Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold382
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: 2572505
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
File 10 of 16
Found at i:1549403 original size:32 final size:32
Alignment explanation
Indices: 1549362--1549424 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 32
1549352 CAATTTGCTA
*
1549362 TGTATCGATACCAAG-ATCATGTATCGATACAG
1 TGTATCGATACAAAGAAT-ATGTATCGATACAG
1549394 TGTATCGATACAAAGCAATATGTATCGATAC
1 TGTATCGATACAAAG-AATATGTATCGATAC
1549425 TTTTGGGTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 14 0.50
33 12 0.43
34 2 0.07
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (32 bp):
TGTATCGATACAAAGAATATGTATCGATACAG
Found at i:1550811 original size:3 final size:3
Alignment explanation
Indices: 1550803--1550827 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1550793 TCAACCATTA
1550803 ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG A
1550828 AGTTGACTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:1557674 original size:48 final size:48
Alignment explanation
Indices: 1557618--1557713 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
1557608 CCAAACCTAT
1557618 ACACCTGTAGCTAGGTTAGAAGCTATTAGAATATTGCTAGCCTTTGCA
1 ACACCTGTAGCTAGGTTAGAAGCTATTAGAATATTGCTAGCCTTTGCA
1557666 ACACCTGTAGCTAGGTTAGAAGCTATTAGAATATTGCTAGCCTTTGCA
1 ACACCTGTAGCTAGGTTAGAAGCTATTAGAATATTGCTAGCCTTTGCA
1557714 TGCTTTTATA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (48 bp):
ACACCTGTAGCTAGGTTAGAAGCTATTAGAATATTGCTAGCCTTTGCA
Found at i:1561628 original size:19 final size:20
Alignment explanation
Indices: 1561581--1561635 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
1561571 ACACCCAGAT
1561581 GTATTGATACATATTGCTTA
1 GTATTGATACATATTGCTTA
* * *
1561601 GTATCGATACATGTT-CTTG
1 GTATTGATACATATTGCTTA
1561620 GTATTGATACATATTG
1 GTATTGATACATATTG
1561636 AATTATATCG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.27, C:0.11, G:0.18, T:0.44
Consensus pattern (20 bp):
GTATTGATACATATTGCTTA
Found at i:1566311 original size:159 final size:157
Alignment explanation
Indices: 1566021--1566497 Score: 595
Period size: 159 Copynumber: 3.0 Consensus size: 157
1566011 TTTTGTCTCT
* * * *
1566021 TTTAGGATTATCGAGATAGTTTTATGTCAAAGGCATACCCATAAGAGCATTTTAGTAATTTTTCC
1 TTTAGGATTATCCAAATACTTTTATGTCAAAGGTATACCCATAAGAGCATTTTAGTAATTTTTCC
* * *
1566086 TAGAACCGAATCTTAAGTTGTCATCGAGATGCTTTTATGCCAAAAGTGTGCATTTACAATAGGTT
66 TAGAACCGAATCTTAGGTTGTCATCGGGATGCTTTTATGCCAAAAGTGTGCATTTAAAATAGGTT
1566151 CATCTTATTTATGATAATTTTAAAGTTC
131 CATCTTATTTATGATAATTTT-AAGTTC
*
1566179 TTTAGGATTATCCAAATACTTTTATGTTAAAGGTATACCCATAAGAGCATTTTAGTAATTTTTTC
1 TTTAGGATTATCCAAATACTTTTATGTCAAAGGTATACCCATAAGAGCATTTTAGTAA-TTTTTC
** * * * *
1566244 CTAGAACTAAATCCTAGGTTGTCATCGGGATGCTTTTATGCCAAAGGTATGCATTTAAAATAAGT
65 CTAGAACCGAATCTTAGGTTGTCATCGGGATGCTTTTATGCCAAAAGTGTGCATTTAAAATAGGT
*
1566309 TCATCTCATTTATGATAATTCTTAAG-TC
130 TCATCTTATTTATGATAATT-TTAAGTTC
* * * * *
1566337 TTTTA-AAGTTAT-CAAGATACTTTCATGTCGAAGGTATACCC-TAAAAGCATTTTTGTAATTTT
1 -TTTAGGA-TTATCCAA-ATACTTTTATGTCAAAGGTATACCCATAAGAGCATTTTAGTAATTTT
* * * * *
1566399 T-CTAGAACCGAGTCTTAGGTTGTCACCAGGATGCTTTTATGCCAAAAGTGTGCATTTAGAACAG
63 TCCTAGAACCGAATCTTAGGTTGTCATCGGGATGCTTTTATGCCAAAAGTGTGCATTTAAAATAG
* * * *
1566463 GTCCATCCTATTTATGATCATTTTTAAGTTT
128 GTTCATCTTATTTATGAT-AATTTTAAGTTC
1566494 TTTA
1 TTTA
1566498 AGGTTAATGA
Statistics
Matches: 275, Mismatches: 37, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
156 76 0.28
157 9 0.03
158 74 0.27
159 114 0.41
160 2 0.01
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (157 bp):
TTTAGGATTATCCAAATACTTTTATGTCAAAGGTATACCCATAAGAGCATTTTAGTAATTTTTCC
TAGAACCGAATCTTAGGTTGTCATCGGGATGCTTTTATGCCAAAAGTGTGCATTTAAAATAGGTT
CATCTTATTTATGATAATTTTAAGTTC
Found at i:1567449 original size:9 final size:9
Alignment explanation
Indices: 1567437--1567469 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1567427 CATAAAACAA
1567437 AGAAAATAG
1 AGAAAATAG
*
1567446 AGAAAATAA
1 AGAAAATAG
1567455 AGAAAATAG
1 AGAAAATAG
1567464 A-AAAAT
1 AGAAAAT
1567470 TCAAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 5 0.23
9 17 0.77
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (9 bp):
AGAAAATAG
Found at i:1567478 original size:18 final size:19
Alignment explanation
Indices: 1567430--1567482 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 19
1567420 CATGGCCCAT
1567430 AAAA-CAAAGAAAATAGAG
1 AAAATCAAAGAAAATAGAG
1567448 AAAAT-AAAGAAAATAGA-
1 AAAATCAAAGAAAATAGAG
*
1567465 AAAATTCAAAAAAAATAG
1 AAAA-TCAAAGAAAATAG
1567483 TAGCATATCA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
17 4 0.13
18 17 0.55
19 10 0.32
ACGTcount: A:0.74, C:0.04, G:0.11, T:0.11
Consensus pattern (19 bp):
AAAATCAAAGAAAATAGAG
Found at i:1570394 original size:89 final size:90
Alignment explanation
Indices: 1570268--1570439 Score: 213
Period size: 89 Copynumber: 1.9 Consensus size: 90
1570258 AAATATTAAA
* * **
1570268 AATTTTCTATTTTGAGGAAACTCCATCCCCACTATTCTCAGGGGATACTCTAACCTTGATCATCA
1 AATTTTATATTTTAAGGAAACTCCATCCCCACTATTCTCAGGCAATACTCTAACCTTGATCATCA
*
1570333 AAAAACTT-AAACTTTTCCTTCATAT
66 AAAAAATTCAAA-TTTTCCTTCATAT
** * * * * *
1570358 AATTTTAT-TTTTAAGGAAACTCCATCCCTTCTATTCTGAGGCAATATTTTAATCTTGATCTTCA
1 AATTTTATATTTTAAGGAAACTCCATCCCCACTATTCTCAGGCAATACTCTAACCTTGATCATCA
1570422 AAAAAATTCAAATTTTCC
66 AAAAAATTCAAATTTTCC
1570440 CTTCGCACAA
Statistics
Matches: 69, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
89 59 0.86
90 10 0.14
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38
Consensus pattern (90 bp):
AATTTTATATTTTAAGGAAACTCCATCCCCACTATTCTCAGGCAATACTCTAACCTTGATCATCA
AAAAAATTCAAATTTTCCTTCATAT
Found at i:1574223 original size:20 final size:21
Alignment explanation
Indices: 1574181--1574229 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
1574171 ATTTAATTTG
* *
1574181 ATTTAATTATATATAATTATT
1 ATTTAAATATATAAAATTATT
*
1574202 ATTTAAATA-ATAAAATTTTT
1 ATTTAAATATATAAAATTATT
1574222 ATTTAAAT
1 ATTTAAAT
1574230 TTAATTATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTTAAATATATAAAATTATT
Found at i:1575574 original size:72 final size:72
Alignment explanation
Indices: 1575363--1575593 Score: 252
Period size: 72 Copynumber: 3.2 Consensus size: 72
1575353 AGGTTCAGTG
* *** * * * * ** *
1575363 CCCAAA-GAAATTAGGAATTTGGTATCTTTGGATC-TGTTTGACCTGTCCAACAATAGGTTAACC
1 CCCAAATGAAATTGGGAATTTGGTATCTTTGGA-CACCCTGGATCTCTCCAACAACACATTAAGC
1575426 GGACCCAT
65 GGACCCAT
* *
1575434 CCCAAATGAAATTGGGAATTTGGTATCTTTGGACACCCTGGATCTCTCCCACAACAGATTAAGCG
1 CCCAAATGAAATTGGGAATTTGGTATCTTTGGACACCCTGGATCTCTCCAACAACACATTAAGCG
1575499 GACCCAT
66 GACCCAT
* * *
1575506 CCCAAATGAAATTGGGAATTTGGTATCTTTGGACGA-CCTGGATCTCTCCAACAATACATTGAGT
1 CCCAAATGAAATTGGGAATTTGGTATCTTTGGAC-ACCCTGGATCTCTCCAACAACACATTAAGC
*
1575570 GGACCGAT
65 GGACCCAT
* *
1575578 CCCAAGTGGAATTGGG
1 CCCAAATGAAATTGGG
1575594 GCTTTACAAA
Statistics
Matches: 138, Mismatches: 19, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
71 7 0.05
72 130 0.94
73 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.27
Consensus pattern (72 bp):
CCCAAATGAAATTGGGAATTTGGTATCTTTGGACACCCTGGATCTCTCCAACAACACATTAAGCG
GACCCAT
Found at i:1577908 original size:23 final size:22
Alignment explanation
Indices: 1577882--1577939 Score: 53
Period size: 24 Copynumber: 2.5 Consensus size: 22
1577872 TTTTTTTGTA
* *
1577882 TGAAAATTTTTATTTTAATTCTT
1 TGAAAATTTTT-TCTAAATTCTT
1577905 TGAAGATATTTTTTCTAAATTCTT
1 TGAA-A-ATTTTTTCTAAATTCTT
* *
1577929 TTAAGATTTTT
1 TGAAAATTTTT
1577940 CTTTGGTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
22 6 0.21
23 4 0.14
24 13 0.45
25 6 0.21
ACGTcount: A:0.29, C:0.05, G:0.07, T:0.59
Consensus pattern (22 bp):
TGAAAATTTTTTCTAAATTCTT
Found at i:1578163 original size:54 final size:54
Alignment explanation
Indices: 1578105--1578212 Score: 132
Period size: 53 Copynumber: 2.0 Consensus size: 54
1578095 TTCACTTTAG
* **
1578105 TTTTTGCAATTTAATTTTTT-TTATTTGAT-TTTTAATT-AAAATTTATTACACAT
1 TTTTTTCAATTTAATTTTTTCTTA--TGATATCATAATTAAAAATTTATTACACAT
* *
1578158 TTTTTTTAATTTAATTTTTTCTTATGATATCATAATTAAAAATTTGTTACACAT
1 TTTTTTCAATTTAATTTTTTCTTATGATATCATAATTAAAAATTTATTACACAT
1578212 T
1 T
1578213 AAAATTTAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
52 4 0.09
53 24 0.51
54 19 0.40
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.58
Consensus pattern (54 bp):
TTTTTTCAATTTAATTTTTTCTTATGATATCATAATTAAAAATTTATTACACAT
Found at i:1578237 original size:22 final size:20
Alignment explanation
Indices: 1578214--1578254 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1578204 TTACACATTA
1578214 AAAT-TTAATTATAAAATATAT
1 AAATATTAA-TATAAAA-ATAT
1578235 AAATATTAATATAAAAATAT
1 AAATATTAATATAAAAATAT
1578255 TTTTTAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 11 0.58
22 4 0.21
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAATATTAATATAAAAATAT
Found at i:1583656 original size:14 final size:16
Alignment explanation
Indices: 1583632--1583664 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1583622 AGTTCATTCA
1583632 TATTGATTTGATT-TT
1 TATTGATTTGATTATT
1583647 TATT-ATTTGATTATT
1 TATTGATTTGATTATT
1583662 TAT
1 TAT
1583665 CCATATACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.67
Consensus pattern (16 bp):
TATTGATTTGATTATT
Found at i:1584324 original size:19 final size:19
Alignment explanation
Indices: 1584300--1584338 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1584290 AAGAATAATT
1584300 ATAAAATTAAA-TTAAATAA
1 ATAAAA-TAAACTTAAATAA
*
1584319 ATAAAATAAACTTTAATAA
1 ATAAAATAAACTTAAATAA
1584338 A
1 A
1584339 GATCACTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (19 bp):
ATAAAATAAACTTAAATAA
Found at i:1587258 original size:35 final size:35
Alignment explanation
Indices: 1587214--1587281 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
1587204 AATTCAAATG
*
1587214 AATGTGGAGGAAGACAAACAAAAGATTACTTCCCA
1 AATGTGGAGGAAGAAAAACAAAAGATTACTTCCCA
1587249 AATGTGGAGGAAGAAAAACAAAAGATTACTTCC
1 AATGTGGAGGAAGAAAAACAAAAGATTACTTCC
1587282 TAAAAGTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.47, C:0.15, G:0.21, T:0.18
Consensus pattern (35 bp):
AATGTGGAGGAAGAAAAACAAAAGATTACTTCCCA
Found at i:1591265 original size:2 final size:2
Alignment explanation
Indices: 1591258--1591305 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1591248 CCTGCAATTT
1591258 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
1591300 TA TA TA
1 TA TA TA
1591306 ATCAAAGAAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1592429 original size:12 final size:14
Alignment explanation
Indices: 1592399--1592444 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
1592389 ATTTTTATCC
1592399 ATTAAAATTATATT
1 ATTAAAATTATATT
1592413 ATTAAAATTAT-TT
1 ATTAAAATTATATT
*
1592426 -TTAATTATTATATT
1 ATTAA-AATTATATT
1592440 ATTAA
1 ATTAA
1592445 GATAGAGGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 4 0.14
13 7 0.25
14 13 0.46
15 4 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
ATTAAAATTATATT
Found at i:1594235 original size:29 final size:29
Alignment explanation
Indices: 1594180--1594238 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
1594170 GCTGTTTATT
** **
1594180 AAATTATTTATTGAAATATTATTGTTTTG
1 AAATTATTTATCAAAATATTACCGTTTTG
*
1594209 AAATTATTTATCAAAATGTTACCGTTTTG
1 AAATTATTTATCAAAATATTACCGTTTTG
1594238 A
1 A
1594239 TCACGTCACA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.49
Consensus pattern (29 bp):
AAATTATTTATCAAAATATTACCGTTTTG
Found at i:1594415 original size:18 final size:20
Alignment explanation
Indices: 1594392--1594430 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
1594382 TTTTTATCTC
*
1594392 ATTATTTAA-AAATA-TAAA
1 ATTATTCAATAAATATTAAA
1594410 ATTATTCAATAAATATTAAA
1 ATTATTCAATAAATATTAAA
1594430 A
1 A
1594431 AAATTATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 5 0.28
20 5 0.28
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
ATTATTCAATAAATATTAAA
Found at i:1594952 original size:17 final size:17
Alignment explanation
Indices: 1594930--1594963 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1594920 AATATATAAC
