Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold72
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: 5928628
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 261288 characters in sequence are not A, C, G, or T
File 37 of 39
Found at i:5347837 original size:11 final size:11
Alignment explanation
Indices: 5347823--5347878 Score: 62
Period size: 11 Copynumber: 5.1 Consensus size: 11
5347813 TAATAAATAA
5347823 ATAATTAAAAT
1 ATAATTAAAAT
*
5347834 ATAATTTAAAGT
1 ATAA-TTAAAAT
5347846 ATAATATAAAA-
1 ATAAT-TAAAAT
*
5347857 ATAATAAAAAT
1 ATAATTAAAAT
5347868 ATAA-TAAAAT
1 ATAATTAAAAT
5347878 A
1 A
5347879 AAAAATTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
10 10 0.26
11 14 0.37
12 14 0.37
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (11 bp):
ATAATTAAAAT
Found at i:5347868 original size:17 final size:16
Alignment explanation
Indices: 5347848--5347882 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
5347838 TTTAAAGTAT
5347848 AATATAAAAATAATAAA
1 AATATAAAAA-AATAAA
*
5347865 AATATAATAAAATAAA
1 AATATAAAAAAATAAA
5347881 AA
1 AA
5347883 ATTTATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
AATATAAAAAAATAAA
Found at i:5347889 original size:19 final size:17
Alignment explanation
Indices: 5347848--5347898 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
5347838 TTTAAAGTAT
5347848 AATATA-AAAATAATAAA
1 AATATATAAAATAA-AAA
5347865 AATATAATAAAATAAAAA
1 AATAT-ATAAAATAAAAA
* *
5347883 ATTTATATAATATAAA
1 A-ATATATAAAATAAA
5347899 TTATTATCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 5 0.17
18 14 0.48
19 10 0.34
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AATATATAAAATAAAAA
Found at i:5347892 original size:18 final size:17
Alignment explanation
Indices: 5347848--5347898 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
5347838 TTTAAAGTAT
*
5347848 AATATAAAAATAAT-AAA
1 AATATAATAA-AATAAAA
5347865 AATATAATAAAATAAAA
1 AATATAATAAAATAAAA
* *
5347882 AATTTATATAATATAAA
1 AATATA-ATAAAATAAA
5347899 TTATTATCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
16 3 0.10
17 17 0.59
18 9 0.31
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AATATAATAAAATAAAA
Found at i:5347899 original size:15 final size:15
Alignment explanation
Indices: 5347881--5347933 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
5347871 ATAAAATAAA
5347881 AAATTTATATAATAT
1 AAATTTATATAATAT
*
5347896 AAA-TTATTATCATATT
1 AAATTTA-TATAATA-T
5347912 AAAATTTATATAAATAT
1 -AAATTTATAT-AATAT
5347929 AAATT
1 AAATT
5347934 ATTTTAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
14 3 0.10
15 9 0.29
16 6 0.19
17 7 0.23
18 6 0.19
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
AAATTTATATAATAT
Found at i:5347931 original size:17 final size:17
Alignment explanation
Indices: 5347874--5347931 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
5347864 AAATATAATA
*
5347874 AAATAAAAAATTTATAT
1 AAATATAAAATTTATAT
5347891 -AATAT-AAA-TTAT-T
1 AAATATAAAATTTATAT
*
5347904 ATCATATTAAAATTTATAT
1 A-AATA-TAAAATTTATAT
5347923 AAATATAAA
1 AAATATAAA
5347932 TTATTTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 12
0.68 0.06 0.26
Matches are distributed among these distances:
13 1 0.03
14 4 0.12
15 6 0.19
16 5 0.16
17 7 0.22
18 7 0.22
19 2 0.06
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATATAAAATTTATAT
Found at i:5347981 original size:24 final size:22
Alignment explanation
Indices: 5347947--5348004 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 22
5347937 TTAAATAAAA
5347947 TTAAAAT--AATTATTTAA-TAT
1 TTAAAATAAAATTATTTAACT-T
*
5347967 ATTAATAATAAAATTTTTTAACTT
1 -TTAA-AATAAAATTATTTAACTT
5347991 TTAAAATAAAATTA
1 TTAAAATAAAATTA
5348005 AAACACTACT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
21 4 0.13
22 12 0.39
23 4 0.13
24 10 0.32
25 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
TTAAAATAAAATTATTTAACTT
Found at i:5355508 original size:27 final size:27
Alignment explanation
Indices: 5355478--5355531 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
5355468 AGCTTAAGGC
*
5355478 TCCAGGGCTCTTGTTTTCTGGTGCAAT
1 TCCAGGGCTCTTGTCTTCTGGTGCAAT
5355505 TCCAGGGCTCTTGTCTTCTGGTGCAAT
1 TCCAGGGCTCTTGTCTTCTGGTGCAAT
5355532 CTGTAGTCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.11, C:0.24, G:0.26, T:0.39
Consensus pattern (27 bp):
TCCAGGGCTCTTGTCTTCTGGTGCAAT
Found at i:5356219 original size:20 final size:21
Alignment explanation
Indices: 5356189--5356227 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
5356179 TTTAAAAATA
*
5356189 AATATAAATAATTTTATTTTT
1 AATATAAATAATATTATTTTT
5356210 AATA-AAATAATATTATTT
1 AATATAAATAATATTATTT
5356228 AATTTCACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AATATAAATAATATTATTTTT
Found at i:5356227 original size:25 final size:25
Alignment explanation
Indices: 5356185--5356232 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
5356175 AAATTTTAAA
*
5356185 AATAAATATAAATAATTTTATTTTT
1 AATAAATATAAATAATTTAATTTTT
*
5356210 AATAAA-ATAATATTATTTAATTT
1 AATAAATATAA-ATAATTTAATTT
5356233 CACAATCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
AATAAATATAAATAATTTAATTTTT
Found at i:5359175 original size:2 final size:2
Alignment explanation
Indices: 5359168--5359205 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5359158 AGAAAGGAAC
5359168 AT 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 AT
5359206 GTAACGTTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5359994 original size:3 final size:3
Alignment explanation
Indices: 5359986--5360015 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5359976 ATTAGCATCA
5359986 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5360016 TTTGTAATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5360824 original size:2 final size:2
Alignment explanation
Indices: 5360817--5360859 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
5360807 AAGTTTTGCT
* *
5360817 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TG 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
5360859 T
1 T
5360860 GCATAGATGC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5362390 original size:2 final size:2
Alignment explanation
Indices: 5362383--5362412 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5362373 ATATACGTAC
5362383 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
5362413 TATTTATGGT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5362876 original size:2 final size:2
Alignment explanation
Indices: 5362869--5362908 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
5362859 GTTTAAACAA
5362869 AT AT 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 AT AT
5362909 GAAAATGATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5363197 original size:15 final size:15
Alignment explanation
Indices: 5363177--5363246 Score: 79
Period size: 15 Copynumber: 4.6 Consensus size: 15
5363167 ACTACGTGAT
5363177 TATTTAATTTAAATA
1 TATTTAATTTAAATA
5363192 TATTTAA-TTAAATTA
1 TATTTAATTTAAA-TA
* * * *
5363207 AATTTAAAATAAAAAA
1 TATTT-AATTTAAATA
5363223 TATTTAATTTAAATA
1 TATTTAATTTAAATA
5363238 TATTTAATT
1 TATTTAATT
5363247 CAATCAACTC
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
14 5 0.11
15 29 0.64
16 7 0.16
17 4 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TATTTAATTTAAATA
Found at i:5369191 original size:15 final size:16
Alignment explanation
Indices: 5369168--5369200 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
5369158 GAAGGAAGGG
5369168 AAAACAAAAA-AAAAA
1 AAAACAAAAAGAAAAA
*
5369183 AAAAGAAAAAGAAAAA
1 AAAACAAAAAGAAAAA
5369199 AA
1 AA
5369201 GAGACCAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.91, C:0.03, G:0.06, T:0.00
Consensus pattern (16 bp):
AAAACAAAAAGAAAAA
Found at i:5375767 original size:21 final size:21
Alignment explanation
Indices: 5375670--5375761 Score: 139
Period size: 21 Copynumber: 4.4 Consensus size: 21
5375660 GCATTGGCCA
*
5375670 AAAATGAAAAGGCAGTGAACC
1 AAAATGAGAAGGCAGTGAACC
*
5375691 AAAGTGAGAAGGCAGTGAACC
1 AAAATGAGAAGGCAGTGAACC
*
5375712 AAAGTGAGAAGGCAGTGAACC
1 AAAATGAGAAGGCAGTGAACC
* *
5375733 AAAATGAAAAAGCAGTGAACC
1 AAAATGAGAAGGCAGTGAACC
5375754 AAAATGAG
1 AAAATGAG
