Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007845.1 Hibiscus syriacus cultivar Beakdansim tig00110201_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: 2731752
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 8 of 13
Found at i:1550860 original size:78 final size:78
Alignment explanation
Indices: 1550776--1550927 Score: 225
Period size: 78 Copynumber: 1.9 Consensus size: 78
1550766 GATGTGAGCT
* * * *
1550776 TTCAAAATGCCCCAAATTTTAATACTGATGTGAGCTTTCAAAATGCCCCACATGAATCATTTCTA
1 TTCAAAATACCCCAAACTTTAATACTAATGTGAGCTTTCAAAACGCCCCACATGAATCATTTCTA
1550841 -TCTGAAATGGGTC
66 GT-TGAAATGGGTC
* * *
1550854 TTCAAAATACCCCAAACTTTCATACTAATGTGAGCTTTCAAAACGCCTCACATGGATCATTTCTA
1 TTCAAAATACCCCAAACTTTAATACTAATGTGAGCTTTCAAAACGCCCCACATGAATCATTTCTA
1550919 GTTGAAATG
66 GTTGAAATG
1550928 TACTTTCAAC
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
78 65 0.98
79 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32
Consensus pattern (78 bp):
TTCAAAATACCCCAAACTTTAATACTAATGTGAGCTTTCAAAACGCCCCACATGAATCATTTCTA
GTTGAAATGGGTC
Found at i:1552409 original size:2 final size:2
Alignment explanation
Indices: 1552402--1552427 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1552392 ATAACAAAGA
1552402 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
1552428 TTGAAAGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1556875 original size:23 final size:23
Alignment explanation
Indices: 1556845--1556904 Score: 120
Period size: 23 Copynumber: 2.6 Consensus size: 23
1556835 GCTTTTAACA
1556845 TTGTCGCTTACTCAGATCCAGGT
1 TTGTCGCTTACTCAGATCCAGGT
1556868 TTGTCGCTTACTCAGATCCAGGT
1 TTGTCGCTTACTCAGATCCAGGT
1556891 TTGTCGCTTACTCA
1 TTGTCGCTTACTCA
1556905 TATTTCTCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.17, C:0.27, G:0.20, T:0.37
Consensus pattern (23 bp):
TTGTCGCTTACTCAGATCCAGGT
Found at i:1561417 original size:26 final size:25
Alignment explanation
Indices: 1561377--1561434 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
1561367 AACTGAAATT
1561377 AAAT-AAATAAAAAGTAAATGACATA
1 AAATAAAATAAAAAGTAAATGAC-TA
* *
1561402 AATTAAAATATAAAGTAAATGACTA
1 AAATAAAATAAAAAGTAAATGACTA
1561427 AAATAAAA
1 AAATAAAA
1561435 AATTAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 12 0.41
26 17 0.59
ACGTcount: A:0.67, C:0.03, G:0.07, T:0.22
Consensus pattern (25 bp):
AAATAAAATAAAAAGTAAATGACTA
Found at i:1561428 original size:20 final size:20
Alignment explanation
Indices: 1561405--1561468 Score: 56
Period size: 20 Copynumber: 3.6 Consensus size: 20
1561395 TGACATAAAT
1561405 TAAAATATAAAGTAAATGAC
1 TAAAATATAAAGTAAATGAC
1561425 T-AAA-ATAAA--AAAT---
1 TAAAATATAAAGTAAATGAC
1561438 TAAAATATAAAGTAAA-GAAC
1 TAAAATATAAAGTAAATG-AC
1561458 TAAAATA-AAAG
1 TAAAATATAAAG
1561469 ATATCATAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 17
0.68 0.00 0.32
Matches are distributed among these distances:
13 1 0.03
14 3 0.08
15 5 0.14
16 4 0.11
17 3 0.08
18 5 0.14
19 7 0.19
20 8 0.22
ACGTcount: A:0.67, C:0.03, G:0.08, T:0.22
Consensus pattern (20 bp):
TAAAATATAAAGTAAATGAC
Found at i:1561441 original size:26 final size:26
Alignment explanation
Indices: 1561377--1561437 Score: 81
Period size: 25 Copynumber: 2.4 Consensus size: 26
1561367 AACTGAAATT
*
1561377 AAATAAATAA-AAAGTAAATGACATA
1 AAATAAAAAATAAAGTAAATGACATA
* *
1561402 AATTAAAATATAAAGTAAATGAC-TA
1 AAATAAAAAATAAAGTAAATGACATA
1561427 AAATAAAAAAT
1 AAATAAAAAAT
1561438 TAAAATATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 18 0.60
26 12 0.40
ACGTcount: A:0.67, C:0.03, G:0.07, T:0.23
Consensus pattern (26 bp):
AAATAAAAAATAAAGTAAATGACATA
Found at i:1561441 original size:33 final size:33
Alignment explanation
Indices: 1561401--1561467 Score: 118
Period size: 33 Copynumber: 2.0 Consensus size: 33
1561391 TAAATGACAT
1561401 AAATTAAAATATAAAGTAAATG-ACTAAAATAAA
1 AAATTAAAATATAAAGTAAA-GAACTAAAATAAA
1561434 AAATTAAAATATAAAGTAAAGAACTAAAATAAA
1 AAATTAAAATATAAAGTAAAGAACTAAAATAAA
1561467 A
1 A
1561468 GATATCATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 1 0.03
33 32 0.97
ACGTcount: A:0.69, C:0.03, G:0.06, T:0.22
Consensus pattern (33 bp):
AAATTAAAATATAAAGTAAAGAACTAAAATAAA
Found at i:1562967 original size:73 final size:72
Alignment explanation
Indices: 1562847--1563020 Score: 267
Period size: 73 Copynumber: 2.4 Consensus size: 72
1562837 CTTCTGGAAA
* * ** *
1562847 TGTTTTAGGAAAAACAATCTCAAGTGAGATAATTTGTTATTTTGAGTGAAACTTTCTCAAGCGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTACTATTTCGAGTGAAACTTTCTCAAGCGAG
*
1562912 AAACAGTT
66 -AACAATT
1562920 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTACTATTTCGAGTGAAACTTTCTCAAGCGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTACTATTTCGAGTGAAACTTTCTCAAGCGAG
1562985 AACAATT
66 AACAATT
* *
1562992 TATTTTAAGAAAAACAATCTCAAGCGAGA
1 TGTTTTAAGAAAAACAATCTCAAGTGAGA
1563021 ACATTTTGTT
Statistics
Matches: 93, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
72 33 0.35
73 60 0.65
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.31
Consensus pattern (72 bp):
TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTACTATTTCGAGTGAAACTTTCTCAAGCGAG
AACAATT
Found at i:1563013 original size:35 final size:35
Alignment explanation
Indices: 1562901--1563036 Score: 130
Period size: 35 Copynumber: 3.8 Consensus size: 35
1562891 AGTGAAACTT
* *
1562901 TCTCAAGCGAGAAACAGTTTGTTTTAAGAAAAACAA
1 TCTCAAGCGAG-AACAATTTATTTTAAGAAAAACAA
* ** ** **
1562937 TCTCAAGTGAGATA-AATTACTATTTCGAGTGAAACTT
1 TCTCAAGCGAGA-ACAATT--TATTTTAAGAAAAACAA
1562974 TCTCAAGCGAGAACAATTTATTTTAAGAAAAACAA
1 TCTCAAGCGAGAACAATTTATTTTAAGAAAAACAA
* *
1563009 TCTCAAGCGAGAACATTTTGTTTTAAGA
1 TCTCAAGCGAGAACAATTTATTTTAAGA
1563037 GAGTCAATTC
Statistics
Matches: 78, Mismatches: 18, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
35 41 0.53
36 12 0.15
37 25 0.32
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.30
Consensus pattern (35 bp):
TCTCAAGCGAGAACAATTTATTTTAAGAAAAACAA
Found at i:1564801 original size:2 final size:2
Alignment explanation
Indices: 1564794--1564842 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
1564784 AGTAGATCTG
1564794 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1564836 AT TT AT A
1 AT AT AT A
1564843 ATTGGTTATA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1566688 original size:27 final size:27
Alignment explanation
Indices: 1566650--1566702 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
1566640 TTGCATACGG
1566650 ATATTTATAGAAGAATGGAGAGTCGCC
1 ATATTTATAGAAGAATGGAGAGTCGCC
1566677 ATATTTATAGAAGAATGGAGAGTCGC
1 ATATTTATAGAAGAATGGAGAGTCGC
1566703 AATAATCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.38, C:0.09, G:0.26, T:0.26
Consensus pattern (27 bp):
ATATTTATAGAAGAATGGAGAGTCGCC
Found at i:1573766 original size:2 final size:2
Alignment explanation
Indices: 1573759--1573786 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1573749 GAATACCATC
1573759 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
1573787 GTCATATTTT
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:1579015 original size:147 final size:143
Alignment explanation
Indices: 1578706--1578997 Score: 426
Period size: 147 Copynumber: 2.0 Consensus size: 143
1578696 AAATACCCTA
*
1578706 AACCATCTTTCTTTCTTTTTCTTTAATGTAAAGCAAAGGGGGTGAATGAGAGCAAAAAAGAAAAA
1 AACCATCTATCTTTCTTTTTCTTTAATGTAAAGCAAAGGGGGTGAATGAGAGCAAAAAAGAAAAA
1578771 AAAAAGAGGGGGTTTAATGAAATATGGAAGATAAATGGGGACATTTTTAAATGTTTGGTATGATT
66 AAAAAGAGGGGGTTTAATGAAATATGGAAGATAAATGGGGACATTTTTAAATGTTTGGTATGA--
* * *
1578836 TATTTTTAAATACCCT
129 TA-TTTAAAAGAACCT
*
1578852 AAACCATCTTTCTTTCTTTTTCTTTAATGTAAAGCAAAGGGGGTGAATGAGAGCAAAAAAGAAAA
1 -AACCATCTATCTTTCTTTTTCTTTAATGTAAAGCAAAGGGGGTGAATGAGAGCAAAAAAG-AAA
1578917 GAAAAAAAGAGGGGGGTTTAATGAAATTATGGAAGAGATAAATGGGGACATTTTTAAATGTATTG
64 -AAAAAAAGA-GGGGGTTTAATGAAA-TATGG-A-AGATAAATGGGGACATTTTTAAATGT-TTG
1578982 GTATGA-A-TTAAAAGAA
123 GTATGATATTTAAAAGAA
1578998 GCTTCTTTTC
Statistics
Matches: 135, Mismatches: 3, Indels: 12
0.90 0.02 0.08
Matches are distributed among these distances:
147 60 0.44
148 3 0.02
149 15 0.11
150 15 0.11
151 6 0.04
152 1 0.01
153 26 0.19
154 9 0.07
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.30
Consensus pattern (143 bp):
AACCATCTATCTTTCTTTTTCTTTAATGTAAAGCAAAGGGGGTGAATGAGAGCAAAAAAGAAAAA
AAAAAGAGGGGGTTTAATGAAATATGGAAGATAAATGGGGACATTTTTAAATGTTTGGTATGATA
TTTAAAAGAACCT
Found at i:1583420 original size:23 final size:23
Alignment explanation
Indices: 1583389--1583435 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1583379 ATTTGTATAC
*
1583389 TCACGAACATGTTCGTTTAGCGT
1 TCACAAACATGTTCGTTTAGCGT
1583412 TCACAAACATGTTCGTTTAGCGT
1 TCACAAACATGTTCGTTTAGCGT
1583435 T
1 T
1583436 TGTTTATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.36
Consensus pattern (23 bp):
TCACAAACATGTTCGTTTAGCGT
Found at i:1585179 original size:15 final size:14
Alignment explanation
Indices: 1585150--1585188 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
1585140 GTACTATTAT
*
1585150 TTTCTTTTACATTTA
1 TTTCTTTTTC-TTTA
1585165 TTTCTATTTTCTTTA
1 TTTCT-TTTTCTTTA
1585180 TTTCTTTTT
1 TTTCTTTTT
1585189 TAATTCATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 4 0.18
15 14 0.64
16 4 0.18
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTCTTTTTCTTTA
Found at i:1586303 original size:28 final size:29
Alignment explanation
Indices: 1586271--1586339 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 29
1586261 TGTTTCCTAA
*
1586271 CCATTTGTTTTTTCTTATGTTT-TTATTG
1 CCATTTATTTTTTCTTATGTTTATTATTG
* * * *
1586299 CCATTTATTTCTTGTTATTTTTATTATTT
1 CCATTTATTTTTTCTTATGTTTATTATTG
1586328 CCATTTATTTTT
1 CCATTTATTTTT
1586340 ATTTTACTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 18 0.53
29 16 0.47
ACGTcount: A:0.14, C:0.12, G:0.06, T:0.68
Consensus pattern (29 bp):
CCATTTATTTTTTCTTATGTTTATTATTG
Found at i:1596082 original size:1 final size:1
Alignment explanation
Indices: 1596076--1596101 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
1596066 AAGCATCTCT
1596076 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
1596102 CCCAGAATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1596992 original size:105 final size:105
Alignment explanation
Indices: 1596315--1596984 Score: 1277
Period size: 105 Copynumber: 6.4 Consensus size: 105
1596305 AGGTTTTACC
*
1596315 CAGAGCCAATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1596380 ACGAAGGGACCGCTGCTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGCTTGTCAACAAACATTTCTCAATTT
1596420 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1596485 ACGAAGGGACCGCTGCTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGCTTGTCAACAAACATTTCTCAATTT
*
1596525 CAGAGCCAATTTCAACTTCACAAAGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1596590 ACGAAGGGACCGCTGCTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGCTTGTCAACAAACATTTCTCAATTT
*
1596630 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1596695 ACGAAGGGACCGCTGCTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGCTTGTCAACAAACATTTCTCAATTT
1596735 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1596800 ACGAAGGGACCGCTGCTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGCTTGTCAACAAACATTTCTCAATTT
*
1596840 CTGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
1596905 ACGAAGAGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGCTTGTCAACAAACATTTCTCAATTT
*
1596945 CAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1596985 GAAACAACAC
Statistics
Matches: 555, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 555 1.00
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGCTTGTCAACAAACATTTCTCAATTT
Found at i:1607797 original size:32 final size:32
Alignment explanation
Indices: 1607724--1608038 Score: 458
Period size: 32 Copynumber: 9.9 Consensus size: 32
1607714 GAATGACCTA
* *
1607724 TCCATATGTTCC-TAAGAACATAGGTAAT--TG
1 TCCATATGTCCCGAAAG-ACATAGGTAATCATG
*
1607754 TCCATATGTCCCGAAAGACATAGGTAATCTTG
1 TCCATATGTCCCGAAAGACATAGGTAATCATG
* *
1607786 TTCATATGTCCCGAAAGACATAGGAAATCATG
1 TCCATATGTCCCGAAAGACATAGGTAATCATG
*
1607818 TCCATATGTCCCGAAAGACATAGGTAATCCTG
1 TCCATATGTCCCGAAAGACATAGGTAATCATG
1607850 TCCATATGTCCCGAAAGACATAGGTAATCATG
1 TCCATATGTCCCGAAAGACATAGGTAATCATG
*
1607882 TCCATATGTCCCGAAAGACATAGGTAATCTTG
1 TCCATATGTCCCGAAAGACATAGGTAATCATG
1607914 TCCATATGTCCCGAAAGACATAGGTAATCATG
1 TCCATATGTCCCGAAAGACATAGGTAATCATG
* * * *
1607946 TTCATATGTCCCAAAAGACATAGGTAATCCTA
1 TCCATATGTCCCGAAAGACATAGGTAATCATG
* *
1607978 TGCATATGTCCCGAAATACATAGGTAAT-ACTG
1 TCCATATGTCCCGAAAGACATAGGTAATCA-TG
*
1608010 TCCATATGTCCCGAAAGACATAAGTAATC
1 TCCATATGTCCCGAAAGACATAGGTAATC
1608039 CTCGACTCTT
Statistics
Matches: 257, Mismatches: 23, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
30 22 0.09
31 3 0.01
32 232 0.90
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.27
Consensus pattern (32 bp):
TCCATATGTCCCGAAAGACATAGGTAATCATG
