Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008488.1 Hibiscus syriacus cultivar Beakdansim tig00111330_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: 12876159
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 38 of 54
Found at i:9165365 original size:19 final size:18
Alignment explanation
Indices: 9165343--9165393 Score: 56
Period size: 16 Copynumber: 3.0 Consensus size: 18
9165333 TATAATCGTT
9165343 TTGCGATTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
*
9165361 ATTGCGA--TTC-TCTCG-
1 -TTGCGATTTTCATTTCGC
9165376 TTGCGATTTTCATTTCGC
1 TTGCGATTTTCATTTCGC
9165394 GTTACGATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 9
0.70 0.05 0.24
Matches are distributed among these distances:
14 6 0.23
16 7 0.27
17 7 0.27
19 6 0.23
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.47
Consensus pattern (18 bp):
TTGCGATTTTCATTTCGC
Found at i:9165902 original size:21 final size:21
Alignment explanation
Indices: 9165878--9165944 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
9165868 TCATTCCTCG
9165878 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
9165899 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
9165920 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
9165941 AGAG
1 AGAG
9165945 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:9165902 original size:42 final size:42
Alignment explanation
Indices: 9165826--9165944 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
9165816 GACTTGCCTG
* * * * * * *
9165826 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
9165868 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
9165910 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
9165945 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:9167316 original size:14 final size:14
Alignment explanation
Indices: 9167297--9167332 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
9167287 ATTGTTTAAT
9167297 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
9167311 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
9167325 TGATTTGT
1 TGATTTGT
9167333 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:9167492 original size:33 final size:33
Alignment explanation
Indices: 9167443--9167537 Score: 109
Period size: 33 Copynumber: 2.9 Consensus size: 33
9167433 ATGACTATCA
* * * *
9167443 CAATGCAAAATGAAAATCGCAACGAGAGAATTG
1 CAATGCGAAATTAAAATCGCAACGAGAAAATCG
*
9167476 CAATGCGAAATTAAAATCGCAACGATAAAATCG
1 CAATGCGAAATTAAAATCGCAACGAGAAAATCG
* * * *
9167509 CAACGCGAAACTAAAATCCCAACGCGAAA
1 CAATGCGAAATTAAAATCGCAACGAGAAA
9167538 CTAAATTCGC
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.48, C:0.21, G:0.17, T:0.14
Consensus pattern (33 bp):
CAATGCGAAATTAAAATCGCAACGAGAAAATCG
Found at i:9167506 original size:14 final size:14
Alignment explanation
Indices: 9167487--9167513 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
9167477 AATGCGAAAT
9167487 TAAAATCGCAACGA
1 TAAAATCGCAACGA
9167501 TAAAATCGCAACG
1 TAAAATCGCAACG
9167514 CGAAACTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.22, G:0.15, T:0.15
Consensus pattern (14 bp):
TAAAATCGCAACGA
Found at i:9167525 original size:19 final size:19
Alignment explanation
Indices: 9167501--9167547 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
9167491 ATCGCAACGA
9167501 TAAAATCGCAACGCGAAAC
1 TAAAATCGCAACGCGAAAC
*
9167520 TAAAATCCCAACGCGAAAC
1 TAAAATCGCAACGCGAAAC
*
9167539 TAAATTCGC
1 TAAAATCGC
9167548 GTTGCGATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.45, C:0.28, G:0.13, T:0.15
Consensus pattern (19 bp):
TAAAATCGCAACGCGAAAC
Found at i:9167565 original size:19 final size:19
Alignment explanation
Indices: 9167543--9167694 Score: 82
Period size: 19 Copynumber: 8.7 Consensus size: 19
9167533 CGAAACTAAA
9167543 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
9167562 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
9167577 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* * *
9167595 TTTGCATTGTGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
9167610 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
9167628 TTCGCATTGCGATAGTCATT
1 TTCGCGTTGCGATTTTCA-T
9167648 TTCGCGTTGCGATTTTCA-
1 TTCGCGTTGCGATTTTCAT
*
9167666 ----AGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
9167681 TTCGCATTGCGATT
1 TTCGCGTTGCGATT
9167695 CTCTCGTTGT
Statistics
Matches: 94, Mismatches: 23, Indels: 32
0.63 0.15 0.21
Matches are distributed among these distances:
14 28 0.30
16 6 0.06
17 6 0.06
19 38 0.40
20 16 0.17
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.45
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:9167589 original size:33 final size:33
Alignment explanation
Indices: 9167547--9167640 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
9167537 ACTAAATTCG
9167547 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
* * *
9167580 CGTTGCGATTTTCATTTTGCATTGTGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
9167613 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
9167641 AGTCATTTTC
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:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:9167664 original size:14 final size:14
Alignment explanation
Indices: 9167653--9167679 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
9167643 TCATTTTCGC
9167653 GTTGCGATTTTCAA
1 GTTGCGATTTTCAA
9167667 GTTGCGATTTTCA
1 GTTGCGATTTTCA
9167680 TTTCGCATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.15, G:0.22, T:0.44
Consensus pattern (14 bp):
GTTGCGATTTTCAA
Found at i:9170049 original size:13 final size:13
Alignment explanation
Indices: 9170016--9170051 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
9170006 ACTCCCGTGC
9170016 ATTTTCTTCGGGG
1 ATTTTCTTCGGGG
*
9170029 ACTTTTCTTTGGGG
1 A-TTTTCTTCGGGG
9170043 ATTTTCTTC
1 ATTTTCTTC
9170052 TTCTTTTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.08, C:0.17, G:0.22, T:0.53
Consensus pattern (13 bp):
ATTTTCTTCGGGG
Found at i:9170302 original size:24 final size:24
Alignment explanation
Indices: 9170251--9170305 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
9170241 AAAATCTGAG
* **
9170251 TATTGACCACGATCAAAGTCCGGG
1 TATTGACCAAGATCAAAGTCCGAA
* *
9170275 TATTGACCAAGATCAAATTTCGAA
1 TATTGACCAAGATCAAAGTCCGAA
9170299 TATTGAC
1 TATTGAC
9170306 TAGTACTCAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (24 bp):
TATTGACCAAGATCAAAGTCCGAA
Found at i:9171125 original size:20 final size:19
Alignment explanation
Indices: 9171104--9171336 Score: 114
Period size: 20 Copynumber: 11.6 Consensus size: 19
9171094 GCGATAGTCA
9171104 GAATCTCGTTGCGATTTAC
1 GAATCTCGTTGCGATTTAC
* * *
9171123 AGATTCGCATTGCGATTTAC
1 -GAATCTCGTTGCGATTTAC
*
9171143 GTAT-TCGAATTGCGATTTAC
1 GAATCTCG--TTGCGATTTAC
*
9171163 GTAT-TCGCATTGCGATTTAC
1 GAATCTCG--TTGCGATTTAC
* *
9171183 -AGATACGCATTGCGATTTAC
1 GA-AT-CTCGTTGCGATTTAC
* *
9171203 GTATTCTCGTTGCAATTTAC
1 G-AATCTCGTTGCGATTTAC
*
9171223 -AGATACGCGTTGCGATTTAC
1 GA-AT-CTCGTTGCGATTTAC
*
9171243 GTATTCTCGTTGCGATTTAC
1 G-AATCTCGTTGCGATTTAC
* * *
9171263 GGATACGCATTGCGATTTTAC
1 GAAT-CTCGTTGCGA-TTTAC
* *
9171284 GTATTGTCGTTGCGATTTAC
1 G-AATCTCGTTGCGATTTAC
* *
9171304 GGATACGCGTTGCGATTTTAC
1 GAAT-CTCGTTGCGA-TTTAC
*
9171325 GGATACTCGTTG
1 GAAT-CTCGTTG
9171337 TGATAGTCAG
Statistics
Matches: 163, Mismatches: 34, Indels: 31
0.71 0.15 0.14
Matches are distributed among these distances:
18 2 0.01
19 5 0.03
20 121 0.74
21 31 0.19
22 4 0.02
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (19 bp):
GAATCTCGTTGCGATTTAC
Found at i:9171156 original size:40 final size:40
Alignment explanation
Indices: 9171112--9171321 Score: 255
Period size: 40 Copynumber: 5.2 Consensus size: 40
9171102 CAGAATCTCG
* *
9171112 TTGCGATTTACAG-ATTCGCATTGCGATTTAC-GTATTCGAA
1 TTGCGATTTAC-GTATTCGCATTGCGATTTACAG-ATACGCA
9171152 TTGCGATTTACGTATTCGCATTGCGATTTACAGATACGCA
1 TTGCGATTTACGTATTCGCATTGCGATTTACAGATACGCA
* * * *
9171192 TTGCGATTTACGTATTCTCGTTGCAATTTACAGATACGCG
1 TTGCGATTTACGTATTCGCATTGCGATTTACAGATACGCA
* * *
9171232 TTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCA
1 TTGCGATTTACGTATTCGCATTGCGATTTACAGATACGCA
* * *
9171272 TTGCGATTTTACGTATT-GTCGTTGCGATTTACGGATACGCG
1 TTGCGA-TTTACGTATTCG-CATTGCGATTTACAGATACGCA
9171313 TTGCGATTT
1 TTGCGATTT
9171322 TACGGATACT
Statistics
Matches: 155, Mismatches: 11, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
39 1 0.01
40 116 0.75
41 38 0.25
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (40 bp):
TTGCGATTTACGTATTCGCATTGCGATTTACAGATACGCA
Found at i:9171176 original size:60 final size:60
Alignment explanation
Indices: 9171110--9171321 Score: 241
Period size: 60 Copynumber: 3.5 Consensus size: 60
9171100 GTCAGAATCT
* *
9171110 CGTTGCGATTTACAGATTCGCATTGCGATTTACGTATTCGAATTGCGATTTACGTATTCG
1 CGTTGCGATTTACAGATACGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCG
* * * * *
9171170 CATTGCGATTTACAGATACGCATTGCGATTTACGTATTCTCGTTGCAATTTACAG-ATACG
1 CGTTGCGATTTACAGATACGCATTGCGATTTACGTATTCGCATTGCGATTTAC-GTATTCG
* * * * *
9171230 CGTTGCGATTTAC-GTATTCTCGTTGCGATTTACGGATACGCATTGCGATTTTACGTATT-G
1 CGTTGCGATTTACAG-ATACGCATTGCGATTTACGTATTCGCATTGCGA-TTTACGTATTCG
* *
9171290 TCGTTGCGATTTACGGATACGCGTTGCGATTT
1 -CGTTGCGATTTACAGATACGCATTGCGATTT
9171322 TACGGATACT
Statistics
Matches: 127, Mismatches: 19, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
59 1 0.01
60 90 0.71
61 35 0.28
62 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (60 bp):
CGTTGCGATTTACAGATACGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCG
Found at i:9181140 original size:21 final size:22
Alignment explanation
Indices: 9181109--9181149 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
9181099 AAAACAAATT
9181109 TCCATAGTACACAAAATACTAC
1 TCCATAGTACACAAAATACTAC
*
9181131 TCCA-AGTACACAAATTACT
1 TCCATAGTACACAAAATACT
9181150 CTTAGGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.44, C:0.27, G:0.05, T:0.24
Consensus pattern (22 bp):
TCCATAGTACACAAAATACTAC
