Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004846.1 Hibiscus syriacus cultivar Beakdansim tig00010927_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: 1467214
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 6
Found at i:930792 original size:20 final size:20
Alignment explanation
Indices: 930767--930810 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
930757 TTGCCACTAT
930767 TATCGATACTA-ACCTTTGAG
1 TATCGATACTAGACC-TTGAG
930787 TATCGATACTAGACCTTGAG
1 TATCGATACTAGACCTTGAG
930807 TATC
1 TATC
930811 ATTTCTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 20 0.87
21 3 0.13
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (20 bp):
TATCGATACTAGACCTTGAG
Found at i:932966 original size:21 final size:20
Alignment explanation
Indices: 932915--932971 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 20
932905 TGGCTCATTC
932915 AGGTGCGGCTAGACTCAGTTT
1 AGGTGCGGCTAG-CTCAGTTT
*
932936 AGGCT-TGGCTCAGCTCAGTTT
1 AGG-TGCGGCT-AGCTCAGTTT
932957 AGGTGCGGCTTAGCT
1 AGGTGCGGC-TAGCT
932972 TAGCTCAGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
20 1 0.03
21 25 0.83
22 4 0.13
ACGTcount: A:0.16, C:0.21, G:0.33, T:0.30
Consensus pattern (20 bp):
AGGTGCGGCTAGCTCAGTTT
Found at i:934859 original size:2 final size:2
Alignment explanation
Indices: 934758--934842 Score: 65
Period size: 2 Copynumber: 43.0 Consensus size: 2
934748 TTTATTTTAT
*
934758 TA TA -A TA TA TA TA TA TA TA TA TA TA TCA TA TT TGA -A GTA TGA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA T-A TA -TA T-A
*
934800 TA AA T- TA -A TCA T- TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
934839 TA TA
1 TA TA
934843 GTTTTCAAAA
Statistics
Matches: 68, Mismatches: 4, Indels: 22
0.72 0.04 0.23
Matches are distributed among these distances:
1 6 0.09
2 55 0.81
3 7 0.10
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:939487 original size:2 final size:2
Alignment explanation
Indices: 939480--939525 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
939470 TTACACGTGC
939480 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
939522 AT AT
1 AT AT
939526 TAATTTTAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:942740 original size:35 final size:34
Alignment explanation
Indices: 942655--942741 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
942645 GGTTAGTATT
*
942655 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
942689 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
942727 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
942742 ACTGAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:943324 original size:18 final size:18
Alignment explanation
Indices: 943301--943346 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
943291 GTGGCGGCGA
943301 CGGCATCATATATGG-CTG
1 CGGCATCATATATGGTC-G
943319 CGGCATCATATATGGTCG
1 CGGCATCATATATGGTCG
943337 CGGCATCATA
1 CGGCATCATA
943347 AATGCTTGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 26 0.96
19 1 0.04
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (18 bp):
CGGCATCATATATGGTCG
Found at i:945128 original size:10 final size:10
Alignment explanation
Indices: 945113--945140 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
945103 CTTAAACAGA
945113 GAGAGAATTT
1 GAGAGAATTT
945123 GAGAGAATTT
1 GAGAGAATTT
945133 GAGAGAAT
1 GAGAGAAT
945141 ATGGTATGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.32, T:0.25
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:949251 original size:90 final size:90
Alignment explanation
Indices: 949098--949275 Score: 284
Period size: 90 Copynumber: 2.0 Consensus size: 90
949088 CCTAACACAC
* * *
949098 CCTTTTATAGCCAAGTTACCCTAGTCATATTAGGCTTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGCATTTTATTATTTCAAATTAATTAAATCTAT
* * *
949163 ATTTAATTAATTGGAATTTAATAAT
66 ACTTAATTAATTGAAATTAAATAAT
* *
949188 CCTTTTATATCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGCATTTTATTATTTCAAATTAATTAAATCTAT
949253 ACTTAATTAATTGAAATTAAATA
66 ACTTAATTAATTGAAATTAAATA
949276 TTCGGGATTA
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 80 1.00
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.44
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATCAGGCATTTTATTATTTCAAATTAATTAAATCTAT
ACTTAATTAATTGAAATTAAATAAT
Found at i:956066 original size:90 final size:90
Alignment explanation
Indices: 955913--956088 Score: 280
Period size: 90 Copynumber: 2.0 Consensus size: 90
955903 TAACACACCT
* * * *
955913 TTTTATAGCCAAGTTACCCTATTCATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTATAT
1 TTTTATAGCCAAGTTACCCTAATCATATCAAGGATTTTATTATTTCAAATTAATTAAATCTATAT
* *
955978 TTAATTAATTGGAATTTAATAATCC
66 TTAATTAATTGAAATTAAATAATCC
* *
956003 TTTTATATCCAAGTTACCCTAATCATATCAATGATTTTATTATTTCAAATTAATTAAATCTATAT
1 TTTTATAGCCAAGTTACCCTAATCATATCAAGGATTTTATTATTTCAAATTAATTAAATCTATAT
956068 TTAATTAATTGAAATTAAATA
66 TTAATTAATTGAAATTAAATA
956089 TTCGGGATTA
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 78 1.00
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.46
Consensus pattern (90 bp):
TTTTATAGCCAAGTTACCCTAATCATATCAAGGATTTTATTATTTCAAATTAATTAAATCTATAT
TTAATTAATTGAAATTAAATAATCC
Found at i:966578 original size:32 final size:26
Alignment explanation
Indices: 966540--966606 Score: 125
Period size: 26 Copynumber: 2.6 Consensus size: 26
966530 TATCAAGTTC
966540 AACTCGAACTCGAAACATAATATTGA
1 AACTCGAACTCGAAACATAATATTGA
966566 AACTCGAACTCGAAACATAATATTGA
1 AACTCGAACTCGAAACATAATATTGA
*
966592 AACTTGAACTCGAAA
1 AACTCGAACTCGAAA
966607 ATGCTTGAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.22
Consensus pattern (26 bp):
AACTCGAACTCGAAACATAATATTGA
Found at i:969121 original size:21 final size:21
Alignment explanation
Indices: 969095--969136 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
969085 GAAATTATTA
*
969095 TAATATTTTAAAATTAATAAT
1 TAATATTTTAAAATAAATAAT
*
969116 TAATATTTTATAATAAATAAT
1 TAATATTTTAAAATAAATAAT
969137 ATTAATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TAATATTTTAAAATAAATAAT
Found at i:972862 original size:127 final size:127
Alignment explanation
Indices: 972520--972990 Score: 736
Period size: 127 Copynumber: 3.7 Consensus size: 127
972510 ATCAGTACCC
* * *
972520 AAAGCGCGTTCCTAGGGGCGCGCCTTCGATTGTTTTGTCAGAGAATATGTTATCATTGCCCTATT
1 AAAGCGCGTTCCCAGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
*
972585 ATGTCACTCATGTCCCCC-GGAGAACTATTCATGTTAGTACCTATTATTTCTGAGGGGACTTG
66 ATGTCACTCATGTCCCCCGGGA-AACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTG
* * *
972647 AAAGAGCGTTCCC-GGGG-GC-ACTTCCATTATTTTTTCAGAGAATATGTTATCATTGCCCTATT
1 AAAGCGCGTTCCCAGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
*
972709 ATGTCACTCATGTCCCACAGGG-AACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTG
66 ATGTCACTCATGTCCC-CCGGGAAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTG
*
972771 AAAGCGCGTTCCCAGGGGCGCGCCTTCCATTATTTTATCAGAGAATATGTTATCATTGCCCTATT
1 AAAGCGCGTTCCCAGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
* * *
972836 ATGTCACTAATGTCCCCCGGGAAACTATTTATGTCAGTACCAATTATTTCTGAGGGGACTTG
66 ATGTCACTCATGTCCCCCGGGAAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTG
* * * *
972898 AAAGCGCGTTCTCGGGGGCGTGCCTTCCATTATTTTGTCAGAGACTATGTTATCATTGCCCTATT
1 AAAGCGCGTTCCCAGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
*
972963 ATGTCACTCATGTCCCCCGGGGAACTAT
66 ATGTCACTCATGTCCCCCGGGAAACTAT
972991 AGATGGATGG
Statistics
Matches: 316, Mismatches: 22, Indels: 12
0.90 0.06 0.03
Matches are distributed among these distances:
124 106 0.34
125 7 0.02
126 12 0.04
127 191 0.60
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (127 bp):
AAAGCGCGTTCCCAGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTATT
ATGTCACTCATGTCCCCCGGGAAACTATTCATGTCAGTACCTATTATTTCTGAGGGGACTTG
Found at i:973184 original size:63 final size:63
Alignment explanation
Indices: 973105--973412 Score: 392
Period size: 63 Copynumber: 4.8 Consensus size: 63
973095 TAACTTAAAT
*
973105 TAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATCAGTTGGTTGTTTGAATAAATTGGA
1 TAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATAAGTTGGTTGTTTGAATAAATTGGA
* *
973168 TAAAATGTTATAGATAAATTGAATAAATGTGAAGTGATAAGTTGGTTG--TGACATTGAAATTGT
1 TAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATAAGTTGGTTGTTTGA-A-T-AAATTGG
973231 A
63 A
** * *
973232 TGGAATG--A-GCATCAACATGTTTTTACAAATAAATGTGAAGTGATAAGTTGGTTGTTTGAATA
1 TAAAATGTTATGGAT-AA-A-----TT--GAATAAATGTGAAGTGATAAGTTGGTTGTTTGAATA
973294 AATTGGA
57 AATTGGA
973301 TAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATAAGTTGGTTGTTTGAATAAATTGGA
1 TAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATAAGTTGGTTGTTTGAATAAATTGGA
* *
973364 TAAAATGTTTTGGATAAATTGAATAAATGTGAAGTGATCAGTTGGTTGT
1 TAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATAAGTTGGTTGT
973413 GACATTGGAA
Statistics
Matches: 213, Mismatches: 15, Indels: 34
0.81 0.06 0.13
Matches are distributed among these distances:
61 5 0.02
62 4 0.02
63 137 0.64
64 12 0.06
65 2 0.01
68 2 0.01
69 12 0.06
70 29 0.14
71 4 0.02
72 6 0.03
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.36
Consensus pattern (63 bp):
TAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATAAGTTGGTTGTTTGAATAAATTGGA
Found at i:973294 original size:31 final size:31
Alignment explanation
Indices: 973259--973359 Score: 100
Period size: 31 Copynumber: 3.2 Consensus size: 31
973249 TGTTTTTACA
973259 AATAAATGTGAAGTGATAAGTTGGTTGTTTG
1 AATAAATGTGAAGTGATAAGTTGGTTGTTTG
* * ***
973290 AATAAAT-TGGA-T-AAAATGTTATGGATAAATTG
1 AATAAATGTGAAGTGATAA-G-T-TGG-TTGTTTG
973322 AATAAATGTGAAGTGATAAGTTGGTTGTTTG
1 AATAAATGTGAAGTGATAAGTTGGTTGTTTG
973353 AATAAAT
1 AATAAAT
973360 TGGATAAAAT
Statistics
Matches: 53, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
28 3 0.06
29 2 0.04
30 4 0.08
31 21 0.40
32 14 0.26
33 4 0.08
34 2 0.04
35 3 0.06
ACGTcount: A:0.40, C:0.00, G:0.24, T:0.37
Consensus pattern (31 bp):
AATAAATGTGAAGTGATAAGTTGGTTGTTTG
Found at i:973318 original size:23 final size:23
Alignment explanation
Indices: 973291--973390 Score: 79
Period size: 23 Copynumber: 4.6 Consensus size: 23
973281 GGTTGTTTGA
973291 ATAAATTGGATAAAATGTTATGG
1 ATAAATTGGATAAAATGTTATGG
* * *
973314 ATAAATTGAAT-AAATGTGAAGTG
1 ATAAATTGGATAAAATGTTATG-G
* *
973337 ATAAGTTGG-T----TGTT-TGA
1 ATAAATTGGATAAAATGTTATGG
*
973354 ATAAATTGGATAAAATGTTTTGG
1 ATAAATTGGATAAAATGTTATGG
*
973377 ATAAATTGAATAAA
1 ATAAATTGGATAAA
973391 TGTGAAGTGA
Statistics
Matches: 59, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
17 8 0.14
18 2 0.03
19 3 0.05
22 13 0.22
23 33 0.56
ACGTcount: A:0.43, C:0.00, G:0.21, T:0.36
Consensus pattern (23 bp):
ATAAATTGGATAAAATGTTATGG
Found at i:973439 original size:196 final size:196
Alignment explanation
Indices: 973105--973480 Score: 689
Period size: 196 Copynumber: 1.9 Consensus size: 196
973095 TAACTTAAAT
*
973105 TAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATCAGTTGGTTGTTTGAATAAATTGGATA
1 TAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATAAGTTGGTTGTTTGAATAAATTGGATA
973170 AAATGTTATAGATAAATTGAATAAATGTGAAGTGATAAGTTGGTTGTGACATTGAAATTGTATGG
66 AAATGTTATAGATAAATTGAATAAATGTGAAGTGATAAGTTGGTTGTGACATTGAAATTGTATGG
973235 AATGAGCATCAACATGTTTTTACAAATAAATGTGAAGTGATAAGTTGGTTGTTTGAATAAATTGG
131 AATGAGCATCAACATGTTTTTACAAATAAATGTGAAGTGATAAGTTGGTTGTTTGAATAAATTGG
973300 A
196 A
973301 TAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATAAGTTGGTTGTTTGAATAAATTGGATA
1 TAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATAAGTTGGTTGTTTGAATAAATTGGATA
* * * *
973366 AAATGTTTTGGATAAATTGAATAAATGTGAAGTGATCAGTTGGTTGTGACATTGGAATTGTATGG
66 AAATGTTATAGATAAATTGAATAAATGTGAAGTGATAAGTTGGTTGTGACATTGAAATTGTATGG
* *
973431 AATGAGCATCGACATGTTTTTACGAATAAATGTGAAGTGATAAGTTGGTT
131 AATGAGCATCAACATGTTTTTACAAATAAATGTGAAGTGATAAGTTGGTT
973481 TTAATGTATA
Statistics
Matches: 173, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
196 173 1.00
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (196 bp):
TAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATAAGTTGGTTGTTTGAATAAATTGGATA
AAATGTTATAGATAAATTGAATAAATGTGAAGTGATAAGTTGGTTGTGACATTGAAATTGTATGG
AATGAGCATCAACATGTTTTTACAAATAAATGTGAAGTGATAAGTTGGTTGTTTGAATAAATTGG
A
Found at i:973629 original size:34 final size:33
Alignment explanation
Indices: 973590--973661 Score: 99
Period size: 34 Copynumber: 2.2 Consensus size: 33
973580 TTAAGTTGAA
*
973590 TTTAATGTTAAATTTTGAACACTATAATTTGTAT
1 TTTAATGTTAAATTTTGAACACCATAA-TTGTAT
* *
973624 TTTAATTTTAAATTTTGAATACCATAATTGTAT
1 TTTAATGTTAAATTTTGAACACCATAATTGTAT
*
973657 ATTAA
1 TTTAA
973662 AAACATTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 10 0.29
34 24 0.71
ACGTcount: A:0.38, C:0.06, G:0.07, T:0.50
Consensus pattern (33 bp):
TTTAATGTTAAATTTTGAACACCATAATTGTAT
Found at i:974239 original size:21 final size:21
Alignment explanation
Indices: 974173--974240 Score: 86
Period size: 21 Copynumber: 3.2 Consensus size: 21
974163 GTCATAAAAT
*
974173 CCTGCGGGCTAGGCATGTAA-
1 CCTGCGGGCTAGGAATGTAAC
974193 CCTGGCGGGCTAGGAATGT-AC
1 CCT-GCGGGCTAGGAATGTAAC
*
974214 TCCTGAGGGCTAGGAATGTAAC
1 -CCTGCGGGCTAGGAATGTAAC
974236 CCTGC
1 CCTGC
974241 AAAGATGACA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
20 4 0.10
21 32 0.78
22 5 0.12
ACGTcount: A:0.21, C:0.25, G:0.34, T:0.21
Consensus pattern (21 bp):
CCTGCGGGCTAGGAATGTAAC
Found at i:975865 original size:24 final size:24
Alignment explanation
Indices: 975832--975888 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
975822 TAAATTCATG
975832 ATAAAT-TTAA-ATTAAAAATAATA
1 ATAAATATTAACATTAAAAATAA-A
**
975855 ATAAATATTAACATTAATTATAAA
1 ATAAATATTAACATTAAAAATAAA
*
975879 AAAAATATTA
1 ATAAATATTA
975889 TCATATCACT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.21
24 14 0.48
25 9 0.31
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (24 bp):
ATAAATATTAACATTAAAAATAAA
Found at i:976066 original size:30 final size:30
Alignment explanation
Indices: 975985--976080 Score: 74
Period size: 30 Copynumber: 3.3 Consensus size: 30
975975 TAATTAGCAC
* *
975985 AAAAAATAATTAATTA-ATAA--ATTTAAAT
1 AAAAAATAA-TATTTATATAATTATTTTAAT
* * *
976013 AAATAATAAT-TATATAAATATTATTTTAAT
1 AAAAAATAATATTTATATA-ATTATTTTAAT
* *
976043 AAAAAATAATATTTATATAATTATATTACT
1 AAAAAATAATATTTATATAATTATTTTAAT
*
976073 ATAAAATA
1 AAAAAATA
976081 TAAAAACTAT
Statistics
Matches: 52, Mismatches: 11, Indels: 8
0.73 0.15 0.11
Matches are distributed among these distances:
26 2 0.04
27 3 0.06
28 9 0.17
30 32 0.62
31 6 0.12
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (30 bp):
AAAAAATAATATTTATATAATTATTTTAAT
Found at i:986046 original size:37 final size:37
Alignment explanation
Indices: 985996--986073 Score: 120
Period size: 37 Copynumber: 2.1 Consensus size: 37
985986 GGATTACATT
* *
985996 GGAACACATTCGTTAATATGGCACCTTAATGAGTTGA
1 GGAACACATTCGTTAACATGGAACCTTAATGAGTTGA
* *
986033 GGAACGCATTCGTTAACGTGGAACCTTAATGAGTTGA
1 GGAACACATTCGTTAACATGGAACCTTAATGAGTTGA
986070 GGAA
1 GGAA
986074 ACGTAATTGG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (37 bp):
GGAACACATTCGTTAACATGGAACCTTAATGAGTTGA
Found at i:987329 original size:16 final size:16
Alignment explanation
Indices: 987308--987354 Score: 94
Period size: 16 Copynumber: 2.9 Consensus size: 16
987298 ATGATTAAGC
987308 GCTGAATGATTCAAAT
1 GCTGAATGATTCAAAT
987324 GCTGAATGATTCAAAT
1 GCTGAATGATTCAAAT
987340 GCTGAATGATTCAAA
1 GCTGAATGATTCAAA
987355 GGCTTTGTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (16 bp):
GCTGAATGATTCAAAT
Found at i:987436 original size:27 final size:27
Alignment explanation
Indices: 987405--987470 Score: 132
Period size: 27 Copynumber: 2.4 Consensus size: 27
987395 ATAATGGCTC
987405 TGAATCATTCAGAATGTACTTCTGTGT
1 TGAATCATTCAGAATGTACTTCTGTGT
987432 TGAATCATTCAGAATGTACTTCTGTGT
1 TGAATCATTCAGAATGTACTTCTGTGT
987459 TGAATCATTCAG
1 TGAATCATTCAG
987471 CACTGTTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.39
Consensus pattern (27 bp):
TGAATCATTCAGAATGTACTTCTGTGT
Found at i:987485 original size:23 final size:23
Alignment explanation
Indices: 987459--987511 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
987449 ACTTCTGTGT
*
987459 TGAATCATTCAGCACTGTTTTTC
1 TGAATCAGTCAGCACTGTTTTTC
* *
987482 TGAATTAGTCAGCATTGTTTTTC
1 TGAATCAGTCAGCACTGTTTTTC
987505 TGAATCA
1 TGAATCA
987512 ATTAGTACTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.43
Consensus pattern (23 bp):
TGAATCAGTCAGCACTGTTTTTC
Found at i:990496 original size:47 final size:47
Alignment explanation
Indices: 990427--990517 Score: 173
Period size: 47 Copynumber: 1.9 Consensus size: 47
990417 GGAGTATTAA
990427 TAGTTGCATTGAGTACATAGTAGATGTGATTTTGGTACTATTGTACG
1 TAGTTGCATTGAGTACATAGTAGATGTGATTTTGGTACTATTGTACG
*
990474 TAGTTGCATTGAGTTCATAGTAGATGTGATTTTGGTACTATTGT
1 TAGTTGCATTGAGTACATAGTAGATGTGATTTTGGTACTATTGT
990518 GCTCTTGGGA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.24, C:0.08, G:0.25, T:0.43
Consensus pattern (47 bp):
TAGTTGCATTGAGTACATAGTAGATGTGATTTTGGTACTATTGTACG
Found at i:995864 original size:29 final size:29
Alignment explanation
Indices: 995832--995904 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
995822 CTCCACAATG
* * *
995832 TTTAATCGTTCATGTTTTACTAAACTGTA
1 TTTAACCGTTCATCTTTTACTAAACAGTA
* * *
995861 TTTAACCTTTCATCTTTTACTCAACAGTG
1 TTTAACCGTTCATCTTTTACTAAACAGTA
*
995890 TTTAACCGTTAATCT
1 TTTAACCGTTCATCT
995905 AACTGGAATA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.26, C:0.19, G:0.08, T:0.47
Consensus pattern (29 bp):
TTTAACCGTTCATCTTTTACTAAACAGTA
Found at i:996013 original size:81 final size:81
Alignment explanation
Indices: 995873--996353 Score: 683
Period size: 81 Copynumber: 5.9 Consensus size: 81
995863 TAACCTTTCA
* * * *
995873 TCTTTTACTCAACAGTGTTTAACCGTTAATCTAACTGGAATAATTGACACCTTTCTGCCAATTGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTGC
995938 ACAGTTAGGCCATTAT
66 ACAGTTAGGCCATTAT
* * ** * *
995954 TCTTTTACCCAACGGTATTTAACCGTTCATCTAGCTGTTATAATTGACACCTTTTTGCCAATTAC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTGC
996019 ACAGTTAGGCCATTAT
66 ACAGTTAGGCCATTAT
* * **
996035 TCTTTTACTCAACGGTATTTAACCGTTAATCTAACTGGTATAATTGACACCTTTCTTTCAATTGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTGC
*
996100 ATAGTTAGGCCATTAT
66 ACAGTTAGGCCATTAT
* *
996116 TCTTTTACCCAAGGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTGC
996181 ACAGTTAGGCCATTAT
66 ACAGTTAGGCCATTAT
* * * * * * *
996197 TCTTTTACTCAACAGTATTTAACCATTCATATAGCTGGCATGATTCACACCTTTCTGTCAATTGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTGC
* *
996262 ACAATTAGACCATTAT
66 ACAGTTAGGCCATTAT
* ** * *
996278 TCTTTTACTCAACGATATTTAATTGTTCATCTAACTGGCATAATTGACACCTTTCTTCCAAATGC
1 TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTGC
996343 ACAGTTAGGCC
66 ACAGTTAGGCC
996354 TCAAAGGCAC
Statistics
Matches: 350, Mismatches: 50, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 350 1.00
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.37
Consensus pattern (81 bp):
TCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTGC
ACAGTTAGGCCATTAT
Found at i:996400 original size:68 final size:67
Alignment explanation
Indices: 996303--996490 Score: 270
Period size: 68 Copynumber: 2.8 Consensus size: 67
996293 TATTTAATTG
*
996303 TTCATCTAACTGGCATAATTGACACCTTTCT-TCCAAATGCACAGTTAGGCCTCAAAGGCACTTA
1 TTCATCTAACTGGCATAAATGACA-CTTTCTGT-CAAATGCACAGTTAGGCCTCAAAGGCACTTA
*
996367 GCCT
64 GCAT
* * * *
996371 TTCATCTAACTAGTATAAATGACTTCTTTCTGTCAAATGCACAATTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGAC-ACTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
996436 CAT
65 CAT
*
996439 TTCATTTAACTGGCATAAATGACACATTTCTGTCAAATGCACAGTTAGGCCT
1 TTCATCTAACTGGCATAAATGACAC-TTTCTGTCAAATGCACAGTTAGGCCT
996491 ATTAATCTTT
Statistics
Matches: 106, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
67 1 0.01
68 104 0.98
69 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.31
Consensus pattern (67 bp):
TTCATCTAACTGGCATAAATGACACTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAGC
AT
Found at i:996715 original size:54 final size:55
Alignment explanation
Indices: 996633--996766 Score: 198
Period size: 55 Copynumber: 2.5 Consensus size: 55
996623 TTTATAGAAA
* * * * **
996633 TCATACACTTGGTATAAATTTCTTAG-TTTGCACACATAGTGCCCATATGAAAAT
1 TCATACACTTAGTATGAATTTCTCAGTTTTGCACACAAAGTGCCCATACAAAAAT
*
996687 TCATACACTTAGTATGAATTTCTCAGTTTTGCACACAAAGTGCCCTTACAAAAAT
1 TCATACACTTAGTATGAATTTCTCAGTTTTGCACACAAAGTGCCCATACAAAAAT
996742 TCATACACTTAGTATGAATTTCTCA
1 TCATACACTTAGTATGAATTTCTCA
996767 ACTTTTTGCA
Statistics
Matches: 72, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
54 23 0.32
55 49 0.68
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.35
Consensus pattern (55 bp):
TCATACACTTAGTATGAATTTCTCAGTTTTGCACACAAAGTGCCCATACAAAAAT
Found at i:997169 original size:19 final size:21
Alignment explanation
Indices: 997130--997179 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 21
997120 CTTACCATGG
997130 TATCGATACTACTATACTATGA
1 TATCGATACTACTATA-TATGA
*
997152 TATCGATACT-CTAT-TATGG
1 TATCGATACTACTATATATGA
*
997171 TACCGATAC
1 TATCGATAC
997180 CATTTTTGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 12 0.46
21 4 0.15
22 10 0.38
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (21 bp):
TATCGATACTACTATATATGA
Found at i:1000859 original size:38 final size:38
Alignment explanation
Indices: 1000808--1000885 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
1000798 ACTTGCCATT
1000808 TAGTAGGATAGATTGAGACTTTGTATCTTGGTTTATTG
1 TAGTAGGATAGATTGAGACTTTGTATCTTGGTTTATTG
1000846 TAGTAGGATAGATTGAGACTTTGTATCTTGGTTTATTG
1 TAGTAGGATAGATTGAGACTTTGTATCTTGGTTTATTG
1000884 TA
1 TA
1000886 AAGGTCATAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.24, C:0.05, G:0.26, T:0.45
Consensus pattern (38 bp):
TAGTAGGATAGATTGAGACTTTGTATCTTGGTTTATTG
Found at i:1003510 original size:14 final size:14
Alignment explanation
Indices: 1003488--1003521 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1003478 GTTCCATACA
*
1003488 ATTTACCTCCCTGG
1 ATTTGCCTCCCTGG
*
1003502 ATTTGCCTCCTTGG
1 ATTTGCCTCCCTGG
1003516 ATTTGC
1 ATTTGC
1003522 ATGAAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.12, C:0.29, G:0.18, T:0.41
Consensus pattern (14 bp):
ATTTGCCTCCCTGG
Found at i:1006511 original size:47 final size:45
Alignment explanation
Indices: 1006417--1006542 Score: 164
Period size: 47 Copynumber: 2.8 Consensus size: 45
1006407 GTAACCATGC
* *
1006417 AAATAAGCTTATAAGCTTACGGAAT-AATGGCAAGTATATTGGAA
1 AAATAAGCTTATAAGCTTATGGAATAAATGGTAAGTATATTGGAA
* * *
1006461 AAATAAGCTTACAAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTATAAGCTTATGGAA--TAAATGGTAAGTATATTGGAA
* *
1006508 AAATAAGCTTATGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTATAAGCTTATGGAATAAATGGTAAG
1006543 AGATTTTATA
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
44 22 0.31
45 11 0.15
46 1 0.01
47 37 0.52
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTATAAGCTTATGGAATAAATGGTAAGTATATTGGAA
Found at i:1012504 original size:43 final size:43
Alignment explanation
Indices: 1012451--1012709 Score: 297
Period size: 43 Copynumber: 6.0 Consensus size: 43
1012441 CGCTATATTC
* * * *
1012451 CAAATCCTATTGCGGCGTTTGTAAGAAAAACGTCG-TGTAATGT
1 CAAAACCTATTGCGGCGTTTGTAAGAAAAACGCCGCT-AAATAT
* * *
1012494 CAAAACCTATTGCGGCGTTTGTAAGACAAATGCCGCTAAATGT
1 CAAAACCTATTGCGGCGTTTGTAAGAAAAACGCCGCTAAATAT
* * *
1012537 CCAAACCTATTGCGGCGTTTGTAATAAAAACGCTGCTAAATAT
1 CAAAACCTATTGCGGCGTTTGTAAGAAAAACGCCGCTAAATAT
* * *
1012580 CAGAACCTTTTGCGGCGTTTGTAAGAAAAATGCCGCTAAATAT
1 CAAAACCTATTGCGGCGTTTGTAAGAAAAACGCCGCTAAATAT
* * *
1012623 CAAAACCTTTTGCGGCATTTGTAAGAAAAAAGCCGCTAAATAT
1 CAAAACCTATTGCGGCGTTTGTAAGAAAAACGCCGCTAAATAT
* * * * *
1012666 CAGAACCTTTTGCGGTGTTTGT-TGAACAAACGCCGCTATATAT
1 CAAAACCTATTGCGGCGTTTGTAAGAA-AAACGCCGCTAAATAT
1012709 C
1 C
1012710 GTTACATATT
Statistics
Matches: 188, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
