Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr7
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: 47983841
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869652 characters in sequence are not A, C, G, or T
File 64 of 153
Found at i:20571136 original size:15 final size:15
Alignment explanation
Indices: 20571116--20571158 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
20571106 AATTATGTTA
20571116 TTATATTTGTTTATT
1 TTATATTTGTTTATT
20571131 TTATATTTGTTTATT
1 TTATATTTGTTTATT
*
20571146 TTAT-TTTCTTTAT
1 TTATATTTGTTTAT
20571159 CAGCTAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
14 8 0.30
15 19 0.70
ACGTcount: A:0.19, C:0.02, G:0.05, T:0.74
Consensus pattern (15 bp):
TTATATTTGTTTATT
Found at i:20572264 original size:20 final size:19
Alignment explanation
Indices: 20572211--20572264 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
20572201 AATTATAAAA
20572211 AAAAATAA-AAAAATTATT
1 AAAAATAATAAAAATTATT
*
20572229 AAGAAAT-ATGAGAAATTATT
1 AA-AAATAAT-AAAAATTATT
20572249 AAAAATTAATAAAAAT
1 AAAAA-TAATAAAAAT
20572265 ATTTAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
18 3 0.10
19 7 0.24
20 17 0.59
21 2 0.07
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.28
Consensus pattern (19 bp):
AAAAATAATAAAAATTATT
Found at i:20572685 original size:30 final size:31
Alignment explanation
Indices: 20572634--20572723 Score: 112
Period size: 30 Copynumber: 2.9 Consensus size: 31
20572624 TGCTAATAAG
* *
20572634 AAAGGCTTAATTAATTTTTAAATTATTTTGC
1 AAAGACTTAATTAATTTTTAAATTATTTTAC
*
20572665 -AAGAACTTAATTAA-TTTTAAATTATTTTAT
1 AAAG-ACTTAATTAATTTTTAAATTATTTTAC
*
20572695 AAAGATTTAATTAATTTTTTAAATTATTT
1 AAAGACTTAATTAA-TTTTTAAATTATTT
20572724 AAGACTAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
30 26 0.51
31 12 0.24
32 13 0.25
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (31 bp):
AAAGACTTAATTAATTTTTAAATTATTTTAC
Found at i:20573081 original size:12 final size:10
Alignment explanation
Indices: 20573045--20573086 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
20573035 ATGTTTTTAT
20573045 ATTTTATA-A
1 ATTTTATATA
*
20573054 TTTTTATATA
1 ATTTTATATA
20573064 ATTTTATATA
1 ATTTTATATA
20573074 ACTCTTTATATA
1 A-T-TTTATATA
20573086 A
1 A
20573087 AATTTATCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
9 7 0.25
10 11 0.39
11 1 0.04
12 9 0.32
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (10 bp):
ATTTTATATA
Found at i:20573321 original size:9 final size:9
Alignment explanation
Indices: 20573307--20573384 Score: 56
Period size: 8 Copynumber: 8.9 Consensus size: 9
20573297 ATTATCTCTG
20573307 ATTTTTTAT
1 ATTTTTTAT
20573316 A-TTTTTAT
1 ATTTTTTAT
*
20573324 A-ATTTTA-
1 ATTTTTTAT
**
20573331 ATAATTTAT
1 ATTTTTTAT
*
20573340 ATTTTCTAT
1 ATTTTTTAT
20573349 -TTTTTTAT
1 ATTTTTTAT
20573357 AGTTTTTTAT
1 A-TTTTTTAT
**
20573367 AACTTTTAT
1 ATTTTTTAT
20573376 AATTTTTTA
1 -ATTTTTTA
20573385 AACTTGTTAT
Statistics
Matches: 54, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
7 1 0.02
8 25 0.46
9 13 0.24
10 15 0.28
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (9 bp):
ATTTTTTAT
Found at i:20573373 original size:19 final size:18
Alignment explanation
Indices: 20573351--20573402 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 18
20573341 TTTTCTATTT
*
20573351 TTTTATAGTTTTTTATAAC
1 TTTTATAATTTTTTA-AAC
20573370 TTTTATAATTTTTTAAAC
1 TTTTATAATTTTTTAAAC
20573388 TTGTTATAATATTTT
1 TT-TTATAAT-TTTT
20573403 CATAATATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 5 0.17
19 21 0.70
20 4 0.13
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (18 bp):
TTTTATAATTTTTTAAAC
Found at i:20576158 original size:17 final size:17
Alignment explanation
Indices: 20576136--20576176 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
20576126 ATTAATATAT
*
20576136 TTTTTTATAATTATTTA
1 TTTTTTAGAATTATTTA
* *
20576153 TTTTTTAGGATTTTTTA
1 TTTTTTAGAATTATTTA
20576170 TTTTTTA
1 TTTTTTA
20576177 AACATTTGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.22, C:0.00, G:0.05, T:0.73
Consensus pattern (17 bp):
TTTTTTAGAATTATTTA
Found at i:20576616 original size:12 final size:12
Alignment explanation
Indices: 20576569--20576655 Score: 51
Period size: 12 Copynumber: 7.5 Consensus size: 12
20576559 TAATATATAC
20576569 AAATATAA-ATAT
1 AAATATAATA-AT
*
20576581 AAGTATAAGT-AT
1 AAATATAA-TAAT
*
20576593 AAGTATATATAAT
1 AAATATA-ATAAT
20576606 AAATATAATAAT
1 AAATATAATAAT
**
20576618 CTATATAATAAT
1 AAATATAATAAT
*
20576630 -AGTATAAT-AT
1 AAATATAATAAT
*
20576640 AAA-ATATTAA-
1 AAATATAATAAT
20576650 AAATAT
1 AAATAT
20576656 CAATTTAAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 15
0.72 0.10 0.18
Matches are distributed among these distances:
10 9 0.15
11 10 0.17
12 32 0.53
13 9 0.15
ACGTcount: A:0.59, C:0.01, G:0.05, T:0.36
Consensus pattern (12 bp):
AAATATAATAAT
Found at i:20577652 original size:16 final size:16
Alignment explanation
Indices: 20577631--20577682 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
20577621 TTTGGTTCGC
20577631 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
20577647 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* * *
20577663 TGTAATGGAATAGATG
1 TGTATTGGATTAGAGG
20577679 TGTA
1 TGTA
20577683 ATAGCAAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.29, C:0.00, G:0.35, T:0.37
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:20577729 original size:45 final size:44
Alignment explanation
Indices: 20577663--20577755 Score: 123
Period size: 45 Copynumber: 2.1 Consensus size: 44
20577653 GGATTAGAGG
* * *
20577663 TGTAATGGAATAGATGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
20577708 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
20577752 TGTA
1 TGTA
20577756 CTAGAGGTGT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 16 0.38
45 26 0.62
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:20577940 original size:18 final size:17
Alignment explanation
Indices: 20577919--20577953 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
20577909 TTATTATTTA
*
20577919 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
20577937 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
20577954 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:20577947 original size:28 final size:27
Alignment explanation
Indices: 20577877--20577949 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
20577867 TTTATTATCA
*
20577877 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
20577905 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
20577932 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
20577950 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:20578087 original size:18 final size:17
Alignment explanation
Indices: 20578066--20578100 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
20578056 TTATTATTAA
*
20578066 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
20578084 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
20578101 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:20578112 original size:147 final size:149
Alignment explanation
Indices: 20577838--20578112 Score: 509
Period size: 147 Copynumber: 1.9 Consensus size: 149
20577828 ATGATTATTG
*
20577838 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
*
20577903 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
66 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
20577968 AGAAATTTGTTTTGGTAAA
131 AGAAATTTGTTTTGGTAAA
*
20577987 TTATT-TTATTTAAATTTTAATAAGATTA-TTAATATCAATAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
20578050 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
20578113 ATATTCTTAT
Statistics
Matches: 123, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
147 95 0.77
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (149 bp):
TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
AGAAATTTGTTTTGGTAAA
Found at i:20578208 original size:18 final size:17
Alignment explanation
Indices: 20578168--20578220 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
20578158 AAATATAAAT
20578168 TAAAATA-ATAA-TT-A
1 TAAAATATATAATTTAA
*
20578182 TTAAATATAT--TTTAA
1 TAAAATATATAATTTAA
20578197 TTAAAATATATAATTTAA
1 -TAAAATATATAATTTAA
20578215 TAAAAT
1 TAAAAT
20578221 TCTAATAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
14 8 0.26
15 3 0.10
16 9 0.29
17 6 0.19
18 5 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAAATATATAATTTAA
Found at i:20578278 original size:60 final size:59
Alignment explanation
Indices: 20578094--20578280 Score: 157
Period size: 60 Copynumber: 3.1 Consensus size: 59
20578084 ATATAATTTA
*
20578094 ATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 ATAAAATTC-TAATAA-TAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
* * ** * * * ** * * * *
20578155 GTAAAATAT-AAATTAA-AATAATAATTAT-TAAATATATTTTAATTAAAATATATAAT-TT
1 ATAAAAT-TCTAA-TAATAAT-ATTCTTATATGAATTTACTAAAATCATAATATATGATACT
20578213 AATAAAATTCTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
1 -ATAAAATTCTAATAAT-AATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
20578274 ATAAAAT
1 ATAAAAT
20578281 ATAATTTGAA
Statistics
Matches: 91, Mismatches: 26, Indels: 19
0.67 0.19 0.14
Matches are distributed among these distances:
58 5 0.05
59 37 0.41
60 38 0.42
61 10 0.11
62 1 0.01
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (59 bp):
ATAAAATTCTAATAATAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
Found at i:20578279 original size:119 final size:120
Alignment explanation
Indices: 20578046--20578340 Score: 495
Period size: 119 Copynumber: 2.5 Consensus size: 120
20578036 TTAATCATAT
*
20578046 TTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTAAA-ATAATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
* * *
20578111 TAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAA
65 CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAAA
20578167 TTAAAATAATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTC-TAATAATC
1 TTAAAATAATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATC
*
20578231 AATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAAT
66 AATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAAA
* *
20578286 TTGAAATAATTAA-TATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 TTAAAATAA-TAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
20578341 TAAAATAATT
Statistics
Matches: 166, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
119 108 0.65
120 53 0.32
121 5 0.03
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.43
Consensus pattern (120 bp):
TTAAAATAATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATC
AATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAAA
Found at i:20579078 original size:16 final size:16
Alignment explanation
Indices: 20579057--20579092 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
20579047 TAAGAAATCA
20579057 CAGCCATGTACTCCTG
1 CAGCCATGTACTCCTG
20579073 CAGCCATGTACTCCTG
1 CAGCCATGTACTCCTG
20579089 CAGC
1 CAGC
20579093 TCCTGAGTTA
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:0.19, C:0.39, G:0.19, T:0.22
Consensus pattern (16 bp):
CAGCCATGTACTCCTG
Found at i:20586983 original size:33 final size:33
Alignment explanation
Indices: 20586928--20587002 Score: 80
Period size: 33 Copynumber: 2.3 Consensus size: 33
20586918 TAGTCCAACT
** * *
20586928 ATGGTCTTACACTTGTATTGCCATGA-CCCAGCC
1 ATGGTCTTACACACGTAGTGCCAT-ATCCCAGAC
* *
20586961 ATGGTCTTACTCACGTAGTGCCATATCCCAGAT
1 ATGGTCTTACACACGTAGTGCCATATCCCAGAC
20586994 ATGGTCTTA
1 ATGGTCTTA
20587003 TCATCTTCAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
32 1 0.03
33 34 0.97
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.32
Consensus pattern (33 bp):
ATGGTCTTACACACGTAGTGCCATATCCCAGAC
Found at i:20587077 original size:108 final size:101
Alignment explanation
Indices: 20586912--20587179 Score: 242
Period size: 102 Copynumber: 2.6 Consensus size: 101
20586902 CGTTTTCTTT
* * *** ** *
20586912 ATGCCATAGTCCAACTATGGTCTTACA--CTTGTA-TTGCCATGACCCAGCCATGGTCTTAC-TC
1 ATGCCATAGCCCAGCTATGGTCTTACATGCACATACTTGCCATGGTCCAACCATGGTCTTACGTC
* *
20586973 ACGTAGTGCCATATCCCAGATATGGTC-TTATCATCTTCATG
66 ACG-A-TGCCATAACCCAGATATGG-CATTATCA-C-TCA-A
20587014 ATGCCATAGCCCAGCTATGGTCTTACACATGCACATA-TACTGCCATGGTCCAACCATGGTCTTA
1 ATGCCATAGCCCAGCTATGGTCTT--ACATGCACATACT--TGCCATGGTCCAACCATGGTCTTA
* * *
20587078 CGTTCACGATGCCATAACCCAGTTATGGCATTTTCACTGAA
62 CG-TCACGATGCCATAACCCAGATATGGCATTATCACTCAA
* ** *
20587119 ATGCTATAGCCCAGCTATGGTCTTACATTTACATACTTGCCATGGTCCAACCACGGTCTTA
1 ATGCCATAGCCCAGCTATGGTCTTACATGCACATACTTGCCATGGTCCAACCATGGTCTTA
20587180 TCCATCAATT
Statistics
Matches: 139, Mismatches: 17, Indels: 20
0.79 0.10 0.11
Matches are distributed among these distances:
102 45 0.32
103 9 0.06
104 4 0.03
105 23 0.17
106 6 0.04
107 2 0.01
108 44 0.32
109 1 0.01
110 5 0.04
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (101 bp):
ATGCCATAGCCCAGCTATGGTCTTACATGCACATACTTGCCATGGTCCAACCATGGTCTTACGTC
ACGATGCCATAACCCAGATATGGCATTATCACTCAA
Found at i:20599166 original size:164 final size:169
Alignment explanation
Indices: 20598873--20599194 Score: 501
Period size: 164 Copynumber: 1.9 Consensus size: 169
20598863 CACAACGCGA
* * *
20598873 AATGTCCGGACCAGTCGGGCCTTCTAGGCCTGCAAATGTTTTAGCGCAATATATAATCTTATTTT
1 AATGTCCGGACCAGTCGGGCCTTCTAGGCCTGCAAATATTTTAGCCCAATACATAATCTTATTTT
* * * *
20598938 CTTTCCTCAGCAGAACTTATCAATTTGGAATTAAAAAGGAGTTAATGGCTTATTTAACTCAAACA
66 CTTTCCTCAACAGAACTTATCAATTCGGAATTAAAAAAGAGTTAATGGCTCATTTAACTCAAACA
20599003 TTAATTTGGGATTAATGGCTCCTTAATTAACAGACATAT
131 TTAATTTGGGATTAATGGCTCCTTAATTAACAGACATAT
* *
20599042 AATGTCTGGACCAGTTGGGCCTTC-AGGCCTGCAAATATTTTAGCCCAATACATAATC-T-TTTT
1 AATGTCCGGACCAGTCGGGCCTTCTAGGCCTGCAAATATTTTAGCCCAATACATAATCTTATTTT
* * *
20599104 -TTT-CTCAACAGAATTTATCAGTTCGGAATTAAAAAAGAGTTAATGGCTCATTTAATTCAAACA
66 CTTTCCTCAACAGAACTTATCAATTCGGAATTAAAAAAGAGTTAATGGCTCATTTAACTCAAACA
20599167 TTAATTTGGGATTAATGGCTCCTTAATT
131 TTAATTTGGGATTAATGGCTCCTTAATT
20599195 CACAAACACA
Statistics
Matches: 141, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
164 81 0.57
165 3 0.02
166 4 0.03
167 1 0.01
168 30 0.21
169 22 0.16
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35
Consensus pattern (169 bp):
AATGTCCGGACCAGTCGGGCCTTCTAGGCCTGCAAATATTTTAGCCCAATACATAATCTTATTTT
CTTTCCTCAACAGAACTTATCAATTCGGAATTAAAAAAGAGTTAATGGCTCATTTAACTCAAACA
TTAATTTGGGATTAATGGCTCCTTAATTAACAGACATAT
Found at i:20600427 original size:27 final size:27
Alignment explanation
Indices: 20600362--20600478 Score: 110
Period size: 27 Copynumber: 4.4 Consensus size: 27
20600352 ACGGACTTTC
* * *
20600362 CCCATATTAGATAGACCTTACAGACTT
1 CCCACATTAGATAGTCCTAACAGACTT
** *
20600389 -CCACAAAAGATGGTCCTAACAGACTT
1 CCCACATTAGATAGTCCTAACAGACTT
* * *
20600415 CCCACATTAGATGGTCCTAACTGGCTT
1 CCCACATTAGATAGTCCTAACAGACTT
* * * *
20600442 CCCACAGTAGATAGTCCTGACGGGCTT
1 CCCACATTAGATAGTCCTAACAGACTT
20600469 CCCACATTAG
1 CCCACATTAG
20600479 TTAGATTGGT
Statistics
Matches: 74, Mismatches: 15, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
26 20 0.27
27 54 0.73
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (27 bp):
CCCACATTAGATAGTCCTAACAGACTT
Found at i:20604472 original size:32 final size:32
Alignment explanation
Indices: 20604431--20604495 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
20604421 TCGGCTGCAA
20604431 TTGGGGGAGTCATTCGAGATGTTGATGGTATT
1 TTGGGGGAGTCATTCGAGATGTTGATGGTATT
20604463 TTGGGGGAGTCATTCGAGATGTTGATGGTATT
1 TTGGGGGAGTCATTCGAGATGTTGATGGTATT
20604495 T
1 T
20604496 AGTTATGTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.18, C:0.06, G:0.37, T:0.38
Consensus pattern (32 bp):
TTGGGGGAGTCATTCGAGATGTTGATGGTATT
Found at i:20606420 original size:3 final size:3
Alignment explanation
Indices: 20606400--20606529 Score: 68
Period size: 3 Copynumber: 42.7 Consensus size: 3
20606390 TTTGTTTTTC
* * *
20606400 TAT TAT CAT TAT TA- TAT TAT TAT TAT TTT TCAT GTACA TAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT -TA-T TAT TAT TAT
* * * * * *
20606446 ATAT TAT TTT TAT GAT TAT TAT T-G TATT TAT TTT TAC TAC TAT TAT
1 -TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
* * * * *
20606492 TTT TAT TAT TAG TAT TAG TAT TAT AAT TAC TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
20606530 CACTTATATA
Statistics
Matches: 93, Mismatches: 26, Indels: 16
0.69 0.19 0.12
Matches are distributed among these distances:
2 4 0.04
3 81 0.87
4 7 0.08
5 1 0.01
ACGTcount: A:0.31, C:0.05, G:0.04, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:20606465 original size:24 final size:24
Alignment explanation
Indices: 20606402--20606501 Score: 87
Period size: 24 Copynumber: 4.0 Consensus size: 24
20606392 TGTTTTTCTA
*
20606402 TTATCATTATTATATTATTATTATTT
1 TTATGATTATTAT-TTA-TATTATTT
*
20606428 TTCATGTACATATTATTTATATTATTT
1 TT-ATG-A-TTATTATTTATATTATTT
20606455 TTATGATTATTATTGTAT-TTATTT
1 TTATGATTATTATT-TATATTATTT
* *
20606479 TTACT-ACTATTATTTTTATTATT
1 TTA-TGATTATTATTTATATTATT
20606502 AGTATTAGTA
Statistics
Matches: 63, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
23 2 0.03
24 29 0.46
25 5 0.08
26 5 0.08
27 12 0.19
28 4 0.06
29 6 0.10
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (24 bp):
TTATGATTATTATTTATATTATTT
Found at i:20606522 original size:39 final size:39
Alignment explanation
Indices: 20606447--20606529 Score: 105
Period size: 39 Copynumber: 2.1 Consensus size: 39
20606437 ATATTATTTA
* **
20606447 TATTATTTTTATGATTATTATTGTATTTATTTTTACTAC
1 TATTATTTTTATGATTAGTATTGTATTTATAATTACTAC
* *
20606486 TATTATTTTTATTATTAGTATTAGTA-TTATAATTACTAT
1 TATTATTTTTATGATTAGTATT-GTATTTATAATTACTAC
20606525 TATTA
1 TATTA
20606530 CACTTATATA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
39 35 0.92
40 3 0.08
ACGTcount: A:0.30, C:0.04, G:0.05, T:0.61
Consensus pattern (39 bp):
TATTATTTTTATGATTAGTATTGTATTTATAATTACTAC
Found at i:20606721 original size:14 final size:14
Alignment explanation
Indices: 20606702--20606728 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20606692 ACATCATGTT
20606702 TTTTAATACTATAC
1 TTTTAATACTATAC
20606716 TTTTAATACTATA
1 TTTTAATACTATA
20606729 TTATGTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (14 bp):
TTTTAATACTATAC
Found at i:20606851 original size:23 final size:23
Alignment explanation
Indices: 20606711--20606794 Score: 53
Period size: 23 Copynumber: 3.3 Consensus size: 23
20606701 TTTTTAATAC
*
20606711 TATACTTTTAATACTATATTATGTA
1 TATATTTTTAATA-TATA-TATGTA
*
20606736 TATATTTTTACATGTAT-TATGTA
1 TATATTTTTA-ATATATATATGTA
*
20606759 CATATTTTCAATAACTATATCATATGTA
1 TATATTTT---TAA-TATAT-ATATGTA
*
20606787 AATATTTT
1 TATATTTT
20606795 ATGTACATAC
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
23 13 0.28
25 13 0.28
26 8 0.17
28 13 0.28
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.51
Consensus pattern (23 bp):
TATATTTTTAATATATATATGTA
Found at i:20607061 original size:27 final size:26
Alignment explanation
Indices: 20607014--20607107 Score: 100
Period size: 27 Copynumber: 3.6 Consensus size: 26
20607004 ATTATATTAC
* *
20607014 ATTTTTTACATATTATCTTATGTATAT
1 ATTTTTTA-ATACTATATTATGTATAT
*
20607041 ATTTTTTAATAACTATATTATGTATGT
1 ATTTTTTAAT-ACTATATTATGTATAT
** * *
20607068 ATTTTTTAACGCTATATTATGTACAC
1 ATTTTTTAATACTATATTATGTATAT
20607094 A-TTTTTAATACTAT
1 ATTTTTTAATACTAT
20607108 GTATATACCT
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
25 11 0.20
26 15 0.27
27 30 0.54
ACGTcount: A:0.32, C:0.09, G:0.05, T:0.54
Consensus pattern (26 bp):
ATTTTTTAATACTATATTATGTATAT
Found at i:20610992 original size:22 final size:22
Alignment explanation
Indices: 20610964--20611018 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
20610954 ATTCATGACT
20610964 AACATTC-TTTCGGCATTTATTC
1 AACATTCATTT-GGCATTTATTC
*
20610986 AACATTCATTTGTCATTTATTC
1 AACATTCATTTGGCATTTATTC
*
20611008 ATTCATTCATT
1 A-ACATTCATT
20611019 CATTGCATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 18 0.62
23 11 0.38
ACGTcount: A:0.25, C:0.20, G:0.05, T:0.49
Consensus pattern (22 bp):
AACATTCATTTGGCATTTATTC
Found at i:20620468 original size:29 final size:28
Alignment explanation
Indices: 20620436--20620490 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
20620426 TTTCATGTTG
*
20620436 TTATTATTAGTAGTATACTATTATATTTA
1 TTATTAATAGTAGTATA-TATTATATTTA
* *
20620465 TTATTAATATTAGTATATATTTTATT
1 TTATTAATAGTAGTATATATTATATT
20620491 ATGTATGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (28 bp):
TTATTAATAGTAGTATATATTATATTTA
Found at i:20620847 original size:21 final size:23
Alignment explanation
Indices: 20620822--20620880 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 23
20620812 ATATTATTGT
*
20620822 TATATTTATTATATA-GTA-GTG
1 TATATTTATTATATATCTATGTG
20620843 TATATTT-TTAT-TATCTATGTG
1 TATATTTATTATATATCTATGTG
*
20620864 TATATATATTTATATAT
1 TATATTTA-TTATATAT
20620881 ATAGTATGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
19 2 0.06
20 6 0.19
21 16 0.52
23 4 0.13
24 3 0.10
ACGTcount: A:0.32, C:0.02, G:0.08, T:0.58
Consensus pattern (23 bp):
TATATTTATTATATATCTATGTG
Found at i:20620852 original size:23 final size:25
Alignment explanation
Indices: 20620822--20620886 Score: 84
Period size: 23 Copynumber: 2.7 Consensus size: 25
20620812 ATATTATTGT
20620822 TATATTTATTATATAGTAGTGTATA
