Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold126
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: 2080828
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.30
Warning! 191490 characters in sequence are not A, C, G, or T
File 11 of 13
Found at i:1728358 original size:33 final size:33
Alignment explanation
Indices: 1728321--1728387 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1728311 TTCAACGATT
1728321 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1728354 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1728387 T
1 T
1728388 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1728359 original size:13 final size:13
Alignment explanation
Indices: 1728341--1728365 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1728331 CATAAAATGT
1728341 TGTATCGATACAA
1 TGTATCGATACAA
1728354 TGTATCGATACA
1 TGTATCGATACA
1728366 TATTTTTTTG
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:1728446 original size:13 final size:13
Alignment explanation
Indices: 1728428--1728452 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1728418 ATTACTCAAA
1728428 TGTATCGATACAT
1 TGTATCGATACAT
1728441 TGTATCGATACA
1 TGTATCGATACA
1728453 CTGATCTTTG
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:1728554 original size:52 final size:52
Alignment explanation
Indices: 1728461--1728590 Score: 192
Period size: 52 Copynumber: 2.5 Consensus size: 52
1728451 CACTGATCTT
* *
1728461 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATT-AAA
1728512 TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATTAAA
* * *
1728564 TGTATCGATACTTGCAAGCAACTTTTC
1 TGTATCGATACATGCAGGCAAATTTTC
1728591 ATATTTCGGG
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
51 19 0.26
52 50 0.69
53 3 0.04
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATTAAA
Found at i:1735052 original size:28 final size:28
Alignment explanation
Indices: 1734974--1735297 Score: 352
Period size: 28 Copynumber: 11.5 Consensus size: 28
1734964 GGCTTTGAAA
*
1734974 AAAAGGTGCCACTAACTTGTGTGGGCTTTG
1 AAAAGATGCCACTAAC-T-TGTGGGCTTTG
* * * *
1735004 AAAGGGTATGCCATTGACTTGTGGGTTTTG
1 AAA-AG-ATGCCACTAACTTGTGGGCTTTG
* *
1735034 AAATGGTGCCACTAACTTGTGGGCTTTG
1 AAAAGATGCCACTAACTTGTGGGCTTTG
1735062 AAAAGATGCCA-TAGACTTGTGGGCTTTG
1 AAAAGATGCCACTA-ACTTGTGGGCTTTG
*
1735090 AAATA-ATGCCACTAACTTGTGGGCTTTT
1 AAA-AGATGCCACTAACTTGTGGGCTTTG
*
1735118 AAAAGATGCCAC-AGACTTATGGGCTTTG
1 AAAAGATGCCACTA-ACTTGTGGGCTTTG
* *
1735146 AAATGATGCCACTAATTTGTGGGCTTTG
1 AAAAGATGCCACTAACTTGTGGGCTTTG
*
1735174 AAAAGATGCCACTGACTTGTGGGCTTT-
1 AAAAGATGCCACTAACTTGTGGGCTTTG
*
1735201 AAAAGGATGCCACTGACTTGTGGGCTTTG
1 AAAA-GATGCCACTAACTTGTGGGCTTTG
* * *
1735230 AAAAGATGCCATTGACTTGT-GGCTTTA
1 AAAAGATGCCACTAACTTGTGGGCTTTG
* * *
1735257 AAAAGATACCACTGACTTGTGAGCTTTG
1 AAAAGATGCCACTAACTTGTGGGCTTTG
* *
1735285 AAATGATGGCACT
1 AAAAGATGCCACT
1735298 TGTTAGGATC
Statistics
Matches: 253, Mismatches: 30, Indels: 24
0.82 0.10 0.08
Matches are distributed among these distances:
27 32 0.13
28 186 0.74
29 9 0.04
30 16 0.06
31 2 0.01
32 8 0.03
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (28 bp):
AAAAGATGCCACTAACTTGTGGGCTTTG
Found at i:1735084 original size:56 final size:56
Alignment explanation
Indices: 1734980--1735292 Score: 396
Period size: 56 Copynumber: 5.5 Consensus size: 56
1734970 GAAAAAAAGG
* * * *
1734980 TGCCACTAACTTGTGTGGGCTTTGAAAGGGTATGCCATTGACTTGTGGGTTTTGAAATGG
1 TGCCACTAAC-T-TGTGGGCTTTGAAA-AG-ATGCCATAGACTTGTGGGCTTTGAAATGA
*
1735040 TGCCACTAACTTGTGGGCTTTGAAAAGATGCCATAGACTTGTGGGCTTTGAAATAA
1 TGCCACTAACTTGTGGGCTTTGAAAAGATGCCATAGACTTGTGGGCTTTGAAATGA
* * *
1735096 TGCCACTAACTTGTGGGCTTTTAAAAGATGCCACAGACTTATGGGCTTTGAAATGA
1 TGCCACTAACTTGTGGGCTTTGAAAAGATGCCATAGACTTGTGGGCTTTGAAATGA
* * *
1735152 TGCCACTAATTTGTGGGCTTTGAAAAGATGCCACT-GACTTGTGGGCTTTAAAAGGA
1 TGCCACTAACTTGTGGGCTTTGAAAAGATGCCA-TAGACTTGTGGGCTTTGAAATGA
* * * *
1735208 TGCCACTGACTTGTGGGCTTTGAAAAGATGCCATTGACTTGT-GGCTTTAAAAAGA
1 TGCCACTAACTTGTGGGCTTTGAAAAGATGCCATAGACTTGTGGGCTTTGAAATGA
* * * *
1735263 TACCACTGACTTGTGAGCTTTGAAATGATG
1 TGCCACTAACTTGTGGGCTTTGAAAAGATG
1735293 GCACTTGTTA
Statistics
Matches: 230, Mismatches: 21, Indels: 9
0.88 0.08 0.03
Matches are distributed among these distances:
55 40 0.17
56 164 0.71
57 1 0.00
58 14 0.06
59 1 0.00
60 10 0.04
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (56 bp):
TGCCACTAACTTGTGGGCTTTGAAAAGATGCCATAGACTTGTGGGCTTTGAAATGA
Found at i:1735698 original size:13 final size:13
Alignment explanation
Indices: 1735680--1735705 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1735670 TACAGCAAGT
1735680 ATGTATCGATACA
1 ATGTATCGATACA
1735693 ATGTATCGATACA
1 ATGTATCGATACA
1735706 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:1737956 original size:21 final size:21
Alignment explanation
Indices: 1737923--1737967 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1737913 TTGCAAGTTG
*
1737923 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1737945 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1737965 AAA
1 AAA
1737968 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1739791 original size:15 final size:15
Alignment explanation
Indices: 1739771--1739801 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1739761 TAAAAATGTC
*
1739771 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1739786 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1739801 C
1 C
1739802 CAAACGAAAT
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1742780 original size:13 final size:13
Alignment explanation
Indices: 1742762--1742787 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1742752 CAATTTTTTG
1742762 TGTATCGATACAT
1 TGTATCGATACAT
1742775 TGTATCGATACAT
1 TGTATCGATACAT
1742788 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:1742872 original size:20 final size:20
Alignment explanation
Indices: 1742847--1742919 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1742837 CAACTTTTTT
1742847 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1742867 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1742888 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1742908 ATGTATCGATAC
1 ATGTATCGATAC
1742920 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:1742885 original size:41 final size:41
Alignment explanation
Indices: 1742826--1742919 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
1742816 CTGCCAAGAA
*
1742826 ATGTATCGATACAACTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
*
1742867 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
1742908 ATGTATCGATAC
1 ATGTATCGATAC
1742920 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
Found at i:1742901 original size:21 final size:21
Alignment explanation
Indices: 1742826--1742901 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
1742816 CTGCCAAGAA
* *
1742826 ATGTATCGATACAACTTTTTT
1 ATGTATCGATACATCTTTTTC
****
1742847 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1742867 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1742888 ATGTATCGATACAT
1 ATGTATCGATACAT
1742902 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1745129 original size:52 final size:52
Alignment explanation
Indices: 1745059--1745179 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
1745049 GAAAATTTAT
*
1745059 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTCGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTCGGCAAATTTGC
* *
1745111 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTCGGCAAATTTGC
1745163 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
1745180 AAGATCAGTG
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTCGGCAAATTTGC
Found at i:1745192 original size:52 final size:51
Alignment explanation
Indices: 1745059--1745199 Score: 203
Period size: 52 Copynumber: 2.7 Consensus size: 51
1745049 GAAAATTTAT
1745059 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTCGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTCGGCAAATTTGC
* * *
1745111 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTCGGCAAATTTGC
*
1745163 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
1745200 ATGTATCGAT
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 79 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTCGGCAAATTTGC
Found at i:1745206 original size:13 final size:13
Alignment explanation
Indices: 1745188--1745212 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1745178 CAAAGATCAG
1745188 TGTATCGATACAA
1 TGTATCGATACAA
1745201 TGTATCGATACA
1 TGTATCGATACA
1745213 TGTGAGTAAT
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:1745294 original size:33 final size:33
Alignment explanation
Indices: 1745252--1745321 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1745242 GGCAGTAGCT
1745252 TACATTGTATCGATACAAAAAAATATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
* ***
1745285 TACATTGTATCGATACAACATTTTATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
1745318 TACA
1 TACA
1745322 AATCGTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (33 bp):
TACATTGTATCGATACAAAAAAATATGTATCGA
Found at i:1745295 original size:13 final size:13
Alignment explanation
Indices: 1745277--1745301 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1745267 CAAAAAAATA
1745277 TGTATCGATACAT
1 TGTATCGATACAT
1745290 TGTATCGATACA
1 TGTATCGATACA
1745302 ACATTTTATG
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:1746673 original size:20 final size:20
Alignment explanation
Indices: 1746594--1746673 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
1746584 AATGTCCAAA
*
1746594 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
1746614 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
1746639 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
1746659 TTGTATCGATACATT
1 ATGTATCGATACATT
1746674 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:1746677 original size:13 final size:13
Alignment explanation
Indices: 1746660--1746710 Score: 93
Period size: 13 Copynumber: 3.9 Consensus size: 13
1746650 CATTTTTCTT
*
1746660 TGTATCGATACAT
1 TGTATCGATACAC
1746673 TGTATCGATACAC
1 TGTATCGATACAC
1746686 TGTATCGATACAC
1 TGTATCGATACAC
1746699 TGTATCGATACA
1 TGTATCGATACA
1746711 GGGTAATTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:1746855 original size:21 final size:21
Alignment explanation
Indices: 1746831--1746877 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1746821 AAATCTTTTG
1746831 CAAAAT-ACTT-GTTTTTCACTT
1 CAAAATAACTTCGTTTTTCA--T
1746852 C-AAATAACTTCGTTTTTCAT
1 CAAAATAACTTCGTTTTTCAT
1746872 CAAAAT
1 CAAAAT
1746878 CAGCATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (21 bp):
CAAAATAACTTCGTTTTTCAT
Found at i:1746874 original size:20 final size:19
Alignment explanation
Indices: 1746833--1746875 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
1746823 ATCTTTTGCA
1746833 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
