Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 31 of 208
Found at i:12276701 original size:13 final size:13
Alignment explanation
Indices: 12276683--12276707 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12276673 TGTCTTTACC
12276683 TATTAAATATATA
1 TATTAAATATATA
12276696 TATTAAATATAT
1 TATTAAATATAT
12276708 TAAAATTTTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TATTAAATATATA
Found at i:12279043 original size:21 final size:21
Alignment explanation
Indices: 12278980--12279052 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 21
12278970 CAGAAATCTC
*
12278980 CCCTCGTTGTTGCTGGTTTCT
1 CCCTCGTTTTTGCTGGTTTCT
* * *
12279001 CCCT--TGTTTACTGGTTTGT
1 CCCTCGTTTTTGCTGGTTTCT
*
12279020 CCCTCGTTTTTGCTAGTTTCT
1 CCCTCGTTTTTGCTGGTTTCT
*
12279041 CCCCTCTTTTTT
1 -CCCTCGTTTTT
12279053 ACTTTGTTCT
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
19 15 0.38
21 15 0.38
22 10 0.25
ACGTcount: A:0.03, C:0.29, G:0.16, T:0.52
Consensus pattern (21 bp):
CCCTCGTTTTTGCTGGTTTCT
Found at i:12281534 original size:6 final size:6
Alignment explanation
Indices: 12281523--12281560 Score: 67
Period size: 6 Copynumber: 6.2 Consensus size: 6
12281513 TATTGTTGAT
12281523 AATGGG AATGGG AATGGG AATGGG AATGGG AAATGGG A
1 AATGGG AATGGG AATGGG AATGGG AATGGG -AATGGG A
12281561 GGAGGGCACG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.37, C:0.00, G:0.47, T:0.16
Consensus pattern (6 bp):
AATGGG
Found at i:12281635 original size:60 final size:59
Alignment explanation
Indices: 12281538--12281734 Score: 242
Period size: 60 Copynumber: 3.3 Consensus size: 59
12281528 GAATGGGAAT
12281538 GGGA-ATGGGAATGGGAAATGGGAGGAGGGCACGGTGGAAGAGGGGAATCGATGGAAGAG
1 GGGAGATGGGAATGGGAAATGGGAGGAGGGCACGGTGGAAGAGGGGAAT-GATGGAAGAG
* * * * *
12281597 GGGAGATGGGAATGGGAAATGGGAGGACGGCATGGTGGAA-TGGGAAAT--TGGAA-TG
1 GGGAGATGGGAATGGGAAATGGGAGGAGGGCACGGTGGAAGAGGGGAATGATGGAAGAG
* * *
12281652 GGTATTGCATGGGAATAGGAAATGGGAGGAGGGAACGGTGGAAGAGGGGAATGATGGAAGAG
1 GGGA--G-ATGGGAATGGGAAATGGGAGGAGGGCACGGTGGAAGAGGGGAATGATGGAAGAG
12281714 GGGAGATGGGAATGGAGAAAT
1 GGGAGATGGGAATGG-GAAAT
12281735 TGCATTGTAT
Statistics
Matches: 114, Mismatches: 15, Indels: 17
0.78 0.10 0.12
Matches are distributed among these distances:
55 4 0.04
56 5 0.04
57 1 0.01
58 31 0.27
59 25 0.22
60 39 0.34
61 5 0.04
62 4 0.04
ACGTcount: A:0.33, C:0.04, G:0.50, T:0.14
Consensus pattern (59 bp):
GGGAGATGGGAATGGGAAATGGGAGGAGGGCACGGTGGAAGAGGGGAATGATGGAAGAG
Found at i:12288070 original size:17 final size:17
Alignment explanation
Indices: 12288035--12288073 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
12288025 TTTTTTGGAG
*
12288035 TTTTATATTCTAATATA
1 TTTTATATTCAAATATA
* *
12288052 TTTTATATTGAAATTTA
1 TTTTATATTCAAATATA
12288069 TTTTA
1 TTTTA
12288074 AATATATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (17 bp):
TTTTATATTCAAATATA
Found at i:12288093 original size:23 final size:23
Alignment explanation
Indices: 12288063--12288156 Score: 78
Period size: 22 Copynumber: 4.3 Consensus size: 23
12288053 TTTATATTGA
12288063 AATT-TAT-TTTAAATATATAA-
1 AATTATATATTTAAATATATAAT
*
12288083 AATTATATATTTAAATTTATAAT
1 AATTATATATTTAAATATATAAT
* * *
12288106 GATTATAT-TTT-AAT-TCTTAT
1 AATTATATATTTAAATATATAAT
12288126 AGATTATATATTTAAAT-TA-AAT
1 A-ATTATATATTTAAATATATAAT
12288148 AATTGATAT
1 AATT-ATAT
12288157 TAATTACTTA
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
20 8 0.13
21 16 0.27
22 25 0.42
23 11 0.18
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (23 bp):
AATTATATATTTAAATATATAAT
Found at i:12291767 original size:20 final size:19
Alignment explanation
Indices: 12291734--12291789 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
12291724 TGAAAAATAA
*
12291734 TAAAATAAATAAATAATACAT
1 TAAATTAAA-AAATAATAC-T
*
12291755 TAAATTAAAAAATAATTCT
1 TAAATTAAAAAATAATACT
*
12291774 TAATTTTAAAAAATAA
1 TAA-ATTAAAAAATAA
12291790 ATATAATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.13
20 19 0.61
21 8 0.26
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (19 bp):
TAAATTAAAAAATAATACT
Found at i:12291796 original size:19 final size:20
Alignment explanation
Indices: 12291759--12291797 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
12291749 ATACATTAAA
* *
12291759 TTAAAAAATAATTCTTAATT
1 TTAAAAAATAAATCATAATT
12291779 TTAAAAAATAAAT-ATAATT
1 TTAAAAAATAAATCATAATT
12291798 ATCTAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (20 bp):
TTAAAAAATAAATCATAATT
Found at i:12299147 original size:2 final size:2
Alignment explanation
Indices: 12299140--12299167 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12299130 ATATAAAAAC
12299140 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
12299168 TTCTGGGTTT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:12303783 original size:11 final size:11
Alignment explanation
Indices: 12303767--12303794 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
12303757 GTCGCCTCTT
12303767 CCTTCGTTCTA
1 CCTTCGTTCTA
12303778 CCTTCGTTCTA
1 CCTTCGTTCTA
12303789 CCTTCG
1 CCTTCG
12303795 CCTCCCGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.07, C:0.39, G:0.11, T:0.43
Consensus pattern (11 bp):
CCTTCGTTCTA
Found at i:12307323 original size:18 final size:17
Alignment explanation
Indices: 12307295--12307329 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12307285 ATTATTAAGA
*
12307295 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
12307312 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
12307330 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:12307669 original size:44 final size:45
Alignment explanation
Indices: 12307604--12307694 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
12307594 ACCTCTATTC
* * *
12307604 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
12307648 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
12307693 CA
1 CA
12307695 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:12307696 original size:16 final size:16
Alignment explanation
Indices: 12307675--12307724 Score: 82
Period size: 16 Copynumber: 3.1 Consensus size: 16
12307665 GATTAGCTAT
12307675 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
12307691 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
*
12307708 TCCACCTCTAATCCAA
1 TACACCTCTAATCCAA
12307724 T
1 T
12307725 TGAATAGTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 17 0.53
17 15 0.47
ACGTcount: A:0.34, C:0.40, G:0.00, T:0.26
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:12307713 original size:17 final size:17
Alignment explanation
Indices: 12307675--12307721 Score: 78
Period size: 17 Copynumber: 2.8 Consensus size: 17
12307665 GATTAGCTAT
12307675 TACACCTCTAAT-CCAA
1 TACACCTCTAATCCCAA
12307691 TACACCTCTAATCCCAA
1 TACACCTCTAATCCCAA
*
12307708 TCCACCTCTAATCC
1 TACACCTCTAATCC
12307722 AATTGAATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 12 0.41
17 17 0.59
ACGTcount: A:0.32, C:0.43, G:0.00, T:0.26
Consensus pattern (17 bp):
TACACCTCTAATCCCAA
Found at i:12311223 original size:17 final size:17
Alignment explanation
Indices: 12311201--12311233 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12311191 CGAAACCCTG
12311201 AGTTTGTTCTGTTTTCT
1 AGTTTGTTCTGTTTTCT
*
12311218 AGTTTGTTCTTTTTTC
1 AGTTTGTTCTGTTTTC
12311234 CTTCTTTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.12, G:0.15, T:0.67
Consensus pattern (17 bp):
AGTTTGTTCTGTTTTCT
Found at i:12315261 original size:24 final size:24
Alignment explanation
Indices: 12315229--12315276 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
12315219 CATTAGTACA
12315229 TGCCAAAATTACAAAAAGAAACGT
1 TGCCAAAATTACAAAAAGAAACGT
12315253 TGCCAAAATTACAAAAAGAAACGT
1 TGCCAAAATTACAAAAAGAAACGT
12315277 CACCAACATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.17, G:0.12, T:0.17
Consensus pattern (24 bp):
TGCCAAAATTACAAAAAGAAACGT
Found at i:12315282 original size:24 final size:24
Alignment explanation
Indices: 12315231--12315282 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
12315221 TTAGTACATG
**
12315231 CCAAAATTACAAAAAGAAACGTTG
1 CCAAAATTACAAAAAGAAACGTCA
12315255 CCAAAATTACAAAAAGAAACGTCA
1 CCAAAATTACAAAAAGAAACGTCA
12315279 CCAA
