Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 129432109
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: 129432109
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 338 of 425
Found at i:104893241 original size:92 final size:92
Alignment explanation
Indices: 104893076--104893243 Score: 250
Period size: 92 Copynumber: 1.8 Consensus size: 92
104893066 GTCTTATAGT
* * * * *
104893076 ATCTTTCAACTATGGTCTTACTCGTTTTCTGTCATGTTGCCATGGTATCTTTCAACCATGGTCTT
1 ATCTTTCAACCATGGTCTTACACGATTTCTATCAGGTTGCCATGGTATCTTTCAACCATGGTCTT
*
104893141 ATTCATTTCATGTCACATTGCCATGGC
66 AATCATTTCATGTCACATTGCCATGGC
104893168 ATCTTTCAACCATGGTCTTACAC-ATTTCATATCAGGTTGCCATGGTATCTTTCAACCATGGTCT
1 ATCTTTCAACCATGGTCTTACACGATTTC-TATCAGGTTGCCATGGTATCTTTCAACCATGGTCT
104893232 TACAT-ATTTCAT
65 TA-ATCATTTCAT
104893244 TTCAAAGAGC
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
91 4 0.06
92 63 0.93
93 1 0.01
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.41
Consensus pattern (92 bp):
ATCTTTCAACCATGGTCTTACACGATTTCTATCAGGTTGCCATGGTATCTTTCAACCATGGTCTT
AATCATTTCATGTCACATTGCCATGGC
Found at i:104893648 original size:24 final size:23
Alignment explanation
Indices: 104893621--104893747 Score: 78
Period size: 23 Copynumber: 5.4 Consensus size: 23
104893611 ATCAGGTAGT
*
104893621 TCACAAAGAACCATATCGTGAAGC
1 TCACAAAGAACC-TATCGGGAAGC
* *
104893645 TCACGAAGAGCCTATCGGGAAGC
1 TCACAAAGAACCTATCGGGAAGC
* * * ** *
104893668 TTCAGATAGCCATATATCGGGAAGT
1 -TCACAAAG-AACCTATCGGGAAGC
* * *
104893693 TCA-AGCGAGAA-CTATCAGGAGGC
1 TCACA--AAGAACCTATCGGGAAGC
*
104893716 TCACAAAGAGCCTATCGGGAAGC
1 TCACAAAGAACCTATCGGGAAGC
104893739 TCACAAAGA
1 TCACAAAGA
104893748 GCTGTATTTC
Statistics
Matches: 76, Mismatches: 21, Indels: 13
0.69 0.19 0.12
Matches are distributed among these distances:
22 3 0.04
23 41 0.54
24 20 0.26
25 12 0.16
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.17
Consensus pattern (23 bp):
TCACAAAGAACCTATCGGGAAGC
Found at i:104895620 original size:21 final size:20
Alignment explanation
Indices: 104895589--104895629 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
104895579 CAATTTTCCC
*
104895589 TTTTCTTCTTTCTTTTCTCT
1 TTTTCTTCTTTCTTTCCTCT
104895609 TTTTCTTTCTTTCTTTCCTCT
1 TTTTC-TTCTTTCTTTCCTCT
104895630 GCTCTCTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTTCTTCTTTCTTTCCTCT
Found at i:104897579 original size:48 final size:48
Alignment explanation
Indices: 104897498--104897595 Score: 124
Period size: 48 Copynumber: 2.0 Consensus size: 48
104897488 CTTATACTTT
** *
104897498 TAAGATTTTCTGAATCTTGTGGCTCATCAATTTAAGATCGCAACCTTA
1 TAAGATTTTCTGAATCTTGTAACTCACCAATTTAAGATCGCAACCTTA
* * * * *
104897546 TAAGATTTTTTGAATCTTGTAACTCACCGATTTAATATCGTAGCCTTA
1 TAAGATTTTCTGAATCTTGTAACTCACCAATTTAAGATCGCAACCTTA
104897594 TA
1 TA
104897596 CTTAAAAGAT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (48 bp):
TAAGATTTTCTGAATCTTGTAACTCACCAATTTAAGATCGCAACCTTA
Found at i:104897940 original size:23 final size:23
Alignment explanation
Indices: 104897881--104897928 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
104897871 TAAAGCATAA
* **
104897881 CTCGTTGAATTTTCATTGTATAG
1 CTCGCTGAATTTTTGTTGTATAG
104897904 CTCGCTGAATTTTTGTTGTATAG
1 CTCGCTGAATTTTTGTTGTATAG
104897927 CT
1 CT
104897929 TGTCTAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.19, C:0.15, G:0.19, T:0.48
Consensus pattern (23 bp):
CTCGCTGAATTTTTGTTGTATAG
Found at i:104898295 original size:17 final size:16
Alignment explanation
Indices: 104898269--104898314 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
104898259 ACTTCGCTCA
*
104898269 TAGCTCGCCATCTTTGC
1 TAGCTCGCCA-CTCTGC
*
104898286 TAGCTTGCCACTCTGC
1 TAGCTCGCCACTCTGC
*
104898302 TAGCTCTCCACTC
1 TAGCTCGCCACTC
104898315 ATGCAAACTG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 16 0.64
17 9 0.36
ACGTcount: A:0.13, C:0.39, G:0.15, T:0.33
Consensus pattern (16 bp):
TAGCTCGCCACTCTGC
Found at i:104901560 original size:27 final size:27
Alignment explanation
Indices: 104901507--104901565 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
104901497 ACAATTACTT
*
104901507 AATATTATTTATTTAATTTGTTGAAAA
1 AATATTATTTATTTAATTTGATGAAAA
104901534 AATATT-TTTATTTAATTTAGAAT-AAAA
1 AATATTATTTATTTAATTT-G-ATGAAAA
104901561 AATAT
1 AATAT
104901566 ATGCTAGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 12 0.41
27 16 0.55
28 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (27 bp):
AATATTATTTATTTAATTTGATGAAAA
Found at i:104907215 original size:26 final size:24
Alignment explanation
Indices: 104907175--104907234 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
104907165 TTATTTCATT
* * *
104907175 AAATAAAAAAATTTAAAAATATAA
1 AAATAAATATATTTAAAAACATAA
104907199 TAAATCAAATATATTTAAAAACATAA
1 -AAAT-AAATATATTTAAAAACATAA
104907225 AAATAAATAT
1 AAATAAATAT
104907235 TAAAACAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.19
25 8 0.26
26 17 0.55
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.28
Consensus pattern (24 bp):
AAATAAATATATTTAAAAACATAA
Found at i:104907239 original size:20 final size:20
Alignment explanation
Indices: 104907224--104907262 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
104907214 TAAAAACATA
*
104907224 AAAATAAATATTAAAACAAAT
1 AAAAT-AATACTAAAACAAAT
104907245 AAAATAATACTAAAACAA
1 AAAATAATACTAAAACAA
104907263 TTCTTAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAATAATACTAAAACAAAT
Found at i:104907249 original size:21 final size:19
Alignment explanation
Indices: 104907216--104907262 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
104907206 AATATATTTA
* *
104907216 AAAACATAAAAATAAATATT
1 AAAACAAAAAAAT-AATACT
104907236 AAAACAAATAAAATAATACT
1 AAAACAAA-AAAATAATACT
104907256 AAAACAA
1 AAAACAA
104907263 TTCTTAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.72, C:0.09, G:0.00, T:0.19
Consensus pattern (19 bp):
AAAACAAAAAAATAATACT
Found at i:104908809 original size:19 final size:21
Alignment explanation
Indices: 104908775--104908813 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
104908765 TTCAATAATT
104908775 ATTAAATAAAATTTTAAAATC
1 ATTAAATAAAATTTTAAAATC
104908796 ATTAAA-AAAA-TTTAAAAT
1 ATTAAATAAAATTTTAAAAT
104908814 TAAATATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
20 4 0.22
21 6 0.33
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (21 bp):
ATTAAATAAAATTTTAAAATC
Found at i:104910877 original size:17 final size:17
Alignment explanation
Indices: 104910855--104910887 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
104910845 ATCCGACAAA
104910855 GCCCGATAAATGATAAT
1 GCCCGATAAATGATAAT
*
104910872 GCCCGATACATGATAA
1 GCCCGATAAATGATAA
104910888 ATGATAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.21
Consensus pattern (17 bp):
GCCCGATAAATGATAAT
Found at i:104917542 original size:10 final size:9
Alignment explanation
Indices: 104917497--104917544 Score: 53
Period size: 9 Copynumber: 5.2 Consensus size: 9
104917487 AGGTGTCAAT
104917497 ATTTTAAAAA
1 ATTTT-AAAA
*
104917507 AATTTAAAA
1 ATTTTAAAA
*
104917516 ATCTT-AAA
1 ATTTTAAAA
104917524 ATTTTAAAA
1 ATTTTAAAA
104917533 ATTATTAAAA
1 ATT-TTAAAA
104917543 AT
1 AT
104917545 AACATCCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
8 7 0.22
9 13 0.41
10 12 0.38
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (9 bp):