Found at i:9183272 original size:28 final size:28
Alignment explanation
Indices: 9183187--9183272 Score: 68
Period size: 28 Copynumber: 3.0 Consensus size: 28
9183177 TTACAAAACT
* *
9183187 TTTTAAAA-TTACATTTTAGTCCCTAAACA
1 TTTTAAAATTTATATTTT-GTCACT-AACA
* * *
9183216 TTTCTAAAGTTTATACTTTGACACTTAAC-
1 TTT-TAAAATTTATATTTTGTCAC-TAACA
9183245 TTTTAAAATTTATATTTTGGTCACTAAC
1 TTTTAAAATTTATATTTT-GTCACTAAC
9183273 CAAAATTTGG
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
28 17 0.38
29 10 0.22
30 10 0.22
31 8 0.18
ACGTcount: A:0.34, C:0.15, G:0.06, T:0.45
Consensus pattern (28 bp):
TTTTAAAATTTATATTTTGTCACTAACA
Found at i:9197613 original size:56 final size:56
Alignment explanation
Indices: 9197527--9197638 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
9197517 ATCATTTTAC
9197527 AATTCAATTTCTCATATGTCCCAACTTAAATTAAAAGAGAACAACCTTTTGTAACA
1 AATTCAATTTCTCATATGTCCCAACTTAAATTAAAAGAGAACAACCTTTTGTAACA
9197583 AATTCAATTTCTCATATGTCCCAACTTAAATTAAAAGAGAACAACCTTTTGTAACA
1 AATTCAATTTCTCATATGTCCCAACTTAAATTAAAAGAGAACAACCTTTTGTAACA
9197639 TATTGTTTTC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.32
Consensus pattern (56 bp):
AATTCAATTTCTCATATGTCCCAACTTAAATTAAAAGAGAACAACCTTTTGTAACA
Found at i:9203923 original size:9 final size:9
Alignment explanation
Indices: 9203909--9203946 Score: 76
Period size: 9 Copynumber: 4.2 Consensus size: 9
9203899 CTTTTTGAAA
9203909 TTCACCTTG
1 TTCACCTTG
9203918 TTCACCTTG
1 TTCACCTTG
9203927 TTCACCTTG
1 TTCACCTTG
9203936 TTCACCTTG
1 TTCACCTTG
9203945 TT
1 TT
9203947 TCTTCACTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.11, C:0.32, G:0.11, T:0.47
Consensus pattern (9 bp):
TTCACCTTG
Found at i:9204825 original size:13 final size:13
Alignment explanation
Indices: 9204807--9204832 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9204797 AAAATATAAC
9204807 AGCACCAACCATT
1 AGCACCAACCATT
9204820 AGCACCAACCATT
1 AGCACCAACCATT
9204833 GGCAAACAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.38, G:0.08, T:0.15
Consensus pattern (13 bp):
AGCACCAACCATT
Found at i:9206354 original size:253 final size:255
Alignment explanation
Indices: 9205889--9206396 Score: 1002
Period size: 253 Copynumber: 2.0 Consensus size: 255
9205879 TCATACTGAA
9205889 CCCTAACAACTTCATTATAGTTGGTACTCCCCGAACACACGACTTCATAACTGGGATTATGCGTA
1 CCCTAACAACTTCATTATAGTTGGTACTCCCCGAACACACGACTTCATAACTGGGATTATGCGTA
9205954 AACCCTTGGCTATACCCAACATCCGTTTTGCTCACCCCTGCAACTCTCTGGAACGCCAATCAACA
66 AACCCTTGGCTATACCCAACATCCGTTTTGCTCACCCCTGCAACTCTCTGGAACGCCAATCAACA
9206019 CCCCAAAAGCAACCTGCATCGAACTGAGCAAACTATTGATCGGGAGCCGGAACGTCGTCGTCTGG
131 CCCCAAAAGCAACCTGCATCGAACTGAGCAAACTATTGATCGGGAGCCGGAACGTCGTCGTCTGG
9206084 ACCCTAAGCAAACAGGAATCCTCTACTGACGTGGCTGGCTTGCTGTTGGCTCTGAAGCCG
196 ACCCTAAGCAAACAGGAATCCTCTACTGACGTGGCTGGCTTGCTGTTGGCTCTGAAGCCG
9206144 CCCTAACAACTTCA-T-TAGTTGGTACTCCCCGAACACACGACTTCATAACTGGGATTATGCGTA
1 CCCTAACAACTTCATTATAGTTGGTACTCCCCGAACACACGACTTCATAACTGGGATTATGCGTA
9206207 AACCCTTGGCTATACCCAACATCCGTTTTGCTCACCCCTGCAACTCTCTGGAACGCCAATCAACA
66 AACCCTTGGCTATACCCAACATCCGTTTTGCTCACCCCTGCAACTCTCTGGAACGCCAATCAACA
9206272 CCCCAAAAGCAACCTGCATCGAACTGAGCAAACTATTGATCGGGAGCCGGAACGTCGTCGTCTGG
131 CCCCAAAAGCAACCTGCATCGAACTGAGCAAACTATTGATCGGGAGCCGGAACGTCGTCGTCTGG
9206337 ACCCTAAGCAAACAGGAATCCTCTACTGACGTGGCTGGCTTGCTGTTGGCTCTGAAGCCG
196 ACCCTAAGCAAACAGGAATCCTCTACTGACGTGGCTGGCTTGCTGTTGGCTCTGAAGCCG
9206397 AGGTTTTTAA
Statistics
Matches: 253, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
253 238 0.94
254 1 0.00
255 14 0.06
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (255 bp):
CCCTAACAACTTCATTATAGTTGGTACTCCCCGAACACACGACTTCATAACTGGGATTATGCGTA
AACCCTTGGCTATACCCAACATCCGTTTTGCTCACCCCTGCAACTCTCTGGAACGCCAATCAACA
CCCCAAAAGCAACCTGCATCGAACTGAGCAAACTATTGATCGGGAGCCGGAACGTCGTCGTCTGG
ACCCTAAGCAAACAGGAATCCTCTACTGACGTGGCTGGCTTGCTGTTGGCTCTGAAGCCG
Found at i:9211936 original size:40 final size:39
Alignment explanation
Indices: 9211878--9211962 Score: 116
Period size: 40 Copynumber: 2.2 Consensus size: 39
9211868 AGTTGACATC
* * *
9211878 TTTGGTTGGTGGCTAACTTGTACACATTGGATATTTCATA
1 TTTGGTAGGTGGCCAACTTGTACACATGGGA-ATTTCATA
* *
9211918 TTTGGTAGGTGGCCAACTTGTGCACATGGGAATTTCATC
1 TTTGGTAGGTGGCCAACTTGTACACATGGGAATTTCATA
9211957 TTTGGT
1 TTTGGT
9211963 TCCTAAAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 13 0.32
40 27 0.68
ACGTcount: A:0.20, C:0.14, G:0.26, T:0.40
Consensus pattern (39 bp):
TTTGGTAGGTGGCCAACTTGTACACATGGGAATTTCATA
Found at i:9215127 original size:16 final size:17
Alignment explanation
Indices: 9215104--9215146 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 17
9215094 TTGTTTCTAC
9215104 ATTTTTAAAAATAAATT
1 ATTTTTAAAAATAAATT
9215121 ATTTTAATAAAAATAAATT
1 ATTTT--TAAAAATAAATT
*
9215140 ATATTTA
1 ATTTTTA
9215147 TTTTCTAGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 7 0.30
19 16 0.70
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTTTTAAAAATAAATT
Found at i:9215133 original size:19 final size:20
Alignment explanation
Indices: 9215109--9215146 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
9215099 TCTACATTTT
9215109 TAAAAATAAATTAT-TTTAA
1 TAAAAATAAATTATATTTAA
9215128 TAAAAATAAATTATATTTA
1 TAAAAATAAATTATATTTA
9215147 TTTTCTAGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAAAATAAATTATATTTAA
Found at i:9215230 original size:234 final size:228
Alignment explanation
Indices: 9214786--9215251 Score: 738
Period size: 228 Copynumber: 2.0 Consensus size: 228
9214776 AAATGCCCAT
9214786 TTTCGGTGTCATTAATTTATGGAACACATTTCAATATTTAGAGTATTATTTCGAGGATTATTTGA
1 TTTCGGTGTCATTAATTTATGGAACACATTTCAATATTTAGAGTATTATTTCGAGGATTATTTGA
*
9214851 GCAAAAAGTATCCTTTTATTTCTGAATTTTTTAAAATAAATTATTTTTAATAAATTATAGTTATT
66 GCAAAAAGTATCCTTTTATTTCTGAATTTTTAAAAATAAATTATTTTTAATAAATTATAGTTATT
*
9214916 TTCTAGGGAATATCTTAAACAAAGAACGATATAAGAGGAAACCCTCAAAATATTTGGAGTTCCTT
131 TTCTAGGGAATATCTTAAACAAAGAACGATACAAGAGGAAACCCTCAAAATATTTGGAGTTCCTT
* *
9214981 TAAGACGTATGAGTGATGGAACGTCACTGTCAA
196 TAAGACGTATGAGTGATGGAACATCACCGTCAA
* *
9215014 TTTCGGTGTCATTAATTTATGGAACGCATTT-AAGTATTTGGAGTATTATTTCGAGGATTATTTG
1 TTTCGGTGTCATTAATTTATGGAACACATTTCAA-TATTTAGAGTATTATTTCGAGGATTATTTG
** * *
9215078 AGTTAAAAGTATTCTTTTGTTTCT-ACATTTTTAAAAATAAATTATTTTAATAAAAATAAATTAT
65 AGCAAAAAGTATCCTTTTATTTCTGA-ATTTTTAAAAATAAATTATTTT--T---AATAAATTAT
* *
9215142 ATTTATTTTCTAGGGGAATATCTTGAACAAAGAACGATACAAGAGGAAACCCTCAAAATATTTGG
124 AGTTATTTTCTA-GGGAATATCTTAAACAAAGAACGATACAAGAGGAAACCCTCAAAATATTTGG
9215207 AGTTCCTTTAAGACGTATGAGTGATGGAACATCACCGTCAA
188 AGTTCCTTTAAGACGTATGAGTGATGGAACATCACCGTCAA
9215248 TTTC
1 TTTC
9215252 AACATAATTA
Statistics
Matches: 218, Mismatches: 12, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
227 3 0.01
228 100 0.46
230 1 0.00
233 21 0.10
234 93 0.43
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (228 bp):
TTTCGGTGTCATTAATTTATGGAACACATTTCAATATTTAGAGTATTATTTCGAGGATTATTTGA
GCAAAAAGTATCCTTTTATTTCTGAATTTTTAAAAATAAATTATTTTTAATAAATTATAGTTATT
TTCTAGGGAATATCTTAAACAAAGAACGATACAAGAGGAAACCCTCAAAATATTTGGAGTTCCTT
TAAGACGTATGAGTGATGGAACATCACCGTCAA
Found at i:9222408 original size:175 final size:176
Alignment explanation
Indices: 9222117--9222467 Score: 686
Period size: 175 Copynumber: 2.0 Consensus size: 176
9222107 GTAAAGTCTC
9222117 CATAGAATTCTGTTGAGTTGTTCCTCTTAGCTTAATTATCTCTTCTAAAGATAACTGCTCTAGTT
1 CATAGAATTCTGTTGAGTTGTTCCTCTTAGCTTAATTATCTCTTCTAAAGATAACTGCTCTAGTT
9222182 TCTCACCACCTTTTACTTTGGCAAATACCTTATTGTTATTTCTCCATTCGTTAGCCA-TTTCTTG
66 TCTCACCACCTTTTACTTTGGCAAATACCTTATTGTTATTTCTCCATTCGTTAGCCATTTTCTTG
9222246 CTATGCCTTCTCTCTTTATGGCTATTACGTTTTCTCATATTACCAT
131 CTATGCCTTCTCTCTTTATGGCTATTACGTTTTCTCATATTACCAT
9222292 CATAGAATTCTGTTGAGTTGTTCCTCTTAGCTTAATTATCTCTTCTAAAGATAACTGCTCTAGTT
1 CATAGAATTCTGTTGAGTTGTTCCTCTTAGCTTAATTATCTCTTCTAAAGATAACTGCTCTAGTT
9222357 TCTCACCACCTTTTACTTTGGCAAATACCTTATTGTTATTTCTCCATTCGTTAGCCATTTTCTTG
66 TCTCACCACCTTTTACTTTGGCAAATACCTTATTGTTATTTCTCCATTCGTTAGCCATTTTCTTG
*
9222422 CTATGCCTTCTCTCTTTATTGCTATTACGTTTTCTCATATTACCAT
131 CTATGCCTTCTCTCTTTATGGCTATTACGTTTTCTCATATTACCAT
9222468 ATAATCCATT
Statistics
Matches: 174, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
175 122 0.70
176 52 0.30
ACGTcount: A:0.21, C:0.23, G:0.11, T:0.46
Consensus pattern (176 bp):
CATAGAATTCTGTTGAGTTGTTCCTCTTAGCTTAATTATCTCTTCTAAAGATAACTGCTCTAGTT
TCTCACCACCTTTTACTTTGGCAAATACCTTATTGTTATTTCTCCATTCGTTAGCCATTTTCTTG
CTATGCCTTCTCTCTTTATGGCTATTACGTTTTCTCATATTACCAT
Found at i:9226624 original size:62 final size:61
Alignment explanation
Indices: 9226527--9226650 Score: 239
Period size: 62 Copynumber: 2.0 Consensus size: 61
9226517 TTGGCGAGGA
9226527 GCCTGAGATACCGACTCACATAGACCCGACACCTCTTGCAGATTTCTTCTGAGGATTTTGAG
1 GCCTGAGATACCGACTCACATAGACCCGACACCTCTTGCAGATTTCTTCTGAGGA-TTTGAG
9226589 GCCTGAGATACCGACTCACATAGACCCGACACCTCTTGCAGATTTCTTCTGAGGATTTGAG
1 GCCTGAGATACCGACTCACATAGACCCGACACCTCTTGCAGATTTCTTCTGAGGATTTGAG
9226650 G
1 G
9226651 ATAGGATACT
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
61 7 0.11
62 55 0.89
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (61 bp):
GCCTGAGATACCGACTCACATAGACCCGACACCTCTTGCAGATTTCTTCTGAGGATTTGAG
Found at i:9227561 original size:42 final size:41
Alignment explanation
Indices: 9227464--9227562 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 41
9227454 CCCTTTACAA
9227464 AAAGGATCGATCCCTCGAGTGAAATGATTGATCCATTCTCT
1 AAAGGATCGATCCCTCGAGTGAAATGATTGATCCATTCTCT
* * *
9227505 AAATAGATCAATCCCTCGA-TGAAAATGATTGATCCCTTC-CATT
1 AAA-GGATCGATCCCTCGAGTG-AAATGATTGATCCATTCTC--T
*
9227548 AAAGGATTGATCCCT
1 AAAGGATCGATCCCT
9227563 TTCTTGCAAC
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
41 6 0.12
42 38 0.79
43 4 0.08
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.29
Consensus pattern (41 bp):
AAAGGATCGATCCCTCGAGTGAAATGATTGATCCATTCTCT
Found at i:9229603 original size:161 final size:165
Alignment explanation
Indices: 9229405--9229733 Score: 596
