Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 60 of 204
Found at i:19153744 original size:49 final size:50
Alignment explanation
Indices: 19153644--19153744 Score: 116
Period size: 49 Copynumber: 2.0 Consensus size: 50
19153634 TCCCGATATT
* ** * *
19153644 TGGCTCGTAAGAGCTTCCCGATATATGGCTCATATGAGCTTCTTGTTATA
1 TGGCTCGGAAGAGCTTCCCGATATACAGCTCATATGAGCTTCATGTCATA
* *
19153694 TGGCTCGGAAGAGCTTCTCG-TTTACAGCTCATATGAGCTTACATG-CATA
1 TGGCTCGGAAGAGCTTCCCGATATACAGCTCATATGAGCTT-CATGTCATA
19153743 TG
1 TG
19153745 AATTGACGGA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
49 22 0.51
50 21 0.49
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.34
Consensus pattern (50 bp):
TGGCTCGGAAGAGCTTCCCGATATACAGCTCATATGAGCTTCATGTCATA
Found at i:19159361 original size:335 final size:334
Alignment explanation
Indices: 19158751--19159404 Score: 1134
Period size: 335 Copynumber: 2.0 Consensus size: 334
19158741 AACCGTCCAT
*
19158751 TAGCATCAGACTTTTACTAACACACAAACACTTACACGACATCAAGCAAAAATATATCCCCCTTT
1 TAGCATCAGACTTTTACTAACACACAAACACTTACACGACATCAAGCAAAAATATATCCCCCCTT
* **
19158816 GCTAAGGCTGGGACTTGAACTCCAGTCCTCCCACATGCCAACTCATGCTTTAGCCACCAGACCAG
66 GCTAACGCAAGGACTTGAACTCCAGTCCTCCCACATGCCAACTCATGCTTTAGCCACCAGACCAG
**
19158881 TAGACCCATTCTGTCATATTTTTATCAACATTTATTTATAAGCCTACTGATTAGAGATAAGAGTT
131 TAGACCCATTCTAACATATTTTTATCAACATTTATTTATAAGCCTACTGATTAGAGATAAGAGTT
*
19158946 TATTCATTTAAAAACAAAAAAATTTCCCAAGCTAAGGTTTGAACTCAAGACTTCTCATACACTCC
196 TATTCATTTAAAAACAAAAAAATTTCCCAAGCTAAGGTTTGAACTCAAGACTTCTCAGACACTCC
19159011 CAGAACACTTAACCACTGAAGCAGATACACAATTATGTCATAAATACACAGAAACAGATAAACAC
261 CAGAACACTTAACCACTGAAGCAGATACACAATTATGTCATAAATA-ACAGAAACAGATAAACAC
19159076 ACTTAACCAC
325 ACTTAACCAC
* *
19159086 TAGCATCAGACTTTTACTAACACACAAACACTTACACGGCATCAAGCAAGAATATATCCCCCCTT
1 TAGCATCAGACTTTTACTAACACACAAACACTTACACGACATCAAGCAAAAATATATCCCCCCTT
19159151 GCTAACGCAAGGACTTGAACTCCAGTCCTCCCACATGCCAACTCATGCTTTAGCCACCAGACCAG
66 GCTAACGCAAGGACTTGAACTCCAGTCCTCCCACATGCCAACTCATGCTTTAGCCACCAGACCAG
*
19159216 TA-AGCCCATTCTAACATA-TTTTATCAACATTTATTTATAAGCCTACTGATTAGAGATAAGGGT
131 TAGA-CCCATTCTAACATATTTTTATCAACATTTATTTATAAGCCTACTGATTAGAGATAAGAGT
*
19159279 TTATTCATTTAAAAACAAAAAAATTTTCCCAAGCTAAGGTTTGAACTCAGGACCTT-TCAGACAC
195 TTATTCATTTAAAAACAAAAAAA-TTTCCCAAGCTAAGGTTTGAACTCAAGA-CTTCTCAGACAC
* *
19159343 TCCCAGAACACTTAACCACTGAAGTAGATACACAATTATGTCATAAATAATAGAAACAGATA
258 TCCCAGAACACTTAACCACTGAAGCAGATACACAATTATGTCATAAATAACAGAAACAGATA
19159405 TACAAATTTC
Statistics
Matches: 303, Mismatches: 13, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
334 80 0.26
335 220 0.73
336 3 0.01
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.26
Consensus pattern (334 bp):
TAGCATCAGACTTTTACTAACACACAAACACTTACACGACATCAAGCAAAAATATATCCCCCCTT
GCTAACGCAAGGACTTGAACTCCAGTCCTCCCACATGCCAACTCATGCTTTAGCCACCAGACCAG
TAGACCCATTCTAACATATTTTTATCAACATTTATTTATAAGCCTACTGATTAGAGATAAGAGTT
TATTCATTTAAAAACAAAAAAATTTCCCAAGCTAAGGTTTGAACTCAAGACTTCTCAGACACTCC
CAGAACACTTAACCACTGAAGCAGATACACAATTATGTCATAAATAACAGAAACAGATAAACACA
CTTAACCAC
Found at i:19160683 original size:17 final size:17
Alignment explanation
Indices: 19160661--19160720 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
19160651 TAAGATAAAC
*
19160661 ATTAAATTAAATATAAT
1 ATTAAATTAAATTTAAT
* *
19160678 ATTAAAATAATCATTTTAAC
1 ATTAAATTAA--A-TTTAAT
19160698 ATTAAATTAAATTTAAT
1 ATTAAATTAAATTTAAT
*
19160715 ACTAAA
1 ATTAAA
19160721 CTATTTGCAG
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
17 19 0.56
18 1 0.03
19 1 0.03
20 13 0.38
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (17 bp):
ATTAAATTAAATTTAAT
Found at i:19160688 original size:37 final size:37
Alignment explanation
Indices: 19160647--19160720 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
19160637 TATTCAAATG
*
19160647 ATAATAAGATAAACATTAAATTAAATATAATATTAAA
1 ATAATAAGATAAACATTAAATTAAATATAATACTAAA
* ** * *
19160684 ATAATCATTTTAACATTAAATTAAATTTAATACTAAA
1 ATAATAAGATAAACATTAAATTAAATATAATACTAAA
19160721 CTATTTGCAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.57, C:0.05, G:0.01, T:0.36
Consensus pattern (37 bp):
ATAATAAGATAAACATTAAATTAAATATAATACTAAA
Found at i:19167824 original size:16 final size:16
Alignment explanation
Indices: 19167803--19167833 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19167793 CTATGTACGC
*
19167803 AAAATATAAAAGACAG
1 AAAATACAAAAGACAG
19167819 AAAATACAAAAGACA
1 AAAATACAAAAGACA
19167834 TAATAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.10, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAATACAAAAGACAG
Found at i:19168706 original size:3 final size:3
Alignment explanation
Indices: 19168698--19168722 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
19168688 TCTCCAACTC
19168698 ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG A
19168723 AGGCTCAAAT
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:19173339 original size:32 final size:32
Alignment explanation
Indices: 19173297--19173358 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
19173287 TTTAGAATGT
* * *
19173297 AGTTCATTTTGAGTTTAAATCACTTCGAGTTCA
1 AGTTCATTTTGAATTCAAATCA-TCCGAGTTCA
19173330 AGTT-ATTTTGAATTCAAATCATCCGAGTT
1 AGTTCATTTTGAATTCAAATCATCCGAGTT
19173359 TAAGGATTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 7 0.27
32 15 0.58
33 4 0.15
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.42
Consensus pattern (32 bp):
AGTTCATTTTGAATTCAAATCATCCGAGTTCA
Found at i:19178064 original size:18 final size:18
Alignment explanation
Indices: 19178043--19178077 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
19178033 AATAAACATC
19178043 TAAATAAATTTAAATTTT
1 TAAATAAATTTAAATTTT
*
19178061 TAAATATATTTAAATTT
1 TAAATAAATTTAAATTT
19178078 AAATAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TAAATAAATTTAAATTTT
Found at i:19178252 original size:14 final size:14
Alignment explanation
Indices: 19178235--19178268 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
19178225 GTTGCAGTTA
19178235 AAAAGTTGTTTTAG
1 AAAAGTTGTTTTAG
* *
19178249 AAAAATTGTTTTTG
1 AAAAGTTGTTTTAG
19178263 AAAAGT
1 AAAAGT
19178269 ATGGTAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (14 bp):
AAAAGTTGTTTTAG
Found at i:19178831 original size:23 final size:23
Alignment explanation
Indices: 19178812--19178853 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
19178802 AAATAATATA
19178812 AATAAAT-T-ATTATTTTTAATT
1 AATAAATGTAATTATTTTTAATT
*
19178833 AATAATTGTAATTATTTTTAA
1 AATAAATGTAATTATTTTTAA
19178854 ATACCTGATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 1 0.06
23 11 0.61
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
AATAAATGTAATTATTTTTAATT
Found at i:19182662 original size:2 final size:2
Alignment explanation
Indices: 19182655--19182680 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19182645 AAAGGAAAGT
19182655 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
19182681 AAATATGTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19184571 original size:132 final size:132
Alignment explanation
Indices: 19184342--19186276 Score: 2870
Period size: 132 Copynumber: 14.6 Consensus size: 132
19184332 CTTCAGTCTG
* * * * * * * *
19184342 CTCCACTGCAACCTCAGGGAGGTAAGA-CAGCCATTTTTTATTTACTCCACTACTGCTTAGGGAG
1 CTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
*
19184406 ACAA-AGTCTGAAATCATCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAAT
66 ACAAGA-TCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAAT
19184470 GTA
130 GTA
* * *
19184473 CTCCACTATAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAG
1 CTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
* * *
19184538 ATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGTG-AGATAGAATTACTGGCTTCAAT
66 ACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAG-TAGAATTACTGGCTTCAAT
19184602 GTA
130 GTA
* * * *
19184605 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATTTTTTATTTGCTCCACTACTGCTTAGGGAG
1 CTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
* *
19184670 ACAA-AGTTTGAAATCATCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAAT
66 ACAAGA-TCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAAT
19184734 GTA
130 GTA
* * * * *
19184737 CTCCACTATAACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGTTCCACTACTGCTTAGGGAG
1 CTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
* * * *
19184802 ATAAGATCTGAAATATTCAATCTATTCCACTGTTGCCCCAGGGAAGTAGAATTACTGGCTTCAAT
66 ACAAGATCTGAAATCTTCAATCTATTCCGCTGCTG-CCCAGGGAAGTAGAATTACTGGCTTCAAT
19184867 GTA
130 GTA
* * *
19184870 CTCCACTGTAATCAC-GAGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTGGGGA
1 CTCCACTGTAACCACAG-GGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTGCTTAGGGA
*
19184934 GACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGAAAGTAGAATTACTGGCTTCAAT
65 GACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAAT
19184999 GTA
130 GTA
* *
19185002 CTCCACTGTAACCAC-GAGGAGGTAAAATCCGCCATCTTCGATCTGTTCCACTACTGCTTAGGGA
1 CTCCACTGTAACCACAG-GGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTGCTTAGGGA
* * *
19185066 GATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGTG-AGATAGAATTACTGGCTTCAA
65 GACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAG-TAGAATTACTGGCTTCAA
19185130 TGTA
129 TGTA
* * * *
19185134 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATTTTTTATTTGCTCCACTACTGCTTAGGGAG
1 CTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
*
19185199 ACAAGGTCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATG
66 ACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATG
19185264 TA
131 TA
* * * * *
19185266 CTCCACTATAACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGTTCCACTACTGCTTAGGGAG
1 CTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
* * *
19185331 ATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCCAGGGAAGTAGAATTACTGGCTTCAAT
66 ACAAGATCTGAAATCTTCAATCTATTCCGCTGCTG-CCCAGGGAAGTAGAATTACTGGCTTCAAT
19185396 GTA
130 GTA
* *
19185399 CTCCACTGTAATCAC-GAGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTGCTTGGGGA
1 CTCCACTGTAACCACAG-GGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTGCTTAGGGA
*
19185463 GACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGAAAGTAGAATTACTGGCTTCAAT
65 GACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAAT
19185528 GTA
130 GTA
* * *
19185531 CTCCACTGTAACCAC-GAGGAGGTAAAATCCGCCATCTTCGATCTGTTCCACTACTGCTGAGGGA
1 CTCCACTGTAACCACAG-GGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTGCTTAGGGA
* * *
19185595 GATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGTG-AGATAGAATTACTGGCTTCAA
65 GACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAG-TAGAATTACTGGCTTCAA
19185659 TGTA
129 TGTA
* * * * *
19185663 CTCCACTGTAACCACAGGGGGGTAAAATCTGCCATTTTTTATTTGCTCCACTACTGCTTAGGGAG
1 CTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
* * *
19185728 ACAAGGTCTGAAATCTTCAATCTATTCCGCTGCTACCCAGGGAAGTAGAATTACCGGCTTCAATG
66 ACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATG
19185793 TA
131 TA
* * * *
19185795 CTCCACTATAACCTCAGAGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAG
1 CTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
* * *
19185860 ATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCTAGGGAAGTAGAATTACTGGCTTCAAT
66 ACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCC-AGGGAAGTAGAATTACTGGCTTCAAT
19185925 GTA
130 GTA
* * *
19185928 CTCCACTGTAACCAC-GAGGAGGTAAAATTCACCATCTTTGATCTGCCCCACTACTGCTTAGGGA
1 CTCCACTGTAACCACAG-GGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTGCTTAGGGA
* *
19185992 GACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCCAAGGAAGTAGAATTACTGGCTTCAAT
