Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 72 of 199
Found at i:20296913 original size:46 final size:43
Alignment explanation
Indices: 20296861--20296992 Score: 123
Period size: 43 Copynumber: 3.1 Consensus size: 43
20296851 CTATGTAAGT
20296861 TATATAAGTTACGTAAGTTATTATGTAAGTTATGCAAGCTTATATA
1 TATATAAGTTAC-T-AGTTATTATGTAAGTTATGCAAG-TTATATA
* **
20296907 TATATAAGTT-CT-G-TATTATGTTA-TTATGTTA-TTATATA
1 TATATAAGTTACTAGTTATTATGTAAGTTATGCAAGTTATATA
* * *
20296945 TTATGTAATTTATTATGTTATTATGTAAGTTATGCAAGTT-TATA
1 -TATATAAGTTACTA-GTTATTATGTAAGTTATGCAAGTTATATA
20296989 TATA
1 TATA
20296993 AGTTTCTATA
Statistics
Matches: 69, Mismatches: 10, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
38 7 0.10
39 8 0.12
40 7 0.10
41 9 0.13
42 2 0.03
43 12 0.17
44 11 0.16
45 3 0.04
46 10 0.14
ACGTcount: A:0.34, C:0.04, G:0.13, T:0.49
Consensus pattern (43 bp):
TATATAAGTTACTAGTTATTATGTAAGTTATGCAAGTTATATA
Found at i:20296931 original size:8 final size:8
Alignment explanation
Indices: 20296920--20296970 Score: 58
Period size: 8 Copynumber: 7.0 Consensus size: 8
20296910 ATAAGTTCTG
20296920 TATTATGT
1 TATTATGT
20296928 TATTATGT
1 TATTATGT
*
20296936 TATTAT-A
1 TATTATGT
20296943 TATTATG-
1 TATTATGT
20296950 TA--AT-T
1 TATTATGT
20296955 TATTATGT
1 TATTATGT
20296963 TATTATGT
1 TATTATGT
20296971 AAGTTATGCA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
5 4 0.11
7 10 0.27
8 23 0.62
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (8 bp):
TATTATGT
Found at i:20296948 original size:15 final size:15
Alignment explanation
Indices: 20296928--20296968 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 15
20296918 TGTATTATGT
20296928 TATTATGTTATTATA
1 TATTATGTTATTATA
*
20296943 TATTATG-TA--ATT
1 TATTATGTTATTATA
20296955 TATTATGTTATTAT
1 TATTATGTTATTAT
20296969 GTAAGTTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
12 9 0.41
13 2 0.09
14 2 0.09
15 9 0.41
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (15 bp):
TATTATGTTATTATA
Found at i:20298797 original size:24 final size:24
Alignment explanation
Indices: 20298718--20298797 Score: 79
Period size: 24 Copynumber: 3.2 Consensus size: 24
20298708 TGTATCTTTC
* * *
20298718 ATTTAAATAATTAATTACATGTCT
1 ATTTAAATAATTAATTACCTATTT
* *
20298742 ACTTAAATAATTAATTACCTAAACATTA
1 ATTTAAATAATTAATTACCT----ATTT
20298770 ATTTAAATAATTAATTACCTATTT
1 ATTTAAATAATTAATTACCTATTT
20298794 ATTT
1 ATTT
20298798 GTTTATTTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
24 25 0.56
28 20 0.44
ACGTcount: A:0.44, C:0.10, G:0.01, T:0.45
Consensus pattern (24 bp):
ATTTAAATAATTAATTACCTATTT
Found at i:20299931 original size:43 final size:42
Alignment explanation
Indices: 20299813--20299966 Score: 188
Period size: 41 Copynumber: 3.7 Consensus size: 42
20299803 TTTTATTATT
* * * * *
20299813 ATTAGCGGCGC-TTTTGAGAAAGCGCCGCTAAAGGTCCGACC
1 ATTAGCGGCGCTTTTTAAAAAAACGCCGCTGAAGGTCCGAAC
*
20299854 ATTAGCGGCGCGTTTT-AAAAAACGCCGCTGAAGGTCCGAAC
1 ATTAGCGGCGCTTTTTAAAAAAACGCCGCTGAAGGTCCGAAC
* * *
20299895 ATTAGCGGCTCTTTTTAAAAAAAACGCTGCTGAAGGTCCGAGC
1 ATTAGCGGCGCTTTTT-AAAAAAACGCCGCTGAAGGTCCGAAC
*
20299938 ATTAGCGGCGCTTTTT-GAAAAACGCCGCT
1 ATTAGCGGCGCTTTTTAAAAAAACGCCGCT
20299967 AAAAGCCCCA
Statistics
Matches: 99, Mismatches: 11, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
41 57 0.58
42 4 0.04
43 38 0.38
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (42 bp):
ATTAGCGGCGCTTTTTAAAAAAACGCCGCTGAAGGTCCGAAC
Found at i:20300096 original size:40 final size:40
Alignment explanation
Indices: 20300032--20300143 Score: 145
Period size: 40 Copynumber: 2.8 Consensus size: 40
20300022 TCTGAGTAAA
* * * *
20300032 CGCCGCTAATGC-CTATTTTTAGCGGGGCTTTTGTAAATG
1 CGCCGCTAATGCTCGATTTTTAGCGGCGCTTTTGGAAAAG
* *
20300071 CGCCGCTACTGCTCGATCTTTAGCGGCGCTTTTGGAAAAG
1 CGCCGCTAATGCTCGATTTTTAGCGGCGCTTTTGGAAAAG
* *
20300111 CGCCGCTAATGCTTGATTTTTAGTGGCGCTTTT
1 CGCCGCTAATGCTCGATTTTTAGCGGCGCTTTT
20300144 TATCAAAATG
Statistics
Matches: 62, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
39 11 0.18
40 51 0.82
ACGTcount: A:0.16, C:0.23, G:0.26, T:0.35
Consensus pattern (40 bp):
CGCCGCTAATGCTCGATTTTTAGCGGCGCTTTTGGAAAAG
Found at i:20300661 original size:88 final size:88
Alignment explanation
Indices: 20300557--20300735 Score: 349
Period size: 88 Copynumber: 2.0 Consensus size: 88
20300547 TCTAATTCTA
20300557 ATGACTATTAGAATTTAAAGTATATCAAAACTTATATAGATCTTGATGGACATTCACTTAATAAA
1 ATGACTATTAGAATTTAAAGTATATCAAAACTTATATAGATCTTGATGGACATTCACTTAATAAA
20300622 ATATTCATGACACTCCCCATTGG
66 ATATTCATGACACTCCCCATTGG
20300645 ATGACTATTAGAATTTAAAGTATATCAAAACTTATATAGATCTTGATGGACATTCACTTAATAAA
1 ATGACTATTAGAATTTAAAGTATATCAAAACTTATATAGATCTTGATGGACATTCACTTAATAAA
*
20300710 ATATTCATGACACTCCTCATTGG
66 ATATTCATGACACTCCCCATTGG
20300733 ATG
1 ATG
20300736 TTCATTTGTA
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 90 1.00
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.35
Consensus pattern (88 bp):
ATGACTATTAGAATTTAAAGTATATCAAAACTTATATAGATCTTGATGGACATTCACTTAATAAA
ATATTCATGACACTCCCCATTGG
Found at i:20307105 original size:42 final size:43
Alignment explanation
Indices: 20307058--20307155 Score: 117
Period size: 43 Copynumber: 2.3 Consensus size: 43
20307048 CACAGAAGTA
* * *
20307058 CATAAGTGCTAAACAG-AAACCCATAATGATTGAACGGAAGCT
1 CATAAGAGCTAAACAGAAAACCCATAAGGATTAAACGGAAGCT
* * * *
20307100 CATAAGAGCTGAACGGAAAACCCATAAGGGTTAAACTGAAGCT
1 CATAAGAGCTAAACAGAAAACCCATAAGGATTAAACGGAAGCT
*
20307143 CAAAAGAGCTAAA
1 CATAAGAGCTAAA
20307156 TGGAAACTCA
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
42 13 0.28
43 33 0.72
ACGTcount: A:0.45, C:0.18, G:0.20, T:0.16
Consensus pattern (43 bp):
CATAAGAGCTAAACAGAAAACCCATAAGGATTAAACGGAAGCT
Found at i:20314786 original size:21 final size:21
Alignment explanation
Indices: 20314757--20314797 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
20314747 AAGCCCGAAG
* *
20314757 GCTACACAGAAGCACATAAGT
1 GCTAAACAGAAACACATAAGT
*
20314778 GCTAAACAGAAACCCATAAG
1 GCTAAACAGAAACACATAAG
20314798 GGTTGAACGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.24, G:0.17, T:0.12
Consensus pattern (21 bp):
GCTAAACAGAAACACATAAGT
Found at i:20314818 original size:42 final size:42
Alignment explanation
Indices: 20314766--20314900 Score: 141
Period size: 42 Copynumber: 3.2 Consensus size: 42
20314756 GGCTACACAG
* * *
20314766 AAGCACATAAGTGCTAAACAGAAACCCATAAGGGTTGAACGA
1 AAGCTCATAAGTGCTAAACGGAAACCCATAAGGGTTAAACGA
* *
20314808 AAGCTCATAAGAT-CTAAATGGAAACCCATAAGGGTTAAATTG-
1 AAGCTCATAAG-TGCTAAACGGAAACCCATAAGGGTTAAA-CGA
* * * *
20314850 AAGCTTAAAAGAGCTAAACGGAAACCCATTAGGGTTAAACGGA
1 AAGCTCATAAGTGCTAAACGGAAACCCATAAGGGTTAAAC-GA
20314893 AA-CTCATA
1 AAGCTCATA
20314901 TGAGTTAATT
Statistics
Matches: 75, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
42 71 0.95
43 4 0.05
ACGTcount: A:0.44, C:0.17, G:0.20, T:0.19
Consensus pattern (42 bp):
AAGCTCATAAGTGCTAAACGGAAACCCATAAGGGTTAAACGA
Found at i:20314846 original size:21 final size:21
Alignment explanation
Indices: 20314771--20314900 Score: 75
Period size: 21 Copynumber: 6.2 Consensus size: 21
20314761 CACAGAAGCA
* * *
20314771 CATAAGTGCTAAACAGAAACC
1 CATAAGGGTTAAACGGAAACC
* *
20314792 CATAAGGGTTGAAC-GAAAGCT
1 CATAAGGGTTAAACGGAAA-CC
* *
20314813 CATAA-GATCTAAATGGAAACC
1 CATAAGGGT-TAAACGGAAACC
** * *
20314834 CATAAGGGTTAAATTGAAGCT
1 CATAAGGGTTAAACGGAAACC
* * * *
20314855 TAAAAGAGCTAAACGGAAACC
1 CATAAGGGTTAAACGGAAACC
* *
20314876 CATTAGGGTTAAACGGAAACT
1 CATAAGGGTTAAACGGAAACC
20314897 CATA
1 CATA
20314901 TGAGTTAATT
Statistics
Matches: 78, Mismatches: 27, Indels: 8
0.69 0.24 0.07
Matches are distributed among these distances:
20 6 0.08
21 66 0.85
22 6 0.08
ACGTcount: A:0.44, C:0.17, G:0.20, T:0.19
Consensus pattern (21 bp):
CATAAGGGTTAAACGGAAACC
Found at i:20314907 original size:21 final size:21
Alignment explanation
Indices: 20314859--20314908 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
20314849 GAAGCTTAAA
*
20314859 AGAGCTAAACGGAAACCCATT
1 AGAGTTAAACGGAAACCCATT
* *
20314880 AGGGTTAAACGGAAACTCA-T
1 AGAGTTAAACGGAAACCCATT
20314900 ATGAGTTAA
1 A-GAGTTAA
20314909 TTGAAGCTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.20
Consensus pattern (21 bp):
AGAGTTAAACGGAAACCCATT
Found at i:20318650 original size:31 final size:32
Alignment explanation
Indices: 20318612--20318687 Score: 102
Period size: 31 Copynumber: 2.4 Consensus size: 32
20318602 GAATCACCCC
*
20318612 GTGTTTACTATCCCGA-CGGACTATCTATTCT
1 GTGTTTACTATCCCGAGCAGACTATCTATTCT
* * *
20318643 GTGTTTACTGT-CCTAGCAGACTATCTATTTT
1 GTGTTTACTATCCCGAGCAGACTATCTATTCT
20318674 GTGTTTACTATCCC
1 GTGTTTACTATCCC
20318688 AATGAACTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
30 3 0.08
31 33 0.87
32 2 0.05
ACGTcount: A:0.18, C:0.24, G:0.16, T:0.42
Consensus pattern (32 bp):
GTGTTTACTATCCCGAGCAGACTATCTATTCT
Found at i:20318697 original size:31 final size:30
Alignment explanation
Indices: 20318612--20318697 Score: 84
Period size: 31 Copynumber: 2.8 Consensus size: 30
20318602 GAATCACCCC
* *
20318612 GTGTTTACTATCCCGACGGACTATCTATTCT
1 GTGTTTACTATCCC-AAGAACTATCTATTCT
* * *
20318643 GTGTTTACTGT-CCTAGCAGACTATCTATTTT
1 GTGTTTACTATCCCAAG-A-ACTATCTATTCT
20318674 GTGTTTACTATCCCAATGAACTAT
1 GTGTTTACTATCCCAA-GAACTAT
20318698 TTTTGTAGAT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
29 1 0.02
30 2 0.05
31 36 0.82
32 4 0.09
33 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (30 bp):
GTGTTTACTATCCCAAGAACTATCTATTCT
Found at i:20320514 original size:10 final size:10
Alignment explanation
Indices: 20320501--20320582 Score: 59
Period size: 10 Copynumber: 8.4 Consensus size: 10
20320491 GAAAAGTTAT
20320501 AAAATTATTCA
1 AAAATTATT-A
*
20320512 AAACTT-TTA
1 AAAATTATTA
20320521 AAAATTA-TA
1 AAAATTATTA
20320530 AGAAATTA-TA
1 A-AAATTATTA
*
20320540 AAAATTTATTT
1 AAAA-TTATTA
*
20320551 AAAAGTA--A
1 AAAATTATTA
20320559 AAAA-TATTTA
1 AAAATTA-TTA
20320569 AAAATTATTA
1 AAAATTATTA
20320579 AAAA
1 AAAA
20320583 AATTCTTGGA
Statistics
Matches: 58, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
7 2 0.03
8 4 0.07
9 12 0.21
10 28 0.48
11 12 0.21
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (10 bp):
AAAATTATTA
Found at i:20320581 original size:20 final size:19
Alignment explanation
Indices: 20320492--20320582 Score: 62
Period size: 19 Copynumber: 4.7 Consensus size: 19
20320482 AAAATTACAG
* * *
20320492 AAAAGTTATAAAATTATTC
1 AAAAATTATAAAAATATTT
* * *
20320511 AAAACTTTTAAAAAT-TAT
1 AAAAATTATAAAAATATTT
20320529 AAGAAATTATAAAAATTTATTT
1 AA-AAATTATAAAAA--TATTT
*
20320551 -AAAAGTA-AAAAATATTT
1 AAAAATTATAAAAATATTT
20320568 AAAAATTATTAAAAA
1 AAAAATTA-TAAAAA
