Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008925.1 Hibiscus syriacus cultivar Beakdansim tig00112230_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: 2702387
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 11
Found at i:1711925 original size:24 final size:22
Alignment explanation
Indices: 1711897--1711976 Score: 83
Period size: 24 Copynumber: 3.5 Consensus size: 22
1711887 CACTTAACAA
1711897 TGCATCGATGCATCTCTTTGAATG
1 TGCATCGATGCATC-C-TTGAATG
* *
1711921 TGCATCGATGTATCC--GCATG
1 TGCATCGATGCATCCTTGAATG
*
1711941 ATGCACCGATGCATGCCTTGAATG
1 -TGCATCGATGCAT-CCTTGAATG
1711965 TGCATCGATGCA
1 TGCATCGATGCA
1711977 CAAGATCATG
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
20 4 0.09
21 11 0.24
22 2 0.04
23 12 0.26
24 17 0.37
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.30
Consensus pattern (22 bp):
TGCATCGATGCATCCTTGAATG
Found at i:1712252 original size:19 final size:19
Alignment explanation
Indices: 1712196--1712258 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
1712186 CTATTTAAAC
**
1712196 TAAAATACCTAAAAAATAAT
1 TAAAATA-CTAAAACCTAAT
* * *
1712216 ATAATATTCTAAATCCTAAT
1 -TAAAATACTAAAACCTAAT
*
1712236 TAAAATACTAAAACCTATT
1 TAAAATACTAAAACCTAAT
1712255 TAAA
1 TAAA
1712259 TTAAAATACA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 9 0.27
21 5 0.15
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAATACTAAAACCTAAT
Found at i:1712296 original size:75 final size:76
Alignment explanation
Indices: 1712216--1712380 Score: 235
Period size: 76 Copynumber: 2.2 Consensus size: 76
1712206 AAAAAATAAT
*
1712216 ATAATATTCTAAATCCTAATTAAAATACT-AAAACCTATTTAAATTAAAATACAAAGATAAAGAT
1 ATAATATTCTAAATCCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAA-AT
1712280 AAAAT-ATAAAA
65 AAAATGATAAAA
* * *
1712291 ATAATATCCTAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATA
1 ATAATATTCTAAATCCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATA
* * *
1712356 TAATGTTTAAA
66 AAATGATAAAA
*
1712367 ATATTATTCTAAAT
1 ATAATATTCTAAAT
1712381 TTGAGTTTAA
Statistics
Matches: 78, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
75 32 0.41
76 46 0.59
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.32
Consensus pattern (76 bp):
ATAATATTCTAAATCCTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGATAAAATA
AAATGATAAAA
Found at i:1715900 original size:16 final size:16
Alignment explanation
Indices: 1715879--1715917 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
1715869 GGTATTACCC
1715879 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
*
1715895 GACCTGTTTTTAACCT
1 GACCTGTTTTCAACCT
1715911 GACCTGT
1 GACCTGT
1715918 AAATGATCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.18, C:0.28, G:0.15, T:0.38
Consensus pattern (16 bp):
GACCTGTTTTCAACCT
Found at i:1716114 original size:13 final size:13
Alignment explanation
Indices: 1716098--1716124 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1716088 GACCTATTAT
1716098 ATAAAATTATTTA
1 ATAAAATTATTTA
1716111 ATAAAATTATTTA
1 ATAAAATTATTTA
1716124 A
1 A
1716125 ATGTAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAAAATTATTTA
Found at i:1716186 original size:14 final size:14
Alignment explanation
Indices: 1716164--1716210 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
1716154 TGCAAAAGAA
*
1716164 AATTAATATAGTTT
1 AATTTATATAGTTT
1716178 AATTTATATA----
1 AATTTATATAGTTT
1716188 AA-TTATATAGTTT
1 AATTTATATAGTTT
1716201 AATTTATATA
1 AATTTATATA
1716211 AAGAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTTATATAGTTT
Found at i:1716197 original size:23 final size:24
Alignment explanation
Indices: 1716163--1716212 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
1716153 ATGCAAAAGA
1716163 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
1716187 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
1716210 AAA
1 AAA
1716213 GAAAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:1716694 original size:19 final size:20
Alignment explanation
Indices: 1716681--1716759 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 20
1716671 AATTTTTCTA
1716681 TTCCCTCTAAATTTCTTAAT
1 TTCCCTCTAAATTTCTTAAT
*
1716701 TTCCCTCTAAA-TTCTCAAT
1 TTCCCTCTAAATTTCTTAAT
*
1716720 TTCTCTATATTCTCAAAATTTCTTAAT
1 TTC-C------CTCTAAATTTCTTAAT
1716747 TTCCCTCTAAATT
1 TTCCCTCTAAATT
1716760 CCCAAATAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 16
0.70 0.06 0.24
Matches are distributed among these distances:
19 10 0.21
20 20 0.43
26 7 0.15
27 10 0.21
ACGTcount: A:0.27, C:0.25, G:0.00, T:0.48
Consensus pattern (20 bp):
TTCCCTCTAAATTTCTTAAT
Found at i:1716841 original size:2 final size:2
Alignment explanation
Indices: 1716834--1716860 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1716824 ACTTTGAATA
1716834 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
1716861 ATTAAACATA
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:1716948 original size:2 final size:2
Alignment explanation
Indices: 1716941--1717131 Score: 90
Period size: 2 Copynumber: 102.0 Consensus size: 2
1716931 CTTGGTGTGA
* * * *
1716941 AT AT AT AT AT AT GT AT AT AC AT AA AT AA AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
1716983 AT AC AT AA AT AT AC AT AT AT AT AT AT AT AT AT TT AA AT GT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
1717024 A- AT GT -T A- AT -T TT AT A- AT AT -T TT AT -T TT AGT CACT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T -A-T AT
* * *
1717059 AT GT TT A- AT -T AT AT AT AT -T AT AT AT AT TT AT AT -T AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1717096 AT AT AT AT AT AT AT AT A- AT -T AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1717132 TAAAGTGAGT
Statistics
Matches: 142, Mismatches: 29, Indels: 36
0.69 0.14 0.17
Matches are distributed among these distances:
1 16 0.11
2 123 0.87
3 1 0.01
4 2 0.01
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1716983 original size:26 final size:28
Alignment explanation
Indices: 1716943--1717013 Score: 119
Period size: 26 Copynumber: 2.6 Consensus size: 28
1716933 TGGTGTGAAT
*
1716943 ATATATATATGTATATACATAAATA-A-
1 ATATATATATATATATACATAAATATAC
1716969 ATATATATATATATATACATAAATATAC
1 ATATATATATATATATACATAAATATAC
1716997 ATATATATATATATATA
1 ATATATATATATATATA
1717014 TTTAAATGTT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
26 24 0.57
27 1 0.02
28 17 0.40
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (28 bp):
ATATATATATATATATACATAAATATAC
Found at i:1717242 original size:18 final size:17
Alignment explanation
Indices: 1717216--1717249 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1717206 AGAGGGAAAT
1717216 TAGGAAAATTTGAGAATA
1 TAGGAAAA-TTGAGAATA
*
1717234 TAGGGAAATTGAGAAT
1 TAGGAAAATTGAGAAT
1717250 TTAGAGGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.47, C:0.00, G:0.26, T:0.26
Consensus pattern (17 bp):
TAGGAAAATTGAGAATA
Found at i:1717510 original size:21 final size:21
Alignment explanation
Indices: 1717486--1717526 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1717476 TATATAGTTA
**
1717486 TATAAACTTTAAACCCTAAAT
1 TATAAACCCTAAACCCTAAAT
1717507 TATAAACCCTAAACCCTAAA
1 TATAAACCCTAAACCCTAAA
1717527 CCGTACACCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (21 bp):
TATAAACCCTAAACCCTAAAT
Found at i:1717571 original size:20 final size:19
Alignment explanation
Indices: 1717539--1717604 Score: 68
Period size: 18 Copynumber: 3.6 Consensus size: 19
1717529 GTACACCCTA
* *
1717539 ATATATGTATAAACCATGT
1 ATATATATATAAACCATAT
1717558 ATAGTATATATAAA-C-TAT
1 ATA-TATATATAAACCATAT
1717576 ATATATATAT--ACCTATAT
1 ATATATATATAAACC-ATAT
1717594 ATATATATATA
1 ATATATATATA
1717605 TATATAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
15 1 0.03
16 1 0.03
17 7 0.17
18 18 0.45
19 4 0.10
20 9 0.22
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.41
Consensus pattern (19 bp):
ATATATATATAAACCATAT
Found at i:1717621 original size:2 final size:2
Alignment explanation
Indices: 1717557--1717610 Score: 63
Period size: 2 Copynumber: 26.0 Consensus size: 2
1717547 ATAAACCATG
* **
1717557 TA TA GTA TA TA TA AA CTA TA TA TA TA TA TA CC 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
1717601 TA TA TA TA TA
1 TA TA TA TA TA
1717611 AAAACTATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
2 41 0.93
3 3 0.07
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1717792 original size:70 final size:67
Alignment explanation
Indices: 1717717--1717850 Score: 189
Period size: 68 Copynumber: 2.0 Consensus size: 67
1717707 TGCACACATA
*
1717717 TATATATATATTAATATAAATTATAACATATAAACTATAT-TTTTATATAGTTATACATATATAG
1 TATATATATATTAATATAAATAATAACATATAAACTATATATTTTA-ATAGTT-TACATATATAG
1717781 TTTT
64 TTTT
*** *
1717785 TATATATATATTAATATAAATAATATTTTATAAACTATATACTTTTAATAGTTTATATATATAGT
1 TATATATATATTAATATAAATAATAACATATAAACTATATA-TTTTAATAGTTTACATATATAGT
1717850 T
65 T
1717851 CACATAAACA
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
68 48 0.81
69 6 0.10
70 5 0.08
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (67 bp):
TATATATATATTAATATAAATAATAACATATAAACTATATATTTTAATAGTTTACATATATAGTT
TT
Found at i:1717910 original size:16 final size:16
Alignment explanation
Indices: 1717867--1718011 Score: 79
Period size: 18 Copynumber: 9.0 Consensus size: 16
1717857 AACATAATTT
*
1717867 ATATATATAGCTTATA
1 ATATATATAGTTTATA
1717883 ATAATTATATAGTTTATA
1 AT-A-TATATAGTTTATA
*
1717901 ATATAAATAGTTTATA
1 ATATATATAGTTTATA
* ** *
1717917 ATTTTATATA-CATAGTT
1 A-TATATATAGTTTA-TA
* *
1717934 ATATATATAGTTCA-C
1 ATATATATAGTTTATA
*
1717949 ATA-A-ATA--TAAT-
1 ATATATATAGTTTATA
*
1717960 TTATATATAGTTTATA
1 ATATATATAGTTTATA
1717976 ATAATTATATAGTTTATA
1 AT-A-TATATAGTTTATA
1717994 ATATAAATATAGTTTATA
1 ATAT--ATATAGTTTATA
1718012 TAATTTTATA
Statistics
Matches: 98, Mismatches: 16, Indels: 28
0.69 0.11 0.20
Matches are distributed among these distances:
11 4 0.04
