Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 54 of 145
Found at i:17602567 original size:33 final size:33
Alignment explanation
Indices: 17602525--17602590 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
17602515 AAATGTCAAA
17602525 GTATAGGGGCATTTTGATAATTTTCTATTCTCC
1 GTATAGGGGCATTTTGATAATTTTCTATTCTCC
17602558 GTATAGGGGCATTTTGATAATTTTCTATTCTCC
1 GTATAGGGGCATTTTGATAATTTTCTATTCTCC
17602591 TCAATTTTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.21, C:0.15, G:0.18, T:0.45
Consensus pattern (33 bp):
GTATAGGGGCATTTTGATAATTTTCTATTCTCC
Found at i:17605159 original size:31 final size:32
Alignment explanation
Indices: 17605121--17605182 Score: 101
Period size: 31 Copynumber: 2.0 Consensus size: 32
17605111 GTTTTTAGAT
17605121 AAATTTGATCC-CCAACCTTT-AAAAAAGAGTA
1 AAATTTGA-CCACCAACCTTTAAAAAAAGAGTA
17605152 AAATTTGACCACCAACCTTTAAAAAAAGAGT
1 AAATTTGACCACCAACCTTTAAAAAAAGAGT
17605183 TGAATTGTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
30 2 0.07
31 17 0.59
32 10 0.34
ACGTcount: A:0.47, C:0.19, G:0.10, T:0.24
Consensus pattern (32 bp):
AAATTTGACCACCAACCTTTAAAAAAAGAGTA
Found at i:17611097 original size:9 final size:9
Alignment explanation
Indices: 17611079--17611198 Score: 82
Period size: 9 Copynumber: 13.0 Consensus size: 9
17611069 AAAAACATAA
*
17611079 TTTATTATT
1 TTTATAATT
17611088 TTTATAA-T
1 TTTATAATT
*
17611096 TTTATTATT
1 TTTATAATT
* *
17611105 TATTATGACT
1 T-TTATAATT
* *
17611115 TTAATTAACT
1 TTTA-TAATT
17611125 TTTAT-ATT
1 TTTATAATT
*
17611133 TTTATAAAT
1 TTTATAATT
17611142 TTTATAATT
1 TTTATAATT
*
17611151 TTAATTAATT
1 TTTA-TAATT
*
17611161 TTTAATGATT
1 TTT-ATAATT
17611171 TTTATAATT
1 TTTATAATT
* *
17611180 TTTTTATGTT
1 TTTATA-ATT
17611190 TTTATAATT
1 TTTATAATT
17611199 CTAGGATGAA
Statistics
Matches: 86, Mismatches: 18, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
8 14 0.16
9 36 0.42
10 35 0.41
11 1 0.01
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.65
Consensus pattern (9 bp):
TTTATAATT
Found at i:17611101 original size:17 final size:17
Alignment explanation
Indices: 17611075--17611164 Score: 74
Period size: 17 Copynumber: 5.1 Consensus size: 17
17611065 TGGAAAAAAC
17611075 ATAA-TTTATTATTTTT
1 ATAATTTTATTATTTTT
17611091 ATAATTTTATTATTTATT
1 ATAATTTTATTATTT-TT
* * *
17611109 ATGACTTTAATTAACTTTT
1 AT-AATTTTATT-ATTTTT
* * *
17611128 ATATTTTTATAAATTTT
1 ATAATTTTATTATTTTT
17611145 ATAATTTTAATTAATTTTT
1 ATAATTTT-ATT-ATTTTT
17611164 A
1 A
17611165 ATGATTTTTA
Statistics
Matches: 58, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
16 4 0.07
17 22 0.38
18 12 0.21
19 17 0.29
20 3 0.05
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.62
Consensus pattern (17 bp):
ATAATTTTATTATTTTT
Found at i:17611154 original size:36 final size:36
Alignment explanation
Indices: 17611087--17611182 Score: 111
Period size: 36 Copynumber: 2.6 Consensus size: 36
17611077 AATTTATTAT
* * *
17611087 TTTTATAATTTTATTATTTATTATGACTTTAATTAAC
1 TTTTATATTTTTATAATTT-TTATAACTTTAATTAAC
* * *
17611124 TTTTATATTTTTATAAATTTTATAATTTTAATTAAT
1 TTTTATATTTTTATAATTTTTATAACTTTAATTAAC
17611160 TTTTAATGATTTTTATAATTTTT
1 TTTT-AT-ATTTTTATAATTTTT
17611183 TTATGTTTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
36 18 0.36
37 18 0.36
38 14 0.28
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (36 bp):
TTTTATATTTTTATAATTTTTATAACTTTAATTAAC
Found at i:17611178 original size:19 final size:18
Alignment explanation
Indices: 17611079--17611198 Score: 84
Period size: 19 Copynumber: 6.5 Consensus size: 18
17611069 AAAAACATAA
* *
17611079 TTTATTATTTTTAT-AAT
1 TTTATAATTTTTATGATT
* *
17611096 TTTATTATTTATTATGACT
1 TTTATAATTT-TTATGATT
* *
17611115 TTAATTAACTTTTAT-ATT
1 TTTA-TAATTTTTATGATT
* *
17611133 TTTATAAATTTTATAATT
1 TTTATAATTTTTATGATT
*
17611151 TTAATTAATTTTTAATGATT
1 TTTA-TAATTTTT-ATGATT
17611171 TTTATAATTTTTTTATG-TT
1 TTTATAA--TTTTTATGATT
17611190 TTTATAATT
1 TTTATAATT
17611199 CTAGGATGAA
Statistics
Matches: 84, Mismatches: 11, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
17 21 0.25
18 15 0.18
19 28 0.33
20 15 0.18
21 5 0.06
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.65
Consensus pattern (18 bp):
TTTATAATTTTTATGATT
Found at i:17611191 original size:29 final size:29
Alignment explanation
Indices: 17611124--17611193 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
17611114 TTTAATTAAC
17611124 TTTTATATTTTT-ATAAATTTTATAATTT
1 TTTTATATTTTTAATAAATTTTATAATTT
* * *
17611152 TAATTA-ATTTTTAATGATTTTTATAATTT
1 T-TTTATATTTTTAATAAATTTTATAATTT
*
17611181 TTTTATGTTTTTA
1 TTTTATATTTTTA
17611194 TAATTCTAGG
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
28 10 0.29
29 24 0.71
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (29 bp):
TTTTATATTTTTAATAAATTTTATAATTT
Found at i:17617734 original size:29 final size:30
Alignment explanation
Indices: 17617702--17617772 Score: 72
Period size: 31 Copynumber: 2.3 Consensus size: 30
17617692 GAAAAGAAGC
*
17617702 AGAAGAAGAAAAAAAATGAGAAAGAAT-AG
1 AGAAGAAGAAAAAAAATGAAAAAGAATGAG
* * *
17617731 AGAAAAAAAAGAAAAAAATGAAAAAGAGTGAG
1 AG-AAGAAGA-AAAAAAATGAAAAAGAATGAG
*
17617763 AAAAGAAGAA
1 AGAAGAAGAA
17617773 TTTAAATTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
29 2 0.06
30 6 0.19
31 21 0.66
32 3 0.09
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.06
Consensus pattern (30 bp):
AGAAGAAGAAAAAAAATGAAAAAGAATGAG
Found at i:17631974 original size:19 final size:19
Alignment explanation
Indices: 17631950--17631987 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
17631940 GTGCCTTGCT
17631950 CGTGTGGG-CCAACACGCCC
1 CGTGTGGGTCC-ACACGCCC
17631969 CGTGTGGGTCCACACGCCC
1 CGTGTGGGTCCACACGCCC
17631988 AGATTGGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 16 0.89
20 2 0.11
ACGTcount: A:0.13, C:0.42, G:0.32, T:0.13
Consensus pattern (19 bp):
CGTGTGGGTCCACACGCCC
Found at i:17632005 original size:33 final size:33
Alignment explanation
Indices: 17631967--17632049 Score: 132
Period size: 33 Copynumber: 2.5 Consensus size: 33
17631957 GCCAACACGC
*
17631967 CCCGTGTGGGTCCACACGCCCAGATTGGCCTTG
1 CCCGTGTGGGCCCACACGCCCAGATTGGCCTTG
*
17632000 CCCGTGTGGGCCCACATGCCCAGATTGGCCTTG
1 CCCGTGTGGGCCCACACGCCCAGATTGGCCTTG
*
17632033 CCCGTGT-GACCCACACG
1 CCCGTGTGGGCCCACACG
17632050 ATCTGGCCTA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
32 8 0.17
33 38 0.83
ACGTcount: A:0.13, C:0.39, G:0.29, T:0.19
Consensus pattern (33 bp):
CCCGTGTGGGCCCACACGCCCAGATTGGCCTTG
Found at i:17635287 original size:35 final size:36
Alignment explanation
Indices: 17635248--17635344 Score: 114
Period size: 34 Copynumber: 2.8 Consensus size: 36
17635238 TCACATGACT
17635248 TATAGGCTTCGCATGTACCTAGGGTTCGCATGG-CA
1 TATAGGCTTCGCATGTACCTAGGGTTCGCATGGTCA
* * *
17635283 TATAGGCTT-GCAGGTACTTAGGGTTTGCATGGTCA
1 TATAGGCTTCGCATGTACCTAGGGTTCGCATGGTCA
* *
17635318 TGTAGGC-TCACAT-T-CCTAGGGTTCGCA
1 TATAGGCTTCGCATGTACCTAGGGTTCGCA
17635345 CTAAGGGGTC
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
33 11 0.21
34 22 0.42
35 19 0.37
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.31
Consensus pattern (36 bp):
TATAGGCTTCGCATGTACCTAGGGTTCGCATGGTCA
Found at i:17635364 original size:13 final size:13
Alignment explanation
Indices: 17635332--17635370 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
17635322 GGCTCACATT
17635332 CCTAGGGTTCGCA
1 CCTAGGGTTCGCA
*
17635345 -CTAAGGGGTCGCA
1 CCT-AGGGTTCGCA
17635358 CCTAGGGTTCGCA
1 CCTAGGGTTCGCA
17635371 TTCTAACATA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 2 0.09
13 18 0.82
14 2 0.09
ACGTcount: A:0.18, C:0.28, G:0.33, T:0.21
Consensus pattern (13 bp):
CCTAGGGTTCGCA
Found at i:17638194 original size:29 final size:27
Alignment explanation
Indices: 17638127--17638221 Score: 79
Period size: 29 Copynumber: 3.4 Consensus size: 27
17638117 AAGTTGTCAT
* *
17638127 AAATTATAAAAATGA-AAAA-ATTATAA
1 AAATTATAAAAATTATAAAATATTA-CA
17638153 AAGATTATTAAAAACTTAT-AAATATTACCA
1 AA-ATTA-TAAAAA-TTATAAAATATTA-CA
* *
17638183 AAACTTATAAAAATTCTAAAATATTATA
1 AAA-TTATAAAAATTATAAAATATTACA
17638211 AAATTATAAAA
1 AAATTATAAAA
17638222 TACATGTAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
26 2 0.04
27 12 0.21
28 13 0.23
29 20 0.35
30 10 0.18
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (27 bp):
AAATTATAAAAATTATAAAATATTACA
Found at i:17638222 original size:8 final size:9
Alignment explanation
Indices: 17638127--17638221 Score: 86
Period size: 9 Copynumber: 10.2 Consensus size: 9
17638117 AAGTTGTCAT
17638127 AAATTATAA
1 AAATTATAA
*
17638136 AAATGA-AA
1 AAATTATAA
17638144 AAATTATAA
1 AAATTATAA
17638153 AAGATTATTAA
1 AA-ATTA-TAA
17638164 AAACTTATAA
1 AAA-TTATAA
* *
17638174 ATATTACCAA
1 AAATTA-TAA
*
17638184 AACTTATAA
1 AAATTATAA
*
17638193 AAATTCTAA
1 AAATTATAA
17638202 AATATTAT-A
1 AA-ATTATAA
17638211 AAATTATAA
1 AAATTATAA
17638220 AA
1 AA
17638222 TACATGTAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
8 12 0.17
9 29 0.42
10 20 0.29
11 8 0.12
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (9 bp):
AAATTATAA
Found at i:17638796 original size:18 final size:19
Alignment explanation
Indices: 17638761--17638799 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
17638751 AGTTTATTAG
17638761 AATTTTTTACAAGTATTTAT
1 AATTTTTTACAAG-ATTTAT
*
17638781 AATTTTTTATAA-ATTTAT
1 AATTTTTTACAAGATTTAT
17638799 A
1 A
17638800 TATCATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
20 11 0.61
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (19 bp):
AATTTTTTACAAGATTTAT
Found at i:17638825 original size:29 final size:28
Alignment explanation
Indices: 17638775--17638849 Score: 77
Period size: 29 Copynumber: 2.8 Consensus size: 28
17638765 TTTTACAAGT
17638775 ATTTATAATTTTTTATAAATTTATATATC
1 ATTTATAATTTTTTATAAATTT-TATATC
* *
17638804 ATTTTTAA-TTTTTAGTATATTTTATAT-
1 ATTTATAATTTTTTA-TAAATTTTATATC
*
17638831 -TTTATTA-TTTTTATAAATT
1 ATTTATAATTTTTTATAAATT
17638850 ATTTGTAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
25 5 0.12
26 11 0.28
28 11 0.28
29 13 0.32
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (28 bp):
