Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr6
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: 44797108
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 921406 characters in sequence are not A, C, G, or T
File 91 of 144
Found at i:27680111 original size:16 final size:18
Alignment explanation
Indices: 27680085--27680117 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
27680075 TTAATTTAAA
27680085 TAAATTAA-TTTCTCAAT
1 TAAATTAATTTTCTCAAT
27680102 TAAA-TAATTTTCTCAA
1 TAAATTAATTTTCTCAA
27680118 CTCAATTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:27681061 original size:24 final size:22
Alignment explanation
Indices: 27681033--27681088 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
27681023 CAACTCTTTC
27681033 CAGCAGATTTCAACTCTTTCACTT
1 CAGCAGATTTC--CTCTTTCACTT
*
27681057 CAGCAGAATT-CTCTTTCACTT
1 CAGCAGATTTCCTCTTTCACTT
*
27681078 CAGTAGATTTC
1 CAGCAGATTTC
27681089 TTCCTCGACA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 19 0.68
24 9 0.32
ACGTcount: A:0.25, C:0.27, G:0.11, T:0.38
Consensus pattern (22 bp):
CAGCAGATTTCCTCTTTCACTT
Found at i:27681072 original size:21 final size:21
Alignment explanation
Indices: 27681046--27681089 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
27681036 CAGATTTCAA
27681046 CTCTTTCACTTCAGCAGAATT
1 CTCTTTCACTTCAGCAGAATT
* *
27681067 CTCTTTCACTTCAGTAGATTT
1 CTCTTTCACTTCAGCAGAATT
27681088 CT
1 CT
27681090 TCCTCGACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.27, G:0.09, T:0.43
Consensus pattern (21 bp):
CTCTTTCACTTCAGCAGAATT
Found at i:27683146 original size:185 final size:184
Alignment explanation
Indices: 27682832--27683389 Score: 836
Period size: 185 Copynumber: 3.0 Consensus size: 184
27682822 ACTATGTTTA
* * *
27682832 TAGTGTAAA-TTGAGACTAAAATTCTCTCTCTTCTTCATGTATGAGTATATTTGATAAGATGTGA
1 TAGTGTAAACTT-AGACCAAAA-T-TCTCTCTTCTTTATGTATGATTATATTTGATAAGATGTGA
* *
27682896 CATTCTTGTAATTGTATGCATGTTTCGAGAAATGTATGTGAATGAATGTATGTAATTAATTTATT
63 CATTCTTGTAATTGTATGCATGTTTCGAGGAATGTATGAGAATGAATGTATGTAATTAATTTATT
*
27682961 GCTATGGATGATAAAGTAATTTTTCCAAATTTGTGATTCCTTGAAAATAAATGTAATT
128 GCTATGGATGATAAAGTAAATTTTCCAAATTT-TGATTCCTTGAAAATAAATGTAATT
* * *
27683019 TAGTGTAAACTTAGACCAAAATTCTCTATTCTTTATGTATGATTATATTTGATAAAATGTAACAT
1 TAGTGTAAACTTAGACCAAAATTCTCTCTTCTTTATGTATGATTATATTTGATAAGATGTGACAT
*
27683084 TCTTGTAATTGTATGCATGTTTCGAGGAATGTATGAGAATGAATGTATGTAATTAGTTTATTGCT
66 TCTTGTAATTGTATGCATGTTTCGAGGAATGTATGAGAATGAATGTATGTAATTAATTTATTGCT
* * *
27683149 ATGGATGATAAAGTAAAATTTCCAAATTTATGATTCCTAGAGAATAAATGTAATT
131 ATGGATGATAAAGTAAATTTTCCAAATTT-TGATTCCTTGAAAATAAATGTAATT
*
27683204 TAGTGTAAACTGAGACCAAAATTCTCTCTTCTTTATGTATGATTATATTTGATAAGATGTGACAT
1 TAGTGTAAACTTAGACCAAAATTCTCTCTTCTTTATGTATGATTATATTTGATAAGATGTGACAT
* * * *
27683269 TCTTGTAATTGTATGCATATTTCGAGGAATGCATGCGAATGAATGTATGTAATTATTTTATTG-T
66 TCTTGTAATTGTATGCATGTTTCGAGGAATGTATGAGAATGAATGTATGTAATTAATTTATTGCT
* *
27683333 CGTGGATGATAAAGTAAATTTTCCAAAATTTTGATT--TTTAGAAATAAATGTAATT
131 -ATGGATGATAAAGTAAATTTTCC-AAATTTTGATTCCTTGA-AAATAAATGTAATT
27683388 TA
1 TA
27683390 TTATTATCTT
Statistics
Matches: 340, Mismatches: 27, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
183 2 0.01
184 16 0.05
185 296 0.87
186 7 0.02
187 17 0.05
188 2 0.01
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.41
Consensus pattern (184 bp):
TAGTGTAAACTTAGACCAAAATTCTCTCTTCTTTATGTATGATTATATTTGATAAGATGTGACAT
TCTTGTAATTGTATGCATGTTTCGAGGAATGTATGAGAATGAATGTATGTAATTAATTTATTGCT
ATGGATGATAAAGTAAATTTTCCAAATTTTGATTCCTTGAAAATAAATGTAATT
Found at i:27683921 original size:22 final size:22
Alignment explanation
Indices: 27683889--27683931 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
27683879 ATGTTCACGC
27683889 ATATATAAGGAAA-ACATGCCAT
1 ATATATAAGGAAAGA-ATGCCAT
*
27683911 ATATATTAGGAAAGAATGCCA
1 ATATATAAGGAAAGAATGCCA
27683932 CATGCACTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.49, C:0.12, G:0.16, T:0.23
Consensus pattern (22 bp):
ATATATAAGGAAAGAATGCCAT
Found at i:27693673 original size:51 final size:51
Alignment explanation
Indices: 27693618--27693970 Score: 492
Period size: 51 Copynumber: 6.7 Consensus size: 51
27693608 AGTGAAAGTG
*
27693618 ATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGTA
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGTA
27693669 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGTA
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGTA
27693720 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGCGTACCA
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAT-G-GT---A
*
27693776 GATAGTTTCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGTA
1 -AT-G----G-TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGTA
* * * * *
27693834 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGATAGT-
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGTA
* * *
27693884 TTCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGTA
1 AT-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGTA
27693936 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
1 ATGGTCACATGTGTAGTACTATGTGCAGGCTACTA
27693971 TGTGAACCGA
Statistics
Matches: 269, Mismatches: 19, Indels: 28
0.85 0.06 0.09
Matches are distributed among these distances:
50 1 0.00
51 209 0.78
52 3 0.01
53 2 0.01
56 2 0.01
57 4 0.01
58 2 0.01
61 2 0.01
62 2 0.01
63 42 0.16
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (51 bp):
ATGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGTA
Found at i:27693734 original size:25 final size:25
Alignment explanation
Indices: 27693654--27693734 Score: 62
Period size: 25 Copynumber: 3.2 Consensus size: 25
27693644 AGGCTACTAC
27693654 GTGTATCGGATGGTAATGGTCACAT
1 GTGTATCGGATGGTAATGGTCACAT
* * *
27693679 GTGTAGTAC-TAT-GTGCA-GG-CTACTAC
1 GTGTA-T-CGGATGGT-AATGGTC-AC-AT
27693705 GTGTATCGGATGGTAATGGTCACAT
1 GTGTATCGGATGGTAATGGTCACAT
27693730 GTGTA
1 GTGTA
27693735 GTACTATGTG
Statistics
Matches: 41, Mismatches: 6, Indels: 18
0.63 0.09 0.28
Matches are distributed among these distances:
24 2 0.05
25 21 0.51
26 16 0.39
27 2 0.05
ACGTcount: A:0.23, C:0.14, G:0.31, T:0.32
Consensus pattern (25 bp):
GTGTATCGGATGGTAATGGTCACAT
Found at i:27693900 original size:165 final size:165
Alignment explanation
Indices: 27693622--27693933 Score: 536
Period size: 165 Copynumber: 1.9 Consensus size: 165
27693612 AAAGTGATGG
27693622 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGTAATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGTAATGGTCACATGTGTAGTA
* * * * *
27693687 CTATGTGCAGGCTACTACGTGTATCGGATGGTAATGGTCACATGTGTAGTACTATGTGCAGGCTA
66 CTATGTGCAGGCTACTACGCGTACCAGATAGTAATGATCACATGTGTAGTACTATGTGCAGGCTA
27693752 CTACGTGTATCGGATGGCGTACCAGATAGTTTCGA
131 CTACGTGTATCGGATGGCGTACCAGATAGTTTCGA
27693787 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGTAATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGTAATGGTCACATGTGTAGTA
* * *
27693852 CTATGTGCAGGCTACTATGCGTACCAGATAGT-TTCGATCACGTGTGTAGTACTATGTGCAGGCT
66 CTATGTGCAGGCTACTACGCGTACCAGATAGTAAT-GATCACATGTGTAGTACTATGTGCAGGCT
27693916 ACTACGTGTATCGGATGG
130 ACTACGTGTATCGGATGG
27693934 TAATGGTCAC
Statistics
Matches: 138, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
164 1 0.01
165 137 0.99
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (165 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGTAATGGTCACATGTGTAGTA
CTATGTGCAGGCTACTACGCGTACCAGATAGTAATGATCACATGTGTAGTACTATGTGCAGGCTA
CTACGTGTATCGGATGGCGTACCAGATAGTTTCGA
Found at i:27693974 original size:26 final size:26
Alignment explanation
Indices: 27693894--27693974 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
27693884 TTCGATCACG
27693894 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
* * *
27693920 CGTGTA-T-CGGATG-GTAATGG-TCAC-A
1 TGTGTAGTAC-TATGTG-CA-GGCT-ACTA
27693945 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
27693971 TGTG
1 TGTG
27693975 AACCGAACAT
Statistics
Matches: 40, Mismatches: 6, Indels: 18
0.62 0.09 0.28
Matches are distributed among these distances:
24 2 0.05
25 16 0.40
26 20 0.50
27 2 0.05
ACGTcount: A:0.22, C:0.15, G:0.30, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:27694027 original size:45 final size:45
Alignment explanation
Indices: 27693976--27694070 Score: 172
Period size: 45 Copynumber: 2.1 Consensus size: 45
27693966 TACTATGTGA
* *
27693976 ACCGAACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
27694021 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
27694066 ACCGA
1 ACCGA
27694071 GTATCTGTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (45 bp):
ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
Found at i:27696915 original size:3 final size:3
Alignment explanation
Indices: 27696901--27696945 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
27696891 TATTTAGTTA
* *
27696901 ATT ATT -TT ATT ATT ATT ATT ACT ATT AATT ATT ATT ACT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT
27696946 TTTTTATTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:27696933 original size:16 final size:16
Alignment explanation
Indices: 27696908--27696943 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
27696898 TTAATTATTT
27696908 TATT-ATTATTATTAC
1 TATTAATTATTATTAC
27696923 TATTAATTATTATTAC
1 TATTAATTATTATTAC
27696939 TATTA
1 TATTA
27696944 TTTTTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTAATTATTATTAC
Found at i:27700414 original size:10 final size:10
Alignment explanation
Indices: 27700389--27700422 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
27700379 ATTTGAGGTT
*
27700389 TTTAAAATTAA
1 TTTAAAA-TCA
27700400 TTTAAAATCA
1 TTTAAAATCA
27700410 TTTAAAATCA
1 TTTAAAATCA
27700420 TTT
1 TTT
27700423 TCTGGTTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 15 0.68
11 7 0.32
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (10 bp):
TTTAAAATCA
Found at i:27709576 original size:20 final size:20
Alignment explanation
Indices: 27709551--27709590 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
27709541 AGTGAGAAGT
27709551 TTTAAGTCTTTTATTTGATA
1 TTTAAGTCTTTTATTTGATA
27709571 TTTAAGTCTTTTATTTGATA
1 TTTAAGTCTTTTATTTGATA
27709591 AAATAAAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.05, G:0.10, T:0.60
