Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009639.1 Hibiscus syriacus cultivar Beakdansim tig00117048_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: 15077257
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 62
Found at i:3536088 original size:23 final size:23
Alignment explanation
Indices: 3536054--3536098 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3536044 ACTGAAGAAG
*
3536054 AAAGAAAAGTGAAGGAAAGGAAT
1 AAAGAAAAGTGAAAGAAAGGAAT
*
3536077 AAAGAAAGGTGAAAGAAAGGAA
1 AAAGAAAAGTGAAAGAAAGGAA
3536099 AGAAAAGGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.31, T:0.07
Consensus pattern (23 bp):
AAAGAAAAGTGAAAGAAAGGAAT
Found at i:3536694 original size:33 final size:33
Alignment explanation
Indices: 3536635--3536697 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
3536625 CGGAAGGTAA
* *
3536635 TATAAATTCTCTATTTTAATATAAAATATTAAT
1 TATAAATTATATATTTTAATATAAAATATTAAT
*
3536668 TATAAATTATATATATTTATTA-AAAATATT
1 TATAAATTATATAT-TTTAATATAAAATATT
3536698 GAAAAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 20 0.77
34 6 0.23
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (33 bp):
TATAAATTATATATTTTAATATAAAATATTAAT
Found at i:3541109 original size:15 final size:15
Alignment explanation
Indices: 3541065--3541126 Score: 62
Period size: 14 Copynumber: 4.5 Consensus size: 15
3541055 TAAGCGGTCT
3541065 CTTCTTCTCCCTTT-
1 CTTCTTCTCCCTTTC
* *
3541079 TTTCTTCTTCCTTT-
1 CTTCTTCTCCCTTTC
3541093 CTTCTT-T--CTTTC
1 CTTCTTCTCCCTTTC
3541105 CTTCTTCTCCCTTTC
1 CTTCTTCTCCCTTTC
*
3541120 TTTCTTC
1 CTTCTTC
3541127 ATAACTGTAC
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
11 4 0.10
12 6 0.15
13 2 0.05
14 17 0.43
15 11 0.28
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (15 bp):
CTTCTTCTCCCTTTC
Found at i:3541509 original size:232 final size:232
Alignment explanation
Indices: 3541100--3541752 Score: 1058
Period size: 232 Copynumber: 2.8 Consensus size: 232
3541090 TTTCTTCTTT
** * *
3541100 CTTTCCTTCTTCTCCCTTTCTTTCTTCATAACTGTACCCCAGACCTAATGACCAATATATAACCC
1 CTTTCCTTCTTCTCTTTTTCTTTCTTCATAACCGTGCCCCAGACC---TGACCAATATATAACCC
* *
3541165 TAAACTGGCCCCATAAACCCCAAATTTACTACAATTATCCATCTATTTTTAATACTACTATTAAA
63 TAAACTGGCCCCATAAACCCTAAATTTGCTACAATTATCCATCTATTTTTAATACTACTATTAAA
3541230 ACGTGAATCATGTAGGCATGCATGAGCAAAATAATGCTCCATATCACGC-AACTATAATTACTAA
128 ACGTGAATCATGTAGGCATGCATGAGCAAAATAATGCTCCATATCACGCGAA-TATAATTACTAA
3541294 ACCAGACCCATAAACCATAATTTAATCCCAACACAGACCAC
192 ACCAGACCCATAAACCATAATTTAATCCCAACACAGACCAC
3541335 CTTTCCTTCTTCTCTTTTTCTTTCTTCATAACCGTGCCCCAGACCTGACCAATATATAACCCTAA
1 CTTTCCTTCTTCTCTTTTTCTTTCTTCATAACCGTGCCCCAGACCTGACCAATATATAACCCTAA
* * * *
3541400 ACTAGCCCCATAAAACCTAAATTTGCTATAATTATCCATCTATTTTTAATACTACTATTAAAATG
66 ACTGGCCCCATAAACCCTAAATTTGCTACAATTATCCATCTATTTTTAATACTACTATTAAAACG
* * **
3541465 TGAATCATGTAGGCATGCTTGAGAAAAATAATGCTCCATATCACGCGAATATAATTACTAAACGG
131 TGAATCATGTAGGCATGCATGAGCAAAATAATGCTCCATATCACGCGAATATAATTACTAAACCA
* *
3541530 GCCCCATAAACCATAATTTAATCCCAACATAGACCAC
196 GACCCATAAACCATAATTTAATCCCAACACAGACCAC
3541567 CTTTCCTTCTTCTCTTTTTCTTTCTTCATAACCGTGCCCCAGACCTGACCAATATATAACCCTAA
1 CTTTCCTTCTTCTCTTTTTCTTTCTTCATAACCGTGCCCCAGACCTGACCAATATATAACCCTAA
* * *
3541632 ACTGGCCCTATAAACCCTAAATTTGCTGCAATAAGT-CATCTATTTTTAATACTACTATTAAAAC
66 ACTGGCCCCATAAACCCTAAATTTGCTACAATTA-TCCATCTATTTTTAATACTACTATTAAAAC
* *
3541696 GTGAATTATGTAGGCATGCATGAGCAAAATAATGCTCCATATCACGTGAATATAATT
130 GTGAATCATGTAGGCATGCATGAGCAAAATAATGCTCCATATCACGCGAATATAATT
3541753 GCTCCCAACA
Statistics
Matches: 389, Mismatches: 27, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
232 345 0.89
233 3 0.01
235 41 0.11
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.31
Consensus pattern (232 bp):
CTTTCCTTCTTCTCTTTTTCTTTCTTCATAACCGTGCCCCAGACCTGACCAATATATAACCCTAA
ACTGGCCCCATAAACCCTAAATTTGCTACAATTATCCATCTATTTTTAATACTACTATTAAAACG
TGAATCATGTAGGCATGCATGAGCAAAATAATGCTCCATATCACGCGAATATAATTACTAAACCA
GACCCATAAACCATAATTTAATCCCAACACAGACCAC
Found at i:3542146 original size:30 final size:30
Alignment explanation
Indices: 3542077--3542187 Score: 197
Period size: 30 Copynumber: 3.7 Consensus size: 30
3542067 CACTACAAGA
3542077 TCGCCCCGACTGCATGGCGACCTTCAAG-T
1 TCGCCCCGACTGCATGGCGACCTTCAAGCT
*
3542106 TCGCTCCGACTGCATGGCGACCTTCAAGCT
1 TCGCCCCGACTGCATGGCGACCTTCAAGCT
*
3542136 TCGCCTCGACTGCATGGCGACCTTCAAGCT
1 TCGCCCCGACTGCATGGCGACCTTCAAGCT
3542166 TCGCCCCGACTGCATGGCGACC
1 TCGCCCCGACTGCATGGCGACC
3542188 AATCTCATCC
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
29 27 0.35
30 50 0.65
ACGTcount: A:0.16, C:0.39, G:0.24, T:0.21
Consensus pattern (30 bp):
TCGCCCCGACTGCATGGCGACCTTCAAGCT
Found at i:3544153 original size:20 final size:20
Alignment explanation
Indices: 3544130--3544167 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3544120 ACAGTTTCCA
*
3544130 AATTTACAACGCGAATTTTG
1 AATTCACAACGCGAATTTTG
*
3544150 AATTCACAATGCGAATTT
1 AATTCACAACGCGAATTT
3544168 CCCAAATTCG
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:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (20 bp):
AATTCACAACGCGAATTTTG
Found at i:3544235 original size:20 final size:20
Alignment explanation
Indices: 3544210--3544261 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
3544200 ACGCGATTTT
3544210 TCAAATTCGCAACACAAAAG
1 TCAAATTCGCAACACAAAAG
*
3544230 TCAAATTCGCAACACAGAAG
1 TCAAATTCGCAACACAAAAG
3544250 TCAAATTCGCAA
1 TCAAATTCGCAA
3544262 AGCTCGTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.46, C:0.25, G:0.12, T:0.17
Consensus pattern (20 bp):
TCAAATTCGCAACACAAAAG
Found at i:3544447 original size:22 final size:22
Alignment explanation
Indices: 3544422--3544468 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
3544412 TCTCTACGGT
* * *
3544422 GACATCCGTCCTCATCTTCGGC
1 GACATCCGTCCCCATATCCGGC
3544444 GACATCCGTCCCCATATCCGGC
1 GACATCCGTCCCCATATCCGGC
3544466 GAC
1 GAC
3544469 CCCTCTCCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.17, C:0.43, G:0.19, T:0.21
Consensus pattern (22 bp):
GACATCCGTCCCCATATCCGGC
Found at i:3544831 original size:20 final size:21
Alignment explanation
Indices: 3544802--3544845 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
3544792 GTAGTTTTTG
*
3544802 AAAATTAAATTCGCAACAC-A
1 AAAATGAAATTCGCAACACGA
3544822 AAAATGAAATTCGCAACACGA
1 AAAATGAAATTCGCAACACGA
3544843 AAA
1 AAA
3544846 GCGCAACGCG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.57, C:0.18, G:0.09, T:0.16
Consensus pattern (21 bp):
AAAATGAAATTCGCAACACGA
Found at i:3544908 original size:19 final size:20
Alignment explanation
Indices: 3544870--3544908 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
3544860 TAGTTTTCGC
* *
3544870 GTTGCGAATTTCATTTTCAA
1 GTTGCGAATTTAAGTTTCAA
3544890 GTTGCGAA-TTAAGTTTCAA
1 GTTGCGAATTTAAGTTTCAA
3544909 AAACTACTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (20 bp):
GTTGCGAATTTAAGTTTCAA
Found at i:3546266 original size:44 final size:41
Alignment explanation
Indices: 3546177--3546270 Score: 143
Period size: 41 Copynumber: 2.3 Consensus size: 41
3546167 TAGGAAGATT
* *
3546177 TACTACCATATACGATGATGAATGATGTAAGTTAATACAAA
1 TACTACCATATACGACGATGAATGATGTAAGTTAACACAAA
* *
3546218 TACTACCATATACGACGATGACTTATGTAAGTTAACACAAA
1 TACTACCATATACGACGATGAATGATGTAAGTTAACACAAA
*
3546259 TACTACTATATA
1 TACTACCATATA
3546271 TAAACAAGTT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.30
Consensus pattern (41 bp):
TACTACCATATACGACGATGAATGATGTAAGTTAACACAAA
Found at i:3546495 original size:42 final size:42
Alignment explanation
Indices: 3546436--3546539 Score: 163
Period size: 42 Copynumber: 2.5 Consensus size: 42
3546426 CACCCCCACT
* *
3546436 TCGACATCGAGATCCATCACCTGATCGAGCCGATTCTACACC
1 TCGACACCGAGAGCCATCACCTGATCGAGCCGATTCTACACC
*
3546478 TCGACACCGAGAGCCATCACCTGATCGAGCTGATTCTACACC
1 TCGACACCGAGAGCCATCACCTGATCGAGCCGATTCTACACC
* *
3546520 TTGACACCTAGAGCCATCAC
1 TCGACACCGAGAGCCATCAC
3546540 ATATTCCATC
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.27, C:0.36, G:0.17, T:0.20
Consensus pattern (42 bp):
TCGACACCGAGAGCCATCACCTGATCGAGCCGATTCTACACC
Found at i:3546802 original size:21 final size:21
Alignment explanation
Indices: 3546641--3546802 Score: 116
Period size: 21 Copynumber: 7.7 Consensus size: 21
3546631 ACCTCCACGG
*
3546641 GATGAGTTAGGTGCTTTACGT
1 GATGAGGTAGGTGCTTTACGT
*
3546662 GATGAGGTCA-ATGCTTTACGT
1 GATGAGGT-AGGTGCTTTACGT
*
3546683 GATGAGGTTGGTGCTTTACGT
1 GATGAGGTAGGTGCTTTACGT
** * **
3546704 GATGA-CAATGGTGCATGGCGT
1 GATGAGGTA-GGTGCTTTACGT
3546725 GATGAGGTAGG-GTCTTTACGT
1 GATGAGGTAGGTG-CTTTACGT
** * * *
3546746 GGCGAGGTAGCTGTTTTACTT
1 GATGAGGTAGGTGCTTTACGT
**
3546767 GATGA-CAATGGTGCTTTACGT
1 GATGAGGTA-GGTGCTTTACGT
*
3546788 GATGAGGTAGCTGCT
1 GATGAGGTAGGTGCT
3546803 CAACGTGAGA
Statistics
Matches: 103, Mismatches: 30, Indels: 16
0.69 0.20 0.11
Matches are distributed among these distances:
20 2 0.02
21 97 0.94
22 4 0.04
ACGTcount: A:0.20, C:0.12, G:0.35, T:0.33
Consensus pattern (21 bp):
GATGAGGTAGGTGCTTTACGT
Found at i:3546809 original size:63 final size:62
Alignment explanation
Indices: 3546650--3546802 Score: 180
Period size: 63 Copynumber: 2.4 Consensus size: 62
3546640 GGATGAGTTA
* * * *
3546650 GGTGCTTTACGTGATGAGGTCAATGCTTTACGTGATGAGGTTGGTGCTTTACGTGATGACAAT
1 GGTGCTTTACGTGATGAGGT-AGTGCTTTACGTGACGAGGTAGCTGCTTTACGTGATGACAAT
* ** * * * *
3546713 GGTGCATGGCGTGATGAGGTAGGGTCTTTACGTGGCGAGGTAGCTGTTTTACTTGATGACAAT
1 GGTGCTTTACGTGATGAGGTAGTG-CTTTACGTGACGAGGTAGCTGCTTTACGTGATGACAAT
3546776 GGTGCTTTACGTGATGAGGTAGCTGCT
1 GGTGCTTTACGTGATGAGGTAG-TGCT
3546803 CAACGTGAGA
Statistics
Matches: 73, Mismatches: 15, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
62 2 0.03
63 70 0.96
64 1 0.01
ACGTcount: A:0.19, C:0.13, G:0.35, T:0.33
Consensus pattern (62 bp):
GGTGCTTTACGTGATGAGGTAGTGCTTTACGTGACGAGGTAGCTGCTTTACGTGATGACAAT
Found at i:3547178 original size:21 final size:21
Alignment explanation
Indices: 3547152--3547197 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
3547142 CATGTCATTA
3547152 TTCAAGAGGCCCATCCCATCG
1 TTCAAGAGGCCCATCCCATCG
*
3547173 TTCAAGAGGCCCCTCCCATCG
1 TTCAAGAGGCCCATCCCATCG
3547194 TTCA
1 TTCA
3547198 GGATCCACCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.39, G:0.17, T:0.22
Consensus pattern (21 bp):
TTCAAGAGGCCCATCCCATCG
Found at i:3547208 original size:21 final size:21
Alignment explanation
Indices: 3547165--3547225 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
3547155 AAGAGGCCCA
* *
3547165 TCCCATCGTTCAAGAGGCC-CC
1 TCCCATCGTTCAGGA-TCCACC
3547186 TCCCATCGTTCAGGATCCACC
1 TCCCATCGTTCAGGATCCACC
*
3547207 TCCCACCGTTCAGGATCCA
1 TCCCATCGTTCAGGATCCA
3547226 TATGACATTC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
20 2 0.06
21 34 0.94
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.21
Consensus pattern (21 bp):
TCCCATCGTTCAGGATCCACC
Found at i:3548447 original size:16 final size:16
Alignment explanation
Indices: 3548418--3548453 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3548408 TGTAAATAAA
* *
3548418 AATTGTTTTTTTGTTT
1 AATTGATTTGTTGTTT
3548434 AATTGATTTGTTGTTT
1 AATTGATTTGTTGTTT
3548450 AATT
1 AATT
3548454 TCAATCTGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.14, T:0.67
Consensus pattern (16 bp):
AATTGATTTGTTGTTT
Found at i:3548602 original size:20 final size:20
Alignment explanation
Indices: 3548518--3548602 Score: 138
Period size: 19 Copynumber: 4.3 Consensus size: 20
3548508 AAGAAAATCG
*
3548518 AATTTGCAACGCGAAAATAA
1 AATTCGCAACGCGAAAATAA
3548538 AATTCG-AACGCGAAAATAA
1 AATTCGCAACGCGAAAATAA
3548557 AATTCG-AACGCGAAAATAA
1 AATTCGCAACGCGAAAATAA
*
3548576 AATTCGCAACGTGAAAATAA
1 AATTCGCAACGCGAAAATAA
3548596 AATTCGC
1 AATTCGC
3548603 GTTACGATTT
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
19 38 0.61
20 24 0.39
ACGTcount: A:0.49, C:0.16, G:0.15, T:0.19
Consensus pattern (20 bp):
AATTCGCAACGCGAAAATAA
Found at i:3548674 original size:20 final size:20
Alignment explanation
Indices: 3548649--3548703 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
