Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007724.1 Hibiscus syriacus cultivar Beakdansim tig00109971_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1221931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:1027431 original size:94 final size:96
Alignment explanation
Indices: 1027259--1027484 Score: 303
Period size: 94 Copynumber: 2.4 Consensus size: 96
1027249 TGGTGATCAT
* * ** * *
1027259 AATCATCAAAATACAAGCATAGCGAAATAAAGGGGAGATCTCATGATGAGCTCAGCATAGAATCT
1 AATCATCAAAATACAATCATAGCGAAATGAAGGGGAGAAATCATCATGA-C-CAGCATAGAATCA
1027324 AACCAAAGAGAGCAGTAGTAGGATATCATTCAC
64 AACCAAAGAGAGCAGTAGTAGGATATCATTCAC
* * *
1027357 AGTCATCAAAATACAATCATAGTGAAATGAAGGGGGGAAATC-TCATGA-CAGCATAGAATCAAA
1 AATCATCAAAATACAATCATAGCGAAATGAAGGGGAGAAATCATCATGACCAGCATAGAATCAAA
* *
1027420 CCAAAGGGAGCAGTAGTAGGATATCATTCGC
66 CCAAAGAGAGCAGTAGTAGGATATCATTCAC
* *
1027451 AATTATCAAAATACAATCATAGCGTAATGAAGGG
1 AATCATCAAAATACAATCATAGCGAAATGAAGGG
1027485 CGTTTTGACT
Statistics
Matches: 113, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
94 73 0.65
97 5 0.04
98 35 0.31
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (96 bp):
AATCATCAAAATACAATCATAGCGAAATGAAGGGGAGAAATCATCATGACCAGCATAGAATCAAA
CCAAAGAGAGCAGTAGTAGGATATCATTCAC
Found at i:1027963 original size:17 final size:17
Alignment explanation
Indices: 1027941--1028001 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
1027931 TATTTTTTAT
1027941 TATTATATTTATATAAA
1 TATTATATTTATATAAA
*
1027958 TATTAT-TTTTTATTAAA
1 TATTATATTTATA-TAAA
* *
1027975 -ATAATATTTATATAAT
1 TATTATATTTATATAAA
*
1027991 TATTTTATTTA
1 TATTATATTTA
1028002 AATTAATTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
16 12 0.34
17 23 0.66
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TATTATATTTATATAAA
Found at i:1028002 original size:29 final size:32
Alignment explanation
Indices: 1027945--1028008 Score: 80
Period size: 33 Copynumber: 2.1 Consensus size: 32
1027935 TTTTATTATT
*
1027945 ATATTTATATAAATATTATTTTTTATTAAAATA
1 ATATTTATAT-AATATTATTTTATATTAAAATA
*
1027978 ATATTTATAT-A-ATTATTTTAT-TTAAATTA
1 ATATTTATATAATATTATTTTATATTAAAATA
1028007 AT
1 AT
1028009 TAATTAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 9 0.31
30 9 0.31
31 1 0.03
33 10 0.34
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (32 bp):
ATATTTATATAATATTATTTTATATTAAAATA
Found at i:1028025 original size:29 final size:28
Alignment explanation
Indices: 1027957--1028025 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 28
1027947 ATTTATATAA
*
1027957 ATATTA-TTTTTTATTAAAATAATATTT
1 ATATTATTTTTTTATTAAAATAATAATT
* * *
1027984 ATATAATTATTTTATTTAAATTAATTAATT
1 ATATTATTTTTTTA-TTAAAATAA-TAATT
1028014 A-ATTATTTTTTT
1 ATATTATTTTTTT
1028026 GTACTAATTA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
27 5 0.15
28 6 0.18
29 17 0.52
30 5 0.15
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (28 bp):
ATATTATTTTTTTATTAAAATAATAATT
Found at i:1030841 original size:42 final size:42
Alignment explanation
Indices: 1030751--1030841 Score: 103
Period size: 42 Copynumber: 2.2 Consensus size: 42
1030741 ATGATGATGC
* * *
1030751 CCAA-CCCTCCAGTTCAGATGCCATCTCCTCAGGGGTATATG
1 CCAAGCCCACCAGTTCAGATGCCATCTCCGCAGGGGTACATG
* * * *
1030792 CCAAGCCCACCAGTTTATATGCCATCTCCGCAGGGTTACATT
1 CCAAGCCCACCAGTTCAGATGCCATCTCCGCAGGGGTACATG
*
1030834 CCTAGCCC
1 CCAAGCCC
1030842 GTCAGGTTAC
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 4 0.10
42 37 0.90
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.24
Consensus pattern (42 bp):
CCAAGCCCACCAGTTCAGATGCCATCTCCGCAGGGGTACATG
Found at i:1030849 original size:21 final size:20
Alignment explanation
Indices: 1030819--1030867 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
1030809 TATGCCATCT
*
1030819 CCGCAGGGTTACATTCCTAGC
1 CCGCA-GGTTACATGCCTAGC
1030840 CCGTCAGGTTACATGCCTAGC
1 CCG-CAGGTTACATGCCTAGC
1030861 CCGCAGG
1 CCGCAGG
1030868 ATTTTATGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 4 0.15
21 20 0.77
22 2 0.08
ACGTcount: A:0.18, C:0.35, G:0.27, T:0.20
Consensus pattern (20 bp):
CCGCAGGTTACATGCCTAGC
Found at i:1030856 original size:42 final size:42
Alignment explanation
Indices: 1030768--1030856 Score: 97
Period size: 42 Copynumber: 2.1 Consensus size: 42
1030758 TCCAGTTCAG
* * * *
1030768 ATGCCATCTCCTCAGGGGTATATGCCAAGCCCACCAGTTTAT
1 ATGCCATCTCCGCAGGGGTACATGCCAAGCCCACCAGGTTAC
* * * **
1030810 ATGCCATCTCCGCAGGGTTACATTCCTAGCCCGTCAGGTTAC
1 ATGCCATCTCCGCAGGGGTACATGCCAAGCCCACCAGGTTAC
1030852 ATGCC
1 ATGCC
1030857 TAGCCCGCAG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.21, C:0.33, G:0.20, T:0.26
Consensus pattern (42 bp):
ATGCCATCTCCGCAGGGGTACATGCCAAGCCCACCAGGTTAC
Found at i:1031507 original size:14 final size:14
Alignment explanation
Indices: 1031472--1031515 Score: 81
Period size: 14 Copynumber: 3.2 Consensus size: 14
1031462 TTTTATCCTT
1031472 AACATATACATTAA
1 AACATATACATTAA
1031486 AA-ATATACATTAA
1 AACATATACATTAA
1031499 AACATATACATTAA
1 AACATATACATTAA
1031513 AAC
1 AAC
1031516 CAACTTATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.45
14 16 0.55
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.27
Consensus pattern (14 bp):
AACATATACATTAA
Found at i:1031683 original size:63 final size:64
Alignment explanation
Indices: 1031581--1031710 Score: 217
Period size: 63 Copynumber: 2.0 Consensus size: 64
1031571 TTTCATGCTC
* * *
1031581 ACAACCAACTTATCACTTCACATTTATTCAATTTGTCCATAACATTTTATCCAATATATTCA-A
1 ACAACCAACTGATCACTTCACATTTATTCAATTTATCCATAAAATTTTATCCAATATATTCATA
*
1031644 ACAACCAACTGATCACTTCACATTTATTCAATTTATCCATAAAATTTTATCCAATTTATTCATA
1 ACAACCAACTGATCACTTCACATTTATTCAATTTATCCATAAAATTTTATCCAATATATTCATA
1031708 ACA
1 ACA
1031711 TTTTATCCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
63 58 0.94
64 4 0.06
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.38
Consensus pattern (64 bp):
ACAACCAACTGATCACTTCACATTTATTCAATTTATCCATAAAATTTTATCCAATATATTCATA
Found at i:1031698 original size:23 final size:23
Alignment explanation
Indices: 1031666--1031725 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
1031656 TCACTTCACA
*
1031666 TTTATTCAATTTATCCATAAAAT
1 TTTATCCAATTTATCCATAAAAT
* *
1031689 TTTATCCAATTTATTCATAACAT
1 TTTATCCAATTTATCCATAAAAT
1031712 TTTATCCAATTTAT
1 TTTATCCAATTTAT
1031726 ACAAACTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (23 bp):
TTTATCCAATTTATCCATAAAAT
Found at i:1031936 original size:116 final size:116
Alignment explanation
Indices: 1031777--1032431 Score: 1143
Period size: 116 Copynumber: 5.7 Consensus size: 116
1031767 AATTTCACAA
*
1031777 GAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGTGCCCCCCGGGAA
1 GAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCGGGAA
1031842 CGCGCTTTCACCACTTTGGGTACTGACATGAATAGTGCCCCCGAGGGACAT
66 CGCGCTTTCACCACTTTGGGTACTGACATGAATAGTGCCCCCGAGGGACAT
1031893 GAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCC-GGAA
1 GAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCGGGAA
*
1031957 CGCGCTTTCACCACTTTGGGTACTGACATGAATAGTGTCCCCGAGGGACAT
66 CGCGCTTTCACCACTTTGGGTACTGACATGAATAGTGCCCCCGAGGGACAT
* *
1032008 GAGTGACATAATAAGGCAATGCTAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCGGGAA
1 GAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCGGGAA
* *
1032073 CGCGCTTTCACCACTTTGGGTACTGACATGAATAATACCCCCGAGGGACAT
66 CGCGCTTTCACCACTTTGGGTACTGACATGAATAGTGCCCCCGAGGGACAT
*
1032124 GAGTGATATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCGGGAA
1 GAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCGGGAA
* *
1032189 CGCGCCTTCACCACTTTGGGTACTGACATGAATAGTGCCCCTGAGGGACAT
66 CGCGCTTTCACCACTTTGGGTACTGACATGAATAGTGCCCCCGAGGGACAT
* *
1032240 GAGTGACATAATAGGGCAATGATAACATATTCTCTGAAAAAATAATGGAAGGTGCCCCCCGGGAA
1 GAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCGGGAA
* *
1032305 CGCGCATTCACCACTTTGGGTTA-TGGCATGAATAGTGCCCCCGAGGGACAT
66 CGCGCTTTCACCACTTTGGG-TACTGACATGAATAGTGCCCCCGAGGGACAT
*
1032356 GAGTGACATAATAGGGCAATGATAACATATTCTCTGATAAAATAATGGAAGGCGCCCCCCGGGAA
1 GAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCGGGAA
* *
1032421 TGCGCATTCAC
66 CGCGCTTTCAC
1032432 ATGAATAGTA
Statistics
Matches: 514, Mismatches: 23, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
115 112 0.22
116 400 0.78
117 2 0.00
ACGTcount: A:0.31, C:0.23, G:0.24, T:0.21
Consensus pattern (116 bp):
GAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCGGGAA
CGCGCTTTCACCACTTTGGGTACTGACATGAATAGTGCCCCCGAGGGACAT
Found at i:1034321 original size:72 final size:72
Alignment explanation
Indices: 1034204--1034347 Score: 288
Period size: 72 Copynumber: 2.0 Consensus size: 72
1034194 TACTTTTTTC
1034204 CAATTTTTCTATCATTTTCGTATTACTTATTTATACTTCATATTAACTATTACATATTCCTAATG
1 CAATTTTTCTATCATTTTCGTATTACTTATTTATACTTCATATTAACTATTACATATTCCTAATG
1034269 GCTTAGG
66 GCTTAGG
1034276 CAATTTTTCTATCATTTTCGTATTACTTATTTATACTTCATATTAACTATTACATATTCCTAATG
1 CAATTTTTCTATCATTTTCGTATTACTTATTTATACTTCATATTAACTATTACATATTCCTAATG
1034341 GCTTAGG
66 GCTTAGG
1034348 TTACGAACTC
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.49
Consensus pattern (72 bp):
CAATTTTTCTATCATTTTCGTATTACTTATTTATACTTCATATTAACTATTACATATTCCTAATG
GCTTAGG
Found at i:1035399 original size:26 final size:26
Alignment explanation
Indices: 1035336--1035431 Score: 77
Period size: 26 Copynumber: 3.5 Consensus size: 26
1035326 GATTAATATT
* *
1035336 AAATAAATTATTTATATTGTAATTTTATA
1 AAAT-AATTAATTATATT-T-ATTTAATA
*
1035365 AAATGATTAATTATATTTATTTAATA
1 AAATAATTAATTATATTTATTTAATA
* *
1035391 TAATAATTAA-TATTATTTATTTTAAAA
1 AAATAATTAATTA-TATTTA-TTTAATA
1035418 AAATATTATTAATT
1 AAATA--ATTAATT
1035432 TTAAAATATT
Statistics
Matches: 55, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
25 2 0.04
26 21 0.38
27 11 0.20
28 11 0.20
29 9 0.16
30 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (26 bp):
AAATAATTAATTATATTTATTTAATA
Found at i:1035424 original size:20 final size:20
Alignment explanation
Indices: 1035399--1035437 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1035389 TATAATAATT
*
1035399 AATATTATTTATTTTAAAAA
1 AATATTATTAATTTTAAAAA
1035419 AATATTATTAATTTTAAAA
1 AATATTATTAATTTTAAAA
