Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001174.1 Hibiscus syriacus cultivar Beakdansim tig00002338_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2182627
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 11
Found at i:1138122 original size:21 final size:21
Alignment explanation
Indices: 1138064--1138122 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
1138054 TGATTTATTA
*
1138064 TTATGGATTTCAAGTTGGTTG
1 TTATGGATTTCAAGTTTGTTG
*
1138085 TTATGAATTTCAAGTTTGTTG
1 TTATGGATTTCAAGTTTGTTG
* *
1138106 TTATGGATGTCATGTTT
1 TTATGGATTTCAAGTTT
1138123 ATTGGATAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.20, C:0.05, G:0.24, T:0.51
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTGTTG
Found at i:1141575 original size:23 final size:23
Alignment explanation
Indices: 1141546--1141608 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
1141536 ATTCCCCTAC
1141546 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
1141569 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
* * *
1141592 GGGGGGTATCGATTCCC
1 AGGGGGAATCGGTTCCC
1141609 TCTGCACTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.25, G:0.33, T:0.22
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCCTTCAA
Found at i:1141593 original size:22 final size:22
Alignment explanation
Indices: 1141537--1141596 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 22
1141527 GGGGTATCAA
*
1141537 TTCCCCTAC-AGGGGGAATCGG
1 TTCCCCTTCAAGGGGGAATCGG
1141558 TTCCCCTTCAAAGGGGGAATCGG
1 TTCCCCTTC-AAGGGGGAATCGG
1141581 TTCCCCTTCAAGGGGG
1 TTCCCCTTCAAGGGGG
1141597 GTATCGATTC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
21 8 0.22
22 7 0.19
23 21 0.58
ACGTcount: A:0.18, C:0.28, G:0.32, T:0.22
Consensus pattern (22 bp):
TTCCCCTTCAAGGGGGAATCGG
Found at i:1149344 original size:19 final size:21
Alignment explanation
Indices: 1149306--1149344 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1149296 CTCTTATGCA
1149306 ACTTAAAAACAATGCAAAATC
1 ACTTAAAAACAATGCAAAATC
*
1149327 ACTTTAAAAC-AT-CAAAAT
1 ACTTAAAAACAATGCAAAAT
1149345 AAGATCACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 2 0.12
21 9 0.53
ACGTcount: A:0.56, C:0.18, G:0.03, T:0.23
Consensus pattern (21 bp):
ACTTAAAAACAATGCAAAATC
Found at i:1167197 original size:54 final size:54
Alignment explanation
Indices: 1167091--1167415 Score: 258
Period size: 57 Copynumber: 6.1 Consensus size: 54
1167081 TTTCTTGATA
* * * * * *
1167091 TGATATTTTCAAATGAA-TTTGAAATAAGTTAAACCTAATTTTCAGGGGTTTCT
1 TGATGTTTTCAAATGAATTTTTAAAAAAGCTAAGCCTAATTTTTAGGGGTTTCT
* * *
1167144 TGATGTTTTCAAATGAATTTTGAAAAAAGGTAAGCCTAATTTTTAGGGTTTTCT
1 TGATGTTTTCAAATGAATTTTTAAAAAAGCTAAGCCTAATTTTTAGGGGTTTCT
* * * * * * *
1167198 TGATGTTTTCAAAAGAGTTTTTTATAAA-CTAAGTCTGATTTTTAGAGGTTTCT
1 TGATGTTTTCAAATGAATTTTTAAAAAAGCTAAGCCTAATTTTTAGGGGTTTCT
* *
1167251 TGA------CATGATGAATTTTTAAAGAAGCTAAG-CTAATTTTTAGGGGTTTCT
1 TGATGTTTTCA-AATGAATTTTTAAAAAAGCTAAGCCTAATTTTTAGGGGTTTCT
* * * *
1167299 CGGTGAT-TATTTCCAATGATTTTTTAAAAAAGCTAA-CCTTGATTTTCAGGGGTTTCT
1 ---TGATGT-TTTCAAATGAATTTTTAAAAAAGCTAAGCC-TAATTTTTAGGGGTTTCT
* * * *
1167356 TGATGATTATTTTAAAAGAATTTTTAAAGAAGCTAAGCCTAATTTTTAGGGGTTTAT
1 TGATG--T-TTTCAAATGAATTTTTAAAAAAGCTAAGCCTAATTTTTAGGGGTTTCT
1167413 TGA
1 TGA
1167416 CGATAACTGT
Statistics
Matches: 216, Mismatches: 38, Indels: 32
0.76 0.13 0.11
Matches are distributed among these distances:
47 2 0.01
48 28 0.13
49 5 0.02
51 3 0.01
53 39 0.18
54 58 0.27
56 20 0.09
57 59 0.27
58 2 0.01
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (54 bp):
TGATGTTTTCAAATGAATTTTTAAAAAAGCTAAGCCTAATTTTTAGGGGTTTCT
Found at i:1167902 original size:240 final size:240
Alignment explanation
Indices: 1167478--1168127 Score: 910
Period size: 240 Copynumber: 2.7 Consensus size: 240
1167468 TCTTGATTTG
1167478 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATACTTAAATCCTTCGGGTCATCTATAA
1 TAAGTCCTTC-GGCCATCAGTAAGTCTTTCGAGCATGATACTTAAATCCTTCGGGTCATCTATAA
* * ** *
1167543 TTCTTTGGAGCAAGATGATAAGTCCTT-GGGCCATCCATAAGACCTTCAGGAAAAATGTTTTCAC
65 TTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGAAGGATGTTTCCAC
* *
1167607 ATGATTTTTGAAAAATAAGAAAGCGATTTCCAAAGTTTCTCATTTAAATCTTTTCTGAAAAA-TG
130 ATGATTTTTGAAAAATAAGAAAGCGATTTACAAAGTTTCTCATTTAAACCTTTTCT-AAAAATTG
* **
1167671 ATTTTTCTTGAATAGTAAGAAAATTATTTCCAAAGTTCCTTACTGAA
194 ATTTTTCTTGAAAAGTAAGAAAACAATTTCCAAAGTTCCTTACTGAA
* *
1167718 TAAGTCCTTCAGGCCATCAGAAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTATAA
1 TAAGTCCTTC-GGCCATCAGTAAGTCTTTCGAGCATGATACTTAAATCCTTCGGGTCATCTATAA
* * * *
1167783 TTCTTTCAAGCAAGATGATAAGTCCTTCAGGCCATCCATAAGACCTTCGGGTAGGATGTTTCCAA
65 TTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGAAGGATGTTTCCAC
* *
1167848 ATGATTTTTG-AAAATGATAAAGCGATTTACAAAGTTTCTCATTTAAACCTTTTCTAAAAATTGA
130 ATGATTTTTGAAAAATAAGAAAGCGATTTACAAAGTTTCTCATTTAAACCTTTTCTAAAAATTGA
* * * *
1167912 TTTTTCTTGAAAAGTAAGAAAGCAATTTCCAAAGTTTCTTACTTAG
195 TTTTTCTTGAAAAGTAAGAAAACAATTTCCAAAGTTCCTTACTGAA
* * * * *
1167958 TAAGTCCTTCGGTCCATCAGTAATTCTTTCGAGAATGATATTTAAATCATTCGGGTTATCTATAA
1 TAAGTCCTTCGG-CCATCAGTAAGTCTTTCGAGCATGATACTTAAATCCTTCGGGTCATCTATAA
* * *
1168023 GTCTTTCGAGCAAGATGATAAGTTCTTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTCCAC
65 TTCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGAAGGATGTTTCCAC
* * * ** * *
1168088 ATGATTTTCGAAGAGTAAGAAAATGATTTCCAAACTTTCT
130 ATGATTTTTGAAAAATAAGAAAGCGATTTACAAAGTTTCT
1168128 TACTTAGTTC
Statistics
Matches: 361, Mismatches: 45, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
239 7 0.02
240 293 0.81
241 61 0.17
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (240 bp):
TAAGTCCTTCGGCCATCAGTAAGTCTTTCGAGCATGATACTTAAATCCTTCGGGTCATCTATAAT
TCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGAAGGATGTTTCCACA
TGATTTTTGAAAAATAAGAAAGCGATTTACAAAGTTTCTCATTTAAACCTTTTCTAAAAATTGAT
TTTTCTTGAAAAGTAAGAAAACAATTTCCAAAGTTCCTTACTGAA
Found at i:1170204 original size:15 final size:15
Alignment explanation
Indices: 1170184--1170216 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1170174 ATTTCCATGT
1170184 TTTATTTATTACTTG
1 TTTATTTATTACTTG
1170199 TTTATTTATTACTTG
1 TTTATTTATTACTTG
1170214 TTT
1 TTT
1170217 TACAATTGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.70
Consensus pattern (15 bp):
TTTATTTATTACTTG
Found at i:1171811 original size:15 final size:15
Alignment explanation
Indices: 1171793--1171822 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1171783 GTGTTTTAAA
1171793 CTGATGTGTATACTT
1 CTGATGTGTATACTT
*
1171808 CTGATTTGTATACTT
1 CTGATGTGTATACTT
1171823 TCTAGTTGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.13, G:0.17, T:0.50
Consensus pattern (15 bp):
CTGATGTGTATACTT
Found at i:1177695 original size:56 final size:55
Alignment explanation
Indices: 1177513--1177697 Score: 273
Period size: 55 Copynumber: 3.3 Consensus size: 55
1177503 GGGGTAAGTG
* * * **
1177513 AGACTTGAAAAATCTTCTAA-AATCGTGTATGCTCTTTATTTCTTCAGAGAGTATA
1 AGACTCGAACAATCTTC-AATAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATA
* * *
1177568 AGACTCGAACAATTTTCAATATTCGTGTCTGCTCCCTATTTCTTCAGAGAGTATG
1 AGACTCGAACAATCTTCAATAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATA
1177623 AGACTCGAACAATCTTCAATAATCGTGTCTGCTCCCTATTTCTTTCAGAGAGTATA
1 AGACTCGAACAATCTTCAATAATCGTGTCTGCTCCCTATTTC-TTCAGAGAGTATA
1177679 AGACTCGAACAATCTTCAA
1 AGACTCGAACAATCTTCAA
1177698 ACGGGTTCAC
Statistics
Matches: 117, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
54 2 0.02
55 84 0.72
56 31 0.26
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.35
Consensus pattern (55 bp):
AGACTCGAACAATCTTCAATAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATA
Found at i:1177807 original size:54 final size:53
Alignment explanation
Indices: 1177743--1178740 Score: 814
Period size: 54 Copynumber: 19.2 Consensus size: 53
1177733 ACACAAATAT
* * * * * *
1177743 TCTTCATCAAATGGGTTAGCTCCTTCTTTCTCTAGGGTGTATGGAACTTGGATA
1 TCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTTGGA-A
* *
1177797 TCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAAAAC-TCGAA
1 TCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTTGGAA
* *
1177849 -CATCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAAAACTT-GAA
1 TCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTTGGAA
* * * ***
1177900 -CATCTTCAAACGGGTTCGCTCCCACTTT-T-TAGGGAGTATGGAACTCAAACA
1 TCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTTGGA-A
** * * *
1177951 TCTTCTTCTTACAGGTTCGCTCCCTCTTTCTCTAGGGAGTATAAAAC-T-CAA
1 TCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTTGGAA
* * * * *
1178002 ACAATCTTCAAATGGGTTCGCTCCCTC--TCTTTAGGGAGTATAGAAC-TCGAA
1 TC-TTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTTGGAA
* * * *
1178053 CTTATTCTTCAAACGGGTTCTCTCCCTCTTTCTCTAAGGAGTATAGAACTCGGACA
1 --TCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTTGGA-A
** *
1178109 TCTTCTTCAAACAAGTTCGCTCCCTCTTTCT-TCAGGAAGTATAGAACTTGGACA
1 TCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTTGGA-A
* *
1178163 TCTTCTTCAAACGGGTTCGCTCCCTCTTTCT-TCAGGAAGTATAGAAC-TCGAA
1 TCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTTGGAA
* * * * *
1178215 -CAATCTTCAAACGGGTTCGCTCCCTC--TCTTTAGGGGGTATGGAAC-TCGAA
1 TC-TTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTTGGAA
* * * ***
1178265 -CAATCTTCAAACGGGTTCGCTCCATCTAT-T-TAGGGAGTATAGAACTCAAACA
1 TC-TTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTTGGA-A
* * *
1178317 TATTCTTCAAACGGGTTCGCTACCTCTTTCTCTAGGGAGTATAGAACTCGGACA
1 TCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTTGGA-A
** * * *
1178371 TCTTCTTCAAACATGTTCGCTCCCTCTTTCT-TCAGGAATTATAGAAC-TCGAA
1 TCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTTGGAA
* * * *
1178423 -CAATCTTCAAACGGGTTCGCTCCCTC--TCTTTAGGGAGTATGGAAC-T-CAA
1 TC-TTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTTGGAA
* * * * *
1178472 ACAATCTTCAAACGGGTTCGCTCCCTCTAT-T-TAGGGAGTATAGAACTCGAACA
1 TC-TTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTTGGA-A
* *
1178525 TATTCTTCAAATGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTTGGACA
1 TCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTTGGA-A
* ** *
1178579 TCTTCTTCAAACGGGTTCGTTCCCTCTTTCT-TCAGAAAGTATAGAAC-TCGAA
1 TCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAACTTGGAA
* * * *
1178631 -CAATCTTCAAACGGGTTCGCTCCCTC--TCTTTAGGGAGTATGGAAC-TCGAA
1 TC-TTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTTGGAA
* * * * * *
1178681 -CAATCTTCAAACGGGTTTGCTCCCTCTAT-T-TAGAGAGTATGGAACTCGGACA
1 TC-TTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTTGGA-A
1178733 TCTTCTTC
1 TCTTCTTC
1178741 TGCTTTATTA
Statistics
Matches: 792, Mismatches: 109, Indels: 88
0.80 0.11 0.09
Matches are distributed among these distances:
49 16 0.02
50 190 0.24
51 92 0.12
52 193 0.24
53 19 0.02
54 279 0.35
55 2 0.00
56 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (53 bp):
TCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTTGGAA
Found at i:1178323 original size:262 final size:258
Alignment explanation
Indices: 1177598--1178727 Score: 1183
Period size: 262 Copynumber: 4.3 Consensus size: 258
1177588 ATTCGTGTCT
* *
1177598 GCTCCCTATTTCTTCA-GAGAGTAT-GAGACTCGAACAATCTTCAATAATCGTG-TCTGCTCCCT
1 GCTCCCTCTTTCTTCAGGA-AGTATAGA-ACTCGAACAATCTTC-A-AA-CGGGTTC-GCTCCCT
* * * * * * * **
1177660 ATTTCTTTCAGAGAGTAT-AAGACTCGAACAATCTTCAAACGGGTTCACTCCCTATTTTTTCAAA
60 CTTTC-TT-AGGGAGTATGGA-ACTCAAACAATCTTCAAACGGGTTCGCTCCCT-CTCTTT-AGG
* * * * * * * * * *
1177724 GAATATAGAACACAAATATTCTTCATCAAATGGGTTAGCTCCTTCTTTCTCTAGGGTGTATGGAA
120 GAGTATAGAACTCGAACAATC-T--TCAAATGGGTTCGCTCCCTCTAT-T-TAGGGAGTATAGAA
* * * * * *
1177789 CTTGGATATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAAAACTC-GA-ACAT
180 CTCGAACATATTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAAGGAGTATAGAACTCGGACACAT
*
1177852 CTTCAAACGGGTTC
245 CTTCAAACAGGTTC
* * * *
1177866 GCTCCCTCTTTC-TCTAGGGAGTATAAAACTTGAAC-ATCTTCAAACGGGTTCGCTCCCACTTT-
1 GCTCCCTCTTTCTTC-AGGAAGTATAGAACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTC
* ** * *
1177928 TTAGGGAGTATGGAACTCAAACATCTTCTTCTTACAGGTTCGCTCCCTCTTTCTCTAGGGAGTAT
65 TTAGGGAGTATGGAACTCAAACA--ATCTTCAAACGGGTTCGCTCCCTC--TCTTTAGGGAGTAT
* * * *
1177993 AAAACTCAAACAATCTTCAAATGGGTTCGCTCCCTCTCTTTAGGGAGTATAGAACTCGAACTTAT
126 AGAACTCGAACAATCTTCAAATGGGTTCGCTCCCTCTATTTAGGGAGTATAGAACTCGAACATAT
* * *
1178058 TCTTCAAACGGGTTCTCTCCCTCTTTCTCTAAGGAGTATAGAACTCGGACATCTTCTTCAAACAA
191 TCTTCAAACGGGTTCGCTCCCTCTTTCTCTAAGGAGTATAGAACTCGGACA-CATCTTCAAACAG
1178123 GTTC
255 GTTC
* * *