65 GACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAAT
19186057 GTA
130 GTA
*
19186060 CTCCACTGTAACCAC-GAGGAGGTAAAATCCGCCATCTTTGATCTGCCCCACTACTGCTTAGGGA
1 CTCCACTGTAACCACAG-GGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTGCTTAGGGA
* *
19186124 GACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCCAGGGAAGTAGAATTATTGGCTTCAAT
65 GACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAAT
19186189 GTA
130 GTA
*
19186192 CTCCACTGTAACCAC-GAGGAGGTAAAATCCGCCATCTTTGATCTGCTCTACTACTGCTTAGGGA
1 CTCCACTGTAACCACAG-GGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTGCTTAGGGA
*
19186256 GACAAGATCTAAAATCTTCAA
65 GACAAGATCTGAAATCTTCAA
19186277 CCTGCTCTAC
Statistics
Matches: 1639, Mismatches: 147, Indels: 35
0.90 0.08 0.02
Matches are distributed among these distances:
131 31 0.02
132 1240 0.76
133 368 0.22
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (132 bp):
CTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
ACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATG
TA
Found at i:19185186 original size:397 final size:396
Alignment explanation
Indices: 19184342--19186276 Score: 2867
Period size: 397 Copynumber: 4.9 Consensus size: 396
19184332 CTTCAGTCTG
* * * * * * * *
19184342 CTCCACTGCAACCTCAGGGAGGTAAGA-CAGCCATTTTTTATTTACTCCACTACTGCTTAGGGAG
1 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
*
19184406 ACAA-AGTCTGAAATCATCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAAT
66 ACAAGA-TCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAAT
* * *
19184470 GTACTCCACTATAACCTCA-G-GGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTA
130 GTACTCCACTGTAA--TCACGAGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTA
* * *
19184533 GGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGTG-AGATAGAATTACTGGCT
193 GGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAG-TAGAATTACTGGCT
* * * *
19184597 TCAATGTACTCCACTGTAACCAC-AGGGAGGTAAAATCTGCCATTTTTTATTTGCTCCACTACTG
257 TCAATGTACTCCACTGTAACCACGA-GGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTG
* * *
19184661 CTTAGGGAGACAA-AGTTTGAAATCATCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACT
321 CTTAGGGAGACAAGA-TCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACT
19184725 GGCTTCAATGTA
385 GGCTTCAATGTA
* * * *
19184737 CTCCACTATAACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGTTCCACTACTGCTTAGGGAG
1 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
* * * *
19184802 ATAAGATCTGAAATATTCAATCTATTCCACTGTTGCCCCAGGGAAGTAGAATTACTGGCTTCAAT
66 ACAAGATCTGAAATCTTCAATCTATTCCGCTGCTG-CCCAGGGAAGTAGAATTACTGGCTTCAAT
*
19184867 GTACTCCACTGTAATCACGAGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTGGG
130 GTACTCCACTGTAATCACGAGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGG
*
19184932 GAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGAAAGTAGAATTACTGGCTTCA
195 GAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCA
* *
19184997 ATGTACTCCACTGTAACCACGAGGAGGTAAAATCCGCCATCTTCGATCTGTTCCACTACTGCTTA
260 ATGTACTCCACTGTAACCACGAGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTGCTTA
* *
19185062 GGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGTG-AGATAGAATTACTGGCT
325 GGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAG-TAGAATTACTGGCT
19185126 TCAATGTA
389 TCAATGTA
* * *
19185134 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATTTTTTATTTGCTCCACTACTGCTTAGGGAG
1 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
*
19185199 ACAAGGTCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATG
66 ACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATG
* * *
19185264 TACTCCACTATAACCTCA-G-GGAGGTAAAATCTGCCATCTTCGATCTGTTCCACTACTGCTTAG
131 TACTCCACTGTAA--TCACGAGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAG
* * *
19185327 GGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCCAGGGAAGTAGAATTACTGGCTT
194 GGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTG-CCCAGGGAAGTAGAATTACTGGCTT
*
19185392 CAATGTACTCCACTGTAATCACGAGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTGCT
258 CAATGTACTCCACTGTAACCACGAGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTGCT
* * *
19185457 TGGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGAAAGTAGAATTACTGGC
323 TAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGC
19185522 TTCAATGTA
388 TTCAATGTA
* * * *
19185531 CTCCACTGTAACCAC-GAGGAGGTAAAATCCGCCATCTTCGATCTGTTCCACTACTGCTGAGGGA
1 CTCCACTGTAACCACAG-GGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGA
* * *
19185595 GATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGTG-AGATAGAATTACTGGCTTCAA
65 GACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAG-TAGAATTACTGGCTTCAA
* * * * *
19185659 TGTACTCCACTGTAACCAC-AGGGGGGTAAAATCTGCCATTTTTTATTTGCTCCACTACTGCTTA
129 TGTACTCCACTGTAATCACGA-GGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTA
* * *
19185723 GGGAGACAAGGTCTGAAATCTTCAATCTATTCCGCTGCTACCCAGGGAAGTAGAATTACCGGCTT
193 GGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTT
* * *
19185788 CAATGTACTCCACTATAACCTC-AGAGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
258 CAATGTACTCCACTGTAACCACGAG-GAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTGC
* *
19185852 TTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCTAGGGAAGTAGAATTACTG
322 TTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCC-AGGGAAGTAGAATTACTG
19185917 GCTTCAATGTA
386 GCTTCAATGTA
* *
19185928 CTCCACTGTAACCAC-GAGGAGGTAAAAT-TCACCATCTTTGATCTGCCCCACTACTGCTTAGGG
1 CTCCACTGTAACCACAG-GGAGGTAAAATCT-GCCATCTTTGATCTGCTCCACTACTGCTTAGGG
* *
19185991 AGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCCAAGGAAGTAGAATTACTGGCTTCAA
64 AGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAA
* * *
19186056 TGTACTCCACTGTAACCACGAGGAGGTAAAATCCGCCATCTTTGATCTGCCCCACTACTGCTTAG
129 TGTACTCCACTGTAATCACGAGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAG
* *
19186121 GGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCCAGGGAAGTAGAATTATTGGCTTC
194 GGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTC
*
19186186 AATGTACTCCACTGTAACCACGAGGAGGTAAAATCCGCCATCTTTGATCTGCTCTACTACTGCTT
259 AATGTACTCCACTGTAACCACGAGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTGCTT
*
19186251 AGGGAGACAAGATCTAAAATCTTCAA
324 AGGGAGACAAGATCTGAAATCTTCAA
19186277 CCTGCTCTAC
Statistics
Matches: 1392, Mismatches: 124, Indels: 46
0.89 0.08 0.03
Matches are distributed among these distances:
395 31 0.02
396 306 0.22
397 1041 0.75
398 14 0.01
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (396 bp):
CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
ACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATG
TACTCCACTGTAATCACGAGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGG
AGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAA
TGTACTCCACTGTAACCACGAGGAGGTAAAATCCGCCATCTTTGATCTGCTCCACTACTGCTTAG
GGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTC
AATGTA
Found at i:19185384 original size:529 final size:529
Alignment explanation
Indices: 19184386--19186276 Score: 3335
Period size: 529 Copynumber: 3.6 Consensus size: 529
19184376 TTTTTATTTA
* *
19184386 CTCCACTACTGCTTAGGGAGACAA-AGTCTGAAATCATCAATCTATTCCGCTGCTGCCCAGGGAA
1 CTCCACTACTGCTTAGGGAGACAAGA-TCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGAAA
* *
19184450 GTAGAATTACTGGCTTCAATGTACTCCACTATAACCTC-AGGGAGGTAAAATCCGCCATCTTCGA
65 GTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACGA-GGAGGTAAAATCCGCCATCTTCGA
19184514 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGT
129 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGT
19184579 GAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATTTTT
194 GAGATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATTTTT
* * *
19184644 TATTTGCTCCACTACTGCTTAGGGAGACAAAGTTTGAAATCATCAATCTATTCCGCTGCTGCCCA
259 TATTTGCTCCACTACTGCTTAGGGAGACAAGGTCTGAAATCTTCAATCTATTCCGCTGCTGCCCA
19184709 GGGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCTCAGGGAGGTAAAATCTGCCATCT
324 GGGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCTCAGGGAGGTAAAATCTGCCATCT
*
19184774 TCGATCTGTTCCACTACTGCTTAGGGAGATAAGATCTGAAATATTCAATCTATTCCACTGTTGCC
389 TCGATCTGTTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCC
19184839 CCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAATCACGAGGAGGTAAAATCTGCCA
454 CCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAATCACGAGGAGGTAAAATCTGCCA
19184904 TCTTTGATCTG
519 TCTTTGATCTG
*
19184915 CTCCACTACTGCTTGGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGAAAG
1 CTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGAAAG
19184980 TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACGAGGAGGTAAAATCCGCCATCTTCGATC
66 TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACGAGGAGGTAAAATCCGCCATCTTCGATC
*
19185045 TGTTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGTGA
131 TGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGTGA
19185110 GATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATTTTTTA
196 GATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATTTTTTA
19185175 TTTGCTCCACTACTGCTTAGGGAGACAAGGTCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGG
261 TTTGCTCCACTACTGCTTAGGGAGACAAGGTCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGG
19185240 GAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCTCAGGGAGGTAAAATCTGCCATCTTC
326 GAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCTCAGGGAGGTAAAATCTGCCATCTTC
19185305 GATCTGTTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCC
391 GATCTGTTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCC
*
19185370 AGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAATCACGAGGAGGTAAAATCCGCCATC
456 AGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAATCACGAGGAGGTAAAATCTGCCATC
19185435 TTTGATCTG
521 TTTGATCTG
*
19185444 CTCCACTACTGCTTGGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGAAAG
1 CTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGAAAG
19185509 TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACGAGGAGGTAAAATCCGCCATCTTCGATC
66 TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACGAGGAGGTAAAATCCGCCATCTTCGATC
* *
19185574 TGTTCCACTACTGCTGAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGTGA
131 TGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGTGA
*
19185639 GATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGGGGTAAAATCTGCCATTTTTTA
196 GATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATTTTTTA
*
19185704 TTTGCTCCACTACTGCTTAGGGAGACAAGGTCTGAAATCTTCAATCTATTCCGCTGCTACCCAGG
261 TTTGCTCCACTACTGCTTAGGGAGACAAGGTCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGG
* * *
19185769 GAAGTAGAATTACCGGCTTCAATGTACTCCACTATAACCTCAGAGAGGTAAAATCCGCCATCTTC
326 GAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCTCAGGGAGGTAAAATCTGCCATCTTC
* *
19185834 GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCT
391 GATCTGTTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCC
* *
19185899 AGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACGAGGAGGTAAAAT-TCACCAT
456 AGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAATCACGAGGAGGTAAAATCT-GCCAT
19185963 CTTTGATCTG
520 CTTTGATCTG
* *
19185973 CCCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCCAAGG-AA
1 CTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTG-CCCAGGAAA
*
19186037 GTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACGAGGAGGTAAAATCCGCCATCTTTGAT
65 GTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACGAGGAGGTAAAATCCGCCATCTTCGAT
* * * * *
19186102 CTGCCCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGTCCAGGG
130 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGTG
* * *
19186167 A-AGTAGAATTATTGGCTTCAATGTACTCCACTGTAACCAC-GAGGAGGTAAAATCCGCCATCTT
195 AGA-TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAG-GGAGGTAAAATCTGCCATTTT
* * * * *
19186230 TGATCTGCTCTACTACTGCTTAGGGAGACAAGATCTAAAATCTTCAA
258 TTATTTGCTCCACTACTGCTTAGGGAGACAAGGTCTGAAATCTTCAA
19186277 CCTGCTCTAC
Statistics
Matches: 1314, Mismatches: 42, Indels: 12
0.96 0.03 0.01
Matches are distributed among these distances:
528 2 0.00
529 1305 0.99
530 7 0.01
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (529 bp):
CTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGAAAG
TAGAATTACTGGCTTCAATGTACTCCACTGTAACCACGAGGAGGTAAAATCCGCCATCTTCGATC
TGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGTGA
GATAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATTTTTTA
TTTGCTCCACTACTGCTTAGGGAGACAAGGTCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGG
GAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCTCAGGGAGGTAAAATCTGCCATCTTC
GATCTGTTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCC
AGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAATCACGAGGAGGTAAAATCTGCCATC
TTTGATCTG
Found at i:19194285 original size:132 final size:132
Alignment explanation
Indices: 19194056--19194801 Score: 1083
Period size: 132 Copynumber: 5.6 Consensus size: 132
19194046 CTTCAGTCTG
* * * * * * *
19194056 CTCCACTGCAACCTCAGGGAGGTAAGA-CAGCCATTTTTTATTTACTCCACTACTGCTTAGGGAG
1 CTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
*
19194120 ACAA-AGTCTGAAATCATCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAAT
66 ACAAGA-TCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAAT
19194184 GTA
130 GTA
* * *
19194187 CTCCACTATAACCTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAG
1 CTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
* * *
19194252 ATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGTG-AGATAGAATTACTGGCTTCAAT
66 ACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAG-TAGAATTACTGGCTTCAAT
19194316 GTA
130 GTA
* * * *
19194319 CTCCACTGTAACCACAGGGAGGTAAAATCTGCCATTTTTTATTTGCTCCACTACTGCTTAGGGAG
1 CTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
* *
19194384 ACAAGGTCTGAAATCTTCAATCTATTCCGCTGCTACCCAGGGAAGTAGAATTACTGGCTTCAATG
66 ACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATG
19194449 TA
131 TA
* * *
19194451 CTCCACTATAACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGTTCCACTACTGCTTAGGGAG
1 CTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
* * * *
19194516 ATAAGATCTGAAATATTCAATCTATTCCACTGTTGCCCCAGGGAAGTAGAATTACTGGCTTCAAT
66 ACAAGATCTGAAATCTTCAATCTATTCCGCTGCTG-CCCAGGGAAGTAGAATTACTGGCTTCAAT
19194581 GTA
130 GTA
*
19194584 CTCCACTGTAA--TCACGAGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTGGGG
1 CTCCACTGTAACCTCA-G-GGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGG
*
19194647 AGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGAAAGTAGAATTAACTGGCTTCA
64 AGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATT-ACTGGCTTCA
19194712 ATGTA
128 ATGTA
* * *
19194717 CTCCACTGTAACCAC-GAGGAGGTAAAAT-TCACCATCTTTGATCTGCCCCACTACTGCTTAGGG
1 CTCCACTGTAACCTCAG-GGAGGTAAAATCT-GCCATCTTTGATCTGCTCCACTACTGCTTAGGG
19194780 AGACAAGATCTGAAATCTTCAA
64 AGACAAGATCTGAAATCTTCAA
19194802 CCTGCTCTAC
Statistics
Matches: 553, Mismatches: 51, Indels: 20
0.89 0.08 0.03
Matches are distributed among these distances:
131 29 0.05
132 311 0.56
133 212 0.38
135 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (132 bp):
CTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
ACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATG
TA
Found at i:19224982 original size:3 final size:3
Alignment explanation
Indices: 19224976--19225009 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
19224966 GTTGTTAACA
19224976 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
19225010 TATGCTAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:19229551 original size:2 final size:2
Alignment explanation
Indices: 19229544--19229576 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
19229534 TCGCTAAATA
19229544 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19229577 GAGTACACCT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:19232709 original size:14 final size:15
Alignment explanation
Indices: 19232691--19232725 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
19232681 TTTTTTAAAT
*
19232691 TATATTATTAATTTA
1 TATATTAATAATTTA
19232706 -ATATTAATAATTTA
1 TATATTAATAATTTA
19232720 TATATT
1 TATATT
19232726 TTTTATTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TATATTAATAATTTA
Found at i:19233106 original size:3 final size:3
Alignment explanation
Indices: 19233098--19233132 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
19233088 AGCATTGCTA
*
19233098 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGG GGT GG
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GG
19233133 AGAAGCATGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.71, T:0.29
Consensus pattern (3 bp):
GGT
Found at i:19235009 original size:461 final size:461
Alignment explanation
Indices: 19234147--19235071 Score: 1841
Period size: 461 Copynumber: 2.0 Consensus size: 461
19234137 TTGGTTTTGG
19234147 AATGTTTTCACTTATTTTATTTTCATTGATTGATATGAGTTTATATACAAAAGACATGCTAAGAA
1 AATGTTTTCACTTATTTTATTTTCATTGATTGATATGAGTTTATATACAAAAGACATGCTAAGAA
19234212 ATCTACTAAAAATAACAGATGTGGACTTATTCTTAAGGAAAACAAATCGCTAAAAATCAGGAATG
66 ATCTACTAAAAATAACAGATGTGGACTTATTCTTAAGGAAAACAAATCGCTAAAAATCAGGAATG
19234277 TAAACAATAAAATCCTAAAGAAATACAAATACTTGAGAGTGCAACTTTATATTCTTATTAGTTCC
131 TAAACAATAAAATCCTAAAGAAATACAAATACTTGAGAGTGCAACTTTATATTCTTATTAGTTCC
19234342 TTCATATAAGAAATCATGAGTATCCTCTTTTAGCAGCATATAATATACTATGGTGGAATTAGGAA
196 TTCATATAAGAAATCATGAGTATCCTCTTTTAGCAGCATATAATATACTATGGTGGAATTAGGAA
19234407 AAGAACTACTTAGTTTAGCTTTCCTATTGCCGTTTTTGCCAAACAATCAGTTACAATGTTACTTC
261 AAGAACTACTTAGTTTAGCTTTCCTATTGCCGTTTTTGCCAAACAATCAGTTACAATGTTACTTC
19234472 CTCGCAAGACATGCCTAAACTTCACTTAACAATCCTTACTACAACATTCATATTTTATTAATAAA
326 CTCGCAAGACATGCCTAAACTTCACTTAACAATCCTTACTACAACATTCATATTTTATTAATAAA
19234537 TTAAACACCAACATAAAAATTTACAAATTATTTAAATAACTTTTTAATGGAAACTAAATTCTCTC
391 TTAAACACCAACATAAAAATTTACAAATTATTTAAATAACTTTTTAATGGAAACTAAATTCTCTC
19234602 AGTGGC
456 AGTGGC
19234608 AATGTTTTCACTTATTTTATTTTCATTGATTGATATGAGTTTATATACAAAAGACATGCTAAGAA
1 AATGTTTTCACTTATTTTATTTTCATTGATTGATATGAGTTTATATACAAAAGACATGCTAAGAA
19234673 ATCTACTAAAAATAACAGATGTGGACTTATTCTTAAGGAAAACAAATCGCTAAAAATCAGGAATG
66 ATCTACTAAAAATAACAGATGTGGACTTATTCTTAAGGAAAACAAATCGCTAAAAATCAGGAATG
19234738 TAAACAATAAAATCCTAAAGAAATACAAATACTTGAGAGTGCAACTTTATATTCTTATTAGTTCC
131 TAAACAATAAAATCCTAAAGAAATACAAATACTTGAGAGTGCAACTTTATATTCTTATTAGTTCC
*
19234803 TTCATATAAGAAATCATGAGTATCCTCTTTTAGCAGCGTATAATATACTATGGTGGAATTAGGAA
196 TTCATATAAGAAATCATGAGTATCCTCTTTTAGCAGCATATAATATACTATGGTGGAATTAGGAA
19234868 AAGAACTACTTAGTTTAGCTTTCCTATTGCCGTTTTTGCCAAACAATCAGTTACAATGTTACTTC
261 AAGAACTACTTAGTTTAGCTTTCCTATTGCCGTTTTTGCCAAACAATCAGTTACAATGTTACTTC
19234933 CTCGCAAGACATGCCTAAACTTCACTTAACAATCCTTACTACAACATTCATATTTTATTAATAAA
326 CTCGCAAGACATGCCTAAACTTCACTTAACAATCCTTACTACAACATTCATATTTTATTAATAAA
19234998 TTAAACACCAACATAAAAATTTACAAATTATTTAAATAACTTTTTAATGGAAACTAAATTCTCTC
391 TTAAACACCAACATAAAAATTTACAAATTATTTAAATAACTTTTTAATGGAAACTAAATTCTCTC
19235063 AGTGGC
456 AGTGGC
19235069 AAT
1 AAT
19235072 ATAACGCTTA
Statistics
Matches: 463, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
461 463 1.00
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (461 bp):
AATGTTTTCACTTATTTTATTTTCATTGATTGATATGAGTTTATATACAAAAGACATGCTAAGAA
ATCTACTAAAAATAACAGATGTGGACTTATTCTTAAGGAAAACAAATCGCTAAAAATCAGGAATG
TAAACAATAAAATCCTAAAGAAATACAAATACTTGAGAGTGCAACTTTATATTCTTATTAGTTCC
TTCATATAAGAAATCATGAGTATCCTCTTTTAGCAGCATATAATATACTATGGTGGAATTAGGAA
AAGAACTACTTAGTTTAGCTTTCCTATTGCCGTTTTTGCCAAACAATCAGTTACAATGTTACTTC
CTCGCAAGACATGCCTAAACTTCACTTAACAATCCTTACTACAACATTCATATTTTATTAATAAA
TTAAACACCAACATAAAAATTTACAAATTATTTAAATAACTTTTTAATGGAAACTAAATTCTCTC
AGTGGC
Found at i:19237214 original size:22 final size:22
Alignment explanation
Indices: 19237181--19237236 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
19237171 ATTTCCTCTC
19237181 AATTCCTCTCAATTTCCTTCCAA
1 AATT-CTCTCAATTTCCTTCCAA
19237204 AATTCTCTCAATTTCCTTCCAA
1 AATTCTCTCAATTTCCTTCCAA
19237226 AATTCTCTCAA
1 AATTCTCTCAA
19237237 ATCCATATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 29 0.88
23 4 0.12
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTCTCTCAATTTCCTTCCAA
Found at i:19239114 original size:18 final size:18
Alignment explanation
Indices: 19239088--19239122 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
19239078 AGGTGCGTTT
*
19239088 CCTAGCCCTTATATGTAC
1 CCTAACCCTTATATGTAC
19239106 CCTAACCCTTATATGTA
1 CCTAACCCTTATATGTA
19239123 TCCTTTTCCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (18 bp):
CCTAACCCTTATATGTAC
Found at i:19239598 original size:43 final size:45
Alignment explanation
Indices: 19239545--19239680 Score: 143
Period size: 50 Copynumber: 3.0 Consensus size: 45
19239535 ATATTTTGAA
*
19239545 TATTTTGATATTATTTTATGTAA-AAAATAGAAATTT-TTTGAGT
1 TATTTTGATATTATTTGATGTAATAAAATAGAAATTTATTTGAGT
* *
19239588 TATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGATT
1 TATTTTGATATTATTTGATGTAATAAAATAGAAATTTATTTGAGT
* * *
19239633 TAATAAAATAGA-AGTTTATTTGATGTAATAAAATAGAAGTTTATTTGA
1 T-AT---TTTGATA--TTATTTGATGTAATAAAATAGAAATTTATTTGA
19239681 TGTAATAAAA
Statistics
Matches: 80, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
43 22 0.28
44 12 0.15
45 7 0.09
46 2 0.03
48 1 0.01
49 3 0.04
50 33 0.41
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (45 bp):
TATTTTGATATTATTTGATGTAATAAAATAGAAATTTATTTGAGT
Found at i:19239636 original size:25 final size:25
Alignment explanation
Indices: 19239598--19239760 Score: 196
Period size: 25 Copynumber: 6.7 Consensus size: 25
19239588 TATTTTGATA
19239598 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
*
19239623 TTATTTGATTTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
19239648 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
*
19239673 TTATTTGATGTAATAAAATAGAAAT
1 TTATTTGATGTAATAAAATAGAAGT
** *
19239698 TT-TTTCGA-GT--T-ATTTTG-A-T
1 TTATTT-GATGTAATAAAATAGAAGT
*
19239717 ATTATTTGATGTAATAAAATATAAGT
1 -TTATTTGATGTAATAAAATAGAAGT
*
19239743 TTATTTGATATAATAAAA
1 TTATTTGATGTAATAAAA
19239761 ACCCTAACCT
Statistics
Matches: 118, Mismatches: 11, Indels: 18
0.80 0.07 0.12
Matches are distributed among these distances:
19 1 0.01
20 5 0.04
21 8 0.07
22 1 0.01
23 1 0.01
24 7 0.06
25 94 0.80
26 1 0.01
ACGTcount: A:0.42, C:0.01, G:0.13, T:0.44
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:19239808 original size:23 final size:23
Alignment explanation
Indices: 19239756--19240043 Score: 155
Period size: 23 Copynumber: 12.0 Consensus size: 23
19239746 TTTGATATAA
* *
19239756 TAAAAACCCTAACCTAATTTAAC
1 TAAAAACCCTAACCTAAATTAAT
***
19239779 CCTAAACCCTAACCTAAATTAAT
1 TAAAAACCCTAACCTAAATTAAT
19239802 TAAAAACCCTAACACTAACCTAATTTAAT
1 TAAAAACCCTAAC-CT-A---AA-TTAAT
19239831 TAAAAACCCTAACCCTAACCTAATTTAAT
1 TAAAAACCCTAA-CCT-A---AA-TTAAT
* *
19239860 TAAAAACCCTAAACCTTAACT--T
1 TAAAAACCCT-AACCTAAATTAAT
*
19239882 TAAAAACCCTAACCTAATTTAA-
1 TAAAAACCCTAACCTAAATTAAT
*
19239904 TACAAAACCCTAACCTAATTTAAT
1 TA-AAAACCCTAACCTAAATTAAT
19239928 TAAAAACCCTAAACC----TTAACT
1 TAAAAACCCT-AACCTAAATTAA-T
* * *
19239949 TAAAAACCTTAAACCTTAACT--T
1 TAAAAACCCT-AACCTAAATTAAT
* *
19239971 TAAAAACCCTAACCTAATTTGA-
1 TAAAAACCCTAACCTAAATTAAT
* *
