Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008756.1 Hibiscus syriacus cultivar Beakdansim tig00111848_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: 4584045
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 21
Found at i:1609290 original size:39 final size:36
Alignment explanation
Indices: 1609213--1609501 Score: 155
Period size: 39 Copynumber: 7.7 Consensus size: 36
1609203 ATATATTATA
* * *
1609213 TTTTCAAAAAT-TATATAATATGTTTTCAAAATAT-G
1 TTTTCAAAACTATATAT-ATACGTTTTCAAAACATCG
1609248 TTTTCAAAACTATATTATATACGTTTTCAAAATCATACG
1 TTTTCAAAACTATA-TATATACGTTTTCAAAA-CAT-CG
* * * **
1609287 TTTTC-AAAGTCATATATTATATGTTTTCAAAACTGTTTT
1 TTTTCAAAACT-ATATA-TATACGTTTTCAAAAC--ATCG
* * * *
1609326 TTTTTAAATCTATATATTATACATTTTCGAAAC--CG
1 TTTTCAAAACTATATA-TATACGTTTTCAAAACATCG
1609361 TTTT-AATAACTATATATTATACGTTTTCAAAACCAT--
1 TTTTCAA-AACTATATA-TATACGTTTTCAAAA-CATCG
* * * **
1609397 TTTTAAAAAACTATATATTATACATTTTCAAAAAAATATA
1 TTTT-CAAAACTATATA-TATACGTTTTC-AAAACAT-CG
*
1609437 TTTTCAAAAACTATATTATATATGTTTTCAAAA-ATACG
1 TTTTC-AAAACTATA-TATATACGTTTTCAAAACAT-CG
*
1609475 TTTTCAAAAACTATATACTTTACGTTT
1 TTTTC-AAAACTATATA-TATACGTTT
1609502 GAACTTATTA
Statistics
Matches: 203, Mismatches: 28, Indels: 43
0.74 0.10 0.16
Matches are distributed among these distances:
34 2 0.01
35 36 0.18
36 20 0.10
37 29 0.14
38 38 0.19
39 50 0.25
40 26 0.13
41 2 0.01
ACGTcount: A:0.39, C:0.11, G:0.04, T:0.45
Consensus pattern (36 bp):
TTTTCAAAACTATATATATACGTTTTCAAAACATCG
Found at i:1609381 original size:35 final size:35
Alignment explanation
Indices: 1609327--1609429 Score: 136
Period size: 35 Copynumber: 2.9 Consensus size: 35
1609317 AACTGTTTTT
* *
1609327 TTTTAAATCTATATATTATACATTTTCGAAACC-G
1 TTTTAAAACTATATATTATACATTTTCAAAACCAG
* *
1609361 TTTTAATAACTATATATTATACGTTTTCAAAACCAT
1 TTTTAA-AACTATATATTATACATTTTCAAAACCAG
1609397 TTTTAAAAAACTATATATTATACATTTTCAAAA
1 TTTT--AAAACTATATATTATACATTTTCAAAA
1609430 AAATATATTT
Statistics
Matches: 60, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
34 6 0.10
35 24 0.40
36 4 0.07
37 24 0.40
38 2 0.03
ACGTcount: A:0.41, C:0.13, G:0.03, T:0.44
Consensus pattern (35 bp):
TTTTAAAACTATATATTATACATTTTCAAAACCAG
Found at i:1611376 original size:30 final size:30
Alignment explanation
Indices: 1611341--1611440 Score: 105
Period size: 30 Copynumber: 3.3 Consensus size: 30
1611331 GGTAACAATA
*
1611341 AAATAAACGAACATGAACACCCTAAAAAAT
1 AAATAAACGAACATGAACACCATAAAAAAT
* * *
1611371 AAATAAACGAACATGAGCACGATATTGAAAAT
1 AAATAAACGAACATGAACACCATA--AAAAAT
* * *
1611403 --TTAAACGAACATGAACACCTTCAAAAAT
1 AAATAAACGAACATGAACACCATAAAAAAT
1611431 AAATAAACGA
1 AAATAAACGA
1611441 TCAGGAAATA
Statistics
Matches: 55, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
28 5 0.09
30 45 0.82
32 5 0.09
ACGTcount: A:0.56, C:0.17, G:0.10, T:0.17
Consensus pattern (30 bp):
AAATAAACGAACATGAACACCATAAAAAAT
Found at i:1612099 original size:2 final size:2
Alignment explanation
Indices: 1612092--1612125 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1612082 ACCTCCTGTT
1612092 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
1612126 ATTGATAGTC
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):
TA
Found at i:1613117 original size:16 final size:16
Alignment explanation
Indices: 1613096--1613126 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1613086 AATTTAAATC
1613096 GAATTTATAAATAGTT
1 GAATTTATAAATAGTT
*
1613112 GAATTTATAACTAGT
1 GAATTTATAAATAGT
1613127 ATGCTCTCCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.03, G:0.13, T:0.42
Consensus pattern (16 bp):
GAATTTATAAATAGTT
Found at i:1613563 original size:7 final size:7
Alignment explanation
Indices: 1613551--1613575 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1613541 TTGTTGTTGA
1613551 AAACCCT
1 AAACCCT
1613558 AAACCCT
1 AAACCCT
1613565 AAACCCT
1 AAACCCT
1613572 AAAC
1 AAAC
1613576 TCTTAATACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.40, G:0.00, T:0.12
Consensus pattern (7 bp):
AAACCCT
Found at i:1613766 original size:7 final size:7
Alignment explanation
Indices: 1613751--1613780 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
1613741 AGGAGAATGG
1613751 TTAGGGT
1 TTAGGGT
*
1613758 TTAGTGT
1 TTAGGGT
1613765 TTAGGGT
1 TTAGGGT
1613772 TTAGGGT
1 TTAGGGT
1613779 TT
1 TT
1613781 TAACAACAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.13, C:0.00, G:0.37, T:0.50
Consensus pattern (7 bp):
TTAGGGT
Found at i:1625997 original size:15 final size:15
Alignment explanation
Indices: 1625950--1625998 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 15
1625940 ATAAGAGATC
1625950 AAAGT-AAATAAGA-G
1 AAAGTAAAATAA-ATG
1625964 AAAGTAAAA-AAATTG
1 AAAGTAAAATAAA-TG
1625979 -AAGTAAAATAAATG
1 AAAGTAAAATAAATG
1625993 AAAGTA
1 AAAGTA
1625999 GAAAATAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
13 1 0.03
14 17 0.57
15 12 0.40
ACGTcount: A:0.65, C:0.00, G:0.16, T:0.18
Consensus pattern (15 bp):
AAAGTAAAATAAATG
Found at i:1631196 original size:47 final size:45
Alignment explanation
Indices: 1631102--1631227 Score: 164
Period size: 47 Copynumber: 2.8 Consensus size: 45
1631092 GTAACCATGC
* * *
1631102 AAATAAGCTTATGAGCTTACGGAAT-AATGGCAAGTATATAGGAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
* * *
1631146 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATAGGAA
*
1631193 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
1631228 AGATTTTATA
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
44 22 0.31
45 11 0.15
46 1 0.01
47 38 0.53
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.29
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
Found at i:1631945 original size:49 final size:49
Alignment explanation
Indices: 1631863--1632346 Score: 475
Period size: 49 Copynumber: 9.9 Consensus size: 49
1631853 ACTGCTTTAA
* * *
1631863 AATGAAAGTTAAATGCCTAACGGTGCATTTTTGGCAGAAAGGTGCCACT
1 AATGCAAGTTAAATGACAAACGGTGCATTTTTGGCAGAAAGGTGCCACT
* *** * * *
1631912 AATGCAAGTTATATGACAAATAATGAATTTTTGGCAAAAAGGTGCCATT
1 AATGCAAGTTAAATGACAAACGGTGCATTTTTGGCAGAAAGGTGCCACT
* * *
1631961 AATGCAAGTTAAATGCCTAACGGTGCATTTTTGGTAGAAAGGTGCCACT
1 AATGCAAGTTAAATGACAAACGGTGCATTTTTGGCAGAAAGGTGCCACT
* * * * * *
1632010 AATGCAAGTTAAAAGCCTAATGGTGCATATTTGGCAGAAAGATGCCACT
1 AATGCAAGTTAAATGACAAACGGTGCATTTTTGGCAGAAAGGTGCCACT
* * *
1632059 AATGCAAGTTAAATG-CATAACGGTGCATTTTCGGCAGAAAGGTACCAAT
1 AATGCAAGTTAAATGACA-AACGGTGCATTTTTGGCAGAAAGGTGCCACT
* * * * *
1632108 AATGCAAGTTAGATGACAAATGGTGAATTTTTGGCAAAAAGGTACCACT
1 AATGCAAGTTAAATGACAAACGGTGCATTTTTGGCAGAAAGGTGCCACT
* * * * * *** *
1632157 AATGCAAGTTAAATGCCTAACGGTACATTTTTGGTAGAAAGTTGTTGCA
1 AATGCAAGTTAAATGACAAACGGTGCATTTTTGGCAGAAAGGTGCCACT
** * * *
1632206 AATGCAAGTTTGATGACAAATGGTGCATTTTTGGAAGAAATGTGCCACT
1 AATGCAAGTTAAATGACAAACGGTGCATTTTTGGCAGAAAGGTGCCACT
* * * * * * * *
1632255 AAGGCAAGCTAAATGCCTAACGGTTCATATTTGGTAGAAATGTGCCACT
1 AATGCAAGTTAAATGACAAACGGTGCATTTTTGGCAGAAAGGTGCCACT
* * *
1632304 AATGCAAGTTACATGACAAACGGTTCATTATTGGCATGAAAGG
1 AATGCAAGTTAAATGACAAACGGTGCATTTTTGGCA-GAAAGG
1632347 ATACCATAAA
Statistics
Matches: 347, Mismatches: 85, Indels: 5
0.79 0.19 0.01
Matches are distributed among these distances:
48 1 0.00
49 339 0.98
50 7 0.02
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (49 bp):
AATGCAAGTTAAATGACAAACGGTGCATTTTTGGCAGAAAGGTGCCACT
Found at i:1632043 original size:98 final size:98
Alignment explanation
Indices: 1631863--1632323 Score: 591
Period size: 98 Copynumber: 4.7 Consensus size: 98
1631853 ACTGCTTTAA
* * *
1631863 AATGAAAGTTAAATGCCTAACGGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTATATGA
1 AATGCAAGTTAAATGCCTAACGGTGCATTTTTGGTAGAAAGGTGCCACTAATGCAAGTTAGATGA
** *
1631928 CAAATAATGAATTTTTGGCAAAAAGGTGCCATT
66 CAAATGGTGAATTTTTGGCAAAAAGGTGCCACT
* * *
1631961 AATGCAAGTTAAATGCCTAACGGTGCATTTTTGGTAGAAAGGTGCCACTAATGCAAGTTAAAAGC
1 AATGCAAGTTAAATGCCTAACGGTGCATTTTTGGTAGAAAGGTGCCACTAATGCAAGTTAGATGA
* * * * *
1632026 CTAATGGTGCATATTTGGCAGAAAGATGCCACT
66 CAAATGGTGAATTTTTGGCAAAAAGGTGCCACT
* * * * *
1632059 AATGCAAGTTAAATGCATAACGGTGCATTTTCGGCAGAAAGGTACCAATAATGCAAGTTAGATGA
1 AATGCAAGTTAAATGCCTAACGGTGCATTTTTGGTAGAAAGGTGCCACTAATGCAAGTTAGATGA
*
1632124 CAAATGGTGAATTTTTGGCAAAAAGGTACCACT
66 CAAATGGTGAATTTTTGGCAAAAAGGTGCCACT
* * *** * *
1632157 AATGCAAGTTAAATGCCTAACGGTACATTTTTGGTAGAAAGTTGTTGCAAATGCAAGTTTGATGA
1 AATGCAAGTTAAATGCCTAACGGTGCATTTTTGGTAGAAAGGTGCCACTAATGCAAGTTAGATGA
* *
1632222 CAAATGGTGCATTTTTGG-AAGAAATGTGCCACT
66 CAAATGGTGAATTTTTGGCAA-AAAGGTGCCACT
* * * * * *
1632255 AAGGCAAGCTAAATGCCTAACGGTTCATATTTGGTAGAAATGTGCCACTAATGCAAGTTACATGA
1 AATGCAAGTTAAATGCCTAACGGTGCATTTTTGGTAGAAAGGTGCCACTAATGCAAGTTAGATGA
1632320 CAAA
66 CAAA
1632324 CGGTTCATTA
Statistics
Matches: 308, Mismatches: 54, Indels: 2
0.85 0.15 0.01
Matches are distributed among these distances:
97 2 0.01
98 306 0.99
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.28
Consensus pattern (98 bp):
AATGCAAGTTAAATGCCTAACGGTGCATTTTTGGTAGAAAGGTGCCACTAATGCAAGTTAGATGA
CAAATGGTGAATTTTTGGCAAAAAGGTGCCACT
Found at i:1632138 original size:147 final size:147
Alignment explanation
Indices: 1631863--1632345 Score: 545
Period size: 147 Copynumber: 3.3 Consensus size: 147
1631853 ACTGCTTTAA
* * *
1631863 AATGAAAGTTAAATGCCTAACGGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTATATGA
1 AATGCAAGTTAAATGCCTAACGGTGCATTTTTGGCAGAAAGATGCCACTAATGCAAGTTAAATGA
** * * *
1631928 CAAATAATGAATTTTTGGCAAAAAGGTGCCATTAATGCAAGTTAAATGCCTAACGGTGCATTTTT
66 CAAATGGTGCATTTTTGGCAGAAAGGTGCCAATAATGCAAGTTAAATGCCTAACGGTGCATTTTT
1631993 GGTAGAAAGGTGCCACT
131 GGTAGAAAGGTGCCACT
* * *
1632010 AATGCAAGTTAAAAGCCTAATGGTGCATATTTGGCAGAAAGATGCCACTAATGCAAGTTAAATG-
1 AATGCAAGTTAAATGCCTAACGGTGCATTTTTGGCAGAAAGATGCCACTAATGCAAGTTAAATGA
* * * * * * * *
1632074 CATAACGGTGCATTTTCGGCAGAAAGGTACCAATAATGCAAGTTAGATGACAAATGGTGAATTTT
66 CA-AATGGTGCATTTTTGGCAGAAAGGTGCCAATAATGCAAGTTAAATGCCTAACGGTGCATTTT
* * *
1632139 TGGCAAAAAGGTACCACT
130 TGGTAGAAAGGTGCCACT
* * * *** * **
1632157 AATGCAAGTTAAATGCCTAACGGTACATTTTTGGTAGAAAGTTGTTGCAAATGCAAGTTTGATGA
1 AATGCAAGTTAAATGCCTAACGGTGCATTTTTGGCAGAAAGATGCCACTAATGCAAGTTAAATGA
* * * * * * *
1632222 CAAATGGTGCATTTTTGGAAGAAATGTGCCACTAAGGCAAGCTAAATGCCTAACGGTTCATATTT
66 CAAATGGTGCATTTTTGGCAGAAAGGTGCCAATAATGCAAGTTAAATGCCTAACGGTGCATTTTT
*
1632287 GGTAGAAATGTGCCACT
131 GGTAGAAAGGTGCCACT
* * * * *
1632304 AATGCAAGTTACATGACAAACGGTTCATTATTGGCATGAAAG
1 AATGCAAGTTAAATGCCTAACGGTGCATTTTTGGCA-GAAAG
1632346 GATACCATAA
Statistics
Matches: 274, Mismatches: 59, Indels: 5
0.81 0.17 0.01
Matches are distributed among these distances:
146 2 0.01
147 265 0.97
148 7 0.03
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (147 bp):
AATGCAAGTTAAATGCCTAACGGTGCATTTTTGGCAGAAAGATGCCACTAATGCAAGTTAAATGA
CAAATGGTGCATTTTTGGCAGAAAGGTGCCAATAATGCAAGTTAAATGCCTAACGGTGCATTTTT
GGTAGAAAGGTGCCACT
Found at i:1632479 original size:92 final size:91
Alignment explanation
Indices: 1632322--1632581 Score: 358
Period size: 92 Copynumber: 2.8 Consensus size: 91
1632312 TTACATGACA
* * * *
1632322 AACGGTTCATTATTGGCATGAAAGGATACCATAAATGAAAATGTATAACAGTACATTATCGGCAT
1 AACGGTGCATTATTGGCATGAAAGGATGCCATAAATGAAAATGTATAACGGTGCATTATCGGCAT
*
1632387 GAAAGGATGCCATAAATGAATATGCAT
66 GAAAGG-TGCCATAAATGAAAATGCAT
*
1632414 AACGGTGCATTATTGGCATGAAATGATGCCATAAATGAAAATGTATAACGGTGCATTATCGGCAT
1 AACGGTGCATTATTGGCATGAAAGGATGCCATAAATGAAAATGTATAACGGTGCATTATCGGCAT
1632479 GAAATGGTGCCATAAATGAAAATGCAT
66 GAAA-GGTGCCATAAATGAAAATGCAT
* * * * ** * * *
1632506 AAAGGTGCATAATTGGCGTGAAAGGATGCCACAAATGAAAATACATAACGGTGTATTAACGACAT
1 AACGGTGCATTATTGGCATGAAAGGATGCCATAAATGAAAATGTATAACGGTGCATTATCGGCAT
*
1632571 AAAAGGTGCCA
66 GAAAGGTGCCA
1632582 CTCATGGTAT
Statistics
Matches: 150, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
91 7 0.05
92 141 0.94
93 2 0.01
ACGTcount: A:0.40, C:0.13, G:0.22, T:0.24
Consensus pattern (91 bp):
AACGGTGCATTATTGGCATGAAAGGATGCCATAAATGAAAATGTATAACGGTGCATTATCGGCAT
GAAAGGTGCCATAAATGAAAATGCAT
Found at i:1632576 original size:46 final size:46
Alignment explanation
Indices: 1632322--1632581 Score: 317
Period size: 46 Copynumber: 5.7 Consensus size: 46
1632312 TTACATGACA
* * * *
1632322 AACGGTTCATTATTGGCATGAAAGGATACCATAAATGAAAATGTAT
1 AACGGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCAT
* * *
1632368 AACAGTACATTATCGGCATGAAAGGATGCCATAAATGAATATGCAT
1 AACGGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCAT
* * *
1632414 AACGGTGCATTATTGGCATGAAATGATGCCATAAATGAAAATGTAT
1 AACGGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCAT
1632460 AACGGTGCATTATCGGCATGAAATGG-TGCCATAAATGAAAATGCAT
1 AACGGTGCATTATCGGCATGAAA-GGATGCCATAAATGAAAATGCAT
* * * * * *
1632506 AAAGGTGCATAATTGGCGTGAAAGGATGCCACAAATGAAAATACAT
1 AACGGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCAT
* * * *
1632552 AACGGTGTATTAACGACATAAAAGG-TGCCA
1 AACGGTGCATTATCGGCATGAAAGGATGCCA
1632582 CTCATGGTAT
Statistics
Matches: 183, Mismatches: 29, Indels: 5
0.84 0.13 0.02
Matches are distributed among these distances:
45 7 0.04
46 175 0.96
47 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.22, T:0.24
Consensus pattern (46 bp):
AACGGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCAT
Found at i:1637927 original size:49 final size:49
Alignment explanation
Indices: 1637868--1638435 Score: 677
Period size: 49 Copynumber: 11.5 Consensus size: 49
1637858 AAATCCTAAC
** *
1637868 GGTGCATTTTTGGCAGAAAGGTGTGACTAATGCAAGTTAGATGACAAAT
1 GGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAAATGACAAAT
* * * * *
1637917 GGTGCATTTTTGGCAAAAATGTGCCACTAATGCAAGTTAAATGCCTAAC
1 GGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAAATGACAAAT
* * * *
1637966 GGTGCATTTTTTGTAGAAAGGTGCCACTAATGCAAGTTAGATGGCAAAT
1 GGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAAATGACAAAT
* * * * *
1638015 GGTGCATTTCTGGTAGAAAGGTGTCACTAATGCAAGTTAAATGCCTAAT
1 GGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAAATGACAAAT
* * *
1638064 GGTGCATTTTTGGTAGAAAGGTGCCACTAATGAAAGTTATATGACAAAT
1 GGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAAATGACAAAT
* * *
1638113 GGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAAATGCCTAAC
1 GGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAAATGACAAAT
* * * ** *
1638162 AGTGCATTTTTGGTAGAAAGGTGCCAGTAATGCAAGTTTGATAACAAAT
1 GGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAAATGACAAAT
* * * *
1638211 GGTTCATTTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAAATGTCTAAC
1 GGTGCA-TTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAAATGACAAAT
* ** * * *
1638261 GGTGCATTTTTGGTAGAAAGACGCCACTAATGTAAGTTAGATGAAAAAT
1 GGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAAATGACAAAT
* * *
1638310 GGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAAATGCCTAAC
1 GGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAAATGACAAAT
* * * * *
1638359 AGTGCATTTTTGGTAGAAAGGTGCCATTAATGCAAGTTAGATGACAAAC
1 GGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAAATGACAAAT
*
1638408 GGTGCATTATTGGCATGAAAGGATGCCA
1 GGTGCATTTTTGGCA-GAAAGG-TGCCA
1638436 TAAATGAAAA
Statistics
Matches: 435, Mismatches: 81, Indels: 4
0.84 0.16 0.01
Matches are distributed among these distances:
49 384 0.88
50 46 0.11
51 5 0.01
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (49 bp):
GGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAAATGACAAAT
Found at i:1638043 original size:98 final size:98
Alignment explanation
Indices: 1637848--1638435 Score: 890
Period size: 98 Copynumber: 6.0 Consensus size: 98
1637838 ACTACTCTAA
* * **
1637848 AATGAAAGTTAAAT-CCTAACGGTGCATTTTTGGCAGAAAGGTGTGACTAATGCAAGTTAGATGA
1 AATGCAAGTTAAATGCCTAACGGTGCATTTTTGGTAGAAAGGTGCCACTAATGCAAGTTAGATGA
* *
1637912 CAAATGGTGCATTTTTGGCAAAAATGTGCCACT
66 CAAATGGTGCATTTTTGGCAGAAAGGTGCCACT
* *
1637945 AATGCAAGTTAAATGCCTAACGGTGCATTTTTTGTAGAAAGGTGCCACTAATGCAAGTTAGATGG
1 AATGCAAGTTAAATGCCTAACGGTGCATTTTTGGTAGAAAGGTGCCACTAATGCAAGTTAGATGA
* * *
1638010 CAAATGGTGCATTTCTGGTAGAAAGGTGTCACT
66 CAAATGGTGCATTTTTGGCAGAAAGGTGCCACT
* * *
1638043 AATGCAAGTTAAATGCCTAATGGTGCATTTTTGGTAGAAAGGTGCCACTAATGAAAGTTATATGA
1 AATGCAAGTTAAATGCCTAACGGTGCATTTTTGGTAGAAAGGTGCCACTAATGCAAGTTAGATGA
1638108 CAAATGGTGCATTTTTGGCAGAAAGGTGCCACT
66 CAAATGGTGCATTTTTGGCAGAAAGGTGCCACT
* * * *
1638141 AATGCAAGTTAAATGCCTAACAGTGCATTTTTGGTAGAAAGGTGCCAGTAATGCAAGTTTGATAA
1 AATGCAAGTTAAATGCCTAACGGTGCATTTTTGGTAGAAAGGTGCCACTAATGCAAGTTAGATGA
*
1638206 CAAATGGTTCATTTTTTGGCAGAAAGGTGCCACT
66 CAAATGGTGCA-TTTTTGGCAGAAAGGTGCCACT
* ** *
1638240 AATGCAAGTTAAATGTCTAACGGTGCATTTTTGGTAGAAAGACGCCACTAATGTAAGTTAGATGA
1 AATGCAAGTTAAATGCCTAACGGTGCATTTTTGGTAGAAAGGTGCCACTAATGCAAGTTAGATGA
*
1638305 AAAATGGTGCATTTTTGGCAGAAAGGTGCCACT
66 CAAATGGTGCATTTTTGGCAGAAAGGTGCCACT
* *
1638338 AATGCAAGTTAAATGCCTAACAGTGCATTTTTGGTAGAAAGGTGCCATTAATGCAAGTTAGATGA
1 AATGCAAGTTAAATGCCTAACGGTGCATTTTTGGTAGAAAGGTGCCACTAATGCAAGTTAGATGA
* *
1638403 CAAACGGTGCATTATTGGCATGAAAGGATGCCA
66 CAAATGGTGCATTTTTGGCA-GAAAGG-TGCCA
1638436 TAAATGAAAA
Statistics
Matches: 441, Mismatches: 46, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
97 13 0.03
98 329 0.75
99 94 0.21
100 5 0.01
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (98 bp):
AATGCAAGTTAAATGCCTAACGGTGCATTTTTGGTAGAAAGGTGCCACTAATGCAAGTTAGATGA
CAAATGGTGCATTTTTGGCAGAAAGGTGCCACT
Found at i:1638461 original size:46 final size:46
Alignment explanation
Indices: 1638409--1638664 Score: 343
Period size: 46 Copynumber: 5.6 Consensus size: 46
1638399 ATGACAAACG
* *
1638409 GTGCATTATTGGCATGAAAGGATGCCATAAATGAAAATGTATAACA
1 GTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAACA
* *
1638455 GTGCATTATTGGCATGAAAGGATGCCATAAATGAAAATGCATAACG
1 GTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAACA
* * * * *
1638501 GTGCATTATCCGCATGAAAGGACGCTATAAATAAAAATGCATAACG
1 GTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAACA
*
1638547 GTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATACATAACA
1 GTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAACA
* * * *
1638593 GTGCATAATCGGCATGAAAGGATGTCATAAATGAAAATACATAATA
1 GTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAACA
* * * *
1638639 GTGTATTAACGGTATAAAAGG-TGCCA
1 GTGCATTATCGGCATGAAAGGATGCCA
1638665 CTCATGGTAT
Statistics
Matches: 188, Mismatches: 22, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
45 4 0.02
46 184 0.98
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.24
Consensus pattern (46 bp):
GTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATGCATAACA
Found at i:1638659 original size:138 final size:138
Alignment explanation
Indices: 1638405--1638659 Score: 384
Period size: 138 Copynumber: 1.8 Consensus size: 138
1638395 TTAGATGACA
* ** * *
1638405 AACGGTGCATTATTGGCATGAAAGGATGCCATAAATGAAAATGTATAACAGTGCATTATTGGCAT
1 AACGGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATACATAACAGTGCATAATCGGCAT
* * * *
1638470 GAAAGGATGCCATAAATGAAAATGCATAACGGTGCATTATCCGCATGAAAGGACGCTATAAATAA
66 GAAAGGATGCCATAAATGAAAATACATAACAGTGCATTAACCGCATAAAAGGACGCTATAAATAA
1638535 AAATGCAT
131 AAATGCAT
1638543 AACGGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATACATAACAGTGCATAATCGGCAT
1 AACGGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATACATAACAGTGCATAATCGGCAT
* * * * *
1638608 GAAAGGATGTCATAAATGAAAATACATAATAGTGTATTAACGGTATAAAAGG
66 GAAAGGATGCCATAAATGAAAATACATAACAGTGCATTAACCGCATAAAAGG
1638660 TGCCACTCAT
Statistics
Matches: 103, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
138 103 1.00
ACGTcount: A:0.42, C:0.13, G:0.22, T:0.24
Consensus pattern (138 bp):
AACGGTGCATTATCGGCATGAAAGGATGCCATAAATGAAAATACATAACAGTGCATAATCGGCAT
GAAAGGATGCCATAAATGAAAATACATAACAGTGCATTAACCGCATAAAAGGACGCTATAAATAA
AAATGCAT
Found at i:1644398 original size:21 final size:21
Alignment explanation
Indices: 1644373--1644424 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
1644363 GTTTGCGAAT
1644373 GTTAAATGAACATTTATGAAC
1 GTTAAATGAACATTTATGAAC
1644394 GTTAAATGAACATTTATGAAC
1 GTTAAATGAACATTTATGAAC
1644415 GTTAAATGAA
1 GTTAAATGAA
1644425 TATGTTTGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (21 bp):
GTTAAATGAACATTTATGAAC
Found at i:1644741 original size:31 final size:31
Alignment explanation
Indices: 1644703--1644764 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
1644693 TACTAAATTA
1644703 TAAGACGTAATTTCTAGAATAAAGCATTACT
1 TAAGACGTAATTTCTAGAATAAAGCATTACT
1644734 TAAGACGTAATTTCTAGAATAAAGCATTACT
1 TAAGACGTAATTTCTAGAATAAAGCATTACT
1644765 GATAACGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (31 bp):
TAAGACGTAATTTCTAGAATAAAGCATTACT
Found at i:1645230 original size:15 final size:15
Alignment explanation
Indices: 1645210--1645249 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
1645200 TGTATTTCTT
1645210 TAATTTAAAAAATTA
1 TAATTTAAAAAATTA
*
1645225 TAATTTAAAAGATTA
1 TAATTTAAAAAATTA
1645240 TAATTTAAAA
1 TAATTTAAAA
1645250 TGATGATGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (15 bp):
TAATTTAAAAAATTA
Found at i:1650594 original size:17 final size:17
Alignment explanation
Indices: 1650572--1650614 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
1650562 GACATTAGTG
1650572 ACTCAACACCTAAATAA
1 ACTCAACACCTAAATAA
1650589 ACTCAACACCTAAATAA
1 ACTCAACACCTAAATAA
*
1650606 ACTTAACAC
1 ACTCAACAC
1650615 AATCACAACC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.51, C:0.30, G:0.00, T:0.19
Consensus pattern (17 bp):
ACTCAACACCTAAATAA
Found at i:1651320 original size:16 final size:17
Alignment explanation
Indices: 1651299--1651341 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
1651289 GCATCATCAG
1651299 CGAAAATATACA-AAAA
1 CGAAAATATACACAAAA
*
1651315 CGAAAACATACACAAAA
1 CGAAAATATACACAAAA
* *
1651332 AGAAGATATA
1 CGAAAATATA
1651342 TCAACGAGAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.65, C:0.14, G:0.09, T:0.12
Consensus pattern (17 bp):
CGAAAATATACACAAAA
Found at i:1663893 original size:16 final size:15
Alignment explanation
Indices: 1663823--1663891 Score: 104
Period size: 15 Copynumber: 4.5 Consensus size: 15
1663813 ACTTGAAGAT
1663823 AAAAAAATGAGAAAATG
1 AAAAAAAT--GAAAATG
1663840 AAATAAAATGAAAATG
1 AAA-AAAATGAAAATG
1663856 AAAAAAATGAAAATG
1 AAAAAAATGAAAATG
1663871 AAAAAAATG-AAATG
1 AAAAAAATGAAAATG
1663885 AAAAAAA
1 AAAAAAA
1663892 AAACGAATAA
Statistics
Matches: 51, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
14 12 0.24
15 21 0.41
16 10 0.20
17 3 0.06
18 5 0.10
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (15 bp):
AAAAAAATGAAAATG
Found at i:1663893 original size:31 final size:32
Alignment explanation
Indices: 1663823--1663891 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 32
1663813 ACTTGAAGAT
1663823 AAAAAAATGAGAAAATGAAATAAAATGAAAATG
1 AAAAAAAT-AGAAAATGAAATAAAATGAAAATG
1663856 AAAAAAAT-GAAAATGAAA-AAAATG-AAATG
1 AAAAAAATAGAAAATGAAATAAAATGAAAATG
1663885 AAAAAAA
1 AAAAAAA
1663892 AAACGAATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
29 12 0.33
30 6 0.17
31 10 0.28
33 8 0.22
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (32 bp):
AAAAAAATAGAAAATGAAATAAAATGAAAATG
Found at i:1665701 original size:55 final size:55
Alignment explanation
Indices: 1665242--1665692 Score: 616
Period size: 55 Copynumber: 8.2 Consensus size: 55
1665232 GCAAAATAAT
* *
1665242 ATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATTGAAG
1 ATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAG
* * *
1665297 ATTGCTCGAGTCTTATACTCTCTAAAGGAATAGGGAGAAGACACGATTGTTGAAG
1 ATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAG
* * *
1665352 ATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGGGCAGACACAATTGATGAAG
1 ATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAG
* * * * *
1665407 ATTGTTTGAGTCTTATACTCTTTGAAGAAATAGGGAACATACACGATTGTTGAAG
1 ATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAG
* *
1665462 ATTGTTCGAATCTTATACTCTCTGAAAGAATAGGGAGCAGACACGATTGTTGAAG
1 ATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAG
* * * * *
1665517 ATTGTTTGAGGCTTAAACTCTCTAAAGGAATAGGGAGCAGACACAATTGTTGAAG
1 ATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAG
* * ** *
1665572 ATTGTTTGAGTCTTATACTATCTGAAGGAATAGGGAGCAGACATTATTGTTGGAG
1 ATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAG
* * * * *
1665627 AATGTTCGATTCATATACTCTCTGATAGGAATAGAGAGCAGACGCGATTGTTGAAG
1 ATTGTTCGAGTCTTATACTCTCTGA-AGGAATAGGGAGCAGACACGATTGTTGAAG
1665683 A-TGTTCGAGT
1 ATTGTTCGAGT
1665693 TCCATACTCC
Statistics
Matches: 344, Mismatches: 51, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
55 318 0.92
56 26 0.08
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (55 bp):
ATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAG
Found at i:1665739 original size:165 final size:163
Alignment explanation
Indices: 1665242--1665747 Score: 588
Period size: 165 Copynumber: 3.1 Consensus size: 163
1665232 GCAAAATAAT
* * *
1665242 ATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTATTGAAGATTGCTCGAG
1 ATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAA
* * *
1665307 TCTTATACTCTCTAAAGGAATAGGGAGAAGACACGATTGTTGAAGATTGTTCGAGTCTTATACTC
66 TCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGT-TCATACTC
* * * *
1665372 TCTGAAGGAATAGGGGGCAGACACAATTGATGAAG
130 TCTAAAGGAATAGGGAGCAGAC-CCATTTATGAAG
* * * *
1665407 ATTGTTTGAGTCTTATACTCTTTGAAGAAATAGGGAACATACACGATTGTTGAAGATTGTTCGAA
1 ATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAA
* * *
1665472 TCTTATACTCTCTGAAAGAATAGGGAGCAGACACGATTGTTGAAGATTGTTTGAGGCTT-AAACT
66 TCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGA-G-TTCATACT
*
1665536 CTCTAAAGGAATAGGGAGCAGACACAATTGT-TGAAG
129 CTCTAAAGGAATAGGGAGCAGAC-CCATT-TATGAAG
* * * ** * * *
1665572 ATTGTTTGAGTCTTATACTATCTGAAGGAATAGGGAGCAGACATTATTGTTGGAGAATGTTCGAT
1 ATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAA
* * *
1665637 TCATATACTCTCTGATAGGAATAGAGAGCAGACGCGATTGTTGAAGA-TGTTCGAGTTCCATACT
66 TCTTATACTCTCTGA-AGGAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTT-CATACT
* * * * *
1665701 CCCTAAAGAAAAAGAGAGC-GAACCCGTTTATAGAAG
129 CTCTAAAGGAATAGGGAGCAG-ACCCATTTAT-GAAG
1665737 ATTGTTCGAGT
1 ATTGTTCGAGT
1665748 TCTACTCGCT
Statistics
Matches: 294, Mismatches: 38, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
163 3 0.01
164 6 0.02
165 254 0.86
166 30 0.10
167 1 0.00
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (163 bp):
ATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAA
TCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTGAAGATTGTTCGAGTTCATACTCT
CTAAAGGAATAGGGAGCAGACCCATTTATGAAG
Found at i:1668695 original size:18 final size:19
Alignment explanation
Indices: 1668664--1668703 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
1668654 ACGCGGACCT
*
1668664 AAATTTATTGTTTTAATTA
1 AAATTAATTGTTTTAATTA
*
1668683 AAATTAATT-TTTTATTTA
1 AAATTAATTGTTTTAATTA
1668701 AAA
1 AAA
1668704 CGACAACATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
AAATTAATTGTTTTAATTA
Found at i:1673617 original size:22 final size:21
Alignment explanation
Indices: 1673592--1673633 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1673582 AAAGGAAAAA
1673592 TAATTAGTATAAAGAAT-ATATG
1 TAATTA-T-TAAAGAATGATATG
1673614 TAATTATTAAAGAATGATAT
1 TAATTATTAAAGAATGATAT
1673634 AAACCAGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.42
21 5 0.26
22 6 0.32
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (21 bp):
TAATTATTAAAGAATGATATG
Found at i:1676370 original size:27 final size:27
Alignment explanation
Indices: 1676329--1676383 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
1676319 CTAGATGAAA
1676329 GTTTGCCATAACATTCTCG-TCTATTTC
1 GTTTGCCATAACATTCTCGTTC-ATTTC
*
1676356 GTTTGCCATAGCATTCTCGTTCATTTC
1 GTTTGCCATAACATTCTCGTTCATTTC
1676383 G
1 G
1676384 ATCTATTTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 24 0.92
28 2 0.08
ACGTcount: A:0.16, C:0.25, G:0.15, T:0.44
Consensus pattern (27 bp):
GTTTGCCATAACATTCTCGTTCATTTC
Found at i:1677164 original size:10 final size:10
Alignment explanation
Indices: 1677146--1677175 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1677136 ATTTAATACA
*
1677146 CCACTGAAAG
1 CCACCGAAAG
1677156 CCACCGAAAG
1 CCACCGAAAG
1677166 CCACCGAAAG
1 CCACCGAAAG
1677176 TCTATTTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.40, C:0.37, G:0.20, T:0.03
Consensus pattern (10 bp):
CCACCGAAAG
Found at i:1677499 original size:32 final size:32
Alignment explanation
Indices: 1677440--1677500 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
1677430 GAAAATATTC
* *
1677440 AAAATATATAAAAAAAAATAAATTTTTTAAGT
1 AAAAAATATAAAAAAAAATAAAATTTTTAAGT
* **
1677472 AAAAAATATATAAAAATTTAAAATTTTTA
1 AAAAAATATAAAAAAAAATAAAATTTTTA
1677501 GGGATATTGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (32 bp):
AAAAAATATAAAAAAAAATAAAATTTTTAAGT
Found at i:1682520 original size:2 final size:2
Alignment explanation
Indices: 1682513--1682537 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1682503 ATATTTTTAT
1682513 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
1682538 GAAGCTCATA
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:1685010 original size:24 final size:24
Alignment explanation
Indices: 1684954--1685011 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
1684944 TCCGTTCGTT
*
1684954 TATGTTCGGTCATTTATGTCTGTG
1 TATGTTCGTTCATTTATGTCTGTG
1684978 TATGTTCGTTCATTTATGTCTGTG
1 TATGTTCGTTCATTTATGTCTGTG
1685002 TATGTTCGTT
1 TATGTTCGTT
1685012 TATGTCCGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.12, C:0.12, G:0.22, T:0.53
Consensus pattern (24 bp):
TATGTTCGTTCATTTATGTCTGTG
Found at i:1685013 original size:20 final size:21
Alignment explanation
Indices: 1684966--1685017 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 21
1684956 TGTTCGGTCA
1684966 TTTATGTCTGTGTATGTTCGTT
1 TTTATGTCTGTGTATGTTCG-T
1684988 CATTTATGTCTGTGTATGTTCG-
1 --TTTATGTCTGTGTATGTTCGT
1685010 TTTATGTC
1 TTTATGTC
1685018 CGTTTGTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.29
24 20 0.71
ACGTcount: A:0.12, C:0.12, G:0.21, T:0.56
Consensus pattern (21 bp):
TTTATGTCTGTGTATGTTCGT
Found at i:1685428 original size:31 final size:31
Alignment explanation
Indices: 1685391--1685470 Score: 151
Period size: 31 Copynumber: 2.6 Consensus size: 31
1685381 TAACGAACAT
*
1685391 GAACGAACACGAACAAGTTGCATTCCTTAAC
1 GAACGAACACGAACAAGCTGCATTCCTTAAC
1685422 GAACGAACACGAACAAGCTGCATTCCTTAAC
1 GAACGAACACGAACAAGCTGCATTCCTTAAC
1685453 GAACGAACACGAACAAGC
1 GAACGAACACGAACAAGC
1685471 AATTTTGTGT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.41, C:0.28, G:0.17, T:0.14
Consensus pattern (31 bp):
GAACGAACACGAACAAGCTGCATTCCTTAAC
Found at i:1695368 original size:15 final size:16
Alignment explanation
Indices: 1695348--1695389 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
1695338 GCTTTTTTTC
1695348 AATAAAATTTAGA-TA
1 AATAAAATTTAGAGTA
*
1695363 AATAAAAGATTAGAGTA
1 AATAAAA-TTTAGAGTA
1695380 AA-AAAATTTA
1 AATAAAATTTA
1695390 AAAAATAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 10 0.43
16 9 0.39
17 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.29
Consensus pattern (16 bp):
AATAAAATTTAGAGTA
Found at i:1695619 original size:24 final size:22
Alignment explanation
Indices: 1695564--1695619 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 22
1695554 TAAAAATGTT
1695564 AATAAAAATGTAAAATAATATA
1 AATAAAAATGTAAAATAATATA
*
1695586 AATAAAAAATATTAAAATAA-ATTA
1 AAT-AAAAAT-GTAAAATAATA-TA
1695610 AGATAAAAAT
1 A-ATAAAAAT
1695620 TTCAAATCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
22 3 0.10
23 7 0.24
24 17 0.59
25 2 0.07
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.27
Consensus pattern (22 bp):
AATAAAAATGTAAAATAATATA
Found at i:1700074 original size:21 final size:23
Alignment explanation
Indices: 1700032--1700077 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1700022 AACACACAAT
*
1700032 AAAAGAGAGAGAAAATGTGGAGA
1 AAAAGAGAGAGAAAAAGTGGAGA
1700055 AAAAGAGAGA-AAAAAG-GGAGA
1 AAAAGAGAGAGAAAAAGTGGAGA
1700076 AA
1 AA
1700078 GAGTCATCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.32
22 5 0.23
23 10 0.45
ACGTcount: A:0.63, C:0.00, G:0.33, T:0.04
Consensus pattern (23 bp):
AAAAGAGAGAGAAAAAGTGGAGA
Found at i:1706038 original size:16 final size:16
Alignment explanation
Indices: 1706019--1706051 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1706009 GGTAGAGATA
1706019 TTGATAATAACTTAGC
1 TTGATAATAACTTAGC
1706035 TTGATAATAACTTAGC
1 TTGATAATAACTTAGC
1706051 T
1 T
1706052 AGGTTATTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.39
Consensus pattern (16 bp):
TTGATAATAACTTAGC
Found at i:1712509 original size:18 final size:18
Alignment explanation
Indices: 1712486--1712522 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1712476 AAGCATGCAC
*
1712486 TTGAATCATTTACTTACA
1 TTGAATCATTTACATACA
1712504 TTGAATCATTTACATACA
1 TTGAATCATTTACATACA
1712522 T
1 T
1712523 ATGTATCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.16, G:0.05, T:0.43
Consensus pattern (18 bp):
TTGAATCATTTACATACA
Found at i:1721418 original size:14 final size:15
Alignment explanation
Indices: 1721395--1721424 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1721385 ATGATATTAG
1721395 AAAATAAAAAATAAA
1 AAAATAAAAAATAAA
1721410 AAAAT-AAAAATAAA
1 AAAATAAAAAATAAA
1721424 A
1 A
1721425 CACTCATGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (15 bp):
AAAATAAAAAATAAA
Found at i:1726824 original size:27 final size:27
Alignment explanation
Indices: 1726743--1726877 Score: 95
Period size: 27 Copynumber: 5.1 Consensus size: 27
1726733 CCTAACTATT
*
1726743 CATATTGGCATAAAGGTGTCAATAATG
1 CATATTGGCAGAAAGGTGTCAATAATG
* **
1726770 CA-AGTTAG-ATGAAAGGCCT-AACT-ATG
1 CATA-TTGGCA-GAAAGGTGTCAA-TAATG
*
1726796 CATATTGGCAAAAAGGTGTCAATAATG
1 CATATTGGCAGAAAGGTGTCAATAATG
* * *
1726823 CA-AGTTAG-ATGAAAGGCGTAAAT-ATG
1 CATA-TTGGCA-GAAAGGTGTCAATAATG
*
1726849 CATATTGGCATAAAGGTGTCAATAATG
1 CATATTGGCAGAAAGGTGTCAATAATG
1726876 CA
1 CA
1726878 AGTTAAATGA
Statistics
Matches: 80, Mismatches: 16, Indels: 24
0.67 0.13 0.20
Matches are distributed among these distances:
26 39 0.49
27 41 0.51
ACGTcount: A:0.39, C:0.12, G:0.23, T:0.26
Consensus pattern (27 bp):
CATATTGGCAGAAAGGTGTCAATAATG
Found at i:1726890 original size:27 final size:27
Alignment explanation
Indices: 1726807--1726891 Score: 86
Period size: 27 Copynumber: 3.2 Consensus size: 27
1726797 ATATTGGCAA
*
1726807 AAAGGTGTCAATAATGCAAGTTAGATG
1 AAAGGTGTCAATAATGCAAGTTAAATG
* * **
1726834 AAAGGCGTAAAT-ATGCATA-TTGGCAT-
1 AAAGGTGTCAATAATGCA-AGTT-AAATG
1726860 AAAGGTGTCAATAATGCAAGTTAAATG
1 AAAGGTGTCAATAATGCAAGTTAAATG
1726887 AAAGG
1 AAAGG
1726892 CCTAACTGTT
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
26 20 0.44
27 25 0.56
ACGTcount: A:0.42, C:0.08, G:0.25, T:0.25
Consensus pattern (27 bp):
AAAGGTGTCAATAATGCAAGTTAAATG
Found at i:1726931 original size:52 final size:53
Alignment explanation
Indices: 1726732--1727040 Score: 382
Period size: 53 Copynumber: 5.9 Consensus size: 53
1726722 AAAGTTAAAC
* * *
1726732 GCCTAACTATTCATATTGGCATAAAGGTGTCAATAATGCAAGTTAGATGAAAG
1 GCCTAACTATGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAAATGAAAG
* *
1726785 GCCTAACTATGCATATTGGCAAAAAGGTGTCAATAATGCAAGTTAGATGAAAG
1 GCCTAACTATGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAAATGAAAG
* * *
1726838 GCGTAAATATGCATATTGGCATAAAGGTGTCAATAATGCAAGTTAAATGAAAG
1 GCCTAACTATGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAAATGAAAG
* *
1726891 GCCTAACTGTTCAT-TTGGCAGAAAGGTGTCAATAATGCAAGTTAAATGAAAG
1 GCCTAACTATGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAAATGAAAG
* * **
1726943 GCTTAACTGTGCAT-TTGGCAGAAAGGTGTCACCAATGCAAGTTAAAT-----
1 GCCTAACTATGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAAATGAAAG
* * * *
1726990 GCCTAACGATGCATTTTTGGCAGAAAGGTG-CTACTAATGCAAGTTAGATGA
1 GCCTAACTATGCA-TATTGGCAGAAAGGTGTC-AATAATGCAAGTTAAATGA
1727041 GAAGTTAAAT
Statistics
Matches: 231, Mismatches: 20, Indels: 12
0.88 0.08 0.05
Matches are distributed among these distances:
47 10 0.04
48 2 0.01
49 29 0.13
52 80 0.35
53 110 0.48
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.27
Consensus pattern (53 bp):
GCCTAACTATGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAAATGAAAG
Found at i:1727108 original size:59 final size:59
Alignment explanation
Indices: 1726981--1727125 Score: 202
Period size: 59 Copynumber: 2.4 Consensus size: 59
1726971 TCACCAATGC
* * * *
1726981 AAGTTAAATGCCTAACGATGCATTTTTGGCAGAAAGGTGCTACTAATGCAAGTTAGATGAG
1 AAGTTAAATGCCTAACGATGCA--TTTGACAGAAAGGTGCCACTAATGCAAGTTAGACGAA
*
1727042 AAGTTAAATGCCTAATGATGCATTTGACA-AAAGAGTGCCACTAATGCAAGTTAGACGAA
1 AAGTTAAATGCCTAACGATGCATTTGACAGAAAG-GTGCCACTAATGCAAGTTAGACGAA
*
1727101 AAGTTAAATGCCTAACGGTGCATTT
1 AAGTTAAATGCCTAACGATGCATTT
1727126 TGGCAAAAAG
Statistics
Matches: 76, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
58 4 0.05
59 51 0.67
61 21 0.28
