Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001978.1 Hibiscus syriacus cultivar Beakdansim tig00004013_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: 2594977
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 10
Found at i:903 original size:29 final size:30
Alignment explanation
Indices: 870--935 Score: 116
Period size: 29 Copynumber: 2.2 Consensus size: 30
860 GAGTATTGCT
870 GAGCTCGACTCGACTCGAAACTCTG-AATG
1 GAGCTCGACTCGACTCGAAACTCTGAAATG
899 GAGCTCGACTCGACTCGAAACTCTGAAATG
1 GAGCTCGACTCGACTCGAAACTCTGAAATG
*
929 AAGCTCG
1 GAGCTCG
936 TGAGCAACTC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 25 0.71
30 10 0.29
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.20
Consensus pattern (30 bp):
GAGCTCGACTCGACTCGAAACTCTGAAATG
Found at i:1996 original size:2 final size:2
Alignment explanation
Indices: 1989--2047 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
1979 ATGTTAGCTG
1989 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
2031 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
2048 CACTGTAAAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2249 original size:2 final size:2
Alignment explanation
Indices: 2242--2267 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2232 TAATTTATGG
2242 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
2268 GTAAAATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3105 original size:19 final size:19
Alignment explanation
Indices: 3081--3127 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
3071 AAAGGCCAAT
3081 GGAGCAGATGAGAACGTGA
1 GGAGCAGATGAGAACGTGA
3100 GGAGCAGATGAGAACGTGA
1 GGAGCAGATGAGAACGTGA
3119 GGAGCAGAT
1 GGAGCAGAT
3128 TTATCTCGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.36, C:0.11, G:0.43, T:0.11
Consensus pattern (19 bp):
GGAGCAGATGAGAACGTGA
Found at i:14711 original size:53 final size:53
Alignment explanation
Indices: 14622--14931 Score: 467
Period size: 53 Copynumber: 5.8 Consensus size: 53
14612 AGAATTCTAC
* * *
14622 CAGAAAATTGTTCGAGTTCTACTCCCTGAAGAAAGAGGGAGCGAACCTGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
** * *
14675 TGGAAGATTGTTCAAGTTCTACTCCCTGAAGTAAGAGGGAGCGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* * *
14728 CAGAAGATTGTCCGAGTTCTACTCCCTGAAGCAAGAGGGAGGGAACCCATAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* * * *
14781 CAGAAGATTGTTTGAGTTCTACACCCTGAAGCAAGAGGGAGTGAACCCATAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* * *
14834 TAGAAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGTGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
14887 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAA
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAA
14932 TGCACTGGTC
Statistics
Matches: 232, Mismatches: 25, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 232 1.00
ACGTcount: A:0.31, C:0.20, G:0.29, T:0.21
Consensus pattern (53 bp):
CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
Found at i:16230 original size:19 final size:19
Alignment explanation
Indices: 16206--16255 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
16196 TATTTATTTC
16206 ATTTGTTTGTTTCTTTGCA
1 ATTTGTTTGTTTCTTTGCA
*
16225 ATTTGTTTGTTGCTTTGCA
1 ATTTGTTTGTTTCTTTGCA
16244 ATTTGTTTGTTT
1 ATTTGTTTGTTT
16256 GTCTTTAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.10, C:0.08, G:0.18, T:0.64
Consensus pattern (19 bp):
ATTTGTTTGTTTCTTTGCA
Found at i:16233 original size:23 final size:21
Alignment explanation
Indices: 16206--16261 Score: 84
Period size: 19 Copynumber: 2.9 Consensus size: 21
16196 TATTTATTTC
16206 ATTTGTTTG-TT-TCTTTGCA
1 ATTTGTTTGTTTGTCTTTGCA
16225 ATTTGTTTG-TTG-CTTTGCA
1 ATTTGTTTGTTTGTCTTTGCA
16244 ATTTGTTTGTTTGTCTTT
1 ATTTGTTTGTTTGTCTTT
16262 AACATTTGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
19 27 0.79
20 3 0.09
21 4 0.12
ACGTcount: A:0.09, C:0.09, G:0.18, T:0.64
Consensus pattern (21 bp):
ATTTGTTTGTTTGTCTTTGCA
Found at i:17745 original size:40 final size:43
Alignment explanation
Indices: 17657--17754 Score: 139
Period size: 40 Copynumber: 2.3 Consensus size: 43
17647 GACACTACTA
*
17657 ATACGTGATGAAGAGGTATGGTCGTCTAAGAGTGACACGGCTC
1 ATACGTGATGAAGAGATATGGTCGTCTAAGAGTGACACGGCTC
* * *
17700 CTACGTGATGAGGAGATATGGTCG-GT-AGA-TGACACGGCTC
1 ATACGTGATGAAGAGATATGGTCGTCTAAGAGTGACACGGCTC
17740 ATACGTGATGAAGAG
1 ATACGTGATGAAGAG
17755 TTTTGGCCAT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
40 24 0.49
41 3 0.06
42 1 0.02
43 21 0.43
ACGTcount: A:0.29, C:0.15, G:0.34, T:0.22
Consensus pattern (43 bp):
ATACGTGATGAAGAGATATGGTCGTCTAAGAGTGACACGGCTC
Found at i:17985 original size:130 final size:131
Alignment explanation
Indices: 17688--18148 Score: 518
Period size: 130 Copynumber: 3.5 Consensus size: 131
17678 TCGTCTAAGA
* * * * * *
17688 GTGACACGGCTCCTACGTGATGAGGAGATATGGTCGGTAGATGACACGGCTCATACGTGATGAAG
1 GTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACACGGTTCCTACGCGATG-AG
* ** * ** * *
17753 AGTTTTG-G-CCATCTTTAGGAAGGGCAATAACATGGTTCCTACGCGTTGAGGACGACTGGTTAT
65 -GATAGGAGACCATCTTTAGGAA-TG--ATAACACAGTTCCTACGTGATGAGGACGACTGGTTAT
*
17816 CTATGG
126 CTAGGG
*
17822 GTGACACGGCTCCTACGTGATGAGGAGGTCTGGTTGGTGGATGACACGGTTCCTACGCGATGAGG
1 GTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACACGGTTCCTACGCGATGAGG
* * *
17887 ATGGGAGACCATCTTTAGGAATGATAACACAGTTCCTACATGATGAGGACGATTGGTTATC-AGG
66 ATAGGAGACCATCTTTAGGAATGATAACACAGTTCCTACGTGATGAGGACGACTGGTTATCTAGG
17951 G
131 G
* * * *
17952 GTGATACGACTCCTACGTGATGAGGAGGTCTGGTCAAG-GGCTGACACGGTTCCTACGCGATGAG
1 GTGACACGGCTCCTACGTGATGAGGAGGTCTGGTC-GGTGGATGACACGGTTCCTACGCGATGAG
* * * * *
18016 GACAGCAAACAATCTTTAGGAGTGATAACACAGTTCCTACGTGATGAGGAC-AGCTGGTTATCTA
65 GATAGGAGACCATCTTTAGGAATGATAACACAGTTCCTACGTGATGAGGACGA-CTGGTTATCTA
18080 GGG
129 GGG
* * * * * *
18083 TTGATACGGCTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGAAACGGTTTCTACTCGATGAGG
1 GTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACACGGTTCCTACGCGATGAGG
18148 A
66 A
18149 CGATATGCCA
Statistics
Matches: 283, Mismatches: 38, Indels: 15
0.84 0.11 0.04
Matches are distributed among these distances:
129 1 0.00
130 113 0.40
131 94 0.33
132 3 0.01
133 4 0.01
134 68 0.24
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (131 bp):
GTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGGTGGATGACACGGTTCCTACGCGATGAGG
ATAGGAGACCATCTTTAGGAATGATAACACAGTTCCTACGTGATGAGGACGACTGGTTATCTAGG
G
Found at i:18278 original size:34 final size:34
Alignment explanation
Indices: 18239--18344 Score: 173
Period size: 34 Copynumber: 3.2 Consensus size: 34
18229 ACCAAATTCA
18239 TTTCAAGGGAAATGACTCAAAGATAGGTGTTTTG
1 TTTCAAGGGAAATGACTCAAAGATAGGTGTTTTG
18273 TTTCAAGGGAAATGACTCAAAGATAGGTGTTTTG
1 TTTCAAGGGAAATGACTCAAAGATAGGTGTTTTG
*
18307 TTTCAAGGGAAACTGACACAAAGAT--G-GTTTTG
1 TTTCAAGGGAAA-TGACTCAAAGATAGGTGTTTTG
18339 TTTCAA
1 TTTCAA
18345 AAAAACATAC
Statistics
Matches: 70, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
32 12 0.17
33 1 0.01
34 46 0.66
35 11 0.16
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.32
Consensus pattern (34 bp):
TTTCAAGGGAAATGACTCAAAGATAGGTGTTTTG
Found at i:18442 original size:67 final size:66
Alignment explanation
Indices: 18356--18555 Score: 238
Period size: 67 Copynumber: 3.1 Consensus size: 66
18346 AAAACATACC
18356 CAAAGATTTTGTTTCTCAAAAGAAATTGTCTCAAGAGAGACAAAAATTTGTTTTCAGAGAAATAG
1 CAAAGATTTT-TTT-TCAAAAGAAATTGTCTCAAGAGAGACAAAAATTTGTTTTCAGAGAAATAG
18421 ACT
64 ACT
* * *
18424 CAAATATTTTTTTATCAAAATAAATTGTCTCAAGAGAGACAAAACTTTGTTTAT-AGAGAAACT-
1 CAAAGATTTTTTT-TCAAAAGAAATTGTCTCAAGAGAGACAAAAATTTGTTT-TCAGAGAAA-TA
18487 GACT
63 GACT
* *
18491 CAAAGATTTTTTTT--AAAGAAACTGTCTC--GAGAGAC-AAAATTTG-TTTCAAGAGAAACA-A
1 CAAAGATTTTTTTTCAAAAGAAATTGTCTCAAGAGAGACAAAAATTTGTTTTC-AGAGAAATAGA
18549 CT
65 CT
18551 CAAAG
1 CAAAG
18556 GATACTGATA
Statistics
Matches: 118, Mismatches: 9, Indels: 18
0.81 0.06 0.12
Matches are distributed among these distances:
59 1 0.01
60 10 0.08
61 14 0.12
62 7 0.06
64 12 0.10
66 1 0.01
67 62 0.53
68 11 0.09
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.31
Consensus pattern (66 bp):
CAAAGATTTTTTTTCAAAAGAAATTGTCTCAAGAGAGACAAAAATTTGTTTTCAGAGAAATAGAC
T
Found at i:18675 original size:32 final size:32
Alignment explanation
Indices: 18626--18694 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
18616 TCACATCAGG
* *
18626 ATGTTGAATCCCAAAAGATACTCCAATATTCA
1 ATGTTGAATCCCAAAAGATACCCCAACATTCA
* *
18658 ATGTTGAATCTCC-AAAGATGCCCCAACATTCG
1 ATGTTGAATC-CCAAAAGATACCCCAACATTCA
18690 ATGTT
1 ATGTT
18695 TCTTGCTTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 30 0.94
33 2 0.06
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (32 bp):
ATGTTGAATCCCAAAAGATACCCCAACATTCA
Found at i:24415 original size:59 final size:59
Alignment explanation
Indices: 24310--24434 Score: 136
Period size: 59 Copynumber: 2.1 Consensus size: 59
24300 TACAAATAGG
24310 AATTTAAAGGAATAAAATGGCAAAAATAGAAACTTAAAGGCTAAAACAATAAAAACCA-A
1 AATTTAAAGGAATAAAATGGCAAAAATAGAAACTTAAAGGCTAAAACAAT-AAAACCATA
* *
24369 AATTTAAA-GAATTAAAATGGCAAAACA-A-AAA-TATAAAGGGGC-AAAACAGTAACACCATA
1 AATTTAAAGGAA-TAAAATGGCAAAA-ATAGAAACT-TAAA--GGCTAAAACAATAAAACCATA
24428 AATTTAA
1 AATTTAA
24435 GGGTCTAAAT
Statistics
Matches: 58, Mismatches: 2, Indels: 12
0.81 0.03 0.17
Matches are distributed among these distances:
57 1 0.02
58 16 0.28
59 37 0.64
60 4 0.07
ACGTcount: A:0.59, C:0.10, G:0.12, T:0.18
Consensus pattern (59 bp):
AATTTAAAGGAATAAAATGGCAAAAATAGAAACTTAAAGGCTAAAACAATAAAACCATA
Found at i:24463 original size:29 final size:30
Alignment explanation
Indices: 24431--24514 Score: 102
Period size: 30 Copynumber: 2.8 Consensus size: 30
24421 CACCATAAAT
*
24431 TTAAGGGTCT-AAATAGAAAATACAGACAA-
1 TTAAGGGACTAAAATAGAAAATACAGA-AAC
*
24460 TTAAAGGACTAAAATAGAAAA-ACTAGAAAC
1 TTAAGGGACTAAAATAGAAAATAC-AGAAAC
*
24490 ATAAGGGACTAAAATAGAAAATACA
1 TTAAGGGACTAAAATAGAAAATACA
24515 AAAAAATAGA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
29 12 0.26
30 33 0.70
31 2 0.04
ACGTcount: A:0.57, C:0.10, G:0.15, T:0.18
