Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold141
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: 2772588
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.32
Warning! 118404 characters in sequence are not A, C, G, or T
File 7 of 18
Found at i:1160629 original size:102 final size:104
Alignment explanation
Indices: 1160493--1160684 Score: 300
Period size: 104 Copynumber: 1.9 Consensus size: 104
1160483 GGTGCTATTT
* *
1160493 TGCTAATTCAACTCAGTGATATTAGACTTAAAG-AA-AAAAAGGTGCCAATGTGTTGATTCGAGG
1 TGCTAATTCAACTCAGCGATATTAGACTTAAAGAAAGAAAAAGGTGCCAATGTGTTGATTCAAGG
1160556 CCAGCGACATTAGACTTAAAGATGAGAAAGATGCCAATA
66 CCAGCGACATTAGACTTAAAGATGAGAAAGATGCCAATA
*
1160595 TGCTAATTCAAGTCTAGCGATATTAGACTT-AAGAAAGAAAAAGGTGCCAATGTGTTGATTCAAG
1 TGCTAATTCAACTC-AGCGATATTAGACTTAAAGAAAGAAAAAGGTGCCAATGTGTTGATTCAAG
* * *
1160659 GCCATCGATATTGGACTTAAAGATGA
65 GCCAGCGACATTAGACTTAAAGATGA
1160685 TAACGATGAG
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
102 16 0.20
103 16 0.20
104 49 0.60
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (104 bp):
TGCTAATTCAACTCAGCGATATTAGACTTAAAGAAAGAAAAAGGTGCCAATGTGTTGATTCAAGG
CCAGCGACATTAGACTTAAAGATGAGAAAGATGCCAATA
Found at i:1161076 original size:52 final size:52
Alignment explanation
Indices: 1160993--1161162 Score: 155
Period size: 52 Copynumber: 3.3 Consensus size: 52
1160983 AATACCACTG
* * * * * * *
1160993 TGCTAATTCAAGGTCAGCAACATTGGGCTT-AAGAATGTTAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAACAATATTGGACTTAAAG-ATGATAAAGGTACCAATA
* *
1161045 TGTTGATTCAAGGCCAACAATATTGGACTTAAAGATGATAAAGGTACTAATA
1 TGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGATAAAGGTACCAATA
* * * * * * *
1161097 TGCTGATTCAAGGCCAACGATATCGGGC-TAAAGAAAGAAAAAGGCACTAATA
1 TGCTGATTCAAGGCCAACAATATTGGACTTAAAG-ATGATAAAGGTACCAATA
*
1161149 TGCTGATCCAAGGC
1 TGCTGATTCAAGGC
1161163 TAGGGAAAAT
Statistics
Matches: 99, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
51 5 0.05
52 91 0.92
53 3 0.03
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (52 bp):
TGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGATAAAGGTACCAATA
Found at i:1161230 original size:105 final size:104
Alignment explanation
Indices: 1160991--1161230 Score: 230
Period size: 104 Copynumber: 2.3 Consensus size: 104
1160981 ATAATACCAC
* * * ** ** * *
1160991 TGTGCTAATTCAAGGTCAGCAACATTGGGCTTAAGAATGTTAAAGGTGCCAATATGTTGATTCAA
1 TGTGCTGATTCAAGGTCAGCAACATTGGGCTAAAGAAAGAAAAAGGCACCAATATGCTGATCCAA
* *
1161056 GGCCAACAATATTGGACTTAAAGATGATAAAGGTACTAA
66 GGCCAACAAAATTGGACTTAAAGATGAGAAAGGTACTAA
* * * * * * *
1161095 TATGCTGATTCAAGGCCAACGATATCGGGCTAAAGAAAGAAAAAGGCACTAATATGCTGATCCAA
1 TGTGCTGATTCAAGGTCAGCAACATTGGGCTAAAGAAAGAAAAAGGCACCAATATGCTGATCCAA
* ** * * *
1161160 GGCTAGGGAAAATTTGACTTGAAGATGAG-AAGAGTGCTAA
66 GGCCA-ACAAAATTGGACTTAAAGATGAGAAAG-GTACTAA
*
1161200 TGTGCTGATTTAAGGTCAGCAACATTGGGCT
1 TGTGCTGATTCAAGGTCAGCAACATTGGGCT
1161231 TAGGAATGAT
Statistics
Matches: 103, Mismatches: 31, Indels: 3
0.75 0.23 0.02
Matches are distributed among these distances:
104 56 0.54
105 47 0.46
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (104 bp):
TGTGCTGATTCAAGGTCAGCAACATTGGGCTAAAGAAAGAAAAAGGCACCAATATGCTGATCCAA
GGCCAACAAAATTGGACTTAAAGATGAGAAAGGTACTAA
Found at i:1161537 original size:33 final size:32
Alignment explanation
Indices: 1161352--1161804 Score: 332
Period size: 32 Copynumber: 14.1 Consensus size: 32
1161342 TAAAAGGAGA
*
1161352 TGCCACTAACTTGTGTGGGCTTTTGAG-AG-GGT
1 TGCCACCAACTTGTGTGGGC--TTGAGAAGAGGT
* ** * * *
1161384 TTCCACCGTCTTGTATGGGCTAT-TGAAG-GGG
1 TGCCACCAACTTGTGTGGGCT-TGAGAAGAGGT
* * * *
1161415 TGCCACCAACTTATGTGAGCTTTAGAA-AGGAG
1 TGCCACCAACTTGTGTGGGCTTGAGAAGAGG-T
* * * *
1161447 TGACACCGACTTATGTGGGTTTTG-G-AGCAGGT
1 TGCCACCAACTTGTGTGGG-CTTGAGAAG-AGGT
*
1161479 TGCCACCGACTTGTGTGGGCTTTGAGAAGAGGT
1 TGCCACCAACTTGTGTGGGC-TTGAGAAGAGGT
1161512 TGCCAACCAACTTGTGTGGGCTTGAGAAGAGGT
1 TGCC-ACCAACTTGTGTGGGCTTGAGAAGAGGT
* * * * *
1161545 TACCACCAACTTGTATGGGCTTTAGAAGGGGG
1 TGCCACCAACTTGTGTGGGCTTGAGAAGAGGT
* * *
1161577 TGCCACCAACTTGTGTGGGCTTTA-AAAAGGG
1 TGCCACCAACTTGTGTGGGCTTGAGAAGAGGT
* *
1161608 TGCCACCGACTTGTGTGGGCTTTAGAAGAGGT
1 TGCCACCAACTTGTGTGGGCTTGAGAAGAGGT
** * *
1161640 TGCCACCGGCTTGTGTGGGCTTTAG-AGGGGT
1 TGCCACCAACTTGTGTGGGCTTGAGAAGAGGT
* * *
1161671 TGCTACCAATTTATGTGGGCTTTGAGAAGAGGT
1 TGCCACCAACTTGTGTGGGC-TTGAGAAGAGGT
* * *
1161704 TGCCACCAACTTATGTGGGCTTTAGAAGGGGT
1 TGCCACCAACTTGTGTGGGCTTGAGAAGAGGT
* **** *
1161736 TTCCATTGTCTTGTGTGGGCTTTGA-AAAAGGGT
1 TGCCACCAACTTGTGTGGGC-TTGAGAAGA-GGT
*
1161769 TGCCACCAGCTTGTGTGGGCTTTAGAGAAGAGGT
1 TGCCACCAACTTGTGTGGGC-TT-GAGAAGAGGT
1161803 TG
1 TG
1161805 AATCCACTAG
Statistics
Matches: 338, Mismatches: 64, Indels: 36
0.77 0.15 0.08
Matches are distributed among these distances:
30 3 0.01
31 74 0.22
32 158 0.47
33 76 0.22
34 24 0.07
35 3 0.01
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (32 bp):
TGCCACCAACTTGTGTGGGCTTGAGAAGAGGT
Found at i:1161642 original size:161 final size:159
Alignment explanation
Indices: 1161359--1161804 Score: 519
Period size: 161 Copynumber: 2.8 Consensus size: 159
1161349 AGATGCCACT
* **
1161359 AACTTGTGTGGGCTTTTGAG-AG-GGTTTCCACCGTCTTGTATGGGCTATT-GAA-GGGGTGCCA
1 AACTTGTGTGGGC-TTTGAGAAGAGGTTACCACCAACTTGTATGGGCT-TTAGAAGGGGGTGCCA
* * * * * * *
1161420 CCAACTTATGTGAGCTTTAGAAAGGAGTGACACCGACTTATGTGGG-TTTTGGAGCAGGTTGCCA
64 CCAACTTGTGTGGGCTTTAAAAAGG-GTGCCACCGACTTGTGTGGGCTTTAGAAG-AGGTTGCCA
1161484 CCGACTTGTGTGGGCTTTGAGAAGAGGTTGCCAACC
127 CCGACTTGTGTGGGCTTT-AG-AGAGGTTG-CAACC
1161520 AACTTGTGTGGGC-TTGAGAAGAGGTTACCACCAACTTGTATGGGCTTTAGAAGGGGGTGCCACC
1 AACTTGTGTGGGCTTTGAGAAGAGGTTACCACCAACTTGTATGGGCTTTAGAAGGGGGTGCCACC
*
1161584 AACTTGTGTGGGCTTTAAAAAGGGTGCCACCGACTTGTGTGGGCTTTAGAAGAGGTTGCCACCGG
66 AACTTGTGTGGGCTTTAAAAAGGGTGCCACCGACTTGTGTGGGCTTTAGAAGAGGTTGCCACCGA
* *
1161649 CTTGTGTGGGCTTTAGAGGGGTTGCTACC
131 CTTGTGTGGGCTTTAGAGAGGTTGCAACC
* * * * * * * **
1161678 AATTTATGTGGGCTTTGAGAAGAGGTTGCCACCAACTTATGTGGGCTTTAGAAGGGGTTTCCATT
1 AACTTGTGTGGGCTTTGAGAAGAGGTTACCACCAACTTGTATGGGCTTTAGAAGGGGGTGCCACC
**
1161743 GTCTTGTGTGGGCTTTGAAAAAGGGTTGCCACC-AGCTTGTGTGGGCTTTAGAGAAGAGGTTG
66 AACTTGTGTGGGCTTT-AAAAAGGG-TGCCACCGA-CTTGTGTGGGCTTT--AGAAGAGGTTG
1161805 AATCCACTAG
Statistics
Matches: 250, Mismatches: 24, Indels: 20
0.85 0.08 0.07
Matches are distributed among these distances:
158 15 0.06
159 70 0.28
160 15 0.06
161 102 0.41
162 37 0.15
163 11 0.04
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (159 bp):
AACTTGTGTGGGCTTTGAGAAGAGGTTACCACCAACTTGTATGGGCTTTAGAAGGGGGTGCCACC
AACTTGTGTGGGCTTTAAAAAGGGTGCCACCGACTTGTGTGGGCTTTAGAAGAGGTTGCCACCGA
CTTGTGTGGGCTTTAGAGAGGTTGCAACC
Found at i:1161725 original size:64 final size:63
Alignment explanation
Indices: 1161352--1161795 Score: 387
Period size: 63 Copynumber: 6.9 Consensus size: 63
1161342 TAAAAGGAGA
* * * ** *
1161352 TGCCACTAACTTGTGTGGGCTTTTG-AGAGGGTTTCCACCGTCTTGTATGGGCTATT-GAAGGGG
1 TGCCACCAACTTGTGTGGGCTTTAGAAGA-GGTTGCCACCAACTTGTGTGGGCT-TTAG-AGGGG
1161415 -
63 T
* * * * * * * * *
1161415 TGCCACCAACTTATGTGAGCTTTAGAA-AGGAGTGACACCGACTTATGTGGGTTTTGGAGCAGGT
1 TGCCACCAACTTGTGTGGGCTTTAGAAGAGG-TTGCCACCAACTTGTGTGGGCTTTAGAG-GGGT
* * *
1161479 TGCCACCGACTTGTGTGGGCTTTGAGAAGAGGTTGCCAACCAACTTGTGTGGGCTTGAGAAGAGG
1 TGCCACCAACTTGTGTGGGCTTT-AGAAGAGGTTGCC-ACCAACTTGTGTGGGCTTTAG-AGGGG
1161544 T
63 T
* * * * * *
1161545 TACCACCAACTTGTATGGGCTTTAGAAGGGGGTGCCACCAACTTGTGTGGGCTTTAAAAAGGG-
1 TGCCACCAACTTGTGTGGGCTTTAGAAGAGGTTGCCACCAACTTGTGTGGGCTTT-AGAGGGGT
* **
1161608 TGCCACCGACTTGTGTGGGCTTTAGAAGAGGTTGCCACCGGCTTGTGTGGGCTTTAGAGGGGT
1 TGCCACCAACTTGTGTGGGCTTTAGAAGAGGTTGCCACCAACTTGTGTGGGCTTTAGAGGGGT
* * * *
1161671 TGCTACCAATTTATGTGGGCTTTGAGAAGAGGTTGCCACCAACTTATGTGGGCTTTAGAAGGGGT
1 TGCCACCAACTTGTGTGGGCTTT-AGAAGAGGTTGCCACCAACTTGTGTGGGCTTTAG-AGGGGT
* **** * *
1161736 TTCCATTGTCTTGTGTGGGCTTT-GAAAAAGGGTTGCCACCAGCTTGTGTGGGCTTTAGAG
1 TGCCACCAACTTGTGTGGGCTTTAG-AAGA-GGTTGCCACCAACTTGTGTGGGCTTTAGAG
1161796 AAGAGGTTGA
Statistics
Matches: 308, Mismatches: 58, Indels: 29
0.78 0.15 0.07
Matches are distributed among these distances:
62 11 0.04
63 108 0.35
64 78 0.25
65 66 0.21
66 43 0.14
67 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.30
Consensus pattern (63 bp):
TGCCACCAACTTGTGTGGGCTTTAGAAGAGGTTGCCACCAACTTGTGTGGGCTTTAGAGGGGT
Found at i:1174755 original size:34 final size:34
Alignment explanation
Indices: 1174717--1174792 Score: 134
Period size: 34 Copynumber: 2.2 Consensus size: 34
1174707 TGGATTCAAA
1174717 ATATTTATATATAAATATAAAAATAAAAAATTTT
1 ATATTTATATATAAATATAAAAATAAAAAATTTT
*
1174751 ATATTTATATATAAATATAAAAATAAAAATTTTT
1 ATATTTATATATAAATATAAAAATAAAAAATTTT
*
1174785 TTATTTAT
1 ATATTTAT
1174793 GTTTGTAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (34 bp):
ATATTTATATATAAATATAAAAATAAAAAATTTT
Found at i:1176199 original size:20 final size:21
Alignment explanation
Indices: 1176174--1176228 Score: 80
Period size: 20 Copynumber: 2.8 Consensus size: 21
1176164 GGAAAGAGAA
1176174 TGTATCAATACATTTTTC-AT
1 TGTATCAATACATTTTTCAAT
*
1176194 TGTATCGATACA-TTTTCAAT
1 TGTATCAATACATTTTTCAAT
1176214 T-TATCAATACATTTT
1 TGTATCAATACATTTT
1176229 GGGTTTTTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.31, C:0.15, G:0.05, T:0.49
Consensus pattern (21 bp):
TGTATCAATACATTTTTCAAT
Found at i:1176211 original size:19 final size:20
Alignment explanation
Indices: 1176174--1176228 Score: 78
Period size: 19 Copynumber: 2.8 Consensus size: 20
1176164 GGAAAGAGAA
1176174 TGTATCAATACATTTTTC-AT
1 TGTATCAATACA-TTTTCAAT
*
1176194 TGTATCGATACATTTTCAAT
1 TGTATCAATACATTTTCAAT
1176214 T-TATCAATACATTTT
1 TGTATCAATACATTTT
1176229 GGGTTTTTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.31, C:0.15, G:0.05, T:0.49
Consensus pattern (20 bp):
TGTATCAATACATTTTCAAT
Found at i:1178821 original size:96 final size:97
Alignment explanation
Indices: 1178622--1178811 Score: 265
Period size: 96 Copynumber: 2.0 Consensus size: 97
1178612 TTTATTTATT
* ** *
1178622 AGGGATACTCCAACCCCATTCATCCGAGCGGATACTCTAACTCCATTTTTAAACTTATTAAGATT
1 AGGGATACTCCAACCTCATTCATCCGAAAGGATACTCTAACTCCATTTTTAAACTTATCAAGATT
* *
1178687 TTAATCTTATTTTTGCTTAAATTTTCATCAAC
66 TAAATCTTATTTTTGCTTAAATTATCATCAAC
* * ** *
1178719 AGGGATACTCCAACCTCATTCTTCCGAAAGGATACTTTAAC-CTGTTTTTAAACTTGTCAAGATT
1 AGGGATACTCCAACCTCATTCATCCGAAAGGATACTCTAACTCCATTTTTAAACTTATCAAGATT
*
1178783 TAAATCTTATTTTTGTTTAAATTATCATC
66 TAAATCTTATTTTTGCTTAAATTATCATC
1178812 GTCGGGGATA
Statistics
Matches: 81, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
96 45 0.56
97 36 0.44
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (97 bp):
AGGGATACTCCAACCTCATTCATCCGAAAGGATACTCTAACTCCATTTTTAAACTTATCAAGATT
TAAATCTTATTTTTGCTTAAATTATCATCAAC
Found at i:1178850 original size:96 final size:96
Alignment explanation
Indices: 1178622--1178838 Score: 254
Period size: 96 Copynumber: 2.2 Consensus size: 96
1178612 TTTATTTATT
* * ** * ** *
1178622 AGGGATACTCCAACCCCATTCATCCGAGCGGATACTCTAACTCCATTTTTAAACTTATTAAGATT
1 AGGGATACTCCAACCTCATTCCTCCGAAAGGATACTTTAAC-CTGTTTTTAAACTTATCAAGATT
* *
1178687 TTAATCTTATTTTTGCTTAAATTTTCATCAAC
65 TAAATCTTATTTTTGCTTAAATTATCATCAAC
* *
1178719 AGGGATACTCCAACCTCATTCTTCCGAAAGGATACTTTAACCTGTTTTTAAACTTGTCAAGATTT
1 AGGGATACTCCAACCTCATTCCTCCGAAAGGATACTTTAACCTGTTTTTAAACTTATCAAGATTT
* **
1178784 AAATCTTATTTTTGTTTAAATTATCATCGTC
66 AAATCTTATTTTTGCTTAAATTATCATCAAC
* * **
1178815 GGGGATATTTTAACCTCATTCCTC
1 AGGGATACTCCAACCTCATTCCTC
1178839 TGAGGGGATA
Statistics
Matches: 101, Mismatches: 19, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
96 65 0.64
97 36 0.36
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (96 bp):
AGGGATACTCCAACCTCATTCCTCCGAAAGGATACTTTAACCTGTTTTTAAACTTATCAAGATTT
AAATCTTATTTTTGCTTAAATTATCATCAAC
Found at i:1179853 original size:67 final size:68
Alignment explanation
Indices: 1179777--1179948 Score: 211
Period size: 67 Copynumber: 2.5 Consensus size: 68
1179767 AAGTGGATAA
* * *
1179777 GTGCTACTAGCCTGTATAGGCTTTGAGGTAGGTAAGCATCATATTCTTTGAGGATTGA-AGTAAG
1 GTGCTACTAGCCTGTATAGGCTTTGAGATGGGTAAGCATCATATTCTTTAAGGATTGAGAGTAAG
1179841 TAG
66 TAG
* * * * * * *
1179844 GTGCCACTAGCCTGTATGGGCTTTGAGATGGGTAACCATCTTGTTCTTTAAGGATTGAGGGTAGG
1 GTGCTACTAGCCTGTATAGGCTTTGAGATGGGTAAGCATCATATTCTTTAAGGATTGAGAGTAAG
1179909 TAG
66 TAG
* * * *
1179912 GTGCTATTAGCTTGTGTAGGCCTTGAGATGGGTAAGC
1 GTGCTACTAGCCTGTATAGGCTTTGAGATGGGTAAGC
1179949 GTTCTACTCT
Statistics
Matches: 87, Mismatches: 17, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
67 50 0.57
68 37 0.43
ACGTcount: A:0.23, C:0.13, G:0.31, T:0.33
Consensus pattern (68 bp):
GTGCTACTAGCCTGTATAGGCTTTGAGATGGGTAAGCATCATATTCTTTAAGGATTGAGAGTAAG
TAG
Found at i:1180155 original size:68 final size:68
Alignment explanation
Indices: 1179748--1180853 Score: 448
Period size: 68 Copynumber: 16.1 Consensus size: 68
