Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008550.1 Hibiscus syriacus cultivar Beakdansim tig00111445_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: 1154708
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 4 of 6
Found at i:557030 original size:102 final size:101
Alignment explanation
Indices: 556924--557188 Score: 404
Period size: 102 Copynumber: 2.6 Consensus size: 101
556914 TGGAACTAAG
* ** *
556924 TTTTGTCTCTCTTGAGATTGTTTCTCTTGAAACATAAACATTGAAAATATTTCCCTTGAAATGAA
1 TTTTGTCTCACTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAA
556989 TTTTGTCTATCTTAAGATAGGTTCCCTTGAAACAAAA
66 TTTTGTCTATCTTAAGATAGGTTCCCTTGAAAC-AAA
*
557026 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAA
1 TTTTGTCTCACTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAA
* * *
557091 TTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAA
66 TTTTGTCTATCTTAAGATAGGTTCCCTTGAAACAAA
* * * *
557127 TTTTGTCTCACTTGAGACAGTTTCTCTTGAAGCATAAACTTTGAAAACGGTTTCCTTTGAAA
1 TTTTGTCTCACTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC-ATTTCCCTTGAAA
557189 CAAAATCTTT
Statistics
Matches: 150, Mismatches: 12, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
101 48 0.32
102 102 0.68
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.39
Consensus pattern (101 bp):
TTTTGTCTCACTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAA
TTTTGTCTATCTTAAGATAGGTTCCCTTGAAACAAA
Found at i:557031 original size:269 final size:257
Alignment explanation
Indices: 556568--557130 Score: 844
Period size: 269 Copynumber: 2.2 Consensus size: 257
556558 TTTAAAGAAG
*
556568 TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAA---TTTTGTCTCTCTTGAAACAAATTTTG
1 TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAATTTTTTTGTCTCTCTTGAAACAAATTTCG
*
556630 TCTCCCTTGAGACATTTTCTTTTAGAACTAAGTTTCGTCTCTCTTGAGACAGTTTCTCTTAAACA
66 TCTCCATTGAGACATTTTCTTTTAGAACTAAGTTTCGTCTCTCTTGAGACAGTTTCTCTTAAACA
* * *
556695 TTGAAAAAATTTCCCTTGAAATTAATTTTGTCTCTCTTGAGATAGGTTCCCTTGAAACAAAATTT
131 TTGAAAAAATTTCCCTTGAAATGAATTTTGTCTATCTTAAGATAGGTTCCCTTGAAACAAAATTT
* **
556760 TGTCTCCCTTGGGAAAGTTTCTCTTGAAACATAAACATTGAAAATGTTTCCCTTGAAATGAA
196 TGTCTCCCTTGAGAAAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAA
* *
556822 TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAATAAAATTTTTGAATATGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAA-CAAATTTTT---T-TGTCTCTCTTGAAACAAA
* * **
556887 TTTCGTCTCCATTGAGACATTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGATTGTTTCTCTT
61 TTTCGTCTCCATTGAGACATTTTCTTTTAGAACTAAGTTTCGTCTCTCTTGAGACAGTTTCTC-T
*
556952 GAAACATAAACATTGAAAATATTTCCCTTGAAATGAATTTTGTCTATCTTAAGATAGGTTCCCTT
125 ------TAAACATTGAAAAAATTTCCCTTGAAATGAATTTTGTCTATCTTAAGATAGGTTCCCTT
*
557017 GAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCT
184 GAAACAAAATTTTGTCTCCCTTGAGAAAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCT
557082 TGAAATGAA
249 TGAAATGAA
*
557091 TTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTT
1 TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAATTTT
557131 GTCTCACTTG
Statistics
Matches: 276, Mismatches: 18, Indels: 16
0.89 0.06 0.05
Matches are distributed among these distances:
254 32 0.12
255 3 0.01
258 2 0.01
261 1 0.00
262 74 0.27
263 1 0.00
268 7 0.03
269 156 0.57
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.41
Consensus pattern (257 bp):
TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAATTTTTTTGTCTCTCTTGAAACAAATTTCG
TCTCCATTGAGACATTTTCTTTTAGAACTAAGTTTCGTCTCTCTTGAGACAGTTTCTCTTAAACA
TTGAAAAAATTTCCCTTGAAATGAATTTTGTCTATCTTAAGATAGGTTCCCTTGAAACAAAATTT
TGTCTCCCTTGAGAAAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAA
Found at i:557055 original size:37 final size:37
Alignment explanation
Indices: 556974--557059 Score: 93
Period size: 37 Copynumber: 2.4 Consensus size: 37
556964 TTGAAAATAT
** * *
556974 TTCCCTTGAAA-TGAATTTTGTCTATCTTAAGATAGG
1 TTCCCTTGAAACAAAATTTTGTCTACCTTAAGACAGG
* * *
557010 TTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGT
1 TTCCCTTGAAACAAAATTTTGTCTACCTTAAGACAGG
*
557047 TTCTCTTGAAACA
1 TTCCCTTGAAACA
557060 TAAACATTGA
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
36 11 0.27
37 30 0.73
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (37 bp):
TTCCCTTGAAACAAAATTTTGTCTACCTTAAGACAGG
Found at i:557097 original size:167 final size:158
Alignment explanation
Indices: 556741--557124 Score: 378
Period size: 167 Copynumber: 2.3 Consensus size: 158
556731 TTGAGATAGG
* * * * *
556741 TTCCCTTGAAACAAAATTTTGTCTCCCTTGGGAAAGTTTCTCTTGAAACATAAACATTGAAAATG
1 TTCCCTTG-AA-ATAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAATA
* * * * * *
556806 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAATAAAATTTTTGAATATG
64 TTTCCCTTGAAATGAATTTTGTCTATCTTAAGATAGGTTCCCTTGAAACAAAATTTTTGAACATG
* *
556871 TTTCTCTTGAAACAAATTTCGTCTCCATTGAGACATT
129 TTTCTCTTGAAACAAA-------TACATTGAAACATT
** * *
556908 TTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGATTGTTTCTCTTGAAACATAAACATTGAAAATA
1 TTCCCTT-GAAATAA-TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAATA
556973 TTTCCCTTGAAATGAATTTTGTCTATCTTAAGATAGGTTCCCTTGAAACAAAATTTTGTCTCCCT
64 TTTCCCTTGAAATGAATTTTGTCTATCTTAAGATAGGTTCCCTTGAAACAAAA---T-T-T---T
557038 TGAGACA-GTTTCTCTTGAAACATAA-ACATTGAAAACA-T
121 TGA-ACATGTTTCTCTTGAAACA-AATACATTG-AAACATT
*
557076 TTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
1 TTCCCTTGAAAT-AATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACA
557125 AATTTTGTCT
Statistics
Matches: 181, Mismatches: 22, Indels: 28
0.78 0.10 0.12
Matches are distributed among these distances:
166 2 0.01
167 135 0.75
168 14 0.08
169 4 0.02
170 1 0.01
171 1 0.01
172 1 0.01
175 19 0.10
176 4 0.02
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (158 bp):
TTCCCTTGAAATAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAATATT
TCCCTTGAAATGAATTTTGTCTATCTTAAGATAGGTTCCCTTGAAACAAAATTTTTGAACATGTT
TCTCTTGAAACAAATACATTGAAACATT
Found at i:557122 original size:36 final size:36
Alignment explanation
Indices: 557075--557157 Score: 121
Period size: 36 Copynumber: 2.3 Consensus size: 36
557065 ATTGAAAACA
** * *
557075 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCTCACTTGAGACAG
557111 TTTCCCTTGAAACAAATTTTGTCTCACTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCACTTGAGACAG
*
557147 TTTCTCTTGAA
1 TTTCCCTTGAA
557158 GCATAAACTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.42
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCACTTGAGACAG
Found at i:557296 original size:36 final size:36
Alignment explanation
Indices: 557254--557322 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
557244 TTTTGGAAGT
* *
557254 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAA
557290 TTTTGTCTCTCTTGAGACAATTTCCCTTGAAAC
1 TTTTGTCTCTCTTGAGACAATTTCCCTTGAAAC
557323 TTCAATCTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.42
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAA
Found at i:557382 original size:36 final size:36
Alignment explanation
Indices: 557340--557425 Score: 131
Period size: 34 Copynumber: 2.4 Consensus size: 36
557330 TTTGAATACA
*
557340 GTTTCTCTTGAAACACAAAAAAAAACCTTTGAAATT
1 GTTTCTCTTGAAACACAAAAAAAAACCTTTGAAAAT
* *
557376 GTTTCTCTT-AAA-ACATAAAAAAATCTTTGAAAAT
1 GTTTCTCTTGAAACACAAAAAAAAACCTTTGAAAAT
557410 GTTTCTCTTGAAACAC
1 GTTTCTCTTGAAACAC
557426 CAAACCTTCG
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
34 28 0.62
35 6 0.13
36 11 0.24
ACGTcount: A:0.42, C:0.16, G:0.08, T:0.34
Consensus pattern (36 bp):
GTTTCTCTTGAAACACAAAAAAAAACCTTTGAAAAT
Found at i:557404 original size:34 final size:34
Alignment explanation
Indices: 557326--557424 Score: 119
Period size: 34 Copynumber: 2.8 Consensus size: 34
557316 TTGAAACTTC
557326 AATCTTTGAATACA-GTTTCTCTTGAAACACAAAAAAA
1 AATCTTTGAA-A-ATGTTTCTCTT-AAA-ACAAAAAAA
* * *
557363 AACCTTTGAAATTGTTTCTCTTAAAACATAAAAA
1 AATCTTTGAAAATGTTTCTCTTAAAACAAAAAAA
*
557397 AATCTTTGAAAATGTTTCTCTTGAAACA
1 AATCTTTGAAAATGTTTCTCTTAAAACA
557425 CCAAACCTTC
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
34 33 0.60
35 3 0.05
36 10 0.18
37 9 0.16
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.34
Consensus pattern (34 bp):
AATCTTTGAAAATGTTTCTCTTAAAACAAAAAAA
Found at i:559945 original size:21 final size:21
Alignment explanation
Indices: 559830--559945 Score: 60
Period size: 21 Copynumber: 5.6 Consensus size: 21
559820 GCGAAATAAA
*
559830 AATCGCAACGCGA-TCTACAG
1 AATCGCAACGCGATTTTACAG
** * **
559850 AATCGCAAATC-AGTTCCCAG
1 AATCGCAACGCGATTTTACAG
* *
559870 AATCGTAACGCGATTATGA-AG
1 AATCGCAACGCGATT-TTACAG
* **
559891 AATCGCAATGCGATAGTACA-
1 AATCGCAACGCGATTTTACAG
** *
559911 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTTTACAG
559933 AATCGCAACGCGA
1 AATCGCAACGCGA
559946 ATATGAAAAT
Statistics
Matches: 68, Mismatches: 22, Indels: 11
0.67 0.22 0.11
Matches are distributed among these distances:
19 1 0.01
20 24 0.35
21 40 0.59
22 3 0.04
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGATTTTACAG
Found at i:559958 original size:20 final size:20
Alignment explanation
Indices: 559933--560144 Score: 128
Period size: 20 Copynumber: 10.6 Consensus size: 20
559923 GATTTTCCAG
*
559933 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGAA
* *
559953 AATCGCAACGCGAACA-TATA
1 AATCGCAACGCGAATACGA-A
* *
559973 AATCGCAACGC-AATTCTGAC
1 AATCGCAACGCGAATAC-GAA
* * * *
559993 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* *
560013 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* *
560033 AATCGCAACGCGTAT-CTATA
1 AATCGCAACGCGAATACGA-A
* * *
560053 AATCGTAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* * * *
560073 AATCGTAATGC-ATATCCGTA
1 AATCGCAACGCGA-ATACGAA
560093 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* * *
560114 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
560134 AATCGCAACGC
1 AATCGCAACGC
560145 AATTTTTAAA
Statistics
Matches: 148, Mismatches: 34, Indels: 20
0.73 0.17 0.10
Matches are distributed among these distances:
19 5 0.03
20 121 0.82
21 22 0.15
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATACGAA
Found at i:559982 original size:40 final size:40
Alignment explanation
Indices: 559933--560143 Score: 201
Period size: 40 Copynumber: 5.2 Consensus size: 40
559923 GATTTTCCAG
* * *
559933 AATCGCAACGCGAATATGAAAATCGCAACGCG-AACATATA
1 AATCGCAACGAGAATACGAAAATCGCAACGCGTATC-TATA
* * ** **
559973 AATCGCAACG-CAATTCTGACTATCGCAACGCGTATCCGTA
1 AATCGCAACGAGAATAC-GAAAATCGCAACGCGTATCTATA
*
560013 AATCGCAACGAGAATACGTAAATCGCAACGCGTATCTATA
1 AATCGCAACGAGAATACGAAAATCGCAACGCGTATCTATA
* * * * * **
560053 AATCGTAACGAGAATACGTAAATCGTAATGCATATCCGTA
1 AATCGCAACGAGAATACGAAAATCGCAACGCGTATCTATA
* **
560093 AATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGAGAATACG-AAAATCGCAACGCGTATCTATA
560134 AATCGCAACG
1 AATCGCAACG
560144 CAATTTTTAA
Statistics
Matches: 140, Mismatches: 27, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
