Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008041.1 Hibiscus syriacus cultivar Beakdansim tig00110528_pilon, whole genome shotgun sequence
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: 4970990
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 21
Found at i:3439282 original size:44 final size:44
Alignment explanation
Indices: 3439232--3439446 Score: 342
Period size: 44 Copynumber: 4.9 Consensus size: 44
3439222 AAATGAATGA
*
3439232 ATAAATGAAAATGCATAACGGTGCATTATTGGGAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* * *
3439276 ATAAATGAAAATGCATAACTGTGTATTATTGGGAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
* ** *
3439320 ATAAATAAAAATGCATAACGGTGCATTATTGAAAGAAAGGTTCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
3439364 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
1 ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
3439408 ATAAAATGAAAATGCATAACGGTGCATT-TTGGCAGAAAG
1 AT-AAATGAAAATGCATAACGGTGCATTATTGGCAGAAAG
3439447 ATGTCACTCC
Statistics
Matches: 158, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
44 133 0.84
45 25 0.16
ACGTcount: A:0.41, C:0.11, G:0.24, T:0.24
Consensus pattern (44 bp):
ATAAATGAAAATGCATAACGGTGCATTATTGGCAGAAAGGTGCC
Found at i:3443217 original size:49 final size:49
Alignment explanation
Indices: 3443164--3443453 Score: 474
Period size: 49 Copynumber: 5.9 Consensus size: 49
3443154 AAAATGAATG
*
3443164 AATGAAAATTAAATGCATAACGGTGCATTTCAGCATAAAAGGTGCCACT
1 AATGAAAATTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACT
* * *
3443213 AATGAAAATCAAATGCATAATGGTGCATTTCAGCATAAAAGGTGCCACT
1 AATGAAAATTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACT
*
3443262 AATGAAAATAAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACT
1 AATGAAAATTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACT
*
3443311 AATGAAAATTAAATGCATAACGGTGCATTTCGGCATAAAAGGAGCCACT
1 AATGAAAATTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACT
* *
3443360 AATGAAAATTAAATGCATAACGGTGCATTTCGACATAAAAGGTGCCACA
1 AATGAAAATTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACT
* *
3443409 AATGAAAATTAAA-GACATAACTGTGCATTTCGGCATACAAGGTGC
1 AATGAAAATTAAATG-CATAACGGTGCATTTCGGCATAAAAGGTGC
3443454 TACTCATGGT
Statistics
Matches: 227, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
48 1 0.00
49 226 1.00
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.23
Consensus pattern (49 bp):
AATGAAAATTAAATGCATAACGGTGCATTTCGGCATAAAAGGTGCCACT
Found at i:3444303 original size:104 final size:105
Alignment explanation
Indices: 3444111--3444311 Score: 271
Period size: 104 Copynumber: 1.9 Consensus size: 105
3444101 AAACACACAC
* * * *
3444111 TGTGACAACATTGGTGGTCACAAAATATACTTTTAGTGTCAAATAAACTTATCACAATTTCTATT
1 TGTGACAACATTGATGGTCACAAAATATACTTTTAGTGTCAAATAAAATCATCACAATTTATATT
* **
3444176 GATAATAGTATCGAACATTTGGTCACTAAAAAATACTTAG
66 AATAATAGTATCGAACAGATGGTCACTAAAAAATACTTAG
* *
3444216 TGTGACAATATTGATGGTCACAAAATATATTTTTTAGTGT-AAA-AAAATCATCACAATTTATAT
1 TGTGACAACATTGATGGTCACAAAATATA-CTTTTAGTGTCAAATAAAATCATCACAATTTATAT
* * *
3444279 TAATAATTGTGTCGAATAGATGGTCACTAAAAA
65 TAATAATAGTATCGAACAGATGGTCACTAAAAA
3444312 GTGAACAGTT
Statistics
Matches: 83, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
104 44 0.53
105 30 0.36
106 9 0.11
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (105 bp):
TGTGACAACATTGATGGTCACAAAATATACTTTTAGTGTCAAATAAAATCATCACAATTTATATT
AATAATAGTATCGAACAGATGGTCACTAAAAAATACTTAG
Found at i:3445327 original size:21 final size:21
Alignment explanation
Indices: 3445301--3445342 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
3445291 ATAGCAATGT
3445301 GGGAGAAACAATATGAACATA
1 GGGAGAAACAATATGAACATA
3445322 GGGAGAAACAATATGAACATA
1 GGGAGAAACAATATGAACATA
3445343 TTCTCAATCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.10, G:0.24, T:0.14
Consensus pattern (21 bp):
GGGAGAAACAATATGAACATA
Found at i:3445880 original size:19 final size:19
Alignment explanation
Indices: 3445856--3445893 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
3445846 CGCAGTTCTC
*
3445856 ATTTAGTGGAATTGTTGAT
1 ATTTAGTGAAATTGTTGAT
3445875 ATTTAGTGAAATTGTTGAT
1 ATTTAGTGAAATTGTTGAT
3445894 CAAACACCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (19 bp):
ATTTAGTGAAATTGTTGAT
Found at i:3447294 original size:24 final size:22
Alignment explanation
Indices: 3447263--3447319 Score: 60
Period size: 25 Copynumber: 2.5 Consensus size: 22
3447253 AATTATTTAT
*
3447263 TATATTTTAAACGATTAAATTAAA
1 TATATTTTAAACAATTAAA-T-AA
* *
3447287 TATATTTTTTAATAATTAAATAA
1 TATA-TTTTAAACAATTAAATAA
3447310 TATATTTTAA
1 TATATTTTAA
3447320 TAATATAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 5 0.18
23 6 0.21
24 5 0.18
25 12 0.43
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
TATATTTTAAACAATTAAATAA
Found at i:3447317 original size:21 final size:20
Alignment explanation
Indices: 3447280--3447328 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
3447270 TAAACGATTA
*
3447280 AATTAAATATATTTTTTAAT
1 AATTAAATATATATTTTAAT
3447300 AATTAAATAATATATTTTAAT
1 AATTAAAT-ATATATTTTAAT
3447321 AATATAAA
1 AAT-TAAA
3447329 AAAATTCTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 8 0.31
21 14 0.54
22 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AATTAAATATATATTTTAAT
Found at i:3447370 original size:13 final size:13
Alignment explanation
Indices: 3447352--3447378 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3447342 TATAAGTAAA
3447352 AATATATTTTAAT
1 AATATATTTTAAT
3447365 AATATATTTTAAT
1 AATATATTTTAAT
3447378 A
1 A
3447379 CAACATATAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AATATATTTTAAT
Found at i:3456083 original size:55 final size:55
Alignment explanation
Indices: 3456018--3456339 Score: 460
Period size: 55 Copynumber: 6.0 Consensus size: 55
3456008 CCAACTAACA
* * * *
3456018 ATACGAAAATTCATAAACTAATTATGAATTTTTTAGTTTTGTACACAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
3456073 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
* * *
3456128 ATACAGAAATTCATAAACTTATTATGAAGTTCTTAGTTTTGCACACAAACTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
* *
3456183 ATATGGAAATTC----A--TATTATGAATTTCTTAGTTTTGCATACAAAGTGCCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
* * *
3456232 ATACAGAAATTCATAAACTTATTATGAATTTATTAGTTTTGCACACAAAGTGTCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
* * *
3456287 ATA-TGAAATTCATAAACTTATTATGAATTTTTTAGTTTTGCACACATAGTGCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCC
3456340 ATTTGGTAAT
Statistics
Matches: 240, Mismatches: 21, Indels: 13
0.88 0.08 0.05
Matches are distributed among these distances:
49 43 0.18
51 1 0.00
53 1 0.00
54 46 0.19
55 149 0.62
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.37
Consensus pattern (55 bp):
ATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCC
Found at i:3456252 original size:104 final size:104
Alignment explanation
Indices: 3456024--3456339 Score: 418
Period size: 104 Copynumber: 2.9 Consensus size: 104
3456014 AACAATACGA
* * * *
3456024 AAATTCATAAACTAATTATGAATTTTTTAGTTTTGTACACAAAGTGCCCATACGGAAATTCATAA
1 AAATTCATAAACTTATTATGAATTTATTAGTTTTGCACACAAAGTGCCCATATGGAAATTC----
3456089 ACTTATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACAG
62 A--TATTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACAG
* * *
3456134 AAATTCATAAACTTATTATGAAGTTCTTAGTTTTGCACACAAACTGCCCATATGGAAATTCATAT
1 AAATTCATAAACTTATTATGAATTTATTAGTTTTGCACACAAAGTGCCCATATGGAAATTCATAT
*
3456199 TATGAATTTCTTAGTTTTGCATACAAAGTGCCCATACAG
66 TATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACAG
*
3456238 AAATTCATAAACTTATTATGAATTTATTAGTTTTGCACACAAAGTGTCCATAT-GAAATTCATAA
1 AAATTCATAAACTTATTATGAATTTATTAGTTTTGCACACAAAGTGCCCATATGGAAATTC----
* *
3456302 ACTTATTATGAATTTTTTAGTTTTGCACACATAGTGCC
62 A--TATTATGAATTTCTTAGTTTTGCACACAAAGTGCC
3456340 ATTTGGTAAT
Statistics
Matches: 186, Mismatches: 14, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
103 7 0.04
104 90 0.48
106 1 0.01
107 1 0.01
109 32 0.17
110 55 0.30
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (104 bp):
AAATTCATAAACTTATTATGAATTTATTAGTTTTGCACACAAAGTGCCCATATGGAAATTCATAT
TATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACAG
Found at i:3463125 original size:54 final size:54
Alignment explanation
Indices: 3463008--3463146 Score: 215
Period size: 54 Copynumber: 2.6 Consensus size: 54
3462998 ACATAAGCAA
*** *
3463008 AATTTCTTAGTTTTGCACACAAAGTGCTCATACGGAAATTCATAAAATTATTATG
1 AATTTCTTAGTTTTGCACACAAAGTGC-CATAAAAAAATTCATAAAATTATAATG
*
3463063 AATTTCTTAGTTTTGCACACAAAGTGCCATAAAAAAATTCATAAACTTATAATG
1 AATTTCTTAGTTTTGCACACAAAGTGCCATAAAAAAATTCATAAAATTATAATG
*
3463117 AATTTCTTAGTTTTGCACACATAGTGCCAT
1 AATTTCTTAGTTTTGCACACAAAGTGCCAT
3463147 TTTGTAATCA
Statistics
Matches: 78, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
54 51 0.65
55 27 0.35
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.36
Consensus pattern (54 bp):
AATTTCTTAGTTTTGCACACAAAGTGCCATAAAAAAATTCATAAAATTATAATG
Found at i:3466907 original size:21 final size:20
Alignment explanation
Indices: 3466846--3466912 Score: 80
Period size: 21 Copynumber: 3.2 Consensus size: 20
3466836 GACTAAGTAT
* *
3466846 CTAGCTAGGTAGGTAGTGTAT
1 CTAGCTAGGTAGCTAG-GTAG
*
3466867 CTAGCTAGGTAAGCGAGGTAG
1 CTAGCTAGGT-AGCTAGGTAG
3466888 CTAGCTAGGTAGCTATGGTAG
1 CTAGCTAGGTAGCTA-GGTAG
3466909 CTAG
1 CTAG
3466913 TTGGGTACCT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.10
21 32 0.80
22 4 0.10
ACGTcount: A:0.25, C:0.13, G:0.34, T:0.27
Consensus pattern (20 bp):
CTAGCTAGGTAGCTAGGTAG
Found at i:3466919 original size:21 final size:21
Alignment explanation
Indices: 3466883--3466924 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3466873 AGGTAAGCGA
*
3466883 GGTAGCTAGCTAGGTAGCTAT
1 GGTAGCTAGCTAGGTACCTAT
* *
3466904 GGTAGCTAGTTGGGTACCTAT
1 GGTAGCTAGCTAGGTACCTAT
3466925 TGTCACTTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.14, G:0.33, T:0.31
Consensus pattern (21 bp):
GGTAGCTAGCTAGGTACCTAT
Found at i:3481456 original size:46 final size:46
Alignment explanation
Indices: 3481389--3481843 Score: 658
Period size: 46 Copynumber: 9.9 Consensus size: 46
3481379 TAAATCGAAT
3481389 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
*
3481435 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATTAAAGGATG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * *
3481481 CCATAATTAAAATACATGAAAGGATGGATTAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * * *
3481527 CCATAACTAAAATTCATGAAAGGATGTATTAAGGTATTAAAGGATG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
** *
3481573 CCATAACTAAAATGCATGAAATAATGCATTAAGGCATGAAAGGATA
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * * *
3481619 CCATAATTAAAATACATGAACGGATGCATTAAGACATGAAAGGATG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * *
3481665 CCATAACTAAAATGCATGAACGAATACATTAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* *
3481711 CCATAATTAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* *
3481757 CCATAATTAAAATGCATGAAAGTATGCATTAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * * * * *
3481803 TCATGATTAAAATGCATGAACGGATGTATTAATGCATGAAA
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAA
3481844 AGAGACCACA
Statistics
Matches: 369, Mismatches: 40, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 369 1.00
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.23
Consensus pattern (46 bp):
CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
Found at i:3481458 original size:26 final size:26
Alignment explanation
Indices: 3481389--3481461 Score: 95
Period size: 26 Copynumber: 3.0 Consensus size: 26
3481379 TAAATCGAAT
3481389 CCATAACTAAAATGCATGAAAGGATG
1 CCATAACTAAAATGCATGAAAGGATG
*
3481415 -CAT---T--AAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAAAGGATG
3481435 CCATAACTAAAATGCATGAAAGGATG
1 CCATAACTAAAATGCATGAAAGGATG
3481461 C
1 C
3481462 ATTAAGGCAT
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
20 15 0.38
21 3 0.08
22 1 0.03
24 1 0.03
