Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold339
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: 1314099
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
File 8 of 9
Found at i:1100989 original size:31 final size:31
Alignment explanation
Indices: 1100951--1101011 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
1100941 CCCGTTTATT
1100951 AAAAAATCTCCCCCTTAATCAAGTAATTCAA
1 AAAAAATCTCCCCCTTAATCAAGTAATTCAA
1100982 AAAAAATCTCCCCCTTAATCAAGTAATTCA
1 AAAAAATCTCCCCCTTAATCAAGTAATTCA
1101012 TATCAAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.44, C:0.26, G:0.03, T:0.26
Consensus pattern (31 bp):
AAAAAATCTCCCCCTTAATCAAGTAATTCAA
Found at i:1102823 original size:13 final size:13
Alignment explanation
Indices: 1102805--1102842 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1102795 ATAAACACCC
1102805 TGTATCGATACAG
1 TGTATCGATACAG
*
1102818 TGTATCGATACAT
1 TGTATCGATACAG
1102831 TGTATCGATACA
1 TGTATCGATACA
1102843 AATAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1104942 original size:15 final size:15
Alignment explanation
Indices: 1104922--1104952 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1104912 ATTTCGTTTG
*
1104922 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1104937 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1104952 G
1 G
1104953 GACATTTTTA
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:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1109036 original size:13 final size:13
Alignment explanation
Indices: 1109018--1109043 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1109008 CAATTTTTTG
1109018 TGTATCGATACAT
1 TGTATCGATACAT
1109031 TGTATCGATACAT
1 TGTATCGATACAT
1109044 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1109108 original size:21 final size:21
Alignment explanation
Indices: 1109082--1109157 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1109072 CTGCCAAGAA
*
1109082 ATGTATCGATACATCTTTTTT
1 ATGTATCGATACATCTTTTTC
****
1109103 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1109123 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1109144 ATGTATCGATACAT
1 ATGTATCGATACAT
1109158 TGCAACATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1109128 original size:20 final size:20
Alignment explanation
Indices: 1109103--1109175 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1109093 CATCTTTTTT
1109103 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1109123 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1109144 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1109164 ATGTATCGATAC
1 ATGTATCGATAC
1109176 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1109139 original size:41 final size:41
Alignment explanation
Indices: 1109082--1109175 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1109072 CTGCCAAGAA
*
1109082 ATGTATCGATACATCTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1109123 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1109164 ATGTATCGATAC
1 ATGTATCGATAC
1109176 TTTGAATTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:1111486 original size:20 final size:20
Alignment explanation
Indices: 1111461--1111515 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
1111451 GTGTGAACAG
* *
1111461 TGATGTATCGATACTATTTA
1 TGATGTATCGATACAAATTA
1111481 TGATGTATCGATACAAATTA
1 TGATGTATCGATACAAATTA
*
1111501 TAATGTATCGATACA
1 TGATGTATCGATACA
1111516 TGCATTTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (20 bp):
TGATGTATCGATACAAATTA
Found at i:1111559 original size:103 final size:103
Alignment explanation
Indices: 1111380--1111598 Score: 429
Period size: 103 Copynumber: 2.1 Consensus size: 103
1111370 ACACGCTCCA
1111380 ATGTATCGATACAAATTATAATGTATCGATACATGCATTTGAATTTATAGCCATTGGGCTTTTAT
1 ATGTATCGATACAAATTATAATGTATCGATACATGCATTTGAATTTATAGCCATTGGGCTTTTAT
1111445 TAAATGGTGTGAACAGTGATGTATCGATACTATTTATG
66 TAAATGGTGTGAACAGTGATGTATCGATACTATTTATG
*
1111483 ATGTATCGATACAAATTATAATGTATCGATACATGCATTTGAATTTATAGCCGTTGGGCTTTTAT
1 ATGTATCGATACAAATTATAATGTATCGATACATGCATTTGAATTTATAGCCATTGGGCTTTTAT
1111548 TAAATGGTGTGAACAGTGATGTATCGATACTATTTATG
66 TAAATGGTGTGAACAGTGATGTATCGATACTATTTATG
1111586 ATGTATCGATACA
1 ATGTATCGATACA
1111599 CTGTATCGAT
Statistics
Matches: 115, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 115 1.00
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (103 bp):
ATGTATCGATACAAATTATAATGTATCGATACATGCATTTGAATTTATAGCCATTGGGCTTTTAT
TAAATGGTGTGAACAGTGATGTATCGATACTATTTATG
Found at i:1111605 original size:13 final size:13
Alignment explanation
Indices: 1111586--1111624 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1111576 ACTATTTATG
1111586 ATGTATCGATACA
1 ATGTATCGATACA
*
1111599 CTGTATCGATACA
1 ATGTATCGATACA
*
1111612 ATGTATTGATACA
1 ATGTATCGATACA
1111625 TGAATAGTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1111704 original size:21 final size:22
Alignment explanation
Indices: 1111667--1111727 Score: 106
Period size: 21 Copynumber: 2.8 Consensus size: 22
1111657 CATGAATAGT
*
1111667 GATACGTGAACAGTGATGTATC
1 GATACATGAACAGTGATGTATC
1111689 GATACATGAA-AGTGATGTATC
1 GATACATGAACAGTGATGTATC
1111710 GATACATGAACAGTGATG
1 GATACATGAACAGTGATG
1111728 AATAGTGATG
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
21 21 0.57
22 16 0.43
ACGTcount: A:0.36, C:0.11, G:0.26, T:0.26
Consensus pattern (22 bp):
GATACATGAACAGTGATGTATC
Found at i:1111734 original size:10 final size:10
Alignment explanation
Indices: 1111715--1111745 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1111705 GTATCGATAC
1111715 ATGAACAGTG
1 ATGAACAGTG
*
1111725 ATGAATAGTG
1 ATGAACAGTG
1111735 ATGAACAGTG
1 ATGAACAGTG
1111745 A
1 A
1111746 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:1111833 original size:53 final size:53
Alignment explanation
Indices: 1111769--1111903 Score: 227
Period size: 53 Copynumber: 2.6 Consensus size: 53
1111759 CTACTACCAA
* *
1111769 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCTAGTGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* *
1111822 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1111875 TGTATCGATACATA-TTTGTGTATCGATAC
1 TGTATCGATACATATTTTGTGTATCGATAC
1111904 TATGCAATCT
Statistics
Matches: 77, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
52 14 0.18
53 63 0.82
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.38
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:1111936 original size:20 final size:20
Alignment explanation
Indices: 1111875--1111943 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
1111865 GCCAATGTCC
1111875 TGTATCGATACATATT--TG
1 TGTATCGATACATATTAATG
* *
1111893 TGTATCGATAC-TATGCAATC
1 TGTATCGATACATAT-TAATG
1111913 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
1111933 TGTATCGATAC
1 TGTATCGATAC
1111944 TTTTCAGGGT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.07
18 11 0.26
20 27 0.64
21 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:1112009 original size:21 final size:21
Alignment explanation
Indices: 1111983--1112023 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1111973 GTCAACCTTG
1111983 TGTATTAATACCAAT-CGTATA
1 TGTATTAATA-CAATACGTATA
*
1112004 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
1112024 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:1113662 original size:13 final size:13
Alignment explanation
Indices: 1113644--1113668 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1113634 ACTGAAGTAA
1113644 TGTATCGATACAT
1 TGTATCGATACAT
1113657 TGTATCGATACA
1 TGTATCGATACA
1113669 ATCTGGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1115321 original size:84 final size:84
Alignment explanation
Indices: 1115168--1115332 Score: 194
Period size: 84 Copynumber: 2.0 Consensus size: 84
1115158 CATTTTCCAC
* * *
1115168 TTGCAACTCATTTCTTTTCTCCTCTAATTCATTTATTTTCTTTTTAAAAGAATTATTTTCTAAAC
1 TTGCAACTCATTTCTATTCTCCTCTAATTCATTTAATTTCTTTTTAAAAGAATTATTCTCTAAAC
1115233 TCATTGATTTACTTTCATT
66 TCATTGATTTACTTTCATT
* *
1115252 TTGCAACTC-TTTCATATTCTTCTCTAATTC-TCTTAATTTC-TTTT-CAAGAATATCATTCTCT
1 TTGCAACTCATTTC-TATTCTCCTCTAATTCAT-TTAATTTCTTTTTAAAAGAAT-T-ATTCTCT
* * *
1115313 ACAGTCATTGATTTATTTTC
62 AAACTCATTGATTTACTTTC
1115333 TTCTTTGAGT
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
82 6 0.09
83 10 0.14
84 53 0.77
ACGTcount: A:0.24, C:0.19, G:0.04, T:0.52
Consensus pattern (84 bp):
TTGCAACTCATTTCTATTCTCCTCTAATTCATTTAATTTCTTTTTAAAAGAATTATTCTCTAAAC
TCATTGATTTACTTTCATT
Found at i:1117487 original size:21 final size:22
Alignment explanation
Indices: 1117450--1117510 Score: 106
Period size: 21 Copynumber: 2.8 Consensus size: 22
1117440 CATGAATAGT
*
1117450 GATACGTGAACAGTGATGTATC
1 GATACATGAACAGTGATGTATC
1117472 GATACATGAA-AGTGATGTATC
1 GATACATGAACAGTGATGTATC
1117493 GATACATGAACAGTGATG
1 GATACATGAACAGTGATG
1117511 AATAGTGATG
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
21 21 0.57
22 16 0.43
ACGTcount: A:0.36, C:0.11, G:0.26, T:0.26
Consensus pattern (22 bp):
GATACATGAACAGTGATGTATC
Found at i:1117517 original size:10 final size:10
Alignment explanation
Indices: 1117498--1117528 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1117488 GTATCGATAC
1117498 ATGAACAGTG
1 ATGAACAGTG
*
1117508 ATGAATAGTG
1 ATGAACAGTG
1117518 ATGAACAGTG
1 ATGAACAGTG
1117528 A
1 A
1117529 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:1117616 original size:53 final size:53
Alignment explanation
Indices: 1117552--1117688 Score: 229
Period size: 53 Copynumber: 2.6 Consensus size: 53
1117542 CTACTACCAA
*
1117552 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAGTAACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATAACC
* **
1117605 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATAACC
1117658 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
1117689 TATGCAATCT
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 65 0.83
54 13 0.17
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATAACC
Found at i:1117721 original size:20 final size:20
Alignment explanation
Indices: 1117658--1117728 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
1117648 GCCAATGTCC
**
1117658 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
1117678 TGTATCGATAC-TATGCAATC
1 TGTATCGATACATAT-TAATG
1117698 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
1117718 TGTATCGATAC
1 TGTATCGATAC
1117729 TTTTTAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:1119122 original size:29 final size:29
Alignment explanation
Indices: 1119035--1119125 Score: 80
Period size: 29 Copynumber: 3.1 Consensus size: 29
1119025 TCAATGAATC
* *
1119035 AGGGACAATTATGTAATTTCATGCATTTT
1 AGGGACTATTATGTAATTTCATGCATATT
* * *
1119064 A-GAACTATTCTAGTAATTTTTCAT--AAATT
1 AGGGACTATTAT-GTAA--TTTCATGCATATT
*
1119093 AGGGATTATTATGTAATTTCATGCATATT
1 AGGGACTATTATGTAATTTCATGCATATT
1119122 AGGG
1 AGGG
1119126 CCATTAAAGT
Statistics
Matches: 47, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
27 6 0.13
28 7 0.15
29 21 0.45
30 7 0.15
31 6 0.13
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (29 bp):
AGGGACTATTATGTAATTTCATGCATATT
Found at i:1119195 original size:29 final size:29
Alignment explanation
Indices: 1119157--1119256 Score: 82
Period size: 29 Copynumber: 3.4 Consensus size: 29
1119147 TTTTAAGACC
1119157 TTTTACGTAATTTTATGCATTTTAAGATTA
1 TTTTACGTAATTTTATGCA-TTTAAGATTA
* *
1119187 TTTTA-GTAATTTGTTATG-ATTTAGGACTA
1 TTTTACGTAA-TT-TTATGCATTTAAGATTA
* * * *
1119216 -TTTATGCAATTTTATGCATTTCAGAGTCA
1 TTTTACGTAATTTTATGCATTTAAGA-TTA
1119245 TTTTA-GTAATTT
1 TTTTACGTAATTT
1119257 GCCATGTTTT
Statistics
Matches: 56, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
27 5 0.09
28 12 0.21
29 22 0.39
30 12 0.21
31 5 0.09
ACGTcount: A:0.28, C:0.07, G:0.13, T:0.52
Consensus pattern (29 bp):
TTTTACGTAATTTTATGCATTTAAGATTA
Found at i:1119195 original size:58 final size:58
Alignment explanation
Indices: 1119148--1119257 Score: 143
Period size: 58 Copynumber: 1.9 Consensus size: 58
1119138 TTTTTCATAT
* *
1119148 TTTAAGACCT-TTTACGTAATTTTATGCATTTTAAGA-TTATTTTAGTAATTTGTTATGA
1 TTTAAGA-CTATTTACGCAATTTTATGCA-TTTAAGAGTCATTTTAGTAATTTGTTATGA
* * *
1119206 TTTAGGACTATTTATGCAATTTTATGCATTTCAGAGTCATTTTAGTAATTTG
1 TTTAAGACTATTTACGCAATTTTATGCATTTAAGAGTCATTTTAGTAATTTG
1119258 CCATGTTTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
57 8 0.18
58 37 0.82
ACGTcount: A:0.28, C:0.08, G:0.14, T:0.50
Consensus pattern (58 bp):
TTTAAGACTATTTACGCAATTTTATGCATTTAAGAGTCATTTTAGTAATTTGTTATGA
Found at i:1119253 original size:116 final size:116
Alignment explanation
Indices: 1119047--1119256 Score: 248