1179738 TAAAAAAATG
* * * * * * * *
1179748 TCCTACTCTTTGAGGACTA-A-AGT-GGATAAGTGCTACTAGCCTGTATAGGCTTTGAGGTAGGT
1 TCCTACTCTTTGAGGA-TAGAGGGTAGG-TAGGTGCCACTAGCTTGTGTGGGCTTTGAGATGGGT
1179810 AAGCA
64 AAGCA
* * * * * * *
1179815 TCATATTCTTTGAGGATTGA-AGTAAGTAGGTGCCACTAGCCTGTATGGGCTTTGAGATGGGTAA
1 TCCTACTCTTTGAGGATAGAGGGTAGGTAGGTGCCACTAGCTTGTGTGGGCTTTGAGATGGGTAA
*
1179879 CCA
66 GCA
* ** * * * * * *
1179882 TCTTGTTCTTTAAGGATTGAGGGTAGGTAGGTGCTATTAGCTTGTGTAGGCCTTGAGATGGGTAA
1 TCCTACTCTTTGAGGATAGAGGGTAGGTAGGTGCCACTAGCTTGTGTGGGCTTTGAGATGGGTAA
*
1179947 GCG
66 GCA
* * * * * * * *
1179950 TTCTACTC-TTGAAGGACTA-AGGGTAGATAGGTGCCACCAACTTGTGTGGACTTTAAGGTGGAT
1 TCCTACTCTTTG-AGGA-TAGAGGGTAGGTAGGTGCCACTAGCTTGTGTGGGCTTTGAGATGGGT
*
1180013 AAGAAAA
64 AAG--CA
* * * * * * * *
1180020 GTGACCTGCTCTTCGATGACTA-A-GATAGGTAGGTGCCACCAACTTGTGTGGGCTTTAAAATGG
1 -T--CCTACTCTTTGAGGA-TAGAGGGTAGGTAGGTGCCACTAGCTTGTGTGGGCTTTGAGATGG
1180083 GTAAGCA
62 GTAAGCA
* * * *
1180090 TCCTACTCTTTGAGGATAGAGGGGAGGTACGTGCCACTAGCTTATGTGGGCTTTGAGGTGGGTAA
1 TCCTACTCTTTGAGGATAGAGGGTAGGTAGGTGCCACTAGCTTGTGTGGGCTTTGAGATGGGT--
*
1180155 GAAAAGTA
64 ---AAGCA
* * * ** * * * * * * ** *
1180163 TCATATTTTTTGAGGACT--TTGGCAGGTAGGTACCATTATCATATGTAAGCTTTGAGATAGGTA
1 TCCTACTCTTTGAGGA-TAGAGGGTAGGTAGGTGCCACTAGCTTGTGTGGGCTTTGAGATGGGTA
**
1180226 AGTG
65 AGCA
** * *
1180230 TTTTACTCTTTGAGGACTA-AGGGTAGGTAGTTGCCA-TCAGCTTATGTGGGCTTTGAGATGGGT
1 TCCTACTCTTTGAGGA-TAGAGGGTAGGTAGGTGCCACT-AGCTTGTGTGGGCTTTGAGATGGGT
1180293 AAGCA
64 AAGCA
** * * * * * * *
1180298 TCCTTTTCTTTGAAGACT-GAGGATAGATAGGTGCCA-TCAACTTGTGTAGGCTTCGAGATAGGT
1 TCCTACTCTTTGAGGA-TAGAGGGTAGGTAGGTGCCACT-AGCTTGTGTGGGCTTTGAGATGGGT
***
1180361 AAATG
64 AAGCA
* * * * *
1180366 TTCTACT-TTCTGAGGACT-GAAGGTAGGCAGGTGCCACTAGCTTATATGGGCTTTGAGATGGGT
1 TCCTACTCTT-TGAGGA-TAGAGGGTAGGTAGGTGCCACTAGCTTGTGTGGGCTTTGAGATGGGT
1180429 AAGCA
64 AAGCA
** * ** * *
1180434 -CCTTGGTCTTTGATGACTA-AGGGTAGACAGGTGCCACT-GACTTGTGTGGGCTTAGAAATGGG
1 TCC-TACTCTTTGAGGA-TAGAGGGTAGGTAGGTGCCACTAG-CTTGTGTGGGCTTTGAGATGGG
**
1180496 TAAGTG
63 TAAGCA
* * * * * * * * * * *
1180502 TCTTATTCTTTGAGGACT-GAAGGTAAGTGGGTGCCCCCAACTTTTTTGGGTTTTGAGATGGGTA
1 TCCTACTCTTTGAGGA-TAGAGGGTAGGTAGGTGCCACTAGCTTGTGTGGGCTTTGAGATGGGTA
*
1180566 AACA
65 AGCA
* * * * * * ** * * * *
1180570 TCTTGCTCTTTAAAGATTGAGGGTAGATAGGCACCACCAGTTTGTGTGGGCTTT-AAAGTGGATA
1 TCCTACTCTTTGAGGATAGAGGGTAGGTAGGTGCCACTAGCTTGTGTGGGCTTTGAGA-TGGGTA
*
1180634 AGAAAA
65 AG--CA
* * * * *
1180640 GTGTCCTACTCTTTGAGGACTA-A-GGTAAGTAGGTGCTACCAGCTTGTATGGGCTTTTAGATGG
1 ---TCCTACTCTTTGAGGA-TAGAGGGTAGGTAGGTGCCACTAGCTTGTGTGGGCTTTGAGATGG
*
1180703 GTAAGTA
62 GTAAGCA
* * **
1180710 TCATACTCTTTGAGGACT-GAGGGTAGGTAGGTG-CAATAAGCTTGTGTAAGCTTTGAGATGGGT
1 TCCTACTCTTTGAGGA-TAGAGGGTAGGTAGGTGCCACT-AGCTTGTGTGGGCTTTGAGATGGGT
* *
1180773 AAACG
64 AAGCA
* * * * ** * *
1180778 TCTTACTCTTTGAGGACTA-A-GGTAGGTAGATGCCTCTGGCTCATGTGGGCTTTGAGATAGGTG
1 TCCTACTCTTTGAGGA-TAGAGGGTAGGTAGGTGCCACTAGCTTGTGTGGGCTTTGAGATGGGTA
1180841 AGCA
65 AGCA
1180845 TCCTACTCT
1 TCCTACTCT
1180854 GTAAGCTCAA
Statistics
Matches: 770, Mismatches: 224, Indels: 90
0.71 0.21 0.08
Matches are distributed among these distances:
66 3 0.00
67 170 0.22
68 435 0.56
69 6 0.01
70 3 0.00
71 1 0.00
72 104 0.14
73 44 0.06
74 4 0.01
ACGTcount: A:0.25, C:0.14, G:0.30, T:0.31
Consensus pattern (68 bp):
TCCTACTCTTTGAGGATAGAGGGTAGGTAGGTGCCACTAGCTTGTGTGGGCTTTGAGATGGGTAA
GCA
Found at i:1180401 original size:136 final size:136
Alignment explanation
Indices: 1179821--1180848 Score: 555
Period size: 136 Copynumber: 7.5 Consensus size: 136
1179811 AGCATCATAT
* * * * * *
1179821 TCTTTGAGGATTGAA-GTAAGTAGGTGCCACTAGCCTGTATGGGCTTTGAGATGGGTAACCAT-C
1 TCTTTGAGGACT-AAGGTAGGTAGGTGCCACCAGCTTATATGGGCTTTGAGATGGGTAAGCATCC
* * * * * * *
1179884 TTGTTCTTT-AAGGATTGAGGGTAGGTAGGTGCTATTAGCTTGTGTAGGCCTT-GAGATGGGTAA
65 TTGCTCTTTGAA-GACTGAGGGTAGATAGGTGCCATCAACTTGTGTAGG-CTTAGAGATAGGTAA
**
1179947 GCGTTCTAC
128 ATGTTCTAC
* * * * * * * * *
1179956 TC-TTGAAGGACTAAGGGTAGATAGGTGCCACCAACTTGTGTGGACTTTAAGGTGGATAAGAAAA
1 TCTTTG-AGGACTAA-GGTAGGTAGGTGCCACCAGCTTATATGGGCTTTGAGATGGGTAAG--CA
* * * * * * * * *
1180020 GTGACC-TGCTCTTCGATGACT-AAGATAGGTAGGTGCCACCAACTTGTGTGGGCTTTA-AAATG
62 -T--CCTTGCTCTTTGAAGACTGAGGGTAGATAGGTGCCATCAACTTGTGTAGGC-TTAGAGATA
*** *
1180082 GGTAAGCATCCTAC
123 GGTAAATGTTCTAC
* * * * * *
1180096 TCTTTGAGGA-TAGAGGGGAGGTACGTGCCACTAGCTTATGTGGGCTTTGAGGTGGGTAAGAAAA
1 TCTTTGAGGACTA-A-GGTAGGTAGGTGCCACCAGCTTATATGGGCTTTGAGATGGGTAAG--CA
* * ** * * ** * * * * * * * * *
1180160 GTATCATATTTTTTGAGGACT-TTGGCAGGTAGGTACCATTATCATATGTAAGCTTTGAGATAGG
62 -T-CCTTGCTCTTTGAAGACTGAGGGTAGATAGGTGCCATCAACTTGTGTAGGCTTAGAGATAGG
* *
1180224 TAAGTGTTTTAC
125 TAAATGTTCTAC
* * *
1180236 TCTTTGAGGACTAAGGGTAGGTAGTTGCCATCAGCTTATGTGGGCTTTGAGATGGGTAAGCATCC
1 TCTTTGAGGACTAA-GGTAGGTAGGTGCCACCAGCTTATATGGGCTTTGAGATGGGTAAGCATCC
* * *
1180301 TT-TTCTTTGAAGACTGAGGATAGATAGGTGCCATCAACTTGTGTAGGCTTCGAGATAGGTAAAT
65 TTGCTCTTTGAAGACTGAGGGTAGATAGGTGCCATCAACTTGTGTAGGCTTAGAGATAGGTAAAT
1180365 GTTCTAC
130 GTTCTAC
* *
1180372 T-TTCTGAGGACTGAAGGTAGGCAGGTGCCACTAGCTTATATGGGCTTTGAGATGGGTAAGCA-C
1 TCTT-TGAGGACT-AAGGTAGGTAGGTGCCACCAGCTTATATGGGCTTTGAGATGGGTAAGCATC
* * * * * * * *
1180435 CTTGGTCTTTGATGACTAAGGGTAGACAGGTGCCA-CTGACTTGTGTGGGCTTAGAAATGGGTAA
64 CTTGCTCTTTGAAGACTGAGGGTAGATAGGTGCCATC-AACTTGTGTAGGCTTAGAGATAGGTAA
* *
1180499 GTG-TCTTAT
128 ATGTTC-TAC
* * * * * * * *
1180508 TCTTTGAGGACTGAAGGTAAGTGGGTGCCCCCAACTTTTTTGGGTTTTGAGATGGGTAAACAT-C
1 TCTTTGAGGACT-AAGGTAGGTAGGTGCCACCAGCTTATATGGGCTTTGAGATGGGTAAGCATCC
* * ** * ** * * * *
1180572 TTGCTCTTTAAAGATTGAGGGTAGATAGGCACCACCAGTTTGTGTGGGCTTTAAAGTGGATAAGA
65 TTGCTCTTTGAAGACTGAGGGTAGATAGGTGCCATCAACTTGTGTAGGC-TT--AG-AGATAGGT
*
1180637 AAAGTGTCCTAC
126 AAA-TGTTCTAC
* * * * * *
1180649 TCTTTGAGGACTAAGGTAAGTAGGTGCTACCAGCTTGTATGGGCTTTTAGATGGGTAAGTAT-CA
1 TCTTTGAGGACTAAGGTAGGTAGGTGCCACCAGCTTATATGGGCTTTGAGATGGGTAAGCATCCT
* * * * * * * *
1180713 TACTCTTTGAGGACTGAGGGTAGGTAGGTGCAAT-AAGCTTGTGTAAGCTTTGAGATGGGTAAAC
66 TGCTCTTTGAAGACTGAGGGTAGATAGGTGCCATCAA-CTTGTGTAGGCTTAGAGATAGGTAAAT
1180777 G-TCTTAC
130 GTTC-TAC
* * ** * * * *
1180784 TCTTTGAGGACTAAGGTAGGTAGATGCCTCTGGCTCATGTGGGCTTTGAGATAGGTGAGCATCCT
1 TCTTTGAGGACTAAGGTAGGTAGGTGCCACCAGCTTATATGGGCTTTGAGATGGGTAAGCATCCT
1180849 ACTCTGTAAG
Statistics
Matches: 681, Mismatches: 177, Indels: 69
0.73 0.19 0.07
Matches are distributed among these distances:
134 6 0.01
135 80 0.12
136 273 0.40
137 9 0.01
138 2 0.00
139 13 0.02
140 265 0.39
141 30 0.04
142 3 0.00
ACGTcount: A:0.25, C:0.14, G:0.30, T:0.31
Consensus pattern (136 bp):
TCTTTGAGGACTAAGGTAGGTAGGTGCCACCAGCTTATATGGGCTTTGAGATGGGTAAGCATCCT
TGCTCTTTGAAGACTGAGGGTAGATAGGTGCCATCAACTTGTGTAGGCTTAGAGATAGGTAAATG
TTCTAC
Found at i:1180763 original size:140 final size:141
Alignment explanation
Indices: 1180497--1180763 Score: 295
Period size: 140 Copynumber: 1.9 Consensus size: 141
1180487 AGAAATGGGT
* * * * * *
1180497 AAGTGTCTTATTCTTTGAGGACTGAAGGTAAGTGGGTGCCCCCAACTTTTTTGGGTTTTGAGATG
1 AAGTGTCCTACTCTTTGAGGACTGAAGGTAAGTAGGTGCCACCAACTTGTATGGGTTTTGAGATG
* * * * * * **
1180562 GGTAAACATCTTGCTCTTTAAAGATTGAGGGTAGATAGGCACCACCAGTTTGTGTGGGCTTTAAA
66 GGTAAACATCATACTCTTTAAAGACTGAGGGTAGATAGGCACAACAAGCTTGTGTAAGCTTTAAA
1180627 GTGGATAAGAA
131 GTGGATAAGAA
* *
1180638 AAGTGTCCTACTCTTTGAGGACT-AAGGTAAGTAGGTGCTACCAGCTTGTATGGGCTTTT-AGAT
1 AAGTGTCCTACTCTTTGAGGACTGAAGGTAAGTAGGTGCCACCAACTTGTATGGG-TTTTGAGAT
** * * * ** *
1180701 GGGTAAGTATCATACTCTTTGAGGACTGAGGGTAGGTAGGTGCAATAAGCTTGTGTAAGCTTT
65 GGGTAAACATCATACTCTTTAAAGACTGAGGGTAGATAGGCACAACAAGCTTGTGTAAGCTTT
1180764 GAGATGGGTA
Statistics
Matches: 101, Mismatches: 24, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
140 76 0.75
141 25 0.25
ACGTcount: A:0.25, C:0.13, G:0.29, T:0.33
Consensus pattern (141 bp):
AAGTGTCCTACTCTTTGAGGACTGAAGGTAAGTAGGTGCCACCAACTTGTATGGGTTTTGAGATG
GGTAAACATCATACTCTTTAAAGACTGAGGGTAGATAGGCACAACAAGCTTGTGTAAGCTTTAAA
GTGGATAAGAA
Found at i:1181203 original size:36 final size:36
Alignment explanation
Indices: 1181131--1181203 Score: 87
Period size: 36 Copynumber: 2.0 Consensus size: 36
1181121 AGATAGAAAC
* * *
1181131 CTCCCTATCTTTTCACGAGCTAAGATGGAAAGCTCT
1 CTCCCTATCTTTTCAAGAGCTAAGATAGAAACCTCT
1181167 CTCCCTATCTTTTTCAA-AGGCTAAGATAG-AACCTCT
1 CTCCCTATC-TTTTCAAGA-GCTAAGATAGAAACCTCT
1181203 C
1 C
1181204 AATCACTTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 17 0.53
37 15 0.47
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.32
Consensus pattern (36 bp):
CTCCCTATCTTTTCAAGAGCTAAGATAGAAACCTCT
Found at i:1181694 original size:24 final size:24
Alignment explanation
Indices: 1181659--1181706 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
1181649 ATAACGTATC
*
1181659 GATACATGAACAGTTATGAACAGT
1 GATACATGAACAGTGATGAACAGT
*
1181683 GATACATTAACAGTGATGAACAGT
1 GATACATGAACAGTGATGAACAGT
1181707 AAAGTATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (24 bp):
GATACATGAACAGTGATGAACAGT
Found at i:1184322 original size:21 final size:20
Alignment explanation
Indices: 1184298--1184354 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
1184288 TCTTAGTTAG
1184298 CTCATTATTTTCATCTTGCAA
1 CTCATTATTTTC-TCTTGCAA
* * *
1184319 CTCATTTCTTTTCTTTTGTAA
1 CTCA-TTATTTTCTCTTGCAA
1184340 CTCATTCATTTTCTC
1 CTCATT-ATTTTCTC
1184355 CTTTAGTTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 2 0.07
21 20 0.69
22 7 0.24
ACGTcount: A:0.18, C:0.25, G:0.04, T:0.54
Consensus pattern (20 bp):
CTCATTATTTTCTCTTGCAA
Found at i:1185996 original size:35 final size:36
Alignment explanation
Indices: 1185955--1186026 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 36
1185945 AGATAGAAAG
*
1185955 CTCCCTAT-TTTTTC-ACGAGCTAAGATAAAACCTCT
1 CTCCCTATCTTTTTCAAAG-GCTAAGATAAAACCTCT
*
1185990 CTCCCTATCTTTTTCAAAGGCTAAGATAGAACCTCT
1 CTCCCTATCTTTTTCAAAGGCTAAGATAAAACCTCT
1186026 C
1 C
1186027 AATCACTTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
35 8 0.24
36 23 0.70
37 2 0.06
ACGTcount: A:0.28, C:0.29, G:0.10, T:0.33
Consensus pattern (36 bp):
CTCCCTATCTTTTTCAAAGGCTAAGATAAAACCTCT
Found at i:1186145 original size:31 final size:31
Alignment explanation
Indices: 1186107--1186171 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
1186097 GAAGCAAAGA
1186107 ATTACAAACTCAATAAACCTCTACAAGGTTG
1 ATTACAAACTCAATAAACCTCTACAAGGTTG
**
1186138 ATTACAAACTCAATAGTCCTCTACAAGGTTG
1 ATTACAAACTCAATAAACCTCTACAAGGTTG
1186169 ATT
1 ATT
1186172 TTTATGGAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.29
Consensus pattern (31 bp):
ATTACAAACTCAATAAACCTCTACAAGGTTG
Found at i:1186668 original size:20 final size:19
Alignment explanation
Indices: 1186642--1186696 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1186632 ACTGCCAGTT
* *
1186642 TATGTATCAATACATTTTA
1 TATGTATCAATACATGTAA
*
1186661 TGATGTATCAATACTAAGTAA
1 T-ATGTATCAATAC-ATGTAA
1186682 TATGTATCAATACAT
1 TATGTATCAATACAT
1186697 CTAGGTGTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 2 0.07
20 24 0.80
21 4 0.13
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (19 bp):
TATGTATCAATACATGTAA
Found at i:1187102 original size:68 final size:68
Alignment explanation
Indices: 1186985--1187273 Score: 208
Period size: 68 Copynumber: 4.2 Consensus size: 68
1186975 TATCCTAATA
** * * * *
1186985 TACTCTTTGAAAATTGAGGGTAGGTAGGTGCCATCAGCTTGTGTGGGCTTTAAGATGGGTAAGTG
1 TACTCTTTGAGGATTAAGGGTAGGTAGGTGCCATCAGCTTATGTAGGCTTTAAGATGCGTAAGTG
1187050 TCC
66 TCC
* * * ** *
1187053 TGCTCTTTGAGGATTAAGGGTAGGTTGGTGTCATTGGCTTATGTAGGCTTTAAGATGCTTAAGTG
1 TACTCTTTGAGGATTAAGGGTAGGTAGGTGCCATCAGCTTATGTAGGCTTTAAGATGCGTAAGTG
1187118 TCC
66 TCC
* * * * * * * * *
1187121 TACTCTTTAAGGACTAAGGGTAGGTAGGTGCTA-CTAGTTTGTGTGGGTTTTAAAATGGGTAAAA
1 TACTCTTTGAGGATTAAGGGTAGGTAGGTGCCATC-AGCTTATGTAGGCTTTAAGATGCGT----
1187185 AAAGTGTCC
61 -AAGTGTCC
* * * * * * * *
1187194 TACTCTTTAAGGACTAA-GGTAGGTAGGTGCCCCTTA-CTTATATGGGCTTTGAGATGGGTAAGT
1 TACTCTTTGAGGATTAAGGGTAGGTAGGTG-CCATCAGCTTATGTAGGCTTTAAGATGCGTAAGT
1187257 G-CC
65 GTCC
*
1187260 TTATTCTTTGAGGA
1 -TACTCTTTGAGGA
1187274 CTAAAGGAAA
Statistics
Matches: 174, Mismatches: 38, Indels: 19
0.75 0.16 0.08
Matches are distributed among these distances:
66 2 0.01
67 16 0.09
68 100 0.57
72 29 0.17
73 27 0.16
ACGTcount: A:0.23, C:0.12, G:0.30, T:0.35
Consensus pattern (68 bp):
TACTCTTTGAGGATTAAGGGTAGGTAGGTGCCATCAGCTTATGTAGGCTTTAAGATGCGTAAGTG
TCC
Found at i:1187268 original size:140 final size:136
Alignment explanation
Indices: 1187001--1187277 Score: 292
Period size: 140 Copynumber: 2.0 Consensus size: 136
1186991 TTGAAAATTG
* * *
1187001 AGGGTAGGTAGGTGCCATCAGCTTGTGTGGGCTTTAAGATGGGTAAGTGTCCTGCTCTTTGAGGA
1 AGGGTAGGTAGGTGCCATCAGCTTGTGTGGGCTTTAAAATGGGTAAGTGTCCTACTCTTTAAGGA
* * * * * *
1187066 TTAAGGGTAGGTTGGTGTCATTGGCTTATGTAGGCTTTAAGATGCTTAAGTGTCCTACTCTTTAA
