Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 176 of 279
Found at i:57984749 original size:41 final size:41
Alignment explanation
Indices: 57984704--57984791 Score: 115
Period size: 41 Copynumber: 2.1 Consensus size: 41
57984694 TGTCAAAAAC
57984704 ACTTTCTAACTATAAAACTTAACATATCAAACATTAGAAA-T
1 ACTTTCTAACTATAAAACTTAACATATCAAACATTA-AAATT
* * * * *
57984745 ACTTTTTAAGTATAAAATTTAATATATTAAACATTAAAATT
1 ACTTTCTAACTATAAAACTTAACATATCAAACATTAAAATT
57984786 ACTTTC
1 ACTTTC
57984792 CTACTAATTA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
40 3 0.08
41 37 0.93
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.39
Consensus pattern (41 bp):
ACTTTCTAACTATAAAACTTAACATATCAAACATTAAAATT
Found at i:58000774 original size:13 final size:13
Alignment explanation
Indices: 58000756--58000795 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
58000746 CATTTTACTT
58000756 GTTGAAACCGTGG
1 GTTGAAACCGTGG
*
58000769 GTTGAAACTGTGG
1 GTTGAAACCGTGG
*
58000782 GTTGAAATCGTGG
1 GTTGAAACCGTGG
58000795 G
1 G
58000796 CAAAACGGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.23, C:0.10, G:0.40, T:0.28
Consensus pattern (13 bp):
GTTGAAACCGTGG
Found at i:58003322 original size:25 final size:25
Alignment explanation
Indices: 58003206--58003309 Score: 136
Period size: 25 Copynumber: 4.2 Consensus size: 25
58003196 GACACACCAC
* * *
58003206 AGCTCTCATGAGCTTCCCGATATAC
1 AGCTCGCATGAGCTTCCCGTTATAT
* *
58003231 AGCTCGCATGAGCTTCCCCTTATTT
1 AGCTCGCATGAGCTTCCCGTTATAT
* *
58003256 AGCTCCCATGAGCTTCCCGTTATTT
1 AGCTCGCATGAGCTTCCCGTTATAT
*
58003281 AGCTCACATGAGCTTCCCGTTATAT
1 AGCTCGCATGAGCTTCCCGTTATAT
58003306 AGCT
1 AGCT
58003310 TGGAAGAGCT
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 70 1.00
ACGTcount: A:0.20, C:0.31, G:0.16, T:0.33
Consensus pattern (25 bp):
AGCTCGCATGAGCTTCCCGTTATAT
Found at i:58011313 original size:15 final size:16
Alignment explanation
Indices: 58011279--58011316 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
58011269 ACGTTTTATT
58011279 TAAAAACTAAACAACA
1 TAAAAACTAAACAACA
*
58011295 -AAAAACTAAA-ACCA
1 TAAAAACTAAACAACA
58011309 TAAAAACT
1 TAAAAACT
58011317 TAGAGCTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 3 0.15
15 17 0.85
ACGTcount: A:0.68, C:0.18, G:0.00, T:0.13
Consensus pattern (16 bp):
TAAAAACTAAACAACA
Found at i:58012271 original size:26 final size:27
Alignment explanation
Indices: 58012242--58012294 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
58012232 ATGTATACCG
* * *
58012242 AATAATACGTAATAATA-TTAAAATAA
1 AATAATAAGTAACAATAGTGAAAATAA
58012268 AATAATAAGTAACAATAGTGAAAATAA
1 AATAATAAGTAACAATAGTGAAAATAA
58012295 TAAGTATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.62, C:0.04, G:0.08, T:0.26
Consensus pattern (27 bp):
AATAATAAGTAACAATAGTGAAAATAA
Found at i:58012603 original size:3 final size:3
Alignment explanation
Indices: 58012585--58012627 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
58012575 AAATATACAT
* * *
58012585 TAA TAT TAA CAA TAA TAA TAA TAA TAC TAA TAA TAA TAA -AA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
58012628 CAAAAAAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:58012875 original size:22 final size:23
Alignment explanation
Indices: 58012829--58012888 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
58012819 GATACTAAAA
* *
58012829 AGAAAATATATAAATATATAGGAT
1 AGAAAATAGAT-AATAAATAGGAT
*
58012853 AGAAAATA-ATAATAAATATGAT
1 AGAAAATAGATAATAAATAGGAT
*
58012875 A-ATAATAGATAATA
1 AGAAAATAGATAATA
58012889 GCAAAAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 5 0.16
22 17 0.53
23 2 0.06
24 8 0.25
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (23 bp):
AGAAAATAGATAATAAATAGGAT
Found at i:58013563 original size:8 final size:7
Alignment explanation
Indices: 58013550--58013598 Score: 50
Period size: 8 Copynumber: 7.0 Consensus size: 7
58013540 GTGTATAAGT
58013550 AGAAAAGA
1 AGAAAA-A
58013558 AGAAAAA
1 AGAAAAA
58013565 TAGAAAAA
1 -AGAAAAA
58013573 TAG--AAA
1 -AGAAAAA
58013579 A-AAAAA
1 AGAAAAA
58013585 AGAAAAA
1 AGAAAAA
58013592 AGAAAAA
1 AGAAAAA
58013599 GACCGATTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
5 1 0.03
6 7 0.19
7 13 0.35
8 16 0.43
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (7 bp):
AGAAAAA
Found at i:58013582 original size:19 final size:18
Alignment explanation
Indices: 58013552--58013598 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 18
58013542 GTATAAGTAG
* *
58013552 AAAAGAAGAAAAATAGAA
1 AAAAGAAAAAAAAAAGAA
58013570 AAATAGAAAAAAAAAAGAA
1 AAA-AGAAAAAAAAAAGAA
58013589 AAAAGAAAAA
1 AAAAGAAAAA
58013599 GACCGATTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (18 bp):
AAAAGAAAAAAAAAAGAA
Found at i:58024328 original size:68 final size:67
Alignment explanation
Indices: 58024243--58024437 Score: 205
Period size: 68 Copynumber: 2.9 Consensus size: 67
58024233 AAGGAGATTT
* * * * *
58024243 AAATGTGTAAGACCATAGTTCGATTATGGCAATATAGAGGGTCCACCAGGACATTAAGCATTTGG
1 AAATGTGTAAGACCATAGCTCGACTATGACAACATAGAGGGTCCACCAGGACATTAA--ATATGG
58024308 -GTA
64 TGTA
* * *
58024311 AAATGTGTGAGACCATAGCTCGACTATGACAACATAGAGGGTCTACCATGACATTAAATATGGTG
1 AAATGTGTAAGACCATAGCTCGACTATGACAACATAGAGGGTCCACCAGGACATTAAATATGGTG
58024376 TA
66 TA
* * * * * * * *
58024378 AAATGTGTAAGACCATGGCTAGGCTATGGCAGCATATG-GAGTTCACCAGGACAATAAATA
1 AAATGTGTAAGACCATAGCTCGACTATGACAACATA-GAGGGTCCACCAGGACATTAAATA
58024438 CGGGGTAGTC
Statistics
Matches: 106, Mismatches: 19, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
66 5 0.05
67 50 0.47
68 51 0.48
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (67 bp):
AAATGTGTAAGACCATAGCTCGACTATGACAACATAGAGGGTCCACCAGGACATTAAATATGGTG
TA
Found at i:58038728 original size:18 final size:18
Alignment explanation
Indices: 58038701--58038996 Score: 193
Period size: 18 Copynumber: 16.1 Consensus size: 18
58038691 TCATTAACAA
* *
58038701 TCAG-AACAATTATTTAT
1 TCAGTAACAATCAATTAT
*
58038718 TCAGTAACAATCACTTAT
1 TCAGTAACAATCAATTAT
*
58038736 TCGGTAACAATCAATTAT
1 TCAGTAACAATCAATTAT
* * * *
58038754 TCAATAATAACCAGTTAT
1 TCAGTAACAATCAATTAT
* *
58038772 TCAGTATCGATCAATTGATCGGTT
1 TCAGTAACAATCAATT-A-----T
* *
58038796 ATCCAATAACAGTCAATTAT
1 -T-CAGTAACAATCAATTAT
*
58038816 TTAGTAA-AATCAGA-TAT
1 TCAGTAACAATCA-ATTAT
* *
58038833 TCAGTAGCAATTAAGTTAT
1 TCAGTAACAATCAA-TTAT
* *
58038852 TCAGTAACAGTCACTTAT
1 TCAGTAACAATCAATTAT
* *
58038870 TCAGTGACAATCAGTTAT
1 TCAGTAACAATCAATTAT
**
58038888 TCAGTAATGATCAATTAT
1 TCAGTAACAATCAATTAT
* * *
58038906 TCAGTAATATTCAGTTAT
1 TCAGTAACAATCAATTAT
* *
58038924 TCAGTAACAGTCTATTAT
1 TCAGTAACAATCAATTAT
* *
58038942 CCAGTAACAGTCAATTAT
1 TCAGTAACAATCAATTAT
* *
58038960 TCGGTAACAGTCAATTAT
1 TCAGTAACAATCAATTAT
* *
58038978 TCAGTAATAATCAGTTAT
1 TCAGTAACAATCAATTAT
58038996 T
1 T
58038997 TTATACCTTT
Statistics
Matches: 215, Mismatches: 51, Indels: 25
0.74 0.18 0.09
Matches are distributed among these distances:
17 17 0.08
18 168 0.78
19 15 0.07
20 1 0.00
24 1 0.00
25 2 0.01
26 11 0.05
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (18 bp):
TCAGTAACAATCAATTAT
Found at i:58038929 original size:72 final size:72
Alignment explanation
Indices: 58038794--58038996 Score: 216
Period size: 72 Copynumber: 2.8 Consensus size: 72
58038784 AATTGATCGG
* * * * ** *
58038794 TTATCCAATAACAGTCAATTATTTAGTAA-AATCAGA-TATTCAGTAGCAATTAAGTTATTCAGT
1 TTATCCAGTAACAATCAATTATTCAGTAACAGTCA-ATTATTCAGTAATAA-TCAGTTATTCAGT
58038857 AACAGTC-A
64 AACAGTCTA
* * * * *
58038865 CTTATTCAGTGACAATCAGTTATTCAGTAA-TGATCAATTATTCAGTAATATTCAGTTATTCAGT
1 -TTATCCAGTAACAATCAATTATTCAGTAACAG-TCAATTATTCAGTAATAATCAGTTATTCAGT
58038929 AACAGTCTA
64 AACAGTCTA
* *
58038938 TTATCCAGTAACAGTCAATTATTCGGTAACAGTCAATTATTCAGTAATAATCAGTTATT
1 TTATCCAGTAACAATCAATTATTCAGTAACAGTCAATTATTCAGTAATAATCAGTTATT
58038997 TTATACCTTT
Statistics
Matches: 108, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
72 93 0.86
73 15 0.14
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (72 bp):
TTATCCAGTAACAATCAATTATTCAGTAACAGTCAATTATTCAGTAATAATCAGTTATTCAGTAA
CAGTCTA
Found at i:58039230 original size:30 final size:30
Alignment explanation
Indices: 58039194--58039254 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
58039184 ACACAAAGTG
58039194 TTGAATCGATAACAGTAACAGTAACAGTAT
1 TTGAATCGATAACAGTAACAGTAACAGTAT
58039224 TTGAATCGATAACAGTAACAGTAACAGTAT
1 TTGAATCGATAACAGTAACAGTAACAGTAT
58039254 T
1 T
58039255 CGACACATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (30 bp):
TTGAATCGATAACAGTAACAGTAACAGTAT
Found at i:58039282 original size:75 final size:75
Alignment explanation
Indices: 58039158--58039297 Score: 217
Period size: 75 Copynumber: 1.9 Consensus size: 75
58039148 TCCAGAACAG
* *
58039158 TAACAATAACAGTAACAGTATTCAACACACAAAGTGTTGAATCGATAACAGTAACAGTAACAGTA
1 TAACAATAACAGTAACAGTATTCAACACACAAAGTGTCGAATAGATAACAGTAACAGTAACAGTA
58039223 TTTGAATCGA
66 TTTGAATCGA
* * * * *
58039233 TAACAGTAACAGTAACAGTATTCGACACATAAAGTGTCGAATAGGTAACAGTAACGGTAACAGTA
1 TAACAATAACAGTAACAGTATTCAACACACAAAGTGTCGAATAGATAACAGTAACAGTAACAGTA
58039298 ACAGTAGTCG
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
75 58 1.00
ACGTcount: A:0.44, C:0.16, G:0.17, T:0.23
Consensus pattern (75 bp):
TAACAATAACAGTAACAGTATTCAACACACAAAGTGTCGAATAGATAACAGTAACAGTAACAGTA
TTTGAATCGA
Found at i:58040011 original size:6 final size:6
Alignment explanation
Indices: 58040000--58040026 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
58039990 AAACCCCAAA
58040000 TTTTTC TTTTTC TTTTTC TTTTTC TTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTT
58040027 CTTTCTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTC
Found at i:58040087 original size:9 final size:10
Alignment explanation
Indices: 58040041--58040090 Score: 57
Period size: 11 Copynumber: 4.9 Consensus size: 10
58040031 CTTTCTCCCA
58040041 TGTTTCTTCTC
1 TGTTTCTT-TC
58040052 TGTTTCGTTTC
1 TGTTTC-TTTC
**
58040063 AATTTCTTTC
1 TGTTTCTTTC
58040073 TGTTTCTTT-
1 TGTTTCTTTC
58040082 TGTTTCTTT
1 TGTTTCTTT
58040091 ACTTATTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
9 9 0.26
10 11 0.32
11 12 0.35
12 2 0.06
ACGTcount: A:0.04, C:0.18, G:0.10, T:0.68
Consensus pattern (10 bp):
TGTTTCTTTC
Found at i:58042193 original size:53 final size:48
Alignment explanation
Indices: 58042114--58042320 Score: 206
Period size: 47 Copynumber: 4.2 Consensus size: 48
58042104 CATGGCAACA
* * *
58042114 TGTGATATGTGATTTCTGTATAAGACCATAGCTGGGCTATGGCATCGGAG
1 TGTGATATGTG-CTTCCGTATAAGACCATAGCTGGGATATGGCATC-GAG
*
58042164 ATATGTGATTATGTGCTTCCGTATAAGACCATATCTGGGATATGGCATCG-G
1 ---TGTGA-TATGTGCTTCCGTATAAGACCATAGCTGGGATATGGCATCGAG
* * *
58042215 TGTGATATGTGCTACTGTATAAGACCATATCTGGGATATGGCATC-AG
1 TGTGATATGTGCTTCCGTATAAGACCATAGCTGGGATATGGCATCGAG
* * * * *
58042262 TGTGATATGTG-ATCCGTGTAAGACCATGGCTGGGCTATGGCTTCG-G
1 TGTGATATGTGCTTCCGTATAAGACCATAGCTGGGATATGGCATCGAG
58042308 TGTGTAATATGTG
1 TGTG--ATATGTG
58042321 ACTATGTGCA
Statistics
Matches: 135, Mismatches: 14, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
46 30 0.22
47 50 0.37
48 12 0.09
51 1 0.01
52 1 0.01
53 35 0.26
54 6 0.04
ACGTcount: A:0.24, C:0.14, G:0.29, T:0.33
Consensus pattern (48 bp):
TGTGATATGTGCTTCCGTATAAGACCATAGCTGGGATATGGCATCGAG
Found at i:58042310 original size:93 final size:98
Alignment explanation
Indices: 58042114--58042339 Score: 257
Period size: 93 Copynumber: 2.3 Consensus size: 98
58042104 CATGGCAACA
* * *
58042114 TGTGATATGTGATTTCTGTATAAGACCATAGCTGGGCTATGGCATCGGAGATATGTGATTATGTG
1 TGTGATATGTGACTACTGTATAAGACCATAGCTGGGATATGGCATC-GAG--ATGTGATTATGTG
* *
58042179 CTTCCGTATAAGACCATATCTGGGATATGGCATCGG
63 CATCCGTATAAGACCATAGCTGGGATATGGCATCGG
*
58042215 TGTGATATGTG-CTACTGTATAAGACCATATCTGGGATATGGCATC-AG-TGTGA-TATGTG-AT
1 TGTGATATGTGACTACTGTATAAGACCATAGCTGGGATATGGCATCGAGATGTGATTATGTGCAT
* * * *
58042275 CCGTGTAAGACCATGGCTGGGCTATGGCTTCGG
66 CCGTATAAGACCATAGCTGGGATATGGCATCGG
**
58042308 TGTGTAATATGTGACTA-TGTGCAAGACCATAG
1 TGTG--ATATGTGACTACTGTATAAGACCATAG
58042340 TTTTACTATG
Statistics
Matches: 109, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
93 33 0.30
94 6 0.06
95 24 0.22
96 3 0.03
98 2 0.02
100 30 0.28
101 11 0.10
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.32
Consensus pattern (98 bp):
TGTGATATGTGACTACTGTATAAGACCATAGCTGGGATATGGCATCGAGATGTGATTATGTGCAT
CCGTATAAGACCATAGCTGGGATATGGCATCGG
Found at i:58049120 original size:9 final size:9
Alignment explanation
Indices: 58049091--58049147 Score: 53
Period size: 9 Copynumber: 6.1 Consensus size: 9
58049081 AATTCATTTT
58049091 AAAATTATA
1 AAAATTATA
*
58049100 AAAA-CATAA
1 AAAATTAT-A
58049109 AAAATTATA
1 AAAATTATA
* *
58049118 AAAATCATT
1 AAAATTATA
58049127 AAAATTGATTA
1 AAAATT-A-TA
58049138 AAAATTATA
1 AAAATTATA
58049147 A
1 A
58049148 TATTAGAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
8 2 0.05
9 25 0.66
10 4 0.11
11 7 0.18
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.30
Consensus pattern (9 bp):
AAAATTATA
Found at i:58049130 original size:18 final size:18
Alignment explanation
Indices: 58049089--58049142 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
58049079 TAAATTCATT
58049089 TTAAAATTATAAAAA-CA
1 TTAAAATTATAAAAATCA
*
58049106 TAAAAAATTATAAAAATCA
1 T-TAAAATTATAAAAATCA
58049125 TTAAAATTGATTAAAAAT
1 TTAAAATT-A-TAAAAAT
58049143 TATAATATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 1 0.03
18 19 0.61
19 4 0.13
20 7 0.23
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (18 bp):
TTAAAATTATAAAAATCA
Found at i:58049281 original size:32 final size:30
Alignment explanation
Indices: 58049237--58049298 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 30
58049227 AATTTGTTAG
**
58049237 AAATTAATTAAATATGAATGTTTTAATAAT
1 AAATTAATTAAATATGAACATTTTAATAAT
58049267 AAATGTAATATAAATATGAACATTTTAATAAT
1 AAAT-TAAT-TAAATATGAACATTTTAATAAT
58049299 CTAAATATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 4 0.14
31 4 0.14
32 20 0.71
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (30 bp):
AAATTAATTAAATATGAACATTTTAATAAT
Found at i:58055115 original size:10 final size:10
Alignment explanation
Indices: 58055054--58055117 Score: 53
Period size: 10 Copynumber: 6.5 Consensus size: 10
58055044 CTAAAAACCC
58055054 TAAAAATTTA
1 TAAAAATTTA
58055064 -AAATAATTTA
1 TAAA-AATTTA
58055074 T-AAAATTTA
1 TAAAAATTTA
* *
58055083 TTAGAAATTAA
1 -TAAAAATTTA
* *
58055094 TGAAAA-TCA
1 TAAAAATTTA
58055103 TAAAAATTTA
1 TAAAAATTTA
58055113 TAAAA
1 TAAAA
58055118 TTATTTTACT
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
9 16 0.38
10 20 0.48
11 6 0.14
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (10 bp):
TAAAAATTTA
Found at i:58055377 original size:15 final size:16
Alignment explanation
Indices: 58055357--58055386 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
58055347 CAGAAAGCCA
58055357 ATATTA-AAATTTTAT
1 ATATTATAAATTTTAT
58055372 ATATTATAAATTTTA
1 ATATTATAAATTTTA
58055387 ATAAAATGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATTATAAATTTTAT
Found at i:58055511 original size:17 final size:17
Alignment explanation
Indices: 58055489--58055545 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
58055479 TAAATTAATT
58055489 TTTTTAAATTTTTATGG
1 TTTTTAAATTTTTATGG
**
58055506 TTTTT-AATAAATTA-GG
1 TTTTTAAAT-TTTTATGG
* *
58055522 TTTTGAAAGTTTTATGG
1 TTTTTAAATTTTTATGG
58055539 TTTTTAA
1 TTTTTAA
58055546 TTTATTTCTA
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
16 12 0.40
17 18 0.60
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.58
Consensus pattern (17 bp):
TTTTTAAATTTTTATGG
Found at i:58062113 original size:18 final size:20
Alignment explanation
Indices: 58062090--58062129 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
58062080 CTTCTGAAAA
58062090 ATTA-TTTCT-GAAAAATTG
1 ATTATTTTCTAGAAAAATTG
*
58062108 ATTATTTTTTAGAAAAATTG
1 ATTATTTTCTAGAAAAATTG
58062128 AT
1 AT
58062130 GTTTTTTGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 4 0.21
20 11 0.58
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (20 bp):
ATTATTTTCTAGAAAAATTG
Found at i:58062275 original size:18 final size:19
Alignment explanation
Indices: 58062249--58062294 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
58062239 GTACAATTCC
*
58062249 TTTTGATAATTAA-ATTATA
1 TTTT-ATAATTAAGATAATA
58062268 TTTTATAA-TAAGATAATA
1 TTTTATAATTAAGATAATA
*
58062286 TTTTGTAAT
1 TTTTATAAT
58062295 AATCAATATC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 3 0.13
18 16 0.70
19 4 0.17
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (19 bp):
TTTTATAATTAAGATAATA
Found at i:58063508 original size:27 final size:27
Alignment explanation
Indices: 58063470--58063526 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
58063460 AAAATAAAAT
* *
58063470 ACTGGTCTTGCCTCTGTCAGAGGCGGC
1 ACTGGTCTTGCCTCTGCCAGAGACGGC
58063497 ACTGGTCTTGCCTCTGCCAGAGACGGC
1 ACTGGTCTTGCCTCTGCCAGAGACGGC
58063524 ACT
1 ACT
58063527 AGTTGATGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.14, C:0.32, G:0.30, T:0.25
Consensus pattern (27 bp):
ACTGGTCTTGCCTCTGCCAGAGACGGC
Found at i:58063669 original size:16 final size:16
Alignment explanation
Indices: 58063641--58063673 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
58063631 AGAGGGAGGG
58063641 AGAAGAGAAGAAAAAA
1 AGAAGAGAAGAAAAAA
58063657 AGAA-AGAAGGAAAAAA
1 AGAAGAGAA-GAAAAAA
58063673 A
1 A
58063674 TTCAGTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (16 bp):
AGAAGAGAAGAAAAAA
Found at i:58067513 original size:12 final size:12
Alignment explanation
Indices: 58067498--58067531 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
58067488 GTCAAGCTCG
58067498 GGATCTGGCTGT
1 GGATCTGGCTGT
*
58067510 GGATCAGGCTGT
1 GGATCTGGCTGT
*
58067522 TGATCTGGCT
1 GGATCTGGCT
58067532 CTATATTAGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.12, C:0.18, G:0.38, T:0.32
Consensus pattern (12 bp):
GGATCTGGCTGT
Found at i:58069664 original size:140 final size:138
Alignment explanation
Indices: 58069514--58069826 Score: 407
Period size: 139 Copynumber: 2.2 Consensus size: 138
58069504 CGGATTCTAT
* * **
58069514 TTTTTAAAATATATTATTTTCTTATTTTTATTTTTTTATCTTATTTTAGTACATAATGTTTCAAA
1 TTTTTAAAATATACTATTTTCATA-TTTTATTTTTTTATCTTATTCCAGTACATAATGTTTCAAA
*
58069579 TATATTATTCTAAAGTTTTTAAAATAA-CCTTGATTTTGTCTC-TTTGTTTGAT-TTTCTAAAAT
65 TATATTATTCTAAAGTTTTT-AAATAATCC-TAATTTTGTC-CATTTGTTT-ATATTTCTAAAAT
58069641 ATTCAAATTTTAA
126 ATTCAAATTTTAA
* *
58069654 TTTTTAAAATATACTATTTTCGTATTTTATTTTATTTATCTTATTCCCGTACATAATGTTTCAAA
1 TTTTTAAAATATACTATTTTCATATTTTATTTT-TTTATCTTATTCCAGTACATAATGTTTCAAA
* * ** * *
58069719 TGTATTATTTTAGTGTTTTTAAATAATCCTAATTTTGTCCATTTGTTTATATTTTTAAAATTTTC
65 TATATTATTCTAAAGTTTTTAAATAATCCTAATTTTGTCCATTTGTTTATATTTCTAAAATATTC
** *
58069784 GGATTTTAT
130 AAATTTTAA
58069793 TTTTTAAAATATACTATTTTCATATTTTATTTTT
1 TTTTTAAAATATACTATTTTCATATTTTATTTTT
58069827 ATATTATTTT
Statistics
Matches: 153, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
138 4 0.03
139 81 0.53
140 68 0.44
ACGTcount: A:0.29, C:0.08, G:0.05, T:0.57
Consensus pattern (138 bp):
TTTTTAAAATATACTATTTTCATATTTTATTTTTTTATCTTATTCCAGTACATAATGTTTCAAAT
ATATTATTCTAAAGTTTTTAAATAATCCTAATTTTGTCCATTTGTTTATATTTCTAAAATATTCA
AATTTTAA
Found at i:58069808 original size:139 final size:140