25 3 0.08
26 16 0.41
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.19
Consensus pattern (26 bp):
CCATAACTAAAATGCATGAAAGGATG
Found at i:3481829 original size:26 final size:26
Alignment explanation
Indices: 3481606--3481829 Score: 111
Period size: 26 Copynumber: 9.5 Consensus size: 26
3481596 ATGCATTAAG
**
3481606 GCATGAAAGGATACCATAATTAAAAT
1 GCATGAAAGGATGTCATAATTAAAAT
* * *
3481632 ACATGAACGGATG-C---ATTAAGA-
1 GCATGAAAGGATGTCATAATTAAAAT
* *
3481653 -CATGAAAGGATGCCATAACTAAAAT
1 GCATGAAAGGATGTCATAATTAAAAT
* *
3481678 GCATG-AACGA----ATACATT--AAG
1 GCATGAAAGGATGTCATA-ATTAAAAT
*
3481698 GCATGAAAGGATGCCATAATTAAAAT
1 GCATGAAAGGATGTCATAATTAAAAT
* *
3481724 GCATGAACGGATG-C---ATT--AAG
1 GCATGAAAGGATGTCATAATTAAAAT
*
3481744 GCATGAAAGGATGCCATAATTAAAAT
1 GCATGAAAGGATGTCATAATTAAAAT
* *
3481770 GCATGAAAGTATG-C---ATT--AAG
1 GCATGAAAGGATGTCATAATTAAAAT
*
3481790 GCATGAAAGGATGTCATGATTAAAAT
1 GCATGAAAGGATGTCATAATTAAAAT
*
3481816 GCATGAACGGATGT
1 GCATGAAAGGATGT
3481830 ATTAATGCAT
Statistics
Matches: 151, Mismatches: 21, Indels: 52
0.67 0.09 0.23
Matches are distributed among these distances:
20 46 0.30
21 10 0.07
22 14 0.09
24 14 0.09
25 10 0.07
26 57 0.38
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.22
Consensus pattern (26 bp):
GCATGAAAGGATGTCATAATTAAAAT
Found at i:3481838 original size:20 final size:20
Alignment explanation
Indices: 3481721--3481843 Score: 75
Period size: 20 Copynumber: 5.5 Consensus size: 20
3481711 CCATAATTAA
* *
3481721 AATGCATGAACGGATGCATT
1 AATGCATGAAAGGATGTATT
*
3481741 AAGGCATGAAAGGATGCCATAATT
1 AATGCATGAAAGGATG---T-ATT
* *
3481765 AAAATGCATGAAAGTATGCATT
1 --AATGCATGAAAGGATGTATT
*
3481787 AAGGCATGAAAGGATGTCATGATT
1 AATGCATGAAAGGATG---T-ATT
*
3481811 AAAATGCATGAACGGATGTATT
1 --AATGCATGAAAGGATGTATT
3481833 AATGCATGAAA
1 AATGCATGAAA
3481844 AGAGACCACA
Statistics
Matches: 79, Mismatches: 12, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
20 38 0.48
22 6 0.08
23 1 0.01
24 6 0.08
26 28 0.35
ACGTcount: A:0.41, C:0.11, G:0.24, T:0.24
Consensus pattern (20 bp):
AATGCATGAAAGGATGTATT
Found at i:3485015 original size:24 final size:24
Alignment explanation
Indices: 3484979--3485085 Score: 106
Period size: 24 Copynumber: 4.5 Consensus size: 24
3484969 ATAAATGGAG
*
3484979 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCATAACAGAATTC
* * *
3485003 ATATCATATATCATAACAGAATCC
1 ATATCAGAAATCATAACAGAATTC
* * * *
3485027 AAATTAGAAATCAGAACATAATTC
1 ATATCAGAAATCATAACAGAATTC
* *
3485051 AGATCATAAATCATAACAGAATTC
1 ATATCAGAAATCATAACAGAATTC
* *
3485075 AAATCGGAAAT
1 ATATCAGAAAT
3485086 TAGATAAAAC
Statistics
Matches: 64, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 64 1.00
ACGTcount: A:0.51, C:0.16, G:0.08, T:0.24
Consensus pattern (24 bp):
ATATCAGAAATCATAACAGAATTC
Found at i:3485085 original size:48 final size:48
Alignment explanation
Indices: 3484981--3485085 Score: 147
Period size: 48 Copynumber: 2.2 Consensus size: 48
3484971 AAATGGAGAT
* *
3484981 ATCAGAAATCAAAACAGAATTCATATCATATATCATAACAGAATCCAA
1 ATCAGAAATCAAAACAGAATTCAGATCATAAATCATAACAGAATCCAA
* * * *
3485029 ATTAGAAATCAGAACATAATTCAGATCATAAATCATAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAGATCATAAATCATAACAGAATCCAA
*
3485077 ATCGGAAAT
1 ATCAGAAAT
3485086 TAGATAAAAC
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.51, C:0.16, G:0.09, T:0.24
Consensus pattern (48 bp):
ATCAGAAATCAAAACAGAATTCAGATCATAAATCATAACAGAATCCAA
Found at i:3487416 original size:18 final size:18
Alignment explanation
Indices: 3487395--3487434 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
3487385 GCGGTCAACG
3487395 GGTCGGGTCAGTCAGTCA
1 GGTCGGGTCAGTCAGTCA
* *
3487413 GGTCGGGTCGGTCAGTCG
1 GGTCGGGTCAGTCAGTCA
3487431 GGTC
1 GGTC
3487435 TAATCGGGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.10, C:0.23, G:0.45, T:0.23
Consensus pattern (18 bp):
GGTCGGGTCAGTCAGTCA
Found at i:3489325 original size:30 final size:30
Alignment explanation
Indices: 3489291--3489354 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
3489281 CAAATGTGTG
3489291 GTCTGCGTTACCAAAAAATTGAGTTCAGGA
1 GTCTGCGTTACCAAAAAATTGAGTTCAGGA
*
3489321 GTCTGCGTTACCAAAAAGTTGAGTTCAGGA
1 GTCTGCGTTACCAAAAAATTGAGTTCAGGA
3489351 GTCT
1 GTCT
3489355 AATACTGAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (30 bp):
GTCTGCGTTACCAAAAAATTGAGTTCAGGA
Found at i:3490590 original size:18 final size:17
Alignment explanation
Indices: 3490564--3490614 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
3490554 ATGATGAACA
*
3490564 ATTTTTTTTTAAAAATAT
1 ATTTATTTTTAAAAA-AT
3490582 ATTTA-TTTTAAAAAAT
1 ATTTATTTTTAAAAAAT
*
3490598 ATTACATTTTTAAAAAA
1 ATT-TATTTTTAAAAAA
3490615 ATCAACGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 5 0.17
17 10 0.34
18 14 0.48
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTATTTTTAAAAAAT
Found at i:3490606 original size:17 final size:17
Alignment explanation
Indices: 3490569--3490614 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
3490559 GAACAATTTT
*
3490569 TTTTTAAAAATATATTTA
1 TTTTTAAAAA-ATATTCA
3490587 -TTTTAAAAAATATTACA
1 TTTTTAAAAAATATT-CA
3490604 TTTTTAAAAAA
1 TTTTTAAAAAA
3490615 ATCAACGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 5 0.20
17 10 0.40
18 10 0.40
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTTAAAAAATATTCA
Found at i:3490730 original size:213 final size:208
Alignment explanation
Indices: 3490353--3490773 Score: 788
Period size: 213 Copynumber: 2.0 Consensus size: 208
3490343 ACTTTTTGGT
*
3490353 ACAATTTTTTTTAAATATATTTATTTTAATAAATATTACATTTTAAAAAATCAACGATTGAAGAA
1 ACAATTTTTTTTAAATATATTTATTTTAAAAAATATTACATTTTAAAAAATCAACGATTGAAGAA
3490418 CACTCAAATGTACCTGTTGATGTTATTTAAGGTTATAAAAATTTTGCAAGTATGAGATTGATTAG
66 CACTCAAATGTACCTGTTGATGTTATTTAAGGTTATAAAAATTTTGCAAGTATGAGATTGATTAG
3490483 TCACATTATATGAAAGTAAAGTTTATCGTTATTATTATCTGTGTTGTTTTTCGTTGCAGACCATT
131 TCACATTATATGAAAGTAAAGTTTATCGTTATTATTATCTGTGTTGTTTTTCGTTGCAGACCATT
3490548 TCATTAATGATGA
196 TCATTAATGATGA
3490561 ACAATTTTTTTTTAAAAATATATTTATTTTAAAAAATATTACATTTTTAAAAAAATCAACGATTG
1 ACAA-TTTTTTTT--AAATATATTTATTTTAAAAAATATTACA-TTTT-AAAAAATCAACGATTG
3490626 AAGAACACTCAAATGTACCTGTTGATGTTATTTAAGGTTATAAAAATTTTGCAAGTATGAGATTG
61 AAGAACACTCAAATGTACCTGTTGATGTTATTTAAGGTTATAAAAATTTTGCAAGTATGAGATTG
3490691 ATTAGTCACATTATATGAAAGTAAAGTTTATCGTTATTATTATCTGTGTTGTTTTTCGTTGCAGA
126 ATTAGTCACATTATATGAAAGTAAAGTTTATCGTTATTATTATCTGTGTTGTTTTTCGTTGCAGA
3490756 CCATTTCATTAATGATGA
191 CCATTTCATTAATGATGA
3490774 TGCCTTCAAA
Statistics
Matches: 207, Mismatches: 1, Indels: 5
0.97 0.00 0.02
Matches are distributed among these distances:
208 4 0.02
209 8 0.04
211 27 0.13
212 4 0.02
213 164 0.79
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.42
Consensus pattern (208 bp):
ACAATTTTTTTTAAATATATTTATTTTAAAAAATATTACATTTTAAAAAATCAACGATTGAAGAA
CACTCAAATGTACCTGTTGATGTTATTTAAGGTTATAAAAATTTTGCAAGTATGAGATTGATTAG
TCACATTATATGAAAGTAAAGTTTATCGTTATTATTATCTGTGTTGTTTTTCGTTGCAGACCATT
TCATTAATGATGA
Found at i:3491734 original size:15 final size:16
Alignment explanation
Indices: 3491714--3491747 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
3491704 TATCTTTGAG
3491714 AAAAAGTAAATAAA-A
1 AAAAAGTAAATAAATA
3491729 AAAAAGTAAATAAATA
1 AAAAAGTAAATAAATA
3491745 AAA
1 AAA
3491748 GAGTGTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (16 bp):
AAAAAGTAAATAAATA
Found at i:3493239 original size:3 final size:3
Alignment explanation
Indices: 3493231--3493299 Score: 131
Period size: 3 Copynumber: 23.3 Consensus size: 3
3493221 CTGCAAGATG
3493231 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3493279 TAA -AA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA T
3493300 TTTTAAGCTT
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 63 0.97
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3493501 original size:69 final size:69
Alignment explanation
Indices: 3493420--3493627 Score: 407
Period size: 69 Copynumber: 3.0 Consensus size: 69
3493410 TCATATTTCG
3493420 ATGAATAATTGAGTTTATTGATAATAAATATTTATATTCTTTTCAGTTACTTTTTTTCTTAACAA
1 ATGAATAATTGAGTTTATTGATAATAAATATTTATATTCTTTTCAGTTACTTTTTTTCTTAACAA
3493485 AGAC
66 AGAC
3493489 ATGAATAATTGAGTTTATTGATAATAAATATTTATATTCTTTTCAGTTACTTTTTTTCTTAACAA
1 ATGAATAATTGAGTTTATTGATAATAAATATTTATATTCTTTTCAGTTACTTTTTTTCTTAACAA
3493554 AGAC
66 AGAC
*
3493558 ATGAATAATTGAGTTTATTGATAATAAATATTTATATTCTTTTCAGTTACTTTTTTTCCTAACAA
1 ATGAATAATTGAGTTTATTGATAATAAATATTTATATTCTTTTCAGTTACTTTTTTTCTTAACAA
3493623 AGAC
66 AGAC
3493627 A
1 A
3493628 GTTATTTTAT
Statistics
Matches: 138, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 138 1.00
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.47
Consensus pattern (69 bp):
ATGAATAATTGAGTTTATTGATAATAAATATTTATATTCTTTTCAGTTACTTTTTTTCTTAACAA
AGAC
Found at i:3499174 original size:186 final size:186
Alignment explanation
Indices: 3498847--3499196 Score: 486
Period size: 186 Copynumber: 1.9 Consensus size: 186
3498837 AAAACCTAGC
* * *
3498847 CAATCTCGAGACCATAATTCCAGAAGGCTTTTTCTGGTATCGATACTATGGTGTTGTATTAATAC
1 CAATCTCGAGACCAGAATTCCAGAAGGCTTTTTCTGATATCGATACCATGGTGTTGTATTAATAC
*** * * * * *
3498912 TGGAAGGTGAGTATCGATACTTCTTCAAATAGTATCAATATCGAGGCCTCAACGACTATATTTTT
66 TGGAAGGTGAGTATCGATAAACCTTCAAACAATATCAATACCAAGGCCTCAACGACTATATTCTT
* * * *
3498977 GAATTTTTTTCATGTTCGGTCTCTATATCAACTTTCCATTATCGATACCAACATGG
131 GAATATTTTTCATGCTCGGTCTCAATACCAACTTTCCATTATCGATACCAACATGG
* * * *
3499033 CAATCTCGAGACGAGAATTCTAGAAGGCTTTTT-TGATATCGGTACCATGGTGTTGGTATTGATA
1 CAATCTCGAGACCAGAATTCCAGAAGGCTTTTTCTGATATCGATACCATGGTGTT-GTATTAATA
* **
3499097 CTGGAAGGTGAGTATTGATAAACCTTCAAACAATATTGATACCAAGGCCTCAACGACTATATTCT
65 CTGGAAGGTGAGTATCGATAAACCTTCAAACAATATCAATACCAAGGCCTCAACGACTATATTCT
3499162 TGAATATTTTTCATGCTCGGTCTCAATACCAACTT
130 TGAATATTTTTCATGCTCGGTCTCAATACCAACTT
3499197 GTCGGTATCG
Statistics
Matches: 141, Mismatches: 22, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
185 18 0.13
186 123 0.87
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.35
Consensus pattern (186 bp):
CAATCTCGAGACCAGAATTCCAGAAGGCTTTTTCTGATATCGATACCATGGTGTTGTATTAATAC
TGGAAGGTGAGTATCGATAAACCTTCAAACAATATCAATACCAAGGCCTCAACGACTATATTCTT
GAATATTTTTCATGCTCGGTCTCAATACCAACTTTCCATTATCGATACCAACATGG
Found at i:3500290 original size:19 final size:20
Alignment explanation
Indices: 3500268--3500309 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
3500258 GATTTTTTTT
3500268 AAAGCAAAATAG-ATTTTGA
1 AAAGCAAAATAGAATTTTGA
*
3500287 AAAGCAAAATGGAATTTTGA
1 AAAGCAAAATAGAATTTTGA
3500307 AAA
1 AAA
3500310 ATGATTTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.55, C:0.05, G:0.17, T:0.24
Consensus pattern (20 bp):
AAAGCAAAATAGAATTTTGA
Found at i:3501709 original size:21 final size:20
Alignment explanation
Indices: 3501677--3501721 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
3501667 CTGAAACAAA
3501677 TAAAATTAAAATA-ATAAGAT
1 TAAAATTAAAATATATAA-AT
3501697 TAAAATGTAAAATATATAAAT
1 TAAAAT-TAAAATATATAAAT
3501718 TAAA
1 TAAA
3501722 GGCCTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.26
21 13 0.57
22 4 0.17
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.31
Consensus pattern (20 bp):
TAAAATTAAAATATATAAAT
Found at i:3502859 original size:3 final size:3
Alignment explanation
Indices: 3502851--3502926 Score: 70
Period size: 3 Copynumber: 26.0 Consensus size: 3
3502841 TATATTTATT
*
3502851 TAA TAA TAA TAA TAT TAA TAA T-A TAA TAGA -AA TAAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA T-AA TAA TAA TAA
* * *
3502896 T-G TAA TAA AAA TAG TAA TAA TAA -AA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3502927 ATAAAAACTG
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
2 6 0.10
3 49 0.83
4 4 0.07
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:3503345 original size:47 final size:47
Alignment explanation
Indices: 3503285--3503843 Score: 879
Period size: 47 Copynumber: 11.9 Consensus size: 47
3503275 CGAAGGATTT
* * *
3503285 AACAT-CTAGCACTGAAGGTCTTATAGATGACCCGAAGGTTTTTTGAA
