Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007733.1 Hibiscus syriacus cultivar Beakdansim tig00109987_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1979160
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 9
Found at i:1428453 original size:14 final size:15
Alignment explanation
Indices: 1428434--1428465 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
1428424 CTAAATTATT
1428434 TTTGAAAACTTA-GA
1 TTTGAAAACTTAGGA
1428448 TTTGAAAACTTAGGA
1 TTTGAAAACTTAGGA
1428463 TTT
1 TTT
1428466 TGGAGTCGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.38, C:0.06, G:0.16, T:0.41
Consensus pattern (15 bp):
TTTGAAAACTTAGGA
Found at i:1430804 original size:11 final size:12
Alignment explanation
Indices: 1430774--1430805 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
1430764 TAATCAACAC
1430774 TCCAATATTAAA
1 TCCAATATTAAA
1430786 TCCAATATTAAA
1 TCCAATATTAAA
1430798 T-CAATATT
1 TCCAATATT
1430806 TTAATATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.35
12 13 0.65
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.38
Consensus pattern (12 bp):
TCCAATATTAAA
Found at i:1431747 original size:10 final size:10
Alignment explanation
Indices: 1431732--1431761 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
1431722 CATCATCCTT
1431732 TAAATTTTTG
1 TAAATTTTTG
1431742 TAAATTTTTG
1 TAAATTTTTG
1431752 TAAATTTTTG
1 TAAATTTTTG
1431762 ATTTGATCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.10, T:0.60
Consensus pattern (10 bp):
TAAATTTTTG
Found at i:1432791 original size:144 final size:145
Alignment explanation
Indices: 1432506--1432791 Score: 520
Period size: 144 Copynumber: 2.0 Consensus size: 145
1432496 AATTTATGAC
*
1432506 TATGGTGGGAATGAGAATTAACGAGGGAAGATGAATAATTGAAGTTTGGTAAAGTGGAGTTATAC
1 TATGGTGGGAATGAGAATTAACGAGAGAAGATGAATAATTGAAGTTTGGTAAAGTGGAGTTATAC
* * *
1432571 AAAAAAAAATGAGATAAGCTTTATAGATGTAGTACTGTACTAATTATTGGTATTTCTCGTATAAC
66 AAAAAAAAATGAGACAAGCTTTACAGATGTAGCACTGTACTAATTATTGGTATTTCTCGTATAAC
1432636 TTCAACAAGATTGAT
131 TTCAACAAGATTGAT
1432651 TATGGTGGGAATGAGAATTAACGAGAGAAGATGAATAATTGAAGTTTGGTAAAGTGGAGTTATAC
1 TATGGTGGGAATGAGAATTAACGAGAGAAGATGAATAATTGAAGTTTGGTAAAGTGGAGTTATAC
*
1432716 -AAAAAAAATGAGACAAGCTTTACAGATGTAGCACTGTACTAATTATTGGTATTTCTCGTATAAT
66 AAAAAAAAATGAGACAAGCTTTACAGATGTAGCACTGTACTAATTATTGGTATTTCTCGTATAAC
1432780 TTCAACAAGATT
131 TTCAACAAGATT
1432792 CGACCGCAGG
Statistics
Matches: 136, Mismatches: 5, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
144 72 0.53
145 64 0.47
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (145 bp):
TATGGTGGGAATGAGAATTAACGAGAGAAGATGAATAATTGAAGTTTGGTAAAGTGGAGTTATAC
AAAAAAAAATGAGACAAGCTTTACAGATGTAGCACTGTACTAATTATTGGTATTTCTCGTATAAC
TTCAACAAGATTGAT
Found at i:1434671 original size:32 final size:31
Alignment explanation
Indices: 1434605--1434688 Score: 109
Period size: 32 Copynumber: 2.7 Consensus size: 31
1434595 TAAAGTTTAG
1434605 TTTTTGTTTCATTTTAGTACCCGTCGTTAAC
1 TTTTTGTTTCATTTTAGTACCCGTCGTTAAC
*
1434636 TTTTTATTTCATTTTAGTACATCAC-T-GTTAAC
1 TTTTTGTTTCATTTTAGTAC--C-CGTCGTTAAC
*
1434668 TTTTTGTTTCGTTTTAGTACC
1 TTTTTGTTTCATTTTAGTACC
1434689 TAATTTTTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
30 1 0.02
31 19 0.40
32 24 0.51
33 2 0.04
34 1 0.02
ACGTcount: A:0.18, C:0.17, G:0.11, T:0.55
Consensus pattern (31 bp):
TTTTTGTTTCATTTTAGTACCCGTCGTTAAC
Found at i:1436015 original size:13 final size:13
Alignment explanation
Indices: 1435997--1436025 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1435987 ACATATAAAT
1435997 TAAATGAATATAA
1 TAAATGAATATAA
1436010 TAAATGAATATAA
1 TAAATGAATATAA
1436023 TAA
1 TAA
1436026 TAATTAATAA
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:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (13 bp):
TAAATGAATATAA
Found at i:1438095 original size:2 final size:2
Alignment explanation
Indices: 1438088--1438118 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1438078 GAAACACCTT
1438088 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1438119 TGTCTGGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1442713 original size:15 final size:16
Alignment explanation
Indices: 1442681--1442713 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1442671 AAAATCTTTC
1442681 TTTCCCGTTCTAGATT
1 TTTCCCGTTCTAGATT
*
1442697 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTAGATT
1442712 TT
1 TT
1442714 GATCTGCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.09, C:0.24, G:0.15, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTAGATT
Found at i:1443490 original size:16 final size:17
Alignment explanation
Indices: 1443463--1443497 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
1443453 TATCGCCGAC
1443463 CGAAATTTCACTATTCA
1 CGAAATTTCACTATTCA
1443480 CGAAA-TTCACTATTCA
1 CGAAATTTCACTATTCA
1443496 CG
1 CG
1443498 TGAATAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.31
Consensus pattern (17 bp):
CGAAATTTCACTATTCA
Found at i:1444823 original size:38 final size:38
Alignment explanation
Indices: 1444781--1444863 Score: 166
Period size: 38 Copynumber: 2.2 Consensus size: 38
1444771 ACAAAATTAG
1444781 ATTTTCAATAAAAAATGTGAAATATAAGATAATTTTAA
1 ATTTTCAATAAAAAATGTGAAATATAAGATAATTTTAA
1444819 ATTTTCAATAAAAAATGTGAAATATAAGATAATTTTAA
1 ATTTTCAATAAAAAATGTGAAATATAAGATAATTTTAA
1444857 ATTTTCA
1 ATTTTCA
1444864 GGAGGACGAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 45 1.00
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.39
Consensus pattern (38 bp):
ATTTTCAATAAAAAATGTGAAATATAAGATAATTTTAA
Found at i:1450642 original size:22 final size:22
Alignment explanation
Indices: 1450600--1450643 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1450590 AATGTGTACT
*
1450600 AAATCCACAAAAATTTGAATTA
1 AAATCCACAAAAATATGAATTA
*
1450622 AAATCCATTAAAAATAT-AATTA
1 AAATCCA-CAAAAATATGAATTA
1450644 TAAGATATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (22 bp):
AAATCCACAAAAATATGAATTA
Found at i:1453813 original size:18 final size:19
Alignment explanation
Indices: 1453778--1453815 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
1453768 CACGGAATGT
1453778 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
1453798 AAGATTACCA-GGGAATAA
1 AAGATTACCAGGGGAATAA
1453816 GATTATTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.47, C:0.11, G:0.24, T:0.18
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:1472375 original size:328 final size:323
Alignment explanation
Indices: 1471789--1472397 Score: 783
Period size: 328 Copynumber: 1.9 Consensus size: 323
1471779 AAACGTGTAA
* *
1471789 TTTAACCTTTTACATATAATAAAGTAAAGGGTAAATTATGCTTATAACCCCCTAACTATTATTCG
1 TTTAACCTTTTACATATAATAAAGTAAAGGGTAAATTATACTTATAACCACCTAACTATTATTCG
* * * * *
1471854 TTTTTATTTTAGTTATTGATCTGTTAATTTTTTTTCAATCAAATCATCTAACTATTTAAGTGTTA
66 TTTTTATTTTAGTTACTAATCTGTTAATTTTTTTTCAATCAAACCATATAACTATTTAAGTATTA
* ** * * * *
1471919 TCAAAACAGTTATTGGTCCTAACATTTAGCGGATGGGATAATATGATTGTTAAAAATTGATATAA
131 CCAAAACAGCCATTCGT-CTAACATTTAGAGGAGGGGATAATATGATTGTTAAAAATTGATACAA
* * * *
1471984 TTATACATTTGAACATCAATATTTACATATTCTATCAGTTTAATATTCATTTTAATGCAATTAAA
195 TCATACATTTGAACATCAATATTTACATATTATATCAATTTAATATTCATTCTAATGCAATTAAA
1472049 TAAATTTAATATCAAATTAGAAAGTGACATGTGACATTACATGATTGATTGACTAAACACATAT
260 TAAATTTAATATCAAATTAGAAAGTGACATGTGACATTACATGATTGATTGACTAAACACATAT
* * * *
1472113 TTTAACCTTTTATATATCATAACGTAAAGGGTAAATTATACTTATAACCACTTAACTATTATTCT
1 TTTAACCTTTTACATATAATAAAGTAAAGGGTAAATTATACTTATAACCACCTAACTATTATTC-
* * * * *
1472178 TTTTTTTTTGTTTTGATTACTAATCTTTTAATTTTTTTTCAATCAAACCATATAATTATTTAAGT
65 -GTTTTTAT-TTTAG-TTACTAATCTGTTAATTTTTTTTCAATCAAACCATATAACTATTTAAGT
* * * *
1472243 ATTGCCAACCAAACCA-CCA-TCGT-TAACTTTTAGAGGAGGGGATAATGTGATTGTTAGAAATT
127 ATT----ACCAAAACAGCCATTCGTCTAACATTTAGAGGAGGGGATAATATGATTGTTAAAAATT
* * * * *
1472305 GATACAATCATACATTTGAGCCTCAATATTTATATATTATATCAATTTAATCTTCATTCTAATTC
188 GATACAATCATACATTTGAACATCAATATTTACATATTATATCAATTTAATATTCATTCTAATGC
*
1472370 AATTAAATAAATTTAATATCGAATTAGA
253 AATTAAATAAATTTAATATCAAATTAGA
1472398 TGATGATATG
Statistics
Matches: 240, Mismatches: 37, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
324 58 0.24
326 6 0.03
327 4 0.02
328 161 0.67
330 3 0.01
331 1 0.00
332 7 0.03
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (323 bp):
TTTAACCTTTTACATATAATAAAGTAAAGGGTAAATTATACTTATAACCACCTAACTATTATTCG
TTTTTATTTTAGTTACTAATCTGTTAATTTTTTTTCAATCAAACCATATAACTATTTAAGTATTA
CCAAAACAGCCATTCGTCTAACATTTAGAGGAGGGGATAATATGATTGTTAAAAATTGATACAAT
CATACATTTGAACATCAATATTTACATATTATATCAATTTAATATTCATTCTAATGCAATTAAAT
AAATTTAATATCAAATTAGAAAGTGACATGTGACATTACATGATTGATTGACTAAACACATAT
Found at i:1473081 original size:32 final size:32
Alignment explanation
Indices: 1473003--1473107 Score: 97
Period size: 32 Copynumber: 3.3 Consensus size: 32
1472993 GTGCTTAATT
* * *
1473003 GGTGATGTGGTACATATCAGGTCATCACTTTG
1 GGTGATGTGGTACATGTCATGTCATCACCTTG
*** *
1473035 GGTGACACGATACATGTCATGTCAAT-ACCTTG
1 GGTGATGTGGTACATGTCATGTC-ATCACCTTG
* * *
1473067 GGTGATGTGGTACATGTCATATTATCA-CTTT
1 GGTGATGTGGTACATGTCATGTCATCACCTTG
1473098 GGTGATGTGG
1 GGTGATGTGG
1473108 CGTATGATAT
Statistics
Matches: 57, Mismatches: 14, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
31 15 0.26
32 40 0.70
33 2 0.04
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.34
Consensus pattern (32 bp):
GGTGATGTGGTACATGTCATGTCATCACCTTG
Found at i:1474924 original size:3 final size:3
Alignment explanation
Indices: 1474916--1474966 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
1474906 CACCTCTAAC
1474916 AGG AGG AGG AGG A-G AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
1474963 AGG A
1 AGG A
1474967 AGAAGAATAG
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:1479125 original size:28 final size:28
Alignment explanation
Indices: 1479063--1479253 Score: 274
Period size: 28 Copynumber: 6.8 Consensus size: 28
1479053 AAAGTCTATT
* * *
1479063 AATAATTACGAAAATATCAACCTTTTCGA
1 AATAATTACCAAAATATC-ACTTTTTCAA
1479092 AATAATTACCAAAATATCACTTTTTCAA
1 AATAATTACCAAAATATCACTTTTTCAA
**
1479120 AATAATTACCAAAATATCACTTTTTTGA
1 AATAATTACCAAAATATCACTTTTTCAA
*
1479148 AATAATTATCAAAATATCACTTTTTCAA
1 AATAATTACCAAAATATCACTTTTTCAA
* *
1479176 AATAATTACCAAAATGTCACTTTTTTAA
1 AATAATTACCAAAATATCACTTTTTCAA
* *
1479204 AATAATTATCAAAATATCACTTTTTCGA
1 AATAATTACCAAAATATCACTTTTTCAA
*
1479232 AATAAATACCAAAATATCACTT
1 AATAATTACCAAAATATCACTT
1479254 GTTTAACAAT
Statistics
Matches: 145, Mismatches: 17, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
28 128 0.88
29 17 0.12
ACGTcount: A:0.46, C:0.16, G:0.03, T:0.36
Consensus pattern (28 bp):
