Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 104 of 106
Found at i:39900221 original size:26 final size:25
Alignment explanation
Indices: 39900166--39900240 Score: 80
Period size: 25 Copynumber: 3.0 Consensus size: 25
39900156 GATATTTTAA
* * * **
39900166 TTTAAAATAATTAAAATTTATTTAA
1 TTTAAAATAATAAAAAATAATTTGG
39900191 TTTAAAATAA-AAATATAATAATTTGG
1 TTTAAAATAATAAA-A-AATAATTTGG
39900217 TTTAAAATAATAAAAAATAATTTG
1 TTTAAAATAATAAAAAATAATTTG
39900241 TAAATATTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
24 2 0.05
25 20 0.48
26 17 0.40
27 3 0.07
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (25 bp):
TTTAAAATAATAAAAAATAATTTGG
Found at i:39903651 original size:12 final size:12
Alignment explanation
Indices: 39903630--39903664 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
39903620 CCATTATTGG
39903630 CCGACGCCGACA
1 CCGACGCCGACA
*
39903642 CCGACACCGACA
1 CCGACGCCGACA
39903654 CCGACGCCGAC
1 CCGACGCCGAC
39903665 GCGGCCTCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.26, C:0.51, G:0.23, T:0.00
Consensus pattern (12 bp):
CCGACGCCGACA
Found at i:39903657 original size:18 final size:18
Alignment explanation
Indices: 39903630--39903664 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39903620 CCATTATTGG
*
39903630 CCGACGCCGACACCGACA
1 CCGACACCGACACCGACA
*
39903648 CCGACACCGACGCCGAC
1 CCGACACCGACACCGAC
39903665 GCGGCCTCAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.51, G:0.23, T:0.00
Consensus pattern (18 bp):
CCGACACCGACACCGACA
Found at i:39914070 original size:14 final size:14
Alignment explanation
Indices: 39914039--39914089 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
39914029 AATGATAATG
*
39914039 ATATTTTTTAT-AT
1 ATATTTTTTATGAA
39914052 A-ATTTTTTATGAA
1 ATATTTTTTATGAA
39914065 ATATTTTGTTA-GAA
1 ATATTTT-TTATGAA
39914079 ATATTTTTTAT
1 ATATTTTTTAT
39914090 ATTAAAAACG
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
12 9 0.27
13 6 0.18
14 15 0.45
15 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (14 bp):
ATATTTTTTATGAA
Found at i:39931409 original size:47 final size:47
Alignment explanation
Indices: 39931351--39931449 Score: 182
Period size: 47 Copynumber: 2.1 Consensus size: 47
39931341 GAAATGAATC
*
39931351 CAAA-TAAATGACTTGGCATTATTATTTTTGAAACTTGAAATTACTT
1 CAAACTAAATGACTTGGCATTATTATTCTTGAAACTTGAAATTACTT
39931397 CAAACTAAATGACTTGGCATTATTATTCTTGAAACTTGAAATTACTT
1 CAAACTAAATGACTTGGCATTATTATTCTTGAAACTTGAAATTACTT
39931444 CAAACT
1 CAAACT
39931450 GTTAGCCATT
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
46 4 0.08
47 47 0.92
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.38
Consensus pattern (47 bp):
CAAACTAAATGACTTGGCATTATTATTCTTGAAACTTGAAATTACTT
Found at i:39937214 original size:24 final size:26
Alignment explanation
Indices: 39937174--39937231 Score: 68
Period size: 24 Copynumber: 2.3 Consensus size: 26
39937164 ATTTGAATGC
39937174 AAAT-TAAGTATGAACTAATAACAA-
1 AAATATAAGTATGAACTAATAACAAT
* *
39937198 AAATATAAGTAT-TACTAATGACAAT
1 AAATATAAGTATGAACTAATAACAAT
39937223 AAATTATAA
1 AAA-TATAA
39937232 TTACAAGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 14 0.48
25 10 0.34
26 5 0.17
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (26 bp):
AAATATAAGTATGAACTAATAACAAT
Found at i:39937428 original size:2 final size:2
Alignment explanation
Indices: 39937421--39937456 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
39937411 CTAATAAATA
39937421 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39937457 TATCTGATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39938673 original size:24 final size:24
Alignment explanation
Indices: 39938626--39938674 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
39938616 AAAAAACTAG
39938626 ACCAAACATGCACTTAAAAGAATT
1 ACCAAACATGCACTTAAAAGAATT
*
39938650 ACCAAACATGCACTTAGAAGAATT
1 ACCAAACATGCACTTAAAAGAATT
39938674 A
1 A
39938675 TATAATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.49, C:0.20, G:0.10, T:0.20
Consensus pattern (24 bp):
ACCAAACATGCACTTAAAAGAATT
Found at i:39944853 original size:54 final size:54
Alignment explanation
Indices: 39944771--39944880 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
39944761 AGATGAATAG
39944771 GACCTTCAATTTCAACTAAGTACTACATGTAAAGGGCTATAGGCCTATAGCAGA
1 GACCTTCAATTTCAACTAAGTACTACATGTAAAGGGCTATAGGCCTATAGCAGA
39944825 GACCTTCAATTTCAACTAAGTACTACATGTAAAGGGCTATAGGCCTATAGCAGA
1 GACCTTCAATTTCAACTAAGTACTACATGTAAAGGGCTATAGGCCTATAGCAGA
39944879 GA
1 GA
39944881 AATAAATTTG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.25
Consensus pattern (54 bp):
GACCTTCAATTTCAACTAAGTACTACATGTAAAGGGCTATAGGCCTATAGCAGA
Found at i:39968813 original size:2 final size:2
Alignment explanation
Indices: 39968754--39968798 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
39968744 AAAATATTAT
39968754 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39968796 TA T
1 TA T
39968799 CAAGCTATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:39971872 original size:39 final size:39
Alignment explanation
Indices: 39971818--39971894 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
39971808 GCTTATATTC
*
39971818 GATTTTAGATATTAAAATCAAAGAAATCCATATAGAAAT
1 GATTTCAGATATTAAAATCAAAGAAATCCATATAGAAAT
*
39971857 GATTTCAGATATTAAAATCAAATAAATCCATATAGAAA
1 GATTTCAGATATTAAAATCAAAGAAATCCATATAGAAA
39971895 CGGAACCGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.30
Consensus pattern (39 bp):
GATTTCAGATATTAAAATCAAAGAAATCCATATAGAAAT
Found at i:39972286 original size:52 final size:52
Alignment explanation
Indices: 39972195--39972321 Score: 141
Period size: 52 Copynumber: 2.4 Consensus size: 52
39972185 ACATAGATGT
* *
39972195 AGAAGAGAAAGAGATCGTGATTTACGTTGGAGAATGGTAATTTG-T-AGAAGAAGAG
1 AGAAGAGAAGGAGATC--GA-TTACGTTGGAGAAGGGTAATTTGCTGAG-AGAAG-G
* * *
39972250 AGAAGAGAGGGAGATCGATTACGTTTGAGAAGGGTAATTTGCTGAGAGATGG
1 AGAAGAGAAGGAGATCGATTACGTTGGAGAAGGGTAATTTGCTGAGAGAAGG
*
39972302 AGAGGAGAAGGAGATCGATT
1 AGAAGAGAAGGAGATCGATT
39972322 GAGAAAAAAG
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
52 40 0.63
53 7 0.11
54 2 0.03
55 14 0.22
ACGTcount: A:0.37, C:0.05, G:0.36, T:0.22
Consensus pattern (52 bp):
AGAAGAGAAGGAGATCGATTACGTTGGAGAAGGGTAATTTGCTGAGAGAAGG
Found at i:39976203 original size:14 final size:14
Alignment explanation
Indices: 39976184--39976213 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
39976174 TCTGATGCAA
39976184 CCACCGCCATCCTT
1 CCACCGCCATCCTT
39976198 CCACCGCCATCCTT
1 CCACCGCCATCCTT
39976212 CC
1 CC
39976214 TTTTATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.60, G:0.07, T:0.20
Consensus pattern (14 bp):
CCACCGCCATCCTT
Found at i:39982986 original size:2 final size:2
Alignment explanation
Indices: 39982979--39983005 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
39982969 CACCCAACAC
39982979 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
39983006 TCAGTCATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:39987627 original size:25 final size:22
Alignment explanation
Indices: 39987579--39987627 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
39987569 ACATAAAACT
* *
39987579 AACAACACCAAATTAAAATTAA
1 AACAACACCAAAATAAAATAAA
39987601 AACAACACCTAAAATAGAACATAAA
1 AACAACACC-AAAATA-AA-ATAAA
39987626 AA
1 AA
39987628 GGTCATCAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 9 0.41
23 5 0.23
24 2 0.09
25 6 0.27
ACGTcount: A:0.65, C:0.18, G:0.02, T:0.14
Consensus pattern (22 bp):
AACAACACCAAAATAAAATAAA
Found at i:39988015 original size:2 final size:2
Alignment explanation
Indices: 39988002--39988035 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
39987992 AAGTAACATG
*
39988002 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39988036 CAATTTATCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:39996360 original size:23 final size:23
Alignment explanation
Indices: 39996334--39996379 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
39996324 ATACAATAAC
* *
39996334 CTTATCCTAATATAATTGGGAAT
1 CTTATCCTAATAAAATTAGGAAT
39996357 CTTATCCTAATAAAATTAGGAAT
1 CTTATCCTAATAAAATTAGGAAT