Period size: 116 Copynumber: 1.8 Consensus size: 116
1119037 GGACAATTAT
* *
1119047 GTAATTTCATGCATTTTAGAACTATTCTAGTAATTTTTCATAAATTAGGGATTATTATGTAATTT
1 GTAATTTCATGCATTTTAGAACTATTCTAGTAATTTTTCATAAATTAGGGACTATTATGCAATTT
*
1119112 CATGCATATTAGGGCCATTAAAGTAATTTTTCATATTTTAAGACCTTTTAC
66 CATGCATATTAGAGCCATTAAAGTAATTTTTCATATTTTAAGACCTTTTAC
* * * * *
1119163 GTAATTTTATGCATTTTA-AGATTATTTTAGTAATTTGTT-ATGATTTA-GGACTATTTATGCAA
1 GTAATTTCATGCATTTTAGA-ACTATTCTAGTAATTT-TTCATAAATTAGGGACTA-TTATGCAA
* * **
1119225 TTTTATGCAT-TTCAGAGTCATTTTAGTAATTT
63 TTTCATGCATATT-AGAGCCATTAAAGTAATTT
1119257 GCCATGTTTT
Statistics
Matches: 78, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
115 8 0.10
116 68 0.87
117 2 0.03
ACGTcount: A:0.30, C:0.09, G:0.13, T:0.48
Consensus pattern (116 bp):
GTAATTTCATGCATTTTAGAACTATTCTAGTAATTTTTCATAAATTAGGGACTATTATGCAATTT
CATGCATATTAGAGCCATTAAAGTAATTTTTCATATTTTAAGACCTTTTAC
Found at i:1121034 original size:21 final size:20
Alignment explanation
Indices: 1121010--1121055 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
1121000 TTCTACAATT
1121010 TGTATCAATACAATAAGTGAA
1 TGTATCAATAC-ATAAGTGAA
**
1121031 TGTATTGATACATAAGTGAA
1 TGTATCAATACATAAGTGAA
1121051 TGTAT
1 TGTAT
1121056 TGATACAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.35
Consensus pattern (20 bp):
TGTATCAATACATAAGTGAA
Found at i:1121047 original size:20 final size:20
Alignment explanation
Indices: 1121017--1121083 Score: 84
Period size: 20 Copynumber: 3.2 Consensus size: 20
1121007 ATTTGTATCA
1121017 ATACAATAAGTGAATGTATTG
1 ATAC-ATAAGTGAATGTATTG
1121038 ATACATAAGTGAATGTATTG
1 ATACATAAGTGAATGTATTG
1121058 ATAC--AAGTTTGAAATGTATTG
1 ATACATAAG--TG-AATGTATTG
1121079 ATACA
1 ATACA
1121084 GGACCATGTC
Statistics
Matches: 42, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.07
20 22 0.52
21 17 0.40
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.34
Consensus pattern (20 bp):
ATACATAAGTGAATGTATTG
Found at i:1124232 original size:59 final size:59
Alignment explanation
Indices: 1124124--1124246 Score: 158
Period size: 59 Copynumber: 2.1 Consensus size: 59
1124114 CTAAAGTATT
* * * * * * *
1124124 GATTTTCCACCATCGAGGATACTCTAACCTCGTTATTTTCGAGGGGATACTCTAACCTC
1 GATTTTCCACCATCAAGGATACTCCAACCTCGTTATTCTCGACGAGATACTCCAACCCC
*
1124183 GATTTTCCACCATCAAGGATACTCCAACCTCGTTGTTC-CTGACGAGATACTCCAACCCC
1 GATTTTCCACCATCAAGGATACTCCAACCTCGTTATTCTC-GACGAGATACTCCAACCCC
1124242 GATTT
1 GATTT
1124247 ATTTCCAAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
58 1 0.02
59 54 0.98
ACGTcount: A:0.24, C:0.30, G:0.15, T:0.30
Consensus pattern (59 bp):
GATTTTCCACCATCAAGGATACTCCAACCTCGTTATTCTCGACGAGATACTCCAACCCC
Found at i:1124355 original size:79 final size:77
Alignment explanation
Indices: 1124181--1124517 Score: 265
Period size: 78 Copynumber: 4.3 Consensus size: 77
1124171 TACTCTAACC
* * * * ** ** * * *
1124181 TCGATTTTCCACCATCAAGGATACTCCAACCTCGTTGTTCCTGACGAGATACTCCAACC-CCGAT
1 TCGATTTTCCACCATCGAGGATACTCTAACC-CATTATTTTTGGGGGGATACTCCAACCTCGGTT
*
1124245 TTATTTCCAAAACA
65 TTA-TTCTAAAACA
** * * *
1124259 -CTGATTTTCCATAATCGAGGATACTCTAACCTCATTATTTTTGGGGGGATGCTCTAACCTTGGT
1 TC-GATTTTCCACCATCGAGGATACTCTAACC-CATTATTTTTGGGGGGATACTCCAACCTCGGT
1124323 TTTACTTCTAAAACA
64 TTTA-TTCTAAAACA
* * * * * * *
1124338 TCGATTTTTCACCATCGAGGATACTCTAACCCATTGTTTCTGAGAGGATACTCCAACCCCGGCTT
1 TCGATTTTCCACCATCGAGGATACTCTAACCCATTATTTTTGGGGGGATACTCCAACCTCGGTTT
1124403 TATATCTAAAACA
66 TAT-TCTAAAACA
* * * * *
1124416 T-GATTTTCCACAATCGAGGATACTCCAACCCTGTTATTTTCGAGGGGG-TACTCCAA-CTCCAG
1 TCGATTTTCCACCATCGAGGATACTCTAACCC-ATTATTTTTG-GGGGGATACTCCAACCT-CGG
1124478 TTTTATTTCTAAAACA
63 TTTTA-TTCTAAAACA
1124494 TCGA-TTTCCACCATC-AGGGATACT
1 TCGATTTTCCACCATCGA-GGATACT
1124518 TCAACCCCAG
Statistics
Matches: 206, Mismatches: 43, Indels: 20
0.77 0.16 0.07
Matches are distributed among these distances:
77 31 0.15
78 128 0.62
79 46 0.22
80 1 0.00
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (77 bp):
TCGATTTTCCACCATCGAGGATACTCTAACCCATTATTTTTGGGGGGATACTCCAACCTCGGTTT
TATTCTAAAACA
Found at i:1124481 original size:156 final size:156
Alignment explanation
Indices: 1124181--1124523 Score: 412
Period size: 156 Copynumber: 2.2 Consensus size: 156
1124171 TACTCTAACC
*
1124181 TCGATTTTCCACCATCAAGGATACTCCAACCTCGTTGTTCCTGACGAGATACTCCAACCCCGATT
1 TCGATTTTCCACCATC-AGGATACTCCAACCTCATTGTTCCTGACGAGATACTCCAACCCCGATT
* * * * *
1124246 TATTTCCAAAACACTGATTTTCCATAATCGAGGATACTCTAACCTCATTATTTTTGGGGGGATGC
65 TATATCCAAAACACTGATTTTCCACAATCGAGGATACTCCAACCTCATTATTTTCGGGGGGATAC
* **
1124311 TCTAACCTTGGTTTTACTTCTAAAACA
130 TCCAACCTCAGTTTTACTTCTAAAACA
* * * *
1124338 TCGATTTTTCACCATCGAGGATACTCTAACC-CATTGTTTCTGA-GAGGATACTCCAACCCCGGC
1 TCGATTTTCCACCATC-AGGATACTCCAACCTCATTGTTCCTGACGA-GATACTCCAACCCC-GA
* *
1124401 TTTATATCTAAAACA-TGATTTTCCACAATCGAGGATACTCCAACC-CTGTTATTTTCGAGGGGG
63 TTTATATCCAAAACACTGATTTTCCACAATCGAGGATACTCCAACCTC-ATTATTTTCG-GGGGG
*
1124464 -TACTCCAA-CTCCAGTTTTATTTCTAAAACA
126 ATACTCCAACCT-CAGTTTTACTTCTAAAACA
*
1124494 TCGA-TTTCCACCATCAGGGATACTTCAACC
1 TCGATTTTCCACCATCA-GGATACTCCAACC
1124524 CCAGTTTTAT
Statistics
Matches: 160, Mismatches: 20, Indels: 14
0.82 0.10 0.07
Matches are distributed among these distances:
154 1 0.01
155 26 0.16
156 86 0.54
157 47 0.29
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (156 bp):
TCGATTTTCCACCATCAGGATACTCCAACCTCATTGTTCCTGACGAGATACTCCAACCCCGATTT
ATATCCAAAACACTGATTTTCCACAATCGAGGATACTCCAACCTCATTATTTTCGGGGGGATACT
CCAACCTCAGTTTTACTTCTAAAACA
Found at i:1124549 original size:50 final size:51
Alignment explanation
Indices: 1124464--1124576 Score: 151
Period size: 50 Copynumber: 2.2 Consensus size: 51
1124454 TTCGAGGGGG
* * *
1124464 TACTCCAACTCCAGTTTTATTTCTAAAACATCGA-TTTCCACCATCAGGGA
1 TACTTCAACCCCAGTTTTATTTCTAAAACATCGATTTTCCACAATCAGGGA
*
1124514 TACTTCAACCCCAGTTTTATTT-TCAAAATATCGATTTTCCACAATCAGGGA
1 TACTTCAACCCCAGTTTTATTTCT-AAAACATCGATTTTCCACAATCAGGGA
1124565 TACTAT-AACCCC
1 TACT-TCAACCCC
1124577 GTTGTTTCTG
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
49 1 0.02
50 29 0.52
51 25 0.45
52 1 0.02
ACGTcount: A:0.31, C:0.27, G:0.09, T:0.33
Consensus pattern (51 bp):
TACTTCAACCCCAGTTTTATTTCTAAAACATCGATTTTCCACAATCAGGGA
Found at i:1124612 original size:129 final size:129
Alignment explanation
Indices: 1124383--1124653 Score: 327
Period size: 129 Copynumber: 2.1 Consensus size: 129
1124373 GTTTCTGAGA
* * *
1124383 GGATACTCCAACCCCGGCTTTATATCTAAAACATGATTTTCCACAATCGAGGATACTCCAACCCT
1 GGATACTCCAACCCCAGCTTTATATCTAAAACATGATTTTCCACAATCGAGGATACTACAACCCC
* *
1124448 GTTATTTTCGAGGGGGTACTCCAACTCCAGTTTTATTTCTAAAACATCGA-TTTCCACCATCAG
66 GTTATTTTCGAGGGGATACTCCAACTCCAGTTTTATTTCTAAAACATCGATTTTCCACAATCAG
* * * * *
1124511 GGATACTTCAACCCCAGTTTTAT-TTTCAAAATATCGATTTTCCACAATC-AGGGATACTATAAC
1 GGATACTCCAACCCCAGCTTTATATCT-AAAACAT-GATTTTCCACAATCGA-GGATACTACAAC
* * *
1124574 CCCGTT-GTTTCTGAGGGGATACTCCAAC-CTCGGTTTTATTTCTAAAACATTGATTTTCCACAA
63 CCCGTTATTTTC-GAGGGGATACTCCAACTC-CAGTTTTATTTCTAAAACATCGATTTTCCACAA
*
1124637 TCGG
126 TCAG
*
1124641 GGATGCTCCAACC
1 GGATACTCCAACC
1124654 TTGTTATATT
Statistics
Matches: 121, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
127 2 0.02
128 32 0.26
129 65 0.54
130 22 0.18
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.32
Consensus pattern (129 bp):
GGATACTCCAACCCCAGCTTTATATCTAAAACATGATTTTCCACAATCGAGGATACTACAACCCC
GTTATTTTCGAGGGGATACTCCAACTCCAGTTTTATTTCTAAAACATCGATTTTCCACAATCAG
Found at i:1124738 original size:79 final size:78
Alignment explanation
Indices: 1124510--1124761 Score: 258
Period size: 79 Copynumber: 3.2 Consensus size: 78
1124500 TCCACCATCA
* * *
1124510 GGGATACTTCAACCCCAGTTTTATTT-TCAAAATATCGATTTTCCACAATC-AGGGATACTATAA
1 GGGATACTCCAACCCCAGTTTTATTTCT-AAAACATCGATTTTCCACAATCGA-GGATACTCTAA
* *
1124573 CCCCGTTGTTTCTGAG
64 CCCTGTTATTTC-GAG
* * * * * *
1124589 GGGATACTCCAACCTCGGTTTTATTTCTAAAACATTGATTTTCCACAATCGGGGATGCTCCAACC
1 GGGATACTCCAACCCCAGTTTTATTTCTAAAACATCGATTTTCCACAATCGAGGATACTCTAACC
*
1124654 TTGTTATATTCGAG
66 CTGTTAT-TTCGAG
* * * * *
1124668 GGGATACTTCAACCCCAGTTTTATTTCTAAAACACCGATTTTTCATC-CTCGAGGATATTCTAAC
1 GGGATACTCCAACCCCAGTTTTATTTCTAAAACATCGATTTTCCA-CAATCGAGGATACTCTAAC
*
1124732 CCTGTTATTTTCGAA
65 CCTGTTA-TTTCGAG
*
1124747 AGGATACTCCAACCC
1 GGGATACTCCAACCC
1124762 TGATTTTGTT
Statistics
Matches: 141, Mismatches: 27, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
79 135 0.96
80 6 0.04
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (78 bp):
GGGATACTCCAACCCCAGTTTTATTTCTAAAACATCGATTTTCCACAATCGAGGATACTCTAACC
CTGTTATTTCGAG
Found at i:1124798 original size:158 final size:158
Alignment explanation
Indices: 1124510--1124816 Score: 345
Period size: 158 Copynumber: 1.9 Consensus size: 158
1124500 TCCACCATCA
* *
1124510 GGGATACTTCAACCCCAGTTTTATTTTCAAAATATCGATTTTCCACAATCAGGGATACTATAACC
1 GGGATACTTCAACCCCAGTTTTATTTTCAAAACACCGATTTTCCACAATCAGGGATACTATAACC
** * * * *
1124575 CCGTTGTTTCTGAGGGGATACTCCAACCTCGGTTTTATTTCTAAAACATTGATTTTCCACAATCG
66 CCGTTGTTTCTGAAAGGATACTCCAACCTCGATTTTATTCCCAAAACATCGATTTTCCACAATCG
*
1124640 GGGATGCTCCAACCTTGTTATATTCGAG
131 GGGATGCTCCAACCCTGTTATATTCGAG
* * * *
1124668 GGGATACTTCAACCCCAGTTTTA-TTTCTAAAACACCGATTTTTCATC-CTC-GAGGATATTCTA
1 GGGATACTTCAACCCCAGTTTTATTTTC-AAAACACCGATTTTCCA-CAATCAG-GGATACTATA
* * * * *
1124730 ACCCTGTTATTT-TCGAAAGGATACTCCAACC-CTGATTTTGTTCCCAAAATATCGATTTTTCAC
63 ACCCCGTTGTTTCT-GAAAGGATACTCCAACCTC-GATTTTATTCCCAAAACATCGATTTTCCAC
* **
1124793 CATCGGGGATTTTCCAACCCTGTT
126 AATCGGGGATGCTCCAACCCTGTT
1124817 TTTTCTCTAA
Statistics
Matches: 123, Mismatches: 21, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
157 7 0.06
158 115 0.93
159 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (158 bp):
GGGATACTTCAACCCCAGTTTTATTTTCAAAACACCGATTTTCCACAATCAGGGATACTATAACC
CCGTTGTTTCTGAAAGGATACTCCAACCTCGATTTTATTCCCAAAACATCGATTTTCCACAATCG
GGGATGCTCCAACCCTGTTATATTCGAG
Found at i:1128725 original size:20 final size:20
Alignment explanation
Indices: 1128684--1128732 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1128674 AGGCATAATT
*
1128684 TATCGATA-AATTCTTCATG
1 TATCGATACAATTCTTCACG
1128703 TATCGATACAATGT-TTCACG
1 TATCGATACAAT-TCTTCACG
1128723 TATCGATACA
1 TATCGATACA
1128733 TTTCACTTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 8 0.30
20 18 0.67
21 1 0.04
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (20 bp):
TATCGATACAATTCTTCACG
Found at i:1128819 original size:20 final size:20
Alignment explanation
Indices: 1128794--1128866 Score: 146
Period size: 20 Copynumber: 3.6 Consensus size: 20
1128784 CTATCAATAC
1128794 AATGTATCGATACTAGGCAT
1 AATGTATCGATACTAGGCAT
1128814 AATGTATCGATACTAGGCAT
1 AATGTATCGATACTAGGCAT
1128834 AATGTATCGATACTAGGCAT
1 AATGTATCGATACTAGGCAT
1128854 AATGTATCGATAC
1 AATGTATCGATAC
1128867 ATCTAGATAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (20 bp):
AATGTATCGATACTAGGCAT
Found at i:1129024 original size:21 final size:20
Alignment explanation
Indices: 1128998--1129049 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 20
1128988 TTAAGGTTTG
*
1128998 AAAACACTTATACGAAACTCT
1 AAAACA-TTATACGAAAATCT
1129019 AAAACATTTATACGAAAATCT
1 AAAACA-TTATACGAAAATCT
1129040 AAAACATTAT
1 AAAACATTAT
1129050 TGATATTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 4 0.14
21 25 0.86
ACGTcount: A:0.52, C:0.17, G:0.04, T:0.27
Consensus pattern (20 bp):
AAAACATTATACGAAAATCT
Found at i:1129705 original size:13 final size:13
Alignment explanation
Indices: 1129687--1129712 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1129677 TACAGCAAGT
1129687 ATGTATCGATACA
1 ATGTATCGATACA
1129700 ATGTATCGATACA
1 ATGTATCGATACA
1129713 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1130955 original size:19 final size:18
Alignment explanation
Indices: 1130905--1130993 Score: 75
Period size: 19 Copynumber: 5.1 Consensus size: 18
1130895 TTGAATTTCA
1130905 ATAA-TTTGTATCGATAC
1 ATAAGTTTGTATCGATAC
*
1130922 A-ACAGTAAATGTATCGATAC
1 ATA-AGT--TTGTATCGATAC
1130942 ATAAGTGTTGTATCGATA-
1 ATAAGT-TTGTATCGATAC
1130960 A-AA---TGTATCGATAC
1 ATAAGTTTGTATCGATAC
1130974 ATAAGTTTTGTATCGATAC
1 ATAAG-TTTGTATCGATAC
1130993 A
1 A
1130994 ATGTATCGCT
Statistics
Matches: 58, Mismatches: 3, Indels: 20
0.72 0.04 0.25
Matches are distributed among these distances:
13 10 0.17
14 1 0.02
15 2 0.03
16 1 0.02
17 4 0.07
18 2 0.03
19 22 0.38
20 15 0.26
21 1 0.02
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (18 bp):
ATAAGTTTGTATCGATAC
Found at i:1130969 original size:32 final size:32
Alignment explanation
Indices: 1130928--1131006 Score: 131
Period size: 32 Copynumber: 2.5 Consensus size: 32