Consensus pattern (30 bp):
TTAAGGGACTAAAATAGAAAATACAGAAAC
Found at i:26834 original size:59 final size:59
Alignment explanation
Indices: 26729--26853 Score: 143
Period size: 59 Copynumber: 2.1 Consensus size: 59
26719 TACAAATAGG
*
26729 AATTTAAAGGAATAAAATGGCAAAAATAGAAACTTAAAGGCTAAAACAATAAAAACCA-A
1 AATTTAAAGGAATAAAATGGCAAAAATAGAAACTTAAAGGCCAAAACAAT-AAAACCATA
* *
26788 AATTTAAA-GAATTAAAATGGCAAAACA-A-AAA-TATAAAGGGCCAAAACAGTAACACCATA
1 AATTTAAAGGAA-TAAAATGGCAAAA-ATAGAAACT-TAAA-GGCCAAAACAATAAAACCATA
26847 AATTTAA
1 AATTTAA
26854 GGGTCTAAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
57 1 0.02
58 16 0.28
59 40 0.69
60 1 0.02
ACGTcount: A:0.59, C:0.11, G:0.11, T:0.18
Consensus pattern (59 bp):
AATTTAAAGGAATAAAATGGCAAAAATAGAAACTTAAAGGCCAAAACAATAAAACCATA
Found at i:26882 original size:29 final size:30
Alignment explanation
Indices: 26850--26933 Score: 102
Period size: 30 Copynumber: 2.8 Consensus size: 30
26840 CACCATAAAT
*
26850 TTAAGGGTCT-AAATAGAAAATACAGACAA-
1 TTAAGGGACTAAAATAGAAAATACAGA-AAC
*
26879 TTAAAGGACTAAAATAGAAAA-ACTAGAAAC
1 TTAAGGGACTAAAATAGAAAATAC-AGAAAC
*
26909 ATAAGGGACTAAAATAGAAAATACA
1 TTAAGGGACTAAAATAGAAAATACA
26934 AAAAATAGAG
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
29 12 0.26
30 33 0.70
31 2 0.04
ACGTcount: A:0.57, C:0.10, G:0.15, T:0.18
Consensus pattern (30 bp):
TTAAGGGACTAAAATAGAAAATACAGAAAC
Found at i:29259 original size:59 final size:59
Alignment explanation
Indices: 29154--29278 Score: 143
Period size: 59 Copynumber: 2.1 Consensus size: 59
29144 TACAAATAGG
*
29154 AATTTAAAGGAATAAAATGGCAAAAATAGAAACTTAAAGGCTAAAACAATAAAAACCA-A
1 AATTTAAAGGAATAAAATGGCAAAAATAGAAACTTAAAGGCCAAAACAAT-AAAACCATA
* *
29213 AATTTAAA-GAATTAAAATGGCAAAACA-A-AAA-TATAAAGGGCCAAAACAGTAACACCATA
1 AATTTAAAGGAA-TAAAATGGCAAAA-ATAGAAACT-TAAA-GGCCAAAACAATAAAACCATA
29272 AATTTAA
1 AATTTAA
29279 GGGTCTAAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
57 1 0.02
58 16 0.28
59 40 0.69
60 1 0.02
ACGTcount: A:0.59, C:0.11, G:0.11, T:0.18
Consensus pattern (59 bp):
AATTTAAAGGAATAAAATGGCAAAAATAGAAACTTAAAGGCCAAAACAATAAAACCATA
Found at i:29307 original size:29 final size:30
Alignment explanation
Indices: 29275--29358 Score: 102
Period size: 30 Copynumber: 2.8 Consensus size: 30
29265 CACCATAAAT
*
29275 TTAAGGGTCT-AAATAGAAAATACAGACAA-
1 TTAAGGGACTAAAATAGAAAATACAGA-AAC
*
29304 TTAAAGGACTAAAATAGAAAA-ACTAGAAAC
1 TTAAGGGACTAAAATAGAAAATAC-AGAAAC
*
29334 ATAAGGGACTAAAATAGAAAATACA
1 TTAAGGGACTAAAATAGAAAATACA
29359 AATAAAATAG
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
29 12 0.26
30 33 0.70
31 2 0.04
ACGTcount: A:0.57, C:0.10, G:0.15, T:0.18
Consensus pattern (30 bp):
TTAAGGGACTAAAATAGAAAATACAGAAAC
Found at i:38192 original size:27 final size:27
Alignment explanation
Indices: 38154--38208 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
38144 CATGTCTATG
38154 TATGCAACTACTTAATTGAAAACCTCT
1 TATGCAACTACTTAATTGAAAACCTCT
* *
38181 TATGCAACTACTTGATTGAAAACTTCT
1 TATGCAACTACTTAATTGAAAACCTCT
38208 T
1 T
38209 TCTCCTTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.36
Consensus pattern (27 bp):
TATGCAACTACTTAATTGAAAACCTCT
Found at i:44271 original size:90 final size:89
Alignment explanation
Indices: 44153--44329 Score: 300
Period size: 90 Copynumber: 2.0 Consensus size: 89
44143 TAATCCTGAA
* * *
44153 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCTTAATATGAT
1 TATTGAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCCTAATATGAT
*
44218 TAGGGTAACTTGGATATAAAAGGAT
65 TAGGATAACTTGGATATAAAAGGAT
44243 TATTGAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
1 TATTGAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
*
44308 AGGATAACTTGGCTATAAAAGG
66 AGGATAACTTGGATATAAAAGG
44330 GTGTGTTAGG
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 32 0.39
90 50 0.61
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.38
Consensus pattern (89 bp):
TATTGAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
AGGATAACTTGGATATAAAAGGAT
Found at i:44949 original size:23 final size:23
Alignment explanation
Indices: 44916--44960 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
44906 CATGTTAATC
* *
44916 ATTCTTGACTCTTTTAAATTTAG
1 ATTCTTCACTCTTGTAAATTTAG
44939 ATTCTTCACTCTTGTAAATTTA
1 ATTCTTCACTCTTGTAAATTTA
44961 ATATAATCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.16, G:0.07, T:0.51
Consensus pattern (23 bp):
ATTCTTCACTCTTGTAAATTTAG
Found at i:54218 original size:24 final size:25
Alignment explanation
Indices: 54191--54247 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 25
54181 TATGCATAGA
* *
54191 ACCAA-AGGCCACTTTAACAACAGT
1 ACCAACAGGCCACCTCAACAACAGT
*
54215 ACCAACTGAGGCCTCCTCAACAACAGT
1 ACCAAC--AGGCCACCTCAACAACAGT
54242 ACCAAC
1 ACCAAC
54248 CGCTGAAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 5 0.19
27 22 0.81
ACGTcount: A:0.39, C:0.35, G:0.12, T:0.14
Consensus pattern (25 bp):
ACCAACAGGCCACCTCAACAACAGT
Found at i:60042 original size:14 final size:14
Alignment explanation
Indices: 60025--60056 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
60015 TTATTTTCTT
60025 TAAAAAATTTAAAC
1 TAAAAAATTTAAAC
*
60039 TAAAACATTTAAAC
1 TAAAAAATTTAAAC
60053 TAAA
1 TAAA
60057 TCGTCTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.28
Consensus pattern (14 bp):
TAAAAAATTTAAAC
Found at i:67001 original size:20 final size:19
Alignment explanation
Indices: 66976--67025 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 19
66966 TGATTAATTC
66976 AGTATCGATACCGAAGGGA
1 AGTATCGATACCGAAGGGA
66995 GAGTATCGATACCGAAGGGA
1 -AGTATCGATACCGAAGGGA
67015 ATGTATCGATA
1 A-GTATCGATA
67026 TCATTTTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.36, C:0.14, G:0.30, T:0.20
Consensus pattern (19 bp):
AGTATCGATACCGAAGGGA
Found at i:67076 original size:19 final size:22
Alignment explanation
Indices: 67052--67105 Score: 69
Period size: 19 Copynumber: 2.6 Consensus size: 22
67042 TGCAAAAATG
67052 GTATCGATACCATAG-A-AG-A
1 GTATCGATACCATAGTATAGTA
**
67071 GTATCGGCACCATAGTATAGTA
1 GTATCGATACCATAGTATAGTA
67093 GTATCGATACCAT
1 GTATCGATACCAT
67106 GGTACGGGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 13 0.46
20 1 0.04
21 2 0.07
22 12 0.43
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (22 bp):
GTATCGATACCATAGTATAGTA
Found at i:67530 original size:55 final size:55
Alignment explanation
Indices: 67446--67760 Score: 351
Period size: 55 Copynumber: 5.9 Consensus size: 55
67436 AGTGTACTAT
* * * * *
67446 AGGCACTATGTGTACAATTTCACGGAATTCATCACGAGTTGATGAATAGCCGTAC
1 AGGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAGCCGTAC
* *
67501 AGGCACTATGTGTGCAATTCCACGAAATTCATCATGAGTTGATGAATAGCCTTAC
1 AGGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAGCCGTAC
* * * *
67556 AGACACTATGTTTACAAAT---C----TTCATCATGAGTTGATGAATAGCCGTAG
1 AGGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAGCCGTAC
* * *
67604 AAGCACTATGTGTGCAAATCCAC-AGAATTCATCATGAGTTGATGAATAGTCATAC
1 AGGCACTATGTGTGCAAATCCACGA-AATTCATCATGAGTTGATGAATAGCCGTAC
* * * *
67659 AGGCACTTTGTGTGCAATTCCACGGAATTCATCATGAGTTGATGAATAGTCGTAC
1 AGGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAGCCGTAC
* * * *
67714 ATGCACTATATGTCCATAAT-CACAAAATTCATCATGAGTTGATGAAT
1 AGGCACTATGTGTGCA-AATCCACGAAATTCATCATGAGTTGATGAAT
67761 TTCCATATAG
Statistics
Matches: 221, Mismatches: 30, Indels: 18
0.82 0.11 0.07
Matches are distributed among these distances:
48 41 0.19
51 1 0.00
52 1 0.00
55 176 0.80
56 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (55 bp):
AGGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAGCCGTAC
Found at i:67611 original size:48 final size:48
Alignment explanation
Indices: 67528--67623 Score: 140
Period size: 48 Copynumber: 2.0 Consensus size: 48
67518 TTCCACGAAA
* * *
67528 TTCATCATGAGTTGATGAATAGCCTTACAGACACTATGTTTACAAATC
1 TTCATCATGAGTTGATGAATAGCCGTAAAGACACTATGTGTACAAATC
*
67576 TTCATCATGAGTTGATGAATAGCCGTAGAAG-CACTATGTGTGCAAATC
1 TTCATCATGAGTTGATGAATAGCCGTA-AAGACACTATGTGTACAAATC
67624 CACAGAATTC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
48 41 0.95
49 2 0.05
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (48 bp):
TTCATCATGAGTTGATGAATAGCCGTAAAGACACTATGTGTACAAATC
Found at i:67652 original size:103 final size:105
Alignment explanation
Indices: 67472--67760 Score: 343
Period size: 103 Copynumber: 2.7 Consensus size: 105
67462 ATTTCACGGA
* * *
67472 ATTCATCACGAGTTGATGAATAGCCGTACAGGCACTATGTGTGCAATTCCAC-GAAATTCATCAT
1 ATTCATCATGAGTTGATGAATAGCCGTACAAGCACTATGTGTGCAAATCCACAG-AATTCATCAT
* *
67536 GAGTTGATGAATAGCCTTACAGACACTATGTTTACAAAT-C
65 GAGTTGATGAATAGCCATACAGACACTATGTGTACAAATCC
*
67576 -TTCATCATGAGTTGATGAATAGCCGTAGAAGCACTATGTGTGCAAATCCACAGAATTCATCATG
1 ATTCATCATGAGTTGATGAATAGCCGTACAAGCACTATGTGTGCAAATCCACAGAATTCATCATG
* * * * *
67640 AGTTGATGAATAGTCATACAGGCACTTTGTGTGCAATTCCAC
66 AGTTGATGAATAGCCATACAGACACTATGTGTACAAAT-C-C
* * * * *
67682 GGAATTCATCATGAGTTGATGAATAGTCGTACATGCACTATATGTCCATAAT-CACAAAATTCAT
1 ---ATTCATCATGAGTTGATGAATAGCCGTACAAGCACTATGTGTGCA-AATCCACAGAATTCAT
67746 CATGAGTTGATGAAT
62 CATGAGTTGATGAAT
67761 TTCCATATAG
Statistics
Matches: 159, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
103 89 0.56
104 1 0.01
106 1 0.01
110 65 0.41
111 3 0.02
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (105 bp):
ATTCATCATGAGTTGATGAATAGCCGTACAAGCACTATGTGTGCAAATCCACAGAATTCATCATG
AGTTGATGAATAGCCATACAGACACTATGTGTACAAATCC
Found at i:72627 original size:165 final size:165
Alignment explanation
Indices: 72341--72744 Score: 528
Period size: 165 Copynumber: 2.4 Consensus size: 165
72331 CCAAGTGTAC
* * * * * *
72341 TACAAAAACTATATGTGCAATTCCACGGAATTCATCGTGAGTTGATGAATAGCCGTACATGCACT
1 TACAAGAACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAGCCGTACAGGCACT
* * * *
72406 ATGTGTGCAATTCCACATAATTCATCATGAGTTGATGAATAGGCATACATGCACTATGTGTGAAA
66 ATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAGCCATACAGGCACTATGTGTGAAA
* * *
72471 TT-CTACGTAATTCATCAGGAGTTGATGAATAGTCG
131 TTAC-ACGAAATTCATCACGAGTTGATGAATAGCCG
* * * *
72506 TACAGGCACTATGTGTGCAAATCCATGAAATTCATCATGAGTTGATGAATAGCCTTACAGGCACT