Consensus pattern (20 bp):
TTTAAGTCTTTTATTTGATA
Found at i:27711645 original size:29 final size:29
Alignment explanation
Indices: 27711523--27711634 Score: 109
Period size: 29 Copynumber: 3.9 Consensus size: 29
27711513 TGCCACCGGT
* * *
27711523 ACATAGTACCTAATAAATATAACACTGGC
1 ACATAGTACCTGATAAATATAACACCGAC
* * * *
27711552 ACATAATGCCTAATAAATATAACACCGAT
1 ACATAGTACCTGATAAATATAACACCGAC
* ** *
27711581 ACAAAGTACCTGAT-AATATGGTCACCGAT
1 ACATAGTACCTGATAAATAT-AACACCGAC
27711610 ACATAGTACCTGATAAATATAACAC
1 ACATAGTACCTGATAAATATAACAC
27711635 TAGCACATAG
Statistics
Matches: 67, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
28 5 0.07
29 57 0.85
30 5 0.07
ACGTcount: A:0.45, C:0.21, G:0.11, T:0.24
Consensus pattern (29 bp):
ACATAGTACCTGATAAATATAACACCGAC
Found at i:27721700 original size:34 final size:34
Alignment explanation
Indices: 27721657--27721724 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
27721647 TGTGTATCCA
27721657 TCATGAATCGCTTGCTTGTAAAATTGCCAAGGCC
1 TCATGAATCGCTTGCTTGTAAAATTGCCAAGGCC
*
27721691 TCATGAATCGCTTGCTTGTCAAATTGCCAAGGCC
1 TCATGAATCGCTTGCTTGTAAAATTGCCAAGGCC
27721725 GTCCCAAATG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (34 bp):
TCATGAATCGCTTGCTTGTAAAATTGCCAAGGCC
Found at i:27728517 original size:12 final size:12
Alignment explanation
Indices: 27728500--27728527 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
27728490 AATTGAAGAT
27728500 AAAATGTGACAC
1 AAAATGTGACAC
27728512 AAAATGTGACAC
1 AAAATGTGACAC
27728524 AAAA
1 AAAA
27728528 GGGTTTGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.14
Consensus pattern (12 bp):
AAAATGTGACAC
Found at i:27730566 original size:26 final size:28
Alignment explanation
Indices: 27730537--27730589 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
27730527 CTGATACTGA
* *
27730537 TTCTG-TAATGGGCTTAGG-TCACCTGG
1 TTCTGTTAAAGGGCTAAGGATCACCTGG
27730563 TTCTGTTAAAGGGCTAAGGATCACCTG
1 TTCTGTTAAAGGGCTAAGGATCACCTG
27730590 ATACTATGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 5 0.22
27 11 0.48
28 7 0.30
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (28 bp):
TTCTGTTAAAGGGCTAAGGATCACCTGG
Found at i:27734851 original size:21 final size:22
Alignment explanation
Indices: 27734809--27734858 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
27734799 AAGGTGGAAG
*
27734809 TTATGTGACAGTTTATCTGCAA
1 TTATGTGACAGTTTATCGGCAA
*
27734831 TTATGTGACTG-TTATCGGCAA
1 TTATGTGACAGTTTATCGGCAA
*
27734852 ATATGTG
1 TTATGTG
27734859 GTGGTTTGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (22 bp):
TTATGTGACAGTTTATCGGCAA
Found at i:27735092 original size:22 final size:22
Alignment explanation
Indices: 27735064--27735108 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
27735054 ATTATGATGA
27735064 TTGATATG-ATGAGATTGATATT
1 TTGATATGTATGAGATT-ATATT
*
27735086 TTGATATGTATGTGATTATATT
1 TTGATATGTATGAGATTATATT
27735108 T
1 T
27735109 GTGTTGATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (22 bp):
TTGATATGTATGAGATTATATT
Found at i:27739876 original size:17 final size:17
Alignment explanation
Indices: 27739850--27739882 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
27739840 GAATAGAATA
27739850 GAATAGAATAAAATAAT
1 GAATAGAATAAAATAAT
*
27739867 GAATATAATAAAATAA
1 GAATAGAATAAAATAA
27739883 AAACAAATGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (17 bp):
GAATAGAATAAAATAAT
Found at i:27742854 original size:29 final size:29
Alignment explanation
Indices: 27742822--27742944 Score: 90
Period size: 29 Copynumber: 4.2 Consensus size: 29
27742812 AATTGTCCCT
*
27742822 TTTCATATTCAATGGTCC-AAACCATCCTA
1 TTTCATATTCAATAG-CCGAAACCATCCTA
* * *
27742851 TTTCAT-TATCAATAGCCGAAGCTATCCCA
1 TTTCATAT-TCAATAGCCGAAACCATCCTA
* * *
27742880 TTTCATATTCGATAGCCGAAGCTATCCCT-
1 TTTCATATTCAATAGCCGAAACCAT-CCTA
* * ** *
27742909 TTTCATATTCAATGGTCGTCACCATCCTT
1 TTTCATATTCAATAGCCGAAACCATCCTA
27742938 TTTCATA
1 TTTCATA
27742945 GTTGATGGTC
Statistics
Matches: 76, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
28 6 0.08
29 67 0.88
30 3 0.04
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.37
Consensus pattern (29 bp):
TTTCATATTCAATAGCCGAAACCATCCTA
Found at i:27742942 original size:58 final size:57
Alignment explanation
Indices: 27742880--27743034 Score: 149
Period size: 58 Copynumber: 2.6 Consensus size: 57
27742870 AGCTATCCCA
27742880 TTTCATATTCGATAGCCGAAGCTATCCCTTTTCATATTCAATGGTCGTCACCAT-CCTT
1 TTTCATATTCGAT-GCC-AAGCTATCCCTTTTCATATTCAATGGTCGTCACCATCCCTT
* * * *
27742938 TTTCATAGTT-GATGGTCATCA-CCATCCCTTTTCAAAGTT-TATGGTCGTCACCATCCCTT
1 TTTCATA-TTCGAT-GCCA--AGCTATCCCTTTTCATA-TTCAATGGTCGTCACCATCCCTT
*
27742997 TTT-ATAATCGATGACCAAAGCTATCCCTTTTCATATTC
1 TTTCATATTCGATG-CC-AAGCTATCCCTTTTCATATTC
27743035 GATAGTCGAA
Statistics
Matches: 78, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
57 6 0.08
58 59 0.76
59 13 0.17
ACGTcount: A:0.23, C:0.26, G:0.12, T:0.39
Consensus pattern (57 bp):
TTTCATATTCGATGCCAAGCTATCCCTTTTCATATTCAATGGTCGTCACCATCCCTT
Found at i:27742952 original size:29 final size:29
Alignment explanation
Indices: 27742903--27742998 Score: 131
Period size: 29 Copynumber: 3.3 Consensus size: 29
27742893 AGCCGAAGCT
27742903 ATCCCTTTTCATA-TTCAATGGTCGTCACC
1 ATCCCTTTTCATAGTT-AATGGTCGTCACC
* * *
27742932 ATCCTTTTTCATAGTTGATGGTCATCACC
1 ATCCCTTTTCATAGTTAATGGTCGTCACC
* *
27742961 ATCCCTTTTCAAAGTTTATGGTCGTCACC
1 ATCCCTTTTCATAGTTAATGGTCGTCACC
27742990 ATCCCTTTT
1 ATCCCTTTT
27742999 TATAATCGAT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
29 57 0.97
30 2 0.03
ACGTcount: A:0.20, C:0.28, G:0.11, T:0.41
Consensus pattern (29 bp):
ATCCCTTTTCATAGTTAATGGTCGTCACC
Found at i:27743022 original size:29 final size:29
Alignment explanation
Indices: 27742990--27743059 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
27742980 GGTCGTCACC
*
27742990 ATCCCTTTTTATAATCGAT-GACCAAAGCT
1 ATCCCTTTTCATAATCGATAG-CCAAAGCT
* * *
27743019 ATCCCTTTTCATATTCGATAGTCGAAGCT
1 ATCCCTTTTCATAATCGATAGCCAAAGCT
27743048 ATCCCTTTTCAT
1 ATCCCTTTTCAT
27743060 TGGTCGATGA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 35 0.97
30 1 0.03
ACGTcount: A:0.26, C:0.26, G:0.10, T:0.39
Consensus pattern (29 bp):
ATCCCTTTTCATAATCGATAGCCAAAGCT
Found at i:27745478 original size:21 final size:22
Alignment explanation
Indices: 27745439--27745479 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
27745429 TACGTTTTAC
*
27745439 CTTAAAAAAAAATATTAAATTA
1 CTTAAAAAAAAACATTAAATTA
27745461 CTTAAAAAAAAACA-TAAAT
1 CTTAAAAAAAAACATTAAAT
27745480 CAAATATGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (22 bp):
CTTAAAAAAAAACATTAAATTA
Found at i:27755428 original size:26 final size:27
Alignment explanation
Indices: 27755399--27755449 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
27755389 GACCGTAATG
27755399 CCCCTAGAGGGTAAATGACT-ATTTTT
1 CCCCTAGAGGGTAAATGACTGATTTTT
*
27755425 CCCCTCGAGGGTAAATGACTGATTT
1 CCCCTAGAGGGTAAATGACTGATTT
27755450 GTGCTATAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (27 bp):
CCCCTAGAGGGTAAATGACTGATTTTT
Found at i:27761297 original size:28 final size:30
Alignment explanation
Indices: 27761247--27761308 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 30
27761237 CATAATTTAA
27761247 CATAAAAAGTCCCAAATGGAAAT-AAAGTT
1 CATAAAAAGTCCCAAATGGAAATAAAAGTT
*
27761276 CATAAAAA-T-CCAAATGATAAATAAAAGTT
1 CATAAAAAGTCCCAAATG-GAAATAAAAGTT
27761305 CATA
1 CATA
27761309 TTTATGTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 7 0.23
28 5 0.17
29 18 0.60
ACGTcount: A:0.55, C:0.13, G:0.10, T:0.23
Consensus pattern (30 bp):
CATAAAAAGTCCCAAATGGAAATAAAAGTT
Found at i:27761708 original size:49 final size:49
Alignment explanation
Indices: 27761630--27761765 Score: 175
Period size: 49 Copynumber: 2.8 Consensus size: 49
27761620 ACACCATTTG
27761630 TGGACAAGCCACCACTG-ATATGCAAATATACTGCCACTGATAAATTTTA
1 TGGACAAGCCACCACTGAAT-TGCAAATATACTGCCACTGATAAATTTTA
* * * * * * *
27761679 TGGACAAGCCACCATTGAATTGTATATATATTGCCATTGGTAAATTTTG
1 TGGACAAGCCACCACTGAATTGCAAATATACTGCCACTGATAAATTTTA
* *
27761728 TGGACAAGCCACCACTGATTTGCAGATATACTGCCACT
1 TGGACAAGCCACCACTGAATTGCAAATATACTGCCACT
27761766 ACTTTGACCT
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
49 71 0.97
50 2 0.03
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.29
Consensus pattern (49 bp):
TGGACAAGCCACCACTGAATTGCAAATATACTGCCACTGATAAATTTTA
Found at i:27765175 original size:57 final size:57
Alignment explanation
Indices: 27765087--27765199 Score: 217
Period size: 57 Copynumber: 2.0 Consensus size: 57
27765077 ATAAATATAA
*
27765087 TAATATTTTAATCTGAAAATTATAATTACATTAATTATAATATAAGTTCGGTAAACT
1 TAATATTTTAATCCGAAAATTATAATTACATTAATTATAATATAAGTTCGGTAAACT
27765144 TAATATTTTAATCCGAAAATTATAATTACATTAATTATAATATAAGTTCGGTAAAC
1 TAATATTTTAATCCGAAAATTATAATTACATTAATTATAATATAAGTTCGGTAAAC
27765200 CATATATTTA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.41
Consensus pattern (57 bp):
TAATATTTTAATCCGAAAATTATAATTACATTAATTATAATATAAGTTCGGTAAACT
Found at i:27787099 original size:25 final size:25
Alignment explanation
Indices: 27787039--27787099 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
27787029 CTCCTAAATT
27787039 TTAATTGAATTATCTAATTTTTCAA
1 TTAATTGAATTATCTAATTTTTCAA
*
27787064 TTTATTGAATTAT-TAATATTTT-ATA
1 TTAATTGAATTATCTAAT-TTTTCA-A
*
27787089 TTAATTAAATT
1 TTAATTGAATT
27787100 TTTGAGAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
24 5 0.16
25 26 0.84
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (25 bp):
TTAATTGAATTATCTAATTTTTCAA
Found at i:27788938 original size:41 final size:42
Alignment explanation
Indices: 27788834--27788942 Score: 125
Period size: 43 Copynumber: 2.6 Consensus size: 42
27788824 TCCATAGTTA
* *
27788834 GGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTGTGAAAG
1 GGGTTGCTAAGTGCTGATTCCACCGTATCCTTGAATAT-AAAG
* *
27788877 GGGTTGTTATGTGCTGATTCC-CCGTATCAC-TGAATAT-AAG
1 GGGTTGCTAAGTGCTGATTCCACCGTATC-CTTGAATATAAAG
*
27788917 GTGGTTGCTAAGTGCTCATTCCACCG
1 G-GGTTGCTAAGTGCTGATTCCACCG
27788943 AGCAACTGTT
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
40 4 0.07
41 17 0.30
42 15 0.27
43 20 0.36
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (42 bp):
GGGTTGCTAAGTGCTGATTCCACCGTATCCTTGAATATAAAG