5375762 GAAGCATTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 65 1.00
ACGTcount: A:0.50, C:0.13, G:0.27, T:0.10
Consensus pattern (21 bp):
AAAATGAGAAGGCAGTGAACC
Found at i:5387611 original size:14 final size:14
Alignment explanation
Indices: 5387592--5387618 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5387582 TTTTTTCAAG
5387592 TTAAAAAAAAAATC
1 TTAAAAAAAAAATC
5387606 TTAAAAAAAAAAT
1 TTAAAAAAAAAAT
5387619 AGCATGACAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (14 bp):
TTAAAAAAAAAATC
Found at i:5392151 original size:24 final size:25
Alignment explanation
Indices: 5392120--5392167 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
5392110 ATTCATGTGA
5392120 CAAAAATG-TCTTT-TAGCTTTAAT
1 CAAAAATGATCTTTATAGCTTTAAT
*
5392143 CAAAGAATGATCTTTATTGCTTTAA
1 CAAA-AATGATCTTTATAGCTTTAA
5392168 ATGAGAGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 4 0.19
25 5 0.24
26 8 0.38
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.42
Consensus pattern (25 bp):
CAAAAATGATCTTTATAGCTTTAAT
Found at i:5393504 original size:17 final size:17
Alignment explanation
Indices: 5393464--5393502 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
5393454 CTCTAAATTA
5393464 ATTTATTATTAAAATATT
1 ATTTA-TATTAAAATATT
*
5393482 ATTTATATTAATATAATT
1 ATTTATATTAAAAT-ATT
5393500 ATT
1 ATT
5393503 ATTAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTATATTAAAATATT
Found at i:5393638 original size:14 final size:14
Alignment explanation
Indices: 5393588--5393640 Score: 72
Period size: 14 Copynumber: 3.8 Consensus size: 14
5393578 ATTATTAAAC
5393588 TAATAAT-TTTTAA
1 TAATAATATTTTAA
*
5393601 TATTAATATTTTAGA
1 TAATAATATTTTA-A
*
5393616 TAGTAATATTTTAA
1 TAATAATATTTTAA
5393630 TAATAATATTT
1 TAATAATATTT
5393641 AATGTTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
13 6 0.17
14 16 0.46
15 13 0.37
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (14 bp):
TAATAATATTTTAA
Found at i:5393661 original size:19 final size:18
Alignment explanation
Indices: 5393626--5393668 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
5393616 TAGTAATATT
5393626 TTAATAATAATATTTAATG
1 TTAA-AATAATATTTAATG
*
5393645 TTAAAATATTATATTAATG
1 TTAAAATAATAT-TTAATG
5393664 TTAAA
1 TTAAA
5393669 TACTTAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (18 bp):
TTAAAATAATATTTAATG
Found at i:5393681 original size:19 final size:19
Alignment explanation
Indices: 5393640--5393681 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
5393630 TAATAATATT
* *
5393640 TAATGTTAAAATATTATAT
1 TAATGTTAAAATATTAAAA
5393659 TAATGTT-AAATACTTAAAA
1 TAATGTTAAAATA-TTAAAA
5393678 TAAT
1 TAAT
5393682 ACTATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (19 bp):
TAATGTTAAAATATTAAAA
Found at i:5393734 original size:18 final size:20
Alignment explanation
Indices: 5393707--5393745 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5393697 AACATAATTA
5393707 TATAAATA-T-TTAAAATAT
1 TATAAATATTATTAAAATAT
*
5393725 TATAATTATTATTAAAATAT
1 TATAAATATTATTAAAATAT
5393745 T
1 T
5393746 TTTTCAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 1 0.06
20 10 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TATAAATATTATTAAAATAT
Found at i:5393775 original size:17 final size:17
Alignment explanation
Indices: 5393725--5393785 Score: 58
Period size: 17 Copynumber: 3.7 Consensus size: 17
5393715 TTTAAAATAT
*
5393725 TATAATTATTATTAAAA
1 TATAATTTTTATTAAAA
5393742 TAT--TTTTTCAATT--AA
1 TATAATTTTT--ATTAAAA
5393757 TATAATTTTTATTAAAA
1 TATAATTTTTATTAAAA
*
5393774 TATTATTTTTAT
1 TATAATTTTTAT
5393786 AATTTTTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
15 12 0.33
17 24 0.67
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
TATAATTTTTATTAAAA
Found at i:5393872 original size:38 final size:38
Alignment explanation
Indices: 5393829--5393912 Score: 91
Period size: 38 Copynumber: 2.2 Consensus size: 38
5393819 AATATTTTAC
*
5393829 TAATATGTTGCAATATATCATTAAAAT-ATAA-ATTATAT
1 TAATAT-TTGCAAT-TATCATTAAAATAATAATATTACAT
** *
5393867 TAATATTTTTAATTATTATTAAAATAATAATATTACAT
1 TAATATTTGCAATTATCATTAAAATAATAATATTACAT
5393905 TATATATT
1 TA-ATATT
5393913 ATTAAAATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
36 11 0.28
37 9 0.23
38 14 0.36
39 5 0.13
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (38 bp):
TAATATTTGCAATTATCATTAAAATAATAATATTACAT
Found at i:5393923 original size:15 final size:15
Alignment explanation
Indices: 5393880--5393923 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
5393870 TATTTTTAAT
5393880 TATTATTAAAATA-A
1 TATTATTAAAATATA
* * *
5393894 TAATATTACATTATA
1 TATTATTAAAATATA
5393909 TATTATTAAAATATA
1 TATTATTAAAATATA
5393924 AATATGTATG
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTATTAAAATATA
Found at i:5395728 original size:2 final size:2
Alignment explanation
Indices: 5395721--5395750 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5395711 GCTGAAAGGG
5395721 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
5395751 TGATCTTCCA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5396468 original size:3 final size:3
Alignment explanation
Indices: 5396460--5396489 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5396450 ATATTTATTC
5396460 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5396490 TTTAGTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5397862 original size:2 final size:2
Alignment explanation
Indices: 5397857--5397897 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
5397847 ATATATAGAT
*
5397857 AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
5397898 AGGAATTGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5398432 original size:12 final size:12
Alignment explanation
Indices: 5398415--5398439 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5398405 AATAAGGTAA
5398415 AGCTCTTTAGTT
1 AGCTCTTTAGTT
5398427 AGCTCTTTAGTT
1 AGCTCTTTAGTT
5398439 A
1 A
5398440 CAAAATTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.48
Consensus pattern (12 bp):
AGCTCTTTAGTT
Found at i:5402131 original size:7 final size:7
Alignment explanation
Indices: 5402119--5402169 Score: 84
Period size: 7 Copynumber: 7.3 Consensus size: 7
5402109 ACCTCCCTTC
*
5402119 CCTTCAA
1 CCTTCAG
5402126 CCTTCAG
1 CCTTCAG
5402133 CCTTCAG
1 CCTTCAG
5402140 CCTTCAG
1 CCTTCAG
5402147 CCTTCAG
1 CCTTCAG
5402154 CCTTCAG
1 CCTTCAG
*
5402161 CCTTAAG
1 CCTTCAG
5402168 CC
1 CC
5402170 ATTCCTAGTA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 42 1.00
ACGTcount: A:0.18, C:0.43, G:0.12, T:0.27
Consensus pattern (7 bp):
CCTTCAG
Found at i:5411380 original size:28 final size:27
Alignment explanation
Indices: 5411348--5411426 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 27
5411338 TAAATGAACA
5411348 AAATTTTTATACTTTAATTTAT-TTAAAT
1 AAATTTTTA-ACTTTAATTTATATT-AAT
* *
5411376 AAATTTTTAATTTTTAATTTATATTCAT
1 AAATTTTTAA-CTTTAATTTATATTAAT
*
5411404 AAATTTTTAACTGTAAATTTATA
1 AAATTTTTAACT-TTAATTTATA
5411427 GCCAAAGAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
27 2 0.05
28 40 0.91
29 2 0.05
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.56
Consensus pattern (27 bp):
AAATTTTTAACTTTAATTTATATTAAT
Found at i:5418355 original size:8 final size:8
Alignment explanation
Indices: 5418342--5418370 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
5418332 TTATTCCCCA
5418342 AAAAAAAT
1 AAAAAAAT
5418350 -AAAAAAT
1 AAAAAAAT
5418357 AAAAAAAT
1 AAAAAAAT
5418365 AAAAAA
1 AAAAAA
5418371 TTCTCGTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:5418362 original size:15 final size:15
Alignment explanation
Indices: 5418342--5418371 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5418332 TTATTCCCCA
5418342 AAAAAAATAAAAAAT
1 AAAAAAATAAAAAAT
5418357 AAAAAAATAAAAAAT
1 AAAAAAATAAAAAAT
5418372 TCTCGTTGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (15 bp):
AAAAAAATAAAAAAT
Found at i:5424937 original size:11 final size:12
Alignment explanation
Indices: 5424877--5424939 Score: 53
Period size: 11 Copynumber: 5.2 Consensus size: 12
5424867 AATTAGTATA
5424877 TTTAATATAATAT
1 TTTAATA-AATAT
5424890 TATT-ATAAATAT
1 T-TTAATAAATAT
*
5424902 TAT-ATAAAT-T
1 TTTAATAAATAT
5424912 TTGCTAATAAATAT
1 TT--TAATAAATAT