Found at i:1612932 original size:129 final size:128
Alignment explanation
Indices: 1612753--1613053 Score: 338
Period size: 129 Copynumber: 2.3 Consensus size: 128
1612743 CTAATTAGTA
* *
1612753 ATTAATTATTTAAAATTACAGTGGCTAAACATGTTATTTTACCCATTTATTAATTTA-GTGACTA
1 ATTAATTA-TTAAAATTAAAG-GACTAAACATGTTATTTTA-CCATTTATTAATTTATG-GACTA
* * * *
1612817 AAATAAA-AT-TATATCAAATTTGTACATAAAATTAAAAGAAATTAAAACATGCTATTCGGGGTT
62 AAATAAATATCTATA--AAATTCGAACATAAAATTAAAAGAAATTAAAACATGC-ATTCAGGATT
*
1612880 TAAAT
124 AAAAT
* * ** *
1612885 ATTAATTATTAAAATTAGAGGACTAAATATGTTATTTTACTTTTTATTCATTTATGGACTAAAAT
1 ATTAATTATTAAAATTAAAGGACTAAACATGTTATTTTACCATTTATTAATTTATGGACTAAAAT
* * * * * *
1612950 AAATATCTATAAAATTCGAATATCAAATTTAAATAAATTAAAACATGCCTTCATGATTAAAAT
66 AAATATCTATAAAATTCGAACATAAAATTAAAAGAAATTAAAACATGCATTCAGGATTAAAAT
* *
1613013 ATTAATTATTAAACTTAAAGGTCTAAACATGTTATTTTACC
1 ATTAATTATTAAAATTAAAGGACTAAACATGTTATTTTACC
1613054 TAAAATATAT
Statistics
Matches: 144, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
128 46 0.32
129 55 0.38
130 20 0.14
131 15 0.10
132 8 0.06
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.39
Consensus pattern (128 bp):
ATTAATTATTAAAATTAAAGGACTAAACATGTTATTTTACCATTTATTAATTTATGGACTAAAAT
AAATATCTATAAAATTCGAACATAAAATTAAAAGAAATTAAAACATGCATTCAGGATTAAAAT
Found at i:1614101 original size:13 final size:13
Alignment explanation
Indices: 1614083--1614118 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1614073 TTTGGGCCTG
1614083 TAATATATAATAA
1 TAATATATAATAA
*
1614096 TAATATTTAATAA
1 TAATATATAATAA
1614109 TAATA-ATAAT
1 TAATATATAAT
1614119 TATTATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 4 0.19
13 17 0.81
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
TAATATATAATAA
Found at i:1615304 original size:13 final size:13
Alignment explanation
Indices: 1615286--1615311 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1615276 ATTTAGCCTG
1615286 CCATTCTAGAATT
1 CCATTCTAGAATT
1615299 CCATTCTAGAATT
1 CCATTCTAGAATT
1615312 TTGACTGACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (13 bp):
CCATTCTAGAATT
Found at i:1628020 original size:6 final size:6
Alignment explanation
Indices: 1628011--1628050 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
1628001 CATTGAGAAT
1628011 GAAAGC GAAAGC GAAAGC GAAAGC GAAAGC GAAAGC GAAA
1 GAAAGC GAAAGC GAAAGC GAAAGC GAAAGC GAAAGC GAAA
1628051 CCATCTAACG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.53, C:0.15, G:0.33, T:0.00
Consensus pattern (6 bp):
GAAAGC
Found at i:1639070 original size:39 final size:39
Alignment explanation
Indices: 1639027--1639103 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
1639017 TTTCCTTTTC
* *
1639027 CTTTATTGTTTGTGTATGTATATTTTTATGTATGTATTG
1 CTTTATTGTTTGTGTATGTATATTTTTATATATATATTG
1639066 CTTTATTGTTTGTGTATGTATATTTTTATATATATATT
1 CTTTATTGTTTGTGTATGTATATTTTTATATATATATT
1639104 AATATTAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.21, C:0.03, G:0.14, T:0.62
Consensus pattern (39 bp):
CTTTATTGTTTGTGTATGTATATTTTTATATATATATTG
Found at i:1650579 original size:36 final size:34
Alignment explanation
Indices: 1650522--1650591 Score: 88
Period size: 36 Copynumber: 2.0 Consensus size: 34
1650512 TTATATTTAA
*
1650522 AAGATAATTTAATTCATTAAAT-TTTAAAAGTTAT
1 AAGATAATTTAATTCAATAAATATTTAAAA-TTAT
*
1650556 AAGATAATAATTAATTTAATAAATATTTAAAATTAT
1 AAGATAAT--TTAATTCAATAAATATTTAAAATTAT
1650592 TTATTAAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
34 8 0.26
36 16 0.52
37 7 0.23
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.43
Consensus pattern (34 bp):
AAGATAATTTAATTCAATAAATATTTAAAATTAT
Found at i:1651350 original size:38 final size:38
Alignment explanation
Indices: 1651260--1651350 Score: 173
Period size: 38 Copynumber: 2.4 Consensus size: 38
1651250 CGGTGTAATA
*
1651260 AAAATAAAATGCCTCTGTCACAACCAAGATAAATAAAT
1 AAAATAAAATGCCTTTGTCACAACCAAGATAAATAAAT
1651298 AAAATAAAATGCCTTTGTCACAACCAAGATAAATAAAT
1 AAAATAAAATGCCTTTGTCACAACCAAGATAAATAAAT
1651336 AAAATAAAATGCCTT
1 AAAATAAAATGCCTT
1651351 GTTTTTCTTA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.53, C:0.16, G:0.08, T:0.23
Consensus pattern (38 bp):
AAAATAAAATGCCTTTGTCACAACCAAGATAAATAAAT
Found at i:1658674 original size:29 final size:29
Alignment explanation
Indices: 1658641--1658730 Score: 162
Period size: 29 Copynumber: 3.1 Consensus size: 29
1658631 TCTACAGTGG
1658641 CCTTGGAGGTCGCCATGGCATCCGGGCGA
1 CCTTGGAGGTCGCCATGGCATCCGGGCGA
*
1658670 CCTTGGAGGTCGCCATGGCATCCAGGCGA
1 CCTTGGAGGTCGCCATGGCATCCGGGCGA
*
1658699 CCTTAGAGGTCGCCATGGCATCCGGGCGA
1 CCTTGGAGGTCGCCATGGCATCCGGGCGA
1658728 CCT
1 CCT
1658731 GTGTGTATTT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 58 1.00
ACGTcount: A:0.16, C:0.32, G:0.34, T:0.18
Consensus pattern (29 bp):
CCTTGGAGGTCGCCATGGCATCCGGGCGA
Found at i:1659349 original size:21 final size:21
Alignment explanation
Indices: 1659324--1659367 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1659314 AATCTAGTTA
1659324 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
1659345 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
1659366 AT
1 AT
1659368 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:1659377 original size:28 final size:30
Alignment explanation
Indices: 1659344--1659406 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
1659334 TAGTATAAAT
*
1659344 TATTAGTTTGTTAGTTTAAG-T-TATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
1659372 TATTAGTTTATTAGTTTAAGTTATATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
1659402 TATTA
1 TATTA
1659407 TATAAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 19 0.59
29 1 0.03
30 12 0.38
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (30 bp):
TATTAGTTTATTAGTTTAAGTTATATATTA
Found at i:1659954 original size:20 final size:21
Alignment explanation
Indices: 1659910--1659954 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1659900 AAATATTGTG
**
1659910 TTTAAAAATATTTAGTGTTGT
1 TTTAAAAATATTTAGTGTTAA
*
1659931 TTTAAAAATATTTTGT-TTAA
1 TTTAAAAATATTTAGTGTTAA
1659951 TTTA
1 TTTA
1659955 CATTGTATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (21 bp):
TTTAAAAATATTTAGTGTTAA
Found at i:1660244 original size:26 final size:25
Alignment explanation
Indices: 1660215--1660273 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
1660205 AAATCATATT
*
1660215 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AGTAAATATCAAATC
*
1660241 ATTAGATT-AATAGTAATTATCAAATC
1 ATT--ATTAAATAGTAAATATCAAATC
1660267 ATTATTA
1 ATTATTA
1660274 GGTTTATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 19 0.68
27 3 0.11
28 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTATTAAATAGTAAATATCAAATC
Found at i:1663187 original size:26 final size:26
Alignment explanation
Indices: 1663158--1663500 Score: 312
Period size: 26 Copynumber: 13.7 Consensus size: 26
1663148 TTTGATGATT
1663158 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
1663184 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
*
1663210 TAATAATGATTT-AGTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
** *
1663236 TAAAAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * * *
1663258 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
1663282 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
1663308 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
*
1663334 TAATAATGATTT-AGTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
* *
1663360 TA-AAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * * *
1663381 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
1663405 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
1663431 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
*
1663457 TAATAATGATTT-AGTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
** *
1663483 TAAAAATGATTTAATAAT
1 TAGTAATGATTTGATAAT
1663501 GATTTAAATA
Statistics
Matches: 275, Mismatches: 20, Indels: 44
0.81 0.06 0.13
Matches are distributed among these distances:
19 2 0.01
20 10 0.04
21 2 0.01
22 14 0.05
23 12 0.04
24 20 0.07
25 22 0.08
26 180 0.65
27 13 0.05
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (26 bp):
TAGTAATGATTTGATAATAATCATTA
Found at i:1663323 original size:124 final size:124
Alignment explanation
Indices: 1663103--1663611 Score: 853
Period size: 124 Copynumber: 4.2 Consensus size: 124
1663093 ATGTATTTAT
1663103 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1663168 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
1663227 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1663292 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
1663351 TAATCATTAT-AAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1663415 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
1663474 TAATCATTATAAAAATGATTTAATAATGA-TT---TA---AAT-ATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
* * * * * *
1663531 TTGATAATAATCATTATAATAATGATTTTATAATAATTATT-TAGTTATTATTTAGTAA
66 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
* * *
1663589 TTAT--TTATAATAATCATTTAATA
1 TAATCATTATAAAAATGATTTAATA
1663612 CTAATGATTT
Statistics
Matches: 375, Mismatches: 9, Indels: 13
0.94 0.02 0.03
Matches are distributed among these distances:
113 17 0.05
115 17 0.05
116 59 0.16
117 3 0.01
120 2 0.01
123 125 0.33
124 152 0.41
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (124 bp):
TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
Found at i:1663428 original size:97 final size:106
Alignment explanation
Indices: 1663308--1663567 Score: 317
Period size: 97 Copynumber: 2.4 Consensus size: 106
1663298 ATAATCATTA
1663308 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAA-AATGA-TT-
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAATAATGATTTA
*
1663370 TAATAATGATT-T-AAAT-A-TT-TAATG-ATTTGATGATT
66 TAATAATCATTATAAAATGATTTATAATGAATTTGATGATT
*
1663405 TAGTAATGATTTGATAATAATCATTATAGTAATGATTT-GATAATAATCATTATAATAATGATTT
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAG-TAATAATCATTATAATAATGATTT
1663469 AGTAATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTGATGATT
65 A-TAATAATCATTAT-AAAATGATTT-ATAATG------A-ATTTGATGATT
1663521 TAGTAATGATTTGATAATAATCATTATAATAATGATTTTA-TAATAAT
1 TAGTAATGATTTGATAATAATCATTATAATAATGA-TTTAGTAATAAT
1663568 TATTTAGTTA
Statistics
Matches: 138, Mismatches: 3, Indels: 25
0.83 0.02 0.15
Matches are distributed among these distances:
96 1 0.01
97 52 0.38
98 5 0.04
99 2 0.01
101 10 0.07
102 1 0.01
104 4 0.03
105 1 0.01
106 2 0.01
108 5 0.04
116 52 0.38
117 3 0.02
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (106 bp):
TAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAATAATGATTTA
TAATAATCATTATAAAATGATTTATAATGAATTTGATGATT
Found at i:1663580 original size:11 final size:11
Alignment explanation
Indices: 1663564--1663599 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
1663554 GATTTTATAA
1663564 TAATTATTTAG
1 TAATTATTTAG
*
1663575 TTATTATTTAG
1 TAATTATTTAG
1663586 TAATTATTTA-
1 TAATTATTTAG
1663596 TAAT
1 TAAT
1663600 AATCATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 4 0.17
11 19 0.83
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (11 bp):
TAATTATTTAG
Found at i:1663596 original size:35 final size:37
Alignment explanation
Indices: 1663557--1663643 Score: 99
Period size: 38 Copynumber: 2.4 Consensus size: 37
1663547 TAATAATGAT
* * *
1663557 TTTATAATAATTATTTAGT-T-ATTATTTAGTAATTA
1 TTTATAATAATTATTTAATATAATGATTTAATAATTA
*
1663592 TTTATAATAATCATTTAATACTAATGATTTAATAATTA
1 TTTATAATAATTATTTAATA-TAATGATTTAATAATTA
1663630 -TTACTAATAATTAT
1 TTTA-TAATAATTAT
1663644 AGAATACTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
35 17 0.40
37 4 0.09
38 22 0.51
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.52
Consensus pattern (37 bp):
TTTATAATAATTATTTAATATAATGATTTAATAATTA
Found at i:1663610 original size:11 final size:12
Alignment explanation
Indices: 1663171--1663643 Score: 92
Period size: 12 Copynumber: 37.9 Consensus size: 12
1663161 TAATGATTTG
*
1663171 ATAATAATCATT
1 ATAATAATTATT
* *
1663183 ATAGTAATGATTT
1 ATAATAATTA-TT
*
1663196 GATAATAATCATT
1 -ATAATAATTATT
*
1663209 ATAATAATGATTT
1 ATAATAATTA-TT
*
1663222 AGTAATAATCATT
1 A-TAATAATTATT
* *
1663235 ATAAAAATGATT
1 ATAATAATTATT
*
1663247 -TAATAATGATT
1 ATAATAATTATT
* *
1663258 -TAAATATTTAATG
1 AT-AATAATT-ATT
* * *
1663271 AT-TTGATGATTT
1 ATAATAATTA-TT
* *
1663283 AGTAATGATT-TG
1 A-TAATAATTATT
*
1663295 ATAATAATCATT
1 ATAATAATTATT
* *
1663307 ATAGTAATGATTT
1 ATAATAATTA-TT
*
1663320 GATAATAATCATT
1 -ATAATAATTATT
*
1663333 ATAATAATGATTT
1 ATAATAATTA-TT
*
1663346 AGTAATAATCATT
1 A-TAATAATTATT
*
1663359 ATAA-AATGATT
1 ATAATAATTATT
*
1663370 -TAATAATGATT
1 ATAATAATTATT
* *
1663381 -TAAATATTTAATG
1 AT-AATAATT-ATT
* * *
1663394 AT-TTGATGATTT
1 ATAATAATTA-TT
* *
1663406 AGTAATGATT-TG
1 A-TAATAATTATT
*
1663418 ATAATAATCATT
1 ATAATAATTATT
* *
1663430 ATAGTAATGATTT
1 ATAATAATTA-TT
*