Period size: 161 Copynumber: 2.0 Consensus size: 165
9229395 AGAAAAATGA
9229405 ATTATTTCTAACAATTCATCGAAGTCAATAATGGCAAAATGTTCACATTACCATTATCATGGTCA
1 ATTATTTCTAACAATT-ATCGAAGTCAATAATGGCAAAATGTTCACATTACCATTATCATGGTCA
9229470 TAATTCTAATACTTTACTATAAAGAAGATAAAATTTTATAAAATAAGACAAATATGAGTTTCTTA
65 TAATTCTAATACTTTACTATAAAGAAGATAAAATTTTATAAAATAAGACAAATATGAG-TTCTTA
9229535 AGGGAACTAGAGGCATTG-AA-AAATATCAAGGACCC
129 AGGGAACTAGAGGCATTGAAACAAATATCAAGGACCC
9229570 ATTA-TTCTAACAA-T-TCGAAGTCAATAATGGCAAAATGTTCACATTACCATTATCATGGTCAT
1 ATTATTTCTAACAATTATCGAAGTCAATAATGGCAAAATGTTCACATTACCATTATCATGGTCAT
9229632 AATTCTAATACTTTACTATAAAGAAGATAAAATTTTATAAAATAAGACAAATATGAGTTCTTAAG
66 AATTCTAATACTTTACTATAAAGAAGATAAAATTTTATAAAATAAGACAAATATGAGTTCTTAAG
9229697 GGAACTAGAGGCATTGAAACTAAATATCAAGGACCC
131 GGAACTAGAGGCATTGAAAC-AAATATCAAGGACCC
9229733 A
1 A
9229734 AAGCAATTTG
Statistics
Matches: 161, Mismatches: 0, Indels: 8
0.95 0.00 0.05
Matches are distributed among these distances:
160 24 0.15
161 107 0.66
163 17 0.11
164 9 0.06
165 4 0.02
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.30
Consensus pattern (165 bp):
ATTATTTCTAACAATTATCGAAGTCAATAATGGCAAAATGTTCACATTACCATTATCATGGTCAT
AATTCTAATACTTTACTATAAAGAAGATAAAATTTTATAAAATAAGACAAATATGAGTTCTTAAG
GGAACTAGAGGCATTGAAACAAATATCAAGGACCC
Found at i:9231034 original size:22 final size:22
Alignment explanation
Indices: 9231006--9231057 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
9230996 GGAAACCCAA
9231006 AAAATTTATTTTAAATTTTTAG
1 AAAATTTATTTTAAATTTTTAG
9231028 AAAATTTATTTTAAATTTTTAG
1 AAAATTTATTTTAAATTTTTAG
9231050 AAAATTTA
1 AAAATTTA
9231058 CGAGAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (22 bp):
AAAATTTATTTTAAATTTTTAG
Found at i:9231995 original size:26 final size:27
Alignment explanation
Indices: 9231966--9232016 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
9231956 ACAATTATGT
*
9231966 TATTTGGATATTTG-ATG-TTTATTTTA
1 TATTTGG-TACTTGAATGTTTTATTTTA
9231992 TATTTGGTACTTGAATGTTTTATTT
1 TATTTGGTACTTGAATGTTTTATTT
9232017 GGTTATTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 5 0.23
26 10 0.45
27 7 0.32
ACGTcount: A:0.22, C:0.02, G:0.16, T:0.61
Consensus pattern (27 bp):
TATTTGGTACTTGAATGTTTTATTTTA
Found at i:9232017 original size:20 final size:20
Alignment explanation
Indices: 9231986--9232034 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
9231976 TTTGATGTTT
9231986 ATTTTATATTTGG-TACTTGA
1 ATTTT-TATTTGGTTACTTGA
*
9232006 ATGTTTTATTTGGTTATTTGA
1 AT-TTTTATTTGGTTACTTGA
9232027 ATTTTTAT
1 ATTTTTAT
9232035 GACTTTGGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.22, C:0.02, G:0.14, T:0.61
Consensus pattern (20 bp):
ATTTTTATTTGGTTACTTGA
Found at i:9242508 original size:29 final size:30
Alignment explanation
Indices: 9242382--9242510 Score: 140
Period size: 30 Copynumber: 4.4 Consensus size: 30
9242372 CCGTTGATCG
* *
9242382 GGTGACATTTTGGGAA-TTAATTCGAAATA
1 GGTGATATTTTGGGAATTTAATTCGAAAAA
*
9242411 GGT-ATTATTTTGGGAATTTAATTTGAAAAA
1 GGTGA-TATTTTGGGAATTTAATTCGAAAAA
* *
9242441 AGTGATACATTT-GGAATTTAATTCGAAAAA
1 GGTGATA-TTTTGGGAATTTAATTCGAAAAA
* *
9242471 GGTGTTATTTTGGGAATTTAATTAG-AAAA
1 GGTGATATTTTGGGAATTTAATTCGAAAAA
*
9242500 TGTGATATTTT
1 GGTGATATTTT
9242511 AGTAATTATT
Statistics
Matches: 83, Mismatches: 12, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
28 1 0.01
29 29 0.35
30 49 0.59
31 4 0.05
ACGTcount: A:0.36, C:0.03, G:0.21, T:0.40
Consensus pattern (30 bp):
GGTGATATTTTGGGAATTTAATTCGAAAAA
Found at i:9243113 original size:20 final size:21
Alignment explanation
Indices: 9243088--9243139 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
9243078 TTTTCCCAAT
*
9243088 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
9243108 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
9243129 TCGCAATGCGA
1 TCGCAATGCGA
9243140 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:9243153 original size:20 final size:20
Alignment explanation
Indices: 9243128--9243241 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
9243118 AATTGGGAAA
9243128 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
9243148 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
9243168 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
9243189 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
9243209 TTCGCAATGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* *
9243229 TTCGCAACGCGAT
1 ATCGCAATGCGAT
9243242 TTACATAGCG
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 62 0.78
21 13 0.16
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:9243172 original size:61 final size:61
Alignment explanation
Indices: 9243125--9243241 Score: 171
Period size: 61 Copynumber: 1.9 Consensus size: 61
9243115 GCGAATTGGG
* * * *
9243125 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
* * *
9243186 AAAATCGCAACGAGATACTGACTTTCGCAATGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAATGCGATACTGACTATCGCAACGCGAT
9243242 TTACATAGCG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
Found at i:9243844 original size:19 final size:19
Alignment explanation
Indices: 9243797--9243838 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
9243787 ACGAGATAAT
*
9243797 CGCAACGCGAAATAAAAAA
1 CGCAACGCGAAACAAAAAA
*
9243816 CGCAACGCGAAACAAAAAT
1 CGCAACGCGAAACAAAAAA
9243835 CGCA
1 CGCA
9243839 TTGCGATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.52, C:0.26, G:0.17, T:0.05
Consensus pattern (19 bp):
CGCAACGCGAAACAAAAAA
Found at i:9243945 original size:19 final size:19
Alignment explanation
Indices: 9243834--9244037 Score: 185
Period size: 19 Copynumber: 11.1 Consensus size: 19
9243824 GAAACAAAAA
* *
9243834 TCGCATTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
9243853 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* * *
9243872 TCACATTGCGTTTTTCATT
1 TCGCGTTGCGATTTTCATT
*
9243891 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
9243910 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
9243930 TCGCGTTGCGATTTTC---
1 TCGCGTTGCGATTTTCATT
* **
9243946 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
9243963 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
9243977 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
9243996 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
9244016 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
9244036 TC
1 TC
9244038 AACCAAAAGA
Statistics
Matches: 150, Mismatches: 22, Indels: 26
0.76 0.11 0.13
Matches are distributed among these distances:
14 19 0.13
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 73 0.49
20 49 0.33
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:9243953 original size:39 final size:38
Alignment explanation
Indices: 9243834--9244037 Score: 155
Period size: 33 Copynumber: 5.6 Consensus size: 38
9243824 GAAACAAAAA
*
9243834 TCGC-ATTGCGATTTTTATTTCGCGTTGCGATTTTCATT
1 TCGCGATTGCGATTTTCATTTCGCGTTGCGATTTTC-TT
* * *
9243872 TCAC-ATTGCGTTTTTCATTTCGCGTTGCGATTTTTATT
1 TCGCGATTGCGATTTTCATTTCGCGTTGCGA-TTTTCTT
*
9243910 TCGCGGTTGCGATTTTCATTTCGCGTTGCGATTTTC--
1 TCGCGATTGCGATTTTCATTTCGCGTTGCGATTTTCTT
* **
9243946 T-G-G-TCGCGATAGTCATTTCGCGTTGCGA--TTC--
1 TCGCGATTGCGATTTTCATTTCGCGTTGCGATTTTCTT
* ** *
9243977 TCTCG-TTGCGATAGTCATTTCCGCGTTGCGATTCTCATT
1 TCGCGATTGCGATTTTCATTT-CGCGTTGCGATTTTC-TT
*
9244016 ATCTCG-TTGCGATTTTCATTTC
1 -TCGCGATTGCGATTTTCATTTC
9244038 AACCAAAAGA
Statistics
Matches: 139, Mismatches: 16, Indels: 21
0.79 0.09 0.12
Matches are distributed among these distances:
31 4 0.03
33 37 0.27
34 11 0.08
35 1 0.01
36 3 0.02
38 36 0.26
39 29 0.21
40 18 0.13
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.46
Consensus pattern (38 bp):
TCGCGATTGCGATTTTCATTTCGCGTTGCGATTTTCTT
Found at i:9244014 original size:20 final size:19
Alignment explanation
Indices: 9243980--9244037 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
9243970 GCGATTCTCT
**
9243980 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTT-CG
* *
9244000 CGTTGCGATTCTCATTATCT
1 CGTTGCGATTTTCATT-TCG
9244020 CGTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
9244038 AACCAAAAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 2 0.06
20 30 0.91
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:9246099 original size:42 final size:42
Alignment explanation
Indices: 9246039--9246160 Score: 120
Period size: 42 Copynumber: 2.9 Consensus size: 42
9246029 GCCTGACTCG
* * *
9246039 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
9246081 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
9246123 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGA
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGA
9246161 AAACCACCCA
Statistics
Matches: 65, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 61 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.17, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:9246119 original size:21 final size:21
Alignment explanation
Indices: 9246095--9246160 Score: 53
Period size: 21 Copynumber: 3.1 Consensus size: 21
9246085 TCATTCCTCG
9246095 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
9246116 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
9246137 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
9246158 AGA
1 AGA
9246161 AAACCACCCA
Statistics
Matches: 31, Mismatches: 13, Indels: 2
0.67 0.28 0.04
Matches are distributed among these distances:
21 30 0.97
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.20, T:0.20
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:9246791 original size:24 final size:24
Alignment explanation
Indices: 9246757--9246809 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
9246747 CTGAAACATC
* *
9246757 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
* *
9246781 ATCAAAGTCCGGGTATTGAGCAAG
1 ATCAAAATCCGGGTATTGACCAAG
9246805 ATCAA
1 ATCAA
9246810 TTTTCGAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.25
