Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008053.1 Hibiscus syriacus cultivar Beakdansim tig00110548_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: 6772376
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 32
Found at i:2724027 original size:199 final size:199
Alignment explanation
Indices: 2723681--2724944 Score: 2307
Period size: 199 Copynumber: 6.3 Consensus size: 199
2723671 AACCACTACC
2723681 TTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCC
1 TTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCC
*
2723746 TGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAAATATATTAGTGTCGACACATTATTTA
66 TGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTA
* * *
2723811 TACATATTTTTTCATAAAACCGGTAGACA-TGTACCGGTTAGATTGAAAAATTACATATTACATT
131 GACATATTTTCTCATAAAACCGGTATA-ATTGTACCGGTTAGATTGAAAAATTACATATTACATT
2723875 ATACT
195 ATACT
2723880 TTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCC
1 TTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCC
*
2723945 TTTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTA
66 TGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTA
* *
2724010 TACATATTATCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTA
131 GACATATTTTCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTA
2724075 TACT
196 TACT
2724079 TTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCC
1 TTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCC
2724144 TGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTA
66 TGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTA
*
2724209 GACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTA
131 GACATATTTTCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTA
2724274 TACT
196 TACT
2724278 TTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCC
1 TTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCC
2724343 TGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTA
66 TGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTA
*
2724408 GACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTA
131 GACATATTTTCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTA
2724473 TACT
196 TACT
* * *
2724477 TTTGGGTTCGATGATTTTGCGATCGACACTTTTTATATATGGATCGACATTTTATGGGTGCACCT
1 TTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCC
*
2724542 TGTTTTCCATTCATTCTGGAAAAGAAATATCGACACAAACTATATTAGTGTCGACACATTATTTA
66 TGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTA
*
2724607 GACATATTTTTTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTA
131 GACATATTTTCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTA
2724672 TACT
196 TACT
2724676 TTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCC
1 TTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCC
*
2724741 TGTTTTCCATTCATTCTGGAAAAGAAATATCGACACAAACTATATTAGTGTCGACACATTATTTA
66 TGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTA
* *
2724806 GACATATTTTTTCATAAAACCGGTAGACA-TGTACCGGTTAGATTGAAAAATTACATATTACATT
131 GACATATTTTCTCATAAAACCGGTATA-ATTGTACCGGTTAGATTGAAAAATTACATATTACATT
2724870 ATACT
195 ATACT
* * *
2724875 TTTGGTTTTCGATGTTTTTGGGATTGACACTTTTTATATATGGATCGACACTTTATGGGTGCACC
1 TTTGG-GTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACC
2724940 CTGTT
65 CTGTT
2724945 GGCCATATTG
Statistics
Matches: 1041, Mismatches: 21, Indels: 5
0.98 0.02 0.00
Matches are distributed among these distances:
198 1 0.00
199 978 0.94
200 62 0.06
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (199 bp):
TTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCC
TGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTTA
GACATATTTTCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTA
TACT
Found at i:2725719 original size:21 final size:21
Alignment explanation
Indices: 2725677--2725719 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2725667 TTTCTGGGTT
* * *
2725677 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
2725698 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
2725719 A
1 A
2725720 CGAATATGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:2725779 original size:66 final size:68
Alignment explanation
Indices: 2725699--2725849 Score: 234
Period size: 67 Copynumber: 2.2 Consensus size: 68
2725689 ACCCATTCAA
*
2725699 GGGGAACCGATACCCCCTCAACGAATATG-ATTTCCAGAATGCTAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
2725763 -GG
66 GGG
* * * *
2725765 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGAATGCTTGTGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
2725830 GGG
66 GGG
*
2725833 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
2725850 ATGAGAAAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
66 27 0.35
67 32 0.42
68 18 0.23
ACGTcount: A:0.27, C:0.28, G:0.26, T:0.18
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
GGG
Found at i:2726533 original size:151 final size:149
Alignment explanation
Indices: 2726335--2726628 Score: 534
Period size: 151 Copynumber: 2.0 Consensus size: 149
2726325 AGGGTCTACG
* *
2726335 CGGTTCTTTAGGACATATGTATATTCTTTGGAACCTGTGTGAAGTCTTGAAAGACACATACTTGA
1 CGGTTCTTTAGGACATATATATATTCTTTGGAACCTGTGTGAAGTCTTCAAAGACACATACTTGA
* *
2726400 TCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTATATGGC
66 TCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATATGGC
2726465 ACTACGGTGCAATCCTATT
131 ACTACGGTGCAATCCTATT
2726484 CGGTTCTTTAGGACATATATATATATTCTTTGGAACCTGTGTGAAGTCTTCAAAGACACATACTT
1 CGGTTCTTTAGGAC--ATATATATATTCTTTGGAACCTGTGTGAAGTCTTCAAAGACACATACTT
2726549 GATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATATG
64 GATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATATG
2726614 GCACTACGGTGCAAT
129 GCACTACGGTGCAAT
2726629 TCTACGGGGC
Statistics
Matches: 139, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
149 14 0.10
151 125 0.90
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (149 bp):
CGGTTCTTTAGGACATATATATATTCTTTGGAACCTGTGTGAAGTCTTCAAAGACACATACTTGA
TCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATATGGC
ACTACGGTGCAATCCTATT
Found at i:2726657 original size:23 final size:23
Alignment explanation
Indices: 2726613--2726657 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2726603 ATCATTATAT
*
2726613 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
2726636 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
2726658 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:2732780 original size:66 final size:68
Alignment explanation
Indices: 2732710--2732860 Score: 225
Period size: 67 Copynumber: 2.2 Consensus size: 68
2732700 ACCCATTAAA
*
2732710 GGGGAACCGATACCCCCTCAACGAATATG-ATTTCCAGAATGCTAGAGGGAAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGAAATCGATACCCCCA
2732774 -GG
66 GGG
* * * * *
2732776 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGAATGCTTGTGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGAAATCGATACCCCCA
2732841 GGG
66 GGG
*
2732844 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
2732861 ATGAGAAAAA
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
66 27 0.36
67 31 0.41
68 18 0.24
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGAAATCGATACCCCCA
GGG
Found at i:2733618 original size:149 final size:149
Alignment explanation
Indices: 2733345--2733636 Score: 548
Period size: 149 Copynumber: 2.0 Consensus size: 149
2733335 AGGGTCTACG
* *
2733345 CGGTTCTTTAGGACATATGTATATTCTTTGGAACCTGTGTGAAGTCTTGAAAGACACATACTTGA
1 CGGTTCTTTAGGACATATATATATTCTTTGGAACCTGTGTGAAGTCTTCAAAGACACATACTTGA
* *
2733410 TCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTATATGGC
66 TCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATATGGC
2733475 ACTACGGTGCAATCCTATT
131 ACTACGGTGCAATCCTATT
2733494 CGGTTCTTTAGGACATATATATATTCTTTGGAACCTGTGTGAAGTCTTCAAAGACACATACTTGA
1 CGGTTCTTTAGGACATATATATATTCTTTGGAACCTGTGTGAAGTCTTCAAAGACACATACTTGA
2733559 TCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATATGGC
66 TCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATATGGC
2733624 ACTACGGTGCAAT
131 ACTACGGTGCAAT
2733637 TCTACGGGGC
Statistics
Matches: 139, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 139 1.00
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (149 bp):
CGGTTCTTTAGGACATATATATATTCTTTGGAACCTGTGTGAAGTCTTCAAAGACACATACTTGA
TCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATATGGC
ACTACGGTGCAATCCTATT
Found at i:2733665 original size:23 final size:23
Alignment explanation
Indices: 2733621--2733665 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2733611 ATCATTATAT
*
2733621 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
2733644 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
2733666 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:2734386 original size:19 final size:19
Alignment explanation
Indices: 2734340--2734388 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
2734330 TTATATTCAC
*
2734340 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
2734359 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
2734378 ATACAAAATTA
1 ATACAAAATTA
2734389 ACCCTACATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:2736218 original size:33 final size:33
Alignment explanation
Indices: 2736181--2736246 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
2736171 CATCTTAATA
*
2736181 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
2736214 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
2736247 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:2736304 original size:21 final size:21
Alignment explanation
Indices: 2736279--2736343 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
2736269 CCCCTTATGC
* *
2736279 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
* *
2736300 CTCTCGAGTTTCTCTACGACT
1 CTCTCAAGTTTCTCTTCGACT
**
2736321 CGATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
2736342 CT
1 CT
2736344 TGATTGTCTT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.17, C:0.31, G:0.14, T:0.38
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:2738623 original size:20 final size:19
Alignment explanation
Indices: 2738577--2738623 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
2738567 TCCGGTATCA
*
2738577 TTTTACCGGTTTTATCCTT
1 TTTTACCGGTTTTATCATT
*
2738596 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
2738617 TTTTACC
1 TTTTACC
2738624 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.17, C:0.19, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:2738781 original size:20 final size:20
Alignment explanation
Indices: 2738758--2738804 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
2738748 TCCGGTAACG
*
2738758 TTTTACCGGTTTTATCATTT
1 TTTTACCGGTTTTATCATAT
2738778 TTTTACCGGTTTTATCATAT
1 TTTTACCGGTTTTATCATAT
2738798 TTTTACC
1 TTTTACC
2738805 TGGTATATCG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.17, C:0.17, G:0.09, T:0.57
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:2738813 original size:20 final size:20
Alignment explanation
Indices: 2738758--2738813 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
2738748 TCCGGTAACG
* *
2738758 TTTTACCGGTTTTATCATTT