1594930 AATTTTTATACATTAAA
1 AATTTTTATACATTAAA
*
1594947 AATTTTTATGCATTAAA
1 AATTTTTATACATTAAA
1594964 TATAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (17 bp):
AATTTTTATACATTAAA
Found at i:1598662 original size:19 final size:18
Alignment explanation
Indices: 1598638--1598673 Score: 63
Period size: 18 Copynumber: 1.9 Consensus size: 18
1598628 TTTAAATACC
1598638 TTTAATTTAAATTTTTATT
1 TTTAATTT-AATTTTTATT
1598657 TTTAATTTAATTTTTAT
1 TTTAATTTAATTTTTAT
1598674 ATAATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTAATTTAATTTTTATT
Found at i:1599894 original size:3 final size:3
Alignment explanation
Indices: 1599886--1599916 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1599876 ACTATTCCAG
1599886 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1599917 ATTAACCTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1600037 original size:66 final size:66
Alignment explanation
Indices: 1599931--1600064 Score: 259
Period size: 66 Copynumber: 2.0 Consensus size: 66
1599921 ACCTCTGTGG
1599931 AATTATTTTATATGAGACCACAACAATTAAAACTTGGAAATTGACCTTCACAAAAAACAATAAAT
1 AATTATTTTATATGAGACCACAACAATTAAAACTTGGAAATTGACCTTCACAAAAAACAATAAAT
1599996 T
66 T
*
1599997 AATTATTTTATATGAGACCACAACAATTAAAACTTGGAAATTGACCTTCACACAAAACAATAAAT
1 AATTATTTTATATGAGACCACAACAATTAAAACTTGGAAATTGACCTTCACAAAAAACAATAAAT
1600062 T
66 T
1600063 AA
1 AA
1600065 GGTTTCAGCT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.49, C:0.16, G:0.07, T:0.28
Consensus pattern (66 bp):
AATTATTTTATATGAGACCACAACAATTAAAACTTGGAAATTGACCTTCACAAAAAACAATAAAT
T
Found at i:1600103 original size:2 final size:2
Alignment explanation
Indices: 1600090--1600153 Score: 103
Period size: 2 Copynumber: 32.5 Consensus size: 2
1600080 TAATCAAAGA
* *
1600090 AT AT AC AT AT AT AT AT AA 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
1600132 AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
1600154 AGGATTTTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
1 1 0.02
2 56 0.98
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1600514 original size:3 final size:3
Alignment explanation
Indices: 1600506--1600540 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1600496 ACATAGCAAG
1600506 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1600541 TACCCTTTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1603502 original size:220 final size:220
Alignment explanation
Indices: 1603110--1603552 Score: 536
Period size: 220 Copynumber: 2.0 Consensus size: 220
1603100 CTGTAACCAA
* * *
1603110 AAATTTATGAAGTTAAGAAGTCGAATTCATGCATCTTAGTACTTAAGAAAACTAAATGAAAACAT
1 AAATTTATGAAGTTAAGAAGTAGAA-TCATGCACCTTAGTACTCAAGAAAACTAAATGAAAACAT
* * * * * * *
1603175 GAAGCTAACATTGAACCATGAGCCAGAAAACAAACTGAGCCAATAGCTTAATTTAATATGCTTCA
65 CAAGCCAACATAGAACCATAAGCCAGAAAACAAACTGAGCCAATAGCCTAAATTAATAAGCTTCA
* * *
1603240 GGCAATGGCCATGATGTAAGGTCAATAGAAGCAGAGTACATGAGCAGTTGCTCATTTTTAACCAT
130 GGCAATAGCCATGATGTAAGGTAAATAGAAGCAGAGTACATGAGCAGTTGCTCA--TTTAAACAT
1603305 GGGAACTGCTAAGATAAGTATAAA-GTTT
193 GGGAACTGCTAAGATAAGTA-AAAGGTTT
* * * * *
1603333 AAATTTATGAAGTTAAGATGTAGCA-CATGCACCTTAGTACTCAAGAAAACTAAGTGAGAATATC
1 AAATTTATGAAGTTAAGAAGTAGAATCATGCACCTTAGTACTCAAGAAAACTAAATGAAAACATC
* * * * *
1603397 ATA-CCAACATAGAACTATAAGCCAGAAAAC-AAGTTAGCCAATCGCCTAAATTAATAAGCTTTA
66 A-AGCCAACATAGAACCATAAGCCAGAAAACAAACTGAGCCAATAGCCTAAATTAATAAGCTTCA
** *
1603460 GGCAATAGTTATGATG-AATGGTAAATAGAAGTAGAGTACATGAGCAGTTGCTCATTTAAACATG
130 GGCAATAGCCATGATGTAA-GGTAAATAGAAGCAGAGTACATGAGCAGTTGCTCATTTAAACATG
* * *
1603524 GGAAGTGCTACGATGAGTAAAAGGTTT
194 GGAACTGCTAAGATAAGTAAAAGGTTT
1603551 AA
1 AA
1603553 GTAGTTCTAA
Statistics
Matches: 188, Mismatches: 29, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
217 3 0.02
218 31 0.16
219 2 0.01
220 72 0.38
221 57 0.30
222 1 0.01
223 22 0.12
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (220 bp):
AAATTTATGAAGTTAAGAAGTAGAATCATGCACCTTAGTACTCAAGAAAACTAAATGAAAACATC
AAGCCAACATAGAACCATAAGCCAGAAAACAAACTGAGCCAATAGCCTAAATTAATAAGCTTCAG
GCAATAGCCATGATGTAAGGTAAATAGAAGCAGAGTACATGAGCAGTTGCTCATTTAAACATGGG
AACTGCTAAGATAAGTAAAAGGTTT
Found at i:1608444 original size:73 final size:73
Alignment explanation
Indices: 1608353--1608497 Score: 281
Period size: 73 Copynumber: 2.0 Consensus size: 73
1608343 ATGGGTAATG
1608353 TATTTATGTAAATAATATTTGAAAGTAATATTGTATGTGATAAATCACATATAAACAGTATTAGA
1 TATTTATGTAAATAATATTTGAAAGTAATATTGTATGTGATAAATCACATATAAACAGTATTAGA
1608418 TTACATAC
66 TTACATAC
*
1608426 TATTTATGTAAATAATATTTGAAAGTAATGTTGTATGTGATAAATCACATATAAACAGTATTAGA
1 TATTTATGTAAATAATATTTGAAAGTAATATTGTATGTGATAAATCACATATAAACAGTATTAGA
1608491 TTACATA
66 TTACATA
1608498 TAAACCCTAC
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (73 bp):
TATTTATGTAAATAATATTTGAAAGTAATATTGTATGTGATAAATCACATATAAACAGTATTAGA
TTACATAC
Found at i:1608907 original size:29 final size:28
Alignment explanation
Indices: 1608833--1608907 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 28
1608823 ATTAAAGTGC
*
1608833 AGGTAATGTTTGTATATAATACATATAAT
1 AGGTAATG-TTGTATGTAATACATATAAT
*
1608862 AGGTAATGTATTTATGTAAATA-ATATTTAA-
1 AGGTAATGT-TGTATGT-AATACATA--TAAT
1608892 AGGTAATGTTGTATGT
1 AGGTAATGTTGTATGT
1608908 GATAAATTGC
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
28 1 0.03
29 22 0.56
30 13 0.33
31 3 0.08
ACGTcount: A:0.39, C:0.01, G:0.17, T:0.43
Consensus pattern (28 bp):
AGGTAATGTTGTATGTAATACATATAAT
Found at i:1608939 original size:517 final size:516
Alignment explanation
Indices: 1607990--1608942 Score: 1506
Period size: 517 Copynumber: 1.8 Consensus size: 516
1607980 ATAAATATTG
*
1607990 CAGTTTTACATAGAACATTATTGAAATTGTAATGTATTTATGTAAAAAATTATTTTAAGAAAATT
1 CAGTTTTACATAGAACATTATTAAAATTGTAATGTATTTATGTAAAAAA-TATTTTAAGAAAATT
1608055 AATACAATTTTTTTAAAACTATTTTTGACTTTTTATTAAATATATTATATATGTAAGAAATTAAT
65 AATACAATTTTTTTAAAACTATTTTTGACTTTTTATTAAATATATTATATATGTAAGAAATTAAT
* *
1608120 ATTTTAATAATTTTTTAGGTTAAAAACTTTATATATTTAATTTATTAATATATTTTTAATATTTA
130 ATTTTAATAATTTTTTAAGTTAAAAACTTAATATATTTAATTTATTAATATATTTTTAATATTTA
1608185 TAATAAATATATTATATTAATAAAAAATAATTTTATGATAAAATTTAGATTTTATTAATTAATAA
195 TAATAAATATATTATATTAATAAAAAATAATTTTATGATAAAATTTAGATTTTATTAATTAATAA
* *
1608250 GAATTACAATTAAAGATTACCCAAAGCATACATAAATATCAAAATTTATATAAATCATTAAAATG
260 GAATTACAACTAAAAATTACCCAAAGCATACATAAATATCAAAATTTATATAAATCATTAAAATG
* * *
1608315 CACGTAATGTTTGCATGTAATGCATATAATGGGTAATGTATTTATGTAAATAATATTTGAAAGTA
325 CACGTAATGTTTGCATATAATACATATAATAGGTAATGTATTTATGTAAATAATATTTGAAAGTA
*
1608380 ATATTGTATGTGATAAATCACATATAAACAGTATTAGATTACATACTATTTATGTAAATAATATT
390 ATATTGTATGTGATAAATCACATATAAACAGTATCAGATTACATACTATTTATGTAAATAATATT
1608445 TGAAAGTAATGTTGTATGTGATAAATCACATATAAACAGTATTAGATTACATATAAACCCTA
455 TGAAAGTAATGTTGTATGTGATAAATCACATATAAACAGTATTAGATTACATATAAACCCTA
*
1608507 CAGTTTTGCATTA-AACATTATTAAAATTGTAATGTATTTATGTAAAAAA-ATTTTAAGAAAATT
1 CAGTTTTACA-TAGAACATTATTAAAATTGTAATGTATTTATGTAAAAAATATTTTAAGAAAATT
* * * * *
1608570 AAATAGAATTTTTTTCAAAATTATTTTTTTATTTTTTATTAAATATATTATATATGTATGAAATT
65 -AATACAATTTTTTT-AAAACTA-TTTTTGACTTTTTATTAAATATATTATATATGTAAGAAATT
* *
1608635 AATTTTTTTAATAA-TTTTTAAGTT-AAAAGTTAATAT-TTTAATTTATTAATATATTTTTAATA
127 AA-TATTTTAATAATTTTTTAAGTTAAAAACTTAATATATTTAATTTATTAATATATTTTTAATA
* *
1608697 TTTGTAATAAATATATTATATTAATAAAAAATAATTTTA-GATAAAATTTAGATTTTTTATTAGT
191 TTTATAATAAATATATTATATTAATAAAAAATAATTTTATGATAAAATTTAGA--TTTTATTAAT
* * *
1608761 TAGTAAGAATTACAACTAAAAATTACCCAAATCATACATAAATATTAAAATTTATATAAATCATT
254 TAATAAGAATTACAACTAAAAATTACCCAAAGCATACATAAATATCAAAATTTATATAAATCATT
* * *
1608826 AAAGTGCAGGTAATGTTTGTATATAATACATATAATAGGTAATGTATTTATGTAAATAATATTT-
319 AAAATGCACGTAATGTTTGCATATAATACATATAATAGGTAATGTATTTATGTAAATAATATTTG
* ** * *
1608890 AAAGGTAATGTTGTATGTGATAAATTGCATATAAACATTATCGGATTACATAC
384 AAA-GTAATATTGTATGTGATAAATCACATATAAACAGTATCAGATTACATAC
1608943 GAACCTTACA
Statistics
Matches: 398, Mismatches: 30, Indels: 16
0.90 0.07 0.04
Matches are distributed among these distances:
515 27 0.07
516 80 0.20
517 230 0.58
518 51 0.13
519 10 0.03
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (516 bp):
CAGTTTTACATAGAACATTATTAAAATTGTAATGTATTTATGTAAAAAATATTTTAAGAAAATTA
ATACAATTTTTTTAAAACTATTTTTGACTTTTTATTAAATATATTATATATGTAAGAAATTAATA
TTTTAATAATTTTTTAAGTTAAAAACTTAATATATTTAATTTATTAATATATTTTTAATATTTAT
AATAAATATATTATATTAATAAAAAATAATTTTATGATAAAATTTAGATTTTATTAATTAATAAG
AATTACAACTAAAAATTACCCAAAGCATACATAAATATCAAAATTTATATAAATCATTAAAATGC
ACGTAATGTTTGCATATAATACATATAATAGGTAATGTATTTATGTAAATAATATTTGAAAGTAA
TATTGTATGTGATAAATCACATATAAACAGTATCAGATTACATACTATTTATGTAAATAATATTT
GAAAGTAATGTTGTATGTGATAAATCACATATAAACAGTATTAGATTACATATAAACCCTA
Found at i:1609007 original size:444 final size:436
Alignment explanation
Indices: 1608426--1609822 Score: 1469
Period size: 444 Copynumber: 3.2 Consensus size: 436
1608416 GATTACATAC
* * * *
1608426 TATTTATGTAAATAATATTTGAAAGTAATGTTGTATGTGATAAATCACATATAAACAGTATTAGA
1 TATTTATGTAAAGAATATTTGAAAATAATGTTGTATGTGATAAATTACATATAAACATTATTAGA
* * * * **
1608491 TTACATATAAACCCTACAGTTTTGCATTAAACATTATTAAAATTGTAATGTATTTATGTAAAAAA
66 TTACATAAAAACCTTACAGTTTTGCATAAAACATTA-TAAAATTGTAATGTATTTATATAAAATT
1608556 ATTTTAAGAAAATTAAATAGAATTTTTTTCAAAATTATTTTTTTATTTTTTATTAAATATATTAT
130 ATTTTAAG-AAATTAAATA-AATTTTTTTCAAAATTA-TTTTTTATTTTTTATTAAATATATTAT
* *
1608621 ATATGTATGAAATTAATTTTTTTAATAATTTTTAAGTTAAAAGTTAATATTTTAATTTATTAATA
192 ATATGTATGAAATTAATTTTTTTAATAATTTTTAAGTTAAAATTTAATATTTTATTTTATTAATA
1608686 TATTTTTAATATTTGTAATAAATATATTATATTAATAAAAAATAATTTTAGATAAAATTTAGATT
257 TATTTTTAATATTTGTAATAAATATATTATATTAATAAAAAATAATTTT-GAT-AAATTTAGATT
** *
1608751 TTTTATTAGTTAGTAAGAATTACAACTAAAAATTACCCAAATCATACATAAATATTAAAATTTAT
320 TTTTATTAGTTAGTAAGAATTACAACTAAAAATTACTAAAAT-ATACATAAATATTAAAATTTAC
* * * * * *
1608816 ATAAATCATTAAAGTGCAGGTAATGTTTGTATATAATACATATAATAGGTAATG
384 ATAAATTATTAGAGTGTAGATAATATTTGTATATAATATATATAAT-GGTAATG
* * * **
1608870 TATTTATGTAAATAATATTT-AAAGGTAATGTTGTATGTGATAAATTGCATATAAACATTATCGG
1 TATTTATGTAAAGAATATTTGAAA-ATAATGTTGTATGTGATAAATTACATATAAACATTATTAG
** * * * *
1608934 ATTACATACGAACCTTACAGTTTTGCATAAAACATTACCAAAACTATAATGTATTCATATAAAAT
65 ATTACATAAAAACCTTACAGTTTTGCATAAAACATTA-TAAAATTGTAATGTATTTATATAAAAT
* *
1608999 TTTTTTAAGCAAATTAAATATAATTTTTTTCAAAATTA-TTTTTATTTTTTATT-AA-ATACTAT
129 TATTTTAAG-AAATTAAATA-AATTTTTTTCAAAATTATTTTTTATTTTTTATTAAATATATTAT
* *
1609061 ATATGTATGAAATTAATTTTTTTAATAATTTTTAAGTCAAAAATTTTGTATATTTTATTTTATTA
192 ATATGTATGAAATTAATTTTTTTAATAATTTTTAAGT-TAAAA-TTT-AATATTTTATTTTATTA
* *
1609126 ATATA-TTATAATATTTGTAAT-AATATATTATATTAATAAAAAATAATTTT-AT-AATTTAAAT
254 ATATATTTTTAATATTTGTAATAAATATATTATATTAATAAAAAATAATTTTGATAAATTTAGAT
* * *
1609187 CTTTTTATTAGTTAGTAAGAATTACAAC-ATAAGATTATTAAAAT-TACATATAACTATTAGAAT
319 -TTTTTATTAGTTAGTAAGAATTACAACTA-AAAATTACTAAAATATACATA-AA-TATTAAAAT
* * * * *
1609250 TTACGTAAATTGTTAGAGTTTAGATAATATTTGTATATAATATTTATAATGGGTAATA
380 TTACATAAATTATTAGAGTGTAGATAATATTTGTATATAATATATATAAT-GGTAATG
* * * * * * *
1609308 TATTTGTGGAAAGAATCTTTGAAAATAGTGTT-TATATGCAACAAATTACATATAAATATTATTA
1 TATTTATGTAAAGAATATTTGAAAATAATGTTGTATGTG--ATAAATTACATATAAACATTATTA
** * * * * * *
1609372 GATTACA-AAAAAAATTATAGTTTTACATAAAATATTATAGAAATTGTGATGTTTTTATGTTAAA
64 GATTACATAAAAACCTTACAGTTTTGCATAAAACATTATA-AAATTGTAATGTATTTAT-AT-AA
*
1609436 AATTCTTTTAAG--A-T--AT-AA-TTTTTTCAAAATTATTTTTTA-TTTTTATTAAATATATTA
126 AATTATTTTAAGAAATTAAATAAATTTTTTTCAAAATTATTTTTTATTTTTTATTAAATATATTA
* *
1609493 TATATGTATGAAATTAA-TTTTTTAATAATTTTAAAGTTAGAAAAATTTATATTTTTTTAGTTTT
191 TATATGTATGAAATTAATTTTTTTAATAATTTTTAAGTT---AAAATTTA-A-TATTTTA-TTTT
** *
1609557 ATTAATATATTTTTTAATATTAATAATAAATATATTATATTAATAAAAAAATAATTTTTTGTTAG
250 ATTAATATA-TTTTTAATATTTGTAATAAATATATTATATTAAT-AAAAAATAA--TTTTGATA-
* * * * * *
1609622 AATTTAGTTTTTTCTATTAGTTGGTATGAATTACAACTAAAAAGTACTAAAATTACACATAAATG
310 AATTTAGATTTTT-TATTAGTTAGTAAGAATTACAACTAAAAATTACTAAAA-TATACATAAATA
* * *
1609687 TTAGAAA-TTACATAAATTATTAGAGTGTAGATAATATTTACT-TGTAATATATATAATGAGTGA
373 TTA-AAATTTACATAAATTATTAGAGTGTAGATAATATTT-GTATATAATATATATAATG-GTAA
1609750 TG
435 TG
* * * * * * *
