Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold19
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: 2266706
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 17655 characters in sequence are not A, C, G, or T
File 12 of 15
Found at i:1576470 original size:118 final size:118
Alignment explanation
Indices: 1576314--1576640 Score: 318
Period size: 118 Copynumber: 2.8 Consensus size: 118
1576304 GCAACTGAAT
* *
1576314 TGTGGGCTTTGAAAGGGTGCAACTGAATTGTGGGCTTTGAGAGAGGTTGCCACCGACTTGTGTGA
1 TGTGGGCTTTGAAAGGGTGCAACTGAATTGTGGACTTTGAGAGAGATTGCCACCGACTTGTG-G-
*
1576379 GCTTTAAG-GGGTGCCACTAACTTATGGGCTTTAAGAGAGGTTGCCATCGACTTG
64 GCTTTAAGAGGATGCCACTAACTTATGGGCTTTAAGAGAGGTTGCCATCGACTTG
* * *
1576433 TGTGGGCTTT-AAGGGGTGCCACTGACTTGTGGACTTTGAGAGAGATTGCCACCGACTTGTGGGC
1 TGTGGGCTTTGAAAGGGTGCAACTGAATTGTGGACTTTGAGAGAGATTGCCACCGACTTGTGGGC
* * *
1576497 TTTAAGAAGGATGCTACTGACTTATGGGCTTTGAA-A-AGG-TGTCAAT-GAC-T-
66 TTTAAG-AGGATGCCACTAACTTATGGGCTTT-AAGAGAGGTTG-CCATCGACTTG
* * * * * * ** * *
1576547 TATGGGCTTTGAAAGGATGCCACT-AACATGTGGGCTTCGA-A-AGGGTACCACTGACTTGTGGG
1 TGTGGGCTTTGAAAGGGTGCAACTGAA-TTGTGGACTTTGAGAGAGATTGCCACCGACTTGTGGG
* *
1576609 CTTTGAA-AGGATGCCACTGACTTGTGGGCTTT
65 CTTT-AAGAGGATGCCACTAACTTATGGGCTTT
1576641 GAAAAAGATG
Statistics
Matches: 179, Mismatches: 22, Indels: 21
0.81 0.10 0.09
Matches are distributed among these distances:
112 23 0.13
113 21 0.12
114 13 0.07
115 22 0.12
116 13 0.07
117 7 0.04
118 68 0.38
119 12 0.07
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.29
Consensus pattern (118 bp):
TGTGGGCTTTGAAAGGGTGCAACTGAATTGTGGACTTTGAGAGAGATTGCCACCGACTTGTGGGC
TTTAAGAGGATGCCACTAACTTATGGGCTTTAAGAGAGGTTGCCATCGACTTG
Found at i:1583835 original size:21 final size:20
Alignment explanation
Indices: 1583807--1583845 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1583797 CACATTTTTA
1583807 TCTAAATGTATCAATACATT
1 TCTAAATGTATCAATACATT
*
1583827 TCTAGAATGTATCGATACA
1 TCTA-AATGTATCAATACA
1583846 AGGTCCCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.36
Consensus pattern (20 bp):
TCTAAATGTATCAATACATT
Found at i:1591870 original size:33 final size:32
Alignment explanation
Indices: 1591828--1591890 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
1591818 CACATCCAGA
* *
1591828 TGTATCGATACATTATGCTTTGTATCAATACCT
1 TGTATCGATACATGAT-CATTGTATCAATACCT
*
1591861 TGTATCGATACATGATCATTGTATCGATAC
1 TGTATCGATACATGATCATTGTATCAATAC
1591891 TTACACAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 12 0.44
33 15 0.56
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATGATCATTGTATCAATACCT
Found at i:1591884 original size:19 final size:21
Alignment explanation
Indices: 1591860--1591914 Score: 71
Period size: 19 Copynumber: 2.8 Consensus size: 21
1591850 TATCAATACC
*
1591860 TTGTATCGATACATGA-TC-A
1 TTGTATCGATACATGACACAA
*
1591879 TTGTATCGATAC-TTACACAA
1 TTGTATCGATACATGACACAA
1591899 TTGTATCGATACATGA
1 TTGTATCGATACATGA
1591915 AACTAGGAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 2 0.07
19 13 0.43
20 13 0.43
21 2 0.07
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (21 bp):
TTGTATCGATACATGACACAA
Found at i:1593607 original size:15 final size:15
Alignment explanation
Indices: 1593587--1593621 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1593577 AACCATCAAA
1593587 GATGATGAAGATAAT
1 GATGATGAAGATAAT
*
1593602 GATGATGATGATAAT
1 GATGATGAAGATAAT
1593617 GATGA
1 GATGA
1593622 AGTTGTCTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (15 bp):
GATGATGAAGATAAT
Found at i:1598104 original size:13 final size:13
Alignment explanation
Indices: 1598086--1598125 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
1598076 ACAATGTTTT
1598086 TTGTATTGATACA
1 TTGTATTGATACA
1598099 TTGTATTGATACA
1 TTGTATTGATACA
*
1598112 TTGTATCGATACA
1 TTGTATTGATACA
1598125 T
1 T
1598126 GGGTTACTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.30, C:0.10, G:0.15, T:0.45
Consensus pattern (13 bp):
TTGTATTGATACA
Found at i:1600679 original size:32 final size:32
Alignment explanation
Indices: 1600642--1600717 Score: 134
Period size: 32 Copynumber: 2.4 Consensus size: 32
1600632 ACATTATGCT
1600642 TTGTATCGATACCTTATATCAATACATGATCA
1 TTGTATCGATACCTTATATCAATACATGATCA
* *
1600674 TTGTATTGATACCTTATATTAATACATGATCA
1 TTGTATCGATACCTTATATCAATACATGATCA
1600706 TTGTATCGATAC
1 TTGTATCGATAC
1600718 TTACACAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.41
Consensus pattern (32 bp):
TTGTATCGATACCTTATATCAATACATGATCA
Found at i:1605168 original size:52 final size:52
Alignment explanation
Indices: 1605090--1605239 Score: 241
Period size: 52 Copynumber: 2.9 Consensus size: 52
1605080 CGAAATATGA
1605090 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
1605142 AAATTTGCCTGTATGTATCGATACATTTCATAGTGTATCGATACATCTTGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
1605194 AAATTTGCCTGCATGTATCGATACAAAGTTC--AGTGTATCGATACAT
1 AAATTTGCCTGCATGTATCGATAC--ATTTCATAGTGTATCGATACAT
1605240 TTTAGTAATG
Statistics
Matches: 92, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
52 88 0.96
54 4 0.04
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:1605324 original size:32 final size:32
Alignment explanation
Indices: 1605283--1605353 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
1605273 AGCTTCGTAG
*
1605283 CGATACATTGTATCGATATAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
* *
1605315 CGATACATTGTATCGGTACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
1605347 CGATACA
1 CGATACA
1605354 AATCGTTGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:1608684 original size:51 final size:50
Alignment explanation
Indices: 1608625--1608739 Score: 176
Period size: 51 Copynumber: 2.3 Consensus size: 50
1608615 AATTAACTAG
*
1608625 ATGTATCGATACATTAAAAAATGTATCGATATATCTAGGTAAAAAAACAGA
1 ATGTATCGATACATTAAAAAATGTATCGATACATCTAGGT-AAAAAACAGA
* * *
1608676 ATGTATCGATACATTGAAAAATGTATCGATACATTTGGGTAAAAAACAGA
1 ATGTATCGATACATTAAAAAATGTATCGATACATCTAGGTAAAAAACAGA
*
1608726 ATGTATTGATACAT
1 ATGTATCGATACAT
1608740 GTACTGTTCA
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
50 23 0.39
51 36 0.61
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.30
Consensus pattern (50 bp):
ATGTATCGATACATTAAAAAATGTATCGATACATCTAGGTAAAAAACAGA
Found at i:1610367 original size:296 final size:290
Alignment explanation
Indices: 1609811--1610462 Score: 970
Period size: 296 Copynumber: 2.2 Consensus size: 290
1609801 AAAAGTTGAG
*
1609811 GAAATTTTTTTCTTGGTCATTTTATAGATAAAGAAAAGCTCGTATTTAAGTCGTTACCAAAAAAT
1 GAAA-TTTTTTCTTGGTCATTTTACAGATAAAGAAAAGCTCGTATTTAAGTCGTTACCAAAAAAT
* *** * * ** *
1609876 GAAATGTGCGTGTTTGTAAATCCGAAATAAGTCGTTATCGAAAAAAGTAATATATTGTTGGCTAA
65 AAAATGTGCACATCTGTAAATCCGAAATAAGTCATTATAAAAAAAAGTAAAATATTGTTGGCTAA
*
1609941 CATAAATTTAAATTCTATCAATTATAAACATGTACAACATTAATTAATTTTAAAAAAATAAATTT
130 CATAAATATAAATTCTATCAATTATAAACATGTACAACATTAATTAATTTTAAAAAAATAAATTT
*
1610006 GTATAATTTATAAATAAATTAAAAATAATTTATAAATAAAAAGTAATAATTCATGCACAATATTA
195 GTATAATTTATAAATAAATTAAAAATAATTTATAAATAAAAAGTAATAATACATGCACAATATTA
1610071 ATTAATTTTAATAAAAATAATACATGTACAA
260 ATTAATTTTAATAAAAATAATACATGTACAA
* *
1610102 -TAATTTTTT-TT-GTCATTTTACAGACAAAGAAAAGCTCGTATTTAAGTCGTTACCAAAAAATA
1 GAAATTTTTTCTTGGTCATTTTACAGATAAAGAAAAGCTCGTATTTAAGTCGTTACCAAAAAATA
* *
1610164 AAATGTGTACATCTGTAAATCTGAAATAAGTCATTATAAAAAAAAAGTAAAATATTGTTGGCTAA
66 AAATGTGCACATCTGTAAATCCGAAATAAGTCATTAT-AAAAAAAAGTAAAATATTGTTGGCTAA
* *
1610229 CATAAATATAAGTTCTATCAATTATAAAAATAATACATGTACAATATTAATTAATTTTAATAAAA
130 CATAAATATAAATTCTATCAA-T-T----ATAA-ACATGTACAACATTAATTAATTTTAA-AAAA
** *
1610294 ATAAATTTGTATAATTTATAAATAAATTAAAAATAATTTATAAATAAAATTTAATAATACATGTA
187 ATAAATTTGTATAATTTATAAATAAATTAAAAATAATTTATAAATAAAAAGTAATAATACATGCA
1610359 CAATATTAATTAATTTTAATAAAAATAATACATGTACAA
252 CAATATTAATTAATTTTAATAAAAATAATACATGTACAA
* **
1610398 GAAATTTTTTCTTGGTCATTTTACAGATAAA-AAAAACTCGTATTTAAGTCGTTACTGAAAAATA
1 GAAATTTTTTCTTGGTCATTTTACAGATAAAGAAAAGCTCGTATTTAAGTCGTTACCAAAAAATA
1610462 A
66 A
1610463 TACGTAGAAA
Statistics
Matches: 323, Mismatches: 26, Indels: 17
0.88 0.07 0.05
Matches are distributed among these distances:
287 78 0.24
288 45 0.14
289 7 0.02
290 3 0.01
294 4 0.01
295 25 0.08
296 104 0.32
297 8 0.02
298 33 0.10
299 16 0.05
ACGTcount: A:0.47, C:0.08, G:0.09, T:0.36
Consensus pattern (290 bp):
GAAATTTTTTCTTGGTCATTTTACAGATAAAGAAAAGCTCGTATTTAAGTCGTTACCAAAAAATA
AAATGTGCACATCTGTAAATCCGAAATAAGTCATTATAAAAAAAAGTAAAATATTGTTGGCTAAC
ATAAATATAAATTCTATCAATTATAAACATGTACAACATTAATTAATTTTAAAAAAATAAATTTG
TATAATTTATAAATAAATTAAAAATAATTTATAAATAAAAAGTAATAATACATGCACAATATTAA
TTAATTTTAATAAAAATAATACATGTACAA
Found at i:1610831 original size:66 final size:68
Alignment explanation
Indices: 1610718--1610846 Score: 165
Period size: 66 Copynumber: 1.9 Consensus size: 68
1610708 TAATTTAATT
* * * *
1610718 TTTTATTTTAAAAAATAATTAATATTTTAATTTATTAATATAAATTTTTTTAAAGTTAATTAAAT
1 TTTTATTATAAAAAATAACTAATATATTAATTTATT-ATATAAATTTTTTAAAAGTTAATTAAAT
1610783 ATTA
65 ATTA
* *
1610787 TTTTATTATAAAATAATAACTAATATATT-A-TTATT-TATTAATTTTTTAAAATTTAATTAA
1 TTTTATTATAAAA-AATAACTAATATATTAATTTATTATATAAATTTTTTAAAAGTTAATTAA
1610847 TTTATAAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
66 22 0.42
68 5 0.09
69 13 0.25
70 13 0.25
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (68 bp):
TTTTATTATAAAAAATAACTAATATATTAATTTATTATATAAATTTTTTAAAAGTTAATTAAATA
TTA
Found at i:1611007 original size:14 final size:14
Alignment explanation
Indices: 1610988--1611030 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
1610978 AATGTATTCA
1610988 TAAAAAAATTATTT
1 TAAAAAAATTATTT
*
1611002 TAAAAAATATT-TTA