1 TTTTACCGGTTATATCATAT
*
2738778 TTTTACCGGTTTTATCATAT
1 TTTTACCGGTTATATCATAT
2738798 TTTTACCTGG-TATATC
1 TTTTACC-GGTTATATC
2738814 GTTTTGGATC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 31 0.94
21 2 0.06
ACGTcount: A:0.18, C:0.16, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTATATCATAT
Found at i:2738848 original size:181 final size:182
Alignment explanation
Indices: 2738544--2739016 Score: 696
Period size: 181 Copynumber: 2.6 Consensus size: 182
2738534 CGTACTTACG
* * * * *
2738544 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCCTTTTGATACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTTATACCGGTTT
* * *
2738609 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
* *
2738674 AGGCGCTATAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* *
2738725 AAAGTATCGACACTTTTAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTTTTACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTTATACCGGTTT
* *
2738790 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** *
2738855 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * * * * *
2738907 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTGACCGATTTTATCATTTCTATACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTTATACCGGTTT
* * *
2738972 TGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
2739017 AATTTGGATC
Statistics
Matches: 262, Mismatches: 29, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
181 164 0.63
182 98 0.37
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (182 bp):
AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTTATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:2743770 original size:40 final size:35
Alignment explanation
Indices: 2743689--2743800 Score: 152
Period size: 35 Copynumber: 3.2 Consensus size: 35
2743679 AAAATAGTCC
* *
2743689 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
2743724 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
** * * *
2743759 TCAATTAAATTTTAAACCCCAAATTCTAAAATACT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
2743794 TCAATTT
1 TCAATTT
2743801 AAGGTTTAGA
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 67 1.00
ACGTcount: A:0.41, C:0.22, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:2743842 original size:35 final size:35
Alignment explanation
Indices: 2743796--2743870 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
2743786 AAAATACTTC
* *
2743796 AATTTAAGGTTTAGAATGTAATTAAATTATTTTGA
1 AATTTAAGGTTTAGAATGAAATTAAAGTATTTTGA
* * *
2743831 AATTTAGGGTTTAGAATGAAATTAAGGTGTTTTGA
1 AATTTAAGGTTTAGAATGAAATTAAAGTATTTTGA
2743866 AATTT
1 AATTT
2743871 TGAACATGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.44
Consensus pattern (35 bp):
AATTTAAGGTTTAGAATGAAATTAAAGTATTTTGA
Found at i:2746330 original size:21 final size:21
Alignment explanation
Indices: 2746263--2746331 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
2746253 CGAAAATATT
* *
2746263 AATATAAAAAATATTCATTTTA
1 AATAAAAAAAATAAT-ATTTTA
* * * *
2746285 CATAGAAAAATTAATATTTTT
1 AATAAAAAAAATAATATTTTA
2746306 AATAAAAAAAATAATATTTTA
1 AATAAAAAAAATAATATTTTA
2746327 AATAA
1 AATAA
2746332 CGCTATACTA
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
21 27 0.71
22 11 0.29
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (21 bp):
AATAAAAAAAATAATATTTTA
Found at i:2751755 original size:20 final size:20
Alignment explanation
Indices: 2751718--2751756 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2751708 TAGTCAAGTG
**
2751718 ATATCGATACTCGGGGCCTA
1 ATATCGATACTCAAGGCCTA
*
2751738 ATATTGATACTCAAGGCCT
1 ATATCGATACTCAAGGCCT
2751757 TGATCAAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (20 bp):
ATATCGATACTCAAGGCCTA
Found at i:2757912 original size:2 final size:2
Alignment explanation
Indices: 2757905--2757939 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2757895 TAATTTTTCA
2757905 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2757940 ATACATAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2758288 original size:18 final size:17
Alignment explanation
Indices: 2758265--2758397 Score: 70
Period size: 18 Copynumber: 7.6 Consensus size: 17
2758255 ATGTTTATAG
*
2758265 TTATCAGACATTTCACCA
1 TTATCAGACATTT-ACAA
* *
2758283 TTATCAAATATTTACAA
1 TTATCAGACATTTACAA
* * *
2758300 TTATCAGATGATTTTCAG
1 TTATCAGA-CATTTACAA
* * *
2758318 TTATCAGATATTTATAT
1 TTATCAGACATTTACAA
* * *
2758335 TTATCAGATGATTTTCAG
1 TTATCAGA-CATTTACAA
*
2758353 TTATCAGATATTTACAGA
1 TTATCAGACATTTACA-A
* **
2758371 -TATCATATGTTTTACAA
1 TTATCAGA-CATTTACAA
2758388 TTATCAGACA
1 TTATCAGACA
2758398 CATATTGATA
Statistics
Matches: 86, Mismatches: 24, Indels: 11
0.71 0.20 0.09
Matches are distributed among these distances:
17 36 0.42
18 50 0.58
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (17 bp):
TTATCAGACATTTACAA
Found at i:2758322 original size:35 final size:35
Alignment explanation
Indices: 2758283--2758395 Score: 149
Period size: 35 Copynumber: 3.2 Consensus size: 35
2758273 CATTTCACCA
*
2758283 TTATCAAATATTTACAATTATCAGATGATTTTCAG
1 TTATCAGATATTTACAATTATCAGATGATTTTCAG
* *
2758318 TTATCAGATATTTATATTTATCAGATGATTTTCAG
1 TTATCAGATATTTACAATTATCAGATGATTTTCAG
* *
2758353 TTATCAGATATTTACAGA-TATCATATG-TTTTACAA
1 TTATCAGATATTTACA-ATTATCAGATGATTTT-CAG
2758388 TTATCAGA
1 TTATCAGA
2758396 CACATATTGA
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
34 4 0.06
35 65 0.94
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (35 bp):
TTATCAGATATTTACAATTATCAGATGATTTTCAG
Found at i:2760048 original size:89 final size:90
Alignment explanation
Indices: 2759932--2760126 Score: 245
Period size: 89 Copynumber: 2.2 Consensus size: 90
2759922 ATCCAAGGCT
* * **
2759932 TTTA-ATTATTGGGTTGCCAAAAGTAAAATCAAAGGATTAGATCATTTTGACTATT-G-TTTTGC
1 TTTATATTATTGGGTTGCAAAAAGTAAAACCAAAGGATTAGATCATTTTGACTATTAGATTACG-
*
2759994 AAAAACAAAATCAAAGGATTAGTTCC
65 AAAAACAAAATCAAAAGATTAGTTCC
* * * *
2760020 TTTATATTATTGGGTTGCAAAAATTAAAACCAAAGGATTAGTTCCTTTTGATTATTAGATTACGA
1 TTTATATTATTGGGTTGCAAAAAGTAAAACCAAAGGATTAGATCATTTTGACTATTAGATTACGA
**
2760085 AAATTAAAATCAAAAGATTAGTTCC
66 AAAACAAAATCAAAAGATTAGTTCC
2760110 -TTATGATTATTGGGTTG
1 TTTAT-ATTATTGGGTTG
2760127 GTGAAATTAA
Statistics
Matches: 92, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
88 4 0.04
89 49 0.53
90 36 0.39
91 3 0.03
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (90 bp):
TTTATATTATTGGGTTGCAAAAAGTAAAACCAAAGGATTAGATCATTTTGACTATTAGATTACGA
AAAACAAAATCAAAAGATTAGTTCC
Found at i:2760063 original size:45 final size:46
Alignment explanation
Indices: 2759936--2760126 Score: 221
Period size: 45 Copynumber: 4.3 Consensus size: 46
2759926 AAGGCTTTTA
* * * *
2759936 ATTATTGGGTTGCCAAAAGTAAAATCAAAGGATTAGATCATTT-TG
1 ATTATTGGGTTGCAAAAATTAAAATCAAAGGATTAGTTCCTTTATG
* ** *
2759981 ACTATTGTTTTGCAAAAA-CAAAATCAAAGGATTAGTTCCTTTAT-
1 ATTATTGGGTTGCAAAAATTAAAATCAAAGGATTAGTTCCTTTATG
*
2760025 ATTATTGGGTTGCAAAAATTAAAACCAAAGGATTAGTTCCTTT-TG
1 ATTATTGGGTTGCAAAAATTAAAATCAAAGGATTAGTTCCTTTATG
* * * * *
2760070 ATTATTAGATTACGAAAATTAAAATCAAAAGATTAGTTCC-TTATG
1 ATTATTGGGTTGCAAAAATTAAAATCAAAGGATTAGTTCCTTTATG
2760115 ATTATTGGGTTG
1 ATTATTGGGTTG
2760127 GTGAAATTAA
Statistics
Matches: 121, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
44 39 0.32
45 82 0.68
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (46 bp):
ATTATTGGGTTGCAAAAATTAAAATCAAAGGATTAGTTCCTTTATG
Found at i:2760360 original size:49 final size:49
Alignment explanation
Indices: 2760294--2760502 Score: 161
Period size: 58 Copynumber: 3.9 Consensus size: 49
2760284 GTTGATTCTA
2760294 ACTTCGTAAGGAAAATAAATAT-TTGAATTTATTTCCTTGAGAATCTTTG
1 ACTTCGTAAGGAAAATAAAT-TGTTGAATTTATTTCCTTGAGAATCTTTG
* *
2760343 ACTTTGTAAGGATAATAAATTGTTGAATTTATTTCCTTGAGAATCTTGAATG
1 ACTTCGTAAGGAAAATAAATTGTTGAATTTATTTCCTTGAGAATCTT---TG
* * * *
2760395 ATTCTAACTTTGTATGGAAAATAAATTGTTAAATTTAATTT-CTTAAGAATCTTGAATG
1 ------ACTTCGTAAGGAAAATAAATTGTTGAATTT-ATTTCCTTGAGAATCTT---TG
*
2760453 ATTCTAACTCGGTACGGAAAATAAATTGTTGAATTTATTTCCTTGAGAAT
1 A--CT---TC-GTAAGGAAAATAAATTGTTGAATTTATTTCCTTGAGAAT
2760503 ATTAAATGAT
Statistics
Matches: 132, Mismatches: 10, Indels: 27
0.78 0.06 0.16
Matches are distributed among these distances:
48 1 0.01
49 43 0.33
52 3 0.02
54 2 0.02
57 5 0.04
58 74 0.56
59 4 0.03
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (49 bp):
ACTTCGTAAGGAAAATAAATTGTTGAATTTATTTCCTTGAGAATCTTTG
Found at i:2760408 original size:58 final size:58
Alignment explanation
Indices: 2760343--2760631 Score: 270
Period size: 58 Copynumber: 5.0 Consensus size: 58
2760333 AGAATCTTTG
* *
2760343 ACTTTGTAAGGATAATAAATTGTTGAATTTATTTCCTTGAGAATCTTGAATGATTCTA
1 ACTTTGTAAGGAAAATAAATTGTTAAATTTATTTCCTTGAGAATCTTGAATGATTCTA
* *
2760401 ACTTTGTATGGAAAATAAATTGTTAAATTTAATTT-CTTAAGAATCTTGAATGATTCTA
1 ACTTTGTAAGGAAAATAAATTGTTAAATTT-ATTTCCTTGAGAATCTTGAATGATTCTA
** * * * * *
2760459 ACTCGGTACGGAAAATAAATTGTTGAATTTATTTCCTTGAGAATATTAAATGATT-TT
1 ACTTTGTAAGGAAAATAAATTGTTAAATTTATTTCCTTGAGAATCTTGAATGATTCTA
* ** * * * *
2760516 ATTTTGTAAAAATAAATAAATTGATT-AATTTATTTTCTTAAGAATCTTGAAGGATCCT-
1 ACTTTGTAAGGA-AAATAAATTG-TTAAATTTATTTCCTTGAGAATCTTGAATGATTCTA
* *
2760574 A-TTATGCAAAAGG-AAATAAATTGTTAAATTTATTTTCC-TGTGAATCTT-ATATGATTCT
1 ACTT-TG--TAAGGAAAATAAATTGTTAAATTTA-TTTCCTTGAGAATCTTGA-ATGATTCT
2760632 GGTTGTAAAA
Statistics
Matches: 188, Mismatches: 32, Indels: 22
0.78 0.13 0.09
Matches are distributed among these distances:
57 16 0.09
58 159 0.85
59 11 0.06
60 2 0.01
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.43
Consensus pattern (58 bp):
ACTTTGTAAGGAAAATAAATTGTTAAATTTATTTCCTTGAGAATCTTGAATGATTCTA
Found at i:2760533 original size:116 final size:116
Alignment explanation
Indices: 2760356--2760566 Score: 318
Period size: 116 Copynumber: 1.8 Consensus size: 116
2760346 TTGTAAGGAT
* * ***
2760356 AATAAATTGTTGAATTTATTTCCTTGAGAATCTTGAATGATTCTAACTTTGTATGGAAAATAAAT
1 AATAAATTGTTGAATTTATTTCCTTGAGAATATTAAATGATTCTAACTTTGTAAAAAAAATAAAT
2760421 TG-TTAAATTTAATTTCTTAAGAATCTTGAATGATTCTAACTCGGTACGGAA
66 TGATT-AATTTAATTTCTTAAGAATCTTGAATGATTCTAACTCGGTACGGAA
* *
2760472 AATAAATTGTTGAATTTATTTCCTTGAGAATATTAAATGATT-TTATTTTGTAAAAATAAATAAA
1 AATAAATTGTTGAATTTATTTCCTTGAGAATATTAAATGATTCTAACTTTGTAAAAA-AAATAAA
*
2760536 TTGATTAATTTATTTTCTTAAGAATCTTGAA
65 TTGATTAATTTAATTTCTTAAGAATCTTGAA
2760567 GGATCCTATT
Statistics
Matches: 85, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
115 9 0.11
116 74 0.87
117 2 0.02
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.43
Consensus pattern (116 bp):
AATAAATTGTTGAATTTATTTCCTTGAGAATATTAAATGATTCTAACTTTGTAAAAAAAATAAAT
TGATTAATTTAATTTCTTAAGAATCTTGAATGATTCTAACTCGGTACGGAA
Found at i:2760591 original size:116 final size:114
Alignment explanation
Indices: 2760350--2760669 Score: 308
Period size: 116 Copynumber: 2.8 Consensus size: 114
2760340 TTGACTTTGT
* * ***
2760350 AAGGATAATAAATTGTTGAATTTATTTCCTTGAGAATCTTGAATGATTCTAACTTTGTATGGAAA
1 AAGGA-AATAAATTGTTGAATTTATTTCCTTGAGAATCTTAAATGATT-TTACTTTGTAAAAAAA
* * * **
2760415 ATAAATTG-TTAAATTTAATTTCTTAAGAATCTTGAATGATTCTAACTCGGT
64 ATAAATTGATT-AATTTATTTTCTTAAGAATCTTGAAGGATCCTAACTCGAA