1663443 GATAATAATCATT
1 -ATAATAATTATT
*
1663456 ATAATAATGATTT
1 ATAATAATTA-TT
*
1663469 AGTAATAATCATT
1 A-TAATAATTATT
* *
1663482 ATAAAAATGATT
1 ATAATAATTATT
*
1663494 -TAATAATGATT
1 ATAATAATTATT
*
1663505 -TAAATATTTGATGAT
1 AT-AATAATT-AT--T
* * *
1663520 TTAGTAATGATTT
1 ATAATAATTA-TT
*
1663533 GATAATAATCATT
1 -ATAATAATTATT
*
1663546 ATAATAATGATTTT
1 ATAATAAT--TATT
1663560 ATAATAATTATT
1 ATAATAATTATT
* *
1663572 -TAGTTATTATT
1 ATAATAATTATT
*
1663583 -TAGTAATTATTT
1 ATAATAATTA-TT
*
1663595 ATAATAATCATTT
1 ATAATAATTA-TT
* *
1663608 AATACTAATGATT
1 -ATAATAATTATT
1663621 -TAATAATTATT
1 ATAATAATTATT
1663632 ACTAATAATTAT
1 A-TAATAATTAT
1663644 AGAATACTAA
Statistics
Matches: 347, Mismatches: 73, Indels: 81
0.69 0.15 0.16
Matches are distributed among these distances:
10 3 0.01
11 76 0.22
12 114 0.33
13 63 0.18
14 84 0.24
15 6 0.02
16 1 0.00
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.45
Consensus pattern (12 bp):
ATAATAATTATT
Found at i:1663621 original size:14 final size:14
Alignment explanation
Indices: 1663524--1663627 Score: 55
Period size: 14 Copynumber: 8.1 Consensus size: 14
1663514 GATGATTTAG
* *
1663524 TAATGATTTGATAA
1 TAATCATTTAATAA
1663538 TAATCA-TT-ATAA
1 TAATCATTTAATAA
* *
1663550 TAATGATTTTATAA
1 TAATCATTTAATAA
* *
1663564 TAATTATTTAGT--
1 TAATCATTTAATAA
* *
1663576 T-ATTATTTAGTAA
1 TAATCATTTAATAA
1663589 T--T-ATTT-ATAA
1 TAATCATTTAATAA
*
1663599 TAATCATTTAATAC
1 TAATCATTTAATAA
*
1663613 TAATGATTTAATAA
1 TAATCATTTAATAA
1663627 T
1 T
1663628 TATTACTAAT
Statistics
Matches: 73, Mismatches: 9, Indels: 16
0.74 0.09 0.16
Matches are distributed among these distances:
10 4 0.05
11 14 0.19
12 12 0.16
13 9 0.12
14 34 0.47
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (14 bp):
TAATCATTTAATAA
Found at i:1663650 original size:38 final size:38
Alignment explanation
Indices: 1663580--1663653 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
1663570 TTTAGTTATT
* **
1663580 ATTTAGTAATTATTTATAATAATCATTTAATACTAATG
1 ATTTAATAATTATTTATAATAATCATAGAATACTAATG
*
1663618 ATTTAATAATTA-TTACTAATAATTATAGAATACTAA
1 ATTTAATAATTATTTA-TAATAATCATAGAATACTAA
1663654 CAAATGAGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 3 0.10
38 28 0.90
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (38 bp):
ATTTAATAATTATTTATAATAATCATAGAATACTAATG
Found at i:1663860 original size:17 final size:17
Alignment explanation
Indices: 1663835--1663867 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1663825 ACTAAATATT
*
1663835 TAATTATTTGATACTAG
1 TAATGATTTGATACTAG
1663852 TAATGATTTGATACTA
1 TAATGATTTGATACTA
1663868 AAAATCATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (17 bp):
TAATGATTTGATACTAG
Found at i:1663860 original size:25 final size:23
Alignment explanation
Indices: 1663781--1663860 Score: 67
Period size: 24 Copynumber: 3.3 Consensus size: 23
1663771 GATTTATTGT
1663781 TAATATTTAATTATTTGATAC--
1 TAATATTTAATTATTTGATACTA
* *
1663802 TAATGATTTAAAATAGTTGATTTACTA
1 TAAT-ATTT-AATTATTTGA--TACTA
1663829 -AATATTTAATTATTTGATACTA
1 TAATATTTAATTATTTGATACTA
1663851 GTAATGATTT
1 -TAAT-ATTT
1663861 GATACTAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
21 4 0.09
22 9 0.20
23 8 0.17
24 11 0.24
25 11 0.24
26 3 0.07
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.49
Consensus pattern (23 bp):
TAATATTTAATTATTTGATACTA
Found at i:1666039 original size:15 final size:14
Alignment explanation
Indices: 1666016--1666046 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
1666006 TACAACACTA
1666016 AACTTTAATATAAT
1 AACTTTAATATAAT
1666030 AACTTATAATATAAT
1 AACTT-TAATATAAT
1666045 AA
1 AA
1666047 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:1666054 original size:16 final size:16
Alignment explanation
Indices: 1666021--1666067 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
1666011 CACTAAACTT
*
1666021 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
1666036 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
1666052 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
1666068 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:1666188 original size:32 final size:34
Alignment explanation
Indices: 1666108--1666189 Score: 93
Period size: 34 Copynumber: 2.5 Consensus size: 34
1666098 CTAAACCCTT
*
1666108 AAAC-AACTAATAAAATATTCTTTTATATAACTA
1 AAACTAACTAATAAACTATTCTTTTATATAACTA
1666141 AAACTAACTAATAAACTATT-TTTTCATTATAA-T-
1 AAACTAACTAATAAACTATTCTTTT-A-TATAACTA
*
1666174 ATACT-ACTAATAAACT
1 AAACTAACTAATAAACT
1666190 TACTAACTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
32 11 0.25
33 12 0.27
34 16 0.36
35 5 0.11
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (34 bp):
AAACTAACTAATAAACTATTCTTTTATATAACTA
Found at i:1666306 original size:45 final size:45
Alignment explanation
Indices: 1666229--1666361 Score: 136
Period size: 45 Copynumber: 3.0 Consensus size: 45
1666219 TCAACAAACA
*
1666229 AATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTT
1 AATATAAC-TAACTA-TTAAC-AAAACAAACTAATTAAATAATTTTTT
* *
1666277 TATATAACTAACTATTAACAAAACAAACTAATT-AATTATTTTTT
1 AATATAACTAACTATTAACAAAACAAACTAATTAAATAATTTTTT
1666321 AACTAT-A-TAACTA-T--C-AAACATATACTAATTAAATAATTTTT
1 AA-TATAACTAACTATTAACAAAACA-A-ACTAATTAAATAATTTTT
1666362 AATTTATGTA
Statistics
Matches: 76, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
39 5 0.07
40 2 0.03
41 7 0.09
42 10 0.13
43 6 0.08
44 12 0.16
45 16 0.21
46 5 0.07
47 6 0.08
48 7 0.09
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (45 bp):
AATATAACTAACTATTAACAAAACAAACTAATTAAATAATTTTTT
Found at i:1666389 original size:41 final size:40
Alignment explanation
Indices: 1666301--1666389 Score: 90
Period size: 41 Copynumber: 2.2 Consensus size: 40
1666291 TTAACAAAAC
* *
1666301 AAACTAATTAATTATTTTTTAACTATATAACTATCAAACAT
1 AAACTAATTAAATAATTTTTAACTATATAACTAT-AAACAT
* * * *
1666342 ATACTAATTAAATAATTTTTAATTTATGTATACTAT-AACTT
1 AAACTAATTAAATAATTTTTAA-CTATATA-ACTATAAACAT
1666383 AAACTAA
1 AAACTAA
1666390 CAATCATATA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 29 0.74
42 5 0.13
43 5 0.13
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.43
Consensus pattern (40 bp):
AAACTAATTAAATAATTTTTAACTATATAACTATAAACAT
Found at i:1666590 original size:23 final size:23
Alignment explanation
Indices: 1666560--1666605 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1666550 TCTTTCTCGG
1666560 CTGCAATCTCTTCTCCCTTTCTT
1 CTGCAATCTCTTCTCCCTTTCTT
1666583 CTGCAATCTCTTCTCCCTTTCTT
1 CTGCAATCTCTTCTCCCTTTCTT
1666606 TCTTTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.09, C:0.39, G:0.04, T:0.48
Consensus pattern (23 bp):
CTGCAATCTCTTCTCCCTTTCTT
Found at i:1666646 original size:25 final size:25
Alignment explanation
Indices: 1666618--1666669 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
1666608 TTTCTTTTAT
1666618 AACCGGCTGCCTCAATTATTTCACC
1 AACCGGCTGCCTCAATTATTTCACC
1666643 AACCGGCTGCCTCAATTATTTCACC
1 AACCGGCTGCCTCAATTATTTCACC
1666668 AA
1 AA
1666670 TAATTGTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.27, C:0.35, G:0.12, T:0.27
Consensus pattern (25 bp):
AACCGGCTGCCTCAATTATTTCACC
Found at i:1666943 original size:13 final size:13
Alignment explanation
Indices: 1666925--1666950 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1666915 GTATAGGACT
1666925 GCATGGCGACCTC
1 GCATGGCGACCTC
1666938 GCATGGCGACCTC
1 GCATGGCGACCTC
1666951 TCCCCATTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.38, G:0.31, T:0.15
Consensus pattern (13 bp):
GCATGGCGACCTC
Found at i:1667337 original size:27 final size:27
Alignment explanation
Indices: 1667290--1667386 Score: 69
Period size: 27 Copynumber: 3.6 Consensus size: 27
1667280 TATTAACTAA
* *
1667290 AAAATGATGAAAATATAAAATTATTT-T
1 AAAATAATTAAAATATAAAA-TATTTAT
*
1667317 TAAATAATTAAAATA-ATAAATATTTAT
1 AAAATAATTAAAATATA-AAATATTTAT
* *
1667344 AAAATAATTGGAAAAAAT-AAA-ATCTAT
1 AAAATAATT--AAAATATAAAATATTTAT
*
1667371 -AAAGAATTAAAATATA
1 AAAATAATTAAAATATA
1667387 CTAAAAAGCC
Statistics
Matches: 56, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
24 6 0.11
26 13 0.23
27 29 0.52
28 3 0.05
29 5 0.09
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.33
Consensus pattern (27 bp):
AAAATAATTAAAATATAAAATATTTAT
Found at i:1668667 original size:2 final size:2
Alignment explanation
Indices: 1668660--1668721 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
1668650 CAATTTTGAC
1668660 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1668702 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
1668722 AGATCCTATT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1676883 original size:16 final size:17
Alignment explanation
Indices: 1676862--1676900 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
1676852 TTAAAAATAA
1676862 TTTAAAAATA-TAAAAT
1 TTTAAAAATATTAAAAT
*
1676878 TTT-AAATTATTAAAAT
1 TTTAAAAATATTAAAAT
1676894 TTTAAAA
1 TTTAAAA
1676901 TATGTATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 5 0.25
16 12 0.60
17 3 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTAAAAATATTAAAAT
Found at i:1678323 original size:2 final size:2
Alignment explanation
Indices: 1678316--1678364 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1678306 TTAATAAATA
1678316 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1678358 AT AT AT A
1 AT AT AT A
1678365 GTTTTAGTAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1680236 original size:61 final size:61
Alignment explanation
Indices: 1680162--1680283 Score: 183
Period size: 61 Copynumber: 2.0 Consensus size: 61
1680152 ACTAAAATTT
* *
1680162 TAAAAAACCATTAACCGTTAATCAATCGAAT-TCAAAATTAAGCAACTAATTAATTAAAATA
1 TAAAAAACCATTAACCGTTAATCAATCGAATCT-AAAATTAAGCAACCAATTAATCAAAATA
* * *
1680223 TAAAAAATCATTAACCGTTAATCAATCGAATCTAAAATTAATCAACCGATTAATCAAAATA
1 TAAAAAACCATTAACCGTTAATCAATCGAATCTAAAATTAAGCAACCAATTAATCAAAATA
1680284 AATTTCAATT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
61 54 0.98
62 1 0.02
ACGTcount: A:0.52, C:0.16, G:0.05, T:0.28
Consensus pattern (61 bp):
TAAAAAACCATTAACCGTTAATCAATCGAATCTAAAATTAAGCAACCAATTAATCAAAATA
Found at i:1687347 original size:21 final size:21
Alignment explanation
Indices: 1687322--1687367 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
1687312 GGAACTTTGA
1687322 AGTCGTCAGAAAAGGAACAAC
1 AGTCGTCAGAAAAGGAACAAC
1687343 AGTCGTCAGAAAAGGAACAAC
1 AGTCGTCAGAAAAGGAACAAC
1687364 AGTC
1 AGTC
1687368 TGCCCGTCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.46, C:0.20, G:0.24, T:0.11
Consensus pattern (21 bp):
AGTCGTCAGAAAAGGAACAAC
Found at i:1717175 original size:27 final size:25
Alignment explanation
Indices: 1717121--1717172 Score: 59
Period size: 27 Copynumber: 1.9 Consensus size: 25
1717111 TTGTATTAAG
*
1717121 TTAATTTGGGTTTTAAAATTTATTTA
1 TTAATTTGAGTTTTAAAATTTA-TTA
1717147 TTAATTTTGAGTTTTAATTAATTTAT
1 TTAA-TTTGAGTTTTAA--AATTTAT
1717173 ATTTGATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
26 4 0.18
27 11 0.50
28 1 0.05
29 6 0.27
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.60
Consensus pattern (25 bp):
TTAATTTGAGTTTTAAAATTTATTA
Found at i:1724096 original size:20 final size:20
Alignment explanation
Indices: 1724071--1724124 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
1724061 GACCAACAAA
1724071 TTCGCAACGCGAATTCCAAT
1 TTCGCAACGCGAATTCCAAT
* *
1724091 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGA-ATTCCAAT
*
1724111 TTCGCAACGTGAAT
1 TTCGCAACGCGAAT
1724125 ATATAAATCG
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.07
20 24 0.89
21 1 0.04
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.28
Consensus pattern (20 bp):
TTCGCAACGCGAATTCCAAT
Found at i:1724171 original size:20 final size:20
Alignment explanation
Indices: 1724148--1724231 Score: 118
Period size: 20 Copynumber: 4.2 Consensus size: 20
1724138 TGCGATTTTC
1724148 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
*
1724168 CAAATTCGCAACAC-AGAAGT
1 CAAATTCGCAACGCGA-AAGT
*
1724188 CAAATTCGC-ACGCGATAGT
1 CAAATTCGCAACGCGAAAGT
*
1724207 CAAATTCGCAATGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
1724227 CAAAT
1 CAAAT
1724232 GTTTTTATGC
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
19 16 0.29
20 40 0.71
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.18
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:1724641 original size:13 final size:13
Alignment explanation
Indices: 1724623--1724654 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
1724613 AGTATTTGTC
1724623 TTTGTTTTGTCTT
1 TTTGTTTTGTCTT
1724636 TTTGTTTTGTCTT
1 TTTGTTTTGTCTT
1724649 TTTGTT
1 TTTGTT
1724655 GAAGAAATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.06, G:0.16, T:0.78
Consensus pattern (13 bp):
TTTGTTTTGTCTT
Found at i:1726943 original size:21 final size:21
Alignment explanation
Indices: 1726894--1726991 Score: 65
Period size: 21 Copynumber: 4.7 Consensus size: 21
1726884 CCGATGCACT
*
1726894 TATCATCATTCAAGAGGCGCC