1035438 TATTAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AATATTATTAATTTTAAAAA
Found at i:1050096 original size:17 final size:18
Alignment explanation
Indices: 1050074--1050109 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1050064 AAGTTGAGGA
*
1050074 AGTAG-AAGAGAAGAACC
1 AGTAGAAAGAGAAAAACC
1050091 AGTAGAAAGAGAAAAACC
1 AGTAGAAAGAGAAAAACC
1050109 A
1 A
1050110 CATTCATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.58, C:0.11, G:0.25, T:0.06
Consensus pattern (18 bp):
AGTAGAAAGAGAAAAACC
Found at i:1052740 original size:15 final size:15
Alignment explanation
Indices: 1052720--1052757 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
1052710 TATAACCTAT
1052720 AAAGCCCAAAACCCG
1 AAAGCCCAAAACCCG
1052735 AAAGCCCAAAACCCG
1 AAAGCCCAAAACCCG
1052750 AAAGCCCA
1 AAAGCCCA
1052758 CTATATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.47, C:0.39, G:0.13, T:0.00
Consensus pattern (15 bp):
AAAGCCCAAAACCCG
Found at i:1055029 original size:29 final size:29
Alignment explanation
Indices: 1054995--1055053 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1054985 CCTAAATTAA
1054995 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1055024 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1055053 T
1 T
1055054 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:1060692 original size:43 final size:42
Alignment explanation
Indices: 1060516--1060824 Score: 221
Period size: 43 Copynumber: 7.3 Consensus size: 42
1060506 TGACAACATA
* * *
1060516 TAGCGGCGTTTGT-TGAACAAACACCGCAATAGGTGTTGTTATT
1 TAGCGGCGTTT-TCTG-ACAAACGCCGCAGTAGGTGTTGATATT
* * * * *
1060559 TAGAGGCGTTTGTCAGAAAAACGCCGCAATAGGTGTTGATGTT
1 TAGCGGCGTTT-TCTGACAAACGCCGCAGTAGGTGTTGATATT
** * * *
1060602 TAGCGGCGTTTTAGGA-AAACGCCACATTAGATGTTGATATT
1 TAGCGGCGTTTTCTGACAAACGCCGCAGTAGGTGTTGATATT
*
1060643 TAGCGGCGTTTTACTTACAAACGCCGCAGTAGGTGTTGATATT
1 TAGCGGCGTTTT-CTGACAAACGCCGCAGTAGGTGTTGATATT
* * * * * * * *
1060686 TTGCGGCATTTTTTTACAAACGCCGCAGTAGTTATTAATTTT
1 TAGCGGCGTTTTCTGACAAACGCCGCAGTAGGTGTTGATATT
** * * * *
1060728 TAGCGGCGTTTTTCCCACAAACGTCGCAGTAGGTTTTCAGATT
1 TAGCGGCG-TTTTCTGACAAACGCCGCAGTAGGTGTTGATATT
* * * * *
1060771 TAGCAGCGTTTTTATCGA-AAACGACGCAATAAGG-GTTGATAAT
1 TAGCGGCG-TTTTCT-GACAAACGCCGCAGT-AGGTGTTGATATT
1060814 TAGCGGCGTTT
1 TAGCGGCGTTT
1060825 ATAGTATACA
Statistics
Matches: 212, Mismatches: 48, Indels: 13
0.78 0.18 0.05
Matches are distributed among these distances:
41 33 0.16
42 38 0.18
43 136 0.64
44 5 0.02
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.33
Consensus pattern (42 bp):
TAGCGGCGTTTTCTGACAAACGCCGCAGTAGGTGTTGATATT
Found at i:1060748 original size:85 final size:84
Alignment explanation
Indices: 1060577--1060761 Score: 208
Period size: 85 Copynumber: 2.2 Consensus size: 84
1060567 TTTGTCAGAA
* * * * * *
1060577 AAACGCCGCAATAGGTGTTGATGTTTAGCGGCGTTTTAGGAAAACGCCACATTAGATGTTGATAT
1 AAACGCCGCAGTAGGTGTTGATATTTAGCGGCATTTTAGGAAAACGCCACAGTAGATATTAATAT
**
1060642 TTAGCGGCGTTTTACTTAC
66 TTAGCGGCGTTTTACCCAC
* *** * * *
1060661 AAACGCCGCAGTAGGTGTTGATATTTTGCGGCATTTTTTTACAAACGCCGCAGTAGTTATTAATT
1 AAACGCCGCAGTAGGTGTTGATATTTAGCGGCATTTTAGGA-AAACGCCACAGTAGATATTAATA
*
1060726 TTTAGCGGCGTTTTTCCCAC
65 TTTAGCGGCGTTTTACCCAC
*
1060746 AAACGTCGCAGTAGGT
1 AAACGCCGCAGTAGGT
1060762 TTTCAGATTT
Statistics
Matches: 83, Mismatches: 17, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
84 34 0.41
85 49 0.59
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (84 bp):
AAACGCCGCAGTAGGTGTTGATATTTAGCGGCATTTTAGGAAAACGCCACAGTAGATATTAATAT
TTAGCGGCGTTTTACCCAC
Found at i:1060865 original size:44 final size:44
Alignment explanation
Indices: 1060816--1060978 Score: 240
Period size: 44 Copynumber: 3.7 Consensus size: 44
1060806 TTGATAATTA
*
1060816 GCGGCGTTTATAGTATACAAACGCCGCTAAATGTATGGTATATT
1 GCGGCGTTTCTAGTATACAAACGCCGCTAAATGTATGGTATATT
* *
1060860 GCGGCGTTTCTAGTATTCAAACGCCTCTAAATGTATGGTATATT
1 GCGGCGTTTCTAGTATACAAACGCCGCTAAATGTATGGTATATT
* *
1060904 GCGGCGTTTCTAGTATACAAACTCCGCTAAATGTATGATATATT
1 GCGGCGTTTCTAGTATACAAACGCCGCTAAATGTATGGTATATT
* *
1060948 GCGGCGTGTT-T-TTTTACAAACGCCGCTAAAT
1 GCGGCGT-TTCTAGTATACAAACGCCGCTAAAT
1060979 AACACAAAAT
Statistics
Matches: 108, Mismatches: 10, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
43 17 0.16
44 89 0.82
45 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (44 bp):
GCGGCGTTTCTAGTATACAAACGCCGCTAAATGTATGGTATATT
Found at i:1061317 original size:21 final size:21
Alignment explanation
Indices: 1061293--1061366 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
1061283 CTGTTGATAT
1061293 GCTGCTTCTCTCTGTGCTACC
1 GCTGCTTCTCTCTGTGCTACC
* **
1061314 GCTGTTTCTCTCTGTGCTGTC
1 GCTGCTTCTCTCTGTGCTACC
* * * *
1061335 GCTGCTTCTTTCTCTGCTTCT
1 GCTGCTTCTCTCTGTGCTACC
*
1061356 ACTGCTTCTCT
1 GCTGCTTCTCT
1061367 GGCTGTTCCG
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.03, C:0.34, G:0.18, T:0.46
Consensus pattern (21 bp):
GCTGCTTCTCTCTGTGCTACC
Found at i:1061389 original size:12 final size:12
Alignment explanation
Indices: 1061368--1061396 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1061358 TGCTTCTCTG
1061368 GCTG-TTCCGCT
1 GCTGCTTCCGCT
1061379 GCTGCTTCCGCT
1 GCTGCTTCCGCT
1061391 GCTGCT
1 GCTGCT
1061397 CTCTCTGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.00, C:0.38, G:0.28, T:0.34
Consensus pattern (12 bp):
GCTGCTTCCGCT
Found at i:1070048 original size:20 final size:20
Alignment explanation
Indices: 1069908--1070060 Score: 86
Period size: 20 Copynumber: 7.7 Consensus size: 20
1069898 AAATGACCAA
* * *
1069908 CAAATTCGCAACGCGAACTA
1 CAAATTCGCAACACGAATTT
* * *
1069928 CAATTTCGCAAC-CCAGTTT
1 CAAATTCGCAACACGAATTT
*
1069947 CCAAATTCGCAACGCGAATCTGT
1 -CAAATTCGCAACACGAAT-T-T
* * *
1069970 -GAA-TCGCAACAAAGAA-GT
1 CAAATTCGCAAC-ACGAATTT
*
1069988 CAAATTCGCAACGCG--TTT
1 CAAATTCGCAACACGAATTT
1070006 GCCAAATTCGCAACACTGAATTT
1 --CAAATTCGCAACAC-GAATTT
1070029 CAAATTCGCAACACGAATTT
1 CAAATTCGCAACACGAATTT
*
1070049 -AATTTCGCAACA
1 CAAATTCGCAACA
1070061 GGTTTTAGTT
Statistics
Matches: 102, Mismatches: 18, Indels: 27
0.69 0.12 0.18
Matches are distributed among these distances:
18 2 0.02
19 17 0.17
20 55 0.54
21 23 0.23
22 1 0.01
23 4 0.04
ACGTcount: A:0.36, C:0.27, G:0.14, T:0.23
Consensus pattern (20 bp):
CAAATTCGCAACACGAATTT
Found at i:1070056 original size:60 final size:61
Alignment explanation
Indices: 1069908--1070059 Score: 152
Period size: 60 Copynumber: 2.5 Consensus size: 61
1069898 AAATGACCAA
* * *
1069908 CAAATTCGCAACGCGAACTACAATTTCGCAACCCAGTTTCCAAATTCGCAACGCGAATCTGT
1 CAAATTCGCAACACGAA-TTCAATTTCGCAACCCAGTTTCCAAATTCGCAACACGAATCTGT
* * * * *
1069970 -GAA-TCGCAACAAAGAAGTCAAATTCGCAACGC-GTTTGCCAAATTCGCAACACTGAAT-T-T
1 CAAATTCGCAAC-ACGAATTCAATTTCGCAACCCAGTTT-CCAAATTCGCAACAC-GAATCTGT
*
1070029 CAAATTCGCAACACGAATTTAATTTCGCAAC
1 CAAATTCGCAACACGAATTCAATTTCGCAAC
1070060 AGGTTTTAGT
Statistics
Matches: 72, Mismatches: 13, Indels: 12
0.74 0.13 0.12
Matches are distributed among these distances:
59 5 0.07
60 51 0.71
61 16 0.22
ACGTcount: A:0.36, C:0.27, G:0.14, T:0.23
Consensus pattern (61 bp):
CAAATTCGCAACACGAATTCAATTTCGCAACCCAGTTTCCAAATTCGCAACACGAATCTGT
Found at i:1070057 original size:19 final size:19
Alignment explanation
Indices: 1070012--1070079 Score: 75
Period size: 18 Copynumber: 3.5 Consensus size: 19
1070002 GTTTGCCAAA
*
1070012 TTCGCAACACTGAATTTCAAA
1 TTCGCAACAC-GAATTT-AAT
1070033 TTCGCAACACGAATTTAAT
1 TTCGCAACACGAATTTAAT
** *
1070052 TTCGCAACA-GGTTTTAGT
1 TTCGCAACACGAATTTAAT
1070070 TTCGCAACAC
1 TTCGCAACAC
1070080 AAATCTTTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
18 15 0.36
19 11 0.26
20 6 0.14
21 10 0.24
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.31
Consensus pattern (19 bp):
TTCGCAACACGAATTTAAT
Found at i:1070251 original size:16 final size:15
Alignment explanation
Indices: 1070216--1070254 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1070206 TCCCCATCTC
*
1070216 TAATTTTTTTTTACA
1 TAATTTTTTTCTACA
*
1070231 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
1070247 TAATTTTT
1 TAATTTTT
1070255 CAATGATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:1072576 original size:77 final size:77
Alignment explanation
Indices: 1072449--1072602 Score: 272
Period size: 77 Copynumber: 2.0 Consensus size: 77
1072439 TGTAACTTTG
* *
1072449 AACTTTTTTGGCTTCTTGTTTCCATAATTAGTCCAATAATCAATTGCATTCAAGTATTTCGCCAA
1 AACTTTTTTGGCTTCTTGTTTCCAGAATTAATCCAATAATCAATTGCATTCAAGTATTTCGCCAA
*
1072514 ATGAGCGTTCCA
66 ATGAGCGCTCCA
*
1072526 AACTTTTTTGGCTTCTTGTTTCCAGAATTAATCCAATAATCAATTGCATTCAAGTATTTTGCCAA
1 AACTTTTTTGGCTTCTTGTTTCCAGAATTAATCCAATAATCAATTGCATTCAAGTATTTCGCCAA
1072591 ATGAGCGCTCCA
66 ATGAGCGCTCCA
1072603 TCCCTTACAA
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
77 73 1.00
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (77 bp):
AACTTTTTTGGCTTCTTGTTTCCAGAATTAATCCAATAATCAATTGCATTCAAGTATTTCGCCAA
ATGAGCGCTCCA
Found at i:1073445 original size:21 final size:19
Alignment explanation
Indices: 1073419--1073533 Score: 86
Period size: 21 Copynumber: 5.5 Consensus size: 19
1073409 GTGAATCGGG
1073419 CTCTTGAACAGTGGGAGGGAC
1 CTCTTGAAC-GTGGGAGGG-C
**
1073440 CTCTTGAACGATGACAAGGGC
1 CTCTTGAACG-TG-GGAGGGC
*
1073461 CTCTTAAACGGTGGGAGGGGC
1 CTCTTGAAC-GTGGGA-GGGC
* *
1073482 CTTTTGAACGATGAGAGGAGC
1 CTCTTGAACG-TGGGAGG-GC
*
1073503 CTCTTGAACGGTGGGAGATGC
1 CTCTTGAAC-GTGGGAG-GGC
1073524 CTCTTGAACG
1 CTCTTGAACG
1073534 ATGACAGATG
Statistics
Matches: 75, Mismatches: 11, Indels: 17
0.73 0.11 0.17
Matches are distributed among these distances:
20 6 0.08
21 63 0.84
22 6 0.08
ACGTcount: A:0.23, C:0.20, G:0.35, T:0.22
Consensus pattern (19 bp):
CTCTTGAACGTGGGAGGGC
Found at i:1073478 original size:42 final size:42
Alignment explanation
Indices: 1073419--1073539 Score: 156
Period size: 42 Copynumber: 2.9 Consensus size: 42
1073409 GTGAATCGGG
*
1073419 CTCTTGAACAGTGGGAGGGACCTCTTGAACGATGACAAGG-GC
1 CTCTTGAACGGTGGGAGGG-CCTCTTGAACGATGACAAGGAGC
* * *
1073461 CTCTTAAACGGTGGGAGGGGCCTTTTGAACGATGA-GAGGAGC
1 CTCTTGAACGGTGGGA-GGGCCTCTTGAACGATGACAAGGAGC
*
1073503 CTCTTGAACGGTGGGAGATGCCTCTTGAACGATGACA
1 CTCTTGAACGGTGGGAG-GGCCTCTTGAACGATGACA