3548639 TGCGATTTTT
* * *
3548649 GAGTTGCGAATTTTATTTTC
1 GAGTTGCGAATTTGAATATC
*
3548669 GCGTTGCGAATTTGAATATC
1 GAGTTGCGAATTTGAATATC
3548689 GAGTTGCGAATTTGA
1 GAGTTGCGAATTTGA
3548704 GTTGTAAATC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.24, C:0.11, G:0.25, T:0.40
Consensus pattern (20 bp):
GAGTTGCGAATTTGAATATC
Found at i:3548675 original size:34 final size:34
Alignment explanation
Indices: 3548598--3548677 Score: 88
Period size: 34 Copynumber: 2.4 Consensus size: 34
3548588 GAAAATAAAA
* *
3548598 TTCGCGTTACGATTTTCGTGTTGCGAATTTAAGT
1 TTCGCGTTGCGATTTTCGAGTTGCGAATTTAAGT
* ** * * *
3548632 ATCAAGTTGCGATTTTTGAGTTGCGAATTTTATT
1 TTCGCGTTGCGATTTTCGAGTTGCGAATTTAAGT
3548666 TTCGCGTTGCGA
1 TTCGCGTTGCGA
3548678 ATTTGAATAT
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.19, C:0.14, G:0.24, T:0.44
Consensus pattern (34 bp):
TTCGCGTTGCGATTTTCGAGTTGCGAATTTAAGT
Found at i:3551232 original size:24 final size:24
Alignment explanation
Indices: 3551198--3551265 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
3551188 CTGAAACATC
*
3551198 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAA
* * *
3551222 ATCAAAGTCCGGGTATTAACCAAA
1 ATCAAAATCCGAGTATTGACCAAA
* * *
3551246 ATCAAATTTCGAATATTGAC
1 ATCAAAATCCGAGTATTGAC
3551266 TAGTACTCGC
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.25
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAA
Found at i:3552225 original size:40 final size:40
Alignment explanation
Indices: 3552181--3552297 Score: 155
Period size: 40 Copynumber: 2.9 Consensus size: 40
3552171 TTGCGAAATT
*
3552181 AAAATTCGTGTTGCGAATTCAGAAATCGAGTTACAAAAAC
1 AAAATTCGTGTTGCGAATTCAGAAATCGAGTTGCAAAAAC
** * *
3552221 AAAATTCGTGTTGCGAATT-AGAAAATCTTGTTGCGAAAAG
1 AAAATTCGTGTTGCGAATTCAG-AAATCGAGTTGCAAAAAC
* *
3552261 GAAATTTGTGTTGCGAATTCAGAAATCGAGTTGCAAA
1 AAAATTCGTGTTGCGAATTCAGAAATCGAGTTGCAAA
3552298 TTTGTGAAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
39 2 0.03
40 61 0.94
41 2 0.03
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.28
Consensus pattern (40 bp):
AAAATTCGTGTTGCGAATTCAGAAATCGAGTTGCAAAAAC
Found at i:3552293 original size:20 final size:20
Alignment explanation
Indices: 3552169--3552299 Score: 76
Period size: 20 Copynumber: 6.5 Consensus size: 20
3552159 AAATAAAAGC
3552169 TGTTGCGAAATT-A-AAATTCG
1 TGTTGCG-AATTCAGAAA-TCG
3552189 TGTTGCGAATTCAGAAATCG
1 TGTTGCGAATTCAGAAATCG
* * * **
3552209 AGTTACAAAAACA-AAATTCG
1 TGTTGCGAATTCAGAAA-TCG
*
3552229 TGTTGCGAATT-AGAAAATCT
1 TGTTGCGAATTCAG-AAATCG
* *
3552249 TGTTGCGAA--AAGGAAATTTG
1 TGTTGCGAATTCA-GAAA-TCG
3552269 TGTTGCGAATTCAGAAATCG
1 TGTTGCGAATTCAGAAATCG
* *
3552289 AGTTGCAAATT
1 TGTTGCGAATT
3552300 TGTGAAATTG
Statistics
Matches: 84, Mismatches: 17, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
19 12 0.14
20 61 0.73
21 10 0.12
22 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.31
Consensus pattern (20 bp):
TGTTGCGAATTCAGAAATCG
Found at i:3552396 original size:21 final size:20
Alignment explanation
Indices: 3552313--3552430 Score: 82
Period size: 20 Copynumber: 5.8 Consensus size: 20
3552303 GAAATTGGAG
* *
3552313 TTCGTGTTGCGAATTTGAAA
1 TTCGCGTTGCGAATTAGAAA
* * *
3552333 ATCGCATTGCGTAA-AAGAAA
1 TTCGCGTTGCG-AATTAGAAA
3552353 TTCGCGTTGCGAAATT-GTCAAA
1 TTCGCGTTGCG-AATTAG--AAA
3552375 TTCGCGTTGCGAATTCAGAAA
1 TTCGCGTTGCGAATT-AGAAA
* *
3552396 -TCGAGTTGCGAATTTGAAA
1 TTCGCGTTGCGAATTAGAAA
3552415 TTC-CGTATTGCGAATT
1 TTCGCG--TTGCGAATT
3552431 TGGAAACTGT
Statistics
Matches: 77, Mismatches: 12, Indels: 17
0.73 0.11 0.16
Matches are distributed among these distances:
19 5 0.06
20 39 0.51
21 18 0.23
22 14 0.18
23 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (20 bp):
TTCGCGTTGCGAATTAGAAA
Found at i:3556859 original size:16 final size:17
Alignment explanation
Indices: 3556838--3556871 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3556828 AAAGGTATCG
3556838 CATTAACCAATT-AAAA
1 CATTAACCAATTGAAAA
*
3556854 CATTAACTAATTGAAAA
1 CATTAACCAATTGAAAA
3556871 C
1 C
3556872 CGATCAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.53, C:0.18, G:0.03, T:0.26
Consensus pattern (17 bp):
CATTAACCAATTGAAAA
Found at i:3558360 original size:14 final size:16
Alignment explanation
Indices: 3558329--3558361 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
3558319 ATATAGGTAA
3558329 TAATGCACTCACCTAG
1 TAATGCACTCACCTAG
3558345 TAATGC-CTCA-CTAG
1 TAATGCACTCACCTAG
3558359 TAA
1 TAA
3558362 ACTTTACGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 4 0.24
16 6 0.35
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.27
Consensus pattern (16 bp):
TAATGCACTCACCTAG
Found at i:3560419 original size:109 final size:109
Alignment explanation
Indices: 3560259--3560460 Score: 300
Period size: 109 Copynumber: 1.9 Consensus size: 109
3560249 AAAACGTCCA
* * * * *
3560259 CTAAACCTATATTTTGAAACTAAGGTAGAAAGATGAAGTTGAGAGCTTAAAATAAAGCTCAGGGA
1 CTAAACCCATATTTTGAAACTAAGGTAGAAAGATAAAGTTGAGAGCCTAAAAGAAAGCCCAGGGA
*
3560324 ATGATGATTTCAT-TTTTTTACCTTGGTGTACCTTAAACCCTAAAC
66 ATGATGATTT--TGTTTCTTACCTTGGTGTACCTTAAACCCTAAAC
*
3560369 CTAAACCCATATTTTGAAACTATGG-AGAAAGATAAAGTTGAGAGCCTAAAAGAAAGCCCAGGGA
1 CTAAACCCATATTTTGAAACTAAGGTAGAAAGATAAAGTTGAGAGCCTAAAAGAAAGCCCAGGGA
*
3560433 ATGTTGATTTTGTTTCTTACCTTGGTGT
66 ATGATGATTTTGTTTCTTACCTTGGTGT
3560461 TACTGGAAAA
Statistics
Matches: 83, Mismatches: 8, Indels: 4
0.87 0.08 0.04
Matches are distributed among these distances:
107 1 0.01
108 15 0.18
109 44 0.53
110 23 0.28
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.31
Consensus pattern (109 bp):
CTAAACCCATATTTTGAAACTAAGGTAGAAAGATAAAGTTGAGAGCCTAAAAGAAAGCCCAGGGA
ATGATGATTTTGTTTCTTACCTTGGTGTACCTTAAACCCTAAAC
Found at i:3581061 original size:64 final size:64
Alignment explanation
Indices: 3580945--3581099 Score: 147
Period size: 64 Copynumber: 2.4 Consensus size: 64
3580935 GAAGGTGTAT
* * * ** *
3580945 CGATGCACAGGTAGTGCATCGATACA-CTCTTTTAAAATAAAAAGATCAAATGCA-ATTAGTGCA
1 CGATGCACAAGCAGTGCATCGATGCATC-CCATTAAAATAAAAACATCAAATGCATATTA-TGCA
*
3581008 T
64 C
* * *
3581009 CGATGCATAAGGCA-TGCATCGATGCATCCCATTAATAAT-AAAACATCGAATGCATTTTATGCA
1 CGATGCACAA-GCAGTGCATCGATGCATCCCATTAA-AATAAAAACATCAAATGCATATTATGCA
3581072 C
64 C
*
3581073 CGATGCACAAGTAGTGCATCGATGCAT
1 CGATGCACAAGCAGTGCATCGATGCAT
3581100 ACCTTTATTA
Statistics
Matches: 74, Mismatches: 12, Indels: 10
0.77 0.12 0.10
Matches are distributed among these distances:
63 2 0.03
64 63 0.85
65 9 0.12
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (64 bp):
CGATGCACAAGCAGTGCATCGATGCATCCCATTAAAATAAAAACATCAAATGCATATTATGCAC
Found at i:3581513 original size:29 final size:29
Alignment explanation
Indices: 3581474--3581583 Score: 159
Period size: 29 Copynumber: 3.8 Consensus size: 29
3581464 TATGTGATAT
3581474 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
* *
3581504 GAGAAATGACATGAGCTATATCATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
*
3581533 GAGAAATGACATGAACTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
* *
3581562 GAGAAATGAAATTAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
3581584 ACATATAAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
28 7 0.10
29 60 0.83
30 5 0.07
ACGTcount: A:0.46, C:0.15, G:0.19, T:0.19
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:3588345 original size:29 final size:29
Alignment explanation
Indices: 3588306--3588444 Score: 253
Period size: 29 Copynumber: 4.8 Consensus size: 29
3588296 TATGTGATAT
3588306 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
3588336 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
3588365 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
*
3588394 GAGAAATGACATGAACTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
3588423 GAGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
3588445 ACATATAAAA
Statistics
Matches: 107, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
28 7 0.07
29 95 0.89
30 5 0.05
ACGTcount: A:0.45, C:0.17, G:0.21, T:0.17
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:3592707 original size:17 final size:17
Alignment explanation
Indices: 3592685--3592737 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 17
3592675 CGGGCCGGGT
3592685 ATATATATTTAAATTAA
1 ATATATATTTAAATTAA
*
3592702 ATATATA---AATATTAT
1 ATATATATTTAA-ATTAA
3592717 ATATATATTTAAATTTAA
1 ATATATATTTAAA-TTAA
3592735 ATA
1 ATA
3592738 AAATTTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 2 0.07
15 11 0.38
17 8 0.28
18 8 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATATATTTAAATTAA
Found at i:3592723 original size:4 final size:4
Alignment explanation
Indices: 3592684--3592775 Score: 52
Period size: 4 Copynumber: 24.5 Consensus size: 4
3592674 TCGGGCCGGG
* * * * * *
3592684 TATA TATA TTTA AAT- TAAA TATA TAAA TAT- TATA TATA TATT TAAA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * *
3592730 TTTA AATA -AAA TTTA T-TA -ATA T-TA TATA TATA TATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
3592774 TA
1 TA
3592776 ATAAGTATTT
Statistics
Matches: 64, Mismatches: 18, Indels: 12
0.68 0.19 0.13
Matches are distributed among these distances:
3 13 0.20
4 51 0.80
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (4 bp):
TATA
Found at i:3592723 original size:6 final size:6
Alignment explanation
Indices: 3592684--3592775 Score: 52
Period size: 6 Copynumber: 16.3 Consensus size: 6
3592674 TCGGGCCGGG
* * * * * *
3592684 TATATA TATTTA AAT-TA AATATA TAAATA T-TATA TATATA TTTAAA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * *
3592730 TTTAAA TA-AAA TTTAT- TA-ATA T-TATA TATATA TATATA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
3592774 TA
1 TA
3592776 ATAAGTATTT
Statistics
Matches: 69, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
4 2 0.03
5 19 0.28
6 48 0.70
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (6 bp):
TATATA
Found at i:3592747 original size:32 final size:33
Alignment explanation
Indices: 3592684--3592776 Score: 93
Period size: 32 Copynumber: 2.8 Consensus size: 33
3592674 TCGGGCCGGG
3592684 TATATATATTTAAATTAAATATATAAATATT-A
1 TATATATATTTAAATTAAATATATAAATATTAA
*
3592716 TATATATATTTAAATTTAAATA-A-AATTTATTAA
1 TATATATATTTAAA-TTAAATATATAA-ATATTAA
* * *
3592749 TATTATATATATATATATATATATATAA
1 TA-TATATATTTAAAT-TAAATATATAA
3592777 TAAGTATTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
31 2 0.04
32 19 0.38
33 11 0.22
34 15 0.30
35 1 0.02
36 2 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (33 bp):
TATATATATTTAAATTAAATATATAAATATTAA
Found at i:3595105 original size:21 final size:19
Alignment explanation
Indices: 3595081--3595119 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
3595071 TAACTATTAT
3595081 TATATTTCTTATCTTATTTTC
1 TATATTTCTT-TCTT-TTTTC
3595102 TATATTTCTTTCTTTTTT
1 TATATTTCTTTCTTTTTT
3595120 GGTTTCCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 4 0.22
21 10 0.56
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (19 bp):
TATATTTCTTTCTTTTTTC
Found at i:3595342 original size:21 final size:22
Alignment explanation
Indices: 3595289--3595342 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
3595279 TTCCATTACT
*
3595289 TTTGTTCATTTTACTTTATTTCA
1 TTTGTT-ATTTTACTTTACTTCA
3595312 TTTGTT-TTTTACTTT-CTTCA
1 TTTGTTATTTTACTTTACTTCA
3595332 TTAT-TTATTTT
1 TT-TGTTATTTT
3595343 TCATTCATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
20 8 0.29
21 14 0.50
23 6 0.21
ACGTcount: A:0.15, C:0.11, G:0.04, T:0.70
Consensus pattern (22 bp):
TTTGTTATTTTACTTTACTTCA
Found at i:3597360 original size:13 final size:13
Alignment explanation
Indices: 3597342--3597366 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3597332 AAAGAACTTG
3597342 AGAAGGGGTAACC
1 AGAAGGGGTAACC
3597355 AGAAGGGGTAAC
1 AGAAGGGGTAAC
3597367 TATACCACCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.12, G:0.40, T:0.08
Consensus pattern (13 bp):
AGAAGGGGTAACC
Found at i:3599369 original size:95 final size:94
Alignment explanation
Indices: 3599195--3599440 Score: 311