5424926 TTTAAT-AATAT
1 TTTAATAAATAT
5424937 TTT
1 TTT
5424940 TTAAAATTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
10 2 0.05
11 15 0.35
12 11 0.26
13 10 0.23
14 5 0.12
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (12 bp):
TTTAATAAATAT
Found at i:5425660 original size:19 final size:19
Alignment explanation
Indices: 5425632--5425668 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5425622 AAGATTTTGG
*
5425632 ATATTTACAATGAAAAATC
1 ATATTGACAATGAAAAATC
*
5425651 ATATTGACAATGAGAAAT
1 ATATTGACAATGAAAAAT
5425669 TAAAGAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.30
Consensus pattern (19 bp):
ATATTGACAATGAAAAATC
Found at i:5431075 original size:12 final size:12
Alignment explanation
Indices: 5431058--5431083 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5431048 AGTTTCTTTT
5431058 GGTTGGGCACCA
1 GGTTGGGCACCA
5431070 GGTTGGGCACCA
1 GGTTGGGCACCA
5431082 GG
1 GG
5431084 CTTCTTTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.23, G:0.46, T:0.15
Consensus pattern (12 bp):
GGTTGGGCACCA
Found at i:5438792 original size:4 final size:4
Alignment explanation
Indices: 5438783--5438808 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
5438773 AGTTCATATG
5438783 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
5438809 AAAAGGTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:5439930 original size:22 final size:22
Alignment explanation
Indices: 5439889--5439931 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5439879 TAAGTTTATT
* *
5439889 ATTTTTTATTTATATTTAAATA
1 ATTTTTTATTTAGATATAAATA
*
5439911 ATTTTTTATTTAGGTATAAAT
1 ATTTTTTATTTAGATATAAAT
5439932 TAAAAATTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (22 bp):
ATTTTTTATTTAGATATAAATA
Found at i:5439950 original size:30 final size:30
Alignment explanation
Indices: 5439928--5439991 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 30
5439918 ATTTAGGTAT
5439928 AAATTAAAAATTAAAGATTTATTGAAATAA
1 AAATTAAAAATTAAAGATTTATTGAAATAA
*
5439958 AAATTAAAGATTAAAG-TTTGATT-ATAATAA
1 AAATTAAAAATTAAAGATTT-ATTGA-AATAA
5439988 AAAT
1 AAAT
5439992 ATTAATATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 4 0.13
30 27 0.87
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (30 bp):
AAATTAAAAATTAAAGATTTATTGAAATAA
Found at i:5440151 original size:11 final size:11
Alignment explanation
Indices: 5440135--5440266 Score: 79
Period size: 10 Copynumber: 12.7 Consensus size: 11
5440125 ACGCAAATTC
5440135 AAATATAATAT
1 AAATATAATAT
*
5440146 AAATAT-TTA-
1 AAATATAATAT
5440155 AAATATAATAT
1 AAATATAATAT
5440166 -AATATAA-A-
1 AAATATAATAT
5440174 AAAT-TAATAT
1 AAATATAATAT
5440184 AAATAT-ATA-
1 AAATATAATAT
* *
5440193 AATTATTA-AT
1 AAATATAATAT
*
5440203 AAATTTATATAT
1 AAATATA-ATAT
*
5440215 AAATATATTAT
1 AAATATAATAT
* *
5440226 -ATTTTAAATAT
1 AAATAT-AATAT
* *
5440237 AATTATAATAA
1 AAATATAATAT
5440248 AAATATAAATAT
1 AAATAT-AATAT
5440260 AAA-ATAA
1 AAATATAA
5440267 ATACGAGAAA
Statistics
Matches: 93, Mismatches: 15, Indels: 27
0.69 0.11 0.20
Matches are distributed among these distances:
8 3 0.03
9 17 0.18
10 28 0.30
11 26 0.28
12 19 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATATAATAT
Found at i:5440160 original size:20 final size:20
Alignment explanation
Indices: 5440135--5440269 Score: 93
Period size: 19 Copynumber: 6.8 Consensus size: 20
5440125 ACGCAAATTC
*
5440135 AAATATAATATAAATATTTA
1 AAATATAATATAAATATATA
*
5440155 AAATATAATAT-AATATAAA
1 AAATATAATATAAATATATA
5440174 AAAT-TAATATAAATATATA
1 AAATATAATATAAATATATA
* *
5440193 AATTATTAATA-AATTTATATA
1 AAATA-TAATATAA-ATATATA
* ** *
5440214 TAAATATATTATATTTTAAATA
1 -AAATATAATATA-AATATATA
*
5440236 TAATTATAATA-AAA-ATAT-
1 -AAATATAATATAAATATATA
*
5440254 AAATATAAAATAAATA
1 AAATATAATATAAATA
5440270 CGAGAAAACA
Statistics
Matches: 90, Mismatches: 16, Indels: 19
0.72 0.13 0.15
Matches are distributed among these distances:
17 8 0.09
18 9 0.10
19 24 0.27
20 13 0.14
21 16 0.18
22 20 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAATATAATATAAATATATA
Found at i:5440164 original size:25 final size:25
Alignment explanation
Indices: 5440136--5440253 Score: 91
Period size: 25 Copynumber: 4.6 Consensus size: 25
5440126 CGCAAATTCA
5440136 AATATAATATAAATATTTAAAATAT
1 AATATAATATAAATATTTAAAATAT
* *
5440161 AATATAATATAAAAAATT--AATAT
1 AATATAATATAAATATTTAAAATAT
* *
5440184 AA-AT-ATATAAATTATTAATAAATTT
1 AATATAATATAAA-TATTTA-AAATAT
* *
5440209 ATATATAAATATATTATATTTTAAATAT
1 A-ATAT-AATATA-AATATTTAAAATAT
*
5440237 AATTATAATAAAAATAT
1 AA-TATAATATAAATAT
5440254 AAATATAAAA
Statistics
Matches: 71, Mismatches: 12, Indels: 19
0.70 0.12 0.19
Matches are distributed among these distances:
21 7 0.10
22 4 0.06
23 7 0.10
25 21 0.30
26 5 0.07
27 8 0.11
28 9 0.13
29 9 0.13
30 1 0.01
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
AATATAATATAAATATTTAAAATAT
Found at i:5440215 original size:31 final size:31
Alignment explanation
Indices: 5440175--5440257 Score: 93
Period size: 31 Copynumber: 2.7 Consensus size: 31
5440165 TAATATAAAA
5440175 AATTA-ATATAAATATATAAATTATT-AATA-
1 AATTATATATAAATATATAAATT-TTAAATAT
*
5440204 AATTTATATATAAATATATTATATTTTAAATAT
1 AA-TTATATATAAATATA-TAAATTTTAAATAT
*
5440237 AATTATA-ATAAAAATATAAAT
1 AATTATATATAAATATATAAAT
5440258 ATAAAATAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
29 2 0.04
30 7 0.15
31 21 0.46
32 14 0.30
33 2 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (31 bp):
AATTATATATAAATATATAAATTTTAAATAT
Found at i:5440236 original size:22 final size:24
Alignment explanation
Indices: 5440188--5440262 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 24
5440178 TAATATAAAT
*
5440188 ATATAAAT-TATTAATAAATTTAT
1 ATATAAATATATTAATAAATTTAA
*
5440211 ATATAAATATATT-AT-ATTTTAA
1 ATATAAATATATTAATAAATTTAA
* * *
5440233 ATATAATTATAATAA-AAATATAA
1 ATATAAATATATTAATAAATTTAA
5440256 ATATAAA
1 ATATAAA
5440263 ATAAATACGA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
22 16 0.38
23 22 0.52
24 4 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
ATATAAATATATTAATAAATTTAA
Found at i:5447991 original size:24 final size:24
Alignment explanation
Indices: 5447964--5448028 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 24
5447954 AATTAATTTA
* *
5447964 TAATTTTTATTTTTAAAATTAAAT
1 TAATTTATATTTTTAAAAATAAAT
*
5447988 TAATTGATATTTTATAAAAATAAAT
1 TAATTTATATTTT-TAAAAATAAAT
*
5448013 AAATTATATATTTTTA
1 TAATT-TATATTTTTA
5448029 TTTATATTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
24 11 0.32
25 16 0.47
26 7 0.21
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TAATTTATATTTTTAAAAATAAAT
Found at i:5448046 original size:29 final size:29
Alignment explanation
Indices: 5448014--5448087 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
5448004 AAAATAAATA
5448014 AATTATATATTTTTAT-TTATATTAA-TTAT
1 AATTATAT-TTTTTATATTATA-TAATTTAT
*
5448043 AATTA-ATTTAATTATATTATATAATTTAT
1 AATTATATTT-TTTATATTATATAATTTAT
5448072 AATTATATTTTTTATA
1 AATTATATTTTTTATA
5448088 ATTAATTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
27 2 0.05
28 9 0.23
29 24 0.62
30 4 0.10
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (29 bp):
AATTATATTTTTTATATTATATAATTTAT
Found at i:5448054 original size:9 final size:9
Alignment explanation
Indices: 5448028--5448209 Score: 57
Period size: 9 Copynumber: 20.4 Consensus size: 9
5448018 ATATATTTTT
5448028 ATTTATATTA
1 ATTTA-ATTA
5448038 ATTATAATTA
1 ATT-TAATTA
5448048 ATTTAATT-
1 ATTTAATTA
5448056 ATATT-ATATA
1 AT-TTAAT-TA
5448066 ATTT-A-TA
1 ATTTAATTA
*
5448073 A-TTATATTT
1 ATTTA-ATTA
*
5448082 TTTATAATTA
1 ATT-TAATTA
* *
5448092 ATTTATTTT
1 ATTTAATTA
5448101 ATTTAATT-
1 ATTTAATTA
* *
5448109 -TATAATCA
1 ATTTAATTA
5448117 ATTGT-ATTA
1 ATT-TAATTA
* *
5448126 AATT-ATTG
1 ATTTAATTA
5448134 ATTTAATTA
1 ATTTAATTA
*
5448143 TTTTAATT-
1 ATTTAATTA
* *
5448151 ATTTACGTAAA
1 ATTTA-AT-TA
5448162 ATTTAATTA
1 ATTTAATTA
*
5448171 ATTTAATAA
1 ATTTAATTA
5448180 ATTT--TT-
1 ATTTAATTA
5448186 ATGTTAAATTA
1 AT-TT-AATTA
*
5448197 ATTTATTTA
1 ATTTAATTA
5448206 ATTT
1 ATTT
5448210 TTTAATTATT
Statistics
Matches: 127, Mismatches: 24, Indels: 43
0.65 0.12 0.22
Matches are distributed among these distances:
6 4 0.03