1 TAAAAAA-ATTATTT
1611016 TAAAAAAACTTATTT
1 TAAAAAAA-TTATTT
1611031 ACAAAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
13 1 0.04
14 18 0.75
15 5 0.21
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (14 bp):
TAAAAAAATTATTT
Found at i:1611733 original size:22 final size:22
Alignment explanation
Indices: 1611678--1611723 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1611668 ATATAATATA
*
1611678 TATTAAATATA-TTATATTAAT
1 TATTTAATATATTTATATTAAT
*
1611699 TATTTAATATATTTATATTTAT
1 TATTTAATATATTTATATTAAT
1611721 TAT
1 TAT
1611724 ATTTTATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TATTTAATATATTTATATTAAT
Found at i:1612317 original size:19 final size:17
Alignment explanation
Indices: 1612295--1612329 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
1612285 TCCAAATTAA
1612295 TATATTTAATAATTTATAT
1 TATATTT-AT-ATTTATAT
1612314 TATATTTATATTTATA
1 TATATTTATATTTATA
1612330 CTATTAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 2 0.12
19 7 0.44
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATATTTATATTTATAT
Found at i:1634708 original size:13 final size:13
Alignment explanation
Indices: 1634690--1634715 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1634680 TACACCAAGT
1634690 ATGTATCGATACA
1 ATGTATCGATACA
1634703 ATGTATCGATACA
1 ATGTATCGATACA
1634716 CCAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1634713 original size:32 final size:33
Alignment explanation
Indices: 1634672--1634735 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1634662 TAGCCAAACT
**
1634672 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACCAAAAATTGTATCGATACAA
1634704 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
1634736 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:1635236 original size:34 final size:35
Alignment explanation
Indices: 1635173--1635239 Score: 93
Period size: 37 Copynumber: 1.9 Consensus size: 35
1635163 CTAAGTGATT
1635173 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
*
1635209 GAGAGGTTTCTATTTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
1635240 TGTTGTAAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 8 0.28
36 9 0.31
37 12 0.41
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.31
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:1638370 original size:13 final size:13
Alignment explanation
Indices: 1638352--1638381 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1638342 AAAAAGGGAG
1638352 GAAAGAAAAAAGT
1 GAAAGAAAAAAGT
*
1638365 GAAAGAAAAGAGT
1 GAAAGAAAAAAGT
1638378 GAAA
1 GAAA
1638382 AAAGAACAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.07
Consensus pattern (13 bp):
GAAAGAAAAAAGT
Found at i:1643155 original size:21 final size:21
Alignment explanation
Indices: 1643131--1643182 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1643121 TTTGCTTAGG
1643131 TATTGATACA-TTCAATCAATA
1 TATTGATACATTTC-ATCAATA
* *
1643152 TATTGATACATTTCATTAATG
1 TATTGATACATTTCATCAATA
1643173 TATTGATACA
1 TATTGATACA
1643183 AGACCTTGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 25 0.89
22 3 0.11
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (21 bp):
TATTGATACATTTCATCAATA
Found at i:1643260 original size:14 final size:14
Alignment explanation
Indices: 1643241--1643267 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1643231 ACCTCTATGC
1643241 CATTTTATTGATGG
1 CATTTTATTGATGG
1643255 CATTTTATTGATG
1 CATTTTATTGATG
1643268 TATCGATACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.52
Consensus pattern (14 bp):
CATTTTATTGATGG
Found at i:1646713 original size:17 final size:17
Alignment explanation
Indices: 1646691--1646746 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
1646681 ATTTCATATT
1646691 TTTTTCTTTTTTTTTTC
1 TTTTTCTTTTTTTTTTC
* *
1646708 TTTTTCTTTCTTTCTTC
1 TTTTTCTTTTTTTTTTC
** * *
1646725 TTCATCTTCTTTCTTTC
1 TTTTTCTTTTTTTTTTC
1646742 TTTTT
1 TTTTT
1646747 TACTTAAATT
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTCTTTTTTTTTTC
Found at i:1647192 original size:17 final size:18
Alignment explanation
Indices: 1647162--1647195 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1647152 CCCCTCTATT
1647162 TTTTCCAATATTTTTCTC
1 TTTTCCAATATTTTTCTC
*
1647180 TTTT-CAATCTTTTTCT
1 TTTTCCAATATTTTTCT
1647196 TCACCCATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTCCAATATTTTTCTC
Found at i:1653313 original size:21 final size:17
Alignment explanation
Indices: 1653274--1653336 Score: 74
Period size: 17 Copynumber: 3.6 Consensus size: 17
1653264 TTCTGATATT
1653274 AAATAATTAAAAAATAA
1 AAATAATTAAAAAATAA
*
1653291 AAATAATTAAGAAAAATTA
1 AAATAATT-A-AAAAATAA
*
1653310 AAA-AATAAAAAAATAA
1 AAATAATTAAAAAATAA
*
1653326 AAATAAATAAA
1 AAATAATTAAA
1653337 TTTTAAAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
16 10 0.26
17 14 0.37
18 4 0.11
19 10 0.26
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.21
Consensus pattern (17 bp):
AAATAATTAAAAAATAA
Found at i:1653315 original size:8 final size:8
Alignment explanation
Indices: 1653271--1653328 Score: 55
Period size: 8 Copynumber: 7.0 Consensus size: 8
1653261 ACCTTCTGAT
*
1653271 ATTAAATA
1 ATTAAAAA
1653279 ATTAAAAA
1 ATTAAAAA
*
1653287 ATAAAAATA
1 ATTAAAA-A
1653296 ATTAAGAAAA
1 ATT-A-AAAA
1653306 ATTAAAAA
1 ATTAAAAA
1653314 A-TAAAAA
1 ATTAAAAA
*
1653321 AATAAAAA
1 ATTAAAAA
1653329 TAAATAAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
7 7 0.16
8 24 0.56
9 4 0.09
10 5 0.12
11 3 0.07
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (8 bp):
ATTAAAAA
Found at i:1653333 original size:10 final size:9
Alignment explanation
Indices: 1653282--1653336 Score: 51
Period size: 10 Copynumber: 6.1 Consensus size: 9
1653272 TTAAATAATT
1653282 AAAAAATAA
1 AAAAAATAA
*
1653291 AAATAATTAA
1 AAA-AAATAA
* *
1653301 GAAAAAT-T
1 AAAAAATAA
1653309 AAAAAAT-A
1 AAAAAATAA
1653317 AAAAAATAA
1 AAAAAATAA
1653326 AAATAAATAA
1 AAA-AAATAA
1653336 A
1 A
1653337 TTTTAAAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
8 13 0.35
9 10 0.27
10 14 0.38
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (9 bp):
AAAAAATAA
Found at i:1653364 original size:19 final size:18
Alignment explanation
Indices: 1653340--1653383 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1653330 AAATAAATTT
*
1653340 TAAAAATTTTAAAGAAAAA
1 TAAAAATTCTAAA-AAAAA
* *
1653359 TAAAAAATCTACAAAAAA
1 TAAAAATTCTAAAAAAAA
1653377 TAAAAAT
1 TAAAAAT
1653384 CTAGTTCTAC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (18 bp):
TAAAAATTCTAAAAAAAA
Found at i:1654320 original size:9 final size:9
Alignment explanation
Indices: 1654302--1654347 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
1654292 ATTAATTAAG
*
1654302 AAAAAATTT
1 AAAAATTTT
1654311 AAAAATTTT
1 AAAAATTTT
1654320 AAAAA---T
1 AAAAATTTT
1654326 AAAATATTTT
1 AAAA-ATTTT
1654336 AAAAATTTT
1 AAAAATTTT
1654345 AAA
1 AAA
1654348 GAAAAATAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
6 5 0.16
7 1 0.03
9 21 0.66
10 5 0.16
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
AAAAATTTT
Found at i:1654328 original size:15 final size:16
Alignment explanation
Indices: 1654310--1654341 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1654300 AGAAAAAATT
1654310 TAAAA-ATTTTAAAAA
1 TAAAATATTTTAAAAA
1654325 TAAAATATTTTAAAAA
1 TAAAATATTTTAAAAA
1654341 T
1 T
1654342 TTTAAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAAATATTTTAAAAA
Found at i:1654353 original size:24 final size:23
Alignment explanation
Indices: 1654299--1654355 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 23
1654289 AAAATTAATT
1654299 AAGAAAAA-ATTTAAAAATTTTA
1 AAGAAAAATATTTAAAAATTTTA
*
1654321 AAAATAAAATATTTTAAAAATTTTA
1 AAGA-AAAATA-TTTAAAAATTTTA
1654346 AAGAAAAATA
1 AAGAAAAATA
1654356 AAAAAAATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 3 0.10
23 4 0.13
24 7 0.23
25 16 0.53
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.32
Consensus pattern (23 bp):
AAGAAAAATATTTAAAAATTTTA
Found at i:1657711 original size:23 final size:22
Alignment explanation
Indices: 1657684--1657761 Score: 90
Period size: 22 Copynumber: 3.5 Consensus size: 22
1657674 TTATTTTTTA
1657684 TATTTTTATATTTGTGTTATATT
1 TATTTTTATATTTGT-TTATATT
1657707 TATTTTTATTATTT-TTTA-ATT
1 TATTTTTA-TATTTGTTTATATT
*
1657728 AATTTTTATATCTTGTTTATA-T
1 TATTTTTATAT-TTGTTTATATT
1657750 TATTTTTCATAT
1 TATTTTT-ATAT
1657762 ATTTAAAATA
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
20 3 0.06
21 12 0.25
22 14 0.29
23 14 0.29
24 5 0.10
ACGTcount: A:0.24, C:0.03, G:0.04, T:0.69
Consensus pattern (22 bp):
TATTTTTATATTTGTTTATATT
Found at i:1657732 original size:21 final size:20
Alignment explanation
Indices: 1657673--1657756 Score: 68
Period size: 22 Copynumber: 4.0 Consensus size: 20
1657663 ATATTTGCAA
1657673 ATTATTTTTT-A-TATTTTT
1 ATTATTTTTTAATTATTTTT
1657691 A-TATTTGTGTTATATTTATTTTT
1 ATTATTT-T-TTA-A-TTATTTTT
1657714 ATTATTTTTTAATTAATTTTT
1 ATTATTTTTTAATT-ATTTTT
1657735 A-TATCTTGTTTATATTATTTTT
1 ATTAT-TT-TTTA-ATTATTTTT
1657757 CATATATTTA
Statistics
Matches: 55, Mismatches: 0, Indels: 18
0.75 0.00 0.25
Matches are distributed among these distances:
17 5 0.09
18 2 0.04
19 2 0.04
20 5 0.09
21 11 0.20
22 13 0.24
23 12 0.22
24 5 0.09
ACGTcount: A:0.24, C:0.01, G:0.04, T:0.71
Consensus pattern (20 bp):
ATTATTTTTTAATTATTTTT
Found at i:1657734 original size:44 final size:41
Alignment explanation
Indices: 1657673--1657765 Score: 118
Period size: 44 Copynumber: 2.2 Consensus size: 41
1657663 ATATTTGCAA
1657673 ATTATTTTTTATATTTTTATAT-TTGTGTTATATTTATTTTT-
1 ATTATTTTTTATATTTTTATATCTTGT-TTATA-TTATTTTTC
1657714 ATTATTTTTTAATTAATTTTTATATCTTGTTTATATTATTTTTC