1130918 ATACAACAGT
1130928 AAATGTATCGATACATAAGTGTTGTATCGATA
1 AAATGTATCGATACATAAGTGTTGTATCGATA
*
1130960 AAATGTATCGATACATAAGTTTTGTATCGATA
1 AAATGTATCGATACATAAGTGTTGTATCGATA
* *
1130992 CAATGTATCGCTACA
1 AAATGTATCGATACA
1131007 AAGCTACTGC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (32 bp):
AAATGTATCGATACATAAGTGTTGTATCGATA
Found at i:1131063 original size:13 final size:13
Alignment explanation
Indices: 1131045--1131072 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1131035 CATTTTTCAA
1131045 TGTATCGATACAT
1 TGTATCGATACAT
1131058 TGTATCGATACAT
1 TGTATCGATACAT
1131071 TG
1 TG
1131073 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1131067 original size:33 final size:33
Alignment explanation
Indices: 1131025--1131090 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1131015 GCCAAGGAAA
**
1131025 TGTATCGATACATTTTTCAATGTATCGATACAT
1 TGTATCGATACATTGATCAATGTATCGATACAT
**
1131058 TGTATCGATACATTGATCTTTGTATCGATACAT
1 TGTATCGATACATTGATCAATGTATCGATACAT
1131091 CTAGGAAGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATTGATCAATGTATCGATACAT
Found at i:1133503 original size:50 final size:51
Alignment explanation
Indices: 1133437--1133611 Score: 221
Period size: 50 Copynumber: 3.4 Consensus size: 51
1133427 AATTTCTCAT
*
1133437 AATCTGGGG-TACTCCAACCCCGATTTTATTTCTAAAACACTAATTTTCCAC
1 AATC-GGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTCCAC
* * * *
1133488 GATCGGGGATA-TCCAACCCCGGTTTTATTT-TCAAAACACCAATTTTCTAT
1 AATCGGGGATACTCCAACCCCGATTTTATTTCT-AAAACACCAATTTTCCAC
* * *
1133538 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCAC
1 AATCGGGGATACTCCAACCCCGATTTTATTT-CTAAAACACCAATTTTCCAC
*
1133590 AATCGAGGATACTCCAACCCCG
1 AATCGGGGATACTCCAACCCCG
1133612 TTAATCATCG
Statistics
Matches: 105, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
49 1 0.01
50 47 0.45
51 22 0.21
52 35 0.33
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.30
Consensus pattern (51 bp):
AATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTCCAC
Found at i:1133617 original size:24 final size:26
Alignment explanation
Indices: 1133591--1133641 Score: 93
Period size: 27 Copynumber: 1.9 Consensus size: 26
1133581 ATTTTTCACA
1133591 ATCGAGGATACTCCAACCCCGTTAATC
1 ATCGAGGATACTCCAACCCCGTTAA-C
1133618 ATCGAGGATACTCCAACCCCGTTA
1 ATCGAGGATACTCCAACCCCGTTA
1133642 TTTTTGAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.29, C:0.33, G:0.16, T:0.22
Consensus pattern (26 bp):
ATCGAGGATACTCCAACCCCGTTAAC
Found at i:1133661 original size:107 final size:106
Alignment explanation
Indices: 1133542--1133745 Score: 277
Period size: 107 Copynumber: 1.9 Consensus size: 106
1133532 TTCTATAATC
* *
1133542 GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACCCCGATTTTATTT-CAAAAACACCAATTTCTCACAATCGAGGATACTCCAA
1133607 CCCCGTTA-ATCATCGA-GGATACTCCAACCCCGTTATTTTTGA
65 CCCCGTTATATC-T-GAGGGATACTCCAACCCCGTTATTTTTGA
* * *** *
1133649 GGGGATACTCCAACCCCGATTTTATTTCTAAAATATTGATTTCTCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCAAAAACACCAATTTCTCACAATCGAGGATACTCCAAC
*
1133714 CCCGTTATTTCTGAGGGGATACTCCAACCCCG
66 CCCGTTATATCTGA-GGGATACTCCAACCCCG
1133746 ACTTTATTCC
Statistics
Matches: 85, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
105 2 0.02
106 39 0.46
107 44 0.52
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (106 bp):
GGGGATACTCCAACCCCGATTTTATTTCAAAAACACCAATTTCTCACAATCGAGGATACTCCAAC
CCCGTTATATCTGAGGGATACTCCAACCCCGTTATTTTTGA
Found at i:1133706 original size:79 final size:79
Alignment explanation
Indices: 1133618--1133901 Score: 446
Period size: 79 Copynumber: 3.6 Consensus size: 79
1133608 CCCGTTAATC
* * *
1133618 ATCGAGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCCAACCCCGATTTTATTTCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTCCTAAAAT
1133683 ATTGATTTCTCACA
66 ATTGATTTCTCACA
*
1133697 ATCGGGGATACTCCAACCCCGTTA-TTTCTGAGGGGATACTCCAACCCCGACTTTATTCCTAAAA
1 ATCGGGGATACTCCAACCCCGTTATTTTC-GAGGGGATACTCCAACCCCGATTTTATTCCTAAAA
* *
1133761 TATTGATTTCTTAAA
65 TATTGATTTCTCACA
* *
1133776 ATCGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCTAACCCC-AGTTTTATTCCTAAAA
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGA-TTTTATTCCTAAAA
*
1133840 TATTGATTTCTCACG
65 TATTGATTTCTCACA
*
1133855 ATCGGGGATACTCCAACCCCGTTATTTTCGCGGGGATACTCCAACCC
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCC
1133902 TGTTATTTTT
Statistics
Matches: 187, Mismatches: 15, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
78 4 0.02
79 179 0.96
80 4 0.02
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.31
Consensus pattern (79 bp):
ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGATTTTATTCCTAAAAT
ATTGATTTCTCACA
Found at i:1133897 original size:28 final size:28
Alignment explanation
Indices: 1133857--1133928 Score: 117
Period size: 28 Copynumber: 2.6 Consensus size: 28
1133847 TTCTCACGAT
1133857 CGGGGATACTCCAACCCCGTTATTTTCG
1 CGGGGATACTCCAACCCCGTTATTTTCG
* *
1133885 CGGGGATACTCCAACCCTGTTATTTTTG
1 CGGGGATACTCCAACCCCGTTATTTTCG
*
1133913 AGGGGATACTCCAACC
1 CGGGGATACTCCAACC
1133929 TCGATTTTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.28
Consensus pattern (28 bp):
CGGGGATACTCCAACCCCGTTATTTTCG
Found at i:1133970 original size:79 final size:79
Alignment explanation
Indices: 1133887--1134059 Score: 233
Period size: 79 Copynumber: 2.2 Consensus size: 79
1133877 TATTTTCGCG
** * *
1133887 GGGATACTCCAACCCTGTTATTTTTGAGGGGATACTCCAA-CCTCGATTTTA-TTCTCAAAACAC
1 GGGATACTCCAACCCTGTTATTTTCAAGGGAATACTCCAACCCT-GAATTTATTTC-CAAAACAC
* *
1133950 CAATTTTCTATAATTA
64 CAATTTTCCATAATCA
* *
1133966 GGGATACTCCAACCCTGTTATTTTCAAGGGAATACTCCAACCCTGAATTTATTTCCAGAACACCG
1 GGGATACTCCAACCCTGTTATTTTCAAGGGAATACTCCAACCCTGAATTTATTTCCAAAACACCA
1134031 ATTTTCCATAATCA
66 ATTTTCCATAATCA
*
1134045 GGGGTACTCCAACCC
1 GGGATACTCCAACCC
1134060 CGTCGTCATC
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
79 77 0.93
80 6 0.07
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (79 bp):
GGGATACTCCAACCCTGTTATTTTCAAGGGAATACTCCAACCCTGAATTTATTTCCAAAACACCA
ATTTTCCATAATCA
Found at i:1134055 original size:186 final size:186
Alignment explanation
Indices: 1133699--1134062 Score: 434
Period size: 186 Copynumber: 2.0 Consensus size: 186
1133689 TTCTCACAAT
* *
1133699 CGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGACTTTATTCCTAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGACTTTATTCCTAAAACAC
** * * * *
1133764 TGATTTCTTAAAATCGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCTAACCCCAGTTT
66 CAATTTCTTAAAATCAGGGATACTCCAACCCCGTTATTTTCAAGGGAATACTCCAACCCCAATTT
* ** *
1133829 TATTCCTAAAATATTGATTTCTCACGATCGGGGATACTCCAACCCCGTTATTTTCG
131 TATTCCTAAAACACCGATTTCTCACAATCGGGGATACTCCAACCCCGTTATTTTCG
* * * *
1133885 CGGGGATACTCCAACCCTGTTATTTTTGAGGGGATACTCCAACCTCGATTTTATT-CTCAAAACA
1 CGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGACTTTATTCCT-AAAACA
* * * *
1133949 CCAATTT-TCTATAATTAGGGATACTCCAACCCTGTTATTTTCAAGGGAATACTCCAACCCTGAA
65 CCAATTTCT-TAAAATCAGGGATACTCCAACCCCGTTATTTTCAAGGGAATACTCCAACCC-CAA
* *
1134013 -TTTATTTCC-AGAACACCGATTT-TCCATAATCAGGGG-TACTCCAACCCCGT
128 TTTTA-TTCCTAAAACACCGATTTCT-CACAATC-GGGGATACTCCAACCCCGT
1134063 CGTCATCTCC
Statistics
Matches: 150, Mismatches: 22, Indels: 12
0.82 0.12 0.07
Matches are distributed among these distances:
185 4 0.03
186 137 0.91
187 9 0.06
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.31
Consensus pattern (186 bp):
CGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCCGACTTTATTCCTAAAACAC
CAATTTCTTAAAATCAGGGATACTCCAACCCCGTTATTTTCAAGGGAATACTCCAACCCCAATTT
TATTCCTAAAACACCGATTTCTCACAATCGGGGATACTCCAACCCCGTTATTTTCG
Found at i:1135249 original size:17 final size:18
Alignment explanation
Indices: 1135227--1135264 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1135217 TTATAAGCAT
*
1135227 AAAGTCA-AAATACAAAG
1 AAAGTCACAAAAACAAAG
*
1135244 AAAGTCACAAAAACAAGG
1 AAAGTCACAAAAACAAAG
1135262 AAA
1 AAA
1135265 AATAAATATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.66, C:0.13, G:0.13, T:0.08
Consensus pattern (18 bp):
AAAGTCACAAAAACAAAG
Found at i:1136936 original size:71 final size:71
Alignment explanation
Indices: 1136855--1136997 Score: 259
Period size: 71 Copynumber: 2.0 Consensus size: 71
1136845 TTGGGTGTTG
*
1136855 GGTATAGATAGAAAAGAAAGAATGAGGCTCGAACTGTTCAAATAGTAACCCATGTATCGATACAA
1 GGTATAGATAGAAAAGAAAGAATGAGGCTCGAACTATTCAAATAGTAACCCATGTATCGATACAA
1136920 TGTATC
66 TGTATC
* *
1136926 GGTATCGATAGAAAAGAAAGAATGAGGCTCGAACTATTCAAATATTAACCCATGTATCGATACAA
1 GGTATAGATAGAAAAGAAAGAATGAGGCTCGAACTATTCAAATAGTAACCCATGTATCGATACAA
1136991 TGTATC
66 TGTATC
1136997 G
1 G
1136998 ATACAAAGAA
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (71 bp):
GGTATAGATAGAAAAGAAAGAATGAGGCTCGAACTATTCAAATAGTAACCCATGTATCGATACAA
TGTATC
Found at i:1136995 original size:13 final size:13
Alignment explanation
Indices: 1136977--1137003 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1136967 ATATTAACCC
1136977 ATGTATCGATACA
1 ATGTATCGATACA
1136990 ATGTATCGATACA
1 ATGTATCGATACA
1137003 A
1 A
1137004 AGAACATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1144145 original size:49 final size:49
Alignment explanation
Indices: 1144087--1144310 Score: 244
Period size: 49 Copynumber: 4.6 Consensus size: 49
1144077 GATGCCAATA
* * * *
1144087 TGCTGATTCAAGGCCAGTGATTTTGGACTCAAAGGTGAAGGTGCTAATG
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCTAATG
* * *
1144136 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGTGTTAATA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG---AAGGTGCTAATG
* * *
1144188 TGCTGATTCAAGGCCAGCGATATTGAACTTAAAGATGAATGTGCCAATG
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCTAATG
* * * * *
1144237 TGCTGATTCAAGGCCATCAACATTGGACTT--A-A--AA-GTGCCAATA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCTAATG
1144280 TGCTGATTCAAGGCCAGCGATATTGGACTTA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTA
1144311 GAAAAAGATG
Statistics
Matches: 150, Mismatches: 21, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
43 35 0.23
44 2 0.01
46 1 0.01
47 1 0.01
49 66 0.44
52 45 0.30
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (49 bp):
TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCTAATG
Found at i:1144159 original size:101 final size:101
Alignment explanation
Indices: 1144027--1144304 Score: 297
Period size: 101 Copynumber: 2.8 Consensus size: 101
1144017 ATGAGAAGAA
* * * * * ** *
1144027 TGCCAATGTGCTGACTCAAGGCCAGGGACATTGG-GTTCAGGAATGTTAGAGATGCCAATATGCT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAG-ATGACAAAGATGCCAATATGCT
* * * *
1144091 GATTCAAGGCCAGTGATTTTGGACTCAAAGGTGAAGG
65 GATTCAAGGCCAGCGATATTGAACTCAAAGATGAAGG
* * **
1144128 TGCTAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGTGTTAATATGCTG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGATGCCAATATGCTG
* *
1144193 ATTCAAGGCCAGCGATATTGAACTTAAAGATGAATG
66 ATTCAAGGCCAGCGATATTGAACTCAAAGATGAAGG
* *
1144229 TGCCAATGTGCTGATTCAAGGCCATCAACATTGGAC-T-----T-A-AAAG-TGCCAATATGCTG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGATGCCAATATGCTG
1144285 ATTCAAGGCCAGCGATATTG
66 ATTCAAGGCCAGCGATATTG
1144305 GACTTAGAAA
Statistics
Matches: 153, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
92 31 0.20
93 4 0.03
94 1 0.01
95 1 0.01
100 1 0.01
101 111 0.73
102 4 0.03
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (101 bp):
TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGATGCCAATATGCTG
ATTCAAGGCCAGCGATATTGAACTCAAAGATGAAGG
Found at i:1144289 original size:43 final size:43
Alignment explanation
Indices: 1144184--1144310 Score: 137
Period size: 43 Copynumber: 2.8 Consensus size: 43
1144174 CAAAGGTGTT
* * *
1144184 AATATGCTGATTCAAGGCCAGCGATATTGAACTTAAAGATGAATGTGCC
1 AATATGCTGATTCAAGGCCAGCAACATTGGACTT--A-A--AA-GTGCC
* *
1144233 AATGTGCTGATTCAAGGCCATCAACATTGGACTTAAAAGTGCC
1 AATATGCTGATTCAAGGCCAGCAACATTGGACTTAAAAGTGCC
* *
1144276 AATATGCTGATTCAAGGCCAGCGATATTGGACTTA
1 AATATGCTGATTCAAGGCCAGCAACATTGGACTTA
1144311 GAAAAAGATG
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
43 36 0.52
44 2 0.03
46 1 0.01
47 1 0.01
49 29 0.42
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (43 bp):
AATATGCTGATTCAAGGCCAGCAACATTGGACTTAAAAGTGCC
Found at i:1144465 original size:29 final size:29
Alignment explanation
Indices: 1144332--1144968 Score: 605
Period size: 29 Copynumber: 22.3 Consensus size: 29
1144322 CACCAACTTG
**
1144332 TGTGGGCTTTTGAAAGGGTTG-CACCAACT
1 TGTGGGCTTTTGAAA-GGTTGCCACTGACT
* *
1144361 TATGTGCTTTTG-AAGGTTGCCACTG-CTT
1 TGTGGGCTTTTGAAAGGTTGCCACTGAC-T
* *