1 CCAA
12315283 CATTGAGTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.56, C:0.21, G:0.10, T:0.13
Consensus pattern (24 bp):
CCAAAATTACAAAAAGAAACGTCA
Found at i:12325958 original size:4 final size:4
Alignment explanation
Indices: 12325949--12325991 Score: 59
Period size: 4 Copynumber: 10.8 Consensus size: 4
12325939 TATCTATATC
* * *
12325949 ACAT ACAT ACAC GCAT ACAT ACAT ACAT ACAT GCAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
12325992 GCATATCTGC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.47, C:0.28, G:0.05, T:0.21
Consensus pattern (4 bp):
ACAT
Found at i:12325967 original size:12 final size:11
Alignment explanation
Indices: 12325950--12325996 Score: 55
Period size: 12 Copynumber: 4.4 Consensus size: 11
12325940 ATCTATATCA
12325950 CATACATACACG
1 CATACATACA-G
12325962 CATACAT--A-
1 CATACATACAG
12325970 CATACATACATG
1 CATACATACA-G
12325982 CATACATACAG
1 CATACATACAG
12325993 CATA
1 CATA
12325997 TCTGCATCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
8 7 0.23
10 2 0.06
11 5 0.16
12 17 0.55
ACGTcount: A:0.45, C:0.28, G:0.06, T:0.21
Consensus pattern (11 bp):
CATACATACAG
Found at i:12326728 original size:2 final size:2
Alignment explanation
Indices: 12326717--12326745 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
12326707 ACTTGTAAAT
12326717 TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
12326746 AAATCATCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:12332918 original size:21 final size:22
Alignment explanation
Indices: 12332871--12332920 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
12332861 TGAAATTAAT
*
12332871 GTTTAATTTTTTTAAAAATCTAA
1 GTTTAATTTTCTTAAAAA-CTAA
12332894 --TTAATTTTCTTAAAAA-TAA
1 GTTTAATTTTCTTAAAAACTAA
12332913 GTTTAATT
1 GTTTAATT
12332921 ATTAAACGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
19 3 0.12
21 21 0.88
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (22 bp):
GTTTAATTTTCTTAAAAACTAA
Found at i:12333509 original size:12 final size:12
Alignment explanation
Indices: 12333492--12333516 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12333482 TTTTTATGGT
12333492 ATTCTTATTTTC
1 ATTCTTATTTTC
12333504 ATTCTTATTTTC
1 ATTCTTATTTTC
12333516 A
1 A
12333517 AACATAGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.16, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTCTTATTTTC
Found at i:12353261 original size:25 final size:26
Alignment explanation
Indices: 12353227--12353275 Score: 91
Period size: 25 Copynumber: 1.9 Consensus size: 26
12353217 AAGTCATCTC
12353227 CAGTTAGATTAC-TTCAAAATGCTGA
1 CAGTTAGATTACTTTCAAAATGCTGA
12353252 CAGTTAGATTACTTTCAAAATGCT
1 CAGTTAGATTACTTTCAAAATGCT
12353276 TTCCAGATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (26 bp):
CAGTTAGATTACTTTCAAAATGCTGA
Found at i:12363004 original size:13 final size:13
Alignment explanation
Indices: 12362986--12363012 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12362976 AGTTATTCAT
12362986 TATTTTTGAAAAG
1 TATTTTTGAAAAG
12362999 TATTTTTGAAAAG
1 TATTTTTGAAAAG
12363012 T
1 T
12363013 TTGGTTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (13 bp):
TATTTTTGAAAAG
Found at i:12363604 original size:31 final size:31
Alignment explanation
Indices: 12363564--12363623 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
12363554 AGTAATGAAA
12363564 AACTAGTCCTAAGACAAATAATAAATAAAAG
1 AACTAGTCCTAAGACAAATAATAAATAAAAG
*
12363595 AACTGGTCCTAAGACAAATAATAAATAAA
1 AACTAGTCCTAAGACAAATAATAAATAAA
12363624 TCACTTTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.57, C:0.13, G:0.10, T:0.20
Consensus pattern (31 bp):
AACTAGTCCTAAGACAAATAATAAATAAAAG
Found at i:12378268 original size:21 final size:21
Alignment explanation
Indices: 12378221--12378261 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
12378211 GTATCAGCAT
12378221 ATTGAACCGGCTAAAAAATCA
1 ATTGAACCGGCTAAAAAATCA
* *
12378242 ATTGAACTGGCTGAAAAATC
1 ATTGAACCGGCTAAAAAATC
12378262 GGTTGAATCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.22
Consensus pattern (21 bp):
ATTGAACCGGCTAAAAAATCA
Found at i:12389113 original size:7 final size:7
Alignment explanation
Indices: 12389103--12389155 Score: 97
Period size: 7 Copynumber: 7.6 Consensus size: 7
12389093 TAAAATATAA
12389103 ATATTCT
1 ATATTCT
12389110 ATATTCT
1 ATATTCT
12389117 ATATTCT
1 ATATTCT
12389124 ATATTCT
1 ATATTCT
12389131 ATATTCT
1 ATATTCT
12389138 ATATTCT
1 ATATTCT
*
12389145 ATATTTT
1 ATATTCT
12389152 ATAT
1 ATAT
12389156 ATTGGGTTGG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
7 45 1.00
ACGTcount: A:0.30, C:0.11, G:0.00, T:0.58
Consensus pattern (7 bp):
ATATTCT
Found at i:12391851 original size:18 final size:18
Alignment explanation
Indices: 12391828--12391864 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
12391818 GGTTTTCTTT
12391828 GGATTCAAACACAATACA
1 GGATTCAAACACAATACA
12391846 GGATTCAAACACAATACA
1 GGATTCAAACACAATACA
12391864 G
1 G
12391865 TGCGTTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.22, G:0.14, T:0.16
Consensus pattern (18 bp):
GGATTCAAACACAATACA
Found at i:12392178 original size:22 final size:22
Alignment explanation
Indices: 12392150--12392222 Score: 114
Period size: 21 Copynumber: 3.4 Consensus size: 22
12392140 CAAAACAACA
12392150 GTTTCTCCCTTCGTTCTTGCTG
1 GTTTCTCCCTTCGTTCTTGCTG
12392172 GTTTCTCCCTT-GTTCTTGCTG
1 GTTTCTCCCTTCGTTCTTGCTG
* *
12392193 GTTTGTCCC-TCGTTTTTGCTG
1 GTTTCTCCCTTCGTTCTTGCTG
12392214 GTTTCTCCC
1 GTTTCTCCC
12392223 CTCTTTTTTG
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
20 1 0.02
21 35 0.74
22 11 0.23
ACGTcount: A:0.00, C:0.30, G:0.19, T:0.51
Consensus pattern (22 bp):
GTTTCTCCCTTCGTTCTTGCTG
Found at i:12392241 original size:22 final size:22
Alignment explanation
Indices: 12392150--12392234 Score: 102
Period size: 21 Copynumber: 4.0 Consensus size: 22
12392140 CAAAACAACA
* *
12392150 GTTTCTCCCTTCGTTCTTGCTG
1 GTTTCTCCCCTCGTTTTTGCTG
* *
12392172 GTTTCT-CCCTTGTTCTTGCTG
1 GTTTCTCCCCTCGTTTTTGCTG
*
12392193 GTTTGT-CCCTCGTTTTTGCTG
1 GTTTCTCCCCTCGTTTTTGCTG
*
12392214 GTTTCTCCCCTCTTTTTTGCT
1 GTTTCTCCCCTCGTTTTTGCT
12392235 TTGTTCTTGG
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
21 36 0.65
22 19 0.35
ACGTcount: A:0.00, C:0.29, G:0.18, T:0.53
Consensus pattern (22 bp):
GTTTCTCCCCTCGTTTTTGCTG
Found at i:12400053 original size:50 final size:50
Alignment explanation
Indices: 12399928--12400171 Score: 256
Period size: 50 Copynumber: 4.7 Consensus size: 50
12399918 GATAATAACA
* * ** * *
12399928 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* * * *
12399979 TCCCCATGCCATGTCCCAGGCATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * * *
12400029 TGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
12400079 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
*
12400134 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA
12400172 TCTTTTTACC
Statistics
Matches: 160, Mismatches: 26, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
49 1 0.01
50 88 0.55
51 31 0.19
53 2 0.01
54 1 0.01
55 2 0.01
56 35 0.22
ACGTcount: A:0.20, C:0.29, G:0.25, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:12400114 original size:100 final size:105
Alignment explanation
Indices: 12399927--12400173 Score: 335
Period size: 100 Copynumber: 2.4 Consensus size: 105
12399917 TGATAATAAC
**
12399927 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTCCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCCTCTCGTGATGGTCCCCATGCCATG
* * *
12399992 TCCCAGGCATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
66 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
* * * *
12400029 -TGCCAACGCCATGTCCTAGACATGGTCTTACATGGGA-CCTCTCGT-CTCGGTGCCCATGCCAT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCCTCTCGTGAT-GGTCCCCATGCCAT
12400091 GTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
65 GTCCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
*
12400134 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATC
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATC
12400174 TTTTTACCCA
Statistics
Matches: 126, Mismatches: 11, Indels: 11
0.85 0.07 0.07
Matches are distributed among these distances:
99 1 0.01