ATTTTAAAA
Found at i:104917940 original size:12 final size:11
Alignment explanation
Indices: 104917928--104917961 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
104917918 ATAACTTTTA
*
104917928 AATAATTTTTT
1 AATAATTATTT
104917939 AA-AATTATTT
1 AATAATTATTT
104917949 AATAATTATTT
1 AATAATTATTT
104917960 AA
1 AA
104917962 AAAAATTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
AATAATTATTT
Found at i:104917969 original size:21 final size:21
Alignment explanation
Indices: 104917928--104917969 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
104917918 ATAACTTTTA
* **
104917928 AATAATTTTTTAAAATTATTT
1 AATAATTATTTAAAAAAATTT
104917949 AATAATTATTTAAAAAAATTT
1 AATAATTATTTAAAAAAATTT
104917970 CTAGGATGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AATAATTATTTAAAAAAATTT
Found at i:104926132 original size:6 final size:6
Alignment explanation
Indices: 104926116--104926146 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
104926106 AAAGGCAACA
104926116 AAGAGTG AAGATG AAGATG AAGATG AAGATG
1 AAGA-TG AAGATG AAGATG AAGATG AAGATG
104926147 CATTACAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.83
7 4 0.17
ACGTcount: A:0.48, C:0.00, G:0.35, T:0.16
Consensus pattern (6 bp):
AAGATG
Found at i:104928072 original size:16 final size:16
Alignment explanation
Indices: 104928051--104928120 Score: 61
Period size: 16 Copynumber: 4.1 Consensus size: 16
104928041 GGTTTGAAAA
*
104928051 AAAGAAAAAGAATAAG
1 AAAGAAAAAGAAGAAG
*
104928067 AAAGAAGAAGAAGAAG
1 AAAGAAAAAGAAGAAG
104928083 AGGAAGAGAAGCAAGAAGAAG
1 A--AAGA-AA--AAGAAGAAG
*
104928104 -AAGAAGAAGAAGAAG
1 AAAGAAAAAGAAGAAG
104928119 AA
1 AA
104928121 GGAGAAGAGG
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
15 9 0.20
16 16 0.36
17 1 0.02
18 8 0.18
19 1 0.02
21 9 0.20
ACGTcount: A:0.67, C:0.01, G:0.30, T:0.01
Consensus pattern (16 bp):
AAAGAAAAAGAAGAAG
Found at i:104928076 original size:3 final size:3
Alignment explanation
Indices: 104928052--104928128 Score: 93
Period size: 3 Copynumber: 25.3 Consensus size: 3
104928042 GTTTGAAAAA
* * *
104928052 AAG AAA AAG AAT AAG AAAG AAG AAG AAG AAG AGG AAG -AG AAG CAAG
1 AAG AAG AAG AAG AAG -AAG AAG AAG AAG AAG AAG AAG AAG AAG -AAG
*
104928098 AAG AAG AAG AAG AAG AAG AAG AAG GAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
104928129 GGAAAAATGG
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
2 2 0.03
3 55 0.87
4 6 0.10
ACGTcount: A:0.65, C:0.01, G:0.32, T:0.01
Consensus pattern (3 bp):
AAG
Found at i:104929252 original size:21 final size:21
Alignment explanation
Indices: 104929219--104929266 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
104929209 GTTGGGGCAC
* *
104929219 CTTGTTGAGTTGGGGTACCCT
1 CTTGCTGACTTGGGGTACCCT
*
104929240 CTTGCTGACTTGGGGTAGCCT
1 CTTGCTGACTTGGGGTACCCT
104929261 CTTGCT
1 CTTGCT
104929267 AGGTTCGGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.08, C:0.23, G:0.31, T:0.38
Consensus pattern (21 bp):
CTTGCTGACTTGGGGTACCCT
Found at i:104930018 original size:83 final size:84
Alignment explanation
Indices: 104929926--104930102 Score: 268
Period size: 83 Copynumber: 2.1 Consensus size: 84
104929916 AAAAAAAAAC
*
104929926 TCATTGCATGCATATTAAAAAATAGGCAAC-AC-ACCAACAATCATTGCATGCATATTAAAAAAT
1 TCATTGCATGCATATTAAAAAATAGGCAACAACTACCAACAATCATTGCATACATATTAAAAAA-
104929989 AGTCAACAGCTTTCCAACAA
65 AGTCAACAGCTTTCCAACAA
* * *
104930009 TCATTGCATGCATATTAAAAAATAGTCAACAACTTTCCAATAATCATTGCATACATATTAAAAAA
1 TCATTGCATGCATATTAAAAAATAGGCAACAAC-TACCAACAATCATTGCATACATATTAAAAAA
*
104930074 AGTCAATAGCTTTCCAACAA
65 AGTCAACAGCTTTCCAACAA
*
104930094 TCACTGCAT
1 TCATTGCAT
104930103 ATGATCAGCA
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
83 29 0.34
84 2 0.02
85 27 0.32
86 27 0.32
ACGTcount: A:0.44, C:0.21, G:0.08, T:0.27
Consensus pattern (84 bp):
TCATTGCATGCATATTAAAAAATAGGCAACAACTACCAACAATCATTGCATACATATTAAAAAAA
GTCAACAGCTTTCCAACAA
Found at i:104930020 original size:43 final size:43
Alignment explanation
Indices: 104929926--104930102 Score: 263
Period size: 43 Copynumber: 4.2 Consensus size: 43
104929916 AAAAAAAAAC
* *
104929926 TCATTGCATGCATATTAAAAAATAGGCAACA-C--ACCAACAA
1 TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
104929966 TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
1 TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
* *
104930009 TCATTGCATGCATATTAAAAAATAGTCAACAACTTTCCAATAA
1 TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
* *
104930052 TCATTGCATACATATTAAAAAA-AGTCAATAGCTTTCCAACAA
1 TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
*
104930094 TCACTGCAT
1 TCATTGCAT
104930103 ATGATCAGCA
Statistics
Matches: 125, Mismatches: 9, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
40 30 0.24
41 1 0.01
42 25 0.20
43 69 0.55
ACGTcount: A:0.44, C:0.21, G:0.08, T:0.27
Consensus pattern (43 bp):
TCATTGCATGCATATTAAAAAATAGTCAACAGCTTTCCAACAA
Found at i:104930102 original size:85 final size:83
Alignment explanation
Indices: 104929930--104930102 Score: 258
Period size: 85 Copynumber: 2.1 Consensus size: 83
104929920 AAAAACTCAT
*
104929930 TGCATGCATATTAAAAAATAGGCAACACACCAACAATCATTGCATGCATATTAAAAAATAGTCAA
1 TGCATGCATATTAAAAAATAGGCAACACACCAACAATCATTGCATACATATTAAAAAATAGTCAA
*
104929995 CAGCTTTCCAACAATCAT
66 CAGCTTTCCAACAATCAC
* * *
104930013 TGCATGCATATTAAAAAATAGTCAACAACTTTCCAATAATCATTGCATACATATTAAAAAA-AGT
1 TGCATGCATATTAAAAAATAGGCAAC-AC--ACCAACAATCATTGCATACATATTAAAAAATAGT
*
104930077 CAATAGCTTTCCAACAATCAC
63 CAACAGCTTTCCAACAATCAC
104930098 TGCAT
1 TGCAT
104930103 ATGATCAGCA
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
83 25 0.31
84 2 0.02
85 27 0.33
86 27 0.33
ACGTcount: A:0.44, C:0.21, G:0.09, T:0.27
Consensus pattern (83 bp):
TGCATGCATATTAAAAAATAGGCAACACACCAACAATCATTGCATACATATTAAAAAATAGTCAA
CAGCTTTCCAACAATCAC
Found at i:104931774 original size:15 final size:15
Alignment explanation
Indices: 104931743--104931784 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
104931733 CATTACTATT
*
104931743 ACTACCAGACGA-TTC
1 ACTACCAGAC-ACATC
*
104931758 ACTCCCAGACACATC
1 ACTACCAGACACATC
104931773 ACTACCAGACAC
1 ACTACCAGACAC
104931785 GTTTTCTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 1 0.04
15 22 0.96
ACGTcount: A:0.36, C:0.40, G:0.10, T:0.14
Consensus pattern (15 bp):
ACTACCAGACACATC
Found at i:104932188 original size:46 final size:46
Alignment explanation
Indices: 104932078--104932180 Score: 188
Period size: 46 Copynumber: 2.2 Consensus size: 46
104932068 GGATACAAAC
*
104932078 AATGACAGATATACACAATAAACATCAGTTTAATAATGTATAATTT
1 AATGACAGATATACACAATAAACATCAGTTTAATAATATATAATTT
*
104932124 AATGGCAGATATACACAATAAACATCAGTTTAATAATATATAATTT
1 AATGACAGATATACACAATAAACATCAGTTTAATAATATATAATTT
104932170 AATGACAGATA
1 AATGACAGATA
104932181 CAAACAATGG
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 54 1.00
ACGTcount: A:0.49, C:0.11, G:0.10, T:0.31
Consensus pattern (46 bp):
AATGACAGATATACACAATAAACATCAGTTTAATAATATATAATTT
Found at i:104932449 original size:64 final size:62
Alignment explanation
Indices: 104932124--104932564 Score: 561
Period size: 62 Copynumber: 7.0 Consensus size: 62
104932114 TGTATAATTT
* *
104932124 AATGGCAGATATACACAATAAACATCAGTTTAATAATATATAATT-TAATGACAGATACAAAC
1 AATGGCAGATATACACAATAAACATCAGTTTAATAAT-GATAATTATAATGGCAGATACAAAC
