCCATAATCAATATCTCGCACACTAAGTGCCA
28591741 AATTTAGCTA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
55 2 0.04
56 48 0.96
ACGTcount: A:0.29, C:0.31, G:0.13, T:0.27
Consensus pattern (56 bp):
CTCAATGTCTTGCACACTAACTGCCATAATCAATATCTCGCACACTAAGTGCCATT
Found at i:28593101 original size:31 final size:31
Alignment explanation
Indices: 28593061--28593134 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
28593051 CGGGTTAGGG
* *
28593061 ACACAGGTGTGTATGACCACACGGCCTACCC
1 ACACGGGTGTGTATGACCACACGACCTACCC
* *
28593092 ACACGGGTGTGTATGTCCACACGACCTGCCC
1 ACACGGGTGTGTATGACCACACGACCTACCC
*
28593123 ACACGGGCGTGT
1 ACACGGGTGTGT
28593135 GACCCCTGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.22, C:0.34, G:0.27, T:0.18
Consensus pattern (31 bp):
ACACGGGTGTGTATGACCACACGACCTACCC
Found at i:28593408 original size:5 final size:5
Alignment explanation
Indices: 28593394--28593430 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
28593384 TATCTTTTGA
*
28593394 ATTTT A-TTT ATTTT ATTTT ATGTT ATTTT ATTTT ATT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATT
28593431 ACTCTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 4 0.14
5 25 0.86
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.76
Consensus pattern (5 bp):
ATTTT
Found at i:28593421 original size:15 final size:14
Alignment explanation
Indices: 28593394--28593430 Score: 65
Period size: 15 Copynumber: 2.6 Consensus size: 14
28593384 TATCTTTTGA
28593394 ATTTTATTTATTTT
1 ATTTTATTTATTTT
28593408 ATTTTATGTTATTTT
1 ATTTTAT-TTATTTT
28593423 ATTTTATT
1 ATTTTATT
28593431 ACTCTAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.76
Consensus pattern (14 bp):
ATTTTATTTATTTT
Found at i:28594449 original size:14 final size:14
Alignment explanation
Indices: 28594430--28594459 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28594420 TTCACAATTA
*
28594430 TGTCTTTTTTATTT
1 TGTCTTTTATATTT
28594444 TGTCTTTTATATTT
1 TGTCTTTTATATTT
28594458 TG
1 TG
28594460 CATGCATAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.10, C:0.07, G:0.10, T:0.73
Consensus pattern (14 bp):
TGTCTTTTATATTT
Found at i:28595904 original size:48 final size:48
Alignment explanation
Indices: 28595849--28595974 Score: 198
Period size: 48 Copynumber: 2.6 Consensus size: 48
28595839 GTGCGAATGA
* *
28595849 TACCTTGATTTGGCTACAGGCCGTGGTTTAGGTATTTCAGAGAGGAGT
1 TACCTTGATTTGGCTACAGGCCATGGTATAGGTATTTCAGAGAGGAGT
*
28595897 TACCTTGATTTGGCTACGGGCCATGGTATAGGTATTTCAGAGAGGAGT
1 TACCTTGATTTGGCTACAGGCCATGGTATAGGTATTTCAGAGAGGAGT
* * *
28595945 TAACTTGATTTGGCTACGGGCGATGGTATA
1 TACCTTGATTTGGCTACAGGCCATGGTATA
28595975 TATACTTATT
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 73 1.00
ACGTcount: A:0.22, C:0.14, G:0.31, T:0.33
Consensus pattern (48 bp):
TACCTTGATTTGGCTACAGGCCATGGTATAGGTATTTCAGAGAGGAGT
Found at i:28600369 original size:46 final size:46
Alignment explanation
Indices: 28600319--28600494 Score: 200
Period size: 46 Copynumber: 3.8 Consensus size: 46
28600309 TGATTGAGCA
28600319 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
28600365 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
28600410 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* **
28600458 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTTGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28600495 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 10, Indels: 20
0.79 0.07 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 5 0.05
46 60 0.55
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:28600475 original size:93 final size:93
Alignment explanation
Indices: 28600316--28600485 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
28600306 GGATGATTGA
*
28600316 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
28600381 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
28600409 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGAG
28600473 TTGAGTCCGAGTT
65 TTGAGTCCGAGTT
28600486 TGCTTATGGG
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 2 0.03
93 72 0.97
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:28605678 original size:14 final size:15
Alignment explanation
Indices: 28605650--28605678 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28605640 CTCTTTCAAG
28605650 GACAAGAATAATCCA
1 GACAAGAATAATCCA
28605665 GACAAGAA-AATCCA
1 GACAAGAATAATCCA
28605679 TATGAACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.55, C:0.21, G:0.14, T:0.10
Consensus pattern (15 bp):
GACAAGAATAATCCA
Found at i:28609146 original size:6 final size:6
Alignment explanation
Indices: 28609135--28609170 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
28609125 TAAAATCTAC
28609135 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
28609171 GTAGTTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
TAAAAA
Found at i:28616019 original size:15 final size:15
Alignment explanation
Indices: 28615999--28616041 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
28615989 GAAGCCCAGA
28615999 ATAAAGAAATCCATG
1 ATAAAGAAATCCATG
*
28616014 ATAAAGAAATCCATT
1 ATAAAGAAATCCATG
*
28616029 ATAAGGAAATCCA
1 ATAAAGAAATCCA
28616042 ATTTACAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.53, C:0.14, G:0.12, T:0.21
Consensus pattern (15 bp):
ATAAAGAAATCCATG
Found at i:28619597 original size:68 final size:67
Alignment explanation
Indices: 28619524--28619673 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
28619514 CATCATGTGT
* * * *
28619524 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
28619586 ATGTAG
62 ATGTAG
** * *
28619592 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
28619657 AG
66 AG
28619659 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
28619674 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:28619629 original size:64 final size:64
Alignment explanation
Indices: 28619548--28619731 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
28619538 AGACATTATG
* *
28619548 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
28619612 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
28619677 AA
63 AA
* * * *
28619679 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
28619732 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:28629732 original size:47 final size:48
Alignment explanation
Indices: 28629622--28629745 Score: 144
Period size: 47 Copynumber: 2.6 Consensus size: 48
28629612 TGATACCTTG
* * ** * **
28629622 ATTTGGCTACGGGCCACGGTATAGGTATTTTAGAGAAGAGTTACCTTG
1 ATTTGGCTACGGGCCATGGTATAGGTACTCCAGAGAAGAGGTACCTCA
*
28629670 ATTTGGCTACAGGCCATGGTATAGGTACTCCAG-GATA-AGGTACCTCA
1 ATTTGGCTACGGGCCATGGTATAGGTACTCCAGAGA-AGAGGTACCTCA
*
28629717 ATTTGGCTACGGGCCATGATATAGGTACT
1 ATTTGGCTACGGGCCATGGTATAGGTACT
28629746 TATCAATTGT
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
47 36 0.55
48 29 0.45
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (48 bp):
ATTTGGCTACGGGCCATGGTATAGGTACTCCAGAGAAGAGGTACCTCA
Found at i:28630962 original size:22 final size:22
Alignment explanation
Indices: 28630937--28630978 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
28630927 GAATGGTATT
28630937 TGAA-TATGAATGCATAAATGTA
1 TGAAGTATGAATG-ATAAATGTA
*
28630959 TGAAGTATGTATGATAAATG
1 TGAAGTATGAATGATAAATG
28630979 ACGTGTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.43, C:0.02, G:0.21, T:0.33
Consensus pattern (22 bp):
TGAAGTATGAATGATAAATGTA
Found at i:28636560 original size:18 final size:17
Alignment explanation
Indices: 28636532--28636565 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
28636522 GGCTTTAACC
28636532 CATTACAGAATAAGAAA
1 CATTACAGAATAAGAAA
*
28636549 CATTATCAGAATCAGAA
1 CATTA-CAGAATAAGAA
28636566 TCAGAATCAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.53, C:0.15, G:0.12, T:0.21
Consensus pattern (17 bp):
CATTACAGAATAAGAAA
Found at i:28636562 original size:6 final size:6