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:9247892 original size:20 final size:20
Alignment explanation
Indices: 9247867--9247904 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
9247857 ATTCATTTGA
*
9247867 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGAGAAAATGG
9247887 CTATCGCAACGAGAAAAT
1 CTATCGCAACGAGAAAAT
9247905 CGCAATGCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:9247964 original size:19 final size:19
Alignment explanation
Indices: 9247923--9248009 Score: 139
Period size: 19 Copynumber: 4.8 Consensus size: 19
9247913 GAAATGAAAA
9247923 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
9247939 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
9247956 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
9247975 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
9247994 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
9248010 TCGTTGCGAT
Statistics
Matches: 66, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.17
16 3 0.05
17 3 0.05
19 49 0.74
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:9247993 original size:38 final size:33
Alignment explanation
Indices: 9247923--9248038 Score: 151
Period size: 33 Copynumber: 3.4 Consensus size: 33
9247913 GAAATGAAAA
9247923 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
9247956 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTC---TCG--TTGCGATTTTCATT
***
9247994 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
*
9248027 TCGCGTTGCGAT
1 TCGCATTGCGAT
9248039 AGTCTGTTTT
Statistics
Matches: 74, Mismatches: 4, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
33 38 0.51
35 3 0.04
36 3 0.04
38 30 0.41
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
Found at i:9248145 original size:14 final size:14
Alignment explanation
Indices: 9248126--9248162 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
9248116 CATCAATTAA
9248126 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
9248140 ACAAATCATCTTTT
1 ACAAATCAACATTT
9248154 ACAAATCAA
1 ACAAATCAA
9248163 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:9250071 original size:20 final size:19
Alignment explanation
Indices: 9250031--9250097 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
9250021 GAAACTTAAA
*
9250031 ATCGCAACGCAAAATGACT
1 ATCGCAACGCGAAATGACT
*
9250050 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
9250070 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
9250089 ATCGCAACG
1 ATCGCAACG
9250098 ACAAAATCGC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
19 24 0.60
20 16 0.40
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:9250105 original size:14 final size:14
Alignment explanation
Indices: 9250086--9250143 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
9250076 ATGCGAAATG
9250086 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
9250100 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
9250116 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
9250132 AAAATCGCAACG
1 AAAATCGCAACG
9250144 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:9250128 original size:32 final size:33
Alignment explanation
Indices: 9250070--9250148 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
9250060 GGAAATGGCT
*
9250070 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
9250103 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
9250135 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
9250149 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:9250196 original size:14 final size:14
Alignment explanation
Indices: 9250177--9250234 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
9250167 TTTCATTTCG
9250177 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
9250191 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
*
9250207 CGCATTGAGATTTTGT
1 CG--TTGCGATTTTGT
9250223 CGTTGCGATTTT
1 CGTTGCGATTTT
9250235 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 8 0.22
18 8 0.22
ACGTcount: A:0.12, C:0.16, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:9250208 original size:32 final size:33
Alignment explanation
Indices: 9250160--9250250 Score: 148
Period size: 32 Copynumber: 2.8 Consensus size: 33
9250150 ACAAATCGCA
* *
9250160 TTGCAATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
9250193 TTGCGA-TTTCATTTCGCATTGAGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
9250225 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
9250251 AGCCATTTCC
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 30 0.57
33 23 0.43
ACGTcount: A:0.14, C:0.18, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:9250257 original size:19 final size:19
Alignment explanation
Indices: 9250235--9250278 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
9250225 TTGCGATTTT
9250235 CATTTCGCA-TTGCGATAGC
1 CATTTC-CACTTGCGATAGC
*
9250254 CATTTCCACTTTGCGATAGT
1 CATTTCCAC-TTGCGATAGC
9250274 CATTT
1 CATTT
9250279 TCGTGTTGCG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 2 0.09
19 6 0.27
20 14 0.64
ACGTcount: A:0.20, C:0.25, G:0.16, T:0.39
Consensus pattern (19 bp):
CATTTCCACTTGCGATAGC
Found at i:9250797 original size:18 final size:18
Alignment explanation
Indices: 9250771--9250815 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
9250761 GTCGATCAGA
*
9250771 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
9250789 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
9250807 TGATGGCTC
1 TGATGGCTC
9250816 CCGATGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:9252160 original size:20 final size:20
Alignment explanation
Indices: 9252135--9252177 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
9252125 AATAGTTTCT
9252135 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
*
9252155 GAAAATGAAAATCGCAACGC
1 GAAAATGAAAATCGCAACAC
9252175 GAA
1 GAA
9252178 TTCGACTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.53, C:0.19, G:0.19, T:0.09
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:9252483 original size:22 final size:22
Alignment explanation
Indices: 9252456--9252499 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
9252446 GATGGAGATA
9252456 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
9252478 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
9252500 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:9252697 original size:21 final size:21
Alignment explanation
Indices: 9252667--9252762 Score: 65
Period size: 20 Copynumber: 4.7 Consensus size: 21
9252657 CGCTTTGAAA
9252667 ATCGCATTGCGATTATGTATT
1 ATCGCATTGCGATTATGTATT
* * *
9252688 ATCGCGTTGCGA--AAGTAAGT
1 ATCGCATTGCGATTATGT-ATT
* * * *
9252708 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGATTATGTATT
**
9252729 ATCGCATTGCGA-TA-GTCAGA
1 ATCGCATTGCGATTATGT-ATT
9252749 ATCGCATTGCGATT
1 ATCGCATTGCGATT
9252763 TTCCCAATTC
Statistics
Matches: 56, Mismatches: 14, Indels: 10
0.70 0.17 0.12
Matches are distributed among these distances:
19 4 0.07
20 27 0.48
21 24 0.43
22 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.38
Consensus pattern (21 bp):
ATCGCATTGCGATTATGTATT
Found at i:9252730 original size:41 final size:41
Alignment explanation
Indices: 9252666--9252764 Score: 126
Period size: 41 Copynumber: 2.4 Consensus size: 41
9252656 GCGCTTTGAA
* *
9252666 AATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTAAG
1 AATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAG
* * * * * *
9252707 TATCTCGTTGCGATTTTTTATTATCGCATTGCGATAGTCAG
1 AATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAG
9252748 AATCGCATTGCGATTTT
1 AATCGCATTGCGATTTT
9252765 CCCAATTCGC
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.38
Consensus pattern (41 bp):
AATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAG
Found at i:9252775 original size:41 final size:41
Alignment explanation
Indices: 9252730--9252823 Score: 118
Period size: 41 Copynumber: 2.3 Consensus size: 41
9252720 TTTTTTATTA
*
9252730 TCGCATTGCGATAGT-CAGAATCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGAT-GTACAGAATCACATTGCGATTTTCCCAAT
* ** *
9252771 TCGCATTGCGATTTACTTATTCACATTGCGATTTTCCCAAT
1 TCGCATTGCGATGTACAGAATCACATTGCGATTTTCCCAAT
*
9252812 TCGCGTTGCGAT
1 TCGCATTGCGAT
9252824 TTACTTATTC
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 1 0.02
41 45 0.98
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.36
Consensus pattern (41 bp):
TCGCATTGCGATGTACAGAATCACATTGCGATTTTCCCAAT
Found at i:9252797 original size:20 final size:20
Alignment explanation
Indices: 9252750--9252842 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
9252740 ATAGTCAGAA
* **
9252750 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
9252771 TCGCATTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* * **
9252791 TCACATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
9252812 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
9252832 TCGCATTGCGA
1 TCGCATTGCGA
9252843 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.19, C:0.25, G:0.16, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:9252824 original size:41 final size:41
Alignment explanation
Indices: 9252753--9252842 Score: 162
Period size: 41 Copynumber: 2.2 Consensus size: 41
9252743 GTCAGAATCG
9252753 CATTGCGATTTTCCCAATTCGCATTGCGATTTACTTATTCA
1 CATTGCGATTTTCCCAATTCGCATTGCGATTTACTTATTCA
* *
9252794 CATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTATTCG
1 CATTGCGATTTTCCCAATTCGCATTGCGATTTACTTATTCA
9252835 CATTGCGA
1 CATTGCGA
9252843 ATTGGGAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.40
Consensus pattern (41 bp):
CATTGCGATTTTCCCAATTCGCATTGCGATTTACTTATTCA
Found at i:9259536 original size:17 final size:18
Alignment explanation
Indices: 9259514--9259556 Score: 79
Period size: 17 Copynumber: 2.4 Consensus size: 18
9259504 ATGACCGGTT
9259514 CCGACCCGACCCGTTGA-
1 CCGACCCGACCCGTTGAC
9259531 CCGACCCGACCCGTTGAC
1 CCGACCCGACCCGTTGAC
9259549 CCGACCCG
1 CCGACCCG
9259557 TTGACCGTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 17 0.68