Period size: 95 Copynumber: 2.7 Consensus size: 94
3599185 CTATTATAAT
* *
3599195 ATTATATATATAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACTCCCCGGCTTTATG
1 ATTATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATG
* *
3599260 GATAATATTCAGCTAGCCTGATAAAGGCG
66 GATAAGATTCAGCTAACCTGATAAAGGCG
3599289 ATTATACTATACAATAAAGCTTGAGTTGTCCCTCTA-AGGCAATTGGTTAAACGCCCCGGCTTTA
1 ATTATA-TATACAATAAAGCTTGAGTTGTCCCTCTAGA-GCAATTGGTTAAACGCCCCGGCTTTA
*
3599353 TGGATAAGATTCAGCTAACCTGATGAA-G-G
64 TGGATAAGATTCAGCTAACCTGATAAAGGCG
* *
3599382 --TAT-T-TAC-AT--A--TGGAGTTG-CCTCTCTAGAGCAATTGGTTAAACACCCCGGCTTTAT
1 ATTATATATACAATAAAGCTTGAGTTGTCC-CTCTAGAGCAATTGGTTAAACGCCCCGGCTTTAT
3599437 GGAT
65 GGAT
3599441 TCAGCTAGCT
Statistics
Matches: 141, Mismatches: 7, Indels: 19
0.84 0.04 0.11
Matches are distributed among these distances:
82 2 0.01
83 42 0.30
84 1 0.01
85 1 0.01
87 2 0.01
88 3 0.02
89 1 0.01
91 3 0.02
93 1 0.01
94 8 0.06
95 77 0.55
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (94 bp):
ATTATATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATG
GATAAGATTCAGCTAACCTGATAAAGGCG
Found at i:3600641 original size:72 final size:72
Alignment explanation
Indices: 3600556--3600737 Score: 301
Period size: 72 Copynumber: 2.5 Consensus size: 72
3600546 CTCAGTTGAG
* *
3600556 ATTGTTATTCTTAAAACAGACTTTGTCTCACTCGAGACTATTTTACTCGAAAGAAGATTTATTTC
1 ATTGTTTTTCTTAAAACAGACTTTGTCTCACTTGAGACTATTTTACTCGAAAGAAGATTTATTTC
3600621 CCTCAAT
66 CCTCAAT
* *
3600628 ATTTTTTTTCTTAAAACAGACTTTGTCTCACTTGAGACTGTTTTACTCGAAAGAAGATTTATTTC
1 ATTGTTTTTCTTAAAACAGACTTTGTCTCACTTGAGACTATTTTACTCGAAAGAAGATTTATTTC
3600693 CCTCAAT
66 CCTCAAT
* *
3600700 ATTGTTTTTCTTAAAACAAGATTTTATCTCACTTGAGA
1 ATTGTTTTTCTTAAAAC-AGACTTTGTCTCACTTGAGA
3600738 TAATTTCCCT
Statistics
Matches: 102, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
72 84 0.82
73 18 0.18
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.42
Consensus pattern (72 bp):
ATTGTTTTTCTTAAAACAGACTTTGTCTCACTTGAGACTATTTTACTCGAAAGAAGATTTATTTC
CCTCAAT
Found at i:3600721 original size:36 final size:36
Alignment explanation
Indices: 3600609--3600723 Score: 106
Period size: 36 Copynumber: 3.2 Consensus size: 36
3600599 TACTCGAAAG
*
3600609 AAGATTTATTTCCCTCAATATTTTTTTTCTTAAAAC
1 AAGATTTATTTCCCTCAATATTGTTTTTCTTAAAAC
* * * ** * * * ** *
3600645 -AGACTTTGTCTCACTTGAGACTGTTTTACTCGAAAG
1 AAGA-TTTATTTCCCTCAATATTGTTTTTCTTAAAAC
3600681 AAGATTTATTTCCCTCAATATTGTTTTTCTTAAAAC
1 AAGATTTATTTCCCTCAATATTGTTTTTCTTAAAAC
3600717 AAGATTT
1 AAGATTT
3600724 TATCTCACTT
Statistics
Matches: 54, Mismatches: 23, Indels: 4
0.67 0.28 0.05
Matches are distributed among these distances:
35 3 0.06
36 48 0.89
37 3 0.06
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.44
Consensus pattern (36 bp):
AAGATTTATTTCCCTCAATATTGTTTTTCTTAAAAC
Found at i:3600960 original size:36 final size:36
Alignment explanation
Indices: 3600913--3600998 Score: 109
Period size: 36 Copynumber: 2.4 Consensus size: 36
3600903 ATTGAAAACA
** * * *
3600913 TTTCCCTTGAAATGAGTTTTGTCTCTCTCGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCTCCCTCGAGACAG
3600949 TTTCCCTTGAAACAAATTTTGTCTCCCTCGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCCCTCGAGACAG
* *
3600985 TTTCTCTTGTAACA
1 TTTCCCTTGAAACA
3600999 TAAACATTGA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTCGAGACAG
Found at i:3600989 original size:101 final size:101
Alignment explanation
Indices: 3600734--3601037 Score: 473
Period size: 101 Copynumber: 3.0 Consensus size: 101
3600724 TATCTCACTT
* *
3600734 GAGATAATTTCCCTCGAAACAGAAAAGTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAC
1 GAGATAGTTTCCCTTGAAAC--AAAA-TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAC
3600799 ATTGAAAAACATTTCCCTTGAAATGAGTTTTGTCTCTCTCTC
63 ATTG-AAAACATTTCCCTTGAAATGAGTTTTG--TCTCTCTC
* *
3600841 GAGATAGTTTCCCTTAAAAAAAAATTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATT
1 GAGATAGTTTCCCTTGAAACAAAATTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATT
3600906 GAAAACATTTCCCTTGAAATGAGTTTTGTCTCTCTC
66 GAAAACATTTCCCTTGAAATGAGTTTTGTCTCTCTC
* * *
3600942 GAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTCGAGACAGTTTCTCTTGTAACATAAACATT
1 GAGATAGTTTCCCTTGAAACAAAATTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATT
* *
3601007 GAAAACATTTCCCTTGAAATAAATTTTGTCT
66 GAAAACATTTCCCTTGAAATGAGTTTTGTCT
3601038 TGAAACAAAT
Statistics
Matches: 186, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
101 97 0.52
103 27 0.15
104 42 0.23
105 4 0.02
107 16 0.09
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.35
Consensus pattern (101 bp):
GAGATAGTTTCCCTTGAAACAAAATTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATT
GAAAACATTTCCCTTGAAATGAGTTTTGTCTCTCTC
Found at i:3601041 original size:17 final size:17
Alignment explanation
Indices: 3601019--3601054 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
3601009 AAACATTTCC
*
3601019 CTTGAAATAAATTTTGT
1 CTTGAAACAAATTTTGT
3601036 CTTGAAACAAATTTTGT
1 CTTGAAACAAATTTTGT
3601053 CT
1 CT
3601055 CCCTTGAGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (17 bp):
CTTGAAACAAATTTTGT
Found at i:3601054 original size:82 final size:82
Alignment explanation
Indices: 3600954--3601119 Score: 305
Period size: 82 Copynumber: 2.0 Consensus size: 82
3600944 GATAGTTTCC
*
3600954 CTTGAAACAAATTTTGTCTCCCTCGAGACAGTTTCTCTTGTAACATAAACATTGAAAACATTTCC
1 CTTGAAACAAATTTTGTCTCCCTCGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCC
3601019 CTTGAAATAAATTTTGT
66 CTTGAAATAAATTTTGT
*
3601036 CTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCC
1 CTTGAAACAAATTTTGTCTCCCTCGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCC
*
3601101 CTTGAAATGAATTTTGT
66 CTTGAAATAAATTTTGT
3601118 CT
1 CT
3601120 CTCTTAAGAT
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 81 1.00
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (82 bp):
CTTGAAACAAATTTTGTCTCCCTCGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCC
CTTGAAATAAATTTTGT
Found at i:3601173 original size:183 final size:184
Alignment explanation
Indices: 3600865--3601209 Score: 602
Period size: 183 Copynumber: 1.9 Consensus size: 184
3600855 TAAAAAAAAA
*
3600865 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAGT
1 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAAT
* * * **
3600930 TTTGTCTCTCTCGAGATAGTTTCCCTTGAAACAAATTTTGTCTCCCTCGAGACAGTTTCTCTTGT
66 TTTGTCTCTCTCAAGATAGCTTCCCTTGAAACAAATTTTCTCTCCCTCGAGACAGTTTCTCTTCA
3600995 AACATAAACATTGAAAAC-ATTTCCCTTGAAATAAATTTTGTCTTGAAACAAAT
131 AACATAAACATTGAAAACAATTTCCCTTGAAATAAATTTTGTCTTGAAACAAAT
3601048 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAAT
1 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAAT
* *
3601113 TTTGTCTCTCTTAAGATAGCTTCCCTTGAAACAAATTTTCTCTCCCTTGAGACAGTTTCTCTTCA
66 TTTGTCTCTCTCAAGATAGCTTCCCTTGAAACAAATTTTCTCTCCCTCGAGACAGTTTCTCTTCA
*
3601178 AACATAAACTTTGAAAACAATTTCCCTTGAAA
131 AACATAAACATTGAAAACAATTTCCCTTGAAA
3601210 CAAAATATTT
Statistics
Matches: 152, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
183 139 0.91
184 13 0.09
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.37
Consensus pattern (184 bp):
TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAAT
TTTGTCTCTCTCAAGATAGCTTCCCTTGAAACAAATTTTCTCTCCCTCGAGACAGTTTCTCTTCA
AACATAAACATTGAAAACAATTTCCCTTGAAATAAATTTTGTCTTGAAACAAAT
Found at i:3601333 original size:42 final size:38
Alignment explanation
Indices: 3601280--3601389 Score: 134
Period size: 42 Copynumber: 2.8 Consensus size: 38
3601270 TGGAGGTATT
*
3601280 GTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTTC
1 GTCTCT-TTGAGACAGTTTCCCTTGAAACAAATTTTG---TC
**
3601322 GTCTCTTTTGAGACAACTTCCCTTGAAACAAATTTTGTC
1 GTCTC-TTTGAGACAGTTTCCCTTGAAACAAATTTTGTC
3601361 -TCTC-TTGAGACAGTTTCCCTTGAAACAAA
1 GTCTCTTTGAGACAGTTTCCCTTGAAACAAA
3601390 ATCTTTAAAT
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
36 23 0.37
38 4 0.06
39 2 0.03
42 32 0.52
43 1 0.02
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (38 bp):
GTCTCTTTGAGACAGTTTCCCTTGAAACAAATTTTGTC
Found at i:3601519 original size:67 final size:64
Alignment explanation
Indices: 3601343--3601522 Score: 202
Period size: 65 Copynumber: 2.7 Consensus size: 64
3601333 GACAACTTCC
* *
3601343 CTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTAAATATGTTTTA
1 CTTGAAACAAATTTTGTCTC-CCTGAGACAGTTTCTCTTGAAACAAAATCTTTAAATATGTTTTA
* * *
3601408 CATT-AAACAAATTTTGTCTCCCCTGAGACAATTTCTCTTGAAACACCAATCTTTGAATATGTTT
1 C-TTGAAACAAATTTTGTCT-CCCTGAGACAGTTTCTCTTGAAACA-AAATCTTTAAATATGTTT
3601472 CT-
63 -TA
* * * *
3601474 CTTGAAACAAAATTTTGCCTCCCTAGAGATAGTTTCTTTTCAAACAAAA
1 CTTGAAAC-AAATTTTGTCTCCCT-GAGACAGTTTCTCTTGAAACAAAA
3601523 AAAAAACATT
Statistics
Matches: 97, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
65 39 0.40
66 30 0.31
67 28 0.29
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (64 bp):
CTTGAAACAAATTTTGTCTCCCTGAGACAGTTTCTCTTGAAACAAAATCTTTAAATATGTTTTA
Found at i:3603313 original size:22 final size:21
Alignment explanation
Indices: 3603256--3603314 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 21
3603246 TACCTTTGTT
*
3603256 ATTATTATATATTATTTATTTAC
1 ATTATTATAT-TT-TTTATTAAC
*
3603279 -TTTTTATATTTTTTATTAAC
1 ATTATTATATTTTTTATTAAC
3603299 ATTATTAGTATTTTTT
1 ATTATTA-TATTTTTT
3603315 TACTATTATC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 8 0.26
21 7 0.23
22 16 0.52
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (21 bp):
ATTATTATATTTTTTATTAAC
Found at i:3603396 original size:17 final size:18
Alignment explanation
Indices: 3603360--3603402 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
3603350 ACGTACATAT
*
3603360 TTTATCATTTTTTGTGTTA
1 TTTAT-ATTTTTTATGTTA
3603379 TTTATATTTTTTAT-TTA
1 TTTATATTTTTTATGTTA
*
3603396 TATATAT
1 TTTATAT
3603403 ATATATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 9 0.41
18 8 0.36
19 5 0.23
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.70
Consensus pattern (18 bp):
TTTATATTTTTTATGTTA
Found at i:3603399 original size:2 final size:2
Alignment explanation
Indices: 3603394--3603532 Score: 114
Period size: 2 Copynumber: 71.5 Consensus size: 2
3603384 ATTTTTTATT
3603394 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
** * * *
3603436 TA TA TA TA TA TA T- TA GG T- TC T- TCA -A TA T- TA T- TA CCA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA -TA TA
* * *
3603474 TT TA GTA T- TT TA T- TC TA CTA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
3603516 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
3603533 TTCATTATTT
Statistics
Matches: 116, Mismatches: 9, Indels: 24
0.78 0.06 0.16
Matches are distributed among these distances:
1 8 0.07
2 103 0.89
3 5 0.04
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3603816 original size:21 final size:22
Alignment explanation
Indices: 3603762--3603816 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
3603752 TGCTATTACT
*
3603762 TTTGTTCATTTTACTTTATTTCA
1 TTTGTT-ATTTTACTTTACTTCA
*
3603785 TTTGTTTTTTTACTTT-CTTCA
1 TTTGTTATTTTACTTTACTTCA
3603806 TTAT-TTATTTT
1 TT-TGTTATTTT
3603817 TCATTCATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 12 0.43
22 10 0.36
23 6 0.21
ACGTcount: A:0.15, C:0.11, G:0.04, T:0.71
Consensus pattern (22 bp):
TTTGTTATTTTACTTTACTTCA
Found at i:3611575 original size:20 final size:21
Alignment explanation
Indices: 3611552--3611634 Score: 87
Period size: 21 Copynumber: 3.9 Consensus size: 21
3611542 TTGGTGCAGA
*
3611552 GGGAATCGATTCCCCCCTGA-
1 GGGAACCGATTCCCCCCTGAG
*
3611572 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC-CTG-AG
**
3611595 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCCTGAG
* *
3611616 GGGAATCGATACCCCCCTG
1 GGGAACCGATTCCCCCCTG
3611635 GGGTTCTGCT
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
20 15 0.29
21 19 0.37
22 1 0.02
23 16 0.31
ACGTcount: A:0.22, C:0.36, G:0.25, T:0.17
Consensus pattern (21 bp):
GGGAACCGATTCCCCCCTGAG
Found at i:3616145 original size:2 final size:2
Alignment explanation