66 CTAAGGGTAGGTAGGTGCCATTGACTTATATAGGCTTTAAGATGCGTAAGTGTCCTACTCTTTAA
1187131 GGACTA
131 GGACTA
* * *
1187137 AGGGTAGGTAGGTGCTA-CTAGTTTGTGTGGGTTTTAAAATGGGTAAAAAAAGTGTCCTACTCTT
1 AGGGTAGGTAGGTGCCATC-AGCTTGTGTGGGCTTTAAAATGGGT-----AAGTGTCCTACTCTT
* * * *
1187201 TAAGGACTAA-GGTAGGTAGGTGCCCCTT-ACTTATATGGGCTTTGAGATGGGTAAGTG-CCTTA
60 TAAGGACTAAGGGTAGGTAGGTG-CCATTGACTTATATAGGCTTTAAGATGCGTAAGTGTCC-TA
* *
1187263 TTCTTTGAGGACTA
123 CTCTTTAAGGACTA
1187277 A
1 A
1187278 AGGAAAATAG
Statistics
Matches: 115, Mismatches: 18, Indels: 12
0.79 0.12 0.08
Matches are distributed among these distances:
135 1 0.01
136 38 0.33
139 2 0.02
140 49 0.43
141 25 0.22
ACGTcount: A:0.23, C:0.13, G:0.30, T:0.34
Consensus pattern (136 bp):
AGGGTAGGTAGGTGCCATCAGCTTGTGTGGGCTTTAAAATGGGTAAGTGTCCTACTCTTTAAGGA
CTAAGGGTAGGTAGGTGCCATTGACTTATATAGGCTTTAAGATGCGTAAGTGTCCTACTCTTTAA
GGACTA
Found at i:1188387 original size:15 final size:15
Alignment explanation
Indices: 1188360--1188404 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
1188350 TTTTTCTCTT
1188360 TTTTTTTGTCTTTTTA
1 TTTTTTTG-CTTTTTA
*
1188376 TTTTTTTGCTTTTTG
1 TTTTTTTGCTTTTTA
* *
1188391 TTTGTTTCCTTTTT
1 TTTTTTTGCTTTTT
1188405 TAGAGTGGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 18 0.69
16 8 0.31
ACGTcount: A:0.02, C:0.09, G:0.09, T:0.80
Consensus pattern (15 bp):
TTTTTTTGCTTTTTA
Found at i:1188778 original size:28 final size:28
Alignment explanation
Indices: 1188741--1188795 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
1188731 TCTTTAATTC
1188741 TTTTCTCCTCAATGAGATTAAGTTACTT
1 TTTTCTCCTCAATGAGATTAAGTTACTT
1188769 TTTTCTCCTCAATGAGATTAAGTTACT
1 TTTTCTCCTCAATGAGATTAAGTTACT
1188796 CATATTGGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.18, G:0.11, T:0.45
Consensus pattern (28 bp):
TTTTCTCCTCAATGAGATTAAGTTACTT
Found at i:1191576 original size:311 final size:311
Alignment explanation
Indices: 1191064--1191670 Score: 767
Period size: 311 Copynumber: 2.0 Consensus size: 311
1191054 TCGAGAATCT
* *
1191064 TAAAGGACTTAAAATGATCATAAATAGGATGAACTTATCCTAAATGCACACCTTTGGCATAAAAG
1 TAAAGAACTTAAAATGATCATAAATAGGATGAACTTATCCTAAATACACACCTTTGGCATAAAAG
* * * *
1191129 CATCCCAGTGACAATGCAGGACTCGATTCTAAGATAATTATGAAAATGCCTTTAGGGTATACCTT
66 CATCCCAGTGACAATCCAAGACTCAATTCTAAGAAAATTATGAAAATGCCTTTAGGGTATACCTT
** * *** * *
1191194 CGACATAAAAGTATCCCCGTAACCTTAATGGACACTAAAATGGTCATAAATTAGACAAACCTATC
131 CGACATAAAAGTATAACAGTAACAGAAAAGGACACTAAAATGATCATAAATTAGACAAACCTATC
* *
1191259 CTAAATGCAC-TCTTTTAGCATAAAAGCATCCTGATGACAACCTAAGACTTAATTTTAACAAAAT
196 CTAAATGCACATC-TTTAGCATAAAAGCATCCTGATGACAACCTAAGACTCAATTTTAAAAAAAT
*
1191323 TATGAAAATACCCTTAGGATATACCTTCAACTTGAAAATATCCTAGTGACCA
260 TATGAAAATACCCTTAGGATATACCTTCAACATGAAAATATCCTAGTGACCA
* * *
1191375 TAAAGAACTTAAAAATGATCGTAAATTGGATGAA-TCT-TCCTAAATACACATCTTTGGCATAAA
1 TAAAGAACTT-AAAATGATCATAAATAGGATGAACT-TATCCTAAATACACACCTTTGGCATAAA
*
1191438 ATCATCCCAGTGACAA-CCTAAGACTCAATTCT-AGAAAAATTATGAAAATGCCTTTAGGGTATA
64 AGCATCCCAGTGACAATCC-AAGACTCAATTCTAAG-AAAATTATGAAAATGCCTTTAGGGTATA
* * * ** ** *
1191501 CTTTCGTCATGAAAGTATAACAGTAACAGAAAAGGA-TTTAAAAATGATTGTAAATTGGACAAAC
127 CCTTCGACATAAAAGTATAACAGTAACAGAAAAGGACACT-AAAATGATCATAAATTAGACAAAC
* * * * * *
1191565 CTATTCTAAATGCACATCTTTGGCATAAAGGCATCTTGGTGACAACCTAGGACTCAATTTTAAAA
191 CTATCCTAAATGCACATCTTTAGCATAAAAGCATCCTGATGACAACCTAAGACTCAATTTTAAAA
* * * *
1191630 AAATTATGAAAATGCCTTTAGGTTATACTTTCAACATGAAA
256 AAATTATGAAAATACCCTTAGGATATACCTTCAACATGAAA
1191671 TTATTCCAAT
Statistics
Matches: 251, Mismatches: 39, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
310 4 0.02
311 223 0.89
312 24 0.10
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (311 bp):
TAAAGAACTTAAAATGATCATAAATAGGATGAACTTATCCTAAATACACACCTTTGGCATAAAAG
CATCCCAGTGACAATCCAAGACTCAATTCTAAGAAAATTATGAAAATGCCTTTAGGGTATACCTT
CGACATAAAAGTATAACAGTAACAGAAAAGGACACTAAAATGATCATAAATTAGACAAACCTATC
CTAAATGCACATCTTTAGCATAAAAGCATCCTGATGACAACCTAAGACTCAATTTTAAAAAAATT
ATGAAAATACCCTTAGGATATACCTTCAACATGAAAATATCCTAGTGACCA
Found at i:1191668 original size:156 final size:154
Alignment explanation
Indices: 1191064--1191670 Score: 580
Period size: 156 Copynumber: 3.9 Consensus size: 154
1191054 TCGAGAATCT
* * * ** * *
1191064 TAAAGGACTT-AAAATGATCATAAATAGGATGAACTTATCCTAAATGCACACCTTTGGCATAAAA
1 TAAAGGAATTAAAAATGATCGTAAATTGGACAAACCTATCCTAAATGCACATCTTTGGCATAAAA
* * * * *
1191128 GCATCCCAGTGACAATGC-AGGACTCGATTCTAAGATAATTATGAAAATGCCTTTAGGGTATACC
66 GCATCCCAGTGACAA-CCTAAGACTCAATTCTAAAAAAATTATGAAAATGCCTTTAGGGTATACC
* * * *
1191192 TTCGACATAAAAGTATCCCCGTAACCT
130 TTCAACATGAAAGTAT-CCAGTAA-CA
* * * * * *
1191219 TAATGGACACT-AAAATGGTCATAAATTAGACAAACCTATCCTAAATGCAC-TCTTTTAGCATAA
1 TAAAGGA-ATTAAAAATGATCGTAAATTGGACAAACCTATCCTAAATGCACATC-TTTGGCATAA
* * * * * * *
1191282 AAGCAT-CCTGATGACAACCTAAGACTTAATTTTAACAAAATTATGAAAATACCCTTAGGATATA
64 AAGCATCCCAG-TGACAACCTAAGACTCAATTCTAAAAAAATTATGAAAATGCCTTTAGGGTATA
* * *
1191346 CCTTCAACTTGAAAATATCCTAGTGACCA
128 CCTTCAACATGAAAGTATCC-AGT-AACA
** * *
1191375 TAAA-GAACTTAAAAATGATCGTAAATTGGATGAATCT-TCCTAAATACACATCTTTGGCATAAA
1 TAAAGGAA-TTAAAAATGATCGTAAATTGGACAAACCTATCCTAAATGCACATCTTTGGCATAAA
* * *
1191438 ATCATCCCAGTGACAACCTAAGACTCAATTCTAGAAAAATTATGAAAATGCCTTTAGGGTATACT
65 AGCATCCCAGTGACAACCTAAGACTCAATTCTAAAAAAATTATGAAAATGCCTTTAGGGTATACC
** *
1191503 TTCGTCATGAAAGTATAACAGTAACA
130 TTCAACATGAAAGTAT-CCAGTAACA
* * * *
1191529 GAAAAGGATTTAAAAATGATTGTAAATTGGACAAACCTATTCTAAATGCACATCTTTGGCATAAA
1 -TAAAGGAATTAAAAATGATCGTAAATTGGACAAACCTATCCTAAATGCACATCTTTGGCATAAA
* *** * * * *
1191594 GGCATCTTGGTGACAACCTAGGACTCAATTTTAAAAAAATTATGAAAATGCCTTTAGGTTATACT
65 AGCATCCCAGTGACAACCTAAGACTCAATTCTAAAAAAATTATGAAAATGCCTTTAGGGTATACC
1191659 TTCAACATGAAA
130 TTCAACATGAAA
1191671 TTATTCCAAT
Statistics
Matches: 364, Mismatches: 74, Indels: 27
0.78 0.16 0.06
Matches are distributed among these distances:
154 4 0.01
155 131 0.36
156 228 0.63
157 1 0.00
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (154 bp):
TAAAGGAATTAAAAATGATCGTAAATTGGACAAACCTATCCTAAATGCACATCTTTGGCATAAAA
GCATCCCAGTGACAACCTAAGACTCAATTCTAAAAAAATTATGAAAATGCCTTTAGGGTATACCT
TCAACATGAAAGTATCCAGTAACA
Found at i:1191697 original size:19 final size:19
Alignment explanation
Indices: 1191673--1191711 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1191663 ACATGAAATT
1191673 ATTCCAATAATCCTAAAAG
1 ATTCCAATAATCCTAAAAG
1191692 ATTCCAATAATCCTAAAAG
1 ATTCCAATAATCCTAAAAG
1191711 A
1 A
1191712 CTTAAAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.21, G:0.05, T:0.26
Consensus pattern (19 bp):
ATTCCAATAATCCTAAAAG
Found at i:1196630 original size:20 final size:20
Alignment explanation
Indices: 1196605--1196679 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
1196595 AAAAAAATAG
1196605 AATGCATCGATACATTGAAA
1 AATGCATCGATACATTGAAA
* *
1196625 AATGCATCGATACATTCATA
1 AATGCATCGATACATTGAAA
* * *
1196645 CATGTATCGATACAATGAAA
1 AATGCATCGATACATTGAAA
*
1196665 AATGTATCGATACAT
1 AATGCATCGATACAT
1196680 CTAGGTAAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.28
Consensus pattern (20 bp):
AATGCATCGATACATTGAAA
Found at i:1196791 original size:21 final size:21
Alignment explanation
Indices: 1196767--1196821 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
1196757 GTTAAGACCT
1196767 TGTATCAATACATTTCTTGAA
1 TGTATCAATACATTTCTTGAA
1196788 TGTATCAATACATTTCTTGAA
1 TGTATCAATACATTTCTTGAA
*
1196809 TGTATCGATACAT
1 TGTATCAATACAT
1196822 CTGGACAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.42
Consensus pattern (21 bp):
TGTATCAATACATTTCTTGAA
Found at i:1198044 original size:19 final size:19
Alignment explanation
Indices: 1198001--1198091 Score: 101
Period size: 19 Copynumber: 4.7 Consensus size: 19
1197991 CACATCCAGA
* *
1198001 TGTATCGATACATTATGCTT
1 TGTATCGATACA-TATTCAT
1198021 TGTATCGATACATATTCAT
1 TGTATCGATACATATTCAT
*
1198040 TGTATCGATACATGTTCAT
1 TGTATCGATACATATTCAT
* **
1198059 TGTTTCGATACATACACAAT
1 TGTATCGATACATATTC-AT
*
1198079 TGTATTGATACAT
1 TGTATCGATACAT
1198092 GAAACTAGCA
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
19 36 0.59
20 25 0.41
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (19 bp):
TGTATCGATACATATTCAT
Found at i:1198050 original size:39 final size:39
Alignment explanation
Indices: 1198001--1198092 Score: 107
Period size: 39 Copynumber: 2.4 Consensus size: 39
1197991 CACATCCAGA
* **
1198001 TGTATCGATACAT-TATGCTTTGTATCGATACATATTC-AT
1 TGTATCGATACATGT-T-CATTGTATCGATACATACACAAT
*
1198040 TGTATCGATACATGTTCATTGTTTCGATACATACACAAT
1 TGTATCGATACATGTTCATTGTATCGATACATACACAAT
*
1198079 TGTATTGATACATG
1 TGTATCGATACATG
1198093 AAACTAGCAG
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
38 16 0.35
39 29 0.63
40 1 0.02
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.41
Consensus pattern (39 bp):
TGTATCGATACATGTTCATTGTATCGATACATACACAAT
Found at i:1198159 original size:33 final size:32
Alignment explanation
Indices: 1198122--1198186 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
1198112 TACTACTATT
1198122 TGTATCGATACAT-AGCACATTGTATCGATACAA
1 TGTATCGATACATAAG-A-ATTGTATCGATACAA
1198155 TGTATCGATACATGAAGAATTGTATCGATACA
1 TGTATCGATACAT-AAGAATTGTATCGATACA
1198187 TTGTCTTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 27 0.90
34 1 0.03
35 2 0.07
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (32 bp):
TGTATCGATACATAAGAATTGTATCGATACAA
Found at i:1198160 original size:13 final size:13
Alignment explanation
Indices: 1198142--1198166 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1198132 CATAGCACAT
1198142 TGTATCGATACAA
1 TGTATCGATACAA
1198155 TGTATCGATACA
1 TGTATCGATACA
1198167 TGAAGAATTG
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:1199798 original size:12 final size:13
Alignment explanation
Indices: 1199783--1199814 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1199773 ACTATCAAAA
1199783 ATGATGAA-AATG
1 ATGATGAATAATG
1199795 ATGAT-AATAATG
1 ATGATGAATAATG
1199807 ATGATGAA
1 ATGATGAA
1199815 GTTGACTCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.11
12 14 0.78
13 2 0.11
ACGTcount: A:0.50, C:0.00, G:0.22, T:0.28
Consensus pattern (13 bp):
ATGATGAATAATG
Found at i:1207220 original size:20 final size:22
Alignment explanation
Indices: 1207176--1207222 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1207166 AATTTTCAAC
1207176 AAAT-TTTCACTTTTTCACTTCA
1 AAATCTTTCACTTTTTCAC-TCA
1207198 AAATCTTTCA-TTTTTCA-TCA
1 AAATCTTTCACTTTTTCACTCA
1207218 AAATC
1 AAATC
1207223 ATCAATAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.33
22 11 0.46
23 5 0.21
ACGTcount: A:0.32, C:0.21, G:0.00, T:0.47
Consensus pattern (22 bp):
AAATCTTTCACTTTTTCACTCA
Found at i:1209527 original size:20 final size:20
Alignment explanation
Indices: 1209504--1209603 Score: 102
Period size: 20 Copynumber: 5.7 Consensus size: 20
1209494 CACACCCAAA
1209504 TGTATCGATACATTATGCTT
1 TGTATCGATACATTATGCTT
1209524 TGTATCGATAC---A----T
1 TGTATCGATACATTATGCTT
1209537 TGTATCGATACATTATGCTT
1 TGTATCGATACATTATGCTT
1209557 TGTATCGATAC---A----T
1 TGTATCGATACATTATGCTT
1209570 TGTATCGATACATTATGCTT
1 TGTATCGATACATTATGCTT
1209590 TGTATCGATACATT
1 TGTATCGATACATT
1209604 GTATCGATAC
Statistics
Matches: 66, Mismatches: 0, Indels: 28
0.70 0.00 0.30
Matches are distributed among these distances:
13 24 0.36
16 2 0.03
17 2 0.03
20 38 0.58
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (20 bp):
TGTATCGATACATTATGCTT
Found at i:1209541 original size:13 final size:13
Alignment explanation
Indices: 1209523--1209614 Score: 82
Period size: 13 Copynumber: 8.0 Consensus size: 13
1209513 ACATTATGCT
1209523 TTGTATCGATACA
1 TTGTATCGATACA
1209536 TTGTATCGATACA
1 TTGTATCGATACA
*
1209549 -T-TAT-G---CT
1 TTGTATCGATACA
1209556 TTGTATCGATACA
1 TTGTATCGATACA
1209569 TTGTATCGATACA
1 TTGTATCGATACA
*
1209582 -T-TAT-G---CT
1 TTGTATCGATACA
1209589 TTGTATCGATACA
1 TTGTATCGATACA
1209602 TTGTATCGATACA
1 TTGTATCGATACA
1209615 ATGATACATG
Statistics
Matches: 63, Mismatches: 4, Indels: 24
0.69 0.04 0.26
Matches are distributed among these distances:
7 2 0.03
8 2 0.03
9 6 0.10
10 4 0.06
11 6 0.10
12 2 0.03
13 41 0.65
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1209546 original size:33 final size:33
Alignment explanation
Indices: 1209504--1209614 Score: 222
Period size: 33 Copynumber: 3.4 Consensus size: 33
1209494 CACACCCAAA
1209504 TGTATCGATACATTATGCTTTGTATCGATACAT
1 TGTATCGATACATTATGCTTTGTATCGATACAT
1209537 TGTATCGATACATTATGCTTTGTATCGATACAT
1 TGTATCGATACATTATGCTTTGTATCGATACAT
1209570 TGTATCGATACATTATGCTTTGTATCGATACAT
1 TGTATCGATACATTATGCTTTGTATCGATACAT
1209603 TGTATCGATACA
1 TGTATCGATACA
1209615 ATGATACATG
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.41
Consensus pattern (33 bp):
TGTATCGATACATTATGCTTTGTATCGATACAT
Found at i:1209718 original size:33 final size:33