1 AACATCCT-GCACTGTAGGTCTTATGGATGACCCGAAGGCTTTTTGAA
* *
3503332 AACATCCTGCACTGAAGGTCTTATGGATGATCCGAAGGCTTTTTGAA
1 AACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGCTTTTTGAA
* *
3503379 AACATCATGCACTGTAGGTCTTATGGATGACCCAAAGGCTTTTTGAA
1 AACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGCTTTTTGAA
* * *
3503426 AACATCCTGCACTGTAGGTCTTATGGATAACTCGAAAGCTTTTTGAA
1 AACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGCTTTTTGAA
*
3503473 AACATCCTGCACTGTAGGTCTTATGGATAACCCGAAGGC-TTTTGAA
1 AACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGCTTTTTGAA
*
3503519 AACATCCTGCACTGTAGGTCTTATGGATGACCCAAAGGCTTTTTGAA
1 AACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGCTTTTTGAA
* *
3503566 AACATCCTGCACTATAGGTCTTATGGATAACCCGAAGGCTTTTTGAA
1 AACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGCTTTTTGAA
* *
3503613 AACATCCTACACTGTAGGTCTTATGGATGACCTGAAGGCTTTTTGAA
1 AACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGCTTTTTGAA
* * * *
3503660 AACATCATGCACTATAGGTCTTATGGATGGCCTGAAGGACTTTTTGAA
1 AACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGG-CTTTTTGAA
3503708 AACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGCTTTTTGAA
1 AACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGCTTTTTGAA
*
3503755 AACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGCTTTTCGAA
1 AACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGCTTTTTGAA
* *
3503802 AACATCCTGCACTGAAGGTCTTATAGATGACCCGAAGGCTTT
1 AACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGCTTT
3503844 AACATCTTGC
Statistics
Matches: 475, Mismatches: 34, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
46 44 0.09
47 386 0.81
48 45 0.09
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (47 bp):
AACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGCTTTTTGAA
Found at i:3503616 original size:187 final size:187
Alignment explanation
Indices: 3503285--3503843 Score: 861
Period size: 187 Copynumber: 3.0 Consensus size: 187
3503275 CGAAGGATTT
* * ** *
3503285 AACAT-CTAGCACTGAAGGTCTTATAGATGACCCGAAGGTTTTTTGAAAACATCCTGCACTGAAG
1 AACATCCT-GCACTGTAGGTCTTATGGATGACCCGAAGGACTTTTGAAAACATCCTGCACTGTAG
* * *
3503349 GTCTTATGGATGATCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTATGGATGACCCAA
65 GTCTTATGGATGACCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGA
* *
3503414 AGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATAACTCGAAAGCTTTTTGAA
130 AGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGAC-CGAAGGCTTTTTGAA
*
3503473 AACATCCTGCACTGTAGGTCTTATGGATAACCCGAAGG-CTTTTGAAAACATCCTGCACTGTAGG
1 AACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGACTTTTGAAAACATCCTGCACTGTAGG
* * *
3503537 TCTTATGGATGACCCAAAGGCTTTTTGAAAACATCCTGCACTATAGGTCTTATGGATAACCCGAA
66 TCTTATGGATGACCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAA
*
3503602 GGCTTTTTGAAAACATCCTACACTGTAGGTCTTATGGATGACCTGAAGGCTTTTTGAA
131 GGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACC-GAAGGCTTTTTGAA
* * * *
3503660 AACATCATGCACTATAGGTCTTATGGATGGCCTGAAGGACTTTTTGAAAACATCCTGCACTGTAG
1 AACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGAC-TTTTGAAAACATCCTGCACTGTAG
3503725 GTCTTATGGATGACCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGA
65 GTCTTATGGATGACCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGA
* * *
3503790 AGGCTTTTCGAAAACATCCTGCACTGAAGGTCTTATAGATGACCCGAAGGCTTT
130 AGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGA-CCGAAGGCTTT
3503844 AACATCTTGC
Statistics
Matches: 340, Mismatches: 26, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
186 1 0.00
187 169 0.50
188 33 0.10
189 135 0.40
190 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (187 bp):
AACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGACTTTTGAAAACATCCTGCACTGTAGG
TCTTATGGATGACCCGAAGGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAA
GGCTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCGAAGGCTTTTTGAA
Found at i:3503909 original size:42 final size:42
Alignment explanation
Indices: 3503802--3503910 Score: 112
Period size: 42 Copynumber: 2.6 Consensus size: 42
3503792 GCTTTTCGAA
* * * * * *
3503802 AACATCCTGCACTGAAGGTCTTATAGATGACCCGAAGGCTTT
1 AACATCATGCACTGAAAGACTTACAAATGACCCGAAGGATTT
* *
3503844 AACATCTTGCACTGAAAGTCTTACAAATGACCCGAAGGATTT
1 AACATCATGCACTGAAAGACTTACAAATGACCCGAAGGATTT
* *
3503886 AAGTATCATGCTCT-AAAGACTTACA
1 AA-CATCATGCACTGAAAGACTTACA
3503911 TATTCAGGAA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
42 49 0.86
43 8 0.14
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (42 bp):
AACATCATGCACTGAAAGACTTACAAATGACCCGAAGGATTT
Found at i:3505039 original size:54 final size:54
Alignment explanation
Indices: 3504975--3505136 Score: 243
Period size: 54 Copynumber: 3.0 Consensus size: 54
3504965 ATAATCACTG
* * *
3504975 GTTCATAAAACATTTGACAACATATTCATCATTTCTTGTGGCTTCTGCCTAGAT
1 GTTCATAAAACATTTGACAACACATTCATCCTTTCTTGTGGCTTCTGCCCAGAT
** *
3505029 GTTTGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCCCAGAT
1 GTTCATAAAACATTTGACAACACATTCATCCTTTCTTGTGGCTTCTGCCCAGAT
* * *
3505083 GTTCATAAAGCATTTGATAATACATTCATCCTTTCTTGTGGCTTCTGCCCAGAT
1 GTTCATAAAACATTTGACAACACATTCATCCTTTCTTGTGGCTTCTGCCCAGAT
3505137 TTCTCAATCA
Statistics
Matches: 96, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 96 1.00
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (54 bp):
GTTCATAAAACATTTGACAACACATTCATCCTTTCTTGTGGCTTCTGCCCAGAT
Found at i:3506152 original size:75 final size:75
Alignment explanation
Indices: 3506009--3506261 Score: 251
Period size: 75 Copynumber: 3.4 Consensus size: 75
3505999 ATAAGATGAT
* * * * * *
3506009 ATGGGCCTTCAACATGCCCCAACATTTGCTAATACAGACGTTCAAAATACGCCAACATTCCTG-A
1 ATGGGCTTTCAACATGCCCCAACATTTGCTGATACAAACATTCAAAATACGTCAATATT-C-GAA
3506073 -TTCTGATTGAA
64 TTTCTGATTGAA
* * * * *
3506084 ATGGGTTTTCAATATGCCCCAACATTTGCTGATAGAAATATTCAAAATGCGTCAATATTCGAATT
1 ATGGGCTTTCAACATGCCCCAACATTTGCTGATACAAACATTCAAAATACGTCAATATTCGAATT
3506149 TCTGATTGAA
66 TCTGATTGAA
* *** * ** * *
3506159 ATTGGCTTTCGGTATGCCCCAGCATTTG-TGGATACAAACATAAACAAATATGTCAATATTCCAA
1 ATGGGCTTTCAACATGCCCCAACATTTGCT-GATACAAACATTCA-AAATACGTCAATATTCGAA
3506223 TTTCTGATTGAA
64 TTTCTGATTGAA
* *
3506235 ATGGGCTTTCAGCATGCCCTAACATTT
1 ATGGGCTTTCAACATGCCCCAACATTT
3506262 TCTTCTTGCT
Statistics
Matches: 146, Mismatches: 28, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
73 1 0.01
74 3 0.02
75 92 0.63
76 50 0.34
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.32
Consensus pattern (75 bp):
ATGGGCTTTCAACATGCCCCAACATTTGCTGATACAAACATTCAAAATACGTCAATATTCGAATT
TCTGATTGAA
Found at i:3508503 original size:72 final size:72
Alignment explanation
Indices: 3508386--3508530 Score: 263
Period size: 72 Copynumber: 2.0 Consensus size: 72
3508376 TATAATAGTA
*
3508386 TAACAGGCTAGCTGAATATTATCCATAAAGCTGGGGCGATTAACCAATTGCTTTAGGGGGACAAC
1 TAACAGGCTAGCTGAATATTATCCATAAAGCTGAGGCGATTAACCAATTGCTTTAGGGGGACAAC
*
3508451 TCCAGCT
66 TCAAGCT
*
3508458 TAACAGGCTAGCTGAATATTATCCATAAAGCTGAGGCGATTAACCAATTGCTTTAGGGGGATAAC
1 TAACAGGCTAGCTGAATATTATCCATAAAGCTGAGGCGATTAACCAATTGCTTTAGGGGGACAAC
3508523 TCAAGCT
66 TCAAGCT
3508530 T
1 T
3508531 TATTGCATAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (72 bp):
TAACAGGCTAGCTGAATATTATCCATAAAGCTGAGGCGATTAACCAATTGCTTTAGGGGGACAAC
TCAAGCT
Found at i:3513713 original size:147 final size:147
Alignment explanation
Indices: 3513546--3513837 Score: 349
Period size: 151 Copynumber: 2.0 Consensus size: 147
3513536 AAAAAATATT
** * *
3513546 AAAATAATTTTTATAAAACT-A-AAGTATATATAT-TTTTAGGGTTTTATAAAT-AGAGTATTTA
1 AAAATAATTTGAATAAAACTAACAACTATATATATATTTT-GGGTTTTATAAATAAG-GAATTTA
* * * * *
3513607 TTTATTTAAAAATATCAGAAAATGACATCTAGTTACTTTAAGACAGCCCCTTTCTTCAATATTAA
64 TTTATTTAAAAATATCAGAAAAGGACATCTAGTTAATTTAAGACA-ACCATTTCCT-AATATTAA
*
3513672 AAAATGAATAAATATTAATAA
127 AAAATAAATAAATATTAATAA
* * *
3513693 AAAATAATTTGAATAAAACTAAAACAACTATATATATATTTTTGTTTTTATAAGTAAGGAATTTA
1 AAAATAATTTGAATAAAACT--AACAACTATATATATATTTTGGGTTTTATAAATAAGGAATTTA
* * * *
3513758 TTTATTTAAAAATATCGGAATAGGACCTCTAGTTAATTTAAGACAACCATTTCCTAATATTTAAA
64 TTTATTTAAAAATATCAGAAAAGGACATCTAGTTAATTTAAGACAACCATTTCCTAATATTAAAA
3513823 AATAAATAAATATTA
129 AATAAATAAATATTA
3513838 TTTAATCAAA
Statistics
Matches: 122, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
147 18 0.15
149 23 0.19
150 8 0.07
151 67 0.55
152 6 0.05
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (147 bp):
AAAATAATTTGAATAAAACTAACAACTATATATATATTTTGGGTTTTATAAATAAGGAATTTATT
TATTTAAAAATATCAGAAAAGGACATCTAGTTAATTTAAGACAACCATTTCCTAATATTAAAAAA
TAAATAAATATTAATAA
Found at i:3514002 original size:21 final size:20
Alignment explanation
Indices: 3513970--3514014 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
3513960 CTGAAACAAA
3513970 TAAAATTAAAATA-ATAAGAT
1 TAAAATTAAAATATATAA-AT
3513990 TAAAATGTAAAATATATAAAT
1 TAAAAT-TAAAATATATAAAT
3514011 TAAA
1 TAAA
3514015 GGCCTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.26
21 13 0.57
22 4 0.17
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.31
Consensus pattern (20 bp):
TAAAATTAAAATATATAAAT
Found at i:3514966 original size:3 final size:3
Alignment explanation
Indices: 3514958--3515059 Score: 95
Period size: 3 Copynumber: 34.3 Consensus size: 3
3514948 TATATTTATT
* * *
3514958 TAA TAA TAA TAAA TAA TAA TAA T-T TAA TAA AAA TTAA TAA TAA AAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
* * *
3515004 T-A TAA TAA TAA TAAA TAA TAA TAA T-G TAA TAA AAA TAG TAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3515048 TAA -AA TAA TAA T
1 TAA TAA TAA TAA T
3515060 TAAAAACTGT
Statistics
Matches: 80, Mismatches: 12, Indels: 14
0.75 0.11 0.13
Matches are distributed among these distances:
2 6 0.08
3 66 0.82
4 8 0.10
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:3514983 original size:24 final size:24
Alignment explanation
Indices: 3514958--3515059 Score: 125
Period size: 24 Copynumber: 4.3 Consensus size: 24
3514948 TATATTTATT
*
3514958 TAATAATAATAAATAATAATAATT
1 TAATAATAATAAATAATAATAATA
* * *
3514982 TAATAAAAATTAATAATAAAAATA
1 TAATAATAATAAATAATAATAATA
*
3515006 TAATAATAATAAATAATAATAATG
1 TAATAATAATAAATAATAATAATA
* * *
3515030 TAATAAAAAT-AGTAATAATAAAA
1 TAATAATAATAAATAATAATAATA
3515053 TAATAAT
1 TAATAAT
3515060 TAAAAACTGT
Statistics
Matches: 65, Mismatches: 13, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
23 16 0.25
24 49 0.75
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (24 bp):
TAATAATAATAAATAATAATAATA
Found at i:3515019 original size:48 final size:47
Alignment explanation
Indices: 3514958--3515059 Score: 161
Period size: 48 Copynumber: 2.1 Consensus size: 47
3514948 TATATTTATT
*
3514958 TAATAATAATAAATAATAATAATTTAATAAAAATTAATAATAA-AAATA
1 TAATAATAATAAATAATAATAATGTAATAAAAA-TAATAATAATAAA-A
*
3515006 TAATAATAATAAATAATAATAATGTAATAAAAATAGTAATAATAAAA
1 TAATAATAATAAATAATAATAATGTAATAAAAATAATAATAATAAAA
3515053 TAATAAT
1 TAATAAT
3515060 TAAAAACTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
47 16 0.31
48 35 0.69
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (47 bp):
TAATAATAATAAATAATAATAATGTAATAAAAATAATAATAATAAAA
Found at i:3516239 original size:6 final size:6
Alignment explanation
Indices: 3516224--3516282 Score: 68
Period size: 6 Copynumber: 10.2 Consensus size: 6
3516214 AGAAACACTA
* * *
3516224 CGATAC CGATAT CGATAT CGATAC CGAT-- CGATAC CGATAC CGATAT
1 CGATAC CGATAC CGATAC CGATAC CGATAC CGATAC CGATAC CGATAC
*
3516270 CGATAC TGATAC C
1 CGATAC CGATAC C
3516283 AACAGTGGCT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
4 4 0.09
6 41 0.91
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (6 bp):
CGATAC
Found at i:3516255 original size:22 final size:22
Alignment explanation
Indices: 3516230--3516282 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
3516220 ACTACGATAC
* *
3516230 CGATATCGATATCGATACCGAT
1 CGATACCGATACCGATACCGAT
*
3516252 CGATACCGATACCGATATCGAT
1 CGATACCGATACCGATACCGAT
3516274 ACTGATACC
1 -C-GATACC
3516283 AACAGTGGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 19 0.73