42 3 0.02
43 184 0.98
44 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (43 bp):
CAAAACCTATTGCGGCGTTTGTAAGAAAAACGCCGCTAAATAT
Found at i:1017868 original size:24 final size:22
Alignment explanation
Indices: 1017834--1017891 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 22
1017824 TGCTATTATG
1017834 TTTTATTTTTAATTAACTATTGCCT
1 TTTTA-TTTT-ATT-ACTATTGCCT
1017859 TTTTA--TT-TTACTATTGCCT
1 TTTTATTTTATTACTATTGCCT
1017878 TTTTATTTTATTAC
1 TTTTATTTTATTAC
1017892 ATTTTAATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
19 15 0.50
20 2 0.07
21 2 0.07
22 6 0.20
25 5 0.17
ACGTcount: A:0.21, C:0.12, G:0.03, T:0.64
Consensus pattern (22 bp):
TTTTATTTTATTACTATTGCCT
Found at i:1017883 original size:19 final size:19
Alignment explanation
Indices: 1017839--1017887 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1017829 TTATGTTTTA
* *
1017839 TTTTTAATTAACTATTGCC
1 TTTTTATTTTACTATTGCC
1017858 TTTTTATTTTACTATTGCC
1 TTTTTATTTTACTATTGCC
1017877 TTTTTATTTTA
1 TTTTTATTTTA
1017888 TTACATTTTA
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:0.20, C:0.12, G:0.04, T:0.63
Consensus pattern (19 bp):
TTTTTATTTTACTATTGCC
Found at i:1019974 original size:11 final size:11
Alignment explanation
Indices: 1019952--1019986 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1019942 TGGTGACTCC
*
1019952 AAAACATTTCA
1 AAAACTTTTCA
*
1019963 AAATCTTTTCA
1 AAAACTTTTCA
1019974 AAAACTTTTCA
1 AAAACTTTTCA
1019985 AA
1 AA
1019987 GAAAAATCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (11 bp):
AAAACTTTTCA
Found at i:1023053 original size:7 final size:7
Alignment explanation
Indices: 1023037--1023120 Score: 71
Period size: 7 Copynumber: 10.9 Consensus size: 7
1023027 AAAGAAATGT
1023037 AAAAATAG
1 AAAAA-AG
1023045 AAAAAAG
1 AAAAAAG
1023052 AAAAAAG
1 AAAAAAG
1023059 AAAAAAATAG
1 --AAAAA-AG
1023069 AAAAAAAG
1 -AAAAAAG
1023077 AAAAACTGAG
1 AAAAA---AG
1023087 AAAAAAG
1 AAAAAAG
*
1023094 -AAAGAG
1 AAAAAAG
1023100 AAAAAAG
1 AAAAAAG
1023107 AAAAAAG
1 AAAAAAG
1023114 AAGAAAA
1 AA-AAAA
1023121 TAGACAGATC
Statistics
Matches: 66, Mismatches: 2, Indels: 16
0.79 0.02 0.19
Matches are distributed among these distances:
6 5 0.08
7 30 0.45
8 11 0.17
9 11 0.17
10 9 0.14
ACGTcount: A:0.80, C:0.01, G:0.15, T:0.04
Consensus pattern (7 bp):
AAAAAAG
Found at i:1023065 original size:10 final size:10
Alignment explanation
Indices: 1023052--1023120 Score: 54
Period size: 10 Copynumber: 7.1 Consensus size: 10
1023042 TAGAAAAAAG
1023052 AAAAAAGAAA
1 AAAAAAGAAA
*
1023062 AAAATAG--A
1 AAAAAAGAAA
1023070 AAAAAAGAAA
1 AAAAAAGAAA
***
1023080 AACTGAGAAA
1 AAAAAAGAAA
*
1023090 AAAGAAAG-AG
1 AAA-AAAGAAA
1023100 AAAAAAGAAA
1 AAAAAAGAAA
*
1023110 AAAGAAGAAA
1 AAAAAAGAAA
1023120 A
1 A
1023121 TAGACAGATC
Statistics
Matches: 44, Mismatches: 11, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
8 7 0.16
9 4 0.09
10 31 0.70
11 2 0.05
ACGTcount: A:0.80, C:0.01, G:0.16, T:0.03
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:1023865 original size:28 final size:28
Alignment explanation
Indices: 1023764--1023857 Score: 143
Period size: 28 Copynumber: 3.4 Consensus size: 28
1023754 GCCAACCCGG
* * *
1023764 AACACATTGCCTCCCCAAATTGACCTGA
1 AACACATTACTTCCCCAAATTAACCTGA
1023792 AACACATTACTTCCCCAAATTAACCTGA
1 AACACATTACTTCCCCAAATTAACCTGA
* *
1023820 AACACATTACTTCCTCAAATTAACCTAA
1 AACACATTACTTCCCCAAATTAACCTGA
1023848 AACACATTAC
1 AACACATTAC
1023858 CTTCTCAAGA
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 61 1.00
ACGTcount: A:0.39, C:0.32, G:0.04, T:0.24
Consensus pattern (28 bp):
AACACATTACTTCCCCAAATTAACCTGA
Found at i:1025167 original size:55 final size:53
Alignment explanation
Indices: 1025097--1025330 Score: 216
Period size: 55 Copynumber: 4.3 Consensus size: 53
1025087 TGTTTTTTTG
* *
1025097 GAAACTAAGTTTGATTTTCAGAATTTTCTTGACAATTTTCAAATGAGCTTTTAAA
1 GAAACTAAGTCTGATTTTCAGAAGTTTCTTGA-AATTTTCAAATGA-CTTTTAAA
* * *
1025152 GAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGACCTTTCAAA
1 GAAACTAAGTCTGATTTTCAGAAGTTTCTTGA-AATTTTCAAATGA-CTTTTAAA
** ** *
1025207 GAAACTAAGTCTGATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTTAAA
1 GAAACTAAGTCTGATTTTCAGAAGTTTCTTGAAATTTTCAAATGACTTTTAAA
* * * * ** * ** * *
1025260 GAAGCTAAGCCTAATTTTTAGGGGTTTCTCGATGTTTTCAAATGAATTTGAAA
1 GAAACTAAGTCTGATTTTCAGAAGTTTCTTGAAATTTTCAAATGACTTTTAAA
* * *
1025313 GAAGCTAAGCCTAATTTT
1 GAAACTAAGTCTGATTTT
1025331 TAGTCTTGAT
Statistics
Matches: 159, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
53 71 0.45
54 10 0.06
55 78 0.49
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.40
Consensus pattern (53 bp):
GAAACTAAGTCTGATTTTCAGAAGTTTCTTGAAATTTTCAAATGACTTTTAAA
Found at i:1025333 original size:53 final size:54
Alignment explanation
Indices: 1025132--1025330 Score: 233
Period size: 53 Copynumber: 3.7 Consensus size: 54
1025122 TTCTTGACAA
* * **
1025132 TTTTCAAATGAGC-TTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATG
1 TTTTCAAATGA-CATTTTAAAGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATG
* * * * *
1025186 ATTTTTAAATGACCTTTCAAAGAAACTAAGTCTGATTTTCAGGGGTTTCTTGATG
1 -TTTTCAAATGACATTTTAAAGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATG
* * *
1025241 TTTTCAAATGA-ATTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTCTCGATG
1 TTTTCAAATGACATTTTAAAGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATG
* *
1025294 TTTTCAAATGA-ATTTGAAAGAAGCTAAGCCTAATTTT
1 TTTTCAAATGACATTTTAAAGAAACTAAGCCTAATTTT
1025331 TAGTCTTGAT
Statistics
Matches: 130, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
53 71 0.55
54 11 0.08
55 48 0.37
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.40
Consensus pattern (54 bp):
TTTTCAAATGACATTTTAAAGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATG
Found at i:1030752 original size:21 final size:22
Alignment explanation
Indices: 1030719--1030766 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
1030709 GACTTTGGAA
1030719 TTTTCCTTGGGATGCAACCAGC
1 TTTTCCTTGGGATGCAACCAGC
* *
1030741 TTTTCC-TGGGATGTAACCATC
1 TTTTCCTTGGGATGCAACCAGC
1030762 TTTTC
1 TTTTC
1030767 TTGTGAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.40
Consensus pattern (22 bp):
TTTTCCTTGGGATGCAACCAGC
Found at i:1033125 original size:20 final size:21
Alignment explanation
Indices: 1033100--1033139 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1033090 AACAAGGAAA
1033100 AGAT-AATTCCTAAA-ATAATG
1 AGATAAATT-CTAAAGATAATG
1033120 AGATAAATTCTAAAGATAAT
1 AGATAAATTCTAAAGATAAT
1033140 TCCTAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (21 bp):
AGATAAATTCTAAAGATAATG
Found at i:1034581 original size:17 final size:16
Alignment explanation
Indices: 1034550--1034590 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1034540 TGGCGCGACT
1034550 AGAAGGGGACGTTGCG
1 AGAAGGGGACGTTGCG
*
1034566 AGAAGGGTGGCGTTGCG
1 AGAAGGG-GACGTTGCG
1034583 AG-AGGGGA
1 AGAAGGGGA
1034591 TGTGGTGCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 1 0.05
16 11 0.50
17 10 0.45
ACGTcount: A:0.24, C:0.10, G:0.54, T:0.12
Consensus pattern (16 bp):
AGAAGGGGACGTTGCG
Found at i:1035004 original size:3 final size:3
Alignment explanation
Indices: 1034996--1035026 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1034986 TAAATCCAAG
*
1034996 AAC AAC AAC AAC AAC AAC AAC AAC AAG AAC A
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC A
1035027 CTCACCAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.68, C:0.29, G:0.03, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:1035134 original size:19 final size:19
Alignment explanation
Indices: 1035110--1035195 Score: 154
Period size: 19 Copynumber: 4.5 Consensus size: 19
1035100 ACAGAAGCAA
1035110 AAGAGAGATGCACCAAACG
1 AAGAGAGATGCACCAAACG
1035129 AAGAGAGATGCACCAAACG
1 AAGAGAGATGCACCAAACG
*
1035148 AAGAGAGATGCACCCAACG
1 AAGAGAGATGCACCAAACG
*
1035167 AAGAGAGATGCACCTAACG
1 AAGAGAGATGCACCAAACG
1035186 AAGAGAGATG
1 AAGAGAGATG
1035196 AGAGAATACC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 65 1.00
ACGTcount: A:0.45, C:0.20, G:0.28, T:0.07
Consensus pattern (19 bp):
AAGAGAGATGCACCAAACG
Found at i:1041160 original size:28 final size:27
Alignment explanation
Indices: 1041125--1041200 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 27
1041115 CTAAATACAC
1041125 CATAAATTATAAATCATAAACTCTAAAA
1 CATAAATTATAAATCATAAACTC-AAAA
* * * *
1041153 CATAAATTCTAGACCTTAAACTCAAAA
1 CATAAATTATAAATCATAAACTCAAAA
* * *
1041180 TATAAACTATAAATCCTAAAC
1 CATAAATTATAAATCATAAAC
1041201 ATTAAATTAT
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
27 19 0.50
28 19 0.50
ACGTcount: A:0.53, C:0.18, G:0.01, T:0.28
Consensus pattern (27 bp):
CATAAATTATAAATCATAAACTCAAAA
Found at i:1041163 original size:14 final size:14
Alignment explanation
Indices: 1041125--1041163 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1041115 CTAAATACAC
* *
1041125 CATAAATTATAAAT
1 CATAAATTCTAAAA
*
1041139 CATAAACTCTAAAA
1 CATAAATTCTAAAA
1041153 CATAAATTCTA
1 CATAAATTCTA
1041164 GACCTTAAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (14 bp):
CATAAATTCTAAAA
Found at i:1041234 original size:28 final size:28
Alignment explanation
Indices: 1041176--1041242 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
1041166 CCTTAAACTC
* * *
1041176 AAAATATAAACTATAAATCCTAAACATT
1 AAAATATAAACAATAAACCCTAAACAGT
* * *
1041204 AAATTATAAACAATAAACCCTTAATAGT
1 AAAATATAAACAATAAACCCTAAACAGT
1041232 AAAATATAAAC
1 AAAATATAAAC
1041243 CCTAAGTCAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.58, C:0.13, G:0.01, T:0.27
Consensus pattern (28 bp):
AAAATATAAACAATAAACCCTAAACAGT
Found at i:1042260 original size:65 final size:63
Alignment explanation
Indices: 1042069--1042271 Score: 173
Period size: 65 Copynumber: 3.1 Consensus size: 63
1042059 AGAGTATATT
** * *
1042069 GATGCATCAAGCGCATTCGATGTTTCA-AAATAGC-CAGAGTGCATCGATGCATGGCTGGTGCAT
1 GATGCATCAAATGCATTCGATGTTTCATAAA-ATCTC--AGTGCATCGATGCATGGTTGGTGCAT
*
1042132 T
63 C
* * *
1042133 GATGAATCAAATGCATTCGATGTTTTCATAAAATCCTCAATGCATCGGTGCATGGTAT-GTGCAT
1 GATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGT-TGGTGCAT
1042197 C
63 C
* **
1042198 GATGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGATTGGTGCA
1 GATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGG-TTGGTGCA
1042261 TC
62 TC
*
1042263 GGTGCATCA
1 GATGCATCA
1042272 CTCTGAAAAA
Statistics
Matches: 113, Mismatches: 16, Indels: 19
0.76 0.11 0.13
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 39 0.35
65 62 0.55
66 5 0.04
67 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (63 bp):
GATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTTGGTGCATC
Found at i:1050863 original size:65 final size:65
Alignment explanation
Indices: 1050743--1050898 Score: 183
Period size: 65 Copynumber: 2.4 Consensus size: 65
1050733 CTAAGAGTGT
* * * *
1050743 ATTGATGCATCAAGTGTATTTGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCT-GGTG
1 ATTGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGG-TAGGTG
1050806 C
65 C
* * * *
1050807 ATTGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGGTATGTG
1 ATTGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATGCATGGTAGGTG
1050871 C
65 C
* *
1050872 ATCGATGCATGAAATGCATTCGATGTT
1 ATTGATGCATCAAATGCATTCGATGTT
1050899 CAATTTAATT
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
64 23 0.29
65 53 0.67
66 3 0.04
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.33
Consensus pattern (65 bp):
ATTGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGTAGGTGC
Found at i:1050937 original size:65 final size:63
Alignment explanation
Indices: 1050783--1050948 Score: 185
Period size: 65 Copynumber: 2.6 Consensus size: 63
1050773 AAATAGCCAG
* *
1050783 AGTGCATCGATGCATGGCTGGTGCATTGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTC
1 AGTGCATCGATGCATGGTTGGTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTC
* * **
1050848 AGTGCATCGGTGCATGGTAT-GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TC