1 TACAAGAACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAGCCGTACAGGCACT
* * *
72571 ATGTGTGCAAATCCACGGAATTCATCATGTGTTGATGAATAGCCATACAGGCACTATGTGTGCAA
66 ATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAGCCATACAGGCACTATGTGTGAAA
72636 TTACACGAAATTCATCACGAGTTGATGAATAGCCG
131 TTACACGAAATTCATCACGAGTTGATGAATAGCCG
* * * *
72671 TGCAAGAACTATGTTTGCATAA-CTACGAAATTCATCATGAGTTGATGAATTA-CCGTATAGGCA
1 TACAAGAACTATGTGTGCA-AATCCACGAAATTCATCATGAGTTGATGAA-TAGCCGTACAGGCA
72734 CTACT-TGTGCA
64 CTA-TGTGTGCA
72745 TGCTAATAAA
Statistics
Matches: 207, Mismatches: 28, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
165 201 0.97
166 6 0.03
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29
Consensus pattern (165 bp):
TACAAGAACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAGCCGTACAGGCACT
ATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAGCCATACAGGCACTATGTGTGAAA
TTACACGAAATTCATCACGAGTTGATGAATAGCCG
Found at i:72745 original size:55 final size:56
Alignment explanation
Indices: 72348--72745 Score: 440
Period size: 55 Copynumber: 7.2 Consensus size: 56
72338 TACTACAAAA
* * * * *
72348 ACTATATGTGCA-ATTCCACGGAATTCATCGTGAGTTGATGAATAGCCGTACATGC
1 ACTATGTGTGCATAATCCACGAAATTCATCATGAGTTGATGAATAGCCGTACAGGC
* * * *
72403 ACTATGTGTGCA-ATTCCAC-ATAATTCATCATGAGTTGATGAATAGGCATACATGC
1 ACTATGTGTGCATAATCCACGA-AATTCATCATGAGTTGATGAATAGCCGTACAGGC
* * * *
72458 ACTATGTGTG-A-AATTCTACGTAATTCATCAGGAGTTGATGAATAGTCGTACAGGC
1 ACTATGTGTGCATAA-TCCACGAAATTCATCATGAGTTGATGAATAGCCGTACAGGC
* *
72513 ACTATGTGTGCA-AATCCATGAAATTCATCATGAGTTGATGAATAGCCTTACAGGC
1 ACTATGTGTGCATAATCCACGAAATTCATCATGAGTTGATGAATAGCCGTACAGGC
* * *
72568 ACTATGTGTGCA-AATCCACGGAATTCATCATGTGTTGATGAATAGCCATACAGGC
1 ACTATGTGTGCATAATCCACGAAATTCATCATGAGTTGATGAATAGCCGTACAGGC
* * * * * *
72623 ACTATGTGTGCA-ATTACACGAAATTCATCACGAGTTGATGAATAGCCGTGCAAGA
1 ACTATGTGTGCATAATCCACGAAATTCATCATGAGTTGATGAATAGCCGTACAGGC
* * *
72678 ACTATGTTTGCATAA-CTACGAAATTCATCATGAGTTGATGAATTA-CCGTATAGGC
1 ACTATGTGTGCATAATCCACGAAATTCATCATGAGTTGATGAA-TAGCCGTACAGGC
72733 ACTACT-TGTGCAT
1 ACTA-TGTGTGCAT
72746 GCTAATAAAT
Statistics
Matches: 295, Mismatches: 41, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
54 2 0.01
55 286 0.97
56 7 0.02
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.30
Consensus pattern (56 bp):
ACTATGTGTGCATAATCCACGAAATTCATCATGAGTTGATGAATAGCCGTACAGGC
Found at i:75365 original size:16 final size:16
Alignment explanation
Indices: 75326--75357 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
75316 ATTTGGTCAT
75326 AACTCTTTTAGCATAA
1 AACTCTTTTAGCATAA
75342 AACTCTTTTAGCATAA
1 AACTCTTTTAGCATAA
75358 TGCTCTTTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.38
Consensus pattern (16 bp):
AACTCTTTTAGCATAA
Found at i:77030 original size:32 final size:32
Alignment explanation
Indices: 76904--77030 Score: 112
Period size: 32 Copynumber: 4.0 Consensus size: 32
76894 ATATTAGTAG
* * *
76904 AGTGTTACATTCAGATAATGCACAATAATGTC
1 AGTGTCACATTCAGATAATACACAATAGTGTC
* * * * *
76936 GGTGTCGCATTCAGATAATGCACAACACTGTC
1 AGTGTCACATTCAGATAATACACAATAGTGTC
* * * * *
76968 AATGTCACAATCAGATAA-AGAACAAAAGTGTT
1 AGTGTCACATTCAGATAATA-CACAATAGTGTC
*
77000 AGTGTCATATTCAGATAATACACAATAGTGT
1 AGTGTCACATTCAGATAATACACAATAGTGT
77031 ACCATGTGTC
Statistics
Matches: 74, Mismatches: 19, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
32 73 0.99
33 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.28
Consensus pattern (32 bp):
AGTGTCACATTCAGATAATACACAATAGTGTC
Found at i:80212 original size:27 final size:30
Alignment explanation
Indices: 80182--80258 Score: 97
Period size: 30 Copynumber: 2.7 Consensus size: 30
80172 AGTGTCTCAA
* *
80182 TTTTTATAAATTATAATAAA-A-C-AAATT
1 TTTTTATAAATCACAATAAACACCTAAATT
*
80209 TTTTTATTAATCACAATAAACACCTAAATT
1 TTTTTATAAATCACAATAAACACCTAAATT
*
80239 TTTTTATAAATCAGAATAAA
1 TTTTTATAAATCACAATAAA
80259 TATGTAATCT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
27 17 0.40
28 1 0.02
29 1 0.02
30 23 0.55
ACGTcount: A:0.48, C:0.09, G:0.01, T:0.42
Consensus pattern (30 bp):
TTTTTATAAATCACAATAAACACCTAAATT
Found at i:80368 original size:30 final size:29
Alignment explanation
Indices: 80293--80371 Score: 90
Period size: 29 Copynumber: 2.7 Consensus size: 29
80283 GTAAAGGCCA
80293 AACTTTTTAT-AATCTACAATAACAACCCG
1 AACTTTTTATAAAT-TACAATAACAACCCG
* *
80322 AACTTTTTATAGATTACAATAACAATCC-
1 AACTTTTTATAAATTACAATAACAACCCG
*
80350 AATTTTTTTTATAAATTACAAT
1 AA--CTTTTTATAAATTACAAT
80372 TACATAGTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
28 2 0.05
29 23 0.53
30 18 0.42
ACGTcount: A:0.42, C:0.16, G:0.03, T:0.39
Consensus pattern (29 bp):
AACTTTTTATAAATTACAATAACAACCCG
Found at i:80406 original size:24 final size:23
Alignment explanation
Indices: 80356--80406 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
80346 ATCCAATTTT
* *
80356 TTTTATAAATTACAATTACATAG
1 TTTTATAAATTACAATAACATAA
80379 TTTTATCAAATTACAATAAC-TCAA
1 TTTTAT-AAATTACAATAACAT-AA
80403 TTTT
1 TTTT
80407 TTTACAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.41, C:0.12, G:0.02, T:0.45
Consensus pattern (23 bp):
TTTTATAAATTACAATAACATAA
Found at i:81094 original size:22 final size:22
Alignment explanation
Indices: 81068--81128 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 22
81058 AACAAACGAT
*
81068 GAAGAAAAAAGGGAAAAAATTA
1 GAAGAAAAAAGGGAAAAAAATA
*
81090 GAAGAAAAAAGGAAAAAAAATA
1 GAAGAAAAAAGGGAAAAAAATA
* *
81112 GAAGAAAAGAGAGAAAA
1 GAAGAAAAAAGGGAAAA
81129 GAGTGCGGCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.05
Consensus pattern (22 bp):
GAAGAAAAAAGGGAAAAAAATA
Found at i:81315 original size:30 final size:30
Alignment explanation
Indices: 81281--81338 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
81271 AAGTATACCC
81281 AATTCTC-AGTTTCATACATAATGTTTTAAA
1 AATTCTCGA-TTTCATACATAATGTTTTAAA
*
81311 AATTCTCGATTTCATACATGATGTTTTA
1 AATTCTCGATTTCATACATAATGTTTTA
81339 TACCATTAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.45
Consensus pattern (30 bp):
AATTCTCGATTTCATACATAATGTTTTAAA
Found at i:81696 original size:2 final size:2
Alignment explanation
Indices: 81683--81713 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
81673 ATGCTTATTG
*
81683 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
81714 GATTAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:84156 original size:17 final size:17
Alignment explanation
Indices: 84099--84160 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
84089 TTTAAGGAAG
* *
84099 TAGTTTATTCATGCATT
1 TAGTTCATTCATGCAAT
* *
84116 TATTTCATTCAATG-AAG
1 TAGTTCATTC-ATGCAAT
* *
84133 TATTTCATTCATGCACT
1 TAGTTCATTCATGCAAT
84150 TAGTTCATTCA
1 TAGTTCATTCA
84161 ATAAGCTACT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
16 3 0.08
17 30 0.83
18 3 0.08
ACGTcount: A:0.27, C:0.16, G:0.10, T:0.47
Consensus pattern (17 bp):
TAGTTCATTCATGCAAT
Found at i:84162 original size:34 final size:34
Alignment explanation
Indices: 84085--84162 Score: 104
Period size: 34 Copynumber: 2.3 Consensus size: 34
84075 AAGCTTTTAC
* * * *
84085 TTCATTTAAGGAAGTAGTTTATTCATGCATTTAT
1 TTCATTCAATGAAGTAGTTTATTCATGCACTTAG
84119 TTCATTCAATGAAGTA-TTTCATTCATGCACTTAG
1 TTCATTCAATGAAGTAGTTT-ATTCATGCACTTAG
84153 TTCATTCAAT
1 TTCATTCAAT
84163 AAGCTACTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
33 3 0.08
34 36 0.92
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (34 bp):
TTCATTCAATGAAGTAGTTTATTCATGCACTTAG
Found at i:87415 original size:7 final size:7
Alignment explanation
Indices: 87403--87444 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
87393 ACATACATTG
87403 TATTTTT
1 TATTTTT
87410 TATTTTT
1 TATTTTT
87417 TATTATTT
1 TATT-TTT
87425 T-TATTTT
1 TAT-TTTT
87432 TATTTTT
1 TATTTTT
*
87439 AATTTT
1 TATTTT
87445 CTGACTGCCT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
7 25 0.81
8 6 0.19
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (7 bp):
TATTTTT
Found at i:89523 original size:18 final size:19
Alignment explanation
Indices: 89488--89524 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
89478 CACGGAATGT
89488 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
89508 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
89525 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:90658 original size:34 final size:34
Alignment explanation
Indices: 90613--90692 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
90603 ATTTAAGGAA
* *
90613 CTATTTTATTCATTCATTTA-TTCCATTCAATGAAG
1 CTATTTCATTCATGCATTTAGTT-CATTCAAT-AAG
90648 -TATTTCATTCATGCATTTAGTTCATTCAATAAG
1 CTATTTCATTCATGCATTTAGTTCATTCAATAAG
*
90681 CTACTTCATTCA
1 CTATTTCATTCA
90693 AGTCAGTAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
33 3 0.08
34 35 0.88
35 2 0.05
ACGTcount: A:0.29, C:0.19, G:0.06, T:0.46
Consensus pattern (34 bp):
CTATTTCATTCATGCATTTAGTTCATTCAATAAG
Found at i:96026 original size:17 final size:17
Alignment explanation
Indices: 96003--96061 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
95993 AAGGAAGTAG
96003 TTCATTCATGCATTTAT
1 TTCATTCATGCATTTAT
* **
96020 TTTATTCAATG-AAGTAT
1 TTCATTC-ATGCATTTAT
*
96037 TTCATTCATGCATTTAG
1 TTCATTCATGCATTTAT
96054 TTCATTCA
1 TTCATTCA
96062 ATAAGCTACT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
16 3 0.09
17 27 0.82
18 3 0.09
ACGTcount: A:0.27, C:0.15, G:0.08, T:0.49
Consensus pattern (17 bp):
TTCATTCATGCATTTAT
Found at i:96078 original size:34 final size:34
Alignment explanation
Indices: 95981--96063 Score: 112
Period size: 34 Copynumber: 2.4 Consensus size: 34
95971 CATTTAAGCT
* * * *
95981 TTTACTTCATTTAAGGAAGTAGTTCATTCATGCA
1 TTTAGTTCATTCAATGAAGTATTTCATTCATGCA
* *
96015 TTTATTTTATTCAATGAAGTATTTCATTCATGCA
1 TTTAGTTCATTCAATGAAGTATTTCATTCATGCA
96049 TTTAGTTCATTCAAT
1 TTTAGTTCATTCAAT
96064 AAGCTACTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.47
Consensus pattern (34 bp):
TTTAGTTCATTCAATGAAGTATTTCATTCATGCA
Found at i:97867 original size:18 final size:18
Alignment explanation
Indices: 97844--97888 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