1 TATATTTATTATATAGTAGTGTATA
*
20620847 T-T-TTTATTATCTA-T-GTGTATA
1 TATATTTATTATATAGTAGTGTATA
20620868 TATATTTATATATATAGTA
1 TATATTTAT-TATATAGTA
20620887 TGATTTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
21 8 0.24
22 2 0.06
23 15 0.45
24 6 0.18
25 2 0.06
ACGTcount: A:0.34, C:0.02, G:0.09, T:0.55
Consensus pattern (25 bp):
TATATTTATTATATAGTAGTGTATA
Found at i:20620910 original size:18 final size:19
Alignment explanation
Indices: 20620889--20620928 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
20620879 ATATAGTATG
20620889 ATTTTTAAT-TACTTTATT
1 ATTTTTAATATACTTTATT
* *
20620907 ATTTTTATTATATTTTATT
1 ATTTTTAATATACTTTATT
20620926 ATT
1 ATT
20620929 CTTTTTTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (19 bp):
ATTTTTAATATACTTTATT
Found at i:20620941 original size:21 final size:22
Alignment explanation
Indices: 20620902--20620952 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
20620892 TTTAATTACT
20620902 TTATTATTTTTATTATATTTTA
1 TTATTATTTTTATTATATTTTA
* *
20620924 TTATTCTTTTT-TTGTATTTTA
1 TTATTATTTTTATTATATTTTA
*
20620945 ATATTATT
1 TTATTATT
20620953 ACTATTATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (22 bp):
TTATTATTTTTATTATATTTTA
Found at i:20622125 original size:21 final size:20
Alignment explanation
Indices: 20622099--20622171 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 20
20622089 ACATATATGT
20622099 ATAATAATGATGAAAATAATA
1 ATAATAAT-ATGAAAATAATA
20622120 ATAATAATAGTGAAAATAAATA
1 ATAATAATA-TGAAAAT-AATA
20622142 AT-ATAATAAT-AAATATAATA
1 ATAATAAT-ATGAAA-ATAATA
* *
20622162 GTAACAATAT
1 ATAATAATAT
20622172 TAGTAATATG
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
20 11 0.24
21 27 0.60
22 7 0.16
ACGTcount: A:0.62, C:0.01, G:0.07, T:0.30
Consensus pattern (20 bp):
ATAATAATATGAAAATAATA
Found at i:20622143 original size:16 final size:15
Alignment explanation
Indices: 20622114--20622156 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
20622104 AATGATGAAA
20622114 ATAATAAT-AATAAT
1 ATAATAATAAATAAT
20622128 AGTGAA-AATAAATAAT
1 A-T-AATAATAAATAAT
20622144 ATAATAATAAATA
1 ATAATAATAAATA
20622157 TAATAGTAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
14 3 0.12
15 13 0.52
16 9 0.36
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (15 bp):
ATAATAATAAATAAT
Found at i:20624774 original size:12 final size:12
Alignment explanation
Indices: 20624759--20624788 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
20624749 ATATTATTAA
*
20624759 TATTATTACTAT
1 TATTATCACTAT
20624771 TATTATCACTAT
1 TATTATCACTAT
20624783 TATTAT
1 TATTAT
20624789 ATCATATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (12 bp):
TATTATCACTAT
Found at i:20624942 original size:15 final size:16
Alignment explanation
Indices: 20624922--20624962 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
20624912 TCTACTATTA
20624922 TATTTATTATTA-TAT
1 TATTTATTATTACTAT
*
20624937 TATTTATTATCACTAT
1 TATTTATTATTACTAT
20624953 TA-TTATTATT
1 TATTTATTATT
20624963 TTTTATCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (16 bp):
TATTTATTATTACTAT
Found at i:20624962 original size:22 final size:22
Alignment explanation
Indices: 20624929--20624977 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
20624919 TTATATTTAT
20624929 TATTA-TATTATTTATTATCAC
1 TATTATTATTATTTATTATCAC
* *
20624950 TATTATTATTATTTTTTATCAT
1 TATTATTATTATTTATTATCAC
20624972 TATTAT
1 TATTAT
20624978 ACATATATGC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (22 bp):
TATTATTATTATTTATTATCAC
Found at i:20625149 original size:28 final size:30
Alignment explanation
Indices: 20625116--20625182 Score: 77
Period size: 28 Copynumber: 2.3 Consensus size: 30
20625106 TTTTTTAAAA
* *
20625116 TATTATATTTTTCATA-TATTATGTAT-TTT
1 TATTATATTTATCATATTATT-CGTATATTT
*
20625145 T-TTATATATATCATATTATTCGTATATTT
1 TATTATATTTATCATATTATTCGTATATTT
20625174 TATTATATT
1 TATTATATT
20625183 ATGTATTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
28 16 0.52
29 9 0.29
30 6 0.19
ACGTcount: A:0.30, C:0.04, G:0.03, T:0.63
Consensus pattern (30 bp):
TATTATATTTATCATATTATTCGTATATTT
Found at i:20625161 original size:37 final size:37
Alignment explanation
Indices: 20625101--20625172 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
20625091 CTTGTATTGG
* *
20625101 GTATATTTTTTAAAATATTATATTTTTCATATATTAT
1 GTATATTTTTTAAAATATCATATTATTCATATATTAT
* *
20625138 GTAT-TTTTTTATATATATCATATTATTCGTATATT
1 GTATATTTTTTA-AAATATCATATTATTCATATATT
20625173 TTATTATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 7 0.23
37 23 0.77
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (37 bp):
GTATATTTTTTAAAATATCATATTATTCATATATTAT
Found at i:20625216 original size:45 final size:47
Alignment explanation
Indices: 20625130--20625219 Score: 132
Period size: 47 Copynumber: 2.0 Consensus size: 47
20625120 ATATTTTTCA
*
20625130 TATATTATGTATTTTTTTATATATATCATATTATTCGTATATTTTAT
1 TATATTATGTATTTTTTTATATATATCATATTATTCATATATTTTAT
*
20625177 TATATTATGTATTTTTTTA-ATA-ATTATATTATGT-ATATATTTT
1 TATATTATGTATTTTTTTATATATATCATATTAT-TCATATATTTT
20625220 TAAATATCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
45 17 0.43
46 4 0.10
47 19 0.47
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62
Consensus pattern (47 bp):
TATATTATGTATTTTTTTATATATATCATATTATTCATATATTTTAT
Found at i:20625266 original size:26 final size:26
Alignment explanation
Indices: 20625237--20625330 Score: 95
Period size: 26 Copynumber: 3.7 Consensus size: 26
20625227 CATACTATTC
*
20625237 ATATATTTTTATGTTATTTCATGTAT
1 ATATATTTTTATATTATTTCATGTAT
20625263 ATATATTTTTATATTA-TT-A-GTTAT
1 ATATATTTTTATATTATTTCATG-TAT
* *
20625287 AAATATTTTTTATACTATTTCATGTAT
1 ATATA-TTTTTATATTATTTCATGTAT
* * *
20625314 GTCTTTTTTTATATTAT
1 ATATATTTTTATATTAT
20625331 CCTTATTATT
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
23 1 0.02
24 8 0.15
25 12 0.22
26 28 0.51
27 5 0.09
28 1 0.02
ACGTcount: A:0.29, C:0.04, G:0.05, T:0.62
Consensus pattern (26 bp):
ATATATTTTTATATTATTTCATGTAT
Found at i:20637122 original size:39 final size:39
Alignment explanation
Indices: 20637078--20637197 Score: 98
Period size: 40 Copynumber: 2.9 Consensus size: 39
20637068 ATTATGCTTG
* *
20637078 AAAAAAGAAAATCAAGATGAAAAACTGAAAAGGGCATCTT
1 AAAAAA-AAGATCAAGATGAAAAACCGAAAAGGGCATCTT
* * *
20637118 AAAAAAAAGGATCAAGGTGAAAACCCGAAAAGGGCGTCTT
1 AAAAAAAA-GATCAAGATGAAAAACCGAAAAGGGCATCTT
* * *
20637158 GATTAACACAAAAGATTAGGATGAAAATCC-AAAAGGGCAT
1 -A--AA-A-AAAAGATCAAGATGAAAAACCGAAAAGGGCAT
20637198 TCTAATGAAG
Statistics
Matches: 64, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
39 2 0.03
40 32 0.50
41 1 0.02
43 11 0.17
44 14 0.22
45 4 0.06
ACGTcount: A:0.52, C:0.12, G:0.21, T:0.15
Consensus pattern (39 bp):
AAAAAAAAGATCAAGATGAAAAACCGAAAAGGGCATCTT
Found at i:20637122 original size:40 final size:40
Alignment explanation
Indices: 20637078--20637157 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
20637068 ATTATGCTTG
*
20637078 AAAAAAGAA-AATCAAGATGAAAAACTGAAAAGGGCATCTT
1 AAAAAA-AAGAATCAAGATGAAAAACCGAAAAGGGCATCTT
* * * *
20637118 AAAAAAAAGGATCAAGGTGAAAACCCGAAAAGGGCGTCTT
1 AAAAAAAAGAATCAAGATGAAAAACCGAAAAGGGCATCTT
20637158 GATTAACACA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
39 2 0.06
40 32 0.94
ACGTcount: A:0.53, C:0.12, G:0.21, T:0.14
Consensus pattern (40 bp):
AAAAAAAAGAATCAAGATGAAAAACCGAAAAGGGCATCTT
Found at i:20639204 original size:142 final size:142
Alignment explanation
Indices: 20638948--20639232 Score: 552
Period size: 142 Copynumber: 2.0 Consensus size: 142
20638938 TAATACACAT
*
20638948 TTGACTTACCTAAATGTTTTAAAAGCCAATAAAAGGAGGATCGCATTTTGAACTTTGTCCAAATT
1 TTGACTTACCTAAATGTTTTAAAAGCCAATAAAAGGAGGATCGCATTTTGAACTCTGTCCAAATT
20639013 TTTAATTTTCGACATTTAAGACACTAATTAATTGATTAAGTACCAATTTTGGGCGTGTCGATGGT
66 TTTAATTTTCGACATTTAAGACACTAATTAATTGATTAAGTACCAATTTTGGGCGTGTCGATGGT
20639078 GCTAATCCTTCC
131 GCTAATCCTTCC
20639090 TTGACTTACCTAAATGTTTTAAAAGCCAATAAAAGGAGGATCGCATTTTGAACTCTGTCCAAATT
1 TTGACTTACCTAAATGTTTTAAAAGCCAATAAAAGGAGGATCGCATTTTGAACTCTGTCCAAATT
*
20639155 TTTAATTTTCGGCATTTAAGACACTAATTAATTGATTAAGTACCAATTTTGGGCGTGTCGATGGT
66 TTTAATTTTCGACATTTAAGACACTAATTAATTGATTAAGTACCAATTTTGGGCGTGTCGATGGT
20639220 GCTAATCCTTCC
131 GCTAATCCTTCC
20639232 T
1 T
20639233 CGTACGTAAC
Statistics
Matches: 141, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
142 141 1.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.36
Consensus pattern (142 bp):
TTGACTTACCTAAATGTTTTAAAAGCCAATAAAAGGAGGATCGCATTTTGAACTCTGTCCAAATT
TTTAATTTTCGACATTTAAGACACTAATTAATTGATTAAGTACCAATTTTGGGCGTGTCGATGGT
GCTAATCCTTCC
Found at i:20643233 original size:24 final size:24
Alignment explanation
Indices: 20643206--20643258 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
20643196 TCAGAGGTTT
20643206 GAGCAACTGCAGGCTCAGATGCAA
1 GAGCAACTGCAGGCTCAGATGCAA
20643230 GAGCAACTGCAGGCTCAGATGCAA
1 GAGCAACTGCAGGCTCAGATGCAA
20643254 GAGCA
1 GAGCA
20643259 GTTGGCTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.34, C:0.25, G:0.30, T:0.11
Consensus pattern (24 bp):
GAGCAACTGCAGGCTCAGATGCAA
Found at i:20652178 original size:135 final size:133
Alignment explanation
Indices: 20651065--20652151 Score: 1467
Period size: 133 Copynumber: 8.1 Consensus size: 133
20651055 GATTACAGAT
* *
20651065 ATCATCAGCCTTATCTTCACTGAGTAGGAGTGGACCAGGCTAAATACCAGATCTTATCTTCGCTG
1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATACCAGATCTTATCTTCGCTG
* * * *
20651130 AGCAGAAGTGAAGCAGATCAAATTTTGGAGAATCTAATCTCCACGTACTGGCGATGGAGCAGATT
66 AGCAGGAGTGAAGCAGATCAAATTTTGGAGAATCTTATCTCCACGTACCGGCAATGGAGCAGATT
20651195 CCA
131 CCA
* *
20651198 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGGGCAGGCTAAATACTAGATCTTATCTTCGCTG
1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATACCAGATCTTATCTTCGCTG
* * * * *
20651263 AGCAAGAGTGGAGCAGATCAAATTTTGGTGAATCTTATCTCCATGTATCGGCAATGGAGCAGATT
66 AGCAGGAGTGAAGCAGATCAAATTTTGGAGAATCTTATCTCCACGTACCGGCAATGGAGCAGATT
*
20651328 TCA
131 CCA
* * * * *
20651331 ACCACCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTATATACTAGATCTTATCTTCGTTG
1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATACCAGATCTTATCTTCGCTG
** * **
20651396 AGCAGGAGCAAAGCAGATCAAATTTT-GATGAATCTTATCTCCATGTATTGGCAATGGAGCAGAT
66 AGCAGGAGTGAAGCAGATCAAATTTTGGA-GAATCTTATCTCCACGTACCGGCAATGGAGCAGAT
20651460 TCCA
130 TCCA
* *
20651464 ATCATCAGCCTTATCTTCACTGAGTAGGAGTGGAGCAGGCTAAATACCAGGTCTTATCTTCGCTG
1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATACCAGATCTTATCTTCGCTG
* * * ** * *
20651529 AGCAGGAGCGGAGCAGATCAAATTTTGGTGAATCTTATCTCCACGTACCGGTGATAGAACAGATT
66 AGCAGGAGTGAAGCAGATCAAATTTTGGAGAATCTTATCTCCACGTACCGGCAATGGAGCAGATT
20651594 CCA
