Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 85040211
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: 85040211
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 163 of 292
Found at i:48550097 original size:19 final size:20
Alignment explanation
Indices: 48550073--48550115 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
48550063 GGTCCTTTCG
* *
48550073 TGAAATTTAATGCATATG-A
1 TGAAATGTAATGCAAATGAA
48550092 TGAAATGTAATGCAAATGAA
1 TGAAATGTAATGCAAATGAA
48550112 TGAA
1 TGAA
48550116 TGCAAAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.47, C:0.05, G:0.19, T:0.30
Consensus pattern (20 bp):
TGAAATGTAATGCAAATGAA
Found at i:48554260 original size:25 final size:25
Alignment explanation
Indices: 48554180--48554264 Score: 70
Period size: 27 Copynumber: 3.4 Consensus size: 25
48554170 TAATATATAT
* *
48554180 AATTTTAAAGTAAATAA--TAAAAC
1 AATTTTAAAATAAATAATGTAAAAG
*
48554203 AA-TTTAAAATGAAA-AATGCATAAAG
1 AATTTTAAAAT-AAATAATGTA-AAAG
* *
48554228 CGAGTTTAAAATAAATAATGTAAAAG
1 -AATTTTAAAATAAATAATGTAAAAG
48554254 AATTTTAAAAT
1 AATTTTAAAAT
48554265 CTATATTACA
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
22 9 0.19
23 5 0.10
24 1 0.02
25 12 0.25
26 8 0.17
27 13 0.27
ACGTcount: A:0.58, C:0.04, G:0.09, T:0.29
Consensus pattern (25 bp):
AATTTTAAAATAAATAATGTAAAAG
Found at i:48554573 original size:17 final size:17
Alignment explanation
Indices: 48554551--48554588 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
48554541 TGAAATACAT
*
48554551 AATATACAATAACTTAA
1 AATATAAAATAACTTAA
*
48554568 AATATAAAATAATTTAA
1 AATATAAAATAACTTAA
48554585 AATA
1 AATA
48554589 AATATATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (17 bp):
AATATAAAATAACTTAA
Found at i:48554620 original size:21 final size:20
Alignment explanation
Indices: 48554567--48554620 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
48554557 CAATAACTTA
*
48554567 AAATATAAAATAATTTAAAAT
1 AAATAT-AAATAATTTAAAAG
*
48554588 AAATATATAATAATTTTTAAAG
1 AAATATA-AATAA-TTTAAAAG
*
48554610 AATTATAAATA
1 AAATATAAATA
48554621 TCTAAAAAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 1 0.04
21 15 0.54
22 12 0.43
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAATATAAATAATTTAAAAG
Found at i:48560660 original size:2 final size:2
Alignment explanation
Indices: 48560655--48560682 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
48560645 ATTTTAATAC
48560655 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
48560683 CTATGTAATA
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:48564063 original size:12 final size:13
Alignment explanation
Indices: 48564041--48564073 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
48564031 TTATTTTCGT
*
48564041 TTTTGTTTATTTA
1 TTTTATTTATTTA
48564054 -TTTATTTATTTA
1 TTTTATTTATTTA
48564066 TTTTATTT
1 TTTTATTT
48564074 CCTTTTGAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (13 bp):
TTTTATTTATTTA
Found at i:48564748 original size:3 final size:3
Alignment explanation
Indices: 48564729--48565218 Score: 171
Period size: 3 Copynumber: 161.7 Consensus size: 3
48564719 TTATTTTCAA
* *
48564729 ATT ACTT ATT TTT ATT ATT ATT -TT ATGT -TGT -TT ATT ATT ACT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT AT-T AT-T ATT ATT ATT ATT ATT
*
48564774 AATT ATA ATT -TCT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 -ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
48564819 ATT ATT ATT ATT ATAT AGT AGTGG ATGT -TT ATT -TAT ATAT ATAT ATGT
1 ATT ATT ATT ATT AT-T ATT A-T-T AT-T ATT ATT AT-T AT-T AT-T AT-T
* * * **
48564867 A-T ATAT AGT ATT ATT TTT AATT ACT -TT ATT -TT AAC ATT ATT ATT
1 ATT AT-T ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * *
48564911 A-T GTT A-T ATTT ACTT -TT -TGT ATT -TC AAT ATT ATT ACT ATT ATT
1 ATT ATT ATT A-TT A-TT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT
* * * *
48564954 ATT ATT ATT ATT AAT ATT AGTGC A-T ATT ATT TTT ATT GTAT ATGT ATGT
1 ATT ATT ATT ATT ATT ATT A-T-T ATT ATT ATT ATT ATT AT-T AT-T AT-T
* * *
48565003 A-T ATGT A-T ACAT ATT -TAT ATAT AGT ATT ATT -TT -TT ATT ACT -TT
1 ATT AT-T ATT A-TT ATT AT-T AT-T ATT ATT ATT ATT ATT ATT ATT ATT
*
48565046 ATT -TT GA-T ATT TTT ATT A-T ATT A-T ATAT ACTT -TT -TGT ATT -TT
1 ATT ATT -ATT ATT ATT ATT ATT ATT ATT AT-T A-TT ATT AT-T ATT ATT
* * * * *
48565088 AAT ATT ATT ACT ATT ATC ATC A-T ATT ATT ATT ACCTT -TT -TT ACT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A--TT ATT ATT ATT
*
48565132 ATCCA ATGT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATTT ATT
1 AT--T AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT
48565181 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
48565219 ATTTTCCTTT
Statistics
Matches: 376, Mismatches: 57, Indels: 108
0.70 0.11 0.20
Matches are distributed among these distances:
2 48 0.13
3 264 0.70
4 57 0.15
5 7 0.02
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:48565077 original size:152 final size:149
Alignment explanation
Indices: 48564781--48565120 Score: 423
Period size: 152 Copynumber: 2.2 Consensus size: 149
48564771 ATTAATTATA
* * *
48564781 ATTTCTATATTATTATTATTATTATTATTATTATTATTATTATTATTATTATATAGTAGTGGATG
1 ATTTCAATATTATTACTATTATTATTATTATTATTAATATTATTATTATTATATAGTAGT-GATG
* * *
48564846 TTTATTTATATATATATATGTATATATAGTATTATTTTTAATTACTTTATTTTAACATTATTATT
65 TATATATATATATACATATGTATATATAGTATTATTTTTAATTACTTTATTTTAACATTATTATT
* *
48564911 ATGTTATATTTACTTTTTGT
130 ATATTATATATACTTTTTGT
* *
48564931 ATTTCAATATTATTACTATTATTATTATTATTATTAATATTAGTGCATATTATTTTTATTGTA-T
1 ATTTCAATATTATTACTATTATTATTATTATTATTAATATTA-T---TATTA-TTATATAGTAGT
* * * * * * *
48564995 -ATGTATGTATATGTATACATATTTATATATAGTATTATTTTTTATTACTTTATTTTGATATTTT
61 GATGTATATATATATATACATATGTATATATAGTATTATTTTTAATTACTTTATTTTAACATTAT
48565059 TATTATATTATATATACTTTTTGT
126 TATTATATTATATATACTTTTTGT
* *
48565083 ATTTTAATATTATTACTATTATCATCATATTATTATTA
1 ATTTCAATATTATTACTATTATTAT--TATTATTATTA
48565121 CCTTTTTTAC
Statistics
Matches: 164, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
150 39 0.24
151 1 0.01
152 99 0.60
154 17 0.10
155 8 0.05
ACGTcount: A:0.32, C:0.04, G:0.05, T:0.59
Consensus pattern (149 bp):
ATTTCAATATTATTACTATTATTATTATTATTATTAATATTATTATTATTATATAGTAGTGATGT
ATATATATATATACATATGTATATATAGTATTATTTTTAATTACTTTATTTTAACATTATTATTA
TATTATATATACTTTTTGT
Found at i:48565401 original size:22 final size:22
Alignment explanation
Indices: 48565380--48565428 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
48565370 CTTAGATTAT
*
48565380 TTATTATTTGT-CTTATCGTTA
1 TTATTATTTGTACTTACCGTTA
* *
48565401 TTACTATTTGTATTTACCGTTA
1 TTATTATTTGTACTTACCGTTA
48565423 TTATTA
1 TTATTA
48565429 CTATTATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.22, C:0.10, G:0.08, T:0.59
Consensus pattern (22 bp):
TTATTATTTGTACTTACCGTTA
Found at i:48565428 original size:3 final size:3
Alignment explanation
Indices: 48565420--48565622 Score: 139
Period size: 3 Copynumber: 68.0 Consensus size: 3
48565410 GTATTTACCG
* * *
48565420 TTA TTA TTA CTA TTA TTT TTA CTT- TTA TTA CTA TTA TTA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA -TTA
* * * * * *
48565466 TTA TTA CTA TTA TTA TCA CTA TT- TTT TTA TT- TTT TTA TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * ** * * * ** *
48565512 TCA TT- TTA -AA ACA TTG TTA CTA TTA TTC TT- TTA CCA TTTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
*
48565555 CGTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA
1 -TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
48565602 TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
48565623 GTGTATGTTT
Statistics
Matches: 155, Mismatches: 34, Indels: 22
0.73 0.16 0.10
Matches are distributed among these distances:
2 11 0.07
3 133 0.86
4 11 0.07
ACGTcount: A:0.30, C:0.07, G:0.01, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:48565487 original size:34 final size:34
Alignment explanation
Indices: 48565444--48565512 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 34
48565434 ATTTTTACTT
*
48565444 TTATTACTATTATTATTA-TTTATTATTACTATTA
1 TTATCACTATT-TTATTATTTTATTATTACTATTA
* *
48565478 TTATCACTATTTTTTTATTTTTTTATTACTATTA
1 TTATCACTATTTTATTATTTTATTATTACTATTA
48565512 T
1 T
48565513 CATTTTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
33 5 0.16
34 26 0.84
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (34 bp):
TTATCACTATTTTATTATTTTATTATTACTATTA
Found at i:48565654 original size:12 final size:12
Alignment explanation
Indices: 48565637--48565670 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
48565627 ATGTTTCTAT
*
48565637 TATACATGTATA
1 TATACATATATA
*
48565649 TATACATATATT
1 TATACATATATA
48565661 TATACATATA
1 TATACATATA
48565671 GTATTATTTT
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:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (12 bp):
TATACATATATA
Found at i:48577893 original size:14 final size:13
Alignment explanation
Indices: 48577858--48577889 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
48577848 CATGCCGAGA
48577858 TATTTTCAATTTC
1 TATTTTCAATTTC
48577871 TATTTTCAATTTC
1 TATTTTCAATTTC
*
48577884 TGTTTT
1 TATTTT
48577890 TCAAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.19, C:0.12, G:0.03, T:0.66
Consensus pattern (13 bp):
TATTTTCAATTTC
Found at i:48577964 original size:90 final size:90
Alignment explanation
Indices: 48577789--48577966 Score: 241
Period size: 90 Copynumber: 2.0 Consensus size: 90
48577779 TGATATTTTT
* * * *
48577789 ATTTCTGTTTTTCAAAAAAATCAACTTATGTTGCGAGAGGTGAGTTGAGCCTCGGGACACATGCC
1 ATTTCTGTTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGACACACGCC
*
48577854 GAGATATTTTCAATTTCTATTTTCA
66 GAGATATTTTCAATTCCTATTTTCA
* * * *
48577879 ATTTCTGTTTTTCAAAAAAATCAACTCATATTATGAGAGGTGAGTTGAGCCTTGGGTCACACGCT
1 ATTTCTGTTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGACACACGCC
* *
48577944 GAGGTATCTTT-AGTTCCTATTTT
66 GAGATAT-TTTCAATTCCTATTTT
48577967 TCAAAAAATC
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
90 73 0.96
91 3 0.04
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (90 bp):
ATTTCTGTTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGACACACGCC
GAGATATTTTCAATTCCTATTTTCA
Found at i:48578082 original size:77 final size:77
Alignment explanation
Indices: 48577871--48578084 Score: 306
Period size: 76 Copynumber: 2.8 Consensus size: 77
48577861 TTTCAATTTC
* * *
48577871 TATTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTATGAGAGGTGAGTTGAGCCTTGGGT
1 TATTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGA
*
48577936 CACACGCTGAGG
66 CACAAGCTGAGG
* * * *
48577948 TATCTTT-AGTTCCTATTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
1 TAT-TTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGG
48578011 ACACAAGCTGAGG
65 ACACAAGCTGAGG
* * *
48578024 TATTTTCAATTTTTGTTTTTCAAAAAAATCAACTCATATTGTGAAAGTTGAGTTGAGCCTC