12 1 0.01
13 6 0.06
14 1 0.01
15 6 0.06
16 26 0.27
17 13 0.13
18 41 0.42
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.47
Consensus pattern (16 bp):
ATATATATAGTTTATA
Found at i:1717989 original size:93 final size:100
Alignment explanation
Indices: 1717832--1718022 Score: 315
Period size: 93 Copynumber: 2.0 Consensus size: 100
1717822 TATACTTTTA
1717832 ATAGTTTATATATATAGTTCACATAAACATAATTTATATATATAGCTTATAATAATTATATAGTT
1 ATAGTTTATATATATAGTTCACATAAACATAATTTATATATATAGCTTATAATAATTATATAGTT
1717897 TATAATAT-AA-ATAG-TT-TATAATTTTATATAC
66 TATAATATAAATATAGTTTATATAATTTTATATAC
* *
1717928 ATAG-TTATATATATAGTTCACATAAATATAA-TT-TATATATAGTTTATAATAATTATATAGTT
1 ATAGTTTATATATATAGTTCACATAAACATAATTTATATATATAGCTTATAATAATTATATAGTT
1717990 TATAATATAAATATAGTTTATATAATTTTATAT
66 TATAATATAAATATAGTTTATATAATTTTATAT
1718023 TATATATATA
Statistics
Matches: 89, Mismatches: 2, Indels: 7
0.91 0.02 0.07
Matches are distributed among these distances:
93 36 0.40
94 4 0.04
95 30 0.34
96 6 0.07
97 13 0.15
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (100 bp):
ATAGTTTATATATATAGTTCACATAAACATAATTTATATATATAGCTTATAATAATTATATAGTT
TATAATATAAATATAGTTTATATAATTTTATATAC
Found at i:1719612 original size:22 final size:22
Alignment explanation
Indices: 1719547--1719599 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
1719537 CAAAAACCCA
1719547 TGAGCCTTTCCGTACTTGAAAC
1 TGAGCCTTTCCGTACTTGAAAC
1719569 TGAGCCTTTCCGTACTTGAAAC
1 TGAGCCTTTCCGTACTTGAAAC
*
1719591 TGCGCCTTT
1 TGAGCCTTT
1719600 TGTGCTTCGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.19, C:0.28, G:0.19, T:0.34
Consensus pattern (22 bp):
TGAGCCTTTCCGTACTTGAAAC
Found at i:1725479 original size:19 final size:19
Alignment explanation
Indices: 1725441--1725485 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1725431 ATATCAAAAA
*
1725441 TATTATTTTTTATCGGTTT
1 TATTATTTTTTATCGATTT
*
1725460 TATTATTTTTTATTGATTT
1 TATTATTTTTTATCGATTT
*
1725479 TGTTATT
1 TATTATT
1725486 GCTAGATACT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.18, C:0.02, G:0.09, T:0.71
Consensus pattern (19 bp):
TATTATTTTTTATCGATTT
Found at i:1737021 original size:10 final size:10
Alignment explanation
Indices: 1737006--1737034 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
1736996 TTATCCGAAT
1737006 ACTTTATCGA
1 ACTTTATCGA
1737016 ACTTTATCGA
1 ACTTTATCGA
1737026 ACTTTATCG
1 ACTTTATCG
1737035 CTTCATAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (10 bp):
ACTTTATCGA
Found at i:1749587 original size:28 final size:28
Alignment explanation
Indices: 1749555--1749611 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
1749545 TTCAGTAATA
* *
1749555 TGTTTGTTTATGTTCTTTCATTTATGTT
1 TGTTTGTTTATGTGCATTCATTTATGTT
*
1749583 TGTTTGTTTATGTGCATTCGTTTATGTT
1 TGTTTGTTTATGTGCATTCATTTATGTT
1749611 T
1 T
1749612 AGCCCAATCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.11, C:0.07, G:0.18, T:0.65
Consensus pattern (28 bp):
TGTTTGTTTATGTGCATTCATTTATGTT
Found at i:1749592 original size:14 final size:15
Alignment explanation
Indices: 1749555--1749595 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
1749545 TTCAGTAATA
1749555 TGTTTGTTTATGTTC
1 TGTTTGTTTATGTTC
**
1749570 T-TTCATTTATGTT-
1 TGTTTGTTTATGTTC
1749583 TGTTTGTTTATGT
1 TGTTTGTTTATGT
1749596 GCATTCGTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
13 1 0.05
14 19 0.90
15 1 0.05
ACGTcount: A:0.10, C:0.05, G:0.17, T:0.68
Consensus pattern (15 bp):
TGTTTGTTTATGTTC
Found at i:1749799 original size:10 final size:10
Alignment explanation
Indices: 1749779--1749815 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
1749769 GATCTATTTC
1749779 CATTTATGTT
1 CATTTATGTT
* *
1749789 CGTTTACGTT
1 CATTTATGTT
1749799 CATTTATGTT
1 CATTTATGTT
1749809 CATTTAT
1 CATTTAT
1749816 TGTGTTTGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.19, C:0.14, G:0.11, T:0.57
Consensus pattern (10 bp):
CATTTATGTT
Found at i:1749850 original size:24 final size:24
Alignment explanation
Indices: 1749815--1749901 Score: 131
Period size: 24 Copynumber: 3.7 Consensus size: 24
1749805 TGTTCATTTA
* *
1749815 TTGTGTTTGTTTACGTTCGTTCAT
1 TTGTGTTCGTTTACATTCGTTCAT
*
1749839 TTATGTTCGTTTACATTCGTTCAT
1 TTGTGTTCGTTTACATTCGTTCAT
*
1749863 TTGTGTTCGTTTACATTCGTTTA-
1 TTGTGTTCGTTTACATTCGTTCAT
1749886 TTGTGTTCGTTTACAT
1 TTGTGTTCGTTTACAT
1749902 CCATCCGTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
23 16 0.28
24 42 0.72
ACGTcount: A:0.13, C:0.14, G:0.17, T:0.56
Consensus pattern (24 bp):
TTGTGTTCGTTTACATTCGTTCAT
Found at i:1752351 original size:35 final size:35
Alignment explanation
Indices: 1752244--1752353 Score: 93
Period size: 36 Copynumber: 3.1 Consensus size: 35
1752234 TTTTAGGGAT
*
1752244 CAAATATGGAATTCCCATATTCAAAGTTTGGCCAC
1 CAAATATGAAATTCCCATATTCAAAGTTTGGCCAC
* * * *
1752279 CTACCAA-A-GAATTTTCCA-ATGTGTACAAG-TTAGCCAC
1 C-A--AATATGAAATTCCCATAT-T-CA-AAGTTTGGCCAC
1752316 CAAATATGAAATTCCCATATTCAAAGTTTGGCCAC
1 CAAATATGAAATTCCCATATTCAAAGTTTGGCCAC
1752351 CAA
1 CAA
1752354 CCAAGATGAA
Statistics
Matches: 56, Mismatches: 9, Indels: 20
0.66 0.11 0.24
Matches are distributed among these distances:
34 5 0.09
35 15 0.27
36 19 0.34
37 12 0.21
38 5 0.09
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (35 bp):
CAAATATGAAATTCCCATATTCAAAGTTTGGCCAC
Found at i:1761550 original size:19 final size:20
Alignment explanation
Indices: 1761512--1761550 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
1761502 ATTCTGCTTG
*
1761512 TTCTTCTTTTCTTCATCATC
1 TTCTTCTTTTCTTCACCATC
*
1761532 TTCTTC-TTTCTTTACCATC
1 TTCTTCTTTTCTTCACCATC
1761551 AACTCATGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.10, C:0.31, G:0.00, T:0.59
Consensus pattern (20 bp):
TTCTTCTTTTCTTCACCATC
Found at i:1764206 original size:686 final size:686
Alignment explanation
Indices: 1762889--1764255 Score: 2608
Period size: 686 Copynumber: 2.0 Consensus size: 686
1762879 TGTAAAGTAA
*
1762889 TATCAATACCTCTTTGGGTATCAATACCTATTTTGCATTATGGAATTTGAGCAAGTTGGTAGTAT
1 TATCAATACCTCTTTGGGTATCAATACCTATTTTGCATTATGGAATTTAAGCAAGTTGGTAGTAT
1762954 AGATACTACCTAGAGAGTATCAATACTTCTCTTATCTAGGGTATCGATACTACATGAATAGTATC
66 AGATACTACCTAGAGAGTATCAATACTTCTCTTATCTAGGGTATCGATACTACATGAATAGTATC
*
1763019 GGTACTGTTCATATAGTATCGATACTGTAAGAACAATATCAGTACATAATACATGAAAATCAGTT
131 GGTACTGTTCATATAGTATCGATACTGTAAGAACAATATCAATACATAATACATGAAAATCAGTT
1763084 TTGTTCTCAAATTCATTTTTAATGGACTTTGAATTATTTTTGAAAACTTTGAATAAATTCAATTC
196 TTGTTCTCAAATTCATTTTTAATGGACTTTGAATTATTTTTGAAAACTTTGAATAAATTCAATTC
*
1763149 AACTCCAAAAAGTTATATCAAATTATTATAAAACATGGTTCAACATAATTCATTTAAGTTAAATA
261 AACTCCAAAAAGTTATATCAAAATATTATAAAACATGGTTCAACATAATTCATTTAAGTTAAATA
1763214 GATACCAAATGTACATGAAATTAACAAGAAATTTCATGACAATTCTTCTTCAAAATCTGCCATGG
326 GATACCAAATGTACATGAAATTAACAAGAAATTTCATGACAATTCTTCTTCAAAATCTGCCATGG
*
1763279 ACATGAGCTTCATAAGGTATGGAGAAAAATTTTTATTTTTCATTTTCAATCGAATTCCTTTGGTT
391 ACATGAGCTTCATAAGGTATAGAGAAAAATTTTTATTTTTCATTTTCAATCGAATTCCTTTGGTT
1763344 TTTGGATTAAATTATGAAATAGAAAATTGTTCTATTCGAAGAGCTATATCATTTGGTACCAATAT
456 TTTGGATTAAATTATGAAATAGAAAATTGTTCTATTCGAAGAGCTATATCATTTGGTACCAATAT
*
1763409 TGCATGCTAATCTTGCTTGAATTCTTAGTTCCGAAATTTTAGCTTTTATGAAGATATTAGGGTTT
521 TGCATGCTAATATTGCTTGAATTCTTAGTTCCGAAATTTTAGCTTTTATGAAGATATTAGGGTTT
1763474 TATGAATTGATGATGTAATTTGATGTTATTAATGTTGTAGAATCATTTCCAAGCTTTTTTGATGA
586 TATGAATTGATGATGTAATTTGATGTTATTAATGTTGTAGAATCATTTCCAAGCTTTTTTGATGA
1763539 TTAAAACACCTAGAAACACATCTATTCAGTTGGTAG
651 TTAAAACACCTAGAAACACATCTATTCAGTTGGTAG
* *
1763575 TATCGATACCTCTTTGGGTATCAATACCTATTTTGCATTCTGGAATTTAAGCAAGTTGGTAGTAT
1 TATCAATACCTCTTTGGGTATCAATACCTATTTTGCATTATGGAATTTAAGCAAGTTGGTAGTAT
*
1763640 CGATACTACCTAGAGAGTATCAATACTTCTCTTATCTAGGGTATCGATACTACATGAATAGTATC
66 AGATACTACCTAGAGAGTATCAATACTTCTCTTATCTAGGGTATCGATACTACATGAATAGTATC
* *
1763705 GGTACTGTTCATATAGTATCGATACTGTAAGAACAATATCAATACTTCATACATGAAAATCAGTT
131 GGTACTGTTCATATAGTATCGATACTGTAAGAACAATATCAATACATAATACATGAAAATCAGTT
1763770 TTGTTCTCAAATTCATTTTTAATGGACTTTGAATTATTTTTGAAAACTTTGAATAAATTCAATTC
196 TTGTTCTCAAATTCATTTTTAATGGACTTTGAATTATTTTTGAAAACTTTGAATAAATTCAATTC
1763835 AACTCCAAAAAGTTATATCAAAATATTATAAAACATGGTTCAACATAATTCATTTAAGTTAAATA
261 AACTCCAAAAAGTTATATCAAAATATTATAAAACATGGTTCAACATAATTCATTTAAGTTAAATA
1763900 GATACCAAATGTACATGAAATTAACAAGAAATTTCATGACAATTCTTCTTCAAAATCTGCCATGG
326 GATACCAAATGTACATGAAATTAACAAGAAATTTCATGACAATTCTTCTTCAAAATCTGCCATGG
** *
1763965 ACATGAGCTTCATAAGGTATAGAGAAATTTTTTTATTTTTCATTTTCAATCGATTTCCTTTGGTT
391 ACATGAGCTTCATAAGGTATAGAGAAAAATTTTTATTTTTCATTTTCAATCGAATTCCTTTGGTT
1764030 TTTGGATTAAATTATGAAATAGAAAATTGTTCTATTCGAAGAGCTATATCATTTGGTACCAATAT
456 TTTGGATTAAATTATGAAATAGAAAATTGTTCTATTCGAAGAGCTATATCATTTGGTACCAATAT
*
1764095 TGCATGCTAATATTGCTTGAATTCTTAGTTTCGAAATTTTAGCTTTTATGAAGATATTAGGGTTT
521 TGCATGCTAATATTGCTTGAATTCTTAGTTCCGAAATTTTAGCTTTTATGAAGATATTAGGGTTT
1764160 TATGAATTGATGATGTAATTTGATGTTATTAATGTTGTAGAATCATTTCCAAGCTTTTTTGATGA
586 TATGAATTGATGATGTAATTTGATGTTATTAATGTTGTAGAATCATTTCCAAGCTTTTTTGATGA
1764225 TTAAAACACCTAGAAACACATCTATTCAGTT
651 TTAAAACACCTAGAAACACATCTATTCAGTT
1764256 CAGCCTAAAC
Statistics
Matches: 667, Mismatches: 14, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
686 667 1.00
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.38
Consensus pattern (686 bp):
TATCAATACCTCTTTGGGTATCAATACCTATTTTGCATTATGGAATTTAAGCAAGTTGGTAGTAT
AGATACTACCTAGAGAGTATCAATACTTCTCTTATCTAGGGTATCGATACTACATGAATAGTATC
GGTACTGTTCATATAGTATCGATACTGTAAGAACAATATCAATACATAATACATGAAAATCAGTT
TTGTTCTCAAATTCATTTTTAATGGACTTTGAATTATTTTTGAAAACTTTGAATAAATTCAATTC
AACTCCAAAAAGTTATATCAAAATATTATAAAACATGGTTCAACATAATTCATTTAAGTTAAATA
GATACCAAATGTACATGAAATTAACAAGAAATTTCATGACAATTCTTCTTCAAAATCTGCCATGG
ACATGAGCTTCATAAGGTATAGAGAAAAATTTTTATTTTTCATTTTCAATCGAATTCCTTTGGTT
TTTGGATTAAATTATGAAATAGAAAATTGTTCTATTCGAAGAGCTATATCATTTGGTACCAATAT
TGCATGCTAATATTGCTTGAATTCTTAGTTCCGAAATTTTAGCTTTTATGAAGATATTAGGGTTT