1 TATCATCATTCAAGAGGCCCC
* *
1726915 T-CCTATCATTTAAGAGGCCCC
1 TATC-ATCATTCAAGAGGCCCC
*
1726936 TATCATCA-TCGAAGAAGCCCC
1 TATCATCATTC-AAGAGGCCCC
** * * *
1726957 TCCCACCGTTCAAGAGGCCCA
1 TATCATCATTCAAGAGGCCCC
* *
1726978 TGTCATCGTTCAAG
1 TATCATCATTCAAG
1726992 TGGTCCCGCC
Statistics
Matches: 58, Mismatches: 15, Indels: 8
0.72 0.19 0.10
Matches are distributed among these distances:
20 2 0.03
21 53 0.91
22 3 0.05
ACGTcount: A:0.27, C:0.33, G:0.17, T:0.23
Consensus pattern (21 bp):
TATCATCATTCAAGAGGCCCC
Found at i:1728443 original size:61 final size:66
Alignment explanation
Indices: 1728360--1728500 Score: 168
Period size: 66 Copynumber: 2.2 Consensus size: 66
1728350 TTTTAAATTG
1728360 AAAGTTGATTTG-TTACAATTGATGAGGAAATAAG-A-T-TTATTTT-TTGATTAATTGATTTGT
1 AAAGTTGATTTGTTTACAATTGATGAGGAAATAAGAATTATTATTTTCTTGATTAATTGATTTGT
1728420 A
66 A
* * ** * * *
1728421 AAAGTTAATTTGTTTA-ATTTGATTTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTG
1 AAAGTTGATTTGTTTACAATTGATGAGGAAATAAGAATTATTATTTT-CTTGATTAATTGATTTG
1728485 TA
65 TA
1728487 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
1728501 GTTTCTAAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
61 25 0.38
62 4 0.06
63 1 0.02
64 6 0.09
66 30 0.45
ACGTcount: A:0.32, C:0.01, G:0.16, T:0.50
Consensus pattern (66 bp):
AAAGTTGATTTGTTTACAATTGATGAGGAAATAAGAATTATTATTTTCTTGATTAATTGATTTGT
A
Found at i:1728584 original size:20 final size:20
Alignment explanation
Indices: 1728559--1728596 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1728549 GTTGAAGGTA
1728559 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
1728579 CAAATTCGCAACGCGAAA
1 CAAATTCGCAACGCGAAA
1728597 TAAGCGTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.26, G:0.18, T:0.13
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:1728872 original size:39 final size:39
Alignment explanation
Indices: 1728816--1728902 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
1728806 TCAAGTTGTA
*
1728816 GATTTTGATTTCTTTTTGCTTGGAACCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGAACCATATGAGATTTG
* *
1728855 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGAACCATATGAGATTTG
1728894 GATTTTGAT
1 GATTTTGAT
1728903 GAGCATCGGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.18, C:0.13, G:0.21, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGAACCATATGAGATTTG
Found at i:1729236 original size:18 final size:18
Alignment explanation
Indices: 1729213--1729249 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1729203 CGAAATTTAT
1729213 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
1729231 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
1729249 A
1 A
1729250 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:1729670 original size:25 final size:25
Alignment explanation
Indices: 1729636--1729685 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
1729626 ATTATTTTTC
*
1729636 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
1729661 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
1729686 TAATTGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:1729776 original size:20 final size:20
Alignment explanation
Indices: 1729751--1729803 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
1729741 TATTGAAGGT
1729751 AAATTCGCAACGCGATAGTC
1 AAATTCGCAACGCGATAGTC
*
1729771 AAATTCGCTACGCGATAGTC
1 AAATTCGCAACGCGATAGTC
1729791 AAATTCGCAACGC
1 AAATTCGCAACGC
1729804 TTATTTCGCG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (20 bp):
AAATTCGCAACGCGATAGTC
Found at i:1730145 original size:18 final size:18
Alignment explanation
Indices: 1730122--1730157 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1730112 AAGCCGGTTG
*
1730122 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1730140 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
1730158 CCTTTTGCTT
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:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1734928 original size:21 final size:21
Alignment explanation
Indices: 1734904--1734980 Score: 75
Period size: 23 Copynumber: 3.5 Consensus size: 21
1734894 CCAGGGGGTT
*
1734904 ATCGATTCCCTTGTGGGGGGA
1 ATCGATTCCCTTGAGGGGGGA
* *
1734925 ATCGATTCCTCTTCAAAGGGGGA
1 ATCGATTCC-CTT-GAGGGGGGA
*
1734948 ATCGGTTCCCTCATGAGGGGGG-
1 ATCGATTCCCT--TGAGGGGGGA
1734970 ATCGATTCCCT
1 ATCGATTCCCT
1734981 CTGCACCAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
21 9 0.20
22 15 0.33
23 20 0.44
24 1 0.02
ACGTcount: A:0.18, C:0.23, G:0.31, T:0.27
Consensus pattern (21 bp):
ATCGATTCCCTTGAGGGGGGA
Found at i:1734945 original size:23 final size:22
Alignment explanation
Indices: 1734919--1734981 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 22
1734909 TTCCCTTGTG
1734919 GGGGGAATCGATTCCTCTTCA-AA
1 GGGGGAATCGATTCC-C-TCATAA
* *
1734942 GGGGGAATCGGTTCCCTCATGA
1 GGGGGAATCGATTCCCTCATAA
*
1734964 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
1734982 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 3 0.09
22 18 0.51
23 14 0.40
ACGTcount: A:0.19, C:0.24, G:0.33, T:0.24
Consensus pattern (22 bp):
GGGGGAATCGATTCCCTCATAA
Found at i:1742965 original size:20 final size:20
Alignment explanation
Indices: 1742929--1743099 Score: 122
Period size: 20 Copynumber: 8.6 Consensus size: 20
1742919 ACTAAAACCT
*
1742929 GTTGCGAAATT-AAATTCGC
1 GTTGCGAATTTGAAATTCGC
*
1742948 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGC
**
1742967 GTTGCGAATTTGACTTTCGC
1 GTTGCGAATTTGAAATTCGC
*
1742987 GTTGCGAATTTG-ACTATCGC
1 GTTGCGAATTTGAAAT-TCGC
1743007 GTTGCGAATTTGGAAAATT-GC
1 GTTGCGAATTT-G-AAATTCGC
** *
1743028 AATACG-ATTT-ACATATTCGC
1 GTTGCGAATTTGA-A-ATTCGC
* * *
1743048 GTTGCGAAATTGGAAACT-GG
1 GTTGCG-AATTTGAAATTCGC
* *
1743068 GTTGCGAAATTGGAATTCGC
1 GTTGCGAATTTGAAATTCGC
1743088 GTTGCGAATTTG
1 GTTGCGAATTTG
1743100 TTGGTCATTT
Statistics
Matches: 116, Mismatches: 23, Indels: 25
0.71 0.14 0.15
Matches are distributed among these distances:
17 1 0.01
18 1 0.01
19 37 0.32
20 61 0.53
21 8 0.07
22 5 0.04
23 3 0.03
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCGC
Found at i:1743238 original size:2 final size:2
Alignment explanation
Indices: 1743231--1743263 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1743221 TTAAATTAAA
1743231 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1743264 AAAGGTTAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1744350 original size:133 final size:133
Alignment explanation
Indices: 1744133--1744668 Score: 623
Period size: 133 Copynumber: 4.0 Consensus size: 133
1744123 GGTATGGTCG
* * * *
1744133 TCTAAGGGTGACACAGCTCCTACGTGATGAGGA-GAACTGGTCGGGGATGACACGGCTCATACGT
1 TCTAGGGGTGACACAACTCCTACGTGATGAGGAGGTA-TGGTCGGGGATGACACGTCTCATACGT
* * * *
1744197 GATGAAGAGTTCTGGCCATCTTTAGGAAGGGTGATAACTCGATTCCTACGCGATGAGAACAACTG
65 GATGAAGAGTTCTGGTCATCTTTAGGAAGGATGATAACTCGATTCCTACGCGATGAGGACGACTG
1744262 GTTA
130 GTTA
*** * *
1744266 TCTAGGGGTGACATGGCTCCTACGTGATGAGGAGGTATGGTCGGGGATGATATGTCTCATACGTG
1 TCTAGGGGTGACACAACTCCTACGTGATGAGGAGGTATGGTCGGGGATGACACGTCTCATACGTG
* * * **
1744331 ATGAAGAGTTTTGGTCATCTTTAGGAAGGATGATAACTTGGTTCCTACGCGATGAGGACGGTTGG
66 ATGAAGAGTTCTGGTCATCTTTAGGAAGGATGATAACTCGATTCCTACGCGATGAGGACGACTGG
1744396 TTA
131 TTA
* *
1744399 TCTAGGGGTGACACAACTCCTACGTGATGATGAGGTATGGTCGGGGATGACACGACTCATACGTG
1 TCTAGGGGTGACACAACTCCTACGTGATGAGGAGGTATGGTCGGGGATGACACGTCTCATACGTG
* ** * * *
1744464 ATGAAGA-TTTTTTTCCATCTTTAGGAAGAATGATAACT-TAGTTCCTACGCGATGAGGATGACT
66 ATGAAGAGTTCTGGT-CATCTTTAGGAAGGATGATAACTCGA-TTCCTACGCGATGAGGACGACT
*
1744527 AGTTA
129 GGTTA
** * * *
1744532 TCTAGGGGTGACACAACTCCTATATGATGAGGAGGTCTGGTCGGGGGATGACACGGT-TCCTACA
1 TCTAGGGGTGACACAACTCCTACGTGATGAGGAGGTATGGTC-GGGGATGACAC-GTCTCATACG
* * *** * * *
1744596 CGATGAGGACAGCTGGTCATCTTTAGG-AGTGGTGATAACTCGATTCCTACGTGATGAGGATGAC
64 TGATGAAGAGTTCTGGTCATCTTTAGGAAG-GATGATAACTCGATTCCTACGCGATGAGGACGAC
1744660 TGGTTA
128 TGGTTA
1744666 TCT
1 TCT
1744669 TTAGGAGTGG
Statistics
Matches: 344, Mismatches: 51, Indels: 15
0.84 0.12 0.04
Matches are distributed among these distances:
132 5 0.01
133 264 0.77
134 71 0.21
135 4 0.01
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.27
Consensus pattern (133 bp):
TCTAGGGGTGACACAACTCCTACGTGATGAGGAGGTATGGTCGGGGATGACACGTCTCATACGTG
ATGAAGAGTTCTGGTCATCTTTAGGAAGGATGATAACTCGATTCCTACGCGATGAGGACGACTGG
TTA
Found at i:1744704 original size:51 final size:51
Alignment explanation
Indices: 1744598--1744719 Score: 140
Period size: 51 Copynumber: 2.4 Consensus size: 51
1744588 TTCCTACACG
* *
1744598 ATGAGGAC-AGCTGGTCATCTTTAGGAGTGGTGATAACTCGATTCCTACGTG
1 ATGAGGACGA-CTGGTTATCTTTAGGAGTGGTGATAACTCGATTCCTACGTA
* ** * *
1744649 ATGAGGATGACTGGTTATCTTTAGGAGTGGTGATAGTTTGGTT-CTGACGTA
1 ATGAGGACGACTGGTTATCTTTAGGAGTGGTGATAACTCGATTCCT-ACGTA
*
1744700 ATGAGGACGGCTGGTTATCT
1 ATGAGGACGACTGGTTATCT
1744720 ATGGATTATG
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
50 2 0.03
51 57 0.95
52 1 0.02
ACGTcount: A:0.22, C:0.13, G:0.32, T:0.33
Consensus pattern (51 bp):
ATGAGGACGACTGGTTATCTTTAGGAGTGGTGATAACTCGATTCCTACGTA
Found at i:1744770 original size:28 final size:28
Alignment explanation
Indices: 1744732--1744811 Score: 101
Period size: 28 Copynumber: 2.9 Consensus size: 28
1744722 GGATTATGGT
*
1744732 TTTAAG-AGAAACCAACTCAAAGATTTG
1 TTTAAGAAGAAACAAACTCAAAGATTTG
** *
1744759 TTTAAGAAGAAACGGACTCCAAGATTTG
1 TTTAAGAAGAAACAAACTCAAAGATTTG
1744787 TTTCAAGAA-AAACAAACTCAAAGAT
1 TTT-AAGAAGAAACAAACTCAAAGAT
1744812 GATGTGTTTC
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
27 6 0.13
28 34 0.76
29 5 0.11
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (28 bp):
TTTAAGAAGAAACAAACTCAAAGATTTG
Found at i:1745039 original size:35 final size:35
Alignment explanation
Indices: 1744983--1745088 Score: 99
Period size: 36 Copynumber: 3.0 Consensus size: 35
1744973 GACAAAATTC
*
1744983 GTTTGAAGGGAAAC-GATCTCAAAGATGTTTGTTTT
1 GTTTCAAGGGAAACAGA-CTCAAAGATGTTTGTTTT
****
1745018 GTTTCAAGGGAAACAGACTCAAAGATGGCAAATTTT
1 GTTTCAAGGGAAACAGACTCAAAGAT-GTTTGTTTT
* *
1745054 GTTTCCAA-AGAAACAGACTCAAAGATTTTATGTTT
1 GTTT-CAAGGGAAACAGACTCAAAGATGTT-TGTTT
1745089 CTAAAGAAAC
Statistics
Matches: 56, Mismatches: 11, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
35 22 0.39
36 31 0.55
37 3 0.05
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (35 bp):
GTTTCAAGGGAAACAGACTCAAAGATGTTTGTTTT
Found at i:1745278 original size:30 final size:29
Alignment explanation
Indices: 1745244--1745318 Score: 107
Period size: 30 Copynumber: 2.6 Consensus size: 29
1745234 AATACAAAAC
1745244 TTTGTTTCAAAAGAAACAACCTCAAAAATT
1 TTTGTTTCAAAAGAAACAA-CTCAAAAATT
* *
1745274 TTTGTTTCAAAAGAAACAACTTAAAGATT
1 TTTGTTTCAAAAGAAACAACTCAAAAATT
*
1745303 TTT-CTTCAAAAGAAAC
1 TTTGTTTCAAAAGAAAC
1745319 TGTCTCAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
28 12 0.29
29 11 0.26
30 19 0.45
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.32
Consensus pattern (29 bp):
TTTGTTTCAAAAGAAACAACTCAAAAATT
Found at i:1745584 original size:36 final size:36
Alignment explanation
Indices: 1745519--1745613 Score: 102
Period size: 36 Copynumber: 2.6 Consensus size: 36
1745509 CAACAAATTT
* * *
1745519 AAATTTGTATCTTAGAGAAAAAATGTCTCAAGCGAGACG
1 AAATTTG--TCTTTGAG-AAAACTGTCTCAAGCGAGACA
*
1745558 AAATTTG-CTTTGAGAGAAACTGTCTCAAGTGAGACA
1 AAATTTGTCTTTGAGA-AAACTGTCTCAAGCGAGACA
*
1745594 AAATTTGTTTTTGAGAAAAC
1 AAATTTGTCTTTGAGAAAAC
1745614 GATCAGTGAG
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
35 1 0.02
36 34 0.69
37 7 0.14
39 7 0.14
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (36 bp):
AAATTTGTCTTTGAGAAAACTGTCTCAAGCGAGACA
Found at i:1745682 original size:16 final size:17
Alignment explanation
Indices: 1745661--1745694 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1745651 TTGAAATTTG
*
1745661 TATCTCAA-AGGGAAAA
1 TATCTCAAGAGAGAAAA
1745677 TATCTCAAGAGAGAAAA
1 TATCTCAAGAGAGAAAA
1745694 T
1 T
1745695 TTGTTTTCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.50, C:0.12, G:0.18, T:0.21
Consensus pattern (17 bp):
TATCTCAAGAGAGAAAA
Found at i:1746171 original size:8 final size:8
Alignment explanation
Indices: 1746162--1747089 Score: 1335
Period size: 8 Copynumber: 116.6 Consensus size: 8
1746152 TGTATCATGC
*
1746162 ATGTATGC
1 ATGTATGT
*
1746170 ATGTATGC
1 ATGTATGT
*
1746178 ATGTATGC
1 ATGTATGT
*
1746186 ATGTATGC
1 ATGTATGT
*
1746194 ATGTATGC
1 ATGTATGT
*
1746202 ATGTATGC
1 ATGTATGT
* *
1746210 ATGTTTGC
1 ATGTATGT
*
1746218 ATGTATGC
1 ATGTATGT
* *
1746226 ATGTTTGC
1 ATGTATGT
*
1746234 ATGTATGC
1 ATGTATGT
* *
1746242 ATGTTTGC
1 ATGTATGT
*
1746250 ATGTATGC
1 ATGTATGT
* *
1746258 ATGTTTGC
1 ATGTATGT
*
1746266 ATGTATGC
1 ATGTATGT
* *
1746274 ATGTTTGC
1 ATGTATGT
*
1746282 ATGTATGC
1 ATGTATGT
* *
1746290 ATGTTTGC
1 ATGTATGT
* *
1746298 ATGTTTGC
1 ATGTATGT
*
1746306 ATGTTTGT
1 ATGTATGT
*
1746314 ATGTATGC
1 ATGTATGT
*
1746322 ATGTATGC
1 ATGTATGT
*
1746330 ATGTATGC
1 ATGTATGT
*
1746338 ATGTATGC