18 8 0.32
ACGTcount: A:0.16, C:0.51, G:0.23, T:0.09
Consensus pattern (18 bp):
CCGACCCGACCCGTTGAC
Found at i:9259549 original size:13 final size:13
Alignment explanation
Indices: 9259533--9259562 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
9259523 CCCGTTGACC
9259533 GACCCGACCCGTT
1 GACCCGACCCGTT
9259546 GACCCGACCCGTT
1 GACCCGACCCGTT
9259559 GACC
1 GACC
9259563 GTTGACCGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.17, C:0.47, G:0.23, T:0.13
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:9259666 original size:30 final size:30
Alignment explanation
Indices: 9259571--9259698 Score: 172
Period size: 29 Copynumber: 4.4 Consensus size: 30
9259561 CCGTTGACCG
* **
9259571 GGTGATATTTTGGGAA-TTAATTCGAAATG
1 GGTGCTATTTTGGGAATTTAATTCGAAAAA
*
9259600 GGTGCTATTTTGGGAATTTAATTTGAAAAA
1 GGTGCTATTTTGGGAATTTAATTCGAAAAA
*
9259630 -GTGCTATATTGGGAATTTAATTCGAAAAA
1 GGTGCTATTTTGGGAATTTAATTCGAAAAA
* *
9259659 TGTGCTATTTTAGGAATTTAATTCG-AAAA
1 GGTGCTATTTTGGGAATTTAATTCGAAAAA
9259688 GGTGCTATTTT
1 GGTGCTATTTT
9259699 AGTAATTATT
Statistics
Matches: 88, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
29 56 0.64
30 32 0.36
ACGTcount: A:0.32, C:0.05, G:0.23, T:0.40
Consensus pattern (30 bp):
GGTGCTATTTTGGGAATTTAATTCGAAAAA
Found at i:9259675 original size:59 final size:58
Alignment explanation
Indices: 9259580--9259726 Score: 170
Period size: 59 Copynumber: 2.5 Consensus size: 58
9259570 GGGTGATATT
** * *
9259580 TTGGGAATTAATTCGAAATGGGTGCTATTTTGGGAATTTAATTTGAAAAAGTGCTATA
1 TTGGGAATTAATTCGAAAAAGGTGCTATTTTAGGAATTTAATTCGAAAAAGTGCTATA
* * *
9259638 TTGGGAATTTAATTCGAAAAATGTGCTATTTTAGGAATTTAATTCGAAAAGGTGCTATT
1 TTGGGAA-TTAATTCGAAAAAGGTGCTATTTTAGGAATTTAATTCGAAAAAGTGCTATA
* * **
9259697 TTAGTAATT-ATTTTAAAAAGTGTGCTATTT
1 TTGGGAATTAATTCGAAAAAG-GTGCTATTT
9259727 CTGTAAAATG
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
57 8 0.11
58 18 0.24
59 49 0.65
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.41
Consensus pattern (58 bp):
TTGGGAATTAATTCGAAAAAGGTGCTATTTTAGGAATTTAATTCGAAAAAGTGCTATA
Found at i:9259721 original size:29 final size:30
Alignment explanation
Indices: 9259576--9259726 Score: 134
Period size: 29 Copynumber: 5.2 Consensus size: 30
9259566 GACCGGGTGA
* * * *
9259576 TATTTTGGGAA-TTAATTCGAAATGGGTGC
1 TATTTTAGGAATTTAATTCAAAAAGTGTGC
* *
9259605 TATTTTGGGAATTTAATTTGAAAAA--GTGC
1 TATTTTAGGAATTTAA-TTCAAAAAGTGTGC
* *
9259634 TATATTGGGAATTTAATTCGAAAAA-TGTGC
1 TATTTTAGGAATTTAATTC-AAAAAGTGTGC
*
9259664 TATTTTAGGAATTTAATTCGAAAAG-GTGC
1 TATTTTAGGAATTTAATTCAAAAAGTGTGC
* * *
9259693 TATTTTAGTAA-TTATTTTAAAAAGTGTGC
1 TATTTTAGGAATTTAATTCAAAAAGTGTGC
9259722 TATTT
1 TATTT
9259727 CTGTAAAATG
Statistics
Matches: 104, Mismatches: 12, Indels: 12
0.81 0.09 0.09
Matches are distributed among these distances:
28 12 0.12
29 62 0.60
30 25 0.24
31 5 0.05
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.42
Consensus pattern (30 bp):
TATTTTAGGAATTTAATTCAAAAAGTGTGC
Found at i:9260492 original size:15 final size:15
Alignment explanation
Indices: 9260472--9260504 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
9260462 TGATACGTGA
9260472 TTCCTGAATAT-TGAT
1 TTCCTG-ATATCTGAT
9260487 TTCCTGATATCTGAT
1 TTCCTGATATCTGAT
9260502 TTC
1 TTC
9260505 TGTATTTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.21, C:0.18, G:0.12, T:0.48
Consensus pattern (15 bp):
TTCCTGATATCTGAT
Found at i:9265016 original size:21 final size:21
Alignment explanation
Indices: 9264973--9265050 Score: 70
Period size: 21 Copynumber: 3.8 Consensus size: 21
9264963 TTTTTGGCTA
**
9264973 AAAGGATTGATCTATTTGACC
1 AAAGGATTGATCCCTTTGACC
9264994 AAAGGATTGATCCCTTT-ACCC
1 AAAGGATTGATCCCTTTGA-CC
* * * *
9265015 AAAAGATCGATCCCCTTGA-A
1 AAAGGATTGATCCCTTTGACC
*
9265035 AAAAGATTGATCCCTT
1 AAAGGATTGATCCCTT
9265051 GGATTCCAGT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
20 15 0.32
21 31 0.66
22 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (21 bp):
AAAGGATTGATCCCTTTGACC
Found at i:9270954 original size:16 final size:16
Alignment explanation
Indices: 9270933--9270971 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
9270923 CGTTTACAAA
9270933 AATGATAGAACAATTC
1 AATGATAGAACAATTC
9270949 AATGATAGAACAATTC
1 AATGATAGAACAATTC
*
9270965 AAGGATA
1 AATGATA
9270972 TCACATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.51, C:0.10, G:0.15, T:0.23
Consensus pattern (16 bp):
AATGATAGAACAATTC
Found at i:9271251 original size:34 final size:34
Alignment explanation
Indices: 9271212--9271287 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 34
9271202 GTCAATTTAA
*
9271212 AAAGATATTTATTAT-CTTTT-TA-ATTTTGAATATT
1 AAAGATAATT-TTATACTTTTGTATATTTT-AA-ATT
9271246 AAAGATAATTTTATACTTTTGTATATTTTAAATT
1 AAAGATAATTTTATACTTTTGTATATTTTAAATT
9271280 AAA-ATAAT
1 AAAGATAAT
9271288 ATCTATTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
33 9 0.24
34 20 0.53
35 4 0.11
36 5 0.13
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (34 bp):
AAAGATAATTTTATACTTTTGTATATTTTAAATT
Found at i:9277888 original size:320 final size:320
Alignment explanation
Indices: 9277300--9277918 Score: 902
Period size: 320 Copynumber: 1.9 Consensus size: 320
9277290 CGTTGACTGG
* * *
9277300 CGTTGACCACTATTGACCAGAACTTTGACTGGTGTTGATCGGGTGTTGAATGACCTTTGACTTTA
1 CGTTGACCACTATTGACCAGAACTTTGAATGGCGTTGATCGGGCGTTGAATGACCTTTGACTTTA
* * * ** ** **
9277365 ACCTAGTATACCTATCCTAACGTTTTTTGACGTTCAGAGTCTGATTCTGCAGTCTGGTTTTCAAA
66 ACCGACTATACCTAACCTAACGTTTTTCAACGTTCAGAGTCCAATTCTGCAGTCCAGTTTTCAAA
* *
9277430 ATTCGAACCCGAAGGCCTCAAAATTACCAGTCAAACCCGTTGACTTTTACTTTGACCGAAAATTC
131 ATTCGAACCCGAAGGCCTCAAAATTACCAGTCAAACCCGTTAACTTTGACTTTGACCGAAAATTC
* * *
9277495 AAAATTTTTGAAAAGTCATATTTTATGTTTTTGATATCCTGAATCCATTTTTGGGGTCTGTTTCA
196 AAAATTTTTAAAAAGTCATATTTTATGTTTTTGACATCCTGAATCCATTTTTGGGGTCCGTTTCA
* * *
9277560 CCAAACTCAAACCTGATAAGCTATTTTTGATTGATTTATGTAAAACGATTGACTATTGAC
261 CAAAACTCAAACCCGATAAGCTATTTTTGACTGATTTATGTAAAACGATTGACTATTGAC
* *
9277620 CGTTGACCACTGTTGACCAGAACTTTGAATGGCGTTGATCGGGCGTTGAATGACCTTTGACTTTG
1 CGTTGACCACTATTGACCAGAACTTTGAATGGCGTTGATCGGGCGTTGAATGACCTTTGACTTTA
* ** *
9277685 ACCGACTATACCTAACCTGACGTTTTTCAACGTTGTGAGTCCAATT-TCGCAGTCCATTTTTCAA
66 ACCGACTATACCTAACCTAACGTTTTTCAACGTTCAGAGTCCAATTCT-GCAGTCCAGTTTTCAA
* * *
9277749 AATTC-AGACCCGGAGGCCTCGAAATTGCCAGTCAAACCCGTTAACTTTGACTTTGACCGAAAAG
130 AATTCGA-ACCCGAAGGCCTCAAAATTACCAGTCAAACCCGTTAACTTTGACTTTGACCGAAAA-
*
9277813 TT-AAAATTTTTAAAAAGTCATATTTTATGTTTTTGACATCTTGAATCCATTTTTGGGGTCCGTT
193 TTCAAAATTTTTAAAAAGTCATATTTTATGTTTTTGACATCCTGAATCCATTTTTGGGGTCCGTT
* *
9277877 TCGCAAAACTCAAACCCGGTAAGCTATTTTTGACTGATTTAT
258 TCACAAAACTCAAACCCGATAAGCTATTTTTGACTGATTTAT
9277919 CCCCCGATTC
Statistics
Matches: 264, Mismatches: 32, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
319 2 0.01
320 260 0.98
321 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (320 bp):
CGTTGACCACTATTGACCAGAACTTTGAATGGCGTTGATCGGGCGTTGAATGACCTTTGACTTTA
ACCGACTATACCTAACCTAACGTTTTTCAACGTTCAGAGTCCAATTCTGCAGTCCAGTTTTCAAA
ATTCGAACCCGAAGGCCTCAAAATTACCAGTCAAACCCGTTAACTTTGACTTTGACCGAAAATTC
AAAATTTTTAAAAAGTCATATTTTATGTTTTTGACATCCTGAATCCATTTTTGGGGTCCGTTTCA
CAAAACTCAAACCCGATAAGCTATTTTTGACTGATTTATGTAAAACGATTGACTATTGAC
Found at i:9279014 original size:27 final size:27
Alignment explanation
Indices: 9278984--9279041 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
9278974 AAATGATTGT
9278984 AATACAC-TAGATATGTAAAATGACC-AG
1 AATACACTTAGA-ATG-AAAATGACCAAG
* *
9279011 AATACCCTTAGAATGCAAATGACCAAG
1 AATACACTTAGAATGAAAATGACCAAG
9279038 AATA
1 AATA
9279042 TCACCAAGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 8 0.30
27 15 0.56
28 4 0.15
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.21
Consensus pattern (27 bp):
AATACACTTAGAATGAAAATGACCAAG
Found at i:9280155 original size:24 final size:24
Alignment explanation
Indices: 9280062--9280144 Score: 87
Period size: 24 Copynumber: 3.5 Consensus size: 24
9280052 AAATATTTTA
* * * *
9280062 TCTGATTTCCGACTTGAATTATGT
1 TCTGATATCTGACCTGAATTCTGT
*
9280086 TCTGATA-CATGACCTGAATTTTGT
1 TCTGATATC-TGACCTGAATTCTGT
* *
9280110 TCTGATTTCTGACCTGGATTCTGT
1 TCTGATATCTGACCTGAATTCTGT
9280134 TCTGATATCTG
1 TCTGATATCTG
9280145 TTTTGAATTC
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
23 1 0.02
24 47 0.96
25 1 0.02
ACGTcount: A:0.19, C:0.18, G:0.18, T:0.45
Consensus pattern (24 bp):
TCTGATATCTGACCTGAATTCTGT
Found at i:9286776 original size:26 final size:26
Alignment explanation
Indices: 9286747--9286799 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
9286737 TAACTTTTCT
9286747 AGTCAA-AGTCAAAGGTTAACGATCAA
1 AGTCAACAGTCAAA-GTTAACGATCAA
* *
9286773 AGTCAACGGTCAAAGTTAACGGTCAA
1 AGTCAACAGTCAAAGTTAACGATCAA
9286799 A
1 A
9286800 CTCAGACGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 18 0.75
27 6 0.25
ACGTcount: A:0.43, C:0.17, G:0.21, T:0.19
Consensus pattern (26 bp):
AGTCAACAGTCAAAGTTAACGATCAA
Found at i:9286785 original size:13 final size:13
Alignment explanation
Indices: 9286754--9286799 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
9286744 TCTAGTCAAA
9286754 GTCAAAGGTTAACG
1 GTCAAA-GTTAACG
* *
9286768 ATCAAAGTCAACG
1 GTCAAAGTTAACG
9286781 GTCAAAGTTAACG
1 GTCAAAGTTAACG
9286794 GTCAAA
1 GTCAAA
9286800 CTCAGACGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
13 23 0.82
14 5 0.18
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (13 bp):
GTCAAAGTTAACG
Found at i:9294798 original size:22 final size:22
Alignment explanation
Indices: 9294755--9294799 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
9294745 AATCCCCGGC
*
9294755 CTCTTCCTCGATTTCTTTAAGT
1 CTCTTCCTCGATTTCTTCAAGT
*
9294777 CTCTTCTTC-ATTTCTTCCAAGT
1 CTCTTCCTCGATTTCTT-CAAGT
9294799 C
1 C
9294800 CTAAAATCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.13, C:0.31, G:0.07, T:0.49
Consensus pattern (22 bp):
CTCTTCCTCGATTTCTTCAAGT
Found at i:9295328 original size:60 final size:60
Alignment explanation