7 11 0.09
8 16 0.13
9 61 0.48
10 24 0.19
11 11 0.09
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (9 bp):
ATTTAATTA
Found at i:5448055 original size:15 final size:15
Alignment explanation
Indices: 5448035--5448110 Score: 70
Period size: 14 Copynumber: 5.2 Consensus size: 15
5448025 TTTATTTATA
5448035 TTAATTATAATTAAT
1 TTAATTATAATTAAT
5448050 TTAATTAT-ATT-AT
1 TTAATTATAATTAAT
*
5448063 ATAATTTATAATTATAT
1 TTAA-TTATAATTA-AT
*
5448080 TT-TTTATAATTAAT
1 TTAATTATAATTAAT
* *
5448094 TT-ATTTTATTTAAT
1 TTAATTATAATTAAT
5448108 TTA
1 TTA
5448111 TAATCAATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
13 5 0.10
14 22 0.44
15 20 0.40
17 3 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTAATTATAATTAAT
Found at i:5448105 original size:20 final size:20
Alignment explanation
Indices: 5448028--5448105 Score: 68
Period size: 20 Copynumber: 3.7 Consensus size: 20
5448018 ATATATTTTT
* *
5448028 ATTTATATTAATTATAATTA
1 ATTTATTTTATTTATAATTA
*
5448048 ATTTAATTATATTATATAATTTA
1 ATTT-ATTTTATT-TATAA-TTA
*
5448071 TAATTATATTT-TTTATAATTA
1 -ATTTAT-TTTATTTATAATTA
5448092 ATTTATTTTATTTA
1 ATTTATTTTATTTA
5448106 ATTTATAATC
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
19 3 0.07
20 13 0.28
21 8 0.17
22 10 0.22
23 7 0.15
24 5 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTATTTTATTTATAATTA
Found at i:5449435 original size:20 final size:21
Alignment explanation
Indices: 5449410--5449448 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5449400 TAAAAACATA
*
5449410 TTTAT-AATCATAATTTAAAT
1 TTTATAAATAATAATTTAAAT
5449430 TTTATAAATAATAATTTAA
1 TTTATAAATAATAATTTAA
5449449 CTTAACCCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTATAAATAATAATTTAAAT
Found at i:5449669 original size:2 final size:2
Alignment explanation
Indices: 5449662--5449693 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5449652 CGTCCTCCTC
5449662 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5449694 GTCTGCATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5451671 original size:30 final size:30
Alignment explanation
Indices: 5451637--5451699 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
5451627 CTCACATAGT
*
5451637 TAAACTTAGTATCATCCAGTATTAATTCAG
1 TAAACTTAGTATCATCCAGTACTAATTCAG
**
5451667 TAAACTTAGTATCATCTGGTACTAATTCAG
1 TAAACTTAGTATCATCCAGTACTAATTCAG
5451697 TAA
1 TAA
5451700 TAGCTTCTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (30 bp):
TAAACTTAGTATCATCCAGTACTAATTCAG
Found at i:5454023 original size:3 final size:3
Alignment explanation
Indices: 5454015--5454051 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
5454005 ACGTAAATTC
5454015 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5454052 GACTACATCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5466330 original size:23 final size:23
Alignment explanation
Indices: 5466279--5466332 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
5466269 TCATTTAATG
* * *
5466279 AAATACTCAAGTATTGTTTACCC
1 AAATATTCAAGTATTATTTAACC
*
5466302 AAATATTCCAGTATTATTTAACC
1 AAATATTCAAGTATTATTTAACC
5466325 AAATATTC
1 AAATATTC
5466333 GGGTGTTGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
AAATATTCAAGTATTATTTAACC
Found at i:5472946 original size:2 final size:2
Alignment explanation
Indices: 5472939--5472966 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5472929 GATGAAATGC
5472939 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
5472967 GGATCTGCCC
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):
TA
Found at i:5475409 original size:16 final size:16
Alignment explanation
Indices: 5475390--5475482 Score: 62
Period size: 16 Copynumber: 5.8 Consensus size: 16
5475380 GTAGCAGCAT
5475390 TCCTTAGCGACAACAC
1 TCCTTAGCGACAACAC
* *
5475406 TCCTTGGC-AGCAGCAC
1 TCCTTAGCGA-CAACAC
* * * *
5475422 TTCTTAGCAAGAGCAC
1 TCCTTAGCGACAACAC
* *
5475438 TCCTTGGCGACAACGC
1 TCCTTAGCGACAACAC
** *
5475454 TCCTTAATGACAGCAC
1 TCCTTAGCGACAACAC
*
5475470 TCCTTAGTGACAA
1 TCCTTAGCGACAA
5475483 AACTATTTGG
Statistics
Matches: 57, Mismatches: 18, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
15 1 0.02
16 55 0.96
17 1 0.02
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.23
Consensus pattern (16 bp):
TCCTTAGCGACAACAC
Found at i:5475418 original size:32 final size:32
Alignment explanation
Indices: 5475373--5475445 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
5475363 GGTAGTAGCG
* *
5475373 CTCCTTGGTAGCAGCA-TTCCTTAGCGACAACA
1 CTCCTTGGCAGCAGCACTT-CTTAGCAACAACA
* *
5475405 CTCCTTGGCAGCAGCACTTCTTAGCAAGAGCA
1 CTCCTTGGCAGCAGCACTTCTTAGCAACAACA
5475437 CTCCTTGGC
1 CTCCTTGGC
5475446 GACAACGCTC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
32 34 0.94
33 2 0.06
ACGTcount: A:0.22, C:0.33, G:0.21, T:0.25
Consensus pattern (32 bp):
CTCCTTGGCAGCAGCACTTCTTAGCAACAACA
Found at i:5476254 original size:32 final size:32
Alignment explanation
Indices: 5476187--5476259 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
5476177 GGTAGTAGCG
* * *
5476187 CTCCTTGGTAGCAGCATTCCTTAGCGACAATA
1 CTCCTTGGCAGCAGCATTCCTTAGCAACAACA
* *
5476219 CTCCTTGGCAGCAGCACTT-CTTAGCAAGAGCA
1 CTCCTTGGCAGCAGCA-TTCCTTAGCAACAACA
5476251 CTCCTTGGC
1 CTCCTTGGC
5476260 GACAACGCTC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
32 33 0.94
33 2 0.06
ACGTcount: A:0.22, C:0.32, G:0.21, T:0.26
Consensus pattern (32 bp):
CTCCTTGGCAGCAGCATTCCTTAGCAACAACA
Found at i:5476796 original size:814 final size:814
Alignment explanation
Indices: 5475228--5476860 Score: 3230
Period size: 814 Copynumber: 2.0 Consensus size: 814
5475218 TTGCACTTAT
5475228 TACCAATCACTCCAGCTGCAGTCTTAACTTTAATTACAATTTATCAAATAGTAGGACTGTATTTC
1 TACCAATCACTCCAGCTGCAGTCTTAACTTTAATTACAATTTATCAAATAGTAGGACTGTATTTC
5475293 AGTGGCTATAGATGCTTGTTTTTGGCTATTAACATGTCAGGCAGGCACATTTGATTGGGCAGTGC
66 AGTGGCTATAGATGCTTGTTTTTGGCTATTAACATGTCAGGCAGGCACATTTGATTGGGCAGTGC
5475358 ACTCTGGTAGTAGCGCTCCTTGGTAGCAGCATTCCTTAGCGACAACACTCCTTGGCAGCAGCACT
131 ACTCTGGTAGTAGCGCTCCTTGGTAGCAGCATTCCTTAGCGACAACACTCCTTGGCAGCAGCACT
5475423 TCTTAGCAAGAGCACTCCTTGGCGACAACGCTCCTTAATGACAGCACTCCTTAGTGACAAAACTA
196 TCTTAGCAAGAGCACTCCTTGGCGACAACGCTCCTTAATGACAGCACTCCTTAGTGACAAAACTA
5475488 TTTGGCAGCAGTGCTCCAGTACTCCAGCACTCTGCCCTCGCTTGCAGTGTATTGCAATATACAGG
261 TTTGGCAGCAGTGCTCCAGTACTCCAGCACTCTGCCCTCGCTTGCAGTGTATTGCAATATACAGG
5475553 TTGTGTGACATATAACAAAGACAATTTTGCACAAGATGCATCAATTCATGACGAACAGTAGATCT
326 TTGTGTGACATATAACAAAGACAATTTTGCACAAGATGCATCAATTCATGACGAACAGTAGATCT
5475618 AACCCCAGAACAAGTGGCTGGATTCTTGGGTTTACTTCACTTCTAGGATGTCCTAGAGAGTATGA
391 AACCCCAGAACAAGTGGCTGGATTCTTGGGTTTACTTCACTTCTAGGATGTCCTAGAGAGTATGA
5475683 CTTTAAGGTTCAAACAGAGAGATTATTACAAAGTCTCTTCTTAACATTTTCCTTTGATACAAGTA
456 CTTTAAGGTTCAAACAGAGAGATTATTACAAAGTCTCTTCTTAACATTTTCCTTTGATACAAGTA
5475748 CTTCCATTTTCCCTCCTGAACTATGGCACATGTCTAGGTGTGCTGTCATGTAACCAACCTTTACT
521 CTTCCATTTTCCCTCCTGAACTATGGCACATGTCTAGGTGTGCTGTCATGTAACCAACCTTTACT
5475813 ACTTGTAACTATAATTCTCCCATGACTGGCTTTAACTCCTTGTAACTATTACCTATTCACCTTGG
586 ACTTGTAACTATAATTCTCCCATGACTGGCTTTAACTCCTTGTAACTATTACCTATTCACCTTGG
5475878 TATATTCTTTTGATGGGACTATAAACAGTGATCCAAAAGCTTCAGTTGGGATCATTGTGGTAAAG
651 TATATTCTTTTGATGGGACTATAAACAGTGATCCAAAAGCTTCAGTTGGGATCATTGTGGTAAAG
5475943 TGAAAACTTGAATTAATAAATTCTCTTCGCAACTTTCTCCATAAAATTATTCATCCACCGCAATT
716 TGAAAACTTGAATTAATAAATTCTCTTCGCAACTTTCTCCATAAAATTATTCATCCACCGCAATT
5476008 TCAATCTTCCTTAGCCATCTTTTTCCTTCACCGC
781 TCAATCTTCCTTAGCCATCTTTTTCCTTCACCGC
5476042 TACCAATCACTCCAGCTGCAGTCTTAACTTTAATTACAATTTATCAAATAGTAGGACTGTATTTC
1 TACCAATCACTCCAGCTGCAGTCTTAACTTTAATTACAATTTATCAAATAGTAGGACTGTATTTC
5476107 AGTGGCTATAGATGCTTGTTTTTGGCTATTAACATGTCAGGCAGGCACATTTGATTGGGCAGTGC
66 AGTGGCTATAGATGCTTGTTTTTGGCTATTAACATGTCAGGCAGGCACATTTGATTGGGCAGTGC
*
5476172 ACTCTGGTAGTAGCGCTCCTTGGTAGCAGCATTCCTTAGCGACAATACTCCTTGGCAGCAGCACT
131 ACTCTGGTAGTAGCGCTCCTTGGTAGCAGCATTCCTTAGCGACAACACTCCTTGGCAGCAGCACT
*
5476237 TCTTAGCAAGAGCACTCCTTGGCGACAACGCTCCTTAATGACAGCACTCCTTAGTGACAAAACTC
196 TCTTAGCAAGAGCACTCCTTGGCGACAACGCTCCTTAATGACAGCACTCCTTAGTGACAAAACTA
5476302 TTTGGCAGCAGTGCTCCAGTACTCCAGCACTCTGCCCTCGCTTGCAGTGTATTGCAATATACAGG
261 TTTGGCAGCAGTGCTCCAGTACTCCAGCACTCTGCCCTCGCTTGCAGTGTATTGCAATATACAGG