1 ATGTATGT
*
1746346 ATGTATGC
1 ATGTATGT
*
1746354 ATGTATGC
1 ATGTATGT
*
1746362 ATGTATGC
1 ATGTATGT
*
1746370 ATGTATGC
1 ATGTATGT
*
1746378 ATGTATGC
1 ATGTATGT
*
1746386 ATGTATGC
1 ATGTATGT
*
1746394 ATGTATGC
1 ATGTATGT
*
1746402 ATGTATGC
1 ATGTATGT
*
1746410 ATGTATGC
1 ATGTATGT
*
1746418 ATGTATGC
1 ATGTATGT
*
1746426 ATGTATGC
1 ATGTATGT
*
1746434 ATGTATGC
1 ATGTATGT
*
1746442 ATGTATGC
1 ATGTATGT
*
1746450 ATGTATGC
1 ATGTATGT
*
1746458 ATGTATGC
1 ATGTATGT
*
1746466 ATGTATGC
1 ATGTATGT
*
1746474 ATGTATGC
1 ATGTATGT
*
1746482 ATGTATGC
1 ATGTATGT
*
1746490 ATGTATGC
1 ATGTATGT
*
1746498 ATGTATGC
1 ATGTATGT
*
1746506 ATGTATGC
1 ATGTATGT
*
1746514 ATGTATGC
1 ATGTATGT
*
1746522 ATGTATGC
1 ATGTATGT
*
1746530 ATGTATGC
1 ATGTATGT
1746538 ATGTATGT
1 ATGTATGT
1746546 ATGTATGT
1 ATGTATGT
1746554 ATGTATGT
1 ATGTATGT
1746562 ATGTATGT
1 ATGTATGT
1746570 ATGTATGT
1 ATGTATGT
1746578 ATGTATGT
1 ATGTATGT
1746586 ATGTATGT
1 ATGTATGT
1746594 ATGTATGT
1 ATGTATGT
1746602 ATGTATGT
1 ATGTATGT
1746610 ATGTATGT
1 ATGTATGT
1746618 ATGTATGT
1 ATGTATGT
1746626 ATGTATGT
1 ATGTATGT
1746634 ATGTATGT
1 ATGTATGT
1746642 ATGTATGT
1 ATGTATGT
1746650 ATGTATGT
1 ATGTATGT
1746658 ATGTATGT
1 ATGTATGT
1746666 ATGTATGT
1 ATGTATGT
1746674 ATGTATGT
1 ATGTATGT
1746682 ATGTATGT
1 ATGTATGT
1746690 ATGTATGT
1 ATGTATGT
1746698 ATGTATGT
1 ATGTATGT
1746706 ATGTATGT
1 ATGTATGT
1746714 ATGTATGT
1 ATGTATGT
1746722 ATGTATGT
1 ATGTATGT
1746730 ATGTATGT
1 ATGTATGT
1746738 ATGTATGT
1 ATGTATGT
1746746 ATGTATGT
1 ATGTATGT
1746754 ATGTATGT
1 ATGTATGT
1746762 ATGTATGT
1 ATGTATGT
1746770 ATGTATGT
1 ATGTATGT
1746778 ATGTATGT
1 ATGTATGT
1746786 ATGTATGT
1 ATGTATGT
1746794 ATGTATGT
1 ATGTATGT
1746802 ATGTATGT
1 ATGTATGT
1746810 ATGTATGT
1 ATGTATGT
1746818 ATGTATGT
1 ATGTATGT
1746826 ATGTATGT
1 ATGTATGT
1746834 ATGTATGT
1 ATGTATGT
1746842 ATGTATGT
1 ATGTATGT
1746850 ATGTATGT
1 ATGTATGT
1746858 ATGTATGT
1 ATGTATGT
1746866 ATGTATGT
1 ATGTATGT
1746874 ATGTATGT
1 ATGTATGT
1746882 ATGTATGT
1 ATGTATGT
1746890 ATGTA-GT
1 ATGTATGT
1746897 ATGTATGT
1 ATGTATGT
1746905 ATGTATGT
1 ATGTATGT
1746913 ATGTATGT
1 ATGTATGT
1746921 ATGTATGT
1 ATGTATGT
1746929 ATGTATGT
1 ATGTATGT
1746937 ATGTATGT
1 ATGTATGT
1746945 ATGTATGT
1 ATGTATGT
1746953 ATGTATG-
1 ATGTATGT
1746960 -TGTATGT
1 ATGTATGT
1746967 ATGTATGT
1 ATGTATGT
1746975 ATGTATGT
1 ATGTATGT
1746983 ATGTATGT
1 ATGTATGT
1746991 ATGTATGT
1 ATGTATGT
1746999 ATGTATGT
1 ATGTATGT
1747007 ATGTATGT
1 ATGTATGT
1747015 ATGTATGT
1 ATGTATGT
1747023 ATGTATGT
1 ATGTATGT
1747031 ATGTATGT
1 ATGTATGT
1747039 ATGTATGT
1 ATGTATGT
1747047 ATGTATGT
1 ATGTATGT
1747055 ATGTATGT
1 ATGTATGT
1747063 ATGTATG-
1 ATGTATGT
1747070 -TGTATGT
1 ATGTATGT
1747077 ATGTATGT
1 ATGTATGT
1747085 ATGTA
1 ATGTA
1747090 CGTACGTACG
Statistics
Matches: 900, Mismatches: 15, Indels: 10
0.97 0.02 0.01
Matches are distributed among these distances:
6 12 0.01
7 7 0.01
8 881 0.98
ACGTcount: A:0.24, C:0.05, G:0.25, T:0.46
Consensus pattern (8 bp):
ATGTATGT
Found at i:1747104 original size:4 final size:4
Alignment explanation
Indices: 1747097--1747169 Score: 146
Period size: 4 Copynumber: 18.2 Consensus size: 4
1747087 GTACGTACGT
1747097 ACGC ACGC ACGC ACGC ACGC ACGC ACGC ACGC ACGC ACGC ACGC ACGC
1 ACGC ACGC ACGC ACGC ACGC ACGC ACGC ACGC ACGC ACGC ACGC ACGC
1747145 ACGC ACGC ACGC ACGC ACGC ACGC A
1 ACGC ACGC ACGC ACGC ACGC ACGC A
1747170 TGTATGTATG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 69 1.00
ACGTcount: A:0.26, C:0.49, G:0.25, T:0.00
Consensus pattern (4 bp):
ACGC
Found at i:1747176 original size:4 final size:4
Alignment explanation
Indices: 1747169--1747234 Score: 96
Period size: 4 Copynumber: 16.5 Consensus size: 4
1747159 GCACGCACGC
* * *
1747169 ATGT ATGT ATGT ATGT ATGT ATGT ATAT ATGT ATGT ATAT ATGC ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
1747217 ATGT ATGT ATAT ATGT AT
1 ATGT ATGT ATGT ATGT AT
1747235 ATGTTGACGT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 54 1.00
ACGTcount: A:0.30, C:0.02, G:0.20, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:1759575 original size:23 final size:23
Alignment explanation
Indices: 1759539--1759757 Score: 214
Period size: 23 Copynumber: 9.5 Consensus size: 23
1759529 CATACGAATT
**
1759539 GAAGAAGGAA-AAATGATTTTATG
1 GAAGAA-GAAGAAATGGGTTTATG
*
1759562 GAAGAAGAAGAAATGTGTTTATG
1 GAAGAAGAAGAAATGGGTTTATG
* *
1759585 GAAGAAAAAGAAATGGGTCTATG
1 GAAGAAGAAGAAATGGGTTTATG
*
1759608 GAAGAAGAAGAAAGGGGTTTATG
1 GAAGAAGAAGAAATGGGTTTATG
* * *
1759631 GAATAAGAATAAAGGGGTTTATG
1 GAAGAAGAAGAAATGGGTTTATG
*
1759654 GAAGAAGAAGAAGAGGGGTTTATG
1 GAAGAAGAAGAA-ATGGGTTTATG
* * *
1759678 AAAGAAGAA-ACAATGAGTTTATC
1 GAAGAAGAAGA-AATGGGTTTATG
* *
1759701 GAATAAGAAGAAAAT--ATTTATG
1 GAAGAAGAAG-AAATGGGTTTATG
*
1759723 GAAGAAGAAGAAATGTGCTTT-TG
1 GAAGAAGAAGAAATG-GGTTTATG
1759746 GAAGAAGAAGAA
1 GAAGAAGAAGAA
1759758 TGGTTCATAA
Statistics
Matches: 166, Mismatches: 22, Indels: 16
0.81 0.11 0.08
Matches are distributed among these distances:
21 4 0.02
22 17 0.10
23 118 0.71
24 26 0.16
25 1 0.01
ACGTcount: A:0.47, C:0.02, G:0.30, T:0.21
Consensus pattern (23 bp):
GAAGAAGAAGAAATGGGTTTATG
Found at i:1761838 original size:18 final size:17
Alignment explanation
Indices: 1761811--1761844 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
1761801 TCCTTCTCAA
1761811 AAATAAAATAAATAAAT
1 AAATAAAATAAATAAAT
1761828 AAATAAAAATAAATAAA
1 AAAT-AAAATAAATAAA
1761845 CTTTCCCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (17 bp):
AAATAAAATAAATAAAT
Found at i:1761839 original size:14 final size:13
Alignment explanation
Indices: 1761811--1761844 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
1761801 TCCTTCTCAA
*
1761811 AAATAAAATAAAT
1 AAATAAAAAAAAT
1761824 AAATAAATAAAAAT
1 AAATAAA-AAAAAT
1761838 AAATAAA
1 AAATAAA
1761845 CTTTCCCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AAATAAAAAAAAT
Found at i:1763520 original size:14 final size:14
Alignment explanation
Indices: 1763501--1763530 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1763491 AGATTTCTTC
1763501 TTTTTCTCTTTATT
1 TTTTTCTCTTTATT
1763515 TTTTTCTCTTTATT
1 TTTTTCTCTTTATT
1763529 TT
1 TT
1763531 GTTTATTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTCTCTTTATT
Found at i:1767029 original size:6 final size:6
Alignment explanation
Indices: 1767015--1767050 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
1767005 AAATGAAAGA
*
1767015 AAGGTG AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG
1 AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG
1767051 GAAAAAAGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.33, C:0.00, G:0.64, T:0.03
Consensus pattern (6 bp):
AAGGGG
Found at i:1768179 original size:21 final size:23
Alignment explanation
Indices: 1768133--1768180 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
1768123 ATCAAGTACA
*
1768133 ATAATATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
1768156 ATAATATAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
1768179 AT
1 AT
1768181 TGACATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.38
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:1769113 original size:182 final size:182
Alignment explanation
Indices: 1768806--1769157 Score: 596
Period size: 182 Copynumber: 1.9 Consensus size: 182
1768796 TTACTATCGG
* *
1768806 TTTTGTCATTTCGAGATCGATTGTGTCATATTCTTACCTGGTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGATTGTGTCATATTCTTACCTGGTATATTGTTATGAATCGATACATT
* * * *
1768871 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTTTCTTTTAAATTCCAAAAGTGTCTA
66 TTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTATCTTTTAAATTCCAAAAGTGCCGA
1768936 TACTTATAATAAAGTATCGACACTATCAACATATCCGGTATCTCTTTACCGA
131 TACTTATAATAAAGTATCGACACTATCAACATATCCGGTATCTCTTTACCGA
* * * *
1768988 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGAATCGATACATT
1 TTTTGTCATTTCGAGACCGATTGTGTCATATTCTTACCTGGTATATTGTTATGAATCGATACATT
1769053 TTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTATCTTTTAAATTCCAAAAGTGCCGA
66 TTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTATCTTTTAAATTCCAAAAGTGCCGA
* *
1769118 TACTTATAATAAAGTATCGATACTATCAACATATCTGGTA
131 TACTTATAATAAAGTATCGACACTATCAACATATCCGGTA
1769158 GCACTTTATT
Statistics
Matches: 158, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
182 158 1.00
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (182 bp):
TTTTGTCATTTCGAGACCGATTGTGTCATATTCTTACCTGGTATATTGTTATGAATCGATACATT
TTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTATCTTTTAAATTCCAAAAGTGCCGA
TACTTATAATAAAGTATCGACACTATCAACATATCCGGTATCTCTTTACCGA
Found at i:1770149 original size:199 final size:199
Alignment explanation
Indices: 1769868--1773189 Score: 3358
Period size: 199 Copynumber: 16.5 Consensus size: 199
1769858 AATGTAAATC
* * *
1769868 GGTATATTTAGACTGGTTATATTGCTAATTTACCTATTACATTATAATTATGGTTTTCGATGTTT
1 GGTATATTTAGACCGGTTATATTGCTAATCTACCTATTACATTATAATTATAGTTTTCGATGTTT
*
1769933 TTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGGGCACTTGGTTTTGAAATACATTC
66 TTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTC
* * *
1769998 TGGACAAAAAGTATCGACACTTGTTTGATTTGTGTCGATACTGTTTGTACACCTGTTTTCTCAAA
131 TGGACCAAAAGTATCGACACTTGTTTGATTTGTGTCGATACTTTTTTTACACCTGTTTTCTCAAA
1770063 AACT
196 AACT
* *
1770067 GGTATATTTAGACCGGTTATATTACTAATCTACCTATTACATTATAATTATGGTTTTCGATGTTT
1 GGTATATTTAGACCGGTTATATTGCTAATCTACCTATTACATTATAATTATAGTTTTCGATGTTT
*
1770132 TTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGGGCACTTGGTTTTGAAATACATTC
66 TTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTC
* * **
1770197 TGGACAAAAAGTATCGACACTTGTTTGATTTGTGTCGATACTGTTCGTACACCTGTTTTCTCAAA
131 TGGACCAAAAGTATCGACACTTGTTTGATTTGTGTCGATACTTTTTTTACACCTGTTTTCTCAAA
1770262 AACT
196 AACT
* *
1770266 GATATATTTAGACCGGTTATATTACTAATCTACCTATTACATTATAATTATAGTTTTCGATGTTT
1 GGTATATTTAGACCGGTTATATTGCTAATCTACCTATTACATTATAATTATAGTTTTCGATGTTT
1770331 TTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTC
66 TTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTC
*
1770396 TGGACTAAAAGTATCGACACTTGTTTGATTTGTGTCGATACTTTTTTTACACCTGTTTTCTCAAA
131 TGGACCAAAAGTATCGACACTTGTTTGATTTGTGTCGATACTTTTTTTACACCTGTTTTCTCAAA
1770461 AA-T
196 AACT
*
1770464 CGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACATTATAATTATAGTTTTCGATGTT
1 -GGTATATTTAGACCGGTTATATTGCTAATCTACCTATTACATTATAATTATAGTTTTCGATGTT
*
1770529 TTTGGGATCGACACTTTTTACAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATT
65 TTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATT
* *
1770594 TTGCACCAAAAGTATCGACACTTGTTTGATTTGTGTCGATACTTTTTTTACACCTGTTTTCTCAA
130 CTGGACCAAAAGTATCGACACTTGTTTGATTTGTGTCGATACTTTTTTTACACCTGTTTTCTCAA
* *
1770659 AACCC
195 AAACT
1770664 GGTATATTTAGACCGGTTATATTGCTAATCTACCTATTACATTATAATTATAGTTTTCGATGTTT
1 GGTATATTTAGACCGGTTATATTGCTAATCTACCTATTACATTATAATTATAGTTTTCGATGTTT
* *
1770729 TTGGGATCGACATTTGTTACAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTT
66 TTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTC
**
1770794 TGGACCAAAAGTATCGACACTTGTTTGATTTGTGTCGATACTTTTTTTACATATGTTTTCTCAAA
131 TGGACCAAAAGTATCGACACTTGTTTGATTTGTGTCGATACTTTTTTTACACCTGTTTTCTCAAA
1770859 AACT
196 AACT
* *
1770863 GGTATATTTAGACCGGTTATATTGCTAATCTACCTATTACATTATAATTATTGTTTTCGATATTT
1 GGTATATTTAGACCGGTTATATTGCTAATCTACCTATTACATTATAATTATAGTTTTCGATGTTT
* * *
1770928 TTGGGATCGACACTTGTTACAAATGTATCGACAGTTTTTAGTGCCCTTGGTTTTGAAATACATTT
66 TTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTC
*
1770993 TGGACCAAAAGTATCGACACTTGTTTGATTTGTGTAGATACTTTTTTTACACCTGTTTTCTCAAA
131 TGGACCAAAAGTATCGACACTTGTTTGATTTGTGTCGATACTTTTTTTACACCTGTTTTCTCAAA
1771058 AACT
196 AACT
1771062 GGTATATTTAGACCGGTTATATTGCTAATCTACCTATTACATTATAATTATAGTTTTCGATGTTT
1 GGTATATTTAGACCGGTTATATTGCTAATCTACCTATTACATTATAATTATAGTTTTCGATGTTT
*
1771127 TTGGGATCGACACTTTTTACAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTC
66 TTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTC
*
1771192 TGGACCAAAAGTATCGACACATGTTTGATTTGTGTCGATACTTTTTTTTACACCTGTTTTCTCAA
131 TGGACCAAAAGTATCGACACTTGTTTGATTTGTGTCGATAC-TTTTTTTACACCTGTTTTCTCAA
1771257 AAACT
195 AAACT
* *
1771262 GGTATATTTAGACCGGTTATATTGCTAATCTACCTATTACATTATGATTATAGTTTTCGATATTT
1 GGTATATTTAGACCGGTTATATTGCTAATCTACCTATTACATTATAATTATAGTTTTCGATGTTT
* *
1771327 TTGGGATCGACACTTGTTACAAATGTATCGACAGTTTTTAGTGCACTTGGTTTTGAAATACATTT
66 TTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTC
*
1771392 TGGACCAAAAGTATCGACACTTGTTTGATTTGTGTCGATACTTTTTTTACACATGTTTTCTCAAA
131 TGGACCAAAAGTATCGACACTTGTTTGATTTGTGTCGATACTTTTTTTACACCTGTTTTCTCAAA
*
1771457 AACC
196 AACT
* * *
1771461 GGTATATTTAGACCGGTTATATTGTTAATATACCTATTACATTATAATTATAGTTTTCGACGTTT
1 GGTATATTTAGACCGGTTATATTGCTAATCTACCTATTACATTATAATTATAGTTTTCGATGTTT
* *
1771526 TTGGGATCGATACTTGTTACAAATGTATCGACACTTTTTAGTGCACTTGGCTTTGAAATACATTC
66 TTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTC
* *