1178127 GCTCCCTCTTTCTTCAGGAAGTATAGAACTTGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTT
1 GCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAACA--ATCTTCAAACGGGTTCGCTCCCTCTTT
* * * * *
1178192 CTTCAGGAAGTATAGAACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTCTTTAGGGGGTATGG
64 CTT-AGGGAGTATGGAACTCAAACAATCTTCAAACGGGTTCGCTCCCTCTCTTTAGGGAGTATAG
* * *
1178257 AACTCGAACAATCTTCAAACGGGTTCGCTCCATCTATTTAGGGAGTATAGAACTCAAACATATTC
128 AACTCGAACAATCTTCAAATGGGTTCGCTCCCTCTATTTAGGGAGTATAGAACTCGAACATATTC
* * * *
1178322 TTCAAACGGGTTCGCTACCTCTTTCTCTAGGGAGTATAGAACTCGGACATCTTCTTCAAACATGT
193 TTCAAACGGGTTCGCTCCCTCTTTCTCTAAGGAGTATAGAACTCGGACA-CATCTTCAAACAGGT
1178387 TC
257 TC
* *
1178389 GCTCCCTCTTTCTTCAGGAATTATAGAACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTCT-T
1 GCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTCT
*
1178453 TAGGGAGTATGGAACTCAAACAATCTTCAAACGGGTTCGCTCCCTCTATTTAGGGAGTATAGAAC
66 TAGGGAGTATGGAACTCAAACAATCTTCAAACGGGTTCGCTCCCTCTCTTTAGGGAGTATAGAAC
* * * *
1178518 TCGAACATATTCTTCAAATGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTTGGACATCTT
131 TCGAACA-A-TCTTCAAATGGGTTCGCTCCCTCTAT-T-TAGGGAGTATAGAACTCGAACATATT
* * * * *
1178583 CTTCAAACGGGTTCGTTCCCTCTTTCT-TCAGAAAGTATAGAACTCGAACA-ATCTTCAAACGGG
192 CTTCAAACGGGTTCGCTCCCTCTTTCTCTAAG-GAGTATAGAACTCGGACACATCTTCAAACAGG
1178646 TTC
256 TTC
* * * * *
1178649 GCTCCCTC--TCTTTAGGGAGTATGGAACTCGAACAATCTTCAAACGGGTTTGCTCCCTCTAT-T
1 GCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTCT
*
1178711 TAGAGAGTATGGAACTC
66 TAGGGAGTATGGAACTC
1178728 GGACATCTTC
Statistics
Matches: 738, Mismatches: 101, Indels: 56
0.82 0.11 0.06
Matches are distributed among these distances:
258 190 0.26
259 6 0.01
260 90 0.12
261 62 0.08
262 236 0.32
263 35 0.05
264 60 0.08
265 6 0.01
266 19 0.03
267 8 0.01
268 24 0.03
269 2 0.00
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.32
Consensus pattern (258 bp):
GCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAACAATCTTCAAACGGGTTCGCTCCCTCTTTCT
TAGGGAGTATGGAACTCAAACAATCTTCAAACGGGTTCGCTCCCTCTCTTTAGGGAGTATAGAAC
TCGAACAATCTTCAAATGGGTTCGCTCCCTCTATTTAGGGAGTATAGAACTCGAACATATTCTTC
AAACGGGTTCGCTCCCTCTTTCTCTAAGGAGTATAGAACTCGGACACATCTTCAAACAGGTTC
Found at i:1178382 original size:208 final size:207
Alignment explanation
Indices: 1177800--1178740 Score: 1327
Period size: 208 Copynumber: 4.5 Consensus size: 207
1177790 TTGGATATCT
* **
1177800 TCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAAAACTCGAAC-ATCTTCAAACGGGT
1 TCTTCAAACGGGTTCGCTCCCTC--TCTTTAGGGAGTATGGAACTCGAACAATCTTCAAACGGGT
* * * *
1177864 TCGCTCCCTCTTTCTCTAGGGAGTATAAAACTTGAAC--A-TCTTCAAACGGGTTCGCTCCCACT
64 TCGCTCCCTCTAT-T-TAGGGAGTATAGAACTCGAACATATTCTTCAAACGGGTTCGCTCCCTCT
* ** ** *
1177926 TT-TTAGGGAGTATGGAACTCAAACATCTTCTTCTTACAGGTTCGCTCCCTCTTTC-TCTAGGGA
127 TTCTTAGGGAGTATAGAACTCGGACATCTTCTTCAAACAGGTTCGCTCCCTCTTTCTTC-AGGAA
* *
1177989 GTATAAAACTCAAACAA
191 GTATAGAACTCGAACAA
* * *
1178006 TCTTCAAATGGGTTCGCTCCCTCTCTTTAGGGAGTATAGAACTCGAACTTATTCTTCAAACGGGT
1 TCTTCAAACGGGTTCGCTCCCTCTCTTTAGGGAGTATGGAACTCGAAC--AATCTTCAAACGGGT
* * * * * **
1178071 TCTCTCCCTCTTTCTCTAAGGAGTATAGAACTCGGACATCTTCTTCAAACAAGTTCGCTCCCTCT
64 TCGCTCCCTCTAT-T-TAGGGAGTATAGAACTCGAACATATTCTTCAAACGGGTTCGCTCCCTCT
* * *
1178136 TTCTTCAGGAAGTATAGAACTTGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTTCAGGAA
127 TTCTT-AGGGAGTATAGAACTCGGACATCTTCTTCAAACAGGTTCGCTCCCTCTTTCTTCAGGAA
1178201 GTATAGAACTCGAACAA
191 GTATAGAACTCGAACAA
*
1178218 TCTTCAAACGGGTTCGCTCCCTCTCTTTAGGGGGTATGGAACTCGAACAATCTTCAAACGGGTTC
1 TCTTCAAACGGGTTCGCTCCCTCTCTTTAGGGAGTATGGAACTCGAACAATCTTCAAACGGGTTC
* * *
1178283 GCTCCATCTATTTAGGGAGTATAGAACTCAAACATATTCTTCAAACGGGTTCGCTACCTCTTTCT
66 GCTCCCTCTATTTAGGGAGTATAGAACTCGAACATATTCTTCAAACGGGTTCGCTCCCTCTTTCT
* *
1178348 CTAGGGAGTATAGAACTCGGACATCTTCTTCAAACATGTTCGCTCCCTCTTTCTTCAGGAATTAT
131 -TAGGGAGTATAGAACTCGGACATCTTCTTCAAACAGGTTCGCTCCCTCTTTCTTCAGGAAGTAT
1178413 AGAACTCGAACAA
195 AGAACTCGAACAA
*
1178426 TCTTCAAACGGGTTCGCTCCCTCTCTTTAGGGAGTATGGAACTCAAACAATCTTCAAACGGGTTC
1 TCTTCAAACGGGTTCGCTCCCTCTCTTTAGGGAGTATGGAACTCGAACAATCTTCAAACGGGTTC
*
1178491 GCTCCCTCTATTTAGGGAGTATAGAACTCGAACATATTCTTCAAATGGGTTCGCTCCCTCTTTCT
66 GCTCCCTCTATTTAGGGAGTATAGAACTCGAACATATTCTTCAAACGGGTTCGCTCCCTCTTTCT
* * * *
1178556 CTAGGGAGTATAGAACTTGGACATCTTCTTCAAACGGGTTCGTTCCCTCTTTCTTCAGAAAGTAT
131 -TAGGGAGTATAGAACTCGGACATCTTCTTCAAACAGGTTCGCTCCCTCTTTCTTCAGGAAGTAT
1178621 AGAACTCGAACAA
195 AGAACTCGAACAA
*
1178634 TCTTCAAACGGGTTCGCTCCCTCTCTTTAGGGAGTATGGAACTCGAACAATCTTCAAACGGGTTT
1 TCTTCAAACGGGTTCGCTCCCTCTCTTTAGGGAGTATGGAACTCGAACAATCTTCAAACGGGTTC
* * * *
1178699 GCTCCCTCTATTTAGAGAGTATGGAACTCGGACATCTTCTTC
66 GCTCCCTCTATTTAGGGAGTATAGAACTCGAACATATTCTTC
1178741 TGCTTTATTA
Statistics
Matches: 664, Mismatches: 61, Indels: 18
0.89 0.08 0.02
Matches are distributed among these distances:
204 23 0.03
206 22 0.03
207 45 0.07
208 414 0.62
209 2 0.00
210 47 0.07
211 2 0.00
212 107 0.16
213 2 0.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (207 bp):
TCTTCAAACGGGTTCGCTCCCTCTCTTTAGGGAGTATGGAACTCGAACAATCTTCAAACGGGTTC
GCTCCCTCTATTTAGGGAGTATAGAACTCGAACATATTCTTCAAACGGGTTCGCTCCCTCTTTCT
TAGGGAGTATAGAACTCGGACATCTTCTTCAAACAGGTTCGCTCCCTCTTTCTTCAGGAAGTATA
GAACTCGAACAA
Found at i:1179004 original size:16 final size:17
Alignment explanation
Indices: 1178983--1179018 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1178973 AGTCATCTTC
1178983 ATCTTCATTATTCAA-T
1 ATCTTCATTATTCAACT
*
1178999 ATCTTCATTCTTCAACT
1 ATCTTCATTATTCAACT
1179016 ATC
1 ATC
1179019 ATTGGGAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (17 bp):
ATCTTCATTATTCAACT
Found at i:1180026 original size:23 final size:23
Alignment explanation
Indices: 1179990--1180038 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
1179980 TCATTTTTCA
*
1179990 TTTTCTTCTTTTTTCTTCTCTTT
1 TTTTCTTCTTTTTTCTTCCCTTT
* *
1180013 TTTTGTTCTTTTTTGTTCCCTTT
1 TTTTCTTCTTTTTTCTTCCCTTT
1180036 TTT
1 TTT
1180039 ATTATCTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.00, C:0.18, G:0.04, T:0.78
Consensus pattern (23 bp):
TTTTCTTCTTTTTTCTTCCCTTT
Found at i:1180037 original size:50 final size:49
Alignment explanation
Indices: 1179949--1180052 Score: 113
Period size: 49 Copynumber: 2.1 Consensus size: 49
1179939 CTCCTTTTTC
* *
1179949 TTTTTCTTCTTCTTTTTTTTTTGCATTTATTTCATTTTTCATTTTCTTCT
1 TTTTTCTTCTTCTTTTTTTGTTGCATTTATTTCATTTTTCATTATC-TCT
* * * *
1179999 TTTTTCTTC-TCTTTTTTTGTT-CTTTTTTGTTCCCTTTTTTATTATCTCT
1 TTTTTCTTCTTCTTTTTTTGTTGCATTTAT-TT-CATTTTTCATTATCTCT
1180048 TTTTT
1 TTTTT
1180053 TTTTATCTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
48 5 0.11
49 21 0.46
50 20 0.43
ACGTcount: A:0.06, C:0.16, G:0.03, T:0.75
Consensus pattern (49 bp):
TTTTTCTTCTTCTTTTTTTGTTGCATTTATTTCATTTTTCATTATCTCT
Found at i:1180064 original size:12 final size:12
Alignment explanation
Indices: 1179990--1180055 Score: 62
Period size: 12 Copynumber: 5.3 Consensus size: 12
1179980 TCATTTTTCA
1179990 TTTTCTTCTTTTT
1 TTTTC-TCTTTTT
*
1180003 TCTTCTCTTTTT
1 TTTTCTCTTTTT
*
1180015 TTGT-TCTTTTT
1 TTTTCTCTTTTT
* *
1180026 TGTTCCCTTTTT
1 TTTTCTCTTTTT
1180038 TATTATCTCTTTTT
1 T-TT-TCTCTTTTT
1180052 TTTT
1 TTTT
1180056 TATCTTTTTC
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
11 9 0.21
12 17 0.40
13 7 0.17
14 9 0.21
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.77
Consensus pattern (12 bp):
TTTTCTCTTTTT
Found at i:1194292 original size:17 final size:17
Alignment explanation
Indices: 1194265--1194409 Score: 105
Period size: 17 Copynumber: 8.4 Consensus size: 17
1194255 ATTTTATATC
1194265 TGTAAATATCTGATAAT
1 TGTAAATATCTGATAAT
*
1194282 TGT-AATCATCTGCT-AT
1 TGTAAAT-ATCTGATAAT
1194298 CTGTAAATATCTGATAAT
1 -TGTAAATATCTGATAAT
**
1194316 TAAAAATCATCTGATAAT
1 TGTAAAT-ATCTGATAAT
* *
1194334 TGTAAATATCTGATCAC
1 TGTAAATATCTGATAAT
* * *
1194351 AGAAAATCATTTGATAAT
1 TGTAAAT-ATCTGATAAT
* * *
1194369 TGTAAATATTTGACAAC
1 TGTAAATATCTGATAAT
* * *
1194386 GGTGAAATGTCTGATAAC
1 TGT-AAATATCTGATAAT
1194404 TGTAAA
1 TGTAAA
1194410 CATTTATAAT
Statistics
Matches: 99, Mismatches: 22, Indels: 14
0.73 0.16 0.10
Matches are distributed among these distances:
16 5 0.05
17 49 0.49
18 45 0.45
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (17 bp):
TGTAAATATCTGATAAT
Found at i:1194302 original size:34 final size:35
Alignment explanation
Indices: 1194238--1194377 Score: 128
Period size: 35 Copynumber: 4.0 Consensus size: 35
1194228 TTAATATGTG
* * *
1194238 TCTGATAAATATAAAA-CATTTTATATCTGTAAATA
1 TCTGATAATTA-AAAATCATCTGATATCTGTAAATA
** *
1194273 TCTGATAATT-GTAATCATCTGCTATCTGTAAATA
1 TCTGATAATTAAAAATCATCTGATATCTGTAAATA
1194307 TCTGATAATTAAAAATCATCTGATAAT-TGTAAATA
1 TCTGATAATTAAAAATCATCTGAT-ATCTGTAAATA
* * *
1194342 TCTGATCA-CAGAAAATCATTTGATAAT-TGTAAATA
1 TCTGATAATTA-AAAATCATCTGAT-ATCTGTAAATA
1194377 T
1 T
1194378 TTGACAACGG
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
33 2 0.02
34 27 0.30
35 58 0.65
36 2 0.02
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (35 bp):
TCTGATAATTAAAAATCATCTGATATCTGTAAATA
Found at i:1194329 original size:18 final size:17
Alignment explanation
Indices: 1194302--1194347 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
1194292 TGCTATCTGT
1194302 AAATATCTGATAATTAA
1 AAATATCTGATAATTAA
**
1194319 AAATCATCTGATAATTGT
1 AAAT-ATCTGATAATTAA
1194337 AAATATCTGAT
1 AAATATCTGAT
1194348 CACAGAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (17 bp):
AAATATCTGATAATTAA
Found at i:1196685 original size:3 final size:3
Alignment explanation
Indices: 1196677--1196704 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1196667 GAATAGGGTT
1196677 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1196705 ATTTATAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:1203375 original size:52 final size:50
Alignment explanation
Indices: 1203292--1203425 Score: 144
Period size: 52 Copynumber: 2.6 Consensus size: 50
1203282 TGATAACTGT
* * ** * * * *
1203292 AAAACATATGATATCTTTAAATATCTTATAATTGTAATTATCTTATATCTG
1 AAAACATCTGATAACTGAAAATATCTGATAATTATAAATATCTAATAT-TG
1203343 TAAAA-ATCTGATAACTGAAAATCATCTGATAATTATAAATATCTAATATTG
1 -AAAACATCTGATAACTGAAAAT-ATCTGATAATTATAAATATCTAATATTG
*
1203394 AAAATCATCTGATAACTGTAAATATCTGATAA
1 AAAA-CATCTGATAACTGAAAATATCTGATAA
1203426 AGGTGAAATG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
50 4 0.06
51 24 0.34
52 42 0.60
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.38
Consensus pattern (50 bp):
AAAACATCTGATAACTGAAAATATCTGATAATTATAAATATCTAATATTG
Found at i:1203413 original size:69 final size:69
Alignment explanation
Indices: 1203280--1203425 Score: 172
Period size: 69 Copynumber: 2.1 Consensus size: 69
1203270 TTAATATGTG
* * * * * *
1203280 TCTGATAACTGTAAAACATATGATATCTTTAAATATCTTATAATTGTAATTATCTTATATCTGTA
1 TCTGATAACTGTAAAACATATGATATCTATAAATATCTAATAATTGAAATCATCTGATAACTGTA
1203345 AAAA
66 AAAA
*
1203349 TCTGATAACTG-AAAATCATCTGATAAT-TATAAATATCTAAT-ATTGAAAATCATCTGATAACT
1 TCTGATAACTGTAAAA-CATATGAT-ATCTATAAATATCTAATAATTG-AAATCATCTGATAACT
*
1203411 GTAAATA
63 GTAAAAA
1203418 TCTGATAA
1 TCTGATAA
1203426 AGGTGAAATG
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
68 8 0.12
69 56 0.85
70 2 0.03
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.38
Consensus pattern (69 bp):
TCTGATAACTGTAAAACATATGATATCTATAAATATCTAATAATTGAAATCATCTGATAACTGTA
AAAA
Found at i:1203421 original size:17 final size:17
Alignment explanation
Indices: 1203280--1203450 Score: 119
Period size: 17 Copynumber: 9.9 Consensus size: 17
1203270 TTAATATGTG
*
1203280 TCTGATAACTGTAAAACA
1 TCTGATAACTGT-AAATA
* * *
1203298 TATGATATCTTTAAATA
1 TCTGATAACTGTAAATA
* * *
1203315 TCTTATAATTGTAATTA
1 TCTGATAACTGTAAATA
* * *
1203332 TCTTATATCTGTAAAAA
1 TCTGATAACTGTAAATA
*
1203349 TCTGATAACTGAAAATCA
1 TCTGATAACTGTAAAT-A
* *
1203367 TCTGATAATTATAAATA
1 TCTGATAACTGTAAATA
* * *
1203384 TCTAAT-ATTGAAAATCA
1 TCTGATAACTGTAAAT-A
1203401 TCTGATAACTGTAAATA
1 TCTGATAACTGTAAATA
** *
1203418 TCTGATAAAGGTGAAATG
1 TCTGATAACTGT-AAATA
*
1203436 TCTGATAATTGTAAA
1 TCTGATAACTGTAAA
1203451 CATTTAGAAT
Statistics
Matches: 117, Mismatches: 32, Indels: 9
0.74 0.20 0.06
Matches are distributed among these distances:
16 7 0.06
17 66 0.56
18 44 0.38
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.37
Consensus pattern (17 bp):
TCTGATAACTGTAAATA
Found at i:1203434 original size:18 final size:17
Alignment explanation
Indices: 1203395--1203443 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
1203385 CTAATATTGA
**
1203395 AAATCATCTGATAACTGT
1 AAAT-ATCTGATAAAGGT
1203413 AAATATCTGATAAAGGT