1 AGTGCATCGATGCATGGT-TGGTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTC
*
1050910 ATGGTGCATCGATGCATGGATTGGTGCATCGGTGCATCA
1 A--GTGCATCGATGCATGG-TTGGTGCATCGATGCATCA
1050949 CTCTGAAAAA
Statistics
Matches: 86, Mismatches: 9, Indels: 12
0.80 0.08 0.11
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 21 0.24
65 58 0.67
66 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (63 bp):
AGTGCATCGATGCATGGTTGGTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTC
Found at i:1051216 original size:14 final size:14
Alignment explanation
Indices: 1051194--1051292 Score: 69
Period size: 14 Copynumber: 7.1 Consensus size: 14
1051184 TTCAACACTT
* *
1051194 AACTTTAAACCCTA
1 AACTATAAACCATA
*
1051208 AACTATAAAACATA
1 AACTATAAACCATA
*
1051222 AACTATAAACCTTA
1 AACTATAAACCATA
**
1051236 AAC-ACTAAAATATA
1 AACTA-TAAACCATA
*
1051250 AA-TATCAACCATA
1 AACTATAAACCATA
*
1051263 TAA-TATAAACCCTA
1 -AACTATAAACCATA
* *
1051277 AACTTTAAACCCTA
1 AACTATAAACCATA
1051291 AA
1 AA
1051293 TGCAAAAAAT
Statistics
Matches: 67, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
13 9 0.13
14 58 0.87
ACGTcount: A:0.54, C:0.21, G:0.00, T:0.25
Consensus pattern (14 bp):
AACTATAAACCATA
Found at i:1051293 original size:41 final size:41
Alignment explanation
Indices: 1051194--1051293 Score: 103
Period size: 41 Copynumber: 2.4 Consensus size: 41
1051184 TTCAACACTT
*
1051194 AACTTTAAACCCTAAACTATAAAACATAAACTATAAACCTTA
1 AACTTTAAACCCTAAA-TATAAAACATAAACTATAAACCCTA
** *** * *
1051236 AACACTAAAATATAAATATCAACCATATAA-TATAAACCCTA
1 AACTTTAAACCCTAAATATAAAACATA-AACTATAAACCCTA
1051277 AACTTTAAACCCTAAAT
1 AACTTTAAACCCTAAAT
1051294 GCAAAAAATA
Statistics
Matches: 44, Mismatches: 13, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
41 31 0.70
42 13 0.30
ACGTcount: A:0.53, C:0.21, G:0.00, T:0.26
Consensus pattern (41 bp):
AACTTTAAACCCTAAATATAAAACATAAACTATAAACCCTA
Found at i:1051687 original size:15 final size:15
Alignment explanation
Indices: 1051669--1051717 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
1051659 AATAGATGGC
*
1051669 CATAAAATATAATAA
1 CATAAAATAAAATAA
* **
1051684 CATAAAATACAATGC
1 CATAAAATAAAATAA
*
1051699 CATAAATTAAAATAA
1 CATAAAATAAAATAA
1051714 CATA
1 CATA
1051718 TATTTCAATA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.61, C:0.12, G:0.02, T:0.24
Consensus pattern (15 bp):
CATAAAATAAAATAA
Found at i:1051689 original size:30 final size:30
Alignment explanation
Indices: 1051640--1051717 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
1051630 TATGAAAAAT
* * * *
1051640 ATAAAATAATATTATATAAAATA-GATGGCC
1 ATAAAATAAAATAACATAAAATACAAT-GCC
*
1051670 ATAAAATATAATAACATAAAATACAATGCC
1 ATAAAATAAAATAACATAAAATACAATGCC
*
1051700 ATAAATTAAAATAACATA
1 ATAAAATAAAATAACATA
1051718 TATTTCAATA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
30 38 0.95
31 2 0.05
ACGTcount: A:0.59, C:0.09, G:0.05, T:0.27
Consensus pattern (30 bp):
ATAAAATAAAATAACATAAAATACAATGCC
Found at i:1055258 original size:40 final size:39
Alignment explanation
Indices: 1055195--1055316 Score: 190
Period size: 40 Copynumber: 3.1 Consensus size: 39
1055185 ACCATAGTGC
1055195 TACACATAAGGTAGTGCCTACCATATACACCGAAGTGTAT
1 TACACATAAGGTAGTGCC-ACCATATACACCGAAGTGTAT
* *
1055235 TACACATAAAGTCGTGTCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTAGTG-CCACCATATACACCGAAGTGTAT
*
1055275 TACACATAAGGTTGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTAGTG-CCACCATATACACCGAAGTGTAT
1055315 TA
1 TA
1055317 TAAACCTGCA
Statistics
Matches: 76, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
40 74 0.97
41 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.25
Consensus pattern (39 bp):
TACACATAAGGTAGTGCCACCATATACACCGAAGTGTAT
Found at i:1057095 original size:20 final size:20
Alignment explanation
Indices: 1057058--1057095 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1057048 AAAATTGGGG
*
1057058 TATTACAAATATTCAATAAA
1 TATTACAAATATTAAATAAA
1057078 TATTA-AAATATTTAAATA
1 TATTACAAATA-TTAAATA
1057096 GACAAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (20 bp):
TATTACAAATATTAAATAAA
Found at i:1058709 original size:6 final size:6
Alignment explanation
Indices: 1058698--1058729 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
1058688 AGGAGAGGAC
1058698 GGGAGA GGGAGA GGGAGA GGGAGA GGGAGA GG
1 GGGAGA GGGAGA GGGAGA GGGAGA GGGAGA GG
1058730 AATGTATGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.69, T:0.00
Consensus pattern (6 bp):
GGGAGA
Found at i:1059827 original size:23 final size:23
Alignment explanation
Indices: 1059790--1059839 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
1059780 ATTTTTATAA
1059790 ATATTTTTTTAAAAATAATA-TT
1 ATATTTTTTTAAAAATAATATTT
*
1059812 ATATTTTTTATTAAAATAATATTT
1 ATATTTTTT-TAAAAATAATATTT
1059836 ATAT
1 ATAT
1059840 AATTATTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 9 0.36
23 10 0.40
24 6 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
ATATTTTTTTAAAAATAATATTT
Found at i:1059845 original size:23 final size:23
Alignment explanation
Indices: 1059801--1059847 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
1059791 TATTTTTTTA
**
1059801 AAAATAATATTATATTTTTTATT
1 AAAATAATATTATATTAATTATT
1059824 AAAATAATATT-TATATAATTATT
1 AAAATAATATTATAT-TAATTATT
1059847 A
1 A
1059848 TTTATTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
AAAATAATATTATATTAATTATT
Found at i:1061020 original size:17 final size:17
Alignment explanation
Indices: 1060998--1061033 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
1060988 GCTTGCTATA
1060998 ATTAGAA-TATTATATTT
1 ATTAGAATTA-TATATTT
1061015 ATTAGAATTATATATTT
1 ATTAGAATTATATATTT
1061032 AT
1 AT
1061034 GTTTCAGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.89
18 2 0.11
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
ATTAGAATTATATATTT
Found at i:1061653 original size:42 final size:42
Alignment explanation
Indices: 1061590--1061684 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 42
1061580 GATGATGCCA
*
1061590 CAAGGGTACATGCCCAACCCACCAGTTTAGATGCCATCTCCG
1 CAAGGGTACATGCCCAACCCACCAGTTCAGATGCCATCTCCG
* * *
1061632 CAAGGGTATATG-CCAAGCCCACCAGTTCATATGTCATCTCCG
1 CAAGGGTACATGCCCAA-CCCACCAGTTCAGATGCCATCTCCG
1061674 C-AGGGTTACAT
1 CAAGGG-TACAT
1061685 TCCTAGCCTA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
41 8 0.17
42 38 0.83
ACGTcount: A:0.26, C:0.32, G:0.20, T:0.22
Consensus pattern (42 bp):
CAAGGGTACATGCCCAACCCACCAGTTCAGATGCCATCTCCG
Found at i:1061718 original size:20 final size:21
Alignment explanation
Indices: 1061671--1061719 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
1061661 TATGTCATCT
* *
1061671 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGGTACATACCTAGC
**
1061692 CTACAGGGGTACATACC-AGC
1 CCGCAGGGGTACATACCTAGC
1061712 CCGCAGGG
1 CCGCAGGG
1061720 TTTTATGACA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.22, C:0.33, G:0.29, T:0.16
Consensus pattern (21 bp):
CCGCAGGGGTACATACCTAGC
Found at i:1062228 original size:35 final size:34
Alignment explanation
Indices: 1062186--1062251 Score: 96
Period size: 35 Copynumber: 1.9 Consensus size: 34
1062176 TACAATAATA
** *
1062186 TTTTTAAAATTTAAATTCAAATTCAACATTAAATG
1 TTTTTAAAATGCAAATCCAAATTCAAC-TTAAATG
1062221 TTTTTAAAATGCAAATCCAAATTCAACTTAA
1 TTTTTAAAATGCAAATCCAAATTCAACTTAA
1062252 TATTCCAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 4 0.14
35 24 0.86
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.39
Consensus pattern (34 bp):
TTTTTAAAATGCAAATCCAAATTCAACTTAAATG
Found at i:1063038 original size:33 final size:33
Alignment explanation
Indices: 1062996--1063074 Score: 149
Period size: 33 Copynumber: 2.4 Consensus size: 33
1062986 GAAGGCACAC
1062996 CCCCTCAAACATGCTTTAACCACATTGCTGCAT
1 CCCCTCAAACATGCTTTAACCACATTGCTGCAT
*
1063029 CCCCTCAAACATGCTTTAACCACATTGCTGTAT
1 CCCCTCAAACATGCTTTAACCACATTGCTGCAT
1063062 CCCCTCAAACATG
1 CCCCTCAAACATG
1063075 ATAGGTATTG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.28, C:0.37, G:0.09, T:0.27
Consensus pattern (33 bp):
CCCCTCAAACATGCTTTAACCACATTGCTGCAT
Found at i:1063280 original size:138 final size:138
Alignment explanation
Indices: 1063029--1063370 Score: 418
Period size: 138 Copynumber: 2.5 Consensus size: 138
1063019 ATTGCTGCAT
* * *** *
1063029 CCCCTCAAACATGCTTTAACCACATTGCTGTATCCCCTCAAACATGATAGGTATTGACATGAATA
1 CCCCTAAAACACGCTTTAACCACATTGCTACGTCCCCTCAAACATGATAGGTACTGACATGAATA
** * * * * *
1063094 GTGTCATTCCGAGGGACATCACACATACTAGGATAATTATAACCTATTCTCTGACAAAAAATGAA
66 GTACCATACCGAGGGACATCACACATAATAGGAAAATTATAACATATTCTCTAACAAAAAA--AA
*
1063159 A-GG-TGCGC
129 AGGGAGGCGC
* *
1063167 CCCCTAAAACGCGCTTTAACCACATTACTACGTCCCCTCAAACATGATAGGTACTGACATGAATA
1 CCCCTAAAACACGCTTTAACCACATTGCTACGTCCCCTCAAACATGATAGGTACTGACATGAATA
* * *
1063232 GTACCCTACCGGGGGACATCACACATAATAGGAAAATTATAACATATTCTCTAATAAAAAAAAAG
66 GTACCATACCGAGGGACATCACACATAATAGGAAAATTATAACATATTCTCTAACAAAAAAAAAG
1063297 GGAAGGCGC
131 GG-AGGCGC
* * * * * *
1063306 CCCCTGAAATACGCTTTAACCACATTGTTTCGTCCCCTCACACATGATAGGTACTGATATGAATA
1 CCCCTAAAACACGCTTTAACCACATTGCTACGTCCCCTCAAACATGATAGGTACTGACATGAATA
1063371 CACATAATAG
Statistics
Matches: 174, Mismatches: 27, Indels: 5
0.84 0.13 0.02
Matches are distributed among these distances:
136 3 0.02
137 2 0.01
138 108 0.62
139 61 0.35
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (138 bp):
CCCCTAAAACACGCTTTAACCACATTGCTACGTCCCCTCAAACATGATAGGTACTGACATGAATA
GTACCATACCGAGGGACATCACACATAATAGGAAAATTATAACATATTCTCTAACAAAAAAAAAG
GGAGGCGC
Found at i:1063547 original size:16 final size:17
Alignment explanation
Indices: 1063522--1063559 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1063512 ACCCAAGCTT
*
1063522 TCAAAATCTC-ATACTC
1 TCAAAATCTCAAAACTC
*
1063538 TCAAATTCTCAAAACTC
1 TCAAAATCTCAAAACTC
1063555 TCAAA
1 TCAAA
1063560 CCTATATTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (17 bp):
TCAAAATCTCAAAACTC
Found at i:1067880 original size:19 final size:19
Alignment explanation
Indices: 1067843--1067880 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1067833 ATTACAATCC
*
1067843 ATTTATTTAACATTGATTA
1 ATTTATTTAACATTAATTA
1067862 ATTTATTTCAA-ATTAATTA
1 ATTTATTT-AACATTAATTA
1067881 TTAGGGAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (19 bp):
ATTTATTTAACATTAATTA
Found at i:1068468 original size:3 final size:3
Alignment explanation
Indices: 1068462--1068611 Score: 286
Period size: 3 Copynumber: 50.7 Consensus size: 3
1068452 ACAAAGACCA
1068462 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1068510 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1068558 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1068605 -AT AAT AA
1 AAT AAT AA
1068612 ACATACATAA
Statistics
Matches: 145, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
2 4 0.03
3 141 0.97
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1070459 original size:20 final size:21
Alignment explanation
Indices: 1070429--1070468 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
1070419 CACGGTATAG
1070429 CTCTATATGAGTATCGATACC
1 CTCTATATGAGTATCGATACC
1070450 CTCT-TATGAGTATCGATAC
1 CTCTATATGAGTATCGATAC
1070469 AAAATCTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.35
Consensus pattern (21 bp):
CTCTATATGAGTATCGATACC
Found at i:1071874 original size:118 final size:118
Alignment explanation
Indices: 1071667--1072138 Score: 452
Period size: 118 Copynumber: 4.1 Consensus size: 118
1071657 TAACATAACC
* * * * * * *
1071667 GGTTAATTACTGGAAATATTATCAGCCATAATAACAT-ATAGGTAGCGCTTATGTAACGTAATTG
1 GGTTAATTACTGGAAACATTATCAACCATAATAACATAACAAGTAGCGCTTATTTAATGTAATAG
* *
1071731 GTAGCACCTTTTTAAAGCTGATGGGGCCTTAGAAATCTGAAGATAACAAAATA
66 GTAGCACATGTTTAAAGCTGATGGGGCCTTAGAAATCTGAAGATAACAAAATA
*
1071784 GGTTAATTATTGGAAACATTATCAACCATAATAACATAACAAGTAGCGCTTATTTAATGTAATAG
1 GGTTAATTACTGGAAACATTATCAACCATAATAACATAACAAGTAGCGCTTATTTAATGTAATAG
* * *
1071849 GTAGCACATGTTTAAAGCTGATGGGGCCTTTGAAATCCGATGATAACAAAATA
66 GTAGCACATGTTTAAAGCTGATGGGGCCTTAGAAATCTGAAGATAACAAAATA