104932186 AATGGCAGATATACACAATAAACATCAGTTTAATAATGTATAATT-TAATGGCAGATACAAAC
1 AATGGCAGATATACACAATAAACATCAGTTTAATAATG-ATAATTATAATGGCAGATACAAAC
*
104932248 AATGGCAGATATACACAATAAACATCAGTGTAATAATGTATAATT-TAATGGCAGATACAAAC
1 AATGGCAGATATACACAATAAACATCAGTTTAATAATG-ATAATTATAATGGCAGATACAAAC
*
104932310 AATTGCAGATATACACAATAAACATCAGTTTAATAATGTATAATT-TAATGGCAGATACAAAC
1 AATGGCAGATATACACAATAAACATCAGTTTAATAATG-ATAATTATAATGGCAGATACAAAC
* * * * *
104932372 AATGGCAGATATACACAATAAACATCAATTTGATAATGACATTTATACAATGGAAGATACAAAC
1 AATGGCAGATATACACAATAAACATCAGTTTAATAATGATAATTAT--AATGGCAGATACAAAC
* * * * *
104932436 AATGGCAGATATACACAATAAAGATCAGTTTGATAATGGCATTCA-TACAATGACAGATACAAAC
1 AATGGCAGATATACACAATAAACATCAGTTTAATAAT-G-A-TAATTATAATGGCAGATACAAAC
* * * * *
104932500 AATGGCAGATACACACAATAAAGATCAGTTTGATAATGGCATTCA-TACAATGGCAGATACAAAC
1 AATGGCAGATATACACAATAAACATCAGTTTAATAAT-G-A-TAATTATAATGGCAGATACAAAC
104932564 A
1 A
104932565 CATCAAAATC
Statistics
Matches: 351, Mismatches: 21, Indels: 12
0.91 0.05 0.03
Matches are distributed among these distances:
61 4 0.01
62 216 0.62
64 127 0.36
65 1 0.00
66 3 0.01
ACGTcount: A:0.47, C:0.14, G:0.13, T:0.26
Consensus pattern (62 bp):
AATGGCAGATATACACAATAAACATCAGTTTAATAATGATAATTATAATGGCAGATACAAAC
Found at i:104932475 original size:34 final size:34
Alignment explanation
Indices: 104932436--104932540 Score: 89
Period size: 32 Copynumber: 3.2 Consensus size: 34
104932426 AGATACAAAC
104932436 AATGGCAGATATACACAATAAAGATCAGTTTGAT
1 AATGGCAGATATACACAATAAAGATCAGTTTGAT
* * * *
104932470 AATGGC--AT-TCATACAATGACAGATACA----AAC
1 AATGGCAGATAT-ACACAAT-AAAGAT-CAGTTTGAT
*
104932500 AATGGCAGATACACACAATAAAGATCAGTTTGAT
1 AATGGCAGATATACACAATAAAGATCAGTTTGAT
104932534 AATGGCA
1 AATGGCA
104932541 TTCATACAAT
Statistics
Matches: 52, Mismatches: 9, Indels: 20
0.64 0.11 0.25
Matches are distributed among these distances:
30 9 0.17
31 6 0.12
32 16 0.31
33 5 0.10
34 16 0.31
ACGTcount: A:0.45, C:0.15, G:0.17, T:0.23
Consensus pattern (34 bp):
AATGGCAGATATACACAATAAAGATCAGTTTGAT
Found at i:104932503 original size:16 final size:16
Alignment explanation
Indices: 104932482--104932518 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
104932472 TGGCATTCAT
104932482 ACAATGACAGATACAA
1 ACAATGACAGATACAA
* *
104932498 ACAATGGCAGATACAC
1 ACAATGACAGATACAA
104932514 ACAAT
1 ACAAT
104932519 AAAGATCAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.22, G:0.14, T:0.14
Consensus pattern (16 bp):
ACAATGACAGATACAA
Found at i:104932712 original size:6 final size:6
Alignment explanation
Indices: 104932703--104932785 Score: 53
Period size: 6 Copynumber: 13.8 Consensus size: 6
104932693 AAATAACCCT
* * * * *
104932703 AAATCG AAATCT AAATCG AAATCA AAATC- AAATTC- TAATCCT AGATCG
1 AAATCG AAATCG AAATCG AAATCG AAATCG AAA-TCG AAAT-CG AAATCG
* * * *
104932751 AGATCG AAATCG AAATTG AAATCA AAATCA AAATC
1 AAATCG AAATCG AAATCG AAATCG AAATCG AAATC
104932786 AGAATCAGTG
Statistics
Matches: 63, Mismatches: 11, Indels: 6
0.79 0.14 0.08
Matches are distributed among these distances:
5 4 0.06
6 57 0.90
7 2 0.03
ACGTcount: A:0.51, C:0.17, G:0.10, T:0.23
Consensus pattern (6 bp):
AAATCG
Found at i:104933408 original size:31 final size:29
Alignment explanation
Indices: 104933369--104933441 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 29
104933359 GGTAACTGTT
*
104933369 AGTTAGTGACTGTTTTGTCACTTTTTTATA
1 AGTTAGTGACTGTTTTGTCACTTTTTGA-A
* *
104933399 ACGTTAGTGACCGTTTTGTTACTTTTTGAA
1 A-GTTAGTGACTGTTTTGTCACTTTTTGAA
104933429 AGTTAAGTGACTG
1 AGTT-AGTGACTG
104933442 AAATAAAACC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
29 3 0.08
30 10 0.27
31 24 0.65
ACGTcount: A:0.22, C:0.11, G:0.21, T:0.47
Consensus pattern (29 bp):
AGTTAGTGACTGTTTTGTCACTTTTTGAA
Found at i:104934155 original size:32 final size:32
Alignment explanation
Indices: 104934090--104934152 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
104934080 GTAAGAGTTA
* *
104934090 ATTTCATTTTTTTAATATTATTTAATATTTTT
1 ATTTCATTTTTGTAATATTAATTAATATTTTT
*
104934122 ATTTTATTTTTGTAATA-TAATTAATATTTTT
1 ATTTCATTTTTGTAATATTAATTAATATTTTT
104934153 TATAATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 13 0.46
32 15 0.54
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (32 bp):
ATTTCATTTTTGTAATATTAATTAATATTTTT
Found at i:104934163 original size:31 final size:30
Alignment explanation
Indices: 104934095--104934163 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 30
104934085 AGTTAATTTC
* *
104934095 ATTTTTTTAATATTATTTAATATTTTTATTTT
1 ATTTTTTTAATATTAATTAATATTTTTA--TA
*
104934127 ATTTTTGTAATA-TAATTAATATTTTTTATA
1 ATTTTTTTAATATTAATTAATA-TTTTTATA
104934157 ATTTTTT
1 ATTTTTT
104934164 ATTACAGTCG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
30 7 0.22
31 8 0.25
32 17 0.53
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.68
Consensus pattern (30 bp):
ATTTTTTTAATATTAATTAATATTTTTATA
Found at i:104935894 original size:47 final size:47
Alignment explanation
Indices: 104935785--104935895 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
104935775 CCGGGATAAG
*
104935785 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
104935832 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
104935879 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
104935896 ACTCAATGTC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
46 1 0.02
47 53 0.95
48 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.25
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:104943145 original size:47 final size:47
Alignment explanation
Indices: 104943036--104943146 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
104943026 CCGGGATAAG
*
104943036 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
104943083 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
104943130 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
104943147 ACTCAATGTC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
46 1 0.02
47 53 0.95
48 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.25
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:104945928 original size:59 final size:59
Alignment explanation
Indices: 104945826--104945942 Score: 191
Period size: 59 Copynumber: 2.0 Consensus size: 59
104945816 ATTGATTTAT
*
104945826 TTTTTAATATTTTTGTACAAATTATTTTTATATTATCTTATTTAATAAAATAGAAGTTC
1 TTTTGAATATTTTTGTACAAATTATTTTTATATTATCTTATTTAATAAAATAGAAGTTC
* *
104945885 TTTTGAATATTTTTGTACAAATTATTTTTATATTGT-TTCATTTAATAAATTAGAAGTT
1 TTTTGAATATTTTTGTACAAATTATTTTTATATTATCTT-ATTTAATAAAATAGAAGTT
104945943 ATTTCAATGT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
58 2 0.04
59 52 0.96
ACGTcount: A:0.34, C:0.04, G:0.07, T:0.55
Consensus pattern (59 bp):
TTTTGAATATTTTTGTACAAATTATTTTTATATTATCTTATTTAATAAAATAGAAGTTC
Found at i:104948863 original size:23 final size:22
Alignment explanation
Indices: 104948831--104948873 Score: 77
Period size: 23 Copynumber: 1.9 Consensus size: 22
104948821 AGATCTTTCC
104948831 TAAATTTATCACTAAATAATCT
1 TAAATTTATCACTAAATAATCT
104948853 TAAATATTATCACTAAATAAT
1 TAAAT-TTATCACTAAATAAT
104948874 TCAAAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATTTATCACTAAATAATCT
Found at i:104948880 original size:23 final size:22
Alignment explanation
Indices: 104948832--104948882 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