1 TATTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTC
48578085 AGGTCATACG
Statistics
Matches: 119, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
75 3 0.03
76 63 0.53
77 50 0.42
78 3 0.03
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (77 bp):
TATTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGA
CACAAGCTGAGG
Found at i:48578098 original size:77 final size:77
Alignment explanation
Indices: 48577871--48578106 Score: 323
Period size: 77 Copynumber: 3.1 Consensus size: 77
48577861 TTTCAATTTC
* *
48577871 TATTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTATGAGAGGTGAGTTGAGCCTTGGGT
1 TATTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGT
48577936 CACACGCTGAGG
66 CACACGCTGAGG
* * * *
48577948 TATCTTT-AGTTCCTATTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG
1 TAT-TTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGG
* *
48578011 ACACAAGCTGAGG
65 TCACACGCTGAGG
* * * *
48578024 TATTTTCAATTTTTGTTTTTCAAAAAAATCAACTCATATTGTGAAAGTTGAGTTGAGCCTCAGGT
1 TATTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGT
* *
48578089 CATACGCTGAGT
66 CACACGCTGAGG
48578101 TATTTT
1 TATTTT
48578107 TAGTTTCTAT
Statistics
Matches: 136, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
75 3 0.02
76 63 0.46
77 67 0.49
78 3 0.02
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (77 bp):
TATTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGT
CACACGCTGAGG
Found at i:48578246 original size:141 final size:140
Alignment explanation
Indices: 48577978--48578247 Score: 294
Period size: 141 Copynumber: 1.9 Consensus size: 140
48577968 CAAAAAATCA
* * *
48577978 ACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACAAGCTGAGGTATTTTCAATTTTTGTTTT
1 ACTCATATTACGAGAGGTGAGTTGAACCTCAGGACACAAGCTGAGGTATTTTCAATTTTTGTTTT
*** * * * *
48578043 TCAAAAAAATCAACTCATATTGTGAAAGTTGAGTTGAGCCTCAGGTCATACGCTGAGTTATTTTT
66 TC-AAAAAATCAACTCATATACCGAAAGATGAGTTGAACCTCAGGTCATACGCCGAGCTATTTTT
48578108 AGTTTCTATCT
130 AGTTTCTATCT
* * *
48578119 ACTCATATTACGAGAGGTGAGTTGAACTTCAGGTCACACA-CTGAGGTATTTTCAATTTTTTAAT
1 ACTCATATTACGAGAGGTGAGTTGAACCTCAGGACACA-AGCTGAGGTATTTTCAA-TTTTT--G
* * * * ** *
48578183 TTTTTC-AAAAATTAACTCATA-ACCGATAGATGAGTTGAACGTCAGTTTGTATGCCGAGCTATT
62 TTTTTCAAAAAATCAACTCATATACCGAAAGATGAGTTGAACCTCAGGTCATACGCCGAGCTATT
48578246 TT
127 TT
48578248 CGATGTTTGT
Statistics
Matches: 105, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
141 79 0.75
142 20 0.19
144 6 0.06
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.36
Consensus pattern (140 bp):
ACTCATATTACGAGAGGTGAGTTGAACCTCAGGACACAAGCTGAGGTATTTTCAATTTTTGTTTT
TCAAAAAATCAACTCATATACCGAAAGATGAGTTGAACCTCAGGTCATACGCCGAGCTATTTTTA
GTTTCTATCT
Found at i:48579344 original size:13 final size:15
Alignment explanation
Indices: 48579312--48579353 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
48579302 AAAAGGTTTA
*
48579312 TTTATTTTCGTTTTTG
1 TTTATTTT-ATTTTTG
48579328 TTTA-TTTATTTTT-
1 TTTATTTTATTTTTG
48579341 TTTATTTTATTTT
1 TTTATTTTATTTT
48579354 ATTTCCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 4 0.17
14 13 0.54
15 3 0.12
16 4 0.17
ACGTcount: A:0.12, C:0.02, G:0.05, T:0.81
Consensus pattern (15 bp):
TTTATTTTATTTTTG
Found at i:48579348 original size:23 final size:24
Alignment explanation
Indices: 48579308--48579357 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
48579298 TGATAAAAGG
*
48579308 TTTATTTATTTTCGTTTT-TGTTTA
1 TTTATTTATTTTCATTTTAT-TTTA
*
48579332 TTTATTT-TTTTTATTTTATTTTA
1 TTTATTTATTTTCATTTTATTTTA
48579355 TTT
1 TTT
48579358 CCTTTTGAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.14, C:0.02, G:0.04, T:0.80
Consensus pattern (24 bp):
TTTATTTATTTTCATTTTATTTTA
Found at i:48579426 original size:2 final size:2
Alignment explanation
Indices: 48579421--48579453 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
48579411 AAAACTACAA
48579421 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
48579454 CCTTTGGCGA
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:48580182 original size:2 final size:2
Alignment explanation
Indices: 48580177--48580206 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
48580167 AGTGTATGTT
*
48580177 TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
48580207 GTATTATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:48580394 original size:3 final size:3
Alignment explanation
Indices: 48580034--48580374 Score: 307
Period size: 3 Copynumber: 112.3 Consensus size: 3
48580024 TTATTTTCAA
* *
48580034 ATT ACTT ATT TTT ATT ATT ATT -TT ATGT -TGT -TT ATT ATT ACT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT AT-T AT-T ATT ATT ATT ATT ATT
*
48580079 AATT ATA ATT -TCT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 -ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
48580124 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATAT AGT AGTGT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT A-T-T
* *
48580172 ATGT -TT A-T ATAT ATAT ATAT ATAT ATGT A-T ATAT AGT ATT ATT TTT
1 AT-T ATT ATT AT-T AT-T AT-T AT-T AT-T ATT AT-T ATT ATT ATT ATT
* ** *
48580218 AATT ACT -TT ATT -TT AAC ATT ATT ATT A-T GTT A-T ATTT ACTT -TT
1 -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT A-TT ATT
*
48580261 -TGT ATT -TC ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
48580305 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
48580353 ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT A
48580375 GTGCATATTA
Statistics
Matches: 289, Mismatches: 24, Indels: 50
0.80 0.07 0.14
Matches are distributed among these distances:
2 21 0.07
3 228 0.79
4 38 0.13
5 2 0.01
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:48580554 original size:12 final size:12
Alignment explanation
Indices: 48580537--48580570 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
48580527 ATGTTTCTAT
*
48580537 TATACATGTATA
1 TATACATATATA
*
48580549 TATACATATATT
1 TATACATATATA
48580561 TATACATATA
1 TATACATATA
48580571 GTATTATTTT
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:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (12 bp):
TATACATATATA
Found at i:48585007 original size:26 final size:26
Alignment explanation
Indices: 48584971--48585080 Score: 177
Period size: 26 Copynumber: 4.2 Consensus size: 26
48584961 TGATACAAAT
48584971 TGATAATAGGTTAGGTAAATG-TTCAA
1 TGATAATAGGTTAGGTAAATGTTTC-A
*
48584997 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
48585023 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
48585049 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
48585075 TGATAA
1 TGATAA
48585081 GAATTTCATG
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
26 78 0.98
27 2 0.03
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:48586762 original size:27 final size:27
Alignment explanation
Indices: 48586695--48586810 Score: 128
Period size: 27 Copynumber: 4.3 Consensus size: 27
48586685 ATGGAGGAAG
* * *
48586695 TGTTCTGGTGGCTATACCACAAATATC
1 TGTTCTGGTGGCTCTGCCACATATATC
*
48586722 TGATCTGGTGGCTCTGCCACATATATC
1 TGTTCTGGTGGCTCTGCCACATATATC
48586749 TGTTCTGGTGGCTCTGCCACGAT-TATC
1 TGTTCTGGTGGCTCTGCCAC-ATATATC
* * * *
48586776 TATATCTGGTGACTCTGTCACA-CTATC
1 TGT-TCTGGTGGCTCTGCCACATATATC
48586803 TGTTCTGG
1 TGTTCTGG
48586811 CAGCCATGCT
Statistics
Matches: 77, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
26 5 0.06
27 55 0.71
28 17 0.22
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (27 bp):
TGTTCTGGTGGCTCTGCCACATATATC
Found at i:48586803 original size:54 final size:54
Alignment explanation
Indices: 48586695--48586810 Score: 144
Period size: 54 Copynumber: 2.1 Consensus size: 54
48586685 ATGGAGGAAG
*
48586695 TGTTCTGGTGGCTATACCACAAATATCTGATCTGGTGGCTCTGCCACATATATC
1 TGTTCTGGTGGCTATACCACAAATATCTGATCTGGTGACTCTGCCACATATATC
* * * * * * *
48586749 TGTTCTGGTGGCTCTGCCACGATTATCTATATCTGGTGACTCTGTCACA-CTATC
1 TGTTCTGGTGGCTATACCACAAATATCT-GATCTGGTGACTCTGCCACATATATC
48586803 TGTTCTGG
1 TGTTCTGG
48586811 CAGCCATGCT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
54 36 0.68
55 17 0.32
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (54 bp):
TGTTCTGGTGGCTATACCACAAATATCTGATCTGGTGACTCTGCCACATATATC
Found at i:48588873 original size:14 final size:14
Alignment explanation
Indices: 48588854--48588883 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
48588844 TGCCTGGCCC
48588854 AACACAAATAAATA
1 AACACAAATAAATA
48588868 AACACAAATAAATA
1 AACACAAATAAATA
48588882 AA
1 AA
48588884 ATAAAATCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.73, C:0.13, G:0.00, T:0.13
Consensus pattern (14 bp):
AACACAAATAAATA
Found at i:48589734 original size:30 final size:30
Alignment explanation
Indices: 48589694--48589752 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
48589684 GTCTGAGAGA
*
48589694 AAAAAAAAGGGAGAAAAGAAGTTTTTTTTTT
1 AAAAAAAGGGGAGAAAAGAA-TTTTTTTTTT
* * *
48589725 AAAACAAGGGGTGAAATGAATTTTTTTT
1 AAAAAAAGGGGAGAAAAGAATTTTTTTT
48589753 AGAAAATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 8 0.33
31 16 0.67
ACGTcount: A:0.44, C:0.02, G:0.20, T:0.34
Consensus pattern (30 bp):
AAAAAAAGGGGAGAAAAGAATTTTTTTTTT
Found at i:48590018 original size:7 final size:7
Alignment explanation
Indices: 48590006--48590031 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
48589996 TCATTTTGGT
48590006 CCATTGA
1 CCATTGA
48590013 CCATTGA
1 CCATTGA
48590020 CCATTGA
1 CCATTGA
48590027 CCATT
1 CCATT
48590032 TTTAGAACTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.31, G:0.12, T:0.31
Consensus pattern (7 bp):
CCATTGA
Found at i:48590465 original size:17 final size:16
Alignment explanation
Indices: 48590413--48590466 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 16
48590403 CTTTGCATAC
48590413 TTATTATTA--TCATT
1 TTATTATTATCTCATT
*
48590427 ATTATT-TTATCTTATT
1 -TTATTATTATCTCATT
48590443 TT-TTATTATCGTCATT
1 TTATTATTATC-TCATT
48590459 TTATTATT
1 TTATTATT
48590467 TCTTTTATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
14 5 0.16
15 12 0.38
16 10 0.31
17 5 0.16
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (16 bp):
TTATTATTATCTCATT
Found at i:48590465 original size:29 final size:29
Alignment explanation
Indices: 48590413--48590478 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
48590403 CTTTGCATAC
*
48590413 TTATTATTATCATTATTATTTTATCTTATT
1 TTATTATTATCATCATTATTTTAT-TTATT
* *
48590443 TT-TTATTATCGTCATT-TTATTATTTCTT
1 TTATTATTATCATCATTATT-TTATTTATT
48590471 TTATTATT
1 TTATTATT
48590479 TCCAGCACTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
28 8 0.26
29 21 0.68
30 2 0.06
ACGTcount: A:0.23, C:0.08, G:0.02, T:0.68
Consensus pattern (29 bp):
TTATTATTATCATCATTATTTTATTTATT
Found at i:48590474 original size:12 final size:13
Alignment explanation
Indices: 48590443--48590480 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
48590433 TTATCTTATT
*
48590443 TTTTATTATCGTCA
1 TTTTATTAT-TTCA