TATGAATTGATGATGTAATTTGATGTTATTAATGTTGTAGAATCATTTCCAAGCTTTTTTGATGA
TTAAAACACCTAGAAACACATCTATTCAGTTGGTAG
Found at i:1764639 original size:19 final size:20
Alignment explanation
Indices: 1764597--1764641 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1764587 ACTATGCTAA
* *
1764597 AAATTAATGTTAGAGTGTTG
1 AAATTGATGTTAGAATGTTG
1764617 AAATTGATGTTAGAATG-TG
1 AAATTGATGTTAGAATGTTG
1764636 AAATTG
1 AAATTG
1764642 GGTCATTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.38, C:0.00, G:0.24, T:0.38
Consensus pattern (20 bp):
AAATTGATGTTAGAATGTTG
Found at i:1770138 original size:20 final size:21
Alignment explanation
Indices: 1770099--1770138 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1770089 ATTGCAGGAA
*
1770099 TTTATGGCTTCGACACAAGAT
1 TTTATGGCTTCAACACAAGAT
1770120 TTTATGGCTTCAACA-AAGA
1 TTTATGGCTTCAACACAAGA
1770139 CCTTGATGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (21 bp):
TTTATGGCTTCAACACAAGAT
Found at i:1780113 original size:34 final size:34
Alignment explanation
Indices: 1780065--1780135 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 34
1780055 GCTACATAGC
* * * *
1780065 ATGTGTTCTTTGATTACGGTTTTTACTGAAAAAT
1 ATGTGTTCTCTGATTACAGTTTTCACTAAAAAAT
*
1780099 ATGTGTTCTCTGATTTCAGTTTTCACTAAAAAAT
1 ATGTGTTCTCTGATTACAGTTTTCACTAAAAAAT
1780133 ATG
1 ATG
1780136 ATTGTTCTGA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.45
Consensus pattern (34 bp):
ATGTGTTCTCTGATTACAGTTTTCACTAAAAAAT
Found at i:1781976 original size:21 final size:20
Alignment explanation
Indices: 1781929--1781978 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 20
1781919 GGTTTCATTA
1781929 TAATAA-TATTATTATTATAT
1 TAATAATTA-TATTATTATAT
1781949 T-AT-ATTATATTATTATAAT
1 TAATAATTATATTATTAT-AT
1781968 TAATAATTATA
1 TAATAATTATA
1781979 ATTTTACAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 10 0.38
19 7 0.27
20 3 0.12
21 6 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TAATAATTATATTATTATAT
Found at i:1781979 original size:13 final size:12
Alignment explanation
Indices: 1781925--1781981 Score: 57
Period size: 13 Copynumber: 4.8 Consensus size: 12
1781915 ATTTGGTTTC
1781925 ATTATAA-TAAT
1 ATTATAATTAAT
*
1781936 ATTATTATT-AT
1 ATTATAATTAAT
1781947 ATTAT-ATTATATT
1 ATTATAATTA-A-T
1781960 ATTATAATTAAT
1 ATTATAATTAAT
1781972 AATTATAATT
1 -ATTATAATT
1781982 TTACAGGCCC
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
10 3 0.08
11 13 0.33
12 3 0.08
13 16 0.41
14 4 0.10
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
ATTATAATTAAT
Found at i:1793747 original size:89 final size:89
Alignment explanation
Indices: 1793637--1793824 Score: 265
Period size: 89 Copynumber: 2.1 Consensus size: 89
1793627 TTCCGATGTT
* *
1793637 GCAAATCCAATCTCTATGGAAGAGTAGTGGAAACAAATCAACCTTGAATTTGATCTTCACA-AAA
1 GCAAATCCAATCTCTACGGAAGAGTAGTGGAAACAAATCAACCTTGAATCTGATCTTCA-AGAAA
1793701 GAGTAGTGAAACAGATTCATCTCAA
65 GAGTAGTGAAACAGATTCATCTCAA
* * * *
1793726 GCAAATCCAGTCT-TCACGGAAGAGTAGTGGAAACAAATCAACCTTGAGTCTGGTCTTCAAGGAA
1 GCAAATCCAATCTCT-ACGGAAGAGTAGTGGAAACAAATCAACCTTGAATCTGATCTTCAAGAAA
*
1793790 GAGTAGTGAAACAGATTCTTCTCAA
65 GAGTAGTGAAACAGATTCATCTCAA
1793815 GTC-AATCCAA
1 G-CAAATCCAA
1793825 CATTCATAAA
Statistics
Matches: 88, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
88 2 0.02
89 85 0.97
90 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (89 bp):
GCAAATCCAATCTCTACGGAAGAGTAGTGGAAACAAATCAACCTTGAATCTGATCTTCAAGAAAG
AGTAGTGAAACAGATTCATCTCAA
Found at i:1793749 original size:46 final size:45
Alignment explanation
Indices: 1793690--1793823 Score: 121
Period size: 43 Copynumber: 3.0 Consensus size: 45
1793680 TTGAATTTGA
**
1793690 TCTTCACAAAAGAGTAGTGAAACAGATTCATCTCAAGCAAATCCAG
1 TCTTCACGGAAGAGTAGTGAAACAGATTCATCTCAAGC-AATCCAG
* * ** * **
1793736 TCTTCACGGAAGAGTAGTGGAAACA-AATCAAC-CTTG-AGTCTGG
1 TCTTCACGGAAGAGTAGT-GAAACAGATTCATCTCAAGCAATCCAG
* *
1793779 TCTTCAAGGAAGAGTAGTGAAACAGATTCTTCTCAAGTCAATCCA
1 TCTTCACGGAAGAGTAGTGAAACAGATTCATCTCAAG-CAATCCA
1793824 ACATTCATAA
Statistics
Matches: 65, Mismatches: 18, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
42 6 0.09
43 25 0.38
44 2 0.03
45 2 0.03
46 24 0.37
47 6 0.09
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (45 bp):
TCTTCACGGAAGAGTAGTGAAACAGATTCATCTCAAGCAATCCAG
Found at i:1793790 original size:43 final size:42
Alignment explanation
Indices: 1793654--1793802 Score: 129
Period size: 43 Copynumber: 3.4 Consensus size: 42
1793644 CAATCTCTAT
* *
1793654 GGAAGAGTAGTGGAAACAAATCAACCTTGAATTTGATCTTCACA
1 GGAAGAGTAGT-GAAACAAATCAACCTTGAATCTGGTCTTCA-A
* * * ** ** *
1793698 -AAAGAGTAGTGAAACAGATTCATCTCAAGCAAATCCAGTCTTCAC
1 GGAAGAGTAGTGAAACA-AATCAAC-CTTG--AATCTGGTCTTCAA
*
1793743 GGAAGAGTAGTGGAAACAAATCAACCTTGAGTCTGGTCTTCAA
1 GGAAGAGTAGT-GAAACAAATCAACCTTGAATCTGGTCTTCAA
1793786 GGAAGAGTAGTGAAACA
1 GGAAGAGTAGTGAAACA
1793803 GATTCTTCTC
Statistics
Matches: 80, Mismatches: 19, Indels: 14
0.71 0.17 0.12
Matches are distributed among these distances:
42 12 0.15
43 35 0.44
44 2 0.03
45 2 0.03
46 23 0.29
47 6 0.08
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (42 bp):
GGAAGAGTAGTGAAACAAATCAACCTTGAATCTGGTCTTCAA
Found at i:1793841 original size:89 final size:89
Alignment explanation
Indices: 1793659--1793843 Score: 232
Period size: 89 Copynumber: 2.1 Consensus size: 89
1793649 TCTATGGAAG
*
1793659 AGTAGTGGAAACAAATCAACCTTGAATTTGATCTTCACAAAAGAGTAGTGAAACAGATTCATCTC
1 AGTAGTGGAAACAAATCAACCTTGAATCTGATCTTCACAAAAGAGTAGTGAAACAGATTCATCTC
* ** *
1793724 AAGCAAATCCAGTCTTCACGGAAG
66 AAGCAAATCCAGACTTCACAAAAA
* * * *
1793748 AGTAGTGGAAACAAATCAACCTTGAGTCTGGTCTTCA-AGGAAGAGTAGTGAAACAGATTCTTCT
1 AGTAGTGGAAACAAATCAACCTTGAATCTGATCTTCACA-AAAGAGTAGTGAAACAGATTCATCT
*
1793812 CAAGTC-AATCCA-ACATTCATAAAAA
65 CAAG-CAAATCCAGAC-TTCACAAAAA
1793837 AGTAGTG
1 AGTAGTG
1793844 AAGCAAGATT
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
88 2 0.02
89 80 0.96
90 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24
Consensus pattern (89 bp):
AGTAGTGGAAACAAATCAACCTTGAATCTGATCTTCACAAAAGAGTAGTGAAACAGATTCATCTC
AAGCAAATCCAGACTTCACAAAAA
Found at i:1795232 original size:27 final size:27
Alignment explanation
Indices: 1795202--1795253 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
1795192 ATTTAATCTT
* *
1795202 AGATTTTTAAT-ATTTTAAATAAATATA
1 AGATTATTAATAATTAT-AATAAATATA
1795229 AGATTATTAATAATTATAATAAATA
1 AGATTATTAATAATTATAATAAATA
1795254 GTATATTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (27 bp):
AGATTATTAATAATTATAATAAATATA
Found at i:1800169 original size:22 final size:21
Alignment explanation
Indices: 1800141--1800181 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1800131 AGCTGCGGAA
1800141 TTGATGGTCTTGATGGATGATG
1 TTGATGGTCTTGAT-GATGATG
*
1800163 TTGATGGTGTTGATGATGA
1 TTGATGGTCTTGATGATGA
1800182 AATGGAGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.20, C:0.02, G:0.37, T:0.41
Consensus pattern (21 bp):
TTGATGGTCTTGATGATGATG
Found at i:1801445 original size:16 final size:15
Alignment explanation
Indices: 1801424--1801462 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
1801414 AACTATAGAT
1801424 ATAATATATATATATG
1 ATAATATAT-TATATG
*
1801440 ATAATA-ATTATATT
1 ATAATATATTATATG
1801454 ATAATATAT
1 ATAATATAT
1801463 GAAATAAGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 11 0.52
15 4 0.19
16 6 0.29
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (15 bp):
ATAATATATTATATG
Found at i:1801479 original size:24 final size:25
Alignment explanation
Indices: 1801428--1801484 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 25
1801418 ATAGATATAA
**
1801428 TATATATATATGATAATAATTATAT
1 TATATATATATGATAATAAGCATAT
1801453 TATA-ATATATGA-AATAAGCATAT
1 TATATATATATGATAATAAGCATAT
*
1801476 T-TATGTATA
1 TATATATATA
1801485 AAGTTAGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 2 0.07
23 14 0.50
24 8 0.29
25 4 0.14
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (25 bp):
TATATATATATGATAATAAGCATAT
Found at i:1804339 original size:24 final size:26
Alignment explanation
Indices: 1804312--1804366 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 26
1804302 AATTCTATTA
*
1804312 TTTTTCTT-TTTTTTTCCTTTCTTT-
1 TTTTTCTTCTTTTTGTCCTTTCTTTC
*
1804336 TTTTTCTTCTTTTTGTCTTTTCTTTC
1 TTTTTCTTCTTTTTGTCCTTTCTTTC
1804362 TTTTT
1 TTTTT
1804367 GTGCTCCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 8 0.30
25 14 0.52
26 5 0.19
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (26 bp):
TTTTTCTTCTTTTTGTCCTTTCTTTC
Found at i:1804347 original size:16 final size:15
Alignment explanation
Indices: 1804314--1804366 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 15
1804304 TTCTATTATT
1804314 TTTCTTTTTTTTTCC
1 TTTCTTTTTTTTTCC
1804329 TTTC-TTTTTTTT-C
1 TTTCTTTTTTTTTCC
*
1804342 -TTCTTTTTGTCTTTTC
1 TTTCTTTTT-T-TTTCC
1804358 TTTCTTTTT
1 TTTCTTTTT
1804367 GTGCTCCAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
12 3 0.09
13 5 0.15
14 9 0.27
15 7 0.21
16 1 0.03
17 8 0.24
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (15 bp):
TTTCTTTTTTTTTCC
Found at i:1804356 original size:17 final size:17
Alignment explanation
Indices: 1804337--1804368 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1804327 CCTTTCTTTT
1804337 TTTTC-TTCTTTTTGTC
1 TTTTCTTTCTTTTTGTC
1804353 TTTTCTTTCTTTTTGT
1 TTTTCTTTCTTTTTGT
1804369 GCTCCAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.00, C:0.16, G:0.06, T:0.78
Consensus pattern (17 bp):
TTTTCTTTCTTTTTGTC
Found at i:1806171 original size:20 final size:20
Alignment explanation
Indices: 1806148--1806194 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1806138 AAAAATGACC
*
1806148 TCCATACCGCAGGACTGGTA
1 TCCATACCGAAGGACTGGTA
* *
1806168 TCCATACCGAAGGATTGGTC
1 TCCATACCGAAGGACTGGTA
1806188 TCCATAC
1 TCCATAC
1806195 TAAAGATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (20 bp):
TCCATACCGAAGGACTGGTA
Found at i:1813254 original size:8 final size:8
Alignment explanation