100 48 0.38
101 35 0.28
103 3 0.02
104 1 0.01
105 2 0.02
106 35 0.28
107 1 0.01
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (105 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCCTCTCGTGATGGTCCCCATGCCATG
TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:12400292 original size:13 final size:13
Alignment explanation
Indices: 12400271--12400302 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
12400261 GCTTGGATCA
*
12400271 TCATCAAATAAAT
1 TCATAAAATAAAT
12400284 TCATAAAATAAAT
1 TCATAAAATAAAT
12400297 TCATAA
1 TCATAA
12400303 TTGCTGGAAA
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:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:12400548 original size:30 final size:30
Alignment explanation
Indices: 12400514--12400571 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
12400504 CCTCGACTCT
**
12400514 AACTTTTTGAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
12400544 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
12400572 AAGGCTCGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.22, G:0.05, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:12401066 original size:4 final size:4
Alignment explanation
Indices: 12401057--12401084 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
12401047 CCTTTTTCTT
12401057 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
12401085 CTTCCTTCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:12401162 original size:15 final size:15
Alignment explanation
Indices: 12401134--12401175 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
12401124 GTTTCGTCTC
* *
12401134 TTCTATTCTGTTTCTT
1 TTCT-TTCTTTTTCTA
12401150 TTCTTTCTTTTTCTA
1 TTCTTTCTTTTTCTA
12401165 TTCTTTCTTTT
1 TTCTTTCTTTT
12401176 GTTTTATGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 20 0.83
16 4 0.17
ACGTcount: A:0.05, C:0.19, G:0.02, T:0.74
Consensus pattern (15 bp):
TTCTTTCTTTTTCTA
Found at i:12401197 original size:5 final size:5
Alignment explanation
Indices: 12401189--12401225 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
12401179 TTATGTGTAT
12401189 ATATA ATATA ATATA ATAT- AT-TA ATGATA ATATA ATA
1 ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA ATA
12401226 GAAAACATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
3 1 0.03
4 4 0.14
5 20 0.69
6 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (5 bp):
ATATA
Found at i:12401218 original size:19 final size:19
Alignment explanation
Indices: 12401186--12401225 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
12401176 GTTTTATGTG
12401186 TATATATAATATAATATAA
1 TATATATAATATAATATAA
12401205 TATAT-TAATGATAATATAA
1 TATATATAAT-ATAATATAA
12401224 TA
1 TA
12401226 GAAAACATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
TATATATAATATAATATAA
Found at i:12404283 original size:15 final size:15
Alignment explanation
Indices: 12404263--12404295 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
12404253 TTAAAGTTTG
12404263 TTATTATAATTTTTT
1 TTATTATAATTTTTT
12404278 TTATTATAATTTTTT
1 TTATTATAATTTTTT
12404293 TTA
1 TTA
12404296 CAAATGCAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTATTATAATTTTTT
Found at i:12405353 original size:22 final size:24
Alignment explanation
Indices: 12405316--12405363 Score: 82
Period size: 22 Copynumber: 2.1 Consensus size: 24
12405306 AACATAGATG
12405316 AAATGATTAATTTAGCTATGCAGA
1 AAATGATTAATTTAGCTATGCAGA
12405340 AAAT-ATT-ATTTAGCTATGCAGA
1 AAATGATTAATTTAGCTATGCAGA
12405362 AA
1 AA
12405364 TTGGACAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 17 0.71
23 3 0.12
24 4 0.17
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (24 bp):
AAATGATTAATTTAGCTATGCAGA
Found at i:12416633 original size:6 final size:6
Alignment explanation
Indices: 12416622--12416649 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
12416612 ATCCAATTCT
12416622 ATCTCC ATCTCC ATCTCC ATCTCC ATCT
1 ATCTCC ATCTCC ATCTCC ATCTCC ATCT
12416650 ACAGGACAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.46, G:0.00, T:0.36
Consensus pattern (6 bp):
ATCTCC
Found at i:12418010 original size:3 final size:3
Alignment explanation
Indices: 12418002--12418189 Score: 65
Period size: 3 Copynumber: 62.7 Consensus size: 3
12417992 AGTTGTTTCT
* * **
12418002 TGC TGC TGC TGC TGC TG- TGGC TGC TGT TGT TG- TAAT TGC TGC TGC
1 TGC TGC TGC TGC TGC TGC T-GC TGC TGC TGC TGC T-GC TGC TGC TGC
* * * * * * ** ** **
12418047 TGT TGC AGC TGT TGT TGC TGA TGA TGC AAC TGC TGC TGC AAC TGC AAC
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC
* * * * ** **
12418095 TGT TGC TGT TGT TGT TGC TGC TGC TGC TGC TGC TGC AAC TGC AAC TGC
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC
* * *** **
12418143 TGC TGT TGT TGC TGC TGC AAT TGC AAC TGC TGC TGC TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
12418190 GTTCATGTAA
Statistics
Matches: 133, Mismatches: 48, Indels: 8
0.70 0.25 0.04
Matches are distributed among these distances:
2 2 0.02
3 129 0.97
4 2 0.02
ACGTcount: A:0.10, C:0.24, G:0.30, T:0.36
Consensus pattern (3 bp):
TGC
Found at i:12418144 original size:30 final size:30
Alignment explanation
Indices: 12418110--12418189 Score: 133
Period size: 30 Copynumber: 2.7 Consensus size: 30
12418100 CTGTTGTTGT
12418110 TGCTGCTGCTGCTGCTGCTGCAACTGCAAC
1 TGCTGCTGCTGCTGCTGCTGCAACTGCAAC
* * *
12418140 TGCTGCTGTTGTTGCTGCTGCAATTGCAAC
1 TGCTGCTGCTGCTGCTGCTGCAACTGCAAC
12418170 TGCTGCTGCTGCTGCTGCTG
1 TGCTGCTGCTGCTGCTGCTG
12418190 GTTCATGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.10, C:0.29, G:0.29, T:0.33
Consensus pattern (30 bp):
TGCTGCTGCTGCTGCTGCTGCAACTGCAAC
Found at i:12418173 original size:45 final size:45
Alignment explanation
Indices: 12418079--12418175 Score: 131
Period size: 45 Copynumber: 2.2 Consensus size: 45
12418069 GATGCAACTG
* * ** **
12418079 CTGCTGCAACTGCAACTGTTGCTGTTGTTGTTGCTGCTGCTGCTG
1 CTGCTGCAACTGCAACTGCTGCTGTTGTTGCTGCTGCAACTGCAA
*
12418124 CTGCTGCAACTGCAACTGCTGCTGTTGTTGCTGCTGCAATTGCAA
1 CTGCTGCAACTGCAACTGCTGCTGTTGTTGCTGCTGCAACTGCAA
12418169 CTGCTGC
1 CTGCTGC
12418176 TGCTGCTGCT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.12, C:0.27, G:0.27, T:0.34
Consensus pattern (45 bp):
CTGCTGCAACTGCAACTGCTGCTGTTGTTGCTGCTGCAACTGCAA
Found at i:12418189 original size:45 final size:43
Alignment explanation
Indices: 12418054--12418181 Score: 125
Period size: 45 Copynumber: 2.8 Consensus size: 43
12418044 TGCTGTTGCA
* *
12418054 GCTGTTGTTGCTGATG-ATGCAACTGCTGCTGCAACTGCAACTGTT
1 GCTGTTGTTGCTGCTGCATGCAACTGCTGCTG---CTGCAACTGCT
* **
12418099 GCTGTTGTTGTTGCTGC-TGCTGCTGCTGCTGCAACTGCAACTGCT
1 GCTGTTGTTGCTGCTGCATGCAACTGCTGCTG---CTGCAACTGCT
12418144 GCTGTTGTTGCTGCTGCAATTGCAACTGCTGCTGCTGC
1 GCTGTTGTTGCTGCTGC-A-TGCAACTGCTGCTGCTGC
12418182 TGCTGCTGGT
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
45 59 0.83
48 12 0.17
ACGTcount: A:0.12, C:0.25, G:0.28, T:0.34
Consensus pattern (43 bp):
GCTGTTGTTGCTGCTGCATGCAACTGCTGCTGCTGCAACTGCT
Found at i:12426246 original size:14 final size:14
Alignment explanation
Indices: 12426227--12426257 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
12426217 CTACCTCCGT
12426227 CCTCCACCGATCCA
1 CCTCCACCGATCCA
*
12426241 CCTCCACCGGTCCA
1 CCTCCACCGATCCA
12426255 CCT
1 CCT
12426258 TCGGTCTACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.58, G:0.10, T:0.16
Consensus pattern (14 bp):
CCTCCACCGATCCA
Found at i:12429191 original size:16 final size:19
Alignment explanation
Indices: 12429166--12429217 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
12429156 TAAAAATAAT
*
12429166 TTAAA-ATATAAAAATTTA
1 TTAAATATATATAAATTTA
12429184 TTAATATATATATAAATTTA
1 TTAA-ATATATATAAATTTA
*
12429204 TT-AATATATGTAAA
1 TTAAATATATATAAA
12429218 ACCAATCTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 14 0.47
19 2 0.07
20 14 0.47
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
TTAAATATATATAAATTTA
Found at i:12429200 original size:20 final size:20
Alignment explanation
Indices: 12429171--12429218 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
12429161 ATAATTTAAA
12429171 ATATAAAAATTTATTAATAT
1 ATATAAAAATTTATTAATAT
*
12429191 ATATATAAATTTATTAATAT
1 ATATAAAAATTTATTAATAT
*
12429211 ATGTAAAA