39 3 0.02
40 103 0.74
41 34 0.24
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (40 bp):
AATCGCAACGAGAATACGAAAATCGCAACGCGTATCTATA
Found at i:560770 original size:21 final size:20
Alignment explanation
Indices: 560709--560805 Score: 126
Period size: 20 Copynumber: 4.8 Consensus size: 20
560699 TTCTAAACTT
*
560709 AAAATCGCAACATGAAAATG
1 AAAATCGCAACACGAAAATG
560729 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
**
560749 ACTATCGCAACGA-GAGAAATG
1 AAAATCGCAAC-ACGA-AAATG
560770 AAAATCGCAACACG-AAATG
1 AAAATCGCAACACGAAAATG
*
560789 AAAATCGCAACGCGAAA
1 AAAATCGCAACACGAAA
560806 CCAAAATCGC
Statistics
Matches: 67, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
19 18 0.27
20 33 0.49
21 16 0.24
ACGTcount: A:0.52, C:0.20, G:0.18, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:560788 original size:19 final size:19
Alignment explanation
Indices: 560709--560816 Score: 117
Period size: 19 Copynumber: 5.5 Consensus size: 19
560699 TTCTAAACTT
*
560709 AAAATCGCAACATGAAAATG
1 AAAATCGCAACACG-AAATG
560729 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACG-AAATG
** *
560749 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAAC-A-CGAAATG
560770 AAAATCGCAACACGAAATG
1 AAAATCGCAACACGAAATG
* **
560789 AAAATCGCAACGCGAAACC
1 AAAATCGCAACACGAAATG
560808 AAAATCGCA
1 AAAATCGCA
560817 TTGCGATTTT
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
19 31 0.41
20 29 0.38
21 15 0.20
22 1 0.01
ACGTcount: A:0.51, C:0.21, G:0.17, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACACGAAATG
Found at i:560882 original size:20 final size:21
Alignment explanation
Indices: 560859--560905 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
560849 GTTGCGAAAG
560859 TCATTTC-CGCGTTGCGATTT
1 TCATTTCTCGCGTTGCGATTT
*
560879 TCA-TTCTCTCGTTGCGATTT
1 TCATTTCTCGCGTTGCGATTT
560899 TCATTTC
1 TCATTTC
560906 AACCAAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 3 0.12
20 18 0.75
21 3 0.12
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.49
Consensus pattern (21 bp):
TCATTTCTCGCGTTGCGATTT
Found at i:562742 original size:94 final size:94
Alignment explanation
Indices: 562581--562960 Score: 611
Period size: 94 Copynumber: 4.1 Consensus size: 94
562571 TATATTGCTT
* * * *
562581 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAATTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTATGTATTCTTTAACACTGTGAAGTTAGT
562646 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
*
562675 AGTAAATTTATTCGGTTGCTGCCAATTTTGCTAAACTATGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTATGTATTCTTTAACACTGTGAAGTTAGT
562740 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * *
562769 AGTAAATTTGTTCGGTTGCTGCCAATTCTGTTAAACTGTATATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTATGTATTCTTTAACACTGTGAAGTTAGT
*
562834 ATTTGTCTTTATTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * *
562863 AGTAAATTTGTTCGGTTGCTGCAAATTCTGCTAAACTATGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTATGTATTCTTTAACACTGTGAAGTTAGT
562928 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
562956 AGTAA
1 AGTAA
562961 TGCAATCCAT
Statistics
Matches: 267, Mismatches: 18, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
93 26 0.10
94 241 0.90
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.48
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTATGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:563064 original size:19 final size:18
Alignment explanation
Indices: 563025--563146 Score: 71
Period size: 19 Copynumber: 6.9 Consensus size: 18
563015 ACGAAACTTA
*
563025 AAATCGCAACGTGAAAAATG
1 AAATCGCAACGCG--AAATG
*
563045 ACTATCGCAACGCGAAATG
1 A-AATCGCAACGCGAAATG
*
563064 AAATTCGCAA--CGAGA-G
1 AAA-TCGCAACGCGAAATG
563080 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
*
563097 AAAATCGCAA--CGACA--
1 -AAATCGCAACGCGAAATG
**
563112 AAATCGCAACGCGAAACCA
1 AAATCGCAACGCGAAA-TG
*
563131 AAATCGCAACGTGAAA
1 AAATCGCAACGCGAAA
563147 CTATAATCGC
Statistics
Matches: 82, Mismatches: 8, Indels: 25
0.71 0.07 0.22
Matches are distributed among these distances:
14 15 0.18
15 2 0.02
16 9 0.11
17 9 0.11
18 1 0.01
19 35 0.43
20 1 0.01
21 10 0.12
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (18 bp):
AAATCGCAACGCGAAATG
Found at i:563090 original size:33 final size:33
Alignment explanation
Indices: 563048--563141 Score: 143
Period size: 33 Copynumber: 2.8 Consensus size: 33
563038 AAAAATGACT
* * *
563048 ATCGCAACGCGAAATGAAATTCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
563081 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
**
563114 ATCGCAACGCGAAACCAAAATCGCAACG
1 ATCGCAACGCGAAATGAAAATCGCAACG
563142 TGAAACTATA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.45, C:0.26, G:0.20, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:563156 original size:19 final size:19
Alignment explanation
Indices: 563080--563147 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 19
563070 GCAACGAGAG
**
563080 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAACCAA
563099 AATCGCAA--CG--A-CAA
1 AATCGCAACGCGAAACCAA
563113 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
*
563132 AATCGCAACGTGAAAC
1 AATCGCAACGCGAAAC
563148 TATAATCGCG
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
14 10 0.24
15 1 0.02
16 2 0.05
17 2 0.05
18 1 0.02
19 26 0.62
ACGTcount: A:0.47, C:0.26, G:0.18, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:563175 original size:19 final size:19
Alignment explanation
Indices: 563153--563246 Score: 82
Period size: 19 Copynumber: 5.5 Consensus size: 19
563143 GAAACTATAA
*
563153 TCGCGTTGTGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
563172 TCGCATTGCGATTTTC---
1 TCGCGTTGCGATTTTCATT
*
563188 T--CGTTGCAATTTTCATT
1 TCGCGTTGCGATTTTCATT
563205 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
563219 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
563238 TCGCGTTGC
1 TCGCGTTGC
563247 AATAGTCATT
Statistics
Matches: 58, Mismatches: 7, Indels: 20
0.68 0.08 0.24
Matches are distributed among these distances:
14 21 0.36
16 4 0.07
17 4 0.07
19 29 0.50
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:563194 original size:14 final size:14
Alignment explanation
Indices: 563177--563234 Score: 53
Period size: 14 Copynumber: 3.8 Consensus size: 14
563167 TCATTTCGCA
563177 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
*
563191 TTGCAATTTTCATTTCGCG
1 TTGCGATTTTC---T--CG
*
563210 TTGCGATTCTCTCG
1 TTGCGATTTTCTCG
563224 TTGCGATTTTC
1 TTGCGATTTTC
563235 ATTTCGCGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
14 22 0.63
16 1 0.03
17 1 0.03
19 11 0.31
ACGTcount: A:0.10, C:0.22, G:0.19, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:563200 original size:33 final size:33
Alignment explanation
Indices: 563163--563246 Score: 141
Period size: 33 Copynumber: 2.5 Consensus size: 33
563153 TCGCGTTGTG
* *
563163 ATTTTCATTTCGCATTGCGATTTTCTCGTTGCA
1 ATTTTCATTTCGCGTTGCGATTCTCTCGTTGCA
*
563196 ATTTTCATTTCGCGTTGCGATTCTCTCGTTGCG
1 ATTTTCATTTCGCGTTGCGATTCTCTCGTTGCA
563229 ATTTTCATTTCGCGTTGC
1 ATTTTCATTTCGCGTTGC
563247 AATAGTCATT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.12, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
ATTTTCATTTCGCGTTGCGATTCTCTCGTTGCA
Found at i:563750 original size:21 final size:21
Alignment explanation
Indices: 563726--563791 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
563716 TCATTCCTCG
563726 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
563747 AGAGGCCACTATCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
563768 AGAGT-CCCTCCCACCATTCA
1 AGAGTCCCCTCCCACCGTTCA
563788 AGAG
1 AGAG
563792 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 1
0.70 0.28 0.02
Matches are distributed among these distances:
20 13 0.41
21 19 0.59
ACGTcount: A:0.26, C:0.36, G:0.18, T:0.20
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:563750 original size:42 final size:42
Alignment explanation
Indices: 563674--563791 Score: 116
Period size: 42 Copynumber: 2.8 Consensus size: 42
563664 GACTCGCCTG
* * * * * *
563674 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC-CTTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCAC-TA
563716 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
563758 TCA-TCGTTGAAGAGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGAGTCCCCTCCCACCGTTCAAGAG
563792 CCCGATTCAC
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
41 22 0.34
42 42 0.65
43 1 0.02
ACGTcount: A:0.24, C:0.36, G:0.17, T:0.24
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:565159 original size:14 final size:14
Alignment explanation
Indices: 565140--565175 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
565130 ATTGTTTAAT
565140 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
565154 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
565168 TGATTTGT
1 TGATTTGT
565176 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:565304 original size:19 final size:19
Alignment explanation
Indices: 565282--565340 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
565272 AAAAATGACT
565282 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
565301 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
565315 ATCGCAATGCGAAATTAAA
1 ATCGCAATGCGAAATGAAA
565334 ATCGCAA
1 ATCGCAA
565341 CGACAAAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 10 0.31
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 16 0.50
ACGTcount: A:0.46, C:0.19, G:0.20, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:565324 original size:33 final size:33
Alignment explanation
Indices: 565282--565361 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
565272 AAAAATGACT
* *
565282 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
565315 ATCGCAATGCGAAATTAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
565348 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
565362 CTAAATTCAC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:565414 original size:33 final size:33
Alignment explanation
Indices: 565371--565517 Score: 177
Period size: 33 Copynumber: 4.3 Consensus size: 33
565361 ACTAAATTCA
* * *
565371 CGTTGTGATTTTCATTTCGTATTGTGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
565404 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
565437 CGTTGCGATTTTCATTTCGCATTGCGATAGTCTTTTCCG
1 CGTTGCGATTTTCATTTCGCATTGCGAT--TC----CCT
* *
565476 CGTTGCGATTTTTATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
565509 CGTTGCGAT
1 CGTTGCGAT
565518 AGTAATTTTC
Statistics
Matches: 99, Mismatches: 9, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
33 67 0.68
35 2 0.02
37 2 0.02
39 28 0.28
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:565430 original size:19 final size:19
Alignment explanation
Indices: 565406--565504 Score: 100
Period size: 19 Copynumber: 5.4 Consensus size: 19
565396 GATTCCCTCG