* * *
2760466 ACGGAAAATAAATTGTTGAATTTATTTCCTTGAGAATATTAAATGATTTTATTTTGTAAAAATAA
1 AAGG-AAATAAATTGTTGAATTTATTTCCTTGAGAATCTTAAATGATTTTACTTTGTAAAAA-AA
2760531 ATAAATTGATTAATTTATTTTCTTAAGAATCTTGAAGGATCCTATTA-T-GCAA
64 ATAAATTGATTAATTTATTTTCTTAAGAATCTTGAAGGATCCTA--ACTCG-AA
* * * * ** *
2760583 AAGGAAATAAATTGTTAAATTTATTTTCC-TGTGAATCTTATATGATTCT-GGTTGTAAAAGGAA
1 AAGGAAATAAATTGTTGAATTTA-TTTCCTTGAGAATCTTAAATGATTTTACTTTGTAAAA-AAA
* **
2760646 ATAAATCGAAGAATTTATTTTCTT
64 ATAAATTGATTAATTTATTTTCTT
2760670 GTTTTGTAAA
Statistics
Matches: 171, Mismatches: 25, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
115 40 0.23
116 118 0.69
117 12 0.07
118 1 0.01
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (114 bp):
AAGGAAATAAATTGTTGAATTTATTTCCTTGAGAATCTTAAATGATTTTACTTTGTAAAAAAAAT
AAATTGATTAATTTATTTTCTTAAGAATCTTGAAGGATCCTAACTCGAA
Found at i:2760688 original size:39 final size:39
Alignment explanation
Indices: 2760634--2760847 Score: 249
Period size: 39 Copynumber: 5.5 Consensus size: 39
2760624 ATGATTCTGG
* * * *
2760634 TTGTAAAAGGAAATAAATCGAAGAATTTATTTTCTTGTT
1 TTGTAAAAGAAAATAAATCGTAGAATTTATTTTCCTATT
*
2760673 TTGTAAAAGAAAATAAATCGTTG-ATTTACTTTT-CTATT
1 TTGTAAAAGAAAATAAATCGTAGAATTTA-TTTTCCTATT
*
2760711 TTGTAGAAAG-AAATAAATCGGAGAATTTATTTTCCTATT
1 TTGTA-AAAGAAAATAAATCGTAGAATTTATTTTCCTATT
* * *
2760750 TTGTAAAAGAAAATAAATCGTTGGATTTACTTTT-TTATT
1 TTGTAAAAGAAAATAAATCGTAGAATTTA-TTTTCCTATT
* * *
2760789 TTGTAAAAGAAAATAAATCGTTGGATTTAGTTTCCTATT
1 TTGTAAAAGAAAATAAATCGTAGAATTTATTTTCCTATT
2760828 TTGTAAAA-AGAAATAAATCG
1 TTGTAAAAGA-AAATAAATCG
2760848 AAACAAATAG
Statistics
Matches: 154, Mismatches: 13, Indels: 16
0.84 0.07 0.09
Matches are distributed among these distances:
38 36 0.23
39 114 0.74
40 4 0.03
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.41
Consensus pattern (39 bp):
TTGTAAAAGAAAATAAATCGTAGAATTTATTTTCCTATT
Found at i:2760761 original size:77 final size:77
Alignment explanation
Indices: 2760634--2760847 Score: 306
Period size: 78 Copynumber: 2.8 Consensus size: 77
2760624 ATGATTCTGG
* *
2760634 TTGTAAAAGGAAATAAATCGAAGAATTTATTTTCTTGTTTTGTAAAAGAAAATAAATCGTT-GAT
1 TTGTAAAA-GAAATAAATCGAAGAATTTATTTTCCTATTTTGTAAAAGAAAATAAATCGTTGGAT
2760698 TTACTTTTCTATT
65 TTACTTTTCTATT
*
2760711 TTGTAGAAAGAAATAAATCGGAGAATTTATTTTCCTATTTTGTAAAAGAAAATAAATCGTTGGAT
1 TTGTA-AAAGAAATAAATCGAAGAATTTATTTTCCTATTTTGTAAAAGAAAATAAATCGTTGGAT
*
2760776 TTACTTTTTTATT
65 TTACTTTTCTATT
** * *
2760789 TTGTAAAAGAAAATAAATCGTTGGATTTAGTTTCCTATTTTGTAAAA-AGAAATAAATCG
1 TTGTAAAAG-AAATAAATCGAAGAATTTATTTTCCTATTTTGTAAAAGA-AAATAAATCG
2760848 AAACAAATAG
Statistics
Matches: 125, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
77 59 0.47
78 66 0.53
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.41
Consensus pattern (77 bp):
TTGTAAAAGAAATAAATCGAAGAATTTATTTTCCTATTTTGTAAAAGAAAATAAATCGTTGGATT
TACTTTTCTATT
Found at i:2761030 original size:38 final size:39
Alignment explanation
Indices: 2760957--2761040 Score: 109
Period size: 38 Copynumber: 2.2 Consensus size: 39
2760947 AATCATTGGG
**
2760957 TTTATTTTTCTATTTTTTAAAAGGAAATAAATTGTT-AGA
1 TTTATTTTTCTATTTTGAAAAAGGAAATAAATTGTTGA-A
* *
2760996 TTTATTTTT-TGTTTTGAAAAAGGAAATAACTTGTTGAA
1 TTTATTTTTCTATTTTGAAAAAGGAAATAAATTGTTGAA
2761034 TTTATTT
1 TTTATTT
2761041 CCTTGATAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
38 30 0.75
39 10 0.25
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.52
Consensus pattern (39 bp):
TTTATTTTTCTATTTTGAAAAAGGAAATAAATTGTTGAA
Found at i:2761162 original size:39 final size:40
Alignment explanation
Indices: 2761067--2761180 Score: 149
Period size: 39 Copynumber: 2.8 Consensus size: 40
2761057 TGATTATGAG
* * *
2761067 TTGTAAAAGGAAAAATAAATCGTTAGATTTTTTTTTCCTATT
1 TTGTAAAA-G-AAAATAAATCGTTGGATTTATTTTTCCTAGT
*
2761109 TTGTAAAAGAAAATAAATCATTGGATTTATTTTT-CTAGT
1 TTGTAAAAGAAAATAAATCGTTGGATTTATTTTTCCTAGT
* *
2761148 TTGTAAAATAAAATAAATCGTTGAATTTATTTT
1 TTGTAAAAGAAAATAAATCGTTGGATTTATTTT
2761181 CTTGGACATT
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
39 34 0.52
40 22 0.34
41 1 0.02
42 8 0.12
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (40 bp):
TTGTAAAAGAAAATAAATCGTTGGATTTATTTTTCCTAGT
Found at i:2764467 original size:14 final size:13
Alignment explanation
Indices: 2764448--2764488 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
2764438 TTAGATTTTT
2764448 TTAAAAATAAATTA
1 TTAAAAAT-AATTA
2764462 TTAAAAAT-A-TA
1 TTAAAAATAATTA
2764473 TTAAAAATACATTA
1 TTAAAAATA-ATTA
2764487 TT
1 TT
2764489 GATGAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
11 10 0.42
12 1 0.04
13 1 0.04
14 12 0.50
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (13 bp):
TTAAAAATAATTA
Found at i:2764764 original size:7 final size:7
Alignment explanation
Indices: 2764752--2764777 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2764742 TGTGGTAAGG
2764752 TTTAGGA
1 TTTAGGA
2764759 TTTAGGA
1 TTTAGGA
2764766 TTTAGGA
1 TTTAGGA
2764773 TTTAG
1 TTTAG
2764778 AGTTTATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (7 bp):
TTTAGGA
Found at i:2764783 original size:14 final size:13
Alignment explanation
Indices: 2764749--2764783 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
2764739 TTATGTGGTA
2764749 AGGTTTAGGATTT
1 AGGTTTAGGATTT
2764762 AGGATTTAGGATTT
1 AGG-TTTAGGATTT
2764776 AGAGTTTA
1 AG-GTTTA
2764784 TATGGTAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 3 0.15
14 16 0.80
15 1 0.05
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.43
Consensus pattern (13 bp):
AGGTTTAGGATTT
Found at i:2764818 original size:21 final size:20
Alignment explanation
Indices: 2764794--2764850 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
2764784 TATGGTAGGA
2764794 TTTAGGGTTTAGAGTTTAGAG
1 TTTAGGGTTTA-AGTTTAGAG
* * *
2764815 TTTA-TGTATTAAAGGTTAGGG
1 TTTAGGGT-TT-AAGTTTAGAG
2764836 TTTAGGGTTTAAGTT
1 TTTAGGGTTTAAGTT
2764851 ATGCACATGA
Statistics
Matches: 28, Mismatches: 5, Indels: 7
0.70 0.12 0.17
Matches are distributed among these distances:
20 6 0.21
21 19 0.68
22 3 0.11
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.46
Consensus pattern (20 bp):
TTTAGGGTTTAAGTTTAGAG
Found at i:2767811 original size:15 final size:15
Alignment explanation
Indices: 2767791--2767846 Score: 67
Period size: 15 Copynumber: 3.5 Consensus size: 15
2767781 AGGGGGTATC
*
2767791 GATTCCCCGGGAACA
1 GATTCCCCGGGTACA
*
2767806 GATTCCCCCAGGGGTACC
1 GATT-CCCC--GGGTACA
2767824 GATTCCCCGGGTACA
1 GATTCCCCGGGTACA
2767839 GATTCCCC
1 GATTCCCC
2767847 CTGCATGGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
15 18 0.51
16 4 0.11
17 4 0.11
18 9 0.26
ACGTcount: A:0.20, C:0.38, G:0.25, T:0.18
Consensus pattern (15 bp):
GATTCCCCGGGTACA
Found at i:2767827 original size:33 final size:34
Alignment explanation
Indices: 2767763--2767847 Score: 127
Period size: 33 Copynumber: 2.5 Consensus size: 34
2767753 ATTGCCCAGA
*
2767763 GGGAACAGATTCTCCCACAGGGGGTATCGATTCCCC
1 GGGAACAGATTC-CCC-CAGGGGGTACCGATTCCCC
2767799 GGGAACAGATTCCCCCA-GGGGTACCGATTCCCC
1 GGGAACAGATTCCCCCAGGGGGTACCGATTCCCC
*
2767832 GGGTACAGATTCCCCC
1 GGGAACAGATTCCCCC
2767848 TGCATGGTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
33 30 0.64
34 2 0.04
35 3 0.06
36 12 0.26
ACGTcount: A:0.21, C:0.34, G:0.27, T:0.18
Consensus pattern (34 bp):
GGGAACAGATTCCCCCAGGGGGTACCGATTCCCC
Found at i:2767990 original size:21 final size:21
Alignment explanation
Indices: 2767960--2768001 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2767950 ATTTGAATAT
*
2767960 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
*
2767981 TATGATGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
2768002 CCCATTATGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:2768068 original size:20 final size:22
Alignment explanation
Indices: 2768030--2768069 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
2768020 TTTTTGCAGA
2768030 AAAATCATTCCCAAACGGCTCC
1 AAAATCATTCCCAAACGGCTCC
2768052 AAAA-CATTCCC-AACGGCT
1 AAAATCATTCCCAAACGGCT
2768070 AGATATGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.35, G:0.10, T:0.17
Consensus pattern (22 bp):
AAAATCATTCCCAAACGGCTCC
Found at i:2770695 original size:15 final size:15
Alignment explanation
Indices: 2770675--2770730 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
2770665 AGGGGGTATC
2770675 GATTCCCCGGGAACA
1 GATTCCCCGGGAACA
*
2770690 GATTCCCCCAGGGGTATC-
1 GATT-CCCC--GGG-AACA
*
2770708 GATTCCCCGGGTACA
1 GATTCCCCGGGAACA
2770723 GATTCCCC
1 GATTCCCC
2770731 CCTGTATGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
14 1 0.03
15 15 0.45
16 4 0.12
17 4 0.12
18 7 0.21
19 2 0.06
ACGTcount: A:0.20, C:0.36, G:0.25, T:0.20
Consensus pattern (15 bp):
GATTCCCCGGGAACA
Found at i:2770709 original size:33 final size:34
Alignment explanation
Indices: 2770647--2770731 Score: 136
Period size: 33 Copynumber: 2.5 Consensus size: 34
2770637 ATTGCCCAGA
2770647 GGGAACAGATTCTCCCCCAGGGGGTATCGATTCCCC
1 GGGAACAGA-T-TCCCCCAGGGGGTATCGATTCCCC
2770683 GGGAACAGATTCCCCCA-GGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCAGGGGGTATCGATTCCCC
*
2770716 GGGTACAGATTCCCCC
1 GGGAACAGATTCCCCC
2770732 CTGTATGGTT
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
33 31 0.65
34 7 0.15
35 1 0.02
36 9 0.19
ACGTcount: A:0.20, C:0.34, G:0.27, T:0.19
Consensus pattern (34 bp):
GGGAACAGATTCCCCCAGGGGGTATCGATTCCCC
Found at i:2770713 original size:18 final size:18
Alignment explanation
Indices: 2770659--2770715 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
2770649 GAACAGATTC
2770659 TCCCCCAGGGGGTATCGAT
1 TCCCCCA-GGGGTATCGAT
*
2770678 T-CCCC--GGG-AACAGAT
1 TCCCCCAGGGGTATC-GAT
2770693 TCCCCCAGGGGTATCGAT
1 TCCCCCAGGGGTATCGAT
2770711 TCCCC
1 TCCCC
2770716 GGGTACAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 11
0.70 0.05 0.25
Matches are distributed among these distances:
14 2 0.06
15 7 0.23
16 4 0.13
18 15 0.48
19 3 0.10
ACGTcount: A:0.18, C:0.37, G:0.26, T:0.19
Consensus pattern (18 bp):
TCCCCCAGGGGTATCGAT
Found at i:2770875 original size:21 final size:21
Alignment explanation
Indices: 2770845--2770886 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2770835 ATTTGAATAT
2770845 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
* *
2770866 TATGATGGGGTTCCGATTCCC
1 TATGAAGGGGTACCGATTCCC
2770887 CCATTCTGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.24, G:0.29, T:0.29
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:2770947 original size:21 final size:21
Alignment explanation
Indices: 2770914--2770953 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
2770904 TTTTTGCAGA
*
2770914 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
2770936 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
2770954 ATATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:2772689 original size:3 final size:3
Alignment explanation
Indices: 2772683--2772798 Score: 115
Period size: 3 Copynumber: 37.7 Consensus size: 3
2772673 TTTATTTTTT
* ** **
2772683 TAA TAA TGA TAA TAA TAA TATA TAA TTT TAA TAA TAA TAA TAA TTT
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
* * *