ATTTATAATTTTTTATAAATTTTATATC
Found at i:17638844 original size:16 final size:17
Alignment explanation
Indices: 17638804--17638845 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
17638794 TTTATATATC
17638804 ATTTTTA-ATTTTTAGT
1 ATTTTTATATTTTTAGT
*
17638820 ATATTTTATA-TTTTATT
1 AT-TTTTATATTTTTAGT
17638837 ATTTTTATA
1 ATTTTTATA
17638846 AATTATTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 9 0.39
17 13 0.57
18 1 0.04
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (17 bp):
ATTTTTATATTTTTAGT
Found at i:17656029 original size:24 final size:23
Alignment explanation
Indices: 17655998--17656043 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
17655988 ATTGAAATGG
*
17655998 ATTGATTTGTATGTGA-TGAATTT
1 ATTGATTTATAT-TGATTGAATTT
17656021 ATTGAATTTATATTGATTGAATT
1 ATTG-ATTTATATTGATTGAATT
17656044 GAATTAAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.52
Consensus pattern (23 bp):
ATTGATTTATATTGATTGAATTT
Found at i:17664015 original size:120 final size:121
Alignment explanation
Indices: 17663802--17664042 Score: 475
Period size: 120 Copynumber: 2.0 Consensus size: 121
17663792 ATTTAAAATT
17663802 CAATACCAAAAACTTCGTTTAAAAATTAAAATATGGATCGAGTTTAAGTTTTAATATTCAAGACT
1 CAATACCAAAAACTTCGTTTAAAAATTAAAATATGGATCGAGTTTAAGTTTTAATATTCAAGACT
17663867 TGAGTTAAGTACGAACCAATTTATTTTGTGCTTATAATATTTGTC-CATAAATTTA
66 TGAGTTAAGTACGAACCAATTTATTTTGTGCTTATAATATTTGTCACATAAATTTA
17663922 CAATACCAAAAACTTCGTTTAAAAATTAAAATATGGATCGAGTTTAAGTTTTAATATTCAAGACT
1 CAATACCAAAAACTTCGTTTAAAAATTAAAATATGGATCGAGTTTAAGTTTTAATATTCAAGACT
17663987 TGAGTTAAGTACGAACCAATTTATTTTGTGCTTATAATATTTGTCACATAAATTTA
66 TGAGTTAAGTACGAACCAATTTATTTTGTGCTTATAATATTTGTCACATAAATTTA
17664043 AATTTGTAAG
Statistics
Matches: 120, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
120 110 0.92
121 10 0.08
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.38
Consensus pattern (121 bp):
CAATACCAAAAACTTCGTTTAAAAATTAAAATATGGATCGAGTTTAAGTTTTAATATTCAAGACT
TGAGTTAAGTACGAACCAATTTATTTTGTGCTTATAATATTTGTCACATAAATTTA
Found at i:17664403 original size:20 final size:20
Alignment explanation
Indices: 17664379--17664424 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
17664369 TAAAAAATAT
*
17664379 TAAAAAT-TACTAAATATTA
1 TAAAAATATTCTAAATATTA
*
17664398 TAAAAATATTGTAAATATTA
1 TAAAAATATTCTAAATATTA
17664418 TAAAAAT
1 TAAAAAT
17664425 TTTAATATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (20 bp):
TAAAAATATTCTAAATATTA
Found at i:17674658 original size:3 final size:3
Alignment explanation
Indices: 17674650--17674693 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
17674640 ATAAGTAAGT
*
17674650 ATA ATA ATA ATA TATA AT- ATA ATA ATA ATA A-A CTA ATA ATA ATA
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
17674694 TAAATAAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
2 3 0.08
3 30 0.83
4 3 0.08
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:17674662 original size:21 final size:18
Alignment explanation
Indices: 17674649--17674693 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
17674639 TATAAGTAAG
17674649 TATAATAATAATATATAA
1 TATAATAATAATATATAA
*
17674667 TATAATAATAATAAACTAA
1 TATAATAATAATATA-TAA
17674686 TAATAATA
1 T-ATAATA
17674694 TAAATAAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 14 0.58
19 4 0.17
20 6 0.25
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
TATAATAATAATATATAA
Found at i:17674677 original size:11 final size:11
Alignment explanation
Indices: 17674649--17674696 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
17674639 TATAAGTAAG
17674649 TATAATAATAA
1 TATAATAATAA
17674660 TAT-ATAAT-A
1 TATAATAATAA
17674669 TAATAATAATAA
1 T-ATAATAATAA
17674681 -ACTAATAATAA
1 TA-TAATAATAA
17674692 TATAA
1 TATAA
17674697 ATAAACAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
9 2 0.06
10 8 0.25
11 20 0.62
12 2 0.06
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (11 bp):
TATAATAATAA
Found at i:17674686 original size:14 final size:14
Alignment explanation
Indices: 17674653--17674693 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
17674643 AGTAAGTATA
17674653 ATAATAATATATAAT
1 ATAATAATA-ATAAT
17674668 ATAATAATAATAA-
1 ATAATAATAATAAT
17674681 ACTAATAATAATA
1 A-TAATAATAATA
17674694 TAAATAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 1 0.04
14 15 0.60
15 9 0.36
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:17675949 original size:44 final size:44
Alignment explanation
Indices: 17675885--17676168 Score: 161
Period size: 44 Copynumber: 6.5 Consensus size: 44
17675875 AGTCTACTCT
17675885 ACTGCAACTTC-GGGAAGATAAGACTTGTAGCTTCAATCTGCCCC
1 ACTGCAACTTCAGGG-AGATAAGACTTGTAGCTTCAATCTGCCCC
* * *** * * *
17675929 ACTGCAACTTCAGGGGGATAAGATTTGTTTTTTTAGTCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAATCTGCCCC
* * ** * * *
17675973 TCTGCAACTTCAAGGAGATAAGAC---TAAATGCGATTTG-CCC
1 ACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAATCTGCCCC
* * * * * * ** *
17676013 TCTGCAACTTCAGAGAAATAAGATTTGT-GATTTTAATCCACTCC
1 ACTGCAACTTCAGGGAGATAAGACTTGTAG-CTTCAATCTGCCCC
* * * * * *
17676057 ACCGCAACTTCAGGAAGATAGGACTAT-TGGCTTTAATCTGCTCC
1 ACTGCAACTTCAGGGAGATAAGACT-TGTAGCTTCAATCTGCCCC
** *
17676101 ACTGCAACTTCAGGGAGATAAGA-TTCACCATCTTCAATCTGCCCC
1 ACTGCAACTTCAGGGAGATAAGACTT--GTAGCTTCAATCTGCCCC
*
17676146 ACTGCAACTTCAGGGGGATAAGA
1 ACTGCAACTTCAGGGAGATAAGA
17676169 TTTGCTTTCT
Statistics
Matches: 176, Mismatches: 53, Indels: 21
0.70 0.21 0.08
Matches are distributed among these distances:
40 22 0.12
41 5 0.03
42 1 0.01
43 5 0.03
44 104 0.59
45 39 0.22
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.28
Consensus pattern (44 bp):
ACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAATCTGCCCC
Found at i:17676264 original size:50 final size:50
Alignment explanation
Indices: 17676210--17676602 Score: 182
Period size: 50 Copynumber: 7.7 Consensus size: 50
17676200 TCGAGGAAAC
* *
17676210 AAGATTCGCCGTCGTGACTTCAATCTGTTCCACTGCACTGCCAGAGAAGT
1 AAGATCCGCCGTCGTGACTTCAATCTGTTCCACTGCACTGCCAGGGAAGT
* * * * ** * * ** *
17676260 AAGATCCGCCATTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGGAA-C
1 AAGATCCGCCGTCGTGACTTCAATCTGTTCCACTGCACTG-CCAGGGAAGT
* * *
17676310 CAGATCCGCCGTCGT-AGCTTCAATCTGTTCCACTACACCGCCAGGGAAGT
1 AAGATCCGCCGTCGTGA-CTTCAATCTGTTCCACTGCACTGCCAGGGAAGT
* * * * ** * * ** *
17676360 AAGATCCGTCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGGAA-C
1 AAGATCCGCCGTCGTGACTTCAATCTGTTCCACTGCACTG-CCAGGGAAGT
* * * *
17676410 CAGATCCGCCGTCGT-AGCTTCAATCTGTTCCCCTACACCGCCAGGGAAGT
1 AAGATCCGCCGTCGTGA-CTTCAATCTGTTCCACTGCACTGCCAGGGAAGT
* * * * ** * * **
17676460 AAGATCCGTCGTTGGGCTTTTATTACTTCAATTTGTTTAACTGCAATGTCAGGGAAAC
1 AAGATCCGCCG-T---C----GTGACTTCAATCTGTTCCACTGCACTGCCAGGGAAGT
* ** * * * *
17676518 AAGATTCGCCGTCACGACTTCAATCTATTCCATTACACCGCCAGGGAAGT
1 AAGATCCGCCGTCGTGACTTCAATCTGTTCCACTGCACTGCCAGGGAAGT
* * * *
17676568 AAGATCCACCGTTGTGGCTTCAATCTTTTCCACTG
1 AAGATCCGCCGTCGTGACTTCAATCTGTTCCACTG
17676603 TAATGCTAAA
Statistics
Matches: 234, Mismatches: 93, Indels: 32
0.65 0.26 0.09
Matches are distributed among these distances:
49 12 0.05
50 173 0.74
51 12 0.05
54 2 0.01
57 1 0.00
58 33 0.14
59 1 0.00
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (50 bp):
AAGATCCGCCGTCGTGACTTCAATCTGTTCCACTGCACTGCCAGGGAAGT
Found at i:17676320 original size:100 final size:100
Alignment explanation
Indices: 17676186--17676596 Score: 497
Period size: 100 Copynumber: 4.0 Consensus size: 100
17676176 TCTCAGTCTG
* * * *
17676186 TTTTAACTGCAATGTCGAGGAAACAAGATTCGCCGTCGT-GACTTCAATCTGTTCCACTGCACTG
1 TTTTAACTGCAATGTCGGGGAAACAAGATCCGCCGTCGTAG-CTTCAATCTGTTCCACTACACCG
* *
17676250 CCAGAGAAGTAAGATCCGCCATTGTGGCTTCAATCT
65 CCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCT
* * *
17676286 TTTTAATTGCAATGTCGGGGGAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGC
1 TTTTAACTGCAATGTCGGGGAAACAAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGC
*
17676351 CAGGGAAGTAAGATCCGTCGTTGTGGCTTCAATCT
66 CAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCT
* * * *
17676386 TTTTAATTGCAATGTCGGGGGAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCCCTACACCGC
1 TTTTAACTGCAATGTCGGGGAAACAAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGC
* *
17676451 CAGGGAAGTAAGATCCGTCGTTG-GGCTTTTATTACTTCAATT
66 CAGGGAAGTAAGATCCGCCGTTGTGGC-TTCA--A--TC---T
* * * *
17676493 TGTTTAACTGCAATGTCAGGGAAACAAGATTCGCCGTC--ACGACTTCAATCTATTCCATTACAC
1 T-TTTAACTGCAATGTCGGGGAAACAAGATCCGCCGTCGTA-G-CTTCAATCTGTTCCACTACAC
*
17676556 CGCCAGGGAAGTAAGATCCACCGTTGTGGCTTCAATCT
63 CGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCT
17676594 TTT
1 TTT
17676597 CCACTGTAAT
Statistics
Matches: 275, Mismatches: 23, Indels: 26
0.85 0.07 0.08
Matches are distributed among these distances:
99 3 0.01
100 180 0.65
101 3 0.01
102 1 0.00
104 4 0.01
106 2 0.01
107 3 0.01
108 76 0.28
109 3 0.01
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (100 bp):
TTTTAACTGCAATGTCGGGGAAACAAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGC
CAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCT
Found at i:17676564 original size:208 final size:200
Alignment explanation
Indices: 17676186--17676596 Score: 497
Period size: 208 Copynumber: 2.0 Consensus size: 200
17676176 TCTCAGTCTG
* * *
17676186 TTTTAACTGCAATGTCGAGGAAACAAGATTCGCCGTCGTGACTTCAATCTGTTCCACTGCACTGC
1 TTTTAACTGCAATGTCGAGGAAACAAGATCCGCCGTCGTGACTTCAATCTGTTCCACTACACCGC
* * * *
17676251 CAGAGAAGTAAGATCCGCCATTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGGAACCAGATC
66 CAGAGAAGTAAGATCCGCCATTGTGGCTTCAATCTTTTTAACTGCAATGTCAGGGAAACAAGATC
* **
17676316 CGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATCCGTCGTTGTGGCTTC
131 CGCCGTCGTAGCTTCAATCTATTCCACTACACCGCCAGGGAAGTAAGATCCACCGTTGTGGCTTC
17676381 AATCT
196 AATCT
* * * * *
17676386 TTTTAATTGCAATGTCGGGGGAACCAGATCCGCCGTCGT-AGCTTCAATCTGTTCCCCTACACCG
1 TTTTAACTGCAATGTCGAGGAAACAAGATCCGCCGTCGTGA-CTTCAATCTGTTCCACTACACCG
* * * *
17676450 CCAGGGAAGTAAGATCCGTCGTTG-GGCTTTTATTACTTCAATTTGTTTAACTGCAATGTCAGGG