565406 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
565425 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
565439 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
** * *
565458 TTGCGATAGTCTTTTCCGCG
1 TTGCGATTTTCATTT-CGCA
*
565478 TTGCGATTTTTATTTCGCA
1 TTGCGATTTTCATTTCGCA
565497 TTGCGATT
1 TTGCGATT
565505 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
14 6 0.10
16 7 0.11
17 7 0.11
19 29 0.46
20 14 0.22
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:569041 original size:20 final size:20
Alignment explanation
Indices: 569018--569243 Score: 244
Period size: 20 Copynumber: 11.2 Consensus size: 20
569008 ATCTCGTTGT
569018 GATTTACAG-ATTCGCATTGC
1 GATTTAC-GTATTCGCATTGC
569038 GATTTACGTATTCGCATTGC
1 GATTTACGTATTCGCATTGC
*
569058 GATTTACGTATTCGCATTGT
1 GATTTACGTATTCGCATTGC
*
569078 GATTTACGTATTCGCATTGT
1 GATTTACGTATTCGCATTGC
569098 GATTTACGTATTCGCATTGC
1 GATTTACGTATTCGCATTGC
* * *
569118 GATTTATGGATACGCATTGC
1 GATTTACGTATTCGCATTGC
* *
569138 GATTTACAG-ATACGCGTTGC
1 GATTTAC-GTATTCGCATTGC
* *
569158 GATTTACGTATTCTCGTTGC
1 GATTTACGTATTCGCATTGC
* * *
569178 GATTTACGGATACGCGTTGC
1 GATTTACGTATTCGCATTGC
*
569198 GATTTTACGTATT-GTCGTTGC
1 GA-TTTACGTATTCG-CATTGC
* *
569219 GATTTACAG-ATACGCGTTGC
1 GATTTAC-GTATTCGCATTGC
569239 GATTT
1 GATTT
569244 TATGGATACT
Statistics
Matches: 184, Mismatches: 15, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.01
20 163 0.89
21 19 0.10
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.39
Consensus pattern (20 bp):
GATTTACGTATTCGCATTGC
Found at i:569078 original size:60 final size:60
Alignment explanation
Indices: 569014--569303 Score: 268
Period size: 60 Copynumber: 4.8 Consensus size: 60
569004 CAGAATCTCG
* *
569014 TTGTGATTTACAGATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCA
1 TTGTGATTTACAGATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGGATACGCA
* *
569074 TTGTGATTTAC-GTATTCGCATTGTGATTTACGTATTCGCATTGCGATTTATGGATACGCA
1 TTGTGATTTACAG-ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGGATACGCA
* * * * * *
569134 TTGCGATTTACAGATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCG
1 TTGTGATTTACAGATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGGATACGCA
* * * * * * *
569194 TTGCGATTTTAC-GTATT-GTCGTTGCGATTTACAG-ATACGCGTTGCGATTTTATGGATACTCG
1 TTGTGA-TTTACAG-ATTCG-CATTGCGATTTAC-GTATTCGCATTGCGA-TTTACGGATACGCA
* * * * *
569256 TTGCGATAGT-CAGAATCGCGTTGCGA-TTATCATATTCGCATTGCGATT
1 TTGTGAT-TTACAGATTCGCATTGCGATTTA-CGTATTCGCATTGCGATT
569304 CTGGAAAATC
Statistics
Matches: 196, Mismatches: 22, Indels: 24
0.81 0.09 0.10
Matches are distributed among these distances:
59 1 0.01
60 117 0.60
61 56 0.29
62 22 0.11
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.39
Consensus pattern (60 bp):
TTGTGATTTACAGATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGGATACGCA
Found at i:569257 original size:41 final size:41
Alignment explanation
Indices: 569010--569283 Score: 204
Period size: 40 Copynumber: 6.8 Consensus size: 41
569000 TAGTCAGAAT
* * * * *
569010 CTCGTTGTGATTTACAGATTCGCATTGCGA-TTTACGTATT
1 CTCGTTGCGATTTACAGATACGCGTTGCGATTTTACGGATA
* * * * * * *
569050 CGCATTGCGATTTAC-GTATTCGCATTGTGA-TTTACGTATT
1 CTCGTTGCGATTTACAG-ATACGCGTTGCGATTTTACGGATA
* * * * * *
569090 CGCATTGTGATTTAC-GTATTCGCATTGCGA-TTTATGGATA
1 CTCGTTGCGATTTACAG-ATACGCGTTGCGATTTTACGGATA
* * * *
569130 CGCATTGCGATTTACAGATACGCGTTGCGA-TTTACGTATT
1 CTCGTTGCGATTTACAGATACGCGTTGCGATTTTACGGATA
* * *
569170 CTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATT
1 CTCGTTGCGATTTACAGATACGCGTTGCGATTTTACGGATA
* *
569211 GTCGTTGCGATTTACAGATACGCGTTGCGATTTTATGGATA
1 CTCGTTGCGATTTACAGATACGCGTTGCGATTTTACGGATA
*
569252 CTCGTTGCGATAGT-CAGA-ATCGCGTTGCGATT
1 CTCGTTGCGAT-TTACAGATA-CGCGTTGCGATT
569284 ATCATATTCG
Statistics
Matches: 204, Mismatches: 25, Indels: 9
0.86 0.11 0.04
Matches are distributed among these distances:
39 1 0.00
40 129 0.63
41 73 0.36
42 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.38
Consensus pattern (41 bp):
CTCGTTGCGATTTACAGATACGCGTTGCGATTTTACGGATA
Found at i:569402 original size:20 final size:19
Alignment explanation
Indices: 569353--569406 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
569343 ATTCTTCATA
569353 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
569372 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
569393 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
569407 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:570459 original size:36 final size:36
Alignment explanation
Indices: 570410--570609 Score: 222
Period size: 36 Copynumber: 5.4 Consensus size: 36
570400 AAAGATTTTG
* *
570410 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAATT
** *
570446 TGTTTCAATG-GAAATTAACGCAAGAGAGACAAAATT
1 TGTTTCAA-GAGAAATTGTCTCAAGAGAGACAAAATT
* * * **
570482 TGTTTCTAGAGAGACAAAATTTATTTCAAGGGAGATGAAATT
1 TGTTTC-A-AGAG---AAA-TTGTCTCAAGAGAGACAAAATT
*
570524 TATTTCAAGAGAAATTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAATT
*
570560 TGTTTCAAGAGAAATTGTCTTAAGAGAGACAAAATT
1 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAATT
570596 TGTTTCAAGAGAAA
1 TGTTTCAAGAGAAA
570610 AAATATCAAG
Statistics
Matches: 138, Mismatches: 18, Indels: 16
0.80 0.10 0.09
Matches are distributed among these distances:
36 101 0.73
37 6 0.04
38 2 0.01
40 4 0.03
41 4 0.03
42 21 0.15
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAATT
Found at i:570493 original size:21 final size:21
Alignment explanation
Indices: 570466--570607 Score: 121
Period size: 21 Copynumber: 7.3 Consensus size: 21
570456 GAAATTAACG
570466 CAAGAGAGACAAAATTTGTTT
1 CAAGAGAGACAAAATTTGTTT
* *
570487 CTAGAGAGACAAAATTTATTT
1 CAAGAGAGACAAAATTTGTTT
* ** *
570508 CAAGGGAGATGAAATTTATTT
1 CAAGAGAGACAAAATTTGTTT
*
570529 C-A-AGAG---AAA-TTGTCT
1 CAAGAGAGACAAAATTTGTTT
570544 CAAGAGAGACAAAATTTGTTT
1 CAAGAGAGACAAAATTTGTTT
570565 C-A-AGAG---AAA-TTGTCTT
1 CAAGAGAGACAAAATTTGT-TT
570581 -AAGAGAGACAAAATTTGTTT
1 CAAGAGAGACAAAATTTGTTT
570601 CAAGAGA
1 CAAGAGA
570608 AAAAATATCA
Statistics
Matches: 97, Mismatches: 10, Indels: 28
0.72 0.07 0.21
Matches are distributed among these distances:
15 9 0.09
16 10 0.10
17 8 0.08
19 7 0.07
20 10 0.10
21 53 0.55
ACGTcount: A:0.42, C:0.09, G:0.20, T:0.29
Consensus pattern (21 bp):
CAAGAGAGACAAAATTTGTTT
Found at i:570604 original size:57 final size:56
Alignment explanation
Indices: 570429--570607 Score: 163
Period size: 57 Copynumber: 3.1 Consensus size: 56
570419 GGAAACTGTC
* **
570429 TCAAGAGAGACAAAATTTGTTTCAATG-GAAATTAACGCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTTTCAA-GAGAAATT-TCTTAAGAGAGACAAAATTTGTT
* * * * *
570486 TCTAGAGAGACAAAATTTATTTCAAGGGAGATGAAATTTATTTCA-AGAG---AAA-TTGTC
1 TCAAGAGAGACAAAATTTGTTTC-A---AGA-GAAATTT-CTTAAGAGAGACAAAATTTGTT
570543 TCAAGAGAGACAAAATTTGTTTCAAGAGAAATTGTCTTAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTTTCAAGAGAAATT-TCTTAAGAGAGACAAAATTTGTT
570600 TCAAGAGA
1 TCAAGAGA
570608 AAAAATATCA
Statistics
Matches: 96, Mismatches: 13, Indels: 26
0.71 0.10 0.19
Matches are distributed among these distances:
52 9 0.09
53 8 0.08
56 4 0.04
57 58 0.60
58 4 0.04
60 1 0.01
61 5 0.05
62 7 0.07
ACGTcount: A:0.42, C:0.09, G:0.20, T:0.28
Consensus pattern (56 bp):
TCAAGAGAGACAAAATTTGTTTCAAGAGAAATTTCTTAAGAGAGACAAAATTTGTT
Found at i:570630 original size:36 final size:36
Alignment explanation
Indices: 570427--570638 Score: 176
Period size: 36 Copynumber: 5.7 Consensus size: 36
570417 AGGGAAACTG
*
570427 TCTCAAGAGAGACAAAATTTGTTTCAATG-GAAATTAA
1 TCTCAAGAGAGACAAAATTTGTTTCAA-GAGAAA-AAA
*
570464 -CGCAAGAGAGACAAAATTTGTTTCTAGAGAGACAAAATTTA
1 TCTCAAGAGAGACAAAATTTGTTTC-A-AGAGA-AAAA---A
* * ** * ***
570505 TTTCAAGGGAGATGAAATTTATTTCAAGAGAAATTG
1 TCTCAAGAGAGACAAAATTTGTTTCAAGAGAAAAAA
***
570541 TCTCAAGAGAGACAAAATTTGTTTCAAGAGAAATTG
1 TCTCAAGAGAGACAAAATTTGTTTCAAGAGAAAAAA
*
570577 TCTTAAGAGAGACAAAATTTGTTTCAAGAGAAAAAA
1 TCTCAAGAGAGACAAAATTTGTTTCAAGAGAAAAAA
* * *
570613 TATCAAGTGAGATAAAATTTTGTTTC
1 TCTCAAGAGAGACAAAA-TTTGTTTC
570639 GAGTAAAAAT
Statistics
Matches: 142, Mismatches: 24, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
36 99 0.70
37 10 0.07
38 4 0.03
39 4 0.03
40 5 0.04
41 2 0.01
42 18 0.13
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.30
Consensus pattern (36 bp):
TCTCAAGAGAGACAAAATTTGTTTCAAGAGAAAAAA
Found at i:570850 original size:86 final size:84
Alignment explanation
Indices: 570690--570894 Score: 254
Period size: 86 Copynumber: 2.4 Consensus size: 84
570680 GTCATCGTTA
* *
570690 ATTCGAAA-TGTTATGAATCAAGCAAA-GAAAATGTTGAAACATCCTTCCTGAAGGTCTTATGGA
1 ATTC-AAAGTGTTGTGAATCGAGCAAATG-AAATGTTGAAACATCCTTCCTGAAGGTCTTATGGA
* *
570753 TGGCCCAAAGGACTTAAGCTG
64 TGGCCCAAAGGACATAAGATG
* *
570774 ATTCAAAGTGTTGTGAATCGAGCAATATGAAATGTTGAAAACAT-TTTGCCTGAAGGTCTTATTG
1 ATTCAAAGTGTTGTGAATCGAGCAA-ATGAAATGTTG-AAACATCCTT-CCTGAAGGTCTTATGG
*
570838 ATGGCCCGAAGGACATAAGATG
63 ATGGCCCAAAGGACATAAGATG
** *
570860 ATTTGAAGTGTTGTGAATCGAGTAAATGAAATGTT
1 ATTCAAAGTGTTGTGAATCGAGCAAATGAAATGTT
570895 AACCCCTCTG
Statistics
Matches: 106, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
83 3 0.03
84 19 0.18
85 21 0.20
86 63 0.59
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (84 bp):
ATTCAAAGTGTTGTGAATCGAGCAAATGAAATGTTGAAACATCCTTCCTGAAGGTCTTATGGATG
GCCCAAAGGACATAAGATG
Found at i:570967 original size:60 final size:60
Alignment explanation
Indices: 570887--571073 Score: 306
Period size: 60 Copynumber: 3.1 Consensus size: 60
570877 TCGAGTAAAT
*
570887 GAAATGTTAACCCCTCTGGTGGGGCATTGTTGATTCAAAGTGTTGTGATTCATGCAATAG
1 GAAATGTTATCCCCTCTGGTGGGGCATTGTTGATTCAAAGTGTTGTGATTCATGCAATAG
* *
570947 GAAATGTTATCCCCTTTGGTGGGGCATTGTTGATTCAAAGTGTTGTGATTCGTGCAATAG
1 GAAATGTTATCCCCTCTGGTGGGGCATTGTTGATTCAAAGTGTTGTGATTCATGCAATAG
* *
571007 GAAATGTTATCCCCTCTGGTGGGGCATTGTTGATTCGAAGTGTTGTGAATCGA-GCAA-AG
1 GAAATGTTATCCCCTCTGGTGGGGCATTGTTGATTCAAAGTGTTGTGATTC-ATGCAATAG
571066 GAAATGTT
1 GAAATGTT
571074 GAAAACATCA
Statistics
Matches: 119, Mismatches: 7, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
59 10 0.08
60 109 0.92
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (60 bp):
GAAATGTTATCCCCTCTGGTGGGGCATTGTTGATTCAAAGTGTTGTGATTCATGCAATAG
Found at i:571261 original size:144 final size:144
Alignment explanation
Indices: 570990--571262 Score: 438
Period size: 144 Copynumber: 1.9 Consensus size: 144
570980 TTCAAAGTGT
* * * *
570990 TGTGATTCGTGCAATAGGAAATGTTATCCCCTCTGGTGGGGCATTGTTGATTCGAAGTGTTGTGA
1 TGTGAATCGAGCAATAGGAAATGTTAACCCCTCTGGTGGGGCATTGCTGATTCGAAGTGTTGTGA
*
571055 ATCGAGCAAAGGAAATGTTGAAAACATCATGCCCAAAGGTCTTATGGATGACTCAAAGGACTTAA
66 ATCGAGCAAAGGAAATGTTGAAAACATCATGCCCAAAGGTCTTATGGATGACCCAAAGGACTTAA
571120 GCTGATTCGAATTG
131 GCTGATTCGAATTG
*
571134 TGTGAATCGAGCAATAGGAAATGTTAACCCCTCTGGTGGGGCGTTGCTGATTCGAAGTGTTGTGA
1 TGTGAATCGAGCAATAGGAAATGTTAACCCCTCTGGTGGGGCATTGCTGATTCGAAGTGTTGTGA
* * * * * *
571199 ATTGAGCAAAGGAAATGTTGAAAACATCCTTCCCAAAGGTCTTATGGATGGCCCGAATGACTTA