1 ATATAAAA
12429219 CCAATCTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
ATATAAAAATTTATTAATAT
Found at i:12429334 original size:20 final size:20
Alignment explanation
Indices: 12429309--12429348 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
12429299 AATATTTTCC
*
12429309 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
12429329 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
12429349 TCATTTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:12429354 original size:34 final size:35
Alignment explanation
Indices: 12429297--12429363 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
12429287 CAAACTCTAG
*
12429297 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
12429332 AAAACATTTTCCAG-AAATCATTTTATAGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
12429364 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:12429355 original size:14 final size:14
Alignment explanation
Indices: 12429332--12429371 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
12429322 ACAGAAAAGT
*
12429332 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
12429346 AAATCATTTTATAG
1 AAAACATTTTACAG
12429360 AAAACATTTTAC
1 AAAACATTTTAC
12429372 TGCCAATCAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:12431152 original size:22 final size:22
Alignment explanation
Indices: 12431127--12431169 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
12431117 GTATTCATAT
* *
12431127 TATTTATAAATTTTATTTAAAA
1 TATTAATAAATTTTAATTAAAA
*
12431149 TATTAATATATTTTAATTAAA
1 TATTAATAAATTTTAATTAAA
12431170 CATAAATTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTAATAAATTTTAATTAAAA
Found at i:12435103 original size:24 final size:24
Alignment explanation
Indices: 12435076--12435125 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
12435066 CCTTGAAGAT
12435076 TTTAGTTCAACTTATGTCTGATTC
1 TTTAGTTCAACTTATGTCTGATTC
*
12435100 TTTAGTTCAACTTGTGTCTGATTC
1 TTTAGTTCAACTTATGTCTGATTC
12435124 TT
1 TT
12435126 CGTTCAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.18, C:0.16, G:0.14, T:0.52
Consensus pattern (24 bp):
TTTAGTTCAACTTATGTCTGATTC
Found at i:12441847 original size:22 final size:22
Alignment explanation
Indices: 12441819--12441889 Score: 80
Period size: 22 Copynumber: 3.4 Consensus size: 22
12441809 TTCTAAAATT
12441819 TTATTATTTTAAAAATATTTTA
1 TTATTATTTTAAAAATATTTTA
*
12441841 TTATTATTTTAAAAA-A--TCA
1 TTATTATTTTAAAAATATTTTA
*
12441860 ATATTTATTTT-AAAATATTTT-
1 TTA-TTATTTTAAAAATATTTTA
12441881 TTATTATTT
1 TTATTATTT
12441890 GATTATTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
19 8 0.20
20 14 0.34
21 3 0.07
22 16 0.39
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (22 bp):
TTATTATTTTAAAAATATTTTA
Found at i:12441867 original size:23 final size:21
Alignment explanation
Indices: 12441818--12441868 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 21
12441808 CTTCTAAAAT
* *
12441818 TTTATTATTTTAAAAATATTT
1 TTTATTATTTTAAAAATAATA
12441839 TATTATTATTTTAAAAAATCAATA
1 T-TTATTATTTT-AAAAAT-AATA
12441863 TTTATT
1 TTTATT
12441869 TTAAAATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 1 0.04
22 10 0.40
23 11 0.44
24 3 0.12
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTATTATTTTAAAAATAATA
Found at i:12441887 original size:20 final size:20
Alignment explanation
Indices: 12441817--12441889 Score: 76
Period size: 20 Copynumber: 3.5 Consensus size: 20
12441807 ACTTCTAAAA
12441817 TTTTATTATTTTAAAAATATT
1 TTTTATTATTTT-AAAATATT
*
12441838 TTATTATTATTTTAAAA-AAT
1 TT-TTATTATTTTAAAATATT
***
12441858 CAATATTTATTTTAAAATATT
1 TTTTA-TTATTTTAAAATATT
12441879 TTTTATTATTT
1 TTTTATTATTT
12441890 GATTATTTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
19 2 0.05
20 19 0.46
21 10 0.24
22 10 0.24
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTATTATTTTAAAATATT
Found at i:12441924 original size:29 final size:29
Alignment explanation
Indices: 12441861--12441925 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
12441851 AAAAAATCAA
12441861 TATTTA-TTTTAAAATATTTTTTATTATT
1 TATTTATTTTTAAAATATTTTTTATTATT
* *
12441889 TGA-TTATTTTTATAAT-TTTTTTCGTTATT
1 T-ATTTATTTTTAAAATATTTTTT-ATTATT
12441918 TATTTATT
1 TATTTATT
12441926 GCTGATAGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
28 11 0.35
29 20 0.65
ACGTcount: A:0.26, C:0.02, G:0.03, T:0.69
Consensus pattern (29 bp):
TATTTATTTTTAAAATATTTTTTATTATT
Found at i:12454332 original size:19 final size:20
Alignment explanation
Indices: 12454305--12454342 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
12454295 ATTTCAATAT
*
12454305 TAATATAAAATTTTTAAAAA
1 TAATATAAAATATTTAAAAA
12454325 TAAT-TAAAATATTTAAAA
1 TAATATAAAATATTTAAAA
12454343 GAGTGGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TAATATAAAATATTTAAAAA
Found at i:12459490 original size:21 final size:22
Alignment explanation
Indices: 12459466--12459510 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
12459456 AGAAAAAGAA
*
12459466 AAATACAAAGAAG-AATAG-ATC
1 AAAT-CAAAAAAGAAATAGAATC
12459487 AAATCAAAAAAGAAATAGAATC
1 AAATCAAAAAAGAAATAGAATC
12459509 AA
1 AA
12459511 CAATTTGTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 7 0.33
21 9 0.43
22 5 0.24
ACGTcount: A:0.67, C:0.09, G:0.11, T:0.13
Consensus pattern (22 bp):
AAATCAAAAAAGAAATAGAATC
Found at i:12462370 original size:34 final size:34
Alignment explanation
Indices: 12462315--12462489 Score: 179
Period size: 34 Copynumber: 5.1 Consensus size: 34
12462305 ATAATACCAA
* *
12462315 AAATAATGTATAAACAGGAGAGGTTCCCTGCAAG
1 AAATAATGTGTAAACAGGAGAGATTCCCTGCAAG
* * *
12462349 AAATGATGTGTAAACATGAGAGATTCCCTGCAACA
1 AAATAATGTGTAAACAGGAGAGATTCCCTGCAA-G
* * * *
12462384 AAATAATGCGTGAACAGGAAAGATTCCATGCAAG
1 AAATAATGTGTAAACAGGAGAGATTCCCTGCAAG
* * * *
12462418 AAATGATTTGTGAACAGGAGAGATTCCCTGCAACA
1 AAATAATGTGTAAACAGGAGAGATTCCCTGCAA-G
* * * *
12462453 AAATAATGCGTGAACAGGAAATATTCCCTGCAAG
1 AAATAATGTGTAAACAGGAGAGATTCCCTGCAAG
12462487 AAA
1 AAA
12462490 AGACAAGTGA
Statistics
Matches: 115, Mismatches: 24, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
34 60 0.52
35 55 0.48
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.21
Consensus pattern (34 bp):
AAATAATGTGTAAACAGGAGAGATTCCCTGCAAG
Found at i:12462416 original size:35 final size:35
Alignment explanation
Indices: 12462327--12462490 Score: 170
Period size: 35 Copynumber: 4.7 Consensus size: 35
12462317 ATAATGTATA
* * * * * *
12462327 AACAGGAGAGGTTCCCTGCAA-GAAATGATGTGTA
1 AACAGGAAAGATTCCCTGCAACAAAATAATGCGTG
* *
12462361 AACATGAGAGATTCCCTGCAACAAAATAATGCGTG
1 AACAGGAAAGATTCCCTGCAACAAAATAATGCGTG
* * * **
12462396 AACAGGAAAGATTCCATGCAA-GAAATGATTTGTG
1 AACAGGAAAGATTCCCTGCAACAAAATAATGCGTG
*
12462430 AACAGGAGAGATTCCCTGCAACAAAATAATGCGTG
1 AACAGGAAAGATTCCCTGCAACAAAATAATGCGTG
* *
12462465 AACAGGAAATATTCCCTGCAAGAAAA
1 AACAGGAAAGATTCCCTGCAACAAAA
12462491 GACAAGTGAA
Statistics
Matches: 106, Mismatches: 22, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
34 47 0.44
35 59 0.56
ACGTcount: A:0.41, C:0.17, G:0.23, T:0.20
Consensus pattern (35 bp):
AACAGGAAAGATTCCCTGCAACAAAATAATGCGTG
Found at i:12462439 original size:69 final size:69
Alignment explanation
Indices: 12462327--12462489 Score: 263
Period size: 69 Copynumber: 2.4 Consensus size: 69
12462317 ATAATGTATA
* * *
12462327 AACAGGAGAGGTTCCCTGCAAGAAATGATGTGTAAACATGAGAGATTCCCTGCAACAAAATAATG
1 AACAGGAAAGATTCCCTGCAAGAAATGATGTGTAAACAGGAGAGATTCCCTGCAACAAAATAATG
12462392 CGTG
66 CGTG
* * *
12462396 AACAGGAAAGATTCCATGCAAGAAATGATTTGTGAACAGGAGAGATTCCCTGCAACAAAATAATG
1 AACAGGAAAGATTCCCTGCAAGAAATGATGTGTAAACAGGAGAGATTCCCTGCAACAAAATAATG
12462461 CGTG
66 CGTG
*
12462465 AACAGGAAATATTCCCTGCAAGAAA
1 AACAGGAAAGATTCCCTGCAAGAAA
12462490 AGACAAGTGA
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
69 86 1.00
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.20
Consensus pattern (69 bp):
AACAGGAAAGATTCCCTGCAAGAAATGATGTGTAAACAGGAGAGATTCCCTGCAACAAAATAATG
CGTG
Found at i:12462753 original size:14 final size:13
Alignment explanation
Indices: 12462722--12462763 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
12462712 TTTAAGTTTC
*
12462722 TAAGTTTTTAAAT
1 TAAGTTTTCAAAT
12462735 TAAGTTTTCAAACT