39996380 TGTTATTCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (23 bp):
CTTATCCTAATAAAATTAGGAAT
Found at i:39999864 original size:23 final size:23
Alignment explanation
Indices: 39999838--39999883 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
39999828 ATACAATAAC
* *
39999838 CTTATCCTAATATAATTGGGAAT
1 CTTATCCTAATAAAATTAGGAAT
39999861 CTTATCCTAATAAAATTAGGAAT
1 CTTATCCTAATAAAATTAGGAAT
39999884 TGTTATTCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (23 bp):
CTTATCCTAATAAAATTAGGAAT
Found at i:40000726 original size:18 final size:18
Alignment explanation
Indices: 40000703--40000742 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
40000693 ACACGTTTAC
40000703 TTAATCGTGTTATCATGT
1 TTAATCGTGTTATCATGT
*
40000721 TTAATCGTGTTATCTTGT
1 TTAATCGTGTTATCATGT
40000739 TTAA
1 TTAA
40000743 ACATATATAC
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:0.23, C:0.10, G:0.15, T:0.53
Consensus pattern (18 bp):
TTAATCGTGTTATCATGT
Found at i:40000937 original size:16 final size:16
Alignment explanation
Indices: 40000918--40000949 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40000908 TTATTTGATG
*
40000918 TTATTATTATTATTTT
1 TTATTATAATTATTTT
40000934 TTATTATAATTATTTT
1 TTATTATAATTATTTT
40000950 CATAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTATTATAATTATTTT
Found at i:40001026 original size:9 final size:9
Alignment explanation
Indices: 40001009--40001038 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
40000999 ATATTTTTAT
40001009 TTAATCGTG
1 TTAATCGTG
*
40001018 TTAAACGTG
1 TTAATCGTG
40001027 TTAATCGTG
1 TTAATCGTG
40001036 TTA
1 TTA
40001039 TTAATCGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.43
Consensus pattern (9 bp):
TTAATCGTG
Found at i:40001116 original size:39 final size:41
Alignment explanation
Indices: 40001039--40001120 Score: 105
Period size: 39 Copynumber: 2.0 Consensus size: 41
40001029 AATCGTGTTA
*
40001039 TTAATCGTGTCATGTCGTATATTAACACGTTTAATAAACGTG
1 TTAATCGTGTCATGTCG-ATATTAACACGTGTAATAAACGTG
* * *
40001081 TTAATCGTGTCGTGTC-ATGTT-ACACGTGTATTAAACGTG
1 TTAATCGTGTCATGTCGATATTAACACGTGTAATAAACGTG
40001120 T
1 T
40001121 ACGTGTATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
39 17 0.47
40 4 0.11
42 15 0.42
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.39
Consensus pattern (41 bp):
TTAATCGTGTCATGTCGATATTAACACGTGTAATAAACGTG
Found at i:40001399 original size:29 final size:27
Alignment explanation
Indices: 40001331--40001387 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
40001321 CAAGTAACAC
*
40001331 CCAAGACTATCACGAGTGAGAATATAT
1 CCAAGACTATCAAGAGTGAGAATATAT
40001358 CCAAGACTATCAAGAGTGAGAATATAT
1 CCAAGACTATCAAGAGTGAGAATATAT
40001385 CCA
1 CCA
40001388 CGATTTTATC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (27 bp):
CCAAGACTATCAAGAGTGAGAATATAT
Found at i:40004332 original size:16 final size:16
Alignment explanation
Indices: 40004311--40004342 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40004301 TCGGATTGAT
*
40004311 TTTCGAGTTTGAATCA
1 TTTCGAGTTTAAATCA
40004327 TTTCGAGTTTAAATCA
1 TTTCGAGTTTAAATCA
40004343 ATTCAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (16 bp):
TTTCGAGTTTAAATCA
Found at i:40005788 original size:3 final size:3
Alignment explanation
Indices: 40005780--40005819 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
40005770 ATAAAAAATA
*
40005780 AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
40005820 CAGACAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:40021630 original size:6 final size:6
Alignment explanation
Indices: 40021619--40021644 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
40021609 ATCCGGAATC
40021619 GGGTTT GGGTTT GGGTTT GGGTTT GG
1 GGGTTT GGGTTT GGGTTT GGGTTT GG
40021645 ATTCCGGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.54, T:0.46
Consensus pattern (6 bp):
GGGTTT
Found at i:40021724 original size:18 final size:18
Alignment explanation
Indices: 40021701--40021738 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
40021691 TTGGGCAGCT
40021701 CTCGCAGACTAACCAGTA
1 CTCGCAGACTAACCAGTA
40021719 CTCGCAGACTAACCAGTA
1 CTCGCAGACTAACCAGTA
40021737 CT
1 CT
40021739 AATGAAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (18 bp):
CTCGCAGACTAACCAGTA
Found at i:40027359 original size:7 final size:7
Alignment explanation
Indices: 40027347--40027374 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
40027337 TATGCATGTA
40027347 TATGGAC
1 TATGGAC
40027354 TATGGAC
1 TATGGAC
40027361 TATGGAC
1 TATGGAC
40027368 TATGGAC
1 TATGGAC
40027375 ATGTCCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (7 bp):
TATGGAC
Found at i:40040163 original size:38 final size:38
Alignment explanation
Indices: 40040113--40040195 Score: 148
Period size: 38 Copynumber: 2.2 Consensus size: 38
40040103 ATCAAATCCA
*
40040113 AAATTCAATCAACAAATGTAAATAATATTGTTCATTACC
1 AAATT-AATCAACAAATGTAAATAATATTGTCCATTACC
40040152 AAATTAATCAACAAATGTAAATAATATTGTCCATTACC
1 AAATTAATCAACAAATGTAAATAATATTGTCCATTACC
40040190 AAATTA
1 AAATTA
40040196 CAATTAACAC
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
38 38 0.88
39 5 0.12
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.33
Consensus pattern (38 bp):
AAATTAATCAACAAATGTAAATAATATTGTCCATTACC
Found at i:40046368 original size:17 final size:17
Alignment explanation
Indices: 40046346--40046380 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
40046336 GGTTCAAGAT
40046346 ATTGAAGATTAAGATGA
1 ATTGAAGATTAAGATGA
* *
40046363 ATTGAAGGTTAAGTTGA
1 ATTGAAGATTAAGATGA
40046380 A
1 A
40046381 ACTCTGTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.26, T:0.31
Consensus pattern (17 bp):
ATTGAAGATTAAGATGA
Found at i:40049990 original size:35 final size:35
Alignment explanation
Indices: 40049952--40050123 Score: 211
Period size: 35 Copynumber: 4.9 Consensus size: 35
40049942 GTGTGGATAG
* * *
40049952 TGATATTGATGTGTGCAAGTAGGGAGTGCAGACGG
1 TGATATTGATGTGTGCGAGTAGGGAGTGCACACGA
* * *
40049987 TGATGTTGATTTGTGCGAGTAGGGAGTGCACAAGA
1 TGATATTGATGTGTGCGAGTAGGGAGTGCACACGA
* * * *
40050022 T-ATTGTTGATGTTTGCAAGTAAGGAGTGCACACGA
1 TGA-TATTGATGTGTGCGAGTAGGGAGTGCACACGA
* *
40050057 TGATATTGAAGTGTGCGAGTAGGGAGTGTACACGA
1 TGATATTGATGTGTGCGAGTAGGGAGTGCACACGA
*
40050092 TGATATTGAAGTGTGCGAGTAGGGAGTGCACA
1 TGATATTGATGTGTGCGAGTAGGGAGTGCACA
40050124 TTGGCTGAGT
Statistics
Matches: 117, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
34 1 0.01
35 115 0.98
36 1 0.01
ACGTcount: A:0.27, C:0.09, G:0.36, T:0.27
Consensus pattern (35 bp):
TGATATTGATGTGTGCGAGTAGGGAGTGCACACGA
Found at i:40077371 original size:21 final size:22
Alignment explanation
Indices: 40077342--40077384 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
40077332 ATAATATTTG
40077342 AAAATA-TTTATAAATTATTTAT
1 AAAATATTTTA-AAATTATTTAT
*
40077364 AAAA-ATTTTAAAATTTTTTAT
1 AAAATATTTTAAAATTATTTAT
40077385 TATATTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AAAATATTTTAAAATTATTTAT
Found at i:40077612 original size:17 final size:17
Alignment explanation
Indices: 40077592--40077633 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
40077582 ATGTTGTATT
40077592 ATATATAA-TAATAAATA
1 ATATATAATTAAT-AATA
*
40077609 ATATTTAATTAATAATA
1 ATATATAATTAATAATA
*
40077626 ATTTATAA
1 ATATATAA
40077634 ATTATTAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATATAATTAATAATA
Found at i:40092183 original size:2 final size:2
Alignment explanation
Indices: 40092176--40092203 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
40092166 TTGTTACGGT
40092176 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
40092204 TTTTGAAGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:40098060 original size:168 final size:169
Alignment explanation
Indices: 40097793--40098105 Score: 472
Period size: 168 Copynumber: 1.9 Consensus size: 169
40097783 CTAGCTGCTA
* *
40097793 GACAAAGCTAGCTGTGTTTGCTCTTTCAGATTGCAATCTTTGCTCACACCACCAAAGGATGCAAA
1 GACAAAGCTAGCTGTGCTTGCTCTTTCAAATTGCAATCTTTGCT-ACACCACCAAAGGATGCAAA
* * *
40097858 TACCATTCACAATTGAAGTGATGGAAGAAAACCCATAATGCCAATCCATGCAAAGAT-TCACAGT