AATAATTACCAAAATATCACTTTTTCAA
Found at i:1482498 original size:21 final size:21
Alignment explanation
Indices: 1482457--1482498 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1482447 GGGGGTTCTG
*
1482457 GTTTTGGGGTTGTTTTGAGAT
1 GTTTTGGGGTTCTTTTGAGAT
1482478 GTTTTGGGGTTCTGTTT-AGAT
1 GTTTTGGGGTTCT-TTTGAGAT
1482499 TGGGTTGGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.10, C:0.02, G:0.36, T:0.52
Consensus pattern (21 bp):
GTTTTGGGGTTCTTTTGAGAT
Found at i:1484145 original size:236 final size:237
Alignment explanation
Indices: 1483701--1484499 Score: 1349
Period size: 237 Copynumber: 3.4 Consensus size: 237
1483691 ATTCATAACT
* * * *
1483701 TGCATACTGGTATGTGTCCATGTTTACAGCAGCTACACATAACATGAGCGCACTGCCAAGAATTA
1 TGCATACTGGTATGTGCCCATGTTTACAGCAGCTACACATAACTTGAGCACTCTGCCAAGAATTA
* * *
1483766 GGACAACTAAAAGAACCATGAACTTC--A--AACAGTATAGTTTGTTCATTGTTATACCATACGA
66 GGACAACTAAAAGAACCATGAACTTCAAATTAACATTATAGTTTGTTCAATGTTATACTATACGA
* * * * *
1483827 GACGATAACGACGAATATAAATGATCGCACACTAAAAGAGACACGATGTTCATGTAATGCAGTTT
131 GAC-AGAACGACAAATATAAGTGATCGCACCCTAAAAGAGACGCGATGTTCATGTAATGCAGTTT
*
1483892 CTTTATGGGCATGCATGTACTAGTGACTCGCCCACCTAAAGCC
195 CTTTATGAGCATGCATGTACTAGTGACTCGCCCACCTAAAGCC
1483935 TGCATACTGGTATGTGCCCATGTTTACAGCAGCTACACATAACTTGAGCACTCTGCCAAGAATTA
1 TGCATACTGGTATGTGCCCATGTTTACAGCAGCTACACATAACTTGAGCACTCTGCCAAGAATTA
1484000 GGACAACT-AAAGAACCATGAACTTCAAATTAACATTATAGTTTGTTCAATGTTATACTATACGA
66 GGACAACTAAAAGAACCATGAACTTCAAATTAACATTATAGTTTGTTCAATGTTATACTATACGA
1484064 GACAGAACGACAAATATAAGTGATCGCACCCTAAAAGAGACGCGATGTTCATGTAATGCAGTTTC
131 GACAGAACGACAAATATAAGTGATCGCACCCTAAAAGAGACGCGATGTTCATGTAATGCAGTTTC
1484129 TTTATGAGCATGCATGTACTAGTGACTCGCCCACCTAAAGCC
196 TTTATGAGCATGCATGTACTAGTGACTCGCCCACCTAAAGCC
1484171 TGCATACTGGTATGTGCCCATGTTTACAGCAGCTACACATAACTTGAGCACTCTGCCAAGAATTA
1 TGCATACTGGTATGTGCCCATGTTTACAGCAGCTACACATAACTTGAGCACTCTGCCAAGAATTA
1484236 GGACAACTAAAAGAACCATGAACTTCAAATTAACATTATAGTTTGTTCAATGTTATACTATACGA
66 GGACAACTAAAAGAACCATGAACTTCAAATTAACATTATAGTTTGTTCAATGTTATACTATACGA
*
1484301 GACAGAACGACAAATATAAGTGATCGCACCCTAAAAGAGATGCGATGTTCATGTAATGCAGTTTC
131 GACAGAACGACAAATATAAGTGATCGCACCCTAAAAGAGACGCGATGTTCATGTAATGCAGTTTC
* * *
1484366 TTTATGAGCATCCATGTACTAATGACTCGCCCACCTAAACCC
196 TTTATGAGCATGCATGTACTAGTGACTCGCCCACCTAAAGCC
* * *
1484408 TGCATACTGGTATGTGTCCATGTTTACAGCAGCTACACATAACTTGAGCACTCTGCCTAGAATAA
1 TGCATACTGGTATGTGCCCATGTTTACAGCAGCTACACATAACTTGAGCACTCTGCCAAGAATTA
* *
1484473 GGACAACT-AAAGAACCATTAACATCAA
66 GGACAACTAAAAGAACCATGAACTTCAA
1484500 CTCTGCGTAA
Statistics
Matches: 538, Mismatches: 22, Indels: 8
0.95 0.04 0.01
Matches are distributed among these distances:
233 17 0.03
234 69 0.13
235 1 0.00
236 188 0.35
237 263 0.49
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (237 bp):
TGCATACTGGTATGTGCCCATGTTTACAGCAGCTACACATAACTTGAGCACTCTGCCAAGAATTA
GGACAACTAAAAGAACCATGAACTTCAAATTAACATTATAGTTTGTTCAATGTTATACTATACGA
GACAGAACGACAAATATAAGTGATCGCACCCTAAAAGAGACGCGATGTTCATGTAATGCAGTTTC
TTTATGAGCATGCATGTACTAGTGACTCGCCCACCTAAAGCC
Found at i:1493465 original size:2 final size:2
Alignment explanation
Indices: 1493458--1493511 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1493448 ACTTAAAAGA
1493458 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1493500 AG AG AG AG AG AG
1 AG AG AG AG AG AG
1493512 CTTTCTATTC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1503194 original size:17 final size:17
Alignment explanation
Indices: 1503172--1503210 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
1503162 TGAATCAAAT
*
1503172 TAATTAGATATTATTTA
1 TAATTAGATATCATTTA
1503189 TAATTAGATATCATTTA
1 TAATTAGATATCATTTA
1503206 -AATTA
1 TAATTA
1503211 ATTGTAAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (17 bp):
TAATTAGATATCATTTA
Found at i:1505756 original size:58 final size:58
Alignment explanation
Indices: 1505658--1505772 Score: 194
Period size: 58 Copynumber: 2.0 Consensus size: 58
1505648 CGAGGTTTTG
* ** *
1505658 GGTTTGAGTATTAAGAATGACAAGGATGTAAGTTTTTAATGTCAAATGATTGAGAATA
1 GGTTCGAGTATTAAGAATGACAAGGATGTAAGCATCTAATGTCAAATGATTGAGAATA
1505716 GGTTCGAGTATTAAGAATGACAAGGATGTAAGCATCTAATGTCAAATGATTGAGAAT
1 GGTTCGAGTATTAAGAATGACAAGGATGTAAGCATCTAATGTCAAATGATTGAGAAT
1505773 TATCTTTGAA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.31
Consensus pattern (58 bp):
GGTTCGAGTATTAAGAATGACAAGGATGTAAGCATCTAATGTCAAATGATTGAGAATA
Found at i:1507081 original size:90 final size:89
Alignment explanation
Indices: 1506926--1507102 Score: 282
Period size: 90 Copynumber: 2.0 Consensus size: 89
1506916 CCTAACACAC
* * *
1506926 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
1 CCTTTTATAGCCAAATTACCCAAATCATATTAGGATTTTATTATTTCAAATTAATTAAATCTATA
* *
1506991 TTTAATTAATTAGAATTTAATAAT
66 TTTAATTAATTAAAATTAAATAAT
* *
1507015 CCTTTTATATCCAAATTACCCAAATCATATTAGAGATTTTATTATTTCAAATTAATTAAATTTAT
1 CCTTTTATAGCCAAATTACCCAAATCATATTAG-GATTTTATTATTTCAAATTAATTAAATCTAT
1507080 ATTTAATTAATTAAAATTAAATA
65 ATTTAATTAATTAAAATTAAATA
1507103 TTTGAGATTA
Statistics
Matches: 80, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
89 30 0.38
90 50 0.62
ACGTcount: A:0.40, C:0.11, G:0.05, T:0.45
Consensus pattern (89 bp):
CCTTTTATAGCCAAATTACCCAAATCATATTAGGATTTTATTATTTCAAATTAATTAAATCTATA
TTTAATTAATTAAAATTAAATAAT
Found at i:1507112 original size:24 final size:21
Alignment explanation
Indices: 1507064--1507133 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 21
1507054 TATTATTTCA
*
1507064 AATTAATT-AAATTTATATTT
1 AATTAATTAAAATTAATATTT
1507084 AATTAATTAAAATTAAATATTT
1 AATTAATTAAAATT-AATATTT
*
1507106 GAGATT-ATTAAAA-CATATATTT
1 -A-ATTAATTAAAATTA-ATATTT
1507128 AATTAA
1 AATTAA
1507134 CTCTAGATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
20 11 0.26
21 8 0.19
22 12 0.29
23 8 0.19
24 3 0.07
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (21 bp):
AATTAATTAAAATTAATATTT
Found at i:1508606 original size:2 final size:2
Alignment explanation
Indices: 1508601--1508625 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1508591 TAGGTGTGTG
1508601 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1508626 TTGTTCTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1513943 original size:216 final size:215
Alignment explanation
Indices: 1513376--1514065 Score: 1075
Period size: 216 Copynumber: 3.2 Consensus size: 215
1513366 AGGTCTTATG
* *
1513376 GATGACCCGAAGGATTTAAGCATCATGCTCAAAAGACTTATTGATGGCCCGAAGGACTTATAAAT
1 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAAT
** * **
1513441 TGTGAAATTTTGAAAATATCATTCTTTGTTTTCAAAAATTTCATCTTC-T--CA-ATTTTTTTTT
66 TGTGAAATTTTGAAAATCGCATTCTTTGTTTTCAAAAATTTCATCTTCTTAAAACATCATTTTTT
* *
1513502 TCATTTTCAAATTCATGTGAAAACATCCTACCCGCAGGTCTTATGGATGGCCCGAATGACTTATC
131 T-ATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATC
1513567 ATCTTGCTCTAAAGGCTTACA
195 ATCTTGCTCTAAAGGCTTACA
*
1513588 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAATGACTTATAAAT
1 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAAT
* * *
1513653 TGTGAAATTTTGAAAATCGCATTCTTTGTTTTCAAAAATTTCATCTTCTCAAACCATCGTTTTTT
66 TGTGAAATTTTGAAAATCGCATTCTTTGTTTTCAAAAATTTCATCTTCTTAAAACATCATTTTTT
* * *
1513718 CATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTACGGATGGCCCGAAGGACTTATTA
131 TATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCA
1513783 TCTTGCTCTAAAGGCTTACA
196 TCTTGCTCTAAAGGCTTACA
* * *
1513803 GATGATCCGAAGGATTTTAAGCATCATGCTTGAAAGACTTATTGATGGCCCGAAGGACTTATAAA
1 GATGACCCGAAGGA-TTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAA
* * *
1513868 TCGTGAAATTTTGAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATTTTT
65 TTGTGAAATTTTGAAAATCGCATTCTTTGTTTTCAAAAATTTCATCTTCTTAAAACATCATTTTT
* * *
1513933 TTATTTTCAAATTCATGTGAAAACATCTTACCCGAAGGTTTTATGGATGGCCTGAAGGACTTATC
130 TTATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATC
1513998 ATCTTGCTCTAAAGGCTTACA
195 ATCTTGCTCTAAAGGCTTACA
* *
1514019 GAAGACCCGAATGATTTAAGCATCATGCTCGGAAAG-CTTACTGATGG
1 GATGACCCGAAGGATTTAAGCATCATGCTC-GAAAGACTTACTGATGG
1514066 ATTTGCTTCA
Statistics
Matches: 436, Mismatches: 36, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
212 108 0.25
215 118 0.27
216 210 0.48
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.34
Consensus pattern (215 bp):
GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAAT
TGTGAAATTTTGAAAATCGCATTCTTTGTTTTCAAAAATTTCATCTTCTTAAAACATCATTTTTT
TATTTTCAAATTCATGTGAAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCA
TCTTGCTCTAAAGGCTTACA
Found at i:1514201 original size:36 final size:37
Alignment explanation
Indices: 1514061--1514247 Score: 200
Period size: 37 Copynumber: 5.1 Consensus size: 37
1514051 AAAGCTTACT
*
1514061 GATGGATTTGCTTCACTACTTTTCGGTGAAGGCTTAA
1 GATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAA
* * * ** *
1514098 AATTGATTTGCTTCATTGTTC-TCAGGTGAAGGCCTAA
1 GATGGATTTGCTTCACTACTCTTC-GGTGAAGGCTTAA
* * * *
1514135 GATGGATTTGCTTCACTATTCTCCGATGAAGGCTTTA
1 GATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAA
*
1514172 GATTGATTT-CTTCACTACTCTTCGGTGAAGGCTTAA
1 GATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAA
* * * *
1514208 GATGGA-TTACTTCACTACTATTTGGTGAAGACTTAA
1 GATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAA
1514244 GATG
1 GATG
1514248 AATTGCTCCA
Statistics
Matches: 123, Mismatches: 24, Indels: 7
0.80 0.16 0.05
Matches are distributed among these distances:
35 2 0.02
36 58 0.47
37 62 0.50
38 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (37 bp):
GATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAA
Found at i:1520421 original size:21 final size:21
Alignment explanation
Indices: 1520397--1520508 Score: 154
Period size: 21 Copynumber: 5.3 Consensus size: 21
1520387 AATGCAAAGT
*
1520397 GGTCTTCATGTCTTTATGAAG
1 GGTCTTCATGTCTTTATGAAC
*
1520418 GGTCTTCATGTCTTTATGAAT
1 GGTCTTCATGTCTTTATGAAC
*
1520439 GGTCTTCATGTCTTTATGAAT
1 GGTCTTCATGTCTTTATGAAC
**
1520460 GGTCTTCATGTCCTTGGTGAAC
1 GGTCTTCATGT-CTTTATGAAC
1520482 GGTCTTC-TCGTCTTTATGAAC
1 GGTCTTCAT-GTCTTTATGAAC
1520503 GGTCTT
1 GGTCTT
1520509 TTTGTCCTTG
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
21 67 0.81
22 16 0.19
ACGTcount: A:0.16, C:0.18, G:0.22, T:0.44
Consensus pattern (21 bp):
GGTCTTCATGTCTTTATGAAC
Found at i:1520500 original size:43 final size:43
Alignment explanation
Indices: 1520397--1520520 Score: 162
Period size: 43 Copynumber: 2.9 Consensus size: 43
1520387 AATGCAAAGT
* ** *
1520397 GGTCTTCATGTCTTTATGAAGGGTCTTCATGT-CTTTATGAAT
1 GGTCTTCATGTCTTTATGAACGGTCTTCATGTCCTTGGTGAAC
*
1520439 GGTCTTCATGTCTTTATGAATGGTCTTCATGTCCTTGGTGAAC
1 GGTCTTCATGTCTTTATGAACGGTCTTCATGTCCTTGGTGAAC