Alignment explanation
Indices: 1209673--1209739 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
1209663 CTTCCATAGT
* *
1209673 TTGTATCGATACATGGT-ACAATGTATCGATACA
1 TTGTATCAATACATGATGA-AATGTATCGATACA
*
1209706 TTGTATCAATACATGATGAATTGTATCGATACA
1 TTGTATCAATACATGATGAAATGTATCGATACA
1209739 T
1 T
1209740 AGCTTGTAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.36
Consensus pattern (33 bp):
TTGTATCAATACATGATGAAATGTATCGATACA
Found at i:1213476 original size:27 final size:26
Alignment explanation
Indices: 1213438--1213488 Score: 84
Period size: 27 Copynumber: 1.9 Consensus size: 26
1213428 TGTCATCTAT
*
1213438 GGGGATACTCCAATCCCATCTTTTCGA
1 GGGGATACTCCAACCCCA-CTTTTCGA
1213465 GGGGATACTCCAACCCCACTTTTC
1 GGGGATACTCCAACCCCACTTTTC
1213489 AACTATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.22, C:0.33, G:0.18, T:0.27
Consensus pattern (26 bp):
GGGGATACTCCAACCCCACTTTTCGA
Found at i:1226214 original size:21 final size:20
Alignment explanation
Indices: 1226185--1226232 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
1226175 CTTCTTTTTT
* *
1226185 AAAAAAAACCAAAA-AAATA
1 AAAAAAAAACAAAACAAAGA
1226204 AAAATAAAAACAAAACAAAGA
1 AAAA-AAAAACAAAACAAAGA
1226225 AAAAAAAA
1 AAAAAAAA
1226233 GAGAGAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.16
20 13 0.52
21 8 0.32
ACGTcount: A:0.85, C:0.08, G:0.02, T:0.04
Consensus pattern (20 bp):
AAAAAAAAACAAAACAAAGA
Found at i:1227473 original size:62 final size:62
Alignment explanation
Indices: 1227321--1228067 Score: 899
Period size: 61 Copynumber: 12.3 Consensus size: 62
1227311 TTTCACTGTT
*
1227321 TAGTCCTCAAAGAGCAGGACGCC-TTT-C----AAAGCCCACACAAGCTGGTGGCA-TTTTC
1 TAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
* *
1227376 -AGTCCTCAAAGAGTAGGACGCCTATTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
1 TAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
* * *
1227437 TAGTCCTCAAAGAGCAGGATGCCTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTC
1 TAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
* *
1227498 TAGTCCTCAAAGA-CAAGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
1 TAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
* * *
1227559 TAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTAGTGGCAC-CTTC
1 TAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
* * * * * *
1227620 CAGTCTTCAAAGAGCAGGATG-CTTTCTCCTTTCAAAGCCCACACAAGCTGGTGGCAC-CTT-
1 TAGTCCTCAAAGAGCAGGACGCCTTT-TCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
* * * *
1227680 TAGTCCTCAAAGAGAAGGACGCCTTTTCCTTTCAAAGCCCACACAAGCTGGTGGCAC-CTTC
1 TAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
* * * *
1227741 -AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCTCACACAAGTTGGCGACATTTTTC
1 TAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
* * ** * *
1227802 TAGTCCTTAAAGAGCAGGACACCTTTTCCTTTCGAAGCCCACGCAAGTTTGG-GGCACCTTTC
1 TAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAG-TTGGTGGCACTTTTC
* * * * * *
1227864 TAGTCCTCAAAGAGCAGTACACCTTTTTCTTTTTAAAGCCCACACAAATTGGTGGCACGTCT-
1 TAGTCCTCAAAGAGCAGGACGCC-TTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
* * * *
1227926 TAGTCCTCAAAGAGCATGACGCCTTTT-TTTTTCAAAGCCCACACGAGTTGGTGGCACCTTT-
1 TAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCACTTTTC
* *
1227987 TAGTCCTCAAAGAGCAGGACGTCTTTT-CTTTTCAAAGCCCACACGAGTTGGTGGCACTTTT-
1 TAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCACTTTTC
*
1228048 TAGTCCTCAAAAAGCAGGAC
1 TAGTCCTCAAAGAGCAGGAC
1228068 ACATTTCATT
Statistics
Matches: 612, Mismatches: 61, Indels: 32
0.87 0.09 0.05
Matches are distributed among these distances:
54 21 0.03
55 2 0.00
56 1 0.00
60 172 0.28
61 201 0.33
62 185 0.30
63 30 0.05
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (62 bp):
TAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTC
Found at i:1228136 original size:40 final size:40
Alignment explanation
Indices: 1228050--1228353 Score: 154
Period size: 41 Copynumber: 7.4 Consensus size: 40
1228040 GCACTTTTTA
* ** *
1228050 GTCCTCAAAAAGCAGGACACATTTCATTTCCTTCTTTTCCGTTTT
1 GTCCTCAAAGAGCAGGATGCATTT--TTTTCTT-TTTTCC--TTT
*
1228095 GTCCACAAAGAGCAGGATGCATTTTTTTCTTTTTTCCTTT
1 GTCCTCAAAGAGCAGGATGCATTTTTTTCTTTTTTCCTTT
* * * * * * *
1228135 GTCCTCAAAGAACAGAACGCACTTCATTTCCTTCTTTCCCCTTCA
1 GTCCTCAAAGAGCAGGATGCA-TT-TTTTTCTT-TTT-TCCTT-T
* * * *
1228180 GTTCTCAAAGAGTAGGATGCATTTTATTCTTCTTTCTTCTTT
1 GTCCTCAAAGAGCAGGATGCATTTTTTTCTT-TTT-TCCTTT
** * * *
1228222 GTCCTCAAA-AGCAGGACACATTTAATTTCCTTTTTCCCTT
1 GTCCTCAAAGAGCAGGATGCATTT-TTTTCTTTTTTCCTTT
* * *
1228262 GTCTTCAAAGGGCAGGATGCA-----TT-TTATTTCCTTT
1 GTCCTCAAAGAGCAGGATGCATTTTTTTCTTTTTTCCTTT
* * ** **
1228296 GTCCTCAAGGAACAGGACCCATTTCATTCTTTTTTTCCTTT
1 GTCCTCAAAGAGCAGGATGCATTTTTTTC-TTTTTTCCTTT
*
1228337 GTCCTTAAAGAGCAGGA
1 GTCCTCAAAGAGCAGGA
1228354 CGCCCCATTC
Statistics
Matches: 195, Mismatches: 50, Indels: 32
0.70 0.18 0.12
Matches are distributed among these distances:
34 23 0.12
35 2 0.01
39 2 0.01
40 32 0.16
41 48 0.25
42 24 0.12
43 22 0.11
44 6 0.03
45 36 0.18
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.39
Consensus pattern (40 bp):
GTCCTCAAAGAGCAGGATGCATTTTTTTCTTTTTTCCTTT
Found at i:1228162 original size:85 final size:87
Alignment explanation
Indices: 1228050--1228289 Score: 253
Period size: 85 Copynumber: 2.8 Consensus size: 87
1228040 GCACTTTTTA
* * * * **
1228050 GTCCTCAAAAAGCAGGACACATTTCATTTCCTTCTTTTCCGTTTTGTCCACAAAGAGCAGGATGC
1 GTCCTCAAAAAGCAGAACACACTTCATTTCCTTCTTTCCCCTTCAGTCCACAAAGAGCAGGATGC
*
1228115 ATTTTTTTCTT-TTT-TCCTTT
66 ATTTTATTCTTCTTTCTCCTTT
* * * *
1228135 GTCCTCAAAGAA-CAGAACGCACTTCATTTCCTTCTTTCCCCTTCAGTTCTCAAAGAGTAGGATG
1 GTCCTCAAA-AAGCAGAACACACTTCATTTCCTTCTTTCCCCTTCAGTCCACAAAGAGCAGGATG
*
1228199 CATTTTATTCTTCTTTCTTCTTT
65 CATTTTATTCTTCTTTCTCCTTT
* * * ** *
1228222 GTCCTC-AAAAGCAGGACACATTTAATTTCCTT-TTT-CCCTT--GTCTTCAAAGGGCAGGATGC
1 GTCCTCAAAAAGCAGAACACACTTCATTTCCTTCTTTCCCCTTCAGTCCACAAAGAGCAGGATGC
1228282 ATTTTATT
66 ATTTTATT
1228290 TCCTTTGTCC
Statistics
Matches: 131, Mismatches: 20, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
82 24 0.18
84 5 0.04
85 67 0.51
86 24 0.18
87 11 0.08
ACGTcount: A:0.23, C:0.24, G:0.13, T:0.40
Consensus pattern (87 bp):
GTCCTCAAAAAGCAGAACACACTTCATTTCCTTCTTTCCCCTTCAGTCCACAAAGAGCAGGATGC
ATTTTATTCTTCTTTCTCCTTT
Found at i:1228942 original size:20 final size:20
Alignment explanation
Indices: 1228917--1228971 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
1228907 TTTTCACAAT
1228917 TTGTATCGATACATTGTCCA
1 TTGTATCGATACATTGTCCA
* * *
1228937 TTGTATCGGTACATTATTCA
1 TTGTATCGATACATTGTCCA
1228957 TTGTA--GATACATTGT
1 TTGTATCGATACATTGT
1228972 ATCGATACAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 8 0.27
20 22 0.73
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.44
Consensus pattern (20 bp):
TTGTATCGATACATTGTCCA
Found at i:1231487 original size:52 final size:51
Alignment explanation
Indices: 1231372--1231487 Score: 133
Period size: 51 Copynumber: 2.3 Consensus size: 51
1231362 ATTTCCGAGG
* * *** * *
1231372 GGATACTCCAACCCCGGCTTTATTTCTAAAATATTTATTTCTCACAATTGG
1 GGATACTCCAACCCCGACTTTATTTCTAAAACACCAATTTCTCACAATCGA
* * *
1231423 GGATACTCCAACCCTGATTTTATTTCTAAAACACCAATCTTTTCACAATCGA
1 GGATACTCCAACCCCGACTTTATTTCTAAAACACCAAT-TTCTCACAATCGA
1231475 GGATACTCCAACC
1 GGATACTCCAACC
1231488 ATGTTATTTT
Statistics
Matches: 54, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
51 31 0.57
52 23 0.43
ACGTcount: A:0.30, C:0.27, G:0.10, T:0.33
Consensus pattern (51 bp):
GGATACTCCAACCCCGACTTTATTTCTAAAACACCAATTTCTCACAATCGA
Found at i:1231525 original size:131 final size:130
Alignment explanation
Indices: 1231291--1231530 Score: 329
Period size: 131 Copynumber: 1.8 Consensus size: 130
1231281 TTTTCATCTC
* * * * *
1231291 GGGGATACTCTCACCCCAGTTTTATTTCCAAAACATCAATTTTTCATAATCGGGGATACTCCAAT
1 GGGGATACTCTCAACCCAGTTTTATTTCCAAAACACCAATTTTTCACAATCGAGGATACTCCAAC
* * * *
1231356 CTTGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTTCTAAAATATTTATTTCTCACAATT
66 CATGTTATTTCCAAAGGGATACTCCAACCCCGACTTTATTTCTAAAATATTTATTTCTCACAATT
* *
1231421 GGGGATACTC-CAACCCTGATTTTATTTCTAAAACACCAATCTTTTCACAATCGAGGATACTCCA
1 GGGGATACTCTCAACCCAG-TTTTATTTCCAAAACACCAAT-TTTTCACAATCGAGGATACTCCA
* * *
1231485 ACCATGTTATTTTCAAAGGGATACTCCAACCCTGATTTTATTTCTA
64 ACCATGTTATTTCCAAAGGGATACTCCAACCCCGACTTTATTTCTA
1231531 GAACACCGAT
Statistics
Matches: 94, Mismatches: 14, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
129 6 0.06
130 29 0.31
131 59 0.63
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.35
Consensus pattern (130 bp):
GGGGATACTCTCAACCCAGTTTTATTTCCAAAACACCAATTTTTCACAATCGAGGATACTCCAAC
CATGTTATTTCCAAAGGGATACTCCAACCCCGACTTTATTTCTAAAATATTTATTTCTCACAATT
Found at i:1231574 original size:80 final size:80
Alignment explanation
Indices: 1231422--1231574 Score: 209
Period size: 80 Copynumber: 1.9 Consensus size: 80
1231412 CTCACAATTG
*
1231422 GGGATACTCCAACCCTGATTTTATTTCTAAAACACCAATCTTTTCACAATCGAGGATACTCCAAC
1 GGGATACTCCAACCCTGATTTTATTTCTAAAACACCAATCTTTCCACAATCGAGGATACTCCAAC
*
1231487 CATGTTATTTTCAAA
66 CACGTTATTTTCAAA
* * * * * *
1231502 GGGATACTCCAACCCTGATTTTATTTCTAGAACACCGAT-TTTCCATAGTCAGGGGATACTCCAG
1 GGGATACTCCAACCCTGATTTTATTTCTAAAACACCAATCTTTCCACAATC-GAGGATACTCCAA
*
1231566 CCCCGTTAT
65 CCACGTTAT
1231575 CATCTCCAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
79 8 0.13
80 55 0.87
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (80 bp):
GGGATACTCCAACCCTGATTTTATTTCTAAAACACCAATCTTTCCACAATCGAGGATACTCCAAC
CACGTTATTTTCAAA
Found at i:1243848 original size:1 final size:1
Alignment explanation
Indices: 1243844--1243895 Score: 50
Period size: 1 Copynumber: 52.0 Consensus size: 1
1243834 CCTTTTTTTT
* * * * * *
1243844 AAAAAAAATAAAAAAAAAACAAAAAACAAAAAAACAAAACAAAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1243896 GAGAGAAAAG
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.88, C:0.08, G:0.02, T:0.02
Consensus pattern (1 bp):
A
Found at i:1243874 original size:15 final size:14
Alignment explanation
Indices: 1243844--1243893 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 14
1243834 CCTTTTTTTT
*
1243844 AAAAAA-AATAAAA
1 AAAAAACAAAAAAA
1243857 AAAAAACAAAAAACA
1 AAAAAACAAAAAA-A
1243872 AAAAAACAAAACAAA
1 AAAAAACAAAA-AAA
1243887 GAAAAAA
1 -AAAAAA
1243894 AAGAGAGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
13 6 0.19
14 5 0.16
15 13 0.41
16 8 0.25
ACGTcount: A:0.88, C:0.08, G:0.02, T:0.02
Consensus pattern (14 bp):
AAAAAACAAAAAAA
Found at i:1243894 original size:20 final size:19
Alignment explanation
Indices: 1243844--1243895 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
1243834 CCTTTTTTTT
1243844 AAAAAAAATAAAAAAAAAAC
1 AAAAAAAA-AAAAAAAAAAC
*
1243864 AAAAAACAAAAAAACAAAAC
1 AAAAAA-AAAAAAAAAAAAC
1243884 AAAGAAAAAAAA
1 AAA-AAAAAAAA
1243896 GAGAGAAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 24 0.83
21 5 0.17
ACGTcount: A:0.88, C:0.08, G:0.02, T:0.02
Consensus pattern (19 bp):
AAAAAAAAAAAAAAAAAAC
Found at i:1243896 original size:9 final size:9
Alignment explanation
Indices: 1243844--1243909 Score: 55
Period size: 9 Copynumber: 7.4 Consensus size: 9
1243834 CCTTTTTTTT
*
1243844 AAAAAAAAT
1 AAAAAAAAG
1243853 AAAAAAAA-
1 AAAAAAAAG
1243861 AACAAAAAA-
1 AA-AAAAAAG
* *
1243870 CAAAAAAAC
1 AAAAAAAAG
*
1243879 AAAACAAAG
1 AAAAAAAAG
1243888 AAAAAAAAG
1 AAAAAAAAG
* *
1243897 AGAGAAAAG
1 AAAAAAAAG
1243906 AAAA
1 AAAA
1243910 GAACCTACTT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
8 8 0.17
9 38 0.83
ACGTcount: A:0.85, C:0.06, G:0.08, T:0.02
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:1245190 original size:61 final size:61
Alignment explanation
Indices: 1245001--1245678 Score: 832
Period size: 62 Copynumber: 11.1 Consensus size: 61
1244991 AAGCTGGATG
* * * * * *
1245001 CCTTTCAAAGCCCACATAAGCTGGTGGCACCTTC-AGCCCTTAAAGAGTAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* * *
1245061 CCTTTTGAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGTAAGG-CGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTCTAGTCCTCAAAGAG-CAGGACGCCTTTT
*
1245123 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTGTAGTCCTCAAAGAGCAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* * * *
1245184 CCTTTTAAAGCCTACACAAGTTGGTGGCACTTTACTAGTCCTCAAAGAGCAAGATGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-CTAGTCCTCAAAGAGCAGGACGCCTTTT
* * *
1245246 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCTTCAAAGAGTAGGATG-CTTTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGCCTTT-T
* *
1245307 CCTTTCAAAGCCCAC-CAAGCTGGTGGCACCTT-TAGTCCTCAAAGAGCAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* * *
1245366 CCTTTCAAAGCCCACACAAGCTGGTGGCACCTT-TAGTCCTCAAAGAGCAGGACGCTTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* * **