104948822 GATCTTTCCT
*
104948832 AAATTTATCACTAAATAATCTT
1 AAATTTATCACTAAATAATCTA
104948854 AAATATTATCACTAAATAAT-TCA
1 AAAT-TTATCACTAAATAATCT-A
104948877 AAATTT
1 AAATTT
104948883 TAAAATCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 7 0.27
23 19 0.73
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (22 bp):
AAATTTATCACTAAATAATCTA
Found at i:104950413 original size:2 final size:2
Alignment explanation
Indices: 104950398--104950437 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
104950388 AGGCCTGAAT
*
104950398 TA TA TA CTA AA TA TA 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 TA TA TA TA TA TA TA T
104950438 TATTTTTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:104950587 original size:24 final size:26
Alignment explanation
Indices: 104950560--104950607 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
104950550 CTAGTTTTAA
*
104950560 TATTTGA-TT-TTATGTTTTTAAATG
1 TATTTGATTTATTATATTTTTAAATG
104950584 TATTTGATTTATTATATTTTTAAA
1 TATTTGATTTATTATATTTTTAAA
104950608 ATTTTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.33
25 2 0.10
26 12 0.57
ACGTcount: A:0.29, C:0.00, G:0.08, T:0.62
Consensus pattern (26 bp):
TATTTGATTTATTATATTTTTAAATG
Found at i:104954097 original size:29 final size:29
Alignment explanation
Indices: 104954043--104954112 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
104954033 AATCCATCTC
*
104954043 GTCAAA-TAATTTTTTCAGAACACATCAT
1 GTCAAATTTATTTTTTCAGAACACATCAT
* * * * *
104954071 GTGAAATTTATTTTTTCATATCCCATCTT
1 GTCAAATTTATTTTTTCAGAACACATCAT
104954100 GTCAAATTTATTT
1 GTCAAATTTATTT
104954113 CTTCCAAAAC
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
28 5 0.15
29 29 0.85
ACGTcount: A:0.31, C:0.16, G:0.07, T:0.46
Consensus pattern (29 bp):
GTCAAATTTATTTTTTCAGAACACATCAT
Found at i:104959640 original size:7 final size:7
Alignment explanation
Indices: 104959628--104959659 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
104959618 TACTACGATT
104959628 AAAAAAC
1 AAAAAAC
104959635 AAAAAAC
1 AAAAAAC
104959642 AAAAAAC
1 AAAAAAC
*
104959649 GAAAAAC
1 AAAAAAC
104959656 AAAA
1 AAAA
104959660 GAAAACAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.84, C:0.12, G:0.03, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:104960395 original size:6 final size:6
Alignment explanation
Indices: 104960369--104960414 Score: 74
Period size: 6 Copynumber: 7.5 Consensus size: 6
104960359 CATTAAATTA
*
104960369 TTTATT TTCTATT TTTGTT TTTATT TTTATT TTTATT TTTATT TTT
1 TTTATT TT-TATT TTTATT TTTATT TTTATT TTTATT TTTATT TTT
104960415 TTCTTTGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
6 31 0.84
7 6 0.16
ACGTcount: A:0.13, C:0.02, G:0.02, T:0.83
Consensus pattern (6 bp):
TTTATT
Found at i:104960401 original size:18 final size:18
Alignment explanation
Indices: 104960369--104960425 Score: 80
Period size: 18 Copynumber: 3.1 Consensus size: 18
104960359 CATTAAATTA
104960369 TTTATTTTCTATTTTTGTT
1 TTTATTTT-TATTTTTGTT
*
104960388 TTTATTTTTATTTTTATT
1 TTTATTTTTATTTTTGTT
104960406 TTTATTTTT-TTCTTTGTT
1 TTTATTTTTATT-TTTGTT
104960424 TT
1 TT
104960426 CACTTAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
17 2 0.06
18 25 0.71
19 8 0.23
ACGTcount: A:0.11, C:0.04, G:0.04, T:0.82
Consensus pattern (18 bp):
TTTATTTTTATTTTTGTT
Found at i:104961803 original size:43 final size:43
Alignment explanation
Indices: 104961752--104961851 Score: 146
Period size: 43 Copynumber: 2.3 Consensus size: 43
104961742 AATCGTCGTA
* *
104961752 AAAGATCATGTTCTTTAACGACGTTTGTAGTAAAAGCGCCGCT
1 AAAGATCATGTTCTATAACGACGTTCGTAGTAAAAGCGCCGCT
** *
104961795 AAAGATCATGTTCTATAGTGGCGTTCGTAGTAAAAGCGCCGCT
1 AAAGATCATGTTCTATAACGACGTTCGTAGTAAAAGCGCCGCT
*
104961838 AAAGAACATGTTCT
1 AAAGATCATGTTCT
104961852 GTAGCAGCGT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 51 1.00
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (43 bp):
AAAGATCATGTTCTATAACGACGTTCGTAGTAAAAGCGCCGCT
Found at i:104961862 original size:43 final size:43
Alignment explanation
Indices: 104961773--104961862 Score: 135
Period size: 43 Copynumber: 2.1 Consensus size: 43
104961763 TCTTTAACGA
* * **
104961773 CGTTTGTAGTAAAAGCGCCGCTAAAGATCATGTTCTATAGTGG
1 CGTTCGTAGTAAAAGCGCCGCTAAAGAACATGTTCTATAGCAG
*
104961816 CGTTCGTAGTAAAAGCGCCGCTAAAGAACATGTTCTGTAGCAG
1 CGTTCGTAGTAAAAGCGCCGCTAAAGAACATGTTCTATAGCAG
104961859 CGTT
1 CGTT
104961863 TGTGAGAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.28
Consensus pattern (43 bp):
CGTTCGTAGTAAAAGCGCCGCTAAAGAACATGTTCTATAGCAG
Found at i:104962217 original size:21 final size:21
Alignment explanation
Indices: 104962174--104962229 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
104962164 CATATTTTCT
* * *
104962174 TGTTGCCTCTGCTGCTCTTGC
1 TGTTGCCTCTGCTTCCCTCGC
104962195 TGTTGCCTCTGCTTCCCTCGC
1 TGTTGCCTCTGCTTCCCTCGC
* *
104962216 TGCTGCCTCCGCTT
1 TGTTGCCTCTGCTT
104962230 TAAGTTGTAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.00, C:0.39, G:0.21, T:0.39
Consensus pattern (21 bp):
TGTTGCCTCTGCTTCCCTCGC
Found at i:104974449 original size:34 final size:34
Alignment explanation
Indices: 104974397--104974463 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
104974387 CACAGTTGAA
* *
104974397 CAGTCTTGGGCCTAAGCCCTTTTTAGTATCAGTGG
1 CAGTCTTGGGCCTAAGCCCATCTTAGTA-CAGTGG
*
104974432 CAGT-TTGGGCCTTAGCCCATCTTAGTACAGTG
1 CAGTCTTGGGCCTAAGCCCATCTTAGTACAGTG
104974464 TCAAAAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 5 0.17
34 20 0.69
35 4 0.14
ACGTcount: A:0.18, C:0.24, G:0.25, T:0.33
Consensus pattern (34 bp):
CAGTCTTGGGCCTAAGCCCATCTTAGTACAGTGG
Found at i:104985075 original size:5 final size:5
Alignment explanation
Indices: 104985065--104985092 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
104985055 CCAATTTGTG
104985065 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
104985093 GAACACACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:104988424 original size:22 final size:24
Alignment explanation
Indices: 104988372--104988425 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 24
104988362 TTTTTTATGA
* *
104988372 TTAAATTGTTGTTATTAAATATGTT
1 TTAAATTATTGTTATT-AATATCTT
*
104988397 TGAAATTATTG-TATT-ATATCTT
1 TTAAATTATTGTTATTAATATCTT
104988419 TTAAATT
1 TTAAATT
104988426 GAATTTATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
22 12 0.48
24 4 0.16
25 9 0.36
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.56
Consensus pattern (24 bp):
TTAAATTATTGTTATTAATATCTT
Found at i:104994765 original size:9 final size:9
Alignment explanation
Indices: 104994732--104994786 Score: 51
Period size: 9 Copynumber: 6.1 Consensus size: 9
104994722 CAAATCCAAC
*
104994732 TCTCTCTAT
1 TCTCTCAAT
104994741 TCTCTCTAA-
1 TCTCTC-AAT
*
104994750 ACTCTCAAT
1 TCTCTCAAT
*
104994759 TCTCTCAAC
1 TCTCTCAAT
104994768 TCTCTCAAAT
1 TCTCTC-AAT
104994778 T-TCTCAAT
1 TCTCTCAAT
104994786 T
1 T
104994787 TTTGTTCAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
8 6 0.16
9 28 0.74
10 4 0.11
ACGTcount: A:0.24, C:0.33, G:0.00, T:0.44
Consensus pattern (9 bp):
TCTCTCAAT
Found at i:104994772 original size:18 final size:18
Alignment explanation
Indices: 104994728--104994784 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
104994718 CACTCAAATC
*
104994728 CAACTCTCTCTATTCTCT
1 CAACTCTCTCAATTCTCT
*