1746853 AAATAACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
1746873 AAA
1 AAA
1746876 ATCAGCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:1749252 original size:22 final size:22
Alignment explanation
Indices: 1749224--1749267 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1749214 TTCTTGGCAG
1749224 TAGCCAAACTTGTATCGATACA
1 TAGCCAAACTTGTATCGATACA
1749246 TAGCCAAACTTGTATCGATACA
1 TAGCCAAACTTGTATCGATACA
1749268 GCAAGTATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (22 bp):
TAGCCAAACTTGTATCGATACA
Found at i:1749292 original size:13 final size:13
Alignment explanation
Indices: 1749274--1749299 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1749264 TACAGCAAGT
1749274 ATGTATCGATACA
1 ATGTATCGATACA
1749287 ATGTATCGATACA
1 ATGTATCGATACA
1749300 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:1750092 original size:28 final size:28
Alignment explanation
Indices: 1750052--1750299 Score: 293
Period size: 28 Copynumber: 8.6 Consensus size: 28
1750042 AAGCTTTCAG
*
1750052 CACTAACTTGTGGGCTTTGAAAAGATGC
1 CACTGACTTGTGGGCTTTGAAAAGATGC
*
1750080 CACTGACTTGTGGGCTTTGAAATGATGC
1 CACTGACTTGTGGGCTTTGAAAAGATGC
*
1750108 CACTAACTTGTGGGCTTT-AAAAGGATGC
1 CACTGACTTGTGGGCTTTGAAAA-GATGC
*
1750136 CACTGATTTGTGGGCTTT-AAAAGGATGC
1 CACTGACTTGTGGGCTTTGAAAA-GATGC
* *
1750164 CACTGACTTGTGGGCTTTGAAATGATAC
1 CACTGACTTGTGGGCTTTGAAAAGATGC
* *
1750192 CACTGACTTATGGGCTTTGAAATGAGTTGC
1 CACTGACTTGTGGGCTTTGAAA--AGATGC
**
1750222 CACCAACTTGTGTGGACTTTGAAAAGAGTGC
1 CACTGACTTGTG-GG-CTTTGAAAAGA-TGC
* *
1750253 CATTGACTTGTGGGCTTTGAAAAGGGTGC
1 CACTGACTTGTGGGCTTTGAAAA-GATGC
*
1750282 CACTAACTTGTGGGCTTT
1 CACTGACTTGTGGGCTTT
1750300 AGAAGGGAAT
Statistics
Matches: 189, Mismatches: 23, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
27 3 0.02
28 116 0.61
29 31 0.16
30 17 0.09
31 14 0.07
32 8 0.04
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (28 bp):
CACTGACTTGTGGGCTTTGAAAAGATGC
Found at i:1750138 original size:56 final size:56
Alignment explanation
Indices: 1750052--1750551 Score: 402
Period size: 56 Copynumber: 8.8 Consensus size: 56
1750042 AAGCTTTCAG
* * * *
1750052 CACTAACTTGTGGGCTTTGAAAA-GATGCCACTGACTTGTGGGCTTTGAAATGATGC
1 CACTAACTTGTGGGCTTT-AAAAGGATGCCACTGACTTGTGGACTTTAAAAGGGTGC
* * *
1750108 CACTAACTTGTGGGCTTTAAAAGGATGCCACTGATTTGTGGGCTTTAAAAGGATGC
1 CACTAACTTGTGGGCTTTAAAAGGATGCCACTGACTTGTGGACTTTAAAAGGGTGC
* * * * * * * *
1750164 CACTGACTTGTGGGCTTTGAAATGATACCACTGACTTATGGGCTTTGAAATGAGTTGC
1 CACTAACTTGTGGGCTTTAAAAGGATGCCACTGACTTGTGGACTTT-AAAAG-GGTGC
* * *
1750222 CACCAACTTGTGTGGACTTTGAAAA-GAGTGCCATTGACTTGTGGGCTTTGAAAAGGGTGC
1 CACTAACTTGTG-GG-CTTT-AAAAGGA-TGCCACTGACTTGTGGACTTT-AAAAGGGTGC
* * *
1750282 CACTAACTTGTGGGCTTTAGAAGGGAATGCCATTAACTTGTGGAC-TTAAAAGGGTGC
1 CACTAACTTGTGGGCTTTA-AAAGG-ATGCCACTGACTTGTGGACTTTAAAAGGGTGC
* * * * * * *
1750339 CA-TGGAGTAGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGGTGC
1 CACT-AACTTGTGGGCTTTAAAAGGATGCCACTGACTTGTGGACTTTAAAAGGGTGC
** * * * * *
1750395 CACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTTAAAAGGGTGC
1 CACTAACTTGTGGGCTTTAAAAGGATGCCACTGACTTGTGGACTTTAAAAGGGTGC
** * * * * * *
1750451 CACGGAGTTGTGGACTTAAAATAGG-TGCCAC-GAATTTGTGGACTTAAAAAAGGTGC
1 CACTAACTTGTGGGCTTTAAA-AGGATGCCACTG-ACTTGTGGACTTTAAAAGGGTGC
* * * * *
1750507 CACTAAGTTGTGGACTTAAAAAGG-TGCCACTGAATCGTGGACTTT
1 CACTAACTTGTGGGCTTTAAAAGGATGCCACTGACTTGTGGACTTT
1750552 GAAGAAGTTA
Statistics
Matches: 383, Mismatches: 45, Indels: 33
0.83 0.10 0.07
Matches are distributed among these distances:
55 38 0.10
56 223 0.58
57 31 0.08
58 22 0.06
59 21 0.05
60 22 0.06
61 26 0.07
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (56 bp):
CACTAACTTGTGGGCTTTAAAAGGATGCCACTGACTTGTGGACTTTAAAAGGGTGC
Found at i:1750206 original size:84 final size:84
Alignment explanation
Indices: 1750052--1750537 Score: 365
Period size: 84 Copynumber: 5.7 Consensus size: 84
1750042 AAGCTTTCAG
* * *
1750052 CACTAACTTGTGGGCTTTGAAAA-GATGCCACTGACTTGTGGGCTTTGAAATGATGCCACTAACT
1 CACTAATTTGTGGACTTT-AAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACT
1750116 TGTGGGCTTTAAAAGGATGC
65 TGTGGGCTTTAAAAGGATGC
* * * * *
1750136 CACTGATTTGTGGGCTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAAATGATACCACTGACTT
1 CACTAATTTGTGGACTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACTT
* * *
1750201 ATGGGCTTTGAAATGAGTTGC
66 GTGGGCTTT-AAAAG-GATGC
* * *
1750222 CACCAACTTGTGTGGACTTTGAAAA-GAGTGCCATTGACTTGTGGGCTTTGAAAAGGGTGCCACT
1 CACTAA-TT-TGTGGACTTT-AAAAGGA-TGCCACTGACTTGTGGGCTTTG-AAAGGATGCCACT
*
1750286 AACTTGTGGGCTTTAGAAGGGAATGC
61 AACTTGTGGGCTTTA-AAAGG-ATGC
* * * * * * * * ** *
1750312 CATTAACTTGTGGAC-TTAAAAGGGTGCCA-TGGAGTAGTGGACTTTAAAAGGGTGCCACGGAGT
1 CACTAATTTGTGGACTTTAAAAGGATGCCACT-GACTTGTGGGCTTTGAAAGGATGCCACTAACT
* *
1750375 TGTGGACTTTAAAAGGGTGC
65 TGTGGGCTTTAAAAGGATGC
** * * * * * * * ** *
1750395 CACGGAGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTT
1 CACTAATTTGTGGACTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACTT
* *
1750460 GTGGACTTAAAATAGG-TGC
66 GTGGGCTTTAAA-AGGATGC
* * * * * **
1750479 CACGAATTTGTGGACTTAAAAAAGG-TGCCACTAAGTTGTGGACTTAAAAAGG-TGCCACT
1 CACTAATTTGTGGACTT-TAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACT
1750538 GAATCGTGGA
Statistics
Matches: 340, Mismatches: 46, Indels: 33
0.81 0.11 0.08
Matches are distributed among these distances:
83 24 0.07
84 167 0.49
85 38 0.11
86 28 0.08
87 5 0.01
88 18 0.05
89 28 0.08
90 32 0.09
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (84 bp):
CACTAATTTGTGGACTTTAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACTT
GTGGGCTTTAAAAGGATGC
Found at i:1750367 original size:28 final size:28
Alignment explanation
Indices: 1750115--1750551 Score: 322
Period size: 28 Copynumber: 15.4 Consensus size: 28
1750105 TGCCACTAAC
* * * *
1750115 TTGTGGGCTTTAAAAGGATGCCACTGAT
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
* * * *
1750143 TTGTGGGCTTTAAAAGGATGCCACTGAC
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
* * * * * * *
1750171 TTGTGGGCTTTGAAATGATACCACTGAC
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
* * * * ** *
1750199 TTATGGGCTTTGAAATGAGTTGCCACCAACT
1 TTGTGGACTTT-AAAAG-GGTGCCACGGA-G
* ** *
1750230 TGTGTGGACTTTGAAAAGAGTGCCATTGAC
1 T-TGTGGACTTT-AAAAGGGTGCCACGGAG
* ** *
1750260 TTGTGGGCTTTGAAAAGGGTGCCACTAAC
1 TTGTGGACTTT-AAAAGGGTGCCACGGAG
* * *** *
1750289 TTGTGGGCTTTAGAAGGGAATGCCATTAAC
1 TTGTGGACTTTAAAAGGG--TGCCACGGAG
*
1750319 TTGTGGAC-TTAAAAGGGTGCCATGGAG
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
*
1750346 TAGTGGACTTTAAAAGGGTGCCACGGAG
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
1750374 TTGTGGACTTTAAAAGGGTGCCACGGAG
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
*
1750402 TTGTGGACTTTAAAAGGGTGCCACAGAG
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
1750430 TTGTGGACTTTAAAAGGGTGCCACGGAG
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
* * *
1750458 TTGTGGAC-TTAAAATAGGTGCCACGAAT
1 TTGTGGACTTTAAAA-GGGTGCCACGGAG
* * **
1750486 TTGTGGACTTAAAAAAGGTGCCACTAAG
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
* * *
1750514 TTGTGGAC-TTAAAAAGGTGCCACTGAA
1 TTGTGGACTTTAAAAGGGTGCCACGGAG
*
1750541 TCGTGGACTTT
1 TTGTGGACTTT
1750552 GAAGAAGTTA
Statistics
Matches: 351, Mismatches: 48, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
27 43 0.12
28 214 0.61
29 50 0.14
30 24 0.07
31 7 0.02
32 13 0.04
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.28
Consensus pattern (28 bp):
TTGTGGACTTTAAAAGGGTGCCACGGAG
Found at i:1751948 original size:25 final size:23
Alignment explanation
Indices: 1751920--1751970 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 23
1751910 TTTTTTGTTC
1751920 TTTTTTTTATTTTGCTTTTGCACTT
1 TTTTTTTTATTTTGCTTTT-CA-TT
* *
1751945 TTTTTTTTGTTTTTCTTTTCATT
1 TTTTTTTTATTTTGCTTTTCATT
1751968 TTT
1 TTT
1751971 GTGCTTTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 5 0.21
24 2 0.08
25 17 0.71
ACGTcount: A:0.06, C:0.10, G:0.06, T:0.78
Consensus pattern (23 bp):
TTTTTTTTATTTTGCTTTTCATT
Found at i:1751978 original size:21 final size:20
Alignment explanation
Indices: 1751946--1751984 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1751936 TTTGCACTTT
* *
1751946 TTTTTTTGTTTTTCTTTTCA
1 TTTTTGTGTTTTGCTTTTCA
1751966 TTTTTGTGCTTTTGCTTTT
1 TTTTTGTG-TTTTGCTTTT
1751985 GACTTTTTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.03, C:0.10, G:0.10, T:0.77
Consensus pattern (20 bp):
TTTTTGTGTTTTGCTTTTCA
Found at i:1759775 original size:21 final size:21
Alignment explanation
Indices: 1759749--1759840 Score: 66
Period size: 22 Copynumber: 4.3 Consensus size: 21
1759739 GCATTCATGT
1759749 CCTTTTTTTGTTTTG-TTGTTA
1 CCTTTTTTTGTTTTGCTT-TTA
* *
1759770 CC-TTTTTTATTTTGCTTTTG
1 CCTTTTTTTGTTTTGCTTTTA
*
1759790 CACTTTTTTTGTTTTTCTTTT-
1 C-CTTTTTTTGTTTTGCTTTTA
* *
1759811 CATTTTTTATACTTTTGCTTTTGA
1 CCTTTTTT-T-GTTTTGCTTTT-A
1759835 -CTTTTT
1 CCTTTTT
1759841 CATAATTTTA
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
20 20 0.36
21 7 0.12
22 24 0.43
23 5 0.09
ACGTcount: A:0.08, C:0.13, G:0.09, T:0.71
Consensus pattern (21 bp):
CCTTTTTTTGTTTTGCTTTTA
Found at i:1759797 original size:22 final size:22
Alignment explanation
Indices: 1759772--1759840 Score: 81
Period size: 22 Copynumber: 3.2 Consensus size: 22
1759762 TGTTGTTACC
1759772 TTTTTTATTTTGCTTTTGCACT
1 TTTTTTATTTTGCTTTTGCACT
* *
1759794 TTTTTTGTTTTTCTTTT-CA-T
1 TTTTTTATTTTGCTTTTGCACT
1759814 TTTTTATACTTTTGCTTTTG-ACT
1 TTTTT-TA-TTTTGCTTTTGCACT
1759837 TTTT
1 TTTT
1759841 CATAATTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
20 6 0.15
21 3 0.08
22 25 0.64
23 5 0.13
ACGTcount: A:0.09, C:0.12, G:0.07, T:0.72
Consensus pattern (22 bp):
TTTTTTATTTTGCTTTTGCACT
Found at i:1764649 original size:27 final size:27
Alignment explanation
Indices: 1764611--1764676 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
1764601 TTAAAAGCGG
1764611 GGTTGGAGTATCTCCTCAGAAGAATGA
1 GGTTGGAGTATCTCCTCAGAAGAATGA
* *
1764638 GGTTGGAGTATCTCCTCGGAGGAATGA
1 GGTTGGAGTATCTCCTCAGAAGAATGA
1764665 GGTTGGAGTATC
1 GGTTGGAGTATC
1764677 CTCGATGAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.24, C:0.14, G:0.35, T:0.27
Consensus pattern (27 bp):
GGTTGGAGTATCTCCTCAGAAGAATGA
Found at i:1765370 original size:26 final size:26
Alignment explanation
Indices: 1765334--1765390 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
1765324 AGATACCATT
1765334 GAAAAGATATTTTGACAAACTTTCAA
1 GAAAAGATATTTTGACAAACTTTCAA
1765360 GAAAAGATATTTTGACAAACTTTCAA
1 GAAAAGATATTTTGACAAACTTTCAA
1765386 GAAAA
1 GAAAA
1765391 AATACAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.49, C:0.11, G:0.12, T:0.28
Consensus pattern (26 bp):
GAAAAGATATTTTGACAAACTTTCAA
Found at i:1766924 original size:25 final size:24
Alignment explanation
Indices: 1766879--1766976 Score: 68
Period size: 20 Copynumber: 4.1 Consensus size: 24
1766869 AATTAACTAG
1766879 ATGTATCGATACAT-T-G--AAAA