Indices: 9295259--9295373 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 60
9295249 AATTCATCCC
**
9295259 TAAACTTTTAAATAATT-TAATTTTATCTTTAAATTATGAT-TATCATTTTAAATTAATCTT
1 TAAACTTTTAAAT-ATTCTAATTTTATCCCTAAATTATGATAT-TCATTTTAAATTAATCTT
* *
9295319 TAAATTTTTAAATATTCTAATTTTATCCCTAAATTATGATATTTATTTTAAATTA
1 TAAACTTTTAAATATTCTAATTTTATCCCTAAATTATGATATTCATTTTAAATTA
9295374 GTCCTCACAC
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
59 3 0.06
60 45 0.92
61 1 0.02
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (60 bp):
TAAACTTTTAAATATTCTAATTTTATCCCTAAATTATGATATTCATTTTAAATTAATCTT
Found at i:9296774 original size:8 final size:8
Alignment explanation
Indices: 9296761--9296791 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
9296751 AATACATTAT
9296761 ATTTTAAA
1 ATTTTAAA
9296769 ATTTTAAA
1 ATTTTAAA
9296777 ATTTTAAA
1 ATTTTAAA
9296785 ATTTTAA
1 ATTTTAA
9296792 TTATGGTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
ATTTTAAA
Found at i:9301411 original size:19 final size:18
Alignment explanation
Indices: 9301392--9301440 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
9301382 GTTGTTTTTA
9301392 AAATAAAAAATAAGAATT
1 AAATAAAAAATAAGAATT
* *
9301410 AAATAAAATAAAAATAATT
1 AAATAAAA-AATAAGAATT
9301429 AAATAAACAAAT
1 AAATAAA-AAAT
9301441 TAAAGAGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 8 0.31
19 17 0.65
20 1 0.04
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (18 bp):
AAATAAAAAATAAGAATT
Found at i:9301435 original size:23 final size:22
Alignment explanation
Indices: 9301390--9301444 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
9301380 AAGTTGTTTT
*
9301390 TAAAATAAAAAATAAGAATTAAA
1 TAAAAT-AAAAATAAGAAATAAA
*
9301413 TAAAATAAAAATAATTAAATAAA
1 TAAAATAAAAATAA-GAAATAAA
* *
9301436 CAAATTAAA
1 TAAAATAAA
9301445 GAGATTGAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 8 0.30
23 19 0.70
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (22 bp):
TAAAATAAAAATAAGAAATAAA
Found at i:9304107 original size:20 final size:20
Alignment explanation
Indices: 9304082--9304128 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
9304072 GTTCAAAGAA
9304082 AAAATAAAATAAAATA-AATG
1 AAAATAAAAT-AAATAGAATG
*
9304102 AAAATAAAGTAAATAGAATG
1 AAAATAAAATAAATAGAATG
9304122 -AAATAAA
1 AAAATAAA
9304129 GTTCGCTACA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (20 bp):
AAAATAAAATAAATAGAATG
Found at i:9304171 original size:12 final size:11
Alignment explanation
Indices: 9304136--9304177 Score: 59
Period size: 12 Copynumber: 3.8 Consensus size: 11
9304126 AAAGTTCGCT
9304136 ACAAAAATAAA
1 ACAAAAATAAA
*
9304147 AC-GAAATAAA
1 ACAAAAATAAA
9304157 ACAAAAATAAAA
1 ACAAAAAT-AAA
9304169 ACAAAAATA
1 ACAAAAATA
9304178 TAACGAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 9 0.33
11 7 0.26
12 11 0.41
ACGTcount: A:0.79, C:0.10, G:0.02, T:0.10
Consensus pattern (11 bp):
ACAAAAATAAA
Found at i:9305496 original size:18 final size:19
Alignment explanation
Indices: 9305465--9305500 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
9305455 AAGATATATT
*
9305465 AAAATAAAATAAATAATAA
1 AAAAGAAAATAAATAATAA
9305484 AAAAGAAAA-AAATAATA
1 AAAAGAAAATAAATAATA
9305501 TAATAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.17
Consensus pattern (19 bp):
AAAAGAAAATAAATAATAA
Found at i:9306398 original size:76 final size:73
Alignment explanation
Indices: 9306236--9306410 Score: 190
Period size: 76 Copynumber: 2.3 Consensus size: 73
9306226 CTAAAATACC
* * * *
9306236 TAAAAAATAATATAATATTCTAAATCATAATTAAAATACTAAAACCCATTTAAACTAAAATACCT
1 TAAAATATAAAATAATATCCTAAAACATAATTAAAATACTAAAACCCATTTAAACTAAAATA-C-
*
9306301 AAAACAAAGA
64 AAAACAAAAA
* *
9306311 TAAAATATAAAAATAATATCCTAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATA-A
1 TAAAATAT-AAAATAATATCCTAAAACATAATTAAAATACTAAAACCCATTTAAACTAAAATACA
*
9306375 AAAGATAAAA
65 AAACA-AAAA
* * *
9306385 TATAATGTTTAAAATATTATCCTAAA
1 TA-AA-ATATAAAATAATATCCTAAA
9306411 CTTGAGTTTA
Statistics
Matches: 85, Mismatches: 11, Indels: 8
0.82 0.11 0.08
Matches are distributed among these distances:
73 5 0.06
74 5 0.06
75 24 0.28
76 51 0.60
ACGTcount: A:0.58, C:0.11, G:0.02, T:0.29
Consensus pattern (73 bp):
TAAAATATAAAATAATATCCTAAAACATAATTAAAATACTAAAACCCATTTAAACTAAAATACAA
AACAAAAA
Found at i:9319773 original size:31 final size:31
Alignment explanation
Indices: 9319735--9319793 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
9319725 CGGTGAATTC
9319735 AATATGTCCTTCTCACTAGGAACTCCCATTT
1 AATATGTCCTTCTCACTAGGAACTCCCATTT
*
9319766 AATATGTCCTTCTCATTAGGAACTCCCA
1 AATATGTCCTTCTCACTAGGAACTCCCA
9319794 AACTCTTGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.34
Consensus pattern (31 bp):
AATATGTCCTTCTCACTAGGAACTCCCATTT
Found at i:9327233 original size:23 final size:23
Alignment explanation
Indices: 9327203--9327252 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
9327193 TGGACCATAT
9327203 GGGATAACGAGCATGTGCAAACA
1 GGGATAACGAGCATGTGCAAACA
* *
9327226 GGGATAACGGGCATGTGCAACCA
1 GGGATAACGAGCATGTGCAAACA
9327249 GGGA
1 GGGA
9327253 AACCAGATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.34, C:0.18, G:0.36, T:0.12
Consensus pattern (23 bp):
GGGATAACGAGCATGTGCAAACA
Found at i:9333334 original size:24 final size:24
Alignment explanation
Indices: 9333300--9333358 Score: 109
Period size: 24 Copynumber: 2.5 Consensus size: 24
9333290 GAACCCTAAT
9333300 TCCATTTCTCCCCCAAATCTCTTC
1 TCCATTTCTCCCCCAAATCTCTTC
*
9333324 TTCATTTCTCCCCCAAATCTCTTC
1 TCCATTTCTCCCCCAAATCTCTTC
9333348 TCCATTTCTCC
1 TCCATTTCTCC
9333359 TGTCACCATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.15, C:0.44, G:0.00, T:0.41
Consensus pattern (24 bp):
TCCATTTCTCCCCCAAATCTCTTC
Found at i:9345365 original size:2 final size:2
Alignment explanation
Indices: 9345358--9345400 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
9345348 AATGGGGAAA
9345358 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
9345400 A
1 A
9345401 GTTTAGGTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9359231 original size:90 final size:90
Alignment explanation
Indices: 9359076--9359243 Score: 232
Period size: 90 Copynumber: 1.9 Consensus size: 90
9359066 TATATTATTG
* * * *
9359076 TATATACAATAAAGCTTGAGTTGTCCCTCTAAAACAATTGGTTAATCACCCTGGCTTTATTGATA
1 TATATACAATAAAGATTGAGTTGTCCCTCTAAAACAATTGGTTAATCACCCCGACTTTATGGATA
9359141 A-TATTCAAATAGCTTATTATACTAT
66 AGT-TTCAAATAGCTTATTATACTAT
* * * *
9359166 TATATGCAATAAAGATTGAGTTGTCCCTTTAGAGCAATTGGTTAAT-AGCCCCGACTTTATGGAT
1 TATATACAATAAAGATTGAGTTGTCCCTCTAAAACAATTGGTTAATCA-CCCCGACTTTATGGAT
9359230 AAGTTTCAAATAGC
65 AAGTTTCAAATAGC
9359244 CAGAAAAAGG
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
89 1 0.01
90 66 0.97
91 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (90 bp):
TATATACAATAAAGATTGAGTTGTCCCTCTAAAACAATTGGTTAATCACCCCGACTTTATGGATA
AGTTTCAAATAGCTTATTATACTAT
Found at i:9361528 original size:73 final size:73
Alignment explanation
Indices: 9361405--9361909 Score: 861
Period size: 73 Copynumber: 6.9 Consensus size: 73
9361395 CAAAGATTTG
9361405 TCTCGCTTGAGATAA-TTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAA
1 TCTCGCTTGAGA-AAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAA
9361469 CAAACTTTT
65 CAAACTTTT
* *
9361478 TCTCGCTTGAGAAAGTTTCACTCGAAATAGAAATTTATCTCACTTAAGATTGTTTTTCTTAAAAC
1 TCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAAC
9361543 AAACTTTT
66 AAACTTTT
* *
9361551 TTTCGCTAGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAAC
1 TCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAAC
9361616 AAACTTTT
66 AAACTTTT
*
9361624 TCTCGCTTGAGAAAGTTTCACTCGAAATAGAAATTTATCTCACTTGAGATTGTTTTTCTTAAAAA
1 TCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTT-AAAA
*
9361689 AAAACTTTT
65 CAAACTTTT
*
9361698 TCTCGCTTGAGAAAGTTTCACTCAAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAAC
1 TCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAAC
9361763 AAACTTTT
66 AAACTTTT
* *
9361771 TCTCACTTGGGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAAC
1 TCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAAC
9361836 AAA-TTGTT
66 AAACTT-TT
* * *
9361844 TCTTGCTTGAGAAAGTTTCACTTGAAATAGCAATTTATCTTACTTGAGATTGTTTTTCTTAAAAC
1 TCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAAC
9361909 A
66 A
9361910 TTTCCAGAAG
Statistics
Matches: 408, Mismatches: 21, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
72 4 0.01
73 334 0.82
74 70 0.17
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.40
Consensus pattern (73 bp):
TCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAAC
AAACTTTT
Found at i:9361787 original size:220 final size:220
Alignment explanation
Indices: 9361405--9361907 Score: 859
Period size: 220 Copynumber: 2.3 Consensus size: 220
9361395 CAAAGATTTG
9361405 TCTCGCTTGAGATAA-TTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTT-AAA
1 TCTCGCTTGAGA-AAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAA
* *
9361468 ACAAACTTTTTCTCGCTTGAGAAAGTTTCACTCGAAATAGAAATTTATCTCACTTAAGATTGTTT
65 AAAAACTTTTTCTCGCTTGAGAAAGTTTCACTCAAAATAGAAATTTATCTCACTTAAGATTGTTT
* *
9361533 TTCTTAAAACAAACTTTTTTTCGCTAGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGA
130 TTCTTAAAACAAACTTTTTCTCACTAGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGA
9361598 GATTGTTTTTCTTAAAACAAACTT-TT
195 GATTGTTTTTCTTAAAACAAA-TTGTT
*
9361624 TCTCGCTTGAGAAAGTTTCACTCGAAATAGAAATTTATCTCACTTGAGATTGTTTTTCTTAAAAA
1 TCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAAA
* *
9361689 AAAACTTTTTCTCGCTTGAGAAAGTTTCACTCAAAATAGCAATTTATCTCACTTGAGATTGTTTT
66 AAAACTTTTTCTCGCTTGAGAAAGTTTCACTCAAAATAGAAATTTATCTCACTTAAGATTGTTTT
* *
9361754 TCTTAAAACAAACTTTTTCTCACTTGGGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAG
131 TCTTAAAACAAACTTTTTCTCACTAGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAG
9361819 ATTGTTTTTCTTAAAACAAATTGTT
196 ATTGTTTTTCTTAAAACAAATTGTT
* * *
9361844 TCTTGCTTGAGAAAGTTTCACTTGAAATAGCAATTTATCTTACTTGAGATTGTTTTTCTTAAAA