131 CCA
* *
20651597 ATCATCAGCCTTATCTTCACTGAGCAAGAGTGGAGCAGGCTAAATACCAGATCTTATCTTCACTG
1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATACCAGATCTTATCTTCGCTG
*
20651662 AGCAGGAGTGAAGCAGATCGAATTTTGGAGAATCTTATCTCCACGTACCGGCAATGGAGCAGATT
66 AGCAGGAGTGAAGCAGATCAAATTTTGGAGAATCTTATCTCCACGTACCGGCAATGGAGCAGATT
20651727 CCA
131 CCA
* * **
20651730 ATCATCAACCTTATCTTCACTGTGCAGGAGTGGAGCAGGCTAAATATACCAGATCTTATCTTCAT
1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCT-AA-ATACCAGATCTTATCTTCGC
* * * *
20651795 TGAGCAGGAGTGAAGCAGATCGAATTTTGGA-ATATCTTACCTCTACGTACCGGCGATGGAGCAG
64 TGAGCAGGAGTGAAGCAGATCAAATTTTGGAGA-ATCTTATCTCCACGTACCGGCAATGGAGCAG
20651859 ATTCCA
128 ATTCCA
** * * *
20651865 ATCATCAGATTTATCTTCACTGAGCAGAAGTGGAGCAGGCTAAATATACCAGGTCTTATCTTTGC
1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCT-AA-ATACCAGATCTTATCTTCGC
* * * * * * *
20651930 TGAGCAGGAGCGGAGCAGATCAAATTTTGGTGAATCTTATCTCCATGTATCGACAATGGAGCAGG
64 TGAGCAGGAGTGAAGCAGATCAAATTTTGGAGAATCTTATCTCCACGTACCGGCAATGGAGCAGA
*
20651995 TTTCA
129 TTCCA
** * * * **
20652000 GCCATCAACCTTATCTTCACTAAGCAGGAGTGGAGCAGACTAAATATACCAGATCTTATCTTCAT
1 ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCT-AA-ATACCAGATCTTATCTTCGC
* * **
20652065 TGAGCAGGAGTGAAGCAGATCGAATTTTGGAGAATTTTATCTCCACGTACCGGTGATGGAGCAGA
64 TGAGCAGGAGTGAAGCAGATCAAATTTTGGAGAATCTTATCTCCACGTACCGGCAATGGAGCAGA
20652130 TTCCA
129 TTCCA
*
20652135 ATCATCAGCTTTATCTT
1 ATCATCAGCCTTATCTT
20652152 TACTAAACAG
Statistics
Matches: 837, Mismatches: 111, Indels: 10
0.87 0.12 0.01
Matches are distributed among these distances:
132 1 0.00
133 511 0.61
134 4 0.00
135 320 0.38
136 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (133 bp):
ATCATCAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAATACCAGATCTTATCTTCGCTG
AGCAGGAGTGAAGCAGATCAAATTTTGGAGAATCTTATCTCCACGTACCGGCAATGGAGCAGATT
CCA
Found at i:20652256 original size:85 final size:85
Alignment explanation
Indices: 20652154--20652358 Score: 342
Period size: 85 Copynumber: 2.4 Consensus size: 85
20652144 TTTATCTTTA
* *
20652154 CTAAACAGTAGGGTAACAGGCTAAAATTTACGGATCCTGGCTCTCCGAGCAGTGGTGGAGCAGGT
1 CTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCCTGGCTCTCCGAGCAGTGGTGGAGCAGGT
20652219 CGAAGA-TCCGCCTTAACCCC
66 CGAAGACT-CGCCTTAACCCC
20652239 CTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCCTGGCTCTCCGAGCAGTGGTGGAGCAGGT
1 CTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCCTGGCTCTCCGAGCAGTGGTGGAGCAGGT
*
20652304 CGAAGACTCGCCTTAATCCC
66 CGAAGACTCGCCTTAACCCC
* *
20652324 CTAAGCAATAGGGTAACAGGTTAAAA-TTACAGATC
1 CTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATC
20652359 TTATCTTCGT
Statistics
Matches: 114, Mismatches: 5, Indels: 3
0.93 0.04 0.02
Matches are distributed among these distances:
84 9 0.08
85 104 0.91
86 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.21
Consensus pattern (85 bp):
CTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCCTGGCTCTCCGAGCAGTGGTGGAGCAGGT
CGAAGACTCGCCTTAACCCC
Found at i:20654156 original size:45 final size:44
Alignment explanation
Indices: 20654051--20654157 Score: 162
Period size: 44 Copynumber: 2.4 Consensus size: 44
20654041 AATACCTTCA
*
20654051 TTTTTTT-GTATATTATTTACTTTTAATCTTTCATGCATATATT
1 TTTTTTTCTTATATTATTTACTTTTAATCTTTCATGCATATATT
*
20654094 TTTTTTTCTTATATTATTTACTTTTAATCTTTTATGCATATATT
1 TTTTTTTCTTATATTATTTACTTTTAATCTTTCATGCATATATT
* *
20654138 TTTTTCTTCTTTTTTTATTT
1 TTTTT-TTCTTATATTATTT
20654158 TTGATACAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
43 7 0.12
44 39 0.67
45 12 0.21
ACGTcount: A:0.20, C:0.09, G:0.03, T:0.68
Consensus pattern (44 bp):
TTTTTTTCTTATATTATTTACTTTTAATCTTTCATGCATATATT
Found at i:20655652 original size:14 final size:15
Alignment explanation
Indices: 20655633--20655694 Score: 76
Period size: 14 Copynumber: 4.3 Consensus size: 15
20655623 NNNNNNATAA
20655633 TATTATTATTATAT-
1 TATTATTATTATATG
20655647 TATTATTATTATTAT-
1 TATTATTATTA-TATG
*
20655662 TATTATTAGTATATG
1 TATTATTATTATATG
*
20655677 TTTTATTA-TATATG
1 TATTATTATTATATG
20655691 TATT
1 TATT
20655695 TATTTTTAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
14 23 0.53
15 20 0.47
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (15 bp):
TATTATTATTATATG
Found at i:20655685 original size:3 final size:3
Alignment explanation
Indices: 20655633--20655669 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
20655623 NNNNNNATAA
20655633 TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
20655670 GTATATGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:20655931 original size:27 final size:26
Alignment explanation
Indices: 20655884--20655977 Score: 100
Period size: 27 Copynumber: 3.6 Consensus size: 26
20655874 ATTATATTAC
* *
20655884 ATTTTTTACATATTATCTTATGTATAT
1 ATTTTTTA-ATACTATATTATGTATAT
*
20655911 ATTTTTTAATAACTATATTATGTATGT
1 ATTTTTTAAT-ACTATATTATGTATAT
** * *
20655938 ATTTTTTAACGCTATATTATGTACAC
1 ATTTTTTAATACTATATTATGTATAT
20655964 A-TTTTTAATACTAT
1 ATTTTTTAATACTAT
20655978 GTATATACCT
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
25 11 0.20
26 15 0.27
27 30 0.54
ACGTcount: A:0.32, C:0.09, G:0.05, T:0.54
Consensus pattern (26 bp):
ATTTTTTAATACTATATTATGTATAT
Found at i:20656085 original size:22 final size:21
Alignment explanation
Indices: 20656037--20656130 Score: 54
Period size: 22 Copynumber: 4.4 Consensus size: 21
20656027 GTATATATTC
20656037 ATATATCATTATTATTAGTTTT
1 ATATAT-ATTATTATTAGTTTT
20656059 -T-TATATTATTATT-GTTTT
1 ATATATATTATTATTAGTTTT
*
20656077 CAATATATATTGTATATATA-TTTT
1 --ATATATATTAT-TAT-TAGTTTT
* * *
20656101 TTAATCTAGTATTA-TATGTTTT
1 AT-ATATATTATTATTA-GTTTT
20656123 ATATATAT
1 ATATATAT
20656131 ATATATGTTC
Statistics
Matches: 54, Mismatches: 8, Indels: 21
0.65 0.10 0.25
Matches are distributed among these distances:
18 5 0.09
19 9 0.17
20 5 0.09
21 6 0.11
22 15 0.28
23 9 0.17
24 5 0.09
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.60
Consensus pattern (21 bp):
ATATATATTATTATTAGTTTT
Found at i:20656087 original size:19 final size:19
Alignment explanation
Indices: 20656044--20656087 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
20656034 TTCATATATC
**
20656044 ATTATTATTAGTTTTTTAT
1 ATTATTATTAGTTTTCAAT
20656063 ATTATTATT-GTTTTCAAT
1 ATTATTATTAGTTTTCAAT
20656081 ATATATT
1 AT-TATT
20656088 GTATATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.64
Consensus pattern (19 bp):
ATTATTATTAGTTTTCAAT
Found at i:20656137 original size:19 final size:18
Alignment explanation
Indices: 20656089--20656139 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
20656079 ATATATATTG
* *
20656089 TATATATATTTTTTAATC
1 TATATATATGTTTTAATA
20656107 TAGTATTATATGTTTTATATA
1 TA-TA-TATATGTTTTA-ATA
20656128 TATATATATGTT
1 TATATATATGTT
20656140 CACTACTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 2 0.07
19 10 0.36
20 12 0.43
21 4 0.14
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.59
Consensus pattern (18 bp):
TATATATATGTTTTAATA
Found at i:20658324 original size:31 final size:29
Alignment explanation
Indices: 20658260--20658328 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
20658250 ACGATACCGT
* ** *
20658260 AAGTGACTAAAATGTAACATTTCAAATAG
1 AAGTGACTAAAATGTAAAATGACAAATAA
20658289 AAGTGACTAAAATGTAAAATGAGACAAATAA
1 AAGTGACTAAAATGTAAAAT--GACAAATAA
20658320 AAGTGACTA
1 AAGTGACTA
20658329 TTTTAATAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 19 0.56
31 15 0.44
ACGTcount: A:0.52, C:0.09, G:0.16, T:0.23
Consensus pattern (29 bp):
AAGTGACTAAAATGTAAAATGACAAATAA
Found at i:20664652 original size:43 final size:44
Alignment explanation
Indices: 20664544--20664663 Score: 131
Period size: 43 Copynumber: 2.8 Consensus size: 44
20664534 ATAGGATTCT
* * *
20664544 GATATGTGATTTACGTGTAAGACCATGTCTGGGACATCGACATC
1 GATATGTGAGTTACATGTAAGACCATGTCTGGGACATCGACACC
* * * *
20664588 G-TATATAAGTT-CATGTAAGACCTTGTCTGGGACAGT-GGCACC
1 GATATGTGAGTTACATGTAAGACCATGTCTGGGACA-TCGACACC
*
20664630 GATATGTGA-TTACATGTAAGACCACGTCTGGGAC
1 GATATGTGAGTTACATGTAAGACCATGTCTGGGAC
20664664 GTTGGCGTTA
Statistics
Matches: 62, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
42 28 0.45
43 33 0.53
44 1 0.02
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (44 bp):
GATATGTGAGTTACATGTAAGACCATGTCTGGGACATCGACACC
Found at i:20666336 original size:20 final size:20
Alignment explanation
Indices: 20666299--20666336 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
20666289 AAAATGTGTG
*
20666299 AATTTGGCTTGATGTTTGCA
1 AATTTGGCTTGATATTTGCA
20666319 AATTTGG-TTGAGTATTTG
1 AATTTGGCTTGA-TATTTG
20666337 TAAAGAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.21, C:0.05, G:0.26, T:0.47
Consensus pattern (20 bp):
AATTTGGCTTGATATTTGCA
Found at i:20667592 original size:20 final size:20
Alignment explanation
Indices: 20667509--20667593 Score: 75
Period size: 20 Copynumber: 4.2 Consensus size: 20
20667499 AGATGCAAAA
*
20667509 CAGGGGCACAGATGTGCAAT
1 CAGGGGCACCGATGTGCAAT
* * *
20667529 CAAGGGTATCGATGTGCAAAT
1 CAGGGGCACCGATGTGC-AAT
* * *
20667550 -AGGGGTACCGATGTGAAAA
1 CAGGGGCACCGATGTGCAAT
20667569 CAGGGGCA-CGATTGTGCAAT
1 CAGGGGCACCGA-TGTGCAAT
20667589 CAGGG
1 CAGGG
20667594 ATACTAAAGT
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
19 5 0.10
20 43 0.84
21 3 0.06
ACGTcount: A:0.31, C:0.16, G:0.35, T:0.18
Consensus pattern (20 bp):
CAGGGGCACCGATGTGCAAT
Found at i:20669862 original size:27 final size:26
Alignment explanation
Indices: 20669832--20669890 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
20669822 TTTTAAATTT
*
20669832 TATTTTACAAATTATTTATAATTTATA
1 TATTTTACAAATTATATAT-ATTTATA
** *
20669859 TATTTTTTAATTTATATATATTTATA
1 TATTTTACAAATTATATATATTTATA
*
20669885 TTTTTT
1 TATTTT
20669891 TAACTTGGAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 12 0.44
27 15 0.56
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (26 bp):
TATTTTACAAATTATATATATTTATA
Found at i:20669887 original size:16 final size:17
Alignment explanation
Indices: 20669844--20669884 Score: 66
Period size: 16 Copynumber: 2.5 Consensus size: 17
20669834 TTTTACAAAT
20669844 TATTTATAATTTATATA
1 TATTTATAATTTATATA
*
20669861 T-TTTTTAATTTATATA
1 TATTTATAATTTATATA
20669877 TATTTATA
1 TATTTATA
20669885 TTTTTTTAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TATTTATAATTTATATA
Found at i:20670232 original size:24 final size:25
Alignment explanation
Indices: 20670192--20670242 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
20670182 AATCCCTCTG
*
20670192 TTCGGATCCCTCGGTTTCTCCCACT
1 TTCGGATCCCTCCGTTTCTCCCACT
*
20670217 TTCGGAT-CCTCCGTTTCTCCCTCT
1 TTCGGATCCCTCCGTTTCTCCCACT
20670241 TT
1 TT