Found at i:27803130 original size:28 final size:28
Alignment explanation
Indices: 27803090--27803188 Score: 153
Period size: 28 Copynumber: 3.5 Consensus size: 28
27803080 AGGGAGATTG
27803090 GCACTAAGTGTGCGAGTTTAATTGTAAA
1 GCACTAAGTGTGCGAGTTTAATTGTAAA
*
27803118 GCACTAAGTGTGCGAGTTTAATGGTAAA
1 GCACTAAGTGTGCGAGTTTAATTGTAAA
* * * *
27803146 GCACTAAGTGTGCGTGTTTGATTATTAA
1 GCACTAAGTGTGCGAGTTTAATTGTAAA
27803174 GCACTAAGTGTGCGA
1 GCACTAAGTGTGCGA
27803189 ACTTATTAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 64 1.00
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.31
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTAATTGTAAA
Found at i:27818292 original size:19 final size:17
Alignment explanation
Indices: 27818243--27818293 Score: 50
Period size: 19 Copynumber: 2.8 Consensus size: 17
27818233 TTTTAATGGT
27818243 TAAA-TAAGTAAATTAG
1 TAAATTAAGTAAATTAG
*
27818259 TAAATAAATGATAAATTAAG
1 TAAATTAA-G-TAAATT-AG
27818279 TAAAATTAAGTAAAT
1 T-AAATTAAGTAAAT
27818294 GTATCATCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
16 4 0.14
17 2 0.07
18 1 0.04
19 11 0.39
20 4 0.14
21 6 0.21
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.31
Consensus pattern (17 bp):
TAAATTAAGTAAATTAG
Found at i:27818936 original size:89 final size:89
Alignment explanation
Indices: 27818783--27819300 Score: 666
Period size: 89 Copynumber: 5.8 Consensus size: 89
27818773 GGGCTAAAGT
** *
27818783 CAGCACAGGAAGGCAAAGCTGGTGTCTTCGATCTGCTTCGCTATCAGTATAGGAAGGCATGATCT
1 CAGCACAGGAAGGCAAAGCTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCATGATCT
* * * *
27818848 GCTATTTTCAGTCTACTCTGCTGT
66 GCTATCTTCAGTCTGCTCCGCTGC
* * * *
27818872 CAGCATAGGAAGGCAAAGCTGGTGTCTTCGATCTGCTTCGTTGCTAGTACAGGAAGGCAAGATCT
1 CAGCACAGGAAGGCAAAGCTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCATGATCT
27818937 GCTATCTT-AGTCTGCTCCGCTGC
66 GCTATCTTCAGTCTGCTCCGCTGC
* * * * *
27818960 CAGTACA-GAGAGGCAAAGCTGGTGTCTTCAATCTGGTTCGCTGTCAGTACAAGAAGGCATGATC
1 CAGCACAGGA-AGGCAAAGCTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCATGATC
* *
27819024 TACTATCTTCAGTCTGCTCTGCTG-
65 TGCTATCTTCAGTCTGCTCCGCTGC
** * * *
27819048 CAATACATGG-AGGCAAAGCTGGTGTGTTCGATTTGCTTCACTGCCAGTACAGGAAGGCATGATC
1 CAGCACA-GGAAGGCAAAGCTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCATGATC
*
27819112 TGCTATCTTCAGTCTGCTCCACTGC
65 TGCTATCTTCAGTCTGCTCCGCTGC
* * * * * * * *
27819137 CAGTACAGGGAGGCAAAACTAGTGTCTTCTATTTGCTTCACTACCAGTACAGGAAGGCATGATCT
1 CAGCACAGGAAGGCAAAGCTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCATGATCT
27819202 GCTATCTTCAGTCTGCTCCGCTGC
66 GCTATCTTCAGTCTGCTCCGCTGC
* * * *
27819226 CAGTACAGGGAGGCAAAGCTGGTGTCTTCGATCTGCTTCGCTGCCAGTATAGGAAGGCAAGATCT
1 CAGCACAGGAAGGCAAAGCTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCATGATCT
27819291 GCTATCTTCA
66 GCTATCTTCA
27819301 CCGATCTGTT
Statistics
Matches: 375, Mismatches: 48, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
87 2 0.01
88 148 0.39
89 224 0.60
90 1 0.00
ACGTcount: A:0.23, C:0.24, G:0.25, T:0.28
Consensus pattern (89 bp):
CAGCACAGGAAGGCAAAGCTGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCATGATCT
GCTATCTTCAGTCTGCTCCGCTGC
Found at i:27818951 original size:44 final size:45
Alignment explanation
Indices: 27818787--27819300 Score: 362
Period size: 44 Copynumber: 11.6 Consensus size: 45
27818777 TAAAGTCAGC
* * * **
27818787 ACAGGAAGGCAA-AGCTGGTGTCTTC-GATCTGCTTCGCTATCAGT
1 ACAGGAAGGCAAGATCTGCTATCTTCAG-TCTGCTTCGCTGCCAGT
* * * * * *
27818831 ATAGGAAGGCATGATCTGCTATTTTCAGTCTAC-TCTGCTGTCAGC
1 ACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTTC-GCTGCCAGT
* * * * * *
27818876 ATAGGAAGGCAA-AGCTGGTGTCTTC-GATCTGCTTCGTTGCTAGT
1 ACAGGAAGGCAAGATCTGCTATCTTCAG-TCTGCTTCGCTGCCAGT
*
27818920 ACAGGAAGGCAAGATCTGCTATCTT-AGTCTGCTCCGCTGCCAGT
1 ACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTTCGCTGCCAGT
* * * * * *
27818964 ACA-GAGAGGCAA-AGCTGGTGTCTTCAATCTGGTTCGCTGTCAGT
1 ACAGGA-AGGCAAGATCTGCTATCTTCAGTCTGCTTCGCTGCCAGT
* * * *
27819008 ACAAGAAGGCATGATCTACTATCTTCAGTCTGC-TCTGCTG-CAAT
1 ACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTTC-GCTGCCAGT
* * * * * *
27819052 ACATGG-AGGCAA-AGCTGGTGTGTTC-GATTTGCTTCACTGCCAGT
1 ACA-GGAAGGCAAGATCTGCTATCTTCAG-TCTGCTTCGCTGCCAGT
* * *
27819096 ACAGGAAGGCATGATCTGCTATCTTCAGTCTGCTCCACTGCCAGT
1 ACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTTCGCTGCCAGT
* * * * * *
27819141 ACAGGGAGGCAA-AACTAG-TGTCTTCTA-TTTGCTTCACTACCAGT
1 ACAGGAAGGCAAGATCT-GCTATCTTC-AGTCTGCTTCGCTGCCAGT
* *
27819185 ACAGGAAGGCATGATCTGCTATCTTCAGTCTGCTCCGCTGCCAGT
1 ACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTTCGCTGCCAGT
* * * *
27819230 ACAGGGAGGCAA-AGCTGGTGTCTTC-GATCTGCTTCGCTGCCAGT
1 ACAGGAAGGCAAGATCTGCTATCTTCAG-TCTGCTTCGCTGCCAGT
*
27819274 ATAGGAAGGCAAGATCTGCTATCTTCA
1 ACAGGAAGGCAAGATCTGCTATCTTCA
27819301 CCGATCTGTT
Statistics
Matches: 359, Mismatches: 84, Indels: 52
0.73 0.17 0.11
Matches are distributed among these distances:
42 1 0.00
43 30 0.08
44 184 0.51
45 142 0.40
46 2 0.01
ACGTcount: A:0.23, C:0.24, G:0.25, T:0.28
Consensus pattern (45 bp):
ACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTTCGCTGCCAGT
Found at i:27819128 original size:177 final size:178
Alignment explanation
Indices: 27818793--27819300 Score: 718
Period size: 177 Copynumber: 2.9 Consensus size: 178
27818783 CAGCACAGGA
* * *
27818793 AGGCAAAGCTGGTGTCTTCGATCTGCTTCGCTATCAGTATAGGAAGGCATGATCTGCTATTTTCA
1 AGGCAAAGCTGGTGTCTTCAATCTGCTTCGCTATCAGTACAGGAAGGCATGATCTGCTATCTTCA
* * * * *
27818858 GTCTACTCTGCTGTC-A-GCATAGGAAGGCAAAGCTGGTGTCTTCGATCTGCTTCGTTGCTAGTA
66 GTCTGCTCTGCTGCCAATACAT-GG-AGGCAAAGCTGGTGTCTTCGATCTGCTTCGCTGCCAGTA
*
27818921 CAGGAAGGCAAGATCTGCTATCTT-AGTCTGCTCCGCTGCCAGTACAGAG
129 CAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCACTGCCAGTACAGAG
* * * *
27818970 AGGCAAAGCTGGTGTCTTCAATCTGGTTCGCTGTCAGTACAAGAAGGCATGATCTACTATCTTCA
1 AGGCAAAGCTGGTGTCTTCAATCTGCTTCGCTATCAGTACAGGAAGGCATGATCTGCTATCTTCA
* * *
27819035 GTCTGCTCTGCTG-CAATACATGGAGGCAAAGCTGGTGTGTTCGATTTGCTTCACTGCCAGTACA
66 GTCTGCTCTGCTGCCAATACATGGAGGCAAAGCTGGTGTCTTCGATCTGCTTCGCTGCCAGTACA
* *
27819099 GGAAGGCATGATCTGCTATCTTCAGTCTGCTCCACTGCCAGTACAGGG
131 GGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCACTGCCAGTACAGAG
* * * * * *
27819147 AGGCAAAACTAGTGTCTTCTATTTGCTTCACTACCAGTACAGGAAGGCATGATCTGCTATCTTCA
1 AGGCAAAGCTGGTGTCTTCAATCTGCTTCGCTATCAGTACAGGAAGGCATGATCTGCTATCTTCA
* * * *
27819212 GTCTGCTCCGCTGCCAGTACAGGGAGGCAAAGCTGGTGTCTTCGATCTGCTTCGCTGCCAGTATA
66 GTCTGCTCTGCTGCCAATACATGGAGGCAAAGCTGGTGTCTTCGATCTGCTTCGCTGCCAGTACA
27819277 GGAAGGCAAGATCTGCTATCTTCA
131 GGAAGGCAAGATCTGCTATCTTCA
27819301 CCGATCTGTT
Statistics
Matches: 292, Mismatches: 35, Indels: 7
0.87 0.10 0.02
Matches are distributed among these distances:
176 58 0.20
177 163 0.56
178 71 0.24
ACGTcount: A:0.23, C:0.24, G:0.25, T:0.29
Consensus pattern (178 bp):
AGGCAAAGCTGGTGTCTTCAATCTGCTTCGCTATCAGTACAGGAAGGCATGATCTGCTATCTTCA
GTCTGCTCTGCTGCCAATACATGGAGGCAAAGCTGGTGTCTTCGATCTGCTTCGCTGCCAGTACA
GGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCACTGCCAGTACAGAG
Found at i:27819622 original size:24 final size:24
Alignment explanation
Indices: 27819572--27819628 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
27819562 CGGATTGCCC
27819572 CCACTGTAATCTTCAAACTTCAAT
1 CCACTGTAATCTTCAAACTTCAAT
* **
27819596 CCATTGTAATCTTCAAGGTT-AAGT
1 CCACTGTAATCTTCAAACTTCAA-T
27819620 CCACTGTAA
1 CCACTGTAA
27819629 CTTTAGGACA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 2 0.07
24 26 0.93
ACGTcount: A:0.32, C:0.25, G:0.11, T:0.33
Consensus pattern (24 bp):
CCACTGTAATCTTCAAACTTCAAT
Found at i:27826990 original size:44 final size:45
Alignment explanation
Indices: 27826927--27827024 Score: 128
Period size: 44 Copynumber: 2.2 Consensus size: 45
27826917 ATCATTTACC
*
27826927 TCCATTCCATTCAACCAAACACA-AGAA-TACTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACA-ATAGAATTACTATTACGCCTCTAT
* **
27826971 TCCATTACATTCAACCAAACAATTGAATTGTTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACAATAGAATTACTATTACGCCTCTAT
*
27827016 TCCAATACA
1 TCCATTACA
27827025 GCGAACCAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
43 1 0.02
44 23 0.49
45 23 0.49
ACGTcount: A:0.36, C:0.29, G:0.05, T:0.31
Consensus pattern (45 bp):
TCCATTACATTCAACCAAACAATAGAATTACTATTACGCCTCTAT
Found at i:27828598 original size:14 final size:14
Alignment explanation
Indices: 27828579--27828623 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
27828569 AAAAAACGTT
27828579 TATAAAGATATATA
1 TATAAAGATATATA
*
27828593 TATAAA-ATA-AGA
1 TATAAAGATATATA
*
27828605 TATATAGATATATA
1 TATAAAGATATATA
27828619 TATAA
1 TATAA
27828624 TAAGATACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 7 0.28
13 6 0.24
14 12 0.48
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
TATAAAGATATATA
Found at i:27828608 original size:26 final size:24
Alignment explanation
Indices: 27828579--27828648 Score: 97
Period size: 24 Copynumber: 2.9 Consensus size: 24
27828569 AAAAAACGTT
27828579 TATAAAGATATATATATAAAATAAGA
1 TATAAAGATATATATAT--AATAAGA
*
27828605 TATATAGATATATATATAATAAGA
1 TATAAAGATATATATATAATAAGA
*
27828629 TACAAAGATATATATA-AATA
1 TATAAAGATATATATATAATA
27828649 GCTATAATAG
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
23 4 0.10
24 21 0.51
26 16 0.39
ACGTcount: A:0.59, C:0.01, G:0.07, T:0.33
Consensus pattern (24 bp):
TATAAAGATATATATATAATAAGA
Found at i:27828725 original size:14 final size:13
Alignment explanation
Indices: 27828699--27828753 Score: 74
Period size: 14 Copynumber: 4.1 Consensus size: 13
27828689 TAATTAAGTA
27828699 AATATAAAATAAT
1 AATATAAAATAAT
27828712 AATATAACAATAAT
1 AATATAA-AATAAT
27828726 AATATAAAACTAAT
1 AATATAAAA-TAAT
* *
27828740 GATATAACATAAT
1 AATATAAAATAAT
27828753 A
1 A
27828754 GCGGTAACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
13 13 0.35
14 24 0.65
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (13 bp):
AATATAAAATAAT
Found at i:27828734 original size:27 final size:27
Alignment explanation
Indices: 27828699--27828753 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
27828689 TAATTAAGTA
27828699 AATATAAAA-TAATAATATAACAATAAT
1 AATATAAAACTAATAATATAAC-ATAAT
*
27828726 AATATAAAACTAATGATATAACATAAT