Indices: 1813241--1813266 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1813231 TTTAATCAAT
1813241 AAACCATA
1 AAACCATA
1813249 AAACCATA
1 AAACCATA
1813257 AAACCATA
1 AAACCATA
1813265 AA
1 AA
1813267 TAATAGCCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.65, C:0.23, G:0.00, T:0.12
Consensus pattern (8 bp):
AAACCATA
Found at i:1814409 original size:3 final size:3
Alignment explanation
Indices: 1814401--1814426 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1814391 TTAGCTCAAA
1814401 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
1814427 AACCCTTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:1828750 original size:33 final size:33
Alignment explanation
Indices: 1828710--1828788 Score: 149
Period size: 33 Copynumber: 2.4 Consensus size: 33
1828700 CTACATTCCA
1828710 AAGATGAATTTTCTAATAAGTTGGCCACCAACC
1 AAGATGAATTTTCTAATAAGTTGGCCACCAACC
*
1828743 AAGATGAAATTTCTAATAAGTTGGCCACCAACC
1 AAGATGAATTTTCTAATAAGTTGGCCACCAACC
1828776 AAGATGAATTTTC
1 AAGATGAATTTTC
1828789 CAACTTGCCA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (33 bp):
AAGATGAATTTTCTAATAAGTTGGCCACCAACC
Found at i:1833386 original size:33 final size:34
Alignment explanation
Indices: 1833318--1833413 Score: 124
Period size: 33 Copynumber: 2.9 Consensus size: 34
1833308 CCCATGTGCA
* *
1833318 AAGTTGGTCACCTACCAAAGAT-AAATTTTTCAAT
1 AAGTTGGTCACCAACC-AAGATGAAATTTCTCAAT
1833352 AAGTTGGTCACCAACCAAGATGAAATTTCT-AAT
1 AAGTTGGTCACCAACCAAGATGAAATTTCTCAAT
* * *
1833385 AAGTTGGCCATCAACCAAGATGAATTTTC
1 AAGTTGGTCACCAACCAAGATGAAATTTC
1833414 CAACTTGCCA
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
33 34 0.61
34 22 0.39
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.29
Consensus pattern (34 bp):
AAGTTGGTCACCAACCAAGATGAAATTTCTCAAT
Found at i:1838840 original size:60 final size:60
Alignment explanation
Indices: 1838747--1838867 Score: 233
Period size: 60 Copynumber: 2.0 Consensus size: 60
1838737 TAGCAGCTCG
*
1838747 TAATTGTGAACCAAAACAGAATGTTTAAAATAATGCTTTTATAGATCTCCATGTTATCGA
1 TAATTGTGAACCAAAACAGAATGTTTAAAATAATGCTTTTATAGATCTCCATATTATCGA
1838807 TAATTGTGAACCAAAACAGAATGTTTAAAATAATGCTTTTATAGATCTCCATATTATCGA
1 TAATTGTGAACCAAAACAGAATGTTTAAAATAATGCTTTTATAGATCTCCATATTATCGA
1838867 T
1 T
1838868 GACTGAAACC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.36
Consensus pattern (60 bp):
TAATTGTGAACCAAAACAGAATGTTTAAAATAATGCTTTTATAGATCTCCATATTATCGA
Found at i:1840914 original size:34 final size:34
Alignment explanation
Indices: 1840876--1841010 Score: 117
Period size: 34 Copynumber: 3.7 Consensus size: 34
1840866 AGAAAAATCC
1840876 ATATAATCAATCTACATAAACAAAACAACTAGGA
1 ATATAATCAATCTACATAAACAAAACAACTAGGA
** * *
1840910 ATATAATCAATGGACATAAACAAAGAAACCACACAAAAAGGCC
1 ATATAATCAATCTACATAAAC--A-AAA-CA-AC---TAGG-A
* *
1840953 ATATAATCAACCTACATAAACAAATCAACTAGGA
1 ATATAATCAATCTACATAAACAAAACAACTAGGA
**
1840987 ATATAATCAATGAACATAAACAAA
1 ATATAATCAATCTACATAAACAAA
1841011 GAAACTACGA
Statistics
Matches: 79, Mismatches: 13, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
34 40 0.51
35 3 0.04
36 1 0.01
37 3 0.04
38 4 0.05
39 4 0.05
40 2 0.03
41 1 0.01
42 3 0.04
43 18 0.23
ACGTcount: A:0.56, C:0.19, G:0.07, T:0.18
Consensus pattern (34 bp):
ATATAATCAATCTACATAAACAAAACAACTAGGA
Found at i:1840982 original size:77 final size:78
Alignment explanation
Indices: 1840830--1841015 Score: 284
Period size: 77 Copynumber: 2.4 Consensus size: 78
1840820 CTCTAACAAC
* * * * *
1840830 GAATATAATCAATCGAGATAAACAAAGAAACTACAAAGAAAAATCCATATAATCAATCTACATAA
1 GAATATAATCAATGGACATAAACAAAGAAACCACAAAGAAAAAGCCATATAATCAACCTACATAA
1840895 ACAAAACAACTAG
66 ACAAAACAACTAG
* *
1840908 GAATATAATCAATGGACATAAACAAAGAAACCACACA-AAAAGGCCATATAATCAACCTACATAA
1 GAATATAATCAATGGACATAAACAAAGAAACCACAAAGAAAAAGCCATATAATCAACCTACATAA
*
1840972 ACAAATCAACTAG
66 ACAAAACAACTAG
*
1840985 GAATATAATCAATGAACATAAACAAAGAAAC
1 GAATATAATCAATGGACATAAACAAAGAAAC
1841016 TACGAAAACA
Statistics
Matches: 99, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
77 66 0.67
78 33 0.33
ACGTcount: A:0.57, C:0.18, G:0.09, T:0.17
Consensus pattern (78 bp):
GAATATAATCAATGGACATAAACAAAGAAACCACAAAGAAAAAGCCATATAATCAACCTACATAA
ACAAAACAACTAG
Found at i:1841353 original size:34 final size:34
Alignment explanation
Indices: 1841315--1841449 Score: 117
Period size: 34 Copynumber: 3.7 Consensus size: 34
1841305 AGAAAAATCC
1841315 ATATAATCAATCTACATAAACAAAACAACTAGGA
1 ATATAATCAATCTACATAAACAAAACAACTAGGA
** * *
1841349 ATATAATCAATGGACATAAACAAAGAAACCACACAAAAAGGCC
1 ATATAATCAATCTACATAAAC--A-AAA-CA-AC---TAGG-A
* *
1841392 ATATAATCAACCTACATAAACAAATCAACTAGGA
1 ATATAATCAATCTACATAAACAAAACAACTAGGA
**
1841426 ATATAATCAATGAACATAAACAAA
1 ATATAATCAATCTACATAAACAAA
1841450 GAAACTACGA
Statistics
Matches: 79, Mismatches: 13, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
34 40 0.51
35 3 0.04
36 1 0.01
37 3 0.04
38 4 0.05
39 4 0.05
40 2 0.03
41 1 0.01
42 3 0.04
43 18 0.23
ACGTcount: A:0.56, C:0.19, G:0.07, T:0.18
Consensus pattern (34 bp):
ATATAATCAATCTACATAAACAAAACAACTAGGA
Found at i:1841421 original size:77 final size:78
Alignment explanation
Indices: 1841269--1841454 Score: 284
Period size: 77 Copynumber: 2.4 Consensus size: 78
1841259 TCTCTAACAA
* * * * *
1841269 GAATATAATCAATCGAGATAAACAAAGAAACTACAAAGAAAAATCCATATAATCAATCTACATAA
1 GAATATAATCAATGGACATAAACAAAGAAACCACAAAGAAAAAGCCATATAATCAACCTACATAA
1841334 ACAAAACAACTAG
66 ACAAAACAACTAG
* *
1841347 GAATATAATCAATGGACATAAACAAAGAAACCACACA-AAAAGGCCATATAATCAACCTACATAA
1 GAATATAATCAATGGACATAAACAAAGAAACCACAAAGAAAAAGCCATATAATCAACCTACATAA
*
1841411 ACAAATCAACTAG
66 ACAAAACAACTAG
*
1841424 GAATATAATCAATGAACATAAACAAAGAAAC
1 GAATATAATCAATGGACATAAACAAAGAAAC
1841455 TACGAAAACA
Statistics
Matches: 99, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
77 66 0.67
78 33 0.33
ACGTcount: A:0.57, C:0.18, G:0.09, T:0.17
Consensus pattern (78 bp):
GAATATAATCAATGGACATAAACAAAGAAACCACAAAGAAAAAGCCATATAATCAACCTACATAA
ACAAAACAACTAG
Found at i:1841561 original size:440 final size:442
Alignment explanation
Indices: 1840740--1841621 Score: 1734
Period size: 439 Copynumber: 2.0 Consensus size: 442
1840730 ATAAGCCTGA
1840740 GCAAAGCCAATTACTAGTTAGCAGATTCAATAGATTTCACTTTAGCATACGAATACCCCATTGTC
1 GCAAAGCCAATTACTAGTTAGCAGATTCAATAGATTTCACTTTAGCATACGAATACCCCATTGTC
1840805 AAATAATCAATCAATCTCTAACAACGAATATAATCAATCGAGATAAACAAAGAAACTACAAAGAA
66 AAATAATCAATCAATCTCTAACAACGAATATAATCAATCGAGATAAACAAAGAAACTACAAAGAA
1840870 AAATCCATATAATCAATCTACATAAACAAAACAACTAGGAATATAATCAATGGACATAAACAAAG
131 AAATCCATATAATCAATCTACATAAACAAAACAACTAGGAATATAATCAATGGACATAAACAAAG
1840935 AAACCACACAAAAAGGCCATATAATCAACCTACATAAACAAATCAACTAGGAATATAATCAATGA
196 AAACCACACAAAAAGGCCATATAATCAACCTACATAAACAAATCAACTAGGAATATAATCAATGA
1841000 ACATAAACAAAGAAACTACGAAAACAGTGGGGGGGGGCAAGAAATTATTTAAATTTATATACAAT
261 ACATAAACAAAGAAACTACGAAAACAGTGGGGGGGGGCAAGAAATTATTTAAATTTATATACAAT
1841065 ATGGAGTGCTGGTTTCACTTGCAGAACCCTCCATTGTTGTCCTTGGAGACAAGCAGTTCCCAAT-
326 ATGGAGTGCTGGTTTCACTTGCAGAACCCTCCATTGTTGTCCTTGGAGACAAGCAGTTCCCAATA
1841129 AACCTAAACTTAATCCAACAACCAGGTTCACCATC-TCACTATGTTTCTTCT
391 AACCTAAACTTAATCCAACAACCAGGTTCACCATCTTCACTATGTTTCTTCT
1841180 GCAAAGCCAATTACTAGTTAGCAGATTCAATAGATTTCACTTTAGCATACGAATACCCCATTGTC
1 GCAAAGCCAATTACTAGTTAGCAGATTCAATAGATTTCACTTTAGCATACGAATACCCCATTGTC
1841245 AAATAATCAATCAATCTCTAACAA-GAATATAATCAATCGAGATAAACAAAGAAACTACAAAGAA
66 AAATAATCAATCAATCTCTAACAACGAATATAATCAATCGAGATAAACAAAGAAACTACAAAGAA
1841309 AAATCCATATAATCAATCTACATAAACAAAACAACTAGGAATATAATCAATGGACATAAACAAAG
131 AAATCCATATAATCAATCTACATAAACAAAACAACTAGGAATATAATCAATGGACATAAACAAAG
1841374 AAACCACACAAAAAGGCCATATAATCAACCTACATAAACAAATCAACTAGGAATATAATCAATGA
196 AAACCACACAAAAAGGCCATATAATCAACCTACATAAACAAATCAACTAGGAATATAATCAATGA
1841439 ACATAAACAAAGAAACTACGAAAACAGTGGGGGGGGGGCAAGAAATTATTTAAATTTATATACAA
261 ACATAAACAAAGAAACTACGAAAACAGT-GGGGGGGGGCAAGAAATTATTTAAATTTATATACAA
1841504 TATGGAGTGCTGGTTTCACTTGCAGAACCCTCCATTGTTGTCCTTGGAGACAAGCAGTTCCCAAT
325 TATGGAGTGCTGGTTTCACTTGCAGAACCCTCCATTGTTGTCCTTGGAGACAAGCAGTTCCCAAT
1841569 AAACCTAAACTTAATCCAACAACCAGGTTCACCATCTTCACTATGTTTCTTCT
390 AAACCTAAACTTAATCCAACAACCAGGTTCACCATCTTCACTATGTTTCTTCT
1841622 TTTTTCCTTT
Statistics
Matches: 439, Mismatches: 0, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
439 198 0.45
440 190 0.43
441 35 0.08
442 16 0.04
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.24
Consensus pattern (442 bp):
GCAAAGCCAATTACTAGTTAGCAGATTCAATAGATTTCACTTTAGCATACGAATACCCCATTGTC
AAATAATCAATCAATCTCTAACAACGAATATAATCAATCGAGATAAACAAAGAAACTACAAAGAA
AAATCCATATAATCAATCTACATAAACAAAACAACTAGGAATATAATCAATGGACATAAACAAAG
AAACCACACAAAAAGGCCATATAATCAACCTACATAAACAAATCAACTAGGAATATAATCAATGA
ACATAAACAAAGAAACTACGAAAACAGTGGGGGGGGGCAAGAAATTATTTAAATTTATATACAAT
ATGGAGTGCTGGTTTCACTTGCAGAACCCTCCATTGTTGTCCTTGGAGACAAGCAGTTCCCAATA
AACCTAAACTTAATCCAACAACCAGGTTCACCATCTTCACTATGTTTCTTCT
Found at i:1853106 original size:31 final size:31
Alignment explanation
Indices: 1853065--1853213 Score: 147
Period size: 31 Copynumber: 4.8 Consensus size: 31
1853055 ACTAATACTC
* *
1853065 CTATGTATTATCTGAATAAAAACCTTACATA
1 CTATGCATTATCTGAATACAAACCTTACATA
* * *
1853096 CTGTGCATTATCTAAATACAAATCTGT-CATA
1 CTATGCATTATCTGAATACAAACCT-TACATA
* * * * *
1853127 CTATACATGATCTGAATGCAAACATGACATA
1 CTATGCATTATCTGAATACAAACCTTACATA
* * *
1853158 TTGTGGATTATCTGAATACAAACCTTACATA
1 CTATGCATTATCTGAATACAAACCTTACATA
* *
1853189 CTATGCATTATCTAAATGCAAACCT
1 CTATGCATTATCTGAATACAAACCT
1853214 GACTAGTATT
Statistics
Matches: 90, Mismatches: 26, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
31 89 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (31 bp):
CTATGCATTATCTGAATACAAACCTTACATA
Found at i:1853176 original size:62 final size:62
Alignment explanation
Indices: 1853091--1853216 Score: 164
Period size: 62 Copynumber: 2.0 Consensus size: 62
1853081 TAAAAACCTT
* *
