Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009610.1 Hibiscus syriacus cultivar Beakdansim tig00116996_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: 3811333
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 18
Found at i:3458119 original size:60 final size:60
Alignment explanation
Indices: 3457932--3458125 Score: 212
Period size: 60 Copynumber: 3.2 Consensus size: 60
3457922 CTTTAAATAT
**
3457932 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATT-ATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACAAGTTGCGA-TTTATGTATTCA-CGTTGCGATTTACGGATA
* * *** * *
3457993 CGCGTTGCGATATACGGATACGCA-TTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATAC-AAGTTGCGATTTATGTATTCACGTTGCGATTTACGGATA
* * * ** *
3458053 CACGTTGCGATTTACGGATACAAGTTGCGATTTATGTGTTCACGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACAAGTTGCGATTTATGTATTCACGTTGCGATTTACGGATA
3458113 CGCGTTGCGATTT
1 CGCGTTGCGATTT
3458126 TGGAAAATCG
Statistics
Matches: 108, Mismatches: 22, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
59 1 0.01
60 81 0.75
61 26 0.24
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACAAGTTGCGATTTATGTATTCACGTTGCGATTTACGGATA
Found at i:3458142 original size:21 final size:21
Alignment explanation
Indices: 3458112--3458194 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
3458102 ATTTTCATAT
*
3458112 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
3458133 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
3458154 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
3458175 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
3458195 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:3459132 original size:22 final size:22
Alignment explanation
Indices: 3459104--3459225 Score: 190
Period size: 22 Copynumber: 5.5 Consensus size: 22
3459094 TAACCACTAT
3459104 GTCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
**
3459126 GTCCCGAAGGACCACAAGATAC
1 GTCCCGAAGGACCACTGGATAC
* *
3459148 GTTCCAAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
3459170 GTCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
* *
3459192 GTCCCGAAGGATCACTAGATAC
1 GTCCCGAAGGACCACTGGATAC
3459214 GTCCCGAAGGAC
1 GTCCCGAAGGAC
3459226 TAATATACCC
Statistics
Matches: 89, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 89 1.00
ACGTcount: A:0.30, C:0.30, G:0.25, T:0.14
Consensus pattern (22 bp):
GTCCCGAAGGACCACTGGATAC
Found at i:3464053 original size:18 final size:18
Alignment explanation
Indices: 3464030--3464079 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
3464020 GTTCAGTATT
3464030 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
3464048 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
3464066 TTTCTCGAAGGACC
1 TGTCCCGAAGGACC
3464080 TCTGGATACG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.26, C:0.32, G:0.22, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:3464096 original size:22 final size:22
Alignment explanation
Indices: 3464068--3464122 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
3464058 GACCACTATT
*
3464068 TCTCGAAGGACCTCTGGATACG
1 TCTCGAAGGACCACTGGATACG
3464090 TCTCGAAGGACCACTGGATACG
1 TCTCGAAGGACCACTGGATACG
3464112 TC-CTGAAGGAC
1 TCTC-GAAGGAC
3464123 TAATATAGCC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 1 0.03
22 30 0.97
ACGTcount: A:0.25, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
TCTCGAAGGACCACTGGATACG
Found at i:3464767 original size:42 final size:40
Alignment explanation
Indices: 3464645--3464768 Score: 130
Period size: 42 Copynumber: 3.1 Consensus size: 40
3464635 ATAATAATAA
* * * *
3464645 ATATA-AATATAAA-TATAAAAAGTATTTTTAAAAAAAC-
1 ATATATAATATAAATTTTCAAAAGTGTTTTTTAAAAAACT
* * *
3464682 A-ATATAATATACATTTTTAAAAATGTTTTTTTAAAAAACT
1 ATATATAATATAAATTTTCAAAAGTG-TTTTTTAAAAAACT
3464722 ATATATTATATATAAATTTTCAAAAGTGTTTTTTAAAAAACT
1 ATATA-TA-ATATAAATTTTCAAAAGTGTTTTTTAAAAAACT
3464764 ATATA
1 ATATA
3464769 ATTTTCAAAA
Statistics
Matches: 71, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
36 3 0.04
37 8 0.11
38 7 0.10
39 12 0.17
40 1 0.01
41 3 0.04
42 21 0.30
43 16 0.23
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (40 bp):
ATATATAATATAAATTTTCAAAAGTGTTTTTTAAAAAACT
Found at i:3464795 original size:31 final size:30
Alignment explanation
Indices: 3464730--3464829 Score: 137
Period size: 30 Copynumber: 3.2 Consensus size: 30
3464720 CTATATATTA
*
3464730 TATATAAATTTTCAAAAGTGTTTTTTAAAAAAC
1 TATAT-AATTTTCAAAAATG-TTTTT-AAAAAC
3464763 TATATAATTTTCAAAAAATGTTTTTAAAAAC
1 TATATAATTTTC-AAAAATGTTTTTAAAAAC
* *
3464794 TATATAATTTTCAAAAATATTTTCAAAAAC
1 TATATAATTTTCAAAAATGTTTTTAAAAAC
3464824 TATATA
1 TATATA
3464830 TTATATAAGT
Statistics
Matches: 63, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
30 22 0.35
31 18 0.29
32 12 0.19
33 11 0.17
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.42
Consensus pattern (30 bp):
TATATAATTTTCAAAAATGTTTTTAAAAAC
Found at i:3464926 original size:36 final size:35
Alignment explanation
Indices: 3464794--3464982 Score: 245
Period size: 37 Copynumber: 5.2 Consensus size: 35
3464784 TTTTAAAAAC
*
3464794 TATATAATTTTCAAAAATATTTTCAAAAACTATATAT
1 TATATAATTTTC-AAAATGTTTT-AAAAACTATATAT
3464831 TATATAAGTTTTCAAAATGATTTTAAAAACTATATAT
1 TATATAA-TTTTCAAAATG-TTTTAAAAACTATATAT
3464868 TATATATATTTTCTAAAATGTTTTAAAAACTATATAT
1 TATATA-ATTTTC-AAAATGTTTTAAAAACTATATAT
* *
3464905 TATATAGTTTTCAAAAGTGTTTTGAAAACTATATAT
1 TATATAATTTTCAAAA-TGTTTTAAAAACTATATAT
* *
3464941 TATACACA-TTTCAAAATGTTTTTAGAAACTATATAT
1 TATATA-ATTTTCAAAATG-TTTTAAAAACTATATAT
3464977 TATATA
1 TATATA
3464983 CGTATTTTCA
Statistics
Matches: 137, Mismatches: 8, Indels: 15
0.86 0.05 0.09
Matches are distributed among these distances:
35 6 0.04
36 56 0.41
37 59 0.43
38 16 0.12
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (35 bp):
TATATAATTTTCAAAATGTTTTAAAAACTATATAT
Found at i:3465745 original size:84 final size:84
Alignment explanation
Indices: 3465655--3467221 Score: 1825
Period size: 84 Copynumber: 18.7 Consensus size: 84
3465645 CTGAATGCTA
* * * * *
3465655 TCGAACTCGAAGGCCTTTTGGTGGCAGATAGCCCTTATTGCCTTGAGCTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGT
** *
3465720 GCCTTTAAGCTGAGCATAG
66 GCCTTGGAGCTGAGCGTAG
* * * * * * * *
3465739 TCGAACTCAAAGGTTTTTTGTCGGCAAATAACCTTTATAGCCTTGCA-TTATGCTGCAAATAATG
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTG-AGTTATGCTGCAAATGATG
*
3465803 TGCCATGGAGCTGAGCGTAG
65 TGCCTTGGAGCTGAGCGTAG
* * * * * * * **
3465823 TCGAACTCGACGGTCTTTTGTTGGCATATAACCCTTCTCGACTTAAGCTATACTATAAATGATGT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGT
* *
3465888 GCCTTAGAGCTAAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* * * * * * *
3465907 TCGAACTCAAAGGTCTTTTATCGGCAGATAATCCTTCTAGCCTTGAGTTATGCTACAAATGATAT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGT
3465972 GCCTTGGAGCTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* * * * *
3465991 TCGAACTCGATGGTCTTTTGGTGGCAGATAACTCTT-TTAGCCTTGAGCTATGCTGCAAATGATA
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTT-GCCTTGAGTTATGCTGCAAATGATG
*
3466055 CGCCTTGGAGCTGAGCGTAG
65 TGCCTTGGAGCTGAGCGTAG
* * * * *
3466075 TCAAACTCGAAGGTCTTTTGGTTGGCAGATAACCCTTCTAGCCTTGATTTATGTTGTAAATGATG
1 TCGAACTCGAAGGTCTTTT-GTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATG
*
3466140 TGCCTTGAAGCTGAGCGTAG
65 TGCCTTGGAGCTGAGCGTAG
* * * * *
3466160 TCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGTGCTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGT
* *
3466225 GCCTTGGAGTTGAGTGTAG
66 GCCTTGGAGCTGAGCGTAG
* * * *
3466244 TCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGCCTTGAGTTATACTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGT
*
3466309 GCCTTGGAGCTGAGCATAG
66 GCCTTGGAGCTGAGCGTAG
* * * *
3466328 TCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCTTTCCTTGAGTTATGTTACAAATGATGT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGT
* *
3466393 GCCTTAGAGTTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* * *
3466412 TCGAACTCAAAGGTCTTTTATTGGCAGATAACCCTTCTCGCCTTGAGTTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGT
* * ** *
3466477 GCCTTTGAGCCGAGTATAA
66 GCCTTGGAGCTGAGCGTAG
* * * *
3466496 TTGAACTCGAAGGTCTTGTGTTGGTAGATAACCC-TCATTGCCTTGAGTTATGCTGTAAATGATG
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTC-TTGCCTTGAGTTATGCTGCAAATGATG
* *
3466560 TGCCTTGGAGCTGAGTGTAA
65 TGCCTTGGAGCTGAGCGTAG
* * * *
3466580 TCGAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTTGCCTTGAGCTATGATGCAAATGTTGT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGT
* * *
3466645 GCCTTTGAGCTGAGTGTAA
66 GCCTTGGAGCTGAGCGTAG
* * * * *
3466664 TCGAACTCGAAGGTCTTTTGTTGGAAAATAACCTTTCTTGCCTTGAGCTATGTTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGT
3466729 GCCTTGGAGCTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* * * * *
3466748 TCGAACTCGAGGGTATTTTGTTGGTAGATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATGT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGT
*
3466813 GCCTTAGAGCTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* * ** * ** * * ** *
3466832 TCAAACT--AAGGTCTTTTGTCGATATATAGTCCTTCTTTCCTTGAGCTATTTTGCAAATAATGT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGT
*
3466895 GCCTTAGAGCTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* *
3466914 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACTCTT-TTAGCCTTGAGTTATGCTGCAAATGAAG
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTT-GCCTTGAGTTATGCTGCAAATGATG
*
3466978 TGCCTTGGAGATGAGCGTAG
65 TGCCTTGGAGCTGAGCGTAG
* * * ** * *
3466998 TTGAACTCGGATGTCTTTTGTTGGCAGATAAATCTTCTAGCCTTGAGTTATGCTGCAAATGAAGT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGT
* * *
3467063 TCCTTGGAGATGAGTGTAG
66 GCCTTGGAGCTGAGCGTAG
* * * * *
3467082 TCGAACTCGAAGGTCTTTTGTTGGCAGTTAGCCCTTCTCGCCTTGA-TCTATGCTACAAATGTTG
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGT-TATGCTGCAAATGATG
* * * *
3467146 TTCCTTTGAGCTGAGTGTAA
65 TGCCTTGGAGCTGAGCGTAG
* *
3467166 TCAAACTCGAAGGTCTTTTGTTGGTAGATAACCCTTCTTGCCTTGAGTTATGCTGC
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGC
3467222 CAATAGTTTC
Statistics
Matches: 1264, Mismatches: 206, Indels: 26
0.84 0.14 0.02
Matches are distributed among these distances:
82 67 0.05
83 7 0.01