20670243 TTCGCCGGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.06, C:0.39, G:0.14, T:0.41
Consensus pattern (25 bp):
TTCGGATCCCTCCGTTTCTCCCACT
Found at i:20671015 original size:34 final size:34
Alignment explanation
Indices: 20670976--20671067 Score: 130
Period size: 34 Copynumber: 2.7 Consensus size: 34
20670966 ACTTAGGAAC
* * *
20670976 TTGTGAATGAGTAATGGTTTACTGTGGAGGAAAG
1 TTGTGAATGAGTGATGGTTTACTCTGAAGGAAAG
*
20671010 TTGTGAATGAGTGATGTTTTACTCTGAAGGAAAG
1 TTGTGAATGAGTGATGGTTTACTCTGAAGGAAAG
* *
20671044 TTGTTAATGATTGATGGTTTACTC
1 TTGTGAATGAGTGATGGTTTACTC
20671068 CAGGGTCTAG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.27, C:0.05, G:0.29, T:0.38
Consensus pattern (34 bp):
TTGTGAATGAGTGATGGTTTACTCTGAAGGAAAG
Found at i:20686063 original size:55 final size:54
Alignment explanation
Indices: 20685957--20686083 Score: 132
Period size: 55 Copynumber: 2.3 Consensus size: 54
20685947 CGAGCCTGCC
* * *
20685957 AAAACAATACGGGCGTGCGAAACGCCCGTGTGGAAGAACCGTGGGTGAACCTATT
1 AAAACAACACGGGCGTGCGAAACGCCCGTGT-GAAAAACCGTGGGTAAACCTATT
* *
20686012 AAAACAACACGGGCGTTCGACACGCCCGTGT-AAAACACC-TGTGGTCAAACCTATT
1 AAAACAACACGGGCGTGCGAAACGCCCGTGTGAAAA-ACCGTG-GGT-AAACCTATT
** *
20686067 AAATTAACAGGGGCGTG
1 AAAACAACACGGGCGTG
20686084 AGGCTTGCAC
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
53 5 0.08
54 6 0.10
55 49 0.82
ACGTcount: A:0.32, C:0.24, G:0.27, T:0.17
Consensus pattern (54 bp):
AAAACAACACGGGCGTGCGAAACGCCCGTGTGAAAAACCGTGGGTAAACCTATT
Found at i:20686470 original size:47 final size:48
Alignment explanation
Indices: 20686399--20686495 Score: 178
Period size: 47 Copynumber: 2.0 Consensus size: 48
20686389 TTGACGCCCA
*
20686399 ATCTCTTTCCCTTAGTGTTTGTTTACTCCTTTCACTTCTATTTTACTT
1 ATCTCTTTCCCTTAGCGTTTGTTTACTCCTTTCACTTCTATTTTACTT
20686447 ATCT-TTTCCCTTAGCGTTTGTTTACTCCTTTCACTTCTATTTTACTT
1 ATCTCTTTCCCTTAGCGTTTGTTTACTCCTTTCACTTCTATTTTACTT
20686494 AT
1 AT
20686496 TTCTAATAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 44 0.92
48 4 0.08
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (48 bp):
ATCTCTTTCCCTTAGCGTTTGTTTACTCCTTTCACTTCTATTTTACTT
Found at i:20696997 original size:67 final size:67
Alignment explanation
Indices: 20696915--20697050 Score: 245
Period size: 67 Copynumber: 2.0 Consensus size: 67
20696905 AATAAGAGAC
*
20696915 GTTTATAATTGAGTTAAAGCTGTACTGCAACTCGAAAAAATTTTAAATTTTTATTATGTCTATTC
1 GTTTATAATTAAGTTAAAGCTGTACTGCAACTCGAAAAAATTTTAAATTTTTATTATGTCTATTC
20696980 AA
66 AA
* *
20696982 GTTTATAATTAAGTTAAAGTTGTACTGCAACTCGAAAAAATTTTAAATTTTTATTATGTTTATTC
1 GTTTATAATTAAGTTAAAGCTGTACTGCAACTCGAAAAAATTTTAAATTTTTATTATGTCTATTC
20697047 AA
66 AA
20697049 GT
1 GT
20697051 GTTTCTCCTC
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.43
Consensus pattern (67 bp):
GTTTATAATTAAGTTAAAGCTGTACTGCAACTCGAAAAAATTTTAAATTTTTATTATGTCTATTC
AA
Found at i:20700975 original size:17 final size:17
Alignment explanation
Indices: 20700953--20700991 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
20700943 ACCAAAATAC
20700953 AAAAAAATACAATAAAT
1 AAAAAAATACAATAAAT
* * *
20700970 AAAAAAATCCATTAATT
1 AAAAAAATACAATAAAT
20700987 AAAAA
1 AAAAA
20700992 GTCCTTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAAAAATACAATAAAT
Found at i:20701296 original size:17 final size:18
Alignment explanation
Indices: 20701264--20701297 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
20701254 TGCAAAAGGG
20701264 ACAAACACAGCAGCAAAT
1 ACAAACACAGCAGCAAAT
20701282 ACAAACACA-CAGCAAA
1 ACAAACACAGCAGCAAA
20701298 ACAGACAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.59, C:0.29, G:0.09, T:0.03
Consensus pattern (18 bp):
ACAAACACAGCAGCAAAT
Found at i:20704068 original size:131 final size:131
Alignment explanation
Indices: 20703752--20704109 Score: 337
Period size: 131 Copynumber: 2.7 Consensus size: 131
20703742 AACTATTAAG
* * * * *
20703752 AATCCTTTAAAACGAAGGCGATATTCGATATTTGGTAATTTGTGGAATCGTGCCCTAACGTGTTG
1 AATCCTTTAAAACGAAGGCGATACTCGAT-TTTGGCAATTCGCGGAATCGTGCCCTAACGTGCTG
* * * * * * *
20703817 GGTTGTAATTTCTCGTTTGCTCAAAGTAATCGAAGGTCCCTTTAAAATTTTATCCATGTCTTTTA
65 GGTTGCAACTTCTCGTTTGCTCAAAATAATCAAAGGTCCCTTCAAAATTTCATCCATGTCTTCTA
20703882 AA
130 AA
* * * * *
20703884 AATCCCTT-AAACGAAGGTGAT-GTGCAATTATTGGCAATTCGCGGAAACGTGCCCTAACGTGCT
1 AATCCTTTAAAACGAAGGCGATACT-CGATT-TTGGCAATTCGCGGAATCGTGCCCTAACGTGCT
* * * * **
20703947 GGGTTGCGACTTCTTGTTTGTTTAAAATAATCAAATTTCCCTTCAAAATTTCA-CTCATGTCTTC
64 GGGTTGCAACTTCTCGTTTGCTCAAAATAATCAAAGGTCCCTTCAAAATTTCATC-CATGTCTTC
20704011 TAAA
128 TAAA
* * * * *
20704015 AATCCTTTAAAACGAAGGCAATACTCGGTGTTTGACAATTCG-GGAATCATGCCCTATCGTGCTG
1 AATCCTTTAAAACGAAGGCGATACTCGAT-TTTGGCAATTCGCGGAATCGTGCCCTAACGTGCTG
*** * * *
20704079 GGTTATGATTTCTCATTTGCTCAAAACAATC
65 GGTTGCAACTTCTCGTTTGCTCAAAATAATC
20704110 GAATATTCCT
Statistics
Matches: 180, Mismatches: 40, Indels: 13
0.77 0.17 0.06
Matches are distributed among these distances:
130 3 0.02
131 145 0.81
132 30 0.17
133 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (131 bp):
AATCCTTTAAAACGAAGGCGATACTCGATTTTGGCAATTCGCGGAATCGTGCCCTAACGTGCTGG
GTTGCAACTTCTCGTTTGCTCAAAATAATCAAAGGTCCCTTCAAAATTTCATCCATGTCTTCTAA
A
Found at i:20705189 original size:10 final size:10
Alignment explanation
Indices: 20705174--20705203 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
20705164 TTTGAAATAT
20705174 TTTAATATAA
1 TTTAATATAA
20705184 TTTAATATAA
1 TTTAATATAA
20705194 TTTAATATAA
1 TTTAATATAA
20705204 AATATTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
TTTAATATAA
Found at i:20705199 original size:15 final size:15
Alignment explanation
Indices: 20705176--20705251 Score: 59
Period size: 15 Copynumber: 5.3 Consensus size: 15
20705166 TGAAATATTT
*
20705176 TAATATAATTTAATA
1 TAATATAATTTAAAA
* *
20705191 TAATTTAATATAAAA
1 TAATATAATTTAAAA
* *
20705206 T-ATTTAATTT-CAA
1 TAATATAATTTAAAA
20705219 -AATATAATTTAAAA
1 TAATATAATTTAAAA
* * *
20705233 TAAAATATTTTAATA
1 TAATATAATTTAAAA
20705248 TAAT
1 TAAT
20705252 TATATTAAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 6
0.73 0.17 0.09
Matches are distributed among these distances:
13 10 0.21
14 10 0.21
15 27 0.57
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (15 bp):
TAATATAATTTAAAA
Found at i:20705266 original size:25 final size:26
Alignment explanation
Indices: 20705185--20705271 Score: 70
Period size: 32 Copynumber: 3.2 Consensus size: 26
20705175 TTAATATAAT
*
20705185 TTAATATAATTTAATATAAAATATTTAA
1 TTAATATAATTTAAAATAAAATA-TT-A
20705213 TTTCAAAATATAATTTAAAATAAAATATT-
1 -TT---AATATAATTTAAAATAAAATATTA
* *
20705242 TTAATATAA-TTATATTAAAACTATTA
1 TTAATATAATTTAAAATAAAA-TATTA
20705268 TTAA
1 TTAA
20705272 AATATGATTA
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
24 9 0.18
25 11 0.22
26 4 0.08
28 2 0.04
29 2 0.04
31 2 0.04
32 20 0.40
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (26 bp):
TTAATATAATTTAAAATAAAATATTA
Found at i:20706997 original size:32 final size:32
Alignment explanation
Indices: 20706956--20707019 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
20706946 AATAGGCCTA
20706956 ACCTTTGCTCATTCTAATCATCCCACATTTGC
1 ACCTTTGCTCATTCTAATCATCCCACATTTGC
20706988 ACCTTTGCTCATTCTAATCATCCCACATTTGC
1 ACCTTTGCTCATTCTAATCATCCCACATTTGC
20707020 CATTCTCTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.22, C:0.34, G:0.06, T:0.38
Consensus pattern (32 bp):
ACCTTTGCTCATTCTAATCATCCCACATTTGC
Found at i:20707420 original size:18 final size:18
Alignment explanation
Indices: 20707397--20707450 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
20707387 CCATTTACGA
20707397 CACTATTCATGTATACAG
1 CACTATTCATGTATACAG
*
20707415 CACTATTCATGTATACGG
1 CACTATTCATGTATACAG
* * *
20707433 TACTGTTCACGTATACAG
1 CACTATTCATGTATACAG
20707451 TAGTTGGGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (18 bp):
CACTATTCATGTATACAG
Found at i:20713057 original size:26 final size:26
Alignment explanation
Indices: 20713028--20713081 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
20713018 AATTGGTAGT
*
20713028 AAAATGTAAAAATAAATTGTTATGTC
1 AAAATGTAAAAATAAATTGCTATGTC
20713054 AAAATGTAAAAATAAATTGCTATGTC
1 AAAATGTAAAAATAAATTGCTATGTC
20713080 AA
1 AA
20713082 TATGAGTGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.52, C:0.06, G:0.11, T:0.31
Consensus pattern (26 bp):
AAAATGTAAAAATAAATTGCTATGTC
Found at i:20713257 original size:3 final size:3
Alignment explanation
Indices: 20713249--20713530 Score: 279
Period size: 3 Copynumber: 94.7 Consensus size: 3
20713239 ATAAACAAGA
* * * *
20713249 AAT AAT AAT AGT AA- AAA AAT AAT AAT AGT AAT AAT GAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
20713296 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AGA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
* *
20713341 AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT AGT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
20713389 AAT TAT TAT AAT AAT AAT AAT AAT AGT AA- ATAC AAT AAT AAC AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT
* * * * *
20713434 AGT AAT AAT AAT AAT AGAA AAT AAT AGT AAT AGT AAA AAT AAT AAT
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * ** *
20713480 AAT AGT AGT AAT AAT AA- ATT AATT AAT TTT AAT AAT AA- AAT AGT
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT
20713524 AA- AAT AA
1 AAT AAT AA
20713531 AAAAAAGGCT
Statistics
Matches: 229, Mismatches: 40, Indels: 20
0.79 0.14 0.07
Matches are distributed among these distances:
2 9 0.04
3 213 0.93
4 7 0.03
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:20713535 original size:8 final size:8
Alignment explanation
Indices: 20713218--20713534 Score: 103
Period size: 9 Copynumber: 36.9 Consensus size: 8
20713208 TAAATAAGCC
20713218 AATAAAAT
1 AATAAAAT
**
20713226 TTTAAAAT
1 AATAAAAT
20713234 AA-AAAAT
1 AATAAAAT
20713241 AA-ACAAGA-
1 AATA-AA-AT
20713249 AATAATAAT
1 AATAA-AAT
*
20713258 AGTAAAA-
1 AATAAAAT
*
20713265 AA-ATAAT
1 AATAAAAT
*
20713272 AATAGTAAT
1 AATA-AAAT
*
20713281 AATGATAAT
1 AAT-AAAAT
20713290 AATAATAAT
1 AATAA-AAT
20713299 AATAATAAT
1 AATAA-AAT
20713308 AATAATAAT
1 AATAA-AAT
20713317 AATAATAAT
1 AATAA-AAT
*
20713326 AATAATAGT
1 AATAA-AAT
20713335 AATAGAAAT
1 AATA-AAAT
20713344 AATAATAAT
1 AATAA-AAT
20713353 AATAATAAT
1 AATAA-AAT
*
20713362 AGTAATAAT
1 AATAA-AAT
*
20713371 AATAGTAAT
1 AATA-AAAT
20713380 AATAATAAT
1 AATAA-AAT
**
20713389 AATTATTAT
1 AA-TAAAAT
20713398 AATAATAAT
1 AATAA-AAT
*
20713407 AATAATAGT
1 AATAA-AAT
*
20713416 AAATACAAT
1 -AATAAAAT
20713425 AATAACAAT
1 AATAA-AAT
*
20713434 AGT--AAT
1 AATAAAAT
20713440 AATAATAAT
1 AATAA-AAT
*
20713449 -AGAAAAT
1 AATAAAAT
*
20713456 AATAGTAAT
1 AATA-AAAT
*
20713465 AGTAAAAAT
1 AAT-AAAAT
20713474 AATAATAAT
1 AATAA-AAT