Alignment explanation
Indices: 58069490--58069826 Score: 450
Period size: 140 Copynumber: 2.4 Consensus size: 140
58069480 TATTTCTAAA
* * *
58069490 ATTTTTAAAATTTTCGGATTCTATTTTTTAAAATATATTATTTTCTTATTTTTATTTTTTTATCT
1 ATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCATA-TTTTATTTTTTTATCT
** *
58069555 TATTTTAGTACATAATGTTTCAAATATATTATTCTAAAGTTTTTAAAATAACCTTGATTTTGTCT
65 TATTCCAGTACATAATGTTTCAAATATATTATTCTAAAGTTTTTAAAATAACCTTAATTTTGTCT
58069620 CTTTGTTTGAT
130 CTTTGTTTGAT
* * ** * *
58069631 -TTTCTAAAATATTCAAATTTTAATTTTTAAAATATACTATTTTCGTATTTTATTTTATTTATCT
1 ATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCATATTTTATTTT-TTTATCT
* * * **
58069695 TATTCCCGTACATAATGTTTCAAATGTATTATTTTAGTGTTTTT-AAATAATCC-TAATTTTGTC
65 TATTCCAGTACATAATGTTTCAAATATATTATTCTAAAGTTTTTAAAATAA-CCTTAATTTTGTC
58069758 -CATTTGTTT-AT
129 TC-TTTGTTTGAT
58069769 ATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCATATTTTATTTTT
1 ATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCATATTTTATTTTT
58069827 ATATTATTTT
Statistics
Matches: 170, Mismatches: 22, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
138 4 0.02
139 81 0.48
140 85 0.50
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.57
Consensus pattern (140 bp):
ATTTTTAAAATTTTCGGATTTTATTTTTTAAAATATACTATTTTCATATTTTATTTTTTTATCTT
ATTCCAGTACATAATGTTTCAAATATATTATTCTAAAGTTTTTAAAATAACCTTAATTTTGTCTC
TTTGTTTGAT
Found at i:58069828 original size:36 final size:33
Alignment explanation
Indices: 58069786--58069868 Score: 87
Period size: 36 Copynumber: 2.4 Consensus size: 33
58069776 AAATTTTCGG
58069786 ATTTTATTTTTTAAAATATACTA-TTTTCATATTTT
1 ATTTTATTTTTT---ATATACTATTTTTCATATTTT
*
58069821 ATTTTTATATTATTTTTATACTATTTTTCATATTTT
1 A-TTTTAT-TT-TTTATATACTATTTTTCATATTTT
*
58069857 ATTCTATTTTTT
1 ATTTTATTTTTT
58069869 TCATATTCTA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
33 3 0.07
34 2 0.05
35 13 0.31
36 19 0.45
37 2 0.05
38 3 0.07
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (33 bp):
ATTTTATTTTTTATATACTATTTTTCATATTTT
Found at i:58069859 original size:14 final size:11
Alignment explanation
Indices: 58069819--58069875 Score: 55
Period size: 11 Copynumber: 5.2 Consensus size: 11
58069809 TTTTCATATT
58069819 TTATTTTTATA
1 TTATTTTTATA
58069830 TTATTTTTATA
1 TTATTTTTATA
*
58069841 CTATTTTTCATA
1 TTATTTTT-ATA
* *
58069853 TT-TTATTCTA
1 TTATTTTTATA
58069863 TT-TTTTTCATA
1 TTATTTTT-ATA
58069874 TT
1 TT
58069876 CTATTTCTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
10 8 0.21
11 26 0.68
12 4 0.11
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (11 bp):
TTATTTTTATA
Found at i:58069877 original size:16 final size:17
Alignment explanation
Indices: 58069856--58069892 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
58069846 TTTCATATTT
58069856 TATTCTATTT-TTTTCA
1 TATTCTATTTCTTTTCA
*
58069872 TATTCTATTTCTTTTCG
1 TATTCTATTTCTTTTCA
58069889 TATT
1 TATT
58069893 TTTTCATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.16, C:0.14, G:0.03, T:0.68
Consensus pattern (17 bp):
TATTCTATTTCTTTTCA
Found at i:58069880 original size:35 final size:37
Alignment explanation
Indices: 58069801--58069881 Score: 100
Period size: 35 Copynumber: 2.3 Consensus size: 37
58069791 ATTTTTTAAA
*
58069801 ATATACTA-TTTTCATATTTTATTTTTATATTATTTT
1 ATATACTATTTTTCATATTTTATTTCTATATTATTTT
58069837 -TATACTATTTTTCATATTTTA-TTCTAT-TT-TTTT
1 ATATACTATTTTTCATATTTTATTTCTATATTATTTT
*
58069870 CATATTCTATTT
1 -ATATACTATTT
58069882 CTTTTCGTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
33 4 0.10
34 2 0.05
35 21 0.52
36 13 0.32
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.67
Consensus pattern (37 bp):
ATATACTATTTTTCATATTTTATTTCTATATTATTTT
Found at i:58069908 original size:28 final size:26
Alignment explanation
Indices: 58069850--58069921 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 26
58069840 ACTATTTTTC
* *
58069850 ATATTTTATTC-TATTTTTTTCATATT
1 ATATTTTTTTCATA-TTTTTTCATAAT
* *
58069876 CTATTTCTTTTCGTATTTTTTCATTAAT
1 ATATTT-TTTTCATATTTTTTCA-TAAT
58069904 ATATTTTTTTCATATTTT
1 ATATTTTTTTCATATTTT
58069922 CTTTTTTATA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
26 5 0.13
27 23 0.61
28 10 0.26
ACGTcount: A:0.21, C:0.10, G:0.01, T:0.68
Consensus pattern (26 bp):
ATATTTTTTTCATATTTTTTCATAAT
Found at i:58071083 original size:11 final size:10
Alignment explanation
Indices: 58071051--58071084 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
58071041 ATAAATTTAT
58071051 AAATTAAATC
1 AAATTAAATC
58071061 TAAATTAAATC
1 -AAATTAAATC
58071072 AAATTCAAATC
1 AAATT-AAATC
58071083 AA
1 AA
58071085 CAATAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 5 0.23
11 17 0.77
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (10 bp):
AAATTAAATC
Found at i:58071464 original size:18 final size:18
Alignment explanation
Indices: 58071441--58071475 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
58071431 TCTGCAGCCT
58071441 TTTTTTTTTCATTTCAGG
1 TTTTTTTTTCATTTCAGG
*
58071459 TTTTTTTTTCGTTTCAG
1 TTTTTTTTTCATTTCAG
58071476 TCAGCTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.09, C:0.11, G:0.11, T:0.69
Consensus pattern (18 bp):
TTTTTTTTTCATTTCAGG
Found at i:58074521 original size:20 final size:21
Alignment explanation
Indices: 58074487--58074530 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
58074477 AACCCTAGCT
*
58074487 TTTTTCTCCTTTTTCTTTCTC
1 TTTTTCTCCTATTTCTTTCTC
*
58074508 TTTTTC-CCTATTTCTTTTTC
1 TTTTTCTCCTATTTCTTTCTC
58074528 TTT
1 TTT
58074531 CGTTTTACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTTTCTCCTATTTCTTTCTC
Found at i:58074618 original size:5 final size:5
Alignment explanation
Indices: 58074608--58074649 Score: 84
Period size: 5 Copynumber: 8.4 Consensus size: 5
58074598 AATTATTATA
58074608 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT
58074650 TAAGTGTTAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:58075527 original size:57 final size:58
Alignment explanation
Indices: 58075429--58075546 Score: 159
Period size: 57 Copynumber: 2.1 Consensus size: 58
58075419 ATAGAAATTG
* **
58075429 TGAAAATGGAGAAATGAGAAACATTTGGAAATAATTATGGTTTTCTGTAAAATAAAAA
1 TGAAAATGGAAAAATGAGAAACATTTGGAAATAATTATGGTTTTCTCCAAAATAAAAA
* * *
58075487 TGAAAATGGAAAAATG-GAATCATTTGGAAATGAA-TGTGGTTTTCTCCAAAATGAAAA
1 TGAAAATGGAAAAATGAGAAACATTTGGAAAT-AATTATGGTTTTCTCCAAAATAAAAA
58075544 TGA
1 TGA
58075547 CCTAAAAATG
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
57 36 0.68
58 17 0.32
ACGTcount: A:0.46, C:0.05, G:0.20, T:0.29
Consensus pattern (58 bp):
TGAAAATGGAAAAATGAGAAACATTTGGAAATAATTATGGTTTTCTCCAAAATAAAAA
Found at i:58084317 original size:12 final size:12
Alignment explanation
Indices: 58084287--58084319 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
58084277 TAAAGTCAGT
*
58084287 ATTGAACTAAAA
1 ATTGAATTAAAA
58084299 ATT-AATTAAAA
1 ATTGAATTAAAA
58084310 ATTGAATTAA
1 ATTGAATTAA
58084320 TAGATACATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (12 bp):
ATTGAATTAAAA
Found at i:58090503 original size:23 final size:23
Alignment explanation
Indices: 58090473--58090522 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
58090463 CTAATGCATT
58090473 TAATGTGAACTATTAGAAATTAC
1 TAATGTGAACTATTAGAAATTAC
58090496 TAATGTGAACTATTAGAAATTAC
1 TAATGTGAACTATTAGAAATTAC
58090519 TAAT
1 TAAT
58090523 ATTTTAGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (23 bp):
TAATGTGAACTATTAGAAATTAC
Found at i:58093192 original size:19 final size:19
Alignment explanation
Indices: 58093170--58093235 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
58093160 GTTTTAAAAT
58093170 TTTTTACAATTTCTAATAA
1 TTTTTACAATTTCTAATAA
*
58093189 TTTTTATAATTT-TAAT-A
1 TTTTTACAATTTCTAATAA
58093206 -TTTTACAATTTCTAATAA
1 TTTTTACAATTTCTAATAA
* *
58093224 CTTTTATAATTT
1 TTTTTACAATTT
58093236 TATAGAGTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
16 10 0.24
17 5 0.12
18 5 0.12
19 21 0.51
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTTACAATTTCTAATAA
Found at i:58093210 original size:35 final size:35
Alignment explanation
Indices: 58093171--58093237 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
58093161 TTTTAAAATT
*
58093171 TTTTACAATTTCTAATAATTTTTATAATTTTAATA
1 TTTTACAATTTCTAATAACTTTTATAATTTTAATA
58093206 TTTTACAATTTCTAATAACTTTTATAATTTTA
1 TTTTACAATTTCTAATAACTTTTATAATTTTA
58093238 TAGAGTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (35 bp):
TTTTACAATTTCTAATAACTTTTATAATTTTAATA
Found at i:58093238 original size:8 final size:8
Alignment explanation
Indices: 58093171--58093239 Score: 50
Period size: 8 Copynumber: 7.9 Consensus size: 8
58093161 TTTTAAAATT
*
58093171 TTTTACAA
1 TTTTATAA
58093179 TTTCTAATAA
1 TTT-T-ATAA
58093189 TTTTTATAA
1 -TTTTATAA
58093198 TTTTA-ATA
1 TTTTATA-A
*
58093206 TTTTACAA
1 TTTTATAA
58093214 TTTCTAATAA
1 TTT-T-ATAA
58093224 CTTTTATAA
1 -TTTTATAA
58093233 TTTTATA
1 TTTTATA
58093240 GAGTTTTTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
7 1 0.02
8 25 0.49
9 11 0.22
10 8 0.16
11 6 0.12
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (8 bp):
TTTTATAA
Found at i:58097061 original size:41 final size:41
Alignment explanation
Indices: 58097016--58097097 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
58097006 CCGTTTGTCT
58097016 AAAAAATATTGTCCAACATAAGCTGCCACATCACCTAGTCA
1 AAAAAATATTGTCCAACATAAGCTGCCACATCACCTAGTCA
*
58097057 AAAAAATATTGTCCAACATAGGCTGCCACATCACCTAGTCA
1 AAAAAATATTGTCCAACATAAGCTGCCACATCACCTAGTCA
58097098 GCTGTATTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.40, C:0.27, G:0.11, T:0.22
Consensus pattern (41 bp):