1073540 GATGCATCAG
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
41 4 0.06
42 60 0.90
43 3 0.04
ACGTcount: A:0.25, C:0.20, G:0.34, T:0.21
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGCCTCTTGAACGATGACAAGGAGC
Found at i:1073920 original size:21 final size:21
Alignment explanation
Indices: 1073896--1073989 Score: 84
Period size: 21 Copynumber: 4.5 Consensus size: 21
1073886 TAAAACATCC
1073896 ACCTCATCACGTAAAG-ACCG
1 ACCTCATCACGTAAAGCACCG
**
1073916 TACCTCATCACGTAGCGCACC-
1 -ACCTCATCACGTAAAGCACCG
** * *
1073937 ATTGTCTTCACGTAAAGTACCG
1 A-CCTCATCACGTAAAGCACCG
* *
1073959 ACCTCATGACGCAAAGCACCG
1 ACCTCATCACGTAAAGCACCG
1073980 ACCTCATCAC
1 ACCTCATCAC
1073990 ATAACTCCCC
Statistics
Matches: 55, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
20 1 0.02
21 50 0.91
22 4 0.07
ACGTcount: A:0.30, C:0.36, G:0.15, T:0.19
Consensus pattern (21 bp):
ACCTCATCACGTAAAGCACCG
Found at i:1076105 original size:22 final size:22
Alignment explanation
Indices: 1076070--1076121 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
1076060 AGATGGAGAT
* * *
1076070 AGACGGCTTTCGTCGGAGATGG
1 AGACGGATTACGTCGGAGATAG
*
1076092 GGACGGATTACGTCGGAGATAG
1 AGACGGATTACGTCGGAGATAG
1076114 AGACGGAT
1 AGACGGAT
1076122 GTCGCTGTAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.25, C:0.15, G:0.40, T:0.19
Consensus pattern (22 bp):
AGACGGATTACGTCGGAGATAG
Found at i:1076269 original size:20 final size:20
Alignment explanation
Indices: 1076244--1076324 Score: 117
Period size: 20 Copynumber: 4.0 Consensus size: 20
1076234 ATAAACGCGC
1076244 TTTGACTTATGTGTTGCGAA
1 TTTGACTTATGTGTTGCGAA
*
1076264 TTTGACTTTTTTGTGTTGCGAA
1 TTTGAC--TTATGTGTTGCGAA
*
1076286 TTTGACTTCTGTGTTGCGAA
1 TTTGACTTATGTGTTGCGAA
*
1076306 TTTAACTTATGTGTTGCGA
1 TTTGACTTATGTGTTGCGA
1076325 TTTACAAATT
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
20 36 0.65
22 19 0.35
ACGTcount: A:0.17, C:0.11, G:0.23, T:0.48
Consensus pattern (20 bp):
TTTGACTTATGTGTTGCGAA
Found at i:1076341 original size:20 final size:20
Alignment explanation
Indices: 1076318--1076362 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
1076308 TAACTTATGT
1076318 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
*
1076338 GTTGCGATTTACATATTCGC
1 GTTGCGATTTACAAATTCGC
1076358 GTTGC
1 GTTGC
1076363 TAATTTGGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:1077158 original size:41 final size:40
Alignment explanation
Indices: 1077098--1077286 Score: 100
Period size: 42 Copynumber: 4.6 Consensus size: 40
1077088 AATTCAAATA
* * * *
1077098 TATTACGGCATTTGGTATAAAACGCCACTATATATTACACC
1 TATTGCGGCGTTTGTTATAAAACGCCACTA-ATATTACAAC
* *
1077139 TATTGCGGCGTTTGTTAT-AAACGCCAATAATATCTA-AAT
1 TATTGCGGCGTTTGTTATAAAACGCCACTAATAT-TACAAC
* * * * *
1077178 TTTTGCGGCATTT-TTATTTAAAAACACCACTAA-AATACAAA
1 TATTGCGGCGTTTGTTA--T-AAAACGCCACTAATATTACAAC
* * * * *
1077219 TATGTTGCGGTGTTTGTTAGAAAAATGCCACTATATATTAGACC
1 TA--TTGCGGCGTTTGTTA-TAAAACGCCACTA-ATATTACAAC
* *
1077263 TATTACGGCGTTTG-TAAAAAACGC
1 TATTGCGGCGTTTGTTATAAAACGC
1077287 TGCTATTGTA
Statistics
Matches: 111, Mismatches: 26, Indels: 23
0.69 0.16 0.14
Matches are distributed among these distances:
38 3 0.03
39 16 0.14
40 22 0.20
41 21 0.19
42 30 0.27
43 10 0.09
44 9 0.08
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (40 bp):
TATTGCGGCGTTTGTTATAAAACGCCACTAATATTACAAC
Found at i:1078704 original size:42 final size:42
Alignment explanation
Indices: 1078631--1078727 Score: 99
Period size: 42 Copynumber: 2.3 Consensus size: 42
1078621 TGCCACTTAA
* * * * *
1078631 ACCACCATATTACGGCGTTTAATATATAAACGCCGCTA-ATTT
1 ACCACTATATTACGGCATTTAATACACAAACGCAGCTACA-TT
1078673 ACCACTATATTACGGCATTT-ATACCACAAACGCAGCTACATT
1 ACCACTATATTACGGCATTTAATA-CACAAACGCAGCTACATT
* *
1078715 AACACTCTATTAC
1 ACCACTATATTAC
1078728 AGCGTTTTAG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
41 3 0.07
42 42 0.91
43 1 0.02
ACGTcount: A:0.35, C:0.27, G:0.09, T:0.29
Consensus pattern (42 bp):
ACCACTATATTACGGCATTTAATACACAAACGCAGCTACATT
Found at i:1085488 original size:58 final size:58
Alignment explanation
Indices: 1085398--1085513 Score: 214
Period size: 58 Copynumber: 2.0 Consensus size: 58
1085388 TTCCGGATAG
1085398 GCCCTCCATGACTATTCTATAAGCATCTATTTATCTCGTATAACCTAGTTGTGTTATC
1 GCCCTCCATGACTATTCTATAAGCATCTATTTATCTCGTATAACCTAGTTGTGTTATC
* *
1085456 GCCCTCCATTACTATTCTATAAGCATCTATTTATCTCGTATCACCTAGTTGTGTTATC
1 GCCCTCCATGACTATTCTATAAGCATCTATTTATCTCGTATAACCTAGTTGTGTTATC
1085514 ATCCCACTCG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.23, C:0.25, G:0.11, T:0.41
Consensus pattern (58 bp):
GCCCTCCATGACTATTCTATAAGCATCTATTTATCTCGTATAACCTAGTTGTGTTATC
Found at i:1085713 original size:16 final size:16
Alignment explanation
Indices: 1085694--1085728 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
1085684 TCTTTCAAAT
1085694 ATTTTTGAAAATAATC
1 ATTTTTGAAAATAATC
1085710 ATTTTTGAAAATAATC
1 ATTTTTGAAAATAATC
1085726 ATT
1 ATT
1085729 AACAGAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.46
Consensus pattern (16 bp):
ATTTTTGAAAATAATC
Found at i:1105080 original size:12 final size:12
Alignment explanation
Indices: 1105065--1105103 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
1105055 TTCATTTTCA
1105065 TTTTCTATTTCTT
1 TTTTCT-TTTCTT
1105078 TTTTCTTTTCTT
1 TTTTCTTTTCTT
1105090 TTTTCTTTTCTT
1 TTTTCTTTTCTT
1105102 TT
1 TT
1105104 CCCTCTTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 20 0.77
13 6 0.23
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTCTTTTCTT
Found at i:1105086 original size:24 final size:25
Alignment explanation
Indices: 1105054--1105103 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
1105044 CTCAAGGTAC
1105054 TTTCATTTTC-ATTTTCTATTTCTTT
1 TTTCATTTTCTATTTTCT-TTTCTTT
*
1105079 TTTC-TTTTCTTTTTTCTTTTCTTT
1 TTTCATTTTCTATTTTCTTTTCTTT
1105103 T
1 T
1105104 CCCTCTTCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (25 bp):
TTTCATTTTCTATTTTCTTTTCTTT
Found at i:1105509 original size:6 final size:6
Alignment explanation
Indices: 1105473--1105588 Score: 90
Period size: 6 Copynumber: 19.3 Consensus size: 6
1105463 CTCAACTCCT
* * * * * ** *
1105473 CCACCG CCACCG CCACCA CAACCA ACTCCA CCACCA CCGTCA CCATCA
1 CCACCA CCACCA CCACCA CCACCA CCACCA CCACCA CCACCA CCACCA
* * **
1105521 CCACCA CCACCA TCATCA CCACCA CCTTCA CCACCA CCACCA TCCA-CA
1 CCACCA CCACCA CCACCA CCACCA CCACCA CCACCA CCACCA -CCACCA
* *
1105569 TCACCA TCACCA CCACCA CC
1 CCACCA CCACCA CCACCA CC
1105589 CCCAACTCAA
Statistics
Matches: 87, Mismatches: 21, Indels: 4
0.78 0.19 0.04
Matches are distributed among these distances:
5 2 0.02
6 82 0.94
7 3 0.03
ACGTcount: A:0.30, C:0.59, G:0.03, T:0.09
Consensus pattern (6 bp):
CCACCA
Found at i:1105522 original size:15 final size:15
Alignment explanation
Indices: 1105513--1105588 Score: 104
Period size: 15 Copynumber: 5.3 Consensus size: 15
1105503 CCACCACCGT
1105513 CACCATCACCACCAC
1 CACCATCACCACCAC
*
1105528 CACCATCATCACCAC
1 CACCATCACCACCAC
*
1105543 CACCTTCACCACCAC
1 CACCATCACCACCAC
*
1105558 CACCAT--CCA-CAT
1 CACCATCACCACCAC
1105570 CACCATCACCACCAC
1 CACCATCACCACCAC
1105585 CACC
1 CACC
1105589 CCCAACTCAA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
12 8 0.15
13 3 0.06
14 3 0.06
15 38 0.73
ACGTcount: A:0.32, C:0.58, G:0.00, T:0.11
Consensus pattern (15 bp):
CACCATCACCACCAC
Found at i:1105613 original size:39 final size:39
Alignment explanation
Indices: 1105570--1105655 Score: 118
Period size: 39 Copynumber: 2.2 Consensus size: 39
1105560 CCATCCACAT
* * *
1105570 CACCATCACCACCACCACCCCCAACTCAACATACTCCGC
1 CACCACCACCAACACCACCCCCAACTCAACATACTCCAC
* * *
1105609 CACCACCATCAACACCACCCCCAACTCATCATATTCCAC
1 CACCACCACCAACACCACCCCCAACTCAACATACTCCAC
1105648 CACCACCA
1 CACCACCA
1105656 AAGTTGACAC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.33, C:0.55, G:0.01, T:0.12
Consensus pattern (39 bp):
CACCACCACCAACACCACCCCCAACTCAACATACTCCAC
Found at i:1105621 original size:27 final size:27
Alignment explanation
Indices: 1105500--1105622 Score: 92
Period size: 27 Copynumber: 4.7 Consensus size: 27
1105490 ACAACCAACT
* *
1105500 CCACCACCACCGTCACCATC-AC--CA
1 CCACCACCACCATCAACATCAACATCA
* * * * *
1105524 CCACCACCATCATCACCACCACCTTCA
1 CCACCACCACCATCAACATCAACATCA
* *
1105551 CCACCACCACCATCCACATCACCATCA
1 CCACCACCACCATCAACATCAACATCA
** *
1105578 CCACCACCACCCCCAAC-TCAACATACT
1 CCACCACCACCATCAACATCAACAT-CA
*
1105605 CCGCCACCACCATCAACA
1 CCACCACCACCATCAACA
1105623 CCACCCCCAA
Statistics
Matches: 77, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
24 17 0.22
25 1 0.01
26 6 0.08
27 53 0.69
ACGTcount: A:0.32, C:0.56, G:0.02, T:0.11
Consensus pattern (27 bp):
CCACCACCACCATCAACATCAACATCA
Found at i:1109127 original size:17 final size:18
Alignment explanation
Indices: 1109107--1109149 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
1109097 AAATTATAAC
*
1109107 ATATTATAA-ATATCATA
1 ATATTATAATATATCAAA
*
1109124 ATA-TATAATTTATCAAA
1 ATATTATAATATATCAAA
1109141 ATATTATAA
1 ATATTATAA
1109150 CATAATCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 5 0.23
17 12 0.55
18 5 0.23
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (18 bp):
ATATTATAATATATCAAA
Found at i:1116054 original size:24 final size:24
Alignment explanation
Indices: 1116022--1116067 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1116012 TTCATATTTT
* *
1116022 ATTAGGAGGTAGGATCCGCTTAAG
1 ATTAAGAGGTAAGATCCGCTTAAG
1116046 ATTAAGAGGTAAGATCCGCTTA
1 ATTAAGAGGTAAGATCCGCTTA
1116068 GATAATGTAA
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:0.33, C:0.13, G:0.28, T:0.26
Consensus pattern (24 bp):
ATTAAGAGGTAAGATCCGCTTAAG
Found at i:1123285 original size:26 final size:25
Alignment explanation
Indices: 1123252--1123306 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
1123242 TTTAAAATAT
1123252 ATTTTCAC-CCCGTAAAATTTTATAA
1 ATTTTCACTCCC-TAAAATTTTATAA
*
1123277 ATTTGTCACTTCCTAAAATTTTATAA
1 ATTT-TCACTCCCTAAAATTTTATAA
1123303 ATTT
1 ATTT
1123307 ATTCCCTAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 4 0.15
26 21 0.78
27 2 0.07
ACGTcount: A:0.35, C:0.16, G:0.04, T:0.45
Consensus pattern (25 bp):