1245426 CCTTTTAAAGCTCACACAAGTTAGTGGCATTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCA-CCTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* ** * * *
1245488 GCTTTCGAAGCCTACACAAGTTTGTGGCACCTTTCTAGTCCTCAAAGAGCAGGACACCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* * *
1245550 TCTTTTCAAAGCCCACACAAATTGGTGGCACC-TCTTAGTCCTCAAAGAGCATGACGCCTTTT
1 CCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTC-TAGTCCTCAAAGAGCAGGACGCCTTTT
** * * * * * *
1245612 -CTTTTCAAAGCCCACATGAGTTGGTGGCACTTTTTAGTCCTCAAAGTGTAGGATGACTTTT
1 CCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
1245673 CCTTTT
1 CCTTTT
1245679 CTCCTTTGTC
Statistics
Matches: 541, Mismatches: 62, Indels: 28
0.86 0.10 0.04
Matches are distributed among these distances:
59 34 0.06
60 121 0.22
61 145 0.27
62 217 0.40
63 24 0.04
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.29
Consensus pattern (61 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
Found at i:1245195 original size:123 final size:121
Alignment explanation
Indices: 1245001--1245678 Score: 808
Period size: 123 Copynumber: 5.5 Consensus size: 121
1244991 AAGCTGGATG
* * * * * *
1245001 CCTTTCAAAGCCCACATAAGCTGGTGGCACCTTCAGCCCTTAAAGAGTAGGACGCCTTTTCCTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTT
*
1245066 TGAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGTAAGGCGCCTTTT
66 TAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAG-AAGGCGCCTTTT
*
1245123 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTGTAGTCCTCAAAGAGCAGGACGCCTTTTCCTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTT-TAGTCCTCAAAGAGCAGGACGCCTTTTCCTT
* * **
1245188 TTAAAGCCTACACAAGTTGGTGGCACTTTACTAGTCCTCAAAGAGCAAGATGCCTTTT
65 TTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAG-AAGGCGCCTTTT
* * * *
1245246 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCTTCAAAGAGTAGGATG-CTTTCTCCT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTT-TAGTCCTCAAAGAGCAGGACGCCTTT-TCCT
* * * *
1245310 TTCAAAGCCCAC-CAAGCTGGTGGCAC-CTT-TAGTCCTCAAAGAGCAGGACGCCTTTT
64 TTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGAAGG-CGCCTTTT
* *
1245366 CCTTTCAAAGCCCACACAAGCTGGTGGCACCTTTAGTCCTCAAAGAGCAGGACGCTTTTTCCTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTT
* * * *
1245431 TAAAGCTCACACAAGTTAGTGGCATTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
66 TAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGAAGG-CGCCTTTT
* * * * * *
1245488 GCTTTCGAAGCCTACACAAGTTTGTGGCACCTTTCTAGTCCTCAAAGAGCAGGACACCTTTTTCT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACC-TT-TAGTCCTCAAAGAGCAGGACGCCTTTTCCT
* * * * *
1245553 TTTCAAAGCCCACACAAATTGGTGGCACCTCT-TAGTCCTCAAAGAGCATGACGCCTTTT
64 TTT-AAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAG-AAGGCGCCTTTT
* ** * * * * *
1245612 CTTTTCAAAGCCCACATGAGTTGGTGGCACTTTTTAGTCCTCAAAGTGTAGGATGACTTTTCCTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCAC-CTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTT
1245677 TT
65 TT
1245679 CTCCTTTGTC
Statistics
Matches: 476, Mismatches: 68, Indels: 23
0.84 0.12 0.04
Matches are distributed among these distances:
119 34 0.07
120 66 0.14
121 3 0.01
122 100 0.21
123 173 0.36
124 77 0.16
125 23 0.05
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.29
Consensus pattern (121 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTTT
TAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGAAGGCGCCTTTT
Found at i:1245822 original size:84 final size:85
Alignment explanation
Indices: 1245647--1245859 Score: 211
Period size: 84 Copynumber: 2.5 Consensus size: 85
1245637 GGCACTTTTT
* * * * * *
1245647 AGTCCTCAAAGTGTAGGATG-AC--TTTTCCTTTTCTCCTTTGTCCTCAAAAAGTAGGACACATT
1 AGTCCTCAAAGAGCAGGATGCACTTTTTTTCTTTTTTCC-TTGTCCTCAAAAAGCAGGACACACT
** *
1245709 TCATTTCCTTCTTTTTTATTT
65 TCATTTCCTTCTTTTCCATTC
* * *
1245730 TGTCCTCAAAGAGCGGGATGC-CTTTTTTTCTTTTTTCCTTGTCCTCAAAGAA-CAGGGCACACT
1 AGTCCTCAAAGAGCAGGATGCACTTTTTTTCTTTTTTCCTTGTCCTCAAA-AAGCAGGACACACT
*
1245793 TCATTTCCTTCTTTTCCCTTC
65 TCATTTCCTTCTTTTCCATTC
* *
1245814 AGTTCTCAAAGAGTAGGATGCACTTTATTCTTCTTTTTTCCCTTGT
1 AGTCCTCAAAGAGCAGGATGCACTTT-TT-TTCTTTTTT-CCTTGT
1245860 TTTCAAAGGG
Statistics
Matches: 105, Mismatches: 17, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
83 17 0.16
84 53 0.50
85 18 0.17
86 2 0.02
87 9 0.09
88 6 0.06
ACGTcount: A:0.19, C:0.24, G:0.14, T:0.43
Consensus pattern (85 bp):
AGTCCTCAAAGAGCAGGATGCACTTTTTTTCTTTTTTCCTTGTCCTCAAAAAGCAGGACACACTT
CATTTCCTTCTTTTCCATTC
Found at i:1246535 original size:20 final size:20
Alignment explanation
Indices: 1246510--1246564 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
1246500 TTTTCACAAT
1246510 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
*
1246530 TTGTATCGATACATTATTCA
1 TTGTATCGATACATTGTTCA
1246550 TTGTA--GATACATTGT
1 TTGTATCGATACATTGT
1246565 ATCGATACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.27
20 24 0.73
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.45
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:1249068 original size:80 final size:78
Alignment explanation
Indices: 1248926--1249127 Score: 260
Period size: 80 Copynumber: 2.5 Consensus size: 78
1248916 TTTTCATCTT
* * * * *
1248926 GGGGATACTCCAAACCCGGTTTTATTTCCAAAACATCAATTTTTCATAATCGGGGATACTCCAAT
1 GGGGATACTCC-AACCCGATTTTATTTCTAAAACACCAATTTTTCACAATCGGGGATACTCCAAC
* *
1248991 CCTGTTATTTTCGA
65 CCCGTTATTTTCAA
* *
1249005 GGGGATACTCCAATCTCGATTTTATTTCTAAATCACCAATCTTTTCACAATCGGGGATACTCCAA
1 GGGGATACTCCAA-CCCGATTTTATTTCTAAAACACCAAT-TTTTCACAATCGGGGATACTCCAA
1249070 CCCCGTTATTTTCAA
64 CCCCGTTATTTTCAA
* * *
1249085 GGGGATACTCCAACCCTTATTTTATTTCTAGAACACCGATTTT
1 GGGGATACTCCAACCC-GATTTTATTTCTAAAACACCAATTTT
1249128 CCATAGTCAT
Statistics
Matches: 106, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
78 2 0.02
79 37 0.35
80 67 0.63
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (78 bp):
GGGGATACTCCAACCCGATTTTATTTCTAAAACACCAATTTTTCACAATCGGGGATACTCCAACC
CCGTTATTTTCAA
Found at i:1249142 original size:80 final size:78
Alignment explanation
Indices: 1248926--1249153 Score: 253
Period size: 80 Copynumber: 2.9 Consensus size: 78
1248916 TTTTCATCTT
* * *
1248926 GGGGATACTCCAAACCC-GGTTTTATTTCCAAAACATCAATTTTTCATAATCGGGGATACTCCAA
1 GGGGATACTCC-AACCCTGATTTTATTT-CTAAACACCAATTTTTCATAATCGGGGATACTCCAA
* * *
1248990 TCCTGTTATTTTCGA
64 CCCCGTTATTTTCAA
* *
1249005 GGGGATACTCCAA-TCTCGATTTTATTTCTAAATCACCAATCTTTTCACAATCGGGGATACTCCA
1 GGGGATACTCCAACCCT-GATTTTATTTCTAAA-CACCAAT-TTTTCATAATCGGGGATACTCCA
1249069 ACCCCGTTATTTTCAA
63 ACCCCGTTATTTTCAA
* * * * * *
1249085 GGGGATACTCCAACCCTTATTTTATTTCTAGAACACCGATTTTCCATAGTCATGGGATACTCCAG
1 GGGGATACTCCAACCCTGATTTTATTTCTA-AACACCAATTTTTCATAATC-GGGGATACTCCAA
1249150 CCCC
64 CCCC
1249154 ACTGTCATCT
Statistics
Matches: 126, Mismatches: 16, Indels: 13
0.81 0.10 0.08
Matches are distributed among these distances:
77 1 0.01
78 6 0.05
79 34 0.27
80 81 0.64
81 4 0.03
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (78 bp):
GGGGATACTCCAACCCTGATTTTATTTCTAAACACCAATTTTTCATAATCGGGGATACTCCAACC
CCGTTATTTTCAA
Found at i:1251783 original size:28 final size:28
Alignment explanation
Indices: 1251724--1251784 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
1251714 ACACATGTTT
* *
1251724 AAGCCTATACTAGCTAGCACATTACTCT
1 AAGCCTATACTAGCTAGCACATGACTCA
* * *
1251752 AAGCCTATACTAGCTGGCAGATGAGTCA
1 AAGCCTATACTAGCTAGCACATGACTCA
1251780 AAGCC
1 AAGCC
1251785 CACATTAGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (28 bp):
AAGCCTATACTAGCTAGCACATGACTCA
Found at i:1251797 original size:28 final size:27
Alignment explanation
Indices: 1251766--1251854 Score: 88
Period size: 28 Copynumber: 3.2 Consensus size: 27
1251756 CTATACTAGC
1251766 TGGCAGATGAGTCAAAGCCCACATTAGT
1 TGGCAG-TGAGTCAAAGCCCACATTAGT
* * * *
1251794 TGGCATTCGTGTTAAAGCCCACATTAAT
1 TGGCAGT-GAGTCAAAGCCCACATTAGT
* * *
1251822 TGACACGTGAATCAAAGCCCATATTAGT
1 TGGCA-GTGAGTCAAAGCCCACATTAGT
1251850 TGGCA
1 TGGCA
1251855 CATAAGTTTG
Statistics
Matches: 47, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
27 1 0.02
28 45 0.96
29 1 0.02
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (27 bp):
TGGCAGTGAGTCAAAGCCCACATTAGT
Found at i:1251898 original size:26 final size:26
Alignment explanation
Indices: 1251865--1251932 Score: 127
Period size: 26 Copynumber: 2.6 Consensus size: 26
1251855 CATAAGTTTG
1251865 AGCCCACACTTGCTGGCACCAAATTA
1 AGCCCACACTTGCTGGCACCAAATTA
1251891 AGCCCACACTTGCTGGCACCAAATTA
1 AGCCCACACTTGCTGGCACCAAATTA
*
1251917 AGCCCACACTAGCTGG
1 AGCCCACACTTGCTGG
1251933 TGCAAAAGTC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.29, C:0.35, G:0.18, T:0.18
Consensus pattern (26 bp):
AGCCCACACTTGCTGGCACCAAATTA
Found at i:1252065 original size:26 final size:27
Alignment explanation
Indices: 1252000--1252066 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 27
1251990 ACATGAATCA
*
1252000 AAGCCCATATTAGCTAGCATCCAAGTTT
1 AAGCCCATACTAGCTAGCATCCAAG-TT
1252028 AAGCCCATACTAGCTAGCA-CCTAAG-T
1 AAGCCCATACTAGCTAGCATCC-AAGTT
*
1252054 AAGCCCACACTAG
1 AAGCCCATACTAG
1252067 TTGGCACACA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
26 13 0.36
27 2 0.06
28 21 0.58
ACGTcount: A:0.34, C:0.30, G:0.15, T:0.21
Consensus pattern (27 bp):
AAGCCCATACTAGCTAGCATCCAAGTT
Found at i:1252244 original size:28 final size:28
Alignment explanation
Indices: 1252210--1252264 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
1252200 GTTGGCACGT
*
1252210 AAGTCAAAGTCCACACTAGCTAGCACTC
1 AAGTCAAAGCCCACACTAGCTAGCACTC
*
1252238 AAGTCAAAGCCCACACTAGCTGGCACT
1 AAGTCAAAGCCCACACTAGCTAGCACT
1252265 TAGTATGGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.35, C:0.33, G:0.16, T:0.16
Consensus pattern (28 bp):
AAGTCAAAGCCCACACTAGCTAGCACTC
Found at i:1254672 original size:21 final size:21
Alignment explanation
Indices: 1254648--1254693 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
1254638 TTTTCATAAT
*
1254648 TTTTTTGGTGTTAATTTATGA
1 TTTTCTGGTGTTAATTTATGA
1254669 TTTTCTGGTGTTAATTTATGA
1 TTTTCTGGTGTTAATTTATGA
1254690 TTTT
1 TTTT
1254694 GTATTATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.17, C:0.02, G:0.17, T:0.63
Consensus pattern (21 bp):
TTTTCTGGTGTTAATTTATGA
Found at i:1257386 original size:17 final size:17
Alignment explanation
Indices: 1257364--1257399 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1257354 GGTGAATGAT
1257364 AGATTAGATATGATCCA
1 AGATTAGATATGATCCA
1257381 AGATTAGATATGATCCA
1 AGATTAGATATGATCCA
1257398 AG
1 AG
1257400 TGCTTCATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.28
Consensus pattern (17 bp):
AGATTAGATATGATCCA
Found at i:1260954 original size:20 final size:20
Alignment explanation
Indices: 1260929--1260966 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1260919 TATCACTATT
1260929 TGTATCGATACATGGTACAA
1 TGTATCGATACATGGTACAA
*
1260949 TGTATCGATACATTGTAC
1 TGTATCGATACATGGTAC
1260967 TGATACATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (20 bp):
TGTATCGATACATGGTACAA
Found at i:1262584 original size:3 final size:3
Alignment explanation
Indices: 1262576--1262600 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1262566 TGAAGAGGAA
1262576 GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT G
1262601 GTAATTCAGA
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:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:1263225 original size:21 final size:21
Alignment explanation
Indices: 1263201--1263240 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1263191 GATATCAAAA
* *
1263201 AATTGGCTAATAAAAATAATG
1 AATTAGCTAAGAAAAATAATG
1263222 AATTAGCTAAGAAAAATAA
1 AATTAGCTAAGAAAAATAA
1263241 AAACTTGCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.05, G:0.12, T:0.25
Consensus pattern (21 bp):
AATTAGCTAAGAAAAATAATG
Found at i:1269165 original size:12 final size:12
Alignment explanation
Indices: 1269148--1269172 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1269138 TATGTATCAA
1269148 ATTACAAGCTTG
1 ATTACAAGCTTG
1269160 ATTACAAGCTTG
1 ATTACAAGCTTG
1269172 A
1 A
1269173 ACAATTTGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (12 bp):
ATTACAAGCTTG
Found at i:1269650 original size:19 final size:20
Alignment explanation
Indices: 1269626--1269679 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 20
1269616 ATATGTTGCT
**
1269626 TTGTATCAATACATGTTC-A
1 TTGTATCAATACATGGACAA
**
1269645 TTGTATGGATACATGGACAA
1 TTGTATCAATACATGGACAA
*
1269665 TTATATCAATACATG
1 TTGTATCAATACATG
1269680 AAACTGGCAG
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (20 bp):
TTGTATCAATACATGGACAA
Found at i:1278243 original size:89 final size:91
Alignment explanation
Indices: 1278093--1278298 Score: 265
Period size: 89 Copynumber: 2.3 Consensus size: 91
1278083 AGGGGAAAGC
* * *