48590457 TTTTATTATTTC-
1 TTTTATTATTTCA
48590469 TTTTATTATTTC
1 TTTTATTATTTC
48590481 CAGCACTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 12 0.52
13 2 0.09
14 9 0.39
ACGTcount: A:0.18, C:0.11, G:0.03, T:0.68
Consensus pattern (13 bp):
TTTTATTATTTCA
Found at i:48592353 original size:15 final size:15
Alignment explanation
Indices: 48592321--48592349 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
48592311 ATTTTCAGTG
48592321 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
48592336 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
48592350 ATTTTCGTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:48593646 original size:43 final size:41
Alignment explanation
Indices: 48593491--48593647 Score: 113
Period size: 43 Copynumber: 3.7 Consensus size: 41
48593481 TGTGTTCTCG
* * *
48593491 TGTAAGACCAAGTCTAGGATGTTGGCATCGGTATGTGATTTCGA
1 TGTAAGACCACGTCTGGGATGTTGGCATC-GAATGTGA-TTC-A
* * ** * *
48593535 -GTAAGACCATGTCTGGAACATTGCCATCGTAATTGTGATTCG
1 TGTAAGACCACGTCTGGGATGTTGGCATCG-AA-TGTGATTCA
*
48593577 TGTAAGACC-CTGTCTGGGACAG-TGGCATCGACATGTGATTACA
1 TGTAAGACCAC-GTCTGGGA-TGTTGGCATCGA-ATGTGATT-CA
*
48593620 TGTAAAACCACGTCTGGGATGTTGGCAT
1 TGTAAGACCACGTCTGGGATGTTGGCAT
48593648 TGTACAATAT
Statistics
Matches: 88, Mismatches: 16, Indels: 19
0.72 0.13 0.15
Matches are distributed among these distances:
42 10 0.11
43 72 0.82
44 6 0.07
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.29
Consensus pattern (41 bp):
TGTAAGACCACGTCTGGGATGTTGGCATCGAATGTGATTCA
Found at i:48598373 original size:26 final size:26
Alignment explanation
Indices: 48598342--48598449 Score: 155
Period size: 26 Copynumber: 4.2 Consensus size: 26
48598332 TGAAATTCCC
48598342 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
*
48598368 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
* *
48598394 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAAACCATT
* *
48598420 GTCAAGGAACATTTACCT-AACTCATT
1 ATCATGGAACATTTACCTAAAC-CATT
48598446 ATCA
1 ATCA
48598450 ATTTGTATCA
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
25 2 0.03
26 71 0.97
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:48598419 original size:52 final size:52
Alignment explanation
Indices: 48598342--48598449 Score: 171
Period size: 52 Copynumber: 2.1 Consensus size: 52
48598332 TGAAATTCCC
*
48598342 ATCATGGAACATTTACCTAAACCATTATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATTATCAAGGAACATTTACCTAACCCATT
* * * *
48598394 ATCATGGAATATTTACCTAATCCATTGTCAAGGAACATTTACCTAACTCATT
1 ATCATGGAACATTTACCTAAACCATTATCAAGGAACATTTACCTAACCCATT
48598446 ATCA
1 ATCA
48598450 ATTTGTATCA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.32
Consensus pattern (52 bp):
ATCATGGAACATTTACCTAAACCATTATCAAGGAACATTTACCTAACCCATT
Found at i:48610531 original size:138 final size:138
Alignment explanation
Indices: 48610300--48610699 Score: 439
Period size: 138 Copynumber: 2.9 Consensus size: 138
48610290 GGTCAGTGAA
* * *
48610300 ACAAATCCTATGCCCCTGAAGTTGCAGTGAGTCGGATTGAATTTACCATAGTGAATCTTATCTCC
1 ACAAATCCTATACCCCTGAAGTTGCAGTGGGTCGGATTGAAATTACCATAGTGAATCTTATCTCC
* * * *
48610365 CTGAAGTTGTAATAGAGTAAGATGAAGCTACAAATCCTATATCCTTAAAGTTGTAGTGGATCAAA
66 CTGAAGTTGCAGTGGAGTAAGATGAAGCTACAAATCCTATATCCTTAAAGTTGTAGTGGAGCAAA
*
48610430 CTGAAGCT
131 CTAAAGCT
* * * * * *
48610438 ACAATTTCTATACCCCTGAAGTTGCAGTGGGTTGGAATGAAATTACGATGGTGAATCTTATCTCC
1 ACAAATCCTATACCCCTGAAGTTGCAGTGGGTCGGATTGAAATTACCATAGTGAATCTTATCTCC
* * * * ** *
48610503 TTGAAGTTGCAGTGGAGTAAGATAAAGCTACGAAT--TTTATCTCTCTGTAGTTGCAGTGGAGCA
66 CTGAAGTTGCAGTGGAGTAAGATGAAGCTACAAATCCTATATC-CT-TAAAGTTGTAGTGGAGCA
*
48610566 AATTAAAGCT
129 AACTAAAGCT
* * * * * *
48610576 ATAAATCCTATACCCCTAAAGTTGTAGTAGGTCAGATTG-AATCTACCATAGCGAATCTTATCTC
1 ACAAATCCTATACCCCTGAAGTTGCAGTGGGTCGGATTGAAAT-TACCATAGTGAATCTTATCTC
* * * * *
48610640 CCTGAAGTTGCTGTGGAGCATA-TTGAAGCTACAAATCCTATACCCCTAAAGTTGTAGTGG
65 CCTGAAGTTGCAGTGGAGTA-AGATGAAGCTACAAATCCTATATCCTTAAAGTTGTAGTGG
48610700 GTCAGATTGA
Statistics
Matches: 210, Mismatches: 46, Indels: 12
0.78 0.17 0.04
Matches are distributed among these distances:
136 5 0.02
137 5 0.02
138 194 0.92
139 2 0.01
140 4 0.02
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Consensus pattern (138 bp):
ACAAATCCTATACCCCTGAAGTTGCAGTGGGTCGGATTGAAATTACCATAGTGAATCTTATCTCC
CTGAAGTTGCAGTGGAGTAAGATGAAGCTACAAATCCTATATCCTTAAAGTTGTAGTGGAGCAAA
CTAAAGCT
Found at i:48610558 original size:44 final size:44
Alignment explanation
Indices: 48610490--48610576 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 44
48610480 TTACGATGGT
*
48610490 GAATCTTATCTCCTTGAAGTTGCAGTGGAGTAAGA-TAAAGCTAC
1 GAATCTTATCTCCTTGAAGTTGCAGTGGAGCAA-ATTAAAGCTAC
* *
48610534 GAATTTTATCT-CTCTGTAGTTGCAGTGGAGCAAATTAAAGCTA
1 GAATCTTATCTCCT-TGAAGTTGCAGTGGAGCAAATTAAAGCTA
48610577 TAAATCCTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 3 0.08
44 35 0.92
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (44 bp):
GAATCTTATCTCCTTGAAGTTGCAGTGGAGCAAATTAAAGCTAC
Found at i:48610649 original size:94 final size:94
Alignment explanation
Indices: 48610533--48610839 Score: 488
Period size: 94 Copynumber: 3.3 Consensus size: 94
48610523 GATAAAGCTA
* * * * * *
48610533 CGAATTTTATCTCTCTGTAGTTGCAGTGGAGCAAATTAAAGCTATAAATCCTATACCCCTAAAGT
1 CGAATCTTATCTCCCTGAAGTTGCAGTGGAGCATATTGAAGCTACAAATCCTATACCCCTAAAGT
*
48610598 TGTAGTAGGTCAGATTGAATCTACCATAG
66 TGTAGTGGGTCAGATTGAATCTACCATAG
*
48610627 CGAATCTTATCTCCCTGAAGTTGCTGTGGAGCATATTGAAGCTACAAATCCTATACCCCTAAAGT
1 CGAATCTTATCTCCCTGAAGTTGCAGTGGAGCATATTGAAGCTACAAATCCTATACCCCTAAAGT
48610692 TGTAGTGGGTCAGATTGAATCTACCATAG
66 TGTAGTGGGTCAGATTGAATCTACCATAG
* **
48610721 CGAATATTATCTCCCTGAAGTTGTTGTGGAGCATATTGAAGCTACAAATCCTATACCCCTAAAGT
1 CGAATCTTATCTCCCTGAAGTTGCAGTGGAGCATATTGAAGCTACAAATCCTATACCCCTAAAGT
* *
48610786 TGTAGTGGGTCTGATTGAATATACCATAG
66 TGTAGTGGGTCAGATTGAATCTACCATAG
*
48610815 CGAATCTTATTTCCCTGAAGTTGCA
1 CGAATCTTATCTCCCTGAAGTTGCA
48610840 ACTGTAACAG
Statistics
Matches: 197, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
94 197 1.00
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.32
Consensus pattern (94 bp):
CGAATCTTATCTCCCTGAAGTTGCAGTGGAGCATATTGAAGCTACAAATCCTATACCCCTAAAGT
TGTAGTGGGTCAGATTGAATCTACCATAG
Found at i:48610803 original size:44 final size:44
Alignment explanation
Indices: 48610571--48610804 Score: 147
Period size: 44 Copynumber: 5.0 Consensus size: 44
48610561 GAGCAAATTA
* * *
48610571 AAGCTATAAATCCTATACCCCTAAAGTTGTAGTAGGTCAGATTG
1 AAGCTACAAATCCTATACCCCTAAAGTTGTAGTGGGTCTGATTG
* * *
48610615 AATCTACCATAGCGAATCTTAT-CTCCCTGAAGTTGCT-GTGGAG-CAT-ATTG
1 AAGCTA-C--A---AATCCTATAC-CCCTAAAGTTG-TAGTGG-GTC-TGATTG
*
48610665 AAGCTACAAATCCTATACCCCTAAAGTTGTAGTGGGTCAGATTG
1 AAGCTACAAATCCTATACCCCTAAAGTTGTAGTGGGTCTGATTG
* * * * * *
48610709 AATCTACCATAGCGAATATTATCTCCCTGAAGTTGTTGTGGAG-CAT-ATTG
1 AAGCTA-CAAATC--CTA-TA-C-CCCTAAAGTTGTAGTGG-GTC-TGATTG
48610759 AAGCTACAAATCCTATACCCCTAAAGTTGTAGTGGGTCTGATTG
1 AAGCTACAAATCCTATACCCCTAAAGTTGTAGTGGGTCTGATTG
48610803 AA
1 AA
48610805 TATACCATAG
Statistics
Matches: 143, Mismatches: 23, Indels: 48
0.67 0.11 0.22
Matches are distributed among these distances:
43 4 0.03
44 58 0.41
45 6 0.04
46 2 0.01
47 6 0.04
48 2 0.01
49 7 0.05
50 55 0.38
51 3 0.02
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (44 bp):
AAGCTACAAATCCTATACCCCTAAAGTTGTAGTGGGTCTGATTG
Found at i:48613040 original size:21 final size:21
Alignment explanation
Indices: 48613015--48613079 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
48613005 TAGCCTCCGG
48613015 GCTTCCGTTTAGCACTTATGT
1 GCTTCCGTTTAGCACTTATGT
* * *
48613036 GCTTCAG-TTAGC-CTT-CGG
1 GCTTCCGTTTAGCACTTATGT
48613054 GCTGT-CGTTTAGCACTTATGT
1 GCT-TCCGTTTAGCACTTATGT
48613075 GCTTC
1 GCTTC
48613080 AGCTAGATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
18 5 0.15
19 9 0.27
20 9 0.27
21 10 0.30
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.40
Consensus pattern (21 bp):
GCTTCCGTTTAGCACTTATGT
Found at i:48613043 original size:39 final size:39
Alignment explanation
Indices: 48612997--48613081 Score: 145
Period size: 39 Copynumber: 2.2 Consensus size: 39
48612987 GCTCTGATGA
48612997 GCTTCAGTTAGCCTCCGGGCT-TCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTCCGGGCTGT-CGTTTAGCACTTATGT
*
48613036 GCTTCAGTTAGCCTTCGGGCTGTCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTCCGGGCTGTCGTTTAGCACTTATGT
48613075 GCTTCAG
1 GCTTCAG
48613082 CTAGATTTCG
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
39 43 0.98
40 1 0.02
ACGTcount: A:0.13, C:0.26, G:0.25, T:0.36
Consensus pattern (39 bp):
GCTTCAGTTAGCCTCCGGGCTGTCGTTTAGCACTTATGT
Found at i:48613092 original size:39 final size:39
Alignment explanation
Indices: 48612997--48613093 Score: 124
Period size: 39 Copynumber: 2.5 Consensus size: 39
48612987 GCTCTGATGA
* * *
48612997 GCTTCAGTTAGCCTCCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGCTAGACTTCGGGCTTCCGTTTAGCACTTATGT
* *
48613036 GCTTCAGTTAGCCTTCGGGCTGT-CGTTTAGCACTTATGT
1 GCTTCAGCTAGACTTCGGGCT-TCCGTTTAGCACTTATGT
*
48613075 GCTTCAGCTAGATTTCGGG
1 GCTTCAGCTAGACTTCGGG
48613094 ATTCAGATCA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
39 52 0.98
40 1 0.02
ACGTcount: A:0.13, C:0.25, G:0.26, T:0.36
Consensus pattern (39 bp):
GCTTCAGCTAGACTTCGGGCTTCCGTTTAGCACTTATGT
Found at i:48615644 original size:15 final size:14
Alignment explanation
Indices: 48615625--48615693 Score: 65
Period size: 14 Copynumber: 5.0 Consensus size: 14
48615615 TCTTTGCATA
48615625 CTTATTATTATTAT
1 CTTATTATTATTAT
48615639 CATTATTA-TATTAT
1 C-TTATTATTATTAT
*
48615653 CTTATTTTTTATTAT
1 CTTA-TTATTATTAT
48615668 CGTTATT-TTATTAT
1 C-TTATTATTATTAT
*
48615682 -TTCTT-TTATTAT
1 CTTATTATTATTAT
48615694 TTTCAGCATT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
12 11 0.22
13 3 0.06
14 17 0.35
15 15 0.31
16 3 0.06
ACGTcount: A:0.25, C:0.07, G:0.01, T:0.67
Consensus pattern (14 bp):
CTTATTATTATTAT
Found at i:48615666 original size:29 final size:29
Alignment explanation
Indices: 48615629--48615694 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
48615619 TGCATACTTA
48615629 TTATTATTATCATTATTATATTATCTTATT
1 TTATTATTATCATTATTATATTAT-TTATT
* * *
48615659 TT-TTATTATCGTTATTTTATTATTTCTT
1 TTATTATTATCATTATTATATTATTTATT
48615687 TTATTATT
1 TTATTATT
48615695 TTCAGCATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 6 0.19
29 24 0.75
30 2 0.06
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.68
Consensus pattern (29 bp):
TTATTATTATCATTATTATATTATTTATT
Found at i:48615682 original size:17 final size:16
Alignment explanation
Indices: 48615629--48615686 Score: 63
Period size: 15 Copynumber: 3.8 Consensus size: 16
48615619 TGCATACTTA
48615629 TTATTATTATC--ATT
1 TTATTATTATCTTATT
48615643 ATTA-TATTATCTTATT
1 -TTATTATTATCTTATT
48615659 TT-TTATTATCGTTATT
1 TTATTATTATC-TTATT
48615675 TTATTATT-TCTT
1 TTATTATTATCTT