66 ATCGAGCAAAGGAAATGTTGAAAACATCATGCCCAAAGGTCTTATGGATGACCCAAAGGACTTA
571263 TTATCTTGCT
Statistics
Matches: 117, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
144 117 1.00
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (144 bp):
TGTGAATCGAGCAATAGGAAATGTTAACCCCTCTGGTGGGGCATTGCTGATTCGAAGTGTTGTGA
ATCGAGCAAAGGAAATGTTGAAAACATCATGCCCAAAGGTCTTATGGATGACCCAAAGGACTTAA
GCTGATTCGAATTG
Found at i:571522 original size:53 final size:53
Alignment explanation
Indices: 571407--571604 Score: 214
Period size: 54 Copynumber: 3.9 Consensus size: 53
571397 TTTCAGTTAT
* * * * * * *
571407 CATCAAGAAACCCCTAAAAATTAGTCTTAACATCTTTAAAAATTCATTTGAAAA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTT-CAAATTCATATGAAAA
* *
571461 CATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCCTTCAAATTCATATGAAAA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTTCAAATTCATATGAAAA
* * *
571514 CATTAAGAAA-CCCTAAAAATTAGGCTTAGCTTCTTTC----TC-TA--AAAA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTTCAAATTCATATGAAAA
*
571559 CATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTTTAAATTCAT
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTTCAAATTCAT
571605 CATGTCAAGA
Statistics
Matches: 120, Mismatches: 18, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
45 13 0.11
46 24 0.20
47 2 0.02
48 2 0.02
50 2 0.02
51 1 0.01
52 23 0.19
53 23 0.19
54 30 0.25
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.29
Consensus pattern (53 bp):
CATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTTCAAATTCATATGAAAA
Found at i:571591 original size:46 final size:49
Alignment explanation
Indices: 571456--571595 Score: 171
Period size: 46 Copynumber: 2.9 Consensus size: 49
571446 AAATTCATTT
* *
571456 GAAAACATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCCTTCAAATTCATA
1 GAAAACATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTTC--A-TCATA
* * *
571508 TGAAAACATTAAGAAA-CCCTAAAAATTAGGCTTAGCTTCTTTC-TC-TA
1 -GAAAACATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTTCATCATA
571555 -AAAACATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTT
1 GAAAACATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTT
571596 TAAATTCATC
Statistics
Matches: 78, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
45 13 0.17
46 24 0.31
47 2 0.03
48 2 0.03
52 23 0.29
53 14 0.18
ACGTcount: A:0.39, C:0.22, G:0.11, T:0.27
Consensus pattern (49 bp):
GAAAACATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTTCATCATA
Found at i:571682 original size:55 final size:55
Alignment explanation
Indices: 571609--571806 Score: 225
Period size: 55 Copynumber: 3.6 Consensus size: 55
571599 ATTCATCATG
* * *
571609 TCAAGAAACCTCTGAAAATCAGACTTAATTTCTTTGAAAGCTCATTTAAAAATCA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTTAAAAATCA
* * * * * *
571664 TTATGAAACTTCTGAAAATAAAACTTAGTTTCTTTAAAAACTCATTTAAAAATCG
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTTAAAAATCA
* * * *
571719 TCAAGAAACTTTTGAAAATCAGACTTAGTTTATTTGAAAATTCATTTAAAAATAA
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTTAAAAATCA
* * * * * *
571774 TCAATAAATTTTTTAAAATCGGATTTAGTTTCT
1 TCAAGAAACTTCTGAAAATCAGACTTAGTTTCT
571807 AAAAAAATCA
Statistics
Matches: 118, Mismatches: 25, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
55 118 1.00
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.37
Consensus pattern (55 bp):
TCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAACTCATTTAAAAATCA
Found at i:573090 original size:28 final size:28
Alignment explanation
Indices: 573049--573111 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
573039 GATATAAAGC
*
573049 TTAGGTTGACTTGGGAAGGTAATGTGTT
1 TTAGGTTAACTTGGGAAGGTAATGTGTT
* *
573077 TTAGGTTAATTTGGGGAGGTAATGTGTT
1 TTAGGTTAACTTGGGAAGGTAATGTGTT
*
573105 TCAGGTT
1 TTAGGTT
573112 GGCTTATTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.21, C:0.03, G:0.35, T:0.41
Consensus pattern (28 bp):
TTAGGTTAACTTGGGAAGGTAATGTGTT
Found at i:582494 original size:149 final size:149
Alignment explanation
Indices: 582244--582705 Score: 840
Period size: 149 Copynumber: 3.1 Consensus size: 149
582234 TATAATTGCA
*
582244 CCGAAGCG-CCGCGTAGAATTGCACTGTAGTGCCATATAATAATGTCCATAAGGACCACATATTA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTA
582308 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
582373 CCACAGAATATATATATATC
130 CCACAGAATATATATATATC
582393 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
582458 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
582523 CACAG-A-ATATATATATC
131 CACAGAATATATATATATC
*
582540 CCGAAGGACCGCGTAGAATTTCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
*
582605 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTT
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
* * *
582670 CAAAGAATATACATATGTC
131 CACAGAATATATATATATC
582689 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
582706 CCCTCGACTC
Statistics
Matches: 304, Mismatches: 6, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
147 143 0.47
148 3 0.01
149 158 0.52
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.28
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CACAGAATATATATATATC
Found at i:584170 original size:63 final size:63
Alignment explanation
Indices: 584064--584222 Score: 201
Period size: 63 Copynumber: 2.5 Consensus size: 63
584054 TAATGGAGGC
* * * * * **
584064 ATGCATCGATGCACTCATGATGCATCGATGCACTGAGGGCATTCGATGTTCATTTTATTAGAA
1 ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTCATATTAAAAGAA
** **
584127 ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTTGTATTAAAATTA
1 ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTCATATTAAAAGAA
* *
584190 ATGCATCGATGCACTTCATATGCATCGATGCAC
1 ATGCATCGATGCACTCCTTATGCATCGATGCAC
584223 CTTCAACAAA
Statistics
Matches: 83, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 83 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.31
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTCATATTAAAAGAA
Found at i:584214 original size:19 final size:20
Alignment explanation
Indices: 584190--584227 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
584180 ATTAAAATTA
584190 ATGCATCGATGCA-CTTCAT
1 ATGCATCGATGCACCTTCAT
584209 ATGCATCGATGCACCTTCA
1 ATGCATCGATGCACCTTCA
584228 ACAAATTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
ATGCATCGATGCACCTTCAT
Found at i:587723 original size:149 final size:149
Alignment explanation
Indices: 587340--587801 Score: 847
Period size: 149 Copynumber: 3.1 Consensus size: 149
587330 TATAATTGCA
* *
587340 CCGAAGTACCACGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
587405 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
*
587470 CACA-TA-ATATATATATC
131 CACAGAATATATATATATC
*
587487 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCTATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
587552 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
587617 CACAGAATATATATATATC
131 CACAGAATATATATATATC
587636 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
587701 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
* * *
587766 CAAAGAATATACATATGTC
131 CACAGAATATATATATATC
587785 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
587802 CCCTCGACTC
Statistics
Matches: 305, Mismatches: 8, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
147 131 0.43
148 1 0.00
149 173 0.57
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CACAGAATATATATATATC
Found at i:589263 original size:63 final size:63
Alignment explanation
Indices: 589157--589315 Score: 210
Period size: 63 Copynumber: 2.5 Consensus size: 63
589147 TAATGGAGGC
* * * * **
589157 ATGCATCGATGCACTCCTGATGCATCGATGCACTGAGGGCATTCGATGTTCATTTTATTAGAA
1 ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTCATATTAAAAGAA
** **
589220 ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTTGTATTAAAATTA
1 ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTCATATTAAAAGAA
* *
589283 ATGCATCGATGCACTTCATATGCATCGATGCAC
1 ATGCATCGATGCACTCCTTATGCATCGATGCAC
589316 CTTCAACAAA
Statistics
Matches: 84, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
63 84 1.00
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.31
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTCATATTAAAAGAA
Found at i:589307 original size:19 final size:20
Alignment explanation
Indices: 589283--589320 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
589273 ATTAAAATTA
589283 ATGCATCGATGCA-CTTCAT
1 ATGCATCGATGCACCTTCAT
589302 ATGCATCGATGCACCTTCA
1 ATGCATCGATGCACCTTCA
589321 ACAAATTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
ATGCATCGATGCACCTTCAT
Found at i:604651 original size:39 final size:41
Alignment explanation
Indices: 604608--604697 Score: 112
Period size: 39 Copynumber: 2.2 Consensus size: 41
604598 TTCTATCTTT
* *
604608 TATGTTATGCTCACGAAACCAAA-TTTTT-TTCTTTTCAAA
1 TATGTTATGCCCACAAAACCAAATTTTTTCTTCTTTTCAAA
**
604647 TATGTTATGCCCACAAAATTAAACTTTTTTTCTTCTTTTCAAA
1 TATGTTATGCCCACAAAACCAAA--TTTTTTCTTCTTTTCAAA
604690 TATGTTAT
1 TATGTTAT
604698 ACACACGGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
39 19 0.44
42 5 0.12
43 19 0.44
ACGTcount: A:0.30, C:0.17, G:0.07, T:0.47
Consensus pattern (41 bp):
TATGTTATGCCCACAAAACCAAATTTTTTCTTCTTTTCAAA
Found at i:604714 original size:43 final size:42
Alignment explanation
Indices: 604631--604719 Score: 115
Period size: 43 Copynumber: 2.1 Consensus size: 42
604621 CGAAACCAAA
* * * *
604631 TTTTTTTCTTTTCAAATATGTTATGCCCACAAAATTAAACTT
1 TTTTTTTCTTTTCAAATATGTTATACACACAAAATAAAACTC
**
604673 TTTTTCTTCTTTTCAAATATGTTATACACACGGAATAAAACTC
1 TTTTT-TTCTTTTCAAATATGTTATACACACAAAATAAAACTC
604716 TTTT
1 TTTT
604720 CTACTCCTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
42 5 0.12
43 35 0.88
ACGTcount: A:0.30, C:0.17, G:0.06, T:0.47
Consensus pattern (42 bp):
TTTTTTTCTTTTCAAATATGTTATACACACAAAATAAAACTC
Found at i:608160 original size:2 final size:2
Alignment explanation
Indices: 608153--608192 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
608143 GGGATAAAGT
* *
608153 TA TA TA TA TA TA TA TA TA CA TA TA TA TA TG TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
608193 TTTAGTTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:609938 original size:12 final size:12
Alignment explanation
Indices: 609905--609939 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
609895 ATCGTGGATC
609905 GAAGAAGAAGAT
1 GAAGAAGAAGAT
* *
609917 GATGATGAAGAT
1 GAAGAAGAAGAT
609929 GAAGAAGAAGA
1 GAAGAAGAAGA
609940 AGAGGGTAGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.34, T:0.11
Consensus pattern (12 bp):
GAAGAAGAAGAT
Found at i:613125 original size:31 final size:31
Alignment explanation
Indices: 613084--613172 Score: 151
Period size: 31 Copynumber: 2.9 Consensus size: 31
613074 GAGTCGAGGG
* *
613084 TTACCAATGTTCTTTGGGACATATGGACTGT
1 TTACCTATGTTCTTTGGGACATATGGACTAT
613115 TTACCTATGTTCTTTGGGACATATGGACTAT