1278093 CCACACATTCCCAACCATAT-CCCTTCACTTAACCACTAGATAGTATTAATGCATCACAAAGCTT
1 CCACACATTCCCAATCATATCCCCTTCACCTAACCACTAGATAGTATTAATGCATCACAAAGCCT
* * *
1278157 GATTTCTTTGGGGTAA-GG-TGCAAA
66 GATTTCCTTGGGGCAAGGGATCCAAA
* ** *
1278181 CCACACATTCCCAATCATATCCCCTTCACCTAACCACTAGATGGTATTGGTGCATCATAAAGCCT
1 CCACACATTCCCAATCATATCCCCTTCACCTAACCACTAGATAGTATTAATGCATCACAAAGCCT
**
1278246 GATTTCCTTGGGGCAAGGGTATCCTGA
66 GATTTCCTTGGGGCAAGGG-ATCCAAA
*
1278273 CCACTCATTCCCAATCATATCCCCTT
1 CCACACATTCCCAATCATATCCCCTT
1278299 TTTTTTAGCC
Statistics
Matches: 101, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
88 19 0.19
89 52 0.51
90 2 0.02
92 28 0.28
ACGTcount: A:0.28, C:0.30, G:0.14, T:0.28
Consensus pattern (91 bp):
CCACACATTCCCAATCATATCCCCTTCACCTAACCACTAGATAGTATTAATGCATCACAAAGCCT
GATTTCCTTGGGGCAAGGGATCCAAA
Found at i:1278811 original size:47 final size:46
Alignment explanation
Indices: 1278758--1278977 Score: 215
Period size: 47 Copynumber: 4.7 Consensus size: 46
1278748 AACCTAGATA
**
1278758 TCAAACTCTTATCAACCTCATTTGATTGTATTGGTGTTAGGACCTGG
1 TCAAACTCTT-TCAACCTCATTTGATTGTATTGGCATTAGGACCTGG
* * * * ** *
1278805 TCAAACTCTTTCTACCCTCATTTAACTATATTGGCATTAAAACCTAG
1 TCAAACTCTTTC-AACCTCATTTGATTGTATTGGCATTAGGACCTGG
* * ** *
1278852 TCAAACTCTTCTCATCTTCATTTGACCGTATTGGCATTAGGACTTGG
1 TCAAACTCTT-TCAACCTCATTTGATTGTATTGGCATTAGGACCTGG
* ** * *
1278899 TCAAACTCTTTCCACCATTGTTTGATTATATTGGCGTTAGGACCTGG
1 TCAAACTCTTTCAACC-TCATTTGATTGTATTGGCATTAGGACCTGG
*
1278946 TTAAACTCTTTCAACCCTCATTTGATTGTATT
1 TCAAACTCTTTCAA-CCTCATTTGATTGTATT
1278978 TGTTATCACC
Statistics
Matches: 136, Mismatches: 33, Indels: 8
0.77 0.19 0.05
Matches are distributed among these distances:
46 5 0.04
47 127 0.93
48 4 0.03
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (46 bp):
TCAAACTCTTTCAACCTCATTTGATTGTATTGGCATTAGGACCTGG
Found at i:1278977 original size:94 final size:94
Alignment explanation
Indices: 1278758--1278977 Score: 253
Period size: 94 Copynumber: 2.3 Consensus size: 94
1278748 AACCTAGATA
** * *
1278758 TCAAACTCTTATCAACCTCATTTGATTGTATTGGTGTTAGGACCTGGTCAAACTCTTTCTACCCT
1 TCAAACTCTTATCAACCTCATTTGATTGTATTGGCATTAGGACCTGGTCAAACTCTTTCCACCAT
1278823 CATTTAACTATATTGGCATTAAAACCTAG
66 CATTTAACTATATTGGCATTAAAACCTAG
* * * ** *
1278852 TCAAACTCTTCTCATCTTCATTTGACCGTATTGGCATTAGGACTTGGTCAAACTCTTTCCACCAT
1 TCAAACTCTTATCAACCTCATTTGATTGTATTGGCATTAGGACCTGGTCAAACTCTTTCCACCAT
** * * * ** *
1278917 TGTTTGATTATATTGGCGTTAGGACCTGG
66 CATTTAACTATATTGGCATTAAAACCTAG
*
1278946 TTAAACTCTT-TCAACCCTCATTTGATTGTATT
1 TCAAACTCTTATCAA-CCTCATTTGATTGTATT
1278978 TGTTATCACC
Statistics
Matches: 102, Mismatches: 23, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
93 3 0.03
94 99 0.97
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (94 bp):
TCAAACTCTTATCAACCTCATTTGATTGTATTGGCATTAGGACCTGGTCAAACTCTTTCCACCAT
CATTTAACTATATTGGCATTAAAACCTAG
Found at i:1279349 original size:92 final size:92
Alignment explanation
Indices: 1279249--1279418 Score: 250
Period size: 92 Copynumber: 1.8 Consensus size: 92
1279239 TCATTTGATT
* * * *
1279249 GTATCGATTACCACCTTGGTCAAACACCTTTTGTTTTTATTTGACTATATCGGCTGCTACCCTAG
1 GTATCGATTACCACCTTAGTCAAACACCTTTTGTTCTTATTTGACTATATCGGCTACCACCCTAG
1279314 TCAAACCCTTTTTATTTTTGTTTAACA
66 TCAAACCCTTTTTATTTTTGTTTAACA
* *** * *
1279341 GTATCGATTACCATCTTAGTCAAACTTTTTTTGTTCTTATTTGACTATATCGGTTACCACCCTGG
1 GTATCGATTACCACCTTAGTCAAACACCTTTTGTTCTTATTTGACTATATCGGCTACCACCCTAG
1279406 TCAAACCCTTTTT
66 TCAAACCCTTTTT
1279419 GTTCTCTATA
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
92 68 1.00
ACGTcount: A:0.22, C:0.23, G:0.12, T:0.43
Consensus pattern (92 bp):
GTATCGATTACCACCTTAGTCAAACACCTTTTGTTCTTATTTGACTATATCGGCTACCACCCTAG
TCAAACCCTTTTTATTTTTGTTTAACA
Found at i:1279418 original size:46 final size:46
Alignment explanation
Indices: 1279025--1279423 Score: 216
Period size: 46 Copynumber: 8.7 Consensus size: 46
1279015 GATTGTATTA
* * * * * *
1279025 GTTACCACCCAGCTTAAACCCTTTTCATTCTTATTTGACTGTATCA
1 GTTACCACCCTGGTCAAACCCTTTTTATTCTTATTTGACTATATCG
** * * * * *
1279071 GTTACCACCCTCATCAAACCTTTTTTGTTTTTGTTTCACTATATCG
1 GTTACCACCCTGGTCAAACCCTTTTTATTCTTATTTGACTATATCG
* * * * * ** *
1279117 ATTACCAACTTGGTCAAA-TCTTTTTCCTTCTCGTTTGACT-TATTG
1 GTTACCACCCTGGTCAAACCCTTTTT-ATTCTTATTTGACTATATCG
* * * * * ** *
1279162 GTTACCACTCTGGTTAAATCCTTTTCCATTCTCATTTGACTGCATTG
1 GTTACCACCCTGGTCAAACCCTTTT-TATTCTTATTTGACTATATCG
* ** * * * * *
1279209 GTTACCACCTTGGTTGAA-CATATTTCATTCTCATTTGATTGTATCG
1 GTTACCACCCTGGTCAAACCCT-TTTTATTCTTATTTGACTATATCG
* *
1279255 ATTACCACCTTGGTCAAACACCTTTTGT-TT-TTATTTGACTATATCG
1 GTTACCACCCTGGTCAAAC-CCTTTT-TATTCTTATTTGACTATATCG
* * * * * * *
1279301 GCTGCTACCCTAGTCAAACCCTTTTTATTTTTGTTTAAC-AGTATCG
1 GTTACCACCCTGGTCAAACCCTTTTTATTCTTATTTGACTA-TATCG
* * * * ** *
1279347 ATTACCATCTTAGTCAAACTTTTTTTGTTCTTATTTGACTATATCG
1 GTTACCACCCTGGTCAAACCCTTTTTATTCTTATTTGACTATATCG
*
1279393 GTTACCACCCTGGTCAAACCCTTTTTGTTCT
1 GTTACCACCCTGGTCAAACCCTTTTTATTCT
1279424 CTATAGACAC
Statistics
Matches: 266, Mismatches: 75, Indels: 24
0.73 0.21 0.07
Matches are distributed among these distances:
44 1 0.00
45 31 0.12
46 204 0.77
47 28 0.11
48 2 0.01
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.44
Consensus pattern (46 bp):
GTTACCACCCTGGTCAAACCCTTTTTATTCTTATTTGACTATATCG
Found at i:1279855 original size:31 final size:32
Alignment explanation
Indices: 1279820--1279896 Score: 138
Period size: 31 Copynumber: 2.4 Consensus size: 32
1279810 CATTTTTTAT
1279820 TGTATCGATACATTTTGGGTTT-TAACCCAAA
1 TGTATCGATACATTTTGGGTTTGTAACCCAAA
1279851 TGTATCGATACATTTTGGGTTTGTAACCCAAA
1 TGTATCGATACATTTTGGGTTTGTAACCCAAA
*
1279883 TGTATCAATACATT
1 TGTATCGATACATT
1279897 CTTCAATGTA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
31 22 0.50
32 22 0.50
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATTTTGGGTTTGTAACCCAAA
Found at i:1282107 original size:14 final size:14
Alignment explanation
Indices: 1282088--1282119 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1282078 TTTAATCAAG
*
1282088 GAAAGCTATACTTT
1 GAAAGCTAAACTTT
1282102 GAAAGCTAAACTTT
1 GAAAGCTAAACTTT
1282116 GAAA
1 GAAA
1282120 TCTCTTAACC
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:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (14 bp):
GAAAGCTAAACTTT
Found at i:1283129 original size:46 final size:45
Alignment explanation
Indices: 1283015--1283142 Score: 118
Period size: 46 Copynumber: 2.8 Consensus size: 45
1283005 CACCTGGGTT
* * *
1283015 AAACCTTTTTGGC-TCTCATTTGACTGTATCTATTACTACCCTGGTC
1 AAACCTTTTT--CATCTCATTTGACTGTATCAATTACTAACCTAGTC
** *
1283061 AAACCTTTTTCATCATTTTTTGACTGTATCGATTA-TCAACCTAGTC
1 AAACCTTTTTCATC-TCATTTGACTGTATCAATTACT-AACCTAGTC
*
1283107 AAATCC-TTTTCATGCTCATTTGATTGTATCAATTAC
1 AAA-CCTTTTTCAT-CTCATTTGACTGTATCAATTAC
1283143 CACCTTAGTA
Statistics
Matches: 67, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
44 1 0.01
45 3 0.04
46 60 0.90
47 3 0.04
ACGTcount: A:0.24, C:0.23, G:0.10, T:0.43
Consensus pattern (45 bp):
AAACCTTTTTCATCTCATTTGACTGTATCAATTACTAACCTAGTC
Found at i:1283173 original size:46 final size:46
Alignment explanation
Indices: 1283079--1283182 Score: 102
Period size: 46 Copynumber: 2.3 Consensus size: 46
1283069 TTCATCATTT
* * * * *
1283079 TTTGACTGTATCGATTATCAACCTAGTCAAATCCTTTTCATGCTCA
1 TTTGATTGTATCAATTATCAACCTAGTAAAAGCCTTTTCATGCCCA
* * *
1283125 TTTGATTGTATCAATTA-CCACCTTAGTAAAAGCCTTTTTATTCCCA
1 TTTGATTGTATCAATTATCAACC-TAGTAAAAGCCTTTTCATGCCCA
* *
1283171 TTTTATGGTATC
1 TTTGATTGTATC
1283183 GGTTAACCTA
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
45 4 0.09
46 43 0.91
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.42
Consensus pattern (46 bp):
TTTGATTGTATCAATTATCAACCTAGTAAAAGCCTTTTCATGCCCA
Found at i:1283438 original size:43 final size:41
Alignment explanation
Indices: 1283389--1283619 Score: 160
Period size: 43 Copynumber: 5.4 Consensus size: 41
1283379 GGTCAACTTG
* * *
1283389 TTTATCCTTTGTTTACCTTTTAGCTCAGTCCCAAGTAAATCCT
1 TTTATCCTTTGTTTA-CTTTCAGCTCAGTCCC-GGTAAATCTT
* * * *
1283432 TTTATCCTTTGTTGACTTGTCAGTTCAATCCCGGTCAA-CTT
1 TTTATCCTTTGTTTACTT-TCAGCTCAGTCCCGGTAAATCTT
* * * *
1283473 CTTTATCCTTTGTTTACCTGTCGGCTCAGTCCTGAGTAAATCCT
1 -TTTATCCTTTGTTTA-CTTTCAGCTCAGTCCCG-GTAAATCTT
* * * ** * * *
1283517 TTTATCTTTTATTGACTTGTTGGTTCAATCCCGGTCAA-CTT
1 TTTATCCTTTGTTTACTT-TCAGCTCAGTCCCGGTAAATCTT
* *
1283558 CTTTATCCTTTGTTTAGCTGTCAGCTCAGTCCTAGGTAAATCTT
1 -TTTATCCTTTGTTTA-CTTTCAGCTCAGTCC-CGGTAAATCTT
*
1283602 TTTATCCTTTGTTGACTT
1 TTTATCCTTTGTTTACTT
1283620 GTCGGTTTAA
Statistics
Matches: 141, Mismatches: 37, Indels: 21
0.71 0.19 0.11
Matches are distributed among these distances:
41 4 0.03
42 59 0.42
43 73 0.52
44 5 0.04
ACGTcount: A:0.17, C:0.23, G:0.14, T:0.45
Consensus pattern (41 bp):
TTTATCCTTTGTTTACTTTCAGCTCAGTCCCGGTAAATCTT
Found at i:1283486 original size:42 final size:42
Alignment explanation
Indices: 1283432--1283738 Score: 194
Period size: 42 Copynumber: 7.2 Consensus size: 42
1283422 AGTAAATCCT
1283432 TTTATCCTTTGTTGACTTGTCAGTTCAATCCCGGTCAACTTC
1 TTTATCCTTTGTTGACTTGTCAGTTCAATCCCGGTCAACTTC
* * * * * * * *
1283474 TTTATCCTTTGTTTACCTGTCGGCTCAGTCCTGAGT-AAATCC
1 TTTATCCTTTGTTGACTTGTCAGTTCAATCCCG-GTCAACTTC
* * **
1283516 TTTTATCTTTTATTGACTTGTTGGTTCAATCCCGGTCAACTTC
1 -TTTATCCTTTGTTGACTTGTCAGTTCAATCCCGGTCAACTTC
* * * * *
1283559 TTTATCCTTTGTTTAGC-TGTCAGCTCAGTCCTAGGTAAATCTT-
1 TTTATCCTTTGTTGA-CTTGTCAGTTCAATCC-CGGTCAA-CTTC
* * **
1283602 TTTATCCTTTGTTGACTTGTCGGTTTAATCTTGGTCAACTTC
1 TTTATCCTTTGTTGACTTGTCAGTTCAATCCCGGTCAACTTC
* * * * * * * * * *
1283644 CTTATCTTTTGTTTACCTAT-TGA-TTTAGTCCTAGG-GAAATCC
1 TTTATCCTTTGTTGA-CT-TGTCAGTTCAATCC-CGGTCAACTTC
* *
1283686 TTTTATCCTTTGTTGACTTGTCAGTTCAATCCCAGTCAACTTA
1 -TTTATCCTTTGTTGACTTGTCAGTTCAATCCCGGTCAACTTC
1283729 TTTATCCTTT
1 TTTATCCTTT
1283739 ATTCACCTCT
Statistics
Matches: 192, Mismatches: 58, Indels: 30
0.69 0.21 0.11
Matches are distributed among these distances:
41 4 0.02
42 98 0.51
43 86 0.45
44 4 0.02
ACGTcount: A:0.18, C:0.22, G:0.14, T:0.46
Consensus pattern (42 bp):
TTTATCCTTTGTTGACTTGTCAGTTCAATCCCGGTCAACTTC
Found at i:1283512 original size:85 final size:85
Alignment explanation
Indices: 1283379--1283759 Score: 469
Period size: 85 Copynumber: 4.5 Consensus size: 85
1283369 GTTCAACCTT
* * * * *
1283379 GGTCAACTTGTTTATCCTTTGTTTACCTTTTAGCTCAGTCCCAAGTAAATCCTTTTATCCTTTGT
1 GGTCAACTTCTTTATCCTTTGTTTACCTGTCAGCTCAGTCCTAGGTAAATCCTTTTATCCTTTGT
1283444 TGACTTGTCAGTTCAATCCC
66 TGACTTGTCAGTTCAATCCC
* * *
1283464 GGTCAACTTCTTTATCCTTTGTTTACCTGTCGGCTCAGTCCT-GAGTAAATCCTTTTATCTTTTA
1 GGTCAACTTCTTTATCCTTTGTTTACCTGTCAGCTCAGTCCTAG-GTAAATCCTTTTATCCTTTG
**
1283528 TTGACTTGTTGGTTCAATCCC
65 TTGACTTGTCAGTTCAATCCC
* *
1283549 GGTCAACTTCTTTATCCTTTGTTTAGCTGTCAGCTCAGTCCTAGGTAAATCTTTTTATCCTTTGT
1 GGTCAACTTCTTTATCCTTTGTTTACCTGTCAGCTCAGTCCTAGGTAAATCCTTTTATCCTTTGT
* * **
1283614 TGACTTGTCGGTTTAATCTT
66 TGACTTGTCAGTTCAATCCC
* * * * * * *
1283634 GGTCAACTTCCTTATCTTTTGTTTACCTAT-TGATTTAGTCCTAGGGAAATCCTTTTATCCTTTG
1 GGTCAACTTCTTTATCCTTTGTTTACCTGTCAG-CTCAGTCCTAGGTAAATCCTTTTATCCTTTG
1283698 TTGACTTGTCAGTTCAATCCC
65 TTGACTTGTCAGTTCAATCCC
* * * * * *
1283719 AGTCAACTTATTTATCCTTTATTCACCTCTCAGCTTAGTCC
1 GGTCAACTTCTTTATCCTTTGTTTACCTGTCAGCTCAGTCC
1283760 CTAGTAACCA
Statistics
Matches: 251, Mismatches: 41, Indels: 8
0.84 0.14 0.03
Matches are distributed among these distances:
84 1 0.00
85 248 0.99
86 2 0.01
ACGTcount: A:0.18, C:0.23, G:0.14, T:0.45
Consensus pattern (85 bp):
GGTCAACTTCTTTATCCTTTGTTTACCTGTCAGCTCAGTCCTAGGTAAATCCTTTTATCCTTTGT
TGACTTGTCAGTTCAATCCC
Found at i:1285032 original size:24 final size:24
Alignment explanation
Indices: 1284982--1285038 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
1284972 CTTTTATTTC
* *
1284982 ATTAATTTTCTTTTTTTCCTTGAA
1 ATTATTTTTCTTTTTTTACTTGAA
*
1285006 ATT-TTTTTCTTTTTTTACTCTGTA
1 ATTATTTTTCTTTTTTTACT-TGAA
1285030 ATTATTTTT
1 ATTATTTTT
1285039 GGGAGGATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 14 0.50
24 9 0.32
25 5 0.18
ACGTcount: A:0.18, C:0.11, G:0.04, T:0.68
Consensus pattern (24 bp):
ATTATTTTTCTTTTTTTACTTGAA
Found at i:1285163 original size:15 final size:15
Alignment explanation
Indices: 1285144--1285173 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1285134 AAGTTTTTTT
1285144 ATTTTTTC-TTTTCA
1 ATTTTTTCATTTTCA
1285158 ATTTTTTCATTTTCA
1 ATTTTTTCATTTTCA
1285173 A
1 A
1285174 GAAACTGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.20, C:0.13, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTTTTTCATTTTCA
Found at i:1286314 original size:18 final size:18
Alignment explanation
Indices: 1286291--1286352 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
1286281 TGGAAAAATC
1286291 AAAAAATCAAAAAATAAT
1 AAAAAATCAAAAAATAAT
* *
1286309 AAAAAATCAAAATTATCAAA
1 AAAAAATCAAAA-AAT-AAT
**
1286329 AAAAAATCTCAAAATAAT
1 AAAAAATCAAAAAATAAT
