Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 136 of 214
Found at i:41296863 original size:30 final size:30
Alignment explanation
Indices: 41296828--41296895 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
41296818 CTTAATTAAA
*
41296828 AAAAGTTACAATT-TAGTCACTGAACTATTC
1 AAAAGTTAC-ATTCAAGTCACTGAACTATTC
* * *
41296858 GAAAGTTTTCATTCAAGTCATTGAACTATTC
1 AAAAG-TTACATTCAAGTCACTGAACTATTC
41296889 AAAAGTT
1 AAAAGTT
41296896 TTTAAAAGTC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
30 9 0.29
31 22 0.71
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (30 bp):
AAAAGTTACATTCAAGTCACTGAACTATTC
Found at i:41299828 original size:2 final size:2
Alignment explanation
Indices: 41299821--41299846 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
41299811 TTGGAATGAA
41299821 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
41299847 TTAGTACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:41306979 original size:21 final size:20
Alignment explanation
Indices: 41306944--41307026 Score: 64
Period size: 21 Copynumber: 4.0 Consensus size: 20
41306934 CTTTTTATAA
**
41306944 TTTTATTTTAAAAAATATGAT
1 TTTTATTTTTTAAAAT-TGAT
41306965 TTTTATTTTTTAAAATT--T
1 TTTTATTTTTTAAAATTGAT
*
41306983 TTATT-TTTATTTAAAATGTGAAA
1 TT-TTATTT-TTTAAAAT-TG-AT
*
41307006 ATTTATTTTTTAAAATTGAT
1 TTTTATTTTTTAAAATTGAT
41307026 T
1 T
41307027 AAACTTTTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 15
0.70 0.09 0.21
Matches are distributed among these distances:
18 6 0.12
19 10 0.20
20 3 0.06
21 16 0.33
22 10 0.20
23 4 0.08
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (20 bp):
TTTTATTTTTTAAAATTGAT
Found at i:41306979 original size:22 final size:22
Alignment explanation
Indices: 41306944--41306994 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
41306934 CTTTTTATAA
41306944 TTTTA-TTTTAAAAAATATGAT
1 TTTTATTTTTAAAAAATATGAT
* * * *
41306965 TTTTATTTTTTAAAATTTTTAT
1 TTTTATTTTTAAAAAATATGAT
41306987 TTTTATTT
1 TTTTATTT
41306995 AAAATGTGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTTATTTTTAAAAAATATGAT
Found at i:41307036 original size:22 final size:21
Alignment explanation
Indices: 41306986--41307037 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 21
41306976 AAAATTTTTA
*
41306986 TTTTTATTTAAAATGTGAAAAT
1 TTTTT-TTTAAAATGTGAAAAC
41307008 TTATTTTTTAAAAT-TGATTAAAC
1 TT-TTTTTTAAAATGTGA--AAAC
41307031 TTTTTTT
1 TTTTTTT
41307038 ATGTACTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 3 0.12
22 15 0.58
23 8 0.31
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.58
Consensus pattern (21 bp):
TTTTTTTTAAAATGTGAAAAC
Found at i:41308113 original size:16 final size:16
Alignment explanation
Indices: 41308092--41308125 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
41308082 CTTCAACCTC
*
41308092 TCATTTCCTTCTCATT
1 TCATTTCCTCCTCATT
41308108 TCATTTCCTCCTCATT
1 TCATTTCCTCCTCATT
41308124 TC
1 TC
41308126 CTCTTCGTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.35, G:0.00, T:0.53
Consensus pattern (16 bp):
TCATTTCCTCCTCATT
Found at i:41309021 original size:13 final size:11
Alignment explanation
Indices: 41308993--41309026 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
41308983 CATTTTTTCT
41308993 CATATATTGTA
1 CATATATTGTA
41309004 CATATATTGTA
1 CATATATTGTA
41309015 CATATATTGTA
1 CATATATTGTA
41309026 C
1 C
41309027 TAATTCCTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (11 bp):
CATATATTGTA
Found at i:41310259 original size:20 final size:20
Alignment explanation
Indices: 41310234--41310273 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
41310224 AATATTTTCC
* *
41310234 AGTAAATCATTTTACAGAAA
1 AGTAAAACACTTTACAGAAA
*
41310254 AGTAAAACACTTTCCAGAAA
1 AGTAAAACACTTTACAGAAA
41310274 TCATTTTACG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.25
Consensus pattern (20 bp):
AGTAAAACACTTTACAGAAA
Found at i:41311179 original size:10 final size:9
Alignment explanation
Indices: 41311164--41311208 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
41311154 TCCAATCAAT
41311164 TTATATAAA
1 TTATATAAA
41311173 TTAATATAAA
1 TT-ATATAAA
*
41311183 TTAGATAAA
1 TTATATAAA
41311192 TTA-ATAAA
1 TTATATAAA
*
41311200 TAATATAAA
1 TTATATAAA
41311209 AACCTATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
8 7 0.22
9 16 0.50
10 9 0.28
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (9 bp):
TTATATAAA
Found at i:41315860 original size:10 final size:10
Alignment explanation
Indices: 41315841--41315874 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
41315831 TAGCTAAAGC
*
41315841 AAATTTAAAA
1 AAATTAAAAA
41315851 AAATTAAAAA
1 AAATTAAAAA
41315861 AAATTAAAAA
1 AAATTAAAAA
41315871 AAAT
1 AAAT
41315875 CCTCTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
AAATTAAAAA
Found at i:41324059 original size:19 final size:19
Alignment explanation
Indices: 41324004--41324061 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
41323994 TTCACGTTGC
41324004 AAACGAAAGAGAT--AAG-
1 AAACGAAAGAGATAGAAGA
* *
41324020 AAACGAAGAAGTGA-AGGAGA
1 AAACG-A-AAGAGATAGAAGA
41324040 AAACGAAAGAGATAGAAGA
1 AAACGAAAGAGATAGAAGA
41324059 AAA
1 AAA
41324062 AAAAAAGGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
16 5 0.16
17 1 0.03
18 10 0.31
19 11 0.34
20 5 0.16
ACGTcount: A:0.62, C:0.05, G:0.28, T:0.05
Consensus pattern (19 bp):
AAACGAAAGAGATAGAAGA
Found at i:41325124 original size:82 final size:81
Alignment explanation
Indices: 41324953--41325195 Score: 326
Period size: 82 Copynumber: 3.0 Consensus size: 81
41324943 AATTGTTAAC
* * * * * *
41324953 AATTGAATTTCTAATTTCAAATCCGAGAAATAAAACGGTTGAATTCCTTAAAA-AAATGTAAGGA
1 AATTGAATTTGTATTTTCAAATCCAAGAAATAAAA-GGCTAAATTCCTTAAAATAAATGTAAGGG
41325017 GATTGAATTCTAAAAAT
65 GATTGAATTCTAAAAAT
* * *
41325034 AATTGAATTTGTATTTTCAAATCCAAAAAATAAAGAGACTAAATTCCTTAAAATAAATATAAGGG
1 AATTGAATTTGTATTTTCAAATCCAAGAAATAAA-AGGCTAAATTCCTTAAAATAAATGTAAGGG
41325099 GATTGAATTCTAAAAAT
65 GATTGAATTCTAAAAAT
* *
41325116 AATTGAATTTGTATTTTCAAATTCAAGAAGTAAAAAGGCTAAATTCCTTAAAATAAATGTAAGGG
1 AATTGAATTTGTATTTTCAAATCCAAGAAAT-AAAAGGCTAAATTCCTTAAAATAAATGTAAGGG
* * *
41325181 AATTAAATTCCAAAA
65 GATTGAATTCTAAAA
41325196 GTACGAAGAA
Statistics
Matches: 142, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
81 44 0.31
82 95 0.67
83 3 0.02
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.31
Consensus pattern (81 bp):
AATTGAATTTGTATTTTCAAATCCAAGAAATAAAAGGCTAAATTCCTTAAAATAAATGTAAGGGG
ATTGAATTCTAAAAAT
Found at i:41326862 original size:64 final size:63
Alignment explanation
Indices: 41326702--41326881 Score: 234
Period size: 64 Copynumber: 2.8 Consensus size: 63
41326692 TGAGCATCCC
* *
41326702 GATCGGTATTGATCCTGCATGTGTTTTGAACATACCATAGCTCTTTGTGAGCGTCCTGTTATAT
1 GATCGGTATTGATCCTGCATGTGTTATG-ACATACCATAACTCTTTGTGAGCGTCCTGTTATAT
* * *
41326766 AATCGGTATTGATCCTGCATGTGTTATGGACATACCACAACTCTTTGTGAGTGTCCTGTTATAT
1 GATCGGTATTGATCCTGCATGTGTTAT-GACATACCATAACTCTTTGTGAGCGTCCTGTTATAT
* * * * * *
41326830 GATCGGTGTTGATCCTACATGTATTGCTGACATACCGTAACTCTTTATGAGC
1 GATCGGTATTGATCCTGCATGTGTT-ATGACATACCATAACTCTTTGTGAGC
41326882 ATCCCGATAT
Statistics
Matches: 100, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
64 98 0.98
65 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.37
Consensus pattern (63 bp):
GATCGGTATTGATCCTGCATGTGTTATGACATACCATAACTCTTTGTGAGCGTCCTGTTATAT
Found at i:41326916 original size:25 final size:24
Alignment explanation
Indices: 41326870--41326922 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
41326860 CATACCGTAA
*
41326870 CTCTTTATGAGCATCCCGATATAGG
1 CTCTTTATGAGCATCCCAATAT-GG
* * *
41326895 CTCTTTGTGAGCTTCCTAATATGG
1 CTCTTTATGAGCATCCCAATATGG
41326919 CTCT
1 CTCT
41326923 CTTGAACTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 6 0.25
25 18 0.75
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.38
Consensus pattern (24 bp):
CTCTTTATGAGCATCCCAATATGG
Found at i:41328890 original size:6 final size:6
Alignment explanation
Indices: 41328881--41328905 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
41328871 TAAAAATGTG
41328881 TGATTA TGATTA TGATTA TGATTA T
1 TGATTA TGATTA TGATTA TGATTA T
41328906 TAAGTAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (6 bp):
TGATTA
Found at i:41338772 original size:25 final size:25
Alignment explanation
Indices: 41338744--41338794 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
41338734 CACGACACGA
41338744 ACCCAAACCACACCTGGCCTTAACC
1 ACCCAAACCACACCTGGCCTTAACC
*
41338769 ACCCAAACCACACTTGGCCTTAACC
1 ACCCAAACCACACCTGGCCTTAACC
41338794 A
1 A
41338795 TCAGACCATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.33, C:0.45, G:0.08, T:0.14
Consensus pattern (25 bp):
ACCCAAACCACACCTGGCCTTAACC
Found at i:41340327 original size:23 final size:23
Alignment explanation
Indices: 41340301--41340399 Score: 153
Period size: 23 Copynumber: 4.3 Consensus size: 23
41340291 ATAAGTGCAA
41340301 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
41340324 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
41340347 CACTGTTATGTAGTCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
41340370 CACTGAAACGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
41340393 CACTGAT
1 CACTGAT
41340400 CAATAACACT
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 67 1.00
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:41340368 original size:46 final size:46
Alignment explanation
Indices: 41340301--41340399 Score: 171
Period size: 46 Copynumber: 2.2 Consensus size: 46
41340291 ATAAGTGCAA
*
41340301 CACTGATATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTACCACTGAAACGTAGCCGAAGCTAC
* *
41340347 CACTGTTATGTAGTCGAAGCTACCACTGAAACGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTACCACTGAAACGTAGCCGAAGCTAC
41340393 CACTGAT
1 CACTGAT
41340400 CAATAACACT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.21
Consensus pattern (46 bp):
CACTGATATGTAGCCGAAGCTACCACTGAAACGTAGCCGAAGCTAC
Found at i:41347733 original size:23 final size:23
Alignment explanation
Indices: 41347707--41347805 Score: 153