1 ATGTATCGATACATCTGGTAAAAA
1766899 ATGTATCGATACATCTGGGTAAAAAAATAGA
1 ATGTATCGATACATCT-GGT----AAA-A-A
1766930 ATGTATCGATACAT-T-G--AAAA
1 ATGTATCGATACATCTGGTAAAAA
1766950 ATGTATCGATACATCTAGGTAAAAA
1 ATGTATCGATACATCT-GGTAAAAA
1766975 AT
1 AT
1766977 ATAGAATGTA
Statistics
Matches: 62, Mismatches: 0, Indels: 27
0.70 0.00 0.30
Matches are distributed among these distances:
20 29 0.47
21 3 0.05
22 2 0.03
23 2 0.03
25 6 0.10
28 1 0.02
29 2 0.03
30 2 0.03
31 15 0.24
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (24 bp):
ATGTATCGATACATCTGGTAAAAA
Found at i:1766936 original size:51 final size:52
Alignment explanation
Indices: 1766879--1766995 Score: 218
Period size: 51 Copynumber: 2.3 Consensus size: 52
1766869 AATTAACTAG
*
1766879 ATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAA-ATAGA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAAAATATAGA
1766930 ATGTATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAAAATATAGA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAAAATATAGA
1766982 ATGTATCGATACAT
1 ATGTATCGATACAT
1766996 GTACTGTTCA
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
51 45 0.70
52 19 0.30
ACGTcount: A:0.44, C:0.10, G:0.16, T:0.29
Consensus pattern (52 bp):
ATGTATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAAAATATAGA
Found at i:1766974 original size:24 final size:20
Alignment explanation
Indices: 1766879--1766963 Score: 71
Period size: 20 Copynumber: 3.7 Consensus size: 20
1766869 AATTAACTAG
1766879 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
1766899 ATGTATCGATACATCTGGGTAAAAAAATAGA
1 ATGTATCGATACAT-T--G------AA-A-A
1766930 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
1766950 ATGTATCGATACAT
1 ATGTATCGATACAT
1766964 CTAGGTAAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 22
0.71 0.00 0.29
Matches are distributed among these distances:
20 29 0.54
21 2 0.04
22 2 0.04
23 1 0.02
28 1 0.02
29 2 0.04
30 2 0.04
31 15 0.28
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.29
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:1767467 original size:10 final size:10
Alignment explanation
Indices: 1767452--1767477 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1767442 GCACCCCTTC
1767452 TTTTTTTGTA
1 TTTTTTTGTA
1767462 TTTTTTTGTA
1 TTTTTTTGTA
1767472 TTTTTT
1 TTTTTT
1767478 CAAATAAGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.08, T:0.85
Consensus pattern (10 bp):
TTTTTTTGTA
Found at i:1771910 original size:15 final size:15
Alignment explanation
Indices: 1771891--1771940 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
1771881 TATCATAATT
1771891 TTAAAAATATAAAAA
1 TTAAAAATATAAAAA
* * *
1771906 AT-AAAATATTAAAT
1 TTAAAAATATAAAAA
*
1771920 TTAATAATATAAAAA
1 TTAAAAATATAAAAA
1771935 TTAAAA
1 TTAAAA
1771941 TATTTTTTAT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
14 11 0.42
15 15 0.58
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
TTAAAAATATAAAAA
Found at i:1771911 original size:14 final size:14
Alignment explanation
Indices: 1771894--1771943 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
1771884 CATAATTTTA
*
1771894 AAAATATAAAAAAT
1 AAAATATAAAAATT
* *
1771908 AAAATATTAAATTT
1 AAAATATAAAAATT
1771922 AATAATATAAAAATT
1 AA-AATATAAAAATT
1771937 AAAATAT
1 AAAATAT
1771944 TTTTTATTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 18 0.60
15 12 0.40
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
AAAATATAAAAATT
Found at i:1771919 original size:21 final size:21
Alignment explanation
Indices: 1771895--1771939 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1771885 ATAATTTTAA
1771895 AAATATAA-AAAATAAAATATT
1 AAATATAATAAAATAAAA-ATT
* *
1771916 AAATTTAATAATATAAAAATT
1 AAATATAATAAAATAAAAATT
1771937 AAA
1 AAA
1771940 ATATTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
AAATATAATAAAATAAAAATT
Found at i:1771956 original size:28 final size:28
Alignment explanation
Indices: 1771890--1771944 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
1771880 TTATCATAAT
*
1771890 TTTAAAAATATAAAAAATAAAATATTAAA
1 TTTAATAATATAAAAAATAAAATATT-AA
*
1771919 TTTAATAATATAAAAATTAAAATATT
1 TTTAATAATATAAAAAATAAAATATT
1771945 TTTTATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (28 bp):
TTTAATAATATAAAAAATAAAATATTAA
Found at i:1772201 original size:27 final size:27
Alignment explanation
Indices: 1772171--1772224 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
1772161 TCCACAAATT
1772171 TGCCGCCTCTAAATTTGATCGTATGAA
1 TGCCGCCTCTAAATTTGATCGTATGAA
* *
1772198 TGCCTCCTTTAAATTTGATCGTATGAA
1 TGCCGCCTCTAAATTTGATCGTATGAA
1772225 CTTTTATCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (27 bp):
TGCCGCCTCTAAATTTGATCGTATGAA
Found at i:1772475 original size:51 final size:50
Alignment explanation
Indices: 1772420--1772519 Score: 112
Period size: 51 Copynumber: 2.0 Consensus size: 50
1772410 TGATATTTAA
* * * **
1772420 ATATTTAATATTTTAATT-TTATATTAAAAATAATATTATTAAATTAAATAT
1 ATATTT-ATA-TTAAATTATTAAATTAAAAATAAAAAAATTAAATTAAATAT
*
1772471 ATATTTTTATTAAATTAATTAAATTAAAAATAAAAAAATTAAATTAAAT
1 ATATTTATATTAAATT-ATTAAATTAAAAATAAAAAAATTAAATTAAAT
1772520 TTTTTATTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
49 6 0.15
50 2 0.05
51 33 0.80
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (50 bp):
ATATTTATATTAAATTATTAAATTAAAAATAAAAAAATTAAATTAAATAT
Found at i:1773149 original size:17 final size:18
Alignment explanation
Indices: 1773122--1773155 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1773112 GGAGTTGAAT
1773122 TTTATATATAAATATATA
1 TTTATATATAAATATATA
1773140 TTTA-ATATAAATATAT
1 TTTATATATAAATATAT
1773156 TTAATTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTATATATAAATATATA
Found at i:1774190 original size:22 final size:22
Alignment explanation
Indices: 1774165--1774237 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 22
1774155 GTTTATTATT
1774165 AATATTATTTAATAAAATTAAA
1 AATATTATTTAATAAAATTAAA
* * **
1774187 AATAATATTTTATTAAGTTTAAA
1 AATATTA-TTTAATAAAATTAAA
1774210 AA-ATATATATTAAT-AAATT-AA
1 AATAT-TAT-TTAATAAAATTAAA
1774231 AATATTA
1 AATATTA
1774238 ATTATGTTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
21 6 0.15
22 13 0.33
23 20 0.51
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (22 bp):
AATATTATTTAATAAAATTAAA
Found at i:1774193 original size:118 final size:109
Alignment explanation
Indices: 1774065--1774342 Score: 317
Period size: 118 Copynumber: 2.5 Consensus size: 109
1774055 TTATTTTTAA
* *
1774065 TAAAAATAATATTTAATTAACTTTAAAAAAATTACATTAATAAATTAAAATATTAATTAT-TTTT
1 TAAAAATAATATTTAATTAAATTTAAAAAAATTATATTAATAAATTAAAATATTAATTATGTTTT
* *
1774129 TAAAATAAAAAATTAAATTAAAAAGGGTTTATTATTAATATTATTTAATAAAAT
66 T---AT-AAAAA-TAAA--AAAAAGGCTCTATTATT-AT-TT-TTTAATAAAAT
* *
1774183 TAAAAATAATATTTTATTAAGTTT-AAAAAATATATATTAATAAATTAAAATATTAATTATGTTT
1 TAAAAATAATATTTAATTAAATTTAAAAAAAT-TATATTAATAAATTAAAATATTAATTATGTTT
** **
1774247 TTATAAAAATAAAAAGTATTCTCTATTATTATTTTTTAATAAAAT
65 TTATAAAAATAAAAAAAAGGCTCTATTATTATTTTTTAATAAAAT
* * *
1774292 AAAAAATGATATTTAATTAAATTTAAAAAATTTTATATTAATAAATTAAAA
1 TAAAAATAATATTTAATTAAATTTAAAAAA-ATTATATTAATAAATTAAAA
1774343 AATAATATTT
Statistics
Matches: 142, Mismatches: 14, Indels: 16
0.83 0.08 0.09
Matches are distributed among these distances:
109 31 0.22
110 25 0.18
111 3 0.02
112 11 0.08
114 4 0.03
115 5 0.04
116 2 0.01
117 7 0.05
118 49 0.35
119 5 0.04
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (109 bp):
TAAAAATAATATTTAATTAAATTTAAAAAAATTATATTAATAAATTAAAATATTAATTATGTTTT
TATAAAAATAAAAAAAAGGCTCTATTATTATTTTTTAATAAAAT
Found at i:1774307 original size:22 final size:22
Alignment explanation
Indices: 1774281--1774366 Score: 100
Period size: 22 Copynumber: 3.8 Consensus size: 22
1774271 ATTATTATTT
* *
1774281 TTTAATAAAATAAAAAATGATA
1 TTTAATAAATTAAAAAATAATA
**
1774303 TTTAATTAAATTTAAAAAATTTTA
1 TTTAA-TAAA-TTAAAAAATAATA
1774327 TATTAATAAATTAAAAAATAATA
1 T-TTAATAAATTAAAAAATAATA
*
1774350 TTTAATGAATTAAAAAA
1 TTTAATAAATTAAAAAA
1774367 ATTATCATGA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
22 20 0.36
23 16 0.29
24 15 0.27
25 4 0.07
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
TTTAATAAATTAAAAAATAATA
Found at i:1774319 original size:23 final size:24
Alignment explanation
Indices: 1774292--1774368 Score: 79
Period size: 23 Copynumber: 3.3 Consensus size: 24
1774282 TTAATAAAAT
* *
1774292 AAAAAATGATATTTAATTAAATTT
1 AAAAAATAATATTTAATTAAATTA
**
1774316 AAAAAATTTTATATTAA-TAAATT-
1 AAAAAATAATAT-TTAATTAAATTA
*
1774339 AAAAAATAATATTTAA-TGAATTA
1 AAAAAATAATATTTAATTAAATTA
1774362 AAAAAAT
1 AAAAAAT
1774369 TATCATGATT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
22 9 0.20
23 17 0.37
24 16 0.35
25 4 0.09
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (24 bp):
AAAAAATAATATTTAATTAAATTA
Found at i:1774478 original size:31 final size:26
Alignment explanation
Indices: 1774440--1774509 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 26
1774430 TAAATTTTAA
1774440 AATTTTAAAAAATAATAATATATTAATT
1 AATTTTAAAAAA-AATAATAT-TTAATT
1774468 ATTATTTTTAATAAAAAATAATATTTAATT
1 A--A-TTTTAA-AAAAAATAATATTTAATT
1774498 AATTTTAAAAAA
1 AATTTTAAAAAA
1774510 CTTTATCTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
26 4 0.11
27 6 0.16
28 2 0.05
30 8 0.21
31 14 0.37
32 4 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
AATTTTAAAAAAAATAATATTTAATT
Found at i:1774654 original size:19 final size:18
Alignment explanation
Indices: 1774595--1774654 Score: 52
Period size: 20 Copynumber: 3.3 Consensus size: 18
1774585 TTTTTAATAA
*
1774595 AATTAAAAA-TAATATTT
1 AATTAAAAATTAAAATTT
* *
1774612 AATT-AAATTTAAAAAATT
1 AATTAAAAATT-AAAATTT
1774630 ACATTAACAAATTAAAATTT
1 A-ATTAA-AAATTAAAATTT
1774650 AATTA
1 AATTA
1774655 TTATATTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 3 0.09
17 5 0.15
18 6 0.18
19 7 0.21
20 8 0.24
21 4 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTAAAAATTAAAATTT
Found at i:1774737 original size:123 final size:119
Alignment explanation
Indices: 1774481--1774833 Score: 443
Period size: 123 Copynumber: 2.9 Consensus size: 119
1774471 ATTTTTAATA
*
1774481 AAAAATAATATTTAATTAATTTTAAAAAACTTTATC-TTAACAAATTAAAA--T-ATTAATTA-T
1 AAAAATAATATTTAATTAAATTTAAAAAA--TTA-CATTAACAAATTAAAATTTAATT-ATTATT
* *
1774541 TTTTAAAAATAAAAAATTT-AAATAAAAAAGGTTTATTATTATTATTTTTAATAAAATT
62 TTTTAAAAATAAAAAATTTAAAATAAAAAA-GTTTATTATTATAATTTTTAATAAAAGT
1774599 AAAAATAATATTTAATTAAATTTAAAAAATTACATTAACAAATTAAAATTTAATTATTATATTTT
1 AAAAATAATATTTAATTAAATTTAAAAAATTACATTAACAAATTAAAATTTAATTA-T-TATTTT
*
1774664 TATAAAAATAAAAAAATTTAAAATATAAAAAGTTTTTTATTATAATTTTTAAT-AAAGT
64 T-TAAAAAT-AAAAAATTTAAAATA-AAAAAGTTTATTATTATAATTTTTAATAAAAGT
* * *
1774722 AAAAATAATATTTAATTAAGTTTAAAAATTTATATTAACAAATTAAAATATTAATTATTATTTTT
1 AAAAATAATATTTAATTAAATTTAAAAAATTACATTAACAAATTAAAAT-TTAATTATTATTTTT
* * * *
1774787 T-AAAATAAAAATTTTAAATTAAAAAAATTTATTATAATATATTTTTA
65 TAAAAATAAAAAATTTAAAATAAAAAAGTTTATTATTATA-ATTTTTA