20320583 AATTCTTGGA
Statistics
Matches: 55, Mismatches: 10, Indels: 13
0.71 0.13 0.17
Matches are distributed among these distances:
17 5 0.09
18 9 0.16
19 27 0.49
20 10 0.18
21 2 0.04
22 2 0.04
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.35
Consensus pattern (19 bp):
AAAAATTATAAAAATATTT
Found at i:20321878 original size:21 final size:21
Alignment explanation
Indices: 20321852--20321900 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
20321842 GTTTCTCTCA
*
20321852 CTGCTTCTCGCACTGCAGGCT
1 CTGCTTCTCGCACTGCAGCCT
* *
20321873 CTGCTTCTCTCGCTGCAGCCT
1 CTGCTTCTCGCACTGCAGCCT
20321894 CTGCTTC
1 CTGCTTC
20321901 CCTCGTTGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.06, C:0.41, G:0.20, T:0.33
Consensus pattern (21 bp):
CTGCTTCTCGCACTGCAGCCT
Found at i:20321905 original size:21 final size:21
Alignment explanation
Indices: 20321864--20321916 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
20321854 GCTTCTCGCA
* *
20321864 CTGCAGGCTCTGCTTCTCTCG
1 CTGCAGCCTCTGCTTCCCTCG
20321885 CTGCAGCCTCTGCTTCCCTCG
1 CTGCAGCCTCTGCTTCCCTCG
* *
20321906 TTGCTGCCTCT
1 CTGCAGCCTCT
20321917 ACTTTAAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.04, C:0.42, G:0.21, T:0.34
Consensus pattern (21 bp):
CTGCAGCCTCTGCTTCCCTCG
Found at i:20323073 original size:114 final size:114
Alignment explanation
Indices: 20322868--20323327 Score: 751
Period size: 114 Copynumber: 4.0 Consensus size: 114
20322858 TAAATTATTT
* *
20322868 TAAATCCCTGAGTATTAGCGGCGCTTACTTAAAAACACCACTAAATCCCCGAAAGCTCAGAAAAC
1 TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACACCACTAAATCCCCGAAAGCTCAGAAAAC
*
20322933 GGCGTCGTTGGGCTTAAGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
66 GGCGTCGTTGGGCTTAGGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
* *
20322982 TAAAGCCCTGAGCTTTAGCGGCGCTTACTTAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAAC
1 TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACACCACTAAATCCCCGAAAGCTCAGAAAAC
* * *
20323047 GGCGTCGTTGGGCTTAGGTATTTTTGCGGCGCTTTACCAAAAACGTCGT
66 GGCGTCGTTGGGCTTAGGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
* *
20323096 TAAAGCCCTGAGCATTAGCGGCGCTTACATAAAAACGCCACTAAATCCCCGAAAGCTCAGAAAAC
1 TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACACCACTAAATCCCCGAAAGCTCAGAAAAC
*
20323161 GGCGTCATTGGGCTTAGGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
66 GGCGTCGTTGGGCTTAGGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
* * *
20323210 CATAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACACCACTAAATCCCCGAAAGCTTAGAAAAC
1 TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACACCACTAAATCCCCGAAAGCTCAGAAAAC
* * *
20323275 GGCATCGTTGGGCTTAGGT-TTTTTGTGGCGCTTCTCTCAAAAACGCCGC
66 GGCGTCGTTGGGCTTAGGTATTTTTGCGGCGCTT-TCCCAAAAACGCCGC
20323324 TAAA
1 TAAA
20323328 TCCCCTAAAG
Statistics
Matches: 320, Mismatches: 25, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
113 13 0.04
114 307 0.96
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.23
Consensus pattern (114 bp):
TAAAGCCCTGAGCATTAGCGGCGCTTACTTAAAAACACCACTAAATCCCCGAAAGCTCAGAAAAC
GGCGTCGTTGGGCTTAGGTATTTTTGCGGCGCTTTCCCAAAAACGCCGC
Found at i:20323328 original size:73 final size:72
Alignment explanation
Indices: 20323227--20323398 Score: 209
Period size: 73 Copynumber: 2.4 Consensus size: 72
20323217 CTGAGCATTA
* * * * *
20323227 GCGGCGCTTACTTAAAAACACCACTAAATCCCCGAAAGCTTAGAAAACGGCATCGTTGGGCTTAG
1 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCATCGTTGGGCTTAG
*
20323292 GTTTTTT
66 GTATTTT
* * * *
20323299 GTGGCGCTTCTCTCAAAAACGCCGCTAAATCCCCTAAAGCTCGGAAAACGGCGTCGTTGGGCTTA
1 GCGGCGCTT-TCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCATCGTTGGGCTTA
20323364 GGTATTTT
65 GGTATTTT
* ** *
20323372 GCGGTGCTTTCTGGAAAATGCCGCTAA
1 GCGGCGCTTTCTCAAAAACGCCGCTAA
20323399 TGCTTATTTT
Statistics
Matches: 84, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
72 23 0.27
73 61 0.73
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (72 bp):
GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCATCGTTGGGCTTAG
GTATTTT
Found at i:20325710 original size:7 final size:7
Alignment explanation
Indices: 20325698--20325731 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
20325688 TTATTATGCC
20325698 TATTATA
1 TATTATA
20325705 TATTATA
1 TATTATA
20325712 TATTATA
1 TATTATA
20325719 TATTATA
1 TATTATA
20325726 TATTAT
1 TATTAT
20325732 TTGTTAAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TATTATA
Found at i:20340699 original size:45 final size:45
Alignment explanation
Indices: 20340635--20340729 Score: 172
Period size: 45 Copynumber: 2.1 Consensus size: 45
20340625 TTCTTCTTCA
* *
20340635 TCTTCGTTTTCTTCTGCTGGATGTAATGATTCCATCAATGGATAT
1 TCTTCGTTTTCTTCTGCTGGATATAATGATTCCATCAAAGGATAT
20340680 TCTTCGTTTTCTTCTGCTGGATATAATGATTCCATCAAAGGATAT
1 TCTTCGTTTTCTTCTGCTGGATATAATGATTCCATCAAAGGATAT
20340725 TCTTC
1 TCTTC
20340730 ATCATCTTCT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.21, C:0.19, G:0.16, T:0.44
Consensus pattern (45 bp):
TCTTCGTTTTCTTCTGCTGGATATAATGATTCCATCAAAGGATAT
Found at i:20340738 original size:45 final size:45
Alignment explanation
Indices: 20340644--20340739 Score: 147
Period size: 45 Copynumber: 2.1 Consensus size: 45
20340634 ATCTTCGTTT
* * * **
20340644 TCTTCTGCTGGATGTAATGATTCCATCAATGGATATTCTTCGTTT
1 TCTTCTGCTGGATATAATGATTCCATCAAAGGATATTCTTCATCA
20340689 TCTTCTGCTGGATATAATGATTCCATCAAAGGATATTCTTCATCA
1 TCTTCTGCTGGATATAATGATTCCATCAAAGGATATTCTTCATCA
20340734 TCTTCT
1 TCTTCT
20340740 TCCCCTGCTG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.43
Consensus pattern (45 bp):
TCTTCTGCTGGATATAATGATTCCATCAAAGGATATTCTTCATCA
Found at i:20343962 original size:15 final size:14
Alignment explanation
Indices: 20343923--20343961 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
20343913 GGGTTGTTAA
*
20343923 TTTTGATTTTAATTT
1 TTTTG-TTTTTATTT
*
20343938 ATTTGTTTTTATTT
1 TTTTGTTTTTATTT
20343952 TTTTGTTTTT
1 TTTTGTTTTT
20343962 TTCAAAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.13, C:0.00, G:0.08, T:0.79
Consensus pattern (14 bp):
TTTTGTTTTTATTT
Found at i:20345374 original size:6 final size:6
Alignment explanation
Indices: 20345363--20345391 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
20345353 ATCATTAATA
20345363 AACCAC AACCAC AACCAC AACCAC AACCA
1 AACCAC AACCAC AACCAC AACCAC AACCA
20345392 TAACACATCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (6 bp):
AACCAC
Found at i:20346641 original size:45 final size:44
Alignment explanation
Indices: 20346456--20346643 Score: 167
Period size: 45 Copynumber: 4.2 Consensus size: 44
20346446 ATACTCGAAT
* *
20346456 AATCACATATATCGAACAATGCCAACGTCCCAGACGTGGTCTTACATG
1 AATCACATATATCG----ATGCCATCGTCCCAGACGTGGTCTTACACG
* *
20346504 -CT-ATATCATATCGATGCCA-CTGTCCCAGACAG-GGTCTTACACG
1 AATCACAT-ATATCGATGCCATC-GTCCCAGAC-GTGGTCTTACACG
* *
20346547 AATCA-A-ATA-CGATGCCAAT-GTCCTAGACATGGTCTTACACG
1 AATCACATATATCGATGCC-ATCGTCCCAGACGTGGTCTTACACG
20346588 TAATCACATATATCGATGCCATCGTCCCAGACGTGGTCTTACACG
1 -AATCACATATATCGATGCCATCGTCCCAGACGTGGTCTTACACG
*
20346633 AGAACACATAT
1 A-ATCACATAT
20346644 TGGAAATCCT
Statistics
Matches: 117, Mismatches: 9, Indels: 31
0.75 0.06 0.20
Matches are distributed among these distances:
41 26 0.22
42 10 0.09
43 26 0.22
44 9 0.08
45 36 0.31
46 3 0.03
47 7 0.06
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.24
Consensus pattern (44 bp):
AATCACATATATCGATGCCATCGTCCCAGACGTGGTCTTACACG
Found at i:20347558 original size:28 final size:31
Alignment explanation
Indices: 20347526--20347584 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 31
20347516 TGTTTTGTTT
20347526 TTATTATAATAA-CATTAT-AAT-ATATAAA
1 TTATTATAATAACCATTATAAATAATATAAA
* *
20347554 TTATTATTATAACCTTTATAAATAATATAAA
1 TTATTATAATAACCATTATAAATAATATAAA
20347585 AACTATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 11 0.42
29 5 0.19
30 3 0.12
31 7 0.27
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (31 bp):
TTATTATAATAACCATTATAAATAATATAAA
Found at i:20357157 original size:40 final size:39
Alignment explanation
Indices: 20357105--20357243 Score: 147
Period size: 40 Copynumber: 3.5 Consensus size: 39
20357095 GGCGTTTGGA
* *
20357105 TAAAAAATGCCGCTAAAAATCAAGCATTAGCGACGTTTT
1 TAAAAAACGCCGCTAAAAATCAAGCATTAGCGGCGTTTT
* *
20357144 TCAAAAAACGCCGCTAAAGATCGAAGCATTAGTGGCGCTTTT
1 T-AAAAAACGCCGCTAAAAATC-AAGCATTAGCGGCG-TTTT
* *
20357186 T-GAAAACGCCGCTAAAAAT-GAGCATTAGCGGCGTTTCT
1 TAAAAAACGCCGCTAAAAATCAAGCATTAGCGGCGTTT-T
* *
20357224 TAGAAAAGCGCCGCAAAAAA
1 TA-AAAAACGCCGCTAAAAA
20357244 CCTAATCCCA
Statistics
Matches: 83, Mismatches: 11, Indels: 11
0.79 0.10 0.10
Matches are distributed among these distances:
37 3 0.04
38 14 0.17
39 1 0.01
40 48 0.58
41 12 0.14
42 5 0.06
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (39 bp):
TAAAAAACGCCGCTAAAAATCAAGCATTAGCGGCGTTTT
Found at i:20357332 original size:41 final size:40
Alignment explanation
Indices: 20357275--20357383 Score: 137
Period size: 41 Copynumber: 2.7 Consensus size: 40
20357265 ACCTTTCGGG
* *
20357275 GCTTTAGCCGCGTTTTTAAAAAAACGCCACTAATGCTCAGA
1 GCTTTAGCGGCGTTTTTAAAAAAGCGCCACTAATGCTC-GA
** ** *
20357316 GCTTTAGCGGCGTTTTTGGAAAAGCGCTGCTAATGCTCGG
1 GCTTTAGCGGCGTTTTTAAAAAAGCGCCACTAATGCTCGA
*
20357356 GATTTAGCGGCGTTTTTAAAAAAGCGCC
1 GCTTTAGCGGCGTTTTTAAAAAAGCGCC
20357384 GCAAAAACAT
Statistics
Matches: 57, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
40 25 0.44
41 32 0.56
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (40 bp):
GCTTTAGCGGCGTTTTTAAAAAAGCGCCACTAATGCTCGA
Found at i:20357808 original size:15 final size:14
Alignment explanation
Indices: 20357788--20357831 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
20357778 AAGGTTTATA
20357788 GATTATGGAATTAAG
1 GATTATGG-ATTAAG
*
20357803 GATTATGGATTAGG
1 GATTATGGATTAAG
* *
20357817 GATTCTGGTTTAAG
1 GATTATGGATTAAG
20357831 G
1 G
20357832 GTTGTGATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
14 17 0.68
15 8 0.32
ACGTcount: A:0.30, C:0.02, G:0.32, T:0.36
Consensus pattern (14 bp):
GATTATGGATTAAG
Found at i:20357979 original size:7 final size:7
Alignment explanation
Indices: 20357967--20358025 Score: 73
Period size: 7 Copynumber: 8.4 Consensus size: 7
20357957 TAAATAATGT
20357967 TTAGGGG
1 TTAGGGG
20357974 TTAGGGG
1 TTAGGGG
*
20357981 TTGGGGG
1 TTAGGGG
**
20357988 TTAGTAG
1 TTAGGGG
20357995 TTAGGGG
1 TTAGGGG
*
20358002 TTTGGGG
1 TTAGGGG
*
20358009 TTTGGGG
1 TTAGGGG
20358016 TTAGGGG
1 TTAGGGG
20358023 TTA
1 TTA
20358026 AGAGTTAGTG
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 44 1.00
ACGTcount: A:0.12, C:0.00, G:0.53, T:0.36
Consensus pattern (7 bp):