Period size: 23 Copynumber: 4.3 Consensus size: 23
41347697 ATAAGTGCAA
41347707 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
41347730 CACTGTTATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
41347753 CACTGTTATGTAGTCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
41347776 CACTGAAACGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
41347799 CACTGAT
1 CACTGAT
41347806 CAATAACACT
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 69 1.00
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:41351497 original size:25 final size:25
Alignment explanation
Indices: 41351468--41351540 Score: 67
Period size: 26 Copynumber: 2.8 Consensus size: 25
41351458 TAGCTCCGGG
41351468 GAGCCATTAAC-ATGAAGCTCACAAA
1 GAGCCATTAACGA-GAAGCTCACAAA
* *
41351493 GAGCCTTTAATCGAGAAGCTCACGAA
1 GAGCCATTAA-CGAGAAGCTCACAAA
* * *
41351519 GAGTCATATAACGGGACGCTCA
1 GAGCCAT-TAACGAGAAGCTCA
41351541 TAAGATATGC
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
25 9 0.23
26 26 0.67
27 4 0.10
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18
Consensus pattern (25 bp):
GAGCCATTAACGAGAAGCTCACAAA
Found at i:41352235 original size:20 final size:20
Alignment explanation
Indices: 41352197--41352236 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
41352187 CCATATATTT
* *
41352197 CATAAAATTTAGAATTTTTC
1 CATAAAATTTACAACTTTTC
*
41352217 CATAAATTTTACAACTTTTC
1 CATAAAATTTACAACTTTTC
41352237 AATTTAGTCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.45
Consensus pattern (20 bp):
CATAAAATTTACAACTTTTC
Found at i:41356661 original size:28 final size:31
Alignment explanation
Indices: 41356610--41356675 Score: 93
Period size: 28 Copynumber: 2.2 Consensus size: 31
41356600 AGGGGTCTGG
*
41356610 TTATAAAAATTGTACTTTATTCTTTTAA-AA
1 TTATAAAAATTGTACTTTAATCTTTTAATAA
*
41356640 TTATAAAATTTG-A-TTTAATCTTTTAATAA
1 TTATAAAAATTGTACTTTAATCTTTTAATAA
41356669 TTATAAA
1 TTATAAA
41356676 GATATAGACT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 12 0.36
29 10 0.30
30 11 0.33
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (31 bp):
TTATAAAAATTGTACTTTAATCTTTTAATAA
Found at i:41358717 original size:31 final size:31
Alignment explanation
Indices: 41358682--41358748 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
41358672 TAAAATAGCA
41358682 ATTAAACTATTAAAAAATTTTCATTCAAGTT
1 ATTAAACTATTAAAAAATTTTCATTCAAGTT
* * * * *
41358713 ATTAAATTATTTAAAAGTTTTTATTTAAGTT
1 ATTAAACTATTAAAAAATTTTCATTCAAGTT
41358744 ATTAA
1 ATTAA
41358749 GTTGTTAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.48
Consensus pattern (31 bp):
ATTAAACTATTAAAAAATTTTCATTCAAGTT
Found at i:41366197 original size:29 final size:29
Alignment explanation
Indices: 41366165--41366264 Score: 89
Period size: 29 Copynumber: 3.4 Consensus size: 29
41366155 TTCTTTTTTA
*
41366165 GTCACTCAACTATGATTTTTTTTATATTG
1 GTCACCCAACTATGATTTTTTTTATATTG
* *
41366194 GTCACCCAACAATGGATTTGTTTCTT-TTTTG
1 GTCACCCAACTAT-GATTT-TTT-TTATATTG
* * *
41366225 GTCACCCAAATATGA-ATTTTTTAAATTTG
1 GTCACCCAACTATGATTTTTTTTATA-TTG
41366254 GTCA-CCAACTA
1 GTCACCCAACTA
41366265 AACAAGATTA
Statistics
Matches: 57, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
27 2 0.04
28 9 0.16
29 19 0.33
30 7 0.12
31 18 0.32
32 2 0.04
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (29 bp):
GTCACCCAACTATGATTTTTTTTATATTG
Found at i:41366227 original size:31 final size:29
Alignment explanation
Indices: 41366153--41366246 Score: 93
Period size: 31 Copynumber: 3.1 Consensus size: 29
41366143 CTATGGGTCA
* * *
41366153 TTTTCTTTTTTAGTCACTCAACTATGATT
1 TTTTCTTTTTTGGTCACCCAACAATGATT
*
41366182 TTTT-TTATATTGGTCACCCAACAATGGATT
1 TTTTCTT-TTTTGGTCACCCAACAAT-GATT
41366212 TGTTTCTTTTTTGGTCACCCAA-ATATGAATT
1 T-TTTCTTTTTTGGTCACCCAACA-ATG-ATT
41366243 TTTT
1 TTTT
41366247 AAATTTGGTC
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
28 2 0.04
29 18 0.33
30 10 0.19
31 22 0.41
32 2 0.04
ACGTcount: A:0.22, C:0.16, G:0.11, T:0.51
Consensus pattern (29 bp):
TTTTCTTTTTTGGTCACCCAACAATGATT
Found at i:41366827 original size:16 final size:16
Alignment explanation
Indices: 41366802--41366852 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
41366792 AGGGATTTGC
*
41366802 TTAATTTAATTTAATA
1 TTAATATAATTTAATA
*
41366818 TTAATATAATTT-TTA
1 TTAATATAATTTAATA
41366833 TTTAATAGTAATATTAATA
1 -TTAATA-TAAT-TTAATA
41366852 T
1 T
41366853 AAGATTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 2 0.07
16 17 0.61
17 4 0.14
18 3 0.11
19 2 0.07
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
TTAATATAATTTAATA
Found at i:41366860 original size:28 final size:27
Alignment explanation
Indices: 41366805--41366860 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
41366795 GATTTGCTTA
* **
41366805 ATTTAATTTAATATTAATATAATTTTT
1 ATTTAATGTAATATTAATATAAGATTT
41366832 ATTTAATAGTAATATTAATATAAGATTT
1 ATTTAAT-GTAATATTAATATAAGATTT
41366860 A
1 A
41366861 AATTTGAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 7 0.28
28 18 0.72
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.52
Consensus pattern (27 bp):
ATTTAATGTAATATTAATATAAGATTT
Found at i:41366899 original size:17 final size:18
Alignment explanation
Indices: 41366862--41366899 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
41366852 TAAGATTTAA
*
41366862 ATTTGAAGATGTTTATGT
1 ATTTGAAGATGTTTATAT
*
41366880 ATTTTAAGAT-TTTATAT
1 ATTTGAAGATGTTTATAT
41366897 ATT
1 ATT
41366900 ATTATTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (18 bp):
ATTTGAAGATGTTTATAT
Found at i:41366969 original size:27 final size:27
Alignment explanation
Indices: 41366918--41366980 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
41366908 TTGTCAACAA
*
41366918 TATATTTTATTTTATATATATTTTAAG
1 TATATTTTATTTTATAAATATTTTAAG
*
41366945 TATATTATTATTTTGA-AAATA-TTTATG
1 TATATT-TTATTTT-ATAAATATTTTAAG
41366972 TAT-TTTTAT
1 TATATTTTAT
41366981 ATATTTCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
25 4 0.12
26 2 0.06
27 14 0.44
28 11 0.34
29 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (27 bp):
TATATTTTATTTTATAAATATTTTAAG
Found at i:41367215 original size:33 final size:32
Alignment explanation
Indices: 41367178--41367241 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
41367168 ACAATCTCAA
* *
41367178 ATAGTTGGATGATCAATTTTTAAAAAAAAAATT
1 ATAGTTCGATGA-CAAGTTTTAAAAAAAAAATT
* *
41367211 ATAGTTCGATGACTAGTTTTAAAAAACAAAT
1 ATAGTTCGATGACAAGTTTTAAAAAAAAAAT
41367242 CATAATTGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 16 0.59
33 11 0.41
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.34
Consensus pattern (32 bp):
ATAGTTCGATGACAAGTTTTAAAAAAAAAATT
Found at i:41368860 original size:25 final size:25
Alignment explanation
Indices: 41368826--41368875 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
41368816 CAAACAAAAG
41368826 TTAGTATATAGAAAAATGGTGAACC
1 TTAGTATATAGAAAAATGGTGAACC
41368851 TTAGTATATAGAAAAATGGTGAACC
1 TTAGTATATAGAAAAATGGTGAACC
41368876 ACCAATGATG
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:0.44, C:0.08, G:0.20, T:0.28
Consensus pattern (25 bp):
TTAGTATATAGAAAAATGGTGAACC
Found at i:41378167 original size:19 final size:20
Alignment explanation
Indices: 41378143--41378195 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
41378133 AGCCTTCACT
41378143 TTTTTATAAATTTGC-AAAA
1 TTTTTATAAATTTGCTAAAA
*
41378162 TTTTTATAAATTCTTCTAAAA
1 TTTTTATAAATT-TGCTAAAA
41378183 TTTTGTA-AAATTT
1 TTTT-TATAAATTT
41378196 TAATTAAGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 12 0.40
20 3 0.10
21 13 0.43
22 2 0.07
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.53
Consensus pattern (20 bp):
TTTTTATAAATTTGCTAAAA
Found at i:41383386 original size:25 final size:25
Alignment explanation
Indices: 41383356--41383484 Score: 81
Period size: 25 Copynumber: 5.2 Consensus size: 25
41383346 AATAAGGGGT
*
41383356 AGCTCTCAAGAGCCATTAATTAGGA
1 AGCTCTCAAGAGCCATTAATCAGGA
** * *
41383381 AGCTCTGGATAGCCA-TATATCGGGA
1 AGCTCTCAAGAGCCATTA-ATCAGGA
*
41383406 AG-T-TCAAGCGAGCCA-T-ATCGGGA
1 AGCTCTCAA--GAGCCATTAATCAGGA
*
41383429 AGCTC-CAGAGAGCCATTAATTAGGA
1 AGCTCTCA-AGAGCCATTAATCAGGA
* * *
41383454 AGCTCACAAATAGCCTTTAATCAGGA
1 AGCTCTC-AAGAGCCATTAATCAGGA
41383480 AGCTC
1 AGCTC
41383485 ACGAGGAGCC
Statistics
Matches: 81, Mismatches: 13, Indels: 19
0.72 0.12 0.17
Matches are distributed among these distances:
23 17 0.21
24 7 0.09
25 36 0.44
26 20 0.25
27 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.22
Consensus pattern (25 bp):
AGCTCTCAAGAGCCATTAATCAGGA
Found at i:41383427 original size:23 final size:23
Alignment explanation
Indices: 41383397--41383444 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
41383387 GGATAGCCAT
* *
41383397 ATATCGGGAAGTTCAAGCGAGCC
1 ATATCGGGAAGCTCAAGAGAGCC
*
41383420 ATATCGGGAAGCTCCAGAGAGCC
1 ATATCGGGAAGCTCAAGAGAGCC
41383443 AT
1 AT
41383445 TAATTAGGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.31, C:0.23, G:0.29, T:0.17
Consensus pattern (23 bp):
ATATCGGGAAGCTCAAGAGAGCC
Found at i:41383473 original size:26 final size:26
Alignment explanation
Indices: 41383426--41383496 Score: 81
Period size: 26 Copynumber: 2.8 Consensus size: 26
41383416 AGCCATATCG
* *
41383426 GGAAGCTC-CAGAGAGCCATTAATTA
1 GGAAGCTCACAAAGAGCCATTAATCA
* *
41383451 GGAAGCTCACAAATAGCCTTTAATCA
1 GGAAGCTCACAAAGAGCCATTAATCA
* *
41383477 GGAAGCTCACGAGGAGCCAT
1 GGAAGCTCACAAAGAGCCAT
41383497 ATATCGGGAT
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
25 8 0.22
26 29 0.78
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (26 bp):
GGAAGCTCACAAAGAGCCATTAATCA
Found at i:41391362 original size:16 final size:16
Alignment explanation
Indices: 41391341--41391388 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 16
41391331 TTAGAAGGAT
41391341 TAAATTGAAAAAAGAC
1 TAAATTGAAAAAAGAC
*
41391357 TAAATTGAGTGAAAAGGAC
1 TAAATTGA---AAAAAGAC
41391376 TAAATT-AAAAAAG
1 TAAATTGAAAAAAG
41391389 GTGTAGAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
15 5 0.19
16 8 0.30
18 1 0.04
19 13 0.48
ACGTcount: A:0.58, C:0.04, G:0.17, T:0.21
Consensus pattern (16 bp):