84 1113 0.88
85 76 0.06
86 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (84 bp):
TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGT
GCCTTGGAGCTGAGCGTAG
Found at i:3468578 original size:100 final size:98
Alignment explanation
Indices: 3468354--3468613 Score: 355
Period size: 100 Copynumber: 2.6 Consensus size: 98
3468344 GGCTAGTTGG
*
3468354 ATCCATAAAGCCGGGGTGTTTAACCAATTGCTCTAGAGGGACAGCTCAA--TATCATTC-TATAG
1 ATCCATAAAG-CGGGGTGTTTAACCAATTGCTCTAGAGGGACAGCTCAAGCT-TTA-TCGTATAG
*
3468416 ATATTATAATCACCTTTATTAGGCTAGCTGAATATT
63 ATATTATAATCACCTTTATCAGGCTAGCTGAATATT
* * * *
3468452 ATCCATACAGCTGGGGCGTTTAACCAATAGCTCTAGAGGGACAACTCAAGCTTTATCGTATAGAT
1 ATCCATAAAGC-GGGGTGTTTAACCAATTGCTCTAGAGGGACAGCTCAAGCTTTATCGTATAGAT
* *
3468517 ATTATAATTACCTTTATCAGGCTTAGCTGAATCTT
65 ATTATAATCACCTTTATCAGGC-TAGCTGAATATT
* *
3468552 ATCCATAAAGTCGGGGTGTTTAACCAATTGCTTTAGAGGGACAGCTCAAGCTTTATTGTATA
1 ATCCATAAAG-CGGGGTGTTTAACCAATTGCTCTAGAGGGACAGCTCAAGCTTTATCGTATA
3468614 TATGTAATAT
Statistics
Matches: 142, Mismatches: 14, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
97 1 0.01
98 45 0.32
99 29 0.20
100 66 0.46
101 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32
Consensus pattern (98 bp):
ATCCATAAAGCGGGGTGTTTAACCAATTGCTCTAGAGGGACAGCTCAAGCTTTATCGTATAGATA
TTATAATCACCTTTATCAGGCTAGCTGAATATT
Found at i:3470111 original size:19 final size:19
Alignment explanation
Indices: 3470078--3470114 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
3470068 TGCAAATGAT
3470078 GAAAATAAAATAAAAGAGA
1 GAAAATAAAATAAAAGAGA
3470097 GAAAA-AAAATGAAAAGAG
1 GAAAATAAAAT-AAAAGAG
3470115 TTAGTGAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.73, C:0.00, G:0.19, T:0.08
Consensus pattern (19 bp):
GAAAATAAAATAAAAGAGA
Found at i:3471504 original size:17 final size:18
Alignment explanation
Indices: 3471495--3471534 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
3471485 AAATAATAGT
3471495 AATTAAAAAATTAAAGTA
1 AATTAAAAAATTAAAGTA
*
3471513 AATTAAATAAGAATAAAGTA
1 AATTAAA-AA-ATTAAAGTA
3471533 AA
1 AA
3471535 ACATACAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 2 0.11
20 10 0.53
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (18 bp):
AATTAAAAAATTAAAGTA
Found at i:3473153 original size:24 final size:22
Alignment explanation
Indices: 3473121--3473169 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
3473111 ACTATTTATT
* *
3473121 ATATATATTTATGAATATATAAAA
1 ATATATATTCAT-AA-AAATAAAA
*
3473145 ATATTTATTCATAAAAATAAAA
1 ATATATATTCATAAAAATAAAA
3473167 ATA
1 ATA
3473170 CTATTAAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 10 0.45
23 2 0.09
24 10 0.45
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (22 bp):
ATATATATTCATAAAAATAAAA
Found at i:3473811 original size:13 final size:13
Alignment explanation
Indices: 3473793--3473819 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3473783 CGTGAGTTCT
3473793 GCCGCCGGCCACC
1 GCCGCCGGCCACC
3473806 GCCGCCGGCCACC
1 GCCGCCGGCCACC
3473819 G
1 G
3473820 TTTCCGGTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.59, G:0.33, T:0.00
Consensus pattern (13 bp):
GCCGCCGGCCACC
Found at i:3474585 original size:3 final size:3
Alignment explanation
Indices: 3474577--3474690 Score: 174
Period size: 3 Copynumber: 37.7 Consensus size: 3
3474567 TTAATATATT
3474577 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
3474625 TAAA TAA TAT TAA TAA TGA TAT TAA TAA TGA TAA TAA TAA TAT TAA
1 T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3474671 TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
3474691 TGGATAAAAA
Statistics
Matches: 100, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
3 97 0.97
4 3 0.03
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3475259 original size:117 final size:115
Alignment explanation
Indices: 3474936--3475614 Score: 1091
Period size: 114 Copynumber: 5.8 Consensus size: 115
3474926 GCTCTTGATG
*
3474936 AGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
* * * *
3475001 TGG-AAACAATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACA
66 TGGAAAAGAATGATCCATCAATGTGATGAATTTAAACAAAAGGTTGAACA
3475050 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
3475115 TGGAAAAGAATGATCCATCAA-GTGATGAATTTAAACAAAAGGTTGAACA
66 TGGAAAAGAATGATCCATCAATGTGATGAATTTAAACAAAAGGTTGAACA
*
3475164 AGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACCTT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACCTT
3475229 CTCTGGAAAAGAATGATCCATCAA-GTGATGAATTTAAACAAAAGGTTGAACA
63 CTCTGGAAAAGAATGATCCATCAATGTGATGAATTTAAACAAAAGGTTGAACA
*
3475281 AGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAAC-CT
* * * *
3475346 TCTCTGG-AAACAATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACA
62 TCTCTGGAAAAGAATGATCCATCAATGTGATGAATTTAAACAAAAGGTTGAACA
3475399 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
3475464 TGGAAAAGAATGATCCATCAA-GTGATGAATTTAAACAAAAGGTTGAACA
66 TGGAAAAGAATGATCCATCAATGTGATGAATTTAAACAAAAGGTTGAACA
3475513 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAAC-CT
*
3475578 TCCTCT-GAAAATGAATGATCCATCAATTTGATGAATT
62 T-CTCTGGAAAA-GAATGATCCATCAATGTGATGAATT
3475615 CAAATCTTTG
Statistics
Matches: 535, Mismatches: 16, Indels: 22
0.93 0.03 0.04
Matches are distributed among these distances:
114 203 0.38
115 52 0.10
117 173 0.32
118 80 0.15
119 18 0.03
120 9 0.02
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (115 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
TGGAAAAGAATGATCCATCAATGTGATGAATTTAAACAAAAGGTTGAACA
Found at i:3475571 original size:349 final size:348
Alignment explanation
Indices: 3474936--3475614 Score: 1267
Period size: 349 Copynumber: 1.9 Consensus size: 348
3474926 GCTCTTGATG
3474936 AGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
1 AGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
3475001 TGGAAACAATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATG
66 TGGAAACAATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATG
3475066 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGAATGATCC
131 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGAATGATCC
*
3475131 ATCAAGTGATGAATTTAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTTC
196 ATCAAGTGATGAATTTAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTC
3475196 TTCAGATGACGAGTTCTTCTCATTATGAAC-CTT-CTCTGGAAAA-GAATGATCCATCAA-GTGA
261 TTCAGATGACGAGTTCTTCTCATTATGAACTCTTCCTCT-GAAAATGAATGATCCATCAATGTGA
3475257 TGAATTTAAACAAAAGGTTGAACA
325 TGAATTTAAACAAAAGGTTGAACA
3475281 AGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
1 AGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAAC-CT
3475346 TCTCTGGAAACAATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCAT
62 TCTCTGGAAACAATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCAT
3475411 TATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGAATG
127 TATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGAATG
3475476 ATCCATCAAGTGATGAATTTAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC
192 ATCCATCAAGTGATGAATTTAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC
*
3475541 CTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTCCTCTGAAAATGAATGATCCATCAATT
257 CTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTCCTCTGAAAATGAATGATCCATCAATG
3475606 TGATGAATT
322 TGATGAATT
3475615 CAAATCTTTG
Statistics
Matches: 324, Mismatches: 2, Indels: 9
0.97 0.01 0.03
Matches are distributed among these distances:
345 39 0.12
348 20 0.06
349 230 0.71
350 8 0.02
351 18 0.06
352 9 0.03
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (348 bp):
AGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTC
TGGAAACAATGATCCATCAATTTGATGAATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATG
AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGAATGATCC
ATCAAGTGATGAATTTAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTC
TTCAGATGACGAGTTCTTCTCATTATGAACTCTTCCTCTGAAAATGAATGATCCATCAATGTGAT
GAATTTAAACAAAAGGTTGAACA
Found at i:3476290 original size:52 final size:52
Alignment explanation
Indices: 3476221--3476483 Score: 385
Period size: 52 Copynumber: 5.1 Consensus size: 52
3476211 TCCACATTCA
* * * *
3476221 ATGCT-TGATTCTATCCAATTAGATCAGATATCTCAAAGAACACTTCCAGAAA
1 ATGCTATG-TTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAG
*
3476273 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAG
* *
3476325 ATGCTATGTTATGAT-CAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTG-TCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAG
*
3476377 ATGCTA--TTCTGTCTAATCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAG
*
3476427 ATGCTA--TTCTGTCTAATCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAG
3476477 ATGCTAT
1 ATGCTAT
3476484 TGGCAAATTC
Statistics
Matches: 198, Mismatches: 9, Indels: 9
0.92 0.04 0.04
Matches are distributed among these distances:
49 1 0.01
50 95 0.48
52 99 0.50
53 3 0.02
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (52 bp):
ATGCTATGTTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAG
Found at i:3476419 original size:50 final size:50
Alignment explanation
Indices: 3476241--3476484 Score: 382
Period size: 50 Copynumber: 4.8 Consensus size: 50
3476231 CTATCCAATT
* * *
3476241 AGATCAGATATCTCAAAGAACACTTCCAGAAAATGCTATGTTCTGTCCAACC
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA--TTCTGTCTAACC
*
3476293 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGATC-AACC
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA--TTCTG-TCTAACC
*
3476345 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATC
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAACC
*
3476395 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATC
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAACC
3476445 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
3476485 GGCAAATTCA
Statistics
Matches: 185, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
49 2 0.01
50 97 0.52
52 84 0.45
53 2 0.01
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.25
Consensus pattern (50 bp):
AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAACC
Found at i:3476694 original size:52 final size:52
Alignment explanation
Indices: 3476515--3476828 Score: 512
Period size: 52 Copynumber: 6.1 Consensus size: 52