TTAGGGG
Found at i:20358159 original size:14 final size:14
Alignment explanation
Indices: 20358140--20358172 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
20358130 TGTAAAAGAG
20358140 GGGTTAGGGGTTAA
1 GGGTTAGGGGTTAA
*
20358154 GGGTTAGGGGTTTA
1 GGGTTAGGGGTTAA
20358168 GGGTT
1 GGGTT
20358173 TATGTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.52, T:0.33
Consensus pattern (14 bp):
GGGTTAGGGGTTAA
Found at i:20358885 original size:113 final size:113
Alignment explanation
Indices: 20358734--20358938 Score: 329
Period size: 113 Copynumber: 1.8 Consensus size: 113
20358724 GCGTTTTATA
* * **
20358734 AAAAACGCCACAAAAAATAATTTTACTATAAAAAAATAGCGCCATTTTATATAGCAAAATTGTGT
1 AAAAACGCCACAAAAAATAATTTTACTATAAAAAAATAGCGCCATTTTACAAAGCAAAACAGTGT
* *
20358799 CATTTTATTTCAAATGAAATAATTTTTGCGTAAGCAATAGCGGCGTTT
66 CATTTTATTCCAAATAAAATAATTTTTGCGTAAGCAATAGCGGCGTTT
* *
20358847 AAAAACGCCACAAAAAATAATTTTACTTTAAAAAAATAGTGCCATTTTACAAAGCAAAACAGTGT
1 AAAAACGCCACAAAAAATAATTTTACTATAAAAAAATAGCGCCATTTTACAAAGCAAAACAGTGT
*
20358912 CGTTTTATTCCAAATAAAATAATTTTT
66 CATTTTATTCCAAATAAAATAATTTTT
20358939 TGCCGCGTTT
Statistics
Matches: 83, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
113 83 1.00
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (113 bp):
AAAAACGCCACAAAAAATAATTTTACTATAAAAAAATAGCGCCATTTTACAAAGCAAAACAGTGT
CATTTTATTCCAAATAAAATAATTTTTGCGTAAGCAATAGCGGCGTTT
Found at i:20359482 original size:11 final size:11
Alignment explanation
Indices: 20359466--20359491 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
20359456 TTTTCCTCAT
20359466 TTTTCTTTTTG
1 TTTTCTTTTTG
20359477 TTTTCTTTTTG
1 TTTTCTTTTTG
20359488 TTTT
1 TTTT
20359492 GTTCTACAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.85
Consensus pattern (11 bp):
TTTTCTTTTTG
Found at i:20359767 original size:22 final size:22
Alignment explanation
Indices: 20359735--20359778 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
20359725 TTAATGTGGG
20359735 TTTATTTTA-TTTTATTTTTTT
1 TTTATTTTATTTTTATTTTTTT
20359756 TTTATTTTTATTTTTATTTTTTT
1 TTTA-TTTTATTTTTATTTTTTT
20359779 GAGGGGGGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.19
22 5 0.24
23 12 0.57
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (22 bp):
TTTATTTTATTTTTATTTTTTT
Found at i:20361169 original size:18 final size:18
Alignment explanation
Indices: 20361146--20361181 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
20361136 TATTTTTCAT
*
20361146 TTGCTTCAATTTCTATGC
1 TTGCTTCAATTTCCATGC
*
20361164 TTGCTTTAATTTCCATGC
1 TTGCTTCAATTTCCATGC
20361182 CTTACAATAA
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:0.17, C:0.22, G:0.11, T:0.50
Consensus pattern (18 bp):
TTGCTTCAATTTCCATGC
Found at i:20362242 original size:43 final size:42
Alignment explanation
Indices: 20362192--20362296 Score: 113
Period size: 43 Copynumber: 2.5 Consensus size: 42
20362182 GTGTTTGTAA
** *
20362192 AAAAGCGTCGCTAAAGGTCAT-TCTTTATAGTGGCGTTTGTGGT
1 AAAAGCGTCGCTAAAGGTCATATC-TT-TAGCAGCGTTTGTGGG
* * *
20362235 AGAAGCGTCGCAAAAAGTCATGATCTTTAGCAGCGTTTGTGGG
1 AAAAGCGTCGCTAAAGGTCAT-ATCTTTAGCAGCGTTTGTGGG
*
20362278 AAAAGCGCCGCTAAAGGTC
1 AAAAGCGTCGCTAAAGGTC
20362297 CTGGCTTTTA
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
43 46 0.92
44 2 0.04
45 2 0.04
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.27
Consensus pattern (42 bp):
AAAAGCGTCGCTAAAGGTCATATCTTTAGCAGCGTTTGTGGG
Found at i:20364342 original size:3 final size:3
Alignment explanation
Indices: 20364334--20364393 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
20364324 CTTTATTACT
20364334 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
20364382 ATC ATC ATC ATC
1 ATC ATC ATC ATC
20364394 GCAACTATTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:20366083 original size:23 final size:23
Alignment explanation
Indices: 20366069--20366112 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
20366059 CACCGATATG
20366069 CCAAAATGAATTGCACCGTAGGT
1 CCAAAATGAATTGCACCGTAGGT
* *
20366092 CCAAAATGAATTACATCGTAG
1 CCAAAATGAATTGCACCGTAG
20366113 TGCTAGAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (23 bp):
CCAAAATGAATTGCACCGTAGGT
Found at i:20366981 original size:30 final size:30
Alignment explanation
Indices: 20366946--20367080 Score: 135
Period size: 30 Copynumber: 4.5 Consensus size: 30
20366936 TTCAAACCAA
* * * *
20366946 ATCATATCATAACAAAACATATTATAATGT
1 ATCATATCATATCATAACGTATTATAACGT
* ** * *
20366976 ATCATATCATATCGTAACGTAACATAGCAT
1 ATCATATCATATCATAACGTATTATAACGT
20367006 ATCATATCATATCATAACGTATTATAACGT
1 ATCATATCATATCATAACGTATTATAACGT
** * ** *
20367036 ATCATATCATATCATGTCATATCGTAACAT
1 ATCATATCATATCATAACGTATTATAACGT
20367066 ATCATATCATATCAT
1 ATCATATCATATCAT
20367081 GTCCTACCCC
Statistics
Matches: 85, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 85 1.00
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (30 bp):
ATCATATCATATCATAACGTATTATAACGT
Found at i:20366983 original size:5 final size:5
Alignment explanation
Indices: 20366975--20367080 Score: 95
Period size: 5 Copynumber: 21.2 Consensus size: 5
20366965 TATTATAATG
* * * * * * *
20366975 TATCA TATCA TATCG TAACG TAACA TAGCA TATCA TATCA TATCA TAACG
1 TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA
* * * * * *
20367025 TATTA TAACG TATCA TATCA TATCA TGTCA TATCG TAACA TATCA TATCA
1 TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA
20367075 TATCA T
1 TATCA T
20367081 GTCCTACCCC
Statistics
Matches: 80, Mismatches: 21, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
5 80 1.00
ACGTcount: A:0.39, C:0.19, G:0.07, T:0.36
Consensus pattern (5 bp):
TATCA
Found at i:20370463 original size:16 final size:16
Alignment explanation
Indices: 20370442--20370480 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
20370432 TTATTAATTC
*
20370442 TATTATTGCTACTTA-T
1 TATTATTGCCA-TTATT
20370458 TATTATTGCCATTATT
1 TATTATTGCCATTATT
20370474 TATTATT
1 TATTATT
20370481 TCTTATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 3 0.14
16 18 0.86
ACGTcount: A:0.26, C:0.10, G:0.05, T:0.59
Consensus pattern (16 bp):
TATTATTGCCATTATT
Found at i:20370585 original size:23 final size:23
Alignment explanation
Indices: 20370548--20370596 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
20370538 ATAATCATTA
* *
20370548 TTATTCTTTATTTGTTATTGTTG
1 TTATTCTTTATTTGTCATTATTG
20370571 TTATTCTATTA-TTGTCATTATTG
1 TTATTCT-TTATTTGTCATTATTG
20370594 TTA
1 TTA
20370597 ATATTGGAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.18, C:0.06, G:0.10, T:0.65
Consensus pattern (23 bp):
TTATTCTTTATTTGTCATTATTG
Found at i:20371639 original size:106 final size:106
Alignment explanation
Indices: 20371500--20371703 Score: 390
Period size: 106 Copynumber: 1.9 Consensus size: 106
20371490 AGGAAAATTT
20371500 TTTTAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTC
1 TTTTAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTC
20371565 GATTTCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAAC
66 GATTTCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAAC
*
20371606 TTTTAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGCTGGGTTTC
1 TTTTAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTC
*
20371671 GATTTCTCGTTCGACTAAATAGCCAAATATCCT
66 GATTTCTCGTTCGACCAAATAGCCAAATATCCT
20371704 CTTAAAGCTT
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
106 96 1.00
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (106 bp):
TTTTAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTC
GATTTCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAAC
Found at i:20377934 original size:12 final size:11
Alignment explanation
Indices: 20377907--20377979 Score: 50
Period size: 10 Copynumber: 6.8 Consensus size: 11
20377897 TATTAAATAC
20377907 AATTTAATAA-
1 AATTTAATAAT
20377917 AA--TAATATAT
1 AATTTAATA-AT
*
20377927 AATTTAATAAC
1 AATTTAATAAT
*
20377938 ATTCTTAAT-AT
1 AAT-TTAATAAT
20377949 AATTATTAATAAT
1 AA-T-TTAATAAT
20377962 -ATTTAATAAT
1 AATTTAATAAT
20377972 AA-TTAATA
1 AATTTAATA
20377980 TAAAATATTA
Statistics
Matches: 50, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
8 5 0.10
9 1 0.02
10 18 0.36
11 7 0.14
12 17 0.34
13 2 0.04
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (11 bp):
AATTTAATAAT
Found at i:20378309 original size:30 final size:32
Alignment explanation
Indices: 20378273--20378332 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
20378263 CATAGTCCTT
20378273 TGTTATTC-AAAAC-CATAGTCCTTAATTTTA
1 TGTTATTCAAAAACTCATAGTCCTTAATTTTA
* *
20378303 TGTTATTCAAAAACTCATAGTTCTTTATTT
1 TGTTATTCAAAAACTCATAGTCCTTAATTT
20378333 ATTCAAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 8 0.31
31 5 0.19
32 13 0.50
ACGTcount: A:0.32, C:0.15, G:0.07, T:0.47
Consensus pattern (32 bp):
TGTTATTCAAAAACTCATAGTCCTTAATTTTA
Found at i:20387134 original size:103 final size:103
Alignment explanation
Indices: 20386928--20387121 Score: 289
Period size: 103 Copynumber: 1.9 Consensus size: 103
20386918 TTGTTCTTTC
* * *
20386928 TGCTACTGCTTGCTTCTAAAAGCATACATCGGCAGGCATTGTTTTTTGAACTTTAAAGGCAACTT
1 TGCTACTGCTTGCTTCTAAAAGCATACATAGGCAGGCATTGGTTTTTGAACCTTAAAGGCAACTT
* *
20386993 GCTTTAACTGCTGCTTAGTTTGTATTAGTTACAATTGT
66 ACTTTAACTGCTGCTTAGCTTGTATTAGTTACAATTGT
* * * * *
20387031 TGCTCCTGCTTGCTTTTATAAGCATACATAGGTAGGCATTGGTTTTTGGACCTTAAAGGCAACTT
1 TGCTACTGCTTGCTTCTAAAAGCATACATAGGCAGGCATTGGTTTTTGAACCTTAAAGGCAACTT
*
20387096 ACTTTTACTGCTGCTTAGCTTGTATT
66 ACTTTAACTGCTGCTTAGCTTGTATT
20387122 GTTGCTGCTT
Statistics
Matches: 80, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
103 80 1.00
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.40
Consensus pattern (103 bp):
TGCTACTGCTTGCTTCTAAAAGCATACATAGGCAGGCATTGGTTTTTGAACCTTAAAGGCAACTT
ACTTTAACTGCTGCTTAGCTTGTATTAGTTACAATTGT
Found at i:20387240 original size:20 final size:20
Alignment explanation
Indices: 20387215--20387255 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
20387205 AAAATACATG
20387215 TATGTCAACATTTGAACTCA
1 TATGTCAACATTTGAACTCA
20387235 TATGTCAACATTTGAACTCA
1 TATGTCAACATTTGAACTCA
20387255 T
1 T
20387256 TTTAGAGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.37
Consensus pattern (20 bp):
TATGTCAACATTTGAACTCA
Found at i:20404803 original size:20 final size:21
Alignment explanation
Indices: 20404778--20404816 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
20404768 TATACGTTGA
20404778 TAATTTTA-ATAACTAAAATG
1 TAATTTTACATAACTAAAATG
*
20404798 TAATTTTACATAGCTAAAA
1 TAATTTTACATAACTAAAA
20404817 GACAAAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.38
Consensus pattern (21 bp):
TAATTTTACATAACTAAAATG
Found at i:20406388 original size:33 final size:34