1774834 TTTTTTAAAT
Statistics
Matches: 210, Mismatches: 12, Indels: 25
0.85 0.05 0.10
Matches are distributed among these distances:
115 1 0.00
116 17 0.08
118 45 0.21
119 24 0.11
120 7 0.03
121 5 0.02
122 14 0.07
123 60 0.29
124 32 0.15
125 5 0.02
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (119 bp):
AAAAATAATATTTAATTAAATTTAAAAAATTACATTAACAAATTAAAATTTAATTATTATTTTTT
AAAAATAAAAAATTTAAAATAAAAAAGTTTATTATTATAATTTTTAATAAAAGT
Found at i:1775601 original size:20 final size:21
Alignment explanation
Indices: 1775568--1775618 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 21
1775558 ATTTTATTTG
1775568 TTAATATAATATTTTT-TTAAAT
1 TTAAT-TAA-ATTTTTGTTAAAT
1775590 TTAATTAAATTTTTGTTAAAT
1 TTAATTAAATTTTTGTTAAAT
1775611 TT-ATTAAA
1 TTAATTAAA
1775619 AAGACTAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 12 0.43
21 11 0.39
22 5 0.18
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
TTAATTAAATTTTTGTTAAAT
Found at i:1777117 original size:21 final size:22
Alignment explanation
Indices: 1777077--1777121 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
1777067 ATATTAAAAA
* *
1777077 TATATATTTTTATGTTAATATT
1 TATATATTTATATATTAATATT
1777099 TATATATTTATA-ATTAATATT
1 TATATATTTATATATTAATATT
1777120 TA
1 TA
1777122 AAATAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
TATATATTTATATATTAATATT
Found at i:1779167 original size:16 final size:17
Alignment explanation
Indices: 1779146--1779178 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1779136 TTTATGATAT
*
1779146 ATTTAAGAATA-AAATA
1 ATTTAAAAATATAAATA
1779162 ATTTAAAAATATAAATA
1 ATTTAAAAATATAAATA
1779179 TATAATTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
ATTTAAAAATATAAATA
Found at i:1779493 original size:26 final size:26
Alignment explanation
Indices: 1779431--1779493 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 26
1779421 ACATTGTATT
*
1779431 TAATTATATATAAAATATTCTTTAAA
1 TAATTATATATAAAATATTCTTAAAA
*
1779457 TAACTATATATAAATATTATT-TTAAAA
1 TAATTATATATAAA-A-TATTCTTAAAA
1779484 TAATTA-ATAT
1 TAATTATATAT
1779494 TTATATTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 17 0.53
27 11 0.34
28 4 0.12
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (26 bp):
TAATTATATATAAAATATTCTTAAAA
Found at i:1779735 original size:23 final size:24
Alignment explanation
Indices: 1779680--1779743 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 24
1779670 ATTTAATTTT
*
1779680 TAATAT-A-AAATAAATAAAAACA
1 TAATATAATAAATAAATATAAACA
* *
1779702 TGAT-TATTAAATAAATATAAA-A
1 TAATATAATAAATAAATATAAACA
1779724 TAATATAATAAATAACATAT
1 TAATATAATAAATAA-ATAT
1779744 GAGACATTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
21 1 0.03
22 7 0.21
23 21 0.64
24 4 0.12
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (24 bp):
TAATATAATAAATAAATATAAACA
Found at i:1782540 original size:50 final size:50
Alignment explanation
Indices: 1782465--1782570 Score: 194
Period size: 50 Copynumber: 2.1 Consensus size: 50
1782455 ATACGAACAA
* *
1782465 ACTTTTCATGATTGTAATGTATCATAGATAATCTACGAAAACTGTTCCTT
1 ACTTTTCATGATCGTAATGTATCATAGATAATCTACAAAAACTGTTCCTT
1782515 ACTTTTCATGATCGTAATGTATCATAGATAATCTACAAAAACTGTTCCTT
1 ACTTTTCATGATCGTAATGTATCATAGATAATCTACAAAAACTGTTCCTT
1782565 ACTTTT
1 ACTTTT
1782571 TAATACCTAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.41
Consensus pattern (50 bp):
ACTTTTCATGATCGTAATGTATCATAGATAATCTACAAAAACTGTTCCTT
Found at i:1785995 original size:29 final size:29
Alignment explanation
Indices: 1785953--1786012 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
1785943 GATAAAAAAC
* *
1785953 TATATACATGGGTTGAATCGAATTCAGTT
1 TATATACATAGGTTGAATCGAATTAAGTT
1785982 TATATACATAGGTTGAATCGAATTAAGTT
1 TATATACATAGGTTGAATCGAATTAAGTT
1786011 TA
1 TA
1786013 GATAACAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.38
Consensus pattern (29 bp):
TATATACATAGGTTGAATCGAATTAAGTT
Found at i:1786172 original size:40 final size:38
Alignment explanation
Indices: 1786118--1786205 Score: 104
Period size: 40 Copynumber: 2.3 Consensus size: 38
1786108 TTTTATCTTA
* * * * *
1786118 AATTGAAATAAAAAATTAATTTTATTTATTAAATAATTTT
1 AATTTAAATTAAAAATTAAATTAATTTA-AAAAT-ATTTT
1786158 AATTTAAATTAAAAATTAAATTAATTTAAAAATATTTT
1 AATTTAAATTAAAAATTAAATTAATTTAAAAATATTTT
*
1786196 ATTTTAAATT
1 AATTTAAATT
1786206 TGATCTAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
38 14 0.33
39 4 0.10
40 24 0.57
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (38 bp):
AATTTAAATTAAAAATTAAATTAATTTAAAAATATTTT
Found at i:1786176 original size:17 final size:17
Alignment explanation
Indices: 1786156--1786190 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1786146 TTAAATAATT
*
1786156 TTAATTTAAATTAAAAA
1 TTAAATTAAATTAAAAA
*
1786173 TTAAATTAATTTAAAAA
1 TTAAATTAAATTAAAAA
1786190 T
1 T
1786191 ATTTTATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAAATTAAATTAAAAA
Found at i:1787502 original size:27 final size:27
Alignment explanation
Indices: 1787467--1787525 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
1787457 GAAATACTAA
*
1787467 AAATATAAA-AAAAGTATTTTTATAATT
1 AAATATAAACAAAAATATTTTT-TAATT
*
1787494 AAATTTAAACAAAAATATTTTTTAATT
1 AAATATAAACAAAAATATTTTTTAATT
1787521 AAATA
1 AAATA
1787526 ATAATTCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 17 0.61
28 11 0.39
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (27 bp):
AAATATAAACAAAAATATTTTTTAATT
Found at i:1787557 original size:65 final size:65
Alignment explanation
Indices: 1787475--1787601 Score: 236
Period size: 65 Copynumber: 2.0 Consensus size: 65
1787465 AAAAATATAA
1787475 AAAAAGTATTTTTATAATTAAATTTAAACAAAAATATTTTTTAATTAAATAATAATTCAAATATT
1 AAAAAGTATTTTTATAATTAAATTTAAACAAAAATATTTTTTAATTAAATAATAATTCAAATATT
* *
1787540 AAAAATTATTTTTATAATTAAATTTAAATAAAAATATTTTTTAATTAAATAATAATTCAAAT
1 AAAAAGTATTTTTATAATTAAATTTAAACAAAAATATTTTTTAATTAAATAATAATTCAAAT
1787602 CAATCTAACT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 60 1.00
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (65 bp):
AAAAAGTATTTTTATAATTAAATTTAAACAAAAATATTTTTTAATTAAATAATAATTCAAATATT
Found at i:1787558 original size:38 final size:35
Alignment explanation
Indices: 1787504--1787601 Score: 113
Period size: 28 Copynumber: 2.9 Consensus size: 35
1787494 AAATTTAAAC
1787504 AAAAATATTTTTTAATTAAATAATAATTCAAATATT
1 AAAAATATTTTTTAATTAAATAATAATTCAAATA-T
1787540 AAAAATTATTTTTATAATT--A-AAT--TT--AA-AT
1 AAAAA-TATTTTT-TAATTAAATAATAATTCAAATAT
1787569 AAAAATATTTTTTAATTAAATAATAATTCAAAT
1 AAAAATATTTTTTAATTAAATAATAATTCAAAT
1787602 CAATCTAACT
Statistics
Matches: 52, Mismatches: 0, Indels: 21
0.71 0.00 0.29
Matches are distributed among these distances:
27 5 0.10
28 7 0.13
29 7 0.13
30 4 0.08
31 2 0.04
32 2 0.04
33 2 0.04
34 2 0.04
35 3 0.06
36 6 0.12
37 7 0.13
38 5 0.10
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (35 bp):
AAAAATATTTTTTAATTAAATAATAATTCAAATAT
Found at i:1788051 original size:83 final size:84
Alignment explanation
Indices: 1787912--1788072 Score: 297
Period size: 83 Copynumber: 1.9 Consensus size: 84
1787902 GCACCAATTG
*
1787912 GAATAAGTTTCTTATGTAAGGAAATGCCTCTTTATTCATTATGTTTAAGCATTGCATGACAT-AA
1 GAATAAGATTCTTATGTAAGGAAATGCCTCTTTATTCATTATGTTTAAGCATTGCATGACATAAA
1787976 AAAAAGGTATATCAAATGA
66 AAAAAGGTATATCAAATGA
*
1787995 GAATAAGATTCTTATGTTAGGAAATGCCTCTTTATTCATTATGTTTAAGCATTGCATGACATAAA
1 GAATAAGATTCTTATGTAAGGAAATGCCTCTTTATTCATTATGTTTAAGCATTGCATGACATAAA
1788060 AAAAAGGTATATC
66 AAAAAGGTATATC
1788073 TATAAGAACT
Statistics
Matches: 75, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
83 60 0.80
84 15 0.20
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (84 bp):
GAATAAGATTCTTATGTAAGGAAATGCCTCTTTATTCATTATGTTTAAGCATTGCATGACATAAA
AAAAAGGTATATCAAATGA
Found at i:1788217 original size:23 final size:23
Alignment explanation
Indices: 1788191--1788234 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1788181 TGCGGTTACT
1788191 TTTAAAAAATAATTTTTAATAAG
1 TTTAAAAAATAATTTTTAATAAG
**
1788214 TTTAAAATTTAATTTTTAATA
1 TTTAAAAAATAATTTTTAATA
1788235 TTTAAATGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
TTTAAAAAATAATTTTTAATAAG
Found at i:1790199 original size:13 final size:13
Alignment explanation
Indices: 1790181--1790207 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1790171 TAATTTTTTT
1790181 ATTTTATATTTAA
1 ATTTTATATTTAA
1790194 ATTTTATATTTAA
1 ATTTTATATTTAA
1790207 A
1 A
1790208 AGGTTGATAT
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:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTTTATATTTAA
Found at i:1792177 original size:28 final size:26
Alignment explanation
Indices: 1792126--1792192 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 26
1792116 CATTTGTACA
*
1792126 TAATTTAAA-AA-ATTAAATTATAAT
1 TAATTTAAATAATATAAAATTATAAT
1792150 TAAATTTAAATAATATAAATATTATAAT
1 T-AATTTAAATAATATAAA-ATTATAAT
*
1792178 TAATTTTAATAATAT
1 TAATTTAAATAATAT
1792193 GATTTAATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
24 1 0.03
25 8 0.22
26 2 0.05
27 17 0.46
28 9 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
TAATTTAAATAATATAAAATTATAAT
Found at i:1794126 original size:23 final size:23
Alignment explanation
Indices: 1794100--1794147 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
1794090 GAGAGTTATA
1794100 TCCCTATACCTATATCTAGATAT
1 TCCCTATACCTATATCTAGATAT
1794123 TCCCTATACCTATATCTAGATAT
1 TCCCTATACCTATATCTAGATAT
1794146 TC
1 TC
1794148 GTCAGACATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.27, G:0.04, T:0.40
Consensus pattern (23 bp):
TCCCTATACCTATATCTAGATAT
Found at i:1794826 original size:153 final size:153
Alignment explanation
Indices: 1794543--1794852 Score: 593
Period size: 153 Copynumber: 2.0 Consensus size: 153
1794533 CTTCATCCGG
1794543 TCTTATAAGACCAGTAGTGAGAATTTTGCATATTGCTTCATCTGTTGCTTTCGATATTCGATGCT
1 TCTTATAAGACCAGTAGTGAGAATTTTGCATATTGCTTCATCTGTTGCTTTCGATATTCGATGCT
1794608 TCTCTTACTCATATCATCAATTTTAAAGCATGAATGTGTTGCAGATAATGAATTCGAAGATAATG
66 TCTCTTACTCATATCATCAATTTTAAAGCATGAATGTGTTGCAGATAATGAATTCGAAGATAATG
1794673 GATCATCCCCAAGGATTTCTGAA
131 GATCATCCCCAAGGATTTCTGAA
*
1794696 TCTTGTAAGACCAGTAGTGAGAATTTTGCATATTGCTTCATCTGTTGCTTTCGATATTCGATGCT
1 TCTTATAAGACCAGTAGTGAGAATTTTGCATATTGCTTCATCTGTTGCTTTCGATATTCGATGCT
* *
1794761 TCTCTTACTCATTTCATCAATTTTAAAGCATGAATGTGTTGCAGATTATGAATTCGAAGATAATG
66 TCTCTTACTCATATCATCAATTTTAAAGCATGAATGTGTTGCAGATAATGAATTCGAAGATAATG
1794826 GATCATCCCCAAGGATTTCTGAA
131 GATCATCCCCAAGGATTTCTGAA
1794849 TCTT
1 TCTT
1794853 CAGTAAAGAT
Statistics
Matches: 154, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
153 154 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (153 bp):
TCTTATAAGACCAGTAGTGAGAATTTTGCATATTGCTTCATCTGTTGCTTTCGATATTCGATGCT
TCTCTTACTCATATCATCAATTTTAAAGCATGAATGTGTTGCAGATAATGAATTCGAAGATAATG
GATCATCCCCAAGGATTTCTGAA
Found at i:1795308 original size:2 final size:2
Alignment explanation
Indices: 1795296--1795339 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1795286 ATTCATGTTT