Alignment explanation
Indices: 28636553--28636628 Score: 66
Period size: 6 Copynumber: 12.3 Consensus size: 6
28636543 AAGAAACATT
* *
28636553 ATCAGA ATCAGA ATCAGA ATCAG- GTGACAGA ATCAGA ATCAGA ATCAGT
1 ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA ATCAGA ATCAGA
* *
28636602 ATCAGGTA A-CAGA ATCAAA ATTAGA AT
1 ATCA-G-A ATCAGA ATCAGA ATCAGA AT
28636629 GTGAATGCAA
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
5 3 0.05
6 46 0.81
7 6 0.11
8 2 0.04
ACGTcount: A:0.47, C:0.14, G:0.18, T:0.20
Consensus pattern (6 bp):
ATCAGA
Found at i:28636589 original size:31 final size:31
Alignment explanation
Indices: 28636553--28636628 Score: 116
Period size: 31 Copynumber: 2.5 Consensus size: 31
28636543 AAGAAACATT
*
28636553 ATCAGAATCAGAATCAGAATCAGGTGACAGA
1 ATCAGAATCAGAATCAGAATCAGGTAACAGA
*
28636584 ATCAGAATCAGAATCAGTATCAGGTAACAGA
1 ATCAGAATCAGAATCAGAATCAGGTAACAGA
* *
28636615 ATCAAAATTAGAAT
1 ATCAGAATCAGAAT
28636629 GTGAATGCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.47, C:0.14, G:0.18, T:0.20
Consensus pattern (31 bp):
ATCAGAATCAGAATCAGAATCAGGTAACAGA
Found at i:28636798 original size:28 final size:26
Alignment explanation
Indices: 28636743--28636824 Score: 92
Period size: 28 Copynumber: 3.0 Consensus size: 26
28636733 AGCATTGCTG
* * *
28636743 CCAGAACAGATATTGTGACAGAGTCA
1 CCAGAACAGATATTGTGGCAAAGCCA
*
28636769 CCAGATACAGATATTTGTGGCATAGCCA
1 CCAGA-ACAGATA-TTGTGGCAAAGCCA
*
28636797 CCAGAATCAGATAATGTGGCAAAGCCA
1 CCAGAA-CAGATATTGTGGCAAAGCCA
28636824 C
1 C
28636825 TTAACAGAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
26 5 0.10
27 21 0.44
28 22 0.46
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.20
Consensus pattern (26 bp):
CCAGAACAGATATTGTGGCAAAGCCA
Found at i:28637449 original size:27 final size:27
Alignment explanation
Indices: 28637419--28637579 Score: 234
Period size: 27 Copynumber: 6.0 Consensus size: 27
28637409 ATCTCTGTAA
*
28637419 TTCTACCCTATAGGGGTATTTC-AGTAT
1 TTCTACCCTACAGGGGTATTTCGA-TAT
* *
28637446 TTCTACCCTACAAGGGTATTTCGATAA
1 TTCTACCCTACAGGGGTATTTCGATAT
*
28637473 TTCTACCCTACAGGGGTATTTCGATAA
1 TTCTACCCTACAGGGGTATTTCGATAT
* * *
28637500 TTCTACCTTATAGGGGTATTTCGGTAT
1 TTCTACCCTACAGGGGTATTTCGATAT
28637527 TTCTACCCTACAGGGGTATTTCGATAT
1 TTCTACCCTACAGGGGTATTTCGATAT
*
28637554 TTCTACCCTACAAGGGTATTTCGATA
1 TTCTACCCTACAGGGGTATTTCGATA
28637580 ATTTTTTAAA
Statistics
Matches: 121, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
27 120 0.99
28 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.37
Consensus pattern (27 bp):
TTCTACCCTACAGGGGTATTTCGATAT
Found at i:28637512 original size:81 final size:81
Alignment explanation
Indices: 28637416--28637582 Score: 289
Period size: 81 Copynumber: 2.1 Consensus size: 81
28637406 GGTATCTCTG
28637416 TAATTCTACCCTATAGGGGTATTTCAGTATTTCTACCCTACAAGGGTATTTCGATAATTCTACCC
1 TAATTCTACCCTATAGGGGTATTTCAGTATTTCTACCCTACAAGGGTATTTCGATAATTCTACCC
*
28637481 TACAGGGGTATTTCGA
66 TACAAGGGTATTTCGA
* * * *
28637497 TAATTCTACCTTATAGGGGTATTTCGGTATTTCTACCCTACAGGGGTATTTCGATATTTCTACCC
1 TAATTCTACCCTATAGGGGTATTTCAGTATTTCTACCCTACAAGGGTATTTCGATAATTCTACCC
28637562 TACAAGGGTATTTCGA
66 TACAAGGGTATTTCGA
28637578 TAATT
1 TAATT
28637583 TTTTAAATCG
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (81 bp):
TAATTCTACCCTATAGGGGTATTTCAGTATTTCTACCCTACAAGGGTATTTCGATAATTCTACCC
TACAAGGGTATTTCGA
Found at i:28637771 original size:80 final size:78
Alignment explanation
Indices: 28637618--28637905 Score: 285
Period size: 81 Copynumber: 3.6 Consensus size: 78
28637608 TTCTGTAAAT
* * * * ** ** *
28637618 CAGGGGTACTTTGGTAATTTTACAAGTCGATGGTATTTCAATAATTTTACAGGTCGAGGGTA-TT
1 CAGGGGTATTTTGGTAATTTTACAA-ACTAGGGTATTTTGATAATTTTACAAATAG-GGGTATTT
* *
28637682 TCAGTAATTTCACAAA
64 TGA-TAATTTTACAAA
28637698 TCAGGGGTATTTTGGTAATTTTACAAACTAGGGTATTTTGATAATTTTACAAACTAGGGGTATTT
1 -CAGGGGTATTTTGGTAATTTTACAAACTAGGGTATTTTGATAATTTTACAAA-TAGGGGTATTT
28637763 TGATAATTTTACAAA
64 TGATAATTTTACAAA
* * * *
28637778 CTAGGGGTATTTTGGTAATTTTACAAAATAGGGGTATTTTGATAATTTCATAAATAAAGGGTATT
1 C-AGGGGTATTTTGGTAATTTTACAAACTA-GGGTATTTTGATAATTTTACAAAT-AGGGGTATT
*
28637843 TTGGTAATTTTACAAA
63 TTGATAATTTTACAAA
* * * *
28637859 -AAGGGTATTTTGGTGATTTTATAAACCAAGGGTATTTT-AGTAATTTT
1 CAGGGGTATTTTGGTAATTTTACAAA-CTAGGGTATTTTGA-TAATTTT
28637906 GTAAATCGAG
Statistics
Matches: 178, Mismatches: 22, Indels: 16
0.82 0.10 0.07
Matches are distributed among these distances:
78 1 0.01
79 38 0.21
80 65 0.37
81 74 0.42
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (78 bp):
CAGGGGTATTTTGGTAATTTTACAAACTAGGGTATTTTGATAATTTTACAAATAGGGGTATTTTG
ATAATTTTACAAA
Found at i:28637810 original size:54 final size:54
Alignment explanation
Indices: 28637674--28637905 Score: 285
Period size: 54 Copynumber: 4.4 Consensus size: 54
28637664 TTACAGGTCG
** * *
28637674 AGGGTATTTCAGTAATTTCAC-AAATCAGGGGTATTTTGGTAATTTTACAAACT-
1 AGGGTATTTTGGTAATTTTACAAAAT-AGGGGTATTTTGATAATTTTACAAACTA
* *
28637727 AGGGTATTTTGATAATTTTACAAACTAGGGGTATTTTGATAATTTTACAAACTA
1 AGGGTATTTTGGTAATTTTACAAAATAGGGGTATTTTGATAATTTTACAAACTA
* * *
28637781 GGGGTATTTTGGTAATTTTACAAAATAGGGGTATTTTGATAATTTCATAAA-TAA
1 AGGGTATTTTGGTAATTTTACAAAATAGGGGTATTTTGATAATTTTACAAACT-A
* * * *
28637835 AGGGTATTTTGGTAATTTTACAAAA-A-GGGTATTTTGGTGATTTTATAAACCA
1 AGGGTATTTTGGTAATTTTACAAAATAGGGGTATTTTGATAATTTTACAAACTA
*
28637887 AGGGTATTTTAGTAATTTT
1 AGGGTATTTTGGTAATTTT
28637906 GTAAATCGAG
Statistics
Matches: 158, Mismatches: 17, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
52 39 0.25
53 45 0.28
54 74 0.47
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.41
Consensus pattern (54 bp):
AGGGTATTTTGGTAATTTTACAAAATAGGGGTATTTTGATAATTTTACAAACTA
Found at i:28637910 original size:27 final size:27
Alignment explanation
Indices: 28637564--28637919 Score: 256
Period size: 27 Copynumber: 13.3 Consensus size: 27
28637554 TTCTACCCTA
* * **
28637564 CAAGGGTATTTCGATAATTTTTTAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* *** * **
28637591 CGAGGGTAAAATGGTAATTCTGTAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* * *
28637618 CAGGGGTACTTTGGTAATTTTACAAGT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* * *** **
28637645 CGATGGTATTTCAATAATTTTACAGGT
1 CAAGGGTATTTTGGTAATTTTACAAAT
* ** *
28637672 CGAGGGTATTTCAGTAATTTCACAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
*
28637699 CAGGGGTATTTTGGTAATTTTACAAA-
1 CAAGGGTATTTTGGTAATTTTACAAAT
* *
28637725 CTAGGGTATTTTGATAATTTTACAAA-
1 CAAGGGTATTTTGGTAATTTTACAAAT
* *
28637751 CTAGGGGTATTTTGATAATTTTACAAA-
1 C-AAGGGTATTTTGGTAATTTTACAAAT
*
28637778 CTAGGGGTATTTTGGTAATTTTACAAAAT
1 C-AAGGGTATTTTGGTAATTTTAC-AAAT
* * * *
28637807 -AGGGGTATTTTGATAATTTCATAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
*
28637833 AAAGGGTATTTTGGTAATTTTACAAA-
1 CAAGGGTATTTTGGTAATTTTACAAAT
* * *
28637859 -AAGGGTATTTTGGTGATTTTATAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAT
* **
28637885 CAAGGGTATTTTAGTAATTTTGTAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAT
*
28637912 CGAGGGTA
1 CAAGGGTA
28637920 AAACAGTAAT
Statistics
Matches: 268, Mismatches: 55, Indels: 12
0.80 0.16 0.04
Matches are distributed among these distances:
25 23 0.09
26 28 0.10
27 214 0.80
28 3 0.01
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.39
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTACAAAT
Found at i:28637927 original size:27 final size:27
Alignment explanation
Indices: 28637898--28638186 Score: 371
Period size: 27 Copynumber: 10.7 Consensus size: 27
28637888 GGGTATTTTA
* *
28637898 GTAATTTTGTAAATCGAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
28637925 GTAATTCTGTAAATCAAGGGTAAAACT
1 GTAATTCTGTAAATCGAGGGTAAAACG
28637952 GTAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
28637979 GTAATTCTATAAATCGAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACG
* * ** * *
28638006 GTAATTTTATAAATTAAAGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* * *
28638033 GTAATTCTATAAATTGAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
28638060 ATAATTCTGTCAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
28638087 GTAATTCTGTAAATTGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
28638114 GTAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* * *
28638141 GTAATTTTGTAACTCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
28638168 GTAATTTTGTAAATTGAGG
1 GTAATTCTGTAAATCGAGG
28638187 ATATTTGGGT
Statistics
Matches: 230, Mismatches: 32, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 230 1.00
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.30
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAACG
Found at i:28640812 original size:26 final size:26
Alignment explanation
Indices: 28640783--28640835 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
28640773 AGTAAACATG
28640783 TAATTGTTTTCTATTTATTTGAACGA
1 TAATTGTTTTCTATTTATTTGAACGA
28640809 TAATTGTTTTCTATTTATTTGAACGA
1 TAATTGTTTTCTATTTATTTGAACGA
28640835 T
1 T
28640836 GAATAAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (26 bp):
TAATTGTTTTCTATTTATTTGAACGA
Found at i:28650336 original size:16 final size:16
Alignment explanation
Indices: 28650315--28650347 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
28650305 ACCATAGAGA
*
28650315 AAGAAGTCTTCGGGTT
1 AAGAAGACTTCGGGTT
28650331 AAGAAGACTTCGGGTT
1 AAGAAGACTTCGGGTT
28650347 A
1 A
28650348 TGTCGCTTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.12, G:0.30, T:0.27
Consensus pattern (16 bp):
AAGAAGACTTCGGGTT
Found at i:28655454 original size:27 final size:27
Alignment explanation
Indices: 28655406--28655752 Score: 385
Period size: 27 Copynumber: 12.9 Consensus size: 27
28655396 AATACTTTAG
* *** *
28655406 TTTACCAAATTACTAAAATACCCTCAA
1 TTTACAAAATTACTATTTTACCCTCGA
28655433 TTTACAAAATTACTATTTTACCCTCGA
1 TTTACAAAATTACTATTTTACCCTCGA
* * **
28655460 TTTACAGAATTA-TCGTTTTAATCTCGA
1 TTTACAAAATTACT-ATTTTACCCTCGA
* * *
28655487 TTTACAGAATTACTGTTTTACCCTTGA
1 TTTACAAAATTACTATTTTACCCTCGA
* * *
28655514 TTTACAAAATTA-TCGTTTTACCTTTGA
1 TTTACAAAATTACT-ATTTTACCCTCGA
*
28655541 TTTACAGAATTACTATTTTACCCTCGA
1 TTTACAAAATTACTATTTTACCCTCGA
28655568 TTTACAAAATTACTATTTTACCCTCGA
1 TTTACAAAATTACTATTTTACCCTCGA
** **
28655595 TTTACAAAATTACCGTTTTACCCTTAA
1 TTTACAAAATTACTATTTTACCCTCGA
28655622 TTTACAAAATTACTATTTTACCCTCGA
1 TTTACAAAATTACTATTTTACCCTCGA
* *
28655649 TTTACAGAATTACTATTTTACCCTTGA
1 TTTACAAAATTACTATTTTACCCTCGA
* * * *
28655676 TTTACAGAATTATTGTTTTACCCTCAA
1 TTTACAAAATTACTATTTTACCCTCGA
*
28655703 TTTACAGAATTA-TCATTTTACCCTCGA
1 TTTACAAAATTACT-ATTTTACCCTCGA
* *
28655730 TTTATAAAATTACCATTTTACCC
1 TTTACAAAATTACTATTTTACCC
28655753 CTAGGGTGTT
Statistics
Matches: 276, Mismatches: 38, Indels: 12
0.85 0.12 0.04
Matches are distributed among these distances:
26 3 0.01
27 271 0.98
28 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (27 bp):
TTTACAAAATTACTATTTTACCCTCGA
Found at i:28656108 original size:26 final size:27
Alignment explanation
Indices: 28656079--28656138 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
28656069 ACATATATAT
*
28656079 ATATCTGT-TCTGGTGGCCTAGCCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
* * *
28656105 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
28656132 ATATCTG
1 ATATCTG
28656139 GCAGCCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (27 bp):
ATATCTGTATCTGGTGACCTAGCCACA
Found at i:28656322 original size:6 final size:6
Alignment explanation
Indices: 28656257--28656387 Score: 72
Period size: 6 Copynumber: 21.3 Consensus size: 6
28656247 TTGCATTCGC
* * * *
28656257 ATTCTG ATTTTG ATTCTG -TTACCTG ATACTA ATTCTG ATTCTA ATTCTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* * * * *
28656306 -TCACCTA ATTCTG ATTCTG ATTCTG ATTTTG ATTCTG -TCACCTG TTTCTG
1 AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG
* *
28656356 ATTCTG ATTCTT ATTTTG ATTCT- AGTTCTG AT
1 ATTCTG ATTCTG ATTCTG ATTCTG A-TTCTG AT
28656388 AATGTTTCTT
Statistics
Matches: 93, Mismatches: 21, Indels: 22
0.68 0.15 0.16
Matches are distributed among these distances:
5 5 0.05
6 76 0.82
7 9 0.10
8 3 0.03
ACGTcount: A:0.19, C:0.18, G:0.13, T:0.50
Consensus pattern (6 bp):
ATTCTG
Found at i:28656355 original size:31 final size:31
Alignment explanation
Indices: 28656257--28656364 Score: 108
Period size: 31 Copynumber: 3.3 Consensus size: 31
28656247 TTGCATTCGC
* * *
28656257 ATTCTGATTTTGATTCTGTTACCTGATACTA
1 ATTCTGATTTTGATTCTGTCACCTGATTCTG
* *
28656288 ATTCTGATTCTAATTCTGTCACCTAATTCTGATTCTG
1 ATTCTGATTTTGATTCTGTCA-C-----CTGATTCTG
*
28656325 ATTCTGATTTTGATTCTGTCACCTGTTTCTG
1 ATTCTGATTTTGATTCTGTCACCTGATTCTG
28656356 ATTCTGATT
1 ATTCTGATT
28656365 CTTATTTTGA
Statistics
Matches: 63, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
31 35 0.56
32 1 0.02
36 1 0.02
37 26 0.41
ACGTcount: A:0.19, C:0.19, G:0.13, T:0.49
Consensus pattern (31 bp):
ATTCTGATTTTGATTCTGTCACCTGATTCTG
Found at i:28656372 original size:37 final size:37
Alignment explanation
Indices: 28656257--28656378 Score: 139
Period size: 37 Copynumber: 3.5 Consensus size: 37
28656247 TTGCATTCGC
* * * *
28656257 ATTCTGATTTTGATTCTGTTACCTGATACTAATTCTG
1 ATTCTGATTTTGATTCTGTCACCTAATTCTGATTCTG
28656294 ATTCT-A-----ATTCTGTCACCTAATTCTGATTCTG
1 ATTCTGATTTTGATTCTGTCACCTAATTCTGATTCTG
**
28656325 ATTCTGATTTTGATTCTGTCACCTGTTTCTGATTCTG
1 ATTCTGATTTTGATTCTGTCACCTAATTCTGATTCTG
*
28656362 ATTCTTATTTTGATTCT
1 ATTCTGATTTTGATTCT
28656379 AGTTCTGATA
Statistics
Matches: 72, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
31 26 0.36
32 1 0.01
36 1 0.01
37 44 0.61
ACGTcount: A:0.19, C:0.18, G:0.12, T:0.51
Consensus pattern (37 bp):
ATTCTGATTTTGATTCTGTCACCTAATTCTGATTCTG
Found at i:28659155 original size:21 final size:21
Alignment explanation
Indices: 28659131--28659173 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
28659121 CGGAAGGGAA
28659131 AGTGGAAACACACAAAGCTAG
1 AGTGGAAACACACAAAGCTAG
28659152 AGTGGAAACACACAAAGCTAG
1 AGTGGAAACACACAAAGCTAG
28659173 A
1 A
28659174 CTTGTAGGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.49, C:0.19, G:0.23, T:0.09
Consensus pattern (21 bp):
AGTGGAAACACACAAAGCTAG
Found at i:28669613 original size:25 final size:26
Alignment explanation
Indices: 28669584--28669645 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 26
28669574 TTTTACTGTA
28669584 TTTATTATTACG-GATATTT-TAAATT
1 TTTATTATTA-GAGATATTTATAAATT
* *
28669609 TTTATGATTAGATATATTTATAAATT
1 TTTATTATTAGAGATATTTATAAATT
28669635 TATTATTATTA
1 T-TTATTATTA
28669646 TAATTATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
24 1 0.03
25 15 0.48
26 7 0.23
27 8 0.26
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.56
Consensus pattern (26 bp):
TTTATTATTAGAGATATTTATAAATT
Found at i:28670681 original size:47 final size:49
Alignment explanation
Indices: 28670611--28670719 Score: 125
Period size: 47 Copynumber: 2.2 Consensus size: 49
28670601 TTCAGTTTTT
**
28670611 TTTCTTCTTCTATTTTCTTTTCTTTTCTC-C-TCTCTTCATCTACTTCC
1 TTTCTTCTTCTATTTTCCCTTCTTTTCTCTCTTCTCTTCATCTACTTCC
*
28670658 TTTCTTCTTCT-TCTTTCCCTTCTTTTCTCTTCTTTTCTCTTCATCTACTTTC
1 TTTCTTCTTCTAT-TTTCCCTTCTTTTCTC-TC--TTCTCTTCATCTACTTCC
28670710 TCTTCTTCTT
1 T-TTCTTCTT
28670720 TTCCCCCATA
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
46 1 0.02
47 25 0.48
49 1 0.02
52 17 0.33
53 8 0.15
ACGTcount: A:0.05, C:0.32, G:0.00, T:0.63
Consensus pattern (49 bp):
TTTCTTCTTCTATTTTCCCTTCTTTTCTCTCTTCTCTTCATCTACTTCC
Found at i:28670689 original size:10 final size:10
Alignment explanation
Indices: 28670623--28670699 Score: 55
Period size: 10 Copynumber: 7.0 Consensus size: 10
28670613 TCTTCTTCTA
*
28670623 TTTTCTTTTC
1 TTTTCTCTTC
28670633 TTTTCTCCTCTC
1 TTTTCT-CT-TC
*
28670645 TTCATCTACTTC