104994746 CTAA-ACTCTCAATTCTCT
1 C-AACTCTCTCAATTCTCT
104994764 CAACTCTCTCAAATT-TCT
1 CAACTCTCTC-AATTCTCT
104994782 CAA
1 CAA
104994785 TTTTTGTTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 2 0.06
18 25 0.76
19 6 0.18
ACGTcount: A:0.26, C:0.35, G:0.00, T:0.39
Consensus pattern (18 bp):
CAACTCTCTCAATTCTCT
Found at i:104996926 original size:24 final size:24
Alignment explanation
Indices: 104996899--104996945 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
104996889 TTTAAAAAAT
* *
104996899 TGTTTTATTAAATATTTAATTTAA
1 TGTTTAATTAAATAATTAATTTAA
*
104996923 TGTTTAATTAATTAATTAATTTA
1 TGTTTAATTAAATAATTAATTTA
104996946 TTTATTTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (24 bp):
TGTTTAATTAAATAATTAATTTAA
Found at i:104997339 original size:3 final size:3
Alignment explanation
Indices: 104997331--104997380 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
104997321 TTTAGATTTC
104997331 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
104997379 AT
1 AT
104997381 ATGTTAGTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:105001587 original size:40 final size:39
Alignment explanation
Indices: 105001538--105001785 Score: 257
Period size: 40 Copynumber: 6.2 Consensus size: 39
105001528 TCTTCGGAAT
* *
105001538 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTAGCACAA-TGCCTTCGGGTC
* * *** *
105001577 TTAACCCGGATTTGGTAACTTGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTAGCAC-AATGCCTTCGGGTC
* *
105001617 TTAGCCCGGATATAACAACTCGCACGAATGCCTCCGGGTC
1 TTAGCCCGGATATAACAACTAGCAC-AATGCCTTCGGGTC
*
105001657 TTAGCCCGGATATAACAACTAGCATGAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTAGCA-CAATGCCTTCGGGTC
* *
105001697 TTAGCCCGGATTTAACAACTCGCACGAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTAGCAC-AATGCCTTCGGGTC
* * * * *
105001737 TTAGCCCGGATAGAATC-GCTAGCATAAATGCCTTCAGGAC
1 TTAGCCCGGATATAA-CAACTAGCA-CAATGCCTTCGGGTC
105001777 TTAGCCCGG
1 TTAGCCCGG
105001786 GTATCATTCA
Statistics
Matches: 174, Mismatches: 29, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
39 3 0.02
40 168 0.97
41 3 0.02
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (39 bp):
TTAGCCCGGATATAACAACTAGCACAATGCCTTCGGGTC
Found at i:105001665 original size:80 final size:80
Alignment explanation
Indices: 105001538--105001785 Score: 295
Period size: 80 Copynumber: 3.1 Consensus size: 80
105001528 TCTTCGGAAT
* ** * * *** *
105001538 TTAG-CCGGATATAACCACAAGCAC-AATTGCCTTCGGGTCTTAACCCGGATTTGGTAACTTGCA
1 TTAGCCCGGATATAACAACTCGCACGAA-TGCCTTCGGGTCTTAGCCCGGATATAACAACTAGCA
105001601 CAAATGCCTTCGGGTC
65 CAAATGCCTTCGGGTC
* *
105001617 TTAGCCCGGATATAACAACTCGCACGAATGCCTCCGGGTCTTAGCCCGGATATAACAACTAGCAT
1 TTAGCCCGGATATAACAACTCGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACAACTAGCAC
*
105001682 GAATGCCTTCGGGTC
66 AAATGCCTTCGGGTC
* * *
105001697 TTAGCCCGGATTTAACAACTCGCACGAATGCCTTCGGGTCTTAGCCCGGATAGAATC-GCTAGCA
1 TTAGCCCGGATATAACAACTCGCACGAATGCCTTCGGGTCTTAGCCCGGATATAA-CAACTAGCA
* * *
105001761 TAAATGCCTTCAGGAC
65 CAAATGCCTTCGGGTC
105001777 TTAGCCCGG
1 TTAGCCCGG
105001786 GTATCATTCA
Statistics
Matches: 147, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
79 4 0.03
80 140 0.95
81 3 0.02
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (80 bp):
TTAGCCCGGATATAACAACTCGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACAACTAGCAC
AAATGCCTTCGGGTC
Found at i:105001767 original size:120 final size:120
Alignment explanation
Indices: 105001538--105001785 Score: 304
Period size: 120 Copynumber: 2.1 Consensus size: 120
105001528 TCTTCGGAAT
* *** *
105001538 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGATTTGGTAACTTGCAC
1 TTAGCCCGGATATAACAACAAGCACAATTGCCTTCGGGTCTTAACCCGGATTTAACAACTCGCAC
* * * * *
105001602 AAATGCCTTCGGGTCTTAGCCCGGATATAACAACTCGCACGAATGCCTCCGGGTC
66 AAATGCCTTCGGGTCTTAGCCCGGATAGAACAACTAGCACAAATGCCTCCAGGAC
* * *
105001657 TTAGCCCGGATATAACAACTAGCATGAA-TGCCTTCGGGTCTTAGCCCGGATTTAACAACTCGCA
1 TTAGCCCGGATATAACAACAAGCA-CAATTGCCTTCGGGTCTTAACCCGGATTTAACAACTCGCA
* * * *
105001721 CGAATGCCTTCGGGTCTTAGCCCGGATAGAATC-GCTAGCATAAATGCCTTCAGGAC
65 CAAATGCCTTCGGGTCTTAGCCCGGATAGAA-CAACTAGCACAAATGCCTCCAGGAC
105001777 TTAGCCCGG
1 TTAGCCCGG
105001786 GTATCATTCA
Statistics
Matches: 109, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
119 4 0.04
120 102 0.94
121 3 0.03
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (120 bp):
TTAGCCCGGATATAACAACAAGCACAATTGCCTTCGGGTCTTAACCCGGATTTAACAACTCGCAC
AAATGCCTTCGGGTCTTAGCCCGGATAGAACAACTAGCACAAATGCCTCCAGGAC
Found at i:105005736 original size:7 final size:7
Alignment explanation
Indices: 105005719--105005846 Score: 81
Period size: 7 Copynumber: 18.6 Consensus size: 7
105005709 ACTTCACCTT
*
105005719 AAAAAAC
1 AAAAAAG
*
105005726 AAAACAAA
1 AAAA-AAG
105005734 AAAAAAG
1 AAAAAAG
105005741 AAAAAAG
1 AAAAAAG
105005748 AAAAGAA-
1 AAAA-AAG
105005755 AAGAAAAG
1 AA-AAAAG
*
105005763 CAAAAACG
1 -AAAAAAG
105005771 AAAAAA-
1 AAAAAAG
105005777 AATAAAA-
1 AA-AAAAG
*
105005784 AAAAGAG
1 AAAAAAG
105005791 AAAAAAG
1 AAAAAAG
105005798 --AAAAG
1 AAAAAAG
*
105005803 AGAAAAG
1 AAAAAAG
* *
105005810 GAACAAG
1 AAAAAAG
*
105005817 AAACAAG
1 AAAAAAG
105005824 AAAAAA-
1 AAAAAAG
*
105005830 AAGAAA-
1 AAAAAAG
105005836 AAAAAAG
1 AAAAAAG
105005843 AAAA
1 AAAA
105005847 GCAAAATAGA
Statistics
Matches: 98, Mismatches: 13, Indels: 20
0.75 0.10 0.15
Matches are distributed among these distances:
5 5 0.05
6 15 0.15
7 62 0.63
8 14 0.14
9 2 0.02
ACGTcount: A:0.81, C:0.05, G:0.13, T:0.01
Consensus pattern (7 bp):
AAAAAAG
Found at i:105005746 original size:12 final size:12
Alignment explanation
Indices: 105005719--105005877 Score: 86
Period size: 13 Copynumber: 12.4 Consensus size: 12
105005709 ACTTCACCTT
* *
105005719 AAAAAACAAAAC
1 AAAAAAAAAAAG
*
105005731 AAAAAAAAAGAAA
1 AAAAAAAAA-AAG
105005744 AAAGAAAAGAAAAG
1 AAA-AAAA-AAAAG
* *
105005758 AAAAGCAAAAACG
1 AAAA-AAAAAAAG
*
105005771 AAAAAAAATAAAA
1 AAAAAAAA-AAAG
105005784 AAAAGAGAAAAAAG
1 AAAA-A-AAAAAAG
* *
105005798 AAAAGAGAAAAGG
1 AAAA-AAAAAAAG
* *
105005811 AACAAGAAACAAG
1 AA-AAAAAAAAAG
105005824 AAAAAAAAGAAA-
1 AAAAAAAA-AAAG
*
105005836 AAAAAAGAAAAG
1 AAAAAAAAAAAG
* *
105005848 CAAAATAGAAAAG
1 -AAAAAAAAAAAG
*
105005861 AAAATAAAAAAG
1 AAAAAAAAAAAG
105005873 AAAAA
1 AAAAA
105005878 GAAGAGGCCA
Statistics
Matches: 115, Mismatches: 21, Indels: 22
0.73 0.13 0.14
Matches are distributed among these distances:
11 3 0.03
12 38 0.33
13 46 0.40
14 23 0.20
15 5 0.04
ACGTcount: A:0.81, C:0.04, G:0.13, T:0.02
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:105005786 original size:40 final size:39
Alignment explanation
Indices: 105005726--105005882 Score: 135
Period size: 40 Copynumber: 3.8 Consensus size: 39
105005716 CTTAAAAAAC
105005726 AAAAC-AAAAAAAA-AGAAAAAAGAAAAGAAAAGAAAAGCA
1 AAAACGAAAAAAAATA-AAAAAAGAAAA-AAAAGAAAAGCA
*
105005765 AAAACGAAAAAAAATAAAAAAAAGAGAAAAAAGAAAAG-A
1 AAAACGAAAAAAAAT-AAAAAAAGAAAAAAAAGAAAAGCA
* *
105005804 GAAAAGGAACAAGAAACAAGAAAAAAAAGAAAAAAAAAGAAAAGCA
1 -AAAACG-A-AA-AAA-AA-TAAAAAAAG-AAAAAAAAGAAAAGCA
*
105005850 AAATA-GAAAAGAAAAT-AAAAAAGAAAAAGAAGA
1 AAA-ACGAAAA-AAAATAAAAAAAGAAAAAAAAGA
105005883 GGCCAAGGTA
Statistics
Matches: 99, Mismatches: 6, Indels: 26
0.76 0.05 0.20
Matches are distributed among these distances:
39 15 0.15
40 30 0.30
41 11 0.11