1 ATTATTTTTT-A-T-ATTTTTATATCTTGTTTATATTATTTTTC
1657758 ATATATTT
1 AT-TATTT
1657766 AAAATACTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
41 10 0.22
42 1 0.02
43 9 0.20
44 17 0.37
45 9 0.20
ACGTcount: A:0.25, C:0.02, G:0.03, T:0.70
Consensus pattern (41 bp):
ATTATTTTTTATATTTTTATATCTTGTTTATATTATTTTTC
Found at i:1657764 original size:11 final size:10
Alignment explanation
Indices: 1657675--1657765 Score: 55
Period size: 11 Copynumber: 8.5 Consensus size: 10
1657665 ATTTGCAAAT
1657675 TATTTTT-TA
1 TATTTTTATA
1657684 TATTTTTATA
1 TATTTTTATA
1657694 T-TTGTGTTATA
1 TATT-T-TTATA
1657705 TTTATTTTTAT-
1 --TATTTTTATA
1657716 TATTTTT-TAA
1 TATTTTTAT-A
1657726 TTAATTTTTATA
1 -T-ATTTTTATA
*
1657738 TCTTGTTTATA
1 TATT-TTTATA
1657749 TTATTTTTCATA
1 -TATTTTT-ATA
1657761 TATTT
1 TATTT
1657766 AAAATACTAA
Statistics
Matches: 66, Mismatches: 2, Indels: 26
0.70 0.02 0.28
Matches are distributed among these distances:
8 1 0.02
9 16 0.24
10 6 0.09
11 21 0.32
12 17 0.26
13 3 0.05
14 2 0.03
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.70
Consensus pattern (10 bp):
TATTTTTATA
Found at i:1658708 original size:26 final size:27
Alignment explanation
Indices: 1658662--1658714 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
1658652 ATTTAATATT
*
1658662 TTTAACTTAAATTTATGTAAATATTAA
1 TTTAACTTAAATTTATATAAATATTAA
1658689 TTTAA-TTAAATATT-TATAAATATTAA
1 TTTAACTTAAAT-TTATATAAATATTAA
1658715 AAATTTTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (27 bp):
TTTAACTTAAATTTATATAAATATTAA
Found at i:1659054 original size:16 final size:18
Alignment explanation
Indices: 1659033--1659077 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1659023 ATTCTTATTT
1659033 TTATATTAT-TTTGATA-
1 TTATATTATATTTGATAG
*
1659049 TTATATTATATTTTATAG
1 TTATATTATATTTGATAG
*
1659067 TTATATAATAT
1 TTATATTATAT
1659078 GATGTTATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 9 0.36
17 6 0.24
18 10 0.40
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (18 bp):
TTATATTATATTTGATAG
Found at i:1659922 original size:15 final size:14
Alignment explanation
Indices: 1659898--1659970 Score: 64
Period size: 15 Copynumber: 5.4 Consensus size: 14
1659888 ATAATTTTAC
*
1659898 AAATACAAAAATTA
1 AAATATAAAAATTA
1659912 ATAATATAAAAATTA
1 A-AATATAAAAATTA
*
1659927 AAATAT----TTTA
1 AAATATAAAAATTA
* *
1659937 AAATATTAAATTTA
1 AAATATAAAAATTA
1659951 ATAATATAAAAATTA
1 A-AATATAAAAATTA
1659966 AAATA
1 AAATA
1659971 AAATAATTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
10 9 0.18
14 15 0.31
15 25 0.51
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (14 bp):
AAATATAAAAATTA
Found at i:1659952 original size:39 final size:40
Alignment explanation
Indices: 1659891--1659970 Score: 126
Period size: 39 Copynumber: 2.0 Consensus size: 40
1659881 ATTTTTTATA
1659891 ATTTTACAAATACAAAAATTAATAATATAAAAATTAAAAT
1 ATTTTACAAATACAAAAATTAATAATATAAAAATTAAAAT
** *
1659931 ATTTTA-AAATATTAAATTTAATAATATAAAAATTAAAAT
1 ATTTTACAAATACAAAAATTAATAATATAAAAATTAAAAT
1659970 A
1 A
1659971 AAATAATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 31 0.84
40 6 0.16
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (40 bp):
ATTTTACAAATACAAAAATTAATAATATAAAAATTAAAAT
Found at i:1660316 original size:11 final size:13
Alignment explanation
Indices: 1660287--1660331 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
1660277 TATATATATA
1660287 TATATTAAAAAAT
1 TATATTAAAAAAT
*
1660300 TATATTAAAAATT
1 TATATTAAAAAAT
*
1660313 TATTTTTAAATAAAT
1 TA-TATTAAA-AAAT
1660328 TATA
1 TATA
1660332 ATATTTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
13 14 0.54
14 7 0.27
15 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TATATTAAAAAAT
Found at i:1660754 original size:25 final size:24
Alignment explanation
Indices: 1660717--1660766 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
1660707 TAAATAATAT
*
1660717 TAATTTAATTAATTAATAATAAAA
1 TAATTTAAATAATTAATAATAAAA
* *
1660741 TAATTTAAAATAATTATTTATAAAA
1 TAATTT-AAATAATTAATAATAAAA
1660766 T
1 T
1660767 TGTATTAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
TAATTTAAATAATTAATAATAAAA
Found at i:1660921 original size:2 final size:2
Alignment explanation
Indices: 1660914--1660940 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1660904 CTAATATAAG
1660914 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 T
1660941 GGAGATTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1662351 original size:7 final size:7
Alignment explanation
Indices: 1662331--1662370 Score: 50
Period size: 6 Copynumber: 6.0 Consensus size: 7
1662321 TGAATCGCAT
1662331 AATTTAA
1 AATTTAA
1662338 AATTTTAA
1 AA-TTTAA
1662346 AATTT-A
1 AATTTAA
1662352 AATTT-A
1 AATTTAA
1662358 AA-TTAA
1 AATTTAA
1662364 AATTTAA
1 AATTTAA
1662371 TTTGATTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 2 0.07
6 12 0.40
7 9 0.30
8 7 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
AATTTAA
Found at i:1662517 original size:30 final size:31
Alignment explanation
Indices: 1662483--1662541 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
1662473 TAAAAATATT
1662483 ATTTT-ATTATATAAATAATA-ATTTAAATCG
1 ATTTTGATTATA-AAATAATATATTTAAATCG
*
1662513 ATTTTGATTATAAAATATTATATTTAAAT
1 ATTTTGATTATAAAATAATATATTTAAAT
1662542 ATTTAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (31 bp):
ATTTTGATTATAAAATAATATATTTAAATCG
Found at i:1664980 original size:2 final size:2
Alignment explanation
Indices: 1664973--1665010 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1664963 CTGAGAGCAG
*
1664973 CT CT CT CT CT CT CT CT CT CT CC CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1665011 TTTCTTCTGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:1665040 original size:6 final size:6
Alignment explanation
Indices: 1665029--1665065 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
1665019 GGCCTTCAAT
*
1665029 GTAGGA GTAGGA GTAGGA GTAGGA GCAGGA GTAGGA G
1 GTAGGA GTAGGA GTAGGA GTAGGA GTAGGA GTAGGA G
1665066 AAGTACAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.32, C:0.03, G:0.51, T:0.14
Consensus pattern (6 bp):
GTAGGA
Found at i:1668587 original size:20 final size:20
Alignment explanation
Indices: 1668562--1668614 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
1668552 GTTACAAGCT
1668562 ATGTATCGATACATT-T-CTTC
1 ATGTATCGATACATTGTAC--C
1668582 ATGTATCGATACATTGTACC
1 ATGTATCGATACATTGTACC
1668602 ATGTATCGATACA
1 ATGTATCGATACA
1668615 AATAATGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 29 0.94
21 1 0.03
22 1 0.03
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTGTACC
Found at i:1668670 original size:21 final size:21
Alignment explanation
Indices: 1668644--1668704 Score: 81
Period size: 19 Copynumber: 3.0 Consensus size: 21
1668634 CTGCCAGTTT
1668644 CATGTATCGATACAATTTATC
1 CATGTATCGATACAATTTATC
* *
1668665 CATGTATCGATACAA-TGA-A
1 CATGTATCGATACAATTTATC
*
1668684 CATGTATCGATACAATGTATC
1 CATGTATCGATACAATTTATC
1668705 GATACAAAGC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
19 15 0.45
20 3 0.09
21 15 0.45
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (21 bp):
CATGTATCGATACAATTTATC
Found at i:1668703 original size:13 final size:13
Alignment explanation
Indices: 1668685--1668711 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1668675 TACAATGAAC
1668685 ATGTATCGATACA
1 ATGTATCGATACA
1668698 ATGTATCGATACA
1 ATGTATCGATACA
1668711 A
1 A
1668712 AGCAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1668726 original size:33 final size:32
Alignment explanation
Indices: 1668666--1668730 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
1668656 CAATTTATCC
*
1668666 ATGTATCGATACAATGAACATGTATCGATACA
1 ATGTATCGATACAAAGAACATGTATCGATACA
*
1668698 ATGTATCGATACAAAGCAGCATGTATCGATACA
1 ATGTATCGATACAAAG-AACATGTATCGATACA
1668731 TCTGGGTGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (32 bp):
ATGTATCGATACAAAGAACATGTATCGATACA
Found at i:1676232 original size:20 final size:20
Alignment explanation
Indices: 1676207--1676281 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
1676197 TTTTCACAAT
*
1676207 TTGTATCGATACATTGTTTA
1 TTGTATCGATACATTGTTCA
1676227 TTGTATCGATACATT-TTGCA
1 TTGTATCGATACATTGTT-CA
*
1676247 TTGTATCGATACATTGCTCA
1 TTGTATCGATACATTGTTCA
1676267 TTGTATCGATACATT
1 TTGTATCGATACATT
1676282 ATATCGATAT
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.04
20 48 0.94
21 1 0.02
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:1676254 original size:40 final size:39
Alignment explanation
Indices: 1676207--1676334 Score: 151
Period size: 40 Copynumber: 3.4 Consensus size: 39
1676197 TTTTCACAAT
*
1676207 TTGTATCGATACATTGTTTATTGTATCGATACATTTTGCA
1 TTGTATCGATACATTGCTTATTGTATCGATACATTTT-CA
*
1676247 TTGTATCGATACATTGCTCATTGTATCGATACA--TT-A
1 TTGTATCGATACATTGCTTATTGTATCGATACATTTTCA
* *
1676283 ---TATCGATATAGTGCTTATTGTATCGATACATTTTACA
1 TTGTATCGATACATTGCTTATTGTATCGATACATTTT-CA
*
1676320 ATGTATCGATACATT
1 TTGTATCGATACATT
1676335 CAAGCATTTT
Statistics
Matches: 74, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
33 27 0.36
35 2 0.03
36 1 0.01
37 1 0.01
38 2 0.03
40 41 0.55
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (39 bp):
TTGTATCGATACATTGCTTATTGTATCGATACATTTTCA
Found at i:1676303 original size:33 final size:33
Alignment explanation
Indices: 1676245--1676314 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1676235 ATACATTTTG
* *
1676245 CATTGTATCGATACATTGCTCATTGTATCGATA
1 CATTATATCGATACAGTGCTCATTGTATCGATA
* *
1676278 CATTATATCGATATAGTGCTTATTGTATCGATA
1 CATTATATCGATACAGTGCTCATTGTATCGATA
1676311 CATT
1 CATT