Indices: 3616138--3616167 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3616128 ATAATTTCTC
3616138 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
3616168 GTGCATTTAC
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):
AT
Found at i:3622378 original size:28 final size:29
Alignment explanation
Indices: 3622358--3622412 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
3622348 TTATTTCAAG
*
3622358 TTAATTACTAAATTTT-TTTTATTGCATA
1 TTAACTACTAAATTTTATTTTATTGCATA
*
3622386 TTAACTACTAACTTTTATTTTATTGCA
1 TTAACTACTAAATTTTATTTTATTGCA
3622413 CTTTAACCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 14 0.58
29 10 0.42
ACGTcount: A:0.31, C:0.11, G:0.04, T:0.55
Consensus pattern (29 bp):
TTAACTACTAAATTTTATTTTATTGCATA
Found at i:3622657 original size:16 final size:16
Alignment explanation
Indices: 3622636--3622681 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
3622626 ACTCTGCTAA
* *
3622636 TTTCTAACGGCTAACT
1 TTTCTAACAGCTAACC
*
3622652 TTTCTAACAACTAACC
1 TTTCTAACAGCTAACC
*
3622668 TTTCTAACCGCTAA
1 TTTCTAACAGCTAA
3622682 TTACTAACTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.30, C:0.28, G:0.07, T:0.35
Consensus pattern (16 bp):
TTTCTAACAGCTAACC
Found at i:3622695 original size:30 final size:31
Alignment explanation
Indices: 3622636--3622700 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
3622626 ACTCTGCTAA
* *
3622636 TTTCTAACGGCTAACTTTTCTAACAACTAACC
1 TTTCTAACCGCTAAC-TTACTAACAACTAACC
*
3622668 TTTCTAACCGCTAA-TTACTAACTACTAACC
1 TTTCTAACCGCTAACTTACTAACAACTAACC
3622698 TTT
1 TTT
3622701 TATTTATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 17 0.57
32 13 0.43
ACGTcount: A:0.31, C:0.28, G:0.05, T:0.37
Consensus pattern (31 bp):
TTTCTAACCGCTAACTTACTAACAACTAACC
Found at i:3624256 original size:23 final size:23
Alignment explanation
Indices: 3624230--3624290 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
3624220 CACCACAGCT
* *
3624230 CGTATAAATGCACCGGAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
3624253 CGTAGAATTGCACTGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
3624276 CGTAGAAATGTACCG
1 CGTAGAAATGCACCG
3624291 TAGTACCATA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.30, C:0.23, G:0.28, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:3624962 original size:2 final size:2
Alignment explanation
Indices: 3624955--3625011 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
3624945 ACTTATAAAC
3624955 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
3624997 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
3625012 CTTCTATTAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3625872 original size:19 final size:19
Alignment explanation
Indices: 3625848--3625894 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
3625838 CTTTAACATG
3625848 TGCATCGATGCACTACCCA
1 TGCATCGATGCACTACCCA
*
3625867 TGCATCGATGTACTACCCA
1 TGCATCGATGCACTACCCA
3625886 TGCATCGAT
1 TGCATCGAT
3625895 ACATCAATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCACTACCCA
Found at i:3629361 original size:23 final size:23
Alignment explanation
Indices: 3629324--3629387 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
3629314 CATCTTGTAT
*
3629324 AAATGCACCGGAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACGTAG
* *
3629347 AATTGCACCGAAGTGCCGCGTAG
1 AAATGCACCGAAGTGCCACGTAG
*
3629370 AAATGCACCGTAGTGCCA
1 AAATGCACCGAAGTGCCA
3629388 TATAAGATGT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.30, C:0.27, G:0.28, T:0.16
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACGTAG
Found at i:3634407 original size:23 final size:23
Alignment explanation
Indices: 3634381--3634449 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
3634371 CACCACAGCT
*
3634381 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
3634404 CGTAGAATTGCACCGGAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
*
3634427 CGTAGAAATGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
3634450 TATAAGATGT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:3635113 original size:2 final size:2
Alignment explanation
Indices: 3635106--3635139 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3635096 ATTTTTAAAC
3635106 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
3635140 TACTTCTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3639399 original size:23 final size:23
Alignment explanation
Indices: 3639373--3639441 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 23
3639363 CACCACAGCT
* * *
3639373 CGTATAAATGCATCGGAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
3639396 CGTAGAATTGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
* * *
3639419 CGTAGAAATTCACTGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
3639442 TATAAGATGT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.22
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:3645133 original size:18 final size:18
Alignment explanation
Indices: 3645107--3645221 Score: 64
Period size: 18 Copynumber: 6.4 Consensus size: 18
3645097 ATATCAAATC
*
3645107 AAAGTAAAAAGAAAAAAG
1 AAAGAAAAAAGAAAAAAG
**
3645125 AAAGAAAAAAGAGCAAAG
1 AAAGAAAAAAGAAAAAAG
*
3645143 --AG--AAAA-CAAAAAG
1 AAAGAAAAAAGAAAAAAG
*
3645156 TAAAGAGAAAAG-AAAAAG
1 -AAAGAAAAAAGAAAAAAG
* *
3645174 TAAAGAGAAAAGAAGCAAAG
1 -AAAGAAAAAAGAA-AAAAG
3645194 AAA-AAAAAAGAAGAATAAAG
1 AAAGAAAAAAG-A-AA-AAAG
3645214 AAAGAAAA
1 AAAGAAAA
3645222 TGGATCAAGT
Statistics
Matches: 76, Mismatches: 9, Indels: 21
0.72 0.08 0.20
Matches are distributed among these distances:
13 4 0.05
14 4 0.05
16 4 0.05
18 43 0.57
19 5 0.07
20 12 0.16
21 4 0.05
ACGTcount: A:0.75, C:0.03, G:0.19, T:0.03
Consensus pattern (18 bp):
AAAGAAAAAAGAAAAAAG
Found at i:3645135 original size:25 final size:23
Alignment explanation
Indices: 3645107--3645205 Score: 74
Period size: 27 Copynumber: 4.0 Consensus size: 23
3645097 ATATCAAATC
3645107 AAAGTAAAAAGAAAAAAGAAAGAAA
1 AAAG-AAAAAGAAAAAA-AAAGAAA
*
3645132 AAAGAGCAAAGAGAAAACAAAAAGTAA
1 AAAGA--AAA-AGAAAA-AAAAAGAAA
* * *
3645159 AGAG-AAAAGAAAAAGTAAAGAGA
1 AAAGAAAAAGAAAAA-AAAAGAAA
3645182 AAAGAAGCAAAGAAAAAAAAAGAA
1 AAAGAA--AAAGAAAAAAAAAGAA
3645206 GAATAAAGAA
Statistics
Matches: 58, Mismatches: 8, Indels: 16
0.71 0.10 0.20
Matches are distributed among these distances:
22 1 0.02
23 14 0.24
24 5 0.09
25 9 0.16
26 12 0.21
27 15 0.26
28 2 0.03
ACGTcount: A:0.75, C:0.03, G:0.19, T:0.03
Consensus pattern (23 bp):
AAAGAAAAAGAAAAAAAAAGAAA
Found at i:3648076 original size:37 final size:37
Alignment explanation
Indices: 3647959--3648092 Score: 125
Period size: 37 Copynumber: 3.6 Consensus size: 37
3647949 GTTTCTCTCG
* * *
3647959 AAACAAAGTTTTGTCTCGCTAGAGACAGTTTTCCTT-G
1 AAACAAA-TTTTGTCTCGCTTGAGACAGTTTTTCTTAA
* * *
3647996 AAACAAA-ATTG-ATCGAACTTGAGATTA-TTTTT-TTAA
1 AAACAAATTTTGTCTCG--CTTGAGA-CAGTTTTTCTTAA
3648032 AAACAAATTTTGTCTCGCTTGAGACAGTTTTTCTTAA
1 AAACAAATTTTGTCTCGCTTGAGACAGTTTTTCTTAA
* *
3648069 AAACAAATTTCGTCTCACTTGAGA
1 AAACAAATTTTGTCTCGCTTGAGA
3648093 TATTCTTCCT
Statistics
Matches: 78, Mismatches: 11, Indels: 16
0.74 0.10 0.15
Matches are distributed among these distances:
34 3 0.04
35 6 0.08
36 29 0.37
37 37 0.47
38 3 0.04
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.37
Consensus pattern (37 bp):
AAACAAATTTTGTCTCGCTTGAGACAGTTTTTCTTAA
Found at i:3648105 original size:37 final size:35
Alignment explanation
Indices: 3648012--3648105 Score: 107
Period size: 37 Copynumber: 2.5 Consensus size: 35
3648002 AATTGATCGA
* *
3648012 ACTTGAGATTATTTTTTTAAAAACAAATTTTGTCTC
1 ACTTGAGA-TATTTTCTTAAAAACAAATTTCGTCTC
* *
3648048 GCTTGAGACAGTTTTTCTTAAAAACAAATTTCGTCTC
1 ACTTGAGATA--TTTTCTTAAAAACAAATTTCGTCTC
3648085 ACTTGAGATATTCTTCCTTAA
1 ACTTGAGATATT-TT-CTTAA
3648106 GACACGAACA
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
35 3 0.06
36 9 0.19
37 36 0.75
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.43
Consensus pattern (35 bp):
ACTTGAGATATTTTCTTAAAAACAAATTTCGTCTC
Found at i:3648187 original size:67 final size:66
Alignment explanation
Indices: 3648058--3648226 Score: 184
Period size: 67 Copynumber: 2.5 Consensus size: 66
3648048 GCTTGAGACA
* * * *
3648058 GTTTTTCTTAAAAACAAATTTCGTCTCACTTGAGATATTCTTCCTTAAGACACGAACATTTGAAA
1 GTTTTTCTTAAAAA-AAATTTCATCTCACTTGAGATATTCTCCCCTAAAACACGAACATTTGAAA
3648123 TT
65 TT
*
3648125 GTTTTTCTTAAAAATAAATTTCATCTCACTTGAGATAGTT-TCCCCTAGAAATAC-AA-ATTTTG
1 GTTTTTCTTAAAAA-AAATTTCATCTCACTTGAGATA-TTCTCCCCTA-AAACACGAACA-TTTG
3648187 AAATT
62 AAATT
** *
3648192 GTTTCACTTGAAACAAAATTT-ATCTCACTTGAGAT
1 GTTTTTCTT-AAAAAAAATTTCATCTCACTTGAGAT
3648227 TGTTCTCAAA
Statistics
Matches: 89, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
66 15 0.17
67 64 0.72
68 10 0.11
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (66 bp):
GTTTTTCTTAAAAAAAATTTCATCTCACTTGAGATATTCTCCCCTAAAACACGAACATTTGAAAT
T
Found at i:3648439 original size:104 final size:102
Alignment explanation
Indices: 3648128--3648470 Score: 276
Period size: 99 Copynumber: 3.3 Consensus size: 102
3648118 TGAAATTGTT
* * * * * *
3648128 TTTCTTAAAAATAAATTTCATCTCACTTGAGATAGTTTCCCCT-AGAAATACAAATTTTGAAATT
1 TTTCTTAAAAACAAATTTCTTCTCACTTGAGACAATTTTCCCTCA-AAACACAAA-TTTGAAATT
**
3648192 GTTTCACTTGAAACAAAATTT-AT-CTCAC-TTGAGATTG
64 GTTTCACTTGAAACAAAATTTGATAAAC-CTTTGAGATTG
* ** * * * * *
3648229 -TTC-TCAAAACAAATTTCGCCTCACTTAAGACAGCTTTT-CTTCGAAACATAAATTCTGAAATT
1 TTTCTTAAAAACAAATTTCTTCTCACTTGAGACA-ATTTTCCCTCAAAACACAAATT-TGAAATT
**
3648291 GTTTCACTTGAAA-AAAA-TTGA-AAATATTTGAGATTG
64 GTTTCACTTGAAACAAAATTTGATAAACCTTTGAGATTG
*
3648327 TTTTTTTCTTAAAAACAAATTTCTTCTCGCTTGAGACAATTTTCCCTCAAAACACAAAATTTGGA
1 ----TTTCTTAAAAACAAATTTCTTCTCACTTGAGACAATTTTCCCTCAAAACAC-AAATTT-GA
*
3648392 AATTGTTTCATTTGAAACAAAATTTGATAAACCTTTGAGATTG
60 AATTGTTTCACTTGAAACAAAATTTGATAAACCTTTGAGATTG
* * *
3648435 TTTCTCACGAAACAAAGTTT-TGTCTCGCTTGAGACA
1 TTTCTTA-AAAACAAA-TTTCT-TCTCACTTGAGACA
3648471 GTTTCTCTTG
Statistics
Matches: 191, Mismatches: 30, Indels: 37
0.74 0.12 0.14
Matches are distributed among these distances:
97 2 0.01
98 16 0.08
99 52 0.27
100 6 0.03
103 7 0.04
104 39 0.20
105 31 0.16
106 21 0.11
107 4 0.02
108 13 0.07
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (102 bp):
TTTCTTAAAAACAAATTTCTTCTCACTTGAGACAATTTTCCCTCAAAACACAAATTTGAAATTGT
TTCACTTGAAACAAAATTTGATAAACCTTTGAGATTG
Found at i:3648484 original size:37 final size:37
Alignment explanation
Indices: 3648434--3648552 Score: 92
Period size: 37 Copynumber: 3.4 Consensus size: 37
3648424 CTTTGAGATT
*
3648434 GTTTCTCACGAAACAAAGTTTTGTCTCGCTTGAGACA
1 GTTTCTCTCGAAACAAAGTTTTGTCTCGCTTGAGACA
* * * **
3648471 GTTTCTCTTGAAACATAA------AC-C-TTTGAGATT
1 GTTTCTCTCGAAACA-AAGTTTTGTCTCGCTTGAGACA
*
3648501 GTTTGTCTCGAAACAAAGTTTTGTCTCGCTTGAGACA
1 GTTTCTCTCGAAACAAAGTTTTGTCTCGCTTGAGACA
* *
3648538 ATTTCTCTTGAAACA
1 GTTTCTCTCGAAACA
3648553 TAAACCCTTG
Statistics
Matches: 58, Mismatches: 15, Indels: 18
0.64 0.16 0.20
Matches are distributed among these distances:
29 2 0.03
30 19 0.33
31 1 0.02
32 1 0.02
35 1 0.02
36 1 0.02
37 31 0.53
38 2 0.03
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (37 bp):
GTTTCTCTCGAAACAAAGTTTTGTCTCGCTTGAGACA
Found at i:3648485 original size:105 final size:100
Alignment explanation
Indices: 3648148--3648504 Score: 273
Period size: 105 Copynumber: 3.5 Consensus size: 100
3648138 ATAAATTTCA
* * *
3648148 TCTCACTTGAGATAGTTTCCCCTAGAAATACAAATTTTGAAATTGTTTCACTTGAAACAAAATTT
1 TCTCACTTGAGACAGTTT-CCCTTGAAACACAAA-TTTGAAATTGTTTCACTTGAAACAAAATTT
** *
3648213 -AT-CTCAC-TTGAGATTG-TTCTCAAAACAAATTTCG
64 GATAAAC-CTTTGAGATTGTTTCTCAAAACAAATTTTG
* * * *
3648247 CCTCACTTAAGACAGCTTT-TCTTCGAAACATAAATTCTGAAATTGTTTCACTTGAAA-AAAA-T
1 TCTCACTTGAGACAG-TTTCCCTT-GAAACACAAATT-TGAAATTGTTTCACTTGAAACAAAATT
** *
3648309 TGA-AAATATTTGAGATTGTTTTTTTCTTAAAAACAAATTTCT-
63 TGATAAACCTTTGAGATTG----TTTC-TCAAAACAAATTT-TG
* * ** *
3648351 TCTCGCTTGAGACAATTTTCCCTCAAAACACAAAATTTGGAAATTGTTTCATTTGAAACAAAATT
1 TCTCACTTGAGAC-AGTTTCCCTTGAAACAC-AAATTT-GAAATTGTTTCACTTGAAACAAAATT
3648416 TGATAAACCTTTGAGATTGTTTCTCACGAAACAAAGTTTTG
