Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009036.1 Hibiscus syriacus cultivar Beakdansim tig00112443_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: 1934717
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 9
Found at i:417250 original size:33 final size:35
Alignment explanation
Indices: 417186--417251 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
417176 AAAATATTTA
* *
417186 TATATTTTCTTTAAAAAATTTAAATTCATAAAATT
1 TATATTTTCTTTAAAAAATTAAAAATCATAAAATT
*
417221 TATATTTT-TTTACAAAATTAAAAAT-ATAAAA
1 TATATTTTCTTTAAAAAATTAAAAATCATAAAA
417252 AGGTTTAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 6 0.21
34 14 0.50
35 8 0.29
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (35 bp):
TATATTTTCTTTAAAAAATTAAAAATCATAAAATT
Found at i:419276 original size:54 final size:54
Alignment explanation
Indices: 419144--419547 Score: 515
Period size: 54 Copynumber: 7.5 Consensus size: 54
419134 ATAAGTTTCA
* * * * * * * *
419144 TGGGGTGCACACGTAGTGCCAATACGATCATTCGTAAACCTTATTATGAATT-CTT
1 TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAA-CTTATTATGAATTAC-G
*
419199 TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACCTATTATGAATTACG
1 TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTTATTATGAATTACG
* * * * * *
419253 TGGGTTCCATACTCAGTGCCGATATGGTCGTTCATAAACTTATTATGAATTCCG
1 TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTTATTATGAATTACG
* **
419307 TGGGTTGCACACTTAGTGTCGATACGGTTGTTCATAAACTTATTATGAATTTTG
1 TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTTATTATGAATTACG
*
419361 TGGGTTGCACACTTAGTGTCGATACGGT-GATTCATAAACTTATTATGAATTTCG
1 TGGGTTGCACACTTAGTGTCGATACGGTCG-TTCATAAACTTATTATGAATTACG
* * *
419415 TAGGTTGCACACTTAGTGCCGATACGGTCATTCATAAACTTATTATGAATTACG
1 TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTTATTATGAATTACG
* * * *
419469 TGGGTTACACACTTAGTGTCGATACGATCGTTCATAAAGTTATTATGAATTATG
1 TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTTATTATGAATTACG
* *
419523 TGGGTTGCACACTTAATGTTGATAC
1 TGGGTTGCACACTTAGTGTCGATAC
419548 ATAAAAATGC
Statistics
Matches: 307, Mismatches: 39, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
53 1 0.00
54 274 0.89
55 32 0.10
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (54 bp):
TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTTATTATGAATTACG
Found at i:429845 original size:31 final size:31
Alignment explanation
Indices: 429807--429869 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
429797 GAGTCGAGGG
429807 TTACCTATGTTCTACGGAACATATGGACAAT
1 TTACCTATGTTCTACGGAACATATGGACAAT
*
429838 TTACCTATGTTCTTCGGAACATATGGACAAT
1 TTACCTATGTTCTACGGAACATATGGACAAT
429869 T
1 T
429870 ACATAAGTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (31 bp):
TTACCTATGTTCTACGGAACATATGGACAAT
Found at i:448927 original size:15 final size:15
Alignment explanation
Indices: 448907--448936 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
448897 ACTTTATTTT
448907 GGTCAGGTCGGGTGG
1 GGTCAGGTCGGGTGG
448922 GGTCAGGTCGGGTGG
1 GGTCAGGTCGGGTGG
448937 ACAAAAAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.07, C:0.13, G:0.60, T:0.20
Consensus pattern (15 bp):
GGTCAGGTCGGGTGG
Found at i:449294 original size:18 final size:16
Alignment explanation
Indices: 449259--449303 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 16
449249 TCAGATTCAT
449259 ATTCCAATTCCTACAG
1 ATTCCAATTCCTACAG
*
449275 ATTCTAATTCCTTCACAG
1 ATTCCAATTCC-T-ACAG
449293 ATTCCAATTCC
1 ATTCCAATTCC
449304 CTCAGAAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 10 0.40
17 1 0.04
18 14 0.56
ACGTcount: A:0.29, C:0.31, G:0.04, T:0.36
Consensus pattern (16 bp):
ATTCCAATTCCTACAG
Found at i:450227 original size:2 final size:2
Alignment explanation
Indices: 450217--450288 Score: 53
Period size: 2 Copynumber: 36.5 Consensus size: 2
450207 AATTGAAAAA
*
450217 AT AT A- AT AT AT AT AT AT AT AT AT A- AT AT A- AGT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* * *
450257 AA ACT AT AT AT AT AA ACT AT AT TT AT AT -T AT A
1 AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT A
450289 AACTATATAA
Statistics
Matches: 55, Mismatches: 8, Indels: 14
0.71 0.10 0.18
Matches are distributed among these distances:
1 4 0.07
2 49 0.89
3 2 0.04
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (2 bp):
AT
Found at i:450241 original size:19 final size:19
Alignment explanation
Indices: 450217--450270 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
450207 AATTGAAAAA
450217 ATATAATATATATATATAT
1 ATATAATATATATATATAT
*
450236 ATATAATATA-AGTTTATAT
1 ATATAATATATA-TATATAT
450255 ATA-AACTATATATATA
1 ATATAA-TATATATATA
450271 AACTATATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
18 3 0.10
19 26 0.87
20 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (19 bp):
ATATAATATATATATATAT
Found at i:450303 original size:18 final size:18
Alignment explanation
Indices: 450261--450319 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
450251 ATATATAAAC
450261 TATATA-TATAAACTATA
1 TATATATTATAAACTATA
*
450278 TTTATATTATAAACTATA
1 TATATATTATAAACTATA
**
450296 TA-ATTATTATAAGTTATA
1 TATA-TATTATAAACTATA
450314 TATATA
1 TATATA
450320 AAATTATGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 6 0.17
18 28 0.80
19 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.47
Consensus pattern (18 bp):
TATATATTATAAACTATA
Found at i:450383 original size:13 final size:13
Alignment explanation
Indices: 450222--450383 Score: 93
Period size: 13 Copynumber: 12.2 Consensus size: 13
450212 AAAAAATATA
*
450222 ATATATATATA-T
1 ATATATATAAACT
*
450234 ATATATAATATAAGT
1 ATATAT-ATA-AACT
*
450249 TTATATATAAACT
1 ATATATATAAACT
450262 ATATATATAAACT
1 ATATATATAAACT
* *
450275 ATAT-T-TATATT
1 ATATATATAAACT
*
450286 ATAAACTATATAA-T
1 ATATA-TATA-AACT
**
450300 -TAT-TATAAGTT
1 ATATATATAAACT
*
450311 ATATATATAAAATT
1 ATATATAT-AAACT
* *
450325 ATGTTTATATGAACT
1 A--TATATATAAACT
450340 ATATATATAAACT
1 ATATATATAAACT
*
450353 ATATATGTAAACT
1 ATATATATAAACT
450366 ATATATGTATAAACT
1 ATATA--TATAAACT
450381 ATA
1 ATA
450384 AAAAGTATAT
Statistics
Matches: 117, Mismatches: 18, Indels: 27
0.72 0.11 0.17
Matches are distributed among these distances:
10 1 0.01
11 12 0.10
12 10 0.09
13 55 0.47
14 12 0.10
15 21 0.18
16 6 0.05
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (13 bp):
ATATATATAAACT
Found at i:450535 original size:19 final size:19
Alignment explanation
Indices: 450511--450572 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 19
450501 TTTTATTTGG
450511 GAATTTAGAGGGAAATTGA
1 GAATTTAGAGGGAAATTGA
*
450530 GAATTTAGAGGG-AATAGAA
1 GAATTTAGAGGGAAATTG-A
* *
450549 AAATTTGGAGGGAAATTGA
1 GAATTTAGAGGGAAATTGA
450568 GAATT
1 GAATT
450573 GAGATTTTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
18 4 0.11
19 28 0.78
20 4 0.11
ACGTcount: A:0.44, C:0.00, G:0.31, T:0.26
Consensus pattern (19 bp):
GAATTTAGAGGGAAATTGA
Found at i:451003 original size:35 final size:35
Alignment explanation
Indices: 450954--451022 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 35
450944 TTTATAAAAA
* * *
450954 AACCCTAAATCCTAAATCATAAACCTTAAACCTTT
1 AACCCTAAACCCTAAACCATAAACCCTAAACCTTT
* *
450989 AACCCTAAACCCTAAACCCTAAACCCTAACCCTT
1 AACCCTAAACCCTAAACCATAAACCCTAAACCTT
451023 GAACTATATA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.41, C:0.36, G:0.00, T:0.23
Consensus pattern (35 bp):
AACCCTAAACCCTAAACCATAAACCCTAAACCTTT
Found at i:451021 original size:6 final size:7
Alignment explanation
Indices: 450953--451021 Score: 77
Period size: 7 Copynumber: 10.0 Consensus size: 7
450943 GTTTATAAAA
450953 AAACCCT
1 AAACCCT
*
450960 AAATCCT
1 AAACCCT
* *
450967 AAATCAT
1 AAACCCT
*
450974 AAACCTT
1 AAACCCT
*
450981 AAACCTT
1 AAACCCT
*
450988 TAACCCT
1 AAACCCT
450995 AAACCCT
1 AAACCCT
451002 AAACCCT
1 AAACCCT
451009 AAACCCT
1 AAACCCT
451016 -AACCCT
1 AAACCCT
451022 TGAACTATAT
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
6 6 0.11
7 49 0.89
ACGTcount: A:0.42, C:0.36, G:0.00, T:0.22
Consensus pattern (7 bp):
AAACCCT
Found at i:451077 original size:2 final size:2
Alignment explanation
Indices: 451066--451100 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
451056 ATAAACCATG
451066 TA TA -A 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 TA TA
451101 ATTACATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:451222 original size:32 final size:32
Alignment explanation
Indices: 451186--451246 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
451176 TTTTATAGAA
* *
451186 ACCATAAACCTTAAATCATAAACCCTAAACTT
1 ACCATAAACCCTAAACCATAAACCCTAAACTT
* *
451218 ACCATAAACCCTAAACCCTAAACCTTAAA
1 ACCATAAACCCTAAACCATAAACCCTAAA
451247 ACCTAATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.48, C:0.31, G:0.00, T:0.21
Consensus pattern (32 bp):
ACCATAAACCCTAAACCATAAACCCTAAACTT
Found at i:452582 original size:23 final size:23
Alignment explanation
Indices: 452556--452647 Score: 123
Period size: 23 Copynumber: 4.0 Consensus size: 23
452546 CACCACAGCT
452556 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
452579 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* **
452602 CATATAATTGTACC-AGAGTGCTG
1 CATATAATTGCACCGA-AGTGCCA
* *
452625 CATAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
452648 TATAACAATG
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
22 1 0.02
23 58 0.98
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:457552 original size:23 final size:23
Alignment explanation
Indices: 457526--457603 Score: 102
Period size: 23 Copynumber: 3.3 Consensus size: 23
457516 CACCACAACT
457526 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
457549 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* *
457572 CATAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