2772729 TAA TAA TAA TAA TAA TAC TAA TATT TAA TAA TAA TAA TAA TAC TAA
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
* *
2772775 TATT TAA TAA TAA TGA TAA TAA TA
1 TA-A TAA TAA TAA TAA TAA TAA TA
2772799 TTTTTTAAAA
Statistics
Matches: 90, Mismatches: 20, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
3 83 0.92
4 7 0.08
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:2772714 original size:25 final size:25
Alignment explanation
Indices: 2772683--2772812 Score: 163
Period size: 25 Copynumber: 5.2 Consensus size: 25
2772673 TTTATTTTTT
* *
2772683 TAATAATGATAATAATAATATATAA
1 TAATAATAATAATAATAATATTTAA
**
2772708 TTTTAATAATAATAATAAT-TTTAA
1 TAATAATAATAATAATAATATTTAA
*
2772732 TAATAATAATAATACTAATATTTAA
1 TAATAATAATAATAATAATATTTAA
*
2772757 TAATAATAATAATACTAATATTTAA
1 TAATAATAATAATAATAATATTTAA
* * *
2772782 TAATAATGATAATAATATTTTTTAA
1 TAATAATAATAATAATAATATTTAA
*
2772807 AAATAA
1 TAATAA
2772813 AATGAAAAAA
Statistics
Matches: 92, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
24 20 0.22
25 72 0.78
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (25 bp):
TAATAATAATAATAATAATATTTAA
Found at i:2773040 original size:45 final size:45
Alignment explanation
Indices: 2772985--2773375 Score: 577
Period size: 45 Copynumber: 8.7 Consensus size: 45
2772975 GAGGTCTTAT
* * *
2772985 CATCTTGCACTGTAA-GTCTTACAGATGACCCGAAGGTTTTGAAAA
1 CATCATGCACTG-AAGGGCTTACAGATGACCCGAAGGCTTTGAAAA
* * **
2773030 CATCATGCACTGAAGGGCTTATAGATGGCTTGAAGGCTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAA
2773075 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAA
* ** *
2773120 CATCATGCACTGAAGGGCTTACAGATGACCCAAAGATTTTGCAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAA
2773165 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAA
*
2773210 CATCATGCACTGAAGGGCTTACAGATGACCCGGAGGCTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAA
* * *
2773255 CATCATGCACTGTAGGGCTTACAGATGACCCGGACGCTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAA
* *
2773300 CATCATGCACTGAAGGGCTTACAGATGACCCGGAGGCTTTAAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAA
* * * *
2773345 TATCATGCACTGTAGGTCTTATAGATGACCC
1 CATCATGCACTGAAGGGCTTACAGATGACCC
2773376 TGAGGTTTAT
Statistics
Matches: 316, Mismatches: 29, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
44 2 0.01
45 314 0.99
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.23
Consensus pattern (45 bp):
CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAA
Found at i:2773495 original size:45 final size:45
Alignment explanation
Indices: 2773410--2773495 Score: 127
Period size: 45 Copynumber: 1.9 Consensus size: 45
2773400 CCTGAAGGCT
* ** *
2773410 TTTTAAAAACATCATGCACTGTAGGTCTTATGGATTACTCGAAGG
1 TTTTAAAAACATCAAGCACTGTAGGTCTTACAGATGACTCGAAGG
*
2773455 TTTTGAAAACATCAAGCACTGTAGGTCTTACAGATGACTCG
1 TTTTAAAAACATCAAGCACTGTAGGTCTTACAGATGACTCG
2773496 GAGAATTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Consensus pattern (45 bp):
TTTTAAAAACATCAAGCACTGTAGGTCTTACAGATGACTCGAAGG
Found at i:2773509 original size:119 final size:119
Alignment explanation
Indices: 2773296--2773609 Score: 441
Period size: 119 Copynumber: 2.6 Consensus size: 119
2773286 GGACGCTTTG
* * ** * * * * *
2773296 AAAACATCATGCACTGAAGGGCTTACAGATGACCCGGAGGCTTTAAAAATATCATGCACTGTAGG
1 AAAACATCATGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCAAGCACTGTAGG
* * * * *
2773361 TCTTATAGATGACCCTGAGGTTTATAATATCAAAAAGCTCCTGAAGGCTTTTTA
66 TCTTACAGATGACCCGGAGATTTATAATATCAAAAAGCTCCCGAAGGCATTTTA
* *
2773415 AAAACATCATGCACTGTAGGTCTTATGGATTACTCGAAGGTTTTGAAAACATCAAGCACTGTAGG
1 AAAACATCATGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCAAGCACTGTAGG
* *
2773480 TCTTACAGATGACTCGGAGAATTTA-AATATCAAAAAGCTCCCGAAGGCATTTTG
66 TCTTACAGATGACCCGGAG-ATTTATAATATCAAAAAGCTCCCGAAGGCATTTTA
*
2773534 AAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCAAGCACTGTAGG
1 AAAACATCATGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCAAGCACTGTAGG
2773599 TCTTACAGATG
66 TCTTACAGATG
2773610 TGGGAAATAG
Statistics
Matches: 173, Mismatches: 21, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
119 169 0.98
120 4 0.02
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.27
Consensus pattern (119 bp):
AAAACATCATGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCAAGCACTGTAGG
TCTTACAGATGACCCGGAGATTTATAATATCAAAAAGCTCCCGAAGGCATTTTA
Found at i:2774306 original size:22 final size:22
Alignment explanation
Indices: 2774281--2774360 Score: 133
Period size: 22 Copynumber: 3.6 Consensus size: 22
2774271 AATAAAGTTT
* *
2774281 TCATCTTTGAAAAGAGAATTTA
1 TCATCTTTGAAGAGAGAATCTA
2774303 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
*
2774325 TCATCTTTGAAGAGAAAATCTA
1 TCATCTTTGAAGAGAGAATCTA
2774347 TCATCTTTGAAGAG
1 TCATCTTTGAAGAG
2774361 TGTATATGTA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 55 1.00
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:2774807 original size:54 final size:54
Alignment explanation
Indices: 2774731--2774933 Score: 307
Period size: 54 Copynumber: 3.8 Consensus size: 54
2774721 ACTGGTTCGG
* * * *
2774731 AAAATATTTGACAACACGTTCATCTTTTCCTGTGGCTTCTGTCCAAAGGTTCAT
1 AAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGTCCAGAGGTTCAT
* *
2774785 AAAACATTTGACAACACATTCATCCTTTCCTATGACTTCTGTCCAGAGGTTCAT
1 AAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGTCCAGAGGTTCAT
* * *
2774839 AAAACATTTGACAACACATTCATCATTTCCTGTGGTTTCTGTCCAGAGGTTCGT
1 AAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGTCCAGAGGTTCAT
* *
2774893 AAAACATTTGACAACACATTCATCCTTTCTTGTGGTTTCTG
1 AAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTG
2774934 CACAGATGTT
Statistics
Matches: 136, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 136 1.00
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (54 bp):
AAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGTCCAGAGGTTCAT
Found at i:2775974 original size:75 final size:75
Alignment explanation
Indices: 2775799--2775976 Score: 225
Period size: 75 Copynumber: 2.4 Consensus size: 75
2775789 AAGATGATAT
** * *
2775799 GGGTCTTCAGCATGCCCCAACATTTACTAATACAAACATTCAAAATGAGTTAATATTCCAATTTC
1 GGGT-TTCAGCATGCCCCAACATTTGTTAATAAAAACATTCAAAATGAGTTAATATTCCAATTTA
2775864 TGATTGAAATG
65 TGATTGAAATG
* ** * * *
2775875 GGCTTTCAGCATGCCCCGTCATTTGTTGATAAAAACATTCAAAATG-TTTCAATATTCCTGA-TT
1 GGGTTTCAGCATGCCCCAACATTTGTTAATAAAAACATTCAAAATGAGTT-AATATTCC-AATTT
2775938 ATGATTGAAATG
64 ATGATTGAAATG
2775950 GGGTTTCAGCATGCCCCAACATTTGTT
1 GGGTTTCAGCATGCCCCAACATTTGTT
2775977 TTTTTTGTTG
Statistics
Matches: 87, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
74 2 0.02
75 81 0.93
76 4 0.05
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.34
Consensus pattern (75 bp):
GGGTTTCAGCATGCCCCAACATTTGTTAATAAAAACATTCAAAATGAGTTAATATTCCAATTTAT
GATTGAAATG
Found at i:2776923 original size:24 final size:24
Alignment explanation
Indices: 2776889--2776943 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
2776879 AATTCTCTAG
*
2776889 GCTTTCTGGCTTCTTAGACCACTT
1 GCTTTCAGGCTTCTTAGACCACTT
*
2776913 GCTTTCAGGCTTCTTGGACCACTT
1 GCTTTCAGGCTTCTTAGACCACTT
2776937 GCTTTCA
1 GCTTTCA
2776944 AGAATGTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.13, C:0.29, G:0.18, T:0.40
Consensus pattern (24 bp):
GCTTTCAGGCTTCTTAGACCACTT
Found at i:2777977 original size:8 final size:9
Alignment explanation
Indices: 2777954--2777994 Score: 66
Period size: 9 Copynumber: 4.7 Consensus size: 9
2777944 ATTCAATTTA
*
2777954 TTTTCTTTC
1 TTTTTTTTC
2777963 TTTTTTTTC
1 TTTTTTTTC
2777972 -TTTTTTTC
1 TTTTTTTTC
2777980 TTTTTTTTC
1 TTTTTTTTC
2777989 TTTTTT
1 TTTTTT
2777995 CTGATGAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 8 0.27
9 22 0.73
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:2777981 original size:17 final size:17
Alignment explanation
Indices: 2777954--2777994 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
2777944 ATTCAATTTA
2777954 TTTTCTTTCTTTTTTTTC
1 TTTT-TTTCTTTTTTTTC
2777972 TTTTTTTCTTTTTTTTC
1 TTTTTTTCTTTTTTTTC
2777989 TTTTTT
1 TTTTTT
2777995 CTGATGAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (17 bp):
TTTTTTTCTTTTTTTTC
Found at i:2783435 original size:14 final size:15
Alignment explanation
Indices: 2783416--2783457 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
2783406 TGAGTGTTTG
2783416 TTTG-TTTATTTTTA
1 TTTGTTTTATTTTTA
2783430 TTTGTTTTA-TTTT-
1 TTTGTTTTATTTTTA
*
2783443 TTTGTTTTAATTTTA
1 TTTGTTTTATTTTTA
2783458 ATATTATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 9 0.36
14 12 0.48
15 4 0.16
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (15 bp):
TTTGTTTTATTTTTA
Found at i:2787896 original size:20 final size:19
Alignment explanation
Indices: 2787873--2787950 Score: 66
Period size: 20 Copynumber: 3.9 Consensus size: 19
2787863 ATTAAAAAAT
2787873 ATAAAAATGCAAATGCAAA
1 ATAAAAATGCAAATGCAAA
*** *
2787892 CATAAAAATATGAATGAAAA
1 -ATAAAAATGCAAATGCAAA
*
2787912 ATGAAAATGCAAAGATGCAAA
1 ATAAAAATGC-AA-ATGCAAA
*
2787933 ATGCAAAATGCAAATGCA
1 AT-AAAAATGCAAATGCA
2787951 TGTATGAAAA
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
19 7 0.16
20 21 0.47
21 10 0.22
22 7 0.16
ACGTcount: A:0.59, C:0.10, G:0.14, T:0.17
Consensus pattern (19 bp):
ATAAAAATGCAAATGCAAA
Found at i:2787898 original size:28 final size:27
Alignment explanation
Indices: 2787842--2787950 Score: 74
Period size: 28 Copynumber: 3.7 Consensus size: 27
2787832 ATGCAAAAAC
* * *
2787842 AAATATAAAATGTAAATGTAAATTAAA
1 AAATATAAAATGCAAATGCAAAATAAA
2787869 AAATATAAAAATGCAAATGCAAACATAAA
1 AAATAT-AAAATGCAAATGCAAA-ATAAA
* **
2787898 AATATGAATGAAAAATGAAAATGCAAAGATGCA
1 AA-AT--AT--AAAATGCAAATGCAAA-ATAAA
**
2787931 AAATGCAAAATGCAAATGCA
1 AAATATAAAATGCAAATGCA
2787951 TGTATGAAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
27 6 0.09
28 27 0.41
29 6 0.09
30 2 0.03
32 4 0.06
33 21 0.32
ACGTcount: A:0.61, C:0.07, G:0.12, T:0.20
Consensus pattern (27 bp):
AAATATAAAATGCAAATGCAAAATAAA
Found at i:2787935 original size:15 final size:14
Alignment explanation
Indices: 2787904--2787950 Score: 62
Period size: 13 Copynumber: 3.4 Consensus size: 14
2787894 TAAAAATATG
*
2787904 AATGAAAAATG-AA
1 AATGCAAAATGCAA
2787917 AATGCAAAGATGCAA
1 AATGCAAA-ATGCAA
2787932 AATGCAAAATGC-A
1 AATGCAAAATGCAA
2787945 AATGCA
1 AATGCA
2787951 TGTATGAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 14 0.45
14 7 0.23
15 10 0.32
ACGTcount: A:0.57, C:0.11, G:0.17, T:0.15
Consensus pattern (14 bp):
AATGCAAAATGCAA
Found at i:2787949 original size:6 final size:7
Alignment explanation
Indices: 2787904--2787950 Score: 62
Period size: 7 Copynumber: 6.9 Consensus size: 7
2787894 TAAAAATATG
*
2787904 AATGAAA
1 AATGCAA
2787911 AATG-AA
1 AATGCAA
2787917 AATGCAA
1 AATGCAA
2787924 AGATGCAA
1 A-ATGCAA
2787932 AATGCAA
1 AATGCAA
2787939 AATGC-A
1 AATGCAA
2787945 AATGCA
1 AATGCA
2787951 TGTATGAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
6 12 0.32
7 18 0.49
8 7 0.19
ACGTcount: A:0.57, C:0.11, G:0.17, T:0.15
Consensus pattern (7 bp):
AATGCAA
Found at i:2792681 original size:3 final size:3
Alignment explanation