1 TAAGTTTTCAAA-T
12462749 TAAGTTTTCAAAT
1 TAAGTTTTCAAAT
12462762 TA
1 TA
12462764 CAAATATCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 14 0.52
14 13 0.48
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (13 bp):
TAAGTTTTCAAAT
Found at i:12480974 original size:46 final size:46
Alignment explanation
Indices: 12480921--12481055 Score: 198
Period size: 46 Copynumber: 2.9 Consensus size: 46
12480911 ATCTATGGCA
* *
12480921 AATTGTGAAAAGTAGGTATGGTGTTTTAGTGAAGAAAATCATACTG
1 AATTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTG
12480967 AATTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTG
1 AATTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTG
* * * * * *
12481013 AGTAGTGAAAAATAGGTATGATATTTCAGTGAAGGAAACCATA
1 AATTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATA
12481056 TTGAGTTATA
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 81 1.00
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.29
Consensus pattern (46 bp):
AATTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTG
Found at i:12500313 original size:64 final size:63
Alignment explanation
Indices: 12500233--12500437 Score: 209
Period size: 65 Copynumber: 3.2 Consensus size: 63
12500223 TTTCATGAAT
* * * *
12500233 TGAATTTAAAGTTATGAATTATATATATATATATAGTTTGAATGTATGATATAAGTTCTTTGAGC
1 TGAATTTAATG-TATGAATT-TATATATATATATGGTTCGAATATATGATATAAGTTCTTTGAGC
* *
12500298 TGAATTTAATGTATGAATTT-TACATACATATGGTTCGAATATAT-ATATTTCAAGTTC-TTGAG
1 TGAATTTAATGTATGAATTTATATATATATATGGTTCGAATATATGATA--T-AAGTTCTTTGAG
12500360 C
63 C
* * * * * * *
12500361 TGAATTTAATGTATGAATTTCACATACATATGTGGTTCGAATATAGGCTACAAATTCTTTGAGC
1 TGAATTTAATGTATGAATTT-ATATATATATATGGTTCGAATATATGATATAAGTTCTTTGAGC
12500425 TGAATTTTAATGT
1 TGAA-TTTAATGT
12500438 TGTAAATTAT
Statistics
Matches: 117, Mismatches: 15, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
61 3 0.03
62 19 0.16
63 33 0.28
64 24 0.21
65 36 0.31
66 2 0.02
ACGTcount: A:0.34, C:0.08, G:0.16, T:0.42
Consensus pattern (63 bp):
TGAATTTAATGTATGAATTTATATATATATATGGTTCGAATATATGATATAAGTTCTTTGAGC
Found at i:12500419 original size:63 final size:62
Alignment explanation
Indices: 12500280--12500437 Score: 196
Period size: 63 Copynumber: 2.5 Consensus size: 62
12500270 TTGAATGTAT
* *
12500280 GATAT-AAGTTCTTTGAGCTGAATTTAATGTATGAATTTTACATACATATGGTTCGAATATA
1 GATATCAAATTCTTTGAGCTGAATTTAATGTATGAATTTCACATACATATGGTTCGAATATA
* *
12500341 TATATTTCAAGTTC-TTGAGCTGAATTTAATGTATGAATTTCACATACATATGTGGTTCGAATAT
1 GATA--TCAAATTCTTTGAGCTGAATTTAATGTATGAATTTCACATACATA--TGGTTCGAATAT
12500405 A
62 A
*
12500406 GGCTA-CAAATTCTTTGAGCTGAATTTTAATGT
1 -GATATCAAATTCTTTGAGCTGAA-TTTAATGT
12500438 TGTAAATTAT
Statistics
Matches: 84, Mismatches: 5, Indels: 12
0.83 0.05 0.12
Matches are distributed among these distances:
61 3 0.04
63 42 0.50
64 16 0.19
65 21 0.25
66 2 0.02
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.41
Consensus pattern (62 bp):
GATATCAAATTCTTTGAGCTGAATTTAATGTATGAATTTCACATACATATGGTTCGAATATA
Found at i:12500717 original size:82 final size:82
Alignment explanation
Indices: 12500620--12500779 Score: 302
Period size: 82 Copynumber: 2.0 Consensus size: 82
12500610 GGTGAATTAT
*
12500620 ATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAGCCTAGCAGGCT
1 ATCAGGTTATAAACCTAGCAAGCTAAGTGCCGGTGATCTAAATCAGGCTATAAGCCTAGCAGGCT
12500685 AAGTGCCGGTGATATGA
66 AAGTGCCGGTGATATGA
*
12500702 ATCAGGTTATAAACCTAGCAAGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCT
1 ATCAGGTTATAAACCTAGCAAGCTAAGTGCCGGTGATCTAAATCAGGCTATAAGCCTAGCAGGCT
12500767 AAGTGCCGGTGAT
66 AAGTGCCGGTGAT
12500780 CCGAATATGA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 76 1.00
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (82 bp):
ATCAGGTTATAAACCTAGCAAGCTAAGTGCCGGTGATCTAAATCAGGCTATAAGCCTAGCAGGCT
AAGTGCCGGTGATATGA
Found at i:12500779 original size:41 final size:41
Alignment explanation
Indices: 12500620--12500785 Score: 260
Period size: 41 Copynumber: 4.0 Consensus size: 41
12500610 GGTGAATTAT
* *
12500620 ATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTAA
1 ATCAGGCTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGA
* *
12500661 ATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGATATGA
1 ATCAGGCTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGA
* *
12500702 ATCAGGTTATAAACCTAGCAAGCTAAGTGCCGGTGATCTGA
1 ATCAGGCTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGA
* *
12500743 ATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGATCCGA
1 ATCAGGCTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGA
12500784 AT
1 AT
12500786 ATGATGAATT
Statistics
Matches: 113, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 113 1.00
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (41 bp):
ATCAGGCTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGA
Found at i:12507658 original size:63 final size:62
Alignment explanation
Indices: 12507589--12507757 Score: 159
Period size: 63 Copynumber: 2.7 Consensus size: 62
12507579 TTTCATGAAT
* * * *
12507589 TGAATTTAAAGTTATGAATTATATATATATATAGTTTGAATGTATGATA-T-AAGTTCTTTGAGC
1 TGAATTTAAAG-TATGAATTATACATACATATAGTTCGAATATAT-ATATTCAAGTTC-TTGAGC
* * *
12507652 TGAATTTAATGTATGAATTTTACATACATATGGTTCGAATATATATATTTCAAGTTCTTGAGC
1 TGAATTTAAAGTATGAATTATACATACATATAGTTCGAATATATATA-TTCAAGTTCTTGAGC
* *
12507715 TGAA--TAATGTATGAATT-TCACATACATATGTGGTTCGAATATA
1 TGAATTTAAAGTATGAATTAT-ACATACATA--TAGTTCGAATATA
12507758 GGCTACAATT
Statistics
Matches: 93, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
60 1 0.01
61 25 0.27
62 27 0.29
63 34 0.37
64 6 0.06
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.42
Consensus pattern (62 bp):
TGAATTTAAAGTATGAATTATACATACATATAGTTCGAATATATATATTCAAGTTCTTGAGC
Found at i:12507774 original size:61 final size:60
Alignment explanation
Indices: 12507634--12507780 Score: 176
Period size: 61 Copynumber: 2.4 Consensus size: 60
12507624 TTGAATGTAT
*
12507634 GATAT-AAGTTCTTTGAGCTGAATTTAATGTATGAATTTTACATACATATGGTTCGAATATA
1 GATATCAAGTTCTTTGAGCTGAA--TAATGTATGAATTTCACATACATATGGTTCGAATATA
*
12507695 TATATTTCAAGTTC-TTGAGCTGAATAATGTATGAATTTCACATACATATGTGGTTCGAATATA
1 GATA--TCAAGTTCTTTGAGCTGAATAATGTATGAATTTCACATACATA--TGGTTCGAATATA
*
12507758 GGCTA-CAA-TTCTTTGAGCTGAAT
1 -GATATCAAGTTCTTTGAGCTGAAT
12507781 TTTAATGTTG
Statistics
Matches: 75, Mismatches: 4, Indels: 14
0.81 0.04 0.15
Matches are distributed among these distances:
60 3 0.04
61 40 0.53
63 24 0.32
64 8 0.11
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (60 bp):
GATATCAAGTTCTTTGAGCTGAATAATGTATGAATTTCACATACATATGGTTCGAATATA
Found at i:12508014 original size:41 final size:41
Alignment explanation
Indices: 12507962--12508127 Score: 269
Period size: 41 Copynumber: 4.0 Consensus size: 41
12507952 CGGTGAATAT
* *
12507962 ATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTAA
1 ATCAGGCTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGA
* *
12508003 ATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGATATGA
1 ATCAGGCTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGA
*
12508044 ATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGA
1 ATCAGGCTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGA
* *
12508085 ATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGATCCGA
1 ATCAGGCTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGA
12508126 AT
1 AT
12508128 ATGATGAATT
Statistics
Matches: 115, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 115 1.00
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (41 bp):
ATCAGGCTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGA
Found at i:12508050 original size:82 final size:82
Alignment explanation
Indices: 12507962--12508121 Score: 311
Period size: 82 Copynumber: 2.0 Consensus size: 82
12507952 CGGTGAATAT
12507962 ATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAGCCTAGCAGGCT
1 ATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAGCCTAGCAGGCT
12508027 AAGTGCCGGTGATATGA
66 AAGTGCCGGTGATATGA
*
12508044 ATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGCCTAGCAGGCT
1 ATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAGCCTAGCAGGCT
12508109 AAGTGCCGGTGAT
66 AAGTGCCGGTGAT