65 TACCATTCACAATTGAAGTGAAGGAAGAAAACCCAAAATGCCAATCCATGCAAAGCTCT-ACAGT
*
40097922 TGTTCCAAGAACTGATATTCCTGAAATTCCTAGCTCCTAGAC
129 TATT-CAAGAACTGATATTCCTGAAATTCCTAGCTCCTAGAC
* * *
40097964 GACAAAGCTTGGCTGTGCTTGCTCTTTCAAATTGCAGTCTTTGCT-CACCACCATA-GATGC-AA
1 GACAAAGC-TAGCTGTGCTTGCTCTTTCAAATTGCAATCTTTGCTACACCACCAAAGGATGCAAA
*
40098026 TACCATTCACAATTGAAGTGAAGGAGGAAAACCCAAAATGCCAATCCATGCAAAGCTCTACAGTT
65 TACCATTCACAATTGAAGTGAAGGAAGAAAACCCAAAATGCCAATCCATGCAAAGCTCTACAGTT
40098091 ATTCAAGAACTGATA
130 ATTCAAGAACTGATA
40098106 CTATCCATAA
Statistics
Matches: 130, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
167 12 0.09
168 63 0.48
169 6 0.05
170 9 0.07
171 8 0.06
172 32 0.25
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.26
Consensus pattern (169 bp):
GACAAAGCTAGCTGTGCTTGCTCTTTCAAATTGCAATCTTTGCTACACCACCAAAGGATGCAAAT
ACCATTCACAATTGAAGTGAAGGAAGAAAACCCAAAATGCCAATCCATGCAAAGCTCTACAGTTA
TTCAAGAACTGATATTCCTGAAATTCCTAGCTCCTAGAC
Found at i:40104250 original size:7 final size:6
Alignment explanation
Indices: 40104233--40104267 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
40104223 GTGTACTGGG
40104233 GAAAAA GAAAAA GCAAAAA GAAAAA -AAAAA GAAAA
1 GAAAAA GAAAAA G-AAAAA GAAAAA GAAAAA GAAAA
40104268 GTCATAATCC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 5 0.19
6 16 0.59
7 6 0.22
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:40106326 original size:2 final size:2
Alignment explanation
Indices: 40106319--40106348 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
40106309 AAGGGCACAA
40106319 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
40106349 GTTGAAAGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:40106877 original size:18 final size:18
Alignment explanation
Indices: 40106854--40106888 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40106844 TTCATTTTTA
* *
40106854 TTTTTATTTTTTAAATTT
1 TTTTTACTTTTGAAATTT
40106872 TTTTTACTTTTGAAATT
1 TTTTTACTTTTGAAATT
40106889 AAAAACATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.71
Consensus pattern (18 bp):
TTTTTACTTTTGAAATTT
Found at i:40110854 original size:67 final size:68
Alignment explanation
Indices: 40110745--40110878 Score: 236
Period size: 67 Copynumber: 2.0 Consensus size: 68
40110735 TCGAGGGCTT
*
40110745 TAGCATGCTGGAAATAAGAGAATGCTGCTAAGAGGATACTTGGACTT-CAGGGATTATGAGAACC
1 TAGCATGCTGGAAATAAGAGAATGCTGCTAAGAGGATACTTGGACTTGCA-GGATTACGAGAACC
40110809 AATA
65 AATA
40110813 TAGCATGCTGGAAATAAGA-AATGCTGCTAAGAGGATACTTGGACTTGCAGGATTACGAGAACCA
1 TAGCATGCTGGAAATAAGAGAATGCTGCTAAGAGGATACTTGGACTTGCAGGATTACGAGAACCA
40110877 AT
66 AT
40110879 GTAGTTAAAA
Statistics
Matches: 64, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
67 43 0.67
68 21 0.33
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (68 bp):
TAGCATGCTGGAAATAAGAGAATGCTGCTAAGAGGATACTTGGACTTGCAGGATTACGAGAACCA
ATA
Found at i:40111533 original size:50 final size:49
Alignment explanation
Indices: 40111472--40111612 Score: 196
Period size: 48 Copynumber: 2.9 Consensus size: 49
40111462 TCTTTTTTTA
*
40111472 GCTTTTCATCCATCTTTACTTTCTTTCCTCCCTTCTCTCATCTAAGTAAT
1 GCTTTTCATCCATCTTTA-TTTCTGTCCTCCCTTCTCTCATCTAAGTAAT
* * *
40111522 GCTTTTTATCCATCTTTATTTTCTGTCCT--CTCCTCTCATCTTAGTAAT
1 GCTTTTCATCCATCTTTA-TTTCTGTCCTCCCTTCTCTCATCTAAGTAAT
*
40111570 GCTTTTCATCCATCTTTATCTTCTGTACTCCCTTCTCTCATCT
1 GCTTTTCATCCATCTTTAT-TTCTGTCCTCCCTTCTCTCATCT
40111613 CCATCCCCTC
Statistics
Matches: 80, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
47 1 0.01
48 42 0.52
50 37 0.46
ACGTcount: A:0.14, C:0.31, G:0.05, T:0.50
Consensus pattern (49 bp):
GCTTTTCATCCATCTTTATTTCTGTCCTCCCTTCTCTCATCTAAGTAAT
Found at i:40111661 original size:18 final size:18
Alignment explanation
Indices: 40111617--40111663 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
40111607 TCATCTCCAT
40111617 CCCCTCCCCCCACAACAC
1 CCCCTCCCCCCACAACAC
* **
40111635 CACAC-CCCCCCACGCCAC
1 C-CCCTCCCCCCACAACAC
40111653 CCCCTCCCCCC
1 CCCCTCCCCCC
40111664 CCAAAAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
17 2 0.09
18 19 0.83
19 2 0.09
ACGTcount: A:0.17, C:0.77, G:0.02, T:0.04
Consensus pattern (18 bp):
CCCCTCCCCCCACAACAC
Found at i:40118601 original size:2 final size:2
Alignment explanation
Indices: 40118588--40118628 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
40118578 AAGGTAAACT
* *
40118588 TA TA TG TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40118629 GTGGAGGGTC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:40122617 original size:6 final size:6
Alignment explanation
Indices: 40122599--40122630 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
40122589 AGCAGAGCAG
40122599 CAGCCA GCAGCCA CAGCCA CAGCCA CAGCCA C
1 CAGCCA -CAGCCA CAGCCA CAGCCA CAGCCA C
40122631 TATGAGATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.31, C:0.50, G:0.19, T:0.00
Consensus pattern (6 bp):
CAGCCA
Found at i:40126689 original size:2 final size:2
Alignment explanation
Indices: 40126682--40126722 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
40126672 CTAATTGATC
40126682 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40126723 GTGTATTCCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:40134469 original size:20 final size:21
Alignment explanation
Indices: 40134431--40134471 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
40134421 TTTGACATAA
*
40134431 TATTTAAAAAAATTATTAAAT
1 TATTTAAAAAAAATATTAAAT
40134452 TATTTAAAAAAAAT-TTAAAT
1 TATTTAAAAAAAATATTAAAT
40134472 AAGTTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TATTTAAAAAAAATATTAAAT
Found at i:40142927 original size:13 final size:13
Alignment explanation
Indices: 40142909--40142939 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
40142899 GGAGAAATTT
40142909 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
*
40142922 AAAAAAAGAAAAG
1 AAAAAAAAAAAAG
40142935 AAAAA
1 AAAAA
40142940 GTTAGTATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:40157270 original size:20 final size:20
Alignment explanation
Indices: 40157222--40157272 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
40157212 TTCTAGACAG
**
40157222 ATCCAAACGCATTGCACTAA
1 ATCCAAACTTATTGCACTAA
40157242 ATCCAAACTTATTGCACTAA
1 ATCCAAACTTATTGCACTAA
40157262 ATCCAAACTTA
1 ATCCAAACTTA
40157273 AAACAATCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.41, C:0.27, G:0.06, T:0.25
Consensus pattern (20 bp):
ATCCAAACTTATTGCACTAA
Found at i:40158109 original size:18 final size:18
Alignment explanation
Indices: 40158082--40158121 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
40158072 AATTACTTTT
**
40158082 AAAA-TAAAATTAGGAAA
1 AAAAGTAAAATTAAAAAA
40158099 AAAAGTAAAATTAAAAAA
1 AAAAGTAAAATTAAAAAA
40158117 AAAAG
1 AAAAG
40158122 AAAGTAGAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.75, C:0.00, G:0.10, T:0.15
Consensus pattern (18 bp):
AAAAGTAAAATTAAAAAA
Found at i:40166725 original size:32 final size:32
Alignment explanation
Indices: 40166684--40166749 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
40166674 TAAAACGTTT
40166684 ATTCTGTGATTGATGAGTTGTATATGCATTAA
1 ATTCTGTGATTGATGAGTTGTATATGCATTAA
40166716 ATTCTGTGATTGATGAGTTGTATATGCATTAA
1 ATTCTGTGATTGATGAGTTGTATATGCATTAA
40166748 AT
1 AT
40166750 GTTCTCTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.29, C:0.06, G:0.21, T:0.44
Consensus pattern (32 bp):
ATTCTGTGATTGATGAGTTGTATATGCATTAA
Found at i:40167536 original size:11 final size:10
Alignment explanation
Indices: 40167516--40167611 Score: 53
Period size: 9 Copynumber: 9.8 Consensus size: 10
40167506 AGGAGGAAAG
40167516 GAAAAAAGAA
1 GAAAAAAGAA
40167526 GAAACAAAGAA
1 GAAA-AAAGAA
*
40167537 -AGAAAAG-A
1 GAAAAAAGAA
*
40167545 -AAAAGAGAA
1 GAAAAAAGAA
40167554 GAAACAAAGAA
1 GAAA-AAAGAA
*
40167565 -AGAAAAGAA
1 GAAAAAAGAA
*
40167574 -AAAGAGGAAGAG
1 GAAA-A--AAGAA
40167586 GAAAAAAGAA
1 GAAAAAAGAA
*
40167596 -AAGAAA-AA
1 GAAAAAAGAA
40167604 GAAAAAAG
1 GAAAAAAG
40167612 GTAAAAAATT
Statistics
Matches: 66, Mismatches: 10, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
8 8 0.12
9 23 0.35
10 16 0.24
11 11 0.17
12 5 0.08
13 3 0.05
ACGTcount: A:0.75, C:0.02, G:0.23, T:0.00