63 TGATAAACCTTTGAGATTGTTTCTCA--AAACAAA-TTTTG
* * * *
3648457 TCTCGCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTT
1 TCTCACTTGAGACAGTTTCCCTTGAAACACAAA--TTTGAAATTGTTT
3648505 GTCTCGAAAC
Statistics
Matches: 201, Mismatches: 31, Indels: 46
0.72 0.11 0.17
Matches are distributed among these distances:
97 2 0.01
98 18 0.09
99 40 0.20
100 3 0.01
103 5 0.02
104 38 0.19
105 55 0.27
106 23 0.11
107 4 0.02
108 13 0.06
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (100 bp):
TCTCACTTGAGACAGTTTCCCTTGAAACACAAATTTGAAATTGTTTCACTTGAAACAAAATTTGA
TAAACCTTTGAGATTGTTTCTCAAAACAAATTTTG
Found at i:3648491 original size:67 final size:67
Alignment explanation
Indices: 3648418--3648661 Score: 339
Period size: 67 Copynumber: 3.6 Consensus size: 67
3648408 ACAAAATTTG
* *
3648418 ATAAACCTTTGAGATTGTTTCTCACGAAACAAAGTTTTGTCTCGCTTGAGACAGTTTCTCTTGAA
1 ATAAACCTTTGAGATTGTTTCTCTCGAAACAAAGTTTTGTCTCGCTTGAGACAATTTCTCTTGAA
3648483 AC
66 AC
*
3648485 ATAAACCTTTGAGATTGTTTGTCTCGAAACAAAGTTTTGTCTCGCTTGAGACAATTTCTCTTGAA
1 ATAAACCTTTGAGATTGTTTCTCTCGAAACAAAGTTTTGTCTCGCTTGAGACAATTTCTCTTGAA
3648550 AC
66 AC
* * * * *
3648552 ATAAACCCTTGAGAATTGTTTCTCTCGAAACAAAGTTTCGTCTCTCTTGAGATAATTATCCCTTG
1 ATAAACCTTTGAG-ATTGTTTCTCTCGAAACAAAGTTTTGTCTCGCTTGAGACAATT-TCTCTTG
3648617 AAAC
64 AAAC
* * * * *
3648621 ATAAA-TTTTGA-AATGTTTCACTCGAAACAAAATTTTATCTC
1 ATAAACCTTTGAGATTGTTTCTCTCGAAACAAAGTTTTGTCTC
3648662 ACCCGAGATA
Statistics
Matches: 159, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
66 25 0.16
67 76 0.48
68 43 0.27
69 15 0.09
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (67 bp):
ATAAACCTTTGAGATTGTTTCTCTCGAAACAAAGTTTTGTCTCGCTTGAGACAATTTCTCTTGAA
AC
Found at i:3648588 original size:135 final size:133
Alignment explanation
Indices: 3648418--3648661 Score: 337
Period size: 135 Copynumber: 1.8 Consensus size: 133
3648408 ACAAAATTTG
* * * *
3648418 ATAAACCTTTGAGATTGTTTCTCACGAAACAAAGTTTTGTCTCGCTTGAGACAGTT-TCTCTTGA
1 ATAAACCCTTGAGATTGTTTCTCACGAAACAAAGTTTCGTCTCGCTTGAGACAATTATCCCTTGA
* ** * *
3648482 AACATAAACCTTTGAGATTGTTTGTCTCGAAACAAAGTTTTGTCTCGCTTGAGACAATTTCTCTT
66 AACATAAA-CTTTGA-AATGTTTCACTCGAAACAAAATTTTATCTCGCTTGAGACAATTTCTCTT
3648547 GAAAC
129 GAAAC
* * *
3648552 ATAAACCCTTGAGAATTGTTTCTCTCGAAACAAAGTTTCGTCTCTCTTGAGATAATTATCCCTTG
1 ATAAACCCTTGAG-ATTGTTTCTCACGAAACAAAGTTTCGTCTCGCTTGAGACAATTATCCCTTG
*
3648617 AAACATAAATTTTGAAATGTTTCACTCGAAACAAAATTTTATCTC
65 AAACATAAACTTTGAAATGTTTCACTCGAAACAAAATTTTATCTC
3648662 ACCCGAGATA
Statistics
Matches: 95, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
134 37 0.39
135 43 0.45
136 15 0.16
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (133 bp):
ATAAACCCTTGAGATTGTTTCTCACGAAACAAAGTTTCGTCTCGCTTGAGACAATTATCCCTTGA
AACATAAACTTTGAAATGTTTCACTCGAAACAAAATTTTATCTCGCTTGAGACAATTTCTCTTGA
AAC
Found at i:3649327 original size:139 final size:139
Alignment explanation
Indices: 3648783--3649319 Score: 655
Period size: 139 Copynumber: 3.9 Consensus size: 139
3648773 AACTGACTAT
* * * * *
3648783 ATCTCCTCAACGCGTAAGAGCAGCGTCATCCTCAGGCAACCAAACTTCCTCATCACTTAAGAACC
1 ATCTCCTCAACGCGTAGGAGCAACGTCATCCTCAGGCAATCAGACTTCCTCATCACGTAAGAACC
* * * * * * * *
3648848 GTATTTTCTCCAAATTATCCCTAAAGACAGA-TAAACGTCCTCATCACGTAAGAATAATGTCATC
66 GTGTTGTCTCCAAAGTATCCCTAAAGAC-GACTAGACATCCTCATCACGTAGGAACAATGTCGTC
* *
3648912 CATCGACTAG
130 CACCGACCAG
* * * * *
3648922 ATCTCCTCAACGTGTAGGAGCAGCGTCATCCTCAGGCAATCAGACTTCCTCGTCATGTAAAAATC
1 ATCTCCTCAACGCGTAGGAGCAACGTCATCCTCAGGCAATCAGACTTCCTCATCACGTAAGAA-C
3648987 C-TGTTGTCTCCAAAGTATCCCTAAAGACGACTAGACATCCTCATCACGTAGGAACAATGTCGTC
65 CGTGTTGTCTCCAAAGTATCCCTAAAGACGACTAGACATCCTCATCACGTAGGAACAATGTCGTC
*
3649051 CACTGACCAG
130 CACCGACCAG
* * ** *
3649061 ATCTTCTCAACGCGTAGGAACAACGTCATCCTCAGGCAATCAGACTTCCTCATCACGTGGGAATC
1 ATCTCCTCAACGCGTAGGAGCAACGTCATCCTCAGGCAATCAGACTTCCTCATCACGTAAGAACC
* * ** * * *
3649126 GTGTTCTCTCTAAAGTATCCCTAAAGACGACTAGACGGCCTTATCACGTAGGAATAATGTTGTCC
66 GTGTTGTCTCCAAAGTATCCCTAAAGACGACTAGACATCCTCATCACGTAGGAACAATGTCGTCC
*
3649191 ACCGGCCAG
131 ACCGACCAG
* * ** * *
3649200 TTCTCCTCAACGCGTAGGAGCAACTTCATCCTCAGGCAATCAGACTTAATTATCACGTAGGAACC
1 ATCTCCTCAACGCGTAGGAGCAACGTCATCCTCAGGCAATCAGACTTCCTCATCACGTAAGAACC
* **
3649265 GTGTTGTCTCCAAAGTATCTCTAAAGACGGTTAGACATCCTCATCACGTAGGAAC
66 GTGTTGTCTCCAAAGTATCCCTAAAGACGACTAGACATCCTCATCACGTAGGAAC
3649320 CGTGTTGTTT
Statistics
Matches: 339, Mismatches: 56, Indels: 6
0.85 0.14 0.01
Matches are distributed among these distances:
138 3 0.01
139 334 0.99
140 2 0.01
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (139 bp):
ATCTCCTCAACGCGTAGGAGCAACGTCATCCTCAGGCAATCAGACTTCCTCATCACGTAAGAACC
GTGTTGTCTCCAAAGTATCCCTAAAGACGACTAGACATCCTCATCACGTAGGAACAATGTCGTCC
ACCGACCAG
Found at i:3649337 original size:56 final size:56
Alignment explanation
Indices: 3649251--3649371 Score: 163
Period size: 56 Copynumber: 2.2 Consensus size: 56
3649241 AGACTTAATT
**
3649251 ATCACGTAGGAACCGTGTTGTCTCCAAAGTA-TCTCTAAAGACGGTTAGACATCCTC
1 ATCACGTAGGAACCGTGTTGTCTCCAAAGTATTC-CTAAAGACGACTAGACATCCTC
* * * *
3649307 ATCACGTAGGAACCGTGTTGTTTTCAAAGTATTCCTTAAGACGACTAGACGTCCTC
1 ATCACGTAGGAACCGTGTTGTCTCCAAAGTATTCCTAAAGACGACTAGACATCCTC
*
3649363 ATCATGTAG
1 ATCACGTAG
3649372 AAACAATATC
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
56 55 0.96
57 2 0.04
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (56 bp):
ATCACGTAGGAACCGTGTTGTCTCCAAAGTATTCCTAAAGACGACTAGACATCCTC
Found at i:3649439 original size:195 final size:195
Alignment explanation
Indices: 3649102--3649514 Score: 553
Period size: 195 Copynumber: 2.1 Consensus size: 195
3649092 TCAGGCAATC
* * *
3649102 AGACTTCCTCATCACGTGGGAATCGTGTTCTCTCTAAAGTATCCCTAAAGACGACTAGACGGCCT
1 AGACATCCTCATCACGTAGGAACCGTGTTCTCTCTAAAGTATCCCTAAAGACGACTAGACGGCCT
* * * * * * *
3649167 TATCACGTAGGAATAATGTTGTCCACCGGCCAGTTCTCCTCAACGCGTAGGAGCAACTTCATCCT
66 CATCACGTAGAAACAATATCGTCCACCGACCAGTTCTCCTCAACGCGTAGGAGCAACGTCATCCT
* * *
3649232 CAGGCAATCAGACTTAATTATCACGTAGGAACCGTGTTGTCTCCAAAGTATCTCTAAAGACGGTT
131 CAGGCAATCAGACTTAATCATCACGTAGGAACCGTGTTGTCTCCAAAGTATCCCTAAAGAAGGTT
* * * * *
3649297 AGACATCCTCATCACGTAGGAACCGTGTTGT-TTTCAAAGTATTCCTTAAGACGACTAGACGTCC
1 AGACATCCTCATCACGTAGGAACCGTGTTCTCTCT-AAAGTATCCCTAAAGACGACTAGACGGCC
* * *
3649361 TCATCATGTAGAAACAATATCGTCCACCGACCA-TATCTCGTCAACGCGTAGGAGCAGCGTCATC
65 TCATCACGTAGAAACAATATCGTCCACCGACCAGT-TCTCCTCAACGCGTAGGAGCAACGTCATC
**
3649425 CT-ATGGCAATCAGACTTTCTCATCACGTAGGAACCGTGTTGTCTCCAAAGTATCCCTAAAGAAG
129 CTCA-GGCAATCAGACTTAATCATCACGTAGGAACCGTGTTGTCTCCAAAGTATCCCTAAAGAAG
3649489 GTT
193 GTT
* *
3649492 AAACATCATCATCACGTAGGAAC
1 AGACATCCTCATCACGTAGGAAC
3649515 AATGTCATCC
Statistics
Matches: 190, Mismatches: 25, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
194 4 0.02
195 186 0.98
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (195 bp):
AGACATCCTCATCACGTAGGAACCGTGTTCTCTCTAAAGTATCCCTAAAGACGACTAGACGGCCT
CATCACGTAGAAACAATATCGTCCACCGACCAGTTCTCCTCAACGCGTAGGAGCAACGTCATCCT
CAGGCAATCAGACTTAATCATCACGTAGGAACCGTGTTGTCTCCAAAGTATCCCTAAAGAAGGTT
Found at i:3649562 original size:139 final size:139
Alignment explanation
Indices: 3649297--3649840 Score: 581
Period size: 139 Copynumber: 3.9 Consensus size: 139
3649287 AAAGACGGTT
* * * * * * * *
3649297 AGACATCCTCATCACGTAGGAACCGTGTTGTTTTCAAAGTATTCCTTAAGACGACTAGACGTCCT
1 AGACTTCCTCATCACGTAGGAACCATGTTGTCTCCAAAGTATCCCTAAAGAAGGCTAGACGTCCT
* * * * *
3649362 CATCATGTAGAAACAATATCGTCCACCGACCATATCTCGTCAACGCGTAGGAGCAGCGTCATCCT
66 CATCACGTAGAAACAATGTCATCCACCGACCAGATCTCCTCAACGCGTAGGAGCAGCGTCATCCT
3649427 -ATGGCAATC
131 CA-GGCAATC
* * * * * *
3649436 AGACTTTCTCATCACGTAGGAACCGTGTTGTCTCCAAAGTATCCCTAAAGAAGGTTAAACATCAT
1 AGACTTCCTCATCACGTAGGAACCATGTTGTCTCCAAAGTATCCCTAAAGAAGGCTAGACGTCCT
* * * * * ** *
3649501 CATCACGTAGGAACAATGTCATCCACCAACCAGATCTCCTCAATGTGTAAGAGTTGTGTCATCCT
66 CATCACGTAGAAACAATGTCATCCACCGACCAGATCTCCTCAACGCGTAGGAGCAGCGTCATCCT
3649566 CAGGCAATC
131 CAGGCAATC
** *
3649575 AGACTTCCTCATCACGTAGGAACCATAATGTCTCCAAAGTATCCCTTAAGAAGGCTAGACGTCCT
1 AGACTTCCTCATCACGTAGGAACCATGTTGTCTCCAAAGTATCCCTAAAGAAGGCTAGACGTCCT
* * * * * * *
3649640 TATCATGTAAAAACAATGTCATCCACTGAGCAGATCTCCTTAACGCGTAGGAGCAGCGTTATCCT
66 CATCACGTAGAAACAATGTCATCCACCGACCAGATCTCCTCAACGCGTAGGAGCAGCGTCATCCT
*
3649705 CAAGCAATC
131 CAGGCAATC
* * * * * *
3649714 AGACTTCCTCATCACATAAGAATCATGTTTTCTCCAGAGTATCCTTAAA-AACGGCTAGACGTCC
1 AGACTTCCTCATCACGTAGGAACCATGTTGTCTCCAAAGTATCCCTAAAGAA-GGCTAGACGTCC
* * * * * * *
3649778 TCATCACATATG-AACAATGTCGTCCACCGATCATATCTCCTCAACCCGTATGAGCAGTGTCAT
65 TCATCACGTA-GAAACAATGTCATCCACCGACCAGATCTCCTCAACGCGTAGGAGCAGCGTCAT
3649841 AAAATATAAT
Statistics
Matches: 330, Mismatches: 72, Indels: 6
0.81 0.18 0.01
Matches are distributed among these distances:
138 2 0.01
139 327 0.99
140 1 0.00
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (139 bp):
AGACTTCCTCATCACGTAGGAACCATGTTGTCTCCAAAGTATCCCTAAAGAAGGCTAGACGTCCT
CATCACGTAGAAACAATGTCATCCACCGACCAGATCTCCTCAACGCGTAGGAGCAGCGTCATCCT
CAGGCAATC
Found at i:3649609 original size:334 final size:334
Alignment explanation
Indices: 3648988--3649644 Score: 825
Period size: 334 Copynumber: 2.0 Consensus size: 334
3648978 GTAAAAATCC
* *
3648988 TGTTGTCTCCAAAGTATCCCTAAAGACGACTAGACATCCTCATCACGTAGGAACAATGTCGTCCA
1 TGTTGTCTCCAAAGTATCCCTAAAGACGACTAGACATCCTCATCACGTAGAAACAATATCGTCCA
*
3649053 CTGACCAGATCTTCTCAACGCGTAGGAACAACGTCATCCTCAGGCAATCAGACTTCCTCATCACG
66 CCGACCAGATCTTCTCAACGCGTAGGAACAACGTCATCCTCAGGCAATCAGACTTCCTCATCACG
* * * * * * * * *
3649118 TGGGAATCGTGTTCTCTCTAAAGTATCCCTAAAGACGACTAGACGGCCTTATCACGTAGGAATAA
131 TAGGAACCGTGTTCTCTCCAAAGTATCCCTAAAGAAGACTAAACAGCATCATCACGTAGGAACAA
** ** * *
3649183 TGTTGTCCACCGGCCAGTTCTCCTCAACGCGTAGGAGCAACTTCATCCTCAGGCAATCAGACTTA
196 TGTCATCCACCAACCAGATCTCCTCAACGCGTAAGAGCAACTTCATCCTCAGGCAATCAGACTTA
* * ** * * *
3649248 ATTATCACGTAGGAACCGTGTTGTCTCCAAAGTATCTCTAAAGACGGTTAGACATCCTCATCACG
261 ATCATCACGTAGGAACCATAATGTCTCCAAAGTATCCCTAAAGAAGGCTAGACATCCTCATCACG
3649313 TAGGAACCG
326 TAGGAACCG
* * * * * *
3649322 TGTTGTTTTCAAAGTATTCCTTAAGACGACTAGACGTCCTCATCATGTAGAAACAATATCGTCCA
1 TGTTGTCTCCAAAGTATCCCTAAAGACGACTAGACATCCTCATCACGTAGAAACAATATCGTCCA
* * * *
3649387 CCGACCATATC-TCGTCAACGCGTAGGAGCAGCGTCATCCT-ATGGCAATCAGACTTTCTCATCA
66 CCGACCAGATCTTC-TCAACGCGTAGGAACAACGTCATCCTCA-GGCAATCAGACTTCCTCATCA
* ** *
3649450 CGTAGGAACCGTGTTGTCTCCAAAGTATCCCTAAAGAAGGTTAAACATCATCATCACGTAGGAAC
129 CGTAGGAACCGTGTTCTCTCCAAAGTATCCCTAAAGAAGACTAAACAGCATCATCACGTAGGAAC
* * ***
3649515 AATGTCATCCACCAACCAGATCTCCTCAATGTGTAAGAG-TTGTGTCATCCTCAGGCAATCAGAC
194 AATGTCATCCACCAACCAGATCTCCTCAACGCGTAAGAGCAACT-TCATCCTCAGGCAATCAGAC
** * * *
3649579 TTCCTCATCACGTAGGAACCATAATGTCTCCAAAGTATCCCTTAAGAAGGCTAGACGTCCTTATC
258 TTAATCATCACGTAGGAACCATAATGTCTCCAAAGTATCCCTAAAGAAGGCTAGACATCCTCATC
3649644 A
323 A
3649645 TGTAAAAACA
Statistics
Matches: 271, Mismatches: 49, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
333 4 0.01
334 267 0.99
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.25
Consensus pattern (334 bp):
TGTTGTCTCCAAAGTATCCCTAAAGACGACTAGACATCCTCATCACGTAGAAACAATATCGTCCA
CCGACCAGATCTTCTCAACGCGTAGGAACAACGTCATCCTCAGGCAATCAGACTTCCTCATCACG
TAGGAACCGTGTTCTCTCCAAAGTATCCCTAAAGAAGACTAAACAGCATCATCACGTAGGAACAA
TGTCATCCACCAACCAGATCTCCTCAACGCGTAAGAGCAACTTCATCCTCAGGCAATCAGACTTA
ATCATCACGTAGGAACCATAATGTCTCCAAAGTATCCCTAAAGAAGGCTAGACATCCTCATCACG
TAGGAACCG
Found at i:3649688 original size:278 final size:278
Alignment explanation
Indices: 3649297--3649821 Score: 676
Period size: 278 Copynumber: 1.9 Consensus size: 278
3649287 AAAGACGGTT
* ** * * * *
3649297 AGACATCCTCATCACGTAGGAACCGTGTTGTTTTCAAAGTATTCCTTAAGACGACTAGACGTCCT
1 AGACATCCTCATCACGTAGGAACCATAATGTCTCCAAAGTATCCCTTAAGAAGACTAGACGTCCT
* * * *
3649362 CATCATGTAGAAACAATATCGTCCACCGACCATATCTCGTCAACGCGTAGGAGCAGCGTCATCCT
66 CATCATGTAAAAACAATATCATCCACCGACCAGATCTCCTCAACGCGTAGGAGCAGCGTCATCCT
* * * * *
3649427 -ATGGCAATCAGACTTTCTCATCACGTAGGAACCGTGTTGTCTCCAAAGTATCCCTAAAGAA-GG
131 CA-AGCAATCAGACTTCCTCATCACATAAGAACCATGTTGTCTCCAAAGTATCCCTAAA-AACGG