19239993 TACAAAATCCTAACCTAAACCCTAAT
1 TA-AAAACCCTAACCTAAA--TTAAT
* *
19240019 TAAAAACCTTAACCCTAACTTAAT
1 TAAAAACCCTAA-CCTAAATTAAT
19240043 T
1 T
19240044 TAATTAAAGA
Statistics
Matches: 213, Mismatches: 27, Indels: 49
0.74 0.09 0.17
Matches are distributed among these distances:
20 4 0.02
21 29 0.14
22 25 0.12
23 70 0.33
24 14 0.07
25 14 0.07
26 7 0.03
28 2 0.01
29 45 0.21
30 3 0.01
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.27
Consensus pattern (23 bp):
TAAAAACCCTAACCTAAATTAAT
Found at i:19239820 original size:29 final size:29
Alignment explanation
Indices: 19239776--19240153 Score: 220
Period size: 29 Copynumber: 13.3 Consensus size: 29
19239766 AACCTAATTT
*
19239776 AACCCTAAACCCTAACCTAAATTAATTAAA
1 AACCCT-AACCCTAACCTAATTTAATTAAA
*
19239806 AACCCTAACACTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
19239835 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
* *
19239864 AACCCTAAACCT----TAA-CT--TTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
19239886 AACCCT-A-----ACCTAATTTAA-TACAA
1 AACCCTAACCCTAACCTAATTTAATTA-AA
19239909 AACCCT-A-----ACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
* * *
19239932 AACCCTAAACCTTAACTTAA--AAACCTTAAA
1 AACCCT-AACCCTAACCTAATTTAA--TTAAA
** *
19239962 CCTTAACTTTAAAAACCCTAACCTAATTTGA-TACAA
1 ----AACCCT---AACCCTAACCTAATTTAATTA-AA
* *
19239998 AATCCTAA-CCTAAACC----CTAATTAAA
1 AACCCTAACCCT-AACCTAATTTAATTAAA
* *
19240023 AACCTTAACCCTAACTTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
*
19240052 GAA-CCTAATCCTAACCTAATTTAATTAAA
1 -AACCCTAACCCTAACCTAATTTAATTAAA
*
19240081 AACCCTAACCCTAATCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
19240110 GTCCTTAACCCTAACCCTAACCTAATTTAATTAAA
1 ------AACCCTAACCCTAACCTAATTTAATTAAA
19240145 AACCCTAAC
1 AACCCTAAC
19240154 TTAAATTAAT
Statistics
Matches: 278, Mismatches: 29, Indels: 83
0.71 0.07 0.21
Matches are distributed among these distances:
20 3 0.01
21 2 0.01
22 13 0.05
23 28 0.10
24 3 0.01
25 17 0.06
26 5 0.02
28 7 0.03
29 130 0.47
30 18 0.06
32 3 0.01
34 4 0.01
35 30 0.11
36 14 0.05
38 1 0.00
ACGTcount: A:0.46, C:0.26, G:0.01, T:0.28
Consensus pattern (29 bp):
AACCCTAACCCTAACCTAATTTAATTAAA
Found at i:19239918 original size:68 final size:66
Alignment explanation
Indices: 19239841--19239990 Score: 232
Period size: 68 Copynumber: 2.2 Consensus size: 66
19239831 TAAAAACCCT
*
19239841 AACCCTAACCTAATTTAATTAAAAACCCTAAACCTTAACTTTAAAAACCCT-AACC-TAATTTAA
1 AACCCTAACCTAATTTAATTAAAAACCCTAAACCTTAAC-TTAAAAACCCTAAACCTTAACTT--
19239904 TACAA
63 TA-AA
*
19239909 AACCCTAACCTAATTTAATTAAAAACCCTAAACCTTAACTTAAAAACCTTAAACCTTAACTTTAA
1 AACCCTAACCTAATTTAATTAAAAACCCTAAACCTTAACTTAAAAACCCTAAACCTTAACTTTAA
19239974 A
66 A
19239975 AACCCTAACCTAATTT
1 AACCCTAACCTAATTT
19239991 GATACAAAAT
Statistics
Matches: 78, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
66 18 0.23
67 12 0.15
68 43 0.55
69 5 0.06
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.29
Consensus pattern (66 bp):
AACCCTAACCTAATTTAATTAAAAACCCTAAACCTTAACTTAAAAACCCTAAACCTTAACTTTAA
A
Found at i:19239963 original size:89 final size:90
Alignment explanation
Indices: 19239855--19240041 Score: 281
Period size: 89 Copynumber: 2.1 Consensus size: 90
19239845 CTAACCTAAT
19239855 TTAA-TTAAAAACCCTAAACCTTAACTTTAAAAACCCTAACCTAATTTAATACAAAACCCTAACC
1 TTAACTTAAAAACCCTAAACCTTAACTTTAAAAACCCTAACCTAATTTAATACAAAACCCTAACC
**
19239919 T-AA-TTTAATTAAAAACCCTAAACC
66 TAAACCCTAATTAAAAA-CCTAAACC
* * *
19239943 TTAACTTAAAAACCTTAAACCTTAACTTTAAAAACCCTAACCTAATTTGATACAAAATCCTAACC
1 TTAACTTAAAAACCCTAAACCTTAACTTTAAAAACCCTAACCTAATTTAATACAAAACCCTAACC
*
19240008 TAAACCCTAATTAAAAACCTTAACC
66 TAAACCCTAATTAAAAACCTAAACC
*
19240033 CTAACTTAA
1 TTAACTTAA
19240042 TTTAATTAAA
Statistics
Matches: 89, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
88 4 0.04
89 58 0.65
90 17 0.19
91 10 0.11
ACGTcount: A:0.47, C:0.25, G:0.01, T:0.28
Consensus pattern (90 bp):
TTAACTTAAAAACCCTAAACCTTAACTTTAAAAACCCTAACCTAATTTAATACAAAACCCTAACC
TAAACCCTAATTAAAAACCTAAACC
Found at i:19239985 original size:21 final size:22
Alignment explanation
Indices: 19239859--19239982 Score: 132
Period size: 22 Copynumber: 5.6 Consensus size: 22
19239849 CCTAATTTAA
19239859 TTAAAAACCCTAAACCTTAACT
1 TTAAAAACCCTAAACCTTAACT
*
19239881 TTAAAAACCCT-AACC-TAATT
1 TTAAAAACCCTAAACCTTAACT
*
19239901 TAATACAAAACCCT-AACC-TAATTT
1 T--TA-AAAACCCTAAACCTTAA-CT
19239925 AATTAAAAACCCTAAACCTTAAC-
1 --TTAAAAACCCTAAACCTTAACT
*
19239948 TTAAAAACCTTAAACCTTAACT
1 TTAAAAACCCTAAACCTTAACT
19239970 TTAAAAACCCTAA
1 TTAAAAACCCTAA
19239983 CCTAATTTGA
Statistics
Matches: 89, Mismatches: 4, Indels: 18
0.80 0.04 0.16
Matches are distributed among these distances:
20 5 0.06
21 24 0.27
22 25 0.28
23 23 0.26
24 8 0.09
25 3 0.03
26 1 0.01
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.27
Consensus pattern (22 bp):
TTAAAAACCCTAAACCTTAACT
Found at i:19240032 original size:19 final size:20
Alignment explanation
Indices: 19240004--19240041 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
19239994 ACAAAATCCT
19240004 AACCTAAACCCTAA-TTAAA
1 AACCTAAACCCTAACTTAAA
*
19240023 AACCTTAACCCTAACTTAA
1 AACCTAAACCCTAACTTAA
19240042 TTTAATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (20 bp):
AACCTAAACCCTAACTTAAA
Found at i:19240148 original size:23 final size:23
Alignment explanation
Indices: 19240122--19240185 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
19240112 CCTTAACCCT
*
19240122 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAAATTAATTAAA
*
19240145 AACCCTAACTTAAATTAATTAAA
1 AACCCTAACCTAAATTAATTAAA
* *
19240168 AACCCTAAACTAAGTTAA
1 AACCCTAACCTAAATTAA
19240186 CAATGTTACA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.50, C:0.20, G:0.02, T:0.28
Consensus pattern (23 bp):
AACCCTAACCTAAATTAATTAAA
Found at i:19240163 original size:58 final size:52
Alignment explanation
Indices: 19240029--19240171 Score: 153
Period size: 64 Copynumber: 2.5 Consensus size: 52
19240019 TAAAAACCTT
*
19240029 AACCCTAACTTAATTTAATTAAAGAACCTAATCCTAACCTAATTTAATTAAA
1 AACCCTAACTTAATTTAATTAAAGAACCTAACCCTAACCTAATTTAATTAAA
19240081 AACCCTAACCCTAATCTAATTTAATTAAAGTCCTTAACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAA--C---T-TAATTTAATTAAAG-----AA-CCTAACCCTAACCTAATTTAATTAAA
*
19240145 AACCCTAACTTAAATTAATTAAA-AACC
1 AACCCTAACTTAATTTAATTAAAGAACC
19240172 CTAAACTAAG
Statistics
Matches: 77, Mismatches: 2, Indels: 25
0.74 0.02 0.24
Matches are distributed among these distances:
51 2 0.03
52 10 0.13
54 1 0.01
57 1 0.01
58 26 0.34
59 1 0.01
62 1 0.01
63 2 0.03
64 33 0.43
ACGTcount: A:0.45, C:0.23, G:0.01, T:0.31
Consensus pattern (52 bp):
AACCCTAACTTAATTTAATTAAAGAACCTAACCCTAACCTAATTTAATTAAA
Found at i:19240334 original size:116 final size:116
Alignment explanation
Indices: 19240182--19240535 Score: 609
Period size: 116 Copynumber: 3.1 Consensus size: 116
19240172 CTAAACTAAG
* * * * *
19240182 TTAACAATGTTACATTGACGTAATGTTAGATTTGGAAAAATGTTTTGACTAGTACTAACAATTAA
1 TTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
19240247 TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
66 TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
* *
19240298 TTAATAATTTTACATTCACATAATGTTAGATCTGGAAAAATGTTTTGATTGGTACTAACAATTAA
1 TTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
19240363 TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
66 TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
* **
19240414 TTAATAATTTTACATTCACATAATGCTAGATTTGGAAAAATGTTTCAACTGGTACTAACAATTAA
1 TTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
*
19240479 TAATTTTATATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
66 TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
19240530 TTAATA
1 TTAATA
19240536 CAATTTATCA
Statistics
Matches: 225, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
116 225 1.00
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.42
Consensus pattern (116 bp):
TTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
Found at i:19240552 original size:17 final size:18
Alignment explanation
Indices: 19240511--19240552 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
19240501 TTTACTAACC
* *
19240511 ATTAATACAATTTTTTGA
1 ATTAATACAATTTTATCA
*
19240529 CTTAATACAA-TTTATCA
1 ATTAATACAATTTTATCA
19240546 ATTAATA
1 ATTAATA
19240553 ATTTCACAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTAATACAATTTTATCA
Found at i:19253689 original size:43 final size:41
Alignment explanation
Indices: 19253614--19253741 Score: 141
Period size: 41 Copynumber: 3.1 Consensus size: 41
19253604 AAACACATAT
* * * *
19253614 ATCACATACAATGCC-ATATCCCAGATATGGTCTTACATGTT
1 ATCACATACGATGCCAATGTCCCAGACATGGTCTTACATG-A
* ** * *
19253655 ATCACATATCGATGTCTCTGTCCCAGACAGGGTCTTACACGA
1 ATCACATA-CGATGCCAATGTCCCAGACATGGTCTTACATGA
*
19253697 ATCATATACGATGCCAATGTCCCAGACATGGTCTTACATGA
1 ATCACATACGATGCCAATGTCCCAGACATGGTCTTACATGA
19253738 ATCA
1 ATCA
19253742 TACCTTGAAA
Statistics
Matches: 71, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
41 40 0.56
42 12 0.17
43 19 0.27
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (41 bp):
ATCACATACGATGCCAATGTCCCAGACATGGTCTTACATGA
Found at i:19264960 original size:5 final size:5
Alignment explanation
Indices: 19264950--19264990 Score: 82
Period size: 5 Copynumber: 8.2 Consensus size: 5
19264940 TGAGCATTCG
19264950 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA A
19264991 AATTTTCGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.20
Consensus pattern (5 bp):
ATCGA
Found at i:19265063 original size:5 final size:5
Alignment explanation
Indices: 19265053--19265100 Score: 53
Period size: 5 Copynumber: 9.4 Consensus size: 5
19265043 TTGAAGTTTT
* *
19265053 ATCGA ATCGA ATCGA GT-GA GATAGA ATTCGA ATCGA ATCGA ATCGA AT
1 ATCGA ATCGA ATCGA ATCGA -ATCGA A-TCGA ATCGA ATCGA ATCGA AT
19265101 ATATTTGTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
4 2 0.05
5 29 0.78
6 6 0.16
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.23
Consensus pattern (5 bp):
ATCGA
Found at i:19268886 original size:9 final size:9
Alignment explanation
Indices: 19268872--19268904 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
19268862 TTGAATTGAT
19268872 TCGATTAAC
1 TCGATTAAC
*
19268881 TCGATTAAT
1 TCGATTAAC
19268890 TCGATTAAC
1 TCGATTAAC
19268899 TCGATT
1 TCGATT
19268905 CGAATAATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (9 bp):
TCGATTAAC
Found at i:19268893 original size:18 final size:18
Alignment explanation
Indices: 19268870--19268904 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
19268860 AATTGAATTG
19268870 ATTCGATTAACTCGATTA
1 ATTCGATTAACTCGATTA
19268888 ATTCGATTAACTCGATT
1 ATTCGATTAACTCGATT
19268905 CGAATAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.40
Consensus pattern (18 bp):
ATTCGATTAACTCGATTA
Found at i:19269106 original size:22 final size:20
Alignment explanation
Indices: 19269078--19269119 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
19269068 AATTTTTTCG
*
19269078 TTATTATTGTTATTGTATTATA
1 TTATTATT-TT-TAGTATTATA
19269100 TTATTATTTTTAGTATTATA
1 TTATTATTTTTAGTATTATA
19269120 GATTGCTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 2 0.11
22 8 0.42
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (20 bp):
TTATTATTTTTAGTATTATA
Found at i:19270959 original size:25 final size:23
Alignment explanation
Indices: 19270931--19270986 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
19270921 ATTTTTTTAT
19270931 TTTTTATAATTCACATACATATATA
1 TTTTTATAA-T-ACATACATATATA
* * **
19270956 TTTTTCTTATATGTACATATATA
1 TTTTTATAATACATACATATATA
19270979 TTTTTATA
1 TTTTTATA