65 CCAGAGAAGTAAGATCCGCCATTGTGGC-TTCA--A--TC---TT-TTTAACTGCAATGTCAGGG
* *
17676514 AAACAAGATTCGCCGTC--ACGACTTCAATCTATTCCATTACACCGCCAGGGAAGTAAGATCCAC
121 AAACAAGATCCGCCGTCGTA-G-CTTCAATCTATTCCACTACACCGCCAGGGAAGTAAGATCCAC
17676577 CGTTGTGGCTTCAATCT
184 CGTTGTGGCTTCAATCT
17676594 TTT
1 TTT
17676597 CCACTGTAAT
Statistics
Matches: 178, Mismatches: 21, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
199 4 0.02
200 78 0.44
202 1 0.01
204 2 0.01
206 1 0.01
207 3 0.02
208 89 0.50
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (200 bp):
TTTTAACTGCAATGTCGAGGAAACAAGATCCGCCGTCGTGACTTCAATCTGTTCCACTACACCGC
CAGAGAAGTAAGATCCGCCATTGTGGCTTCAATCTTTTTAACTGCAATGTCAGGGAAACAAGATC
CGCCGTCGTAGCTTCAATCTATTCCACTACACCGCCAGGGAAGTAAGATCCACCGTTGTGGCTTC
AATCT
Found at i:17676581 original size:108 final size:109
Alignment explanation
Indices: 17676377--17676587 Score: 277
Period size: 108 Copynumber: 1.9 Consensus size: 109
17676367 GTCGTTGTGG
* * * * * *
17676377 CTTCAATCTTTTTAATTGCAATGTCGGGGGAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCC
1 CTTCAATCTTTTTAACTGCAATGTCAGGGAAACAAGATCCGCCGTCGTAGCTTCAATCTATTCCA
**
17676442 CTACACCGCCAGGGAAGTAAGATCCGTCGTTG-GGCTTTTATTA
66 CTACACCGCCAGGGAAGTAAGATCCACCGTTGTGGCTTTTATTA
*
17676485 CTTCAAT-TTGTTTAACTGCAATGTCAGGGAAACAAGATTCGCCGTC--ACGACTTCAATCTATT
1 CTTCAATCTT-TTTAACTGCAATGTCAGGGAAACAAGATCCGCCGTCGTA-G-CTTCAATCTATT
*
17676547 CCATTACACCGCCAGGGAAGTAAGATCCACCGTTGTGGCTT
63 CCACTACACCGCCAGGGAAGTAAGATCCACCGTTGTGGCTT
17676588 CAATCTTTTC
Statistics
Matches: 89, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
106 1 0.01
107 3 0.03
108 80 0.90
109 5 0.06
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (109 bp):
CTTCAATCTTTTTAACTGCAATGTCAGGGAAACAAGATCCGCCGTCGTAGCTTCAATCTATTCCA
CTACACCGCCAGGGAAGTAAGATCCACCGTTGTGGCTTTTATTA
Found at i:17677509 original size:16 final size:16
Alignment explanation
Indices: 17677488--17677520 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
17677478 AAAGTCTTAA
17677488 TTTAGACTCTTCATTC
1 TTTAGACTCTTCATTC
17677504 TTTAGACTCTTCATTC
1 TTTAGACTCTTCATTC
17677520 T
1 T
17677521 CAGATTTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.24, G:0.06, T:0.52
Consensus pattern (16 bp):
TTTAGACTCTTCATTC
Found at i:17678220 original size:23 final size:23
Alignment explanation
Indices: 17678190--17678239 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
17678180 TAATTTTTTA
17678190 TTTTGATTTTGATTTTTTCT-GAT
1 TTTTGATTTTG-TTTTTTCTAGAT
*
17678213 TTTTGATTTTGTTTTTTTTAGAT
1 TTTTGATTTTGTTTTTTCTAGAT
17678236 TTTT
1 TTTT
17678240 CTTTGATTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 7 0.28
23 18 0.72
ACGTcount: A:0.12, C:0.02, G:0.12, T:0.74
Consensus pattern (23 bp):
TTTTGATTTTGTTTTTTCTAGAT
Found at i:17679064 original size:25 final size:25
Alignment explanation
Indices: 17679014--17679079 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
17679004 AAGAAAATCC
* *
17679014 AAAAGAATGAAAAAATAATTATTCA
1 AAAAGAATGAAAGAATAATTACTCA
*
17679039 AAAAGAATGAAAGAAT-ATTGGCTCA
1 AAAAGAATGAAAGAATAATT-ACTCA
17679064 AAAATGAATGCAAAGA
1 AAAA-GAATG-AAAGA
17679080 TGTATTTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 3 0.09
25 22 0.63
26 5 0.14
27 5 0.14
ACGTcount: A:0.59, C:0.06, G:0.15, T:0.20
Consensus pattern (25 bp):
AAAAGAATGAAAGAATAATTACTCA
Found at i:17683035 original size:3 final size:3
Alignment explanation
Indices: 17683027--17683070 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
17683017 ATAAGTAAGT
*
17683027 ATA ATA ATA ATA TATA AT- ATA ATA ATA ATA A-A CTA ATA ATA ATA
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
17683071 TAAATAAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
2 3 0.08
3 30 0.83
4 3 0.08
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:17683039 original size:21 final size:18
Alignment explanation
Indices: 17683026--17683070 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
17683016 TATAAGTAAG
17683026 TATAATAATAATATATAA
1 TATAATAATAATATATAA
*
17683044 TATAATAATAATAAACTAA
1 TATAATAATAATATA-TAA
17683063 TAATAATA
1 T-ATAATA
17683071 TAAATAAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 14 0.58
19 4 0.17
20 6 0.25
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
TATAATAATAATATATAA
Found at i:17683054 original size:11 final size:11
Alignment explanation
Indices: 17683026--17683073 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
17683016 TATAAGTAAG
17683026 TATAATAATAA
1 TATAATAATAA
17683037 TAT-ATAAT-A
1 TATAATAATAA
17683046 TAATAATAATAA
1 T-ATAATAATAA
17683058 -ACTAATAATAA
1 TA-TAATAATAA
17683069 TATAA
1 TATAA
17683074 ATAAACAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
9 2 0.06
10 8 0.25
11 20 0.62
12 2 0.06
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (11 bp):
TATAATAATAA
Found at i:17683063 original size:14 final size:14
Alignment explanation
Indices: 17683030--17683070 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
17683020 AGTAAGTATA
17683030 ATAATAATATATAAT
1 ATAATAATA-ATAAT
17683045 ATAATAATAATAA-
1 ATAATAATAATAAT
17683058 ACTAATAATAATA
1 A-TAATAATAATA
17683071 TAAATAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 1 0.04
14 15 0.60
15 9 0.36
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:17683750 original size:1 final size:1
Alignment explanation
Indices: 17683744--17683771 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
17683734 AAACACTCAA
17683744 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
17683772 TTTTTCTCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:17687549 original size:12 final size:12
Alignment explanation
Indices: 17687514--17687550 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
17687504 AATATATCAT
17687514 AAAAATTATA-A
1 AAAAATTATATA
17687525 AAAAATTAT-TA
1 AAAAATTATATA
*
17687536 AAAAATTGTATA
1 AAAAATTATATA
17687548 AAA
1 AAA
17687551 TCATAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 18 0.78
12 5 0.22
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (12 bp):
AAAAATTATATA
Found at i:17687730 original size:21 final size:22
Alignment explanation
Indices: 17687692--17687732 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
17687682 AAAATTACAA
*
17687692 AAAAATATTATTACAATTATTC
1 AAAAATAATATTACAATTATTC
*
17687714 AAAAATAATA-TAGAATTAT
1 AAAAATAATATTACAATTAT
17687733 AAAAAGAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (22 bp):
AAAAATAATATTACAATTATTC
Found at i:17687772 original size:17 final size:17
Alignment explanation
Indices: 17687664--17687773 Score: 62
Period size: 17 Copynumber: 5.9 Consensus size: 17
17687654 AAAAGCGTAA
*
17687664 AAAATTATAAAAATATAG
1 AAAATTATAAAAA-ATAT
*
17687682 AAAATTACAAAAAAATATT
1 AAAATTA-TAAAAAATA-T
17687701 ATTACAATTATTCAAAAATAATAT
1 A--A-AATTA-T--AAAA-AATAT
*
17687725 AGAATTATAAAAAGA-AT
1 AAAATTATAAAAA-ATAT
*
17687742 AAAATTATATAAAATAT
1 AAAATTATAAAAAATAT
17687759 AACAA-TATAAAAAAT
1 AA-AATTATAAAAAAT
17687774 GTTTACAATT
Statistics
Matches: 73, Mismatches: 8, Indels: 23
0.70 0.08 0.22
Matches are distributed among these distances:
16 1 0.01
17 27 0.37
18 17 0.23
19 6 0.08
20 1 0.01
21 6 0.08
22 5 0.07
24 6 0.08
25 4 0.05
ACGTcount: A:0.65, C:0.04, G:0.03, T:0.29
Consensus pattern (17 bp):
AAAATTATAAAAAATAT
Found at i:17708618 original size:89 final size:90
Alignment explanation
Indices: 17708467--17708645 Score: 324
Period size: 89 Copynumber: 2.0 Consensus size: 90
17708457 TTTTAAATGG
*
17708467 CAATTAGGCCATTTAAATGATAGTGGGTGAATATGGACAACTTTATCCTTATGTTATATGAAATA
1 CAATTAGACCATTTAAATGATAGTGGGTGAATATGGACAACTTTATCCTTATGTTATATGAAATA
17708532 TAAATTATTTAAT-AAGGTTAATAA
66 TAAATTATTTAATAAAGGTTAATAA
**
17708556 CAATTAGACCATTTAAATGATAGTGGGTGGCTATGGACAACTTTATCCTTATGTTATATGAAATA
1 CAATTAGACCATTTAAATGATAGTGGGTGAATATGGACAACTTTATCCTTATGTTATATGAAATA
17708621 TAAATTATTTAATAAAGGTTAATAA
66 TAAATTATTTAATAAAGGTTAATAA
17708646 GGTAAATAAA
Statistics
Matches: 86, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
89 75 0.87
90 11 0.13
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.37
Consensus pattern (90 bp):
CAATTAGACCATTTAAATGATAGTGGGTGAATATGGACAACTTTATCCTTATGTTATATGAAATA
TAAATTATTTAATAAAGGTTAATAA
Found at i:17710256 original size:41 final size:41
Alignment explanation
Indices: 17710203--17710314 Score: 136
Period size: 41 Copynumber: 2.7 Consensus size: 41
17710193 TAAGGTGATT
* * *
17710203 AAATGTTTCAGACTTTACGTCTAGCAGG-TCTGATGCCGGTG
1 AAATATTTCAGACTTTAAGTCTAGCAGGCT-TAATGCCGGTG
*
17710244 AAATATTTCAGACTTTATGTCTAGCAGGCTTAATGCCGGTG
1 AAATATTTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG
* * * *
17710285 AAACAATTCGGACTATAAGTCTAGCAGGCT
1 AAATATTTCAGACTTTAAGTCTAGCAGGCT
17710315 AAAAGCTGGT
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
41 61 0.98
42 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (41 bp):
AAATATTTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTG
Found at i:17710513 original size:69 final size:67
Alignment explanation
Indices: 17710438--17710657 Score: 277
Period size: 63 Copynumber: 3.2 Consensus size: 67
17710428 TTTAAGAACA
* * *
17710438 TGTATATACATTCGGTGATAATACTTGTTAGGCATATGTATATATGCATTCAGCTATTTATGTTT
1 TGTATATACATTCGGTGATAATATTTGTTA-GCATATGTATATA-GCATTCGGCTATTCATGTTT
17710503 AAAG
64 AAAG
*
17710507 TGTATATACATTCGGTGATAATATTTGTT---ATGTGTATA-AGCATTCGGCTATTCATGTTTAA
1 TGTATATACATTCGGTGATAATATTTGTTAGCATATGTATATAGCATTCGGCTATTCATGTTTAA
17710568 AG
66 AG
* *
17710570 TGTATATACATTCGATGATAATATTTGTTAAGCATATATGTATATACACATTCGGCTATTCATGT
1 TGTATATACATTCGGTGATAATATTTGTT-AGC--ATATGTATATA-GCATTCGGCTATTCATG-
*
17710635 TTTAAAT
61 TTTAAAG
*
17710642 TGTATATGCATTCGGT
1 TGTATATACATTCGGT
17710658 TTTAAGTGTT
Statistics
Matches: 132, Mismatches: 10, Indels: 15
0.84 0.06 0.10
Matches are distributed among these distances:
63 50 0.38
64 1 0.01
65 8 0.06
69 36 0.27
70 1 0.01
71 16 0.12
72 20 0.15
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.43
Consensus pattern (67 bp):
TGTATATACATTCGGTGATAATATTTGTTAGCATATGTATATAGCATTCGGCTATTCATGTTTAA
AG
Found at i:17710519 original size:31 final size:30