* *
3649490 TTAAACATCATCATCACGTAGGAACAATGTCATCCACCAACCAGATCTCCTCAATGTGTAAGAGT
194 CTAAACATCATCATCACATAGGAACAATGTCATCCACCAACCAGATCTCCTCAATGTGTAAGAGT
3649555 TGTGTCATCCTCAGGCAATC
259 TGTGTCATCCTCAGGCAATC
* *
3649575 AGACTTCCTCATCACGTAGGAACCATAATGTCTCCAAAGTATCCCTTAAGAAGGCTAGACGTCCT
1 AGACATCCTCATCACGTAGGAACCATAATGTCTCCAAAGTATCCCTTAAGAAGACTAGACGTCCT
* * * * * *
3649640 TATCATGTAAAAACAATGTCATCCACTGAGCAGATCTCCTTAACGCGTAGGAGCAGCGTTATCCT
66 CATCATGTAAAAACAATATCATCCACCGACCAGATCTCCTCAACGCGTAGGAGCAGCGTCATCCT
* * * *
3649705 CAAGCAATCAGACTTCCTCATCACATAAGAATCATGTTTTCTCCAGAGTATCCTTAAAAACGGCT
131 CAAGCAATCAGACTTCCTCATCACATAAGAACCATGTTGTCTCCAAAGTATCCCTAAAAACGGCT
* * * * * * * *
3649770 AGACGTCCTCATCACATATGAACAATGTCGTCCACCGATCATATCTCCTCAA
196 AAACATCATCATCACATAGGAACAATGTCATCCACCAACCAGATCTCCTCAA
3649822 CCCGTATGAG
Statistics
Matches: 207, Mismatches: 38, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
277 2 0.01
278 204 0.99
279 1 0.00
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.26
Consensus pattern (278 bp):
AGACATCCTCATCACGTAGGAACCATAATGTCTCCAAAGTATCCCTTAAGAAGACTAGACGTCCT
CATCATGTAAAAACAATATCATCCACCGACCAGATCTCCTCAACGCGTAGGAGCAGCGTCATCCT
CAAGCAATCAGACTTCCTCATCACATAAGAACCATGTTGTCTCCAAAGTATCCCTAAAAACGGCT
AAACATCATCATCACATAGGAACAATGTCATCCACCAACCAGATCTCCTCAATGTGTAAGAGTTG
TGTCATCCTCAGGCAATC
Found at i:3649714 original size:473 final size:473
Alignment explanation
Indices: 3648829--3649784 Score: 1127
Period size: 473 Copynumber: 2.0 Consensus size: 473
3648819 CAACCAAACT
* *
3648829 TCCTCATCACTTAAGAACCGTATTTTCTCCAAATTATCCCTAAAGACAGATAAACGTCCTCATCA
1 TCCTCATCACGTAAGAACCGTATTTTCTCCAAAGTATCCCTAAAGACAGATAAACGTCCTCATCA
* * * * *
3648894 CGTAAGAATAATGTCATCCATCGACTAGATCTCCTCAACGTGTAGGAGCAGCGTCATCCTCAGGC
66 CGTAAGAACAATATCATCCACCGACCAGATCTCCTCAACGCGTAGGAGCAGCGTCATCCTCAGGC
* * * *
3648959 AATCAGACTTCCTCGTCATGTAAAAATCCTGTTGTCTCCAAAGTATCCCTAAAGACGACTAGACA
131 AATCAGACTTCCTCATCACGTAAAAATCCTGTTGTCTCCAAAGTATCCCTAAAGAAGACTAAACA
* * ** * *
3649024 TCCTCATCACGTAGGAACAATGTCGTCCACTGACCAGATCTTCTCAACGCGTAGGAACAACGTCA
196 TCATCATCACGTAGGAACAATGTCATCCACCAACCAGATCTCCTCAACGCGTAAGAACAACGTCA
* * * ** * *
3649089 TCCTCAGGCAATCAGACTTCCTCATCACGTGGGAATCGTGTTCTCTCTAAAGTATCCCTAAAGAC
261 TCCTCAGGCAATCAGACTTCCTCATCACGTAGGAACCATAATCTCTCCAAAGTATCCCTAAAGAA
** * ** *
3649154 GACTAGACGGCCTTATCACGTAGGAATAATGTTGTCCACCGGCCAGTTCTCCTCAACGCGTAGGA
326 GACTAGACGGCCTTATCACGTAAAAACAATGTCATCCACCGGCCAGATCTCCTCAACGCGTAGGA
* * * * *
3649219 GCAACTTCATCCTCAGGCAATCAGACTTAATTATCACGTAGGAACCGTGTTGTCTCCAAAGTAT-
391 GCAACTTCATCCTCAAGCAATCAGACTTAATCATCACATAAGAACCATGTTGTCTCCAAAGTATC
* *
3649283 CTCTAAAGACGGTTAGACA
456 CT-TAAAAACGGCTAGACA
* * * * * *
3649302 TCCTCATCACGTAGGAACCGTGTTGTT-TTCAAAGTATTCCTTAAGAC-GACTAGACGTCCTCAT
1 TCCTCATCACGTAAGAACCGTATT-TTCTCCAAAGTATCCCTAAAGACAGA-TAAACGTCCTCAT
* * * *
3649365 CATGT-AGAAACAATATCGTCCACCGACCATATCTCGTCAACGCGTAGGAGCAGCGTCATCCT-A
64 CACGTAAG-AACAATATCATCCACCGACCAGATCTCCTCAACGCGTAGGAGCAGCGTCATCCTCA
* ** **
3649428 TGGCAATCAGACTTTCTCATCACGTAGGAA-CCGTGTTGTCTCCAAAGTATCCCTAAAGAAGGTT
128 -GGCAATCAGACTTCCTCATCACGTAAAAATCC-TGTTGTCTCCAAAGTATCCCTAAAGAAGACT
* * ****
3649492 AAACATCATCATCACGTAGGAACAATGTCATCCACCAACCAGATCTCCTCAATGTGTAAGAGTTG
191 AAACATCATCATCACGTAGGAACAATGTCATCCACCAACCAGATCTCCTCAACGCGTAAGAACAA
* * *
3649557 TGTCATCCTCAGGCAATCAGACTTCCTCATCACGTAGGAACCATAATGTCTCCAAAGTATCCCTT
256 CGTCATCCTCAGGCAATCAGACTTCCTCATCACGTAGGAACCATAATCTCTCCAAAGTATCCCTA
* * * * *
3649622 AAGAAGGCTAGACGTCCTTATCATGTAAAAACAATGTCATCCACTGAG-CAGATCTCCTTAACGC
321 AAGAAGACTAGACGGCCTTATCACGTAAAAACAATGTCATCCACCG-GCCAGATCTCCTCAACGC
* ** * *
3649686 GTAGGAGCAGCGTT-ATCCTCAAGCAATCAGACTTCCTCATCACATAAGAATCATGTTTTCTCCA
385 GTAGGAGCAAC-TTCATCCTCAAGCAATCAGACTTAATCATCACATAAGAACCATGTTGTCTCCA
* *
3649750 GAGTATCCTTAAAAACGGCTAGACG
449 AAGTATCCTTAAAAACGGCTAGACA
3649775 TCCTCATCAC
1 TCCTCATCAC
3649785 ATATGAACAA
Statistics
Matches: 402, Mismatches: 73, Indels: 16
0.82 0.15 0.03
Matches are distributed among these distances:
472 7 0.02
473 388 0.97
474 7 0.02
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (473 bp):
TCCTCATCACGTAAGAACCGTATTTTCTCCAAAGTATCCCTAAAGACAGATAAACGTCCTCATCA
CGTAAGAACAATATCATCCACCGACCAGATCTCCTCAACGCGTAGGAGCAGCGTCATCCTCAGGC
AATCAGACTTCCTCATCACGTAAAAATCCTGTTGTCTCCAAAGTATCCCTAAAGAAGACTAAACA
TCATCATCACGTAGGAACAATGTCATCCACCAACCAGATCTCCTCAACGCGTAAGAACAACGTCA
TCCTCAGGCAATCAGACTTCCTCATCACGTAGGAACCATAATCTCTCCAAAGTATCCCTAAAGAA
GACTAGACGGCCTTATCACGTAAAAACAATGTCATCCACCGGCCAGATCTCCTCAACGCGTAGGA
GCAACTTCATCCTCAAGCAATCAGACTTAATCATCACATAAGAACCATGTTGTCTCCAAAGTATC
CTTAAAAACGGCTAGACA
Found at i:3653815 original size:29 final size:29
Alignment explanation
Indices: 3653793--3653848 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
3653783 TTATTTCAAG
* *
3653793 TTAACTACTAATTTTTGTTTTATTGCATA
1 TTAACTACTAACTTTTATTTTATTGCATA
3653822 TTAACTACTAACTTTTATTTTATTGCA
1 TTAACTACTAACTTTTATTTTATTGCA
3653849 CTCTAACCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.29, C:0.12, G:0.05, T:0.54
Consensus pattern (29 bp):
TTAACTACTAACTTTTATTTTATTGCATA
Found at i:3673799 original size:9 final size:9
Alignment explanation
Indices: 3673787--3673833 Score: 51
Period size: 9 Copynumber: 5.1 Consensus size: 9
3673777 AATAAATACT
3673787 AAAATTAAA
1 AAAATTAAA
*
3673796 AAAATTACA
1 AAAATTAAA
3673805 AAAATTACAA
1 AAAATTA-AA
*
3673815 ATAA-TAAA
1 AAAATTAAA
3673823 GAAAATTAAA
1 -AAAATTAAA
3673833 A
1 A
3673834 TATACAAGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
8 2 0.06
9 21 0.68
10 8 0.26
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (9 bp):
AAAATTAAA
Found at i:3673810 original size:18 final size:17
Alignment explanation
Indices: 3673771--3673833 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 17
3673761 ATTACAAAAT
* *
3673771 AAATTAAATAAATACTA
1 AAATTAAAAAAATACAA
3673788 AAATTAAAAAAATTACAA
1 AAATTAAAAAAA-TACAA
* *
3673806 AAATTACAAATAATAAAGA
1 AAATTA-AAAAAATACA-A
3673825 AAATTAAAA
1 AAATTAAAA
3673834 TATACAAGGA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
17 11 0.28
18 16 0.41
19 12 0.31
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.24
Consensus pattern (17 bp):
AAATTAAAAAAATACAA
Found at i:3675258 original size:33 final size:33
Alignment explanation
Indices: 3675215--3675679 Score: 367
Period size: 33 Copynumber: 13.9 Consensus size: 33
3675205 GCAAAAAGTT
* * * *
3675215 GATGTTGATCCAGCTCCTTCTGTGATAGATTAA
1 GATGTCGATCCACCTCTTTCTGTGATGGATTAA
* * * * *
3675248 GATGTCGATCCATCTATTTCTGTCATGAATT-T
1 GATGTCGATCCACCTCTTTCTGTGATGGATTAA
* * *
3675280 GAATATCAATCCGCCTCTTTCTGTGATGGATTTGAA
1 G-ATGTCGATCCACCTCTTTCTGTGATGGA-TT-AA
*
3675316 -ATGTCGATCCACCTCTTTCTGTGATGGAATT-T
1 GATGTCGATCCACCTCTTTCTGTGATGG-ATTAA
** * *
3675348 GAATGTTAATTCACCTCTTTCTGTGATGGATCAA
1 G-ATGTCGATCCACCTCTTTCTGTGATGGATTAA
* * * *
3675382 AATATCGATCCACCTCTTTCTGTGATAGATT-T
1 GATGTCGATCCACCTCTTTCTGTGATGGATTAA
* * *
3675414 GAATATCGATCCACCTCTTTATGTGATGGATT-T
1 G-ATGTCGATCCACCTCTTTCTGTGATGGATTAA
*
3675447 GAACGTCGATCCACCTCTTTCTGTGATGGATTTAA
1 G-ATGTCGATCCACCTCTTTCTGTGATGGA-TTAA
* *
3675482 -ATGTCGATCCACCTCTTTTTGTGATGGATT-T
1 GATGTCGATCCACCTCTTTCTGTGATGGATTAA
*
3675513 GAATGTCGATCCACCTCCTTCTGTGATGGATTTGAA
1 G-ATGTCGATCCACCTCTTTCTGTGATGGA-TT-AA
* *
3675549 -ATATCGATCCACCTTTTTCTGTGATGGATTTGAA
1 GATGTCGATCCACCTCTTTCTGTGATGGA-TT-AA
* * * * *
3675583 -ATATTGATCCACCTCTTTTTGTAATGGATT-T
1 GATGTCGATCCACCTCTTTCTGTGATGGATTAA
*
3675614 GAATGTCGATCCGCCTCTTTCTGTGATGGATTTGAA
1 G-ATGTCGATCCACCTCTTTCTGTGATGGA-TT-AA
* *
3675650 -ATGTCGATCCACCTCCTTCTGGGATGGATT
1 GATGTCGATCCACCTCTTTCTGTGATGGATT
3675680 TGAATGTCGA
Statistics
Matches: 348, Mismatches: 63, Indels: 42
0.77 0.14 0.09
Matches are distributed among these distances:
32 3 0.01
33 206 0.59
34 138 0.40
35 1 0.00
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (33 bp):
GATGTCGATCCACCTCTTTCTGTGATGGATTAA
Found at i:3675639 original size:233 final size:234
Alignment explanation
Indices: 3675221--3675690 Score: 631
Period size: 233 Copynumber: 2.0 Consensus size: 234
3675211 AGTTGATGTT
* *
3675221 GATCCAGCTCCTTCTGTGATAGATTAAGATGTCGATCCATCTATTTCTGTCATGAATTTGAATAT
1 GATCCACCTCCTTCTGTGATAGATTAAGATGTCGATCCACCTATTTCTGTCATGAATTTGAATAT
* * *
3675286 CAATCCGCCTCTTTCTGTGATGGATTTGAAATGTCGATCCACCTCTTTCTGTGATGGAATTTGAA
66 CAATCCACCTCCTTCTGTGATGGATTTGAAATATCGATCCACCTCTTTCTGTGATGGAATTTGAA
* * *
3675351 TGTTAATTCACCTCTTTCTGTGATGGATCAAAATATCGATCCACCTCTTTCTGTGATAGATTTG-
131 TATTAATCCACCTCTTTCTGTAATGGATCAAAATATCGATCCACCTCTTTCTGTGATAGATTTGA
* *
3675415 AATATCGATCCACCTCTTTATGTGATGGATTTGAACGTC
196 AATATCGATCCACCTCCTTATGGGATGGATTTGAACGTC
* * * * * * *
3675454 GATCCACCTCTTTCTGTGATGGATTTAA-ATGTCGATCCACCTCTTTTTGTGATGGATTTGAATG
1 GATCCACCTCCTTCTGTGATAGA-TTAAGATGTCGATCCACCTATTTCTGTCATGAATTTGAATA
* *
3675518 TCGATCCACCTCCTTCTGTGATGGATTTGAAATATCGATCCACCTTTTTCTGTGATGG-ATTTGA
65 TCAATCCACCTCCTTCTGTGATGGATTTGAAATATCGATCCACCTCTTTCTGTGATGGAATTTG-
* * *** * * *
3675582 AATATTGATCCACCTCTTTTTGTAATGGATTTGAATGTCGATCCGCCTCTTTCTGTGATGGATTT
129 AATATTAATCCACCTCTTTCTGTAATGGATCAAAATATCGATCCACCTCTTTCTGTGATAGATTT
* * *
3675647 GAAATGTCGATCCACCTCCTTCTGGGATGGATTTGAATGTC
194 GAAATATCGATCCACCTCCTTATGGGATGGATTTGAACGTC
3675688 GAT
1 GAT
3675691 TCTGATCTAC
Statistics
Matches: 204, Mismatches: 30, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
232 5 0.02
233 158 0.77
234 41 0.20
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (234 bp):
GATCCACCTCCTTCTGTGATAGATTAAGATGTCGATCCACCTATTTCTGTCATGAATTTGAATAT
CAATCCACCTCCTTCTGTGATGGATTTGAAATATCGATCCACCTCTTTCTGTGATGGAATTTGAA
TATTAATCCACCTCTTTCTGTAATGGATCAAAATATCGATCCACCTCTTTCTGTGATAGATTTGA
AATATCGATCCACCTCCTTATGGGATGGATTTGAACGTC
Found at i:3675687 original size:67 final size:67
Alignment explanation
Indices: 3675216--3675690 Score: 591
Period size: 67 Copynumber: 7.1 Consensus size: 67
3675206 CAAAAAGTTG
* * * * * * * *
3675216 ATGTTGATCCAGCTCCTTCTGTGATAGA-TT-AAGATGTCGATCCATCTATTTCTGTCATGAATT
1 ATGTCGATCCACCTCTTTCTGTGATGGATTTGAA-ATGTCGATCCACCTCTTTCTGTGATGGATT
3675279 TGA
65 TGA
* * *
3675282 ATATCAATCCGCCTCTTTCTGTGATGGATTTGAAATGTCGATCCACCTCTTTCTGTGATGGAATT
1 ATGTCGATCCACCTCTTTCTGTGATGGATTTGAAATGTCGATCCACCTCTTTCTGTGATGG-ATT
3675347 TGA
65 TGA
** * ** * *
3675350 ATGTTAATTCACCTCTTTCTGTGATGGA-TCAAAATATCGATCCACCTCTTTCTGTGATAGATTT
1 ATGTCGATCCACCTCTTTCTGTGATGGATTTGAAATGTCGATCCACCTCTTTCTGTGATGGATTT
3675414 GA
66 GA
* * *
3675416 ATATCGATCCACCTCTTTATGTGATGGATTTG-AACGTCGATCCACCTCTTTCTGTGATGGATTT
1 ATGTCGATCCACCTCTTTCTGTGATGGATTTGAAATGTCGATCCACCTCTTTCTGTGATGGATTT
*
3675480 AA
66 GA
* *
3675482 ATGTCGATCCACCTCTTTTTGTGATGGATTTG-AATGTCGATCCACCTCCTTCTGTGATGGATTT
1 ATGTCGATCCACCTCTTTCTGTGATGGATTTGAAATGTCGATCCACCTCTTTCTGTGATGGATTT
3675546 GAA
66 G-A
* * * * * *
3675549 ATATCGATCCACCTTTTTCTGTGATGGATTTGAAATATTGATCCACCTCTTTTTGTAATGGATTT
1 ATGTCGATCCACCTCTTTCTGTGATGGATTTGAAATGTCGATCCACCTCTTTCTGTGATGGATTT
3675614 GA
66 GA
* * *
3675616 ATGTCGATCCGCCTCTTTCTGTGATGGATTTGAAATGTCGATCCACCTCCTTCTGGGATGGATTT
1 ATGTCGATCCACCTCTTTCTGTGATGGATTTGAAATGTCGATCCACCTCTTTCTGTGATGGATTT
3675681 GA
66 GA
3675683 ATGTCGAT
1 ATGTCGAT
3675691 TCTGATCTAC
Statistics
Matches: 351, Mismatches: 52, Indels: 11
0.85 0.13 0.03
Matches are distributed among these distances:
66 140 0.40
67 151 0.43
68 60 0.17
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (67 bp):
ATGTCGATCCACCTCTTTCTGTGATGGATTTGAAATGTCGATCCACCTCTTTCTGTGATGGATTT
GA
Found at i:3677887 original size:11 final size:11
Alignment explanation
Indices: 3677867--3677928 Score: 70
Period size: 11 Copynumber: 5.4 Consensus size: 11
3677857 CTTGATTCAA
*
3677867 TTTCTTTTTTT
1 TTTCTCTTTTT
3677878 TTTCTCTTTTCT
1 TTTCTCTTTT-T
* *
3677890 CTTTTTTTCTTTT
1 -TTTCTCT-TTTT
3677903 TTTCTCTTTTT
1 TTTCTCTTTTT
3677914 TTTCTCTTTTT
1 TTTCTCTTTTT
3677925 TTTC
1 TTTC
3677929 CTGATAGATG
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
11 28 0.65
12 6 0.14
13 6 0.14
14 3 0.07
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTCTCTTTTT
Found at i:3677894 original size:18 final size:18
Alignment explanation
Indices: 3677867--3677923 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
3677857 CTTGATTCAA
*
3677867 TTTCTTTTTTTTTTCTCT
1 TTTCTCTTTTTTTTCTCT
*
3677885 TTTCTC-TTTTTTTCTTTT
1 TTTCTCTTTTTTTTC-TCT
3677903 TTTCTCTTTTTTTTCTCT
1 TTTCTCTTTTTTTTCTCT
3677921 TTT
1 TTT
3677924 TTTTCCTGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
17 8 0.24
18 18 0.53
19 8 0.24
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTCTCTTTTTTTTCTCT
Found at i:3677896 original size:9 final size:9
Alignment explanation
Indices: 3677875--3677925 Score: 61
Period size: 8 Copynumber: 5.7 Consensus size: 9
3677865 AATTTCTTTT
3677875 TTTTTTCTC
1 TTTTTTCTC
*
3677884 TTTTCTCT-
1 TTTTTTCTC
3677892 TTTTTTCT-
1 TTTTTTCTC
3677900 TTTTTTCTC
1 TTTTTTCTC
3677909 TTTTTTTTCTC
1 --TTTTTTCTC
3677920 TTTTTT
1 TTTTTT
3677926 TTCCTGATAG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
8 15 0.41
9 13 0.35
11 9 0.24
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTTCTC
Found at i:3678407 original size:3 final size:3
Alignment explanation
Indices: 3678392--3678437 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
3678382 TTTCATTCAT
*
3678392 TTC TTC TTA TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
3678438 ATTTGCCCCC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:3695350 original size:20 final size:20
Alignment explanation
Indices: 3695222--3695334 Score: 172
Period size: 20 Copynumber: 5.7 Consensus size: 20
3695212 TTTCCCACGA
3695222 ATTTGTAAAACCTCTGGGTC
1 ATTTGTAAAACCTCTGGGTC
*
3695242 ATTTGTAAGACCTCTGGGTC
1 ATTTGTAAAACCTCTGGGTC
*
3695262 ATTTGTAAAACCTCTGAGTC
1 ATTTGTAAAACCTCTGGGTC
**
3695282 ATTTGTAAAACCTCCAGGTC
1 ATTTGTAAAACCTCTGGGTC
**
3695302 ATTTGTAAAACCTCCAGGTC
1 ATTTGTAAAACCTCTGGGTC
3695322 ATTTGTAAAACCT
1 ATTTGTAAAACCT
3695335 TCGGGTAATT
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 87 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (20 bp):
ATTTGTAAAACCTCTGGGTC
Found at i:3695362 original size:60 final size:60
Alignment explanation
Indices: 3695221--3695363 Score: 153
Period size: 60 Copynumber: 2.4 Consensus size: 60
3695211 ATTTCCCACG
* * * **
3695221 AATTTGTAAAACCTCTGGGTCATTTGTAAGACCTCTGGGTCATTTGTAAAACCTCTGAGT
1 AATTTATAAAACATCTGGGTCATTTGTAAAACCTCCAGGTCATTTGTAAAACCTCTGAGT
* * * ** *
3695281 CATTTGTAAAACCTCCAGGTCATTTGTAAAACCTCCAGGTCATTTGTAAAACCT-TCGGGT
1 AATTTATAAAACATCTGGGTCATTTGTAAAACCTCCAGGTCATTTGTAAAACCTCT-GAGT
* *
3695341 AATTTATAAATCATTTGGGTCAT
1 AATTTATAAAACATCTGGGTCAT
3695364 CTGTCAGTCT
Statistics
Matches: 68, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
59 1 0.01
60 67 0.99
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (60 bp):
AATTTATAAAACATCTGGGTCATTTGTAAAACCTCCAGGTCATTTGTAAAACCTCTGAGT
Found at i:3695363 original size:40 final size:40
Alignment explanation
Indices: 3695222--3695350 Score: 170
Period size: 40 Copynumber: 3.2 Consensus size: 40
3695212 TTTCCCACGA
*
3695222 ATTTGTAAAACCTCTGGGTCATTTGTAAGACC-TCTGGGTC
1 ATTTGTAAAACCTCTGGGTCATTTGTAAAACCTTC-GGGTC
* * *
3695262 ATTTGTAAAACCTCTGAGTCATTTGTAAAACCTCCAGGTC
1 ATTTGTAAAACCTCTGGGTCATTTGTAAAACCTTCGGGTC
** *
3695302 ATTTGTAAAACCTCCAGGTCATTTGTAAAACCTTCGGGTA
1 ATTTGTAAAACCTCTGGGTCATTTGTAAAACCTTCGGGTC
*
3695342 ATTTATAAA
1 ATTTGTAAA
3695351 TCATTTGGGT
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
40 76 0.99
41 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.34
Consensus pattern (40 bp):
ATTTGTAAAACCTCTGGGTCATTTGTAAAACCTTCGGGTC
Found at i:3695545 original size:36 final size:36
Alignment explanation
Indices: 3695496--3696040 Score: 699
Period size: 36 Copynumber: 15.1 Consensus size: 36
3695486 CTAAAATTAA
* *
3695496 TCATTCTCGACCTTCACGGAAGAGTAGTGAAGTAAG
1 TCATTTTCAACCTTCACGGAAGAGTAGTGAAGTAAG
*
3695532 TCATTTTCAACCTTCACGGAAGAGTAGTAAAGTTAA-
1 TCATTTTCAACCTTCACGGAAGAGTAGTGAAG-TAAG
* *
3695568 TCATTTTCAACCTTCAC-GAATGAGTAGTAAAGTTAG
1 TCATTTTCAACCTTCACGGAA-GAGTAGTGAAGTAAG
3695604 TCATTTTCAACCTTCACGGAAGAGTAGTGAAGTCAA-
1 TCATTTTCAACCTTCACGGAAGAGTAGTGAAGT-AAG
* *
3695640 TCATTTTCAACCTTCACGGAAGAGTAGTGAAGTTAC
1 TCATTTTCAACCTTCACGGAAGAGTAGTGAAGTAAG
* *
3695676 TCATTATCAACCTTCACGGAAGAGTAGTGAAGTTAG
1 TCATTTTCAACCTTCACGGAAGAGTAGTGAAGTAAG
*
3695712 TAATTTTCAACCTTCACGGAAGAGTAGTGAAGTCAA-
1 TCATTTTCAACCTTCACGGAAGAGTAGTGAAGT-AAG
3695748 TCATTTTCAACCTTCACGGAAGAGTAGTGAAGTTAA-
1 TCATTTTCAACCTTCACGGAAGAGTAGTGAAG-TAAG
*
3695784 TCATTTTCAACCTTCACGGAAGAGTAGTGAAGTCAG
1 TCATTTTCAACCTTCACGGAAGAGTAGTGAAGTAAG
* * *
3695820 TCAGTTTCGACCTTCACAGAAGAGTAGTGAAGTCAA-
1 TCATTTTCAACCTTCACGGAAGAGTAGTGAAGT-AAG
*
3695856 TCATTTTCAACCTTCATGGAAGAGTAGTGAAGTTAA-
1 TCATTTTCAACCTTCACGGAAGAGTAGTGAAG-TAAG
* * * *
3695892 TAAATTTCAACCTTCACAGAAGAGTAGTGAAGTTAG
1 TCATTTTCAACCTTCACGGAAGAGTAGTGAAGTAAG
* * *
3695928 TCATTTTCAACATTCACGAAAGAGTAGTGAAGTCAG
1 TCATTTTCAACCTTCACGGAAGAGTAGTGAAGTAAG
* * * *
3695964 TCATTTCCAGCCTTCATGGAAGAGTAGTGAAGTCAG
1 TCATTTTCAACCTTCACGGAAGAGTAGTGAAGTAAG
* * * *
3696000 TCATTTCCAGCCTTCACAGAAGAGTAGTGAAGCAAG
1 TCATTTTCAACCTTCACGGAAGAGTAGTGAAGTAAG
3696036 ATCAT
1 -TCAT
3696041 ATCAAAATTT
Statistics
Matches: 454, Mismatches: 42, Indels: 25
0.87 0.08 0.05
Matches are distributed among these distances:
35 10 0.02
36 429 0.94
37 15 0.03
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.28
Consensus pattern (36 bp):
TCATTTTCAACCTTCACGGAAGAGTAGTGAAGTAAG
Found at i:3695686 original size:108 final size:107
Alignment explanation
Indices: 3695496--3696031 Score: 788
Period size: 108 Copynumber: 5.0 Consensus size: 107
3695486 CTAAAATTAA
* *
3695496 TCATTCTCGACCTTCACGGAAGAGTAGTGAAGT-AAGTCATTTTCAACCTTCACGGAAGAGTAGT
1 TCATTTTCAACCTTCACGGAAGAGTAGTGAAGTCAA-TCATTTTCAACCTTCACGGAAGAGTAGT
* *
3695560 AAAGTTAATCATTTTCAACCTTCAC-GAATGAGTAGTAAAGTTAG
65 GAAGTTAATCA-TTTCAACCTTCACAGAA-GAGTAGTGAAGTTAG
3695604 TCATTTTCAACCTTCACGGAAGAGTAGTGAAGTCAATCATTTTCAACCTTCACGGAAGAGTAGTG
1 TCATTTTCAACCTTCACGGAAGAGTAGTGAAGTCAATCATTTTCAACCTTCACGGAAGAGTAGTG
* *
3695669 AAGTTACTCATTATCAACCTTCACGGAAGAGTAGTGAAGTTAG
66 AAGTTAATCATT-TCAACCTTCACAGAAGAGTAGTGAAGTTAG
*
3695712 TAATTTTCAACCTTCACGGAAGAGTAGTGAAGTCAATCATTTTCAACCTTCACGGAAGAGTAGTG
1 TCATTTTCAACCTTCACGGAAGAGTAGTGAAGTCAATCATTTTCAACCTTCACGGAAGAGTAGTG
* *
3695777 AAGTTAATCATTTTCAACCTTCACGGAAGAGTAGTGAAGTCAG
66 AAGTTAATCA-TTTCAACCTTCACAGAAGAGTAGTGAAGTTAG
* * * *
3695820 TCAGTTTCGACCTTCACAGAAGAGTAGTGAAGTCAATCATTTTCAACCTTCATGGAAGAGTAGTG
1 TCATTTTCAACCTTCACGGAAGAGTAGTGAAGTCAATCATTTTCAACCTTCACGGAAGAGTAGTG
*
3695885 AAGTTAATAAATTTCAACCTTCACAGAAGAGTAGTGAAGTTAG
66 AAGTTAAT-CATTTCAACCTTCACAGAAGAGTAGTGAAGTTAG
* * * * * *
3695928 TCATTTTCAACATTCACGAAAGAGTAGTGAAGTCAGTCATTTCCAGCCTTCATGGAAGAGTAGTG
1 TCATTTTCAACCTTCACGGAAGAGTAGTGAAGTCAATCATTTTCAACCTTCACGGAAGAGTAGTG
* * *
3695993 AAGTCAGTCATTTCCAGCCTTCACAGAAGAGTAGTGAAG
66 AAGTTAATCATTT-CAACCTTCACAGAAGAGTAGTGAAG
3696032 CAAGATCATA
Statistics
Matches: 394, Mismatches: 28, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
107 6 0.02
108 380 0.96
109 8 0.02
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.29
Consensus pattern (107 bp):
TCATTTTCAACCTTCACGGAAGAGTAGTGAAGTCAATCATTTTCAACCTTCACGGAAGAGTAGTG
AAGTTAATCATTTCAACCTTCACAGAAGAGTAGTGAAGTTAG
Found at i:3696239 original size:3 final size:3
Alignment explanation
Indices: 3696233--3696267 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3696223 TACAATAATA
3696233 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3696268 CAAGACCTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3697436 original size:52 final size:52
Alignment explanation
Indices: 3697376--3697481 Score: 203
Period size: 52 Copynumber: 2.0 Consensus size: 52
3697366 TATGTTCATA
*
3697376 ATTTATATTTTAACCCCGTATTATATATGGTTAAATTACATTAACAAGACTT
1 ATTTATATTTTAACCCCGTAATATATATGGTTAAATTACATTAACAAGACTT
3697428 ATTTATATTTTAACCCCGTAATATATATGGTTAAATTACATTAACAAGACTT
1 ATTTATATTTTAACCCCGTAATATATATGGTTAAATTACATTAACAAGACTT
3697480 AT
1 AT
3697482 ATTTTATAAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.42
Consensus pattern (52 bp):
ATTTATATTTTAACCCCGTAATATATATGGTTAAATTACATTAACAAGACTT
Found at i:3703218 original size:12 final size:12
Alignment explanation
Indices: 3703203--3703258 Score: 50
Period size: 12 Copynumber: 5.1 Consensus size: 12
3703193 TAAATCAAAA
3703203 AATAATATTAAT
1 AATAATATTAAT
*
3703215 AATAA-ATAAAT
1 AATAATATTAAT
* *
3703226 AATACTATAAAT
1 AATAATATTAAT
3703238 AAT-ATA-TAAT
1 AATAATATTAAT
3703248 -ATAATA-TAAT
1 AATAATATTAAT
3703258 A
1 A
3703259 TGTACTATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
9 2 0.05
10 10 0.27
11 11 0.30
12 14 0.38
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (12 bp):
AATAATATTAAT
Found at i:3703325 original size:22 final size:22
Alignment explanation
Indices: 3703290--3703338 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
3703280 ACTATATAAC
* *
3703290 ATATATTATATTTTTAAAAACT
1 ATATAATATATTTTCAAAAACT
* *
3703312 ATATAATATGTTTTCAAAAATT
1 ATATAATATATTTTCAAAAACT
3703334 ATATA
1 ATATA
3703339 TATTATATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (22 bp):
ATATAATATATTTTCAAAAACT
Found at i:3703394 original size:62 final size:63
Alignment explanation
Indices: 3703301--3703448 Score: 169
Period size: 64 Copynumber: 2.3 Consensus size: 63
3703291 TATATTATAT
* * ** *
3703301 TTTTAAAAACTATATA-ATATGTTTTCAAAAATTATATATAT-TA-TATATTTTTTCAAAAACCG
1 TTTTAAAAACTATATATATATGTTTT-AAAAATTAAAAATATATATTATACGTTTTCAAAAA-CA
*
3703363 TTTTAAAAACTATATATTATATGTTTT-AAAATTAAAAATATATATTATACGTTTTCAAAAATA
1 TTTTAAAAACTATATA-TATATGTTTTAAAAATTAAAAATATATATTATACGTTTTCAAAAACA
3703426 TTTTCAAAAACTATACTATATAT
1 TTTT-AAAAACTATA-TATATAT
3703449 TATTATATAT
Statistics
Matches: 74, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
62 28 0.38
63 6 0.08
64 38 0.51
65 2 0.03
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (63 bp):
TTTTAAAAACTATATATATATGTTTTAAAAATTAAAAATATATATTATACGTTTTCAAAAACA
Found at i:3703406 original size:28 final size:30
Alignment explanation
Indices: 3703365--3703422 Score: 93
Period size: 28 Copynumber: 2.0 Consensus size: 30
3703355 AAAAACCGTT
*
3703365 TTAAAAACTATATATTATATGTTTT-AAAA
1 TTAAAAACTATATATTATACGTTTTCAAAA
3703394 TTAAAAA-TATATATTATACGTTTTCAAAA
1 TTAAAAACTATATATTATACGTTTTCAAAA
3703423 ATATTTTCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 16 0.59
29 11 0.41
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.43
Consensus pattern (30 bp):
TTAAAAACTATATATTATACGTTTTCAAAA
Found at i:3703473 original size:14 final size:12
Alignment explanation
Indices: 3703442--3703472 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
3703432 AAAACTATAC
3703442 TATATATTATTA
1 TATATATTATTA
*
3703454 TATATATTATCA
1 TATATATTATTA
3703466 TATATAT
1 TATATAT
3703473 ACTAAATAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (12 bp):
TATATATTATTA
Found at i:3708374 original size:20 final size:20
Alignment explanation
Indices: 3708349--3708392 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
3708339 TCTTGCAAAG
3708349 TTGGTTATTAGCTATATAAC
1 TTGGTTATTAGCTATATAAC
3708369 TTGGTTATTAGCTATATAAC
1 TTGGTTATTAGCTATATAAC
3708389 TTGG
1 TTGG
3708393 CCAATATCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.27, C:0.09, G:0.18, T:0.45
Consensus pattern (20 bp):
TTGGTTATTAGCTATATAAC
Found at i:3710575 original size:174 final size:173
Alignment explanation
Indices: 3710285--3710634 Score: 691
Period size: 174 Copynumber: 2.0 Consensus size: 173
3710275 GTTTTCTTTT
3710285 GAAAATAACATAAAACCATAGTTTTTTCTCATTTTTTCGATCTTGATCCGAAAATTAAGCAAAAC
1 GAAAATAACATAAAACCATAGTTTTTTCTCATTTTTTCGATCTTGATCCGAAAATTAAGCAAAAC
3710350 AAAGGCATGAAAAAGAAAGATTGAGAAGAGAGTAAAGGAGTTACCTTCGACCGGAGCCTTTGCCA
66 AAAGGCATGAAAAAGAAAGATTGAGAAGAGAGTAAAGGAGTTACCTTCGACCGGAGCCTTTGCCA
3710415 GCGACAGAGATCCTCTGTTCGCAGATCCGAACGGTCAGAAGAGA
131 GCGACAGAGA-CCTCTGTTCGCAGATCCGAACGGTCAGAAGAGA
3710459 GAAAATAACATAAAACCATAGTTTTTTCTCATTTTTTCGATCTTGATCCGAAAATTAAGCAAAAC
1 GAAAATAACATAAAACCATAGTTTTTTCTCATTTTTTCGATCTTGATCCGAAAATTAAGCAAAAC