19270987 TTTTATAATT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
23 17 0.68
24 1 0.04
25 7 0.28
ACGTcount: A:0.34, C:0.09, G:0.02, T:0.55
Consensus pattern (23 bp):
TTTTTATAATACATACATATATA
Found at i:19272500 original size:17 final size:19
Alignment explanation
Indices: 19272478--19272514 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
19272468 AAGAAAAATA
19272478 ATTTT-ATATTA-TGAGAT
1 ATTTTAATATTAGTGAGAT
*
19272495 ATTTTAATTTTAGTGAGAT
1 ATTTTAATATTAGTGAGAT
19272514 A
1 A
19272515 GGGCCAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 5 0.29
18 5 0.29
19 7 0.41
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (19 bp):
ATTTTAATATTAGTGAGAT
Found at i:19272966 original size:15 final size:15
Alignment explanation
Indices: 19272946--19272977 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
19272936 TAACTAGCAC
19272946 GGGTTACATTAAAAT
1 GGGTTACATTAAAAT
19272961 GGGTTACATTAAAAT
1 GGGTTACATTAAAAT
19272976 GG
1 GG
19272978 ATCACGAGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.31
Consensus pattern (15 bp):
GGGTTACATTAAAAT
Found at i:19275876 original size:30 final size:28
Alignment explanation
Indices: 19275840--19275901 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
19275830 AAAAAAGCCC
19275840 TTTTTTTCAAAATTTACCGAAATGGGCCAA
1 TTTTTTT-AAAATTTACCGAAATGGGCC-A
** * *
19275870 TTTTTTTATTATTTACCGGAATGGTCCA
1 TTTTTTTAAAATTTACCGAAATGGGCCA
19275898 TTTT
1 TTTT
19275902 CTGGGAAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 5 0.18
29 16 0.57
30 7 0.25
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.47
Consensus pattern (28 bp):
TTTTTTTAAAATTTACCGAAATGGGCCA
Found at i:19276142 original size:22 final size:22
Alignment explanation
Indices: 19276114--19276163 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
19276104 ACAAATCCTA
19276114 TCTCAATTTCCTTCCAAAATCC
1 TCTCAATTTCCTTCCAAAATCC
*
19276136 TCTCAATTTCCTTCCAAAATTC
1 TCTCAATTTCCTTCCAAAATCC
19276158 TCTCAA
1 TCTCAA
19276164 AATCACAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.28, C:0.34, G:0.00, T:0.38
Consensus pattern (22 bp):
TCTCAATTTCCTTCCAAAATCC
Found at i:19276189 original size:52 final size:52
Alignment explanation
Indices: 19276117--19276216 Score: 191
Period size: 52 Copynumber: 1.9 Consensus size: 52
19276107 AATCCTATCT
*
19276117 CAATTTCCTTCCAAAATCCTCTCAATTTCCTTCCAAAATTCTCTCAAAATCA
1 CAATTTCCTTCCAAAATCCTCTCAATTTCCTTCCAAAAATCTCTCAAAATCA
19276169 CAATTTCCTTCCAAAATCCTCTCAATTTCCTTCCAAAAATCTCTCAAA
1 CAATTTCCTTCCAAAATCCTCTCAATTTCCTTCCAAAAATCTCTCAAA
19276217 TCCATATTAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.34
Consensus pattern (52 bp):
CAATTTCCTTCCAAAATCCTCTCAATTTCCTTCCAAAAATCTCTCAAAATCA
Found at i:19276197 original size:22 final size:22
Alignment explanation
Indices: 19276169--19276215 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 22
19276159 CTCAAAATCA
19276169 CAATTTCCTTCC-AAAATCCTCT
1 CAATTTCCTTCCAAAAAT-CTCT
19276191 CAATTTCCTTCCAAAAATCTCT
1 CAATTTCCTTCCAAAAATCTCT
19276213 CAA
1 CAA
19276216 ATCCATATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.32, C:0.34, G:0.00, T:0.34
Consensus pattern (22 bp):
CAATTTCCTTCCAAAAATCTCT
Found at i:19276287 original size:31 final size:31
Alignment explanation
Indices: 19276249--19276315 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
19276239 CCTCAATTTC
*
19276249 ATTTTTTTTAAATAATTTTAAATTTTTTTAT
1 ATTTTTTTAAAATAATTTTAAATTTTTTTAT
19276280 ATTTTTTTAAAATAATTTTAAATTTTTTTAT
1 ATTTTTTTAAAATAATTTTAAATTTTTTTAT
19276311 ATTTT
1 ATTTT
19276316 CAACAATGGC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (31 bp):
ATTTTTTTAAAATAATTTTAAATTTTTTTAT
Found at i:19276308 original size:10 final size:10
Alignment explanation
Indices: 19276251--19276315 Score: 67
Period size: 10 Copynumber: 6.4 Consensus size: 10
19276241 TCAATTTCAT
19276251 TTTTTTTAAA
1 TTTTTTTAAA
**
19276261 TAATTTTAAA
1 TTTTTTTAAA
*
19276271 TTTTTTTATA
1 TTTTTTTAAA
19276281 TTTTTTTAAAA
1 TTTTTTT-AAA
**
19276292 TAATTTTAAA
1 TTTTTTTAAA
*
19276302 TTTTTTTATA
1 TTTTTTTAAA
19276312 TTTT
1 TTTT
19276316 CAACAATGGC
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
10 36 0.84
11 7 0.16
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTTTTAAA
Found at i:19277496 original size:14 final size:14
Alignment explanation
Indices: 19277479--19277510 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
19277469 TTGATATTTA
19277479 GTATTTAGTATTAT
1 GTATTTAGTATTAT
*
19277493 GTATTTTGTATTAT
1 GTATTTAGTATTAT
19277507 GTAT
1 GTAT
19277511 ATAACTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.16, T:0.59
Consensus pattern (14 bp):
GTATTTAGTATTAT
Found at i:19278806 original size:30 final size:30
Alignment explanation
Indices: 19278709--19279484 Score: 961
Period size: 30 Copynumber: 25.8 Consensus size: 30
19278699 TAATAAAAAT
19278709 CCTAATTTAATTAAAAACCCT-AACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAA
*
19278738 CCTAATTTATTTAAAAACCCTAAACTCTAACACTAA
1 CCTAATTTAATTAAAAACCCTAAA--C---C-CTAA
19278774 CCTAATTTAATTAAAAACCCTAAACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAA
19278804 CCTAA--TAA--AAAAACCCT-AACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAA
19278829 CCTAATTTAATTAAAAACCCTAAACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAA
*
19278859 CCTAATTTAATCAAAAACCCTAAACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAA
*
19278889 CTTAATTTAATTAAAAACCCT-AACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAA
*
19278918 CTTAA-TTAATTAAAAACCCTAAACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAA
19278947 CCTAATTTAATTAAAAACCCT-AACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAA
19278976 CCTAATTTAATT-AAAACCCTAAACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAA
* *
19279005 CTTAATTTAATTAAAAACCTTAAACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAA
*
19279035 CTTAATTTAATTAAAAACCCT-AA--CT--
1 CCTAATTTAATTAAAAACCCTAAACCCTAA
*
19279060 --TAATTTAATTAAAAACCCT-AATCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAA
19279087 CCTAATTTAATTAAAAACCTTAAACCTTAAACCCTAA
1 CCTAATTTAATTAAAAA-C-----CC-TAAACCCTAA
*
19279124 CCTAATTTAATTAAAAACCTTAAACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAA
19279154 CCTAATTTAATTAAAAACCCT-AACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAA
*
19279183 CTTAATTTAATTAAAAACCCTAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCT--A----AACCCTAA
19279219 CCTAATTTAATTAAAAACCCTAAACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAA
19279249 CCTAATTTAATTAAAAACCCT-AACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAA
*
19279278 CTTAATTTAATTAAACAAACCCTAAACCCTAA
1 CCTAATTTAATT-AA-AAACCCTAAACCCTAA
* *
19279310 TCTAATTTATTTAAAAACCCTAAACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAA
* *
19279340 TCTAATTTATTTAAAAACCCTAAACCCTAGCCCTAA
1 CCTAATTTAATTAAAAACCCT-AA----A-CCCTAA
**
19279376 CCTAATTTAATTAAAAACTGTAAACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAA
*
19279406 CTTAATTTAATTAAAAACCCT-AA--C-AA
1 CCTAATTTAATTAAAAACCCTAAACCCTAA
*
19279432 CCTAATTTAATTGAAAACCCTAAACCCTAA
1 CCTAATTTAATTAAAAACCCTAAACCCTAA
*
19279462 CTTAATTTAATTAAAAACCCTAA
1 CCTAATTTAATTAAAAACCCTAA
19279485 CCATTAACAA
Statistics
Matches: 668, Mismatches: 29, Indels: 99
0.84 0.04 0.12
Matches are distributed among these distances:
23 21 0.03
25 15 0.02
26 30 0.04
27 8 0.01
28 26 0.04
29 160 0.24
30 264 0.40
31 14 0.02
32 18 0.03
34 2 0.00
35 6 0.01
36 80 0.12
37 24 0.04
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.29
Consensus pattern (30 bp):
CCTAATTTAATTAAAAACCCTAAACCCTAA
Found at i:19279282 original size:24 final size:23
Alignment explanation
Indices: 19279240--19279284 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
19279230 TAAAAACCCT
*
19279240 AAACCCTAACCTAATTTAATTAA
1 AAACCCTAACCTAACTTAATTAA
19279263 AAACCCTAACCCTAACTTAATT
1 AAACCCTAA-CCTAACTTAATT
19279285 TAATTAAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (23 bp):
AAACCCTAACCTAACTTAATTAA
Found at i:19279456 original size:56 final size:56
Alignment explanation
Indices: 19279374--19279485 Score: 197
Period size: 56 Copynumber: 2.0 Consensus size: 56
19279364 CCCTAGCCCT
**
19279374 AACCTAATTTAATTAAAAACTGTAAACCCTAACTTAATTTAATTAAAAACCCTAAC
1 AACCTAATTTAATTAAAAACCCTAAACCCTAACTTAATTTAATTAAAAACCCTAAC
*
19279430 AACCTAATTTAATTGAAAACCCTAAACCCTAACTTAATTTAATTAAAAACCCTAAC
1 AACCTAATTTAATTAAAAACCCTAAACCCTAACTTAATTTAATTAAAAACCCTAAC
19279486 CATTAACAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.47, C:0.21, G:0.02, T:0.29
Consensus pattern (56 bp):
AACCTAATTTAATTAAAAACCCTAAACCCTAACTTAATTTAATTAAAAACCCTAAC
Found at i:19282902 original size:123 final size:124
Alignment explanation
Indices: 19282682--19282957 Score: 493
Period size: 123 Copynumber: 2.2 Consensus size: 124
19282672 CGAGGGCGCG
*
19282682 ATTTTATACTATTTGCTCAGAAATGTCAAAAAAAATTATTTCTTACATGACCAACTGTAGCGAAA
1 ATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACCAACTGTAGCGAAA
* *
19282747 TCGCTTCCACGAGGGCATGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAAGCA
66 TCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAAGCA
19282806 ATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATT-TTTCTTACATGACCAACTGTAGCGAAA
1 ATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACCAACTGTAGCGAAA
*
19282870 TCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAAGCG
66 TCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAAGCA
19282929 ATTTTATACTATTTGAC-CAGAAACGTCAA
1 ATTTTATACTATTTG-CTCAGAAACGTCAA
19282958 CTCGAAATAA
Statistics
Matches: 147, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
123 110 0.75
124 37 0.25
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.31
Consensus pattern (124 bp):
ATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACCAACTGTAGCGAAA
TCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAAGCA
Found at i:19285330 original size:30 final size:30
Alignment explanation
Indices: 19285296--19285354 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
19285286 TTATTTTATT
*
19285296 GTTAATTTTGTTATTATTTTAAAGACATTG
1 GTTAATTTTGTTACTATTTTAAAGACATTG
*
19285326 GTTAATTTTGTTACTATTTTAGAGACATT
1 GTTAATTTTGTTACTATTTTAAAGACATT
19285355 TGCTTGTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.53
Consensus pattern (30 bp):
GTTAATTTTGTTACTATTTTAAAGACATTG
Found at i:19288467 original size:207 final size:204
Alignment explanation
Indices: 19288062--19288480 Score: 730
Period size: 207 Copynumber: 2.0 Consensus size: 204
19288052 GAGGATTGGT
* *
19288062 GGATGAGCTGTGTAAAGGCATAAGAAAGATAAGCATGACAGAGATGTCCACGGGAAAGCAGACGA
1 GGATGAGCTGTGTAAAGGCAAAAGAAAGATAAGCATGACAGAGATGTCCACGGGAAAGCACACGA
19288127 GATTTGTTGACAACAGCGATGATGAGATTGAAGAAGAAGAAGAATGGGGAGAGAATGGGGAGTAT
66 GATTTGTTGACAACAGCGATGATGAGATTGAAGAAGAAGAAGAATGGGGAGAGAATGGGGAGTAT
*
19288192 TCAAGTGATATAATGAGGTTGAAGGGGTTGCCAACACCCAAAGGAAAGCACCTGCGCTTTCCTCT
131 TCAAGTGATATAATGAGGTTGAAGGGGTTGCCAACACCCAAAAGAAAGCACCTGCGCTTTCCTCT
19288257 GGAGGAGGA
196 GGAGGAGGA
* * *
19288266 GGCTGAGCTGTGTAAAGGCAAAAGAAAGATAAGCATGACAGAGATGTTCATGGGAAAGCACACGA
1 GGATGAGCTGTGTAAAGGCAAAAGAAAGATAAGCATGACAGAGATGTCCACGGGAAAGCACACGA
* * *
19288331 GATTTGTTTACAACAGCGATGATGAGATTGAAGAAGAAGAAGAAGAATGGGGGGAGCATGGGGAG
66 GATTTGTTGACAACAGCGATGATGAGATT---GAAGAAGAAGAAGAATGGGGAGAGAATGGGGAG
19288396 TATTCAAGTGATATAATGAGGTTGAAGGGGTTGCCAACACCCAAAAGAAAGCACCTGCGCTTTCC
128 TATTCAAGTGATATAATGAGGTTGAAGGGGTTGCCAACACCCAAAAGAAAGCACCTGCGCTTTCC
19288461 TCTGGAGGAGGA
193 TCTGGAGGAGGA
19288473 GGATGAGC
1 GGATGAGC
19288481 AAGATTAAGT
Statistics
Matches: 202, Mismatches: 10, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