97834 ATCATGCATC
97844 TAGTTCATTGAATAAAGT
1 TAGTTCATTGAATAAAGT
*
97862 TAGTTCATTGAATAATGT
1 TAGTTCATTGAATAAAGT
97880 TAGTTCATT
1 TAGTTCATT
97889 AATCAAACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (18 bp):
TAGTTCATTGAATAAAGT
Found at i:98688 original size:54 final size:54
Alignment explanation
Indices: 98628--98819 Score: 233
Period size: 54 Copynumber: 3.6 Consensus size: 54
98618 TAAACAAATT
*** * *
98628 ATGAATTTCGTGCTTTGCACACTTAGTGCCGAAACGGTTATTCATCCATATAGG
1 ATGAATTTCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGA
* * * * *
98682 ATGAATTACGTGGAATGTACACTTAGTGCTGAAAAGGTTATTCATCCACATAGA
1 ATGAATTTCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGA
* * *
98736 ATGAA-TTCTGTGAAATGCACACTTAGTACTGACACGGTTATTCATCCACATAGA
1 ATGAATTTC-GTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGA
* *
98790 ATGAATTCCATGAAATGCACACTTAGTGCC
1 ATGAATTTCGTGAAATGCACACTTAGTGCC
98820 TATTGGGTAT
Statistics
Matches: 117, Mismatches: 19, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
53 2 0.02
54 113 0.97
55 2 0.02
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (54 bp):
ATGAATTTCGTGAAATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGA
Found at i:99387 original size:22 final size:19
Alignment explanation
Indices: 99331--99380 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
99321 CGATGTTACC
* *
99331 TGGTAACGATAACTCACCA
1 TGGTATCGATACCTCACCA
99350 TGGTATCGATACCTCACCA
1 TGGTATCGATACCTCACCA
*
99369 TGGTATCAATAC
1 TGGTATCGATAC
99381 TACCTCATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (19 bp):
TGGTATCGATACCTCACCA
Found at i:110814 original size:18 final size:17
Alignment explanation
Indices: 110791--110824 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
110781 TCCTCTTGAG
110791 CTCTTTTAATCATCTTCA
1 CTCTTTTAATCA-CTTCA
110809 CTCTTTTAATCACTTC
1 CTCTTTTAATCACTTC
110825 TTGTAGACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.21, C:0.29, G:0.00, T:0.50
Consensus pattern (17 bp):
CTCTTTTAATCACTTCA
Found at i:111955 original size:54 final size:54
Alignment explanation
Indices: 111897--112173 Score: 347
Period size: 54 Copynumber: 5.1 Consensus size: 54
111887 TTTCGTGCTT
* * **
111897 TGCACACTTAGCGCCGAAATAGTTATTCATCCATGTAGGATGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACAGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * * * *
111951 TGCACACTTAGCGACAAAACGGTTATTCATCCACATAGGATGAATTCCATGAAA
1 TGCACACTTAGTGCCGAAACAGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * * *
112005 TGCACACTTAGTACCGAAACAGTTATTCATCGACATATGATGAATTCTGTGAAA
1 TGCACACTTAGTGCCGAAACAGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * * * *
112059 TACGCATTTAGTGCCGAAACAATTATTCATCCACATAGGATGAATTTCGTGAAA
1 TGCACACTTAGTGCCGAAACAGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * * * *
112113 TGCACACTTAGTGTCAAAACGGTTATTCATCCAAATAGGATGCATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACAGTTATTCATCCACATAGGATGAATTCCGTGAAA
112167 TGCACAC
1 TGCACAC
112174 GTAATGCCTA
Statistics
Matches: 188, Mismatches: 35, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 188 1.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (54 bp):
TGCACACTTAGTGCCGAAACAGTTATTCATCCACATAGGATGAATTCCGTGAAA
Found at i:112534 original size:20 final size:20
Alignment explanation
Indices: 112505--112556 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
112495 TGACCCTTCA
*
112505 GTATCGATACATA-TACCATG
1 GTATCTATAC-TACTACCATG
*
112525 GTATCTATACTACCCTACTATG
1 GTATCTATACTA--CTACCATG
112547 GTATCTATAC
1 GTATCTATAC
112557 CCCCTTCCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 2 0.07
20 9 0.33
22 16 0.59
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.35
Consensus pattern (20 bp):
GTATCTATACTACTACCATG
Found at i:112670 original size:95 final size:95
Alignment explanation
Indices: 112519--112728 Score: 280
Period size: 95 Copynumber: 2.2 Consensus size: 95
112509 CGATACATAT
* * * * *
112519 ACCATGGTATCTATACTACCCTACTATGGTATCTATACCCCCTTCCAGTATCGATACCAAAATTA
1 ACCATGGTATCAATACTACCATACTAGGGTACCGATACCCCCTTCCAGTATCGATACCAAAATTA
*
112584 GCTTCGATG-TGCCTTGGTATCGATACCCTC
66 GCTTCGATGTTACC-TGGTATCGATACCCTC
* * * * *
112614 ACCATGGTATCAATACTACTATGCTAGGGTACCGATACCCCCTTTC-GATATTGATACCAAATTT
1 ACCATGGTATCAATACTACCATACTAGGGTACCGATACCCCCTTCCAG-TATCGATACCAAAATT
*
112678 AGGTTCGATGTTACCTGGTATCGATACCCTC
65 AGCTTCGATGTTACCTGGTATCGATACCCTC
112709 ACCATGGTATCAATACTACC
1 ACCATGGTATCAATACTACC
112729 TCATTAGTAC
Statistics
Matches: 100, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
94 1 0.01
95 96 0.96
96 3 0.03
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.31
Consensus pattern (95 bp):
ACCATGGTATCAATACTACCATACTAGGGTACCGATACCCCCTTCCAGTATCGATACCAAAATTA
GCTTCGATGTTACCTGGTATCGATACCCTC
Found at i:118466 original size:17 final size:17
Alignment explanation
Indices: 118446--118504 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
118436 AAGAAAGTAG
118446 TTCATTCATGCATTTAA
1 TTCATTCATGCATTTAA
** *
118463 TTCATTCAATG-AAGTAT
1 TTCATTC-ATGCATTTAA
**
118480 TTCATTCATGCATTTCG
1 TTCATTCATGCATTTAA
118497 TTCATTCA
1 TTCATTCA
118505 ATAAGCTACT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
16 3 0.09
17 27 0.82
18 3 0.09
ACGTcount: A:0.27, C:0.19, G:0.08, T:0.46
Consensus pattern (17 bp):
TTCATTCATGCATTTAA
Found at i:118467 original size:34 final size:34
Alignment explanation
Indices: 118440--118521 Score: 112
Period size: 34 Copynumber: 2.4 Consensus size: 34
118430 TCATTTAAGA
118440 AAGTAGTTCATTCATGCATTTAATTCATTCAATG
1 AAGTAGTTCATTCATGCATTTAATTCATTCAATG
* **
118474 AAGTATTTCATTCATGCATTTCGTTCATTCAAT-
1 AAGTAGTTCATTCATGCATTTAATTCATTCAATG
*
118507 AAGCTACTTCATTCA
1 AAG-TAGTTCATTCA
118522 AGTCAGTAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
33 3 0.07
34 40 0.93
ACGTcount: A:0.30, C:0.18, G:0.10, T:0.41
Consensus pattern (34 bp):
AAGTAGTTCATTCATGCATTTAATTCATTCAATG
Found at i:119373 original size:24 final size:24
Alignment explanation
Indices: 119343--119394 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
119333 TTCCATTATT
* *
119343 TATATTG-TTGGTTCTATGCTCATA
1 TATATTGTTTGCTCCTA-GCTCATA
119367 TATATTGTTTGCTCCTAGCTCATA
1 TATATTGTTTGCTCCTAGCTCATA
119391 TATA
1 TATA
119395 GCAAATGGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.23, C:0.15, G:0.13, T:0.48
Consensus pattern (24 bp):
TATATTGTTTGCTCCTAGCTCATA
Found at i:121040 original size:32 final size:32
Alignment explanation
Indices: 121004--121065 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
120994 TACTAGCAGA
121004 GTGTCACATTAAGATAATGCACAATAATGTTT
1 GTGTCACATTAAGATAATGCACAATAATGTTT
* * * *
121036 GTGTCACATTCATATAATGCATAGTAATGT
1 GTGTCACATTAAGATAATGCACAATAATGT
121066 CATTGTCGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (32 bp):
GTGTCACATTAAGATAATGCACAATAATGTTT
Found at i:123434 original size:15 final size:16
Alignment explanation
Indices: 123395--123435 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
123385 TTCATGCATA
123395 TATATTT-TTATATAT
1 TATATTTATTATATAT
123410 TATATATTATTATAT-T
1 TATAT-TTATTATATAT
*
123426 TGTATTTATT
1 TATATTTATT
123436 TGCTGTAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 10 0.43
16 7 0.30
17 6 0.26
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (16 bp):
TATATTTATTATATAT
Found at i:123807 original size:34 final size:34
Alignment explanation
Indices: 123758--123836 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 34
123748 TATGATGTGC
* *
123758 CATCTAAAGGTTGTCTCTAAAG-GAAACAATGCTT
1 CATCCAAAGGGTGTCTC-AAAGAGAAACAATGCTT
* * *
123792 CATCCAAAGGGTGTCTCCAAGAGACACAATGTTT
1 CATCCAAAGGGTGTCTCAAAGAGAAACAATGCTT
123826 CATCCGAAAGG
1 CATCC-AAAGG
123837 TGCCTCCAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
33 3 0.08
34 30 0.79
35 5 0.13
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (34 bp):
CATCCAAAGGGTGTCTCAAAGAGAAACAATGCTT
Found at i:123844 original size:34 final size:32
Alignment explanation
Indices: 123783--123882 Score: 96
Period size: 34 Copynumber: 3.0 Consensus size: 32
123773 TCTAAAGGAA
* *
123783 ACAATGCTTCATCCAAAGGGTGTCTCCAAGAGAC
1 ACAATGTTTCATCCAAA-GGTGCCTCCAA-AGAC
*
123817 ACAATGTTTCATCCGAAAGGTGCCTCCAAA-AG
1 ACAATGTTTCATCC-AAAGGTGCCTCCAAAGAC
* *
123849 AC-ATGTTTCATCCAAAATGTGCCTCTAAAAGAC
1 ACAATGTTTCATCC-AAAGGTGCCTC-CAAAGAC
123882 A
1 A
123883 TATTTTGTCA
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
31 21 0.38
32 6 0.11
33 3 0.05
34 23 0.41
35 3 0.05
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (32 bp):
ACAATGTTTCATCCAAAGGTGCCTCCAAAGAC
Found at i:123858 original size:31 final size:31
Alignment explanation
Indices: 123790--123883 Score: 107
Period size: 31 Copynumber: 2.9 Consensus size: 31
123780 GAAACAATGC
* * *
123790 TTCATCCAAAGGGTGTCTCCAAGAGACACAATGT
1 TTCATCCAAAAGGTGCCTCCAA-A-AGAC-ATGT
*
123824 TTCATCCGAAAGGTGCCTCCAAAAGACATGT
1 TTCATCCAAAAGGTGCCTCCAAAAGACATGT
* *
123855 TTCATCCAAAATGTGCCTCTAAAAGACAT
1 TTCATCCAAAAGGTGCCTCCAAAAGACAT
123884 ATTTTGTCAC
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
31 30 0.57
32 3 0.06
33 1 0.02
34 19 0.36
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (31 bp):
TTCATCCAAAAGGTGCCTCCAAAAGACATGT
Found at i:124772 original size:24 final size:23
Alignment explanation
Indices: 124726--124772 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
124716 ATTGCTTAAT
* * *
124726 GTTGTTTTGGTTGGAATTTTTGA
1 GTTGTTTTGGCTGAAATTGTTGA
124749 GTTGTTTTGGGCTGAAATTGTTGA
1 GTTGTTTT-GGCTGAAATTGTTGA
124773 ATCAATGCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.15, C:0.02, G:0.32, T:0.51
Consensus pattern (23 bp):
GTTGTTTTGGCTGAAATTGTTGA
Found at i:125043 original size:17 final size:17
Alignment explanation
Indices: 125021--125062 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
125011 TGAATTTGAC
125021 CAAAAAGTCAAAATATT
1 CAAAAAGTCAAAATATT
*
125038 CAAAAAGTGAAAATATT
1 CAAAAAGTCAAAATATT
125055 CAAAAAGT
1 CAAAAAGT
125063 AATTTTTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.60, C:0.10, G:0.10, T:0.21