1 AATATAAAACTAATAATATAACATAAT
27828753 A
1 A
27828754 GCGGTAACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 15 0.58
28 11 0.42
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (27 bp):
AATATAAAACTAATAATATAACATAAT
Found at i:27829466 original size:8 final size:9
Alignment explanation
Indices: 27829440--27829470 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
27829430 ATATGCGGAT
27829440 AAATAAACAA
1 AAATAAA-AA
27829450 AAATAAAAA
1 AAATAAAAA
27829459 AAATAAAAA
1 AAATAAAAA
27829468 AAA
1 AAA
27829471 GATTTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 14 0.67
10 7 0.33
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.10
Consensus pattern (9 bp):
AAATAAAAA
Found at i:27833202 original size:51 final size:50
Alignment explanation
Indices: 27833075--27833204 Score: 136
Period size: 50 Copynumber: 2.6 Consensus size: 50
27833065 AAAGTGATGG
* * *
27833075 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAAAGATAGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACGACGCGTACCAGAAAGATAGA
* * * * * * * *
27833125 TCGCATGTGTAGTATTATGAGTAGGCTACGATGCGTACC-GAATAGCTTCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACGACGCGTACCAGAA-AG-ATAGA
27833176 TCACGTGTGTAGTACTATGTGCAGGCTAC
1 TCACGTGTGTAGTACTATGTGCAGGCTAC
27833205 TACGTGTATC
Statistics
Matches: 62, Mismatches: 16, Indels: 3
0.77 0.20 0.04
Matches are distributed among these distances:
49 3 0.05
50 33 0.53
51 26 0.42
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.28
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACGACGCGTACCAGAAAGATAGA
Found at i:27833236 original size:51 final size:52
Alignment explanation
Indices: 27833067--27833267 Score: 180
Period size: 51 Copynumber: 4.0 Consensus size: 52
27833057 TGAAAGTGAA
* *
27833067 AGTGAT-GGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-
1 AGTGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT
* * * * * * * * *
27833117 A-AGATAGGTCGCATGTGTAGTATTATGAGTAGGCTACGATGCGTACCGAAT
1 AGTGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT
* * * *
27833168 AGCT--TCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAT
1 AG-TGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT
* * * *
27833219 AGTGAT-GGTCACATGTGTAGTATTGTGTGCAGGCTACTATGTGAACCGG
1 AGTGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGG
27833268 TATCATTAAT
Statistics
Matches: 114, Mismatches: 31, Indels: 11
0.73 0.20 0.07
Matches are distributed among these distances:
49 3 0.03
50 36 0.32
51 74 0.65
52 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.29
Consensus pattern (52 bp):
AGTGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT
Found at i:27833531 original size:37 final size:38
Alignment explanation
Indices: 27833462--27833534 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 38
27833452 ATGTGTGGAA
* **
27833462 TTGAATTGAATATTGACTTGAAAATGGCAAAGTGAATT
1 TTGAATTGAATAGTGACTTGAAAATGAAAAAGTGAATT
*
27833500 TTGAATTGAATAGTGA-TTGAAAGTGAAAAAGTGAA
1 TTGAATTGAATAGTGACTTGAAAATGAAAAAGTGAA
27833535 ATTATGAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 16 0.52
38 15 0.48
ACGTcount: A:0.42, C:0.03, G:0.23, T:0.32
Consensus pattern (38 bp):
TTGAATTGAATAGTGACTTGAAAATGAAAAAGTGAATT
Found at i:27839264 original size:21 final size:21
Alignment explanation
Indices: 27839240--27839287 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
27839230 CGATGTCGTG
27839240 ACACTGGA-CCCTGATGTTGCA
1 ACACTGGAGCCCTG-TGTTGCA
** *
27839261 ACACTATAGGCCTGTGTTGCA
1 ACACTGGAGCCCTGTGTTGCA
27839282 ACACTG
1 ACACTG
27839288 CCCCTGTTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (21 bp):
ACACTGGAGCCCTGTGTTGCA
Found at i:27843010 original size:50 final size:50
Alignment explanation
Indices: 27842899--27843145 Score: 221
Period size: 50 Copynumber: 4.8 Consensus size: 50
27842889 ATTTGCGTAA
* *
27842899 AGAGATCCCATGTAAGACCATGTTTGGGACACGGCATTGGCACCATTGAGGTTATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACC---GA-G--ATG
* *
27842955 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* ** * *
27843005 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * * * *
27843055 AGA-ACTCTTATGTAAGACCATATCTGGGATATGGAATTGGTA--GTACAAG
1 AGAGA-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* * *
27843104 AAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
27843146 TGTTATTATC
Statistics
Matches: 159, Mismatches: 29, Indels: 13
0.79 0.14 0.06
Matches are distributed among these distances:
48 1 0.01
49 35 0.22
50 80 0.50
52 1 0.01
53 2 0.01
56 40 0.25
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.23
Consensus pattern (50 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:27851496 original size:175 final size:176
Alignment explanation
Indices: 27851186--27851540 Score: 507
Period size: 175 Copynumber: 2.0 Consensus size: 176
27851176 CTTCAATTAT
* * * *
27851186 TCAACAATGGTAACATTCTCAAACTATAACAGTACCAAAAATTACGACATGGATCAGCTAGTTTA
1 TCAAAAATGGTAACATTCTCAAAATATAACAGTACAAAAAATTACGACATGGATCAGCTAGCTTA
* *
27851251 AGTTTCCAACATTTTGAAAAACATAAAAATTTCAAGAAAAGGAATAAATTAAACTAACCAAATTG
66 AGTTTCCAACATTCTGAAAAACATAAAAATTTCAAAAAAAGGAATAAATTAAACTAACCAAATTG
* * *
27851316 AAGCTTCAAAAATTGGAGCCCTAGCCATGCTTTGAGAGTTTCTCCC
131 AAGCTTCAAAAATTAGAGCCCTAGCCATGCGTCGAGAGTTTCTCCC
*
27851362 TCAAAAATGGTAACATTCTCAAAATTTAACAGTACAAAAAATTACGACATAGG-TCAGCTAGCTT
1 TCAAAAATGGTAACATTCTCAAAATATAACAGTACAAAAAATTACGACAT-GGATCAGCTAGCTT
* ** ** * *
27851426 AATTTTCCAGGATTCTG-AAAACATAATGATTTCAAAAAAAGGACTAAATTAAACTAGCCAAATT
65 AAGTTTCCAACATTCTGAAAAACATAAAAATTTCAAAAAAAGGAATAAATTAAACTAACCAAATT
* * *
27851490 GAAGCTTGAAAATTTAGAGCCCTAGCCGTGCGTCGAGAGTTTCTCCC
130 GAAGCTTCAAAAATTAGAGCCCTAGCCATGCGTCGAGAGTTTCTCCC
27851537 TCAA
1 TCAA
27851541 TGGTTTCGAT
Statistics
Matches: 158, Mismatches: 20, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
175 87 0.55
176 69 0.44
177 2 0.01
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.27
Consensus pattern (176 bp):
TCAAAAATGGTAACATTCTCAAAATATAACAGTACAAAAAATTACGACATGGATCAGCTAGCTTA
AGTTTCCAACATTCTGAAAAACATAAAAATTTCAAAAAAAGGAATAAATTAAACTAACCAAATTG
AAGCTTCAAAAATTAGAGCCCTAGCCATGCGTCGAGAGTTTCTCCC
Found at i:27852175 original size:28 final size:28
Alignment explanation
Indices: 27852143--27852202 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
27852133 CTCGGATCGT
* * *
27852143 ACATATGTAGATTACGAAGTCGGTTTGC
1 ACATAGGTAGATTACGAAGTCAGTTTAC
*
27852171 ACATAGGTAGATTACGGAGTCAGTTTAC
1 ACATAGGTAGATTACGAAGTCAGTTTAC
27852199 ACAT
1 ACAT
27852203 GGATGCTTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (28 bp):
ACATAGGTAGATTACGAAGTCAGTTTAC
Found at i:27852474 original size:52 final size:52
Alignment explanation
Indices: 27852418--27852561 Score: 173
Period size: 52 Copynumber: 2.8 Consensus size: 52
27852408 ACAATTCACA
* * **
27852418 CATTCAATACAATGACAACTCACGTATACATTTCATCACAAAA-TAGTTCAAG
1 CATTCAATGCAATGAAAACTTGCGTATACATTTCATCACAAAACT-GTTCAAG
* * * * *
27852470 CATTCGATGCAAAGAAAATTTGTGTATACATTTCATCACAAAACTGTTCATG
1 CATTCAATGCAATGAAAACTTGCGTATACATTTCATCACAAAACTGTTCAAG
* *
27852522 CATTTAATGCAATGAAAACTTGCATATACATTTCATCACA
1 CATTCAATGCAATGAAAACTTGCGTATACATTTCATCACA
27852562 CAAAAAATTT
Statistics
Matches: 76, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
52 75 0.99
53 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.31
Consensus pattern (52 bp):
CATTCAATGCAATGAAAACTTGCGTATACATTTCATCACAAAACTGTTCAAG
Found at i:27860177 original size:20 final size:20
Alignment explanation
Indices: 27860152--27860208 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
27860142 GAAAGTTAAA
27860152 TTGAGCTCGAATGAGCTGAT
1 TTGAGCTCGAATGAGCTGAT
*
27860172 TTGAGCTCAAATGAGCTGAT
1 TTGAGCTCGAATGAGCTGAT
*
27860192 TGGAGCT-GAAATGAGCT
1 TTGAGCTCG-AATGAGCT
27860209 AAAGGAGCTG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.28, C:0.14, G:0.30, T:0.28
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTGAT
Found at i:27861717 original size:13 final size:13
Alignment explanation
Indices: 27861689--27861744 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
27861679 TAATAAATTT
*
27861689 TTAATTTT-AATT
1 TTAATTTTAAATA
27861701 TTAATTTTAAATA
1 TTAATTTTAAATA
* *
27861714 TTAATATCAAATA
1 TTAATTTTAAATA
*
27861727 TTATAATTTTCAATA
1 -T-TAATTTTAAATA
27861742 TTA
1 TTA
27861745 TTAAATATAT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
12 8 0.23
13 16 0.46
14 2 0.06
15 9 0.26
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (13 bp):
TTAATTTTAAATA
Found at i:27861826 original size:30 final size:29
Alignment explanation
Indices: 27861780--27861844 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
27861770 TTTAATAATA
* *
27861780 TAATAAATTGTTAATA-TAATTTATTATTT
1 TAATAAATTGTTAATATTAAATT-GTATTT
*
27861809 TAATAAATTATTTAATATTAAATTGTATTT
1 TAATAAATT-GTTAATATTAAATTGTATTT
27861839 TAATAA
1 TAATAA
27861845 TAAATTTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 9 0.29
30 17 0.55
31 5 0.16
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (29 bp):
TAATAAATTGTTAATATTAAATTGTATTT
Found at i:27863716 original size:4 final size:4
Alignment explanation
Indices: 27863709--27863758 Score: 100
Period size: 4 Copynumber: 12.5 Consensus size: 4
27863699 ATATGTCCAG
27863709 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
27863757 AT
1 AT
27863759 GAAAACAAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 46 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:27863984 original size:4 final size:4
Alignment explanation
Indices: 27863975--27864004 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
27863965 TAAATAATTT
*
27863975 CATA CATA CATA CGTA CATA CATA CATA CA
1 CATA CATA CATA CATA CATA CATA CATA CA
27864005 CATACAGTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.47, C:0.27, G:0.03, T:0.23
Consensus pattern (4 bp):
CATA
Found at i:27874190 original size:13 final size:13
Alignment explanation
Indices: 27874172--27874196 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27874162 GGTAGGATTT
27874172 TGTATATTTGATA
1 TGTATATTTGATA
27874185 TGTATATTTGAT
1 TGTATATTTGAT
27874197 TCTGTCATCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (13 bp):
TGTATATTTGATA
Found at i:27877421 original size:13 final size:13
Alignment explanation