12508122 CCGAATATGA
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 77 1.00
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (82 bp):
ATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAGCCTAGCAGGCT
AAGTGCCGGTGATATGA
Found at i:12509564 original size:24 final size:23
Alignment explanation
Indices: 12509533--12509579 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
12509523 TATTCACACA
12509533 TATTCTTA-CTTAATTTCAAATGT
1 TATTCTTACCTTAATTT-AAATGT
*
12509556 TATTACTTACCTTACTTTAAATGT
1 TATT-CTTACCTTAATTTAAATGT
12509580 CCCATGATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 10 0.48
25 7 0.33
ACGTcount: A:0.30, C:0.15, G:0.04, T:0.51
Consensus pattern (23 bp):
TATTCTTACCTTAATTTAAATGT
Found at i:12510756 original size:9 final size:9
Alignment explanation
Indices: 12510701--12510792 Score: 59
Period size: 9 Copynumber: 10.3 Consensus size: 9
12510691 TTGGTTTATT
*
12510701 TAATAATAA
1 TAATTATAA
*
12510710 TAATAATAA
1 TAATTATAA
12510719 TAA-TATAA
1 TAATTATAA
**
12510727 -AACCATAA
1 TAATTATAA
*
12510735 TAATGTTTAA
1 TAAT-TATAA
12510745 TAATTATAA
1 TAATTATAA
12510754 TAATTAT-A
1 TAATTATAA
12510762 TACA-TATAA
1 TA-ATTATAA
*
12510771 TATTTATATA
1 TAATTATA-A
12510781 TAACTTA-AA
1 TAA-TTATAA
12510790 TAA
1 TAA
12510793 AATCTTAAAT
Statistics
Matches: 67, Mismatches: 8, Indels: 16
0.74 0.09 0.18
Matches are distributed among these distances:
7 2 0.03
8 14 0.21
9 37 0.55
10 11 0.16
11 3 0.04
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.39
Consensus pattern (9 bp):
TAATTATAA
Found at i:12511280 original size:46 final size:46
Alignment explanation
Indices: 12511212--12511350 Score: 210
Period size: 46 Copynumber: 3.0 Consensus size: 46
12511202 ACATTGCTAT
*
12511212 AACTCAGTATGGTTTTCTTCACGGAAATACCATACCTACTTTTTA-
1 AACTCAGTATGGTTTTCTTCACGGAAATACCATACCTACTTTTCAC
*
12511257 AGACTCAGTATGGTTTTATTCACGGAAATACCATACCTACTTTTCAC
1 A-ACTCAGTATGGTTTTCTTCACGGAAATACCATACCTACTTTTCAC
* *
12511304 AACAT-AGTATGGTTTTCTTCACTGAAATACCATACCTACGTTTCAC
1 AAC-TCAGTATGGTTTTCTTCACGGAAATACCATACCTACTTTTCAC
12511350 A
1 A
12511351 CTTTGCCATG
Statistics
Matches: 86, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
45 1 0.01
46 83 0.97
47 2 0.02
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACGGAAATACCATACCTACTTTTCAC
Found at i:12513959 original size:11 final size:11
Alignment explanation
Indices: 12513943--12513968 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
12513933 AGAAAGGAAC
12513943 GAAACAGGGGA
1 GAAACAGGGGA
12513954 GAAACAGGGGA
1 GAAACAGGGGA
12513965 GAAA
1 GAAA
12513969 GAAGAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.08, G:0.42, T:0.00
Consensus pattern (11 bp):
GAAACAGGGGA
Found at i:12514641 original size:6 final size:6
Alignment explanation
Indices: 12514624--12514672 Score: 71
Period size: 6 Copynumber: 8.2 Consensus size: 6
12514614 ATGTGAGGTA
* * *
12514624 AGTATT AATATT AGTATT AGTATT ATTATT AGTATT ATTATT AGTATT
1 AGTATT AGTATT AGTATT AGTATT AGTATT AGTATT AGTATT AGTATT
12514672 A
1 A
12514673 TTAAGATGAG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (6 bp):
AGTATT
Found at i:12514641 original size:12 final size:12
Alignment explanation
Indices: 12514626--12514675 Score: 82
Period size: 12 Copynumber: 4.2 Consensus size: 12
12514616 GTGAGGTAAG
* *
12514626 TATTAATATTAG
1 TATTAGTATTAT
12514638 TATTAGTATTAT
1 TATTAGTATTAT
12514650 TATTAGTATTAT
1 TATTAGTATTAT
12514662 TATTAGTATTAT
1 TATTAGTATTAT
12514674 TA
1 TA
12514676 AGATGAGTGG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (12 bp):
TATTAGTATTAT
Found at i:12514652 original size:3 final size:3
Alignment explanation
Indices: 12514626--12514675 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
12514616 GTGAGGTAAG
* * * * *
12514626 TAT TAA TAT TAG TAT TAG TAT TAT TAT TAG TAT TAT TAT TAG TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
12514674 TA
1 TA
12514676 AGATGAGTGG
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (3 bp):
TAT
Found at i:12514853 original size:23 final size:26
Alignment explanation
Indices: 12514827--12514875 Score: 77
Period size: 23 Copynumber: 2.0 Consensus size: 26
12514817 ATTGCGGATT
12514827 AATTATTG-ATTGAAAA-GTG-GAAA
1 AATTATTGAATTGAAAATGTGAGAAA
12514850 AATTATTGAATTGAAAATGTGAGAAA
1 AATTATTGAATTGAAAATGTGAGAAA
12514876 TTGTGATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 8 0.35
24 8 0.35
25 3 0.13
26 4 0.17
ACGTcount: A:0.49, C:0.00, G:0.20, T:0.31
Consensus pattern (26 bp):
AATTATTGAATTGAAAATGTGAGAAA
Found at i:12521011 original size:22 final size:22
Alignment explanation
Indices: 12520986--12521037 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
12520976 GAATTAAACT
12520986 TAAAAATTTAAAAT-TTATAAAA
1 TAAAAATTTAAAATCTTA-AAAA
* *
12521008 TAAAATAATTAAATTCTTAAAAA
1 TAAAA-ATTTAAAATCTTAAAAA
12521031 TAAAAAT
1 TAAAAAT
12521038 AAGAAAGATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
22 6 0.24
23 16 0.64
24 3 0.12
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
TAAAAATTTAAAATCTTAAAAA
Found at i:12521932 original size:11 final size:11
Alignment explanation
Indices: 12521916--12521946 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
12521906 AAGTATGGGT
12521916 AGGTATGGGAA
1 AGGTATGGGAA
*
12521927 AGGTATGGGCA
1 AGGTATGGGAA
12521938 AGGTATGGG
1 AGGTATGGG
12521947 GTATGGGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.29, C:0.03, G:0.48, T:0.19
Consensus pattern (11 bp):
AGGTATGGGAA
Found at i:12526023 original size:18 final size:18
Alignment explanation
Indices: 12526000--12526110 Score: 195
Period size: 18 Copynumber: 6.2 Consensus size: 18
12525990 CCCAACTACT
*
12526000 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
12526018 GTATACGTGAATAGTTCC
1 GTATACGTGAATAGTACC
12526036 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
12526054 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
*
12526072 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
12526090 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
12526108 GTA
1 GTA
12526111 AACGGTCGTA
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 88 1.00
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:12526672 original size:11 final size:11
Alignment explanation
Indices: 12526656--12526686 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
12526646 AAGTATGGGT
12526656 AGGTATGGGAA
1 AGGTATGGGAA
*
12526667 AGGTATGGGCA
1 AGGTATGGGAA
12526678 AGGTATGGG
1 AGGTATGGG
12526687 GTATGGGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.29, C:0.03, G:0.48, T:0.19
Consensus pattern (11 bp):
AGGTATGGGAA
Found at i:12531284 original size:6 final size:6
Alignment explanation
Indices: 12531275--12531310 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
12531265 TAGATATAAG
12531275 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
12531311 TTATAATGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
AAATAT
Found at i:12538850 original size:6 final size:6
Alignment explanation
Indices: 12538839--12538892 Score: 108
Period size: 6 Copynumber: 9.0 Consensus size: 6
12538829 AAAAAATTGG
12538839 ATTTGA ATTTGA ATTTGA ATTTGA ATTTGA ATTTGA ATTTGA ATTTGA
1 ATTTGA ATTTGA ATTTGA ATTTGA ATTTGA ATTTGA ATTTGA ATTTGA
12538887 ATTTGA
1 ATTTGA
12538893 GTAAATTCAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
ATTTGA
Found at i:12539131 original size:18 final size:18
Alignment explanation
Indices: 12539108--12539166 Score: 91
Period size: 18 Copynumber: 3.3 Consensus size: 18
12539098 ACCACCAACT
12539108 ATCGATTCAACCAGTTCG
1 ATCGATTCAACCAGTTCG
*
12539126 ATCGATTCAACCGGTTCG
1 ATCGATTCAACCAGTTCG
* *
12539144 ATCAATTCAATCAGTTCG
1 ATCGATTCAACCAGTTCG
12539162 ATCGA
1 ATCGA
12539167 ATAAATTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (18 bp):
ATCGATTCAACCAGTTCG
Found at i:12543875 original size:6 final size:6
Alignment explanation
Indices: 12543859--12543897 Score: 69
Period size: 6 Copynumber: 6.3 Consensus size: 6
12543849 CGATGCATTT
12543859 GGCTAGA GGCTGA GGCTGA GGCTGA GGCTGA GGCTGA GG
1 GGCT-GA GGCTGA GGCTGA GGCTGA GGCTGA GGCTGA GG
12543898 ATGGGGTTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 28 0.88