Consensus pattern (10 bp):
GAAAAAAGAA
Found at i:40167593 original size:27 final size:28
Alignment explanation
Indices: 40167511--40167605 Score: 133
Period size: 28 Copynumber: 3.5 Consensus size: 28
40167501 TAAAAAGGAG
*
40167511 GAAAGGAAAAA-AGAAGAAACAAAGAAA
1 GAAAAGAAAAAGAGAAGAAACAAAGAAA
40167538 GAAAAGAAAAAGAGAAGAAACAAAGAAA
1 GAAAAGAAAAAGAGAAGAAACAAAGAAA
**
40167566 GAAAAGAAAAAGAGGAAG-AGGAAA-AAA
1 GAAAAGAAAAAGA-GAAGAAACAAAGAAA
40167593 GAAAAGAAAAAGA
1 GAAAAGAAAAAGA
40167606 AAAAAGGTAA
Statistics
Matches: 63, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
27 26 0.41
28 33 0.52
29 4 0.06
ACGTcount: A:0.74, C:0.02, G:0.24, T:0.00
Consensus pattern (28 bp):
GAAAAGAAAAAGAGAAGAAACAAAGAAA
Found at i:40167599 original size:32 final size:29
Alignment explanation
Indices: 40167502--40167609 Score: 114
Period size: 28 Copynumber: 3.7 Consensus size: 29
40167492 ATTAAAAGGT
* * *
40167502 AAAAAGGAGGAAAGGAAAAA-AGAAGA-A
1 AAAAAGAAAGAAAAGAAAAAGAGAAGAGA
*
40167529 ACAAAGAAAGAAAAGAAAAAGAGAAGA-A
1 AAAAAGAAAGAAAAGAAAAAGAGAAGAGA
*
40167557 ACAAAGAAAGAAAAGAAAAAGAGGAAGAGGA
1 AAAAAGAAAGAAAAGAAAAAGA-GAAGA-GA
40167588 AAAAAGAAAAGAAAAAGAAAAA
1 AAAAAG-AAAG-AAAAGAAAAA
40167610 AGGTAAAAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 6
0.86 0.06 0.07
Matches are distributed among these distances:
27 16 0.23
28 29 0.41
29 5 0.07
31 6 0.09
32 4 0.06
33 10 0.14
ACGTcount: A:0.74, C:0.02, G:0.24, T:0.00
Consensus pattern (29 bp):
AAAAAGAAAGAAAAGAAAAAGAGAAGAGA
Found at i:40167617 original size:27 final size:27
Alignment explanation
Indices: 40167535--40167619 Score: 102
Period size: 27 Copynumber: 3.1 Consensus size: 27
40167525 AGAAACAAAG
*
40167535 AAAGAAAAGAAAAAGAGAAGAAA-CAAA
1 AAAGAAAAGAAAAAGAGAA-AAAGGAAA
* *
40167562 GAAAGAAAAGAAAAAGAGGAAGAGGAAA
1 -AAAGAAAAGAAAAAGAGAAAAAGGAAA
40167590 AAAGAAAAGAAAAAGA-AAAAAGGTAAA
1 AAAGAAAAGAAAAAGAGAAAAAGG-AAA
40167617 AAA
1 AAA
40167620 TTGTCCATTG
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
26 5 0.10
27 24 0.48
28 21 0.42
ACGTcount: A:0.75, C:0.01, G:0.22, T:0.01
Consensus pattern (27 bp):
AAAGAAAAGAAAAAGAGAAAAAGGAAA
Found at i:40168179 original size:2 final size:2
Alignment explanation
Indices: 40168174--40168206 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
40168164 TCTCATTATT
40168174 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40168207 TTTTAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40168338 original size:2 final size:2
Alignment explanation
Indices: 40168333--40168365 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
40168323 TCTCATTATT
40168333 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40168366 TTAAAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40168362 original size:159 final size:157
Alignment explanation
Indices: 40168073--40168383 Score: 595
Period size: 159 Copynumber: 2.0 Consensus size: 157
40168063 TTTTATGTTC
40168073 TTGTTGCTCATTTCCTTGTAAGACTTGTTTTTGTTTAGAGGTCATCTTTGAGTTTATGCTCGACA
1 TTGTTGCTCATTTCCTTGTAAGACTTGTTTTTGTTTAGAGGTCATCTTTGAGTTTATGCTCGACA
40168138 TGCTTTTTGGCTCAAGTTAGGGTCTCTCTCATTATTTATATATATATATATATATATATATATAT
66 TGCTTTTTGGCTCAAGTTAGGGTCTCTCTCATTATTTATATATATATATATATATATATATATAT
40168203 ATATTTTTAAAAAAAAAGGAAAAAGTAAA
131 ATA--TTTAAAAAAAAAGGAAAAAGTAAA
*
40168232 TTGTTNCTCATTTCCTTGTAAGACTTGTTTTTGTTTAGAGGTCATCTTTGAGTTTATGCTCGACA
1 TTGTTGCTCATTTCCTTGTAAGACTTGTTTTTGTTTAGAGGTCATCTTTGAGTTTATGCTCGACA
40168297 TGCTTTTTGGCTCAAGTTAGGGTCTCTCTCATTATTTATATATATATATATATATATATATATAT
66 TGCTTTTTGGCTCAAGTTAGGGTCTCTCTCATTATTTATATATATATATATATATATATATATAT
40168362 ATATTTAAAAAAAAAGGAAAAA
131 ATATTTAAAAAAAAAGGAAAAA
40168384 AGAGTGGAAA
Statistics
Matches: 151, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
157 19 0.13
159 132 0.87
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44
Consensus pattern (157 bp):
TTGTTGCTCATTTCCTTGTAAGACTTGTTTTTGTTTAGAGGTCATCTTTGAGTTTATGCTCGACA
TGCTTTTTGGCTCAAGTTAGGGTCTCTCTCATTATTTATATATATATATATATATATATATATAT
ATATTTAAAAAAAAAGGAAAAAGTAAA
Found at i:40170772 original size:19 final size:20
Alignment explanation
Indices: 40170750--40170792 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
40170740 ATATTAACAT
40170750 TTATAAATTTTATTC-ATAA
1 TTATAAATTTTATTCTATAA
* *
40170769 TTAT-ATTTTTATTCTTTAA
1 TTATAAATTTTATTCTATAA
40170788 TTATA
1 TTATA
40170793 TTTCATCCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (20 bp):
TTATAAATTTTATTCTATAA
Found at i:40170780 original size:18 final size:19
Alignment explanation
Indices: 40170757--40170795 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
40170747 CATTTATAAA
40170757 TTTTATTC-ATAATTATAT
1 TTTTATTCTATAATTATAT
*
40170775 TTTTATTCTTTAATTATAT
1 TTTTATTCTATAATTATAT
40170794 TT
1 TT
40170796 CATCCATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTATTCTATAATTATAT
Found at i:40192139 original size:50 final size:50
Alignment explanation
Indices: 40192052--40192201 Score: 228
Period size: 50 Copynumber: 3.0 Consensus size: 50
40192042 CCTTTTAGAT
* * * *
40192052 TGATAGTGTCTCAAGCAACTCACTACAGCCGTTAATGCCAAACAGTCCAG
1 TGATCGTGTCTTAAGCAACTCACTACAGCCGTCAATGCAAAACAGTCCAG
*
40192102 TGATCGTGTCTTAAGCAACTCACTACAGCTGTCAATGCAAAACAGTCCAG
1 TGATCGTGTCTTAAGCAACTCACTACAGCCGTCAATGCAAAACAGTCCAG
* * *
40192152 TGATCGTGTCTTAAGCAACCCACTACAACCGTCAACGCAAAACAGTCCAG
1 TGATCGTGTCTTAAGCAACTCACTACAGCCGTCAATGCAAAACAGTCCAG
40192202 CTCACGATCA
Statistics
Matches: 91, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 91 1.00
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.21
Consensus pattern (50 bp):
TGATCGTGTCTTAAGCAACTCACTACAGCCGTCAATGCAAAACAGTCCAG
Found at i:40195457 original size:17 final size:16
Alignment explanation
Indices: 40195415--40195459 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 16
40195405 AAATATTAAT
40195415 AATTCAAAATCAAAATAA
1 AATTCAAAA--AAAATAA
*
40195433 AATCCAAAAAAAATGAA
1 AATTCAAAAAAAAT-AA
40195450 AATTCAAAAA
1 AATTCAAAAA
40195460 CCCAATCCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 5 0.21
17 11 0.46
18 8 0.33
ACGTcount: A:0.69, C:0.11, G:0.02, T:0.18
Consensus pattern (16 bp):
AATTCAAAAAAAATAA
Found at i:40201314 original size:9 final size:9
Alignment explanation
Indices: 40201280--40201320 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
40201270 TAAAAGGTTG
40201280 TAAAATTTA
1 TAAAATTTA
*
40201289 -AAAATTAA
1 TAAAATTTA
*
40201297 TAAACTTTA
1 TAAAATTTA
40201306 TAAAATTTA
1 TAAAATTTA
40201315 -AAAATT
1 TAAAATT
40201321 CAACCGACAG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
8 13 0.48
9 14 0.52
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (9 bp):
TAAAATTTA
Found at i:40201840 original size:29 final size:28
Alignment explanation
Indices: 40201800--40201865 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 28
40201790 TTAATCGTAT
*
40201800 TTTTTAAAAATAATTAATATTAAAAAAAATA
1 TTTTT-AATATAA-TAAT-TTAAAAAAAATA
* *
40201831 TTATTTAATATAATAATTTTAGAAAAATA
1 TT-TTTAATATAATAATTTAAAAAAAATA
40201860 TTTTTA
1 TTTTTA
40201866 GAATATCCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
28 4 0.13
29 12 0.39
30 4 0.13
31 8 0.26
32 3 0.10
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (28 bp):
TTTTTAATATAATAATTTAAAAAAAATA
Found at i:40203400 original size:3 final size:3
Alignment explanation
Indices: 40203394--40203426 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
40203384 CCGAGGAGGC
*
40203394 GAG GAG GAG GAG GAC GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
40203427 CCGCTGATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.03, G:0.64, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:40203413 original size:15 final size:15
Alignment explanation
Indices: 40203386--40203422 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
40203376 GAGGTCGTCC
40203386 GAGGAGG-CGAGGAG
1 GAGGAGGACGAGGAG
40203400 GAGGAGGACGAGGAG
1 GAGGAGGACGAGGAG
40203415 GAGGAGGA
1 GAGGAGGA
40203423 GGAGCCGCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 7 0.32
15 15 0.68
ACGTcount: A:0.32, C:0.05, G:0.62, T:0.00
Consensus pattern (15 bp):
GAGGAGGACGAGGAG