1853091 ACATACTGTGCATTATCTAAATACAAATCTGT-CATACTATACATGATCTGAATGCAAACATG
1 ACATACTGTGCATTATCTAAATACAAACCT-TACATACTATACATGATCTAAATGCAAACATG
* * * * * *
1853153 ACATATTGTGGATTATCTGAATACAAACCTTACATACTATGCATTATCTAAATGCAAACCTG
1 ACATACTGTGCATTATCTAAATACAAACCTTACATACTATACATGATCTAAATGCAAACATG
1853215 AC
1 AC
1853217 TAGTATTTGG
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
61 1 0.02
62 54 0.98
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (62 bp):
ACATACTGTGCATTATCTAAATACAAACCTTACATACTATACATGATCTAAATGCAAACATG
Found at i:1854492 original size:19 final size:20
Alignment explanation
Indices: 1854468--1854506 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1854458 TTTACCCCGA
1854468 TTCATC-TAGTATCGATACT
1 TTCATCATAGTATCGATACT
1854487 TTCATCATAGTATCGATACT
1 TTCATCATAGTATCGATACT
1854507 CAAACCCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (20 bp):
TTCATCATAGTATCGATACT
Found at i:1863429 original size:18 final size:18
Alignment explanation
Indices: 1863406--1863441 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1863396 AAATAAAAAA
*
1863406 AAGTGTTTTTGTTTTAAT
1 AAGTGTTTTTGATTTAAT
1863424 AAGTGTTTTTGATTTAAT
1 AAGTGTTTTTGATTTAAT
1863442 TATATTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.17, T:0.58
Consensus pattern (18 bp):
AAGTGTTTTTGATTTAAT
Found at i:1863504 original size:12 final size:13
Alignment explanation
Indices: 1863477--1863509 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1863467 ATATTATAAA
*
1863477 TTTTCAAACTTAG
1 TTTTCAAACATAG
1863490 TTTTCAAA-ATAG
1 TTTTCAAACATAG
1863502 TTTTCAAA
1 TTTTCAAA
1863510 TTTTCCCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.45
Consensus pattern (13 bp):
TTTTCAAACATAG
Found at i:1867456 original size:111 final size:111
Alignment explanation
Indices: 1867263--1867581 Score: 392
Period size: 111 Copynumber: 2.9 Consensus size: 111
1867253 GGTGCCCCTA
* * * * *
1867263 ATGAAAGTTATCGATCAATTTTG-TTAATGCATAACAGTGCATTTTCGCCATCAAATGTGCCACC
1 ATGAAAGTTATCGATCGATTTTGTTTAATGCATAACAGTGCATTATCGACATAAAAGGTGCCACC
* * *
1867327 TATGGAATTCATAAAAGGTGAATTACCATTTCGACATACCTCATGT
66 CATGGTATTCATAAAAGGTGAATTACCATTTCGACATACCTCATAT
* * * *
1867373 ATGAAAGTTATCGATCGTTTTTGTTTAATACATAACGGTGCATTATCGACATAAAAGGTGCTACC
1 ATGAAAGTTATCGATCGATTTTGTTTAATGCATAACAGTGCATTATCGACATAAAAGGTGCCACC
* **
1867438 CATGGTATTCATAAAAGGTGAATTACCATTTTGACATACCTTGTAT
66 CATGGTATTCATAAAAGGTGAATTACCATTTCGACATACCTCATAT
* * *
1867484 ATGAAAGTTATCGATCGGTTTTGTTTAATGCATAACTA-TGCATTAT-TAGCATAAAAGGAGCCA
1 ATGAAAGTTATCGATCGATTTTGTTTAATGCATAAC-AGTGCATTATCGA-CATAAAAGGTGCCA
* * * * *
1867547 CTCATGGTATTCTTAAAAGGTAAATGACTATTTCG
64 CCCATGGTATTCATAAAAGGTGAATTACCATTTCG
1867582 GCACTTCGGT
Statistics
Matches: 179, Mismatches: 27, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
110 22 0.12
111 157 0.88
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (111 bp):
ATGAAAGTTATCGATCGATTTTGTTTAATGCATAACAGTGCATTATCGACATAAAAGGTGCCACC
CATGGTATTCATAAAAGGTGAATTACCATTTCGACATACCTCATAT
Found at i:1874626 original size:111 final size:110
Alignment explanation
Indices: 1874448--1874769 Score: 450
Period size: 111 Copynumber: 2.9 Consensus size: 110
1874438 GGTGCCATTA
* * *
1874448 ATGAAAGTTATCGATCGATTTTG-TTAATGCATAACTATGCATTTTCAGCATAAAAGGTGCCACC
1 ATGAAAGTTATCGATCGATTTTGTTTAATGCATAACTATGCATTATCGGCATAAAAGGTG-CAAC
1874512 CATGGTATTCATAAAAGGTGAATTACCATTTCGACATACCTCGTGT
65 CATGGTATTCATAAAAGGTGAATTACCATTTCGACATACCTCGTGT
* * *
1874558 ATGAAAGTTATCGATCGATTTTGTTTTATGAATAACGGA-GCATTATCGGCATAAAAGGTGACAA
1 ATGAAAGTTATCGATCGATTTTGTTTAATGCATAAC-TATGCATTATCGGCATAAAAGGTG-CAA
* *
1874622 CCATGGTATTCATAAAAGGTGAATTACCATTTCAACATGCCTCGTGT
64 CCATGGTATTCATAAAAGGTGAATTACCATTTCGACATACCTCGTGT
* * * * *
1874669 ATGAAAGTTACCGATTGATTTTGTTTAATGCATAAATATGCATTATCGGCATAAAAGGCGCCACT
1 ATGAAAGTTATCGATCGATTTTGTTTAATGCATAACTATGCATTATCGGCATAAAAGGTGCAAC-
* * *
1874734 AATTGTATTCATAAAAGGTGAATGACCATTTCGACA
65 CATGGTATTCATAAAAGGTGAATTACCATTTCGACA
1874770 CTTCGATGCA
Statistics
Matches: 187, Mismatches: 21, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
110 27 0.14
111 159 0.85
112 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (110 bp):
ATGAAAGTTATCGATCGATTTTGTTTAATGCATAACTATGCATTATCGGCATAAAAGGTGCAACC
ATGGTATTCATAAAAGGTGAATTACCATTTCGACATACCTCGTGT
Found at i:1875843 original size:32 final size:32
Alignment explanation
Indices: 1875798--1875858 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
1875788 AATGTAAAAT
1875798 TGACACTAATGTGCATTATCTT-AATGCAATAA
1 TGACACTAATGTGCATTAT-TTGAATGCAATAA
**
1875830 TGACACTGGTGTGCATTATTTGAATGCAA
1 TGACACTAATGTGCATTATTTGAATGCAA
1875859 CACTTCTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 2 0.08
32 24 0.92
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (32 bp):
TGACACTAATGTGCATTATTTGAATGCAATAA
Found at i:1876267 original size:20 final size:20
Alignment explanation
Indices: 1876242--1876279 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1876232 GCTCATCTTA
*
1876242 GTTCATCCATTATCGATATT
1 GTTCATCCAGTATCGATATT
1876262 GTTCATCCAGTATCGATA
1 GTTCATCCAGTATCGATA
1876280 CTCAAACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.39
Consensus pattern (20 bp):
GTTCATCCAGTATCGATATT
Found at i:1878060 original size:15 final size:16
Alignment explanation
Indices: 1878033--1878064 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1878023 GCTTTCAAAA
1878033 TTGAAAAATGAAAATT
1 TTGAAAAATGAAAATT
1878049 TTGAAAAA-GAAAATT
1 TTGAAAAATGAAAATT
1878064 T
1 T
1878065 GATTAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.31
Consensus pattern (16 bp):
TTGAAAAATGAAAATT
Found at i:1878065 original size:14 final size:15
Alignment explanation
Indices: 1878029--1878066 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
1878019 GAGAGCTTTC
1878029 AAAA-TTGAAAAATG
1 AAAATTTGAAAAATG
1878043 AAAATTTTGAAAAA-G
1 AAAA-TTTGAAAAATG
1878058 AAAATTTGA
1 AAAATTTGA
1878067 TTAAAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 9 0.41
15 5 0.23
16 8 0.36
ACGTcount: A:0.61, C:0.00, G:0.13, T:0.26
Consensus pattern (15 bp):
AAAATTTGAAAAATG
Found at i:1881301 original size:21 final size:20
Alignment explanation
Indices: 1881277--1881340 Score: 74
Period size: 21 Copynumber: 3.1 Consensus size: 20
1881267 CCATGCATTT
*
1881277 TTAGCTCAAATGATCAATCTC
1 TTAGC-CAAATGATCAATCCC
* *
1881298 TTAGCAAAAGGATCAATCCC
1 TTAGCCAAATGATCAATCCC
*
1881318 TTTGACCAAATGATCAATCCC
1 TTAG-CCAAATGATCAATCCC
1881339 TT
1 TT
1881341 GAAAAAGGAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
20 15 0.42
21 21 0.58
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.30
Consensus pattern (20 bp):
TTAGCCAAATGATCAATCCC
Found at i:1881356 original size:19 final size:20
Alignment explanation
Indices: 1881288--1881360 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 20
1881278 TAGCTCAAAT
*
1881288 GATCAATCTCTT-AGCAAAAG
1 GATCAATCCCTTGA-CAAAAG
* *
1881308 GATCAATCCCTTTGACCAAAT
1 GATCAATCCC-TTGACAAAAG
1881329 GATCAATCCCTTGA-AAAAG
1 GATCAATCCCTTGACAAAAG
*
1881348 GATCGATCCCTTG
1 GATCAATCCCTTG
1881361 GATTCTGATA
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
19 15 0.33
20 13 0.29
21 16 0.36
22 1 0.02
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.26
Consensus pattern (20 bp):
GATCAATCCCTTGACAAAAG
Found at i:1881357 original size:40 final size:41
Alignment explanation
Indices: 1881283--1881359 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 41
1881273 ATTTTTAGCT
* *
1881283 CAAATGATCAATCTCTTAGCAAAAGGATCAATCCCTTTGAC
1 CAAATGATCAATCCCTTAGAAAAAGGATCAATCCCTTTGAC
*
1881324 CAAATGATCAATCCCTT-GAAAAAGGATCGATCCCTT
1 CAAATGATCAATCCCTTAGAAAAAGGATCAATCCCTT
1881360 GGATTCTGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 17 0.52
41 16 0.48
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (41 bp):
CAAATGATCAATCCCTTAGAAAAAGGATCAATCCCTTTGAC
Found at i:1883807 original size:16 final size:16
Alignment explanation
Indices: 1883786--1883818 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1883776 AAGTAAGTCT
1883786 AATTAT-ATTGTTTATC
1 AATTATCATT-TTTATC
1883802 AATTATCATTTTTATC
1 AATTATCATTTTTATC
1883818 A
1 A
1883819 CATTCTCTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.33, C:0.09, G:0.03, T:0.55
Consensus pattern (16 bp):
AATTATCATTTTTATC
Found at i:1884639 original size:30 final size:31
Alignment explanation
Indices: 1884576--1884639 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
1884566 GTTAACTCGG
1884576 AGTGACCACATCTTAATTAAATAAAAACGAA
1 AGTGACCACATCTTAATTAAATAAAAACGAA
* * *
1884607 AGTGACTATATCTTAATTAAA-AAAACCGAA
1 AGTGACCACATCTTAATTAAATAAAAACGAA
1884637 AGT
1 AGT
1884640 CAACATGTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 11 0.37
31 19 0.63
ACGTcount: A:0.50, C:0.14, G:0.11, T:0.25
Consensus pattern (31 bp):
AGTGACCACATCTTAATTAAATAAAAACGAA
Found at i:1884651 original size:30 final size:31
Alignment explanation
Indices: 1884585--1884652 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 31
1884575 GAGTGACCAC
*
1884585 ATCTTAATTAAATAAAAACGAAAGTGACTAT
1 ATCTTAATTAAATAAAAACGAAAGTAACTAT
*
1884616 ATCTTAATTAAA-AAAACCGAAAGTCAAC-AT
1 ATCTTAATTAAATAAAAACGAAAGT-AACTAT
*
1884646 GTCTTAA
1 ATCTTAA
1884653 GTTTTTTGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 19 0.58
31 14 0.42
ACGTcount: A:0.50, C:0.13, G:0.09, T:0.28
Consensus pattern (31 bp):
ATCTTAATTAAATAAAAACGAAAGTAACTAT
Found at i:1888684 original size:34 final size:34
Alignment explanation
Indices: 1888615--1888685 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 34
1888605 TTTAATCAAT
* **
1888615 ATAATATATAAACACATTACTGCTACAACATACA
1 ATAATACATAAACACATTACTGAAACAACATACA
1888649 ATAATACATAAACACATTA-TAGAAACAGACA-ACA
1 ATAATACATAAACACATTACT-GAAACA-ACATACA
1888683 ATA
1 ATA
1888686 CGCGAACGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 1 0.03
34 28 0.88
35 3 0.09
ACGTcount: A:0.55, C:0.18, G:0.04, T:0.23
Consensus pattern (34 bp):