Indices: 2792667--2792747 Score: 90
Period size: 3 Copynumber: 26.3 Consensus size: 3
2792657 TTTATTTAGT
* ** *
2792667 TAA TAA TGA TAA TAA TAA TATA TAA TAA TAA TAA TAA TTT TAT TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
* *
2792713 TAA TAA TAC TAA TATT TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA T
2792748 TTTTAAAAAT
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
3 61 0.92
4 5 0.08
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:2792735 original size:43 final size:44
Alignment explanation
Indices: 2792661--2792750 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 44
2792651 TAATTATTTA
*
2792661 TTTAGTTAATAATGATAATAATAATATATAATAATAATAATAAT
1 TTTAGTTAATAATAATAATAATAATATATAATAATAATAATAAT
* *
2792705 TTTA-TTAATAATAATACTAAT-ATTTAATAATAATAATAATAAT
1 TTTAGTTAATAATAATAATAATAATAT-ATAATAATAATAATAAT
2792748 TTT
1 TTT
2792751 TAAAAATAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
42 3 0.07
43 35 0.83
44 4 0.10
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.44
Consensus pattern (44 bp):
TTTAGTTAATAATAATAATAATAATATATAATAATAATAATAAT
Found at i:2792752 original size:22 final size:21
Alignment explanation
Indices: 2792666--2792759 Score: 111
Period size: 22 Copynumber: 4.5 Consensus size: 21
2792656 ATTTATTTAG
*
2792666 TTAATAATGATAATAATAA-T
1 TTAATAATAATAATAATAATT
*
2792686 AT-ATAATAATAATAATAATT
1 TTAATAATAATAATAATAATT
* *
2792706 TTATTAATAATAATACTAATAT
1 TTAATAATAATAATAATAAT-T
2792728 TTAATAATAATAATAATAATTT
1 TTAATAATAATAATAATAA-TT
*
2792750 TTAAAAATAA
1 TTAATAATAA
2792760 AATGAAAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
19 15 0.24
20 3 0.05
21 15 0.24
22 28 0.45
23 1 0.02
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (21 bp):
TTAATAATAATAATAATAATT
Found at i:2801020 original size:22 final size:24
Alignment explanation
Indices: 2800994--2801043 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 24
2800984 TTTTTTAGGT
2800994 AAAACAATTA-AA-TATTATTTT-A
1 AAAACAATTACAACT-TTATTTTGA
*
2801016 AAAACGATTACAACTTTATTTTGA
1 AAAACAATTACAACTTTATTTTGA
2801040 AAAA
1 AAAA
2801044 ATGGGTGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 9 0.38
23 9 0.38
24 6 0.25
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.36
Consensus pattern (24 bp):
AAAACAATTACAACTTTATTTTGA
Found at i:2802023 original size:29 final size:29
Alignment explanation
Indices: 2801991--2802050 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
2801981 TGGTAATAAT
* * *
2801991 AAATTAAAGGGCTAAAACAGAAAAATAGA
1 AAATTAAAAGACTAAAACAGAAAAACAGA
* *
2802020 AAATTAAAAGACTAAAATAGCAAAACAGA
1 AAATTAAAAGACTAAAACAGAAAAACAGA
2802049 AA
1 AA
2802051 CGTAGGGACT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.65, C:0.08, G:0.13, T:0.13
Consensus pattern (29 bp):
AAATTAAAAGACTAAAACAGAAAAACAGA
Found at i:2803484 original size:25 final size:27
Alignment explanation
Indices: 2803432--2803484 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 27
2803422 GGCACTCACT
* *
2803432 CGGCTGAGAGGCTGGAACGTCAAGCGG
1 CGGCTGAGAGGCTGGAACGCCAAACGG
*
2803459 CGGCTG-GA-GCTGGAAGGCCAAACGG
1 CGGCTGAGAGGCTGGAACGCCAAACGG
2803484 C
1 C
2803485 TGAGCTGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 15 0.65
26 2 0.09
27 6 0.26
ACGTcount: A:0.23, C:0.25, G:0.43, T:0.09
Consensus pattern (27 bp):
CGGCTGAGAGGCTGGAACGCCAAACGG
Found at i:2803617 original size:25 final size:25
Alignment explanation
Indices: 2803582--2803658 Score: 136
Period size: 25 Copynumber: 3.1 Consensus size: 25
2803572 CAGCTGGAAC
2803582 ATTTAGGGTTTGAAACCCTAATCTG
1 ATTTAGGGTTTGAAACCCTAATCTG
*
2803607 TTTTAGGGTTTGAAACCCTAATCTG
1 ATTTAGGGTTTGAAACCCTAATCTG
*
2803632 ATTTAGGGTTTGAAACCCTAATATG
1 ATTTAGGGTTTGAAACCCTAATCTG
2803657 AT
1 AT
2803659 GGGTTGATTG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 49 1.00
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (25 bp):
ATTTAGGGTTTGAAACCCTAATCTG
Found at i:2803749 original size:3 final size:3
Alignment explanation
Indices: 2803741--2803798 Score: 80
Period size: 3 Copynumber: 19.0 Consensus size: 3
2803731 ATTTGTAAAT
**
2803741 TAA TAA TAA TAA TAA TAA TAAA TAA TAA TAA TAA TAA TAA CGA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
*
2803787 AAA TAA TAA TAA
1 TAA TAA TAA TAA
2803799 AGAAGACCCG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
3 45 0.94
4 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:2804158 original size:43 final size:43
Alignment explanation
Indices: 2804111--2804288 Score: 148
Period size: 41 Copynumber: 4.1 Consensus size: 43
2804101 ATGGGGACGA
2804111 CTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGAT
1 CTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGAT
** * *
2804154 CTGG---TCTGGGGAATGACACGGCTCATACGTGATGAAGAGTT
1 CTGGTTATCTATGG-TTGACACGGCTCATACGTGATGAAGAGAT
** * * * * * *
2804195 CTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACG-G
1 CTGGTTATCT-ATGGT--TGACACGGCTCATACGTGATGAAGA-GAT
* * *
2804241 CTGGTTATCTATGGTTGACACTGCTCCTACGTGATGAGGAGAT
1 CTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGAT
2804284 CTGGT
1 CTGGT
2804289 CTGGGGATGA
Statistics
Matches: 107, Mismatches: 19, Indels: 18
0.74 0.13 0.12
Matches are distributed among these distances:
40 5 0.05
41 31 0.29
42 1 0.01
43 31 0.29
44 3 0.03
45 6 0.06
46 29 0.27
47 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.28
Consensus pattern (43 bp):
CTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGAT
Found at i:2804245 original size:130 final size:131
Alignment explanation
Indices: 2804003--2804333 Score: 434
Period size: 130 Copynumber: 2.5 Consensus size: 131
2803993 ACTCGGTTCC
* * ** *
2804003 TACGTGATGAAGACATCTGGTC-GAAGGATGACACTACTCATACATGATGAAGAGTTCTTGGCCA
1 TACGTGATGAAGAGATCTGGTCTG-GGGATGACACGGCTCATACGTGATGAAGAGTTC-TGGCCA
* *
2804067 TCTTTAGGAAGGGTGATAACTCGGTTCCTACGTGATGGGGACGACTGGTTATCTATGGTTGACAC
64 TC--TA-GAAGGGTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTATGGTTGACAC
2804132 GGCTCA
126 GGCTCA
2804138 TACGTGATGAAGAGATCTGGTCTGGGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCAT
1 TACGTGATGAAGAGATCTGGTCTGGGG-ATGACACGGCTCATACGTGATGAAGAGTTCTGGCCAT
* *
2804203 CTA-AA-GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACTGCT
65 CTAGAAGGGTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTATGGTTGACACGGCT
*
2804266 CC
130 CA
* * * * * * *
2804268 TACGTGATGAGGAGATCTGGTCTGGGGATGACACGGTTCCTATGTGATGAGGACTACTGGCCATC
1 TACGTGATGAAGAGATCTGGTCTGGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATC
2804333 T
66 T
2804334 TAGGAATAAT
Statistics
Matches: 177, Mismatches: 17, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
129 33 0.19
130 81 0.46
131 2 0.01
133 2 0.01
135 31 0.18
136 28 0.16
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (131 bp):
TACGTGATGAAGAGATCTGGTCTGGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATC
TAGAAGGGTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTATGGTTGACACGGCTC
A
Found at i:2804784 original size:15 final size:15
Alignment explanation
Indices: 2804760--2804803 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
2804750 AAGATGATCT
*
2804760 TGTTTTAAGAGAAAA
1 TGTTTCAAGAGAAAA
2804775 TGTTTCAAGAGAAAA
1 TGTTTCAAGAGAAAA
*
2804790 TGTTTCAAGTGAAA
1 TGTTTCAAGAGAAA
2804804 CGACTCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (15 bp):
TGTTTCAAGAGAAAA
Found at i:2805378 original size:30 final size:30
Alignment explanation
Indices: 2805344--2805440 Score: 97
Period size: 35 Copynumber: 3.1 Consensus size: 30
2805334 GAGAGACAAA
2805344 TTTGTTTCAAAAGAAACAAACTCAAAGATT
1 TTTGTTTCAAAAGAAACAAACTCAAAGATT
*** *
2805374 TTTGTTTCAAAAGAAACTATCTTAAGAGAAAGAAT
1 TTTGTTTCAAAAGAAAC-A----AACTCAAAGATT
*
2805409 TTTGTTTCCAAAGAAACAAACTC-AAGATT
1 TTTGTTTCAAAAGAAACAAACTCAAAGATT
2805438 TTT
1 TTT
2805441 TTCGCAAAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
29 8 0.15
30 19 0.36
31 1 0.02
34 1 0.02
35 24 0.45
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.33
Consensus pattern (30 bp):
TTTGTTTCAAAAGAAACAAACTCAAAGATT
Found at i:2805413 original size:35 final size:35
Alignment explanation
Indices: 2805302--2805425 Score: 123
Period size: 35 Copynumber: 3.7 Consensus size: 35
2805292 AAACAGATTC
* *
2805302 AAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAG
1 AAAGAATTTTGTTTCAAAAGAAACTATCTTAAGAG
* * * ***
2805337 AGACAAATTTGTTTCAAAAGAAAC-A----AACTC
1 AAAGAATTTTGTTTCAAAAGAAACTATCTTAAGAG
*
2805367 AAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAG
1 AAAGAATTTTGTTTCAAAAGAAACTATCTTAAGAG
*
2805402 AAAGAATTTTGTTTCCAAAGAAAC
1 AAAGAATTTTGTTTCAAAAGAAAC
2805426 AAACTCAAGA
Statistics
Matches: 67, Mismatches: 17, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
30 22 0.33
31 1 0.01
34 1 0.01
35 43 0.64
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.31
Consensus pattern (35 bp):
AAAGAATTTTGTTTCAAAAGAAACTATCTTAAGAG
Found at i:2805441 original size:65 final size:65
Alignment explanation
Indices: 2805290--2805440 Score: 232
Period size: 65 Copynumber: 2.3 Consensus size: 65
2805280 TCAATTTAAG
* * * *
2805290 AGAAACAGATTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAATTTGTTTCAAA
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAAACAAATTTGTTTCAAA
* * *
2805355 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAAAGAATTTTGTTTCCAA
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAAACAAATTTGTTTCAAA
2805420 AGAAACAAACTC-AAGATTTTT
1 AGAAACAAACTCAAAGATTTTT
2805441 TTCGCAAAAT
Statistics
Matches: 79, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
64 9 0.11
65 70 0.89
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (65 bp):
AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAAACAAATTTGTTTCAAA
Found at i:2805507 original size:52 final size:52
Alignment explanation
Indices: 2805428--2805672 Score: 198
Period size: 52 Copynumber: 5.0 Consensus size: 52
2805418 AAAGAAACAA
* * *
2805428 ACTCAAGATTTTTTTCGCAAAATTGTCTCAAGAGATACAAAACTTTGTTTCAG
1 ACTCAA-ATATTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAG
* *
2805481 ACTCAAATATTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAA
1 ACTCAAATATTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAG
* *** * * * *
2805533 AAT-AAATAGACTT---AAAGTTTTTTCAA-A-AGA-AACAA-----TCTCA-
1 ACTCAAATATTTTTCACAAAATTGTCTCAAGAGAGACAA-AACTTTGTTTCAG
* *
2805573 A---AGATTTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAG
1 ACTCAAATATTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAG
** *
2805622 ACTCAAAGCTTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
1 ACTCAAATATTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
2805673 AAATAAATAG
Statistics
Matches: 149, Mismatches: 27, Indels: 33
0.71 0.13 0.16
Matches are distributed among these distances:
38 5 0.03
40 1 0.01
41 14 0.09
42 1 0.01
43 5 0.03
44 2 0.01
45 2 0.01
46 5 0.03
47 1 0.01
48 13 0.09
49 1 0.01
51 7 0.05
52 86 0.58
53 6 0.04
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.33
Consensus pattern (52 bp):
ACTCAAATATTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAG
Found at i:2805595 original size:141 final size:140