1 TT-TTCT-CTTC
*
28670657 CTTTCTTCTTC
1 TTTTC-TCTTC
*
28670668 TTCTTTCCCTTC
1 -T-TTTCTCTTC
28670680 TTTTCTCTTC
1 TTTTCTCTTC
28670690 TTTTCTCTTC
1 TTTTCTCTTC
28670700 ATCTACTTTC
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
10 24 0.45
11 8 0.15
12 12 0.23
13 9 0.17
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.64
Consensus pattern (10 bp):
TTTTCTCTTC
Found at i:28670720 original size:47 final size:49
Alignment explanation
Indices: 28670625--28670720 Score: 124
Period size: 52 Copynumber: 1.9 Consensus size: 49
28670615 TTCTTCTATT
*
28670625 TTCTTTTCTTTTCTCCTCTCTTCATCTACTTCCTTTCTTCTTCTTCTTTCCC
1 TTCTTTTCTCTTCTCCTCTCTTCATCTA---CCTTTCTTCTTCTTCTTTCCC
**
28670677 TTCTTTTCTCTTCTTTTCTCTTCATCTA-CTTTC-TCTTCTTCTTT
1 TTCTTTTCTCTTCTCCTCTCTTCATCTACCTTTCTTCTTCTTCTTT
28670721 TCCCCCATAG
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
47 11 0.27
48 5 0.12
52 25 0.61
ACGTcount: A:0.04, C:0.33, G:0.00, T:0.62
Consensus pattern (49 bp):
TTCTTTTCTCTTCTCCTCTCTTCATCTACCTTTCTTCTTCTTCTTTCCC
Found at i:28672478 original size:274 final size:274
Alignment explanation
Indices: 28671989--28672532 Score: 1088
Period size: 274 Copynumber: 2.0 Consensus size: 274
28671979 TTTTACCCTT
28671989 AGGAGCAAAATTACTGATATACCCCTAGGGTTAAGGTTGACCTGAATGCATGTTTGACTGTTACT
1 AGGAGCAAAATTACTGATATACCCCTAGGGTTAAGGTTGACCTGAATGCATGTTTGACTGTTACT
28672054 GTTTACTGCATGCCATGTTATTATTATTTGATGCATGGGACTGGGTTATTGATGGAGGAAGTACT
66 GTTTACTGCATGCCATGTTATTATTATTTGATGCATGGGACTGGGTTATTGATGGAGGAAGTACT
28672119 GAAAGTGGCTTGACCACGTACTGGAGGCTTTGCCTCAACTTACTGATATCTGAGCAACTATGCTG
131 GAAAGTGGCTTGACCACGTACTGGAGGCTTTGCCTCAACTTACTGATATCTGAGCAACTATGCTG
28672184 CAACTGTGGAGTGTAGGGCTGGGTGGGTTGAGCTATTCCCCACATGGAGTGTAGCGATTGGTTAT
196 CAACTGTGGAGTGTAGGGCTGGGTGGGTTGAGCTATTCCCCACATGGAGTGTAGCGATTGGTTAT
28672249 AGGCTGGGTTGGGC
261 AGGCTGGGTTGGGC
28672263 AGGAGCAAAATTACTGATATACCCCTAGGGTTAAGGTTGACCTGAATGCATGTTTGACTGTTACT
1 AGGAGCAAAATTACTGATATACCCCTAGGGTTAAGGTTGACCTGAATGCATGTTTGACTGTTACT
28672328 GTTTACTGCATGCCATGTTATTATTATTTGATGCATGGGACTGGGTTATTGATGGAGGAAGTACT
66 GTTTACTGCATGCCATGTTATTATTATTTGATGCATGGGACTGGGTTATTGATGGAGGAAGTACT
28672393 GAAAGTGGCTTGACCACGTACTGGAGGCTTTGCCTCAACTTACTGATATCTGAGCAACTATGCTG
131 GAAAGTGGCTTGACCACGTACTGGAGGCTTTGCCTCAACTTACTGATATCTGAGCAACTATGCTG
28672458 CAACTGTGGAGTGTAGGGCTGGGTGGGTTGAGCTATTCCCCACATGGAGTGTAGCGATTGGTTAT
196 CAACTGTGGAGTGTAGGGCTGGGTGGGTTGAGCTATTCCCCACATGGAGTGTAGCGATTGGTTAT
28672523 AGGCTGGGTT
261 AGGCTGGGTT
28672533 CGGCTTGCAT
Statistics
Matches: 270, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
274 270 1.00
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.31
Consensus pattern (274 bp):
AGGAGCAAAATTACTGATATACCCCTAGGGTTAAGGTTGACCTGAATGCATGTTTGACTGTTACT
GTTTACTGCATGCCATGTTATTATTATTTGATGCATGGGACTGGGTTATTGATGGAGGAAGTACT
GAAAGTGGCTTGACCACGTACTGGAGGCTTTGCCTCAACTTACTGATATCTGAGCAACTATGCTG
CAACTGTGGAGTGTAGGGCTGGGTGGGTTGAGCTATTCCCCACATGGAGTGTAGCGATTGGTTAT
AGGCTGGGTTGGGC
Found at i:28677759 original size:43 final size:43
Alignment explanation
Indices: 28677712--28677819 Score: 180
Period size: 43 Copynumber: 2.5 Consensus size: 43
28677702 CATTATGCCC
*
28677712 GCTAGGCACGAAGGCCCGAATACACATCACCGACATGAAGCCT
1 GCTAGGCACGAAGGCCCGAATACACATCACCGACACGAAGCCT
* * *
28677755 GCTAGGCACAAAGGCCTGAATACACATCACCGGCACGAAGCCT
1 GCTAGGCACGAAGGCCCGAATACACATCACCGACACGAAGCCT
28677798 GCTAGGCACGAAGGCCCGAATA
1 GCTAGGCACGAAGGCCCGAATA
28677820 TAATAGTAGC
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.32, C:0.31, G:0.25, T:0.11
Consensus pattern (43 bp):
GCTAGGCACGAAGGCCCGAATACACATCACCGACACGAAGCCT
Found at i:28677860 original size:38 final size:38
Alignment explanation
Indices: 28677812--28677935 Score: 122
Period size: 38 Copynumber: 3.2 Consensus size: 38
28677802 GGCACGAAGG
* ** * * *
28677812 CCCGAATATAATAGTAGCACTAGGCCTGCGGGATTTAT
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
28677850 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
* ** * * *
28677888 CCCAGATATTTTACCAGCACGAAGCTTACGGGTCTTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGG-ATTTAA
28677927 GCCCGGATA
1 -CCCGGATA
28677936 CACATCAAAT
Statistics
Matches: 71, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
38 59 0.83
39 5 0.07
40 7 0.10
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (38 bp):
CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
Found at i:28688200 original size:27 final size:27
Alignment explanation
Indices: 28688170--28688660 Score: 574
Period size: 27 Copynumber: 18.2 Consensus size: 27
28688160 AAAGTACTCC
*
28688170 CGATTTAAAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
28688197 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** *
28688224 CGATTTTTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
28688251 CGACTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
28688278 C-AGTTTACAGAATTACCGTTTTACCTT
1 CGA-TTTACAGAATTACCGTTTTACCCT
*
28688305 CGATTTACAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
28688332 C-AGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
* *
28688359 CGATTTATAGAATTATCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** *
28688386 CGATTTGTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
28688413 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* * **
28688440 CAATTTATAGAATTACTATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
28688467 CGATTTATAGAATTACCATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* * ***
28688494 CAATTTATAGAATTATTATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
28688521 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* ** * *
28688548 CAATTTGTAAAATTACCATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* * * *
28688575 TGATTTACAGAATTACTGGTTTACCTT
1 CGATTTACAGAATTACCGTTTTACCCT
* * *
28688602 C-AGTTTACAAAATTATCGTTTTACCTT
1 CGA-TTTACAGAATTACCGTTTTACCCT
* *
28688629 TGATTTATAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
28688656 TGATT
1 CGATT
28688661 GTGAAATTAC
Statistics
Matches: 395, Mismatches: 63, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
26 3 0.01
27 389 0.98
28 3 0.01
ACGTcount: A:0.28, C:0.22, G:0.09, T:0.41
Consensus pattern (27 bp):
CGATTTACAGAATTACCGTTTTACCCT
Found at i:28688731 original size:54 final size:54
Alignment explanation
Indices: 28688665--28688861 Score: 234
Period size: 54 Copynumber: 3.6 Consensus size: 54
28688655 TTGATTGTGA
* ** *
28688665 AATTACTGAAATACCCCTATAGGGTAGAATTTTCGAAATACCCCTATAGGGTAG
1 AATTACTGAAATACCCTTATAGGGTAGAATTACCAAAATACCCCTATAGGGTAG
* * * *
28688719 AATTACTAAAATACCCTTATAGGATAGAATTACCAAAATACCCCTGTAAGGTAG
1 AATTACTGAAATACCCTTATAGGGTAGAATTACCAAAATACCCCTATAGGGTAG
* * *
28688773 AATTA-TCGAAACACCCTTGTAGGGTAGAAATACCAAAATACCCCTATAGGGTAG
1 AATTACT-GAAATACCCTTATAGGGTAGAATTACCAAAATACCCCTATAGGGTAG
* * * * *
28688827 AATTACCGAGATACCCTTGTGGGGTAAAATTACCA
1 AATTACTGAAATACCCTTATAGGGTAGAATTACCA
28688862 TTTTGCCCCT
Statistics
Matches: 120, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
53 1 0.01
54 119 0.99
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.25
Consensus pattern (54 bp):
AATTACTGAAATACCCTTATAGGGTAGAATTACCAAAATACCCCTATAGGGTAG
Found at i:28688851 original size:27 final size:27
Alignment explanation
Indices: 28688673--28688861 Score: 198
Period size: 27 Copynumber: 7.0 Consensus size: 27
28688663 GAAATTACTG
** *
28688673 AAATACCCCTATAGGGTAGAATTTTCG
1 AAATACCCCTATAGGGTAGAATTACCA
*
28688700 AAATACCCCTATAGGGTAGAATTACTA
1 AAATACCCCTATAGGGTAGAATTACCA
* *
28688727 AAATACCCTTATAGGATAGAATTACCA
1 AAATACCCCTATAGGGTAGAATTACCA
* * * *
28688754 AAATACCCCTGTAAGGTAGAATTATCG
1 AAATACCCCTATAGGGTAGAATTACCA
* * * *
28688781 AAACACCCTTGTAGGGTAGAAATACCA
1 AAATACCCCTATAGGGTAGAATTACCA
*
28688808 AAATACCCCTATAGGGTAGAATTACCG
1 AAATACCCCTATAGGGTAGAATTACCA
* * * * *
28688835 AGATACCCTTGTGGGGTAAAATTACCA