Consensus pattern (17 bp):
CAAAAAGTCAAAATATT
Found at i:129213 original size:17 final size:17
Alignment explanation
Indices: 129190--129248 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
129180 AAGGAAGTAG
129190 TTCATTCATGCATTTAT
1 TTCATTCATGCATTTAT
* **
129207 TTTATTCAATG-AAGTAT
1 TTCATTC-ATGCATTTAT
*
129224 TTCATTCATGCATTTAG
1 TTCATTCATGCATTTAT
129241 TTCATTCA
1 TTCATTCA
129249 ATAAGCTACT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
16 3 0.09
17 27 0.82
18 3 0.09
ACGTcount: A:0.27, C:0.15, G:0.08, T:0.49
Consensus pattern (17 bp):
TTCATTCATGCATTTAT
Found at i:129228 original size:34 final size:34
Alignment explanation
Indices: 129168--129265 Score: 117
Period size: 34 Copynumber: 2.9 Consensus size: 34
129158 CATTTAACCT
* * * *
129168 TTTACTTCATTTAAGGAAGTAGTTCATTCATGCA
1 TTTAGTTCATTCAATGAAGTACTTCATTCATGCA
* * *
129202 TTTATTTTATTCAATGAAGTATTTCATTCATGCA
1 TTTAGTTCATTCAATGAAGTACTTCATTCATGCA
129236 TTTAGTTCATTCAAT-AAGCTACTTCATTCA
1 TTTAGTTCATTCAATGAAG-TACTTCATTCA
129266 AGTCAGTAAG
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
33 3 0.05
34 52 0.95
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (34 bp):
TTTAGTTCATTCAATGAAGTACTTCATTCATGCA
Found at i:131014 original size:18 final size:18
Alignment explanation
Indices: 130991--131036 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
130981 AATCATGCAT
130991 TTAGTTCATTGAATAAAG
1 TTAGTTCATTGAATAAAG
*
131009 TTAGTTCATTGAATAATG
1 TTAGTTCATTGAATAAAG
131027 TTAGTTCATT
1 TTAGTTCATT
131037 AATCAAACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.46
Consensus pattern (18 bp):
TTAGTTCATTGAATAAAG
Found at i:131857 original size:54 final size:54
Alignment explanation
Indices: 131776--131967 Score: 235
Period size: 54 Copynumber: 3.6 Consensus size: 54
131766 TAAACAAATT
* *
131776 ATGAATTCCGT-ACATTGTACACTTAGTGCCGAAACAGTTATTCATCCATATAGG
1 ATGAATTCCGTGA-AATGTACACTTAGTGCCGAAACAGTTATTCATCCACATAGG
* * * * * *
131830 ATGAATTACATGAAATGTGCACATAGTGCTGAAA-AGGTTATTCATCCACATAGA
1 ATGAATTCCGTGAAATGTACACTTAGTGCCGAAACA-GTTATTCATCCACATAGG
* * * * *
131884 ATGAATTCCGTGAAATGCACCCTTCGTGCGGACACAGTTATTCATCCACATAGG
1 ATGAATTCCGTGAAATGTACACTTAGTGCCGAAACAGTTATTCATCCACATAGG
131938 ATGAATTCCGTGAAATGTACACTTAGTGCC
1 ATGAATTCCGTGAAATGTACACTTAGTGCC
131968 TATTGGGTAT
Statistics
Matches: 113, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
53 1 0.01
54 110 0.97
55 2 0.02
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (54 bp):
ATGAATTCCGTGAAATGTACACTTAGTGCCGAAACAGTTATTCATCCACATAGG
Found at i:132460 original size:95 final size:91
Alignment explanation
Indices: 132305--132511 Score: 224
Period size: 95 Copynumber: 2.2 Consensus size: 91
132295 CAATACCTAT
* *
132305 ACCATGGTATCGATACTATCCTACTATGGTATCGATACCCACTTCCACTATCGATACCAAAACTT
1 ACCATGGTATCGATACTA--CTACCATGGTACCGATACCCACTTCCACTATCGATACC-AAACTT
* * *
132370 -GTTTTGATG-TGCCTTAGTATCGATACCCTC
63 AGGTTCGATGTTACC-T-GTATCGATA-CCTC
* *
132400 ACCATGGTATCGATACTACTATCCATGGGTACCGATATCCC-CTTTCGA-TATCGATACCAAATT
1 ACCATGGTATCGATACTACTA-CCAT-GGTACCGATA-CCCAC-TTCCACTATCGATACCAAACT
*
132463 TAGGTTCGATGTTACCTGTATTGATACCTC
62 TAGGTTCGATGTTACCTGTATCGATACCTC
132493 ACCATGGTATCGATACTAC
1 ACCATGGTATCGATACTAC
132512 CTCATCAGTA
Statistics
Matches: 98, Mismatches: 8, Indels: 14
0.82 0.07 0.12
Matches are distributed among these distances:
93 26 0.27
94 16 0.16
95 46 0.47
96 10 0.10
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (91 bp):
ACCATGGTATCGATACTACTACCATGGTACCGATACCCACTTCCACTATCGATACCAAACTTAGG
TTCGATGTTACCTGTATCGATACCTC
Found at i:133032 original size:11 final size:11
Alignment explanation
Indices: 133016--133040 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
133006 GGTTACGGGA
133016 AAAAGAGAAAG
1 AAAAGAGAAAG
133027 AAAAGAGAAAG
1 AAAAGAGAAAG
133038 AAA
1 AAA
133041 CTTTTATCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
AAAAGAGAAAG
Found at i:136113 original size:21 final size:21
Alignment explanation
Indices: 136067--136113 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
136057 TCGAACAACC
*
136067 TTTTTTTTCGTTCAAACTGTT
1 TTTTTTTTCATTCAAACTGTT
* *
136088 GTTTTTTTGCATTCAACCT-TT
1 -TTTTTTTTCATTCAAACTGTT
136109 TTTTT
1 TTTTT
136114 CGATGGAGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 5 0.23
21 2 0.09
22 15 0.68
ACGTcount: A:0.13, C:0.15, G:0.09, T:0.64
Consensus pattern (21 bp):
TTTTTTTTCATTCAAACTGTT
Found at i:145549 original size:54 final size:54
Alignment explanation
Indices: 145491--145775 Score: 435
Period size: 54 Copynumber: 5.3 Consensus size: 54
145481 TTATGTGCTT
* * * * *
145491 TGCACACTTAGCGCCAAAACAGTTATTCATCCATATAGGGTGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * *
145545 TGCACACTTAGCGACGAAACGGTTATTCATCCACATAGGATGAATTCCATGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * *
145599 TGCACACTTAGTACCGAAATGGTTATTCATCCACATATGATGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * * *
145653 TACACATTTATTGCCGAAACAGTTATTCATCCACATAGGATGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
145707 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
145761 TGCACACTTAGTGCC
1 TGCACACTTAGTGCC
145776 TATTGGGTAA
Statistics
Matches: 208, Mismatches: 23, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 208 1.00
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (54 bp):
TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
Found at i:146128 original size:20 final size:20
Alignment explanation
Indices: 146099--146150 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
146089 TGGCCCTCCA
*
146099 GTATCGATACATA-TACCATG
1 GTATCTATAC-TACTACCATG
*
146119 GTATCTATACTACCCTACTATG
1 GTATCTATACTA--CTACCATG
146141 GTATCTATAC
1 GTATCTATAC
146151 CCCCTTCCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 2 0.07
20 9 0.33
22 16 0.59
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.35
Consensus pattern (20 bp):
GTATCTATACTACTACCATG
Found at i:146298 original size:94 final size:95
Alignment explanation
Indices: 146112--146321 Score: 253
Period size: 94 Copynumber: 2.2 Consensus size: 95
146102 TCGATACATA
* * * * *
146112 TACCATGGTATCTATACTACCCTACTATGGTATCTATACCCCCTTCCAGTATCGATACCAAAATT
1 TACCATGGTATCAATACTACCATACTAGGGTACCGATACCCCCTTCCAGTATCGATACCAAAATT
* * *
146177 AGCTTCGATGTGCCTTGGTATCGATACCCT
66 AGCTTCGATGTACCTTGCTATCAATACCCT
* * * * *
146207 TACCATGGTATCAATACTACTATGCTAGGGTACCGATACCCCTTTCGA-TATCGATACCAAATTT
1 TACCATGGTATCAATACTACCATACTAGGGTACCGATACCCCCTTCCAGTATCGATACCAAAATT
*
146271 AGGTTCGATGTTACC-TGCTATCAATACCCT
66 AGCTTCGATG-TACCTTGCTATCAATACCCT
* *
146301 CACCATGGTATCAAAACTACC
1 TACCATGGTATCAATACTACC
146322 TCATTAGTAC
Statistics
Matches: 97, Mismatches: 17, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
94 55 0.57
95 42 0.43
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (95 bp):
TACCATGGTATCAATACTACCATACTAGGGTACCGATACCCCCTTCCAGTATCGATACCAAAATT
AGCTTCGATGTACCTTGCTATCAATACCCT
Found at i:152000 original size:17 final size:17
Alignment explanation
Indices: 151980--152038 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
151970 AAGAAAGTAG
151980 TTCATTCATGCATTTAA
1 TTCATTCATGCATTTAA
** *
151997 TTCATTCAATG-AAGTAT
1 TTCATTC-ATGCATTTAA
*
152014 TTCATTCATGCATTTCA
1 TTCATTCATGCATTTAA
152031 TTCATTCA
1 TTCATTCA
152039 ATAAGCTACT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
16 3 0.09
17 27 0.82
18 3 0.09
ACGTcount: A:0.29, C:0.19, G:0.07, T:0.46
Consensus pattern (17 bp):
TTCATTCATGCATTTAA
Found at i:152001 original size:34 final size:34
Alignment explanation
Indices: 151974--152055 Score: 121
Period size: 34 Copynumber: 2.4 Consensus size: 34
151964 TCATTTAAGA
151974 AAGTAGTTCATTCATGCATTTAATTCATTCAATG
1 AAGTAGTTCATTCATGCATTTAATTCATTCAATG
* *
152008 AAGTATTTCATTCATGCATTTCATTCATTCAAT-
1 AAGTAGTTCATTCATGCATTTAATTCATTCAATG
*
152041 AAGCTACTTCATTCA
1 AAG-TAGTTCATTCA
152056 AGTCAGTAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
33 3 0.07
34 41 0.93
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (34 bp):
AAGTAGTTCATTCATGCATTTAATTCATTCAATG
Found at i:152921 original size:24 final size:24
Alignment explanation
Indices: 152876--152921 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
152866 TTCCATTGTT
* *
152876 TATATTGTTGGTTCTAAGCTCATA
1 TATATTGTTGCTCCTAAGCTCATA
152900 TATATTGTTTGCTCCTAA-CTCA
1 TATATTG-TTGCTCCTAAGCTCA
152922 CCTATAGCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.24, C:0.17, G:0.13, T:0.46
Consensus pattern (24 bp):
TATATTGTTGCTCCTAAGCTCATA
Found at i:154618 original size:32 final size:32
Alignment explanation
Indices: 154558--154648 Score: 89
Period size: 32 Copynumber: 2.9 Consensus size: 32
154548 ACTAGTAGAG
* *
154558 TGTCACATTAAGATAATGCACAACAATGT-TT
1 TGTCACATTCAGATAATGCACAACAATGTCAT
* * **
154589 CTGTCACATTCATATAATGCATATTAATGTCAT
1 -TGTCACATTCAGATAATGCACAACAATGTCAT
*
154622 TGTCGCATTCAGATAATGCA-AA-AATGT
1 TGTCACATTCAGATAATGCACAACAATGT
154649 GTCAGTGTCG
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
30 5 0.10
31 1 0.02
32 42 0.86
33 1 0.02
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.34
Consensus pattern (32 bp):
TGTCACATTCAGATAATGCACAACAATGTCAT
Found at i:157209 original size:34 final size:34
Alignment explanation
Indices: 157160--157248 Score: 99
Period size: 34 Copynumber: 2.6 Consensus size: 34
157150 TATGATGTGC
* * *
157160 CATCTAAAGGTTGTCTCTAAAGGAAACAATGCTT
1 CATCCAAAGGGTGTCTCCAAAGGAAACAATGCTT
* * *
157194 CATCCAAAGGGTGTCTCCAAGGGACACAATGTTT
1 CATCCAAAGGGTGTCTCCAAAGGAAACAATGCTT
*
157228 CATCCGAAA-GGTGCCTCCAAA
1 CATCC-AAAGGGTGTCTCCAAA
157249 AGACATGTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
34 43 0.93
35 3 0.07
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (34 bp):
CATCCAAAGGGTGTCTCCAAAGGAAACAATGCTT
Found at i:157260 original size:31 final size:31
Alignment explanation
Indices: 157222--157285 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
157212 AAGGGACACA
*
157222 ATGTTTCATCCGAAAGGTGCCTCCAAAAGAC
1 ATGTTTCATCCAAAAGGTGCCTCCAAAAGAC
*
157253 ATGTTTCATCCAAAATGTGCCTCCAAAAGAC
1 ATGTTTCATCCAAAAGGTGCCTCCAAAAGAC