* *
20713483 AGTAGTAAT
1 AATA-AAAT
*
20713492 AATAAATT
1 AATAAAAT
20713500 AATTAATTTTAAT
1 AA-TAA----AAT
20713513 AATAAAAT
1 AATAAAAT
*
20713521 AGTAAAAT
1 AATAAAAT
20713529 AA-AAAA
1 AATAAAA
20713535 AAGGCTAAAT
Statistics
Matches: 240, Mismatches: 38, Indels: 63
0.70 0.11 0.18
Matches are distributed among these distances:
6 8 0.03
7 18 0.08
8 45 0.19
9 153 0.64
10 9 0.04
12 3 0.01
13 4 0.02
ACGTcount: A:0.63, C:0.01, G:0.05, T:0.31
Consensus pattern (8 bp):
AATAAAAT
Found at i:20715053 original size:44 final size:44
Alignment explanation
Indices: 20714997--20715263 Score: 159
Period size: 44 Copynumber: 6.0 Consensus size: 44
20714987 ATCCTGCTCT
* * *
20714997 ACTGCAACTTCAGAGAGATAAGGATTGTGGCTTCGATCTGCTCC
1 ACTGTAACTTCAGAGAGATAAGGATTGTAGCTTCGATCTACTCC
* * *
20715041 AATGTAATTTCAGGGAGA-AGAGG-TATGTAGCTTCGATCTACTCC
1 ACTGTAACTTCAGAGAGATA-AGGAT-TGTAGCTTCGATCTACTCC
* * * * * ** * * *
20715085 GCTGGAACTTCAAAGAGGTAAGAATTGGTAATTTCAACCTGCTCC
1 ACTGTAACTTCAGAGAGATAAGGATT-GTAGCTTCGATCTACTCC
* * * ** * *
20715130 ACTGCAACTTCA-AGGAGATAAGGTTTGT-GTATTTTTATCCTGCTCT
1 ACTGTAACTTCAGA-GAGATAAGGATTGTAG--CTTCGAT-CTACTCC
* *
20715176 ACTGTAACTTCAGAGAGATAAGGATTGTGGCTTCTATCTACTCC
1 ACTGTAACTTCAGAGAGATAAGGATTGTAGCTTCGATCTACTCC
* * *
20715220 AATGTAATTTCAG-G-GAGAAGAGATTTGTAGCTTCGATCTACTCC
1 ACTGTAACTTCAGAGAGATAAG-GA-TTGTAGCTTCGATCTACTCC
20715264 GCTAGAACTT
Statistics
Matches: 170, Mismatches: 40, Indels: 26
0.72 0.17 0.11
Matches are distributed among these distances:
42 5 0.03
43 5 0.03
44 85 0.50
45 43 0.25
46 30 0.18
47 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (44 bp):
ACTGTAACTTCAGAGAGATAAGGATTGTAGCTTCGATCTACTCC
Found at i:20715185 original size:46 final size:46
Alignment explanation
Indices: 20714968--20715204 Score: 141
Period size: 44 Copynumber: 5.3 Consensus size: 46
20714958 ACTGAGGGAA
* * * *
20714968 ATAAGGTTTGTGTATTTTTATCCTGCTCTACTGCAACTTC-AGAGAG
1 ATAAGGATTGTGTACTTTGATCCTGCTCCACTGCAACTTCAAG-GAG
* * * * * *
20715014 ATAAGGATTGTG-GCTTCGAT-CTGCTCCAATGTAATTTCAGGGAG
1 ATAAGGATTGTGTACTTTGATCCTGCTCCACTGCAACTTCAAGGAG
* * * * * *
20715058 A-AGAGG--TATGTAGCTTCGAT-CTACTCCGCTGGAACTTCAAAGAG
1 ATA-AGGATTGTGTA-CTTTGATCCTGCTCCACTGCAACTTCAAGGAG
* * * * *
20715102 GTAAGAATTG-GTAATTTCAACCTGCTCCACTGCAACTTCAAGGAG
1 ATAAGGATTGTGTACTTTGATCCTGCTCCACTGCAACTTCAAGGAG
* * * * *
20715147 ATAAGGTTTGTGTATTTTTATCCTGCTCTACTGTAACTTC-AGAGAG
1 ATAAGGATTGTGTACTTTGATCCTGCTCCACTGCAACTTCAAG-GAG
20715193 ATAAGGATTGTG
1 ATAAGGATTGTG
20715205 GCTTCTATCT
Statistics
Matches: 142, Mismatches: 39, Indels: 20
0.71 0.19 0.10
Matches are distributed among these distances:
42 3 0.02
43 1 0.01
44 50 0.35
45 38 0.27
46 50 0.35
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (46 bp):
ATAAGGATTGTGTACTTTGATCCTGCTCCACTGCAACTTCAAGGAG
Found at i:20715208 original size:179 final size:178
Alignment explanation
Indices: 20714822--20715335 Score: 734
Period size: 179 Copynumber: 2.9 Consensus size: 178
20714812 GTTCCAATCC
* * * * *
20714822 ACTGCATCTTCAGAG-GTATAAGAATTG-GTGCTTCGATAC-GCTCCAATGTAATTTTAGAGAAA
1 ACTGCAACTTCAGAGAG-ATAAGGATTGTG-GCTTCGAT-CTGCTCCAATGTAATTTCAGGGAGA
* * * * *
20714884 AGAGTTTTGTAGCTTCGACCTACTCCACTGAAACTTCAAGGAGATAAGAATTGGTAATTTCAACT
63 AGAGATTTGTAGCTTCGATCTACTCCGCTGGAACTTCAAGGAGGTAAGAATTGGTAATTTCAACT
* * *
20714949 TGCCCCACT--AC-TGAGGGAAATAAGGTTTGTGTATTTTTATCCTGCTCT
128 TGCTCCACTCAACTTCAGGGAGATAAGGTTTGTGTATTTTTATCCTGCTCT
20714997 ACTGCAACTTCAGAGAGATAAGGATTGTGGCTTCGATCTGCTCCAATGTAATTTCAGGGAGAAGA
1 ACTGCAACTTCAGAGAGATAAGGATTGTGGCTTCGATCTGCTCCAATGTAATTTCAGGGAGAAGA
* * * *
20715062 GGTATGTAGCTTCGATCTACTCCGCTGGAACTTCAAAGAGGTAAGAATTGGTAATTTCAACCTGC
66 GATTTGTAGCTTCGATCTACTCCGCTGGAACTTCAAGGAGGTAAGAATTGGTAATTTCAACTTGC
*
20715127 TCCACTGCAACTTCAAGGAGATAAGGTTTGTGTATTTTTATCCTGCTCT
131 TCCACT-CAACTTCAGGGAGATAAGGTTTGTGTATTTTTATCCTGCTCT
* * *
20715176 ACTGTAACTTCAGAGAGATAAGGATTGTGGCTTCTATCTACTCCAATGTAATTTCAGGGAGAAGA
1 ACTGCAACTTCAGAGAGATAAGGATTGTGGCTTCGATCTGCTCCAATGTAATTTCAGGGAGAAGA
* *
20715241 GATTTGTAGCTTCGATCTACTCCGCTAGAACTTCAAGGAGGTAAGAACTGGTAATTTCAACTTGC
66 GATTTGTAGCTTCGATCTACTCCGCTGGAACTTCAAGGAGGTAAGAATTGGTAATTTCAACTTGC
20715306 TCCACTACAACTTCAGGGAGATAAGGTTTG
131 TCCACT-CAACTTCAGGGAGATAAGGTTTG
20715336 CGGCTTGTAG
Statistics
Matches: 304, Mismatches: 28, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
174 1 0.00
175 116 0.38
176 2 0.01
178 2 0.01
179 183 0.60
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (178 bp):
ACTGCAACTTCAGAGAGATAAGGATTGTGGCTTCGATCTGCTCCAATGTAATTTCAGGGAGAAGA
GATTTGTAGCTTCGATCTACTCCGCTGGAACTTCAAGGAGGTAAGAATTGGTAATTTCAACTTGC
TCCACTCAACTTCAGGGAGATAAGGTTTGTGTATTTTTATCCTGCTCT
Found at i:20716103 original size:46 final size:46
Alignment explanation
Indices: 20716053--20716196 Score: 198
Period size: 46 Copynumber: 3.1 Consensus size: 46
20716043 GGTTTCTTTC
* * * *
20716053 ATCCACCCCACTGCAACTCAAGGCTATAGGATTTGTATCACCTTCA
1 ATCCATCCCACTGCAACTCAGGGATATAGGATTTGTATCATCTTCA
*
20716099 ATCCATCCCACTGCAACTCAGGGATATGGGATTTGTATCATCTTCA
1 ATCCATCCCACTGCAACTCAGGGATATAGGATTTGTATCATCTTCA
* * * * *
20716145 ATTCATCCCACTGTAACTCAGGGGTACAGGATTTGTATCTTCTTCA
1 ATCCATCCCACTGCAACTCAGGGATATAGGATTTGTATCATCTTCA
20716191 ATCCAT
1 ATCCAT
20716197 TGATCTGTGT
Statistics
Matches: 86, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 86 1.00
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (46 bp):
ATCCATCCCACTGCAACTCAGGGATATAGGATTTGTATCATCTTCA
Found at i:20722532 original size:26 final size:25
Alignment explanation
Indices: 20722503--20722562 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
20722493 TTTTAAAATA
20722503 AAAAATAAACAAGAAATAATAATAGT
1 AAAAATAAACAA-AAATAATAATAGT
* * *
20722529 AAAAAAATAATAATAATAATAATAGT
1 AAAAATA-AACAAAAATAATAATAGT
*
20722555 AATAATAA
1 AAAAATAA
20722563 TAGTAATAGT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
25 1 0.04
26 23 0.82
27 4 0.14
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (25 bp):
AAAAATAAACAAAAATAATAATAGT
Found at i:20722638 original size:3 final size:3
Alignment explanation
Indices: 20722517--20722617 Score: 87
Period size: 3 Copynumber: 33.7 Consensus size: 3
20722507 ATAAACAAGA
* * *
20722517 AAT AAT AAT AGT AA- AAA AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * * *
20722564 AGT AAT AGT AGAA AAT AAT AGT AAT AGT AAA AAT AAC AAT AAT AGT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
20722610 AAT AAT AA
1 AAT AAT AA
20722618 ATTAATAAAT
Statistics
Matches: 75, Mismatches: 21, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
2 2 0.03
3 72 0.96
4 1 0.01
ACGTcount: A:0.63, C:0.01, G:0.08, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:20733357 original size:17 final size:18
Alignment explanation
Indices: 20733328--20733370 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
20733318 AAATTAATTT
20733328 TTTTA-AAAAAATTAT-A
1 TTTTATAAAAAATTATAA
*
20733344 TTTTATAAATAATTATAA
1 TTTTATAAAAAATTATAA
*
20733362 TTTAATAAA
1 TTTTATAAA
20733371 CCAAAAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 5 0.22
17 9 0.39
18 9 0.39
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTTATAAAAAATTATAA
Found at i:20736555 original size:85 final size:85
Alignment explanation
Indices: 20736412--20736581 Score: 331
Period size: 85 Copynumber: 2.0 Consensus size: 85
20736402 CAAGGCCTAG
20736412 CTTGCACCCTGGCTATACCTCAGATACTTCAGGATTTTGGTACTAGTGTTTCACTTGCACTCTTG
1 CTTGCACCCTGGCTATACCTCAGATACTTCAGGATTTTGGTACTAGTGTTTCACTTGCACTCTTG
20736477 TTTTCGATCGGTTTTGCCTC
66 TTTTCGATCGGTTTTGCCTC
*
20736497 CTTGCCCCCTGGCTATACCTCAGATACTTCAGGATTTTGGTACTAGTGTTTCACTTGCACTCTTG
1 CTTGCACCCTGGCTATACCTCAGATACTTCAGGATTTTGGTACTAGTGTTTCACTTGCACTCTTG
20736562 TTTTCGATCGGTTTTGCCTC
66 TTTTCGATCGGTTTTGCCTC
20736582 ACTTTGGTCA
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 84 1.00
ACGTcount: A:0.15, C:0.26, G:0.19, T:0.40
Consensus pattern (85 bp):
CTTGCACCCTGGCTATACCTCAGATACTTCAGGATTTTGGTACTAGTGTTTCACTTGCACTCTTG
TTTTCGATCGGTTTTGCCTC
Found at i:20736704 original size:13 final size:13
Alignment explanation
Indices: 20736667--20736705 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
20736657 TCTGCTTAAC
20736667 TTTGAATTTTGATT
1 TTTGAATTTT-ATT
*
20736681 TTAGAATTTTATT
1 TTTGAATTTTATT
*
20736694 TTTGAAATTTAT
1 TTTGAATTTTAT
20736706 GATTCTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
TTTGAATTTTATT
Found at i:20743571 original size:42 final size:42
Alignment explanation
Indices: 20743512--20743600 Score: 151
Period size: 42 Copynumber: 2.1 Consensus size: 42
20743502 TTCTAATTGG
*
20743512 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAATATAAAA
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAA
*
20743554 GAAAATAGTTTCCTTATTCTAATAAACTACTAAAAGATAAAA
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAA
*
20743596 TAAAA
1 GAAAA
20743601 ATATTCTTAG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.52, C:0.12, G:0.06, T:0.30
Consensus pattern (42 bp):
GAAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAA
Found at i:20743647 original size:19 final size:18
Alignment explanation
Indices: 20743625--20743664 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 18
20743615 TGAATAAAAC
20743625 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAA-AT
20743644 TTATCTACCTAAATAAAT
1 TTATCTACCTAAATAAAT
20743662 TTA
1 TTA
20743665 AAATATATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (18 bp):
TTATCTACCTAAATAAAT
Found at i:20747530 original size:42 final size:42
Alignment explanation
Indices: 20747471--20747558 Score: 140
Period size: 42 Copynumber: 2.1 Consensus size: 42
20747461 CCTAATTGGT
* *
20747471 AAAATAGTTCCCTTATTCTAATAAACTACTCAAATATAAAAG
1 AAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAAG
* *
20747513 AAAATAGTTCTCTTATTCTAATAAACTACTAAAAGATAAAAT
1 AAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAAG
20747555 AAAA
1 AAAA
20747559 ATATTCTTAG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.31
Consensus pattern (42 bp):
AAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAAG
Found at i:20747605 original size:19 final size:19
Alignment explanation
Indices: 20747583--20748401 Score: 1538
Period size: 19 Copynumber: 43.2 Consensus size: 19
20747573 TGAATAAAAC