TAAATTGAAAAAAGAC
Found at i:41391389 original size:16 final size:17
Alignment explanation
Indices: 41391335--41391389 Score: 60
Period size: 16 Copynumber: 3.2 Consensus size: 17
41391325 ATTTCGTTAG
*
41391335 AAGGATTAAATTGAAAA
1 AAGGACTAAATTGAAAA
*
41391352 AA-GACTAAATTGAGTGAA
1 AAGGACTAAATTGA--AAA
41391370 AAGGACTAAATT-AAAA
1 AAGGACTAAATTGAAAA
41391386 AAGG
1 AAGG
41391390 TGTAGAAGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
16 16 0.50
17 2 0.06
18 5 0.16
19 9 0.28
ACGTcount: A:0.56, C:0.04, G:0.20, T:0.20
Consensus pattern (17 bp):
AAGGACTAAATTGAAAA
Found at i:41393644 original size:20 final size:20
Alignment explanation
Indices: 41393619--41393659 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
41393609 AAGTTTGTTT
41393619 TATTTTTTCTTTCTCTGATA
1 TATTTTTTCTTTCTCTGATA
41393639 TATTTTTTCTTTCTCTGATA
1 TATTTTTTCTTTCTCTGATA
41393659 T
1 T
41393660 CCCAGTACAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.15, G:0.05, T:0.66
Consensus pattern (20 bp):
TATTTTTTCTTTCTCTGATA
Found at i:41394482 original size:12 final size:12
Alignment explanation
Indices: 41394465--41394499 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 12
41394455 AGTTTAGTGT
41394465 AATTTAATTAAA
1 AATTTAATTAAA
41394477 AATTTAATTTTAAA
1 AATTTAA--TTAAA
41394491 AATTTAATT
1 AATTTAATT
41394500 TAATATCGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 9 0.43
14 12 0.57
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
AATTTAATTAAA
Found at i:41394491 original size:14 final size:14
Alignment explanation
Indices: 41394472--41394500 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
41394462 TGTAATTTAA
41394472 TTAAAAATTTAATT
1 TTAAAAATTTAATT
41394486 TTAAAAATTTAATT
1 TTAAAAATTTAATT
41394500 T
1 T
41394501 AATATCGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TTAAAAATTTAATT
Found at i:41394764 original size:13 final size:13
Alignment explanation
Indices: 41394748--41394797 Score: 68
Period size: 13 Copynumber: 3.9 Consensus size: 13
41394738 ATAGCCATTA
*
41394748 TTTCTTACATTTG
1 TTTCTTACATTTC
41394761 TTTCTGTA-ATTTC
1 TTTCT-TACATTTC
41394774 TTTCTTACA-TTC
1 TTTCTTACATTTC
41394786 TTTCTTACATTT
1 TTTCTTACATTT
41394798 ATATTTATCT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
12 14 0.42
13 17 0.52
14 2 0.06
ACGTcount: A:0.16, C:0.18, G:0.04, T:0.62
Consensus pattern (13 bp):
TTTCTTACATTTC
Found at i:41394788 original size:12 final size:12
Alignment explanation
Indices: 41394743--41394796 Score: 56
Period size: 12 Copynumber: 4.3 Consensus size: 12
41394733 TATGCATAGC
*
41394743 CATTATTTCTTA
1 CATTCTTTCTTA
*
41394755 CATTTGTTTCTGTA
1 CA-TTCTTTCT-TA
41394769 -ATTTCTTTCTTA
1 CA-TTCTTTCTTA
41394781 CATTCTTTCTTA
1 CATTCTTTCTTA
41394793 CATT
1 CATT
41394797 TATATTTATC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
12 18 0.49
13 17 0.46
14 2 0.05
ACGTcount: A:0.19, C:0.19, G:0.04, T:0.59
Consensus pattern (12 bp):
CATTCTTTCTTA
Found at i:41397773 original size:9 final size:9
Alignment explanation
Indices: 41397759--41397793 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
41397749 TTGCAAAAAG
41397759 GACGATGAC
1 GACGATGAC
41397768 GACGATGAC
1 GACGATGAC
*
41397777 GACAATGAC
1 GACGATGAC
41397786 GACGATGA
1 GACGATGA
41397794 TGTTTCTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.37, C:0.20, G:0.31, T:0.11
Consensus pattern (9 bp):
GACGATGAC
Found at i:41399165 original size:32 final size:32
Alignment explanation
Indices: 41399129--41399193 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
41399119 AGTATAATTC
41399129 TTGTTACATGAGCTTACTAAGCACAAAATGCT
1 TTGTTACATGAGCTTACTAAGCACAAAATGCT
41399161 TTGTTACATGAGCTTACTAAGCACAAAATGCT
1 TTGTTACATGAGCTTACTAAGCACAAAATGCT
41399193 T
1 T
41399194 ACCCTGTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.32
Consensus pattern (32 bp):
TTGTTACATGAGCTTACTAAGCACAAAATGCT
Found at i:41407503 original size:25 final size:23
Alignment explanation
Indices: 41407451--41407533 Score: 58
Period size: 24 Copynumber: 3.4 Consensus size: 23
41407441 CAGCTTGAAA
* * * *
41407451 GAGCGTCCCGATATTAGCTCTTAC
1 GAGCATCCCGTTAATAGCTATT-C
* *
41407475 GAGCATCCCGTTATATGGTTATTGC
1 GAGCATCCCGTTA-ATAGCTATT-C
* *
41407500 GAGCTTCTCGTTAATAGCTATTC
1 GAGCATCCCGTTAATAGCTATTC
41407523 GAAGCATCCCG
1 G-AGCATCCCG
41407534 ATTGTTTGTG
Statistics
Matches: 44, Mismatches: 13, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
23 2 0.05
24 25 0.57
25 17 0.39
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (23 bp):
GAGCATCCCGTTAATAGCTATTC
Found at i:41407707 original size:25 final size:24
Alignment explanation
Indices: 41407653--41407766 Score: 99
Period size: 25 Copynumber: 4.7 Consensus size: 24
41407643 ATTGGCTTGT
* *
41407653 ATGAGCTTCCCATTAATGGCTCTC
1 ATGAGCTTCCCGTTAATGGCTCAC
** *
41407677 CGGAGCTTCCTGTTACATGGCTCAC
1 ATGAGCTTCCCGTTA-ATGGCTCAC
*
41407702 ATGAGCTTCCCG-TATATGGCTTAC
1 ATGAGCTTCCCGTTA-ATGGCTCAC
41407726 ATGAGCTTCCCAG-TATATGGCTCGA-
1 ATGAGCTTCCC-GTTA-ATGGCTC-AC
*
41407751 AAGAGCTTCCCGTTAA
1 ATGAGCTTCCCGTTAA
41407767 GTGCTCGTAT
Statistics
Matches: 74, Mismatches: 12, Indels: 8
0.79 0.13 0.09
Matches are distributed among these distances:
24 34 0.46
25 39 0.53
26 1 0.01
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (24 bp):
ATGAGCTTCCCGTTAATGGCTCAC
Found at i:41407780 original size:24 final size:24
Alignment explanation
Indices: 41407702--41407787 Score: 77
Period size: 25 Copynumber: 3.5 Consensus size: 24
41407692 CATGGCTCAC
* *
41407702 ATGAGCTTCCCGTATATGGCT-TA
1 ATGAGCTTCCCGTATAAGGCTCGA
*
41407725 CATGAGCTTCCCAGTATATGGCTCGA
1 -ATGAGCTTCCC-GTATAAGGCTCGA
* *
41407751 AAGAGCTTCCCGT-TAAGTGCTCGT
1 ATGAGCTTCCCGTATAAG-GCTCGA
41407775 ATGAGCATTCCCG
1 ATGAGC-TTCCCG
41407788 AATATGAATT
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
23 3 0.06
24 23 0.43
25 26 0.49
26 1 0.02
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.29
Consensus pattern (24 bp):
ATGAGCTTCCCGTATAAGGCTCGA
Found at i:41410047 original size:43 final size:43
Alignment explanation
Indices: 41409982--41410110 Score: 165
Period size: 43 Copynumber: 3.0 Consensus size: 43
41409972 TAGGATCTGC
* *
41409982 GATATGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATT
1 GATATGTGTTTACGTGTAAGACCACGTCTAGGACGTTGGCATT
* *
41410025 GACT-TGTGTTTACGTGTAAGACC-TGTCTAGGACAG-TGGCATC
1 GA-TATGTGTTTACGTGTAAGACCACGTCTAGGAC-GTTGGCATT
* *
41410067 GATATGTGATTACATGTAAGACCACGTCTAGGACGTTGGCATT
1 GATATGTGTTTACGTGTAAGACCACGTCTAGGACGTTGGCATT
41410110 G
1 G
41410111 TACGAGCTTT
Statistics
Matches: 73, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
41 1 0.01
42 34 0.47
43 37 0.51
44 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.29, T:0.32
Consensus pattern (43 bp):
GATATGTGTTTACGTGTAAGACCACGTCTAGGACGTTGGCATT
Found at i:41417546 original size:22 final size:23
Alignment explanation
Indices: 41417515--41417571 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
41417505 GCCAATGAAT
41417515 AAAAAAATA-TTATTATTTTTTG
1 AAAAAAATATTTATTATTTTTTG
* * *
41417537 AATAAAATATTTTTTATTTTTTT
1 AAAAAAATATTTATTATTTTTTG
41417560 AAAAAAAT-TTTA
1 AAAAAAATATTTA
41417572 AAAAAATATG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
22 11 0.38
23 18 0.62
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
AAAAAAATATTTATTATTTTTTG
Found at i:41417688 original size:25 final size:27
Alignment explanation
Indices: 41417617--41417681 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
41417607 CCTATCAGCT
* *
41417617 AGGCGCTAATGAAGGTGCCTCATAGAG
1 AGGCGCCAATGAATGTGCCTCATAGAG
*
41417644 AGGCGCCAATGAATGTGCCTCTTAGAG
1 AGGCGCCAATGAATGTGCCTCATAGAG
41417671 AGGCGCCAATG
1 AGGCGCCAATG
41417682 GTGGCCTTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.28, C:0.22, G:0.32, T:0.18
Consensus pattern (27 bp):
AGGCGCCAATGAATGTGCCTCATAGAG
Found at i:41417823 original size:3 final size:3
Alignment explanation
Indices: 41417817--41417849 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
41417807 GAGAGAAAGG
41417817 AGA AGA AGA AGA AGA AG- AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
41417850 ATAAAGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:41417838 original size:17 final size:17
Alignment explanation
Indices: 41417816--41417849 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
41417806 AGAGAGAAAG
41417816 GAGAAGAAGAAGAAGAA
1 GAGAAGAAGAAGAAGAA
41417833 GAGAAGAAGAAGAAGAA
1 GAGAAGAAGAAGAAGAA
41417850 ATAAAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (17 bp):
GAGAAGAAGAAGAAGAA
Found at i:41417839 original size:14 final size:14
Alignment explanation
Indices: 41417820--41417848 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
41417810 AGAAAGGAGA
41417820 AGAAGAAGAAGAAG
1 AGAAGAAGAAGAAG
41417834 AGAAGAAGAAGAAG
1 AGAAGAAGAAGAAG
41417848 A
1 A
41417849 AATAAAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (14 bp):
AGAAGAAGAAGAAG
Found at i:41418019 original size:19 final size:20
Alignment explanation
Indices: 41417995--41418032 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
41417985 TACTTTATAT
*
41417995 GAATATTGTGATT-TTTTAA
1 GAATATTGTAATTATTTTAA
41418014 GAATATTGTAATTATTTTA
1 GAATATTGTAATTATTTTA
41418033 TAATTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (20 bp):
GAATATTGTAATTATTTTAA
Found at i:41418128 original size:80 final size:79
Alignment explanation
Indices: 41417968--41418114 Score: 203
Period size: 80 Copynumber: 1.9 Consensus size: 79
41417958 ATATTTAGTG
* * *
41417968 TTTATAGTTTGGATTAGTACTTTATATGAATATTGTGATTTTTTAAGAATATTGTAATTATTTTA
1 TTTATAGTTTGGATTAGTACTTTATATGAATATTGTGATATTTCAAGAATATTGTAATTATTGTA
41418033 TAATTAAATTTATA
66 TAATTAAATTTATA
* *
41418047 TTTATAGTTTTGGATTAGTATTTTGTATGAATATTGT-A-ATTTCAAGATATATTGTAA-TATTG
1 TTTATAG-TTTGGATTAGTACTTTATATGAATATTGTGATATTTCAAGA-ATATTGTAATTATTG
41418109 TA-AATT
64 TATAATT
41418115 TTTGTATGAA
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
77 4 0.07
78 13 0.21
79 17 0.28
80 27 0.44
ACGTcount: A:0.33, C:0.01, G:0.13, T:0.52
Consensus pattern (79 bp):