* *** ** * ** ** *
1071902 GGTTAATTACT-TAATTTGTTATC-AGTATTATTAACATATTAAGTA--GC--ACCT-A-G-AAC
1 GGTTAATTACTGGAA-ACATTATCAACCA-TAATAACATAACAAGTAGCGCTTATTTAATGTAAT
* * * * * *
1071958 A-TTACCA-AAGTTT-AAGGTGATGGAGCCTTAGAAAT-TCAACGATAACAAAATA
64 AGGTAGCACATGTTTAAAGCTGATGGGGCCTTAGAAATCTGAA-GATAACAAAATA
* *
1072010 GGTTAATTACTGGAAACATTATCAACCATAATAATATAACAAGTAGCGCTTAATTAATGTAATAG
1 GGTTAATTACTGGAAACATTATCAACCATAATAACATAACAAGTAGCGCTTATTTAATGTAATAG
* ** * * *
1072075 GTTGTGCCTGTTTAAAGCTAATGGGGCCTTAGAAATCTGACGATAA-AAACATA
66 GTAGCACATGTTTAAAGCTGATGGGGCCTTAGAAATCTGAAGATAACAAA-ATA
1072128 GGTTAATTACT
1 GGTTAATTACT
1072139 TAATTTGTTA
Statistics
Matches: 277, Mismatches: 60, Indels: 35
0.74 0.16 0.09
Matches are distributed among these distances:
107 1 0.00
108 60 0.22
109 9 0.03
110 6 0.02
111 3 0.01
112 3 0.01
113 2 0.01
114 3 0.01
115 3 0.01
116 3 0.01
117 45 0.16
118 137 0.49
119 2 0.01
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (118 bp):
GGTTAATTACTGGAAACATTATCAACCATAATAACATAACAAGTAGCGCTTATTTAATGTAATAG
GTAGCACATGTTTAAAGCTGATGGGGCCTTAGAAATCTGAAGATAACAAAATA
Found at i:1072070 original size:226 final size:227
Alignment explanation
Indices: 1071741--1072247 Score: 770
Period size: 226 Copynumber: 2.2 Consensus size: 227
1071731 GTAGCACCTT
* * *
1071741 TTTAAAGCTGATGGGGCCTTAGAAATCTGAA-GATAACAAAATAGGTTAATTATTGGAAACATTA
1 TTTAAAGCTGATGGAGCCTTAGAAAT-TCAACGATAACAAAATAGGTTAATTACTGGAAACATTA
* *
1071805 TCAACCATAATAACATAACAAGTAGCGCTTATTTAATGTAATAGGTAGCACATGTTTAAAGCTGA
65 TCAACCATAATAACATAACAAGTAGCGCTTAATTAATGTAATAGGTAGCACATGTTTAAAGCTAA
* * *
1071870 TGGGGCCTTTGAAATCCGATGATAACAAA-ATAGGTTAATTACTTAATTTGTTATCAGTATTATT
130 TGGGGCCTTAGAAATCCGACGATAA-AAACATAGGTTAATTACTTAATTTGTTATCAGTATTATC
*
1071934 AACATATTAAGTAGCACCTAGAACATTACCAAAG
194 AACATATTAAGTAGCACCTAAAACATTACCAAAG
*
1071968 TTT-AAGGTGATGGAGCCTTAGAAATTCAACGATAACAAAATAGGTTAATTACTGGAAACATTAT
1 TTTAAAGCTGATGGAGCCTTAGAAATTCAACGATAACAAAATAGGTTAATTACTGGAAACATTAT
* * ** *
1072032 CAACCATAATAATATAACAAGTAGCGCTTAATTAATGTAATAGGTTGTGCCTGTTTAAAGCTAAT
66 CAACCATAATAACATAACAAGTAGCGCTTAATTAATGTAATAGGTAGCACATGTTTAAAGCTAAT
*
1072097 GGGGCCTTAGAAATCTGACGATAAAAACATAGGTTAATTACTTAATTTGTTATCAGTATTATCAA
131 GGGGCCTTAGAAATCCGACGATAAAAACATAGGTTAATTACTTAATTTGTTATCAGTATTATCAA
* * **
1072162 CATATTATGTAGCGCCTAAAATGTTACCAAAG
196 CATATTAAGTAGCACCTAAAACATTACCAAAG
*
1072194 TTTAAAGCTGATGGAGCCTTAGAAA-TCTGACGATAACAAAATAGGTTAATTACT
1 TTTAAAGCTGATGGAGCCTTAGAAATTC-AACGATAACAAAATAGGTTAATTACT
1072248 TGATTTGTTA
Statistics
Matches: 254, Mismatches: 22, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
225 6 0.02
226 200 0.79
227 48 0.19
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (227 bp):
TTTAAAGCTGATGGAGCCTTAGAAATTCAACGATAACAAAATAGGTTAATTACTGGAAACATTAT
CAACCATAATAACATAACAAGTAGCGCTTAATTAATGTAATAGGTAGCACATGTTTAAAGCTAAT
GGGGCCTTAGAAATCCGACGATAAAAACATAGGTTAATTACTTAATTTGTTATCAGTATTATCAA
CATATTAAGTAGCACCTAAAACATTACCAAAG
Found at i:1072817 original size:200 final size:200
Alignment explanation
Indices: 1072431--1072886 Score: 664
Period size: 200 Copynumber: 2.3 Consensus size: 200
1072421 GTTTAGATCG
1072431 AAAGTATCGATACCTATACAAAAAGTATCAATACTTTATGTTTACGCCTATTATCATTAAACTAG
1 AAAGTATCGATACCTATACAAAAAGTATCAATACTTTATGTTTACGCCTATTATCATTAAACTAG
* * * *
1072496 TAGATTTTTACAGTTTACATTTTAAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATA
66 TAGATTTTTACAGTTTACATTGTAAATTTACCTATAACTTTAAAGTAATAGGTATCAAAATTATA
* * * ** *
1072561 AGTATCGATACTTGTGATTCGTGTATCGATACTTTATGCGTGCATGTTGTTTGAGAAGTATAATG
131 AGTATCGATACTTGTGATTCATATATCGATACTTTATGCATGCAAATTGTTTGAGAAGCATAATG
1072626 GACTA
196 GACTA
* * *
1072631 AAATTATCGATACCTATACAAATAGTATCAATACTTTATGTTTACGCCTATTATCATTAAA-TTG
1 AAAGTATCGATACCTATACAAAAAGTATCAATACTTTATGTTTACGCCTATTATCATTAAACTAG
* ** *
1072695 ATAGTTTTTTTACTTTTTACATTGTAAATTTACCTATAACTTTAAAGTAATCGGTATCAAAATTA
66 -TAG-ATTTTTACAGTTTACATTGTAAATTTACCTATAACTTTAAAGTAATAGGTATCAAAATTA
* * *
1072760 TAAGTATCGATACTTGTTATTCATATATCGATACTTTGTGCATGCAAATTG-TTGAGAAGCATAC
129 TAAGTATCGATACTTGTGATTCATATATCGATACTTTATGCATGCAAATTGTTTGAGAAGCATAA
1072824 TGGACTA
194 TGGACTA
* * * *
1072831 AAAGTATCGATGCCTATACAAAGAGTATCAATAATTTATGTTTACTCCTATTATCA
1 AAAGTATCGATACCTATACAAAAAGTATCAATACTTTATGTTTACGCCTATTATCA
1072887 GATACTGAGG
Statistics
Matches: 229, Mismatches: 25, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
199 2 0.01
200 131 0.57
201 96 0.42
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.39
Consensus pattern (200 bp):
AAAGTATCGATACCTATACAAAAAGTATCAATACTTTATGTTTACGCCTATTATCATTAAACTAG
TAGATTTTTACAGTTTACATTGTAAATTTACCTATAACTTTAAAGTAATAGGTATCAAAATTATA
AGTATCGATACTTGTGATTCATATATCGATACTTTATGCATGCAAATTGTTTGAGAAGCATAATG
GACTA
Found at i:1073001 original size:200 final size:199
Alignment explanation
Indices: 1072431--1073002 Score: 658
Period size: 200 Copynumber: 2.9 Consensus size: 199
1072421 GTTTAGATCG
1072431 AAAGTATCGATACCTATACAAAAAGTATCAATACTTTATGTTTACGCCTATTATCATTAAACT-A
1 AAAGTATCGATACCTATACAAAAAGTATCAATACTTTATGTTTACGCCTATTATCATTAAACTGA
1072495 G-TAGATTTTTA-CAGTTTACATT-TTAAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAAT
66 GTTA-ATTTTTACCA-TTTACATTGTT-AATTTACCTATTACTTTAAAGTAATAGGTTTCGAAAT
* ** * * ** *
1072557 TATAAGTATCGATACTTGTGATTCGTGTATCGATACTTTATGCGTGCATGTTGTTTGAGAAGTAT
128 TATAAGTATCGATACTTAT-ATTC-AATATCGATACTTTGTGCATGCAAATTGTTTGAGAAGCAT
1072622 AATGGACTA
191 AATGGACTA
* * *
1072631 AAATTATCGATACCTATACAAATAGTATCAATACTTTATGTTTACGCCTATTATCATTAAATTGA
1 AAAGTATCGATACCTATACAAAAAGTATCAATACTTTATGTTTACGCCTATTATCATTAAACTG-
** * * * * *
1072696 TAGTT--TTTTTACTTTTTACATTGTAAATTTACCTATAACTTTAAAGTAATCGGTATCAAAATT
65 -AGTTAATTTTTACCATTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATT
*
1072759 ATAAGTATCGATACTTGTTATTCATATATCGATACTTTGTGCATGCAAATTG-TTGAGAAGCATA
129 ATAAGTATCGATACTT-ATATTCA-ATATCGATACTTTGTGCATGCAAATTGTTTGAGAAGCATA
*
1072823 CTGGACTA
192 ATGGACTA
* * * * * *
1072831 AAAGTATCGATGCCTATACAAAGAGTATCAATAATTTATGTTTACTCCTATTATCA-GATACTGA
1 AAAGTATCGATACCTATACAAAAAGTATCAATACTTTATGTTTACGCCTATTATCATTAAACTGA
* * * * * *
1072895 GGTTCAACATATTACCATGTATATTGTTAATTTACCTATTACTTTAAAGTAATAGTTTTTGAAAT
66 -GTT-AA-TTTTTACCATTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAAT
* *
1072960 TATAAGAATCGATACTTATATGACAATATCGATAC-TTGTGCAT
128 TATAAGTATCGATACTTATAT-TCAATATCGATACTTTGTGCAT
1073003 TTACGCCTAT
Statistics
Matches: 315, Mismatches: 43, Indels: 28
0.82 0.11 0.07
Matches are distributed among these distances:
197 1 0.00
198 3 0.01
199 4 0.01
200 137 0.43
201 103 0.33
202 64 0.20
203 2 0.01
204 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (199 bp):
AAAGTATCGATACCTATACAAAAAGTATCAATACTTTATGTTTACGCCTATTATCATTAAACTGA
GTTAATTTTTACCATTTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTAT
AAGTATCGATACTTATATTCAATATCGATACTTTGTGCATGCAAATTGTTTGAGAAGCATAATGG
ACTA
Found at i:1073136 original size:130 final size:129
Alignment explanation
Indices: 1072906--1073155 Score: 301
Period size: 130 Copynumber: 1.9 Consensus size: 129
1072896 GTTCAACATA
* ** *
1072906 TTACCATGTATATTGTTAATTTACCTATTACTTTAAAGTAATAGTTTTTGAAATTATAAGAATCG
1 TTACCATGTACATTGTTAATTTACCTATTACTTTAAAGTAATAGTTTTCAAAATTACAAGAATCG
* * *
1072971 ATACTTATATGACAATATCGATACTTGTGCATTTACGCCTATTTTCATTATACCGGTAGAAACGT
66 ATACTTATATGACAATATCAATACTTGTG-ATTTACGCATATTATCATTATACCGGTAGAAACGT
* * * *
1073036 TTACCGTGTACATTGTTAATTTACCTATTACTTTAAAGTAATAAG-TTTCAAAATTCCACGTATC
1 TTACCATGTACATTGTTAATTTACCTATTACTTTAAAGTAAT-AGTTTTCAAAATTACAAGAATC
* *
1073100 GATACTT-TAT-ACATGTGTATCAATGCTTGATG-TTTACGCATATTATCATTATACCG
65 GATACTTATATGACA---ATATCAATACTTG-TGATTTACGCATATTATCATTATACCG
1073156 ATTGACTTTT
Statistics
Matches: 102, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
128 3 0.03
129 3 0.03
130 82 0.80
131 12 0.12
132 2 0.02
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (129 bp):
TTACCATGTACATTGTTAATTTACCTATTACTTTAAAGTAATAGTTTTCAAAATTACAAGAATCG
ATACTTATATGACAATATCAATACTTGTGATTTACGCATATTATCATTATACCGGTAGAAACGT
Found at i:1075724 original size:20 final size:20
Alignment explanation
Indices: 1075701--1075765 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
1075691 CGTTTTTATG
*
1075701 AAATTTCAATCAGTTTTGTC
1 AAATTTCAATCGGTTTTGTC
*
1075721 AAA-TTCTAACCGGTTTTGTC
1 AAATTTC-AATCGGTTTTGTC
*
1075741 -AATTTCCAATCGGTTTTGTT
1 AAATTT-CAATCGGTTTTGTC
1075761 AAATT
1 AAATT
1075766 CGTTACCTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
19 5 0.14
20 27 0.73
21 5 0.14
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.45
Consensus pattern (20 bp):
AAATTTCAATCGGTTTTGTC
Found at i:1076231 original size:178 final size:177
Alignment explanation
Indices: 1075930--1076297 Score: 436
Period size: 178 Copynumber: 2.1 Consensus size: 177
1075920 TTATACATGT
* * *
1075930 GTATCGATACTTTGTGCGTGCAAATTGTTGAGAATCATACTGGACTATAAGTATCGATACGTATA
1 GTATCGATACTTTGTGCGTGCAAATTGTTGAGAATCATACTGGAATAAAAGTATCGATACATATA
* * *
1075995 CAAAACGTATTAATAATTGATGTTTACGCCTATCATCATTAAACCGGTAGACTTTTACCATTTAC
66 CAAAACGTATCAATAATTGATATTTACGCCTATCATCATTAAACCGATAGACTTTTACCATTTAC
* *
1076060 ATTATAAAGCTACCTATAACTTTAAAGCAATCGGTTTCTAAATTCCGC
131 ATGATAAA-CTACCTATAACTTTAAAGCAATCGGTTTCAAAATTCCGC
* * * *
1076108 GTATCGATACTTTTTGCGTGCTAATTATTTGA-TATGCATACTGGAATAAAAGTATCGATA-ATA
1 GTATCGATACTTTGTGCGTGCAAATT-GTTGAGAAT-CATACTGGAATAAAAGTATCGATACATA
* * * * * * * * *
1076171 TATAATAA-GTATCGATACTTTATATTTGCGCCTATTATCATTAAACTGATAGATTTTTACCGTT
64 TACAA-AACGTATCAATAATTGATATTTACGCCTATCATCATTAAACCGATAGACTTTTACCATT
* * * * *
1076235 TCCATGGTAAATTACCTATAACTTTAAAGTAATCGGTTTCAAAATTTCGC
128 TACATGATAAACTACCTATAACTTTAAAGCAATCGGTTTCAAAATTCCGC
*
1076285 ATATCGATACTTT
1 GTATCGATACTTT
1076298 ATACAAGTGA
Statistics
Matches: 160, Mismatches: 27, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
177 47 0.29
178 85 0.53
179 28 0.17
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (177 bp):
GTATCGATACTTTGTGCGTGCAAATTGTTGAGAATCATACTGGAATAAAAGTATCGATACATATA
CAAAACGTATCAATAATTGATATTTACGCCTATCATCATTAAACCGATAGACTTTTACCATTTAC
ATGATAAACTACCTATAACTTTAAAGCAATCGGTTTCAAAATTCCGC
Found at i:1076374 original size:199 final size:199
Alignment explanation
Indices: 1076110--1076565 Score: 566
Period size: 199 Copynumber: 2.3 Consensus size: 199
1076100 AATTCCGCGT
* *
1076110 ATCGATACTTTTTGCGTGCTAATTATTTGATATGCATACTGGAATAAAAGTATCGATAATATATA
1 ATCGATACTTTTTGCGTGCAAATTATTTGAGATGCATACTGGAATAAAAGTATCGATAATATATA
* * *
1076175 ATAAGTATCGATACTTTATATTTGCGCCTATTATCATTAAACT-GATAGATTTTTACCGTTTCCA
66 ATAAGTATCGATACTTTATATTTACGCCTACTATCATTAAACTAG-TAGATTTTTACCGTTTACA
* *
1076239 TGGTAAA-TTACCTATAACTTTAAAGTAATCGGTTTCAAAATTTCGCATATCGATACTTTATACA
130 TGGTAAATTTACCTATAACTTTAAAGAAATAGGTTTCAAAATTTCGCATATCGATACTTTATACA
1076303 AGTGA
195 AGTGA
* * * *
1076308 ATCGATATTTTTTTGCGTGCAAATTGTTTGAGATGCGTACTGGAATAAAAGTATCGATACTATAT
1 ATCGATA-CTTTTTGCGTGCAAATTATTTGAGATGCATACTGGAATAAAAGTATCGATAATATAT
* * * *
1076373 AATAAGTATTGTTACTTTATGTTTACGCCTACTATCATTAAACTAGTAGATTTTTACTGTTTACA
65 AATAAGTATCGATACTTTATATTTACGCCTACTATCATTAAACTAGTAGATTTTTACCGTTTACA
* * * * * *
1076438 TTGTAAATTTACCTATTATTTTAAAGAAATAGGTTTCGAAATTAT--AAGTATCTATACGTTTTA
130 TGGTAAATTTACCTATAACTTTAAAGAAATAGGTTTCAAAATT-TCGCA-TATCGATAC--TTTA
* *
1076501 TGC-A-TGT
191 TACAAGTGA
* *
1076508 ATCGATACTTTGTGCGT-CGAAATTATTTGAGATGCATACTAGAATAATAAGTATCGAT
1 ATCGATACTTTTTGCGTGC-AAATTATTTGAGATGCATACTGGAATAA-AAGTATCGAT
1076566 GCATTATGTT
Statistics
Matches: 221, Mismatches: 28, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
198 8 0.04
199 147 0.67
200 58 0.26
201 2 0.01
202 6 0.03
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.40
Consensus pattern (199 bp):
ATCGATACTTTTTGCGTGCAAATTATTTGAGATGCATACTGGAATAAAAGTATCGATAATATATA
ATAAGTATCGATACTTTATATTTACGCCTACTATCATTAAACTAGTAGATTTTTACCGTTTACAT
GGTAAATTTACCTATAACTTTAAAGAAATAGGTTTCAAAATTTCGCATATCGATACTTTATACAA
GTGA
Found at i:1082244 original size:15 final size:15
Alignment explanation