1609752 CATTTGTGTAAAGAATATTT-AAAGATAATGTTTGTA--TAACAAATTATATATAAATATTATCA
1 TATTTATGTAAAGAATATTTGAAA-ATAATG-TTGTATGTGATAAATTACATATAAACATTATTA
*
1609814 GAATACATA
64 GATTACATA
1609823 TACAGTTTTA
Statistics
Matches: 803, Mismatches: 107, Indels: 87
0.81 0.11 0.09
Matches are distributed among these distances:
431 22 0.03
432 29 0.04
433 26 0.03
434 12 0.01
435 13 0.02
436 7 0.01
437 31 0.04
438 164 0.20
439 41 0.05
440 56 0.07
441 39 0.05
442 61 0.08
443 32 0.04
444 254 0.32
445 9 0.01
446 7 0.01
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (436 bp):
TATTTATGTAAAGAATATTTGAAAATAATGTTGTATGTGATAAATTACATATAAACATTATTAGA
TTACATAAAAACCTTACAGTTTTGCATAAAACATTATAAAATTGTAATGTATTTATATAAAATTA
TTTTAAGAAATTAAATAAATTTTTTTCAAAATTATTTTTTATTTTTTATTAAATATATTATATAT
GTATGAAATTAATTTTTTTAATAATTTTTAAGTTAAAATTTAATATTTTATTTTATTAATATATT
TTTAATATTTGTAATAAATATATTATATTAATAAAAAATAATTTTGATAAATTTAGATTTTTTAT
TAGTTAGTAAGAATTACAACTAAAAATTACTAAAATATACATAAATATTAAAATTTACATAAATT
ATTAGAGTGTAGATAATATTTGTATATAATATATATAATGGTAATG
Found at i:1609150 original size:22 final size:21
Alignment explanation
Indices: 1609116--1609157 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
1609106 TTGTATATTT
*
1609116 TATTTTATTAATATATTATAA
1 TATTTTAATAATATATTATAA
1609137 TATTTGTAATAATATATTATA
1 TATTT-TAATAATATATTATA
1609158 TTAATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
TATTTTAATAATATATTATAA
Found at i:1609376 original size:21 final size:21
Alignment explanation
Indices: 1609352--1609409 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
1609342 TATGCAACAA
1609352 ATTACATATAAATATTATTAG-
1 ATTACATA-AAATATTATTAGT
* *
1609373 ATTACAAAAAAAATTA-TAGT
1 ATTACATAAAATATTATTAGT
*
1609393 TTTACATAAAATATTAT
1 ATTACATAAAATATTAT
1609410 AGAAATTGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
19 3 0.10
20 20 0.67
21 7 0.23
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (21 bp):
ATTACATAAAATATTATTAGT
Found at i:1609583 original size:21 final size:21
Alignment explanation
Indices: 1609540--1609602 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
1609530 TAGAAAAATT
* * *
1609540 TATATTTTTTTAGTTTTATTAA
1 TATA-TTTTTTAATATTAATAA
1609562 TATATTTTTTAATATTAATAA
1 TATATTTTTTAATATTAATAA
* * *
1609583 TAAATATATT-ATATTAATAA
1 TATATTTTTTAATATTAATAA
1609603 AAAAATAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 10 0.29
21 21 0.60
22 4 0.11
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
TATATTTTTTAATATTAATAA
Found at i:1612823 original size:13 final size:13
Alignment explanation
Indices: 1612805--1612834 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1612795 ACAATTCTTC
1612805 ATGTATCGATACA
1 ATGTATCGATACA
*
1612818 ATGTATCGATATA
1 ATGTATCGATACA
1612831 ATGT
1 ATGT
1612835 CCCATGTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1615441 original size:19 final size:20
Alignment explanation
Indices: 1615417--1615456 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1615407 TTTAAATAGT
1615417 AACCC-ATGTATCAATACAA
1 AACCCAATGTATCAATACAA
*
1615436 AACCCAGATGTATCGATACAA
1 AACCCA-ATGTATCAATACAA
1615457 TGTTCTTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
21 13 0.72
ACGTcount: A:0.45, C:0.25, G:0.10, T:0.20
Consensus pattern (20 bp):
AACCCAATGTATCAATACAA
Found at i:1617091 original size:79 final size:79
Alignment explanation
Indices: 1616955--1617158 Score: 266
Period size: 79 Copynumber: 2.6 Consensus size: 79
1616945 GAGATAATAA
* * ** * *
1616955 CGGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCGGTTGTGAGAAATCGATGA
1 CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAAT-A
*
1617020 -TTAGGAAAAAAAAT
65 TTTAGGAAAAAAAAC
*
1617034 CGGGATTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
* * * *
1617099 TTTGGGAATAAAGC
66 TTAGGAAAAAAAAC
**
1617113 CGGGGTTGGAGTATCCCCTCGGAGGTAACGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCC
1617159 GATGAACTAA
Statistics
Matches: 109, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
78 1 0.01
79 108 0.99
ACGTcount: A:0.28, C:0.17, G:0.31, T:0.24
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATAT
TTAGGAAAAAAAAC
Found at i:1617169 original size:28 final size:28
Alignment explanation
Indices: 1617113--1617189 Score: 82
Period size: 28 Copynumber: 2.8 Consensus size: 28
1617103 GGAATAAAGC
*** **
1617113 CGGGGTTGGAGTATCCCCTCGGAGGTAA
1 CGGGGTTGGAGTATCCCCGATGAACTAA
1617141 CGGGGTTGGAGTATCCCCGATGAACTAA
1 CGGGGTTGGAGTATCCCCGATGAACTAA
** *
1617169 CAAGGTTGGAGTATCCTCGAT
1 CGGGGTTGGAGTATCCCCGAT
1617190 TGTGAAAAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.22, C:0.21, G:0.34, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAACTAA
Found at i:1617262 original size:52 final size:53
Alignment explanation
Indices: 1617173--1617295 Score: 169
Period size: 52 Copynumber: 2.4 Consensus size: 53
1617163 AACTAACAAG
* ** * *
1617173 GTTGGAGTATCCTCGATT-GTGAAAAATTGGTGTTTTTGGAAATCAAATCGGA
1 GTTGGAGTATCCCCGATTAAAGAAAAATTGGTGTTTTTGAAAATAAAATCGGA
* *
1617225 GTTGGAGTATCCCCGATTAAAGGAAAATTGGTG-TTTTGAAAATAAAATCGGG
1 GTTGGAGTATCCCCGATTAAAGAAAAATTGGTGTTTTTGAAAATAAAATCGGA
1617277 GTTGGAGTATCCCCGATTA
1 GTTGGAGTATCCCCGATTA
1617296 TGAACAATTG
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
52 52 0.83
53 11 0.17
ACGTcount: A:0.30, C:0.11, G:0.27, T:0.32
Consensus pattern (53 bp):
GTTGGAGTATCCCCGATTAAAGAAAAATTGGTGTTTTTGAAAATAAAATCGGA
Found at i:1624847 original size:129 final size:130
Alignment explanation
Indices: 1624492--1624847 Score: 513
Period size: 130 Copynumber: 2.7 Consensus size: 130
1624482 ATTTTTCATC
* *
1624492 TCGGGGATACTCCAACCCTAGTTTTATTTTCAAAACATCAATTTTTCATAATC-AGGGATACTCC
1 TCGGGGATACTCCAACCCCAATTTTATTTTCAAAACATCAATTTTTCATAATCGA-GGATACTCC
*
1624556 AATCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTTCTAAAATATTGATTTCTCACA
65 AATCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTTCTAAAATATTGATTTCTCACA
1624621 A
130 A
* * * * * *
1624622 TCAGGGATACTCTACCCCCAATTTTATTTCCAAAACATTAATTTTTTATAATCG-GAGATACTCC
1 TCGGGGATACTCCAACCCCAATTTTATTTTCAAAACATCAATTTTTCATAATCGAG-GATACTCC
*
1624686 AATCCCGTTATTTCCGAGGGGATACTCTAACCCCGACTTTATTTCTAAAATATTGA-TTCTCACA
65 AATCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTTCTAAAATATTGATTTCTCACA
1624750 A
130 A
* * * *
1624751 TCGGGGATACTCCAACCCCAATTTTATTTTTAAAACACCAATCTTTTCACAATCGAGGATACTCT
1 TCGGGGATACTCCAACCCCAATTTTATTTTCAAAACATCAAT-TTTTCATAATCGAGGATACTCC
**
1624816 AATCCCGTTATTTTTGA-GGGATACTCCAACCC
65 AATCCCGTTATTTCCGAGGGGATACTCCAACCC
1624848 AGTTTTATTT
Statistics
Matches: 199, Mismatches: 23, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
129 59 0.30
130 139 0.70
131 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (130 bp):
TCGGGGATACTCCAACCCCAATTTTATTTTCAAAACATCAATTTTTCATAATCGAGGATACTCCA
ATCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTTCTAAAATATTGATTTCTCACAA
Found at i:1624882 original size:130 final size:129
Alignment explanation
Indices: 1624492--1624899 Score: 500
Period size: 130 Copynumber: 3.1 Consensus size: 129
1624482 ATTTTTCATC
* *
1624492 TCGGGGATACTCCAACCCTAGTTTTATTTTCAAAACATCAATTTTTCATAATC-AGGGATACTCC
1 TCGGGGATACTCCAACCCCAATTTTATTTTCAAAACATCAATTTTTCATAATCGA-GGATACTCC
*
1624556 AATCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTTCTAAAATATTGATTTCTCACA
65 AATCCCGTTATTTCCGAGGGGATACTCCAA-CCCAGCTTTATTTCTAAAATATTGATTTCTCACA
1624621 A
129 A
* * * * * *
1624622 TCAGGGATACTCTACCCCCAATTTTATTTCCAAAACATTAATTTTTTATAATCG-GAGATACTCC
1 TCGGGGATACTCCAACCCCAATTTTATTTTCAAAACATCAATTTTTCATAATCGAG-GATACTCC
* *
1624686 AATCCCGTTATTTCCGAGGGGATACTCTAACCCCGACTTTATTTCTAAAATATTGA-TTCTCACA
65 AATCCCGTTATTTCCGAGGGGATACTCCAACCCAG-CTTTATTTCTAAAATATTGATTTCTCACA
1624750 A
129 A
* * * *
1624751 TCGGGGATACTCCAACCCCAATTTTATTTTTAAAACACCAATCTTTTCACAATCGAGGATACTCT
1 TCGGGGATACTCCAACCCCAATTTTATTTTCAAAACATCAAT-TTTTCATAATCGAGGATACTCC
** * * * * ** *
1624816 AATCCCGTTATTTTTGA-GGGATACTCCAACCCAGTTTTATTTCCAGAACACCGATTTTTTCACA
65 AATCCCGTTATTTCCGAGGGGATACTCCAACCCAGCTTTATTTCTAAAATATTGA-TTTCTCACA
1624880 A
129 A
* *
1624881 TCGAGGATACTCCAGCCCC
1 TCGGGGATACTCCAACCCC
1624900 TTTCTTATCC
Statistics
Matches: 238, Mismatches: 33, Indels: 14
0.84 0.12 0.05
Matches are distributed among these distances:
128 14 0.06
129 64 0.27
130 159 0.67
131 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.33
Consensus pattern (129 bp):
TCGGGGATACTCCAACCCCAATTTTATTTTCAAAACATCAATTTTTCATAATCGAGGATACTCCA
ATCCCGTTATTTCCGAGGGGATACTCCAACCCAGCTTTATTTCTAAAATATTGATTTCTCACAA
Found at i:1637308 original size:1 final size:1
Alignment explanation
Indices: 1637304--1637362 Score: 55
Period size: 1 Copynumber: 59.0 Consensus size: 1
1637294 GCCTTTTTTT
* * * * * * *
1637304 AAAAAAAATAAAAAAATAAAAAAAACAAAAAAAACAAAAAAACAAAACAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1637363 GAGAAAAGAA
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.88, C:0.07, G:0.02, T:0.03
Consensus pattern (1 bp):
A
Found at i:1637325 original size:17 final size:17
Alignment explanation
Indices: 1637303--1637362 Score: 77
Period size: 17 Copynumber: 3.5 Consensus size: 17
1637293 CGCCTTTTTT
*
1637303 TAAAAAAAATAAAAAAA
1 TAAAAAAAACAAAAAAA
1637320 TAAAAAAAACAAAAAAA
1 TAAAAAAAACAAAAAAA
1637337 -ACAAAAAAACAAAACAAA
1 TA-AAAAAAACAAAA-AAA
*
1637355 GAAAAAAA
1 TAAAAAAA
1637363 GAGAAAAGAA
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
16 1 0.03
17 28 0.72
18 9 0.23
19 1 0.03
ACGTcount: A:0.87, C:0.07, G:0.02, T:0.05
Consensus pattern (17 bp):
TAAAAAAAACAAAAAAA
Found at i:1637359 original size:9 final size:8
Alignment explanation
Indices: 1637305--1637362 Score: 62
Period size: 8 Copynumber: 6.9 Consensus size: 8
1637295 CCTTTTTTTA
*
1637305 AAAAAAAT
1 AAAAAAAC
*
1637313 AAAAAAATA
1 AAAAAAA-C
1637322 AAAAAAAC
1 AAAAAAAC
1637330 AAAAAAAAC
1 -AAAAAAAC
1637339 AAAAAAAC
1 AAAAAAAC
*
1637347 AAAACAAAG
1 AAAA-AAAC
1637356 AAAAAAA
1 AAAAAAA
1637363 GAGAAAAGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
8 22 0.50
9 22 0.50
ACGTcount: A:0.88, C:0.07, G:0.02, T:0.03
Consensus pattern (8 bp):
AAAAAAAC
Found at i:1637363 original size:8 final size:8
Alignment explanation
Indices: 1637305--1637374 Score: 52
Period size: 8 Copynumber: 8.5 Consensus size: 8
1637295 CCTTTTTTTA
*
1637305 AAAAAAAT
1 AAAAAAAG
*
1637313 AAAAAAATA
1 AAAAAAA-G
*
1637322 AAAAAAACA
1 AAAAAAA-G
*
1637331 AAAAAAAC
1 AAAAAAAG
*
1637339 AAAAAAAC
1 AAAAAAAG
1637347 AAAACAAAG
1 AAAA-AAAG
1637356 AAAAAAAG
1 AAAAAAAG
*
1637364 -AGAAAAG
1 AAAAAAAG
1637371 AAAA
1 AAAA
1637375 GAACCTGCTT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
7 6 0.11
8 25 0.47
9 22 0.42
ACGTcount: A:0.86, C:0.06, G:0.06, T:0.03
Consensus pattern (8 bp):
AAAAAAAG
Found at i:1637377 original size:10 final size:9
Alignment explanation
Indices: 1637304--1637377 Score: 62
Period size: 9 Copynumber: 8.2 Consensus size: 9
1637294 GCCTTTTTTT
1637304 AAAAAAAA-
1 AAAAAAAAG
* *
1637312 TAAAAAAAT
1 AAAAAAAAG
*
1637321 AAAAAAAAC
1 AAAAAAAAG
1637330 AAAAAAAA-
1 AAAAAAAAG
* *
1637338 CAAAAAAAC
1 AAAAAAAAG
*
1637347 AAAACAAAG
1 AAAAAAAAG
1637356 AAAAAAAGAG
1 AAAAAAA-AG
1637366 AAAAGAAAAG
1 AAAA-AAAAG
1637376 AA
1 AA
1637378 CCTGCTTAAG
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
8 14 0.26
9 27 0.50
10 10 0.19
11 3 0.06
ACGTcount: A:0.85, C:0.05, G:0.07, T:0.03
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:1638655 original size:121 final size:121
Alignment explanation
Indices: 1638462--1638887 Score: 460
Period size: 121 Copynumber: 3.5 Consensus size: 121
1638452 GAGCAGGACG
* ** * *
1638462 CCTTTCAAAGCCCACACCAGTTGGTGGCA-TTTTCCAATCCTCAAAGAGCAGGACG------CCT
1 CCTTTTAAAGCCCACATAAGTTGGTGGCACTTTT-CAGTCTTCAAAGAGCAGGACGACTTTTCCT
* *
1638520 TTTAAAGCCTACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGTAGGACGTCTTTT
65 TTTAAAGCCCACACAAGTTGGTGGCACTTT-CAGTCCTCAAAGAGCAGGACGTCTTTT
* * * * *
1638578 CCTTTTAAAGTCCACATAAGCTGGTGGCTC-CTTCAGTCTTCAAAGAGCAGGACGTCTTTTCCTT
1 CCTTTTAAAGCCCACATAAGTTGGTGGCACTTTTCAGTCTTCAAAGAGCAGGACGACTTTTCCTT
* *
1638642 TTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTC-AAGGGACAGGACGCCTTTT
66 TTAAAGCCCACACAAGTTGGTGGCAC-TTTCAGTCCTCAAAGAG-CAGGACGTCTTTT