AAAAAATATTGTCCAACATAAGCTGCCACATCACCTAGTCA
Found at i:58097282 original size:30 final size:32
Alignment explanation
Indices: 58097246--58097313 Score: 79
Period size: 30 Copynumber: 2.2 Consensus size: 32
58097236 GGTTTCATTG
* *
58097246 CAGTCACCAAAC-TTTTGAAAAA-TAACAAAA
1 CAGTCACCAAACGTTATAAAAAAGTAACAAAA
* *
58097276 CAGTCA-CTAACGTTATAAAAAAGTGACAAAA
1 CAGTCACCAAACGTTATAAAAAAGTAACAAAA
58097307 CAGTCAC
1 CAGTCAC
58097314 TGACTAACAG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
29 4 0.13
30 14 0.45
31 13 0.42
ACGTcount: A:0.50, C:0.21, G:0.10, T:0.19
Consensus pattern (32 bp):
CAGTCACCAAACGTTATAAAAAAGTAACAAAA
Found at i:58097369 original size:21 final size:21
Alignment explanation
Indices: 58097345--58097385 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
58097335 TAACATAACC
*
58097345 GCTGATGTGACAAGTTAACTA
1 GCTGAAGTGACAAGTTAACTA
* *
58097366 GCTGAAGTGGCCAGTTAACT
1 GCTGAAGTGACAAGTTAACT
58097386 TGCCACATTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (21 bp):
GCTGAAGTGACAAGTTAACTA
Found at i:58104959 original size:19 final size:20
Alignment explanation
Indices: 58104921--58104960 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
58104911 CCTACAAAAC
58104921 AGAAACAGAAAAGAAAGCAA
1 AGAAACAGAAAAGAAAGCAA
* *
58104941 AGAAGCAGAAACG-AAGCAA
1 AGAAACAGAAAAGAAAGCAA
58104960 A
1 A
58104961 ACAGTAGCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.65, C:0.12, G:0.23, T:0.00
Consensus pattern (20 bp):
AGAAACAGAAAAGAAAGCAA
Found at i:58111777 original size:19 final size:19
Alignment explanation
Indices: 58111750--58111787 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
58111740 TTGCACTCAT
* *
58111750 TCATTTGCACTACATTTCA
1 TCATATGCACTAAATTTCA
58111769 TCATATGCACTAAATTTCA
1 TCATATGCACTAAATTTCA
58111788 CGAAAAGGCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (19 bp):
TCATATGCACTAAATTTCA
Found at i:58120068 original size:44 final size:44
Alignment explanation
Indices: 58119908--58120304 Score: 235
Period size: 44 Copynumber: 8.7 Consensus size: 44
58119898 AGTCTTATGC
* * ** *
58119908 CCCTAAAGTTGCAGTGGAGCAGACTGAAGATAGCGAA-TCTTATCT
1 CCCTGAAGTTGCAGTGGAGCAGATTGAAGCCA-C-AAGCCTTATCT
* * * * * * * *
58119953 CCTTGTAGTCGCAGTAGTGCAGATTGAAGTCACAAACCTTATCC
1 CCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACAAGCCTTATCT
* * * * * *
58119997 CCCTGAATTTGTAGTGGGGTAGGTTGAAGCCACCAGCCTTATCT
1 CCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACAAGCCTTATCT
* *
58120041 CCCTGAAGTTGCAGTGGAGCAAATTGAAGCTGAAAATCACAAACCTTATCT
1 CCCTGAAGTTGCAGTGGAGCAGATTGAAGC-------CACAAGCCTTATCT
* * *
58120092 CCCTGAAGTTGCAGTGGAGCAGGTTGAA-CTTACAAGTCTTATCT
1 CCCTGAAGTTGCAGTGGAGCAGATTGAAGC-CACAAGCCTTATCT
* * ** *
58120136 CCCTAAAGTTGCAGTGGAGCAGACTGAAGATAGCGAA-TCTTATCT
1 CCCTGAAGTTGCAGTGGAGCAGATTGAAGCCA-C-AAGCCTTATCT
* * *
58120181 CCCTGAAGTTACAGTGGAGTAGATTGAA-CCTAGAAATTACAGACCTTATCT
1 CCCTGAAGTTGCAGTGGAGCAGATTGAAGCC-----A-CA-AG-CCTTATCT
* * * * *
58120232 CTCTGAAGTTTCAGTGGAGCAGGTTGAAGCTACAAGTCTTATCT
1 CCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACAAGCCTTATCT
* *
58120276 CCCTGAAGTTGCAGTGAAGCAGACTGAAG
1 CCCTGAAGTTGCAGTGGAGCAGATTGAAG
58120305 TGGAGCATAT
Statistics
Matches: 270, Mismatches: 62, Indels: 41
0.72 0.17 0.11
Matches are distributed among these distances:
43 2 0.01
44 132 0.49
45 58 0.21
46 3 0.01
47 1 0.00
48 1 0.00
49 2 0.01
50 1 0.00
51 69 0.26
52 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (44 bp):
CCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACAAGCCTTATCT
Found at i:58120098 original size:95 final size:95
Alignment explanation
Indices: 58119982--58120156 Score: 253
Period size: 95 Copynumber: 1.8 Consensus size: 95
58119972 CAGATTGAAG
* * * * * *
58119982 TCACAAACCTTATCCCCCTGAATTTGTAGTGGGGTAGGTTGAAGC-CACCAGCCTTATCTCCCTG
1 TCACAAACCTTATCCCCCTGAAGTTGCAGTGGAGCAGGTTGAA-CTCACAAGCCTTATCTCCCTA
58120046 AAGTTGCAGTGGAGCAAATTGAAGCTGAAAA
65 AAGTTGCAGTGGAGCAAATTGAAGCTGAAAA
* * *
58120077 TCACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAACTTACAAGTCTTATCTCCCTAA
1 TCACAAACCTTATCCCCCTGAAGTTGCAGTGGAGCAGGTTGAACTCACAAGCCTTATCTCCCTAA
58120142 AGTTGCAGTGGAGCA
66 AGTTGCAGTGGAGCA
58120157 GACTGAAGAT
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
94 1 0.01
95 69 0.99
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.26
Consensus pattern (95 bp):
TCACAAACCTTATCCCCCTGAAGTTGCAGTGGAGCAGGTTGAACTCACAAGCCTTATCTCCCTAA
AGTTGCAGTGGAGCAAATTGAAGCTGAAAA
Found at i:58120227 original size:140 final size:140
Alignment explanation
Indices: 58120034--58120304 Score: 420
Period size: 140 Copynumber: 1.9 Consensus size: 140
58120024 AGCCACCAGC
* *
58120034 CTTATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAGCTGAAAATCACAAACCTTATCTCCCTGAA
1 CTTATCTCCCTGAAGTTACAGTGGAGCAAATTGAACCTGAAAATCACAAACCTTATCTCCCTGAA
*
58120099 GTTGCAGTGGAGCAGGTTGAA-CTTACAAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGA
66 GTTGCAGTGGAGCAGGTTGAAGC-TACAAGTCTTATCTCCCTAAAGTTGCAGTGAAGCAGACTGA
58120163 AGATAGCGAAT
130 AGATAGCGAAT
* * * * *
58120174 CTTATCTCCCTGAAGTTACAGTGGAGTAGATTGAACCT-AGAAATTACAGACCTTATCTCTCTGA
1 CTTATCTCCCTGAAGTTACAGTGGAGCAAATTGAACCTGA-AAATCACAAACCTTATCTCCCTGA
* *
58120238 AGTTTCAGTGGAGCAGGTTGAAGCTACAAGTCTTATCTCCCTGAAGTTGCAGTGAAGCAGACTGA
65 AGTTGCAGTGGAGCAGGTTGAAGCTACAAGTCTTATCTCCCTAAAGTTGCAGTGAAGCAGACTGA
58120303 AG
130 AG
58120305 TGGAGCATAT
Statistics
Matches: 119, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
139 1 0.01
140 117 0.98
141 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (140 bp):
CTTATCTCCCTGAAGTTACAGTGGAGCAAATTGAACCTGAAAATCACAAACCTTATCTCCCTGAA
GTTGCAGTGGAGCAGGTTGAAGCTACAAGTCTTATCTCCCTAAAGTTGCAGTGAAGCAGACTGAA
GATAGCGAAT
Found at i:58123363 original size:40 final size:40
Alignment explanation
Indices: 58123287--58123367 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
58123277 CTTCATTAGA
* ** *
58123287 AATTTTACAGTTCAATACAATATACGTAACATTATTCAGT
1 AATTTCACAGTTCAATACAATATACAAAACAATATTCAGT
* * *
58123327 AATTTCACAGTTCAATTCAGTATTCAAAACAATATTCAGT
1 AATTTCACAGTTCAATACAATATACAAAACAATATTCAGT
58123367 A
1 A
58123368 TCCCATAATT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (40 bp):
AATTTCACAGTTCAATACAATATACAAAACAATATTCAGT
Found at i:58124157 original size:5 final size:5
Alignment explanation
Indices: 58124147--58124343 Score: 394
Period size: 5 Copynumber: 39.4 Consensus size: 5
58124137 TTTCTTTTAT
58124147 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
58124197 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
58124247 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
58124297 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA AT
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA AT
58124344 TATTAAACAA
Statistics
Matches: 192, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 192 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:58138767 original size:30 final size:30
Alignment explanation
Indices: 58138731--58138792 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
58138721 AAAAATTAAT
58138731 ATATGTTAACTTTGCTAACGTAACATCCAC
1 ATATGTTAACTTTGCTAACGTAACATCCAC
*
58138761 ATATGTTAACTTTGCTAACGTGACATCCAC
1 ATATGTTAACTTTGCTAACGTAACATCCAC
58138791 AT
1 AT
58138793 TAATTTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.34
Consensus pattern (30 bp):
ATATGTTAACTTTGCTAACGTAACATCCAC
Found at i:58146979 original size:47 final size:49
Alignment explanation
Indices: 58146902--58147129 Score: 185
Period size: 47 Copynumber: 4.9 Consensus size: 49
58146892 TGGGTAAGGT
* *
58146902 GCCGATGT-CATGTCCTAGACATGGTTTTACACTGGCTCAT-ATCTC-AA
1 GCCGAT-TACATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCGAA
* * * *
58146949 GTCGATTCCATGTCCCAGACATGGTCTTACACTGACT-ATCATCTCGTA
1 GCCGATTACATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCGAA
* * * * *
58146997 GCC-AATACATGTCCCA-ACAT-GTCTTACACTAGCTTAT-GTCTCGAG
1 GCCGATTACATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCGAA
* * *
58147042 GCCGA-TACATGTCCCAGACAT-GTCTTACACTAGC-CCTCGTCTC-AA
1 GCCGATTACATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCGAA
** * *
58147087 TGCCGATGCCATGTCCCAGACATGGTCTTATATTGGCTC-TCAT
1 -GCCGATTACATGTCCCAGACATGGTCTTACACTGGCTCATCAT
58147130 AATGTGGCCG
Statistics
Matches: 148, Mismatches: 22, Indels: 21
0.77 0.12 0.11
Matches are distributed among these distances:
45 33 0.22
46 37 0.25
47 61 0.41
48 16 0.11
49 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.18, T:0.30
Consensus pattern (49 bp):
GCCGATTACATGTCCCAGACATGGTCTTACACTGGCTCATCATCTCGAA
Found at i:58147039 original size:45 final size:46
Alignment explanation
Indices: 58146957--58147116 Score: 157
Period size: 46 Copynumber: 3.4 Consensus size: 46
58146947 AAGTCGATTC
58146957 CATGTCCCAGACATGGTCTTACACT-GACTATCATCTCGTA-GCCAATA
1 CATGTCCCAGACAT-GTCTTACACTAG-CTATCATCTCG-AGGCCAATA
* *
58147004 CATGTCCCA-ACATGTCTTACACTAGCTTAT-GTCTCGAGGCCGATA
1 CATGTCCCAGACATGTCTTACACTAGC-TATCATCTCGAGGCCAATA
** * * * * *
58147049 CATGTCCCAGACATGTCTTACACTAGCCCTCGTCTCAATGCCGATGC
1 CATGTCCCAGACATGTCTTACACTAGCTATCATCTCGAGGCCAAT-A
58147096 CATGTCCCAGACATGGTCTTA
1 CATGTCCCAGACAT-GTCTTA
58147117 TATTGGCTCT
Statistics
Matches: 99, Mismatches: 7, Indels: 13
0.83 0.06 0.11
Matches are distributed among these distances:
44 1 0.01
45 32 0.32
46 37 0.37
47 23 0.23
48 6 0.06
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.28
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTAGCTATCATCTCGAGGCCAATA
Found at i:58152596 original size:33 final size:33
Alignment explanation
Indices: 58152559--58152694 Score: 149