1 AAATATCTGATAAAGGT
*
1203430 GAAATGTCTGATAA
1 -AAATATCTGATAA
1203444 TTGTAAACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 11 0.41
18 16 0.59
ACGTcount: A:0.43, C:0.10, G:0.16, T:0.31
Consensus pattern (17 bp):
AAATATCTGATAAAGGT
Found at i:1204492 original size:15 final size:16
Alignment explanation
Indices: 1204460--1204492 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1204450 AATTTAAACT
*
1204460 TAAATATAAAATTCAA
1 TAAAAATAAAATTCAA
1204476 TAAAAATAAAA-TCAA
1 TAAAAATAAAATTCAA
1204491 TA
1 TA
1204493 CTTAAATTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (16 bp):
TAAAAATAAAATTCAA
Found at i:1204499 original size:28 final size:27
Alignment explanation
Indices: 1204468--1204522 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
1204458 CTTAAATATA
1204468 AAATTCA-ATAAAAATAAAATCAATACTT
1 AAATTCATATAAAAAT-AAATC-ATACTT
* *
1204496 AAATTGATATAAAACTAAATCATACTT
1 AAATTCATATAAAAATAAATCATACTT
1204523 CCATCGTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 6 0.25
28 11 0.46
29 7 0.29
ACGTcount: A:0.56, C:0.11, G:0.02, T:0.31
Consensus pattern (27 bp):
AAATTCATATAAAAATAAATCATACTT
Found at i:1205298 original size:18 final size:20
Alignment explanation
Indices: 1205275--1205317 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
1205265 CTTGATTTCC
*
1205275 ATTCAA-TTTCAAGCAT-GA
1 ATTCAACTTCCAAGCATCGA
*
1205293 ATTCAACTTCCTAGCATCGA
1 ATTCAACTTCCAAGCATCGA
1205313 ATTCA
1 ATTCA
1205318 TGCAATTCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 6 0.29
19 8 0.38
20 7 0.33
ACGTcount: A:0.35, C:0.23, G:0.09, T:0.33
Consensus pattern (20 bp):
ATTCAACTTCCAAGCATCGA
Found at i:1206531 original size:21 final size:21
Alignment explanation
Indices: 1206507--1206550 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1206497 GTGTGAGAAT
1206507 AAGGACGAGAGATAGAAGATG
1 AAGGACGAGAGATAGAAGATG
* *
1206528 AAGGGCGAGAGATCGAAGATG
1 AAGGACGAGAGATAGAAGATG
1206549 AA
1 AA
1206551 TTGGGGGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.45, C:0.07, G:0.39, T:0.09
Consensus pattern (21 bp):
AAGGACGAGAGATAGAAGATG
Found at i:1207634 original size:13 final size:13
Alignment explanation
Indices: 1207613--1207645 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1207603 CAAACCCACC
*
1207613 CTACTTAAACCCT
1 CTACCTAAACCCT
1207626 CTACCTAAACCCT
1 CTACCTAAACCCT
1207639 CTACCTA
1 CTACCTA
1207646 TTTCTAAGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.30, C:0.42, G:0.00, T:0.27
Consensus pattern (13 bp):
CTACCTAAACCCT
Found at i:1211302 original size:21 final size:21
Alignment explanation
Indices: 1211272--1211312 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1211262 AGTGGGAGAA
1211272 GAAGGACGAGAGATAGAAGAG
1 GAAGGACGAGAGATAGAAGAG
* *
1211293 GAAGGGCGAGAGATCGAAGA
1 GAAGGACGAGAGATAGAAGA
1211313 TGAATTGGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.07, G:0.44, T:0.05
Consensus pattern (21 bp):
GAAGGACGAGAGATAGAAGAG
Found at i:1218829 original size:12 final size:13
Alignment explanation
Indices: 1218811--1218845 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
1218801 AAAAGTAAAA
1218811 ATTTTAAAAATAT
1 ATTTTAAAAATAT
1218824 -TTTTAAAAA-AT
1 ATTTTAAAAATAT
1218835 ATTTTAAAAAT
1 ATTTTAAAAAT
1218846 GATAAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 2 0.10
12 18 0.90
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATTTTAAAAATAT
Found at i:1218834 original size:13 final size:12
Alignment explanation
Indices: 1218807--1218844 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
1218797 ATATAAAAGT
1218807 AAAA-ATTTT-A
1 AAAATATTTTAA
1218817 AAAATATTTTTAA
1 AAAATA-TTTTAA
1218830 AAAATATTTTAA
1 AAAATATTTTAA
1218842 AAA
1 AAA
1218845 TGATAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 4 0.16
11 1 0.04
12 13 0.52
13 7 0.28
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
AAAATATTTTAA
Found at i:1219012 original size:68 final size:68
Alignment explanation
Indices: 1218934--1219070 Score: 256
Period size: 68 Copynumber: 2.0 Consensus size: 68
1218924 TTTGTAAAAA
1218934 AATAAAAATTATTAAAGTTCCGTTATTTTTATATTAATTGATTCAATTTTTTTAAAAAATGTTCA
1 AATAAAAATTATTAAAGTTCCGTTATTTTTATATTAATTGATTCAATTTTTTTAAAAAATGTTCA
1218999 AAG
66 AAG
* *
1219002 AATAAAAATTATTAAATTTCCGTTATTTTTATATTAATTGATTCAATTTTTTTTAAAAATGTTCA
1 AATAAAAATTATTAAAGTTCCGTTATTTTTATATTAATTGATTCAATTTTTTTAAAAAATGTTCA
1219067 AAG
66 AAG
1219070 A
1 A
1219071 TTAATTTTTT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.41, C:0.06, G:0.07, T:0.47
Consensus pattern (68 bp):
AATAAAAATTATTAAAGTTCCGTTATTTTTATATTAATTGATTCAATTTTTTTAAAAAATGTTCA
AAG
Found at i:1224243 original size:95 final size:95
Alignment explanation
Indices: 1224080--1224270 Score: 382
Period size: 95 Copynumber: 2.0 Consensus size: 95
1224070 ACCTAAATGG
1224080 GCCAAGGAATGGGTGGAAGTGGTTCAGATTCAACTCTTAGCTATAACAGTAGCTAATGGTGAAAA
1 GCCAAGGAATGGGTGGAAGTGGTTCAGATTCAACTCTTAGCTATAACAGTAGCTAATGGTGAAAA
1224145 ACTTTTTAGTACTGTAAAAAGTAATAGGAT
66 ACTTTTTAGTACTGTAAAAAGTAATAGGAT
1224175 GCCAAGGAATGGGTGGAAGTGGTTCAGATTCAACTCTTAGCTATAACAGTAGCTAATGGTGAAAA
1 GCCAAGGAATGGGTGGAAGTGGTTCAGATTCAACTCTTAGCTATAACAGTAGCTAATGGTGAAAA
1224240 ACTTTTTAGTACTGTAAAAAGTAATAGGAT
66 ACTTTTTAGTACTGTAAAAAGTAATAGGAT
1224270 G
1 G
1224271 AGCTGGAAGA
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 96 1.00
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.28
Consensus pattern (95 bp):
GCCAAGGAATGGGTGGAAGTGGTTCAGATTCAACTCTTAGCTATAACAGTAGCTAATGGTGAAAA
ACTTTTTAGTACTGTAAAAAGTAATAGGAT
Found at i:1225709 original size:18 final size:19
Alignment explanation
Indices: 1225686--1225722 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
1225676 TTCATTGAAA
1225686 AACCGAAAAA-CCGAACCG
1 AACCGAAAAACCCGAACCG
1225704 AACCGAAAAACCCGAACCG
1 AACCGAAAAACCCGAACCG
1225723 TTAAAAAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.49, C:0.35, G:0.16, T:0.00
Consensus pattern (19 bp):
AACCGAAAAACCCGAACCG
Found at i:1229325 original size:13 final size:13
Alignment explanation
Indices: 1229307--1229350 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
1229297 AAAAATAAAA
1229307 AAATAAATATTAT
1 AAATAAATATTAT
1229320 AAATAAAT-TTA-
1 AAATAAATATTAT
*
1229331 AAAAAAATATTAT
1 AAATAAATATTAT
*
1229344 ATATAAA
1 AAATAAA
1229351 ATATATCAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 7 0.27
12 6 0.23
13 13 0.50
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
AAATAAATATTAT
Found at i:1229396 original size:14 final size:11
Alignment explanation
Indices: 1229367--1229397 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1229357 CAATTTAAAC
1229367 TATAATAAAAA
1 TATAATAAAAA
1229378 TATAATAAAAA
1 TATAATAAAAA
*
1229389 TAAAATAAA
1 TATAATAAA
1229398 TTTTATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
TATAATAAAAA
Found at i:1231325 original size:126 final size:126
Alignment explanation
Indices: 1231177--1231429 Score: 506
Period size: 126 Copynumber: 2.0 Consensus size: 126
1231167 TTCATATATA
1231177 TTAGCATCATAATCTATCTCCAAGGGTTTGTTTTGATAATTATTTGATATTTTAAATGCTTGGAC
1 TTAGCATCATAATCTATCTCCAAGGGTTTGTTTTGATAATTATTTGATATTTTAAATGCTTGGAC
1231242 GGCTAAAGGACATTTCATGCACAAAATTAGAGTTTTAGTCAGATTTGGACACTATAGAGTT
66 GGCTAAAGGACATTTCATGCACAAAATTAGAGTTTTAGTCAGATTTGGACACTATAGAGTT
1231303 TTAGCATCATAATCTATCTCCAAGGGTTTGTTTTGATAATTATTTGATATTTTAAATGCTTGGAC
1 TTAGCATCATAATCTATCTCCAAGGGTTTGTTTTGATAATTATTTGATATTTTAAATGCTTGGAC
1231368 GGCTAAAGGACATTTCATGCACAAAATTAGAGTTTTAGTCAGATTTGGACACTATAGAGTT
66 GGCTAAAGGACATTTCATGCACAAAATTAGAGTTTTAGTCAGATTTGGACACTATAGAGTT
1231429 T
1 T
1231430 CTACCGCACA
Statistics
Matches: 127, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
126 127 1.00
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (126 bp):
TTAGCATCATAATCTATCTCCAAGGGTTTGTTTTGATAATTATTTGATATTTTAAATGCTTGGAC
GGCTAAAGGACATTTCATGCACAAAATTAGAGTTTTAGTCAGATTTGGACACTATAGAGTT
Found at i:1231981 original size:17 final size:17
Alignment explanation
Indices: 1231945--1231984 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1231935 ACATGCTAAG
1231945 AAATA-AAAATTAACAT
1 AAATAGAAAATTAACAT
1231961 -AATAGAAAATTGAA-AT
1 AAATAGAAAATT-AACAT
1231977 AAATAGAA
1 AAATAGAA
1231985 TAAAAACAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 4 0.19
16 8 0.38
17 9 0.43
ACGTcount: A:0.68, C:0.03, G:0.07, T:0.23
Consensus pattern (17 bp):
AAATAGAAAATTAACAT
Found at i:1233293 original size:20 final size:20
Alignment explanation
Indices: 1233265--1233302 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1233255 CCAAATAAAG
*
1233265 AAAACGAAAATAAATAAATA
1 AAAAAGAAAATAAATAAATA
*
1233285 AAAAAGAAAATGAATAAA
1 AAAAAGAAAATAAATAAA
1233303 ATATAATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.76, C:0.03, G:0.08, T:0.13
Consensus pattern (20 bp):
AAAAAGAAAATAAATAAATA
Found at i:1233293 original size:26 final size:26
Alignment explanation
Indices: 1233261--1233312 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1233251 TGGACCAAAT
1233261 AAAGAAAACGAAAATAAATA-AATAAA
1 AAAGAAAACGAAAA-AAATATAATAAA
* *
1233287 AAAGAAAATGAATAAAATATAATAAA
1 AAAGAAAACGAAAAAAATATAATAAA
1233313 TAATATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (26 bp):
AAAGAAAACGAAAAAAATATAATAAA
Found at i:1233506 original size:75 final size:75
Alignment explanation
Indices: 1233355--1233601 Score: 363
Period size: 77 Copynumber: 3.2 Consensus size: 75
1233345 TATTTTTTTT
* * *
1233355 AAAACTATATAATATATATATTTTCCAAATATTTTTCAAAAATTATATATTATATATATATATTC
1 AAAACTATATATTATATATATTTTCAAAATATTTTTCAAAAATTATATATTATATATGT-T-TTC
1233420 AAAATGTTTTCA
64 AAAATGTTTTCA
* *
1233432 AAAACTATATATTATATATATTTTCAAAATATTTTTCAAAAATTTTATATTATATATGTTTTTAA
1 AAAACTATATATTATATATATTTTCAAAATATTTTTCAAAAATTATATATTATATATGTTTTCAA
1233497 AATGTTTTCA
66 AATGTTTTCA
*
1233507 AAAACTATATATTATATATATTTTTCAAAATATTTTT-AAAAACTATATATTATATATATGTTTT
1 AAAACTATATATTATATATA-TTTTCAAAATATTTTTCAAAAATTATATA-T-TATATATGTTTT
*
1233571 CAAAAT-TTTATAA
63 CAAAATGTTT-TCA
1233584 AAAACTATATATTATATA
1 AAAACTATATATTATATA
1233602 CTATATATAT
Statistics
Matches: 157, Mismatches: 9, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
75 44 0.28
76 21 0.13
77 92 0.59
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (75 bp):
AAAACTATATATTATATATATTTTCAAAATATTTTTCAAAAATTATATATTATATATGTTTTCAA
AATGTTTTCA
Found at i:1233606 original size:14 final size:15
Alignment explanation
Indices: 1233587--1233618 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
1233577 TTTATAAAAA
1233587 ACTATATAT-TATAT
1 ACTATATATATATAT
1233601 ACTATATATATATAT
1 ACTATATATATATAT
1233616 ACT
1 ACT
1233619 CTAAATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (15 bp):
ACTATATATATATAT
Found at i:1236818 original size:18 final size:18
Alignment explanation
Indices: 1236795--1236839 Score: 81
Period size: 18 Copynumber: 2.4 Consensus size: 18
1236785 AATTTAACAT
1236795 TATCAAATTACATGCCAC
1 TATCAAATTACATGCCAC
1236813 TATCAAATTACATGCCAC
1 TATCAAATTACATGCCAC
1236831 TATCTAAAT
1 TATC-AAAT
1236840 CAAATTTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 22 0.85
19 4 0.15
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.31
Consensus pattern (18 bp):
TATCAAATTACATGCCAC
Found at i:1237196 original size:44 final size:44
Alignment explanation
Indices: 1237088--1237242 Score: 249
Period size: 44 Copynumber: 3.5 Consensus size: 44
1237078 CATTTATTAA
* *
1237088 CCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATT-TGT
1 CCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCATTAT-T
1237132 ACCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCATTATT
1 -CCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCATTATT
*
1237177 CCATAAGCTCGTAAGCTTATTTTACCCATATACTTGCCATTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCATTATT
*
1237221 CCATAAGCTCGTAAACTTATTT
1 CCATAAGCTCGTAAGCTTATTT
1237243 GCATGCTTAC
Statistics
Matches: 105, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
44 64 0.61
45 40 0.38
46 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.37
Consensus pattern (44 bp):
CCATAAGCTCGTAAGCTTATTTTACCAATATACTTGCCATTATT
Found at i:1244631 original size:55 final size:55
Alignment explanation
Indices: 1244556--1245781 Score: 1562
Period size: 55 Copynumber: 22.4 Consensus size: 55
1244546 TTCTTTCAAG
* ** * **
1244556 GAGTAT-AGAACTCAAACAATCTTCTGCTAA-CGTGTCTACTCTATATTCCTTCAGA
1 GAGTATAAG-ACTCGAACAATCTTCAAC-AATCGTGTCTGCTCCCTATTCCTTCAGA
* * * *
1244611 GAGTATAAGACTCGATCAATCTTCAACAATCATGTTTGCTCTCTATTCCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
* * * * * *