TTTATAGTTTGGATTAGTACTTTATATGAATATTGTGATATTTCAAGAATATTGTAATTATTGTA
TAATTAAATTTATA
Found at i:41418197 original size:60 final size:60
Alignment explanation
Indices: 41418127--41418248 Score: 183
Period size: 60 Copynumber: 2.0 Consensus size: 60
41418117 TGTATGAATA
* * * *
41418127 TTGTAATTATTTTATAA-TTAATTTGTTAGTAATTTAGGATTATGTTATAAATTTTTGTGT
1 TTGTAATTA-TTTAAAATTTAATTTATTAGTAATTTAGGATTAAGTTATAAATTGTTGTGT
*
41418187 TTGTAATTATTTAAAATTTAATTTATTAGTAATTTAGGATTAAGTTATAAGTTGTTGTGT
1 TTGTAATTATTTAAAATTTAATTTATTAGTAATTTAGGATTAAGTTATAAATTGTTGTGT
41418247 TT
1 TT
41418249 AGTTTAGTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
59 6 0.11
60 50 0.89
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (60 bp):
TTGTAATTATTTAAAATTTAATTTATTAGTAATTTAGGATTAAGTTATAAATTGTTGTGT
Found at i:41418386 original size:16 final size:15
Alignment explanation
Indices: 41418365--41418401 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
41418355 CTCATTTAAT
41418365 TTTTATATAATATAA
1 TTTTATATAATATAA
*
41418380 CTTTTATATAATTTAA
1 -TTTTATATAATATAA
41418396 TTTTAT
1 TTTTAT
41418402 TTGATTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTTATATAATATAA
Found at i:41421466 original size:27 final size:28
Alignment explanation
Indices: 41421425--41421493 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 28
41421415 GAAAAATCAG
**
41421425 ACCATTGGCATCTCTTAACAT-GGCACC
1 ACCATTGGCGCCTCTTAACATAGGCACC
* * *
41421452 ACTATTGGCGCCTC-TCAGATAGGCACC
1 ACCATTGGCGCCTCTTAACATAGGCACC
*
41421479 ACCATTGGCTCCTCT
1 ACCATTGGCGCCTCT
41421494 GAGATAGGCG
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
26 4 0.12
27 29 0.88
ACGTcount: A:0.22, C:0.35, G:0.17, T:0.26
Consensus pattern (28 bp):
ACCATTGGCGCCTCTTAACATAGGCACC
Found at i:41421498 original size:27 final size:27
Alignment explanation
Indices: 41421446--41421502 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
41421436 CTCTTAACAT
*
41421446 GGCACCACTATTGGCGCCTCTCAGATA
1 GGCACCACCATTGGCGCCTCTCAGATA
* *
41421473 GGCACCACCATTGGCTCCTCTGAGATA
1 GGCACCACCATTGGCGCCTCTCAGATA
41421500 GGC
1 GGC
41421503 GCCAATACTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.21, C:0.33, G:0.25, T:0.21
Consensus pattern (27 bp):
GGCACCACCATTGGCGCCTCTCAGATA
Found at i:41434341 original size:30 final size:30
Alignment explanation
Indices: 41434263--41434358 Score: 93
Period size: 31 Copynumber: 3.1 Consensus size: 30
41434253 TTGGTAACTA
* * * *
41434263 TTCCTATATTGGGGTTTGAACTTGGCAATTG
1 TTCCCATATTGGGGCTTAAAC-TAGCAATTG
* * * *
41434294 TTCTCATGTTGGAGCTTAAACTAGCAAGTG
1 TTCCCATATTGGGGCTTAAACTAGCAATTG
*
41434324 TTCCCATATTGGGGCTTAAGCTAAGCAATTG
1 TTCCCATATTGGGGCTTAAACT-AGCAATTG
41434355 TTCC
1 TTCC
41434359 TACATTAGGC
Statistics
Matches: 51, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
30 25 0.49
31 26 0.51
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (30 bp):
TTCCCATATTGGGGCTTAAACTAGCAATTG
Found at i:41434357 original size:31 final size:30
Alignment explanation
Indices: 41434287--41434358 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
41434277 TTTGAACTTG
* *
41434287 GCAATTGTTCTCATGTTGGAGCTTAAACTA
1 GCAATTGTTCCCATATTGGAGCTTAAACTA
* * *
41434317 GCAAGTGTTCCCATATTGGGGCTTAAGCTAA
1 GCAATTGTTCCCATATTGGAGCTTAAACT-A
41434348 GCAATTGTTCC
1 GCAATTGTTCC
41434359 TACATTAGGC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
30 24 0.69
31 11 0.31
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.33
Consensus pattern (30 bp):
GCAATTGTTCCCATATTGGAGCTTAAACTA
Found at i:41437664 original size:17 final size:18
Alignment explanation
Indices: 41437635--41437669 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
41437625 ATTGGTTCAA
41437635 TTAAAAATCATTAAAAAT
1 TTAAAAATCATTAAAAAT
*
41437653 TTAAAAAT-ATTACAAAT
1 TTAAAAATCATTAAAAAT
41437670 ATAGACAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (18 bp):
TTAAAAATCATTAAAAAT
Found at i:41437669 original size:9 final size:9
Alignment explanation
Indices: 41437634--41437671 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
41437624 TATTGGTTCA
41437634 ATTAAAAAT
1 ATTAAAAAT
41437643 CATTAAAAAT
1 -ATTAAAAAT
41437653 -TTAAAAAT
1 ATTAAAAAT
*
41437661 ATTACAAAT
1 ATTAAAAAT
41437670 AT
1 AT
41437672 AGACAAATCC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
8 8 0.31
9 9 0.35
10 9 0.35
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (9 bp):
ATTAAAAAT
Found at i:41444237 original size:5 final size:5
Alignment explanation
Indices: 41444227--41444251 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
41444217 TTTGGCCCCA
41444227 GCCCG GCCCG GCCCG GCCCG GCCCG
1 GCCCG GCCCG GCCCG GCCCG GCCCG
41444252 AATATATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.60, G:0.40, T:0.00
Consensus pattern (5 bp):
GCCCG
Found at i:41444302 original size:12 final size:11
Alignment explanation
Indices: 41444274--41444303 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
41444264 ATATATTTTT
41444274 TATTTTTAAAA
1 TATTTTTAAAA
41444285 TATTTTTAAAA
1 TATTTTTAAAA
41444296 TACTTTTT
1 TA-TTTTT
41444304 TTTATTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:41444340 original size:26 final size:27
Alignment explanation
Indices: 41444285--41444342 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 27
41444275 ATTTTTAAAA
* *
41444285 TATTTTTAAAATACTTTTTTTTATTTTT
1 TATTTTTAAAATAC-TTTTTTTAGTGTT
*
41444313 TATTTTTAAAATA-TTTTTTTGGTGTT
1 TATTTTTAAAATACTTTTTTTAGTGTT
41444339 TATT
1 TATT
41444343 AAAAAATAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 14 0.52
28 13 0.48
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.69
Consensus pattern (27 bp):
TATTTTTAAAATACTTTTTTTAGTGTT
Found at i:41445247 original size:126 final size:125
Alignment explanation
Indices: 41444967--41445652 Score: 896
Period size: 126 Copynumber: 5.5 Consensus size: 125
41444957 GATAAAATCA
* * * * * * * * *
41444967 AAGCAGGATGATTGATCG-GAAGGATTTTTGAAGTCACGCCCACGTGTACGTGCTTTTGCTACAG
1 AAGCAGGATGCTTTAT-GAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
* * *
41445031 TAGGTTCTGGAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTTTAAAAAA-GCTTC
65 TTGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAACGCTTC
* * *
41445091 AAGCAGGATGCTTTGTGAGAAGAATTTGTGAAATCGCGCCTTCGTGGACGCGCTTTTACTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
* *
41445156 TGGTCCTAGAAGAAATAATTTCGAGTTGACGTTTTTGAGCAAATAGTTTAAAAAACGCTTC
66 TGGTCCTGGAA-AAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAACGCTTC
* * * *
41445217 AAGCAGGATGCTTTGTGAGAAGAATTTGTGAAATCGCGTCCTCGTGGACGTGCTTTTACTACAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
*
41445282 TGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTTTGAGCAAATAGTTTAAAAAACGCTTC
66 TGGTCCTGGAA-AAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAACGCTTC
* * * * *
41445343 AAGCAGGATGCTTTATAAGAAGAATTTGTGAAGTCGCGCCCACGTGGACGCGATTTTGCTATAGT
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
* * * * *
41445408 AGGTCCTGAAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAACAACGCTGC
66 TGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAA-AACGCTTC
** *
41445469 AAGCAACATGCTATT-TGAGAAGAATTTGTGAAATCGCACCCTCGTGGACGCGC-TTTGCTACAG
1 AAGCAGGATGCT-TTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
* * * *
41445532 TTGGTCCTGGAAAAATAATTTCGACTTGACGTTTCTGAGTAAATAGTAT-AAAATCGCTTC
65 TTGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAACGCTTC
* * * **
41445592 TAGCAAGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACATGCTTTTGCTA
1 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTA
41445653 TAGTAACGTG
Statistics
Matches: 498, Mismatches: 57, Indels: 14
0.88 0.10 0.02
Matches are distributed among these distances:
122 2 0.00
123 51 0.10
124 69 0.14
125 132 0.27
126 242 0.49
127 2 0.00
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.30
Consensus pattern (125 bp):
AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
TGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAACGCTTC
Found at i:41448858 original size:21 final size:21
Alignment explanation
Indices: 41448832--41449423 Score: 652
Period size: 22 Copynumber: 27.7 Consensus size: 21
41448822 TCAAATTATA
41448832 TTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
41448853 TTTAAGTTAAGGGTTTAAGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
*
41448875 TTAAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
*
41448897 TTAAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
41448918 TTTAGGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
* * *
41448940 TTTAATTTAATGGTTAAGG-T
1 TTTAAGTTAAGGGTTAGGGTT
41448960 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
* * *
41448982 TTAAAGTTAAAAGTTTAGGGTT
1 TTTAAGTT-AAGGGTTAGGGTT
* * * *
41449004 ATTAGGTTAAAGGTTAGGATT
1 TTTAAGTTAAGGGTTAGGGTT
*
41449025 TTTAGGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
* * *
41449047 TTTAATTTAAGGGCTAGAG-T
1 TTTAAGTTAAGGGTTAGGGTT
*
41449067 TTAAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
*
41449089 TTTAAGTTAAGGGTTAGTGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
41449110 TTTAGGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* * *
41449131 TTGAGGTTAAGAGTTTAGGGTT
1 TTTAAGTTAAG-GGTTAGGGTT
*
41449153 TTTAATTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
* *
41449174 TTTAAGTTAAGGGTTTATGGTG
1 TTTAAGTTAAGGG-TTAGGGTT
41449196 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
* *
41449218 TTAAAGTTAAGGTTTAGGG-T
1 TTTAAGTTAAGGGTTAGGGTT
* *
41449238 TTTAGGTTAAGGGTTAGAGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
41449259 TTTAGGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
* * *
41449281 TGTAATTTAAGGATTA-GGTT
1 TTTAAGTTAAGGGTTAGGGTT
* *
41449301 TTTAAGTTAAGAGTTTAGGATT
1 TTTAAGTTAAG-GGTTAGGGTT
41449323 TTTAAGTTAAGGGTCTAGGGTT
1 TTTAAGTTAAGGGT-TAGGGTT
* *
41449345 TTAAAGTTAATGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
41449366 TTTAGGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTT
*
41449388 TTAAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
*
41449409 TTTAGGTTAAGGGTT