1676315 TTACAATGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (33 bp):
CATTATATCGATACAGTGCTCATTGTATCGATA
Found at i:1678775 original size:28 final size:27
Alignment explanation
Indices: 1678707--1678783 Score: 102
Period size: 28 Copynumber: 2.8 Consensus size: 27
1678697 TGGATTTTTC
1678707 ATTTTCGAGGGATACTCCAACCCCGTT
1 ATTTTCGAGGGATACTCCAACCCCGTT
* *
1678734 ATGTCATCGA-GGATACTCCAATCCCGTT
1 AT-T-TTCGAGGGATACTCCAACCCCGTT
1678762 ATTTTCGAGGGGATACTCCAAC
1 ATTTTCGA-GGGATACTCCAAC
1678784 TCCGATTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
26 4 0.10
27 3 0.07
28 31 0.74
29 4 0.10
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (27 bp):
ATTTTCGAGGGATACTCCAACCCCGTT
Found at i:1679071 original size:122 final size:122
Alignment explanation
Indices: 1678875--1679112 Score: 311
Period size: 122 Copynumber: 2.0 Consensus size: 122
1678865 ATTTCTAAAA
* *
1678875 TACCAATTTTTCACAATCAGAGATATTCAAACTCCTGTTTTATTTCCAAAACACCAATTTCTCAC
1 TACCAATTTTCCACAATCAGAGATACTCAAACTCCTGTTTTATTTCCAAAACACCAATTTCTCAC
* *
1678940 AATCGGGGATACTCCAACCCCGTTA-TTTCTGAGGGGATACTCCAACCCCGACTTTAT
66 AATCAGGGATACTCCAACCCCGTTATTTTC-GAGAGGATACTCCAACCCCGACTTTAT
* * ** * * *
1678997 TACCAATTTTCCACAATCGGGGATACTCCCACTCC-GATTTTATTTTCAAAATACCGATTT-TCT
1 TACCAATTTTCCACAATCAGAGATACTCAAACTCCTG-TTTTATTTCCAAAACACCAATTTCTC-
* *
1679060 ATAATCAGGGATACTCCAACCCTGTTATTTTCGAGAGGATACTCCAACCCCGA
64 ACAATCAGGGATACTCCAACCCCGTTATTTTCGAGAGGATACTCCAACCCCGA
1679113 TTTTCATTTC
Statistics
Matches: 100, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
121 3 0.03
122 93 0.93
123 4 0.04
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.31
Consensus pattern (122 bp):
TACCAATTTTCCACAATCAGAGATACTCAAACTCCTGTTTTATTTCCAAAACACCAATTTCTCAC
AATCAGGGATACTCCAACCCCGTTATTTTCGAGAGGATACTCCAACCCCGACTTTAT
Found at i:1684911 original size:21 final size:20
Alignment explanation
Indices: 1684868--1684913 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
1684858 ACTATTATTT
* * *
1684868 TTTAAAATATTTTTATTTTA
1 TTTAAAATAATTTAATTTAA
1684888 TTTAAAATTAATTTAATTTAA
1 TTTAAAA-TAATTTAATTTAA
1684909 TTTAA
1 TTTAA
1684914 TTTTTAAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTAAAATAATTTAATTTAA
Found at i:1685712 original size:26 final size:26
Alignment explanation
Indices: 1685657--1685722 Score: 62
Period size: 26 Copynumber: 2.5 Consensus size: 26
1685647 ATTTATAAAA
* **
1685657 AAATAAATATTAATATTTTAAAATTT
1 AAATAAATATTAATACTTTAAAATAC
*
1685683 AAATAAATATATAATACTTT-GAATAC
1 AAATAAATAT-TAATACTTTAAAATAC
*
1685709 AAATATGATATTAA
1 AAATA-AATATTAA
1685723 AAATAACATG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
26 21 0.64
27 12 0.36
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (26 bp):
AAATAAATATTAATACTTTAAAATAC
Found at i:1686101 original size:17 final size:17
Alignment explanation
Indices: 1686051--1686103 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
1686041 ATAAATAAAT
1686051 ATATCAAAACTTATATAA
1 ATATCAAAA-TTATATAA
*
1686069 A-AT--GAATTATCA-AA
1 ATATCAAAATTAT-ATAA
1686083 ATATCAAAATTATATAA
1 ATATCAAAATTATATAA
1686100 ATAT
1 ATAT
1686104 ATAATATCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 11
0.68 0.05 0.27
Matches are distributed among these distances:
14 7 0.25
15 5 0.18
16 1 0.04
17 14 0.50
18 1 0.04
ACGTcount: A:0.57, C:0.08, G:0.02, T:0.34
Consensus pattern (17 bp):
ATATCAAAATTATATAA
Found at i:1686837 original size:24 final size:26
Alignment explanation
Indices: 1686810--1686858 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
1686800 CACATTTTCT
*
1686810 ATTTTTATATAATTT-TT-ATTTAAA
1 ATTTTTAAATAATTTATTCATTTAAA
*
1686834 ATTTTTAAATTATTTATTCATTTAA
1 ATTTTTAAATAATTTATTCATTTAA
1686859 TACAATGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 13 0.62
25 2 0.10
26 6 0.29
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (26 bp):
ATTTTTAAATAATTTATTCATTTAAA
Found at i:1686999 original size:25 final size:25
Alignment explanation
Indices: 1686971--1687021 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
1686961 ATATAGATAA
* **
1686971 TTTATCTATATATTTTTACTTATTG
1 TTTATCTATACAACTTTACTTATTG
1686996 TTTATCTATACAACTTTACTTATTG
1 TTTATCTATACAACTTTACTTATTG
1687021 T
1 T
1687022 CTCTAATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.25, C:0.12, G:0.04, T:0.59
Consensus pattern (25 bp):
TTTATCTATACAACTTTACTTATTG
Found at i:1690855 original size:23 final size:24
Alignment explanation
Indices: 1690829--1690877 Score: 82
Period size: 23 Copynumber: 2.1 Consensus size: 24
1690819 AAAAGTATAA
1690829 TTAAATATATTTATA-TAATTTAT
1 TTAAATATATTTATATTAATTTAT
*
1690852 TTAAATATATTTATATTATTTTAT
1 TTAAATATATTTATATTAATTTAT
1690876 TT
1 TT
1690878 TATTTTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
TTAAATATATTTATATTAATTTAT
Found at i:1691296 original size:21 final size:20
Alignment explanation
Indices: 1691265--1691305 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1691255 ATTTAATTAT
1691265 TTTTTAATT-AATAATAAATA
1 TTTTTAATTAAAT-ATAAATA
1691285 TTTTTAATTTAAATATAAATA
1 TTTTTAA-TTAAATATAAATA
1691306 ATTAAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.37
21 9 0.47
22 3 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTTTAATTAAATATAAATA
Found at i:1691740 original size:18 final size:19
Alignment explanation
Indices: 1691700--1691740 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
1691690 AAGTTTGAAT
1691700 ATTTT-AAATTCAATTAAG
1 ATTTTAAAATTCAATTAAG
*
1691718 A-TTTAAAATTTAATTAA-
1 ATTTTAAAATTCAATTAAG
1691735 ATTTTA
1 ATTTTA
1691741 TTTTTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (19 bp):
ATTTTAAAATTCAATTAAG
Found at i:1694355 original size:22 final size:22
Alignment explanation
Indices: 1694321--1694376 Score: 89
Period size: 21 Copynumber: 2.6 Consensus size: 22
1694311 CTGGACATGT
*
1694321 TAAAAAAA-ACATGAAACATAA
1 TAAAAAAATGCATGAAACATAA
1694342 TAAAAAAATGCATGAAACATAA
1 TAAAAAAATGCATGAAACATAA
1694364 T-AAAAAATGCATG
1 TAAAAAAATGCATG
1694377 GTCAAAGGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
21 20 0.61
22 13 0.39
ACGTcount: A:0.64, C:0.09, G:0.09, T:0.18
Consensus pattern (22 bp):
TAAAAAAATGCATGAAACATAA
Found at i:1694371 original size:21 final size:21
Alignment explanation
Indices: 1694321--1694376 Score: 85
Period size: 22 Copynumber: 2.6 Consensus size: 21
1694311 CTGGACATGT
**
1694321 TAAAAAAAACATGAAACATAA
1 TAAAAAATGCATGAAACATAA
1694342 TAAAAAAATGCATGAAACATAA
1 T-AAAAAATGCATGAAACATAA
1694364 TAAAAAATGCATG
1 TAAAAAATGCATG
1694377 GTCAAAGGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 13 0.41
22 19 0.59
ACGTcount: A:0.64, C:0.09, G:0.09, T:0.18
Consensus pattern (21 bp):
TAAAAAATGCATGAAACATAA
Found at i:1695337 original size:20 final size:20
Alignment explanation
Indices: 1695290--1695364 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
1695280 AAAAAGACAT
*
1695290 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
1695309 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
1695330 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
1695350 AATGTATCGATACAT
1 AATGTATCGATACAT
1695365 CAAGGTAAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:1695358 original size:40 final size:39
Alignment explanation
Indices: 1695287--1695364 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1695277 GGTAAAAAGA
* *
1695287 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
1695326 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
1695365 CAAGGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:1696671 original size:43 final size:43
Alignment explanation
Indices: 1696623--1696708 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
1696613 AATCGCCAAT
1696623 CTGATTGATCTTCAATGGTCACTACGAAGTGACCGAAAGTTTG
1 CTGATTGATCTTCAATGGTCACTACGAAGTGACCGAAAGTTTG
1696666 CTGATTGATCTTCAATGGTCACTACGAAGTGACCGAAAGTTTG
1 CTGATTGATCTTCAATGGTCACTACGAAGTGACCGAAAGTTTG
1696709 GAGTCGCCAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (43 bp):
CTGATTGATCTTCAATGGTCACTACGAAGTGACCGAAAGTTTG
Found at i:1699686 original size:52 final size:52
Alignment explanation
Indices: 1699595--1699693 Score: 137
Period size: 52 Copynumber: 1.9 Consensus size: 52
1699585 CCCGAAATAT
* **
1699595 GAAAATTTGCCTGCATGTATCGATATATTTCATAATGTATCGATACATCTGA
1 GAAAATTTGCCTGCATGTATCGATACATAACATAATGTATCGATACATCTGA
* *
1699647 GAAAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 GAAAATTTGCCTGCATGTATCGATACATAACAT-AATGTATCGATACA
1699694 ATGTATCGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
51 2 0.05
52 39 0.95
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Consensus pattern (52 bp):
GAAAATTTGCCTGCATGTATCGATACATAACATAATGTATCGATACATCTGA
Found at i:1699700 original size:13 final size:13
Alignment explanation
Indices: 1699682--1699706 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1699672 CAAAGATCAG
1699682 TGTATCGATACAA
1 TGTATCGATACAA
1699695 TGTATCGATACA
1 TGTATCGATACA
1699707 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1704639 original size:23 final size:22
Alignment explanation
Indices: 1704609--1704677 Score: 69
Period size: 21 Copynumber: 3.3 Consensus size: 22
1704599 TAGCCTTATT
1704609 TTTTTTCTACTTCTTTGT-TTT-TA
1 TTTTTTCT-C-TCTTT-TCTTTCTA
1704632 TTTTTTCTCTCTTTTCTTTCTA
1 TTTTTTCTCTCTTTTCTTTCTA
1704654 TTTTTT-TCT-TTTT-TTTCT-
1 TTTTTTCTCTCTTTTCTTTCTA
1704672 TTTTTT
1 TTTTTT
1704678 GTAAAACCTT
Statistics
Matches: 44, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
18 6 0.14
19 5 0.11
20 5 0.11
21 11 0.25
22 9 0.20
23 8 0.18
ACGTcount: A:0.04, C:0.14, G:0.01, T:0.80
Consensus pattern (22 bp):
TTTTTTCTCTCTTTTCTTTCTA