23 1 0.04
24 6 0.23
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (22 bp):
CGATACCGATACCGATACCGAT
Found at i:3516889 original size:13 final size:14
Alignment explanation
Indices: 3516854--3516917 Score: 56
Period size: 16 Copynumber: 4.2 Consensus size: 14
3516844 AAAATATAAT
3516854 TTTATATTATTTTTAA
1 TTTATA-TA-TTTTAA
3516870 TTTATATATTTTAA
1 TTTATATATTTTAA
*
3516884 TTATATATATATATATA
1 TT-TATATAT-TTTA-A
* *
3516901 TATATATATTTTTA
1 TTTATATATTTTAA
3516915 TTT
1 TTT
3516918 CTCTAAAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
14 11 0.28
15 11 0.28
16 16 0.40
17 2 0.05
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTATATATTTTAA
Found at i:3516890 original size:2 final size:2
Alignment explanation
Indices: 3516885--3516909 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3516875 ATATTTTAAT
3516885 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3516910 TTTTATTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3518756 original size:25 final size:24
Alignment explanation
Indices: 3518710--3518756 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
3518700 AAATTTGTAT
*
3518710 ATATAATTATATTAATAAATTTAA
1 ATATAATTAAATTAATAAATTTAA
*
3518734 ATATAATTTAAATTAATATATTT
1 ATATAA-TTAAATTAATAAATTT
3518757 TTAATTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
ATATAATTAAATTAATAAATTTAA
Found at i:3518798 original size:16 final size:15
Alignment explanation
Indices: 3518779--3518810 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
3518769 TATTATATCT
3518779 AAAAAATATTTTCTTA
1 AAAAAATATTTT-TTA
3518795 AAAAAATATTTTTTA
1 AAAAAATATTTTTTA
3518810 A
1 A
3518811 CAACAATCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (15 bp):
AAAAAATATTTTTTA
Found at i:3521982 original size:23 final size:23
Alignment explanation
Indices: 3521923--3522068 Score: 96
Period size: 23 Copynumber: 6.6 Consensus size: 23
3521913 CTCATCTTAT
3521923 TATATATATATATAATTTTAAAA
1 TATATATATATATAATTTTAAAA
* *
3521946 TATGTATAT-TATATGTTTTAAAA
1 TATATATATATATA-ATTTTAAAA
* * *
3521969 -ATATATATACAT-A-TAT-ATA
1 TATATATATATATAATTTTAAAA
3521988 TATATATATTATATAATTTTAAAA
1 TATATATA-TATATAATTTTAAAA
**
3522012 TATATATAGT-T-T--TTAGAAAA
1 TATATATA-TATATAATTTTAAAA
* *
3522032 TATATAT-TATATAGTTTTGAAA
1 TATATATATATATAATTTTAAAA
*
3522054 TATGTTATATATATA
1 TAT-ATATATATATA
3522069 TATATTACAC
Statistics
Matches: 93, Mismatches: 17, Indels: 25
0.69 0.13 0.19
Matches are distributed among these distances:
18 1 0.01
19 3 0.03
20 23 0.25
21 4 0.04
22 21 0.23
23 24 0.26
24 17 0.18
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.49
Consensus pattern (23 bp):
TATATATATATATAATTTTAAAA
Found at i:3522019 original size:2 final size:2
Alignment explanation
Indices: 3521969--3522002 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
3521959 TGTTTTAAAA
*
3521969 AT AT AT AT AC AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3522003 ATTTTAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3522054 original size:22 final size:21
Alignment explanation
Indices: 3521923--3522064 Score: 73
Period size: 20 Copynumber: 6.6 Consensus size: 21
3521913 CTCATCTTAT
*
3521923 TATATATATATATAATTTTAAAA
1 TATATAT-TATATAGTTTT-AAA
3521946 TATGTATATTATAT-GTTTTAAA
1 TA--TATATTATATAGTTTTAAA
* * * *
3521968 AATATATATACATA-TATATATA
1 TATATAT-TATATAGT-TTTAAA
*
3521990 TATATATTATATAATTTT-AA
1 TATATATTATATAGTTTTAAA
3522010 -A-ATA-TATATAGTTTTTAGAAAA
1 TATATATTATATAG-TTTT---AAA
*
3522032 TATATATTATATAGTTTTGAA
1 TATATATTATATAGTTTTAAA
*
3522053 -ATATGTTATATA
1 TATATATTATATA
3522065 TATATATATT
Statistics
Matches: 93, Mismatches: 12, Indels: 31
0.68 0.09 0.23
Matches are distributed among these distances:
17 6 0.06
18 7 0.08
19 1 0.01
20 17 0.18
21 14 0.15
22 17 0.18
23 7 0.08
24 12 0.13
25 12 0.13
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.49
Consensus pattern (21 bp):
TATATATTATATAGTTTTAAA
Found at i:3522070 original size:35 final size:34
Alignment explanation
Indices: 3522031--3522100 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 34
3522021 TTTTTAGAAA
* *
3522031 ATATATATT-ATATAGTTTTGAAATATGTTATATAT
1 ATATATATTAACATA-TTTTGAAAAATG-TATATAT
3522066 ATATATATTACACATATTTTGAAAAATGTATATAT
1 ATATATATTA-ACATATTTTGAAAAATGTATATAT
3522101 TAAAGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 16 0.52
36 11 0.35
37 4 0.13
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (34 bp):
ATATATATTAACATATTTTGAAAAATGTATATAT
Found at i:3533898 original size:48 final size:48
Alignment explanation
Indices: 3533842--3533939 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
3533832 CCTACCTTAG
3533842 GCCCAACACCTATATAACTTGGTACAAATATCTTGAGATGTTTAATTT
1 GCCCAACACCTATATAACTTGGTACAAATATCTTGAGATGTTTAATTT
3533890 GCCCAACACCTATATAACTTGGTACAAATATCTTGAGATGTTTAATTT
1 GCCCAACACCTATATAACTTGGTACAAATATCTTGAGATGTTTAATTT
3533938 GC
1 GC
3533940 TTGACTTAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (48 bp):
GCCCAACACCTATATAACTTGGTACAAATATCTTGAGATGTTTAATTT
Found at i:3534774 original size:2 final size:2
Alignment explanation
Indices: 3534769--3534793 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3534759 TGTGTGTTTG
3534769 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3534794 TCCTTAGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3537624 original size:225 final size:224
Alignment explanation
Indices: 3537264--3537872 Score: 608
Period size: 225 Copynumber: 2.7 Consensus size: 224
3537254 TTTCTAGTCA
* * * * * *
3537264 AATCTTTTCAAAGACAATCTAAACTCCACGGAGGAGGATATTGGTTTCGAAAACCAACTAAGAAT
1 AATCTTTT-TAAGTCAATCTCAACTCCAAGGAGGAGGATATTGGGTTC-AAAACCAACTCAGAAT
* * ** * **
3537329 CTG--TTGCATTCTATCTTAATTCATTGATGAGGAGCTAGTTTCCAGTTAAGGTTTTCATTCTAG
64 C-GACTT-CATTCTAGCTTAACTCAACGATGAGGAGCTAGTTTCTAGTTAAGGTTTTCAGGCTAG
** * *
3537392 CTTTCAACTTCAAGATGAATGATACTTGACCTTGAAGAACATCAAGAATTAACTAC-ATTTTGTC
127 CTTTCAACTTCAAGATGAATGATACTTGACCCAGAAGAACACCAAGAATTAACTACAATTTAG-C
** * * *
3537456 TTAACTCTGCAGCGAGGAGCCAC-TTTCCATTCG
191 TTAACTCAACAGCGAAGAGCCACTTTTCAATCCG
3537489 AATCTTTTTGAAGTCAATCTCAACTCCAAGGAGGAGGATATTGGGTTCAAAAGCCAACTCAGAAT
1 AATCTTTTT-AAGTCAATCTCAACTCCAAGGAGGAGGATATTGGGTTCAAAA-CCAACTCAGAAT
* * * * *
3537554 CGACTTCATTCTAGCTTAACTAAACGATGAGGAGTTAGTTTCTAGTTGAA-GTTTTTAGGCTCGG
64 CGACTTCATTCTAGCTTAACTCAACGATGAGGAGCTAGTTTCTAGTT-AAGGTTTTCAGGCTAGC
* * * * *
3537618 TTTCAACTTCACGATGAATGATACTTGACCCAGAAGCACACCAAGAATTGATTGCAATTTAGCTT
128 TTTCAACTTCAAGATGAATGATACTTGACCCAGAAGAACACCAAGAATTAACTACAATTTAGCTT
* * *
3537683 AACTCAACGGTGAAGAGCCACTTTTTAATCCG
193 AACTCAACAGCGAAGAGCCACTTTTCAATCCG
* * * *
3537715 ATAT-TTTTTAAGTCAATCTCAACTCC-ATGA-CACTGATATTGGGTTTGAAAACCAACTCAGAA
1 A-ATCTTTTTAAGTCAATCTCAACTCCAAGGAGGA-GGATATTGGG-TTCAAAACCAACTCAGAA
* * * * * *
3537777 TTGACTTCATTCTAGCTTAACTCAACAACGAGGAGCTAGTTTCTAGTTAAAGCTTTCAGGACAAG
63 TCGACTTCATTCTAGCTTAACTCAACGATGAGGAGCTAGTTTCTAGTTAAGGTTTTCAGG-CTAG
* *
3537842 -TTTTAACTT-AATGATGAAGGATACTTGACCC
127 CTTTCAACTTCAA-GATGAATGATACTTGACCC
3537873 TAAAGCACAT
Statistics
Matches: 320, Mismatches: 51, Indels: 27
0.80 0.13 0.07
Matches are distributed among these distances:
223 4 0.01
224 104 0.32
225 188 0.59
226 22 0.07
227 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (224 bp):
AATCTTTTTAAGTCAATCTCAACTCCAAGGAGGAGGATATTGGGTTCAAAACCAACTCAGAATCG
ACTTCATTCTAGCTTAACTCAACGATGAGGAGCTAGTTTCTAGTTAAGGTTTTCAGGCTAGCTTT
CAACTTCAAGATGAATGATACTTGACCCAGAAGAACACCAAGAATTAACTACAATTTAGCTTAAC
TCAACAGCGAAGAGCCACTTTTCAATCCG
Found at i:3537979 original size:224 final size:222
Alignment explanation
Indices: 3537493--3538035 Score: 501
Period size: 224 Copynumber: 2.4 Consensus size: 222
3537483 CATTCGAATC
* * *
3537493 TTTTTGAAGTCAATCTCAACTCCAAGGAGGAGGATATTGGG-TTCAAAAGCCAACTCAGAATCGA
1 TTTTTAAAGTCAATCTCAACTCC-A--TGGAGGATATTGGGTTTCAAAA-CCAACTCAGAATTGA
* * * * * * * **
3537557 CTTCATTCTAGCTTAACTAAACGATGAGGAGTTAGTTTCTAGTTGAAGTTTTTAGGCTCGGTTTC
62 CTTCATTCTAGCTTAACTCAACAACGAGGAGCTAGTTTCTAGTTAAAGCTTTCAGGCTAAGTTTC
* * * *
3537622 AACTTCACGATGAATGATACTTGACCCAGAAGCACACCAAGAATTGATTGCAATTTAGCTTAACT
127 AACTTAACGATGAAGGATACTTGACCCAGAAGCACACCAAGAACTGACTGCAATTTAGCTTAACT
*** * * * *
3537687 CAACGGTGAAGAGCCACTTTTTAATCCGATA
192 CAACGAAAAAGAGCCACTCTTCAAGCCGAAA
* * * *
3537718 TTTTTTAAGTCAATCTCAACTCCATGACACTGATATTGGGTTTGAAAACCAACTCAGAATTGACT
1 TTTTTAAAGTCAATCTCAACTCCATG-GA-GGATATTGGGTTTCAAAACCAACTCAGAATTGACT
*
3537783 TCATTCTAGCTTAACTCAACAACGAGGAGCTAGTTTCTAGTTAAAGCTTTCAGGAC-AAGTTTTA
64 TCATTCTAGCTTAACTCAACAACGAGGAGCTAGTTTCTAGTTAAAGCTTTCAGG-CTAAGTTTCA
* *** * * *
3537847 ACTTAATGATGAAGGATACTTGACCCTA-AAGCACATTTAGAACTGACTGTATTTTGGCTTAACT
128 ACTTAACGATGAAGGATACTTGACCC-AGAAGCACACCAAGAACTGACTGCAATTTAGCTTAACT
3537911 CAAC-AAAAAGAGCCAC-CTTCAAGCC-AAA
192 CAACGAAAAAGAGCCACTCTTCAAGCCGAAA
* * * *
3537939 TCTTTTAAAATTCAATTTTAACTCCACATTGGAGGATATTGGGTTCCAAAA-CAGACTCA-AGAT
1 T-TTTT-AAAGTCAATCTCAACT-C-CA-TGGAGGATATTGGGTTTCAAAACCA-ACTCAGA-AT
* * *
3538002 TAACTTCAATT-TAGCTTAGCTCAACCACGAGGAG
59 TGACTTC-ATTCTAGCTTAACTCAACAACGAGGAG
3538036 TTACTTCCTA
Statistics
Matches: 260, Mismatches: 45, Indels: 27
0.78 0.14 0.08
Matches are distributed among these distances:
221 3 0.01
222 11 0.04
223 25 0.10
224 183 0.70
225 36 0.14
226 2 0.01
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (222 bp):
TTTTTAAAGTCAATCTCAACTCCATGGAGGATATTGGGTTTCAAAACCAACTCAGAATTGACTTC
ATTCTAGCTTAACTCAACAACGAGGAGCTAGTTTCTAGTTAAAGCTTTCAGGCTAAGTTTCAACT
TAACGATGAAGGATACTTGACCCAGAAGCACACCAAGAACTGACTGCAATTTAGCTTAACTCAAC
GAAAAAGAGCCACTCTTCAAGCCGAAA
Found at i:3538380 original size:24 final size:23
Alignment explanation
Indices: 3538337--3538386 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
3538327 CTTATTATTT
*
3538337 TATATATATAGTTTTGAAATATG
1 TATATATATAGTTTTAAAATATG
*
3538360 TATAT-TATATGTTTTAAAA-ATA
1 TATATATATA-GTTTTAAAATATG
3538382 TATAT
1 TATAT
3538387 GCACATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (23 bp):
TATATATATAGTTTTAAAATATG
Found at i:3538385 original size:22 final size:22
Alignment explanation
Indices: 3538337--3538386 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
3538327 CTTATTATTT
*
3538337 TATATA-TATAGTTTTGAAATA
1 TATATATTATAGTTTTGAAAAA
*
3538358 TGTATATTATATGTTTT-AAAAA
1 TATATATTATA-GTTTTGAAAAA
3538380 TATATAT
1 TATATAT
3538387 GCACATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 5 0.21
22 14 0.58
23 5 0.21
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (22 bp):
TATATATTATAGTTTTGAAAAA
Found at i:3541565 original size:20 final size:20
Alignment explanation
Indices: 3541540--3541586 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
3541530 CAATCGGCAA
3541540 CGATACCGAAAGGGGAA-TAT
1 CGATACCGAAA-GGGAAGTAT
3541560 CGATA-CGAAAGGGAAGGTAT
1 CGATACCGAAAGGGAA-GTAT
3541580 CGATACC
1 CGATACC
3541587 ATTTAAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 5 0.21
19 5 0.21
20 13 0.54
21 1 0.04
ACGTcount: A:0.38, C:0.17, G:0.30, T:0.15
Consensus pattern (20 bp):
CGATACCGAAAGGGAAGTAT
Found at i:3541633 original size:19 final size:20
Alignment explanation
Indices: 3541609--3541681 Score: 60
Period size: 19 Copynumber: 3.6 Consensus size: 20
3541599 AGGAAAAAAT
3541609 GGTATCAATACCATAATA-G
1 GGTATCAATACCATAATAGG
**
3541628 GGTATCAGA-ACCATTGTATGG
1 GGTATCA-ATACCATAATA-GG
* * *
3541649 TAGTATCGATACCATGATAGG
1 -GGTATCAATACCATAATAGG
3541670 GGTATCAATACC
1 GGTATCAATACC
3541682 GAGGAGCCAA
Statistics
Matches: 41, Mismatches: 8, Indels: 9
0.71 0.14 0.16
Matches are distributed among these distances:
19 14 0.34
20 11 0.27
21 4 0.10
22 12 0.29
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.27
Consensus pattern (20 bp):
GGTATCAATACCATAATAGG
Found at i:3542141 original size:47 final size:47
Alignment explanation
Indices: 3542072--3542324 Score: 346
Period size: 47 Copynumber: 5.4 Consensus size: 47
3542062 TAAATCAAAT
* *
3542072 CCATAATTTAAAATGCATGAAAGGATGCATTAAGGCGTGAAATGATG
1 CCATAATTTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* *
3542119 CCATAATTTAAAATGCATGAAAGGATGCATTAAGGCATTAAAGGTTG