42 6 0.06
43 7 0.07
44 11 0.11
45 17 0.17
46 2 0.02
ACGTcount: A:0.80, C:0.04, G:0.15, T:0.02
Consensus pattern (39 bp):
AAAACGAAAAAAAATAAAAAAAGAAAAAAAAGAAAAGCA
Found at i:105005876 original size:5 final size:5
Alignment explanation
Indices: 105005743--105005869 Score: 82
Period size: 5 Copynumber: 23.8 Consensus size: 5
105005733 AAAAAAAGAA
*
105005743 AAAAG AAAAG AAAAG AAAAG CAAAAACG AAAA- AAAAT AAAA- AAAAG
1 AAAAG AAAAG AAAAG AAAAG --AAAA-G AAAAG AAAAG AAAAG AAAAG
* *
105005789 AGAA- AAAAG AAAAGAG AAAAGG AACAAG AAACAAG AAAA- AAAAG AAAAA
1 AAAAG AAAAG -AAA-AG AAAA-G AA-AAG -AA-AAG AAAAG AAAAG AAAAG
*
105005838 AAAAG AAAAG CAAAATAG AAAAG AAAAT AAAA
1 AAAAG AAAAG --AAA-AG AAAAG AAAAG AAAA
105005870 AAGAAAAAGA
Statistics
Matches: 102, Mismatches: 5, Indels: 30
0.74 0.04 0.22
Matches are distributed among these distances:
4 15 0.15
5 48 0.47
6 19 0.19
7 17 0.17
8 3 0.03
ACGTcount: A:0.79, C:0.04, G:0.15, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:105006411 original size:65 final size:65
Alignment explanation
Indices: 105006307--105006430 Score: 185
Period size: 65 Copynumber: 1.9 Consensus size: 65
105006297 TTTAGCAAAG
* * * * * * *
105006307 TTTGCTATCTTTGATTAATTTCTTCGTTTCGCGCTATGCTCTCAATCAATTTCTTTCTTATTGTT
1 TTTGCCATCTTGGATTAACTTATTCGTCTCGAGCTATGCTCTCAATCAATTTCCTTCTTATTGTT
105006372 TTTGCCATCTTGGATTAACTTATTCGTCTCGAGCTATGCTCTCAATCAATTTCCTTCTT
1 TTTGCCATCTTGGATTAACTTATTCGTCTCGAGCTATGCTCTCAATCAATTTCCTTCTT
105006431 GTCCATCATT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
65 52 1.00
ACGTcount: A:0.17, C:0.23, G:0.11, T:0.49
Consensus pattern (65 bp):
TTTGCCATCTTGGATTAACTTATTCGTCTCGAGCTATGCTCTCAATCAATTTCCTTCTTATTGTT
Found at i:105007331 original size:142 final size:143
Alignment explanation
Indices: 105007006--105007388 Score: 488
Period size: 143 Copynumber: 2.7 Consensus size: 143
105006996 GAAGATGGTG
* * * *
105007006 GATCTTACCTTCCTAAAGTTGTAGTGGAGCAGATTGAAGCCACCAGCCTTGTCTCCCTGAAGTTG
1 GATCTTATCTTCCTAAAGTTGTAGTGGAACAGATTGAAGCCACCAGCCTTATCTCCCTAAAGTTG
* * *
105007071 TAGCGGAGTAGACTGAAGACAGCGAATCTTATTTTCTGGACATTACAGTGGAATAGGTTGAAGCT
66 CAGCGGAGTAGACTGAAGACAGCGAATCTTATTTTCTGGACATTACAGTGGAATAGATTAAAGCT
*
105007136 ACAAGTTATGGCA
131 ACAAATTATGGCA
* * * ** **
105007149 GATCTCATCTTCCTGAAGTTGCAGT-GAAGCAGATCAAAGCCACCAGCCTTATCTATCTAAAGTT
1 GATCTTATCTTCCTAAAGTTGTAGTGGAA-CAGATTGAAGCCACCAGCCTTATCTCCCTAAAGTT
* * * * *
105007213 GCAACAGAGCATACTGAAGACAGCGAATCTTATTTTCCT-GACGTTAC-GTGGAATAGATTAAAG
65 GCAGCGGAGTAGACTGAAGACAGCGAATCTTATTTT-CTGGACATTACAGTGGAATAGATTAAAG
105007276 CTACAAATTATGG-A
129 CTACAAATTATGGCA
* *
105007290 GAATCTTATCTTCTTAAAGTTGTAGTGGAACAGATTGAAGCCACCAGCTTTATCTCCCTAAAGTT
1 G-ATCTTATCTTCCTAAAGTTGTAGTGGAACAGATTGAAGCCACCAGCCTTATCTCCCTAAAGTT
* *
105007355 -CAGCGGAGTAGACTGAAGATAGCAAATCTTATTT
65 GCAGCGGAGTAGACTGAAGACAGCGAATCTTATTT
105007389 CCCTTTTCCT
Statistics
Matches: 201, Mismatches: 35, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
141 30 0.15
142 78 0.39
143 91 0.45
144 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.28
Consensus pattern (143 bp):
GATCTTATCTTCCTAAAGTTGTAGTGGAACAGATTGAAGCCACCAGCCTTATCTCCCTAAAGTTG
CAGCGGAGTAGACTGAAGACAGCGAATCTTATTTTCTGGACATTACAGTGGAATAGATTAAAGCT
ACAAATTATGGCA
Found at i:105009819 original size:24 final size:23
Alignment explanation
Indices: 105009792--105009868 Score: 66
Period size: 25 Copynumber: 3.2 Consensus size: 23
105009782 TATCATTTCC
105009792 GCTCTTTCGAGCTATGATCAGTAA
1 GCTCTTTCGAGCTATGA-CAGTAA
* *
105009816 GCTCCTCCTGAGCTGATGACAGTAA
1 GCTCTTTC-GAGCT-ATGACAGTAA
** *
105009841 GCTCTATT-GAGCTAAAACGGTAA
1 GCTCT-TTCGAGCTATGACAGTAA
105009864 GCTCT
1 GCTCT
105009869 GACAAACCGA
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
23 12 0.28
24 11 0.26
25 15 0.35
26 5 0.12
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (23 bp):
GCTCTTTCGAGCTATGACAGTAA
Found at i:105012804 original size:54 final size:54
Alignment explanation
Indices: 105012718--105012858 Score: 232
Period size: 54 Copynumber: 2.6 Consensus size: 54
105012708 AGGAAGCGTC
*
105012718 CTGGTGGCTATGCCACAATTATCTGATTTGGTGGCTCTGCCACATATATCTG-T
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
105012771 CATGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 C-TGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
*
105012826 CTGGTGGCTCTGCCACAA-TATCTGTATCTGGTG
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTG
105012859 ACTTCGTCAC
Statistics
Matches: 83, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
53 7 0.08
54 74 0.89
55 2 0.02
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.35
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
Found at i:105012854 original size:32 final size:27
Alignment explanation
Indices: 105012718--105012858 Score: 182
Period size: 27 Copynumber: 5.2 Consensus size: 27
105012708 AGGAAGCGTC
*
105012718 CTGGTGGCTATGCCACA-ATTATCTGAT
1 CTGGTGGCTCTGCCACATA-TATCTGAT
*
105012745 TTGGTGGCTCTGCCACATATATCTG-T
1 CTGGTGGCTCTGCCACATATATCTGAT
*
105012771 CATGGTGGCTATGCCACA-ATTATCTGAT
1 C-TGGTGGCTCTGCCACATA-TATCTGAT
*
105012799 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACATATATCTGAT
105012826 CTGGTGGCTCTGCCACA-ATATCTGTAT
1 CTGGTGGCTCTGCCACATATATCTG-AT
105012853 CTGGTG
1 CTGGTG
105012859 ACTTCGTCAC
Statistics
Matches: 101, Mismatches: 7, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
26 9 0.09
27 88 0.87
28 4 0.04
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.35
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACATATATCTGAT
Found at i:105012869 original size:27 final size:27
Alignment explanation
Indices: 105012718--105012875 Score: 175
Period size: 27 Copynumber: 5.9 Consensus size: 27
105012708 AGGAAGCGTC
*
105012718 CTGGTGGCTATGCCACAATTATCTG-AT
1 CTGGTGGCTCTGCCACAA-TATCTGTAT
*
105012745 TTGGTGGCTCTGCCACATATATCTG--T
1 CTGGTGGCTCTGCCACA-ATATCTGTAT
*
105012771 CATGGTGGCTATGCCACAATTATCTG-AT
1 C-TGGTGGCTCTGCCACAA-TATCTGTAT
105012799 CTGGTGGCTCTGCCACATATATCTGT-T
1 CTGGTGGCTCTGCCACA-ATATCTGTAT
105012826 CTGGTGGCTCTGCCACAATATCTGTAT
1 CTGGTGGCTCTGCCACAATATCTGTAT
* *
105012853 CTGGTGACT-TCGTCACAATATCT
1 CTGGTGGCTCT-GCCACAATATCT
105012876 AGCAGCGTCG
Statistics
Matches: 116, Mismatches: 7, Indels: 16
0.83 0.05 0.12
Matches are distributed among these distances:
26 11 0.09
27 101 0.87
28 4 0.03
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.35
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATATCTGTAT
Found at i:105012870 original size:81 final size:80
Alignment explanation
Indices: 105012718--105012875 Score: 200
Period size: 81 Copynumber: 2.0 Consensus size: 80
105012708 AGGAAGCGTC
*
105012718 CTGGTGGCTATGCCACAATTATCTGATTTGGTGGCTCTGCCACATATATCTGTCATGGTGGCTAT
1 CTGGTGGCTATGCCACAATTATCTGATTTGGTGGCTCTGCCACATATATCTGTCATGGTGACTAT
105012783 GCCACAATTATCTGAT
66 GCCACAA-TATCTGAT
*
105012799 CTGGTGGCTCTGCCAC-ATATATCTG-TTCTGGTGGCTCTGCCACA-ATATCTGT-ATCTGGTGA
1 CTGGTGGCTATGCCACAAT-TATCTGATT-TGGTGGCTCTGCCACATATATCTGTCA--TGGTGA
*
105012860 CT-TCGTCACAATATCT
62 CTAT-GCCACAATATCT
105012876 AGCAGCGTCG
Statistics
Matches: 69, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
79 1 0.01
80 18 0.26
81 50 0.72
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.35
Consensus pattern (80 bp):