* *
1638699 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCTTCAAAGAGCAGGAC-ACTTTTTTC
1 CCTTTTAAAGCCCACATAAGTTGGTGGCACTTTTC-AGTCTTCAAAGAGCAGGACGAC-TTTTCC
* * *
1638763 TTTTCAAAGCCCACACGAGTTGGTGGTACCTTTTAGTCCTCAAAGAGCAGGACGTCTTTT
64 TTTT-AAAGCCCACACAAGTTGGTGGCA-CTTTCAGTCCTCAAAGAGCAGGACGTCTTTT
* * * * * * *
1638823 -CTTTTCAAAACCCATATGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGACGCCTTTACCT
1 CCTTTT-AAAGCCCACATAAGTTGGTGGCACTTTTCAGTCTTCAAAGAGCAGGACGACTTTTCCT
1638887 T
65 T
1638888 CTCTCTTTCG
Statistics
Matches: 259, Mismatches: 34, Indels: 27
0.81 0.11 0.08
Matches are distributed among these distances:
115 19 0.07
116 25 0.10
120 4 0.02
121 74 0.29
122 7 0.03
123 57 0.22
124 68 0.26
125 5 0.02
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (121 bp):
CCTTTTAAAGCCCACATAAGTTGGTGGCACTTTTCAGTCTTCAAAGAGCAGGACGACTTTTCCTT
TTAAAGCCCACACAAGTTGGTGGCACTTTCAGTCCTCAAAGAGCAGGACGTCTTTT
Found at i:1638704 original size:61 final size:61
Alignment explanation
Indices: 1638442--1638887 Score: 476
Period size: 61 Copynumber: 7.5 Consensus size: 61
1638432 TTCACCCTTT
*
1638442 AGTCCTCAAAGAGCAGGACGCC-TTT-C----AAAGCCCACACCAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTT-C
* * *
1638497 AATCCTCAAAGAGCAGGACG------CCTTTTAAAGCCTACACAAGTTGGTGGCACTTTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
* * * * * * *
1638552 AGTCCTCAAAGAGTAGGACGTCTTTTCCTTTTAAAGTCCACATAAGCTGGTGGCTC-CTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
* *
1638612 AGTCTTCAAAGAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
*
1638673 AGTCCTC-AAGGGACAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
1 AGTCCTCAAAGAG-CAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
* * * * * *
1638734 TAGTCTTCAAAGAGCAGGACACTTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGTACCTTTT-
1 -AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCA-CTTTTC
* * * ** *
1638797 AGTCCTCAAAGAGCAGGACGTCTTTT-CTTTTCAAAACCCATATGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCACTTTTC
*
1638858 AGTCCTCAAAGAGCAGGACGCCTTTACCTT
1 AGTCCTCAAAGAGCAGGACGCCTTTTCCTT
1638888 CTCTCTTTCG
Statistics
Matches: 331, Mismatches: 40, Indels: 33
0.82 0.10 0.08
Matches are distributed among these distances:
51 1 0.00
55 59 0.18
56 3 0.01
60 61 0.18
61 130 0.39
62 47 0.14
63 25 0.08
64 5 0.02
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (61 bp):
AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
Found at i:1638850 original size:185 final size:182
Alignment explanation
Indices: 1638462--1638887 Score: 496
Period size: 185 Copynumber: 2.4 Consensus size: 182
1638452 GAGCAGGACG
* * * *
1638462 CCTTTCAAAGCCCACACCAGTTGGTGGCA-TTTTCCAATCCTCAAAGAGCAGGACG------CCT
1 CCTTTTAAAACCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAGGACGCCTTTACCT
* * *
1638520 TTTAAAGCCTACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGTAGGACGTCTTTTCCTTTTA
65 TTTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGACCTCTTTTCCTTTTA
* * *
1638585 AAGTCCACATAAGCTGGTGGCTCCTTCAGTCTTCAAAGAGCAGGACGTCTTTT
130 AAGCCCACACAAGCTGGTGGCTCCTTCAGTCCTCAAAGAGCAGGACGTCTTTT
* * *
1638638 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTC-AAGGGACAGGACGCCTTTTCCT
1 CCTTTTAAAACCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAG-CAGGACGCCTTTACCT
* * *
1638702 TTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCTTCAAAGAGCAGGACACT-TTTTTCTTT
65 TTTAAAGCCCACACAAGTTGGTGGCAC-TTTCCAGTCCTCAAAGAGCAGGAC-CTCTTTTCCTTT
* * *
1638766 TCAAAGCCCACACGAGTTGGTGG-TACCTTTTAGTCCTCAAAGAGCAGGACGTCTTTT
128 T-AAAGCCCACACAAGCTGGTGGCT-CC-TTCAGTCCTCAAAGAGCAGGACGTCTTTT
* ** *
1638823 -CTTTTCAAAACCCATATGAGTTGGTGGCACTTTTTAGTCCTCAAAGAGCAGGACGCCTTTACCT
1 CCTTTT-AAAACCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTACCT
1638887 T
65 T
1638888 CTCTCTTTCG
Statistics
Matches: 212, Mismatches: 23, Indels: 21
0.83 0.09 0.08
Matches are distributed among these distances:
175 4 0.02
176 41 0.19
177 4 0.02
182 29 0.14
183 31 0.15
184 25 0.12
185 74 0.35
186 4 0.02
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (182 bp):
CCTTTTAAAACCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTTACCTT
TTAAAGCCCACACAAGTTGGTGGCACTTTCCAGTCCTCAAAGAGCAGGACCTCTTTTCCTTTTAA
AGCCCACACAAGCTGGTGGCTCCTTCAGTCCTCAAAGAGCAGGACGTCTTTT
Found at i:1638965 original size:42 final size:42
Alignment explanation
Indices: 1638918--1639165 Score: 191
Period size: 41 Copynumber: 5.9 Consensus size: 42
1638908 CAGGACGCCT
* * *
1638918 TTTCCTTTTTTCCTTTGTCCTCAAAGAGTAGGATGCACTTCA
1 TTTCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCATTTCA
* *
1638960 TTTCCTTCTTTTCCTTTCTAATTCTCAAAGAGCAGGACGCACTTT-A
1 TTTCCTT-TTTTCC-TT-T-GTCCTCAAAGAGCAGGACGCA-TTTCA
* * * * *
1639006 TTCTCC-TTTTTCCTTTGTCTTTAAAAAGCAGGACACATTTAA
1 TT-TCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCATTTCA
* * * * *
1639048 TTTCC-TTTTTCCTTTGTCTTTAAAGGGCAGGATGCATTTTA
1 TTTCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCATTTCA
* * * * *
1639089 TTTCCTTTTTTCCTTAGTCCCCAAGGAGCATGACCCATTTCA
1 TTTCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCATTTCA
** *
1639131 -TT-CTCTTTTTCCTTAATCCTCAAAGAGTAGGACGC
1 TTTCCT-TTTTTCCTTTGTCCTCAAAGAGCAGGACGC
1639166 CCCCTTCCTT
Statistics
Matches: 165, Mismatches: 32, Indels: 19
0.76 0.15 0.09
Matches are distributed among these distances:
40 2 0.01
41 68 0.41
42 51 0.31
43 7 0.04
44 4 0.02
45 7 0.04
46 21 0.13
47 5 0.03
ACGTcount: A:0.21, C:0.24, G:0.13, T:0.42
Consensus pattern (42 bp):
TTTCCTTTTTTCCTTTGTCCTCAAAGAGCAGGACGCATTTCA
Found at i:1639723 original size:13 final size:13
Alignment explanation
Indices: 1639707--1639736 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1639697 ATACATTGTT
*
1639707 CATTGTATCGATA
1 CATTGTATCAATA
1639720 CATTGTATCAATA
1 CATTGTATCAATA
1639733 CATT
1 CATT
1639737 CAAGCATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (13 bp):
CATTGTATCAATA
Found at i:1642239 original size:51 final size:51
Alignment explanation
Indices: 1642114--1642335 Score: 239
Period size: 51 Copynumber: 4.4 Consensus size: 51
1642104 TTATTTTCGA
* * ** *
1642114 GGGGATACTCCAACCCCGGCTTTATTTCTAAAATATTGATTTCTCATAATC
1 GGGGATACTCCAACCCCGACTTTATTTCTAAAACATCAATTTCTCACAATC
* * * * *
1642165 -GGGATACTCCAACCCCAATTTTATTTCCAAAACATCAATTTTTCATAATC
1 GGGGATACTCCAACCCCGACTTTATTTCTAAAACATCAATTTCTCACAATC
* * * **
1642215 GGGGATACTCCAACCCCGGCTTTATTTTTAAAATATTGATTTCTCACAATC
1 GGGGATACTCCAACCCCGACTTTATTTCTAAAACATCAATTTCTCACAATC
** * * * *
1642266 GGAAATACTCCAACCCCAATTTTATTTCTAAAACACCAATCTTTTCACAATC
1 GGGGATACTCCAACCCCGACTTTATTTCTAAAACATCAAT-TTCTCACAATC
1642318 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
1642336 TTATTTTTGA
Statistics
Matches: 137, Mismatches: 32, Indels: 3
0.80 0.19 0.02
Matches are distributed among these distances:
50 42 0.31
51 70 0.51
52 25 0.18
ACGTcount: A:0.31, C:0.27, G:0.11, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGACTTTATTTCTAAAACATCAATTTCTCACAATC
Found at i:1642402 original size:78 final size:78
Alignment explanation
Indices: 1642272--1642415 Score: 225
Period size: 78 Copynumber: 1.8 Consensus size: 78
1642262 AATCGGAAAT
* *
1642272 ACTCCAACCCCAATTTTATTTCTAAAACACCAATCTTTTCACAATCGGGGATACTCCAACCCCGT
1 ACTCCAACCCCAATTTTATTTCCAAAACACCAATCTTTTCACAATCGAGGATACTCCAACCCCGT
1642337 TATTTTTGAAGGA
66 TATTTTTGAAGGA
* * * * *
1642350 ACTCCAACCCCAGTTTTATTTCCAAAACATCGATTTTTTCATAATCGAGGATACTCCAACCCCGT
1 ACTCCAACCCCAATTTTATTTCCAAAACACCAATCTTTTCACAATCGAGGATACTCCAACCCCGT
1642415 T
66 T
1642416 GTTATTCCCG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
78 59 1.00
ACGTcount: A:0.30, C:0.29, G:0.10, T:0.31
Consensus pattern (78 bp):
ACTCCAACCCCAATTTTATTTCCAAAACACCAATCTTTTCACAATCGAGGATACTCCAACCCCGT
TATTTTTGAAGGA
Found at i:1645211 original size:13 final size:13
Alignment explanation
Indices: 1645188--1645222 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1645178 AGTACCTTTA
*
1645188 TATCAATACAATG
1 TATCGATACAATG
*
1645201 TATTGATACAATG
1 TATCGATACAATG
1645214 TATCGATAC
1 TATCGATAC
1645223 TAAGATCCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:1645284 original size:20 final size:21
Alignment explanation
Indices: 1645254--1645292 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1645244 TCTGTGTTTT
*
1645254 TTCAGATGTATTGATACATCA
1 TTCAGATGTATCGATACATCA
1645275 TTCA-ATGTATCGATACAT
1 TTCAGATGTATCGATACAT
1645293 TCTAGAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (21 bp):
TTCAGATGTATCGATACATCA
Found at i:1646005 original size:167 final size:167
Alignment explanation
Indices: 1645729--1646068 Score: 554
Period size: 167 Copynumber: 2.0 Consensus size: 167
1645719 ATCTCCTTTT
* * * *
1645729 TGCACATGATCTCTAATGAAGTGATGTCTAATTTCAATGTGCTTAGTCCTAGAGTGTTGTATGAG
1 TGCACATGATCTCTAATGAAATGATGTCTAATTTCAATATGCTTAGTCCTAGAGTATTGTACGAG
* *
1645794 ATTTTTGGTAATACAAATGGCACTAACATTGTCATATTTAATGGGAATATAATCCATGGTGATAC
66 ATTTTTGGTAAGACAAATGGCACTAACATTGTCACATTTAATGGGAATATAATCCATGGTGATAC
*
1645859 CAAAATCCTTTAATTGTTGTTTTATCCACAATATCTG
131 CAAAATCCTTTAATTGTTGTTTTATCCACAATACCTG
* * *
1645896 TGCACATGATCTCTAATGAAATGATGTTTAATTTCAATATGCTTAGTCTTAGAGTATTGTACGAT
1 TGCACATGATCTCTAATGAAATGATGTCTAATTTCAATATGCTTAGTCCTAGAGTATTGTACGAG
* *
1645961 ATTTTTGGTAAGACAAATGGCACTAGCATTGTCACATTTAATGGGAATATGATCCATGGTGATAC
66 ATTTTTGGTAAGACAAATGGCACTAACATTGTCACATTTAATGGGAATATAATCCATGGTGATAC
* *
1646026 CAAAATTCTTTAATTGTTGTTTTATCCATAATACCTG
131 CAAAATCCTTTAATTGTTGTTTTATCCACAATACCTG
1646063 TGCACA
1 TGCACA
1646069 ACAACTTCCT
Statistics
Matches: 159, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
167 159 1.00
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (167 bp):
TGCACATGATCTCTAATGAAATGATGTCTAATTTCAATATGCTTAGTCCTAGAGTATTGTACGAG
ATTTTTGGTAAGACAAATGGCACTAACATTGTCACATTTAATGGGAATATAATCCATGGTGATAC
CAAAATCCTTTAATTGTTGTTTTATCCACAATACCTG
Found at i:1651717 original size:33 final size:32
Alignment explanation
Indices: 1651654--1651717 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
1651644 CTTTTTAAGG
* * * *
1651654 TGTATCGATGCTATGAATGTGTATCGATACAA
1 TGTATCGATACTAAGAATATGTATCAATACAA
1651686 TGTATCGATACTAAGCAATATGTATCAATACA
1 TGTATCGATACTAAG-AATATGTATCAATACA
1651718 TCTAGGTGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (32 bp):
TGTATCGATACTAAGAATATGTATCAATACAA
Found at i:1651829 original size:24 final size:24
Alignment explanation
Indices: 1651797--1651869 Score: 146
Period size: 24 Copynumber: 3.0 Consensus size: 24
1651787 CAAATACCTA
1651797 TGTATCGATACTTTGGATTATTTT
1 TGTATCGATACTTTGGATTATTTT
1651821 TGTATCGATACTTTGGATTATTTT
1 TGTATCGATACTTTGGATTATTTT
1651845 TGTATCGATACTTTGGATTATTTT
1 TGTATCGATACTTTGGATTATTTT
1651869 T
1 T
1651870 ACTTGAAAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.21, C:0.08, G:0.16, T:0.55
Consensus pattern (24 bp):
TGTATCGATACTTTGGATTATTTT
Found at i:1653740 original size:20 final size:20
Alignment explanation
Indices: 1653716--1653768 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
1653706 ATATTTATAG
1653716 ATGTATCGATACATTATG-T
1 ATGTATCGATACATTATGAT
*
1653735 ATTGTATCGATACATTTTGAT
1 A-TGTATCGATACATTATGAT
*
1653756 ATGTATCAATACA
1 ATGTATCGATACA
1653769 AATAAGAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 1 0.03
20 27 0.90
21 2 0.07
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTATGAT
Found at i:1655470 original size:21 final size:21
Alignment explanation
Indices: 1655445--1655488 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1655435 CTTAGAACAT
* *
1655445 ATATTATATTGATATAAGGTC
1 ATATTATATCGATACAAGGTC
* *
1655466 ATATTGTATCGATACAATGTC
1 ATATTATATCGATACAAGGTC
1655487 AT
1 AT
1655489 GTTTTTCATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (21 bp):
ATATTATATCGATACAAGGTC
Found at i:1657163 original size:58 final size:57
Alignment explanation
Indices: 1657018--1657171 Score: 177
Period size: 58 Copynumber: 2.6 Consensus size: 57
1657008 TTTTTTTGTC
** *
1657018 ATTTCATATATTTTAAGGTCATTTTAGTAATTTGACATGTTTTAGGACCGTTTATGCA
1 ATTTCATGCATTTTAAGGTC-TTTTAGTAATTTGTCATGTTTTAGGACCGTTTATGCA
* * *
1657076 ATTTCATGCGTTTTGAAGTTATTTTAGTAATTTGTCATGTTTTAGGA-C-TATTATGCA