7 4 0.12
ACGTcount: A:0.18, C:0.15, G:0.51, T:0.15
Consensus pattern (6 bp):
GGCTGA
Found at i:12546259 original size:3 final size:3
Alignment explanation
Indices: 12546251--12546284 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
12546241 GATAGGAAAG
12546251 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
12546285 TAAGATATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:12556038 original size:25 final size:25
Alignment explanation
Indices: 12555986--12556034 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 25
12555976 ACATGGAAGG
12555986 TAATTAAAATCACCATGATAAAAGC
1 TAATTAAAATCACCATGATAAAAGC
12556011 TAATT-AAAT-ACCAT-AGTAAAAGC
1 TAATTAAAATCACCATGA-TAAAAGC
12556034 T
1 T
12556035 CTAAACCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 1 0.04
23 13 0.57
24 4 0.17
25 5 0.22
ACGTcount: A:0.51, C:0.14, G:0.08, T:0.27
Consensus pattern (25 bp):
TAATTAAAATCACCATGATAAAAGC
Found at i:12559043 original size:17 final size:18
Alignment explanation
Indices: 12559021--12559055 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
12559011 AATATGTTTC
*
12559021 TCATAAAATATA-AAAAA
1 TCATAAAAAATAGAAAAA
12559038 TCATAAAAAATAGAAAAA
1 TCATAAAAAATAGAAAAA
12559056 AAGAAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.71, C:0.06, G:0.03, T:0.20
Consensus pattern (18 bp):
TCATAAAAAATAGAAAAA
Found at i:12559127 original size:24 final size:27
Alignment explanation
Indices: 12559093--12559158 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 27
12559083 TAATATTGAT
12559093 ATAAACTTATAA-TTATT-ATAAAA-TA
1 ATAAA-TTATAATTTATTGATAAAATTA
*
12559118 ATAAATTATAATTTTTTGATAAAATTA
1 ATAAATTATAATTTATTGATAAAATTA
*
12559145 ATAAAATAT-ATTTA
1 ATAAATTATAATTTA
12559159 AATTGTTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
24 6 0.17
25 9 0.26
26 10 0.29
27 10 0.29
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (27 bp):
ATAAATTATAATTTATTGATAAAATTA
Found at i:12559734 original size:19 final size:18
Alignment explanation
Indices: 12559694--12559739 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
12559684 AAGTTTGATA
* *
12559694 TTTTTAAAATTTTAATAT
1 TTTTTAAAATTCTAATAC
*
12559712 TTTTTAAGAATTCTAATGC
1 TTTTTAA-AATTCTAATAC
12559731 TTTTTAAAA
1 TTTTTAAAA
12559740 AAAATTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (18 bp):
TTTTTAAAATTCTAATAC
Found at i:12560921 original size:9 final size:8
Alignment explanation
Indices: 12560904--12560928 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
12560894 GAGAGGGACT
12560904 AAGAAAAA
1 AAGAAAAA
12560912 AAGAAAAA
1 AAGAAAAA
12560920 AAGAAAAA
1 AAGAAAAA
12560928 A
1 A
12560929 GAGCGCCTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AAGAAAAA
Found at i:12567028 original size:18 final size:18
Alignment explanation
Indices: 12566988--12567030 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
12566978 CAAAAGCCCA
* *
12566988 AGCTTTTTCCCAGTATTG
1 AGCTTGTTCCCAGTATAG
12567006 AGCTTGTTCCCAGTACTAG
1 AGCTTGTTCCCAGTA-TAG
12567025 -GCTTGT
1 AGCTTGT
12567031 GATTTTGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.16, C:0.23, G:0.21, T:0.40
Consensus pattern (18 bp):
AGCTTGTTCCCAGTATAG
Found at i:12567863 original size:16 final size:16
Alignment explanation
Indices: 12567844--12567876 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
12567834 GGTATTGGAT
*
12567844 TGGATTAGAGGTGTAA
1 TGGAATAGAGGTGTAA
12567860 TGGAATAGAGGTGTAA
1 TGGAATAGAGGTGTAA
12567876 T
1 T
12567877 AGCAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (16 bp):
TGGAATAGAGGTGTAA
Found at i:12567863 original size:21 final size:21
Alignment explanation
Indices: 12567821--12567863 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
12567811 GGTTCGTTGT
*
12567821 ATTGGATTAGAGAGGTATTGG
1 ATTGGATTAGAGAGGTAATGG
12567842 ATTGGATTAGAG-GTGTAATGG
1 ATTGGATTAGAGAG-GTAATGG
12567863 A
1 A
12567864 ATAGAGGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (21 bp):
ATTGGATTAGAGAGGTAATGG
Found at i:12567921 original size:45 final size:44
Alignment explanation
Indices: 12567855--12567949 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
12567845 GGATTAGAGG
* *
12567855 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
12567900 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
12567944 TGTAAT
1 TGTAAT
12567950 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:12568138 original size:28 final size:28
Alignment explanation
Indices: 12568068--12568150 Score: 80
Period size: 27 Copynumber: 3.0 Consensus size: 28
12568058 TTTATTATCA
* *
12568068 AAAATAAATAATTTAATCATA-TTTAAAC
1 AAAATATATAATTTAAT-ATATTTTAATC
* * *
12568096 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATATTTTAATC
*
12568123 AAAATATATAATTTAATAAATTCTTAAT
1 AAAATATATAATTTAATATATT-TTAAT
12568151 AATTAGCAGA
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
26 3 0.07
27 18 0.41
28 18 0.41
29 5 0.11
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (28 bp):
AAAATATATAATTTAATATATTTTAATC
Found at i:12568275 original size:18 final size:17
Alignment explanation
Indices: 12568253--12568287 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12568243 TTATTATTAA
*
12568253 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
12568271 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
12568288 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:12568331 original size:54 final size:54
Alignment explanation
Indices: 12568273--12568451 Score: 128
Period size: 55 Copynumber: 3.1 Consensus size: 54
12568263 ATTAAAATAT
*
12568273 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAACC
1 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAAAC
** * * * * *
12568327 ATAATATATGATACTGTAAAATAT-AAAATAACATAATTATTATTAAATAT-AATATAATTAAAA
1 ATAAT-T-T-A-A---TAAAAT-TCTTAATAA-TTAA-TATTCTT--ATATGAAT-TTACTCAAA
*
12568390 TAT
53 -AC
*
12568393 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATC
1 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAAAC
12568447 ATAAT
1 ATAAT
12568452 ATATGATTAT
Statistics
Matches: 91, Mismatches: 18, Indels: 32
0.65 0.13 0.23
Matches are distributed among these distances:
54 10 0.11
55 11 0.12
56 4 0.04
57 7 0.08
58 5 0.05
59 11 0.12
61 11 0.12
62 5 0.05
63 7 0.08
64 4 0.04
65 11 0.12
66 5 0.05
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (54 bp):
ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAAAC
Found at i:12568347 original size:61 final size:61
Alignment explanation
Indices: 12568268--12568458 Score: 178
Period size: 61 Copynumber: 3.2 Consensus size: 61
12568258 TTTTAATTAA
* * *
12568268 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAACCAT
1 AATATATGATCTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
* * * * * * * * *
12568329 AATATATGATACT-GTAAAA-T-ATAA-AATAACATAATTATTAT-TAAATATAAT-ATAATTAA
1 AATATATGAT-CTAATAAAATTCTTAATAATTA-AT-ATTCTTATATGAATTTACTCA-AATCAT
* *
12568388 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATGATCTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
12568449 AATATATGAT
1 AATATATGAT
12568459 TATAACTAAT
Statistics
Matches: 96, Mismatches: 24, Indels: 20
0.69 0.17 0.14
Matches are distributed among these distances:
58 6 0.06
59 29 0.30
60 16 0.17
61 39 0.41
62 6 0.06
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (61 bp):
AATATATGATCTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
Found at i:12568370 original size:120 final size:120
Alignment explanation
Indices: 12568239--12568458 Score: 413
Period size: 120 Copynumber: 1.8 Consensus size: 120
12568229 ATATTTAAAT
* *
12568239 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
1 ATAATTATTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
12568304 TCTTATATGAATTTACTCAAACCATAATATATGATACTGTAAAATATAAAATAAC
66 TCTTATATGAATTTACTCAAACCATAATATATGATACTGTAAAATATAAAATAAC
12568359 ATAATTATTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
1 ATAATTATTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
*
12568424 TCTTATATGAATTTACTCAAATCATAATATATGAT
66 TCTTATATGAATTTACTCAAACCATAATATATGAT
12568459 TATAACTAAT
Statistics
Matches: 97, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 97 1.00