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (59 bp):
AAGTTAAATGCCTAACGATGCATTTGACAGAAAGGTGCCACTAATGCAAGTTAGACGAA
Found at i:1727218 original size:46 final size:46
Alignment explanation
Indices: 1727166--1727272 Score: 151
Period size: 46 Copynumber: 2.3 Consensus size: 46
1727156 ATGAAAAATA
** * *
1727166 GTGCATTATCGGTATGAAAGGATGCCATAAATGAAAATACATAATG
1 GTGCATTATCGACATGAAAGGATGACATAAATGAAAATACATAACG
*
1727212 GTGCATTATCGACATGAAATGATGACATAAATGAAAATACATAACG
1 GTGCATTATCGACATGAAAGGATGACATAAATGAAAATACATAACG
* *
1727258 GTGTATTAACGACAT
1 GTGCATTATCGACAT
1727273 ATAAGGTACC
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 54 1.00
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.26
Consensus pattern (46 bp):
GTGCATTATCGACATGAAAGGATGACATAAATGAAAATACATAACG
Found at i:1732167 original size:27 final size:27
Alignment explanation
Indices: 1732137--1732328 Score: 100
Period size: 27 Copynumber: 7.2 Consensus size: 27
1732127 CATATTGGCA
1732137 GAAAGGTGTCAATAATGCAAGTTAGAT
1 GAAAGGTGTCAATAATGCAAGTTAGAT
** ** *
1732164 GAAAGGCCT-AATTGTGCATA-TTGACAT
1 GAAAGGTGTCAATAATGCA-AGTT-AGAT
* *
1732191 -AAAAGTGTCAATAATGCAAGTTAGTT
1 GAAAGGTGTCAATAATGCAAGTTAGAT
** * *
1732217 GAAAGGCCT-AACT-GTGCATA-TTGGCA-
1 GAAAGGTGTCAA-TAATGCA-AGTTAG-AT
*
1732243 GAAAGGTGTCAATAATGCAAGTTAAAT
1 GAAAGGTGTCAATAATGCAAGTTAGAT
* *
1732270 GAAAGGTGT-AACT-GTGCATA-TTGGCAT
1 GAAAGGTGTCAA-TAATGCA-AGTTAG-AT
*
1732297 -AAAGGTGTCAATAATGCAAGTTAAAT
1 GAAAGGTGTCAATAATGCAAGTTAGAT
1732323 GAAAGG
1 GAAAGG
1732329 CCTGACTGTG
Statistics
Matches: 117, Mismatches: 29, Indels: 38
0.64 0.16 0.21
Matches are distributed among these distances:
26 56 0.48
27 61 0.52
ACGTcount: A:0.39, C:0.10, G:0.24, T:0.27
Consensus pattern (27 bp):
GAAAGGTGTCAATAATGCAAGTTAGAT
Found at i:1732185 original size:53 final size:53
Alignment explanation
Indices: 1732119--1732590 Score: 660
Period size: 53 Copynumber: 8.9 Consensus size: 53
1732109 GTTAAATGCT
1732119 TAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGCC
1 TAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGCC
* * * * *
1732172 TAATTGTGCATATTGACATAAAAGTGTCAATAATGCAAGTTAGTTGAAAGGCC
1 TAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGCC
* **
1732225 TAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAAATGAAAGGTG
1 TAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGCC
* *
1732278 TAACTGTGCATATTGGCATAAAGGTGTCAATAATGCAAGTTAAATGAAAGGCC
1 TAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGCC
* * *
1732331 TGACTGTGCATATTGGCAGAAAGGTGTCAATAATACAAGTTAGATGAGAA-ACC
1 TAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGA-AAGGCC
* * * * * * *
1732384 TAATTGTGCATATTGGTATAAAGGTCTCAATAATACATGTTAGATGAAACGCC
1 TAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGCC
* * *
1732437 TAACTGTGCATATTAGCATAAAGGTGTCAATAATGCAAGTTAGATGAAACGCC
1 TAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGCC
* * *
1732490 TAACTGTTCATATTGGTAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGTCC
1 TAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGCC
* * *
1732543 TACCTGTGCAT-TTGGCAGAAAGGTGTCATTAATGCTAGTTAGATGAAA
1 TAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAA
1732591 AGTTAAATGC
Statistics
Matches: 372, Mismatches: 45, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
52 36 0.10
53 334 0.90
54 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.28
Consensus pattern (53 bp):
TAACTGTGCATATTGGCAGAAAGGTGTCAATAATGCAAGTTAGATGAAAGGCC
Found at i:1732715 original size:12 final size:12
Alignment explanation
Indices: 1732698--1732723 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1732688 CCATTAATGT
1732698 AAGTTAGATGAA
1 AAGTTAGATGAA
1732710 AAGTTAGATGAA
1 AAGTTAGATGAA
1732722 AA
1 AA
1732724 ATGGTGAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.00, G:0.23, T:0.23
Consensus pattern (12 bp):
AAGTTAGATGAA
Found at i:1733402 original size:26 final size:25
Alignment explanation
Indices: 1733372--1733423 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
1733362 TATCATCGAA
* *
1733372 TGTTTTAATTTTGTATTAAAATGTTT
1 TGTTTTAATTTTGAAATAAAAT-TTT
1733398 TGTTTTAATTTTGAAATAAAATTTT
1 TGTTTTAATTTTGAAATAAAATTTT
1733423 T
1 T
1733424 ATGGGTTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 4 0.17
26 20 0.83
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.60
Consensus pattern (25 bp):
TGTTTTAATTTTGAAATAAAATTTT
Found at i:1734037 original size:21 final size:20
Alignment explanation
Indices: 1734013--1734051 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1734003 TATCAAGGTA
*
1734013 TTTGTTGAAGCCATGAAATCT
1 TTTGTCGAAGCCAT-AAATCT
*
1734034 TTTGTCGAGGCCATAAAT
1 TTTGTCGAAGCCATAAAT
1734052 TCATGCAGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (20 bp):
TTTGTCGAAGCCATAAATCT
Found at i:1742085 original size:95 final size:94
Alignment explanation
Indices: 1741959--1742163 Score: 277
Period size: 95 Copynumber: 2.2 Consensus size: 94
1741949 ATATCGACGA
* * *
1741959 GGTAGTATCGATACCATGATAAGGGTATCGATACCAAGCAACATCGAATCTAATTTTGGTATCGA
1 GGTAGTATCGATACCATGATAAAGGTATCGATACCAAGAAACATCGAACCTAATTTTGGTATCGA
* * * *
1742024 TACCGAGAGGGGGTATCGGTATCATGGTAT
66 TACC-AGAAGAGGTATCGGTACCATAGTAT
* *
1742054 GGTAGTATCGATACCAT-AGTAAAGGTATCGATACCAGGAAACATCGAACCTAATTTTGGTATGG
1 GGTAGTATCGATACCATGA-TAAAGGTATCGATACCAAGAAACATCGAACCTAATTTTGGTATCG
1742118 ATACCAGAAGAGGTATCGGTACCATAGTAT
65 ATACCAGAAGAGGTATCGGTACCATAGTAT
* * *
1742148 AGAAGTATCGGTACCA
1 GGTAGTATCGATACCA
1742164 GGGTAGTAGT
Statistics
Matches: 97, Mismatches: 12, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
94 35 0.36
95 62 0.64
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (94 bp):
GGTAGTATCGATACCATGATAAAGGTATCGATACCAAGAAACATCGAACCTAATTTTGGTATCGA
TACCAGAAGAGGTATCGGTACCATAGTAT
Found at i:1742600 original size:55 final size:55
Alignment explanation
Indices: 1742516--1742829 Score: 339
Period size: 55 Copynumber: 5.8 Consensus size: 55
1742506 TACTACAAGT
* ** *
1742516 ACTTTATGTGGATATCCACGGCATTCATCATGGGTTGATGAATCATCGTACATGC
1 ACTTTATGTGCATATCCACGAAATTCATCATGGGTTGATGAATCACCGTACATGC
* * * * * * *
1742571 ACTTTATGTGCATATTCATGAAATTCATCATGTGTTGATGAATCATCGTATAGGA
1 ACTTTATGTGCATATCCACGAAATTCATCATGGGTTGATGAATCACCGTACATGC
* *
1742626 ACTTTATGTGCATATCCACAAAATTCATCATGGGTTGATGAATCAACGTACATGC
1 ACTTTATGTGCATATCCACGAAATTCATCATGGGTTGATGAATCACCGTACATGC
* * ** *
1742681 ACTTAATGTGTATATCCTTGGAA-T--TCATGGGTTGATGAATCACCGTACATGC
1 ACTTTATGTGCATATCCACGAAATTCATCATGGGTTGATGAATCACCGTACATGC
* * * * *
1742733 ACTTTGTGTGCAAACCCACGAAATTCATCATGAGTTGATGAATCACCGTACAGGC
1 ACTTTATGTGCATATCCACGAAATTCATCATGGGTTGATGAATCACCGTACATGC
* * * * * *
1742788 ACTATGTGTGCA-ACCCACAAAATTCATCACGAGTTGATGAAT
1 ACTTTATGTGCATATCCACGAAATTCATCATGGGTTGATGAAT
1742830 TTCTGTATAG
Statistics
Matches: 219, Mismatches: 37, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
52 42 0.19
53 1 0.00
54 29 0.13
55 147 0.67
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (55 bp):
ACTTTATGTGCATATCCACGAAATTCATCATGGGTTGATGAATCACCGTACATGC
Found at i:1742773 original size:107 final size:109
Alignment explanation
Indices: 1742538--1742790 Score: 321
Period size: 107 Copynumber: 2.3 Consensus size: 109
1742528 TATCCACGGC
* * *
1742538 ATTCATCATGGGTTGATGAATCATCGTACATGCACTTTATGTGCATATTCATGAAATTCATCATG
1 ATTCATCATGGGTTGATGAATCAACGTACATGCACTTAATGTGCATATCCATGAAATT-ATCATG
* * * * *
1742603 TGTTGATGAATCATCGTATAGGAACTTTATGTGCATATCCACAAA
65 GGTTGATGAATCACCGTACAGGAACTTTATGTGCAAACCCACAAA
* * *
1742648 ATTCATCATGGGTTGATGAATCAACGTACATGCACTTAATGTGTATATCCTTGGAA-T-TCATGG
1 ATTCATCATGGGTTGATGAATCAACGTACATGCACTTAATGTGCATATCCATGAAATTATCATGG
* * * *
1742711 GTTGATGAATCACCGTACATGCACTTTGTGTGCAAACCCACGAA
66 GTTGATGAATCACCGTACAGGAACTTTATGTGCAAACCCACAAA
* * *
1742755 ATTCATCATGAGTTGATGAATCACCGTACAGGCACT
1 ATTCATCATGGGTTGATGAATCAACGTACATGCACT
1742791 ATGTGTGCAA
Statistics
Matches: 125, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
107 74 0.59
109 1 0.01
110 50 0.40
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (109 bp):
ATTCATCATGGGTTGATGAATCAACGTACATGCACTTAATGTGCATATCCATGAAATTATCATGG
GTTGATGAATCACCGTACAGGAACTTTATGTGCAAACCCACAAA
Found at i:1745112 original size:95 final size:95
Alignment explanation
Indices: 1744976--1745161 Score: 250
Period size: 95 Copynumber: 2.0 Consensus size: 95
1744966 ATACCGATGA
* * *
1744976 GGTAGTATCGATACCATGATAAGGGTATCGATATCAAGCAACACCAAATCTAATTT-TGGTATCG
1 GGTAGTATCGATACCATGATAAGGGTATCAATATCAAGCAACACCAAACCTAATTTAT-GTATCA
*
1745040 ATACCGGGAGGGGGTATCGATACCATAGTTT
65 ATACCGGAAGGGGGTATCGATACCATAGTTT
* * ***
1745071 GGTAGTATCGATACCATGGTAAGGGTATCAATA-CTAGGCAACATTGAACCTAATTTATGTATCA
1 GGTAGTATCGATACCATGATAAGGGTATCAATATC-AAGCAACACCAAACCTAATTTATGTATCA
*
1745135 ATACCGGAAGGGGGTATCGGTACCATA
65 ATACCGGAAGGGGGTATCGATACCATA
1745162 ATATAGAAGT
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
94 1 0.01
95 77 0.97
96 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (95 bp):
GGTAGTATCGATACCATGATAAGGGTATCAATATCAAGCAACACCAAACCTAATTTATGTATCAA
TACCGGAAGGGGGTATCGATACCATAGTTT
Found at i:1745194 original size:95 final size:95
Alignment explanation
Indices: 1745025--1745200 Score: 214
Period size: 95 Copynumber: 1.9 Consensus size: 95
1745015 AACACCAAAT
* * * * * * *
1745025 CTAATTTTGGTATCGATACCGGGAGGGGGTATCGATACCATAGTTTGGTAGTATCGATACCATGG
1 CTAATTTTGGTATCAATACCGGAAGGGGGTATCGATACCATAATATAGAAGTATCGATACCAGGG
*
1745090 TAAGGGTATCAATACTAGGCAACATTGAAC
66 TAAGAGTATCAATACTAGGCAACATTGAAC
*
1745120 CTAATTTAT-GTATCAATACCGGAAGGGGGTATCGGTACCATAATATAGAAGTATC-AGTACCAG
1 CTAATTT-TGGTATCAATACCGGAAGGGGGTATCGATACCATAATATAGAAGTATCGA-TACCAG
*
1745183 GGT-AGTAGTATCGATACT
64 GGTAAG-AGTATCAATACT
1745201 GTAGAGTCAG
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
94 3 0.04
95 64 0.94
96 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.28
Consensus pattern (95 bp):
CTAATTTTGGTATCAATACCGGAAGGGGGTATCGATACCATAATATAGAAGTATCGATACCAGGG
TAAGAGTATCAATACTAGGCAACATTGAAC
Found at i:1745795 original size:110 final size:110
Alignment explanation
Indices: 1745544--1745894 Score: 351
Period size: 110 Copynumber: 3.2 Consensus size: 110
1745534 ATATCCACGA
* * *
1745544 AATTCATCATGGGTTGACGAATCA-TCGTAC-TGGCACTTTATCTGCATATCCAT-AGAATTCAT
1 AATTCATCATGGGTTGATGAATCACT-GTACAT-GCACTTTATGTGAATATCCATGA-AATTCAT
* *
1745606 CATGGGTTGATGAATCACCGTACTGGCACATTATGTT-CATAACCACAT--
63 CATGGGTTGATGAATCACCGTACAGGCACATTGT-TTGCA-AACC-CATGG
* * * *
1745654 AATTCATTATGGGTTGATGAATCACCGTACATGCACGTTATGTGAATATCCTTGAAATTCATCAT
1 AATTCATCATGGGTTGATGAATCACTGTACATGCACTTTATGTGAATATCCATGAAATTCATCAT
* *
1745719 GGGTTAATGAATCATCGTACAGGCACATTGTTTGCAAACCCATGG
66 GGGTTGATGAATCACCGTACAGGCACATTGTTTGCAAACCCATGG
* * * * * *
1745764 AATTCATCATGGGTTGATGAATCACTATACATACACTTTGTGTGCAA-ACCCACGAAATTCATCG
1 AATTCATCATGGGTTGATGAATCACTGTACATGCACTTTATGTG-AATATCCATGAAATTCATCA
* * * * *
1745828 TGAGTTGATGAATCACCGTATAGGGAC-TATGTGTGC-AACCCACGG
65 TGGGTTGATGAATCACCGTACAGGCACAT-TGTTTGCAAACCCATGG
* *
1745873 AATTCATTATGAGTTGATGAAT
1 AATTCATCATGGGTTGATGAAT
1745895 TTCCGTATAG
Statistics
Matches: 203, Mismatches: 30, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
108 3 0.01
109 35 0.17
110 161 0.79
111 4 0.02
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Consensus pattern (110 bp):
AATTCATCATGGGTTGATGAATCACTGTACATGCACTTTATGTGAATATCCATGAAATTCATCAT
GGGTTGATGAATCACCGTACAGGCACATTGTTTGCAAACCCATGG
Found at i:1745810 original size:55 final size:55
Alignment explanation
Indices: 1745544--1745894 Score: 300
Period size: 55 Copynumber: 6.4 Consensus size: 55
1745534 ATATCCACGA
* * * * * *
1745544 AATTCATCATGGGTTGACGAATCATCGTAC-TGGCACTTTATCTGCATATCCATAG
1 AATTCATCATGGGTTGATGAATCACCGTACAT-GCACTTTATGTGCAAACCCATGG
* *
1745599 AATTCATCATGGGTTGATGAATCACCGTAC-TGGCACATTATGTTCATAACCACAT--
1 AATTCATCATGGGTTGATGAATCACCGTACAT-GCACTTTATGTGCA-AACC-CATGG
* * * * *
1745654 AATTCATTATGGGTTGATGAATCACCGTACATGCACGTTATGTG-AATATCCTTGA
1 AATTCATCATGGGTTGATGAATCACCGTACATGCACTTTATGTGCAA-ACCCATGG
* * * * * *
1745709 AATTCATCATGGGTTAATGAATCATCGTACAGGCACATTGTTTGCAAACCCATGG
1 AATTCATCATGGGTTGATGAATCACCGTACATGCACTTTATGTGCAAACCCATGG
** * * * *
1745764 AATTCATCATGGGTTGATGAATCACTATACATACACTTTGTGTGCAAACCCACGA
1 AATTCATCATGGGTTGATGAATCACCGTACATGCACTTTATGTGCAAACCCATGG
* * * * * * * *