1244666 GAGTAAAAGACTCGAACAATCTCCAACTAA-AGTATCCGCTCCCTATCCCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAAC-AATCGTGTCTGCTCCCTATTCCTTCAGA
* * *
1244721 GAGTATAAGACTCCAACTATCTTCAACAATTGTGTCTGCTCCCTATTCCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
* * *
1244776 GAGT-T-----T-GAACATTCTTCAATAATCGTGTCTGCTCCCTACTCCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
* * * *
1244824 GAGTATAAGACTTGAACAATCTTCAATAATCGTGTCTACTTCCTATTCCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
* * *
1244879 GAGTATAAGACTCGAACAATGTTCAATAATCGTGTCTGCTCCCTATTCCTTCACA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
* * * *
1244934 GATTATAAGACTCGAACAATCTTCAAAAATCATGTCTGCTCCCTATTTCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
** * * *
1244989 GAGTATAAGACTCGAACAATCTTCAACTTTCCTGTCTACTCCCTATTCCTTCACA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
* * *
1245044 GAGTATAAGACTTGATCAACCTTCAACAATCGTGT-TCGCTCCCTATTCCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCT-GCTCCCTATTCCTTCAGA
* * *
1245099 GAGTATAAGACTCAAATAAT-TATCAACAATCGTGTCTGCTCCATATTCCTTCAGA
1 GAGTATAAGACTCGAACAATCT-TCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
*
1245154 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTATGCTCCCTATTCCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
* *
1245209 GAGTATAAGACTCAAACAATCTTCAACAATCGTGTCTAG-TCCCTATTCCTTTAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCT-GCTCCCTATTCCTTCAGA
* * *
1245264 GAGTATAAGACTCAAACAATCTTCAACAATCGTGTATGTTCCCTATTCCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
* * *
1245319 GAGTATAAGACTCGATCAATCTTCAACAATCGTGTCTGCTCCCTATTTCATCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
* * * *
1245374 GAGTATAAGACTCGATCAATCTTCAACAATTGTGTATGCTCCCTATTCCTTCAGT
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
* * *
1245429 GAGTATAAGACTCGAACAATCTTCAACAATCGTTTCTGTTCCCTATTCCTTTAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
* * * * *
1245484 GAGTATAAGACTCGATCAATCTCCAACAATAGTGTCTGTTACCTATTCCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
*
1245539 GAGTATAAGACTC-AATCAATCTTCAACAATCGTGTCCGCTCCCTATTCCTTCAGA
1 GAGTATAAGACTCGAA-CAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
* * * * **
1245594 GAGTATAAGACTCGATCTATCTTTAACAATTGTGTCTAATCCCTATTCCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
* * * * *
1245649 GTGTATAAGACTCAAACAATCTTCAACAATCATGTATGTTCCCTATTCCTTCAGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
* * * *
1245704 GAGTATAAGACTCGATCAATCTTCAACAATCGCGTCCGCTCCCTATTCCTTCGGA
1 GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
1245759 GAGTATAAGACTCGAACAATCTT
1 GAGTATAAGACTCGAACAATCTT
1245782 GATGCTTCAA
Statistics
Matches: 1017, Mismatches: 135, Indels: 38
0.85 0.11 0.03
Matches are distributed among these distances:
48 40 0.04
49 2 0.00
54 10 0.01
55 957 0.94
56 8 0.01
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (55 bp):
GAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCCTTCAGA
Found at i:1246840 original size:11 final size:11
Alignment explanation
Indices: 1246819--1246891 Score: 73
Period size: 10 Copynumber: 6.8 Consensus size: 11
1246809 TAAACCCTCC
1246819 TTTTTTACTTCA
1 TTTTTT-CTTCA
1246831 TTTTTTCTTCA
1 TTTTTTCTTCA
*
1246842 TTTTTTC-TCT
1 TTTTTTCTTCA
*
1246852 TTTTTTATTCA
1 TTTTTTCTTCA
*
1246863 CTCTTTTC-TC-
1 -TTTTTTCTTCA
1246873 TTTTTTCTTC-
1 TTTTTTCTTCA
1246883 TTTTTTCTT
1 TTTTTTCTT
1246892 TTTTCATTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
9 6 0.12
10 19 0.37
11 16 0.31
12 11 0.21
ACGTcount: A:0.07, C:0.19, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTTTCTTCA
Found at i:1246854 original size:32 final size:31
Alignment explanation
Indices: 1246818--1246888 Score: 83
Period size: 31 Copynumber: 2.2 Consensus size: 31
1246808 ATAAACCCTC
*
1246818 CTTTTTTACTTCA-TTTTTTCTTCATTTTTTC-T
1 CTTTTTTA-TTCACTCTTTTC-TC-TTTTTTCTT
1246850 CTTTTTTTATTCACTCTTTTCTCTTTTTTCTT
1 C-TTTTTTATTCACTCTTTTCTCTTTTTTCTT
1246882 CTTTTTT
1 CTTTTTT
1246889 CTTTTTTCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
31 13 0.37
32 9 0.26
33 13 0.37
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.73
Consensus pattern (31 bp):
CTTTTTTATTCACTCTTTTCTCTTTTTTCTT
Found at i:1246902 original size:16 final size:16
Alignment explanation
Indices: 1246866--1246927 Score: 54
Period size: 17 Copynumber: 3.8 Consensus size: 16
1246856 TTATTCACTC
* *
1246866 TTTTCTCTTTTTTCTT
1 TTTTTTCTTTTTTCAT
1246882 CTTTTTTCTTTTTTCA-
1 -TTTTTTCTTTTTTCAT
*
1246898 TTTTTTCATTTTTCCAT
1 TTTTTTC-TTTTTTCAT
* *
1246915 TTCTTCCTTTTTT
1 TTTTTTCTTTTTT
1246928 TCTCTTTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
15 7 0.19
16 12 0.32
17 18 0.49
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTTCTTTTTTCAT
Found at i:1246903 original size:17 final size:18
Alignment explanation
Indices: 1246846--1246903 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 18
1246836 TCTTCATTTT
* *
1246846 TTCTCTTTT-TTTATTCA
1 TTCTTTTTTCTTTTTTCA
* *
1246863 CTCTTTTCTCTTTTTTC-
1 TTCTTTTTTCTTTTTTCA
1246880 TTCTTTTTTCTTTTTTCA
1 TTCTTTTTTCTTTTTTCA
1246898 TT-TTTT
1 TTCTTTT
1246904 CATTTTTCCA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
17 25 0.76
18 8 0.24
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (18 bp):
TTCTTTTTTCTTTTTTCA
Found at i:1246944 original size:41 final size:41
Alignment explanation
Indices: 1246834--1246950 Score: 120
Period size: 41 Copynumber: 2.9 Consensus size: 41
1246824 TACTTCATTT
*
1246834 TTTCTTCATTTTTTCTCTTTTTTTA---TTCACTCTTTTCTC
1 TTTCTTCTTTTTTTCTCTTTTTTTATTTTTCA-TCTTTTCTC
* *
1246873 TTTTTTCTTCTTTTT-TCTTTTTTCATTTTTTCAT-TTTTC-C
1 TTTCTTCTT-TTTTTCTCTTTTTTTA-TTTTTCATCTTTTCTC
1246913 ATTTCTTCCTTTTTTTCTCTTTTTTTATTTTTCATCTT
1 -TTTCTT-CTTTTTTTCTCTTTTTTTATTTTTCATCTT
1246951 CAAGCAAAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
39 16 0.25
40 6 0.09
41 23 0.36
42 15 0.23
43 4 0.06
ACGTcount: A:0.07, C:0.20, G:0.00, T:0.74
Consensus pattern (41 bp):
TTTCTTCTTTTTTTCTCTTTTTTTATTTTTCATCTTTTCTC
Found at i:1249766 original size:56 final size:55
Alignment explanation
Indices: 1249663--1249768 Score: 133
Period size: 56 Copynumber: 1.9 Consensus size: 55
1249653 TTCTAAAAAT
* *
1249663 AGGTTCGCTCCCTATCGCTTCAGGGAGCATAGAACATGAAGAATCTTCTGGGGAC
1 AGGTTCGCTCCCTATCGCTTCAGGGAGCATAGAACATAAACAATCTTCTGGGGAC
* ** *
1249718 AGGTTCGCTCCCTCTTTCTTTCAGGGAGTATAGAAC-TCAAACAATCTTCTG
1 AGGTTCGCTCCCTATCGC-TTCAGGGAGCATAGAACAT-AAACAATCTTCTG
1249769 CTAACGTGTC
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
55 16 0.37
56 27 0.63
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (55 bp):
AGGTTCGCTCCCTATCGCTTCAGGGAGCATAGAACATAAACAATCTTCTGGGGAC
Found at i:1249818 original size:55 final size:55
Alignment explanation
Indices: 1249737--1251030 Score: 1727
Period size: 55 Copynumber: 23.5 Consensus size: 55
1249727 CCCTCTTTCT
* * ** * ** *
1249737 TTCAGGGAGTAT-AGAACTCAAACAATCTTCTGCTAA-CGTGTCTACTCTATATTCA
1 TTCAGAGAGTATAAG-ACTCGAACAATCTTCAAC-AATCGTGTCTGCTCCCTATTCC
* * *
1249792 TTCAGAGAGTATAAGACTCGATCAATCTTCAACAATCATGTTTGCTCCCTATTCC
1 TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCC
* * ** * * *
1249847 TTCAGAGAGTAAAAGACTCGAACAATCTCCAACAAAAGTATCCGCTCCCTATCCC
1 TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCC
* * *
1249902 TTCAGAGAGTATAAGACTCCAACTATCTTCAACAATTGTGTCTGCTCCCTATTCC
1 TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCC
* *
1249957 TTTAGAGAGTATAAGACTCGAACAATCTTCAATAATCGTGTCTGCTCCCT-TCTCC
1 TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTAT-TCC
* * *
1250012 TTCAGAGAGTATAAGACTTGAACAATCTTCAACAATCGTGTCTACTTCCTATTCC
1 TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCC
* *
1250067 TTCAGAGAGTATAAGACTCGAACAATGTTCAATAATCGTGTCTGCTCCCTATTCC
1 TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCC
* * * *
1250122 TTCACAGAGTATAAGACTCGAACAATCTTCAACAATCATGTCAGCTCCCTATTTC
1 TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCC
* * *
1250177 TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCCTGTCTACTCCATATTCC
1 TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCC
* * * *
1250232 TTCACAGAGTATAAGACTTGATCAACCTTCAACAATCGTGT-TCGCTCCCTATTCC
1 TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCT-GCTCCCTATTCC
* * * *
1250287 TTCAGAGAGTATAAGACTCAAATAAT-TATCAATAATCGTGTCTGCTCCATATTCC
1 TTCAGAGAGTATAAGACTCGAACAATCT-TCAACAATCGTGTCTGCTCCCTATTCC
*
1250342 TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTATGCTCCCTATTCC
1 TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCC
*
1250397 TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTACTCCCTATTCC
1 TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCC
* * * **
1250452 TTGAGAGAGTATAAGACTCAAACAATCTTCAACAATCGTGTTTGCTATCTATTCC
1 TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCC
* * *
1250507 TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTATGTTCCCTATTTC
1 TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCC
*
1250562 TTCAGAGAGTATAAGACTCGATCAATCTTCAACAATCGTGTCTGCTCCCTATTCC
1 TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCC
* * * *
1250617 ATCAGAGAGTATAAGACTCGATCAATCTTCAACAATTGTGTATGCTCCCTATTCC
1 TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCC
* * *
1250672 TTCAGTGAGTATAAGACTCGAACAATCTTCAACAATCGTGTTTGTTCCCTATTCC
1 TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCC
* * * * * **
1250727 TTTAGAGAGTATAAGACTCGATCAATCTCCAACAATAGTGTCTGTTATCTATTCC
1 TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCC
* * * *
1250782 TTCAAAGAGTATAAGACTC-AATTAATCTTCAACAATCGTGTCCGCTCTCTATTCC
1 TTCAGAGAGTATAAGACTCGAA-CAATCTTCAACAATCGTGTCTGCTCCCTATTCC
* * * **
1250837 TTCAGAGAGTATAAGACTCGATCAATCTTTAACAATTGTGTCTAATCCCTATTCC
1 TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCC
* * * * *
1250892 TTCAGAGTGTATAAGACTCAAACAATCTTCAACAATCATGTATGTTCCCTATTCC
1 TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCC
* *
1250947 TTCAGAGAGTATAAGACTCGATCAATCTTCAACAATCGTGTCCGCTCCCTATTCC
1 TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCC
*
1251002 TTCAGAGAGTATAAGACTCAAACAATCTT
1 TTCAGAGAGTATAAGACTCGAACAATCTT
1251031 GATGCTTCAA
Statistics
Matches: 1080, Mismatches: 149, Indels: 20
0.86 0.12 0.02
Matches are distributed among these distances:
54 6 0.01
55 1068 0.99
56 6 0.01
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.31
Consensus pattern (55 bp):
TTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCC
Found at i:1252126 original size:7 final size:7
Alignment explanation
Indices: 1252114--1252172 Score: 50
Period size: 8 Copynumber: 8.1 Consensus size: 7
1252104 TTTTATTCAC
1252114 TCTTTTT
1 TCTTTTT
1252121 TC-TTTT
1 TCTTTTT
*
1252127 T-TTTCT
1 TCTTTTT
1252133 TCTTTTT
1 TCTTTTT
1252140 TCATTTTT
1 TC-TTTTT
*
1252148 CCATTTCTT
1 TC-TTT-TT
1252157 TCTTTTT
1 TCTTTTT
1252164 CTCTTTTT
1 -TCTTTTT
1252172 T
1 T
1252173 TATTTTTCAT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
6 9 0.21
7 11 0.26
8 20 0.47
9 3 0.07
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (7 bp):
TCTTTTT
Found at i:1252138 original size:11 final size:11
Alignment explanation
Indices: 1252068--1252140 Score: 55
Period size: 11 Copynumber: 6.6 Consensus size: 11
1252058 TTGAACCCTC
*
1252068 CTTTTTTACTT
1 CTTTTTTTCTT
*
1252079 CATTTTTTCTT
1 CTTTTTTTCTT
1252090 -TATTTTTTC-T
1 CT-TTTTTTCTT
*
1252100 CTTTTTTTATT
1 CTTTTTTTCTT
1252111 CACTCTTTTTTC-T
1 --CT-TTTTTTCTT
1252124 -TTTTTTTCTT
1 CTTTTTTTCTT
1252134 CTTTTTT
1 CTTTTTT
1252141 CATTTTTCCA
Statistics
Matches: 49, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
9 7 0.14
10 9 0.18
11 24 0.49
13 3 0.06
14 6 0.12
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (11 bp):
CTTTTTTTCTT
Found at i:1252155 original size:32 final size:32
Alignment explanation
Indices: 1252119--1252180 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
1252109 TTCACTCTTT
1252119 TTTCTTT-TTTTTCTTCTTTTTTCATTTTTCCA
1 TTTCTTTCTTTTTC-TCTTTTTTCATTTTTCCA
*
1252151 TTTCTTTCTTTTTCTCTTTTTTTATTTTTC
1 TTTCTTTCTTTTTCTCTTTTTTCATTTTTC
1252181 ATCTTCAAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 22 0.79
33 6 0.21
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.77
Consensus pattern (32 bp):
TTTCTTTCTTTTTCTCTTTTTTCATTTTTCCA
Found at i:1252365 original size:20 final size:20
Alignment explanation
Indices: 1252321--1252568 Score: 167
Period size: 20 Copynumber: 12.2 Consensus size: 20
1252311 AATGACCAAC
*
1252321 AAAATCGCAACGCGA--AATA
1 AAAATCGCAACGCGATTAA-G
*
1252340 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* *
1252360 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