Found at i:1704665 original size:19 final size:18
Alignment explanation
Indices: 1704641--1704677 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
1704631 ATTTTTTCTC
1704641 TCTTTTCTTTCTATTTTTT
1 TCTTTTCTTTCT-TTTTTT
*
1704660 TCTTTTTTTTCTTTTTTT
1 TCTTTTCTTTCTTTTTTT
1704678 GTAAAACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.84
Consensus pattern (18 bp):
TCTTTTCTTTCTTTTTTT
Found at i:1704667 original size:8 final size:9
Alignment explanation
Indices: 1704619--1704677 Score: 64
Period size: 9 Copynumber: 6.1 Consensus size: 9
1704609 TTTTTTCTAC
1704619 TTCTTTGTTT
1 TTCTTT-TTT
*
1704629 TTATTTTTT
1 TTCTTTTTT
*
1704638 CTCTCTTTTCT
1 -T-TCTTTTTT
1704649 TTCTATTTTT
1 TTCT-TTTTT
1704659 TTCTTTTTT
1 TTCTTTTTT
1704668 TTCTTTTTT
1 TTCTTTTTT
1704677 T
1 T
1704678 GTAAAACCTT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
9 21 0.50
10 15 0.36
11 6 0.14
ACGTcount: A:0.03, C:0.14, G:0.02, T:0.81
Consensus pattern (9 bp):
TTCTTTTTT
Found at i:1707429 original size:20 final size:20
Alignment explanation
Indices: 1707401--1707472 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 20
1707391 TACCCTGATG
1707401 TATCGATACATTTTTCAATA
1 TATCGATACATTTTTCAATA
* * * *
1707421 TATCAATACATGTATGAATA
1 TATCGATACATTTTTCAATA
* * * *
1707441 TATCGATATATTCTGCAATG
1 TATCGATACATTTTTCAATA
1707461 TATCGATACATT
1 TATCGATACATT
1707473 ATGTCTTTTT
Statistics
Matches: 39, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
TATCGATACATTTTTCAATA
Found at i:1708419 original size:23 final size:23
Alignment explanation
Indices: 1708383--1708434 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
1708373 AGCCTTTGAC
1708383 CATGCA-TTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
1708405 CATGCATTTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
1708428 CATGCAT
1 CATGCAT
1708435 CTTTAACATG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 6 0.21
23 23 0.79
ACGTcount: A:0.19, C:0.12, G:0.10, T:0.60
Consensus pattern (23 bp):
CATGCATTTTTTTTATTATGTTT
Found at i:1713756 original size:15 final size:15
Alignment explanation
Indices: 1713736--1713765 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1713726 ATGTTCCGTG
1713736 TCCAAAATTTCGTTA
1 TCCAAAATTTCGTTA
*
1713751 TCCAAAATTTTGTTA
1 TCCAAAATTTCGTTA
1713766 CAAAAATCGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.43
Consensus pattern (15 bp):
TCCAAAATTTCGTTA
Found at i:1718560 original size:11 final size:10
Alignment explanation
Indices: 1718523--1718559 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
1718513 ACCTAATCCT
*
1718523 AAAAAAAA-G
1 AAAAAAAACC
1718532 AAAAAAAACC
1 AAAAAAAACC
1718542 AAAAAAAACC
1 AAAAAAAACC
1718552 AAAAAAAA
1 AAAAAAAA
1718560 AAACCTTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 8 0.31
10 18 0.69
ACGTcount: A:0.86, C:0.11, G:0.03, T:0.00
Consensus pattern (10 bp):
AAAAAAAACC
Found at i:1719676 original size:28 final size:28
Alignment explanation
Indices: 1719632--1720167 Score: 344
Period size: 28 Copynumber: 19.1 Consensus size: 28
1719622 AGTCCACAAC
* *
1719632 TCCTTTT-ATGTCCACAACTCTGTGGCA
1 TCCTTTTAAAGTCCACAACTCAGTGGCA
*
1719659 TCCTTTTAAAGTCCACAACTCTGTGGCA
1 TCCTTTTAAAGTCCACAACTCAGTGGCA
*
1719687 TCCTTTT-AAGTCCACAACTCCGTGGCA
1 TCCTTTTAAAGTCCACAACTCAGTGGCA
* * *
1719714 CCCTTTTAAAGTCCACAACTCCGTGACA
1 TCCTTTTAAAGTCCACAACTCAGTGGCA
*
1719742 -CCTTTTAAAGTCCACAACTCCGTGGCA
1 TCCTTTTAAAGTCCACAACTCAGTGGCA
* *
1719769 CCCTTTT-AAGTCCACAACTCCGTGGCA
1 TCCTTTTAAAGTCCACAACTCAGTGGCA
* * * *
1719796 -CCTTTTTAAGTCTACAACTCTGTAGCA
1 TCCTTTTAAAGTCCACAACTCAGTGGCA
* *
1719823 CCCTTTT-AAGTCCACAAGTCAGTGGCA
1 TCCTTTTAAAGTCCACAACTCAGTGGCA
* *
1719850 TTCC-TTCAAAGTCCACAAGTCAGTGGCA
1 -TCCTTTTAAAGTCCACAACTCAGTGGCA
* * * *
1719878 ACCTTTCAAAGCCCACAAGTCAGTGGCA
1 TCCTTTTAAAGTCCACAACTCAGTGGCA
* * * *
1719906 CTCCTCTCAAAGCCAACACAAGTCAGTGGCA
1 -TCCTTTTAAAGTC--CACAACTCAGTGGCA
* * *
1719937 TCCTTTCAAAGCCCACACAAGTCAGTGGCAA
1 TCCTTTTAAAG-TC-CACAACTCAGTGGC-A
* * * * *
1719968 CCCATTTCAA-TGCTCACAAGTCGGTGGC-
1 TCCTTTTAAAGT-C-CACAACTCAGTGGCA
* * *
1719996 TTCTTTTCAAAGCCCACAAGTCAGTGGCA
1 TCCTTTT-AAAGTCCACAACTCAGTGGCA
* * * * *
1720025 CCCTTTTAAAGCCCACGAGTCAATGGCA
1 TCCTTTTAAAGTCCACAACTCAGTGGCA
* * *
1720053 -CTCTTTCAAAGCCCACAAGTCAGTGGCA
1 TC-CTTTTAAAGTCCACAACTCAGTGGCA
* *
1720081 T-CTTTTCAAAGCCCACGCAAGTCAGTGGCA
1 TCCTTTT-AAAGTCCA--CAACTCAGTGGCA
* * *
1720111 -CCTTTTCAAA-CCCACGAGTCAGTGGCA
1 TCCTTTT-AAAGTCCACAACTCAGTGGCA
* * * *
1720138 -CTCTTTCAAAGCCCACAAGTTAGTGGCA
1 TC-CTTTTAAAGTCCACAACTCAGTGGCA
1720166 TC
1 TC
1720168 TTCAAAGCCC
Statistics
Matches: 439, Mismatches: 44, Indels: 50
0.82 0.08 0.09
Matches are distributed among these distances:
26 6 0.01
27 136 0.31
28 188 0.43
29 24 0.05
30 61 0.14
31 24 0.05
ACGTcount: A:0.27, C:0.32, G:0.16, T:0.25
Consensus pattern (28 bp):
TCCTTTTAAAGTCCACAACTCAGTGGCA
Found at i:1719705 original size:27 final size:27
Alignment explanation
Indices: 1719632--1719910 Score: 292
Period size: 27 Copynumber: 10.1 Consensus size: 27
1719622 AGTCCACAAC
* *
1719632 TCCTTTTATGTCCACAACTCTGTGGCA
1 TCCTTTTAAGTCCACAACTCCGTGGCA
*
1719659 TCCTTTTAAAGTCCACAACTCTGTGGCA
1 TCCTTTT-AAGTCCACAACTCCGTGGCA
1719687 TCCTTTTAAGTCCACAACTCCGTGGCA
1 TCCTTTTAAGTCCACAACTCCGTGGCA
* *
1719714 CCCTTTTAAAGTCCACAACTCCGTGACA
1 TCCTTTT-AAGTCCACAACTCCGTGGCA
1719742 -CCTTTTAAAGTCCACAACTCCGTGGCA
1 TCCTTTT-AAGTCCACAACTCCGTGGCA
*
1719769 CCCTTTTAAGTCCACAACTCCGTGGCA
1 TCCTTTTAAGTCCACAACTCCGTGGCA
* * *
1719796 -CCTTTTTAAGTCTACAACTCTGTAGCA
1 TCC-TTTTAAGTCCACAACTCCGTGGCA
* * *
1719823 CCCTTTTAAGTCCACAAGTCAGTGGCA
1 TCCTTTTAAGTCCACAACTCCGTGGCA
** * *
1719850 TTCCTTCAAAGTCCACAAGTCAGTGGCA
1 -TCCTTTTAAGTCCACAACTCCGTGGCA
* * * * *
1719878 ACCTTTCAAAGCCCACAAGTCAGTGGCA
1 TCCTTT-TAAGTCCACAACTCCGTGGCA
1719906 CTCCT
1 -TCCT
1719911 CTCAAAGCCA
Statistics
Matches: 225, Mismatches: 19, Indels: 14
0.87 0.07 0.05
Matches are distributed among these distances:
26 2 0.01
27 123 0.55
28 97 0.43
29 3 0.01
ACGTcount: A:0.25, C:0.32, G:0.15, T:0.28
Consensus pattern (27 bp):
TCCTTTTAAGTCCACAACTCCGTGGCA
Found at i:1719719 original size:55 final size:55
Alignment explanation
Indices: 1719632--1719910 Score: 323
Period size: 55 Copynumber: 5.1 Consensus size: 55
1719622 AGTCCACAAC
* * * *
1719632 TCCTTTTATGTCCACAACTCTGTGGCATCCTTTTAAAGTCCACAACTCTGTGGCA
1 TCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCAGTGGCA
* *
1719687 TCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCCGTGACA
1 TCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCAGTGGCA
*
1719742 -CCTTTTAAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCA
1 TCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCAGTGGCA
* * * *
1719796 -CCTTTTTAAGTCTACAACTCTGTAGCACCCTTTT-AAGTCCACAAGTCAGTGGCA
1 TCC-TTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCAGTGGCA
** * * * * * *
1719850 TTCCTTCAAAGTCCACAAGTCAGTGGCAACCTTTCAAAGCCCACAAGTCAGTGGCA
1 -TCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCAGTGGCA
1719906 CTCCT
1 -TCCT
1719911 CTCAAAGCCA
Statistics
Matches: 198, Mismatches: 21, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
54 69 0.35
55 104 0.53
56 25 0.13
ACGTcount: A:0.25, C:0.32, G:0.15, T:0.28
Consensus pattern (55 bp):
TCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAAGTCCACAACTCAGTGGCA
Found at i:1720209 original size:32 final size:28
Alignment explanation
Indices: 1719698--1721335 Score: 715
Period size: 28 Copynumber: 56.2 Consensus size: 28
1719688 CCTTTTAAGT
* * * * *
1719698 CCACAACTCCGTGGCACCCTTTTAAAGT
1 CCACAAGTCAGTGGCACTCTTTCAAAGC
* * * * *
1719726 CCACAACTCCGTGACAC-CTTTTAAAGT
1 CCACAAGTCAGTGGCACTCTTTCAAAGC
* * * * *
1719753 CCACAACTCCGTGGCACCCTTT-TAAGT
1 CCACAAGTCAGTGGCACTCTTTCAAAGC
* * ** *
1719780 CCACAACTCCGTGGCAC-CTTTTTAAGT
1 CCACAAGTCAGTGGCACTCTTTCAAAGC
* * * * * * *
1719807 CTACAACTCTGTAGCACCCTTT-TAAGT
1 CCACAAGTCAGTGGCACTCTTTCAAAGC
* * *
1719834 CCACAAGTCAGTGGCATTCCTTCAAAGT
1 CCACAAGTCAGTGGCACTCTTTCAAAGC
1719862 CCACAAGTCAGTGGCAAC-CTTTCAAAGC
1 CCACAAGTCAGTGGC-ACTCTTTCAAAGC
*
1719890 CCACAAGTCAGTGGCACTCCTCTCAAAGC
1 CCACAAGTCAGTGGCACT-CTTTCAAAGC
1719919 CAACACAAGTCAGTGGCA-TCCTTTCAAAGCC
1 C--CACAAGTCAGTGGCACT-CTTTCAAAG-C
* *
1719950 CACACAAGTCAGTGGCAACCCATTTCAATGC
1 C-CACAAGTCAGTGGC-ACTC-TTTCAAAGC
* * *
1719981 TCACAAGTCGGTGGC-TTCTTTTCAAAGC
1 CCACAAGTCAGTGGCACTC-TTTCAAAGC
* *
1720009 CCACAAGTCAGTGGCACCCTTTTAAAGC
1 CCACAAGTCAGTGGCACTCTTTCAAAGC
* *
1720037 CCACGAGTCAATGGCACTCTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTCAAAGC
1720065 CCACAAGTCAGTGGCA-TCTTTTCAAAGC
1 CCACAAGTCAGTGGCACTC-TTTCAAAGC
1720093 CCACGCAAGTCAGTGGCAC-CTTTTCAAA-C
1 CCA--CAAGTCAGTGGCACTC-TTTCAAAGC
*
1720122 CCACGAGTCAGTGGCACTCTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTCAAAGC
*
1720150 CCACAAGTTAGTGGCA-TC-TTCAAAGCC
1 CCACAAGTCAGTGGCACTCTTTCAAAG-C
*
1720177 CACACAAGTCGGTGGCAACTCATTTCAAAGCC
1 C-CACAAGTCAGTGGC-ACTC-TTTCAAAG-C
** *
1720209 CACACAAGTTGGTGGCAACCCATTTCAAAGCC
1 C-CACAAGTCAGTGGC-ACTC-TTTCAAAG-C
** *
1720241 CACACAAGTTGGTGGCAAC-CTAT--AAG-
1 C-CACAAGTCAGTGGC-ACTCTTTCAAAGC
*** ** *
1720267 ---TTGGT--G-GCAACTCATTTGAAAGCC
1 CCACAAGTCAGTGGCACTC-TTTCAAAG-C
* *
1720291 CACACAAGTTAGTGGCAACCCATTTCAAAGCC
1 C-CACAAGTCAGTGGC-ACTC-TTTCAAAG-C
** *
1720323 CACACAAGTTGGTGGCAACTTATTTCAAAGCC
1 C-CACAAGTCAGTGGC-AC-TCTTTCAAAG-C
* * *
1720355 CACACAAGTTAGTGGCAACCCATTTTAAAGC
1 C-CACAAGTCAGTGGC-ACTC-TTTCAAAGC
** * *
1720386 CTACACAAGTTGGTGGCAAGTTATTTCAAAGCC
1 C--CACAAGTCAGTGGC-A-CTCTTTCAAAG-C
** * *
1720419 CACACAAGTTGGTGGCAACCCACTTCAAAGCC
1 C-CACAAGTCAGTGGC-ACTC-TTTCAAAG-C
**
1720451 CACACAAGTTGGTGGCAACT-TACTTCAAAGCC