Indices: 27877403--27877430 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
27877393 TACTTTTACC
27877403 ATTATTATATATA
1 ATTATTATATATA
27877416 ATTATTATATATA
1 ATTATTATATATA
27877429 AT
1 AT
27877431 CATGTGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTATTATATATA
Found at i:27878741 original size:34 final size:34
Alignment explanation
Indices: 27878703--27878793 Score: 103
Period size: 41 Copynumber: 2.5 Consensus size: 34
27878693 CAAGTACAAT
27878703 AAAAACTAGAAACGTATTATA-CCAAAAAAAAAAA
1 AAAAACTAGAAACGTATTA-ACCCAAAAAAAAAAA
27878737 AAAAACTAGAAACGTAAAACAGATTAACCCAAAAAAAAAAA
1 AAAAACTAGAAACGT-------ATTAACCCAAAAAAAAAAA
27878778 AAAAACTAGAAACGTA
1 AAAAACTAGAAACGTA
27878794 AAACAGACAA
Statistics
Matches: 49, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
34 16 0.33
40 1 0.02
41 32 0.65
ACGTcount: A:0.67, C:0.13, G:0.08, T:0.12
Consensus pattern (34 bp):
AAAAACTAGAAACGTATTAACCCAAAAAAAAAAA
Found at i:27878806 original size:40 final size:41
Alignment explanation
Indices: 27878724--27878808 Score: 154
Period size: 41 Copynumber: 2.1 Consensus size: 41
27878714 ACGTATTATA
*
27878724 CCAAAAAAAAAAAAAAAACTAGAAACGTAAAACAGATTAAC
1 CCAAAAAAAAAAAAAAAACTAGAAACGTAAAACAGATCAAC
27878765 CCAAAAAAAAAAAAAAAACTAGAAACGTAAAACAGA-CAAC
1 CCAAAAAAAAAAAAAAAACTAGAAACGTAAAACAGATCAAC
27878805 CCAA
1 CCAA
27878809 TCAATTGATT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 7 0.16
41 36 0.84
ACGTcount: A:0.68, C:0.18, G:0.07, T:0.07
Consensus pattern (41 bp):
CCAAAAAAAAAAAAAAAACTAGAAACGTAAAACAGATCAAC
Found at i:27881054 original size:13 final size:15
Alignment explanation
Indices: 27881030--27881061 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
27881020 TTTAAGTGAA
27881030 AATATGTTAATTA-T
1 AATATGTTAATTAGT
27881044 AATAT-TTAATTAGT
1 AATATGTTAATTAGT
27881058 AATA
1 AATA
27881062 AAATAAGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (15 bp):
AATATGTTAATTAGT
Found at i:27893800 original size:113 final size:113
Alignment explanation
Indices: 27893602--27893827 Score: 407
Period size: 113 Copynumber: 2.0 Consensus size: 113
27893592 GGTTTCTCAG
* * *
27893602 ACAATAACTTGGAACAACTTATCTGCTTAAAATCTTAGAGGATCTAACTAGAAGAACTAGATAAG
1 ACAATAACTTGGAACAACTTATCTGCTTAAAATCTTAGAGGATCTAACCAAAAGAACCAGATAAG
27893667 AAACACCAATTCATGGAATGAAAAACTTCTAATATTGTATGATTAACT
66 AAACACCAATTCATGGAATGAAAAACTTCTAATATTGTATGATTAACT
*
27893715 ACAATGACTTGGAACAACTTATCTGCTTAAAATCTTAGAGGATCTAACCAAAAGAACCAGATAAG
1 ACAATAACTTGGAACAACTTATCTGCTTAAAATCTTAGAGGATCTAACCAAAAGAACCAGATAAG
*
27893780 AAACACCAATTCATGGAATGAAAAACTTCTAATATTGTATGCTTAACT
66 AAACACCAATTCATGGAATGAAAAACTTCTAATATTGTATGATTAACT
27893828 GACATGTTGC
Statistics
Matches: 108, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
113 108 1.00
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.27
Consensus pattern (113 bp):
ACAATAACTTGGAACAACTTATCTGCTTAAAATCTTAGAGGATCTAACCAAAAGAACCAGATAAG
AAACACCAATTCATGGAATGAAAAACTTCTAATATTGTATGATTAACT
Found at i:27909300 original size:21 final size:23
Alignment explanation
Indices: 27909253--27909300 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
27909243 TAATTAAAAG
27909253 GTAAAA-TAAGTAAATAAATAAA
1 GTAAAACTAAGTAAATAAATAAA
27909275 -T-AAACTAAGT-AA-AAATAAA
1 GTAAAACTAAGTAAATAAATAAA
27909294 GTAAAAC
1 GTAAAAC
27909301 AAATTTTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 7 0.30
20 6 0.26
21 10 0.43
ACGTcount: A:0.67, C:0.04, G:0.08, T:0.21
Consensus pattern (23 bp):
GTAAAACTAAGTAAATAAATAAA
Found at i:27910126 original size:30 final size:29
Alignment explanation
Indices: 27910075--27910136 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
27910065 CGACCAATGA
* *
27910075 AAAGGGATGACTTCAGTTATCAAAATATAG
1 AAAGGGATAACTTCAGCTATCAAAATAT-G
*
27910105 AAAGGGATAACTTC-GACTATCAAATTATG
1 AAAGGGATAACTTCAG-CTATCAAAATATG
27910134 AAA
1 AAA
27910137 AAGGATGGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.18
30 23 0.82
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.26
Consensus pattern (29 bp):
AAAGGGATAACTTCAGCTATCAAAATATG
Found at i:27910157 original size:30 final size:30
Alignment explanation
Indices: 27910123--27910382 Score: 196
Period size: 30 Copynumber: 8.7 Consensus size: 30
27910113 AACTTCGACT
* *
27910123 ATCAAATTATGAAAAAGGATGGTGATGACC
1 ATCAAATTATGAAAAGGGATGGTGATGGCC
** * *
27910153 ATC-AACCATGAAAAGGAATGGTGACGGCC
1 ATCAAATTATGAAAAGGGATGGTGATGGCC
* * * *
27910182 ATCGAATTTTGAAAAGGGATGGCT-TTGGCT
1 ATCAAATTATGAAAAGGGATGG-TGATGGCC
* *
27910212 ATCAAATTATGAAAAGGGATGG-GTTTGGCT
1 ATCAAATTATGAAAAGGGATGGTG-ATGGCC
*
27910242 ATCAAATTATGAAAAGGGATGGCT--TCGGCT
1 ATCAAATTATGAAAAGGGATGG-TGAT-GGCC
* * *
27910272 ATCCAATTATGAAAAGGGATAGCT--TCGGCT
1 ATCAAATTATGAAAAGGGAT-GGTGAT-GGCC
* *
27910302 ATCAAATTATGAAAAGGGATGGTGACGACC
1 ATCAAATTATGAAAAGGGATGGTGATGGCC
* * *
27910332 ATTAACA--ATGAAAAGGGATGGTGACGACC
1 ATCAA-ATTATGAAAAGGGATGGTGATGGCC
*
27910361 ATCGAATTATGAAAAGGGATGG
1 ATCAAATTATGAAAAGGGATGG
27910383 CTTTGGCTCT
Statistics
Matches: 192, Mismatches: 25, Indels: 26
0.79 0.10 0.11
Matches are distributed among these distances:
28 1 0.01
29 51 0.27
30 137 0.71
31 3 0.02
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.24
Consensus pattern (30 bp):
ATCAAATTATGAAAAGGGATGGTGATGGCC
Found at i:27910255 original size:60 final size:60
Alignment explanation
Indices: 27910071--27910436 Score: 253
Period size: 60 Copynumber: 6.1 Consensus size: 60
27910061 TCATCGACCA
* ** * * *
27910071 ATGAAAAGGGATGACTTCAGTTATCAAAATAT-AGAAAGGGATAACTTCGACTATCAAATT
1 ATGAAAAGGGATGGCTTTGGCTATCAAATTATGA-AAAGGGATAGCTTCGACTATCAAATT
* * * * ** * * * * * *
27910131 ATGAAAAAGGATGG-TGATGACCATC-AACCATGAAAAGGAAT-GGTGACGGCCATCGAATT
1 ATGAAAAGGGATGGCT-TTGGCTATCAAATTATGAAAAGGGATAGCT-TCGACTATCAAATT
* * * * *
27910190 TTGAAAAGGGATGGCTTTGGCTATCAAATTATGAAAAGGGATGGGTTTGGCTATCAAATT
1 ATGAAAAGGGATGGCTTTGGCTATCAAATTATGAAAAGGGATAGCTTCGACTATCAAATT
* * *
27910250 ATGAAAAGGGATGGCTTCGGCTATCCAATTATGAAAAGGGATAGCTTCGGCTATCAAATT
1 ATGAAAAGGGATGGCTTTGGCTATCAAATTATGAAAAGGGATAGCTTCGACTATCAAATT
* * * ** * * * *
27910310 ATGAAAAGGGATGG---TGACGACCATTAACAATGAAAAGGGAT-GGTGACGACCATCGAATT
1 ATGAAAAGGGATGGCTTTGGCTATCA--AATTATGAAAAGGGATAGCT-TCGACTATCAAATT
* * * * * *
27910369 ATGAAAAGGGATGGCTTTGGCTCTCAAAATATGGAAAGGGATAGCTTTGACTATCGAACT
1 ATGAAAAGGGATGGCTTTGGCTATCAAATTATGAAAAGGGATAGCTTCGACTATCAAATT
27910429 ATGAAAAG
1 ATGAAAAG
27910437 TGGTGGTAAC
Statistics
Matches: 234, Mismatches: 59, Indels: 26
0.73 0.18 0.08
Matches are distributed among these distances:
57 4 0.02
58 3 0.01
59 78 0.33
60 139 0.59
61 5 0.02
62 5 0.02
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.25
Consensus pattern (60 bp):
ATGAAAAGGGATGGCTTTGGCTATCAAATTATGAAAAGGGATAGCTTCGACTATCAAATT
Found at i:27910352 original size:29 final size:30
Alignment explanation
Indices: 27910310--27910382 Score: 112
Period size: 29 Copynumber: 2.5 Consensus size: 30
27910300 CTATCAAATT
*
27910310 ATGAAAAGGGATGGTGACGACCAT-TAACA
1 ATGAAAAGGGATGGTGACGACCATCGAACA
**
27910339 ATGAAAAGGGATGGTGACGACCATCGAATT
1 ATGAAAAGGGATGGTGACGACCATCGAACA
27910369 ATGAAAAGGGATGG
1 ATGAAAAGGGATGG
27910383 CTTTGGCTCT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 24 0.60
30 16 0.40
ACGTcount: A:0.40, C:0.11, G:0.32, T:0.18
Consensus pattern (30 bp):
ATGAAAAGGGATGGTGACGACCATCGAACA
Found at i:27910376 original size:179 final size:179
Alignment explanation
Indices: 27910071--27910436 Score: 518
Period size: 179 Copynumber: 2.0 Consensus size: 179
27910061 TCATCGACCA
*
27910071 ATGAAAAGGGATGACTTCAGTTATCAAAATATAGAAAGGGATAACTTCGACTATCAAATTATGAA
1 ATGAAAAGGGATGACTTCAGCTATCAAAATATAGAAAGGGATAACTTCGACTATCAAATTATGAA
* * * *
27910136 AAAGGATGGTGATGACCATCAACCATGAAAAGGAATGGTGACGGCCATCGAATTTTGAAAAGGGA
66 AAAGGATGGTGACGACCATCAACAATGAAAAGGAATGGTGACGACCATCGAATTATGAAAAGGGA
* * * * *
27910201 TGGCTTTGGCTATCAAATTATGAAAAGGGATGGGTTTGGCTATCAAATT
131 TGGCTTTGGCTATCAAAATATGAAAAGGGATAGCTTTGACTATCAAACT
* * * * * *
27910250 ATGAAAAGGGATGGCTTCGGCTATCCAATTAT-GAAAAGGGATAGCTTCGGCTATCAAATTATGA
1 ATGAAAAGGGATGACTTCAGCTATCAAAATATAG-AAAGGGATAACTTCGACTATCAAATTATGA
* * *
27910314 AAAGGGATGGTGACGACCATTAACAATGAAAAGGGATGGTGACGACCATCGAATTATGAAAAGGG
65 AAAAGGATGGTGACGACCATCAACAATGAAAAGGAATGGTGACGACCATCGAATTATGAAAAGGG
* * *
27910379 ATGGCTTTGGCTCTCAAAATATGGAAAGGGATAGCTTTGACTATCGAACT
130 ATGGCTTTGGCTATCAAAATATGAAAAGGGATAGCTTTGACTATCAAACT
27910429 ATGAAAAG
1 ATGAAAAG
27910437 TGGTGGTAAC
Statistics
Matches: 164, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
178 1 0.01
179 163 0.99
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.25
Consensus pattern (179 bp):
ATGAAAAGGGATGACTTCAGCTATCAAAATATAGAAAGGGATAACTTCGACTATCAAATTATGAA
AAAGGATGGTGACGACCATCAACAATGAAAAGGAATGGTGACGACCATCGAATTATGAAAAGGGA
TGGCTTTGGCTATCAAAATATGAAAAGGGATAGCTTTGACTATCAAACT
Found at i:27918392 original size:27 final size:28
Alignment explanation
Indices: 27918311--27918405 Score: 129
Period size: 27 Copynumber: 3.4 Consensus size: 28
27918301 GAGATTGGCG
* * * *
27918311 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
27918340 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
27918368 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
27918395 CTGAGTGTGCG
1 CTAAGTGTGCG
27918406 GACTTAATAT
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.39
28 22 0.36
29 15 0.25
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.33
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:27918419 original size:29 final size:27
Alignment explanation
Indices: 27918336--27918419 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
27918326 TAAATTGTAC
* *
27918336 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTAATTATAT
* *
27918364 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTAATTATAT
*
27918391 AGCACTGAGTGTGCGGACTTAATATATAT
1 AGCACTAAGTGTGC-GACTTAAT-TATAT
27918420 TTTTGAATCA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 23 0.46
28 22 0.44
29 5 0.10
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTAATTATAT
Found at i:27923550 original size:20 final size:21
Alignment explanation
Indices: 27923513--27923551 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
27923503 TTTTGTAAAG
*
27923513 AAAACACAAACAATCAAAACT