*
1252380 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TAAG
***
1252400 AAAATCGCAACGCGATATTCC
1 AAAATCGCAACGCGAT-TAAG
*
1252421 AAGAATCGCAATGCGATTAAG
1 AA-AATCGCAACGCGATTAAG
* ***
1252442 AGAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGAT-TAAG
1252463 AAGAATCGCAACGCGATTCCAAG
1 AA-AATCGCAACGCGATT--AAG
1252486 --AATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
1252506 --AATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTAAG
1252524 AAAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGATT--AAG
*
1252546 --AATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTAAG
1252564 AAAAT
1 AAAAT
1252569 GAGTAAATTC
Statistics
Matches: 187, Mismatches: 23, Indels: 37
0.76 0.09 0.15
Matches are distributed among these distances:
18 6 0.03
19 15 0.08
20 123 0.66
21 12 0.06
22 31 0.17
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:1252566 original size:40 final size:40
Alignment explanation
Indices: 1252321--1252568 Score: 249
Period size: 40 Copynumber: 6.1 Consensus size: 40
1252311 AATGACCAAC
* * *
1252321 AAAATCGCAACGCGAAAT--AAAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCG-ATTCCAAGAATCGCAACGCGATTAAG
* **** *
1252360 AAAATCGCAACGTTGAAAAGAA-AATCGCAACG-G-TCAAAAG
1 AAAATCGCAACG-CGATTCCAAGAATCGCAACGCGAT--TAAG
*
1252400 AAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATTAAG
1 AAAATCGCAACGCG--ATTCCAAGAATCGCAACGCGATTAAG
*
1252442 AGAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTCCAAG
1 AAAATCGCAACGCGA--TTCCAAGAATCGCAACGCGATT--AAG
1252486 --AATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
*
1252524 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
1252564 AAAAT
1 AAAAT
1252569 GAGTAAATTC
Statistics
Matches: 179, Mismatches: 14, Indels: 31
0.80 0.06 0.14
Matches are distributed among these distances:
38 4 0.02
39 16 0.09
40 90 0.50
41 5 0.03
42 59 0.33
43 1 0.01
44 4 0.02
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.16
Consensus pattern (40 bp):
AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTAAG
Found at i:1252675 original size:6 final size:6
Alignment explanation
Indices: 1252664--1252744 Score: 162
Period size: 6 Copynumber: 13.5 Consensus size: 6
1252654 GACACGTATT
1252664 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1252712 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1252745 CGAGACGAGA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 75 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1253250 original size:6 final size:6
Alignment explanation
Indices: 1253239--1253325 Score: 174
Period size: 6 Copynumber: 14.5 Consensus size: 6
1253229 TCTCGTCTCG
1253239 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1253287 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1253326 AATACGTGTC
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 81 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:1253453 original size:20 final size:20
Alignment explanation
Indices: 1253428--1253927 Score: 677
Period size: 20 Copynumber: 24.8 Consensus size: 20
1253418 CTCATTTTCT
1253428 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
1253448 GAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
1253469 -AATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
1253488 GAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
1253509 -AATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
1253528 GAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
1253549 -AATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
1253568 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
1253588 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
1253608 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
1253628 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
1253648 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
1253668 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
1253688 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
*
1253708 GAATCGTGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
*
1253729 -AATCGCATTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
*
1253748 GAATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTCTT-G
*
1253768 GAATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTCTT-G
*
1253788 GAATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTCTT-G
1253808 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
1253828 GAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
1253849 -AATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
1253868 GAAGATCGCGTTGCGATTCTCT-
1 G-A-ATCGCGTTGCGATTCT-TG
* *
1253890 TAATCGCATTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
1253910 GAATATCGCGTTGCGATT
1 G-A-ATCGCGTTGCGATT
1253928 TTCTTTTGAC
Statistics
Matches: 442, Mismatches: 10, Indels: 54
0.87 0.02 0.11
Matches are distributed among these distances:
18 25 0.06
19 3 0.01
20 354 0.80
21 5 0.01
22 54 0.12
23 1 0.00
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.38
Consensus pattern (20 bp):
GAATCGCGTTGCGATTCTTG
Found at i:1253476 original size:40 final size:40
Alignment explanation
Indices: 1253421--1254006 Score: 549
Period size: 40 Copynumber: 14.6 Consensus size: 40
1253411 GAATTTACTC
*
1253421 ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1253461 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1253501 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1253541 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1253581 A--TTCTTGGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTT--AATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1253621 A--TTCTTGGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTT--AATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1253661 A--TTCTTGGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTT--AATCGCGTTGCGATTCTTGGAATCGCGTTGCG
* *
1253701 A--TTCTTGGAATCGTGTTGCGATTTTCTT--AATCGCATTGCG
1 ATTTTCTT--AATCGCGTTGCGA--TTCTTGGAATCGCGTTGCG
*
1253741 A--TTCTTGGAATCGCGTTGCGATT-TTCTGAATCGCGTTGCG
1 ATTTTCTT--AATCGCGTTGCGATTCTT-GGAATCGCGTTGCG
* *
1253781 ATTTTCTGAATCGCGTTGCGATT-TTCTGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTT-GGAATCGCGTTGCG
1253821 A--TTCTTGGAATCGCGTTGCGATTTTCTT--AATCGCGTTGCG
1 ATTTTCTT--AATCGCGTTGCGA--TTCTTGGAATCGCGTTGCG
*** * *
1253861 ATTCTTGGAAGATCGCGTTGCGATTCTCT-TAATCGCATTGCG
1 ATT-TTCTTA-ATCGCGTTGCGATTCT-TGGAATCGCGTTGCG
*** *
1253903 ATTCTTGGAATATCGCGTTGCGATTTTCTTTTG-A-C-CGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCGA--TTC-TTGGAATCGCGTTGCG
* * **
1253945 ATTTTCTT-TTCAACGTTGCGATT-TTCTAAATCGCGTTGCG
1 ATTTTCTTAATC-GCGTTGCGATTCTT-GGAATCGCGTTGCG
*
1253985 A-TTT-TTATTTCGCGTTGCGATT
1 ATTTTCTTA-ATCGCGTTGCGATT
1254007 TTGTTGGTCA
Statistics
Matches: 494, Mismatches: 21, Indels: 63
0.85 0.04 0.11
Matches are distributed among these distances:
36 2 0.00
37 3 0.01
38 16 0.03
39 16 0.03
40 377 0.76
41 4 0.01
42 65 0.13
43 5 0.01
44 5 0.01
45 1 0.00
ACGTcount: A:0.16, C:0.20, G:0.25, T:0.40
Consensus pattern (40 bp):
ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
Found at i:1253943 original size:20 final size:20
Alignment explanation
Indices: 1253918--1253971 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
1253908 TGGAATATCG
* *
1253918 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTCAA
1253938 CGTTGCGATTTTCTTTTCAA
1 CGTTGCGATTTTCTTTTCAA
1253958 CGTTGCGATTTTCT
1 CGTTGCGATTTTCT
1253972 AAATCGCGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.20, G:0.19, T:0.50
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTCAA
Found at i:1260577 original size:20 final size:21
Alignment explanation
Indices: 1260540--1260578 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1260530 TGAGAAATTA
1260540 TTTTAAAATATAAAAATGATG
1 TTTTAAAATATAAAAATGATG
*
1260561 TTTTAAAAT-TGAAAATGA
1 TTTTAAAATATAAAAATGA
1260579 AAAAAAACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.38
Consensus pattern (21 bp):
TTTTAAAATATAAAAATGATG
Found at i:1264425 original size:23 final size:21
Alignment explanation
Indices: 1264373--1264434 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
1264363 TTTTGGTGTA
*
1264373 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
1264393 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
1264414 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
1264435 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:1266281 original size:169 final size:169
Alignment explanation
Indices: 1266002--1266341 Score: 680
Period size: 169 Copynumber: 2.0 Consensus size: 169
1265992 CACAAGCTCC
1266002 ACCCGAAGCTAACGAAGATCTCGAGCTTAAGCAATTAATGCGAGACATCGATGAAGCCGAAGATG
1 ACCCGAAGCTAACGAAGATCTCGAGCTTAAGCAATTAATGCGAGACATCGATGAAGCCGAAGATG
1266067 AGCCTGAGCAGCCCGAGGAGCAGCCCGAAGAGCAAGCACAACAAACGCATCCAATGCCTCCATAT
66 AGCCTGAGCAGCCCGAGGAGCAGCCCGAAGAGCAAGCACAACAAACGCATCCAATGCCTCCATAT
1266132 TTCCAATCCTTTATGGAGACATTCGATTTTTGATACGCT
131 TTCCAATCCTTTATGGAGACATTCGATTTTTGATACGCT
1266171 ACCCGAAGCTAACGAAGATCTCGAGCTTAAGCAATTAATGCGAGACATCGATGAAGCCGAAGATG
1 ACCCGAAGCTAACGAAGATCTCGAGCTTAAGCAATTAATGCGAGACATCGATGAAGCCGAAGATG
1266236 AGCCTGAGCAGCCCGAGGAGCAGCCCGAAGAGCAAGCACAACAAACGCATCCAATGCCTCCATAT
66 AGCCTGAGCAGCCCGAGGAGCAGCCCGAAGAGCAAGCACAACAAACGCATCCAATGCCTCCATAT
1266301 TTCCAATCCTTTATGGAGACATTCGATTTTTGATACGCT
131 TTCCAATCCTTTATGGAGACATTCGATTTTTGATACGCT
1266340 AC
1 AC
1266342 TATAGATTCG
Statistics
Matches: 171, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
169 171 1.00
ACGTcount: A:0.33, C:0.26, G:0.22, T:0.19
Consensus pattern (169 bp):
ACCCGAAGCTAACGAAGATCTCGAGCTTAAGCAATTAATGCGAGACATCGATGAAGCCGAAGATG
AGCCTGAGCAGCCCGAGGAGCAGCCCGAAGAGCAAGCACAACAAACGCATCCAATGCCTCCATAT
TTCCAATCCTTTATGGAGACATTCGATTTTTGATACGCT
Found at i:1267185 original size:19 final size:19
Alignment explanation
Indices: 1267155--1267207 Score: 88
Period size: 19 Copynumber: 2.7 Consensus size: 19
1267145 TTTACACTTA
1267155 GGGAACCGATTCCCCATAGG
1 GGGAA-CGATTCCCCATAGG
1267175 GGGAACGATTCCCCATAGG
1 GGGAACGATTCCCCATAGG
*
1267194 GGGTACGATTCCCC
1 GGGAACGATTCCCC
1267208 CCACGCTCCA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 27 0.84
20 5 0.16
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.17
Consensus pattern (19 bp):
GGGAACGATTCCCCATAGG
Found at i:1267635 original size:55 final size:55
Alignment explanation
Indices: 1267566--1267673 Score: 216
Period size: 55 Copynumber: 2.0 Consensus size: 55
1267556 TCTCTTTGAG
1267566 AAAGAGTGTTCTCAAGAATTGGGGTATATTCTTGAGGGAGTTGTAAGGTTATCGA
1 AAAGAGTGTTCTCAAGAATTGGGGTATATTCTTGAGGGAGTTGTAAGGTTATCGA
1267621 AAAGAGTGTTCTCAAGAATTGGGGTATATTCTTGAGGGAGTTGTAAGGTTATC
1 AAAGAGTGTTCTCAAGAATTGGGGTATATTCTTGAGGGAGTTGTAAGGTTATC
1267674 TCTTTGGCCT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.29, C:0.07, G:0.31, T:0.33
Consensus pattern (55 bp):
AAAGAGTGTTCTCAAGAATTGGGGTATATTCTTGAGGGAGTTGTAAGGTTATCGA
Found at i:1271224 original size:22 final size:21
Alignment explanation
Indices: 1271172--1271225 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
1271162 GTACATATAT
*
1271172 ATAAAATAATAATATTAAAAA
1 ATAAAAAAATAATATTAAAAA
**
1271193 ATAACCAAATGAATA-TAAATAA
1 ATAAAAAAAT-AATATTAAA-AA
1271215 ATAAAAAAATA
1 ATAAAAAAATA
1271226 TGTATATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (21 bp):
ATAAAAAAATAATATTAAAAA
Found at i:1271749 original size:37 final size:38
Alignment explanation
Indices: 1271708--1271812 Score: 151
Period size: 37 Copynumber: 2.8 Consensus size: 38
1271698 GTGCTTGTGG
* *
1271708 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAA-CTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAATCTCT
* *
1271745 ATCCTATTTTTAGGAGTTTAAATCCTAGCA-AATTTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAATCTCT
*
1271782 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAG
1271813 GACGAAAAGA
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
36 2 0.03
37 58 0.97
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (38 bp):
ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAATCTCT
Found at i:1272742 original size:106 final size:106
Alignment explanation
Indices: 1272405--1273877 Score: 2138
Period size: 106 Copynumber: 14.0 Consensus size: 106
1272395 GCATTGTTCT
* * ** * *
1272405 GAGTCCAATATCCTTCG-TCGTGAAGTTGAAATTCGCTCTGGAACCGGGAAATTGTTTGTTGATA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* * * * *
1272469 ACCAGCCGTCCCTTCGTTGTGAAGTTGAATTTGTGTTGTCTT
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1272511 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-GA-T--GAA-AT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * * *
1272570 TCAGCCG-CCTCTTCGTCGTGAAGTTGAGCTTGTGTTGCCTTG
66 CCAGCGGTCC-CTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * * * *
1272612 G-GTTCAAGATCATTCACTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
1272676 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
1272717 GAGTCCAATATCCTACGCTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1272782 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1272823 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
1272888 TCAGCGGTCCCTTCATCGTGAAGTTAAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1272929 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
1272994 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1273035 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1273100 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1273141 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTG-TGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1273205 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1273246 GAGTCCAATATCCTTCG-TGTGAAGTTAAAATT-GCTCTGAAATTGAGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
1273309 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1273350 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
1273415 CCAGCGGTCCCATCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1273456 GAGTCCAATATCCTTCGTTGTAAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTG---A
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1273517 -CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1273557 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTTTGAAATTGGAAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
1273622 CCAGCGGTCACTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
1273663 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGATCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
1273728 CCAGCGGTCTCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1273769 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGAAAATTG-TTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
1273833 CCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1273874 GAGT
1 GAGT
1273878 GGCACGATAT
Statistics
Matches: 1243, Mismatches: 104, Indels: 41
0.90 0.07 0.03
Matches are distributed among these distances:
99 2 0.00
100 73 0.06
101 92 0.07
102 10 0.01
103 23 0.02
104 80 0.06
105 136 0.11
106 824 0.66
107 3 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1273846 original size:628 final size:631
Alignment explanation
Indices: 1272405--1273877 Score: 2277
Period size: 628 Copynumber: 2.3 Consensus size: 631
1272395 GCATTGTTCT
* * * ** *
1272405 GAGTCCAATATCCTTCGTCGTGAAGTTGAAATTCGCTCTGGAACCGGGAAATTGTTTGTTGATAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * * * *
1272470 CCAGCCGTCCCTTCGTTGTGAAGTTGAATTTGTGTTGTCTTGAGTCCAATATCCTTCGCTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
* * *
1272535 GTTGAAATTGACTCTG-GA-TG-AAATT-TTGTTGACAATCAGCCG-CCTCTTCGTCGTGAAGTT
131 GTTGAAATTGGCTCTGAAATTGAAAATTGTTGTTGACAACCAG-CGTCC-CTTCGTCGTGAAGTT
* * * * *
1272595 GAGCTTGTGTTGCCTTGG-GTTCAAGATCATTCACTGAGAAGTTGAAATTGGCTCTGAAATTGGG
194 GAACTTGTGTTGTC-TGGAGTCCAAGATCATTCACTGAGAAGTTAAAATTGGCTCTGAAATTGAG
* *
1272659 AAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCA
258 AAGTTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
1272724 ATATCCTACGCTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAACCAGCGG
323 ATATCCTACGCTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAACCAGCGG
* *
1272789 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
388 TCCCATCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTAAAGTTGAAA
*
1272854 TTGGCTCTAAAATTGAGAAGTTATTTGTTGACAATCAGCGGTCCCTTCATCGTGAAGTTAAACTT
453 TTGGCTCTAAAATTGAGAAGTTAGTTGTTG--AATCAGCGGTCCCTTCATCGTGAAGTTAAACTT
* *
1272919 GCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGT
516 GCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAGTTGT
* *
1272984 TTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
581 TTATTGACAACCAGCGGTCACTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1273035 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
1273100 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
*
1273165 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTT-TGTGACAACCAGCGGTCCCTTCGTCGTGAAGT
131 GTTGAAATTGGCTCTGAAATTGA-AAATTGTTGT-TGACAACCAGC-GTCCCTTCGTCGTGAAGT
* * * * *
1273229 TGAACTTGCGTTGTCTGGAGTCCAATATCCTTC-GTGTGAAGTTAAAATT-GCTCTGAAATTGAG
193 TGAACTTGTGTTGTCTGGAGTCCAAGATCATTCACTGAGAAGTTAAAATTGGCTCTGAAATTGAG
* *
1273292 AAGTTATTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
258 AAGTTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA
* * * *
1273357 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGG
323 ATATCCTACGCTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAACCAGCGG
1273422 TCCCATCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTAAAGTTGAAA
388 TCCCATCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTAAAGTTGAAA
* * *
1273487 TTGGCTCTGAAATTGAGAAGTT-GTTGTTG-A-CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
453 TTGGCTCTAAAATTGAGAAGTTAGTTGTTGAATCAGCGGTCCCTTCATCGTGAAGTTAAACTTGC
*
1273549 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTTTGAAATTGGAAAGTTGTTT
518 GTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAGTTGTTT
*
1273614 ATTGACAACCAGCGGTCACTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
583 ATTGACAACCAGCGGTCACTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1273663 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGATCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
1273728 CCAGCGGTCTCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
* *
1273793 GTTGAAATTGGCTCCGAAATTGGAAAATTGTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTT
131 GTTGAAATTGGCTCTGAAATT-GAAAATTGTTGTTGACAACCAG-CGTCCCTTCGTCGTGAAGTT
*
1273858 GAACTTGTGTTGTCTTGAGT
194 GAACTTGTGTTGTCTGGAGT
1273878 GGCACGATAT
Statistics
Matches: 770, Mismatches: 61, Indels: 26
0.90 0.07 0.03
Matches are distributed among these distances:
628 334 0.43
629 5 0.01
630 130 0.17
631 1 0.00
632 8 0.01
633 219 0.28
634 22 0.03
635 49 0.06
636 2 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (631 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAA
GTTGAAATTGGCTCTGAAATTGAAAATTGTTGTTGACAACCAGCGTCCCTTCGTCGTGAAGTTGA
ACTTGTGTTGTCTGGAGTCCAAGATCATTCACTGAGAAGTTAAAATTGGCTCTGAAATTGAGAAG
TTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATA
TCCTACGCTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAACCAGCGGTCC
CATCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTAAAGTTGAAATTG
GCTCTAAAATTGAGAAGTTAGTTGTTGAATCAGCGGTCCCTTCATCGTGAAGTTAAACTTGCGTT
GTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAGTTGTTTATT
GACAACCAGCGGTCACTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1275389 original size:16 final size:15
Alignment explanation
Indices: 1275320--1275392 Score: 62
Period size: 16 Copynumber: 4.8 Consensus size: 15
1275310 ATCTTGCATG
*
1275320 TTCTTTTTTGTCCCTT
1 TTCTTTTTTGT-TCTT
*
1275336 TTC-TTTTTGATTTTT
1 TTCTTTTTTG-TTCTT
*
1275351 TTCTTTCTT-TT-TT
1 TTCTTTTTTGTTCTT
1275364 TTCTTCTTTTGCTTCTT
1 TTCTT-TTTTG-TTCTT
1275381 TTCTTTTTTGTT
1 TTCTTTTTTGTT
1275393 TTTGCCCTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
13 7 0.15
14 5 0.11
15 13 0.28
16 15 0.32
17 7 0.15
ACGTcount: A:0.01, C:0.16, G:0.05, T:0.77
Consensus pattern (15 bp):
TTCTTTTTTGTTCTT
Found at i:1279405 original size:4 final size:4
Alignment explanation
Indices: 1279373--1279451 Score: 53
Period size: 4 Copynumber: 20.2 Consensus size: 4
1279363 GTTAGAGGGA
* *
1279373 AAAT GAAT AAAT GAAA- AAA- AAAT -AA- AAAT AAAT -AA- AAAT AAAAGG
1 AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAA-T
*
1279418 AAAA AAAT AAAT AAAT AAAT AAAT AAAT GAAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT A
1279452 TTAATATATA
Statistics
Matches: 61, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
3 14 0.23
4 34 0.56
5 13 0.21
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (4 bp):
AAAT
Found at i:1279517 original size:34 final size:35
Alignment explanation
Indices: 1279447--1279536 Score: 96
Period size: 34 Copynumber: 2.5 Consensus size: 35
1279437 TAAATAAATG
* *
1279447 AAATATTAATATATATATATATATATGAGTAAAATAGA
1 AAATATAAATA-ATATA-AAATA-ATGAGTAAAATAGA
1279485 AAA-AT-AATAATCATAAAATAATGA-TAATAATAGA
1 AAATATAAATAAT-ATAAAATAATGAGTAA-AATAGA
1279519 AAATATAAATAATATAAA
1 AAATATAAATAATATAAA
1279537 CAAATAAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 11
0.80 0.02 0.19
Matches are distributed among these distances:
33 3 0.06
34 13 0.28
35 13 0.28
36 13 0.28
37 2 0.04
38 3 0.06
ACGTcount: A:0.62, C:0.01, G:0.06, T:0.31
Consensus pattern (35 bp):
AAATATAAATAATATAAAATAATGAGTAAAATAGA
Found at i:1280345 original size:37 final size:37
Alignment explanation
Indices: 1280304--1280400 Score: 140
Period size: 37 Copynumber: 2.6 Consensus size: 37
1280294 GGATCTTATC
* *
1280304 TTTAGGAGTTTAAATCATAGTAGAACTCTATCCTATT
1 TTTAGGAGTTTAAATCCTAGTAGAACTCTATACTATT
* * *
1280341 TTTAGGAGTTTAAATCCTAGCAAAATTCTATACTATT
1 TTTAGGAGTTTAAATCCTAGTAGAACTCTATACTATT
*
1280378 TTTAGGAGTTTGAATCCTAGTAG
1 TTTAGGAGTTTAAATCCTAGTAG
1280401 GACGAAAAGG
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.40
Consensus pattern (37 bp):
TTTAGGAGTTTAAATCCTAGTAGAACTCTATACTATT
Found at i:1282570 original size:18 final size:18
Alignment explanation
Indices: 1282534--1282568 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1282524 AATTAAAATG
1282534 CAAACAAGAAATTCAAAA
1 CAAACAAGAAATTCAAAA
*
1282552 CAAACAAGGAA-TCAAAA
1 CAAACAAGAAATTCAAAA
1282569 ACCAAATTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.66, C:0.17, G:0.09, T:0.09
Consensus pattern (18 bp):
CAAACAAGAAATTCAAAA
Found at i:1285059 original size:2 final size:2
Alignment explanation
Indices: 1285052--1285077 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1285042 TACTTATTGC
1285052 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1285078 TAATAATTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1288566 original size:17 final size:18
Alignment explanation
Indices: 1288535--1288571 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
1288525 AAAAATTACT
*
1288535 AAAATTAAAATAAAATAA
1 AAAAATAAAATAAAATAA
1288553 AAAAATAAAA-AAAATAA
1 AAAAATAAAATAAAATAA
1288570 AA
1 AA
1288572 GAACTATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (18 bp):
AAAAATAAAATAAAATAA
Found at i:1289861 original size:7 final size:7
Alignment explanation
Indices: 1289815--1289865 Score: 59
Period size: 7 Copynumber: 7.3 Consensus size: 7
1289805 ATGAAAATGA
*
1289815 ATAAAAT
1 ATAATAT
*
1289822 ATAATAA
1 ATAATAT
1289829 ATAATAT
1 ATAATAT
1289836 ATAATACT
1 ATAATA-T
*
1289844 ATACTAT
1 ATAATAT
1289851 ATAATAT
1 ATAATAT
1289858 ATAA-AT
1 ATAATAT
1289864 AT
1 AT
1289866 TTTTTTTTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
6 4 0.11
7 28 0.74
8 6 0.16
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (7 bp):
ATAATAT
Found at i:1289915 original size:37 final size:37
Alignment explanation
Indices: 1289874--1290085 Score: 237
Period size: 37 Copynumber: 5.5 Consensus size: 37
1289864 ATTTTTTTTT
* * *
1289874 AAAACTATATAATATATATATATTCATAATATTTTCA
1 AAAACTATATATTATATATATTTTCAAAATATTTTCA
1289911 AAAACTATATATTATATATATTTTCAAAATATTTTCA
1 AAAACTATATATTATATATATTTTCAAAATATTTTCA
* *
1289948 AAAACTATATATTATGTATGTTTTCAAAATATTTTCA
1 AAAACTATATATTATATATATTTTCAAAATATTTTCA
* * * *
1289985 AAAACTATATATTATGTATGTTTTCAAAACAGTTTTTAAAA
1 AAAACTATATATTATATATATTTTCAAAATA--TTTT--CA
1290026 AAAACTATATTATATATATATATATATTCAAAAT-TTTATCAA
1 AAAACTATA-TAT-TATATATAT-T-TTCAAAATATTT-TC-A
*
1290068 AAAAGTATATATTATATA
1 AAAACTATATATTATATA
1290086 CTATATATAT
Statistics
Matches: 153, Mismatches: 12, Indels: 17
0.84 0.07 0.09
Matches are distributed among these distances:
37 99 0.65
39 4 0.03
40 6 0.04
41 13 0.08
42 15 0.10
43 8 0.05
44 1 0.01
45 7 0.05
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (37 bp):
AAAACTATATATTATATATATTTTCAAAATATTTTCA
Found at i:1289919 original size:26 final size:26
Alignment explanation
Indices: 1289890--1289939 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
1289880 ATATAATATA
1289890 TATATATTCATA-ATATTTTCAAAAAC
1 TATATATT-ATATATATTTTCAAAAAC
1289916 TATATATTATATATATTTTCAAAA
1 TATATATTATATATATTTTCAAAA
1289940 TATTTTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 3 0.13
26 20 0.87