**
1520482 GGTCTTC-TCGTCTTTATGAACGGTCTTTTTGTCCTTGGT
1 GGTCTTCAT-GTCTTTATGAACGGTCTTCATGTCCTTGGT
1520521 ATGACTGTAT
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
42 32 0.44
43 41 0.56
ACGTcount: A:0.15, C:0.18, G:0.23, T:0.45
Consensus pattern (43 bp):
GGTCTTCATGTCTTTATGAACGGTCTTCATGTCCTTGGTGAAC
Found at i:1525866 original size:20 final size:20
Alignment explanation
Indices: 1525841--1525881 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1525831 TTTGATAGCT
1525841 GCAGTTTAGATTCGATTAGA
1 GCAGTTTAGATTCGATTAGA
1525861 GCAGTTTAGATTCGATTAGA
1 GCAGTTTAGATTCGATTAGA
1525881 G
1 G
1525882 TCGGTTAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.10, G:0.27, T:0.34
Consensus pattern (20 bp):
GCAGTTTAGATTCGATTAGA
Found at i:1527365 original size:59 final size:60
Alignment explanation
Indices: 1527283--1527398 Score: 153
Period size: 59 Copynumber: 1.9 Consensus size: 60
1527273 ACAAATAGTC
* * *
1527283 CCCCAACTATAGGGTATTACTTTGTCGAGTC-CCCGACTATTAAAAGTTATAAAATGATT
1 CCCCAACTATAGGATATTACTTTGTCGAGTCTACCGACTATTAAAAGTTACAAAATGATT
* * * * *
1527342 CCCCGACTATAGGATGTTGCTTTGTTGAGTCTATCGACTATTAAAAGTTACAAAATG
1 CCCCAACTATAGGATATTACTTTGTCGAGTCTACCGACTATTAAAAGTTACAAAATG
1527399 GTCACTCGAT
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
59 26 0.54
60 22 0.46
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (60 bp):
CCCCAACTATAGGATATTACTTTGTCGAGTCTACCGACTATTAAAAGTTACAAAATGATT
Found at i:1531430 original size:13 final size:13
Alignment explanation
Indices: 1531412--1531456 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
1531402 TAGTAACTGG
*
1531412 TTTGATCAATTGA
1 TTTGATAAATTGA
* *
1531425 TTTGATTAGTTGA
1 TTTGATAAATTGA
*
1531438 TTTGAGAAATTGA
1 TTTGATAAATTGA
1531451 TTTGAT
1 TTTGAT
1531457 TAACTGTTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.29, C:0.02, G:0.20, T:0.49
Consensus pattern (13 bp):
TTTGATAAATTGA
Found at i:1532491 original size:2 final size:2
Alignment explanation
Indices: 1532479--1532539 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
1532469 TTCTCTAGCC
1532479 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1532520 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
1532540 TATTTTCACA
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 57 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1541213 original size:16 final size:16
Alignment explanation
Indices: 1541184--1541220 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
1541174 TGCTGTGTTC
1541184 TCTTTCTCTGTTTTTT
1 TCTTTCTCTGTTTTTT
1541200 TCTTT-TCTGTTTTTT
1 TCTTTCTCTGTTTTTT
1541215 T-TTTCT
1 TCTTTCT
1541221 TGTCGTTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 3 0.15
15 12 0.60
16 5 0.25
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.78
Consensus pattern (16 bp):
TCTTTCTCTGTTTTTT
Found at i:1541495 original size:27 final size:27
Alignment explanation
Indices: 1541459--1541549 Score: 173
Period size: 27 Copynumber: 3.4 Consensus size: 27
1541449 GCAGTGAGGC
*
1541459 GGCGGCTGGGATTCTTGAAGCATCAGA
1 GGCGGCTGGGATTCTGGAAGCATCAGA
1541486 GGCGGCTGGGATTCTGGAAGCATCAGA
1 GGCGGCTGGGATTCTGGAAGCATCAGA
1541513 GGCGGCTGGGATTCTGGAAGCATCAGA
1 GGCGGCTGGGATTCTGGAAGCATCAGA
1541540 GGCGGCTGGG
1 GGCGGCTGGG
1541550 GGTGGCTAGG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 63 1.00
ACGTcount: A:0.20, C:0.19, G:0.43, T:0.19
Consensus pattern (27 bp):
GGCGGCTGGGATTCTGGAAGCATCAGA
Found at i:1541675 original size:3 final size:3
Alignment explanation
Indices: 1541667--1541772 Score: 140
Period size: 3 Copynumber: 34.7 Consensus size: 3
1541657 TTATTTATTA
* * *
1541667 AAT AAT AAT ATAT ATT GAT AAT AAT AAT AAT AAAT AAT GAT AAT AAT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT
* **
1541714 AAT AAT AAT TAT AAT AAT AAT AAT AAT AAT AAT AAT AAT TTT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1541762 AAT AAT AAT AA
1 AAT AAT AAT AA
1541773 ATTTAAATGA
Statistics
Matches: 89, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
3 83 0.93
4 6 0.07
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:1542779 original size:118 final size:114
Alignment explanation
Indices: 1542420--1543908 Score: 2121
Period size: 118 Copynumber: 13.0 Consensus size: 114
1542410 AGAATTATGC
*
1542420 AAAAA-GTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 AAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* ** * *
1542484 TTATGAACT-T-CTCTGG-AAAAGCTGCTCCATCAAGTGATGGATT-TGA
66 TTATGAACTCTACTCTGGCAAAA-ATAATCCATCAAGTGATGAATTCAGA
* * *
1542530 GCAAAAGGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTT
1 -AAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
**
1542595 ATTATGAAC-CTTTTCTGGCAAAAATAATCCATCAAGTGATGAATTCAGA
65 ATTATGAACTCTACTCTGGCAAAAATAATCCATCAAGTGATGAATTCAGA
*
1542644 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
1 AAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTC
1542709 TCATTATGAACTCTACCTCTGGCAAAAATAATCCATCAAGTGATGAATTCAGA
63 TCATTATGAACTCTA-CTCTGGCAAAAATAATCCATCAAGTGATGAATTCAGA
1542762 AAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 AAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
1542827 TTATGGACT-T-CTCTGGCAAAAATAATCCATCAAGTGATGAATTCAGA
66 TTATGAACTCTACTCTGGCAAAAATAATCCATCAAGTGATGAATTCAGA
*
1542874 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
1 AAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTC
1542939 TCATTATGAACTCTACCTCTGGCAAAAATAATCCATCAAGTGATGAATTCAGA
63 TCATTATGAACTCTA-CTCTGGCAAAAATAATCCATCAAGTGATGAATTCAGA
1542992 AAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 AAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * *
1543057 TTATGAACT-T-CTCTGG-AAAAGTTGATTCATCAAGTGATGGATT-TGA
66 TTATGAACTCTACTCTGGCAAAA-ATAATCCATCAAGTGATGAATTCAGA
* *
1543103 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTT
1 -AAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTT
1543168 CTCATTATGAACTCTACCTCTGGCAAAAATAATCCATCAAGTGATGAATTCAGA
62 CTCATTATGAACTCTA-CTCTGGCAAAAATAATCCATCAAGTGATGAATTCAGA
1543222 AAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 AAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
1543287 TTATGGACT-T-CTCTGGCAAAAATAATCCATCAAGTGATGAATTCAGA
66 TTATGAACTCTACTCTGGCAAAAATAATCCATCAAGTGATGAATTCAGA
*
1543334 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
1 AAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTC
1543399 TCATTATGAACTCTACCTCTGGCAAAAATAATCCATCAAGTGATGAATTCAGA
63 TCATTATGAACTCTA-CTCTGGCAAAAATAATCCATCAAGTGATGAATTCAGA
1543452 AAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 AAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * * *
1543517 TTATGAACT-T-CTCTGG-AAAAGTTGATTCATCAAGTGATGGATT-TGA
66 TTATGAACTCTACTCTGGCAAAA-ATAATCCATCAAGTGATGAATTCAGA
* *
1543563 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTT
1 -AAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTT
*
1543628 CTCATTATGAACTCTACCTCTGGCAACAATAATCCATCAAGTGATGAATTCA-A
62 CTCATTATGAACTCTA-CTCTGGCAAAAATAATCCATCAAGTGATGAATTCAGA
*
1543681 ACAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 A-AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
** * * * *
1543746 ATTATGAACTCTAC-CTGG-AAAGGCTGATCCAGCAAATGATGGATTCA-A
65 ATTATGAACTCTACTCTGGCAAA-AATAATCCATCAAGTGATGAATTCAGA
*
1543794 GTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTT
1 -AAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTT
*
1543859 CTCATTATGAACTCTAC-CTGG-AAATACTGAAT-CATCGAA-TGATGAATTCA
62 CTCATTATGAACTCTACTCTGGCAAA-AAT-AATCCATC-AAGTGATGAATTCA
1543909 AGCGAAAAGT
Statistics
Matches: 1263, Mismatches: 65, Indels: 95
0.89 0.05 0.07
Matches are distributed among these distances:
111 16 0.01
112 397 0.31
113 150 0.12
114 11 0.01
115 188 0.15
116 70 0.06
117 6 0.00
118 416 0.33
119 9 0.01
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (114 bp):
AAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTCTACTCTGGCAAAAATAATCCATCAAGTGATGAATTCAGA
Found at i:1542912 original size:230 final size:230
Alignment explanation
Indices: 1542418--1543877 Score: 2394
Period size: 230 Copynumber: 6.4 Consensus size: 230
1542408 ATAGAATTAT
* *
1542418 GCAAAAAGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTT
* ** * * *
1542480 CTCATTATGAACT-T--CTCTGG-AAAAGCTGCTCCATCAAGTGATGGATT-TGAGCAAAAGGTT
66 CTCATTATGAACTCTACCTCTGGCAAAA-ATAATCCATCAAGTGATGAATTCAGA-AAAAAGGTT
* *
1542540 GAACAAATTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACC
129 GAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA-C
*
1542605 TTTTCTGGCAAAAATAATCCATCAAGTGATGAATTCAGA
193 TTCTCTGG-AAAAATAATCCATCAAGTGATGAATTCAGA
1542644 -CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTT
1542708 CTCATTATGAACTCTACCTCTGGCAAAAATAATCCATCAAGTGATGAATTCAGAAAAAAGGTTGA
66 CTCATTATGAACTCTACCTCTGGCAAAAATAATCCATCAAGTGATGAATTCAGAAAAAAGGTTGA
*
1542773 ACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGGACTTC
131 ACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTC
1542838 TCTGGCAAAAATAATCCATCAAGTGATGAATTCAGA
196 TCTGG-AAAAATAATCCATCAAGTGATGAATTCAGA
1542874 -CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTT
1542938 CTCATTATGAACTCTACCTCTGGCAAAAATAATCCATCAAGTGATGAATTCAGAAAAAAGGTTGA
66 CTCATTATGAACTCTACCTCTGGCAAAAATAATCCATCAAGTGATGAATTCAGAAAAAAGGTTGA
1543003 ACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTC
131 ACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTC
* * * * *
1543068 TCTGGAAAAGTTGATTCATCAAGTGATGGATT-TGA
196 TCTGGAAAA-ATAATCCATCAAGTGATGAATTCAGA
*
1543103 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTT
1543168 CTCATTATGAACTCTACCTCTGGCAAAAATAATCCATCAAGTGATGAATTCAGAAAAAAGGTTGA
66 CTCATTATGAACTCTACCTCTGGCAAAAATAATCCATCAAGTGATGAATTCAGAAAAAAGGTTGA
*
1543233 ACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGGACTTC
131 ACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTC
1543298 TCTGGCAAAAATAATCCATCAAGTGATGAATTCAGA
196 TCTGG-AAAAATAATCCATCAAGTGATGAATTCAGA
1543334 -CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTT
1543398 CTCATTATGAACTCTACCTCTGGCAAAAATAATCCATCAAGTGATGAATTCAGAAAAAAGGTTGA
66 CTCATTATGAACTCTACCTCTGGCAAAAATAATCCATCAAGTGATGAATTCAGAAAAAAGGTTGA
1543463 ACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTC
131 ACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTC
* * * * *
1543528 TCTGGAAAAGTTGATTCATCAAGTGATGGATT-TGA
196 TCTGGAAAA-ATAATCCATCAAGTGATGAATTCAGA
*
1543563 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTT
*
1543628 CTCATTATGAACTCTACCTCTGGCAACAATAATCCATCAAGTGATGAATTCA-AACAAAAGGTTG
66 CTCATTATGAACTCTACCTCTGGCAAAAATAATCCATCAAGTGATGAATTCAGAA-AAAAGGTTG
*
1543692 AACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-T