3476505 TCACTAATTG
*
3476515 GTTCTGTTCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-
1 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
* *
3476566 -TTCTGTCTAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-
1 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
* * *
3476616 -TTCTGTCTAATCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTAT
1 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
3476667 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
* *
3476719 GTTATGAT-CAACCAGATCAGATAACTCAAAGAACACTTCTAGAAGATGCTAT
1 GTTCTG-TCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
3476771 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
3476823 GTTCTG
1 GTTCTG
3476829 ATGCTTTTCC
Statistics
Matches: 248, Mismatches: 11, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
50 96 0.39
51 1 0.00
52 150 0.60
53 1 0.00
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.25
Consensus pattern (52 bp):
GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
Found at i:3477821 original size:9 final size:9
Alignment explanation
Indices: 3477807--3477888 Score: 62
Period size: 9 Copynumber: 9.0 Consensus size: 9
3477797 ACCTTAACCC
3477807 CTTTTTTTT
1 CTTTTTTTT
3477816 CTTTTTCTTT
1 CTTTTT-TTT
3477826 -TTCTTCTTTT
1 CTT-TT-TTTT
*
3477836 CCTTTTTTT
1 CTTTTTTTT
*
3477845 -TTTCTTTT
1 CTTTTTTTT
* *
3477853 CTTTCTCTT
1 CTTTTTTTT
3477862 CTTTTTCTTT
1 CTTTTT-TTT
*
3477872 -TCTTTTTT
1 CTTTTTTTT
3477880 CTTTTTTTT
1 CTTTTTTTT
3477889 TTCAAGCATA
Statistics
Matches: 58, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
8 9 0.16
9 35 0.60
10 12 0.21
11 2 0.03
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:3477822 original size:6 final size:6
Alignment explanation
Indices: 3477811--3477891 Score: 71
Period size: 5 Copynumber: 13.0 Consensus size: 6
3477801 TAACCCCTTT
3477811 TTTTTC TTTTTC TTTTTC TTCTTTTCC TTTTT- TTTTTC -TTTTC TTTCTCTTC
1 TTTTTC TTTTTC TTTTTC -T-TTTT-C TTTTTC TTTTTC TTTTTC -TT-T-TTC
3477863 TTTTTC -TTTTC TTTTTTC TTTTT- TTTTTC
1 TTTTTC TTTTTC -TTTTTC TTTTTC TTTTTC
3477892 AAGCATAATA
Statistics
Matches: 64, Mismatches: 0, Indels: 22
0.74 0.00 0.26
Matches are distributed among these distances:
5 20 0.31
6 20 0.31
7 12 0.19
8 8 0.12
9 4 0.06
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTTC
Found at i:3477846 original size:31 final size:32
Alignment explanation
Indices: 3477808--3477891 Score: 111
Period size: 31 Copynumber: 2.7 Consensus size: 32
3477798 CCTTAACCCC
3477808 TTTTTTTTCTTTTTCTTTTTCTTC-TTTTCCT
1 TTTTTTTTCTTTTTCTTTTTCTTCTTTTTCCT
* *
3477839 TTTTTTTT-TCTTTTCTTTCTCTTCTTTTTCTT
1 TTTTTTTTCT-TTTTCTTTTTCTTCTTTTTCCT
3477871 TTCTTTTTTCTTTTT-TTTTTC
1 TT-TTTTTTCTTTTTCTTTTTC
3477892 AAGCATAATA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
30 1 0.02
31 21 0.46
32 13 0.28
33 10 0.22
34 1 0.02
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (32 bp):
TTTTTTTTCTTTTTCTTTTTCTTCTTTTTCCT
Found at i:3477855 original size:37 final size:37
Alignment explanation
Indices: 3477808--3477889 Score: 114
Period size: 37 Copynumber: 2.2 Consensus size: 37
3477798 CCTTAACCCC
*
3477808 TTTTTTTTCTTTTTCTT-TTTCTTCTTTTCCTTTTT-T
1 TTTTTTTTCTTTCTCTTCTTT-TTCTTTTCCTTTTTCT
*
3477844 TTTTCTTTTCTTTCTCTTCTTTTTCTTTTCTTTTTTCT
1 TTTT-TTTTCTTTCTCTTCTTTTTCTTTTCCTTTTTCT
3477882 TTTTTTTT
1 TTTTTTTT
3477890 TCAAGCATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
36 4 0.10
37 29 0.71
38 8 0.20
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (37 bp):
TTTTTTTTCTTTCTCTTCTTTTTCTTTTCCTTTTTCT
Found at i:3488474 original size:13 final size:15
Alignment explanation
Indices: 3488452--3488488 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
3488442 TAGACAGAAA
3488452 AAAT-AAATAC-TG-
1 AAATAAAATACTTGC
3488464 AAATAAAATACTTGC
1 AAATAAAATACTTGC
3488479 AAATAAAATA
1 AAATAAAATA
3488489 AAACATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 6 0.27
14 2 0.09
15 10 0.45
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.24
Consensus pattern (15 bp):
AAATAAAATACTTGC
Found at i:3488520 original size:22 final size:23
Alignment explanation
Indices: 3488481--3488523 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
3488471 ATACTTGCAA
*
3488481 ATAAAATAAAACATATAAATATT
1 ATAAAATAAAACAAATAAATATT
*
3488504 ATAAAA-AAAATAAATAAATA
1 ATAAAATAAAACAAATAAATA
3488524 AAAATTTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (23 bp):
ATAAAATAAAACAAATAAATATT
Found at i:3488535 original size:22 final size:22
Alignment explanation
Indices: 3488510--3488551 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3488500 TATTATAAAA
* *
3488510 AAAATAAATAAATAAAAATTTG
1 AAAAGAAAGAAATAAAAATTTG
*
3488532 AAAAGAAAGAATTAAAAATT
1 AAAAGAAAGAAATAAAAATT
3488552 AAATATATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (22 bp):
AAAAGAAAGAAATAAAAATTTG
Found at i:3489291 original size:17 final size:18
Alignment explanation
Indices: 3489269--3489302 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
3489259 AATATATTTA
3489269 AAAACATA-AAATAAAAG
1 AAAACATATAAATAAAAG
3489286 AAAACATATAAATAAAA
1 AAAACATATAAATAAAA
3489303 TGACTAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.15
Consensus pattern (18 bp):
AAAACATATAAATAAAAG
Found at i:3490641 original size:3 final size:3
Alignment explanation
Indices: 3490628--3490712 Score: 86
Period size: 3 Copynumber: 28.7 Consensus size: 3
3490618 TTTAATATAT
* *
3490628 TAA TAAA TAA TAA T-A TAA TAA TAA TAA TAA -AA AAA T-A TAA TGA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
3490671 TAT TAA TAA TGA TAA TAA TAA TAT TAA TAA TAAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TA
3490713 TGGATAAAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
2 6 0.09
3 56 0.82
4 6 0.09
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3490708 original size:40 final size:39
Alignment explanation
Indices: 3490621--3490713 Score: 107
Period size: 40 Copynumber: 2.3 Consensus size: 39
3490611 ATATGTATTT
* *
3490621 AATATATTAATAAATAATAATATAATAATAATAATAAAAA
1 AATATAATAAT-ATTAATAATATAATAATAATAATAAAAA
* * *
3490661 AATATAATGATATTAATAATGATAATAATAATATTAATAAT
1 AATATAATAATATTAATAAT-ATAATAATAATAATAA-AAA
3490702 AA-ATAATAATAT
1 AATATAATAATAT
3490714 GGATAAAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.18
40 33 0.73
41 4 0.09
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (39 bp):
AATATAATAATATTAATAATATAATAATAATAATAAAAA
Found at i:3490719 original size:19 final size:19
Alignment explanation
Indices: 3490644--3490725 Score: 60
Period size: 19 Copynumber: 4.2 Consensus size: 19
3490634 ATAATAATAT
3490644 AATAATAATAAT-AA-AAAA
1 AATAATAAT-ATGAATAAAA
* * *
3490662 ATATAATGATATTAATAATGAT
1 A-ATAATAATATGAATAA--AA
* *
3490684 AATAATAATATTAATAATA
1 AATAATAATATGAATAAAA
*
3490703 AATAATAATATGGATAAAA
1 AATAATAATATGAATAAAA
3490722 AATA
1 AATA
3490726 GTATCTTCAG
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
18 3 0.06
19 29 0.57
20 2 0.04
21 15 0.29
22 2 0.04
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (19 bp):
AATAATAATATGAATAAAA
Found at i:3490832 original size:12 final size:12
Alignment explanation
Indices: 3490804--3490843 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
3490794 AAAAAAACAA
3490804 AAATAATAATAAT
1 AAATAATAAT-AT
3490817 AAATAATAATAT
1 AAATAATAATAT
3490829 AAAT-ATAAATAT
1 AAATAAT-AATAT
3490841 AAA
1 AAA
3490844 AAGTGTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 2 0.08
12 14 0.54
13 10 0.38
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATAATAATAT
Found at i:3490881 original size:37 final size:38
Alignment explanation
Indices: 3490825--3490940 Score: 118
Period size: 37 Copynumber: 3.1 Consensus size: 38
3490815 ATAAATAATA
* *
3490825 ATATAAATAT-AAA-TATAAAAAGTGTAATTTTAAAACT
1 ATATATATATAAAATTATAAAAAGTGT-TTTTTAAAACT
**
3490862 AT-T-TATATAAAATTATAAAAA-TGTTTTTTTTAACT
1 ATATATATATAAAATTATAAAAAGTGTTTTTTAAAACT
*
3490897 ATATATATATAAAATT-TCAAAAGTGTTTTTTAAAAAACT
1 ATATATATATAAAATTATAAAAAGTGTTTTTT--AAAACT
3490936 ATATA
1 ATATA
3490941 ATTTTCAAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
35 14 0.22
36 13 0.20
37 29 0.45
39 9 0.14
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.42
Consensus pattern (38 bp):
ATATATATATAAAATTATAAAAAGTGTTTTTTAAAACT
Found at i:3490928 original size:35 final size:35
Alignment explanation
Indices: 3490858--3490929 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 35
3490848 GTAATTTTAA
*
3490858 AACTATTTATATAAAATTATAAAAATGTTTTTTTT
1 AACTATTTATATAAAATTATAAAAATGTGTTTTTT
*
3490893 AACTATATATATATAAAATT-TCAAAA-GTGTTTTTT
1 AACTAT-T-TATATAAAATTATAAAAATGTGTTTTTT
3490928 AA
1 AA
3490930 AAAACTATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 16 0.48
36 6 0.18
37 11 0.33
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (35 bp):
AACTATTTATATAAAATTATAAAAATGTGTTTTTT
Found at i:3490939 original size:35 final size:35
Alignment explanation
Indices: 3490856--3490972 Score: 91
Period size: 32 Copynumber: 3.3 Consensus size: 35
3490846 GTGTAATTTT
* *
3490856 AAAACTATTTATATAAAATTATAAAAATGTTTTTTTTAA
1 AAAACTA--TATATAAAATT-TCAAAA-GTGTTTTTTAA
* *
3490895 CTATA-TATATATAAAATTTCAAAAGTGTTTTTTAA
1 -AAAACTATATATAAAATTTCAAAAGTGTTTTTTAA
* *
3490930 AAAAC--TATAT-AATTTTCAAAAAATG-TTTTTAA
1 AAAACTATATATAAAATTTC-AAAAGTGTTTTTTAA
3490962 AAAACTATATA
1 AAAACTATATA
3490973 ATTTTCAAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
32 18 0.28
33 11 0.17
34 6 0.09
35 10 0.15
36 5 0.08
37 11 0.17
39 2 0.03
40 2 0.03
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (35 bp):
AAAACTATATATAAAATTTCAAAAGTGTTTTTTAA
Found at i:3490964 original size:31 final size:31
Alignment explanation
Indices: 3490902--3490994 Score: 132
Period size: 32 Copynumber: 2.9 Consensus size: 31
3490892 TAACTATATA
* *
3490902 TATATAAAATTTCAAAAGTGTTTTTTAAAAAAC
1 TATAT-AATTTTCAAAAATG-TTTTTAAAAAAC
3490935 TATATAATTTTCAAAAAATGTTTTTAAAAAAC
1 TATATAATTTTC-AAAAATGTTTTTAAAAAAC
*
3490967 TATATAATTTTCAAAAATGTTTTCAAAA
1 TATATAATTTTCAAAAATGTTTTTAAAA
3490995 TTATATATTA
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
31 15 0.27
32 30 0.54
33 11 0.20
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.41
Consensus pattern (31 bp):
TATATAATTTTCAAAAATGTTTTTAAAAAAC
Found at i:3491080 original size:37 final size:36