Indices: 1082223--1082269 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
1082213 CTTTGATATA
1082223 ATTTCTTTCCATTTC
1 ATTTCTTTCCATTTC
*
1082238 CTTTCTTAT-CATTTC
1 ATTTCTT-TCCATTTC
1082253 ATTTCTTCTTCCATTTC
1 ATTTC-T-TTCCATTTC
1082270 TTATTTCATA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 16 0.62
16 3 0.12
17 7 0.27
ACGTcount: A:0.13, C:0.28, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTCTTTCCATTTC
Found at i:1084093 original size:2 final size:2
Alignment explanation
Indices: 1084086--1084113 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1084076 TAGATTCTAG
1084086 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1084114 CATTCACTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1085431 original size:21 final size:20
Alignment explanation
Indices: 1085381--1085440 Score: 102
Period size: 20 Copynumber: 2.9 Consensus size: 20
1085371 ATACTGGACT
1085381 AAAAGTATCGATACCTATAC
1 AAAAGTATCGATACCTATAC
1085401 AAAAGTATCGATACCTATAC
1 AAAAGTATCGATACCTATAC
1085421 AAAATGTATCGATACTCTAT
1 AAAA-GTATCGATAC-CTAT
1085441 GTTTACGCCT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
20 24 0.63
21 10 0.26
22 4 0.11
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.28
Consensus pattern (20 bp):
AAAAGTATCGATACCTATAC
Found at i:1085588 original size:219 final size:219
Alignment explanation
Indices: 1085182--1085634 Score: 574
Period size: 219 Copynumber: 2.1 Consensus size: 219
1085172 ATATTGGACT
* * * * *
1085182 AAAAGTATCGATACCTATAGAAAGAGTGTTGGTACTTTATGTTTACGCCTATTATCATTAAACCG
1 AAAAGTATCGATACCTATACAAAGAGTGTTGATACTCTATGTTTACGCCTAATATCATTAAACCA
* ** * *
1085247 GTAAATTTTTATCATTTTCATTGTAAAATTACCTATTACTATAAAGTAATCGTTTCGAAATTATA
66 GTAAACTTTTATCATTGACATTATAAAATTACCTATAACTATAAAGTAATCGTTTCGAAATTATA
* * * * * ** *
1085312 AGTATTGATACTTGTGGCACGTGTATCGATTCTTTCTGCATGCATGTTGTTTGAGAAGCATACTG
131 AGTATTGATACTGGTGACACATGTATCGATACTTTCTGCAGGCAAATTGTATGAGAAGCATACTG
*
1085377 GACTAAAAGTATCGATACCTATAC
196 GACTAAAAGTATCGATACCCATAC
1085401 AAAAGTATCGATACCTATACAAA-A-TGTATCGATACTCTATGTTTACGCCTAATATCATTAAAC
1 AAAAGTATCGATACCTATACAAAGAGTGT-T-GATACTCTATGTTTACGCCTAATATCATTAAAC
* * *
1085464 CAGTAGACTTTTA-CTATTGACATTATAAATTTACCTATAAC-ATTAAAGTAATCGGTTTTGAAA
64 CAGTAAACTTTTATC-ATTGACATTATAAAATTACCTATAACTA-TAAAGTAATC-GTTTCGAAA
* * * *
1085527 TTATAAGTATTGATACTGGTTATACATGTATCGATACTTTGTGCGGGCAAATTG-ATGAGAAGCA
126 TTATAAGTATTGATACTGGTGACACATGTATCGATACTTTCTGCAGGCAAATTGTATGAGAAGCA
1085591 TACTGGACTAAAAGTATCGATACCCATAC
191 TACTGGACTAAAAGTATCGATACCCATAC
*
1085620 AAAGAGTATCAATAC
1 AAA-AGTATCGATAC
1085635 TTTATATTTA
Statistics
Matches: 201, Mismatches: 27, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
217 3 0.01
218 4 0.02
219 133 0.66
220 61 0.30
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (219 bp):
AAAAGTATCGATACCTATACAAAGAGTGTTGATACTCTATGTTTACGCCTAATATCATTAAACCA
GTAAACTTTTATCATTGACATTATAAAATTACCTATAACTATAAAGTAATCGTTTCGAAATTATA
AGTATTGATACTGGTGACACATGTATCGATACTTTCTGCAGGCAAATTGTATGAGAAGCATACTG
GACTAAAAGTATCGATACCCATAC
Found at i:1085758 original size:199 final size:199
Alignment explanation
Indices: 1085401--1085765 Score: 473
Period size: 199 Copynumber: 1.8 Consensus size: 199
1085391 ATACCTATAC
* * * * *
1085401 AAAAGTATCGATACCTATACAAAATGTATCGATACTCTATGTTTACGCCTAATATCATTAAACCA
1 AAAAGTATCGATACCCATACAAAATGTATCAATACTCTATATTTAAGCCCAATATCATTAAACCA
* * * * * *
1085466 GTAGACTTTTACTATTGACATTATAAATTTACCTATAACATTAAAGTAATCGGTTTTGAAATTAT
66 GTAGACTTTTACCATTGACATTATAAAATTACCAATAACATTAAAATAATAGGTTTCGAAATTAT
**
1085531 AAGTATTGATACTGGTTATACATGTATCGATACTTTGTGCGGGCAAATTGATGAGAAGCATACTG
131 AAGTACCGATACTGGTTATACATGTATCGATACTTTGTGCGGGCAAATTGATGAGAAGCATACTG
1085596 GACT
196 GACT
* *
1085600 AAAAGTATCGATACCCATACAAAGA-GTATCAATACTTTATATTTAAGCCCATTATCATTAAACC
1 AAAAGTATCGATACCCATACAAA-ATGTATCAATACTCTATATTTAAGCCCAATATCATTAAACC
* * * ** * * *
1085664 GGTAGATTTTTACCGTTTTCATTGTAAAATTAGCAAT-TCATTTAAAATAATAGGTTTCGAAATT
65 AGTAGACTTTTACCATTGACATTATAAAATTACCAATAACA-TTAAAATAATAGGTTTCGAAATT
* *
1085728 ATAAGTACCGATACTTGTTATACGTGTATCGATACTTT
129 ATAAGTACCGATACTGGTTATACATGTATCGATACTTT
1085766 TTTTGTGTTC
Statistics
Matches: 139, Mismatches: 25, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
198 2 0.01
199 136 0.98
200 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.36
Consensus pattern (199 bp):
AAAAGTATCGATACCCATACAAAATGTATCAATACTCTATATTTAAGCCCAATATCATTAAACCA
GTAGACTTTTACCATTGACATTATAAAATTACCAATAACATTAAAATAATAGGTTTCGAAATTAT
AAGTACCGATACTGGTTATACATGTATCGATACTTTGTGCGGGCAAATTGATGAGAAGCATACTG
GACT
Found at i:1092936 original size:199 final size:196
Alignment explanation
Indices: 1092379--1092944 Score: 531
Period size: 199 Copynumber: 2.9 Consensus size: 196
1092369 CCAAAGTCTC
* * *
1092379 GATACTTTTGTGTAAGGTATCGATACTTTCGAAATGTTTTCACTTTTTTCATTTC--TT---TTC
1 GATACTTGTGTGTAAGGTATCGATACTTTCGAGA-CTTTTC-CTTTTTTCATTTCTTTTAAATTC
* * * * * * *
1092439 ATAAAGTATTGATACTATGATACATATACTTATAAAAGTATTGATAC-A-GTCAGCATATCTGGT
64 CTAAAGTACTGATACTTTGGTACATATACTTATAAAAGTATCGATACAATTTCAACAT-TCTGGT
* * * * * * * * *
1092502 AGCGCTTTACCGATTTTGTCATATTGAAACCAATTTTGTTAAATTTTAACTTGTTATATTGTCAT
128 AGCTCTTTACAGATTTTG-CAAATTAAAACCGATTTTGTCAAATTTCAACCTGTTATATTGTCAA
1092567 GTATT
192 GTATT
* * * * ** * ** * * *
1092572 GATACATGTGTCTCAGGTACCGATACTTTATAGGC-GCT-ATTATTTCAATTCTTTTAAATTCCT
1 GATACTTGTGTGTAAGGTATCGATACTTTCGAGACTTTTCCTTTTTTCATTTCTTTTAAATTCCT
* ** *
1092635 AAAGTACCGATACTTTGGTGTATATACTTATAAAAGTATCGATACAAATTTCAACCATTC-GATA
66 AAAGTACTGATACTTTGGTACATATACTTATAAAAGTATCGATAC-AATTTCAA-CATTCTGGTA
* * * * * * * * *
1092699 TCTATTTACCAGTTTTTTCACACTAAAATCGGTTTTGTCAAACTTCAACCTGTTATATTGTCAAG
129 GCTCTTTA-CAGATTTTGCAAATTAAAACCGATTTTGTCAAATTTCAACCTGTTATATTGTCAAG
1092764 TATT
193 TATT
1092768 GATACTTGTGTGTAAGGTATCGATACTTTCGAGACATTTTCCTTTTTTCATTTCTTTTAAATTCC
1 GATACTTGTGTGTAAGGTATCGATACTTTCGAGAC-TTTTCCTTTTTTCATTTCTTTTAAATTCC
* * * *
1092833 TACAGTACTGATGCTTTGGTACATATACTTATACACGTATCGATACATATTTCAACAATTCTGGT
65 TAAAGTACTGATACTTTGGTACATATACTTATAAAAGTATCGATACA-ATTTCAAC-ATTCTGGT
*
1092898 AGCTCTTTACTGATTTTGCAAATTAAAACCGATTTTGTCAAATTTCA
128 AGCTCTTTACAGATTTTGCAAATTAAAACCGATTTTGTCAAATTTCA
1092945 CCGGTTTTGT
Statistics
Matches: 284, Mismatches: 73, Indels: 26
0.74 0.19 0.07
Matches are distributed among these distances:
189 10 0.04
191 3 0.01
193 25 0.09
194 42 0.15
196 77 0.27
197 11 0.04
198 6 0.02
199 101 0.36
200 9 0.03
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (196 bp):
GATACTTGTGTGTAAGGTATCGATACTTTCGAGACTTTTCCTTTTTTCATTTCTTTTAAATTCCT
AAAGTACTGATACTTTGGTACATATACTTATAAAAGTATCGATACAATTTCAACATTCTGGTAGC
TCTTTACAGATTTTGCAAATTAAAACCGATTTTGTCAAATTTCAACCTGTTATATTGTCAAGTAT
T
Found at i:1093778 original size:42 final size:42
Alignment explanation
Indices: 1093726--1093875 Score: 176
Period size: 42 Copynumber: 3.5 Consensus size: 42
1093716 ACCACAAATA
* * * *
1093726 CCGCTAAAGGTTATGTTTTTTGGCGGTGTTGTTTTACAAACG
1 CCGCTAAAGGTTATGATATTTAGCGATGTTGTTTTACAAACG
* * *
1093768 CCGCTAAAGGTAAT-ACTATTTAGCGATGTTTTTTTTACAAATG
1 CCGCTAAAGGTTATGA-TATTTAGCGATG-TTGTTTTACAAACG
** *
1093811 CCGCTAAAGGTTATGATATTTAGCGACATTGTTTTCCAAACG
1 CCGCTAAAGGTTATGATATTTAGCGATGTTGTTTTACAAACG
*
1093853 TCGCTAAAGGTTATGATATTTAG
1 CCGCTAAAGGTTATGATATTTAG
1093876 TTGTGTTTTT
Statistics
Matches: 91, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
42 55 0.60
43 35 0.38
44 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.38
Consensus pattern (42 bp):
CCGCTAAAGGTTATGATATTTAGCGATGTTGTTTTACAAACG
Found at i:1106096 original size:14 final size:15
Alignment explanation
Indices: 1106077--1106106 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1106067 AATATAAGCC
1106077 AAATTTT-TGGGGCA
1 AAATTTTGTGGGGCA
1106091 AAATTTTGTGGGGCA
1 AAATTTTGTGGGGCA
1106106 A
1 A
1106107 GTAAAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.30, C:0.07, G:0.30, T:0.33
Consensus pattern (15 bp):
AAATTTTGTGGGGCA
Found at i:1106581 original size:60 final size:60
Alignment explanation
Indices: 1106471--1106626 Score: 163
Period size: 60 Copynumber: 2.6 Consensus size: 60
1106461 CACAAGATTG
* * * * * ** *
1106471 GATTTCAACTTCACAATGAAGGATATCTAACTTAAAGCCCATTTGGTGAAACAA-TACTT-
1 GATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAATTTCATGAAAAAACT-CTTA
* *
1106530 GTATTTTAACTTCACAACGAAGGATTTCCAACTCAAAACCAATTTCATGAAAAAACTCTTA
1 G-ATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAATTTCATGAAAAAACTCTTA
* * *
1106591 GATTTCAACTTCACGACAAAGGATATCCAATTCAAA
1 GATTTCAACTTCACAACGAAGGATATCCAACTCAAA
1106627 GCTAAACTTC
Statistics
Matches: 79, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
59 1 0.01
60 76 0.96
61 2 0.03
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.29
Consensus pattern (60 bp):
GATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAATTTCATGAAAAAACTCTTA
Found at i:1106734 original size:121 final size:121
Alignment explanation
Indices: 1106582--1106937 Score: 480
Period size: 121 Copynumber: 2.9 Consensus size: 121
1106572 TTTCATGAAA
* *
1106582 AAACTCTTAGATTTCAACTTCACGACAAAGGATATCCAATTCAAAGCTAAACTTCACAACGAAGG
1 AAAC-CTTGGATTTCAACTTCACGACAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGG
* **
1106647 AGTCATCCATGATTTCAACTTCACAACAAAGGATATCGTGCCCACAAGAAGCAATGC
65 AGCCATCCATGATTTCAACTTCACAATGAAGGATATCGTGCCCACAAGAAGCAATGC
** *
1106704 AAACCTTGGATTTCAACTTCACGATGAAGGATATCCAATTCAAAGCTCAACTTCACAAAGAAGGA
1 AAACCTTGGATTTCAACTTCACGACAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGA
* * * *
1106769 GCCATCCACGATTTCAACTTCA-AGATGAATGATATCATGCCCACAAGCAGCAATGC
66 GCCATCCATGATTTCAACTTCACA-ATGAAGGATATCGTGCCCACAAGAAGCAATGC
* * * * * * *
1106825 AACCCTAGGATTTCAACTTCACGACAAATGATATCCAATTTAAAGCTCAACATCACGACGAAGAA
1 AAACCTTGGATTTCAACTTCACGACAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGA
* * * *
1106890 GCCATTCATGATTTCATCTTCACAATGAAGGATATCGTACCCAAAAGA
66 GCCATCCATGATTTCAACTTCACAATGAAGGATATCGTGCCCACAAGA
1106938 TTGACCCAAA
Statistics
Matches: 202, Mismatches: 30, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
120 1 0.00
121 196 0.97
122 5 0.02
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.23
Consensus pattern (121 bp):
AAACCTTGGATTTCAACTTCACGACAAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGA
GCCATCCATGATTTCAACTTCACAATGAAGGATATCGTGCCCACAAGAAGCAATGC
Found at i:1107505 original size:3 final size:3
Alignment explanation
Indices: 1107497--1107529 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
1107487 TAAATATAAA
1107497 TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TA
1107530 CAACTATTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1109460 original size:16 final size:17
Alignment explanation
Indices: 1109422--1109460 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
1109412 ACGCGGTCTA
1109422 GTTTTTGTCTTAAAAAT
1 GTTTTTGTCTTAAAAAT
* *
1109439 GATTTT-TCTTAAAATT
1 GTTTTTGTCTTAAAAAT
1109455 GTTTTT
1 GTTTTT
1109461 AAAAGACATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.26, C:0.05, G:0.10, T:0.59
Consensus pattern (17 bp):
GTTTTTGTCTTAAAAAT
Found at i:1113537 original size:26 final size:26
Alignment explanation
Indices: 1113503--1113693 Score: 166
Period size: 26 Copynumber: 8.0 Consensus size: 26
1113493 ATGCCTTAAT
*
1113503 GCATTCTTTCATGCATTTCAATTATG
1 GCATCCTTTCATGCATTTCAATTATG
1113529 GCATCCTTTCATGCATTTCAATTATG
1 GCATCCTTTCATGCATTTCAATTATG
* *
1113555 GCATCATTTCATGC-CTT--A--AT-
1 GCATCCTTTCATGCATTTCAATTATG
* *
1113575 GTATCCTTTCATGCATTTCATTTATG
1 GCATCCTTTCATGCATTTCAATTATG
* *
1113601 GCATCATTTCATGC-CTT--A--AT-
1 GCATCCTTTCATGCATTTCAATTATG
1113621 GCATCCTTTCATGCATTTCAATTATG
1 GCATCCTTTCATGCATTTCAATTATG
* *
1113647 GCATCCTTTCATTC-CTT--A--AT-
1 GCATCCTTTCATGCATTTCAATTATG
*
1113667 GCATCCTTTCATGCATTTTAATTATG
1 GCATCCTTTCATGCATTTCAATTATG
1113693 G
1 G
1113694 ATTCATTTTA
Statistics
Matches: 130, Mismatches: 17, Indels: 36
0.71 0.09 0.20
Matches are distributed among these distances:
20 38 0.29
21 12 0.09
23 4 0.03
25 12 0.09
26 64 0.49