Alignment explanation
Indices: 17710478--17710583 Score: 90
Period size: 31 Copynumber: 3.4 Consensus size: 30
17710468 GGCATATGTA
*
17710478 TATATGCATTCAGCTATTTATGTTTAAAGTG
1 TATATACATTC-GCTATTTATGTTTAAAGTG
* * * *
17710509 TATATACATTCGGTGATAATAT-TTGTTATGTG
1 TATATACATTCGCT-AT-TTATGTT-TAAAGTG
*
17710541 TATA-AGCATTCGGCTATTCATGTTTAAAGTG
1 TATATA-CATTC-GCTATTTATGTTTAAAGTG
17710572 TATATACATTCG
1 TATATACATTCG
17710584 ATGATAATAT
Statistics
Matches: 58, Mismatches: 10, Indels: 15
0.70 0.12 0.18
Matches are distributed among these distances:
30 3 0.05
31 31 0.53
32 22 0.38
33 2 0.03
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.43
Consensus pattern (30 bp):
TATATACATTCGCTATTTATGTTTAAAGTG
Found at i:17714487 original size:17 final size:17
Alignment explanation
Indices: 17714465--17714520 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
17714455 TATATTATAA
17714465 TTTTAATAAATTTTTAT
1 TTTTAATAAATTTTTAT
* **
17714482 TTTTAAAAAATTCATAT
1 TTTTAATAAATTTTTAT
* *
17714499 TTTTTATAATTTTTTAT
1 TTTTAATAAATTTTTAT
17714516 ATTTT
1 -TTTT
17714521 TCTCGTAATT
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
17 26 0.87
18 4 0.13
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTAATAAATTTTTAT
Found at i:17714520 original size:18 final size:18
Alignment explanation
Indices: 17714499--17714546 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
17714489 AAATTCATAT
17714499 TTTTTATAATTTTTTATA
1 TTTTTATAATTTTTTATA
* ** **
17714517 TTTTTCTCGTAATTTATA
1 TTTTTATAATTTTTTATA
17714535 TTTTTATAATTT
1 TTTTTATAATTT
17714547 ATATAAAATC
Statistics
Matches: 20, Mismatches: 10, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (18 bp):
TTTTTATAATTTTTTATA
Found at i:17714600 original size:19 final size:20
Alignment explanation
Indices: 17714578--17714618 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
17714568 TTTTTGCAAT
17714578 TTTTTTATCATTTAT-ATAA
1 TTTTTTATCATTTATAATAA
*
17714597 TTTTTTGTCATTTATAATAA
1 TTTTTTATCATTTATAATAA
17714617 TT
1 TT
17714619 GTTATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTTTTATCATTTATAATAA
Found at i:17715685 original size:169 final size:169
Alignment explanation
Indices: 17715399--17715885 Score: 688
Period size: 169 Copynumber: 2.9 Consensus size: 169
17715389 TTCTTCAATT
* * * * * *
17715399 TTAACGCCAGGGAGATGAGATTCGCTGCCTTCAGCTTTAATCTGCTCTGCTACAACACCAGGGAA
1 TTAACACCAGGGAGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTGCAACGCCAGGGAA
* * * *
17715464 ACCAGATTTGCTACCTTTAGCCTTAATCTGTTCCACTGTAATGCAAAAGAGATAGGATTCGCTGC
66 ACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTATAATGCAAAAGAGATAGGATTCGCTGC
* *
17715529 CCACAGCTTTAATCCGCTCCACTTCAGCTATTCCAAGTC
131 CCACAGCTTTAATCCGCTCAACCTCAGCTATTCCAAGTC
*** * * *
17715568 TTAATGTCAGGGAGATAAGATTCTCTGCCCT-ATGCTCTAATCTGCTCCGCTGCAACGCTAGGGA
1 TTAACACCAGGGAGATAAGATTCGCTGCCCTCA-GCTTTAATCTGCTCCGCTGCAACGCCAGGGA
* *
17715632 AACAAGATTCGCTACCTTTAGCTTTAATATGTTCCACTATAATGCCAAAGAGATAGGATTCGCTG
65 AACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTATAATGCAAAAGAGATAGGATTCGCTG
* * *
17715697 TCCGCAGCTTTAATCCACTCAACCTCAGCTATTCCAAGTC
130 CCCACAGCTTTAATCCGCTCAACCTCAGCTATTCCAAGTC
*
17715737 TTAACACCAGGGAGATAAGATTCGCTGCCCTCAGCTTTAGTCTGCTCCGCTGCAACGCCAGGGAA
1 TTAACACCAGGGAGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTGCAACGCCAGGGAA
* * * * * *
17715802 AGAAGATTCACTACCTTTAGCTTTAATCTATTCCACTATAAGGCTAAATAGATAGGATTCGCTGC
66 ACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTATAATGCAAAAGAGATAGGATTCGCTGC
17715867 CCACAGCTTTAATCCGCTC
131 CCACAGCTTTAATCCGCTC
17715886 TACTCTAGCA
Statistics
Matches: 278, Mismatches: 38, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
168 1 0.00
169 276 0.99
170 1 0.00
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (169 bp):
TTAACACCAGGGAGATAAGATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTGCAACGCCAGGGAA
ACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTATAATGCAAAAGAGATAGGATTCGCTGC
CCACAGCTTTAATCCGCTCAACCTCAGCTATTCCAAGTC
Found at i:17716165 original size:45 final size:45
Alignment explanation
Indices: 17716116--17716256 Score: 126
Period size: 45 Copynumber: 3.1 Consensus size: 45
17716106 AAGATTTGTC
* *
17716116 ATCTTCGATCTGCTTCGCTGTCAGTACAGAAAAGCAAGATCTGCT
1 ATCTTCGATCTGCTTCGCTGACAATACAGAAAAGCAAGATCTGCT
* * * * *
17716161 ATCTTC-AGTCTGCTCCGCTAACAATACAGGAATA-TAAGATCTACT
1 ATCTTCGA-TCTGCTTCGCTGACAATACA-GAAAAGCAAGATCTGCT
* * * * *
17716206 ATCTTTGATCTACTTCGCTGCCAATACAG-TAAGACAAGATTTGCT
1 ATCTTCGATCTGCTTCGCTGACAATACAGAAAAG-CAAGATCTGCT
17716251 ATCTTC
1 ATCTTC
17716257 AATCCACTTC
Statistics
Matches: 73, Mismatches: 18, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
43 1 0.01
44 2 0.03
45 65 0.89
46 5 0.07
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (45 bp):
ATCTTCGATCTGCTTCGCTGACAATACAGAAAAGCAAGATCTGCT
Found at i:17717576 original size:6 final size:6
Alignment explanation
Indices: 17717530--17717560 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
17717520 CATTTTTCCA
17717530 TCATTT TCATTT TCATTT TCATTT TCATTT T
1 TCATTT TCATTT TCATTT TCATTT TCATTT T
17717561 TTTATTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (6 bp):
TCATTT
Found at i:17720167 original size:16 final size:16
Alignment explanation
Indices: 17720142--17720176 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
17720132 TTCTATGATG
*
17720142 AAATGCCATGCAGTCA
1 AAATGCCATGCAGCCA
*
17720158 AAATGTCATGCAGCCA
1 AAATGCCATGCAGCCA
17720174 AAA
1 AAA
17720177 CAAACACAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.17
Consensus pattern (16 bp):
AAATGCCATGCAGCCA
Found at i:17721690 original size:23 final size:23
Alignment explanation
Indices: 17721662--17721706 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
17721652 GTTCAAAATT
*
17721662 TTAAAATAAACAATATATATGAG
1 TTAAAACAAACAATATATATGAG
*
17721685 TTAAAACAAATAATATATATGA
1 TTAAAACAAACAATATATATGA
17721707 ATGTACAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.31
Consensus pattern (23 bp):
TTAAAACAAACAATATATATGAG
Found at i:17723612 original size:20 final size:20
Alignment explanation
Indices: 17723561--17723617 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
17723551 TTAATAATTT
* * *
17723561 ATAAGCCTAATGTATTATAG
1 ATAAGTCTAATATATTAGAG
*
17723581 AT-AGATCCAATATATTAGAG
1 ATAAG-TCTAATATATTAGAG
*
17723601 ATAAGTCTAATACATTA
1 ATAAGTCTAATATATTA
17723618 CATAAGCCCA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
19 2 0.07
20 25 0.86
21 2 0.07
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.33
Consensus pattern (20 bp):
ATAAGTCTAATATATTAGAG
Found at i:17723822 original size:21 final size:22
Alignment explanation
Indices: 17723776--17723822 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
17723766 AATGTAAGGT
*
17723776 TTGTTATTATGTTTTAATTTAG
1 TTGTTATTATGTGTTAATTTAG
17723798 -TGTTATTATTGTGTT-ATTT-G
1 TTGTTATTA-TGTGTTAATTTAG
17723818 TTGTT
1 TTGTT
17723823 TTAAATTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
20 1 0.05
21 16 0.73
22 5 0.23
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (22 bp):
TTGTTATTATGTGTTAATTTAG
Found at i:17730597 original size:32 final size:32
Alignment explanation
Indices: 17730556--17730645 Score: 162
Period size: 32 Copynumber: 2.8 Consensus size: 32
17730546 CAATCATTTC
17730556 AATATCCAACAAGCTTAAAACATAATAAATTA
1 AATATCCAACAAGCTTAAAACATAATAAATTA
*
17730588 AATATCCAACAAGCTTAAAACATAATAAATTC
1 AATATCCAACAAGCTTAAAACATAATAAATTA
*
17730620 AATATCTAACAAGCTTAAAACATAAT
1 AATATCCAACAAGCTTAAAACATAAT
17730646 CAATATCTAA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 56 1.00
ACGTcount: A:0.54, C:0.17, G:0.03, T:0.26
Consensus pattern (32 bp):
AATATCCAACAAGCTTAAAACATAATAAATTA
Found at i:17730652 original size:27 final size:30
Alignment explanation
Indices: 17730553--17730658 Score: 128
Period size: 32 Copynumber: 3.5 Consensus size: 30
17730543 TGTCAATCAT
17730553 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCCAACAAGCTTAAAAC--AATAAA
*
17730585 TTAAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCCAACAAGCTTAAAAC--AATAAA
*
17730617 TTCAATATCTAACAAGCTTAAAAC-AT-AA
1 TTCAATATCCAACAAGCTTAAAACAATAAA
*
17730645 -TCAATATCTAACAA
1 TTCAATATCCAACAA
17730659 ATTCAAGACA
Statistics
Matches: 71, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
27 14 0.20
28 2 0.03
29 2 0.03
32 53 0.75
ACGTcount: A:0.53, C:0.18, G:0.03, T:0.26
Consensus pattern (30 bp):
TTCAATATCCAACAAGCTTAAAACAATAAA
Found at i:17730669 original size:27 final size:27
Alignment explanation
Indices: 17730618--17730672 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
17730608 CATAATAAAT
*
17730618 TCAATATCTAACAAGCTTAAAACATAA
1 TCAATATCTAACAAGATTAAAACATAA
*
17730645 TCAATATCTAACAA-ATTCAAGACATAA
1 TCAATATCTAACAAGATT-AAAACATAA
17730672 T
1 T
17730673 AATTTCAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 2 0.08
27 23 0.92
ACGTcount: A:0.51, C:0.18, G:0.04, T:0.27
Consensus pattern (27 bp):
TCAATATCTAACAAGATTAAAACATAA
Found at i:17730680 original size:59 final size:62
Alignment explanation
Indices: 17730551--17730690 Score: 162
Period size: 59 Copynumber: 2.3 Consensus size: 62
17730541 ATTGTCAATC
*
17730551 ATTTCAATATCCAACAAGCTTAAAACATAATAAATTAAATATCCAACAAGCTTAAAACATAATA
1 ATTTCAATATCCAACAAGCTTAAAAC--AATAAATTAAATATCCAACAAGATTAAAACATAATA
* * * * *
17730615 AATTCAATATCTAACAAGCTTAAAAC-AT-AA-TCAATATCTAACAA-ATTCAAGACATAATA
1 ATTTCAATATCCAACAAGCTTAAAACAATAAATTAAATATCCAACAAGATT-AAAACATAATA
*
17730674 ATTTCAAAATCCAACAA
1 ATTTCAATATCCAACAA
17730691 ACTAAAATTT
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
58 2 0.03
59 36 0.55
60 2 0.03
61 2 0.03
64 24 0.36
ACGTcount: A:0.53, C:0.18, G:0.03, T:0.26
Consensus pattern (62 bp):
ATTTCAATATCCAACAAGCTTAAAACAATAAATTAAATATCCAACAAGATTAAAACATAATA
Found at i:17733908 original size:17 final size:17
Alignment explanation
Indices: 17733886--17733938 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
17733876 TCTTCAACAG
17733886 ACAGATGCAAAATCCAA
1 ACAGATGCAAAATCCAA
*
17733903 ACAGAT--TAAA--CAA