1 CCATAATTTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
3542166 CCATAATTTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
1 CCATAATTTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * * *
3542213 CCATAATTTAAAATGCATGAAATGATGGATTAAGGGATGAAAAGATG
1 CCATAATTTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * * * *
3542260 CCATAATTT-AAATGAATGAAATGATGGATTAAGGCATTAAAAGATG
1 CCATAATTTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
** *
3542306 GAAAAATTTTAAAATGCAT
1 CCATAA-TTTAAAATGCAT
3542325 AAATGGTTGT
Statistics
Matches: 187, Mismatches: 17, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
46 37 0.20
47 143 0.76
48 7 0.04
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.26
Consensus pattern (47 bp):
CCATAATTTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
Found at i:3542145 original size:27 final size:27
Alignment explanation
Indices: 3542109--3542239 Score: 110
Period size: 27 Copynumber: 5.4 Consensus size: 27
3542099 CATTAAGGCG
*
3542109 TGAAATGATGCCATAATTTAAAATGCA
1 TGAAAGGATGCCATAATTTAAAATGCA
*
3542136 TGAAAGGATG-C---A-TT--AAGGCA
1 TGAAAGGATGCCATAATTTAAAATGCA
* *
3542156 TTAAAGGTTGCCATAATTTAAAATGCA
1 TGAAAGGATGCCATAATTTAAAATGCA
*
3542183 TGAAAGGATG-C---A-TT--AAGGCA
1 TGAAAGGATGCCATAATTTAAAATGCA
3542203 TGAAAGGATGCCATAATTTAAAATGCA
1 TGAAAGGATGCCATAATTTAAAATGCA
*
3542230 TGAAATGATG
1 TGAAAGGATG
3542240 GATTAAGGGA
Statistics
Matches: 80, Mismatches: 10, Indels: 28
0.68 0.08 0.24
Matches are distributed among these distances:
20 28 0.35
21 2 0.03
22 4 0.05
23 2 0.03
24 2 0.03
25 4 0.05
26 2 0.03
27 36 0.45
ACGTcount: A:0.42, C:0.10, G:0.21, T:0.27
Consensus pattern (27 bp):
TGAAAGGATGCCATAATTTAAAATGCA
Found at i:3542161 original size:20 final size:20
Alignment explanation
Indices: 3542086--3542213 Score: 76
Period size: 20 Copynumber: 5.7 Consensus size: 20
3542076 AATTTAAAAT
3542086 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* * *
3542106 GCGTGAAATGATGCCATAATTTAAAAT
1 GCATGAAAGGATG-C---A-TT--AAG
3542133 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* * *
3542153 GCATTAAAGGTTGCCATAATTTAAAAT
1 GCATGAAAGGATG-C---A-TT--AAG
3542180 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
3542200 GCATGAAAGGATGC
1 GCATGAAAGGATGC
3542214 CATAATTTAA
Statistics
Matches: 82, Mismatches: 12, Indels: 28
0.67 0.10 0.23
Matches are distributed among these distances:
20 40 0.49
21 2 0.02
22 4 0.05
23 2 0.02
24 2 0.02
25 4 0.05
26 2 0.02
27 26 0.32
ACGTcount: A:0.40, C:0.11, G:0.25, T:0.24
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:3547699 original size:20 final size:20
Alignment explanation
Indices: 3547674--3547720 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
3547664 TTAATCAGTT
3547674 TCGATACCGAAAGAGG-A-GTA
1 TCGATACC-AAAG-GGAAGGTA
3547694 TCGATACCAAAGGGAAGGTA
1 TCGATACCAAAGGGAAGGTA
3547714 TCGATAC
1 TCGATAC
3547721 AATTTCAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.08
19 5 0.20
20 18 0.72
ACGTcount: A:0.38, C:0.17, G:0.28, T:0.17
Consensus pattern (20 bp):
TCGATACCAAAGGGAAGGTA
Found at i:3548210 original size:22 final size:23
Alignment explanation
Indices: 3548185--3548238 Score: 56
Period size: 27 Copynumber: 2.2 Consensus size: 23
3548175 GCTCTAAATC
3548185 GAAA-CAATAATTTAAAATGCAT
1 GAAAGCAATAATTTAAAATGCAT
*
3548207 GAAAGGATGCCATAATTTAAAATGCAT
1 G-AA--A-GCAATAATTTAAAATGCAT
3548234 GAAAG
1 GAAAG
3548239 GATGCATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 9
0.72 0.03 0.25
Matches are distributed among these distances:
22 1 0.04
23 3 0.12
24 1 0.04
25 1 0.04
26 2 0.08
27 18 0.69
ACGTcount: A:0.50, C:0.09, G:0.17, T:0.24
Consensus pattern (23 bp):
GAAAGCAATAATTTAAAATGCAT
Found at i:3548229 original size:27 final size:25
Alignment explanation
Indices: 3548194--3548384 Score: 126
Period size: 27 Copynumber: 7.9 Consensus size: 25
3548184 CGAAACAATA
3548194 ATTTAAAATGCATGAAAGGATGCCAT
1 ATTT-AAATGCATGAAAGGATGCCAT
3548220 AATTTAAAATGCATGAAAGGATG-C--
1 -ATTT-AAATGCATGAAAGGATGCCAT
* *
3548244 A-TT-AAGGCATGAAAGGATGACAT
1 ATTTAAATGCATGAAAGGATGCCAT
3548267 GATTTAAAATGCATGAAAGGATG-C--
1 -ATTT-AAATGCATGAAAGGATGCCAT
*
3548291 A-TT-AAGGCATGAAAGGATGCCAT
1 ATTTAAATGCATGAAAGGATGCCAT
* *
3548314 GATTTAAAAAGCATAAAAGGATGCC--
1 -ATTT-AAATGCATGAAAGGATGCCAT
* *
3548339 --TT-AAGGCAAGAAAGGATGCCAT
1 ATTTAAATGCATGAAAGGATGCCAT
3548361 AATTTAAATGCAT-AAATGGATGCC
1 -ATTTAAATGCATGAAA-GGATGCC
3548385 TTAAGGCATG
Statistics
Matches: 133, Mismatches: 10, Indels: 43
0.72 0.05 0.23
Matches are distributed among these distances:
20 45 0.34
21 2 0.02
22 6 0.05
23 2 0.02
24 2 0.02
25 9 0.07
26 14 0.11
27 53 0.40
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.24
Consensus pattern (25 bp):
ATTTAAATGCATGAAAGGATGCCAT
Found at i:3548255 original size:20 final size:20
Alignment explanation
Indices: 3548230--3548310 Score: 90
Period size: 20 Copynumber: 3.7 Consensus size: 20
3548220 AATTTAAAAT
3548230 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
3548250 GCATGAAAGGATGACATGATTTAAAAT
1 GCATGAAAGGATG-C---A-TT--AAG
3548277 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
3548297 GCATGAAAGGATGC
1 GCATGAAAGGATGC
3548311 CATGATTTAA
Statistics
Matches: 52, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
20 29 0.56
21 1 0.02
22 2 0.04
23 1 0.02
24 1 0.02
25 2 0.04
26 1 0.02
27 15 0.29
ACGTcount: A:0.41, C:0.10, G:0.28, T:0.21
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:3548272 original size:47 final size:47
Alignment explanation
Indices: 3548203--3548421 Score: 325
Period size: 47 Copynumber: 4.7 Consensus size: 47
3548193 AATTTAAAAT
3548203 GCATGAAAGGATGCCATAATTTAAAATGCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCCATAATTTAAAATGCATGAAAGGATGCATTAAG
* *
3548250 GCATGAAAGGATGACATGATTTAAAATGCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCCATAATTTAAAATGCATGAAAGGATGCATTAAG
* * * *
3548297 GCATGAAAGGATGCCATGATTTAAAAAGCATAAAAGGATGCCTTAAG
1 GCATGAAAGGATGCCATAATTTAAAATGCATGAAAGGATGCATTAAG
* *
3548344 GCAAGAAAGGATGCCATAATTT-AAATGCAT-AAATGGATGCCTTAAG
1 GCATGAAAGGATGCCATAATTTAAAATGCATGAAA-GGATGCATTAAG
*
3548390 GCATGAAAGGATGCCAAAATTTTAAAATGCAT
1 GCATGAAAGGATGCCATAA-TTTAAAATGCAT
3548422 AAATGGAAGT
Statistics
Matches: 158, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
45 3 0.02
46 36 0.23
47 111 0.70
48 8 0.05
ACGTcount: A:0.42, C:0.11, G:0.23, T:0.23
Consensus pattern (47 bp):
GCATGAAAGGATGCCATAATTTAAAATGCATGAAAGGATGCATTAAG
Found at i:3548401 original size:20 final size:20
Alignment explanation
Indices: 3548230--3548404 Score: 82
Period size: 20 Copynumber: 7.8 Consensus size: 20
3548220 AATTTAAAAT
*
3548230 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCCTTAAG
* *
3548250 GCATGAAAGGATGACATGATTTAAAAT
1 GCATGAAAGGATG-C----CTT--AAG
*
3548277 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCCTTAAG
*
3548297 GCATGAAAGGATGCCATGATTTAAAAA
1 GCATGAAAGGATGCC-----TT--AAG
*
3548324 GCATAAAAGGATGCCTTAAG
1 GCATGAAAGGATGCCTTAAG
* *
3548344 GCAAGAAAGGATGCCATAATTTAAAT
1 GCATGAAAGGATGCC-----TT-AAG
3548370 GCAT-AAATGGATGCCTTAAG
1 GCATGAAA-GGATGCCTTAAG
3548390 GCATGAAAGGATGCC
1 GCATGAAAGGATGCC
3548405 AAAATTTTAA
Statistics
Matches: 120, Mismatches: 13, Indels: 44
0.68 0.07 0.25
Matches are distributed among these distances:
20 57 0.47
21 6 0.05
22 4 0.03
25 9 0.08
26 13 0.11
27 31 0.26
ACGTcount: A:0.41, C:0.12, G:0.25, T:0.22
Consensus pattern (20 bp):
GCATGAAAGGATGCCTTAAG
Found at i:3550705 original size:36 final size:36
Alignment explanation
Indices: 3550652--3550721 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
3550642 TTTCATAGTT
*
3550652 TCTTGATGATGAATTTACATCATTATTTGTACAAAA
1 TCTTGATGACGAATTTACATCATTATTTGTACAAAA
*
3550688 TCTTGATGACGAGTTTACATCATTATTTGTACAA
1 TCTTGATGACGAATTTACATCATTATTTGTACAA
3550722 TCTTCATGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (36 bp):
TCTTGATGACGAATTTACATCATTATTTGTACAAAA
Found at i:3553684 original size:25 final size:25
Alignment explanation
Indices: 3553633--3553686 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
3553623 TCAGAAAAGA
* **
3553633 AAAATATAAAATATAAAAAAATGTT
1 AAAAGATAAAATATAAAAAAAAATT
3553658 AAAAGATAAAATA-AAATAAAAAATT
1 AAAAGATAAAATATAAA-AAAAAATT
3553683 AAAA
1 AAAA
3553687 AAGAAGTGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 3 0.12
25 22 0.88
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (25 bp):
AAAAGATAAAATATAAAAAAAAATT
Found at i:3553734 original size:6 final size:5
Alignment explanation
Indices: 3553700--3553733 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
3553690 AAGTGGGAAA
3553700 AAAAT -AAAT AAAAT AAAAT AAAAT AAAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAAA
3553734 AAATTAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 18 0.67
6 5 0.19
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:3553736 original size:19 final size:19
Alignment explanation
Indices: 3553700--3553742 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
3553690 AAGTGGGAAA
*
3553700 AAAATAAATAAAATAAAAT
1 AAAATAAATAAAAAAAAAT
3553719 AAAATAAA-AATAAAAAAAT
1 AAAATAAATAA-AAAAAAAT
*
3553738 TAAAT
1 AAAAT
3553743 TTAGTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (19 bp):
AAAATAAATAAAAAAAAAT
Found at i:3553915 original size:18 final size:18
Alignment explanation
Indices: 3553894--3553936 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
3553884 GTTGTTTTTA
*
3553894 AAATAAAAGATAAGAAGT
1 AAATAAAAGAAAAGAAGT
* *
3553912 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAAGT
3553930 AAATAAA
1 AAATAAA
3553937 TAATGTAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (18 bp):
AAATAAAAGAAAAGAAGT
Found at i:3555566 original size:270 final size:270
Alignment explanation
Indices: 3555085--3555674 Score: 914
Period size: 270 Copynumber: 2.2 Consensus size: 270
3555075 ATACTTCTTC
3555085 GTGAAGTTGAAATCGT-GAGTGGCTCATTCGTTGTGAAGTTGAGCTTTGAACTAAAAAATCCCGA
1 GTGAAGTTGAAATCGTAG-GTGGCTCATTCGTTGTGAAGTTGAGCTTTGAACTAAAAAATCCCGA
** * * * **
3555149 GCACGATATCCTTCATCGTGAAGTTGAATCCGGGCTCAAAGCATTGGAAAGTCGCTCCTGGATTG
65 GCAAAATATCATTCATCGTGAAGTTGAAACCAGGCTCAAAGCATTGGAAAGTCGCTCCTGGATCA
*
3555214 TCTTCTAGCCCAATATACTTCATCGTGAAGCTGAAATTTGACCTGAAGACTTTGGTATGAAACTG
130 TCTTCTAGCCCAATATACTTCATCGTGAAGCTAAAATTTGACCTGAAGACTTTGGTATGAAACTG
* * * * *
3555279 GTTTTTCATTTTTGTGTTATAGATGAGTCAC-TCTTCGTGAAGTTGGGTCAATCTTTTAGGTACG
195 ATTTTTCATTGTTGTGTTACAGATGACTC-CTTCTTCGTGAAGTTGGATCAATCTTTTAGGTACG
3555343 ATATCCTTCGAT
259 ATATCCTTCGAT
* * * * *
3555355 GTGAAGTTTAAATTGTAGGTGGCTCATTCGTTGTGAAGTTGAACTTTGAACTGAAAAATCCTGAG
1 GTGAAGTTGAAATCGTAGGTGGCTCATTCGTTGTGAAGTTGAGCTTTGAACTAAAAAATCCCGAG
* * *
3555420 CAAAATATCATTCCTTGTGAAGTTGAAACTAGGCTCAAAGCATTGGAAAGTCGCTCCTGGATCAT
66 CAAAATATCATTCATCGTGAAGTTGAAACCAGGCTCAAAGCATTGGAAAGTCGCTCCTGGATCAT
* *
3555485 CTTTTAGCCCAATATACTTCGTCGTGAAGCTAAAATTTGACCTGAAGACTTTGGTATGAAACTGA
131 CTTCTAGCCCAATATACTTCATCGTGAAGCTAAAATTTGACCTGAAGACTTTGGTATGAAACTGA
* *
3555550 TTTTTCATTGTTGTGTTACAGATGACTCCTTCTTCGTGAAGTTGGATCAATGTTTTGGGTACGAT
196 TTTTTCATTGTTGTGTTACAGATGACTCCTTCTTCGTGAAGTTGGATCAATCTTTTAGGTACGAT
*
3555615 ATCCTTCGTT
261 ATCCTTCGAT
3555625 GTGAAGTTGAAATCGTAGGTGGCTCATTCGTTGTGAAGTTGAGCTTTGAA
1 GTGAAGTTGAAATCGTAGGTGGCTCATTCGTTGTGAAGTTGAGCTTTGAA
3555675 TTGGATATCC
Statistics
Matches: 289, Mismatches: 29, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
269 1 0.00
270 287 0.99
271 1 0.00
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.34
Consensus pattern (270 bp):
GTGAAGTTGAAATCGTAGGTGGCTCATTCGTTGTGAAGTTGAGCTTTGAACTAAAAAATCCCGAG
CAAAATATCATTCATCGTGAAGTTGAAACCAGGCTCAAAGCATTGGAAAGTCGCTCCTGGATCAT
CTTCTAGCCCAATATACTTCATCGTGAAGCTAAAATTTGACCTGAAGACTTTGGTATGAAACTGA
TTTTTCATTGTTGTGTTACAGATGACTCCTTCTTCGTGAAGTTGGATCAATCTTTTAGGTACGAT
ATCCTTCGAT
Found at i:3555876 original size:123 final size:122
Alignment explanation
Indices: 3555613--3555877 Score: 282
Period size: 123 Copynumber: 2.1 Consensus size: 122
3555603 TTTGGGTACG
* * * *