1795296 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1795337 TA T
1 TA T
1795340 GAATGATACG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1795396 original size:19 final size:18
Alignment explanation
Indices: 1795362--1795400 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1795352 TGAATAATTT
1795362 TTTAAATATAAAAAAAAA
1 TTTAAATATAAAAAAAAA
*
1795380 TTTAAA-ATAAATTAAAAA
1 TTTAAATATAAA-AAAAAA
1795398 TTT
1 TTT
1795401 TAATTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TTTAAATATAAAAAAAAA
Found at i:1795402 original size:19 final size:18
Alignment explanation
Indices: 1795361--1795403 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
1795351 TTGAATAATT
1795361 TTTTAAATATAAAAAAAA
1 TTTTAAATATAAAAAAAA
*
1795379 ATTTAAA-ATAAATTAAAAA
1 TTTTAAATATAAA--AAAAA
1795398 TTTTAA
1 TTTTAA
1795404 TTTTAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 5 0.24
18 6 0.29
19 10 0.48
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TTTTAAATATAAAAAAAA
Found at i:1795426 original size:16 final size:16
Alignment explanation
Indices: 1795403--1795439 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1795393 AAAAATTTTA
*
1795403 ATTT-TAAATTAATTT
1 ATTTATAAATTAAATT
1795418 ATTTATAAATTAAATT
1 ATTTATAAATTAAATT
1795434 ATTTAT
1 ATTTAT
1795440 CTGAAGTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTTATAAATTAAATT
Found at i:1800384 original size:80 final size:80
Alignment explanation
Indices: 1800251--1800410 Score: 302
Period size: 80 Copynumber: 2.0 Consensus size: 80
1800241 GGTGCCGTAG
*
1800251 ATACCAGAGTTTGAGCATAACTAAACTAGGCTACTAAATCAGATAATCGAATAAACAAAAATATA
1 ATACCAGAGATTGAGCATAACTAAACTAGGCTACTAAATCAGATAATCGAATAAACAAAAATATA
1800316 GAAAAAAGAAACTAA
66 GAAAAAAGAAACTAA
*
1800331 ATACCAGAGATTGAGCATAACTAAACTAGGCTATTAAATCAGATAATCGAATAAACAAAAATATA
1 ATACCAGAGATTGAGCATAACTAAACTAGGCTACTAAATCAGATAATCGAATAAACAAAAATATA
1800396 GAAAAAAGAAACTAA
66 GAAAAAAGAAACTAA
1800411 GTGTTTAGCA
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
80 78 1.00
ACGTcount: A:0.54, C:0.13, G:0.12, T:0.20
Consensus pattern (80 bp):
ATACCAGAGATTGAGCATAACTAAACTAGGCTACTAAATCAGATAATCGAATAAACAAAAATATA
GAAAAAAGAAACTAA
Found at i:1801963 original size:20 final size:20
Alignment explanation
Indices: 1801938--1801979 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1801928 ATTAGAAACC
1801938 GTGGGATACTGGAATTCCGA
1 GTGGGATACTGGAATTCCGA
* *
1801958 GTGGGATATTGGAATTTCGA
1 GTGGGATACTGGAATTCCGA
1801978 GT
1 GT
1801980 ATGGATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.10, G:0.36, T:0.31
Consensus pattern (20 bp):
GTGGGATACTGGAATTCCGA
Found at i:1803238 original size:19 final size:19
Alignment explanation
Indices: 1803197--1803239 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1803187 GTTTTTAATG
* **
1803197 TATATATATATATAATTTT
1 TATATATATATATAAATCA
1803216 TATATATATATATAAATCA
1 TATATATATATATAAATCA
1803235 TATAT
1 TATAT
1803240 TTACTAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
TATATATATATATAAATCA
Found at i:1804167 original size:16 final size:15
Alignment explanation
Indices: 1804134--1804171 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1804124 ATTAATTAAT
1804134 TAAAAAATAAAAACA
1 TAAAAAATAAAAACA
1804149 TAAAATAATAAAATA-A
1 TAAAA-AATAAAA-ACA
1804165 TAAAAAA
1 TAAAAAA
1804172 AGAGACAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 7 0.33
16 13 0.62
17 1 0.05
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (15 bp):
TAAAAAATAAAAACA
Found at i:1804820 original size:8 final size:8
Alignment explanation
Indices: 1804798--1804874 Score: 50
Period size: 8 Copynumber: 9.2 Consensus size: 8
1804788 AAGGAATGAG
1804798 AGAAGAAGA
1 AGAAGAA-A
1804807 GAGAAGAAA
1 -AGAAGAAA
*
1804816 GGAAGAAA
1 AGAAGAAA
*
1804824 AAAAGAAA
1 AGAAGAAA
1804832 AGAAGAAGA
1 AGAAGAA-A
*
1804841 ATGAAGGAA
1 A-GAAGAAA
1804850 A-AA-AAA
1 AGAAGAAA
*
1804856 AGGAGAAAA
1 AGAAG-AAA
*
1804865 AAAAGAAA
1 AGAAGAAA
1804873 AG
1 AG
1804875 GGGTGGCTTG
Statistics
Matches: 52, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
6 3 0.06
7 3 0.06
8 23 0.44
9 11 0.21
10 12 0.23
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.01
Consensus pattern (8 bp):
AGAAGAAA
Found at i:1804862 original size:27 final size:30
Alignment explanation
Indices: 1804800--1804857 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1804790 GGAATGAGAG
1804800 AAGAAGAGAGAAGAAAGGAAGAAAAAAAGAA
1 AAGAAGAGAGAAGAAAGGAAGAAAAAAAG-A
1804831 AAGAAGA-AGAATG-AAGGAA-AAAAAAAG
1 AAGAAGAGAGAA-GAAAGGAAGAAAAAAAG
1804858 GAGAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 8 0.31
30 10 0.38
31 8 0.31
ACGTcount: A:0.71, C:0.00, G:0.28, T:0.02
Consensus pattern (30 bp):
AAGAAGAGAGAAGAAAGGAAGAAAAAAAGA
Found at i:1804871 original size:30 final size:30
Alignment explanation
Indices: 1804814--1804871 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
1804804 AGAGAGAAGA
*
1804814 AAGGAAGAAAAAAAGAAAAGAAGAAGAATG
1 AAGGAAGAAAAAAAGAAAAGAAAAAGAATG
1804844 AAGGAA-AAAAAAAGGAGAAA-AAAAAGAA
1 AAGGAAGAAAAAAA-GA-AAAGAAAAAGAA
1804872 AAGGGGTGGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 7 0.28
30 15 0.60
31 3 0.12
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (30 bp):
AAGGAAGAAAAAAAGAAAAGAAAAAGAATG
Found at i:1808568 original size:21 final size:20
Alignment explanation
Indices: 1808542--1808611 Score: 79
Period size: 21 Copynumber: 3.5 Consensus size: 20
1808532 CAATTTGTAT
1808542 ATAAGTGAATGTATTGATATA
1 ATAAGTGAATGTATTGATA-A
* *
1808563 ATAAGTGAATGTATCGA-AC
1 ATAAGTGAATGTATTGATAA
* *
1808582 ATAAGTAAATGTATTGATAC
1 ATAAGTGAATGTATTGATAA
*
1808602 ATAAATGAAT
1 ATAAGTGAAT
1808612 CGATATATGC
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 15 0.36
20 11 0.26
21 16 0.38
ACGTcount: A:0.46, C:0.04, G:0.17, T:0.33
Consensus pattern (20 bp):
ATAAGTGAATGTATTGATAA
Found at i:1811143 original size:20 final size:20
Alignment explanation
Indices: 1811032--1811145 Score: 77
Period size: 20 Copynumber: 5.5 Consensus size: 20
1811022 TTTTTACCCG
* **
1811032 ATGTATCGATACTTTTTTCA
1 ATGTATCGATACATTGATCA
* *
1811052 ATGTATCGATACATGGATGA
1 ATGTATCGATACATTGATCA
* **
1811072 ATGTATAGATACATTCTTCA
1 ATGTATCGATACATTGATCA
* *
1811092 GTGTATCGATACATCCT-ACCCA
1 ATGTATCGATACAT--TGA-TCA
* *
1811114 GATATATCGATACATTGAACA
1 -ATGTATCGATACATTGATCA
1811135 ATGTATCGATA
1 ATGTATCGATA
1811146 TATCTATTTA
Statistics
Matches: 71, Mismatches: 18, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
20 52 0.73
21 3 0.04
22 4 0.06
23 12 0.17
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACATTGATCA
Found at i:1825097 original size:22 final size:22
Alignment explanation
Indices: 1825043--1825083 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1825033 ACAAAAGCTA
*
1825043 ACTTAGTTT-TTCTATTTTTCT
1 ACTTATTTTCTTCTATTTTTCT
1825064 ACTTATTTTCTTCTATTTTT
1 ACTTATTTTCTTCTATTTTT
1825084 TTCTTGCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.15, C:0.15, G:0.02, T:0.68
Consensus pattern (22 bp):
ACTTATTTTCTTCTATTTTTCT
Found at i:1827273 original size:48 final size:48
Alignment explanation
Indices: 1827087--1827390 Score: 301
Period size: 48 Copynumber: 6.4 Consensus size: 48
1827077 AGTGGTAATC
* * * * *
1827087 ATAT-GTCAAATGAGTG-TAAAAAGAGTTTAACTAGGTCCTAACACCA
1 ATATAGTCAAACGAGGGATAAAAAGAGTTTGACCAGGCCCTAACACCA
* * * * * * *
1827133 ATACAATCAAACAAGGGGAAAAAAAGAGTTTAACTAGGCCCTAACAACA
1 ATATAGTCAAACGA-GGGATAAAAAGAGTTTGACCAGGCCCTAACACCA
* * * **
1827182 ATACAATCAAACGAGGGAT-GAAAGAGTTTGACCAAACCCTAACACCA
1 ATATAGTCAAACGAGGGATAAAAAGAGTTTGACCAGGCCCTAACACCA
* *
1827229 ATATAGTCAAACGAGGGATAAAAAGAGTTTGGCTAGGCCCTAACACCA
1 ATATAGTCAAACGAGGGATAAAAAGAGTTTGACCAGGCCCTAACACCA
* * * * *
1827277 ATATAGTCAAACAAAGGAT-GAAAGAGTTTGACCAGGCCTTGACACCA
1 ATATAGTCAAACGAGGGATAAAAAGAGTTTGACCAGGCCCTAACACCA
* * * * *
1827324 ATACAGTCAAACGAGTGATGAAAAGAGTTTGGCCAGACCCTAACACCA
1 ATATAGTCAAACGAGGGATAAAAAGAGTTTGACCAGGCCCTAACACCA
*
1827372 ATATAGTCAAACGAAGGAT
1 ATATAGTCAAACGAGGGAT
1827391 GAAAGAACAC
Statistics
Matches: 211, Mismatches: 42, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
46 3 0.01
47 83 0.39
48 85 0.40
49 40 0.19
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.18
Consensus pattern (48 bp):
ATATAGTCAAACGAGGGATAAAAAGAGTTTGACCAGGCCCTAACACCA
Found at i:1827288 original size:95 final size:95
Alignment explanation
Indices: 1827123--1827396 Score: 368
Period size: 95 Copynumber: 2.9 Consensus size: 95
1827113 TTAACTAGGT
* * * ** * * *
1827123 CCTAACACCAATACAATCAAACAAGGGGAAAAAAAGAGTTTAACTAGGCCCTAACAACAATACAA
1 CCTAACACCAATACAGTCAAACGA-GGGATAAAAAGAGTTTGGCTAGGCCCTAACACCAATATAG
*
1827188 TCAAACGAGGGATGAAAGAGTTTGACCAAAC
65 TCAAACGAAGGATGAAAGAGTTTGACCAAAC
*
1827219 CCTAACACCAATATAGTCAAACGAGGGATAAAAAGAGTTTGGCTAGGCCCTAACACCAATATAGT
1 CCTAACACCAATACAGTCAAACGAGGGATAAAAAGAGTTTGGCTAGGCCCTAACACCAATATAGT
* **
1827284 CAAACAAAGGATGAAAGAGTTTGACCAGGC
66 CAAACGAAGGATGAAAGAGTTTGACCAAAC
* * * * * *
1827314 CTTGACACCAATACAGTCAAACGAGTGATGAAAAGAGTTTGGCCAGACCCTAACACCAATATAGT
1 CCTAACACCAATACAGTCAAACGAGGGATAAAAAGAGTTTGGCTAGGCCCTAACACCAATATAGT
1827379 CAAACGAAGGATGAAAGA
66 CAAACGAAGGATGAAAGA
1827397 ACACCAATAC
Statistics
Matches: 157, Mismatches: 21, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
95 136 0.87
96 21 0.13
ACGTcount: A:0.44, C:0.20, G:0.19, T:0.16
Consensus pattern (95 bp):
CCTAACACCAATACAGTCAAACGAGGGATAAAAAGAGTTTGGCTAGGCCCTAACACCAATATAGT
CAAACGAAGGATGAAAGAGTTTGACCAAAC
Found at i:1827451 original size:78 final size:79
Alignment explanation
Indices: 1827318--1827463 Score: 186
Period size: 78 Copynumber: 1.9 Consensus size: 79
1827308 CCAGGCCTTG
* * * ** *
1827318 ACACCAATACAGTCAAACGAGTGATGAAAAGAGTTTGGCCAGACCCTAACACCAATATAGTCAAA
1 ACACCAATACAGTCAAACAAGGGATGAAAAAAGTTTAACCAGACCCTAACACCAATACAGTCAAA
1827383 CGAAGGATGAAAGA
66 CGAAGGATGAAAGA
* * * * *
1827397 ACACCAATACAGTCAAATAAGGGAT-AAAAAAGTTTAACTAGGCCCTAACGCCAATACAGTTAAA
1 ACACCAATACAGTCAAACAAGGGATGAAAAAAGTTTAACCAGACCCTAACACCAATACAGTCAAA
1827461 CGA
66 CGA
1827464 GAGAAGATAA
Statistics
Matches: 56, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
78 34 0.61
79 22 0.39
ACGTcount: A:0.45, C:0.21, G:0.18, T:0.16
Consensus pattern (79 bp):
ACACCAATACAGTCAAACAAGGGATGAAAAAAGTTTAACCAGACCCTAACACCAATACAGTCAAA
CGAAGGATGAAAGA
Found at i:1827495 original size:126 final size:126
Alignment explanation
Indices: 1827270--1827509 Score: 329
Period size: 126 Copynumber: 1.9 Consensus size: 126
1827260 GCTAGGCCCT
* * * * * *
1827270 AACACCAATATAGTCAAACAAAGGATGAAAGAGTTTGACCAGGCCTTGACACCAATACAGTCAAA
1 AACACCAATACAGTCAAACAAAGGATAAAAAAGTTTAACCAGGCCCTAACACCAATACAGTCAAA
* * *
1827335 CGAGTGATGAAAAGAGTTTGGCCAGACCCTAACACCAATATAGTCAAACGAAGGATGAAAG
66 CGAGAGAAGAAAAGAGTTTGACCAGACCCTAACACCAATATAGTCAAACGAAGGATGAAAG
* * * * *
1827396 AACACCAATACAGTCAAATAAGGGATAAAAAAGTTTAACTAGGCCCTAACGCCAATACAGTTAAA
1 AACACCAATACAGTCAAACAAAGGATAAAAAAGTTTAACCAGGCCCTAACACCAATACAGTCAAA