1745819 AATTCATCGTGAGTTGATGAATCACCGTATAGGGACTATGTGTGC-AACCCACGG
1 AATTCATCATGGGTTGATGAATCACCGTACATGCACTTTATGTGCAAACCCATGG
* *
1745873 AATTCATTATGAGTTGATGAAT
1 AATTCATCATGGGTTGATGAAT
1745895 TTCCGTATAG
Statistics
Matches: 245, Mismatches: 44, Indels: 15
0.81 0.14 0.05
Matches are distributed among these distances:
53 3 0.01
54 31 0.13
55 203 0.83
56 5 0.02
57 3 0.01
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Consensus pattern (55 bp):
AATTCATCATGGGTTGATGAATCACCGTACATGCACTTTATGTGCAAACCCATGG
Found at i:1745825 original size:165 final size:165
Alignment explanation
Indices: 1745542--1745847 Score: 402
Period size: 165 Copynumber: 1.9 Consensus size: 165
1745532 GCATATCCAC
* * * * *
1745542 GAAATTCATCATGGGTTGACGAATCATCGTACTGGCACTTTATCTGCATATCCATAGAATTCATC
1 GAAATTCATCATGGGTTAACGAATCATCGTACAGGCACATTATCTGCAAACCCATAGAATTCATC
* * * * *
1745607 ATGGGTTGATGAATCACCGTACTGGCACATTATGTTCATAACCACATAATTCATTATGGGTTGAT
66 ATGGGTTGATGAATCACCATACTGACACATTATGTGCATAACCACATAATTCATCATGAGTTGAT
1745672 GAATCACCGTACATGCACGTTATGTGAATATCCTT
131 GAATCACCGTACATGCACGTTATGTGAATATCCTT
* * * *
1745707 GAAATTCATCATGGGTTAATGAATCATCGTACAGGCACATTGTTTGCAAACCCATGGAATTCATC
1 GAAATTCATCATGGGTTAACGAATCATCGTACAGGCACATTATCTGCAAACCCATAGAATTCATC
* * * *
1745772 ATGGGTTGATGAATCACTATACAT-ACACTTTGTGTGCA-AACCCACGA-AATTCATCGTGAGTT
66 ATGGGTTGATGAATCACCATAC-TGACACATTATGTGCATAA-CCAC-ATAATTCATCATGAGTT
1745834 GATGAATCACCGTA
128 GATGAATCACCGTA
1745848 TAGGGACTAT
Statistics
Matches: 120, Mismatches: 18, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
164 2 0.02
165 116 0.97
166 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (165 bp):
GAAATTCATCATGGGTTAACGAATCATCGTACAGGCACATTATCTGCAAACCCATAGAATTCATC
ATGGGTTGATGAATCACCATACTGACACATTATGTGCATAACCACATAATTCATCATGAGTTGAT
GAATCACCGTACATGCACGTTATGTGAATATCCTT
Found at i:1746424 original size:147 final size:147
Alignment explanation
Indices: 1746157--1746450 Score: 588
Period size: 147 Copynumber: 2.0 Consensus size: 147
1746147 ACATCAAGTC
1746157 AGAGTCGCCTAATCAGAAACGGTATGGCATACCTGTCTACTTTTGATATATTTTAGTTGTCATGC
1 AGAGTCGCCTAATCAGAAACGGTATGGCATACCTGTCTACTTTTGATATATTTTAGTTGTCATGC
1746222 AATAGGTTTAGTAAAACGCTATGTAAAACTTTGGAATTAAACTACTGTAAAACAGTGAAATGTGG
66 AATAGGTTTAGTAAAACGCTATGTAAAACTTTGGAATTAAACTACTGTAAAACAGTGAAATGTGG
1746287 AGTATCTTTTTTTATTT
131 AGTATCTTTTTTTATTT
1746304 AGAGTCGCCTAATCAGAAACGGTATGGCATACCTGTCTACTTTTGATATATTTTAGTTGTCATGC
1 AGAGTCGCCTAATCAGAAACGGTATGGCATACCTGTCTACTTTTGATATATTTTAGTTGTCATGC
1746369 AATAGGTTTAGTAAAACGCTATGTAAAACTTTGGAATTAAACTACTGTAAAACAGTGAAATGTGG
66 AATAGGTTTAGTAAAACGCTATGTAAAACTTTGGAATTAAACTACTGTAAAACAGTGAAATGTGG
1746434 AGTATCTTTTTTTATTT
131 AGTATCTTTTTTTATTT
1746451 GTATATGTAA
Statistics
Matches: 147, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
147 147 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (147 bp):
AGAGTCGCCTAATCAGAAACGGTATGGCATACCTGTCTACTTTTGATATATTTTAGTTGTCATGC
AATAGGTTTAGTAAAACGCTATGTAAAACTTTGGAATTAAACTACTGTAAAACAGTGAAATGTGG
AGTATCTTTTTTTATTT
Found at i:1747104 original size:73 final size:71
Alignment explanation
Indices: 1746975--1747237 Score: 239
Period size: 73 Copynumber: 3.6 Consensus size: 71
1746965 CGGATTCCCT
* * * * * *
1746975 TGAAACAAAAATTTTAATCTCACTTGAGATACTTTTTTCATAGAACAAGT-AT-TCTCACTCGAG
1 TGAAA-AAAAATTTT-ATCTCGCTTGAGATAGTTTTCTC-TTGAA-AATTCTTGTCTCACTCGAG
1747038 ACAGTTTCTCC
62 ACAGTTTCT-C
* *
1747049 TGAAAGAAAAATGTAATCTCGCTTGAGATAGTTTTCTCTTGAAAATT-TTCGTCTCACTCGAGAC
1 TGAAA-AAAAATTTTATCTCGCTTGAGATAGTTTTCTCTTGAAAATTCTT-GTCTCACTCGAGAC
1747113 AGTTTCTC
64 AGTTTCTC
* * * * * * *
1747121 TCAAAACTAAATTTTATCTCGTTTGAGATAGGTTTTCTCTTGAAAATTCTTGTGTCACTCAATAT
1 TGAAAA-AAAATTTTATCTCGCTTGAGATA-GTTTTCTCTTGAAAATTCTTGTCTCACTCGAGAC
1747186 AGTTTCTC
64 AGTTTCTC
* * *
1747194 TCGAAATAAAATTTTATCTCACTTGAGATAATTTT-TCTT-AAAAT
1 T-GAAAAAAAATTTTATCTCGCTTGAGATAGTTTTCTCTTGAAAAT
1747238 AAATTTTGTC
Statistics
Matches: 159, Mismatches: 24, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
70 5 0.03
71 9 0.06
72 32 0.20
73 96 0.60
74 17 0.11
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (71 bp):
TGAAAAAAAATTTTATCTCGCTTGAGATAGTTTTCTCTTGAAAATTCTTGTCTCACTCGAGACAG
TTTCTC
Found at i:1747253 original size:36 final size:37
Alignment explanation
Indices: 1747188--1747269 Score: 105
Period size: 36 Copynumber: 2.2 Consensus size: 37
1747178 CTCAATATAG
** *
1747188 TTTCTCTCGAAATAAAATTTTATCTCACTTGAGATAAT
1 TTTCTCTTAAAATAAAATTTTATCCCACTTGAGAT-AT
*
1747226 TTT-TCTTAAAAT-AAATTTTGTCCCACTTGAGATAT
1 TTTCTCTTAAAATAAAATTTTATCCCACTTGAGATAT
1747261 TTTCTCTTA
1 TTTCTCTTA
1747270 TAAAAGTTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
35 5 0.13
36 24 0.62
37 7 0.18
38 3 0.08
ACGTcount: A:0.30, C:0.16, G:0.07, T:0.46
Consensus pattern (37 bp):
TTTCTCTTAAAATAAAATTTTATCCCACTTGAGATAT
Found at i:1749490 original size:24 final size:24
Alignment explanation
Indices: 1749463--1749516 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
1749453 ATAGTGTCAA
*
1749463 GAGTACACAAATTTACTAATATAG
1 GAGTACACAAATGTACTAATATAG
1749487 GAGTACACAAATGTACTAATATAG
1 GAGTACACAAATGTACTAATATAG
1749511 GA-TACA
1 GAGTACA
1749517 AGTGTTATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 4 0.14
24 25 0.86
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (24 bp):
GAGTACACAAATGTACTAATATAG
Found at i:1749501 original size:147 final size:145
Alignment explanation
Indices: 1749196--1749593 Score: 436
Period size: 147 Copynumber: 2.7 Consensus size: 145
1749186 TGGTGCCAGT
* *
1749196 AGTACACGAATGTACTGAACATA-ATACAAGT-ATTGTAGAACACAACATCAGGTATAGATAATC
1 AGTACACGAATGTACT-AA-AAAGATACAAGTGA-TGTAGAACACATCATCA-GTATAGATAATC
* * * * * *
1749259 AAGATGGTAGTT--CAACGTTAAAACATTATGAAACTAATAATGCACATATAGTGTCAGGAGTAC
62 AAGATGGTAGTTCACAACGTCAAAACATTATGAACCCAATAATACAAATATAGTGTCAAGAGTAC
*
1749322 ACGAATGTACTAATACAAG
127 ACAAATGTACTAATACAAG
*
1749341 AGTACATGAATGTACTAAAAAGATTACAAGTGATGTAGAACACATCATCAAGTATAGATAATCAA
1 AGTACACGAATGTACTAAAAAGA-TACAAGTGATGTAGAACACATCATC-AGTATAGATAATCAA
* * *
1749406 GATGGTAGTTCACAATGTCAAAACATTATGAACCCACTAATATAAATATAGTGTCAAGAGTACAC
64 GATGGTAGTTCACAACGTCAAAACATTATGAACCCAATAATACAAATATAGTGTCAAGAGTACAC
* * *
1749471 AAATTTACTAATATAGG
129 AAATGTACTAATACAAG
* * * * * *
1749488 AGTACACAAATGTACTAATATAGGATACAAGTGTTATAGAACACGGT-ATC---ATGGATAAT-A
1 AGTACACGAATGTACTAA-A-AAGATACAAGTGATGTAGAACAC-ATCATCAGTATAGATAATCA
*
1749548 AGGATGGTAGTTCACAACGTCAAAACATTATGAACCCCATAATACA
63 A-GATGGTAGTTCACAACGTCAAAACATTATGAACCCAATAATACA
1749594 TATACAGTAC
Statistics
Matches: 216, Mismatches: 27, Indels: 21
0.82 0.10 0.08
Matches are distributed among these distances:
143 4 0.02
144 51 0.24
145 61 0.28
146 2 0.01
147 73 0.34
148 21 0.10
149 4 0.02
ACGTcount: A:0.44, C:0.15, G:0.16, T:0.25
Consensus pattern (145 bp):
AGTACACGAATGTACTAAAAAGATACAAGTGATGTAGAACACATCATCAGTATAGATAATCAAGA
TGGTAGTTCACAACGTCAAAACATTATGAACCCAATAATACAAATATAGTGTCAAGAGTACACAA
ATGTACTAATACAAG
Found at i:1749591 original size:144 final size:143
Alignment explanation
Indices: 1749196--1749593 Score: 387
Period size: 145 Copynumber: 2.7 Consensus size: 143
1749186 TGGTGCCAGT
* * * * * * *
1749196 AGTACACGAATGTACTGAACATAATACAAGT-ATTGTAGAACACAACATCAGGTATAGATAATCA
1 AGTACACAAATGTACTAAAAAGATTACAAGTGA-TATAGAACACATCATCA---ATAGATAATCA
* ** * * *
1749260 AGATGGTAGTT--CAACGTTAAAACATTATGAAACTAATAATGCACATATAGTGTCAGGAGTACA
62 AGATGGTAGTTCACAACGTCAAAACATTATG-AACCCATAATACAAATATAGTGTCAAGAGTACA
*
1749323 CGAATGTACTAATACAAG
126 CAAATGTACTAATACAAG
** *
1749341 AGTACATGAATGTACTAAAAAGATTACAAGTGATGTAGAACACATCATCAAGTATAGATAATCAA
1 AGTACACAAATGTACTAAAAAGATTACAAGTGATATAGAACACATCATC-A--ATAGATAATCAA
* *
1749406 GATGGTAGTTCACAATGTCAAAACATTATGAACCCACTAATATAAATATAGTGTCAAGAGTACAC
63 GATGGTAGTTCACAACGTCAAAACATTATGAACCCA-TAATACAAATATAGTGTCAAGAGTACAC
* * *
1749471 AAATTTACTAATATAGG
127 AAATGTACTAATACAAG
* * * *
1749488 AGTACACAAATGTACTAATATAGGA-TACAAGTGTTATAGAACACGGT-ATC-ATGGATAAT-AA
1 AGTACACAAATGTACTAA-A-AAGATTACAAGTGATATAGAACAC-ATCATCAATAGATAATCAA
1749549 GGATGGTAGTTCACAACGTCAAAACATTATGAACCCCATAATACA
63 -GATGGTAGTTCACAACGTCAAAACATTATGAA-CCCATAATACA
1749594 TATACAGTAC
Statistics
Matches: 216, Mismatches: 27, Indels: 21
0.82 0.10 0.08
Matches are distributed among these distances:
143 2 0.01
144 45 0.21
145 69 0.32
146 6 0.03
147 69 0.32
148 21 0.10
149 4 0.02
ACGTcount: A:0.44, C:0.15, G:0.16, T:0.25
Consensus pattern (143 bp):
AGTACACAAATGTACTAAAAAGATTACAAGTGATATAGAACACATCATCAATAGATAATCAAGAT
GGTAGTTCACAACGTCAAAACATTATGAACCCATAATACAAATATAGTGTCAAGAGTACACAAAT
GTACTAATACAAG
Found at i:1756961 original size:40 final size:40
Alignment explanation
Indices: 1756897--1757047 Score: 205
Period size: 40 Copynumber: 3.8 Consensus size: 40
1756887 TATGCATTTT
* *
1756897 AGTGC-TTACAGATAAGGTCCTGCCCACCATATGCATCGA
1 AGTGCATTACACATAAGGTCGTGCCCACCATATGCATCGA
* * *
1756936 AGTGCTTTACACATAAGGTTGTGCCCACCATATGCACCGA
1 AGTGCATTACACATAAGGTCGTGCCCACCATATGCATCGA
* *
1756976 AGTGCATTACACATAAGGTCGTGCCCACCATATTCATGGA
1 AGTGCATTACACATAAGGTCGTGCCCACCATATGCATCGA
* * *
1757016 AGTGCATTACACATAGGGTTGTGTCCACCATA
1 AGTGCATTACACATAAGGTCGTGCCCACCATA
1757048 AGAACCGAAG
Statistics
Matches: 99, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
39 5 0.05
40 94 0.95
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (40 bp):
AGTGCATTACACATAAGGTCGTGCCCACCATATGCATCGA
Found at i:1756994 original size:80 final size:79
Alignment explanation
Indices: 1756897--1757063 Score: 235
Period size: 80 Copynumber: 2.1 Consensus size: 79
1756887 TATGCATTTT
* *
1756897 AGTGCTTACAGATAAGGTCCTGCCCACCATATGCATCGAAGTGCTTTACACATAAGGTTGTGCCC
1 AGTGCTTACACATAAGGTCCTGCCCACCATATGCATCGAAGTGCATTACACATAAGGTTGTGCCC
* *
1756962 ACCATATGCACCGA
66 ACCATAAGAACCGA
* * * * *
1756976 AGTGCATTACACATAAGGTCGTGCCCACCATATTCATGGAAGTGCATTACACATAGGGTTGTGTC
1 AGTGC-TTACACATAAGGTCCTGCCCACCATATGCATCGAAGTGCATTACACATAAGGTTGTGCC
1757041 CACCATAAGAACCGA
65 CACCATAAGAACCGA
*
1757056 AGTTCTTA
1 AGTGCTTA
1757064 ATTGATATGC
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
79 8 0.10
80 69 0.90
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.25
Consensus pattern (79 bp):
AGTGCTTACACATAAGGTCCTGCCCACCATATGCATCGAAGTGCATTACACATAAGGTTGTGCCC
ACCATAAGAACCGA
Found at i:1757192 original size:19 final size:21
Alignment explanation
Indices: 1757168--1757218 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
1757158 GGCAAAGTAT
1757168 ATTATCATA-A-TTCATGATA
1 ATTATCATATAGTTCATGATA
1757187 ATTATCATATATGTTCATGATA
1 ATTATCATATA-GTTCATGATA
**
1757209 AACATCATAT
1 ATTATCATAT
1757219 GTAAAGATCG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 9 0.33
20 1 0.04
22 17 0.63
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (21 bp):
ATTATCATATAGTTCATGATA
Found at i:1760826 original size:2 final size:2
Alignment explanation
Indices: 1760819--1760895 Score: 140
Period size: 2 Copynumber: 39.5 Consensus size: 2
1760809 CGTAACAACG
1760819 TA TA TA TA TA TA -A TA TA TA T- 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
1760859 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
1760896 GTTTATTTTG
Statistics
Matches: 73, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.03
2 71 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1766097 original size:2 final size:2
Alignment explanation
Indices: 1766092--1766119 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1766082 ATTTTTTAAC
1766092 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
1766120 TATCCCTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1766316 original size:81 final size:81
Alignment explanation
Indices: 1766208--1766636 Score: 576
Period size: 81 Copynumber: 5.3 Consensus size: 81
1766198 GCTTTTCACT
* * * * * **
1766208 TAACTTGCATATTTGACA-CTTTCCTGTCAAATGCATAGCTAATCCATTATTCTTTTACTCAACA
1 TAACTGGCATAATTGACACCTTT-CTGTCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACA
* *
1766272 GTGTTTAACCGATCATC
65 GTATTTAACCGTTCATC
* *
1766289 TAACTGGCATAGTTGACACCTTTCTGTCAATTGCA-AATTAGGCCATTATTCTTTTACTCAACAG
1 TAACTGGCATAATTGACACCTTTCTGTCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACAG
* *
1766353 TGTTTAACCGTACATC
66 TATTTAACCGTTCATC
* * * * *
1766369 TAACTGGCATAGTTGACACCTTTCTATCAATTGCACAATTAGGCCATTATTATTTTACTCAACGG