1 ACAGATGCAAAATCCAA
* *
17733916 ATAGATGCAAAATCTAA
1 ACAGATGCAAAATCCAA
17733933 ACAGAT
1 ACAGAT
17733939 TCTTCAACAA
Statistics
Matches: 27, Mismatches: 5, Indels: 8
0.68 0.12 0.20
Matches are distributed among these distances:
13 8 0.30
15 6 0.22
17 13 0.48
ACGTcount: A:0.55, C:0.17, G:0.11, T:0.17
Consensus pattern (17 bp):
ACAGATGCAAAATCCAA
Found at i:17734515 original size:56 final size:55
Alignment explanation
Indices: 17734440--17734569 Score: 163
Period size: 56 Copynumber: 2.3 Consensus size: 55
17734430 AAAATTTTAT
* * *
17734440 AAAATATTAAAAATTATATAAACTTATAAAAAGATATAAAAATCCTAGAAAATAAA
1 AAAATATTAAAAATAATATAAACTTATAAAAAGATAAAAAAATCATA-AAAATAAA
* * *
17734496 AAAATATTAGAGATAATATAAACTTATAAAAATATAAAAAAATCATAAAAATATAA
1 AAAATATTAAAAATAATATAAACTTATAAAAAGATAAAAAAATCATAAAAATA-AA
*
17734552 AAACT-TATAAAAATAATA
1 AAAATAT-TAAAAATAATA
17734570 AATTAAAAAT
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
55 7 0.11
56 56 0.89
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.27
Consensus pattern (55 bp):
AAAATATTAAAAATAATATAAACTTATAAAAAGATAAAAAAATCATAAAAATAAA
Found at i:17734545 original size:9 final size:8
Alignment explanation
Indices: 17734440--17734582 Score: 65
Period size: 10 Copynumber: 16.0 Consensus size: 8
17734430 AAAATTTTAT
17734440 AAAATATTA
1 AAAATA-TA
17734449 AAAATTATA
1 AAAA-TATA
*
17734458 TAAACTTATAA
1 -AAA-ATAT-A
17734469 AAAGATATA
1 AAA-ATATA
*
17734478 AAAATCCTA
1 AAAAT-ATA
*
17734487 GAAAATAAA
1 -AAAATATA
17734496 AAAATATTA
1 AAAATA-TA
17734505 GAGATAATATA
1 -A-A-AATATA
**
17734516 AACTTATA
1 AAAATATA
17734524 AAAATATAAA
1 AAAATAT--A
17734534 AAAATCATA
1 AAAAT-ATA
17734543 AAAATATA
1 AAAATATA
17734551 AAAACTTATA
1 AAAA--TATA
17734561 AAAATA-A
1 AAAATATA
*
17734568 TAAAT-TA
1 AAAATATA
17734575 AAAATATA
1 AAAATATA
17734583 TAATTACAAA
Statistics
Matches: 104, Mismatches: 13, Indels: 35
0.68 0.09 0.23
Matches are distributed among these distances:
7 10 0.10
8 28 0.27
9 21 0.20
10 35 0.34
11 6 0.06
12 4 0.04
ACGTcount: A:0.66, C:0.04, G:0.03, T:0.27
Consensus pattern (8 bp):
AAAATATA
Found at i:17734585 original size:18 final size:17
Alignment explanation
Indices: 17734522--17734582 Score: 56
Period size: 19 Copynumber: 3.6 Consensus size: 17
17734512 TATAAACTTA
*
17734522 TAAAAATATAAAAAAAT
1 TAAAAATATAAATAAAT
*
17734539 CATAAAAATATAAA-AACT
1 --TAAAAATATAAATAAAT
17734557 TATAAAA-AT-AATAAAT
1 TA-AAAATATAAATAAAT
17734573 TAAAAATATA
1 TAAAAATATA
17734583 TAATTACAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
15 6 0.17
16 11 0.31
17 4 0.11
18 3 0.08
19 12 0.33
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.26
Consensus pattern (17 bp):
TAAAAATATAAATAAAT
Found at i:17739258 original size:21 final size:21
Alignment explanation
Indices: 17739234--17739283 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
17739224 TGTTTCTAAA
* *
17739234 CTCACCGCTATAGTATCCAAT
1 CTCACCGCTACAGTAACCAAT
** *
17739255 CTCATTGCTACAGTAACTAAT
1 CTCACCGCTACAGTAACCAAT
17739276 CTCACCGC
1 CTCACCGC
17739284 CACCACTGTT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.34, G:0.10, T:0.28
Consensus pattern (21 bp):
CTCACCGCTACAGTAACCAAT
Found at i:17739776 original size:19 final size:19
Alignment explanation
Indices: 17739756--17739804 Score: 73
Period size: 18 Copynumber: 2.5 Consensus size: 19
17739746 TTTAAATTAA
17739756 TTTTATAAGTTTTTATGAATT
1 TTTTATAAGTTTTTAT-AA-T
17739777 TTTTATAAG-TTTTATAAT
1 TTTTATAAGTTTTTATAAT
17739795 TTTTATAAGT
1 TTTTATAAGT
17739805 ATACATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 10 0.37
19 2 0.07
20 6 0.22
21 9 0.33
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (19 bp):
TTTTATAAGTTTTTATAAT
Found at i:17739789 original size:9 final size:9
Alignment explanation
Indices: 17739756--17739804 Score: 53
Period size: 9 Copynumber: 5.1 Consensus size: 9
17739746 TTTAAATTAA
17739756 TTTTATAAG
1 TTTTATAAG
*
17739765 TTTTTATGAATT
1 -TTTTAT-AA-G
17739777 TTTTATAAG
1 TTTTATAAG
*
17739786 TTTTATAAT
1 TTTTATAAG
17739795 TTTTATAAG
1 TTTTATAAG
17739804 T
1 T
17739805 ATACATAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
9 17 0.52
10 8 0.24
11 8 0.24
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (9 bp):
TTTTATAAG
Found at i:17739836 original size:18 final size:19
Alignment explanation
Indices: 17739751--17739868 Score: 66
Period size: 18 Copynumber: 6.2 Consensus size: 19
17739741 GATTTTTTAA
17739751 ATTAATTTT-ATAAGTTTTT
1 ATTAATTTTAATAA-TTTTT
* * *
17739770 ATGAATTTTTTATAAGTTTT
1 ATTAA-TTTTAATAATTTTT
* * **
17739790 A-TAATTTTTATAAGTATAC
1 ATTAATTTTAATAA-TTTTT
*
17739809 ATAAAATTTTAAT-ATTTTT
1 AT-TAATTTTAATAATTTTT
17739828 ATTAATTTTAAATAATTTTT
1 ATTAATTTT-AATAATTTTT
* *
17739848 A-T-ATTTTAATGATTCTT
1 ATTAATTTTAATAATTTTT
17739865 ATTA
1 ATTA
17739869 GAAAATGAAA
Statistics
Matches: 75, Mismatches: 15, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
17 9 0.12
18 21 0.28
19 16 0.21
20 17 0.23
21 12 0.16
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTAATTTTAATAATTTTT
Found at i:17758447 original size:19 final size:19
Alignment explanation
Indices: 17758404--17758447 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
17758394 TTCATTTCTC
*
17758404 TCTTCCATTTCCTTCATTT
1 TCTTCCATTTCCTTCATCT
* **
17758423 TTTTCCATTTCCTTTGTCT
1 TCTTCCATTTCCTTCATCT
17758442 TCTTCC
1 TCTTCC
17758448 CTTATCGATT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.07, C:0.32, G:0.02, T:0.59
Consensus pattern (19 bp):
TCTTCCATTTCCTTCATCT
Found at i:17759305 original size:13 final size:13
Alignment explanation
Indices: 17759289--17759313 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17759279 TTTACTTTTT
17759289 CTTAGTTAATTTA
1 CTTAGTTAATTTA
17759302 CTTAGTTAATTT
1 CTTAGTTAATTT
17759314 TTAGTTTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (13 bp):
CTTAGTTAATTTA
Found at i:17763882 original size:25 final size:25
Alignment explanation
Indices: 17763848--17763897 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
17763838 CTAACTTTGT
17763848 TATCTTAGACTTTGAAGTAGATAAA
1 TATCTTAGACTTTGAAGTAGATAAA
17763873 TATCTTAGACTTTGAAGTAGATAAA
1 TATCTTAGACTTTGAAGTAGATAAA
17763898 GAGGTACCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (25 bp):
TATCTTAGACTTTGAAGTAGATAAA
Found at i:17766622 original size:21 final size:20
Alignment explanation
Indices: 17766598--17766636 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
17766588 GTTTTGATGA
17766598 AGGTATCAATACCTTAGGCCT
1 AGGTATCAATACC-TAGGCCT
*
17766619 AGGTATCGATACCTAGGC
1 AGGTATCAATACCTAGGC
17766637 TTATATTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (20 bp):
AGGTATCAATACCTAGGCCT
Found at i:17767488 original size:28 final size:27
Alignment explanation
Indices: 17767434--17767546 Score: 99
Period size: 30 Copynumber: 4.2 Consensus size: 27
17767424 CATATATCAC
*
17767434 TAAGCA-CAAAGTGCAAA-TAAT--GA
1 TAAGCACCAAAGTGCAAATTAATACAA
17767457 TAAGCACCAAAGTGCAAATTAATAACAA
1 TAAGCACCAAAGTGCAAATTAAT-ACAA
* * *
17767485 TAAGCATCAAAGTGCAAATTTTTACAGCAA
1 TAAGCACCAAAGTGCAAA--TTAATA-CAA
* * *
17767515 TAAGCACCAATGTGCAAAATAATACGA
1 TAAGCACCAAAGTGCAAATTAATACAA
17767542 TAAGC
1 TAAGC
17767547 GCGCTAATTT
Statistics
Matches: 72, Mismatches: 10, Indels: 12
0.77 0.11 0.13
Matches are distributed among these distances:
23 6 0.08
24 11 0.15
25 4 0.06
27 7 0.10
28 21 0.29
29 1 0.01
30 22 0.31
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.20
Consensus pattern (27 bp):
TAAGCACCAAAGTGCAAATTAATACAA
Found at i:17767518 original size:30 final size:28
Alignment explanation
Indices: 17767434--17767546 Score: 103
Period size: 28 Copynumber: 4.2 Consensus size: 28
17767424 CATATATCAC
*
17767434 TAAGCA-CAAAGTGCAAA-TAAT---GA
1 TAAGCACCAAAGTGCAAATTAATAACAA
17767457 TAAGCACCAAAGTGCAAATTAATAACAA
1 TAAGCACCAAAGTGCAAATTAATAACAA
* **
17767485 TAAGCATCAAAGTGCAAATTTTTACAGCAA
1 TAAGCACCAAAGTGCAAATTAATA-A-CAA
* * *
17767515 TAAGCACCAATGTGCAAAATAAT-ACGA
1 TAAGCACCAAAGTGCAAATTAATAACAA
17767542 TAAGC
1 TAAGC
17767547 GCGCTAATTT
Statistics
Matches: 73, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
23 6 0.08
24 11 0.15
25 4 0.05
27 7 0.10
28 23 0.32
29 1 0.01
30 21 0.29
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.20
Consensus pattern (28 bp):
TAAGCACCAAAGTGCAAATTAATAACAA
Found at i:17770283 original size:15 final size:16
Alignment explanation
Indices: 17770263--17770292 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
17770253 TAACAACTAA
17770263 TATATAA-ATATATTT
1 TATATAATATATATTT
17770278 TATATAATATATATT
1 TATATAATATATATT
17770293 AATTGTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATATAATATATATTT
Found at i:17773234 original size:4 final size:4
Alignment explanation
Indices: 17773217--17773253 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
17773207 ATATGCTCGA
*
17773217 AAAG AAAG AGAG AAAG AAAG AAAG AAAG AAAG AAAG A
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG A
17773254 GCATATGTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:17773980 original size:111 final size:111
Alignment explanation
Indices: 17773786--17774007 Score: 435
Period size: 111 Copynumber: 2.0 Consensus size: 111
17773776 CATCTATGCA
17773786 TTACTCGGGACGAGCAATGAATTAAGCTTGGGGTGTAGAAACACAAAAATATATAGACTTTTTAA
1 TTACTCGGGACGAGCAATGAATTAAGCTTGGGGTGTAGAAACACAAAAATATATAGACTTTTTAA
17773851 CATCTTTTGAGCTCTAATTCGTGCAGTTTCGTAGTAATTTTTTTTT
66 CATCTTTTGAGCTCTAATTCGTGCAGTTTCGTAGTAATTTTTTTTT
17773897 TTACTCGGGACGAGCAATGAATTAAGCTTGGGGTGTAGAAACACAAAAATATATAGACTTTTTAA
1 TTACTCGGGACGAGCAATGAATTAAGCTTGGGGTGTAGAAACACAAAAATATATAGACTTTTTAA
*
17773962 CATCTTTTGAGCTCTAATTTGTGCAGTTTCGTAGTAATTTTTTTTT
66 CATCTTTTGAGCTCTAATTCGTGCAGTTTCGTAGTAATTTTTTTTT
17774008 GAAATTCATA
Statistics
Matches: 110, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
111 110 1.00
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.38
Consensus pattern (111 bp):
TTACTCGGGACGAGCAATGAATTAAGCTTGGGGTGTAGAAACACAAAAATATATAGACTTTTTAA
CATCTTTTGAGCTCTAATTCGTGCAGTTTCGTAGTAATTTTTTTTT