1286347 CAAAAA
1 -AAAAA
1286353 GATTATTACT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
18 14 0.40
19 9 0.26
20 12 0.34
ACGTcount: A:0.73, C:0.10, G:0.00, T:0.18
Consensus pattern (18 bp):
AAAAAATCAAAAAATAAT
Found at i:1286351 original size:9 final size:8
Alignment explanation
Indices: 1286284--1286331 Score: 51
Period size: 8 Copynumber: 5.6 Consensus size: 8
1286274 ATTTGTTTGG
1286284 AAAAATCA
1 AAAAATCA
1286292 AAAAATCA
1 AAAAATCA
*
1286300 AAAAATAATA
1 AAAAAT--CA
1286310 AAAAATCA
1 AAAAATCA
*
1286318 AAATTATCA
1 AAA-AATCA
1286327 AAAAA
1 AAAAA
1286332 AAATCTCAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
8 19 0.58
9 7 0.21
10 7 0.21
ACGTcount: A:0.75, C:0.08, G:0.00, T:0.17
Consensus pattern (8 bp):
AAAAATCA
Found at i:1286419 original size:20 final size:20
Alignment explanation
Indices: 1286394--1286461 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
1286384 GAAAGTTGTG
* *
1286394 AAAGCATGAAATGAAGACGC
1 AAAGCATGAAATGATGATGC
*
1286414 AAAGCATGAAA-GTTG-TG-
1 AAAGCATGAAATGATGATGC
1286431 AAAGCATGAAATGATGATGC
1 AAAGCATGAAATGATGATGC
1286451 AAAGCATGAAA
1 AAAGCATGAAA
1286462 GTTGTGAAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
17 11 0.27
18 4 0.10
19 4 0.10
20 22 0.54
ACGTcount: A:0.49, C:0.10, G:0.25, T:0.16
Consensus pattern (20 bp):
AAAGCATGAAATGATGATGC
Found at i:1286424 original size:37 final size:37
Alignment explanation
Indices: 1286382--1286476 Score: 172
Period size: 37 Copynumber: 2.6 Consensus size: 37
1286372 TGATGAATGA
1286382 ATGAAAGTTGTGAAAGCATGAAATGAAGACGCAAAGC
1 ATGAAAGTTGTGAAAGCATGAAATGAAGACGCAAAGC
* *
1286419 ATGAAAGTTGTGAAAGCATGAAATGATGATGCAAAGC
1 ATGAAAGTTGTGAAAGCATGAAATGAAGACGCAAAGC
1286456 ATGAAAGTTGTGAAAGCATGA
1 ATGAAAGTTGTGAAAGCATGA
1286477 TATCATGCAA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.44, C:0.08, G:0.27, T:0.20
Consensus pattern (37 bp):
ATGAAAGTTGTGAAAGCATGAAATGAAGACGCAAAGC
Found at i:1290437 original size:21 final size:21
Alignment explanation
Indices: 1290396--1290438 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1290386 GTGATATTTA
* *
1290396 TCATGTTATATATTTGTTGAT
1 TCATGTTAAATATTAGTTGAT
1290417 TCATGTTGAAATATTAG-TGAT
1 TCATGTT-AAATATTAGTTGAT
1290438 T
1 T
1290439 TCATTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.28, C:0.05, G:0.16, T:0.51
Consensus pattern (21 bp):
TCATGTTAAATATTAGTTGAT
Found at i:1298862 original size:1 final size:1
Alignment explanation
Indices: 1298858--1298919 Score: 61
Period size: 1 Copynumber: 62.0 Consensus size: 1
1298848 CCTTCTTTTT
* * * * * * *
1298858 AAAAAAAACAAAAAAAAAAACAAAAAACAAAAAAACAAAAAAACAAAACAAAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1298920 GAGAGAAAAG
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.89, C:0.10, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:1298872 original size:8 final size:8
Alignment explanation
Indices: 1298858--1298917 Score: 72
Period size: 8 Copynumber: 7.8 Consensus size: 8
1298848 CCTTCTTTTT
1298858 AAAAAA-A
1 AAAAAACA
*
1298865 ACAAAA-A
1 AAAAAACA
1298872 AAAAAAC-
1 AAAAAACA
1298879 AAAAAACA
1 AAAAAACA
1298887 AAAAAACA
1 AAAAAACA
1298895 AAAAAACA
1 AAAAAACA
*
1298903 AAACAAAGA
1 AAA-AAACA
1298912 AAAAAA
1 AAAAAA
1298918 AAGAGAGAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
7 18 0.38
8 22 0.47
9 7 0.15
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (8 bp):
AAAAAACA
Found at i:1298889 original size:27 final size:27
Alignment explanation
Indices: 1298859--1298919 Score: 97
Period size: 27 Copynumber: 2.3 Consensus size: 27
1298849 CTTCTTTTTA
1298859 AAAAAAACAAAAAAA-AAAACAAAAAA
1 AAAAAAACAAAAAAACAAAACAAAAAA
*
1298885 CAAAAAAACAAAAAAACAAAACAAAGAA
1 -AAAAAAACAAAAAAACAAAACAAAAAA
1298913 AAAAAAA
1 AAAAAAA
1298920 GAGAGAAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 22 0.69
28 10 0.31
ACGTcount: A:0.89, C:0.10, G:0.02, T:0.00
Consensus pattern (27 bp):
AAAAAAACAAAAAAACAAAACAAAAAA
Found at i:1298889 original size:28 final size:28
Alignment explanation
Indices: 1298859--1298919 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
1298849 CTTCTTTTTA
*
1298859 AAAAAAACAAAAAAA-AAAACAAAAAAC
1 AAAAAAACAAAAAAACAAAACAAAAAAA
*
1298886 AAAAAAACAAAAAAACAAAACAAAGAAA
1 AAAAAAACAAAAAAACAAAACAAAAAAA
1298914 AAAAAA
1 AAAAAA
1298920 GAGAGAAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 15 0.48
28 16 0.52
ACGTcount: A:0.89, C:0.10, G:0.02, T:0.00
Consensus pattern (28 bp):
AAAAAAACAAAAAAACAAAACAAAAAAA
Found at i:1300219 original size:123 final size:123
Alignment explanation
Indices: 1300030--1300768 Score: 904
Period size: 122 Copynumber: 6.0 Consensus size: 123
1300020 GAACAAGATG
* * * *
1300030 CCTTTCAAAGCCCACACAAGCTGGTGGCACC-TTCAGTCCTCAAAGAGTATGATGCCTTTTCCTT
1 CCTTTTAAAGCCCACACAAGCTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTT
* ** *
1300094 TTAAAGCCCACATAAGTTGGTGGCACTTTTTTAGTCCTCAAAGAGCAAGATACCTTTC
66 TTAAAGCCCACACAAGTTGGTGGCACTTTTTTAGTCCTCAAAGAGCAAGACGCCTTTT
** * *
1300152 CCTTTTAAAGCCCATGCAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTCCTT
1 CCTTTTAAAGCCCACACAAGCTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTT
** *
1300217 TTAAAGCCCACACAAGTTGGTGGCACTTTACTAGTCCTCAAAGAGCAAGATGCCTTTT
66 TTAAAGCCCACACAAGTTGGTGGCACTTTTTTAGTCCTCAAAGAGCAAGACGCCTTTT
* * *
1300275 CCTTTTAAAGCCCACACAAGCTGGTGGCACCTTCCAGTCTTCAAAGAGCAGGATG-CTTTCTCCT
1 CCTTTTAAAGCCCACACAAGCTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTT-TCCT
* * * * *
1300339 TTCAAAGCCCAC-CAAGCTAGTGGCAC--CTTTAGTCCTCAAAGAGCAGGACGCCTTTT
65 TTTAAAGCCCACACAAGTTGGTGGCACTTTTTTAGTCCTCAAAGAGCAAGACGCCTTTT
* *
1300395 CCTTTCAAAGCCCACACAAGCTGGTGGCACC-TTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTT
1 CCTTTTAAAGCCCACACAAGCTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTT
* ** * *
1300459 TTAAAGCTCACACAAGTTGGTGGCTTTTTTTTAGTCCTCAAAGAGCAGGACGACTTTT
66 TTAAAGCCCACACAAGTTGGTGGCACTTTTTTAGTCCTCAAAGAGCAAGACGCCTTTT
* * * * * *
1300517 CCTTTTGAAGCCCACACAAGTTTGTGGCACCTTTCTAGTCCTCAAAGAGCAAGACACCTTTTTCT
1 CCTTTTAAAGCCCACACAAGCTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGACGCCTTTTCCT
* * * *
1300582 TTTCAAAGCCCACACAAATTGGTGGCAC-CTCTTAGTCCTCAAAGAGCATGACGCCTTTT
65 TTT-AAAGCCCACACAAGTTGGTGGCACTTTTTTAGTCCTCAAAGAGCAAGACGCCTTTT
* * * * *
1300641 TCTTTTCAAAGCCTACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACG-CTTTT-CT
1 CCTTTT-AAAGCCCACACAAGCTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCT
* * * * *
1300704 TTTCAAAGCCCACACGAGTTGGTGGTA-GTTTTTAGTCCTCAAAGAGGAGGACGCCTTTT
65 TTT-AAAGCCCACACAAGTTGGTGGCACTTTTTTAGTCCTCAAAGAGCAAGACGCCTTTT
*
1300763 CTTTTT
1 CCTTTT
1300769 CTTCTTTGTC
Statistics
Matches: 534, Mismatches: 72, Indels: 22
0.85 0.11 0.04
Matches are distributed among these distances:
119 35 0.07
120 69 0.13
122 155 0.29
123 153 0.29
124 78 0.15
125 44 0.08
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (123 bp):
CCTTTTAAAGCCCACACAAGCTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTT
TTAAAGCCCACACAAGTTGGTGGCACTTTTTTAGTCCTCAAAGAGCAAGACGCCTTTT
Found at i:1300415 original size:60 final size:60
Alignment explanation
Indices: 1300030--1300763 Score: 835
Period size: 62 Copynumber: 12.0 Consensus size: 60
1300020 GAACAAGATG
* * * * *
1300030 CCTTTCAAAGCCCACACAAGCTGGTGGCACCTTCAGTCCTCAAAGAGTATGATGCCTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGACGCCTTTT
* * * * ** *
1300090 CCTTTTAAAGCCCACATAAGTTGGTGGCACTTTTTTAGTCCTCAAAGAGCAAGATACCTTTC
1 CCTTTCAAAGCCCACACAAGTTGGTGGCAC--CTTTAGTCCTCAAAGAGCAGGACGCCTTTT
* **
1300152 CCTTTTAAAGCCCATGCAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACGCCTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACC-TTTAGTCCTCAAAGAGCAGGACGCCTTTT
* * * *
1300213 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTACTAGTCCTCAAAGAGCAAGATGCCTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTT--TAGTCCTCAAAGAGCAGGACGCCTTTT
* * * * *
1300275 CCTTTTAAAGCCCACACAAGCTGGTGGCACCTTCCAGTCTTCAAAGAGCAGGATG-CTTTCT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTT-TAGTCCTCAAAGAGCAGGACGCCTTT-T
* *
1300336 CCTTTCAAAGCCCAC-CAAGCTAGTGGCACCTTTAGTCCTCAAAGAGCAGGACGCCTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGACGCCTTTT
* * *
1300395 CCTTTCAAAGCCCACACAAGCTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCCTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGACGCCTTTT
* * *** *
1300455 CCTTTTAAAGCTCACACAAGTTGGTGGCTTTTTTTTAGTCCTCAAAGAGCAGGACGACTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGC--ACCTTTAGTCCTCAAAGAGCAGGACGCCTTTT
** * * *
1300517 CCTTTTGAAGCCCACACAAGTTTGTGGCACCTTTCTAGTCCTCAAAGAGCAAGACACCTTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACC-TT-TAGTCCTCAAAGAGCAGGACGCC-TTTT
* * *
1300580 CTTTTCAAAGCCCACACAAATTGGTGGCACCTCTTAGTCCTCAAAGAGCATGACGCCTTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCT-TTAGTCCTCAAAGAGCAGGACGCC-TTTT
* * *
1300642 CTTTTCAAAGCCTACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACG-CTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACC-TTTAGTCCTCAAAGAGCAGGACGCCTTTT
* * * ** *
1300702 CTTTTCAAAGCCCACACGAGTTGGTGGTAGTTTTTAGTCCTCAAAGAGGAGGACGCCTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCA-CCTTTAGTCCTCAAAGAGCAGGACGCCTTTT
1300763 C
1 C
1300764 TTTTTCTTCT
Statistics
Matches: 588, Mismatches: 69, Indels: 33
0.85 0.10 0.05
Matches are distributed among these distances:
59 34 0.06
60 172 0.29
61 96 0.16
62 254 0.43
63 32 0.05
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (60 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTAGTCCTCAAAGAGCAGGACGCCTTTT
Found at i:1300851 original size:40 final size:39
Alignment explanation
Indices: 1300738--1300880 Score: 135
Period size: 40 Copynumber: 3.5 Consensus size: 39
1300728 GTAGTTTTTA
* * *
1300738 GTCCTCAAAGAGGAGGACGCCTTTTCTT-TTTCTTCTTT
1 GTCCTCAAAGAGCAGGACGCCTTTTTTTCTTTTTTCTTT
* * *
1300776 GTCCTCAAAGAGCAGGACACATTTCATTTCCTTCTTTTTTGTTTT
1 GTCCTCAAAGAGCAGGACGC-CTT--TTT--TTCTTTTTT-CTTT
*
1300821 GTCCTCAAAGAGCAGGATGCCTTTTTTTCTTTTTTCCTTT
1 GTCCTCAAAGAGCAGGACGCCTTTTTTTCTTTTTT-CTTT
* *
1300861 GTCCTCAAAGAACATGACGC
1 GTCCTCAAAGAGCAGGACGC
1300881 ACTTCATTTC
Statistics
Matches: 84, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
38 18 0.21
39 2 0.02
40 29 0.35
41 2 0.02
42 3 0.04
43 2 0.02
44 7 0.08
45 21 0.25
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.41
Consensus pattern (39 bp):
GTCCTCAAAGAGCAGGACGCCTTTTTTTCTTTTTTCTTT
Found at i:1300870 original size:85 final size:84
Alignment explanation
Indices: 1300733--1300893 Score: 225
Period size: 85 Copynumber: 1.9 Consensus size: 84
1300723 TGGTGGTAGT
* * *
1300733 TTTTAGTCCTCAAAGAGGAGGACGCCTTTTCTTTTTCTTCTTTGTCCTCAAAGAGCAGGACACAT
1 TTTTAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTTCTTCTTTGTCCTCAAAGAACAGGACACAC
1300798 TTCATTTCCTTCTTTTTTG
66 TTCATTTCCTTCTTTTTTG
* * * * *
1300817 TTTT-GTCCTCAAAGAGCAGGATGCCTTTTTTTCTTTTTTCCTTTGTCCTCAAAGAACATGACGC
1 TTTTAGTCCTCAAAGAGCAGGACGCCTTTTCTT-TTTCTT-CTTTGTCCTCAAAGAACAGGACAC
1300881 ACTTCATTTCCTT
64 ACTTCATTTCCTT
1300894 TTAGTTCTCA
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
83 25 0.37
84 9 0.13
85 33 0.49
ACGTcount: A:0.19, C:0.24, G:0.14, T:0.43
Consensus pattern (84 bp):
TTTTAGTCCTCAAAGAGCAGGACGCCTTTTCTTTTTCTTCTTTGTCCTCAAAGAACAGGACACAC
TTCATTTCCTTCTTTTTTG
Found at i:1301629 original size:20 final size:20
Alignment explanation
Indices: 1301604--1301656 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
1301594 TTTTCACAAT
1301604 TTGTATCGATACATTATTCA
1 TTGTATCGATACATTATTCA
1301624 TTGTATCGATACATTATTCA
1 TTGTATCGATACATTATTCA
1301644 TTGTA--GATACATT
1 TTGTATCGATACATT
1301657 GTATCGATAC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.24
20 25 0.76
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.45
Consensus pattern (20 bp):
TTGTATCGATACATTATTCA
Found at i:1304174 original size:80 final size:78
Alignment explanation
Indices: 1304024--1304254 Score: 291
Period size: 80 Copynumber: 2.9 Consensus size: 78
1304014 TTTTCATCTC
* * * * *
1304024 GGGGATACTCCAAACCTGGTTTTATTTCCAAAACATCAATTTTTCATAATCGGGGATACTCCAAT
1 GGGGATACTCC-AACCCGATTTTATTTCTAAAACACCAATTTTTCATAATCGGGGATACTCCAAC
*
1304089 CCCGTTATTTACGA
65 CCCGTTATTTACAA
* * *
1304103 GGGGATACTCCAATCCCGATTTTATTGCTAAAACACCAATCTTTTCACAATCGGGGATACTCTAA
1 GGGGATACTCCAA-CCCGATTTTATTTCTAAAACACCAAT-TTTTCATAATCGGGGATACTCCAA
*
1304168 CCCCGTTATTTTCAA
64 CCCCGTTATTTACAA
* * * *
1304183 GGGGATACTCCAACCCTGATTTTATTTCTAGAACACCGATTTTTCATAGTCAGGGGATACTCCAG
1 GGGGATACTCCAACCC-GATTTTATTTCTAAAACACCAATTTTTCATAATC-GGGGATACTCCAA
1304248 CCCCGTT
64 CCCCGTT
1304255 GTCATCTCAA
Statistics
Matches: 131, Mismatches: 17, Indels: 7
0.85 0.11 0.05
Matches are distributed among these distances:
78 2 0.02
79 44 0.34
80 85 0.65
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (78 bp):