204 88 0.44
207 114 0.56
ACGTcount: A:0.36, C:0.13, G:0.33, T:0.18
Consensus pattern (204 bp):
GGATGAGCTGTGTAAAGGCAAAAGAAAGATAAGCATGACAGAGATGTCCACGGGAAAGCACACGA
GATTTGTTGACAACAGCGATGATGAGATTGAAGAAGAAGAAGAATGGGGAGAGAATGGGGAGTAT
TCAAGTGATATAATGAGGTTGAAGGGGTTGCCAACACCCAAAAGAAAGCACCTGCGCTTTCCTCT
GGAGGAGGA
Found at i:19299735 original size:42 final size:42
Alignment explanation
Indices: 19299676--19299790 Score: 151
Period size: 42 Copynumber: 2.7 Consensus size: 42
19299666 ATTTAACTCA
* *
19299676 TATGAGTTTCATTTTAACCC-TATTGGGTTTCCGTTCAGCTCT
1 TATGAGCTTCAGTTTAACCCTTA-TGGGTTTCCGTTCAGCTCT
* * *
19299718 TTTGAGCTTTAGTTTAACCCTTATAGGTTTCCGTTCAGCTCT
1 TATGAGCTTCAGTTTAACCCTTATGGGTTTCCGTTCAGCTCT
* *
19299760 TATGAGCTTCCGTTCAACCCTTATGGGTTTC
1 TATGAGCTTCAGTTTAACCCTTATGGGTTTC
19299791 TTTTTAGCAC
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
42 60 0.97
43 2 0.03
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.43
Consensus pattern (42 bp):
TATGAGCTTCAGTTTAACCCTTATGGGTTTCCGTTCAGCTCT
Found at i:19299770 original size:21 final size:21
Alignment explanation
Indices: 19299704--19299784 Score: 65
Period size: 21 Copynumber: 3.9 Consensus size: 21
19299694 CCTATTGGGT
* * *
19299704 TTCCGTTCAGCTCTTTTGAGC
1 TTCCGTTCAACCCTTATGAGC
** * *
19299725 TTTAGTTTAACCCTTAT-AGGT
1 TTCCGTTCAACCCTTATGA-GC
* *
19299746 TTCCGTTCAGCTCTTATGAGC
1 TTCCGTTCAACCCTTATGAGC
19299767 TTCCGTTCAACCCTTATG
1 TTCCGTTCAACCCTTATG
19299785 GGTTTCTTTT
Statistics
Matches: 43, Mismatches: 15, Indels: 4
0.69 0.24 0.06
Matches are distributed among these distances:
20 1 0.02
21 41 0.95
22 1 0.02
ACGTcount: A:0.16, C:0.26, G:0.16, T:0.42
Consensus pattern (21 bp):
TTCCGTTCAACCCTTATGAGC
Found at i:19302018 original size:16 final size:17
Alignment explanation
Indices: 19301981--19302022 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
19301971 CTTATATCAA
*
19301981 TAAAA-TAAAATAATTT
1 TAAAATTAAAATAACTT
19301997 TAAAAATTAAAAT-ACTT
1 T-AAAATTAAAATAACTT
19302014 TAAAATTAA
1 TAAAATTAA
19302023 CTTAATTGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 9 0.39
17 8 0.35
18 6 0.26
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAAATTAAAATAACTT
Found at i:19330159 original size:20 final size:20
Alignment explanation
Indices: 19330119--19330159 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
19330109 TTCTTTATAT
**
19330119 TTTTTAGAATTTTTTTGAAA
1 TTTTTAGAATTTTTTAAAAA
*
19330139 TTTTTATAATTTTTTAAAAA
1 TTTTTAGAATTTTTTAAAAA
19330159 T
1 T
19330160 ATAAATTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (20 bp):
TTTTTAGAATTTTTTAAAAA
Found at i:19330193 original size:19 final size:20
Alignment explanation
Indices: 19330112--19330235 Score: 70
Period size: 19 Copynumber: 6.5 Consensus size: 20
19330102 TTTAACTTTC
* *
19330112 TTTATATTTTT-TAGAATTTT
1 TTTAAATTTTTATA-AATTAT
19330132 TTTGAAATTTTTAT-AATT-T
1 TTT-AAATTTTTATAAATTAT
**
19330151 TTTAAA--AATATAAA-T-T
1 TTTAAATTTTTATAAATTAT
*
19330167 TTTGAATTTTTATAAA-TAT
1 TTTAAATTTTTATAAATTAT
*
19330186 TTTAAA-TTTTAAAAATTAT
1 TTTAAATTTTTATAAATTAT
* *
19330205 TTTGAACTTTTGA-AAATTAT
1 TTT-AAATTTTTATAAATTAT
*
19330225 TTTGAATTTTT
1 TTTAAATTTTT
19330236 TTTGTATTTT
Statistics
Matches: 82, Mismatches: 13, Indels: 19
0.72 0.11 0.17
Matches are distributed among these distances:
16 10 0.12
17 2 0.02
18 18 0.22
19 21 0.26
20 19 0.23
21 11 0.13
22 1 0.01
ACGTcount: A:0.36, C:0.01, G:0.05, T:0.58
Consensus pattern (20 bp):
TTTAAATTTTTATAAATTAT
Found at i:19330235 original size:20 final size:19
Alignment explanation
Indices: 19330166--19330235 Score: 88
Period size: 19 Copynumber: 3.6 Consensus size: 19
19330156 AAATATAAAT
19330166 TTTTGAATTTTTATAAA-TA
1 TTTTGAATTTTTA-AAATTA
* *
19330185 TTTTAAATTTTAAAAATTA
1 TTTTGAATTTTTAAAATTA
*
19330204 TTTTGAACTTTTGAAAATTA
1 TTTTGAA-TTTTTAAAATTA
19330224 TTTTGAATTTTT
1 TTTTGAATTTTT
19330236 TTTGTATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
18 3 0.07
19 23 0.52
20 18 0.41
ACGTcount: A:0.36, C:0.01, G:0.06, T:0.57
Consensus pattern (19 bp):
TTTTGAATTTTTAAAATTA
Found at i:19335697 original size:3 final size:3
Alignment explanation
Indices: 19335689--19335714 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
19335679 CAAGGCCTCA
19335689 CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CA
19335715 AAGTAGCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:19341971 original size:15 final size:15
Alignment explanation
Indices: 19341951--19341980 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
19341941 GGTATATTAT
19341951 AATATTAAAAAAATA
1 AATATTAAAAAAATA
19341966 AATATTAAAAAAATA
1 AATATTAAAAAAATA
19341981 CATGACAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AATATTAAAAAAATA
Found at i:19342903 original size:23 final size:23
Alignment explanation
Indices: 19342859--19342906 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
19342849 TTATCCCATT
** *
19342859 ATTGAAATTCTATTTTTTAAAAC
1 ATTGAAATTCTAAATTTCAAAAC
*
19342882 ATTGAAATTTTAAATTTCAAAAC
1 ATTGAAATTCTAAATTTCAAAAC
19342905 AT
1 AT
19342907 AAAAAAAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (23 bp):
ATTGAAATTCTAAATTTCAAAAC
Found at i:19343308 original size:26 final size:26
Alignment explanation
Indices: 19343271--19343327 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
19343261 AAAACCCTAA
19343271 AGTCTGTCGCTTGGCACGGTGTTCTT
1 AGTCTGTCGCTTGGCACGGTGTTCTT
19343297 AGTCTG-CTGCTTGGCACGGTGTTCTT
1 AGTCTGTC-GCTTGGCACGGTGTTCTT
19343323 AGTCT
1 AGTCT
19343328 ACCGCCTGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 1 0.03
26 29 0.97
ACGTcount: A:0.09, C:0.23, G:0.30, T:0.39
Consensus pattern (26 bp):
AGTCTGTCGCTTGGCACGGTGTTCTT
Found at i:19343337 original size:26 final size:26
Alignment explanation
Indices: 19343282--19343340 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
19343272 GTCTGTCGCT
* * *
19343282 TGGCACGGTGTTCTTAGTCTGCTGCT
1 TGGCACGGTGTTCTTAGTCTACCGCC
19343308 TGGCACGGTGTTCTTAGTCTACCGCC
1 TGGCACGGTGTTCTTAGTCTACCGCC
19343334 TGGCACG
1 TGGCACG
19343341 TTTTTTCTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.10, C:0.27, G:0.31, T:0.32
Consensus pattern (26 bp):
TGGCACGGTGTTCTTAGTCTACCGCC
Found at i:19352435 original size:182 final size:182
Alignment explanation
Indices: 19352128--19352491 Score: 728
Period size: 182 Copynumber: 2.0 Consensus size: 182
19352118 AGAACTATAA
19352128 CCAATGAGCTTGTTGCTTTAGAAGCTGAACAAAAGGAGGGGGTCTTCTACTCGGTAAAAGAATGA
1 CCAATGAGCTTGTTGCTTTAGAAGCTGAACAAAAGGAGGGGGTCTTCTACTCGGTAAAAGAATGA
19352193 AAAACTCGCTGCAAATTATATGGAAGTCTTGGGAATGAAATCGAGCATTTCAGTAAATTATTTCT
66 AAAACTCGCTGCAAATTATATGGAAGTCTTGGGAATGAAATCGAGCATTTCAGTAAATTATTTCT
19352258 CAGACAGGGTCTAAAACCAGGACACAGGAAATCAGGGCCATGAGGCTAATGT
131 CAGACAGGGTCTAAAACCAGGACACAGGAAATCAGGGCCATGAGGCTAATGT
19352310 CCAATGAGCTTGTTGCTTTAGAAGCTGAACAAAAGGAGGGGGTCTTCTACTCGGTAAAAGAATGA
1 CCAATGAGCTTGTTGCTTTAGAAGCTGAACAAAAGGAGGGGGTCTTCTACTCGGTAAAAGAATGA
19352375 AAAACTCGCTGCAAATTATATGGAAGTCTTGGGAATGAAATCGAGCATTTCAGTAAATTATTTCT
66 AAAACTCGCTGCAAATTATATGGAAGTCTTGGGAATGAAATCGAGCATTTCAGTAAATTATTTCT
19352440 CAGACAGGGTCTAAAACCAGGACACAGGAAATCAGGGCCATGAGGCTAATGT
131 CAGACAGGGTCTAAAACCAGGACACAGGAAATCAGGGCCATGAGGCTAATGT
19352492 TTCTGTCTTT
Statistics
Matches: 182, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
182 182 1.00
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (182 bp):
CCAATGAGCTTGTTGCTTTAGAAGCTGAACAAAAGGAGGGGGTCTTCTACTCGGTAAAAGAATGA
AAAACTCGCTGCAAATTATATGGAAGTCTTGGGAATGAAATCGAGCATTTCAGTAAATTATTTCT
CAGACAGGGTCTAAAACCAGGACACAGGAAATCAGGGCCATGAGGCTAATGT
Found at i:19359930 original size:9 final size:9
Alignment explanation
Indices: 19359916--19359966 Score: 93
Period size: 9 Copynumber: 5.7 Consensus size: 9
19359906 GCTTGTTGTC
19359916 GAGAAATAA
1 GAGAAATAA
19359925 GAGAAATAA
1 GAGAAATAA
*
19359934 GAAAAATAA
1 GAGAAATAA
19359943 GAGAAATAA
1 GAGAAATAA
19359952 GAGAAATAA
1 GAGAAATAA
19359961 GAGAAA
1 GAGAAA
19359967 ATGATGTGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 40 1.00
ACGTcount: A:0.69, C:0.00, G:0.22, T:0.10
Consensus pattern (9 bp):
GAGAAATAA
Found at i:19364524 original size:17 final size:17
Alignment explanation
Indices: 19364502--19364534 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
19364492 ACATGTTTAT
19364502 TTATTAGAA-AATTTAAA
1 TTATTA-AATAATTTAAA
19364519 TTATTAAATAATTTAA
1 TTATTAAATAATTTAA
19364535 TTAAAGTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
TTATTAAATAATTTAAA
Found at i:19364690 original size:89 final size:89
Alignment explanation
Indices: 19364588--19364763 Score: 325
Period size: 89 Copynumber: 2.0 Consensus size: 89
19364578 ACCCATTTTA
*
19364588 AAAAAAAAATACGAAAATGGGTCGTTTTGTTCAAAAATTATTGAAAGGACCGATTTCCCTAAAAC
1 AAAAAAAAATACGAAAATGGGTCGTTTTGTTAAAAAATTATTGAAAGGACCGATTTCCCTAAAAC
19364653 ACACTGAGTTGGCATTGTTTTTCC
66 ACACTGAGTTGGCATTGTTTTTCC
* *
19364677 AAAAAAAATTACGAAAATGGGTCGTTTTGTTAAAAAATTATTGAAAGGACCGATTTCCCTAAAAG
1 AAAAAAAAATACGAAAATGGGTCGTTTTGTTAAAAAATTATTGAAAGGACCGATTTCCCTAAAAC
19364742 ACACTGAGTTGGCATTGTTTTT
66 ACACTGAGTTGGCATTGTTTTT
19364764 AGGGGAAACG
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
89 84 1.00
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.31
Consensus pattern (89 bp):
AAAAAAAAATACGAAAATGGGTCGTTTTGTTAAAAAATTATTGAAAGGACCGATTTCCCTAAAAC
ACACTGAGTTGGCATTGTTTTTCC
Found at i:19374619 original size:23 final size:23
Alignment explanation
Indices: 19374585--19374635 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
19374575 GTGGAGATGG
*
19374585 TGTAATATCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
19374608 TGTAATACCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
*
19374631 AGTAA
1 TGTAA
19374636 GAAAGTAGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (23 bp):
TGTAATACCCCGAAAATTACTAC
Found at i:19377953 original size:13 final size:13
Alignment explanation
Indices: 19377935--19377963 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
19377925 GCCTGGCACA
19377935 TGGACGTGTGGCT
1 TGGACGTGTGGCT
19377948 TGGACGTGTGGCT
1 TGGACGTGTGGCT
19377961 TGG
1 TGG
19377964 CCATATGACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.14, G:0.48, T:0.31
Consensus pattern (13 bp):
TGGACGTGTGGCT
Found at i:19378722 original size:12 final size:12
Alignment explanation
Indices: 19378692--19378730 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
19378682 ACCTCCACCC
*
19378692 CCAATTGTACCA
1 CCAATTGTACCT
*
19378704 CCTATTGTACCT
1 CCAATTGTACCT
*
19378716 CCAATTGCACCT
1 CCAATTGTACCT
19378728 CCA
1 CCA
19378731 CCTTCTCATG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.26, C:0.38, G:0.08, T:0.28
Consensus pattern (12 bp):
CCAATTGTACCT
Found at i:19382252 original size:20 final size:21
Alignment explanation
Indices: 19382229--19382276 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 21
19382219 TTATTCCTTT
19382229 ATTTTCTTTTTCT-TCTTCCC
1 ATTTTCTTTTTCTCTCTTCCC
* *
19382249 A-TTTATTTTTCTCTCTTCTC
1 ATTTTCTTTTTCTCTCTTCCC
*
19382269 ATATTCTT
1 ATTTTCTT
19382277 CACTGCAGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
19 10 0.45
20 8 0.36
21 4 0.18
ACGTcount: A:0.10, C:0.25, G:0.00, T:0.65
Consensus pattern (21 bp):
ATTTTCTTTTTCTCTCTTCCC
Found at i:19383169 original size:16 final size:16
Alignment explanation
Indices: 19383150--19383183 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
19383140 GAGAATGGAA
19383150 AATAAAGAAAAAAAGT
1 AATAAAGAAAAAAAGT
19383166 AATAAAGAAAAAAAGT
1 AATAAAGAAAAAAAGT
19383182 AA
1 AA
19383184 AAGAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (16 bp):
AATAAAGAAAAAAAGT
Found at i:19383172 original size:8 final size:8