1 TCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAA
9361908 CATTTCCAGA
Statistics
Matches: 268, Mismatches: 13, Indels: 5
0.94 0.05 0.02
Matches are distributed among these distances:
218 2 0.01
219 58 0.22
220 208 0.78
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.40
Consensus pattern (220 bp):
TCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAAA
AAAACTTTTTCTCGCTTGAGAAAGTTTCACTCAAAATAGAAATTTATCTCACTTAAGATTGTTTT
TCTTAAAACAAACTTTTTCTCACTAGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAG
ATTGTTTTTCTTAAAACAAATTGTT
Found at i:9362835 original size:28 final size:28
Alignment explanation
Indices: 9362783--9362836 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
9362773 ACATCAAAGG
*
9362783 TTATTTTTATATTTAGTTTTCATTTTAT
1 TTATTTTTATACTTAGTTTTCATTTTAT
*
9362811 TTATTTTT-TACTTAGTATTTTATTTT
1 TTATTTTTATACTTAGT-TTTCATTTT
9362837 TTTCAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.72
Consensus pattern (28 bp):
TTATTTTTATACTTAGTTTTCATTTTAT
Found at i:9369324 original size:22 final size:22
Alignment explanation
Indices: 9369299--9369342 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
9369289 CCAAGACAAA
9369299 ATCCTCATCTCAAAGCCTACTT
1 ATCCTCATCTCAAAGCCTACTT
*
9369321 ATCCTTATCTCAAAGCCTACTT
1 ATCCTCATCTCAAAGCCTACTT
9369343 TCGCTGAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.34, G:0.05, T:0.34
Consensus pattern (22 bp):
ATCCTCATCTCAAAGCCTACTT
Found at i:9381966 original size:2 final size:2
Alignment explanation
Indices: 9381959--9381990 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
9381949 ATACAAAGGT
9381959 TA TA TA TA TA TA 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
9381991 AGAACTGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9388423 original size:169 final size:169
Alignment explanation
Indices: 9388144--9388481 Score: 676
Period size: 169 Copynumber: 2.0 Consensus size: 169
9388134 AACATCTACG
9388144 GTGTTCAGAATATACTGCAAAATCCATTTCACAGCTTCCCAATGCTCCTTTCGAGGATCATACAT
1 GTGTTCAGAATATACTGCAAAATCCATTTCACAGCTTCCCAATGCTCCTTTCGAGGATCATACAT
9388209 ATACCTGCTCACAACCCTAACTGCCTGTGAAATATCGGGTCTCGTACATACCATTGCATACATTA
66 ATACCTGCTCACAACCCTAACTGCCTGTGAAATATCGGGTCTCGTACATACCATTGCATACATTA
9388274 AGGTACCAACAGCACTTGCATACGAAACCTTTGATATGT
131 AGGTACCAACAGCACTTGCATACGAAACCTTTGATATGT
9388313 GTGTTCAGAATATACTGCAAAATCCATTTCACAGCTTCCCAATGCTCCTTTCGAGGATCATACAT
1 GTGTTCAGAATATACTGCAAAATCCATTTCACAGCTTCCCAATGCTCCTTTCGAGGATCATACAT
9388378 ATACCTGCTCACAACCCTAACTGCCTGTGAAATATCGGGTCTCGTACATACCATTGCATACATTA
66 ATACCTGCTCACAACCCTAACTGCCTGTGAAATATCGGGTCTCGTACATACCATTGCATACATTA
9388443 AGGTACCAACAGCACTTGCATACGAAACCTTTGATATGT
131 AGGTACCAACAGCACTTGCATACGAAACCTTTGATATGT
9388482 ATTCCCGTTC
Statistics
Matches: 169, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
169 169 1.00
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (169 bp):
GTGTTCAGAATATACTGCAAAATCCATTTCACAGCTTCCCAATGCTCCTTTCGAGGATCATACAT
ATACCTGCTCACAACCCTAACTGCCTGTGAAATATCGGGTCTCGTACATACCATTGCATACATTA
AGGTACCAACAGCACTTGCATACGAAACCTTTGATATGT
Found at i:9392685 original size:14 final size:14
Alignment explanation
Indices: 9392659--9392691 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
9392649 GTATTTAGGG
*
9392659 ATTGTGGTTTAGTT
1 ATTGCGGTTTAGTT
9392673 ATTGCGGTTTAGTT
1 ATTGCGGTTTAGTT
9392687 ATTGC
1 ATTGC
9392692 CCTTATTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.15, C:0.06, G:0.27, T:0.52
Consensus pattern (14 bp):
ATTGCGGTTTAGTT
Found at i:9396285 original size:4 final size:4
Alignment explanation
Indices: 9396269--9396316 Score: 53
Period size: 4 Copynumber: 11.8 Consensus size: 4
9396259 CATTATTATT
* *
9396269 TTTA TTTA -GTA TTTA TTTA TTTTA ATTA TTTA TTTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA -TTTA TTTA TTTA TTT
9396317 TCATTAATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
3 2 0.05
4 27 0.73
5 8 0.22
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:9396297 original size:13 final size:13
Alignment explanation
Indices: 9396281--9396322 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
9396271 TATTTAGTAT
9396281 TTATTTATTTTAA
1 TTATTTATTTTAA
*
9396294 TTATTTATTTTAT
1 TTATTTATTTTAA
*
9396307 TTATTTATTTTCA
1 TTATTTATTTTAA
9396320 TTA
1 TTA
9396323 ATTTTAAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (13 bp):
TTATTTATTTTAA
Found at i:9396314 original size:17 final size:16
Alignment explanation
Indices: 9396246--9396316 Score: 58
Period size: 17 Copynumber: 4.4 Consensus size: 16
9396236 TTTATCTACT
* *
9396246 TTATTTATTTT-CTCA
1 TTATTTATTTTATTTA
9396261 TTA-TTATTTTTATTTA
1 TTATTTA-TTTTATTTA
*
9396277 GTATTTA-TTTATTTTAA
1 TTATTTATTTTA-TTT-A
9396294 TTATTTATTTTATTTA
1 TTATTTATTTTATTTA
9396310 TTTATTT
1 -TTATTT
9396317 TCATTAATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
14 3 0.07
15 11 0.24
16 8 0.18
17 19 0.42
18 4 0.09
ACGTcount: A:0.24, C:0.03, G:0.01, T:0.72
Consensus pattern (16 bp):
TTATTTATTTTATTTA
Found at i:9402679 original size:13 final size:13
Alignment explanation
Indices: 9402650--9402693 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
9402640 AAGTTCTACT
9402650 TTTCTTTCATCTTTC
1 TTTCTTT-AT-TTTC
9402665 TTTCTTTATTTTC
1 TTTCTTTATTTTC
*
9402678 TTTCATTATTTT-
1 TTTCTTTATTTTC
9402690 TTTC
1 TTTC
9402694 ACAATACTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 4 0.14
13 15 0.54
14 2 0.07
15 7 0.25
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTCTTTATTTTC
Found at i:9403625 original size:13 final size:13
Alignment explanation
Indices: 9403607--9403631 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9403597 TGGTGCCCGC
9403607 AACTCATGGCATT
1 AACTCATGGCATT
9403620 AACTCATGGCAT
1 AACTCATGGCAT
9403632 GTGGGCACTA
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:0.24, G:0.16, T:0.28
Consensus pattern (13 bp):
AACTCATGGCATT
Found at i:9406767 original size:17 final size:18
Alignment explanation
Indices: 9406745--9406791 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
9406735 TATGTAATTG
*
9406745 GATTCCAATTTC-TAACA
1 GATTCCAATTCCTTAACA
*
9406762 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTAACA
9406780 GATTCCAATTCC
1 GATTCCAATTCC
9406792 CTCATAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 11 0.41
18 16 0.59
ACGTcount: A:0.30, C:0.30, G:0.06, T:0.34
Consensus pattern (18 bp):
GATTCCAATTCCTTAACA
Found at i:9407470 original size:11 final size:11
Alignment explanation
Indices: 9407454--9407485 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
9407444 TAATCTGATG
9407454 GGAGCAATTTT
1 GGAGCAATTTT
9407465 GGAGCAATTTT
1 GGAGCAATTTT
*
9407476 GGACCAATTT
1 GGAGCAATTT
9407486 AGCAGATTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.28, C:0.12, G:0.25, T:0.34
Consensus pattern (11 bp):
GGAGCAATTTT
Found at i:9421836 original size:13 final size:13
Alignment explanation
Indices: 9421818--9421859 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
9421808 TCTCAATATT
9421818 ATTTAAAAGATTG
1 ATTTAAAAGATTG
*
9421831 ATTT--AATATT-
1 ATTTAAAAGATTG
9421841 ATTTAAAAGATTG
1 ATTTAAAAGATTG
9421854 ATTTAA
1 ATTTAA
9421860 CTTTTAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
10 4 0.17
11 5 0.21
12 5 0.21
13 10 0.42
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (13 bp):
ATTTAAAAGATTG
Found at i:9421838 original size:23 final size:23
Alignment explanation
Indices: 9421812--9421859 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
9421802 AAAATATCTC
9421812 AATATTATTTAAAAGATTGATTT
1 AATATTATTTAAAAGATTGATTT
9421835 AATATTATTTAAAAGATTGATTT
1 AATATTATTTAAAAGATTGATTT
9421858 AA
1 AA
9421860 CTTTTAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (23 bp):
AATATTATTTAAAAGATTGATTT
Found at i:9422008 original size:19 final size:19
Alignment explanation
Indices: 9421984--9422036 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
9421974 AAAATATGTT
*
9421984 ATTAGTTGAAATCACGATC
1 ATTAGTTGAGATCACGATC
9422003 ATTAGTTGAGATCACGATC
1 ATTAGTTGAGATCACGATC
9422022 ATTAGTTGAGATCAC
1 ATTAGTTGAGATCAC
9422037 ATGTCATTAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (19 bp):
ATTAGTTGAGATCACGATC
Found at i:9422100 original size:170 final size:168
Alignment explanation
Indices: 9421880--9422187 Score: 501
Period size: 170 Copynumber: 1.8 Consensus size: 168
9421870 GTTATCCATA
* *
9421880 TTTTATTTATACGTATGAATTACACATGAAAGAGGTGATGATTTACCTTAAAAAATGAGATGTAA
1 TTTTATTTACAAGTATGAATTACACATGAAAGAGGTGATGATTTACCTTAAAAAATGAGATGTAA
* *
9421945 AAATGTTATTGGTTGAGATAGACAATATGAAAATATGTTATTAGTTGAAATCACGATCATTAGTT
66 AAATGTTATTGGTTGAGATAGACAAGATGAAAATATGTTATTAGTTGAAATCACGATCACTAGTT
9422010 GAGATCACGATCATTAGTTGAGATCACATGTCATTAGT
131 GAGATCACGATCATTAGTTGAGATCACATGTCATTAGT
* * *
9422048 TTTTATTTACAAGTATGATTTACACATAAGAAAGAGGTGAAT-ATTTACCTTAAACATTGAGATG
1 TTTTATTTACAAGTATGAATTACACAT--GAAAGAGGTG-ATGATTTACCTTAAAAAATGAGATG
* *
9422112 TAAAAATGTTATTGGTTGATATCGACAAGATGAAAATATGTTATTAGTTGAAATCACGATCACTA
63 TAAAAATGTTATTGGTTGAGATAGACAAGATGAAAATATGTTATTAGTTGAAATCACGATCACTA
9422177 GTTGAGATCAC
128 GTTGAGATCAC
9422188 ATGTTATTAG
Statistics
Matches: 128, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
168 24 0.19
170 102 0.80
171 2 0.02
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (168 bp):
TTTTATTTACAAGTATGAATTACACATGAAAGAGGTGATGATTTACCTTAAAAAATGAGATGTAA
AAATGTTATTGGTTGAGATAGACAAGATGAAAATATGTTATTAGTTGAAATCACGATCACTAGTT
GAGATCACGATCATTAGTTGAGATCACATGTCATTAGT
Found at i:9422204 original size:39 final size:40
Alignment explanation
Indices: 9422149--9422228 Score: 108
Period size: 39 Copynumber: 2.0 Consensus size: 40
9422139 AGATGAAAAT
* * * *
9422149 ATGTTATTAGTTGAAATCACG-ATCACTAGTTGAGATCAC
1 ATGTTATTAGTAGAAATAACGAAACACTAGTTAAGATCAC
*
9422188 ATGTTATTAGTAGAAATAACGAAACATTAGTTAAGATCAC
1 ATGTTATTAGTAGAAATAACGAAACACTAGTTAAGATCAC
9422228 A
1 A
9422229 GATGATGTAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
39 19 0.54
40 16 0.46