Found at i:17774047 original size:27 final size:28
Alignment explanation
Indices: 17774017--17774069 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
17774007 TGAAATTCAT
*
17774017 ACTTTAATTA-TAAAATAATTAATTTGC
1 ACTTAAATTATTAAAATAATTAATTTGC
* *
17774044 ACTTAAATTATTAACATATTTAATTT
1 ACTTAAATTATTAAAATAATTAATTT
17774070 TAATTATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (28 bp):
ACTTAAATTATTAAAATAATTAATTTGC
Found at i:17777138 original size:18 final size:18
Alignment explanation
Indices: 17777114--17777157 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
17777104 TGTCATTCGT
17777114 TTTCAAAACATTATTC-A
1 TTTCAAAACATTATTCAA
* *
17777131 TTTACAAATCGTTATTCAA
1 TTT-CAAAACATTATTCAA
17777150 TTTCAAAA
1 TTTCAAAA
17777158 TGTTTTCTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 3 0.14
18 15 0.68
19 4 0.18
ACGTcount: A:0.41, C:0.16, G:0.02, T:0.41
Consensus pattern (18 bp):
TTTCAAAACATTATTCAA
Found at i:17777716 original size:23 final size:24
Alignment explanation
Indices: 17777672--17777716 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
17777662 AAAATCCTGC
* *
17777672 CCATCCAGCCTCTACTCACCATCT
1 CCATCCAACCTCTACACACCATCT
*
17777696 CCATCCAACC-CTACACTCCAT
1 CCATCCAACCTCTACACACCAT
17777717 GTGGGGATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 9 0.50
24 9 0.50
ACGTcount: A:0.24, C:0.51, G:0.02, T:0.22
Consensus pattern (24 bp):
CCATCCAACCTCTACACACCATCT
Found at i:17779704 original size:33 final size:33
Alignment explanation
Indices: 17779653--17779716 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
17779643 ACAAGCACTG
* * *
17779653 ACAGTCTGGGCCTGAGCCCTATTCAGTAACAGT
1 ACAGTCTGGACCTGAGCCCAATACAGTAACAGT
* *
17779686 ACAGTGTGGACCTTAGCCCAATACAGTAACA
1 ACAGTCTGGACCTGAGCCCAATACAGTAACA
17779717 ATGTGGGCCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.22
Consensus pattern (33 bp):
ACAGTCTGGACCTGAGCCCAATACAGTAACAGT
Found at i:17779727 original size:28 final size:27
Alignment explanation
Indices: 17779681--17779738 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 27
17779671 CTATTCAGTA
*
17779681 ACAGTACAGTGTGGACCTTAGCCCAAT
1 ACAGTACAATGTGGACCTTAGCCCAAT
* *
17779708 ACAGTAACAATGTGGGCCTTAGCCCAGT
1 ACAGT-ACAATGTGGACCTTAGCCCAAT
17779736 ACA
1 ACA
17779739 ATATCAGTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.21
Consensus pattern (27 bp):
ACAGTACAATGTGGACCTTAGCCCAAT
Found at i:17780099 original size:27 final size:26
Alignment explanation
Indices: 17780069--17780258 Score: 165
Period size: 27 Copynumber: 7.2 Consensus size: 26
17780059 TATAACAGTT
17780069 ATTTTACCCTATGAGGGTATTTAAGTC
1 ATTTTACCCTATGAGGGTATTT-AGTC
*
17780096 ATTTTATCCTAT-AGGGGTATTTTAGTC
1 ATTTTACCCTATGA-GGGTA-TTTAGTC
*
17780123 ATTTTACCCTAT-AGGGGTATTTTGATC
1 ATTTTACCCTATGA-GGGTATTTAG-TC
* * *
17780150 ATTTTACCCTATGAGGGTGTTTCAATT
1 ATTTTACCCTATGAGGGTATTT-AGTC
* * *
17780177 AATTTATCCTA-G-GGGTATTTCGGTC
1 ATTTTACCCTATGAGGGTATTT-AGTC
*
17780202 ATTTTACCCTATGAGGGTATTTTGATC
1 ATTTTACCCTATGAGGGTATTTAG-TC
* *
17780229 A-TTTAACCTATGGGGGTATTTTAGTC
1 ATTTTACCCTATGAGGGTA-TTTAGTC
17780255 ATTT
1 ATTT
17780259 ATTAACCTCT
Statistics
Matches: 134, Mismatches: 19, Indels: 20
0.77 0.11 0.12
Matches are distributed among these distances:
25 18 0.13
26 26 0.19
27 86 0.64
28 4 0.03
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.44
Consensus pattern (26 bp):
ATTTTACCCTATGAGGGTATTTAGTC
Found at i:17780222 original size:79 final size:80
Alignment explanation
Indices: 17780069--17780260 Score: 250
Period size: 79 Copynumber: 2.4 Consensus size: 80
17780059 TATAACAGTT
* *
17780069 ATTTTACCCTATGAGGGTATTTAAGTCATTTTATCCTATAGGGGTATTTTAGTCATTTTACCCTA
1 ATTTTACCCTATGAGGGTATTTAAGTCAATTTATCC-ATAGGGGTATTTCAGTCATTTTACCCTA
17780134 TAGGGGTATTTTGATC
65 TAGGGGTATTTTGATC
* * *
17780150 ATTTTACCCTATGAGGGTGTTTCAA-TTAATTTATCC-TAGGGGTATTTCGGTCATTTTACCCTA
1 ATTTTACCCTATGAGGGTATTT-AAGTCAATTTATCCATAGGGGTATTTCAGTCATTTTACCCTA
17780213 T-GAGGGTATTTTGATC
65 TAG-GGGTATTTTGATC
* * *
17780229 A-TTTAACCTATGGGGGTATTTTAGTC-ATTTAT
1 ATTTTACCCTATGAGGGTATTTAAGTCAATTTAT
17780261 TAACCTCTTA
Statistics
Matches: 98, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
77 7 0.07
78 19 0.19
79 40 0.41
81 30 0.31
82 2 0.02
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.44
Consensus pattern (80 bp):
ATTTTACCCTATGAGGGTATTTAAGTCAATTTATCCATAGGGGTATTTCAGTCATTTTACCCTAT
AGGGGTATTTTGATC
Found at i:17790005 original size:30 final size:30
Alignment explanation
Indices: 17789971--17790030 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
17789961 GAGACAGTTT
*
17789971 GAAAGAAGTTTCAGATCGACAGAAATCTTA
1 GAAAGAAGATTCAGATCGACAGAAATCTTA
17790001 GAAAGAAGATTCAGATCGACAGAAATCTTA
1 GAAAGAAGATTCAGATCGACAGAAATCTTA
17790031 TTGGGATTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.45, C:0.13, G:0.20, T:0.22
Consensus pattern (30 bp):
GAAAGAAGATTCAGATCGACAGAAATCTTA
Found at i:17791405 original size:16 final size:16
Alignment explanation
Indices: 17791384--17791414 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17791374 TATTAGGGGA
17791384 AAAAGTGTAAATTTTC
1 AAAAGTGTAAATTTTC
*
17791400 AAAAGTGTGAATTTT
1 AAAAGTGTAAATTTT
17791415 GGATTGAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.03, G:0.16, T:0.39
Consensus pattern (16 bp):
AAAAGTGTAAATTTTC
Found at i:17795561 original size:42 final size:43
Alignment explanation
Indices: 17795491--17795605 Score: 153
Period size: 43 Copynumber: 2.7 Consensus size: 43
17795481 TTGAGATTTT
* *
17795491 CATGTATGACCATGTCTGGGACATTGGCATCG-TATATGATTA
1 CATGTAAGACCATGTCTGGGACAGTGGCATCGTTATATGATTA
* * * *
17795533 CGTGTAAGACCCTGTCTTGGACAGTGGCATCGTTATTTGATTA
1 CATGTAAGACCATGTCTGGGACAGTGGCATCGTTATATGATTA
17795576 CATGTAAGACCATGTCTGGGAC-GTTGGCAT
1 CATGTAAGACCATGTCTGGGACAG-TGGCAT
17795606 TGAACGAGCT
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
42 28 0.45
43 34 0.55
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.32
Consensus pattern (43 bp):
CATGTAAGACCATGTCTGGGACAGTGGCATCGTTATATGATTA
Found at i:17802474 original size:13 final size:13
Alignment explanation
Indices: 17802456--17802480 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17802446 GAATTAAAGT
17802456 GTGTGAAAATTTC
1 GTGTGAAAATTTC
17802469 GTGTGAAAATTT
1 GTGTGAAAATTT
17802481 TATCGTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:17803664 original size:42 final size:42
Alignment explanation
Indices: 17803598--17803720 Score: 147
Period size: 43 Copynumber: 2.9 Consensus size: 42
17803588 GATTTGAGAT
* * *
17803598 TTACGTGTAAGACCATGTCAAGGACATTGGCATCGTATATGA
1 TTACGTGTAAGACCATATCTAGGACATTGGCATTGTATATGA
* * *
17803640 TTACGTGTAAGACCCTATCTAGGACAGTGGCATTGTTATTTGA
1 TTACGTGTAAGACCATATCTAGGACATTGGCATTG-TATATGA
* * * *
17803683 TTACATGTAAGACCATATTTGGGACGTTGGCATTGTAT
1 TTACGTGTAAGACCATATCTAGGACATTGGCATTGTAT
17803721 GAGCTTTTTG
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
42 33 0.49
43 35 0.51
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (42 bp):
TTACGTGTAAGACCATATCTAGGACATTGGCATTGTATATGA
Found at i:17810215 original size:27 final size:27
Alignment explanation
Indices: 17810088--17810259 Score: 186
Period size: 27 Copynumber: 6.4 Consensus size: 27
17810078 GGTATAACAG
* * * *
17810088 TCATTTTACCGTATAGGGGTATTTAGG
1 TCATTTTACCCTATAGGAGTATTTCGA
*
17810115 TCATTTTACCCTATAGGGGTATTTCGA
1 TCATTTTACCCTATAGGAGTATTTCGA
* * *
17810142 TCATTTTACCCTATGGGGGTATTTCAA
1 TCATTTTACCCTATAGGAGTATTTCGA
17810169 TCATTTTACCCTATAGGAGTATTTCGA
1 TCATTTTACCCTATAGGAGTATTTCGA
* *
17810196 TCATTTTACCATAT-GAGAGTATTTCGG
1 TCATTTTACCCTATAG-GAGTATTTCGA
* * * *
17810223 CCATTTTACCTTATGGGAGTATTTTTG-
1 TCATTTTACCCTATAGGAGTA-TTTCGA
17810250 TCATTTTACC
1 TCATTTTACC
17810260 TATTTTGGGA
Statistics
Matches: 128, Mismatches: 14, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
26 1 0.01
27 122 0.95
28 5 0.04
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42
Consensus pattern (27 bp):
TCATTTTACCCTATAGGAGTATTTCGA
Found at i:17810254 original size:81 final size:81
Alignment explanation
Indices: 17810085--17810259 Score: 217
Period size: 81 Copynumber: 2.2 Consensus size: 81
17810075 AGGGGTATAA
* * * * * *
17810085 CAGTCATTTTACCGTATAGGGGTATTTAGGTCATTTTACCCTATAGGGGTATTTCGATCATTTTA
1 CAGTCATTTTACCCTATAGGAGTATTTAGATCATTTTACCATATAGGAGTATTTCGACCATTTTA
*
17810150 CCCTATGGGGGTATTT
66 CCCTATGGGAGTATTT
* * *
17810166 CAATCATTTTACCCTATAGGAGTATTTCGATCATTTTACCATAT-GAGAGTATTTCGGCCATTTT
1 CAGTCATTTTACCCTATAGGAGTATTTAGATCATTTTACCATATAG-GAGTATTTCGACCATTTT
*
17810230 ACCTTATGGGAGTATTT
65 ACCCTATGGGAGTATTT
**
17810247 TTGTCATTTTACC
1 CAGTCATTTTACC
17810260 TATTTTGGGA
Statistics
Matches: 79, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
80 1 0.01
81 78 0.99
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42
Consensus pattern (81 bp):
CAGTCATTTTACCCTATAGGAGTATTTAGATCATTTTACCATATAGGAGTATTTCGACCATTTTA
CCCTATGGGAGTATTT
Found at i:17811405 original size:13 final size:14
Alignment explanation
Indices: 17811382--17811410 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
17811372 CTCCTCAAAT
17811382 CTCTCCAAATATCC
1 CTCTCCAAATATCC
17811396 CTCT-CAAATATCC
1 CTCTCCAAATATCC
17811409 CT
1 CT
17811411 AAATCATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.28, C:0.41, G:0.00, T:0.31
Consensus pattern (14 bp):
CTCTCCAAATATCC
Found at i:17813345 original size:21 final size:21
Alignment explanation
Indices: 17813321--17813362 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
17813311 ACCCTATGAG
*
17813321 GGTATTTCGGTCATTTTACCC
1 GGTATTTCGATCATTTTACCC
17813342 GGTATTTCGATCATTTTACCC
1 GGTATTTCGATCATTTTACCC
17813363 TATGGGGGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.43
Consensus pattern (21 bp):
GGTATTTCGATCATTTTACCC
Found at i:17813497 original size:27 final size:26
Alignment explanation
Indices: 17813303--17813496 Score: 236
Period size: 27 Copynumber: 7.4 Consensus size: 26
17813293 GGGTATAATA
17813303 GTCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATG-GGGTATTTCG
17813330 GTCATTTTACCC-----GGTATTTCG
1 GTCATTTTACCCTATGGGGTATTTCG