1 TTACCTATGTTCTTTGGGACATATGGACTAT
*
613146 TTACCTATGTTCTTTGGAACATATGGA
1 TTACCTATGTTCTTTGGGACATATGGA
613173 TTGGTCCTTC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (31 bp):
TTACCTATGTTCTTTGGGACATATGGACTAT
Found at i:619885 original size:19 final size:19
Alignment explanation
Indices: 619863--619905 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
619853 TCCTATTATT
*
619863 TTATTTTTTTTAGTTAAAA
1 TTATTTTTTTTAGATAAAA
* *
619882 TTATATTTTTTAGATAAAC
1 TTATTTTTTTTAGATAAAA
619901 TTATT
1 TTATT
619906 AATTGACTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (19 bp):
TTATTTTTTTTAGATAAAA
Found at i:622455 original size:79 final size:79
Alignment explanation
Indices: 622319--622477 Score: 300
Period size: 79 Copynumber: 2.0 Consensus size: 79
622309 TGAGATCCCA
*
622319 TATTGGCAAGTAAAAGATTTTGTATATCATTTAAAAATCCCAATATTAGACACTTACACTGCCCC
1 TATTGGCAAGTAAAAGATTTTGTATATCATTTAAAAATCCCAATATTAGACAATTACACTGCCCC
622384 TCCAAGTTGAGCAC
66 TCCAAGTTGAGCAC
*
622398 TATTGGCAAGTAAAAGATTTTGTATATCATTTAAAAATCCCAATATTAGACAATTACATTGCCCC
1 TATTGGCAAGTAAAAGATTTTGTATATCATTTAAAAATCCCAATATTAGACAATTACACTGCCCC
622463 TCCAAGTTGAGCAC
66 TCCAAGTTGAGCAC
622477 T
1 T
622478 GGTTGAGAGC
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (79 bp):
TATTGGCAAGTAAAAGATTTTGTATATCATTTAAAAATCCCAATATTAGACAATTACACTGCCCC
TCCAAGTTGAGCAC
Found at i:626844 original size:69 final size:69
Alignment explanation
Indices: 626733--626865 Score: 257
Period size: 69 Copynumber: 1.9 Consensus size: 69
626723 TACTTGCCAC
*
626733 AAACTAAATGGCCGCCATTACTACCCTAAGGTTTGATTCGGTTATAGTGTATAAATGCAAAAACT
1 AAACTAAATGGCCACCATTACTACCCTAAGGTTTGATTCGGTTATAGTGTATAAATGCAAAAACT
626798 AACT
66 AACT
626802 AAACTAAATGGCCACCATTACTACCCTAAGGTTTGATTCGGTTATAGTGTATAAATGCAAAAAC
1 AAACTAAATGGCCACCATTACTACCCTAAGGTTTGATTCGGTTATAGTGTATAAATGCAAAAAC
626866 CAACCGTTAA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
69 63 1.00
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.29
Consensus pattern (69 bp):
AAACTAAATGGCCACCATTACTACCCTAAGGTTTGATTCGGTTATAGTGTATAAATGCAAAAACT
AACT
Found at i:629584 original size:153 final size:153
Alignment explanation
Indices: 629310--629585 Score: 401
Period size: 153 Copynumber: 1.8 Consensus size: 153
629300 CAAGATGCTG
* * *
629310 AAGCTTTGAAAGTCGAGTAAGGGACGGATGTATGCTGATGAAATTGTTACCACTAAGATTAAGAT
1 AAGCTTGGAAAGTCGAGTAAGGGACGGAGGTATGCTGATGAAATTGTTACCACTAAGATCAAGAT
* * *
629375 GGGCCAAAGAGGATAGATAAGAAACATCATTAGGAATATCTAATTCACCAATATTGCACATGCCA
66 GGGCCAAAGAGGATAGACAAGAAACATCACTAGGAATATCTAATTCACCAAGATTGCACATGCCA
629440 CAATTTGATAATCTAAGAGATTC
131 CAATTTGATAATCTAAGAGATTC
*
629463 AAGCTTGGAAAGTCGAGTAAGGGACGGAGGTATGCTGATGAAATTGTTACCAGTAAGATCAAG-T
1 AAGCTTGGAAAGTCGAGTAAGGGACGGAGGTATGCTGATGAAATTGTTACCACTAAGATCAAGAT
** ** * ** *
629527 CGTTCCAAAGAGGATAGACGTGAAATATCACTAGGAATATCTTCTTCTCCAAGATTGCA
66 -GGGCCAAAGAGGATAGACAAGAAACATCACTAGGAATATCTAATTCACCAAGATTGCA
629586 GTCCTTTAGT
Statistics
Matches: 107, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
152 1 0.01
153 106 0.99
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.26
Consensus pattern (153 bp):
AAGCTTGGAAAGTCGAGTAAGGGACGGAGGTATGCTGATGAAATTGTTACCACTAAGATCAAGAT
GGGCCAAAGAGGATAGACAAGAAACATCACTAGGAATATCTAATTCACCAAGATTGCACATGCCA
CAATTTGATAATCTAAGAGATTC
Found at i:631583 original size:35 final size:36
Alignment explanation
Indices: 631537--631630 Score: 122
Period size: 35 Copynumber: 2.7 Consensus size: 36
631527 CACAATCATT
* *
631537 AATTACATTCTAAACCCT-ATATTCCAAAATATTTC
1 AATTACATTCTAAACCCTCAAATTCCAAAATACTTC
*
631572 AATTACATTCTAAA-TCTCAAATTCCAAAATACTTC
1 AATTACATTCTAAACCCTCAAATTCCAAAATACTTC
* *
631607 AATTACATGCTCAACCC-CAAATTC
1 AATTACATTCTAAACCCTCAAATTC
631631 ATAATACATT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
34 2 0.04
35 48 0.94
36 1 0.02
ACGTcount: A:0.40, C:0.26, G:0.01, T:0.33
Consensus pattern (36 bp):
AATTACATTCTAAACCCTCAAATTCCAAAATACTTC
Found at i:637979 original size:15 final size:15
Alignment explanation
Indices: 637959--637988 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
637949 GCATATTGAA
*
637959 ATTAGACATCATTTC
1 ATTAGAAATCATTTC
637974 ATTAGAAATCATTTC
1 ATTAGAAATCATTTC
637989 GCTAAAGAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.40
Consensus pattern (15 bp):
ATTAGAAATCATTTC
Found at i:638420 original size:23 final size:22
Alignment explanation
Indices: 638390--638468 Score: 88
Period size: 23 Copynumber: 3.5 Consensus size: 22
638380 CACTAGCTAG
638390 TGCATCGATGCATCCTTTGAATA
1 TGCATCGATGCATCC-TTGAATA
* * *
638413 TGCATCGATACAT-CATGAAGA
1 TGCATCGATGCATCCTTGAATA
* *
638434 TGCACCGATGCATTCCTTGAATG
1 TGCATCGATGCA-TCCTTGAATA
638457 TGCATCGATGCA
1 TGCATCGATGCA
638469 CTCTGCCGTG
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
21 15 0.33
22 2 0.04
23 28 0.62
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (22 bp):
TGCATCGATGCATCCTTGAATA
Found at i:638981 original size:13 final size:13
Alignment explanation
Indices: 638963--638987 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
638953 ACACATTGAT
638963 TTTTCAAAATTTG
1 TTTTCAAAATTTG
638976 TTTTCAAAATTT
1 TTTTCAAAATTT
638988 TTCAAAACTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.04, T:0.56
Consensus pattern (13 bp):
TTTTCAAAATTTG
Found at i:642199 original size:149 final size:147
Alignment explanation
Indices: 642009--642275 Score: 435
Period size: 149 Copynumber: 1.8 Consensus size: 147
641999 TTAACTCAAC
* *
642009 ATATTATAAATATTTATAATTAAATTTAAACAGAAACTCAAAAATTCAATTCAATTCGACTTGAT
1 ATATGATAAATATTTATAATTAAATTTAAACAGAAAATCAAAAATTCAATTCAATTCGACTTGAT
* *
642074 TTAAATTTTATAAAAATCAAATCGAAAAAATTTCGAGTCAACTATTTTATAAACTAAACTTAATT
66 TTAAATTTTAT-AAAATCAAAT-AAAAAAAATTCGAGTCAACTATTTTATAAACTAAACTTAATT
642139 AGAATCAAATAATATTATA
129 AGAATCAAATAATATTATA
* * *
642158 ATATGATAAATATTTATATTTAAATTTAAACAGAAAATCAAAAATTTAATTCAATTCGACTTTAT
1 ATATGATAAATATTTATAATTAAATTTAAACAGAAAATCAAAAATTCAATTCAATTCGACTTGAT
* *
642223 TTAAATTTTATAAACTCAAATAAAAAAAATTCGAGTTAACTATTTTATAAACT
66 TTAAATTTTATAAAATCAAATAAAAAAAATTCGAGTCAACTATTTTATAAACT
642276 GAATTGAGTA
Statistics
Matches: 109, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
147 29 0.27
148 9 0.08
149 71 0.65
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.37
Consensus pattern (147 bp):
ATATGATAAATATTTATAATTAAATTTAAACAGAAAATCAAAAATTCAATTCAATTCGACTTGAT
TTAAATTTTATAAAATCAAATAAAAAAAATTCGAGTCAACTATTTTATAAACTAAACTTAATTAG
AATCAAATAATATTATA
Found at i:642433 original size:35 final size:35
Alignment explanation
Indices: 642394--642461 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
642384 TTGCTGCTTC
642394 AAGTATTTTGGAATTTGAGATTTAGAATGTAATCA
1 AAGTATTTTGGAATTTGAGATTTAGAATGTAATCA
*
642429 AAGTATTTTGGAATTTGGGATTTAGAATGTAAT
1 AAGTATTTTGGAATTTGAGATTTAGAATGTAAT
642462 TGATGACTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.35, C:0.01, G:0.22, T:0.41
Consensus pattern (35 bp):
AAGTATTTTGGAATTTGAGATTTAGAATGTAATCA
Found at i:642743 original size:29 final size:29
Alignment explanation
Indices: 642710--642769 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
642700 ATATTATAAA
642710 CTAAATATGAGATTAAACGAAAATCAGGC
1 CTAAATATGAGATTAAACGAAAATCAGGC
642739 CTAAATATGAGATTAAACGAAAATCAGGC
1 CTAAATATGAGATTAAACGAAAATCAGGC
642768 CT
1 CT
642770 GTCCTAATAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.47, C:0.15, G:0.17, T:0.22
Consensus pattern (29 bp):
CTAAATATGAGATTAAACGAAAATCAGGC
Found at i:644359 original size:59 final size:61
Alignment explanation
Indices: 644265--644378 Score: 137
Period size: 59 Copynumber: 1.9 Consensus size: 61
644255 AGAACATATG
** *
644265 AATAATCGAGTGACTCAACAAAGCAACATATTATAAT-CAGAGACTATTT-TATAACTTAT
1 AATAATCGAGAAACTCAACAAAGCAACATATTATAATAAAGAGACTATTTGTATAACTTAT
* *
644324 AATAATCGAGAAACTCAACTAAA-CAATATCA-TATAATAAAGAGATTATTTGTATA
1 AATAATCGAGAAACTCAAC-AAAGCAACAT-ATTATAATAAAGAGACTATTTGTATA
644379 CTTTCTCCTA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
59 28 0.61
60 14 0.30
61 4 0.09
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.30
Consensus pattern (61 bp):
AATAATCGAGAAACTCAACAAAGCAACATATTATAATAAAGAGACTATTTGTATAACTTAT
Found at i:644882 original size:60 final size:60
Alignment explanation
Indices: 644791--644909 Score: 157
Period size: 60 Copynumber: 2.0 Consensus size: 60
644781 TACAGAAACA
* * * * * *
644791 GTCCCCCGACCATAGGGTGATGTTTTTTTAAGTCTCTCGACTATTAAAAGTTATAAAATG
1 GTCCCCCGACCATAGGGTGATGCTTTGTTAAGTCCCCCAACTATTAAAAGTTACAAAATG
* * *
644851 GTCCCCTGACTATAGGGTGTTGCTTTGTTAAGTCCCCCAACTATTAAAAGTTACAAAAT
1 GTCCCCCGACCATAGGGTGATGCTTTGTTAAGTCCCCCAACTATTAAAAGTTACAAAAT
644910 AGTCACCAAC
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.34
Consensus pattern (60 bp):
GTCCCCCGACCATAGGGTGATGCTTTGTTAAGTCCCCCAACTATTAAAAGTTACAAAATG
Found at i:652844 original size:153 final size:153
Alignment explanation
Indices: 652589--652864 Score: 419
Period size: 153 Copynumber: 1.8 Consensus size: 153
652579 CAAGATGCTG
* *
652589 AAGCTTCGAAAGTCGAGTAAGGGACGGATGTATGCTGATGAAATTGTTACCACTAAGATCAAGAT
1 AAGCTTCGAAAGTCGAGCAAGGGACGGAGGTATGCTGATGAAATTGTTACCACTAAGATCAAGAT
*
652654 GGCACAAAGAGGATAGATAAGAAACATCACTAGGAATATCTAATTCACCAAGATTGCACATGCCA
66 GGCACAAAGAGGATAGACAAGAAACATCACTAGGAATATCTAATTCACCAAGATTGCACATGCCA
652719 CAATTTGATAATCTAAGATATGT
131 CAATTTGATAATCTAAGATATGT
*
652742 AAGCTTGGAAAGTCGAGCAAGGGACGGAGGTATGCTGATGAAATTGTTACCACTAAGATCAAG-T
1 AAGCTTCGAAAGTCGAGCAAGGGACGGAGGTATGCTGATGAAATTGTTACCACTAAGATCAAGAT
*** ** * ** *
652806 CGTTTCAAAGAGGATAGACGTGAAATATCACTAGGAATATCTTCTTCTCCAAGATTGCA
66 -GGCACAAAGAGGATAGACAAGAAACATCACTAGGAATATCTAATTCACCAAGATTGCA
652865 GTCCCTTATT
Statistics
Matches: 109, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
152 1 0.01
153 108 0.99
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (153 bp):
AAGCTTCGAAAGTCGAGCAAGGGACGGAGGTATGCTGATGAAATTGTTACCACTAAGATCAAGAT
GGCACAAAGAGGATAGACAAGAAACATCACTAGGAATATCTAATTCACCAAGATTGCACATGCCA
CAATTTGATAATCTAAGATATGT
Found at i:658675 original size:57 final size:58
Alignment explanation
Indices: 658603--658715 Score: 149
Period size: 59 Copynumber: 1.9 Consensus size: 58
658593 TACACAAACA
* *
658603 GTCCCCCGACCATAGGGTATT-TTT-TTAAGTCTCTCGACTATTAAAAGTTACAAAATG
1 GTCCCCCGACCATAGGGTATTCTTTGTTAAGTC-CCCGACTATTAAAAATTACAAAATG
* * *
658660 GTCCCCTGACTATAGGGTGTTGCTTTGTTAAGTCCCCGACTATTAAAAATTACAAA
1 GTCCCCCGACCATAGGGTATT-CTTTGTTAAGTCCCCGACTATTAAAAATTACAAA
658716 TTAGTCACCC
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
57 18 0.38
59 23 0.48
60 7 0.15
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (58 bp):
GTCCCCCGACCATAGGGTATTCTTTGTTAAGTCCCCGACTATTAAAAATTACAAAATG
Found at i:661640 original size:23 final size:23
Alignment explanation
Indices: 661610--661654 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
661600 TTACTATCTT
661610 TACAGGGAGAGGCACCGTTATTC
1 TACAGGGAGAGGCACCGTTATTC
661633 TACAGGGAGAGGCACCGTTATT