5476367 TTGTGTGACATATAACAAAGACAATTTTGCACAAGATGCATCAATTCATGACGAACAGTAGATCT
326 TTGTGTGACATATAACAAAGACAATTTTGCACAAGATGCATCAATTCATGACGAACAGTAGATCT
*
5476432 AACCCCAGAACAAGTGGCTGGATTCTTGGGTTTACTTCACTTTTAGGATGTCCTAGAGAGTATGA
391 AACCCCAGAACAAGTGGCTGGATTCTTGGGTTTACTTCACTTCTAGGATGTCCTAGAGAGTATGA
5476497 CTTTAAGGTTCAAACAGAGAGATTATTACAAAGTCTCTTCTTAACATTTTCCTTTGATACAAGTA
456 CTTTAAGGTTCAAACAGAGAGATTATTACAAAGTCTCTTCTTAACATTTTCCTTTGATACAAGTA
5476562 CTTCCATTTTCCCTCCTGAACTATGGCACATGTCTAGGTGTGCTGTCATGTAACCAACCTTTACT
521 CTTCCATTTTCCCTCCTGAACTATGGCACATGTCTAGGTGTGCTGTCATGTAACCAACCTTTACT
*
5476627 ACTTGTAACTATAATTCTCCCATGACTGGCTTTAACTCCTTGTAACTATTACCTATTCACCTTTG
586 ACTTGTAACTATAATTCTCCCATGACTGGCTTTAACTCCTTGTAACTATTACCTATTCACCTTGG
5476692 TATATTCTTTTGATGGGACTATAAACAGTGATCCAAAAGCTTCAGTTGGGATCATTGTGGTAAAG
651 TATATTCTTTTGATGGGACTATAAACAGTGATCCAAAAGCTTCAGTTGGGATCATTGTGGTAAAG
5476757 TGAAAACTTGAATTAATAAATTCTCTTCGCAACTTTCTCCATAAAATTATTCATCCACCGCAATT
716 TGAAAACTTGAATTAATAAATTCTCTTCGCAACTTTCTCCATAAAATTATTCATCCACCGCAATT
5476822 TCAATCTTCCTTAGCCATCTTTTTCCTTCACCGC
781 TCAATCTTCCTTAGCCATCTTTTTCCTTCACCGC
5476856 TACCA
1 TACCA
5476861 TCATCGCACT
Statistics
Matches: 815, Mismatches: 4, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
814 815 1.00
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.32
Consensus pattern (814 bp):
TACCAATCACTCCAGCTGCAGTCTTAACTTTAATTACAATTTATCAAATAGTAGGACTGTATTTC
AGTGGCTATAGATGCTTGTTTTTGGCTATTAACATGTCAGGCAGGCACATTTGATTGGGCAGTGC
ACTCTGGTAGTAGCGCTCCTTGGTAGCAGCATTCCTTAGCGACAACACTCCTTGGCAGCAGCACT
TCTTAGCAAGAGCACTCCTTGGCGACAACGCTCCTTAATGACAGCACTCCTTAGTGACAAAACTA
TTTGGCAGCAGTGCTCCAGTACTCCAGCACTCTGCCCTCGCTTGCAGTGTATTGCAATATACAGG
TTGTGTGACATATAACAAAGACAATTTTGCACAAGATGCATCAATTCATGACGAACAGTAGATCT
AACCCCAGAACAAGTGGCTGGATTCTTGGGTTTACTTCACTTCTAGGATGTCCTAGAGAGTATGA
CTTTAAGGTTCAAACAGAGAGATTATTACAAAGTCTCTTCTTAACATTTTCCTTTGATACAAGTA
CTTCCATTTTCCCTCCTGAACTATGGCACATGTCTAGGTGTGCTGTCATGTAACCAACCTTTACT
ACTTGTAACTATAATTCTCCCATGACTGGCTTTAACTCCTTGTAACTATTACCTATTCACCTTGG
TATATTCTTTTGATGGGACTATAAACAGTGATCCAAAAGCTTCAGTTGGGATCATTGTGGTAAAG
TGAAAACTTGAATTAATAAATTCTCTTCGCAACTTTCTCCATAAAATTATTCATCCACCGCAATT
TCAATCTTCCTTAGCCATCTTTTTCCTTCACCGC
Found at i:5478197 original size:29 final size:30
Alignment explanation
Indices: 5478162--5478222 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
5478152 ACAAAATAAA
* * *
5478162 ATTTTAATTTTTAATATTT-ATAATTTTTT
1 ATTTTAAATTATAATATTTAATAACTTTTT
*
5478191 ATTTTAAATTATAATTTTTAATAACTTTTT
1 ATTTTAAATTATAATATTTAATAACTTTTT
5478221 AT
1 AT
5478223 CTATAAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (30 bp):
ATTTTAAATTATAATATTTAATAACTTTTT
Found at i:5481801 original size:2 final size:2
Alignment explanation
Indices: 5481794--5481820 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5481784 GATAATATGC
5481794 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 A
5481821 GAGAGAGAGA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5481825 original size:2 final size:2
Alignment explanation
Indices: 5481820--5481850 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5481810 ATATATATAT
5481820 AG AG 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 AG AG A
5481851 CACACACACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5488413 original size:2 final size:2
Alignment explanation
Indices: 5488406--5488444 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
5488396 GTGACAAAAT
* *
5488406 GA GA GA GA GA GA GA GA GA GA GA CA GA GA GA GA GA AA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
5488445 GTCAGATAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.46, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5491225 original size:30 final size:30
Alignment explanation
Indices: 5491191--5491257 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
5491181 TGTATTTGCG
5491191 GCCGCCTTTTCCAAGAAAGACTTCGTCTCC
1 GCCGCCTTTTCCAAGAAAGACTTCGTCTCC
* *
5491221 GCCGCCTTTTCCATGAAAGGCTTCGTCTCC
1 GCCGCCTTTTCCAAGAAAGACTTCGTCTCC
5491251 GCCGCCT
1 GCCGCCT
5491258 CCTTCTATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.15, C:0.39, G:0.19, T:0.27
Consensus pattern (30 bp):
GCCGCCTTTTCCAAGAAAGACTTCGTCTCC
Found at i:5493597 original size:18 final size:20
Alignment explanation
Indices: 5493548--5493601 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
5493538 ATTAAAATTG
* *
5493548 ATTTGTAAATTTATTTTATT
1 ATTTATAAATTAATTTTATT
*
5493568 ATTTAAAAATTAATTTTA-T
1 ATTTATAAATTAATTTTATT
5493587 ATTT-TAAATTAATTT
1 ATTTATAAATTAATTT
5493602 AAATAAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 10 0.33
19 5 0.17
20 15 0.50
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
ATTTATAAATTAATTTTATT
Found at i:5493631 original size:24 final size:26
Alignment explanation
Indices: 5493603--5493650 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
5493593 AATTAATTTA
5493603 AATAA-AAATAAAATT-TATCAAATT
1 AATAATAAATAAAATTATATCAAATT
* *
5493627 AATAATAATTTAAATTATATCAAA
1 AATAATAAATAAAATTATATCAAA
5493651 CTGAATCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.25
25 8 0.40
26 7 0.35
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.35
Consensus pattern (26 bp):
AATAATAAATAAAATTATATCAAATT
Found at i:5493802 original size:17 final size:18
Alignment explanation
Indices: 5493780--5493816 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
5493770 TTTTTTAATA
*
5493780 TATTTAATAATTT-TATT
1 TATTTAAAAATTTATATT
5493797 TATTTAAAAATTTATATT
1 TATTTAAAAATTTATATT
5493815 TA
1 TA
5493817 ATGTATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TATTTAAAAATTTATATT
Found at i:5493878 original size:20 final size:20
Alignment explanation
Indices: 5493853--5493890 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5493843 TTAATAAATT
*
5493853 AAATAATATTATTTTATTAA
1 AAATAAAATTATTTTATTAA
5493873 AAATAAAATTATTTTATT
1 AAATAAAATTATTTTATT
5493891 TATTTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AAATAAAATTATTTTATTAA
Found at i:5493881 original size:25 final size:26
Alignment explanation
Indices: 5493841--5493891 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
5493831 TTTTATATAA
*
5493841 TATTAATAAATTAAATAATATTATTT
1 TATTAATAAATAAAATAATATTATTT
* *
5493867 TATTAA-AAATAAAATTATTTTATTT
1 TATTAATAAATAAAATAATATTATTT
5493892 ATTTTTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
TATTAATAAATAAAATAATATTATTT
Found at i:5494330 original size:22 final size:21
Alignment explanation
Indices: 5494299--5494339 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
5494289 GATTGTCCAG
*
5494299 CTCACAACTCAGTGACTCACCA
1 CTCACAACTCACTG-CTCACCA
*
5494321 CTCACTACTCACTGCTCAC
1 CTCACAACTCACTGCTCAC
5494340 TCATCTTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.27, C:0.44, G:0.07, T:0.22
Consensus pattern (21 bp):
CTCACAACTCACTGCTCACCA
Found at i:5520705 original size:19 final size:19
Alignment explanation
Indices: 5520678--5520716 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
5520668 ATGACTTCAG
*
5520678 ATTAGACCAATACAGCATA
1 ATTAAACCAATACAGCATA
* *
5520697 ATTAAACCAGTATAGCATA
1 ATTAAACCAATACAGCATA
5520716 A
1 A
5520717 CGTCAAGAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.18, G:0.10, T:0.23
Consensus pattern (19 bp):
ATTAAACCAATACAGCATA
Found at i:5525082 original size:463 final size:462
Alignment explanation
Indices: 5524183--5525086 Score: 1790
Period size: 463 Copynumber: 2.0 Consensus size: 462
5524173 AATTCACTCT
5524183 CCACAAAAATGTGTTTAATCTGCAAATATGAATGTCTGCCCCCTCCAAATCTGTTTACAAGAGCT
1 CCACAAAAATGTGTTTAATCTGCAAATATGAATGTCTGCCCCCTCCAAATCTGTTTACAAGAGCT
5524248 TATATATGCCCTCATAAGTCATAGATAACACAAACCCTAAGGGGCTTATTATGCTAACAAGCCCA
66 TATATATGCCCTCATAAGTCATAGATAACACAAACCCTAAGGGGCTTATTATGCTAACAAGCCCA
5524313 ACTCTTACTTAAACCCAAATAACAAGTTTTTATGCTAAATAAAGCCCAAAGCAAGTCACAACCAG
131 ACTCTTACTTAAACCCAAATAACAAGTTTTTATGCTAAATAAAGCCCAAAGCAAGTCACAACCAG
5524378 CAGGCCCTTTATTACAAAATAACCAAGTCCTAATTCAATCCATTGGAGCCCATATCTTCCAAATA
196 CAGGCCCTTTATTACAAAATAACCAAGTCCTAATTCAATCCATTGGAGCCCATATCTTCCAAATA
5524443 TATGCAATTAACTAGCTTGGGCTCTTCTAACTCCAAATTGGGTCTACTTTCAAATAGGCTAGCAA
261 TATGCAATTAACTAGCTTGGGCTCTTCTAACTCCAAATTGGGTCTACTTTCAAATAGGCTAGCAA