ATAATACATAAACACATTACTGAAACAACATACA
Found at i:1889666 original size:14 final size:14
Alignment explanation
Indices: 1889644--1889681 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
1889634 ACGGCCGTAA
1889644 TGCAACGTAATGCC
1 TGCAACGTAATGCC
*
1889658 TGCAGCGTAATGCC
1 TGCAACGTAATGCC
*
1889672 TGCATCGTAA
1 TGCAACGTAA
1889682 CGTTTTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (14 bp):
TGCAACGTAATGCC
Found at i:1890975 original size:19 final size:20
Alignment explanation
Indices: 1890931--1890975 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1890921 ATTTGTTTTT
*
1890931 AATAAATTTTTATCTGTGAA
1 AATAAATTTTTATCTCTGAA
* *
1890951 ATTAAATTTTTATTTCT-AA
1 AATAAATTTTTATCTCTGAA
1890970 AATAAA
1 AATAAA
1890976 ATATTAAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (20 bp):
AATAAATTTTTATCTCTGAA
Found at i:1892950 original size:3 final size:3
Alignment explanation
Indices: 1892942--1892973 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1892932 TTTATGGTTA
*
1892942 AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1892974 AAAGTAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1894299 original size:3 final size:3
Alignment explanation
Indices: 1894291--1894372 Score: 73
Period size: 3 Copynumber: 28.0 Consensus size: 3
1894281 CCGGTTTGTA
* *
1894291 AAT AAT AAT TAT -TT AAT AAT AAT -AT AAT -AT ATAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT
* **
1894333 AAT AAT ATTT AAT AAT AAT AAT AAT AAT TTT AAT AAT AAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1894373 TTAAGTAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
2 7 0.11
3 52 0.81
4 5 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
AAT
Found at i:1894332 original size:25 final size:22
Alignment explanation
Indices: 1894291--1894372 Score: 106
Period size: 21 Copynumber: 4.0 Consensus size: 22
1894281 CCGGTTTGTA
1894291 AATAATAATTATTTAATAATAAT
1 AATAATAA-TATTTAATAATAAT
1894314 -ATAAT-ATA--T-ATAAT-AT
1 AATAATAATATTTAATAATAAT
1894330 AATAATAATATTTAATAATAAT
1 AATAATAATATTTAATAATAAT
1894352 AATAATAAT-TTTAATAATAAT
1 AATAATAATATTTAATAATAAT
1894373 TTAAGTAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 14
0.79 0.00 0.21
Matches are distributed among these distances:
16 2 0.04
17 10 0.19
18 4 0.08
20 3 0.06
21 18 0.34
22 16 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AATAATAATATTTAATAATAAT
Found at i:1895074 original size:302 final size:305
Alignment explanation
Indices: 1894526--1895238 Score: 1333
Period size: 302 Copynumber: 2.3 Consensus size: 305
1894516 GAGGTCTTAA
*
1894526 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
* *
1894591 AGGCTTTTTGGAAACATTATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACTTCAA
66 AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
* *
1894656 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTT
131 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTACAGGACGTACAGATGACCCTAAGGCTTT
*
1894721 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCGCTGCAGGACTTACAGATGAC
196 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGAC
*
1894786 CCTAAGG-TTT-TAAACATCAAAAAGCTCCCGAAGGC-TTTTTGG
261 CCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTTGG
1894828 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1894893 AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
1894958 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTACAGGACGTACAGATGACCCTAAGGCTTT
131 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTACAGGACGTACAGATGACCCTAAGGCTTT
1895023 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGAC
196 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGAC
1895088 CCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTTGG
261 CCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTTGG
1895133 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
1895198 AGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATG
66 AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
1895239 TGGGAAATAG
Statistics
Matches: 400, Mismatches: 8, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
302 261 0.65
303 3 0.01
304 24 0.06
305 112 0.28
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (305 bp):
AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTACAGGACGTACAGATGACCCTAAGGCTTT
GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGAC
CCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTTGG
Found at i:1895265 original size:76 final size:76
Alignment explanation
Indices: 1894526--1895238 Score: 1331
Period size: 76 Copynumber: 9.4 Consensus size: 76
1894516 GAGGTCTTAA
*
1894526 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1894591 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
1894602 AAACATTATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACTTCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1894667 AGGCTTTTTGG
66 AGGCTTTTTGG
1894678 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1894743 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
1894754 AAACATCATGCGCTGCAGGACTTACAGATGACCCTAAGG-TTT-TAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1894817 AGGCTTTTTGG
66 AGGCTTTTTGG
1894828 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1894893 AGGCTTTTTGG
66 AGGCTTTTTGG
1894904 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1894969 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
1894980 AAACATCATGCACTACAGGACGTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1895045 AGGCTTTTTGG
66 AGGCTTTTTGG
1895056 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1895121 AGGCTTTTTTGG
66 AGGC-TTTTTGG
1895133 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1895198 AGGCTTTTTGG
66 AGGCTTTTTGG
*
1895209 AAACATCATGCACTGTAGGACTTACAGATG
1 AAACATCATGCACTGCAGGACTTACAGATG
1895239 TGGGAAATAG
Statistics
Matches: 620, Mismatches: 14, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
74 69 0.11
75 6 0.01
76 469 0.76
77 76 0.12
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (76 bp):
AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:1895874 original size:22 final size:22
Alignment explanation
Indices: 1895849--1895903 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
1895839 CATAAAGCTT
1895849 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
1895871 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
1895893 TCATCTTTGAA
1 TCATCTTTGAA
1895904 GAGTGTAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:1897976 original size:13 final size:13
Alignment explanation
Indices: 1897976--1898017 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
1897966 CCGTTGACCC
*
1897976 GACCCAACCCGTT
1 GACCCGACCCGTT
*
1897989 TACCCGACCCGTT
1 GACCCGACCCGTT
1898002 GACCCGACCCGTT
1 GACCCGACCCGTT
1898015 GAC
1 GAC
1898018 TCGTTGACCG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.19, C:0.45, G:0.19, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1898012 original size:18 final size:18
Alignment explanation
Indices: 1897954--1897999 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
1897944 ACCAGTCACA
1897954 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
* *
1897972 ACCCGACCCAACCCGTTT
1 ACCCGACCCGACCCGTTG
1897990 ACCCGACCCG
1 ACCCGACCCG
1898000 TTGACCCGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.20, C:0.52, G:0.17, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:1898030 original size:15 final size:17
Alignment explanation
Indices: 1898010--1898043 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1898000 TTGACCCGAC
1898010 CCGTTGA-C-TCGTTGA
1 CCGTTGACCGTCGTTGA
1898025 CCGTTGACCGTCGTTGA
1 CCGTTGACCGTCGTTGA
1898042 CC
1 CC
1898044 ACTGTTGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 1 0.06
17 9 0.53
ACGTcount: A:0.12, C:0.32, G:0.26, T:0.29
Consensus pattern (17 bp):
CCGTTGACCGTCGTTGA
Found at i:1900318 original size:12 final size:12
Alignment explanation
Indices: 1900303--1900341 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
1900293 GATACGTTAC
1900303 CTGAATTCTGTT
1 CTGAATTCTGTT
*
1900315 CTG-ATTCTGAT
1 CTGAATTCTGTT
*
1900326 CTGGATTCTGTT
1 CTGAATTCTGTT
1900338 CTGA
1 CTGA
1900342 TATCTGATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.15, C:0.18, G:0.21, T:0.46
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:1900347 original size:12 final size:11
Alignment explanation
Indices: 1900307--1900347 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
1900297 CGTTACCTGA
1900307 ATTCTGTTCTG
1 ATTCTGTTCTG
*
1900318 ATTCTGATCTGG
1 ATTCTGTTCT-G
1900330 ATTCTGTTCTG
1 ATTCTGTTCTG
1900341 ATATCTG
1 AT-TCTG
1900348 ATATGAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
11 12 0.46
12 14 0.54
ACGTcount: A:0.15, C:0.17, G:0.20, T:0.49
Consensus pattern (11 bp):
ATTCTGTTCTG
Found at i:1900361 original size:24 final size:23
Alignment explanation
Indices: 1900304--1900367 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 23
1900294 ATACGTTACC
*
1900304 TGAATTCTGTTCTGATTCTGATC
1 TGAATTCTGTTCTGATTCTGATA
*
1900327 TGGATTCTGTTCTGATATCTGATA
1 TGAATTCTGTTCTGAT-TCTGATA
* *
1900351 TGAATTATGTTTTGATT
1 TGAATTCTGTTCTGATT
1900368 TTTGATATCT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 16 0.46
24 19 0.54
ACGTcount: A:0.20, C:0.11, G:0.19, T:0.50
Consensus pattern (23 bp):
TGAATTCTGTTCTGATTCTGATA
Found at i:1903857 original size:18 final size:18
Alignment explanation
Indices: 1903831--1903866 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1903821 TCGAAAGGAC
*
1903831 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1903849 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
1903867 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1904805 original size:24 final size:23
Alignment explanation
Indices: 1904778--1904864 Score: 66
Period size: 24 Copynumber: 3.7 Consensus size: 23
1904768 ATTTCCGAAT
*