Period size: 33 Copynumber: 4.3 Consensus size: 33
58152549 GTCTGCTTTA
*
58152559 TGTTTCTCTATTTTCTGTTTCTGTACCGTGTTT
1 TGTTTCTCTATTTTCTGTTTCTGTACCATGTTT
* *
58152592 TGTTTCTTTATTTTCTGTTTCTGTACCATATTT
1 TGTTTCTCTATTTTCTGTTTCTGTACCATGTTT
* * * *
58152625 TGTTCCTCTATTTTCTATAGT-GGT----T-TTT
1 TGTTTCTCTATTTTCTGT-TTCTGTACCATGTTT
58152653 TGTTTCTCTATTTTCTGTTTCTGTACCATGTTT
1 TGTTTCTCTATTTTCTGTTTCTGTACCATGTTT
*
58152686 TGTTCCTCT
1 TGTTTCTCT
58152695 TGCCATTTTT
Statistics
Matches: 83, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
27 1 0.01
28 21 0.25
29 1 0.01
32 1 0.01
33 58 0.70
34 1 0.01
ACGTcount: A:0.09, C:0.18, G:0.12, T:0.61
Consensus pattern (33 bp):
TGTTTCTCTATTTTCTGTTTCTGTACCATGTTT
Found at i:58161404 original size:93 final size:92
Alignment explanation
Indices: 58161246--58161527 Score: 298
Period size: 93 Copynumber: 3.0 Consensus size: 92
58161236 TTGATTTTAG
* ** *
58161246 TAAATTCATATAAGAACA-TTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTA
1 TAAATTCATATAAGAAAATTTTTATTA-TAAGAATTTTAAAAAATTATATATTATTATTAAATTA
*
58161310 TATTTAATATTAATTATTTTAAATTGTA
65 TATTTAATATTAATTATTTTAAATTATA
58161338 TAAATTCATATAAGAAAATTTTTATTATCAAGAATTTTAAAAAATTATATATTATTATTAAATTA
1 TAAATTCATATAAGAAAATTTTTATTAT-AAGAATTTTAAAAAATTATATATTATTATTAAATTA
*
58161403 TATGTAATAATT-ATTATTTTAAATTATA
65 TATTTAAT-ATTAATTATTTTAAATTATA
* * * * ** ** *
58161431 CAAATTCATAAAATATAATTTATTAGTTATAATTATTTTAAATTTTATTAAATCATATATTTAAT
1 TAAATTCATATAAGAAAATTT-TTA-TTATAAGAATTTTAAA--AAATTATAT-AT-TA-TT-AT
* *
58161496 TAAATCATATTTAATATTAATTATTTGAAATT
58 TAAATTATATTTAATATTAATTATTTTAAATT
58161528 TTCTTTTATA
Statistics
Matches: 160, Mismatches: 18, Indels: 16
0.82 0.09 0.08
Matches are distributed among these distances:
92 18 0.11
93 80 0.50
94 16 0.10
95 4 0.03
96 6 0.04
97 2 0.01
98 2 0.01
99 5 0.03
100 27 0.17
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (92 bp):
TAAATTCATATAAGAAAATTTTTATTATAAGAATTTTAAAAAATTATATATTATTATTAAATTAT
ATTTAATATTAATTATTTTAAATTATA
Found at i:58161497 original size:17 final size:17
Alignment explanation
Indices: 58161472--58161505 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
58161462 ATTATTTTAA
*
58161472 ATTTTATTAAATCATAT
1 ATTTAATTAAATCATAT
58161489 ATTTAATTAAATCATAT
1 ATTTAATTAAATCATAT
58161506 TTAATATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATTAAATCATAT
Found at i:58161507 original size:15 final size:16
Alignment explanation
Indices: 58161472--58161510 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
58161462 ATTATTTTAA
*
58161472 ATTTTATTAAATCATAT
1 ATTTAATTAAATCA-AT
58161489 ATTTAATTAAATC-AT
1 ATTTAATTAAATCAAT
58161504 ATTTAAT
1 ATTTAAT
58161511 ATTAATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.43
17 12 0.57
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTTAATTAAATCAAT
Found at i:58161514 original size:17 final size:18
Alignment explanation
Indices: 58161476--58161515 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
58161466 TTTTAAATTT
*
58161476 TATTAAATCATATATTTA
1 TATTAAATCATATATTAA
58161494 -ATTAAATCATAT-TTAA
1 TATTAAATCATATATTAA
58161510 TATTAA
1 TATTAA
58161516 TTATTTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTAAATCATATATTAA
Found at i:58161624 original size:16 final size:16
Alignment explanation
Indices: 58161603--58161644 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
58161593 TTATTAAATT
*
58161603 ATATATTTTAATTATA
1 ATATATTTTAATAATA
58161619 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
58161634 AT-TATGTTTAA
1 ATATAT-TTTAA
58161645 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:58161629 original size:15 final size:15
Alignment explanation
Indices: 58161594--58161635 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
58161584 TTAAGAATTT
*
58161594 TATTAAATTAT-ATA
1 TATTTAATTATAATA
58161608 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
58161622 TATTTAATAATAAT
1 TATTTAATTATAAT
58161636 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:58161662 original size:154 final size:153
Alignment explanation
Indices: 58161571--58161881 Score: 489
Period size: 154 Copynumber: 2.0 Consensus size: 153
58161561 AAATTCATAT
* *
58161571 AAGAATATTAATT-TTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAA
1 AAGAATACTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAA
*
58161635 TTATGTTTAAATATGATTAAATTATTTATTATTGATATTAATCTTATTAAAATTTAAATAACAAT
66 TTATGTTTAAATATGATTAAATTATTTATTATTGATATTAA-CTTATGAAAATTTAAATAACAAT
58161700 AACAATAATAATTTACCAAAACAA
130 AACAATAATAATTTACCAAAACAA
*** *
58161724 ATTTATGCTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAA
1 AAGAATACTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAA
*
58161789 TTATGTTTAAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAAC
66 TTATGTTTAAATATGATTAAATTATTTATTATTGAT-AT--TAA-CTTATGAAAATTTAAATAAC
*
58161854 AATAACAATAATCATTTACCAAAACAA
127 AATAACAATAATAATTTACCAAAACAA
58161881 A
1 A
58161882 TTTCTGCTAA
Statistics
Matches: 147, Mismatches: 7, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
153 8 0.05
154 86 0.59
155 2 0.01
157 51 0.35
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (153 bp):
AAGAATACTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAA
TTATGTTTAAATATGATTAAATTATTTATTATTGATATTAACTTATGAAAATTTAAATAACAATA
ACAATAATAATTTACCAAAACAA
Found at i:58161772 original size:18 final size:17
Alignment explanation
Indices: 58161744--58161778 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
58161734 ATTATTAAGA
*
58161744 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
58161761 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
58161779 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:58162032 original size:16 final size:16
Alignment explanation
Indices: 58162011--58162049 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
58162001 TTGATTTGCT
*
58162011 ATTACACAGCTTTTCC
1 ATTACACAGCTATTCC
**
58162027 ATTACACCTCTATTCC
1 ATTACACAGCTATTCC
58162043 ATTACAC
1 ATTACAC
58162050 CTCTAATCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.33, G:0.03, T:0.36
Consensus pattern (16 bp):
ATTACACAGCTATTCC
Found at i:58162050 original size:16 final size:16
Alignment explanation
Indices: 58162023--58162064 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
58162013 TACACAGCTT
58162023 TTCCATTACACCTCTA
1 TTCCATTACACCTCTA
58162039 TTCCATTACACCTCTA
1 TTCCATTACACCTCTA
* *
58162055 ATCCAATACA
1 TTCCATTACA
58162065 GCGAACCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.31, C:0.36, G:0.00, T:0.33
Consensus pattern (16 bp):
TTCCATTACACCTCTA
Found at i:58163771 original size:21 final size:21
Alignment explanation
Indices: 58163747--58163790 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
58163737 AAAATAATAA
58163747 AATTTTGATATAAAA-AGTGTT
1 AATTTTGAT-TAAAATAGTGTT
* *
58163768 AATTTTTATTAAAATAGTTTT
1 AATTTTGATTAAAATAGTGTT
58163789 AA
1 AA
58163791 AATACAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (21 bp):
AATTTTGATTAAAATAGTGTT
Found at i:58163947 original size:19 final size:18
Alignment explanation
Indices: 58163924--58163989 Score: 82
Period size: 19 Copynumber: 3.7 Consensus size: 18
58163914 GTTTTAAAAC
58163924 ATTTTACAATTTCTAATA
1 ATTTTACAATTTCTAATA
*
58163942 ATTTTTATAATTT-TAAT-
1 A-TTTTACAATTTCTAATA
58163959 ATTTTACAATTTCTAATA
1 ATTTTACAATTTCTAATA
*
58163977 ACTTTTATAATTT
1 A-TTTTACAATTT
58163990 TTTAGAGCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
16 10 0.24
17 5 0.12
18 6 0.15
19 20 0.49
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTTACAATTTCTAATA
Found at i:58163986 original size:35 final size:35
Alignment explanation
Indices: 58163924--58163990 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
58163914 GTTTTAAAAC
*
58163924 ATTTTACAATTTCTAATAATTTTTATAATTTTAAT
1 ATTTTACAATTTCTAATAACTTTTATAATTTTAAT
58163959 ATTTTACAATTTCTAATAACTTTTATAATTTT
1 ATTTTACAATTTCTAATAACTTTTATAATTTT
58163991 TTAGAGCTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (35 bp):
ATTTTACAATTTCTAATAACTTTTATAATTTTAAT
Found at i:58165018 original size:2 final size:2
Alignment explanation
Indices: 58165011--58165036 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
58165001 GTTGTTTCTT
58165011 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
58165037 AATAATTAAG
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:58180860 original size:18 final size:18
Alignment explanation
Indices: 58180832--58180873 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
58180822 TACTATGCAA
*
58180832 AAAATAATTTAAAATTTAT
1 AAAA-AATTTAAAATATAT
58180851 AAAAAATTTAAAATATAT
1 AAAAAATTTAAAATATAT
58180869 AAAAA
1 AAAAA
58180874 GTTAATTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAAAATTTAAAATATAT
Found at i:58180878 original size:17 final size:18
Alignment explanation
Indices: 58180840--58180878 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
58180830 AAAAAATAAT
* *
58180840 TTAAAATTTATAAAAAAT
1 TTAAAATATATAAAAAAG
58180858 TTAAAATATAT-AAAAAG
1 TTAAAATATATAAAAAAG
58180875 TTAA
1 TTAA
58180879 TTTGATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
TTAAAATATATAAAAAAG
Found at i:58190123 original size:21 final size:19
Alignment explanation
Indices: 58190088--58190130 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
58190078 TTGCATAAAC
58190088 TCAAATTAGCACATCACTCGA
1 TCAAATTAGCACAT--CTCGA
**
58190109 TCAAATTAGTGCATCTCGA
1 TCAAATTAGCACATCTCGA
58190128 TCA
1 TCA
58190131 TTGCAAAAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 8 0.40
21 12 0.60
ACGTcount: A:0.35, C:0.26, G:0.12, T:0.28
Consensus pattern (19 bp):