Alignment explanation
Indices: 2805413--2805726 Score: 522
Period size: 141 Copynumber: 2.2 Consensus size: 140
2805403 AAGAATTTTG
* * *
2805413 TTTCCAAAGAAACAAACTC-AAGATTTTTTTCGCAAAATTGTCTCAAGAGATACAAAACTTTGTT
1 TTTCAAAAGAAAC-AACTCAAAGATTTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTT
*
2805477 TCAGACTCAAATATTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAG
65 TCAGACTCAAAGATTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAG
* *
2805542 ACTTAAAGTTT
130 ACTCAAAGATT
2805553 TTTCAAAAGAAACAATCTCAAAGATTTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTT
1 TTTCAAAAGAAACAA-CTCAAAGATTTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTT
*
2805618 TCAGACTCAAAGCTTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAG
65 TCAGACTCAAAGATTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAG
2805683 ACTCAAAGATT
130 ACTCAAAGATT
*
2805694 TTTCAAAAGAAACAACTCAAAGATATTTATTCA
1 TTTCAAAAGAAACAACTCAAAGAT-TTTTTTCA
2805727 AAAGGAACAA
Statistics
Matches: 163, Mismatches: 8, Indels: 5
0.93 0.05 0.03
Matches are distributed among these distances:
139 2 0.01
140 24 0.15
141 137 0.84
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (140 bp):
TTTCAAAAGAAACAACTCAAAGATTTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTT
CAGACTCAAAGATTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAAATAAATAGA
CTCAAAGATT
Found at i:2805715 original size:25 final size:27
Alignment explanation
Indices: 2805668--2805791 Score: 119
Period size: 29 Copynumber: 4.5 Consensus size: 27
2805658 CAAAACTTTG
* * *
2805668 TTTCAAAATAAATAGACTCAAAG-ATT
1 TTTCAAAAGAAACAAACTCAAAGAATT
2805694 TTTCAAAAGAAAC-AACTCAAAGATATT
1 TTTCAAAAGAAACAAACTCAAAGA-ATT
* *
2805721 TATTCAAAAGGAACAAACTCCAAGAATTT
1 T-TTCAAAAGAAACAAACTCAAAGAA-TT
2805750 TATTCAAAATG-AACAAACTCAAAGATATT
1 T-TTCAAAA-GAAACAAACTCAAAGA-ATT
*
2805779 TTTCAAGAGAAAC
1 TTTCAAAAGAAAC
2805792 TGTCTCAAGA
Statistics
Matches: 83, Mismatches: 7, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
25 8 0.10
26 11 0.13
27 5 0.06
28 21 0.25
29 36 0.43
30 2 0.02
ACGTcount: A:0.50, C:0.15, G:0.09, T:0.27
Consensus pattern (27 bp):
TTTCAAAAGAAACAAACTCAAAGAATT
Found at i:2806104 original size:36 final size:35
Alignment explanation
Indices: 2806020--2806123 Score: 129
Period size: 36 Copynumber: 3.0 Consensus size: 35
2806010 GAGAAAATGA
* * *
2806020 TGTCTCAAGCGAGACGAAATTTGCTTTT-AGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTGAGAAAT
* **
2806054 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTT-GAGAAAT
*
2806090 TGTCTCAAGCGAGACAAAGTTTGTTTTTGAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTGAGAAA
2806124 CGATCTCAAG
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
34 23 0.40
35 6 0.10
36 29 0.50
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.34
Consensus pattern (35 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTGAGAAAT
Found at i:2806131 original size:35 final size:32
Alignment explanation
Indices: 2806021--2806150 Score: 109
Period size: 35 Copynumber: 3.8 Consensus size: 32
2806011 AGAAAATGAT
*
2806021 GTCTCAAGCGAGACGAAATTTGCTTTT-AGATATA
1 GTCTCAAGCGAGAC-AAATTTGTTTTTGAGA-A-A
**
2806055 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAA
1 GTCTCAAGCGAGAC-AAATTTGTTTTT-GAGAAA
2806089 TTGTCTCAAGCGAGACAAAGTTTGTTTTTGAGAAA
1 --GTCTCAAGCGAGACAAA-TTTGTTTTTGAGAAA
* *
2806124 CGATCTCAAGTGAGATCAACTTTGTTT
1 -G-TCTCAAGCGAGA-CAAATTTGTTT
2806151 AATGTGAAAC
Statistics
Matches: 80, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
34 25 0.31
35 28 0.35
36 27 0.34
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (32 bp):
GTCTCAAGCGAGACAAATTTGTTTTTGAGAAA
Found at i:2806286 original size:101 final size:99
Alignment explanation
Indices: 2806091--2806317 Score: 271
Period size: 101 Copynumber: 2.3 Consensus size: 99
2806081 TAGAGAAATT
* *
2806091 GTCTCAAGCGAGACAAAGTTTGTTTTTGAGAAACGATCTCAAGTGAGATCAACTTTGTTTAATGT
1 GTCTCAAGCGAGACAAAATTTG-TTTTGAGAAACAATCTCAAGTGAGATCAACTTTGTTTAATGT
*
2806156 GAAACAAATCCGAAATTTGGATCTCAAAGGGAAAAG
65 GAAACAAATCCGAAAATTGGATCTCAAA-GGAAAAG
* * *
2806192 GTCTCAAGCGAGACAAAATTTGTTTTGAAAGAAACAATCT-AAGGTGAGATTAATTTTGTTT-TT
1 GTCTCAAGCGAGACAAAATTTGTTTTG--AGAAACAATCTCAA-GTGAGATCAACTTTGTTTAAT
* * * *
2806255 AGTGAATCAAATTC-AAAATTGTATCTCAAAGGAAAAT
63 -GTGAAACAAATCCGAAAATTGGATCTCAAAGGAAAAG
* *
2806292 GTCTCAAGCGAAACACAATTTGTTTT
1 GTCTCAAGCGAGACAAAATTTGTTTT
2806318 AAAATTCTCA
Statistics
Matches: 110, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
100 35 0.32
101 38 0.35
102 37 0.34
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (99 bp):
GTCTCAAGCGAGACAAAATTTGTTTTGAGAAACAATCTCAAGTGAGATCAACTTTGTTTAATGTG
AAACAAATCCGAAAATTGGATCTCAAAGGAAAAG
Found at i:2806784 original size:4 final size:4
Alignment explanation
Indices: 2806775--2806813 Score: 60
Period size: 4 Copynumber: 9.5 Consensus size: 4
2806765 TGTATCATGG
*
2806775 ATGT ATGT ATGT ATGT ATGT ATGT ATGT GTTGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT -ATGT ATGT AT
2806814 ATACTTTTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 29 0.91
5 3 0.09
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.51
Consensus pattern (4 bp):
ATGT
Found at i:2808001 original size:21 final size:22
Alignment explanation
Indices: 2807957--2808007 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
2807947 TTTGTATGTG
2807957 CTCTTTGTCCACTTTCTCTTCTTT
1 CTCTTT-T-CACTTTCTCTTCTTT
* *
2807981 TTCTTTTCACTTTGT-TTCTTT
1 CTCTTTTCACTTTCTCTTCTTT
2808002 CTCTTT
1 CTCTTT
2808008 GCTTTTCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 11 0.46
22 7 0.29
23 1 0.04
24 5 0.21
ACGTcount: A:0.04, C:0.27, G:0.04, T:0.65
Consensus pattern (22 bp):
CTCTTTTCACTTTCTCTTCTTT
Found at i:2808792 original size:163 final size:164
Alignment explanation
Indices: 2808602--2808930 Score: 642
Period size: 163 Copynumber: 2.0 Consensus size: 164
2808592 AAAGAAAGGT
2808602 ACGGGTATGACTTTTGTGTCTCAAAAAATAAATACAGTGTTTCAAGGTGGAAAGAATGTTTCAAG
1 ACGGGTATGACTTTTGTGTCTCAAAAAATAAATACAGTGTTTCAAGGTGGAAAGAATGTTTCAAG
2808667 GTCTCAAAGAGAGGGAATGTCAAAAATTGGTTATTTGGTAGTGACCAGGAATTATTTCGAGTAAA
66 GTCTCAAAGAGAGGGAATGTCAAAAATTGGTTATTTGGTAGTGACCAGGAATTATTTCGAGTAAA
2808732 AAAATC-GATTTTGTTTTGGGTTTAGACAGAATA
131 AAAATCAGATTTTGTTTTGGGTTTAGACAGAATA
2808765 ACGGGTATGACTTTTGTGTCTCAAAAAATAAATACAGTGTTTCAAGGTGGAAAGAATGTTTCAAG
1 ACGGGTATGACTTTTGTGTCTCAAAAAATAAATACAGTGTTTCAAGGTGGAAAGAATGTTTCAAG
2808830 GTCTCAAAGAGAGGGAATGTCAAAAATTGGTTATTTGGTAGTGACCAGGAATTATTTCGAGTAAA
66 GTCTCAAAGAGAGGGAATGTCAAAAATTGGTTATTTGGTAGTGACCAGGAATTATTTCGAGTAAA
2808895 AAAATCGAGATTTTGTTTTGGGTTTAGACAGAATA
131 AAAATC-AGATTTTGTTTTGGGTTTAGACAGAATA
2808930 A
1 A
2808931 AAAAAAGGTC
Statistics
Matches: 164, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
163 136 0.83
165 28 0.17
ACGTcount: A:0.35, C:0.09, G:0.24, T:0.32
Consensus pattern (164 bp):
ACGGGTATGACTTTTGTGTCTCAAAAAATAAATACAGTGTTTCAAGGTGGAAAGAATGTTTCAAG
GTCTCAAAGAGAGGGAATGTCAAAAATTGGTTATTTGGTAGTGACCAGGAATTATTTCGAGTAAA
AAAATCAGATTTTGTTTTGGGTTTAGACAGAATA
Found at i:2811115 original size:31 final size:31
Alignment explanation
Indices: 2811059--2811151 Score: 177
Period size: 31 Copynumber: 3.0 Consensus size: 31
2811049 TGACAAAATG
2811059 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAA-AAATAAGTTAGTAT
2811091 ACACAAACAAAAGAGAAAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAAAATAAGTTAGTAT
2811122 ACACAAACAAAAGAGAAAAATAAGTTAGTA
1 ACACAAACAAAAGAGAAAAATAAGTTAGTA
2811152 CATGTAAAAT
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
31 44 0.72
32 17 0.28
ACGTcount: A:0.61, C:0.10, G:0.14, T:0.15
Consensus pattern (31 bp):
ACACAAACAAAAGAGAAAAATAAGTTAGTAT
Found at i:2812079 original size:22 final size:24
Alignment explanation
Indices: 2812053--2812102 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 24
2812043 TTTTTTAGGT
2812053 AAAACAATTA-AA-TATTATTTT-A
1 AAAACAATTACAACT-TTATTTTGA
*
2812075 AAAACGATTACAACTTTATTTTGA
1 AAAACAATTACAACTTTATTTTGA
2812099 AAAA
1 AAAA
2812103 ATGGGTGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 9 0.38
23 9 0.38
24 6 0.25
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.36
Consensus pattern (24 bp):
AAAACAATTACAACTTTATTTTGA
Found at i:2813083 original size:29 final size:29
Alignment explanation
Indices: 2813051--2813110 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
2813041 TGGTAATAAT
* * *
2813051 AAATTAAAGGGCTAAAACAGAAAAATAGA
1 AAATTAAAAGACTAAAACAGAAAAACAGA
* *
2813080 AAATTAAAAGACTAAAATAGCAAAACAGA
1 AAATTAAAAGACTAAAACAGAAAAACAGA
2813109 AA
1 AA
2813111 CGTAGGGACT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.65, C:0.08, G:0.13, T:0.13
Consensus pattern (29 bp):
AAATTAAAAGACTAAAACAGAAAAACAGA
Found at i:2814538 original size:25 final size:27
Alignment explanation
Indices: 2814486--2814538 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 27
2814476 GGCACTCACT
* *
2814486 CGGCTGAGAGGCTGGAACGTCAAGCGG
1 CGGCTGAGAGGCTGGAACGCCAAACGG
*
2814513 CGGCTG-GA-GCTGGAAGGCCAAACGG
1 CGGCTGAGAGGCTGGAACGCCAAACGG
2814538 C
1 C
2814539 TGAGCTGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 15 0.65
26 2 0.09
27 6 0.26
ACGTcount: A:0.23, C:0.25, G:0.43, T:0.09
Consensus pattern (27 bp):
CGGCTGAGAGGCTGGAACGCCAAACGG
Found at i:2814671 original size:25 final size:25
Alignment explanation
Indices: 2814636--2814712 Score: 136
Period size: 25 Copynumber: 3.1 Consensus size: 25
2814626 CGGCTGGAAC
2814636 ATTTAGGGTTTGAAACCCTAATCTG
1 ATTTAGGGTTTGAAACCCTAATCTG
*
2814661 TTTTAGGGTTTGAAACCCTAATCTG
1 ATTTAGGGTTTGAAACCCTAATCTG
*
2814686 ATTTAGGGTTTGAAACCCTAATATG
1 ATTTAGGGTTTGAAACCCTAATCTG
2814711 AT
1 AT
2814713 GGGTTGATTG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 49 1.00
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (25 bp):
ATTTAGGGTTTGAAACCCTAATCTG
Found at i:2814803 original size:3 final size:3
Alignment explanation
Indices: 2814795--2814852 Score: 80
Period size: 3 Copynumber: 19.0 Consensus size: 3
2814785 ATTTGTAAAT
**
2814795 TAA TAA TAA TAA TAA TAA TAAA TAA TAA TAA TAA TAA TAA CGA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
*
2814841 AAA TAA TAA TAA
1 TAA TAA TAA TAA
2814853 AGAAGACCCG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
3 45 0.94
4 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:2815958 original size:20 final size:20
Alignment explanation
Indices: 2815933--2816211 Score: 143
Period size: 20 Copynumber: 13.6 Consensus size: 20
2815923 AATGACCAAT
*
2815933 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTGAG
** ***
2815953 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTGAG
**
2815973 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TGAG
**
2815993 AAAATCGCAACGCGAGCTT-CC
1 AAAATCGCAACGCGA--TTGAG
**
2816014 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGA-TT-G-AG
* *
2816037 AAAATCGCAATGCGATTCA-
1 AAAATCGCAACGCGATTGAG
* *
2816056 ATCAATCGCAATGCGATTGAG
1 A-AAATCGCAACGCGATTGAG
* *
2816077 AGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGA-TT-G-AG
* * *
2816100 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTGAG
* * * *
2816120 AGATTCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTGAG
* * *
2816140 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTGAG
* *
2816160 AGAATCGCAAAGCGATTGAG
1 AAAATCGCAACGCGATTGAG
* *
2816180 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTGAG
2816200 AAAATCGCAACG
1 AAAATCGCAACG
2816212 TTAAAAAGAA
Statistics
Matches: 211, Mismatches: 34, Indels: 28
0.77 0.12 0.10
Matches are distributed among these distances:
19 1 0.00
20 160 0.76
21 18 0.09
22 4 0.02
23 27 0.13
24 1 0.00
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTGAG
Found at i:2816093 original size:40 final size:40
Alignment explanation
Indices: 2816059--2816211 Score: 189
Period size: 40 Copynumber: 3.8 Consensus size: 40
2816049 CGATTCAATC
* *
2816059 AATCGCAATGCGATTGAGAGAGTCGCAACGCGATTTAGAAGAG
1 AATCGCAATGCGACTGAGAGAATCGCAACGCGA-TT-G-AGAG
* * *
2816102 AATCGCAATGCGACTGAGAGATTCGCAATGCGACTGAGAG
1 AATCGCAATGCGACTGAGAGAATCGCAACGCGATTGAGAG
*
2816142 AATCGCAATGCGACTGAGAGAATCGCAAAGCGATTGAGAG
1 AATCGCAATGCGACTGAGAGAATCGCAACGCGATTGAGAG
* * * *
2816182 AATCGCAACGCGATTTAGAAAATCGCAACG
1 AATCGCAATGCGACTGAGAGAATCGCAACG
2816212 TTAAAAAGAA
Statistics
Matches: 98, Mismatches: 12, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
40 66 0.67
41 1 0.01
42 1 0.01
43 30 0.31
ACGTcount: A:0.36, C:0.19, G:0.28, T:0.17
Consensus pattern (40 bp):
AATCGCAATGCGACTGAGAGAATCGCAACGCGATTGAGAG
Found at i:2816106 original size:63 final size:63
Alignment explanation
Indices: 2816018--2816211 Score: 234
Period size: 63 Copynumber: 3.1 Consensus size: 63
2816008 GCTTCCAAGT
* * * *
2816018 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTCA-ATCAATCGCAATGCGATTGAGAGAG
1 TCGCAACGCGATTTAGAAGAGAATCGCAATGCGATTGAGA-GAATCGCAATGCGATTGAGAGAA
* * *
2816081 TCGCAACGCGATTTAGAAGAGAATCGCAATGCGACTGAGAGATTCGCAATGCGACTGAGAGAA
1 TCGCAACGCGATTTAGAAGAGAATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAGAA
* * * * * *
2816144 TCGCAATGCGA-CT-G-AGAGAATCGCAAAGCGATTGAGAGAATCGCAACGCGATTTAGAAAA
1 TCGCAACGCGATTTAGAAGAGAATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAGAA
2816204 TCGCAACG
1 TCGCAACG
2816212 TTAAAAAGAA
Statistics
Matches: 113, Mismatches: 17, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
60 46 0.41
61 1 0.01
62 1 0.01
63 64 0.57
64 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.26, T:0.18
Consensus pattern (63 bp):
TCGCAACGCGATTTAGAAGAGAATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAGAA
Found at i:2816221 original size:20 final size:20
Alignment explanation
Indices: 2816198--2816241 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
2816188 AACGCGATTT
*
2816198 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
*
2816218 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTAAAA
2816238 AGAA
1 AGAA
2816242 TAGTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.55, C:0.16, G:0.18, T:0.11
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:2816226 original size:60 final size:60
Alignment explanation
Indices: 2815935--2816229 Score: 164
Period size: 60 Copynumber: 4.8 Consensus size: 60
2815925 TGACCAATAA
* ** *
2815935 AATCGCAACGCGATTTAGAAAATCGCAACGTTAAAAAGAAAATCGC-AA-CGGTCAAAAGAA
1 AATCGCAACGCGATTTAGAAAATCGCAACGTTAAAAAGAAAATCGCAAAGCGAT--TGAGAG
* ** ** * * * * *
2815995 AATCGCAACGCGAGCTTCCAAGTTCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTCA-ATC
1 AATCGCAACGCGA-TTTAGAAAATCGCAA--CG-TTAAAAAGAAAATCGCAAAGCGATTGAGA-G
* * * * * * * * *
2816059 AATCGCAATGCGATTGAGAGAGTCGCAACGCGATTTAGAAGAGAATCGCAATGCGACTGAGAG
1 AATCGCAACGCGATTTAGAAAATCGCAA--CG-TTAAAAAGAAAATCGCAAAGCGATTGAGAG
* * * * * * ** *** *
2816122 ATTCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCGCAAAGCGATTGAGAG
1 AATCGCAACGCGATTTAGAAAATCGCAACGTTAAAAAGAAAATCGCAAAGCGATTGAGAG
2816182 AATCGCAACGCGATTTAGAAAATCGCAACGTTAAAAAGAAAATCGCAA
1 AATCGCAACGCGATTTAGAAAATCGCAACGTTAAAAAGAAAATCGCAA
2816230 CGGTCAAAAG
Statistics
Matches: 179, Mismatches: 48, Indels: 16
0.74 0.20 0.07
Matches are distributed among these distances:
60 71 0.40
61 11 0.06
63 65 0.36
64 28 0.16
65 1 0.01
66 3 0.02
ACGTcount: A:0.40, C:0.20, G:0.23, T:0.17
Consensus pattern (60 bp):
AATCGCAACGCGATTTAGAAAATCGCAACGTTAAAAAGAAAATCGCAAAGCGATTGAGAG
Found at i:2816330 original size:6 final size:6
Alignment explanation
Indices: 2816319--2816369 Score: 102
Period size: 6 Copynumber: 8.5 Consensus size: 6
2816309 GACACGTATT
2816319 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
2816367 ACC
1 ACC
2816370 CGAGACGAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:2817060 original size:6 final size:6
Alignment explanation
Indices: 2817049--2817101 Score: 79
Period size: 6 Copynumber: 8.8 Consensus size: 6
2817039 CGGGTCGGGT
* * *
2817049 CGTGGC CGTGGC CGTGGC CGTGGC CGTGGC CGTGGT CGTGGT CGTGGT
1 CGTGGC CGTGGC CGTGGC CGTGGC CGTGGC CGTGGC CGTGGC CGTGGC
2817097 CGTGG
1 CGTGG
2817102 TAATACGTGT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.00, C:0.26, G:0.51, T:0.23
Consensus pattern (6 bp):
CGTGGC
Found at i:2817102 original size:6 final size:6
Alignment explanation
Indices: 2817041--2817102 Score: 72
Period size: 6 Copynumber: 10.5 Consensus size: 6
2817031 CGCCGCCTCG
* * * * *
2817041 GGTCG- GGTCGT GGCCGT GGCCGT GGCCGT GGCCGT GGCCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
2817088 GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGT
2817103 AATACGTGTC
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
5 5 0.09
6 49 0.91
ACGTcount: A:0.00, C:0.24, G:0.52, T:0.24
Consensus pattern (6 bp):
GGTCGT
Found at i:2817102 original size:18 final size:18
Alignment explanation
Indices: 2817046--2817102 Score: 87
Period size: 18 Copynumber: 3.2 Consensus size: 18
2817036 CCTCGGGTCG
2817046 GGTCGTGGCCGTGGCCGT
1 GGTCGTGGCCGTGGCCGT
*
2817064 GGCCGTGGCCGTGGCCGT
1 GGTCGTGGCCGTGGCCGT
* *
2817082 GGTCGTGGTCGTGGTCGT
1 GGTCGTGGCCGTGGCCGT
2817100 GGT
1 GGT
2817103 AATACGTGTC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.00, C:0.25, G:0.51, T:0.25
Consensus pattern (18 bp):
GGTCGTGGCCGTGGCCGT
Found at i:2817204 original size:20 final size:20
Alignment explanation
Indices: 2817179--2817222 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
2817169 TTTTTAACTA
*
2817179 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
2817199 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
2817219 TTCT
1 TTCT
2817223 AAATCGCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:2817232 original size:20 final size:20
Alignment explanation
Indices: 2817209--2817506 Score: 152
Period size: 20 Copynumber: 14.6 Consensus size: 20
2817199 TTCTTTTTAA
2817209 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
2817229 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
2817249 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
2817269 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
2817289 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
* * *
2817312 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * **
2817332 CATTGCGATTCTAAAAATCG
1 CGTTGCGATTTTCTAAATCG
* *** *
2817352 CATTGCGATTCAATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
2817372 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
2817395 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
2817416 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
2817434 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
2817456 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
2817476 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
2817495 CGTTGCGATTTT
1 CGTTGCGATTTT
2817507 ATTGGTCATT
Statistics
Matches: 223, Mismatches: 44, Indels: 23
0.77 0.15 0.08
Matches are distributed among these distances:
18 2 0.01
19 17 0.08
20 157 0.70
21 14 0.06
22 6 0.03
23 27 0.12
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:2817255 original size:40 final size:40
Alignment explanation
Indices: 2817211--2817402 Score: 222
Period size: 40 Copynumber: 4.7 Consensus size: 40
2817201 CTTTTTAACG
2817211 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
* * * * *
2817251 TTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
*
2817291 TTGCGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCA
1 TTGCGA--TT-TTCTAAATCGCGTTGCGATTCTCTCAATCGCA
* ** * **
2817334 TTGCGATTCTAAAAATCGCATTGCGATTCAATCAATCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
2817374 TTGCGATTTTCTTCTAAATCGCGTTGCGA
1 TTGCGA--TT-TTCTAAATCGCGTTGCGA
2817403 ACTTGGAAGC
Statistics
Matches: 124, Mismatches: 22, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
40 72 0.58
41 2 0.02
42 4 0.03
43 46 0.37
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.36
Consensus pattern (40 bp):
TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
Found at i:2817327 original size:83 final size:83
Alignment explanation
Indices: 2817219--2817402 Score: 296
Period size: 83 Copynumber: 2.2 Consensus size: 83
2817209 CGTTGCGATT
* *** * **
2817219 TTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTCTC
1 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTAAAAATCGCATTGCGATTCAATC
*
2817284 AGTCGCATTGCGATTTTC
66 AATCGCATTGCGATTTTC
2817302 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTAAAAATCGCATTGCGATTCAATC
1 TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTAAAAATCGCATTGCGATTCAATC
2817367 AATCGCATTGCGATTTTC
66 AATCGCATTGCGATTTTC
2817385 TTCTAAATCGCGTTGCGA
1 TTCTAAATCGCGTTGCGA
2817403 ACTTGGAAGC
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
83 93 1.00
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.35
Consensus pattern (83 bp):
TTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTAAAAATCGCATTGCGATTCAATC
AATCGCATTGCGATTTTC
Found at i:2817395 original size:63 final size:59
Alignment explanation
Indices: 2817223--2817381 Score: 174
Period size: 63 Copynumber: 2.6 Consensus size: 59
2817213 GCGATTTTCT
* * * **
2817223 AAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTCT
1 AAATCGCATTGCGATTC-ATCAATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTAA
* * * * *
2817283 CAGTCGCATTGCGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCTAA
1 AAATCGCATTGCGA--TTCATC--AATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTAA
2817346 AAATCGCATTGCGATTCAATCAATCGCATTGCGATT
1 AAATCGCATTGCGATTC-ATCAATCGCATTGCGATT
2817382 TTCTTCTAAA
Statistics
Matches: 80, Mismatches: 14, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
60 24 0.30
61 5 0.06
62 5 0.06
63 46 0.57
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.34
Consensus pattern (59 bp):
AAATCGCATTGCGATTCATCAATCGCATTGCGATTCTCTCAATCGCATTGCGATTCTAA
Found at i:2817496 original size:19 final size:20
Alignment explanation
Indices: 2817456--2817506 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
2817446 TTCTTTTTAA
*
2817456 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
2817476 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
2817495 CGTTGCGATTTT
1 CGTTGCGATTTT
2817507 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:2817827 original size:14 final size:16