ATTTTCACTCCCTAAAATTTTATAA
Found at i:1126068 original size:21 final size:23
Alignment explanation
Indices: 1126042--1126093 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 23
1126032 TGAAAAATTA
1126042 CTCCCCTTT-AC-TTTAACACTT
1 CTCCCCTTTAACATTTAACACTT
1126063 CTCCCCTTTAAAACATTTAACACTT
1 CTCCCCTTT--AACATTTAACACTT
1126088 CTCCCC
1 CTCCCC
1126094 CTTTTTGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 9 0.33
24 2 0.07
25 16 0.59
ACGTcount: A:0.23, C:0.40, G:0.00, T:0.37
Consensus pattern (23 bp):
CTCCCCTTTAACATTTAACACTT
Found at i:1126741 original size:18 final size:18
Alignment explanation
Indices: 1126718--1126758 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1126708 AGGCATTCGA
1126718 TCCTCTGGCTATGCTTGT
1 TCCTCTGGCTATGCTTGT
** *
1126736 TCCTCTGTTTGTGCTTGT
1 TCCTCTGGCTATGCTTGT
1126754 TCCTC
1 TCCTC
1126759 GTGCTGTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.02, C:0.29, G:0.20, T:0.49
Consensus pattern (18 bp):
TCCTCTGGCTATGCTTGT
Found at i:1139261 original size:12 final size:12
Alignment explanation
Indices: 1139241--1139282 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
1139231 TAAATAAAAG
*
1139241 AGAATAGTAACA
1 AGAAGAGTAACA
1139253 AGAAGAGTAACA
1 AGAAGAGTAACA
*
1139265 AGTAACAGTAACA
1 AG-AAGAGTAACA
1139278 A-AAGA
1 AGAAGA
1139283 ACAGATCAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
11 3 0.12
12 13 0.50
13 10 0.38
ACGTcount: A:0.60, C:0.10, G:0.19, T:0.12
Consensus pattern (12 bp):
AGAAGAGTAACA
Found at i:1139771 original size:30 final size:30
Alignment explanation
Indices: 1139737--1139795 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
1139727 TAATAAATTT
*
1139737 GCATAATTATATATTTGGT-CTGTAATATTG
1 GCATAATTATATATTTAGTCCT-TAATATTG
1139767 GCATAATTATATATTTAGTCCTTAATATT
1 GCATAATTATATATTTAGTCCTTAATATT
1139796 TATATATTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 25 0.93
31 2 0.07
ACGTcount: A:0.32, C:0.08, G:0.12, T:0.47
Consensus pattern (30 bp):
GCATAATTATATATTTAGTCCTTAATATTG
Found at i:1140502 original size:183 final size:183
Alignment explanation
Indices: 1140187--1140572 Score: 643
Period size: 183 Copynumber: 2.1 Consensus size: 183
1140177 ATTAAATTTT
* *
1140187 AAATTTTAAATATATTATATATAACATATGGGCTCAACCCAAATCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAAACCCAATTAATAA
* *
1140252 TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATACATTTTT
66 TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTT
* *
1140317 TATTTTATAATTATATATTATTTAAATTATTTGTAAACTGTTTTTT-AATTAAA
131 TATTTTATAATTATATATTATTTAAATTAATTATAAACT-TTTTTTGAATTAAA
1140370 AAATATTAAATATATTATATATAACATATGGGCT-AAGCCCAAACCATTTAAAACCCAATTAATA
1 AAATATTAAATATATTATATATAACATATGGGCTCAA-CCCAAACCATTTAAAACCCAATTAATA
* *
1140434 ATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAACTTATCTAAAATTT
65 ATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAAATTT
1140499 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
130 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
* *
1140553 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
1140573 AATTAGAAAA
Statistics
Matches: 191, Mismatches: 10, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
182 16 0.08
183 175 0.92
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (183 bp):
AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTT
TATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
Found at i:1140718 original size:15 final size:15
Alignment explanation
Indices: 1140698--1140726 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1140688 AAAAAAAGTT
1140698 TGGTTAATTCGGTTA
1 TGGTTAATTCGGTTA
1140713 TGGTTAATTCGGTT
1 TGGTTAATTCGGTT
1140727 CGGTCGGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.07, G:0.28, T:0.48
Consensus pattern (15 bp):
TGGTTAATTCGGTTA
Found at i:1141121 original size:24 final size:24
Alignment explanation
Indices: 1141094--1141143 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
1141084 GTTAATTCGG
* *
1141094 TTCGGTGAATAATTTTCAAATTAA
1 TTCGGTGAATAATTTACAAATAAA
*
1141118 TTCGGTTAATAATTTACAAATAAA
1 TTCGGTGAATAATTTACAAATAAA
1141142 TT
1 TT
1141144 TTGGTTCCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (24 bp):
TTCGGTGAATAATTTACAAATAAA
Found at i:1141223 original size:116 final size:118
Alignment explanation
Indices: 1141095--1141342 Score: 356
Period size: 121 Copynumber: 2.1 Consensus size: 118
1141085 TTAATTCGGT
* *
1141095 TCGGTGAATAATTTTCAAATTAA-TTCGGTTAATAATTTACAAATAAATTTTGGTTCCATTAACC
1 TCGGTTAATAATTTTCAAATTAAGTTCGGTTAATAATTTACAAATAAATTTTGGTTCCATTAACA
*
1141159 GAACCGAATTAGCCGAATTTTTGCTTCGATTAATTCAATTAATAATT-AAAAA
66 GAACCGAATTAACCGAATTTTTGCTTCGATTAATTCAATTAATAATTAAAAAA
* *
1141211 TCGGTTAATAATTTTCAAATTAATTCGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATT
1 TCGGTTAATAATTTTCAAATTAA----GTTCGGTTAATAATTTACAAATAAATTTTGGTTCCATT
** * *
1141276 AACAGAGTCGAATTAACCGAATTTTTTCTTCGATTAATTCGATTAATAATTAAAAAAA
62 AACAGAACCGAATTAACCGAATTTTTGCTTCGATTAATTCAATTAATAATT-AAAAAA
1141334 TCGGTTAAT
1 TCGGTTAAT
1141343 TCGGTTTGGT
Statistics
Matches: 116, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
116 22 0.19
121 80 0.69
123 14 0.12
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.40
Consensus pattern (118 bp):
TCGGTTAATAATTTTCAAATTAAGTTCGGTTAATAATTTACAAATAAATTTTGGTTCCATTAACA
GAACCGAATTAACCGAATTTTTGCTTCGATTAATTCAATTAATAATTAAAAAA
Found at i:1141379 original size:137 final size:139
Alignment explanation
Indices: 1141211--1141530 Score: 475
Period size: 137 Copynumber: 2.3 Consensus size: 139
1141201 TAATTAAAAA
*
1141211 TCGGTTAATAATTTTCAAATTAATTCGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATT
1 TCGGTTAATAATTTTCAAAATAATTCGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATT
* * *
1141276 AA-CAGAGTCGAATTAACCGAATTTTTTCTTCGATTAATTCGATTAATAA-TT-AAAAAAATCGG
66 AACCAAACT-GAATTAACCGAATTTTTGCTTCGATTAATTCGATTAATAATTTAAAAAAAATCGG
1141338 TTAATTCGGT
130 TTAATTCGGT
* * * * *
1141348 TTGGTTAATAATTTTTAAAATAATTCAGTTCGGTTAATAAATTTCTAATAAATTTTGGTTCGATT
1 TCGGTTAATAATTTTCAAAATAATTCGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATT
*
1141413 AACCAAACTGAATTAACCGAATTTTTGCTTCGATTAATTCGGTTAATAATTTTAAAAAAAATCGG
66 AACCAAACTGAATTAACCGAATTTTTGCTTCGATTAATTCGATTAATAA-TTTAAAAAAAATCGG
1141478 TTAATTCGGT
130 TTAATTCGGT
* * *
1141488 TCGGTTAATAATTTTCAAAAAAATTTTGGTTCGATTAATAATT
1 TCGGTTAATAATTTTCAAAATAA-TTCGGTTCGGTTAATAATT
1141531 AAAAAAATAA
Statistics
Matches: 161, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
137 99 0.61
138 4 0.02
139 2 0.01
140 41 0.25
141 15 0.09
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (139 bp):
TCGGTTAATAATTTTCAAAATAATTCGGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATT
AACCAAACTGAATTAACCGAATTTTTGCTTCGATTAATTCGATTAATAATTTAAAAAAAATCGGT
TAATTCGGT
Found at i:1141401 original size:29 final size:29
Alignment explanation
Indices: 1141339--1141395 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
1141329 AAAAATCGGT
* * *
1141339 TAATTCGGTTTGGTTAATAATTTTTAAAA
1 TAATTCAGTTCGGTTAATAATTTCTAAAA
1141368 TAATTCAGTTCGGTTAATAAATTTCTAA
1 TAATTCAGTTCGGTTAAT-AATTTCTAA
1141396 TAAATTTTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.46
Consensus pattern (29 bp):
TAATTCAGTTCGGTTAATAATTTCTAAAA
Found at i:1141500 original size:37 final size:34
Alignment explanation
Indices: 1141450--1141604 Score: 118
Period size: 29 Copynumber: 4.7 Consensus size: 34
1141440 CTTCGATTAA
1141450 TTCGGTTAATAATTTTAAAAAAAATCGGTTAATTCGG
1 TTCGGTTAATAATTTT-AAAAAAAT--GTTAATTCGG
1141487 TTCGGTTAATAATTTTCAAAAAAA--TT--TT-GG
1 TTCGGTTAATAATTTT-AAAAAAATGTTAATTCGG
*
1141517 TTCGATTAATAA--TTAAAAAAATAAGTTAATTCGG
1 TTCGGTTAATAATTTTAAAAAAAT--GTTAATTCGG
* * *
1141551 TTTGGTTAATAATTTT---CAAA--TTAATTCAG
1 TTCGGTTAATAATTTTAAAAAAATGTTAATTCGG
*
1141580 TTCGGTTAATAATTTTCAAATAAAT
1 TTCGGTTAATAATTTT-AAAAAAAT
1141605 TTTGGTTCGA
Statistics
Matches: 96, Mismatches: 8, Indels: 31
0.71 0.06 0.23
Matches are distributed among these distances:
27 7 0.07
28 2 0.02
29 23 0.24
30 13 0.14
31 4 0.04
33 10 0.10
34 12 0.12
36 2 0.02
37 23 0.24
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.41
Consensus pattern (34 bp):
TTCGGTTAATAATTTTAAAAAAATGTTAATTCGG
Found at i:1141547 original size:204 final size:202
Alignment explanation
Indices: 1141313--1141732 Score: 698
Period size: 204 Copynumber: 2.1 Consensus size: 202
1141303 CTTCGATTAA
** *
1141313 TTCGATTAATAATTAAAAAAATCGGTTAATTCGGTTTGGTTAATAATTTTTAAAATAATTCAGTT
1 TTCGATTAATAATTAAAAAAATAAGTTAATTCGGTTTGGTTAATAATTTTCAAAATAATTCAGTT
*
1141378 CGGTTAATAAATTTCTAATAAATTTTGGTTCGATTAACCAAA-CTGAATTAACCGAATTTTTGCT
66 CGGTTAATAAATTTCAAATAAATTTTGGTTCGATTAACCAAATC-GAATTAACCGAATTTTTGCT
1141442 TCGATTAATTCGGTTAATAATTTTAAAAAAAATCGGTTAATTCGGTTCGGTTAATAATTTTCAAA
130 TCGATTAATTCGGTTAATAA-TTTAAAAAAAATCGGTTAATTCGGTTCGGTTAATAATTTTCAAA
1141507 AAAATTTTGG
194 AAAA-TTTGG
*
1141517 TTCGATTAATAATTAAAAAAATAAGTTAATTCGGTTTGGTTAATAATTTTCAAATTAATTCAGTT
1 TTCGATTAATAATTAAAAAAATAAGTTAATTCGGTTTGGTTAATAATTTTCAAAATAATTCAGTT
* *
1141582 CGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACCAAATCGAATTAACCGAATTTTTTCTT
66 CGGTTAATAAATTTCAAATAAATTTTGGTTCGATTAACCAAATCGAATTAACCGAATTTTTGCTT
* **
1141647 CGATTAATTCGGTTAATAATTTAAAAAAAATTGGTTAATTCGGTTCGGTTAATAATTTTCAAATT
131 CGATTAATTCGGTTAATAATTTAAAAAAAATCGGTTAATTCGGTTCGGTTAATAATTTTCAAAAA
1141712 AATTTGG
196 AATTTGG
* *
1141719 TTAGGTTAATAATT
1 TTCGATTAATAATT
1141733 TTCAAATAAA
Statistics
Matches: 203, Mismatches: 12, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
202 17 0.08
203 45 0.22
204 140 0.69
205 1 0.00
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.42
Consensus pattern (202 bp):
TTCGATTAATAATTAAAAAAATAAGTTAATTCGGTTTGGTTAATAATTTTCAAAATAATTCAGTT
CGGTTAATAAATTTCAAATAAATTTTGGTTCGATTAACCAAATCGAATTAACCGAATTTTTGCTT
CGATTAATTCGGTTAATAATTTAAAAAAAATCGGTTAATTCGGTTCGGTTAATAATTTTCAAAAA
AATTTGG
Found at i:1141725 original size:29 final size:29
Alignment explanation
Indices: 1141681--1141750 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
1141671 AAAAAATTGG
* *
1141681 TTAATTCGGTTCGGTTAATAATTTTCAAA
1 TTAATTTGGTTAGGTTAATAATTTTCAAA
1141710 TTAATTTGGTTAGGTTAATAATTTTCAAA