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (26 bp):
TATATATTATATATATTTTCAAAAAC
Found at i:1297964 original size:24 final size:24
Alignment explanation
Indices: 1297932--1297995 Score: 80
Period size: 22 Copynumber: 2.8 Consensus size: 24
1297922 CATAAGGAAT
*
1297932 GTGTTACAAGAGCAAAGAAAAAAA
1 GTGTCACAAGAGCAAAGAAAAAAA
*
1297956 GTGTCACAAGAAC-AA-AAAAAAA
1 GTGTCACAAGAGCAAAGAAAAAAA
1297978 GTGTCACAA-AGACAAAGA
1 GTGTCACAAGAG-CAAAGA
1297996 TTCATATAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
21 1 0.03
22 17 0.50
23 4 0.12
24 12 0.35
ACGTcount: A:0.58, C:0.12, G:0.19, T:0.11
Consensus pattern (24 bp):
GTGTCACAAGAGCAAAGAAAAAAA
Found at i:1298511 original size:44 final size:44
Alignment explanation
Indices: 1298461--1298556 Score: 174
Period size: 44 Copynumber: 2.2 Consensus size: 44
1298451 GTATAAAAAT
1298461 AATTATTAATATACTAAAATTTATATAAATATATAATACCCTTA
1 AATTATTAATATACTAAAATTTATATAAATATATAATACCCTTA
*
1298505 AATTATTAATATACTAAAATTTTTATAAATATATAATACCCTTA
1 AATTATTAATATACTAAAATTTATATAAATATATAATACCCTTA
*
1298549 AATGATTA
1 AATTATTA
1298557 TAAAAAATTG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 50 1.00
ACGTcount: A:0.49, C:0.08, G:0.01, T:0.42
Consensus pattern (44 bp):
AATTATTAATATACTAAAATTTATATAAATATATAATACCCTTA
Found at i:1298785 original size:18 final size:18
Alignment explanation
Indices: 1298764--1298826 Score: 53
Period size: 18 Copynumber: 3.6 Consensus size: 18
1298754 TCAAAAATTT
1298764 TATAAATATTAATTAAAA
1 TATAAATATTAATTAAAA
*
1298782 TATATAATA-T-CTT-AAA
1 TATA-AATATTAATTAAAA
* *
1298798 TATAATTATTATATAAAAA
1 TATAAATATTA-ATTAAAA
1298817 TA-AAATATTA
1 TATAAATATTA
1298827 CAGATATTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
15 3 0.09
16 8 0.23
17 2 0.06
18 13 0.37
19 9 0.26
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
TATAAATATTAATTAAAA
Found at i:1301802 original size:21 final size:21
Alignment explanation
Indices: 1301776--1301818 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1301766 TGACCAAAGG
*
1301776 TGAAGCAATGGTAAGCAGGAT
1 TGAAGCAATGGTAAGAAGGAT
1301797 TGAAGCAATGGTAAGAAGGAT
1 TGAAGCAATGGTAAGAAGGAT
1301818 T
1 T
1301819 CCAACATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.07, G:0.33, T:0.21
Consensus pattern (21 bp):
TGAAGCAATGGTAAGAAGGAT
Found at i:1305456 original size:24 final size:24
Alignment explanation
Indices: 1305424--1305471 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1305414 TTCTGTTTGG
* *
1305424 GTTTTAGGTTTGGGCCTGGTTGTA
1 GTTTTAGGTTGGGGCATGGTTGTA
*
1305448 GTTTTAGGTTGGGGCATGTTTGTA
1 GTTTTAGGTTGGGGCATGGTTGTA
1305472 TAAAAGGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.10, C:0.06, G:0.38, T:0.46
Consensus pattern (24 bp):
GTTTTAGGTTGGGGCATGGTTGTA
Found at i:1306133 original size:28 final size:27
Alignment explanation
Indices: 1306075--1306134 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 27
1306065 GAGTTTAGAG
* *
1306075 TTTTAAACTTTTCGTGAGTTTTAAACT
1 TTTTAAACTTTTCATGAATTTTAAACT
1306102 TTTTAAATCTTTTCATGAATTTTAAAACT
1 TTTTAAA-CTTTTCATGAATTTT-AAACT
1306131 TTTT
1 TTTT
1306135 TCCTTATATG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 7 0.24
28 13 0.45
29 9 0.31
ACGTcount: A:0.28, C:0.10, G:0.07, T:0.55
Consensus pattern (27 bp):
TTTTAAACTTTTCATGAATTTTAAACT
Found at i:1306500 original size:2 final size:2
Alignment explanation
Indices: 1306493--1306524 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1306483 CAAGCAAAGC
1306493 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1306525 ATATATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1306529 original size:2 final size:2
Alignment explanation
Indices: 1306524--1306558 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1306514 TCTCTCTCTC
1306524 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1306559 TAAGATAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1306843 original size:19 final size:19
Alignment explanation
Indices: 1306819--1306855 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1306809 TCTATCACAA
*
1306819 ACTTTTGATAAGATTATTG
1 ACTTTTGACAAGATTATTG
1306838 ACTTTTGACAAGATTATT
1 ACTTTTGACAAGATTATT
1306856 TCCAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.46
Consensus pattern (19 bp):
ACTTTTGACAAGATTATTG
Found at i:1307208 original size:20 final size:20
Alignment explanation
Indices: 1307183--1307234 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
1307173 TAATTTCTAT
1307183 TAATTAACCGATCTTGAACA
1 TAATTAACCGATCTTGAACA
1307203 TAATTAACCGATCTTGAACA
1 TAATTAACCGATCTTGAACA
1307223 TAATTAACCGAT
1 TAATTAACCGAT
1307235 AACCGAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (20 bp):
TAATTAACCGATCTTGAACA
Found at i:1312449 original size:69 final size:67
Alignment explanation
Indices: 1312336--1312617 Score: 264
Period size: 69 Copynumber: 4.1 Consensus size: 67
1312326 AATGTCGGAA
* * *
1312336 TGACTCGCAC-GAGAGCCCCG-AAGCGTTAGAGTGACTCATACGGGAGCACCTAATCATATTTAT
1 TGACTCGCACGGA-AG-CCCGAAAG-GTTAGAGTGACTCACACGGAAGCACCTAATCACATTTA-
1312399 TTCCGG
62 TTCCGG
* * * *
1312405 TTACTCGCACGGGAGCTCCGAAAGGTTAGAGTGACTTACACGGGAGCACCTAA-CGACATTTATT
1 TGACTCGCACGGAAGC-CCGAAAGGTTAGAGTGACTCACACGGAAGCACCTAATC-ACATTTATT
*
1312469 CTAGG
64 C-CGG
* * * * * * *
1312474 TGACTCGCATGGAAGCCCTGAAGGGTTATAGTGACTCGCACAGAAGAACATAATCACATTTATTC
1 TGACTCGCACGGAAGCCC-GAAAGGTTAGAGTGACTCACACGGAAGCACCTAATCACATTTATTC
1312539 CGGG
65 C-GG
* * * * *
1312543 TGACTAGCACGGAAGCCTCGAAGGGTTAGAATGACTCACATGAAAGCACCTAATCACATTTATTC
1 TGACTCGCACGGAAGCC-CGAAAGGTTAGAGTGACTCACACGGAAGCACCTAATCACATTTATTC
1312608 CGGG
65 C-GG
1312612 TGACTC
1 TGACTC
1312618 ATATGGAAGC
Statistics
Matches: 175, Mismatches: 29, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
68 7 0.04
69 162 0.93
70 6 0.03
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.23
Consensus pattern (67 bp):
TGACTCGCACGGAAGCCCGAAAGGTTAGAGTGACTCACACGGAAGCACCTAATCACATTTATTCC
GG
Found at i:1314817 original size:59 final size:60
Alignment explanation
Indices: 1314697--1314847 Score: 173
Period size: 60 Copynumber: 2.5 Consensus size: 60
1314687 GTATATACAT
* * * * *
1314697 ATAGTTTAGGATAAAATT-AGAATGTTCAAAAAGTTTGGGGACTAATATAGAATGAAGGTC
1 ATAGTTTGGGATAAAATTGA-AATTTTAAAAAAGTTTGAGGACTAATATAGAATGAAAGTC
* *
1314757 ATAGTTTGGGATGAAATTGAAATTTTAAAAAAG-TTGAGGACTAATTTAGAAT-AATAGTC
1 ATAGTTTGGGATAAAATTGAAATTTTAAAAAAGTTTGAGGACTAATATAGAATGAA-AGTC
*
1314816 ATAATTTAGGGATAAAATTGAAATATTTAAAA
1 ATAGTTT-GGGATAAAATTGAAAT-TTTAAAA
1314848 GTTTAGAGAC
Statistics
Matches: 78, Mismatches: 9, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
58 2 0.03
59 26 0.33
60 42 0.54
61 8 0.10
ACGTcount: A:0.44, C:0.03, G:0.20, T:0.32
Consensus pattern (60 bp):
ATAGTTTGGGATAAAATTGAAATTTTAAAAAAGTTTGAGGACTAATATAGAATGAAAGTC
Found at i:1314848 original size:59 final size:57
Alignment explanation
Indices: 1314705--1314870 Score: 156
Period size: 60 Copynumber: 2.8 Consensus size: 57
1314695 ATATAGTTTA
* * * * *
1314705 GGATAAAATT-AGAATGTTCAAAAAGTTTGGGGACTAATATAGAATGAAGGTCATAGTTTG
1 GGATAAAATTGA-AAT-TTTAAAAAG-TTGAGGACTAATTTAGAAT-AAAGTCATAATTTG
*
1314765 GGATGAAATTGAAATTTTAAAAAAGTTGAGGACTAATTTAGAATAATAGTCATAATTTAG
1 GGATAAAATTGAAATTTT-AAAAAGTTGAGGACTAATTTAGAATAA-AGTCATAATTT-G
* * *
1314825 GGATAAAATTGAAATATTT-AAAAGTTTAGAGACCAATTTAAAATAA
1 GGATAAAATTGAAAT-TTTAAAAAGTTGAG-GACTAATTTAGAATAA
1314871 GAATCATACT
Statistics
Matches: 90, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
58 2 0.02
59 37 0.41
60 47 0.52
61 4 0.04
ACGTcount: A:0.45, C:0.04, G:0.19, T:0.31
Consensus pattern (57 bp):
GGATAAAATTGAAATTTTAAAAAGTTGAGGACTAATTTAGAATAAAGTCATAATTTG
Found at i:1314878 original size:60 final size:58
Alignment explanation
Indices: 1314755--1314883 Score: 143
Period size: 60 Copynumber: 2.2 Consensus size: 58
1314745 AGAATGAAGG
* * * * * *
1314755 TCATAGTTTGGGATGAAATTGAAATTTTAAAAAAGTTGAGGACTAATTTAGAATAATAG
1 TCATAATTTGGGATAAAATTGAAATTTT-AAAAAGTTGAGGACCAATTTAAAATAAGAA
*
1314814 TCATAATTTAGGGATAAAATTGAAATATTT-AAAAGTTTAGAGACCAATTTAAAATAAGAA
1 TCATAATTT-GGGATAAAATTGAAAT-TTTAAAAAGTTGAG-GACCAATTTAAAATAAGAA
*
1314874 TCATACTTTG
1 TCATAATTTG
1314884 AGGACATATG
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
59 18 0.31
60 38 0.64
61 3 0.05
ACGTcount: A:0.44, C:0.05, G:0.16, T:0.34
Consensus pattern (58 bp):
TCATAATTTGGGATAAAATTGAAATTTTAAAAAGTTGAGGACCAATTTAAAATAAGAA
Found at i:1315966 original size:2 final size:2
Alignment explanation
Indices: 1315959--1316002 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1315949 TATCTAATCC
1315959 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1316001 AT
1 AT
1316003 CACTTCATAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1316178 original size:2 final size:2
Alignment explanation
Indices: 1316171--1316200 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1316161 TAATATAAAT
1316171 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
1316201 GATGGACGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1320162 original size:37 final size:37
Alignment explanation
Indices: 1320112--1320189 Score: 147
Period size: 37 Copynumber: 2.1 Consensus size: 37
1320102 TTACTATAAC
*
1320112 AACATATTATTGTTGTGCTTAGTTTTTCTACAACTAA
1 AACATATTATTGTTCTGCTTAGTTTTTCTACAACTAA
1320149 AACATATTATTGTTCTGCTTAGTTTTTCTACAACTAA
1 AACATATTATTGTTCTGCTTAGTTTTTCTACAACTAA
1320186 AACA
1 AACA
1320190 ACCTTAAATT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.44
Consensus pattern (37 bp):
AACATATTATTGTTCTGCTTAGTTTTTCTACAACTAA
Found at i:1322184 original size:2 final size:2
Alignment explanation
Indices: 1322177--1322206 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1322167 GTTTTAATTA
*
1322177 AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1322207 GAAAATCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1323182 original size:6 final size:6
Alignment explanation
Indices: 1323149--1323193 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
1323139 AAATAACAAT
* * *
1323149 TAATAA TAATAA TAA-TA TAATTA TAATTA TAATTA TGATTA TAAT
1 TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA TAATTA TAAT
1323194 ATTTTTTTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
5 4 0.11
6 31 0.89
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (6 bp):
TAATTA
Found at i:1323605 original size:89 final size:88
Alignment explanation
Indices: 1323470--1323729 Score: 335
Period size: 90 Copynumber: 2.9 Consensus size: 88
1323460 AAATATAATC
* * * *
1323470 TGAAAATATCTTGTACTAAAGGTCTTATGGATGGTCCC-AAGGACTTAAAAATAAAGAAACCCCG
1 TGAAAATATCTTGCACTGAAGGTCTTATGGAT-GACCCGAA-GACTTAAAAATCAAGAAACCCCG
1323534 AAGGTTTAGTTTCTTAGATCTCATT
64 AAGGTTTAGTTTCTTAGATCTCATT
* *
1323559 TGAAAACATCCTGCACTGAAGGTCTTATGGATGACCCGAAGAACTTAAAAATCAAGAAACTCCCG
1 TGAAAATATCTTGCACTGAAGGTCTTATGGATGACCCGAAG-ACTTAAAAATCAAGAAAC-CCCG
*
1323624 AA-ATCTTAGTTTCTTAGATCTCATT
64 AAGGT-TTAGTTTCTTAGATCTCATT
* ** *
1323649 TGAAAATATCTTACACTGAAGGTCTTATGGATGGTCCGAATGACTTAAAAATCAAGAAACCCTTG
1 TGAAAATATCTTGCACTGAAGGTCTTATGGATGACCCGAA-GACTTAAAAATCAAGAAACCC-CG
*
1323714 AAGGCTTAGTTTCTTA
64 AAGGTTTAGTTTCTTA
1323730 ATTGTTACCA
Statistics
Matches: 149, Mismatches: 15, Indels: 13
0.84 0.08 0.07
Matches are distributed among these distances:
88 5 0.03
89 50 0.34
90 93 0.62
91 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (88 bp):
TGAAAATATCTTGCACTGAAGGTCTTATGGATGACCCGAAGACTTAAAAATCAAGAAACCCCGAA
GGTTTAGTTTCTTAGATCTCATT
Found at i:1323842 original size:43 final size:43
Alignment explanation
Indices: 1323777--1323930 Score: 202
Period size: 43 Copynumber: 3.6 Consensus size: 43
1323767 CAAGTGTTCA
*
1323777 TCAAGTTTGTCATCAAGGAACCCCTACATATCACGATGGTCCC
1 TCAAGTTTGTCATCAAGAAACCCCTACATATCACGATGGTCCC
* * * **
1323820 TTAAGTTTTTCATTAAGAAACCCCTACATATCACGATGGTTTC
1 TCAAGTTTGTCATCAAGAAACCCCTACATATCACGATGGTCCC
*
1323863 TCAAGTTTGTCATCAA-AGAACCCCTACATATCACGATGGTCCT
1 TCAAGTTTGTCATCAAGA-AACCCCTACATATCACGATGGTCCC
* * *
1323906 TCAAGCTTGCCATCAAGGAACCCCT
1 TCAAGTTTGTCATCAAGAAACCCCT
1323931 TAAAATCAGG
Statistics
Matches: 94, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
42 1 0.01
43 93 0.99
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (43 bp):
TCAAGTTTGTCATCAAGAAACCCCTACATATCACGATGGTCCC
Found at i:1324005 original size:39 final size:38
Alignment explanation
Indices: 1323952--1324255 Score: 249
Period size: 39 Copynumber: 7.6 Consensus size: 38
1323942 TTAGTTTCTA
* * *
1323952 AAAATATTGTGTTTCGAGCGAAACTATCTCAAGCGAGAT
1 AAAATCTTTTGTTTCAAG-GAAACTATCTCAAGCGAGAT
* *
1323991 AAAATCTTCTGTTTCAAGTGAAACAATCTCAAGCGAGAT