CTGGTGGCTATGCCACAATTATCTGATTTGGTGGCTCTGCCACATATATCTGTCATGGTGACTAT
GCCACAATATCTGAT
Found at i:105019872 original size:54 final size:54
Alignment explanation
Indices: 105019790--105019936 Score: 215
Period size: 54 Copynumber: 2.7 Consensus size: 54
105019780 TGGAGGAAGC
* * *
105019790 GTCCTGATGGCTATGCCACAATTATCTGATTTGGTGGCTCTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCT
*
105019844 GTCCTGGTGACTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCT
** *
105019898 GTTTTGGTGGCTCTGCCACAA-TATCTGTATCTGGTGACT
1 GTCCTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACT
105019937 TCGTCACAAT
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
53 6 0.07
54 78 0.93
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35
Consensus pattern (54 bp):
GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCT
Found at i:105019944 original size:27 final size:26
Alignment explanation
Indices: 105019803--105019950 Score: 156
Period size: 27 Copynumber: 5.5 Consensus size: 26
105019793 CTGATGGCTA
*
105019803 TGCCACAATTATCTGATT-TGGTGGCTC
1 TGCCACAA-TATCTG-TTCTGGTGACTC
* *
105019830 TGCCACATATATCTGTCCTGGTGACTA
1 TGCCACA-ATATCTGTTCTGGTGACTC
*
105019857 TGCCACAATTATCTGATCTGGTGACTC
1 TGCCACAA-TATCTGTTCTGGTGACTC
* *
105019884 TGCCACATATATCTGTTTTGGTGGCTC
1 TGCCACA-ATATCTGTTCTGGTGACTC
105019911 TGCCACAATATCTGTATCTGGTGACT-
1 TGCCACAATATCTGT-TCTGGTGACTC
*
105019937 TCGTCACAATATCT
1 T-GCCACAATATCT
105019951 AGCAGCCTCG
Statistics
Matches: 103, Mismatches: 12, Indels: 12
0.81 0.09 0.09
Matches are distributed among these distances:
26 11 0.11
27 90 0.87
28 2 0.02
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.36
Consensus pattern (26 bp):
TGCCACAATATCTGTTCTGGTGACTC
Found at i:105022140 original size:24 final size:24
Alignment explanation
Indices: 105022113--105022159 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
105022103 ATATGTTGAC
105022113 ATTCAAATCAGCACACATAGTGCT
1 ATTCAAATCAGCACACATAGTGCT
* *
105022137 ATTCAACTCCGCACACATAGTGC
1 ATTCAAATCAGCACACATAGTGC
105022160 CATACTACAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.34, C:0.30, G:0.13, T:0.23
Consensus pattern (24 bp):
ATTCAAATCAGCACACATAGTGCT
Found at i:105022194 original size:24 final size:24
Alignment explanation
Indices: 105022123--105022185 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
105022113 ATTCAAATCA
* * * * *
105022123 GCACACATAGTGCTATTCAACTCC
1 GCACACATAGTGCCATACTACACT
105022147 GCACACATAGTGCCATACTACACT
1 GCACACATAGTGCCATACTACACT
105022171 GCACACATAGTGCCA
1 GCACACATAGTGCCA
105022186 ATGTACACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.32, C:0.33, G:0.14, T:0.21
Consensus pattern (24 bp):
GCACACATAGTGCCATACTACACT
Found at i:105030011 original size:24 final size:24
Alignment explanation
Indices: 105029984--105030030 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
105029974 ATATGTTGAC
105029984 ATTCAAATCAGCACACATAGTGCT
1 ATTCAAATCAGCACACATAGTGCT
* *
105030008 ATTCAACTCCGCACACATAGTGC
1 ATTCAAATCAGCACACATAGTGC
105030031 CATACTACAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.34, C:0.30, G:0.13, T:0.23
Consensus pattern (24 bp):
ATTCAAATCAGCACACATAGTGCT
Found at i:105030064 original size:24 final size:24
Alignment explanation
Indices: 105029994--105030056 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
105029984 ATTCAAATCA
* * * *
105029994 GCACACATAGTGCTATTCAACTCC
1 GCACACATAGTGCCATACTACACC
105030018 GCACACATAGTGCCATACTACACC
1 GCACACATAGTGCCATACTACACC
*
105030042 GCACACATTGTGCCA
1 GCACACATAGTGCCA
105030057 ATGTACACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.30, C:0.35, G:0.14, T:0.21
Consensus pattern (24 bp):
GCACACATAGTGCCATACTACACC
Found at i:105034347 original size:11 final size:11
Alignment explanation
Indices: 105034326--105034354 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
105034316 ACCTTGTGTG
105034326 AAAAT-AAAAT
1 AAAATAAAAAT
105034336 AAAATAAAAAT
1 AAAATAAAAAT
105034347 AAAATAAA
1 AAAATAAA
105034355 GAACACACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:105040329 original size:8 final size:8
Alignment explanation
Indices: 105040283--105040345 Score: 50
Period size: 7 Copynumber: 8.8 Consensus size: 8
105040273 TTAAGTTTAT
105040283 TTAAAATA
1 TTAAAATA
*
105040291 --AAAACA
1 TTAAAATA
105040297 TT-AAAT-
1 TTAAAATA
105040303 TTAAAAT-
1 TTAAAATA
105040310 TTAAAA-A
1 TTAAAATA
*
105040317 ATAAAATA
1 TTAAAATA
105040325 TT-AAATA
1 TTAAAATA
*
105040332 TTTAAATA
1 TTAAAATA
105040340 TTAAAA
1 TTAAAA
105040346 ACACTTTTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
6 7 0.16
7 25 0.57
8 12 0.27
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (8 bp):
TTAAAATA
Found at i:105040334 original size:23 final size:22
Alignment explanation
Indices: 105040281--105040337 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
105040271 AATTAAGTTT
*
105040281 ATTTAAAA--TAAAAACATTAA
1 ATTTAAAATTTAAAAACATAAA
105040301 ATTTAAAATTTAAAAA-ATAAA
1 ATTTAAAATTTAAAAACATAAA
105040322 ATATTAAATATTTAAA
1 AT-TTAAA-ATTTAAA
105040338 TATTAAAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 8 0.25
21 6 0.19
22 11 0.34
23 7 0.22
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
ATTTAAAATTTAAAAACATAAA
Found at i:105040538 original size:23 final size:24
Alignment explanation
Indices: 105040486--105040552 Score: 75
Period size: 23 Copynumber: 2.8 Consensus size: 24
105040476 TATATAATAC
*
105040486 ATAAAA-ATATTTTTAAAAAAGTTT
1 ATAAAATATATTTTTATAAAAG-TT
* *
105040510 AAAAAATATTTTTTTATAAAA-TT
1 ATAAAATATATTTTTATAAAAGTT
*
105040533 ATAAAATATATATTTATAAA
1 ATAAAATATATTTTTATAAA
105040553 TTTTAAGGAG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
23 19 0.53
24 5 0.14
25 12 0.33
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (24 bp):
ATAAAATATATTTTTATAAAAGTT
Found at i:105040608 original size:10 final size:11
Alignment explanation
Indices: 105040581--105040617 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
105040571 ATATATAAAA
105040581 TTAAAAAATAT
1 TTAAAAAATAT
105040592 TGT-AAAAAT-T
1 T-TAAAAAATAT
105040602 TTAAAAAATAT
1 TTAAAAAATAT
105040613 TTAAA
1 TTAAA
105040618 TTTCAAGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
9 1 0.04
10 8 0.35
11 13 0.57
12 1 0.04
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (11 bp):
TTAAAAAATAT
Found at i:105040750 original size:22 final size:21
Alignment explanation
Indices: 105040703--105040750 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
105040693 TTATAAAAAA
* *
105040703 TATTTTAAAAATTATTTATAG
1 TATTTTAAAAATAATTTATAC
*
105040724 T-TTTTCAAAAATAATTTTTAC
1 TATTTT-AAAAATAATTTATAC
105040745 TATTTT
1 TATTTT
105040751 TTACATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 4 0.18
21 14 0.64
22 4 0.18
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (21 bp):
TATTTTAAAAATAATTTATAC
Found at i:105041599 original size:67 final size:67
Alignment explanation
Indices: 105041491--105041651 Score: 304
Period size: 67 Copynumber: 2.4 Consensus size: 67
105041481 AGTGAAAAGT
*
105041491 TTTTGCCATTTTAATTCAATTTAAATTGAGGGAAAAATTTTTGAGTTAATTAAATTGATGATTTC
1 TTTTGTCATTTTAATTCAATTTAAATTGAGGGAAAAATTTTTGAGTTAATTAAATTGATGATTTC
105041556 TA
66 TA
105041558 TTTTGTCATTTTAATTCAATTTAAATTGAGGGAAAAATTTTTGAGTTAATTAAATTGATGATTTC
1 TTTTGTCATTTTAATTCAATTTAAATTGAGGGAAAAATTTTTGAGTTAATTAAATTGATGATTTC