1 TTAATTTGGTTAGGTTAATAATTTTCAAA
*
1141739 TAAATTTTGGTT
1 TTAA-TTTGGTT
1141751 CGATTAACCG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
29 30 0.81
30 7 0.19
ACGTcount: A:0.31, C:0.06, G:0.14, T:0.49
Consensus pattern (29 bp):
TTAATTTGGTTAGGTTAATAATTTTCAAA
Found at i:1150514 original size:117 final size:117
Alignment explanation
Indices: 1150025--1150526 Score: 442
Period size: 120 Copynumber: 4.3 Consensus size: 117
1150015 GAACTCCCTA
* * ** * *
1150025 TTAATCCACCTTC-TTCTGTGATGG-TTTAAATAAAA-GTCGAACAAATTCTTCTCATTGTGAAC
1 TTAATCCACC-TCATTCTATGATGGATTTGAGCAAAAGGTCGAACAAGTTCTTCTCATTATGAAC
* * * * * ** *
1150087 TTTTTATCCCTCTGTCGACGAGTTCTTCTCATTATGAATTCACCGTTTAGAAATG
65 TTCTTCTCCCTC-GTGGATGAGTTCTTCTCATTATGAACTCACC-AATGGAAATG
* * * * * *
1150142 TTGATCCACCTCTTTCTGTGATGGATTTGAGCAAAAGGTTGAATATGTTCTTCTCATTATGAACC
1 TTAATCCACCTCATTCTATGATGGATTTGAGCAAAAGGTCGAACAAGTTCTTCTCATTATGAA-C
* * * *
1150207 TGT-TTTTCCCTCCGTAGATGAGTTCTTCTCATTATGAACTCACCATTTGGAAATA
65 T-TCTTCTCCCT-CGTGGATGAGTTCTTCTCATTATGAACTCACCA-ATGGAAATG
* * * * * *
1150262 TTAATCCATCTCATTCTGTGATGGATTTGAGTAAAAAGATCGAA-TAGATTCTTTTCATTATGAA
1 TTAATCCACCTCATTCTATGATGGATTTGAG-CAAAAGGTCGAACAAG-TTCTTCTCATTATGAA
* * * *
1150326 CTTCTTCTCACTTCGTGAATGAGTTATTCTCATTATGAACTC-CTC-ATTGAAATG
64 CTTCTTCTC-CCTCGTGGATGAGTTCTTCTCATTATGAACTCAC-CAATGGAAATG
* * * *
1150380 TTAATCCACCTTATTCTATGATAGATTTGAGCGAAAGGTCGAACAAGTTCTTCTCATTATGATCT
1 TTAATCCACCTCATTCTATGATGGATTTGAGCAAAAGGTCGAACAAGTTCTTCTCATTATGAACT
* * *
1150445 TCTTCTCCCTCTTGGATGGGTTCTTCTCATTATGAACTCTCCAATGGAAATG
66 TCTTCTCCCTCGTGGATGAGTTCTTCTCATTATGAACTCACCAATGGAAATG
* * * * *
1150497 TTGATCTAACTCCTTCTATGATGAATTTGA
1 TTAATCCACCTCATTCTATGATGGATTTGA
1150527 TCCCTTTTTT
Statistics
Matches: 314, Mismatches: 56, Indels: 30
0.79 0.14 0.08
Matches are distributed among these distances:
116 30 0.10
117 84 0.27
118 43 0.14
119 23 0.07
120 106 0.34
121 28 0.09
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (117 bp):
TTAATCCACCTCATTCTATGATGGATTTGAGCAAAAGGTCGAACAAGTTCTTCTCATTATGAACT
TCTTCTCCCTCGTGGATGAGTTCTTCTCATTATGAACTCACCAATGGAAATG
Found at i:1159400 original size:20 final size:20
Alignment explanation
Indices: 1159375--1159427 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
1159365 TCCTTGAATG
1159375 TGCATCGATGCACACTGCCA
1 TGCATCGATGCACACTGCCA
1159395 TGCATCGATGCACACTGCCA
1 TGCATCGATGCACACTGCCA
1159415 TGCATCGATGCAC
1 TGCATCGATGCAC
1159428 CCGTCGGGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.25, C:0.34, G:0.21, T:0.21
Consensus pattern (20 bp):
TGCATCGATGCACACTGCCA
Found at i:1159617 original size:20 final size:20
Alignment explanation
Indices: 1159592--1159639 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
1159582 AAATTCTGCT
1159592 AACATCATTAAATCATGCAA
1 AACATCATTAAATCATGCAA
1159612 AACATCATTAAATCATGCAA
1 AACATCATTAAATCATGCAA
1159632 AACATCAT
1 AACATCAT
1159640 CATATTCCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.50, C:0.21, G:0.04, T:0.25
Consensus pattern (20 bp):
AACATCATTAAATCATGCAA
Found at i:1162267 original size:45 final size:46
Alignment explanation
Indices: 1162176--1162274 Score: 166
Period size: 45 Copynumber: 2.2 Consensus size: 46
1162166 TGCATATTGC
1162176 ATGCATCGATGCACTCAGGATTTTATAAAAACATCGAATGCATTTT
1 ATGCATCGATGCACTCAGGATTTTATAAAAACATCGAATGCATTTT
*
1162222 ATGCATCGATGCACTCAGGCTATTT-T-AAAACATCGAATGCATTTT
1 ATGCATCGATGCACTCAGGAT-TTTATAAAAACATCGAATGCATTTT
1162267 ATGCATCG
1 ATGCATCG
1162275 TTTACAGATA
Statistics
Matches: 51, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
45 27 0.53
46 21 0.41
47 3 0.06
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Consensus pattern (46 bp):
ATGCATCGATGCACTCAGGATTTTATAAAAACATCGAATGCATTTT
Found at i:1164853 original size:54 final size:56
Alignment explanation
Indices: 1164697--1164864 Score: 182
Period size: 56 Copynumber: 3.0 Consensus size: 56
1164687 TACCAAATGA
* * * *
1164697 CACTAAGTGTGCAAAAAATGTAAG-ATATTCATACTAAGTGTAT-AAATTTCTATATGGG
1 CACTATGTGTGC-AAAAA--TAAGAAAATTCATACTAAGTGTATGAATTTTC-GTATGGG
*
1164755 CACTTTGTGTGCAAAAATAAGAAAATTCATACTAAGTGTATGAATTTTCGTATGGG
1 CACTATGTGTGCAAAAATAAGAAAATTCATACTAAGTGTATGAATTTTCGTATGGG
* * * * *
1164811 CACTATGTGTGC-TAACTAA-TAAATTCATACCAAGTGTATGAATGTTCGTATGGG
1 CACTATGTGTGCAAAAATAAGAAAATTCATACTAAGTGTATGAATTTTCGTATGGG
1164865 AAAATATATG
Statistics
Matches: 97, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
54 32 0.33
55 9 0.09
56 35 0.36
57 11 0.11
58 10 0.10
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (56 bp):
CACTATGTGTGCAAAAATAAGAAAATTCATACTAAGTGTATGAATTTTCGTATGGG
Found at i:1165188 original size:67 final size:68
Alignment explanation
Indices: 1165080--1165258 Score: 238
Period size: 68 Copynumber: 2.6 Consensus size: 68
1165070 ATTAATAGGT
* *
1165080 CTAACTGTGCATTT-ATCAGAAATGTGTCATTTATGCCAGTTAGACGAAAGG-TAAGTGCCTTTG
1 CTAACTGTGCATTTGA-CAGAAAGGTGTCATTTATGCCAGTTAGACGAAAGGCTAACTGCCTTTG
1165143 AGGC
65 AGGC
* *
1165147 CTAACTGTG-ATTATGACAGAAAGGTGTCATTTAAGCCAGTTAGATGAAAGGCTAACTGCCTTTG
1 CTAACTGTGCATT-TGACAGAAAGGTGTCATTTATGCCAGTTAGACGAAAGGCTAACTGCCTTTG
1165211 AGGC
65 AGGC
* ** * *
1165215 CTAACTGTGCAATTGGTAGAAAGGTGACAATTATGCCAGTTAGA
1 CTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGA
1165259 TGAACTATTA
Statistics
Matches: 98, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
66 3 0.03
67 42 0.43
68 51 0.52
69 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.29
Consensus pattern (68 bp):
CTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGACGAAAGGCTAACTGCCTTTGA
GGC
Found at i:1165280 original size:68 final size:68
Alignment explanation
Indices: 1165096--1165280 Score: 149
Period size: 68 Copynumber: 2.7 Consensus size: 68
1165086 GTGCATTTAT
* * * * * * * * * *
1165096 CAGAAATGTGTCATTTATGCCAGTTAGACGAAAG-GTAAGTGCCTTTGAGGCCTAACTGTGATTA
1 CAGAAAGGTGACAATTAAGCCAGTTAGATGAAAGACTAAATACCGTTGAGGCCTAACTGTGAATA
1165160 TGA
66 TGA
* * * * * *
1165163 CAGAAAGGTGTCATTTAAGCCAGTTAGATGAAAGGCTAACTGCCTTTGAGGCCTAACTGTGCAAT
1 CAGAAAGGTGACAATTAAGCCAGTTAGATGAAAGACTAAATACCGTTGAGGCCTAACTGTG-AAT
*
1165228 -TGG
65 ATGA
* * ** *
1165231 TAGAAAGGTGACAATTATGCCAGTTAGATGAACTATTAAATACCGTTGAG
1 CAGAAAGGTGACAATTAAGCCAGTTAGATGAAAGACTAAATACCGTTGAG
1165281 TAAAGAATAA
Statistics
Matches: 98, Mismatches: 18, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
67 31 0.32
68 65 0.66
69 2 0.02
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (68 bp):
CAGAAAGGTGACAATTAAGCCAGTTAGATGAAAGACTAAATACCGTTGAGGCCTAACTGTGAATA
TGA
Found at i:1165407 original size:81 final size:81
Alignment explanation
Indices: 1165212--1165689 Score: 690
Period size: 81 Copynumber: 5.9 Consensus size: 81
1165202 CTGCCTTTGA
* **
1165212 GGCCTAACTGTGCAATTGGTAGAAAGGTGACAATTATGCCAGTTAGATGAACTATTAAATACCGT
1 GGCCTAACTGTGCAATTGGTAGAAAGGTGCCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
1165277 TGAGT-AAAGAATAAT
66 TGAGTAAAAGAATAAT
* * * * *
1165292 GGCCTGATTGTACAATTGGTAGAAAGGTGTCAATTATGCCAGTTAGGTGAACGGTTAAATACCGT
1 GGCCTAACTGTGCAATTGGTAGAAAGGTGCCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
1165357 TGAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
* * *
1165373 GGCCTAACTGTACAATTGGTAAAAAGGTGCCAATTATG-TAGTTAGATGAACGGTTAAATACCGT
1 GGCCTAACTGTGCAATTGGTAGAAAGGTGCCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
1165437 TGAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
* * *
1165453 GGCCTAATTGTGCAATTGGTAGAAATGTGCCAATTATGCCAGTTAGATGAACGGTTAAATACTGT
1 GGCCTAACTGTGCAATTGGTAGAAAGGTGCCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
1165518 TGAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
* * **
1165534 GGCCTAACTGTGCAATTGGTAGAAAGATGCCAATTATGACAGTTAGATGAACGGTTAAATAATGT
1 GGCCTAACTGTGCAATTGGTAGAAAGGTGCCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
*
1165599 TGAGTAAAATAATAAT
66 TGAGTAAAAGAATAAT
* * * * * * **
1165615 GGCCTAACTGTGCAATTGGTAAAAAAAGTACCATTTATGCCAGTTAGATGAAAGGTTAAACACTT
1 GGCCTAACTGTGCAATTGGT-AGAAAGGTGCCAATTATGCCAGTTAGATGAACGGTTAAATACCG
1165680 TTGAGTAAAA
65 TTGAGTAAAA
1165690 ATGAAATGTT
Statistics
Matches: 360, Mismatches: 35, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
80 137 0.38
81 179 0.50
82 44 0.12
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (81 bp):
GGCCTAACTGTGCAATTGGTAGAAAGGTGCCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
TGAGTAAAAGAATAAT
Found at i:1165477 original size:161 final size:162
Alignment explanation
Indices: 1165212--1165689 Score: 708
Period size: 161 Copynumber: 3.0 Consensus size: 162
1165202 CTGCCTTTGA
* * **
1165212 GGCCTAACTGTGCAATTGGTAGAAAGGTGACAATTATGCCAGTTAGATGAACTATTAAATACCGT
1 GGCCTAACTGTGCAATTGGTAGAAAGGTGCCAATTATGACAGTTAGATGAACGGTTAAATACCGT
* * * * *
1165277 TGAGT-AAAGAATAATGGCCTGATTGTACAATTGGTAGAAAGGTGTCAATTATGCCAGTTAGGTG
66 TGAGTAAAAGAATAATGGCCTAATTGTGCAATTGGTAGAAAAGTGCCAATTATGCCAGTTAGATG
*
1165341 AACGGTTAAATACCGTTGAGTAAAAGAATAAT
131 AACGGTTAAATACTGTTGAGTAAAAGAATAAT
* * *
1165373 GGCCTAACTGTACAATTGGTAAAAAGGTGCCAATTATG-TAGTTAGATGAACGGTTAAATACCGT
1 GGCCTAACTGTGCAATTGGTAGAAAGGTGCCAATTATGACAGTTAGATGAACGGTTAAATACCGT
*
1165437 TGAGTAAAAGAATAATGGCCTAATTGTGCAATTGGTAGAAATGTGCCAATTATGCCAGTTAGATG
66 TGAGTAAAAGAATAATGGCCTAATTGTGCAATTGGTAGAAAAGTGCCAATTATGCCAGTTAGATG
1165502 AACGGTTAAATACTGTTGAGTAAAAGAATAAT
131 AACGGTTAAATACTGTTGAGTAAAAGAATAAT
* **
1165534 GGCCTAACTGTGCAATTGGTAGAAAGATGCCAATTATGACAGTTAGATGAACGGTTAAATAATGT
1 GGCCTAACTGTGCAATTGGTAGAAAGGTGCCAATTATGACAGTTAGATGAACGGTTAAATACCGT
* * * * *
1165599 TGAGTAAAATAATAATGGCCTAACTGTGCAATTGGTAAAAAAAGTACCATTTATGCCAGTTAGAT
66 TGAGTAAAAGAATAATGGCCTAATTGTGCAATTGGT-AGAAAAGTGCCAATTATGCCAGTTAGAT
* * *
1165664 GAAAGGTTAAACACTTTTGAGTAAAA
130 GAACGGTTAAATACTGTTGAGTAAAA
1165690 ATGAAATGTT
Statistics
Matches: 287, Mismatches: 27, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
160 28 0.10
161 155 0.54
162 57 0.20
163 47 0.16
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (162 bp):
GGCCTAACTGTGCAATTGGTAGAAAGGTGCCAATTATGACAGTTAGATGAACGGTTAAATACCGT
TGAGTAAAAGAATAATGGCCTAATTGTGCAATTGGTAGAAAAGTGCCAATTATGCCAGTTAGATG
AACGGTTAAATACTGTTGAGTAAAAGAATAAT