1 AAAACACAAACAAACAAAACT
*
27923534 AAAA-ACAAATAAACAAAA
1 AAAACACAAACAAACAAAA
27923552 ACACAGATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.74, C:0.18, G:0.00, T:0.08
Consensus pattern (21 bp):
AAAACACAAACAAACAAAACT
Found at i:27924915 original size:15 final size:15
Alignment explanation
Indices: 27924895--27924950 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
27924885 AGAATGTATC
27924895 TAAAAATAAAAAAAA
1 TAAAAATAAAAAAAA
27924910 TAAAAA-AACAAAAAA
1 TAAAAATAA-AAAAAA
*
27924925 TAATGAAAATAAAAATAAT
1 T-A--AAAATAAAAA-AAA
27924944 TAAAAAT
1 TAAAAAT
27924951 TAATACACTA
Statistics
Matches: 34, Mismatches: 1, Indels: 11
0.74 0.02 0.24
Matches are distributed among these distances:
14 2 0.06
15 13 0.38
16 6 0.18
18 8 0.24
19 5 0.15
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.18
Consensus pattern (15 bp):
TAAAAATAAAAAAAA
Found at i:27927728 original size:13 final size:13
Alignment explanation
Indices: 27927710--27927734 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27927700 AATTTATATA
27927710 TGTGAAAATTTTG
1 TGTGAAAATTTTG
27927723 TGTGAAAATTTT
1 TGTGAAAATTTT
27927735 ATCGTTTGTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (13 bp):
TGTGAAAATTTTG
Found at i:27928903 original size:44 final size:43
Alignment explanation
Indices: 27928852--27928973 Score: 115
Period size: 44 Copynumber: 2.8 Consensus size: 43
27928842 GAATGAGTTA
* *
27928852 TCGTGTAAGACCACGTCTGGGACATTGGCATCGATTTGA-GATT
1 TCGTGTAAGACCACGTCTGGGACATTGGCATCGATAT-ACAATT
* * * * *
27928895 TACGTGTAAGACCATGTCTAGGATATCGACATCG-TATACAATT
1 T-CGTGTAAGACCACGTCTGGGACATTGGCATCGATATACAATT
* *
27928938 TCGTGTAAGACC-CTGTTTGGGACAGTGGCATCGATA
1 TCGTGTAAGACCAC-GTCTGGGACATTGGCATCGATA
27928974 CATGTAAGAT
Statistics
Matches: 61, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
42 25 0.41
43 9 0.15
44 27 0.44
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (43 bp):
TCGTGTAAGACCACGTCTGGGACATTGGCATCGATATACAATT
Found at i:27929849 original size:13 final size:13
Alignment explanation
Indices: 27929831--27929855 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27929821 ATGTTTCATT
27929831 ATTGTTTTGGTAG
1 ATTGTTTTGGTAG
27929844 ATTGTTTTGGTA
1 ATTGTTTTGGTA
27929856 CGGATCCAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.28, T:0.56
Consensus pattern (13 bp):
ATTGTTTTGGTAG
Found at i:27935299 original size:28 final size:29
Alignment explanation
Indices: 27935267--27935365 Score: 107
Period size: 28 Copynumber: 3.5 Consensus size: 29
27935257 ATAATAAGCC
*
27935267 CGCACACTTAGTGCTTA-ATAGTCGAACT
1 CGCACACTTAGTGCTTACATAATCGAACT
*
27935295 CGCACACTTAGTGC-TATATAATC-AACCT
1 CGCACACTTAGTGCTTACATAATCGAA-CT
* * *
27935323 CGCACACTTAGTGCTATACA-ATTTGAACC
1 CGCACACTTAGTGCT-TACATAATCGAACT
27935352 CGCACACTTAGTGC
1 CGCACACTTAGTGC
27935366 CAATCTCATG
Statistics
Matches: 61, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
27 4 0.07
28 35 0.57
29 17 0.28
30 5 0.08
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCTTACATAATCGAACT
Found at i:27938895 original size:13 final size:13
Alignment explanation
Indices: 27938877--27938901 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27938867 TAATTTATAT
27938877 GTGTGAAAATTTC
1 GTGTGAAAATTTC
27938890 GTGTGAAAATTT
1 GTGTGAAAATTT
27938902 TATCGTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:27941015 original size:13 final size:13
Alignment explanation
Indices: 27940999--27941024 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27940989 ATATGTTTCA
27940999 TGATTGTTTTGGT
1 TGATTGTTTTGGT
27941012 TGATTGTTTTGGT
1 TGATTGTTTTGGT
27941025 ATGGATCCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.00, G:0.31, T:0.62
Consensus pattern (13 bp):
TGATTGTTTTGGT
Found at i:27945437 original size:50 final size:50
Alignment explanation
Indices: 27945383--27945482 Score: 146
Period size: 50 Copynumber: 2.0 Consensus size: 50
27945373 TACAGAAGAA
* * *
27945383 GTATCTGGAAATAAATCTACAAATTTTTGGTGGCATGTCCACATTATTCT
1 GTATCTGGAAATAAATCTACAAATATTTGGTGGCATGACCACACTATTCT
* * *
27945433 GTATCTGGCAGTAAATCTACAAATATTTGGTGGCTTGACCACACTATTCT
1 GTATCTGGAAATAAATCTACAAATATTTGGTGGCATGACCACACTATTCT
27945483 ATTTCTGACA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (50 bp):
GTATCTGGAAATAAATCTACAAATATTTGGTGGCATGACCACACTATTCT
Found at i:27954109 original size:18 final size:19
Alignment explanation
Indices: 27954079--27954115 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
27954069 TTTGCAAAAA
*
27954079 CATCACAATCACATAATAT
1 CATCACAATCACACAATAT
27954098 CATCAC-ATCACACAATAT
1 CATCACAATCACACAATAT
27954116 ACTTTTCAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.24
Consensus pattern (19 bp):
CATCACAATCACACAATAT
Found at i:27964016 original size:27 final size:27
Alignment explanation
Indices: 27963986--27964163 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
27963976 ATATTGAGTC
* * * *
27963986 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
27964013 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
27964040 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
27964068 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
27964095 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
27964122 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
27964149 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
27964164 GTACAATTTA
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:27964125 original size:82 final size:81
Alignment explanation
Indices: 27964007--27964162 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
27963997 TGCTATATAA
* *
27964007 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
27964072 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
27964089 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
27964153 CACTTAGTGC
65 CACTTAGTGC
27964163 TGTACAATTT
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:27968300 original size:32 final size:32
Alignment explanation
Indices: 27968245--27968380 Score: 168
Period size: 32 Copynumber: 4.3 Consensus size: 32
27968235 AAATGGCTAC
* *
27968245 AAGCCATAAGT-ACAGTAATATGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* *
27968276 AAGCCATCAGTAGCAGTGATATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * *
27968308 TAGTCATCAGTAAC-GATAATATGATCGGTACA
1 AAGCCATCAGTAACAG-TAATATGATCGGCACA
* *
27968340 AAACCATCAGTAACAGTGATATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
27968372 AAGCCATCA
1 AAGCCATCA
27968381 ATAGCATCAC
Statistics
Matches: 87, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
31 11 0.13
32 75 0.86
33 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTAATATGATCGGCACA
Found at i:27968361 original size:64 final size:64
Alignment explanation
Indices: 27968260--27968380 Score: 188
Period size: 64 Copynumber: 1.9 Consensus size: 64
27968250 ATAAGTACAG
* * * * *
27968260 TAATATGATTGGCACAAAGCCATCAGTAGCAGTGATATGATCGGCACATAGTCATCAGTAACGA
1 TAATATGATCGGCACAAAACCATCAGTAACAGTGATATGATCGGCACAAAGCCATCAGTAACGA
*
27968324 TAATATGATCGGTACAAAACCATCAGTAACAGTGATATGATCGGCACAAAGCCATCA
1 TAATATGATCGGCACAAAACCATCAGTAACAGTGATATGATCGGCACAAAGCCATCA
27968381 ATAGCATCAC
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
64 51 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (64 bp):
TAATATGATCGGCACAAAACCATCAGTAACAGTGATATGATCGGCACAAAGCCATCAGTAACGA
Found at i:27968408 original size:23 final size:24
Alignment explanation
Indices: 27968382--27968432 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 24
27968372 AAGCCATCAA
27968382 TAGC-ATCACAGCAAAGCTGCCAG
1 TAGCAATCACAGCAAAGCTGCCAG
*
27968405 TAGCAATATCGCAGCAAAGCTGCCAG
1 TAGC-A-ATCACAGCAAAGCTGCCAG
27968431 TA
1 TA
27968433 ATAGTATATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 4 0.17
26 20 0.83
ACGTcount: A:0.35, C:0.27, G:0.22, T:0.16
Consensus pattern (24 bp):
TAGCAATCACAGCAAAGCTGCCAG
Found at i:27968628 original size:23 final size:23
Alignment explanation
Indices: 27968555--27968637 Score: 76
Period size: 24 Copynumber: 3.5 Consensus size: 23
27968545 CCATGCTCAG
**
27968555 AATCAGTCATACAAATCACAGACA
1 AATCAGTCATTTAAA-CACAGACA
* ** *
27968579 AACCAGTCATACCAAACATAGACA
1 AATCAGTCAT-TTAAACACAGACA
*
27968603 AATCAGTCATTTAACCACAGACA
1 AATCAGTCATTTAAACACAGACA
*
27968626 AATCAATCATTT
1 AATCAGTCATTT
27968638 GACCTCGAGG
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
23 20 0.41
24 25 0.51
25 4 0.08
ACGTcount: A:0.47, C:0.25, G:0.07, T:0.20
Consensus pattern (23 bp):
AATCAGTCATTTAAACACAGACA
Found at i:27968716 original size:27 final size:27
Alignment explanation
Indices: 27968680--27968853 Score: 188
Period size: 27 Copynumber: 6.4 Consensus size: 27
27968670 CAAGGCATTC
* * *
27968680 CGGTTATTTTATCCTACAAGGGTATTA
1 CGGTCATTTTACCCTACAGGGGTATTA
** * * *
27968707 CAATCATTTTACCTTATAGGGGCATTA
1 CGGTCATTTTACCCTACAGGGGTATTA
* * *
27968734 TGGTCATTTTACCTTATAGGGGTATTA
1 CGGTCATTTTACCCTACAGGGGTATTA
* * *
27968761 CGGTTATTTTACCCTACAAGGGCATTA
1 CGGTCATTTTACCCTACAGGGGTATTA
*
27968788 CAGTCATTTT-CCACTACAGGGGTATTA
1 CGGTCATTTTACC-CTACAGGGGTATTA
27968815 CGGTCATTTTACCCTACAGGGGTATTA
1 CGGTCATTTTACCCTACAGGGGTATTA
*
27968842 CGATCATTTTAC
1 CGGTCATTTTAC
27968854 AAGCTTTTCG
Statistics
Matches: 121, Mismatches: 24, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
26 2 0.02
27 117 0.97
28 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.37
Consensus pattern (27 bp):
CGGTCATTTTACCCTACAGGGGTATTA
Found at i:27968769 original size:81 final size:81
Alignment explanation
Indices: 27968680--27968853 Score: 233
Period size: 81 Copynumber: 2.1 Consensus size: 81
27968670 CAAGGCATTC
* * * * *
27968680 CGGTTATTTTATCCTACAAGGGTATTACAATCATTTTACC-TTATAGGGGCATTATGGTCATTTT
1 CGGTTATTTTACCCTACAAGGGCATTACAATCATTTT-CCACTACAGGGGCATTACGGTCATTTT
* *
27968744 ACCTTATAGGGGTATTA
65 ACCCTACAGGGGTATTA
* *
27968761 CGGTTATTTTACCCTACAAGGGCATTACAGTCATTTTCCACTACAGGGGTATTACGGTCATTTTA
1 CGGTTATTTTACCCTACAAGGGCATTACAATCATTTTCCACTACAGGGGCATTACGGTCATTTTA
27968826 CCCTACAGGGGTATTA
66 CCCTACAGGGGTATTA
* *
27968842 CGATCATTTTAC
1 CGGTTATTTTAC
27968854 AAGCTTTTCG
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
80 2 0.02
81 79 0.98
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.37
Consensus pattern (81 bp):