1771591 TGGACTAAAAGTATCGACACTTGTTTGATTTGTGTCGATACTTTTTTTACACATGTTTTCTCAAA
131 TGGACCAAAAGTATCGACACTTGTTTGATTTGTGTCGATACTTTTTTTACACCTGTTTTCTCAAA
1771656 AACT
196 AACT
* * * *
1771660 AGTATATTTAGACTGATTATATTGCTAATATACCTATTACATTATAATTATAGTTTTCGATGTTT
1 GGTATATTTAGACCGGTTATATTGCTAATCTACCTATTACATTATAATTATAGTTTTCGATGTTT
*
1771725 TTGGGATCGACACTTTTTACAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAAT---TTG
66 TTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATT-
* * * ** * * * **
1771787 CT-AATC-TACCTAT-TACA-TTATAATT-ATAGTT-T-TCGAT-GTTTTTGGGATCGACACT-T
130 CTGGACCAAAAGTATCGACACTTGT--TTGAT--TTGTGTCGATACTTTTT-TTA-C-AC-CTGT
* * *
1771843 GTT-ACAAATGTA-T
187 TTTCTCAAA--AACT
** * ** ** * * * * * ** ** * * * *
1771856 CGACAATTTTTAGTGCACTTGGTTTTG--AA-ATACATTTTGGACCAAAAGTATCGATACTT-G-
1 -G-GTATATTTAGACCGGTT-ATATTGCTAATCTACCTATTACATTATAATTATAG-T-TTTCGA
* * * ** * * * ** **
1771916 T-TTGATTTGTG-TCGATACTTTTTTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTT
61 TGTT--TTTGGGATCGACAC-TTGTTACAAATG---TATC-GACA-C--T-T-TTTAGTGCACTT
* * * * ** ** * * * * *
1771979 -ATATTGCTAATCTACCTAT-TACATTATAATTAT--A-A-TT-TTCGATGTTTTTGGGATCGAC
114 GGTTTTG--AA-ATACAT-TCTGGACCAAAAGTATCGACACTTGTT---TG-ATTTGTG-TCGAT
* * *****
1772037 ACTTGTTACAAATGTATCGACACT-TTTTAGTGCACTTGGTTT
170 ACTT-TT-----TTTA-C-AC-CTGTTTT-CT-CA--AAAACT
* * * * * * * ** * * *
1772079 GAAATACATTTTGGACCAGAAGTATCGACACTTGTTCGATTTGTGTCGA-TAC-TT-T-TTTACA
1 G--GTATA-TTTAGACC-G--GT-T--ATA-TTG--CTA-ATCTACCTATTACATTATAATTATA
* ******* * ** * ** * * *
1772140 CCTGTTTTCTAAAAAACCGGTATATTTAGACCGGTTA-TATTGCTAATCTAC-CTATTACATTA-
53 ---GTTTTCGATGTTTTTGG--GATCGACACTTGTTACAAATG-T-ATCGACACT-TT---TTAG
* * * * ** ** * *
1772202 T-AATTATGGTTTTCG--ATA-TTTTTGG-------G-ATCGACACTTGTTACAAATGTATCGAC
107 TGCACT-TGGTTTT-GAAATACATTCTGGACCAAAAGTATCGACACTTGTTTGATTTGTGTCGAT
*** * * *
1772255 ACTTTTTAGGGCACTTGGTTT-TGAAATACATTCT
170 ACTTTTT-TTACACCTGTTTTCTCAAA-A-A--CT
* * * * * * ** * *
1772289 GGACAAAAAGTATCGACACTTGTT-TGATTTG-T-GTCTA--TACTT-TTTTTTACA-CAT-GTT
1 GG---TATA-TTTAGAC-C-GGTTAT-A-TTGCTAATCTACCTA-TTACATTATA-ATTATAG-T
* * * * *
1772346 TTCTCAAAAACTAGTATATTT-AGA-C--CGCTTGATACAAATGTATCGACACTTTTTAGGGCAC
55 TT-TC---GA-T-GT-T-TTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGTGCAC
*
1772407 TTGGTTTTGAAATACATTCTGGA-CAAAATGTATCGACACTTGTTTGATTTGTGTCTATACTTTT
112 TTGGTTTTGAAATACATTCTGGACCAAAA-GTATCGACACTTGTTTGATTTGTGTCGATACTTTT
* *
1772471 TTTACACATGTTTTCTCAAAAACC
176 TTTACACCTGTTTTCTCAAAAACT
* *
1772495 GGTATATTTAGATCGGTTATATTGCTAATCTATCTATTACATTATAATTATAGTTTTCGATGTTT
1 GGTATATTTAGACCGGTTATATTGCTAATCTACCTATTACATTATAATTATAGTTTTCGATGTTT
*
1772560 TTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTA
66 TTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTC
* * * *
1772625 TGGACCAAAAGTATCGACACTTATTCGATTTGTGTGGATACTTTTTTTACATCTG-TTTCTCAAA
131 TGGACCAAAAGTATCGACACTTGTTTGATTTGTGTCGATACTTTTTTTACACCTGTTTTCTCAAA
*
1772689 AATT
196 AACT
* *
1772693 GATATATTTAGACCGGTTATATTGCTAATCTACCTATTACATTATAATTATAGTTTTCGATATTT
1 GGTATATTTAGACCGGTTATATTGCTAATCTACCTATTACATTATAATTATAGTTTTCGATGTTT
* *
1772758 TTGGGATCGACACTTGTTACAAATGTATTGACACTTTTTAGGGCACTTGGTTTTGAAATACATTC
66 TTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTC
* *
1772823 TGGACCAAAAGTATCGATACTTGTTCGATTTGTGTCGATACTTTTTTTACACCTGTTTTCTCAAA
131 TGGACCAAAAGTATCGACACTTGTTTGATTTGTGTCGATACTTTTTTTACACCTGTTTTCTC-AA
1772888 AAAC-
195 AAACT
* * *
1772892 GGTATATTCAGACTGATTATATTGCTAATCTACCTATTACATTATAATTATAGTTTTCGATGTTT
1 GGTATATTTAGACCGGTTATATTGCTAATCTACCTATTACATTATAATTATAGTTTTCGATG-TT
*
1772957 TTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATGCATT
65 TTTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATT
* * * *
1773022 CTGGACCAAAAGTATCGACACTTGTTCGA-TTGTGTCAATACTTTTTTTATACATGTTTTCTCAA
130 CTGGACCAAAAGTATCGACACTTGTTTGATTTGTGTCGATACTTTTTTTACACCTGTTTTCTCAA
*
1773086 AAACC
195 AAACT
* *
1773091 GGTATATTTAGACCGGTTATATTGTTAATTTACCTATTACATTATAATTAT-GATTTTCGATGTT
1 GGTATATTTAGACCGGTTATATTGCTAATCTACCTATTACATTATAATTATAG-TTTTCGATGTT
*
1773155 TTTGGGATCGACACTTGTTATAAATGTATCGACAC
65 TTTGGGATCGACACTTGTTACAAATGTATCGACAC
1773190 ATAAGTTTAC
Statistics
Matches: 2639, Mismatches: 327, Indels: 315
0.80 0.10 0.10
Matches are distributed among these distances:
193 8 0.00
194 11 0.00
195 17 0.01
196 36 0.01
197 26 0.01
198 241 0.09
199 1703 0.65
200 312 0.12
201 16 0.01
202 29 0.01
203 21 0.01
204 6 0.00
205 6 0.00
206 12 0.00
207 7 0.00
208 3 0.00
209 13 0.00
210 43 0.02
211 16 0.01
212 10 0.00
213 5 0.00
214 2 0.00
215 2 0.00
217 2 0.00
218 11 0.00
219 15 0.01
220 2 0.00
221 1 0.00
222 5 0.00
223 5 0.00
224 5 0.00
225 1 0.00
226 2 0.00
227 3 0.00
228 2 0.00
229 5 0.00
230 4 0.00
231 7 0.00
232 3 0.00
233 4 0.00
234 5 0.00
235 4 0.00
236 4 0.00
237 4 0.00
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (199 bp):
GGTATATTTAGACCGGTTATATTGCTAATCTACCTATTACATTATAATTATAGTTTTCGATGTTT
TTGGGATCGACACTTGTTACAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTC
TGGACCAAAAGTATCGACACTTGTTTGATTTGTGTCGATACTTTTTTTACACCTGTTTTCTCAAA
AACT
Found at i:1771743 original size:104 final size:104
Alignment explanation
Indices: 1771634--1771861 Score: 257
Period size: 103 Copynumber: 2.2 Consensus size: 104
1771624 GTCGATACTT
* * * * * *
1771634 TTTTTACACATGTTTTC-TCAAAAACTAGTATATTTAG-ACTGATTATATTGCTAATATACCTAT
1 TTTTTACAAATGTTATCGACAAAAACTAGTACACTTAGTACTGA-AAT-TTGCTAATATACCTAT
1771697 TACATTATAATTATAGTTTTCGATGTTTTTGGGATCGACAC
64 TACATTATAATTATAGTTTTCGATGTTTTTGGGATCGACAC
***** * * ** *
1771738 TTTTTACAAATG-TATCGACACTTTTTAGTGCACTTGGTTTTGAAATTTGCTAATCTACCTATTA
1 TTTTTACAAATGTTATCGACAAAAACTAGTACACTTAGTACTGAAATTTGCTAATATACCTATTA
1771802 CATTATAATTATAGTTTTCGATGTTTTTGGGATCGACAC
66 CATTATAATTATAGTTTTCGATGTTTTTGGGATCGACAC
*
1771841 TTGTTACAAATG-TATCGACAA
1 TTTTTACAAATGTTATCGACAA
1771862 TTTTTAGTGC
Statistics
Matches: 104, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
103 78 0.75
104 23 0.22
105 3 0.03
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.43
Consensus pattern (104 bp):
TTTTTACAAATGTTATCGACAAAAACTAGTACACTTAGTACTGAAATTTGCTAATATACCTATTA
CATTATAATTATAGTTTTCGATGTTTTTGGGATCGACAC
Found at i:1771799 original size:103 final size:103
Alignment explanation
Indices: 1771681--1771886 Score: 385
Period size: 103 Copynumber: 2.0 Consensus size: 103
1771671 ACTGATTATA
*
1771681 TTGCTAATATACCTATTACATTATAATTATAGTTTTCGATGTTTTTGGGATCGACACTTTTTACA
1 TTGCTAATATACCTATTACATTATAATTATAGTTTTCGATGTTTTTGGGATCGACACTTGTTACA
*
1771746 AATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAAT
66 AATGTATCGACAATTTTTAGTGCACTTGGTTTTGAAAT
*
1771784 TTGCTAATCTACCTATTACATTATAATTATAGTTTTCGATGTTTTTGGGATCGACACTTGTTACA
1 TTGCTAATATACCTATTACATTATAATTATAGTTTTCGATGTTTTTGGGATCGACACTTGTTACA
1771849 AATGTATCGACAATTTTTAGTGCACTTGGTTTTGAAAT
66 AATGTATCGACAATTTTTAGTGCACTTGGTTTTGAAAT
1771887 ACATTTTGGA
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 100 1.00
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (103 bp):
TTGCTAATATACCTATTACATTATAATTATAGTTTTCGATGTTTTTGGGATCGACACTTGTTACA
AATGTATCGACAATTTTTAGTGCACTTGGTTTTGAAAT
Found at i:1772077 original size:301 final size:301
Alignment explanation
Indices: 1771486--1772083 Score: 1036
Period size: 302 Copynumber: 2.0 Consensus size: 301
1771476 GTTATATTGT
*
1771486 TAATATACCTATTACATTATAATTATAGTTTTCGACGTTTTTGGGATCGATACTTGTTACAAATG
1 TAATATACCTATTACATTATAATTATAGTTTTCGACGTTTTTGGGATCGACACTTGTTACAAATG
* *
1771551 TATCGACACTTTTTAGTGCACTTGGCTTTGAAATACATTCTGGACTAAAAGTATCGACACTTGTT
66 TATCGACAATTTTTAGTGCACTTGGCTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTT
* *
1771616 TGATTTGTGTCGATACTTTTTTTACACATGTTTTCTCAAAAACTAGTATATTTAGACTGATTATA
131 TGATTTGTGTCGATACTTTTTTTACACATGTTTTCTCAAAAACCAGTATATTTAGACCGATTATA
* *
1771681 TTGCTAATATACCTATTACATTATAATTATAGTTTTCGATGTTTTTGGGATCGACACTTTTTACA
196 TTGCTAATATACCTATTACATTATAATTATAATTTTCGATGTTTTTGGGATCGACACTTGTTACA
1771746 AATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATTTGC
261 AATGTATCGACACTTTTTAGTGCACTTGG-TTTGAAATTTGC
* *
1771788 TAATCTACCTATTACATTATAATTATAGTTTTCGATGTTTTTGGGATCGACACTTGTTACAAATG
1 TAATATACCTATTACATTATAATTATAGTTTTCGACGTTTTTGGGATCGACACTTGTTACAAATG
* * *
1771853 TATCGACAATTTTTAGTGCACTTGGTTTTGAAATACATTTTGGACCAAAAGTATCGATACTTGTT
66 TATCGACAATTTTTAGTGCACTTGGCTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTT
* * *
1771918 TGATTTGTGTCGATAC-TTTTTTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTTATA
131 TGATTTGTGTCGATACTTTTTTTACACATGTTTTCTCAAAAACCAGTATATTTAGACCGATTATA
*
1771982 TTGCTAATCTACCTATTACATTATAATTATAATTTTCGATGTTTTTGGGATCGACACTTGTTACA
196 TTGCTAATATACCTATTACATTATAATTATAATTTTCGATGTTTTTGGGATCGACACTTGTTACA
1772047 AATGTATCGACACTTTTTAGTGCACTTGGTTTGAAAT
261 AATGTATCGACACTTTTTAGTGCACTTGGTTTGAAAT
1772084 ACATTTTGGA
Statistics
Matches: 280, Mismatches: 16, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
300 8 0.03
301 134 0.48
302 138 0.49
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.43
Consensus pattern (301 bp):
TAATATACCTATTACATTATAATTATAGTTTTCGACGTTTTTGGGATCGACACTTGTTACAAATG
TATCGACAATTTTTAGTGCACTTGGCTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTT
TGATTTGTGTCGATACTTTTTTTACACATGTTTTCTCAAAAACCAGTATATTTAGACCGATTATA
TTGCTAATATACCTATTACATTATAATTATAATTTTCGATGTTTTTGGGATCGACACTTGTTACA
AATGTATCGACACTTTTTAGTGCACTTGGTTTGAAATTTGC
Found at i:1772126 original size:197 final size:198
Alignment explanation
Indices: 1771784--1772372 Score: 1018
Period size: 197 Copynumber: 3.0 Consensus size: 198
1771774 GTTTTGAAAT
1771784 TTGCTAATCTACCTATTACATTATAATTATAGTTTTCGATGTTTTTGGGATCGACACTTGTTACA
1 TTGCTAATCTACCTATTACATTATAATTATAGTTTTCGATGTTTTTGGGATCGACACTTGTTACA
* *
1771849 AATGTATCGACAATTTTTAGTGCACTTGGTTTTGAAATACATTTTGGACCAAAAGTATCGATACT
66 AATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTTTGGACCAAAAGTATCGACACT
1771914 TGTTTGATTTGTGTCGATACTTTTTTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTT
131 TGTTTGATTTGTGTCGATACTTTTTTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTT
1771979 ATA
196 ATA
*
1771982 TTGCTAATCTACCTATTACATTATAATTATAATTTTCGATGTTTTTGGGATCGACACTTGTTACA
1 TTGCTAATCTACCTATTACATTATAATTATAGTTTTCGATGTTTTTGGGATCGACACTTGTTACA
*
1772047 AATGTATCGACACTTTTTAGTGCACTTGG-TTTGAAATACATTTTGGACCAGAAGTATCGACACT
66 AATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTTTGGACCAAAAGTATCGACACT
* *
1772111 TGTTCGATTTGTGTCGATACTTTTTTACACCTGTTTTCTAAAAAACCGGTATATTTAGACCGGTT
131 TGTTTGATTTGTGTCGATACTTTTTTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTT
1772176 ATA
196 ATA
* *
1772179 TTGCTAATCTACCTATTACATTATAATTATGGTTTTCGATATTTTTGGGATCGACACTTGTTACA
1 TTGCTAATCTACCTATTACATTATAATTATAGTTTTCGATGTTTTTGGGATCGACACTTGTTACA
* * *
1772244 AATGTATCGACACTTTTTAGGGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACT
66 AATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTTTGGACCAAAAGTATCGACACT
* * **
1772309 TGTTTGATTTGTGTCTATACTTTTTTTTACACATGTTTTCTCAAAAACTAGTATATTTAGACCG
131 TGTTTGATTTGTGTCGATAC--TTTTTTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCG
1772373 CTTGATACAA
Statistics
Matches: 369, Mismatches: 19, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
197 189 0.51
198 142 0.38
200 38 0.10
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (198 bp):
TTGCTAATCTACCTATTACATTATAATTATAGTTTTCGATGTTTTTGGGATCGACACTTGTTACA
AATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTTTGGACCAAAAGTATCGACACT
TGTTTGATTTGTGTCGATACTTTTTTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTT
ATA
Found at i:1772855 original size:535 final size:532
Alignment explanation
Indices: 1771840--1772889 Score: 1807
Period size: 535 Copynumber: 2.0 Consensus size: 532
1771830 GGGATCGACA
* * *
1771840 CTTGTTACAAATGTATCGACAATTTTTAGTGCACTTGGTTTTGAAATACATTTTGGACCAAAAGT
1 CTTGATACAAATGTATCGACAATTTTTAGGGCACTTGGTTTTGAAATACATTCTGGACCAAAAGT
* *
1771905 ATCGATACTTGTTTGATTTGTGTCGATACTTTTTTACACCTGTTTTCTCAAAAACCGGTATATTT
66 ATCGACACTTGTTTGATTTGTGTCGATACTTTTTTACACATGTTTTCTCAAAAACCGGTATATTT
1771970 AGACCGGTTATATTGCTAATCTACCTATTACATTATAATTATAATTTTCGATGTTTTTGGGATCG
131 AGACCGGTTATATTGCTAATCTACCTATTACATTATAATTATAATTTTCGATGTTTTTGGGATCG
* *
1772035 ACACTTGTTACAAATGTATCGACACTTTTTAGTGCACTTGGTTTGAAATACATTTTGGACCAGAA
196 ACACTTGTTACAAATGTATCGACACTTTTTAGTGCACTTGGTTTGAAATACATTATGGACCAAAA
* *
1772100 GTATCGACACTTGTTCGATTTGTGTCGATACTTTTTTACACCTGTTTTCTAAAAAACCGGTATAT
261 GTATCGACACTTATTCGATTTGTGTCGATACTTTTTTACACCTGTTTTCTAAAAAACCGATATAT
*
1772165 TTAGACCGGTTATATTGCTAATCTACCTATTACATTATAATTATGGTTTTCGATATTTTTGGGAT
326 TTAGACCGGTTATATTGCTAATCTACCTATTACATTATAATTATAGTTTTCGATATTTTTGGGAT
1772230 CGACACTTGTTACAAATGTATCGACACTTTTTAGGGCACTTGGTTTTGAAATACATTCTGGACAA
391 CGACACTTGTTACAAATGTATCGACACTTTTTAGGGCACTTGGTTTTGAAATACATTCTGGACAA
* *
1772295 AAAGTATCGACACTTGTTTGATTTGTGTCTATACTTTTTTTTACACATGTTTTCTCAAAAACTAG
456 AAAGTATCGACACTTGTTCGATTTGTGTCGATAC-TTTTTTTACACATGTTTTCTCAAAAACTAG