Found at i:1165702 original size:28 final size:28
Alignment explanation
Indices: 1165662--1165716 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
1165652 TGCCAGTTAG
* *
1165662 ATGAAAGGTTAAACACTTTTGAGTAAAA
1 ATGAAAGGTTAAACACTGTTGAATAAAA
*
1165690 ATGAAATGTTAAACACTGTTGAATAAA
1 ATGAAAGGTTAAACACTGTTGAATAAA
1165717 GAAGTGATGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.47, C:0.07, G:0.16, T:0.29
Consensus pattern (28 bp):
ATGAAAGGTTAAACACTGTTGAATAAAA
Found at i:1165860 original size:2 final size:2
Alignment explanation
Indices: 1165853--1165889 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1165843 TGAAGGGATG
1165853 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1165890 AGGTACAACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1169059 original size:18 final size:17
Alignment explanation
Indices: 1169018--1169059 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
1169008 AATCTAGAAA
*
1169018 ATATATATAAAAAACAC
1 ATATAAATAAAAAACAC
1169035 A-AGTAAATAAACAAACAC
1 ATA-TAAATAAA-AAACAC
1169053 ATATAAA
1 ATATAAA
1169060 ATACCAAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
16 1 0.05
17 8 0.38
18 11 0.52
19 1 0.05
ACGTcount: A:0.67, C:0.12, G:0.02, T:0.19
Consensus pattern (17 bp):
ATATAAATAAAAAACAC
Found at i:1171787 original size:60 final size:60
Alignment explanation
Indices: 1171721--1171889 Score: 166
Period size: 59 Copynumber: 2.8 Consensus size: 60
1171711 GTATGATTCA
* * *
1171721 CATTTTAAATTGGTCCTTAAACTTTTAAATATTTTAATTTCA-TCCCTAAATCGTGACTAT
1 CATTTTAAATTGGTCCTTAAACTTTTAAACATTTCAATTTCATTCCC-AAATCATGACTAT
* ** * * * *
1171781 CATTTTAAATTAGTCCTCGAAC-GTTGAACATTTCAATTTCATTCCCAAATTATGACTTT
1 CATTTTAAATTGGTCCTTAAACTTTTAAACATTTCAATTTCATTCCCAAATCATGACTAT
* * *
1171840 CATTCTAAATTGGT-CTCTAAACTTTTTGAACATTACAATTTCA-TCCCAAA
1 CATTTTAAATTGGTCCT-TAAAC-TTTTAAACATTTCAATTTCATTCCCAAA
1171890 CTATACATAT
Statistics
Matches: 89, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
58 2 0.02
59 40 0.45
60 30 0.34
61 17 0.19
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (60 bp):
CATTTTAAATTGGTCCTTAAACTTTTAAACATTTCAATTTCATTCCCAAATCATGACTAT
Found at i:1172084 original size:60 final size:61
Alignment explanation
Indices: 1172014--1172226 Score: 204
Period size: 60 Copynumber: 3.5 Consensus size: 61
1172004 TTTGGATGAA
* *
1172014 TTTAGGGATGAAATTGAAATATTCAAGAGTTTGGGGACCAAATTAAGAAGATAGG-CAT-G
1 TTTAGGGATGAAATTGAAATATTCAAAAGTTTGGGGACCAAATTAAAAAGATAGGTCATAG
* * * *
1172073 TTATAGGGATGAAATTGGAAGATTCAAAAATTTGGGGACCATATTAAAAAGATAGGTCATAG
1 TT-TAGGGATGAAATTGAAATATTCAAAAGTTTGGGGACCAAATTAAAAAGATAGGTCATAG
* ** * * * *
1172135 TTTAGGGATAAAATT-AGAATATTCAAAAGTTTAAGGACTAATTTAGAATAA-A-A-TTCATAA
1 TTTAGGGATGAAATTGA-AATATTCAAAAGTTTGGGGACCAAATTA-AA-AAGATAGGTCATAG
* * *
1172195 TTTAAGAATGAAATTGAATTATTCAAAAGTTT
1 TTTAGGGATGAAATTGAAATATTCAAAAGTTT
1172227 AAAGATCAAT
Statistics
Matches: 126, Mismatches: 21, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
59 2 0.02
60 78 0.62
61 38 0.30
62 6 0.05
63 2 0.02
ACGTcount: A:0.43, C:0.06, G:0.20, T:0.31
Consensus pattern (61 bp):
TTTAGGGATGAAATTGAAATATTCAAAAGTTTGGGGACCAAATTAAAAAGATAGGTCATAG
Found at i:1172166 original size:29 final size:28
Alignment explanation
Indices: 1172133--1172237 Score: 79
Period size: 29 Copynumber: 3.6 Consensus size: 28
1172123 GATAGGTCAT
*
1172133 AGTTTAGGGATAAAATTAGAATATTCAAA
1 AGTTTAAGGAT-AAATTAGAATATTCAAA
* *
1172162 AGTTTAAGGACTAATTTAGAATAAAATTCATA
1 AGTTTAAGGA-TAAATTAGAAT---ATTCAAA
*
1172194 A-TTTAAGAATGAAATT-GAATTATTCAAA
1 AGTTTAAGGAT-AAATTAGAA-TATTCAAA
* *
1172222 AGTTTAAAGATCAATT
1 AGTTTAAGGATAAATT
1172238 TAAAATAAGA
Statistics
Matches: 60, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
28 11 0.18
29 25 0.42
30 5 0.08
31 12 0.20
32 7 0.12
ACGTcount: A:0.48, C:0.05, G:0.13, T:0.34
Consensus pattern (28 bp):
AGTTTAAGGATAAATTAGAATATTCAAA
Found at i:1172227 original size:60 final size:60
Alignment explanation
Indices: 1172145--1172258 Score: 153
Period size: 60 Copynumber: 1.9 Consensus size: 60
1172135 TTTAGGGATA
* *
1172145 AAATTAGAATATTCAAAAGTTTAAGGA-CTAATTTAGAATAA-AATTCATAATTTAAGAATG
1 AAATTAGAATATTCAAAAGTTTAAAGATC-AATTTAAAATAAGAATT-ATAATTTAAGAATG
*
1172205 AAATT-GAATTATTCAAAAGTTTAAAGATCAATTTAAAATAAGAGTTATAATTTA
1 AAATTAGAA-TATTCAAAAGTTTAAAGATCAATTTAAAATAAGAATTATAATTTA
1172259 GAGACATATG
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
59 3 0.06
60 41 0.85
61 4 0.08
ACGTcount: A:0.50, C:0.04, G:0.11, T:0.35
Consensus pattern (60 bp):
AAATTAGAATATTCAAAAGTTTAAAGATCAATTTAAAATAAGAATTATAATTTAAGAATG
Found at i:1176369 original size:31 final size:31
Alignment explanation
Indices: 1176331--1176398 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
1176321 TAAAAAAATA
1176331 TAAGATTTAGTCACTTTT-GTTTCATTTTAAT
1 TAAGATTTAGT-ACTTTTCGTTTCATTTTAAT
** *
1176362 TAAGATTTAGTTGTTTTCGTTTCATTTTACT
1 TAAGATTTAGTACTTTTCGTTTCATTTTAAT
1176393 TAAGAT
1 TAAGAT
1176399 GTGGTCAGTG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 4 0.12
31 29 0.88
ACGTcount: A:0.25, C:0.09, G:0.12, T:0.54
Consensus pattern (31 bp):
TAAGATTTAGTACTTTTCGTTTCATTTTAAT
Found at i:1177388 original size:31 final size:31
Alignment explanation
Indices: 1177350--1177420 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
1177340 TACATTCATC
* * * *
1177350 TGACCAAAACTTAATAAAATGGTAACGTAAG
1 TGACCAAAACTTAATAAAACGATAACATAAA
1177381 TGACCAAAACTTAATAAAACGATAACATAAA
1 TGACCAAAACTTAATAAAACGATAACATAAA
1177412 TGACCAAAA
1 TGACCAAAA
1177421 GTGTACAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.54, C:0.15, G:0.11, T:0.20
Consensus pattern (31 bp):
TGACCAAAACTTAATAAAACGATAACATAAA
Found at i:1178804 original size:18 final size:17
Alignment explanation
Indices: 1178761--1178804 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1178751 TATAAATCAG
*
1178761 GTTCAAACTCAATTTAA
1 GTTCAAACTCAATTCAA
*
1178778 GTTCGAACTCAAGTTCAA
1 GTTCAAACTCAA-TTCAA
*
1178796 GTTTAAACT
1 GTTCAAACT
1178805 TTAAATACAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.34
Consensus pattern (17 bp):
GTTCAAACTCAATTCAA
Found at i:1180019 original size:16 final size:16
Alignment explanation
Indices: 1179982--1180025 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
1179972 TTTAGGAAAT
1179982 AATAAGAAAATTAAAAG
1 AATAAGAAAA-TAAAAG
1179999 AATAAGAAAAT-AAAG
1 AATAAGAAAATAAAAG
*
1180014 ATATAAAAAAAT
1 A-ATAAGAAAAT
1180026 CAATTATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 5 0.20
16 10 0.40
17 10 0.40
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (16 bp):
AATAAGAAAATAAAAG
Found at i:1184697 original size:8 final size:8
Alignment explanation
Indices: 1184688--1184762 Score: 105
Period size: 8 Copynumber: 9.4 Consensus size: 8
1184678 GTGACAATGT
*
1184688 ATGTATGT
1 ATGTATGC
1184696 ATGTATGC
1 ATGTATGC
*
1184704 ATGCATGC
1 ATGTATGC
*
1184712 ATGGATGC
1 ATGTATGC
1184720 ATGTATGC
1 ATGTATGC
*
1184728 ATGGATGC
1 ATGTATGC
1184736 ATGTATGC
1 ATGTATGC
*
1184744 ATGGATGC
1 ATGTATGC
1184752 ATGTATGC
1 ATGTATGC
1184760 ATG
1 ATG
1184763 GATGGTTTAG
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 59 1.00
ACGTcount: A:0.25, C:0.12, G:0.29, T:0.33
Consensus pattern (8 bp):
ATGTATGC
Found at i:1184699 original size:4 final size:4
Alignment explanation
Indices: 1184700--1184762 Score: 72
Period size: 4 Copynumber: 15.8 Consensus size: 4
1184690 GTATGTATGT
* * * * *
1184700 ATGC ATGC ATGC ATGG ATGC ATGT ATGC ATGG ATGC ATGT ATGC ATGG
1 ATGC ATGC ATGC ATGC ATGC ATGC ATGC ATGC ATGC ATGC ATGC ATGC
*
1184748 ATGC ATGT ATGC ATG
1 ATGC ATGC ATGC ATG
1184763 GATGGTTTAG
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.25, C:0.14, G:0.30, T:0.30
Consensus pattern (4 bp):
ATGC
Found at i:1184721 original size:16 final size:16
Alignment explanation
Indices: 1184688--1184766 Score: 131
Period size: 16 Copynumber: 4.9 Consensus size: 16
1184678 GTGACAATGT
* *
1184688 ATGTATGTATGTATGC
1 ATGTATGCATGGATGC
*
1184704 ATGCATGCATGGATGC
1 ATGTATGCATGGATGC
1184720 ATGTATGCATGGATGC
1 ATGTATGCATGGATGC
1184736 ATGTATGCATGGATGC
1 ATGTATGCATGGATGC
1184752 ATGTATGCATGGATG
1 ATGTATGCATGGATG
1184767 GTTTAGATAA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 59 1.00
ACGTcount: A:0.25, C:0.11, G:0.30, T:0.33
Consensus pattern (16 bp):
ATGTATGCATGGATGC
Found at i:1190428 original size:12 final size:12
Alignment explanation
Indices: 1190411--1190441 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
1190401 TTTCATAGAT
1190411 AAACAAAAAACA
1 AAACAAAAAACA
1190423 AAACAAAAAACA
1 AAACAAAAAACA
1190435 ACAACAA
1 A-AACAA
1190442 CAAAGTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.72
13 5 0.28
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (12 bp):
AAACAAAAAACA
Found at i:1194560 original size:21 final size:21
Alignment explanation
Indices: 1194523--1194562 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1194513 TCTGTTGAAA
**
1194523 CTCCACCTGCTTTGGAGTATG
1 CTCCACCTGCTGCGGAGTATG
1194544 CTCCACCTGCTGCGGAGTA
1 CTCCACCTGCTGCGGAGTA
1194563 CTACTTGTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.33, G:0.25, T:0.28
Consensus pattern (21 bp):
CTCCACCTGCTGCGGAGTATG
Found at i:1203246 original size:21 final size:21
Alignment explanation
Indices: 1203222--1203275 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
1203212 AGTGACTGAC
*
1203222 GGTGCGATGGTGGTCACTGGA
1 GGTGCGATGATGGTCACTGGA
** * *
1203243 GGTGCGACAATGGTGACTGGC
1 GGTGCGATGATGGTCACTGGA
1203264 GGTGCGATGATG
1 GGTGCGATGATG
1203276 ATGATTGGCG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.17, C:0.15, G:0.46, T:0.22
Consensus pattern (21 bp):
GGTGCGATGATGGTCACTGGA
Found at i:1203507 original size:41 final size:42
Alignment explanation
Indices: 1203419--1203533 Score: 117
Period size: 41 Copynumber: 2.8 Consensus size: 42
1203409 TTTTCACAAA
* * * * * **
1203419 AAACGCCACTAATGTACACGTTTATTTCGACGTTTGTATAAC
1 AAACGCCACTATTGTACAAGTCTATTGCGGCGCGTGTATAAC
** *
1203461 AAACGCCACTATT-TACGCGTCTATTGTGGCGCGTGTATGAA-
1 AAACGCCACTATTGTACAAGTCTATTGCGGCGCGTGTAT-AAC
1203502 AAACGCCACTATTGTACAAGTCTATTGCGGCG
1 AAACGCCACTATTGTACAAGTCTATTGCGGCG
1203534 TTCCATTAAC