3555613 ATATCCTTCGTTGTGAAGTTGAAATCGTAGGTGGCTCATTCGTTGTGAAGTTGAGCTTTGAATTG
1 ATAT-CTTCGCTGTGAAGTTGAAATCGTAGGTGGCTCATTCGCTATGAAGTTGAGCTTCGAATTG
* * ** *
3555678 GATATCCTTCGTTGTGAAGTTGAAATCCAATCTTGTAAATTGAATCACTTTGAGATTA
65 GATATCCTTCGTTATGAAGTTGAAATCCAATCTTGAAAATTGAATCACTTCAACATTA
** * * * * *
3555736 ATATCTTTTTCTATGAAGTTGAGATTG-GGGATGGCTCATTTGCTATGAAGTTGAGCTTCGAATT
1 ATATC-TTCGCTGTGAAGTTGAAATCGTAGG-TGGCTCATTCGCTATGAAGTTGAGCTTCGAATT
* * * * *
3555800 GGATGTCCTTTGTTATGAAGTTGAAATCCAATCTTGAAAATTGCATTAGC-TCAACTTTA
64 GGATATCCTTCGTTATGAAGTTGAAATCCAATCTTGAAAATTGAATCA-CTTCAACATTA
3555859 ATATGCTTCGCTGTGAAGT
1 ATAT-CTTCGCTGTGAAGT
3555878 GGATATTTAC
Statistics
Matches: 114, Mismatches: 24, Indels: 8
0.78 0.16 0.05
Matches are distributed among these distances:
122 3 0.03
123 109 0.96
124 2 0.02
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.38
Consensus pattern (122 bp):
ATATCTTCGCTGTGAAGTTGAAATCGTAGGTGGCTCATTCGCTATGAAGTTGAGCTTCGAATTGG
ATATCCTTCGTTATGAAGTTGAAATCCAATCTTGAAAATTGAATCACTTCAACATTA
Found at i:3556896 original size:6 final size:6
Alignment explanation
Indices: 3556885--3556919 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
3556875 TTCCTTCCCT
*
3556885 TTTTTC TTTTTC TTTTTC TTTTTC TATTT- TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
3556920 AAACGAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:3561288 original size:9 final size:9
Alignment explanation
Indices: 3561274--3561309 Score: 72
Period size: 9 Copynumber: 4.0 Consensus size: 9
3561264 ACAATCAATG
3561274 AATTAGGAA
1 AATTAGGAA
3561283 AATTAGGAA
1 AATTAGGAA
3561292 AATTAGGAA
1 AATTAGGAA
3561301 AATTAGGAA
1 AATTAGGAA
3561310 TTTAAAGACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.22, T:0.22
Consensus pattern (9 bp):
AATTAGGAA
Found at i:3561600 original size:4 final size:4
Alignment explanation
Indices: 3561591--3561616 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3561581 ACAAGTGGGA
3561591 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
3561617 TTGGGGGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:3561830 original size:17 final size:17
Alignment explanation
Indices: 3561810--3561843 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3561800 TTTTTAAAAT
*
3561810 AAAAGATAAGAATTAAA
1 AAAAGAAAAGAATTAAA
*
3561827 AAAAGAAAATAATTAAA
1 AAAAGAAAAGAATTAAA
3561844 TAAATAATCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.18
Consensus pattern (17 bp):
AAAAGAAAAGAATTAAA
Found at i:3563004 original size:119 final size:119
Alignment explanation
Indices: 3562788--3563025 Score: 386
Period size: 119 Copynumber: 2.0 Consensus size: 119
3562778 TCCAACAATC
* * *
3562788 CCCCATATGAATAAAATTGATGGTTCAAAACACTAACTTTATATGGTGATAGATTCTAGGTTTGA
1 CCCCACATGAATAAAATTGATGGTTCAAAACACTAACTTGATATGGTGAGAGATTCTAGGTTTGA
*
3562853 TATTTGCATAAGAGAGGTAGACATCCCTATTTGAACATTCCCTTGTGAAAATAT
66 TATTTGCATAAGAGAGGTAGACATCCCCATTTGAACATTCCCTTGTGAAAATAT
* * * *
3562907 CCCCACATGAATAATATTGATGGTTCAAAACACTGACTTGATATGGTGAGAGATTCTAGTTTTTA
1 CCCCACATGAATAAAATTGATGGTTCAAAACACTAACTTGATATGGTGAGAGATTCTAGGTTTGA
* *
3562972 TATTTGCATAAGATAGGTAGACATCCCCATTTGAACCTTCCCTTGTGAAAATAT
66 TATTTGCATAAGAGAGGTAGACATCCCCATTTGAACATTCCCTTGTGAAAATAT
3563026 GTTTTTAAAT
Statistics
Matches: 109, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
119 109 1.00
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (119 bp):
CCCCACATGAATAAAATTGATGGTTCAAAACACTAACTTGATATGGTGAGAGATTCTAGGTTTGA
TATTTGCATAAGAGAGGTAGACATCCCCATTTGAACATTCCCTTGTGAAAATAT
Found at i:3563567 original size:141 final size:142
Alignment explanation
Indices: 3563297--3563583 Score: 549
Period size: 141 Copynumber: 2.0 Consensus size: 142
3563287 AAGGACTTGG
3563297 GATAAGGACCCTAGTAATCTCAAAAGATTTATGCAAGTAGTTTGTCCAATTGAACCTAGATCTTG
1 GATAAGGACCCTAGTAATCTCAAAAGATTTATGCAAGTAGTTTGTCCAATTGAACCTAGATCTTG
*
3563362 AGATCTACAGTCAACAAAATTGGGTTTTCCTTTACATAACGCCTTAAATATTTATGGGTTTTAGT
66 AGATCTACAGTCAACAAAATTGGGTTTTCCTTTACATAACGCCTTAAATATTTATAGGTTTTAGT
3563427 CATATTCCTTTC
131 CATATTCCTTTC
3563439 GATAAGGACCCTAGT-ATCTCAAAAGATTTATGCAAGTAGTTTGTCCAATTGAACCTAGATCTTG
1 GATAAGGACCCTAGTAATCTCAAAAGATTTATGCAAGTAGTTTGTCCAATTGAACCTAGATCTTG
*
3563503 AGATCTACAGTCAACAAAATTGGGTTTTCCTTTACATAACGCCTTAAATATTTATAGTTTTTAGT
66 AGATCTACAGTCAACAAAATTGGGTTTTCCTTTACATAACGCCTTAAATATTTATAGGTTTTAGT
3563568 CATATTCCTTTC
131 CATATTCCTTTC
3563580 GATA
1 GATA
3563584 TTTTATCAAA
Statistics
Matches: 143, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
141 128 0.90
142 15 0.10
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.36
Consensus pattern (142 bp):
GATAAGGACCCTAGTAATCTCAAAAGATTTATGCAAGTAGTTTGTCCAATTGAACCTAGATCTTG
AGATCTACAGTCAACAAAATTGGGTTTTCCTTTACATAACGCCTTAAATATTTATAGGTTTTAGT
CATATTCCTTTC
Found at i:3566695 original size:94 final size:93
Alignment explanation
Indices: 3566532--3566707 Score: 225
Period size: 94 Copynumber: 1.9 Consensus size: 93
3566522 CAAGGGTAAA
*
3566532 TATCGATACCATGAATCCAGAATGTCAAAATAGTATCGATACTAAAGGGAGTAACGGTACCATAG
1 TATCGATACCATGAATCCAGAATATCAAAATAGTATCGATACTAAAGGGAGTAACGGTACCATAG
*
3566597 TATAGTAGTATAGATACTGAAAGAAAGG
66 TATAGAAGTATAGATACTGAAAGAAAGG
* **
3566625 TATCGATACCATGCAA-CACAGAATAT-AGAAATGGTATCGATACTGAGAAGGG-GTATTGGTAC
1 TATCGATACCATG-AATC-CAGAATATCA-AAATAGTATCGATACT-A-AAGGGAGTAACGGTAC
*
3566687 CATA-TATAGAAGTATCGATAC
61 CATAGTATAGAAGTATAGATAC
3566708 CAGGGTAGTA
Statistics
Matches: 72, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
93 15 0.21
94 39 0.54
95 13 0.18
96 5 0.07
ACGTcount: A:0.40, C:0.14, G:0.22, T:0.24
Consensus pattern (93 bp):
TATCGATACCATGAATCCAGAATATCAAAATAGTATCGATACTAAAGGGAGTAACGGTACCATAG
TATAGAAGTATAGATACTGAAAGAAAGG
Found at i:3567203 original size:46 final size:46
Alignment explanation
Indices: 3567142--3567475 Score: 533
Period size: 46 Copynumber: 7.3 Consensus size: 46
3567132 ATTAAAATGG
*
3567142 ATGAAAGGATACCATAACTAAAATGCATGAAATGATGCATTAAGGC
1 ATGAAAGGATGCCATAACTAAAATGCATGAAATGATGCATTAAGGC
*
3567188 ATGAAATGATGCCATAACTAAAATGCATGAAATGATGCATTAAGGC
1 ATGAAAGGATGCCATAACTAAAATGCATGAAATGATGCATTAAGGC
* * * *
3567234 ATGAAAGGATTCCATAAATAAAATGCATGAAAGGATGCATTAAGGA
1 ATGAAAGGATGCCATAACTAAAATGCATGAAATGATGCATTAAGGC
*
3567280 ATGAAAGGATGCCATAACTAAAATGCATGAAATGATGCATTAATGC
1 ATGAAAGGATGCCATAACTAAAATGCATGAAATGATGCATTAAGGC
* * *
3567326 ATGAAAAGATGCCATAACTAAAATGCATGAATTGATGGATTAAGGC
1 ATGAAAGGATGCCATAACTAAAATGCATGAAATGATGCATTAAGGC
* * *
3567372 ATGAAAGGATGACATAACTAAAATGCATGAAAGGATCCATTAAGGC
1 ATGAAAGGATGCCATAACTAAAATGCATGAAATGATGCATTAAGGC
* *
3567418 ATGAAAAGATGCCATAACTAAAATGCATGAAAGGATGCATTAAGGC
1 ATGAAAGGATGCCATAACTAAAATGCATGAAATGATGCATTAAGGC
3567464 ATGAAAGGATGC
1 ATGAAAGGATGC
3567476 TTTAAGGCAT
Statistics
Matches: 262, Mismatches: 26, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 262 1.00
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.22
Consensus pattern (46 bp):
ATGAAAGGATGCCATAACTAAAATGCATGAAATGATGCATTAAGGC
Found at i:3567490 original size:20 final size:20
Alignment explanation
Indices: 3567166--3567492 Score: 150
Period size: 20 Copynumber: 14.6 Consensus size: 20
3567156 TAACTAAAAT
*
3567166 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
3567186 GCATGAAATGATGCCATAACTAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
*
3567212 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
3567232 GCATGAAAGGATTCCATAAATAAAAT
1 GCATGAAAGGA-TGCAT---T--AAG
3567258 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
3567278 GAATGAAAGGATGCCATAACTAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
* *
3567304 GCATGAAATGATGCATTAAT
1 GCATGAAAGGATGCATTAAG
* *
3567324 GCATGAAAAGATGCCATAACTAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
** *
3567350 GCATGAATTGATGGATTAAG
1 GCATGAAAGGATGCATTAAG
*
3567370 GCATGAAAGGATGACATAACTAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
*
3567396 GCATGAAAGGATCCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
3567416 GCATGAAAAGATGCCATAACTAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
3567442 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
3567462 GCATGAAAGGATGCTTTAAG
1 GCATGAAAGGATGCATTAAG
3567482 GCATGAAAGGA
1 GCATGAAAGGA
3567493 GGCCATAAAT
Statistics
Matches: 243, Mismatches: 28, Indels: 72
0.71 0.08 0.21
Matches are distributed among these distances:
20 112 0.46
21 18 0.07
22 6 0.02
24 6 0.02
25 18 0.07
26 83 0.34
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.22
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:3574330 original size:26 final size:25
Alignment explanation
Indices: 3574294--3574507 Score: 147
Period size: 26 Copynumber: 9.0 Consensus size: 25
3574284 TGCATTAAGA
3574294 CATGAAAGGATGACATAACTAAAATG
1 CATGAAAGGATG-CATAACTAAAATG
* *
3574320 CATGAAAGGATG--T-A-T-TAAGG
1 CATGAAAGGATGCATAACTAAAATG
*
3574340 CATGAAAAGATGTCATAACTAAAATG
1 CATGAAAGGATG-CATAACTAAAATG
*
3574366 CATGAAAGGATTCCATAACTAAAATG
1 CATGAAAGGA-TGCATAACTAAAATG
* *
3574392 CATGAAAGGATG--T-A-T-TAAGG
1 CATGAAAGGATGCATAACTAAAATG
3574412 CATGAAA-GATGCCATAACTAAAATG
1 CATGAAAGGATG-CATAACTAAAATG
* *
3574437 CATGAAAGGATG--T-A-T-TAAGG
1 CATGAAAGGATGCATAACTAAAATG
*
3574457 CATGAAAAGATGCCATAACTAAAAT-
1 CATGAAAGGATG-CATAACTAAAATG
* *
3574482 CAATGAAAGGAGGCCATAACTGAAAT
1 C-ATGAAAGGATG-CATAACTAAAAT
3574508 TAAAGAATAA
Statistics
Matches: 147, Mismatches: 20, Indels: 42
0.70 0.10 0.20
Matches are distributed among these distances:
19 4 0.03
20 38 0.26
21 3 0.02
22 4 0.03
23 6 0.04
24 3 0.02
25 14 0.10
26 74 0.50
27 1 0.01
ACGTcount: A:0.46, C:0.12, G:0.21, T:0.21
Consensus pattern (25 bp):
CATGAAAGGATGCATAACTAAAATG
Found at i:3574374 original size:46 final size:46
Alignment explanation
Indices: 3574201--3574376 Score: 253
Period size: 46 Copynumber: 3.8 Consensus size: 46
3574191 TAATTAAAAT
* * *
3574201 GCATGAAAGGGTGCCATAATTAAAATGCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAG
* * *
3574247 GCATTAAAGGATGCCATAACTAAAATGCATTAAAGAATGCATTAAG
1 GCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAG
* * *
3574293 ACATGAAAGGATGACATAACTAAAATGCATGAAAGGATGTATTAAG
1 GCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAG
* *
3574339 GCATGAAAAGATGTCATAACTAAAATGCATGAAAGGAT
1 GCATGAAAGGATGCCATAACTAAAATGCATGAAAGGAT
3574377 TCCATAACTA
Statistics
Matches: 115, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 115 1.00
ACGTcount: A:0.45, C:0.11, G:0.21, T:0.23
Consensus pattern (46 bp):
GCATGAAAGGATGCCATAACTAAAATGCATGAAAGGATGCATTAAG
Found at i:3574383 original size:72 final size:71
Alignment explanation
Indices: 3574294--3574448 Score: 274
Period size: 72 Copynumber: 2.2 Consensus size: 71
3574284 TGCATTAAGA
*
3574294 CATGAAAGGATGACATAACTAAAATGCATGAAAGGATGTATTAAGGCATGAAAAGATGTCATAAC
1 CATGAAAGGATGACATAACTAAAATGCATGAAAGGATGTATTAAGGCATG-AAAGATGCCATAAC
3574359 TAAAATG
65 TAAAATG
**
3574366 CATGAAAGGATTCCATAACTAAAATGCATGAAAGGATGTATTAAGGCATGAAAGATGCCATAACT
1 CATGAAAGGATGACATAACTAAAATGCATGAAAGGATGTATTAAGGCATGAAAGATGCCATAACT
3574431 AAAATG
66 AAAATG
3574437 CATGAAAGGATG
1 CATGAAAGGATG
3574449 TATTAAGGCA
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
71 31 0.39
72 48 0.61
ACGTcount: A:0.46, C:0.11, G:0.21, T:0.22
Consensus pattern (71 bp):
CATGAAAGGATGACATAACTAAAATGCATGAAAGGATGTATTAAGGCATGAAAGATGCCATAACT
AAAATG
Found at i:3574416 original size:20 final size:20
Alignment explanation
Indices: 3574391--3574468 Score: 68
Period size: 20 Copynumber: 3.6 Consensus size: 20
3574381 TAACTAAAAT
3574391 GCATGAAAGGATGTATTAAG
1 GCATGAAAGGATGTATTAAG
* *
3574411 GCATGAAA-GATGCCATAACTAAAAT
1 GCATGAAAGGATG---T-A-T-TAAG
3574436 GCATGAAAGGATGTATTAAG
1 GCATGAAAGGATGTATTAAG
*
3574456 GCATGAAAAGATG
1 GCATGAAAGGATG
3574469 CCATAACTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 14
0.71 0.08 0.22
Matches are distributed among these distances:
19 4 0.09
20 22 0.48
21 1 0.02
22 2 0.04
23 2 0.04
24 1 0.02
25 10 0.22
26 4 0.09
ACGTcount: A:0.44, C:0.09, G:0.26, T:0.22
Consensus pattern (20 bp):
GCATGAAAGGATGTATTAAG
Found at i:3574431 original size:45 final size:45