48615687 TTATTATTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 7 0.18
15 14 0.37
16 12 0.32
17 5 0.13
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (16 bp):
TTATTATTATCTTATT
Found at i:48620050 original size:2 final size:2
Alignment explanation
Indices: 48620043--48620068 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
48620033 GAAAAAGATA
48620043 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
48620069 GCAGCAATGA
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:48626200 original size:131 final size:132
Alignment explanation
Indices: 48625880--48626389 Score: 595
Period size: 132 Copynumber: 3.9 Consensus size: 132
48625870 TTTAGAGAGT
* * * *
48625880 ATGAATGAAATTCT-AAAGGAATCTTCGATCATTTTG-GACAAAC-AGGAAATCGCAACCCAGCA
1 ATGAGTGAAATTCTAAAAGG-ACCTTCGATTATTTTGAG-CAAACGA-GAAATTGCAACCCAGCA
* * * * * ** * *
48625942 CGATAGGGCACGATTCCCCGAATTGCCAAACATCGAATATTACCTTCGTTTTGAAGAGTTTTTAG
63 CGTTAGGGCACGATTCCGCGAATTGCCAAATATAGAACATCGCCTTCGTTTTAAAGAATTTTTAG
48626007 AAAAC
128 AAAAC
* * *
48626012 ATAAGTGAAATTC-AAAAGGGACCTTTGATTATTTTGAACAAACGAGAAATTGCAACCCAGCACG
1 ATGAGTGAAATTCTAAAA-GGACCTTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAGCACG
* *
48626076 TTAAGGCACGATTCCGCGAATTGCCAAATATAGAACATCGCCTTC-ATTTAAAGAATTTTTA-AA
65 TTAGGGCACGATTCCGCGAATTGCCAAATATAGAACATCGCCTTCGTTTTAAAGAATTTTTAGAA
*
48626139 GGAC
130 -AAC
* * * *
48626143 ATGGGTGAAATTCTAAAAGGACCTTCAATTACTTTGAGCAAACGAGAAATTGCAACCCAACACGT
1 ATGAGTGAAATTCTAAAAGGACCTTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAGCACGT
* * * *
48626208 TAGGGCACGATTCCTCGAATTGCCAAATATTGAACATCGCCTTCGTTTTAAAGGATTTTTAGAAT
66 TAGGGCACGATTCCGCGAATTGCCAAATATAGAACATCGCCTTCGTTTTAAAGAATTTTTAGAAA
48626273 AC
131 AC
* * * ** *
48626275 ATGAGTGAAATTTTGAAGGGATATTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAGCACAT
1 ATGAGTGAAATTCTAAAAGGACCTTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAGCACGT
*
48626340 TAGGGCACAATTCCGCGAATTGCCAAATATCA-AATC-TCGCCTTCGTTTTA
66 TAGGGCACGATTCCGCGAATTGCCAAATAT-AGAA-CATCGCCTTCGTTTTA
48626390 TAAAACATAT
Statistics
Matches: 323, Mismatches: 45, Indels: 20
0.83 0.12 0.05
Matches are distributed among these distances:
130 2 0.01
131 109 0.34
132 206 0.64
133 6 0.02
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.27
Consensus pattern (132 bp):
ATGAGTGAAATTCTAAAAGGACCTTCGATTATTTTGAGCAAACGAGAAATTGCAACCCAGCACGT
TAGGGCACGATTCCGCGAATTGCCAAATATAGAACATCGCCTTCGTTTTAAAGAATTTTTAGAAA
AC
Found at i:48629514 original size:30 final size:30
Alignment explanation
Indices: 48629478--48629576 Score: 144
Period size: 30 Copynumber: 3.3 Consensus size: 30
48629468 CTAGCATTTG
*
48629478 CCACCACCAACTCCACTAGCTACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
*
48629508 CCACCACAAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
* **
48629538 CCACCACCTACTCCTTTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
*
48629568 CTACCACCA
1 CCACCACCA
48629577 CTTATACTTA
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 61 1.00
ACGTcount: A:0.26, C:0.47, G:0.06, T:0.20
Consensus pattern (30 bp):
CCACCACCAACTCCACTAGCCACACTTGCT
Found at i:48629776 original size:21 final size:22
Alignment explanation
Indices: 48629751--48629803 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
48629741 CAAAGGCTAG
48629751 TTTTTGGAGAGGCTAGTTTTTT
1 TTTTTGGAGAGGCTAGTTTTTT
48629773 TTTTTGGAGAGGCTAG-TTTTT
1 TTTTTGGAGAGGCTAGTTTTTT
48629794 TTTTTGGAGA
1 TTTTTGGAGA
48629804 TTAATCAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 15 0.48
22 16 0.52
ACGTcount: A:0.15, C:0.04, G:0.28, T:0.53
Consensus pattern (22 bp):
TTTTTGGAGAGGCTAGTTTTTT
Found at i:48630094 original size:15 final size:15
Alignment explanation
Indices: 48630074--48630117 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
48630064 TTTTTGTTAT
48630074 TATTATATTTTTTAA
1 TATTATATTTTTTAA
*
48630089 TATTATA--TTAT-A
1 TATTATATTTTTTAA
48630101 TA-TATATTTTTTAA
1 TATTATATTTTTTAA
48630115 TAT
1 TAT
48630118 ATTAGGTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 8
0.70 0.06 0.24
Matches are distributed among these distances:
11 4 0.17
12 3 0.13
13 6 0.26
14 3 0.13
15 7 0.30
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TATTATATTTTTTAA
Found at i:48630163 original size:23 final size:25
Alignment explanation
Indices: 48630115--48630190 Score: 70
Period size: 23 Copynumber: 3.2 Consensus size: 25
48630105 TATTTTTTAA
* * *
48630115 TATATTAGGTATAT-TC-TAAATTC
1 TATATTACGTATATATCATTAATAC
48630138 TATATTACGTATATAT-ATT-ATAC
1 TATATTACGTATATATCATTAATAC
* * *
48630161 TATTTTATGTATATATCTTTAATAC
1 TATATTACGTATATATCATTAATAC
48630186 TATAT
1 TATAT
48630191 ATTTACATAT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
23 30 0.71
24 4 0.10
25 8 0.19
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.51
Consensus pattern (25 bp):
TATATTACGTATATATCATTAATAC
Found at i:48630244 original size:22 final size:23
Alignment explanation
Indices: 48630214--48630279 Score: 80
Period size: 22 Copynumber: 2.9 Consensus size: 23
48630204 TTTCTACATG
*
48630214 TTATCTTATGTATATATTTTA-A
1 TTATATTATGTATATATTTTACA
*
48630236 TTATATTATGTATGTATTTTTACA
1 TTATATTATGTATATA-TTTTACA
* *
48630260 CTATATTATGTACATATTTT
1 TTATATTATGTATATATTTT
48630280 TTTATATCTA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
22 14 0.38
23 9 0.24
24 14 0.38
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.58
Consensus pattern (23 bp):
TTATATTATGTATATATTTTACA
Found at i:48630280 original size:24 final size:23
Alignment explanation
Indices: 48630219--48630280 Score: 81
Period size: 24 Copynumber: 2.7 Consensus size: 23
48630209 ACATGTTATC
*
48630219 TTATGTATATA-TTTTAATTATA
1 TTATGTATATATTTTTAACTATA
*
48630241 TTATGTATGTATTTTTACACTATA
1 TTATGTATATATTTTTA-ACTATA
*
48630265 TTATGTACATATTTTT
1 TTATGTATATATTTTT
48630281 TTATATCTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 10 0.29
23 5 0.15
24 19 0.56
ACGTcount: A:0.31, C:0.05, G:0.06, T:0.58
Consensus pattern (23 bp):
TTATGTATATATTTTTAACTATA
Found at i:48630317 original size:76 final size:75
Alignment explanation
Indices: 48630149--48630317 Score: 175
Period size: 76 Copynumber: 2.2 Consensus size: 75
48630139 ATATTACGTA
* * * *
48630149 TATATATTATACTATTTTATGTATATATCTTTAATACTATATATTTACATATTTTTTTCTACATG
1 TATATATTATACTATATTATGTATATATCTTTAACACTATATATGTACATATTTTTTTATACATG
*
48630214 TTATCTTATG
66 TTATCTAATG
* * * *
48630224 TATATATTTTAATTATATTATGTATGTAT-TTTTACACTATATTATGTACATATTTTTTTATATC
1 TATATATTAT-ACTATATTATGTATATATCTTTAACACTATA-TATGTACATATTTTTTTATA-C
48630288 TAT-TTCATAC-AATG
63 -ATGTT-AT-CTAATG
48630302 TATATATTATA-TATAT
1 TATATATTATACTATAT
48630318 CTTAACATTA
Statistics
Matches: 78, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
75 19 0.24
76 38 0.49
77 4 0.05
78 16 0.21
79 1 0.01
ACGTcount: A:0.33, C:0.08, G:0.04, T:0.56
Consensus pattern (75 bp):
TATATATTATACTATATTATGTATATATCTTTAACACTATATATGTACATATTTTTTTATACATG
TTATCTAATG
Found at i:48630369 original size:25 final size:24
Alignment explanation
Indices: 48630341--48630396 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
48630331 GTTATATTTT
*
48630341 CACTATTTTAT-GTATATACTTCAAA
1 CACTATTATATAGTATAT--TTCAAA
*
48630366 CACTA-TATATAGTATATTTCTAA
1 CACTATTATATAGTATATTTCAAA
48630389 CACTATTA
1 CACTATTA
48630397 CTATTTTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 10 0.37
24 6 0.22
25 11 0.41
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.43
Consensus pattern (24 bp):
CACTATTATATAGTATATTTCAAA
Found at i:48641466 original size:17 final size:17
Alignment explanation
Indices: 48641446--48641478 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
48641436 AGGGCATCTT
48641446 AAAA-AAAAAGAGAAAAG
1 AAAAGAAAAA-AGAAAAG
48641463 AAAAGAAAAAAGAAAA
1 AAAAGAAAAAAGAAAA
48641479 AGAGAGAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAAAGAAAAG
Found at i:48642528 original size:13 final size:13
Alignment explanation
Indices: 48642485--48642528 Score: 70
Period size: 13 Copynumber: 3.3 Consensus size: 13
48642475 CACCGAGGTA
48642485 TTTTAATTTCTGT
1 TTTTAATTTCTGT
*
48642498 TTTTCAATTTCTGC
1 TTTT-AATTTCTGT
48642512 TTTTAATTTCTGT
1 TTTTAATTTCTGT
48642525 TTTT
1 TTTT
48642529 CAAAAATCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 16 0.57
14 12 0.43
ACGTcount: A:0.14, C:0.11, G:0.07, T:0.68
Consensus pattern (13 bp):
TTTTAATTTCTGT
Found at i:48642706 original size:99 final size:100
Alignment explanation
Indices: 48642423--48642692 Score: 393
Period size: 99 Copynumber: 2.7 Consensus size: 100
48642413 TTTCAATTTA
* * * *
48642423 TGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGCTGAGCCTCGGGGCACACCGAGGTATTT
1 TGCTTTTC-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTT
* ** *
48642488 T-AATTTCTGTTTTTCAA-TTTCTGCTTTTAATTTC
65 TCAATTTCTGTTTTTCAATTTTCTCCTTACAAATTC
* *
48642522 TGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAGGGCACGCTGAGGTATTT
1 TGCTTTTC-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTT
*
48642587 TCAATTTCTGTTTTTCAATTTTTTCCTTACAAATTC
65 TCAATTTCTGTTTTTCAATTTTCTCCTTACAAATTC
*
48642623 TGCTTTTC-AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTT
1 TGCTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTT
48642687 CAATTT
66 CAATTT
48642693 TCATTTTTTA
Statistics
Matches: 155, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
99 120 0.77
100 16 0.10
101 19 0.12
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (100 bp):
TGCTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTT
CAATTTCTGTTTTTCAATTTTCTCCTTACAAATTC
Found at i:48642902 original size:75 final size:73
Alignment explanation
Indices: 48642697--48643153 Score: 550
Period size: 75 Copynumber: 6.2 Consensus size: 73
48642687 CAATTTTCAT
* * * * * *
48642697 TTTTTAATTTATGTTTCT-AAAAAATCAATTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACAC
1 TTTTCAATTTCTGTTT-TAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACAC
*
48642761 GCTGAGGTA
65 GTTGAGGTA
* * * * *
48642770 ATTTCAATTTTTGTTTGT-CAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACAC
1 TTTTCAATTTCTGTTT-TAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACAC
48642834 GTTGAGGTA
65 GTTGAGGTA
* *
48642843 TTTTCAATTTCTGTCTTTAAAAAAAATTAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACA
1 TTTTCAATTTCTGT-TTT-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACA
48642908 CGTTGAGGTA
64 CGTTGAGGTA
* *
48642918 TTTTCAATTTCTGTTTTTCAAAAAAATCAACTTATATTGCGATAGGTGAGTTGAACCTCAAG--A
1 TTTTCAATTTCTG-TTTT-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACA
*
48642981 CGCTGAGGTA
64 CGTTGAGGTA
* * * *
48642991 ATTTCAATTTTTGTTTGT-CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACAC
1 TTTTCAATTTCTGTTT-TAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACAC
48643055 GTTGAGGTA
65 GTTGAGGTA
* * *
48643064 TTTTCAATTTCTGTCTTTAAAAAAAATCAGCTCATATTGCAAGAGGTGAGTTGAACCTCAAGACG