20747583 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20747602 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20747621 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20747640 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20747659 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20747678 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20747697 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20747716 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20747735 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20747754 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20747773 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20747792 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20747811 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20747830 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20747849 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20747868 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20747887 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20747906 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20747925 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20747944 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20747963 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20747982 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20748001 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20748020 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20748039 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20748058 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20748077 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20748096 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20748115 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20748134 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20748153 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20748172 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20748191 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20748210 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20748229 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20748248 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20748267 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20748286 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20748305 TTATCTACCTAAATAA-ATT
1 TTATCTACCTAAATAAGA-T
** * * *
20748324 CTTAGAATA--TGAATAAAAC
1 -TTA-TCTACCTAAATAAGAT
20748343 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20748362 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAAGAT
20748381 TTATCTACCTAAATAA-AT
1 TTATCTACCTAAATAAGAT
20748399 TTA
1 TTA
20748402 AAATATATAC
Statistics
Matches: 785, Mismatches: 9, Indels: 13
0.97 0.01 0.02
Matches are distributed among these distances:
17 2 0.00
18 9 0.01
19 768 0.98
20 4 0.01
21 2 0.00
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.37
Consensus pattern (19 bp):
TTATCTACCTAAATAAGAT
Found at i:20754738 original size:53 final size:53
Alignment explanation
Indices: 20754657--20754758 Score: 188
Period size: 53 Copynumber: 1.9 Consensus size: 53
20754647 ATCGACATTT
20754657 CATCAAAGAAAAGTTAACTGCCCGCATCTTAGGCTTAAGTCATGTAGCCACTG
1 CATCAAAGAAAAGTTAACTGCCCGCATCTTAGGCTTAAGTCATGTAGCCACTG
20754710 CATCAAAGAAAAGTTAACTG-CCGACATCTTAGGCTTAAGTCATGTAGCC
1 CATCAAAGAAAAGTTAACTGCCCG-CATCTTAGGCTTAAGTCATGTAGCC
20754759 TCTGACAAGC
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
52 3 0.06
53 45 0.94
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.25
Consensus pattern (53 bp):
CATCAAAGAAAAGTTAACTGCCCGCATCTTAGGCTTAAGTCATGTAGCCACTG
Found at i:20755332 original size:22 final size:22
Alignment explanation
Indices: 20755304--20755348 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
20755294 ACCCCGAAAC
*
20755304 TCTTAAGTGTTACTTTTAGTAA
1 TCTTAAGTGCTACTTTTAGTAA
20755326 TCTTAAGTGCTACTTTTAGTAA
1 TCTTAAGTGCTACTTTTAGTAA
20755348 T
1 T
20755349 AATAAGAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.11, G:0.13, T:0.49
Consensus pattern (22 bp):
TCTTAAGTGCTACTTTTAGTAA
Found at i:20755354 original size:22 final size:22
Alignment explanation
Indices: 20755307--20755354 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
20755297 CCGAAACTCT
* **
20755307 TAAGTGTTACTTTTAGTAATCT
1 TAAGTGCTACTTTTAGTAATAA
20755329 TAAGTGCTACTTTTAGTAATAA
1 TAAGTGCTACTTTTAGTAATAA
20755351 TAAG
1 TAAG
20755355 AAAGAATGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.44
Consensus pattern (22 bp):
TAAGTGCTACTTTTAGTAATAA
Found at i:20759267 original size:14 final size:14
Alignment explanation
Indices: 20759248--20759277 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
20759238 AAGATTGTAT
20759248 TATTCAAACGGATA
1 TATTCAAACGGATA
20759262 TATTCAAACGGATA
1 TATTCAAACGGATA
20759276 TA
1 TA
20759278 AAGCCAGGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (14 bp):
TATTCAAACGGATA
Found at i:20760126 original size:19 final size:19
Alignment explanation
Indices: 20760102--20760140 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
20760092 TTTTGGATTG
20760102 ATTCTAATTAAATCCTCTT
1 ATTCTAATTAAATCCTCTT
20760121 ATTCTAATTAAATCCTCTT
1 ATTCTAATTAAATCCTCTT
20760140 A
1 A
20760141 GTTCATAGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.21, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTCTAATTAAATCCTCTT
Found at i:20761104 original size:26 final size:24
Alignment explanation
Indices: 20761074--20761123 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
20761064 AAATAAAAAA
*
20761074 ATTTAAAAATATAATAAATCAAATAT
1 ATTTAAAAACATAA-AAA-CAAATAT
20761100 ATTTAAAAACATAAAAACAAATAT
1 ATTTAAAAACATAAAAACAAATAT
20761124 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (24 bp):
ATTTAAAAACATAAAAACAAATAT
Found at i:20761143 original size:21 final size:21
Alignment explanation
Indices: 20761094--20761152 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
20761084 ATAATAAATC
*
20761094 AAAT-ATATTTAAAA-ACATAA
1 AAATAATA-TTAAAACAAATAA
*
20761114 AAACAAATATTAAAACAAATAA
1 AAA-TAATATTAAAACAAATAA
*
20761136 AAATAATACTAAAACAA
1 AAATAATATTAAAACAA
20761153 TTCTTAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 3 0.09
21 18 0.56
22 11 0.34
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.22
Consensus pattern (21 bp):
AAATAATATTAAAACAAATAA
Found at i:20761229 original size:15 final size:16
Alignment explanation
Indices: 20761199--20761231 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
20761189 AAATGGTTAT
20761199 ATTAAAAATTTAAAATA
1 ATTAAAAA-TTAAAATA
20761216 ATTAAAAA-TAAAATA
1 ATTAAAAATTAAAATA
20761231 A
1 A
20761232 AACAATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATTAAAAATTAAAATA
Found at i:20762331 original size:131 final size:129
Alignment explanation
Indices: 20762137--20762609 Score: 443
Period size: 131 Copynumber: 3.6 Consensus size: 129
20762127 GTTTCACAAT
* * * * * *
20762137 TTTTAAGAATCCTTTAAAACGAAGGCGATATTCGA-TACATGGTAAGTCGAGGAATAGTGCCCTA
1 TTTTAAAAATCCTTTAAAACGAAGGCG--AGTCGATTA-TTGGCAATTCGA-GAATCGTGCCCTA
* * * ** *
20762201 ACGTGTTGGGTTGCAATTTCTCGTTTGCTCAAAGTAATCGAAGGTCCCTTTAGAATTTCACCCAT
62 ACGTGCTGGGTTGCAACTTCTCGTTTGCTCAAAATAATCGAATATCCCTTTAGAATTTCACTCAT
20762266 GTC
127 GTC
*
20762269 TTTTAAAAATCCCTT-AAACGAAGGCGATGTGCGATTATTGGCAATTCGCAGAATCGTGCCCTAA
1 TTTTAAAAATCCTTTAAAACGAAGGCGA-GT-CGATTATTGGCAATTCG-AGAATCGTGCCCTAA
* * * * *
20762333 CGTGCTGGGTTGCAACTTCTCGTTTGCTTAAAATAATCAAATATCCCTTCAAAATCTCACTCATG
63 CGTGCTGGGTTGCAACTTCTCGTTTGCTCAAAATAATCGAATATCCCTTTAGAATTTCACTCATG
20762398 TC
128 TC
* * * * * * *
20762400 TTCTAAAAATCCTTTAAAACGAAGGCAAGACTCG-GTATTTGACAATTCGGGAATCATGCCCTAT
1 TTTTAAAAATCCTTTAAAACGAAGGC--GAGTCGATTA-TTGGCAATTCGAGAATCGTGCCCTAA
** * * * **
20762464 CGTGCTGGGTTGTGACTTCTCGTTTGTTCAAAACAATCGAATATTCCTTTAGGTTTTCACTCATG
63 CGTGCTGGGTTGCAACTTCTCGTTTGCTCAAAATAATCGAATATCCCTTTAGAATTTCACTCATG
*
20762529 TTT
128 -TC
*
20762532 TTTTAAGGAAA-CCTTTTAAAACAAAGGCGACGTTCGATGT-TTGGCAATTCGAGAATCGTGCCC
1 TTTTAA--AAATCC-TTTAAAACGAAGGCGA-G-TCGAT-TATTGGCAATTCGAGAATCGTGCCC
*
20762595 TATCGTGCTGGGTTG
60 TAACGTGCTGGGTTG
20762610 TGCTTTTTCA
Statistics
Matches: 279, Mismatches: 46, Indels: 30
0.79 0.13 0.08
Matches are distributed among these distances:
129 1 0.00
130 1 0.00
131 171 0.61
132 46 0.16
133 3 0.01
134 56 0.20
136 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (129 bp):
TTTTAAAAATCCTTTAAAACGAAGGCGAGTCGATTATTGGCAATTCGAGAATCGTGCCCTAACGT
GCTGGGTTGCAACTTCTCGTTTGCTCAAAATAATCGAATATCCCTTTAGAATTTCACTCATGTC
Found at i:20762603 original size:134 final size:131
Alignment explanation
Indices: 20762183--20762743 Score: 390
Period size: 131 Copynumber: 4.2 Consensus size: 131
20762173 ACATGGTAAG
* * * ** * * ** ** *
20762183 TCGAGGAATAGTGCCCTAACGTGTTGGGTTGCAATTTCTCGTTTGCTCAAAGTAATCGAAGGTCC
1 TCGA-GAATCGTGCCCTATCGTGCTGGGTTGTGACTTCTCGTTTGTTCAAAACAATCGAATATTC
* * * * * *
20762248 CTTTAGAATTTCACCCATGTCTTT-TAAAAATCC-CTT-AAACGAAGGCGATGTGCGAT-TATTG
65 CTTTAGGATTTCACTCATGT-TTTCTAAAAA-CCTTTTAAAACAAAGGCGACGTTCGATGT-TTG
20762309 GCAAT
127 GCAAT
* ** * * *
20762314 TCGCAGAATCGTGCCCTAACGTGCTGGGTTGCAACTTCTCGTTTGCTT-AAAATAATCAAATATC
1 TCG-AGAATCGTGCCCTATCGTGCTGGGTTGTGACTTCTCGTTTG-TTCAAAACAATCGAATATT
* ** * * * * *
20762378 CCTTCAAAATCTCACTCATGTCTTCTAAAAATCC-TTTAAAACGAAGGCAAGAC--TCGGTATTT
64 CCTTTAGGATTTCACTCATGTTTTCTAAAAA-CCTTTTAAAACAAAGGC--GACGTTCGATGTTT
*
20762440 GACAAT
126 GGCAAT
* *
20762446 TCGGGAATCATGCCCTATCGTGCTGGGTTGTGACTTCTCGTTTGTTCAAAACAATCGAATATTCC
1 TCGAGAATCGTGCCCTATCGTGCTGGGTTGTGACTTCTCGTTTGTTCAAAACAATCGAATATTCC
* *
20762511 TTTAGGTTTTCACTCATGTTTTTTTAAGGAAACCTTTTAAAACAAAGGCGACGTTCGATGTTTGG
66 TTTAGGATTTCACTCATG-TTTTCTAA--AAACCTTTTAAAACAAAGGCGACGTTCGATGTTTGG
20762576 CAAT
128 CAAT
* ** * * *
20762580 TCGAGAATCGTGCCCTATCGTGCTGGGTTGTG-CTTTTTCACTTGTTCAGAACGATCGAAGA-TC
1 TCGAGAATCGTGCCCTATCGTGCTGGGTTGTGAC-TTCTCGTTTGTTCAAAACAATCGAATATTC
* * * * ** *
20762643 CCTTCGGAATTTCACTCACGTTTTCTAAAAAAAACTCTTTAAAACGAAA-GAAATGTTCGATGTT
65 CTTTAGG-ATTTCACTCATGTTTTCT--AAAAACCT-TTTAAAAC-AAAGGCGACGTTCGATGTT
* *
20762707 TGGAAAC
125 TGGCAAT
20762714 TCGAGGAATCGTGCCCTA-CTGTGCTGGGTT
1 TCGA-GAATCGTGCCCTATC-GTGCTGGGTT
20762744 TCGGTTTTCG
Statistics
Matches: 352, Mismatches: 56, Indels: 40
0.79 0.12 0.09
Matches are distributed among these distances:
130 4 0.01
131 144 0.41
132 34 0.10
133 21 0.06
134 121 0.34
135 28 0.08
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.33
Consensus pattern (131 bp):
TCGAGAATCGTGCCCTATCGTGCTGGGTTGTGACTTCTCGTTTGTTCAAAACAATCGAATATTCC
TTTAGGATTTCACTCATGTTTTCTAAAAACCTTTTAAAACAAAGGCGACGTTCGATGTTTGGCAA
T
Found at i:20767054 original size:3 final size:3
Alignment explanation
Indices: 20767032--20767101 Score: 63
Period size: 3 Copynumber: 23.0 Consensus size: 3
20767022 GTACAATTTG
20767032 TAA TAA -AA TATA TAAA TAA TAA TAA TAA TAGA TAA -AA TAA TAA TAA
1 TAA TAA TAA TA-A T-AA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
* * * *
20767078 TAG GAA TAG TAA TAG TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