*
1827461 CGAGAGAAGATAAGAGTTTGACCA-AGCCCTAACACCAATATAGTCAAAC
66 CGAGAGAAGAAAAGAGTTTGACCAGA-CCCTAACACCAATATAGTCAAAC
1827510 AGGGGATGTA
Statistics
Matches: 98, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
125 1 0.01
126 97 0.99
ACGTcount: A:0.44, C:0.20, G:0.18, T:0.17
Consensus pattern (126 bp):
AACACCAATACAGTCAAACAAAGGATAAAAAAGTTTAACCAGGCCCTAACACCAATACAGTCAAA
CGAGAGAAGAAAAGAGTTTGACCAGACCCTAACACCAATATAGTCAAACGAAGGATGAAAG
Found at i:1827598 original size:47 final size:47
Alignment explanation
Indices: 1827400--1827939 Score: 427
Period size: 48 Copynumber: 11.3 Consensus size: 47
1827390 TGAAAGAACA
** * * * *
1827400 CCAATACAGTCAAATAAGGGATAAAAAAGTTTAACTAGGCCCTAACG
1 CCAATACAGTCAAACGAGGGATGAAAGAGTTTGACCAGGCCCTAACG
* * * * *
1827447 CCAATACAGTTAAACGAGAGAAGATAAGAGTTTGACCAAGCCCTAACA
1 CCAATACAGTCAAACGAGGGATGA-AAGAGTTTGACCAGGCCCTAACG
* *
1827495 CCAATATAGTCAAAC-AGGGGATGTAAAGAGAGTTTGACCAGGCCCTAACA
1 CCAATACAGTCAAACGA-GGGATG--AA-AGAGTTTGACCAGGCCCTAACG
* * * *
1827545 CTAATACAGTCAAACGAGGGATGAAAAAGTTTTACCAGGCCTTAACG
1 CCAATACAGTCAAACGAGGGATGAAAGAGTTTGACCAGGCCCTAACG
* * * * *
1827592 TCAATACAGTCAAACGAGGGATAAAAAGAGTTTGACTAGGTCCTGA-G
1 CCAATACAGTCAAACGAGGGAT-GAAAGAGTTTGACCAGGCCCTAACG
* *
1827639 ACCAATACAGTCAAACGAGGGATGAAAGAGTTTGACCAAGCCCTGACG
1 -CCAATACAGTCAAACGAGGGATGAAAGAGTTTGACCAGGCCCTAACG
* * ** * * * * *
1827687 CTAATACAATCAAATAAGAGATGAAAAAATTTGACTAGGCCCTAACA
1 CCAATACAGTCAAACGAGGGATGAAAGAGTTTGACCAGGCCCTAACG
* * * * * * * * *
1827734 TCAATATAGTGAAATGAGGCATGAAAGAGTTTGATCGGGCCTTAATG
1 CCAATACAGTCAAACGAGGGATGAAAGAGTTTGACCAGGCCCTAACG
** * * * *
1827781 CCAATACAGTCAAACGAGAAAAGATAAGAGTTTGACTAGACCCTAACA
1 CCAATACAGTCAAACGAGGGATGA-AAGAGTTTGACCAGGCCCTAACG
* * * * *
1827829 CTAATACAGTCAAATGAGGGATGGAAAGAGTTTGACTAGGTCCGAACG
1 CCAATACAGTCAAACGAGGGAT-GAAAGAGTTTGACCAGGCCCTAACG
* * * * *** *
1827877 CCAATATAATCAAACGAGGGATGGAAAGAGTTTGACTAAGTTTTAACA
1 CCAATACAGTCAAACGAGGGAT-GAAAGAGTTTGACCAGGCCCTAACG
1827925 CCAATACAGTCAAAC
1 CCAATACAGTCAAAC
1827940 AAAAAAAGAT
Statistics
Matches: 385, Mismatches: 97, Indels: 21
0.77 0.19 0.04
Matches are distributed among these distances:
47 161 0.42
48 179 0.46
49 3 0.01
50 41 0.11
51 1 0.00
ACGTcount: A:0.41, C:0.18, G:0.21, T:0.20
Consensus pattern (47 bp):
CCAATACAGTCAAACGAGGGATGAAAGAGTTTGACCAGGCCCTAACG
Found at i:1827660 original size:95 final size:95
Alignment explanation
Indices: 1827400--1827939 Score: 507
Period size: 95 Copynumber: 5.7 Consensus size: 95
1827390 TGAAAGAACA
** * * *
1827400 CCAATACAGTCAAATAAGGGATAAAAA-AGTTTAACTAGGCCCTAACGCCAATACAGTTAAACGA
1 CCAATACAGTCAAACGAGGGATAAAAAGAGTTTGACTAGGCCCTAACACCAATACAGTCAAACGA
* * * *
1827464 GAGAAGATAAGAGTTTGACCAAGCCCTAACA
66 GGGATGA-AAGAGTTTGACCAGGCCCTAACG
* * * *
1827495 CCAATATAGTCAAAC-AGGGGATGTAAAGAGAGTTTGACCAGGCCCTAACACTAATACAGTCAAA
1 CCAATACAGTCAAACGA-GGGA--TAAAAAGAGTTTGACTAGGCCCTAACACCAATACAGTCAAA
* * *
1827559 CGAGGGATGAAAAAGTTTTACCAGGCCTTAACG
63 CGAGGGATGAAAGAGTTTGACCAGGCCCTAACG
* * * *
1827592 TCAATACAGTCAAACGAGGGATAAAAAGAGTTTGACTAGGTCCTGAGACCAATACAGTCAAACGA
1 CCAATACAGTCAAACGAGGGATAAAAAGAGTTTGACTAGGCCCTAACACCAATACAGTCAAACGA
* *
1827657 GGGATGAAAGAGTTTGACCAAGCCCTGACG
66 GGGATGAAAGAGTTTGACCAGGCCCTAACG
* * ** * * * * *
1827687 CTAATACAATCAAATAAGAGATGAAAAA-A-TTTGACTAGGCCCTAACATCAATATAGTGAAATG
1 CCAATACAGTCAAACGAGGGAT-AAAAAGAGTTTGACTAGGCCCTAACACCAATACAGTCAAACG
* * * * *
1827750 AGGCATGAAAGAGTTTGATCGGGCCTTAATG
65 AGGGATGAAAGAGTTTGACCAGGCCCTAACG
* * * *
1827781 CCAATACAGTCAAACGA--GAAAAGATAAGAGTTTGACTAGACCCTAACACTAATACAGTCAAAT
1 CCAATACAGTCAAACGAGGGATAA-A-AAGAGTTTGACTAGGCCCTAACACCAATACAGTCAAAC
* * *
1827844 GAGGGATGGAAAGAGTTTGACTAGGTCCGAACG
64 GAGGGAT-GAAAGAGTTTGACCAGGCCCTAACG
* * ** * ***
1827877 CCAATATAATCAAACGAGGGATGGAAAGAGTTTGACTAAGTTTTAACACCAATACAGTCAAAC
1 CCAATACAGTCAAACGAGGGATAAAAAGAGTTTGACTAGGCCCTAACACCAATACAGTCAAAC
1827940 AAAAAAAGAT
Statistics
Matches: 354, Mismatches: 78, Indels: 25
0.77 0.17 0.05
Matches are distributed among these distances:
91 2 0.01
92 3 0.01
93 2 0.01
94 66 0.19
95 131 0.37
96 69 0.19
97 41 0.12
98 40 0.11
ACGTcount: A:0.41, C:0.18, G:0.21, T:0.20
Consensus pattern (95 bp):
CCAATACAGTCAAACGAGGGATAAAAAGAGTTTGACTAGGCCCTAACACCAATACAGTCAAACGA
GGGATGAAAGAGTTTGACCAGGCCCTAACG
Found at i:1829663 original size:32 final size:32
Alignment explanation
Indices: 1829622--1829703 Score: 164
Period size: 32 Copynumber: 2.6 Consensus size: 32
1829612 CGTGATTGAA
1829622 AGGTTCTATCTTAGCCTTGAAAGATAGTGTAG
1 AGGTTCTATCTTAGCCTTGAAAGATAGTGTAG
1829654 AGGTTCTATCTTAGCCTTGAAAGATAGTGTAG
1 AGGTTCTATCTTAGCCTTGAAAGATAGTGTAG
1829686 AGGTTCTATCTTAGCCTT
1 AGGTTCTATCTTAGCCTT
1829704 TATAAAAGAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.37
Consensus pattern (32 bp):
AGGTTCTATCTTAGCCTTGAAAGATAGTGTAG
Found at i:1841137 original size:34 final size:34
Alignment explanation
Indices: 1841093--1841184 Score: 123
Period size: 34 Copynumber: 2.7 Consensus size: 34
1841083 TATAATCTTA
*
1841093 CAACTCTATCTTTTCAAAGGCTTAGATAGAACCT
1 CAACACTATCTTTTCAAAGGCTTAGATAGAACCT
*
1841127 CAACACTATCTTTTCGAAA-GCTAAGATAGAACCT
1 CAACACTATCTTTTC-AAAGGCTTAGATAGAACCT
* * *
1841161 CTATACTATCTTTTCGAAGGCTTA
1 CAACACTATCTTTTCAAAGGCTTA
1841185 AATAAAATCT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
33 2 0.04
34 45 0.90
35 3 0.06
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.33
Consensus pattern (34 bp):
CAACACTATCTTTTCAAAGGCTTAGATAGAACCT
Found at i:1843250 original size:20 final size:20
Alignment explanation
Indices: 1843188--1843259 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
1843178 AACTCTTGTA
*
1843188 TGTATCGATACACATCCAGA-
1 TGTATCGATACATATCCA-AT
* *
1843208 TGTATCGATACATGTTC-AT
1 TGTATCGATACATATCCAAT
*
1843227 TGTATCGATACATACCCAAT
1 TGTATCGATACATATCCAAT
*
1843247 TGTATCAATACAT
1 TGTATCGATACAT
1843260 GAAACTGGCA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
18 1 0.02
19 14 0.33
20 28 0.65
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (20 bp):
TGTATCGATACATATCCAAT
Found at i:1846591 original size:37 final size:37
Alignment explanation
Indices: 1846541--1846644 Score: 199
Period size: 37 Copynumber: 2.8 Consensus size: 37
1846531 GGTACCTAAA
1846541 ATCAAGACTTGATCCTTGTGTTTGTAGGAGGTGGAGC
1 ATCAAGACTTGATCCTTGTGTTTGTAGGAGGTGGAGC
*
1846578 ATCAAGACTTGATCCTTGTGTTTATAGGAGGTGGAGC
1 ATCAAGACTTGATCCTTGTGTTTGTAGGAGGTGGAGC
1846615 ATCAAGACTTGATCCTTGTGTTTGTAGGAG
1 ATCAAGACTTGATCCTTGTGTTTGTAGGAG
1846645 CATTGCTACA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 65 1.00
ACGTcount: A:0.23, C:0.13, G:0.30, T:0.34
Consensus pattern (37 bp):
ATCAAGACTTGATCCTTGTGTTTGTAGGAGGTGGAGC
Found at i:1852061 original size:13 final size:13
Alignment explanation
Indices: 1852043--1852068 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1852033 TTATCAAGGG
1852043 GGAGAAAATCTTT
1 GGAGAAAATCTTT
1852056 GGAGAAAATCTTT
1 GGAGAAAATCTTT
1852069 TTAAACCGAT
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:0.08, G:0.23, T:0.31
Consensus pattern (13 bp):
GGAGAAAATCTTT
Found at i:1852715 original size:32 final size:33
Alignment explanation
Indices: 1852674--1852738 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
1852664 CACACCCAGA
*
1852674 TGTATCGATACATTATG-TTTGTATTGATACAT
1 TGTATCGATACATTATGCTTTGTATCGATACAT
1852706 TGTATCGATACATTATGCTTTGTATCGATACAT
1 TGTATCGATACATTATGCTTTGTATCGATACAT
1852739 GCACAATTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 17 0.55
33 14 0.45
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATTATGCTTTGTATCGATACAT
Found at i:1856450 original size:243 final size:242
Alignment explanation
Indices: 1855811--1856540 Score: 1309
Period size: 242 Copynumber: 3.0 Consensus size: 242
1855801 GATGGGAGAA
*
1855811 TTAGCATTCTTTTTGGGACTTCAAGTGAAGCAAACAAAGGACAGAATCTTCATCAATCAAGCAAA
1 TTAGCATTCTTTTTGGGACTTCAAGTGAAGAAAACAAAGGACA-AATCTTCATCAATCAAGCAAA
1855876 ATATACAAAGGAGTTACTCAAAAGGTTTCAAATGGATCAAGTCAAACCATGTGAAACACCAATGA
65 ATATACAAAGGAGTTACTCAAAAGGTTTCAAATGGATCAAGTCAAACCATGTGAAACACCAATGA
*
1855941 GTACTTCAACAAAGCTTGAAAAGGATGAAGGAGGCAATTTTATCGACACTAAACTTTATAGGTCT
130 GTACTTCAACAAAGCTTGAAAAGGATGAAGGAGGTAATTTTATCGACACTAAACTTTATAGGTCT
1856006 ATGATAGGTTCATTGTTATATCTCACTGCTAGTATACCAGATATTATG
195 ATGATAGGTTCATTGTTATATCTCACTGCTAGTATACCAGATATTATG
* * *
1856054 TTAGAATTCTTTTTGGGACTT-AAGTGAAGTAAACAAAGGACGGAATCTTCATCAATCAAGCAAA
1 TTAGCATTCTTTTTGGGACTTCAAGTGAAGAAAACAAAGGAC-AAATCTTCATCAATCAAGCAAA
* *
1856118 ATATACAAAGGAGTTACTCAAAAGGTTTCAAATAGATCAAGTCAAACCATGCGAAACACCAATGA
65 ATATACAAAGGAGTTACTCAAAAGGTTTCAAATGGATCAAGTCAAACCATGTGAAACACCAATGA
*
1856183 GTACTTCAACAAAACTTGAAAAGGATGAAGGAGGTAATTTTATCGACACTAAACTTTATAGGTCT
130 GTACTTCAACAAAGCTTGAAAAGGATGAAGGAGGTAATTTTATCGACACTAAACTTTATAGGTCT
*
1856248 ACGATAGGTTCATTGTTATATCTCACTGCTAGTATACCAGATATTATG
195 ATGATAGGTTCATTGTTATATCTCACTGCTAGTATACCAGATATTATG
* *
1856296 TTAGCATTCTTTTTGGGACTTCAAGTGAAGAAAAAAAAGGACAATATCTTCATCAATCAAGTAAA
1 TTAGCATTCTTTTTGGGACTTCAAGTGAAGAAAACAAAGGACAA-ATCTTCATCAATCAAGCAAA
*
1856361 ATATACAAAGGAGTTACTCAAAAGGTTTCAAATGGATAAAGTCAAACCATGTGAAACACCAATGA
65 ATATACAAAGGAGTTACTCAAAAGGTTTCAAATGGATCAAGTCAAACCATGTGAAACACCAATGA
1856426 GTACTTCAACAAAGCTTGAAAAGGATGAAGGAGGTAATTTTATCGACACTAAACTTTATAGGTCT
130 GTACTTCAACAAAGCTTGAAAAGGATGAAGGAGGTAATTTTATCGACACTAAACTTTATAGGTCT
*
1856491 ATGATGGGTTCATTGTTATATCTCACTGCTAGTATACCAGATATTATG
195 ATGATAGGTTCATTGTTATATCTCACTGCTAGTATACCAGATATTATG
1856539 TT
1 TT
1856541 TAGTGTATGC
Statistics
Matches: 465, Mismatches: 19, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
242 234 0.50
243 231 0.50
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (242 bp):
TTAGCATTCTTTTTGGGACTTCAAGTGAAGAAAACAAAGGACAAATCTTCATCAATCAAGCAAAA
TATACAAAGGAGTTACTCAAAAGGTTTCAAATGGATCAAGTCAAACCATGTGAAACACCAATGAG
TACTTCAACAAAGCTTGAAAAGGATGAAGGAGGTAATTTTATCGACACTAAACTTTATAGGTCTA
TGATAGGTTCATTGTTATATCTCACTGCTAGTATACCAGATATTATG
Found at i:1857558 original size:13 final size:13
Alignment explanation
Indices: 1857540--1857566 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1857530 ACAATGTTCT
1857540 TTGTATCGATACA
1 TTGTATCGATACA
1857553 TTGTATCGATACA
1 TTGTATCGATACA
1857566 T
1 T
1857567 GGGTTACTAT
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1860036 original size:13 final size:13
Alignment explanation
Indices: 1860018--1860044 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1860008 ACATTATGCT
1860018 TTGTATCAATACA
1 TTGTATCAATACA
1860031 TTGTATCAATACA
1 TTGTATCAATACA
1860044 T
1 T
1860045 GCACAATTGT
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:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (13 bp):
TTGTATCAATACA
Found at i:1860137 original size:13 final size:13
Alignment explanation
Indices: 1860121--1860151 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
1860111 CATTGTATAT
1860121 ATACAATGTATCG
1 ATACAATGTATCG
1860134 ATACAATGTATCG
1 ATACAATGTATCG
1860147 ATACA
1 ATACA