1 AAATACCCCTATAGGGTAGAATTACCA
28688862 TTTTGCCCCT
Statistics
Matches: 132, Mismatches: 30, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 132 1.00
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (27 bp):
AAATACCCCTATAGGGTAGAATTACCA
Found at i:28688858 original size:81 final size:81
Alignment explanation
Indices: 28688673--28688858 Score: 237
Period size: 81 Copynumber: 2.3 Consensus size: 81
28688663 GAAATTACTG
* * * * * *
28688673 AAATACCCCTATAGGGTAGAATTTTCGAAATACCCCTATAGGGTAGAATTACTAAAATACCCTTA
1 AAATACCCCTGTAGGGTAGAATTATCGAAACACCCCTATAGGGTAGAAATACCAAAATACCCCTA
28688738 TAGGATAGAATTACCA
66 TAGGATAGAATTACCA
* * *
28688754 AAATACCCCTGTAAGGTAGAATTATCGAAACACCCTTGTAGGGTAGAAATACCAAAATACCCCTA
1 AAATACCCCTGTAGGGTAGAATTATCGAAACACCCCTATAGGGTAGAAATACCAAAATACCCCTA
* *
28688819 TAGGGTAGAATTACCG
66 TAGGATAGAATTACCA
* * * *
28688835 AGATACCCTTGTGGGGTAAAATTA
1 AAATACCCCTGTAGGGTAGAATTA
28688859 CCATTTTGCC
Statistics
Matches: 89, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
81 89 1.00
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (81 bp):
AAATACCCCTGTAGGGTAGAATTATCGAAACACCCCTATAGGGTAGAAATACCAAAATACCCCTA
TAGGATAGAATTACCA
Found at i:28689101 original size:27 final size:27
Alignment explanation
Indices: 28689062--28689140 Score: 99
Period size: 27 Copynumber: 3.0 Consensus size: 27
28689052 GGAAGCGTTC
* *
28689062 TGGTGGCTATGCCACAAATATATGTTT
1 TGGTGGCTCTGCCACAAATATCTGTTT
28689089 TGGTGGCTCTGCCA-AAATATCTGTATT
1 TGGTGGCTCTGCCACAAATATCTGT-TT
* *
28689116 TGGTGACTCTGTCAC-AATATCTGTT
1 TGGTGGCTCTGCCACAAATATCTGTT
28689141 GACCGATCAC
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
26 10 0.22
27 36 0.78
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.38
Consensus pattern (27 bp):
TGGTGGCTCTGCCACAAATATCTGTTT
Found at i:28689244 original size:22 final size:22
Alignment explanation
Indices: 28689210--28689268 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 22
28689200 CCCGTTATTA
* *
28689210 ATGGCTCTATGCCAACCTAAAT
1 ATGGCTTTGTGCCAACCTAAAT
* * * *
28689232 ATGGCTTTGTGCCATCTTGACT
1 ATGGCTTTGTGCCAACCTAAAT
*
28689254 ATGGCTTCGTGCCAA
1 ATGGCTTTGTGCCAA
28689269 ACGTATTTAC
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.32
Consensus pattern (22 bp):
ATGGCTTTGTGCCAACCTAAAT
Found at i:28689455 original size:27 final size:27
Alignment explanation
Indices: 28689433--28689501 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
28689423 TAGGTGGGTT
*
28689433 TGCCACATTATCTG-ATTCTGGTGGCTC
1 TGCCACAATATCTGTA-TCTGGTGGCTC
*
28689460 TGCCACAATATCTGTATCTGGTGACTC
1 TGCCACAATATCTGTATCTGGTGGCTC
* *
28689487 TGTCACGATATCTGT
1 TGCCACAATATCTGT
28689502 TTTGGCAGCC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
27 36 0.97
28 1 0.03
ACGTcount: A:0.19, C:0.25, G:0.20, T:0.36
Consensus pattern (27 bp):
TGCCACAATATCTGTATCTGGTGGCTC
Found at i:28689633 original size:6 final size:6
Alignment explanation
Indices: 28689624--28689798 Score: 148
Period size: 6 Copynumber: 28.8 Consensus size: 6
28689614 TTGCATTCAC
* * * * *
28689624 ATTCTG ATTCTG ATTCTG -TCACATA ATTCTG ATTCTG -TTACTA ATACTA
1 ATTCTG ATTCTG ATTCTG AT-TC-TG ATTCTG ATTCTG ATT-CTG ATTCTG
* *
28689673 ATTCTG ATTCTG ATTCTG -TTACTG ATTCTG ATTCTG ATTCT- ATCACCTA
1 ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG ATTCTG AT--TCTG
*
28689722 ATTCTG ATTCTG ATTCTG ATTCTG -TTACTA ATAT-TG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATT-CTG AT-TCTG ATTCTG ATTCTG
28689770 ATTCTG -TTACTG ATTCTG ATTCTG ATTCT
1 ATTCTG ATT-CTG ATTCTG ATTCTG ATTCT
28689799 CATTTTGGTT
Statistics
Matches: 140, Mismatches: 13, Indels: 32
0.76 0.07 0.17
Matches are distributed among these distances:
5 12 0.09
6 114 0.81
7 10 0.07
8 4 0.03
ACGTcount: A:0.22, C:0.18, G:0.13, T:0.48
Consensus pattern (6 bp):
ATTCTG
Found at i:28689723 original size:49 final size:49
Alignment explanation
Indices: 28689624--28689739 Score: 166
Period size: 49 Copynumber: 2.4 Consensus size: 49
28689614 TTGCATTCAC
28689624 ATTCTGATTCTGATTCTGTCACATAATTCTGATTCTGTTACTAATACTA
1 ATTCTGATTCTGATTCTGTCACATAATTCTGATTCTGTTACTAATACTA
* *
28689673 ATTCTGATTCTGATTCTGTTAC-TGATTCTGATTCTGATT-CT-ATCACCTA
1 ATTCTGATTCTGATTCTGTCACATAATTCTGATTCTG-TTACTAAT-A-CTA
28689722 ATTCTGATTCTGATTCTG
1 ATTCTGATTCTGATTCTG
28689740 ATTCTGTTAC
Statistics
Matches: 62, Mismatches: 2, Indels: 6
0.89 0.03 0.09
Matches are distributed among these distances:
47 2 0.03
48 16 0.26
49 44 0.71
ACGTcount: A:0.22, C:0.19, G:0.12, T:0.47
Consensus pattern (49 bp):
ATTCTGATTCTGATTCTGTCACATAATTCTGATTCTGTTACTAATACTA
Found at i:28689760 original size:73 final size:73
Alignment explanation
Indices: 28689624--28689786 Score: 192
Period size: 73 Copynumber: 2.2 Consensus size: 73
28689614 TTGCATTCAC
* *
28689624 ATTCTGATTCTGATTCTGTCACATAATTCTGATTCTGTTACTAATACTAATTCTGATTCTGATTC
1 ATTCTGATTCTGATTCTATCACATAATTCTGATTCTGTTACTAATACTAATTCTAATTCTGATTC
28689689 TG-TTACTG
66 TGATT-CTG
* * * *
28689697 ATTCTGATTCTGATTCTATCACCTAATTCTGATTCTGATT-CTGATTCT-GTTACTAATAT-TGA
1 ATTCTGATTCTGATTCTATCACATAATTCTGATTCTG-TTACTAATACTAATT-CTAAT-TCTGA
28689759 TTCTGATTCTG
63 TTCTGATTCTG
28689770 ATTCTG-TTACTGATTCT
1 ATTCTGATT-CTGATTCT
28689787 GATTCTGATT
Statistics
Matches: 79, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
72 4 0.05
73 70 0.89
74 5 0.06
ACGTcount: A:0.22, C:0.18, G:0.12, T:0.48
Consensus pattern (73 bp):
ATTCTGATTCTGATTCTATCACATAATTCTGATTCTGTTACTAATACTAATTCTAATTCTGATTC
TGATTCTG
Found at i:28689819 original size:30 final size:30
Alignment explanation
Indices: 28689649--28689798 Score: 197
Period size: 30 Copynumber: 5.2 Consensus size: 30
28689639 CTGTCACATA
* *
28689649 ATTCTGATTCTGTTACTAATACTAATTCTG
1 ATTCTGATTCTGTTACTAATTCTGATTCTG
*
28689679 ATTCTGATTCTGTTACTGATTCTGATTCTG
1 ATTCTGATTCTGTTACTAATTCTGATTCTG
28689709 ATTCT-A-TC----ACCTAATTCTGATTCTG
1 ATTCTGATTCTGTTA-CTAATTCTGATTCTG
28689734 ATTCTGATTCTGTTACTAATAT-TGATTCTG
1 ATTCTGATTCTGTTACTAAT-TCTGATTCTG
*
28689764 ATTCTGATTCTGTTACTGATTCTGATTCTG
1 ATTCTGATTCTGTTACTAATTCTGATTCTG
28689794 ATTCT
1 ATTCT
28689799 CATTTTGGTT
Statistics
Matches: 106, Mismatches: 5, Indels: 18
0.82 0.04 0.14
Matches are distributed among these distances:
24 1 0.01
25 19 0.18
26 1 0.01
27 2 0.02
28 2 0.02
29 2 0.02
30 77 0.73
31 2 0.02
ACGTcount: A:0.21, C:0.17, G:0.13, T:0.49
Consensus pattern (30 bp):
ATTCTGATTCTGTTACTAATTCTGATTCTG
Found at i:28691845 original size:27 final size:27
Alignment explanation
Indices: 28691815--28692304 Score: 610
Period size: 27 Copynumber: 18.1 Consensus size: 27
28691805 AAGTACTCCT
*
28691815 GATTTACAGAATTACTGTTTTACCCTC
1 GATTTACAGAATTACCGTTTTACCCTC
28691842 GATTTACAGAATTACCGTTTTACCCTC
1 GATTTACAGAATTACCGTTTTACCCTC
** *
28691869 GATTTTTAAAATTACCGTTTTACCCTC
1 GATTTACAGAATTACCGTTTTACCCTC
*
28691896 GATTTATAGAATTACCGTTTTACCCTC
1 GATTTACAGAATTACCGTTTTACCCTC
* * *
28691923 -AGTTTATAGAATTACCATTTTACCTTC
1 GA-TTTACAGAATTACCGTTTTACCCTC
*
28691950 GATTTATAGAATTACCGTTTTACCCTC
1 GATTTACAGAATTACCGTTTTACCCTC
* **
28691977 AATTTACAGAATTACTATTTTACCCTC
1 GATTTACAGAATTACCGTTTTACCCTC
*
28692004 GATTTATAGAATTACCGTTTTACCCTC
1 GATTTACAGAATTACCGTTTTACCCTC
** * *
28692031 GATTTGTAAAATTACCGTTTTACCCTT
1 GATTTACAGAATTACCGTTTTACCCTC
*
28692058 GATTTACAGAATTATCGTTTTACCCTC
1 GATTTACAGAATTACCGTTTTACCCTC
**
28692085 -AGTTTACAGAATTACTATTTTACCCTC
1 GA-TTTACAGAATTACCGTTTTACCCTC
**
28692112 GATTTACAGAATTATTGTTTTACCCTC
1 GATTTACAGAATTACCGTTTTACCCTC
*
28692139 -AGTTTACAGAATTACTGTTTTACCCTC
1 GA-TTTACAGAATTACCGTTTTACCCTC
28692166 GATTTACAGAATTACCGTTTTACCCTC
1 GATTTACAGAATTACCGTTTTACCCTC
* ** * *
28692193 AATTTGTAAAATTACCGTTTTACCCTT
1 GATTTACAGAATTACCGTTTTACCCTC
* *
28692220 GATTTACAGAATTACTGGTTTACCCTC
1 GATTTACAGAATTACCGTTTTACCCTC
* *
28692247 -AGTTTACAAAATTATCGTTTTACCCTC
1 GA-TTTACAGAATTACCGTTTTACCCTC
* *
28692274 GATTTACAGAATTACCATTTTACCCTT