1144389 TATGGGC-TTTG-AAGGTTGCCACTAACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
* *
1144416 TGTGGGC-TTTGAAA-ATGTGCCACTAACT
1 TGTGGGCTTTTGAAAGGT-TGCCACTGACT
* *
1144444 TGTGGGCTTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
* * *
1144473 TGTGGACTTTTG-GAGGTTGCCACTAACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
* * *
1144501 TGTGGGC-TTTGAAAGGGGTGCCACCGATT
1 TGTGGGCTTTTGAAA-GGTTGCCACTGACT
*
1144530 TGTGGGCTTTTGAAA-ATATGCCACTGACT
1 TGTGGGCTTTTGAAAGGT-TGCCACTGACT
1144559 TGTGGGCTTTTG-AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
* * * *
1144587 TGTGGGCGTTTGTAAGGGGTGCCACCGACT
1 TGTGGGCTTTTG-AAAGGTTGCCACTGACT
**
1144617 TGTGGGCTTTTGAAAATTTGCCACTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
*
1144646 TGTGGACTTTTG-AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
* *
1144674 TGTGGGCGTTTGAAA-ATATGCCACTGACT
1 TGTGGGCTTTTGAAAGGT-TGCCACTGACT
1144703 TGTGGGCTTTTG-AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
* * *
1144731 TGTGGGC-CTTGAAAGAGGTGCCACCGACT
1 TGTGGGCTTTTGAAAG-GTTGCCACTGACT
* * * *
1144760 TATGGGCTTTTGAAAAGATG-CATTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
1144788 TGTGGGCTTTTG-AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
* *
1144816 TGTGGGC-TTTGAAAGGGGTGCCACCGACT
1 TGTGGGCTTTTGAAA-GGTTGCCACTGACT
* * * *
1144845 TATGGGCTTTTAAAAAGATGCCACTGACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
*
1144874 TGTGGGCTTTTG-AAGG-TGCCACTAACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
* * * *
1144901 TATAGGC-TTTGAAAGGGGTGCCACCGACT
1 TGTGGGCTTTTGAAA-GGTTGCCACTGACT
* * *
1144930 TGTGGGCTTTTGAAAAGATGCCACTAACT
1 TGTGGGCTTTTGAAAGGTTGCCACTGACT
*
1144959 TATGGGCTTT
1 TGTGGGCTTT
1144969 GGAAGGTGAG
Statistics
Matches: 500, Mismatches: 80, Indels: 56
0.79 0.13 0.09
Matches are distributed among these distances:
26 4 0.01
27 67 0.13
28 162 0.32
29 217 0.43
30 50 0.10
ACGTcount: A:0.20, C:0.18, G:0.29, T:0.32
Consensus pattern (29 bp):
TGTGGGCTTTTGAAAGGTTGCCACTGACT
Found at i:1144494 original size:57 final size:57
Alignment explanation
Indices: 1144366--1144968 Score: 573
Period size: 57 Copynumber: 10.6 Consensus size: 57
1144356 CAACTTATGT
* * * *
1144366 GCTTTTGAAGGTTGCCACTG-CTTTATGGGC-TTTG-AAGGTTGCCACTAACTTGTGG
1 GCTTTTGAAGGTTGCCACTGAC-TTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGG
** *
1144421 GC-TTTGAAAATGTGCCACTAACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGG
1 GCTTTTGAAGGT-TGCCACTGACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGG
* * * * * * *
1144478 ACTTTTGGAGGTTGCCACTAACTTGTGGGC-TTTGAAAGGGGTGCCACCGATTTGTGG
1 GCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAA-AGATGCCACTGACTTGTGG
** * *
1144535 GCTTTTGAAAATATGCCACTGACTTGTGGGCTTTTG-AAGGTTGCCACTGACTTGTGG
1 GCTTTTGAAGGT-TGCCACTGACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGG
* * * **
1144592 GCGTTTGTAAGGGGTGCCACCGACTTGTGGGCTTTTGAAAATTTGCCACTGACTTGTGG
1 GCTTTTG-AA-GGTTGCCACTGACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGG
* * *
1144651 ACTTTTGAAGGTTGCCACTGACTTGTGGGCGTTTGAAAATATGCCACTGACTTGTGG
1 GCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGG
* * * *
1144708 GCTTTTGAAGGTTGCCACTGACTTGTGGGC-CTTGAAAGAGGTGCCACCGACTTATGG
1 GCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAA-AGATGCCACTGACTTGTGG
* * * * *
1144765 GCTTTTGAAAAGATG-CATTGACTTGTGGGCTTTTG-AAGGTTGCCACTGACTTGTGG
1 GCTTTTG-AAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGG
* * * *
1144821 GC-TTTGAAAGGGGTGCCACCGACTTATGGGCTTTTAAAAAGATGCCACTGACTTGTGG
1 GCTTTTG-AA-GGTTGCCACTGACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGG
* * * * * *
1144879 GCTTTTGAAGG-TGCCACTAACTTATAGGC-TTTGAAAGGGGTGCCACCGACTTGTGG
1 GCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAA-AGATGCCACTGACTTGTGG
* * * *
1144935 GCTTTTGAAAAGATGCCACTAACTTATGGGCTTT
1 GCTTTTG-AAGGTTGCCACTGACTTGTGGGCTTT
1144969 GGAAGGTGAG
Statistics
Matches: 459, Mismatches: 67, Indels: 40
0.81 0.12 0.07
Matches are distributed among these distances:
54 7 0.02
55 29 0.06
56 76 0.17
57 214 0.47
58 99 0.22
59 34 0.07
ACGTcount: A:0.20, C:0.18, G:0.29, T:0.32
Consensus pattern (57 bp):
GCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGG
Found at i:1144506 original size:85 final size:83
Alignment explanation
Indices: 1144366--1144968 Score: 613
Period size: 85 Copynumber: 7.1 Consensus size: 83
1144356 CAACTTATGT
* * *
1144366 GCTTTTGAAGGTTGCCACTG-CTTTATGGGCTTTGAAGGTTGCCACTAACTTGTGGGC-TTTGAA
1 GCTTTTGAAAGTTGCCACTGAC-TTGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCGTTTGAA
*
1144429 AATGTGCCACTAACTTGTGG
65 AA-GTGCCACTGACTTGTGG
* * * *
1144449 GCTTTTGAAAAGATGCCACTGACTTGTGGACTTTTGGAGGTTGCCACTAACTTGTGGGC-TTTGA
1 GCTTTTG-AAAGTTGCCACTGACTTGTGGGC-TTTGAAGGTTGCCACTGACTTGTGGGCGTTTGA
* * *
1144513 AAGGGGTGCCACCGATTTGTGG
64 AA--AGTGCCACTGACTTGTGG
*
1144535 GCTTTTGAAAATATGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCGTTTGT
1 GCTTTTGAAAGT-TGCCACTGACTTGTGGGC-TTTGAAGGTTGCCACTGACTTGTGGGCGTTTG-
** *
1144600 AAGGGGTGCCACCGACTTGTGG
63 AA-AAGTGCCACTGACTTGTGG
* *
1144622 GCTTTTGAAAATTTGCCACTGACTTGTGGACTTTTGAAGGTTGCCACTGACTTGTGGGCGTTTGA
1 GCTTTTG-AAAGTTGCCACTGACTTGTGGGC-TTTGAAGGTTGCCACTGACTTGTGGGCGTTTGA
*
1144687 AAATATGCCACTGACTTGTGG
64 AAA-GTGCCACTGACTTGTGG
* * * * * *
1144708 GCTTTTGAAGGTTGCCACTGACTTGTGGGCCTTGAAAGAGGTGCCACCGACTTATGGGCTTTTGA
1 GCTTTTGAAAGTTGCCACTGACTTGTGGGCTTTG-AAG-GTTGCCACTGACTTGTGGGCGTTTGA
*
1144773 AAAGATG-CATTGACTTGTGG
64 AAAG-TGCCACTGACTTGTGG
* * * * * *
1144793 GCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGAAAGGGGTGCCACCGACTTATGGGCTTTTAA
1 GCTTTTGAAAGTTGCCACTGACTTGTGGGCTTTG-AA-GGTTGCCACTGACTTGTGGGCGTTTGA
1144858 AAAGATGCCACTGACTTGTGG
64 AAAG-TGCCACTGACTTGTGG
* * * * * * *
1144879 GCTTTTG-AAGGTGCCACTAACTTATAGGCTTTGAAAGGGGTGCCACCGACTTGTGGGCTTTTGA
1 GCTTTTGAAAGTTGCCACTGACTTGTGGGCTTTG-AA-GGTTGCCACTGACTTGTGGGCGTTTGA
* *
1144943 AAAGATGCCACTAACTTATGG
64 AAAG-TGCCACTGACTTGTGG
1144964 GCTTT
1 GCTTT
1144969 GGAAGGTGAG
Statistics
Matches: 460, Mismatches: 44, Indels: 30
0.86 0.08 0.06
Matches are distributed among these distances:
83 7 0.02
84 20 0.04
85 214 0.47
86 135 0.29
87 78 0.17
88 6 0.01
ACGTcount: A:0.20, C:0.18, G:0.29, T:0.32
Consensus pattern (83 bp):
GCTTTTGAAAGTTGCCACTGACTTGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCGTTTGAAA
AGTGCCACTGACTTGTGG
Found at i:1161233 original size:13 final size:13
Alignment explanation
Indices: 1161215--1161245 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1161205 CGTTAGGCAT
1161215 AATGTATCAATAC
1 AATGTATCAATAC
*
1161228 AATGTATCGATAC
1 AATGTATCAATAC
1161241 AATGT
1 AATGT
1161246 CCCATGTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (13 bp):
AATGTATCAATAC
Found at i:1161332 original size:19 final size:19
Alignment explanation
Indices: 1161290--1161345 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
1161280 CTGCCCGTTT
*
1161290 CATGTATCGATACAATTAAG
1 CATGTATCGATACAA-TGAG
1161310 CATGTATCGATACAATGAG
1 CATGTATCGATACAATGAG
*
1161329 CATGTGTCGATACAATG
1 CATGTATCGATACAATG
1161346 TATCGATACT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAG
Found at i:1162906 original size:32 final size:32
Alignment explanation
Indices: 1162870--1162940 Score: 142
Period size: 32 Copynumber: 2.2 Consensus size: 32
1162860 GAAACAAGCA
1162870 AAGAAAGAAAAAGAAGGAAAAGGTAAGAGAGG
1 AAGAAAGAAAAAGAAGGAAAAGGTAAGAGAGG
1162902 AAGAAAGAAAAAGAAGGAAAAGGTAAGAGAGG
1 AAGAAAGAAAAAGAAGGAAAAGGTAAGAGAGG
1162934 AAGAAAG
1 AAGAAAG
1162941 GAAAGGAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.63, C:0.00, G:0.34, T:0.03
Consensus pattern (32 bp):
AAGAAAGAAAAAGAAGGAAAAGGTAAGAGAGG
Found at i:1164653 original size:29 final size:31
Alignment explanation
Indices: 1164591--1164653 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 31
1164581 TACTCAATCC
1164591 TAAA-AAAAAAATTTAACAATTAGAAATTAA
1 TAAATAAAAAAATTTAACAATTAGAAATTAA
* * *
1164621 -AAATAAAAAATTTTAA-AA-TATAACTTAA
1 TAAATAAAAAAATTTAACAATTAGAAATTAA
1164649 TAAAT
1 TAAAT
1164654 TTTAATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
28 8 0.29
29 9 0.32
30 11 0.39
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (31 bp):
TAAATAAAAAAATTTAACAATTAGAAATTAA
Found at i:1165454 original size:18 final size:19
Alignment explanation
Indices: 1165416--1165457 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
1165406 CTGAGAATAA
* *
1165416 AATAATCTTTTAAATATAT
1 AATAATCTCTTAAATAAAT
1165435 AATAATCTCTT-AATAAAT
1 AATAATCTCTTAAATAAAT
1165453 AATAA
1 AATAA
1165458 AATATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.40
Consensus pattern (19 bp):
AATAATCTCTTAAATAAAT
Found at i:1168357 original size:20 final size:20
Alignment explanation
Indices: 1168344--1168381 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1168334 CAACAATGGG
1168344 GATCTTTTGGCAACAAAAGA
1 GATCTTTTGGCAACAAAAGA
1168364 GATCTTTTGGCAACAAAA
1 GATCTTTTGGCAACAAAA
1168382 AAAGTTCTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.26
Consensus pattern (20 bp):
GATCTTTTGGCAACAAAAGA
Found at i:1170454 original size:51 final size:51
Alignment explanation
Indices: 1170392--1170504 Score: 172
Period size: 51 Copynumber: 2.2 Consensus size: 51
1170382 TTTCGAGAAA
* * * * *
1170392 ATACTCTAACCTCGGTTTTATTTCCAAAACACTAATTTTTCACAATCGGGG
1 ATACTCCAACCTCAGTTTTATTTCCAAAACACTAATTCTTCACAACCGAGG
*
1170443 ATACTCCAACCTCAGTTTTATTTCCAAAACACTGATTCTTCACAACCGAGG
1 ATACTCCAACCTCAGTTTTATTTCCAAAACACTAATTCTTCACAACCGAGG
1170494 ATACTCCAACC
1 ATACTCCAACC
1170505 CTGTTATTTT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.31, C:0.28, G:0.10, T:0.31
Consensus pattern (51 bp):
ATACTCCAACCTCAGTTTTATTTCCAAAACACTAATTCTTCACAACCGAGG
Found at i:1170522 original size:79 final size:78
Alignment explanation
Indices: 1170440--1171102 Score: 661
Period size: 79 Copynumber: 8.4 Consensus size: 78
1170430 TTCACAATCG
* *
1170440 GGGATACTCCAACCTCAGTTTTATTTCCAAAACACTGATTCTTCACAACCGAGGATACTCCAACC
1 GGGATACTCCAACCCCAGTTTTATTTCCAAAACACTGATT-TTCACAATCGAGGATACTCCAACC
* * *
1170505 CTGTTATTTTTTAG
65 CCGTTATTTTTGAA
* * *
1170519 GGGATACTCTAACCCCAGTTTTATTTCCAAAACA-TCGATTTTCCACAATCGGGGATACTCTAAC
1 GGGATACTCCAACCCCAGTTTTATTTCCAAAACACT-GATTTT-CACAATCGAGGATACTCCAAC
*
1170583 CCCGTTATTTCTGAA
64 CCCGTTATTTTTGAA
* * * * * *
1170598 GGGATACTCTAACCTCGGTTTTATTTCTAAAACA-TCAATTTTCCATAATC-AGGGATACTCCAA
1 GGGATACTCCAACCCCAGTTTTATTTCCAAAACACT-GATTTT-CACAATCGA-GGATACTCCAA
1170661 CCCCGTTATTTTTGAA
63 CCCCGTTATTTTTGAA
*
1170677 GGGATACTCCAACCCCGGTTTTATTTCCAAAACACTGATTTTTCACAATC-AGGGATACTCCAAC
1 GGGATACTCCAACCCCAGTTTTATTTCCAAAACACTGA-TTTTCACAATCGA-GGATACTCCAAC
* * *
1170741 CCCATTATTTTCGAG
64 CCCGTTATTTTTGAA
* * * * * * *
1170756 GGGATACTCTAACCCCAGTTTTATTTTCAAAACACCGATTTTTCATAATTGGGGATACCCCAACC
1 GGGATACTCCAACCCCAGTTTTATTTCCAAAACACTGA-TTTTCACAATCGAGGATACTCCAACC
**
1170821 CCGTTATTTCCGAA
65 CCGTTATTTTTGAA
** * * * * *
1170835 GGGATACTTTAACCCTAGTTTTATTTCGAAAACATTAATTTTCACAATCAAGGATACTCCAACCC
1 GGGATACTCCAACCCCAGTTTTATTTCCAAAACACTGATTTTCACAATCGAGGATACTCCAACCC
**
1170900 CGTTATTTTCAAA
66 CGTTATTTTTGAA
* * * * *
1170913 GGGATACTCCAACCCCGGTTTTATTTCCAAAACACCGATTTTCCACCATCTAGGATACTCTAACC
1 GGGATACTCCAACCCCAGTTTTATTTCCAAAACACTGATTTT-CACAATCGAGGATACTCCAACC
1170978 CCGTTATTTTTGAA
65 CCGTTATTTTTGAA
* * * *** ** ** *
1170992 AGGATACTCCAACCTCGGTTTTATTTTTTAAACACCAATTTTTCACCGTCGAGAATACTCCAACC
1 GGGATACTCCAACCCCAGTTTTATTTCCAAAACACTGA-TTTTCACAATCGAGGATACTCCAACC
**
1171057 CCGTTATTTCCGAA
65 CCGTTATTTTTGAA
* * *
1171071 GAGATACTCCAATCCC-GTTTTTATCTCCAAAA
1 GGGATACTCCAACCCCAG-TTTTATTTCCAAAA
1171103 TATTAAATTT
Statistics
Matches: 492, Mismatches: 83, Indels: 18
0.83 0.14 0.03
Matches are distributed among these distances:
78 71 0.14
79 412 0.84
80 9 0.02
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.33
Consensus pattern (78 bp):
GGGATACTCCAACCCCAGTTTTATTTCCAAAACACTGATTTTCACAATCGAGGATACTCCAACCC
CGTTATTTTTGAA
Found at i:1170566 original size:130 final size:130
Alignment explanation
Indices: 1170328--1170583 Score: 327
Period size: 130 Copynumber: 2.0 Consensus size: 130
1170318 TCATTCATGT
* * * * * *
1170328 TTTTATTTCTAAAATACTGATTTTCCACCATCGGGGATACTCTAACCCCGTTATTTTCGAGAAAA
1 TTTTATTTCCAAAACACTGATTTTCCACAACCGAGGATACTCCAACCCCGTTATTTTCGAGAAAA
* * *
1170393 TACTCTAACCTCGGTTTTATTTCCAAAACACTAATTTTTCACAATCGGGGATACTCCAACCTCAG
66 TACTCTAACCCCAGTTTTATTTCCAAAACACTAATTTTCCACAATCGGGGATACTCCAACCTCAG
* ** ***
1170458 TTTTATTTCCAAAACACTGATTCTT-CACAACCGAGGATACTCCAACCCTGTTATTTTTTAGGGG
1 TTTTATTTCCAAAACACTGATT-TTCCACAACCGAGGATACTCCAACCCCGTTATTTTCGAGAAA
* *
1170522 ATACTCTAACCCCAGTTTTATTTCCAAAACA-TCGATTTTCCACAATCGGGGATACTCTAACC