157284 AT
1 AT
157286 ATTTTGTCAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (31 bp):
ATGTTTCATCCAAAAGGTGCCTCCAAAAGAC
Found at i:158172 original size:24 final size:24
Alignment explanation
Indices: 158126--158172 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
158116 TTTCGATTGC
* *
158126 TTAATGTTGTTTTGGTTGGAATTT
1 TTAATGTTGTTTTGGCTGAAATTT
158150 TTAA-GTTGTTTTGGGCTGAAATT
1 TTAATGTTGTTTT-GGCTGAAATT
158173 GTTGAATCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.19, C:0.02, G:0.26, T:0.53
Consensus pattern (24 bp):
TTAATGTTGTTTTGGCTGAAATTT
Found at i:168887 original size:29 final size:30
Alignment explanation
Indices: 168828--168887 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 30
168818 TAAATAATCA
* * *
168828 AATATAATTAATAATATTTTTTATTTTAAT
1 AATATAATTAAAAATATTTTTTATATAAAT
168858 AATAT-ATTAAAAATATTATTTTA-ATAAAT
1 AATATAATTAAAAATATT-TTTTATATAAAT
168887 A
1 A
168888 TCTAATATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (30 bp):
AATATAATTAAAAATATTTTTTATATAAAT
Found at i:168927 original size:64 final size:64
Alignment explanation
Indices: 168807--168926 Score: 190
Period size: 62 Copynumber: 1.9 Consensus size: 64
168797 TTATTATTAT
*
168807 TATTATTTTAATAAATAATCAAATATAATTAATAATATTTTTTATTTTAATAATATATTAAAAA
1 TATTATTTTAATAAATAATCAAATATAATTAATAATATTTGTTATTTTAATAATATATTAAAAA
* * *
168871 TATTATTTTAATAAAT-ATCTAATATAATTTATAATA-TTGTTATTTTAATAAAATAT
1 TATTATTTTAATAAATAATCAAATATAATTAATAATATTTGTTATTTTAATAATATAT
168927 ACTAATCCTA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
62 18 0.35
63 18 0.35
64 16 0.31
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (64 bp):
TATTATTTTAATAAATAATCAAATATAATTAATAATATTTGTTATTTTAATAATATATTAAAAA
Found at i:168979 original size:24 final size:23
Alignment explanation
Indices: 168936--168983 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
168926 TACTAATCCT
*
168936 AATTTATAAAATTTTAGAAATAA
1 AATTTATAAAATATTAGAAATAA
168959 AATTTAATAATAATATT-GAAATAA
1 AATTT-ATAA-AATATTAGAAATAA
168983 A
1 A
168984 TAATAATGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 5 0.23
24 12 0.55
25 5 0.23
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (23 bp):
AATTTATAAAATATTAGAAATAA
Found at i:171132 original size:16 final size:16
Alignment explanation
Indices: 171111--171141 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
171101 AGTATAATCA
171111 CTAATCTAGATCATCG
1 CTAATCTAGATCATCG
171127 CTAATCTAGATCATC
1 CTAATCTAGATCATC
171142 ATATGAATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.26, G:0.10, T:0.32
Consensus pattern (16 bp):
CTAATCTAGATCATCG
Found at i:176338 original size:54 final size:54
Alignment explanation
Indices: 176254--176624 Score: 609
Period size: 54 Copynumber: 6.9 Consensus size: 54
176244 TTACCGAATG
176254 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
*
176308 GACACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* *
176362 GGTACTATGTGTGCAACTTAAGAATTTCATAATAAGTTTATGAATTTCCGTATT
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* *
176416 GGCACTATGTGTGCAACTTAAGGAATTCATAATAAGTTTATGAATTTCTGTATT
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* * * *
176470 GGCACTGTG-GATGCAACTTAATAAATTTATAATAGGTTTATGAATTTCCGTATT
1 GGCACTATGTG-TGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
*
176524 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCTGTATT
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* * *
176578 AGCACTATGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTT
1 GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTT
176625 GTGAATTACT
Statistics
Matches: 293, Mismatches: 22, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
53 1 0.00
54 291 0.99
55 1 0.00
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (54 bp):
GGCACTATGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
Found at i:177846 original size:18 final size:17
Alignment explanation
Indices: 177807--177849 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
177797 ATTATATGGA
177807 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
177823 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
177841 TATTATTAT
1 TATTATTAT
177850 ACATATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:178299 original size:42 final size:40
Alignment explanation
Indices: 178234--178312 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 40
178224 GAGTACCCAT
* *
178234 TTTTTTGTTTTATTTCTAGCTAAAGTCTCTCCCACTTTCCTC
1 TTTTTTGTCTTATTTCTAGCTAAAG-C-CCCCCACTTTCCTC
178276 TTTTTTGTCTTATTTCT-GACTAAAGCCCCCCACTTTC
1 TTTTTTGTCTTATTTCTAG-CTAAAGCCCCCCACTTTC
178313 GGTGAAGTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 10 0.29
41 2 0.06
42 22 0.65
ACGTcount: A:0.15, C:0.28, G:0.08, T:0.49
Consensus pattern (40 bp):
TTTTTTGTCTTATTTCTAGCTAAAGCCCCCCACTTTCCTC
Found at i:178379 original size:38 final size:40
Alignment explanation
Indices: 178328--178407 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 40
178318 AGTGAGAGGG
*
178328 TAGCTTTTCTATTTT-TAAATA-TTTGTTGTATATATATA
1 TAGCTTTTCTATTTTATAAATACTTTGATGTATATATATA
*
178366 TAGCTTATT-TATTTTATTAATACTTTGATGTATATATATA
1 TAGCTT-TTCTATTTTATAAATACTTTGATGTATATATATA
178406 TA
1 TA
178408 TTTTCATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
38 12 0.32
39 7 0.19
40 18 0.49
ACGTcount: A:0.31, C:0.05, G:0.07, T:0.56
Consensus pattern (40 bp):
TAGCTTTTCTATTTTATAAATACTTTGATGTATATATATA
Found at i:178496 original size:14 final size:14
Alignment explanation
Indices: 178477--178515 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
178467 TATTATTTAT
*
178477 TTTATTTTTTTCCC
1 TTTATTTTATTCCC
*
178491 TTTATTTTATTCTC
1 TTTATTTTATTCCC
*
178505 TTTATCTTATT
1 TTTATTTTATT
178516 TGTTTTCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.13, C:0.15, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTATTTTATTCCC
Found at i:184243 original size:18 final size:18
Alignment explanation
Indices: 184220--184255 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
184210 TTCAACATCA
*
184220 ATATTGGGGCATTTTTGG
1 ATATTGGGGCATCTTTGG
184238 ATATTGGGGCATCTTTGG
1 ATATTGGGGCATCTTTGG
184256 GGATTCAACA
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:0.17, C:0.08, G:0.33, T:0.42
Consensus pattern (18 bp):
ATATTGGGGCATCTTTGG
Found at i:185800 original size:426 final size:424
Alignment explanation
Indices: 185258--186082 Score: 1249
Period size: 426 Copynumber: 1.9 Consensus size: 424
185248 CACCCGAGAC
*
185258 AACACAAGTTCAACTTCACAACGAAGAGACGGCTGGTTGTCAACAAACAACTTCCCAATTTCAGA
1 AACACAAGTTCAACTTCACAACGAAGAGACGGCTGGTCGTCAACAAACAACTTCCCAATTTCAGA
185323 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAAAACAAGTTCAACTTCACAACGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAAAACAAGTTCAACTTCACAACGA
* * *
185388 AGGGACGGTTATTTGTCAAAAAACCAATTT-TCAATTTCAGAGCCAATTTCAACTTCACAGCGAA
131 AGGGACGGCTAGTTGTCAAAAAA-CAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAA
* * *
185452 GGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGATGACTGGTTGTCAACAAA
195 GGATATTGGACTCAAGACAACACAAGTTCAAATTCACAACGAAGGGACGACTGGTTGTCAACAAA
* * *
185517 CAATTTCCCAATTTCAGAGTCAATTTCAACTTCACAATGAAGGATATTAGACTCAAGACAAAACA
260 CAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAAACTCAAGACAAAACA
* * * * * *
185582 AGTTCAACTTCACAACAAAGGGACGGCTGGTTGTCAACAAAACAATTTCCCAGTTTCAGAGCCAA
325 AGCTCAACTTCACAACAAAGGGACAGCCGGCTGTCAAC-AAACAATTTCACAGTTCCAGAGCCAA
185647 TTTCAACTTCACAGCGAAGATTATTGGACTCAAGAT
389 TTTCAACTTCACAGCGAAGATTATTGGACTCAAGAT
* * ** *
185683 AACACAAGTTCAACTTCACAACGAAGGGATGGCTTGGTCGTCAACAAACCAA-TTTTCAGTTTCA
1 AACACAAGTTCAACTTCACAACGAAGAGACGGC-TGGTCGTCAACAAA-CAACTTCCCAATTTCA
** **
185747 GAGCCAATTTCAACTTCACAGTGAAGGATATTGGACTCAAGACAACCCAAGTTCAACTTCACAAC
64 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAAAACAAGTTCAACTTCACAAC
* **
185812 GAAGGGACGGCTGGTTGTCAGCAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGA
129 GAAGGGACGGCTAGTTGTCAAAAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGA
** *
185877 AGGATATTGGACTCAAGATGACACAAGTTCAAATTCACAACGAAGGGACGGCTGGTTGTCAACAA
194 AGGATATTGGACTCAAGACAACACAAGTTCAAATTCACAACGAAGGGACGACTGGTTGTCAACAA
* * * *
185942 ACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAAACTCGAGATAACAC
259 ACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAAACTCAAGACAAAAC
* * * *
186007 AAGCTCAACTTCACAGCGAAGGGGCAGCCGGCTGTCAACAAACAATTTCACAGTTCCGGAGCCAA
324 AAGCTCAACTTCACAACAAAGGGACAGCCGGCTGTCAACAAACAATTTCACAGTTCCAGAGCCAA
186072 TTTCAACTTCA
389 TTTCAACTTCA
186083 TGACAGAGGA
Statistics
Matches: 358, Mismatches: 39, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
425 71 0.20
426 284 0.79
427 3 0.01
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (424 bp):
AACACAAGTTCAACTTCACAACGAAGAGACGGCTGGTCGTCAACAAACAACTTCCCAATTTCAGA
GCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAAAACAAGTTCAACTTCACAACGA
AGGGACGGCTAGTTGTCAAAAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAG
GATATTGGACTCAAGACAACACAAGTTCAAATTCACAACGAAGGGACGACTGGTTGTCAACAAAC
AATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAAACTCAAGACAAAACAA
GCTCAACTTCACAACAAAGGGACAGCCGGCTGTCAACAAACAATTTCACAGTTCCAGAGCCAATT
TCAACTTCACAGCGAAGATTATTGGACTCAAGAT
Found at i:186103 original size:106 final size:106
Alignment explanation
Indices: 185254--186082 Score: 1196
Period size: 106 Copynumber: 7.8 Consensus size: 106
185244 TCTCCACCCG
* *
185254 AGACAACACAAGTTCAACTTCACAACGAAGAGACGGCTGGTTGTCAACAAACAACTTCCCAATTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTT
*
185319 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCA
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
* * ** * *
185360 AGACAAAACAAGTTCAACTTCACAACGAAGGGACGGTTATTTGTCAAAAAACCAATTT-TCAATT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAA-CAATTTCCCAATT
*
185424 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCG
65 TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
* *
185466 AGACAACACAAGTTCAACTTCACAACGAAGGGATGACTGGTTGTCAACAAACAATTTCCCAATTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTT
* ** *
185531 CAGAGTCAATTTCAACTTCACAATGAAGGATATTAGACTCA
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
* * *
185572 AGACAAAACAAGTTCAACTTCACAACAAAGGGACGGCTGGTTGTCAACAAAACAATTTCCCAGTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AAACAATTTCCCAATT
185637 TCAGAGCCAATTTCAACTTCACAGCGAA-GATTATTGGACTCA
65 TCAGAGCCAATTTCAACTTCACAGCGAAGGA-TATTGGACTCA
* * * * *
185679 AGATAACACAAGTTCAACTTCACAACGAAGGGATGGCTTGGTCGTCAACAAACCAATTT-TCAGT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGC-TGGTTGTCAACAAA-CAATTTCCCAAT
*
185743 TTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGGACTCA
64 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
* *
185786 AGACAACCCAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAGCAAACAATTTCCCAATTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTT
185851 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
** *
185892 AGATGACACAAGTTCAAATTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTT
** *
185957 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTAAACTCG
66 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
* * * * * * * * * *
185998 AGATAACACAAGCTCAACTTCACAGCGAAGGGGCAGCCGGCTGTCAACAAACAATTTCACAGTTC
1 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTT
*
186063 CGGAGCCAATTTCAACTTCA
66 CAGAGCCAATTTCAACTTCA
186083 TGACAGAGGA
Statistics
Matches: 648, Mismatches: 67, Indels: 16
0.89 0.09 0.02
Matches are distributed among these distances:
105 12 0.02
106 450 0.69
107 168 0.26
108 18 0.03
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (106 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATTT
CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
Found at i:190447 original size:23 final size:23
Alignment explanation
Indices: 190420--190466 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
190410 ACTTCCTCAG
190420 TGGCAAACGTGCACTTTTCCTTC
1 TGGCAAACGTGCACTTTTCCTTC
*
190443 TGGCAAACGTGTACTTTTCCTTC
1 TGGCAAACGTGCACTTTTCCTTC
190466 T
1 T
190467 TCACGTACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.38
Consensus pattern (23 bp):
TGGCAAACGTGCACTTTTCCTTC
Found at i:199166 original size:34 final size:32
Alignment explanation
Indices: 199121--199192 Score: 90
Period size: 34 Copynumber: 2.2 Consensus size: 32
199111 CCTTTTGTAA
*
199121 AGGGAAAAGGTTCTAGCTTAGCCCGTGTAAAAGCT
1 AGGG-AAAGGTTCTAGCTTAGCCCG-G-AAAAACT
* *
199156 AGGGAAAGGTTCTTGTTTAGCCCGGAAAAACT
1 AGGGAAAGGTTCTAGCTTAGCCCGGAAAAACT
199188 AGGGA
1 AGGGA
199193 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 18 0.53
35 4 0.12
ACGTcount: A:0.32, C:0.15, G:0.31, T:0.22
Consensus pattern (32 bp):
AGGGAAAGGTTCTAGCTTAGCCCGGAAAAACT
Found at i:202603 original size:34 final size:32
Alignment explanation
Indices: 202564--202633 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
202554 TTTTGTAAAG
* *
202564 GGGAAATGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
202598 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
202630 GGGA
1 GGGA
202634 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:207992 original size:49 final size:49
Alignment explanation
Indices: 207924--208258 Score: 472
Period size: 49 Copynumber: 6.8 Consensus size: 49
207914 ATTAATGAAT
**
207924 GTTAAATGCATAATAGTGCATTTCGGCATAAAAGGTGCCACTAATAAAA
1 GTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATAAAA
** * *
207973 GTTAAATATATAACGGTGCATTTAGGCTTAAAAGGTGCCACTAATAAAA
1 GTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATAAAA
* * * *
208022 GTTAAATGCATAACAGTGCATTGCGACATAAAAGGTGCCAGTAATAAAA
1 GTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATAAAA
* * * * *
208071 GTTAAATGCATAATGGTGCATTTCAGCTTAAAAGGTGCCATTAATGAAA
1 GTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATAAAA
* * *
208120 GTTAAATGCATAACGGTGCATTTAGGCATAAAAGGTGCTACTAATGAAA
1 GTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATAAAA
** * *
208169 GTTAAATGCATAACATTGCATTTAGGCATAAAAGGTGCCACTAATGAAA
1 GTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATAAAA
208218 GTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCAC
1 GTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCAC
208259 CCATGGTATT
Statistics
Matches: 252, Mismatches: 34, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 252 1.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (49 bp):
GTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACTAATAAAA
Found at i:214947 original size:49 final size:49
Alignment explanation
Indices: 214885--215227 Score: 488
Period size: 49 Copynumber: 7.0 Consensus size: 49
214875 TAAAATGAAT
* *
214885 TAATGAAAGTTAAATGCATAATGGTGCATTTCGGCATAAAAGGTGACAC
1 TAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCAC
* * * *
214934 TAATAAAAGTTAAATGCATATCGGTGTATTTCGGCATAAAAGGTGTCAC
1 TAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCAC
* * * * *
214983 TGATAAAAGTTAAAAGCATGACGGTGCATTTTGGCATAAAAGGTGCCAC
1 TAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCAC
* * * *
215032 TAATAAAAGTTAAATGCATAACGATGCATTTCGGCATAATAGGTGCCAT
1 TAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCAC
* * *
215081 TAATGAAAGTTAAATGCACAACAGTGCATTTAGGCATAAAAGGTGCCAC
1 TAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCAC
*
215130 TAATGAAAGTTAAATGTATAACGGTGCATTTCGGCATAAAAGGTGCCAC
1 TAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCAC
* **
215179 GAATGAAAGTTAAATGCATAACGGTATATTTCGGCATAAAAGGTGCCAC
1 TAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCAC
215228 CCATGGTATT
Statistics
Matches: 260, Mismatches: 34, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 260 1.00
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (49 bp):
TAATGAAAGTTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCAC
Found at i:219784 original size:51 final size:51
Alignment explanation
Indices: 219727--219825 Score: 153
Period size: 51 Copynumber: 1.9 Consensus size: 51
219717 TTTTTATTTG
* * * *
219727 TATTTTTTATATTTTATTATAGTTTAAATTGATATAATTCATATATAATAA
1 TATTTTTTAAAATTTATTATAGTTTAAACTAATATAATTCATATATAATAA
*
219778 TATTTTTTAAAATTTATTATAGTTTAAACTAATATGATTCATATATAA
1 TATTTTTTAAAATTTATTATAGTTTAAACTAATATAATTCATATATAA
219826 GTGTAAATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (51 bp):
TATTTTTTAAAATTTATTATAGTTTAAACTAATATAATTCATATATAATAA
Found at i:219957 original size:26 final size:25
Alignment explanation
Indices: 219926--219980 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
219916 AACAGTTAAA
* * *
219926 TTTTAAACTGCTCTTTTGTACAACAT
1 TTTTAAA-AGCTCATTTCTACAACAT
*
219952 TTTTAAAAGTTCATTTCTACAACAT
1 TTTTAAAAGCTCATTTCTACAACAT
219977 TTTT
1 TTTT
219981 TTTAAAGTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 18 0.72
26 7 0.28
ACGTcount: A:0.29, C:0.16, G:0.05, T:0.49
Consensus pattern (25 bp):
TTTTAAAAGCTCATTTCTACAACAT
Found at i:220279 original size:17 final size:18
Alignment explanation
Indices: 220257--220293 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
220247 AAATACAAAC
220257 AAAAATATA-ATTATAAT
1 AAAAATATATATTATAAT
*
220274 AAAAATATATTTTATAAT
1 AAAAATATATATTATAAT
220292 AA
1 AA
220294 CTCACTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAAATATATATTATAAT
Found at i:221478 original size:2 final size:2
Alignment explanation
Indices: 221473--221536 Score: 119
Period size: 2 Copynumber: 31.5 Consensus size: 2
221463 TAGGGATGTG
221473 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
221515 AT AT AT AT AT AT AT AT GAT AT A
1 AT AT AT AT AT AT AT AT -AT AT A
221537 ATCAAACGAT
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 59 0.97
3 2 0.03
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:222947 original size:15 final size:16
Alignment explanation
Indices: 222924--222959 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
222914 AATACTTTCA
*
222924 TATTTTATTAA-ATTT
1 TATTATATTAACATTT
222939 TATTATATTAACATTT
1 TATTATATTAACATTT
222955 TATTA
1 TATTA
222960 ATTTTTGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTATATTAACATTT
Found at i:225032 original size:3 final size:3
Alignment explanation
Indices: 225019--225064 Score: 58
Period size: 3 Copynumber: 15.3 Consensus size: 3
225009 TATCTTCTTC
* *
225019 TGA TGA CGA TGA TGA TGA TGGA T-A TGA TAA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA T-GA TGA TGA TGA TGA TGA TGA TGA TGA
225064 T
1 T
225065 ATAGTGATGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.35, C:0.02, G:0.30, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:225301 original size:26 final size:26
Alignment explanation
Indices: 225232--225301 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
225222 AATTATTGAC
*
225232 TTTTTATTTATTTTGTT-TCTTAATTT
1 TTTTTA-TTATTTTGTTGTCTTAATTG
* **
225258 TTTTTATTACTTAATTGT-TTGAATTG
1 TTTTTATTATTTTGTTGTCTT-AATTG
225284 TTTTTATTATTTTGTTGT
1 TTTTTATTATTTTGTTGT
225302 ATCATTTTCT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
25 9 0.26
26 26 0.74
ACGTcount: A:0.17, C:0.03, G:0.09, T:0.71
Consensus pattern (26 bp):
TTTTTATTATTTTGTTGTCTTAATTG
Found at i:227670 original size:60 final size:60
Alignment explanation
Indices: 227570--227686 Score: 137
Period size: 60 Copynumber: 1.9 Consensus size: 60
227560 CATGATGTTT
* * * * * *
227570 ACATTTAGGTCGAACAAGCTGGTAGTTGCATGCATTCCCTTTGAACTTGAAGGCATCTCG
1 ACATTAAGGTCGAACAAGCTCGCAGTTGAATGCATTCCCTTGGAACTTGAAGACATCTCG
* * *
227630 ACATTAAGGTTGAAGAAGCTCGCAGTTGAATGC-TTCCCCTTGGAGCTTGAAGACATC
1 ACATTAAGGTCGAACAAGCTCGCAGTTGAATGCATT-CCCTTGGAACTTGAAGACATC
227687 ATGTCAAATG
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
59 2 0.04
60 45 0.96
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.28
Consensus pattern (60 bp):
ACATTAAGGTCGAACAAGCTCGCAGTTGAATGCATTCCCTTGGAACTTGAAGACATCTCG
Found at i:229879 original size:45 final size:46
Alignment explanation
Indices: 229794--229881 Score: 142
Period size: 45 Copynumber: 1.9 Consensus size: 46
229784 AAATAGCCCG
* *
229794 AGTGCATCGATGCATGGTCTTGTGCATCGATGCATTAAATGCACTA
1 AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCACTA
*
229840 AGTGCATCGATTCATGGT-ATGTGCATCGATGCATAAAATGCA