* *
17813351 ATCATTTTACCCTATGGGGGTATTTCA
1 GTCATTTTACCCTAT-GGGGTATTTCG
*
17813378 GTCATTTTACCCTATGGGGATATTTTG
1 GTCATTTTACCCTATGGGG-TATTTCG
* *
17813405 GTCATTTTACCTTATGAGGGTATTTCA
1 GTCATTTTACCCTATG-GGGTATTTCG
17813432 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTAT-GGGGTATTTCG
* *
17813459 GTCATTTTACCTTATGGGAGTATTTTG
1 GTCATTTTACCCTATGGG-GTATTTCG
17813486 GTCATTTTACC
1 GTCATTTTACC
17813497 TATTTTGGGG
Statistics
Matches: 145, Mismatches: 12, Indels: 20
0.82 0.07 0.11
Matches are distributed among these distances:
21 20 0.14
26 7 0.05
27 114 0.79
28 4 0.03
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.43
Consensus pattern (26 bp):
GTCATTTTACCCTATGGGGTATTTCG
Found at i:17819084 original size:41 final size:41
Alignment explanation
Indices: 17819027--17819166 Score: 219
Period size: 41 Copynumber: 3.4 Consensus size: 41
17819017 GAGATAATTT
*
17819027 AGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATGTTTC
1 AGACTTTACGTCTAGCAAGCTTGATGCCGGTGAAATGTTTC
*
17819068 AGACTTTACATCTAGCAAGCTTGATGCCGAG-GAAATGTTTC
1 AGACTTTACGTCTAGCAAGCTTGATGCCG-GTGAAATGTTTC
*
17819109 AGACTTTACGTCTAGCAAGCTTGATGCCGGTGAAATATTTC
1 AGACTTTACGTCTAGCAAGCTTGATGCCGGTGAAATGTTTC
* *
17819150 GGACTTTAGGTCTAGCA
1 AGACTTTACGTCTAGCA
17819167 GGCTAATTGT
Statistics
Matches: 91, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
40 1 0.01
41 89 0.98
42 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (41 bp):
AGACTTTACGTCTAGCAAGCTTGATGCCGGTGAAATGTTTC
Found at i:17819343 original size:2 final size:2
Alignment explanation
Indices: 17819336--17819370 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
17819326 AGTTGAAAAG
*
17819336 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17819371 GGGTGCATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:17820236 original size:48 final size:48
Alignment explanation
Indices: 17820165--17820260 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
17820155 GGTTTAGATG
17820165 GATTGAAATTCTAAGTTTTGTTTTAAATGGTTTAAGTAAAATTTTTAA
1 GATTGAAATTCTAAGTTTTGTTTTAAATGGTTTAAGTAAAATTTTTAA
17820213 GATTGAAATTCTAAGTTTTGTTTTAAATGGTTTAAGTAAAATTTTTAA
1 GATTGAAATTCTAAGTTTTGTTTTAAATGGTTTAAGTAAAATTTTTAA
17820261 TTATGCTTAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (48 bp):
GATTGAAATTCTAAGTTTTGTTTTAAATGGTTTAAGTAAAATTTTTAA
Found at i:17822364 original size:41 final size:40
Alignment explanation
Indices: 17822297--17822376 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 40
17822287 AATACCGACC
* *
17822297 TTTTCATTGATATCTTCTTTGTATATCGTCCTTTTCAACA
1 TTTTCATTGATATCTTCTTTGGATATCATCCTTTTCAACA
17822337 TTTTCATTTGATATCCTT-TTTGGATATCATCCTTTTCAAC
1 TTTTCA-TTGATAT-CTTCTTTGGATATCATCCTTTTCAAC
17822377 CTATTATTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 6 0.17
41 27 0.75
42 3 0.08
ACGTcount: A:0.20, C:0.20, G:0.07, T:0.53
Consensus pattern (40 bp):
TTTTCATTGATATCTTCTTTGGATATCATCCTTTTCAACA
Found at i:17825598 original size:37 final size:37
Alignment explanation
Indices: 17825548--17825630 Score: 139
Period size: 37 Copynumber: 2.2 Consensus size: 37
17825538 CTTAGTGTCA
* *
17825548 TGGCGTGTTATCGATTAGATTAGCTTTTATGAGCGAT
1 TGGCGTGTTATCGAGTAGATTAGCTCTTATGAGCGAT
*
17825585 TGGCGTGTTATCGAGTGGATTAGCTCTTATGAGCGAT
1 TGGCGTGTTATCGAGTAGATTAGCTCTTATGAGCGAT
17825622 TGGCGTGTT
1 TGGCGTGTT
17825631 TCAGTTGGAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.18, C:0.12, G:0.31, T:0.39
Consensus pattern (37 bp):
TGGCGTGTTATCGAGTAGATTAGCTCTTATGAGCGAT
Found at i:17825942 original size:11 final size:12
Alignment explanation
Indices: 17825916--17825953 Score: 76
Period size: 12 Copynumber: 3.2 Consensus size: 12
17825906 CAAAACAGGA
17825916 TTTTAGCGGCGT
1 TTTTAGCGGCGT
17825928 TTTTAGCGGCGT
1 TTTTAGCGGCGT
17825940 TTTTAGCGGCGT
1 TTTTAGCGGCGT
17825952 TT
1 TT
17825954 AGACAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.08, C:0.16, G:0.32, T:0.45
Consensus pattern (12 bp):
TTTTAGCGGCGT
Found at i:17826048 original size:39 final size:39
Alignment explanation
Indices: 17825942--17826053 Score: 120
Period size: 39 Copynumber: 2.8 Consensus size: 39
17825932 AGCGGCGTTT
* *
17825942 TTAGCGGCGTTTAGACAAAAAATGCCACTAAAAATCAAGCA
1 TTAGCGGCGTTT-TAC-AAAAATGCCGCTAAAAATCAAGCA
* * *
17825983 TTAGCGGTGCCTTTACAAAAACGCCGCTAAAAAT-AAGCA
1 TTAGCGGCG-TTTTACAAAAATGCCGCTAAAAATCAAGCA
*
17826022 TTAGCGGCGTTTTCCAAAAAGTGCCGC-AAAAA
1 TTAGCGGCGTTTTACAAAAA-TGCCGCTAAAAA
17826054 GCCTAAGCCC
Statistics
Matches: 60, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
38 14 0.23
39 18 0.30
40 16 0.27
41 10 0.17
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (39 bp):
TTAGCGGCGTTTTACAAAAATGCCGCTAAAAATCAAGCA
Found at i:17826148 original size:41 final size:41
Alignment explanation
Indices: 17826103--17826303 Score: 348
Period size: 41 Copynumber: 4.9 Consensus size: 41
17826093 CTTTACCAGT
17826103 GTTTTTGAAGAAGCGCCGCTAATGCTCTGGCCTTTAGCGGC
1 GTTTTTGAAGAAGCGCCGCTAATGCTCTGGCCTTTAGCGGC
*
17826144 GTTTTTAAAGAAGCGCCGCTAATGCTCTGGCCTTTAGCGGC
1 GTTTTTGAAGAAGCGCCGCTAATGCTCTGGCCTTTAGCGGC
* *
17826185 GTTTTTGAAGAAGCGCCGCTAATGCTCTGGCCGTTAGCGGT
1 GTTTTTGAAGAAGCGCCGCTAATGCTCTGGCCTTTAGCGGC
* *
17826226 GTTTTTGAAAAAGCGCCGCTAATGCTCTGGCCGTTAGCGGC
1 GTTTTTGAAGAAGCGCCGCTAATGCTCTGGCCTTTAGCGGC
*
17826267 GTTTTTGAAGAAGCGCCGCTAATGCTCGGGCCTTTAG
1 GTTTTTGAAGAAGCGCCGCTAATGCTCTGGCCTTTAG
17826304 AATAAAATCT
Statistics
Matches: 151, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 151 1.00
ACGTcount: A:0.18, C:0.23, G:0.29, T:0.29
Consensus pattern (41 bp):
GTTTTTGAAGAAGCGCCGCTAATGCTCTGGCCTTTAGCGGC
Found at i:17826656 original size:41 final size:41
Alignment explanation
Indices: 17826569--17826684 Score: 135
Period size: 41 Copynumber: 2.8 Consensus size: 41
17826559 AATGCTCTAT
* * ** *
17826569 CCTTTAGCGACGTTTTTGAAGAAGCGCCGGC-ATTGCTCTGG
1 CCTTTAGCGGCGTTTTTGAAGAAGCGCC-GCTAATGCTAAGA
*
17826610 CCTTTAGCGGCATTTTTGAAGAAGCGCCGCTAATGCTAAGA
1 CCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTAAGA
* * *
17826651 TCTTTAGCAGCGTTTTTGAAAAAGCGCCGCTAAT
1 CCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAAT
17826685 ATATTTTTTA
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
40 2 0.03
41 62 0.97
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.29
Consensus pattern (41 bp):
CCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTAAGA
Found at i:17827391 original size:15 final size:15
Alignment explanation
Indices: 17827371--17827399 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
17827361 TTAAGATCAG
17827371 TTATGGATTTAGGGT
1 TTATGGATTTAGGGT
17827386 TTATGGATTTAGGG
1 TTATGGATTTAGGG
17827400 GTTAGAGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.34, T:0.45
Consensus pattern (15 bp):
TTATGGATTTAGGGT
Found at i:17827506 original size:33 final size:33
Alignment explanation
Indices: 17827460--17827531 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
17827450 ATTAAATAAT
*
17827460 GTTTAGGGGTTAGGGATTCGAGG-TCAGGTTAGG
1 GTTTAGGGATTAGGGATTC-AGGATCAGGTTAGG
*
17827493 GTTTAGGGATTAGGGATTCAGGATCGGGTTAGG
1 GTTTAGGGATTAGGGATTCAGGATCAGGTTAGG
17827526 GTTTAG
1 GTTTAG
17827532 AATTTAGATT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 3 0.08
33 33 0.92
ACGTcount: A:0.19, C:0.06, G:0.43, T:0.32
Consensus pattern (33 bp):
GTTTAGGGATTAGGGATTCAGGATCAGGTTAGG
Found at i:17828643 original size:132 final size:130
Alignment explanation
Indices: 17828491--17828732 Score: 396
Period size: 130 Copynumber: 1.8 Consensus size: 130
17828481 TAATTTTTTG
*
17828491 AATAGCGGCGTTTTTATAAAAAACGCCACAAAAAATAATTTTACTTTAAAAAAATAACGCCCTTT
1 AATAGCGGCGTTTTTATAAAAAACGCCACAAAAAATAATTTTA-TTTAAAAAAATAACGCCATTT
17828556 TAGCATAGCAAAACAGTGTCGTTTCATTCCAAATAAAATAATTTTTTTGCAGCCGAAAAAGTTAA
65 TA-CATAGCAAAACAGTGTCGTTTCATTCCAAATAAAATAATTTTTTTGCAGCCGAAAAAGTTAA
17828621 GC
129 GC
* *
17828623 AATAGCGGCGCTTTTT-TAAAAAACGCCACAAAAAATAATTTTATTTTAAAAAATAGCGCCATTT
1 AATAGCGGCG-TTTTTATAAAAAACGCCACAAAAAATAATTTTATTTAAAAAAATAACGCCATTT
* * *
17828687 TATATAGTAAAACAGTGTCGTTTTATTCCAAATAAAATAATTTTTT
65 TACATAGCAAAACAGTGTCGTTTCATTCCAAATAAAATAATTTTTT
17828733 GTGACATTTT
Statistics
Matches: 103, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
130 41 0.40
131 20 0.19
132 37 0.36
133 5 0.05
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (130 bp):
AATAGCGGCGTTTTTATAAAAAACGCCACAAAAAATAATTTTATTTAAAAAAATAACGCCATTTT
ACATAGCAAAACAGTGTCGTTTCATTCCAAATAAAATAATTTTTTTGCAGCCGAAAAAGTTAAGC
Found at i:17835000 original size:43 final size:42
Alignment explanation
Indices: 17834947--17835176 Score: 307
Period size: 43 Copynumber: 5.4 Consensus size: 42
17834937 AAGGTTATGC
* * *
17834947 CTTTAGCGGCGTTTTTGCGAGAAGCGCCGCTAAAGGTTATGGT
1 CTTTAGCGGCGTTTGTG-GAAAAGCGCCGCTAAAGGTCATGGT
*
17834990 CTTTAGCGGCGTTTGTGGGAAAAGCGCTGCTAAAGGTCATGGT
1 CTTTAGCGGCGTTTGT-GGAAAAGCGCCGCTAAAGGTCATGGT
** *
17835033 CTTTAATGGCGTTTGTGGGAAAAGCGCTGCTAAAGGTCATGGT
1 CTTTAGCGGCGTTTGT-GGAAAAGCGCCGCTAAAGGTCATGGT
*
17835076 CTTTAGCGGCGTTTGTGGAAAAGCGCCGCTAAAGGTCTTGGT
1 CTTTAGCGGCGTTTGTGGAAAAGCGCCGCTAAAGGTCATGGT
* ** *
17835118 TTTTAAAGGCGATTGTAGGAAAAGCGCCGCTAAAGGTCATGGT
1 CTTTAGCGGCGTTTGT-GGAAAAGCGCCGCTAAAGGTCATGGT
*
17835161 CTTTGGCGGCGTTTGT
1 CTTTAGCGGCGTTTGT
17835177 TTCTAAAAAC
Statistics
Matches: 165, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
42 36 0.22
43 128 0.78
44 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.30
Consensus pattern (42 bp):
CTTTAGCGGCGTTTGTGGAAAAGCGCCGCTAAAGGTCATGGT
Found at i:17835150 original size:85 final size:86
Alignment explanation
Indices: 17834968--17835176 Score: 330
Period size: 85 Copynumber: 2.4 Consensus size: 86
17834958 TTTTTGCGAG
* *
17834968 AAGCGCCGCTAAAGGTTATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCTGCTAAAGGTCATGGT
1 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGT
* * *
17835033 CTTTAATGGCGTTTGTGGGAA
66 CTTTAAAGGCGATTGTAGGAA
* *
17835054 AAGCGCTGCTAAAGGTCATGGTCTTTAGCGGCGTTTGT-GGAAAAGCGCCGCTAAAGGTCTTGGT
1 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGT
*
17835118 TTTTAAAGGCGATTGTAGGAA