1 C-CACAAGTCAGTGGC-ACTCT--TTCAAAG-C
**
1720483 CACACAAGTTGGTGGCAACT-TACTTCAAAGCC
1 C-CACAAGTCAGTGGC-ACTCT--TTCAAAG-C
** *
1720515 CACACAAGTTGGTGGCAACTCATTTGAAAGC
1 C-CACAAGTCAGTGGC-ACTC-TTTCAAAGC
** *
1720546 CCATACAAGTTGGTGGCAACCCATTTCAAAGCC
1 CC--ACAAGTCAGTGGC-ACTC-TTTCAAAG-C
** *
1720579 CACACAAGTTGGTGGCAACTTATTTCAAAGC
1 C-CACAAGTCAGTGGC-AC-TCTTTCAAAGC
** * *
1720610 CCAGACAAGTTGGTGGCAACCCATTTTAAAGC
1 CC--ACAAGTCAGTGGC-ACTC-TTTCAAAGC
** *
1720642 CTACACAAGTTGGTGGCAAGTCATTTCAAAGCC
1 C--CACAAGTCAGTGGC-ACTC-TTTCAAAG-C
** *
1720675 CACACAAGTTGGTGGCAACCTATTTCAAAGCC
1 C-CACAAGTCAGTGGC-A-CTCTTTCAAAG-C
** * *
1720707 CACACAAGTTGGTGGCAACCCATTTGAAAGC
1 C-CACAAGTCAGTGGC-ACTC-TTTCAAAGC
* *
1720738 CCATACAAGTTAGTGGGAACTCATTTCAAAGC
1 CC--ACAAGTCAGT-GGCACTC-TTTCAAAGC
* * *
1720770 CTACAAAGGT-GGTGGCAACCTATTTCAAAGCC
1 CCAC-AA-GTCAGTGGC-A-CTCTTTCAAAG-C
*
1720802 CACACAAGTCGGTGGCA-TCTTTTCAAAGC
1 C-CACAAGTCAGTGGCACTC-TTTCAAAGC
*
1720831 CCACAAGTCAGTGGTA-TCCTTTCAAAGC
1 CCACAAGTCAGTGGCACT-CTTTCAAAGC
** *
1720859 CCGTAAGTCTGTGGCA-TCCTTTCAAAGCC
1 CCACAAGTCAGTGGCACT-CTTTCAAAG-C
* *
1720888 CACACAAGTCGGTGGCAACCCATTTCAAAGC
1 C-CACAAGTCAGTGGC-ACTC-TTTCAAAGC
* * *
1720919 TCACAAGTCGGTGGC-TTCTTTTCAAAGC
1 CCACAAGTCAGTGGCACTC-TTTCAAAGC
* *
1720947 CCACAAGTCAATGGCACCCTTTCAAAGC
1 CCACAAGTCAGTGGCACTCTTTCAAAGC
* *
1720975 CCACAAGTCAGTGGCACCCTTTCCAAGC
1 CCACAAGTCAGTGGCACTCTTTCAAAGC
* *
1721003 CCACAAGTCAGTGGCACCCTTTCCAAGC
1 CCACAAGTCAGTGGCACTCTTTCAAAGC
*
1721031 CCACAAGTCAGTGGCA-TCCTTTCCAAG-
1 CCACAAGTCAGTGGCACT-CTTTCAAAGC
1721058 -C-C----CA-TGGCAACT-TTTCAAAGC
1 CCACAAGTCAGTGGC-ACTCTTTCAAAGC
* *
1721079 CCACGAGTCAGTAGCA-TCCTTTCAAAGC
1 CCACAAGTCAGTGGCACT-CTTTCAAAGC
*
1721107 CCACAAGTCGGTGGCA-TCTTTTCAAAGC
1 CCACAAGTCAGTGGCACTC-TTTCAAAGC
* * *
1721135 CCACAAATCAGTGGCACCCTTTCAAAAC
1 CCACAAGTCAGTGGCACTCTTTCAAAGC
* * * *
1721163 CCACAAGTCAATGGTA-TCTTTTCCATGC
1 CCACAAGTCAGTGGCACTC-TTTCAAAGC
1721191 CCACAAGTCAGTGGCAACT-TTTCAAAGC
1 CCACAAGTCAGTGGC-ACTCTTTCAAAGC
**
1721219 CCATGAGTCAGTGGCAACT-TTTCAAAGC
1 CCACAAGTCAGTGGC-ACTCTTTCAAAGC
* *
1721247 CCACGAGTCAGTGGCA-TCCTTCTAAAGC
1 CCACAAGTCAGTGGCACTCTTTC-AAAGC
*
1721275 CCACAAGTTAGTGGCA-TCCTTTCAAAGC
1 CCACAAGTCAGTGGCACT-CTTTCAAAGC
*
1721303 CCACAAGTCAGTGGCA-TCTCTTGAAAGC
1 CCACAAGTCAGTGGCACTCT-TTCAAAGC
1721331 CCACA
1 CCACA
1721336 GAAGTTAGTG
Statistics
Matches: 1353, Mismatches: 154, Indels: 206
0.79 0.09 0.12
Matches are distributed among these distances:
18 2 0.00
19 2 0.00
20 14 0.01
21 3 0.00
22 7 0.01
23 1 0.00
25 1 0.00
26 14 0.01
27 125 0.09
28 524 0.39
29 30 0.02
30 106 0.08
31 50 0.04
32 460 0.34
33 11 0.01
34 3 0.00
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (28 bp):
CCACAAGTCAGTGGCACTCTTTCAAAGC
Found at i:1720289 original size:50 final size:50
Alignment explanation
Indices: 1720214--1720310 Score: 167
Period size: 50 Copynumber: 1.9 Consensus size: 50
1720204 AAGCCCACAC
*
1720214 AAGTTGGTGGCAACCCATTTCAAAGCCCACACAAGTTGGTGGCAACCTAT
1 AAGTTGGTGGCAACCCATTTCAAAGCCCACACAAGTTAGTGGCAACCTAT
* *
1720264 AAGTTGGTGGCAACTCATTTGAAAGCCCACACAAGTTAGTGGCAACC
1 AAGTTGGTGGCAACCCATTTCAAAGCCCACACAAGTTAGTGGCAACC
1720311 CATTTCAAAG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.22
Consensus pattern (50 bp):
AAGTTGGTGGCAACCCATTTCAAAGCCCACACAAGTTAGTGGCAACCTAT
Found at i:1720289 original size:82 final size:82
Alignment explanation
Indices: 1720182--1720341 Score: 293
Period size: 82 Copynumber: 2.0 Consensus size: 82
1720172 AAGCCCACAC
*
1720182 AAGTCGGTGGCAACTCATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCACACA
1 AAGTCGGTGGCAACTCATTTCAAAGCCCACACAAGTTAGTGGCAACCCATTTCAAAGCCCACACA
1720247 AGTTGGTGGCAACCTAT
66 AGTTGGTGGCAACCTAT
* *
1720264 AAGTTGGTGGCAACTCATTTGAAAGCCCACACAAGTTAGTGGCAACCCATTTCAAAGCCCACACA
1 AAGTCGGTGGCAACTCATTTCAAAGCCCACACAAGTTAGTGGCAACCCATTTCAAAGCCCACACA
1720329 AGTTGGTGGCAAC
66 AGTTGGTGGCAAC
1720342 TTATTTCAAA
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 75 1.00
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.21
Consensus pattern (82 bp):
AAGTCGGTGGCAACTCATTTCAAAGCCCACACAAGTTAGTGGCAACCCATTTCAAAGCCCACACA
AGTTGGTGGCAACCTAT
Found at i:1720365 original size:64 final size:64
Alignment explanation
Indices: 1720264--1720835 Score: 817
Period size: 64 Copynumber: 9.0 Consensus size: 64
1720254 GGCAACCTAT
* * *
1720264 AAGTTGGTGGCAACTCATTTGAAAGCCCACACAAGTTAGTGGCAACCCATTTCAAAGCCCACAC
1 AAGTTGGTGGCAACTTATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCACAC
* * *
1720328 AAGTTGGTGGCAACTTATTTCAAAGCCCACACAAGTTAGTGGCAACCCATTTTAAAGCCTACAC
1 AAGTTGGTGGCAACTTATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCACAC
* *
1720392 AAGTTGGTGGCAAGTTATTTCAAAGCCCACACAAGTTGGTGGCAACCCACTTCAAAGCCCACAC
1 AAGTTGGTGGCAACTTATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCACAC
* ** *
1720456 AAGTTGGTGGCAACTTACTTCAAAGCCCACACAAGTTGGTGGCAACTTACTTCAAAGCCCACAC
1 AAGTTGGTGGCAACTTATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCACAC
* * *
1720520 AAGTTGGTGGCAACTCATTTGAAAGCCCATACAAGTTGGTGGCAACCCATTTCAAAGCCCACAC
1 AAGTTGGTGGCAACTTATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCACAC
* * *
1720584 AAGTTGGTGGCAACTTATTTCAAAGCCCAGACAAGTTGGTGGCAACCCATTTTAAAGCCTACAC
1 AAGTTGGTGGCAACTTATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCACAC
* * *
1720648 AAGTTGGTGGCAAGTCATTTCAAAGCCCACACAAGTTGGTGGCAACCTATTTCAAAGCCCACAC
1 AAGTTGGTGGCAACTTATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCACAC
** * * * * * *
1720712 AAGTTGGTGGCAACCCATTTGAAAGCCCATACAAGTTAGTGGGAACTCATTTCAAAGCCTACA-
1 AAGTTGGTGGCAACTTATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCACAC
* * * * *
1720775 AAGGTGGTGGCAACCTATTTCAAAGCCCACACAAGTCGGTGGC-A-TCTTTTCAAAGCCCACA
1 AAGTTGGTGGCAACTTATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCACA
1720836 AGTCAGTGGT
Statistics
Matches: 459, Mismatches: 49, Indels: 3
0.90 0.10 0.01
Matches are distributed among these distances:
61 15 0.03
62 1 0.00
63 36 0.08
64 407 0.89
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (64 bp):
AAGTTGGTGGCAACTTATTTCAAAGCCCACACAAGTTGGTGGCAACCCATTTCAAAGCCCACAC
Found at i:1720428 original size:96 final size:96
Alignment explanation
Indices: 1720264--1720951 Score: 841
Period size: 96 Copynumber: 7.3 Consensus size: 96
1720254 GGCAACCTAT
* * *
1720264 AAGTTGGTGGCAACTCATTTGAAAGCCCACACAAGTTAGTGGCAACCCATTTCAAAGCCCACACA
1 AAGTTGGTGGCAACTCATTTCAAAGCCCACACAAGTTGGTGGCAACCTATTTCAAAGCCCACACA
**
1720329 AGTTGGTGGCAACTTATTTCAAAGCCCACAC
66 AGTTGGTGGCAACCCATTTCAAAGCCCACAC
* * * * **
1720360 AAGTTAGTGGCAACCCATTTTAAAGCCTACACAAGTTGGTGGCAAGTTATTTCAAAGCCCACACA
1 AAGTTGGTGGCAACTCATTTCAAAGCCCACACAAGTTGGTGGCAACCTATTTCAAAGCCCACACA
*
1720425 AGTTGGTGGCAACCCACTTCAAAGCCCACAC
66 AGTTGGTGGCAACCCATTTCAAAGCCCACAC
* * * *
1720456 AAGTTGGTGGCAACTTACTTCAAAGCCCACACAAGTTGGTGGCAACTTACTTCAAAGCCCACACA
1 AAGTTGGTGGCAACTCATTTCAAAGCCCACACAAGTTGGTGGCAACCTATTTCAAAGCCCACACA
* * *
1720521 AGTTGGTGGCAACTCATTTGAAAGCCCATAC
66 AGTTGGTGGCAACCCATTTCAAAGCCCACAC
* * *
1720552 AAGTTGGTGGCAACCCATTTCAAAGCCCACACAAGTTGGTGGCAACTTATTTCAAAGCCCAGACA
1 AAGTTGGTGGCAACTCATTTCAAAGCCCACACAAGTTGGTGGCAACCTATTTCAAAGCCCACACA
* *
1720617 AGTTGGTGGCAACCCATTTTAAAGCCTACAC
66 AGTTGGTGGCAACCCATTTCAAAGCCCACAC
*
1720648 AAGTTGGTGGCAAGTCATTTCAAAGCCCACACAAGTTGGTGGCAACCTATTTCAAAGCCCACACA
1 AAGTTGGTGGCAACTCATTTCAAAGCCCACACAAGTTGGTGGCAACCTATTTCAAAGCCCACACA
* *
1720713 AGTTGGTGGCAACCCATTTGAAAGCCCATAC
66 AGTTGGTGGCAACCCATTTCAAAGCCCACAC
* * * *
1720744 AAGTTAGTGGGAACTCATTTCAAAGCCTACA-AAGGTGGTGGCAACCTATTTCAAAGCCCACACA
1 AAGTTGGTGGCAACTCATTTCAAAGCCCACACAAGTTGGTGGCAACCTATTTCAAAGCCCACACA
* * *
1720808 AGTCGGTGGC-A-TCTTTTCAAAG-CC-CAC
66 AGTTGGTGGCAACCCATTTCAAAGCCCACAC
** * * ** *
1720835 AAGTCAGTGG-TA-TCCTTTCAAAG-CC-CGTAAGTCT-GTGGCATCC--TTTCAAAGCCCACAC
1 AAGTTGGTGGCAACTCATTTCAAAGCCCACACAAGT-TGGTGGCAACCTATTTCAAAGCCCACAC
* *
1720893 AAGTCGGTGGCAACCCATTTCAAAG--CTCAC
65 AAGTTGGTGGCAACCCATTTCAAAGCCCACAC
* * *
1720923 AAGTCGGTGGC--TTCTTTTCAAAGCCCACA
1 AAGTTGGTGGCAACTCATTTCAAAGCCCACA
1720952 AGTCAATGGC
Statistics
Matches: 522, Mismatches: 61, Indels: 24
0.86 0.10 0.04
Matches are distributed among these distances:
86 26 0.05
87 3 0.01
88 43 0.08
89 13 0.02
90 2 0.00
91 11 0.02
92 2 0.00
93 8 0.02
94 1 0.00
95 41 0.08
96 372 0.71
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.23
Consensus pattern (96 bp):
AAGTTGGTGGCAACTCATTTCAAAGCCCACACAAGTTGGTGGCAACCTATTTCAAAGCCCACACA
AGTTGGTGGCAACCCATTTCAAAGCCCACAC
Found at i:1721065 original size:20 final size:20
Alignment explanation
Indices: 1721042--1721081 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1721032 CACAAGTCAG
* *
1721042 TGGCATCCTTTCCAAGCCCA
1 TGGCAACCTTTCAAAGCCCA
*
1721062 TGGCAACTTTTCAAAGCCCA
1 TGGCAACCTTTCAAAGCCCA
1721082 CGAGTCAGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.25, C:0.35, G:0.15, T:0.25
Consensus pattern (20 bp):
TGGCAACCTTTCAAAGCCCA
Found at i:1721524 original size:47 final size:46
Alignment explanation
Indices: 1721426--1721587 Score: 186
Period size: 45 Copynumber: 3.5 Consensus size: 46
1721416 AAATCCGATA
* * *
1721426 TCGCTGGCATTGAATCAGCATATTG-GCACCTTTA-TTAGCTCAATG
1 TCGCTGGCCTTGAATCAGCACATTGTCCA-CTTTACTTAGCTCAATG
* * *
1721471 TCGCTGGCCTTGAATCAGCACATTTTCCATTTTCCCTTAGCTCAATG
1 TCGCTGGCCTTGAATCAGCACATTGTCCACTTT-ACTTAGCTCAATG
* * *
1721518 TTGCTGGCCTTGAATCAGCACGTTGTCCACTTTAC-TAGCCCAATG
1 TCGCTGGCCTTGAATCAGCACATTGTCCACTTTACTTAGCTCAATG
**
1721563 TCGCTGGCCTTGAATTGGCACATTG
1 TCGCTGGCCTTGAATCAGCACATTG
1721588 GTAATCATCT
Statistics
Matches: 98, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
45 55 0.56
46 3 0.03
47 40 0.41