Alignment explanation
Indices: 20406325--20406403 Score: 97
Period size: 33 Copynumber: 2.3 Consensus size: 34
20406315 TTTTCAAAAA
* * * *
20406325 TTAAAAATATTTATAAAATTTTCAAATTTTATATT
1 TTAAAAAT-TTTAAAAAAGTATCAAATTTTAAATT
20406360 TTAAAAATTTTAAAAAAGTAT-AAATTTTAAATT
1 TTAAAAATTTTAAAAAAGTATCAAATTTTAAATT
*
20406393 TTAAAATTTTT
1 TTAAAAATTTT
20406404 TCTAAAGTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 21 0.54
34 10 0.26
35 8 0.21
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (34 bp):
TTAAAAATTTTAAAAAAGTATCAAATTTTAAATT
Found at i:20410846 original size:27 final size:27
Alignment explanation
Indices: 20410781--20410859 Score: 70
Period size: 27 Copynumber: 2.9 Consensus size: 27
20410771 CATGCGTTTA
* * *
20410781 ACGTAGCAGTAAGAATAAAGTGTAATC
1 ACGTAGCAGTAAGCACAAAGTGCAATC
* * *
20410808 ACATA-AAGGTAAGCACATAGTGCAATC
1 ACGTAGCA-GTAAGCACAAAGTGCAATC
*
20410835 ACGTAGCAGTAAGCACCGAAGTGCA
1 ACGTAGCAGTAAGCA-CAAAGTGCA
20410860 TAAAATATGG
Statistics
Matches: 39, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
26 1 0.03
27 30 0.77
28 8 0.21
ACGTcount: A:0.42, C:0.18, G:0.23, T:0.18
Consensus pattern (27 bp):
ACGTAGCAGTAAGCACAAAGTGCAATC
Found at i:20412626 original size:23 final size:23
Alignment explanation
Indices: 20412589--20412637 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
20412579 ATAATCATTA
*
20412589 TTATTCTTTATTTGTTATTGTTG
1 TTATTCTTTATTTGTCATTGTTG
20412612 TTATTCTATTA-TTGTCATTGTTG
1 TTATTCT-TTATTTGTCATTGTTG
20412635 TTA
1 TTA
20412638 ATATTGGAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 21 0.88
24 3 0.12
ACGTcount: A:0.16, C:0.06, G:0.12, T:0.65
Consensus pattern (23 bp):
TTATTCTTTATTTGTCATTGTTG
Found at i:20413676 original size:106 final size:106
Alignment explanation
Indices: 20413540--20413740 Score: 375
Period size: 106 Copynumber: 1.9 Consensus size: 106
20413530 AAGATTTTTC
20413540 TAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
1 TAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
*
20413605 TTCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAACTTT
66 TTCTCGTTCGACCAAACAGCCAAATATCCTTTTTAAACTTT
*
20413646 TAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGCTGGGTTTCGAT
1 TAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
*
20413711 TTCTCGTTCGACTAAACAGCCAAATATCCT
66 TTCTCGTTCGACCAAACAGCCAAATATCCT
20413741 CTTAAAGCTT
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
106 92 1.00
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.30
Consensus pattern (106 bp):
TAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
TTCTCGTTCGACCAAACAGCCAAATATCCTTTTTAAACTTT
Found at i:20425160 original size:43 final size:43
Alignment explanation
Indices: 20425087--20425740 Score: 610
Period size: 43 Copynumber: 15.1 Consensus size: 43
20425077 GTCATAAAGT
20425087 AGATCTTGTCTTCC-ATATTGGT-GCGAAGTAGATCGAAGAAGC
1 AGATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAGAAGC
* * * *
20425129 AGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGATATC
1 AGATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAGA-AGC
* * *
20425173 AGATCCTATCTTCCTATATTGGTAGGAAGTAGATCGAAGTAGC
1 AGATCTTGTCTTCCTATATTGGTAGGAAGTAGATCGAAGAAGC
* * *
20425216 AGATC-TATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGC
1 AGATCTTGTCTTCCTATATTGGTAGGAAGTAGATCGAAGAAGC
* * *
20425258 AGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGC
1 AGATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAG-AAGC
* * * *
20425303 AGATCTTGTCTTCATGT-TTGG-CGTGAAGTAGATCGAAGTAGC
1 AGATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAGAAGC
* * * *
20425345 AGATCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGC
1 AGATCTTGTCTTCCTATATTGGTAGGAAGTAGATCGAAGAAGC
* * *
20425388 AGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGC
1 AGATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAG-AAGC
* * * *
20425433 AGATCTTGTCTTCATGT-TTGG-CGTGAAGTAGATCGAAGTAGC
1 AGATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAGAAGC
* * * *
20425475 AGATCCTATCTTCCTATATTGGTAGGAA-TGGATCGAAGATGC
1 AGATCTTGTCTTCCTATATTGGTAGGAAGTAGATCGAAGAAGC
* *
20425517 AGATCTTGTCTTCCCATATTGGTGGTGAAGTAGATCGAAGAAAGC
1 AGATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAG-AAGC
* * * *
20425562 AGATCTTGTCTTCATGTATTGG-CGTGAA-TAGATCGAAGATATC
1 AGATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAGA-AGC
* * * * * *
20425605 AGATCCTATCTTCCTATATTGGTAGGAAGTGGACCGACGATGC
1 AGATCTTGTCTTCCTATATTGGTAGGAAGTAGATCGAAGAAGC
* * * * *
20425648 AGATTTTGTCTTCCCATACTGGTAGGAAGTGGATCGAAGATGC
1 AGATCTTGTCTTCCTATATTGGTAGGAAGTAGATCGAAGAAGC
** * * *
20425691 AGATCTTGTCTTCCCGTACTGGTGGTGAAGAAGATCGAAGAAAGC
1 AGATCTTGTCTTCCTATATTGGTAG-GAAGTAGATCGAAG-AAGC
20425736 AGATC
1 AGATC
20425741 GACGATGGCG
Statistics
Matches: 500, Mismatches: 91, Indels: 39
0.79 0.14 0.06
Matches are distributed among these distances:
42 117 0.23
43 215 0.43
44 103 0.21
45 65 0.13
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (43 bp):
AGATCTTGTCTTCCTATATTGGTAGGAAGTAGATCGAAGAAGC
Found at i:20425204 original size:87 final size:89
Alignment explanation
Indices: 20425095--20425740 Score: 596
Period size: 87 Copynumber: 7.5 Consensus size: 89
20425085 GTAGATCTTG
*
20425095 TCTTCC-ATATTGGT-GCGAAGTAGATCGAAGAAGCAGATCTTGTCTTCATGTATTGG-CGTGAA
1 TCTTCCTATATTGGTAGCGAAGTAGATCGAAGAAGCAGATCTTGTCTTCATATATTGGTCGTGAA
*
20425157 GTAGATCGAAGATATCAGATCCTA
66 GTAGATCGAAGATAGCAGATCCTA
* * * *
20425181 TCTTCCTATATTGGTAG-GAAGTAGATCGAAGTAGCAGATC-TATCTTCCTATATTGGTAG-GAA
1 TCTTCCTATATTGGTAGCGAAGTAGATCGAAGAAGCAGATCTTGTCTTCATATATTGGTCGTGAA
* * *
20425243 GTGGATCGAAGAT-GCAGATCTTG
66 GTAGATCGAAGATAGCAGATCCTA
* * * *
20425266 TCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGT-TTGG-CGTGA
1 TCTTCCTATATTGGTAGCGAAGTAGATCGAAG-AAGCAGATCTTGTCTTCATATATTGGTCGTGA
20425329 AGTAGATCGAAG-TAGCAGATCCTA
65 AGTAGATCGAAGATAGCAGATCCTA
* * ** * *
20425353 TCTTCCTATATTGGTAG-GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAA
1 TCTTCCTATATTGGTAGCGAAGTAGATCGAAGAAGCAGATCTTGTCTTCATATATTGGTCGTGAA
* * * *
20425417 GTAGATCGCAGAAAGCAGATCTTG
66 GTAGATCGAAGATAGCAGATCCTA
* * * * * * * * *
20425441 TCTTCATGT-TTGG-CGTGAAGTAGATCGAAGTAGCAGATCCTATCTTCCTATATTGGTAG-GAA
1 TCTTCCTATATTGGTAGCGAAGTAGATCGAAGAAGCAGATCTTGTCTTCATATATTGGTCGTGAA
* * *
20425503 -TGGATCGAAGAT-GCAGATCTTG
66 GTAGATCGAAGATAGCAGATCCTA
* * * *
20425525 TCTTCCCATATTGGTGGTGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG-CGTGA
1 TCTTCCTATATTGGTAGCGAAGTAGATCGAAG-AAGCAGATCTTGTCTTCATATATTGGTCGTGA
*
20425589 A-TAGATCGAAGATATCAGATCCTA
65 AGTAGATCGAAGATAGCAGATCCTA
* * * * * ** * *
20425613 TCTTCCTATATTGGTAG-GAAGTGGACCGACGATGCAGATTTTGTCTTCCCATACTGGTAG-GAA
1 TCTTCCTATATTGGTAGCGAAGTAGATCGAAGAAGCAGATCTTGTCTTCATATATTGGTCGTGAA
* * *
20425676 GTGGATCGAAGAT-GCAGATCTTG
66 GTAGATCGAAGATAGCAGATCCTA
** * * * *
20425699 TCTTCCCGTACTGGTGGTGAAGAAGATCGAAGAAAGCAGATC
1 TCTTCCTATATTGGTAGCGAAGTAGATCGAAG-AAGCAGATC
20425741 GACGATGGCG
Statistics
Matches: 452, Mismatches: 87, Indels: 40
0.78 0.15 0.07
Matches are distributed among these distances:
84 16 0.04
85 52 0.12
86 129 0.29
87 201 0.44
88 54 0.12
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (89 bp):
TCTTCCTATATTGGTAGCGAAGTAGATCGAAGAAGCAGATCTTGTCTTCATATATTGGTCGTGAA
GTAGATCGAAGATAGCAGATCCTA
Found at i:20425380 original size:130 final size:131
Alignment explanation
Indices: 20425095--20425740 Score: 891
Period size: 130 Copynumber: 5.0 Consensus size: 131
20425085 GTAGATCTTG
* * *** * *
20425095 TCTTCC-ATATTGGT-GCGAAGTAGATCGAAGAAGCAGATCTTGTCTTCATGTATTGG-CGTGAA
1 TCTTCCTATATTGGTAG-GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAA
* * * * * * *
20425157 GTAGATCGAAGATATCAGATCCTATCTTCCTATATTGGTAG-GAAGTAGATCGAAGTAGCAGAT-
65 GTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGTAGCAGATC
20425220 CTA
129 CTA
20425223 TCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAG
1 TCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAG
*
20425288 TAGATCGCAGAAAGCAGATCTTGTCTTCATGT-TTGGCGTGAAGTAGATCGAAGTAGCAGATCCT
66 TAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGTAGCAGATCCT
20425352 A
131 A
20425353 TCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAG
1 TCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAG
*
20425418 TAGATCGCAGAAAGCAGATCTTGTCTTCATGT-TTGGCGTGAAGTAGATCGAAGTAGCAGATCCT
66 TAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGTAGCAGATCCT
20425482 A
131 A
*
20425483 TCTTCCTATATTGGTAGGAA-TGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGTGAAG
1 TCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAG
*
20425547 TAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAA-TAGATCGAAGATATCAGATCC
66 TAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAG-TAGCAGATCC
20425611 TA
130 TA
* * * * *
20425613 TCTTCCTATATTGGTAGGAAGTGGACCGACGATGCAGATTTTGTCTTCCCATACTGGTAG-GAAG
1 TCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAG
* * ** * * * *
20425677 TGGATCGAAG-ATGCAGATCTTGTCTTCCCGTACTGGTGGTGAAGAAGATCGAAGAAAGCAGATC
66 TAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAG-TAGCAGATC
20425741 GACGATGGCG
Statistics
Matches: 476, Mismatches: 32, Indels: 17
0.91 0.06 0.03
Matches are distributed among these distances:
128 7 0.01
129 175 0.37
130 243 0.51
131 51 0.11
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (131 bp):
TCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAG
TAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGTAGCAGATCCT
A
Found at i:20425561 original size:259 final size:260
Alignment explanation
Indices: 20425095--20425703 Score: 885
Period size: 259 Copynumber: 2.4 Consensus size: 260
20425085 GTAGATCTTG
* * *** *
20425095 TCTTCC-ATATTGGT-GCGAAGTAGATCGAAGAAGCAGATCTTGTCTTCATGTATTGG-CGTGAA
1 TCTTCCTATATTGGTAG-GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTAG-GAA
* * * * *
20425157 GTAGATCGAAGATATCAGATCCTATCTTCCTATATTGGTAGGAAGTAGATCGAAGTAGCAGATCT
64 GTAGATCGAAGAAAGCAGATCTTGTCTTCATATATTGGTAGGAAGTAGATCGAAGTAGCAGATCT
20425222 ATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAA
129 ATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAA
*
20425287 GTAGATCGCAGAAAGCAGATCTTGTCTTCATGT-TTGGCGTGAAGTAGATCGAAG-TAGCAGATC
194 GTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAA-TAGATCGAAGATAGCAGATC
20425350 CTA
258 CTA
*
20425353 TCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAG
1 TCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTAG-GAAG
* * *
20425418 TAGATCGCAGAAAGCAGATCTTGTCTTCATGT-TTGG-CGTGAAGTAGATCGAAGTAGCAGATCC
65 TAGATCGAAGAAAGCAGATCTTGTCTTCATATATTGGTAG-GAAGTAGATCGAAGTAGCAGAT-C
*