1860152 TAATGAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (13 bp):
ATACAATGTATCG
Found at i:1864968 original size:50 final size:50
Alignment explanation
Indices: 1864893--1865027 Score: 207
Period size: 50 Copynumber: 2.7 Consensus size: 50
1864883 TTCCACAATT
1864893 TGTATCGATACATTATTCATTGTATCGATACATTCTGGGTTTTACCCAGA
1 TGTATCGATACATTATTCATTGTATCGATACATTCTGGGTTTTACCCAGA
* * * * *
1864943 TGTATCAATTCATTGTTCATTGTATCGATACATTTTGGGTTTTACCTAGA
1 TGTATCGATACATTATTCATTGTATCGATACATTCTGGGTTTTACCCAGA
* *
1864993 TGTATCGATACATTTTTCAATGTATCGATACATTC
1 TGTATCGATACATTATTCATTGTATCGATACATTC
1865028 AGGCATTTTT
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 75 1.00
ACGTcount: A:0.26, C:0.16, G:0.15, T:0.43
Consensus pattern (50 bp):
TGTATCGATACATTATTCATTGTATCGATACATTCTGGGTTTTACCCAGA
Found at i:1866873 original size:13 final size:13
Alignment explanation
Indices: 1866855--1866880 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1866845 ATTTGTAGAA
1866855 TGTATCGATACAT
1 TGTATCGATACAT
1866868 TGTATCGATACAT
1 TGTATCGATACAT
1866881 CGATCTTTGT
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:1869303 original size:52 final size:52
Alignment explanation
Indices: 1869240--1869368 Score: 179
Period size: 52 Copynumber: 2.5 Consensus size: 52
1869230 CTCAATTTTT
* *
1869240 CATAATCGGGGATACTCCAACCCCGGTTTTATTTTC-AAAACACCAAGTTTC
1 CATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAAGTTTC
* * * *
1869291 CTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTT
1 C-ATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAAGTTTC
*
1869344 CACAATCGGGGATACTCCAACCCCG
1 CATAATCGGGGATACTCCAACCCCG
1869369 TTAATCAACT
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
51 1 0.01
52 52 0.78
53 14 0.21
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.29
Consensus pattern (52 bp):
CATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAAGTTTC
Found at i:1869476 original size:51 final size:50
Alignment explanation
Indices: 1869407--1869522 Score: 142
Period size: 51 Copynumber: 2.3 Consensus size: 50
1869397 TATTTTTGAG
* *
1869407 GGGATACTCGAACCCCGATTTTATTTCTAAAACACCAATTCTCCACAATC
1 GGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTCTCCACAATC
* * * * * *
1869457 AGGGATATTCCAACTCCGATTTTATTTCCAAAATACTAATTTTTCACAATC
1 -GGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTCTCCACAATC
1869508 GAGGATACTCCAACC
1 G-GGATACTCCAACC
1869523 TCGTTATTTC
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
50 1 0.02
51 53 0.98
ACGTcount: A:0.33, C:0.27, G:0.10, T:0.30
Consensus pattern (50 bp):
GGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTCTCCACAATC
Found at i:1869541 original size:28 final size:28
Alignment explanation
Indices: 1869505--1869579 Score: 100
Period size: 28 Copynumber: 2.7 Consensus size: 28
1869495 ATTTTTCACA
* *
1869505 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGAGGATACTCCAACCCCGTTACTTC
1869533 ATCGAGGATACTCCAACCCCGTTACTTC
1 ATCGAGGATACTCCAACCCCGTTACTTC
1869561 --CGAGGGGATACTCCAACCC
1 ATCGA--GGATACTCCAACCC
1869580 TGGCTTTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
26 3 0.07
28 40 0.93
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.24
Consensus pattern (28 bp):
ATCGAGGATACTCCAACCCCGTTACTTC
Found at i:1869542 original size:158 final size:159
Alignment explanation
Indices: 1869247--1869596 Score: 458
Period size: 158 Copynumber: 2.2 Consensus size: 159
1869237 TTTCATAATC
* ** *
1869247 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAAGTTTCCTTTAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAAGTTTCCTACAATCAGGGATACTCCAA
*
1869312 CTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAACCCCGTTAATCAA
66 CTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCCCGTTAATCAA
* * **
1869377 CTGGGATACTCCAACCTCGTTATTTTTGA
131 CTGGGATACTCCAACCCCGTTACTTCCGA
* *
1869406 GGGGATACTCGAACCCCGATTTTA-TTTCTAAAACACCAA-TTCTCC-ACAATCAGGGATATTCC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAACACCAAGTT-TCCTACAATCAGGGATACTCC
* * * *
1869468 AACTCCGATTTTATTTCC-AAAATACTAATTTTTCACAATCGAGGATACTCCAACCTCGTTATTT
64 AACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCCCGTTA-AT
*
1869532 CATC-GAGGATACTCCAACCCCGTTACTTCCGA
128 CAACTG-GGATACTCCAACCCCGTTACTTCCGA
* **
1869564 GGGGATACTCCAACCCTGGCTTTATTTTCAAAA
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAA
1869597 TATTGATTTC
Statistics
Matches: 166, Mismatches: 20, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
157 40 0.24
158 87 0.52
159 39 0.23
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (159 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAAGTTTCCTACAATCAGGGATACTCCAA
CTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCCCGTTAATCAA
CTGGGATACTCCAACCCCGTTACTTCCGA
Found at i:1869692 original size:79 final size:79
Alignment explanation
Indices: 1869533--1869710 Score: 175
Period size: 79 Copynumber: 2.3 Consensus size: 79
1869523 TCGTTATTTC
* ** * *
1869533 ATCGAGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCTGGCTTTATTTTCAAAAT
1 ATCGGGGATACTCCAACCCTATTACTTCCGAGGGGATACTCCAACCCTGACTTTATTTTCAAAAC
1869598 ATTGATTTCTCATA
66 ATTGATTTCTCATA
* * * **
1869612 ATTGGGGATACTCCAACCCTATTATTTTC-ACGGGGATACTCCAATCCC-GACTTTATTTTTGAA
1 ATCGGGGATACTCCAACCCTATTACTTCCGA-GGGGATACTCCAA-CCCTGACTTTATTTTCAAA
1869675 ACATCT-ATTT-TCTATA
64 ACAT-TGATTTCTC-ATA
* * *
1869691 ATCGGAGACACTTCAACCCT
1 ATCGGGGATACTCCAACCCT
1869711 TGTCTTATTT
Statistics
Matches: 81, Mismatches: 14, Indels: 8
0.79 0.14 0.08
Matches are distributed among these distances:
78 3 0.04
79 74 0.91
80 4 0.05
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (79 bp):
ATCGGGGATACTCCAACCCTATTACTTCCGAGGGGATACTCCAACCCTGACTTTATTTTCAAAAC
ATTGATTTCTCATA
Found at i:1877257 original size:52 final size:52
Alignment explanation
Indices: 1877124--1877264 Score: 230
Period size: 52 Copynumber: 2.7 Consensus size: 52
1877114 TGAAAAGTTA
1877124 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
1877176 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
**
1877228 CTGCATGTATCGATACA-AAAATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTTAAT-AGTGTATCGATACA
1877265 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:1877271 original size:13 final size:13
Alignment explanation
Indices: 1877253--1877277 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1877243 CAAAAATCAG
1877253 TGTATCGATACAA
1 TGTATCGATACAA
1877266 TGTATCGATACA
1 TGTATCGATACA
1877278 TGTGAGTAAT
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:1877361 original size:13 final size:13
Alignment explanation
Indices: 1877343--1877367 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1877333 CAAAAAAATA
1877343 TGTATCGATACAT
1 TGTATCGATACAT
1877356 TGTATCGATACA
1 TGTATCGATACA
1877368 ACATTTTATG
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:1877363 original size:33 final size:33
Alignment explanation
Indices: 1877321--1877387 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1877311 AGTAGCTTAA
1877321 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1877354 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1877387 A
1 A
1877388 AATCATTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1877466 original size:21 final size:21
Alignment explanation
Indices: 1877425--1877466 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1877415 GTTGGGACCT
*
1877425 TGTATCGATACATTTTAACAA
1 TGTATCGATACATTTGAACAA
*
1877446 TGTATCGATACATTTGGACAA
1 TGTATCGATACATTTGAACAA
1877467 AAATGTAATT
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:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTGAACAA
Found at i:1879852 original size:123 final size:118
Alignment explanation
Indices: 1879561--1880250 Score: 838
Period size: 123 Copynumber: 5.7 Consensus size: 118
1879551 TTAGCCTTTC
*
1879561 CAGTCCTCAAAGAGCAGGACGCCTTTTTCCTTTTAAAGCCCACACAAATTGGTGGCACTTTTCAG
1 CAGTCCTCAAAGAGCAGGACGCC--TTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC-TTTCAG
* **
1879626 TCCTCAAAGAGCAAGACG----C-CTTTTAAAGCCCACACAAGCCGGTGGCACCTT
63 TCCTCAAAGAGCAGGACGCTTTCTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT
*
1879677 CAGTCCTCAAAGAGCAGGATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAG
1 CAGTCCTCAAAGAGCAGGACGCCTT-TCCTTTTAAAGCCCACACAAGTTGGTGGCAC-TTTC-AG
* *
1879742 TCCTCAAAGAGCAGGATGCTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTT
63 TCCTCAAAGAGCAGGACGCTTTCTCTTT-TAAAGCCCACACAAGTTGGTGGCACCTT
* * * *
1879799 CCAGTCCTCAAAGAGCAGGGCACCTTTCCTTTTTAAAGCCCACATAA-TCTGGTGGCACCTTCAG
1 -CAGTCCTCAAAGAGCAGGACGCCTTTCC-TTTTAAAGCCCACACAAGT-TGGTGGCACTTTCAG
* *
1879863 TCCTCAAAGAGCAGGACGCCTTTTTCTTTTAGAGCCCACACAAGTTGGTGGCACCTT
63 TCCTCAAAGAGCAGGACG-CTTTCTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT
* * * *
1879920 TAGTCCTCAAAGAGCAGGACGTCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTT-AG
1 CAGTCCTCAAAGAGCAGGACG-CCTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCA-CTTTCAG
* *
1879984 TCCTCAAAGAGCAGGACACTTTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTT
63 TCCTCAAAGAGCAGGACGC--TTTCTC-TTTTAAAGCCCACACAAGTTGGTGGCACCTT
* *
1880043 TAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGT
1 CAGTCCTCAAAGAGCAGGACGCC-TTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTTCAGT
* * * *
1880108 CCTCAAAGAGTAGGACACCTTCTTCCCTTTTAAAGCCCACACAAGTTAGTGGCA-CTT
64 CCTCAAAGAGCAGGAC-GC-T-TTCTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT
* * *
1880165 CCCAGTCCTCAGAGAGCATGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTA
1 --CAGTCCTCAAAGAGCAGGACGCCTT-TCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTC-A
1880230 GTCCTCAAAGAGCAGGACGCT
62 GTCCTCAAAGAGCAGGACGCT
1880251 CCCTCCTTTC
Statistics
Matches: 505, Mismatches: 42, Indels: 48
0.85 0.07 0.08
Matches are distributed among these distances:
114 2 0.00
115 35 0.07
116 40 0.08
120 24 0.05
121 92 0.18
122 83 0.16
123 158 0.31
124 71 0.14
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.27
Consensus pattern (118 bp):
CAGTCCTCAAAGAGCAGGACGCCTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCAGTCC
TCAAAGAGCAGGACGCTTTCTCTTTTAAAGCCCACACAAGTTGGTGGCACCTT
Found at i:1880249 original size:61 final size:61
Alignment explanation
Indices: 1879562--1880249 Score: 838
Period size: 61 Copynumber: 11.3 Consensus size: 61
1879552 TAGCCTTTCC
* *
1879562 AGTCCTCAAAGAGCAGGACGCCTTTTTCCTTTTAAAGCCCACACAAATTGGTGGCA-CTTTT
1 AGTCCTCAAAGAGCAGGACGCC-TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCT
* **
1879623 CAGTCCTCAAAGAGCAAGACG------CCTTTTAAAGCCCACACAAGCCGGTGGCACCTTC-
1 -AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCT
* * *
1879678 AGTCCTCAAAGAGCAGGATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCT
1 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTCT
* * *
1879740 AGTCCTCAAAGAGCAGGATG-C-TTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTTC-CTTT-TAAAGCCCACACAAGTTGGTGGCACCTTCT
* * *