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (46 bp):
TCGCTGGCCTTGAATCAGCACATTGTCCACTTTACTTAGCTCAATG
Found at i:1722010 original size:20 final size:19
Alignment explanation
Indices: 1721964--1722041 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 19
1721954 TTTTACCCTG
* *
1721964 ATGTATCGATACATTTTTCA
1 ATGTATCGATACA-TTATGA
* *
1721984 ATATATCAATACATGTATGA
1 ATGTATCGATACAT-TATGA
* *
1722004 ATGTATCGATATATTCTGCA
1 ATGTATCGATACATTATG-A
1722024 ATGTATCGATACATTATG
1 ATGTATCGATACATTATG
1722042 TCTTTTTACC
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
19 4 0.09
20 42 0.91
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (19 bp):
ATGTATCGATACATTATGA
Found at i:1722036 original size:40 final size:39
Alignment explanation
Indices: 1721964--1722041 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
1721954 TTTTACCCTG
* *
1721964 ATGTATCGATACATTTTTCAATATATCAATACATGTATGA
1 ATGTATCGATACATTCTGCAATATATCAATACAT-TATGA
* * *
1722004 ATGTATCGATATATTCTGCAATGTATCGATACATTATG
1 ATGTATCGATACATTCTGCAATATATCAATACATTATG
1722042 TCTTTTTACC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTGCAATATATCAATACATTATGA
Found at i:1722964 original size:23 final size:23
Alignment explanation
Indices: 1722928--1722979 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
1722918 AGCCTTTGAC
1722928 CATGCA-TTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
1722950 CATGCATTTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
1722973 CATGCAT
1 CATGCAT
1722980 CTTTAACATG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 6 0.21
23 23 0.79
ACGTcount: A:0.19, C:0.12, G:0.10, T:0.60
Consensus pattern (23 bp):
CATGCATTTTTTTTATTATGTTT
Found at i:1732675 original size:14 final size:14
Alignment explanation
Indices: 1732652--1732689 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
1732642 ACTTTGATCG
1732652 TTGATC-ATTGACT
1 TTGATCTATTGACT
1732665 TTGATCTATTGACT
1 TTGATCTATTGACT
1732679 TTGA-CTATTGA
1 TTGATCTATTGA
1732690 TTATTGACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.24, C:0.13, G:0.16, T:0.47
Consensus pattern (14 bp):
TTGATCTATTGACT
Found at i:1732682 original size:20 final size:20
Alignment explanation
Indices: 1732639--1732703 Score: 80
Period size: 20 Copynumber: 3.2 Consensus size: 20
1732629 CGGTTGATAG
* *
1732639 TTGACTTTGATC-GTTGATCA
1 TTGACTTTGATCTATTGA-CT
1732659 TTGACTTTGATCTATTGACT
1 TTGACTTTGATCTATTGACT
1732679 TTGACTATTGAT-TATTGACT
1 TTGACT-TTGATCTATTGACT
1732699 TTGAC
1 TTGAC
1732704 CTTAAAAATC
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
20 32 0.78
21 9 0.22
ACGTcount: A:0.22, C:0.14, G:0.17, T:0.48
Consensus pattern (20 bp):
TTGACTTTGATCTATTGACT
Found at i:1732694 original size:7 final size:7
Alignment explanation
Indices: 1732658--1732703 Score: 53
Period size: 6 Copynumber: 6.9 Consensus size: 7
1732648 ATCGTTGATC
1732658 ATTGACT
1 ATTGACT
1732665 -TTGATCT
1 ATTGA-CT
1732672 ATTGACT
1 ATTGACT
1732679 -TTGACT
1 ATTGACT
*
1732685 ATTGATT
1 ATTGACT
1732692 ATTGACT
1 ATTGACT
1732699 -TTGAC
1 ATTGAC
1732704 CTTAAAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
6 15 0.44
7 15 0.44
8 4 0.12
ACGTcount: A:0.24, C:0.13, G:0.15, T:0.48
Consensus pattern (7 bp):
ATTGACT
Found at i:1737614 original size:2 final size:2
Alignment explanation
Indices: 1737607--1737637 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1737597 TTATGAAGTG
*
1737607 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1737638 GTCCAAGTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1738208 original size:3 final size:3
Alignment explanation
Indices: 1738202--1738253 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
1738192 AAAAAAATCA
* * * * *
1738202 TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT TGT TGT TAT TGT TAT TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1738250 TAT T
1 TAT T
1738254 GTAAAATACA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1739809 original size:14 final size:14
Alignment explanation
Indices: 1739790--1739835 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
1739780 TTTTTCTTCA
1739790 AATATAATATATTT
1 AATATAATATATTT
1739804 AATATAATATAAATTT
1 AATATAATAT--ATTT
1739820 -ATATAA-AT-TTT
1 AATATAATATATTT
1739831 AATAT
1 AATAT
1739836 GATAATAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
11 3 0.10
12 4 0.14
14 12 0.41
15 6 0.21
16 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATATAATATATTT
Found at i:1740871 original size:18 final size:19
Alignment explanation
Indices: 1740850--1740887 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1740840 AATTATATTT
*
1740850 TTAAATTAT-CAATAAAAA
1 TTAAAATATGCAATAAAAA
*
1740868 TTAAAATATGGAATAAAAA
1 TTAAAATATGCAATAAAAA
1740887 T
1 T
1740888 ATGAGATGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.32
Consensus pattern (19 bp):
TTAAAATATGCAATAAAAA
Found at i:1746294 original size:27 final size:25
Alignment explanation
Indices: 1746264--1746329 Score: 64
Period size: 27 Copynumber: 2.6 Consensus size: 25
1746254 ACAACATGAA
1746264 AAAAATAATTAAAATACGATATATTAT
1 AAAAATAATTAAAATACGA-ATA-TAT
**
1746291 AAAAA-ATATTATGATACGAATATAT
1 AAAAATA-ATTAAAATACGAATATAT
*
1746316 AAATAT-ATTAAAAT
1 AAAAATAATTAAAAT
1746330 TATTAAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
24 6 0.19
25 7 0.22
26 4 0.12
27 15 0.47
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (25 bp):
AAAAATAATTAAAATACGAATATAT
Found at i:1746294 original size:28 final size:25
Alignment explanation
Indices: 1746263--1746329 Score: 73
Period size: 24 Copynumber: 2.6 Consensus size: 25
1746253 TACAACATGA
1746263 AAAAAATAATTAAAATACGATATATTAT
1 AAAAAAT-ATTAAAATACGA-ATA-TAT
**
1746291 AAAAAATATTATGATACGAATATAT
1 AAAAAATATTAAAATACGAATATAT
*
1746316 -AAATATATTAAAAT
1 AAAAAATATTAAAAT
1746330 TATTAAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
24 11 0.32
25 3 0.09
26 3 0.09
27 10 0.29
28 7 0.21
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.33
Consensus pattern (25 bp):
AAAAAATATTAAAATACGAATATAT
Found at i:1746447 original size:11 final size:11
Alignment explanation
Indices: 1746431--1746470 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
1746421 ATAATATCTT
*
1746431 TAATATAATTA
1 TAATATAAATA
*
1746442 TAATATAAAAA
1 TAATATAAATA
1746453 TAATATAAATA
1 TAATATAAATA
1746464 TAATATA
1 TAATATA
1746471 TTATAATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TAATATAAATA
Found at i:1751289 original size:14 final size:16
Alignment explanation
Indices: 1751270--1751301 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
1751260 ATAAAATCGA
1751270 TAAAAAT-TA-ATTTT
1 TAAAAATATATATTTT
1751284 TAAAAATATATATTTT
1 TAAAAATATATATTTT
1751300 TA
1 TA
1751302 TTAATTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 2 0.12
16 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TAAAAATATATATTTT
Found at i:1751360 original size:19 final size:18
Alignment explanation
Indices: 1751329--1751377 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
1751319 TTATTAATAA
1751329 TTTAAAATTAAAATCATT
1 TTTAAAATTAAAATCATT
*
1751347 TTTAAAATTTAAAATTATT
1 TTTAAAA-TTAAAATCATT
*
1751366 TTATTAAATTAA
1 TT-TAAAATTAA
1751378 CTAATAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 7 0.26
19 16 0.59
20 4 0.15
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTAAAATTAAAATCATT
Found at i:1752630 original size:21 final size:22
Alignment explanation
Indices: 1752604--1752649 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
1752594 GTTAGGTTTG
1752604 TTTATGCTTGAAG-TTTGA-TTA
1 TTTATG-TTGAAGATTTGATTTA
*
1752625 TTTATGTTTAAGATTTGATTTA
1 TTTATGTTGAAGATTTGATTTA
1752647 TTT
1 TTT
1752650 TTTAGATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 5 0.23
21 11 0.50
22 6 0.27
ACGTcount: A:0.24, C:0.02, G:0.15, T:0.59
Consensus pattern (22 bp):
TTTATGTTGAAGATTTGATTTA
Found at i:1752647 original size:18 final size:19
Alignment explanation
Indices: 1752624--1752664 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
1752614 AAGTTTGATT
1752624 ATTTATGTTTAAGATTT-G
1 ATTTATGTTTAAGATTTAG
* *
1752642 ATTTATTTTTTAGATTTAG
1 ATTTATGTTTAAGATTTAG
1752661 ATTT
1 ATTT
1752665 GTCATTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.61
Consensus pattern (19 bp):
ATTTATGTTTAAGATTTAG
Found at i:1759587 original size:26 final size:26
Alignment explanation
Indices: 1759556--1759614 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
1759546 GCTCCTATAT
*
1759556 AGATTCATATCATCTACCCTACTTGA
1 AGATTCACATCATCTACCCTACTTGA
* * * *
1759582 ATATTCACATTATCTACCTTATTTGA
1 AGATTCACATCATCTACCCTACTTGA
1759608 AGATTCA
1 AGATTCA
1759615 ATTTCAACCA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (26 bp):
AGATTCACATCATCTACCCTACTTGA
Found at i:1769919 original size:12 final size:13
Alignment explanation
Indices: 1769902--1769930 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1769892 GCAGCCCAAG
1769902 AAGAAAG-AAAGA
1 AAGAAAGAAAAGA
1769914 AAGAAAGAAAAGA
1 AAGAAAGAAAAGA
1769927 AAGA
1 AAGA
1769931 CATTAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AAGAAAGAAAAGA
Found at i:1771204 original size:32 final size:30
Alignment explanation
Indices: 1771130--1771204 Score: 71
Period size: 32 Copynumber: 2.4 Consensus size: 30
1771120 AGCCTATTTC
* *
1771130 AATTTAATTTT-TGTTTTAAAATTAAAAGAC
1 AATTT-ATTTTATGTTTTAAAATAAAAAGAA
*
1771160 AATATAGTTTTTATGTTTTAAAATAAAAAAGAAA
1 AATTTA--TTTTATGTTTTAAAAT-AAAAAG-AA
1771194 AATTTATTTTA
1 AATTTATTTTA
1771205 AAATTGTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
29 1 0.03
30 4 0.11
31 4 0.11
32 16 0.44
33 5 0.14
34 6 0.17
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.45