1 TTTTCAATTTCTGT-TTT-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACA
*
48643129 C-TT-AGGTG
64 CGTTGAGGTA
*
48643137 TTTTCTATTTCTGTTTT
1 TTTTCAATTTCTGTTTT
48643154 TCAATTTCTG
Statistics
Matches: 335, Mismatches: 39, Indels: 21
0.85 0.10 0.05
Matches are distributed among these distances:
71 38 0.11
72 6 0.02
73 138 0.41
74 6 0.02
75 146 0.44
76 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.35
Consensus pattern (73 bp):
TTTTCAATTTCTGTTTTAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACG
TTGAGGTA
Found at i:48643100 original size:221 final size:220
Alignment explanation
Indices: 48642710--48643157 Score: 747
Period size: 221 Copynumber: 2.0 Consensus size: 220
48642700 TTAATTTATG
* *
48642710 TTTCTAAAAAATCAATTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
1 TTTCAAAAAAATCAATTCATATTGCGAGAAGTGAGTTGAACCTCA-GACACGCTGAGGTAATTTC
48642775 AATTTTTGTTTGTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACACGTTGAG
65 AATTTTTGTTTGTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACACGTTGAG
* *
48642840 GTATTTTCAATTTCTGTCTTTAAAAAAAATTAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAG
130 GTATTTTCAATTTCTGTCTTTAAAAAAAATCAGCTCATATTGCAAGAGGTGAGTTGAACCTCAAG
48642905 ACACGTTGAGGTATTTTCAATTTCTGTT
195 ACAC-TT-AGGTATTTTCAATTTCTGTT
* * *
48642933 TTTCAAAAAAATCAACTT-ATATTGCGATAGGTGAGTTGAACCTCA-AGACGCTGAGGTAATTTC
1 TTTCAAAAAAATCAA-TTCATATTGCGAGAAGTGAGTTGAACCTCAGACACGCTGAGGTAATTTC
*
48642996 AATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAG
65 AATTTTTGTTTGTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACACGTTGAG
48643061 GTATTTTCAATTTCTGTCTTTAAAAAAAATCAGCTCATATTGCAAGAGGTGAGTTGAACCTCAAG
130 GTATTTTCAATTTCTGTCTTTAAAAAAAATCAGCTCATATTGCAAGAGGTGAGTTGAACCTCAAG
* * *
48643126 ACGCTTAGGTGTTTTCTATTTCTGTT
195 ACACTTAGGTATTTTCAATTTCTGTT
48643152 TTTCAA
1 TTTCAA
48643158 TTTCTGTGTT
Statistics
Matches: 213, Mismatches: 11, Indels: 6
0.93 0.05 0.03
Matches are distributed among these distances:
219 24 0.11
220 2 0.01
221 147 0.69
223 38 0.18
224 2 0.01
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (220 bp):
TTTCAAAAAAATCAATTCATATTGCGAGAAGTGAGTTGAACCTCAGACACGCTGAGGTAATTTCA
ATTTTTGTTTGTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACACGTTGAGG
TATTTTCAATTTCTGTCTTTAAAAAAAATCAGCTCATATTGCAAGAGGTGAGTTGAACCTCAAGA
CACTTAGGTATTTTCAATTTCTGTT
Found at i:48643160 original size:14 final size:14
Alignment explanation
Indices: 48643137--48643171 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
48643127 CGCTTAGGTG
*
48643137 TTTTCTATTTCTGT
1 TTTTCAATTTCTGT
48643151 TTTTCAATTTCTGT
1 TTTTCAATTTCTGT
*
48643165 GTTTCAA
1 TTTTCAA
48643172 AAAAATCAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.14, C:0.14, G:0.09, T:0.63
Consensus pattern (14 bp):
TTTTCAATTTCTGT
Found at i:48643264 original size:15 final size:14
Alignment explanation
Indices: 48643228--48643260 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
48643218 CGCTGAGGTA
48643228 TTTTCAAATTCTGT
1 TTTTCAAATTCTGT
*
48643242 TTTTCAAATTTTGT
1 TTTTCAAATTCTGT
48643256 TTTTC
1 TTTTC
48643261 CAAAAAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.64
Consensus pattern (14 bp):
TTTTCAAATTCTGT
Found at i:48643269 original size:91 final size:90
Alignment explanation
Indices: 48643126--48643616 Score: 384
Period size: 91 Copynumber: 5.3 Consensus size: 90
48643116 GAACCTCAAG
* * * * * *
48643126 ACGCTTAGGTGTTTTCTATTTCTGTTTTTCAATTTCTGTGTTTCAAAAAAATCAGCTCATATTGC
1 ACGCTGAGGTATTTTCAATTTCTGTTTTTCAATTTATGTTTTTCAAAAAAATCAACTCATATTGC
*
48643191 GAGTGGTGAGTTGAGCCTTGACTCAC
66 GAGAGGTGAGTTGAGCCTTGA-TCAC
* *
48643217 ACGCTGAGGTATTTTCAAATTCTGTTTTTCAAATTT-TGTTTTTCCAAAAAATCAACTCATATTG
1 ACGCTGAGGTATTTTCAATTTCTGTTTTTC-AATTTATGTTTTTCAAAAAAATCAACTCATATTG
* * **
48643281 CGAGAGGTGAGTTCAGCC-TCAGGAC
65 CGAGAGGTGAGTTGAGCCTTGATCAC
* * *
48643306 ACGCTGAGATATTTTCAATTTCTTTTTTTTTCAATTTATGTTTGTCAAAAAAATCAACTCATATT
1 ACGCTGAGGTATTTTCAATTTC--TGTTTTTCAATTTATGTTTTTCAAAAAAATCAACTCATATT
*
48643371 GCGAGAGGTGAGTTGAGCCTCAGATCAC
64 GCGAGAGGTGAGTTGAGCCT-TGATCAC
* * * * * * * **
48643399 ACGCCGAGGTATTTTCAATTGATTTTTATTTTTATTTTTTTTCAATTTATGCTTTGCAAAAATCA
1 ACGCTGAGGTATTTTCAATT--TCTGT-TTTTCAATTTATGT---TTT-T-C---AAAAAAATCA
* * * *
48643464 ACTCATATTACGAGAGGTAAGTTGAGCCTCGGGTCAC
55 ACTCATATTGCGAGAGGTGAGTTGAGCCT-TGATCAC
** * ** *
48643501 ATACCGAGGTATTTTCAAAATCTGTTTTACAAATTT-TG-TTTT---AAAAATCAACTCATATTG
1 ACGCTGAGGTATTTTCAATTTCTGTTTTTC-AATTTATGTTTTTCAAAAAAATCAACTCATATTG
* * *
48643561 CGAGAAGTGAGTTGAGCCTTAGTTTAC
65 CGAGAGGTGAGTTGAGCCTT-GATCAC
** *
48643588 GTGCTGAGCTATTTTCAATTTCTGTTTTT
1 ACGCTGAGGTATTTTCAATTTCTGTTTTT
48643617 AATGTTTAGT
Statistics
Matches: 322, Mismatches: 59, Indels: 42
0.76 0.14 0.10
Matches are distributed among these distances:
87 60 0.19
89 22 0.07
90 7 0.02
91 117 0.36
92 5 0.02
93 24 0.07
94 11 0.03
95 4 0.01
97 2 0.01
98 1 0.00
99 5 0.02
100 7 0.02
102 57 0.18
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (90 bp):
ACGCTGAGGTATTTTCAATTTCTGTTTTTCAATTTATGTTTTTCAAAAAAATCAACTCATATTGC
GAGAGGTGAGTTGAGCCTTGATCAC
Found at i:48643383 original size:182 final size:178
Alignment explanation
Indices: 48643084--48643416 Score: 463
Period size: 182 Copynumber: 1.8 Consensus size: 178
48643074 CTGTCTTTAA
* * * * * * *
48643084 AAAAAATCAGCTCATATTGCAAGAGGTGAGTTGAACCTCAAGACGCTTAGGTGTTTTCTATTTCT
1 AAAAAATCAACTCATATTGCAAGAGGTGAGTTCAACCTCAACACGCTGAGATATTTTCAATTTCT
* * * *
48643149 GTTTTTCAATTTCTGTGTTTCAAAAAAATCAGCTCATATTGCGAGTGGTGAGTTGAGCCT-TGAC
66 GTTTTTCAATTTATGTGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGA-
*
48643213 TCACACGCTGAGGTATTTTCAAATTCTGTTTTTCAAATTTTGTTTTTCC
130 TCACACGCCGAGGTATTTTCAAATTCTGTTTTTCAAATTTTGTTTTTCC
* *
48643262 AAAAAATCAACTCATATTGCGAGAGGTGAGTTCAGCCTCAGGACACGCTGAGATATTTTCAATTT
1 AAAAAATCAACTCATATTGCAAGAGGTGAGTTCAACCTCA--ACACGCTGAGATATTTTCAATTT
*
48643327 CTTTTTTTTTCAATTTATGT-TTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
64 C--TGTTTTTCAATTTATGTGTT-TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
48643391 CAGATCACACGCCGAGGTATTTTCAA
126 CAGATCACACGCCGAGGTATTTTCAA
48643417 TTGATTTTTA
Statistics
Matches: 134, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
178 36 0.27
180 19 0.14
181 2 0.01
182 75 0.56
183 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (178 bp):
AAAAAATCAACTCATATTGCAAGAGGTGAGTTCAACCTCAACACGCTGAGATATTTTCAATTTCT
GTTTTTCAATTTATGTGTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGAT
CACACGCCGAGGTATTTTCAAATTCTGTTTTTCAAATTTTGTTTTTCC
Found at i:48643501 original size:102 final size:103
Alignment explanation
Indices: 48643329--48643518 Score: 294
Period size: 102 Copynumber: 1.8 Consensus size: 103
48643319 TTCAATTTCT
* *
48643329 TTTTTTTTCAATTTATGTTTGTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
1 TTTTTTTTCAATTTATGTTTGTC-AAAAAATCAACTCATATTACGAGAGGTAAGTTGAGCCTCAG
*
48643394 ATCACACGCCGAGGTATTTTCAATTGATTTTTATTTTTA
65 ATCACACACCGAGGTATTTTCAATTGATTTTTATTTTTA
*
48643433 TTTTTTTTCAATTTATGCTTTG-C-AAAAATCAACTCATATTACGAGAGGTAAGTTGAGCCTCGG
1 TTTTTTTTCAATTTATG-TTTGTCAAAAAATCAACTCATATTACGAGAGGTAAGTTGAGCCTCAG
* *
48643496 GTCACATACCGAGGTATTTTCAA
65 ATCACACACCGAGGTATTTTCAA
48643519 AATCTGTTTT
Statistics
Matches: 79, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
102 57 0.72
104 18 0.23
105 4 0.05
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (103 bp):
TTTTTTTTCAATTTATGTTTGTCAAAAAATCAACTCATATTACGAGAGGTAAGTTGAGCCTCAGA
TCACACACCGAGGTATTTTCAATTGATTTTTATTTTTA
Found at i:48643602 original size:87 final size:87
Alignment explanation
Indices: 48643456--48643683 Score: 210
Period size: 87 Copynumber: 2.6 Consensus size: 87
48643446 TATGCTTTGC
* * * * *
48643456 AAAAATCAACTCATATTACGAGAGGTAAGTTGAGCCTCGGGTCACATACCGAGGTATTTTCAAAA
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGTCACATACCGAGCTATTTTCAAAA
48643521 TCTGTTTTACAAAT-TTT-GTTTT
66 TCTGTTTT--AAATGTTTAGTTTT
* * * * * * **
48643543 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTAGTTTACGTGCTGAGCTATTTTCAATT
1 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGTCACATACCGAGCTATTTTCAAAA
*
48643608 TCTGTTTTTAATGTTTAGTTTT
66 TCTGTTTTAAATGTTTAGTTTT
* * * * * * *
48643630 AAAGAGTCAATTCATATTGTGAGAAATGAGTTAAG-CTCAAGATCACATGCCGAG
1 AAA-AATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC-AGGTCACATACCGAG
48643684 TAAAGAATAA
Statistics
Matches: 113, Mismatches: 24, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
85 3 0.03
86 3 0.03
87 70 0.62
88 37 0.33
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (87 bp):
AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGTCACATACCGAGCTATTTTCAAAA
TCTGTTTTAAATGTTTAGTTTT
Found at i:48644334 original size:30 final size:30
Alignment explanation
Indices: 48644298--48644396 Score: 162
Period size: 30 Copynumber: 3.3 Consensus size: 30
48644288 CTAGCCTTTG
48644298 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
*
48644328 CCACCACCTACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
* * *
48644358 CTACCACCTACTCCATTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
48644388 CCACCACCA
1 CCACCACCA
48644397 CTTGTACCTA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 64 1.00
ACGTcount: A:0.25, C:0.49, G:0.06, T:0.19
Consensus pattern (30 bp):
CCACCACCAACTCCACTAGCCACACTTGCT
Found at i:48644962 original size:23 final size:25
Alignment explanation
Indices: 48644914--48644989 Score: 70
Period size: 23 Copynumber: 3.2 Consensus size: 25
48644904 ATTCTTTTAA
* * *
48644914 TATATTAGGTATAT-TC-TAAATTC
1 TATATTACGTATATATCATTAATAC
48644937 TATATTACGTATATAT-ATT-ATAC
1 TATATTACGTATATATCATTAATAC
* * *
48644960 TATTTTATGTATATATCTTTAATAC
1 TATATTACGTATATATCATTAATAC
48644985 TATAT
1 TATAT
48644990 GATTTACATA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
23 30 0.71
24 4 0.10
25 8 0.19
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.51
Consensus pattern (25 bp):
TATATTACGTATATATCATTAATAC
Found at i:48645045 original size:22 final size:23
Alignment explanation
Indices: 48645015--48645081 Score: 73
Period size: 25 Copynumber: 2.9 Consensus size: 23
48645005 TTTCTACATG
*
48645015 TTATCTTATGTATATATTTTA-A
1 TTATATTATGTATATATTTTACA
*
48645037 TTATATTATGTATGTATTTTTTACA
1 TTATATTATGTA--TATATTTTACA
* *
48645062 CTATATTATGTACATATTTT
1 TTATATTATGTATATATTTT
48645082 TTTATATCTA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
22 11 0.30
23 6 0.16
24 8 0.22
25 12 0.32
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.58
Consensus pattern (23 bp):
TTATATTATGTATATATTTTACA
Found at i:48645120 original size:78 final size:77
Alignment explanation
Indices: 48644948--48645120 Score: 172
Period size: 78 Copynumber: 2.2 Consensus size: 77
48644938 ATATTACGTA
* * * *
48644948 TATATATTATACTATTTTATGTATATATCTTTAATACTATATGATTTACATATTTTTTTTCTACA