CGGTTATTTTACCCTACAAGGGCATTACAATCATTTTCCACTACAGGGGCATTACGGTCATTTTA
CCCTACAGGGGTATTA
Found at i:27977664 original size:54 final size:56
Alignment explanation
Indices: 27977606--27977734 Score: 163
Period size: 62 Copynumber: 2.2 Consensus size: 56
27977596 TTTAAAGTGA
** *
27977606 GAAAACTAGTTTAATT-TGCA-GATAAAAGTGCTTGTATTCAAGCTCCTTAACTAT
1 GAAAACTAGTTTAATTAAACATAATAAAAGTGCTTGTATTCAAGCTCCTTAACTAT
27977660 GAAAACTAGGAAAATTTAATTAAAACATAATAAAAGTGCTTGTATTCAAGCTCCTTAACTAT
1 GAAAACTA-G----TTTAATT-AAACATAATAAAAGTGCTTGTATTCAAGCTCCTTAACTAT
27977722 GAAAACTAGTTTA
1 GAAAACTAGTTTA
27977735 GTCTACTACA
Statistics
Matches: 64, Mismatches: 3, Indels: 13
0.80 0.04 0.16
Matches are distributed among these distances:
54 8 0.12
55 1 0.02
57 4 0.06
59 7 0.11
61 3 0.05
62 41 0.64
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (56 bp):
GAAAACTAGTTTAATTAAACATAATAAAAGTGCTTGTATTCAAGCTCCTTAACTAT
Found at i:27981404 original size:12 final size:14
Alignment explanation
Indices: 27981387--27981419 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
27981377 TAATGGTCAC
27981387 ATGTGTA-G-TACT
1 ATGTGTAGGCTACT
27981399 ATGTGTAGGCTACT
1 ATGTGTAGGCTACT
27981413 ATGTGTA
1 ATGTGTA
27981420 CCGGATGGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 1 0.05
14 11 0.58
ACGTcount: A:0.24, C:0.09, G:0.27, T:0.39
Consensus pattern (14 bp):
ATGTGTAGGCTACT
Found at i:27981413 original size:51 final size:50
Alignment explanation
Indices: 27981337--27981553 Score: 163
Period size: 51 Copynumber: 4.3 Consensus size: 50
27981327 TATGAAGACG
* * * * *
27981337 TGTGTAGTACTAAGTGCAAGCTACTATGTGTATC-GATAGATAATGGTCACA
1 TGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGATAGAT--TGGTCACA
* * * *
27981388 TGTGTAGTACTATGTGTAGGCTACTATGTGTACCGGATGGCCTTGGTCACG
1 TGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGATAG-ATTGGTCACA
* * * * * * * *
27981439 TGTGTAGTATTATGTGTA-G-TACTGCATGAACCGGAAAGCTTGATCACG
1 TGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGATAGATTGGTCACA
* * *
27981487 TGTGTAGTACTATGTGTAGGCTAATACGTGTATCGAAT-GATAATGGTCACA
1 TGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGATAGAT--TGGTCACA
* *
27981538 TGGGTGGTACTATGTG
1 TGTGTAGTACTATGTG
27981554 CAAACCACCG
Statistics
Matches: 132, Mismatches: 28, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
48 26 0.20
49 16 0.12
50 11 0.08
51 74 0.56
52 4 0.03
53 1 0.01
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.33
Consensus pattern (50 bp):
TGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGATAGATTGGTCACA
Found at i:27981501 original size:48 final size:50
Alignment explanation
Indices: 27981383--27981505 Score: 142
Period size: 48 Copynumber: 2.5 Consensus size: 50
27981373 TAGATAATGG
* ** * ** *
27981383 TCACATGTGTAGTACTATGTGTAGGCTACTATGTGTACCGGATGGCCTTGG
1 TCACGTGTGTAGTACTATGTGTA-GCTACTACATGAACCGGAAAGCCTTGA
* *
27981434 TCACGTGTGTAGTATTATGTGTAG-TACTGCATGAACCGGAAAG-CTTGA
1 TCACGTGTGTAGTACTATGTGTAGCTACTACATGAACCGGAAAGCCTTGA
27981482 TCACGTGTGTAGTACTATGTGTAG
1 TCACGTGTGTAGTACTATGTGTAG
27981506 GCTAATACGT
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
48 27 0.44
49 13 0.21
50 1 0.02
51 21 0.34
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.33
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTGTAGCTACTACATGAACCGGAAAGCCTTGA
Found at i:27988799 original size:9 final size:9
Alignment explanation
Indices: 27988785--27988826 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
27988775 TTTGGTTAAA
*
27988785 AATTAATCG
1 AATTAACCG
*
27988794 AATTAACCA
1 AATTAACCG
27988803 AATTAACCG
1 AATTAACCG
27988812 AATT-ACTCG
1 AATTAAC-CG
27988821 AATTAA
1 AATTAA
27988827 AAGAATTGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
8 2 0.07
9 25 0.89
10 1 0.04
ACGTcount: A:0.48, C:0.17, G:0.07, T:0.29
Consensus pattern (9 bp):
AATTAACCG
Found at i:27988979 original size:13 final size:13
Alignment explanation
Indices: 27988961--27988985 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27988951 TATGATTAGG
27988961 TTGGGTTGGGTAA
1 TTGGGTTGGGTAA
27988974 TTGGGTTGGGTA
1 TTGGGTTGGGTA
27988986 GGATACTTGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
TTGGGTTGGGTAA
Found at i:27988982 original size:18 final size:18
Alignment explanation
Indices: 27988959--27988998 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
27988949 TTTATGATTA
* *
27988959 GGTTGGGTTGGGTAATTG
1 GGTTGGGTAGGATAATTG
*
27988977 GGTTGGGTAGGATACTTG
1 GGTTGGGTAGGATAATTG
27988995 GGTT
1 GGTT
27988999 TGGATTAGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.12, C:0.03, G:0.47, T:0.38
Consensus pattern (18 bp):
GGTTGGGTAGGATAATTG
Found at i:27989204 original size:18 final size:19
Alignment explanation
Indices: 27989177--27989228 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
27989167 AACCGACCGA
*
27989177 TTAACTGAATTTTGTCGG-
1 TTAACCGAATTTTGTCGGT
*
27989195 TTAACCGAATTTTTTCGGTT
1 TTAACCGAATTTTGTCGG-T
*
27989215 TTACCCGAATTTTG
1 TTAACCGAATTTTG
27989229 CACACCTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 16 0.57
20 12 0.43
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.46
Consensus pattern (19 bp):
TTAACCGAATTTTGTCGGT
Found at i:27993780 original size:15 final size:16
Alignment explanation
Indices: 27993747--27993777 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27993737 TTAAAATTTC
27993747 TTTTCTGCATTTAAAA
1 TTTTCTGCATTTAAAA
*
27993763 TTTTCTTCATTTAAA
1 TTTTCTGCATTTAAA
27993778 TTTAAATTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.13, G:0.03, T:0.55
Consensus pattern (16 bp):
TTTTCTGCATTTAAAA
Found at i:28015417 original size:29 final size:29
Alignment explanation
Indices: 28015361--28015419 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
28015351 CCCTCCAAGC
28015361 TTTGATTTTTAAATTTTCATGATCATTCAT
1 TTTGATTTTTAAATTTTCATGA-CATTCAT
**
28015391 TTTGATTTTTATCTATTTCATG-CATTCAT
1 TTTGATTTTTAAAT-TTTCATGACATTCAT
28015420 GTAGTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 7 0.27
30 12 0.46
31 7 0.27
ACGTcount: A:0.24, C:0.12, G:0.07, T:0.58
Consensus pattern (29 bp):
TTTGATTTTTAAATTTTCATGACATTCAT
Found at i:28017563 original size:20 final size:20
Alignment explanation
Indices: 28017538--28017656 Score: 105
Period size: 20 Copynumber: 6.0 Consensus size: 20
28017528 GATGCATAAT
* *
28017538 AGGGGCACTGAAGTGCAGAC
1 AGGGGCACTAAAGTGCAAAC
28017558 AGGGGCAC-AAATGTGCAAAC
1 AGGGGCACTAAA-GTGCAAAC
**
28017578 AGGGGCACTGTAGTGCAAAC
1 AGGGGCACTAAAGTGCAAAC
* * * *
28017598 AGAGACACTAAAGTGTATAC
1 AGGGGCACTAAAGTGCAAAC
* *
28017618 AGGGGCACCAAATTGCAAAC
1 AGGGGCACTAAAGTGCAAAC
* **
28017638 AAGGGCACCGAAGTGCAAA
1 AGGGGCACTAAAGTGCAAA
28017657 TCTCGTACAA
Statistics
Matches: 78, Mismatches: 19, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
19 2 0.03
20 75 0.96
21 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.30, T:0.12
Consensus pattern (20 bp):
AGGGGCACTAAAGTGCAAAC
Found at i:28025031 original size:40 final size:40
Alignment explanation
Indices: 28024948--28025132 Score: 164
Period size: 40 Copynumber: 4.7 Consensus size: 40
28024938 TTGAATGCTG
* * * *
28024948 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGA-T-ACTAAA
*
28024988 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCCTTTGTGCGAGATACTAAA
* * **
28025028 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGA-ATTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGA-TACTAAA
* * * *
28025068 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAA
* *
28025107 TCCGGGCTATGTCCCGAAGGCCTTTG
1 TCCGGGTTAAGTCCCGAAGGCCTTTG
28025133 AACGAGGAGC
Statistics
Matches: 118, Mismatches: 20, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
39 32 0.27
40 74 0.63
41 11 0.09
42 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAA
Found at i:28025126 original size:79 final size:80
Alignment explanation
Indices: 28024948--28025127 Score: 213
Period size: 80 Copynumber: 2.3 Consensus size: 80
28024938 TTGAATGCTG
* * * *
28024948 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGATTAAGATCCGAAGGCCTTT
1 TCCGGGCTAAGTCCCGAAGGCTTCGTGCGAAGTGAATAAATCCGGATTAAGATCCGAAGGCCATT
28025013 GTGCGAGATACTAAA
66 GTGCGAGATACTAAA
* * * * *
28025028 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAATTG-TTAAATCCGGGTTATG-TCCCGAAGG-CA
1 TCCGGGCTAAGTCCCGAAGGC-TTCGTGCGAAGTGAATAAATCCGGATTAAGAT-CCGAAGGCCA
* *
28025090 TTGTGTGAGTTACTAAA
64 TTGTGCGAGATACTAAA
*
28025107 TCCGGGCTATGTCCCGAAGGC
1 TCCGGGCTAAGTCCCGAAGGC
28025128 CTTTGAACGA
Statistics
Matches: 85, Mismatches: 13, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
79 36 0.42
80 39 0.46
81 10 0.12
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCTTCGTGCGAAGTGAATAAATCCGGATTAAGATCCGAAGGCCATT
GTGCGAGATACTAAA
Found at i:28026713 original size:21 final size:21
Alignment explanation
Indices: 28026664--28026716 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
28026654 CAATTTGGTT
*
28026664 TTTTATTTTTATTTTTATTTA
1 TTTTATTTTTATTTTTATTGA
* *
28026685 ATTAATTTTTATTTTT-TGTGA
1 TTTTATTTTTATTTTTAT-TGA
28026706 TTTTATTTTTA
1 TTTTATTTTTA
28026717 GGTGTTTATG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 1 0.04
21 25 0.96
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (21 bp):
TTTTATTTTTATTTTTATTGA
Found at i:28034659 original size:56 final size:57
Alignment explanation
Indices: 28034593--28034754 Score: 220
Period size: 56 Copynumber: 2.9 Consensus size: 57
28034583 GAACATGCTA
* * *
28034593 GAAAAATGGAAGCCTTTGTGGTAGTCTAT-AAAATGGAAGCCTTTGTGGCAATCTAT
1 GAAAAATGGAAGCCTTTGTGGCAATCTATGAAAATGGAAGCCTTTGTGGCAATATAT
* *
28034649 GAAAAATGGAAGCTTTTGTGGCAATCTATGAGAAATGGAAGCTTTTGTGGCAATATAT
1 GAAAAATGGAAGCCTTTGTGGCAATCTATGA-AAATGGAAGCCTTTGTGGCAATATAT
* * * *
28034707 G-AAAATGGTAGCCTTTATGGCAATTTGTGAAAATGGAAGCCTTTGTGG
1 GAAAAATGGAAGCCTTTGTGGCAATCTATGAAAATGGAAGCCTTTGTGG
28034755 AGAACTATGA
Statistics
Matches: 93, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
56 43 0.46
57 25 0.27
58 25 0.27
ACGTcount: A:0.32, C:0.10, G:0.27, T:0.31
Consensus pattern (57 bp):
GAAAAATGGAAGCCTTTGTGGCAATCTATGAAAATGGAAGCCTTTGTGGCAATATAT
Found at i:28034727 original size:28 final size:28
Alignment explanation
Indices: 28034595--28034775 Score: 215
Period size: 29 Copynumber: 6.5 Consensus size: 28