3710524 AAAGGCATGAAAAAGAAAGATTGAGAAGAGAGTAAAGGAGTTACCTTCGACCGGAGCCTTTGCCA
66 AAAGGCATGAAAAAGAAAGATTGAGAAGAGAGTAAAGGAGTTACCTTCGACCGGAGCCTTTGCCA
3710589 GCGACAGAGACCTCTGTTCGCAGATCCGAACGGTCAGAAGAGA
131 GCGACAGAGACCTCTGTTCGCAGATCCGAACGGTCAGAAGAGA
3710632 GAA
1 GAA
3710635 GGGAAGCTGA
Statistics
Matches: 176, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
173 36 0.20
174 140 0.80
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (173 bp):
GAAAATAACATAAAACCATAGTTTTTTCTCATTTTTTCGATCTTGATCCGAAAATTAAGCAAAAC
AAAGGCATGAAAAAGAAAGATTGAGAAGAGAGTAAAGGAGTTACCTTCGACCGGAGCCTTTGCCA
GCGACAGAGACCTCTGTTCGCAGATCCGAACGGTCAGAAGAGA
Found at i:3711594 original size:4 final size:4
Alignment explanation
Indices: 3711585--3711609 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3711575 ATATTAACCA
3711585 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
3711610 GCATTAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:3713945 original size:135 final size:134
Alignment explanation
Indices: 3713697--3713969 Score: 501
Period size: 135 Copynumber: 2.0 Consensus size: 134
3713687 ATGCGGTTAT
3713697 GACTCTTAATTACCTTTGTACGCTTATTTTTCAGTATCAACTTTGAGTCATATGTAATTATTTTT
1 GACTCTTAATTACCTTTGTACGCTTATTTTTCAGTATCAACTTTGAGTCATATGTAATTATTTTT
3713762 TTCTAAGATTACATTTCTTTGACTATCATTTCAACTACTTGATTTTTTTTGTCTTGTTTCTACTA
66 TTCTAAGATTACATTTCTTTGACTATCATTTCAACTACTTGA-TTTTTTTGTCTTGTTTCTACTA
3713827 ACTTG
130 ACTTG
3713832 GACTCTTAATTACCTTTGTACGCTTATTTTTCAGTATCAACTTTGAGTCATATGTAATTATTTTT
1 GACTCTTAATTACCTTTGTACGCTTATTTTTCAGTATCAACTTTGAGTCATATGTAATTATTTTT
3713897 TTCTAAGATTACATTTCTTTGACTAATCATTTCAACTAACTTGATTTTTTTTTGTCTTGTTTCTA
66 TTCTAAGATTACATTTCTTTGACT-ATCATTTCAACT-ACTTGA--TTTTTTTGTCTTGTTTCTA
3713962 CTAACTTG
127 CTAACTTG
3713970 ATTTCCTTTT
Statistics
Matches: 135, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
135 89 0.66
136 12 0.09
137 6 0.04
138 28 0.21
ACGTcount: A:0.23, C:0.16, G:0.10, T:0.51
Consensus pattern (134 bp):
GACTCTTAATTACCTTTGTACGCTTATTTTTCAGTATCAACTTTGAGTCATATGTAATTATTTTT
TTCTAAGATTACATTTCTTTGACTATCATTTCAACTACTTGATTTTTTTGTCTTGTTTCTACTAA
CTTG
Found at i:3713967 original size:30 final size:30
Alignment explanation
Indices: 3713926--3713983 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
3713916 TGACTAATCA
**
3713926 TTTCAACTAACTTGATTTTTTTTTGTCTTG
1 TTTCAACTAACTTGATTTCCTTTTGTCTTG
*
3713956 TTTCTACTAACTTGATTTCCTTTTGTCT
1 TTTCAACTAACTTGATTTCCTTTTGTCT
3713984 GGTCTTGTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.16, C:0.17, G:0.09, T:0.59
Consensus pattern (30 bp):
TTTCAACTAACTTGATTTCCTTTTGTCTTG
Found at i:3714469 original size:14 final size:14
Alignment explanation
Indices: 3714450--3714512 Score: 69
Period size: 14 Copynumber: 4.6 Consensus size: 14
3714440 ACTTGTTGCA
3714450 TTTGCATCTCATAT
1 TTTGCATCTCATAT
*
3714464 TTTGCA-CTCCTATT
1 TTTGCATCTCATA-T
*
3714478 TTTGCATCTCGTAT
1 TTTGCATCTCATAT
*
3714492 TTTGCACCT-AT-T
1 TTTGCATCTCATAT
3714504 TTTGCATCT
1 TTTGCATCT
3714513 TTGCATTTGC
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
12 9 0.21
13 6 0.14
14 22 0.52
15 5 0.12
ACGTcount: A:0.16, C:0.24, G:0.10, T:0.51
Consensus pattern (14 bp):
TTTGCATCTCATAT
Found at i:3714501 original size:26 final size:27
Alignment explanation
Indices: 3714450--3714512 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 27
3714440 ACTTGTTGCA
3714450 TTTGCATCTCATATTTTGCACTCCTATT
1 TTTGCATCTCATATTTTGCAC-CCTATT
*
3714478 TTTGCATCTCGTATTTTGCA-CCTATT
1 TTTGCATCTCATATTTTGCACCCTATT
3714504 TTTGCATCT
1 TTTGCATCT
3714513 TTGCATTTGC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
26 15 0.44
28 19 0.56
ACGTcount: A:0.16, C:0.24, G:0.10, T:0.51
Consensus pattern (27 bp):
TTTGCATCTCATATTTTGCACCCTATT
Found at i:3717527 original size:54 final size:53
Alignment explanation
Indices: 3717439--3717604 Score: 194
Period size: 54 Copynumber: 3.1 Consensus size: 53
3717429 CCAAACAATG
* * * *
3717439 TGATGTTTTTAAATAAATTTTGAGAGAAATTAAGCTTGATTTTGAGGAGTTTCT
1 TGATGTTTTCAAATGAATTTTGAGA-AAACTAAGCTTGATTTTAAGGAGTTTCT
3717493 TGATGTTTTCAAATGAATTTTGAGATAAACTAAGCTTGATTTTCAAGG-GTTTCT
1 TGATGTTTTCAAATGAATTTTGAGA-AAACTAAGCTTGATTTT-AAGGAGTTTCT
* * *
3717547 TGATGTTTTCAAATGGA-TTTGGGAAGGAACTAAGCTTGATTTTCAGGTA-TTTCT
1 TGATGTTTTCAAATGAATTTTGAGAA--AACTAAGCTTGATTTTAAGG-AGTTTCT
3717601 TGAT
1 TGAT
3717605 TACTTCCGAT
Statistics
Matches: 99, Mismatches: 8, Indels: 10
0.85 0.07 0.09
Matches are distributed among these distances:
52 1 0.01
53 9 0.09
54 86 0.87
55 3 0.03
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.43
Consensus pattern (53 bp):
TGATGTTTTCAAATGAATTTTGAGAAAACTAAGCTTGATTTTAAGGAGTTTCT
Found at i:3718561 original size:35 final size:34
Alignment explanation
Indices: 3718518--3718590 Score: 85
Period size: 35 Copynumber: 2.1 Consensus size: 34
3718508 ATAAAGTCTA
* *
3718518 TTTTGAAAAACTATTT-TGTCCTTCTTAGGATCAT
1 TTTTG-AAAACTATTTAAGTCCTTCTTAGGACCAT
* *
3718552 TTTTAGAAAATTGTTTAAGTCCTTCTTAGGACCAT
1 TTTT-GAAAACTATTTAAGTCCTTCTTAGGACCAT
3718587 TTTT
1 TTTT
3718591 CTGGGATGTC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
34 12 0.36
35 21 0.64
ACGTcount: A:0.26, C:0.14, G:0.12, T:0.48
Consensus pattern (34 bp):
TTTTGAAAACTATTTAAGTCCTTCTTAGGACCAT
Found at i:3719584 original size:140 final size:135
Alignment explanation
Indices: 3719011--3719689 Score: 806
Period size: 135 Copynumber: 5.0 Consensus size: 135
3719001 AGATAAACCA
* * *
3719011 ATTAACATTTCCAATTGAGAGTTCATATTGAGAAGAATTCATCCGATAAAGGGAGAAGAAGTTCG
1 ATTAACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCG
* * * *
3719076 TAATGAGAAGAACTTGTTCAACCTTTGCTCAATTCA-CGGTATTTCAAATCAGTGATGCCTCACT
66 TAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCATCGATATTT-GAATCAGTGACGCCTCACT
3719140 TGAGGG
130 TGAGGG
* *
3719146 ATTAACATTTCCAATTGAGAGTTCATACTGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTTG
1 ATTAACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCG
* * * * * *
3719211 TAATGAGAAAAACTTGTTCAAACTTTGCTCGATTCATGGCAT-TTCGAATCAGCGATGCCTCACT
66 TAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCATCG-ATATTTGAATCAGTGACGCCTCACT
3719275 TGAGGG
130 TGAGGG
* * * * *
3719281 ATTAACATTTCCAATGGAGAGTTCATAATTAGACGAACTCATCTGATAGAGGGAGAAGAAGTTCA
1 ATTAACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCG
** ** *
3719346 TAGGGAGAATCACTTGTTCAACCTTTGCTCGATTCA-CGATATTTTGAATCAGTGACACCTCACT
66 TAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCATCGATA-TTTGAATCAGTGACGCCTCACT
*
3719410 TTAGGG
130 TGAGGG
* * * * *
3719416 ATTAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCAACCAATCGAGGGAGAAGAAGTTCA
1 ATTAACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCG
* * * ** *
3719481 TAATGGGAAGAACTTATTCAACCTTTTCTTAATTCATCGCATATGGAGTTAAATCAGTGACGCCT
66 TAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCATCG-ATAT----TTGAATCAGTGACGCCT
*
3719546 CACTTTAGGG
126 CACTTGAGGG
* * * * * *
3719556 ATTAACATTTCCAATTAAGAGTTTATAATGACAAGAACTCATCAGATAGAGGGAGAATAAGTTTG
1 ATTAACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCG
* *
3719621 TAATGAGAAGAACTTGTTCAACCTTTTCTCGATTCATCGTATTTAGAGTTGAATCAGTGACGCCT
66 TAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCATCG-A--T--ATTTGAATCAGTGACGCCT
3719686 CACT
126 CACT
3719690 CGAGAGACCA
Statistics
Matches: 465, Mismatches: 65, Indels: 23
0.84 0.12 0.04
Matches are distributed among these distances:
133 2 0.00
134 1 0.00
135 315 0.68
136 6 0.01
137 4 0.01
140 135 0.29
142 1 0.00
144 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.29
Consensus pattern (135 bp):
ATTAACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCG
TAATGAGAAGAACTTGTTCAACCTTTGCTCGATTCATCGATATTTGAATCAGTGACGCCTCACTT
GAGGG
Found at i:3724535 original size:13 final size:13
Alignment explanation
Indices: 3724496--3724528 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
3724486 ATTAAGAAAG
3724496 TTGAAAGTTTAAA
1 TTGAAAGTTTAAA
3724509 TTGAAAGTTTAAA
1 TTGAAAGTTTAAA
3724522 TTGAAAG
1 TTGAAAG
3724529 GTAAAATAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.18, T:0.36
Consensus pattern (13 bp):
TTGAAAGTTTAAA
Found at i:3724701 original size:26 final size:25
Alignment explanation
Indices: 3724672--3724740 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 25
3724662 GTAAAATGAT
3724672 AAAAAAAAAAGATAAAATAGTA-AGTA
1 AAAAAAAAAAGATAAAATA-TATA-TA
3724698 AAAAAACAAATA-ATAAAATATATATA
1 AAAAAA-AAA-AGATAAAATATATATA
3724724 AAAAAGAAAAAGA-AAAA
1 AAAAA-AAAAAGATAAAA
3724741 GAAAAAGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
25 5 0.13
26 19 0.50
27 13 0.34
28 1 0.03
ACGTcount: A:0.77, C:0.01, G:0.07, T:0.14
Consensus pattern (25 bp):
AAAAAAAAAAGATAAAATATATATA
Found at i:3724702 original size:27 final size:26
Alignment explanation
Indices: 3724672--3724740 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 26
3724662 GTAAAATGAT
3724672 AAAAAAAAAAGATAAAATAGTA-AGTAA
1 AAAAAAAAAAGATAAAATA-TATA-TAA
*
3724699 AAAAACAAATA-ATAAAATATATATAA
1 AAAAA-AAAAAGATAAAATATATATAA
*
3724725 AAAAGAAAAAGA-AAAA
1 AAAAAAAAAAGATAAAA
3724741 GAAAAAGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
25 8 0.22
26 10 0.28
27 14 0.39
28 4 0.11
ACGTcount: A:0.77, C:0.01, G:0.07, T:0.14
Consensus pattern (26 bp):
AAAAAAAAAAGATAAAATATATATAA
Found at i:3724735 original size:6 final size:6
Alignment explanation
Indices: 3724724--3724751 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
3724714 AATATATATA
3724724 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
3724752 TAAATAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:3725055 original size:15 final size:16
Alignment explanation
Indices: 3725004--3725080 Score: 65
Period size: 15 Copynumber: 4.9 Consensus size: 16
3724994 AAAAAATGAA
* *
3725004 AATAATTATATATAT-
1 AATAATAATATACATG
3725019 AATATATACATATA-AT-
1 AATA-ATA-ATATACATG
3725035 AATAATAATA-ACATG
1 AATAATAATATACATG
*
3725050 AATAATAAAAATACATG
1 AATAAT-AATATACATG
3725067 AATAA-AATATACAT
1 AATAATAATATACAT
3725081 ATAATAAATA
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
13 1 0.02
14 5 0.09
15 21 0.40
16 11 0.21
17 15 0.28
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.32
Consensus pattern (16 bp):
AATAATAATATACATG
Found at i:3725055 original size:18 final size:17
Alignment explanation
Indices: 3725017--3725080 Score: 69
Period size: 18 Copynumber: 3.7 Consensus size: 17
3725007 AATTATATAT
*
3725017 ATAATATATACATATAATA
1 ATAATA-ATACAT-GAATA
3725036 ATAATAATAACATGAATA
1 ATAATAAT-ACATGAATA
*
3725054 ATAAAAATACATGAATA
1 ATAATAATACATGAATA
3725071 A-AAT-ATACAT
1 ATAATAATACAT
3725081 ATAATAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
15 6 0.15
16 2 0.05
17 10 0.24
18 13 0.32
19 10 0.24
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.30
Consensus pattern (17 bp):
ATAATAATACATGAATA
Found at i:3725089 original size:15 final size:15
Alignment explanation
Indices: 3725011--3725090 Score: 54
Period size: 15 Copynumber: 4.8 Consensus size: 15
3725001 GAAAATAATT
3725011 ATATATATAATATATAC
1 ATATA-ATAA-ATATAC
3725028 ATATAATAATAATAATAAC
1 ATATAAT-A-AAT-AT-AC
*
3725047 ATGAATAATAAAAATAC
1 AT--ATAATAAATATAC
*
3725064 AT-GAATAAAATATAC
1 ATATAAT-AAATATAC
3725079 ATATAATAAATA
1 ATATAATAAATA
3725091 AAGGGACTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 18
0.70 0.05 0.25
Matches are distributed among these distances:
14 3 0.06
15 14 0.27
16 5 0.10
17 12 0.24
18 5 0.10
19 6 0.12
20 1 0.02
21 5 0.10
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.31
Consensus pattern (15 bp):
ATATAATAAATATAC
Found at i:3725482 original size:37 final size:37
Alignment explanation
Indices: 3725432--3725536 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
3725422 GTTCTTTTGG
* * *
3725432 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
* * * *
3725469 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
*
3725506 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAG
3725537 GACGAAAATG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
Done.