1 TAACTGGCATAATTGACACCTTTCTGTCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACAG
1766434 TATTTAACCGTTCATC
66 TATTTAACCGTTCATC
* * *
1766450 TAACTGGTATAATTGACACC-TTCTGCCAATTGCACAGGTAGGCCATTATTCTTTTACTCAACAG
1 TAACTGGCATAATTGACACCTTTCTGTCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACAG
1766514 TATTTAACCGTTCATC
66 TATTTAACCGTTCATC
* * * * **
1766530 TAACTAGCATAATTGACACCTTTCTGCCAATTACACAGTTAGACCATTATTCTTTTACTCAATGG
1 TAACTGGCATAATTGACACCTTTCTGTCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACAG
1766595 TATTTAACCGTTCATC
66 TATTTAACCGTTCATC
*
1766611 TAACTGGCATAATTGACACATTTCTG
1 TAACTGGCATAATTGACACCTTTCTG
1766637 CCATTTAGAT
Statistics
Matches: 314, Mismatches: 31, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
80 145 0.46
81 165 0.53
82 4 0.01
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (81 bp):
TAACTGGCATAATTGACACCTTTCTGTCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACAG
TATTTAACCGTTCATC
Found at i:1766442 original size:161 final size:162
Alignment explanation
Indices: 1766251--1766639 Score: 584
Period size: 161 Copynumber: 2.4 Consensus size: 162
1766241 CATAGCTAAT
* * * * *
1766251 CCATTATTCTTTTACTCAACAGTGTTTAACCGATCATCTAACTGGCATAGTTGACACCTTTCTGT
1 CCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGC
* * *
1766316 CAATTGCA-AATTAGGCCATTATTCTTTTACTCAACAGTGTTTAACCGTACATCTAACTGGCATA
66 CAATTGCACAAGTAGGCCATTATTCTTTTACTCAACAGTATTTAACCGTACATCTAACTAGCATA
* * * *
1766380 GTTGACACCTTTCTATCAATTGCACAATTAGG
131 ATTGACACCTTTCTACCAATTACACAATTAGA
* *
1766412 CCATTATTATTTTACTCAACGGTATTTAACCGTTCATCTAACTGGTATAATTGACACC-TTCTGC
1 CCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGC
* *
1766476 CAATTGCACAGGTAGGCCATTATTCTTTTACTCAACAGTATTTAACCGTTCATCTAACTAGCATA
66 CAATTGCACAAGTAGGCCATTATTCTTTTACTCAACAGTATTTAACCGTACATCTAACTAGCATA
* *
1766541 ATTGACACCTTTCTGCCAATTACACAGTTAGA
131 ATTGACACCTTTCTACCAATTACACAATTAGA
* *
1766573 CCATTATTCTTTTACTCAATGGTATTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGC
1 CCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGC
1766638 CA
66 CA
1766640 TTTAGATAGT
Statistics
Matches: 204, Mismatches: 22, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
160 13 0.06
161 183 0.90
162 8 0.04
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.36
Consensus pattern (162 bp):
CCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGC
CAATTGCACAAGTAGGCCATTATTCTTTTACTCAACAGTATTTAACCGTACATCTAACTAGCATA
ATTGACACCTTTCTACCAATTACACAATTAGA
Found at i:1766652 original size:81 final size:81
Alignment explanation
Indices: 1766251--1766639 Score: 575
Period size: 80 Copynumber: 4.8 Consensus size: 81
1766241 CATAGCTAAT
* * * *
1766251 CCATTATTCTTTTACTCAACAGTGTTTAACCGATCATCTAACTGGCATAGTTGACACCTTTCTGT
1 CCATTATTCTTTTACTCAACAGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGC
*
1766316 CAATTGCA-AATTAGG
66 CAATTGCACAGTTAGG
* * * **
1766331 CCATTATTCTTTTACTCAACAGTGTTTAACCGTACATCTAACTGGCATAGTTGACACCTTTCTAT
1 CCATTATTCTTTTACTCAACAGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGC
*
1766396 CAATTGCACAATTAGG
66 CAATTGCACAGTTAGG
* * *
1766412 CCATTATTATTTTACTCAACGGTATTTAACCGTTCATCTAACTGGTATAATTGACACC-TTCTGC
1 CCATTATTCTTTTACTCAACAGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGC
*
1766476 CAATTGCACAGGTAGG
66 CAATTGCACAGTTAGG
*
1766492 CCATTATTCTTTTACTCAACAGTATTTAACCGTTCATCTAACTAGCATAATTGACACCTTTCTGC
1 CCATTATTCTTTTACTCAACAGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGC
* *
1766557 CAATTACACAGTTAGA
66 CAATTGCACAGTTAGG
** *
1766573 CCATTATTCTTTTACTCAATGGTATTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTGC
1 CCATTATTCTTTTACTCAACAGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGC
1766638 CA
66 CA
1766640 TTTAGATAGT
Statistics
Matches: 283, Mismatches: 24, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
80 142 0.50
81 141 0.50
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.36
Consensus pattern (81 bp):
CCATTATTCTTTTACTCAACAGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGC
CAATTGCACAGTTAGG
Found at i:1766780 original size:68 final size:68
Alignment explanation
Indices: 1766605--1766792 Score: 261
Period size: 68 Copynumber: 2.8 Consensus size: 68
1766595 TATTTAACCG
* * *
1766605 TTCATCTAACTGGCATAATTGACACATTTCTGCCATTTAG-ATAGTTAGGCCTCAAAGTCACTTA
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCATTT-GCATAGTTAGGCCTCAAAGGCACTTA
1766669 GCCT
65 GCCT
* * *
1766673 TTCATCTAACTGGCATAAATGACACATTTGTGTCTTTTGCATAGTTAAGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCATTTGCATAGTTAGGCCTCAAAGGCACTTAG
1766738 CCT
66 CCT
* * * * *
1766741 TTCATCTAACTGGTATAAATAACACCTCTCTGTCATTTGCACAGTTAGGCCT
1 TTCATCTAACTGGCATAAATGACACATTTCTGTCATTTGCATAGTTAGGCCT
1766793 ATAATCGTTT
Statistics
Matches: 105, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
67 1 0.01
68 104 0.99
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACATTTCTGTCATTTGCATAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:1767576 original size:95 final size:95
Alignment explanation
Indices: 1767462--1767658 Score: 256
Period size: 95 Copynumber: 2.1 Consensus size: 95
1767452 CCTAGTACCG
* * * * **
1767462 ATACTTCTATACTATGGTATCGATACCCCCTTATGGTATCGATACTTATTTTATG-TTCGATGTT
1 ATACTACTATACTAAGGTATCGATACCCCCTTACGGTATCAATACCGATTTT-TGATTCGATGTT
* *
1767526 GCCTA-GTATTGATACTCTTA-CTATGATATCA
65 G-CTAGGTATCGATACCCTTATC-ATGATATCA
1767557 ATACTACTATACTAAGGTATCGATACCCCCTTACGGTATCAATACCGATTTTTGATTCGATGTTG
1 ATACTACTATACTAAGGTATCGATACCCCCTTACGGTATCAATACCGATTTTTGATTCGATGTTG
* *
1767622 CTAGGTATCGATACCCTTATCATGGTATCG
66 CTAGGTATCGATACCCTTATCATGATATCA
1767652 ATACTAC
1 ATACTAC
1767659 CTCTTCGGTA
Statistics
Matches: 89, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
94 5 0.06
95 83 0.93
96 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (95 bp):
ATACTACTATACTAAGGTATCGATACCCCCTTACGGTATCAATACCGATTTTTGATTCGATGTTG
CTAGGTATCGATACCCTTATCATGATATCA
Found at i:1779524 original size:146 final size:148
Alignment explanation
Indices: 1779260--1779553 Score: 574
Period size: 146 Copynumber: 2.0 Consensus size: 148
1779250 AATTGGTATC
1779260 ATTTGAACTTAAATTTGCATCCCAAAAAGTTTCAGACACATAGCAATACAAATTATGATAGAAAC
1 ATTTGAACTTAAATTTGCATCCCAAAAAGTTTCAGACACATAGCAATACAAATTATGATAGAAAC
1779325 ATAATTTAAACGTGAAACTTAATATCGAATTGGGAGAAAAAACATCAAACACAACTTATC-GG-T
66 ATAATTTAAACGTGAAACTTAATATCGAATTGGGAGAAAAAACATCAAACACAACTTATCGGGTT
1779388 TGAATTTGGTGAAACAAA
131 TGAATTTGGTGAAACAAA
1779406 ATTTGAACTTAAATTTGCATCCCAAAAAGTTTCAGACACATAGCAATACAAATTATGATAGAAAC
1 ATTTGAACTTAAATTTGCATCCCAAAAAGTTTCAGACACATAGCAATACAAATTATGATAGAAAC
1779471 ATAATTTAAACGTGAAACTTAATATCGAATTGGGAGAAAAAACATCAAACACAACTTATCGGGTT
66 ATAATTTAAACGTGAAACTTAATATCGAATTGGGAGAAAAAACATCAAACACAACTTATCGGGTT
1779536 TGAATTTGGTGAAACAAA
131 TGAATTTGGTGAAACAAA
1779554 CTTCGGATTC
Statistics
Matches: 146, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
146 125 0.86
147 2 0.01
148 19 0.13
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (148 bp):
ATTTGAACTTAAATTTGCATCCCAAAAAGTTTCAGACACATAGCAATACAAATTATGATAGAAAC
ATAATTTAAACGTGAAACTTAATATCGAATTGGGAGAAAAAACATCAAACACAACTTATCGGGTT
TGAATTTGGTGAAACAAA
Found at i:1780715 original size:5 final size:5
Alignment explanation
Indices: 1780705--1780731 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1780695 TAGTTTTGTA
1780705 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
1780732 TTCTTTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:1782903 original size:24 final size:24
Alignment explanation
Indices: 1782851--1782903 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
1782841 AACAACTAAG
**
1782851 GATAAAATCCTAAAACATTCAAAT
1 GATAAAATCCTAAAACAAACAAAT
* * *
1782875 AATAAAATCCTAAAATAAACAAGT
1 GATAAAATCCTAAAACAAACAAAT
1782899 GATAA
1 GATAA
1782904 TTCCCAAAAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.58, C:0.13, G:0.06, T:0.23
Consensus pattern (24 bp):
GATAAAATCCTAAAACAAACAAAT
Found at i:1785309 original size:176 final size:176
Alignment explanation
Indices: 1785015--1785376 Score: 679
Period size: 176 Copynumber: 2.1 Consensus size: 176
1785005 AAATGATAAG
1785015 AATTTGAATTAAATGGGATAGGTTTGGTGATAAAATCGTGTGGGGACTACAGATTTTTAAAATGG
1 AATTTGAATTAAATGGGATAGGTTTGGTGATAAAATCGTGTGGGGACTACAGATTTTTAAAATGG
*
1785080 TAAAGAGTTTGAAGTGAATAAAATTATTGTGCAAAAGAAAATGTCGGGTTTTAAGTTTCCAGGAG
66 TAAAGAGTTTGAAGTAAATAAAATTATTGTGCAAAAGAAAATGTCGGGTTTTAAGTTTCCAGGAG
*
1785145 AGTGGAATTTGATTTGGCACCTGGGACCAAGGGGCATTTTAAAAAT
131 AGTGGAATTTGATTTGGCACCTGGGACCAAGGGGCATTCTAAAAAT
*
1785191 AATTTGAATTAAATGGGATAGGTTTGGTGATAAAATCGTGTGGGGACTACAGATTTTTAAATTGG
1 AATTTGAATTAAATGGGATAGGTTTGGTGATAAAATCGTGTGGGGACTACAGATTTTTAAAATGG
*
1785256 TAAAGAGTTTGAAGTAAATAAAATTATTGTGGAAAAGAAAATGTCGGGTTTTAAGTTTCCAGGAG
66 TAAAGAGTTTGAAGTAAATAAAATTATTGTGCAAAAGAAAATGTCGGGTTTTAAGTTTCCAGGAG
*
1785321 AGTGGAATTTGATTTGGCACCTGGGACCAAGGGGTATTCTAAAAAT
131 AGTGGAATTTGATTTGGCACCTGGGACCAAGGGGCATTCTAAAAAT
1785367 AATTTGAATT
1 AATTTGAATT
1785377 GGTCAAATGG
Statistics
Matches: 181, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
176 181 1.00
ACGTcount: A:0.35, C:0.07, G:0.26, T:0.32
Consensus pattern (176 bp):
AATTTGAATTAAATGGGATAGGTTTGGTGATAAAATCGTGTGGGGACTACAGATTTTTAAAATGG
TAAAGAGTTTGAAGTAAATAAAATTATTGTGCAAAAGAAAATGTCGGGTTTTAAGTTTCCAGGAG
AGTGGAATTTGATTTGGCACCTGGGACCAAGGGGCATTCTAAAAAT
Found at i:1785661 original size:5 final size:5
Alignment explanation
Indices: 1785647--1785722 Score: 50
Period size: 5 Copynumber: 14.8 Consensus size: 5
1785637 AAATTCAAGG
* * * *
1785647 AAAAT AAAAAT AAAAT AAACATT CAATT AAAAT -AAAT ATATT AAAAT
1 AAAAT -AAAAT AAAAT AAA-A-T AAAAT AAAAT AAAAT AAAAT AAAAT
1785694 AAAA- ATAAAT AAAAT -AAAT GAAAAT AAAA
1 AAAAT A-AAAT AAAAT AAAAT -AAAAT AAAA
1785723 ATGGGTTGCC
Statistics
Matches: 55, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
4 9 0.16
5 32 0.58
6 11 0.20
7 3 0.05
ACGTcount: A:0.72, C:0.03, G:0.01, T:0.24
Consensus pattern (5 bp):
AAAAT
Found at i:1785672 original size:28 final size:31
Alignment explanation
Indices: 1785639--1785696 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 31
1785629 GTACTTGAAA
1785639 ATTCAAGGAAAATAAA-A-A-TAAAATAAAC
1 ATTCAAGGAAAATAAATATATTAAAATAAAC
**
1785667 ATTCAATTAAAATAAATATATTAAAATAAA
1 ATTCAAGGAAAATAAATATATTAAAATAAA
1785697 AATAAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 14 0.56
29 1 0.04
30 1 0.04
31 9 0.36
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (31 bp):
ATTCAAGGAAAATAAATATATTAAAATAAAC
Found at i:1785691 original size:14 final size:15
Alignment explanation
Indices: 1785657--1785712 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 15
1785647 AAAATAAAAA
*
1785657 TAAAATAAACATTCAAT
1 TAAAATAAATA-T-AAT
1785674 TAAAATAAATAT-AT
1 TAAAATAAATATAAT
* *
1785688 TAAAATAAAAATAAA
1 TAAAATAAATATAAT
1785703 TAAAATAAAT
1 TAAAATAAAT
1785713 GAAAATAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
14 13 0.38
15 10 0.29
16 1 0.03
17 10 0.29
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.29
Consensus pattern (15 bp):
TAAAATAAATATAAT
Found at i:1785708 original size:25 final size:24
Alignment explanation
Indices: 1785676--1785724 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
1785666 CATTCAATTA
* *
1785676 AAATAAATATATTAAAATAAAAAT
1 AAATAAATAAATGAAAATAAAAAT
1785700 AAATAAAATAAATGAAAATAAAAAT
1 AAAT-AAATAAATGAAAATAAAAAT
1785725 GGGTTGCCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (24 bp):
AAATAAATAAATGAAAATAAAAAT
Found at i:1786162 original size:191 final size:192
Alignment explanation
Indices: 1785792--1786181 Score: 633
Period size: 191 Copynumber: 2.0 Consensus size: 192
1785782 AAACGACAAT
1785792 TTCTAAGAGAGATGCTTCCTCCACATCATATATTTTTTCCAACTAAGAAATTTCTTATGAGAAAT
1 TTCTAAGAGAGATGCTTCCTCCACATCATATATTTTTTCCAACTAAGAAATTTCTTATGAGAAAT
* *
1785857 TCTATGATTAATAATTTCCTTCAGTTTTTCCTTGTAGATTCTAACATTCTCATAAGCATTTATTC
66 TCTATGATTAACAA--T-CTTCAGTTTTTCCTTGTAGATTCAAACATTCTCATAAGCATTTATTC
* * *
1785922 GGATCTTTTTCAGCATTGGAAGTTTATCCGAAATCTATAAATTATCAACTTCACCCAAAAATGTG
128 GGATCTTTTTCAGAATTGGAAGTTTATACGAAATCGATAAATTATCAACTTCACCCAAAAATGTG
* *
1785987 TTCTAAGAGAGATGCTTCCTCCACTTCATATATTTTTTCCAACTAAGTAATTTCTTATGAGAAAT
1 TTCTAAGAGAGATGCTTCCTCCACATCATATATTTTTTCCAACTAAGAAATTTCTTATGAGAAAT
*