1 TACAGGGAGAGGCACCGTTATT
661655 AAATAACCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22
Consensus pattern (23 bp):
TACAGGGAGAGGCACCGTTATTC
Found at i:663502 original size:34 final size:35
Alignment explanation
Indices: 663459--663527 Score: 122
Period size: 34 Copynumber: 2.0 Consensus size: 35
663449 AAACCTGCAG
663459 GGGGAATCGGTACCCCCTG-GGGGAATCTGTTCCC
1 GGGGAATCGGTACCCCCTGAGGGGAATCTGTTCCC
*
663493 GGGGAATCGGTACCCCCTGAGGGGAATTTGTTCCC
1 GGGGAATCGGTACCCCCTGAGGGGAATCTGTTCCC
663528 TCTGGGCAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 19 0.58
35 14 0.42
ACGTcount: A:0.16, C:0.28, G:0.35, T:0.22
Consensus pattern (35 bp):
GGGGAATCGGTACCCCCTGAGGGGAATCTGTTCCC
Found at i:663745 original size:19 final size:20
Alignment explanation
Indices: 663721--663760 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
663711 AATTTAATCG
*
663721 AATATATAAT-TTAAAATTC
1 AATATAAAATCTTAAAATTC
663740 AATATAAAATCTTAAAATTC
1 AATATAAAATCTTAAAATTC
663760 A
1 A
663761 TTAACACTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
AATATAAAATCTTAAAATTC
Found at i:667259 original size:19 final size:20
Alignment explanation
Indices: 667235--667274 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
667225 AATTTAATCG
*
667235 AATATATAAT-TTAAAATTC
1 AATATAAAATCTTAAAATTC
667254 AATATAAAATCTTAAAATTC
1 AATATAAAATCTTAAAATTC
667274 A
1 A
667275 TTAACACTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
AATATAAAATCTTAAAATTC
Found at i:671813 original size:20 final size:20
Alignment explanation
Indices: 671788--671827 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
671778 TCATTTAGGA
*
671788 TGATCTGGGTGTAAATGGGC
1 TGATCTGGGTATAAATGGGC
671808 TGATCTGGGTATAAATGGGC
1 TGATCTGGGTATAAATGGGC
671828 CTCCGGGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.10, G:0.38, T:0.30
Consensus pattern (20 bp):
TGATCTGGGTATAAATGGGC
Found at i:672430 original size:115 final size:116
Alignment explanation
Indices: 672283--673062 Score: 955
Period size: 115 Copynumber: 6.7 Consensus size: 116
672273 TAAGGCAAGT
* *
672283 TTGAATAAATTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
*
672348 ACTTCTGGAAATGTTGATCTATCTCTTTCTGTGATAGAATCATGCAAAAGG
66 ACTTCTGGAAATGTTGATCTATCTCCTTCTGTGATAGAATCATGCAAAAGG
*
672399 TTGAACAAGTTCTT-TCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTTATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
* *
672463 ACTTCTGGAAATGTTGATATATCTCCTTCTGTGATAGAATCATGTAAAAGG
66 ACTTCTGGAAATGTTGATCTATCTCCTTCTGTGATAGAATCATGCAAAAGG
672514 TTGAACAAGTTCTTCTCATTATGAACTT-TTCTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
672578 ACTTCTGGAAATGTTGATCTATCTCCTTCTGTGATAGAATCATGCAAAAGG
66 ACTTCTGGAAATGTTGATCTATCTCCTTCTGTGATAGAATCATGCAAAAGG
* *
672629 TTGAATAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGTGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
*
672694 ACTTCTGGAAATGTTTATCTTGATCTATCTCCTTCTGTGATAGAATCA--AATAAAGG
66 ACTTCTGGAAATG------TTGATCTATCTCCTTCTGTGATAGAATCATGCA-AAAGG
*
672750 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATTATGAA
** ** * ** *
672814 CTTTCTCTGGAAAAATTGATCCA--T-C--GAGTGAT-GAATTCAAGCAAAAGG
65 CACT-TCTGGAAATGTTGATCTATCTCCTTCTGTGATAGAA-TCATGCAAAAGG
*
672862 TTGAACCAAGTTCTTCTCATTATGAACTTCTCCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 TTGAA-CAAGTTCTTCTCATTATGAACTTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATTATGA
* * ** * *** ** * * * *
672927 ACTCTCCCT-GACAATACTGATCCATCGAATAATGAGTTTG-AGCA---AAAAGG
64 ACACT-TCTGGA-AATGTTGATCTATCTCCTTCTGTGATAGAATCATGCAAAAGG
* * *
672977 TTGAACAAATTCTTCTCATTACGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAA
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATTATGAA
*
673042 C-TTTACCTGGAAATGTTGATC
65 CACTT--CTGGAAATGTTGATC
673063 CATTGAGTGA
Statistics
Matches: 594, Mismatches: 44, Indels: 54
0.86 0.06 0.08
Matches are distributed among these distances:
110 3 0.01
111 8 0.01
112 10 0.02
113 35 0.06
114 111 0.19
115 235 0.40
116 80 0.13
118 2 0.00
119 4 0.01
120 2 0.00
121 64 0.11
122 40 0.07
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (116 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
ACTTCTGGAAATGTTGATCTATCTCCTTCTGTGATAGAATCATGCAAAAGG
Found at i:672948 original size:114 final size:114
Alignment explanation
Indices: 672745--673081 Score: 482
Period size: 114 Copynumber: 3.0 Consensus size: 114
672735 AGAATCAAAT
672745 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATT
* *
672809 ATGAACTTTCTCTGGAAAAATTGATCCATCGAGTGATGAATTCAAGC-A
66 ATGAACTTTCCCTGGAAATATTGATCCATCGAGTGATGAATTCAAGCAA
* *
672857 AAAGGTTGAACCAAGTTCTTCTCATTATGAACTTCTCCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAGGTTGAA-CAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCAT
* * * * * **
672922 TATGAACTCTCCCT-GACAATACTGATCCATCGAATAATGAGTTTGAGCAA
65 TATGAACTTTCCCTGGA-AATATTGATCCATCGAGTGATGAATTCAAGCAA
* *
672972 AAAGGTTGAACAAATTCTTCTCATTACGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATT
* * * *
673037 ATGAACTTTACCTGGAAATGTTGATCCATTGAGTGATGGATTCAA
66 ATGAACTTTCCCTGGAAATATTGATCCATCGAGTGATGAATTCAA
673082 ATTTTTGCTA
Statistics
Matches: 194, Mismatches: 26, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
112 10 0.05
113 32 0.16
114 139 0.72
115 13 0.07
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.36
Consensus pattern (114 bp):
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATT
ATGAACTTTCCCTGGAAATATTGATCCATCGAGTGATGAATTCAAGCAA
Found at i:674259 original size:18 final size:18
Alignment explanation
Indices: 674222--674259 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
674212 TATGTGAAAG
*
674222 AATAAATTGAATTTCGAA
1 AATAAATTGAATTTCAAA
674240 AATAAATTGAATTTCAAA
1 AATAAATTGAATTTCAAA
674258 AA
1 AA
674260 GATAATCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.55, C:0.05, G:0.08, T:0.32
Consensus pattern (18 bp):
AATAAATTGAATTTCAAA
Found at i:681955 original size:15 final size:15
Alignment explanation
Indices: 681918--681966 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
681908 AACTATAAAG
681918 AAAAT-AATGTAATG-
1 AAAATGAATGT-ATGC
681932 AATAATGAATGTATGC
1 AA-AATGAATGTATGC
681948 AAAATGAATGTATGC
1 AAAATGAATGTATGC
681963 AAAA
1 AAAA
681967 GGTATTGATC
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
14 2 0.06
15 23 0.72
16 7 0.22
ACGTcount: A:0.53, C:0.04, G:0.16, T:0.27
Consensus pattern (15 bp):
AAAATGAATGTATGC
Found at i:684757 original size:4 final size:4
Alignment explanation
Indices: 684748--684774 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
684738 TTCATAAAGA
684748 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
684775 AAGGAAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:685287 original size:29 final size:27
Alignment explanation
Indices: 685254--685338 Score: 80
Period size: 28 Copynumber: 3.0 Consensus size: 27
685244 TAAAAACATT
685254 AATAAAAAGTAATATATAAATATTATGAA
1 AATAAAAAGT-ATATATAAA-ATTATGAA
* *
685283 AATAATAAGTATATATAAAATTTTGAA
1 AATAAAAAGTATATATAAAATTATGAA
* * * *
685310 AAGAAAGAATTATAAATTAAATATATGAA
1 AATAAA-AAGTATATATAAAAT-TATGAA
685339 TTTTTAATTT
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
27 11 0.24
28 21 0.46
29 14 0.30
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (27 bp):
AATAAAAAGTATATATAAAATTATGAA
Found at i:685288 original size:22 final size:23
Alignment explanation
Indices: 685233--685289 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 23
685223 ATTTAATACT
*
685233 TGAAAATAAAATAAAAACATTAA
1 TGAAAATAATATAAAAACATTAA
* * *
685256 TAAAAAGTAATATATAAATATT-A
1 TGAAAA-TAATATAAAAACATTAA
685279 TGAAAATAATA
1 TGAAAATAATA
685290 AGTATATATA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
22 5 0.18
23 11 0.39
24 12 0.43
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (23 bp):
TGAAAATAATATAAAAACATTAA
Found at i:686002 original size:128 final size:126
Alignment explanation
Indices: 685800--686033 Score: 278
Period size: 127 Copynumber: 1.8 Consensus size: 126
685790 TAATTTTATG
* * * * * * *
685800 AAAATATATTAATTTATATATATAAGATATTTATTTATTTAGAAATATCAGAAAAAGGCTTCTAG
1 AAAATAGATTAATTTATATAAATAAGATATTTAATTATTTAGAAATATCAGAAAAAGACATCCAA
*
685865 GTACTTTAAGACAAT-TCTTTTCTTAATATT-AAGAAATAAATAAATATTAATAAAATTTATCT
66 GTACTTTAAGAC--TGTCCTTTCTTAATATTGAA-AAATAAATAAATATTAATAAAATTTATCT
* *
685927 AAAATAGATATAATTTATA-AAAGTAATATATTTAATTATTTA-AAATATCAGAAAATTGACATC
1 AAAATAGAT-TAATTTATATAAA-TAAGATATTTAATTATTTAGAAATATCAGAAAA-AGACATC
* *
685990 CAATTATTTTAAGACTGTCCTTTCTTAATATTGAAAAATAAATA
63 CAAGTACTTTAAGACTGTCCTTTCTTAATATTGAAAAATAAATA
686034 TTAAAATATG
Statistics
Matches: 90, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
126 1 0.01
127 46 0.51
128 43 0.48
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (126 bp):
AAAATAGATTAATTTATATAAATAAGATATTTAATTATTTAGAAATATCAGAAAAAGACATCCAA
GTACTTTAAGACTGTCCTTTCTTAATATTGAAAAATAAATAAATATTAATAAAATTTATCT
Found at i:687662 original size:3 final size:3
Alignment explanation
Indices: 687652--687702 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
687642 GTAATAATTT
* * * * *
687652 ATA A-A ATA ATA ATA ATT ATA ATT ATA ATA ATA ATA ATT ATT ATT ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
687699 ATA A
1 ATA A
687703 ATAAAAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
ATA
Found at i:687666 original size:18 final size:19
Alignment explanation
Indices: 687643--687685 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
687633 TTTGGGCCTG
687643 TAATAATTTATAA-AATAA
1 TAATAATTTATAATAATAA
*
687661 TAATAA-TTATAATTATAA
1 TAATAATTTATAATAATAA
687679 TAATAAT
1 TAATAAT
687686 AATTATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TAATAATTTATAATAATAA
Found at i:687678 original size:15 final size:15
Alignment explanation
Indices: 687660--687702 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
687650 TTATAAAATA
*
687660 ATAATAATTATAATT
1 ATAATAATAATAATT
687675 ATAATAATAATAATT
1 ATAATAATAATAATT
* *
687690 ATTATTATAATAA
1 ATAATAATAATAA
687703 ATAAAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATAATAATAATT
Found at i:687680 original size:21 final size:21
Alignment explanation
Indices: 687656--687702 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
687646 TAATTTATAA
687656 AATAATAATAATTATAATTAT
1 AATAATAATAATTATAATTAT
*
687677 AATAATAATAATTATTATTAT
1 AATAATAATAATTATAATTAT
687698 AATAA
1 AATAA
687703 ATAAAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AATAATAATAATTATAATTAT
Found at i:701760 original size:19 final size:20
Alignment explanation
Indices: 701736--701783 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
701726 AATGATTTTC
*
701736 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
701755 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
701775 TTTTGAAAA
1 TTTTGAAAA
701784 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:712483 original size:2 final size:2
Alignment explanation