457595 TATAATAAT
1 CAT-ATAAT
457604 GTCTATAAGG
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 43 0.91
24 4 0.09
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:460853 original size:14 final size:14
Alignment explanation
Indices: 460834--460880 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
460824 TTTTTTTCTT
460834 TATATAAATTAAAC
1 TATATAAATTAAAC
460848 TATAT-AATT----
1 TATATAAATTAAAC
460857 TATATAAATTAAAC
1 TATATAAATTAAAC
*
460871 TATATTAATT
1 TATATAAATT
460881 TTCCTTTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
13 4 0.15
14 14 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAAATTAAAC
Found at i:460858 original size:23 final size:24
Alignment explanation
Indices: 460832--460881 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
460822 TATTTTTTTC
460832 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
460855 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
460879 TTT
1 TTT
460882 TCCTTTTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:461180 original size:16 final size:16
Alignment explanation
Indices: 461149--461203 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
461139 CGGATCATTT
*
461149 ACAGGTTAGGTTAAAA
1 ACAGGTCAGGTTAAAA
* *
461165 ACATGTCAGTTTAAAA
1 ACAGGTCAGGTTAAAA
*
461181 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTAAAA
461197 ACAGGTC
1 ACAGGTC
461204 GGGTAATACC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.40, C:0.13, G:0.24, T:0.24
Consensus pattern (16 bp):
ACAGGTCAGGTTAAAA
Found at i:461450 original size:18 final size:18
Alignment explanation
Indices: 461427--461488 Score: 106
Period size: 18 Copynumber: 3.4 Consensus size: 18
461417 TCAATTTCAA
*
461427 TCAGTTTTACATGTTGGG
1 TCAGTTTTACATGTCGGG
461445 TCAGTTTTACATGTCGGG
1 TCAGTTTTACATGTCGGG
461463 TCAGTTTTACATGTCGGG
1 TCAGTTTTACATGTCGGG
*
461481 TCAATTTT
1 TCAGTTTT
461489 TTACACCCAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.18, C:0.15, G:0.24, T:0.44
Consensus pattern (18 bp):
TCAGTTTTACATGTCGGG
Found at i:462137 original size:80 final size:80
Alignment explanation
Indices: 462051--462203 Score: 261
Period size: 80 Copynumber: 1.9 Consensus size: 80
462041 ATTCCTGCTA
*
462051 AACCAACCAAACACAAAATATAACATTCTCAGTAATCCTATTATCTGATAATCTTTTATTCCCAC
1 AACCAACCAAACACAAAATATAACATTCTCAATAATCCTATTATCTGATAATCTTTTATTCCCAC
462116 TAATAATCTTACGGG
66 TAATAATCTTACGGG
* * * *
462131 AACCAACCAAACACAAAATATAACATTCTTAATAATCCTATTCTCTTATAATCTTTTATTCCGAC
1 AACCAACCAAACACAAAATATAACATTCTCAATAATCCTATTATCTGATAATCTTTTATTCCCAC
462196 TAATAATC
66 TAATAATC
462204 AAACGCACTT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
80 68 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.33
Consensus pattern (80 bp):
AACCAACCAAACACAAAATATAACATTCTCAATAATCCTATTATCTGATAATCTTTTATTCCCAC
TAATAATCTTACGGG
Found at i:463697 original size:212 final size:212
Alignment explanation
Indices: 463330--464179 Score: 1292
Period size: 212 Copynumber: 4.0 Consensus size: 212
463320 TGGCCCTGGA
** * *
463330 TGGATTGGAGAAGTGGGAAATGTGGCGTCTGA-ATGAGGATTGTGATCAAAATGTCAGATAGCCA
1 TGGATTGGAGAAGTGGGAAATGTGGCGTCTGATA-GAGGATTGCAATCAAAATATCAGATAACCA
* * *
463394 TCTCCCTCTTTGTATCTTCTCCTGATATTAAATCAGAAATTAATGCTTGTGCTCTACTTCTCATG
65 TCTCCCTCTTTGTATCTTCTCCAGATATTAAATCAGAAGTTAATGCTTGTGCTCTGCTTCTCATG
* *
463459 GAGTTCAAGTTTGGCTCTTCTTTTACATAATTCTCAATATGGGAAAGGCATTGGCCTTAATTTAC
130 GAGTTCAAGTTTGGCTCTTCTTTTACATAATTCTCAATATGGAAAAGGCATTGACCTTAATTTAC
* ** * *
463524 TTAAGAGTGATTAGAAAG
195 TGAAGAGAAATAAGAATG
* *** *
463542 TGGATTGGAGAAGTGGGAAATGTGGCGTCTGATAGAGAATTGTGGTCAAAATATCAGATAGCCAT
1 TGGATTGGAGAAGTGGGAAATGTGGCGTCTGATAGAGGATTGCAATCAAAATATCAGATAACCAT
* *
463607 CACCCTCTTTGTATCTTCTCCAGATATTAAATCGGAAGTTAATGCTTGTGCTCTGCTTCTCATGG
66 CTCCCTCTTTGTATCTTCTCCAGATATTAAATCAGAAGTTAATGCTTGTGCTCTGCTTCTCATGG
* *
463672 AGTTCAAGTTTGGCTCTTATTTTACATAATTCTCAATATGGAAAAGACATTGACCTTAATTTA-T
131 AGTTCAAGTTTGGCTCTTCTTTTACATAATTCTCAATATGGAAAAGGCATTGACCTTAATTTACT
463736 GGAAGAGAAATAAGAATG
196 -GAAGAGAAATAAGAATG
*
463754 TGGATTGGAGAAGTGGGAAATGTGGTGTCTGATAGAGGATTGCAATCAAAATATCAGATAACCAT
1 TGGATTGGAGAAGTGGGAAATGTGGCGTCTGATAGAGGATTGCAATCAAAATATCAGATAACCAT
* * * *
463819 CTCCCCCATCGTATCTTCTCCAGATATTAATTCAGAAGTTAATGCTTGTGCTCTGCTTCTCATGG
66 CTCCCTCTTTGTATCTTCTCCAGATATTAAATCAGAAGTTAATGCTTGTGCTCTGCTTCTCATGG
* *
463884 AGTGCAAGTTTGGCTCTTCTTTTACATAATTCTCAATATGGAAAAGGCATTGACCTTAATTTACG
131 AGTTCAAGTTTGGCTCTTCTTTTACATAATTCTCAATATGGAAAAGGCATTGACCTTAATTTACT
463949 GAAGAGAAATAAGAATG
196 GAAGAGAAATAAGAATG
* *
463966 TGGATTGGAGAAGTGGGAAATGTGGTGTCTGACAGAGGATTGCAATCAAAATATCAGATAACCAT
1 TGGATTGGAGAAGTGGGAAATGTGGCGTCTGATAGAGGATTGCAATCAAAATATCAGATAACCAT
* * *
464031 CTTCCT-TATTGTATCTTCTCCAGATATTAGATCAGAAGTTAATGCTTGTGCTCTGCTTCTCTTG
66 CTCCCTCT-TTGTATCTTCTCCAGATATTAAATCAGAAGTTAATGCTTGTGCTCTGCTTCTCATG
* * *
464095 GAGTTCAAGTTTGGCTCTTCTTTTTCATAATTCTCAATATGGAAAAGGCATTGGCCTTAATTAAC
130 GAGTTCAAGTTTGGCTCTTCTTTTACATAATTCTCAATATGGAAAAGGCATTGACCTTAATTTAC
**
464160 TGAAGAGTGATAAGAATG
195 TGAAGAGAAATAAGAATG
464178 TG
1 TG
464180 TTAACAGAGT
Statistics
Matches: 586, Mismatches: 48, Indels: 8
0.91 0.07 0.01
Matches are distributed among these distances:
211 1 0.00
212 584 1.00
213 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (212 bp):
TGGATTGGAGAAGTGGGAAATGTGGCGTCTGATAGAGGATTGCAATCAAAATATCAGATAACCAT
CTCCCTCTTTGTATCTTCTCCAGATATTAAATCAGAAGTTAATGCTTGTGCTCTGCTTCTCATGG
AGTTCAAGTTTGGCTCTTCTTTTACATAATTCTCAATATGGAAAAGGCATTGACCTTAATTTACT
GAAGAGAAATAAGAATG
Found at i:467100 original size:21 final size:21
Alignment explanation
Indices: 467075--467125 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
467065 TGAATTAGTA
467075 CTAAAGTAAAATAATTAAATG
1 CTAAAGTAAAATAATTAAATG
467096 CTAAAGTAAAATAATTAAATG
1 CTAAAGTAAAATAATTAAATG
*
467117 -TAAATTAAA
1 CTAAAGTAAA
467126 TTGAAAGATA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 8 0.28
21 21 0.72
ACGTcount: A:0.59, C:0.04, G:0.08, T:0.29
Consensus pattern (21 bp):
CTAAAGTAAAATAATTAAATG
Found at i:469871 original size:20 final size:20
Alignment explanation
Indices: 469834--469871 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
469824 TTACTTTATG
* *
469834 AATTTTGAAAATATTTTTAA
1 AATTTTGAAAACAGTTTTAA
469854 AATTTTGAAAACAGTTTT
1 AATTTTGAAAACAGTTTT
469872 CCAAGAAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (20 bp):
AATTTTGAAAACAGTTTTAA
Found at i:471112 original size:3 final size:3
Alignment explanation
Indices: 471106--471143 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
471096 TAAAAAAATA
471106 TAT TAT TAT TAT TAT TAT TAT TAT T-T TAAT TAT ATAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT -TAT T
471144 TTGCAGGCCC
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 2 0.06
3 25 0.78
4 5 0.16
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:472722 original size:27 final size:27
Alignment explanation
Indices: 472682--472747 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
472672 ATGTGATATG
472682 AGAGTTGAGGGTACAATTGGCATGCCA
1 AGAGTTGAGGGTACAATTGGCATGCCA
*
472709 AGAGTTGAGTGTACAATTGGCATGCCA
1 AGAGTTGAGGGTACAATTGGCATGCCA
*
472736 AGAGTCGAGGGT
1 AGAGTTGAGGGT
472748 TCTATGTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.29, C:0.14, G:0.35, T:0.23
Consensus pattern (27 bp):
AGAGTTGAGGGTACAATTGGCATGCCA
Found at i:472779 original size:23 final size:23
Alignment explanation
Indices: 472748--472791 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
472738 AGTCGAGGGT
*
472748 TCTATGTGGTCCTTCGGGACAAC
1 TCTACGTGGTCCTTCGGGACAAC
472771 TCTACGTGGTCCTTCGGGACA
1 TCTACGTGGTCCTTCGGGACA
472792 TTATATGTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (23 bp):
TCTACGTGGTCCTTCGGGACAAC
Found at i:472827 original size:23 final size:23
Alignment explanation
Indices: 472801--472862 Score: 115
Period size: 23 Copynumber: 2.7 Consensus size: 23
472791 ATTATATGTG
*
472801 GCACTTTGGTGCATTTCTATGCA
1 GCACTTCGGTGCATTTCTATGCA
472824 GCACTTCGGTGCATTTCTATGCA
1 GCACTTCGGTGCATTTCTATGCA
472847 GCACTTCGGTGCATTT
1 GCACTTCGGTGCATTT
472863 TATACGAGCT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.37
Consensus pattern (23 bp):
GCACTTCGGTGCATTTCTATGCA
Found at i:477499 original size:2 final size:2
Alignment explanation
Indices: 477492--477519 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
477482 CATGAAGCTC
477492 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
477520 GTCACGAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:488249 original size:660 final size:660
Alignment explanation
Indices: 486983--488299 Score: 2442
Period size: 660 Copynumber: 2.0 Consensus size: 660
486973 AAGATGTTGC
* *
486983 ATTATTTAAATTACCAATATTTTTATCATTACATTTTAAACGATAATATAGGCTAATTAGACTAC
1 ATTATTTAAATTACCAATATTTTTATCATTACATTGTAAACGATAATATAGGCTAATTAGACTAA
487048 GTTTTTATCTTGATTTTTCATAATATTCGTAACACCCTAAACCAGTACAACACACAGTGACCAAT
66 GTTTTTATCTTGATTTTTCATAATATTCGTAACACCCTAAACCAGTACAACACACAGTGACCAAT
*
487113 CAGAATGCTACACGGAACCACCGGAGTGGCTAATCAAAAAATTTCTTTTAAATTTCTCCATTTTA
131 CAGAATGCTACACAGAACCACCGGAGTGGCTAATCAAAAAATTTCTTTTAAATTTCTCCATTTTA
487178 AAAATGACCATTTGTAAATATTGATGCTAAAATAAATTAACCACAATTTAAATAAAATAATTTAC
196 AAAATGACCATTTGTAAATATTGATGCTAAAATAAATTAACCACAATTTAAATAAAATAATTTAC
*
487243 ATCAAGAGCTCCCAAAATAACATTTATAACATACATACCATTGTTTAAAATGAGTTACAACTCAT
261 ATCAAGAGCTCCCAAAATAACATTTATAACATACAGACCATTGTTTAAAATGAGTTACAACTCAT
487308 ACAAAAATATACAAAGGGTCTACAAGTATACATACCCTCTAAAAAGATGACCTGAGACGTACTCT
326 ACAAAAATATACAAAGGGTCTACAAGTATACATACCCTCTAAAAAGATGACCTGAGACGTACTCT
*
487373 AGACTATCTGGGTCTGGATCATTGCTAGCAAAAAGTCCTCGGATTGCTCCTCGACTAACATGCGT
391 ACACTATCTGGGTCTGGATCATTGCTAGCAAAAAGTCCTCGGATTGCTCCTCGACTAACATGCGT
*
487438 AAGGAAGCAAATTCCAAACGCTGAGCTAACTAGGTCAGTGTCACACTAACAACTAAGCCATACTA