Consensus pattern (30 bp):
AATTTATTTTATGTTTTAAAATAAAAAGAA
Found at i:1772271 original size:20 final size:20
Alignment explanation
Indices: 1772231--1772271 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1772221 ATGTTAATGT
* * *
1772231 TGATATCAAATTTTTTGTTA
1 TGATAACAAATTTTCTATTA
1772251 TGATAACAAATTTTCTATTA
1 TGATAACAAATTTTCTATTA
1772271 T
1 T
1772272 TAATAATGCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.51
Consensus pattern (20 bp):
TGATAACAAATTTTCTATTA
Found at i:1774903 original size:20 final size:20
Alignment explanation
Indices: 1774835--1774910 Score: 57
Period size: 20 Copynumber: 3.8 Consensus size: 20
1774825 AATTAAATTA
* *
1774835 TTTTTATATATATTCATA-AT
1 TTTTTATTTA-ATTTATATAT
* *
1774855 TTTTTATATAATTTATATAA
1 TTTTTATTTAATTTATATAT
* *
1774875 GTTTAATTTAATTGT-TATAT
1 TTTTTATTTAATT-TATATAT
*
1774895 TTTTTATTTTATTTAT
1 TTTTTATTTAATTTAT
1774911 TTAAATTATG
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
19 7 0.16
20 36 0.82
21 1 0.02
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTTATTTAATTTATATAT
Found at i:1775219 original size:17 final size:17
Alignment explanation
Indices: 1775199--1775267 Score: 50
Period size: 19 Copynumber: 3.9 Consensus size: 17
1775189 AAATATGATA
1775199 ATAAATAAAAATATAAG
1 ATAAATAAAAATATAAG
* *
1775216 ATAAAATTAAATATATAAA
1 AT-AAA-TAAAAATATAAG
*
1775235 AT-AATATAAATATGAAG
1 ATAAATAAAAATAT-AAG
* *
1775252 TTAATATATAAATATA
1 ATAA-ATAAAAATATA
1775268 TTAAATTATG
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
16 7 0.17
17 7 0.17
18 5 0.12
19 22 0.54
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (17 bp):
ATAAATAAAAATATAAG
Found at i:1775226 original size:19 final size:20
Alignment explanation
Indices: 1775185--1775240 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
1775175 AAAAATACAG
*
1775185 TAAAAA-ATATGATAATAAA
1 TAAAAATATAAGATAATAAA
*
1775204 TAAAAATATAAGATAA-AAT
1 TAAAAATATAAGATAATAAA
* *
1775223 TAAATATATAAAATAATA
1 TAAAAATATAAGATAATA
1775241 TAAATATGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 22 0.71
20 9 0.29
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.29
Consensus pattern (20 bp):
TAAAAATATAAGATAATAAA
Found at i:1775277 original size:29 final size:31
Alignment explanation
Indices: 1775225--1775304 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 31
1775215 GATAAAATTA
1775225 AATATATAAA-ATAATATAAA-TATGAAG-T-T
1 AATATATAAATAT-AT-TAAATTATGAAGATAT
*
1775254 AATATATAAATATATTAAATTATGTAGATAT
1 AATATATAAATATATTAAATTATGAAGATAT
*
1775285 AAT-TATTAATATATTAAATT
1 AATATATAAATATATTAAATT
1775305 TATATAAATA
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
28 4 0.09
29 18 0.40
30 19 0.42
31 4 0.09
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (31 bp):
AATATATAAATATATTAAATTATGAAGATAT
Found at i:1775298 original size:38 final size:38
Alignment explanation
Indices: 1775221--1775366 Score: 122
Period size: 38 Copynumber: 3.8 Consensus size: 38
1775211 ATAAGATAAA
*
1775221 ATTAAATATATA-AAATAATATAAATATGAA--GTTAATAT
1 ATTAAATATATATAAAT-ATAT-AATAT-AATTATTAATAT
*
1775259 A-TAAATATAT-TAAATTATGTAGATATAATTATTAATAT
1 ATTAAATATATATAAA-TATATA-ATATAATTATTAATAT
* * *
1775297 ATTAAATTTATATAAATATATAATATTATTTTTAATAT
1 ATTAAATATATATAAATATATAATATAATTATTAATAT
* *
1775335 GATTATAATATTTAAAAATATATAAATATAAT
1 -ATTA-AATATATATAAATATAT-AATATAAT
1775367 AAAAATATAT
Statistics
Matches: 88, Mismatches: 10, Indels: 17
0.77 0.09 0.15
Matches are distributed among these distances:
36 3 0.03
37 19 0.22
38 24 0.27
39 17 0.19
40 18 0.20
41 7 0.08
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (38 bp):
ATTAAATATATATAAATATATAATATAATTATTAATAT
Found at i:1775310 original size:49 final size:46
Alignment explanation
Indices: 1775254--1775369 Score: 126
Period size: 49 Copynumber: 2.4 Consensus size: 46
1775244 ATATGAAGTT
1775254 AATATATAAATATATTAAATTA-TGTAGATATAATTATTAATATATTAAA
1 AATATATAAATATA-TAAATTATTGTA-ATATAATTA-TAATAT-TTAAA
** * *
1775303 TTTATATAAATATATAATATTATTTTTAATATGATTATAATATTTAAA
1 AATATATAAATATATAA-ATTA-TTGTAATATAATTATAATATTTAAA
1775351 AATATATAAATATAATAAA
1 AATATATAAATAT-ATAAA
1775370 AATATATAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
48 20 0.35
49 26 0.46
50 8 0.14
51 3 0.05
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (46 bp):
AATATATAAATATATAAATTATTGTAATATAATTATAATATTTAAA
Found at i:1788876 original size:3 final size:3
Alignment explanation
Indices: 1788868--1788903 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1788858 TCTTTATCAT
1788868 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1788904 GCGGTAGTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1793536 original size:3 final size:3
Alignment explanation
Indices: 1793528--1793552 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1793518 CCCGAGTCAC
1793528 CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT C
1793553 TTTGATGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:1795295 original size:13 final size:13
Alignment explanation
Indices: 1795277--1795303 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1795267 TATAGTGAAC
1795277 ATGTATCGATACA
1 ATGTATCGATACA
1795290 ATGTATCGATACA
1 ATGTATCGATACA
1795303 A
1 A
1795304 AGCATGATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1798574 original size:22 final size:23
Alignment explanation
Indices: 1798530--1798574 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
1798520 ATATTCATGG
*
1798530 CATTCATTCAACATTTTCATAAT
1 CATTCATTCAACATTTGCATAAT
* *
1798553 CATTCA-TCAATATTTGCTTAAT
1 CATTCATTCAACATTTGCATAAT
1798575 TACTAAGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.33, C:0.20, G:0.02, T:0.44
Consensus pattern (23 bp):
CATTCATTCAACATTTGCATAAT
Found at i:1807618 original size:42 final size:42
Alignment explanation
Indices: 1806794--1807638 Score: 794
Period size: 42 Copynumber: 20.2 Consensus size: 42
1806784 ATTAAACTTC
* * * * *
1806794 TGGAGAC-TTTCTTTCCCTTAGTTTGTCTGTCGACTTTAACCC
1 TGGAGACTTTTC-TTCCCTTAGTCTGCCTGTCGGCTTTGACCT
* * * * **
1806836 TGGAGAC-TTTCTTTCTTTAGTCTACCTATTAGCTTTGACCT
1 TGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCT
* * *
1806877 TGGAGACTTTTCTTCCCTTAGTCTGCCTATCGACTTTGACCC
1 TGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCT
* *
1806919 TGGAGACTTTCCTTCCCTTAGTCTGCCTGTTGGCTTTGACCT
1 TGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCT
*
1806961 T-AAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACGC-
1 TGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGAC-CT
** * * * * * *
1807002 TAAAGACTTTCCTTCTCTTAGTCTGCCTATTGACTTTGACCC
1 TGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCT
* * * * *
1807044 TAGAGACTTTCCTTCCCTCAGTCTGCCTGTCGACTTTGACCC
1 TGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCT
* * * * *
1807086 TAGAGACTTTTCTTCCCTTGGTTTGCTTGTCGGCTTTGACCC
1 TGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCT
**
1807128 TGGAGA-TTTTCTTTCTTTTAGTCTGCCTGTCGGCTTTGACCCT
1 TGGAGACTTTTC-TTCCCTTAGTCTGCCTGTCGGCTTTGA-CCT
* * * *
1807171 TGCA-ACTTTTCTTCCCTTAGTCTGTCTGTCGACTTTGACCC
1 TGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCT
* * * *
1807212 TGGAGACTTTCCTTCCCTTAGTCTGCCTATCGACTTTGAACT
1 TGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCT
* * * **
1807254 TAGAGACTTTCCTTCCCTTAGTTTG-CTCGTCGATTTTGACCT
1 TGGAGACTTTTCTTCCCTTAGTCTGCCT-GTCGGCTTTGACCT
* * ** *
1807296 TAGAGAC-TTTCATACCCTTAGTCTGCCTGTCAACTTTGACCC
1 TGGAGACTTTTC-TTCCCTTAGTCTGCCTGTCGGCTTTGACCT
* ** *
1807338 TAGAGACTTCCCTTCCCTCAGTCTGCCTGTCGGCTTTGACCT
1 TGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCT
* * * *
1807380 TAGAGACTTTTTTTCCCTCAGCCTGCCTGTCGGCTTTGACCT
1 TGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCT
* * *
1807422 TGGAGACTTTCCTT-CCTTCAATCTGCCTGTCGGCTTTGACCC
1 TGGAGACTTTTCTTCCCTT-AGTCTGCCTGTCGGCTTTGACCT
** * * *
1807464 TAAAGACTTTCCTTCCCTCAGTCTGCCCGTCGGC-TTGACCT
1 TGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCT
* * *
1807505 TGGAGACTTTTCTACCCTTAGTCTGCCCGTCAGCTTTGACCT
1 TGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCT
* * *
1807547 TGGAGACTTTTCTACCTTTAGCCTGCCTGTCGG-TCTTGACCT
1 TGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCT-TTGACCT
* * * * *
1807589 TGGAGACTTTTCTACCCTTAGTCTACCTGTCGACATTGACCC
1 TGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCT
*
1807631 TGAAGACT
1 TGGAGACT
1807639 GCCTCATCTA
Statistics
Matches: 673, Mismatches: 113, Indels: 34
0.82 0.14 0.04
Matches are distributed among these distances:
41 116 0.17
42 540 0.80
43 17 0.03
ACGTcount: A:0.14, C:0.30, G:0.18, T:0.38
Consensus pattern (42 bp):
TGGAGACTTTTCTTCCCTTAGTCTGCCTGTCGGCTTTGACCT
Found at i:1808268 original size:31 final size:31
Alignment explanation
Indices: 1808230--1808288 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1808220 TGCATGCAAG
1808230 GCAATGTAGCATGCAATAATGGGAGACACAT
1 GCAATGTAGCATGCAATAATGGGAGACACAT
* *
1808261 GCAATGTAGCATGCAATCATGGGGGACA
1 GCAATGTAGCATGCAATAATGGGAGACA
1808289 TAAGCAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.36, C:0.17, G:0.29, T:0.19
Consensus pattern (31 bp):
GCAATGTAGCATGCAATAATGGGAGACACAT
Found at i:1808930 original size:24 final size:24
Alignment explanation
Indices: 1808902--1808955 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1808892 TTCCACGAAC
* *
1808902 ACAGCAACAGCATCTACGCACACG
1 ACAGCAACAGCATCCACGAACACG
1808926 ACAGCAACAGCATCCACGAACACG
1 ACAGCAACAGCATCCACGAACACG
*
1808950 GCAGCA
1 ACAGCA
1808956 GCTCGAGCCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.37, G:0.19, T:0.06
Consensus pattern (24 bp):
ACAGCAACAGCATCCACGAACACG
Done.