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
41 31 0.52
42 29 0.48
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (42 bp):
AAACGCCACTATTGTACAAGTCTATTGCGGCGCGTGTATAAC
Found at i:1203819 original size:83 final size:83
Alignment explanation
Indices: 1203603--1203833 Score: 284
Period size: 83 Copynumber: 2.8 Consensus size: 83
1203593 ATTGTAGCGT
* * * **
1203603 TTTTTACATAAA-AACACTAAAGTATGTGTTTGTGGCGGCATTTTAACAAAAACACCACTATATA
1 TTTTTACATAAACACCACTAAAGTATGTGTTTGTAGCGGCGTTTTAACAAAAATGCCACTATATA
* * **
1203667 TCTGGCTATCGCGGCATT
66 TCTAGCTATCGCAGCACG
* * * * * *
1203685 TTTTTACATAAACGCCACTAAAGTACGTGTTTTTAGCGGTGTTTTGACAAAAATGCCACTATATG
1 TTTTTACATAAACACCACTAAAGTATGTGTTTGTAGCGGCGTTTTAACAAAAATGCCACTATATA
1203750 TCTAGCTATCGCAGCACG
66 TCTAGCTATCGCAGCACG
* ** *
1203768 TTTTTACATAAACACCACTAAAGTATGCGTTTGTAGCGGCGTTTTCCCAAAAATGACACTATATA
1 TTTTTACATAAACACCACTAAAGTATGTGTTTGTAGCGGCGTTTTAACAAAAATGCCACTATATA
1203833 T
66 T
1203834 TAGGATATCC
Statistics
Matches: 124, Mismatches: 24, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
82 12 0.10
83 112 0.90
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (83 bp):
TTTTTACATAAACACCACTAAAGTATGTGTTTGTAGCGGCGTTTTAACAAAAATGCCACTATATA
TCTAGCTATCGCAGCACG
Found at i:1204488 original size:21 final size:21
Alignment explanation
Indices: 1204464--1204518 Score: 94
Period size: 20 Copynumber: 2.7 Consensus size: 21
1204454 ATTGGCCTAA
1204464 AGGTTTCGAAACCCCCCTCAT
1 AGGTTTCGAAACCCCCCTCAT
*
1204485 AGGTTTC-AAAACCCCCTCAT
1 AGGTTTCGAAACCCCCCTCAT
1204505 AGGTTTCGAAACCC
1 AGGTTTCGAAACCC
1204519 TCCATGTTCC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 19 0.61
21 12 0.39
ACGTcount: A:0.27, C:0.35, G:0.15, T:0.24
Consensus pattern (21 bp):
AGGTTTCGAAACCCCCCTCAT
Found at i:1204923 original size:31 final size:30
Alignment explanation
Indices: 1204875--1204950 Score: 93
Period size: 31 Copynumber: 2.4 Consensus size: 30
1204865 ACAAATCAAA
1204875 CCTTGAAAAATAGGAGTGGTTCTAGT-TTAG
1 CCTTGAAAAATAGGAGTGGTTCTA-TCTTAG
1204905 CCTTAGAAAAACTA-GAGTGGTTCTATCTTAG
1 CCTT-GAAAAA-TAGGAGTGGTTCTATCTTAG
1204936 CCATTGAAAAGATAG
1 CC-TTGAAAA-ATAG
1204951 ATTTGTAAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
30 5 0.12
31 30 0.75
32 5 0.12
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.30
Consensus pattern (30 bp):
CCTTGAAAAATAGGAGTGGTTCTATCTTAG
Found at i:1208114 original size:31 final size:31
Alignment explanation
Indices: 1208079--1208144 Score: 84
Period size: 31 Copynumber: 2.1 Consensus size: 31
1208069 CGAAAAAGGG
1208079 GAGTGATTCTAGT-TTAGCC-TTAGAAAA-ACTA
1 GAGTGATTCTA-TCTTAGCCATT-GAAAATA-TA
1208110 GAGTGATTCTATCTTAGCCATTGAAAATATA
1 GAGTGATTCTATCTTAGCCATTGAAAATATA
1208141 GAGT
1 GAGT
1208145 TGTAAGGTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
30 1 0.03
31 28 0.88
32 3 0.09
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (31 bp):
GAGTGATTCTATCTTAGCCATTGAAAATATA
Found at i:1210617 original size:20 final size:19
Alignment explanation
Indices: 1210594--1210639 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
1210584 CGATATACCA
1210594 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
1210614 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
1210634 GGTAAA
1 GGTAAA
1210640 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1210783 original size:20 final size:19
Alignment explanation
Indices: 1210760--1210806 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
1210750 CGATATAACA
1210760 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
1210780 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
1210800 GGTAAAA
1 GGTAAAA
1210807 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1210808 original size:17 final size:19
Alignment explanation
Indices: 1210769--1210811 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
1210759 AGGTAAAAAT
1210769 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
1210789 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
1210806 ATGATA
1 ATGATA
1210812 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:1213062 original size:21 final size:21
Alignment explanation
Indices: 1213015--1213079 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
1213005 AAGACAATCA
* *
1213015 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
1213037 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
1213057 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
1213078 AG
1 AG
1213080 GCATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:1213155 original size:33 final size:33
Alignment explanation
Indices: 1213113--1213178 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1213103 AAATAGATGG
*
1213113 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
1213146 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
1213179 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:1214997 original size:19 final size:19
Alignment explanation
Indices: 1214973--1215021 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1214963 AATGTAGGGT
1214973 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1214992 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
1215011 TATTTTTGTAT
1 TAATTTTGTAT
1215022 GTGAATATAA
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:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1215670 original size:198 final size:198
Alignment explanation
Indices: 1215140--1216306 Score: 2230
Period size: 198 Copynumber: 5.9 Consensus size: 198
1215130 CAATATGGCC
* *
1215140 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAAACATCGAAA
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCG-AA
* *
1215205 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACTGGTACAATTATACCGGTTTTATGAG
64 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
1215270 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAA
129 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAA
1215335 TGGAA
194 TGGAA
1215340 AACAGGGTGCACCCATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1215403 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
1215468 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
1215533 GAA
196 GAA
1215536 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
1215601 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATATCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
1215666 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAAT
1215731 GGAA
195 GGAA
1215735 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1215800 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
1215865 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
1215930 GAA
196 GAA
1215933 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1215998 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
1216063 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
1216128 GAA
196 GAA
1216131 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1216196 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
1216261 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
1216307 CTAATTTAAA
Statistics
Matches: 954, Mismatches: 10, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
196 163 0.17
197 24 0.03
198 542 0.57
199 196 0.21
200 29 0.03
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (198 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
GAA
Found at i:1215882 original size:397 final size:396
Alignment explanation
Indices: 1215140--1216306 Score: 2239
Period size: 397 Copynumber: 2.9 Consensus size: 396
1215130 CAATATGGCC
* *
1215140 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAAACATCGAAA
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCG-AA
* *
1215205 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACTGGTACAATTATACCGGTTTTATGAG
64 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
1215270 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAA
129 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAA
1215335 TGGAAAACAGGGTGCACCCATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATC
194 TGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATC
1215398 GAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTAT
259 GAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTAT
1215463 GAGAGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAAT
324 GAGAGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAAT
1215528 GAATGGAA
389 GAATGGAA
1215536 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
1215601 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATATCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
1215666 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAAT
1215731 GGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
195 GGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCG
1215796 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
260 AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATG
1215861 AGAGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATG
325 AGAGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATG
1215926 AATGGAA
390 AATGGAA
1215933 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1215998 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
1216063 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
1216128 GAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGA
196 GAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGA
1216193 ACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGA
261 ACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGA
*
1216258 GAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
326 GAGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
1216307 CTAATTTAAA
Statistics
Matches: 761, Mismatches: 7, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
394 112 0.15
395 75 0.10
396 232 0.30
397 342 0.45
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (396 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATG
GAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGA
ACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGA
GAGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGA
ATGGAA