5524508 CCATCTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCGTTATTGGTCCTTGAAATCCT
326 CCATCTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCGTTATTGGTCCTTGAAATCCT
5524573 TCCAATGCCTTCAGGTCTTTGTCTTCAATGGACCTTCCTTGGTTTTCATCAACTCCTCCTTCTTC
391 TCCAATGCCTTCAGGTCTTTGTCTTCAATGGACCTTCCTTGGTTTTCATCAACTCCTCCTTCTTC
5524638 AAGAGAA
456 AAGAGAA
5524645 CCACAAAAATGTGTTTAATCTGCAAATATGAATGTCTGCCCCCTCCAAATCTGTTTACAAGAGCT
1 CCACAAAAATGTGTTTAATCTGCAAATATGAATGTCTGCCCCCTCCAAATCTGTTTACAAGAGCT
5524710 TATATATGCCCTCATAAGTCATAGATAACACAAACCCTAAGGGGCTTATTATGCTAACAAGCCCA
66 TATATATGCCCTCATAAGTCATAGATAACACAAACCCTAAGGGGCTTATTATGCTAACAAGCCCA
5524775 ACTCTTACTTAAACCCAAATAACAAGTTTTTATGCTAAATAAAGCCCAAAGCAAGTCACAACCAG
131 ACTCTTACTTAAACCCAAATAACAAGTTTTTATGCTAAATAAAGCCCAAAGCAAGTCACAACCAG
5524840 CAGGCCCTTTATTACAAAATAACCCAAGTCCTAATTCAATCCATTGGAGCCCATATCTTCCAAAT
196 CAGGCCCTTTATTACAAAATAA-CCAAGTCCTAATTCAATCCATTGGAGCCCATATCTTCCAAAT
*
5524905 ATATGCAATTAACTAGCTTGGGCTCTTCTAACTCCAAATTGGGTCTACTTTCAAATAGGCTAGTA
260 ATATGCAATTAACTAGCTTGGGCTCTTCTAACTCCAAATTGGGTCTACTTTCAAATAGGCTAGCA
5524970 ACCATCTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCGTTATTGGTCCTTGAAATCC
325 ACCATCTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCGTTATTGGTCCTTGAAATCC
5525035 TTCCAATGCCTTCAGGTCTTTGTCTTCAATGGACCTTCCTTGGTTTTCATCA
390 TTCCAATGCCTTCAGGTCTTTGTCTTCAATGGACCTTCCTTGGTTTTCATCA
5525087 GAGCCAAACC
Statistics
Matches: 440, Mismatches: 1, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
462 217 0.49
463 223 0.51
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (462 bp):
CCACAAAAATGTGTTTAATCTGCAAATATGAATGTCTGCCCCCTCCAAATCTGTTTACAAGAGCT
TATATATGCCCTCATAAGTCATAGATAACACAAACCCTAAGGGGCTTATTATGCTAACAAGCCCA
ACTCTTACTTAAACCCAAATAACAAGTTTTTATGCTAAATAAAGCCCAAAGCAAGTCACAACCAG
CAGGCCCTTTATTACAAAATAACCAAGTCCTAATTCAATCCATTGGAGCCCATATCTTCCAAATA
TATGCAATTAACTAGCTTGGGCTCTTCTAACTCCAAATTGGGTCTACTTTCAAATAGGCTAGCAA
CCATCTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCGTTATTGGTCCTTGAAATCCT
TCCAATGCCTTCAGGTCTTTGTCTTCAATGGACCTTCCTTGGTTTTCATCAACTCCTCCTTCTTC
AAGAGAA
Found at i:5533340 original size:2 final size:2
Alignment explanation
Indices: 5533333--5533373 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
5533323 CAGTTCCATA
5533333 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
5533374 AAAGAAAGAA
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:5553183 original size:2 final size:2
Alignment explanation
Indices: 5553170--5553205 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
5553160 CCGATAAAGA
*
5553170 AT AT AA 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
5553206 CTTATCACAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5556703 original size:8 final size:8
Alignment explanation
Indices: 5556690--5556728 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
5556680 GATTATTAAT
5556690 AAAAAGAA
1 AAAAAGAA
5556698 AAAAAGAA
1 AAAAAGAA
5556706 AAAAA-AA
1 AAAAAGAA
*
5556713 AGAAAGAA
1 AAAAAGAA
*
5556721 GAAAAGAA
1 AAAAAGAA
5556729 GTTGAGAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:5556712 original size:11 final size:12
Alignment explanation
Indices: 5556692--5556728 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
5556682 TTATTAATAA
5556692 AAAGAAAAAAAG
1 AAAGAAAAAAAG
5556704 AAA-AAAAAAAG
1 AAAGAAAAAAAG
*
5556715 AAAGAAGAAAAG
1 AAAGAAAAAAAG
5556727 AA
1 AA
5556729 GTTGAGAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.48
12 12 0.52
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAGAAAAAAAG
Found at i:5569378 original size:15 final size:15
Alignment explanation
Indices: 5569360--5569390 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5569350 ATAACAAGCC
5569360 TCTTTGATGTCCATG
1 TCTTTGATGTCCATG
*
5569375 TCTTTGATGTTCATG
1 TCTTTGATGTCCATG
5569390 T
1 T
5569391 ACATGCAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.16, G:0.19, T:0.52
Consensus pattern (15 bp):
TCTTTGATGTCCATG
Found at i:5573815 original size:24 final size:24
Alignment explanation
Indices: 5573788--5573837 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
5573778 AATATAAATA
* *
5573788 TTAAATGTTTTATATT-TTTTATAT
1 TTAAATATATTATATTATTTT-TAT
5573812 TTAAATATATTATATTATTTTTAT
1 TTAAATATATTATATTATTTTTAT
5573836 TT
1 TT
5573838 GTTAAGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (24 bp):
TTAAATATATTATATTATTTTTAT
Found at i:5573830 original size:27 final size:26
Alignment explanation
Indices: 5573788--5573870 Score: 68
Period size: 25 Copynumber: 3.3 Consensus size: 26
5573778 AATATAAATA
*
5573788 TTAAATGT-TTTA-TATTTTTTATAT
1 TTAAATATATTTATTATTTTTTATAT
*
5573812 TTAAATATATTATATTA-TTTTTATTT
1 TTAAATATATT-TATTATTTTTTATAT
* *
5573838 GTTAAGT-TATTTATT-TATTTTATAT
1 -TTAAATATATTTATTATTTTTTATAT
*
5573863 TTTAATAT
1 TTAAATAT
5573871 TATATTTAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
24 11 0.24
25 14 0.30
26 14 0.30
27 7 0.15
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (26 bp):
TTAAATATATTTATTATTTTTTATAT
Found at i:5573873 original size:26 final size:27
Alignment explanation
Indices: 5573796--5573873 Score: 78
Period size: 26 Copynumber: 3.0 Consensus size: 27
5573786 TATTAAATGT
*
5573796 TTTATATT-TTTTATATTTAAATA-TA
1 TTTATATTATTTTATATTTTAATATTA
*
5573821 -TTATATTATTTT-TATTTGTTAA-GTTA
1 TTTATATTATTTTATA-TT-TTAATATTA
5573847 TTTAT-TTATTTTATATTTTAATATTA
1 TTTATATTATTTTATATTTTAATATTA
5573873 T
1 T
5573874 ATTTAAATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
24 9 0.21
25 10 0.23
26 18 0.42
27 6 0.14
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (27 bp):
TTTATATTATTTTATATTTTAATATTA
Found at i:5574071 original size:3 final size:3
Alignment explanation
Indices: 5574065--5574109 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
5574055 TGTGTAGTAG
5574065 AAT AAT AAT AAT AAT AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5574110 CATATATAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5574539 original size:12 final size:11
Alignment explanation
Indices: 5574518--5574552 Score: 54
Period size: 12 Copynumber: 3.2 Consensus size: 11
5574508 TATGGTATGA
5574518 TTTC-TTTTCT
1 TTTCTTTTTCT
5574528 TTTCTTTTTTCT
1 TTTC-TTTTTCT
5574540 TTTCTTTTTCT
1 TTTCTTTTTCT
5574551 TT
1 TT
5574553 CTGTCAACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 4 0.17
11 9 0.39
12 10 0.43
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTCTTTTTCT
Found at i:5574540 original size:17 final size:18
Alignment explanation
Indices: 5574518--5574552 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
5574508 TATGGTATGA
5574518 TTTCTTTTC-TTTTCTTT
1 TTTCTTTTCTTTTTCTTT
5574535 TTTCTTTTCTTTTTCTTT
1 TTTCTTTTCTTTTTCTTT
5574553 CTGTCAACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTCTTTTCTTTTTCTTT
Found at i:5576077 original size:2 final size:2
Alignment explanation
Indices: 5576070--5576094 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5576060 CTTTTTCTTT
5576070 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 T
5576095 GTAAGGAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5580842 original size:6 final size:6
Alignment explanation
Indices: 5580833--5580889 Score: 60
Period size: 6 Copynumber: 9.2 Consensus size: 6
5580823 ATATTAAAAT
* * *
5580833 ATTTAA ATTTAA ATTTAA ATTTAA ATATAA ATAATTAA GTTTAA AATTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT--TTAA ATTTAA ATTTAA
*
5580883 ATATAA A
1 ATTTAA A
5580890 AATTAATTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
6 38 0.90
8 4 0.10
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (6 bp):
ATTTAA
Found at i:5580870 original size:26 final size:25
Alignment explanation
Indices: 5580841--5580895 Score: 83
Period size: 26 Copynumber: 2.2 Consensus size: 25
5580831 ATATTTAAAT
*
5580841 TTAAATTTAAATTTAAATATAAATAA
1 TTAAATTTAAAATTAAATATAAA-AA
*
5580867 TTAAGTTTAAAATTAAATATAAAAA
1 TTAAATTTAAAATTAAATATAAAAA
5580892 TTAA
1 TTAA
5580896 TTTTTTTACT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 6 0.22
26 21 0.78
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
TTAAATTTAAAATTAAATATAAAAA
Found at i:5588893 original size:2 final size:2
Alignment explanation
Indices: 5588886--5588921 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5588876 ACCCCGCGGC