456 AAGGAAGCAAATTCCAAACGCTGAGCTAACTAGGTCAGTGCCACACTAACAACTAAGCCATACTA
487503 AAAGTGTTCATGACATGCTCAAGCTAACTAATAACTGAAATAGTGAGTATACTCGTATACTACAC
521 AAAGTGTTCATGACATGCTCAAGCTAACTAATAACTGAAATAGTGAGTATACTCGTATACTACAC
487568 TTTCTACACTATGACATACATCATGTGTGGCTAAGGGTTCTGCATCTCAGAGCTCACACACCCTC
586 TTTCTACACTATGACATACATCATGTGTGGCTAAGGGTTCTGCATCTCAGAGCTCACACACCCTC
487633 TAGTCTATCG
651 TAGTCTATCG
487643 ATTATTTAAATTACCAATATTTTTTATCATTACATTGTAAACGATAATATAGGCTAATTAGACTA
1 ATTATTTAAATTACCAATA-TTTTTATCATTACATTGTAAACGATAATATAGGCTAATTAGACTA
* * *
487708 AGTTTTTTATCTTGATTTTTCATAATATTTGTAA-ACTCTAAACCAGTACGACACACAGTCGACC
65 AG-TTTTTATCTTGATTTTTCATAATATTCGTAACACCCTAAACCAGTACAACACACAGT-GACC
487772 AATCAGAATGCTACACAGAACCACCGGAGT-GCTAATCAAAAAATTTCTTTTAAATTTCTCCATT
128 AATCAGAATGCTACACAGAACCACCGGAGTGGCTAATCAAAAAATTTCTTTTAAATTTCTCCATT
487836 TTAAAAATGACCATTTGTAAATATTGATGCTAAAATAAATTAACCACAATTTAAATAAAATAATT
193 TTAAAAATGACCATTTGTAAATATTGATGCTAAAATAAATTAACCACAATTTAAATAAAATAATT
*
487901 TACATCAAGAGCT-CCAAAATAACATTTATAACATGCAGACCATTGTTTAAAATGAGTTACAACT
258 TACATCAAGAGCTCCCAAAATAACATTTATAACATACAGACCATTGTTTAAAATGAGTTACAACT
*
487965 CATACAAAAATATACAAAGGGTCTACAAGTATACATGCCCTCTAAAAAGATGACCTGAGACGTAC
323 CATACAAAAATATACAAAGGGTCTACAAGTATACATACCCTCTAAAAAGATGACCTGAGACGTAC
*
488030 TCTACACTATCTGGGTCTGGATCATTGCTGGCAAAAAGTCCTCGGATTGCTCCTCGACTAACATG
388 TCTACACTATCTGGGTCTGGATCATTGCTAGCAAAAAGTCCTCGGATTGCTCCTCGACTAACATG
488095 CGTAAGGAAGCAAATTCCAAACGCTGAGCTAACTAGGTCAGTGCCACACTAACAACTAAGCCATA
453 CGTAAGGAAGCAAATTCCAAACGCTGAGCTAACTAGGTCAGTGCCACACTAACAACTAAGCCATA
*
488160 CTAAAAGTGTTCATGACATGTTCAAGCTAACTAATAACTGAAATAGTGAGTATACTCGTATACTA
518 CTAAAAGTGTTCATGACATGCTCAAGCTAACTAATAACTGAAATAGTGAGTATACTCGTATACTA
* * *
488225 CACTTTCTACAGTATGATATACATCATGTGTGGCTAAGGGTTCTGCATCTCGGAGCTCACACACC
583 CACTTTCTACACTATGACATACATCATGTGTGGCTAAGGGTTCTGCATCTCAGAGCTCACACACC
488290 CTCTAGTCTA
648 CTCTAGTCTA
488300 CCGAGGCTAG
Statistics
Matches: 638, Mismatches: 16, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
660 395 0.62
661 180 0.28
662 63 0.10
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (660 bp):
ATTATTTAAATTACCAATATTTTTATCATTACATTGTAAACGATAATATAGGCTAATTAGACTAA
GTTTTTATCTTGATTTTTCATAATATTCGTAACACCCTAAACCAGTACAACACACAGTGACCAAT
CAGAATGCTACACAGAACCACCGGAGTGGCTAATCAAAAAATTTCTTTTAAATTTCTCCATTTTA
AAAATGACCATTTGTAAATATTGATGCTAAAATAAATTAACCACAATTTAAATAAAATAATTTAC
ATCAAGAGCTCCCAAAATAACATTTATAACATACAGACCATTGTTTAAAATGAGTTACAACTCAT
ACAAAAATATACAAAGGGTCTACAAGTATACATACCCTCTAAAAAGATGACCTGAGACGTACTCT
ACACTATCTGGGTCTGGATCATTGCTAGCAAAAAGTCCTCGGATTGCTCCTCGACTAACATGCGT
AAGGAAGCAAATTCCAAACGCTGAGCTAACTAGGTCAGTGCCACACTAACAACTAAGCCATACTA
AAAGTGTTCATGACATGCTCAAGCTAACTAATAACTGAAATAGTGAGTATACTCGTATACTACAC
TTTCTACACTATGACATACATCATGTGTGGCTAAGGGTTCTGCATCTCAGAGCTCACACACCCTC
TAGTCTATCG
Found at i:489145 original size:27 final size:27
Alignment explanation
Indices: 489107--489160 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
489097 CTATTGACTC
489107 AGTAAAGGTATAAAAGAGTTATGAATG
1 AGTAAAGGTATAAAAGAGTTATGAATG
489134 AGTAAAGGTATAAAAGAGTTATGAATG
1 AGTAAAGGTATAAAAGAGTTATGAATG
489161 TGTTACCTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.26, T:0.26
Consensus pattern (27 bp):
AGTAAAGGTATAAAAGAGTTATGAATG
Found at i:491745 original size:21 final size:21
Alignment explanation
Indices: 491719--491796 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
491709 CTGAAGTTAG
* * *
491719 TGTAGCAATGCATCGGTATAT
1 TGTAGCAGTGCATCGGTACAC
491740 TGTAGCAGTGCATCGGTACAC
1 TGTAGCAGTGCATCGGTACAC
491761 TGTAGCAGTGCATCGGTACAC
1 TGTAGCAGTGCATCGGTACAC
* * *
491782 TATAACAGTGTATCG
1 TGTAGCAGTGCATCG
491797 ATACGCATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (21 bp):
TGTAGCAGTGCATCGGTACAC
Found at i:491945 original size:19 final size:20
Alignment explanation
Indices: 491897--491949 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
491887 TTGCTGTTCA
*
491897 CAGTACTATTTATACAATAT
1 CAGTACTATTCATACAATAT
*
491917 CAGTACTATTCATACATTAT
1 CAGTACTATTCATACAATAT
*
491937 -AGTATTATTCATA
1 CAGTACTATTCATA
491950 AAAACGTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.42
Consensus pattern (20 bp):
CAGTACTATTCATACAATAT
Found at i:494032 original size:21 final size:21
Alignment explanation
Indices: 494008--494054 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
493998 AATATGTAAA
494008 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
494029 TCGCGTTGCGATTTTCCAATT
1 TCGCATTGCGATTTTCCAAAT
494050 TCGCA
1 TCGCA
494055 ACGCGAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.19, C:0.26, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:494060 original size:21 final size:21
Alignment explanation
Indices: 493947--494060 Score: 63
Period size: 20 Copynumber: 5.6 Consensus size: 21
493937 GACCAACAAA
**
493947 TTCGCAACGCGA-ACTCCAAT
1 TTCGCAACGCGATTTTCCAAT
* *
493967 TTCGCAACTC-AGTTTCCAAT
1 TTCGCAACGCGATTTTCCAAT
* * * **
493987 TTCGCAACTCGAATATGTAA-
1 TTCGCAACGCGATTTTCCAAT
* ** *
494007 ATCGCATTGCGATTTTCCAAA
1 TTCGCAACGCGATTTTCCAAT
***
494028 TTCGCGTTGCGATTTTCCAAT
1 TTCGCAACGCGATTTTCCAAT
494049 TTCGCAACGCGA
1 TTCGCAACGCGA
494061 ATTTGTAAAT
Statistics
Matches: 70, Mismatches: 21, Indels: 5
0.73 0.22 0.05
Matches are distributed among these distances:
19 1 0.01
20 37 0.53
21 32 0.46
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.31
Consensus pattern (21 bp):
TTCGCAACGCGATTTTCCAAT
Found at i:494093 original size:40 final size:40
Alignment explanation
Indices: 494049--494228 Score: 192
Period size: 40 Copynumber: 4.5 Consensus size: 40
494039 ATTTTCCAAT
*
494049 TTCGCAACGCGAATTTGT-AAA-TCGCAACACAGAAGTCAAA
1 TTCGCAACGCG-A-TAGTCAAATTCGCAACACAGAAGTCAAA
* *
494089 TTCGCAACGCGATAGTCAAATTCGTAGCACA-AAGTCAAA
1 TTCGCAACGCGATAGTCAAATTCGCAACACAGAAGTCAAA
* *
494128 TTCACAACGCGAATTTGT-AAA-TCGCAACACAGAAGTCAAA
1 TTCGCAACGCG-A-TAGTCAAATTCGCAACACAGAAGTCAAA
* *
494168 TTCGCAACACGATAGTCAAATTCGCAACGC-GATAGTCAAA
1 TTCGCAACGCGATAGTCAAATTCGCAACACAGA-AGTCAAA
* *
494208 TTCGCAACGCAAAAGTCAAAT
1 TTCGCAACGCGATAGTCAAAT
494229 GTTTTTACGC
Statistics
Matches: 118, Mismatches: 14, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
38 6 0.05
39 36 0.31
40 73 0.62
41 3 0.03
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (40 bp):
TTCGCAACGCGATAGTCAAATTCGCAACACAGAAGTCAAA
Found at i:494216 original size:20 final size:20
Alignment explanation
Indices: 494082--494228 Score: 149
Period size: 20 Copynumber: 7.4 Consensus size: 20
494072 GCAACACAGA
494082 AGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACGCGAT
* * * *
494102 AGTCAAATTCGTAGCAC-AA
1 AGTCAAATTCGCAACGCGAT
*
494121 AGTCAAATTCACAACGCGAATT
1 AGTCAAATTCGCAACGCG-A-T
* *
494143 TGT-AAA-TCGCAACACAGA-
1 AGTCAAATTCGCAACGC-GAT
*
494161 AGTCAAATTCGCAACACGAT
1 AGTCAAATTCGCAACGCGAT
494181 AGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACGCGAT
* *
494201 AGTCAAATTCGCAACGCAAA
1 AGTCAAATTCGCAACGCGAT
494221 AGTCAAAT
1 AGTCAAAT
494229 GTTTTTACGC
Statistics
Matches: 104, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
18 2 0.02
19 19 0.18
20 76 0.73
21 5 0.05
22 2 0.02
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.20
Consensus pattern (20 bp):
AGTCAAATTCGCAACGCGAT
Found at i:494381 original size:22 final size:22
Alignment explanation
Indices: 494356--494406 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
494346 CTACGGCGAC
494356 ATCCATCCCCATCTCCGACGAA
1 ATCCATCCCCATCTCCGACGAA
494378 ATCCATCCCCATCTCCGACGAA
1 ATCCATCCCCATCTCCGACGAA
494400 ATCCATC
1 ATCCATC
494407 TATCTCCATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.27, C:0.45, G:0.08, T:0.20
Consensus pattern (22 bp):
ATCCATCCCCATCTCCGACGAA
Found at i:494687 original size:12 final size:13
Alignment explanation
Indices: 494670--494700 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
494660 AGTATTTGTC
494670 TTTGTTTT-TCTT
1 TTTGTTTTGTCTT
494682 TTTGTTTTGTCTT
1 TTTGTTTTGTCTT
494695 TTTGTT
1 TTTGTT
494701 GAAGAAACCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.00, C:0.06, G:0.13, T:0.81
Consensus pattern (13 bp):
TTTGTTTTGTCTT
Found at i:494750 original size:14 final size:14
Alignment explanation
Indices: 494712--494751 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
494702 AAGAAACCCT
*
494712 AAATCGCAACACCA
1 AAATCGCAACGCCA
* *
494726 AATTCGCAACGCGA
1 AAATCGCAACGCCA
494740 AAATCGCAACGC
1 AAATCGCAACGC
494752 AATTTTAGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.33, G:0.15, T:0.10
Consensus pattern (14 bp):
AAATCGCAACGCCA
Found at i:494792 original size:20 final size:20
Alignment explanation
Indices: 494760--494825 Score: 114
Period size: 20 Copynumber: 3.3 Consensus size: 20
494750 GCAATTTTAG
*
494760 TTTCGCGTTGCGATTTTCAT
1 TTTCGCATTGCGATTTTCAT
*
494780 TTTTGCATTGCGATTTTCAT
1 TTTCGCATTGCGATTTTCAT
494800 TTTCGCATTGCGATTTTCAT
1 TTTCGCATTGCGATTTTCAT
494820 TTTCGC
1 TTTCGC
494826 GTTACGAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.12, C:0.20, G:0.17, T:0.52
Consensus pattern (20 bp):
TTTCGCATTGCGATTTTCAT
Found at i:496913 original size:21 final size:21
Alignment explanation
Indices: 496894--496992 Score: 103
Period size: 21 Copynumber: 4.7 Consensus size: 21
496884 GATGCACCTA
* *
496894 TCATCATTCAAGAGGCACCTC
1 TCATCGTTCAAGAGGCCCCTC
*
496915 TTATCGTTCAAGAGGCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* *
496936 TCATC-ATCGAAGAAGCCCCTC
1 TCATCGTTC-AAGAGGCCCCTC
* *
496957 CCACCGTTCAAGAGGCCCC-C
1 TCATCGTTCAAGAGGCCCCTC
496977 ATCATCGTTCAAGAGG
1 -TCATCGTTCAAGAGG
496993 TCCTGCCCGC
Statistics
Matches: 63, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
20 3 0.05
21 58 0.92
22 2 0.03
ACGTcount: A:0.25, C:0.35, G:0.18, T:0.21