Found at i:40205864 original size:4 final size:4
Alignment explanation
Indices: 40205855--40206015 Score: 176
Period size: 4 Copynumber: 41.8 Consensus size: 4
40205845 AAGATTCTTT
*
40205855 ATAC ATAC ATAC AT-- ATAT ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
40205901 ATAT ATAC --AC ATAC ATAC ATAC AT-- ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * *
40205945 AT-- ATAT ATAC ATAC ATAC ATAT ATAT ATAN ATATC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA-C ATAC ATAC ATAC
* *
40205992 ATAC ATAT ATAT ACTAC ATAC ATA
1 ATAC ATAC ATAC A-TAC ATAC ATA
40206016 TATATATATA
Statistics
Matches: 138, Mismatches: 9, Indels: 20
0.83 0.05 0.12
Matches are distributed among these distances:
2 8 0.06
4 124 0.90
5 6 0.04
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.30
Consensus pattern (4 bp):
ATAC
Found at i:40205883 original size:22 final size:22
Alignment explanation
Indices: 40205855--40206021 Score: 186
Period size: 22 Copynumber: 7.8 Consensus size: 22
40205845 AAGATTCTTT
*
40205855 ATACATACATACATATATATAC
1 ATACATACATACATATACATAC
40205877 ATACATACATAC--ATACATAC
1 ATACATACATACATATACATAC
* *
40205897 ATACATATATACACATACATAC
1 ATACATACATACATATACATAC
40205919 ATACAT--ATAC--ATACATAC
1 ATACATACATACATATACATAC
*
40205937 ATACATACATATATATACATAC
1 ATACATACATACATATACATAC
* *
40205959 ATACATATATATATANATATCATAC
1 ATACATACATACAT--ATA-CATAC
*
40205984 ATACATACATACATATATATAC
1 ATACATACATACATATACATAC
*
40206006 -TACATACATATATATA
1 ATACATACATACATATA
40206022 TATATAATAT
Statistics
Matches: 128, Mismatches: 8, Indels: 19
0.83 0.05 0.12
Matches are distributed among these distances:
18 14 0.11
20 25 0.20
21 15 0.12
22 51 0.40
23 3 0.02
24 3 0.02
25 17 0.13
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (22 bp):
ATACATACATACATATACATAC
Found at i:40206020 original size:4 final size:4
Alignment explanation
Indices: 40205867--40206060 Score: 113
Period size: 4 Copynumber: 48.5 Consensus size: 4
40205857 ACATACATAC
* * * * * * * * * *
40205867 ATAT ATAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ATAT ACAC ATAC
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * * * * * * * *
40205915 ATAC ATAC ATAT ACAT ACAT ACAT ACAT ACAT ATAT ATAC ATAC ATAC
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * * * * *
40205963 ATAT ATAT ATAN ATAT CATAC ATAC ATAC ATAC ATAT ATAT ACTAC ATAC
1 ATAT ATAT ATAT ATAT -ATAT ATAT ATAT ATAT ATAT ATAT A-TAT ATAT
40206013 ATAT ATAT ATAT ATA- ATAT ATAT ATAT ATAT -TAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
40206059 AT
1 AT
40206061 CTTGTGGCTT
Statistics
Matches: 170, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
3 6 0.04
4 158 0.93
5 6 0.04
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.36
Consensus pattern (4 bp):
ATAT
Found at i:40206034 original size:30 final size:31
Alignment explanation
Indices: 40205869--40206057 Score: 136
Period size: 30 Copynumber: 6.0 Consensus size: 31
40205859 ATACATACAT
* * *
40205869 ATATATACATACATACATACATACATACATAC
1 ATATATAC-TACATACATATATATATATATAC
* *
40205901 ATATATAC-ACATAC--ATACATACATATAC
1 ATATATACTACATACATATATATATATATAC
* *
40205929 ATACATACATACATACATATATATACATACATAC
1 ATATATAC-TACATACATATATAT--ATATATAC
* * * * *
40205963 ATATATATATANATATCATACATACATACATAC
1 ATATATA-CTACATA-CATATATATATATATAC
40205996 ATATATATACTACATACATATATATATATATA-
1 --ATATATACTACATACATATATATATATATAC
* *
40206028 ATATATA-TATATATATTATATATATATATA
1 ATATATACTACATACA-TATATATATATATA
40206058 TATCTTGTGG
Statistics
Matches: 125, Mismatches: 21, Indels: 24
0.74 0.12 0.14
Matches are distributed among these distances:
28 16 0.13
29 6 0.05
30 33 0.26
32 13 0.10
33 21 0.17
34 22 0.18
35 14 0.11
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (31 bp):
ATATATACTACATACATATATATATATATAC
Found at i:40206058 original size:15 final size:15
Alignment explanation
Indices: 40206014--40206058 Score: 81
Period size: 15 Copynumber: 3.0 Consensus size: 15
40206004 ACTACATACA
*
40206014 TATATATATATATAA
1 TATATATATATATAT
40206029 TATATATATATATAT
1 TATATATATATATAT
40206044 TATATATATATATAT
1 TATATATATATATAT
40206059 ATCTTGTGGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TATATATATATATAT
Found at i:40206060 original size:21 final size:21
Alignment explanation
Indices: 40205945--40206060 Score: 92
Period size: 21 Copynumber: 5.5 Consensus size: 21
40205935 ACATACATAC
* * *
40205945 ATATATATACATA-CATACAT
1 ATATATATATATATTATATAT
* * *
40205965 ATATATATANATATCATACAT
1 ATATATATATATATTATATAT
* * *
40205986 ACATACATACATA-TATATACT
1 ATATATATATATATTATATA-T
* *
40206007 ACATACATATATATATATATAAT
1 ATATATATATATAT-TATAT-AT
40206030 ATATATATATATATTATATAT
1 ATATATATATATATTATATAT
40206051 ATATATATAT
1 ATATATATAT
40206061 CTTGTGGCTT
Statistics
Matches: 82, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
20 16 0.20
21 42 0.51
22 5 0.06
23 18 0.22
24 1 0.01
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.41
Consensus pattern (21 bp):
ATATATATATATATTATATAT
Found at i:40218344 original size:43 final size:43
Alignment explanation
Indices: 40218276--40218363 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 43
40218266 GCCAAAATGG
* *
40218276 AACAACAGAATTCCAAATTAAAGGCAAGGTCACAGACCATGTT
1 AACAAAAGAATTCCAAATTAAAGGCAAGGTCACAGACCATATT
* * * *
40218319 AACAAAAGAATTCTAAGTTACAGGCAAGGTCACGGACCATATT
1 AACAAAAGAATTCCAAATTAAAGGCAAGGTCACAGACCATATT
40218362 AA
1 AA
40218364 GCATGAATCC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.19
Consensus pattern (43 bp):
AACAAAAGAATTCCAAATTAAAGGCAAGGTCACAGACCATATT
Found at i:40234262 original size:13 final size:13
Alignment explanation
Indices: 40234244--40234279 Score: 51
Period size: 11 Copynumber: 3.0 Consensus size: 13
40234234 ATAGTTTTAT
40234244 GAAAGAAGAAAAA
1 GAAAGAAGAAAAA
40234257 GAAAGAAG-AAAA
1 GAAAGAAGAAAAA
40234269 G-AAGAA-AAAAA
1 GAAAGAAGAAAAA
40234280 ATTCAAGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 9 0.41
12 5 0.23
13 8 0.36
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (13 bp):
GAAAGAAGAAAAA
Found at i:40245014 original size:29 final size:27
Alignment explanation
Indices: 40244935--40245014 Score: 70
Period size: 29 Copynumber: 2.8 Consensus size: 27
40244925 AAAAAATAAA
* *
40244935 AAAAATTAATTTATATAAATTATTATAC
1 AAAAATTAA-TTATATAATTTATAATAC
* **
40244963 AAAAATTAAATCAATATTTTTTATAAAATAC
1 AAAAATT-AAT-TATATAATTTAT--AATAC
40244994 AAAAATTAATTATATAATTTA
1 AAAAATTAATTATATAATTTA
40245015 ATCTTTTATG
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
28 8 0.20
29 18 0.45
30 3 0.08
31 11 0.28
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (27 bp):
AAAAATTAATTATATAATTTATAATAC
Found at i:40262376 original size:16 final size:16
Alignment explanation
Indices: 40262355--40262388 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
40262345 AATATGTTAA
40262355 TATTTTTAAATAATTT
1 TATTTTTAAATAATTT
*
40262371 TATTTTTAATTAATTT
1 TATTTTTAAATAATTT
40262387 TA
1 TA
40262389 AAATTATTAT
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTTTAAATAATTT
Found at i:40262424 original size:13 final size:13
Alignment explanation
Indices: 40262406--40262431 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40262396 TATTATATAA
40262406 ATTATAATTTTTT
1 ATTATAATTTTTT
40262419 ATTATAATTTTTT
1 ATTATAATTTTTT
40262432 TCTTCTTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATTATAATTTTTT
Found at i:40269487 original size:16 final size:17
Alignment explanation
Indices: 40269456--40269487 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
40269446 TTCAATCATG
40269456 ACTTTTCATCAAATAAC
1 ACTTTTCATCAAATAAC
40269473 ACTTTTCAT-AAATAA
1 ACTTTTCATCAAATAA
40269488 TCTTTTATTT
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:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (17 bp):
ACTTTTCATCAAATAAC
Found at i:40280916 original size:21 final size:20
Alignment explanation
Indices: 40280890--40280933 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
40280880 TAAGATTGTT
40280890 AGAAATATTTGA-AAAGAAAGA
1 AGAAAT-TTTGAGAAA-AAAGA
*
40280911 AGAAATTTTTAGAAAAAAGA
1 AGAAATTTTGAGAAAAAAGA