130 AACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTT
** * * * *
1543756 CTACCTGGAAAGGCTGATCCAGCAAATGATGGATTCA-A
195 CT--CTGGAAA-AATAATCCATCAAGTGATGAATTCAGA
*
1543794 GTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTT
1543859 CTCATTATGAACTCTACCT
66 CTCATTATGAACTCTACCT
1543878 GGAAATACTG
Statistics
Matches: 1172, Mismatches: 43, Indels: 33
0.94 0.03 0.03
Matches are distributed among these distances:
225 51 0.04
228 21 0.02
229 18 0.02
230 870 0.74
231 206 0.18
232 6 0.01
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (230 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTT
CTCATTATGAACTCTACCTCTGGCAAAAATAATCCATCAAGTGATGAATTCAGAAAAAAGGTTGA
ACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTC
TCTGGAAAAATAATCCATCAAGTGATGAATTCAGA
Found at i:1544367 original size:22 final size:22
Alignment explanation
Indices: 1544342--1544396 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
1544332 CATAAAGTTT
*
1544342 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
*
1544364 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
1544386 TCATCTTTGAA
1 TCATCTTTGAA
1544397 GAGTGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:1544892 original size:54 final size:54
Alignment explanation
Indices: 1544768--1544968 Score: 243
Period size: 54 Copynumber: 3.8 Consensus size: 54
1544758 CACTGGTTCA
* * *
1544768 TAAAACATTTGACAATACATTCATCTTTTCTTGTGGTTTCTG-TC-GA-G-ATG
1 TAAAACATTTGACAACACATTCATCTTTTCTTGTGGCTTCTGCTCAGATGTTTG
*
1544818 TAAAACACTTGACAACACATTCATCCTTTTC-TGTGGCTTCTGCTCAGATGTTTG
1 TAAAACATTTGACAACACATTCAT-CTTTTCTTGTGGCTTCTGCTCAGATGTTTG
* * * **
1544872 TAAAACATTTGACAACACATTCATCATTTCTTGTGGTTTTTGCTCAGATGTTCA
1 TAAAACATTTGACAACACATTCATCTTTTCTTGTGGCTTCTGCTCAGATGTTTG
* *
1544926 TAAAGCGTTTGACAACACATTCATCCTTTTC-TGTGGCTTCTGC
1 TAAAACATTTGACAACACATTCAT-CTTTTCTTGTGGCTTCTGC
1544969 CAAGATTTCT
Statistics
Matches: 129, Mismatches: 15, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
50 32 0.25
51 8 0.06
52 2 0.02
53 6 0.05
54 76 0.59
55 5 0.04
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (54 bp):
TAAAACATTTGACAACACATTCATCTTTTCTTGTGGCTTCTGCTCAGATGTTTG
Found at i:1547269 original size:84 final size:84
Alignment explanation
Indices: 1547128--1547350 Score: 394
Period size: 84 Copynumber: 2.7 Consensus size: 84
1547118 ATTCCTACCG
* * *
1547128 AACCAGATCAGATAACTCAAAGAACATTTCCAAAAGATGCTATTGAACACATTATTCTTCCAAAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAAAT
*
1547193 TCAATGATTAG-TCTTGTTC
66 TCAATGATTAGTTC-TGTCC
1547212 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAAAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAAAT
1547277 TCAATGATTAGTTCTGTCC
66 TCAATGATTAGTTCTGTCC
1547296 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTAT
1547351 ATTTGTTCCA
Statistics
Matches: 134, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
84 132 0.99
85 2 0.01
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.28
Consensus pattern (84 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTATTCTTCCAAAT
TCAATGATTAGTTCTGTCC
Found at i:1556105 original size:14 final size:14
Alignment explanation
Indices: 1556080--1556115 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1556070 TGCTGTGTTC
1556080 TCTTTCTCTGTTTTT
1 TCTTT-TCTGTTTTT
1556095 TCTTTTCTGTTTTT
1 TCTTTTCTGTTTTT
1556109 T-TTTTCT
1 TCTTTTCT
1556116 TGTCGTTCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 6 0.29
14 10 0.48
15 5 0.24
ACGTcount: A:0.00, C:0.17, G:0.06, T:0.78
Consensus pattern (14 bp):
TCTTTTCTGTTTTT
Found at i:1556385 original size:27 final size:27
Alignment explanation
Indices: 1556349--1556439 Score: 164
Period size: 27 Copynumber: 3.4 Consensus size: 27
1556339 GCAGTGAGGC
**
1556349 GGCGGCTGGGATTCTTAAAGCATCAGA
1 GGCGGCTGGGATTCTGGAAGCATCAGA
1556376 GGCGGCTGGGATTCTGGAAGCATCAGA
1 GGCGGCTGGGATTCTGGAAGCATCAGA
1556403 GGCGGCTGGGATTCTGGAAGCATCAGA
1 GGCGGCTGGGATTCTGGAAGCATCAGA
1556430 GGCGGCTGGG
1 GGCGGCTGGG
1556440 GTGGCTAGGG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 62 1.00
ACGTcount: A:0.21, C:0.19, G:0.42, T:0.19
Consensus pattern (27 bp):
GGCGGCTGGGATTCTGGAAGCATCAGA
Found at i:1556564 original size:3 final size:3
Alignment explanation
Indices: 1556556--1556670 Score: 140
Period size: 3 Copynumber: 37.7 Consensus size: 3
1556546 TTATTTATTA
* * *
1556556 AAT AAT AAT ATAT AAT ATT GAT AAT AAT AAT AAT AAAT AAT GAT AAT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
* * *
1556603 AAT AAT AAT TAT TAT AAT AAT AAT AAT AAT ACT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
**
1556651 TTT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
1556671 ATTTAAATGA
Statistics
Matches: 96, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
3 90 0.94
4 6 0.06
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:1558067 original size:172 final size:172
Alignment explanation
Indices: 1557781--1558126 Score: 674
Period size: 172 Copynumber: 2.0 Consensus size: 172
1557771 GCACCAAGGC
1557781 TTCTTTATGGCAGCTCATAAGCATGAATCGTTTGGATGAAAAAGGCCAAGCTAAAAAATGCTTGA
1 TTCTTTATGGCAGCTCATAAGCATGAATCGTTTGGATGAAAAAGGCCAAGCTAAAAAATGCTTGA
1557846 TCAAGTGGAAAGGACCGACGAAAATCAATAGGATTTACGGGGATCGGCTCGATGATACGCCGTTG
66 TCAAGTGGAAAGGACCGACGAAAATCAATAGGATTTACGGGGATCGGCTCGATGATACGCCGTTG
*
1557911 GCGCACAATTTGGCGAGTCGGGTGGAAAGCTGAGTTTCGAGT
131 GCGCACAATTTGGCCAGTCGGGTGGAAAGCTGAGTTTCGAGT
1557953 TTCTTTATGGCAGCTCATAAGCATGAATCGTTTGGATGAAAAAGGCCAAGCTAAAAAATGCTTGA
1 TTCTTTATGGCAGCTCATAAGCATGAATCGTTTGGATGAAAAAGGCCAAGCTAAAAAATGCTTGA
1558018 TCAAGTGGAAAGGACCGACGAAAATCAATAGGATTTACGGGGATCGGCTCGATGATACGCCGTTG
66 TCAAGTGGAAAGGACCGACGAAAATCAATAGGATTTACGGGGATCGGCTCGATGATACGCCGTTG
*
1558083 GCGCACAATTTGGCCAGTCGGGTGGAGAGCTGAGTTTCGAGT
131 GCGCACAATTTGGCCAGTCGGGTGGAAAGCTGAGTTTCGAGT
1558125 TT
1 TT
1558127 AAAGAGCAGG
Statistics
Matches: 172, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
172 172 1.00
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.24
Consensus pattern (172 bp):
TTCTTTATGGCAGCTCATAAGCATGAATCGTTTGGATGAAAAAGGCCAAGCTAAAAAATGCTTGA
TCAAGTGGAAAGGACCGACGAAAATCAATAGGATTTACGGGGATCGGCTCGATGATACGCCGTTG
GCGCACAATTTGGCCAGTCGGGTGGAAAGCTGAGTTTCGAGT
Found at i:1560155 original size:32 final size:35
Alignment explanation
Indices: 1560100--1560172 Score: 98
Period size: 33 Copynumber: 2.2 Consensus size: 35
1560090 AATATATTAA
*
1560100 AATTTTAAAATAATTAAAATAATAT-ATTTATTAT
1 AATTTTAAAATAATTAAAATAATATGATTTATAAT
* *
1560134 -ATTTTAAAA-AGTTAAATTAATATGATTTATAAT
1 AATTTTAAAATAATTAAAATAATATGATTTATAAT
1560167 AATTTT
1 AATTTT
1560173 TATGTTTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 12 0.35
33 17 0.50
34 5 0.15
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (35 bp):
AATTTTAAAATAATTAAAATAATATGATTTATAAT
Found at i:1560218 original size:23 final size:23
Alignment explanation
Indices: 1560172--1560216 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
1560162 ATAATAATTT
1560172 TTATGTTTTAATAATATAAAATA
1 TTATGTTTTAATAATATAAAATA
*
1560195 TTAT-TTTTAA-AATATTAAATA
1 TTATGTTTTAATAATATAAAATA
1560216 T
1 T
1560217 ATATATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.52
22 6 0.29
23 4 0.19
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
TTATGTTTTAATAATATAAAATA
Found at i:1560220 original size:2 final size:2
Alignment explanation
Indices: 1560213--1560251 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1560203 AAAATATTAA
1560213 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1560252 AATTAATCGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1567660 original size:17 final size:17
Alignment explanation
Indices: 1567628--1567672 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
1567618 AGAAATATGT
*
1567628 CTGGTGGGTCACCAGTTG
1 CTGGCGGGT-ACCAGTTG
1567646 CTGGCGGGTACCAGTTG
1 CTGGCGGGTACCAGTTG
1567663 CTGGCGGGTA
1 CTGGCGGGTA
1567673 TGTGAGGCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 18 0.69
18 8 0.31
ACGTcount: A:0.11, C:0.22, G:0.42, T:0.24
Consensus pattern (17 bp):
CTGGCGGGTACCAGTTG
Found at i:1574297 original size:19 final size:20
Alignment explanation
Indices: 1574273--1574314 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1574263 CTTCTATTTT
*
1574273 TAATAA-AATTAGCCCTAAA
1 TAATAATAATTAACCCTAAA
*
1574292 TAATAATACTTAACCCTAAA
1 TAATAATAATTAACCCTAAA
1574312 TAA
1 TAA
1574315 GTACCGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.52, C:0.17, G:0.02, T:0.29
Consensus pattern (20 bp):
TAATAATAATTAACCCTAAA
Found at i:1575455 original size:2 final size:2
Alignment explanation
Indices: 1575448--1575532 Score: 161
Period size: 2 Copynumber: 42.5 Consensus size: 2
1575438 TTGGTTCTCA
*
1575448 AT AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1575490 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1575532 A
1 A
1575533 ATGAGTTGTT
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1583077 original size:14 final size:14
Alignment explanation
Indices: 1583055--1583096 Score: 75
Period size: 14 Copynumber: 3.0 Consensus size: 14
1583045 CATATCATAA
*
1583055 CAACCAAAATCCAT
1 CAACTAAAATCCAT
1583069 CAACTAAAATCCAT
1 CAACTAAAATCCAT
1583083 CAACTAAAATCCAT
1 CAACTAAAATCCAT
1583097 TAAGTCATCG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (14 bp):
CAACTAAAATCCAT
Found at i:1593965 original size:26 final size:27
Alignment explanation
Indices: 1593936--1593989 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 27
1593926 ATCTAAAATT
1593936 TAAAATAATAAAATTGAAA-TAA-TTCA
1 TAAAA-AATAAAATTGAAACTAACTTCA
* *
1593962 TAAAAAATTAAATTTAAACTAACTTCA
1 TAAAAAATAAAATTGAAACTAACTTCA
1593989 T
1 T
1593990 TGACTGGTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 11 0.46
26 8 0.33
27 5 0.21
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.33
Consensus pattern (27 bp):
TAAAAAATAAAATTGAAACTAACTTCA
Found at i:1612902 original size:14 final size:14
Alignment explanation
Indices: 1612883--1612912 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1612873 AATGAAATAA
1612883 ATTTAGGATTTATG
1 ATTTAGGATTTATG
*
1612897 ATTTAGGGTTTATG
1 ATTTAGGATTTATG
1612911 AT
1 AT
1612913 AGTTAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (14 bp):
ATTTAGGATTTATG
Found at i:1627089 original size:50 final size:50
Alignment explanation
Indices: 1627016--1627110 Score: 145
Period size: 50 Copynumber: 1.9 Consensus size: 50
1627006 TAACCATATC
*
1627016 GATTCCATTATAGACCTTCAGGGATATTTTAGACATGTTGATTTCGGATG
1 GATTCCATTATAGACCTTCAGGGATATTTCAGACATGTTGATTTCGGATG
* ** *
1627066 GATTTCATTATAGGTCTTTAGGGATATTTCAGACATGTTGATTTC
1 GATTCCATTATAGACCTTCAGGGATATTTCAGACATGTTGATTTC