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:496941 original size:42 final size:42
Alignment explanation
Indices: 496893--497012 Score: 120
Period size: 42 Copynumber: 2.9 Consensus size: 42
496883 CGATGCACCT
** *
496893 ATCATCATTCAAGAGGCACCTCTTATCGTTCAAGAGGCCCCTC
1 ATCATCATTCAAGAGGCACCTCCCACCGTTCAAGAGGCCCC-C
* *
496936 -TCATCA-TCGAAGAAGCCCCTCCCACCGTTCAAGAGGCCCCC
1 ATCATCATTC-AAGAGGCACCTCCCACCGTTCAAGAGGCCCCC
* * *
496977 ATCATCGTTCAAGAGG-TCCTGCCCGCCGTTCAAGAG
1 ATCATCATTCAAGAGGCACCT-CCCACCGTTCAAGAG
497013 CCCGATTCAT
Statistics
Matches: 64, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
41 6 0.09
42 56 0.88
43 2 0.03
ACGTcount: A:0.24, C:0.36, G:0.19, T:0.21
Consensus pattern (42 bp):
ATCATCATTCAAGAGGCACCTCCCACCGTTCAAGAGGCCCCC
Found at i:498458 original size:28 final size:28
Alignment explanation
Indices: 498413--498466 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
498403 TTTTGATTAA
*
498413 TTGATTTGTAAAAGTTGATTTGTAAAAG
1 TTGATTTGTAAAAGTTGATGTGTAAAAG
** *
498441 TTGATTTGTTTAATTTGATGTGTAAA
1 TTGATTTGTAAAAGTTGATGTGTAAA
498467 TAAGAATTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.48
Consensus pattern (28 bp):
TTGATTTGTAAAAGTTGATGTGTAAAAG
Found at i:498459 original size:14 final size:14
Alignment explanation
Indices: 498413--498449 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
498403 TTTTGATTAA
498413 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
498427 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
498441 TTGATTTGT
1 TTGATTTGT
498450 TTAATTTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:498642 original size:20 final size:20
Alignment explanation
Indices: 498617--498687 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 20
498607 GATTTTTGGT
498617 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTTTCGCG
*
498637 TTGCGAATTTGACTTTCACG
1 TTGCGAATTTGACTTTCGCG
* * *
498657 TTGCGAATTTGGCTTTTGTG
1 TTGCGAATTTGACTTTCGCG
*
498677 TTGTGAATTTG
1 TTGCGAATTTG
498688 GCTATCACAA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.15, C:0.14, G:0.25, T:0.45
Consensus pattern (20 bp):
TTGCGAATTTGACTTTCGCG
Found at i:499036 original size:6 final size:6
Alignment explanation
Indices: 499025--499093 Score: 88
Period size: 6 Copynumber: 11.8 Consensus size: 6
499015 GTTGTGATTG
**
499025 GATTTT GATTTT GA--TT GATTGC GATTTT GATTTT GATTTT GATTTT
1 GATTTT GATTTT GATTTT GATTTT GATTTT GATTTT GATTTT GATTTT
**
499071 GATTGC GATTTT GATTTT GATTT
1 GATTTT GATTTT GATTTT GATTT
499094 CCTTTTGCTT
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
4 4 0.08
6 49 0.92
ACGTcount: A:0.17, C:0.03, G:0.20, T:0.59
Consensus pattern (6 bp):
GATTTT
Found at i:499052 original size:22 final size:21
Alignment explanation
Indices: 499019--499074 Score: 82
Period size: 22 Copynumber: 2.8 Consensus size: 21
499009 AAGCCGGTTG
499019 TGATTGGATTTTGATTTTGAT
1 TGATTGGATTTTGATTTTGAT
499040 TGATTGCGATTTTGATTTTGAT
1 TGATTG-GATTTTGATTTTGAT
499062 T--TT-GATTTTGATT
1 TGATTGGATTTTGATT
499075 GCGATTTTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
18 10 0.29
20 2 0.06
21 6 0.18
22 16 0.47
ACGTcount: A:0.18, C:0.02, G:0.21, T:0.59
Consensus pattern (21 bp):
TGATTGGATTTTGATTTTGAT
Found at i:501534 original size:12 final size:12
Alignment explanation
Indices: 501513--501546 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
501503 GGTTGTGGGT
*
501513 TTTGAGATTGTG
1 TTTGATATTGTG
501525 TTTGATATTGTG
1 TTTGATATTGTG
*
501537 TTTGGTATTG
1 TTTGATATTG
501547 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:502132 original size:14 final size:15
Alignment explanation
Indices: 502096--502133 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
502086 GAAATCATTG
502096 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
502111 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
502126 AAAAATTA
1 AAAAATTA
502134 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:502336 original size:21 final size:20
Alignment explanation
Indices: 502292--502364 Score: 103
Period size: 21 Copynumber: 3.6 Consensus size: 20
502282 TAAATTCATG
*
502292 TTGCGAATTTGAAATTC-AA
1 TTGCGAATTTGAAATTCGCA
502311 TTGCGAATTTGAAATTCTGCA
1 TTGCGAATTTGAAATTC-GCA
502332 TTGCGAATTTGAAATTCCGCA
1 TTGCGAATTTGAAATT-CGCA
*
502353 TTGCAAATTTGA
1 TTGCGAATTTGA
502365 CTTTTGTGTT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
19 17 0.35
21 31 0.63
22 1 0.02
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.37
Consensus pattern (20 bp):
TTGCGAATTTGAAATTCGCA
Found at i:502381 original size:20 final size:20
Alignment explanation
Indices: 502353--502475 Score: 124
Period size: 20 Copynumber: 6.2 Consensus size: 20
502343 AAATTCCGCA
502353 TTGCAAATTTGACTTTTGTG
1 TTGCAAATTTGACTTTTGTG
*
502373 TTGCGAATTTGACTTTTGTG
1 TTGCAAATTTGACTTTTGTG
* * * *
502393 TTGC-GATTT-ACAAATTCGCG
1 TTGCAAATTTGAC--TTTTGTG
*
502413 TTGCGAATTTGACTTTTGTG
1 TTGCAAATTTGACTTTTGTG
* * *
502433 TTGCAAATTTGACTATCGCG
1 TTGCAAATTTGACTTTTGTG
*
502453 TTGCAAATTTGACTTCTGTG
1 TTGCAAATTTGACTTTTGTG
502473 TTG
1 TTG
502476 TGATTTACAA
Statistics
Matches: 82, Mismatches: 17, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
18 2 0.02
19 4 0.05
20 70 0.85
21 4 0.05
22 2 0.02
ACGTcount: A:0.20, C:0.14, G:0.22, T:0.45
Consensus pattern (20 bp):
TTGCAAATTTGACTTTTGTG
Found at i:502423 original size:40 final size:40
Alignment explanation
Indices: 502372--502494 Score: 169
Period size: 40 Copynumber: 3.1 Consensus size: 40
502362 TGACTTTTGT
502372 GTTGCGAATTTGACTTTTGTGTTGCGATTTACAAATTCGC
1 GTTGCGAATTTGACTTTTGTGTTGCGATTTACAAATTCGC
* *
502412 GTTGCGAATTTGACTTTTGTGTTGCAAATTTGAC-TA-TCGC
1 GTTGCGAATTTGACTTTTGTGTTGC-GATTT-ACAAATTCGC
* * *
502452 GTTGCAAATTTGACTTCTGTGTTGTGATTTACAAATTCGC
1 GTTGCGAATTTGACTTTTGTGTTGCGATTTACAAATTCGC
502492 GTT
1 GTT
502495 ACGATTTACA
Statistics
Matches: 72, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
38 2 0.03
39 5 0.07
40 58 0.81
41 5 0.07
42 2 0.03
ACGTcount: A:0.20, C:0.15, G:0.22, T:0.43
Consensus pattern (40 bp):
GTTGCGAATTTGACTTTTGTGTTGCGATTTACAAATTCGC
Found at i:502456 original size:60 final size:61
Alignment explanation
Indices: 502343--502456 Score: 167
Period size: 60 Copynumber: 1.9 Consensus size: 61
502333 TGCGAATTTG
* * * *
502343 AAATTCCGCATTGCAAATTTGACTTTTGTGTTGCGAATTTGACTTTTGTGTTGCGATTTAC
1 AAATTCCGCATTGCAAATTTGACTTTTGTGTTGCAAATTTGACTATCGCGTTGCGATTTAC
* *
502404 AAATT-CGCGTTGCGAATTTGACTTTTGTGTTGCAAATTTGACTATCGCGTTGC
1 AAATTCCGCATTGCAAATTTGACTTTTGTGTTGCAAATTTGACTATCGCGTTGC
502457 AAATTTGACT
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
60 42 0.89
61 5 0.11
ACGTcount: A:0.21, C:0.16, G:0.21, T:0.42
Consensus pattern (61 bp):
AAATTCCGCATTGCAAATTTGACTTTTGTGTTGCAAATTTGACTATCGCGTTGCGATTTAC
Found at i:502502 original size:20 final size:20
Alignment explanation
Indices: 502477--502514 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
502467 TCTGTGTTGT
502477 GATTTACAAATTCGCGTTAC
1 GATTTACAAATTCGCGTTAC
*
502497 GATTTACAGATTCGCGTT
1 GATTTACAAATTCGCGTT
502515 GCGAAATTGG
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:0.26, C:0.18, G:0.18, T:0.37
Consensus pattern (20 bp):
GATTTACAAATTCGCGTTAC
Found at i:502516 original size:80 final size:80
Alignment explanation
Indices: 502335--502522 Score: 218
Period size: 80 Copynumber: 2.3 Consensus size: 80
502325 TTCTGCATTG
* * * * * * *
502335 CGAATTTGAAATTCCGCATTGCAAATTTGACTTTTGTGTTGCGAATTTGACTTTTGTGTTGCGAT
1 CGAATTTGACATT-CGCGTTGCAAATTTGACTATCGCGTTGCAAATTTGACTTCTGTGTTGCGAT
*
502400 TTACAAATTCGCGTTG
65 TTACAAATTCGCGTTA
* * * *
502416 CGAATTTGACTTTTGTGTTGCAAATTTGACTATCGCGTTGCAAATTTGACTTCTGTGTTGTGATT
1 CGAATTTGACATTCGCGTTGCAAATTTGACTATCGCGTTGCAAATTTGACTTCTGTGTTGCGATT
502481 TACAAATTCGCGTTA
66 TACAAATTCGCGTTA
502496 CG-ATTT-ACAGATTCGCGTTGCGAAATT
1 CGAATTTGAC--ATTCGCGTTGC-AAATT
502523 GGAAAATCGC
Statistics
Matches: 89, Mismatches: 15, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
78 2 0.02
79 4 0.04
80 67 0.75
81 16 0.18
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.41
Consensus pattern (80 bp):
CGAATTTGACATTCGCGTTGCAAATTTGACTATCGCGTTGCAAATTTGACTTCTGTGTTGCGATT
TACAAATTCGCGTTA
Found at i:506963 original size:39 final size:39
Alignment explanation
Indices: 506919--506997 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
506909 AAGTCTCAAC
506919 TATCATGGTGTTTCAATTATTTCAAAAATTAGTGTTGAA
1 TATCATGGTGTTTCAATTATTTCAAAAATTAGTGTTGAA
506958 TATCATGGTGTTTCAATTATTTCAAAAATTAGTGTTGAA
1 TATCATGGTGTTTCAATTATTTCAAAAATTAGTGTTGAA
506997 T
1 T
506998 CAGTTTGTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.44
Consensus pattern (39 bp):
TATCATGGTGTTTCAATTATTTCAAAAATTAGTGTTGAA
Found at i:508267 original size:20 final size:20
Alignment explanation
Indices: 508218--508290 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
508208 GCAGCCTTCG
* * * *
508218 TGCATGGATGCACAGCAGGG
1 TGCATCGATGCACAACATGA
*
508238 TGCATAGATGCACAACATGA
1 TGCATCGATGCACAACATGA
* *
508258 TGGATCGATGCACATCATGA
1 TGCATCGATGCACAACATGA
*
508278 TGCATCAATGCAC
1 TGCATCGATGCAC
508291 TAAGTGTATT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.21
Consensus pattern (20 bp):
TGCATCGATGCACAACATGA
Found at i:508335 original size:20 final size:21
Alignment explanation
Indices: 508310--508365 Score: 87
Period size: 20 Copynumber: 2.7 Consensus size: 21
508300 TCGAAATTGA
*
508310 GTGCATGGATGCACTACA-TG
1 GTGCATGGATGCACTACAGGG
*
508330 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTACAGGG
508351 GTGCATGGATGCACT
1 GTGCATGGATGCACT
508366 TTGACACCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
20 17 0.52
21 16 0.48
ACGTcount: A:0.21, C:0.20, G:0.36, T:0.23
Consensus pattern (21 bp):
GTGCATGGATGCACTACAGGG
Found at i:508612 original size:21 final size:21