Alignment explanation
Indices: 3490967--3491162 Score: 260
Period size: 37 Copynumber: 5.5 Consensus size: 36
3490957 TTTAAAAAAC
*
3490967 TATATAA-TTTTCAAAAATGTTTTCAAAATTATATA-
1 TATATAAGTTTTC-AAAATGTTTTCAAAACTATATAT
*
3491002 T-TATAAGTTTCCAAAATGTTTTCAAAACTATATAT
1 TATATAAGTTTTCAAAATGTTTTCAAAACTATATAT
* *
3491037 TTTATAAGTTTTCAAAATGTTTTCAAAAACTAAATAT
1 TATATAAGTTTTCAAAATGTTTTC-AAAACTATATAT
*
3491074 TATATAAGTTTTCAAAATGATTTTAAAAACTATATAT
1 TATATAAGTTTTCAAAATG-TTTTCAAAACTATATAT
3491111 TATAT-AGTTTTCAAAAGTGTTTT-AAAACTATATAT
1 TATATAAGTTTTCAAAA-TGTTTTCAAAACTATATAT
3491146 TATATACA-TTTTCAAAA
1 TATATA-AGTTTTCAAAA
3491163 AAAATTTAGA
Statistics
Matches: 146, Mismatches: 7, Indels: 15
0.87 0.04 0.09
Matches are distributed among these distances:
34 26 0.18
35 23 0.16
36 45 0.31
37 48 0.33
38 4 0.03
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.44
Consensus pattern (36 bp):
TATATAAGTTTTCAAAATGTTTTCAAAACTATATAT
Found at i:3491120 original size:73 final size:72
Alignment explanation
Indices: 3490967--3491187 Score: 258
Period size: 73 Copynumber: 3.1 Consensus size: 72
3490957 TTTAAAAAAC
* * * *
3490967 TATATAATTTTCAAAAATGTTTTCAAAATTATATA-T-TATAAGTTTCCAAAATG-TTTTCAAAA
1 TATATAGTTTTC-AAAATGTTTTCAAAACTATATATTATATAAGTTTTCAAAATGATTTTAAAAA
3491029 CTATATAT
65 CTATATAT
* *
3491037 TTTATAAGTTTTCAAAATGTTTTCAAAAACTAAATATTATATAAGTTTTCAAAATGATTTTAAAA
1 TATAT-AGTTTTCAAAATGTTTTC-AAAACTATATATTATATAAGTTTTCAAAATGATTTTAAAA
3491102 ACTATATAT
64 ACTATATAT
** *
3491111 TATATAGTTTTCAAAAGTGTTTT-AAAACTATATATTATATACA-TTTTCAAAAAAAATTTAGAA
1 TATATAGTTTTCAAAA-TGTTTTCAAAACTATATATTATATA-AGTTTTCAAAATGATTTTA-AA
3491174 AACT-T-TAT
63 AACTATATAT
3491182 TATATA
1 TATATA
3491188 CATATTTTCA
Statistics
Matches: 132, Mismatches: 11, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
70 15 0.11
71 24 0.18
72 33 0.25
73 34 0.26
74 26 0.20
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.43
Consensus pattern (72 bp):
TATATAGTTTTCAAAATGTTTTCAAAACTATATATTATATAAGTTTTCAAAATGATTTTAAAAAC
TATATAT
Found at i:3491905 original size:3 final size:3
Alignment explanation
Indices: 3491899--3491962 Score: 56
Period size: 3 Copynumber: 21.0 Consensus size: 3
3491889 TTATTATTAT
* * * * *
3491899 TAA TAA TAA TAA TAT TAT TAA TAA TAT TAA TAAA TAA TAG TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
* *
3491945 TAA TAA TAT TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA
3491963 AATGGAAAAA
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:3491922 original size:12 final size:12
Alignment explanation
Indices: 3491905--3491961 Score: 69
Period size: 12 Copynumber: 4.7 Consensus size: 12
3491895 TTATTAATAA
3491905 TAATAATATTAT
1 TAATAATATTAT
3491917 TAATAATATTAAT
1 TAATAATATT-AT
* *
3491930 AAATAATAGTAT
1 TAATAATATTAT
*
3491942 TAATAATAATAT
1 TAATAATATTAT
*
3491954 TAAAAATA
1 TAATAATA
3491962 AAATGGAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
12 29 0.74
13 10 0.26
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (12 bp):
TAATAATATTAT
Found at i:3491942 original size:16 final size:15
Alignment explanation
Indices: 3491896--3491952 Score: 75
Period size: 16 Copynumber: 3.9 Consensus size: 15
3491886 TAATTATTAT
3491896 TATTAATAATAATAA
1 TATTAATAATAATAA
3491911 TATT-AT--TAATAA
1 TATTAATAATAATAA
*
3491923 TATTAATAAATAATAG
1 TATTAAT-AATAATAA
3491939 TATTAATAATAATA
1 TATTAATAATAATA
3491953 TTAAAAATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
12 10 0.27
13 2 0.05
14 2 0.05
15 11 0.30
16 12 0.32
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (15 bp):
TATTAATAATAATAA
Found at i:3491957 original size:25 final size:25
Alignment explanation
Indices: 3491890--3491961 Score: 85
Period size: 25 Copynumber: 3.0 Consensus size: 25
3491880 ATTTTTTAAT
* * *
3491890 TATTATTATTAATAAT-AATAATAT
1 TATTAATAATAATAATAAATAATAG
*
3491914 TATTAATAATATTAATAAATAATAG
1 TATTAATAATAATAATAAATAATAG
*
3491939 TATTAATAATAATATTAAA-AATA
1 TATTAATAATAATAATAAATAATA
3491962 AAATGGAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
24 17 0.41
25 24 0.59
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (25 bp):
TATTAATAATAATAATAAATAATAG
Found at i:3492426 original size:15 final size:15
Alignment explanation
Indices: 3492406--3492462 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
3492396 AACCAGGTAT
3492406 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
**
3492421 CGGGTACCCGCAAAATC
1 CGGGTACCCG-ATTA-C
*
3492438 CGGGTACCCGATTAT
1 CGGGTACCCGATTAC
3492453 CGGGTACCCG
1 CGGGTACCCG
3492463 TAACATCCGG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
15 20 0.57
16 4 0.11
17 11 0.31
ACGTcount: A:0.21, C:0.33, G:0.28, T:0.18
Consensus pattern (15 bp):
CGGGTACCCGATTAC
Found at i:3492442 original size:17 final size:16
Alignment explanation
Indices: 3492406--3492474 Score: 61
Period size: 15 Copynumber: 4.3 Consensus size: 16
3492396 AACCAGGTAT
**
3492406 CGGGTACCCGATTA-C
1 CGGGTACCCGAAAATC
3492421 CGGGTACCCGCAAAATC
1 CGGGTACCCG-AAAATC
**
3492438 CGGGTACCCGATTAT-
1 CGGGTACCCGAAAATC
*
3492453 CGGGTACCCGTAACATC
1 CGGGTACCCG-AAAATC
3492470 CGGGT
1 CGGGT
3492475 CGGGACACGG
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
15 20 0.45
16 8 0.18
17 16 0.36
ACGTcount: A:0.22, C:0.32, G:0.28, T:0.19
Consensus pattern (16 bp):
CGGGTACCCGAAAATC
Found at i:3492447 original size:32 final size:32
Alignment explanation
Indices: 3492406--3492474 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
3492396 AACCAGGTAT
3492406 CGGGTACCCGATTACCGGGTACCCGCAAAATC
1 CGGGTACCCGATTACCGGGTACCCGCAAAATC
* * *
3492438 CGGGTACCCGATTATCGGGTACCCGTAACATC
1 CGGGTACCCGATTACCGGGTACCCGCAAAATC
3492470 CGGGT
1 CGGGT
3492475 CGGGACACGG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.22, C:0.32, G:0.28, T:0.19
Consensus pattern (32 bp):
CGGGTACCCGATTACCGGGTACCCGCAAAATC
Found at i:3498147 original size:6 final size:6
Alignment explanation
Indices: 3498126--3498205 Score: 67
Period size: 6 Copynumber: 13.8 Consensus size: 6
3498116 ACCCCCACTC
* * * *
3498126 CCACCT CCGCCG CCACCT CCACCT CCCCCT CCGCCT CCA--- CCACCT
1 CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT CCACCT
* * * *
3498171 CCTCCT CCTCCT CCTCCA CCACCT CCACCT CCACC
1 CCACCT CCACCT CCACCT CCACCT CCACCT CCACC
3498206 GCCCCCTCCC
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
3 3 0.05
6 57 0.95
ACGTcount: A:0.11, C:0.69, G:0.04, T:0.16
Consensus pattern (6 bp):
CCACCT
Found at i:3498156 original size:24 final size:24
Alignment explanation
Indices: 3498123--3498202 Score: 88
Period size: 24 Copynumber: 3.2 Consensus size: 24
3498113 ACTACCCCCA
*
3498123 CTCCCACCTCCGCCGCCACCTCCAC
1 CTCCC-CCTCCGCCACCACCTCCAC
*
3498148 CTCCCCCTCCGCCTCCACCACCTCCTC
1 CTCCCCCTCCG---CCACCACCTCCAC
* *
3498175 CTCCTCCTCCTCCACCACCTCCAC
1 CTCCCCCTCCGCCACCACCTCCAC
3498199 CTCC
1 CTCC
3498203 ACCGCCCCCT
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
24 22 0.47
25 5 0.11
27 20 0.43
ACGTcount: A:0.10, C:0.69, G:0.04, T:0.17
Consensus pattern (24 bp):
CTCCCCCTCCGCCACCACCTCCAC
Found at i:3498168 original size:21 final size:21
Alignment explanation
Indices: 3498135--3498202 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 21
3498125 CCCACCTCCG
* *
3498135 CCGCCACCTCCACCTCCCCCT
1 CCGCCTCCACCACCTCCCCCT
3498156 CCGCCTCCACCACCTCCTCCTCCT
1 CCGCCTCCACCACCT-C-CC-CCT
* *
3498180 CCTCCTCCACCACCTCCACCT
1 CCGCCTCCACCACCTCCCCCT
3498201 CC
1 CC
3498203 ACCGCCCCCT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
21 18 0.45
22 2 0.05
23 3 0.08
24 17 0.43
ACGTcount: A:0.10, C:0.69, G:0.03, T:0.18
Consensus pattern (21 bp):
CCGCCTCCACCACCTCCCCCT
Found at i:3498174 original size:3 final size:3
Alignment explanation
Indices: 3498141--3498202 Score: 52
Period size: 3 Copynumber: 20.7 Consensus size: 3
3498131 TCCGCCGCCA
* * * * * *
3498141 CCT CCA CCT CCC CCT CCG CCT CCA CCA CCT CCT CCT CCT CCT CCT CCA
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT
* *
3498189 CCA CCT CCA CCT CC
1 CCT CCT CCT CCT CC
3498203 ACCGCCCCCT
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.10, C:0.69, G:0.02, T:0.19
Consensus pattern (3 bp):
CCT
Found at i:3499368 original size:16 final size:17
Alignment explanation
Indices: 3499325--3499370 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
3499315 TTAGGTAATT
*
3499325 TTATGATAATTTTATTTA
1 TTATGATTA-TTTATTTA
3499343 TTAT-ACTTATTT-TTTA
1 TTATGA-TTATTTATTTA
3499359 TTATGATTATTT
1 TTATGATTATTT
3499371 GAAAAAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
16 14 0.56
17 5 0.20
18 6 0.24
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.65
Consensus pattern (17 bp):
TTATGATTATTTATTTA
Found at i:3502813 original size:13 final size:13
Alignment explanation
Indices: 3502795--3502863 Score: 56
Period size: 13 Copynumber: 5.5 Consensus size: 13
3502785 TTAAATGATA
*
3502795 AATAAAAAATTAC
1 AATAAAAAACTAC
*
3502808 AAT--AAAAGT-C
1 AATAAAAAACTAC
3502818 AATAAAACAACTAC
1 AATAAAA-AACTAC
* *
3502832 AAT-AAAAAGTCC
1 AATAAAAAACTAC
*
3502844 AATAAACAACTAC
1 AATAAAAAACTAC
3502857 AATAAAA
1 AATAAAA
3502864 GTACTAAATA
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
10 4 0.09
11 5 0.12
12 9 0.21
13 21 0.49
14 4 0.09
ACGTcount: A:0.65, C:0.14, G:0.03, T:0.17
Consensus pattern (13 bp):
AATAAAAAACTAC
Found at i:3502836 original size:14 final size:13
Alignment explanation
Indices: 3502817--3502862 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
3502807 CAATAAAAGT
3502817 CAATAAAACAACTA
1 CAAT-AAACAACTA
* *
3502831 CAATAAA-AAGTC
1 CAATAAACAACTA
3502843 CAATAAACAACTA
1 CAATAAACAACTA
3502856 CAATAAA
1 CAATAAA
3502863 AGTACTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 10 0.37
13 13 0.48
14 4 0.15
ACGTcount: A:0.63, C:0.20, G:0.02, T:0.15
Consensus pattern (13 bp):
CAATAAACAACTA
Found at i:3502850 original size:25 final size:24
Alignment explanation
Indices: 3502795--3502863 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 24
3502785 TTAAATGATA
* *
3502795 AATAAAAAATTACAAT-AAAAGTC
1 AATAAACAACTACAATAAAAAGTC
3502818 AATAAAACAACTACAATAAAAAGTCC
1 AAT-AAACAACTACAATAAAAAGT-C
3502844 AATAAACAACTACAATAAAA
1 AATAAACAACTACAATAAAA
3502864 GTACTAAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
23 3 0.07