66 CTTTAAAGGCGATTGTAGGAA
*
17835139 AAGCGCCGCTAAAGGTCATGGTCTTTGGCGGCGTTTGT
1 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGT
17835177 TTCTAAAAAC
Statistics
Matches: 113, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
85 77 0.68
86 36 0.32
ACGTcount: A:0.22, C:0.16, G:0.33, T:0.29
Consensus pattern (86 bp):
AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGT
CTTTAAAGGCGATTGTAGGAA
Found at i:17836778 original size:2 final size:2
Alignment explanation
Indices: 17836771--17836800 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17836761 GAGCACACTA
17836771 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
17836801 CATGTTCTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:17838733 original size:36 final size:36
Alignment explanation
Indices: 17838693--17838761 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
17838683 ATGTCATTCA
*
17838693 ATGGTTTAGCATTTGTTGTGAATCATCAAATGTGTG
1 ATGGTTTAGCATTTGTTGCGAATCATCAAATGTGTG
17838729 ATGGTTTAGCATTTGTTGCGAATCATCAAATGT
1 ATGGTTTAGCATTTGTTGCGAATCATCAAATGT
17838762 ACACTCTCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.41
Consensus pattern (36 bp):
ATGGTTTAGCATTTGTTGCGAATCATCAAATGTGTG
Found at i:17841603 original size:22 final size:22
Alignment explanation
Indices: 17841577--17841621 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
17841567 TAGAATAAGT
17841577 ATAAACCAAAACCAATGCCATA
1 ATAAACCAAAACCAATGCCATA
17841599 ATAAACCAAAACCAATGCCATA
1 ATAAACCAAAACCAATGCCATA
17841621 A
1 A
17841622 GCTTATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.56, C:0.27, G:0.04, T:0.13
Consensus pattern (22 bp):
ATAAACCAAAACCAATGCCATA
Found at i:17845487 original size:19 final size:18
Alignment explanation
Indices: 17845463--17845503 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 18
17845453 TAGGATTCTG
17845463 TATATCTGT-TCTGCATATC
1 TATATCTGTATCTG--TATC
17845482 TATATCTGTATCTGTATC
1 TATATCTGTATCTGTATC
17845500 TATA
1 TATA
17845504 AAGGACTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.24, C:0.17, G:0.10, T:0.49
Consensus pattern (18 bp):
TATATCTGTATCTGTATC
Found at i:17846306 original size:160 final size:161
Alignment explanation
Indices: 17846042--17846364 Score: 639
Period size: 160 Copynumber: 2.0 Consensus size: 161
17846032 GGCATCTCCG
17846042 AATTCGGCCATAACATCTAGGTTGGGTTTGGGGTGTTACACAAAATCTCATCCCAATGCACATGC
1 AATTCGGCCATAACATCTAGGTTGGGTTTGGGGTGTTACACAAAATCTCATCCCAATGCACATGC
17846107 AATATGTCATACAAATTCATACATAATCATATTCCAACCCTTTTCACATTTATTCGACATGTTCA
66 AATATGTCATACAAATTCATACATAATCATATTCCAACCCTTTTCACATTTATTCGACATGTTCA
17846172 ACATGTCCTCAATAATCACAT-CTTACAGAA
131 ACATGTCCTCAATAATCACATACTTACAGAA
17846202 AATTCGGCCATAACATCTAGGTTGGGTTTGGGGTGTTACACAAAATCTCATCCCAATGCACATGC
1 AATTCGGCCATAACATCTAGGTTGGGTTTGGGGTGTTACACAAAATCTCATCCCAATGCACATGC
17846267 AATATGTCATACAAATTCATACATAATCATATTCCAACCCTTTTCACATTTATTCGACATGTTCA
66 AATATGTCATACAAATTCATACATAATCATATTCCAACCCTTTTCACATTTATTCGACATGTTCA
17846332 ACATGTCCTCAATAATCACATACTTACAGAA
131 ACATGTCCTCAATAATCACATACTTACAGAA
17846363 AA
1 AA
17846365 AGGAAGCAGT
Statistics
Matches: 162, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
160 151 0.93
161 11 0.07
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.31
Consensus pattern (161 bp):
AATTCGGCCATAACATCTAGGTTGGGTTTGGGGTGTTACACAAAATCTCATCCCAATGCACATGC
AATATGTCATACAAATTCATACATAATCATATTCCAACCCTTTTCACATTTATTCGACATGTTCA
ACATGTCCTCAATAATCACATACTTACAGAA
Found at i:17848562 original size:26 final size:23
Alignment explanation
Indices: 17848508--17848562 Score: 56
Period size: 26 Copynumber: 2.3 Consensus size: 23
17848498 TAGCATAAGT
*
17848508 TAAATTTCAAAATCTTTATTTAT
1 TAAATTTCAAAATCTTTATTTAA
* *
17848531 TGAATTTACTAAATACTATTATTTAA
1 TAAATTT-CAAAAT-CT-TTATTTAA
17848557 TAAATT
1 TAAATT
17848563 CGTTAAATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
23 6 0.24
24 5 0.20
25 2 0.08
26 12 0.48
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (23 bp):
TAAATTTCAAAATCTTTATTTAA
Found at i:17849668 original size:18 final size:18
Alignment explanation
Indices: 17849645--17849679 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
17849635 GGCCTAGTAC
17849645 CCAAAC-TAAAGCCCAAAA
1 CCAAACTTAAA-CCCAAAA
17849663 CCAAACTTAAACCCAAA
1 CCAAACTTAAACCCAAA
17849680 CCTACCCCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.54, C:0.34, G:0.03, T:0.09
Consensus pattern (18 bp):
CCAAACTTAAACCCAAAA
Found at i:17850143 original size:100 final size:99
Alignment explanation
Indices: 17849966--17850261 Score: 389
Period size: 100 Copynumber: 3.0 Consensus size: 99
17849956 AAATAAAAGC
17849966 TACAGTGGATCAGATTAAAGCTACGACGGCAAATCTTGCTTCCCTGATATTGCAATTTAAAAGAT
1 TACAGTGGATCAGATTAAAGCTACGACGG-AAATCTTGCTTCCCTGATATTGCAATTTAAAAGAT
* * *
17850031 TGAAGCCACAACGGCGAATCTCAGTTCCCTGGCA-A
65 TGAAGCCGCAACGGCGAATCTTACTTCCCTGG-AGA
* * *
17850066 TACAGTGGAGCATATTAAAGCTATGACGGTAAATCTTGCTTCCCTGATATTGCAATTTAAAAGAT
1 TACAGTGGATCAGATTAAAGCTACGACGG-AAATCTTGCTTCCCTGATATTGCAATTTAAAAGAT
* *
17850131 TGAAGCCGCAACGGTGAATCTTACTTTCCTGGAGA
65 TGAAGCCGCAACGGCGAATCTTACTTCCCTGGAGA
* * * * * ** * *
17850166 TGCAGTGGATCAGATTGAAGCTACAACGGAGAATCTTG-TTCCCCGACATTATAATTAAAAATAT
1 TACAGTGGATCAGATTAAAGCTACGACGGA-AATCTTGCTTCCCTGATATTGCAATTTAAAAGAT
17850230 TGAAGCCGCAACGGCGAATCTTACTTCCCTGG
65 TGAAGCCGCAACGGCGAATCTTACTTCCCTGG
17850262 TGGTGTAATG
Statistics
Matches: 171, Mismatches: 23, Indels: 5
0.86 0.12 0.03
Matches are distributed among these distances:
99 52 0.30
100 119 0.70
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (99 bp):
TACAGTGGATCAGATTAAAGCTACGACGGAAATCTTGCTTCCCTGATATTGCAATTTAAAAGATT
GAAGCCGCAACGGCGAATCTTACTTCCCTGGAGA
Found at i:17850145 original size:50 final size:50
Alignment explanation
Indices: 17849977--17850260 Score: 144
Period size: 50 Copynumber: 5.7 Consensus size: 50
17849967 ACAGTGGATC
* * * * *
17849977 AGATTAAAGCTACGACGGCAAATCTTGCTTCCCTGATATTGCAATTTAAA
1 AGATTGAAGCCACAACGGCAAATCTTGCTTCCCTGACATTGCAATTGAAA
* * * * * * * **
17850027 AGATTGAAGCCACAACGGCGAATCTCAG-TTCCCTGGCAATACAGTGGAGC
1 AGATTGAAGCCACAACGGCAAATCT-TGCTTCCCTGACATTGCAATTGAAA
* * * ** * * *
17850077 ATATTAAAGCTATGACGGTAAATCTTGCTTCCCTGATATTGCAATTTAAA
1 AGATTGAAGCCACAACGGCAAATCTTGCTTCCCTGACATTGCAATTGAAA
* ** * * * * * **
17850127 AGATTGAAGCCGCAACGGTGAATCTTACTTTCCTGGAGA-TGCAGTGGATC
1 AGATTGAAGCCACAACGGCAAATCTTGCTTCCCT-GACATTGCAATTGAAA
* * ** *
17850177 AGATTGAAGCTACAACGG-AGAATCTTG-TTCCCCGACATTATAATTAAAA
1 AGATTGAAGCCACAACGGCA-AATCTTGCTTCCCTGACATTGCAATTGAAA
* * * *
17850226 ATATTGAAGCCGCAACGGCGAATCTTACTTCCCTG
1 AGATTGAAGCCACAACGGCAAATCTTGCTTCCCTG
17850261 GTGGTGTAAT
Statistics
Matches: 161, Mismatches: 66, Indels: 14
0.67 0.27 0.06
Matches are distributed among these distances:
48 3 0.02
49 30 0.19
50 124 0.77
51 4 0.02
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (50 bp):
AGATTGAAGCCACAACGGCAAATCTTGCTTCCCTGACATTGCAATTGAAA
Found at i:17850251 original size:99 final size:100
Alignment explanation
Indices: 17849968--17850326 Score: 384
Period size: 100 Copynumber: 3.6 Consensus size: 100
17849958 ATAAAAGCTA
* * *
17849968 CAGTGGATCAGATTAAAGCTACGACGGCAAATCTTGCTTCCCTGATATTGCAATTTAAAAGATTG
1 CAGTGGATCAGATTAAAGCTACAACGGCAAATCTTGCTTCCCCGACATTGCAATTTAAAAGATTG
* * * *
17850033 AAGCCACAACGGCGAATCTCAGTTCCCTGGCA-ATA
66 AAGCCGCAACGGCGAATCTTACTTCCCTGG-AGATG
* * ** * * *
17850068 CAGTGGAGCATATTAAAGCTATGACGGTAAATCTTGCTTCCCTGATATTGCAATTTAAAAGATTG
1 CAGTGGATCAGATTAAAGCTACAACGGCAAATCTTGCTTCCCCGACATTGCAATTTAAAAGATTG
* *
17850133 AAGCCGCAACGGTGAATCTTACTTTCCTGGAGATG
66 AAGCCGCAACGGCGAATCTTACTTCCCTGGAGATG
* ** * *
17850168 CAGTGGATCAGATTGAAGCTACAACGG-AGAATCTTG-TTCCCCGACATTATAATTAAAAATATT
1 CAGTGGATCAGATTAAAGCTACAACGGCA-AATCTTGCTTCCCCGACATTGCAATTTAAAAGATT
* *
17850231 GAAGCCGCAACGGCGAATCTTACTTCCCTGGTGGTG
65 GAAGCCGCAACGGCGAATCTTACTTCCCTGGAGATG
* * * * ** * *
17850267 TAATGGGA-CAGATTGAAGCTACAACAGTGAATCTTGCTTCCCCGACATCGCAGTTTAAAA
1 CAGT-GGATCAGATTAAAGCTACAACGGCAAATCTTGCTTCCCCGACATTGCAATTTAAAA
17850327 ATTTTGAAGC
Statistics
Matches: 220, Mismatches: 34, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
99 82 0.37
100 138 0.63
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (100 bp):
CAGTGGATCAGATTAAAGCTACAACGGCAAATCTTGCTTCCCCGACATTGCAATTTAAAAGATTG
AAGCCGCAACGGCGAATCTTACTTCCCTGGAGATG
Found at i:17850749 original size:18 final size:18
Alignment explanation
Indices: 17850726--17850760 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
17850716 GGCCTAGTAC
17850726 CCAAAC-TAAAGCCCAAAA
1 CCAAACTTAAA-CCCAAAA
17850744 CCAAACTTAAACCCAAA
1 CCAAACTTAAACCCAAA
17850761 CCTACCCCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.54, C:0.34, G:0.03, T:0.09
Consensus pattern (18 bp):
CCAAACTTAAACCCAAAA
Found at i:17859539 original size:20 final size:20
Alignment explanation
Indices: 17859514--17859555 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
17859504 TTTATGTTAG
17859514 TATATATTTATAATTGAAAA
1 TATATATTTATAATTGAAAA
*
17859534 TATATATTTATAGTTGAAAA
1 TATATATTTATAATTGAAAA
17859554 TA
1 TA
17859556 AGTTATTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
TATATATTTATAATTGAAAA
Found at i:17859590 original size:3 final size:3
Alignment explanation
Indices: 17859582--17859633 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
17859572 TGTTGCTAAA
* * *
17859582 TAT TAT TAT GAT TAT TAT TAT CAT TAT TAT TAC TACT T-T TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TA-T TAT
17859628 TAT TAT
1 TAT TAT
17859634 GGTAATTACT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
2 2 0.05
3 34 0.85
4 4 0.10
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:17861037 original size:26 final size:26
Alignment explanation
Indices: 17861008--17861059 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
17860998 TAACAAACAT
17861008 GGATTTATTTCAATACAAAAATTTAC
1 GGATTTATTTCAATACAAAAATTTAC
17861034 GGATTTATTTCAATACAAAAATTTAC
1 GGATTTATTTCAATACAAAAATTTAC
17861060 TTTTAAATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (26 bp):
GGATTTATTTCAATACAAAAATTTAC
Done.