1 ATTTCATGCATTTT-AAGGTCTTTTAGTAATTTGTCATGTTTTAGGACCGT-TTATGCA
* *
1657133 ATTTCATGCATTTTAGGGTCTTTTAAAGTAATTTTTCAT
1 ATTTCATGCATTTTAAGGTCTTTT--AGTAATTTGTCAT
1657172 AATTGAAGGG
Statistics
Matches: 81, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
56 8 0.10
57 21 0.26
58 48 0.59
59 4 0.05
ACGTcount: A:0.26, C:0.10, G:0.16, T:0.49
Consensus pattern (57 bp):
ATTTCATGCATTTTAAGGTCTTTTAGTAATTTGTCATGTTTTAGGACCGTTTATGCA
Found at i:1657251 original size:58 final size:58
Alignment explanation
Indices: 1657169--1657287 Score: 159
Period size: 58 Copynumber: 2.1 Consensus size: 58
1657159 AGTAATTTTT
* * *
1657169 CATAATTGAAGGGTTATTATGTAATTTCACGTATTTTAGCATCATTTTAGTCATCTT-C
1 CATAATTGAAGGGTAATTACGTAATTTCACGCATTTTAGCATCATTTTAGTCA-CTTGC
* ** *
1657227 CATAATTGAGGGGTAATTACGTAATTTCGTGCATTTTTGCATCATTTTAGTCACTTGC
1 CATAATTGAAGGGTAATTACGTAATTTCACGCATTTTAGCATCATTTTAGTCACTTGC
1657285 CAT
1 CAT
1657288 GATTTAGGAC
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
57 3 0.06
58 50 0.94
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.43
Consensus pattern (58 bp):
CATAATTGAAGGGTAATTACGTAATTTCACGCATTTTAGCATCATTTTAGTCACTTGC
Found at i:1657309 original size:58 final size:58
Alignment explanation
Indices: 1657184--1657350 Score: 151
Period size: 58 Copynumber: 2.9 Consensus size: 58
1657174 TTGAAGGGTT
* * * * * ***
1657184 ATTATGTAATTTCACGTATTTTAGCATCATTTTAGTCATCTT-CCATAATTGAGGGGTA
1 ATTATGTAATTTCATGCATTTTTGCATCATTTTAGTCA-CTTGCCATGATTTAGGACCA
* *
1657242 ATTACGTAATTTCGTGCATTTTTGCATCATTTTAGTCACTTGCCATGATTTAGGACCA
1 ATTATGTAATTTCATGCATTTTTGCATCATTTTAGTCACTTGCCATGATTTAGGACCA
* * * * * *
1657300 TTTATGTAATTTTATGCAATTTAT-AATCATTTTAGT-AATTGCCATGTTTTA
1 ATTATGTAATTTCATGC-ATTTTTGCATCATTTTAGTCACTTGCCATGATTTA
1657351 AAAACTTTTA
Statistics
Matches: 89, Mismatches: 18, Indels: 5
0.79 0.16 0.04
Matches are distributed among these distances:
57 16 0.18
58 68 0.76
59 5 0.06
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.46
Consensus pattern (58 bp):
ATTATGTAATTTCATGCATTTTTGCATCATTTTAGTCACTTGCCATGATTTAGGACCA
Found at i:1658377 original size:17 final size:17
Alignment explanation
Indices: 1658334--1658382 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
1658324 TTTTTATTGT
1658334 TTTTAT-TTTTAAAATA
1 TTTTATATTTTAAAATA
1658350 ---TA-ATTTT-AAATA
1 TTTTATATTTTAAAATA
1658362 TTTTATATTTTAAAATA
1 TTTTATATTTTAAAATA
1658379 TTTT
1 TTTT
1658383 TTTCTATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 11
0.71 0.00 0.29
Matches are distributed among these distances:
12 5 0.19
13 6 0.22
15 2 0.07
16 5 0.19
17 9 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTATATTTTAAAATA
Found at i:1659369 original size:29 final size:29
Alignment explanation
Indices: 1659318--1659547 Score: 192
Period size: 29 Copynumber: 7.8 Consensus size: 29
1659308 GTTGCCATAA
* * *
1659318 TACTCTTTGGCATAAGTACTTTTTGTACAGG
1 TACT-TTTGGCACAAGTA-TTTTGGCACAGG
* *
1659349 TACTTTTTGCACAAGTATTTTGGCACAAG
1 TACTTTTGGCACAAGTATTTTGGCACAGG
* * * *
1659378 TACTTTTGGCACAGGTACTTTGACATAGG
1 TACTTTTGGCACAAGTATTTTGGCACAGG
* * **
1659407 TACTTTTGGCACAAGTACTTTGGCATATA
1 TACTTTTGGCACAAGTATTTTGGCACAGG
* *
1659436 TACTTTTGGCATAAATATTTTGGCACAGG
1 TACTTTTGGCACAAGTATTTTGGCACAGG
* * * *
1659465 TACCTTTAGCATAAGTACTTTTGGTACAGG
1 TACTTTTGGCACAAGTA-TTTTGGCACAGG
* * * *
1659495 TACCTTTGGCACAGGTACTTTTAGCATAGG
1 TACTTTTGGCACAAGTA-TTTTGGCACAGG
*
1659525 TA-TTTTCAGCACAAGTATTTTGG
1 TACTTTT-GGCACAAGTATTTTGG
1659548 GAACAACATA
Statistics
Matches: 162, Mismatches: 35, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
29 102 0.63
30 56 0.35
31 4 0.02
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.38
Consensus pattern (29 bp):
TACTTTTGGCACAAGTATTTTGGCACAGG
Found at i:1659392 original size:44 final size:44
Alignment explanation
Indices: 1659323--1659547 Score: 195
Period size: 44 Copynumber: 5.1 Consensus size: 44
1659313 CATAATACTC
* * * * *
1659323 TTTGGCATAAGTACTTTTTGTACAGGTACTTTTTGCACAAGTAT
1 TTTGGCACAAGTACTTTTAGCATAGGTACTTTTGGCACAAGTAT
* * * * *
1659367 TTTGGCACAAGTACTTTTGGCACAGGTAC-TTTGACATAGGTACT
1 TTTGGCACAAGTACTTTTAGCATAGGTACTTTTGGCACAAGTA-T
* ** * *
1659411 TTTGGCACAAGTAC-TTTGGCATATATACTTTTGGCATAAATAT
1 TTTGGCACAAGTACTTTTAGCATAGGTACTTTTGGCACAAGTAT
* * * * * *
1659454 TTTGGCACAGGTACCTTTAGCATAAGTACTTTTGGTACAGGTACC
1 TTTGGCACAAGTACTTTTAGCATAGGTACTTTTGGCACAAGTA-T
* *
1659499 TTTGGCACAGGTACTTTTAGCATAGGTA-TTTTCAGCACAAGTAT
1 TTTGGCACAAGTACTTTTAGCATAGGTACTTTT-GGCACAAGTAT
1659543 TTTGG
1 TTTGG
1659548 GAACAACATA
Statistics
Matches: 148, Mismatches: 28, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
43 34 0.23
44 81 0.55
45 33 0.22
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.38
Consensus pattern (44 bp):
TTTGGCACAAGTACTTTTAGCATAGGTACTTTTGGCACAAGTAT
Found at i:1659497 original size:15 final size:15
Alignment explanation
Indices: 1659318--1659530 Score: 166
Period size: 15 Copynumber: 14.5 Consensus size: 15
1659308 GTTGCCATAA
* *
1659318 TACTCTTTGGCATAAG
1 TACT-TTTGGCACAGG
* *
1659334 TACTTTTTGTACAGG
1 TACTTTTGGCACAGG
* *
1659349 TACTTTTTGCACAAG
1 TACTTTTGGCACAGG
*
1659364 TA-TTTTGGCACAAG
1 TACTTTTGGCACAGG
1659378 TACTTTTGGCACAGG
1 TACTTTTGGCACAGG
* *
1659393 TAC-TTTGACATAGG
1 TACTTTTGGCACAGG
*
1659407 TACTTTTGGCACAAG
1 TACTTTTGGCACAGG
* **
1659422 TAC-TTTGGCATATA
1 TACTTTTGGCACAGG
* **
1659436 TACTTTTGGCATAAA
1 TACTTTTGGCACAGG
1659451 TA-TTTTGGCACAGG
1 TACTTTTGGCACAGG
* * * *
1659465 TACCTTTAGCATAAG
1 TACTTTTGGCACAGG
*
1659480 TACTTTTGGTACAGG
1 TACTTTTGGCACAGG
*
1659495 TACCTTTGGCACAGG
1 TACTTTTGGCACAGG
* *
1659510 TACTTTTAGCATAGG
1 TACTTTTGGCACAGG
1659525 TA-TTTT
1 TACTTTT
1659531 CAGCACAAGT
Statistics
Matches: 159, Mismatches: 34, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
14 51 0.32
15 104 0.65
16 4 0.03
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.38
Consensus pattern (15 bp):
TACTTTTGGCACAGG
Found at i:1659535 original size:15 final size:14
Alignment explanation
Indices: 1659451--1659545 Score: 55
Period size: 15 Copynumber: 6.4 Consensus size: 14
1659441 TTGGCATAAA
*
1659451 TATTTTGGCACAGG
1 TATTTTAGCACAGG
* * *
1659465 TACCTTTAGCATAAG
1 TA-TTTTAGCACAGG
* *
1659480 TACTTTTGGTACAGG
1 TA-TTTTAGCACAGG
* *
1659495 TACCTTTGGCACAGG
1 TA-TTTTAGCACAGG
*
1659510 TACTTTTAGCATAGG
1 TA-TTTTAGCACAGG
*
1659525 TATTTTCAGCACAAG
1 TATTTT-AGCACAGG
1659540 TATTTT
1 TATTTT
1659546 GGGAACAACA
Statistics
Matches: 63, Mismatches: 16, Indels: 3
0.77 0.20 0.04
Matches are distributed among these distances:
14 6 0.10
15 57 0.90
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (14 bp):
TATTTTAGCACAGG
Found at i:1661499 original size:13 final size:13
Alignment explanation
Indices: 1661481--1661506 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1661471 TACACAAAGT
1661481 ATGTATCGATACA
1 ATGTATCGATACA
1661494 ATGTATCGATACA
1 ATGTATCGATACA
1661507 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1661525 original size:34 final size:32
Alignment explanation
Indices: 1661463--1661527 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
1661453 TAGCCAAACT
**
1661463 TGTATCGATACACAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAATGTATCGATACAA
1661495 TGTATCGATACACAAAAAAATTGTATCGATACA
1 TGTATCGATACAC-AAAAAA-TGTATCGATACA
1661528 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 13 0.45
33 4 0.14
34 12 0.41
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACAAAAAATGTATCGATACAA
Found at i:1663399 original size:19 final size:19
Alignment explanation
Indices: 1663375--1663425 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
1663365 TTTCAACGAT
1663375 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
*
1663394 TTGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTG
1663413 TTGTATCGATACA
1 TTGTATCGATACA
1663426 GTGTAAGCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:1663485 original size:13 final size:13
Alignment explanation
Indices: 1663467--1663491 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1663457 ATTACTCAAA
1663467 TGTATCGATACAT
1 TGTATCGATACAT
1663480 TGTATCGATACA
1 TGTATCGATACA
1663492 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1663541 original size:52 final size:52
Alignment explanation
Indices: 1663500--1663680 Score: 353
Period size: 52 Copynumber: 3.5 Consensus size: 52
1663490 CACTGATCTT
1663500 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1663552 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATATACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1663604 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1663656 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1663681 TCATATTTCG
Statistics
Matches: 127, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 127 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1670338 original size:18 final size:18
Alignment explanation
Indices: 1670281--1670347 Score: 63
Period size: 18 Copynumber: 3.9 Consensus size: 18
1670271 CCGGAACAGT
*
1670281 CAAAAGT-AAACACACAAA
1 CAAAAGTCAAA-AAACAAA
*
1670299 CAAAAGACAAAAGAA-AAA
1 CAAAAGTCAAAA-AACAAA
1670317 -AAAAGTCAAAAAACAAA
1 CAAAAGTCAAAAAACAAA
1670334 CAAAA--CAAAAAACA
1 CAAAAGTCAAAAAACA
1670348 CACACAAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
16 11 0.26
17 13 0.31
18 14 0.33
19 4 0.10
ACGTcount: A:0.75, C:0.16, G:0.06, T:0.03
Consensus pattern (18 bp):
CAAAAGTCAAAAAACAAA
Found at i:1670626 original size:20 final size:21
Alignment explanation
Indices: 1670597--1670639 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
1670587 GTTCTTTTCC
*
1670597 AAACACAAAAA-AAAAAAGAA
1 AAACAAAAAAACAAAAAAGAA
*
1670617 AAACAAAAAAACAAAATAGAA
1 AAACAAAAAAACAAAAAAGAA
1670638 AA
1 AA
1670640 TCTCGGTCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.84, C:0.09, G:0.05, T:0.02
Consensus pattern (21 bp):
AAACAAAAAAACAAAAAAGAA
Found at i:1671684 original size:31 final size:31
Alignment explanation
Indices: 1671643--1671725 Score: 94
Period size: 31 Copynumber: 2.7 Consensus size: 31
1671633 ATACCTTTTT
*
1671643 AAAGTCCACGACTCAGTGGCAATTTCTTCTC
1 AAAGTCCACGACTCAGTGGCAACTTCTTCTC
* * * *
1671674 AAAGTGCACGACTCCGTGGCACCTTCTTTTC
1 AAAGTCCACGACTCAGTGGCAACTTCTTCTC
* * *
1671705 AAAGCCCACAACTCCGTGGCA
1 AAAGTCCACGACTCAGTGGCA
1671726 CTCTTTGTTC
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.24
Consensus pattern (31 bp):
AAAGTCCACGACTCAGTGGCAACTTCTTCTC
Found at i:1671916 original size:100 final size:101
Alignment explanation
Indices: 1671674--1672402 Score: 616
Period size: 100 Copynumber: 7.3 Consensus size: 101
1671664 ATTTCTTCTC
* * * *
1671674 AAAGTGCACGACTCCGTGGCACC---TTCTTTTCAAAGCCCACAACTCCGTGGCACTCTTTGTTC
1 AAAGTCCACAACTCCGTGGCACCTTGTTCCTTTCAAAGTCCACAACTCCGTGGCAC-CTTT-TT-
* * * *
1671736 CTTTT--AAGTCCACGACCCCGTGGCATCTTGTTCCTTTT
63 CTTTTCAAAGCCCACAACTCCGTGGCACCTT-TTCCTTTT
* * * *
1671774 -AAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
1 AAAGTCCACAACTCCGTGGCACCTTGTTCCTTTCAAAGTCCACAACTCCGTGGCACCTTTTTCTT
* *
1671838 TTCAAAGCCCACCACTCCGTGGTACCTTTTCCTTTT
66 TTCAAAGCCCACAACTCCGTGGCACCTTTTCCTTTT
* *
1671874 -AAGTCCACGACCCCGTGGCACCTTGTTCCTTTCAAAGTCCACAACTCCGTGGCACTCTTTTTCC
1 AAAGTCCACAACTCCGTGGCACCTTGTTCCTTTCAAAGTCCACAACTCCGTGGCAC-CTTTTT--
* * *
1671938 CTTTT-AAAGTCCACAACCCCGTGGCTCCTTGTTCCTTTT
63 CTTTTCAAAGCCCACAACTCCGTGGCACCTT-TTCCTTTT
* * *
1671977 -AAGTCCACGACTCCGTGGCACC---TTCCTTTCAAAGTCCGCGACTCCGTGGCACC---TTCTT
1 AAAGTCCACAACTCCGTGGCACCTTGTTCCTTTCAAAGTCCACAACTCCGTGGCACCTTTTTCTT
*
1672035 TTCAAAGCCCACAACTCTGTGGCACTCTTTTTCCTTTTT
66 TTCAAAGCCCACAACTCCGTGGCAC-C-TTTTCC-TTTT
** * *
1672074 AAAGTCCACAACTCCGTGGCACCTTGTT-CTTTTTAAGTCCACGACTCCATGGCACC---TTCTT
1 AAAGTCCACAACTCCGTGGCACCTTGTTCCTTTCAAAGTCCACAACTCCGTGGCACCTTTTTCTT
1672135 TTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
66 TTCAAAGCCCACAACTCCGTGGCAC-C-TTTT-CCTTTT
* * * ** * *
1672174 AAAGTCCACAACCCCATGGCACCTTGTTCCTTT-TAAGTCCATGACTCTGTGGCACC---TTCCT
1 AAAGTCCACAACTCCGTGGCACCTTGTTCCTTTCAAAGTCCACAACTCCGTGGCACCTTTTTCTT
* * * *
1672235 TTCAAAGTCCGCGACTTCGTGGCACC--TT-CTTTT
66 TTCAAAGCCCACAACTCCGTGGCACCTTTTCCTTTT
* * * *
1672268 CAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAAGCCCACAACTCCGTGGCACCTTGTT