1 TTTAAGTTAAGGGTT
41449424 TAAGGTTTGT
Statistics
Matches: 483, Mismatches: 72, Indels: 32
0.82 0.12 0.05
Matches are distributed among these distances:
20 53 0.11
21 196 0.41
22 231 0.48
23 3 0.01
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.43
Consensus pattern (21 bp):
TTTAAGTTAAGGGTTAGGGTT
Found at i:41448899 original size:43 final size:43
Alignment explanation
Indices: 41448832--41449431 Score: 636
Period size: 43 Copynumber: 14.0 Consensus size: 43
41448822 TCAAATTATA
*
41448832 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAAGGTT
1 TTTAAGTTAAGGGTTTAGGG-TTTTAAGTTAAGGGTTTAGGGTT
*
41448875 TTAAAGTTAAGGGTTTAGGGTTTTAAAGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTTTT-AAGTTAAGGGTTTAGGGTT
* * * *
41448918 TTTAGGTTAAGGGTTTAGGGTTTTTAATTTAATGG-TTAAGG-T
1 TTTAAGTTAAGGGTTTAGGG-TTTTAAGTTAAGGGTTTAGGGTT
**
41448960 TTTAAGTTAAGGGTTTAGGGTTTTAAAGTTAAAAGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTTTT-AAGTTAAGGGTTTAGGGTT
* * * * *
41449004 ATTAGGTTAAAGG-TTAGGATTTTTAGGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGG-GTTTTAAGTTAAGGGTTTAGGGTT
* * * *
41449047 TTTAATTTAAGGG-CTAGAGTTTAAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTTTTAAGTTAAGGGTTTAGGGTT
* *
41449089 TTTAAGTTAAGGG-TTAGTGTTTTTAGGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAG-GGTTTTAAGTTAAGGGTTTAGGGTT
* * * *
41449131 TTGAGGTTAAGAGTTTAGGGTTTTTAATTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGG-TTTTAAGTTAAGGGTTTAGGGTT
*
41449174 TTTAAGTTAAGGGTTTATGGTGTTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGT-TTTAAGTTAAGGGTTTAGGGTT
* * *
41449218 TTAAAGTTAA-GGTTTAGGGTTTTAGGTTAAGGG-TTAGAGTT
1 TTTAAGTTAAGGGTTTAGGGTTTTAAGTTAAGGGTTTAGGGTT
* * *
41449259 TTTAGGTTAAGGGTTTAGGGTTTGTAATTTAA-GGATTA-GGTT
1 TTTAAGTTAAGGGTTTAGGGTTT-TAAGTTAAGGGTTTAGGGTT
* * *
41449301 TTTAAGTTAAGAGTTTAGGATTTTTAAGTTAAGGGTCTAGGGTT
1 TTTAAGTTAAGGGTTTAGG-GTTTTAAGTTAAGGGTTTAGGGTT
* * *
41449345 TTAAAGTTAATGG-TTAGGGTTTTTAGGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGG-TTTTAAGTTAAGGGTTTAGGGTT
* * *
41449388 TTAAAGTTAAGGG-TTAGGGTTTTTAGGTTAAGGGTTTAAGGTT
1 TTTAAGTTAAGGGTTTAGGG-TTTTAAGTTAAGGGTTTAGGGTT
41449431 T
1 T
41449432 GTCAATTAAA
Statistics
Matches: 470, Mismatches: 68, Indels: 38
0.82 0.12 0.07
Matches are distributed among these distances:
41 19 0.04
42 136 0.29
43 249 0.53
44 66 0.14
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.43
Consensus pattern (43 bp):
TTTAAGTTAAGGGTTTAGGGTTTTAAGTTAAGGGTTTAGGGTT
Found at i:41448988 original size:107 final size:107
Alignment explanation
Indices: 41448832--41449431 Score: 739
Period size: 107 Copynumber: 5.6 Consensus size: 107
41448822 TCAAATTATA
* *
41448832 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAAGGTTTTAAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTAGGG-TTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
41448897 TTAAAGTTAAGGGTTAGGGTTTTTAGGTTAAGGGTTTAGGGTT
65 TTAAAGTTAAGGGTTAGGGTTTTTAGGTTAAGGGTTTAGGGTT
* * * * **
41448940 TTTAATTTAATGGTTAAGGTTTTAAGTTAAGGGTTTAGGGTTTTAAAGTTAAAAGTTTAGGGTTA
1 TTTAAGTTAAGGGTTAGGGTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT-
* * *
41449005 TT-AGGTTAAAGGTTAGGATTTTTAGGTTAAGGGTTTAGGGTT
65 TTAAAGTTAAGGGTTAGGGTTTTTAGGTTAAGGGTTTAGGGTT
* * * * *
41449047 TTTAATTTAAGGGCTAGAGTTTAAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGG-TTAGTGTTT
1 TTTAAGTTAAGGGTTAGGGTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTT
* * * *
41449111 TTAGGTTAAGGGTTAGGGTTTTGAGGTTAAGAGTTTAGGGTT
66 TAAAGTTAAGGGTTAGGGTTTTTAGGTTAAGGGTTTAGGGTT
* * *
41449153 TTTAATTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTATGGTGTTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTAGGG-TTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* *
41449218 TTAAAGTTAAGGTTTAGGG-TTTTAGGTTAAGGG-TTAGAGTT
65 TTAAAGTTAAGGGTTAGGGTTTTTAGGTTAAGGGTTTAGGGTT
* * * * *
41449259 TTTAGGTTAAGGGTTTAGGGTTTGTAATTTAA-GGATTA-GGTTTTTAAGTTAAGAGTTTAGGAT
1 TTTAAGTTAAGGG-TTAGGGTTT-TAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTTAGGGT
* * * *
41449322 TTTTAAGTTAAGGGTCTAGGGTTTTAAAGTTAATGG-TTAGGGTT
64 TTTAAAGTTAAGGGT-TAGGGTTTTTAGGTTAAGGGTTTAGGGTT
* * *
41449366 TTTAGGTTAAGGGTTTAGGGTTTTAAAGTTAAGGG-TTAGGGTTTTTAGGTTAAGGGTTTAAGGT
1 TTTAAGTTAAGGG-TTAGGGTTTT-AAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTTAGGGT
41449430 TT
64 TT
41449432 GTCAATTAAA
Statistics
Matches: 429, Mismatches: 52, Indels: 22
0.85 0.10 0.04
Matches are distributed among these distances:
105 37 0.09
106 92 0.21
107 234 0.55
108 66 0.15
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.43
Consensus pattern (107 bp):
TTTAAGTTAAGGGTTAGGGTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTT
TAAAGTTAAGGGTTAGGGTTTTTAGGTTAAGGGTTTAGGGTT
Found at i:41449440 original size:22 final size:21
Alignment explanation
Indices: 41448832--41449440 Score: 436
Period size: 21 Copynumber: 28.5 Consensus size: 21
41448822 TCAAATTATA
*
41448832 TTTAAGTTAAGGG-TTAGGGTT
1 TTTAAATTAAGGGTTTAGGG-T
* *
41448853 TTTAAGTTAAGGGTTTAAGGT
1 TTTAAATTAAGGGTTTAGGGT
41448874 TTTAAAGTTAAGGGTTTAGGGT
1 TTTAAA-TTAAGGGTTTAGGGT
41448896 TTTAAAGTTAAGGG-TTAGGGTT
1 TTTAAA-TTAAGGGTTTAGGG-T
**
41448918 TTTAGGTTAAGGGTTTAGGGTT
1 TTTAAATTAAGGGTTTAGGG-T
* * *
41448940 TTTAATTTAATGG-TTAAGGT
1 TTTAAATTAAGGGTTTAGGGT
*
41448960 TTTAAGTTAAGGGTTTAGGGT
1 TTTAAATTAAGGGTTTAGGGT
**
41448981 TTTAAAGTTAAAAGTTTAGGGT
1 TTTAAA-TTAAGGGTTTAGGGT
** * *
41449003 TATTAGGTTAAAGG-TTAGGATT
1 T-TTAAATTAAGGGTTTAGG-GT
**
41449025 TTTAGGTTAAGGGTTTAGGGTT
1 TTTAAATTAAGGGTTTAGGG-T
* * *
41449047 TTTAATTTAAGGG-CTAGAG-
1 TTTAAATTAAGGGTTTAGGGT
41449066 TTTAAAGTTAAGGGTTTAGGGTT
1 TTTAAA-TTAAGGGTTTAGGG-T
* *
41449089 TTTAAGTTAAGGG-TTAGTGTT
1 TTTAAATTAAGGGTTTAG-GGT
**
41449110 TTTAGGTTAAGGG-TTAGGGT
1 TTTAAATTAAGGGTTTAGGGT
** *
41449130 TTTGAGGTTAAGAGTTTAGGGTT
1 TTT-AAATTAAGGGTTTAGGG-T
*
41449153 TTTAATTTAAGGG-TTAGGGTT
1 TTTAAATTAAGGGTTTAGGG-T
* *
41449174 TTTAAGTTAAGGGTTTATGGT
1 TTTAAATTAAGGGTTTAGGGT
*
41449195 GTTTAAGTTAAGGGTTTAGGGT
1 -TTTAAATTAAGGGTTTAGGGT
41449217 TTTAAAGTTAA-GGTTTAGGGT
1 TTTAAA-TTAAGGGTTTAGGGT
** *
41449238 TTTAGGTTAAGGG-TTAGAGTT
1 TTTAAATTAAGGGTTTAG-GGT
**
41449259 TTTAGGTTAAGGGTTTAGGGT
1 TTTAAATTAAGGGTTTAGGGT
* * *
41449280 TTGTAATTTAA-GGATTAGGTT
1 TT-TAAATTAAGGGTTTAGGGT
* * *
41449301 TTTAAGTTAAGAGTTTAGGATT
1 TTTAAATTAAGGGTTTAGG-GT
* *
41449323 TTTAAGTTAAGGGTCTAGGGT
1 TTTAAATTAAGGGTTTAGGGT
*
41449344 TTTAAAGTTAATGG-TTAGGGTT
1 TTTAAA-TTAAGGGTTTAGGG-T
**
41449366 TTTAGGTTAAGGGTTTAGGGT
1 TTTAAATTAAGGGTTTAGGGT
41449387 TTTAAAGTTAAGGG-TTAGGGTT
1 TTTAAA-TTAAGGGTTTAGGG-T
** *
41449409 TTTAGGTTAAGGGTTTAAGGT
1 TTTAAATTAAGGGTTTAGGGT
*
41449430 TTGTCAATTAA
1 TT-TAAATTAA
41449441 ATTATGCATT
Statistics
Matches: 486, Mismatches: 68, Indels: 67
0.78 0.11 0.11
Matches are distributed among these distances:
19 5 0.01
20 39 0.08
21 217 0.45
22 213 0.44
23 12 0.02
ACGTcount: A:0.26, C:0.00, G:0.31, T:0.43
Consensus pattern (21 bp):
TTTAAATTAAGGGTTTAGGGT
Found at i:41449991 original size:18 final size:18
Alignment explanation
Indices: 41449965--41450007 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
41449955 GACTCGAAAA
* *
41449965 AGGAAACATATAAGGGTT
1 AGGAAACATAAAAGGGCT
*
41449983 AGGATACATAAAAGGGCT
1 AGGAAACATAAAAGGGCT
41450001 AGGAAAC
1 AGGAAAC
41450008 GCACCTGGCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.47, C:0.09, G:0.28, T:0.16
Consensus pattern (18 bp):
AGGAAACATAAAAGGGCT
Found at i:41450826 original size:20 final size:20
Alignment explanation
Indices: 41450789--41450826 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41450779 TTTATTTTTA
*
41450789 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
41450809 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
41450827 TACCTTGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:41451839 original size:11 final size:11
Alignment explanation
Indices: 41451825--41451901 Score: 63
Period size: 11 Copynumber: 6.9 Consensus size: 11
41451815 ATAAATATGG
41451825 ATTTGAGAGAA
1 ATTTGAGAGAA
*
41451836 ATTTTGA-AGGA
1 A-TTTGAGAGAA
*
41451847 ATTTGAGTGCAA
1 ATTTGAGAG-AA
41451859 A-TTGAGAGGAA
1 ATTTGAGA-GAA
41451870 ATTT-AGAAGAA
1 ATTTGAG-AGAA
41451881 A-TTGAGAGGAA
1 ATTTGAGA-GAA
41451892 ATTTGAGAGA
1 ATTTGAGAGA
41451902 TGATTAGTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
10 8 0.15
11 28 0.53
12 17 0.32
ACGTcount: A:0.43, C:0.01, G:0.29, T:0.27
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:41451847 original size:51 final size:51
Alignment explanation
Indices: 41451766--41451863 Score: 126
Period size: 51 Copynumber: 1.9 Consensus size: 51
41451756 AATTATTTAA
*
41451766 AAATAGGGATTTAAGAGAAATTTAAGAGGAACTTGTGAGCAAATTGAAAAT
1 AAATAGGGATTTAAGAGAAATTTAAGAGGAACTTGAGAGCAAATTGAAAAT
* * * * *
41451817 AAATATGGATTTGAGAGAAATTT-TGAAGGAATTTGAGTGCAAATTGA
1 AAATAGGGATTTAAGAGAAATTTAAG-AGGAACTTGAGAGCAAATTGA
41451864 GAGGAAATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
50 1 0.03
51 39 0.98
ACGTcount: A:0.44, C:0.03, G:0.24, T:0.29
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAAGAGGAACTTGAGAGCAAATTGAAAAT
Found at i:41451868 original size:22 final size:23
Alignment explanation
Indices: 41451825--41451899 Score: 79
Period size: 22 Copynumber: 3.3 Consensus size: 23
41451815 ATAAATATGG
41451825 ATTTGAG-AGAAATTTTGA-AGG-A
1 ATTTGAGAAGAAA--TTGAGAGGAA
*
41451847 ATTTGAG-TGCAAATTGAGAGGAA
1 ATTTGAGAAG-AAATTGAGAGGAA
41451870 ATTT-AGAAGAAATTGAGAGGAA
1 ATTTGAGAAGAAATTGAGAGGAA
41451892 ATTTGAGA
1 ATTTGAGA
41451900 GATGATTAGT
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
21 4 0.09
22 30 0.65
23 12 0.26
ACGTcount: A:0.43, C:0.01, G:0.28, T:0.28
Consensus pattern (23 bp):
ATTTGAGAAGAAATTGAGAGGAA
Found at i:41451873 original size:34 final size:34
Alignment explanation
Indices: 41451825--41451900 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 34
41451815 ATAAATATGG
* * *
41451825 ATTTGAGA-GAAATTTTGAAGGAATTTGAGTGCAA
1 ATTTGAGAGGAAATTTAGAA-GAAATTGAGAGCAA
*
41451859 A-TTGAGAGGAAATTTAGAAGAAATTGAGAGGAA