1786052 TCTATGATTAACAA-GTTCA-TTTTATCCTTGTAGATTCAAACATTCTCATAAGCATTTATTCGG
66 TCTATGATTAACAATCTTCAGTTTT-TCCTTGTAGATTCAAACATTCTCATAAGCATTTATTCGG
*
1786115 ATCTTTTTCA-AATTTGGAAGTTTATATGAAATCGATAAATTATCAACTTCACCCAAAAATGTG
130 ATCTTTTTCAGAA-TTGGAAGTTTATACGAAATCGATAAATTATCAACTTCACCCAAAAATGTG
1786178 TTCT
1 TTCT
1786182 TTAAATATTT
Statistics
Matches: 184, Mismatches: 9, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
190 5 0.03
191 103 0.56
195 76 0.41
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.40
Consensus pattern (192 bp):
TTCTAAGAGAGATGCTTCCTCCACATCATATATTTTTTCCAACTAAGAAATTTCTTATGAGAAAT
TCTATGATTAACAATCTTCAGTTTTTCCTTGTAGATTCAAACATTCTCATAAGCATTTATTCGGA
TCTTTTTCAGAATTGGAAGTTTATACGAAATCGATAAATTATCAACTTCACCCAAAAATGTG
Found at i:1793448 original size:97 final size:97
Alignment explanation
Indices: 1793282--1793478 Score: 394
Period size: 97 Copynumber: 2.0 Consensus size: 97
1793272 TTTTAGCGGC
1793282 ATTTTTTAACCCTATAGCGGCGTTTATAAATGCCGTTAAAAACTTTCCCGACGCTTGCAAAACCA
1 ATTTTTTAACCCTATAGCGGCGTTTATAAATGCCGTTAAAAACTTTCCCGACGCTTGCAAAACCA
1793347 CCGCAAGTAGTGCCGCTATAACGAGCGCCGCA
66 CCGCAAGTAGTGCCGCTATAACGAGCGCCGCA
1793379 ATTTTTTAACCCTATAGCGGCGTTTATAAATGCCGTTAAAAACTTTCCCGACGCTTGCAAAACCA
1 ATTTTTTAACCCTATAGCGGCGTTTATAAATGCCGTTAAAAACTTTCCCGACGCTTGCAAAACCA
1793444 CCGCAAGTAGTGCCGCTATAACGAGCGCCGCA
66 CCGCAAGTAGTGCCGCTATAACGAGCGCCGCA
1793476 ATT
1 ATT
1793479 GTTAGCGGCA
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 100 1.00
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.25
Consensus pattern (97 bp):
ATTTTTTAACCCTATAGCGGCGTTTATAAATGCCGTTAAAAACTTTCCCGACGCTTGCAAAACCA
CCGCAAGTAGTGCCGCTATAACGAGCGCCGCA
Found at i:1793682 original size:43 final size:43
Alignment explanation
Indices: 1793526--1793656 Score: 199
Period size: 43 Copynumber: 3.0 Consensus size: 43
1793516 TCGAGACATA
* * *
1793526 TAGCGACGTTTGTCTTTACAAACGCCGTTATTAACTGTGTATT
1 TAGCGACGTTTGTCTTTATAAACGCCGCTATTGACTGTGTATT
* * *
1793569 TAGCGGCGTTTGTCTTTATAAACGTCGCTATTGACTGCGTATT
1 TAGCGACGTTTGTCTTTATAAACGCCGCTATTGACTGTGTATT
*
1793612 TAGCGACGTTTGTCTTTGTAAACGCCGCTATTGACTGTGTATT
1 TAGCGACGTTTGTCTTTATAAACGCCGCTATTGACTGTGTATT
1793655 TA
1 TA
1793657 ATGTCATTTG
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 78 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.40
Consensus pattern (43 bp):
TAGCGACGTTTGTCTTTATAAACGCCGCTATTGACTGTGTATT
Found at i:1796778 original size:42 final size:42
Alignment explanation
Indices: 1796690--1797096 Score: 235
Period size: 42 Copynumber: 9.9 Consensus size: 42
1796680 AGTATATTTA
* * * * **
1796690 TTTAACGGTGTTTGTGTTTAAAACGCTACTAAAGTACAAG-C
1 TTTAGCGGCGTTTGTGCTAAAAACGCCGCTAAAGTACAAGTC
* * * *
1796731 ATTTAGCGGCGTTTGTGCTTAAAATGCCACTAAAGTACGAGTC
1 -TTTAGCGGCGTTTGTGCTAAAAACGCCGCTAAAGTACAAGTC
**** * * * * * *
1796774 TTTAGCAATATTTGT-ATAAAAATGACACTTAAGTACGAGTC
1 TTTAGCGGCGTTTGTGCTAAAAACGCCGCTAAAGTACAAGTC
* *
1796815 TTTA-CTAGCGTTTGT-ATAAAAACGCCGCTAAA-TACAAGTAC
1 TTTAGC-GGCGTTTGTGCTAAAAACGCCGCTAAAGTACAAGT-C
** * * * * * * *
1796856 TTTAGC-GTATTTTTACTTAAAATGCCGTTAATA-TACAGGAC
1 TTTAGCGGCGTTTGTGCTAAAAACGCCGCTAA-AGTACAAGTC
** * * *
1796897 TTTAGCAACGATTGTGCTTAAAACGCCGCTAAAGTACAAGTT
1 TTTAGCGGCGTTTGTGCTAAAAACGCCGCTAAAGTACAAGTC
* * * *
1796939 TTTAGCGGCGTTTGTAC-AAAAACACCGCTAAAGTA-TAGTA
1 TTTAGCGGCGTTTGTGCTAAAAACGCCGCTAAAGTACAAGTC
* * * * * *
1796979 ATTAGTGGCGTTTAT-ATAAAAACGCCACTAATGTACAAGTC
1 TTTAGCGGCGTTTGTGCTAAAAACGCCGCTAAAGTACAAGTC
* *
1797020 TTTAGCGGCGTTTGTGCTTAAAACGCCGCTAGAGTA-AGAGTC
1 TTTAGCGGCGTTTGTGCTAAAAACGCCGCTAAAGTACA-AGTC
* *
1797062 TTTAGCGGCGTTTGTAC-AAAAATGCCGCTAAAGTA
1 TTTAGCGGCGTTTGTGCTAAAAACGCCGCTAAAGTA
1797097 TATTAATTAG
Statistics
Matches: 282, Mismatches: 71, Indels: 25
0.75 0.19 0.07
Matches are distributed among these distances:
40 42 0.15
41 117 0.41
42 122 0.43
43 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (42 bp):
TTTAGCGGCGTTTGTGCTAAAAACGCCGCTAAAGTACAAGTC
Found at i:1796829 original size:41 final size:41
Alignment explanation
Indices: 1796751--1796836 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 41
1796741 GTTTGTGCTT
* *
1796751 AAAATGCCACTAAAGTACGAGTCTTTAGCAATATTTGTATA
1 AAAATGACACTAAAGTACGAGTCTTTAGCAACATTTGTATA
* * *
1796792 AAAATGACACTTAAGTACGAGTCTTTA-CTAGCGTTTGTATA
1 AAAATGACACTAAAGTACGAGTCTTTAGC-AACATTTGTATA
1796833 AAAA
1 AAAA
1796837 CGCCGCTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 1 0.03
41 38 0.97
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (41 bp):
AAAATGACACTAAAGTACGAGTCTTTAGCAACATTTGTATA
Found at i:1797000 original size:40 final size:40
Alignment explanation
Indices: 1796916--1797214 Score: 251
Period size: 40 Copynumber: 7.3 Consensus size: 40
1796906 GATTGTGCTT
* * *
1796916 AAAACGCCGCTAAAGTACAAGTTTTTAGCGGCGTTTGTACA
1 AAAACGCCGCTAAAGTA-TAGTATTTAGCGGCGTTTGTATA
* * * *
1796957 AAAACACCGCTAAAGTATAGTAATTAGTGGCGTTTATATA
1 AAAACGCCGCTAAAGTATAGTATTTAGCGGCGTTTGTATA
* * * * * *
1796997 AAAACGCCACTAATGTACAAGTCTTTAGCGGCGTTTGTGCTT
1 AAAACGCCGCTAAAGTA-TAGTATTTAGCGGCGTTTGT-ATA
* * * *
1797039 AAAACGCCGCTAGAGTAAGAGTCTTTAGCGGCGTTTGTACA
1 AAAACGCCGCTAAAGT-ATAGTATTTAGCGGCGTTTGTATA
* * * * * * *
1797080 AAAATGCCGCTAAAGTATATTAATTAGTGGTGTTTATATG
1 AAAACGCCGCTAAAGTATAGTATTTAGCGGCGTTTGTATA
* * * * *
1797120 AAAACACCACTAAACTATAGTATTTAGCGGCTTTTATATA
1 AAAACGCCGCTAAAGTATAGTATTTAGCGGCGTTTGTATA
*
1797160 AAAACGCCACTAAAGTATGAGTATTTA-CTGGCGTTTGT-TCA
1 AAAACGCCGCTAAAGTAT-AGTATTTAGC-GGCGTTTGTAT-A
1797201 AAAACGCCGCTAAA
1 AAAACGCCGCTAAA
1797215 AATACCGCTA
Statistics
Matches: 202, Mismatches: 50, Indels: 12
0.77 0.19 0.05
Matches are distributed among these distances:
40 94 0.47
41 74 0.37
42 33 0.16
43 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.29
Consensus pattern (40 bp):
AAAACGCCGCTAAAGTATAGTATTTAGCGGCGTTTGTATA
Found at i:1797066 original size:123 final size:122
Alignment explanation
Indices: 1796908--1797214 Score: 386
Period size: 123 Copynumber: 2.5 Consensus size: 122
1796898 TTAGCAACGA
* *
1796908 TTGTGCTTAAAACGCCGCTAAAGTACA-AGTTTTTAGCGGCGTTTGTACAAAAACACCGCTAAAG
1 TTGTGCTTAAAACGCCGCTAAAGTA-AGAGTATTTAGCGGCGTTTGTACAAAAACGCCGCTAAAG
* ** *
1796972 TATAGTAATTAGTGGCGTTTATATAAAAACGCCACTAATGTACAAGTCTTTAGCGGCGT
65 TATAGTAATTAGTGGCGTTTATATAAAAACACCACTAAACTA-AAGTATTTAGCGGCGT
* * *
1797031 TTGTGCTTAAAACGCCGCTAGAGTAAGAGTCTTTAGCGGCGTTTGTACAAAAATGCCGCTAAAGT
1 TTGTGCTTAAAACGCCGCTAAAGTAAGAGTATTTAGCGGCGTTTGTACAAAAACGCCGCTAAAGT
* * * * *
1797096 ATATTAATTAGTGGTGTTTATATGAAAACACCACTAAACTATAGTATTTAGCGGCTT
66 ATAGTAATTAGTGGCGTTTATATAAAAACACCACTAAACTAAAGTATTTAGCGGCGT
* * * * * *
1797153 TTAT-ATAAAAACGCCACTAAAGTATGAGTATTTA-CTGGCGTTTGTTCAAAAACGCCGCTAAA
1 TTGTGCTTAAAACGCCGCTAAAGTAAGAGTATTTAGC-GGCGTTTGTACAAAAACGCCGCTAAA
1797215 AATACCGCTA
Statistics
Matches: 160, Mismatches: 22, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
120 1 0.01
121 48 0.30
122 17 0.11
123 94 0.59
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (122 bp):
TTGTGCTTAAAACGCCGCTAAAGTAAGAGTATTTAGCGGCGTTTGTACAAAAACGCCGCTAAAGT
ATAGTAATTAGTGGCGTTTATATAAAAACACCACTAAACTAAAGTATTTAGCGGCGT
Found at i:1799910 original size:21 final size:22
Alignment explanation
Indices: 1799885--1799928 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
1799875 TTAAGGCCAA
* *
1799885 ATTCAGCTTCAAATTG-TCTAG
1 ATTCAGCTCCAAAATGATCTAG
*
1799906 ATTCATCTCCAAAATGATCTAG
1 ATTCAGCTCCAAAATGATCTAG
1799928 A
1 A
1799929 ATATTCATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.34
Consensus pattern (22 bp):
ATTCAGCTCCAAAATGATCTAG
Found at i:1805335 original size:14 final size:15
Alignment explanation
Indices: 1805316--1805350 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
1805306 TTTATAAAAG
1805316 TTATTT-CTTTTTCT
1 TTATTTACTTTTTCT
1805330 TTATTTACTTTTTCT
1 TTATTTACTTTTTCT
1805345 TTATTT
1 TTATTT
1805351 TTGTCTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.77
Consensus pattern (15 bp):
TTATTTACTTTTTCT
Found at i:1808798 original size:184 final size:185
Alignment explanation
Indices: 1808452--1808820 Score: 731
Period size: 184 Copynumber: 2.0 Consensus size: 185
1808442 GAACATTTTC
1808452 CTATCGACGGATGCCTTTTAGAATTTGCAATGCACTCGGCACATTCCAGAGATGCATGCTAAGAA
1 CTATCGACGGATGCCTTTTAGAATTTGCAATGCACTCGGCACATTCCAGAGATGCATGCTAAGAA
1808517 TCTTTGCGGATTATGTTTGAGAAAGATATCAAAGTCTTCAAGGATGACTTCACCGTATATGGTGA
66 TCTTTGCGGATTATGTTTGAGAAAGATATCAAAGTCTTCAAGGATGACTTCACCGTATATGGTGA
1808582 TTCTTTTAACGAGTGCTTTATTAATTCAACTACCGTATTAAAATGATGCCTAGAA
131 TTCTTTTAACGAGTGCTTTATTAATTCAACTACCGTATTAAAATGATGCCTAGAA
1808637 CTATCGACGGATGCCTTTTAGAATTTGCAATGCACTCGGCACATTCCAGAGATGCATGCTAAGAA
1 CTATCGACGGATGCCTTTTAGAATTTGCAATGCACTCGGCACATTCCAGAGATGCATGCTAAGAA
1808702 TCTTTGCGGATTATG-TTGAGAAAGATATCAAAGTCTTCAAGGATGACTTCACCGTATATGGTGA
66 TCTTTGCGGATTATGTTTGAGAAAGATATCAAAGTCTTCAAGGATGACTTCACCGTATATGGTGA
1808766 TTCTTTTAACGAGTGCTTTATTAATTCAACTACCGTATTAAAATGATGCCTAGAA
131 TTCTTTTAACGAGTGCTTTATTAATTCAACTACCGTATTAAAATGATGCCTAGAA
1808821 TTCAACATAG
Statistics
Matches: 184, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
184 104 0.57
185 80 0.43
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (185 bp):
CTATCGACGGATGCCTTTTAGAATTTGCAATGCACTCGGCACATTCCAGAGATGCATGCTAAGAA
TCTTTGCGGATTATGTTTGAGAAAGATATCAAAGTCTTCAAGGATGACTTCACCGTATATGGTGA
TTCTTTTAACGAGTGCTTTATTAATTCAACTACCGTATTAAAATGATGCCTAGAA
Found at i:1810276 original size:57 final size:57
Alignment explanation
Indices: 1810167--1810278 Score: 152
Period size: 57 Copynumber: 2.0 Consensus size: 57
1810157 CCAGGTTTGA
* * ** * *
1810167 CACACCATGAGCAATAATAAAATATCAAGGATCTCATTTCATTAACCGAATAATCGG
1 CACACCACGAGCAATAATAAAAGATCAAGGAAATCATTTCATCAACCAAATAATCGG
* *
1810224 CACACCACGAGCAATAATAAAAGATCGAGGAAATCATTTCATCAATCAAATAATC
1 CACACCACGAGCAATAATAAAAGATCAAGGAAATCATTTCATCAACCAAATAATC
1810279 AAGGCGTTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
57 47 1.00
ACGTcount: A:0.45, C:0.21, G:0.12, T:0.22
Consensus pattern (57 bp):
CACACCACGAGCAATAATAAAAGATCAAGGAAATCATTTCATCAACCAAATAATCGG
Found at i:1818139 original size:2 final size:2
Alignment explanation
Indices: 1818132--1818158 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1818122 CCCAATTACA
1818132 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1818159 AAGAAAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1819254 original size:13 final size:13
Alignment explanation
Indices: 1819210--1819254 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
1819200 TACTTTCTAT
1819210 ATTAATTATAATC
1 ATTAATTATAATC
*
1819223 CTTATATTATAAATC
1 ATTA-ATTAT-AATC
1819238 -TTAATTATAATC
1 ATTAATTATAATC
1819250 ATTAA
1 ATTAA
1819255 ATTTTAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
12 4 0.14
13 12 0.43
14 8 0.29
15 4 0.14
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTAATTATAATC
Found at i:1819262 original size:27 final size:27
Alignment explanation
Indices: 1819211--1819262 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
1819201 ACTTTCTATA
* *
1819211 TTAATTATAATCCTTATATTATAAATC
1 TTAATTATAATCATTAAATTATAAATC
*
1819238 TTAATTATAATCATTAAATTTTAAA
1 TTAATTATAATCATTAAATTATAAA
1819263 ATATGCGTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (27 bp):
TTAATTATAATCATTAAATTATAAATC
Found at i:1819730 original size:2 final size:2
Alignment explanation
Indices: 1819723--1819843 Score: 108
Period size: 2 Copynumber: 61.0 Consensus size: 2
1819713 CGTGTTTAAT
1819723 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
1819764 TA TA TA CT- TG TA TA TA TA CT- TA TG TG TA TA TA CA 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
* * *
1819806 TA CT- TA TA TA TA TA CT- TA TG TG TA TA TA CA TA TA TA TA
1 TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
1819844 CTTGTGTACA
Statistics
Matches: 101, Mismatches: 9, Indels: 18
0.79 0.07 0.14
Matches are distributed among these distances:
1 5 0.05
2 92 0.91
3 4 0.04
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1819856 original size:24 final size:24
Alignment explanation
Indices: 1819811--1819866 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
1819801 ATATATACTT
**
1819811 ATATATATACTTATGTGTATATAC
1 ATATATATACTTATGTACATATAC
* *
1819835 ATATATATACTTGTGTACATATCC
1 ATATATATACTTATGTACATATAC
*
1819859 TTATATAT
1 ATATATAT
1819867 TATATACTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.46