1627111 ATGATCAGCA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.41
Consensus pattern (50 bp):
GATTCCATTATAGACCTTCAGGGATATTTCAGACATGTTGATTTCGGATG
Found at i:1636262 original size:14 final size:14
Alignment explanation
Indices: 1636245--1636276 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1636235 ATTTCAACCG
1636245 TCTATTTTCACTCA
1 TCTATTTTCACTCA
*
1636259 TCTATTTTCACTGA
1 TCTATTTTCACTCA
1636273 TCTA
1 TCTA
1636277 AGGTGTAAAA
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:0.22, C:0.25, G:0.03, T:0.50
Consensus pattern (14 bp):
TCTATTTTCACTCA
Found at i:1637061 original size:3 final size:3
Alignment explanation
Indices: 1637055--1637081 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1637045 GCTCAAGGAG
1637055 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1637082 ATGGAGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1638597 original size:72 final size:69
Alignment explanation
Indices: 1638448--1638600 Score: 177
Period size: 72 Copynumber: 2.2 Consensus size: 69
1638438 TAACTTTTTT
* * * * *
1638448 TTATAAATTATAGTTATTAAATAAAAAAATTATTTATTTCATTAACAAAAGTAATAATACATAAA
1 TTATAAATTATAGTTAATAAATAAAAAAATTAATTATTCCATTAACAAAACTAATAATACACAAA
1638513 AATG
66 AATG
1638517 TTATAAATTATAGTTAATAAA-AAATTAATAATTAGATT-TTCCATTAACAAAATTCTAA-AATA
1 TTATAAATTATAGTTAATAAATAAA--AA-AATTA-ATTATTCCATTAACAAAA--CTAATAATA
*
1638579 TACAAAAATG
60 CACAAAAATG
1638589 TTATAAATTATA
1 TTATAAATTATA
1638601 TTCAAACATA
Statistics
Matches: 72, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
68 3 0.04
69 20 0.28
70 2 0.03
71 18 0.25
72 26 0.36
73 3 0.04
ACGTcount: A:0.53, C:0.05, G:0.04, T:0.38
Consensus pattern (69 bp):
TTATAAATTATAGTTAATAAATAAAAAAATTAATTATTCCATTAACAAAACTAATAATACACAAA
AATG
Found at i:1639300 original size:20 final size:22
Alignment explanation
Indices: 1639255--1639300 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 22
1639245 ATATCACGAT
*
1639255 TTAATTGGAGATTAAATTTATT
1 TTAATTGGAGATTAAATTTATA
1639277 TTAATT-GA-ATTAAA-TTATGA
1 TTAATTGGAGATTAAATTTAT-A
1639297 TTAA
1 TTAA
1639301 AATGATAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 4 0.18
20 10 0.45
21 2 0.09
22 6 0.27
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (22 bp):
TTAATTGGAGATTAAATTTATA
Found at i:1641020 original size:25 final size:25
Alignment explanation
Indices: 1640992--1641039 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1640982 CTCCAAAATA
* *
1640992 CAAATACAAATAAGAGTTTATGACT
1 CAAATAAAAATAAGAGTCTATGACT
*
1641017 CAAATAAAAATAAGGGTCTATGA
1 CAAATAAAAATAAGAGTCTATGA
1641040 TAGTACATGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.25
Consensus pattern (25 bp):
CAAATAAAAATAAGAGTCTATGACT
Found at i:1644141 original size:26 final size:24
Alignment explanation
Indices: 1644095--1644142 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 24
1644085 AATATTATAA
1644095 AATATATTAATTATTTATTAAAGT
1 AATATATTAATTATTTATTAAAGT
1644119 AATAGTATTATATTATATT-TTAAA
1 AATA-TATTA-ATTAT-TTATTAAA
1644143 AAGTATTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 4 0.19
25 5 0.24
26 10 0.48
27 2 0.10
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (24 bp):
AATATATTAATTATTTATTAAAGT
Found at i:1644225 original size:24 final size:26
Alignment explanation
Indices: 1644197--1644278 Score: 73
Period size: 27 Copynumber: 3.2 Consensus size: 26
1644187 GGATTATTAA
1644197 ATTATTC-TTA-AATACATAAATAAT
1 ATTATTCATTATAATACATAAATAAT
* *
1644221 ATTATTCATTATTAATACTTTAATAAT
1 ATTATTCATTA-TAATACATAAATAAT
*
1644248 ATTATT-TTTATGAAATTA-ATAAATAAT
1 ATTATTCATTAT--AA-TACATAAATAAT
1644275 ATTA
1 ATTA
1644279 ATTTTATTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
24 7 0.15
25 4 0.09
26 3 0.06
27 31 0.66
28 2 0.04
ACGTcount: A:0.46, C:0.05, G:0.01, T:0.48
Consensus pattern (26 bp):
ATTATTCATTATAATACATAAATAAT
Found at i:1644322 original size:54 final size:53
Alignment explanation
Indices: 1644206--1644322 Score: 128
Period size: 54 Copynumber: 2.2 Consensus size: 53
1644196 AATTATTCTT
* *** *
1644206 AAATACATAAATAATATTATTCATTATTAATACTTTAATAATATTATTTTTATGA
1 AAATA-ATAAATAATATTATT-ATTATTAATAATTTAATAATATTATTAAAATAA
* *
1644261 AATTAATAAATAATATTAATT-TTATTAATAATTTATTATATATTATTAAAATAA
1 AAATAATAAATAATATT-ATTATTATTAATAATTTAATA-ATATTATTAAAATAA
1644315 AAATAATA
1 AAATAATA
1644323 TCTTATTATA
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
53 15 0.29
54 30 0.58
55 7 0.13
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (53 bp):
AAATAATAAATAATATTATTATTATTAATAATTTAATAATATTATTAAAATAA
Found at i:1646050 original size:17 final size:17
Alignment explanation
Indices: 1646028--1646061 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1646018 TATGTTAAGA
1646028 GACTAATTTATAAAATT
1 GACTAATTTATAAAATT
1646045 GACTAATTTATAAAATT
1 GACTAATTTATAAAATT
1646062 TTAGAATGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (17 bp):
GACTAATTTATAAAATT
Found at i:1647984 original size:36 final size:39
Alignment explanation
Indices: 1647940--1648013 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 39
1647930 TACAACATTC
* *
1647940 CCAGTAATC-ATATT-CC-CTGGTAATTTTACATTCCCA
1 CCAGTAATCTACATTCCCACTGGTAATCTTACATTCCCA
1647976 CCAGTAATCTTACATTCCCACTGGTAATCTTACATTCC
1 CCAGTAATC-TACATTCCCACTGGTAATCTTACATTCC
1648014 GTGAACCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 9 0.28
38 4 0.12
39 2 0.06
40 17 0.53
ACGTcount: A:0.27, C:0.30, G:0.08, T:0.35
Consensus pattern (39 bp):
CCAGTAATCTACATTCCCACTGGTAATCTTACATTCCCA
Found at i:1647988 original size:20 final size:20
Alignment explanation
Indices: 1647959--1648013 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
1647949 ATATTCCCTG
*
1647959 GTAATTTTACATTCCCACCA
1 GTAATCTTACATTCCCACCA
**
1647979 GTAATCTTACATTCCCACTG
1 GTAATCTTACATTCCCACCA
1647999 GTAATCTTACATTCC
1 GTAATCTTACATTCC
1648014 GTGAACCAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.27, C:0.29, G:0.07, T:0.36
Consensus pattern (20 bp):
GTAATCTTACATTCCCACCA
Found at i:1655393 original size:2 final size:2
Alignment explanation
Indices: 1655379--1655541 Score: 74
Period size: 2 Copynumber: 84.5 Consensus size: 2
1655369 CGTCCCTGGG
* * *
1655379 GA GA GA G- GA -A GA GA GA GA -A TGA GG GA GA GT GA GA GA GA CA
1 GA GA GA GA GA GA GA GA GA GA GA -GA GA GA GA GA GA GA GA GA GA
* * * *
1655419 GA G- GA GG GA GA TGA -A GA TA GA GA GG GG GA GA GA GA GA GA TG-
1 GA GA GA GA GA GA -GA GA GA GA GA GA GA GA GA GA GA GA GA GA -GA
* * * * * * *
1655460 GA GG GA GA GG GA GA GA GA GG GG GA GA GA AA GG GA GA G- GG GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* * * *
1655501 GA GA GA GA GG GA -A G- GA GA GA GA GA GA GG GG GA GT GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1655541 G
1 G
1655542 CCTCAGGATT
Statistics
Matches: 120, Mismatches: 29, Indels: 24
0.69 0.17 0.14
Matches are distributed among these distances:
1 9 0.08
2 107 0.89
3 4 0.03
ACGTcount: A:0.40, C:0.01, G:0.56, T:0.04
Consensus pattern (2 bp):
GA
Found at i:1655467 original size:18 final size:17
Alignment explanation
Indices: 1655379--1655541 Score: 115
Period size: 16 Copynumber: 9.3 Consensus size: 17
1655369 CGTCCCTGGG
*
1655379 GAGAGAGGA-AGAGAGA
1 GAGAGAGGAGGGAGAGA
1655395 GA-ATGAGGGAGAGTGAGAGA
1 GAGA-GA-GGAG-G-GAGAGA
*
1655415 GACAGAGGAGGGAGATGAA
1 GAGAGAGGAGGGAGA-G-A
1655434 GATAGAGAGG-GGGAGAGA
1 G--AGAGAGGAGGGAGAGA
1655452 GAGAGATGGAGGGAGAGGGA
1 GAGAGA-GGAGGGAGA--GA
1655472 GAGAGAGG-GGGAGAGA
1 GAGAGAGGAGGGAGAGA
* *
1655488 AAGGGA-GAGGG-GAGA
1 GAGAGAGGAGGGAGAGA
*
1655503 GAGAGAGGGAAGGAGAGA
1 GAGAGA-GGAGGGAGAGA
*
1655521 GAGAGAGG-GGGAGTGA
1 GAGAGAGGAGGGAGAGA
1655537 GAGAG
1 GAGAG
1655542 CCTCAGGATT
Statistics
Matches: 120, Mismatches: 9, Indels: 36
0.73 0.05 0.22
Matches are distributed among these distances:
15 10 0.08
16 29 0.24
17 15 0.12
18 26 0.22
19 9 0.08
20 24 0.20
21 7 0.06
ACGTcount: A:0.40, C:0.01, G:0.56, T:0.04
Consensus pattern (17 bp):
GAGAGAGGAGGGAGAGA
Found at i:1655538 original size:20 final size:20
Alignment explanation
Indices: 1655388--1655541 Score: 84
Period size: 20 Copynumber: 7.3 Consensus size: 20
1655378 GGAGAGAGGA
*
1655388 AGAGAGAGAATGAGGGAGAGTG
1 AGAGAGAG-A-GAGGGGGAGTG
*
1655410 AGAGAGACAGAGGAGGGAGATG
1 AGAGAGAGAGAGG-GGGAG-TG
* *
1655432 A-AGATAGAGAGGGGGAGAG
1 AGAGAGAGAGAGGGGGAGTG
*
1655451 AGAGAGATG-GAGGGAGAG-G
1 AGAGAGA-GAGAGGGGGAGTG
* *
1655470 -GAGAGAGAGGGGGAGAGAAAGGG
1 AGAGAGAGAGAGGG-G-G--AGTG
*
1655493 AGAGGGGAGAGAGAGAGGGAAG-G
1 AGA---GAGAGAGAG-GGGGAGTG
1655516 AGAGAGAGAGAGGGGGAGTG
1 AGAGAGAGAGAGGGGGAGTG
1655536 AGAGAG
1 AGAGAG
1655542 CCTCAGGATT
Statistics
Matches: 104, Mismatches: 12, Indels: 34
0.69 0.08 0.23
Matches are distributed among these distances:
17 1 0.01
18 10 0.10
19 8 0.08
20 38 0.37
21 15 0.14
22 12 0.12
23 5 0.05
24 4 0.04
27 9 0.09
28 2 0.02
ACGTcount: A:0.40, C:0.01, G:0.56, T:0.04
Consensus pattern (20 bp):
AGAGAGAGAGAGGGGGAGTG
Found at i:1658353 original size:20 final size:20
Alignment explanation
Indices: 1658328--1658405 Score: 138
Period size: 20 Copynumber: 3.9 Consensus size: 20
1658318 ATCATATTCC
* *
1658328 CTGGTAATTTTACATTTCCA
1 CTGGTAATCTTACATTCCCA
1658348 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
1658368 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
1658388 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1658406 GTGAACCAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.24, C:0.27, G:0.10, T:0.38
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1665805 original size:22 final size:22
Alignment explanation
Indices: 1665773--1665898 Score: 73
Period size: 22 Copynumber: 5.7 Consensus size: 22
1665763 TCCCTGGGGA
*
1665773 GAGAGGAAGAGAGAGAATGAGG
1 GAGAGGGAGAGAGAGAATGAGG
* * *
1665795 GAGAGTGAGAGAGACAGAGGAGG
1 GAGAGGGAGAGAGAGA-ATGAGG
* * * *
1665818 GAGATGAAGATAGAG-A-GGGG
1 GAGAGGGAGAGAGAGAATGAGG
* *
1665838 GAGAGAGAGAGATGGAGGGA-GAGG
1 GAGAGGGAGAGA--GA-GAATGAGG
1665862 GAGAGGGAGATG-GAG-ATGGAGG
1 GAGAGGGAGA-GAGAGAAT-GAGG
1665884 GAGAGGGAGAGAGAG
1 GAGAGGGAGAGAGAG
1665899 GGGGAGAGAA
Statistics
Matches: 79, Mismatches: 16, Indels: 18
0.70 0.14 0.16
Matches are distributed among these distances:
20 12 0.15
21 3 0.04
22 34 0.43
23 16 0.20
24 13 0.16
25 1 0.01
ACGTcount: A:0.39, C:0.01, G:0.55, T:0.06
Consensus pattern (22 bp):
GAGAGGGAGAGAGAGAATGAGG
Found at i:1665847 original size:6 final size:6
Alignment explanation
Indices: 1665771--1665958 Score: 72
Period size: 6 Copynumber: 32.2 Consensus size: 6
1665761 CGTCCCTGGG
* * *
1665771 GAGAGA G-GA-A GAGAGA GA-ATGA GGGAGA GTGAGA GAGACA GAG-GA
1 GAGAGA GAGAGA GAGAGA GAGA-GA GAGAGA GAGAGA GAGAGA GAGAGA