GGGGATACTCCAACCCGATTTTATTTCTAAAACACCAATTTTTCATAATCGGGGATACTCCAACC
CCGTTATTTACAA
Found at i:1305440 original size:15 final size:14
Alignment explanation
Indices: 1305420--1305452 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1305410 TAAGATCTAG
*
1305420 AAAAAAAAGGCAAA
1 AAAAAAAAAGCAAA
1305434 AAAAAAAAAGCAAA
1 AAAAAAAAAGCAAA
1305448 AAAAA
1 AAAAA
1305453 GCCAAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.85, C:0.06, G:0.09, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAGCAAA
Found at i:1306887 original size:28 final size:28
Alignment explanation
Indices: 1306828--1306888 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
1306818 ACACATGTTT
* *
1306828 AAGCCTATACTAGCTAGCACATTACTCT
1 AAGCCTATACTAGCTAGCACATGACTCA
* *
1306856 AAGCCTATACTAGCTGGCACATGAGTCA
1 AAGCCTATACTAGCTAGCACATGACTCA
1306884 AAGCC
1 AAGCC
1306889 CACATTAGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (28 bp):
AAGCCTATACTAGCTAGCACATGACTCA
Found at i:1306901 original size:28 final size:28
Alignment explanation
Indices: 1306870--1306961 Score: 96
Period size: 28 Copynumber: 3.3 Consensus size: 28
1306860 CTATACTAGC
1306870 TGGCACATGAGTCAAAGCCCACATTAGT
1 TGGCACATGAGTCAAAGCCCACATTAGT
* * * *
1306898 TGGCA-TTCGTGTTAAAGCCCACATTAAT
1 TGGCACAT-GAGTCAAAGCCCACATTAGT
* * * *
1306926 TGACACGTGAATCAAAGCCCATATTAGT
1 TGGCACATGAGTCAAAGCCCACATTAGT
1306954 TGGCACAT
1 TGGCACAT
1306962 AAGTTTGAGC
Statistics
Matches: 49, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
27 1 0.02
28 47 0.96
29 1 0.02
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.26
Consensus pattern (28 bp):
TGGCACATGAGTCAAAGCCCACATTAGT
Found at i:1307104 original size:138 final size:137
Alignment explanation
Indices: 1306886--1307144 Score: 322
Period size: 138 Copynumber: 1.9 Consensus size: 137
1306876 ATGAGTCAAA
* ** * * *
1306886 GCCCACATTAGTTGGCATTCGTGTTAAAGCCCACATTAATTGACACGTGAATCAAAGCCCATATT
1 GCCCACATTAATTGGCATTCACGTTAAAACCAACATTAATTGACACATGAATCAAAGCCCATATT
* * * * * *
1306951 AGTTGGCACATAAGTTTGAGCCCACACTTGCTGGCACCAAATTAAGCCCACACTAGCTGGTGCAA
66 AGCT-GAACATAAGTTTAAGCCCACACTAGCTAGCACCAAAGTAAGCCCACACTAGCTGGTGCAA
1307016 AAGTCGAT
130 AAGTCGAT
* * *
1307024 GCCCACGTTAATTGGCATTCACGTTAAAACCAATATTAATTGGCACATGAATCAAAGCCCATATT
1 GCCCACATTAATTGGCATTCACGTTAAAACCAACATTAATTGACACATGAATCAAAGCCCATATT
* * *
1307089 AGCT-AACATCCAAGTTTAAGCCCATACTAGCTAGCACCTAAGTAAGCCCAGACTAG
66 AGCTGAACAT--AAGTTTAAGCCCACACTAGCTAGCACCAAAGTAAGCCCACACTAG
1307145 TTGGCATACA
Statistics
Matches: 101, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
136 4 0.04
138 97 0.96
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.24
Consensus pattern (137 bp):
GCCCACATTAATTGGCATTCACGTTAAAACCAACATTAATTGACACATGAATCAAAGCCCATATT
AGCTGAACATAAGTTTAAGCCCACACTAGCTAGCACCAAAGTAAGCCCACACTAGCTGGTGCAAA
AGTCGAT
Found at i:1307131 original size:28 final size:26
Alignment explanation
Indices: 1307078--1307144 Score: 73
Period size: 28 Copynumber: 2.5 Consensus size: 26
1307068 ACATGAATCA
*
1307078 AAGCCCATATTAGCTAACATCCAAGTTT
1 AAGCCCATACTAGCTAACATCCAAG--T
*
1307106 AAGCCCATACTAGCTAGCA-CCTAAGT
1 AAGCCCATACTAGCTAACATCC-AAGT
*
1307132 AAGCCCAGACTAG
1 AAGCCCATACTAG
1307145 TTGGCATACA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 13 0.37
27 2 0.06
28 20 0.57
ACGTcount: A:0.36, C:0.28, G:0.15, T:0.21
Consensus pattern (26 bp):
AAGCCCATACTAGCTAACATCCAAGT
Found at i:1307322 original size:28 final size:28
Alignment explanation
Indices: 1307282--1307372 Score: 155
Period size: 28 Copynumber: 3.2 Consensus size: 28
1307272 ATGTTAGTTG
* *
1307282 GCACATAAGTCAAAGTCCACACTAGCTA
1 GCACTTAAGTCAAAGCCCACACTAGCTA
1307310 GCACTTAAGTCAAAGCCCACACTAGCTA
1 GCACTTAAGTCAAAGCCCACACTAGCTA
*
1307338 GCACTTAAGTCAAAGCCCACACTAGCTG
1 GCACTTAAGTCAAAGCCCACACTAGCTA
1307366 GCACTTA
1 GCACTTA
1307373 GTATGGAGGT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 60 1.00
ACGTcount: A:0.35, C:0.31, G:0.15, T:0.19
Consensus pattern (28 bp):
GCACTTAAGTCAAAGCCCACACTAGCTA
Found at i:1309804 original size:21 final size:21
Alignment explanation
Indices: 1309780--1309827 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
1309770 TTTTCATAAT
*
1309780 TTTTTTGGTGTTAATTTATGA
1 TTTTCTGGTGTTAATTTATGA
1309801 TTTTCTGGTGTTAATTTATGA
1 TTTTCTGGTGTTAATTTATGA
1309822 TTTTCT
1 TTTTCT
1309828 ATTATATAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.17, C:0.04, G:0.17, T:0.62
Consensus pattern (21 bp):
TTTTCTGGTGTTAATTTATGA
Found at i:1312513 original size:17 final size:17
Alignment explanation
Indices: 1312491--1312526 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1312481 GGTGAATGAT
1312491 AGATTAGATATGATCCA
1 AGATTAGATATGATCCA
1312508 AGATTAGATATGATCCA
1 AGATTAGATATGATCCA
1312525 AG
1 AG
1312527 TTCTTCATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.28
Consensus pattern (17 bp):
AGATTAGATATGATCCA
Found at i:1314792 original size:2 final size:2
Alignment explanation
Indices: 1314781--1314822 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1314771 CAAATCCATC
1314781 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1314822 T
1 T
1314823 TTAAAGTGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1321416 original size:13 final size:13
Alignment explanation
Indices: 1321398--1321423 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1321388 CAATTTTTTG
1321398 TGTATCGATACAT
1 TGTATCGATACAT
1321411 TGTATCGATACAT
1 TGTATCGATACAT
1321424 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1323983 original size:13 final size:13
Alignment explanation
Indices: 1323961--1323999 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1323951 ATAATCACCC
1323961 TGTATCGATACAA
1 TGTATCGATACAA
*
1323974 TGTATTGATACAA
1 TGTATCGATACAA
*
1323987 TCTATCGATACAA
1 TGTATCGATACAA
1324000 AGAAAAATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1326087 original size:15 final size:15
Alignment explanation
Indices: 1326051--1326088 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1326041 TTCATCAATT
* *
1326051 TCATTTGGAGCTTCT
1 TCATTTTGAGCTTCC
1326066 TCATTTTGAGCTTCC
1 TCATTTTGAGCTTCC
1326081 TCATTTTG
1 TCATTTTG
1326089 GACATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.13, C:0.21, G:0.16, T:0.50
Consensus pattern (15 bp):
TCATTTTGAGCTTCC
Found at i:1327939 original size:21 final size:21
Alignment explanation
Indices: 1327892--1327936 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
1327882 AAGTTTTCAT
1327892 TTTTC-TTAGCTAACTCATTA
1 TTTTCATTAGCTAACTCATTA
*
1327912 TTTTCATTAGCTAACTTCTTTA
1 TTTTCATTAGCTAAC-TCATTA
1327934 TTT
1 TTT
1327937 CATCTTGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.22, C:0.18, G:0.04, T:0.56
Consensus pattern (21 bp):
TTTTCATTAGCTAACTCATTA
Found at i:1330172 original size:13 final size:13
Alignment explanation
Indices: 1330154--1330179 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1330144 CAATTTTTTG
1330154 TGTATCGATACAT
1 TGTATCGATACAT
1330167 TGTATCGATACAT
1 TGTATCGATACAT
1330180 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1333287 original size:89 final size:88
Alignment explanation
Indices: 1333137--1333307 Score: 252
Period size: 89 Copynumber: 1.9 Consensus size: 88
1333127 AGGGGGCAGC
* * *
1333137 CCACACATTCCTAACCATATCCCTTCACTTAACCACTAGATAGTATTAATGCATCACAAAGCTTG
1 CCACACATTCCCAACCATATCCCTTCACATAACCACTAGATAGTATTAATGCATCACAAAGCCTG
*
1333202 ATTTCTTTGGGGCAAGGTGCAAA
66 ATTTCCTTGGGGCAAGGTGCAAA
* * **
1333225 CCACACATTCCCAATCATATCCCCTTCACATAACCACTAGATGGTATTGGTGCATCACAAAGCCT
1 CCACACATTCCCAACCATAT-CCCTTCACATAACCACTAGATAGTATTAATGCATCACAAAGCCT
*
1333290 GTTTTCCTTGGGGCAAGG
65 GATTTCCTTGGGGCAAGG
1333308 GTATCCCGAC
Statistics
Matches: 73, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
88 18 0.25
89 55 0.75
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (88 bp):
CCACACATTCCCAACCATATCCCTTCACATAACCACTAGATAGTATTAATGCATCACAAAGCCTG
ATTTCCTTGGGGCAAGGTGCAAA
Found at i:1333854 original size:47 final size:46
Alignment explanation
Indices: 1333801--1334020 Score: 217
Period size: 47 Copynumber: 4.7 Consensus size: 46
1333791 AACCTAGATA
**
1333801 TCAAACTCTTATCAACCTCATTTGATTGTATTGGTGTTAAGACCTGG
1 TCAAACTCTT-TCAACCTCATTTGATTGTATTGGCATTAAGACCTGG
* * * * * *
1333848 TCAAACTCTTTCTACCCTCATTTAACTATATTAGCATTAAGACCTAG
1 TCAAACTCTTTC-AACCTCATTTGATTGTATTGGCATTAAGACCTGG
* * * * *
1333895 TCAAACTCTTCTCATCTTCATTTGATCGTATTGGCATTAGGACTTGG
1 TCAAACTCTT-TCAACCTCATTTGATTGTATTGGCATTAAGACCTGG
* ** * *
1333942 TCAAACTCTTTCCACCATTGTTTGATTATATTGGCATTAGGACCTGG
1 TCAAACTCTTTCAACC-TCATTTGATTGTATTGGCATTAAGACCTGG
1333989 -CTAAACTCTTTCAACCCTCATTTGATTGTATT
1 TC-AAACTCTTTCAA-CCTCATTTGATTGTATT
1334021 TCTTATCACC
Statistics
Matches: 138, Mismatches: 30, Indels: 10
0.78 0.17 0.06
Matches are distributed among these distances:
46 6 0.04
47 128 0.93
48 4 0.03
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.39
Consensus pattern (46 bp):
TCAAACTCTTTCAACCTCATTTGATTGTATTGGCATTAAGACCTGG
Found at i:1333972 original size:94 final size:92
Alignment explanation
Indices: 1333801--1334020 Score: 251
Period size: 94 Copynumber: 2.3 Consensus size: 92
1333791 AACCTAGATA
** * *
1333801 TCAAACTCTTATCAACCTCATTTGATTGTATTGGTGTTAAGACCTGGTCAAACTCTTTCTACCCT
1 TCAAACTCTT-TCAACCTCATTTGATTGTATTGGCATTAAGACCTGGTCAAACTCTTTCCACCAT
1333866 CATTTAACTATATTAGCATTAAGACCTAG
65 CATTTAACTATATTAGCATTAAGACCT-G
* * * * *
1333895 TCAAACTCTTCTCATCTTCATTTGATCGTATTGGCATTAGGACTTGGTCAAACTCTTTCCACCAT
1 TCAAACTCTT-TCAACCTCATTTGATTGTATTGGCATTAAGACCTGGTCAAACTCTTTCCACCAT
** * * * *
1333960 TGTTTGATTATATTGGCATTAGGACCTG
65 CATTTAACTATATTAGCATTAAGACCTG
*
1333988 GCTAAACTCTTTCAACCCTCATTTGATTGTATT
1 TC-AAACTCTTTCAA-CCTCATTTGATTGTATT
1334021 TCTTATCACC
Statistics
Matches: 104, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
93 5 0.05
94 99 0.95
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.39
Consensus pattern (92 bp):
TCAAACTCTTTCAACCTCATTTGATTGTATTGGCATTAAGACCTGGTCAAACTCTTTCCACCATC
ATTTAACTATATTAGCATTAAGACCTG
Found at i:1334131 original size:46 final size:46
Alignment explanation
Indices: 1334068--1334460 Score: 238
Period size: 46 Copynumber: 8.5 Consensus size: 46
1334058 GATTGTATTA
* *
1334068 GTTACCACCCAGCTCAAACCCTTTTCATTCTCATTTGACTGTATCG
1 GTTACCACCCTGGTCAAACCCTTTTCATTCTCATTTGACTGTATCG
** * * * * *
1334114 GTTACCACCCTCATCAAA-CCTTCTTCGTTTTCGTTTCACTATATCG
1 GTTACCACCCTGGTCAAACCCTT-TTCATTCTCATTTGACTGTATCG
* * * * * * * * *
1334160 ATTACCAACTTGGTCAAATCTTTTTCCTTATCGTTTGACT-TATTG
1 GTTACCACCCTGGTCAAACCCTTTTCATTCTCATTTGACTGTATCG
* * * * *
1334205 GTTACCACTCTGGTTAAATCCTTTTCCATTCTCATTTGACTGCATTG
1 GTTACCACCCTGGTCAAACCCTTTT-CATTCTCATTTGACTGTATCG
* ** * * *
1334252 GTTACCACCTTGGTTGAA-CATATTTCATTCTCATTTGATTGTATCA
1 GTTACCACCCTGGTCAAACCCT-TTTCATTCTCATTTGACTGTATCG
* * * *
1334298 ATTACCA-CCTCGGTCAAACACCTTTT-GTTCTTATTTGACTATATCG
1 GTTACCACCCT-GGTCAAAC-CCTTTTCATTCTCATTTGACTGTATCG
* * * * * ** *
1334344 GCTGCTACCCTAGTCAAACCCTTTTCATTTTTGTTTGACAGTATCG
1 GTTACCACCCTGGTCAAACCCTTTTCATTCTCATTTGACTGTATCG
* * * * * ** ** * *
1334390 ATTACCATCTTAGTCACACTTTTTTTGTTCTTATTTGACTATATCG
1 GTTACCACCCTGGTCAAACCCTTTTCATTCTCATTTGACTGTATCG
1334436 GTTACCACCCTGGTCAAACCCTTTT
1 GTTACCACCCTGGTCAAACCCTTTT
1334461 TGTTCTCTGT
Statistics
Matches: 259, Mismatches: 78, Indels: 20
0.73 0.22 0.06
Matches are distributed among these distances:
45 35 0.14
46 191 0.74
47 31 0.12
48 2 0.01
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.41
Consensus pattern (46 bp):
GTTACCACCCTGGTCAAACCCTTTTCATTCTCATTTGACTGTATCG
Found at i:1334224 original size:45 final size:46
Alignment explanation
Indices: 1334161--1334265 Score: 124
Period size: 45 Copynumber: 2.3 Consensus size: 46
1334151 ACTATATCGA
* * *
1334161 TTACCAACTTGGTCAAATCTTTTTCC-TTATCGTTTGACT-TATTGG
1 TTACC-ACTTGGTCAAATCCTTTTCCATTATCATTTGACTGCATTGG
* *
1334206 TTACCACTCTGGTTAAATCCTTTTCCATTCTCATTTGACTGCATTGG
1 TTACCACT-TGGTCAAATCCTTTTCCATTATCATTTGACTGCATTGG
1334253 TTACCACCTTGGT
1 TTACCA-CTTGGT
1334266 TGAACATATT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
44 3 0.06
45 20 0.39
46 11 0.22
47 15 0.29
48 2 0.04
ACGTcount: A:0.19, C:0.24, G:0.13, T:0.44
Consensus pattern (46 bp):
TTACCACTTGGTCAAATCCTTTTCCATTATCATTTGACTGCATTGG
Found at i:1334896 original size:31 final size:32
Alignment explanation
Indices: 1334861--1334939 Score: 115
Period size: 31 Copynumber: 2.5 Consensus size: 32
1334851 TACATTTTTT
1334861 ATTGTATCGATACATTCGAGGTTT-TAACCCA
1 ATTGTATCGATACATTCGAGGTTTCTAACCCA
** *
1334892 ATTGTATCGATACATTTTAGGTTTCTGACCCA
1 ATTGTATCGATACATTCGAGGTTTCTAACCCA
*
1334924 AATGTATCGATACATT
1 ATTGTATCGATACATT
1334940 TTGGGTTTCT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
31 22 0.51
32 21 0.49
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (32 bp):
ATTGTATCGATACATTCGAGGTTTCTAACCCA
Done.