1 ATTTGAGAGGAAATTTAGAAGAAATTGAGAGCAA
41451892 ATTTGAGAG
1 ATTTGAGAG
41451901 ATGATTAGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
33 18 0.50
34 18 0.50
ACGTcount: A:0.42, C:0.01, G:0.29, T:0.28
Consensus pattern (34 bp):
ATTTGAGAGGAAATTTAGAAGAAATTGAGAGCAA
Found at i:41452977 original size:27 final size:27
Alignment explanation
Indices: 41452914--41452984 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
41452904 GAAATCCAGA
**
41452914 TGCCACAGGCGGCACCAAAGGTACCTG
1 TGCCACAGGCGGCACCAAAGGTACCAC
* * *
41452941 TGGCAGAGGCGGCACCAAAGGTGCCAC
1 TGCCACAGGCGGCACCAAAGGTACCAC
41452968 TGCCACAGGCGGCACCA
1 TGCCACAGGCGGCACCA
41452985 CTTGTATTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.25, C:0.34, G:0.32, T:0.08
Consensus pattern (27 bp):
TGCCACAGGCGGCACCAAAGGTACCAC
Found at i:41453029 original size:3 final size:3
Alignment explanation
Indices: 41453016--41453049 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
41453006 CCGTCCAGCT
* *
41453016 GAA GGA GAA GAA GAA GAA GAA GAA GGA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
41453050 GAGGAGGAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:41453462 original size:42 final size:40
Alignment explanation
Indices: 41453386--41453492 Score: 119
Period size: 40 Copynumber: 2.6 Consensus size: 40
41453376 TAGTTTTTAC
* *
41453386 ATTA-TATTATTGTTAGTTATTATTTTTAGTAAAACTCTA
1 ATTATTATTATTGTTAGTTATTATTTTGAGTAAAACTATA
*
41453425 ATTATTATTATTAGTTAG-TATTATTTTGAGTATAAAACTATT
1 ATTATTATTATT-GTTAGTTATTATTTTGAG--TAAAACTATA
*
41453467 ATTATTGTTAATGTGTTAGTTATTAT
1 ATTATTATT-AT-TGTTAGTTATTAT
41453493 GATTAGTGGT
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
39 4 0.07
40 18 0.32
41 5 0.09
42 16 0.28
43 7 0.12
44 7 0.12
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.54
Consensus pattern (40 bp):
ATTATTATTATTGTTAGTTATTATTTTGAGTAAAACTATA
Found at i:41453470 original size:76 final size:76
Alignment explanation
Indices: 41453268--41453476 Score: 201
Period size: 76 Copynumber: 2.7 Consensus size: 76
41453258 GTTTAGTTAT
* * *
41453268 TAATAATTATTGTTACTTAGTATTATTGTTAGTA-AAACACTAATATTATTATGGTTAGTTATTA
1 TAATTATTATT-TTAGTTAGTATTATTGTTAGTATAAA-AC---TATTATTATTGTTAGTTATTA
41453332 GGATTAGTAAAAACCC
61 GGATTAGTAAAAACCC
* * * * * * ***
41453348 TGATTATTATTTTAGTTAGTATGATTGTTAGTTTTTACATTA-TATTATTGTTAGTTATTATTTT
1 TAATTATTATTTTAGTTAGTATTATTGTTAG-TATAAAACTATTATTATTGTTAGTTATTAGGAT
*
41453412 TAGT-AAAACTC
65 TAGTAAAAACCC
41453423 TAATTATTATTATTAGTTAGTATTATT-TTGAGTATAAAACTATTATTATTGTTA
1 TAATTATTATT-TTAGTTAGTATTATTGTT-AGTATAAAACTATTATTATTGTTA
41453477 ATGTGTTAGT
Statistics
Matches: 105, Mismatches: 19, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
75 24 0.23
76 49 0.47
77 2 0.02
79 18 0.17
80 11 0.10
81 1 0.01
ACGTcount: A:0.33, C:0.05, G:0.11, T:0.50
Consensus pattern (76 bp):
TAATTATTATTTTAGTTAGTATTATTGTTAGTATAAAACTATTATTATTGTTAGTTATTAGGATT
AGTAAAAACCC
Found at i:41456394 original size:16 final size:17
Alignment explanation
Indices: 41456367--41456398 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
41456357 CTGTCAAATT
41456367 GATGTGTGTAATGTTGG
1 GATGTGTGTAATGTTGG
41456384 GATGT-TGTAATGTTG
1 GATGTGTGTAATGTTG
41456399 TTTTAAGACC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.19, C:0.00, G:0.38, T:0.44
Consensus pattern (17 bp):
GATGTGTGTAATGTTGG
Found at i:41458777 original size:154 final size:153
Alignment explanation
Indices: 41458499--41459270 Score: 937
Period size: 152 Copynumber: 5.0 Consensus size: 153
41458489 AACTTCAAGA
* ** * * **
41458499 AAAATTTAGTAAAAACCCTTATTTCAACCATTTGTTCGTA-TTTTTTCCTAAATTTTATTACTTT
1 AAAATTTAGAAAAAACCCTTATTTCGGCCCTTTGCTCGTATTTTTTTCCCGAATTTTATTACTTT
*
41458563 -TAAAAATATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTT
66 ATAAAAATATACTATTTTCTTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTT
41458627 AAATAAATTTAGTGTTTTTTAAAT
131 -AATAAATTTAGTGTTTTTTAAAT
* *
41458651 AAATTTTA-AAAAAACCCTTATTTCGGCCCTTTGCTCATATTTTTTTCCCGAATTTTATTACTTT
1 AAAATTTAGAAAAAACCCTTATTTCGGCCCTTTGCTCGTATTTTTTTCCCGAATTTTATTACTTT
* *
41458715 CAATAAAAATATATTATTTT-TTATTTTATTATTTTACTTTATTTTAGTACATTATGTTTGAAAT
66 --ATAAAAATATACTATTTTCTTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAAT
* * * * *
41458779 GT-ATTAATTAAGTCTATTTTTAAAA
129 TTAATAAATTTAGTGT-TTTTTAAAT
* *
41458804 AAAATTTAGTAAAAAACCCTTATTTCGGCTCTTT-ATCGTA-TTTTTTCCCGAATTTTATTACTT
1 AAAATTTAG-AAAAAACCCTTATTTCGGCCCTTTGCTCGTATTTTTTTCCCGAATTTTATTACTT
*
41458867 T-TAAAAAATATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAAT
65 TAT-AAAAATATACTATTTTCTTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAAT
41458931 TTAAATAAATTTAGTGTGTTTTTTAAAT
129 TT-AATAAATTTA--GTGTTTTTTAAAT
* *
41458959 -AAA-TTAAAAAAAACCCTTATTTCGGCCCTTTGCTCGTATTTTTTTTCCGAATTTTATTACTTT
1 AAAATTTAGAAAAAACCCTTATTTCGGCCCTTTGCTCGTATTTTTTTCCCGAATTTTATTACTTT
* * *
41459022 CAATAAAAATATATTATTTTCGTATTTTATTTTTTTACATTATTTTAGTACATTATGTTTGAAAT
66 --ATAAAAATATACTATTTTCTTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAA-
* * *
41459087 GTTTTAAT-TATTTCTGTTTCTTTTTAAA-
128 --TTTAATAAATTT-AGTGT-TTTTTAAAT
* * * *
41459115 AAAATTTAGTAAAAAACTCTTACTTCGGCCCTTTGTTCGTATTTTTTTCTCCGCATTTTATTACT
1 AAAATTTAG-AAAAAACCCTTATTTCGGCCCTTTGCTCGTATTTTTTTC-CCGAATTTTATTACT
41459180 TTA-AAAAATAT-CATATTTTC-TATTTTTATTATTTTACATTATTTTAGTACATTATGTTTGAA
64 TTATAAAAATATAC-TATTTTCTTA-TTTTATTATTTTACATTATTTTAGTACATTATGTTTGAA
*
41459242 ATTT-ATTAATTTAGTATGTTTTTTAAAT
127 ATTTAATAAATTTAG--TGTTTTTTAAAT
41459270 A
1 A
41459271 TACAATTTTT
Statistics
Matches: 536, Mismatches: 51, Indels: 63
0.82 0.08 0.10
Matches are distributed among these distances:
150 1 0.00
151 40 0.07
152 105 0.20
153 50 0.09
154 95 0.18
155 50 0.09
156 64 0.12
157 70 0.13
158 7 0.01
159 38 0.07
160 16 0.03
ACGTcount: A:0.32, C:0.10, G:0.06, T:0.51
Consensus pattern (153 bp):
AAAATTTAGAAAAAACCCTTATTTCGGCCCTTTGCTCGTATTTTTTTCCCGAATTTTATTACTTT
ATAAAAATATACTATTTTCTTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTT
AATAAATTTAGTGTTTTTTAAAT
Found at i:41460908 original size:17 final size:17
Alignment explanation
Indices: 41460882--41460946 Score: 62
Period size: 17 Copynumber: 3.8 Consensus size: 17
41460872 TTAATTTTTT
41460882 AAAAAT-TAAAAATTAA
1 AAAAATATAAAAATTAA
41460898 AAAAATATAAAAATT-A
1 AAAAATATAAAAATTAA
* *
41460914 GAAATTATTAAAAAGTATAA
1 AAAAATA-TAAAAA-T-TAA
*
41460934 AAAAGTATAAAAA
1 AAAAATATAAAAA
41460947 ATATTTTGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
16 12 0.30
17 14 0.35
18 1 0.03
19 7 0.17
20 6 0.15
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.25
Consensus pattern (17 bp):
AAAAATATAAAAATTAA
Found at i:41460910 original size:24 final size:25
Alignment explanation
Indices: 41460881--41460936 Score: 78
Period size: 24 Copynumber: 2.2 Consensus size: 25
41460871 ATTAATTTTT
41460881 TAAAAATTAAAAATTA-AAAAAATA
1 TAAAAATTAAAAATTATAAAAAATA
* *
41460905 TAAAAATTAGAAATTATTAAAAAGTA
1 TAAAAATTAAAAATTA-TAAAAAATA
41460931 TAAAAA
1 TAAAAA
41460937 AGTATAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 15 0.54
26 13 0.46
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.27
Consensus pattern (25 bp):
TAAAAATTAAAAATTATAAAAAATA
Found at i:41465668 original size:75 final size:75
Alignment explanation
Indices: 41465584--41465969 Score: 502
Period size: 75 Copynumber: 5.1 Consensus size: 75
41465574 TTAACTTTTT
** * * *
41465584 TTTTTGAAAAATAGAAATTGAAAATAGCTTGGCGTGCGATCCGAAGCTCAACTCACCTCTCGGAT
1 TTTTTGAAAAATAGAAATTGAAAATAGCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGGAT
41465649 TATGAGTTGA
66 TATGAGTTGA
* * * * * * * * *
41465659 TTTTTGAAAAACAGAAATTGAAAATAGCTCGGCATACAATCCAAAGCTCAACTCACTTCTCGAAT
1 TTTTTGAAAAATAGAAATTGAAAATAGCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGGAT
41465724 TATGAGTTGA
66 TATGAGTTGA
* * * * * *
41465734 TTTTTTAAAAACAGAAATTGTAAATAGCTTAGCGTGCGACTCGGGGCTCAACTCACTTCTCGGAT
1 TTTTTGAAAAATAGAAATTGAAAATAGCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGGAT
41465799 TATGAGTTGA
66 TATGAGTTGA
* * * * *
41465809 TTTTTGAAAAATAGAAATTGTAAATACCTCAGCGTGCGACCCGAGGCTCAAATTACTTCTAGGAT
1 TTTTTGAAAAATAGAAATTGAAAATAGCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGGAT
41465874 TATGAGTTGA
66 TATGAGTTGA
* * * * *
41465884 TTTTTGAAAAATAGAAATTAAAAATACCTCAGCATGGGACCCGAGGCTCAACTCACTTCTTGGAT
1 TTTTTGAAAAATAGAAATTGAAAATAGCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGGAT
41465949 TATGAGTTGA
66 TATGAGTTGA
41465959 TTTTTGAAAAA
1 TTTTTGAAAAA
41465970 CAAAAAAAGA
Statistics
Matches: 274, Mismatches: 37, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
75 274 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (75 bp):
TTTTTGAAAAATAGAAATTGAAAATAGCTCAGCGTGCGACCCGAGGCTCAACTCACTTCTCGGAT
TATGAGTTGA
Found at i:41474235 original size:27 final size:27
Alignment explanation
Indices: 41474197--41474250 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
41474187 ATGTACATGC
*
41474197 AATGAATGAATGAATGACTAATGAATG
1 AATGAATGAATGAATGACCAATGAATG
*
41474224 AATGGATGAATGAATGACCAATGAATG
1 AATGAATGAATGAATGACCAATGAATG
41474251 TTAGTCATGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.46, C:0.06, G:0.24, T:0.24
Consensus pattern (27 bp):
AATGAATGAATGAATGACCAATGAATG
Found at i:41474246 original size:23 final size:23
Alignment explanation
Indices: 41474196--41474250 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
41474186 TATGTACATG
* *
41474196 CAATGAATGAATGAATGACTAAT
1 CAATGAATGAATGAATGAATAAC
* * *
41474219 GAATGAATGGATGAATGAATGAC
1 CAATGAATGAATGAATGAATAAC
41474242 CAATGAATG
1 CAATGAATG
41474251 TTAGTCATGC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.45, C:0.07, G:0.24, T:0.24
Consensus pattern (23 bp):
CAATGAATGAATGAATGAATAAC
Found at i:41474250 original size:4 final size:4
Alignment explanation
Indices: 41474197--41474240 Score: 63
Period size: 4 Copynumber: 11.2 Consensus size: 4
41474187 ATGTACATGC
* *
41474197 AATG AATG AATG AATG ACT- AATG AATG AATG GATG AATG AATG A
1 AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG A
41474241 CCAATGAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 2 0.06