40280931 AGA
1 AGA
40280934 GTATGGCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.61, C:0.00, G:0.18, T:0.20
Consensus pattern (20 bp):
AGAAATTTTGAGAAAAAAGA
Found at i:40281522 original size:26 final size:26
Alignment explanation
Indices: 40281493--40281542 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
40281483 TTTGTGAGAT
40281493 TTTTAACACATGTGGCATATGTTTAA
1 TTTTAACACATGTGGCATATGTTTAA
40281519 TTTTAACACATGTGGCATATGTTT
1 TTTTAACACATGTGGCATATGTTT
40281543 GTTCCACTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (26 bp):
TTTTAACACATGTGGCATATGTTTAA
Found at i:40283380 original size:2 final size:2
Alignment explanation
Indices: 40283375--40283449 Score: 114
Period size: 2 Copynumber: 37.5 Consensus size: 2
40283365 CTCAAAAATC
* **
40283375 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT NC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
40283417 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40283450 GAAATTTTTT
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40286863 original size:35 final size:35
Alignment explanation
Indices: 40286835--40287126 Score: 293
Period size: 35 Copynumber: 8.3 Consensus size: 35
40286825 CTTAATTGTT
40286835 TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
1 TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
* * * *
40286870 CAATTTAATCAATTAAGCCCAACAATTTAATTAAA
1 TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
* * * *
40286905 CAATTTTAATCAACTAGGTCCAATGACTTAATTAAA
1 TAA-TTTAATCAATTAGGCCCAATAACTTAATTAAA
* * * ***
40286941 CAAATTTAATCAATTATGCCCAATAATTTAATTGTT
1 -TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
** *
40286977 TAATTTAATTGATTAGGCCCAATGACTTAATTAAA
1 TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
** *
40287012 TAATTTAATTGATTAGGCCCAATGACTTAATTAAA
1 TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
* *
40287047 TAATTTAATTAATTAGGCCCAATAATTTAATTAAA
1 TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
* * * *
40287082 CAATTTAGTTAATTAGG--C-ACAACTTAATTAAA
1 TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
*
40287114 CAATTTTAATCAA
1 TAA-TTTAATCAA
40287127 GTGCTTGAGA
Statistics
Matches: 217, Mismatches: 37, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
32 15 0.07
33 8 0.04
35 142 0.65
36 50 0.23
37 2 0.01
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.36
Consensus pattern (35 bp):
TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
Found at i:40286992 original size:142 final size:140
Alignment explanation
Indices: 40286826--40287088 Score: 364
Period size: 142 Copynumber: 1.9 Consensus size: 140
40286816 CCCATTTAAC
40286826 TTAATTGTTTAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATCAATTAAGCCCA
1 TTAATTGTTTAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATCAATTAAGCCCA
* * *
40286891 ACAATTTAATTAAACAATTTTAATCAACTAGGTCCAATGACTTAATTAAACAAATTTAATCAATT
66 ACAACTTAATTAAACAA-TTTAATCAACTAGGCCCAATAACTTAATTAAAC-AATTTAATCAATT
40286956 ATGCCCAATAAT
129 ATGCCCAATAAT
** * * ** *
40286968 TTAATTGTTTAATTTAATTGATTAGGCCCAATGACTTAATTAAATAATTTAATTGATTAGGCCCA
1 TTAATTGTTTAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATCAATTAAGCCCA
** * * * *
40287033 ATGACTTAATTAAATAATTTAATTAATTAGGCCCAATAATTTAATTAAACAATTTA
66 ACAACTTAATTAAACAATTTAATCAACTAGGCCCAATAACTTAATTAAACAATTTA
40287089 GTTAATTAGG
Statistics
Matches: 105, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
140 6 0.06
141 28 0.27
142 71 0.68
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.38
Consensus pattern (140 bp):
TTAATTGTTTAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATCAATTAAGCCCA
ACAACTTAATTAAACAATTTAATCAACTAGGCCCAATAACTTAATTAAACAATTTAATCAATTAT
GCCCAATAAT
Found at i:40288468 original size:18 final size:20
Alignment explanation
Indices: 40288431--40288470 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
40288421 TAAGATACAA
*
40288431 ATTTTTTATTCATAATTCAT
1 ATTTATTATTCATAATTCAT
40288451 ATTTATTATTC-T-ATTCAT
1 ATTTATTATTCATAATTCAT
40288469 AT
1 AT
40288471 AAATAATGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 1 0.05
20 10 0.53
ACGTcount: A:0.30, C:0.10, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTATTATTCATAATTCAT
Found at i:40292780 original size:30 final size:29
Alignment explanation
Indices: 40292701--40292800 Score: 87
Period size: 29 Copynumber: 3.4 Consensus size: 29
40292691 TTATTTAAAA
*
40292701 AAATTCAAATAAGTCTTTATACTTTTA--TT
1 AAATT-AAATAAGTCCTTATA-TTTTATTTT
* *
40292730 ACATTCAATCAAGTCCTTATATTTTTATTTT
1 AAATTAAAT-AAGTCCTTATA-TTTTATTTT
* *
40292761 AAATTAAATAAGCCCTTATATTTGATTTT
1 AAATTAAATAAGTCCTTATATTTTATTTT
* *
40292790 GAGTTAAATAA
1 AAATTAAATAA
40292801 ACATTTATTA
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
28 3 0.05
29 36 0.62
30 10 0.17
31 9 0.16
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (29 bp):
AAATTAAATAAGTCCTTATATTTTATTTT
Found at i:40297162 original size:6 final size:6
Alignment explanation
Indices: 40297151--40297179 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
40297141 ACACGTAAAC
40297151 GAGGAA GAGGAA GAGGAA GAGGAA GAGGA
1 GAGGAA GAGGAA GAGGAA GAGGAA GAGGA
40297180 GGTTTTGATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (6 bp):
GAGGAA
Found at i:40309548 original size:3 final size:3
Alignment explanation
Indices: 40309542--40309579 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
40309532 AGAAGAAGGG
*
40309542 GGA GGA GGA GGA GGA GGA GGA GGA GAA GGA GGA GGA GG
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GG
40309580 GGGGGGGGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:40313449 original size:2 final size:2
Alignment explanation
Indices: 40313442--40313469 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
40313432 TTTGAAAGAA
40313442 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
40313470 GGGGTGGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:40315985 original size:2 final size:2
Alignment explanation
Indices: 40315978--40316013 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
40315968 CATTCTGAAT
40315978 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40316014 CATAGTTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40317359 original size:2 final size:2
Alignment explanation
Indices: 40317354--40317443 Score: 123
Period size: 2 Copynumber: 46.0 Consensus size: 2
40317344 TATATAGAAA
* *
40317354 AT AT AT AA ACT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
40317397 AT AT AT -T NT -T AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40317436 AT AT AT AT
1 AT AT AT AT
40317444 TTCAAAATAC
Statistics
Matches: 80, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
1 3 0.04
2 76 0.95
3 1 0.01
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:40319108 original size:24 final size:24
Alignment explanation
Indices: 40319081--40319128 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
40319071 CATGAAAGGT
* * *
40319081 GAAACCTTTCTTCTCAAATTGTAA
1 GAAAACTTTCTTCTAAAATAGTAA
*
40319105 GAAAATTTTCTTCTAAAATAGTAA
1 GAAAACTTTCTTCTAAAATAGTAA
40319129 AAAGTAAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.38
Consensus pattern (24 bp):
GAAAACTTTCTTCTAAAATAGTAA
Found at i:40322213 original size:2 final size:2
Alignment explanation
Indices: 40322208--40322233 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40322198 CACACACATG
40322208 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
40322234 ACATTAAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:40328239 original size:29 final size:29
Alignment explanation
Indices: 40328189--40328288 Score: 94
Period size: 29 Copynumber: 3.5 Consensus size: 29
40328179 AAATTAATAT
** ** *
40328189 TTATATTTTTATTACATTCAAATTAGCTC
1 TTATATTTTTATTTGAGCCAAATAAGCTC
*
40328218 TTATATTTTTATTTGAGCCAAATAAGCTT
1 TTATATTTTTATTTGAGCCAAATAAGCTC
* * **
40328247 TTATACTTTT-TTTGAGCTAAATAAATTC
1 TTATATTTTTATTTGAGCCAAATAAGCTC
*
40328275 TTATGTTTTTATTT
1 TTATATTTTTATTT
40328289 ATAGTCAAAT
Statistics
Matches: 57, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
28 22 0.39
29 35 0.61