1 -AAAGTCCACAACTCCGTGGCAC-CTTGTT-CCTTTCAAAGTCCACAACTCCGTGGCACCTT-TT
* * * * * *
1672333 CCTTTT--AAGTCCACAACTTCATGGCATCTTTCACCCTTTTT
62 TCTTTTCAAAGCCCACAACTCCGTGGCACCTTT--TCC-TTTT
* *
1672374 AAAGCCCACAACTCCGTGGCATCTT-TTCC
1 AAAGTCCACAACTCCGTGGCACCTTGTTCC
1672403 CTTCTCTAAA
Statistics
Matches: 537, Mismatches: 59, Indels: 64
0.81 0.09 0.10
Matches are distributed among these distances:
94 10 0.02
95 37 0.07
96 14 0.03
97 11 0.02
98 39 0.07
99 27 0.05
100 240 0.45
101 37 0.07
102 57 0.11
103 36 0.07
104 3 0.01
105 22 0.04
106 4 0.01
ACGTcount: A:0.19, C:0.34, G:0.14, T:0.32
Consensus pattern (101 bp):
AAAGTCCACAACTCCGTGGCACCTTGTTCCTTTCAAAGTCCACAACTCCGTGGCACCTTTTTCTT
TTCAAAGCCCACAACTCCGTGGCACCTTTTCCTTTT
Found at i:1672149 original size:231 final size:230
Alignment explanation
Indices: 1671639--1672419 Score: 954
Period size: 231 Copynumber: 3.3 Consensus size: 230
1671629 TCAAATACCT
** * ** *
1671639 TTTTAAAGTCCACGACT-CAGTGGCAATTTCTTCTCAAAGTGCACGACTCCGTGGCAC-C--TT-
1 TTTT-AAGTCCACGACTCCA-TGGCACCTTCTTTTCAAAGCCCACAACTCCGTGGCACTCTTTTC
* * *
1671699 -CTTTTCAAAGCCCACAACTCCGTGGCACTCTTTGTTCCTTTTAAGTCCACGACCCCGTGGCATC
64 CCTTTT-AAAGCCCACAACCCCGTGG--CTCCTTGTTCCTTTTAAGTCCACGACTCCGTGGCA-C
* * * * *
1671763 TTGTTCCTTT-TAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGC
125 --CTTCCTTTCAAAGTCCGCGACTCCGTGGCACC---TTCTTTTCAAAGCCCACAACTCCGTGGC
* * *
1671827 AC-CTTTTT-CTTTTCAAAGCCCACCACTCCGTGGTACCTT-TTCC
185 ACTCTTTTTCCTTTTTAAAGCCCACAACTCCGTGGCACCTTGTTCC
* * * *
1671870 TTTTAAGTCCACGACCCCGTGGCACCTTGTTCCTTTCAAAGTCCACAACTCCGTGGCACTCTTTT
1 TTTTAAGTCCACGACTCCATGGCACC---TTCTTTTCAAAGCCCACAACTCCGTGGCACTC-TTT
*
1671935 TCCCTTTTAAAGTCCACAACCCCGTGGCTCCTTGTTCCTTTTAAGTCCACGACTCCGTGGCACCT
62 TCCCTTTTAAAGCCCACAACCCCGTGGCTCCTTGTTCCTTTTAAGTCCACGACTCCGTGGCACCT
*
1672000 TCCTTTCAAAGTCCGCGACTCCGTGGCACCTTCTTTTCAAAGCCCACAACTCTGTGGCACTCTTT
127 TCCTTTCAAAGTCCGCGACTCCGTGGCACCTTCTTTTCAAAGCCCACAACTCCGTGGCACTCTTT
* *
1672065 TTCCTTTTTAAAGTCCACAACTCCGTGGCACCTTGTTCT
192 TTCCTTTTTAAAGCCCACAACTCCGTGGCACCTTGTTCC
1672104 TTTTAAGTCCACGACTCCATGGCACCTTCTTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTCC
1 TTTTAAGTCCACGACTCCATGGCACCTTCTTTTCAAAGCCCACAACTCCGTGGCACTC-TTTTCC
* * * * *
1672169 CTTTTAAAGTCCACAACCCCATGGCACCTTGTTCCTTTTAAGTCCATGACTCTGTGGCACCTTCC
65 CTTTTAAAGCCCACAACCCCGTGGCTCCTTGTTCCTTTTAAGTCCACGACTCCGTGGCACCTTCC
*
1672234 TTTCAAAGTCCGCGACTTCGTGGCACCTTCTTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTC
130 TTTCAAAGTCCGCGACTCCGTGGCACCTTCTTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTC
*
1672299 CCTTTTAAAGCCCACAACTCCGTGGCACCTTGTTCC
195 CTTTTTAAAGCCCACAACTCCGTGGCACCTTGTTCC
* * * *
1672335 TTTTAAGTCCACAACTTCATGGCATCTTTCACCCTTTTTAAAGCCCACAACTCCGTGGCA-TCTT
1 TTTTAAGTCCACGACTCCATGGCA-CCTT----CTTTTCAAAGCCCACAACTCCGTGGCACTCTT
1672399 TTCCCTTCTCTAAAGCCCACA
61 TTCCCTT-T-TAAAGCCCACA
1672420 CAAGTCAGTG
Statistics
Matches: 488, Mismatches: 41, Indels: 37
0.86 0.07 0.07
Matches are distributed among these distances:
230 16 0.03
231 249 0.51
232 9 0.02
233 60 0.12
234 57 0.12
235 4 0.01
236 69 0.14
237 2 0.00
238 17 0.03
239 5 0.01
ACGTcount: A:0.19, C:0.34, G:0.14, T:0.32
Consensus pattern (230 bp):
TTTTAAGTCCACGACTCCATGGCACCTTCTTTTCAAAGCCCACAACTCCGTGGCACTCTTTTCCC
TTTTAAAGCCCACAACCCCGTGGCTCCTTGTTCCTTTTAAGTCCACGACTCCGTGGCACCTTCCT
TTCAAAGTCCGCGACTCCGTGGCACCTTCTTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTCC
TTTTTAAAGCCCACAACTCCGTGGCACCTTGTTCC
Found at i:1672358 original size:131 final size:132
Alignment explanation
Indices: 1671674--1672364 Score: 665
Period size: 131 Copynumber: 5.2 Consensus size: 132
1671664 ATTTCTTCTC
* * * * * *
1671674 AAAGTGCACGACTCCGTGGCACC-TTCTTTTCAAAGCCCACAACTCCGTGGCACTCTTTGTTCCT
1 AAAGTCCACAACTCCGTGGCACCTTTCCTTTCAAAGTCCACGACTCCGTGGCAC-C-TTCTT--T
** * * *
1671738 TTTAAGTCCACGACCCCGTGGCA-TCTTGTTCCTTTT-AAGTCCACAACTCCGTGGCACCTTTTT
62 TCAAAGCCCACAACTCCGTGGCACTCTTGTTCCTTTTAAAGTCCACAACTCCGTGGCACCTTTTT
*
1671801 CTTTTT
127 CCTTTT
* * * * *
1671807 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTCAAAGCCCACCACTCCGTGGTACCTTTTCCTT
1 AAAGTCCACAACTCCGTGGCACC--TTTCCTTTCAAAGTCCACGACTCCGTGGCACC--TT-CTT
* * * *
1671872 TT--AAGTCCACGACCCCGTGGCAC-CTTGTTCCTTTCAAAGTCCACAACTCCGTGGCACTCTTT
61 TTCAAAGCCCACAACTCCGTGGCACTCTTGTTCCTTTTAAAGTCCACAACTCCGTGGCAC-CTTT
1671934 TTCCCTTTT
125 TT-CCTTTT
* * * *
1671943 AAAGTCCACAACCCCGTGGCTCCTTGTTCCTTT-TAAGTCCACGACTCCGTGGCACCTTCCTTTC
1 AAAGTCCACAACTCCGTGGCACC-T-TTCCTTTCAAAGTCCACGACTCCGTGGCACCTTCTTTTC
* * * * *
1672007 AAAGTCCGCGACTCCGTGGCAC-C---TT-CTTTTCAAAGCCCACAACTCTGTGGCACTCTTTTT
64 AAAGCCCACAACTCCGTGGCACTCTTGTTCCTTTT-AAAGTCCACAACTCCGTGGCAC-CTTTTT
1672067 CCTTTTT
127 CC-TTTT
* ** *
1672074 AAAGTCCACAACTCCGTGGCACCTTGTTCTTTTTAAGTCCACGACTCCATGGCACCTTCTTTTCA
1 AAAGTCCACAACTCCGTGGCACCTT-TCCTTTCAAAGTCCACGACTCCGTGGCACCTTCTTTTCA
* * * *
1672139 AAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAAGTCCACAACCCCATGGCACCTTGTTCC
65 AAGCCCACAACTCCGTGGCACTCTTGTT-CCTTTTAAAGTCCACAACTCCGTGGCACCTTTTTCC
1672204 TTTT
129 TTTT
** * * *
1672208 -AAGTCCATGACTCTGTGGCACC-TTCCTTTCAAAGTCCGCGACTTCGTGGCACCTTCTTTTCAA
1 AAAGTCCACAACTCCGTGGCACCTTTCCTTTCAAAGTCCACGACTCCGTGGCACCTTCTTTTCAA
* * *
1672271 AGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAAGCCCACAACTCCGTGGCACCTTGTTCCT
66 AGCCCACAACTCCGTGGCACTCTTGTT-CCTTTTAAAGTCCACAACTCCGTGGCACCTTTTTCCT
1672336 TTT
130 TTT
* * *
1672339 -AAGTCCACAACTTCATGGCATCTTTC
1 AAAGTCCACAACTCCGTGGCACCTTTC
1672365 ACCCTTTTTA
Statistics
Matches: 482, Mismatches: 53, Indels: 47
0.83 0.09 0.08
Matches are distributed among these distances:
129 1 0.00
130 12 0.02
131 217 0.45
132 9 0.02
133 72 0.15
134 45 0.09
135 39 0.08
136 80 0.17
137 7 0.01
ACGTcount: A:0.19, C:0.34, G:0.14, T:0.32
Consensus pattern (132 bp):
AAAGTCCACAACTCCGTGGCACCTTTCCTTTCAAAGTCCACGACTCCGTGGCACCTTCTTTTCAA
AGCCCACAACTCCGTGGCACTCTTGTTCCTTTTAAAGTCCACAACTCCGTGGCACCTTTTTCCTT
TT
Found at i:1672445 original size:33 final size:32
Alignment explanation
Indices: 1672402--1672675 Score: 428
Period size: 33 Copynumber: 8.5 Consensus size: 32
1672392 GCATCTTTTC
*
1672402 CCTTCTCTAAAGCCCACACAAGTCAGTGGCAA
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAA
1672434 CCTTCTTCTAAAGCCCACACAAGTCGGTGGCAA
1 CCTTC-TCTAAAGCCCACACAAGTCGGTGGCAA
1672467 CCCTTCTCTAAAGCCCACACAAGTCGGTGGCAA
1 -CCTTCTCTAAAGCCCACACAAGTCGGTGGCAA
*
1672500 CCTTTTTCTAAAGCCCACACAAGTCGGTGGCAA
1 CC-TTCTCTAAAGCCCACACAAGTCGGTGGCAA
1672533 CCCTTCTC-AAAGCCCACACAAGTCGGTGGCAA
1 -CCTTCTCTAAAGCCCACACAAGTCGGTGGCAA
*
1672565 CCCTCTCTAAAGCCCACACAAGTCGGTGGCAA
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAA
* *
1672597 CCCTCTCTAAAGCCCACACAAGTTGGTGGCAA
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAA
1672629 CCATTCTCTAAAGCCCACACAAGTCGGTGGCAA
1 CC-TTCTCTAAAGCCCACACAAGTCGGTGGCAA
*
1672662 CCCT-TCT-AAGCCCA
1 CCTTCTCTAAAGCCCA
1672676 ATATCGCTAG
Statistics
Matches: 228, Mismatches: 8, Indels: 14
0.91 0.03 0.06
Matches are distributed among these distances:
30 7 0.03
31 9 0.04
32 89 0.39
33 116 0.51
34 7 0.03
ACGTcount: A:0.28, C:0.35, G:0.18, T:0.19
Consensus pattern (32 bp):
CCTTCTCTAAAGCCCACACAAGTCGGTGGCAA
Found at i:1672777 original size:43 final size:43
Alignment explanation
Indices: 1672663--1673603 Score: 707
Period size: 43 Copynumber: 20.1 Consensus size: 43
1672653 CGGTGGCAAC
* *
1672663 CCTTCTAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCA
1 CCTT-TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
* * *
1672707 CCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA
1 ----C--CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
* *
1672756 CCTTTAAGTCCAATATCGCTGGTCTTGAATCAGTATATTGGCA
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
* * *
1672799 CCTTTGTCTTTAAGTCCAATA-CAGTTGGCCTTGAATCAGCACATTGACA
1 -C-----CTTTAAGTCCAATATC-GCTGGCCTTGAATCAGCATATTGGCA
* * *
1672848 CCTCTAAGTCCAATATAGCTGGCCTTGAATTAGCATATTGGCGCCTTTGTCA
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATT---G-----G-CA
*
1672900 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTAGCA
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
* * * * *
1672943 CCTTTGTCTTTAAGTCCAATGTAGCTGGCCCTGAATCAGTACATTGGCA
1 -C-----CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
**
1672992 CCTCCAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
* * * *
1673035 CCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATCGGCA
1 -C-----CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
* *
1673084 CCTTTAAGTCCGATATCGCTGGCCTTGAATCAGCATATTAGCA
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
* * * *
1673127 CCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATCGGCA
1 -C-----CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
1673176 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
* * * * *
1673219 CCTTTATCTTTAAGTCCAATGTAGCTGGCCTTAAATCAGCACATCGGCA
1 -C-----CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
* *
1673268 CCTTTAAGTCTAATATCGCTGGCCTTGAATCAACATATTGGCA
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
* * * *
1673311 CCTTTATCTTTAAGTCCAATGTAGTTGGCCTTGAATCAGCACATTGGCA
1 -C-----CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
1673360 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
* *
1673403 CCCTCATCTTTTAAG-CCTAATGTCGCTGGCCTTGAATCAGCACATTGGCA
1 ----C--C-TTTAAGTCC-AATATCGCTGGCCTTGAATCAGCATATTGGCA
* *
1673453 CCTTTAAGTCCAATATCGCTGGCTTTGAATCCGCATATTGGCGCCTTTGTCA
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATT---G-----G-CA
*
1673505 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGTCTTTGTCA
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATT---G-----G-CA
* * *
1673557 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
1673600 CCTT
1 CCTT
1673604 CATCTTTAAC
Statistics
Matches: 731, Mismatches: 95, Indels: 139
0.76 0.10 0.14
Matches are distributed among these distances:
43 288 0.39
44 11 0.02
45 1 0.00
46 3 0.00
47 1 0.00
48 8 0.01
49 254 0.35
50 39 0.05
51 1 0.00
52 125 0.17
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (43 bp):
CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
Found at i:1672830 original size:92 final size:92
Alignment explanation
Indices: 1672663--1673603 Score: 626
Period size: 92 Copynumber: 10.0 Consensus size: 92
1672653 CGGTGGCAAC
* * * ** *
1672663 CCTTCTAAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
1 CCTT-TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGTCCAATA
*
1672728 TAGCTGGCCTTGAATCAGCACATTGGCA
65 TCGCTGGCCTTGAATCAGCACATTGGCA
* * *
1672756 CCTTTAAGTCCAATATCGCTGGTCTTGAATCAGTATATTGGCACCTTTGTCTTTAAGTCCAATA-
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGTCCAATAT
* *
1672820 CAGTTGGCCTTGAATCAGCACATTGACA
66 C-GCTGGCCTTGAATCAGCACATTGGCA
* * *
1672848 CCTCTAAGTCCAATATAGCTGGCCTTGAATTAGCATATTGGCGCCTTTGTCACCTTTAAGTCCAA
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTGT---CTTTAAGTCCAA
* *
1672913 TATCGCTGGCCTTGAATCAGCATATTAGCA
63 TATCGCTGGCCTTGAATCAGCACATTGGCA
* * * * *
1672943 CCTTTGTCTTTAAGTCCAATGTAGCTGGCCCTGAATCAGTACATTGGCACC----TC--CAAGTC
1 -C-----CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGTC
*
1673002 CAATATCGCTGGCCTTGAATCAGCATATTGGCA
60 CAATATCGCTGGCCTTGAATCAGCACATTGGCA
* * *
1673035 CCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATCGGCA-C-----CTTTAAGTC
1 -C-----CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGTC
* * *
1673094 CGATATCGCTGGCCTTGAATCAGCATATTAGCA
60 CAATATCGCTGGCCTTGAATCAGCACATTGGCA
* * *
1673127 CCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATCGGCA-C-----CTTTAAGTC
1 -C-----CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGTC
*
1673186 CAATATCGCTGGCCTTGAATCAGCATATTGGCA
60 CAATATCGCTGGCCTTGAATCAGCACATTGGCA
* * * *
1673219 CCTTTATCTTTAAGTCCAATGTAGCTGGCCTTAAATCAGCACATCGGCA-C-----CTTTAAGTC
1 -C-----CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGTC
* * *
1673278 TAATATCGCTGGCCTTGAATCAACATATTGGCA
60 CAATATCGCTGGCCTTGAATCAGCACATTGGCA
* * *
1673311 CCTTTATCTTTAAGTCCAATGTAGTTGGCCTTGAATCAGCACATTGGCA-C-----CTTTAAGTC
1 -C-----CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGTC
*
1673370 CAATATCGCTGGCCTTGAATCAGCATATTGGCA
60 CAATATCGCTGGCCTTGAATCAGCACATTGGCA
* * *
1673403 CCCTCATCTTTTAAG-CCTAATGTCGCTGGCCTTGAATCAGCACATTGGCA-C-----CTTTAAG
1 ----C--C-TTTAAGTCC-AATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAG
* * *
1673461 TCCAATATCGCTGGCTTTGAATCCGCATATTGGCGCCTTTGTCA
58 TCCAATATCGCTGGCCTTGAATCAGCACATT---G-----G-CA
* * **
1673505 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGTCTTTGTCATCTTTAAGTCCAA
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTG---TCTTTAAGTCCAA
*
1673570 TGTCGCTGGCCTTGAATCAGCACATTGGCA
63 TATCGCTGGCCTTGAATCAGCACATTGGCA
1673600 CCTT
1 CCTT
1673604 CATCTTTAAC
Statistics
Matches: 751, Mismatches: 60, Indels: 72
0.85 0.07 0.08
Matches are distributed among these distances:
90 1 0.00
91 1 0.00
92 510 0.68
93 77 0.10
94 1 0.00
95 77 0.10
96 8 0.01
97 1 0.00
101 39 0.05
102 2 0.00
104 34 0.05
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (92 bp):
CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGTCCAATAT
CGCTGGCCTTGAATCAGCACATTGGCA
Found at i:1673121 original size:22 final size:22
Alignment explanation
Indices: 1673058--1673121 Score: 53
Period size: 21 Copynumber: 3.0 Consensus size: 22
1673048 GTCCAATGTA
*
1673058 GCTGGCCTTGAATCAGCACATC
1 GCTGGCCTTGAATCAGCATATC
* * *
1673080 G--GCACCTTTAAGTCCG-ATATC
1 GCTG-GCCTTGAA-TCAGCATATC
1673101 GCTGGCCTTGAATCAGCATAT
1 GCTGGCCTTGAATCAGCATAT
1673122 TAGCACCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 10
0.64 0.15 0.21
Matches are distributed among these distances:
20 1 0.03
21 14 0.47
22 14 0.47
23 1 0.03
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.27
Consensus pattern (22 bp):
GCTGGCCTTGAATCAGCATATC
Found at i:1673141 original size:184 final size:184
Alignment explanation
Indices: 1672898--1673612 Score: 1045
Period size: 184 Copynumber: 3.8 Consensus size: 184
1672888 GCGCCTTTGT
*
1672898 CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTAGCACCTTTGTCTTTAAGTCCAAT
1 CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTAGCACCTTTATCTTTAAGTCCAAT
* * *
1672963 GTAGCTGGCCCTGAATCAGTACATTGGCACCTCCAAGTCCAATATCGCTGGCCTTGAATCAGCAT
66 GTAGCTGGCCTTGAATCAGCACATTGGCACCTCTAAGTCCAATATCGCTGGCCTTGAATCAGCAT
*
1673028 ATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATCGG
131 ATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATCGG
*
1673082 CACCTTTAAGTCCGATATCGCTGGCCTTGAATCAGCATATTAGCACCTTTATCTTTAAGTCCAAT
1 CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTAGCACCTTTATCTTTAAGTCCAAT
* *
1673147 GTAGCTGGCCTTGAATCAGCACATCGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCAT
66 GTAGCTGGCCTTGAATCAGCACATTGGCACCTCTAAGTCCAATATCGCTGGCCTTGAATCAGCAT
* *
1673212 ATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTAAATCAGCACATCGG
131 ATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATCGG
* * *
1673266 CACCTTTAAGTCTAATATCGCTGGCCTTGAATCAACATATTGGCACCTTTATCTTTAAGTCCAAT
1 CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTAGCACCTTTATCTTTAAGTCCAAT
* *
1673331 GTAGTTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCAT
66 GTAGCTGGCCTTGAATCAGCACATTGGCACCTCTAAGTCCAATATCGCTGGCCTTGAATCAGCAT
* * *
1673396 ATTGGCACCCTCATCTTTTAAG-CCTAATGTCGCTGGCCTTGAATCAGCACATTGG
131 ATTGGCACCTTCATC-TTTAAGTCC-AATGTAGCTGGCCTTGAATCAGCACATCGG
* * * *
1673451 CACCTTTAAGTCCAATATCGCTGGCTTTGAATCCGCATATTGGCGCCTTTGTCATCTTTAAGTCC
1 CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTAGCACC-TT-T-ATCTTTAAGTCC
* * * * *
1673516 AATATCGCTGGCCTTGAATCAGCATATTGGCGTCTTTGTCATCTTTAAGTCCAATGTCGCTGGCC
63 AATGTAGCTGGCCTTGAATCAGCACATTGGC-AC-----C-TC--TAAGTCCAATATCGCTGGCC
*
1673581 TTGAATCAGCACATTGGCACCTTCATCTTTAA
119 TTGAATCAGCATATTGGCACCTTCATCTTTAA
1673613 CATTCCTAAG
Statistics
Matches: 484, Mismatches: 33, Indels: 16
0.91 0.06 0.03
Matches are distributed among these distances:
184 315 0.65
185 75 0.15
186 2 0.00
187 1 0.00
188 39 0.08
189 1 0.00
194 1 0.00
195 1 0.00
196 5 0.01
197 44 0.09
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (184 bp):
CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTAGCACCTTTATCTTTAAGTCCAAT
GTAGCTGGCCTTGAATCAGCACATTGGCACCTCTAAGTCCAATATCGCTGGCCTTGAATCAGCAT
ATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATCGG
Found at i:1674424 original size:13 final size:13
Alignment explanation
Indices: 1674406--1674430 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1674396 CATAAAGTGT
1674406 TGTATCGATACAA
1 TGTATCGATACAA
1674419 TGTATCGATACA
1 TGTATCGATACA
1674431 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1674446 original size:32 final size:33
Alignment explanation
Indices: 1674386--1674454 Score: 122
Period size: 32 Copynumber: 2.1 Consensus size: 33
1674376 TTCAACGATT
1674386 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*
1674419 TGTATCGATACAT-AAGTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
1674451 TGTA
1 TGTA
1674455 AGCTACTGCC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 22 0.63
33 13 0.37
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:1674509 original size:13 final size:13
Alignment explanation
Indices: 1674491--1674515 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1674481 ATTACTCAAA
1674491 TGTATCGATACAT
1 TGTATCGATACAT
1674504 TGTATCGATACA
1 TGTATCGATACA
1674516 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1674561 original size:52 final size:52
Alignment explanation
Indices: 1674524--1674652 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
1674514 CACTGATCTT
1674524 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1674576 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1674628 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1674653 TCATATTTCG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 76 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1677994 original size:67 final size:68
Alignment explanation
Indices: 1677899--1678203 Score: 240
Period size: 67 Copynumber: 4.6 Consensus size: 68
1677889 TCTCCTAATG
* * * *
1677899 CAAGTACTATTAATAGAGAA-TTCGACCATTGTGGTCTCATGTGCCACTCCTGTCACTCT-CTCA
1 CAAGTACTATTAATGGAGAAGTT-AACCATTGTGGTCTCATGTGCCACTTCTGTCACTCTCCCCA
*
1677962 TTTA
65 TATA
* *
1677966 CAAGTACTATTAATGGAGAAGTTAACCATTGTGATCTCATGTGCCACTTCTGTCATTCTCCCCAT
1 CAAGTACTATTAATGGAGAAGTTAACCATTGTGGTCTCATGTGCCACTTCTGTCACTCTCCCCAT
1678031 ATA
66 ATA
* * * * * *
1678034 CAAGT--TTTTAACATGGAGAAGTCAACCATTGTGGTCTTATGCGCCACTTCTGTCACTTTCCCT
1 CAAGTACTATT-A-ATGGAGAAGTTAACCATTGTGGTCTCATGTGCCACTTCTGTCACTCTCCCC
1678097 A-ATA
64 ATATA
* * * * * * *
1678101 TAAGTA-TTTTCAATAGAGAAG---GCCATTATGGTCT--TGTGCGTCACTTTTGTCACTCTCCT
1 CAAGTACTATT-AATGGAGAAGTTAACCATTGTGGTCTCATGTGC--CACTTCTGTCACTCTCCC
1678160 CA-ATA
63 CATATA
* * * * *
1678165 CAAATACTCTTAATGG-GGAGTTGACTATTGTGGTCTCAT
1 CAAGTACTATTAATGGAGAAGTTAACCATTGTGGTCTCAT
1678204 ACACAATTTC
Statistics
Matches: 192, Mismatches: 33, Indels: 25
0.77 0.13 0.10
Matches are distributed among these distances:
62 4 0.02
63 3 0.02
64 38 0.20
65 3 0.02
66 13 0.07
67 67 0.35
68 64 0.33
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (68 bp):
CAAGTACTATTAATGGAGAAGTTAACCATTGTGGTCTCATGTGCCACTTCTGTCACTCTCCCCAT
ATA
Found at i:1678065 original size:68 final size:66
Alignment explanation
Indices: 1677846--1678121 Score: 236
Period size: 67 Copynumber: 4.1 Consensus size: 66
1677836 TCTTACATTG
* * ** * * * *
1677846 TGGAGAAGTCGACCGTTGTGGTC-CTATGCACCATTTCTATCACTCTCCTA-ATGCAAGTACTAT
1 TGGAGAAGTCAACCATTGTGGTCTC-ATGTGCCACTTCTGTCACTCTCCCATATACAAGTA-TAT
1677909 TAA
64 TAA
* * * * * *
1677912 TAGAGAATTCGACCATTGTGGTCTCATGTGCCACTCCTGTCACTCTCTCATTTACAAGTACTATT
1 TGGAGAAGTCAACCATTGTGGTCTCATGTGCCACTTCTGTCACTCTCCCATATACAAGTA-TATT
1677977 AA
65 AA
* * * *
1677979 TGGAGAAGTTAACCATTGTGATCTCATGTGCCACTTCTGTCATTCTCCCCATATACAAGT-TTTT
1 TGGAGAAGTCAACCATTGTGGTCTCATGTGCCACTTCTGTCACTCT-CCCATATACAAGTATATT
1678043 AACA
65 -A-A
* * * * *
1678047 TGGAGAAGTCAACCATTGTGGTCTTATGCGCCACTTCTGTCACTTTCCC-TAATATAAGTATTTT
1 TGGAGAAGTCAACCATTGTGGTCTCATGTGCCACTTCTGTCACTCTCCCAT-ATACAAGTATATT
1678111 CAA
65 -AA
*
1678114 TAGAGAAG
1 TGGAGAAG
1678122 GCCATTATGG
Statistics
Matches: 172, Mismatches: 31, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
66 42 0.24
67 73 0.42
68 57 0.33
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (66 bp):
TGGAGAAGTCAACCATTGTGGTCTCATGTGCCACTTCTGTCACTCTCCCATATACAAGTATATTA
A
Found at i:1678721 original size:15 final size:15
Alignment explanation
Indices: 1678701--1678754 Score: 90
Period size: 15 Copynumber: 3.6 Consensus size: 15
1678691 CCATAGTACT
1678701 CTTTTGGCACAAGTA
1 CTTTTGGCACAAGTA
*
1678716 CTTTTGGCACAGGTA
1 CTTTTGGCACAAGTA
1678731 CTTTTGGCACAAGTA
1 CTTTTGGCACAAGTA
*
1678746 CTTTAGGCA
1 CTTTTGGCA
1678755 ACAACATTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (15 bp):
CTTTTGGCACAAGTA
Found at i:1679358 original size:20 final size:21
Alignment explanation
Indices: 1679317--1679361 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1679307 TTCAATAATT
*
1679317 TGTATTGATACAATAAAGGAA
1 TGTACTGATACAATAAAGGAA
1679338 TGTACTGATAC-AT-AAGTGAA
1 TGTACTGATACAATAAAG-GAA
1679358 TGTA
1 TGTA
1679362 TCGACACATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.42, C:0.07, G:0.20, T:0.31
Consensus pattern (21 bp):
TGTACTGATACAATAAAGGAA
Found at i:1679460 original size:20 final size:20
Alignment explanation
Indices: 1679437--1679484 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1679427 AATATATCAT
1679437 TACATTTTTCATTGTATCGA
1 TACATTTTTCATTGTATCGA
*
1679457 TACATTCTTCATTGTATCGA
1 TACATTTTTCATTGTATCGA
*
1679477 TTCATTTT
1 TACATTTT
1679485 GGGTATCTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.23, C:0.17, G:0.08, T:0.52
Consensus pattern (20 bp):
TACATTTTTCATTGTATCGA
Found at i:1680444 original size:18 final size:18
Alignment explanation
Indices: 1680421--1680456 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
1680411 TCATGCATTG
1680421 TTTCCATG-TTCCATACAT
1 TTTCCATGCTT-CATACAT
1680439 TTTCCATGCTTCATACAT
1 TTTCCATGCTTCATACAT
1680457 GCATAAAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.88
19 2 0.12
ACGTcount: A:0.22, C:0.28, G:0.06, T:0.44
Consensus pattern (18 bp):
TTTCCATGCTTCATACAT
Found at i:1680921 original size:20 final size:21
Alignment explanation
Indices: 1680877--1680927 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
1680867 TTTTACAATT
1680877 TGTATCGATATAAATAGTAAA
1 TGTATCGATATAAATAGTAAA
* *
1680898 TGTATCGATATATA-AGTGAA
1 TGTATCGATATAAATAGTAAA
*
1680918 TGTATAGATA
1 TGTATCGATA
1680928 CATGCCTGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.43, C:0.04, G:0.18, T:0.35
Consensus pattern (21 bp):
TGTATCGATATAAATAGTAAA
Found at i:1688772 original size:16 final size:17
Alignment explanation
Indices: 1688751--1688789 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1688741 AGTAATTATG
1688751 ATGAATGT-T-TAGATTC
1 ATGAATGTATATA-ATTC
1688767 ATGAATGTATATAATTC
1 ATGAATGTATATAATTC
1688784 ATGAAT
1 ATGAAT
1688790 ATACTTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.38
17 11 0.52
18 2 0.10
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.41
Consensus pattern (17 bp):
ATGAATGTATATAATTC
Found at i:1688798 original size:17 final size:17
Alignment explanation
Indices: 1688763--1688870 Score: 60
Period size: 17 Copynumber: 6.1 Consensus size: 17
1688753 GAATGTTTAG
*
1688763 ATTCATGAATGTATATA
1 ATTCATGAATATATATA
1688780 ATTCATGAATATACTTAATA
1 ATTCATGAATATA--T-ATA
*
1688800 TCATTCATGTATAT-TCATA
1 --ATTCATGAATATAT-ATA
* *
1688819 GTTCATGAAT-TTTCA-A
1 ATTCATGAATATAT-ATA
* *
1688835 ATTCATGAATTTACATA
1 ATTCATGAATATATATA
* *
1688852 ATTTATGAATATACATA
1 ATTCATGAATATATATA
1688869 AT
1 AT
1688871 AACATGCATG
Statistics
Matches: 73, Mismatches: 10, Indels: 16
0.74 0.10 0.16
Matches are distributed among these distances:
16 12 0.16
17 42 0.58
19 5 0.07
20 3 0.04
22 11 0.15
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (17 bp):
ATTCATGAATATATATA
Found at i:1688841 original size:16 final size:17
Alignment explanation
Indices: 1688802--1688870 Score: 70
Period size: 17 Copynumber: 4.1 Consensus size: 17
1688792 ACTTAATATC
*