20425481 TATCTTCCTATATTGGTAGGAA-TGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGTGA
128 TATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGA
*
20425545 AGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAATAGATCGAAGATATCAGATC
193 AGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAATAGATCGAAGATAGCAGATC
20425610 CTA
258 CTA
* * * *
20425613 TCTTCCTATATTGGTAGGAAGTGGACCGACGATGCAGATTTTGTCTTCCCATACTGGTAGGAAGT
1 TCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTAGGAAGT
* *
20425678 GGATCGAAG-ATGCAGATCTTGTCTTC
66 AGATCGAAGAAAGCAGATCTTGTCTTC
20425704 CCGTACTGGT
Statistics
Matches: 318, Mismatches: 26, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
258 23 0.07
259 165 0.52
260 130 0.41
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.31
Consensus pattern (260 bp):
TCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTAGGAAGT
AGATCGAAGAAAGCAGATCTTGTCTTCATATATTGGTAGGAAGTAGATCGAAGTAGCAGATCTAT
CTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGT
AGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAATAGATCGAAGATAGCAGATCCTA
Found at i:20427364 original size:23 final size:23
Alignment explanation
Indices: 20427327--20427375 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
20427317 ATAATCATTA
* *
20427327 TTATTCTTTATTTGTTATTGTTG
1 TTATTCTTTATTTGTCATTATTG
20427350 TTATTCTATTA-TTGTCATTATTG
1 TTATTCT-TTATTTGTCATTATTG
20427373 TTA
1 TTA
20427376 ATATTGGAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.18, C:0.06, G:0.10, T:0.65
Consensus pattern (23 bp):
TTATTCTTTATTTGTCATTATTG
Found at i:20428414 original size:106 final size:106
Alignment explanation
Indices: 20428275--20428478 Score: 390
Period size: 106 Copynumber: 1.9 Consensus size: 106
20428265 AAGGAAAATT
20428275 TTTTAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTC
1 TTTTAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTC
20428340 GATTTCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAAC
66 GATTTCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAAC
*
20428381 TTTTAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGCTGGGTTTC
1 TTTTAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTC
*
20428446 GATTTCTCGTTCGACTAAATAGCCAAATATCCT
66 GATTTCTCGTTCGACCAAATAGCCAAATATCCT
20428479 CTTAAAGCTT
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
106 96 1.00
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (106 bp):
TTTTAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTC
GATTTCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAAC
Found at i:20450168 original size:159 final size:159
Alignment explanation
Indices: 20449923--20450242 Score: 532
Period size: 159 Copynumber: 2.0 Consensus size: 159
20449913 CGGACTAAAA
* * **
20449923 TCGATCTTGACTTTCTATCGAATAGCCTTATCAGTTATTCTCAAATTACGAACTGCTTTGAGTGT
1 TCGATCTTGACTTTCTATCGAACAACCTTATCAGTTATTCTCAAACCACGAACTGCTTTGAGTGT
* * * *
20449988 GTGCTCAAAATTTATCAAACCAATTGTATAGAATGAAAAACTTTATTTACTTTTAGTAGGAAGGC
66 GTACTCAAAATTTATCAAACCAATTGTATAGAATGAAAAACTTTATTAACTTTCAGAAGGAAGGC
*
20450053 TAATTCTCTCTATAAACGGAAACTATGCG
131 TAATTCTCTCTATAAACGAAAACTATGCG
*
20450082 TCGATCTTGACTTTCTATCGAACAACCTTATCAGTTATTCTCAAACCACGAATTGCTTTGAGTGT
1 TCGATCTTGACTTTCTATCGAACAACCTTATCAGTTATTCTCAAACCACGAACTGCTTTGAGTGT
*
20450147 GTACTCAAAATTTATCAAACCAATTGTATAGAATGAAAAACTTTATTAACTTTCAGAAGGAAGGT
66 GTACTCAAAATTTATCAAACCAATTGTATAGAATGAAAAACTTTATTAACTTTCAGAAGGAAGGC
*
20450212 TAATTCTCTCTATGAACGAAAACTATGCG
131 TAATTCTCTCTATAAACGAAAACTATGCG
20450241 TC
1 TC
20450243 TTTGAAATTA
Statistics
Matches: 149, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
159 149 1.00
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (159 bp):
TCGATCTTGACTTTCTATCGAACAACCTTATCAGTTATTCTCAAACCACGAACTGCTTTGAGTGT
GTACTCAAAATTTATCAAACCAATTGTATAGAATGAAAAACTTTATTAACTTTCAGAAGGAAGGC
TAATTCTCTCTATAAACGAAAACTATGCG
Found at i:20450625 original size:16 final size:17
Alignment explanation
Indices: 20450596--20450631 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
20450586 TTAATCAATT
20450596 AATTAAATTAATTTCTC
1 AATTAAATTAATTTCTC
*
20450613 AATTAAA-TAATTTTTC
1 AATTAAATTAATTTCTC
20450629 AAT
1 AAT
20450632 CCAATTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTAAATTAATTTCTC
Found at i:20450776 original size:14 final size:15
Alignment explanation
Indices: 20450757--20450790 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
20450747 CTTTGAGCTT
*
20450757 TAATTATTTAATT-A
1 TAATTAATTAATTAA
20450771 TAATTAATTAATTAA
1 TAATTAATTAATTAA
20450786 TAATT
1 TAATT
20450791 TGAAGAACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TAATTAATTAATTAA
Found at i:20452781 original size:43 final size:43
Alignment explanation
Indices: 20452672--20452786 Score: 128
Period size: 43 Copynumber: 2.7 Consensus size: 43
20452662 AGCTCGTACA
* * * *
20452672 ATGCCAACGTCTCAGACATGGTCTTACATGTAATCACATATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACAAATCG
20452715 ATGCC-ACTGTCCCA-A-ATTGGGTCTTACACGTAAACACAAATCG
1 ATGCCAAC-GTCCCAGACA-T-GGTCTTACACGTAAACACAAATCG
* *
20452758 ATGCCAACATCCCAGACGTGGTCTTACAC
1 ATGCCAACGTCCCAGACATGGTCTTACAC
20452787 AAAAAACACA
Statistics
Matches: 60, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
41 1 0.02
42 4 0.07
43 51 0.85
44 4 0.07
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACAAATCG
Found at i:20465360 original size:43 final size:43
Alignment explanation
Indices: 20465251--20465370 Score: 127
Period size: 43 Copynumber: 2.8 Consensus size: 43
20465241 AGAAAAAGAC
* * * * *
20465251 CAAAAAAGGAAGCTATATGGAAGAAACCACA-ATTGCATCCAGA
1 CAAAAAAGGAAGCAACATGGAAGCAACCACATCTTG-ATCCAAA
* **
20465294 CAAAAAAAAGAAGCAACGGGGAAGCAACCACATCTATG-TCCAAA
1 C-AAAAAAGGAAGCAACATGGAAGCAACCACATCT-TGATCCAAA
20465338 CAAAAAAGGAAGCAACATGGAAGCAACCACATC
1 CAAAAAAGGAAGCAACATGGAAGCAACCACATC
20465371 AGGACAAAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 6
0.79 0.14 0.08
Matches are distributed among these distances:
43 30 0.48
44 30 0.48
45 1 0.02
46 2 0.03
ACGTcount: A:0.50, C:0.22, G:0.18, T:0.10
Consensus pattern (43 bp):
CAAAAAAGGAAGCAACATGGAAGCAACCACATCTTGATCCAAA
Found at i:20465724 original size:83 final size:83
Alignment explanation
Indices: 20465585--20465745 Score: 279
Period size: 83 Copynumber: 1.9 Consensus size: 83
20465575 TAAAGGAACG
20465585 GTTTTACAAAATAGGGAAGGATAGTGGATGAAAAGTAACTTGGAGAAAAAATTCAAACCCACTTG
1 GTTTTACAAAATAGGGAAGGATAGTGGATGAAAAGTAACTTGGAGAAAAAATTCAAACCCACTTG
20465650 AATGCCCCTCTTATACTA
66 AATGCCCCTCTTATACTA
* * *
20465668 GTTTTACAAAATAGAGG-AGGATGGTGGATGAGAAGTAACTTGGAGAAAAATTTCAAACCCACTT
1 GTTTTACAAAATAG-GGAAGGATAGTGGATGAAAAGTAACTTGGAGAAAAAATTCAAACCCACTT
20465732 GAATGCCCCTCTTA
65 GAATGCCCCTCTTA
20465746 GGCTTCCTCC
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
83 72 0.97
84 2 0.03
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (83 bp):
GTTTTACAAAATAGGGAAGGATAGTGGATGAAAAGTAACTTGGAGAAAAAATTCAAACCCACTTG
AATGCCCCTCTTATACTA
Found at i:20469975 original size:25 final size:25
Alignment explanation
Indices: 20469930--20469981 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
20469920 AAAAAAATTA
20469930 TTTTTTTATCTTTTCCTTCTTTCTTT
1 TTTTTTTATCTTTTCCTTC-TTCTTT
*
20469956 TTTTTTTCCTCTTTT-C-TCTTCTTT
1 TTTTTTT-ATCTTTTCCTTCTTCTTT
20469980 TT
1 TT
20469982 GCCATCCCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 8 0.33
25 2 0.08
26 8 0.33
27 6 0.25
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (25 bp):
TTTTTTTATCTTTTCCTTCTTCTTT
Found at i:20469980 original size:19 final size:19
Alignment explanation
Indices: 20469940--20469981 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
20469930 TTTTTTTATC
* *
20469940 TTTTCCTTCTTTCTTTTTT
1 TTTTCCTTCTTTCTCTTCT
20469959 TTTTCC-TCTTTTCTCTTCT
1 TTTTCCTTC-TTTCTCTTCT
20469978 TTTT
1 TTTT
20469982 GCCATCCCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTCCTTCTTTCTCTTCT
Found at i:20475889 original size:6 final size:6
Alignment explanation
Indices: 20475845--20475893 Score: 53
Period size: 6 Copynumber: 7.8 Consensus size: 6
20475835 CCAAACACAC
* * *
20475845 CAGTAAA CAGTAA TCAGTAA CGGTAG CAGTAA CAATAA CAGTAA CAGTA
1 CAGT-AA CAGTAA -CAGTAA CAGTAA CAGTAA CAGTAA CAGTAA CAGTA
20475894 TTCAACACAC
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
6 25 0.71
7 10 0.29
ACGTcount: A:0.47, C:0.16, G:0.18, T:0.18
Consensus pattern (6 bp):
CAGTAA
Found at i:20475929 original size:45 final size:45
Alignment explanation
Indices: 20475873--20476028 Score: 195
Period size: 45 Copynumber: 3.3 Consensus size: 45
20475863 AACGGTAGCA
* * **
20475873 GTAACAATAACAGTAACAGTATTCAACACACAAAGTGTTGAATCT
1 GTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCT
* *
20475918 GTAACAGTAACAGTAATAGTATTCGACACACAAAGTGCCGAGTCGGT
1 GTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATC--T
*
20475965 AACAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCA
1 ----GTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCT
20476014 GTAACAGTAACAGTA
1 GTAACAGTAACAGTA
20476029 GTCGGCACAT
Statistics
Matches: 96, Mismatches: 9, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
45 53 0.55
47 1 0.01
51 42 0.44
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (45 bp):
GTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCT
Found at i:20475973 original size:51 final size:51
Alignment explanation
Indices: 20475865--20476028 Score: 214
Period size: 51 Copynumber: 3.3 Consensus size: 51
20475855 TAATCAGTAA
* * * **
20475865 CGGTAGCAGTAACAATAACAGTAACAGTATTCAACACACAAAGTGTTGAAT
1 CGGTAACAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
* *
20475916 C--T----GTAACAGTAACAGTAATAGTATTCGACACACAAAGTGCCGAGT
1 CGGTAACAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
20475961 CGGTAACAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
1 CGGTAACAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
*
20476012 CAGTAACAGTAACAGTA
1 CGGTAACAGTAACAGTA
20476029 GTCGGCACAT
Statistics
Matches: 98, Mismatches: 9, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
45 38 0.39
47 1 0.01
49 1 0.01
51 58 0.59
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (51 bp):
CGGTAACAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
Found at i:20475974 original size:6 final size:6
Alignment explanation
Indices: 20475963--20475989 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
20475953 TGCCGAGTCG
20475963 GTAACA GTAACA GTAACA GTAACA GTA
1 GTAACA GTAACA GTAACA GTAACA GTA
20475990 TTCGACACAC
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:0.48, C:0.15, G:0.19, T:0.19
Consensus pattern (6 bp):
GTAACA
Found at i:20476052 original size:38 final size:39
Alignment explanation