* * * * * *
1665816 GGGAGA TGA-AGA TAGAGA GGGGGA GAGAGA GAGATG- GAGGGA GAGGGA
1 GAGAGA -GAGAGA GAGAGA GAGAGA GAGAGA GAGA-GA GAGAGA GAGAGA
* * * * * * *
1665864 GAGGGA GATG-GA GATG-GA GGGAGA GGGAGA GAGAGG GGGAGA GAAAGG
1 GAGAGA GA-GAGA GA-GAGA GAGAGA GAGAGA GAGAGA GAGAGA GAGAGA
* * * * *
1665912 GAGAGG GAGAGA GAGAGG GA-AG- GAGAGA GAGAGG GGGAGT GAGAGA
1 GAGAGA GAGAGA GAGAGA GAGAGA GAGAGA GAGAGA GAGAGA GAGAGA
1665958 G
1 G
1665959 CCTCAGGATT
Statistics
Matches: 139, Mismatches: 30, Indels: 26
0.71 0.15 0.13
Matches are distributed among these distances:
4 4 0.03
5 15 0.11
6 116 0.83
7 4 0.03
ACGTcount: A:0.39, C:0.01, G:0.56, T:0.04
Consensus pattern (6 bp):
GAGAGA
Found at i:1665859 original size:18 final size:17
Alignment explanation
Indices: 1665771--1665958 Score: 99
Period size: 16 Copynumber: 11.1 Consensus size: 17
1665761 CGTCCCTGGG
*
1665771 GAGAGAGGA-AGAGAGA
1 GAGAGAGGAGGGAGAGA
1665787 GA-ATGAGGGAGAGTGAGAGA
1 GAGA-GA-GGAG-G-GAGAGA
*
1665807 GACAGAGGAGGGAGATGA
1 GAGAGAGGAGGGAGA-GA
* *
1665825 -AGATAGAGAGGGGGAGA
1 GAGAGAG-GAGGGAGAGA
* *
1665842 GAGAGA-GATGGAGGGA
1 GAGAGAGGAGGGAGAGA
*
1665858 GAGGGA-GAGGGAGATG-
1 GAGAGAGGAGGGAGA-GA
*
1665874 GAGA-TGGAGGGAGAGGGA
1 GAGAGAGGAGGGAGA--GA
1665892 GAGAGAGG-GGGAGAGA
1 GAGAGAGGAGGGAGAGA
* *
1665908 AAGGGA-GAGGGAGAGA
1 GAGAGAGGAGGGAGAGA
*
1665924 GAGAG-GGAAGGAGAGA
1 GAGAGAGGAGGGAGAGA
* *
1665940 GAGAGGGGGAGTGAGAGA
1 GAGA-GAGGAGGGAGAGA
1665958 G
1 G
1665959 CCTCAGGATT
Statistics
Matches: 132, Mismatches: 22, Indels: 34
0.70 0.12 0.18
Matches are distributed among these distances:
15 2 0.02
16 63 0.48
17 16 0.12
18 34 0.26
19 6 0.05
20 10 0.08
21 1 0.01
ACGTcount: A:0.39, C:0.01, G:0.56, T:0.04
Consensus pattern (17 bp):
GAGAGAGGAGGGAGAGA
Found at i:1665860 original size:28 final size:28
Alignment explanation
Indices: 1665829--1665958 Score: 92
Period size: 28 Copynumber: 4.7 Consensus size: 28
1665819 AGATGAAGAT
1665829 AGAGAGGGGGAGAGAGAGAGATGGAGGG
1 AGAGAGGGGGAGAGAGAGAGATGGAGGG
1665857 AGAG-GGAGAGG-GAGATG-GAGATGGAGGG
1 AGAGAGG-G-GGAGAGA-GAGAGATGGAGGG
* * * * *
1665885 AGAG-GGAGAGAGAGGGGGAGA-GAAAGG
1 AGAGAGG-GGGAGAGAGAGAGATGGAGGG
* * * *
1665912 -GAGAGGGAGAGAGAGAGGGAAGGAGAG
1 AGAGAGGGGGAGAGAGAGAGATGGAGGG
*
1665939 AGAGAGGGGGAGTGAGAGAG
1 AGAGAGGGGGAGAGAGAGAG
1665959 CCTCAGGATT
Statistics
Matches: 81, Mismatches: 13, Indels: 16
0.74 0.12 0.15
Matches are distributed among these distances:
26 14 0.17
27 13 0.16
28 51 0.63
29 3 0.04
ACGTcount: A:0.37, C:0.00, G:0.60, T:0.03
Consensus pattern (28 bp):
AGAGAGGGGGAGAGAGAGAGATGGAGGG
Found at i:1668985 original size:29 final size:29
Alignment explanation
Indices: 1668950--1669031 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
1668940 AAACTAAATT
1668950 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTACTTACATCATTTAATTAAA
* *
1668979 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTACTTACATCATTTAATTAAA
1669008 GATGTCATTACTTACATCAATTTA
1 GATGTCATTACTTACATC-ATTTA
1669032 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.43
Consensus pattern (29 bp):
GATGTCATTACTTACATCATTTAATTAAA
Found at i:1673214 original size:6 final size:6
Alignment explanation
Indices: 1673203--1673319 Score: 55
Period size: 6 Copynumber: 19.8 Consensus size: 6
1673193 TAGAGAGGGG
* * * *
1673203 GAGAGA GAGAGA TG-GAGG GAGAGG GAGATG- GAGATG- GAGGGA GAGGGA
1 GAGAGA GAGAGA -GAGAGA GAGAGA GAGA-GA GAGA-GA GAGAGA GAGAGA
* * * * * *
1673251 GAGAGA GGGGGA GAGAAA GGGAGA GGGAGA GAGAGA GGGA-A G-GAGA
1 GAGAGA GAGAGA GAGAGA GAGAGA GAGAGA GAGAGA GAGAGA GAGAGA
* * *
1673297 GAGAGA GAGGGG GAGTGA GAGAG
1 GAGAGA GAGAGA GAGAGA GAGAG
1673320 CCTCAGGATT
Statistics
Matches: 88, Mismatches: 17, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
4 2 0.02
5 6 0.07
6 78 0.89
7 2 0.02
ACGTcount: A:0.38, C:0.00, G:0.59, T:0.03
Consensus pattern (6 bp):
GAGAGA
Found at i:1673224 original size:18 final size:17
Alignment explanation
Indices: 1673194--1673319 Score: 109
Period size: 16 Copynumber: 7.2 Consensus size: 17
1673184 TGTTGGATAT
1673194 AGAGAGG-GGGAGAGAG
1 AGAGAGGAGGGAGAGAG
1673210 AGAGATGGAGGGAGAGGGAG
1 AGAGA-GGAGGGAGA--GAG
1673230 ATGGAGATGGAGGGAGAGGGAG
1 A--GAGA-GGAGGGAGA--GAG
*
1673252 AGAGAGG-GGGAGAGAA
1 AGAGAGGAGGGAGAGAG
*
1673268 AGGGA-GAGGGAGAGAG
1 AGAGAGGAGGGAGAGAG
*
1673284 AGAG-GGAAGGAGAGAG
1 AGAGAGGAGGGAGAGAG
*
1673300 AGAGAGG-GGGAGTGAG
1 AGAGAGGAGGGAGAGAG
1673316 AGAG
1 AGAG
1673320 CCTCAGGATT
Statistics
Matches: 94, Mismatches: 7, Indels: 18
0.79 0.06 0.15
Matches are distributed among these distances:
15 1 0.01
16 47 0.50
17 4 0.04
18 12 0.13
19 2 0.02
20 8 0.09
22 20 0.21
ACGTcount: A:0.37, C:0.00, G:0.60, T:0.03
Consensus pattern (17 bp):
AGAGAGGAGGGAGAGAG
Found at i:1673248 original size:28 final size:26
Alignment explanation
Indices: 1673195--1673301 Score: 82
Period size: 26 Copynumber: 4.2 Consensus size: 26
1673185 GTTGGATATA
*
1673195 GAGAGGGGGAGAGAGA-GAGATGGAGG
1 GAGAGGGAGAGAGAGAGGAGA-GGAGG
* *
1673221 GAGAGGGAGA-TG-GA-GA-TGGAGG
1 GAGAGGGAGAGAGAGAGGAGAGGAGG
* *
1673243 GAGAGGGAGAGAGAGGGGGAGAGAAAGG
1 GAGAGGGAGAGAGA-GAGGAGAG-GAGG
*
1673271 GAGAGGGAGAGAGAGAGG-GAAGGAGA
1 GAGAGGGAGAGAGAGAGGAG-AGGAGG
1673297 GAGAG
1 GAGAG
1673302 AGAGGGGGAG
Statistics
Matches: 64, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
22 15 0.23
23 1 0.02
24 4 0.06
25 2 0.03
26 19 0.30
27 6 0.09
28 17 0.27
ACGTcount: A:0.37, C:0.00, G:0.60, T:0.03
Consensus pattern (26 bp):
GAGAGGGAGAGAGAGAGGAGAGGAGG
Found at i:1673263 original size:22 final size:22
Alignment explanation
Indices: 1673205--1673307 Score: 102
Period size: 22 Copynumber: 4.6 Consensus size: 22
1673195 GAGAGGGGGA
*
1673205 GAGAGAGAGATGGAGGGAGAGG
1 GAGAGAGAGAGGGAGGGAGAGG
*
1673227 GAGATG-GAGATGGAGGGAGAGG
1 GAGA-GAGAGAGGGAGGGAGAGG
* * *
1673249 GAGAGAGAGGGGGAGAGAAAGG
1 GAGAGAGAGAGGGAGGGAGAGG
*
1673271 GAGAGGGAGAGAGAGAGGGA-AGG
1 GAGA--GAGAGAGGGAGGGAGAGG
1673294 AGAGAGAGAGAGGG
1 -GAGAGAGAGAGGG
1673308 GGAGTGAGAG
Statistics
Matches: 68, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
21 1 0.01
22 48 0.71
23 4 0.06
24 15 0.22
ACGTcount: A:0.38, C:0.00, G:0.59, T:0.03
Consensus pattern (22 bp):
GAGAGAGAGAGGGAGGGAGAGG
Found at i:1674344 original size:10 final size:10
Alignment explanation
Indices: 1674317--1674410 Score: 57
Period size: 10 Copynumber: 9.2 Consensus size: 10
1674307 TGGATATAGA
* *
1674317 GAGGGGGAGA
1 GAGGGAGAGG
* *
1674327 GAGAGAGATG
1 GAGGGAGAGG
1674337 GAGGGAGAGG
1 GAGGGAGAGG
* *
1674347 GAGATAGAGATG
1 GAG--GGAGAGG
1674359 GAGGGAGAGG
1 GAGGGAGAGG
*
1674369 GAGAGAGAGG
1 GAGGGAGAGG
*
1674379 G-GGG-GAGA
1 GAGGGAGAGG
*
1674387 AAGGGAGAGG
1 GAGGGAGAGG
1674397 GAGAGAGAGAGG
1 GAG-G-GAGAGG
1674409 GA
1 GA
1674411 ATGAGCTTTC
Statistics
Matches: 62, Mismatches: 16, Indels: 10
0.70 0.18 0.11
Matches are distributed among these distances:
8 3 0.05
9 5 0.08
10 37 0.60
11 1 0.02
12 16 0.26
ACGTcount: A:0.36, C:0.00, G:0.61, T:0.03
Consensus pattern (10 bp):
GAGGGAGAGG
Found at i:1674355 original size:22 final size:22
Alignment explanation
Indices: 1674325--1674377 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
1674315 GAGAGGGGGA
1674325 GAGAGAGAGATGGAGGGAGAGG
1 GAGAGAGAGATGGAGGGAGAGG
*
1674347 GAGATAGAGATGGAGGGAGAGG
1 GAGAGAGAGATGGAGGGAGAGG
1674369 GAGAGAGAG
1 GAGAGAGAG
1674378 GGGGGGAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.57, T:0.06
Consensus pattern (22 bp):
GAGAGAGAGATGGAGGGAGAGG
Found at i:1675412 original size:4 final size:4
Alignment explanation
Indices: 1675405--1675429 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1675395 AATATATATA
1675405 TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG T
1675430 TGAGATCAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:1676260 original size:8 final size:8
Alignment explanation
Indices: 1676247--1676274 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
1676237 GCATGATTTT
1676247 AGTAAAGG
1 AGTAAAGG
1676255 AGTAAAGG
1 AGTAAAGG
1676263 AGTAAAGG
1 AGTAAAGG
1676271 AGTA
1 AGTA
1676275 TGGTATTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.36, T:0.14
Consensus pattern (8 bp):
AGTAAAGG
Found at i:1676897 original size:14 final size:15
Alignment explanation
Indices: 1676878--1676915 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
1676868 ATAATTCGGA
*
1676878 TATTTTATAA-TATT
1 TATTTTATAACTATG
1676892 TATTTTATAACTATG
1 TATTTTATAACTATG
1676907 TATATTTAT
1 TAT-TTTAT
1676916 TTTAAATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.48
15 6 0.29
16 5 0.24
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (15 bp):
TATTTTATAACTATG
Found at i:1677523 original size:19 final size:19
Alignment explanation
Indices: 1677489--1677537 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
1677479 TTTTCTATTG
*
1677489 AAAATTTGTTTTCGCCCCCT
1 AAAATTT-TATTCGCCCCCT
*
1677509 AAAATTTTATTCGCCCCTT
1 AAAATTTTATTCGCCCCCT
*
1677528 GAAATTTTAT
1 AAAATTTTAT
1677538 AAGTTCAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.27, C:0.22, G:0.08, T:0.43
Consensus pattern (19 bp):
AAAATTTTATTCGCCCCCT
Found at i:1679377 original size:19 final size:19
Alignment explanation
Indices: 1679353--1679389 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1679343 ATTTTTTTTG
* *
1679353 AAAATTATTTTTTAAAAAT
1 AAAATTAATATTTAAAAAT
1679372 AAAATTAATATTTAAAAA
1 AAAATTAATATTTAAAAA
1679390 AACTTTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAATTAATATTTAAAAAT
Found at i:1680948 original size:3 final size:3
Alignment explanation
Indices: 1680940--1681008 Score: 138
Period size: 3 Copynumber: 23.0 Consensus size: 3
1680930 TTTTACTTTA
1680940 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1680988 AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT
1681009 GGTAAACAAC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1681172 original size:31 final size:31
Alignment explanation
Indices: 1681095--1681183 Score: 106
Period size: 31 Copynumber: 2.9 Consensus size: 31
1681085 GTCACCAATG
* * * *
1681095 TTATCAATTTGTATCAAATTGGTTACTAACA
1 TTATCGATTTGTAACAAAATGGTCACTAACA
* * *
1681126 TTATCGATTTATAACAAAATGGTCATTAACG
1 TTATCGATTTGTAACAAAATGGTCACTAACA
*
1681157 TTATTGATTTGTAACAAAATGGTCACT
1 TTATCGATTTGTAACAAAATGGTCACT
1681184 CCACCATTAT
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.39
Consensus pattern (31 bp):
TTATCGATTTGTAACAAAATGGTCACTAACA
Found at i:1683432 original size:31 final size:31
Alignment explanation
Indices: 1683397--1683492 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
1683387 TATTGGAGTT
*
1683397 AATGTCATACCTACGACGACGATAACTGTCA