1688802 ATTCATGTATATT-CATA
1 ATTCATGAAT-TTACATA
* *
1688819 GTTCATGAATTTTCA-A
1 ATTCATGAATTTACATA
1688835 ATTCATGAATTTACATA
1 ATTCATGAATTTACATA
* *
1688852 ATTTATGAATATACATA
1 ATTCATGAATTTACATA
1688869 AT
1 AT
1688871 AACATGCATG
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
16 16 0.36
17 28 0.64
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.43
Consensus pattern (17 bp):
ATTCATGAATTTACATA
Found at i:1692153 original size:8 final size:8
Alignment explanation
Indices: 1692140--1692169 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1692130 TAAGTAACCC
1692140 AACAAAGA
1 AACAAAGA
1692148 AACAAAGA
1 AACAAAGA
*
1692156 AACAAATA
1 AACAAAGA
1692164 AACAAA
1 AACAAA
1692170 ATAAATAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.77, C:0.13, G:0.07, T:0.03
Consensus pattern (8 bp):
AACAAAGA
Found at i:1695257 original size:17 final size:17
Alignment explanation
Indices: 1695217--1695270 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
1695207 AAATATTTTT
1695217 TAAAATTTATAT-AA--
1 TAAAATTTATATAAATG
* *
1695231 TAAAAATTAT-TACATG
1 TAAAATTTATATAAATG
1695247 TCAAAATTTATATAAATG
1 T-AAAATTTATATAAATG
1695265 TAAAAT
1 TAAAAT
1695271 ATTTTAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
13 1 0.03
14 10 0.32
16 1 0.03
17 13 0.42
18 6 0.19
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.39
Consensus pattern (17 bp):
TAAAATTTATATAAATG
Found at i:1697195 original size:19 final size:19
Alignment explanation
Indices: 1697171--1697208 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
1697161 CTATCATGCC
1697171 ATTAC-TATCTTTTAAAATT
1 ATTACTTAT-TTTTAAAATT
1697190 ATTACTTTATTTTTAAAAT
1 ATTAC-TTATTTTTAAAAT
1697209 ATTTTATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.29
20 9 0.53
21 3 0.18
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTACTTATTTTTAAAATT
Found at i:1697220 original size:18 final size:19
Alignment explanation
Indices: 1697197--1697246 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
1697187 ATTATTACTT
1697197 TATTTTTAAAATATTTT-A
1 TATTTTTAAAATATTTTAA
1697215 TATTTTGT-AAAT-TTTTAA
1 TATTTT-TAAAATATTTTAA
* *
1697233 TATATTTAATATAT
1 TATTTTTAAAATAT
1697247 ATATACACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
17 5 0.19
18 19 0.73
19 2 0.08
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
TATTTTTAAAATATTTTAA
Found at i:1697246 original size:2 final size:2
Alignment explanation
Indices: 1697232--1697307 Score: 52
Period size: 2 Copynumber: 39.0 Consensus size: 2
1697222 TAAATTTTTA
* * *
1697232 AT AT AT TT A- AT AT AT AT AT AC ACT A- AG AT CAT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT -AT AT AT AT AT AT
* * *
1697274 AT AT AT GT AA AA AT AT -T AT AT A- 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
1697308 GCTTTTAGTA
Statistics
Matches: 59, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
1 4 0.07
2 52 0.88
3 3 0.05
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (2 bp):
AT
Found at i:1698970 original size:15 final size:16
Alignment explanation
Indices: 1698945--1698987 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 16
1698935 ATTTTAGGGT
1698945 ATATATATATACACTA
1 ATATATATATACACTA
*
1698961 ATAT-TATATACACTTT
1 ATATATATATACAC-TA
1698977 ATATATATATA
1 ATATATATATA
1698988 TTATATAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 9 0.38
16 9 0.38
17 6 0.25
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (16 bp):
ATATATATATACACTA
Found at i:1698994 original size:15 final size:15
Alignment explanation
Indices: 1698944--1698994 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
1698934 AATTTTAGGG
*
1698944 TATATATATATACAC
1 TATATATATATACAT
1698959 TA-ATATTATATACACT
1 TATATA-TATATACA-T
*
1698975 T-TATATATATATAT
1 TATATATATATACAT
1698989 TATATA
1 TATATA
1698995 AACTAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
14 5 0.17
15 21 0.70
16 4 0.13
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (15 bp):
TATATATATATACAT
Found at i:1702475 original size:20 final size:18
Alignment explanation
Indices: 1702441--1702507 Score: 73
Period size: 18 Copynumber: 3.6 Consensus size: 18
1702431 TATATATTAT
1702441 TAATATTTTTTATTTTTA
1 TAATATTTTTTATTTTTA
1702459 TAATATTTTAATTATTTTTA
1 TAATATTTT--TTATTTTTA
* *
1702479 TAATATATTATATATTTTA
1 TAATATTTTTTAT-TTTTA
*
1702498 -ATTATTTTTT
1 TAATATTTTTT
1702508 TACCTATGTT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
18 19 0.46
19 5 0.12
20 17 0.41
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TAATATTTTTTATTTTTA
Found at i:1702837 original size:24 final size:23
Alignment explanation
Indices: 1702810--1702883 Score: 62
Period size: 24 Copynumber: 3.1 Consensus size: 23
1702800 AACAGTAAGT
1702810 ATAACATTTATAAAATTAAAAATA
1 ATAA-ATTTATAAAATTAAAAATA
** *
1702834 AT-AATGATTATAAAATTAATTATT
1 ATAAAT--TTATAAAATTAAAAATA
*
1702858 ATAATTTTATAAAA-TAAAAATTA
1 ATAAATTTATAAAATTAAAAA-TA
1702881 ATA
1 ATA
1702884 GTAAAATATA
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
22 6 0.15
23 13 0.33
24 18 0.46
25 2 0.05
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (23 bp):
ATAAATTTATAAAATTAAAAATA
Found at i:1703116 original size:28 final size:28
Alignment explanation
Indices: 1703055--1703116 Score: 99
Period size: 27 Copynumber: 2.2 Consensus size: 28
1703045 TTGTTGAATA
* *
1703055 ATAATTAAAAATTATTAAAATTATATTT
1 ATAATTAAAAAATATTAAAATTATAATT
1703083 AT-ATTAAAAAATATTAAAATTATAATT
1 ATAATTAAAAAATATTAAAATTATAATT
1703110 ATAATTA
1 ATAATTA
1703117 TATTAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 25 0.81
28 6 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
ATAATTAAAAAATATTAAAATTATAATT
Found at i:1703118 original size:33 final size:34
Alignment explanation
Indices: 1703068--1703145 Score: 104
Period size: 33 Copynumber: 2.3 Consensus size: 34
1703058 ATTAAAAATT
* * *
1703068 ATTAAAATTATATTTATATTAAAAAAT-ATTAAA
1 ATTATAATTATAATTATATTAAAAAATAAATAAA
*
1703101 ATTATAATTATAATTATATTAAAATATAAATAAA
1 ATTATAATTATAATTATATTAAAAAATAAATAAA
*
1703135 ATTATATTTAT
1 ATTATAATTAT
1703146 GTTGAATAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
33 24 0.62
34 15 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (34 bp):
ATTATAATTATAATTATATTAAAAAATAAATAAA
Found at i:1703128 original size:22 final size:23
Alignment explanation
Indices: 1703093--1703142 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
1703083 ATATTAAAAA
* *
1703093 ATATTAAAATTATAATTATAATT
1 ATATTAAAATTATAAATAAAATT
1703116 ATATTAAAA-TATAAATAAAATT
1 ATATTAAAATTATAAATAAAATT
1703138 ATATT
1 ATATT
1703143 TATGTTGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
ATATTAAAATTATAAATAAAATT
Found at i:1704833 original size:18 final size:17
Alignment explanation
Indices: 1704824--1704873 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
1704814 ATTAATATAT
1704824 TAAAATTTATATAAATA
1 TAAAATTTATATAAATA
1704841 TAAAATATT-T-TAAATA
1 TAAAAT-TTATATAAATA
1704857 T--AATTTAATATAAATA
1 TAAAATTT-ATATAAATA
1704873 T
1 T
1704874 TATATAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
13 2 0.07
14 3 0.10
15 1 0.03
16 14 0.48
17 7 0.24
18 2 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:1706645 original size:97 final size:97
Alignment explanation
Indices: 1706522--1706848 Score: 462
Period size: 97 Copynumber: 3.4 Consensus size: 97
1706512 TTGAAAAACA
* * *
1706522 GGGTTGGAGCATCCCCTCGGAGGAATGGGGTTGGAGTGTCCTCGATGATGACAATTTAAGTGAGT
1 GGGTTAGAGTATCCCCTCGGAGGAATAGGGTTGGAGTGTCCTCGATGATGACAATTTAAGTGAGT
* *
1706587 ATAAAATTTAAACTTTGATGCGTTTAAAAGCG
66 ATAAGATTTAAACTTTGATGTGTTTAAAAGCG
* * * * *
1706619 GGGTTAGAGTATCCTCTCGGAAGAATGGGGTTGAAGTG-CCTCTAATGATGACAATTTAAGTGAG
1 GGGTTAGAGTATCCCCTCGGAGGAATAGGGTTGGAGTGTCCTC-GATGATGACAATTTAAGTGAG
1706683 TATAAGATTTAAACTTTGATGTGTTTAAAAGCG
65 TATAAGATTTAAACTTTGATGTGTTTAAAAGCG
* * *
1706716 GGGTTGGAGTATCCCCTCGGAGGAATAGGGTTGCAGTGT-CTCCGATGATGACAATTTAAGTAAG
1 GGGTTAGAGTATCCCCTCGGAGGAATAGGGTTGGAGTGTCCT-CGATGATGACAATTTAAGTGAG
* *
1706780 AATAAGATTTAAATTTTGATGTGTTTAAAAGCG
65 TATAAGATTTAAACTTTGATGTGTTTAAAAGCG
* *
1706813 GGGTTAGAGTAT-CCTTCGGAGGAATAGGGTTAGAGT
1 GGGTTAGAGTATCCCCTCGGAGGAATAGGGTTGGAGT
1706849 ATCCCTAATA
Statistics
Matches: 206, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
96 25 0.12
97 180 0.87
98 1 0.00
ACGTcount: A:0.29, C:0.11, G:0.29, T:0.30
Consensus pattern (97 bp):
GGGTTAGAGTATCCCCTCGGAGGAATAGGGTTGGAGTGTCCTCGATGATGACAATTTAAGTGAGT
ATAAGATTTAAACTTTGATGTGTTTAAAAGCG
Found at i:1708900 original size:13 final size:13
Alignment explanation
Indices: 1708882--1708907 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1708872 ATATTTTTTG
1708882 TGTATCGATACAT
1 TGTATCGATACAT
1708895 TGTATCGATACAT
1 TGTATCGATACAT
1708908 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1708918 original size:32 final size:33
Alignment explanation
Indices: 1708861--1708925 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
1708851 TACAAGCCAA
1708861 TGTATCGATACATATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-TTTTTGTGTATCGATACAT
1708895 TGTATCGATACATA-TTTTGTGTATCGATACA
1 TGTATCGATACATATTTTTGTGTATCGATACA
1708926 AGTTTGGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 17 0.55
34 14 0.45
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATATTTTTGTGTATCGATACAT
Found at i:1708919 original size:19 final size:19
Alignment explanation
Indices: 1708861--1708925 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 19
1708851 TACAAGCCAA
1708861 TGTATCGATACATATTTTTTG
1 TGTATCGATACATA--TTTTG
1708882 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
1708895 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
1708914 TGTATCGATACA
1 TGTATCGATACA
1708926 AGTTTGGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
15 1 0.03
18 1 0.03
19 13 0.34
21 11 0.29
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:1709627 original size:39 final size:40
Alignment explanation
Indices: 1709552--1709632 Score: 110
Period size: 39 Copynumber: 2.0 Consensus size: 40
1709542 TTTTCTTTCT
**
1709552 CCCTTAACTAAAGTAATTTTAACAAATTTGTACATTCTCC
1 CCCTTAACTAAAGTAATTTTAACAAATTTACACATTCTCC
* * *
1709592 CCCTTAA-TAAGGTAATTTTAGCAAATTTACGCATTCTCC
1 CCCTTAACTAAAGTAATTTTAACAAATTTACACATTCTCC
1709631 CC
1 CC
1709633 TTTTATTAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
39 29 0.81
40 7 0.19
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.36
Consensus pattern (40 bp):
CCCTTAACTAAAGTAATTTTAACAAATTTACACATTCTCC
Found at i:1709711 original size:29 final size:29
Alignment explanation
Indices: 1709671--1709734 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
1709661 GGTAATTTAA
*
1709671 ACACATATCAAAAATTTATTTGCACTTAC
1 ACACATATCAAAAATTTATTTGCACATAC
1709700 ACACATATCAAAAATTTATTTGCACATAC
1 ACACATATCAAAAATTTATTTGCACATAC
*
1709729 ATACAT
1 ACACAT
1709735 CTATTCTCTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.44, C:0.20, G:0.03, T:0.33
Consensus pattern (29 bp):
ACACATATCAAAAATTTATTTGCACATAC
Found at i:1711517 original size:13 final size:13
Alignment explanation
Indices: 1711499--1711536 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1711489 ATAATCCCCC
1711499 TGTATCGATACAG
1 TGTATCGATACAG
*
1711512 TGTATCGATACAT
1 TGTATCGATACAG
1711525 TGTATCGATACA
1 TGTATCGATACA
1711537 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1717712 original size:13 final size:13
Alignment explanation
Indices: 1717694--1717719 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1717684 ATATTTTTTG
1717694 TGTATCGATACAT
1 TGTATCGATACAT
1717707 TGTATCGATACAT
1 TGTATCGATACAT
1717720 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1717730 original size:32 final size:33
Alignment explanation
Indices: 1717673--1717737 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
1717663 TACAAGCCAA
1717673 TGTATCGATACATATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-TTTTTGTGTATCGATACAT
1717707 TGTATCGATACATA-TTTTGTGTATCGATACA
1 TGTATCGATACATATTTTTGTGTATCGATACA
1717738 AGTTTGGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 17 0.55
34 14 0.45
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATATTTTTGTGTATCGATACAT
Done.