Indices: 20475973--20476055 Score: 116
Period size: 39 Copynumber: 2.2 Consensus size: 39
20475963 GTAACAGTAA
*
20475973 CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
1 CAGTAACAGTAACAGTAGTCGACACACAAAGTGCCGAAT
* *
20476012 CAGTAACAGTAACAGTAGTCGGCACA-TAAGTGCCTG-AT
1 CAGTAACAGTAACAGTAGTCGACACACAAAGTGCC-GAAT
20476050 CAGTAA
1 CAGTAA
20476056 GCCGACAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
38 15 0.38
39 25 0.62
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (39 bp):
CAGTAACAGTAACAGTAGTCGACACACAAAGTGCCGAAT
Found at i:20476457 original size:26 final size:25
Alignment explanation
Indices: 20476428--20476477 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
20476418 CAATTCAATG
20476428 ATTCAATTAAA-ACCATTTCAATTTCT
1 ATTCAA-TAAACA-CATTTCAATTTCT
*
20476454 ATTCAATAATCACATTTCAATTTC
1 ATTCAATAAACACATTTCAATTTC
20476478 ACTTTCTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.38, C:0.20, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTCAATAAACACATTTCAATTTCT
Found at i:20477269 original size:13 final size:13
Alignment explanation
Indices: 20477251--20477291 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
20477241 CTCAATTTTC
20477251 TCTTTTCTTTCTT
1 TCTTTTCTTTCTT
20477264 TCTTTTCTTTCTT
1 TCTTTTCTTTCTT
* *
20477277 TC-CTTCTTTCCT
1 TCTTTTCTTTCTT
20477289 TCT
1 TCT
20477292 CTGTTTCGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (13 bp):
TCTTTTCTTTCTT
Found at i:20477499 original size:5 final size:5
Alignment explanation
Indices: 20477489--20477561 Score: 76
Period size: 5 Copynumber: 13.8 Consensus size: 5
20477479 TTTGTTTATT
*
20477489 TATAA TATAA TA-ATA TAATAA TATAA TATAA TATAA TATAA TATAA TTTACAA
1 TATAA TATAA TATA-A T-ATAA TATAA TATAA TATAA TATAA TATAA --TATAA
*
20477542 TATAA TAAAA TAATAA TATA
1 TATAA TATAA T-ATAA TATA
20477562 CTTCGAAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
4 1 0.02
5 45 0.78
6 7 0.12
7 5 0.09
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (5 bp):
TATAA
Found at i:20477503 original size:8 final size:8
Alignment explanation
Indices: 20477490--20477561 Score: 69
Period size: 8 Copynumber: 9.0 Consensus size: 8
20477480 TTGTTTATTT
20477490 ATAATATA
1 ATAATATA
20477498 ATAATATA
1 ATAATATA
20477506 ATAATATA
1 ATAATATA
20477514 AT-ATA-A
1 ATAATATA
20477520 TATAATATA
1 -ATAATATA
*
20477529 AT-ATAATTT
1 ATAAT-A-TA
*
20477538 ACAATATA
1 ATAATATA
*
20477546 ATAAAATA
1 ATAATATA
20477554 ATAATATA
1 ATAATATA
20477562 CTTCGAAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
6 1 0.02
7 7 0.13
8 38 0.73
9 4 0.08
10 2 0.04
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (8 bp):
ATAATATA
Found at i:20478556 original size:18 final size:18
Alignment explanation
Indices: 20478535--20478572 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
20478525 TAAAGTTAGT
*
20478535 AATTATGGTTTTGTTAAC
1 AATTATGGTTTTATTAAC
20478553 AATTATGGTTTTATTAAC
1 AATTATGGTTTTATTAAC
20478571 AA
1 AA
20478573 ATTGTGAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.05, G:0.13, T:0.47
Consensus pattern (18 bp):
AATTATGGTTTTATTAAC
Found at i:20479457 original size:19 final size:20
Alignment explanation
Indices: 20479433--20479471 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
20479423 TCCCTTTCCC
20479433 TCCTTT-TCTT-TCTTGCTTT
1 TCCTTTCTCTTAT-TTGCTTT
20479452 TCCTTTCTCTTATTTGCTTT
1 TCCTTTCTCTTATTTGCTTT
20479472 GAAACTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 11 0.61
21 1 0.06
ACGTcount: A:0.03, C:0.26, G:0.05, T:0.67
Consensus pattern (20 bp):
TCCTTTCTCTTATTTGCTTT
Found at i:20482166 original size:165 final size:160
Alignment explanation
Indices: 20481893--20482218 Score: 415
Period size: 165 Copynumber: 2.0 Consensus size: 160
20481883 TCAAGTCAAG
** * * *
20481893 TCAAGCATATGATTGTCAAATCTCAAAATCTAAAATATCTTCATTGCAAAACTCGCATAATTCTT
1 TCAAGCATACAATTGTCAAATCGCAAAATCTAAAATATCTTCATTGCAAAACTCACATAATTCAT
* * *
20481958 ATCTATAATTTTTATAGTCTTAGGAAATAAAGAGATTTGGCCTTTCAAATGAGTAGTGCAGAAAA
66 ATCTATAATTTTTATAGTCATAGGAAATAAAAAGAATTGGCCTTTCAAATGAGTAGTGCAGAAAA
*
20482023 TTTACAGATTCAGATTTTG-AAGCGTTGAAA
131 TTTACACATTCA-ATTTTGTAAGCGTTGAAA
* * * *
20482053 TCAAGCATACAATTTTCAAATCGCAAAGTCTAAGAATATTTTTCATTGCAAAAACTCACCTAATT
1 TCAAGCATACAATTGTCAAATCGCAAAATCTAA-AATA-TCTTCATTGC-AAAACTCACATAATT
* *
20482118 CATA-CTTATAA-TTTTAGTGAAGTCATATGAAATAAAAAGAATTGGCCTTTCAAATGATTAGTG
63 CATATC-TATAATTTTTA-T--AGTCATAGGAAATAAAAAGAATTGGCCTTTCAAATGAGTAGTG
*
20482181 CAGAAAATTTACACATTCAATTTTGTAAGTGTTGAAA
124 CAGAAAATTTACACATTCAATTTTGTAAGCGTTGAAA
20482218 T
1 T
20482219 TAAATGAATG
Statistics
Matches: 142, Mismatches: 16, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
160 28 0.20
161 4 0.03
162 15 0.11
163 22 0.15
164 6 0.04
165 67 0.47
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (160 bp):
TCAAGCATACAATTGTCAAATCGCAAAATCTAAAATATCTTCATTGCAAAACTCACATAATTCAT
ATCTATAATTTTTATAGTCATAGGAAATAAAAAGAATTGGCCTTTCAAATGAGTAGTGCAGAAAA
TTTACACATTCAATTTTGTAAGCGTTGAAA
Found at i:20484190 original size:2 final size:2
Alignment explanation
Indices: 20484185--20484211 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20484175 TATATATATT
20484185 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
20484212 AGAGAGAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:20493309 original size:4 final size:4
Alignment explanation
Indices: 20493300--20493324 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
20493290 TGCCCAACTC
20493300 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
20493325 CGTATAATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:20497634 original size:11 final size:10
Alignment explanation
Indices: 20497607--20497679 Score: 74
Period size: 11 Copynumber: 6.7 Consensus size: 10
20497597 ACTTAAATCC
20497607 TTTCTCTCAA
1 TTTCTCTCAA
*
20497617 ATTCTCTCATA
1 TTTCTCTCA-A
20497628 TTTCTCTCCAA
1 TTTCTCT-CAA
20497639 TATTCTCTCATA
1 T-TTCTCTCA-A
20497651 TTTCTCTCAAA
1 TTTCTCTC-AA
*
20497662 TTCCTCTCAAA
1 TTTCTCTC-AA
20497673 TTTCTCT
1 TTTCTCT
20497680 TAAAACTCTC
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
10 8 0.15
11 35 0.65
12 11 0.20
ACGTcount: A:0.22, C:0.30, G:0.00, T:0.48
Consensus pattern (10 bp):
TTTCTCTCAA
Found at i:20497643 original size:23 final size:21
Alignment explanation
Indices: 20497607--20497679 Score: 110
Period size: 22 Copynumber: 3.3 Consensus size: 21
20497597 ACTTAAATCC
20497607 TTTCTCTCAAATTCTCTCATA
1 TTTCTCTCAAATTCTCTCATA
20497628 TTTCTCTCCAATATTCTCTCATA
1 TTTCTCT-CAA-ATTCTCTCATA
*
20497651 TTTCTCTCAAATTCCTCTCAAA
1 TTTCTCTCAAATT-CTCTCATA
20497673 TTTCTCT
1 TTTCTCT
20497680 TAAAACTCTC
Statistics
Matches: 48, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
21 10 0.21
22 20 0.42
23 18 0.38
ACGTcount: A:0.22, C:0.30, G:0.00, T:0.48
Consensus pattern (21 bp):
TTTCTCTCAAATTCTCTCATA
Found at i:20498830 original size:7 final size:7
Alignment explanation
Indices: 20498818--20498842 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
20498808 AGCCGATTCA
20498818 TATTTAG
1 TATTTAG
20498825 TATTTAG
1 TATTTAG
20498832 TATTTAG
1 TATTTAG
20498839 TATT
1 TATT
20498843 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:20499394 original size:30 final size:30
Alignment explanation
Indices: 20499340--20499396 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
20499330 CGACGACGCA
** *
20499340 GGCCCATCAACAGTGCCTACACAATCATTC
1 GGCCCATCAACAGCACCCACACAATCATTC
*
20499370 GGCCCATCAACAGCACCCATACAATCA
1 GGCCCATCAACAGCACCCACACAATCA
20499397 CCAGGCTCAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.33, C:0.39, G:0.12, T:0.16
Consensus pattern (30 bp):
GGCCCATCAACAGCACCCACACAATCATTC
Found at i:20499512 original size:18 final size:18
Alignment explanation
Indices: 20499489--20499531 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
20499479 TGCCAGGTGC
* *
20499489 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
20499507 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
20499525 GTTTCCT
1 GTATCCT
20499532 TTTTCTAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:20499992 original size:34 final size:34
Alignment explanation
Indices: 20499951--20500023 Score: 137
Period size: 34 Copynumber: 2.1 Consensus size: 34
20499941 TTTTGAATAT
*
20499951 TTTTATATTATTTTATGTAATAAAATAGAAATTC
1 TTTTATATTATTTCATGTAATAAAATAGAAATTC
20499985 TTTTATATTATTTCATGTAATAAAATAGAAATTC
1 TTTTATATTATTTCATGTAATAAAATAGAAATTC
20500019 TTTTA
1 TTTTA
20500024 AATAAGGTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.51
Consensus pattern (34 bp):
TTTTATATTATTTCATGTAATAAAATAGAAATTC
Found at i:20500033 original size:29 final size:32
Alignment explanation
Indices: 20499967--20500035 Score: 81
Period size: 34 Copynumber: 2.2 Consensus size: 32
20499957 ATTATTTTAT
* *
20499967 GTAATAAAATAGAAATTCTTTTATATTATTTCAT
1 GTAATAAAATAGAAATTCTTTTATA-TA-TTAAG
20500001 GTAATAAAATAGAAATTCTTTTA-A-A-TAAG
1 GTAATAAAATAGAAATTCTTTTATATATTAAG
20500030 GTAATA
1 GTAATA
20500036 TTTTGAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
29 8 0.24
31 1 0.03
33 1 0.03
34 23 0.70
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.41
Consensus pattern (32 bp):
GTAATAAAATAGAAATTCTTTTATATATTAAG
Found at i:20500057 original size:61 final size:61
Alignment explanation
Indices: 20499988--20500193 Score: 230
Period size: 61 Copynumber: 3.5 Consensus size: 61
20499978 GAAATTCTTT
* *
20499988 TATATTATTTCATGTAATAAAATAGAAATTCTTTTAAATAAGGTAATATTTTGAATATTTC
1 TATATTATTTCATTTAATAAAATATAAATTCTTTTAAATAAGGTAATATTTTGAATATTTC
* * * * *
20500049 TATATTATTTCATTTAATAAAATA-AAACGTTGTTTTGAATAAAGT-A-ATTGT-AAT-TTAC
1 TATATTATTTCATTTAATAAAATATAAA--TTCTTTTAAATAAGGTAATATTTTGAATATTTC
* * **
20500107 TTTAATA-TT--TTTAATAAAATATAAATTCTTTTAAATAAGACAATATTTTGAATATTTC
1 TATATTATTTCATTTAATAAAATATAAATTCTTTTAAATAAGGTAATATTTTGAATATTTC
*
20500165 TATATTATTTCATTTAAAAAAATATAAAT
1 TATATTATTTCATTTAATAAAATATAAAT
20500194 AATACAATAT
Statistics
Matches: 117, Mismatches: 18, Indels: 20
0.75 0.12 0.13
Matches are distributed among these distances:
54 11 0.09
55 13 0.11
56 7 0.06
57 5 0.04
58 16 0.14
59 5 0.04
60 7 0.06
61 40 0.34
62 13 0.11
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (61 bp):
TATATTATTTCATTTAATAAAATATAAATTCTTTTAAATAAGGTAATATTTTGAATATTTC
Found at i:20502546 original size:125 final size:125
Alignment explanation
Indices: 20502324--20502614 Score: 492
Period size: 125 Copynumber: 2.3 Consensus size: 125
20502314 TCAGGCCAAA
* * * *
20502324 TAGGAACTACTGTAGCAAAAGAGCGTCCACGTGTGAGCTTCTTTCAGTACTTTTGCTGACAAAGC
1 TAGGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTCCAGTACTTTTACTAACAAAGC
* *