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.31
Consensus pattern (40 bp):
ATGTTATTAGTAGAAATAACGAAACACTAGTTAAGATCAC
Found at i:9423488 original size:23 final size:23
Alignment explanation
Indices: 9423459--9423518 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
9423449 GATAATTTAA
9423459 AAATAATATTATTTCA-AATAAAT
1 AAATAATATTATTT-AGAATAAAT
* * *
9423482 AATTAATACTATTTAGTATAAAT
1 AAATAATATTATTTAGAATAAAT
*
9423505 AAATAATATGATTT
1 AAATAATATTATTT
9423519 TTGAAATTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
22 1 0.03
23 29 0.97
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (23 bp):
AAATAATATTATTTAGAATAAAT
Found at i:9424482 original size:21 final size:22
Alignment explanation
Indices: 9424457--9424509 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
9424447 AAATCATTCA
9424457 GGGGGAATCGGTACCCCCTTGG
1 GGGGGAATCGGTACCCCCTTGG
9424479 GGGGGAATCGGTACCCCCTT-G
1 GGGGGAATCGGTACCCCCTTGG
9424500 GGGGGAATCG
1 GGGGGAATCG
9424510 ATTCCCTCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 11 0.35
22 20 0.65
ACGTcount: A:0.15, C:0.25, G:0.43, T:0.17
Consensus pattern (22 bp):
GGGGGAATCGGTACCCCCTTGG
Found at i:9426670 original size:23 final size:22
Alignment explanation
Indices: 9426599--9426701 Score: 111
Period size: 21 Copynumber: 4.7 Consensus size: 22
9426589 AGAACCCGTG
* * *
9426599 GGGGGTATCGATTCCCC-TACA
1 GGGGGAATCGGTTCCCCTTAAA
*
9426620 GGGGGAATCGGTTCCCC-TACA
1 GGGGGAATCGGTTCCCCTTAAA
*
9426641 GGGGGAATCAGTTCCCCTTTAAA
1 GGGGGAATCGGTTCCCC-TTAAA
*
9426664 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGAATCGGTTCCCCTTAAA
* *
9426686 GGGGGTATCGATTCCC
1 GGGGGAATCGGTTCCC
9426702 TCTGTACTAA
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
21 35 0.49
22 18 0.25
23 19 0.26
ACGTcount: A:0.19, C:0.26, G:0.31, T:0.23
Consensus pattern (22 bp):
GGGGGAATCGGTTCCCCTTAAA
Found at i:9435582 original size:55 final size:55
Alignment explanation
Indices: 9435437--9435696 Score: 378
Period size: 55 Copynumber: 4.7 Consensus size: 55
9435427 GGCACTAAGC
*
9435437 GTGCAAAAACTAAGAAATTCTTACTAAGTGTATGAATTTCCGTATTGACACTATGT
1 GTGC-AAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGACACTATGT
* * * *
9435493 ATGCAAAAACTAAGAAATTCATATTAAATGTATGAATTTTCGTATTGACACTATGT
1 GTGC-AAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGACACTATGT
* * *
9435549 GTGCAAAACTAAGAAATTCATACTAAATGTATGAATATCCGTATTGGCACTATGT
1 GTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGACACTATGT
* * *
9435604 GTGCAAAACTAAGAAATTCATACGAAGTGTATGAATTTCCGTATGGGCACTATGT
1 GTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGACACTATGT
* *
9435659 GTGC-AAACTAAGAAATCCATACTAAGTGTATTAATTTC
1 GTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTC
9435697 GTTTGAGAAA
Statistics
Matches: 187, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
54 31 0.17
55 102 0.55
56 54 0.29
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (55 bp):
GTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGACACTATGT
Found at i:9435988 original size:81 final size:81
Alignment explanation
Indices: 9435902--9436605 Score: 1023
Period size: 81 Copynumber: 8.7 Consensus size: 81
9435892 TGGTCTAAAT
* * * *
9435902 TAAAAGATAAATGGCCTAACTGTGCATTTGGTAGAAAGGTGTTAATTATGCCAGTTAGATGAATG
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACG
9435967 GTTAAAGACCGTTGAG
66 GTTAAAGACCGTTGAG
* * *
9435983 TAAAAGATAAATGGCCTAGCTGTGCACTTGGCAGAAAGGTGTCAGTTATGCCAATTAGATGAACG
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACG
9436048 GTTAAAGACCGTTGAG
66 GTTAAAGACCGTTGAG
*
9436064 TAAAAGATAAATGGCCTAGCTGTTCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACG
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACG
*
9436129 GTTAAAGATCGTTGAG
66 GTTAAAGACCGTTGAG
* * * * *
9436145 TAAAAGATAAATGGTCTAGCTATGCATTTGGCAGAAATGTGCCAATTATGCCAGTTAGATGAATG
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACG
9436210 GTTAAAGACCGTTGAG
66 GTTAAAGACCGTTGAG
* * * *
9436226 TAAAAGATAAATGGTCTAGTTGTGCATTTGGTAGAAAGGTGTCAATTATGCCAGTTAGATGAATG
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACG
* *
9436291 GTTAAAGACTGCTGAG
66 GTTAAAGACCGTTGAG
* * * * *
9436307 TAAAAGATAAATGACCTAGCTCTGCATTTGGCAAAAATGTGTCAATTATG-CAGTTAGATGAATG
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACG
9436371 GTTAAAGACCGTTGAG
66 GTTAAAGACCGTTGAG
* * * * * *
9436387 TAAAAGACAAATGACCTAGCTATGCATTTGGAAGAAAGGTGTTAATTATGCCAATTAGATGAACG
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACG
9436452 GTTAAAGACCGTTGAG
66 GTTAAAGACCGTTGAG
* * * * *
9436468 TAAAAAATAAATGGCCTAGTTATGCATTTGGCAGAAAGGTGTCAATTATGCTAGATAGATGAACG
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACG
9436533 GTTAAAGACCGTTGAG
66 GTTAAAGACCGTTGAG
* * * * * *
9436549 TAAAAGATAAATGGACTAGTTGTGCATTTGGTAGAAAAGTGTCAATCATGCAAGTTA
1 TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTA
9436606 ATTGAAAAGT
Statistics
Matches: 562, Mismatches: 60, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
80 72 0.13
81 490 0.87
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (81 bp):
TAAAAGATAAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACG
GTTAAAGACCGTTGAG
Found at i:9446143 original size:12 final size:12
Alignment explanation
Indices: 9446126--9446152 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
9446116 CTTTTTTTTA
9446126 ATTATGTCTAAC
1 ATTATGTCTAAC
9446138 ATTATGTCTAAC
1 ATTATGTCTAAC
9446150 ATT
1 ATT
9446153 TACTTTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.44
Consensus pattern (12 bp):
ATTATGTCTAAC
Found at i:9447101 original size:41 final size:41
Alignment explanation
Indices: 9446962--9447101 Score: 108
Period size: 42 Copynumber: 3.4 Consensus size: 41
9446952 AAAATGATAC
** * *
9446962 TTTAGCGGCATTTTTCCAACAAGCGCCGAAATAAATTGGTAA
1 TTTAGCGGTGTTTTTCCAACAAACGCCGCAATAAATT-GTAA
* * * * *
9447004 TTTAGCGGTGTTTATTGCAA-AAACGTCGGAATAGACTTGT-T
1 TTTAGCGGTGTTT-TTCCAACAAACGCCGCAATA-AATTGTAA
*
9447045 TTTAGTCGCGT-TTTTT-CAACAAACGCCGCAATATATTAGTAA
1 TTTAG-CG-GTGTTTTTCCAACAAACGCCGCAATAAATT-GTAA
9447087 TTTAGCGGTGTTTTT
1 TTTAGCGGTGTTTTT
9447102 ATACAAATGC
Statistics
Matches: 77, Mismatches: 13, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
40 7 0.09
41 27 0.35
42 33 0.43
43 10 0.13
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (41 bp):
TTTAGCGGTGTTTTTCCAACAAACGCCGCAATAAATTGTAA
Found at i:9447301 original size:132 final size:133
Alignment explanation
Indices: 9447082--9447331 Score: 330
Period size: 132 Copynumber: 1.9 Consensus size: 133
9447072 GCAATATATT
* * * *
9447082 AGTAATTTAGCGGTGTTTTTATACAAATGCCGCAACAGGATTGTTTATAGTGGCATTTGTCAAAC
1 AGTAATTTAGCGGTGTTTTCAGACAAACGCCGAAACAGGATTGTTTATAGTGGCATTTGTCAAAC
* * *
9447147 AAACGTCGTTATACATAAGTAATTTAGCGGCATTTTTA-TACAAACGCCGCAAACGCTGCTATAC
66 AAACGTCGCTATAAATAAGTAATTTAGCGGCATTTTTACTACAAACACCGCAAACGCTGCTATAC
9447211 AGA
131 AGA
* *
9447214 AGTAATTTAGCGGTGTTTATCAGACAAACGCCGAAATAGG-TTGTTTATAGTGGCGTTTGTACAA
1 AGTAATTTAGCGGTGTTT-TCAGACAAACGCCGAAACAGGATTGTTTATAGTGGCATTTGT-CAA
* *
9447278 A-AAATGAT-GCTATAAAGT-AGTAATTTAGCGGCGTTTTTACTACAAACACCGCAA
64 ACAAACG-TCGCTATAAA-TAAGTAATTTAGCGGCATTTTTACTACAAACACCGCAA
9447332 TATGGTTGTT
Statistics
Matches: 102, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
132 67 0.66
133 35 0.34
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (133 bp):
AGTAATTTAGCGGTGTTTTCAGACAAACGCCGAAACAGGATTGTTTATAGTGGCATTTGTCAAAC
AAACGTCGCTATAAATAAGTAATTTAGCGGCATTTTTACTACAAACACCGCAAACGCTGCTATAC
AGA
Found at i:9447365 original size:82 final size:82
Alignment explanation
Indices: 9447203--9447363 Score: 207
Period size: 82 Copynumber: 2.0 Consensus size: 82
9447193 CCGCAAACGC
* * *
9447203 TGCTATACAGAAGTAATTTAGCGGTGTTTATCAGACAAACGCCGAAATAGGTTGTTTATAGTGGC
1 TGCTATAAAGAAGTAATTTAGCGGCGTTTATCAGACAAACACCGAAATAGGTTGTTTATAGTGGC
*
9447268 GTTTGTACAAAAAATGA
66 ATTTGTACAAAAAATGA
* * * *
9447285 TGCTATAAAGTAGTAATTTAGCGGCGTTT-TTACTACAAACACCGCAATATGGTTGTTTATAGTG
1 TGCTATAAAGAAGTAATTTAGCGGCGTTTATCA-GACAAACACCGAAATA-GGTTGTTTATAGTG
* *
9447349 GCATTTTTATAAAAA
64 GCATTTGTACAAAAA
9447364 TGCCACAAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
81 2 0.03
82 39 0.58
83 26 0.39
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (82 bp):
TGCTATAAAGAAGTAATTTAGCGGCGTTTATCAGACAAACACCGAAATAGGTTGTTTATAGTGGC
ATTTGTACAAAAAATGA
Found at i:9448935 original size:43 final size:43
Alignment explanation
Indices: 9448835--9448936 Score: 150
Period size: 43 Copynumber: 2.4 Consensus size: 43
9448825 TTTTGGATAC
*
9448835 AAACGCCGCTATAGATATAACTTTTTGTGGAGTTTGTCTCCAG
1 AAACGCCGCTATAGATATAACTTTTTATGGAGTTTGTCTCCAG
* * *
9448878 AAACGCCACTATAGATATGACTTTTTATGGCGTTTGTCTCCAG
1 AAACGCCGCTATAGATATAACTTTTTATGGAGTTTGTCTCCAG
* *
9448921 AAATGCCGCAATAGAT
1 AAACGCCGCTATAGAT
9448937 TTATCCATAG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (43 bp):
AAACGCCGCTATAGATATAACTTTTTATGGAGTTTGTCTCCAG
Found at i:9450550 original size:31 final size:32
Alignment explanation
Indices: 9450503--9450588 Score: 133
Period size: 31 Copynumber: 2.8 Consensus size: 32
9450493 GAGTATTGTT
*
9450503 GAGC-TCGACTCGACTCGAAAACTCTGAAATG
1 GAGCTTCGACTCGACTCGAAAACTCGGAAATG
*
9450534 GAG-TTCGATTCGACTCGAAAACTCGGAAATG
1 GAGCTTCGACTCGACTCGAAAACTCGGAAATG
9450565 GAGCTT-GACTCGACTCGAAAACTC
1 GAGCTTCGACTCGACTCGAAAACTC
9450589 ACGAGCTTAA
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
31 48 0.96
32 2 0.04
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.21
Consensus pattern (32 bp):
GAGCTTCGACTCGACTCGAAAACTCGGAAATG
Found at i:9451501 original size:11 final size:11
Alignment explanation
Indices: 9451485--9451521 Score: 74
Period size: 11 Copynumber: 3.4 Consensus size: 11
9451475 GATCACACTT
9451485 TCTCAGGTTCA
1 TCTCAGGTTCA
9451496 TCTCAGGTTCA
1 TCTCAGGTTCA
9451507 TCTCAGGTTCA
1 TCTCAGGTTCA
9451518 TCTC
1 TCTC
9451522 TTGGTAACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.16, C:0.30, G:0.16, T:0.38
Consensus pattern (11 bp):
TCTCAGGTTCA
Done.