4 33 0.94
ACGTcount: A:0.48, C:0.02, G:0.25, T:0.25
Consensus pattern (4 bp):
AATG
Found at i:41477236 original size:13 final size:13
Alignment explanation
Indices: 41477218--41477244 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
41477208 TGCATGACTT
41477218 TTCAAAAACAAAA
1 TTCAAAAACAAAA
41477231 TTCAAAAACAAAA
1 TTCAAAAACAAAA
41477244 T
1 T
41477245 ATTATTGTTT
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:0.67, C:0.15, G:0.00, T:0.19
Consensus pattern (13 bp):
TTCAAAAACAAAA
Found at i:41477796 original size:17 final size:17
Alignment explanation
Indices: 41477757--41477788 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
41477747 TAGGCTGTTA
41477757 TATTTTTATATTTTTTT
1 TATTTTTATATTTTTTT
41477774 TATTTTTAT-TTTTTT
1 TATTTTTATATTTTTT
41477789 CTTCTTTTCG
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (17 bp):
TATTTTTATATTTTTTT
Found at i:41478307 original size:303 final size:304
Alignment explanation
Indices: 41477751--41478319 Score: 881
Period size: 303 Copynumber: 1.9 Consensus size: 304
41477741 TGGACCTAGG
* * * **
41477751 CTGTTATATTTTTATATTTTTTTTATTTTTATTTTTTTCTTCTTTTCGCTGTTGGGGCGCGCAAG
1 CTGTTATATTTCTATATTATTTTTATTTTTATTTTTTTCTTCTTTTCACTGTTGGCCCGCGCAAG
* * *
41477816 TTGTGGCCTGTTGCAATACTACTGGGTCGCTAGGACGGGCCTAGCTGTGGCCTGCTTGATGAATC
66 TTGTGGCCTGTTGCAATACTACTGGGCCGCTAGGACGAGCCTAGCTGTGGCCTGCTTGACGAATC
* * * *
41477881 GGATCCGATTCTAGTCAGATTCTGCTGGCCTACTGGGTTGCTGGCATGTTGATGCTGCTGGATGT
131 GGATCCGATTCAAGTCAGAGTCTGCTGGCCTACTAGGTCGCTGGCATGTTGATGCTGCTGGATGT
*
41477946 GGGCCCGCTGTTTTGGGCCGACCTGTTGGTGCTGGCTGGGTTACTGTTCGGGTCAGGTTGGGTCA
196 GGGCCCGCTGTTTTGGGCCGACCTGTTGGTGCTGGCTGGGTTACTATTCGGGTCAGGTTGGGTCA
*
41478011 TTGGTCAGTTGGAGAAAGGTCTGATCCGGGTCGGGTGAACCCGA
261 GTGGTCAGTTGGAGAAAGGTCTGATCCGGGTCGGGTGAACCCGA
*
41478055 CTGTTATATTTCTATATATATTTTTATTTTTATTTTTTTCTTCTTTTCACTGTTGGCCCGCGCAG
1 CTGTTATATTTCTATAT-TATTTTTATTTTTATTTTTTTCTTCTTTTCACTGTTGGCCCGCGCAA
* * *
41478120 GTTGTGGCCTGTTGCAGTACTACTGGGCCGCTAGGACGAG-CTGGCTGTGGCCTGCTTGACGGAT
65 GTTGTGGCCTGTTGCAATACTACTGGGCCGCTAGGACGAGCCTAGCTGTGGCCTGCTTGACGAAT
* * *
41478184 TGGATCCGCTTCAAGTC-GGGTCTGCTGGCCTACTAGGTCGCTGGCATGTTGATGCTGCTGGATG
130 CGGATCCGATTCAAGTCAGAGTCTGCTGGCCTACTAGGTCGCTGGCATGTTGATGCTGCTGGATG
* * * **
41478248 TGGGCCTGCTGTTTTGGGCCGACCTGTTGGTGTTGGCTGGGTTGCTATTCGTTTCAGGTTGGGTC
195 TGGGCCCGCTGTTTTGGGCCGACCTGTTGGTGCTGGCTGGGTTACTATTCGGGTCAGGTTGGGTC
41478313 AGTGGTC
260 AGTGGTC
41478320 GGGTCGATTC
Statistics
Matches: 238, Mismatches: 26, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
303 108 0.45
304 51 0.21
305 79 0.33
ACGTcount: A:0.12, C:0.20, G:0.31, T:0.37
Consensus pattern (304 bp):
CTGTTATATTTCTATATTATTTTTATTTTTATTTTTTTCTTCTTTTCACTGTTGGCCCGCGCAAG
TTGTGGCCTGTTGCAATACTACTGGGCCGCTAGGACGAGCCTAGCTGTGGCCTGCTTGACGAATC
GGATCCGATTCAAGTCAGAGTCTGCTGGCCTACTAGGTCGCTGGCATGTTGATGCTGCTGGATGT
GGGCCCGCTGTTTTGGGCCGACCTGTTGGTGCTGGCTGGGTTACTATTCGGGTCAGGTTGGGTCA
GTGGTCAGTTGGAGAAAGGTCTGATCCGGGTCGGGTGAACCCGA
Found at i:41478564 original size:16 final size:14
Alignment explanation
Indices: 41478533--41478569 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
41478523 CGAAGGTGAG
41478533 TTTTTTTTTAAATT
1 TTTTTTTTTAAATT
*
41478547 TTTTATTTTTGAATT
1 TTTT-TTTTTAAATT
41478562 TTTTTTTT
1 TTTTTTTT
41478570 CTTTTGTTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (14 bp):
TTTTTTTTTAAATT
Found at i:41478947 original size:30 final size:29
Alignment explanation
Indices: 41478877--41478955 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 29
41478867 ACAACTTTTG
*
41478877 GGGTCAAAATGTAATTTTAGGAAAATTTA
1 GGGTCAAAATGTAATTTTAGGAAAATTAA
* *
41478906 GGGTTAAAATGTAATTTTAGGAAAGTTAA
1 GGGTCAAAATGTAATTTTAGGAAAATTAA
*
41478935 GATGTCAAAATGTAAATTTTA
1 G-GGTCAAAATGT-AATTTTA
41478956 AATTTTGTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 27 0.63
30 9 0.21
31 7 0.16
ACGTcount: A:0.42, C:0.03, G:0.20, T:0.35
Consensus pattern (29 bp):
GGGTCAAAATGTAATTTTAGGAAAATTAA
Found at i:41479277 original size:27 final size:27
Alignment explanation
Indices: 41479237--41479288 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
41479227 CTCAACTTTC
* *
41479237 ATTATTTTAGGTAAGTGGGTGAAAGTG
1 ATTATTTTACGTAAGTGGGTAAAAGTG
41479264 ATTATTTTACGTAAGTGGGTAAAAG
1 ATTATTTTACGTAAGTGGGTAAAAG
41479289 GAGGGAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.33, C:0.02, G:0.29, T:0.37
Consensus pattern (27 bp):
ATTATTTTACGTAAGTGGGTAAAAGTG
Found at i:41481930 original size:17 final size:16
Alignment explanation
Indices: 41481895--41481939 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 16
41481885 TAGCATAAAT
* *
41481895 AATAAAATGAAATTAC
1 AATAATATGAAAATAC
41481911 AATAATATGATAAATAC
1 AATAATATGA-AAATAC
*
41481928 AATAATAAGAAA
1 AATAATATGAAA
41481940 TAATAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 11 0.44
17 14 0.56
ACGTcount: A:0.64, C:0.04, G:0.07, T:0.24
Consensus pattern (16 bp):
AATAATATGAAAATAC
Found at i:41484319 original size:50 final size:50
Alignment explanation
Indices: 41484245--41484359 Score: 126
Period size: 50 Copynumber: 2.3 Consensus size: 50
41484235 GCTCCACTGT
* * * * *
41484245 AACTTCGGGGAGATAGGATTTGCTACTGTACTTCCAAT-TCATTCCACTAC
1 AACTTCAGGGATATAAGATATGCTACTGTAATTCCAATCT-ATTCCACTAC
* * *
41484295 AA-TTCTAGGGATATAAGATATGCTATTGTAATTTCAATCTATTCCACTGC
1 AACTTC-AGGGATATAAGATATGCTACTGTAATTCCAATCTATTCCACTAC
41484345 AACTTCAGGGATATA
1 AACTTCAGGGATATA
41484360 GGATTCGAGG
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
49 3 0.06
50 47 0.87
51 4 0.07
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (50 bp):
AACTTCAGGGATATAAGATATGCTACTGTAATTCCAATCTATTCCACTAC
Found at i:41486462 original size:25 final size:25
Alignment explanation
Indices: 41486434--41486489 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
41486424 ATGTAAACGG
* *
41486434 GAAGCTCTTTTGAACCATATAACAA
1 GAAGCTCATGTGAACCATATAACAA
* * *
41486459 GAAGCTCATGTGAGCCATGTAACAG
1 GAAGCTCATGTGAACCATATAACAA
41486484 GAAGCT
1 GAAGCT
41486490 TATGAGAGCC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (25 bp):
GAAGCTCATGTGAACCATATAACAA
Found at i:41486498 original size:25 final size:24
Alignment explanation
Indices: 41486448--41486522 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 24
41486438 CTCTTTTGAA
* *
41486448 CCATATAACAAGAAGCTCATGTGAG
1 CCAT-TAACAGGAAGCTCATGAGAG
*
41486473 CCATGTAACAGGAAGCTTATGAGAG
1 CCAT-TAACAGGAAGCTCATGAGAG
* *
41486498 CCAATTAACGGGAAGCTCGTGAGAG
1 CC-ATTAACAGGAAGCTCATGAGAG
41486523 ACAAATAATG
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
25 40 0.95
26 2 0.05
ACGTcount: A:0.36, C:0.19, G:0.27, T:0.19
Consensus pattern (24 bp):
CCATTAACAGGAAGCTCATGAGAG
Found at i:41486535 original size:25 final size:25
Alignment explanation
Indices: 41486459--41486541 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
41486449 CATATAACAA
* * ** *
41486459 GAAGCTCATGTGAGCCATGTAACAG
1 GAAGCTCATGAGAGACAAATAACGG
* * *
41486484 GAAGCTTATGAGAGCCAATTAACGG
1 GAAGCTCATGAGAGACAAATAACGG
* *
41486509 GAAGCTCGTGAGAGACAAATAATGG
1 GAAGCTCATGAGAGACAAATAACGG
41486534 GAAGCTCA
1 GAAGCTCA
41486542 AAAGAGAGCC
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.36, C:0.17, G:0.29, T:0.18
Consensus pattern (25 bp):
GAAGCTCATGAGAGACAAATAACGG
Found at i:41487952 original size:79 final size:80
Alignment explanation
Indices: 41487866--41488023 Score: 178
Period size: 79 Copynumber: 2.0 Consensus size: 80
41487856 GTATGAGGGT
* * * ** *
41487866 TATATATGAATATACAAGATTCGAATACATATATGTATATACATGTATAAA-TTCTT-GGTTTAA
1 TATATATGAATACACAAGACTCCAATACATATATAAATATACACGTATAAACTT-TTGGGTTTAA
41487929 -TCAAAGGTATGTATAA
65 CT-AAAGGTATGTATAA
* * * * *
41487945 TATATATGTATACATAAGGCTCCAATATATATATAAATATACACGTATAAACTTTTGGGTTTGAC
1 TATATATGAATACACAAGACTCCAATACATATATAAATATACACGTATAAACTTTTGGGTTTAAC
41488010 TAAAGGTATGTATA
66 TAAAGGTATGTATA
41488024 TTGTATTTGT
Statistics
Matches: 65, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
79 43 0.66
80 21 0.32
81 1 0.02
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (80 bp):
TATATATGAATACACAAGACTCCAATACATATATAAATATACACGTATAAACTTTTGGGTTTAAC
TAAAGGTATGTATAA
Found at i:41488703 original size:41 final size:41
Alignment explanation
Indices: 41488658--41488743 Score: 136
Period size: 41 Copynumber: 2.1 Consensus size: 41
41488648 GGCTTAGCAC
** *
41488658 CTAGCAGGCTTATTGCCAGTGAAACAATTCAGACTTTATGT
1 CTAGCAGGCTTAAGGCCAGTGAAACAATTCAGACTATATGT
*
41488699 CTAGCAGGCTTAAGGCCAGTGAAACATTTCAGACTATATGT
1 CTAGCAGGCTTAAGGCCAGTGAAACAATTCAGACTATATGT
41488740 CTAG
1 CTAG
41488744 TATGCTAAGT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (41 bp):
CTAGCAGGCTTAAGGCCAGTGAAACAATTCAGACTATATGT
Found at i:41490794 original size:15 final size:15
Alignment explanation
Indices: 41490755--41490796 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
41490745 ATTTTATTCA
*
41490755 TTTATCATCCTTTGT
1 TTTATCATCTTTTGT
41490770 TTTATCATCTTTTGT
1 TTTATCATCTTTTGT
41490785 TTTATCATCTTT
1 TTTATCATCTTT
41490797 CCAATTTAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.14, C:0.17, G:0.05, T:0.64
Consensus pattern (15 bp):
TTTATCATCTTTTGT
Found at i:41499317 original size:22 final size:24
Alignment explanation
Indices: 41499292--41499346 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 24
41499282 CCCAATTTAA
*
41499292 TTCTAAC-TAAG-CTTACTTATTT
1 TTCTAACTTAAGTCATACTTATTT
41499314 TTCTAACTTAAGTCATACTTA-TT
1 TTCTAACTTAAGTCATACTTATTT
41499337 TTCT-ACTTAA
1 TTCTAACTTAA
41499347 TGTCTTATCA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 13 0.43
23 10 0.33
24 7 0.23
ACGTcount: A:0.29, C:0.18, G:0.04, T:0.49
Consensus pattern (24 bp):
TTCTAACTTAAGTCATACTTATTT
Found at i:41499953 original size:5 final size:5
Alignment explanation
Indices: 41499932--41500004 Score: 71
Period size: 5 Copynumber: 14.4 Consensus size: 5
41499922 TTACTTTATT
41499932 TAATA TATATAA TAATA TAATA TAATA TAATA TAAT- TAATA TATTATA
1 TAATA TA-AT-A TAATA TAATA TAATA TAATA TAATA TAATA TA--ATA
* *
41499980 TTATA TTATA TAATA -AA-A TAATA TA