Alignment explanation
Indices: 19383147--19383204 Score: 55
Period size: 8 Copynumber: 7.1 Consensus size: 8
19383137 GATGAGAATG
19383147 GAAAATAAA
1 GAAAA-AAA
19383156 GAAAAAAA
1 GAAAAAAA
* *
19383164 GTAATAAA
1 GAAAAAAA
19383172 GAAAAAAA
1 GAAAAAAA
*
19383180 GTAAAAGAA
1 G-AAAAAAA
*
19383189 -AATAAAA
1 GAAAAAAA
19383196 GAAAAAAA
1 GAAAAAAA
19383204 G
1 G
19383205 TAAATTGCTC
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
7 5 0.13
8 23 0.59
9 11 0.28
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.09
Consensus pattern (8 bp):
GAAAAAAA
Found at i:19384700 original size:19 final size:19
Alignment explanation
Indices: 19384676--19384718 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
19384666 CGTCACATAA
19384676 ATTTATTTCGTTGATCGAT
1 ATTTATTTCGTTGATCGAT
19384695 ATTTATTTCGTTGATCGAT
1 ATTTATTTCGTTGATCGAT
19384714 ATTTA
1 ATTTA
19384719 ACTGACGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.23, C:0.09, G:0.14, T:0.53
Consensus pattern (19 bp):
ATTTATTTCGTTGATCGAT
Found at i:19385473 original size:21 final size:21
Alignment explanation
Indices: 19385449--19385496 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
19385439 TTTCACATCA
*
19385449 ATTTAATATTAAAAAAATAAT
1 ATTTAATATCAAAAAAATAAT
** *
19385470 ATTTTCTATCAAAAGAATAAT
1 ATTTAATATCAAAAAAATAAT
19385491 ATTTAA
1 ATTTAA
19385497 ATATATATTC
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (21 bp):
ATTTAATATCAAAAAAATAAT
Found at i:19386641 original size:13 final size:13
Alignment explanation
Indices: 19386623--19386647 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19386613 TTAGAGGGGG
19386623 ATTAAATTAATTA
1 ATTAAATTAATTA
19386636 ATTAAATTAATT
1 ATTAAATTAATT
19386648 TTAATATTAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTAAATTAATTA
Found at i:19391461 original size:23 final size:23
Alignment explanation
Indices: 19391418--19391461 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
19391408 TAAGATAACT
* *
19391418 ATATAAAAATTTTCAATAATATA
1 ATATAAAAATTTTAAAAAATATA
*
19391441 ATATAAATATTTTAAAAAATA
1 ATATAAAAATTTTAAAAAATA
19391462 AAAAATAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
ATATAAAAATTTTAAAAAATATA
Found at i:19391469 original size:23 final size:23
Alignment explanation
Indices: 19391420--19391469 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
19391410 AGATAACTAT
* * * *
19391420 ATAAAAATTTTCAATAATATAAT
1 ATAAAAATTTTAAAAAATAAAAA
*
19391443 ATAAATATTTTAAAAAATAAAAA
1 ATAAAAATTTTAAAAAATAAAAA
19391466 ATAA
1 ATAA
19391470 TATGAGTGGG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (23 bp):
ATAAAAATTTTAAAAAATAAAAA
Found at i:19391968 original size:13 final size:12
Alignment explanation
Indices: 19391950--19392023 Score: 61
Period size: 12 Copynumber: 6.5 Consensus size: 12
19391940 AAAAAATAAT
19391950 TAATTATAAAAA
1 TAATTATAAAAA
19391962 GTAA-T-TAAAAA
1 -TAATTATAAAAA
*
19391973 TAATTAT-AATA
1 TAATTATAAAAA
19391984 TAA-TATAATAAA
1 TAATTATAA-AAA
19391996 TAATT-T-AAAA
1 TAATTATAAAAA
*
19392006 CAATTATAAAAA
1 TAATTATAAAAA
*
19392018 CAATTA
1 TAATTA
19392024 ACTAAAGTAT
Statistics
Matches: 51, Mismatches: 3, Indels: 15
0.74 0.04 0.22
Matches are distributed among these distances:
10 13 0.25
11 16 0.31
12 18 0.35
13 4 0.08
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (12 bp):
TAATTATAAAAA
Found at i:19391972 original size:11 final size:10
Alignment explanation
Indices: 19391956--19392016 Score: 50
Period size: 11 Copynumber: 5.6 Consensus size: 10
19391946 TAATTAATTA
19391956 TAAAAAGTAAT
1 TAAAAA-TAAT
19391967 TAAAAATAAT
1 TAAAAATAAT
*
19391977 TATAATATAAT
1 TA-AAAATAAT
19391988 ATAATAAATAAT
1 -TAA-AAATAAT
* *
19392000 TTAAAACAAT
1 TAAAAATAAT
19392010 TATAAAA
1 TA-AAAA
19392017 ACAATTAACT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
10 13 0.32
11 20 0.49
12 8 0.20
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (10 bp):
TAAAAATAAT
Found at i:19391976 original size:23 final size:24
Alignment explanation
Indices: 19391944--19392005 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 24
19391934 GATATAAAAA
*
19391944 AATAATTAATTATAAAAAGTAAT-T
1 AATAAATAATTATAAAAA-TAATAT
*
19391968 AA-AAATAATTAT-AATATAATAT
1 AATAAATAATTATAAAAATAATAT
19391990 AATAAATAATT-TAAAA
1 AATAAATAATTATAAAA
19392006 CAATTATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
21 4 0.12
22 7 0.22
23 19 0.59
24 2 0.06
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (24 bp):
AATAAATAATTATAAAAATAATAT
Found at i:19391991 original size:33 final size:33
Alignment explanation
Indices: 19391945--19392014 Score: 90
Period size: 33 Copynumber: 2.1 Consensus size: 33
19391935 ATATAAAAAA
*
19391945 ATAATTAATTATAA-AAAGTAATTAAAAATAATT
1 ATAATTAATTATAATAAA-TAATTAAAAACAATT
*
19391978 ATAATATAA-TATAATAAATAATTTAAAACAATT
1 ATAAT-TAATTATAATAAATAATTAAAAACAATT
19392011 ATAA
1 ATAA
19392015 AAACAATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 27 0.82
34 6 0.18
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (33 bp):
ATAATTAATTATAATAAATAATTAAAAACAATT
Found at i:19392013 original size:23 final size:22
Alignment explanation
Indices: 19391950--19392023 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 22
19391940 AAAAAATAAT
*
19391950 TAATTATAAAA-AGTAATTAAAAA
1 TAATTATAAAACAAT-A-TAAAAA
* *
19391973 TAATTATAATATAATATAATAAA
1 TAATTATAAAACAATATAA-AAA
19391996 TAATT-TAAAACAATTATAAAAA
1 TAATTATAAAACAA-TATAAAAA
*
19392018 CAATTA
1 TAATTA
19392024 ACTAAAGTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
22 16 0.38
23 24 0.57
24 2 0.05
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (22 bp):
TAATTATAAAACAATATAAAAA
Found at i:19393016 original size:20 final size:20
Alignment explanation
Indices: 19392993--19393030 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
19392983 TACACATTTC
19392993 ACAATTCATATCAAAATCTG
1 ACAATTCATATCAAAATCTG
* *
19393013 ACAATTGATATTAAAATC
1 ACAATTCATATCAAAATC
19393031 CCGTTATTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.32
Consensus pattern (20 bp):
ACAATTCATATCAAAATCTG
Found at i:19395497 original size:23 final size:24
Alignment explanation
Indices: 19395471--19395538 Score: 93
Period size: 23 Copynumber: 2.9 Consensus size: 24
19395461 TTCATTTAAC
19395471 TTAATCGAACATGTTCACGAACA-
1 TTAATCGAACATGTTCACGAACAT
* * *
19395494 TTAAACGAACATATTCATGAACAT
1 TTAATCGAACATGTTCACGAACAT
*
19395518 TTAATTGAACATGTTCACGAA
1 TTAATCGAACATGTTCACGAA
19395539 TAATGTTAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 20 0.54
24 17 0.46
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (24 bp):
TTAATCGAACATGTTCACGAACAT
Found at i:19395584 original size:4 final size:4
Alignment explanation
Indices: 19395577--19395601 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
19395567 CAAGCAATAA
19395577 ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC A
19395602 AACACATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:19395765 original size:12 final size:11
Alignment explanation
Indices: 19395736--19395780 Score: 54
Period size: 12 Copynumber: 3.9 Consensus size: 11
19395726 ATTATTAATA
19395736 AATAAACGAGT
1 AATAAACGAGT
*
19395747 CATAAACGAGCT
1 AATAAACGAG-T
*
19395759 AATAAACAAGT
1 AATAAACGAGT
19395770 CAATAAACGAG
1 -AATAAACGAG
19395781 CTTGTTTGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
11 10 0.36
12 18 0.64
ACGTcount: A:0.53, C:0.16, G:0.16, T:0.16
Consensus pattern (11 bp):
AATAAACGAGT
Found at i:19395770 original size:23 final size:24
Alignment explanation
Indices: 19395736--19395782 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
19395726 ATTATTAATA
*
19395736 AATAAACGAGTC-ATAAACGAGCT
1 AATAAACAAGTCAATAAACGAGCT
19395759 AATAAACAAGTCAATAAACGAGCT
1 AATAAACAAGTCAATAAACGAGCT
19395783 TGTTTGTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.51, C:0.17, G:0.15, T:0.17
Consensus pattern (24 bp):
AATAAACAAGTCAATAAACGAGCT
Found at i:19403435 original size:30 final size:30
Alignment explanation
Indices: 19403397--19403456 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
19403387 AAAAAGCAAA
19403397 CATT-TTTTTTT--TAATTTAGTCCTAACC
1 CATTGTTTTTTTGGTAATTTAGTCCTAACC
*
19403424 CATTGTTTTTTTGGTAATTTAGTCGTAACC
1 CATTGTTTTTTTGGTAATTTAGTCCTAACC
19403454 CAT
1 CAT
19403457 CATAAAAGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 4 0.14
28 7 0.24
30 18 0.62
ACGTcount: A:0.22, C:0.17, G:0.10, T:0.52
Consensus pattern (30 bp):
CATTGTTTTTTTGGTAATTTAGTCCTAACC
Found at i:19406703 original size:11 final size:11
Alignment explanation
Indices: 19406686--19406715 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
19406676 GGTGCAATTG
19406686 ATATTATTGCT
1 ATATTATTGCT
*
19406697 CTATTATTGCT
1 ATATTATTGCT
19406708 ATATTATT
1 ATATTATT
19406716 TAACAAAAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.27, C:0.10, G:0.07, T:0.57
Consensus pattern (11 bp):
ATATTATTGCT
Found at i:19411430 original size:3 final size:3
Alignment explanation
Indices: 19411422--19411476 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
19411412 CCACGAAACC
19411422 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
19411470 ATA ATA A
1 ATA ATA A
19411477 AACAAACTTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:19411875 original size:18 final size:18
Alignment explanation
Indices: 19411849--19411897 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
19411839 CTGCGAATTG
*
19411849 CGAGCTCACCAAGAA-CTA
1 CGAGCTCACCAA-AATATA
*
19411867 CGAGTTCACCAAAATATA
1 CGAGCTCACCAAAATATA
19411885 CGAGCTCACCAAA
1 CGAGCTCACCAAA
19411898 TGTGCGAGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 2 0.07
18 25 0.93
ACGTcount: A:0.41, C:0.31, G:0.14, T:0.14
Consensus pattern (18 bp):
CGAGCTCACCAAAATATA
Found at i:19411905 original size:17 final size:17
Alignment explanation
Indices: 19411847--19411931 Score: 73
Period size: 17 Copynumber: 4.9 Consensus size: 17
19411837 AACTGCGAAT
*
19411847 TGCGAGCTCACCAAGAAC
1 TGCGAGCTCACCAA-ATC
* * *
19411865 TACGAGTTCACCAAAATA
1 TGCGAGCTCACC-AAATC
* *
19411883 TACGAGCTCACCAAATG
1 TGCGAGCTCACCAAATC
*
19411900 TGCGAGCTCATCAACA-C
1 TGCGAGCTCACCAA-ATC
19411917 TGCGAGCTCACCAAA
1 TGCGAGCTCACCAAA
19411932 GCCTGAGAGC
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
16 1 0.02
17 29 0.53
18 23 0.42
19 2 0.04
ACGTcount: A:0.35, C:0.31, G:0.18, T:0.16
Consensus pattern (17 bp):
TGCGAGCTCACCAAATC
Found at i:19411983 original size:29 final size:30
Alignment explanation
Indices: 19411916--19411983 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
19411906 CTCATCAACA
* * *
19411916 CTGCGAGCTCACCAAAGCCTGAGAGCTCAT
1 CTGCGAGCTAACCAAAGCATGAGAGCTCAC
* *
19411946 TTGCAAGCTAACC-AAGCATGAGAGCTCAC
1 CTGCGAGCTAACCAAAGCATGAGAGCTCAC
19411975 CTGCGAGCT
1 CTGCGAGCT
19411984 CTTCACTTTG
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
29 21 0.68
30 10 0.32
ACGTcount: A:0.28, C:0.31, G:0.24, T:0.18
Consensus pattern (30 bp):
CTGCGAGCTAACCAAAGCATGAGAGCTCAC
Found at i:19414695 original size:25 final size:24
Alignment explanation
Indices: 19414612--19414746 Score: 118
Period size: 25 Copynumber: 5.6 Consensus size: 24
19414602 TTGATATGCA
* *
19414612 CTAATGAACAGAGAGCACTAAAGTG
1 CTAAT-AACAGAGAGCACCAACGTG
*
19414637 CT-AT-ACAGAGAGCA-CAGATGTG
1 CTAATAACAGAGAGCACCA-ACGTG
**
19414659 CT-A-AACAGAGAGCACTGACGTG
1 CTAATAACAGAGAGCACCAACGTG
19414681 CTAATAATCAGAGAGCACCAACGTG
1 CTAATAA-CAGAGAGCACCAACGTG
* * *
19414706 CTAGTAGCCAGAGAGCACCAATGTG
1 CTAATA-ACAGAGAGCACCAACGTG
19414731 CTAATAATCAGAGAGC
1 CTAATAA-CAGAGAGC
19414747 GCGCTAAAGT
Statistics
Matches: 90, Mismatches: 12, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
21 1 0.01