TCAAATTAGCACATCTCGA
Found at i:58201084 original size:253 final size:252
Alignment explanation
Indices: 58200587--58201085 Score: 752
Period size: 253 Copynumber: 2.0 Consensus size: 252
58200577 ATAGAATGAG
* *
58200587 AGATTTTTGTTCTCATCACAGAACCCCGGGCCTAAGTTACTATTCCTTTAAAATGTAATCCTCAA
1 AGATTTTTGTTCTCATCACAGAACCCCAGGCCTAAGTTACAATTCCTTTAAAATGTAATCCTCAA
*
58200652 CCTGAAGAATTCAGTCAAACTACTTTCTACTCAACTTCCAAAGACCTTTACAAATATTTGGCCCC
66 CCTGAAGAATTCAGTCAAACTACTTTCCACTCAACTTCCAAAGACCTTTACAAATATTTGGCCCC
* * * *
58200717 ATCTTTCAACCTAAAGCTGATACTGCAATCTAGCTGGTACTTAGCAAAACTCATCCTACCCAACT
131 ATCCTTCAACCTAAAGCTGATACTACAACCTAGCTGCTACTTAGCAAAACTCATCCTACCCAACT
* * *
58200782 GGTTCGGTTCAGACCCAAAGCGATTGAATCAAATTCAAAATATTAAAAACAAATTCA
196 GGTTCAGTTCAGACCCAAAGCAATTGAATCAAATTCAAAATACTAAAAACAAATTCA
***
58200839 AGATTTTTGTTCT-AGTCACAGAACCCCAGTTTTAAGTTACAATTCCTTTAAAATGTAATCCTCA
1 AGATTTTTGTTCTCA-TCACAGAACCCCAGGCCTAAGTTACAATTCCTTTAAAATGTAATCCTCA
** * * *
58200903 ACCTGAAGAATTTGGTCAAACTACTTTCCACTCGACTTCCAAAGGCCTTCTTCAAATATTTGGCC
65 ACCTGAAGAATTCAGTCAAACTACTTTCCACTCAACTTCCAAAGACCTT-TACAAATATTTGGCC
*
58200968 CCATCCTTCAACCTAAAGCTGATA-TCACAACCTAGCTGCTACATTA-CAAAATTCATCCTACCC
129 CCATCCTTCAACCTAAAGCTGATACT-ACAACCTAGCTGCTAC-TTAGCAAAACTCATCCTACCC
* *
58201031 AACTTGTTCAGTTCAGACCCAAAGCAATTGAATCAAATTCGAAATACTAAAAACA
192 AACTGGTTCAGTTCAGACCCAAAGCAATTGAATCAAATTCAAAATACTAAAAACA
58201086 TCAAGAAAGA
Statistics
Matches: 222, Mismatches: 21, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
251 1 0.00
252 102 0.46
253 116 0.52
254 3 0.01
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (252 bp):
AGATTTTTGTTCTCATCACAGAACCCCAGGCCTAAGTTACAATTCCTTTAAAATGTAATCCTCAA
CCTGAAGAATTCAGTCAAACTACTTTCCACTCAACTTCCAAAGACCTTTACAAATATTTGGCCCC
ATCCTTCAACCTAAAGCTGATACTACAACCTAGCTGCTACTTAGCAAAACTCATCCTACCCAACT
GGTTCAGTTCAGACCCAAAGCAATTGAATCAAATTCAAAATACTAAAAACAAATTCA
Found at i:58201619 original size:2 final size:2
Alignment explanation
Indices: 58201614--58201648 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
58201604 TTCCCCCCAA
58201614 AG AG 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 AG AG A
58201649 TCAAACTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:58203615 original size:13 final size:13
Alignment explanation
Indices: 58203594--58203644 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
58203584 TTAAAGTTAG
*
58203594 ATTATTATATTAT
1 ATTAGTATATTAT
58203607 ATTAGTATATTAT
1 ATTAGTATATTAT
* *
58203620 ATTTATTATTTTA-
1 A-TTAGTATATTAT
58203633 ATTAG-ATATTAT
1 ATTAGTATATTAT
58203645 TGTTAAGTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
11 5 0.16
12 3 0.10
13 14 0.45
14 9 0.29
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (13 bp):
ATTAGTATATTAT
Found at i:58204622 original size:153 final size:153
Alignment explanation
Indices: 58204344--58204649 Score: 585
Period size: 153 Copynumber: 2.0 Consensus size: 153
58204334 TTAGAAACTC
*
58204344 TTTATGCGACTAAGTCTCTAGCTAACCATTTAGTGTTGAAACAACGTCTATTTAAATTTTGCATT
1 TTTATGCGACTAAGTCTCTAGCTAACCATTTAGTGTTGAAACAACGTCTATTTAAATTTTGCATG
*
58204409 AACGAATGTAAGCTTCCTAGAGTTCACACCAGTCAATTCATTACTCTTTTAAATGATTTAAAGAA
66 AACGAATGTAAGCTTCCTAGAGATCACACCAGTCAATTCATTACTCTTTTAAATGATTTAAAGAA
58204474 TGTTGAGGTTCATATTGACCCAG
131 TGTTGAGGTTCATATTGACCCAG
58204497 TTTATGCGACTAAGTCTCTAGCTAACCATTTAGTGTTGAAACAACGTCTATTTAAATTTTGCATG
1 TTTATGCGACTAAGTCTCTAGCTAACCATTTAGTGTTGAAACAACGTCTATTTAAATTTTGCATG
*
58204562 AACGAATGTGAGCTTCCTAGAGATCACACCAGTCAATTCATTACTCTTTTAAATGATTTAAAGAA
66 AACGAATGTAAGCTTCCTAGAGATCACACCAGTCAATTCATTACTCTTTTAAATGATTTAAAGAA
58204627 TGTTGAGGTTCATATTGACCCAG
131 TGTTGAGGTTCATATTGACCCAG
58204650 AAGATCAAGC
Statistics
Matches: 150, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
153 150 1.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (153 bp):
TTTATGCGACTAAGTCTCTAGCTAACCATTTAGTGTTGAAACAACGTCTATTTAAATTTTGCATG
AACGAATGTAAGCTTCCTAGAGATCACACCAGTCAATTCATTACTCTTTTAAATGATTTAAAGAA
TGTTGAGGTTCATATTGACCCAG
Found at i:58207013 original size:20 final size:20
Alignment explanation
Indices: 58206977--58207014 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
58206967 CCAATGTTGA
*
58206977 CCCATTTTCTCTATTTTTGG
1 CCCATTTTCACTATTTTTGG
*
58206997 CCCATTTTCACTCTTTTT
1 CCCATTTTCACTATTTTT
58207015 ACTCTCATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.29, G:0.05, T:0.55
Consensus pattern (20 bp):
CCCATTTTCACTATTTTTGG
Found at i:58208929 original size:11 final size:11
Alignment explanation
Indices: 58208909--58208952 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
58208899 ATGATGAAAT
*
58208909 AAAATTAAAAG
1 AAAATAAAAAG
* *
58208920 AAAAGAAAAAT
1 AAAATAAAAAG
*
58208931 AAAATAAAAAT
1 AAAATAAAAAG
58208942 AAAATAAAAAG
1 AAAATAAAAAG
58208953 TAGTTTTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.14
Consensus pattern (11 bp):
AAAATAAAAAG
Found at i:58208931 original size:22 final size:22
Alignment explanation
Indices: 58208905--58208951 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
58208895 CCTAATGATG
*
58208905 AAATAAAATTAAAAGAAAAGAA
1 AAATAAAATAAAAAGAAAAGAA
* *
58208927 AAATAAAATAAAAATAAAATAA
1 AAATAAAATAAAAAGAAAAGAA
58208949 AAA
1 AAA
58208952 GTAGTTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (22 bp):
AAATAAAATAAAAAGAAAAGAA
Found at i:58208976 original size:14 final size:13
Alignment explanation
Indices: 58208959--58208998 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
58208949 AAAGTAGTTT
58208959 TAAAAAGATAAAAA
1 TAAAAA-ATAAAAA
58208973 TAAAAACATAAAAA
1 TAAAAA-ATAAAAA
*
58208987 TAATAAATAAAA
1 TAAAAAATAAAA
58208999 GTCTTTAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 6 0.25
14 18 0.75
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (13 bp):
TAAAAAATAAAAA
Found at i:58212785 original size:42 final size:42
Alignment explanation
Indices: 58212736--58212819 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
58212726 AAGTGTGAAA
*
58212736 GTTTAATTATAGAATAAAGAAAATTGAAAGGACTAAATAAGT
1 GTTTAATTATAGAATAAAGAAAACTGAAAGGACTAAATAAGT
58212778 GTTTAATTATAGAATAAAGAAAACTGAAAGGACTAAATAAGT
1 GTTTAATTATAGAATAAAGAAAACTGAAAGGACTAAATAAGT
58212820 AAATAAACCA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.52, C:0.04, G:0.17, T:0.27
Consensus pattern (42 bp):
GTTTAATTATAGAATAAAGAAAACTGAAAGGACTAAATAAGT
Found at i:58213522 original size:20 final size:20
Alignment explanation
Indices: 58213475--58213515 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
58213465 AAAAGCAGGG
58213475 AAAGAAAGAAAGAAAGGAGA
1 AAAGAAAGAAAGAAAGGAGA
58213495 AAAGAAAG-AAGAAAGG-GA
1 AAAGAAAGAAAGAAAGGAGA
58213513 AAA
1 AAA
58213516 TTGAAAGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 5 0.24
19 8 0.38
20 8 0.38
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (20 bp):
AAAGAAAGAAAGAAAGGAGA
Found at i:58214892 original size:20 final size:21
Alignment explanation
Indices: 58214869--58214917 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
58214859 AATTATATTG
58214869 AATTGAAAAAAAATAT-AATT
1 AATTGAAAAAAAATATGAATT
**
58214889 AATT-AATTAAAATATGAATT
1 AATTGAAAAAAAATATGAATT
*
58214909 AACTGAAAA
1 AATTGAAAA
58214918 CTCAAAAGTC
Statistics
Matches: 22, Mismatches: 5, Indels: 3
0.73 0.17 0.10
Matches are distributed among these distances:
19 9 0.41
20 11 0.50
21 2 0.09
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (21 bp):
AATTGAAAAAAAATATGAATT
Found at i:58215059 original size:12 final size:12
Alignment explanation
Indices: 58215042--58215066 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
58215032 TCCGACTACT
58215042 GTTACTGTTACC
1 GTTACTGTTACC
58215054 GTTACTGTTACC
1 GTTACTGTTACC
58215066 G
1 G
58215067 ATTCGGTATT
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:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (12 bp):
GTTACTGTTACC
Found at i:58215218 original size:53 final size:47
Alignment explanation
Indices: 58215097--58215205 Score: 166
Period size: 47 Copynumber: 2.3 Consensus size: 47
58215087 GATATTGTTA
* * * *
58215097 CTGT-TACCGTTACTGTTACTATTTCGGATTTGTTCCGATGAGGTACT
1 CTGTGTACCG-TACTGTTACTGTTCCGGATTTGTTCCGATGAGGCACC
58215144 CTGTGTACCGTACTGTTACTGTTCCGGATTTGTTCCGATGAGGCACC
1 CTGTGTACCGTACTGTTACTGTTCCGGATTTGTTCCGATGAGGCACC
58215191 CTGTGTACCGTACTG
1 CTGTGTACCGTACTG
58215206 CTATTGTTAC
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
47 52 0.91
48 5 0.09
ACGTcount: A:0.16, C:0.23, G:0.24, T:0.38
Consensus pattern (47 bp):
CTGTGTACCGTACTGTTACTGTTCCGGATTTGTTCCGATGAGGCACC
Found at i:58215353 original size:18 final size:18
Alignment explanation
Indices: 58215330--58215532 Score: 157
Period size: 18 Copynumber: 11.3 Consensus size: 18
58215320 AAAAGTATAA
* *
58215330 AATAATTGATTATTACTG
1 AATAATTGACTGTTACTG
*
58215348 AATAATTGACTGTTAC-C
1 AATAATTGACTGTTACTG
*
58215365 AGATAATTAACTGTTACTG
1 A-ATAATTGACTGTTACTG
*
58215384 GAT-ATTAGACTGTTACTG
1 AATAATT-GACTGTTACTG
* * *
58215402 AATAACTGAATATTACTG
1 AATAATTGACTGTTACTG
*
58215420 AATAATTGA-TCATTACTG
1 AATAATTGACT-GTTACTG
* * *
58215438 AATAACTGATTGTCACTG
1 AATAATTGACTGTTACTG
*
58215456 AATGAA-TGACTGCTACTG
1 AAT-AATTGACTGTTACTG
* *
58215474 AATAACTTAATTGTTACTG
1 AATAA-TTGACTGTTACTG
*
58215493 AAT-ATCTGA-TTTTACTG
1 AATAAT-TGACTGTTACTG
58215510 AATAATTGACTGTTACTG
1 AATAATTGACTGTTACTG
*
58215528 GATAA
1 AATAA
58215533 CCGATCAATT
Statistics
Matches: 148, Mismatches: 25, Indels: 24
0.75 0.13 0.12
Matches are distributed among these distances:
17 21 0.14
18 110 0.74
19 17 0.11
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (18 bp):
AATAATTGACTGTTACTG
Found at i:58221313 original size:21 final size:21