1772360 TATATTTAGACCG
520 TATATTTAGACCG
*
1772373 CTTGATACAAATGTATCGACACTTTTTAGGGCACTTGGTTTTGAAATACATTCTGGA-CAAAATG
1 CTTGATACAAATGTATCGACAATTTTTAGGGCACTTGGTTTTGAAATACATTCTGGACCAAAA-G
*
1772437 TATCGACACTTGTTTGATTTGTGTCTATACTTTTTTTACACATGTTTTCTCAAAAACCGGTATAT
65 TATCGACACTTGTTTGATTTGTGTCGATAC-TTTTTTACACATGTTTTCTCAAAAACCGGTATAT
* * *
1772502 TTAGATCGGTTATATTGCTAATCTATCTATTACATTATAATTATAGTTTTCGATGTTTTTGGGAT
129 TTAGACCGGTTATATTGCTAATCTACCTATTACATTATAATTATAATTTTCGATGTTTTTGGGAT
1772567 CGACACTTGTTACAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTATGGACCA
194 CGACACTTGTTACAAATGTATCGACACTTTTTAGTGCACTTGG-TTTGAAATACATTATGGACCA
* * * **
1772632 AAAGTATCGACACTTATTCGATTTGTGTGGATACTTTTTTTACATCTG-TTTCTCAAAAATTGAT
258 AAAGTATCGACACTTATTCGATTTGTGTCGATAC-TTTTTTACACCTGTTTTCTAAAAAACCGAT
1772696 ATATTTAGACCGGTTATATTGCTAATCTACCTATTACATTATAATTATAGTTTTCGATATTTTTG
322 ATATTTAGACCGGTTATATTGCTAATCTACCTATTACATTATAATTATAGTTTTCGATATTTTTG
*
1772761 GGATCGACACTTGTTACAAATGTATTGACACTTTTTAGGGCACTTGGTTTTGAAATACATTCTGG
387 GGATCGACACTTGTTACAAATGTATCGACACTTTTTAGGGCACTTGGTTTTGAAATACATTCTGG
* * *
1772826 ACCAAAAGTATCGATACTTGTTCGATTTGTGTCGATACTTTTTTTACACCTGTTTTCTCAAAAA
452 ACAAAAAGTATCGACACTTGTTCGATTTGTGTCGATACTTTTTTTACACATGTTTTCTCAAAAA
1772890 ACGGTATATT
Statistics
Matches: 487, Mismatches: 26, Indels: 7
0.94 0.05 0.01
Matches are distributed among these distances:
532 5 0.01
533 82 0.17
534 163 0.33
535 225 0.46
536 12 0.02
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.41
Consensus pattern (532 bp):
CTTGATACAAATGTATCGACAATTTTTAGGGCACTTGGTTTTGAAATACATTCTGGACCAAAAGT
ATCGACACTTGTTTGATTTGTGTCGATACTTTTTTACACATGTTTTCTCAAAAACCGGTATATTT
AGACCGGTTATATTGCTAATCTACCTATTACATTATAATTATAATTTTCGATGTTTTTGGGATCG
ACACTTGTTACAAATGTATCGACACTTTTTAGTGCACTTGGTTTGAAATACATTATGGACCAAAA
GTATCGACACTTATTCGATTTGTGTCGATACTTTTTTACACCTGTTTTCTAAAAAACCGATATAT
TTAGACCGGTTATATTGCTAATCTACCTATTACATTATAATTATAGTTTTCGATATTTTTGGGAT
CGACACTTGTTACAAATGTATCGACACTTTTTAGGGCACTTGGTTTTGAAATACATTCTGGACAA
AAAGTATCGACACTTGTTCGATTTGTGTCGATACTTTTTTTACACATGTTTTCTCAAAAACTAGT
ATATTTAGACCG
Found at i:1773582 original size:18 final size:19
Alignment explanation
Indices: 1773535--1773583 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
1773525 TTACATTCAC
*
1773535 ATACAAAATTATAAATCAT
1 ATACAAAATTAAAAATCAT
* *
1773554 ATTCAAAATTAAAAATCTT
1 ATACAAAATTAAAAATCAT
1773573 ATAC-AAATTAA
1 ATACAAAATTAA
1773584 CCATGCATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 7 0.27
19 19 0.73
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (19 bp):
ATACAAAATTAAAAATCAT
Found at i:1775147 original size:12 final size:12
Alignment explanation
Indices: 1775126--1775163 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
1775116 CATCTCTTTT
*
1775126 ATTTCACCCTTC
1 ATTTCCCCCTTC
1775138 ATTTCCCCCTTC
1 ATTTCCCCCTTC
1775150 ATTTCCCCCTTC
1 ATTTCCCCCTTC
1775162 AT
1 AT
1775164 CCAAGTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.13, C:0.45, G:0.00, T:0.42
Consensus pattern (12 bp):
ATTTCCCCCTTC
Found at i:1776643 original size:18 final size:18
Alignment explanation
Indices: 1776620--1776658 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1776610 TACTATCAAC
1776620 ATTTAAAATTTGTAAT-CA
1 ATTTAAAATTT-TAATCCA
*
1776638 ATTTAAAGTTTTAATCCA
1 ATTTAAAATTTTAATCCA
1776656 ATT
1 ATT
1776659 ACCATTTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (18 bp):
ATTTAAAATTTTAATCCA
Found at i:1777714 original size:21 final size:22
Alignment explanation
Indices: 1777658--1777722 Score: 87
Period size: 23 Copynumber: 3.0 Consensus size: 22
1777648 CACCACAGCT
*
1777658 CGTATAATGCACCGAAGTGCCA
1 CGTAGAATGCACCGAAGTGCCA
* *
1777680 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAA-TGCACCGAAGTGCCA
1777703 CG-AGAATGCACCGAAGTGCC
1 CGTAGAATGCACCGAAGTGCC
1777723 TATAAGATGT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 13 0.34
22 10 0.26
23 15 0.39
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.17
Consensus pattern (22 bp):
CGTAGAATGCACCGAAGTGCCA
Found at i:1778315 original size:135 final size:134
Alignment explanation
Indices: 1778028--1778298 Score: 479
Period size: 135 Copynumber: 2.0 Consensus size: 134
1778018 ACTTTCAGAT
1778028 ATCACGTAGCTCATATTCACTTTTTATACTATTTCATATTTCTTGTCACATTACTTATATCTTAC
1 ATCACG-AGCTCATATTCACTTTTTATACTATTTCATATTTCTTGTCACATTACTTATATCTTAC
1778093 TTTTATGTCTTATCCTATATATATAGATATGCACATGTTCATAACCCATCTTCCTATATATATAT
65 TTTTATGTCTTATCCTATATATATAGATATGCACATGTTCATAACCCATCTTCCTATATATATAT
*
1778158 ATGAT
130 ATGAC
1778163 ATCACGTAGCTCATATTCACTTTTTATACTATTTCATATTTCTTGTCACATTACTTATATCTTAC
1 ATCACG-AGCTCATATTCACTTTTTATACTATTTCATATTTCTTGTCACATTACTTATATCTTAC
1778228 TTTTATGTCTTATCCTATATATATATAGATATGCACATGTTCATATAACCCATCTTCCTATATAT
65 TTTTATGTCTTATCC--TATATATATAGATATGCACATGTTC--ATAACCCATCTTCCTATATAT
1778293 ATATAT
126 ATATAT
1778299 ACACATCATT
Statistics
Matches: 132, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
135 80 0.61
137 25 0.19
139 27 0.20
ACGTcount: A:0.29, C:0.19, G:0.06, T:0.46
Consensus pattern (134 bp):
ATCACGAGCTCATATTCACTTTTTATACTATTTCATATTTCTTGTCACATTACTTATATCTTACT
TTTATGTCTTATCCTATATATATAGATATGCACATGTTCATAACCCATCTTCCTATATATATATA
TGAC
Found at i:1780319 original size:19 final size:20
Alignment explanation
Indices: 1780272--1780320 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
1780262 CATTTATACA
1780272 ACCTA-AAATATCATTTTCT
1 ACCTATAAATATCATTTTCT
1780291 ACCTAT-AATATCATTTT-T
1 ACCTATAAATATCATTTTCT
1780309 ACCTATAAATAT
1 ACCTATAAATAT
1780321 TAACTAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.25
19 21 0.75
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.43
Consensus pattern (20 bp):
ACCTATAAATATCATTTTCT
Found at i:1781207 original size:183 final size:182
Alignment explanation
Indices: 1780706--1781911 Score: 1627
Period size: 183 Copynumber: 6.6 Consensus size: 182
1780696 TACGCGTACT
* * ** *
1780706 TATTAAAGTATCGACACTTTCATCATATCTTGTATCTATTTACCGGTTTTGTC-ATTTTGAGACC
1 TATTAAATTATCGACACTTTCAACATATCCGGTAGCT-TTTACCGGTTTTGTCAATTTTGAGA-C
* * *
1780770 A-GTTTTATCATATTTTTACCTATTATATTGTTCTGGATCGATATATTTTCATAAAGTGTCGACA
64 ATGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACA
* *
1780834 CTTTTTAAGCGTTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
129 CTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
* ** * **
1780888 TATTAAATTATCGACACTTTCAACATATCCGGTAACTTTTTTCGGTTTTTTCTTTTTTGAGACAT
1 TATTAAATTATCGACACTTTCAACATATCCGGTAGCTTTTACCGGTTTTGTCAATTTTGAGACAT
* * *
1780953 GTTTTATCATATTTTTACCTGTTATATTGGTAAGGATCGATACATTTTCATAAAGCGTCGACACT
66 GTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACACT
* *
1781018 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAAAAAGTGTCGATACTAA
131 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
* *
1781070 TATTAAATTATCGACACTTTCAATATATCCGGTAGCGTTTTACTGGTTTTGTCAATTTTGAGACA
1 TATTAAATTATCGACACTTTCAACATATCCGGTAGC-TTTTACCGGTTTTGTCAATTTTGAGACA
* *
1781135 TGTTTTATTATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCAACAC
65 TGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACAC
1781200 TTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
130 TTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
* * * * * *
1781253 TATTAAATTATCGACACTTTTAACATATCCGGTAACTTTTTCCGATTTTGTCATTTTTGAGACCT
1 TATTAAATTATCGACACTTTCAACATATCCGGTAGCTTTTACCGGTTTTGTCAATTTTGAGACAT
* * * * ** * *
1781318 GTTTTATCATATTTTTATCTGTTATATTATTGTAGATCGAT--ATTTTTTTAAAATATCGACACT
66 GTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACACT
* * *
1781381 TTATAGGCGCTATAACTTCATCTCTTTTAAATTCAGAAAGTTTCGATACTTA
131 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
* * * *
1781433 TATTAAATTATCGACACTTTCAATATATCTGGTAGCATTTTACTGGTTTTGTCAATTTTGAGACC
1 TATTAAATTATCGACACTTTCAACATATCCGGTAGC-TTTTACCGGTTTTGTCAATTTTGAGACA
*
1781498 TGTTTTATCATATTTTTACCCGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACAC
65 TGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACAC
* * *
1781563 TTTTTAAGCGCAATAACTTTTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
130 TTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
* * ** ** * *
1781616 TATTAAATTATCGATACTTTTAACATATCCTCATAATTTTTTCCGGTTTTGTCATTTTTGAGACA
1 TATTAAATTATCGACACTTTCAACATATCC-GGTAGCTTTTACCGGTTTTGTCAATTTTGAGACA
* * * *
1781681 TGTTTTATCATATTTTTACCTGTTACATTGGTAAGAATCGATACATTTTCATAAAGTGTCGACAC
65 TGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACAC
*
1781746 TTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTTTCGATACTTA
130 TTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
*
1781799 TATTAAATTATCGACAC--TCGACACATATCCGGTAGCGTTTTACCGGTTTTGTC-ATTTTGGGA
1 TATTAAATTATCGACACTTTC-A-ACATATCCGGTAGC-TTTTACCGGTTTTGTCAATTTTGAGA
** * * * * * *
1781861 CCGGTTTT-GCAATATTTGTACCTGTAATATTGCTATGGGTCGATCCATTTT
63 CATGTTTTATC-ATATTTTTACCTGTTATATTGTTATGGATCGATACATTTT
1781912 TCATTTGTAT
Statistics
Matches: 894, Mismatches: 119, Indels: 22
0.86 0.11 0.02
Matches are distributed among these distances:
180 98 0.11
181 77 0.09
182 289 0.32
183 428 0.48
184 2 0.00
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (182 bp):
TATTAAATTATCGACACTTTCAACATATCCGGTAGCTTTTACCGGTTTTGTCAATTTTGAGACAT
GTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACACT
TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
Found at i:1781733 original size:546 final size:547
Alignment explanation
Indices: 1780706--1781856 Score: 1684
Period size: 546 Copynumber: 2.1 Consensus size: 547
1780696 TACGCGTACT
* * ** *
1780706 TATTAAAGTATCGACACTTTCATCATATCTTGTATCTATTTACCGGTTTTGTCA-TTTTGAGACC
1 TATTAAATTATCGACACTTTCAACATATCCGGTAACT-TTTACCGGTTTTGTCATTTTTGAGACC
* * * *
1780770 AGTTTTATCATATTTTTACCTATTATATTGTTCTGGATCGATATATTTTCATAAAGTGTCGACAC
65 AGTTTTATCATATTTTTACCTATTATATTATTCTAGATCGATATATTTTCATAAAATATCGACAC
* * *
1780835 TTTTTAAGCGTTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATC
130 TTTATAAGCGCTATAACTTCATCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATC
* * * **
1780900 GACACTTTCAACATATCCGGTAACTTTTTTCGGTTTTTTCTTTTTTGAGACATGTTTTATCATAT
195 GACACTTTCAACATATCCGGTAACATTTTACGGTTTTGTCAATTTTGAGACATGTTTTATCATAT
* * *
1780965 TTTTACCTGTTATATTGGTAAGGATCGATACATTTTCATAAAGCGTCGACACTTTTTAGGCGCTA
260 TTTTACCCGTTATATTGGTAAGGATCGATACATTTTCATAAAGCGTCGACACTTTTTAAGCGCAA
*
1781030 TAACTTCTTCTCTTTTAAATTCAAAAAGTGTCGATACTAATATTAAATTATCGACACTTTCAATA
325 TAACTTCTTCTCTTTTAAATTCAAAAAGTGTCGATACTAATATTAAATTATCGACACTTTCAACA
** * * *
1781095 TATCCGGTAGCGTTTTACTGGTTTTGTCAATTTTGAGACATGTTTTATTATATTTTTACCTGTTA
390 TATCCCATAGAGTTTTACCGGTTTTGTCAATTTTGAGACATGTTTTATCATATTTTTACCTGTTA
* * * *
1781160 TATTGTTATGGATCGATACATTTTCATAAAGTGTCAACACTTTTTAGGCGCTATAACTTCTTCTC
455 CATTGGTAAGAATCGATACATTTTCATAAAGTGTCAACACTTTTTAGGCGCTATAACTTCTTCTC
1781225 TTTTAAATTCAGAAAGTGTCGATACTTA
520 TTTTAAATTCAGAAAGTGTCGATACTTA
* * * *
1781253 TATTAAATTATCGACACTTTTAACATATCCGGTAACTTTTTCCGATTTTGTCATTTTTGAGACCT
1 TATTAAATTATCGACACTTTCAACATATCCGGTAACTTTTACCGGTTTTGTCATTTTTGAGACCA
* * * *
1781318 GTTTTATCATATTTTTATCTGTTATATTATTGTAGATCGATAT-TTTT-TTAAAATATCGACACT
66 GTTTTATCATATTTTTACCTATTATATTATTCTAGATCGATATATTTTCATAAAATATCGACACT
* *
1781381 TTATAGGCGCTATAACTTCATCTCTTTTAAATTCAGAAAGTTTCGATACTTATATTAAATTATCG
131 TTATAAGCGCTATAACTTCATCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCG
* * * *
1781446 ACACTTTCAATATATCTGGTAGCATTTTACTGGTTTTGTCAATTTTGAGACCTGTTTTATCATAT
196 ACACTTTCAACATATCCGGTAACATTTTAC-GGTTTTGTCAATTTTGAGACATGTTTTATCATAT
* * *
1781511 TTTTACCCGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACACTTTTTAAGCGCAA
260 TTTTACCCGTTATATTGGTAAGGATCGATACATTTTCATAAAGCGTCGACACTTTTTAAGCGCAA
* * * * *
1781576 TAACTTTTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGATACTTTTAACA
325 TAACTTCTTCTCTTTTAAATTCAAAAAGTGTCGATACTAATATTAAATTATCGACACTTTCAACA
* * *
1781641 TATCCTCATA-ATTTTTTCCGGTTTTGTCATTTTTGAGACATGTTTTATCATATTTTTACCTGTT
390 TATCC-CATAGAGTTTTACCGGTTTTGTCAATTTTGAGACATGTTTTATCATATTTTTACCTGTT
*
1781705 ACATTGGTAAGAATCGATACATTTTCATAAAGTGTCGACACTTTTTAGGCGCTATAACTTCTTCT
454 ACATTGGTAAGAATCGATACATTTTCATAAAGTGTCAACACTTTTTAGGCGCTATAACTTCTTCT
*
1781770 CTTTTAAATTCAGAAAGTTTCGATACTTA
519 CTTTTAAATTCAGAAAGTGTCGATACTTA
*
1781799 TATTAAATTATCGACAC--TCGACACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTT
1 TATTAAATTATCGACACTTTC-A-ACATATCCGGTAAC-TTTTACCGGTTTTGTCATTTT
1781857 GGGACCGGTT
Statistics
Matches: 537, Mismatches: 61, Indels: 12
0.88 0.10 0.02
Matches are distributed among these distances:
544 1 0.00
545 99 0.18
546 337 0.63
547 100 0.19
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.44
Consensus pattern (547 bp):
TATTAAATTATCGACACTTTCAACATATCCGGTAACTTTTACCGGTTTTGTCATTTTTGAGACCA
GTTTTATCATATTTTTACCTATTATATTATTCTAGATCGATATATTTTCATAAAATATCGACACT
TTATAAGCGCTATAACTTCATCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCG
ACACTTTCAACATATCCGGTAACATTTTACGGTTTTGTCAATTTTGAGACATGTTTTATCATATT
TTTACCCGTTATATTGGTAAGGATCGATACATTTTCATAAAGCGTCGACACTTTTTAAGCGCAAT