20502389 ATCCTGCTTAAAGTGTTTTTGACACTATTTGCTCAGAAACATCTTCTCCAAATTATTTTT
66 ATCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTT
*
20502449 TAGGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTCCAGTACTTTTACTAACAATGC
1 TAGGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTCCAGTACTTTTACTAACAAAGC
*
20502514 ATCCTGCTTAAAGCGTTTTTGCCACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTT
66 ATCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTT
*
20502574 TCAGGAACTACTGTAGCAAAAGAGCGTCCACATGGGAGCTT
1 T-AGGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTT
20502615 TTTTAAATTA
Statistics
Matches: 156, Mismatches: 9, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
125 118 0.76
126 38 0.24
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (125 bp):
TAGGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTCCAGTACTTTTACTAACAAAGC
ATCCTGCTTAAAGCGTTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTT
Found at i:20502787 original size:97 final size:97
Alignment explanation
Indices: 20502657--20502956 Score: 374
Period size: 96 Copynumber: 3.1 Consensus size: 97
20502647 CCTAAATCTC
* *
20502657 AAACCTTAATTTATTTAAGTTTTTCCTTAAAAACCTTAAACACTAAACCCTAATCAAAATTTTTT
1 AAACCCTAATTTATTTAAGTTTTTCCTTAAAAACCTTAAACACTAAACCCTAATC-TAATTTTTT
* * * * *
20502722 TAAAACTTATAATTAATTTACTTAGGTAATCCT
65 AAAAATTTATAATTAATTTACTCAAGTAACCCT
* * *
20502755 AAACCCTAATTTATTTGA-TTTTTCCTTAAAAACTCTT-AACACTAAACCTTAATCTGATTTTTT
1 AAACCCTAATTTATTTAAGTTTTTCCTTAAAAAC-CTTAAACACTAAACCCTAATCTAATTTTTT
20502818 AAAAATTTATAATTAATTTACTCAAGTAACCCT
65 AAAAATTTATAATTAATTTACTCAAGTAACCCT
* * * *
20502851 AAACCCTAATTTAATTAATTTTTTCCTTAAAAA-CTATAAACACAAAACCCTAATCTAA-TTTTG
1 AAACCCTAATTTATTTAAGTTTTTCCTTAAAAACCT-TAAACACTAAACCCTAATCTAATTTTTT
* * * *
20502914 AAAAATTTATAATTAATTTAATTAAGAAACTCT
65 AAAAATTTATAATTAATTTACTCAAGTAACCCT
*
20502947 AAACCTTAAT
1 AAACCCTAAT
20502957 CCCTTATTTA
Statistics
Matches: 177, Mismatches: 21, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
95 2 0.01
96 94 0.53
97 62 0.35
98 19 0.11
ACGTcount: A:0.41, C:0.16, G:0.03, T:0.40
Consensus pattern (97 bp):
AAACCCTAATTTATTTAAGTTTTTCCTTAAAAACCTTAAACACTAAACCCTAATCTAATTTTTTA
AAAATTTATAATTAATTTACTCAAGTAACCCT
Found at i:20507326 original size:5 final size:5
Alignment explanation
Indices: 20507316--20507343 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
20507306 GGACTTTGGG
20507316 TAGCT TAGCT TAGCT TAGCT TAGCT TAG
1 TAGCT TAGCT TAGCT TAGCT TAGCT TAG
20507344 ACTTCAGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.39
Consensus pattern (5 bp):
TAGCT
Found at i:20508376 original size:21 final size:20
Alignment explanation
Indices: 20508327--20508366 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
20508317 GGCACACAAG
20508327 AAAACATGGTCACAGCAATC
1 AAAACATGGTCACAGCAATC
20508347 AAAACATGGTCACAGCAATC
1 AAAACATGGTCACAGCAATC
20508367 TTTTACATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.25, G:0.15, T:0.15
Consensus pattern (20 bp):
AAAACATGGTCACAGCAATC
Found at i:20508603 original size:24 final size:24
Alignment explanation
Indices: 20508570--20508620 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
20508560 CAATAAGTAA
*
20508570 TAATACTTAAAAAATGTAGATTTT
1 TAATACTTAAAAAATGTAGATTAT
* *
20508594 TAATAGTTAAAAGATGTAGATTAT
1 TAATACTTAAAAAATGTAGATTAT
20508618 TAA
1 TAA
20508621 CCTTGGTTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.47, C:0.02, G:0.12, T:0.39
Consensus pattern (24 bp):
TAATACTTAAAAAATGTAGATTAT
Found at i:20531181 original size:43 final size:43
Alignment explanation
Indices: 20531133--20531331 Score: 326
Period size: 43 Copynumber: 4.6 Consensus size: 43
20531123 TTTTAGAAAT
*
20531133 AAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGAACAAGACCTTTAGCCGCGCTTTTCCCAC
* * *
20531176 AAACGCCGCTATAGAACAAGACCTTTAGCCGCGCTTTTTCCAA
1 AAACGCCGCTAAAGAACAAGACCTTTAGCCGCGCTTTTCCCAC
*
20531219 AAACGCCGCTAAAGAACAAGACCTTTAGCAGCGCTTTTCCCAC
1 AAACGCCGCTAAAGAACAAGACCTTTAGCCGCGCTTTTCCCAC
* *
20531262 AAACGCCGCTATAGAACAAGACCTTTAGCCGCGCTTTTTCCAC
1 AAACGCCGCTAAAGAACAAGACCTTTAGCCGCGCTTTTCCCAC
*
20531305 AAACGCCGCTAAAGAACATGACCTTTA
1 AAACGCCGCTAAAGAACAAGACCTTTA
20531332 AAAAAATATT
Statistics
Matches: 143, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 143 1.00
ACGTcount: A:0.32, C:0.31, G:0.17, T:0.21
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACAAGACCTTTAGCCGCGCTTTTCCCAC
Found at i:20531278 original size:86 final size:86
Alignment explanation
Indices: 20531133--20531331 Score: 371
Period size: 86 Copynumber: 2.3 Consensus size: 86
20531123 TTTTAGAAAT
*
20531133 AAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAACAAGAC
1 AAACGCCGCTAAAGAACAAGACCTTTAGCAGCGCTTTTCCCACAAACGCCGCTATAGAACAAGAC
20531198 CTTTAGCCGCGCTTTTTCCAA
66 CTTTAGCCGCGCTTTTTCCAA
20531219 AAACGCCGCTAAAGAACAAGACCTTTAGCAGCGCTTTTCCCACAAACGCCGCTATAGAACAAGAC
1 AAACGCCGCTAAAGAACAAGACCTTTAGCAGCGCTTTTCCCACAAACGCCGCTATAGAACAAGAC
*
20531284 CTTTAGCCGCGCTTTTTCCAC
66 CTTTAGCCGCGCTTTTTCCAA
*
20531305 AAACGCCGCTAAAGAACATGACCTTTA
1 AAACGCCGCTAAAGAACAAGACCTTTA
20531332 AAAAAATATT
Statistics
Matches: 110, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
86 110 1.00
ACGTcount: A:0.32, C:0.31, G:0.17, T:0.21
Consensus pattern (86 bp):
AAACGCCGCTAAAGAACAAGACCTTTAGCAGCGCTTTTCCCACAAACGCCGCTATAGAACAAGAC
CTTTAGCCGCGCTTTTTCCAA
Found at i:20532031 original size:4 final size:4
Alignment explanation
Indices: 20532022--20532056 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
20532012 GGTATATTAG
20532022 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
20532057 TATCTATATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:20535302 original size:14 final size:14
Alignment explanation
Indices: 20535283--20535363 Score: 56
Period size: 14 Copynumber: 5.7 Consensus size: 14
20535273 ACCCTTGAAT
20535283 CCCTAAATCCTAAC
1 CCCTAAATCCTAAC
20535297 CCCTAAATCCCTAAC
1 CCCTAAAT-CCTAAC
* * ** *
20535312 TCTTAACCCCTAAA
1 CCCTAAATCCTAAC
* *
20535326 CCTTAAATCCCAAC
1 CCCTAAATCCTAAC
* *
20535340 CCTTAAA-CCATAAT
1 CCCTAAATCC-TAAC
20535354 CCCTAAATCC
1 CCCTAAATCC
20535364 ATATATAATT
Statistics
Matches: 51, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
13 2 0.04
14 37 0.73
15 12 0.24
ACGTcount: A:0.36, C:0.41, G:0.00, T:0.23
Consensus pattern (14 bp):
CCCTAAATCCTAAC
Found at i:20535305 original size:22 final size:22
Alignment explanation
Indices: 20535280--20535346 Score: 82
Period size: 22 Copynumber: 3.1 Consensus size: 22
20535270 CCGACCCTTG
20535280 AATCCCTAAATCCTAACCCCTA
1 AATCCCTAAATCCTAACCCCTA
* *
20535302 AATCCCTAACTCTTAACCCCTA
1 AATCCCTAAATCCTAACCCCTA
* * *
20535324 AA-CCTTAAATCCCAACCCTTA
1 AATCCCTAAATCCTAACCCCTA
20535345 AA
1 AA
20535347 CCATAATCCC
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 16 0.42
22 22 0.58
ACGTcount: A:0.37, C:0.39, G:0.00, T:0.24
Consensus pattern (22 bp):
AATCCCTAAATCCTAACCCCTA
Found at i:20535346 original size:21 final size:20
Alignment explanation
Indices: 20535288--20535356 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 20
20535278 TGAATCCCTA
* *
20535288 AATCCTAACCCCTAAATCCCT
1 AATCCCAACCCCTAAA-CCAT
** *
20535309 AACTCTTAACCCCTAAACCTT
1 AA-TCCCAACCCCTAAACCAT
*
20535330 AAATCCCAACCCTTAAACCAT
1 -AATCCCAACCCCTAAACCAT
20535351 AATCCC
1 AATCCC
20535357 TAAATCCATA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
20 6 0.15
21 19 0.47
22 15 0.38
ACGTcount: A:0.36, C:0.41, G:0.00, T:0.23
Consensus pattern (20 bp):
AATCCCAACCCCTAAACCAT
Found at i:20535360 original size:28 final size:29
Alignment explanation
Indices: 20535297--20535363 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
20535287 AAATCCTAAC
* * *
20535297 CCCTAAATCCCTAACTCTTAACCCCTAAA
1 CCCTAAATCCCTAACCCTTAAACCATAAA
* *
20535326 CCTTAAATCCC-AACCCTTAAACCATAAT
1 CCCTAAATCCCTAACCCTTAAACCATAAA
20535354 CCCTAAATCC
1 CCCTAAATCC
20535364 ATATATAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 22 0.69
29 10 0.31
ACGTcount: A:0.36, C:0.40, G:0.00, T:0.24
Consensus pattern (29 bp):
CCCTAAATCCCTAACCCTTAAACCATAAA
Found at i:20535446 original size:21 final size:18
Alignment explanation
Indices: 20535404--20535457 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 18
20535394 CAAAACACGT
*
20535404 AAAAAACTGAACTGGATA
1 AAAAAACTGAACCGGATA
20535422 AAAAAACTGAACCGAGCACTA
1 AAAAAACTGAACCG-G-A-TA
*
20535443 AAAATACTGAACCGG
1 AAAAAACTGAACCGG
20535458 GATGGGATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 13 0.42
19 1 0.03
20 2 0.06
21 15 0.48
ACGTcount: A:0.52, C:0.19, G:0.17, T:0.13
Consensus pattern (18 bp):
AAAAAACTGAACCGGATA
Found at i:20535885 original size:41 final size:41
Alignment explanation
Indices: 20535823--20535901 Score: 140
Period size: 41 Copynumber: 1.9 Consensus size: 41
20535813 TAAATTATTT
* *
20535823 TAAATCCCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCAC
1 TAAAGCCCTGAGCATTAGCGGCCCTTTCTCAAAAACGCCAC
20535864 TAAAGCCCTGAGCATTAGCGGCCCTTTCTCAAAAACGC
1 TAAAGCCCTGAGCATTAGCGGCCCTTTCTCAAAAACGC
20535902 TGTTAAATCC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.22
Consensus pattern (41 bp):
TAAAGCCCTGAGCATTAGCGGCCCTTTCTCAAAAACGCCAC
Found at i:20536039 original size:102 final size:102
Alignment explanation
Indices: 20535863--20536054 Score: 321
Period size: 102 Copynumber: 1.9 Consensus size: 102
20535853 AAAAACGCCA
* * *
20535863 CTAAAGCCCTGAGCATTAGCGGCCCTTTCTCAAAAACGCTGTTAAATCCCCGAAAGCTTAGAAAA
1 CTAAAGCCCTGAGCATTAGCGGCCCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAA
*
20535928 CGGCGTCGTTGGGCTTAGGTTTTTTTTGCGGCGTTCG
66 CGACGTCGTTGGGCTTAGGTTTTTTTTGCGGCGTTCG
* * *
20535965 CTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCTGAAAGCTCAGAAAA
1 CTAAAGCCCTGAGCATTAGCGGCCCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAA
20536030 CGACGTCGTTGGGCTTAGGTTTTTT
66 CGACGTCGTTGGGCTTAGGTTTTTT
20536055 GTGGCGCTTT
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
102 83 1.00
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.28
Consensus pattern (102 bp):
CTAAAGCCCTGAGCATTAGCGGCCCTTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAA
CGACGTCGTTGGGCTTAGGTTTTTTTTGCGGCGTTCG
Found at i:20536102 original size:72 final size:72
Alignment explanation
Indices: 20535983--20536154 Score: 299
Period size: 72 Copynumber: 2.4 Consensus size: 72
20535973 CTGAGCATTA
*
20535983 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCTGAAAGCTCAGAAAACGACGTCGTTGGGCTTAG
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCTGAAAGCTCAGAAAACGACGTCGCTGGGCTTAG
20536048 GTTTTTT
66 GTTTTTT
* *
20536055 GTGGCGCTTTCTTAAAAACGCCGCTAAATCCCTGAAAGCTCAGAAAACGGCGTCGCTGGGCTTAG