Alignment explanation
Indices: 508588--508627 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
508578 ATGTTTAATG
508588 AAAAAGATATCAATTGTTAAC
1 AAAAAGATATCAATTGTTAAC
*
508609 AAAATGATATCAATTGTTA
1 AAAAAGATATCAATTGTTA
508628 CCAATTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (21 bp):
AAAAAGATATCAATTGTTAAC
Found at i:509739 original size:23 final size:23
Alignment explanation
Indices: 509693--509739 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
509683 TAAATCAACA
* *
509693 TTTTATTTTTCAAAACTTTCAAT
1 TTTTATTTTTCAAAACTCTAAAT
* *
509716 TTTTATTTTTGAAAGCTCTAAAT
1 TTTTATTTTTCAAAACTCTAAAT
509739 T
1 T
509740 CTTTTTCAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.11, G:0.04, T:0.55
Consensus pattern (23 bp):
TTTTATTTTTCAAAACTCTAAAT
Found at i:510935 original size:20 final size:22
Alignment explanation
Indices: 510910--510949 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
510900 TGTTGTATAT
510910 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
510930 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
510950 TCTACTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:511094 original size:32 final size:33
Alignment explanation
Indices: 511052--511115 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
511042 TAGCCTTCGT
*
511052 GTATGGATGCACAGCAGGGTGCATCGATGCACA
1 GTATGGATGCACAGCAGGATGCATCGATGCACA
*
511085 GTAT-GATGCACATCAGGATGCATCGATGCAC
1 GTATGGATGCACAGCAGGATGCATCGATGCAC
511116 TAAGTGTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 25 0.86
33 4 0.14
ACGTcount: A:0.28, C:0.22, G:0.30, T:0.20
Consensus pattern (33 bp):
GTATGGATGCACAGCAGGATGCATCGATGCACA
Found at i:511180 original size:21 final size:21
Alignment explanation
Indices: 511135--511211 Score: 120
Period size: 21 Copynumber: 3.7 Consensus size: 21
511125 TCGAAATGGA
* *
511135 GTGCATGGATGCACTACA-TG
1 GTGCATGGATGCACTGCAGGG
511155 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
*
511176 GTGCATAGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
511197 GTGCATGGATGCACT
1 GTGCATGGATGCACT
511212 TTGACACTCT
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
20 17 0.33
21 35 0.67
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.22
Consensus pattern (21 bp):
GTGCATGGATGCACTGCAGGG
Found at i:511602 original size:39 final size:39
Alignment explanation
Indices: 511548--511625 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
511538 ACTGATTTGC
511548 ACACTGATGATGATGTTACGCAAGAACATTTGGTGTCTA
1 ACACTGATGATGATGTTACGCAAGAACATTTGGTGTCTA
** *
511587 ACACTGATGATGATGTTGTGCAAGAACCTTTGGTGTCTA
1 ACACTGATGATGATGTTACGCAAGAACATTTGGTGTCTA
511626 TTGTACCTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.32
Consensus pattern (39 bp):
ACACTGATGATGATGTTACGCAAGAACATTTGGTGTCTA
Found at i:514275 original size:30 final size:30
Alignment explanation
Indices: 514221--514290 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
514211 GGAGACCTAG
* **
514221 ATTTTAAAAATTATAATTTAGATTCTTAAA
1 ATTTTAAAAAATATAATTTAGATTCCCAAA
514251 ATTTTCAAAAAATATAATTT-GATTCCCAAA
1 ATTTT-AAAAAATATAATTTAGATTCCCAAA
*
514281 ATTTTTAAAA
1 ATTTTAAAAA
514291 TTCAGATTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 4 0.11
30 18 0.51
31 13 0.37
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (30 bp):
ATTTTAAAAAATATAATTTAGATTCCCAAA
Found at i:514891 original size:3 final size:3
Alignment explanation
Indices: 514883--514941 Score: 66
Period size: 3 Copynumber: 18.7 Consensus size: 3
514873 CTCTCGTGTA
*
514883 TAT TAT TAT TAT TA- CAT ATAT TAT ATAT TAT ATAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT -TAT TAT -TAT TAT -TAT TAT TAT TAT TAT
514930 TAT TATT TAT TA
1 TAT TA-T TAT TA
514942 CAAACCCATT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
2 1 0.02
3 37 0.76
4 11 0.22
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:515445 original size:2 final size:2
Alignment explanation
Indices: 515438--515470 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
515428 TTCAAATACA
515438 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 A
515471 CGAAAAAAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:516475 original size:25 final size:23
Alignment explanation
Indices: 516446--516507 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 23
516436 TAACCACTAG
*
516446 ATTAATTTATATTTATTAATTTAA
1 ATTAATTT-TATTTATTAAATTAA
**
516470 TATTAATTTGGTTTATTAAATTAA
1 -ATTAATTTTATTTATTAAATTAA
516494 ATTAAATTTTATTT
1 ATT-AATTTTATTT
516508 TTTAGTTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 3 0.10
24 20 0.65
25 8 0.26
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (23 bp):
ATTAATTTTATTTATTAAATTAA
Found at i:521216 original size:64 final size:63
Alignment explanation
Indices: 521105--521303 Score: 201
Period size: 64 Copynumber: 3.1 Consensus size: 63
521095 TTTCAGAGTG
* *
521105 ATGCACCAATCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCGAATGCATTTCATGCA
1 ATGCA-CAA-CCATGCATCGATGCACTCAGGATATT---TTGAAACATCGAATGCATTTGATGCA
521167 TCA
61 TCA
*
521170 ATGCACATACCATGCATCGATGCACT-AGGAT-TTTATGAAAACATCGAATGCATTTGATGCACC
1 ATGCACA-ACCATGCATCGATGCACTCAGGATATTT-TG-AAACATCGAATGCATTTGATGCATC
521233 A
63 A
* * * * * *
521234 ATACACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTGATGCATCG
1 ATGCA-CAACCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATTTGATGCATCA
521298 ATGCAC
1 ATGCAC
521304 TCTTAGTGCA
Statistics
Matches: 114, Mismatches: 11, Indels: 20
0.79 0.08 0.14
Matches are distributed among these distances:
61 1 0.01
62 2 0.02
63 1 0.01
64 94 0.82
65 13 0.11
66 3 0.03
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.26
Consensus pattern (63 bp):
ATGCACAACCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATTTGATGCATCA
Found at i:521303 original size:17 final size:19
Alignment explanation
Indices: 521275--521323 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
521265 TATTTTGAAA
521275 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
521293 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
521312 CACCGATGCACT
1 CATCGATGCACT
521324 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:527125 original size:21 final size:21
Alignment explanation
Indices: 527080--527154 Score: 80
Period size: 23 Copynumber: 3.4 Consensus size: 21
527070 CACCTAACAA
*
527080 TGCATCGATGCATCCTTGAATG
1 TGCATCGATACA-CCTTGAATG
* *
527102 TGCATCGATACACCATGAAGG
1 TGCATCGATACACCTTGAATG
527123 TGCA-CTGATGCACACCTTGAATG
1 TGCATC-GAT--ACACCTTGAATG
527146 TGCATCGAT
1 TGCATCGAT
527155 GCACAGGGTC
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
20 1 0.02
21 14 0.32
22 11 0.25
23 17 0.39
24 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.27
Consensus pattern (21 bp):
TGCATCGATACACCTTGAATG
Found at i:532307 original size:3 final size:3
Alignment explanation
Indices: 532299--532345 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
532289 CTCTCATGTA
* *
532299 TAT TAT TAT TAT TAT TA- TAT TACA TAT TAT TAT TAT TAT TGT TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
532344 TA
1 TA
532346 CAAATAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 34 0.89
4 2 0.05
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:541414 original size:24 final size:24
Alignment explanation
Indices: 541369--541429 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
541359 CTGAATTTTG
* * *
541369 TGATTTATGATCTGGATTCTGTTC
1 TGATTTATGATATGAATACTGTTC
* *
541393 TGATATATGATATGAATACTGTTT
1 TGATTTATGATATGAATACTGTTC
*
541417 TGATTTCTGATAT
1 TGATTTATGATAT
541430 CTCCGTTTAT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.25, C:0.08, G:0.18, T:0.49
Consensus pattern (24 bp):
TGATTTATGATATGAATACTGTTC
Found at i:543123 original size:20 final size:21
Alignment explanation
Indices: 543098--543137 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
543088 TATAATCACC
*
543098 AATAAGATCAT-AAATAAATT
1 AATAAGATAATCAAATAAATT
543118 AATAAGATAATCAAATAAAT
1 AATAAGATAATCAAATAAAT
543138 ATATCTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (21 bp):
AATAAGATAATCAAATAAATT
Found at i:548337 original size:473 final size:473
Alignment explanation
Indices: 547452--548392 Score: 1715
Period size: 473 Copynumber: 2.0 Consensus size: 473
547442 AATAAATACA
*
547452 AAAGATAAGGGATAATTAAAAGATAATTATCAAAGAAAATTCCTAAAAATGCAAAAGATAATTGT
1 AAAGATAAGGGATAATTAAAAGATAATTATCAAAGAAAATTCCTAAAAATACAAAAGATAATTGT
* *
547517 TTGAATTAAATCTAAAATAAAAGATAATTCCTAAATCTTGAATTTGAAATGTTCTTGGAATGCTC
66 TTGAATTAAATCTAAAATAAAAGATAATTCCTAAATCTTGAATTTGAAATGTGCTTGAAATGCTC
*
547582 AGTCGTCTGCACATCTTCTAGAAGCCTGCTGACTGGGCACTTCTAGAAACTGTTGATGTGACAGT
131 AGTCGTCTACACATCTTCTAGAAGCCTGCTGACTGGGCACTTCTAGAAACTGTTGATGTGACAGT
*
547647 GAGTCAACATTTCATGCTCAATTTTATGTCCATTGTTCCAGACTTAGTTCCAGAATAAAAATTAC
196 GAGTCAACATTTCATGCTCAATTTTATGTCCATTGTTCCAGACTTAGTTCCAGAACAAAAATTAC
547712 ATTTTTCAGCAAATCGTCCTGCACAAAAAACATATAAAAAACATCCAATTCAGTAGTAAACATGG
261 ATTTTTCAGCAAATCGTCCTGCACAAAAAACATATAAAAAACATCCAATTCAGTAGTAAACATGG
*
547777 ATAAACAAATAAAATTTAAGCACAAAAAGTAGCATAAAATAAACACTAGTCACTCCTTCGTTGAG
326 ATAAACAAATAAAATTTAAGCACAAAAAGTAACATAAAATAAACACTAGTCACTCCTTCGTTGAG
547842 AAATAAAGACATGGTGTCCAATATAATTAAATGAAATAGGTACAAGGGTTGAGATTATTATAGGA
391 AAATAAAGACATGGTGTCCAATATAATTAAATGAAATAGGTACAAGGGTTGAGATTATTATAGGA
*
547907 AATCTTAAGAGAGTTCTC
456 AATCTTAAAAGAGTTCTC
*
547925 AAAGATAAGGGATAATTAAAAGATAATTATCAAAGATAATTCCTAAAAATACAAAAGATAATTGT
1 AAAGATAAGGGATAATTAAAAGATAATTATCAAAGAAAATTCCTAAAAATACAAAAGATAATTGT
*
547990 TTGAATTAAATCTAAAATAAAATATAATTCCTAAATCTTGAATTTGAAATGTGCTTGAAATGCTC
66 TTGAATTAAATCTAAAATAAAAGATAATTCCTAAATCTTGAATTTGAAATGTGCTTGAAATGCTC
* *
548055 AGTCGTCTACACATCTTCTAGAAGCCTGTTGACTGGGCACTTCTAGAAACTGTTGATGTGGCAGT