1 TATATATTATACTATATTATGTATATATCTTTAACACTATATGATGTACATATTTTTTTTATACA
**
48645013 TGTTATCTTATG
66 TGTTATCAAATG
* * * * * *
48645025 TATATATTTTAATTATATTATGTATGTATTTTTTACACTATATTATGTACATA-TTTTTTTATAT
1 TATATATTAT-ACTATATTATGTATATATCTTTAACACTATATGATGTACATATTTTTTTTATA-
48645089 CTAT-TTCATACAAATG
64 C-ATGTT-AT-CAAATG
48645105 TATATATTATA-TATAT
1 TATATATTATACTATAT
48645121 CTTAACATTA
Statistics
Matches: 78, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
77 18 0.23
78 42 0.54
79 5 0.06
80 13 0.17
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.55
Consensus pattern (77 bp):
TATATATTATACTATATTATGTATATATCTTTAACACTATATGATGTACATATTTTTTTTATACA
TGTTATCAAATG
Found at i:48645172 original size:25 final size:24
Alignment explanation
Indices: 48645144--48645199 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
48645134 GTTATATTTT
*
48645144 CACTATTTTAT-GTATATACTTCAAA
1 CACTATTATATAGTATAT--TTCAAA
*
48645169 CACTA-TATATAGTATATTTCTAA
1 CACTATTATATAGTATATTTCAAA
48645192 CACTATTA
1 CACTATTA
48645200 CTATTTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 10 0.37
24 6 0.22
25 11 0.41
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.43
Consensus pattern (24 bp):
CACTATTATATAGTATATTTCAAA
Found at i:48650584 original size:30 final size:31
Alignment explanation
Indices: 48650550--48650608 Score: 95
Period size: 30 Copynumber: 1.9 Consensus size: 31
48650540 ACCAGCTAAC
48650550 AGCTAACCATACTAACTG-AAGAC-GTTACAA
1 AGCTAACCA-ACTAACTGTAAGACAGTTACAA
48650580 AGCTAACCAACTAACTGTAAGACAGTTAC
1 AGCTAACCAACTAACTGTAAGACAGTTAC
48650609 TCCTAACATC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 8 0.30
30 14 0.52
31 5 0.19
ACGTcount: A:0.42, C:0.24, G:0.14, T:0.20
Consensus pattern (31 bp):
AGCTAACCAACTAACTGTAAGACAGTTACAA
Found at i:48651102 original size:5 final size:5
Alignment explanation
Indices: 48651092--48651121 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
48651082 GGTTTTATAC
48651092 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
48651122 ATGTAATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:48651147 original size:10 final size:10
Alignment explanation
Indices: 48651092--48651147 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 10
48651082 GGTTTTATAC
*
48651092 TTTTATTTTA
1 TTTTATTTAA
*
48651102 TTTTATTTTA
1 TTTTATTTAA
48651112 TTTTATTTTAA
1 TTTTA-TTTAA
* * *
48651123 -TGTAATTAT
1 TTTTATTTAA
48651132 TTTTATTTAA
1 TTTTATTTAA
48651142 TTTTAT
1 TTTTAT
48651148 AATTTTTTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
9 3 0.08
10 30 0.81
11 4 0.11
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (10 bp):
TTTTATTTAA
Found at i:48651152 original size:19 final size:20
Alignment explanation
Indices: 48651092--48651174 Score: 64
Period size: 19 Copynumber: 4.2 Consensus size: 20
48651082 GGTTTTATAC
* **
48651092 TTTTATTTTATTTTATTTTA
1 TTTTATTTAATTTTATAATA
* * *
48651112 TTTTATTTTAATGTAATTAT-
1 TTTTA-TTTAATTTTATAATA
48651132 TTTTATTTAATTTTATAAT-
1 TTTTATTTAATTTTATAATA
*
48651151 TTTT-TATAATTCTTATAATA
1 TTTTATTTAATT-TTATAATA
48651171 TTTT
1 TTTT
48651175 TATATTTTAA
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
18 6 0.12
19 22 0.42
20 14 0.27
21 10 0.19
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.70
Consensus pattern (20 bp):
TTTTATTTAATTTTATAATA
Found at i:48651154 original size:20 final size:20
Alignment explanation
Indices: 48651092--48651177 Score: 63
Period size: 20 Copynumber: 4.3 Consensus size: 20
48651082 GGTTTTATAC
* *
48651092 TTTTATTTTATTTTAT-TTT
1 TTTTATTTAATTTTATAATT
* * *
48651111 ATTTTATTTTAATGTAATTA-T
1 -TTTTA-TTTAATTTTATAATT
48651132 TTTTATTTAATTTTATAATT
1 TTTTATTTAATTTTATAATT
48651152 TTTTA--TAATTCTTATAATAT
1 TTTTATTTAATT-TTATAAT-T
48651172 TTTTAT
1 TTTTAT
48651178 ATTTTAATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
18 5 0.09
19 17 0.32
20 22 0.42
21 9 0.17
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.70
Consensus pattern (20 bp):
TTTTATTTAATTTTATAATT
Found at i:48651155 original size:10 final size:10
Alignment explanation
Indices: 48651142--48651182 Score: 50
Period size: 9 Copynumber: 4.2 Consensus size: 10
48651132 TTTTATTTAA
48651142 TTTTATAATT
1 TTTTATAATT
48651152 TTTTATAA-T
1 TTTTATAATT
*
48651161 TCTTATAATAT
1 TTTTATAAT-T
48651172 TTTTAT-ATT
1 TTTTATAATT
48651181 TT
1 TT
48651183 AATTTATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 11 0.41
10 10 0.37
11 6 0.22
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTATAATT
Found at i:48651178 original size:20 final size:19
Alignment explanation
Indices: 48651129--48651183 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 19
48651119 TTAATGTAAT
48651129 TATTTTTATTTAATTTTATAA
1 TATTTTTA--TAATTTTATAA
48651150 T-TTTTTATAATTCTTATAA
1 TATTTTTATAATT-TTATAA
48651169 TATTTTTAT-ATTTTA
1 TATTTTTATAATTTTA
48651184 ATTTATTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
18 8 0.25
19 10 0.31
20 13 0.41
21 1 0.03
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (19 bp):
TATTTTTATAATTTTATAA
Found at i:48651225 original size:13 final size:13
Alignment explanation
Indices: 48651204--48651244 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
48651194 AAGATTTTTT
48651204 TATATCAAAATAA
1 TATATCAAAATAA
*
48651217 TATAACAAAAATAA
1 TATATC-AAAATAA
*
48651231 TATTTCAAAATAA
1 TATATCAAAATAA
48651244 T
1 T
48651245 GTCAATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (13 bp):
TATATCAAAATAA
Found at i:48656992 original size:16 final size:15
Alignment explanation
Indices: 48656968--48657019 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 15
48656958 AAATTTATAT
48656968 TTTTCATCCTTTCAA
1 TTTTCATCCTTTCAA
*
48656983 TTTTCTATCCCTTCAAA
1 TTTTC-ATCCTTTC-AA
48657000 TTTTCAT-CTTTCCAA
1 TTTTCATCCTTT-CAA
48657015 TTTTC
1 TTTTC
48657020 TTTCCACTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 15 0.47
16 10 0.31
17 7 0.22
ACGTcount: A:0.19, C:0.27, G:0.00, T:0.54
Consensus pattern (15 bp):
TTTTCATCCTTTCAA
Found at i:48657001 original size:17 final size:15
Alignment explanation
Indices: 48656968--48657007 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
48656958 AAATTTATAT
*
48656968 TTTTCATCCTTTCAA
1 TTTTCATCCCTTCAA
48656983 TTTTCTATCCCTTCAAA
1 TTTTC-ATCCCTTC-AA
48657000 TTTTCATC
1 TTTTCATC
48657008 TTTCCAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 5 0.23
16 10 0.45
17 7 0.32
ACGTcount: A:0.20, C:0.28, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTTCATCCCTTCAA
Found at i:48660616 original size:17 final size:17
Alignment explanation
Indices: 48660594--48660628 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
48660584 ATATCATATC
48660594 AACTTACTATCCCTGAT
1 AACTTACTATCCCTGAT
48660611 AACTTACTATCCCTGAT
1 AACTTACTATCCCTGAT
48660628 A
1 A
48660629 GCTTTCAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.29, G:0.06, T:0.34
Consensus pattern (17 bp):
AACTTACTATCCCTGAT
Found at i:48660972 original size:21 final size:21
Alignment explanation
Indices: 48660946--48661024 Score: 77
Period size: 21 Copynumber: 3.7 Consensus size: 21
48660936 TGATCAGAGT
*
48660946 ACGACACATAAAGTGCCTAAA
1 ACGACACACAAAGTGCCTAAA
* *
48660967 ACGACACACGAGGTGCCTAAA
1 ACGACACACAAAGTGCCTAAA
* *
48660988 ACGACACACGAGGTGCCTGAAA
1 ACGACACACAAAGTGCCT-AAA
* *
48661010 TATGACACATAAAGT
1 -ACGACACACAAAGT
48661025 TCCTGATCGG
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
21 36 0.73
22 3 0.06
23 10 0.20
ACGTcount: A:0.42, C:0.24, G:0.20, T:0.14
Consensus pattern (21 bp):
ACGACACACAAAGTGCCTAAA
Found at i:48661018 original size:23 final size:21
Alignment explanation
Indices: 48660958--48661005 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
48660948 GACACATAAA
48660958 GTGCCTAAAACGACACACGAG
1 GTGCCTAAAACGACACACGAG
48660979 GTGCCTAAAACGACACACGAG
1 GTGCCTAAAACGACACACGAG
48661000 GTGCCT
1 GTGCCT
48661006 GAAATATGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.33, C:0.29, G:0.25, T:0.12
Consensus pattern (21 bp):
GTGCCTAAAACGACACACGAG
Found at i:48661423 original size:15 final size:15
Alignment explanation
Indices: 48661398--48661455 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
48661388 TCATATATAT
48661398 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
48661414 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
48661429 AATAATTTCAATCAA
1 TATAAATTCAATCAA
48661444 TATAAATTCAAT
1 TATAAATTCAAT
48661456 AAATTCATCG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:48662738 original size:5 final size:5
Alignment explanation
Indices: 48662725--48662761 Score: 65
Period size: 5 Copynumber: 7.2 Consensus size: 5
48662715 TTCTTTAGTT
48662725 TATATA TATAA TATAA TATAA TATAA TATAA TATAA T
1 TATA-A TATAA TATAA TATAA TATAA TATAA TATAA T
48662762 TAAAACATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 27 0.87
6 4 0.13
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TATAA
Found at i:48662796 original size:8 final size:8
Alignment explanation
Indices: 48662783--48662811 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
48662773 ATATTTTATT
48662783 ATATAATA
1 ATATAATA
48662791 ATATAATA
1 ATATAATA
48662799 ATATAATA
1 ATATAATA
48662807 ATATA
1 ATATA
48662812 CTAAACATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATAATA
Found at i:48670238 original size:75 final size:75
Alignment explanation
Indices: 48670115--48670264 Score: 264
Period size: 75 Copynumber: 2.0 Consensus size: 75
48670105 CATTTGCAAG
*
48670115 ATTGCTTGTTTAAACAATTAATTTCAGATCATGCAATAAAGACAATTCATCTTACTAATACTGAT
1 ATTGCTTGTTTAAACAATTAATTTCAAATCATGCAATAAAGACAATTCATCTTACTAATACTGAT
48670180 GAGTTTATAT
66 GAGTTTATAT
* **
48670190 ATTGCTTGTTTAAATAATTAATTTCAAATCATGCAATAAAGACAATTCATCTTGGTAATACTGAT
1 ATTGCTTGTTTAAACAATTAATTTCAAATCATGCAATAAAGACAATTCATCTTACTAATACTGAT
48670255 GAGTTTATAT
66 GAGTTTATAT
48670265 CTTAGTCTTT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 71 1.00
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.39
Consensus pattern (75 bp):
ATTGCTTGTTTAAACAATTAATTTCAAATCATGCAATAAAGACAATTCATCTTACTAATACTGAT
GAGTTTATAT
Found at i:48674005 original size:131 final size:130
Alignment explanation
Indices: 48673836--48674167 Score: 429
Period size: 131 Copynumber: 2.6 Consensus size: 130
48673826 TAACTATTCA
* * * * *
48673836 TTTAAAAATT-TTCAAAACGAAGGCAACATTCAAGGTTTGGGAATTTGGGGAATCGTGCCCAATC
1 TTTAAAAATTCTTTAAAACGAAGGCAACGTTCAATGTTTGGAAATTCGGGGAATCGTGCCCAATC
* * * * *
48673900 TTGTTGGGTTGCAATTTCTCGTTTCTTCAAAATAATCGAATATTCTTTTCGAATTTCAATCATGC
66 GTGCTGGGTTGCAATTTCCCGTTTCTTCAAAATAATCGAATATTCATTTAGAATTTCAATCATG-
48673965 C
130 C
* * *
48673966 TTTAAAAATTCTTTAAAACGAAGGCAACGTTCGATGTTTGGCAATTCGGGGAATCGTGCCCTATC
1 TTTAAAAATTCTTTAAAACGAAGGCAACGTTCAATGTTTGGAAATTCGGGGAATCGTGCCCAATC
* *
48674031 GTGCTGGGTTGCAATTTCCCGTTTCTTCAAAATAATCGAATATTCATTTAGAATTTCACTCATGT
66 GTGCTGGGTTGCAATTTCCCGTTTCTTCAAAATAATCGAATATTCATTTAGAATTTCAATCATGC