5588886 GA GA GA GA GA 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 GA GA GA GA GA
5588922 ATCTAAGTCG
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5589978 original size:2 final size:2
Alignment explanation
Indices: 5589973--5590014 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
5589963 TTATATATAA
5589973 AG AG AG AG AG AG 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 AG AG AG AG AG AG
5590015 TTTACACATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5590090 original size:2 final size:2
Alignment explanation
Indices: 5590083--5590124 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
5590073 AAAGTACCAA
5590083 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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
5590124 A
1 A
5590125 CTAAATAAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5592010 original size:12 final size:12
Alignment explanation
Indices: 5591993--5592033 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
5591983 TTTACAATTA
5591993 ATAATAAATAAT
1 ATAATAAATAAT
*
5592005 ATAATAAATAAA
1 ATAATAAATAAT
5592017 ATTAATAAAATAAT
1 A-TAAT-AAATAAT
5592031 ATA
1 ATA
5592034 TATTTTTGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 12 0.48
13 6 0.24
14 7 0.28
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAATAAATAAT
Found at i:5595823 original size:20 final size:21
Alignment explanation
Indices: 5595774--5595824 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 21
5595764 AATTATTTTT
*
5595774 ATTTTA-ATAA-AATGATATA
1 ATTTTATATAATAATGATAAA
5595793 ATTTTAT-TAATAATG-TAAA
1 ATTTTATATAATAATGATAAA
5595812 ATTTTATATAATA
1 ATTTTATATAATA
5595825 TATATTAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 19 0.68
20 9 0.32
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (21 bp):
ATTTTATATAATAATGATAAA
Found at i:5605234 original size:13 final size:13
Alignment explanation
Indices: 5605216--5605304 Score: 70
Period size: 13 Copynumber: 5.9 Consensus size: 13
5605206 CATAAAGTGT
5605216 TGTATCGATACAA
1 TGTATCGATACAA
5605229 TGTATCGATACATAA
1 TGTATCGATAC--AA
5605244 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
5605261 TGTATCGATACATAA
1 TGTATCGATAC--AA
5605276 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
5605293 TGTATCGATACA
1 TGTATCGATACA
5605305 TAAGTTTTGT
Statistics
Matches: 64, Mismatches: 0, Indels: 24
0.73 0.00 0.27
Matches are distributed among these distances:
13 34 0.53
15 4 0.06
17 4 0.06
19 22 0.34
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5605251 original size:32 final size:32
Alignment explanation
Indices: 5605196--5605325 Score: 242
Period size: 32 Copynumber: 4.0 Consensus size: 32
5605186 TTCAACAATT
5605196 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
5605229 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
5605261 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
5605293 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
5605325 T
1 T
5605326 ATAAGCTACT
Statistics
Matches: 96, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
32 83 0.86
33 13 0.14
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:5605253 original size:19 final size:18
Alignment explanation
Indices: 5605194--5605323 Score: 110
Period size: 19 Copynumber: 7.8 Consensus size: 18
5605184 ATTTCAACAA
5605194 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
5605213 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
5605229 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
5605245 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
5605261 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
5605277 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
5605293 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
5605309 TTTTGTATCGATACA
1 -TTTGTATCGATACA
5605324 ATATAAGCTA
Statistics
Matches: 92, Mismatches: 0, Indels: 38
0.71 0.00 0.29
Matches are distributed among these distances:
13 33 0.36
15 6 0.07
17 6 0.07
19 35 0.38
20 12 0.13
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:5605428 original size:52 final size:52
Alignment explanation
Indices: 5605344--5605494 Score: 212
Period size: 52 Copynumber: 2.9 Consensus size: 52
5605334 CTGCCAAAAA
* * * *
5605344 ATGTATCGATACATTACTTAAATGCATCGATACACGCAGGTAAATTTGTCCAG
1 ATGTATCGATACACTA-TTAAATGTATCGATACACGCAGGCAAATTTGCCCAG
* *
5605397 ATGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAG
1 ATGTATCGATACACTATTAAATGTATCGATACACGCAGGCAAATTTGCCCAG
* * *
5605449 ATATATCGATACACTATTAAATGTATCGATACATGTAGGCAAATTT
1 ATGTATCGATACACTATTAAATGTATCGATACACGCAGGCAAATTT
5605495 TCATATTTCG
Statistics
Matches: 89, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
52 74 0.83
53 15 0.17
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.30
Consensus pattern (52 bp):
ATGTATCGATACACTATTAAATGTATCGATACACGCAGGCAAATTTGCCCAG
Found at i:5605586 original size:21 final size:21
Alignment explanation
Indices: 5605560--5605609 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
5605550 GTCAGGATTA
5605560 ATGTCAAATATCAATTGCTAC
1 ATGTCAAATATCAATTGCTAC
5605581 ATGTCAAATATCAATTGCTAC
1 ATGTCAAATATCAATTGCTAC
*
5605602 ATGCCAAA
1 ATGTCAAA
5605610 ACACACTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (21 bp):
ATGTCAAATATCAATTGCTAC
Found at i:5609045 original size:11 final size:11
Alignment explanation
Indices: 5609029--5609061 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
5609019 AATTTTTTTA
5609029 TATTTAAAATT
1 TATTTAAAATT
*
5609040 TATTTATAATT
1 TATTTAAAATT
5609051 T-TTTAAAATT
1 TATTTAAAATT
5609061 T
1 T
5609062 TATCTAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TATTTAAAATT
Found at i:5609498 original size:18 final size:19
Alignment explanation
Indices: 5609463--5609509 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
5609453 TTTTAAAAAA
5609463 ATTTATATAATTCATCATT
1 ATTTATATAATTCATCATT
5609482 ATTT-TATAATGTC-TCATGT
1 ATTTATATAAT-TCATCAT-T
*
5609501 ATATATATA
1 ATTTATATA
5609510 TATATACACA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 10 0.42
19 10 0.42
20 4 0.17
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.51
Consensus pattern (19 bp):
ATTTATATAATTCATCATT
Found at i:5610010 original size:5 final size:5
Alignment explanation
Indices: 5610000--5610154 Score: 61
Period size: 5 Copynumber: 30.6 Consensus size: 5
5609990 CAATTAAACG
* * *
5610000 TAATA TAATA TGATA TTAAAA TAATA TAATA TAA-A -AAGTA AAATA -AATA
1 TAATA TAATA TAATA -TAATA TAATA TAATA TAATA TAA-TA TAATA TAATA
* * * * * * *
5610049 AAATA TAATT TTATA TAATA TAA-A TTAT- TAATA TATTA AAAT- TTATA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA
* * * * *
5610096 TAAACA TAAAA TATTT TAAATA TAATAA TAATAA AAATA TAAATA TAATA
1 T-AATA TAATA TAATA T-AATA TAAT-A TAAT-A TAATA T-AATA TAATA
5610146 TAAATA TAA
1 T-AATA TAA
5610155 AAATTATGAA
Statistics
Matches: 111, Mismatches: 26, Indels: 26
0.68 0.16 0.16
Matches are distributed among these distances:
3 2 0.02
4 13 0.12
5 65 0.59
6 31 0.28
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (5 bp):
TAATA
Found at i:5610025 original size:16 final size:15
Alignment explanation
Indices: 5610004--5610156 Score: 59
Period size: 17 Copynumber: 10.1 Consensus size: 15
5609994 TAAACGTAAT
*
5610004 ATAATATGATATTAAA
1 ATAATATAATA-TAAA
5610020 ATAATATAATATAAA
1 ATAATATAATATAAA
*
5610035 A-AGTA-AA-ATAAA
1 ATAATATAATATAAA
* * * *
5610047 TAAAATATAATTTTAT
1 -ATAATATAATATAAA
*
5610063 ATAATATAA-AT-TA
1 ATAATATAATATAAA
*
5610076 TTAATAT-AT-TAAA
1 ATAATATAATATAAA
* *
5610089 ATTTATATAAACATAAA
1 A-TAATAT-AATATAAA
* *
5610106 ATATTTTAAATATAATA
1 ATAATAT-AATATAA-A
*
5610123 ATAATAAAAATATAAA
1 ATAAT-ATAATATAAA
5610139 TATAATATAAATATAAA
1 -ATAATAT-AATATAAA
5610156 A
1 A
5610157 ATTATGAATA
Statistics
Matches: 100, Mismatches: 23, Indels: 28
0.66 0.15 0.19
Matches are distributed among these distances:
12 7 0.07
13 10 0.10
14 12 0.12
15 15 0.15
16 26 0.26
17 30 0.30
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (15 bp):
ATAATATAATATAAA
Found at i:5610133 original size:17 final size:17
Alignment explanation
Indices: 5610113--5610155 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