131 AGTCGTCTACACATCTTCTAGAAGCCTGCTGACTGGGCACTTCTAGAAACTGTTGATGTGACAGT
*
548120 GAGTCAACATTTCATGCTCAATTTTATGTCCACTT-TTCCAGACTT-GATTCCATAACAAAAATT
196 GAGTCAACATTTCATGCTCAATTTTATGTCCA-TTGTTCCAGACTTAG-TTCCAGAACAAAAATT
* *
548183 ACATTTTTCAGCAGATCGTCCTGCACAAAAAACATGTAAAAAACATCCAATTCAGTAGTAAACAT
259 ACATTTTTCAGCAAATCGTCCTGCACAAAAAACATATAAAAAACATCCAATTCAGTAGTAAACAT
*
548248 GGATAAACAAATAAAATTTAAGCACGAAAAGTAACATAAAATAAACACTAGTCACTCCTTCGTTG
324 GGATAAACAAATAAAATTTAAGCACAAAAAGTAACATAAAATAAACACTAGTCACTCCTTCGTTG
548313 AGAAATAAAGACATGGTGTCCAATATAATTAAATGAAATAGGTACAAGGGTTGAGATTATTATAG
389 AGAAATAAAGACATGGTGTCCAATATAATTAAATGAAATAGGTACAAGGGTTGAGATTATTATAG
548378 GAAATCTTAAAAGAG
454 GAAATCTTAAAAGAG
548393 GGCCAACATG
Statistics
Matches: 451, Mismatches: 15, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
472 1 0.00
473 448 0.99
474 2 0.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (473 bp):
AAAGATAAGGGATAATTAAAAGATAATTATCAAAGAAAATTCCTAAAAATACAAAAGATAATTGT
TTGAATTAAATCTAAAATAAAAGATAATTCCTAAATCTTGAATTTGAAATGTGCTTGAAATGCTC
AGTCGTCTACACATCTTCTAGAAGCCTGCTGACTGGGCACTTCTAGAAACTGTTGATGTGACAGT
GAGTCAACATTTCATGCTCAATTTTATGTCCATTGTTCCAGACTTAGTTCCAGAACAAAAATTAC
ATTTTTCAGCAAATCGTCCTGCACAAAAAACATATAAAAAACATCCAATTCAGTAGTAAACATGG
ATAAACAAATAAAATTTAAGCACAAAAAGTAACATAAAATAAACACTAGTCACTCCTTCGTTGAG
AAATAAAGACATGGTGTCCAATATAATTAAATGAAATAGGTACAAGGGTTGAGATTATTATAGGA
AATCTTAAAAGAGTTCTC
Found at i:550471 original size:24 final size:24
Alignment explanation
Indices: 550423--550497 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 24
550413 CAGCTCGTAA
* *
550423 AAATTGCACCGAAGTACCGCGTAG
1 AAATTGCACCGAAGTACCACATAG
* *
550447 AAATTGCACCGTAGTGCCACATAG
1 AAATTGCACCGAAGTACCACATAG
550471 AAA-TGTC-CCGAA-TGACCACATAG
1 AAATTG-CACCGAAGT-ACCACATAG
550494 AAAT
1 AAAT
550498 GTCTCGAAGG
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
22 1 0.02
23 17 0.40
24 24 0.57
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (24 bp):
AAATTGCACCGAAGTACCACATAG
Found at i:550492 original size:23 final size:23
Alignment explanation
Indices: 550463--550587 Score: 135
Period size: 23 Copynumber: 5.4 Consensus size: 23
550453 CACCGTAGTG
550463 CCACATAGAAATGTCCCGAATGA
1 CCACATAGAAATGTCCCGAATGA
* *
550486 CCACATAGAAATGTCTCGAAGGA
1 CCACATAGAAATGTCCCGAATGA
* * *
550509 CCACATA-ATATTATCCCGAAGGA
1 CCACATAGA-AATGTCCCGAATGA
* *
550532 CCGCATAAAAATGTCCCGAATGA
1 CCACATAGAAATGTCCCGAATGA
* * *
550555 CCACGTAGAATTCTCCCGAATGA
1 CCACATAGAAATGTCCCGAATGA
*
550578 CCGCATAGAA
1 CCACATAGAA
550588 CCCTCAACTC
Statistics
Matches: 84, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
22 1 0.01
23 82 0.98
24 1 0.01
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (23 bp):
CCACATAGAAATGTCCCGAATGA
Found at i:550526 original size:46 final size:46
Alignment explanation
Indices: 550463--550587 Score: 153
Period size: 46 Copynumber: 2.7 Consensus size: 46
550453 CACCGTAGTG
* * * *
550463 CCACATAGAAATGTCCCGAATGACCACATAGAAATGTCTCGAAGGA
1 CCACATAGAATTATCCCGAATGACCGCATAGAAATGTCCCGAAGGA
* * *
550509 CCACATA-ATATTATCCCGAAGGACCGCATAAAAATGTCCCGAATGA
1 CCACATAGA-ATTATCCCGAATGACCGCATAGAAATGTCCCGAAGGA
* *
550555 CCACGTAGAATTCTCCCGAATGACCGCATAGAA
1 CCACATAGAATTATCCCGAATGACCGCATAGAA
550588 CCCTCAACTC
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
45 1 0.02
46 64 0.97
47 1 0.02
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (46 bp):
CCACATAGAATTATCCCGAATGACCGCATAGAAATGTCCCGAAGGA
Found at i:550770 original size:19 final size:19
Alignment explanation
Indices: 550746--550796 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
550736 CCACATAGAT
550746 CATGTAACACATAGGATAA
1 CATGTAACACATAGGATAA
550765 CATGTAACACATAGGATAA
1 CATGTAACACATAGGATAA
550784 CATGTAACACATA
1 CATGTAACACATA
550797 TCTCATGTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.47, C:0.18, G:0.14, T:0.22
Consensus pattern (19 bp):
CATGTAACACATAGGATAA
Found at i:557437 original size:194 final size:191
Alignment explanation
Indices: 557083--557456 Score: 658
Period size: 194 Copynumber: 1.9 Consensus size: 191
557073 AATAACATGA
*
557083 TTTTGAAGAGTTCAACACCACCTAAGAAATAAAAGACAAAATTACATGGAAAAAGAACACAACAA
1 TTTTGAAGAGTTCAACACCACCTAAGAAATAAAAGACAAAATTACATGGAAAAAGAACAAAACAA
* *
557148 TTTGTGGAAAGTAGGTCGTATGATTTAGACCGAGCTATCTCCTTGTATTAACAAACAGCTATAAC
66 TTTGTGGAAAGTAGGTCGTATAATTTAGACCAAGCTATCTCCTTGTATTAACAAACAGCTATAAC
*
557213 AAGAACACAACACAAGACAGACATGAGATTTGGAAACCCCTTGAAAAAAAAAACATTTATG
131 AAGAACACAACACAAGACAGACAAGAGATTTGGAAACCCCTTGAAAAAAAAAACATTTATG
* *
557274 TTTTGAAGAGTTCAACACCACCTATGTAATAAAAGACAAAATTACATGGAAAAAGAACAAAACAA
1 TTTTGAAGAGTTCAACACCACCTAAGAAATAAAAGACAAAATTACATGGAAAAAGAACAAAACAA
*
557339 TTTGTGGAAAGTAGAAGGTCGTATAATTTAGACCAAGCTATCTCCTTGTATTAACAAACAGTTAT
66 TTTGTGGAAAGT---AGGTCGTATAATTTAGACCAAGCTATCTCCTTGTATTAACAAACAGCTAT
557404 AACAAGAACACAACACAAGACAGACAAGAGATTTGGAAACCCCTTGAAAAAAA
128 AACAAGAACACAACACAAGACAGACAAGAGATTTGGAAACCCCTTGAAAAAAA
557457 TACAAAATCA
Statistics
Matches: 173, Mismatches: 7, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
191 74 0.43
194 99 0.57
ACGTcount: A:0.46, C:0.17, G:0.16, T:0.22
Consensus pattern (191 bp):
TTTTGAAGAGTTCAACACCACCTAAGAAATAAAAGACAAAATTACATGGAAAAAGAACAAAACAA
TTTGTGGAAAGTAGGTCGTATAATTTAGACCAAGCTATCTCCTTGTATTAACAAACAGCTATAAC
AAGAACACAACACAAGACAGACAAGAGATTTGGAAACCCCTTGAAAAAAAAAACATTTATG
Found at i:570494 original size:12 final size:12
Alignment explanation
Indices: 570466--570504 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
570456 TTATTTGCAA
570466 ATTTTT-ATCTT
1 ATTTTTAATCTT
570477 -TTTTTAATCTT
1 ATTTTTAATCTT
570488 ATTTTTAATCTT
1 ATTTTTAATCTT
*
570500 GTTTT
1 ATTTT
570505 CAACACCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 5 0.20
11 5 0.20
12 15 0.60
ACGTcount: A:0.18, C:0.08, G:0.03, T:0.72
Consensus pattern (12 bp):
ATTTTTAATCTT
Found at i:573828 original size:28 final size:27
Alignment explanation
Indices: 573797--573862 Score: 89
Period size: 26 Copynumber: 2.4 Consensus size: 27
573787 ACGAATCCCA
* * *
573797 TACATAACAGAGTGGGGAACAAATCTTG
1 TACAGAACAGAG-GCGGAACAAATCTCG
573825 TACAGAACAGA-GCGGAACAAATCTCG
1 TACAGAACAGAGGCGGAACAAATCTCG
573851 TACAGAACAGAG
1 TACAGAACAGAG
573863 AAGGGAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 24 0.71
28 10 0.29
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.15
Consensus pattern (27 bp):
TACAGAACAGAGGCGGAACAAATCTCG
Found at i:573848 original size:26 final size:26
Alignment explanation
Indices: 573812--573862 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
573802 AACAGAGTGG
*
573812 GGAACAAATCTTGTACAGAACAGAGC
1 GGAACAAATCTCGTACAGAACAGAGC
573838 GGAACAAATCTCGTACAGAACAGAG
1 GGAACAAATCTCGTACAGAACAGAG
573863 AAGGGAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.14
Consensus pattern (26 bp):
GGAACAAATCTCGTACAGAACAGAGC
Found at i:573895 original size:28 final size:28
Alignment explanation
Indices: 573854--573929 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 28
573844 AATCTCGTAC
* *
573854 AGAA-CAGAGAAGGGAAAATAT-TGATGA
1 AGAATCAG-GAAGGGAAAAAATCTCATGA
*
573881 AGAATCAGGACAGGGAAAAAATCTCATGC
1 AGAATCAGGA-AGGGAAAAAATCTCATGA
*
573910 AGAATCAGGATGGGAAAAAA
1 AGAATCAGGAAGGGAAAAAA
573930 GTCCCATACA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
27 6 0.14
28 22 0.52
29 14 0.33
ACGTcount: A:0.50, C:0.09, G:0.28, T:0.13
Consensus pattern (28 bp):
AGAATCAGGAAGGGAAAAAATCTCATGA
Found at i:573913 original size:29 final size:28
Alignment explanation
Indices: 573838--573973 Score: 91
Period size: 29 Copynumber: 4.8 Consensus size: 28
573828 AGAACAGAGC
* * *
573838 GGAACAAATCTCGTACAGAA-CAGAGAAG
1 GGAAAAAATCTCATGCAGAATCAG-GAAG
* * *
573866 GGAAAATAT-TGATGAAGAATCAGGACAG
1 GGAAAAAATCTCATGCAGAATCAGGA-AG
*
573894 GGAAAAAATCTCATGCAGAATCAGGATG
1 GGAAAAAATCTCATGCAGAATCAGGAAG
* * *
573922 GGAAAAAAGTCCCATACAAAATCA-GAATG
1 GGAAAAAA-TCTCATGCAGAATCAGGAA-G
573951 GGAAACAAAGTC-CTATGCAGAAT
1 GGAAA-AAA-TCTC-ATGCAGAAT
573974 GGCAGAACTA
Statistics
Matches: 85, Mismatches: 16, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
27 8 0.09
28 31 0.36
29 33 0.39
30 13 0.15
ACGTcount: A:0.46, C:0.15, G:0.24, T:0.15
Consensus pattern (28 bp):
GGAAAAAATCTCATGCAGAATCAGGAAG
Found at i:579885 original size:29 final size:29
Alignment explanation
Indices: 579800--579885 Score: 131
Period size: 28 Copynumber: 3.0 Consensus size: 29
579790 GTGAGAACTC
*
579800 TAAAGTCTAGGGACCTAAGTGTAAAAAAC
1 TAAAGTCTAGGGACCTAAGTGTAAAAAAT
579829 TAAAGTCTAGGG-CCTATA-TGTAAAAAAT
1 TAAAGTCTAGGGACCTA-AGTGTAAAAAAT
*
579857 TAAAGTCTAGGGACCTAAGTGTGAAAAAT
1 TAAAGTCTAGGGACCTAAGTGTAAAAAAT
579886 ATAATCCTAG
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
28 26 0.50
29 26 0.50
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.24
Consensus pattern (29 bp):
TAAAGTCTAGGGACCTAAGTGTAAAAAAT
Found at i:579895 original size:29 final size:29
Alignment explanation
Indices: 579802--579889 Score: 112
Period size: 29 Copynumber: 3.1 Consensus size: 29
579792 GAGAACTCTA
579802 AAGTCTAGGGACCTAAGTGTAAAAAACTA-
1 AAGTCTAGGGACCTAAGTGTAAAAAA-TAT
579831 AAGTCTAGGG-CCTATA-TGTAAAAAAT-T
1 AAGTCTAGGGACCTA-AGTGTAAAAAATAT
*
579858 AAAGTCTAGGGACCTAAGTGTGAAAAATAT
1 -AAGTCTAGGGACCTAAGTGTAAAAAATAT
579888 AA
1 AA
579890 TCCTAGAGGG
Statistics
Matches: 52, Mismatches: 1, Indels: 12
0.80 0.02 0.18
Matches are distributed among these distances:
27 1 0.02
28 24 0.46
29 26 0.50
30 1 0.02
ACGTcount: A:0.44, C:0.11, G:0.20, T:0.24
Consensus pattern (29 bp):
AAGTCTAGGGACCTAAGTGTAAAAAATAT
Found at i:581392 original size:65 final size:65
Alignment explanation
Indices: 581310--581440 Score: 201
Period size: 65 Copynumber: 2.0 Consensus size: 65
581300 TCATATTTAT
* * * * *
581310 TAAATTTTGATTTGATTTAATTTTAGAGAGTTGAAG-TTTTTTCTATATAAAGAGATTGAATTCG