65 ATACTCTAACCCCAGTTTTATTTCCAAAACACT-AATTTTCCACAATCGGGGATACTCCAACC
1170584 CCGTTATTTC
Statistics
Matches: 107, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
129 1 0.01
130 104 0.97
131 2 0.02
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (130 bp):
TTTTATTTCCAAAACACTGATTTTCCACAACCGAGGATACTCCAACCCCGTTATTTTCGAGAAAA
TACTCTAACCCCAGTTTTATTTCCAAAACACTAATTTTCCACAATCGGGGATACTCCAACCTCAG
Found at i:1170776 original size:237 final size:236
Alignment explanation
Indices: 1170440--1171079 Score: 854
Period size: 236 Copynumber: 2.7 Consensus size: 236
1170430 TTCACAATCG
* * * *
1170440 GGGATACTCCAACCTCAGTTTTATTTCCAAAACACTGATTCTTCACAA-CCGAGGATACTCCAAC
1 GGGATACTCCAACCCCGGTTTTATTTCCAAAACACTGATTTTTCACAATCAG-GGATACTCCAAC
* * * * *
1170504 CCTGTTATTTTTTAGGGGATACTCTAACCCCAGTTTTATTTCCAAAACATCGATTTTCCACAATC
65 CCCGTTATTTTTGAGGGGATACTCTAACCCCAGTTTTATTTTCAAAACACCGATTTTTCACAATC
* * * *
1170569 GGGGATACTCTAACCCCGTTATTTCTGAAGGGATACTCTAA-CCTCGGTTTTATTTCTAAAACAT
130 GGGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCTAACCCT-AGTTTTATTTCGAAAACAT
* * **
1170633 CAATTTTCCATAATCAGGGATACTCCAACCCCGTTATTTTTGAA
194 CAATTTT-CACAATCAAGGATACTCCAACCCCGTTATTTTCAAA
1170677 GGGATACTCCAACCCCGGTTTTATTTCCAAAACACTGATTTTTCACAATCAGGGATACTCCAACC
1 GGGATACTCCAACCCCGGTTTTATTTCCAAAACACTGATTTTTCACAATCAGGGATACTCCAACC
* * * *
1170742 CCATTATTTTCGAGGGGATACTCTAACCCCAGTTTTATTTTCAAAACACCGATTTTTCATAATTG
66 CCGTTATTTTTGAGGGGATACTCTAACCCCAGTTTTATTTTCAAAACACCGATTTTTCACAATCG
* * *
1170807 GGGATACCCCAACCCCGTTATTTCCGAAGGGATACTTTAACCCTAGTTTTATTTCGAAAACATTA
131 GGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCTAACCCTAGTTTTATTTCGAAAACATCA
1170872 ATTTTCACAATCAAGGATACTCCAACCCCGTTATTTTCAAA
196 ATTTTCACAATCAAGGATACTCCAACCCCGTTATTTTCAAA
* * * *
1170913 GGGATACTCCAACCCCGGTTTTATTTCCAAAACACCGATTTTCCACCATCTA-GGATACTCTAAC
1 GGGATACTCCAACCCCGGTTTTATTTCCAAAACACTGATTTTTCACAATC-AGGGATACTCCAAC
** * * * ** * **
1170977 CCCGTTATTTTTGAAAGGATACTCCAACCTCGGTTTTATTTTTTAAACACCAATTTTTCACCGTC
65 CCCGTTATTTTTGAGGGGATACTCTAACCCCAGTTTTATTTTCAAAACACCGATTTTTCACAATC
* * *
1171042 GAGAATACTCCAACCCCGTTATTTCCGAAGAGATACTC
130 GGGGATACTCCAACCCCGTTATTTCCGAAGGGATACTC
1171080 CAATCCCGTT
Statistics
Matches: 353, Mismatches: 47, Indels: 7
0.87 0.12 0.02
Matches are distributed among these distances:
236 174 0.49
237 174 0.49
238 5 0.01
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.33
Consensus pattern (236 bp):
GGGATACTCCAACCCCGGTTTTATTTCCAAAACACTGATTTTTCACAATCAGGGATACTCCAACC
CCGTTATTTTTGAGGGGATACTCTAACCCCAGTTTTATTTTCAAAACACCGATTTTTCACAATCG
GGGATACTCCAACCCCGTTATTTCCGAAGGGATACTCTAACCCTAGTTTTATTTCGAAAACATCA
ATTTTCACAATCAAGGATACTCCAACCCCGTTATTTTCAAA
Found at i:1172533 original size:31 final size:31
Alignment explanation
Indices: 1172498--1172558 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
1172488 CTTTATGTTA
1172498 CTAAACTAGTAAAGGGTATGCAATTAATTGG
1 CTAAACTAGTAAAGGGTATGCAATTAATTGG
* *
1172529 CTAAACTAGTAATGGGTATTCAATTAATTG
1 CTAAACTAGTAAAGGGTATGCAATTAATTG
1172559 ACTATGTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.33
Consensus pattern (31 bp):
CTAAACTAGTAAAGGGTATGCAATTAATTGG
Found at i:1173153 original size:33 final size:32
Alignment explanation
Indices: 1173110--1173172 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 32
1173100 CCACTGTTTA
1173110 TATCGATACATG-GCACATTGTATCGATACAATG
1 TATCGATACATGAG-A-ATTGTATCGATACAATG
*
1173143 TATCGGTACATGATGAATTGTATCGATACA
1 TATCGATACATGA-GAATTGTATCGATACA
1173173 TTGCTTCTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 25 0.93
34 1 0.04
35 1 0.04
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (32 bp):
TATCGATACATGAGAATTGTATCGATACAATG
Found at i:1179097 original size:13 final size:13
Alignment explanation
Indices: 1179079--1179104 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1179069 ACAATATTTT
1179079 TGTATCGATACAA
1 TGTATCGATACAA
1179092 TGTATCGATACAA
1 TGTATCGATACAA
1179105 GGGTTACTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1186330 original size:80 final size:79
Alignment explanation
Indices: 1186246--1186563 Score: 336
Period size: 80 Copynumber: 4.0 Consensus size: 79
1186236 AGTCAAACCC
* * * *
1186246 CGTTTTTACTTCTAAAATACCGAATTTTTCATCT-TAGGGGACACTCCAATCCCACCATCTCCGA
1 CGTTTTTACTTCTAAAACATCAAATTTTTCATCTCT-GGGGACACTCCAACCCCACCATCTCCGA
1186310 GGGGATACTCCAACTT
65 GGGGATACTCCAAC-T
* * * * *
1186326 CGTTTTTACTT-TCAAAACATTAAATTTTTTATCTCTAGGGACATTCCAACCCCACCATCTTCGA
1 CGTTTTTACTTCT-AAAACATCAAATTTTTCATCTCTGGGGACACTCCAACCCCACCATCTCCGA
* *
1186390 GGGGATACTCTAACCC
65 GGGGATACTCCAA-CT
* * * * *
1186406 CATTTTTACTTCTAAAACATCAAACTTTTGATCTCTGGGGATACTCCAACCCCACCATCTCCGAA
1 CGTTTTTACTTCTAAAACATCAAATTTTTCATCTCTGGGGACACTCCAACCCCACCATCTCCGAG
* *
1186471 GGTATACTTCAACT
66 GGGATACTCCAACT
** * ** *
1186485 CTGTTTTTACTTCTAAAACATTGAATTGTTCATCTCTGAAGACACTCTAACCCCCACCATCTCCG
1 C-GTTTTTACTTCTAAAACATCAAATTTTTCATCTCTGGGGACACTCCAA-CCCCACCATCTCCG
1186550 AGGAGG-TACTCCAA
64 AGG-GGATACTCCAA
1186564 TCCTGGTTTT
Statistics
Matches: 194, Mismatches: 37, Indels: 13
0.80 0.15 0.05
Matches are distributed among these distances:
79 3 0.02
80 164 0.85
81 26 0.13
82 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.12, T:0.32
Consensus pattern (79 bp):
CGTTTTTACTTCTAAAACATCAAATTTTTCATCTCTGGGGACACTCCAACCCCACCATCTCCGAG
GGGATACTCCAACT
Found at i:1186462 original size:160 final size:161
Alignment explanation
Indices: 1186241--1186560 Score: 391
Period size: 160 Copynumber: 2.0 Consensus size: 161
1186231 GGGGTAGTCA
* * * * *
1186241 AACCCCGTTTTTACTTCTAAAATACCGAATTTTTCATCTTAGGGGACACTCCAATCCCACCATCT
1 AACCCCATTTTTACTTCTAAAACACCAAACTTTTCATCTTAGGGGACACTCCAACCCCACCATCT
* * * *
1186306 CCGAGGGGATACTCCAACT-TCGTTTTTACTT-TCAAAACATTAAATTTTTTATCTCT-AGGGAC
66 CCGAAGGGATACTCCAACTCT-GTTTTTACTTCT-AAAACATTAAATTGTTCATCTCTGA-AGAC
* *
1186368 ATTCCAA-CCCCACCATCTTCGAGG-GGATACTCT
128 ACTCCAACCCCCACCATCTCCGAGGAGG-TACTCT
* * *
1186401 AACCCCATTTTTACTTCTAAAACATCAAACTTTTGATCTCT-GGGGATACTCCAACCCCACCATC
1 AACCCCATTTTTACTTCTAAAACACCAAACTTTTCATCT-TAGGGGACACTCCAACCCCACCATC
* * *
1186465 TCCGAAGGTATACTTCAACTCTGTTTTTACTTCTAAAACATTGAATTGTTCATCTCTGAAGACAC
65 TCCGAAGGGATACTCCAACTCTGTTTTTACTTCTAAAACATTAAATTGTTCATCTCTGAAGACAC
*
1186530 TCTAACCCCCACCATCTCCGAGGAGGTACTC
130 TCCAACCCCCACCATCTCCGAGGAGGTACTC
1186561 CAATCCTGGT
Statistics
Matches: 136, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
160 109 0.80
161 25 0.18
162 2 0.01
ACGTcount: A:0.28, C:0.29, G:0.12, T:0.32
Consensus pattern (161 bp):
AACCCCATTTTTACTTCTAAAACACCAAACTTTTCATCTTAGGGGACACTCCAACCCCACCATCT
CCGAAGGGATACTCCAACTCTGTTTTTACTTCTAAAACATTAAATTGTTCATCTCTGAAGACACT
CCAACCCCCACCATCTCCGAGGAGGTACTCT
Found at i:1189708 original size:25 final size:25
Alignment explanation
Indices: 1189674--1189723 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1189664 TAAAGTGGTA
1189674 CATAGAAAAATTAACTACAGTCATT
1 CATAGAAAAATTAACTACAGTCATT
1189699 CATAGAAAAATTAACTACAGTCATT
1 CATAGAAAAATTAACTACAGTCATT
1189724 ATTATCCACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (25 bp):
CATAGAAAAATTAACTACAGTCATT
Found at i:1190779 original size:18 final size:18
Alignment explanation
Indices: 1190756--1190791 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1190746 CCTTTTTTAA
*
1190756 TTATATAATATATTATTT
1 TTATATAATATATAATTT
*
1190774 TTATATATTATATAATTT
1 TTATATAATATATAATTT
1190792 ATATCATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TTATATAATATATAATTT
Found at i:1192113 original size:60 final size:60
Alignment explanation
Indices: 1192044--1192169 Score: 234
Period size: 60 Copynumber: 2.1 Consensus size: 60
1192034 CATACTACAT
*
1192044 AATTTTTTTCAAAAACATAAACTAATTGATATATATAAAGTTGATAAAAATTGAAATATA
1 AATTTTTTTCAAAAACATAAACTAATTGATATACATAAAGTTGATAAAAATTGAAATATA
*
1192104 AATTTTTTTCAAAAACATAAACTAATTGATATACATAAAGTTGATAAAAATTGAAATATG
1 AATTTTTTTCAAAAACATAAACTAATTGATATACATAAAGTTGATAAAAATTGAAATATA
1192164 AATTTT
1 AATTTT
1192170 GTCATGTCTC
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 64 1.00
ACGTcount: A:0.50, C:0.06, G:0.07, T:0.37
Consensus pattern (60 bp):
AATTTTTTTCAAAAACATAAACTAATTGATATACATAAAGTTGATAAAAATTGAAATATA
Found at i:1192268 original size:30 final size:31
Alignment explanation
Indices: 1192244--1192307 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
1192234 ACGAAATAGT
1192244 AAATATAA-TTTTAAAAAATTACGAATGATAA
1 AAATATAACTTTTAAAAAATTACGAA-GATAA
*
1192275 AAATATAACTTTT-AAAAATTA-TAA-ATAA
1 AAATATAACTTTTAAAAAATTACGAAGATAA
1192303 AAATA
1 AAATA
1192308 AACATCAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
28 9 0.29
30 2 0.06
31 16 0.52
32 4 0.13
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (31 bp):
AAATATAACTTTTAAAAAATTACGAAGATAA
Found at i:1198358 original size:18 final size:18
Alignment explanation
Indices: 1198271--1198359 Score: 54
Period size: 18 Copynumber: 4.5 Consensus size: 18
1198261 TTAAAAGATT
*
1198271 TTATATTTTAAAAACTAC
1 TTATATTTTAAAAAATAC
*
1198289 TTA-AATTTAAAAAATTAC
1 TTATATTTTAAAAAA-TAC
*
1198307 TCAATCATTTTACTTTAAAAATAAC
1 T-TAT-ATTTTA----AAAAAT-AC
*
1198332 TAATCATTTTAAAAAATAC
1 TTAT-ATTTTAAAAAATAC
1198351 TTATATTTT
1 TTATATTTT
1198360 TTTATATATT
Statistics
Matches: 57, Mismatches: 5, Indels: 18
0.71 0.06 0.22
Matches are distributed among these distances:
17 9 0.16
18 12 0.21
19 6 0.11
20 6 0.11
21 5 0.09
24 11 0.19
25 8 0.14
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (18 bp):
TTATATTTTAAAAAATAC
Found at i:1198369 original size:12 final size:12
Alignment explanation
Indices: 1198352--1198398 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
1198342 AAAAAATACT
1198352 TATATTTTTTTA
1 TATATTTTTTTA
*
1198364 TATATTTATTTA
1 TATATTTTTTTA
*
1198376 TTATATTTTTTAA
1 -TATATTTTTTTA
*
1198389 AATATTTTTT
1 TATATTTTTT
1198399 GAAAAAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
12 20 0.67
13 10 0.33
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TATATTTTTTTA
Found at i:1198834 original size:25 final size:25
Alignment explanation
Indices: 1198793--1198859 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
1198783 TCTCGATAAC
*
1198793 ATTATATAT-GATT-ATAAAAATAT
1 ATTATATATAAATTAATAAAAATAT
1198816 ATTATATATAAATTAATAAAAATAT
1 ATTATATATAAATTAATAAAAATAT
** *
1198841 AACATAATATAAAATAATA
1 ATTAT-ATATAAATTAATA
1198860 TAATATGAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
23 9 0.24
24 3 0.08
25 13 0.35
26 12 0.32
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (25 bp):
ATTATATATAAATTAATAAAAATAT
Found at i:1198924 original size:6 final size:6
Alignment explanation
Indices: 1198884--1198983 Score: 68
Period size: 6 Copynumber: 16.7 Consensus size: 6
1198874 TTTTAAATTT
*
1198884 TATATAA TATAAA TTATTAATA TATTAAA -ATAAA TATAAA TATAAA -ATATA
1 TATA-AA TATAAA -TA-TAA-A TA-TAAA TATAAA TATAAA TATAAA TATAAA
* * *
1198935 T-TAAAA TATAAT TAT-AA TAT-AA TAAAAA TATAAA TAT-AA TATTAA
1 TAT-AAA TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA
1198980 TATA
1 TATA
1198984 TGAAATATTC
Statistics
Matches: 77, Mismatches: 7, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
5 22 0.29
6 37 0.48
7 8 0.10
8 9 0.12
9 1 0.01
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (6 bp):
TATAAA
Found at i:1198929 original size:17 final size:17
Alignment explanation
Indices: 1198885--1198983 Score: 59
Period size: 17 Copynumber: 5.9 Consensus size: 17
1198875 TTTAAATTTT
*
1198885 ATATAATATAAATTATTAA
1 ATATAAAATAAA-TA-TAA
1198904 TATATTAAAATAAATATAA
1 -ATA-TAAAATAAATATAA
*
1198923 ATATAAAATATAT-TAA
1 ATATAAAATAAATATAA
*
1198939 A-AT---ATAATTAT-A
1 ATATAAAATAAATATAA
1198951 ATATAATAA-AAATATAA
1 ATATAA-AATAAATATAA
* *
1198968 ATATAATATTAATATA
1 ATATAAAATAAATATA
1198984 TGAAATATTC
Statistics
Matches: 63, Mismatches: 7, Indels: 21
0.69 0.08 0.23
Matches are distributed among these distances:
12 6 0.10
13 3 0.05
15 2 0.03
16 10 0.16
17 23 0.37
18 3 0.05
19 3 0.05
20 5 0.08
21 8 0.13
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATATAAAATAAATATAA
Found at i:1199987 original size:16 final size:18
Alignment explanation
Indices: 1199954--1199988 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1199944 ATAATTTAAA
1199954 ATTATAAATTATTATTAT
1 ATTATAAATTATTATTAT
1199972 ATTA-AAATTATT-TTAT
1 ATTATAAATTATTATTAT
1199988 A
1 A
1199989 AATATTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 8 0.47
18 4 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTATAAATTATTATTAT
Found at i:1200002 original size:19 final size:21
Alignment explanation
Indices: 1199970--1200011 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
1199960 AATTATTATT