28034585 ACATGCTAGA
* *
28034595 AAAATGGAAGCCTTTGTGGTAGTCTAT-
1 AAAATGGAAGCCTTTGTGGCAATCTATG
28034622 AAAATGGAAGCCTTTGTGGCAATCTATG
1 AAAATGGAAGCCTTTGTGGCAATCTATG
*
28034650 AAAAATGGAAGCTTTTGTGGCAATCTATG
1 -AAAATGGAAGCCTTTGTGGCAATCTATG
* *
28034679 AGAAATGGAAGCTTTTGTGGCAATATATG
1 A-AAATGGAAGCCTTTGTGGCAATCTATG
* * * *
28034708 AAAATGGTAGCCTTTATGGCAATTTGTG
1 AAAATGGAAGCCTTTGTGGCAATCTATG
*
28034736 AAAATGGAAGCCTTTGTGG-AGAACTATG
1 AAAATGGAAGCCTTTGTGGCA-ATCTATG
*
28034764 -AGATGGAAGCCT
1 AAAATGGAAGCCT
28034776 CTATGGAGAT
Statistics
Matches: 135, Mismatches: 15, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
27 37 0.27
28 44 0.33
29 54 0.40
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.30
Consensus pattern (28 bp):
AAAATGGAAGCCTTTGTGGCAATCTATG
Found at i:28034763 original size:85 final size:85
Alignment explanation
Indices: 28034596--28034775 Score: 224
Period size: 85 Copynumber: 2.1 Consensus size: 85
28034586 CATGCTAGAA
* * * *
28034596 AAATGGAAGCCTTTGTGGTAGTCTATAAAATGGAAGCCTTTGTGGCAATCTATGAAAAATGGAAG
1 AAATGGAAGCCTTTGTGGCAATATATAAAATGGAAGCCTTTATGGCAATCTATGAAAAATGGAAG
* *
28034661 CTTTTGTGGCAATCTATGAG
66 CCTTTGTGGCAAACTATGAG
* * * *
28034681 AAATGGAAGCTTTTGTGGCAATATATGAAAATGGTAGCCTTTATGGCAATTTGTG-AAAATGGAA
1 AAATGGAAGCCTTTGTGGCAATATAT-AAAATGGAAGCCTTTATGGCAATCTATGAAAAATGGAA
28034745 GCCTTTGTGG-AGAACTATGAG
65 GCCTTTGTGGCA-AACTATGAG
28034766 --ATGGAAGCCT
1 AAATGGAAGCCT
28034776 CTATGGAGAT
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
83 9 0.11
84 1 0.01
85 48 0.59
86 24 0.29
ACGTcount: A:0.32, C:0.11, G:0.27, T:0.30
Consensus pattern (85 bp):
AAATGGAAGCCTTTGTGGCAATATATAAAATGGAAGCCTTTATGGCAATCTATGAAAAATGGAAG
CCTTTGTGGCAAACTATGAG
Found at i:28037419 original size:33 final size:33
Alignment explanation
Indices: 28037382--28037493 Score: 152
Period size: 33 Copynumber: 3.4 Consensus size: 33
28037372 GTCGGGTTGA
* *
28037382 CACTCCACCATCGACGCACTGCCGTCAGACCAC
1 CACTCCACCATCGACGCACCGCTGTCAGACCAC
* *
28037415 CACTCCACCATTGTCGCACCGCTGTCAGACCAC
1 CACTCCACCATCGACGCACCGCTGTCAGACCAC
* * **
28037448 CACTCCACCATCGCCACACCGCTGTTGGACCAC
1 CACTCCACCATCGACGCACCGCTGTCAGACCAC
28037481 CACTCCACCATCG
1 CACTCCACCATCG
28037494 TTGGACCTCC
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 70 1.00
ACGTcount: A:0.22, C:0.48, G:0.14, T:0.15
Consensus pattern (33 bp):
CACTCCACCATCGACGCACCGCTGTCAGACCAC
Found at i:28039992 original size:29 final size:30
Alignment explanation
Indices: 28039940--28040016 Score: 95
Period size: 29 Copynumber: 2.6 Consensus size: 30
28039930 ATGGAGATTA
* * * *
28039940 CCACAAAGGCTTTTCCTGT-CCAGAGTTTG
1 CCACAAAGGCTTTTCCTTTGACAGAGATCG
*
28039969 CCACAGAGGC-TTTCCTTTGACAGAGATCG
1 CCACAAAGGCTTTTCCTTTGACAGAGATCG
28039998 CCACAAAGGCTTTTCCTTT
1 CCACAAAGGCTTTTCCTTT
28040017 TAGATATTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
28 7 0.17
29 25 0.62
30 8 0.20
ACGTcount: A:0.22, C:0.29, G:0.19, T:0.30
Consensus pattern (30 bp):
CCACAAAGGCTTTTCCTTTGACAGAGATCG
Found at i:28040091 original size:29 final size:29
Alignment explanation
Indices: 28040054--28040179 Score: 116
Period size: 28 Copynumber: 4.4 Consensus size: 29
28040044 AAGAAGTTCA
28040054 CCACAAAGGCTTACCTTTCTAAAGTTTTG
1 CCACAAAGGCTTACCTTTCTAAAGTTTTG
* * ***
28040083 CCACAAAGG-TTGACCTTTC-ACAGGTACA
1 CCACAAAGGCTT-ACCTTTCTAAAGTTTTG
*
28040111 CCACAAAGGCTTACCTTTCCAAAGTTTTG
1 CCACAAAGGCTTACCTTTCTAAAGTTTTG
* ** *
28040140 CCACAAAGGC-GACCTTAAATAAAG-ATTG
1 CCACAAAGGCTTACCTT-TCTAAAGTTTTG
28040168 CCACAAAGGCTT
1 CCACAAAGGCTT
28040180 TTCTTTTCCT
Statistics
Matches: 76, Mismatches: 16, Indels: 10
0.75 0.16 0.10
Matches are distributed among these distances:
28 40 0.53
29 36 0.47
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (29 bp):
CCACAAAGGCTTACCTTTCTAAAGTTTTG
Found at i:28040154 original size:28 final size:29
Alignment explanation
Indices: 28040054--28040155 Score: 109
Period size: 29 Copynumber: 3.6 Consensus size: 29
28040044 AAGAAGTTCA
* *
28040054 CCACAAAGGCTTACCTTTCTAAAGTTTTG
1 CCACAAAGGCTGACCTTTCCAAAGTTTTG
* * * ***
28040083 CCACAAAGGTTGACCTTT-CACAGGTACA
1 CCACAAAGGCTGACCTTTCCAAAGTTTTG
*
28040111 CCACAAAGGCTTACCTTTCCAAAGTTTTG
1 CCACAAAGGCTGACCTTTCCAAAGTTTTG
28040140 CCACAAAGGC-GACCTT
1 CCACAAAGGCTGACCTT
28040156 AAATAAAGAT
Statistics
Matches: 56, Mismatches: 16, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
28 25 0.45
29 31 0.55
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.26
Consensus pattern (29 bp):
CCACAAAGGCTGACCTTTCCAAAGTTTTG
Found at i:28046587 original size:12 final size:12
Alignment explanation
Indices: 28046572--28046599 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
28046562 TACTTACTTT
28046572 CTTACTTGTTTA
1 CTTACTTGTTTA
28046584 CTTACTTGTTTA
1 CTTACTTGTTTA
28046596 CTTA
1 CTTA
28046600 AATAACTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.18, C:0.18, G:0.07, T:0.57
Consensus pattern (12 bp):
CTTACTTGTTTA
Found at i:28046953 original size:50 final size:50
Alignment explanation
Indices: 28046850--28046995 Score: 157
Period size: 50 Copynumber: 2.9 Consensus size: 50
28046840 TTTCCTGCAC
* * * * *
28046850 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATATCCCAGACATGGTCTTACAGGGGACTTCTCATATCAG
* * * * * * * *
28046900 TGCCCATGTCATGTCCCAGACATGGCCTTACGGGGGACTTCTTATCTCAG
1 TGCCAACGCCATATCCCAGACATGGTCTTACAGGGGACTTCTCATATCAG
* *
28046950 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATA
1 TGCCAACGCCATATCCCAGACATGGTCTTACAGGGGACTTCTCATA
28046996 ATCTCAATGA
Statistics
Matches: 75, Mismatches: 21, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
50 75 1.00
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATATCCCAGACATGGTCTTACAGGGGACTTCTCATATCAG
Found at i:28054485 original size:24 final size:24
Alignment explanation
Indices: 28054458--28054503 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
28054448 AAATTACAAT
* *
28054458 TAAAATTTAATTTAATATTTAATA
1 TAAAATATAATTCAATATTTAATA
28054482 TAAAATATAATTCAATATTTAA
1 TAAAATATAATTCAATATTTAA
28054504 ACTATTAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
TAAAATATAATTCAATATTTAATA
Found at i:28054654 original size:29 final size:31
Alignment explanation
Indices: 28054622--28054689 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 31
28054612 TTAATATAAA
28054622 ATTTAAATTTA-TTAT-TATATTTTTAAAAT
1 ATTTAAATTTACTTATATATATTTTTAAAAT
* *
28054651 ATTT--ATGTACTTTTATATATTTTTAAAAT
1 ATTTAAATTTACTTATATATATTTTTAAAAT
*
28054680 TTTTAGAATT
1 ATTTA-AATT
28054690 AGATCAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
27 4 0.13
28 3 0.10
29 21 0.70
32 2 0.07
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (31 bp):
ATTTAAATTTACTTATATATATTTTTAAAAT
Found at i:28064122 original size:26 final size:26
Alignment explanation
Indices: 28064064--28064122 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
28064054 GACTAAAATA
* *
28064064 TGAATTTTTATAAAAAAATTAAAAAAG
1 TGAA-TTTAATAAAAAAATCAAAAAAG
*
28064091 TTAATTTAATAAAAAAATCATAAAAAG
1 TGAATTTAATAAAAAAATCA-AAAAAG
28064118 -GAATT
1 TGAATT
28064123 ACATTTGAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 18 0.67
27 9 0.33
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (26 bp):
TGAATTTAATAAAAAAATCAAAAAAG
Found at i:28065787 original size:98 final size:98
Alignment explanation
Indices: 28065610--28065804 Score: 327
Period size: 98 Copynumber: 2.0 Consensus size: 98
28065600 TACAATAAAA
* *
28065610 CTTTAAAAGAACATTCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATTC
1 CTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTC
* *
28065675 CTCTAGAATCCCAAACTCGGAATATTTCCTTTT
66 CTCTAAAATCCCAAACTCAGAATATTTCCTTTT
*
28065708 CTTTAAAAGAACCTCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTC
1 CTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTC
* *
28065773 CTTTAAAATTCCAAACTCAGAATATTTCCTTT
66 CTCTAAAATCCCAAACTCAGAATATTTCCTTT
28065805 ATTATTTAAA
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 90 1.00
ACGTcount: A:0.36, C:0.25, G:0.10, T:0.30
Consensus pattern (98 bp):
CTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTC
CTCTAAAATCCCAAACTCAGAATATTTCCTTTT
Found at i:28066097 original size:9 final size:9
Alignment explanation
Indices: 28066083--28066107 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
28066073 TGCAAATGCT
28066083 ATAATAACA
1 ATAATAACA
28066092 ATAATAACA
1 ATAATAACA
28066101 ATAATAA
1 ATAATAA
28066108 ATACATCGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (9 bp):
ATAATAACA
Found at i:28067130 original size:22 final size:21
Alignment explanation
Indices: 28067095--28067171 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 21
28067085 AAAGGGTATC
* *
28067095 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
28067116 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
*
28067139 TACATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
28067158 TGCATATCATATCT
1 TACAAATCATATCT
28067172 AGGATTGCAT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
19 18 0.38
21 4 0.08
22 15 0.31
23 11 0.23
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.36
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:28067138 original size:23 final size:22
Alignment explanation
Indices: 28067095--28067152 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
28067085 AAAGGGTATC
* *
28067095 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
28067116 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
28067139 TACATATCATATCT
1 TACAAATCATATCT
28067153 AAGATTGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.09
22 18 0.56
23 11 0.34
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:28067155 original size:19 final size:19
Alignment explanation
Indices: 28067131--28067203 Score: 128
Period size: 19 Copynumber: 3.8 Consensus size: 19
28067121 AATCATATCT
*
28067131 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
28067150 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
28067169 TCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
28067188 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
28067204 TTCAAAAATT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 51 1.00
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Done.