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (120 bp):
ATAATTATTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATAT
TCTTATATGAATTTACTCAAACCATAATATATGATACTGTAAAATATAAAATAAC
Found at i:12568394 original size:18 final size:17
Alignment explanation
Indices: 12568373--12568407 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12568363 TTATTATTAA
12568373 ATATAATATAATTAAAAT
1 ATATAATATAA-TAAAAT
*
12568391 ATATAATTTAATAAAAT
1 ATATAATATAATAAAAT
12568408 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATAATATAATAAAAT
Found at i:12568470 original size:17 final size:16
Alignment explanation
Indices: 12568448--12568494 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
12568438 ACTCAAATCA
12568448 TAATATATGATTATAAC
1 TAATATATGATT-TAAC
*
12568465 T-A-ATATGATTTAAT
1 TAATATATGATTTAAC
12568479 TAAATATATGATTTAA
1 T-AATATATGATTTAA
12568495 TAAAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 4 0.15
15 8 0.31
16 2 0.08
17 12 0.46
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (16 bp):
TAATATATGATTTAAC
Found at i:12568495 original size:17 final size:17
Alignment explanation
Indices: 12568467--12568500 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
12568457 ATTATAACTA
*
12568467 ATATGATTTAATTAAAT
1 ATATGATTTAATAAAAT
12568484 ATATGATTTAATAAAAT
1 ATATGATTTAATAAAAT
12568501 TTAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
ATATGATTTAATAAAAT
Found at i:12572864 original size:17 final size:16
Alignment explanation
Indices: 12572836--12572867 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
12572826 CAAATTCATA
12572836 TAAGAATATTAATTAT
1 TAAGAATATTAATTAT
12572852 TAAGAATTATTAATTA
1 TAAGAA-TATTAATTA
12572868 AATTAGTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (16 bp):
TAAGAATATTAATTAT
Found at i:12572900 original size:18 final size:18
Alignment explanation
Indices: 12572840--12572901 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 18
12572830 TTCATATAAG
* *
12572840 AATATTAATTAT-TAAGA
1 AATATTAATTATATTATA
* *
12572857 ATTATTAATTAAATTAGTA
1 AATATTAATTATATTA-TA
*
12572876 TAT-TTAATTATATTATA
1 AATATTAATTATATTATA
12572893 AATATTAAT
1 AATATTAAT
12572902 AATAATGTTA
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
17 14 0.41
18 18 0.53
19 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (18 bp):
AATATTAATTATATTATA
Found at i:12573026 original size:27 final size:27
Alignment explanation
Indices: 12572975--12573058 Score: 66
Period size: 27 Copynumber: 3.1 Consensus size: 27
12572965 AGAGTCGTAA
* *
12572975 TATAAGTT-ATTAAAAAT-TTTATTAAT
1 TATAAATTAATTAAAAATATAT-TTAAT
*
12573001 TATAATTTAATTAAAAATATATTTAAT
1 TATAAATTAATTAAAAATATATTTAAT
* * *
12573028 AATAAATTATATT-TAAATATGATTAAAT
1 TATAAATTA-ATTAAAAATAT-ATTTAAT
12573056 TAT
1 TAT
12573059 TTATATTGAT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
26 7 0.15
27 27 0.57
28 13 0.28
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (27 bp):
TATAAATTAATTAAAAATATATTTAAT
Found at i:12573038 original size:17 final size:17
Alignment explanation
Indices: 12572998--12573043 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
12572988 AAATTTTATT
12572998 AATTATAATTTAATTAAA
1 AATTAT-ATTTAATTAAA
12573016 AA-TATATTTAA-TAATA
1 AATTATATTTAATTAA-A
12573032 AATTATATTTAA
1 AATTATATTTAA
12573044 ATATGATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 3 0.12
16 9 0.35
17 12 0.46
18 2 0.08
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTATATTTAATTAAA
Found at i:12573061 original size:19 final size:19
Alignment explanation
Indices: 12573037--12573084 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
12573027 TAATAAATTA
12573037 TATTTAAATATGAT-TAAAT
1 TATTTAAAT-TGATATAAAT
* *
12573056 TATTTATATTGATATAACT
1 TATTTAAATTGATATAAAT
*
12573075 TATTAAAATT
1 TATTTAAATT
12573085 TAAATAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 4 0.17
19 20 0.83
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (19 bp):
TATTTAAATTGATATAAAT
Found at i:12573155 original size:18 final size:17
Alignment explanation
Indices: 12573127--12573161 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12573117 CTAATTTAGA
*
12573127 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
12573144 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
12573162 TAATAATACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:12579997 original size:9 final size:8
Alignment explanation
Indices: 12579978--12580002 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
12579968 TGAGGCGCTC
12579978 TTTTTTCT
1 TTTTTTCT
12579986 TTTTTTCT
1 TTTTTTCT
12579994 TTTTTTCT
1 TTTTTTCT
12580002 T
1 T
12580003 AGTCCCTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTTCT
Found at i:12581062 original size:17 final size:16
Alignment explanation
Indices: 12581017--12581062 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
12581007 TATATTTTAT
*
12581017 AAAATATTAAAATTTAA
1 AAAATATTAACA-TTAA
12581034 AAAATA--AACATTAA
1 AAAATATTAACATTAA
12581048 AATAATATTAACATT
1 AA-AATATTAACATT
12581063 TTTATTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
14 6 0.24
15 7 0.28
17 12 0.48
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAATATTAACATTAA
Found at i:12581775 original size:25 final size:26
Alignment explanation
Indices: 12581724--12581785 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
12581714 ACAATTTAAA
*
12581724 TATATTTTATTAATTTTATCAAAAAT
1 TATAATTTATTAATTTTATCAAAAAT
* *
12581750 TATAATTTATTATTTTTAT-AATAAT
1 TATAATTTATTAATTTTATCAAAAAT
12581775 TATAAGTTTAT
1 TATAA-TTTAT
12581786 ATCAATATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
25 10 0.31
26 22 0.69
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (26 bp):
TATAATTTATTAATTTTATCAAAAAT
Found at i:12581852 original size:17 final size:18
Alignment explanation
Indices: 12581822--12581856 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
12581812 ATAAATTTCT
*
12581822 TTTTTCTATTTTTTATGA
1 TTTTTCTATATTTTATGA
12581840 TTTTT-TATATTTTATGA
1 TTTTTCTATATTTTATGA
12581857 GAACATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.20, C:0.03, G:0.06, T:0.71
Consensus pattern (18 bp):
TTTTTCTATATTTTATGA
Found at i:12582077 original size:26 final size:27
Alignment explanation
Indices: 12582031--12582082 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
12582021 TTTAATTAAT
12582031 TTTTTTACATTTCTTACATATAACCTTC
1 TTTTTTACATTTCTTA-ATATAACCTTC
* *
12582059 TTTTTTATATTTCTT-ATATCACCT
1 TTTTTTACATTTCTTAATATAACCT
12582083 ATCCAATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 8 0.36
28 14 0.64
ACGTcount: A:0.23, C:0.19, G:0.00, T:0.58
Consensus pattern (27 bp):
TTTTTTACATTTCTTAATATAACCTTC
Found at i:12607167 original size:25 final size:25
Alignment explanation
Indices: 12607115--12607163 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 25
12607105 AACATGGAAG
12607115 TAATTAAAATCACCATGATAAAAGC
1 TAATTAAAATCACCATGATAAAAGC
12607140 TAATT-AAAT-ACCAT-AGTAAAAGC
1 TAATTAAAATCACCATGA-TAAAAGC
12607163 T
1 T
12607164 CTAAACCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 1 0.04
23 13 0.57
24 4 0.17
25 5 0.22
ACGTcount: A:0.51, C:0.14, G:0.08, T:0.27
Consensus pattern (25 bp):
TAATTAAAATCACCATGATAAAAGC
Found at i:12610142 original size:17 final size:18
Alignment explanation
Indices: 12610120--12610154 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
12610110 AATATGTTTC
*
12610120 TCATAAAATATA-AAAAA
1 TCATAAAAAATAGAAAAA
12610137 TCATAAAAAATAGAAAAA
1 TCATAAAAAATAGAAAAA
12610155 AGAAATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.71, C:0.06, G:0.03, T:0.20
Consensus pattern (18 bp):
TCATAAAAAATAGAAAAA
Found at i:12610803 original size:16 final size:17
Alignment explanation
Indices: 12610782--12610828 Score: 60
Period size: 16 Copynumber: 2.7 Consensus size: 17
12610772 ATCAAGTTTG
12610782 ATATTTTTAAAATT-TA
1 ATATTTTTAAAATTCTA
12610798 ATATTTTTAAGAATTCTA
1 ATATTTTTAA-AATTCTA
*
12610816 ATGCTTTTTAAAA
1 AT-ATTTTTAAAA
12610829 AAATTAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 10 0.37
17 4 0.15
18 6 0.22
19 7 0.26
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.51
Consensus pattern (17 bp):
ATATTTTTAAAATTCTA
Done.