Indices: 712476--712549 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
712466 CCTGAATGGC
712476 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
712518 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
712550 CACTTGAATG
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:714603 original size:20 final size:20
Alignment explanation
Indices: 714578--714615 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
714568 TTTGGTTCAC
714578 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
714598 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
714616 GGAATAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:715927 original size:11 final size:12
Alignment explanation
Indices: 715897--715938 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
715887 GTTATTTAAA
715897 CGGGTATTGGGC
1 CGGGTATTGGGC
*
715909 CGGGTATTGGGT
1 CGGGTATTGGGC
715921 C-GGTATTGGGC
1 CGGGTATTGGGC
715932 CGGGTAT
1 CGGGTAT
715939 ATATATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.10, C:0.14, G:0.48, T:0.29
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:715943 original size:2 final size:2
Alignment explanation
Indices: 715936--716026 Score: 66
Period size: 2 Copynumber: 48.0 Consensus size: 2
715926 TTGGGCCGGG
* * * * * *
715936 TA TA TA TA TA TA TA TT TA AA T- TA AA TA TA TA TT TT TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
715977 AA T- TA AA TT TA T- TA -A TA T- TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
716015 TA TA TA TA TA TA
1 TA TA TA TA TA TA
716027 ATTATTTTTA
Statistics
Matches: 68, Mismatches: 16, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
1 5 0.07
2 63 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:717418 original size:2 final size:2
Alignment explanation
Indices: 717411--717451 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
717401 ATCGTTTAGT
717411 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
717452 GTAATCAAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:722903 original size:6 final size:7
Alignment explanation
Indices: 722883--722909 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
722873 GTGAAGCTCG
722883 AGGAAAA
1 AGGAAAA
722890 AGGAAAA
1 AGGAAAA
722897 AGGAAAA
1 AGGAAAA
722904 AGGAAA
1 AGGAAA
722910 CGAAGTCAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (7 bp):
AGGAAAA
Found at i:728951 original size:11 final size:11
Alignment explanation
Indices: 728928--728999 Score: 60
Period size: 11 Copynumber: 6.4 Consensus size: 11
728918 GCTTGAAGAT
728928 AAAAAAATG-A
1 AAAAAAATGAA
*
728938 AAAAAGA-GAA
1 AAAAAAATGAA
728948 AAAAAAATGAAAAA
1 AAAAAAATG---AA
728962 AGAAAAAATGAA
1 A-AAAAAATGAA
*
728974 GAAAAAATGAA
1 AAAAAAATGAA
728985 AAAGAAAA-GAA
1 AAA-AAAATGAA
728996 AAAA
1 AAAA
729000 TGAAGAATAA
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
9 1 0.02
10 14 0.27
11 19 0.37
12 6 0.12
14 3 0.06
15 8 0.16
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.06
Consensus pattern (11 bp):
AAAAAAATGAA
Found at i:729003 original size:19 final size:18
Alignment explanation
Indices: 728923--728999 Score: 77
Period size: 19 Copynumber: 4.1 Consensus size: 18
728913 ATTTTGCTTG
*
728923 AAGATAAAAAAATGAAAAA
1 AAGAAAAAAAAATG-AAAA
728942 AGAGAAAAAAAAATGAAAA
1 A-AGAAAAAAAAATGAAAA
*
728961 AAGAAAAAATGAA-GAAAA
1 AAGAAAAAA-AAATGAAAA
728979 AATGAAAAAGAAAA-GAAAA
1 AA-GAAAAA-AAAATGAAAA
728998 AA
1 AA
729000 TGAAGAATAA
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
18 15 0.29
19 23 0.45
20 13 0.25
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.06
Consensus pattern (18 bp):
AAGAAAAAAAAATGAAAA
Found at i:729005 original size:11 final size:11
Alignment explanation
Indices: 728961--729011 Score: 63
Period size: 11 Copynumber: 4.8 Consensus size: 11
728951 AAAATGAAAA
728961 AAGAAAAAATG
1 AAGAAAAAATG
728972 AAGAAAAAATG
1 AAGAAAAAATG
*
728983 AA-AAAGAA--
1 AAGAAAAAATG
728991 AAGAAAAAATG
1 AAGAAAAAATG
729002 AAGAATAAAA
1 AAGAA-AAAA
729012 GTTGAATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
8 2 0.06
9 5 0.15
10 5 0.15
11 18 0.53
12 4 0.12
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (11 bp):
AAGAAAAAATG
Found at i:730402 original size:53 final size:53
Alignment explanation
Indices: 730256--731185 Score: 1346
Period size: 53 Copynumber: 17.6 Consensus size: 53
730246 AGTGAAGCAA
* *
730256 AAGAAGATTGATCGAGTTCCTACTCCCTGAAGAAAGAGAGAGAGAACCCGTAGG
1 AAGAAGATTGTTCGAGTT-CTACTCCCTGAAGAAAGAGAGAGCGAACCCGTAGG
*
730310 TAGAAGATTGTTCGAG-TCTACTCCCTGAAGAAAGAGAGAGCGAACCCGTAGG
1 AAGAAGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGAACCCGTAGG
* *
730362 AAGAAGATTGTTAGAGTTTTACTCCCTGAAGAAAGAGAGAGCGAACCCGTAGG
1 AAGAAGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGAACCCGTAGG
*
730415 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGAACCCGTAGG
1 AAGAAGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGAACCCGTAGG
*
730468 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGAACCCGTAGG
1 AAGAAGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGAACCCGTAGG
* * * * *
730521 CAGAAGATTGTTTGAGTTCTACTCCCTGAAAAAAAAAAGAGCGAACCCGTAGG
1 AAGAAGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGAACCCGTAGG
730574 AAGAAGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGAACCCGTAGG
1 AAGAAGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGAACCCGTAGG
* * * * * *
730627 GAGAAGATTGTTCGAGTTATACTCCCTAAAGAAAGAGATAGTGAACCCGTAGA
1 AAGAAGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGAACCCGTAGG
*
730680 AAGAAGATTGTTCGATTTCTACTCCCTGAAGAAAGAGAGAGCGAACCCGTA-G
1 AAGAAGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGAACCCGTAGG
*
730732 ACAGAAGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAACGAACCCGTAGG
1 A-AGAAGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGAACCCGTAGG
*
730786 AAGAAGATTGTTTGAGTTCTACTCCCTGAAGAAAGAGAGAGCGAACCCGTAGG
1 AAGAAGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGAACCCGTAGG
* * * * * * *
730839 CAGAAGATTGTTCGAGTTATACTCCTTGAA-AAAAAAAGAGTGAACCCGTAAG
1 AAGAAGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGAACCCGTAGG
* * *
730891 AAGAAGATTGTTCGATTTCTACTCCATTAAGAAAGAGAGAGCGAACCCGTAGG
1 AAGAAGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGAACCCGTAGG
*
730944 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGAACCCGTAGG
1 AAGAAGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGAACCCGTAGG
* *
730997 TAGAAGATTGTTCGAGTTCTACTCCCTGAAGAACGAGAGAGCGAACCCGTAGG
1 AAGAAGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGAACCCGTAGG
* * * * *
731050 CAGAAGATTGTTCGAGTTCTACTCCCTAAAGAAACAGAGAGCAAACCCATAGG
1 AAGAAGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGAACCCGTAGG
* * * * * * ***
731103 CAGAAGATTATTCGAGTTCTACTCCCTGAA-ACGATAGAGATCAAACCCGTTTT
1 AAGAAGATTGTTCGAGTTCTACTCCCTGAAGA-AAGAGAGAGCGAACCCGTAGG
** *
731156 CTGAAGATTGTTTGAGTTCTACTCCCTGAA
1 AAGAAGATTGTTCGAGTTCTACTCCCTGAA
731186 ACGATAGAGA
Statistics
Matches: 795, Mismatches: 76, Indels: 11
0.90 0.09 0.01
Matches are distributed among these distances:
52 93 0.12
53 686 0.86
54 16 0.02
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.21
Consensus pattern (53 bp):
AAGAAGATTGTTCGAGTTCTACTCCCTGAAGAAAGAGAGAGCGAACCCGTAGG
Found at i:731425 original size:2 final size:2
Alignment explanation
Indices: 731418--731452 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
731408 TTGGTTATTA
731418 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
731453 ATCAAGTAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:734004 original size:22 final size:19
Alignment explanation
Indices: 733979--734046 Score: 75
Period size: 19 Copynumber: 3.4 Consensus size: 19
733969 ACCCTCTATT
733979 TATTATTTTTCAATTAAATCA
1 TATTATTTTTCAA-TAAAT-A
*
734000 CTATT-TTTATTGAATAAATA
1 -TATTATTT-TTCAATAAATA
*
734020 TAATATTTTTCAATAAATA
1 TATTATTTTTCAATAAATA
734039 TATTATTT
1 TATTATTT
734047 CAAGTCAGGT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
19 20 0.50
20 4 0.10
21 8 0.20
22 8 0.20
ACGTcount: A:0.40, C:0.06, G:0.01, T:0.53
Consensus pattern (19 bp):
TATTATTTTTCAATAAATA
Found at i:737418 original size:21 final size:19
Alignment explanation
Indices: 737392--737436 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
737382 TAAAACAAAG
737392 AAAATAAAATGAATAAAAATA
1 AAAATAAAA-GAA-AAAAATA
*
737413 AAAATAAAAGAAATAAATA
1 AAAATAAAAGAAAAAAATA
737432 AAAAT
1 AAAAT
737437 GTTGGATCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.48
20 3 0.13
21 9 0.39
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (19 bp):
AAAATAAAAGAAAAAAATA
Found at i:738826 original size:41 final size:38
Alignment explanation
Indices: 738733--738886 Score: 193
Period size: 39 Copynumber: 3.9 Consensus size: 38
738723 ATATAAATAT
* * *
738733 TTTTTAAAAACTATA-TAATATATATATTTTCAAAATG
1 TTTTCAAAAATTATATTTATATATATATTTTCAAAATG
*
738770 TTTTCAAAAATTATATGTTATATATATTTTTTCAAAATG
1 TTTTCAAAAATTATAT-TTATATATATATTTTCAAAATG
* *
738809 TTTTTAAAAACTATATATTATATATATATTTTTTCAAAATG
1 TTTTCAAAAA-T-TATATT-TATATATATATTTTCAAAATG
*
738850 TTTTCAAAAATTATATATTATATAAATATTTTCAAAA
1 TTTTCAAAAATTATAT-TTATATATATATTTTCAAAA
738887 ATTATATATT
Statistics
Matches: 103, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
37 13 0.13
39 51 0.50
40 4 0.04
41 35 0.34
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.49
Consensus pattern (38 bp):
TTTTCAAAAATTATATTTATATATATATTTTCAAAATG
Found at i:738864 original size:28 final size:28
Alignment explanation
Indices: 738845--738961 Score: 168
Period size: 28 Copynumber: 4.2 Consensus size: 28
738835 TATTTTTTCA
*
738845 AAATGTTTTCAAAAATTATATATTATAT
1 AAATATTTTCAAAAATTATATATTATAT
738873 AAATATTTTCAAAAATTATATATTATAT
1 AAATATTTTCAAAAATTATATATTATAT
*
738901 AAATATTTTCAAAAATTATATATTGTAT
1 AAATATTTTCAAAAATTATATATTATAT
* *
738929 --ATGTTTTCAAAATTTTATATATTATAT
1 AAATATTTTCAAAA-ATTATATATTATAT
738956 -AATATT
1 AAATATT
738962 AAATAGCACC
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
26 11 0.14
27 12 0.15
28 58 0.72
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (28 bp):
AAATATTTTCAAAAATTATATATTATAT
Found at i:741461 original size:24 final size:23
Alignment explanation
Indices: 741434--741514 Score: 72
Period size: 24 Copynumber: 3.4 Consensus size: 23
741424 TATATCAAAA
* *
741434 ATCAAAACATAATTCATGTCAAGT
1 ATCAAATCA-AATTCAAGTCAAGT
* * *
741458 ATCATATCAAAATCTAGGTCAAGT
1 ATCAAATCAAATTC-AAGTCAAGT
*
741482 ATCAAATCAGAATCCAAGTCAAGT
1 ATCAAATCA-AATTCAAGTCAAGT
*
741506 ATCATATCA
1 ATCAAATCA
741515 GAATCCATGT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
23 4 0.09
24 39 0.85
25 3 0.07
ACGTcount: A:0.44, C:0.19, G:0.10, T:0.27
Consensus pattern (23 bp):
ATCAAATCAAATTCAAGTCAAGT
Found at i:741515 original size:24 final size:24
Alignment explanation
Indices: 741448--741561 Score: 142
Period size: 24 Copynumber: 4.8 Consensus size: 24
741438 AAACATAATT
*
741448 CATGTCAAGTATCATATCAAAATC
1 CATGTCAAGTATCATATCAGAATC
* * *
741472 TAGGTCAAGTATCAAATCAGAATC