Found at i:1216271 original size:595 final size:595
Alignment explanation
Indices: 1215140--1216306 Score: 2239
Period size: 595 Copynumber: 2.0 Consensus size: 595
1215130 CAATATGGCC
1215140 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAAACATCGAAA
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAAACATCGAAA
*
1215205 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACTGGTACAATTATACCGGTTTTATGAG
66 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
*
1215270 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAA
131 AGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAA
1215335 TGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATAAAAAGTGTCGATCCCAAAATCATCGA
196 TGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATAAAAAGTGTCGATCCCAAAATCATCGA
1215400 ACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGA
261 ACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGA
1215465 GAGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGA
326 GAGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGA
1215530 ATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCAT
391 ATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCAT
*
1215595 CGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATATCGGTTTTA
456 CGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTA
1215660 TGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGA
521 TGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGA
1215725 ATGAATGGAA
586 ATGAATGGAA
* *
1215735 AACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCG-AA
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAAACATCGAAA
*
1215798 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
66 ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
1215863 AGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAA
131 AGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAA
1215928 TGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATC
196 TGGAAAACAGGGTGCACCCATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATC
1215993 GAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTAT
259 GAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTAT
*
1216058 GAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAAT
324 GAGAGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAAT
1216123 GAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATC
389 GAATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATC
1216188 ATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTT
454 ATCGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTT
1216253 TATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
519 TATGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATA
1216307 CTAATTTAAA
Statistics
Matches: 563, Mismatches: 7, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
593 163 0.29
594 24 0.04
595 376 0.67
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (595 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAAACATCGAAA
ACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
AGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAA
TGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATAAAAAGTGTCGATCCCAAAATCATCGA
ACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGA
GAGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGA
ATGGAAAACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCAT
CGAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTA
TGAGAGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGA
ATGAATGGAA
Found at i:1217781 original size:18 final size:18
Alignment explanation
Indices: 1217760--1217821 Score: 88
Period size: 18 Copynumber: 3.4 Consensus size: 18
1217750 AGCGGTCGCA
1217760 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* *
1217778 GAAGATGACGATGACGAT
1 GAAGATGAAGCTGACGAT
* *
1217796 GACGATGAAGCTGGCGAT
1 GAAGATGAAGCTGACGAT
1217814 GAAGATGA
1 GAAGATGA
1217822 TGACGATGAT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.37, C:0.11, G:0.35, T:0.16
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:1217784 original size:6 final size:6
Alignment explanation
Indices: 1217760--1217851 Score: 67
Period size: 6 Copynumber: 15.3 Consensus size: 6
1217750 AGCGGTCGCA
* * * * * *
1217760 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GACGAT GACGAT GAAGCT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
** * * * * *
1217808 GGCGAT GAAGAT GATGAC GATGAT GATGAT GATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA
1217852 TGATCCAAAC
Statistics
Matches: 70, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 70 1.00
ACGTcount: A:0.37, C:0.09, G:0.35, T:0.20
Consensus pattern (6 bp):
GAAGAT
Found at i:1217832 original size:3 final size:3
Alignment explanation
Indices: 1217811--1217855 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
1217801 TGAAGCTGGC
* * *
1217811 GAT GAA GAT GAT GAC GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1217856 CCAAACAAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.38, C:0.02, G:0.33, T:0.27
Consensus pattern (3 bp):
GAT
Found at i:1217855 original size:12 final size:12
Alignment explanation
Indices: 1217763--1217851 Score: 88
Period size: 12 Copynumber: 7.4 Consensus size: 12
1217753 GGTCGCAGAA
*
1217763 GATGAAGCTGAC
1 GATGAAGATGAC
1217775 GATGAAGATGAC
1 GATGAAGATGAC
*
1217787 GATGACGATGAC
1 GATGAAGATGAC
* *
1217799 GATGAAGCTGGC
1 GATGAAGATGAC
*
1217811 GATGAAGATGAT
1 GATGAAGATGAC
* * *
1217823 GACGATGATGAT
1 GATGAAGATGAC
* *
1217835 GATGATGATGAA
1 GATGAAGATGAC
1217847 GATGA
1 GATGA
1217852 TGATCCAAAC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 65 1.00
ACGTcount: A:0.36, C:0.09, G:0.35, T:0.20
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:1217855 original size:18 final size:18
Alignment explanation
Indices: 1217760--1217851 Score: 85
Period size: 18 Copynumber: 5.1 Consensus size: 18
1217750 AGCGGTCGCA
*
1217760 GAAGATGAAGCTGACGAT
1 GAAGATGAAGATGACGAT
*
1217778 GAAGATGACGATGACGAT
1 GAAGATGAAGATGACGAT
* * *
1217796 GACGATGAAGCTGGCGAT
1 GAAGATGAAGATGACGAT
* * *
1217814 GAAGATGATGACGATGAT
1 GAAGATGAAGATGACGAT
* * *
1217832 GATGATGATGATGAAGAT
1 GAAGATGAAGATGACGAT
1217850 GA
1 GA
1217852 TGATCCAAAC
Statistics
Matches: 59, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 59 1.00
ACGTcount: A:0.37, C:0.09, G:0.35, T:0.20
Consensus pattern (18 bp):
GAAGATGAAGATGACGAT
Found at i:1219617 original size:183 final size:182
Alignment explanation
Indices: 1219309--1220008 Score: 1246
Period size: 183 Copynumber: 3.9 Consensus size: 182
1219299 CTTTCAACAT
** * * *
1219309 ATTATAATAAAATAGGTAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1219374 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
1219439 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATA
131 AATGTGTCGATACGATTTAAAAAAGTATCGACATTTACACATCGGAACCCA-A
1219492 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1219557 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
1219622 AA--TGTCGATACGATTTAAAAAAGTATCGACATTTACACATCGGAACCC-A
131 AATGTGTCGATACGATTTAAAAAAGTATCGACATTTACACATCGGAACCCAA
1219671 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1219736 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
1219801 AATATGTCGATACGATTTAAAAAAGTATCGACATTTACACATCGGAACCCAGA
131 AATGTGTCGATACGATTTAAAAAAGTATCGACATTTACACATCGGAACCCA-A
* *
1219854 TTTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
* *
1219919 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAG-AA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
1219983 AATGTGTCGATACCATTTAAAAAAGT
131 AATGTGTCGATACGATTTAAAAAAGT
1220009 GTCGGTAATT
Statistics
Matches: 501, Mismatches: 12, Indels: 9
0.96 0.02 0.02
Matches are distributed among these distances:
179 133 0.27
181 91 0.18
182 26 0.05
183 251 0.50
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (182 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATGTGTCGATACGATTTAAAAAAGTATCGACATTTACACATCGGAACCCAA
Found at i:1219979 original size:362 final size:363
Alignment explanation
Indices: 1219309--1220008 Score: 1267
Period size: 362 Copynumber: 1.9 Consensus size: 363
1219299 CTTTCAACAT
*
1219309 ATTATAATAAAATAGGTAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATAAAATAGATAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1219374 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
* * *
1219439 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATAATTATAATGTAA
131 AATATGTCGATACGATTTAAAAAAGTATCGACATTTACACATCGGAACCCAGAATTATAATGTAA
*
1219504 TAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCT
196 TAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCT
* *
1219569 ATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAA-ATGTCGATAC
261 ATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAATATGTCGATAC
*
1219633 GATTTAAAAAAGTATCGACATTTACACATCGGAACCCA
326 CATTTAAAAAAGTATCGACATTTACACATCGGAACCCA
** * *
1219671 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1 ATTATAATAAAATAGATAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
1219736 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
*
1219801 AATATGTCGATACGATTTAAAAAAGTATCGACATTTACACATCGGAACCCAGATTTATAATGTAA
131 AATATGTCGATACGATTTAAAAAAGTATCGACATTTACACATCGGAACCCAGAATTATAATGTAA
1219866 TAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCT
196 TAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCT
*
1219931 ATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAATGTGTCGATAC
261 ATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAATATGTCGATAC
1219996 CATTTAAAAAAGT
326 CATTTAAAAAAGT
1220009 GTCGGTAATT
Statistics
Matches: 323, Mismatches: 14, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
362 302 0.93
363 21 0.07
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (363 bp):
ATTATAATAAAATAGATAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
AATATGTCGATACGATTTAAAAAAGTATCGACATTTACACATCGGAACCCAGAATTATAATGTAA
TAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCT
ATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAATATGTCGATAC
CATTTAAAAAAGTATCGACATTTACACATCGGAACCCA
Done.