1 GATTTACAGAATTACCGTTTTACCCTC
28692301 GATT
1 GATT
28692305 GTGAAATTAC
Statistics
Matches: 402, Mismatches: 53, Indels: 16
0.85 0.11 0.03
Matches are distributed among these distances:
26 4 0.01
27 394 0.98
28 4 0.01
ACGTcount: A:0.27, C:0.22, G:0.10, T:0.41
Consensus pattern (27 bp):
GATTTACAGAATTACCGTTTTACCCTC
Found at i:28692339 original size:27 final size:27
Alignment explanation
Indices: 28692309--28692503 Score: 196
Period size: 27 Copynumber: 7.2 Consensus size: 27
28692299 TTGATTGTGA
28692309 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * *
28692336 AATTTCCGAAATACCCCTCTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * *
28692363 AATTACTGAAATACCCTTATAGGATAG
1 AATTACTGAAATACCCCTGTAGGGTAG
**
28692390 AATTACCAAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
28692417 AATTA-TCGAAATACCCTTGTAGGGTAG
1 AATTACT-GAAATACCCCTGTAGGGTAG
* ** * *
28692444 AAATACCAAAATACCACTATAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * * *
28692471 AATTA-TCGACATACCCTTGTGGGGTAA
1 AATTACT-GAAATACCCCTGTAGGGTAG
28692498 AATTAC
1 AATTAC
28692504 CATTTTGCCC
Statistics
Matches: 133, Mismatches: 31, Indels: 7
0.78 0.18 0.04
Matches are distributed among these distances:
27 133 1.00
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.26
Consensus pattern (27 bp):
AATTACTGAAATACCCCTGTAGGGTAG
Found at i:28692377 original size:54 final size:54
Alignment explanation
Indices: 28692316--28692505 Score: 256
Period size: 54 Copynumber: 3.5 Consensus size: 54
28692306 TGAAATTACT
* * * *
28692316 GAAATACCCCTGTAGGGTAGAATTTCCGAAATACCCCTCTAGGGTAGAATTA-C
1 GAAATACCCTTGTAGGGTAGAATTACCAAAATACCCCTATAGGGTAGAATTATC
* * *
28692369 TGAAATACCCTTATAGGATAGAATTACCAAAATACCCCTGTAGGGTAGAATTATC
1 -GAAATACCCTTGTAGGGTAGAATTACCAAAATACCCCTATAGGGTAGAATTATC
* *
28692424 GAAATACCCTTGTAGGGTAGAAATACCAAAATACCACTATAGGGTAGAATTATC
1 GAAATACCCTTGTAGGGTAGAATTACCAAAATACCCCTATAGGGTAGAATTATC
* * *
28692478 GACATACCCTTGTGGGGTAAAATTACCA
1 GAAATACCCTTGTAGGGTAGAATTACCA
28692506 TTTTGCCCCT
Statistics
Matches: 120, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
54 119 0.99
55 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.25
Consensus pattern (54 bp):
GAAATACCCTTGTAGGGTAGAATTACCAAAATACCCCTATAGGGTAGAATTATC
Found at i:28692406 original size:81 final size:81
Alignment explanation
Indices: 28692317--28692502 Score: 232
Period size: 81 Copynumber: 2.3 Consensus size: 81
28692307 GAAATTACTG
* **
28692317 AAATACCCCTGTAGGGTAGAATT-TCCGAAATACCCCTCTAGGGTAGAATTACTGAAATACC-CT
1 AAATACCCCTGTAGGGTAGAATTAT-CGAAATACCCCTCTAGGGTAGAAATACCAAAATACCAC-
28692380 TATAGGATAGAATTACCA
64 TATAGGATAGAATTACCA
* *
28692398 AAATACCCCTGTAGGGTAGAATTATCGAAATACCCTTGTAGGGTAGAAATACCAAAATACCACTA
1 AAATACCCCTGTAGGGTAGAATTATCGAAATACCCCTCTAGGGTAGAAATACCAAAATACCACTA
* * *
28692463 TAGGGTAGAATTATCG
66 TAGGATAGAATTACCA
* * * *
28692479 ACATACCCTTGTGGGGTAAAATTA
1 AAATACCCCTGTAGGGTAGAATTA
28692503 CCATTTTGCC
Statistics
Matches: 91, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
81 89 0.98
82 2 0.02
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.26
Consensus pattern (81 bp):
AAATACCCCTGTAGGGTAGAATTATCGAAATACCCCTCTAGGGTAGAAATACCAAAATACCACTA
TAGGATAGAATTACCA
Found at i:28692741 original size:27 final size:27
Alignment explanation
Indices: 28692703--28692785 Score: 107
Period size: 27 Copynumber: 3.1 Consensus size: 27
28692693 CGGAGGAAGC
*
28692703 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCACAAATATCT
28692730 GTTCTGGTGGCTCTGCCA-AAATATCT
1 GTTCTGGTGGCTCTGCCACAAATATCT
* * *
28692756 GTATTTGGTGACTCTGTCAC-AATATCT
1 GT-TCTGGTGGCTCTGCCACAAATATCT
28692783 GTT
1 GTT
28692786 GACCGATCAC
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
26 11 0.22
27 39 0.78
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.37
Consensus pattern (27 bp):
GTTCTGGTGGCTCTGCCACAAATATCT
Found at i:28692887 original size:22 final size:22
Alignment explanation
Indices: 28692855--28692913 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
28692845 CCCGTTATTA
*
28692855 ATGGCTCTGTGCCAACCTAAAT
1 ATGGCTTTGTGCCAACCTAAAT
* * * *
28692877 ATGGCTTTGTGCCATCTTGACT
1 ATGGCTTTGTGCCAACCTAAAT
*
28692899 ATGGCTTCGTGCCAA
1 ATGGCTTTGTGCCAA
28692914 ACGTATTTAC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.32
Consensus pattern (22 bp):
ATGGCTTTGTGCCAACCTAAAT
Found at i:28693088 original size:25 final size:26
Alignment explanation
Indices: 28693060--28693147 Score: 79
Period size: 27 Copynumber: 3.3 Consensus size: 26
28693050 TTGTGCTACG
* * *
28693060 TATCTGTT-AGGTGGGTTTGCCACAT
1 TATCTGTTCAGGTGGCTCTGCCACAA
*
28693085 TATCTGATTCTGGTGGCTCTGCCACAA
1 TATCTG-TTCAGGTGGCTCTGCCACAA
* * * *
28693112 TATCTGTATCTGGTGACTCTGTCACGA
1 TATCTGT-TCAGGTGGCTCTGCCACAA
28693139 TATCTGTTC
1 TATCTGTTC
28693148 TGGCAGCCAT
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
25 6 0.11
26 5 0.09
27 42 0.79
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.39
Consensus pattern (26 bp):
TATCTGTTCAGGTGGCTCTGCCACAA
Found at i:28693107 original size:27 final size:25
Alignment explanation
Indices: 28693077--28693150 Score: 85
Period size: 27 Copynumber: 2.8 Consensus size: 25
28693067 TAGGTGGGTT
*
28693077 TGCCACATTATCTGATTCTGGTGGCTC
1 TGCCACA-TATCTG-TTCTGGTGACTC
28693104 TGCCACAATATCTGTATCTGGTGACTC
1 TGCCAC-ATATCTGT-TCTGGTGACTC
*
28693131 TGTCACGATATCTGTTCTGG
1 TGCCAC-ATATCTGTTCTGG
28693151 CAGCCATGCT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
26 6 0.14
27 35 0.83
28 1 0.02
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (25 bp):
TGCCACATATCTGTTCTGGTGACTC
Found at i:28693277 original size:6 final size:6
Alignment explanation
Indices: 28693268--28693527 Score: 191
Period size: 6 Copynumber: 42.8 Consensus size: 6
28693258 TTGCATTCAC
* * * * *
28693268 ATTCTG ATTCTG ATTCTG -TCACGTA ATTCTG ATTATG -TTACTA ATACTG
1 ATTCTG ATTCTG ATTCTG AT-TC-TG ATTCTG ATTCTG ATT-CTG ATTCTG
* * * * *
28693317 ATTCTG ATTCTG ATTTTG -TTACTG ATTCTA ATTCTG ATTTTG -TCACCTA
1 ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG ATTCTG AT--TCTG
*
28693366 ATTCTG ATTCTG ATTCTG ATTCTG -TTACTA ATAT-TG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATT-CTG AT-TCTG ATTCTG ATTCTG
* *
28693414 ATTCTG -TTACTG ATTCTG ATTCTG ATTCTG -TCACCTA ATTCTG ATTCTG
1 ATTCTG ATT-CTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG
*
28693463 ATTCTG ATTCTG -TTACTA ATAT-TG ATTCTG ATTCTG ATTCTG -TTACTG
1 ATTCTG ATTCTG ATT-CTG AT-TCTG ATTCTG ATTCTG ATTCTG ATT-CTG
28693511 ATTCTG ATTCTG ATTCT
1 ATTCTG ATTCTG ATTCT
28693528 CATTTTGGTT
Statistics
Matches: 201, Mismatches: 28, Indels: 50
0.72 0.10 0.18
Matches are distributed among these distances:
5 17 0.08
6 165 0.82
7 14 0.07
8 5 0.02
ACGTcount: A:0.21, C:0.17, G:0.14, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:28693317 original size:18 final size:19
Alignment explanation
Indices: 28693277--28693319 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
28693267 CATTCTGATT
* *
28693277 CTGATTCTGTCACGTAATT
1 CTGATTATGTCACGTAATA
*
28693296 CTGATTATGTTAC-TAATA
1 CTGATTATGTCACGTAATA
28693314 CTGATT
1 CTGATT
28693320 CTGATTCTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.44
Consensus pattern (19 bp):
CTGATTATGTCACGTAATA
Found at i:28693329 original size:30 final size:30
Alignment explanation
Indices: 28693293--28693527 Score: 260
Period size: 30 Copynumber: 8.2 Consensus size: 30
28693283 CTGTCACGTA
*
28693293 ATTCTGATTATGTTACTAATACTGATTCTG
1 ATTCTGATTCTGTTACTAATACTGATTCTG
* *
28693323 ATTCTGA-T-T-TT-GT--TACTGATTCTA
1 ATTCTGATTCTGTTACTAATACTGATTCTG
* * *
28693347 ATTCTGATTTTGTCACCTAATTCTGATTCTG
1 ATTCTGATTCTGTTA-CTAATACTGATTCTG
*
28693378 ATTCTGATTCTGTTACTAATATTGATTCTG
1 ATTCTGATTCTGTTACTAATACTGATTCTG
28693408 ATTCTGATTCTG----T--TACTGATTCTG
1 ATTCTGATTCTGTTACTAATACTGATTCTG
* *
28693432 ATTCTGATTCTGTCACCTAATTCTGATTCTG