5610103 AAAATATTTT
5610113 AAATAT-AATAATAATAA
1 AAATATAAAT-ATAATAA
*
5610130 AAATATAAATATAATAT
1 AAATATAAATATAATAA
5610147 AAATATAAA
1 AAATATAAA
5610156 AATTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 21 0.88
18 3 0.12
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AAATATAAATATAATAA
Found at i:5610137 original size:11 final size:11
Alignment explanation
Indices: 5610112--5610154 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
5610102 TAAAATATTT
5610112 TAAATATAATA
1 TAAATATAATA
*
5610123 -ATAATAAAAATA
1 TA-AAT-ATAATA
5610135 TAAATATAATA
1 TAAATATAATA
5610146 TAAATATAA
1 TAAATATAA
5610155 AAATTATGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
10 1 0.04
11 17 0.63
12 8 0.30
13 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAATATAATA
Found at i:5610142 original size:23 final size:26
Alignment explanation
Indices: 5610061--5610168 Score: 91
Period size: 25 Copynumber: 4.2 Consensus size: 26
5610051 ATATAATTTT
*
5610061 ATATAATATAAATTATTAATATATTA-AA
1 ATATAATATAAA-TA-TAA-AAATTATAA
* * *
5610089 AT-TTATATAAACATAAAATATTTTAA
1 ATATAATATAAATATAAAA-ATTATAA
*
5610115 ATATAATA-ATA-ATAAAAA-TATAA
1 ATATAATATAAATATAAAAATTATAA
*
5610138 ATATAATATAAATATAAAAATTATGA
1 ATATAATATAAATATAAAAATTATAA
5610164 ATATA
1 ATATA
5610169 TGTGTGCATA
Statistics
Matches: 65, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
23 12 0.18
24 4 0.06
25 19 0.29
26 16 0.25
27 12 0.18
28 2 0.03
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (26 bp):
ATATAATATAAATATAAAAATTATAA
Found at i:5614710 original size:2 final size:2
Alignment explanation
Indices: 5614705--5614740 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
5614695 ATGTGTGTGT
*
5614705 GA GA GA GA GA GA AA GA GA GA GA GA GA GA GA GTA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G-A GA G
5614741 GTTAAGCTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.47, T:0.03
Consensus pattern (2 bp):
GA
Found at i:5622961 original size:90 final size:90
Alignment explanation
Indices: 5622860--5623036 Score: 291
Period size: 90 Copynumber: 2.0 Consensus size: 90
5622850 AAAAAATTTG
* * * * * *
5622860 ATTATTACTTTATTTAGATAGTTTTTAATTTATTATATTTAAATAAATTTTTAACATTTAATTTA
1 ATTATTACTTTATTTAAATAATATTTAATTAACTACATTTAAATAAATTTTTAACATTTAATTTA
5622925 TATCTAAATAAAAATCATTAACTCT
66 TATCTAAATAAAAATCATTAACTCT
*
5622950 ATTATTACTTTATTTAAATAATATTTAATTAACTACATTTAAATAAATTTTTAATATTTAATTTA
1 ATTATTACTTTATTTAAATAATATTTAATTAACTACATTTAAATAAATTTTTAACATTTAATTTA
5623015 TATCTAAATAAAAATCATTAAC
66 TATCTAAATAAAAATCATTAAC
5623037 ATTTAATTTG
Statistics
Matches: 80, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 80 1.00
ACGTcount: A:0.43, C:0.07, G:0.01, T:0.49
Consensus pattern (90 bp):
ATTATTACTTTATTTAAATAATATTTAATTAACTACATTTAAATAAATTTTTAACATTTAATTTA
TATCTAAATAAAAATCATTAACTCT
Found at i:5624379 original size:15 final size:14
Alignment explanation
Indices: 5624359--5624388 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
5624349 GACGTGTCGC
5624359 ATGATATAATATAAT
1 ATGATATAAT-TAAT
5624374 ATGATATAATTAAT
1 ATGATATAATTAAT
5624388 A
1 A
5624389 AAAAGAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (14 bp):
ATGATATAATTAAT
Found at i:5635181 original size:19 final size:18
Alignment explanation
Indices: 5635157--5635193 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
5635147 CTCGCGCAGG
5635157 TTTTTTTTTCCTCTCTTTT
1 TTTTTTTTTCCT-TCTTTT
5635176 TTTTTTTTTCCTTCTTTT
1 TTTTTTTTTCCTTCTTTT
5635194 GGGCTATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTTTTTTTCCTTCTTTT
Found at i:5637239 original size:24 final size:24
Alignment explanation
Indices: 5637194--5637239 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
5637184 ATTATTTATA
* *
5637194 TAATTAAAAAAATTTATTTAAATT
1 TAATTAAAAAAATTAATATAAATT
* *
5637218 TAATTATAAATATTAATATAAA
1 TAATTAAAAAAATTAATATAAA
5637240 AATTTTTAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
TAATTAAAAAAATTAATATAAATT
Found at i:5643057 original size:16 final size:15
Alignment explanation
Indices: 5643031--5643065 Score: 61
Period size: 16 Copynumber: 2.3 Consensus size: 15
5643021 TATAATATAA
5643031 AATTTTAATTTTTAT
1 AATTTTAATTTTTAT
5643046 AATTTATAATTTTTAT
1 AATTT-TAATTTTTAT
5643062 AATT
1 AATT
5643066 CAAATTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
AATTTTAATTTTTAT
Found at i:5643149 original size:18 final size:19
Alignment explanation
Indices: 5643126--5643162 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
5643116 AAATAACTTA
*
5643126 ATTATTTTTAAT-TTTTTT
1 ATTATTTTAAATATTTTTT
5643144 ATTATTTTAAATATTTTTT
1 ATTATTTTAAATATTTTTT
5643163 TTCTTACATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (19 bp):
ATTATTTTAAATATTTTTT
Found at i:5647752 original size:16 final size:15
Alignment explanation
Indices: 5647731--5647797 Score: 52
Period size: 14 Copynumber: 4.5 Consensus size: 15
5647721 ATAAAATTTT
5647731 TAATTAAATAATATTA
1 TAATTAAATAA-ATTA
*
5647747 TAATT-AATAAATTT
1 TAATTAAATAAATTA
*
5647761 TATTTAAA-AATATT-
1 TAATTAAATAA-ATTA
5647775 TAA-TAAATAAATTTA
1 TAATTAAATAAA-TTA
*
5647790 AAATTAAA
1 TAATTAAA
5647798 ATTTACTCAT
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
13 5 0.12
14 15 0.37
15 12 0.29
16 9 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TAATTAAATAAATTA
Found at i:5647799 original size:28 final size:29
Alignment explanation
Indices: 5647732--5647798 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
5647722 TAAAATTTTT
* *
5647732 AATTAAATAATATTATAATTAATAAATTTT
1 AATTAAA-AATATTATAATAAATAAATTTA
*
5647762 ATTTAAAAATATT-TAATAAATAAATTTAA
1 AATTAAAAATATTATAATAAATAAATTT-A
5647791 AATTAAAA
1 AATTAAAA
5647799 TTTACTCATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 13 0.41
29 13 0.41
30 6 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
AATTAAAAATATTATAATAAATAAATTTA
Found at i:5647846 original size:17 final size:17
Alignment explanation
Indices: 5647821--5647854 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5647811 AAAAATTATA
*
5647821 TAAATTATGAGATAAAT
1 TAAAATATGAGATAAAT
*
5647838 TAAAATATGATATAAAT
1 TAAAATATGAGATAAAT
5647855 ATAATATAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (17 bp):
TAAAATATGAGATAAAT
Found at i:5648275 original size:11 final size:12
Alignment explanation
Indices: 5648228--5648279 Score: 65
Period size: 12 Copynumber: 4.5 Consensus size: 12
5648218 ATACATGAAT
5648228 ATAATATAAAGA
1 ATAATATAAAGA
5648240 ATAAT-TAAAGCA
1 ATAATATAAAG-A
*
5648252 A-AATATAAAAA
1 ATAATATAAAGA
5648263 ATAATATAAA-A
1 ATAATATAAAGA
5648274 ATAATA
1 ATAATA
5648280 CAAATAAGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
11 17 0.47
12 19 0.53
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (12 bp):
ATAATATAAAGA
Found at i:5648279 original size:23 final size:23
Alignment explanation
Indices: 5648228--5648279 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
5648218 ATACATGAAT
*
5648228 ATAATATAAAGAATAATTAAAGCA
1 ATAATATAAAAAATAATTAAA-CA
5648252 A-AATATAAAAAATAATATAAA-A
1 ATAATATAAAAAATAAT-TAAACA
5648274 ATAATA
1 ATAATA
5648280 CAAATAAGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 2 0.08
23 18 0.72
24 5 0.20
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (23 bp):
ATAATATAAAAAATAATTAAACA
Found at i:5648801 original size:20 final size:20
Alignment explanation
Indices: 5648762--5648799 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
5648752 ATATGATATA
*
5648762 ATACATAAAAATATAAAAAT
1 ATACATAAAAATAAAAAAAT
5648782 ATACAT-AAAATAAAAAAA
1 ATACATAAAAATAAAAAAA
5648800 ATTATTAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (20 bp):
ATACATAAAAATAAAAAAAT
Found at i:5648893 original size:16 final size:15
Alignment explanation
Indices: 5648872--5648923 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
5648862 AACACACAAA
5648872 TTTTTTTATCTCTCTT
1 TTTTTTTAT-TCTCTT
*
5648888 TTTTTTTCTTCTTCTT
1 TTTTTTTATTC-TCTT
* *
5648904 TTCTTTCATTC-CTT
1 TTTTTTTATTCTCTT
5648918 TTTTTT
1 TTTTTT
5648924 CTCTCCTTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
14 8 0.27
15 2 0.07
16 20 0.67
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTTTATTCTCTT
Done.