Alignment explanation
Indices: 58221272--58221313 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
58221262 CACTACAATA
* *
58221272 TTTCCTATCACTTCCTTTTAT
1 TTTCCTATCACTTCATATTAT
58221293 TTTCCT-TCACTATCATATTAT
1 TTTCCTATCACT-TCATATTAT
58221314 GAACATAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.19, C:0.26, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTCCTATCACTTCATATTAT
Found at i:58222226 original size:40 final size:38
Alignment explanation
Indices: 58222142--58222257 Score: 115
Period size: 40 Copynumber: 2.9 Consensus size: 38
58222132 TGAGTTACCA
* * *
58222142 TAGTGAATCAGAAACAAATCCTATCCACTTTATATATTTC
1 TAGTGAATCAG-AATAAATCCTATTCACTTTA-ATTTTTC
* *
58222182 TAGTGAATCACGAATAAATCATATTCACTTTAATTTCTTT
1 TAGTGAATCA-GAATAAATCCTATTCACTTTAATTT-TTC
* *
58222222 TAGTGAATTAGGAATAGATCCTATTCACTTTTAATT
1 TAGTGAATCA-GAATAAATCCTATTCAC-TTTAATT
58222258 CTTGAGAAGG
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
39 3 0.05
40 53 0.83
41 8 0.12
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (38 bp):
TAGTGAATCAGAATAAATCCTATTCACTTTAATTTTTC
Found at i:58223396 original size:35 final size:32
Alignment explanation
Indices: 58223357--58223426 Score: 79
Period size: 32 Copynumber: 2.1 Consensus size: 32
58223347 TTAATTATTT
*
58223357 ATTTTA-TTTAATTAATATAATATAATAATATAATA
1 ATTTTACTTAAATT-ATAT-ATA-AAT-ATATAATA
*
58223392 ATTTTACTTAAATTATATGTAAATATATAATA
1 ATTTTACTTAAATTATATATAAATATATAATA
58223424 ATT
1 ATT
58223427 ACTAATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
32 11 0.34
33 3 0.09
34 2 0.06
35 10 0.31
36 6 0.19
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (32 bp):
ATTTTACTTAAATTATATATAAATATATAATA
Found at i:58226293 original size:42 final size:42
Alignment explanation
Indices: 58226245--58226325 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
58226235 AGGTGTCATG
58226245 ACATTGGACATGTAATTAGAGTAATCTGCCCCTAGTGTTGCA
1 ACATTGGACATGTAATTAGAGTAATCTGCCCCTAGTGTTGCA
* *
58226287 ACATTGGACATGTAATTAGAGTAATTTTCCCCTAGTGTT
1 ACATTGGACATGTAATTAGAGTAATCTGCCCCTAGTGTT
58226326 TTGCACACTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (42 bp):
ACATTGGACATGTAATTAGAGTAATCTGCCCCTAGTGTTGCA
Found at i:58227288 original size:23 final size:23
Alignment explanation
Indices: 58227226--58227291 Score: 60
Period size: 23 Copynumber: 2.9 Consensus size: 23
58227216 TAATGCACCG
** *
58227226 AAGTGCTAGAATGAATCACACCA
1 AAGTGCTAGAATGAATTGCAACA
* * * **
58227249 TAGTACCAGAACAAATTGCAACA
1 AAGTGCTAGAATGAATTGCAACA
58227272 AAGTGCTAGAATGAATTGCA
1 AAGTGCTAGAATGAATTGCA
58227292 TCGAAGTGTC
Statistics
Matches: 30, Mismatches: 13, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.44, C:0.18, G:0.18, T:0.20
Consensus pattern (23 bp):
AAGTGCTAGAATGAATTGCAACA
Found at i:58227298 original size:23 final size:22
Alignment explanation
Indices: 58227210--58227299 Score: 56
Period size: 23 Copynumber: 3.9 Consensus size: 22
58227200 TACATTCCAC
58227210 AGAATGTAA-TGCACCGAAGTGCT
1 AGAATG-AATTGCA-CGAAGTGCT
** * * *
58227233 AGAATGAATCACACCATAGTACC
1 AGAATGAATTGCACGA-AGTGCT
** *
58227256 AGAACAAATTGCAACAAAGTGCT
1 AGAATGAATTGC-ACGAAGTGCT
58227279 AGAATGAATTGCATCGAAGTG
1 AGAATGAATTGCA-CGAAGTG
58227300 TCAAATGCTC
Statistics
Matches: 48, Mismatches: 15, Indels: 8
0.68 0.21 0.11
Matches are distributed among these distances:
22 5 0.10
23 40 0.83
24 3 0.06
ACGTcount: A:0.41, C:0.18, G:0.21, T:0.20
Consensus pattern (22 bp):
AGAATGAATTGCACGAAGTGCT
Found at i:58232349 original size:94 final size:94
Alignment explanation
Indices: 58232239--58232422 Score: 314
Period size: 94 Copynumber: 2.0 Consensus size: 94
58232229 CAAGCCAATT
* * *
58232239 TGACTTTTCATATGTAAAAGGAGTTTAGTGGTCCAAAAAGAAAAACAAATGAAGTATTACGGGCT
1 TGACTTTTCACATGTAAAAGCAGTTTAGTGGTCCAAAAAGAAAAACAAATGAAGCATTACGGGCT
58232304 TGACCAATTTGCATCCTTCAATGCTAATC
66 TGACCAATTTGCATCCTTCAATGCTAATC
**
58232333 TGACTTTTCACATGTAAAAGCAGTTTAGTGGTCCAAAAAGAAAAACAAATGAAGCATTGTGGGCT
1 TGACTTTTCACATGTAAAAGCAGTTTAGTGGTCCAAAAAGAAAAACAAATGAAGCATTACGGGCT
*
58232398 TGACCAATTTGTATCCTTCAATGCT
66 TGACCAATTTGCATCCTTCAATGCT
58232423 TCCTCCACAC
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
94 84 1.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.30
Consensus pattern (94 bp):
TGACTTTTCACATGTAAAAGCAGTTTAGTGGTCCAAAAAGAAAAACAAATGAAGCATTACGGGCT
TGACCAATTTGCATCCTTCAATGCTAATC
Found at i:58237266 original size:21 final size:21
Alignment explanation
Indices: 58237238--58237281 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
58237228 TTTTAGTTTT
58237238 ATTTT-AT-TTTG-TTTCTCC
1 ATTTTCATATTTGTTTTCTCC
*
58237256 ATTTTCATATTTGTTTTCTCT
1 ATTTTCATATTTGTTTTCTCC
58237277 ATTTT
1 ATTTT
58237282 ATGTTTCTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 5 0.23
19 2 0.09
20 4 0.18
21 11 0.50
ACGTcount: A:0.14, C:0.14, G:0.05, T:0.68
Consensus pattern (21 bp):
ATTTTCATATTTGTTTTCTCC
Found at i:58239266 original size:2 final size:2
Alignment explanation
Indices: 58239259--58239292 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
58239249 AGGAAACAGG
58239259 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
58239293 CCCTCCTACC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:58240160 original size:20 final size:20
Alignment explanation
Indices: 58240105--58240160 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
58240095 ATGTCACATC
*
58240105 AAAAATAATTTAAAAATTAT
1 AAAAATAATTTAAAAAATAT
*
58240125 AAAAAT-ATTTAGAAAATA-
1 AAAAATAATTTAAAAAATAT
58240143 AAAAATTAATTTAAAAAA
1 AAAAA-TAATTTAAAAAA
58240161 ATATTTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 5 0.16
19 11 0.35
20 15 0.48
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (20 bp):
AAAAATAATTTAAAAAATAT
Found at i:58240166 original size:12 final size:13
Alignment explanation
Indices: 58240141--58240173 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
58240131 ATTTAGAAAA
*
58240141 TAAAAAATTAATT
1 TAAAAAAATAATT
58240154 TAAAAAAAT-ATT
1 TAAAAAAATAATT
58240166 TAAAAAAA
1 TAAAAAAA
58240174 ACATGATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
TAAAAAAATAATT
Found at i:58247942 original size:74 final size:74
Alignment explanation
Indices: 58247821--58247966 Score: 283
Period size: 74 Copynumber: 2.0 Consensus size: 74
58247811 TTGGCCAAGG
58247821 CTAAATTAGCAGAAGTTAAATCCTTATAACCCATGATGAACTGGTTATGTAGATTACAATGACCT
1 CTAAATTAGCAGAAGTTAAATCCTTATAACCCATGATGAACTGGTTATGTAGATTACAATGACCT
58247886 GTAATTGGC
66 GTAATTGGC
*
58247895 CTAAATTAGCAGAAGTTAAATCCTTATAACCCATGGTGAACTGGTTATGTAGATTACAATGACCT
1 CTAAATTAGCAGAAGTTAAATCCTTATAACCCATGATGAACTGGTTATGTAGATTACAATGACCT
58247960 GTAATTG
66 GTAATTG
58247967 AGCTAGCTTT
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 71 1.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.32
Consensus pattern (74 bp):
CTAAATTAGCAGAAGTTAAATCCTTATAACCCATGATGAACTGGTTATGTAGATTACAATGACCT
GTAATTGGC
Found at i:58255611 original size:31 final size:29
Alignment explanation
Indices: 58255566--58255623 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 29
58255556 TCTCAAAATT
*
58255566 ATATATTAACTTTGATTTAATGTGTAATTTG
1 ATATATAAACTTTGATTT-A-GTGTAATTTG
*
58255597 ATATATAAATTTTGATTTAGTGTAATT
1 ATATATAAACTTTGATTTAGTGTAATT
58255624 ATACACCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.32
30 1 0.04
31 16 0.64
ACGTcount: A:0.34, C:0.02, G:0.12, T:0.52
Consensus pattern (29 bp):
ATATATAAACTTTGATTTAGTGTAATTTG
Found at i:58255817 original size:29 final size:32
Alignment explanation
Indices: 58255766--58255838 Score: 102
Period size: 30 Copynumber: 2.4 Consensus size: 32
58255756 ATTGTGTTAA
*
58255766 TAATTTATAAGAATTAGATC-AAATTAAAATT
1 TAATATATAAGAATTAGATCAAAATTAAAATT
58255797 TAATATATAA-AATTAGA-CAAAATTAAAATT
1 TAATATATAAGAATTAGATCAAAATTAAAATT
58255827 T-ATATAT-AGAAT
1 TAATATATAAGAAT
58255839 AACACATTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
28 1 0.03
29 10 0.26
30 19 0.49
31 9 0.23
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (32 bp):
TAATATATAAGAATTAGATCAAAATTAAAATT
Found at i:58255855 original size:31 final size:30
Alignment explanation
Indices: 58255790--58255866 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 30
58255780 TAGATCAAAT
* * *
58255790 TAAAATTTAATATATAAAATTAGACAAAAT
1 TAAAATTTAATATATAAAATAACACAAAAC
*
58255820 TAAAATTT-ATATATAGAATAACACATTAAAC
1 TAAAATTTAATATATAAAATAACACA--AAAC
*
58255851 TAAAA-TTAATGTATAA
1 TAAAATTTAATATATAA
58255867 TTTTAAGATT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
29 14 0.37
30 10 0.26
31 14 0.37
ACGTcount: A:0.57, C:0.05, G:0.04, T:0.34
Consensus pattern (30 bp):
TAAAATTTAATATATAAAATAACACAAAAC
Found at i:58256630 original size:18 final size:18
Alignment explanation
Indices: 58256599--58256634 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
58256589 TAAGGTAAAA
58256599 AAATTTAAATACTAAATT
1 AAATTTAAATACTAAATT
58256617 AAATATTAAA-ACTAAATT
1 AAAT-TTAAATACTAAATT
58256635 GAGGTACCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATTTAAATACTAAATT
Found at i:58257004 original size:3 final size:3
Alignment explanation
Indices: 58256996--58257029 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
58256986 GAATCCCAGG
*
58256996 TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
58257030 GGCATTGACG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:58272898 original size:18 final size:18
Alignment explanation
Indices: 58272875--58272967 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
58272865 CCCAACTACT
*
58272875 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
58272893 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