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.44
Consensus pattern (26 bp):
GCATCCTTTCATGCATTTCAATTATG
Found at i:1113581 original size:46 final size:46
Alignment explanation
Indices: 1113529--1113701 Score: 285
Period size: 46 Copynumber: 3.8 Consensus size: 46
1113519 TTCAATTATG
1113529 GCATCCTTTCATGCATTTCAATTATGGCATCATTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTCAATTATGGCATCATTTCATGCCTTAAT
* *
1113575 GTATCCTTTCATGCATTTCATTTATGGCATCATTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTCAATTATGGCATCATTTCATGCCTTAAT
* *
1113621 GCATCCTTTCATGCATTTCAATTATGGCATCCTTTCATTCCTTAAT
1 GCATCCTTTCATGCATTTCAATTATGGCATCATTTCATGCCTTAAT
*
1113667 GCATCCTTTCATGCATTTTAATTATGG-ATTCATTT
1 GCATCCTTTCATGCATTTCAATTATGGCA-TCATTT
1113702 TAGAACAGTT
Statistics
Matches: 118, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
45 1 0.01
46 117 0.99
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.45
Consensus pattern (46 bp):
GCATCCTTTCATGCATTTCAATTATGGCATCATTTCATGCCTTAAT
Found at i:1113586 original size:20 final size:20
Alignment explanation
Indices: 1113555--1113680 Score: 90
Period size: 20 Copynumber: 5.7 Consensus size: 20
1113545 TTCAATTATG
*
1113555 GCATCATTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
* *
1113575 GTATCCTTTCATGCATTTCATTTAT
1 GCATCCTTTCATGC----C-TTAAT
*
1113600 GGCATCATTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
*
1113621 GCATCCTTTCATGCATTTCAATTAT
1 GCATCCTTTCATGC-CTT--A--AT
*
1113646 GGCATCCTTTCATTCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
1113667 GCATCCTTTCATGC
1 GCATCCTTTCATGC
1113681 ATTTTAATTA
Statistics
Matches: 83, Mismatches: 11, Indels: 24
0.70 0.09 0.20
Matches are distributed among these distances:
20 38 0.46
21 8 0.10
22 1 0.01
23 2 0.02
24 1 0.01
25 8 0.10
26 25 0.30
ACGTcount: A:0.21, C:0.25, G:0.10, T:0.43
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:1113588 original size:72 final size:72
Alignment explanation
Indices: 1113471--1113614 Score: 227
Period size: 72 Copynumber: 2.0 Consensus size: 72
1113461 TTATTAATTA
* * *
1113471 ATTTCATTTATGGCATTCTTTCATGCCTTAATGCATTCTTTCATGCATTTCAATTATGGCATCCT
1 ATTTCAATTATGGCATTCTTTCATGCCTTAATGCATCCTTTCATGCATTTCAATTATGGCATCAT
1113536 TTCATGC
66 TTCATGC
* *
1113543 ATTTCAATTATGGCA-TCATTTCATGCCTTAATGTATCCTTTCATGCATTTCATTTATGGCATCA
1 ATTTCAATTATGGCATTC-TTTCATGCCTTAATGCATCCTTTCATGCATTTCAATTATGGCATCA
1113607 TTTCATGC
65 TTTCATGC
1113615 CTTAATGCAT
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
71 2 0.03
72 64 0.97
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.45
Consensus pattern (72 bp):
ATTTCAATTATGGCATTCTTTCATGCCTTAATGCATCCTTTCATGCATTTCAATTATGGCATCAT
TTCATGC
Found at i:1114142 original size:22 final size:22
Alignment explanation
Indices: 1114112--1114168 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
1114102 TACCTCTACC
*
1114112 ATGGTATCGATACTTTTATACT
1 ATGGTATCGATACTTCTATACT
*
1114134 ATGGCATCGATACTTCTATACT
1 ATGGTATCGATACTTCTATACT
*
1114156 ATGGTATTGATAC
1 ATGGTATCGATAC
1114169 CTTTCTCTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (22 bp):
ATGGTATCGATACTTCTATACT
Found at i:1120490 original size:46 final size:46
Alignment explanation
Indices: 1120440--1120675 Score: 312
Period size: 46 Copynumber: 5.1 Consensus size: 46
1120430 TTAATAATTA
* *
1120440 TTCATTAATTTCATTTATGGCATCATTTCATGCCTTAATGCATCCT
1 TTCATGAATTTCAATTATGGCATCATTTCATGCCTTAATGCATCCT
* *
1120486 TTCATGCATTTCAATTATGACATCATTTCATGCCTTAATGCATCCT
1 TTCATGAATTTCAATTATGGCATCATTTCATGCCTTAATGCATCCT
* * * *
1120532 TTCCTGGATTTCAATTATGGCATCCTTTCATGTCTTAATGCATCCT
1 TTCATGAATTTCAATTATGGCATCATTTCATGCCTTAATGCATCCT
* * * *
1120578 TTCATGCAA-ATCATTTATGGCATCCTTTCATGCCTTAATGCATCTT
1 TTCATG-AATTTCAATTATGGCATCATTTCATGCCTTAATGCATCCT
* * * *
1120624 TTCATGAATTTCAATTATGACATCTTTTCATGCTTTAATGCATCAT
1 TTCATGAATTTCAATTATGGCATCATTTCATGCCTTAATGCATCCT
1120670 TTCATG
1 TTCATG
1120676 CCTTAATGCA
Statistics
Matches: 167, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
45 2 0.01
46 164 0.98
47 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.44
Consensus pattern (46 bp):
TTCATGAATTTCAATTATGGCATCATTTCATGCCTTAATGCATCCT
Found at i:1120667 original size:66 final size:66
Alignment explanation
Indices: 1120459--1120742 Score: 285
Period size: 66 Copynumber: 4.2 Consensus size: 66
1120449 TTCATTTATG
*
1120459 GCATCATTTCATGCCTTAATGCATCCTTTCATGCATTTCAATTATGACATCATTTCATGCCTTAA
1 GCATCATTTCATGCCTTAATGCATCCTTTCATGCATTTCAATTATGACATCCTTTCATGCCTTAA
1120524 T
66 T
* * **
1120525 GCATCCTTTCCTGGATTTCAATTATGGCATCCTTTCATG----TC--TTAATG-CATCCTTTCAT
1 GCATCATTTCAT-GCCTT--A--AT-GCATCCTTTCATGCATTTCAATT-ATGACATCCTTTCAT
*
1120583 GCAAATCATTTAT
59 GC----C-TTAAT
* * * * *
1120596 GGCATCCTTTCATGCCTTAATGCATCTTTTCATGAATTTCAATTATGACATCTTTTCATGCTTTA
1 -GCATCATTTCATGCCTTAATGCATCCTTTCATGCATTTCAATTATGACATCCTTTCATGCCTTA
1120661 AT
65 AT
* *
1120663 GCATCATTTCATGCCTTAATGCATCCTTTCATGCATTTCAATTATGGCATCCTTTCATTCCTTAA
1 GCATCATTTCATGCCTTAATGCATCCTTTCATGCATTTCAATTATGACATCCTTTCATGCCTTAA
1120728 T
66 T
1120729 GCATCATTTCATGC
1 GCATCATTTCATGC
1120743 ATTTTAATTA
Statistics
Matches: 178, Mismatches: 20, Indels: 40
0.75 0.08 0.17
Matches are distributed among these distances:
66 109 0.61
67 12 0.07
68 2 0.01
69 2 0.01
70 3 0.02
71 12 0.07
72 38 0.21
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.42
Consensus pattern (66 bp):
GCATCATTTCATGCCTTAATGCATCCTTTCATGCATTTCAATTATGACATCCTTTCATGCCTTAA
T
Found at i:1120673 original size:112 final size:112
Alignment explanation
Indices: 1120551--1120755 Score: 329
Period size: 112 Copynumber: 1.8 Consensus size: 112
1120541 TTCAATTATG
* * *
1120551 GCATCCTTTCATGTCTTAATGCATCCTTTCATGCAAATCATTTATGGCATCCTTTCATGCCTTAA
1 GCATCATTTCATGCCTTAATGCATCCTTTCATGCAAATCAATTATGGCATCCTTTCATGCCTTAA
*
1120616 TGCATCTTTTCATGAATTTCAATTATGACATCTTTTCATGCTTTAAT
66 TGCATCATTTCATGAATTTCAATTATGACATCTTTTCATGCTTTAAT
** *
1120663 GCATCATTTCATGCCTTAATGCATCCTTTCATGCATTTCAATTATGGCATCCTTTCATTCCTTAA
1 GCATCATTTCATGCCTTAATGCATCCTTTCATGCAAATCAATTATGGCATCCTTTCATGCCTTAA
* *
1120728 TGCATCATTTCATGCATTTTAATTATGA
66 TGCATCATTTCATGAATTTCAATTATGA
1120756 ATTCATTTTA
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
112 84 1.00
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.43
Consensus pattern (112 bp):
GCATCATTTCATGCCTTAATGCATCCTTTCATGCAAATCAATTATGGCATCCTTTCATGCCTTAA
TGCATCATTTCATGAATTTCAATTATGACATCTTTTCATGCTTTAAT
Found at i:1120713 original size:46 final size:46
Alignment explanation
Indices: 1120663--1120754 Score: 148
Period size: 46 Copynumber: 2.0 Consensus size: 46
1120653 ATGCTTTAAT
*
1120663 GCATCATTTCATGCCTTAATGCATCCTTTCATGCATTTCAATTATG
1 GCATCATTTCATGCCTTAATGCATCATTTCATGCATTTCAATTATG
* * *
1120709 GCATCCTTTCATTCCTTAATGCATCATTTCATGCATTTTAATTATG
1 GCATCATTTCATGCCTTAATGCATCATTTCATGCATTTCAATTATG
1120755 AATTCATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.24, C:0.23, G:0.10, T:0.43
Consensus pattern (46 bp):
GCATCATTTCATGCCTTAATGCATCATTTCATGCATTTCAATTATG
Found at i:1120720 original size:138 final size:136
Alignment explanation
Indices: 1120450--1120695 Score: 365
Period size: 138 Copynumber: 1.8 Consensus size: 136
1120440 TTCATTAATT
*
1120450 TCATTTATGGCATCATTTCATGCCTTAATGCATCCTTTCATGCATTTCAATTATGACATCATTTC
1 TCATTTATGGCATCATTTCATGCCTTAATGCATCCTTTCATGAATTTCAATTATGACATCATTTC
* * *
1120515 ATGCCTTAATGCATCCTTTCCTGGATTTCAATTATGGCATCCTTTCATGTCTTAATGCATCCTTT
66 ATGCCTTAATGCATCATTTCATGGACTT-AA-TATGGCATCCTTTCATGTCTTAATGCATCCTTT
1120580 CATGCAAA
129 CATGCAAA
* * *
1120588 TCATTTATGGCATCCTTTCATGCCTTAATGCATCTTTTCATGAATTTCAATTATGACATCTTTTC
1 TCATTTATGGCATCATTTCATGCCTTAATGCATCCTTTCATGAATTTCAATTATGACATCATTTC
* *
1120653 ATGCTTTAATGCATCATTTCAT-GCCTT-A-AT-GCATCCTTTCATG
66 ATGCCTTAATGCATCATTTCATGGACTTAATATGGCATCCTTTCATG
1120696 CATTTCAATT
Statistics
Matches: 99, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
132 13 0.13
133 2 0.02
135 1 0.01
137 3 0.03
138 80 0.81
ACGTcount: A:0.24, C:0.23, G:0.11, T:0.43
Consensus pattern (136 bp):
TCATTTATGGCATCATTTCATGCCTTAATGCATCCTTTCATGAATTTCAATTATGACATCATTTC
ATGCCTTAATGCATCATTTCATGGACTTAATATGGCATCCTTTCATGTCTTAATGCATCCTTTCA
TGCAAA
Found at i:1124604 original size:28 final size:28
Alignment explanation
Indices: 1124565--1124618 Score: 60
Period size: 28 Copynumber: 1.9 Consensus size: 28
1124555 TTAGTATAAT
1124565 TAAAGTATTT-AAGTATATAAAGTATAATT
1 TAAAGTATTTAAAGTATAT-AAGTATAA-T
1124594 ATAAAG-A-TTAAAGTATATAAGTATA
1 -TAAAGTATTTAAAGTATATAAGTATA
1124619 TAATATAACG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
28 9 0.39
29 9 0.39
30 5 0.22
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (28 bp):
TAAAGTATTTAAAGTATATAAGTATAAT
Found at i:1124618 original size:22 final size:22
Alignment explanation
Indices: 1124579--1124640 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
1124569 GTATTTAAGT
*
1124579 ATATAAAG--TATAATTATAAA
1 ATATAAAGTATATAAGTATAAA
*
1124599 GAT-TAAAGTATATAAGTATATA
1 -ATATAAAGTATATAAGTATAAA
* *
1124621 ATATAACGTTTATAAGTATA
1 ATATAAAGTATATAAGTATA
1124641 TATATATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
20 5 0.15
21 4 0.12
22 25 0.74
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.37
Consensus pattern (22 bp):
ATATAAAGTATATAAGTATAAA
Found at i:1124621 original size:30 final size:28
Alignment explanation
Indices: 1124559--1124653 Score: 90
Period size: 29 Copynumber: 3.4 Consensus size: 28
1124549 TGTCAGTTAG
*
1124559 TATAAT-TAAAGTATTTAAGTATATAA-A
1 TATAATATAAAG-ATTAAAGTATATAATA
1124586 GTATAATTATAAAGATTAAAGTATATAAGTA
1 -TATAA-TATAAAGATTAAAGTATATAA-TA
* *
1124617 TATAATATAACGTTTATAAGTATAT-ATA
1 TATAATATAAAGATTA-AAGTATATAATA
1124645 TAT-ATATAA
1 TATAATATAA
1124654 TATAAACTAT
Statistics
Matches: 59, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
27 6 0.10
28 10 0.17
29 24 0.41
30 18 0.31
31 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.08, T:0.40
Consensus pattern (28 bp):
TATAATATAAAGATTAAAGTATATAATA
Found at i:1124723 original size:22 final size:21
Alignment explanation
Indices: 1124689--1124757 Score: 54
Period size: 22 Copynumber: 3.4 Consensus size: 21
1124679 AGTTTATATT
* *
1124689 TAAATTATTATATGCTATGTA
1 TAAACTATTATATACTATGTA
*
1124710 TAAACTATATATATATTATGTA
1 TAAACTAT-TATATACTATGTA
* * *
1124732 T--AGT-TTATATACCATTTA
1 TAAACTATTATATACTATGTA
1124750 TAAACTAT
1 TAAACTAT
1124758 AGAGTTTATA
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
18 11 0.31
19 1 0.03
20 4 0.11
21 8 0.22
22 12 0.33
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.46
Consensus pattern (21 bp):
TAAACTATTATATACTATGTA
Found at i:1124836 original size:13 final size:13
Alignment explanation
Indices: 1124813--1125216 Score: 143
Period size: 13 Copynumber: 29.8 Consensus size: 13
1124803 TACTTATTAA
*
1124813 TATAAATTATATAG
1 TATAAA-TATAAAG
*
1124827 TTTAAATATAAAG
1 TATAAATATAAAG
*
1124840 TATAATTATAAAG
1 TATAAATATAAAG
* *
1124853 AATAAAATATATAG
1 TAT-AAATATAAAG
1124867 TATATAATATAAAG
1 TATA-AATATAAAG
1124881 TATATAAGTATATAA-
1 TATA-AA-TATA-AAG
* *
1124896 -ACATATATAAAG
1 TATAAATATAAAG
* * *
1124908 TTTTAGTATAAAG
1 TATAAATATAAAG
* * *
1124921 TATATATACATA-
1 TATAAATATAAAG
1124933 TATAATAATATAAAG
1 TAT-A-AATATAAAG
* * *
1124948 CATAAGTATATCA-
1 TATAAATATA-AAG
1124961 TATAAATATAAAG
1 TATAAATATAAAG
*
1124974 TATAATTATAAAG
1 TATAAATATAAAG
*
1124987 AATAAAGTATATAAG
1 TATAAA-TATA-AAG
*
1125002 CATATAATATAAAG
1 TATA-AATATAAAG
1125016 --TAAATATACATA-
1 TATAAATATA-A-AG
1125028 TATAATAATATAAAG
1 TAT-A-AATATAAAG
1125043 TATATAAGTACTAAA-
1 TATA-AA-TA-TAAAG
1125058 TATAAAGTATATAAG
1 TATAAA-TATA-AAG
*
1125073 AATAAAATATAAAG
1 TAT-AAATATAAAG
*
1125087 TATATATGTATTAAA-
1 TATA-A-ATA-TAAAG
* * *
1125102 AATAAGTAAATAAG
1 TATAAATATA-AAG
*
1125116 TATTAAATATAAAATA
1 TA-TAAATAT-AAA-G
*
1125132 TATAAATATATA-
1 TATAAATATAAAG
1125144 TATAAACTATAAAG
1 TATAAA-TATAAAG
*
1125158 TATATATATATAAG
1 TATAAATATA-AAG
*
1125172 TAT--ATATATA-
1 TATAAATATAAAG
* *
1125182 TATATATATATA-