Consensus pattern (24 bp):
ATATATATACTTATGTACATATAC
Found at i:1819862 original size:38 final size:37
Alignment explanation
Indices: 1819755--1819862 Score: 141
Period size: 38 Copynumber: 2.9 Consensus size: 37
1819745 TATATATATA
1819755 TATATA-ATATATATAC-TTGTATATATACTTATGTG
1 TATATACATATATATACTTTGTATATATACTTATGTG
*
1819790 TATATACATATATATA-TACTTATATATATACTTATGTG
1 TATATACATATATATACT--TTGTATATATACTTATGTG
* *
1819828 TATATACATATATATACTTGTGTACATATCCTTAT
1 TATATACATATATATACTT-TGTATATATACTTAT
1819863 ATATTATATA
Statistics
Matches: 63, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
35 6 0.10
36 9 0.14
37 1 0.02
38 46 0.73
39 1 0.02
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.47
Consensus pattern (37 bp):
TATATACATATATATACTTTGTATATATACTTATGTG
Found at i:1819902 original size:24 final size:22
Alignment explanation
Indices: 1819858--1819902 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1819848 TGTACATATC
* *
1819858 CTTATATATTATATACTTTATA
1 CTTATATATTATACACCTTATA
1819880 CTTATATATATATACACACTTAT
1 CTTATATAT-TATACAC-CTTAT
1819903 TTATACTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 9 0.47
23 6 0.32
24 4 0.21
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (22 bp):
CTTATATATTATACACCTTATA
Found at i:1820041 original size:11 final size:11
Alignment explanation
Indices: 1820025--1820059 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1820015 ATATAAATAT
1820025 ATACATGCATC
1 ATACATGCATC
*
1820036 ATACATACATC
1 ATACATGCATC
*
1820047 ATATATGCATC
1 ATACATGCATC
1820058 AT
1 AT
1820060 TAATCATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.40, C:0.23, G:0.06, T:0.31
Consensus pattern (11 bp):
ATACATGCATC
Found at i:1823387 original size:90 final size:90
Alignment explanation
Indices: 1823272--1823447 Score: 289
Period size: 90 Copynumber: 2.0 Consensus size: 90
1823262 TAATCACAAA
* * * * * *
1823272 TATTTAATTTCAATTAATTAAATATATATTTAATTAATTTGAAATAATAAAATCCCTGATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
1823337 TAGGGTAACTTGGATATAAAAGGAT
66 TAGGGTAACTTGGATATAAAAGGAT
1823362 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
*
1823427 TAGGGTAACTTGGCTATAAAA
66 TAGGGTAACTTGGATATAAAA
1823448 TGGTGTGTTA
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 79 1.00
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
TAGGGTAACTTGGATATAAAAGGAT
Found at i:1828484 original size:89 final size:90
Alignment explanation
Indices: 1828322--1828498 Score: 266
Period size: 89 Copynumber: 2.0 Consensus size: 90
1828312 TAATCCCGAA
* * ** * *
1828322 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATTCCTGATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
*
1828387 TAGGGTAACTTGGATATAAAAGGAT
66 TAGGGTAACTTAGATATAAAAGGAT
*
1828412 TATTAAATTCCAATTAATTAAATATATA-TTAATTAATTTGAAATAATAAAAACCCTAATATGAC
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
*
1828476 TAGGGTAACTTAGCTATAAAAGG
66 TAGGGTAACTTAGATATAAAAGG
1828499 GTGTGTAGGT
Statistics
Matches: 78, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
89 53 0.68
90 25 0.32
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.37
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
TAGGGTAACTTAGATATAAAAGGAT
Found at i:1835215 original size:90 final size:90
Alignment explanation
Indices: 1835062--1835242 Score: 362
Period size: 90 Copynumber: 2.0 Consensus size: 90
1835052 TTCGATTGAT
1835062 GTTTTGTCACAACATAAAAAAGCCTTACGTTTGATGATGGCTTATTTAAAAGGCATAATCCCTAC
1 GTTTTGTCACAACATAAAAAAGCCTTACGTTTGATGATGGCTTATTTAAAAGGCATAATCCCTAC
1835127 CATTTGTATGCATAAGATTATGCTC
66 CATTTGTATGCATAAGATTATGCTC
1835152 GTTTTGTCACAACATAAAAAAGCCTTACGTTTGATGATGGCTTATTTAAAAGGCATAATCCCTAC
1 GTTTTGTCACAACATAAAAAAGCCTTACGTTTGATGATGGCTTATTTAAAAGGCATAATCCCTAC
1835217 CATTTGTATGCATAAGATTATGCTC
66 CATTTGTATGCATAAGATTATGCTC
1835242 G
1 G
1835243 AATAATGCTA
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 91 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (90 bp):
GTTTTGTCACAACATAAAAAAGCCTTACGTTTGATGATGGCTTATTTAAAAGGCATAATCCCTAC
CATTTGTATGCATAAGATTATGCTC
Found at i:1836188 original size:21 final size:20
Alignment explanation
Indices: 1836164--1836216 Score: 79
Period size: 21 Copynumber: 2.6 Consensus size: 20
1836154 TTCGTGCATG
**
1836164 GATGCATCGATGCACAGCCTT
1 GATGCATCGATGCACAG-AAT
1836185 GATGCATCGATGCACAGAAT
1 GATGCATCGATGCACAGAAT
1836205 GATGCATCGATG
1 GATGCATCGATG
1836217 AACTAATTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 13 0.43
21 17 0.57
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (20 bp):
GATGCATCGATGCACAGAAT
Found at i:1836260 original size:16 final size:16
Alignment explanation
Indices: 1836239--1836270 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1836229 TCGGTGTTTG
1836239 AGTGCATGGATGCACT
1 AGTGCATGGATGCACT
1836255 AGTGCATGGATGCACT
1 AGTGCATGGATGCACT
1836271 GCAAGGATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (16 bp):
AGTGCATGGATGCACT
Found at i:1836273 original size:21 final size:19
Alignment explanation
Indices: 1836239--1836312 Score: 91
Period size: 21 Copynumber: 3.8 Consensus size: 19
1836229 TCGGTGTTTG
1836239 AGTGCATGGATGCACT---
1 AGTGCATGGATGCACTGCA
1836255 AGTGCATGGATGCACTGCA
1 AGTGCATGGATGCACTGCA
1836274 AGGATGCATGGATGCACTGCA
1 A-G-TGCATGGATGCACTGCA
1836295 AGGGTGCATGGATGCACT
1 A--GTGCATGGATGCACT
1836313 TTGACACCCT
Statistics
Matches: 52, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
16 16 0.31
19 1 0.02
20 1 0.02
21 32 0.62
22 2 0.04
ACGTcount: A:0.26, C:0.19, G:0.34, T:0.22
Consensus pattern (19 bp):
AGTGCATGGATGCACTGCA
Found at i:1836439 original size:30 final size:29
Alignment explanation
Indices: 1836381--1836449 Score: 111
Period size: 29 Copynumber: 2.3 Consensus size: 29
1836371 GAAACCTTTT
**
1836381 AAAACATTGAATAAATTCAATTAAGTCCA
1 AAAACATTTTATAAATTCAATTAAGTCCA
1836410 AAAACATTTTATAAATTCAATTCAAGTCCA
1 AAAACATTTTATAAATTCAATT-AAGTCCA
1836440 AAAACATTTT
1 AAAACATTTT
1836450 GCCTTAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
29 20 0.54
30 17 0.46
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.32
Consensus pattern (29 bp):
AAAACATTTTATAAATTCAATTAAGTCCA
Found at i:1836584 original size:21 final size:21
Alignment explanation
Indices: 1836560--1836599 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1836550 ATGTTTAATG
1836560 AAAAAGATACCAATTGTTAAC
1 AAAAAGATACCAATTGTTAAC
* *
1836581 AAAATGATATCAATTGTTA
1 AAAAAGATACCAATTGTTA
1836600 CCAATTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (21 bp):
AAAAAGATACCAATTGTTAAC
Found at i:1838409 original size:19 final size:19
Alignment explanation
Indices: 1838385--1838436 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
1838375 AATGCATTTG
1838385 ATGCATCGATGCACCAGCC
1 ATGCATCGATGCACCAGCC
1838404 ATGCATCGATGCACCAGCC
1 ATGCATCGATGCACCAGCC
1838423 ATGCATCGATGCAC
1 ATGCATCGATGCAC
1838437 TCTGGCTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.27, C:0.35, G:0.21, T:0.17
Consensus pattern (19 bp):
ATGCATCGATGCACCAGCC
Found at i:1838409 original size:84 final size:82
Alignment explanation
Indices: 1838319--1838481 Score: 215
Period size: 83 Copynumber: 2.0 Consensus size: 82
1838309 GAATGCATTT
1838319 CATGCATCGATGCA-CATACCATGCACCGATGCA-CT-GCAAATTTTATGAAAACATCGAATGCA
1 CATGCATCGATGCACCA-ACCATGCACCGATGCACCTGGC-AA-TTT-TG-AAACATCGAATGCA
*
1838381 TTTGATGCATCGATGCACCAGC
61 CTTGATGCATCGATGCACCAGC
* * *
1838403 CATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTG
1 CATGCATCGATGCACCAACCATGCACCGATGCAC-CTGGCAATTTTGAAACATCGAATGCACTTG
1838468 ATGCATCGATGCAC
65 ATGCATCGATGCAC
1838482 TCTTAGTGTA
Statistics
Matches: 71, Mismatches: 4, Indels: 9
0.85 0.05 0.11
Matches are distributed among these distances:
83 31 0.44
84 30 0.42
85 5 0.07
86 3 0.04
87 2 0.03
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (82 bp):
CATGCATCGATGCACCAACCATGCACCGATGCACCTGGCAATTTTGAAACATCGAATGCACTTGA
TGCATCGATGCACCAGC
Found at i:1845945 original size:21 final size:21
Alignment explanation
Indices: 1845903--1845946 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1845893 ACTCCGGGAG
* *
1845903 CTAGTTCCTCACGAGCTGCTC
1 CTAGATCCTCACGAGCTCCTC
* *
1845924 CTAGATCCTCTCGTGCTCCTC
1 CTAGATCCTCACGAGCTCCTC
1845945 CT
1 CT
1845947 CCTCCAGCTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.11, C:0.41, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGATCCTCACGAGCTCCTC
Found at i:1847082 original size:64 final size:64
Alignment explanation
Indices: 1847007--1847131 Score: 155
Period size: 65 Copynumber: 1.9 Consensus size: 64
1846997 TGAACCAATC
* *
1847007 CATGCATCGATGCAC-CATGAATTAAATTG-AACATCGAATGCATTTCATGCATCGATGCACATA
1 CATGCACCGATGCACTCA-GAATTAAA-TGAAACATCAAATGCATTTCATGCATCGATGCACATA
1847070 T
64 T
* ** *
1847071 CATGCACCGATGCACTGAGAATTTTATGAAAACATCAAATGCATTTGATGCATCGATGCAC
1 CATGCACCGATGCACTCAGAATTAAATG-AAACATCAAATGCATTTCATGCATCGATGCAC
1847132 CAGCCATGCA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
63 2 0.04
64 20 0.38
65 30 0.58
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (64 bp):
CATGCACCGATGCACTCAGAATTAAATGAAACATCAAATGCATTTCATGCATCGATGCACATAT
Found at i:1847166 original size:65 final size:64
Alignment explanation
Indices: 1847036--1847192 Score: 147
Period size: 65 Copynumber: 2.4 Consensus size: 64
1847026 AATTAAATTG
* * * *
1847036 AACATCGAATGCATTTCATGCATCGATGCACATATCATGCACCGATGCACTGAGAATTTTATGAA
1 AACATCGAATGCATTTGATGCATCGATGCACATACCATGCACCAATGCACTCAGAATTTTATG-A
* * * * **
1847101 AACATCAAATGCATTTGATGCATCGATGCACCA-GCCATGCATCAATGCACTCTGGCTATTT-TG
1 AACATCGAATGCATTTGATGCATCGATGCA-CATACCATGCACCAATGCACTCAGAAT-TTTATG
1847164 A
64 A
* * * *
1847165 AACTTTGAATGCACTTGATGCACCGATG
1 AACATCGAATGCATTTGATGCATCGATG
1847193 TACTCTTAGT
Statistics
Matches: 75, Mismatches: 15, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
64 24 0.32
65 46 0.61
66 5 0.07
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCGATGCACATACCATGCACCAATGCACTCAGAATTTTATGA
Found at i:1848834 original size:20 final size:22
Alignment explanation
Indices: 1848809--1848848 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1848799 TGTTGTATAT
1848809 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
1848829 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
1848849 TCTACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:1849114 original size:21 final size:21
Alignment explanation
Indices: 1849046--1849143 Score: 90
Period size: 21 Copynumber: 4.7 Consensus size: 21
1849036 GGTGTTTGAG
* *
1849046 TGCATGGATGCACTGCATGG-
1 TGCATGGATGCACTACAGGGA
* ** **
1849066 TGCATCGATGCACTAGTGCAA
1 TGCATGGATGCACTACAGGGA
* *
1849087 GTGCATGAATGCACTGCAGGGA
1 -TGCATGGATGCACTACAGGGA
*
1849109 TGCATGGATGCACTACAGGGG
1 TGCATGGATGCACTACAGGGA
1849130 TGCATGGATGCACT
1 TGCATGGATGCACT
1849144 TTGACACCCT
Statistics
Matches: 59, Mismatches: 17, Indels: 3
0.75 0.22 0.04
Matches are distributed among these distances:
20 13 0.22
21 32 0.54
22 14 0.24
ACGTcount: A:0.24, C:0.20, G:0.33, T:0.22
Consensus pattern (21 bp):
TGCATGGATGCACTACAGGGA
Found at i:1849133 original size:42 final size:42
Alignment explanation
Indices: 1849044--1849143 Score: 121
Period size: 42 Copynumber: 2.4 Consensus size: 42
1849034 TCGGTGTTTG
* **
1849044 AGTGCATGGATGCACTGCATGGTGCATCGATGCACTAGTGCA
1 AGTGCATGGATGCACTGCAGGGTGCATCGATGCACTACAGCA
* * *
1849086 AGTGCATGAATGCACTGCAGGGATGCATGGATGCACTACAG-G
1 AGTGCATGGATGCACTGCAGGG-TGCATCGATGCACTACAGCA
*
1849128 GGTGCATGGATGCACT
1 AGTGCATGGATGCACT
1849144 TTGACACCCT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 34 0.69
43 15 0.31
ACGTcount: A:0.25, C:0.20, G:0.33, T:0.22
Consensus pattern (42 bp):
AGTGCATGGATGCACTGCAGGGTGCATCGATGCACTACAGCA
Found at i:1849244 original size:29 final size:30
Alignment explanation
Indices: 1849212--1849275 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 30
1849202 GAAACCTTTT
1849212 AAAACATTGAATAAATTCAATT-AAGTCCA
1 AAAACATTGAATAAATTCAATTCAAGTCCA
***
1849241 AAAACATTTTGTAAATTCAATTCAAGTCCA
1 AAAACATTGAATAAATTCAATTCAAGTCCA
1849271 AAAAC
1 AAAAC
1849276 CATTTTTCCT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
29 19 0.61
30 12 0.39
ACGTcount: A:0.50, C:0.16, G:0.06, T:0.28
Consensus pattern (30 bp):
AAAACATTGAATAAATTCAATTCAAGTCCA
Done.