1 TAAATTTTAATTTGATTTAATTTTACAGAGTTGAAGCATTTTTC-ATATAAAAAGATCGAATTCG
581374 G
65 G
581375 TAAATTTTAATTTGATTTAATTTTACAGAGTTGAAGCATTTTTCATATAAAAAGATCGAATTCGG
1 TAAATTTTAATTTGATTTAATTTTACAGAGTTGAAGCATTTTTCATATAAAAAGATCGAATTCGG
581440 T
1 T
581441 TTAGTTTGAA
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
65 54 0.90
66 6 0.10
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.44
Consensus pattern (65 bp):
TAAATTTTAATTTGATTTAATTTTACAGAGTTGAAGCATTTTTCATATAAAAAGATCGAATTCGG
Found at i:581717 original size:53 final size:53
Alignment explanation
Indices: 581646--581753 Score: 182
Period size: 53 Copynumber: 2.0 Consensus size: 53
581636 TTAGTATAAT
*
581646 TACACATCTAATCATTGATACTTACATA-TATATTAATTTAATCCTAATTTTAA
1 TACACATCTAATAATTGATACTTACATATTATATTAATTTAATCCTAA-TTTAA
*
581699 TACACATCTAATAATTGATACTTACATATTATATTAATTTAATCTTAATTTAA
1 TACACATCTAATAATTGATACTTACATATTATATTAATTTAATCCTAATTTAA
581752 TA
1 TA
581754 AATTAAAATA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
53 34 0.65
54 18 0.35
ACGTcount: A:0.41, C:0.13, G:0.02, T:0.44
Consensus pattern (53 bp):
TACACATCTAATAATTGATACTTACATATTATATTAATTTAATCCTAATTTAA
Found at i:582000 original size:2 final size:2
Alignment explanation
Indices: 581993--582020 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
581983 AAGTTACACA
581993 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
582021 CACAACTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:582129 original size:35 final size:35
Alignment explanation
Indices: 582078--582147 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
582068 AATAGAAACT
582078 TATTCTATTGTATTAGTAG-ACGAGATTTTACGAAA
1 TATTCTATTGTATTAGTAGTA-GAGATTTTACGAAA
* *
582113 TATTGTATTGTATTAGTAGTAGATATTTTACGAAA
1 TATTCTATTGTATTAGTAGTAGAGATTTTACGAAA
582148 AAGGGTCTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 31 0.97
36 1 0.03
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (35 bp):
TATTCTATTGTATTAGTAGTAGAGATTTTACGAAA
Found at i:582452 original size:2 final size:2
Alignment explanation
Indices: 582445--582477 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
582435 TTGTACTTTC
582445 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
582478 CACTGTGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:582634 original size:30 final size:30
Alignment explanation
Indices: 582579--582735 Score: 166
Period size: 30 Copynumber: 5.5 Consensus size: 30
582569 ATCTTAACTT
*
582579 ATAAAA-ATATCTTA-AA-TTAAAATAAAA
1 ATAAAATATATTTTATAAGTTAAAATAAAA
* *
582606 GTAAAATATATTTTATAAGTTAAGATAAAA
1 ATAAAATATATTTTATAAGTTAAAATAAAA
* * * *
582636 GT-AAA-ATACTTT-TAAGCTAAAATAAGA
1 ATAAAATATATTTTATAAGTTAAAATAAAA
* *
582663 TTAAAATATATTTT-TAAGCTAAAATAAAA
1 ATAAAATATATTTTATAAGTTAAAATAAAA
* *
582692 ATAAAATATATTTAATAAGTTAAGATAAAA
1 ATAAAATATATTTTATAAGTTAAAATAAAA
582722 ATAAAATATATTTT
1 ATAAAATATATTTT
582736 TTAAATGTTA
Statistics
Matches: 109, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
27 18 0.17
28 16 0.15
29 37 0.34
30 38 0.35
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.35
Consensus pattern (30 bp):
ATAAAATATATTTTATAAGTTAAAATAAAA
Found at i:583247 original size:244 final size:242
Alignment explanation
Indices: 582952--583584 Score: 960
Period size: 244 Copynumber: 2.6 Consensus size: 242
582942 CAGGGTGACA
* *
582952 TATGATTGGTTAAAAGTGTATTGAATTAAAAAATAAATTAAAATATAATTATTCCTTCAATTCGA
1 TATGATTGGTTGAAAGTATATTGAATT-AAAAATAAATTAAAATATAATTATTCCTTCAATT-GA
* * * * * *
583017 TGATGACACATGATTTCATCTAATTTGATGATAAAATTTATTTAAATTTGTTAAAATTATGACCA
64 TGATGACACATGACTTCATCTGATTCGATGATAAAATTTATTTTAATTTATTAAAATTATGAACA
* * *
583082 AGTTAAAATAATATGTAAATGTCAGTGATTAGATGTGTAATTATAGGTTCGAACCCATTTGCTTA
129 AATTAAAATAATATGTAAATGTCAGTGATTAGACGTGTAATTATAAGTTCGAACCCATTTGCTTA
* *
583147 CATTTGATGTGTTTTATTTTCTTTCCACCTTAGGGTGACACATGTCACCC
194 CATTTGATGTGCTTTATTTTCTTTCCACC-TAGGATGACACATGTCACCC
**
583197 TATGATTGGTTGAAAGTATATCAAATTAAAAATAAATTAAAATATAATTATTCCTTCAATTGGAT
1 TATGATTGGTTGAAAGTATATTGAATTAAAAATAAATTAAAATATAATTATTCCTTCAATT-GAT
* *
583262 GAGGACACATGACTTCATCTGATTCGATGATTAAATTTATTTTAATTTATTAAAATTATGAACAA
65 GATGACACATGACTTCATCTGATTCGATGATAAAATTTATTTTAATTTATTAAAATTATGAACAA
* * * *
583327 ATTAAAATAATATATAAGTGTCAGTGATTAGACGTGTAATTATAAGTTTGAACCCTTTTGCTTAC
130 ATTAAAATAATATGTAAATGTCAGTGATTAGACGTGTAATTATAAGTTCGAACCCATTTGCTTAC
*
583392 ATTTGATGTGCTTTATTTTCTTTCCACCTCGGATGACACATGTCACCC
195 ATTTGATGTGCTTTATTTTCTTTCCACCTAGGATGACACATGTCACCC
*
583440 TATGATTGATTGAAAGTATATTGAATTAAAAATAAATTAAAATATAATTATTCCTTCAATTGAAT
1 TATGATTGGTTGAAAGTATATTGAATTAAAAATAAATTAAAATATAATTATTCCTTCAATTG-AT
* * * * *
583505 GATGACACAAGGCTTCATTTGATTCAATAATTAAAATTTATTTTAATTTATTAAAATTATGAACA
65 GATGACACATGACTTCATCTGATTCGATGA-TAAAATTTATTTTAATTTATTAAAATTATGAACA
583570 AATTAAAATAATATG
129 AATTAAAATAATATG
583585 CAGTGGTTAG
Statistics
Matches: 352, Mismatches: 34, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
242 1 0.00
243 102 0.29
244 226 0.64
245 23 0.07
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (242 bp):
TATGATTGGTTGAAAGTATATTGAATTAAAAATAAATTAAAATATAATTATTCCTTCAATTGATG
ATGACACATGACTTCATCTGATTCGATGATAAAATTTATTTTAATTTATTAAAATTATGAACAAA
TTAAAATAATATGTAAATGTCAGTGATTAGACGTGTAATTATAAGTTCGAACCCATTTGCTTACA
TTTGATGTGCTTTATTTTCTTTCCACCTAGGATGACACATGTCACCC
Found at i:583702 original size:19 final size:20
Alignment explanation
Indices: 583667--583716 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
583657 ATTTGATACT
583667 CGATTCAAAAAGCTCGTGAG
1 CGATTCAAAAAGCTCGTGAG
*
583687 CGATTC-AAAAGTTCGTGAG
1 CGATTCAAAAAGCTCGTGAG
* *
583706 CAACTCAAAAA
1 CGATTCAAAAA
583717 TATAATATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (20 bp):
CGATTCAAAAAGCTCGTGAG
Found at i:583756 original size:27 final size:25
Alignment explanation
Indices: 583712--583762 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
583702 TGAGCAACTC
583712 AAAAATATAATATATTAA-ATTTAA
1 AAAAATATAATATATTAACATTTAA
583736 AAAAATTATGAATAATATTAACATTTA
1 AAAAA-TAT-AAT-ATATTAACATTTA
583763 TGTGTTGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 5 0.22
25 3 0.13
26 3 0.13
27 7 0.30
28 5 0.22
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (25 bp):
AAAAATATAATATATTAACATTTAA
Found at i:591105 original size:13 final size:13
Alignment explanation
Indices: 591087--591111 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
591077 AAAAATTGAT
591087 AAACATAAAATTG
1 AAACATAAAATTG
591100 AAACATAAAATT
1 AAACATAAAATT
591112 CAAATCAAGT
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:0.64, C:0.08, G:0.04, T:0.24
Consensus pattern (13 bp):
AAACATAAAATTG
Found at i:601622 original size:16 final size:16
Alignment explanation
Indices: 601603--601659 Score: 69
Period size: 16 Copynumber: 3.6 Consensus size: 16
601593 TTAGCCAAAC
601603 CGAAAGCAACTTGAAT
1 CGAAAGCAACTTGAAT
*
601619 CGAAAGTAACTTGAAT
1 CGAAAGCAACTTGAAT
* ** *
601635 CGAAAGTAACCCGAAC
1 CGAAAGCAACTTGAAT
601651 CGAAAGCAA
1 CGAAAGCAA
601660 TCCGAACCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.46, C:0.21, G:0.19, T:0.14
Consensus pattern (16 bp):
CGAAAGCAACTTGAAT
Found at i:601664 original size:16 final size:15
Alignment explanation
Indices: 601600--601686 Score: 66
Period size: 16 Copynumber: 5.5 Consensus size: 15
601590 ATTTTAGCCA
*
601600 AACCGAAAGCAACTTG
1 AACCGAAAGCAAC-CG
* * *
601616 AATCGAAAGTAACTTG
1 AACCGAAAGCAAC-CG
* *
601632 AATCGAAAGTAACCCG
1 AACCGAAAGCAA-CCG
601648 AACCGAAAGCAATCCG
1 AACCGAAAGCAA-CCG
*
601664 AACCAAAAGCAACCG
1 AACCGAAAGCAACCG
*
601679 ATCCGAAA
1 AACCGAAA
601687 ATAATCTATC
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
15 9 0.15
16 51 0.84
17 1 0.02
ACGTcount: A:0.46, C:0.25, G:0.17, T:0.11
Consensus pattern (15 bp):
AACCGAAAGCAACCG
Found at i:601742 original size:18 final size:18
Alignment explanation
Indices: 601708--601745 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
601698 CGAATAAGAT
*
601708 TTTTTTAAAAATGACATA
1 TTTTTTAAAAATAACATA
601726 TTTTTTACAAAA-AACATA
1 TTTTTTA-AAAATAACATA
601744 TT
1 TT
601746 AATAATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.45
Consensus pattern (18 bp):
TTTTTTAAAAATAACATA
Found at i:602166 original size:36 final size:36
Alignment explanation
Indices: 602110--602250 Score: 187
Period size: 36 Copynumber: 3.9 Consensus size: 36
602100 AGATGAACAA
* * *
602110 TTGAGTCGAAAGTGTTGATGCTTCATTCCGTTCACT
1 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCACT
* * *
602146 TTGAATCGAAAGTGTCGATGCTTTCTTTCGTTC-TT
1 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCACT
602181 CTTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCACT
1 -TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCACT
*
602218 TTGAATCGAAAGTG-CTGATGCTTCCTTTCGTTC
1 TTGAATCGAAAGTGTC-GATGCTTCCTTCCGTTC
602251 TTCTTATTCA
Statistics
Matches: 92, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
35 2 0.02
36 89 0.97
37 1 0.01
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.40
Consensus pattern (36 bp):
TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCACT
Found at i:602202 original size:72 final size:72
Alignment explanation
Indices: 602110--602255 Score: 240
Period size: 72 Copynumber: 2.0 Consensus size: 72
602100 AGATGAACAA
* * *
602110 TTGAGTCGAAAGTGTTGATGCTTCATTCCGTTCACTTTGAATCGAAAGTG-TCGATGCTTTCTTT
1 TTGAATCGAAAGTGTCGATGCTTCATTCCGTTCACTTTGAATCGAAAGTGCT-GATGCTTCCTTT
602174 CGTTCTTC
65 CGTTCTTC
*
602182 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCACTTTGAATCGAAAGTGCTGATGCTTCCTTTC
1 TTGAATCGAAAGTGTCGATGCTTCATTCCGTTCACTTTGAATCGAAAGTGCTGATGCTTCCTTTC
602247 GTTCTTC
66 GTTCTTC
602254 TT
1 TT
602256 ATTCACCTTC
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
72 68 0.99
73 1 0.01
ACGTcount: A:0.18, C:0.21, G:0.20, T:0.41