24 11 0.27
25 23 0.56
26 4 0.10
ACGTcount: A:0.65, C:0.14, G:0.03, T:0.17
Consensus pattern (24 bp):
AATAAACAACTACAATAAAAAGTC
Found at i:3502876 original size:24 final size:23
Alignment explanation
Indices: 3502797--3502887 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 23
3502787 AAATGATAAA
* *
3502797 TAAAA-AATTACAATAAAAGTCAA
1 TAAAACAACTACAATAAAAGT-AC
*
3502820 TAAAACAACTACAATAAAAAGTCC
1 TAAAACAACTACAAT-AAAAGTAC
*
3502844 AATAAACAACTACAATAAAAGTAC
1 TA-AAACAACTACAATAAAAGTAC
* *
3502868 TAAATACAAATATAATAAAA
1 TAAA-ACAACTACAATAAAA
3502888 AACAAAATCC
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
23 7 0.12
24 30 0.54
25 19 0.34
ACGTcount: A:0.64, C:0.13, G:0.03, T:0.20
Consensus pattern (23 bp):
TAAAACAACTACAATAAAAGTAC
Found at i:3502885 original size:49 final size:49
Alignment explanation
Indices: 3502795--3502888 Score: 127
Period size: 49 Copynumber: 1.9 Consensus size: 49
3502785 TTAAATGATA
* *
3502795 AATAAAAAATTACAATAAAAGTCAATAAAACAACTACAATAAAAAGTCC
1 AATAAAAAACTACAATAAAAGTCAATAAAACAAATACAATAAAAAGTCC
* * *
3502844 AATAAACAACTACAATAAAAGT-ACTAAATACAAATATAATAAAAA
1 AATAAAAAACTACAATAAAAGTCAATAAA-ACAAATACAATAAAAA
3502889 ACAAAATCCA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
48 5 0.13
49 34 0.87
ACGTcount: A:0.65, C:0.13, G:0.03, T:0.19
Consensus pattern (49 bp):
AATAAAAAACTACAATAAAAGTCAATAAAACAAATACAATAAAAAGTCC
Found at i:3505647 original size:21 final size:22
Alignment explanation
Indices: 3505591--3505648 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 22
3505581 CACCACAGCT
* *
3505591 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCG-AGTACCA
*
3505614 CGTAGAA-TGCACCG-GTACCG
1 CGTAGAATTGCACCGAGTACCA
3505634 CGTAGAATTGCACCG
1 CGTAGAATTGCACCG
3505649 TAGTGCCTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 11 0.35
21 7 0.23
22 7 0.23
23 6 0.19
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (22 bp):
CGTAGAATTGCACCGAGTACCA
Found at i:3505836 original size:98 final size:96
Alignment explanation
Indices: 3505660--3505876 Score: 312
Period size: 98 Copynumber: 2.2 Consensus size: 96
3505650 AGTGCCTATA
** * * *
3505660 TAATGTCCATAAGGACCATATCATTCCTTAAGAATCATATATATACTAGGGATCAAGTATGTGTC
1 TAATGTCCCGAAGGACCACAT-ATTCCTTAAGAATCATATATATACCAGAGATCAAGTATGTGTC
*
3505725 TCACCAGACTTCACACATGTTCCAAAGAATAC
65 TCACCAGAATTCACACATGTTCCAAAGAATAC
*
3505757 ATATATGTCCCGAAGGACCACATATTCCTTAAGAATCATATACATATGCCA-AGATCAAGTA-GT
1 -TA-ATGTCCCGAAGGACCACATATTCCTTAAGAATCATAT--ATATACCAGAGATCAAGTATGT
3505820 GTCTCACCAGAATTCACACATGTTCCAAAGAATAC
62 GTCTCACCAGAATTCACACATGTTCCAAAGAATAC
3505855 TAATGTCCCGAAGGACCACATA
1 TAATGTCCCGAAGGACCACATA
3505877 GACCCTCGAC
Statistics
Matches: 109, Mismatches: 7, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
96 20 0.18
97 2 0.02
98 56 0.51
99 25 0.23
100 6 0.06
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (96 bp):
TAATGTCCCGAAGGACCACATATTCCTTAAGAATCATATATATACCAGAGATCAAGTATGTGTCT
CACCAGAATTCACACATGTTCCAAAGAATAC
Found at i:3506174 original size:57 final size:58
Alignment explanation
Indices: 3506073--3506195 Score: 232
Period size: 57 Copynumber: 2.2 Consensus size: 58
3506063 TATAATCTCA
3506073 TAGTCATATAATATTTCATATAAACATATATTTTCTCTTTCATATATCTCATATCATG
1 TAGTCATATAATATTTCATATAAACATATATTTTCTCTTTCATATATCTCATATCATG
3506131 TAGTCATATAATATTTCATAT-AACATATATTTTCTCTTTCATATATCTCATATCATG
1 TAGTCATATAATATTTCATATAAACATATATTTTCTCTTTCATATATCTCATATCATG
3506188 TA-TCATAT
1 TAGTCATAT
3506196 CTTGTGATCA
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
56 6 0.09
57 38 0.58
58 21 0.32
ACGTcount: A:0.34, C:0.15, G:0.03, T:0.47
Consensus pattern (58 bp):
TAGTCATATAATATTTCATATAAACATATATTTTCTCTTTCATATATCTCATATCATG
Found at i:3510918 original size:23 final size:22
Alignment explanation
Indices: 3510864--3510921 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
3510854 TCGTATATTA
3510864 CACCGAAGTGCCACGTAGAATT
1 CACCGAAGTGCCACGTAGAATT
* *
3510886 CACCGGAGTGCCGCGTAGAATT
1 CACCGAAGTGCCACGTAGAATT
*
3510908 GCACCGTAGTGCCA
1 -CACCGAAGTGCCA
3510922 TATAATAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 20 0.65
23 11 0.35
ACGTcount: A:0.26, C:0.29, G:0.28, T:0.17
Consensus pattern (22 bp):
CACCGAAGTGCCACGTAGAATT
Found at i:3511131 original size:100 final size:99
Alignment explanation
Indices: 3510937--3511148 Score: 338
Period size: 100 Copynumber: 2.1 Consensus size: 99
3510927 TAATGTCCAT
* *
3510937 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTA-GTGTCTCACCA
3511002 GACTTCACACATGTTCAAAGAATACATATGTCCCG
65 GACTTCACACATGTTCAAAGAATACATATGTCCCG
*
3511037 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTA-TGTCTCACCAG
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGTGTCTCACCAG
*
3511101 ACTT-ACACATGTTCCAAAGAATGCATATATGTCCCG
66 ACTTCACACATGTT-CAAAGAAT--ACATATGTCCCG
3511137 AAGGACCACATA
1 AAGGACCACATA
3511149 GACCCTCGAC
Statistics
Matches: 105, Mismatches: 4, Indels: 6
0.91 0.03 0.05
Matches are distributed among these distances:
97 9 0.09
98 23 0.22
100 73 0.70
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.25
Consensus pattern (99 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTAGTGTCTCACCAG
ACTTCACACATGTTCAAAGAATACATATGTCCCG
Found at i:3513361 original size:9 final size:9
Alignment explanation
Indices: 3513347--3513380 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
3513337 TAAGTAAAAT
3513347 ATTAAATAA
1 ATTAAATAA
3513356 ATTAAAT-A
1 ATTAAATAA
*
3513364 CTTAAATAA
1 ATTAAATAA
3513373 ATTAAATA
1 ATTAAATA
3513381 CAAAATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (9 bp):
ATTAAATAA
Found at i:3513379 original size:17 final size:17
Alignment explanation
Indices: 3513343--3513381 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
3513333 TAATTAAGTA
3513343 AAATA-TTAAATAAATT
1 AAATACTTAAATAAATT
3513359 AAATACTTAAATAAATT
1 AAATACTTAAATAAATT
3513376 AAATAC
1 AAATAC
3513382 AAAATATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATACTTAAATAAATT
Found at i:3516465 original size:43 final size:43
Alignment explanation
Indices: 3516413--3516545 Score: 151
Period size: 43 Copynumber: 3.1 Consensus size: 43
3516403 CTATGGTTTC
* * * *
3516413 GAAATCCAAAATGGTTAGTATCGAAAACCTTATATTCATCATT
1 GAAATCCAAAACGATCAGTATCGAAAACCTTATATTCATTATT
* * * * *
3516456 GAACTCCAAAACGATCACTATCGAAAGA-CATGTATTCATTATC
1 GAAATCCAAAACGATCAGTATCGAAA-ACCTTATATTCATTATT
* *
3516499 GAAATCCAAAACGATCGGTATCGAAAACCTTATATCCATTATT
1 GAAATCCAAAACGATCAGTATCGAAAACCTTATATTCATTATT
3516542 GAAA
1 GAAA
3516546 CCCTTATATC
Statistics
Matches: 72, Mismatches: 16, Indels: 4
0.78 0.17 0.04
Matches are distributed among these distances:
42 1 0.01
43 70 0.97
44 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.28
Consensus pattern (43 bp):
GAAATCCAAAACGATCAGTATCGAAAACCTTATATTCATTATT
Found at i:3519256 original size:23 final size:25
Alignment explanation
Indices: 3519229--3519279 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 25
3519219 TGAGTTGTAA
*
3519229 AATAAGA-C-TCAACTCGACAAATC
1 AATAAGACCGTCAACTAGACAAATC
3519252 AATAAGACTCGTCAACTAGACAAATC
1 AATAAGAC-CGTCAACTAGACAAATC
3519278 AA
1 AA
3519280 AATTCTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 7 0.29
25 1 0.04
26 16 0.67
ACGTcount: A:0.49, C:0.24, G:0.10, T:0.18
Consensus pattern (25 bp):
AATAAGACCGTCAACTAGACAAATC
Found at i:3519654 original size:39 final size:38
Alignment explanation
Indices: 3519611--3519718 Score: 126
Period size: 39 Copynumber: 2.8 Consensus size: 38
3519601 AGCCAAATAT
* * * *
3519611 GAAGACTCCACGATTGCATGGCGTCTTCAGTAAAATGGA
1 GAAGAC-CCATGACTGCATGGCGTCTTCAGGAAAACGGA
*
3519650 GAAGACCCTATGACTGCATGGCGTCTTCAGGCAAACGGA
1 GAAGACCC-ATGACTGCATGGCGTCTTCAGGAAAACGGA
* *
3519689 GAAGACCCCATGAGTGCACGGCGTCTTCAG
1 GAAGA-CCCATGACTGCATGGCGTCTTCAG
3519719 ACCAATAGGA
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
38 2 0.03
39 55 0.92
40 3 0.05
ACGTcount: A:0.28, C:0.25, G:0.28, T:0.19
Consensus pattern (38 bp):
GAAGACCCATGACTGCATGGCGTCTTCAGGAAAACGGA
Found at i:3531285 original size:20 final size:21
Alignment explanation
Indices: 3531257--3531329 Score: 89
Period size: 20 Copynumber: 3.6 Consensus size: 21
3531247 AAATAACCAA
3531257 CAAATTCGCAACGCAG-TTTT
1 CAAATTCGCAACGCAGATTTT
* *
3531277 CAAAATCGCAACG-AGATTCT
1 CAAATTCGCAACGCAGATTTT
*
3531297 CAAATTCGTAACGC-GATTTT
1 CAAATTCGCAACGCAGATTTT
*
3531317 CAAATTCGTAACG
1 CAAATTCGCAACG
3531330 TGAATTTCAT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 2 0.04
20 44 0.96
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.27
Consensus pattern (21 bp):
CAAATTCGCAACGCAGATTTT
Found at i:3531337 original size:20 final size:20
Alignment explanation
Indices: 3531274--3531338 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
3531264 GCAACGCAGT
* *
3531274 TTTCAAAATCGCAACGAG-A
1 TTTCAAATTCGTAACGAGAA
* *
3531293 TTCTCAAATTCGTAACGCGAT
1 TT-TCAAATTCGTAACGAGAA
*
3531314 TTTCAAATTCGTAACGTGAA
1 TTTCAAATTCGTAACGAGAA
3531334 TTTCA
1 TTTCA
3531339 TTTTTGTAAC
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.05
20 34 0.89
21 2 0.05
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (20 bp):
TTTCAAATTCGTAACGAGAA
Found at i:3531546 original size:21 final size:20
Alignment explanation
Indices: 3531522--3531575 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
3531512 ACTCAGTTTT
* *
3531522 CAAATTTGCAATGCGATTCTC
1 CAAATTCGCAACGCGATT-TC
*
3531543 CAAATTCGCAACGCGATTTT
1 CAAATTCGCAACGCGATTTC
3531563 CAAATTCGCAACG
1 CAAATTCGCAACG
3531576 ATAATTATCG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (20 bp):
CAAATTCGCAACGCGATTTC
Found at i:3531568 original size:20 final size:20
Alignment explanation
Indices: 3531505--3531575 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
3531495 GAACACAACT
*
3531505 ATTCGCAACTC-AGTTTTCAA
1 ATTCGCAACGCGA-TTTTCAA
* * *
3531525 ATTTGCAATGCGATTCTCCAA
1 ATTCGCAACGCGATT-TTCAA
3531546 ATTCGCAACGCGATTTTCAA
1 ATTCGCAACGCGATTTTCAA
3531566 ATTCGCAACG
1 ATTCGCAACG
3531576 ATAATTATCG
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
20 24 0.57
21 18 0.43
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (20 bp):
ATTCGCAACGCGATTTTCAA
Found at i:3531571 original size:113 final size:112
Alignment explanation
Indices: 3531363--3531574 Score: 264