1199970 ATATTAAAATTATTTTA-TAA
1 ATATTAAAATTATTTTATTAA
*
1199990 ATATTTAAA-TATTTTATTAA
1 ATATTAAAATTATTTTATTAA
1200010 AT
1 AT
1200012 TGATCAATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
ATATTAAAATTATTTTATTAA
Found at i:1200856 original size:36 final size:36
Alignment explanation
Indices: 1200807--1200877 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
1200797 AATCTACACG
* * *
1200807 AATTTTTATTAAAAAAGAATTAATATT-AAATTTTA
1 AATTATTATTAAAAAAGAATAAAAATTAAAATTTTA
*
1200842 AATTATTATTTAAAAAATAATAAAAATTAAAATTTT
1 AATTATTA-TTAAAAAAGAATAAAAATTAAAATTTT
1200878 TTATTAAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 7 0.23
36 16 0.53
37 7 0.23
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (36 bp):
AATTATTATTAAAAAAGAATAAAAATTAAAATTTTA
Found at i:1200952 original size:45 final size:44
Alignment explanation
Indices: 1200842--1201187 Score: 214
Period size: 45 Copynumber: 7.6 Consensus size: 44
1200832 TTAAATTTTA
* *
1200842 AATTATTATTTAAAAAATAATAAAAATTAAAATTTTTTATTAAATCTCA
1 AATTATTATTTAAAAAATAATAAAAA-T---A-TTTATATTAAATCTCG
* *
1200891 AATTATTATCTTAAAAAAGT-TTAAAAAATATTTATATTAAATCTTG
1 AATTATTAT-TTAAAAAA-TAAT-AAAAATATTTATATTAAATCTCG
* *
1200937 AATTAGTATTTAAAAAATAATAAAAATATTTTATATTAAATATCG
1 AATTATTATTTAAAAAATAATAAAAATA-TTTATATTAAATCTCG
* **
1200982 AATTATTATTT-AAAAATAAT-AAAA-ATTTA-A-GAATAT-TTT
1 AATTATTATTTAAAAAATAATAAAAATATTTATATTAA-ATCTCG
* *
1201021 ATATTACTATTTAAAAAATAATAAAAATTAAAAATTTATA-TAAATCTCA
1 A-ATTATTATTTAAAAAATAATAAAAA-T----ATTTATATTAAATCTCG
* * **
1201070 AATTACTATTTAAAAATAAAAAATTAAAAAATATTTTATATTAAATCTTA
1 AATTATTATTT--AAA-AAATAA-T-AAAAATA-TTTATATTAAATCTCG
* * * *
1201120 AATTACTATTT-TAAAATACTAAAAA-ATTATATATTACATCT-G
1 AATTATTATTTAAAAAATAATAAAAATATT-TATATTAAATCTCG
1201162 AAATTATTATTT--AAAATAATAAAAAT
1 -AATTATTATTTAAAAAATAATAAAAAT
1201188 TAAAAAATTT
Statistics
Matches: 245, Mismatches: 25, Indels: 60
0.74 0.08 0.18
Matches are distributed among these distances:
39 4 0.02
40 12 0.05
41 13 0.05
42 19 0.08
43 26 0.11
44 22 0.09
45 34 0.14
46 25 0.10
47 2 0.01
48 18 0.07
49 20 0.08
50 32 0.13
51 11 0.04
52 2 0.01
53 5 0.02
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (44 bp):
AATTATTATTTAAAAAATAATAAAAATATTTATATTAAATCTCG
Found at i:1201153 original size:43 final size:43
Alignment explanation
Indices: 1201096--1201232 Score: 143
Period size: 43 Copynumber: 3.1 Consensus size: 43
1201086 TAAAAAATTA
* *
1201096 AAAAATATTTTATATTAAATCTTAAATTACTATTTTAAAATACT
1 AAAAA-ATTATATATTAAATCTTAAATTACTATTTTAAAATAAT
* * *
1201140 AAAAAATTATATATTACATCTGAAATTATTA-TTTAAAATAAT
1 AAAAAATTATATATTAAATCTTAAATTACTATTTTAAAATAAT
* * * *
1201182 -AAAAATTAAAAAATTTTAAATTTTAAATTACTATTTAAAAATAAT
1 AAAAAATT---ATATATTAAATCTTAAATTACTATTTTAAAATAAT
1201227 AAAAAA
1 AAAAAA
1201233 ATTTAAAATA
Statistics
Matches: 76, Mismatches: 12, Indels: 8
0.79 0.12 0.08
Matches are distributed among these distances:
41 7 0.09
42 10 0.13
43 22 0.29
44 22 0.29
45 10 0.13
46 5 0.07
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (43 bp):
AAAAAATTATATATTAAATCTTAAATTACTATTTTAAAATAAT
Found at i:1201323 original size:107 final size:106
Alignment explanation
Indices: 1201198--1201392 Score: 295
Period size: 106 Copynumber: 1.8 Consensus size: 106
1201188 TAAAAAATTT
* * *
1201198 TAAATTTTAAATTACTATTT-AAAAATAATAAAAAAATTTAAAATATATTTTATATTAAATCTCA
1 TAAATTTTAAATCACTATTTAAAAAATAAT-AAAAAATTAAAAAAATA-TTTATATTAAATCT-A
* *
1201262 -AATTACTATTTAAAAATAACAAAAAATAAAAAATATTTTATAC
63 GAATTAATATTGAAAAATAACAAAAAATAAAAAATATTTTATAC
1201305 TAAATTTTAAATCACTATTTAAAAAATAATAAAAAATTAAAAAAATATTTATATTAAATCTAGAA
1 TAAATTTTAAATCACTATTTAAAAAATAATAAAAAATTAAAAAAATATTTATATTAAATCTAGAA
*
1201370 TTAATATTGAAAAATAAGAAAAA
66 TTAATATTGAAAAATAACAAAAA
1201393 TATTTTATAT
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
105 1 0.01
106 36 0.45
107 34 0.43
108 9 0.11
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.36
Consensus pattern (106 bp):
TAAATTTTAAATCACTATTTAAAAAATAATAAAAAATTAAAAAAATATTTATATTAAATCTAGAA
TTAATATTGAAAAATAACAAAAAATAAAAAATATTTTATAC
Found at i:1201383 original size:54 final size:51
Alignment explanation
Indices: 1201140--1201392 Score: 220
Period size: 53 Copynumber: 4.9 Consensus size: 51
1201130 TTAAAATACT
* * * *
1201140 AAAAA-ATTATATATTACATCTGAAATTATTATTTAAAATAAT-AAAAATT-
1 AAAAATATTTTATATTAAATCT-AAATTACTATTAAAAATAATAAAAAATTA
*
1201189 AAAAA-ATTTTAAATT---T-TAAATTACTATTTAAAAATAATAAAAAAATTTA
1 AAAAATATTTTATATTAAATCTAAATTACTA-TTAAAAATAAT-AAAAAA-TTA
* *
1201238 AAATATATTTTATATTAAATCTCAAATTACTATTTAAAAATAACAAAAAA-TA
1 AAAAATATTTTATATTAAATCT-AAATTACTA-TTAAAAATAATAAAAAATTA
* * *
1201290 AAAAATATTTTATACTAAATTTTAAATCACTATTTAAAAAATAATAAAAAATTA
1 AAAAATATTTTATATTAAA-TCTAAATTACTA-TT-AAAAATAATAAAAAATTA
* *
1201344 AAAAA-ATATTTATATTAAATCTAGAATTAATATTGAAAAATAAGAAAAA
1 AAAAATAT-TTTATATTAAATCTA-AATTACTATT-AAAAATAATAAAAA
1201393 TATTTTATAT
Statistics
Matches: 170, Mismatches: 18, Indels: 28
0.79 0.08 0.13
Matches are distributed among these distances:
44 8 0.05
45 11 0.06
46 1 0.01
47 5 0.03
48 2 0.01
49 17 0.10
50 9 0.05
52 30 0.18
53 37 0.22
54 30 0.18
55 20 0.12
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (51 bp):
AAAAATATTTTATATTAAATCTAAATTACTATTAAAAATAATAAAAAATTA
Found at i:1201436 original size:44 final size:45
Alignment explanation
Indices: 1201334--1201437 Score: 124
Period size: 44 Copynumber: 2.4 Consensus size: 45
1201324 TAAAAAATAA
*
1201334 TAAAAA-ATTAAAAAAATATTTATATTAAATCTAGAATTAATATT
1 TAAAAATATTAAAAATATATTTATATTAAATCTAGAATTAATATT
* ** * *
1201378 GAAAAATAAGAAAAATAT-TTTATATTAAAATTTA-AATTATTATT
1 TAAAAATATTAAAAATATATTTATATT-AAATCTAGAATTAATATT
1201422 TAAAAATATTAAAAAT
1 TAAAAATATTAAAAAT
1201438 TAAAAATATT
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
44 35 0.71
45 14 0.29
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (45 bp):
TAAAAATATTAAAAATATATTTATATTAAATCTAGAATTAATATT
Found at i:1201455 original size:16 final size:16
Alignment explanation
Indices: 1201388--1201455 Score: 57
Period size: 16 Copynumber: 4.1 Consensus size: 16
1201378 GAAAAATAAG
1201388 AAAAATATTTTATATT
1 AAAAATATTTTATATT
*
1201404 AAAATTTAAATTATTAT-TT
1 AAAA---ATATT-TTATATT
** *
1201423 AAAAATATTAAAAATT
1 AAAAATATTTTATATT
1201439 AAAAATATTTTATATT
1 AAAAATATTTTATATT
1201455 A
1 A
1201456 TTATTATATA
Statistics
Matches: 39, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
15 1 0.03
16 24 0.62
19 10 0.26
20 4 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
AAAAATATTTTATATT
Found at i:1201458 original size:98 final size:96
Alignment explanation
Indices: 1201283--1201455 Score: 253
Period size: 98 Copynumber: 1.8 Consensus size: 96
1201273 AAAAATAACA
*
1201283 AAAAATAAAAAATATTTTATACTAAATTTTAAATCACTATTTAAAAAATAATAAAAAATTAAAAA
1 AAAAATAAAAAATATTTTATACTAAAATTTAAATCACTATTTAAAAAATAATAAAAAATTAAAAA
1201348 AATATTTATATTAAATCTAGAATTAATATTG
66 AATATTTATATTAAATCTAGAATTAATATTG
* * * *
1201379 AAAAATAAGAAAAATATTTTATATTAAAATTTAAATTATTATTT-AAAAAT-ATTAAAAATTAAA
1 AAAAAT-A-AAAAATATTTTATACTAAAATTTAAATCACTATTTAAAAAATAATAAAAAATTAAA
*
1201442 AATAT-TTTATATTA
64 AAAATATTTATATTA
1201456 TTATTATATA
Statistics
Matches: 69, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
95 9 0.13
96 22 0.32
97 7 0.10
98 31 0.45
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (96 bp):
AAAAATAAAAAATATTTTATACTAAAATTTAAATCACTATTTAAAAAATAATAAAAAATTAAAAA
AATATTTATATTAAATCTAGAATTAATATTG
Found at i:1201499 original size:19 final size:19
Alignment explanation
Indices: 1201475--1201524 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
1201465 ATTTATATAA
** *
1201475 TTTTTAATTTAAAATTAAT
1 TTTTTAATAAAAAATCAAT
1201494 TTTTT-ATAAAAAATCAAT
1 TTTTTAATAAAAAATCAAT
1201512 TTTTTAAATAAAA
1 TTTTT-AATAAAA
1201525 TAATATATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 15 0.58
19 5 0.19
20 6 0.23
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTTTAATAAAAAATCAAT
Found at i:1201524 original size:18 final size:19
Alignment explanation
Indices: 1201484--1201525 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
1201474 ATTTTTAATT
*
1201484 TAAAATTAATTTTTTATAA
1 TAAAATCAATTTTTTATAA
1201503 -AAAATCAATTTTTTA-AA
1 TAAAATCAATTTTTTATAA
1201520 TAAAAT
1 TAAAAT
1201526 AATATATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
TAAAATCAATTTTTTATAA
Found at i:1201537 original size:13 final size:13
Alignment explanation
Indices: 1201521--1201573 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
1201511 TTTTTTAAAT
1201521 AAAATAATATATA
1 AAAATAATATATA
*
1201534 AAAATAATAAATA
1 AAAATAATATATA
* * *
1201547 TATATAATTTTAATA
1 AAAATAA-TAT-ATA
1201562 AAAATAATATAT
1 AAAATAATATAT
1201574 GCATGTAACT
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
13 19 0.63
14 3 0.10
15 8 0.27
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAAATAATATATA
Found at i:1201571 original size:22 final size:22
Alignment explanation
Indices: 1201513--1201573 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 22
1201503 AAAATCAATT
1201513 TTTTAA-ATAAAATAATATATAA
1 TTTTAATA-AAAATAATATATAA
*
1201535 ---AAATAATAAAT-ATATATAA
1 TTTTAATAA-AAATAATATATAA
1201554 TTTTAATAAAAATAATATAT
1 TTTTAATAAAAATAATATAT
1201574 GCATGTAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
19 11 0.35
20 5 0.16
21 4 0.13
22 11 0.35
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
TTTTAATAAAAATAATATATAA
Found at i:1201586 original size:28 final size:28
Alignment explanation
Indices: 1201531--1201587 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
1201521 AAAATAATAT
* *
1201531 ATAAAAATAATAAATATATATAATTTTA
1 ATAAAAATAATAAATACATATAACTTTA
* * *
1201559 ATAAAAATAATATATGCATGTAACTTTA
1 ATAAAAATAATAAATACATATAACTTTA
1201587 A
1 A
1201588 ACAAAAACAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.37
Consensus pattern (28 bp):
ATAAAAATAATAAATACATATAACTTTA
Found at i:1206744 original size:13 final size:13
Alignment explanation
Indices: 1206726--1206753 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1206716 AAGATCACAT
1206726 ATCATACTATAAA
1 ATCATACTATAAA
1206739 ATCATACTATAAA
1 ATCATACTATAAA
1206752 AT
1 AT
1206754 TTATCTAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (13 bp):
ATCATACTATAAA
Found at i:1207366 original size:32 final size:32
Alignment explanation
Indices: 1207269--1207377 Score: 95
Period size: 32 Copynumber: 3.5 Consensus size: 32
1207259 ATATTGCACC
* *
1207269 ATTAATCATAAATTTGATAG--ATTAGACATA
1 ATTACTCATAAATTTAATAGATATTAGACATA
* * *
1207299 TTTTCTTATAAATTTAAT-GAATATT-GA-ATAAA
1 ATTACTCATAAATTTAATAG-ATATTAGACAT--A
1207331 ATTACTCATAAATTTAATAGATATTAGACATA
1 ATTACTCATAAATTTAATAGATATTAGACATA
1207363 ATTACT-ACTAAATTT
1 ATTACTCA-TAAATTT
1207378 GAAAATTATT
Statistics
Matches: 62, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
29 1 0.02
30 15 0.24
31 3 0.05
32 38 0.61
33 3 0.05
34 2 0.03
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.41
Consensus pattern (32 bp):
ATTACTCATAAATTTAATAGATATTAGACATA
Found at i:1207579 original size:26 final size:26
Alignment explanation
Indices: 1207496--1207580 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
1207486 ATGAATTATT
1207496 TAATCTTATTTATTTTATTTTTGAAATA
1 TAATCTTATTTATTTTATTTTT-AAA-A
* * ** * * *
1207524 TGATTCATATAGAATTTATTTTTTATA
1 T-AATCTTATTTATTTTATTTTTAAAA
*
1207551 TAATCTTATTTATTTTATATTTAAAA
1 TAATCTTATTTATTTTATTTTTAAAA
1207577 TAAT
1 TAAT
1207581 TTTCATATAA
Statistics
Matches: 41, Mismatches: 15, Indels: 4
0.68 0.25 0.07
Matches are distributed among these distances:
26 21 0.51
27 2 0.05
28 2 0.05
29 16 0.39
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (26 bp):
TAATCTTATTTATTTTATTTTTAAAA
Found at i:1208262 original size:13 final size:13
Alignment explanation
Indices: 1208244--1208268 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1208234 CATTATGCTT
1208244 TGTATCGATACAA
1 TGTATCGATACAA
1208257 TGTATCGATACA
1 TGTATCGATACA
1208269 TGTTTATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1208419 original size:33 final size:35
Alignment explanation
Indices: 1208339--1208420 Score: 118
Period size: 33 Copynumber: 2.5 Consensus size: 35
1208329 TACCACTGTT
*
1208339 TGTATCGATACATG--GCACATTTTATCGATACAA
1 TGTATCGATACATGCTGCACATTATATCGATACAA
*
1208372 TGTATTGATACATGCTG-A-ATTATATCGATACAA
1 TGTATCGATACATGCTGCACATTATATCGATACAA
1208405 TGTATCGATACATGCT
1 TGTATCGATACATGCT
1208421 TCTAACGGCT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
33 42 0.95
34 1 0.02
35 1 0.02
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (35 bp):
TGTATCGATACATGCTGCACATTATATCGATACAA
Found at i:1210284 original size:21 final size:21