Alignment explanation
Indices: 3574365--3574492 Score: 213
Period size: 45 Copynumber: 2.8 Consensus size: 45
3574355 TAACTAAAAT
*
3574365 GCATGAAAGGATTCCATAACTAAAATGCATGAAAGGATGTATTAAG
1 GCATGAAA-GATGCCATAACTAAAATGCATGAAAGGATGTATTAAG
3574411 GCATGAAAGATGCCATAACTAAAATGCATGAAAGGATGTATTAAG
1 GCATGAAAGATGCCATAACTAAAATGCATGAAAGGATGTATTAAG
3574456 GCATGAAAAGATGCCATAACTAAAAT-CAATGAAAGGA
1 GCATG-AAAGATGCCATAACTAAAATGC-ATGAAAGGA
3574493 GGCCATAACT
Statistics
Matches: 79, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
45 42 0.53
46 37 0.47
ACGTcount: A:0.46, C:0.12, G:0.21, T:0.21
Consensus pattern (45 bp):
GCATGAAAGATGCCATAACTAAAATGCATGAAAGGATGTATTAAG
Found at i:3574461 original size:117 final size:118
Alignment explanation
Indices: 3574247--3574507 Score: 409
Period size: 117 Copynumber: 2.2 Consensus size: 118
3574237 ATGCATTAAG
* *
3574247 GCATTAAAGGATGCCATAACTAAAATGCATTAAAGAATGCATTAAGACATGAAAGGATGACATAA
1 GCATGAAAGGATGCCATAACTAAAATGCATGAAAGAATGCATTAAGACATGAAAGGATGACATAA
*
3574312 CTAAAATGCATGAAAGGATGTATTAAGGCATGAAAAGATGTCATAACTAAAAT
66 CTAAAATGCATGAAAGGATGTATTAAGGCATGAAAAGATGCCATAACTAAAAT
* * * * *
3574365 GCATGAAAGGATTCCATAACTAAAATGCATGAAAGGATGTATTAAGGCATGAAA-GATGCCATAA
1 GCATGAAAGGATGCCATAACTAAAATGCATGAAAGAATGCATTAAGACATGAAAGGATGACATAA
3574429 CTAAAATGCATGAAAGGATGTATTAAGGCATGAAAAGATGCCATAACTAAAAT
66 CTAAAATGCATGAAAGGATGTATTAAGGCATGAAAAGATGCCATAACTAAAAT
* *
3574482 -CAATGAAAGGAGGCCATAACTGAAAT
1 GC-ATGAAAGGATGCCATAACTAAAAT
3574508 TAAAGAATAA
Statistics
Matches: 131, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
116 1 0.01
117 82 0.63
118 48 0.37
ACGTcount: A:0.46, C:0.12, G:0.20, T:0.22
Consensus pattern (118 bp):
GCATGAAAGGATGCCATAACTAAAATGCATGAAAGAATGCATTAAGACATGAAAGGATGACATAA
CTAAAATGCATGAAAGGATGTATTAAGGCATGAAAAGATGCCATAACTAAAAT
Found at i:3580018 original size:46 final size:46
Alignment explanation
Indices: 3579946--3580571 Score: 815
Period size: 46 Copynumber: 13.3 Consensus size: 46
3579936 TTATTCGTTA
* *
3579946 ATTTCAGTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* *
3579992 ATTTTAGTTACGGCATCTTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
*
3580038 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGGATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * *
3580084 ATTTTAGTTATGTCATCCTTTCATGCCTTAATGTATCGTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * *
3580130 ATTTTAGTTATGGCATCTTTTCATGCATTAATGCATCATTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * *
3580176 ATTTTAGTTATGGCATCCTTTTATTCCTTAATGCATCCTTTCATAC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * * * * * *
3580222 ATTTTATTTATGGAATCCTTTCATACCGTAATGAATCATTTCATGA
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
3580268 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
*
3580314 ATTTTAGTTATGGCATCCTTTCATGCATTTTAGCCATGGCATCCTTTAATGCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGC--CTT----A----AT--------GCATCCTTTCATGC
* *
3580378 ATTTTAGTTCTGGC--CCTTTCATGCCTTAATGCATCTTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
*
3580422 ATTTTAGTTATGCCATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* *
3580468 ATTTTAGTTATGGCATCCTTTCATGACTTAATGCATCCTTTCATGT
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* *
3580514 ATTTTAGTTACGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
1 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
3580560 ATTTTAGTTATG
1 ATTTTAGTTATG
3580572 AATTCATTTT
Statistics
Matches: 508, Mismatches: 52, Indels: 40
0.85 0.09 0.07
Matches are distributed among these distances:
44 25 0.05
46 436 0.86
48 2 0.00
52 3 0.01
56 3 0.01
60 2 0.00
62 10 0.02
64 27 0.05
ACGTcount: A:0.21, C:0.22, G:0.13, T:0.44
Consensus pattern (46 bp):
ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
Found at i:3580315 original size:12 final size:12
Alignment explanation
Indices: 3580298--3580379 Score: 53
Period size: 12 Copynumber: 6.5 Consensus size: 12
3580288 TCATGCCTTA
3580298 ATGCATCCTTTC
1 ATGCATCCTTTC
* *
3580310 ATGCAT-TTTAGTT
1 ATGCATCCTT--TC
3580323 ATGGCATCCTTTC
1 AT-GCATCCTTTC
3580336 ATGCAT--TTTAGCC
1 ATGCATCCTTT---C
*
3580349 ATGGCATCCTTTA
1 AT-GCATCCTTTC
3580362 ATGCATCCTTTC
1 ATGCATCCTTTC
3580374 ATGCAT
1 ATGCAT
3580380 TTTAGTTCTG
Statistics
Matches: 54, Mismatches: 6, Indels: 20
0.68 0.08 0.25
Matches are distributed among these distances:
10 3 0.06
11 2 0.04
12 25 0.46
13 11 0.20
14 8 0.15
15 2 0.04
16 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.13, T:0.41
Consensus pattern (12 bp):
ATGCATCCTTTC
Found at i:3580412 original size:108 final size:109
Alignment explanation
Indices: 3580250--3580447 Score: 326
Period size: 108 Copynumber: 1.8 Consensus size: 109
3580240 TTTCATACCG
3580250 TAATGAATCATTTCATGAATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCA
1 TAATGAATCATTTCATGAATTTTAGTTATGGCA-CCTTTCATGCCTTAATGCATCCTTTCATGCA
*
3580315 TTTTAGTTATGGCATCCTTTCATGCATTTTAGCCATGGCATCCTT
65 TTTTAGTTATGCCATCCTTTCATGCATTTTAGCCATGGCATCCTT
* * * * *
3580360 TAATGCATCCTTTCATGCATTTTAGTTCTGGC-CCTTTCATGCCTTAATGCATCTTTTCATGCAT
1 TAATGAATCATTTCATGAATTTTAGTTATGGCACCTTTCATGCCTTAATGCATCCTTTCATGCAT
3580424 TTTAGTTATGCCATCCTTTCATGC
66 TTTAGTTATGCCATCCTTTCATGC
3580448 CTTAATGCAT
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
108 54 0.66
110 28 0.34
ACGTcount: A:0.21, C:0.23, G:0.13, T:0.43
Consensus pattern (109 bp):
TAATGAATCATTTCATGAATTTTAGTTATGGCACCTTTCATGCCTTAATGCATCCTTTCATGCAT
TTTAGTTATGCCATCCTTTCATGCATTTTAGCCATGGCATCCTT
Found at i:3580419 original size:20 final size:20
Alignment explanation
Indices: 3580392--3580559 Score: 102
Period size: 20 Copynumber: 7.5 Consensus size: 20
3580382 TAGTTCTGGC
3580392 CCTTTCATGCCTTAATGCAT
1 CCTTTCATGCCTTAATGCAT
* *
3580412 CTTTTCATGCATTTTAGTTATGCCAT
1 CCTTTCATGC--CTTA---ATG-CAT
3580438 CCTTTCATGCCTTAATGCAT
1 CCTTTCATGCCTTAATGCAT
*
3580458 CCTTTCATGCATTTTAGTTATGGCAT
1 CCTTTCATGC--CTTA---AT-GCAT
*
3580484 CCTTTCATGACTTAATGCAT
1 CCTTTCATGCCTTAATGCAT
** *
3580504 CCTTTCATGTATTTTAGTTACGGCAT
1 CCTTTCATG--CCTTA---A-TGCAT
3580530 CCTTTCATGCCTTAATGCAT
1 CCTTTCATGCCTTAATGCAT
*
3580550 CATTTCATGC
1 CCTTTCATGC
3580560 ATTTTAGTTA
Statistics
Matches: 116, Mismatches: 14, Indels: 36
0.70 0.08 0.22
Matches are distributed among these distances:
20 48 0.41
21 6 0.05
22 9 0.08
24 9 0.08
25 6 0.05
26 38 0.33
ACGTcount: A:0.20, C:0.24, G:0.12, T:0.43
Consensus pattern (20 bp):
CCTTTCATGCCTTAATGCAT
Found at i:3580426 original size:154 final size:155
Alignment explanation
Indices: 3580203--3580492 Score: 474
Period size: 154 Copynumber: 1.9 Consensus size: 155
3580193 CTTTTATTCC
* *
3580203 TTAATGCATCCTTTCATACATTTTATTTATGGAATCCTTTCATACCGTAATGAATCATTTCATGA
1 TTAATGCATCCTTTCATACATTTTAGTTATGG-ACCCTTTCATACCGTAATGAATCATTTCATGA
*
3580268 ATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGGCATCCT
65 ATTTTAGTTATGCCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGGCATCCT
3580333 TTCATGCATTTTAGCCATGGCATCCT
130 TTCATGCATTTTAGCCATGGCATCCT
* * * * * * *
3580359 TTAATGCATCCTTTCATGCATTTTAGTTCTGG-CCCTTTCATGCCTTAATGCATCTTTTCATGCA
1 TTAATGCATCCTTTCATACATTTTAGTTATGGACCCTTTCATACCGTAATGAATCATTTCATGAA
3580423 TTTTAGTTATGCCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGGCATCCTT
66 TTTTAGTTATGCCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGGCATCCTT
3580488 TCATG
131 TCATG
3580493 ACTTAATGCA
Statistics
Matches: 124, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
154 95 0.77
156 29 0.23
ACGTcount: A:0.21, C:0.22, G:0.12, T:0.44
Consensus pattern (155 bp):
TTAATGCATCCTTTCATACATTTTAGTTATGGACCCTTTCATACCGTAATGAATCATTTCATGAA
TTTTAGTTATGCCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGGCATCCTT
TCATGCATTTTAGCCATGGCATCCT
Found at i:3580441 original size:246 final size:247
Alignment explanation
Indices: 3580111--3580571 Score: 728
Period size: 246 Copynumber: 1.9 Consensus size: 247
3580101 CTTTCATGCC
* * *
3580111 TTAATGTATCGTTTCATGCATTTTAGTTATGGCATCTTTTCATGCATTAATGCATCATTTCATGC
1 TTAATGCATCCTTTCATGCATTTTAGTTATGGCA-CCTTTCATGCATTAATGCATCATTTCATGC
* * * *
3580176 ATTTTAGTTATGGCATCCTTTTATTCCTTAATGCATCCTTTCATACATTTTATTTATGGAATCCT
65 ATTTTAGTTATGCCATCCTTTCATGCCTTAATGCATCCTTTCATACATTTTAGTTATGGAATCCT
*
3580241 TTCAT-ACCGTAATGAATCATTTCATGAATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATC
130 TTCATGA-CGTAATGAATCATTTCATGAATTTTAGTTACGGCATCCTTTCATGCCTTAATGCATC
*
3580305 CTTTCATGCATTTTAGTTATGGCATCCTTTCATGCATTTTAGCCATGGCATCCT
194 ATTTCATGCATTTTAGTTATGGCATCCTTTCATGCATTTTAGCCATGGCATCCT
* * *
3580359 TTAATGCATCCTTTCATGCATTTTAGTTCTGGC-CCTTTCATGCCTTAATGCATCTTTTCATGCA
1 TTAATGCATCCTTTCATGCATTTTAGTTATGGCACCTTTCATGCATTAATGCATCATTTCATGCA
* *
3580423 TTTTAGTTATGCCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGGCATCCTT
66 TTTTAGTTATGCCATCCTTTCATGCCTTAATGCATCCTTTCATACATTTTAGTTATGGAATCCTT
* * * *
3580488 TCATGACTTAATGCATCCTTTCATGTATTTTAGTTACGGCATCCTTTCATGCCTTAATGCATCAT
131 TCATGACGTAATGAATCATTTCATGAATTTTAGTTACGGCATCCTTTCATGCCTTAATGCATCAT
3580553 TTCATGCATTTTAGTTATG
196 TTCATGCATTTTAGTTATG
3580572 AATTCATTTT
Statistics
Matches: 194, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
246 163 0.84
247 1 0.01
248 30 0.15
ACGTcount: A:0.22, C:0.21, G:0.13, T:0.45
Consensus pattern (247 bp):
TTAATGCATCCTTTCATGCATTTTAGTTATGGCACCTTTCATGCATTAATGCATCATTTCATGCA
TTTTAGTTATGCCATCCTTTCATGCCTTAATGCATCCTTTCATACATTTTAGTTATGGAATCCTT
TCATGACGTAATGAATCATTTCATGAATTTTAGTTACGGCATCCTTTCATGCCTTAATGCATCAT
TTCATGCATTTTAGTTATGGCATCCTTTCATGCATTTTAGCCATGGCATCCT
Found at i:3580466 original size:200 final size:201
Alignment explanation
Indices: 3580157--3580539 Score: 597
Period size: 200 Copynumber: 1.9 Consensus size: 201
3580147 TTTTCATGCA
* *
3580157 TTAATGCATCATTTCATGCATTTTAGTTATGGCATCCTTTTATTCCTTAATGCATCCTTTCATAC
1 TTAATGCATCATTTCATGCATTTTAGTTATGGCA-CCTTTCATGCCTTAATGCATCCTTTCATAC
* *
3580222 ATTTTATTTATGGAATCCTTTCATACCGTAATGAATCATTTCATGAATTTTAGTTATGGCATCCT
65 ATTTTAGTTATGCAATCCTTTCATACCGTAATGAATCATTTCATGAATTTTAGTTATGGCATCCT
* *
3580287 TTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCATTTTAGCCATG
130 TTCATGACTTAATGCATCCTTTCATGCATTTTAGTTACGGCATCCTTTCATGCATTTTAGCCATG
3580352 GCATCCT
195 GCATCCT
* * * *
3580359 TTAATGCATCCTTTCATGCATTTTAGTTCTGGC-CCTTTCATGCCTTAATGCATCTTTTCATGCA
1 TTAATGCATCATTTCATGCATTTTAGTTATGGCACCTTTCATGCCTTAATGCATCCTTTCATACA
* * * * * *
3580423 TTTTAGTTATGCCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGGCATCCTT
66 TTTTAGTTATGCAATCCTTTCATACCGTAATGAATCATTTCATGAATTTTAGTTATGGCATCCTT
*
3580488 TCATGACTTAATGCATCCTTTCATGTATTTTAGTTACGGCATCCTTTCATGC
131 TCATGACTTAATGCATCCTTTCATGCATTTTAGTTACGGCATCCTTTCATGC
3580540 CTTAATGCAT
Statistics
Matches: 164, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
200 133 0.81
202 31 0.19
ACGTcount: A:0.21, C:0.22, G:0.12, T:0.44
Consensus pattern (201 bp):
TTAATGCATCATTTCATGCATTTTAGTTATGGCACCTTTCATGCCTTAATGCATCCTTTCATACA
TTTTAGTTATGCAATCCTTTCATACCGTAATGAATCATTTCATGAATTTTAGTTATGGCATCCTT
TCATGACTTAATGCATCCTTTCATGCATTTTAGTTACGGCATCCTTTCATGCATTTTAGCCATGG
CATCCT
Found at i:3582846 original size:2 final size:2
Alignment explanation
Indices: 3582841--3583052 Score: 125
Period size: 2 Copynumber: 111.5 Consensus size: 2
3582831 TCTCAAAAAC
3582841 TA TA TA TA TA TA T- TA TA TA T- TA TA -A TA TA T- TA TGA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
*
3582880 TA -A TT TA T- TA TA TA TA TA -A TA TA TA CTA 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
* * * * * *
3582920 TA TG T- TT TCA GA -A AA CTA TA TA T- TT TCA AA TA TA TA T- TA
1 TA TA TA TA T-A TA TA TA -TA TA TA TA TA T-A TA TA TA TA TA TA
* *
3582959 TA TA -A TA TA TA TGA TA TA TA TA TA TA TA TA TG T- TA -A TA TC
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
3582999 TA CA T- TT TT TA -A AA TA T- TA TA TT 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
3583038 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
3583053 TAAAACTCCA
Statistics
Matches: 169, Mismatches: 18, Indels: 46
0.73 0.08 0.20