1 ATTCTGATTCTGTTA-CTAATACTGATTCTG
*
28693463 ATTCTGATTCTGTTACTAATATTGATTCTG
1 ATTCTGATTCTGTTACTAATACTGATTCTG
* *
28693493 ATTCTGATTCTGTTACTGATTCTGATTCTG
1 ATTCTGATTCTGTTACTAATACTGATTCTG
28693523 ATTCT
1 ATTCT
28693528 CATTTTGGTT
Statistics
Matches: 173, Mismatches: 18, Indels: 28
0.79 0.08 0.13
Matches are distributed among these distances:
24 39 0.23
25 1 0.01
26 3 0.02
27 3 0.02
28 1 0.01
29 3 0.02
30 77 0.45
31 46 0.27
ACGTcount: A:0.21, C:0.16, G:0.14, T:0.49
Consensus pattern (30 bp):
ATTCTGATTCTGTTACTAATACTGATTCTG
Found at i:28693404 original size:73 final size:73
Alignment explanation
Indices: 28693268--28693431 Score: 167
Period size: 73 Copynumber: 2.2 Consensus size: 73
28693258 TTGCATTCAC
* * * *
28693268 ATTCTGATTCTGATTCTGTCACGTAATTCTGATTATGTTACTAATACTGATTCTGATTCTGATTT
1 ATTCTAATTCTGATTCTGTCACCTAATTCTGATTATGTTACTAATACTGATTCTAATTCTGATTC
28693333 TG-TTACTG
66 TGATT-CTG
* * * *
28693341 ATTCTAATTCTGATTTTGTCACCTAATTCTGATTCTGATT-CTGATTCTG-TTACTAATAT-TGA
1 ATTCTAATTCTGATTCTGTCACCTAATTCTGATTATG-TTACTAATACTGATT-CTAAT-TCTGA
28693403 TTCTGATTCTG
63 TTCTGATTCTG
*
28693414 ATTCT-GTTACTGATTCTG
1 ATTCTAATT-CTGATTCTG
28693432 ATTCTGATTC
Statistics
Matches: 76, Mismatches: 10, Indels: 10
0.79 0.10 0.10
Matches are distributed among these distances:
72 4 0.05
73 67 0.88
74 5 0.07
ACGTcount: A:0.21, C:0.16, G:0.14, T:0.49
Consensus pattern (73 bp):
ATTCTAATTCTGATTCTGTCACCTAATTCTGATTATGTTACTAATACTGATTCTAATTCTGATTC
TGATTCTG
Found at i:28693405 original size:85 final size:85
Alignment explanation
Indices: 28693293--28693527 Score: 425
Period size: 85 Copynumber: 2.8 Consensus size: 85
28693283 CTGTCACGTA
* * * * *
28693293 ATTCTGATTATGTTACTAATACTGATTCTGATTCTGATTTTGTTACTGATTCTAATTCTGATTTT
1 ATTCTGATTCTGTTACTAATATTGATTCTGATTCTGATTCTGTTACTGATTCTGATTCTGATTCT
28693358 GTCACCTAATTCTGATTCTG
66 GTCACCTAATTCTGATTCTG
28693378 ATTCTGATTCTGTTACTAATATTGATTCTGATTCTGATTCTGTTACTGATTCTGATTCTGATTCT
1 ATTCTGATTCTGTTACTAATATTGATTCTGATTCTGATTCTGTTACTGATTCTGATTCTGATTCT
28693443 GTCACCTAATTCTGATTCTG
66 GTCACCTAATTCTGATTCTG
28693463 ATTCTGATTCTGTTACTAATATTGATTCTGATTCTGATTCTGTTACTGATTCTGATTCTGATTCT
1 ATTCTGATTCTGTTACTAATATTGATTCTGATTCTGATTCTGTTACTGATTCTGATTCTGATTCT
28693528 CATTTTGGTT
Statistics
Matches: 145, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
85 145 1.00
ACGTcount: A:0.21, C:0.16, G:0.14, T:0.49
Consensus pattern (85 bp):
ATTCTGATTCTGTTACTAATATTGATTCTGATTCTGATTCTGTTACTGATTCTGATTCTGATTCT
GTCACCTAATTCTGATTCTG
Found at i:28699022 original size:32 final size:32
Alignment explanation
Indices: 28698956--28699023 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 32
28698946 TTTTTGTTAA
* *
28698956 TGTTGGATTCTAAAATTTTAGTTTATTATATT
1 TGTTGGATTCTAAAATTTTAGTCTATGATATT
28698988 TGTTGGATTCTAAAATTATTATGTCT-TGAT-TT
1 TGTTGGATTCTAAAATT-TTA-GTCTATGATATT
28699020 TGTT
1 TGTT
28699024 AGATATTGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 23 0.72
33 6 0.19
34 3 0.09
ACGTcount: A:0.25, C:0.04, G:0.15, T:0.56
Consensus pattern (32 bp):
TGTTGGATTCTAAAATTTTAGTCTATGATATT
Found at i:28699049 original size:27 final size:27
Alignment explanation
Indices: 28699019--28699091 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 27
28699009 TGTCTTGATT
28699019 TTGTTAGATATTGATTATGTTTCAAGC
1 TTGTTAGATATTGATTATGTTTCAAGC
*
28699046 TTGTTAGATATTGAATTTATTATGTTTTAAGC
1 TTGTTAGATATTG-----ATTATGTTTCAAGC
*
28699078 TTGTTGGATATTGA
1 TTGTTAGATATTGA
28699092 AATGATTGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
27 14 0.36
32 25 0.64
ACGTcount: A:0.26, C:0.04, G:0.19, T:0.51
Consensus pattern (27 bp):
TTGTTAGATATTGATTATGTTTCAAGC
Found at i:28699071 original size:32 final size:32
Alignment explanation
Indices: 28699032--28699092 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
28699022 TTAGATATTG
28699032 ATTATGTTTCAAGCTTGTTAGATATTGAATTT
1 ATTATGTTTCAAGCTTGTTAGATATTGAATTT
* *
28699064 ATTATGTTTTAAGCTTGTTGGATATTGAA
1 ATTATGTTTCAAGCTTGTTAGATATTGAA
28699093 ATGATTGACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.28, C:0.05, G:0.18, T:0.49
Consensus pattern (32 bp):
ATTATGTTTCAAGCTTGTTAGATATTGAATTT
Found at i:28700110 original size:22 final size:22
Alignment explanation
Indices: 28700042--28700130 Score: 92
Period size: 22 Copynumber: 4.0 Consensus size: 22
28700032 GATACTTTTA
28700042 ATGTGGTGTAATATTAGTTATGC
1 ATGTGGTGTAATATTAGTTAT-C
** *
28700065 ACT-TGG-ACAATATTGTTGTTATC
1 A-TGTGGTGTAATA-T-TAGTTATC
28700088 ATGTGGTGTAATATTAGTTATC
1 ATGTGGTGTAATATTAGTTATC
*
28700110 ATATGGTGTAATATTAGTTAT
1 ATGTGGTGTAATATTAGTTAT
28700131 GCACTTGGAT
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
22 32 0.59
23 11 0.20
24 11 0.20
ACGTcount: A:0.28, C:0.06, G:0.21, T:0.45
Consensus pattern (22 bp):
ATGTGGTGTAATATTAGTTATC
Found at i:28700193 original size:68 final size:68
Alignment explanation
Indices: 28700045--28700176 Score: 210
Period size: 68 Copynumber: 1.9 Consensus size: 68
28700035 ACTTTTAATG
* * *
28700045 TGGTGTAATATTAGTTATGCACTTGGACAATATTGTTGTTATCATGTGGTGTAATATTAGTTATC
1 TGGTATAATATTAGTTATGCACTTGGACAATATTGTTGTTATCATGTGGTGTAATACTAATTATC
28700110 ATA
66 ATA
* * *
28700113 TGGTGTAATATTAGTTATGCACTTGGATAATGTTGTTGTTATCATGTGGTGTAATACTAATTAT
1 TGGTATAATATTAGTTATGCACTTGGACAATATTGTTGTTATCATGTGGTGTAATACTAATTAT
28700177 GTATTTGGAT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 60 1.00
ACGTcount: A:0.27, C:0.07, G:0.21, T:0.45
Consensus pattern (68 bp):
TGGTATAATATTAGTTATGCACTTGGACAATATTGTTGTTATCATGTGGTGTAATACTAATTATC
ATA
Found at i:28700605 original size:14 final size:14
Alignment explanation
Indices: 28700586--28700623 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
28700576 CCAGAAAAGT
28700586 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
28700600 AAATCATTTTCTAG
1 AAATCATTTTCCAG
*
28700614 AAAACATTTT
1 AAATCATTTT
28700624 ACCTGCAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.39
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:28702669 original size:30 final size:30
Alignment explanation
Indices: 28702635--28702734 Score: 76
Period size: 30 Copynumber: 3.2 Consensus size: 30
28702625 AATACTGAAT
28702635 CGAATTTTATGATTATATATACATAATGAC
1 CGAATTTTATGATTATATATACATAATGAC
* * * * * * *
28702665 CGAATGCGTACATAT-ATAATTTTTAAATACTGAAT
1 CGAAT---T--TTATGATTATATATACATAATG-AC
28702700 CGAATTTTATGATTATATATACATAATGAC
1 CGAATTTTATGATTATATATACATAATGAC
28702730 CGAAT
1 CGAAT
28702735 GCGTACATAC
Statistics
Matches: 49, Mismatches: 14, Indels: 14
0.64 0.18 0.18
Matches are distributed among these distances:
30 14 0.29
31 12 0.24
32 1 0.02
33 1 0.02
34 12 0.24
35 9 0.18
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (30 bp):
CGAATTTTATGATTATATATACATAATGAC
Found at i:28702687 original size:65 final size:65
Alignment explanation
Indices: 28702611--28702743 Score: 266
Period size: 65 Copynumber: 2.0 Consensus size: 65
28702601 TTTTGGATAT
28702611 ATATATAATTTTTAAATACTGAATCGAATTTTATGATTATATATACATAATGACCGAATGCGTAC
1 ATATATAATTTTTAAATACTGAATCGAATTTTATGATTATATATACATAATGACCGAATGCGTAC
28702676 ATATATAATTTTTAAATACTGAATCGAATTTTATGATTATATATACATAATGACCGAATGCGTAC
1 ATATATAATTTTTAAATACTGAATCGAATTTTATGATTATATATACATAATGACCGAATGCGTAC
28702741 ATA
1 ATA
28702744 CTTGAGAATT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 68 1.00
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.38
Consensus pattern (65 bp):
ATATATAATTTTTAAATACTGAATCGAATTTTATGATTATATATACATAATGACCGAATGCGTAC
Found at i:28702845 original size:21 final size:21
Alignment explanation
Indices: 28702815--28702855 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
28702805 AACCTTAGGT
28702815 ATGGCTAGGATAC-ATATGTC
1 ATGGCTAGGATACGATATGTC
*
28702835 ATGGCATAGGATCCGATATGT
1 ATGGC-TAGGATACGATATGT
28702856 GTTTTCATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 7 0.39
22 6 0.33