1 TAATA TAATA TAATA TAATA TAATA TA
41500005 CATAACATAA
Statistics
Matches: 59, Mismatches: 2, Indels: 14
0.79 0.03 0.19
Matches are distributed among these distances:
3 1 0.02
4 8 0.14
5 39 0.66
6 4 0.07
7 7 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
TAATA
Found at i:41499979 original size:24 final size:23
Alignment explanation
Indices: 41499928--41500004 Score: 77
Period size: 24 Copynumber: 3.3 Consensus size: 23
41499918 CTATTTACTT
41499928 TATT-TAATAT-ATATAATAATA
1 TATTATAATATAATATAATAATA
*
41499949 TAATATAATATAATATAATTAATA
1 TATTATAATATAATATAA-TAATA
* *
41499973 TATTATATTATATTATATAATAAAA
1 TATTATA--ATATAATATAATAATA
*
41499998 TAATATA
1 TATTATA
41500005 CATAACATAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
21 3 0.07
22 6 0.13
23 6 0.13
24 11 0.24
25 10 0.22
26 10 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATTATAATATAATATAATAATA
Found at i:41499991 original size:36 final size:36
Alignment explanation
Indices: 41499931--41499999 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
41499921 TTTACTTTAT
*
41499931 TTAATATATATAATAATATAATATAATATAATATAA
1 TTAATATATATAATAATATAATATAATAAAATATAA
* *
41499967 TTAATATAT-TATATTATATTATATAATAAAATA
1 TTAATATATATA-ATAATATAATATAATAAAATA
41500000 ATATACATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 2 0.07
36 27 0.93
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (36 bp):
TTAATATATATAATAATATAATATAATAAAATATAA
Found at i:41500014 original size:14 final size:13
Alignment explanation
Indices: 41499932--41500014 Score: 53
Period size: 14 Copynumber: 6.2 Consensus size: 13
41499922 TTACTTTATT
*
41499932 TAATAT-ATATAA
1 TAATATAATAAAA
41499944 TAATATAATATAATA
1 TAATATAATA-AA-A
*
41499959 TAATATAATTAATA
1 TAATATAA-TAAAA
* * *
41499973 TATTAT-ATTATA
1 TAATATAATAAAA
*
41499985 TTATATAATAAAA
1 TAATATAATAAAA
*
41499998 TAATATACATAACA
1 TAATATA-ATAAAA
41500012 TAA
1 TAA
41500015 AAATCTCATA
Statistics
Matches: 55, Mismatches: 10, Indels: 10
0.73 0.13 0.13
Matches are distributed among these distances:
12 14 0.25
13 14 0.25
14 15 0.27
15 10 0.18
16 2 0.04
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (13 bp):
TAATATAATAAAA
Found at i:41503255 original size:7 final size:7
Alignment explanation
Indices: 41503243--41503276 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
41503233 AACATTTACT
41503243 AATTTTA
1 AATTTTA
41503250 AATTTTA
1 AATTTTA
41503257 AATTTTA
1 AATTTTA
41503264 AATTTTA
1 AATTTTA
41503271 AATTTT
1 AATTTT
41503277 TTTAAAGGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
AATTTTA
Found at i:41505205 original size:14 final size:15
Alignment explanation
Indices: 41505186--41505227 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
41505176 TAGTCGATTG
41505186 GTATTTAGTATATA-
1 GTATTTAGTATATAT
41505200 GTATTTAGTAT-TAT
1 GTATTTAGTATATAT
41505214 GTA-TTATGTATATA
1 GTATTTA-GTATATA
41505228 ACTAATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 5 0.20
14 18 0.72
15 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.52
Consensus pattern (15 bp):
GTATTTAGTATATAT
Found at i:41505877 original size:18 final size:18
Alignment explanation
Indices: 41505836--41505877 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
41505826 GATAGTTGCG
* *
41505836 TATCCTAACCCTTTTATG
1 TATCCTAACCCTTATATA
41505854 TATCCTAACCCTTATATA
1 TATCCTAACCCTTATATA
*
41505872 TTTCCT
1 TATCCT
41505878 TTTTCTAGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.24, C:0.29, G:0.02, T:0.45
Consensus pattern (18 bp):
TATCCTAACCCTTATATA
Found at i:41507009 original size:124 final size:124
Alignment explanation
Indices: 41506804--41507138 Score: 573
Period size: 124 Copynumber: 2.7 Consensus size: 124
41506794 GTTTTGTATC
*
41506804 AAATAGTATAAAATCGCTTCTAGCTGGATGCTATTTGAGAATAATTTGTGAAATCGCGCCCTCGT
1 AAATAGTATAAAATCGCTTCTAGCTGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGT
41506869 GGACGCGCTTTTGCTACAGTAGGTCATGAAAGAAATAAATTTTTT-TGACGTTTCTGAGG
66 GGACGCGCTTTTGCTACAGTAGGTCATGAAAGAAAT-AATTTTTTCTGACGTTTCTGAGG
* *
41506928 AAATAGTATAAAATCGCTTATAGCTGGATGCTATTTGAGAAGAATTTGTGAAATTGCGCCCTCGT
1 AAATAGTATAAAATCGCTTCTAGCTGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGT
* *
41506993 GGACGCGCTTTTGCTACAGTAGGTCATGGAAGAAATAATTTTTTCTGACGTTTCTGAGT
66 GGACGCGCTTTTGCTACAGTAGGTCATGAAAGAAATAATTTTTTCTGACGTTTCTGAGG
* * *
41507052 AAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCACACCCTCGT
1 AAATAGTATAAAATCGCTTCTAGCTGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGT
*
41507117 GGACGCGCTTTTTCTACAGTAG
66 GGACGCGCTTTTGCTACAGTAG
41507139 CATGTTTGGG
Statistics
Matches: 199, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
123 8 0.04
124 191 0.96
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (124 bp):
AAATAGTATAAAATCGCTTCTAGCTGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGT
GGACGCGCTTTTGCTACAGTAGGTCATGAAAGAAATAATTTTTTCTGACGTTTCTGAGG
Found at i:41509571 original size:24 final size:25
Alignment explanation
Indices: 41509523--41509579 Score: 98
Period size: 24 Copynumber: 2.3 Consensus size: 25
41509513 GACATATAAC
*
41509523 TCAAATAAACTTTTATTTTATTACA
1 TCAAATAAACTTCTATTTTATTACA
41509548 TCAAATAAACTTCTA-TTTATTACA
1 TCAAATAAACTTCTATTTTATTACA
41509572 TCAAATAA
1 TCAAATAA
41509580 TATCAAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 17 0.55
25 14 0.45
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (25 bp):
TCAAATAAACTTCTATTTTATTACA
Found at i:41510075 original size:18 final size:18
Alignment explanation
Indices: 41510052--41510091 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
41510042 GACTCGGAAA
*
41510052 AGGATACATATAAGGGTT
1 AGGATACATATAAGGGCT
41510070 AGGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
41510088 AGGA
1 AGGA
41510092 AACACACTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.40, C:0.07, G:0.30, T:0.23
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:41510960 original size:20 final size:20
Alignment explanation
Indices: 41510923--41510960 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41510913 TTTATTTTTA
*
41510923 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
41510943 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
41510961 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:41511748 original size:26 final size:26
Alignment explanation
Indices: 41511687--41511748 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
41511677 CTTTTATAAC
* *
41511687 AAATA-ATAAATTAATAATTATCTAA
1 AAATATATAAATAAAAAATTATCTAA
*
41511712 AAATGTATAAATAAAAAATTAT-TAA
1 AAATATATAAATAAAAAATTATCTAA
*
41511737 ATAATATTTAAA
1 A-AATATATAAA
41511749 AATTATATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
25 8 0.27
26 22 0.73
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (26 bp):
AAATATATAAATAAAAAATTATCTAA
Found at i:41511993 original size:12 final size:11
Alignment explanation
Indices: 41511957--41512011 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
41511947 TTAAATATAG
41511957 ATTTGAGAGAA
1 ATTTGAGAGAA
*
41511968 ATTTTGA-AGGA
1 A-TTTGAGAGAA
41511979 ATTTGAGAGCAA
1 ATTTGAGAG-AA
41511991 A-TTGAGAGGAA
1 ATTTGAGA-GAA
41512002 ATTTGAGAGA
1 ATTTGAGAGA
41512012 GGATTAGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
10 5 0.14
11 18 0.49
12 14 0.38
ACGTcount: A:0.42, C:0.02, G:0.29, T:0.27
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:41512004 original size:23 final size:21
Alignment explanation
Indices: 41511957--41512011 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 21
41511947 TTAAATATAG
41511957 ATTTGAGAGAAATTTTGAAGGA
1 ATTTGAGAGAAA-TTTGAAGGA
41511979 ATTTGAGAGCAAA-TTGAGAGGAA
1 ATTTGAGAG-AAATTTGA-AGG-A
41512002 ATTTGAGAGA
1 ATTTGAGAGA
41512012 GGATTAGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
21 4 0.13
22 13 0.43
23 13 0.43
ACGTcount: A:0.42, C:0.02, G:0.29, T:0.27
Consensus pattern (21 bp):
ATTTGAGAGAAATTTGAAGGA
Found at i:41514388 original size:40 final size:40
Alignment explanation
Indices: 41514333--41514412 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
41514323 AAAACTATCC
41514333 TTGTTGGAAAACTCATTATTAATTTCAAATTCACCCGAAT
1 TTGTTGGAAAACTCATTATTAATTTCAAATTCACCCGAAT
41514373 TTGTTGGAAAACTCATTATTAATTTCAAATTCACCCGAAT
1 TTGTTGGAAAACTCATTATTAATTTCAAATTCACCCGAAT
41514413 CCAGTAGCGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (40 bp):
TTGTTGGAAAACTCATTATTAATTTCAAATTCACCCGAAT
Found at i:41515723 original size:125 final size:126
Alignment explanation
Indices: 41515418--41515834 Score: 622
Period size: 126 Copynumber: 3.3 Consensus size: 126
41515408 TCAGGCCAAA
* * *
41515418 CAGGAGCTACTGTAGCAAAAGCGCGTCCATGTGGGAGCTTCTTTCAGTACTCTTGTTGACAAAGC
1 CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGC
* * * * *
41515483 ATCCTGCTTAAAGCGTTTTCGACACTATTTTCTTAGAAACGTCTATTCGAAATTATTTTTT
66 ATCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTTTACTCGAAATTATTTTTT
* * *
41515544 CAAGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGTTTCTTTCAGTACTTTTGCAGACAAAGC
1 CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGC
* *
41515609 ATCCTGCTTAAAGTGTTTTTGTCACTATTTGCTCAGAAACGTTTACTCGAAATTA-TTTTT
66 ATCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTTTACTCGAAATTATTTTTT
* * *
41515669 CAGGAGCTACTGTAACAAAAGTGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGATAAAGC
1 CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGC
41515734 ATCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTCTT-CTCGAAATTATTTTTT
66 ATCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGT-TTACTCGAAATTATTTTTT
* ** * *
41515795 CAGGAGCTACTGTAGTAAAAGAACGTCCATGTAGGAGCTT
1 CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTT
41515835 TTTAAAATTA
Statistics
Matches: 262, Mismatches: 27, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
125 114 0.44
126 148 0.56
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (126 bp):
CAGGAGCTACTGTAGCAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAAAGC
ATCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACGTTTACTCGAAATTATTTTTT
Done.