20767102 GAACAATATA
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
2 4 0.07
3 42 0.78
4 7 0.13
5 1 0.02
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:20767206 original size:14 final size:15
Alignment explanation
Indices: 20767182--20767210 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20767172 CAAATAGATG
20767182 AATAGATAATAATAA
1 AATAGATAATAATAA
20767197 AATA-ATAATAATAA
1 AATAGATAATAATAA
20767211 TGGCATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (15 bp):
AATAGATAATAATAA
Found at i:20769648 original size:17 final size:16
Alignment explanation
Indices: 20769617--20769671 Score: 58
Period size: 17 Copynumber: 3.4 Consensus size: 16
20769607 AATAAGAAAC
20769617 AAAGAAGAAAAAACAA
1 AAAGAAGAAAAAACAA
*
20769633 AAAGAAGCAGAAAACAA
1 AAAGAAG-AAAAAACAA
* *
20769650 AACGAA-AAAAAAAAA
1 AAAGAAGAAAAAACAA
20769665 CAAAGAA
1 -AAAGAA
20769672 CGAATCTTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
15 7 0.22
16 12 0.38
17 13 0.41
ACGTcount: A:0.78, C:0.09, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAGAAGAAAAAACAA
Found at i:20770714 original size:26 final size:25
Alignment explanation
Indices: 20770665--20770854 Score: 116
Period size: 26 Copynumber: 7.2 Consensus size: 25
20770655 AAAACTGCTA
* * *
20770665 ATATTATTCATTTTAAGTTTTTTTAT
1 ATATTATTTATTTTAA-ATATTTTAT
20770691 ATATTATTTATTTTAAATCATTTTATT
1 ATATTATTTATTTTAAAT-ATTTTA-T
** *
20770718 ATTACTTATTCTAATCCTTT-TCTATTTTAAA
1 A-TA-TTATT-T-AT--TTTAAATATTTT-AT
* *
20770749 ATATTATCTATTTTAAATATGTTACAT
1 ATATTATTTATTTTAAATAT-TT-TAT
* *
20770776 ATATTATTTATTTTAAACTATTATAC
1 ATATTATTTATTTTAAA-TATTTTAT
* *
20770802 ATATTACTTATTTTAAAT-TTTTTT
1 ATATTATTTATTTTAAATATTTTAT
*
20770826 ATCTT-TTTATTTTAAAATATTTTAT
1 ATATTATTTATTTT-AAATATTTTAT
20770851 ATAT
1 ATAT
20770855 AATAGGTATT
Statistics
Matches: 126, Mismatches: 23, Indels: 31
0.70 0.13 0.17
Matches are distributed among these distances:
23 7 0.06
24 11 0.09
25 13 0.10
26 40 0.32
27 24 0.19
28 6 0.05
29 9 0.07
30 3 0.02
31 8 0.06
32 2 0.02
33 3 0.02
ACGTcount: A:0.33, C:0.07, G:0.01, T:0.59
Consensus pattern (25 bp):
ATATTATTTATTTTAAATATTTTAT
Found at i:20770779 original size:27 final size:28
Alignment explanation
Indices: 20770749--20770805 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
20770739 CTATTTTAAA
20770749 ATATTATCTATTTTAAA-TATGT-TACAT
1 ATATTATCTATTTTAAACTAT-TATACAT
*
20770776 ATATTATTTATTTTAAACTATTATACAT
1 ATATTATCTATTTTAAACTATTATACAT
20770804 AT
1 AT
20770806 TACTTATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 17 0.63
28 10 0.37
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.53
Consensus pattern (28 bp):
ATATTATCTATTTTAAACTATTATACAT
Found at i:20771038 original size:2 final size:2
Alignment explanation
Indices: 20771031--20771055 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20771021 CCTTGGGTTT
20771031 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
20771056 TATTTAAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20774598 original size:19 final size:19
Alignment explanation
Indices: 20774576--20774613 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
20774566 ACATTAGATT
20774576 TTTAA-AATATATAAATATA
1 TTTAATAATATA-AAATATA
20774595 TTTAATAATATAAAATATA
1 TTTAATAATATAAAATATA
20774614 AAAATTAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TTTAATAATATAAAATATA
Found at i:20775953 original size:17 final size:17
Alignment explanation
Indices: 20775931--20775967 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
20775921 TAAGAAAGAA
20775931 TAATTAAAATTTTTAAT
1 TAATTAAAATTTTTAAT
*
20775948 TAATTAAATTTTTTAAT
1 TAATTAAAATTTTTAAT
20775965 TAA
1 TAA
20775968 AAATCTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TAATTAAAATTTTTAAT
Found at i:20784239 original size:37 final size:37
Alignment explanation
Indices: 20784198--20784271 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
20784188 TCATTAAACA
20784198 ACTATTACAGGTGCTAATGAAGGGTCTAATTGTCAAT
1 ACTATTACAGGTGCTAATGAAGGGTCTAATTGTCAAT
*
20784235 ACTATTGCAGGTGCTAATGAAGGGTCTAATTGTCAAT
1 ACTATTACAGGTGCTAATGAAGGGTCTAATTGTCAAT
20784272 GAGATTGATG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32
Consensus pattern (37 bp):
ACTATTACAGGTGCTAATGAAGGGTCTAATTGTCAAT
Found at i:20786074 original size:22 final size:22
Alignment explanation
Indices: 20786028--20786080 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
20786018 CATAATAAAA
**
20786028 CACATATAGATAGTTCAAGTGC
1 CACATATAGATAGTTCAAGCAC
* *
20786050 CACATATTGATAGTTTAAGCAC
1 CACATATAGATAGTTCAAGCAC
20786072 CACAT-TAGA
1 CACATATAGA
20786081 CATTTTTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 3 0.12
22 23 0.88
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (22 bp):
CACATATAGATAGTTCAAGCAC
Found at i:20786104 original size:29 final size:31
Alignment explanation
Indices: 20786071--20786133 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 31
20786061 AGTTTAAGCA
*
20786071 CCACATTAGACATTTT-T-AAAGTACATGTG
1 CCACATTAGACATTTTATGAAAGTACAGGTG
* * *
20786100 CCACATTGGATATTTTATGAAAGTATAGGTG
1 CCACATTAGACATTTTATGAAAGTACAGGTG
20786131 CCA
1 CCA
20786134 AATGTGACAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 14 0.50
30 1 0.04
31 13 0.46
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Consensus pattern (31 bp):
CCACATTAGACATTTTATGAAAGTACAGGTG
Found at i:20787206 original size:16 final size:16
Alignment explanation
Indices: 20787185--20787252 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
20787175 TTTGGTTCGC
20787185 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
20787201 TGTATTGGATTAGAGA
1 TGTATTGGATTAGAGG
*
20787217 TGTATTAGATTAGAGG
1 TGTATTGGATTAGAGG
20787233 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
20787249 TGTA
1 TGTA
20787253 ATAGCAAATC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.28, C:0.00, G:0.34, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:20787504 original size:16 final size:16
Alignment explanation
Indices: 20787480--20787521 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
20787470 AACATAATTA
20787480 TTATT-AAATA-TATT
1 TTATTAAAATATTATT
20787494 TTAATTAAAATATTTATT
1 TT-ATTAAAATA-TTATT
20787512 TTATTAAAAT
1 TTATTAAAAT
20787522 TCTTAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 2 0.08
15 3 0.12
16 5 0.21
17 8 0.33
18 6 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTATTAAAATATTATT
Found at i:20787728 original size:26 final size:26
Alignment explanation
Indices: 20787699--20787789 Score: 94
Period size: 26 Copynumber: 3.4 Consensus size: 26
20787689 TGATACTGTA
* *
20787699 AAATATAAATTAACATAATTATTATT
1 AAATATAATTTAAAATAATTATTATT
* *
20787725 AAATATATTTTAATTAA-AATATATGATT
1 AAATATAATTTAA--AATAAT-TATTATT
* *
20787753 TAATACAATTTAAAATAATTATTATT
1 AAATATAATTTAAAATAATTATTATT
20787779 AAATATAATTT
1 AAATATAATTT
20787790 CATAAAATGT
Statistics
Matches: 51, Mismatches: 10, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
26 28 0.55
27 6 0.12
28 17 0.33
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (26 bp):
AAATATAATTTAAAATAATTATTATT
Found at i:20787773 original size:120 final size:120
Alignment explanation
Indices: 20787470--20787762 Score: 523
Period size: 120 Copynumber: 2.4 Consensus size: 120
20787460 ATCATATTTA
* * * *
20787470 AACATAATTATTATTAAATATATTTTAATTAAAATATTTATTTTATTAAAATTCTTAATAATGAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
20787535 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
*
20787590 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
20787655 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
* *
20787710 AACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATACAATT
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
20787763 TAAAATAATT
Statistics
Matches: 165, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
120 165 1.00
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:20797712 original size:5 final size:5
Alignment explanation
Indices: 20797702--20797733 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
20797692 GTTAGTGTGA
20797702 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
20797734 GAACACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:20797727 original size:9 final size:9
Alignment explanation
Indices: 20797703--20797733 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
20797693 TTAGTGTGAA
20797703 AAATAAAAT
1 AAATAAAAT
20797712 AAAATAAAAT
1 -AAATAAAAT
20797722 AAATAAAAT
1 AAATAAAAT
20797731 AAA
1 AAA
20797734 GAACACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:20798862 original size:295 final size:295
Alignment explanation
Indices: 20798332--20798918 Score: 1102
Period size: 295 Copynumber: 2.0 Consensus size: 295
20798322 AAAGGCTCTT
20798332 GAGTGGAAAGATTATCTAAGCTTGTTTTACGTCTCTGAAGAAGAAGCTTCTGCACTATGGCCTTC
1 GAGTGGAAAGATTATCTAAGCTTGTTTTACGTCTCTGAAGAAGAAGCTTCTGCACTATGGCCTTC
20798397 CATCTGCAGGTAGAAAAATGTTACTTGTTAGATTTTCTTTAATCCTTAAACATCATACCATGCAT
66 CATCTGCAGGTAGAAAAATGTTACTTGTTAGATTTTCTTTAATCCTTAAACATCATACCATGCAT
20798462 CCTTTTTGTTGACAAATATATTAATAAACCTTTTTGGTATTCTTTTGTAGGGAGAAAGTGTTAGA
131 CCTTTTTGTTGACAAATATATTAATAAACCTTTTTGGTATTCTTTTGTAGGGAGAAAGTGTTAGA
* *
20798527 TTACATGAAGAAGTCTGAAGTTGTCATTAAACAACTATTACAGGTGCTAATGAAGGGCCTAAATG
196 TTACATGAAGAAGTCCGAAGTTGTCATTAAACAACTATTACAGGTGCTAATGAAGGGCCTAAACG
*
20798592 TCGATGAAATTGATGAGGCAAAAGAATCATTACTA
261 TCAATGAAATTGATGAGGCAAAAGAATCATTACTA
20798627 GAGTGGAAAGATTATCTAAGCTTGTTTTACGTCTCTGAAGAAGAAGCTTCTGCACTATGGCCTTC
1 GAGTGGAAAGATTATCTAAGCTTGTTTTACGTCTCTGAAGAAGAAGCTTCTGCACTATGGCCTTC
20798692 CATCTGCAGGTAGAAAAATGTTACTTGTTAGATTTTCTTTAATCCTTAAACATCATACCATGCAT
66 CATCTGCAGGTAGAAAAATGTTACTTGTTAGATTTTCTTTAATCCTTAAACATCATACCATGCAT
*
20798757 CCTTTTTGTTGACAAATATATTAATAAACCTTTTTGGTATTCTTTTGTAGGGAGCAAGTGTTAGA
131 CCTTTTTGTTGACAAATATATTAATAAACCTTTTTGGTATTCTTTTGTAGGGAGAAAGTGTTAGA
* *
20798822 TTACATGAAGAAGTCCGAAGTTGTCATTAAACAGCTATTACAGGTGCTAATGAAGGGTCTAAACG
196 TTACATGAAGAAGTCCGAAGTTGTCATTAAACAACTATTACAGGTGCTAATGAAGGGCCTAAACG
**
20798887 TCAATGAGGTTGATGAGGCAAAAGAATCATTA
261 TCAATGAAATTGATGAGGCAAAAGAATCATTA
20798919 TTGATGGGTT
Statistics
Matches: 284, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
295 284 1.00
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (295 bp):
GAGTGGAAAGATTATCTAAGCTTGTTTTACGTCTCTGAAGAAGAAGCTTCTGCACTATGGCCTTC
CATCTGCAGGTAGAAAAATGTTACTTGTTAGATTTTCTTTAATCCTTAAACATCATACCATGCAT
CCTTTTTGTTGACAAATATATTAATAAACCTTTTTGGTATTCTTTTGTAGGGAGAAAGTGTTAGA
TTACATGAAGAAGTCCGAAGTTGTCATTAAACAACTATTACAGGTGCTAATGAAGGGCCTAAACG
TCAATGAAATTGATGAGGCAAAAGAATCATTACTA
Done.