* * * * * * *
48674096 TTTCAAGATTC--TAAAGCG-AGGCAATGTTCAATGTTTGGAAATTCGAGGAATCGTGCCCTACC
1 TTTAAAAATTCTTTAAAACGAAGGCAACGTTCAATGTTTGGAAATTCGGGGAATCGTGCCCAATC
48674158 GTGCTGGGTT
66 GTGCTGGGTT
48674168 TCATTTTTTC
Statistics
Matches: 179, Mismatches: 22, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
127 49 0.27
128 6 0.03
130 19 0.11
131 105 0.59
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.35
Consensus pattern (130 bp):
TTTAAAAATTCTTTAAAACGAAGGCAACGTTCAATGTTTGGAAATTCGGGGAATCGTGCCCAATC
GTGCTGGGTTGCAATTTCCCGTTTCTTCAAAATAATCGAATATTCATTTAGAATTTCAATCATGC
Found at i:48682343 original size:26 final size:27
Alignment explanation
Indices: 48682309--48682369 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
48682299 ATAAAATATA
* *
48682309 ATTA-TATTATCTATTTTTAA-TTCTT
1 ATTATTATTATATATTTTAAACTTCTT
48682334 -TTATGTATTATATATTTTAAACTTCTT
1 ATTAT-TATTATATATTTTAAACTTCTT
48682361 ATTATTATT
1 ATTATTATT
48682370 TTTAAATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
26 14 0.47
27 9 0.30
28 4 0.13
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.62
Consensus pattern (27 bp):
ATTATTATTATATATTTTAAACTTCTT
Found at i:48682372 original size:21 final size:21
Alignment explanation
Indices: 48682339--48682393 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 21
48682329 TTCTTTTATG
48682339 TATTA-TATATTTTAAACTT-CT
1 TATTATTAT-TTTTAAA-TTACT
48682360 TATTATTATTTTTAAATTAACT
1 TATTATTATTTTTAAATT-ACT
48682382 TATATATTATTT
1 TAT-TATTATTT
48682394 ATTTTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
20 2 0.07
21 12 0.40
22 8 0.27
23 8 0.27
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTATTATTTTTAAATTACT
Found at i:48682517 original size:22 final size:20
Alignment explanation
Indices: 48682491--48682540 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
48682481 TTGTTTTATG
*
48682491 TATTATTCATTTTAAATTGTTT
1 TATTATTCACTTT-AATT-TTT
*
48682513 TATTATTTACTTTAATTTTT
1 TATTATTCACTTTAATTTTT
48682533 TATATATT
1 TAT-TATT
48682541 ATCAATTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.24
21 8 0.32
22 11 0.44
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (20 bp):
TATTATTCACTTTAATTTTT
Found at i:48682566 original size:26 final size:25
Alignment explanation
Indices: 48682458--48682574 Score: 75
Period size: 26 Copynumber: 4.7 Consensus size: 25
48682448 TTTAAAATAC
* * *
48682458 TTTATACATTATCTATTTTAAACTTGT
1 TTTATATATTATCAATTTCAAA-TT-T
* *
48682485 TTTATGTATTATTC-ATTTTAAATTGT
1 TTTATATATTA-TCAATTTCAAATT-T
*
48682511 TTTAT-TATT-T-ACTTT--AATTT
1 TTTATATATTATCAATTTCAAATTT
48682531 TTTATATATTATCAATTTCAAATTT
1 TTTATATATTATCAATTTCAAATTT
* *
48682556 TTATATGTATTATCTATTT
1 TT-TATATATTATCAATTT
48682575 TTTATATACC
Statistics
Matches: 76, Mismatches: 6, Indels: 17
0.77 0.06 0.17
Matches are distributed among these distances:
20 6 0.08
21 8 0.11
22 1 0.01
23 8 0.11
25 11 0.14
26 23 0.30
27 17 0.22
28 2 0.03
ACGTcount: A:0.29, C:0.07, G:0.03, T:0.61
Consensus pattern (25 bp):
TTTATATATTATCAATTTCAAATTT
Found at i:48686620 original size:12 final size:12
Alignment explanation
Indices: 48686603--48686633 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
48686593 AATATTGAAG
48686603 AAGACGAGGAAA
1 AAGACGAGGAAA
48686615 AAGACGAGGAAA
1 AAGACGAGGAAA
48686627 AAGACGA
1 AAGACGA
48686634 TCACTCTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.58, C:0.10, G:0.32, T:0.00
Consensus pattern (12 bp):
AAGACGAGGAAA
Found at i:48688904 original size:78 final size:78
Alignment explanation
Indices: 48688775--48688931 Score: 262
Period size: 78 Copynumber: 2.0 Consensus size: 78
48688765 CCTGAAGTTG
*
48688775 CAGTGGAACAGATCAAAGAAGCAAGCCTTAACCCCCTAAGTAGTAGGGTAAC-AGACTGAAGATT
1 CAGTGGAACAGATCAAAAAAGCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAAG-CTGAAGATT
48688839 GCAGATCTCGTCTC
65 GCAGATCTCGTCTC
* * *
48688853 CAGTGGAGCAGATCAAAAAAGCAGGCCTTAACCCCCTAAGTAGTAGGGTAACAAGCTGAAGATTT
1 CAGTGGAACAGATCAAAAAAGCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAAGCTGAAGATTG
48688918 CAGATCTCGTCTC
66 CAGATCTCGTCTC
48688931 C
1 C
48688932 CTGAAATTGC
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
78 72 0.97
79 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.23, T:0.20
Consensus pattern (78 bp):
CAGTGGAACAGATCAAAAAAGCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAAGCTGAAGATTG
CAGATCTCGTCTC
Found at i:48689026 original size:44 final size:45
Alignment explanation
Indices: 48688908--48689040 Score: 155
Period size: 45 Copynumber: 3.0 Consensus size: 45
48688898 GGGTAACAAG
** ** *
48688908 CTGAAGATTTCAGATCTCGTCTCCCTGAAATTGCAGTAGAGCAGA
1 CTGAAGATAGCAGATCTTATCTCCCTGAAGTTGCAGTAGAGCAGA
*
48688953 CTGAAGATAGCAGATCTTATCTCCCTGAAGTTGCAGTAGAGTAGA
1 CTGAAGATAGCAGATCTTATCTCCCTGAAGTTGCAGTAGAGCAGA
* *
48688998 -TCGAAGTTA-CA-ATCCTTATCTCTCTGAAGTTGCAGTAGAGCAG
1 CT-GAAGATAGCAGAT-CTTATCTCCCTGAAGTTGCAGTAGAGCAG
48689041 CATTAAAATA
Statistics
Matches: 77, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
43 2 0.03
44 30 0.39
45 45 0.58
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (45 bp):
CTGAAGATAGCAGATCTTATCTCCCTGAAGTTGCAGTAGAGCAGA
Found at i:48696437 original size:21 final size:20
Alignment explanation
Indices: 48696413--48696464 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
48696403 AAAAATGGGG
48696413 TTTATAAGAAATTACTTGG-TT
1 TTTATAAGAAATT--TTGGATT
*
48696434 TTTATATGAAAATTTTGGATT
1 TTTATAAG-AAATTTTGGATT
48696455 TTTAT-AGAAA
1 TTTATAAGAAA
48696465 AAGTTATTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
19 3 0.11
20 5 0.19
21 14 0.52
22 5 0.19
ACGTcount: A:0.37, C:0.02, G:0.13, T:0.48
Consensus pattern (20 bp):
TTTATAAGAAATTTTGGATT
Found at i:48696466 original size:21 final size:20
Alignment explanation
Indices: 48696428--48696465 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
48696418 AAGAAATTAC
48696428 TTGGTTTTTATATGAAAATT
1 TTGGTTTTTATATGAAAATT
48696448 TTGGATTTTTATA-GAAAA
1 TTGG-TTTTTATATGAAAA
48696466 AGTTATTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (20 bp):
TTGGTTTTTATATGAAAATT
Found at i:48696795 original size:31 final size:31
Alignment explanation
Indices: 48696760--48696820 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
48696750 GTATGACGGG
* *
48696760 TGACTAAAATGATAAATGTATGTAACAATAA
1 TGACTAAAATAATAAAAGTATGTAACAATAA
*
48696791 TGACTAAAATAATAAAAGTATGTAAGAATA
1 TGACTAAAATAATAAAAGTATGTAACAATA
48696821 GTGTTTGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.54, C:0.05, G:0.13, T:0.28
Consensus pattern (31 bp):
TGACTAAAATAATAAAAGTATGTAACAATAA
Found at i:48709811 original size:14 final size:14
Alignment explanation
Indices: 48709792--48709859 Score: 57
Period size: 14 Copynumber: 4.6 Consensus size: 14
48709782 AATTGTTGGT
48709792 TTCTTTTGTTCTTG
1 TTCTTTTGTTCTTG
*
48709806 TTCTTTTGGTTTTTG
1 TTCTTTT-GTTCTTG
* *
48709821 AATCTTTTATTTTTCTT-
1 --T-TCTT-TTGTTCTTG
48709838 TTCTTTTGTTCTTG
1 TTCTTTTGTTCTTG
48709852 TTCTTTTG
1 TTCTTTTG
48709860 GTTTTTGAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
13 7 0.17
14 18 0.43
15 7 0.17
17 1 0.02
18 7 0.17
19 2 0.05
ACGTcount: A:0.04, C:0.12, G:0.12, T:0.72
Consensus pattern (14 bp):
TTCTTTTGTTCTTG
Found at i:48709828 original size:16 final size:15
Alignment explanation
Indices: 48709793--48709880 Score: 54
Period size: 15 Copynumber: 5.8 Consensus size: 15
48709783 ATTGTTGGTT
* *
48709793 TCTTTTGTTCTTG-T
1 TCTTTTGTTTTTGAA
48709807 TCTTTTGGTTTTTGAA
1 TCTTTT-GTTTTTGAA
* ***
48709823 TCTTTTATTTTTCTTT
1 TCTTTTGTTTTT-GAA
* *
48709839 TCTTTTGTTCTTG-T
1 TCTTTTGTTTTTGAA
48709853 TCTTTTGGTTTTTGAA
1 TCTTTT-GTTTTTGAA
*
48709869 TCTTTTATTTTT
1 TCTTTTGTTTTT
48709881 CTTTCTTATT
Statistics
Matches: 57, Mismatches: 12, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
14 13 0.23
15 22 0.39
16 22 0.39
ACGTcount: A:0.07, C:0.10, G:0.11, T:0.72
Consensus pattern (15 bp):
TCTTTTGTTTTTGAA
Found at i:48709841 original size:46 final size:46
Alignment explanation
Indices: 48709791--48709884 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
48709781 GAATTGTTGG
48709791 TTTCTTTTGTTCTTGTTCTTTTGGTTTTTGAATCTTTTATTTTTCT
1 TTTCTTTTGTTCTTGTTCTTTTGGTTTTTGAATCTTTTATTTTTCT
48709837 TTTCTTTTGTTCTTGTTCTTTTGGTTTTTGAATCTTTTATTTTTCT
1 TTTCTTTTGTTCTTGTTCTTTTGGTTTTTGAATCTTTTATTTTTCT
48709883 TT
1 TT
48709885 CTTATTTCTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.06, C:0.11, G:0.11, T:0.72
Consensus pattern (46 bp):
TTTCTTTTGTTCTTGTTCTTTTGGTTTTTGAATCTTTTATTTTTCT
Found at i:48712226 original size:187 final size:182
Alignment explanation
Indices: 48711904--48712274 Score: 643
Period size: 187 Copynumber: 2.0 Consensus size: 182
48711894 TGATTAAATA
*
48711904 TTGTGATTTAATGCATCCAAGTCCAATAAGCTCATGTTCATATAGTTGCACAGTACCATCTGCGA
1 TTGTGATTTAATGCATCCAAGTCCAATAAGCTCATGTTCATATAGTTGCACAGTACCATATGCGA
*
48711969 TATCTTAAACCTAGATTTGACATTCTATTTATATTCCATAGTAGCTATAGTTCCATTTGTTAAAG
66 TATCTTAAACCTAGATTTGACATGCTATTTATATTCCATAGTAGCTATAGTTCCATTTGTTAAAG
48712034 GGCAGATTAAAAGGACACTCTAGTCTAGATGCTCATGTTTTGACTTGGTCTATATTT
131 GGCAGATTAAAAGGACA--C---TCTAGATGCTCATGTTTTGACTTGGTCTATATTT
48712091 TTGTGATTTAATGCATCCAAGTCCAATAAGCTCATGTTCATATAGTTGCACAGTACCATATGCGA
1 TTGTGATTTAATGCATCCAAGTCCAATAAGCTCATGTTCATATAGTTGCACAGTACCATATGCGA
* * *
48712156 TATCTTAAACCTAGATTTGATATGCTATTTATGTTCCATAGTAGCTATAGTTCCATTTGTTAATG
66 TATCTTAAACCTAGATTTGACATGCTATTTATATTCCATAGTAGCTATAGTTCCATTTGTTAAAG
*
48712221 GGCAGATTAAAAGGACACTCTAGATGCTGATGTTTTGACTTGGTCTATATTT
131 GGCAGATTAAAAGGACACTCTAGATGCTCATGTTTTGACTTGGTCTATATTT
48712273 TT
1 TT
48712275 AAACATTGTT
Statistics
Matches: 178, Mismatches: 6, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
182 35 0.20
185 1 0.01
187 142 0.80
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.38
Consensus pattern (182 bp):
TTGTGATTTAATGCATCCAAGTCCAATAAGCTCATGTTCATATAGTTGCACAGTACCATATGCGA
TATCTTAAACCTAGATTTGACATGCTATTTATATTCCATAGTAGCTATAGTTCCATTTGTTAAAG
GGCAGATTAAAAGGACACTCTAGATGCTCATGTTTTGACTTGGTCTATATTT
Found at i:48713249 original size:17 final size:17
Alignment explanation
Indices: 48713227--48713267 Score: 75
Period size: 16 Copynumber: 2.5 Consensus size: 17
48713217 GTACAACGAG
48713227 TTAGAAAAGTTGGAACT
1 TTAGAAAAGTTGGAACT
48713244 TTAG-AAAGTTGGAACT
1 TTAGAAAAGTTGGAACT
48713260 TTAGAAAA
1 TTAGAAAA
48713268 CATAGGGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 16 0.70
17 7 0.30
ACGTcount: A:0.44, C:0.05, G:0.22, T:0.29
Consensus pattern (17 bp):
TTAGAAAAGTTGGAACT
Found at i:48713499 original size:20 final size:22
Alignment explanation
Indices: 48713459--48713508 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 22
48713449 GAAAATAACT
48713459 AAAATAAAAAATTTAAGAATAA
1 AAAATAAAAAATTTAAGAATAA
*
48713481 AAAATAAATAA-TTAA-AATAA
1 AAAATAAAAAATTTAAGAATAA
*
48713501 TAAATAAA
1 AAAATAAA
48713509 CAGATAGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 12 0.46