Period size: 113 Copynumber: 1.9 Consensus size: 112
3531353 ATTTCAAAAC
* ** *
3531363 GTTAATTACCGATATAGGTAAACACAATTATTCACAGTTCAGTTTTCATATTCACAACGCGATTC
1 GTTAATTACCGATATAGGTAAACACAACTATTCACAACTCAGTTTTCAAATTCACAACGCGATTC
***
3531428 TCTAAAAATTCAACGCGAATTTCGTTTTCGCAACTCGAATTTCGCAAT
66 TC-AAAAATTCAACGCGAATTTCAAATTCGCAACTCGAATTTCGCAAT
* * ** *
3531476 GTTAATTACCGATATAGGTGAACACAACTATTCGCAACTCAGTTTTCAAATTTGCAATGCGATTC
1 GTTAATTACCGATATAGGTAAACACAACTATTCACAACTCAGTTTTCAAATTCACAACGCGATTC
* *
3531541 TC-CAAATTCGCAACGCGATTTTCAAATTCGCAAC
66 TCAAAAATT--CAACGCGAATTTCAAATTCGCAAC
3531575 GATAATTATC
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
111 5 0.06
113 78 0.94
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32
Consensus pattern (112 bp):
GTTAATTACCGATATAGGTAAACACAACTATTCACAACTCAGTTTTCAAATTCACAACGCGATTC
TCAAAAATTCAACGCGAATTTCAAATTCGCAACTCGAATTTCGCAAT
Found at i:3531775 original size:79 final size:74
Alignment explanation
Indices: 3531567--3531775 Score: 217
Period size: 79 Copynumber: 2.8 Consensus size: 74
3531557 GATTTTCAAA
* * * *
3531567 TTCGCAACGATAATTATCGATATAGGTAAATACAATTATTTGCAACTCAGTTTTC-AAATTCCCA
1 TTCGCAACGATAATTATCGATATAGGTAAAAACAACTATTCGCAACTCAGTTTTCAAAAATCCCA
* * *
3531631 GCTCGAATT
66 ACGCAAATT
* * * *
3531640 TT-GCAACAATAATTATCGATATAGGTAAAAACAACTATTCGCAACGC-GATTCTCAAAAATCGC
1 TTCGCAACGATAATTATCGATATAGGTAAAAACAACTATTCGCAACTCAG-TTTTCAAAAATCCC
3531703 AACGCAAATTTTGTT
65 AACGCAAA-----TT
* * *
3531718 TTCGCAACGTTAATTACCGATATAGGTAAACACAACTATTCGCAACTCAGTTTTCAAA
1 TTCGCAACGATAATTATCGATATAGGTAAAAACAACTATTCGCAACTCAGTTTTCAAA
3531776 TTCGTAACGC
Statistics
Matches: 110, Mismatches: 17, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
71 1 0.01
72 44 0.40
73 13 0.12
78 4 0.04
79 47 0.43
80 1 0.01
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.31
Consensus pattern (74 bp):
TTCGCAACGATAATTATCGATATAGGTAAAAACAACTATTCGCAACTCAGTTTTCAAAAATCCCA
ACGCAAATT
Found at i:3544161 original size:2 final size:2
Alignment explanation
Indices: 3544073--3544145 Score: 132
Period size: 2 Copynumber: 37.5 Consensus size: 2
3544063 CAAAGTAATC
3544073 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3544115 TA TA TA TA TA TA TA TA TA TA T- TA -A TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3544146 CATGGTATAC
Statistics
Matches: 69, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.03
2 67 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3544255 original size:17 final size:17
Alignment explanation
Indices: 3544227--3544262 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 17
3544217 TTCAATATAA
3544227 AATTTAAATAAATTATTT
1 AATTTAAATAAA-TATTT
3544245 AATTT-AATAAATATTT
1 AATTTAAATAAATATTT
3544261 AA
1 AA
3544263 ATTTTAAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 6 0.33
18 5 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTTAAATAAATATTT
Found at i:3544265 original size:17 final size:19
Alignment explanation
Indices: 3544226--3544266 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
3544216 ATTCAATATA
3544226 AAATTTAAATAAATTATTT
1 AAATTTAAATAAATTATTT
3544245 -AATTT-AATAAA-TATTT
1 AAATTTAAATAAATTATTT
3544261 AAATTT
1 AAATTT
3544267 TAAGGAAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 5 0.24
17 11 0.52
18 5 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AAATTTAAATAAATTATTT
Found at i:3546988 original size:222 final size:225
Alignment explanation
Indices: 3546544--3546994 Score: 849
Period size: 222 Copynumber: 2.0 Consensus size: 225
3546534 CAAGAAAAAT
3546544 AAAAGACAATAAAAATAACGGCGCGATCGACAACTAATATTAAAGTTATGTTTGTCGTCGATCAA
1 AAAAGACAATAAAAATAACGGCGCGATCGACAACTAATATTAAAGTTATGTTTGTCGTCGATCAA
3546609 CAAAAAAAAAAAGAAAAAAAAAAGATAAACGACTTACTAATGAGATAAAAGTAAGGGATAACTAG
66 CAAAAAAAAAAAGAAAAAAAAAAGATAAACGACTTACTAATGAGATAAAAGTAAGGGATAACTAG
3546674 GTTAATCCCGCGTGAGAATTAAAATTGAAATCGTCCTTTAAAAGTTTAAAACGACCAAGGATTTT
131 GTTAATCCCGCGTGAGAATTAAAATTGAAATCGTCCTTTAAAAGTTTAAAACGACCAAGGATTTT
3546739 ACTATGTAAAAGTGGAGCGAAGTAACAAAG
196 ACTATGTAAAAGTGGAGCGAAGTAACAAAG
3546769 AAAAGACAATAAAAAATAAC-G-GCGATCGACAACTAATATTAAAGTTATG-TTGTCGTCGATCA
1 AAAAGACAAT-AAAAATAACGGCGCGATCGACAACTAATATTAAAGTTATGTTTGTCGTCGATCA
3546831 AC-AAAAAAAAAAGAAAAAAAAAAGATAAACGACTTACTAATGAGATAAAAGTAAGGGATAACTA
65 ACAAAAAAAAAAAGAAAAAAAAAAGATAAACGACTTACTAATGAGATAAAAGTAAGGGATAACTA
3546895 GGTTTAATCCCGCGTGAGAATTAAAATTGAAATCGTCCTTTAAAAGTTTAAAACGACCAAGGA-T
130 GG-TTAATCCCGCGTGAGAATTAAAATTGAAATCGTCCTTTAAAAGTTTAAAACGACCAAGGATT
3546959 TTACTATGTAAAAGTGGAGCGAAGTAACAAAG
194 TTACTATGTAAAAGTGGAGCGAAGTAACAAAG
3546991 AAAA
1 AAAA
3546995 ATGAGGGTGG
Statistics
Matches: 224, Mismatches: 0, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
222 101 0.45
223 75 0.33
224 28 0.12
225 11 0.05
226 9 0.04
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.22
Consensus pattern (225 bp):
AAAAGACAATAAAAATAACGGCGCGATCGACAACTAATATTAAAGTTATGTTTGTCGTCGATCAA
CAAAAAAAAAAAGAAAAAAAAAAGATAAACGACTTACTAATGAGATAAAAGTAAGGGATAACTAG
GTTAATCCCGCGTGAGAATTAAAATTGAAATCGTCCTTTAAAAGTTTAAAACGACCAAGGATTTT
ACTATGTAAAAGTGGAGCGAAGTAACAAAG
Found at i:3549178 original size:2 final size:2
Alignment explanation
Indices: 3549171--3549255 Score: 163
Period size: 2 Copynumber: 43.0 Consensus size: 2
3549161 TATCAACTTT
3549171 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A 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
3549212 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3549254 TA
1 TA
3549256 GATCATAAAG
Statistics
Matches: 82, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 81 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3549438 original size:3 final size:3
Alignment explanation
Indices: 3549430--3549473 Score: 54
Period size: 3 Copynumber: 14.3 Consensus size: 3
3549420 TCTACAAAAA
*
3549430 TAT TAT TA- TATT TAT TAT TAT TAT TAT TAT TATT TAT TTT TAT T
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT T
3549474 TTTGCAGGCC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
2 2 0.06
3 29 0.81
4 5 0.14
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:3549446 original size:9 final size:10
Alignment explanation
Indices: 3549432--3549474 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
3549422 TACAAAAATA
3549432 TTATTA-TAT
1 TTATTATTAT
3549441 TTATTATTATT
1 TTATTATTA-T
3549452 ATTATTATTAT
1 -TTATTATTAT
*
3549463 TTATTTTTAT
1 TTATTATTAT
3549473 TT
1 TT
3549475 TTGCAGGCCC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
9 6 0.20
10 13 0.43
11 2 0.07
12 9 0.30
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TTATTATTAT
Found at i:3550331 original size:6 final size:6
Alignment explanation
Indices: 3550320--3550346 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3550310 ATCGAATACT
3550320 TTTTAA TTTTAA TTTTAA TTTTAA TTT
1 TTTTAA TTTTAA TTTTAA TTTTAA TTT
3550347 GAAATTTTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTTAA
Found at i:3552999 original size:11 final size:12
Alignment explanation
Indices: 3552966--3553025 Score: 52
Period size: 11 Copynumber: 4.9 Consensus size: 12
3552956 GATCTAATCA
3552966 AGAACAAAAATAG
1 AGAACAAAAA-AG
*
3552979 AAGAAGAAAAAAG
1 -AGAACAAAAAAG
3552992 AGAA-AAAAAAG
1 AGAACAAAAAAG
*
3553003 AGAA-AAAAACAA
1 AGAACAAAAA-AG
*
3553015 AAAACAAAAAA
1 AGAACAAAAAA
3553026 CAAAAAACAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
11 16 0.39
12 9 0.22
13 7 0.17
14 9 0.22
ACGTcount: A:0.80, C:0.05, G:0.13, T:0.02
Consensus pattern (12 bp):
AGAACAAAAAAG
Found at i:3553000 original size:12 final size:12
Alignment explanation
Indices: 3552966--3553073 Score: 57
Period size: 12 Copynumber: 9.1 Consensus size: 12
3552956 GATCTAATCA
*
3552966 AGAACAAAAATAG
1 AGAA-AAAAAAAG
*
3552979 AAGAAGAAAAAAG
1 -AGAAAAAAAAAG
3552992 AG-AAAAAAAAG
1 AGAAAAAAAAAG
3553003 AGAAAAAAACAA-
1 AGAAAAAAA-AAG
*
3553015 A-AAACAAAAAAC
1 AGAAA-AAAAAAG
*
3553027 A-AAAAACAAATG
1 AGAAAAA-AAAAG
*
3553039 A-AAAAACAAA-
1 AGAAAAAAAAAG
* *
3553049 TGAAAAATAAAG
1 AGAAAAAAAAAG
*
3553061 AAAAAAAAAAAG
1 AGAAAAAAAAAG
3553073 A
1 A
3553074 CGCTATGCAA
Statistics
Matches: 75, Mismatches: 12, Indels: 16
0.73 0.12 0.16
Matches are distributed among these distances:
11 27 0.36
12 36 0.48
13 8 0.11
14 4 0.05
ACGTcount: A:0.80, C:0.06, G:0.11, T:0.04
Consensus pattern (12 bp):
AGAAAAAAAAAG
Found at i:3553016 original size:7 final size:7
Alignment explanation
Indices: 3553006--3553036 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
3552996 AAAAAAGAGA
3553006 AAAAAAC
1 AAAAAAC
3553013 AAAAAAC
1 AAAAAAC
3553020 AAAAAAC
1 AAAAAAC
3553027 AAAAAAC
1 AAAAAAC
3553034 AAA
1 AAA
3553037 TGAAAAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:3553066 original size:11 final size:10
Alignment explanation
Indices: 3552979--3553069 Score: 74
Period size: 11 Copynumber: 8.2 Consensus size: 10
3552969 ACAAAAATAG
3552979 AAGAAGAAAAA
1 AAGAA-AAAAA
3552990 AGAGAAAAAAA
1 A-AGAAAAAAA
3553001 AGAGAAAAAAA
1 A-AGAAAAAAA
*
3553012 CAAAAAACAAAA
1 -AAGAAA-AAAA
*
3553024 AACAAAAAACA
1 AAGAAAAAA-A
3553035 AATGAAAAAACA
1 AA-GAAAAAA-A
*
3553047 AATGAAAAATA
1 AA-GAAAAAAA
3553058 AAGAAAAAAA
1 AAGAAAAAAA
3553068 AA
1 AA
3553070 AAGACGCTAT
Statistics
Matches: 70, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
10 12 0.17
11 32 0.46
12 26 0.37
ACGTcount: A:0.81, C:0.05, G:0.10, T:0.03
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:3553897 original size:23 final size:21
Alignment explanation
Indices: 3553866--3553927 Score: 61
Period size: 23 Copynumber: 2.8 Consensus size: 21
3553856 TGAAAGGGGC
* *
3553866 AATAGTTTCAAACTTTTGATT
1 AATATTTTCAAACTTTTAATT
3553887 AAATATTTTTCAAACTCTTTAATT
1 -AATA-TTTTCAAACT-TTTAATT
*
3553911 GATATTTTCAGAACTTT
1 AATATTTTCA-AACTTT
3553928 GAAAATAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
22 12 0.35
23 16 0.47
24 6 0.18
ACGTcount: A:0.34, C:0.11, G:0.06, T:0.48
Consensus pattern (21 bp):
AATATTTTCAAACTTTTAATT
Found at i:3554760 original size:36 final size:36
Alignment explanation
Indices: 3554709--3555035 Score: 193
Period size: 36 Copynumber: 8.8 Consensus size: 36
3554699 AATTTACTCA
*
3554709 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTATCATG
1 AAACAAA-TTTTGTCTCTCTTGAGACAGTTTACCATG
* * *
3554746 AAATAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTACCATG
* *
3554782 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTACCATG
* * * * * *
3554818 AAACAAATCTTTGAATATTTTTTCCTTGAAACAAATTTCGTCTCCCTTG
1 AAACAAAT-TTTG-----TCTCT-CTTGAGAC--A----GTTTACCATG
* * **
3554867 AAACAAATTTCGTCTCCCTTGAGACAGTTT-CTTTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTAC-CATG
* * * *
3554903 GAACTAAGTTTTGTCTCTTTTGAGACAGTTT-CTCTTG
1 AAAC-AAATTTTGTCTCTCTTGAGACAGTTTAC-CATG
* * * *
3554940 AAACAAATCTTATCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTACCATG
* * *
3554976 AAACAAA-GTT-T-TCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTGTCTCTCTTGAGACAGTTTACCATG
*
3555009 -AACAAAGTTT-TCTCTC-TGAGACAGTTT
1 AAACAAATTTTGTCTCTCTTGAGACAGTTT
3555036 CTATTGAAAC
Statistics
Matches: 243, Mismatches: 29, Indels: 40
0.78 0.09 0.13
Matches are distributed among these distances:
32 6 0.02
33 36 0.15
34 5 0.02
35 3 0.01
36 111 0.46
37 41 0.17
40 1 0.00
42 10 0.04
43 9 0.04
45 1 0.00
48 3 0.01
49 17 0.07
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (36 bp):
AAACAAATTTTGTCTCTCTTGAGACAGTTTACCATG
Found at i:3554865 original size:21 final size:21
Alignment explanation
Indices: 3554841--3554888 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
3554831 AATATTTTTT
3554841 CCTTGAAACAAATTTCGTCTC
1 CCTTGAAACAAATTTCGTCTC
3554862 CCTTGAAACAAATTTCGTCTC
1 CCTTGAAACAAATTTCGTCTC
3554883 CCTTGA
1 CCTTGA
3554889 GACAGTTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.33
Consensus pattern (21 bp):
CCTTGAAACAAATTTCGTCTC
Found at i:3554947 original size:73 final size:67
Alignment explanation
Indices: 3554860--3555046 Score: 216
Period size: 73 Copynumber: 2.7 Consensus size: 67
3554850 AAATTTCGTC
* * * *
3554860 TCCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTTTTG
1 TCCCTTGAAACAAATTT--TCTCTCTTGAGACAGTTTCTCTTGAAACAAAG-TTT-TCTC--TTG
3554925 AGACAGTT
60 AGACAGTT
* *
3554933 TCTCTTGAAACAAATCTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAAGTTTTCTCTTGAGAC
1 TCCCTTGAAACAAAT-TT-TCTCTCTTGAGACAGTTTCTCTTGAAACAAAGTTTTCTCTTGAGAC
3554998 AGTT
64 AGTT
*
3555002 TCCCTTG-AACAAAGTTTTCTCTC-TGAGACAGTTTCTATTGAAACA
1 TCCCTTGAAACAAA-TTTTCTCTCTTGAGACAGTTTCTCTTGAAACA
3555047 CCAACCTTTG
Statistics
Matches: 102, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
66 20 0.20
67 6 0.06
68 8 0.08
69 18 0.18
71 4 0.04
72 3 0.03
73 41 0.40
74 2 0.02
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (67 bp):
TCCCTTGAAACAAATTTTCTCTCTTGAGACAGTTTCTCTTGAAACAAAGTTTTCTCTTGAGACAG
TT
Found at i:3555008 original size:15 final size:15
Alignment explanation
Indices: 3554957--3555036 Score: 63
Period size: 15 Copynumber: 4.9 Consensus size: 15
3554947 TCTTATCTCT
3554957 CTTGAGACAGTTTCC
1 CTTGAGACAGTTTCC
* *
3554972 CTTGAAACAAAGTTTTCT
1 CTTGAGAC--AG-TTTCC
3554990 CTTGAGACAGTTTCC
1 CTTGAGACAGTTTCC
*
3555005 CTTGA-ACAAAGTTTTCT
1 CTTGAGAC--AG-TTTCC
3555022 CTCTGAGACAGTTTC
1 CT-TGAGACAGTTTC
3555037 TATTGAAACA
Statistics
Matches: 52, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
14 2 0.04
15 16 0.31
16 8 0.15
17 10 0.19
18 14 0.27
19 2 0.04
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (15 bp):
CTTGAGACAGTTTCC
Found at i:3555017 original size:16 final size:16
Alignment explanation
Indices: 3554965--3555018 Score: 58
Period size: 18 Copynumber: 3.3 Consensus size: 16
3554955 CTCTTGAGAC
3554965 AGTTTCCCTTGAAACAA
1 AGTTTCCCTTG-AACAA
*
3554982 AGTTTTCTCTTGAGAC--
1 AG-TTTCCCTTGA-ACAA
3554998 AGTTTCCCTTGAACAA
1 AGTTTCCCTTGAACAA
3555014 AGTTT
1 AGTTT
3555019 TCTCTCTGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
14 2 0.06
15 9 0.29
16 7 0.23
17 3 0.10
18 10 0.32
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (16 bp):
AGTTTCCCTTGAACAA
Found at i:3555294 original size:84 final size:84
Alignment explanation
Indices: 3555149--3555315 Score: 226
Period size: 84 Copynumber: 2.0 Consensus size: 84
3555139 TCTTGAAACA
* *
3555149 AAAAGACCTTCGAGTTCGACTACACACAGCTCGAATGCACATCATTTGCAACAAAGCTCAAGGCA
1 AAAAGACCTTCGAGTTCGACTACACACAGCTCAAAGGCACATCATTTGCAACAAAGCTCAAGGCA
*
3555214 AAAAGGGTTATTTGCCAAC
66 AAAAGGGTTATCTGCCAAC
* * * * ** * *
3555233 AAAAGACCTTTGAGTTCGATTGCACTCAGCTCAAAGGCACATCATTTGCAGTATAGGTCAAGGCA
1 AAAAGACCTTCGAGTTCGACTACACACAGCTCAAAGGCACATCATTTGCAACAAAGCTCAAGGCA
*
3555298 AGAAGGGTTATCTGCCAA
66 AAAAGGGTTATCTGCCAA
3555316 AGACCTTCGA
Statistics
Matches: 71, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
84 71 1.00
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (84 bp):
AAAAGACCTTCGAGTTCGACTACACACAGCTCAAAGGCACATCATTTGCAACAAAGCTCAAGGCA
AAAAGGGTTATCTGCCAAC
Found at i:3555661 original size:3 final size:3
Alignment explanation
Indices: 3555646--3555702 Score: 84
Period size: 3 Copynumber: 19.7 Consensus size: 3
3555636 ACAAAAACAT
3555646 TTA TTA -TA TTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3555691 TT- TTA TT- TTA TT
1 TTA TTA TTA TTA TT
3555703 TTTGCAGGCC
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
2 6 0.12
3 42 0.84
4 2 0.04
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:3571381 original size:21 final size:22
Alignment explanation
Indices: 3571331--3571384 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
3571321 ATTAATTAAT
* * *
3571331 TTTATAGTTTAATTTATAATTA
1 TTTATAATATAATTAATAATTA
3571353 TTTATAATATAATTAAT-ATTA
1 TTTATAATATAATTAATAATTA
3571374 TATT-TAATATA
1 T-TTATAATATA
3571385 TTTTTATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 12 0.43
22 16 0.57
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTATAATATAATTAATAATTA
Found at i:3571392 original size:34 final size:38
Alignment explanation
Indices: 3571323--3571394 Score: 98
Period size: 39 Copynumber: 2.0 Consensus size: 38
3571313 TAAACTATAT
*
3571323 TAATTAATTTTATAGTTTAATTTATAATTATTTATAATA
1 TAATTAATATTATAGTTTAA-TTATAATTATTTATAATA
3571362 TAATTAATATTATA-TTTAA-TAT-ATT-TTTATAAT
1 TAATTAATATTATAGTTTAATTATAATTATTTATAAT
3571395 GTAAATATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
34 8 0.25
35 3 0.09
36 3 0.09
38 5 0.16
39 13 0.41
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (38 bp):
TAATTAATATTATAGTTTAATTATAATTATTTATAATA
Found at i:3578476 original size:54 final size:54
Alignment explanation
Indices: 3578394--3578504 Score: 195
Period size: 54 Copynumber: 2.1 Consensus size: 54
3578384 AAACTTAACC
*
3578394 TCAGAACAGGAGATCCTAAGTAAACCAAATGCAGAAGATATAAACAACAGAAAA
1 TCAGAACAGGAGATCCTAAGTAAACCAAATACAGAAGATATAAACAACAGAAAA
* *
3578448 TCAGAACAGGAGATCCTAAGTAAACCAAATACAGAAGATATAGACAACATAAAA
1 TCAGAACAGGAGATCCTAAGTAAACCAAATACAGAAGATATAAACAACAGAAAA
3578502 TCA
1 TCA
3578505 TTCTTTCGAA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.53, C:0.17, G:0.15, T:0.14
Consensus pattern (54 bp):
TCAGAACAGGAGATCCTAAGTAAACCAAATACAGAAGATATAAACAACAGAAAA
Found at i:3579778 original size:14 final size:14
Alignment explanation
Indices: 3579759--3579786 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3579749 AAGTGAAAGA
3579759 ATAGTTATATAATT
1 ATAGTTATATAATT
3579773 ATAGTTATATAATT
1 ATAGTTATATAATT
3579787 TTGTTATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:3583231 original size:2 final size:2
Alignment explanation
Indices: 3583226--3583267 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
3583216 AAGTTATTAA
3583226 AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3583267 A
1 A
3583268 CGACTATGAG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3583808 original size:23 final size:23
Alignment explanation
Indices: 3583781--3583847 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
3583771 ATTTTATATG
*
3583781 GCACTTCGGTGCATTTCTATGCA
1 GCACTTCGGTGCATTTCTACGCA
* * *
3583804 GCACTTTGGTGCAATTCTACGTA
1 GCACTTCGGTGCATTTCTACGCA
*
3583827 GCACTTCGGTGCATTTATACG
1 GCACTTCGGTGCATTTCTACG
3583848 AGTTGTGGTG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.34
Consensus pattern (23 bp):
GCACTTCGGTGCATTTCTACGCA
Found at i:3584288 original size:12 final size:13
Alignment explanation
Indices: 3584271--3584299 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3584261 CGTAGGTTAC
3584271 AGAAGCG-AGAAG
1 AGAAGCGAAGAAG
3584283 AGAAGCGAAGAAG
1 AGAAGCGAAGAAG
3584296 AGAA
1 AGAA
3584300 AGACAGGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.55, C:0.07, G:0.38, T:0.00
Consensus pattern (13 bp):
AGAAGCGAAGAAG
Found at i:3588218 original size:21 final size:22
Alignment explanation
Indices: 3588178--3588219 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
3588168 TTTTCCAAAA
*
3588178 TACTACAGAGGTATCGATACCC
1 TACTACAGAGGTACCGATACCC
*
3588200 TACTACAG-TGTACCGATACC
1 TACTACAGAGGTACCGATACC
3588220 TTGCTACAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.24
Consensus pattern (22 bp):
TACTACAGAGGTACCGATACCC
Found at i:3588965 original size:31 final size:31
Alignment explanation
Indices: 3588927--3589049 Score: 167
Period size: 31 Copynumber: 4.0 Consensus size: 31
3588917 CCCGAATGAC
** * *
3588927 CAGTCCATAAGTCCATAACAACCTAGGTAAT
1 CAGTCCATAAGTCCCGAAGAACATAGGTAAT
3588958 CAGTCCATATA-TCCCGAAGAACATAGGTAAT
1 CAGTCCATA-AGTCCCGAAGAACATAGGTAAT
* *
3588989 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATAAGTCCCGAAGAACATAGGTAAT
*
3589020 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATAAGTCCCGAAGAACATAGGTAA
3589050 CCCTCGACTC
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
31 83 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (31 bp):
CAGTCCATAAGTCCCGAAGAACATAGGTAAT
Found at i:3591575 original size:31 final size:31
Alignment explanation
Indices: 3591529--3591693 Score: 233
Period size: 31 Copynumber: 5.3 Consensus size: 31
3591519 ATAGGTCAAT
* * * *
3591529 AAGAACCTAGGTAATCAGTACATATGTCCCG
1 AAGAACATAGATAAACAGTCCATATGTCCCG
* *
3591560 AAGAACATAGATAATCAGTCCATATGTCCCA
1 AAGAACATAGATAAACAGTCCATATGTCCCG
*
3591591 AAGAACATATATAAACAGTCCATATGTCCCG
1 AAGAACATAGATAAACAGTCCATATGTCCCG
*
3591622 AAGAACATAGGTAAACAGTCCATATGTCCCG
1 AAGAACATAGATAAACAGTCCATATGTCCCG
*
3591653 AAGAACATATG-TAAACAGTCCATATGTCTCG
1 AAGAACATA-GATAAACAGTCCATATGTCCCG
3591684 AAGAACATAG
1 AAGAACATAG
3591694 GTAACCCTCG
Statistics
Matches: 123, Mismatches: 10, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
30 1 0.01
31 121 0.98
32 1 0.01
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.22