Alignment explanation
Indices: 2817799--2817829 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
2817789 AAATTATATA
2817799 TATATATTTTAAAAAT
1 TATATATTTTAAAAAT
2817815 TATA-ATTTTAAAAAT
1 TATATATTTTAAAAAT
2817830 ATTTTACTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TATATATTTTAAAAAT
Found at i:2818013 original size:22 final size:22
Alignment explanation
Indices: 2817960--2818011 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 22
2817950 TTTTTAAATA
*
2817960 TTAAAATAATTTATTTATTTATTG
1 TTAAAAT-A-TTATTTATTAATTG
*
2817984 TTAAAATATTATTTATATAATTT
1 TTAAAATATTATTTAT-TAATTG
2818007 TTAAA
1 TTAAA
2818012 TAAAATATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 8 0.32
23 10 0.40
24 7 0.28
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TTAAAATATTATTTATTAATTG
Found at i:2818127 original size:22 final size:23
Alignment explanation
Indices: 2818084--2818164 Score: 71
Period size: 22 Copynumber: 3.6 Consensus size: 23
2818074 AAAGTAAGGA
**
2818084 TATTATATT-ATATATTAAAAAT
1 TATTATATTAATATATTTTAAAT
2818106 TATTA-ATTAATATATTTTAAA-
1 TATTATATTAATATATTTTAAAT
* **
2818127 TATCTTTATTAA-ATATTATTGGAT
1 TAT-TATATTAATATATT-TTAAAT
2818151 TATTATATTAATAT
1 TATTATATTAATAT
2818165 TAAATACATA
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
21 6 0.13
22 21 0.45
23 15 0.32
24 5 0.11
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.53
Consensus pattern (23 bp):
TATTATATTAATATATTTTAAAT
Found at i:2825465 original size:155 final size:154
Alignment explanation
Indices: 2825278--2825588 Score: 597
Period size: 155 Copynumber: 2.0 Consensus size: 154
2825268 GAGTGGATCT
2825278 TTTCTAGATCTACCCTCCCGAGGCCTCATTTTCACAAAATCAGTATGTTTTTTTTAAACGATGGT
1 TTTCTAGATCTACCCTCCCGAGGCCTCATTTTCACAAAATCAGTATGTTTTTTTTAAACGATGGT
2825343 ACAAAGACCTCTCGGAAAAATGAAAAATTTTGATTTTTTTTGCCGCCGATGAACGGCGGCC-GGC
66 ACAAAGACCTCTCGGAAAAATGAAAAATTTTGA--TTTTTTGCCGCCGATGAACGGCGGCCGGGC
2825407 CCGTTCAACGGCGGCGGTGAGGCGGC
129 CCGTTCAACGGCGGCGGTGAGGCGGC
2825433 TTTCTAGATCTACCCTCCCGAGGCCTCATTTTCACAAAATCAGTATGTTTTTTTTAAACGATGGT
1 TTTCTAGATCTACCCTCCCGAGGCCTCATTTTCACAAAATCAGTATGTTTTTTTTAAACGATGGT
2825498 ACAAAGACCTCTCGGAAAAATGAAAAATTTTGATTTTTTGCCGCCGATGAACGGCGGCCGGGCCC
66 ACAAAGACCTCTCGGAAAAATGAAAAATTTTGATTTTTTGCCGCCGATGAACGGCGGCCGGGCCC
2825563 GTTCAACGGCGGCGGTGAGGCGGC
131 GTTCAACGGCGGCGGTGAGGCGGC
2825587 TT
1 TT
2825589 GCGGCGGCTG
Statistics
Matches: 155, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
153 26 0.17
154 31 0.20
155 98 0.63
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.28
Consensus pattern (154 bp):
TTTCTAGATCTACCCTCCCGAGGCCTCATTTTCACAAAATCAGTATGTTTTTTTTAAACGATGGT
ACAAAGACCTCTCGGAAAAATGAAAAATTTTGATTTTTTGCCGCCGATGAACGGCGGCCGGGCCC
GTTCAACGGCGGCGGTGAGGCGGC
Found at i:2836881 original size:47 final size:46
Alignment explanation
Indices: 2836812--2836900 Score: 142
Period size: 47 Copynumber: 1.9 Consensus size: 46
2836802 AATATTTCGC
*
2836812 TTAGGATGAAAACCCGAGAGGGCGCCCTAAATTGAAAAAAAAAACGT
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATT-AAAAAAAAAACGT
* *
2836859 TTAGGGTGAAAACTCGAAAGGGCGCCCTAAATTAAAAAAAAA
1 TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTAAAAAAAAA
2836901 TAGGAAAACA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
46 9 0.23
47 30 0.77
ACGTcount: A:0.46, C:0.16, G:0.22, T:0.16
Consensus pattern (46 bp):
TTAGGATGAAAACCCGAAAGGGCGCCCTAAATTAAAAAAAAAACGT
Found at i:2837936 original size:98 final size:98
Alignment explanation
Indices: 2837680--2838435 Score: 1090
Period size: 98 Copynumber: 7.5 Consensus size: 98
2837670 AGGTTTTACC
*
2837680 CAGAGCCAATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC-
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
2837744 AGCGAAGGGACCGCTGGTTGTCAACAGACATTTCTCAATTT
66 A-CGAAGGGACCGCTGGTTGTCAATA-A-A-----CAATTT
*
2837785 CAGAGCCAATTTCAACTTCATAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
2837850 ACGAAGGGACCGCTGGTTGTCAATAAACAATTT
66 ACGAAGGGACCGCTGGTTGTCAATAAACAATTT
*
2837883 CAGGGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
2837948 ACGAAGGGACCGCTGGTTGTCAATAAACAATTT
66 ACGAAGGGACCGCTGGTTGTCAATAAACAATTT
*
2837981 CAGGGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
2838046 ATGAAGGGACCGCTGGTTGTCAATAAACAATTT
66 ACGAAGGGACCGCTGGTTGTCAATAAACAATTT
2838079 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
2838144 ACGAAGGGACCGCTGGTTGTCAATAAACAATTT
66 ACGAAGGGACCGCTGGTTGTCAATAAACAATTT
*
2838177 C----CCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
2838238 ACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAAT--A-AA-----CAATTT
* * * * *
2838279 TAGAGCCAATTTCAACTTCACAACGAAGGAGATTGGGCTCCAGACAACACAAGTTCAACTTCACA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
2838344 ACGAAGGGACCGCTGGTTGTCAACAAGTAATTTCCCAGTTT
66 ACGAAGGGACCGCTGGTTGT---CAA-TAA----ACAATTT
* * * * *
2838385 TAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGCCTCGAAACAACGCA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
2838436 TATTGCATTG
Statistics
Matches: 607, Mismatches: 23, Indels: 41
0.90 0.03 0.06
Matches are distributed among these distances:
94 83 0.14
96 1 0.00
97 2 0.00
98 296 0.49
102 6 0.01
103 1 0.00
104 1 0.00
105 85 0.14
106 126 0.21
107 1 0.00
108 1 0.00
109 3 0.00
110 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (98 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAATAAACAATTT
Found at i:2837954 original size:43 final size:43
Alignment explanation
Indices: 2837893--2838244 Score: 137
Period size: 43 Copynumber: 7.4 Consensus size: 43
2837883 CAGGGCCAAT
2837893 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* *** ** * * *
2837936 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCAGGGCCAAT
1 TTCAACTTCACAACGAA-GGA-TATTGG-ACTC--CAGACAA---C---G-CAAG
2837991 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* * *** ** * * *
2838034 TTCAACTTCACGATGAAGGGACCGCTGGTTGTCAATAAACAATTTCAGAGCCAAT
1 TTCAACTTCACAACGAA-GGA-TATTGG-ACTC--CAGACAA---C---G-CAAG
2838089 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* *** ** * * * *
2838132 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
1 TTCAACTTCACAACGAA-GGA-TATTGG-ACTC--CAGACAA---CGCAAG
*
2838183 TTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
*
2838226 TTCAACTTCACGACGAAGG
1 TTCAACTTCACAACGAAGG
2838245 GACCGCTGGT
Statistics
Matches: 216, Mismatches: 61, Indels: 64
0.63 0.18 0.19
Matches are distributed among these distances:
43 74 0.34
44 11 0.05
45 9 0.04
46 11 0.05
47 2 0.01
48 17 0.08
49 3 0.01
50 13 0.06
51 21 0.10
52 4 0.02
53 6 0.03
54 8 0.04
55 37 0.17
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.22
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:2838432 original size:106 final size:106
Alignment explanation
Indices: 2838178--2838420 Score: 387
Period size: 106 Copynumber: 2.3 Consensus size: 106
2838168 AAACAATTTC
* * *
2838178 CCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAA
*
2838243 GGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTTAGAG
66 GGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTTAGAG
* *
2838284 CCAATTTCAACTTCACAACGAAGGAGATTGGGCTCCAGACAACACAAGTTCAACTTCACAACGAA
1 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAA
** * *
2838349 GGGACCGCTGGTTGTCAACAAGTAATTTCCCAGTTTTAGAG
66 GGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTTAGAG
*
2838390 CCAATTTCAACTTCACAGCGAAGGATATTGG
1 CCAATTTCAACTTCACAACGAAGGATATTGG
2838421 CCTCGAAACA
Statistics
Matches: 125, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
106 125 1.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.23
Consensus pattern (106 bp):
CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAA
GGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTTAGAG
Found at i:2840156 original size:2 final size:2
Alignment explanation
Indices: 2840144--2840195 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
2840134 ACTTATATGC
2840144 TA TA T- 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
*
2840185 TA TA TG TA TA T
1 TA TA TA TA TA T
2840196 TTTGTATTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2840246 original size:19 final size:18
Alignment explanation
Indices: 2840209--2840282 Score: 55
Period size: 18 Copynumber: 4.1 Consensus size: 18
2840199 GTATTTTATC
*
2840209 TTATTATTTCTTTACTTTT
1 TTATTATTTATTTA-TTTT
2840228 TTATTATTATATTTA-TTT
1 TTATTATT-TATTTATTTT
* *
2840246 TCATTATTTAGTTT-TTCTA
1 TTATTATTTA-TTTATT-TT
*
2840265 TTATTA-TTATATATTTT
1 TTATTATTTATTTATTTT
2840282 T
1 T
2840283 CCTCTCTCTC
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
17 6 0.14
18 19 0.43
19 14 0.32
20 5 0.11
ACGTcount: A:0.23, C:0.05, G:0.01, T:0.70
Consensus pattern (18 bp):
TTATTATTTATTTATTTT
Found at i:2848103 original size:16 final size:16
Alignment explanation
Indices: 2848082--2848112 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2848072 GCTTGCTTCC
2848082 CCCATTTTTCTCTTTT
1 CCCATTTTTCTCTTTT
2848098 CCCATTTTTCTCTTT
1 CCCATTTTTCTCTTT
2848113 GTAACCTCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.32, G:0.00, T:0.61
Consensus pattern (16 bp):
CCCATTTTTCTCTTTT
Found at i:2852923 original size:28 final size:29
Alignment explanation
Indices: 2852894--2852949 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
2852884 CAAATTTTAG
*
2852894 TTAGTAACCAAAATATAAATTTTGAAAGT
1 TTAGTAACCAAAATATAAAGTTTGAAAGT
** *
2852923 TTAGTGGCCAAAGTATAAAGTTTGAAA
1 TTAGTAACCAAAATATAAAGTTTGAAA
2852950 AAAAATAAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.45, C:0.07, G:0.16, T:0.32
Consensus pattern (29 bp):
TTAGTAACCAAAATATAAAGTTTGAAAGT
Found at i:2855126 original size:12 final size:12
Alignment explanation
Indices: 2855109--2855139 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
2855099 GTTATGATAT
2855109 TATTAAGTTTTA
1 TATTAAGTTTTA
2855121 TATTAAGTTTTA
1 TATTAAGTTTTA
2855133 TA-TAAGT
1 TATTAAGT
2855140 GAATACGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.26
12 14 0.74
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (12 bp):
TATTAAGTTTTA
Found at i:2856366 original size:20 final size:20
Alignment explanation
Indices: 2856341--2856379 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2856331 ATTTTATAAT
2856341 TCCACCATTACAAAATAACA
1 TCCACCATTACAAAATAACA
2856361 TCCACCATTACAAAATAAC
1 TCCACCATTACAAAATAAC
2856380 CTCATTCAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.49, C:0.31, G:0.00, T:0.21
Consensus pattern (20 bp):
TCCACCATTACAAAATAACA
Found at i:2859854 original size:23 final size:23
Alignment explanation
Indices: 2859764--2859846 Score: 139
Period size: 23 Copynumber: 3.6 Consensus size: 23
2859754 CATTTTATAT
2859764 GGCACTTCGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
*
2859787 GGCACTTCAGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
* *
2859810 GGTACTTCGGTGCAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
2859833 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
2859847 TTTATACGAG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.18, C:0.28, G:0.27, T:0.28
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Done.