AACTTCTTCTCTTTTAAATTCAAAAAGTGTCGATACTAATATTAAATTATCGACACTTTCAACAT
ATCCCATAGAGTTTTACCGGTTTTGTCAATTTTGAGACATGTTTTATCATATTTTTACCTGTTAC
ATTGGTAAGAATCGATACATTTTCATAAAGTGTCAACACTTTTTAGGCGCTATAACTTCTTCTCT
TTTAAATTCAGAAAGTGTCGATACTTA
Found at i:1782431 original size:2 final size:2
Alignment explanation
Indices: 1782424--1782451 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1782414 TTTCATTTAC
1782424 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
1782452 GCACGCGCGT
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:1782978 original size:2 final size:2
Alignment explanation
Indices: 1782973--1783017 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
1782963 AATTAAAAAA
*
1782973 AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1783014 AT AT
1 AT AT
1783018 TAAAAATTCA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1787039 original size:85 final size:85
Alignment explanation
Indices: 1786751--1787088 Score: 389
Period size: 85 Copynumber: 4.0 Consensus size: 85
1786741 CATGCCTTGT
* * * *
1786751 AGAGAATCTACATTATTCACATCATTTGCTTTTCATTGACATTTCACATAAACTCAGATAAACTG
1 AGAGAATCTACACTATTCACGTCATTTGCTTTTCATTGACATATCACATCAACTCAGATAAACTG
1786816 AAATAATTTACATTCAAATC
66 AAATAATTTACATTCAAATC
* * * * *
1786836 AGATAACCTACACTATTCACGTCATTTTCTTTTCATTAACATATCACATCAACTCAGATAAATTG
1 AGAGAATCTACACTATTCACGTCATTTGCTTTTCATTGACATATCACATCAACTCAGATAAACTG
*
1786901 -AATAATTT-TA-T-AGAATC
66 AAATAATTTACATTCA-AATC
* * * ** *
1786918 AGAGAATCTACACTATTCACGTCCTTTGCTTTTCATTGACATTTCATATCAACTCTTATAAACCG
1 AGAGAATCTACACTATTCACGTCATTTGCTTTTCATTGACATATCACATCAACTCAGATAAACTG
*
1786983 AAATAATTTACATTCAAATA
66 AAATAATTTACATTCAAATC
* * * * * * * **
1787003 AAAGAATATATACTATTCACGTCCTTTACTTGTCATTGACATATCACATCAACTCAGATTATTTG
1 AGAGAATCTACACTATTCACGTCATTTGCTTTTCATTGACATATCACATCAACTCAGATAAACTG
1787068 AAATAATATT-CATTCAAATC
66 AAATAAT-TTACATTCAAATC
1787088 A
1 A
1787089 TATAAGAGTA
Statistics
Matches: 210, Mismatches: 37, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
81 1 0.00
82 59 0.28
83 9 0.04
84 9 0.04
85 129 0.61
86 3 0.01
ACGTcount: A:0.38, C:0.20, G:0.07, T:0.36
Consensus pattern (85 bp):
AGAGAATCTACACTATTCACGTCATTTGCTTTTCATTGACATATCACATCAACTCAGATAAACTG
AAATAATTTACATTCAAATC
Found at i:1787047 original size:167 final size:167
Alignment explanation
Indices: 1786751--1787061 Score: 460
Period size: 167 Copynumber: 1.9 Consensus size: 167
1786741 CATGCCTTGT
* *
1786751 AGAGAATCTACATTATTCACATCATTTGCTTTTCATTGACATTTCACATAAACTCAGATAAACTG
1 AGAGAATCTACACTATTCACATCATTTGCTTTTCATTGACATTTCACATAAACTCAGATAAACCG
* * * * * *
1786816 AAATAATTTACATTCAAATCAGATAACCTACACTATTCACGTCATTTTCTTTTCATTAACATATC
66 AAATAATTTACATTCAAATAAAAGAACATACACTATTCACGTCATTTACTTGTCATTAACATATC
1786881 ACATCAACTCAGATAAATTGAATAATTTTATAGAATC
131 ACATCAACTCAGATAAATTGAATAATTTTATAGAATC
* * * * **
1786918 AGAGAATCTACACTATTCACGTCCTTTGCTTTTCATTGACATTTCATATCAACTCTTATAAACCG
1 AGAGAATCTACACTATTCACATCATTTGCTTTTCATTGACATTTCACATAAACTCAGATAAACCG
* * * *
1786983 AAATAATTTACATTCAAATAAAAGAATATATACTATTCACGTCCTTTACTTGTCATTGACATATC
66 AAATAATTTACATTCAAATAAAAGAACATACACTATTCACGTCATTTACTTGTCATTAACATATC
1787048 ACATCAACTCAGAT
131 ACATCAACTCAGAT
1787062 TATTTGAAAT
Statistics
Matches: 126, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
167 126 1.00
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.36
Consensus pattern (167 bp):
AGAGAATCTACACTATTCACATCATTTGCTTTTCATTGACATTTCACATAAACTCAGATAAACCG
AAATAATTTACATTCAAATAAAAGAACATACACTATTCACGTCATTTACTTGTCATTAACATATC
ACATCAACTCAGATAAATTGAATAATTTTATAGAATC
Found at i:1791697 original size:59 final size:56
Alignment explanation
Indices: 1791634--1791801 Score: 168
Period size: 59 Copynumber: 2.9 Consensus size: 56
1791624 AGTGGGGATT
1791634 ATTTTATAAAATTGAAAATTATTAAAGGCCTTTAATAATTAAGGTAGAAAGTTGA-GACA
1 ATTTTATAAAATTGAAAA--A-TAAAGGCC-TTAATAATTAAGGTAGAAAGTTGAGGACA
** * *
1791693 ATTTTATAAAATTGAAAAACACTAGGGGCCCTTAATAATTAA-TTAGAAAG-TGAGGATA
1 ATTTTATAAAATTG-AAAA-A-TAAAGG-CCTTAATAATTAAGGTAGAAAGTTGAGGACA
*
1791751 ATTTTATAAAATT-AAAAA-CAAGAGCCTTAATAATTAAGGTAGAAAG-TGAGG
1 ATTTTATAAAATTGAAAAATAAAG-GCCTTAATAATTAAGGTAGAAAGTTGAGG
1791802 GCCTTGCGAT
Statistics
Matches: 94, Mismatches: 10, Indels: 15
0.79 0.08 0.13
Matches are distributed among these distances:
53 14 0.15
54 13 0.14
55 1 0.01
56 4 0.04
57 3 0.03
58 23 0.24
59 30 0.32
60 6 0.06
ACGTcount: A:0.46, C:0.07, G:0.17, T:0.30
Consensus pattern (56 bp):
ATTTTATAAAATTGAAAAATAAAGGCCTTAATAATTAAGGTAGAAAGTTGAGGACA
Found at i:1793744 original size:4 final size:4
Alignment explanation
Indices: 1793735--1793759 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1793725 TTTACTACTC
1793735 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
1793760 TTTGAGGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:1794419 original size:2 final size:2
Alignment explanation
Indices: 1794412--1794436 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1794402 ATTTTTGGGT
1794412 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
1794437 GAGTTAATTA
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:1794466 original size:16 final size:16
Alignment explanation
Indices: 1794440--1794499 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 16
1794430 TATATATGAG
1794440 TTAATTATTAGTTATTA
1 TTAA-TATTAGTTATTA
*
1794457 TTAATATTAGTTATGA
1 TTAATATTAGTTATTA
1794473 TT-ATGATTA--TA-TA
1 TTAAT-ATTAGTTATTA
*
1794486 TTATTATTAGTTAT
1 TTAATATTAGTTAT
1794500 ATATATATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 11
0.71 0.06 0.22
Matches are distributed among these distances:
13 7 0.20
14 3 0.09
15 4 0.11
16 17 0.49
17 4 0.11
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (16 bp):
TTAATATTAGTTATTA
Found at i:1794489 original size:19 final size:18
Alignment explanation
Indices: 1794467--1794512 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
1794457 TTAATATTAG
1794467 TTATGATTATGATTATATA
1 TTATGATTATG-TTATATA
*
1794486 TTATTATTA-GTTATATA
1 TTATGATTATGTTATATA
1794503 TATATG-TTAT
1 T-TATGATTAT
1794513 AGTATTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 11 0.48
18 4 0.17
19 8 0.35
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.57
Consensus pattern (18 bp):
TTATGATTATGTTATATA
Found at i:1797543 original size:21 final size:21
Alignment explanation
Indices: 1797519--1797559 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1797509 AGGGAAATAG
1797519 AGGAATTTGA-AAATAAAATTA
1 AGGAATTTGAGAAA-AAAATTA
*
1797540 AGGAGTTTGAGAAAAAAATT
1 AGGAATTTGAGAAAAAAATT
1797560 CAATTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.54, C:0.00, G:0.20, T:0.27
Consensus pattern (21 bp):
AGGAATTTGAGAAAAAAATTA
Found at i:1797927 original size:31 final size:30
Alignment explanation
Indices: 1797889--1797979 Score: 102
Period size: 30 Copynumber: 3.1 Consensus size: 30
1797879 GAGACAACCC
1797889 ATTTCATTTTATTTCATTTTTAGTAAATTTT
1 ATTTCATTTTATTT-ATTTTTAGTAAATTTT
* *
1797920 ATTTCA-TTTA---ATTTTTCGCAAATTTT
1 ATTTCATTTTATTTATTTTTAGTAAATTTT
*
1797946 AATTT-ATTTCATTTATTTTTAGTAAATTTT
1 -ATTTCATTTTATTTATTTTTAGTAAATTTT
1797976 ATTT
1 ATTT
1797980 TATTAGGTAC
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
26 15 0.30
27 7 0.14
29 4 0.08
30 18 0.36
31 6 0.12
ACGTcount: A:0.27, C:0.07, G:0.03, T:0.63
Consensus pattern (30 bp):
ATTTCATTTTATTTATTTTTAGTAAATTTT
Found at i:1797928 original size:26 final size:25
Alignment explanation
Indices: 1797896--1797979 Score: 87
Period size: 26 Copynumber: 3.1 Consensus size: 25
1797886 CCCATTTCAT
1797896 TTTATTTCATTTTTAGTAAATTTTA
1 TTTATTTCATTTTTAGTAAATTTTA
* * *
1797921 TTTCATTTAATTTTTCGCAAATTTTAA
1 TTT-ATTTCATTTTTAGTAAATTTT-A
1797948 TTTATTTCATTTATTTTTAGTAAATTTTA
1 TTTATTTC----ATTTTTAGTAAATTTTA
1797977 TTT
1 TTT
1797980 TATTAGGTAC
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
25 3 0.06
26 22 0.47
27 4 0.09
29 4 0.09
30 14 0.30
ACGTcount: A:0.27, C:0.06, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTATTTCATTTTTAGTAAATTTTA
Found at i:1798893 original size:31 final size:31
Alignment explanation
Indices: 1798857--1798915 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1798847 AACTTAAAAG
* *
1798857 AGTTTTGCAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATAATGAAATTTAAATAATTTT
*
1798888 AGTTTTATAATAATGAAATTTAAATAAT
1 AGTTTTACAATAATGAAATTTAAATAAT
1798916 CCATACAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATAATGAAATTTAAATAATTTT
Found at i:1798969 original size:22 final size:22
Alignment explanation
Indices: 1798939--1799034 Score: 131
Period size: 22 Copynumber: 4.4 Consensus size: 22
1798929 ATAATAATTT
*
1798939 TTTTTAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
1798961 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
*
1798983 TTTTAAAATAAATCAATCGATA
1 TTTTAAAATAAATCAATCCATA
**
1799005 TTTTAAAATGAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
1799027 TTTTAAAA
1 TTTTAAAA
1799035 ATACAATTTA
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
22 62 0.94
23 4 0.06
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:1798995 original size:44 final size:42
Alignment explanation
Indices: 1798939--1799308 Score: 289
Period size: 44 Copynumber: 9.3 Consensus size: 42
1798929 ATAATAATTT
* *
1798939 TTTTTAAATAAATCAATCCATATTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAAT-AATCCATATTTTAAAATAAATC-ATCCATA
* **
1798983 TTTTAAAATAAATCAATCGATATTTTAAAATGAAATTTTCCATA
1 TTTTAAAATAAAT-AATCCATATTTTAAAAT-AAATCATCCATA
*
1799027 TTTT--AA-AAAT-A--CA-ATTTAAAAAT-AA--AT--ATA
1 TTTTAAAATAAATAATCCATATTTTAAAATAAATCATCCATA
*
1799057 TTTTAAAATAAATCATCCATA-TTTAAAATAAAT-A---A-A
1 TTTTAAAATAAATAATCCATATTTTAAAATAAATCATCCATA
** *
1799093 TTTTAAAATAAAT-ATCCATATTTTAAAATAAAATTTTTCATA
1 TTTTAAAATAAATAATCCATATTTTAAAAT-AAATCATCCATA
1799135 TTTTAAAAT-AA-AATCCATATTTT-AAATAAA--ATCCATA
1 TTTTAAAATAAATAATCCATATTTTAAAATAAATCATCCATA
* *
1799172 CTTT----T-AA-CA-CCATATTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATAATCCATATTTTAAAATAAATC-ATCCATA
* **
1799208 TTTTAAAATAATTCAATCCATATTTTAAAATAAAATTTTCCATA
1 TTTTAAAATAAAT-AATCCATATTTTAAAAT-AAATCATCCATA
*
1799252 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCAATA
1 TTTTAAAATAAAT-AATCCATATTTTAAAATAAATC-ATCCATA
1799296 TTTTAAAATAAAT
1 TTTTAAAATAAAT
1799309 TTTAAAATAG
Statistics
Matches: 271, Mismatches: 23, Indels: 64
0.76 0.06 0.18
Matches are distributed among these distances:
30 7 0.03
32 12 0.04
33 15 0.06
34 3 0.01
35 7 0.03
36 50 0.18
37 17 0.06
38 1 0.00
39 4 0.01
40 5 0.02
41 19 0.07
42 12 0.04
43 5 0.02
44 106 0.39
45 8 0.03
ACGTcount: A:0.50, C:0.10, G:0.01, T:0.40
Consensus pattern (42 bp):
TTTTAAAATAAATAATCCATATTTTAAAATAAATCATCCATA
Found at i:1799064 original size:16 final size:16
Alignment explanation
Indices: 1799040--1799107 Score: 82
Period size: 16 Copynumber: 4.0 Consensus size: 16
1799030 TAAAAATACA
*
1799040 ATTTAAAAATAAATAT
1 ATTTTAAAATAAATAT
1799056 ATTTTAAAATAAATCAT
1 ATTTTAAAATAAAT-AT
*
1799073 CCATATTTAAAATAAATAA
1 --AT-TTTAAAATAAATAT
1799092 ATTTTAAAATAAATAT
1 ATTTTAAAATAAATAT
1799108 CCATATTTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
16 26 0.58
17 4 0.09
19 3 0.07
20 12 0.27
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (16 bp):
ATTTTAAAATAAATAT
Found at i:1799088 original size:36 final size:35
Alignment explanation
Indices: 1799040--1799164 Score: 144
Period size: 36 Copynumber: 3.3 Consensus size: 35
1799030 TAAAAATACA
1799040 ATTTAAAAATAAATATATTTTAAAATAAATCATCCAT
1 ATTT-AAAATAAATATATTTTAAAATAAAT-ATCCAT
*
1799077 ATTTAAAATAAATAAATTTTAAAATAAATATCCAT
1 ATTTAAAATAAATATATTTTAAAATAAATATCCAT
1799112 ATTTTAAAATAAAATTTTTCATATTTTAAAATAAA-ATCCAT
1 A-TTTAAAAT-AAA----T-ATATTTTAAAATAAATATCCAT
*
1799153 ATTTTAAATAAA
1 ATTTAAAATAAA
1799165 ATCCATACTT
Statistics
Matches: 78, Mismatches: 3, Indels: 12
0.84 0.03 0.13
Matches are distributed among these distances:
35 7 0.09
36 32 0.41
37 7 0.09
39 3 0.04
40 7 0.09
41 8 0.10
42 14 0.18
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (35 bp):
ATTTAAAATAAATATATTTTAAAATAAATATCCAT
Found at i:1799137 original size:22 final size:22
Alignment explanation
Indices: 1799054--1799166 Score: 101
Period size: 20 Copynumber: 5.8 Consensus size: 22
1799044 AAAAATAAAT
*
1799054 ATATTTTAAAAT-AAATCATCC
1 ATATTTTAAAATAAAATTATCC
1799075 ATA-TTTAAAAT-AAA-TA---
1 ATATTTTAAAATAAAATTATCC
1799091 A-ATTTTAAAAT-AAA-TATCC
1 ATATTTTAAAATAAAATTATCC
* *
1799110 ATATTTTAAAATAAAATTTTTC
1 ATATTTTAAAATAAAATTATCC
1799132 ATATTTTAAAAT-AAA--ATCC
1 ATATTTTAAAATAAAATTATCC
1799151 ATATTTT-AAATAAAAT
1 ATATTTTAAAATAAAAT
1799167 CCATACTTTT
Statistics
Matches: 78, Mismatches: 5, Indels: 19
0.76 0.05 0.19
Matches are distributed among these distances:
15 1 0.01
16 14 0.18
18 4 0.05
19 14 0.18
20 21 0.27
21 9 0.12
22 15 0.19
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (22 bp):
ATATTTTAAAATAAAATTATCC
Done.