1 AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
229882 TTCGATGTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 22 0.56
46 17 0.44
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (46 bp):
AGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCACTA
Found at i:245756 original size:25 final size:25
Alignment explanation
Indices: 245722--245769 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
245712 CCAAGGCGGT
*
245722 AGAGAACCCTAATATCGAGTAGAAA
1 AGAGAACCCTAATACCGAGTAGAAA
*
245747 AGAGAACCCTAATACCGGGTAGA
1 AGAGAACCCTAATACCGAGTAGA
245770 TTATTTTAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.15
Consensus pattern (25 bp):
AGAGAACCCTAATACCGAGTAGAAA
Found at i:246133 original size:18 final size:18
Alignment explanation
Indices: 246112--246146 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
246102 AACTTGATCT
246112 AAAATAATATATTTATTA
1 AAAATAATATATTTATTA
* *
246130 AAAATATTATTTTTATT
1 AAAATAATATATTTATT
246147 CAATAAAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AAAATAATATATTTATTA
Found at i:246326 original size:42 final size:41
Alignment explanation
Indices: 246267--246360 Score: 163
Period size: 42 Copynumber: 2.3 Consensus size: 41
246257 CCCTAAGCCA
246267 AACCCAACCCGACATGAACATAACTTTAAAAAATCCGGCCCG
1 AACCCAACCCGACATGAACATAACTTT-AAAAATCCGGCCCG
246309 AACCCAACCCGACATGAACATAACTTTAAAAATCCGGCCCG
1 AACCCAACCCGACATGAACATAACTTTAAAAATCCGGCCCG
*
246350 -ACCCGACCCGA
1 AACCCAACCCGA
246361 ATCCATAATT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 10 0.20
41 14 0.27
42 27 0.53
ACGTcount: A:0.38, C:0.36, G:0.13, T:0.13
Consensus pattern (41 bp):
AACCCAACCCGACATGAACATAACTTTAAAAATCCGGCCCG
Found at i:246712 original size:15 final size:15
Alignment explanation
Indices: 246692--246740 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
246682 ATATATTTTA
246692 ATATATTTTTTAAAT
1 ATATATTTTTTAAAT
*
246707 ATATATTATTTAAAT
1 ATATATTTTTTAAAT
*
246722 -TAAAATTTTTTAAA-
1 AT-ATATTTTTTAAAT
246736 ATATA
1 ATATA
246741 AAATTTCTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
14 3 0.11
15 25 0.89
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATATTTTTTAAAT
Found at i:247507 original size:59 final size:60
Alignment explanation
Indices: 247442--247586 Score: 238
Period size: 59 Copynumber: 2.4 Consensus size: 60
247432 TCAGGTGAAA
*
247442 ATTTTATAACTTTTAATAGTTGGGAGACTCAATAAAATAGTATCATATAGT-AAGGAACC
1 ATTTTATAACTTTTAATAGTTGAGAGACTCAATAAAATAGTATCATATAGTAAAGGAACC
* *
247501 ATTTTATAACTTTTAATAGTTGAGAGACTCAATAAAATAGTGTCATATAGTAAAGGGACC
1 ATTTTATAACTTTTAATAGTTGAGAGACTCAATAAAATAGTATCATATAGTAAAGGAACC
247561 ATTTTATAACCTTTATAATAGTTGAG
1 ATTTTATAA-CTTT-TAATAGTTGAG
247587 GATCAACAAA
Statistics
Matches: 80, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
59 49 0.61
60 16 0.20
61 4 0.05
62 11 0.14
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (60 bp):
ATTTTATAACTTTTAATAGTTGAGAGACTCAATAAAATAGTATCATATAGTAAAGGAACC
Found at i:249991 original size:2 final size:2
Alignment explanation
Indices: 249951--249979 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
249941 CGTTAATAAA
249951 AT AT -T 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
249980 TTTCATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:254412 original size:2 final size:2
Alignment explanation
Indices: 254405--254435 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
254395 CCACAAAAAC
*
254405 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
254436 CTTTTTGACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:256232 original size:46 final size:46
Alignment explanation
Indices: 256168--256255 Score: 149
Period size: 46 Copynumber: 1.9 Consensus size: 46
256158 ACCTCTACAT
* * *
256168 ATTTTCATTTGTGGCATCCTTTCCTGTCAATTATGCATTGTTATAC
1 ATTTTCATTTATGGCATCCTTTCCTGCCAATTATGCACTGTTATAC
256214 ATTTTCATTTATGGCATCCTTTCCTGCCAATTATGCACTGTT
1 ATTTTCATTTATGGCATCCTTTCCTGCCAATTATGCACTGTT
256256 CTTCATCTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.19, C:0.22, G:0.12, T:0.47
Consensus pattern (46 bp):
ATTTTCATTTATGGCATCCTTTCCTGCCAATTATGCACTGTTATAC
Found at i:256534 original size:54 final size:55
Alignment explanation
Indices: 256476--256802 Score: 212
Period size: 55 Copynumber: 6.0 Consensus size: 55
256466 AGTCTATAGT
* * * *
256476 TTGCACACATAGTATCAATACGGTAATTCACAAACTTATTAT-AATTTATGT-GGG
1 TTGCACACAAAGTAACAATACGGAAATTCATAAACTTATTATGAATTTAT-TAGGG
* * * * **
256530 TTGCACATC-CACTAACAATACGGAAATTCATAAACTTATTTTGAATTTCTTAGTT
1 TTGCACA-CAAAGTAACAATACGGAAATTCATAAACTTATTATGAATTTATTAGGG
** * * * ***
256585 TTGCACACAAAGTGCCCATACGGGAATTCATAAACTTATTATGAATTTGTTAACT
1 TTGCACACAAAGTAACAATACGGAAATTCATAAACTTATTATGAATTTATTAGGG
** * * * **
256640 TTGCACACAAAGTGCCCATACGAAAATTCA-ATAACTTATTATGAATTTCTTAGTT
1 TTGCACACAAAGTAACAATACGGAAATTCATA-AACTTATTATGAATTTATTAGGG
** * ** * **
256695 TTGCACACAAAGTGCCCATACATAAATTCATAAACTTATTATGAATTTGTTAGTT
1 TTGCACACAAAGTAACAATACGGAAATTCATAAACTTATTATGAATTTATTAGGG
* ** ** * ** * *
256750 TTACACTTAAAGTGCCCATACAAAAATTCATAAACTAATTATGAATTTCTTAG
1 TTGCACACAAAGTAACAATACGGAAATTCATAAACTTATTATGAATTTATTAG
256803 TTTTGCACGC
Statistics
Matches: 234, Mismatches: 33, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
54 37 0.16
55 196 0.84
56 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.35
Consensus pattern (55 bp):
TTGCACACAAAGTAACAATACGGAAATTCATAAACTTATTATGAATTTATTAGGG
Found at i:256606 original size:55 final size:55
Alignment explanation
Indices: 256547--256820 Score: 381
Period size: 55 Copynumber: 5.0 Consensus size: 55
256537 TCCACTAACA
* *
256547 ATACGGAAATTCATAAACTTATTTTGAATTTCTTAGTTTTGCACACAAAGTGCCC
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
** * **
256602 ATACGGGAATTCATAAACTTATTATGAATTTGTTAACTTTGCACACAAAGTGCCC
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
256657 ATACGAAAATTCA-ATAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
1 ATACGAAAATTCATA-AACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
* * **
256712 ATAC-ATAAATTCATAAACTTATTATGAATTTGTTAGTTTTACACTTAAAGTGCCC
1 ATACGA-AAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
* * * *
256767 ATACAAAAATTCATAAACTAATTATGAATTTCTTAGTTTTGCACGCATAGTGCC
1 ATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCC
256821 ATTTGGAAAT
Statistics
Matches: 195, Mismatches: 20, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
54 2 0.01
55 191 0.98
56 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (55 bp):
ATACGAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
Found at i:256614 original size:109 final size:110
Alignment explanation
Indices: 256475--256820 Score: 310
Period size: 110 Copynumber: 3.2 Consensus size: 110
256465 AAGTCTATAG
* ** * * * **
256475 TTTGCACACATAGTATCAATACGGTAATTCACAAACTTATTAT-AATTTATGT-GGGTTGCACAT
1 TTTGCACACAAAGTGCCCATACGGAAATTCATAAACTTATTATGAATTTAT-TAACGTTGCACA-
* * *
256538 C-CACTAACAATACGGAAATTC-ATAAACTTATTTTGAATTTCTTAGT
64 CAAACTAACAATACGAAAATTCAAT-AACTTATTATGAATTTCTTAGT
* * *
256584 TTTGCACACAAAGTGCCCATACGGGAATTCATAAACTTATTATGAATTTGTTAACTTTGCACACA
1 TTTGCACACAAAGTGCCCATACGGAAATTCATAAACTTATTATGAATTTATTAACGTTGCACACA
* ** *
256649 AAGTGCCCATACGAAAATTCAATAACTTATTATGAATTTCTTAGT
66 AACTAACAATACGAAAATTCAATAACTTATTATGAATTTCTTAGT
** * **
256694 TTTGCACACAAAGTGCCCATACATAAATTCATAAACTTATTATGAATTTGTT-A-GTTTTACACT
1 TTTGCACACAAAGTGCCCATACGGAAATTCATAAACTTATTATGAATTTATTAACGTTGCACAC-
* ** * * *
256757 TAAAGTGCCCATACAAAAATTC-ATAAACTAATTATGAATTTCTTAGT
65 -AAACTAACAATACGAAAATTCAAT-AACTTATTATGAATTTCTTAGT
* *
256804 TTTGCACGCATAGTGCC
1 TTTGCACACAAAGTGCC
256821 ATTTGGAAAT
Statistics
Matches: 203, Mismatches: 27, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
108 6 0.03
109 42 0.21
110 153 0.75
111 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (110 bp):
TTTGCACACAAAGTGCCCATACGGAAATTCATAAACTTATTATGAATTTATTAACGTTGCACACA
AACTAACAATACGAAAATTCAATAACTTATTATGAATTTCTTAGT
Found at i:274990 original size:18 final size:17
Alignment explanation
Indices: 274962--275032 Score: 72
Period size: 18 Copynumber: 4.1 Consensus size: 17
274952 ACAATAGTAT
* *
274962 TACACGCTTAACTGAAG
1 TACATGCTTAAATGAAG
*
274979 TAGCATGCTTAAATG-AC
1 TA-CATGCTTAAATGAAG
274996 TACATGCTTAAATGAAG
1 TACATGCTTAAATGAAG
* *
275013 TAAATGCTTTAGATGAAG
1 TACATGC-TTAAATGAAG
275031 TA
1 TA
275033 GCATACTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
16 12 0.27
17 12 0.27
18 21 0.47
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (17 bp):
TACATGCTTAAATGAAG
Found at i:276386 original size:50 final size:50
Alignment explanation
Indices: 276332--276428 Score: 149
Period size: 50 Copynumber: 1.9 Consensus size: 50
276322 ACTCACTGAC
* *
276332 GTGGTGGTAGTTGGCATCAATGGAGTGGTGGAACATTTATGGTTGGACGA
1 GTGGTGGTAGTTGGAATCAATGAAGTGGTGGAACATTTATGGTTGGACGA
* * *
276382 GTGGTGGTAGTTGGAATCAGTGAAGTTGTGGTACATTTATGGTTGGA
1 GTGGTGGTAGTTGGAATCAATGAAGTGGTGGAACATTTATGGTTGGA
276429 GGATGTCAGA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.22, C:0.06, G:0.39, T:0.33
Consensus pattern (50 bp):
GTGGTGGTAGTTGGAATCAATGAAGTGGTGGAACATTTATGGTTGGACGA
Found at i:284772 original size:17 final size:18
Alignment explanation
Indices: 284746--284793 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 18
284736 ATTAGGTTAC
*
284746 AGTAAGAAT-AATATTGT
1 AGTAACAATAAATATTGT
284763 AGTAACAATAAAATATTGT
1 AGTAACAAT-AAATATTGT
* *
284782 AGCAATAATAAA
1 AGTAACAATAAA
284794 CAATATAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 8 0.31
18 3 0.12
19 15 0.58
ACGTcount: A:0.54, C:0.04, G:0.12, T:0.29
Consensus pattern (18 bp):
AGTAACAATAAATATTGT
Found at i:284779 original size:19 final size:19
Alignment explanation
Indices: 284755--284793 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
284745 CAGTAAGAAT
*
284755 AATATTGTAGTAACAATAA
1 AATATTGTAGCAACAATAA
*
284774 AATATTGTAGCAATAATAA
1 AATATTGTAGCAACAATAA
284793 A
1 A
284794 CAATATAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.54, C:0.05, G:0.10, T:0.31
Consensus pattern (19 bp):
AATATTGTAGCAACAATAA
Done.