1904778 TGAATTCTGTTATGATACGTTACC
1 TGAATTCTGTTATGATAC-TGACC
* * * *
1904802 TGAATTTTGTTCTGATTCTGATC
1 TGAATTCTGTTATGATACTGACC
* **
1904825 TGGATTCTGTTATGATATCTGATA
1 TGAATTCTGTTATGATA-CTGACC
* *
1904849 TGAATTATGTTTTGAT
1 TGAATTCTGTTATGAT
1904865 TTTTGATATC
Statistics
Matches: 49, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
23 16 0.33
24 33 0.67
ACGTcount: A:0.23, C:0.10, G:0.18, T:0.48
Consensus pattern (23 bp):
TGAATTCTGTTATGATACTGACC
Found at i:1907039 original size:13 final size:13
Alignment explanation
Indices: 1906992--1907028 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1906982 AACCCGACCC
1906992 GACCTGACCCGTT
1 GACCTGACCCGTT
*
1907005 TACCTGACCCGTT
1 GACCTGACCCGTT
*
1907018 GACCCGACCCG
1 GACCTGACCCG
1907029 ACCCGTTGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.16, C:0.43, G:0.22, T:0.19
Consensus pattern (13 bp):
GACCTGACCCGTT
Found at i:1908381 original size:18 final size:18
Alignment explanation
Indices: 1908355--1908390 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1908345 TCGAAAGGAC
*
1908355 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1908373 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
1908391 CTGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1909329 original size:24 final size:23
Alignment explanation
Indices: 1909302--1909388 Score: 66
Period size: 24 Copynumber: 3.7 Consensus size: 23
1909292 ATTTCCGAAT
*
1909302 TGAATTCTGTTATGATACGTTACC
1 TGAATTCTGTTATGATAC-TGACC
* * * *
1909326 TGAATTTTGTTCTGATTCTGATC
1 TGAATTCTGTTATGATACTGACC
* **
1909349 TGGATTCTGTTATGATATCTGATA
1 TGAATTCTGTTATGATA-CTGACC
* *
1909373 TGAATTATGTTTTGAT
1 TGAATTCTGTTATGAT
1909389 TTTTGATATC
Statistics
Matches: 49, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
23 16 0.33
24 33 0.67
ACGTcount: A:0.23, C:0.10, G:0.18, T:0.48
Consensus pattern (23 bp):
TGAATTCTGTTATGATACTGACC
Found at i:1911530 original size:18 final size:18
Alignment explanation
Indices: 1911507--1911576 Score: 78
Period size: 18 Copynumber: 4.2 Consensus size: 18
1911497 ACCGGTCACA
1911507 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
1911525 ACCCGACCTGACCCGTT-
1 ACCCGACCCGACCCGTTG
* *
1911542 ----TACCTGACCCGTTG
1 ACCCGACCCGACCCGTTG
1911556 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1911574 ACC
1 ACC
1911577 GTTGACCGTC
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
13 12 0.28
18 31 0.72
ACGTcount: A:0.17, C:0.47, G:0.20, T:0.16
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:1911576 original size:13 final size:13
Alignment explanation
Indices: 1911529--1911565 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1911519 CCGTTGACCC
1911529 GACCTGACCCGTT
1 GACCTGACCCGTT
*
1911542 TACCTGACCCGTT
1 GACCTGACCCGTT
*
1911555 GACCCGACCCG
1 GACCTGACCCG
1911566 ACCCGTTGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.16, C:0.43, G:0.22, T:0.19
Consensus pattern (13 bp):
GACCTGACCCGTT
Found at i:1912918 original size:18 final size:18
Alignment explanation
Indices: 1912892--1912927 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1912882 TCGAAAGGAC
*
1912892 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1912910 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
1912928 CTGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1913867 original size:24 final size:23
Alignment explanation
Indices: 1913840--1913926 Score: 84
Period size: 24 Copynumber: 3.7 Consensus size: 23
1913830 ATTTCCGAAT
*
1913840 TGAATTCTGTTCTGATACGTTACC
1 TGAATTCTGTTCTGATAC-TGACC
* *
1913864 TGAATTCTGTTCTGATTCTGATC
1 TGAATTCTGTTCTGATACTGACC
* **
1913887 TGGATTCTGTTCTGATATCTGATA
1 TGAATTCTGTTCTGATA-CTGACC
* *
1913911 TGAATTATGTTTTGAT
1 TGAATTCTGTTCTGAT
1913927 TTTTGATATC
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
23 18 0.34
24 35 0.66
ACGTcount: A:0.21, C:0.14, G:0.18, T:0.47
Consensus pattern (23 bp):
TGAATTCTGTTCTGATACTGACC
Found at i:1913907 original size:12 final size:11
Alignment explanation
Indices: 1913843--1913907 Score: 60
Period size: 12 Copynumber: 5.5 Consensus size: 11
1913833 TCCGAATTGA
1913843 ATTCTGTTCTG
1 ATTCTGTTCTG
*
1913854 ATAC-GTTACCTG
1 ATTCTGTT--CTG
1913866 AATTCTGTTCTG
1 -ATTCTGTTCTG
*
1913878 ATTCTGATCTGG
1 ATTCTGTTCT-G
1913890 ATTCTGTTCTG
1 ATTCTGTTCTG
1913901 ATATCTG
1 AT-TCTG
1913908 ATATGAATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
10 3 0.07
11 15 0.34
12 20 0.45
13 3 0.07
14 3 0.07
ACGTcount: A:0.17, C:0.18, G:0.18, T:0.46
Consensus pattern (11 bp):
ATTCTGTTCTG
Found at i:1916065 original size:18 final size:18
Alignment explanation
Indices: 1916042--1916111 Score: 78
Period size: 18 Copynumber: 4.2 Consensus size: 18
1916032 ACCGGTCACA
1916042 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1916060 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
* * *
1916077 ----TACCTGACCTGTTG
1 ACCCGACCCGACCCGTTG
1916091 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1916109 ACC
1 ACC
1916112 GTTGACCGTT
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
13 10 0.24
18 31 0.76
ACGTcount: A:0.17, C:0.47, G:0.20, T:0.16
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:1917450 original size:18 final size:18
Alignment explanation
Indices: 1917424--1917459 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1917414 TCGAAAGGAC
*
1917424 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1917442 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
1917460 CTGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1918399 original size:24 final size:23
Alignment explanation
Indices: 1918372--1918458 Score: 84
Period size: 24 Copynumber: 3.7 Consensus size: 23
1918362 ATTTCCGAAT
*
1918372 TGAATTCTGTTCTGATACGTTACC
1 TGAATTCTGTTCTGATAC-TGACC
* *
1918396 TGAATTCTGTTCTGATTCTGATC
1 TGAATTCTGTTCTGATACTGACC
* **
1918419 TGGATTCTGTTCTGATATCTGATA
1 TGAATTCTGTTCTGATA-CTGACC
* *
1918443 TGAATTATGTTTTGAT
1 TGAATTCTGTTCTGAT
1918459 TTTTGATATC
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
23 18 0.34
24 35 0.66
ACGTcount: A:0.21, C:0.14, G:0.18, T:0.47
Consensus pattern (23 bp):
TGAATTCTGTTCTGATACTGACC
Found at i:1918439 original size:12 final size:11
Alignment explanation
Indices: 1918375--1918439 Score: 60
Period size: 12 Copynumber: 5.5 Consensus size: 11
1918365 TCCGAATTGA
1918375 ATTCTGTTCTG
1 ATTCTGTTCTG
*
1918386 ATAC-GTTACCTG
1 ATTCTGTT--CTG
1918398 AATTCTGTTCTG
1 -ATTCTGTTCTG
*
1918410 ATTCTGATCTGG
1 ATTCTGTTCT-G
1918422 ATTCTGTTCTG
1 ATTCTGTTCTG
1918433 ATATCTG
1 AT-TCTG
1918440 ATATGAATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
10 3 0.07
11 15 0.34
12 20 0.45
13 3 0.07
14 3 0.07
ACGTcount: A:0.17, C:0.18, G:0.18, T:0.46
Consensus pattern (11 bp):
ATTCTGTTCTG
Found at i:1920639 original size:13 final size:13
Alignment explanation
Indices: 1920579--1920626 Score: 87
Period size: 13 Copynumber: 3.7 Consensus size: 13
1920569 GTCACAACCC
1920579 GACCCGACCCGTT
1 GACCCGACCCGTT
1920592 GACCCGACCCGTT
1 GACCCGACCCGTT
*
1920605 TACCCGACCCGTT
1 GACCCGACCCGTT
1920618 GACCCGACC
1 GACCCGACC
1920627 TGACCCGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.17, C:0.48, G:0.21, T:0.15
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1921981 original size:18 final size:18
Alignment explanation
Indices: 1921955--1921990 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1921945 TCGAAAGGAC
*
1921955 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1921973 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
1921991 CTGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1922929 original size:24 final size:23
Alignment explanation
Indices: 1922902--1922988 Score: 84
Period size: 24 Copynumber: 3.7 Consensus size: 23
1922892 ATTTCCGAAT
*
1922902 TGAATTCTGTTCTGATACGTTACC
1 TGAATTCTGTTCTGATAC-TGACC
* *
1922926 TGAATTCTGTTCTGATTCTGATC
1 TGAATTCTGTTCTGATACTGACC
* **
1922949 TGGATTCTGTTCTGATATCTGATA
1 TGAATTCTGTTCTGATA-CTGACC
* *
1922973 TGAATTATGTTTTGAT
1 TGAATTCTGTTCTGAT
1922989 TTTTGATATC
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
23 18 0.34
24 35 0.66
ACGTcount: A:0.21, C:0.14, G:0.18, T:0.47
Consensus pattern (23 bp):
TGAATTCTGTTCTGATACTGACC
Found at i:1922969 original size:12 final size:11
Alignment explanation
Indices: 1922905--1922969 Score: 60
Period size: 12 Copynumber: 5.5 Consensus size: 11
1922895 TCCGAATTGA
1922905 ATTCTGTTCTG
1 ATTCTGTTCTG
*
1922916 ATAC-GTTACCTG
1 ATTCTGTT--CTG
1922928 AATTCTGTTCTG
1 -ATTCTGTTCTG
*
1922940 ATTCTGATCTGG
1 ATTCTGTTCT-G
1922952 ATTCTGTTCTG
1 ATTCTGTTCTG
1922963 ATATCTG
1 AT-TCTG
1922970 ATATGAATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
10 3 0.07
11 15 0.34
12 20 0.45
13 3 0.07
14 3 0.07
ACGTcount: A:0.17, C:0.18, G:0.18, T:0.46
Consensus pattern (11 bp):
ATTCTGTTCTG
Found at i:1925173 original size:114 final size:114
Alignment explanation
Indices: 1924973--1925193 Score: 361
Period size: 114 Copynumber: 1.9 Consensus size: 114
1924963 GATCATGCAG
* * *
1924973 TTCATCTTTCAATTCCAATGATTGGTTCTGAGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGAGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1925038 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
* * * * *
1925087 TTCATCTTTCAAATCTAATGATTGGTTTTGGGGTTTATACCAAACCAGATCATATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGAGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
1925152 ACACTTTCAGAAGATGCTATTGGGTCTCCTTATTTCTACTAT
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTAT
1925194 AAGAACGTGG
Statistics
Matches: 98, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 98 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTGAGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
Found at i:1932578 original size:3 final size:3
Alignment explanation
Indices: 1932570--1932601 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1932560 TTTATGGTTA
*