1 TATAAATATAAAG
*
1125194 TATATATATAAAG
1 TATAAATATAAAG
*
1125207 TATATATATA
1 TATAAATATA
1125217 TGCTTTATAT
Statistics
Matches: 301, Mismatches: 49, Indels: 81
0.70 0.11 0.19
Matches are distributed among these distances:
10 3 0.01
11 9 0.03
12 41 0.14
13 92 0.31
14 80 0.27
15 52 0.17
16 24 0.08
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (13 bp):
TATAAATATAAAG
Found at i:1124893 original size:22 final size:21
Alignment explanation
Indices: 1124810--1125212 Score: 166
Period size: 22 Copynumber: 18.7 Consensus size: 21
1124800 TTATACTTAT
*
1124810 TAATATAAAT-TATATAGTTTA
1 TAATATAAATATATA-AGTATA
* *
1124831 -AATATAAA-GTATAATTATA
1 TAATATAAATATATAAGTATA
*
1124850 -AAGAATAAA-ATATATAGTATA
1 TAA-TATAAATATATA-AGTATA
1124871 TAATATAAAGTATATAAGTATA
1 TAATATAAA-TATATAAGTATA
* * *
1124893 TAA-ACATATATA-AAGT-TT
1 TAATATAAATATATAAGTATA
* *
1124911 TAGTATAAAGTATATATACATATA
1 TAATATAAA-TATATA-A-GTATA
*
1124935 TAATAATATAA-AGCATAAGTATA
1 TAAT-ATA-AATA-TATAAGTATA
*
1124958 TCATATAAATATA-AAGTATA
1 TAATATAAATATATAAGTATA
* *
1124978 -ATTATAAAGA-ATAAAGTATA
1 TAATATAAATATAT-AAGTATA
*
1124998 TAAGCATATAATATA-AAGTAAATA
1 TAA-TATA-AATATATAAGT--ATA
1125022 TACATATATAATAATATAAAGTATA
1 TA-ATATA-AAT-ATAT-AAGTATA
1125047 TAAGTACTAAATATA-AAGTATA
1 TAA-TA-TAAATATATAAGTATA
*
1125069 TAAGAATAAA-ATATAAAGTATA
1 TAA-TATAAATATAT-AAGTATA
* *
1125091 TATGTATTAAA-A-ATAAGTAAA
1 TA-ATA-TAAATATATAAGTATA
*
1125112 TAAGTATTAAATATA-AAATATA
1 TAA-TA-TAAATATATAAGTATA
* *
1125134 TAA-ATATATATATAAACTATA
1 TAATATAAATATAT-AAGTATA
*
1125155 -AAGTATATATATATAAGTATA
1 TAA-TATAAATATATAAGTATA
*
1125176 T-ATATATATATATATA-TATA
1 TAATATAAATATATA-AGTATA
1125196 TATATATAAAGTATATA
1 TA-ATATAAA-TATATA
1125213 TATATGCTTT
Statistics
Matches: 299, Mismatches: 37, Indels: 90
0.70 0.09 0.21
Matches are distributed among these distances:
18 4 0.01
19 27 0.09
20 66 0.22
21 51 0.17
22 72 0.24
23 28 0.09
24 23 0.08
25 20 0.07
26 4 0.01
27 4 0.01
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.36
Consensus pattern (21 bp):
TAATATAAATATATAAGTATA
Found at i:1124905 original size:32 final size:32
Alignment explanation
Indices: 1124867--1124978 Score: 87
Period size: 32 Copynumber: 3.6 Consensus size: 32
1124857 AAATATATAG
1124867 TATATAATA-TAAAGTATATAAGTATATAAACA
1 TATATAATAGTAAAGTATA-AAGTATATAAACA
** *
1124899 TATATAA-AGTTTTAGTATAAAGTATATATACA
1 TATATAATAG-TAAAGTATAAAGTATATAAACA
* *
1124931 TATATAATAATATAAAGCAT-AAGTATAT---CA
1 TATATAAT-A-GTAAAGTATAAAGTATATAAACA
1124961 TATA-AATA-TAAAGTATAA
1 TATATAATAGTAAAGTATAA
1124979 TTATAAAGAA
Statistics
Matches: 66, Mismatches: 8, Indels: 17
0.73 0.09 0.19
Matches are distributed among these distances:
26 7 0.11
27 1 0.02
28 1 0.02
29 3 0.05
30 6 0.09
31 1 0.02
32 26 0.39
33 15 0.23
34 6 0.09
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.36
Consensus pattern (32 bp):
TATATAATAGTAAAGTATAAAGTATATAAACA
Found at i:1124956 original size:40 final size:40
Alignment explanation
Indices: 1124870--1124957 Score: 92
Period size: 40 Copynumber: 2.2 Consensus size: 40
1124860 TATATAGTAT
* *
1124870 ATAA-TATAAAGTATATAAGTATATAAACATATATAAAGT
1 ATAAGTATAAAGTATATAAATATATAAACATATATAAAGC
* * *
1124909 TTTAGTATAAAGTATATATACATATAT-AATA-ATATAAAGC
1 ATAAGTATAAAGTATATA-A-ATATATAAACATATATAAAGC
1124949 ATAAGTATA
1 ATAAGTATA
1124958 TCATATAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
39 2 0.05
40 28 0.72
41 4 0.10
42 5 0.13
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.35
Consensus pattern (40 bp):
ATAAGTATAAAGTATATAAATATATAAACATATATAAAGC
Found at i:1125063 original size:71 final size:64
Alignment explanation
Indices: 1124988--1125154 Score: 183
Period size: 65 Copynumber: 2.5 Consensus size: 64
1124978 ATTATAAAGA
*
1124988 ATAAAGTATATAAGCATATAATATAAAGTAAATATACATATATAATAATATAAAGTATATAAGTA
1 ATAAAGTATATAAG-ATATAATATAAAGT--ATATACATAT-TAA-AA-AT-AAGTAAATAAGTA
1125053 CTAAAT
59 CTAAAT
* ** *
1125059 ATAAAGTATATAAGAATAAAATATAAAGTATATATGTATTAAAAATAAGTAAATAAGTATTAAAT
1 ATAAAGTATATAAG-ATATAATATAAAGTATATACATATTAAAAATAAGTAAATAAGTACTAAAT
* *
1125124 ATAAAATATATAA-ATATATATATAAACTATA
1 ATAAAGTATATAAGATATA-ATATAAAGTATA
1125155 AAGTATATAT
Statistics
Matches: 86, Mismatches: 9, Indels: 9
0.83 0.09 0.09
Matches are distributed among these distances:
63 4 0.05
64 11 0.13
65 29 0.34
66 2 0.02
67 2 0.02
68 3 0.03
69 8 0.09
71 27 0.31
ACGTcount: A:0.58, C:0.02, G:0.07, T:0.33
Consensus pattern (64 bp):
ATAAAGTATATAAGATATAATATAAAGTATATACATATTAAAAATAAGTAAATAAGTACTAAAT
Found at i:1125109 original size:134 final size:135
Alignment explanation
Indices: 1124811--1125163 Score: 351
Period size: 134 Copynumber: 2.6 Consensus size: 135
1124801 TATACTTATT
* *
1124811 AATATAAATTATATAGT-TTAAATATAAAGTATAATTATAAAGAATAAAATATATAGTATATAAT
1 AATATAAAGTATATAGTATTAAATATAAAGTATAATTATAAAGAATAAAATATATAGCATATAAT
* *
1124875 ATAAAGTATATAAGTATATAAACATATATAAAGTTTTAGTATAAAGTATATATACATATATAATA
66 ATAAAGTATATAAGTATATAAACATATATAAAGTTTAAGTATAAAGTATATATACATATATAAGA
1124940 ATATA
131 ATATA
* *
1124945 AAGCAT-AAGTATATCA-TA-TAAATATAAAGTATAATTATAAAGAATAAAGTATATAAGCATAT
1 AA-TATAAAGTATAT-AGTATTAAATATAAAGTATAATTATAAAGAATAAAATATAT-AGCATAT
* *
1125007 AATATAAAGTAAATATACA-TATAT-AATA-ATATAAAGTATATAAGTACTAAA-TATA-A-A-G
63 AATATAAAGT--ATATA-AGTATATAAACATATATAAAGT-T-TAAGTA-TAAAGTATATATACA
1125065 TATATAAGAATA-A
122 TATATAAGAATATA
* * * *
1125078 AATATAAAGTATATATGTATTAAAAAT-AAGTAAATAAGTATTAAA-TATAAAATATATA-AATA
1 AATATAAAGTATATA-GTATTAAATATAAAGT--ATAATTA-TAAAGAATAAAATATATAGCATA
*
1125140 TATATATAAACTATA-AAGTATATA
62 TA-ATATAAAGTATATAAGTATATA
1125164 TATATAAGTA
Statistics
Matches: 184, Mismatches: 15, Indels: 41
0.77 0.06 0.17
Matches are distributed among these distances:
131 1 0.01
132 9 0.05
133 14 0.08
134 67 0.36
135 44 0.24
136 21 0.11
137 23 0.12
138 5 0.03
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.34
Consensus pattern (135 bp):
AATATAAAGTATATAGTATTAAATATAAAGTATAATTATAAAGAATAAAATATATAGCATATAAT
ATAAAGTATATAAGTATATAAACATATATAAAGTTTAAGTATAAAGTATATATACATATATAAGA
ATATA
Found at i:1125117 original size:65 final size:70
Alignment explanation
Indices: 1124988--1125136 Score: 191
Period size: 65 Copynumber: 2.2 Consensus size: 70
1124978 ATTATAAAGA
* * *
1124988 ATAAAGTATATAAGCATATAATATAAAGTAAATATACATATATAATAATATAAAGTATATAAGTA
1 ATAAAGTATATAAGAATAAAATATAAAGT-AATATACATATATAATAATATAAAGTAAATAAGTA
1125053 CTAAAT
65 CTAAAT
** *
1125059 ATAAAGTATATAAGAATAAAATATAAAGT-ATATATGTAT-TAA-AA-AT-AAGTAAATAAGTAT
1 ATAAAGTATATAAGAATAAAATATAAAGTAATATACATATATAATAATATAAAGTAAATAAGTAC
1125119 TAAAT
66 TAAAT
*
1125124 ATAAAATATATAA
1 ATAAAGTATATAA
1125137 ATATATATAT
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
65 29 0.41
66 2 0.03
67 2 0.03
68 3 0.04
69 8 0.11
71 27 0.38
ACGTcount: A:0.58, C:0.02, G:0.07, T:0.32
Consensus pattern (70 bp):
ATAAAGTATATAAGAATAAAATATAAAGTAATATACATATATAATAATATAAAGTAAATAAGTAC
TAAAT
Found at i:1125142 original size:2 final size:2
Alignment explanation
Indices: 1125129--1125380 Score: 107
Period size: 2 Copynumber: 125.0 Consensus size: 2
1125119 TAAATATAAA
* * *
1125129 AT AT AT AA AT AT AT AT AT AA ACT AT AA AGT AT AT AT AT AT A- AGT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT A-T
*
1125173 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AGT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* * * *
1125216 AT GCT TT AT AT -T AT AT ACT -T AT AT ACT -T TT AT ACT CT AT -T
1 AT -AT AT AT AT AT AT AT A-T AT AT AT A-T AT AT AT A-T AT AT AT
* * * * * *
1125256 TT TT GT -T CT -T AT ACT TT AT AT -T AT -T AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
1125295 ACT TT AT ACT A- AA ACT TT AT AT AT AT AT AT AT AT AT AT AT AT
1 A-T AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
1125337 AT AT AGT TT AT AT AT AT ACT -T AT AT ACT TT AT AT -T AT -T AT
1 AT AT A-T AT AT AT AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT
1125377 AT AT
1 AT AT
1125381 GTATGTATGC
Statistics
Matches: 194, Mismatches: 28, Indels: 56
0.70 0.10 0.20
Matches are distributed among these distances:
1 13 0.07
2 166 0.86
3 15 0.08
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1125364 original size:94 final size:89
Alignment explanation
Indices: 1125265--1125459 Score: 291
Period size: 94 Copynumber: 2.1 Consensus size: 89
1125255 TTTTTGTTCT
1125265 TATACTTTATATTATTATATATGTATATATACTTTATACTAAAACTTTATATATATATATATATA
1 TATACTTTATATTATTATATATGTATATATACTTTATACTAAAAC-TT-TATATATATATATATA
*
1125330 TATATATATATAGTTTATATATATACTTA
64 CA-AT-T-TATAGTTTATATATATACTTA
* * *
1125359 TATACTTTATATTATTATATATGTATGTATGCTTTATACTAAAACTTTATGTATATATATATACA
1 TATACTTTATATTATTATATATGTATATATACTTTATACTAAAACTTTATATATATATATATACA
*
1125424 CTTTATAGTTTATATATATACTTA
66 ATTTATAGTTTATATATATACTTA
1125448 TATACTTATATA
1 TATACTT-TATA
1125460 CTTTAGTCTT
Statistics
Matches: 95, Mismatches: 5, Indels: 6
0.90 0.05 0.06
Matches are distributed among these distances:
89 28 0.29
90 5 0.05
91 1 0.01
92 16 0.17
93 2 0.02
94 43 0.45
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.51
Consensus pattern (89 bp):
TATACTTTATATTATTATATATGTATATATACTTTATACTAAAACTTTATATATATATATATACA
ATTTATAGTTTATATATATACTTA
Found at i:1125440 original size:22 final size:21
Alignment explanation
Indices: 1125402--1125444 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
1125392 TTATACTAAA
1125402 ACTTTATGTATATATATATAC
1 ACTTTATGTATATATATATAC
*
1125423 ACTTTATAGTTTATATATATAC
1 ACTTTAT-GTATATATATATAC
1125445 TTATATACTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.37, C:0.09, G:0.05, T:0.49
Consensus pattern (21 bp):
ACTTTATGTATATATATATAC
Found at i:1125450 original size:36 final size:37
Alignment explanation
Indices: 1125410--1125494 Score: 88
Period size: 36 Copynumber: 2.3 Consensus size: 37
1125400 AAACTTTATG
*
1125410 TATATATATATACACTTTA-TAGTTTAT-ATATATAC-T
1 TATATATATATACACTTTAGT-CTTTATAAT-TATACTT
*
1125446 TATATACT-TATATACTTTAGTCTTTATAATTATACTT
1 TATATA-TATATACACTTTAGTCTTTATAATTATACTT
*
1125483 TTTATATATATA
1 TATATATATATA
1125495 ATGTACTTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
36 27 0.66
37 14 0.34
ACGTcount: A:0.36, C:0.08, G:0.02, T:0.53
Consensus pattern (37 bp):
TATATATATATACACTTTAGTCTTTATAATTATACTT
Found at i:1125451 original size:8 final size:8
Alignment explanation
Indices: 1125438--1125462 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1125428 ATAGTTTATA
1125438 TATATACT
1 TATATACT
1125446 TATATACT
1 TATATACT
1125454 TATATACT
1 TATATACT
1125462 T
1 T
1125463 TAGTCTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (8 bp):
TATATACT
Found at i:1125454 original size:28 final size:29
Alignment explanation
Indices: 1125316--1125464 Score: 78
Period size: 29 Copynumber: 5.1 Consensus size: 29
1125306 AAACTTTATA
* *
1125316 TATATATATATATATATA-TATATATAGTT
1 TATATATATATATATACACT-TATATACTT
*
1125345 TATATATATACT-TATATACTT-TATA--T
1 TATATATATA-TATATACACTTATATACTT
* * **
1125371 TATTATATATGTATGTATGCTTTATACTAAAACTT
1 TA-TATATATATATATACAC-TTATA-T---ACTT
* *
1125406 TATGTATATATATATACACTT-TATAGTT
1 TATATATATATATATACACTTATATACTT
*
1125434 TATATATATACT-TATATACTTATATACTT
1 TATATATATA-TATATACACTTATATACTT
1125463 TA
1 TA
1125465 GTCTTTATAA
Statistics
Matches: 94, Mismatches: 12, Indels: 28
0.70 0.09 0.21
Matches are distributed among these distances:
26 4 0.04
27 12 0.13
28 26 0.28
29 28 0.30
30 3 0.03
31 1 0.01
32 2 0.02
33 3 0.03
34 12 0.13
35 3 0.03
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.51
Consensus pattern (29 bp):
TATATATATATATATACACTTATATACTT
Found at i:1125456 original size:20 final size:20
Alignment explanation
Indices: 1125414--1125459 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1125404 TTTATGTATA
*
1125414 TATATATACACTTTATAGTT
1 TATATATACACTTTATAGCT
*
1125434 TATATATATACTTATATA-CT
1 TATATATACACTT-TATAGCT
1125454 TATATA
1 TATATA
1125460 CTTTAGTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (20 bp):
TATATATACACTTTATAGCT
Done.