1 AAAATCTTTTGTTTCAAG-GAAACTATCTCAAGCGAGAT
* * * *
1324030 AAAATCTTTTGTTTCAAATGAAATTGTCTCAAGGGAGAT
1 AAAATCTTTTGTTTC-AAGGAAACTATCTCAAGCGAGAT
* *
1324069 AAAA---TTTGTTTCAAAGGAAACTGTCTCAAGCGAAACTGTCT
1 AAAATCTTTTGTTTC-AAGGAAACTATCTCAAGCG--A--G-AT
1324110 CAAGCGACA-CTAAATTTGTTTCAATGGAAACTATCTCAAGCGAGAT
1 -AA---A-ATCT---TTTGTTTCAA-GGAAACTATCTCAAGCGAGAT
* *
1324156 AAAATCTTTTGTTTCGAGGAAAACTATCTCAAGTGAGAT
1 AAAATCTTTTGTTTCAAGG-AAACTATCTCAAGCGAGAT
* *
1324195 AAAATCTTTTGTTTCAAGGAAAACAATCTTGAA-CGAGAT
1 AAAATCTTTTGTTTCAAGG-AAACTATC-TCAAGCGAGAT
1324234 AAAATCTTTTGTTTCAAGGAAA
1 AAAATCTTTTGTTTCAAGGAAA
1324256 AACAATCTTG
Statistics
Matches: 222, Mismatches: 23, Indels: 41
0.78 0.08 0.14
Matches are distributed among these distances:
36 25 0.11
38 6 0.03
39 145 0.65
40 6 0.03
41 2 0.01
42 5 0.02
45 3 0.01
46 2 0.01
47 1 0.00
49 1 0.00
50 2 0.01
51 24 0.11
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.31
Consensus pattern (38 bp):
AAAATCTTTTGTTTCAAGGAAACTATCTCAAGCGAGAT
Found at i:1324103 original size:15 final size:15
Alignment explanation
Indices: 1324085--1324116 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1324075 TGTTTCAAAG
1324085 GAAACTGTCTCAAGC
1 GAAACTGTCTCAAGC
1324100 GAAACTGTCTCAAGC
1 GAAACTGTCTCAAGC
1324115 GA
1 GA
1324117 CACTAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.25, G:0.22, T:0.19
Consensus pattern (15 bp):
GAAACTGTCTCAAGC
Found at i:1324196 original size:126 final size:128
Alignment explanation
Indices: 1323968--1324216 Score: 321
Period size: 126 Copynumber: 1.9 Consensus size: 128
1323958 TTGTGTTTCG
*
1323968 AGCGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCAAGTGAAACAATCTCAAGCGAGATAAA
1 AGCGAAACTATCTCAAGCGACATAAAA-CTTCTGTTTCAAGTGAAACAATCTCAAGCGAGATAAA
* * *
1324033 ATCTTTTGTTTCAAATGAAATTGTCTCAAGGGAGATAAAA-TTTGTTTCAAAGGAAACTGTCTCA
65 ATCTTTTGTTTCAAAGGAAACTATCTCAAGGGAGATAAAATTTTGTTTC-AAGGAAACTGTCTCA
* *
1324097 AGCGAAACTGTCTCAAGCGACACT-AAA-TT-TGTTTCAA-TGGAAACTATCTCAAGCGAGATAA
1 AGCGAAACTATCTCAAGCGACA-TAAAACTTCTGTTTCAAGT-GAAACAATCTCAAGCGAGATAA
* *
1324158 AATCTTTTGTTTC-GAGGAAAACTATCTCAAGTGAGATAAAATCTTTTGTTTCAAGGAAA
64 AATCTTTTGTTTCAAAGG-AAACTATCTCAAGGGAGATAAAA--TTTTGTTTCAAGGAAA
1324217 ACAATCTTGA
Statistics
Matches: 106, Mismatches: 8, Indels: 13
0.83 0.06 0.10
Matches are distributed among these distances:
125 3 0.03
126 62 0.58
127 2 0.02
128 7 0.07
129 31 0.29
130 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (128 bp):
AGCGAAACTATCTCAAGCGACATAAAACTTCTGTTTCAAGTGAAACAATCTCAAGCGAGATAAAA
TCTTTTGTTTCAAAGGAAACTATCTCAAGGGAGATAAAATTTTGTTTCAAGGAAACTGTCTCA
Found at i:1324232 original size:78 final size:77
Alignment explanation
Indices: 1324124--1324336 Score: 250
Period size: 78 Copynumber: 2.7 Consensus size: 77
1324114 CGACACTAAA
* * *
1324124 TTTGTTTCAATGG-AAACTATC-TCAAGCGAGATAAAATCTTTTGTTTCGAGGAAAACTATCTCA
1 TTTGTTTCAA-GGAAAACAATCTTGAA-CGAGATAAAATCTTTTGTTTCGAGGAAAACAATCTCA
*
1324187 AGTGAGATAAAATCT
64 AGTAAGAT-AAATCT
* **
1324202 TTTGTTTCAAGGAAAACAATCTTGAACGAGATAAAATCTTTTGTTTCAAGGAAAAACAATCTTGA
1 TTTGTTTCAAGGAAAACAATCTTGAACGAGATAAAATCTTTTGTTTCGAGG-AAAACAATCTCAA
1324267 GTAAGATAAATCT
65 GTAAGATAAATCT
* ** * *
1324280 TCTGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTCTTATTTCGAGTAAAA
1 TTTGTTTCAAGG-AAAACAATCTTGAACGAGATAAAATCTT-TTGTTTCGAGGAAAA
1324337 AAATGTCTCA
Statistics
Matches: 117, Mismatches: 13, Indels: 9
0.84 0.09 0.06
Matches are distributed among these distances:
77 2 0.02
78 58 0.50
79 49 0.42
80 8 0.07
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (77 bp):
TTTGTTTCAAGGAAAACAATCTTGAACGAGATAAAATCTTTTGTTTCGAGGAAAACAATCTCAAG
TAAGATAAATCT
Found at i:1324256 original size:39 final size:39
Alignment explanation
Indices: 1324151--1324320 Score: 227
Period size: 39 Copynumber: 4.3 Consensus size: 39
1324141 TATCTCAAGC
* * *
1324151 GAGATAAAATCTTTTGTTTCGAGGAAAACTATC-TCAAGT
1 GAGATAAAATCTTTTGTTTCAAGGAAAACAATCTTGAA-T
*
1324190 GAGATAAAATCTTTTGTTTCAAGGAAAACAATCTTGAAC
1 GAGATAAAATCTTTTGTTTCAAGGAAAACAATCTTGAAT
*
1324229 GAGATAAAATCTTTTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTTTGTTTCAAGG-AAAACAATCTTGAAT
* * *
1324269 AAGAT-AAATCTTCTGTTTCAAGGAAAAACAATCTTGAGT
1 GAGATAAAATCTTTTGTTTCAAGG-AAAACAATCTTGAAT
1324308 GAGATAAAATCTT
1 GAGATAAAATCTT
1324321 CTTATTTCGA
Statistics
Matches: 119, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
39 92 0.77
40 27 0.23
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (39 bp):
GAGATAAAATCTTTTGTTTCAAGGAAAACAATCTTGAAT
Found at i:1324312 original size:79 final size:78
Alignment explanation
Indices: 1324150--1324320 Score: 245
Period size: 79 Copynumber: 2.2 Consensus size: 78
1324140 CTATCTCAAG
* * * *
1324150 CGAGATAAAATCTTTTGTTTCGAGGAAAACTATCTCAAGTGAGATAAAATCTTTTGTTTCAAGGA
1 CGAGATAAAATCTTTTGTTTCAAGGAAAACAATCTCAAGTAAGATAAAATCTTCTGTTTCAAGGA
1324215 AAACAATCTTGAA
66 AAACAATCTTGAA
**
1324228 CGAGATAAAATCTTTTGTTTCAAGGAAAAACAATCTTGAGTAAGAT-AAATCTTCTGTTTCAAGG
1 CGAGATAAAATCTTTTGTTTCAAGG-AAAACAATCTCAAGTAAGATAAAATCTTCTGTTTCAAGG
*
1324292 AAAAACAATCTTGAG
65 -AAAACAATCTTGAA
*
1324307 TGAGATAAAATCTT
1 CGAGATAAAATCTT
1324321 CTTATTTCGA
Statistics
Matches: 83, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
78 41 0.49
79 42 0.51
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (78 bp):
CGAGATAAAATCTTTTGTTTCAAGGAAAACAATCTCAAGTAAGATAAAATCTTCTGTTTCAAGGA
AAACAATCTTGAA
Found at i:1324365 original size:79 final size:77
Alignment explanation
Indices: 1324105--1324458 Score: 226
Period size: 78 Copynumber: 4.6 Consensus size: 77
1324095 CAAGCGAAAC
* * ** *
1324105 TGTCTCAAGCGACACTAAA-TTTGTTTCAATGG--AAACTATCTCAAGCGAGATAAAATCTTTTG
1 TGTCTCAAGCGAGAC-AAATTTTGTTTCAA-GGAAAAACAATCTTGAGTGAGATAAAATCTTTTG
* *
1324167 TTTCGAG-GAAAAC
64 TTTCGAGTAAAAAA
* * * **
1324180 TATCTCAAGTGAGATAAAATCTTTTGTTTCAAGG-AAAACAATCTTGAACGAGATAAAATCTTTT
1 TGTCTCAAGCGAGA-CAAA--TTTTGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTTT
* *
1324244 GTTTCAAGGAAAAACA
63 GTTTCGAGTAAAAA-A
* ** ** *
1324260 -ATCTTGAGTAAGATAAATCTTCTGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTCTT
1 TGTCTCAAGCGAGACAAAT-TT-TGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTT-TT
*
1324324 ATTTCGAGTAAAAAAA
63 GTTTCGAGT-AAAAAA
* * * * * * *
1324340 TGTCTCAAGCGAGACAAATGTTGTTTTAA-GAAAAAC-AT-GT-AGTGAAATGAAATGTCTTGTT
1 TGTCTCAAGCGAGACAAATTTTGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTTTGTT
* * **
1324401 TTGAATAAAACC
66 TCGAGTAAAAAA
* * *
1324413 TGTCTCAAGCGAGACAAATCTTGTTTTAA-GAAAAACAATATTGAGT
1 TGTCTCAAGCGAGACAAATTTTGTTTCAAGGAAAAACAATCTTGAGT
1324459 CAAATGAAAT
Statistics
Matches: 223, Mismatches: 40, Indels: 31
0.76 0.14 0.11
Matches are distributed among these distances:
73 39 0.17
74 10 0.04
75 27 0.12
76 5 0.02
77 6 0.03
78 62 0.28
79 47 0.21
80 10 0.04
81 17 0.08
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (77 bp):
TGTCTCAAGCGAGACAAATTTTGTTTCAAGGAAAAACAATCTTGAGTGAGATAAAATCTTTTGTT
TCGAGTAAAAAA
Found at i:1324448 original size:37 final size:37
Alignment explanation
Indices: 1324333--1324449 Score: 105
Period size: 37 Copynumber: 3.2 Consensus size: 37
1324323 TATTTCGAGT
* *
1324333 AAAAAAATGTCTCAAGCGAGACAAATGTTGTTTTAAG
1 AAAAACATGTCTCAAGCGAGACAAATCTTGTTTTAAG
* * ** **
1324370 AAAAACATGTAGTGAAATGA-A-ATGTCTTGTTTTGAA-
1 AAAAACATGT-CTCAAGCGAGACAAATCTTGTTTT-AAG
* *
1324406 TAAAACCTGTCTCAAGCGAGACAAATCTTGTTTTAAG
1 AAAAACATGTCTCAAGCGAGACAAATCTTGTTTTAAG
1324443 AAAAACA
1 AAAAACA
1324450 ATATTGAGTC
Statistics
Matches: 57, Mismatches: 18, Indels: 10
0.67 0.21 0.12
Matches are distributed among these distances:
35 5 0.09
36 20 0.35
37 27 0.47
38 5 0.09
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (37 bp):
AAAAACATGTCTCAAGCGAGACAAATCTTGTTTTAAG
Found at i:1324514 original size:75 final size:73
Alignment explanation
Indices: 1324341--1324522 Score: 201
Period size: 73 Copynumber: 2.5 Consensus size: 73
1324331 GTAAAAAAAT
* * **
1324341 GTCTCAAGCGAGACAAATGT-TGTTTTAAGAAAAACATGTAGTGAAATGAAATGTCTTGTTTTGA
1 GTCTCAAGCGAGACAAA-GTCTGTTTTAAGAAAAACATGTAGTCAAATGAAATGTCTTCTTCAGA
*
1324405 ATAAAACCT
65 ATAAAACCA
*
1324414 GTCTCAAGCGAGACAAA-TCTTGTTTTAAGAAAAACAATATTGAGTCAAATGAAATGTCTTCCTT
1 GTCTCAAGCGAGACAAAGTC-TGTTTTAAGAAAAAC-AT-GT-AGTCAAATGAAATGTCTT-CTT
*
1324478 CAG-GTAAAA-CA
61 CAGAATAAAACCA
* *
1324489 GTCTCAAGTGAGACAAAGTCAGTTTTAAGAAAAA
1 GTCTCAAGCGAGACAAAGTCTGTTTTAAGAAAAA
1324523 TAATCTACAG
Statistics
Matches: 93, Mismatches: 9, Indels: 12
0.82 0.08 0.11
Matches are distributed among these distances:
71 1 0.01
73 32 0.34
74 2 0.02
75 31 0.33
76 24 0.26
77 3 0.03
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (73 bp):
GTCTCAAGCGAGACAAAGTCTGTTTTAAGAAAAACATGTAGTCAAATGAAATGTCTTCTTCAGAA
TAAAACCA
Found at i:1331952 original size:93 final size:94
Alignment explanation
Indices: 1331793--1331969 Score: 293
Period size: 93 Copynumber: 1.9 Consensus size: 94
1331783 TCTGAAGCTT
* * *
1331793 CTTATGCATTTATGTTGTTGGTTTTCCTTGTTTCGTGTTTCCGCTTGTCTCAGCGGCAATTGTAA
1 CTTATGCATTTATGCTGTTGGTTTTCCTTGTTTCGTGTTTCCGCTTGTCTCAACGGCAACTGTAA
*
1331858 AAAG-TGTCTAGTGTTCATGTTTTTGTTA
66 AAAGTTGTCAAGTGTTCATGTTTTTGTTA
*
1331886 CTTATGCATTTATGCTGTTGGTTTTCCTTGTTTCGTGTTTCCTCTTGTCTCAACGGCAACTGTAA
1 CTTATGCATTTATGCTGTTGGTTTTCCTTGTTTCGTGTTTCCGCTTGTCTCAACGGCAACTGTAA
1331951 AAAGTTTGTCAAGTGTTCA
66 AAAG-TTGTCAAGTGTTCA
1331970 CGTGCTTGTT
Statistics
Matches: 77, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
93 65 0.84
95 12 0.16
ACGTcount: A:0.16, C:0.17, G:0.20, T:0.46
Consensus pattern (94 bp):
CTTATGCATTTATGCTGTTGGTTTTCCTTGTTTCGTGTTTCCGCTTGTCTCAACGGCAACTGTAA
AAAGTTGTCAAGTGTTCATGTTTTTGTTA
Found at i:1333848 original size:15 final size:15
Alignment explanation
Indices: 1333828--1333858 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1333818 CAACAAATAG
1333828 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
1333843 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
1333858 A
1 A
1333859 TTTAAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:1335337 original size:2 final size:2
Alignment explanation
Indices: 1335299--1335326 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1335289 TTAATATTAA
1335299 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1335327 TAGTTATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1335344 original size:15 final size:15
Alignment explanation
Indices: 1335300--1335337 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1335290 TAATATTAAA
1335300 TATATATATATATA-T
1 TATATATATAT-TAGT
1335315 ATATATATATATTAGT
1 -TATATATATATTAGT
1335331 TATATAT
1 TATATAT
1335338 TACTTAGCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
TATATATATATTAGT
Found at i:1343347 original size:16 final size:14
Alignment explanation
Indices: 1343321--1343359 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 14
1343311 GATTAATTTA
1343321 TTTTCTTTTTTCACT
1 TTTTCTTTTTTCA-T
1343336 TTTTCATTTTTTCA-
1 TTTTC-TTTTTTCAT
1343350 TTTTCTTTTT
1 TTTTCTTTTT
1343360 CGTATCAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 5 0.22
14 5 0.22
15 5 0.22
16 8 0.35
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTCTTTTTTCAT
Found at i:1343745 original size:44 final size:44
Alignment explanation
Indices: 1343663--1343776 Score: 122
Period size: 44 Copynumber: 2.6 Consensus size: 44
1343653 CTTCTATCGC
* * *
1343663 GTTGATCCA-CTTCTTTCTATGATGGAACCGAGCGAAATGACAAT
1 GTTGATCCATC-TCCTTCTATGATGGAACCGAACAAAATGACAAT
* * *
1343707 GTTGATCCATCTCCTTCTATGATGGAATCGAACAAAATGTCGAT
1 GTTGATCCATCTCCTTCTATGATGGAACCGAACAAAATGACAAT
* ** *
1343751 ATTGATGTATCTCCTTCTGTGATGGA
1 GTTGATCCATCTCCTTCTATGATGGA
1343777 TTTGAACTAA
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 58 0.98
45 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.33
Consensus pattern (44 bp):
GTTGATCCATCTCCTTCTATGATGGAACCGAACAAAATGACAAT
Found at i:1346359 original size:15 final size:14
Alignment explanation
Indices: 1346323--1346357 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
1346313 CTTTCTTTTA
1346323 CTTTTTTATTTTCT
1 CTTTTTTATTTTCT
1346337 CTTTTTTATTTTCT
1 CTTTTTTATTTTCT
1346351 CTTTTTT
1 CTTTTTT
1346358 TAAGTGTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (14 bp):
CTTTTTTATTTTCT
Found at i:1350632 original size:4 final size:4
Alignment explanation
Indices: 1350623--1350660 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
1350613 TATTAGAAAC
*
1350623 AATA AATA AATA AATA AGTA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AA
1350661 AATGATTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (4 bp):
AATA
Done.