Consensus pattern (31 bp):
AAGAACATAGATAAACAGTCCATATGTCCCG
Found at i:3591694 original size:62 final size:62
Alignment explanation
Indices: 3591529--3591697 Score: 257
Period size: 62 Copynumber: 2.7 Consensus size: 62
3591519 ATAGGTCAAT
* * * * * *
3591529 AAGAACCTAGGTAATCAGTACATATGTCCCGAAGAACATAGATAATCAGTCCATATGTCCCA
1 AAGAACATATGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCCCA
* *
3591591 AAGAACATATATAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCCCG
1 AAGAACATATGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCCCA
*
3591653 AAGAACATATGTAAACAGTCCATATGTCTCGAAGAACATAGGTAA
1 AAGAACATATGTAAACAGTCCATATGTCCCGAAGAACATAGGTAA
3591698 CCCTCGACTC
Statistics
Matches: 97, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 97 1.00
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.22
Consensus pattern (62 bp):
AAGAACATATGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATGTCCCA
Found at i:3592926 original size:11 final size:11
Alignment explanation
Indices: 3592912--3592944 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
3592902 TTTCCTTAAG
*
3592912 CTTAAGTATCA
1 CTTAAGGATCA
3592923 CTTAAGGATCA
1 CTTAAGGATCA
3592934 CTTAAGGATCA
1 CTTAAGGATCA
3592945 AAACCCATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.30
Consensus pattern (11 bp):
CTTAAGGATCA
Found at i:3594203 original size:33 final size:34
Alignment explanation
Indices: 3594144--3594233 Score: 139
Period size: 33 Copynumber: 2.7 Consensus size: 34
3594134 CTCATGTGTA
* *
3594144 AAGTTGGTCA-CATACCAAAGATGAATTTTCTAAT
1 AAGTTGGCCACCA-ACCAAAGATGAATTTTCCAAT
3594178 AAGTTGGCCACCAACC-AAGATGAATTTTCCAAT
1 AAGTTGGCCACCAACCAAAGATGAATTTTCCAAT
3594211 AAGTTGGCCACCAACCAAAGATG
1 AAGTTGGCCACCAACCAAAGATG
3594234 TCAACTTTGC
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
33 32 0.62
34 18 0.35
35 2 0.04
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (34 bp):
AAGTTGGCCACCAACCAAAGATGAATTTTCCAAT
Found at i:3594249 original size:9 final size:9
Alignment explanation
Indices: 3594235--3594266 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
3594225 CCAAAGATGT
3594235 CAACTTTGC
1 CAACTTTGC
3594244 CAACTTT--
1 CAACTTTGC
3594251 CAACTTTGC
1 CAACTTTGC
3594260 CAACTTT
1 CAACTTT
3594267 CAAGCCAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
7 7 0.33
9 14 0.67
ACGTcount: A:0.25, C:0.31, G:0.06, T:0.38
Consensus pattern (9 bp):
CAACTTTGC
Found at i:3594255 original size:16 final size:16
Alignment explanation
Indices: 3594234--3594269 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
3594224 ACCAAAGATG
3594234 TCAACTTTGCCAACTT
1 TCAACTTTGCCAACTT
3594250 TCAACTTTGCCAACTT
1 TCAACTTTGCCAACTT
3594266 TCAA
1 TCAA
3594270 GCCAAACATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.31, G:0.06, T:0.36
Consensus pattern (16 bp):
TCAACTTTGCCAACTT
Found at i:3596645 original size:31 final size:31
Alignment explanation
Indices: 3596610--3596668 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
3596600 TTCTTTTTTT
*
3596610 ATTTTTT-TGTTTTATTATTTTCTCTTTTAAC
1 ATTTTTTATATTTTATTATTTT-TCTTTTAAC
3596641 ATTTTTTATATTTTATTATTTTTCTTTT
1 ATTTTTTATATTTTATTATTTTTCTTTT
3596669 CTGAAATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 13 0.50
32 13 0.50
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.75
Consensus pattern (31 bp):
ATTTTTTATATTTTATTATTTTTCTTTTAAC
Found at i:3598654 original size:11 final size:11
Alignment explanation
Indices: 3598638--3598671 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
3598628 TCTTCTTTTT
3598638 TAAAAAATTAA
1 TAAAAAATTAA
3598649 TAAAAAATTAA
1 TAAAAAATTAA
*
3598660 TAGAAAATTAA
1 TAAAAAATTAA
3598671 T
1 T
3598672 TTTATTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (11 bp):
TAAAAAATTAA
Found at i:3600308 original size:29 final size:29
Alignment explanation
Indices: 3600266--3600336 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 29
3600256 GATGTTAATA
*
3600266 ATGCATTATTACATTCAGCAAAAGTATGC
1 ATGCATTATTACATTCAGAAAAAGTATGC
3600295 ATGCATTATTACATTCAGAAAAAGTATGC
1 ATGCATTATTACATTCAGAAAAAGTATGC
3600324 ATGCATTATTACA
1 ATGCATTATTACA
3600337 AGATTAACAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.32
Consensus pattern (29 bp):
ATGCATTATTACATTCAGAAAAAGTATGC
Found at i:3602647 original size:35 final size:34
Alignment explanation
Indices: 3602601--3602702 Score: 134
Period size: 35 Copynumber: 2.9 Consensus size: 34
3602591 TTTGATAATG
* *
3602601 TATTTTGAATTTGGGGTTGAGCATGTAATTGAAA
1 TATTTTGAATTTGGGGTTTAGAATGTAATTGAAA
* *
3602635 TATTTTAGAATTTGAGGTTTAGAATGTAATTGAAG
1 TATTTT-GAATTTGGGGTTTAGAATGTAATTGAAA
3602670 TATTTTGGAATTCT-GGGTTTAGAATGTAATTGA
1 TATTTT-GAATT-TGGGGTTTAGAATGTAATTGA
3602703 TAATCGTGTT
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
34 6 0.10
35 53 0.88
36 1 0.02
ACGTcount: A:0.30, C:0.02, G:0.25, T:0.43
Consensus pattern (34 bp):
TATTTTGAATTTGGGGTTTAGAATGTAATTGAAA
Found at i:3608391 original size:22 final size:21
Alignment explanation
Indices: 3608365--3608418 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
3608355 GCAAACAAAT
*
3608365 ATAAAATATAAATTTCTTTTAA
1 ATAAAATATAAATTTC-TTGAA
* *
3608387 ATAAATTA-AAAATTCTTGAA
1 ATAAAATATAAATTTCTTGAA
3608407 A-AAAATATAAAT
1 ATAAAATATAAAT
3608419 AAACGAACAT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 5 0.19
20 8 0.31
21 6 0.23
22 7 0.27
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (21 bp):
ATAAAATATAAATTTCTTGAA
Found at i:3608417 original size:21 final size:22
Alignment explanation
Indices: 3608367--3608417 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
3608357 AAACAAATAT
* *
3608367 AAAATAT-AAATTTCTTTTAAA
1 AAAATATAAAAATTCTTTGAAA
*
3608388 TAAAT-TAAAAATTC-TTGAAA
1 AAAATATAAAAATTCTTTGAAA
3608408 AAAATATAAA
1 AAAATATAAA
3608418 TAAACGAACA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (22 bp):
AAAATATAAAAATTCTTTGAAA
Found at i:3615243 original size:24 final size:24
Alignment explanation
Indices: 3615226--3615351 Score: 107
Period size: 24 Copynumber: 5.2 Consensus size: 24
3615216 ATCAAAATAT
*
3615226 AAATCAGGTCAAGTATCATATCAG
1 AAATCAGGTCAAGTATCAAATCAG
* *
3615250 AAATCAGGTCAAGTAACAGATCAG
1 AAATCAGGTCAAGTATCAAATCAG
* *
3615274 -AATCCAAGTCAAGTATCAGATCAG
1 AAAT-CAGGTCAAGTATCAAATCAG
* *
3615298 -AATCCATGTC-AGATATCAGATCAG
1 AAAT-CAGGTCAAG-TATCAAATCAG
* *
3615322 -AATCCATGTCAAGTATCAGATCAG
1 AAAT-CAGGTCAAGTATCAAATCAG
3615346 AAATCA
1 AAATCA
3615352 AATCGAAAAT
Statistics
Matches: 93, Mismatches: 5, Indels: 8
0.88 0.05 0.08
Matches are distributed among these distances:
23 5 0.05
24 83 0.89
25 5 0.05
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (24 bp):
AAATCAGGTCAAGTATCAAATCAG
Found at i:3615318 original size:48 final size:47
Alignment explanation
Indices: 3615233--3615347 Score: 160
Period size: 48 Copynumber: 2.4 Consensus size: 47
3615223 TATAAATCAG
*
3615233 GTCAAGTATCATATCAGAAATCAGGTCAAGTAACAGATCAGAATCCAA
1 GTCAAGTATCAGATCAG-AATCAGGTCAAGTAACAGATCAGAATCCAA
* * *
3615281 GTCAAGTATCAGATCAGAATCCATGTC-AGATATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAAT-CAGGTCAAG-TAACAGATCAGAATCCAA
3615329 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
3615348 ATCAAATCGA
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
47 5 0.08
48 56 0.92
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (47 bp):
GTCAAGTATCAGATCAGAATCAGGTCAAGTAACAGATCAGAATCCAA
Found at i:3615364 original size:48 final size:47
Alignment explanation
Indices: 3615233--3615364 Score: 151
Period size: 48 Copynumber: 2.7 Consensus size: 47
3615223 TATAAATCAG
* *
3615233 GTCAAGTATCATATCAGAAATCAGGTCAAGTAA-CAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAAATCAAGTCAA--AATCAGATCAGAATCCAA
* * *
3615281 GTCAAGTATCAGATCAG-AATCCATGTCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAAAT-CAAGTCA-AAATCAGATCAGAATCCAA
*
3615329 GTCAAGTATCAGATCAGAAATCAAATCGAAAATCAG
1 GTCAAGTATCAGATCAGAAATCAAGTC-AAAATCAG
3615365 GTAAAATATT
Statistics
Matches: 72, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
47 4 0.06
48 63 0.88
49 5 0.07
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (47 bp):
GTCAAGTATCAGATCAGAAATCAAGTCAAAATCAGATCAGAATCCAA
Found at i:3616477 original size:18 final size:18
Alignment explanation
Indices: 3616456--3616491 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3616446 CTTCCATCCG
*
3616456 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
3616474 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
3616492 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:3617808 original size:15 final size:15
Alignment explanation
Indices: 3617788--3617821 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
3617778 GGTCAACTCC
3617788 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
3617803 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
3617818 GGTC
1 GGTC
3617822 GGGTAAACGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.24, C:0.26, G:0.35, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:3617821 original size:8 final size:7
Alignment explanation
Indices: 3617787--3617818 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
3617777 TGGTCAACTC
3617787 CGGTCAA
1 CGGTCAA
3617794 CGGTCAA
1 CGGTCAA
3617801 CGGGTCAA
1 C-GGTCAA
3617809 CGGTCAA
1 CGGTCAA
3617816 CGG
1 CGG
3617819 GTCGGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:3617832 original size:13 final size:13
Alignment explanation
Indices: 3617814--3617851 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
3617804 GTCAACGGTC
3617814 AACGGGTCGGGTA
1 AACGGGTCGGGTA
3617827 AACGGGTCGGGTA
1 AACGGGTCGGGTA
3617840 AACGGGTCGGGT
1 AACGGGTCGGGT
3617852 CGGGTCAACG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.21, C:0.16, G:0.47, T:0.16
Consensus pattern (13 bp):
AACGGGTCGGGTA
Found at i:3617850 original size:18 final size:18
Alignment explanation
Indices: 3617829--3617874 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
3617819 GTCGGGTAAA
3617829 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
*
3617847 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTAAACGGGT
*
3617865 CAGGTCGGGT
1 CGGGTCGGGT
3617875 TGTGACCGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.13, C:0.20, G:0.50, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Done.