1 CATGTCAAGTATCATATCAGAATC
*
741496 CAAGTCAAGTATCATATCAGAATC
1 CATGTCAAGTATCATATCAGAATC
*
741520 CATGTC-AGATATCATATCTGAATC
1 CATGTCAAG-TATCATATCAGAATC
*
741544 CATGTCAAGT-TCAGATCA
1 CATGTCAAGTATCATATCA
741562 TAATTCAAAT
Statistics
Matches: 77, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
23 8 0.10
24 67 0.87
25 2 0.03
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.28
Consensus pattern (24 bp):
CATGTCAAGTATCATATCAGAATC
Found at i:746129 original size:2 final size:2
Alignment explanation
Indices: 746122--746157 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
746112 ATTATTTAAA
746122 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
746158 TTTAAATATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:746711 original size:2 final size:2
Alignment explanation
Indices: 746704--746747 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
746694 TTATCTAATC
746704 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
746746 AT
1 AT
746748 TCATATTCTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:747788 original size:24 final size:24
Alignment explanation
Indices: 747752--747806 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
747742 TCCTTCTGCC
* *
747752 TTTAATTTCTTATAAAG-AAAAAT
1 TTTAAATTATTATAAAGTAAAAAT
* *
747775 ATTTAAATTATTATCAAGTTAAAAT
1 -TTTAAATTATTATAAAGTAAAAAT
747800 TTTAAAT
1 TTTAAAT
747807 ATAAAATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 21 0.81
25 5 0.19
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (24 bp):
TTTAAATTATTATAAAGTAAAAAT
Found at i:747992 original size:31 final size:31
Alignment explanation
Indices: 747954--748017 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
747944 TCAGGGGCAA
*
747954 AATTGCATAT-CAAAGCCAAAATCAATGGCCT
1 AATTGCATATGC-AAGCCAAAATCAAGGGCCT
* *
747985 AATTGCATATGCAAGTCAAAATCAGGGGCCT
1 AATTGCATATGCAAGCCAAAATCAAGGGCCT
748016 AA
1 AA
748018 AAGTCCATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 28 0.97
32 1 0.03
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (31 bp):
AATTGCATATGCAAGCCAAAATCAAGGGCCT
Found at i:751570 original size:32 final size:32
Alignment explanation
Indices: 751530--751605 Score: 122
Period size: 29 Copynumber: 2.5 Consensus size: 32
751520 CAGATAATAT
751530 ATTGAATTTACAAAAAAATATATATGTATGAA
1 ATTGAATTTACAAAAAAATATATATGTATGAA
*
751562 ATTGAATTTAC---AAAATATCTATGTATGAA
1 ATTGAATTTACAAAAAAATATATATGTATGAA
751591 ATTGAATTTACAAAA
1 ATTGAATTTACAAAA
751606 TCGAACTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
29 28 0.70
32 12 0.30
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.36
Consensus pattern (32 bp):
ATTGAATTTACAAAAAAATATATATGTATGAA
Found at i:755833 original size:16 final size:17
Alignment explanation
Indices: 755809--755841 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
755799 TCATTTGGAT
*
755809 TTCCTTTGTT-TATTTC
1 TTCCATTGTTGTATTTC
755825 TTCCATTGTTGTATTTC
1 TTCCATTGTTGTATTTC
755842 CTTTGGATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.09, C:0.18, G:0.09, T:0.64
Consensus pattern (17 bp):
TTCCATTGTTGTATTTC
Found at i:759659 original size:60 final size:60
Alignment explanation
Indices: 759580--759696 Score: 189
Period size: 60 Copynumber: 1.9 Consensus size: 60
759570 AAATAGTCCA
* * *
759580 TCGACTATAGGATGATGCTTTGTTGAGTCCCTTGACTATTAAAAGTTATAAAATGATTCT
1 TCGACTATAAGATGATGCTTTGTTGAGTCCCTTGACTATTAAAAGATACAAAATGATTCT
* *
759640 TCGACTATAAGATGTTGCTTTGTTGAGTCTCTTGACTATTAAAAGATACAAAATGAT
1 TCGACTATAAGATGATGCTTTGTTGAGTCCCTTGACTATTAAAAGATACAAAATGAT
759697 CACTTAACTA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.38
Consensus pattern (60 bp):
TCGACTATAAGATGATGCTTTGTTGAGTCCCTTGACTATTAAAAGATACAAAATGATTCT
Found at i:778732 original size:20 final size:22
Alignment explanation
Indices: 778702--778753 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 22
778692 AAAATTTTAA
*
778702 ATAATAAAATATTTATAAAAT-T
1 ATAA-AAAATATATATAAAATAT
*
778724 A-AAAAAATATATCTAAAATAT
1 ATAAAAAATATATATAAAATAT
778745 ATAAAAAAT
1 ATAAAAAAT
778754 TAAAACTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 14 0.54
21 4 0.15
22 8 0.31
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
ATAAAAAATATATATAAAATAT
Found at i:779639 original size:111 final size:110
Alignment explanation
Indices: 779441--779789 Score: 538
Period size: 111 Copynumber: 3.1 Consensus size: 110
779431 TTGTCGGTTT
** *
779441 GTGTCGATACTTTATAAAAATATATTAATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATTCATAACAATATAACAGGT-AAAAAATGACAAAACC
779506 GGTCTATAAATGACAAAACAGGTAAAGCGCTACTAGATATATTGAAA
65 GGTCTATAAATGACAAAACAGGTAAAGCGCTAC-AGATATATTGAAA
* *
779553 GTGTCGATACTTTAAAAAAATGTATCGATTCATAACAATATAACAGGTAAAAAATGACAAAACCG
1 GTGTCGATACTTTATAAAAATATATCGATTCATAACAATATAACAGGTAAAAAATGACAAAACCG
*
779618 GTCTATAAATGACAAAACAGGTAAAGCGCTACCGTATATATTGAAA
66 GTCTATAAATGACAAAACAGGTAAAGCGCTACAG-ATATATTGAAA
*
779664 GTGTCGATATTTTATAAAAATATATCGA-TCTATAACAATATAACAGGTAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATATATCGATTC-ATAACAATATAACAGGTAAAAAATGACAAAACC
* * * * *
779728 GGTTTATAAATGACAAAATAGGTAAAGCGCTACCGGATATGTTGATA
65 GGTCTATAAATGACAAAACAGGTAAAGCGCTA-CAGATATATTGAAA
779775 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
779790 TATAAGTATC
Statistics
Matches: 219, Mismatches: 15, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
110 3 0.01
111 171 0.78
112 45 0.21
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.27
Consensus pattern (110 bp):
GTGTCGATACTTTATAAAAATATATCGATTCATAACAATATAACAGGTAAAAAATGACAAAACCG
GTCTATAAATGACAAAACAGGTAAAGCGCTACAGATATATTGAAA
Found at i:779967 original size:182 final size:182
Alignment explanation
Indices: 779661--780298 Score: 994
Period size: 182 Copynumber: 3.5 Consensus size: 182
779651 GTATATATTG
* *
779661 AAAGTGTCGATATTTTATAAAAATATATCGA-TCTATAACAATATAACAGGTAAAAA-ATGACAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATTC-ATAACAATATAACAGGTAAAAATATGACAA
* * ** ** * * *
779724 AACCGGTTTATAAATGACAAAATAGGTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTA
65 AACCGATCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGAAAGTGTCGATACTTTA
* *
779789 TTATAAGTATCGACACTTTTAAAATTTAAAAGAGAAGAAGTTACAGCGCTAAT
130 TTATAAGTATCGACACTTTTGAAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
*
779842 AAAGTGTCGATACTTTATAAAAATGTATCGATTAATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATTCATAACAATATAACAGGTAAAAATATGACAAA
* * *
779907 ACCGGTATCGAAATGACAAAATCGGTAAAGAGCTACCAGATATGTTGAAAGTGTCGATACTTTAT
66 ACCGATCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGAAAGTGTCGATACTTTAT
*
779972 TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCG-TCAAT
131 TATAAGTATCGACACTTTTGAAATTTAAAAGAGAAGAAGTTATAGCGCT-AAT
* *
780024 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAAATATGACAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATTCATAACAATATAACAGGT-AAAAATATGACAA
*
780089 AACCGATCTCGAGATGACAAAACCGGTAAAGAGCTACCAGATATGTTGAAAGTGTCGATACTTTA
65 AACCGATCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGAAAGTGTCGATACTTTA
* * * *
780154 TTATAAGTATCGACACTTTTGAAATTTAAAAGAAAATAATTTATAGCGCCAAT
130 TTATAAGTATCGACACTTTTGAAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
780207 AAAGTGTCGATACTTTATAAAAATGTATCGATTCATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATTCATAACAATATAACAGGTAAAAATATGACAAA
*
780272 ATCGATCTCGAAATGACAAAACCGGTA
66 ACCGATCTCGAAATGACAAAACCGGTA
780299 GTAAAAAAGT
Statistics
Matches: 423, Mismatches: 29, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
181 52 0.12
182 201 0.48
183 170 0.40
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.28
Consensus pattern (182 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATTCATAACAATATAACAGGTAAAAATATGACAAA
ACCGATCTCGAAATGACAAAACCGGTAAAGAGCTACCAGATATGTTGAAAGTGTCGATACTTTAT
TATAAGTATCGACACTTTTGAAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
Found at i:780982 original size:23 final size:23
Alignment explanation
Indices: 780936--780983 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
780926 AAATAGGTCA
* *
780936 ATATAAGCGCTACCTATTACATT
1 ATATAAGCGCTACATAATACATT
*
780959 ATATAAGCGCTACATAATATATT
1 ATATAAGCGCTACATAATACATT
780982 AT
1 AT
780984 TGTACTTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (23 bp):
ATATAAGCGCTACATAATACATT
Found at i:781420 original size:17 final size:17
Alignment explanation
Indices: 781396--781466 Score: 58
Period size: 17 Copynumber: 4.2 Consensus size: 17
781386 TTCTTTTTTT
781396 TTTA-ATTTAATTTTAA
1 TTTAGATTTAATTTTAA
*
781412 TTTAGATTTAA--ATAA
1 TTTAGATTTAATTTTAA
* * *
781427 GCATTATGTTTTTATTTTAA
1 --TTTA-GATTTAATTTTAA
781447 TTTAGATTTAATTTTAA
1 TTTAGATTTAATTTTAA
781464 TTT
1 TTT
781467 TATCTTGCTA
Statistics
Matches: 41, Mismatches: 8, Indels: 11
0.68 0.13 0.18
Matches are distributed among these distances:
15 3 0.07
16 4 0.10
17 23 0.56
18 8 0.20
20 3 0.07
ACGTcount: A:0.34, C:0.01, G:0.06, T:0.59
Consensus pattern (17 bp):
TTTAGATTTAATTTTAA
Found at i:781804 original size:19 final size:19
Alignment explanation
Indices: 781782--781820 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
781772 TTTTTACGTC
*
781782 ATTTGAGTTTTTATGTTAG
1 ATTTGAGGTTTTATGTTAG
*
781801 ATTTGGGGTTTTATGTTAG
1 ATTTGAGGTTTTATGTTAG
781820 A
1 A
781821 GTATGTTGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.54
Consensus pattern (19 bp):
ATTTGAGGTTTTATGTTAG
Found at i:786391 original size:64 final size:63
Alignment explanation
Indices: 786295--786418 Score: 187
Period size: 64 Copynumber: 2.0 Consensus size: 63
786285 ACATTTAATT
* * *
786295 TAAGTTGACAAGTGGTATGATGGATTCTAAATATTGGAAAGTTGATTCAAGTTGGTAAGTTGG
1 TAAGTTGACAAATGGTATGATGGATTCTAAATATTGGAAAGTTGATTAAAGTTGGCAAGTTGG
*
786358 TAAGTTGACAAATGGCTATGATGGATATC-AAATATTGGAAAGTTGTTTAAAGTTGGCAAGT
1 TAAGTTGACAAATGG-TATGATGGAT-TCTAAATATTGGAAAGTTGATTAAAGTTGGCAAGT
786419 GACCAACTTG
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
63 14 0.25
64 39 0.71
65 2 0.04
ACGTcount: A:0.34, C:0.06, G:0.27, T:0.34
Consensus pattern (63 bp):
TAAGTTGACAAATGGTATGATGGATTCTAAATATTGGAAAGTTGATTAAAGTTGGCAAGTTGG
Found at i:788305 original size:19 final size:19
Alignment explanation
Indices: 788272--788310 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
788262 GGTCAAATTT
* *
788272 AAAGTCAACATGTAGGTCA
1 AAAGTCAACAGGTAGATCA
*
788291 AAAGTCAACGGGTAGATCA
1 AAAGTCAACAGGTAGATCA
788310 A
1 A
788311 CGACCAGGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.44, C:0.15, G:0.23, T:0.18
Consensus pattern (19 bp):
AAAGTCAACAGGTAGATCA
Found at i:789496 original size:20 final size:20
Alignment explanation
Indices: 789471--789515 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
789461 TTGTTTTTAA
789471 TAAATTTTTATCTATAAAAT
1 TAAATTTTTATCTATAAAAT
* *
789491 TAAATTTTTATTTTTAAAAT
1 TAAATTTTTATCTATAAAAT
*
789511 AAAAT
1 TAAAT
789516 ATTAAAAGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
TAAATTTTTATCTATAAAAT
Done.