Consensus pattern (72 bp):
TTGAATCGAAAGTGTCGATGCTTCATTCCGTTCACTTTGAATCGAAAGTGCTGATGCTTCCTTTC
GTTCTTC
Found at i:605209 original size:22 final size:22
Alignment explanation
Indices: 605177--605242 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
605167 GGGAGCGTAT
605177 GGGTATCGGTACTCCTTTATAG
1 GGGTATCGGTACTCCTTTATAG
* *
605199 GGGTATTGGTACTCCTTCATAG
1 GGGTATCGGTACTCCTTTATAG
*
605221 GGGTATCGGTACTACCTGTATA
1 GGGTATCGGTACT-CCTTTATA
605243 AAATTCAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
22 32 0.84
23 6 0.16
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.35
Consensus pattern (22 bp):
GGGTATCGGTACTCCTTTATAG
Found at i:609438 original size:23 final size:23
Alignment explanation
Indices: 609412--609480 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
609402 CACCACAGCT
*
609412 CATATAAATGCACCGAAGTGCCA
1 CATAGAAATGCACCGAAGTGCCA
* * *
609435 CATAGAATTGCACCGTAGTGCCG
1 CATAGAAATGCACCGAAGTGCCA
* *
609458 CGTAGAATTGCACC-ATAGTGCCA
1 CATAGAAATGCACCGA-AGTGCCA
609481 TATAATAATG
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.20
Consensus pattern (23 bp):
CATAGAAATGCACCGAAGTGCCA
Found at i:609614 original size:18 final size:18
Alignment explanation
Indices: 609591--609626 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
609581 GAATACATAT
609591 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
609609 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
609627 TATCATTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.22, T:0.11
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACA
Found at i:609662 original size:59 final size:58
Alignment explanation
Indices: 609579--609770 Score: 146
Period size: 59 Copynumber: 3.2 Consensus size: 58
609569 ACATGTTCCA
*
609579 AAGAATACATAT-ATGTCCCGAAGGACCACAATGTCCCGAAGGACCACATATCATTCCTT
1 AAGAAT-CATATAATATCCCGAAGGACCACAATGTCCCGAA-GACCACATATCATTCCTT
* * * * *
609638 AAGAATCATATACATATGCC-AAGGATCA-AGTATGTGTCTCAC-CAGACTTCACACAT-GTTCC
1 AAGAATCATATA-ATATCCCGAAGGACCACA--A--TGTC-C-CGAAGAC--CACATATCATTCC
*
609699 -A
57 TT
*
609700 AAGAATACATAT-ATGTCCCGAAGGACCACAATGTCCCGAAAGACCACATATCATTCCTT
1 AAGAAT-CATATAATATCCCGAAGGACCACAATGTCCCG-AAGACCACATATCATTCCTT
609759 AAGAATCATATA
1 AAGAATCATATA
609771 TATACTAGGG
Statistics
Matches: 101, Mismatches: 14, Indels: 36
0.67 0.09 0.24
Matches are distributed among these distances:
57 7 0.07
58 16 0.16
59 27 0.27
60 6 0.06
61 6 0.06
62 20 0.20
63 12 0.12
64 7 0.07
ACGTcount: A:0.38, C:0.25, G:0.14, T:0.23
Consensus pattern (58 bp):
AAGAATCATATAATATCCCGAAGGACCACAATGTCCCGAAGACCACATATCATTCCTT
Found at i:609701 original size:121 final size:121
Alignment explanation
Indices: 609487--609848 Score: 647
Period size: 121 Copynumber: 3.0 Consensus size: 121
609477 GCCATATAAT
** *
609487 AATGTCCATAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGC
1 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGT
609552 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
66 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
* * *
609608 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGT
1 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGT
609673 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
66 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
*
609729 AATGTCCCGAAAGACCACATATCATTCCTTAAGAATCATAT--ATATACTAGGGATCAAGTATGT
1 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGT
609792 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
66 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
609848 A
1 A
609849 GAGACCCTCG
Statistics
Matches: 231, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
119 76 0.33
121 155 0.67
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (121 bp):
AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGT
GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
Found at i:609735 original size:18 final size:18
Alignment explanation
Indices: 609712--609747 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
609702 GAATACATAT
*
609712 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAAGACCACA
609730 ATGTCCCGAAAGACCACA
1 ATGTCCCGAAAGACCACA
609748 TATCATTCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.33, G:0.19, T:0.11
Consensus pattern (18 bp):
ATGTCCCGAAAGACCACA
Found at i:616596 original size:21 final size:21
Alignment explanation
Indices: 616570--616610 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
616560 ATGAGATCTT
616570 TTTCATTTTTCAATTTTGAAG
1 TTTCATTTTTCAATTTTGAAG
**
616591 TTTCATTTTTGTATTTTGAA
1 TTTCATTTTTCAATTTTGAA
616611 AATAACTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.07, G:0.10, T:0.61
Consensus pattern (21 bp):
TTTCATTTTTCAATTTTGAAG
Found at i:618898 original size:19 final size:19
Alignment explanation
Indices: 618860--618899 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
618850 CGAATAATTG
* * *
618860 AATCGAATATAATATTTTA
1 AATCAAATATAAAATCTTA
618879 AATCAAATATAAAATCTTA
1 AATCAAATATAAAATCTTA
618898 AA
1 AA
618900 ATTACTTAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.35
Consensus pattern (19 bp):
AATCAAATATAAAATCTTA
Found at i:619400 original size:11 final size:11
Alignment explanation
Indices: 619384--619409 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
619374 TAATTAGATA
619384 TATTTTATTTT
1 TATTTTATTTT
619395 TATTTTATTTT
1 TATTTTATTTT
619406 TATT
1 TATT
619410 ACATTCACTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (11 bp):
TATTTTATTTT
Found at i:624711 original size:13 final size:13
Alignment explanation
Indices: 624693--624719 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
624683 TTACAGATGC
624693 GCATATGAAGACT
1 GCATATGAAGACT
624706 GCATATGAAGACT
1 GCATATGAAGACT
624719 G
1 G
624720 TTCAACTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (13 bp):
GCATATGAAGACT
Found at i:624956 original size:2 final size:2
Alignment explanation
Indices: 624949--624985 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
624939 TACTTGTTAA
624949 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
624986 CAAGGATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:637674 original size:23 final size:23
Alignment explanation
Indices: 637603--637681 Score: 92
Period size: 23 Copynumber: 3.5 Consensus size: 23
637593 ACACTTAACA
637603 GTGCATCGATGCA-TCCCTTTGAAT
1 GTGCATCGATGCACT-CC-TTGAAT
* * *
637627 GTGCATCGAT--ACACCATGAAG
1 GTGCATCGATGCACTCCTTGAAT
637648 GTGCATCGATGCACTCCTTGAAT
1 GTGCATCGATGCACTCCTTGAAT
637671 GTGCATCGATG
1 GTGCATCGATG
637682 TACAAGGCCA
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
21 14 0.30
22 3 0.07
23 19 0.41
24 10 0.22
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (23 bp):
GTGCATCGATGCACTCCTTGAAT
Found at i:640492 original size:15 final size:15
Alignment explanation
Indices: 640472--640500 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
640462 AGGAGGTTAA
640472 TATATGTATGTATGT
1 TATATGTATGTATGT
640487 TATATGTATGTATG
1 TATATGTATGTATG
640501 ATACCCTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TATATGTATGTATGT
Found at i:641050 original size:60 final size:60
Alignment explanation
Indices: 640956--641094 Score: 197
Period size: 60 Copynumber: 2.3 Consensus size: 60
640946 GATCCTATTT
* *** *
640956 TAAATTAGTCCTTAAACTTTTAAACATTCTAATTTCATCCCAAAAATATGGCTCTCATTC
1 TAAATTAGTCCTTAAACTTTTAAACATTCCAATTTCATCCCAAAAATATCAATATCATTC
* * *
641016 TAAATTAATCCTTAAACTTTTAAACATTCCAATTTCATCCCCAAACTATCAATATCATTC
1 TAAATTAGTCCTTAAACTTTTAAACATTCCAATTTCATCCCAAAAATATCAATATCATTC
*
641076 TAAATTAGTCCCTAAACTT
1 TAAATTAGTCCTTAAACTT
641095 CTGCATCTTC
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 69 1.00
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (60 bp):
TAAATTAGTCCTTAAACTTTTAAACATTCCAATTTCATCCCAAAAATATCAATATCATTC
Found at i:641093 original size:31 final size:29
Alignment explanation
Indices: 641010--641093 Score: 71
Period size: 29 Copynumber: 2.8 Consensus size: 29
641000 AATATGGCTC
* * *
641010 TCATTCTAAATTAATCCTTAAACTTTTAAA
1 TCATTCTAAATT-ATCCCTAAACTATCAAA
* * *
641040 -CATTCCAATTTCATCCCCAAACTATCAATA
1 TCATTCTAAATT-ATCCCTAAACTATCAA-A
641070 TCATTCTAAATTAGTCCCTAAACT
1 TCATTCTAAATTA-TCCCTAAACT
641094 TCTGCATCTT
Statistics
Matches: 41, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
29 21 0.51
30 2 0.05
31 18 0.44
ACGTcount: A:0.37, C:0.25, G:0.01, T:0.37
Consensus pattern (29 bp):
TCATTCTAAATTATCCCTAAACTATCAAA
Found at i:641106 original size:60 final size:59
Alignment explanation
Indices: 640956--641124 Score: 151
Period size: 60 Copynumber: 2.8 Consensus size: 59
640946 GATCCTATTT
* * * * * * *** *
640956 TAAATTAGTCCTTAAACTTTTAAACATTCTAATTTCATCCCAAAAATATGGCTCTCATTC
1 TAAATTAATCCCTAAACTTTGAAACATTC-CATTTCATCCCCAAACTATCAATATCATTC
* *
641016 TAAATTAATCCTTAAACTTTTAAACATTCCAATTTCATCCCCAAACTATCAATATCATTC
1 TAAATTAATCCCTAAACTTTGAAACATTCC-ATTTCATCCCCAAACTATCAATATCATTC
* * * * *
641076 TAAATTAGTCCCTAAACTTCTGCATC-TTCCATTTTATCCCCAAATTATC
1 TAAATTAATCCCTAAACTT-TGAAACATTCCATTTCATCCCCAAACTATC
641125 CAAATATGTA
Statistics
Matches: 92, Mismatches: 15, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
59 17 0.18
60 72 0.78
61 3 0.03
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (59 bp):
TAAATTAATCCCTAAACTTTGAAACATTCCATTTCATCCCCAAACTATCAATATCATTC
Found at i:641632 original size:23 final size:23
Alignment explanation
Indices: 641602--641653 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
641592 CAATTTTGTT
641602 CAATTAAAATTATTATAAACATA
1 CAATTAAAATTATTATAAACATA
*
641625 CAATTAAAATTATTATAACCATA
1 CAATTAAAATTATTATAAACATA
641648 CAATTA
1 CAATTA
641654 TATATATAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.35
Consensus pattern (23 bp):
CAATTAAAATTATTATAAACATA
Done.