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCTGAAAGCTCAGAAAACGACGTCGCTGGGCTTAG
20536120 GTTTTTT
66 GTTTTTT
* *
20536127 GCGGCGCTTTCTCAAAAACACCGCTAAA
1 GCGGCGCTTTCTTAAAAACGCCGCTAAA
20536155 GCCCAAGCAT
Statistics
Matches: 94, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 94 1.00
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (72 bp):
GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCTGAAAGCTCAGAAAACGACGTCGCTGGGCTTAG
GTTTTTT
Found at i:20536436 original size:113 final size:113
Alignment explanation
Indices: 20536057--20536728 Score: 952
Period size: 114 Copynumber: 5.9 Consensus size: 113
20536047 GGTTTTTTGT
* * * * *
20536057 GGCGCTTTCTTAAAAACGCCGCTAAATCCCTGAAAGCTCAGAAAACGGCGTCGCTGGGCTTAGG-
1 GGCGCTTTCTTAAAAACGCCGCTAAATCCCAGAATGCTCAGAAAACAGCATCGTTGGGCTTAGGT
*
20536121 TTTTTTGCGGCGCTTTCTCAAAAACACCGCTAAAGCCCAAGCATTAGC
66 TTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCAAGCATTAGC
* * *
20536169 AGCGCTTTCTTAAAAACGCCGCTAAATCCGAAAATGCTCAGAAAACAGCATCGTTGGGCTTAGGT
1 GGCGCTTTCTTAAAAACGCCGCTAAATCCCAGAATGCTCAGAAAACAGCATCGTTGGGCTTAGGT
* *
20536234 TTTTTTGCGGTGCTTTCTCAAAAACGCCGCTAAAGCCCTGAGCATTAGC
66 TTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCC-AAGCATTAGC
* * * * * *
20536283 GGCGCTTTCTTAAAAACGCCGCTAAATCCCCGACTACTCAGAAAACAACGTCGCTGGGCTTAGGT
1 GGCGCTTTCTTAAAAACGCCGCTAAATCCCAGAATGCTCAGAAAACAGCATCGTTGGGCTTAGGT
* *
20536348 TTTTTTGCAGCGCTTTCTCAAAAACGCTGCTAAAGCCCAAGCATTAGC
66 TTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCAAGCATTAGC
* *
20536396 GGCGCTTTTTTAAAAACGCCGCTAAATCCCAGAATGCTCAGAAAACGGCATCGTTGGGCTTAGGT
1 GGCGCTTTCTTAAAAACGCCGCTAAATCCCAGAATGCTCAGAAAACAGCATCGTTGGGCTTAGG-
* * * * *
20536461 TTTTTTTACGGCACTTTCTCAAAAATGCCGCTAAAGCCCTGAGCATTTGC
65 TTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCC-AAGCATTAGC
* *
20536511 GGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACAGCATCGTTGGGCTTAGGT
1 GGCGCTTTCTTAAAAACGCCGCTAAATCCCAGAATGCTCAGAAAACAGCATCGTTGGGCTTAGG-
**
20536576 TTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCTTGAGCATT-GC
65 TTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCC-CAAGCATTAGC
* * * *
20536625 GGCGCTTTCTTAAAAACACCGCTAAATCCCTGAATGCTCAGAAAACGGCATCGTTGGGATTAGGT
1 GGCGCTTTCTTAAAAACGCCGCTAAATCCCAGAATGCTCAGAAAACAGCATCGTTGGGCTTAGGT
* * *
20536690 TTTTTTGCAGCGCTTTCTCAAAATCGCCTCTAAAGCCCA
66 TTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCA
20536729 GAATGCTCAG
Statistics
Matches: 498, Mismatches: 57, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
112 56 0.11
113 136 0.27
114 195 0.39
115 111 0.22
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (113 bp):
GGCGCTTTCTTAAAAACGCCGCTAAATCCCAGAATGCTCAGAAAACAGCATCGTTGGGCTTAGGT
TTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCAAGCATTAGC
Found at i:20536733 original size:73 final size:72
Alignment explanation
Indices: 20536621--20536794 Score: 222
Period size: 73 Copynumber: 2.4 Consensus size: 72
20536611 GCCTTGAGCA
* * * *
20536621 TTGCGGCGCTTTCTTAAAAACACCGCTAAATCCCTGAATGCTCAGAAAACGGCATCGTTGGGATT
1 TTGCGGCGCTTTCTCAAAAACACCGCTAAAGCCCAGAATGCTCAGAAAACGACATCGTTGGGATT
20536686 AGGTTTTT
66 AGG-TTTT
* * * * * *
20536694 TTGCAGCGCTTTCTCAAAATCGCCTCTAAAGCCCAGAATGCTCAGAAAACGACGTCGTTGGGCTT
1 TTGCGGCGCTTTCTCAAAAACACCGCTAAAGCCCAGAATGCTCAGAAAACGACATCGTTGGGATT
20536759 AGGTTTT
66 AGGTTTT
** *
20536766 TTGCGGCGCTTTCTGGAAAACGCCGCTAA
1 TTGCGGCGCTTTCTCAAAAACACCGCTAA
20536795 TGCTTATTTT
Statistics
Matches: 86, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
72 28 0.33
73 58 0.67
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.28
Consensus pattern (72 bp):
TTGCGGCGCTTTCTCAAAAACACCGCTAAAGCCCAGAATGCTCAGAAAACGACATCGTTGGGATT
AGGTTTT
Found at i:20538106 original size:7 final size:7
Alignment explanation
Indices: 20538091--20538120 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
20538081 TGAGTACTTT
*
20538091 TGATTAG
1 TGATAAG
20538098 TGATAAG
1 TGATAAG
20538105 TGATAAG
1 TGATAAG
20538112 TGATAAG
1 TGATAAG
20538119 TG
1 TG
20538121 GTAGCTTAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.30, T:0.33
Consensus pattern (7 bp):
TGATAAG
Found at i:20538201 original size:51 final size:50
Alignment explanation
Indices: 20538091--20538368 Score: 412
Period size: 51 Copynumber: 5.5 Consensus size: 50
20538081 TGAGTACTTT
* *
20538091 TGATTAGTGATAAGTGATAAGTGATAAGTGGTAGCTTAGCTACACTTATC
1 TGATCAGTGACAAGTGATAAGTGATAAGTGGTAGCTTAGCTACACTTATC
** *
20538141 TGATCAGTGACAAGTGGCAAGTGATAAGTGATAGCTTCAGCTACACTTATC
1 TGATCAGTGACAAGTGATAAGTGATAAGTGGTAGCTT-AGCTACACTTATC
* *
20538192 TGATCAGTGACAAGTGGTAAGTGATAAGTGATAGCTTCAGCTACACTTATC
1 TGATCAGTGACAAGTGATAAGTGATAAGTGGTAGCTT-AGCTACACTTATC
* * *
20538243 TGATCAGTGACAAGTGACAAGTGATAAGCGGTAGTTGTAGCTACACTTATC
1 TGATCAGTGACAAGTGATAAGTGATAAGTGGTAGCT-TAGCTACACTTATC
*
20538294 TGATCAGTGACAAGTGGTAAGTGATAAGTGGTAGCTTAGCTACACTTATC
1 TGATCAGTGACAAGTGATAAGTGATAAGTGGTAGCTTAGCTACACTTATC
* *
20538344 TGATCTGGGACAAGTGATAAGTGAT
1 TGATCAGTGACAAGTGATAAGTGAT
20538369 CATACGTAAG
Statistics
Matches: 208, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
50 68 0.33
51 139 0.67
52 1 0.00
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.29
Consensus pattern (50 bp):
TGATCAGTGACAAGTGATAAGTGATAAGTGGTAGCTTAGCTACACTTATC
Found at i:20542077 original size:19 final size:18
Alignment explanation
Indices: 20542040--20542080 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 18
20542030 TTATAGCAAA
20542040 TTTTAATTTTAATCATTT
1 TTTTAATTTTAATCATTT
*
20542058 TTTTAATTTT--TAATTT
1 TTTTAATTTTAATCATTT
20542074 TTTTAAT
1 TTTTAAT
20542081 AAAAGAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 12 0.55
18 10 0.45
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTAATTTTAATCATTT
Found at i:20545029 original size:9 final size:9
Alignment explanation
Indices: 20545017--20545079 Score: 56
Period size: 9 Copynumber: 6.8 Consensus size: 9
20545007 AAATAATTTA
20545017 AAAAATTAT
1 AAAAATTAT
*
20545026 AAAAA-TAG
1 AAAAATTAT
*
20545034 AAAATAATAT
1 AAAA-ATTAT
20545044 AAAAATTAT
1 AAAAATTAT
20545053 AAAAAAATTAT
1 --AAAAATTAT
*
20545064 AAAAAGTAT
1 AAAAATTAT
*
20545073 AAGAATT
1 AAAAATT
20545080 CAAAAAAGTA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
8 6 0.14
9 23 0.52
10 6 0.14
11 9 0.20
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (9 bp):
AAAAATTAT
Found at i:20545044 original size:18 final size:20
Alignment explanation
Indices: 20545016--20545068 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
20545006 CAAATAATTT
20545016 AAAAAATTATAAAAA-TAGA
1 AAAAAATTATAAAAATTAGA
* *
20545035 AAATAA-TATAAAAATTATA
1 AAAAAATTATAAAAATTAGA
20545054 AAAAAATTATAAAAA
1 AAAAAATTATAAAAA
20545069 GTATAAGAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 8 0.28
19 13 0.45
20 8 0.28
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.25
Consensus pattern (20 bp):
AAAAAATTATAAAAATTAGA
Found at i:20545374 original size:44 final size:44
Alignment explanation
Indices: 20545320--20545407 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 44
20545310 TATACCTTCT
*
20545320 AAAATTTATCATATAAGCTATTTTATATCATTATTACTTATTAG
1 AAAAGTTATCATATAAGCTATTTTATATCATTATTACTTATTAG
* *
20545364 AAAAGTTATCATGTAAGCTATTTTATATCATTATTGCTTATTAG
1 AAAAGTTATCATATAAGCTATTTTATATCATTATTACTTATTAG
20545408 GCATATTCAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.47
Consensus pattern (44 bp):
AAAAGTTATCATATAAGCTATTTTATATCATTATTACTTATTAG
Found at i:20545807 original size:31 final size:31
Alignment explanation
Indices: 20545728--20545808 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 31
20545718 TATTTGAGAA
* *
20545728 GCTCTTATTTGAACACTTTTAAAAAGGTTTG
1 GCTCTTATTTGAACACTTTCAAAAACGTTTG
* * *
20545759 GCTCTTACTAGAACACTTTCAAAAACTTTTG
1 GCTCTTATTTGAACACTTTCAAAAACGTTTG
* *
20545790 GCTCGTATTTGAGCACTTT
1 GCTCTTATTTGAACACTTT
20545809 GAAAGTTTTG
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.40
Consensus pattern (31 bp):
GCTCTTATTTGAACACTTTCAAAAACGTTTG
Found at i:20547889 original size:15 final size:15
Alignment explanation
Indices: 20547869--20547897 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
20547859 AAGAGAAAAT
20547869 GATGATGAAGATGAA
1 GATGATGAAGATGAA
20547884 GATGATGAAGATGA
1 GATGATGAAGATGA
20547898 CGAGGGGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.34, T:0.21
Consensus pattern (15 bp):
GATGATGAAGATGAA
Found at i:20551044 original size:6 final size:6
Alignment explanation
Indices: 20551033--20551063 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
20551023 AGAAACGCAT
20551033 GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG G
1 GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG G
20551064 ACCATCCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (6 bp):
GTTTGG
Found at i:20558378 original size:21 final size:21
Alignment explanation
Indices: 20558348--20558390 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
20558338 AATGTAATAA
* *
20558348 TAAAATTATATTTTAACCTTT
1 TAAAAATATAATTTAACCTTT
*
20558369 TAAAAATATAATTTAATCTTT
1 TAAAAATATAATTTAACCTTT
20558390 T
1 T
20558391 CCCCAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (21 bp):
TAAAAATATAATTTAACCTTT
Found at i:20558925 original size:16 final size:17
Alignment explanation
Indices: 20558907--20558947 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
20558897 AAAATTTTAA
20558907 TTTAAATCTTTTATAATT
1 TTTAAATCTTTTATAA-T
*
20558925 TTTAAATTTTTTA-AAT
1 TTTAAATCTTTTATAAT
20558941 TTTAAAT
1 TTTAAAT
20558948 TAATAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.36
17 2 0.09
18 12 0.55
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTAAATCTTTTATAAT
Found at i:20558927 original size:9 final size:8
Alignment explanation
Indices: 20558907--20558948 Score: 50
Period size: 9 Copynumber: 5.0 Consensus size: 8
20558897 AAAATTTTAA
20558907 TTTAAATCT
1 TTTAAAT-T
20558916 TTTATAATT
1 TTTA-AATT
20558925 TTTAAATTT
1 TTTAAA-TT
20558934 TTTAAA-T
1 TTTAAATT
20558941 TTTAAATT
1 TTTAAATT
20558949 AATAATAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
7 7 0.23
8 3 0.10
9 17 0.57
10 3 0.10
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (8 bp):
TTTAAATT
Found at i:20558948 original size:16 final size:17
Alignment explanation
Indices: 20558907--20558948 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
20558897 AAAATTTTAA
*
20558907 TTTAAATCTTTTATAATT
1 TTTAAAT-TTTTATAAAT
20558925 TTTAAATTTTT-TAAAT
1 TTTAAATTTTTATAAAT
20558941 TTTAAATT
1 TTTAAATT
20558949 AATAATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 12 0.52
17 4 0.17
18 7 0.30
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTAAATTTTTATAAAT
Done.