1 AATGTCATACCTACGATGACGATAACTGTCA
1683428 AATGTCATACCTACGATGACGATAACTGTCA
1 AATGTCATACCTACGATGACGATAACTGTCA
*
1683459 AATGTCATATCTACGATGACGATAACTGTCA
1 AATGTCATACCTACGATGACGATAACTGTCA
1683490 AAT
1 AAT
1683493 TTATCTCTAG
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (31 bp):
AATGTCATACCTACGATGACGATAACTGTCA
Found at i:1683848 original size:16 final size:16
Alignment explanation
Indices: 1683827--1683860 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1683817 ATTTTGTCTC
* *
1683827 TACGTTTATTTTATTT
1 TACGTTGATATTATTT
1683843 TACGTTGATATTATTT
1 TACGTTGATATTATTT
1683859 TA
1 TA
1683861 ATTATTTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.06, G:0.09, T:0.62
Consensus pattern (16 bp):
TACGTTGATATTATTT
Found at i:1685137 original size:2 final size:2
Alignment explanation
Indices: 1685096--1685126 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1685086 TAAAGGGAGT
1685096 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1685127 TAGAAATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1690646 original size:67 final size:67
Alignment explanation
Indices: 1690534--1691003 Score: 665
Period size: 67 Copynumber: 7.0 Consensus size: 67
1690524 ACCTAAACTG
* * * *
1690534 ATTCAGCTTCAGCTTTTCGTTGTTGCTGTCTATCGTATAAAGGCCTTGCTCAGTTTGACATGAGC
1 ATTCAGCTTCAGCCTTTCGTTGTTGCTTTCGATCGTATAAAGGCCTTGCTCAGTGTGACATGAGC
1690599 TA
66 TA
* * * * *
1690601 ATTCAACTTCAGCCTTTCGTTGTTGCTTTCGATCGTACAAGGGCCTTCCTCAGTGTGGCA-GAAG
1 ATTCAGCTTCAGCCTTTCGTTGTTGCTTTCGATCGTATAAAGGCCTTGCTCAGTGTGACATG-AG
1690665 CTA
65 CTA
* * * * *
1690668 ATTCAACTTCAGCCTTTCGTTGTTGCTTTCAATCATATAAAGGCCTTGCTCAGTGTGATAGGAGC
1 ATTCAGCTTCAGCCTTTCGTTGTTGCTTTCGATCGTATAAAGGCCTTGCTCAGTGTGACATGAGC
1690733 TA
66 TA
* * * *
1690735 ATTCAGCTTCAACCTATCGTTGTTGCTATCGATCGTATAAAGGCCTTGCTCAGTGTGACTTGAGC
1 ATTCAGCTTCAGCCTTTCGTTGTTGCTTTCGATCGTATAAAGGCCTTGCTCAGTGTGACATGAGC
1690800 TA
66 TA
*
1690802 ATTCAGCTTCAGCCTTTCGTTGTTGCTTTCGATCATATAAAGGCCTTGCTCAGTGTGACATGAGC
1 ATTCAGCTTCAGCCTTTCGTTGTTGCTTTCGATCGTATAAAGGCCTTGCTCAGTGTGACATGAGC
1690867 TA
66 TA
* * * *
1690869 ATTCAGCTTCAGCCTTTTGTTGTTGCTTCCTA-CTGTATAAAGGCCTTGCTCAGTGTGGCATGAG
1 ATTCAGCTTCAGCCTTTCGTTGTTGCTTTCGATC-GTATAAAGGCCTTGCTCAGTGTGACATGAG
*
1690933 ATA
65 CTA
* * *
1690936 ATTCAGCTTCAGCCTTCCGTTGTTGATTTCGATCGTATAAAAGCCTTGCTCAGTGTGACATGAGC
1 ATTCAGCTTCAGCCTTTCGTTGTTGCTTTCGATCGTATAAAGGCCTTGCTCAGTGTGACATGAGC
1691001 TA
66 TA
1691003 A
1 A
1691004 CTGAGCATCA
Statistics
Matches: 355, Mismatches: 44, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
66 2 0.01
67 351 0.99
68 2 0.01
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (67 bp):
ATTCAGCTTCAGCCTTTCGTTGTTGCTTTCGATCGTATAAAGGCCTTGCTCAGTGTGACATGAGC
TA
Found at i:1691558 original size:41 final size:41
Alignment explanation
Indices: 1691481--1691561 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 41
1691471 GCCTGACTTT
* * *
1691481 TTTAACTAAACAGGCCAGGCCCATGCCTTTTTAAAAGCCTA
1 TTTAACTAAACAGGCCAGGCCCAGGCCTATTAAAAAGCCTA
* **
1691522 TTTAACTAAACAGGTCAGGCTTAGGCCTATTAAAAAGCCT
1 TTTAACTAAACAGGCCAGGCCCAGGCCTATTAAAAAGCCT
1691562 TATAAGCCTG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.27
Consensus pattern (41 bp):
TTTAACTAAACAGGCCAGGCCCAGGCCTATTAAAAAGCCTA
Found at i:1703369 original size:30 final size:30
Alignment explanation
Indices: 1703301--1703369 Score: 124
Period size: 29 Copynumber: 2.4 Consensus size: 30
1703291 ACCATGACCA
1703301 CATAA-CTATTTAAGTGGTTTTAATGTAGT
1 CATAAGCTATTTAAGTGGTTTTAATGTAGT
1703330 CAT-AGCTATTTAAGTGGTTTTAATGTAGT
1 CATAAGCTATTTAAGTGGTTTTAATGTAGT
1703359 CATAAGCTATT
1 CATAAGCTATT
1703370 ATAGAACAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
28 1 0.03
29 30 0.79
30 7 0.18
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.43
Consensus pattern (30 bp):
CATAAGCTATTTAAGTGGTTTTAATGTAGT
Found at i:1712908 original size:60 final size:60
Alignment explanation
Indices: 1712798--1712921 Score: 162
Period size: 60 Copynumber: 2.1 Consensus size: 60
1712788 CGAGTGACCG
* * *
1712798 TTTGATAACTTTTAATAGTTGAGGGACTTAATAAAATAACTCTCTATAGTCAATGGACTA
1 TTTGATAACTTTTAATAGTCGACGGACTTAATAAAATAACTCTCTATAGTCAAGGGACTA
* * *
1712858 TTTGATAACTTTTAGTAGTCGACGGACTTAATAAAATAGTA-TCT-TGTAGTCAGGGGACTA
1 TTTGATAACTTTTAATAGTCGACGGACTTAATAAAATA--ACTCTCTATAGTCAAGGGACTA
1712918 TTTG
1 TTTG
1712922 TGTAATTTGT
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
60 52 0.93
61 3 0.05
62 1 0.02
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (60 bp):
TTTGATAACTTTTAATAGTCGACGGACTTAATAAAATAACTCTCTATAGTCAAGGGACTA
Found at i:1714032 original size:96 final size:96
Alignment explanation
Indices: 1713868--1714064 Score: 322
Period size: 96 Copynumber: 2.1 Consensus size: 96
1713858 TGCGGTCAAG
* *
1713868 TGATAACGGTTTCGGATGGCACCAAAACCGCTATATAACAGCCGCTATTCCAACAGCGGATAGCT
1 TGATAACGGTTTCAGATGGCACCAAAACCACTATATAACAGCCGCTATTCCAACAGCGGATAGCT
1713933 ATTTAAATCCCTGCTCCTAATCACTTCATTT
66 ATTTAAATCCCTGCTCCTAATCACTTCATTT
* * * * * *
1713964 TGATAACGTTTTCAGATGGCACCAAAATCATTATATAACGGCCGCTATTCCAATAGCGGATCGCT
1 TGATAACGGTTTCAGATGGCACCAAAACCACTATATAACAGCCGCTATTCCAACAGCGGATAGCT
1714029 ATTTAAATCCCTGCTCCTAATCACTTCATTT
66 ATTTAAATCCCTGCTCCTAATCACTTCATTT
1714060 TGATA
1 TGATA
1714065 CTTGAGAGCA
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
96 93 1.00
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.30
Consensus pattern (96 bp):
TGATAACGGTTTCAGATGGCACCAAAACCACTATATAACAGCCGCTATTCCAACAGCGGATAGCT
ATTTAAATCCCTGCTCCTAATCACTTCATTT
Found at i:1732274 original size:2 final size:2
Alignment explanation
Indices: 1732267--1732324 Score: 82
Period size: 2 Copynumber: 29.0 Consensus size: 2
1732257 TGACCCTAAC
* *
1732267 AT AT AT AT AT AT AT AT CCT A- AC AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
1732309 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
1732325 GTATCCGTCA
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
1 1 0.02
2 49 0.96
3 1 0.02
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1732286 original size:22 final size:22
Alignment explanation
Indices: 1732261--1732324 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
1732251 GGGTATTGAC
1732261 CCTAACATATATATATATATAT
1 CCTAACATATATATATATATAT
1732283 CCTAACATATATATATATATAT
1 CCTAACATATATATATATATAT
* *
1732305 -AT-ATATATATATATATATAT
1 CCTAACATATATATATATATAT
1732325 GTATCCGTCA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
20 17 0.43
21 1 0.03
22 22 0.55
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (22 bp):
CCTAACATATATATATATATAT
Found at i:1733706 original size:31 final size:31
Alignment explanation
Indices: 1733628--1733730 Score: 99
Period size: 31 Copynumber: 3.4 Consensus size: 31
1733618 TTCATATAAG
*
1733628 TACCTAAAGTA--TTTTTTGGTCAAAATAAA
1 TACCTAAAGTATTTTTTTTGGTCAAAATAGA
**
1733657 TATATAAA-T-TTATCTTTTTGGTCAAAATAGA
1 TACCTAAAGTATT-T-TTTTTGGTCAAAATAGA
*
1733688 TACCTAAAGTATTTTTTTT-GTCAAAATAGG
1 TACCTAAAGTATTTTTTTTGGTCAAAATAGA
* *
1733718 TATCTAAAATATT
1 TACCTAAAGTATT
1733731 CGATTTTTTT
Statistics
Matches: 60, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
28 1 0.02
29 6 0.10
30 22 0.37
31 27 0.45
32 2 0.03
33 2 0.03
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.43
Consensus pattern (31 bp):
TACCTAAAGTATTTTTTTTGGTCAAAATAGA
Found at i:1733711 original size:30 final size:30
Alignment explanation
Indices: 1733628--1733730 Score: 109
Period size: 30 Copynumber: 3.4 Consensus size: 30
1733618 TTCATATAAG
*
1733628 TACCTAAAGTA-TTTTTTGGTCAAAATAAA
1 TACCTAAAGTATTTTTTTGGTCAAAATAGA
** * *
1733657 TATATAAATTTATCTTTTTGGTCAAAATAGA
1 TACCTAAA-GTATTTTTTTGGTCAAAATAGA
* *
1733688 TACCTAAAGTATTTTTTTTGTCAAAATAGG
1 TACCTAAAGTATTTTTTTGGTCAAAATAGA
* *
1733718 TATCTAAAATATT
1 TACCTAAAGTATT
1733731 CGATTTTTTT
Statistics
Matches: 59, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
29 6 0.10
30 31 0.53
31 22 0.37
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.43
Consensus pattern (30 bp):
TACCTAAAGTATTTTTTTGGTCAAAATAGA
Found at i:1734181 original size:17 final size:17
Alignment explanation
Indices: 1734154--1734186 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1734144 ACCCACCATT
1734154 ACCTCACCCACTCAAACA
1 ACCTCACCCACT-AAACA
1734172 ACCT-ACCCACTAAAC
1 ACCTCACCCACTAAAC
1734187 CACTACTCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 7 0.47
18 4 0.27
ACGTcount: A:0.39, C:0.48, G:0.00, T:0.12
Consensus pattern (17 bp):
ACCTCACCCACTAAACA
Found at i:1739568 original size:21 final size:20
Alignment explanation
Indices: 1739482--1739639 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
1739472 AAATGACCAA
**
1739482 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1739501 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1739521 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1739541 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
1739562 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1739583 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1739603 CAATAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
1739624 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1739640 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 42 0.41
21 44 0.43
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1739649 original size:20 final size:19
Alignment explanation
Indices: 1739607--1739780 Score: 105
Period size: 20 Copynumber: 8.7 Consensus size: 19
1739597 GATTTTCAAT
** *
1739607 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAA-CCGTA
*
1739627 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAAC-CGTA
* *
1739647 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCG-AACCGTA
***
1739667 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCG-AACCGTA
* *
1739687 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCG-AACCGTA
* *
1739707 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCG-AACCGTA
** * *
1739727 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAA-CCGT-A
*
1739748 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCG-AACCGTA
1739768 AATCGCAACGCGA
1 AATCGCAACGCGA
1739781 TATTTAAAGC
Statistics
Matches: 123, Mismatches: 26, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
19 2 0.02
20 105 0.85
21 15 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (19 bp):
AATCGCAACGCGAACCGTA
Found at i:1739670 original size:40 final size:39
Alignment explanation
Indices: 1739607--1739779 Score: 141
Period size: 40 Copynumber: 4.3 Consensus size: 39
1739597 GATTTTCAAT
* ** * *
1739607 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CGTA
* ***
1739647 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCGTA
* * *
1739687 AATCGCAATGCGTATCCGTATATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCGTA
* * * *
1739727 AATCGCAACG-ATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGT-ATCCGT-AAATCGCAACGCG-AACCGTA
1739768 AATCGCAACGCG
1 AATCGCAACGCG
1739780 ATATTTAAAG
Statistics
Matches: 109, Mismatches: 20, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
39 1 0.01
40 77 0.71
41 31 0.28
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (39 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACCGTA
Found at i:1739690 original size:60 final size:60
Alignment explanation
Indices: 1739607--1739779 Score: 186
Period size: 60 Copynumber: 2.9 Consensus size: 60
1739597 GATTTTCAAT
* *
1739607 AATCGCAACGCGAATATGAAAATCGCAACGCG-AACACATAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGAATAGGAAAATCGCAACGCGTAAC-CATAAATCGCAACGCGTATCCGTA
* * * * * * *
1739667 AATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTATATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATAGGAAAATCGCAACGCGTAACCATAAATCGCAACGCGTATCCGTA
** ** * *
1739727 AATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCG
1 AATCGCAACGCGAATA-GGAAAATCGCAACGCGTAACCATAAATCGCAACGCG
1739780 ATATTTAAAG
Statistics
Matches: 93, Mismatches: 18, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
60 60 0.65
61 33 0.35
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGAATAGGAAAATCGCAACGCGTAACCATAAATCGCAACGCGTATCCGTA
Found at i:1739761 original size:41 final size:38
Alignment explanation
Indices: 1739626--1739777 Score: 144
Period size: 40 Copynumber: 3.8 Consensus size: 38
1739616 GCGAATATGA
* * * *
1739626 AAATCGCAACGCG-AACACATAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATC-CGTAAATCGCAAC--GTATACAT
** * *
1739666 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAA--CGTATACAT
*
1739706 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACG-T-ATACAT
1739746 AAAATCGCAACGCGTATCCGTAAATCGCAACG
1 -AAATCGCAACGCGTATCCGTAAATCGCAACG
1739778 CGATATTTAA
Statistics
Matches: 96, Mismatches: 10, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
38 2 0.02
39 1 0.01
40 61 0.64
41 31 0.32
42 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.20
Consensus pattern (38 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGTATACAT
Found at i:1740200 original size:33 final size:33
Alignment explanation
Indices: 1740161--1740231 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1740151 TTCACTTAGA
*
1740161 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1740194 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1740227 TTTCA
1 TTTCA
1740232 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1740371 original size:14 final size:14
Alignment explanation
Indices: 1740352--1740405 Score: 63
Period size: 14 Copynumber: 3.6 Consensus size: 14
1740342 AGAATGACTG
1740352 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
1740366 TCGCAACGCGAAATGAAA
1 TCGCAA--CGAGA-G-AA
1740384 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
1740398 TCGCAACG
1 TCGCAACG
1740406 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 8 0.24
17 1 0.03
18 8 0.24
ACGTcount: A:0.41, C:0.24, G:0.26, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:1740387 original size:18 final size:16
Alignment explanation
Indices: 1740362--1740410 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
1740352 TCGCAACGAG
1740362 AGAATCGCAACGCGAA
1 AGAATCGCAACGCGAA
*
1740378 ATGAAATCGCAA--CGAG
1 A-G-AATCGCAACGCGAA
1740394 AGAATCGCAACGCGAA
1 AGAATCGCAACGCGAA
1740410 A
1 A
1740411 CCAAAATCGC
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 8 0.30
15 1 0.04
16 9 0.33
17 1 0.04
18 8 0.30
ACGTcount: A:0.45, C:0.22, G:0.24, T:0.08
Consensus pattern (16 bp):
AGAATCGCAACGCGAA
Found at i:1740439 original size:19 final size:19
Alignment explanation
Indices: 1740417--1740514 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
1740407 GAAACCAAAA
*
1740417 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1740436 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1740450 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1740469 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
1740483 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
1740502 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1740515 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1740458 original size:14 final size:14
Alignment explanation
Indices: 1740439--1740528 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1740429 TTTCATTTCG
1740439 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1740453 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1740472 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1740486 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
1740503 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
1740519 CGTTGCGATT
1 CGTTGCGATT
1740529 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1740464 original size:33 final size:33
Alignment explanation
Indices: 1740422--1740536 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1740412 CAAAATCGCA
1740422 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1740455 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
1740488 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1740521 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1740537 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1742391 original size:92 final size:93
Alignment explanation
Indices: 1742232--1742608 Score: 717
Period size: 92 Copynumber: 4.1 Consensus size: 93
1742222 TAGATTGCTT
*
1742232 AGTAAATTTATTCGGTTGCTGCCAATTCTGCT-AACTGTGTATTCTTTAACACTGTG-AATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1742295 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1742323 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1742387 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1742415 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1742479 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1742507 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1742572 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1742600 AGTAAATTT
1 AGTAAATTT
1742609 ATCCATTCAA
Statistics
Matches: 282, Mismatches: 1, Indels: 4
0.98 0.00 0.01
Matches are distributed among these distances:
91 31 0.11
92 208 0.74
93 43 0.15
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.47
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1742692 original size:19 final size:19
Alignment explanation
Indices: 1742652--1742780 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1742642 TAGTTTACTT
* *
1742652 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1742672 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1742691 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1742710 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
1742724 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
1742743 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
1742757 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1742776 TCGCA
1 TCGCA
1742781 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1742731 original size:33 final size:32
Alignment explanation
Indices: 1742688--1742780 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
1742678 CGCGAAACCA
**
1742688 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
1742720 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
1742753 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
1742781 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:1742778 original size:52 final size:52
Alignment explanation
Indices: 1742652--1742780 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
1742642 TAGTTTACTT
**
1742652 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
1742704 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
1742757 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
1742781 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:1742798 original size:19 final size:19
Alignment explanation
Indices: 1742776--1742910 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1742766 GAAACCAAAA
*
1742776 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1742795 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
1742811 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1742828 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1742844 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1742861 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
1742880 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1742900 TCGTGTTGCGA
1 TCGCGTTGCGA
1742911 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1742817 original size:14 final size:14
Alignment explanation
Indices: 1742798--1742854 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1742788 TTTCATTTCG
1742798 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1742812 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
1742829 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
1742845 CGTTGCGATT
1 CGTTGCGATT
1742855 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1742823 original size:33 final size:33
Alignment explanation
Indices: 1742781--1742873 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1742771 CAAAATCGCA
*
1742781 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
1742814 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1742847 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1742874 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:1744827 original size:14 final size:14
Alignment explanation
Indices: 1744808--1744843 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1744798 ATTGTTTAAT
1744808 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1744822 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1744836 TGATTTGT
1 TGATTTGT
1744844 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1745017 original size:20 final size:19
Alignment explanation
Indices: 1744949--1745031 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
1744939 CAAAATGACT
1744949 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1744968 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1744982 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1745001 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1745021 ATCGCAATGCG
1 ATCGCAATGCG
1745032 TTTATAATTT
Statistics
Matches: 56, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 21 0.38
20 19 0.34
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Done.