ACGTcount: A:0.29, C:0.10, G:0.07, T:0.54
Consensus pattern (29 bp):
TTATATTTTTATTTGAGCCAAATAAGCTC
Found at i:40328269 original size:28 final size:29
Alignment explanation
Indices: 40328207--40328288 Score: 85
Period size: 28 Copynumber: 2.9 Consensus size: 29
40328197 TTATTACATT
* *
40328207 CAAATTAGCTCTTATATTTTTATTTGAGC
1 CAAATAAGCTCTTATACTTTTATTTGAGC
*
40328236 CAAATAAGCTTTTATACTTTT-TTTGAGC
1 CAAATAAGCTCTTATACTTTTATTTGAGC
* ** **
40328264 TAAATAAATTCTTATGTTTTTATTT
1 CAAATAAGCTCTTATACTTTTATTT
40328289 ATAGTCAAAT
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
28 22 0.51
29 21 0.49
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.51
Consensus pattern (29 bp):
CAAATAAGCTCTTATACTTTTATTTGAGC
Found at i:40331584 original size:10 final size:10
Alignment explanation
Indices: 40331569--40331601 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
40331559 AATTCCAAGT
40331569 AGAAAGAGAG
1 AGAAAGAGAG
40331579 AGAAAGAGAG
1 AGAAAGAGAG
*
40331589 AGAGAGAGAG
1 AGAAAGAGAG
40331599 AGA
1 AGA
40331602 GGATGGGGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (10 bp):
AGAAAGAGAG
Found at i:40331621 original size:2 final size:2
Alignment explanation
Indices: 40331573--40331602 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
40331563 CCAAGTAGAA
*
40331573 AG AG AG AG AA AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
40331603 GATGGGGGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:40333664 original size:22 final size:22
Alignment explanation
Indices: 40333639--40333702 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 22
40333629 TACGTAACCG
* *
40333639 ATTTTTGGGTATTGCGTGACTA
1 ATTTTTAGGTATTGAGTGACTA
*
40333661 A-TTTTAGGTATTGAGTAACTA
1 ATTTTTAGGTATTGAGTGACTA
* * *
40333682 TTTTTTAGGCATTGTGTGACT
1 ATTTTTAGGTATTGAGTGACT
40333703 TAAGTATTGT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 17 0.50
22 17 0.50
ACGTcount: A:0.22, C:0.08, G:0.23, T:0.47
Consensus pattern (22 bp):
ATTTTTAGGTATTGAGTGACTA
Found at i:40345831 original size:162 final size:162
Alignment explanation
Indices: 40345548--40345868 Score: 448
Period size: 162 Copynumber: 2.0 Consensus size: 162
40345538 CAAAATCTCT
* *
40345548 TTTCTTTTAAATCAAAAACCAATTCAATAATGATCGTGACGTTGTCAAAACCTTAAAGACTATAT
1 TTTCTCTTAAATCAAAAACCAATTCAATAATGATCGTGACGCTGTCAAAACCTTAAAGACTATAT
* * * * *
40345613 TTATTTTCAACAATATTAAAATCATGTTATCGACATTTATCAGTAACTTGAAATTTTGATCAAAT
66 TTATTTTCAACAACATTAAAATCATGTTATCAACATATATCAATAACTTAAAATTTTGATCAAAT
*
40345678 TTATGCCAATAAAGTGTATGTCCAAAACCTAC
131 TTATGCCAATAAAGTGTATGTCAAAAACCTAC
* * * * *
40345710 TTTCTCTTAAATCAAAAATCAATTCAATAATGATTGTGATGCTGTCAAAACTTTAAAGA-TCATG
1 TTTCTCTTAAATCAAAAACCAATTCAATAATGATCGTGACGCTGTCAAAACCTTAAAGACT-ATA
*
40345774 TTTATTTTCAACAACATTAAAATCGTGTTATCAACATATA-CGAATAACTTAAAATTTTGATCAA
65 TTTATTTTCAACAACATTAAAATCATGTTATCAACATATATC-AATAACTTAAAATTTTGATCAA
* * * *
40345838 ATTTATGTCGATGAAGTGTTTGTCAAAAACC
129 ATTTATGCCAATAAAGTGTATGTCAAAAACC
40345869 AATACCCTTT
Statistics
Matches: 139, Mismatches: 18, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
161 2 0.01
162 137 0.99
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (162 bp):
TTTCTCTTAAATCAAAAACCAATTCAATAATGATCGTGACGCTGTCAAAACCTTAAAGACTATAT
TTATTTTCAACAACATTAAAATCATGTTATCAACATATATCAATAACTTAAAATTTTGATCAAAT
TTATGCCAATAAAGTGTATGTCAAAAACCTAC
Found at i:40350121 original size:2 final size:2
Alignment explanation
Indices: 40350114--40350141 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
40350104 AAAATCAGAC
40350114 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40350142 GTACACATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40357349 original size:16 final size:16
Alignment explanation
Indices: 40357326--40357359 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
40357316 AAAGGCAAAA
40357326 AAAAAAAAAAGAG-AG
1 AAAAAAAAAAGAGAAG
*
40357341 AAAAGAAAAAGAGAAG
1 AAAAAAAAAAGAGAAG
40357357 AAA
1 AAA
40357360 TTCATTTCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAGAGAAG
Found at i:40361033 original size:4 final size:4
Alignment explanation
Indices: 40361026--40361055 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
40361016 ACATACAAAC
40361026 ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
40361056 TTGAGGGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:40364515 original size:35 final size:35
Alignment explanation
Indices: 40364469--40364538 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
40364459 TGGTGGGACA
*
40364469 GTTATCCTTAACATGGGACAGGTGAAGTGCTATAT
1 GTTATCCTTAACATAGGACAGGTGAAGTGCTATAT
40364504 GTTATCCTTAACATAGGACAGGTGAAGTGCTATAT
1 GTTATCCTTAACATAGGACAGGTGAAGTGCTATAT
40364539 ATATATATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.31
Consensus pattern (35 bp):
GTTATCCTTAACATAGGACAGGTGAAGTGCTATAT
Found at i:40370034 original size:2 final size:2
Alignment explanation
Indices: 40370027--40370068 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
40370017 ATTATTATTA
*
40370027 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40370069 TGAGTTAAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40389532 original size:21 final size:21
Alignment explanation
Indices: 40389491--40389532 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
40389481 ATATCTATAT
*
40389491 TATAAAAAAAATAAATTTTAA
1 TATAAAAAAAATAAATATTAA
*
40389512 TATAAAATAAATTAAA-ATTAA
1 TATAAAA-AAAATAAATATTAA
40389533 AACTTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
TATAAAAAAAATAAATATTAA
Found at i:40390530 original size:27 final size:27
Alignment explanation
Indices: 40390500--40390551 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
40390490 TGAATCGTAA
* * *
40390500 ATTATATAATAATTATTTTATTTTATT
1 ATTATAAAATAATGATTTCATTTTATT
40390527 ATTATAAAATAATGATTTCATTTTA
1 ATTATAAAATAATGATTTCATTTTA
40390552 CGAACCAAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (27 bp):
ATTATAAAATAATGATTTCATTTTATT
Found at i:40397301 original size:21 final size:22
Alignment explanation
Indices: 40397277--40397319 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
40397267 CGCTCCCCCC
*
40397277 CTTT-TTTTTTTTTTCCCTTTT
1 CTTTGTTTTGTTTTTCCCTTTT
*
40397298 CTTTGTTTTGTTTTTCCTTTTT
1 CTTTGTTTTGTTTTTCCCTTTT
40397320 TTCCCCCTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.79
Consensus pattern (22 bp):
CTTTGTTTTGTTTTTCCCTTTT
Found at i:40401758 original size:2 final size:2
Alignment explanation
Indices: 40401751--40401777 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
40401741 AGATTAACAA
40401751 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
40401778 AAGTGAGGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:40410940 original size:31 final size:30
Alignment explanation
Indices: 40410872--40410940 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
40410862 ATAGTTTTTT
*
40410872 TATTCTCAATTAACACCTAATAAATATTTT
1 TATTCTCAATTAACACCTAATAAATATTTC
* *
40410902 TATTCTCAATTAACATCC-CATGAATAATTTC
1 TATTCTCAATTAACA-CCTAATAAAT-ATTTC
40410933 TATTCTCA
1 TATTCTCA
40410941 CAATATACTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 20 0.59
31 14 0.41
ACGTcount: A:0.36, C:0.20, G:0.01, T:0.42
Consensus pattern (30 bp):
TATTCTCAATTAACACCTAATAAATATTTC
Found at i:40411711 original size:38 final size:38
Alignment explanation
Indices: 40411669--40411744 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
40411659 ATTTTTGAGA
40411669 TGGTATTAGTTTTAAAGGGCCATTATCAATTACAATTT
1 TGGTATTAGTTTTAAAGGGCCATTATCAATTACAATTT
*
40411707 TGGTATTAGTTTTAAAGGGCTATTATCAATTACAATTT
1 TGGTATTAGTTTTAAAGGGCCATTATCAATTACAATTT
40411745 GATTTAATAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (38 bp):
TGGTATTAGTTTTAAAGGGCCATTATCAATTACAATTT
Found at i:40418524 original size:43 final size:42
Alignment explanation
Indices: 40418463--40418548 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 42
40418453 GTTGCAGTCG
* * *
40418463 ACAGCAAGAGTTATAACACTCA-CAGTCCCTCAAGTTTTTAAAC
1 ACAGCAAGAGATATAACACCCATCA-T-CCTCAAGTTTCTAAAC
40418506 ACAGCAAGAGATATAACACCCATCATCCTCAAGTTTCTAAAC
1 ACAGCAAGAGATATAACACCCATCATCCTCAAGTTTCTAAAC