Alignment explanation
Indices: 1210243--1210284 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1210233 CACATGGAGT
* *
1210243 GATTGTCAAACTTGAAGAAAA
1 GATTGTCAAACTTCAAAAAAA
1210264 GATTGTCAAACTTCAAAAAAA
1 GATTGTCAAACTTCAAAAAAA
1210285 ACTCTCTCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.12, G:0.14, T:0.24
Consensus pattern (21 bp):
GATTGTCAAACTTCAAAAAAA
Found at i:1214853 original size:13 final size:13
Alignment explanation
Indices: 1214835--1214860 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1214825 CAGGGCAACT
1214835 TTGTATCGATACA
1 TTGTATCGATACA
1214848 TTGTATCGATACA
1 TTGTATCGATACA
1214861 ACACTTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1214873 original size:19 final size:21
Alignment explanation
Indices: 1214849--1214901 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
1214839 ATCGATACAT
1214849 TGTATCGATACAAC-ACT-TA
1 TGTATCGATACAACTACTGTA
* *
1214868 TGTATCAATAC-ACTTACTGTT
1 TGTATCGATACAAC-TACTGTA
1214889 TGTATCGATACAA
1 TGTATCGATACAA
1214902 ATTATGAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 2 0.07
19 10 0.37
20 3 0.11
21 11 0.41
22 1 0.04
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (21 bp):
TGTATCGATACAACTACTGTA
Found at i:1215758 original size:52 final size:49
Alignment explanation
Indices: 1215640--1216493 Score: 401
Period size: 48 Copynumber: 18.8 Consensus size: 49
1215630 CGAAGAATGA
* * * * * *
1215640 CAATGTGCTGATTCATGGCCAGCGACATTAGACTTGAAGA-AGA-ATGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGATAAAGATGC
* * ** *
1215687 TAATGTGCTGAGACAAGGCCAGCGACATTGGGCTTAGGAATGTTAAAGATGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGGCTTA--AA-GATAAAGATGC
* * * * * *
1215739 CAATATGCTGATTCAAGGCCAACGATATCGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGATAAAGATGC
* **
1215788 CAATATGTTGATTCAAGTTCAGCGACATTGGGC-T-----T----ATGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGATAAAGATGC
* * * * *
1215827 TAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA-CAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGATAAAGATGC
*
1215875 CAATATGCTGATTCAAGGCCAGCGATATTGGGCTT----AT---G-T--
1 CAATATGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGATAAAGATGC
* * * * *
1215914 CAATGTGCTGATTCAAGGCCAGGGACATTGGTCTTAGAA-A-CAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGGCTTA-AAGATAAAGATGC
*
1215962 CAATATGCTGATTCAAGGCCAGCGATATTGGGC-T-----T---G-TGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGATAAAGATGC
* * * * *
1216001 CATTGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA-CAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGATAAAGATGC
* * * * * **
1216049 CAATATGCTGATTCAAAGCCAGTGATATTGGAC-TCAAGATGGAGATGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGATAAAGATGC
* * * * * * *
1216097 TAATGTGGTGATTCAAGGCAAGTGACATTGGTCTTAAAGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGATAAAGATGC
* * * *
1216146 CAATGTGTTGATTCAAGGCCAACGATATTGGGC-T-----T----ATGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGATAAAGATGC
* * * * *
1216185 CAATGTGCTGATTTAAGGCCAGTGACATTGGTCTTAAAGACAAAG-TGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGATAAAGATGC
* * * *
1216233 TAATATGTTGATTCAAGGCCAGCAATATTGGGCTT----AT---G-T--
1 CAATATGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGATAAAGATGC
* * * * * *
1216272 TAATGTGCTGATTCAAGTCCAGCGACATTGGTCTTAAAGA-CAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGATAAAGATGC
* * ** ** *
1216320 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT-GTG-CCAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGATAAAGATGC
* * *
1216367 CAATATGTTGATTCAAGGCCAGCGATATTGGAC-T-----T----ATGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGATAAAGATGC
* * *
1216406 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGATAAAGATGC
* * *
1216455 CAATATGCTGATTCAAAGCCAGCGATATTGGACTTAAAG
1 CAATATGCTGATTCAAGGCCAGCGACATTGGGCTTAAAG
1216494 GTGCCATTGA
Statistics
Matches: 616, Mismatches: 121, Indels: 138
0.70 0.14 0.16
Matches are distributed among these distances:
39 184 0.30
40 5 0.01
41 3 0.00
42 1 0.00
43 4 0.01
44 2 0.00
45 3 0.00
46 3 0.00
47 77 0.12
48 186 0.30
49 111 0.18
50 3 0.00
51 2 0.00
52 32 0.05
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.27
Consensus pattern (49 bp):
CAATATGCTGATTCAAGGCCAGCGACATTGGGCTTAAAGATAAAGATGC
Found at i:1215898 original size:87 final size:87
Alignment explanation
Indices: 1215735--1216350 Score: 795
Period size: 87 Copynumber: 7.0 Consensus size: 87
1215725 AATGTTAAAG
* * * * * * * *
1215735 ATGCCAATATGCTGATTCAAGGCCAACGATATCGGACTTAAAGATGAAGGTGCCAATATGTTGAT
1 ATGCTAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA-CAAGGTGCCAATATGCTGAT
** *
1215800 TCAAGTTCAGCGACATTGGGCTT
65 TCAAGGCCAGCGATATTGGGCTT
1215823 ATGCTAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
1 ATGCTAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
1215888 CAAGGCCAGCGATATTGGGCTT
66 CAAGGCCAGCGATATTGGGCTT
*
1215910 ATG-TCAATGTGCTGATTCAAGGCCAGGGACATTGGTCTTAGAA-ACAAGGTGCCAATATGCTGA
1 ATGCT-AATGTGCTGATTCAAGGCCAGCGACATTGGTCTTA-AAGACAAGGTGCCAATATGCTGA
1215973 TTCAAGGCCAGCGATATTGGGCTT
64 TTCAAGGCCAGCGATATTGGGCTT
* * *
1215997 GTGCCATTGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
1 ATGCTAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
* * *
1216062 CAAAGCCAGTGATATTGGACTCAAGAT
66 CAAGGCCAGCGATATTGGGCT-----T
* * * * * *
1216089 GGAGATGCTAATGTGGTGATTCAAGGCAAGTGACATTGGTCTTAAAGATAAAGGTGCCAATGTGT
1 ----ATGCTAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA-CAAGGTGCCAATATGC
*
1216154 TGATTCAAGGCCAACGATATTGGGCTT
61 TGATTCAAGGCCAGCGATATTGGGCTT
* * * * * *
1216181 ATGCCAATGTGCTGATTTAAGGCCAGTGACATTGGTCTTAAAGACAAAGTGCTAATATGTTGATT
1 ATGCTAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
*
1216246 CAAGGCCAGCAATATTGGGCTT
66 CAAGGCCAGCGATATTGGGCTT
* *
1216268 ATGTTAATGTGCTGATTCAAGTCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
1 ATGCTAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
1216333 CAAGGCCAGCGATATTGG
66 CAAGGCCAGCGATATTGG
1216351 ACTTGTGCCA
Statistics
Matches: 463, Mismatches: 51, Indels: 29
0.85 0.09 0.05
Matches are distributed among these distances:
86 3 0.01
87 305 0.66
88 80 0.17
92 2 0.00
96 38 0.08
97 35 0.08
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (87 bp):
ATGCTAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
CAAGGCCAGCGATATTGGGCTT
Found at i:1216182 original size:271 final size:270
Alignment explanation
Indices: 1215823--1216353 Score: 848
Period size: 271 Copynumber: 2.0 Consensus size: 270
1215813 CATTGGGCTT
* *
1215823 ATGCTAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
1 ATGCTAATGTGCTGATTCAAGGCAAGCGACATTGGTCTTAAAGAAAAGGTGCCAATATGCTGATT
* *
1215888 CAAGGCCAGCGATATTGGGCTTATGTCAATGTGCTGATTCAAGGCCAGGGACATTGGTCTTAGAA
66 CAAGGCCAACGATATTGGGCTTATGCCAATGTGCTGATTCAAGGCCAGGGACATTGGTCTTA-AA
* * * *
1215953 -ACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTGTGCCATTGTGCTGATTCAA
130 GACAAAGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGGCTTATGCCAATGTGCTGATTCAA
*
1216017 GGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAAGCCAGTGATATTGGAC
195 GGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAAGCCAGCGATATTGGAC
1216082 TCAAGATGGAG
260 TCAAGATGGAG
* * * *
1216093 ATGCTAATGTGGTGATTCAAGGCAAGTGACATTGGTCTTAAAGATAAAGGTGCCAATGTGTTGAT
1 ATGCTAATGTGCTGATTCAAGGCAAGCGACATTGGTCTTAAAGA-AAAGGTGCCAATATGCTGAT
* *
1216158 TCAAGGCCAACGATATTGGGCTTATGCCAATGTGCTGATTTAAGGCCAGTGACATTGGTCTTAAA
65 TCAAGGCCAACGATATTGGGCTTATGCCAATGTGCTGATTCAAGGCCAGGGACATTGGTCTTAAA
* * **
1216223 GACAAAGTGCTAATATGTTGATTCAAGGCCAGCAATATTGGGCTTATGTTAATGTGCTGATTCAA
130 GACAAAGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGGCTTATGCCAATGTGCTGATTCAA
* *
1216288 GTCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
195 GGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAAGCCAGCGATATTGGAC
1216353 T
260 T
1216354 TGTGCCAAGG
Statistics
Matches: 238, Mismatches: 21, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
270 43 0.18
271 195 0.82
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (270 bp):
ATGCTAATGTGCTGATTCAAGGCAAGCGACATTGGTCTTAAAGAAAAGGTGCCAATATGCTGATT
CAAGGCCAACGATATTGGGCTTATGCCAATGTGCTGATTCAAGGCCAGGGACATTGGTCTTAAAG
ACAAAGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGGCTTATGCCAATGTGCTGATTCAAG
GCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAAGCCAGCGATATTGGACT
CAAGATGGAG
Found at i:1216381 original size:47 final size:47
Alignment explanation
Indices: 1216277--1216493 Score: 236
Period size: 47 Copynumber: 4.7 Consensus size: 47
1216267 TATGTTAATG
* * *
1216277 TGCTGATTCAAGTCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAG-CAAGGTGCCAATA
**
1216325 TGCTGATTCAAGGCCAGCGATATTGGACTT-GTGCCAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAG-CAAGGTGCCAATA
* *
1216372 TGTTGATTCAAGGCCAGCGATATTGGACTT------A--TGCCAATG
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGCAAGGTGCCAATA
* * *
1216411 TGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAG--CAAGGTGCCAATA
*
1216460 TGCTGATTCAAAGCCAGCGATATTGGACTTAAAG
1 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
1216494 GTGCCATTGA
Statistics
Matches: 144, Mismatches: 15, Indels: 19
0.81 0.08 0.11
Matches are distributed among these distances:
39 34 0.24
41 1 0.01
47 44 0.31
48 27 0.19
49 38 0.26
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.26
Consensus pattern (47 bp):
TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGCAAGGTGCCAATA
Found at i:1216469 original size:358 final size:351
Alignment explanation
Indices: 1215682--1216493 Score: 1011
Period size: 358 Copynumber: 2.3 Consensus size: 351
1215672 CTTGAAGAAG
* ** * *
1215682 AATGCTAATGTGCTGAGACAAGGCCAGCGACATTGGGCTTAGGAATGTTAAAGATGCCAATATGC
1 AATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTA--AA-GATAAAGATGCCAATATGC
* * ** *
1215747 TGATTCAAGGCCAA-CGATATCGGACTTAAAGATGAAGGTGCCAATATGTTGATTCAAGTTCAGC
63 TGATTCAAGG-CAAGCGATATTGGACTTAAAGATAAAGGTGCCAATATGTTGATTCAAGGCCAAC
* *
1215811 GACATTGGGCTTATGCTAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCC
127 GACATTGGGCTTATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGTGCC
* *
1215876 AATATGCTGATTCAAGGCCAGCGATATTGGGCTTATGTCAATGTGCTGATTCAAGGCCAGGGACA
192 AATATGCTGATTCAAGGCCAGCAATATTGGGCTTATGTCAATGTGCTGATTCAAGGCCAGCGACA
* *
1215941 TTGGTCTTAGAAACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTGTGCCATTG
257 TTGGTCTTAGAAACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTGTGCCATTA
*
1216006 TGCTGATTCAAGGCCAGCGACATTGGTCTT
322 TGCTGATTCAAGGCCAGCGACATTGGACTT
* * * * * ** *
1216036 AAAGACAAGGTGCCAATATGCTGATTCAAAGCCAGTGATATTGGAC-TCAAGATGGAGATGCTAA
1 ------AA--TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAAGATGCCAA
* * * * * *
1216100 TGTGGTGATTCAAGGCAAGTGACATTGGTCTTAAAGATAAAGGTGCCAATGTGTTGATTCAAGGC
58 TATGCTGATTCAAGGCAAGCGATATTGGACTTAAAGATAAAGGTGCCAATATGTTGATTCAAGGC
* * *
1216165 CAACGATATTGGGCTTATGCCAATGTGCTGATTTAAGGCCAGTGACATTGGTCTTAAAGACAAAG
123 CAACGACATTGGGCTTATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAG
* * * *
1216230 TGCTAATATGTTGATTCAAGGCCAGCAATATTGGGCTTATGTTAATGTGCTGATTCAAGTCCAGC
188 TGCCAATATGCTGATTCAAGGCCAGCAATATTGGGCTTATGTCAATGTGCTGATTCAAGGCCAGC
1216295 GACATTGGTCTTA-AAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTGTGC
253 GACATTGGTCTTAGAA-ACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTGTGC
* *
1216359 CAAGGTGCCAATATGTTGATTCAAGGCCAGCGATATTGGACTT
317 C-A--T-----TATGCTGATTCAAGGCCAGCGACATTGGACTT
* *
1216402 -ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGCCAATATGCTGA
1 AATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAAGATGCCAATATGCTGA
* *
1216466 TTCAAAGCCAGCGATATTGGACTTAAAG
66 TTCAAGGCAAGCGATATTGGACTTAAAG
1216494 GTGCCATTGA
Statistics
Matches: 382, Mismatches: 57, Indels: 28
0.82 0.12 0.06
Matches are distributed among these distances:
357 36 0.09
358 282 0.74
359 4 0.01
360 2 0.01
361 2 0.01
362 28 0.07
366 28 0.07
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (351 bp):
AATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAAGATGCCAATATGCTGA
TTCAAGGCAAGCGATATTGGACTTAAAGATAAAGGTGCCAATATGTTGATTCAAGGCCAACGACA
TTGGGCTTATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGTGCCAATA
TGCTGATTCAAGGCCAGCAATATTGGGCTTATGTCAATGTGCTGATTCAAGGCCAGCGACATTGG
TCTTAGAAACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTGTGCCATTATGCT
GATTCAAGGCCAGCGACATTGGACTT
Found at i:1216481 original size:88 final size:86
Alignment explanation
Indices: 1216317--1216490 Score: 249
Period size: 88 Copynumber: 2.0 Consensus size: 86