1879801 AGTCCTCAAAGAGCAGGGCACC-TTTCCTTTTTAAAGCCCACATAA-TCTGGTGGCACCTTC-
1 AGTCCTCAAAGAGCAGGACGCCTTTTCC-TTTTAAAGCCCACACAAGT-TGGTGGCACCTTCT
* *
1879861 AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAGAGCCCACACAAGTTGGTGGCACCTT-T
1 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCT
* * *
1879921 AGTCCTCAAAGAGCAGGACGTCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTT-T
1 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTCT
* * *
1879982 AGTCCTCAAAGAGCAGGACACTTTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACCTT-T
1 AGTCCTCAAAGAGCAGGACGC--CTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCT
*
1880044 AGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-T
1 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCT
* * * *
1880104 CAGTCCTCAAAGAGTAGGACACCTTCTTCCCTTTTAAAGCCCACACAAGTTAGTGGCA-CTTCCC
1 -AGTCCTCAAAGAGCAGGACGCCTT-TT-CCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CT
* * *
1880168 AGTCCTCAGAGAGCATGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCT
1 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CT
1880229 AGTCCTCAAAGAGCAGGACGC
1 AGTCCTCAAAGAGCAGGACGC
1880250 TCCCTCCTTT
Statistics
Matches: 550, Mismatches: 51, Indels: 51
0.84 0.08 0.08
Matches are distributed among these distances:
54 18 0.03
55 26 0.05
56 3 0.01
60 147 0.27
61 177 0.32
62 123 0.22
63 56 0.10
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (61 bp):
AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCT
Found at i:1880282 original size:163 final size:163
Alignment explanation
Indices: 1880097--1880454 Score: 599
Period size: 163 Copynumber: 2.2 Consensus size: 163
1880087 AAGTTGGTGG
*
1880097 CACCTTTCAGTCCTCAAAGAGTAGGACACCTTCTTCCCTTTTAAAGCCCACACAAGTTAGTGGCA
1 CACCTTTTAGTCCTCAAAGAGTAGGACACCTTCTTCCCTTTTAAAGCCCACACAAGTTAGTGGCA
* ** *
1880162 CTTCCCAGTCCTCAGAGAGCATGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTC
66 CTTCCCAGTCCTCAGAGAGCAGGAAACCTTCTCCTTTTAAAGCCCACACAAATTGGTGGCACTTC
1880227 CTAGTCCTCAAAGAGCAGGACGCTCCCTCCTTT
131 CTAGTCCTCAAAGAGCAGGACGCTCCCTCCTTT
*
1880260 CACCTTTTAGTCCTCAAAGAGTAGGACACCTTCTTCCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CACCTTTTAGTCCTCAAAGAGTAGGACACCTTCTTCCCTTTTAAAGCCCACACAAGTTAGTGGCA
* *
1880325 CTTCCCGGTCCTCAGAGAGTAGGAAACCTTCTCCTTTTAAAGCCCACACAAATTGGTGGCACTTC
66 CTTCCCAGTCCTCAGAGAGCAGGAAACCTTCTCCTTTTAAAGCCCACACAAATTGGTGGCACTTC
*
1880390 CTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTT
131 CTAGTCCTCAAAGAGCAGGACGCTCCCTCCTTT
* * * *
1880423 CACCCTTTAATCCTCAAAGAGCAGGACGCCTT
1 CACCTTTTAGTCCTCAAAGAGTAGGACACCTT
1880455 TTAAAGCCCA
Statistics
Matches: 182, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
163 182 1.00
ACGTcount: A:0.25, C:0.32, G:0.17, T:0.26
Consensus pattern (163 bp):
CACCTTTTAGTCCTCAAAGAGTAGGACACCTTCTTCCCTTTTAAAGCCCACACAAGTTAGTGGCA
CTTCCCAGTCCTCAGAGAGCAGGAAACCTTCTCCTTTTAAAGCCCACACAAATTGGTGGCACTTC
CTAGTCCTCAAAGAGCAGGACGCTCCCTCCTTT
Found at i:1880381 original size:61 final size:63
Alignment explanation
Indices: 1880268--1880409 Score: 216
Period size: 61 Copynumber: 2.3 Consensus size: 63
1880258 TTCACCTTTT
* *
1880268 AGTCCTCAAAGAGTAGGACACCTTCTTCCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCC
1 AGTCCTCAAAGAGTAGGAAACCTTCTTCCCTTTTAAAGCCCACACAAATTGGTGGCACTTCCC
* * *
1880331 GGTCCTCAGAGAGTAGGAAACCTTC-T-CCTTTTAAAGCCCACACAAATTGGTGGCACTTCCT
1 AGTCCTCAAAGAGTAGGAAACCTTCTTCCCTTTTAAAGCCCACACAAATTGGTGGCACTTCCC
*
1880392 AGTCCTCAAAGAGCAGGA
1 AGTCCTCAAAGAGTAGGA
1880410 CGCTCTCTCC
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
61 48 0.68
62 1 0.01
63 22 0.31
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (63 bp):
AGTCCTCAAAGAGTAGGAAACCTTCTTCCCTTTTAAAGCCCACACAAATTGGTGGCACTTCCC
Found at i:1880604 original size:61 final size:61
Alignment explanation
Indices: 1880451--1880679 Score: 260
Period size: 61 Copynumber: 3.9 Consensus size: 61
1880441 GAGCAGGACG
* *
1880451 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-T-AGTCCTCAAAGAGCAGGA---C---G
1 CCTTTCAAAGCCCACACAAGTTGGTGGCA-CTTCTCAGTCCTCAAAGAGCAGGATGCCTATT
* * * *
1880505 CCTTTCAAAGCCCACACAAGTTAGTGGCA-TTTTCCAGTCCTGAAAAAGCAGGATGCCTATT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTCT-CAGTCCTCAAAGAGCAGGATGCCTATT
* * *
1880566 CCTTTCAAAGCCCACACGAGTTGGTGGCACTTCTCAGTCCTCAAAGAGCAGGATGCTTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTCTCAGTCCTCAAAGAGCAGGATGCCTATT
* * * *
1880627 CCTTTTAAAGCCCACACAAGTTGGTGGCGCTTCCCAGTCCTTAAAGAGCAGGA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTCTCAGTCCTCAAAGAGCAGGA
1880680 CACTCCCTCC
Statistics
Matches: 148, Mismatches: 17, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
52 2 0.01
53 1 0.01
54 27 0.18
55 16 0.11
58 1 0.01
61 98 0.66
62 3 0.02
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (61 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACTTCTCAGTCCTCAAAGAGCAGGATGCCTATT
Found at i:1880664 original size:122 final size:115
Alignment explanation
Indices: 1880451--1880679 Score: 289
Period size: 122 Copynumber: 1.9 Consensus size: 115
1880441 GAGCAGGACG
*
1880451 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGC
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGC
* *
1880516 CCACACAAGTTAGTGGCATTTTCCAGTCCTGAAAAAGCAGGATGCCTATT
66 CCACACAAGTTAGTGGCACTTCCCAGTCCTGAAAAAGCAGGATGCCTATT
* *
1880566 CCTTTCAAAGCCCACACGAGTTGGTGGCA-CTTCTCAGTCCTCAAAGAGCAGGATGCTTTTTCCT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTT-T-AGTCCTCAAAGAGCAGGA--C----GCCT
* * * * *
1880630 TTTAAAGCCCACACAAGTTGGTGGCGCTTCCCAGTCCTTAAAGAGCAGGA
58 TTCAAAGCCCACACAAGTTAGTGGCACTTCCCAGTCCTGAAAAAGCAGGA
1880680 CACTCCCTCC
Statistics
Matches: 96, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
114 3 0.03
115 28 0.29
116 18 0.19
118 1 0.01
122 46 0.48
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (115 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAGC
CCACACAAGTTAGTGGCACTTCCCAGTCCTGAAAAAGCAGGATGCCTATT
Found at i:1880766 original size:55 final size:55
Alignment explanation
Indices: 1880696--1881463 Score: 794
Period size: 55 Copynumber: 13.5 Consensus size: 55
1880686 CTCCTTTCGC
1880696 CTTTT-AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * ** *
1880750 CTTCTCAGTCCTCAAAGAGTAGGATGCCACTTAAAGCCCGCACAAGTTGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
1880805 -TTTTCCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTTGTGGCA
1 CTTTT-CAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
1880860 -TTTTACAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CTTTT-CAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
1880915 -TTTTCCAGTCCTCAAAAAGCAGGATGCCTTTCAAAGCCTACACAAGTTGGTGGCA
1 CTTTT-CAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
1880970 TTTTTCAGTCCTCAAAGAGTAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
*
1881025 -TTTTCCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CTTTT-CAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * * * * *
1881080 TTTTTCAATCCTCAAAGAGCAAGATGCTTTTTCTCTTCAAATCCCACATAAGTCGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGACGC-----CT-TTTAAAGCCCACACAAGTTGGTGGCA
*
1881141 -TTTTCCAGTCCTCAAAGGGCAGGACGCCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
1 CTTTT-CAGTCCTCAAAGAGCAGGACG-C----CTTTT-AAAGCCCACACAAGTTGGTGGCA
* * **
1881202 CTTTTCAGTCCTTAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGCCGGTGGCA
1 CTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
1881257 C-CTTCAATCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGACA
1 CTTTTCAGTCCTCAAAGAGCAGGACG------CCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
1881317 CTTTTCAGTCTTCAAAGAGCAGGATGCTTTCTTTTTGCAAAGCCCACACAAGTTGGTAGCA
1 CTTTTCAGTCCTCAAAGAGCAGGACGC---C-TTTT--AAAGCCCACACAAGTTGGTGGCA
* * * * * *
1881378 CCTTCCAGTCCTCAAAGGGCAGGACACCTTTTCTTTTCAAAGCCCACACGAGTTGGTGGTA
1 CTTTTCAGTCCTCAAAGAGCAGGAC-GC----CTTTT-AAAGCCCACACAAGTTGGTGGCA
*
1881439 CTTTTCAGTCCTCAAAGAGTAGGAC
1 CTTTTCAGTCCTCAAAGAGCAGGAC
1881464 ACACTTCCTT
Statistics
Matches: 610, Mismatches: 74, Indels: 53
0.83 0.10 0.07
Matches are distributed among these distances:
54 32 0.05
55 324 0.53
56 12 0.02
58 1 0.00
59 4 0.01
60 35 0.06
61 188 0.31
62 10 0.02
63 4 0.01
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (55 bp):
CTTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:1880894 original size:110 final size:110
Alignment explanation
Indices: 1880701--1881462 Score: 880
Period size: 110 Copynumber: 6.7 Consensus size: 110
1880691 TTCGCCTTTT
* *
1880701 AGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCTCAGTCCTCAAA
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAA
* ** *
1880766 GAGTAGGATGCCACTTAAAGCCCGCACAAGTTGGTGGCATTTTCC
66 GAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
*
1880811 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTTGTGGCA-TTTTACAGTCCTCAA
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAA
*
1880875 AGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
65 AGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
* * * *
1880921 AGTCCTCAAAAAGCAGGATGCCTTTCAAAGCCTACACAAGTTGGTGGCATTTTTCAGTCCTCAAA
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAA
*
1880986 GAGTAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
66 GAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
* *
1881031 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAATCCTCAAA
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAA
* * * * *
1881096 GAGCAAGATGCTTTTTCTCTTCAAATCCCACATAAGTCGGTGGCATTTTCC
66 GAGCAGGATGC-----CT-TTTAAAGCCCACACAAGTTGGTGGCATTTTCC
*
1881147 AGTCCTCAAAGGGCAGGACGCCTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTC
1 AGTCCTCAAAGAGCAGGACG-C----C-TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTC
* * * ** **
1881212 CTTAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGCCGGTGGCACCTT-C
60 CTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
* *
1881262 AATCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGACACTTTTCAGTC
1 AGTCCTCAAAGAGCAGGACGCCTT-T-C----AAAGCCCACACAAGTTGGTGGCACTTTTCAGTC
* * **
1881327 TTCAAAGAGCAGGATGCTTTCTTTTTGCAAAGCCCACACAAGTTGGTAGCACCTTCC
60 CTCAAAGAGCAGGATGC---C-TTTT--AAAGCCCACACAAGTTGGTGGCATTTTCC
* * * *
1881384 AGTCCTCAAAGGGCAGGACACCTTTTCTTTTCAAAGCCCACACGAGTTGGTGGTACTTTTCAGTC
1 AGTCCTCAAAGAGCAGGAC-GC----C-TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTC
*
1881449 CTCAAAGAGTAGGA
60 CTCAAAGAGCAGGA
1881463 CACACTTCCT
Statistics
Matches: 566, Mismatches: 53, Indels: 54
0.84 0.08 0.08
Matches are distributed among these distances:
109 5 0.01
110 269 0.48
111 5 0.01
114 1 0.00
115 67 0.12
116 72 0.13
117 3 0.01
118 1 0.00
119 3 0.01
121 25 0.04
122 109 0.19
123 1 0.00
126 1 0.00
127 2 0.00
128 2 0.00
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (110 bp):
AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAA
GAGCAGGATGCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCC
Done.