21 4 0.15
22 10 0.38
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (22 bp):
AAAATAAAAAATTTAAGAATAA
Found at i:48713502 original size:16 final size:15
Alignment explanation
Indices: 48713478--48713507 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
48713468 AATTTAAGAA
48713478 TAAAAAATAAATAAT
1 TAAAAAATAAATAAT
48713493 TAAAATAATAAATAA
1 TAAAA-AATAAATAA
48713508 ACAGATAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
TAAAAAATAAATAAT
Found at i:48713519 original size:20 final size:20
Alignment explanation
Indices: 48713459--48713520 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
48713449 GAAAATAACT
*
48713459 AAAATAAAAAATTTAAGAATAA
1 AAAATAAACAA-TT-AGAATAA
* *
48713481 AAAATAAATAATTAAAATAA
1 AAAATAAACAATTAGAATAA
*
48713501 TAAATAAACAGA-TAGAATAA
1 AAAATAAACA-ATTAGAATAA
48713521 GAAGTGGAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 21 0.62
21 3 0.09
22 10 0.29
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.23
Consensus pattern (20 bp):
AAAATAAACAATTAGAATAA
Found at i:48720041 original size:34 final size:34
Alignment explanation
Indices: 48719998--48720068 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
48719988 TAACAAAAAG
48719998 TCCTTAGTTTAACCATTTTTAACCAGTAACCAAT
1 TCCTTAGTTTAACCATTTTTAACCAGTAACCAAT
48720032 TCCTTAGTTTAACCATTTTTAACCAGTAACCAAT
1 TCCTTAGTTTAACCATTTTTAACCAGTAACCAAT
48720066 TCC
1 TCC
48720069 GAGATCCCAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.38
Consensus pattern (34 bp):
TCCTTAGTTTAACCATTTTTAACCAGTAACCAAT
Found at i:48720216 original size:18 final size:20
Alignment explanation
Indices: 48720195--48720237 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
48720185 ACAAAATCAA
*
48720195 ATTCAACTACA-A-ATGCAG
1 ATTCAAATACATATATGCAG
*
48720213 ATTCAAATACATATATGTAG
1 ATTCAAATACATATATGCAG
48720233 ATTCA
1 ATTCA
48720238 GAACAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 10 0.48
19 1 0.05
20 10 0.48
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.30
Consensus pattern (20 bp):
ATTCAAATACATATATGCAG
Found at i:48722533 original size:35 final size:34
Alignment explanation
Indices: 48722494--48722612 Score: 96
Period size: 35 Copynumber: 3.4 Consensus size: 34
48722484 ATGTAGATAA
48722494 AACAGATCAGAACATACTAGTTGCACATATAGTTT
1 AACAGATCAGAACATACTA-TTGCACATATAGTTT
* * **
48722529 AACAGATCAAAAACATGCTATTG-ACATATTCAGATAA
1 AACAGATC-AGAACATACTATTGCACATA-T-AG-TTT
* * * * *
48722566 AACATATTAGGACATATTAATTGCAAATATAGTTT
1 AACAGATCAGAACATACT-ATTGCACATATAGTTT
48722601 AACAGATCAGAA
1 AACAGATCAGAA
48722613 ACAGGTATTG
Statistics
Matches: 62, Mismatches: 16, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
34 5 0.08
35 22 0.35
36 19 0.31
37 12 0.19
38 4 0.06
ACGTcount: A:0.45, C:0.14, G:0.13, T:0.28
Consensus pattern (34 bp):
AACAGATCAGAACATACTATTGCACATATAGTTT
Found at i:48726144 original size:50 final size:50
Alignment explanation
Indices: 48726069--48726169 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
48726059 ATATTCTATG
48726069 AACCTTCAACATGGGATAAATTGCCGATGCCATGTCCCAGACATGGTCTT
1 AACCTTCAACATGGGATAAATTGCCGATGCCATGTCCCAGACATGGTCTT
48726119 AACCTTCAACATGGGATAAATTGCCGATGCCATGTCCCAGACATGGTCTT
1 AACCTTCAACATGGGATAAATTGCCGATGCCATGTCCCAGACATGGTCTT
48726169 A
1 A
48726170 CACTGGTTCT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.26
Consensus pattern (50 bp):
AACCTTCAACATGGGATAAATTGCCGATGCCATGTCCCAGACATGGTCTT
Found at i:48726363 original size:48 final size:46
Alignment explanation
Indices: 48726140--48726457 Score: 172
Period size: 47 Copynumber: 6.8 Consensus size: 46
48726130 TGGGATAAAT
** *
48726140 TGCCGATGCCATGT-CCCAGACATGGTCTTACACTGGTTCTCATATATGCG
1 TGCCGATG-CATGTCCCCAGACAT-GTCTTACACTGGCACTCATCT-T--G
* * * * *
48726190 TGCTGATGCATGT-CCTAGACATGTCTTACACTAGCAC-AACCCTTG
1 TGCCGATGCATGTCCCCAGACATGTCTTACACTGGCACTCA-TCTTG
* * * *
48726235 -GCCGATACGTAT-CCCAGACACGTCTTACACTGGCTA-TC-TCTGTCG
1 TGCCGATGCATGTCCCCAGACATGTCTTACACTGGC-ACTCATCT-T-G
* * * *
48726280 AGGCCGATGAATGT-CCCAAACATGTCTTACTCTGGCACTCATCTCTG
1 -TGCCGATGCATGTCCCCAGACATGTCTTACACTGGCACTCATCT-TG
* * ** *
48726327 TGCCGATGCCATGTCCCCA-ACATGGTCTTACACTGGCTCTTATAATA
1 TGCCGATG-CATGTCCCCAGACAT-GTCTTACACTGGCACTCATCTTG
* * * *
48726374 TAGCTGATGCATGT-CCCAGACATGTCTTACACTAGCCCTCATCTGG
1 T-GCCGATGCATGTCCCCAGACATGTCTTACACTGGCACTCATCTTG
*
48726420 ATGCCAATGCCATG-CCCCAGACATGGTCTTACACTGGC
1 -TGCCGATG-CATGTCCCCAGACAT-GTCTTACACTGGC
48726458 GCACAAATCA
Statistics
Matches: 206, Mismatches: 44, Indels: 38
0.72 0.15 0.13
Matches are distributed among these distances:
43 2 0.01
44 28 0.14
45 3 0.01
46 33 0.16
47 65 0.32
48 55 0.27
49 13 0.06
50 7 0.03
ACGTcount: A:0.22, C:0.31, G:0.19, T:0.28
Consensus pattern (46 bp):
TGCCGATGCATGTCCCCAGACATGTCTTACACTGGCACTCATCTTG
Found at i:48726398 original size:94 final size:94
Alignment explanation
Indices: 48726285--48726457 Score: 251
Period size: 94 Copynumber: 1.8 Consensus size: 94
48726275 TGTCGAGGCC
* * * *
48726285 GATGAATGTCCCAAACATGTCTTACTCTGGCACTCATCTCTG-TGCCGATGCCATGTCCCCA-AC
1 GATGAATGTCCCAAACATGTCTTACACTAGCACTCATCT-GGATGCCAATGCCATG-CCCCAGAC
48726348 ATGGTCTTACACTGGCTCTTATAATATAGCT
64 ATGGTCTTACACTGGCTCTTATAATATAGCT
* * *
48726379 GATGCATGTCCCAGACATGTCTTACACTAGCCCTCATCTGGATGCCAATGCCATGCCCCAGACAT
1 GATGAATGTCCCAAACATGTCTTACACTAGCACTCATCTGGATGCCAATGCCATGCCCCAGACAT
48726444 GGTCTTACACTGGC
66 GGTCTTACACTGGC
48726458 GCACAAATCA
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
93 6 0.09
94 64 0.91
ACGTcount: A:0.23, C:0.31, G:0.18, T:0.28
Consensus pattern (94 bp):
GATGAATGTCCCAAACATGTCTTACACTAGCACTCATCTGGATGCCAATGCCATGCCCCAGACAT
GGTCTTACACTGGCTCTTATAATATAGCT
Found at i:48732861 original size:43 final size:43
Alignment explanation
Indices: 48732798--48732970 Score: 188
Period size: 43 Copynumber: 4.0 Consensus size: 43
48732788 GGCTCATACA
* * * * * *
48732798 ATGCC-ATATCCCAGATATGGTCTAACATGTTACCACATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCACATATCG
* * * *
48732840 ATGCCACTGTCCCAGACATGGTCTTACACGAAATCATATAACG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCACATATCG
* *
48732883 ATGCCAATGTCCTAGACATGGTCTTACACGTAATCACA-ATACA
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCACATAT-CG
* * *
48732926 ATGCCAATGTCTCAGACATGGTCTTACATGTAATCACATCTCG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCACATATCG
48732969 AT
1 AT
48732971 AACTTAATGT
Statistics
Matches: 107, Mismatches: 21, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
42 6 0.06
43 100 0.93
44 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGTAATCACATATCG
Found at i:48739337 original size:46 final size:46
Alignment explanation
Indices: 48739261--48739519 Score: 340
Period size: 46 Copynumber: 5.6 Consensus size: 46
48739251 TGATGTCATA
* * * * * *
48739261 GTATCTTTGAACTATGGTTTTACTCGTTTTC-TGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTATTC-ATTTCATGTCACGTTGCCATG
* ** *
48739307 GTATCTTTCAACCATTGTCTTATTCATTTTCCCGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTATTCA-TTTCATGTCACGTTGCCATG
* *
48739354 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGTTGCCATG
*
48739400 GTATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGTTGCCATG
** * *
48739446 GTATCTTTCAACCATGGTCTTACACATTTCATATCACGCTGCCATG
1 GTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGTTGCCATG
48739492 GTATCTTTCAACCATGGTCTTATTCATT
1 GTATCTTTCAACCATGGTCTTATTCATT
48739520 CCATATCAGA
Statistics
Matches: 191, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
46 153 0.80
47 38 0.20
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.42
Consensus pattern (46 bp):
GTATCTTTCAACCATGGTCTTATTCATTTCATGTCACGTTGCCATG
Found at i:48739525 original size:46 final size:46
Alignment explanation
Indices: 48739298--48739527 Score: 343
Period size: 46 Copynumber: 5.0 Consensus size: 46
48739288 TTTCTGTCAT
* *** *
48739298 GTTGCCATGGTATCTTTCAACCATTGTCTTATTCATTTTCCCGTCAT
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTTCATATCAC
* * *
48739345 GTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCAC
48739391 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCAC
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCAC
**
48739437 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAC
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCAC
* *
48739483 GCTGCCATGGTATCTTTCAACCATGGTCTTATTCATTCCATATCA
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCA
48739528 GAGAGCACAC
Statistics
Matches: 169, Mismatches: 14, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
46 136 0.80
47 33 0.20
ACGTcount: A:0.21, C:0.25, G:0.14, T:0.40
Consensus pattern (46 bp):
GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCAC
Found at i:48742355 original size:70 final size:70
Alignment explanation
Indices: 48742242--48742465 Score: 288
Period size: 70 Copynumber: 3.2 Consensus size: 70
48742232 CAATTTATTA
* * *
48742242 CTAATTAATATGCTGCTATTATATTGTAAATCATTGGTTGTCCAAATTAGGACAAATTCGTGGTG
1 CTAATTAATATGCTGCTGTTATATTGTAAATCATTGGCTGTCCAAATTAGGACAAATTCATGGTG
48742307 TTTAG
66 TTTAG
* *
48742312 CTAATTAATATGCTGCTGTTATATTGTAAACCATTGACTGTCCAAATTAGGACAAATTCATGGTG
1 CTAATTAATATGCTGCTGTTATATTGTAAATCATTGGCTGTCCAAATTAGGACAAATTCATGGTG
48742377 TTTAG
66 TTTAG
* * * * * * * *
48742382 CTAATGAAAATGCTGTTGTTATAGTATGAATCATTGGCTGTCCAAATTAGGGCATACTT-ATGGT
1 CTAATTAATATGCTGCTGTTATATTGTAAATCATTGGCTGTCCAAATTAGGACA-AATTCATGGT
*
48742446 ATTTAG
65 GTTTAG
* *
48742452 ATAATTAAAATGCT
1 CTAATTAATATGCT
48742466 AATGTTATGA
Statistics
Matches: 135, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
70 132 0.98
71 3 0.02
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (70 bp):
CTAATTAATATGCTGCTGTTATATTGTAAATCATTGGCTGTCCAAATTAGGACAAATTCATGGTG
TTTAG
Found at i:48743791 original size:2 final size:2
Alignment explanation
Indices: 48743784--48743822 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
48743774 GTGAATCGAC
48743784 AT 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 AT A
48743823 GTTGGAATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:48745747 original size:43 final size:43
Alignment explanation
Indices: 48745652--48745790 Score: 158
Period size: 43 Copynumber: 3.3 Consensus size: 43
48745642 ATAGGTTATA
* *
48745652 CTTTGGTTTATCCGATGATGCACTG-ATGTGCCAGTATATTTA
1 CTTTGGTTTATCCGATGATGCACTGTGTGTGCCAGTATATTTT
* * * *
48745694 ATTCGGTTTATCCGGTGATGCATTGTGTGTGCC-GATATATTTT
1 CTTTGGTTTATCCGATGATGCACTGTGTGTGCCAG-TATATTTT
* * *
48745737 CTTTGATTTATTCGATGATGTACTGTGTGTGCCAGTATATTTT
1 CTTTGGTTTATCCGATGATGCACTGTGTGTGCCAGTATATTTT
48745780 -TTTGGGTTTAT
1 CTTT-GGTTTAT
48745791 TTGATTTCTG
Statistics
Matches: 79, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
42 25 0.32
43 53 0.67
44 1 0.01
ACGTcount: A:0.18, C:0.13, G:0.23, T:0.46
Consensus pattern (43 bp):
CTTTGGTTTATCCGATGATGCACTGTGTGTGCCAGTATATTTT
Done.