1216307 AAAGACAAGG
* ** * *
1216317 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTGTGCCAAGGTGCCAATATGTTGATTCA
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAGCAAAGGTGCCAATATGCTGATTCA
*
1216382 AGGCCAGCGATATTGGACTTA
66 AAGCCAGCGATATTGGACTTA
* * *
1216403 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGCCAATATGCTGATT
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT-AAG-CAAAGGTGCCAATATGCTGATT
1216468 CAAAGCCAGCGATATTGGACTTA
64 CAAAGCCAGCGATATTGGACTTA
1216491 AAGGTGCCAT
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
86 35 0.45
87 1 0.01
88 41 0.53
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.27
Consensus pattern (86 bp):
TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAGCAAAGGTGCCAATATGCTGATTCA
AAGCCAGCGATATTGGACTTA
Found at i:1216562 original size:33 final size:34
Alignment explanation
Indices: 1216506--1216620 Score: 105
Period size: 33 Copynumber: 3.5 Consensus size: 34
1216496 GCCATTGAGT
*
1216506 TGTGGACTT-ACA-GGAAAATGGGTG-CAC-GAAGG
1 TGTGGACTTAAAAGGGAAAA-GGGTGTCACAG-AGG
* *
1216538 TGTGGGCTTAAAAGGGAAAAGGGTGTCACAGAGT
1 TGTGGACTTAAAAGGGAAAAGGGTGTCACAGAGG
* * ** *
1216572 TGTGGACTTAAAAGGGAAAA-GATGCCATGGAGT
1 TGTGGACTTAAAAGGGAAAAGGGTGTCACAGAGG
1216605 TGTGGACTTAAAAGGG
1 TGTGGACTTAAAAGGG
1216621 TGCCACGGAG
Statistics
Matches: 71, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
32 8 0.11
33 32 0.45
34 30 0.42
35 1 0.01
ACGTcount: A:0.33, C:0.10, G:0.37, T:0.21
Consensus pattern (34 bp):
TGTGGACTTAAAAGGGAAAAGGGTGTCACAGAGG
Found at i:1216617 original size:26 final size:26
Alignment explanation
Indices: 1216588--1216645 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 26
1216578 CTTAAAAGGG
* *
1216588 AAAAGATGCCATGGAGTTGTGGACTT
1 AAAAGATGCCACGGAGTTATGGACTT
*
1216614 AAAAGGGTGCCACGGAGTTATGGACTT
1 AAAA-GATGCCACGGAGTTATGGACTT
1216641 AAAAG
1 AAAAG
1216646 GAAAAAGAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 5 0.18
27 23 0.82
ACGTcount: A:0.34, C:0.12, G:0.31, T:0.22
Consensus pattern (26 bp):
AAAAGATGCCACGGAGTTATGGACTT
Found at i:1216625 original size:27 final size:27
Alignment explanation
Indices: 1216594--1216646 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
1216584 AGGGAAAAGA
* *
1216594 TGCCATGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTATGGACTTAAAAGGG
1216621 TGCCACGGAGTTATGGACTTAAAAGG
1 TGCCACGGAGTTATGGACTTAAAAGG
1216647 AAAAAGAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.28, C:0.13, G:0.34, T:0.25
Consensus pattern (27 bp):
TGCCACGGAGTTATGGACTTAAAAGGG
Found at i:1216658 original size:34 final size:34
Alignment explanation
Indices: 1216614--1217027 Score: 415
Period size: 34 Copynumber: 12.8 Consensus size: 34
1216604 TTGTGGACTT
* *
1216614 AAAAGGGTGCCACGGAGTTATGGACTTAAAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
* * * * *
1216648 AAAAGAGTGCCATGAAGTTGTGGGCCTAAAA-AA
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
* *
1216681 AAAAGA-TGTCATGGAGTTGTGGACTTAAAA-G-
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
* *
1216712 ----G-GTGCTACGAAGTTGTGGACTTAAAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
* * *
1216741 AAAAGAGTGCCACGAAGTTGTGGGCTTAAAAAGA
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
*
1216775 AAAAGA-TGCCATGGAGTTGTGGACTTAAAA-G-
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
* * *
1216806 ----G-GTGCCACGGAGTTATGGGCTTGAAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
*
1216835 AAAAGAGTGCCACAGAGTTGT-GAGCTTAAAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGA-CTTAAAAGGA
*
1216869 AAAAGA-TGCCACGGAGTTGTGGACTTAAAAAG-
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
1216901 AAAAG-GTGCCACGGAGTTGTGGACTTAAAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
* *
1216934 ACAAG-GTGCCACGGACTTGTGGACTTAAAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
* *
1216967 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGA
1 AAAAGAGTGCCACGGAGTTGTGGAC-TTAAAAGGA
* *
1217002 AAAA-AGTGCCACTGAGTCGTGGACTT
1 AAAAGAGTGCCACGGAGTTGTGGACTT
1217028 TGGGAAAAAA
Statistics
Matches: 316, Mismatches: 42, Indels: 45
0.78 0.10 0.11
Matches are distributed among these distances:
27 42 0.13
28 2 0.01
32 51 0.16
33 89 0.28
34 120 0.38
35 12 0.04
ACGTcount: A:0.37, C:0.12, G:0.31, T:0.20
Consensus pattern (34 bp):
AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
Found at i:1216696 original size:93 final size:94
Alignment explanation
Indices: 1216544--1216998 Score: 560
Period size: 94 Copynumber: 4.8 Consensus size: 94
1216534 AAGGTGTGGG
* * * * **
1216544 CTTAAAAGGGAAAAGGGTGTCAC-AGAGTTGTGGACTTAAAAGGGAAAAGATGCCATGGAGTTGT
1 CTTAAAAGGAAAAAGAGTGCCACGA-AGTTGTGGGCTTAAAAGAAAAAAGATGCCATGGAGTTGT
1216608 GGACTTAAAAGGGTGCCACGGAGTTATGGA
65 GGACTTAAAAGGGTGCCACGGAGTTATGGA
* * *
1216638 CTTAAAAGGAAAAAGAGTGCCATGAAGTTGTGGGCCTAAAA-AAAAAAGATGTCATGGAGTTGTG
1 CTTAAAAGGAAAAAGAGTGCCACGAAGTTGTGGGCTTAAAAGAAAAAAGATGCCATGGAGTTGTG
* * *
1216702 GACTTAAAAGGGTGCTACGAAGTTGTGGA
66 GACTTAAAAGGGTGCCACGGAGTTATGGA
1216731 CTTAAAAGGAAAAAGAGTGCCACGAAGTTGTGGGCTTAAAA-AGAAAAAGATGCCATGGAGTTGT
1 CTTAAAAGGAAAAAGAGTGCCACGAAGTTGTGGGCTTAAAAGA-AAAAAGATGCCATGGAGTTGT
*
1216795 GGACTTAAAAGGGTGCCACGGAGTTATGGG
65 GGACTTAAAAGGGTGCCACGGAGTTATGGA
* * * *
1216825 CTTGAAAGGAAAAAGAGTGCCAC-AGAGTTGTGAGCTTAAAAGGAAAAAGATGCCACGGAGTTGT
1 CTTAAAAGGAAAAAGAGTGCCACGA-AGTTGTGGGCTTAAAAGAAAAAAGATGCCATGGAGTTGT
*
1216889 GGACTTAAAAAGAAAAGGTGCCACGGAGTTGTGGA
65 GGACTT-AAAAG----GGTGCCACGGAGTTATGGA
* * * * * *
1216924 CTTAAAAGGAACAAG-GTGCCACGGACTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGT
1 CTTAAAAGGAAAAAGAGTGCCACGAAGTTGTGGGCTTAAAAGAAAAAAGA-TGCCATGGAGTTGT
*
1216988 GGGCTTTAAAA
65 GGAC-TTAAAA
1216999 AGAAAAAAGT
Statistics
Matches: 317, Mismatches: 32, Indels: 19
0.86 0.09 0.05
Matches are distributed among these distances:
93 87 0.27
94 142 0.45
95 6 0.02
98 29 0.09
99 51 0.16
100 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.31, T:0.20
Consensus pattern (94 bp):
CTTAAAAGGAAAAAGAGTGCCACGAAGTTGTGGGCTTAAAAGAAAAAAGATGCCATGGAGTTGTG
GACTTAAAAGGGTGCCACGGAGTTATGGA
Found at i:1216793 original size:33 final size:33
Alignment explanation
Indices: 1216722--1217583 Score: 363
Period size: 31 Copynumber: 27.4 Consensus size: 33
1216712 GGTGCTACGA
*
1216722 AGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGA
1 AGTTGTGGACTTAAAAGGAAAAAGA-TGCCACGG
* * *
1216756 AGTTGTGGGCTTAAAAAGAAAAAGATGCCATGG
1 AGTTGTGGACTTAAAAGGAAAAAGATGCCACGG
1216789 AGTTGTGGACTTAAAAGG-----G-TGCCACGG
1 AGTTGTGGACTTAAAAGGAAAAAGATGCCACGG
* * * *
1216816 AGTTATGGGCTTGAAAGGAAAAAGAGTGCCACAG
1 AGTTGTGGACTTAAAAGGAAAAAGA-TGCCACGG
1216850 AGTTGT-GAGCTTAAAAGGAAAAAGATGCCACGG
1 AGTTGTGGA-CTTAAAAGGAAAAAGATGCCACGG
* *
1216883 AGTTGTGGACTTAAAAAG-AAAAGGTGCCACGG
1 AGTTGTGGACTTAAAAGGAAAAAGATGCCACGG
* *
1216915 AGTTGTGGACTTAAAAGGAACAAGGTGCCACGG
1 AGTTGTGGACTTAAAAGGAAAAAGATGCCACGG
*
1216948 ACTTGTGGACTTAAAAGGAAAAAGAGTGCCACGG
1 AGTTGTGGACTTAAAAGGAAAAAGA-TGCCACGG
* * *
1216982 AGTTGTGGGCTTTAAAAAGAAAAA-AGTGCCACTG
1 AGTTGTGGAC-TTAAAAGGAAAAAGA-TGCCACGG
* ** *
1217016 AGTCGTGGACTT--TGGGAAAAA-ATGCCACTG
1 AGTTGTGGACTTAAAAGGAAAAAGATGCCACGG
* ** **
1217046 AGTCGTGGACTT-TGA-G-AAAAGATTGCCATTG
1 AGTTGTGGACTTAAAAGGAAAAAGA-TGCCACGG
* ** **
1217077 AGTCGTGGACTTCGAA-G-AAAAGATGCCATTG
1 AGTTGTGGACTTAAAAGGAAAAAGATGCCACGG
* ** * **
1217108 AGTCGTGGACTTCGAA-G-AAGAGATGCCATTG
1 AGTTGTGGACTTAAAAGGAAAAAGATGCCACGG
* * * * *
1217139 AGTCGTGGACTT---TGGGAAGAGATGCCACTG
1 AGTTGTGGACTTAAAAGGAAAAAGATGCCACGG
** ** * *
1217169 AGTCATGGACTTTGAAGAAAAAAGATGCCACCG
1 AGTTGTGGACTTAAAAGGAAAAAGATGCCACGG
* * * * *
1217202 AGTCGTGGACTT---GGGGAAGAGATGCCACTG
1 AGTTGTGGACTTAAAAGGAAAAAGATGCCACGG
* *
1217232 AGTCGTGGACTT---A-GAAAAGAGATGCCACTG
1 AGTTGTGGACTTAAAAGGAAAA-AGATGCCACGG
** **
1217262 AGTTGTGGACTTTGAA-G-AAAAGATGCCACTA
1 AGTTGTGGACTTAAAAGGAAAAAGATGCCACGG
* * * * *
1217293 AGTCGTGGACTT---TGGGACAAGATGCCACTG
1 AGTTGTGGACTTAAAAGGAAAAAGATGCCACGG
* * * *
1217323 AGTCGTGGACTT-TAA-G-AAGAGATTGCCACTG
1 AGTTGTGGACTTAAAAGGAAAAAGA-TGCCACGG
* ** *
1217354 AGTCGTGGACTTTGAA-G-AAAAGATGCCACTG
1 AGTTGTGGACTTAAAAGGAAAAAGATGCCACGG
** * ** **
1217385 AGTCATGGACTT---TGGAACTAGATGCCATTG
1 AGTTGTGGACTTAAAAGGAAAAAGATGCCACGG
* * * *
1217415 AGTCGTGGACTT-TAA-G-AAGAGATTGCCACTG
1 AGTTGTGGACTTAAAAGGAAAAAGA-TGCCACGG
* * *
1217446 AGTCGTGGACTTAGAA-G-AAAAGATGCCACTG
1 AGTTGTGGACTTAAAAGGAAAAAGATGCCACGG
* **
1217477 AGTCGTGGACTT---A-GAAAAGAGATGCCACTA
1 AGTTGTGGACTTAAAAGGAAAA-AGATGCCACGG
* ** *
1217507 AGTTGTGGGCTTTTAA-G-AAAAGATGCCACTG
1 AGTTGTGGACTTAAAAGGAAAAAGATGCCACGG
* ** * **
1217538 AGTCGTGGACTTTGAAGAAAAAAAGATGCCACTA
1 AGTTGTGGACTTAAAAG-GAAAAAGATGCCACGG
1217572 AGTTGTGGACTT
1 AGTTGTGGACTT
1217584 TGAGAAGAGA
Statistics
Matches: 696, Mismatches: 87, Indels: 90
0.80 0.10 0.10
Matches are distributed among these distances:
27 22 0.03
28 3 0.00
29 13 0.02
30 167 0.24
31 200 0.29
32 61 0.09
33 109 0.16
34 109 0.16
35 12 0.02
ACGTcount: A:0.33, C:0.15, G:0.30, T:0.22
Consensus pattern (33 bp):
AGTTGTGGACTTAAAAGGAAAAAGATGCCACGG
Found at i:1216812 original size:27 final size:27
Alignment explanation
Indices: 1216781--1216833 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
1216771 AAGAAAAAGA
* *
1216781 TGCCATGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTATGGACTTAAAAGGG
* *
1216808 TGCCACGGAGTTATGGGCTTGAAAGG
1 TGCCACGGAGTTATGGACTTAAAAGG
1216834 AAAAAGAGTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.25, C:0.13, G:0.38, T:0.25
Consensus pattern (27 bp):
TGCCACGGAGTTATGGACTTAAAAGGG
Found at i:1216934 original size:65 final size:67
Alignment explanation
Indices: 1216808--1217027 Score: 277
Period size: 65 Copynumber: 3.3 Consensus size: 67
1216798 CTTAAAAGGG
* * * *
1216808 TGCCACGGAGTTATGGGCTTGAAAGGAAAAAGAGTGCCACAGAGTTGT-GAGCTTAAAAGGAAAA
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGA-CTTAAAAGGAAAA
1216872 AGA
65 AGA
* *
1216875 TGCCACGGAGTTGTGGACTTAAAAAG-AAAAG-GTGCCACGGAGTTGTGGACTTAAAAGGAACAA
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAAAAA
*
1216938 GG
66 GA
* * *
1216940 TGCCACGGACTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAA
1 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGAC-TTAAAAGGAAAA
1217005 A-A
65 AGA
* *
1217007 GTGCCACTGAGTCGTGGACTT
1 -TGCCACGGAGTTGTGGACTT
1217028 TGGGAAAAAA
Statistics
Matches: 132, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
65 52 0.39
66 12 0.09
67 40 0.30
68 28 0.21
ACGTcount: A:0.35, C:0.14, G:0.31, T:0.20
Consensus pattern (67 bp):
TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAAAAA
GA
Found at i:1217079 original size:61 final size:60
Alignment explanation
Indices: 1217003--1217619 Score: 702
Period size: 61 Copynumber: 10.0 Consensus size: 60
1216993 TTAAAAAGAA
* *
1217003 AAAAG-TGCCACTGAGTCGTGGACTTTGGGAAAAAATGCCACTGAGTCGTGGACTTTGAG
1 AAAAGATGCCACTGAGTCGTGGACTTTGAGAAAAGATGCCACTGAGTCGTGGACTTTGAG
* * * *
1217062 AAAAGATTGCCATTGAGTCGTGGACTTCGAAGAAAAGATGCCATTGAGTCGTGGACTTCGAAG
1 AAAAGA-TGCCACTGAGTCGTGGACTTTG-AGAAAAGATGCCACTGAGTCGTGGACTTTG-AG
* * * * *
1217125 AAGAGATGCCATTGAGTCGTGGACTTTGGGAAGAGATGCCACTGAGTCATGGACTTTGAAG
1 AAAAGATGCCACTGAGTCGTGGACTTTGAGAAAAGATGCCACTGAGTCGTGGACTTTG-AG
* * * * *
1217186 AAAAAAGATGCCACCGAGTCGTGGACTTGGGGAAGAGATGCCACTGAGTCGTGGACTTAGA-
1 --AAAAGATGCCACTGAGTCGTGGACTTTGAGAAAAGATGCCACTGAGTCGTGGACTTTGAG
* * *
1217247 AAAGAGATGCCACTGAGTTGTGGACTTTGAAGAAAAGATGCCACTAAGTCGTGGACTTTGGG
1 AAA-AGATGCCACTGAGTCGTGGACTTTG-AGAAAAGATGCCACTGAGTCGTGGACTTTGAG
* * *
1217309 ACAAGATGCCACTGAGTCGTGGACTTTAAGAAGAGATTGCCACTGAGTCGTGGACTTTGAAG
1 AAAAGATGCCACTGAGTCGTGGACTTTGAGAAAAGA-TGCCACTGAGTCGTGGACTTTG-AG
* * * *
1217371 AAAAGATGCCACTGAGTCATGGACTTTG-GAACTAGATGCCATTGAGTCGTGGACTTTAAG
1 AAAAGATGCCACTGAGTCGTGGACTTTGAGAA-AAGATGCCACTGAGTCGTGGACTTTGAG
* * *
1217431 AAGAGATTGCCACTGAGTCGTGGACTTAGAAGAAAAGATGCCACTGAGTCGTGGACTTAGA-
1 AAAAGA-TGCCACTGAGTCGTGGACTTTG-AGAAAAGATGCCACTGAGTCGTGGACTTTGAG
* * * *
1217492 AAAGAGATGCCACTAAGTTGTGGGCTTTTAAGAAAAGATGCCACTGAGTCGTGGACTTTGAAG
1 AAA-AGATGCCACTGAGTCGTGGAC-TTTGAGAAAAGATGCCACTGAGTCGTGGACTTTG-AG
* * * *
1217555 AAAAAAAGATGCCACTAAGTTGTGGACTTTGAGAAGAGATGCCACTAAGTCGTGGACTTTGAG
1 ---AAAAGATGCCACTGAGTCGTGGACTTTGAGAAAAGATGCCACTGAGTCGTGGACTTTGAG
1217618 AA
1 AA
1217620 GAGAGATTTG
Statistics
Matches: 479, Mismatches: 57, Indels: 43
0.83 0.10 0.07
Matches are distributed among these distances:
59 8 0.02
60 38 0.08
61 207 0.43
62 108 0.23
63 64 0.13
64 31 0.06
65 20 0.04
66 3 0.01
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (60 bp):
AAAAGATGCCACTGAGTCGTGGACTTTGAGAAAAGATGCCACTGAGTCGTGGACTTTGAG
Done.