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (21 bp):
ATGGCTAGGATACGATATGTC
Found at i:28702911 original size:43 final size:43
Alignment explanation
Indices: 28702863--28703017 Score: 129
Period size: 43 Copynumber: 3.7 Consensus size: 43
28702853 TGTGTTTTCA
* *
28702863 TGTAAGACCACGTCTGGGACTTTGGCATCAATATGTGGTTACG
1 TGTAAGACCACGTCTGGGACATTGGCATCAGTATGTGGTTACG
* * * * * *
28702906 TGTAAGACCATGTTTGGGACATCGGTATC-GTATTTGATT-CG
1 TGTAAGACCACGTCTGGGACATTGGCATCAGTATGTGGTTACG
* * * *
28702947 TGTAAGACC-CTGTCTGGGACAGTGGCATCAGTATG-AGATAGCA
1 TGTAAGACCAC-GTCTGGGACATTGGCATCAGTATGTGGTTA-CG
* **
28702990 TGTAAGACCACGTTTGGGATGTTGGCAT
1 TGTAAGACCACGTCTGGGACATTGGCAT
28703018 TGTGTGATAA
Statistics
Matches: 85, Mismatches: 22, Indels: 10
0.73 0.19 0.09
Matches are distributed among these distances:
41 26 0.31
42 11 0.13
43 47 0.55
44 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACATTGGCATCAGTATGTGGTTACG
Found at i:28704119 original size:22 final size:21
Alignment explanation
Indices: 28704073--28704120 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
28704063 TTGATGTATA
* *
28704073 TATATATTGGTTTATTAAATG
1 TATATATTGGCTTATTAAAAG
*
28704094 -ATATTTTGGCTTATTATAAAG
1 TATATATTGGCTTATTA-AAAG
28704115 TATATA
1 TATATA
28704121 AAATTTGTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
20 14 0.67
21 3 0.14
22 4 0.19
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.50
Consensus pattern (21 bp):
TATATATTGGCTTATTAAAAG
Found at i:28706156 original size:45 final size:45
Alignment explanation
Indices: 28706055--28706416 Score: 536
Period size: 45 Copynumber: 8.1 Consensus size: 45
28706045 TTTTCTCAAA
* * *
28706055 TCACCGGCATT-TCGCCTGCTAGGCTC-GAGGCCCG-AT-ATCATT
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAAT-ATC
* * *
28706097 TCACCAGCATTATAGCCTGTTAGGCTCGAAA-GCCCGAATAGTATC
1 TCACCGGCATTATAGCCTGCTAGGCTC-AAAGGCCCGAATAATATC
28706142 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC
*
28706187 TCCCCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC
*
28706232 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCAAATAATATC
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC
* *
28706277 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACATT
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC
* * *
28706322 TCACCGGCATTATAGCCTGCTAGGCTCAAAAGCCCGAATAACATT
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC
* *
28706367 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAACATT
1 TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC
28706412 TCACC
1 TCACC
28706417 AGTTCTTTCC
Statistics
Matches: 297, Mismatches: 17, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
42 10 0.03
43 13 0.04
44 8 0.03
45 265 0.89
46 1 0.00
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.23
Consensus pattern (45 bp):
TCACCGGCATTATAGCCTGCTAGGCTCAAAGGCCCGAATAATATC
Found at i:28709717 original size:18 final size:18
Alignment explanation
Indices: 28709694--28709728 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
28709684 TGCGACGACG
28709694 GCATCCC-AGTGGCTGACA
1 GCATCCCGA-TGGCTGACA
28709712 GCATCCCGATGGCTGAC
1 GCATCCCGATGGCTGAC
28709729 GACGGTTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.94
19 1 0.06
ACGTcount: A:0.20, C:0.34, G:0.29, T:0.17
Consensus pattern (18 bp):
GCATCCCGATGGCTGACA
Found at i:28710355 original size:14 final size:13
Alignment explanation
Indices: 28710322--28710351 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
28710312 TTTCATTCTA
*
28710322 TTTTCAAAACTTG
1 TTTTCCAAACTTG
28710335 TTTTCCAAACTTG
1 TTTTCCAAACTTG
28710348 TTTT
1 TTTT
28710352 TCCAGCAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.17, G:0.07, T:0.53
Consensus pattern (13 bp):
TTTTCCAAACTTG
Found at i:28710614 original size:36 final size:36
Alignment explanation
Indices: 28710567--28710639 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
28710557 TAGAAAATAA
28710567 ACCGTGGACTATCATATCCACGTAGGGCTATTTTTT
1 ACCGTGGACTATCATATCCACGTAGGGCTATTTTTT
*
28710603 ACCGTGGACTATCATATCCATGTAGGGCTATTTTTT
1 ACCGTGGACTATCATATCCACGTAGGGCTATTTTTT
28710639 A
1 A
28710640 AAAGAATTCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (36 bp):
ACCGTGGACTATCATATCCACGTAGGGCTATTTTTT
Found at i:28712593 original size:18 final size:18
Alignment explanation
Indices: 28712570--28712604 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28712560 CCCTTCTCCT
* *
28712570 CTAAGGGGAAATAGAAAG
1 CTAAGGGAAAAAAGAAAG
28712588 CTAAGGGAAAAAAGAAA
1 CTAAGGGAAAAAAGAAA
28712605 CCGGGTAGGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.06, G:0.29, T:0.09
Consensus pattern (18 bp):
CTAAGGGAAAAAAGAAAG
Found at i:28716285 original size:40 final size:40
Alignment explanation
Indices: 28716248--28716432 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
28716238 GCTACTCGTT
* *
28716248 CAAACGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
28716288 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
28716328 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
28716367 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
28716408 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28716433 CATCATTCAA
Statistics
Matches: 124, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
38 2 0.02
39 33 0.27
40 76 0.61
41 13 0.10
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:28716350 original size:79 final size:80
Alignment explanation
Indices: 28716248--28716432 Score: 216
Period size: 79 Copynumber: 2.3 Consensus size: 80
28716238 GCTACTCGTT
* * *
28716248 CAAACGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAA-GCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
28716311 GGATTTAGTAAC-TCGCA
63 GGATATAGTAACTTAGCA
* **
28716328 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAA-GCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
* *
28716392 ATATGGTCACTTAGCA
65 ATATAGTAACTTAGCA
28716408 CAAAGCCTTCGGGACTTAGCCCGGA
1 CAAAGCCTTCGGGACTTAGCCCGGA
28716433 CATCATTCAA
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.60
80 33 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (80 bp):
CAAAGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCA
Found at i:28723149 original size:77 final size:77
Alignment explanation
Indices: 28723022--28723176 Score: 301
Period size: 77 Copynumber: 2.0 Consensus size: 77
28723012 TGGCATGTAT
*
28723022 AGCTAGACCCAACGCATTACGGTAGTCCTAGAATCGACTAAAGCGTAGCTCTGATACCAATCAAA
1 AGCTAGACCCAACGCATTACGGTAGTCCTAGAATCGACTAAACCGTAGCTCTGATACCAATCAAA
28723087 TGTAACACACCG
66 TGTAACACACCG
28723099 AGCTAGACCCAACGCATTACGGTAGTCCTAGAATCGACTAAACCGTAGCTCTGATACCAATCAAA
1 AGCTAGACCCAACGCATTACGGTAGTCCTAGAATCGACTAAACCGTAGCTCTGATACCAATCAAA
28723164 TGTAACACACCG
66 TGTAACACACCG
28723176 A
1 A
28723177 ACCCGAGACC
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.35, C:0.28, G:0.17, T:0.19
Consensus pattern (77 bp):
AGCTAGACCCAACGCATTACGGTAGTCCTAGAATCGACTAAACCGTAGCTCTGATACCAATCAAA
TGTAACACACCG
Found at i:28724581 original size:39 final size:40
Alignment explanation
Indices: 28724533--28724715 Score: 189
Period size: 39 Copynumber: 4.6 Consensus size: 40
28724523 GCTATTCGTT
* *
28724533 CAAACGCCTTCGGGACATAGCCCGGTTATAGTAACTCG-A
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* *
28724572 CAATTGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCA
* *
28724612 CAAATGCCTTCGGG-CTTAGCCCGG-AATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
* * * * *
28724651 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTAAC-TCGCA
28724692 CAAA-GCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
28724716 ACATCATTCA
Statistics
Matches: 120, Mismatches: 15, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
38 2 0.02
39 62 0.52
40 44 0.37
41 12 0.10
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Done.