*
58272911 GTATACGTGAATAGTACT
1 GTATACGTGAATAGTACC
*
58272929 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
58272947 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
58272965 GTA
1 GTA
58272968 AACGGTCGTA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:58272927 original size:36 final size:36
Alignment explanation
Indices: 58272875--58272967 Score: 168
Period size: 36 Copynumber: 2.6 Consensus size: 36
58272865 CCCAACTACT
*
58272875 GTATACGTGAACAGTACCGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
*
58272911 GTATACGTGAATAGTACTGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
58272947 GTATACGTGAATAGTACCGTA
1 GTATACGTGAATAGTACCGTA
58272968 AACGGTCGTA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (36 bp):
GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
Found at i:58274599 original size:120 final size:120
Alignment explanation
Indices: 58274402--58275401 Score: 1860
Period size: 120 Copynumber: 8.3 Consensus size: 120
58274392 TTTTCAAGTT
*
58274402 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
* *
58274467 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
*
58274522 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
*
58274587 TAATATAAGAATATTAATTATTAAGAAATTTT-TTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAG-AATTTTATTAAATTATATATTTTAATTAAA
*
58274642 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
* *
58274707 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
58274762 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
*
58274827 TAATATAAGAATATTAATTATTAAGAATTTCATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
58274882 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
* *
58274947 TAATATAAGAATATT-ATCCAATTAAGAATTTCATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAAT--TATTAAGAATTTTATTAAATTATATATTTTAATTAAA
58275003 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
58275068 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
58275123 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
58275188 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
58275243 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
58275308 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
58275363 ATATATTTAATAATAATTATGTTAATTTATATTTTACAG
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAG
58275402 AATACAAGTG
Statistics
Matches: 868, Mismatches: 7, Indels: 10
0.98 0.01 0.01
Matches are distributed among these distances:
119 8 0.01
120 736 0.85
121 122 0.14
122 2 0.00
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.48
Consensus pattern (120 bp):
ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
Found at i:58275122 original size:18 final size:17
Alignment explanation
Indices: 58275094--58275128 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
58275084 ATTATTAAGA
*
58275094 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
58275111 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
58275129 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:58275242 original size:18 final size:17
Alignment explanation
Indices: 58275214--58275248 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
58275204 ATTATTAAGA
*
58275214 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
58275231 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
58275249 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:58275303 original size:481 final size:480
Alignment explanation
Indices: 58274402--58275401 Score: 1860
Period size: 481 Copynumber: 2.1 Consensus size: 480
58274392 TTTTCAAGTT
*
58274402 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
* **
58274467 TAATATAAGAATATTAATTATTAAGAATTTTTTTAAATTATATAGTTTAATTAAAATATATTTAA
66 TAATATAAGAATATTAATAATTAAGAATTTCATTAAATTATATAGTTTAATTAAAATATATTTAA
*
58274532 TAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTAATATAAGA
131 TAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGA
58274597 ATATTAATTATTAAGAAATTTTTTAAATTATATAGTTTAATTAAAATATATTTAATAATAATTAT
196 ATATTAATTATTAAGAAATTTTTTAAATTATATAGTTTAATTAAAATATATTTAATAATAATTAT
*
58274662 GTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTA
261 GTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTA
*
58274727 TTAAGAATTTTTTTAAATTATATAGTTTAATTAAAATATATTTAATAATAATTATGTTAATTTAT
326 TTAAGAATTTTATTAAATTATATAGTTTAATTAAAATATATTTAATAATAATTATGTTAATTTAT
58274792 ATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTT
391 ATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTT
58274857 CATTAAATTATATATTTTAATTAAA
456 CATTAAATTATATATTTTAATTAAA
58274882 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
*
58274947 TAATATAAGAATATT-ATCCAATTAAGAATTTCATTAAATTATATATTTTAATTAAAATATATTT
66 TAATATAAGAATATTAAT--AATTAAGAATTTCATTAAATTATATAGTTTAATTAAAATATATTT
58275011 AATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAA
129 AATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAA
*
58275076 GAATATTAATTATTAAG-AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAAT
194 GAATATTAATTATTAAGAAATTTT-TTAAATTATATAGTTTAATTAAAATATATTTAATAATAAT
58275140 TATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAA
258 TATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAA
*
58275205 TTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATT
323 TTATTAAGAATTTTATTAAATTATATAGTTTAATTAAAATATATTTAATAATAATTATGTTAATT
58275270 TATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAA
388 TATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAA
*
58275335 TTTTATTAAATTATATATTTTAATTAAA
453 TTTCATTAAATTATATATTTTAATTAAA
58275363 ATATATTTAATAATAATTATGTTAATTTATATTTTACAG
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAG
58275402 AATACAAGTG
Statistics
Matches: 506, Mismatches: 11, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
479 2 0.00
480 85 0.17
481 419 0.83
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.48
Consensus pattern (480 bp):
ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
TAATATAAGAATATTAATAATTAAGAATTTCATTAAATTATATAGTTTAATTAAAATATATTTAA
TAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGA
ATATTAATTATTAAGAAATTTTTTAAATTATATAGTTTAATTAAAATATATTTAATAATAATTAT
GTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTA
TTAAGAATTTTATTAAATTATATAGTTTAATTAAAATATATTTAATAATAATTATGTTAATTTAT
ATTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTT
CATTAAATTATATATTTTAATTAAA
Found at i:58275362 original size:18 final size:17
Alignment explanation
Indices: 58275334--58275368 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
58275324 ATTATTAAGA
*
58275334 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
58275351 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
58275369 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:58287523 original size:20 final size:19
Alignment explanation
Indices: 58287498--58287541 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
58287488 AAATTTAAAA
*
58287498 TTTTATTATATGTCTTAT-TT
1 TTTTATT-TATAT-TTATATT
58287518 TTTTATTTATATTTATATT
1 TTTTATTTATATTTATATT
58287537 TTTTA
1 TTTTA
58287542 ATATGTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 4 0.18
19 11 0.50
20 7 0.32
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTTATTTATATTTATATT
Found at i:58292921 original size:71 final size:71
Alignment explanation
Indices: 58292838--58292973 Score: 245
Period size: 71 Copynumber: 1.9 Consensus size: 71
58292828 ACGGTAAGTT
* * *
58292838 GAAACCCAGCAGGATTAGGTATGATTTCTCGAATTTCCAAACACAAAATATTGCCTTATTTTAAT
1 GAAACCCAGCAGGATTAGGCACGATTTCTCAAATTTCCAAACACAAAATATTGCCTTATTTTAAT
58292903 AATGTC
66 AATGTC
58292909 GAAACCCAGCAGGATTAGGCACGATTTCTCAAATTTCCAAACACAAAATATTGCCTTATTTTAAT
1 GAAACCCAGCAGGATTAGGCACGATTTCTCAAATTTCCAAACACAAAATATTGCCTTATTTTAAT
58292974 TTAAGAAAAC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
71 62 1.00
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (71 bp):
GAAACCCAGCAGGATTAGGCACGATTTCTCAAATTTCCAAACACAAAATATTGCCTTATTTTAAT
AATGTC
Found at i:58293431 original size:18 final size:18
Alignment explanation
Indices: 58293390--58293432 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
58293380 AAGATAAAAT
*
58293390 AATATATAAAAACTCTTTA
1 AATATATAAAAACTC-TAA
58293409 AATATATAAACAACTC-AA
1 AATATATAAA-AACTCTAA
58293427 AATATA
1 AATATA
58293433 ATGTGTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 7 0.32
19 10 0.45
20 5 0.23
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (18 bp):
AATATATAAAAACTCTAA
Found at i:58293503 original size:24 final size:24
Alignment explanation
Indices: 58293436--58293534 Score: 99
Period size: 24 Copynumber: 4.0 Consensus size: 24
58293426 AAATATAATG
* *
58293436 TGTAAAAAAAGTTTAAAATACATAA
1 TGTATAAAAA-TTTAAAATAAATAA
* *
58293461 TATATGAAAATATTAAAATAAATAA
1 TGTATAAAAAT-TTAAAATAAATAA
* * **
58293486 TGTATAAAAATTTGAAATGAATGT
1 TGTATAAAAATTTAAAATAAATAA
*
58293510 TGTATAAAAAGTTAAAATAAATAA
1 TGTATAAAAATTTAAAATAAATAA
58293534 T
1 T
58293535 AACAAAAAAA
Statistics
Matches: 58, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
24 30 0.52
25 28 0.48
ACGTcount: A:0.58, C:0.01, G:0.09, T:0.32
Consensus pattern (24 bp):
TGTATAAAAATTTAAAATAAATAA
Found at i:58293640 original size:15 final size:15
Alignment explanation
Indices: 58293620--58293651 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
58293610 ATATAAATAG
58293620 AAATAGAAATATAAT
1 AAATAGAAATATAAT
58293635 AAATAGAAATATAAT
1 AAATAGAAATATAAT
58293650 AA
1 AA
58293652 TAGTTGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (15 bp):
AAATAGAAATATAAT
Done.