1932570 AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1932602 AAAGTAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1933929 original size:3 final size:3
Alignment explanation
Indices: 1933921--1933990 Score: 67
Period size: 3 Copynumber: 24.0 Consensus size: 3
1933911 CCGGTTTGTA
* *
1933921 AAT AAT AAT TAT -TT AAT AAT AAT -AT AAT -AT ATAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT
*
1933963 AAT AAT ATTT AAT AAT AAT AAT AAT AAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT
1933991 TTAAGTAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
2 7 0.12
3 44 0.79
4 5 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
AAT
Found at i:1933939 original size:11 final size:12
Alignment explanation
Indices: 1933922--1933990 Score: 63
Period size: 11 Copynumber: 5.7 Consensus size: 12
1933912 CGGTTTGTAA
1933922 ATAATAAT-TAT
1 ATAATAATATAT
*
1933933 TTAATAATA-AT
1 ATAATAATATAT
1933944 ATAATATATATAAT
1 ATAATA-ATAT-AT
1933958 ATAATAATAATAT
1 ATAATAAT-ATAT
*
1933971 TTAATAATA-AT
1 ATAATAATATAT
1933982 AATAATAAT
1 -ATAATAAT
1933991 TTAAGTAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
11 16 0.33
12 11 0.23
13 11 0.23
14 10 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
ATAATAATATAT
Found at i:1933962 original size:25 final size:22
Alignment explanation
Indices: 1933921--1933990 Score: 89
Period size: 22 Copynumber: 3.4 Consensus size: 22
1933911 CCGGTTTGTA
1933921 AATAATAATTATTTAATAATAAT
1 AATAATAA-TATTTAATAATAAT
1933944 -ATAAT-ATA--T-ATAAT-AT
1 AATAATAATATTTAATAATAAT
1933960 AATAATAATATTTAATAATAAT
1 AATAATAATATTTAATAATAAT
1933982 AATAATAAT
1 AATAATAAT
1933991 TTAAGTAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
16 2 0.05
17 10 0.24
18 4 0.10
20 3 0.07
21 6 0.15
22 16 0.39
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
AATAATAATATTTAATAATAAT
Found at i:1937883 original size:42 final size:41
Alignment explanation
Indices: 1937797--1937889 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 41
1937787 TGTCAAAATG
* * * * **
1937797 GTATTGATACTGAAAGAGAGTATTGGTACCATAGTGTAGTA
1 GTATTGATACTGAAAGAAAGTATCGATACCATAGTATAAAA
* *
1937838 GTATCGATACTGAGAGAAAGGTATCGATACCATAGTATAAAA
1 GTATTGATACTGAAAGAAA-GTATCGATACCATAGTATAAAA
1937880 GTATTGATAC
1 GTATTGATAC
1937890 CATGGTAGGG
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
41 16 0.38
42 26 0.62
ACGTcount: A:0.38, C:0.10, G:0.24, T:0.29
Consensus pattern (41 bp):
GTATTGATACTGAAAGAAAGTATCGATACCATAGTATAAAA
Found at i:1938339 original size:20 final size:20
Alignment explanation
Indices: 1938314--1938455 Score: 115
Period size: 20 Copynumber: 6.5 Consensus size: 20
1938304 TGAAATGCAT
1938314 GAAAGGATGCATTAAGGCAC
1 GAAAGGATGCATTAAGGCAC
1938334 GAAAGGATGCATTAAGGCAC
1 GAAAGGATGCATTAAGGCAC
* *
1938354 GAAAGGATGCCATAAATGAAATGCAT
1 GAAAGGATG-CAT---T--AAGGCAC
*
1938380 GAAAGGATGCATTAAGGCAT
1 GAAAGGATGCATTAAGGCAC
*
1938400 GAAAGGATGCCATAAATGAAATGCATC
1 GAAAGGATG-CAT---T--AAGGCA-C
*
1938427 -AAAGGATGCATTAAGGCAG
1 GAAAGGATGCATTAAGGCAC
1938446 GAAAGGATGC
1 GAAAGGATGC
1938456 CATAAATGAA
Statistics
Matches: 101, Mismatches: 7, Indels: 28
0.74 0.05 0.21
Matches are distributed among these distances:
20 58 0.57
21 6 0.06
22 2 0.02
24 2 0.02
25 6 0.06
26 27 0.27
ACGTcount: A:0.42, C:0.13, G:0.28, T:0.17
Consensus pattern (20 bp):
GAAAGGATGCATTAAGGCAC
Found at i:1938404 original size:46 final size:46
Alignment explanation
Indices: 1938334--1938467 Score: 241
Period size: 46 Copynumber: 2.9 Consensus size: 46
1938324 ATTAAGGCAC
1938334 GAAAGGATGCATTAAGGCACGAAAGGATGCCATAAATGAAATGCAT
1 GAAAGGATGCATTAAGGCACGAAAGGATGCCATAAATGAAATGCAT
*
1938380 GAAAGGATGCATTAAGGCATGAAAGGATGCCATAAATGAAATGCAT
1 GAAAGGATGCATTAAGGCACGAAAGGATGCCATAAATGAAATGCAT
* *
1938426 CAAAGGATGCATTAAGGCAGGAAAGGATGCCATAAATGAAAT
1 GAAAGGATGCATTAAGGCACGAAAGGATGCCATAAATGAAAT
1938468 TAACGAATAA
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 85 1.00
ACGTcount: A:0.44, C:0.12, G:0.26, T:0.18
Consensus pattern (46 bp):
GAAAGGATGCATTAAGGCACGAAAGGATGCCATAAATGAAATGCAT
Found at i:1938949 original size:81 final size:81
Alignment explanation
Indices: 1938814--1939063 Score: 349
Period size: 81 Copynumber: 3.1 Consensus size: 81
1938804 TGTTCTAAAA
* * ** *
1938814 TAAAAGATTAATGGCCTAGCTGTGCACTTGGTAGAAATTTGTCAATTATGCCAGTTAGATGGAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAAGTGTCAATTATGCCAGTTAGATGAAAG
1938879 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
*
1938895 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAAGTGTCAATTATGCCAGTTAGATGAAAG
1938960 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * *
1938976 TAAAAGATTAAGGGTCTAGCTGTGCATTTGCCAAAAAAGTGTCAATCATG-CAGGTTAGATGAAA
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAAGTGTCAATTATGCCA-GTTAGATGAAA
* * * *
1939040 GGTTGAATGCCTTCGGG
65 GGTTAAATACCTTTGAG
1939057 TAAAAGA
1 TAAAAGA
1939064 CTAAAGGAAT
Statistics
Matches: 153, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
80 2 0.01
81 151 0.99
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (81 bp):
TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAAGTGTCAATTATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAG
Found at i:1941039 original size:2 final size:2
Alignment explanation
Indices: 1941032--1941059 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1941022 TGTCAAAAAG
1941032 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
1941060 CTTTTATAGC
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:1943849 original size:46 final size:46
Alignment explanation
Indices: 1943797--1944006 Score: 296
Period size: 46 Copynumber: 4.6 Consensus size: 46
1943787 AGTATTTCAT
1943797 CCATAAATGAAATGCATGAAAGGATGCATTAAGGAATGAAAGGATG
1 CCATAAATGAAATGCATGAAAGGATGCATTAAGGAATGAAAGGATG
* * *
1943843 CCATAAATGAAATGCATGAAAGGTTGCATTAAGGCATGAAATGATG
1 CCATAAATGAAATGCATGAAAGGATGCATTAAGGAATGAAAGGATG
* * * *
1943889 CCATAAATGAAATGCACGAAAGGTTGCATTAAGGCATGAAAGGATT
1 CCATAAATGAAATGCATGAAAGGATGCATTAAGGAATGAAAGGATG
* * **
1943935 CCATAAATGAAACGCATGAAAGGATGCATT-ACGACATGAAATAATG
1 CCATAAATGAAATGCATGAAAGGATGCATTAAGGA-ATGAAAGGATG
*
1943981 TCATAAATGAAATGCATGAAAGGATG
1 CCATAAATGAAATGCATGAAAGGATG
1944007 ACATAAATGA
Statistics
Matches: 147, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
45 2 0.01
46 145 0.99
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.21
Consensus pattern (46 bp):
CCATAAATGAAATGCATGAAAGGATGCATTAAGGAATGAAAGGATG
Found at i:1943881 original size:20 final size:20
Alignment explanation
Indices: 1943810--1943933 Score: 77
Period size: 20 Copynumber: 5.6 Consensus size: 20
1943800 TAAATGAAAT
1943810 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
1943830 GAATGAAAGGATGCCATAAATGAAAT
1 GCATGAAAGGATG-CAT---T--AAG
*
1943856 GCATGAAAGGTTGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
1943876 GCATGAAATGATGCCATAAATGAAAT
1 GCATGAAAGGATG-CAT---T--AAG
* *
1943902 GCACGAAAGGTTGCATTAAG
1 GCATGAAAGGATGCATTAAG
1943922 GCATGAAAGGAT
1 GCATGAAAGGAT
1943934 TCCATAAATG
Statistics
Matches: 78, Mismatches: 14, Indels: 24
0.67 0.12 0.21
Matches are distributed among these distances:
20 37 0.47
21 6 0.08
22 2 0.03
24 2 0.03
25 6 0.08
26 25 0.32
ACGTcount: A:0.42, C:0.10, G:0.27, T:0.21
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:1943910 original size:92 final size:92
Alignment explanation
Indices: 1943797--1944006 Score: 330
Period size: 92 Copynumber: 2.3 Consensus size: 92
1943787 AGTATTTCAT
*
1943797 CCATAAATGAAATGCATGAAAGGATGCATTAAGGAATGAAAGGATGCCATAAATGAAATGCATGA
1 CCATAAATGAAATGCATGAAAGGATGCATTAAGGAATGAAAGGATGCCATAAATGAAACGCATGA
* * *
1943862 AAGGTTGCATTAAGGCATGAAATGATG
66 AAGGATGCATTAAGACATGAAATAATG
* * * *
1943889 CCATAAATGAAATGCACGAAAGGTTGCATTAAGGCATGAAAGGATTCCATAAATGAAACGCATGA
1 CCATAAATGAAATGCATGAAAGGATGCATTAAGGAATGAAAGGATGCCATAAATGAAACGCATGA
*
1943954 AAGGATGCATTACGACATGAAATAATG
66 AAGGATGCATTAAGACATGAAATAATG
*
1943981 TCATAAATGAAATGCATGAAAGGATG
1 CCATAAATGAAATGCATGAAAGGATG
1944007 ACATAAATGA
Statistics
Matches: 106, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
92 106 1.00
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.21
Consensus pattern (92 bp):
CCATAAATGAAATGCATGAAAGGATGCATTAAGGAATGAAAGGATGCCATAAATGAAACGCATGA
AAGGATGCATTAAGACATGAAATAATG
Found at i:1944000 original size:26 final size:26
Alignment explanation
Indices: 1943969--1944019 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
1943959 TGCATTACGA
* *
1943969 CATGAAATAATGTCATAAATGAAATG
1 CATGAAAGAATGACATAAATGAAATG
*
1943995 CATGAAAGGATGACATAAATGAAAT
1 CATGAAAGAATGACATAAATGAAAT
1944020 TAATGAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.51, C:0.08, G:0.18, T:0.24
Consensus pattern (26 bp):
CATGAAAGAATGACATAAATGAAATG
Found at i:1944611 original size:81 final size:81
Alignment explanation
Indices: 1944365--1944614 Score: 306
Period size: 81 Copynumber: 3.1 Consensus size: 81
1944355 TGTTCTAAAA
* * * * ** *
1944365 TAAAAGATTAATGGCCTAACTATGCATTTGGTAGAAATTTGTCAATTATGCCAGTTAGATGGAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAAAAAAATGTCAATTATGCCAGTTAGATGAAAG
*
1944430 GTTAAACACCTTTGAG
66 GTTAAATACCTTTGAG
* * * *
1944446 TAAAAGATTAATGGCCTAGTTGTGCATTTGGCATAAAGATGTCAATTATGTCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAAAAAAATGTCAATTATGCCAGTTAGATGAAAG
1944511 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* *
1944527 TAAAAGATTAA-GGTTCTAGCTGTGCATTTGGCAAAAAAATGTCAATCATG-CAGGTTAGATGAA
1 TAAAAGATTAATGG-CCTAGCTGTGCATTTGGCAAAAAAATGTCAATTATGCCA-GTTAGATGAA
* * * *
1944590 AGGTTGAATGCCTTCGGG
64 AGGTTAAATACCTTTGAG
1944608 TAAAAGA
1 TAAAAGA
1944615 CTAAAGGAAT
Statistics
Matches: 148, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
80 4 0.03
81 144 0.97
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.31
Consensus pattern (81 bp):
TAAAAGATTAATGGCCTAGCTGTGCATTTGGCAAAAAAATGTCAATTATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAG
Done.