Matches are distributed among these distances:
1 17 0.10
2 145 0.86
3 7 0.04
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3582963 original size:65 final size:63
Alignment explanation
Indices: 3582885--3583057 Score: 210
Period size: 65 Copynumber: 2.7 Consensus size: 63
3582875 ATATATAATT
* * * *
3582885 TATTATA-TATATAATATATACTATATATATATATATATGTTTTCAGAAAACTATATATTTTCAA
1 TATTATATTATATAATATATA-TATATATATATATATATATGTT-A-AAAACTACATATTTTAAA
3582949 A
63 A
* * *
3582950 TA-TATATTATATAATATATATGATATATATATATATATATGTTAATATCTACATTTTTTAAAA
1 TATTATATTATATAATATATAT-ATATATATATATATATATGTTAAAAACTACATATTTTAAAA
*
3583013 TATTATATT-TAT-ATATATATATATATATATATATATATATTAAAA
1 TATTATATTATATAATATATATATATATATATATATATATGTTAAAA
3583058 CTCCAAAATA
Statistics
Matches: 96, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
61 23 0.24
62 8 0.08
63 19 0.20
64 12 0.12
65 34 0.35
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (63 bp):
TATTATATTATATAATATATATATATATATATATATATATGTTAAAAACTACATATTTTAAAA
Found at i:3583455 original size:44 final size:44
Alignment explanation
Indices: 3583339--3583456 Score: 121
Period size: 44 Copynumber: 2.7 Consensus size: 44
3583329 TATTTTTTGA
* ** * *
3583339 ACGACTCCCCTTCGTGGGTTTAATAAAAGTGACATATTCTTCGT
1 ACGACTCCCCTTCATGGGTTTAATCCATGTGACATATTCTTCGG
* * ** *
3583383 ATGACTCCCCTTCACGGGTTCGATCCATGTGA-AGTGTTCTTCGG
1 ACGACTCCCCTTCATGGGTTTAATCCATGTGACA-TATTCTTCGG
*
3583427 ACGACTCCCCTTCATGGGTTTAAGCCATGT
1 ACGACTCCCCTTCATGGGTTTAATCCATGT
3583457 TCTTCGGATG
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
43 1 0.02
44 57 0.98
ACGTcount: A:0.20, C:0.26, G:0.21, T:0.32
Consensus pattern (44 bp):
ACGACTCCCCTTCATGGGTTTAATCCATGTGACATATTCTTCGG
Found at i:3583756 original size:42 final size:43
Alignment explanation
Indices: 3583660--3583756 Score: 112
Period size: 42 Copynumber: 2.3 Consensus size: 43
3583650 CCCCTTCAGA
* * *
3583660 AGTTTAAGCC-AGTCTAGATTCTTTATATGACTCCCTTTTGCG
1 AGTTTAAGCCAAGTCTAGATTCTTTAGATGACTCCCATTTACG
* *
3583702 AGTTTAAG-CAAGTCTTGATTCTTTGGATGA-TCCCATTTAC-
1 AGTTTAAGCCAAGTCTAGATTCTTTAGATGACTCCCATTTACG
3583742 AGGTTTAAGCCAAGT
1 A-GTTTAAGCCAAGT
3583757 GAGATTACTC
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
40 1 0.02
41 16 0.34
42 30 0.64
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.38
Consensus pattern (43 bp):
AGTTTAAGCCAAGTCTAGATTCTTTAGATGACTCCCATTTACG
Found at i:3583927 original size:13 final size:13
Alignment explanation
Indices: 3583909--3583934 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3583899 ACGATATTCT
3583909 TCTAGACTTGAAG
1 TCTAGACTTGAAG
3583922 TCTAGACTTGAAG
1 TCTAGACTTGAAG
3583935 ACCTTGGTTA
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:0.23, T:0.31
Consensus pattern (13 bp):
TCTAGACTTGAAG
Found at i:3590527 original size:14 final size:14
Alignment explanation
Indices: 3590502--3590557 Score: 62
Period size: 14 Copynumber: 4.1 Consensus size: 14
3590492 TGTATACTAC
3590502 AATATAT-A-TTAT
1 AATATATAATTTAT
3590514 AATATATAATTTAT
1 AATATATAATTTAT
* *
3590528 TATATATAATGTAT
1 AATATATAATTTAT
*
3590542 ATTATATATATTTAT
1 AATATATA-ATTTAT
3590557 A
1 A
3590558 TATGTTTTCA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
12 7 0.19
13 1 0.03
14 22 0.61
15 6 0.17
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (14 bp):
AATATATAATTTAT
Found at i:3590542 original size:28 final size:26
Alignment explanation
Indices: 3590503--3590560 Score: 73
Period size: 28 Copynumber: 2.2 Consensus size: 26
3590493 GTATACTACA
3590503 ATATATATTATAATATATA-ATTTATT
1 ATATATATTATAATATATATATTTA-T
*
3590529 ATATATAATGTATATTATATATATTTAT
1 ATATAT-AT-TATAATATATATATTTAT
3590557 ATAT
1 ATAT
3590561 GTTTTCAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 6 0.21
27 2 0.07
28 15 0.54
29 5 0.18
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
ATATATATTATAATATATATATTTAT
Found at i:3598304 original size:19 final size:19
Alignment explanation
Indices: 3598269--3598318 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
3598259 GTGGTTGTTA
3598269 TGATTATATGT-TCTATAT
1 TGATTATATGTATCTATAT
3598287 GTGATTATATGTAT-TATAT
1 -TGATTATATGTATCTATAT
* *
3598306 TAATTGTATGTAT
1 TGATTATATGTAT
3598319 GCATGACTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 11 0.39
19 16 0.57
20 1 0.04
ACGTcount: A:0.30, C:0.02, G:0.14, T:0.54
Consensus pattern (19 bp):
TGATTATATGTATCTATAT
Found at i:3599469 original size:18 final size:18
Alignment explanation
Indices: 3599446--3599480 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
3599436 GTTCTTAAGG
3599446 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
3599464 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
3599481 AATATACAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.23, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:3610638 original size:16 final size:16
Alignment explanation
Indices: 3610615--3610653 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3610605 AAATTAAAAA
3610615 AATATATAATAAATAT
1 AATATATAATAAATAT
* * *
3610631 ATTATATATTATATAT
1 AATATATAATAAATAT
3610647 AATATAT
1 AATATAT
3610654 GTACGATGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
AATATATAATAAATAT
Found at i:3611047 original size:2 final size:2
Alignment explanation
Indices: 3611040--3611088 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
3611030 TGAACTCTAT
3611040 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3611082 TA TA TA T
1 TA TA TA T
3611089 GGATTTTATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3611242 original size:2 final size:2
Alignment explanation
Indices: 3611235--3611268 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3611225 CATCTTACAA
3611235 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3611269 TAAAGTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3611334 original size:40 final size:42
Alignment explanation
Indices: 3611282--3611360 Score: 101
Period size: 40 Copynumber: 1.9 Consensus size: 42
3611272 AGTTTTAAGT
* *
3611282 TAAATTATATTTA-AATTATT-AA-TCAATTATTATATAAAAA
1 TAAATTAAATTTATAAATATTCAACTCAATT-TTATATAAAAA
*
3611322 TAAATTAAATTTATAAATATTCAACTTAATTTTATATAA
1 TAAATTAAATTTATAAATATTCAACTCAATTTTATATAA
3611361 TCTAATAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 12 0.36
41 6 0.18
42 10 0.30
43 5 0.15
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (42 bp):
TAAATTAAATTTATAAATATTCAACTCAATTTTATATAAAAA
Found at i:3611420 original size:14 final size:13
Alignment explanation
Indices: 3611403--3611445 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
3611393 TTAACAAAAT
3611403 TAATTTAATGATTA
1 TAATTTAA-GATTA
3611417 TAATTTAA-ATTA
1 TAATTTAAGATTA
*
3611429 TAATATAAAGATTA
1 TAAT-TTAAGATTA
3611443 TAA
1 TAA
3611446 ATAATATAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 8 0.31
13 3 0.12
14 15 0.58
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (13 bp):
TAATTTAAGATTA
Found at i:3614034 original size:96 final size:96
Alignment explanation
Indices: 3613890--3614066 Score: 228
Period size: 96 Copynumber: 1.8 Consensus size: 96
3613880 TAGATTCCTA
* * * * **
3613890 GATCCATAAATCAGGAACAATCATATTTTCCAGTGAAAACAGAAAACCATATAACAGATTTCAAG
1 GATCCATAAATCAAGAACAATCATATTTTCCAGTAAAAACAGAAAACCAAAGAACAGATACCAAG
3613955 TAACCATAGTTCATAAACCAGTAGATTTCAT
66 TAACCATAGTTCATAAACCAGTAGATTTCAT
* * * ** * *
3613986 GATCCATATATCAAGAACTATTATATTTTCCAGTAAAAACAGCTAACCAAAGAACATATACCATG
1 GATCCATAAATCAAGAACAATCATATTTTCCAGTAAAAACAGAAAACCAAAGAACAGATACCAAG
*
3614051 TAGCCATAGTTCATAA
66 TAACCATAGTTCATAA
3614067 GCCAAAAATC
Statistics
Matches: 67, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
96 67 1.00
ACGTcount: A:0.44, C:0.19, G:0.11, T:0.27
Consensus pattern (96 bp):
GATCCATAAATCAAGAACAATCATATTTTCCAGTAAAAACAGAAAACCAAAGAACAGATACCAAG
TAACCATAGTTCATAAACCAGTAGATTTCAT
Found at i:3615555 original size:96 final size:96
Alignment explanation
Indices: 3615375--3615563 Score: 229
Period size: 96 Copynumber: 2.0 Consensus size: 96
3615365 CATTTCAATT
* * * * * *
3615375 AGTAGATTTCTTTATCCATAAATCAGGAACATTCATATTTTCCAGTGGAAACAGAAAACCATATA
1 AGTAGATTTCATGATCCATAAATCAAGAACATTCATATTTTCCAGTGAAAACAGAAAACCAAAGA
**
3615440 ACACATTTCAAGTAACCATAGTTCATAAACA
66 ACACATACCAAGTAACCATAGTTCATAAACA
* *
3615471 AGTAGATTTCATGATCCATATATCAAGAACTATT-ATATTTTCCAGTGAAAACA-AGTAACCAAA
1 AGTAGATTTCATGATCCATAAATCAAGAAC-ATTCATATTTTCCAGTGAAAACAGA-AAACCAAA
* * *
3615534 GAACATATACCATGTAGCCATAGTTCATAA
64 GAACACATACCAAGTAACCATAGTTCATAA
3615564 GCCAGAAATT
Statistics
Matches: 78, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
95 1 0.01
96 74 0.95
97 3 0.04
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (96 bp):
AGTAGATTTCATGATCCATAAATCAAGAACATTCATATTTTCCAGTGAAAACAGAAAACCAAAGA
ACACATACCAAGTAACCATAGTTCATAAACA
Found at i:3620050 original size:96 final size:97
Alignment explanation
Indices: 3619879--3620055 Score: 230
Period size: 96 Copynumber: 1.8 Consensus size: 97
3619869 TAGTTCCCTG
* * * ** *
3619879 ATCCATAAATCAGGGAACAATCATATTTTCCAATGAAAATAGGAAACCAGATAACACATTTCAGG
1 ATCCATAAATCAGGAAACAATAATATTTTCCAATGAAAACAGGAAACCAGATAACACATACCAGA
*
3619944 TAACCGTAGTTCATAAACTAGTAGATTCCATT
66 TAACCATAGTTCATAAACTAGTAGATTCCATT
* * * * *
3619976 ATCCATAAATCA-GAAACTATAATATTTTCCAATGAAAACATGTAACCAGATAACATATACCATA
1 ATCCATAAATCAGGAAACAATAATATTTTCCAATGAAAACAGGAAACCAGATAACACATACCAGA
*
3620040 TAGCCATAGTTCATAA
66 TAACCATAGTTCATAA
3620056 GCCAGACAAT
Statistics
Matches: 67, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
96 55 0.82
97 12 0.18
ACGTcount: A:0.44, C:0.19, G:0.11, T:0.27
Consensus pattern (97 bp):
ATCCATAAATCAGGAAACAATAATATTTTCCAATGAAAACAGGAAACCAGATAACACATACCAGA
TAACCATAGTTCATAAACTAGTAGATTCCATT
Found at i:3629888 original size:3 final size:3
Alignment explanation
Indices: 3629880--3629937 Score: 100
Period size: 3 Copynumber: 19.7 Consensus size: 3
3629870 TACTTATTTA
*
3629880 TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3629927 TAT TAT TAT TA
1 TAT TAT TAT TA
3629938 CTACAAAACA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 50 0.96
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:3630423 original size:3 final size:3
Alignment explanation
Indices: 3630415--3630457 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
3630405 TACTTATTTA
*
3630415 TAT TAT TAT TAT TA- TAT TAC TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3630458 CTACTACTAC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:3630432 original size:20 final size:20
Alignment explanation
Indices: 3630415--3630454 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 20
3630405 TACTTATTTA
3630415 TATTATTATTATTATATTAC
1 TATTATTATTATTATATTAC
3630435 TATTATTATTATTATTATTA
1 TATTATTATTATTA-TATTA
3630455 TTACTACTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTATTATTATTATATTAC
Found at i:3633063 original size:45 final size:47
Alignment explanation
Indices: 3632974--3633063 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 47
3632964 ATAGTATTAC
* * * *
3632974 TTTATTTTCCGAACAAATGTATGCGAACTAGAAATCATGTGGTTAGG
1 TTTATTTTCCAAACAAATGCATGCGAACTAGAAAGCATGAGGTTAGG
3633021 TTTATTTTCCAAACAAA-GCATG-GAACTAGAAAGCATGAGGTTA
1 TTTATTTTCCAAACAAATGCATGCGAACTAGAAAGCATGAGGTTA
3633064 AGATGTATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 19 0.49
46 4 0.10
47 16 0.41
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (47 bp):
TTTATTTTCCAAACAAATGCATGCGAACTAGAAAGCATGAGGTTAGG
Found at i:3645280 original size:42 final size:42
Alignment explanation
Indices: 3645233--3645314 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
3645223 TATAGAGGTG
3645233 TTTTTA-ACTACAAACACCATAAAAGG-TAGGGTTTTTAGTGGT
1 TTTTTAGAC-ACAAACA-CATAAAAGGTTAGGGTTTTTAGTGGT
*
3645275 TTTTTAGACACAAACACGTAAAAGGTTAGGGTTTTTAGTG
1 TTTTTAGACACAAACACATAAAAGGTTAGGGTTTTTAGTG
3645315 ACGGGTTTAG
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
41 8 0.22
42 27 0.73
43 2 0.05
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35
Consensus pattern (42 bp):
TTTTTAGACACAAACACATAAAAGGTTAGGGTTTTTAGTGGT
Done.