22 33 0.37
23 1 0.01
24 4 0.04
25 51 0.57
ACGTcount: A:0.39, C:0.21, G:0.24, T:0.16
Consensus pattern (24 bp):
CTAATAACAGAGAGCACCAACGTG
Found at i:19415830 original size:5 final size:5
Alignment explanation
Indices: 19415812--19415851 Score: 53
Period size: 5 Copynumber: 7.6 Consensus size: 5
19415802 TGTTTTATGT
*
19415812 ATATA ATAATA ATATA ATATT ATAATA ATATA ATATA ATA
1 ATATA AT-ATA ATATA ATATA AT-ATA ATATA ATATA ATA
19415852 ACTTACTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 22 0.71
6 9 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:19415836 original size:16 final size:16
Alignment explanation
Indices: 19415812--19415852 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
19415802 TGTTTTATGT
19415812 ATATAATAATAATATA
1 ATATAATAATAATATA
*
19415828 ATATTATAATAATATA
1 ATATAATAATAATATA
19415844 ATATAATAA
1 ATATAATAA
19415853 CTTACTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATATAATAATAATATA
Found at i:19415852 original size:8 final size:8
Alignment explanation
Indices: 19415817--19415846 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
19415807 TATGTATATA
19415817 ATAATAAT
1 ATAATAAT
*
19415825 ATAATATT
1 ATAATAAT
19415833 ATAATAAT
1 ATAATAAT
19415841 ATAATA
1 ATAATA
19415847 TAATAACTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
ATAATAAT
Found at i:19419850 original size:3 final size:3
Alignment explanation
Indices: 19419842--19419872 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
19419832 CTTGTTTTTC
*
19419842 CTT CTT CTT CTT TTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
19419873 ACTTGTTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
CTT
Found at i:19419860 original size:15 final size:16
Alignment explanation
Indices: 19419836--19419868 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
19419826 TTTTTACTTG
19419836 TTTTTCCTTCTTCTTC
1 TTTTTCCTTCTTCTTC
19419852 TTTTT-CTTCTTCTTC
1 TTTTTCCTTCTTCTTC
19419867 TT
1 TT
19419869 CTTCACTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTCCTTCTTCTTC
Found at i:19421217 original size:1 final size:1
Alignment explanation
Indices: 19421211--19421325 Score: 59
Period size: 1 Copynumber: 115.0 Consensus size: 1
19421201 TATTAACATT
* * * * * * * * * * *
19421211 AAAAAAATAGAAAAATAAAAATAAAAATAAAAATAAAAATAAAAATAAAAATAAAAATAAAAATA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * * *
19421276 AAAATAAAAATAAATAAAAATAAAAATAAAAATAAAAATAAAAATAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
19421326 TTGGGTTGCT
Statistics
Matches: 76, Mismatches: 38, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
1 76 1.00
ACGTcount: A:0.83, C:0.00, G:0.01, T:0.16
Consensus pattern (1 bp):
A
Found at i:19421230 original size:6 final size:6
Alignment explanation
Indices: 19421221--19421326 Score: 198
Period size: 6 Copynumber: 18.0 Consensus size: 6
19421211 AAAAAAATAG
19421221 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
19421269 AAAAAT AAAAAT AAAAAT --AAAT AAAAAT AAAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
19421315 AAAAAT AAAAAT
1 AAAAAT AAAAAT
19421327 TGGGTTGCTT
Statistics
Matches: 98, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.04
6 94 0.96
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:19430196 original size:25 final size:26
Alignment explanation
Indices: 19430158--19430220 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
19430148 ATTGCTCGTG
19430158 TGAGCTT-CTCGTTAGTCAGCTCACA
1 TGAGCTTCCTCGTTAGTCAGCTCACA
* * *
19430183 TGAGCTTCCT-GTTATTCATCTCAGA
1 TGAGCTTCCTCGTTAGTCAGCTCACA
*
19430208 GGAGCTTCC-CGTT
1 TGAGCTTCCTCGTT
19430221 TACAGCTCGT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 30 0.94
26 2 0.06
ACGTcount: A:0.17, C:0.27, G:0.21, T:0.35
Consensus pattern (26 bp):
TGAGCTTCCTCGTTAGTCAGCTCACA
Found at i:19442409 original size:18 final size:18
Alignment explanation
Indices: 19442383--19442425 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
19442373 GACTGAGAAA
* *
19442383 AGGAAACATATAAGGGTT
1 AGGATACATATAAGGGCT
19442401 AGGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
19442419 AGGATAC
1 AGGATAC
19442426 GCACCTGGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.42, C:0.09, G:0.28, T:0.21
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:19444490 original size:30 final size:30
Alignment explanation
Indices: 19444448--19444535 Score: 106
Period size: 30 Copynumber: 2.9 Consensus size: 30
19444438 AAAATCAGTC
* *
19444448 TGGGCC-TGAGCCCTATACAGTAGCAGTGTG
1 TGGGCCAT-AGCCCAATACAGTAACAGTGTG
* * *
19444478 TGTGCCATAGCCCAATATAGTAACAGAGTG
1 TGGGCCATAGCCCAATACAGTAACAGTGTG
*
19444508 TGGGCCTTAGCCCAATACAGTAACAGTG
1 TGGGCCATAGCCCAATACAGTAACAGTG
19444536 CAAATACAGT
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
30 47 0.98
31 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (30 bp):
TGGGCCATAGCCCAATACAGTAACAGTGTG
Found at i:19444704 original size:26 final size:26
Alignment explanation
Indices: 19444647--19444743 Score: 86
Period size: 26 Copynumber: 3.7 Consensus size: 26
19444637 ATATCGCAAC
* * ** *
19444647 AAAGTTGCCAGTAATAGTAACGTAGT
1 AAAGCTGCCAGTAACAGTAACACAAT
*
19444673 AAAGCTGCCAGTAACAGTAATACAAT
1 AAAGCTGCCAGTAACAGTAACACAAT
* * * * *
19444699 AGAGCTGTCAGTATCAGTAACGCAGT
1 AAAGCTGCCAGTAACAGTAACACAAT
*
19444725 AAAGCTTCCAGTAACAGTA
1 AAAGCTGCCAGTAACAGTA
19444744 TTTGTGGCAA
Statistics
Matches: 55, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.23
Consensus pattern (26 bp):
AAAGCTGCCAGTAACAGTAACACAAT
Found at i:19444982 original size:27 final size:27
Alignment explanation
Indices: 19444936--19445079 Score: 141
Period size: 27 Copynumber: 5.3 Consensus size: 27
19444926 AGGTATAACG
* *
19444936 GTCATTTTACCCTA-TAAGGGTATTTCG
1 GTCATTTTA-CCTATTGAGGGTATTTCA
*
19444963 GTAATTTTACCTATTGAGGGTATTTCA
1 GTCATTTTACCTATTGAGGGTATTTCA
* * * *
19444990 GTTATTTTACCCATCGAGGATATTTCA
1 GTCATTTTACCTATTGAGGGTATTTCA
* * *
19445017 ATCATTTTACCCATCGAGGGTATTTC-
1 GTCATTTTACCTATTGAGGGTATTTCA
*
19445043 GATCATTTTACCCT-TTAAGGGTATTTCA
1 G-TCATTTTA-CCTATTGAGGGTATTTCA
19445071 GTCATTTTA
1 GTCATTTTA
19445080 GAGGCCTACT
Statistics
Matches: 99, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
26 4 0.04
27 92 0.93
28 3 0.03
ACGTcount: A:0.24, C:0.17, G:0.16, T:0.42
Consensus pattern (27 bp):
GTCATTTTACCTATTGAGGGTATTTCA
Found at i:19444985 original size:54 final size:54
Alignment explanation
Indices: 19444934--19445079 Score: 177
Period size: 54 Copynumber: 2.7 Consensus size: 54
19444924 AGAGGTATAA
* * * *
19444934 CGGTCATTTTACCCTATAAGGGTATTTCGGTAATTTTACCTATTGAGGGTATTT
1 CGGTCATTTTACCCTATAAGGGTATTTCAGTCATTTTACCCATCGAGGGTATTT
* * * * *
19444988 CAGTTATTTTACCC-ATCGAGGATATTTCAATCATTTTACCCATCGAGGGTATTT
1 CGGTCATTTTACCCTAT-AAGGGTATTTCAGTCATTTTACCCATCGAGGGTATTT
* *
19445042 CGATCATTTTACCCTTTAAGGGTATTTCAGTCATTTTA
1 CGGTCATTTTACCCTATAAGGGTATTTCAGTCATTTTA
19445080 GAGGCCTACT
Statistics
Matches: 74, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
53 2 0.03
54 71 0.96
55 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (54 bp):
CGGTCATTTTACCCTATAAGGGTATTTCAGTCATTTTACCCATCGAGGGTATTT
Found at i:19446805 original size:22 final size:22
Alignment explanation
Indices: 19446780--19446849 Score: 113
Period size: 22 Copynumber: 3.2 Consensus size: 22
19446770 TGGCCTCTAC
19446780 CATGGCTAACGTACTAAGCTCT
1 CATGGCTAACGTACTAAGCTCT
19446802 CATGGCTAACGTACTAAGCTCT
1 CATGGCTAACGTACTAAGCTCT
** *
19446824 CATGTTTCACGTACTAAGCTCT
1 CATGGCTAACGTACTAAGCTCT
19446846 CATG
1 CATG
19446850 TTTGAACAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.30
Consensus pattern (22 bp):
CATGGCTAACGTACTAAGCTCT
Found at i:19447617 original size:30 final size:29
Alignment explanation
Indices: 19447575--19447662 Score: 95
Period size: 30 Copynumber: 2.9 Consensus size: 29
19447565 AGAATCAATC
* * *
19447575 TGGGCCTAAGCCCTATACAGTAGCAGTGTG
1 TGGGCCT-AGCCCAATACAGTAACAGTGTA
* *
19447605 TGGGCCATAGCCCAATATAGTAACAGAGTA
1 TGGGCC-TAGCCCAATACAGTAACAGTGTA
*
19447635 TGGGTCTTAGCCCAATACAGTAACAGTG
1 TGGG-CCTAGCCCAATACAGTAACAGTG
19447663 CAAATGCAGT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
30 46 0.96
31 2 0.04
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.23
Consensus pattern (29 bp):
TGGGCCTAGCCCAATACAGTAACAGTGTA
Found at i:19447824 original size:26 final size:26
Alignment explanation
Indices: 19447754--19447850 Score: 72
Period size: 26 Copynumber: 3.7 Consensus size: 26
19447744 CCCACGCAGC
* * *
19447754 AAAGCTGCCAGTAACAATAATGTAGC
1 AAAGCTACCAGTAACAGTAATGTAGG
* ** **
19447780 AGAGCTGTCAGTATTAGTAATGTAGG
1 AAAGCTACCAGTAACAGTAATGTAGG
*
19447806 AAAGCTACCAGTAACAGTATTTGT-GG
1 AAAGCTACCAGTAACAGTA-ATGTAGG
*
19447832 CAAAGCCACCAGT-ACAGTA
1 -AAAGCTACCAGTAACAGTA
19447851 TACTTCCCCT
Statistics
Matches: 56, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
26 42 0.75
27 14 0.25
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.23
Consensus pattern (26 bp):
AAAGCTACCAGTAACAGTAATGTAGG
Found at i:19448077 original size:27 final size:27
Alignment explanation
Indices: 19448015--19448078 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
19448005 AGGGGTATAA
19448015 CGGTCATTTTACCCTATAGAGGTATTT
1 CGGTCATTTTACCCTATAGAGGTATTT
* * * *
19448042 CGATAATTTTATCC-ATCGAGGGTATTT
1 CGGTCATTTTACCCTATAGA-GGTATTT
19448069 CGGTCATTTT
1 CGGTCATTTT
19448079 CGAGGCCCAT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
26 4 0.13
27 26 0.87
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (27 bp):
CGGTCATTTTACCCTATAGAGGTATTT
Found at i:19453340 original size:27 final size:26
Alignment explanation
Indices: 19453294--19453344 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
19453284 ATGGGGGTAG
19453294 GATTATGTATATCTGTTCTGCTTATCT
1 GATTATGTATATCTGTTCTG-TTATCT
*
19453321 GATTATG-CTATCTGTATCTGTTAT
1 GATTATGTATATCTGT-TCTGTTAT
19453345 GGACTTAGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.20, C:0.14, G:0.16, T:0.51
Consensus pattern (26 bp):
GATTATGTATATCTGTTCTGTTATCT
Found at i:19461286 original size:33 final size:33
Alignment explanation
Indices: 19461232--19461322 Score: 112
Period size: 33 Copynumber: 2.8 Consensus size: 33
19461222 GCATCCACAA
*
19461232 AGTAAGTCCACCAGGATAGTAAACACAGAATAG
1 AGTAAGTCCACCAGGACAGTAAACACAGAATAG
* * *
19461265 AGTAAGTTCACCGGGACAGTAAACACGGAATAG
1 AGTAAGTCCACCAGGACAGTAAACACAGAATAG
* *
19461298 AG-ATAGTCCATCAAGACAGTAAACA
1 AGTA-AGTCCACCAGGACAGTAAACA
19461323 TGAGATAGTC
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
32 1 0.02
33 48 0.98
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (33 bp):
AGTAAGTCCACCAGGACAGTAAACACAGAATAG
Found at i:19463080 original size:28 final size:28
Alignment explanation
Indices: 19463014--19463068 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
19463004 AACTTGACGT
*
19463014 ACAGCTCGTGTGAGCAAATTCAAATATC
1 ACAGCTCGTGTGAACAAATTCAAATATC
*
19463042 ACAACTCGTGTGAACAAATTCAAATAT
1 ACAGCTCGTGTGAACAAATTCAAATAT
19463069 TATAGCTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (28 bp):
ACAGCTCGTGTGAACAAATTCAAATATC
Found at i:19463087 original size:28 final size:28
Alignment explanation
Indices: 19463014--19463088 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 28
19463004 AACTTGACGT
*
19463014 ACAGCTCGTGTGAGCAAATTCAAATATC
1 ACAGCTCGTGTAAGCAAATTCAAATATC
* *
19463042 ACAACTCGTGTGAA-CAAATTCAAATATT
1 ACAGCTCGTGT-AAGCAAATTCAAATATC
* *
19463070 ATAGCTTGTGTAAGCAAAT
1 ACAGCTCGTGTAAGCAAAT
19463089 CGGCCTCGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
27 2 0.05
28 36 0.92
29 1 0.03
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (28 bp):
ACAGCTCGTGTAAGCAAATTCAAATATC
Done.