40418548 A
1 A
40418549 GAGACAACAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
42 16 0.41
43 21 0.54
44 2 0.05
ACGTcount: A:0.40, C:0.27, G:0.10, T:0.23
Consensus pattern (42 bp):
ACAGCAAGAGATATAACACCCATCATCCTCAAGTTTCTAAAC
Found at i:40422335 original size:21 final size:21
Alignment explanation
Indices: 40422309--40422354 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
40422299 AATAAGCATC
40422309 TTTTTTTTAACTATATTTTCT
1 TTTTTTTTAACTATATTTTCT
40422330 TTTTTTTTAACTATATTTTCT
1 TTTTTTTTAACTATATTTTCT
40422351 TTTT
1 TTTT
40422355 CTTTCTTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTTTTTAACTATATTTTCT
Found at i:40427874 original size:24 final size:24
Alignment explanation
Indices: 40427829--40427875 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
40427819 CTCAAACTTA
* *
40427829 TTTTATATTTATTATTTTTGTAAT
1 TTTTATATTTATTATATATGTAAT
40427853 TTTTAT-TTTATTAATATATGTAA
1 TTTTATATTTATT-ATATATGTAA
40427876 AGGATGTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (24 bp):
TTTTATATTTATTATATATGTAAT
Found at i:40442225 original size:396 final size:395
Alignment explanation
Indices: 40441493--40442283 Score: 1564
Period size: 396 Copynumber: 2.0 Consensus size: 395
40441483 TCAAATTTAC
40441493 GAAAAAATAATAAAATAATTCCCAATTTTTTGACACTAAGATCCACCCCTATCTCATAGTATTTT
1 GAAAAAATAATAAAATAATTCCCAATTTTTTGACACTAAGATCCACCCCTATCTCATAGTATTTT
*
40441558 ATTGTAATAAAAACAAATTATTTGTATTTGATAAAAACAAAAATAAATTATGCTTGGTAAGATTT
66 ATTGTAATAAAAACAAATTATTTGTATTTGATAAAAACAAAAACAAATTATGCTTGGTAAGATTT
40441623 ATTAGGTTGTTGATATTTTATAATATTGTCAAATTATATATGTATCATTTTTCAATAACTGAAAA
131 ATTAGGTTGTTGATATTTTATAATATTGTCAAATTATATATGTATCATTTTTCAATAACTGAAAA
40441688 GAAAATAAATTATCGAAATTTTTTTAATTTGAGGAATGAGATTGAAATTTACTTTAAGTGAGTGA
196 GAAAATAAATTATCGAAATTTTTTTAATTTGAGGAATGAGATTGAAATTTACTTTAAGTGAGTGA
40441753 TATATTATCTTACCTATAAATATAATACTTAAAGTACAAAAAAATACTTTATTTTGTTAAATAAA
261 TATATTATCTTACCTATAAATATAATACTTAAAGTACAAAAAAATACTTTATTTTGTTAAATAAA
40441818 AAATATTAATACTTAAATTCAAAACGTAATGAGAAGAAAACCTCTTCAAAAGCAATTAACTAGTT
326 AAATATTAATACTTAAATTCAAAACGTAATGAGAAGAAAACCTCTTCAAAAGCAATTAACTAGTT
40441883 ACCCA
391 ACCCA
40441888 NGAAAAAATAATAAAATAATTCCCAATTTTTTGACACTAAGATCCACCCCTATCTCATAGTATTT
1 -GAAAAAATAATAAAATAATTCCCAATTTTTTGACACTAAGATCCACCCCTATCTCATAGTATTT
40441953 TATTGTAATAAAAACAAATTATTTGTATTTGATAAAAACAAAAACAAATTATGCTTGGTAAGATT
65 TATTGTAATAAAAACAAATTATTTGTATTTGATAAAAACAAAAACAAATTATGCTTGGTAAGATT
40442018 TATTAGGTTGTTGATATTTTATAATATTGTCAAATTATATATGTATCATTTTTCAATAACTGAAA
130 TATTAGGTTGTTGATATTTTATAATATTGTCAAATTATATATGTATCATTTTTCAATAACTGAAA
40442083 AGAAAATAAATTATCGAAATTTTTTTAATTTGAGGAATGAGATTGAAATTTACTTTAAGTGAGTG
195 AGAAAATAAATTATCGAAATTTTTTTAATTTGAGGAATGAGATTGAAATTTACTTTAAGTGAGTG
40442148 ATATATTATCTTACCTATAAATATAATACTTAAAGTACAAAAAAATACTTTATTTTGTTAAATAA
260 ATATATTATCTTACCTATAAATATAATACTTAAAGTACAAAAAAATACTTTATTTTGTTAAATAA
40442213 AAAATATTAATACTTAAATTCAAAACGTAATGAGAAGAAAACCTCTTCAAAAGCAATTAACTAGT
325 AAAATATTAATACTTAAATTCAAAACGTAATGAGAAGAAAACCTCTTCAAAAGCAATTAACTAGT
40442278 TACCCA
390 TACCCA
40442284 AAATAAAACT
Statistics
Matches: 394, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
396 394 1.00
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (395 bp):
GAAAAAATAATAAAATAATTCCCAATTTTTTGACACTAAGATCCACCCCTATCTCATAGTATTTT
ATTGTAATAAAAACAAATTATTTGTATTTGATAAAAACAAAAACAAATTATGCTTGGTAAGATTT
ATTAGGTTGTTGATATTTTATAATATTGTCAAATTATATATGTATCATTTTTCAATAACTGAAAA
GAAAATAAATTATCGAAATTTTTTTAATTTGAGGAATGAGATTGAAATTTACTTTAAGTGAGTGA
TATATTATCTTACCTATAAATATAATACTTAAAGTACAAAAAAATACTTTATTTTGTTAAATAAA
AAATATTAATACTTAAATTCAAAACGTAATGAGAAGAAAACCTCTTCAAAAGCAATTAACTAGTT
ACCCA
Found at i:40448230 original size:15 final size:16
Alignment explanation
Indices: 40448205--40448237 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
40448195 CTGGAAGCTG
40448205 AAAAACAAAAAAGAAA
1 AAAAACAAAAAAGAAA
40448221 AAAAAC-AAAAAGAAA
1 AAAAACAAAAAAGAAA
40448236 AA
1 AA
40448238 GGTCTTCACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.88, C:0.06, G:0.06, T:0.00
Consensus pattern (16 bp):
AAAAACAAAAAAGAAA
Found at i:40451607 original size:55 final size:55
Alignment explanation
Indices: 40451523--40451632 Score: 175
Period size: 55 Copynumber: 2.0 Consensus size: 55
40451513 GATAGCAGAT
40451523 GGAATTGATCTCAAGCAAGAATTCGAGATAAACCTTGTGTTCCAAGTCGTTTAAA
1 GGAATTGATCTCAAGCAAGAATTCGAGATAAACCTTGTGTTCCAAGTCGTTTAAA
* * * * *
40451578 GGAATTGGTGTCAATCAAGAATTTGAGATAAACCTTGTGTTCCAAGTTGTTTAAA
1 GGAATTGATCTCAAGCAAGAATTCGAGATAAACCTTGTGTTCCAAGTCGTTTAAA
40451633 TTTAACCATG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.32
Consensus pattern (55 bp):
GGAATTGATCTCAAGCAAGAATTCGAGATAAACCTTGTGTTCCAAGTCGTTTAAA
Found at i:40463929 original size:2 final size:2
Alignment explanation
Indices: 40463922--40464002 Score: 52
Period size: 2 Copynumber: 43.5 Consensus size: 2
40463912 ATAGAGATAA
* *
40463922 AT AT AT AT AT AT AT AT AT AT AT AT AC AT GT -T NAGT -T AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -A-T AT AT AT AT
* *
40463963 -T A- AT -T A- AT AG AG AT A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40464000 AT A
1 AT A
40464003 CATGATTTTG
Statistics
Matches: 64, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
1 8 0.12
2 55 0.86
4 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.05, T:0.44
Consensus pattern (2 bp):
AT
Found at i:40464335 original size:3 final size:3
Alignment explanation
Indices: 40464323--40464353 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
40464313 ATTTATTTTT
*
40464323 TTA TTT TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
40464354 ATGTTAGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:40465785 original size:15 final size:16
Alignment explanation
Indices: 40465760--40465796 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
40465750 TAATTTTTTA
40465760 TATTATTACATAAATT
1 TATTATTACATAAATT
40465776 TATT-TTACATAAATT
1 TATTATTACATAAATT
40465791 T-TTATT
1 TATTATT
40465797 TTTATATTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 2 0.10
15 14 0.70
16 4 0.20
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTATTACATAAATT
Found at i:40467887 original size:29 final size:28
Alignment explanation
Indices: 40467820--40467887 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 28
40467810 TTTTTACAAA
* *
40467820 TTATAATATTAAAATTTATAAACTTCAT
1 TTATAATATAAAAATATATAAACTTCAT
*
40467848 TTATAATTATAAAAATATATAAA-TTTAT
1 TTATAA-TATAAAAATATATAAACTTCAT
40467876 ATATATAATATA
1 -T-TATAATATA
40467888 TTACTTTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 10 0.29
29 19 0.56
30 5 0.15
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
TTATAATATAAAAATATATAAACTTCAT
Found at i:40467900 original size:22 final size:22
Alignment explanation
Indices: 40467853--40467904 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
40467843 TTCATTTATA
*
40467853 ATTATA-AAAATATATAAATTT
1 ATTATATATAATATATAAATTT
* *
40467874 A-TATATATAATATATTACTTT
1 ATTATATATAATATATAAATTT
40467895 ATTATATATA
1 ATTATATATA
40467905 TAAAATTTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 4 0.15
21 14 0.54
22 8 0.31
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTATATATAATATATAAATTT
Found at i:40470520 original size:23 final size:23
Alignment explanation
Indices: 40470470--40470522 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
40470460 AGTTCCAGTT
* * *
40470470 AGAGAGAGAATGAGAGAGGGAGA
1 AGAGAGAGAAAGAGAAAGGGAAA
40470493 AGAGAGAGAAAGA-AAAGGGAAA
1 AGAGAGAGAAAGAGAAAGGGAAA
40470515 ATGAGAGA
1 A-GAGAGA
40470523 AAAAAAGTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 8 0.31
23 18 0.69
ACGTcount: A:0.55, C:0.00, G:0.42, T:0.04
Consensus pattern (23 bp):
AGAGAGAGAAAGAGAAAGGGAAA
Found at i:40482848 original size:4 final size:4
Alignment explanation
Indices: 40482839--40482869 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
40482829 TGAAAATCCA
40482839 AAAT AAAT AAAT AAAT ACAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AA
40482870 CGCTGAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Done.