105041623 TA
66 TA
*
105041625 TTTTGTCATTTTAATTTAATTTAAATT
1 TTTTGTCATTTTAATTCAATTTAAATT
105041652 TTTTCTAATC
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
67 92 1.00
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.50
Consensus pattern (67 bp):
TTTTGTCATTTTAATTCAATTTAAATTGAGGGAAAAATTTTTGAGTTAATTAAATTGATGATTTC
TA
Found at i:105042470 original size:26 final size:27
Alignment explanation
Indices: 105042441--105042492 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
105042431 AAGCACAACT
105042441 GTGCC-CCTATCTGACACCCTCCACTG
1 GTGCCGCCTATCTGACACCCTCCACTG
* * *
105042467 GTGCCGCTTATCTGGCACCGTCCACT
1 GTGCCGCCTATCTGACACCCTCCACT
105042493 ACTAAAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.13, C:0.42, G:0.19, T:0.25
Consensus pattern (27 bp):
GTGCCGCCTATCTGACACCCTCCACTG
Found at i:105042832 original size:22 final size:21
Alignment explanation
Indices: 105042803--105042846 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
105042793 AAATTAAAAA
*
105042803 TTTAACTT-TCTTTATAATTTT
1 TTTAACTTAT-TTTAAAATTTT
105042824 TTTAGACTTATTTTAAAATTTT
1 TTTA-ACTTATTTTAAAATTTT
105042846 T
1 T
105042847 ATAATTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 4 0.20
22 15 0.75
23 1 0.05
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTAACTTATTTTAAAATTTT
Found at i:105042868 original size:25 final size:24
Alignment explanation
Indices: 105042840--105042888 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
105042830 CTTATTTTAA
*
105042840 AATTTTTATAATTTTCTAAAAATAT
1 AATTTTTAGAATTTT-TAAAAATAT
* *
105042865 AATTTTTGGAATTTTTATAAATAT
1 AATTTTTAGAATTTTTAAAAATAT
105042889 TTTTAATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (24 bp):
AATTTTTAGAATTTTTAAAAATAT
Found at i:105043335 original size:18 final size:17
Alignment explanation
Indices: 105043309--105043354 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
105043299 TTTATATATT
*
105043309 TTTAGAATTTTTTAAAAA
1 TTTA-AATTTTCTAAAAA
105043327 TTTATAATTTTCTAAAAA
1 TTTA-AATTTTCTAAAAA
105043345 TATTAAATTT
1 T-TTAAATTT
105043355 GAAATTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 22 0.88
19 3 0.12
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (17 bp):
TTTAAATTTTCTAAAAA
Found at i:105043348 original size:40 final size:39
Alignment explanation
Indices: 105043269--105043348 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 39
105043259 AAAATTATTA
** *
105043269 TTTTAGAAAATTTTTAAAATTTTAATTTTCTTTATATAT
1 TTTTAGAAAATTTTTAAAATTTTAATTTTCTAAAAATAT
*
105043308 TTTTAG-AATTTTTTAAAAATTTATAATTTTCTAAAAATAT
1 TTTTAGAAAATTTTT-AAAATTT-TAATTTTCTAAAAATAT
105043348 T
1 T
105043349 AAATTTGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
38 7 0.20
39 13 0.37
40 15 0.43
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (39 bp):
TTTTAGAAAATTTTTAAAATTTTAATTTTCTAAAAATAT
Found at i:105043360 original size:25 final size:24
Alignment explanation
Indices: 105043324--105043372 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
105043314 AATTTTTTAA
105043324 AAATTTATAATTTTCTAAAAATATT
1 AAATTTATAATTTT-TAAAAATATT
*
105043349 AAATTTGA-AATTTTTATAAATATT
1 AAATTT-ATAATTTTTAAAAATATT
105043373 TTTATTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 9 0.41
25 12 0.55
26 1 0.05
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (24 bp):
AAATTTATAATTTTTAAAAATATT
Found at i:105043574 original size:11 final size:11
Alignment explanation
Indices: 105043558--105043584 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
105043548 TTAACTCAAA
105043558 ATTTTATTTTT
1 ATTTTATTTTT
105043569 ATTTTATTTTT
1 ATTTTATTTTT
105043580 ATTTT
1 ATTTT
105043585 TCAGAATCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (11 bp):
ATTTTATTTTT
Found at i:105043846 original size:22 final size:20
Alignment explanation
Indices: 105043820--105043868 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
105043810 TAAATAATAA
105043820 ATTATTTGATGTATAATAATT
1 ATTATTT-ATGTATAATAATT
105043841 ATTTATTTATGTATAGATAA-T
1 A-TTATTTATGTATA-ATAATT
105043862 ATTATTT
1 ATTATTT
105043869 CAAGTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 6 0.23
21 10 0.38
22 10 0.38
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (20 bp):
ATTATTTATGTATAATAATT
Found at i:105046746 original size:20 final size:19
Alignment explanation
Indices: 105046724--105046781 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 19
105046714 ACTTGTTTTA
105046724 AAACAATTTTAACTTGATT
1 AAACAATTTTAACTTGATT
*
105046743 AAA-AATGCTTAACTAT-ATT
1 AAACAAT-TTTAACT-TGATT
*
105046762 GAAACCATTTTAACTTGATT
1 -AAACAATTTTAACTTGATT
105046782 TTATCATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
18 3 0.10
19 13 0.42
20 13 0.42
21 2 0.06
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.40
Consensus pattern (19 bp):
AAACAATTTTAACTTGATT
Found at i:105046843 original size:23 final size:24
Alignment explanation
Indices: 105046808--105046855 Score: 64
Period size: 22 Copynumber: 2.0 Consensus size: 24
105046798 TTTGTTCAAC
105046808 TTTAACTTTTATA-CAAAA-ATAT
1 TTTAACTTTTATATCAAAACATAT
*
105046830 TTTAATTTGTTATATCAAAACATAT
1 TTTAACTT-TTATATCAAAACATAT
105046855 T
1 T
105046856 ATCAAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
23 5 0.23
24 5 0.23
25 5 0.23
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.48
Consensus pattern (24 bp):
TTTAACTTTTATATCAAAACATAT
Found at i:105049132 original size:38 final size:37
Alignment explanation
Indices: 105049080--105049161 Score: 114
Period size: 38 Copynumber: 2.2 Consensus size: 37
105049070 ATGTTTAACC
*
105049080 TTACAATCTCCCTTAAGAG-TTCTACCCAAAATCTTAAGA
1 TTACAA-CTCCCTTAAG-GTTTCTACCC-AAACCTTAAGA
105049119 TTACAACTCCCTTAAGGTTTCTACCCAAACCTTAAGA
1 TTACAACTCCCTTAAGGTTTCTACCCAAACCTTAAGA
105049156 TT-CAAC
1 TTACAAC
105049162 ACTCAAAGAG
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
36 4 0.10
37 13 0.32
38 18 0.44
39 6 0.15
ACGTcount: A:0.34, C:0.28, G:0.07, T:0.30
Consensus pattern (37 bp):
TTACAACTCCCTTAAGGTTTCTACCCAAACCTTAAGA
Found at i:105049652 original size:18 final size:18
Alignment explanation
Indices: 105049629--105049663 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
105049619 TTAAAACAGC
105049629 TTTAACTTC-ATTGAAATG
1 TTTAAC-TCAATTGAAATG
105049647 TTTAACTCAATTGAAAT
1 TTTAACTCAATTGAAAT
105049664 CATTTTAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (18 bp):
TTTAACTCAATTGAAATG
Found at i:105049731 original size:22 final size:24
Alignment explanation
Indices: 105049703--105049746 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
105049693 GTTTTGTTCA
105049703 ATTTTAACTT-TTAT-TCAAAAAC
1 ATTTTAACTTGTTATATCAAAAAC
*
105049725 ATTTTAATTTGTTATATCAAAA
1 ATTTTAACTTGTTATATCAAAA
105049747 CATATTATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (24 bp):
ATTTTAACTTGTTATATCAAAAAC
Found at i:105051969 original size:36 final size:36
Alignment explanation
Indices: 105051922--105051991 Score: 140
Period size: 36 Copynumber: 1.9 Consensus size: 36
105051912 ATACCAACTA
105051922 AAAGTGCTCCAATACTTATTGATGTCACAATAGTTG
1 AAAGTGCTCCAATACTTATTGATGTCACAATAGTTG
105051958 AAAGTGCTCCAATACTTATTGATGTCACAATAGT
1 AAAGTGCTCCAATACTTATTGATGTCACAATAGT
105051992 ACAAACTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (36 bp):
AAAGTGCTCCAATACTTATTGATGTCACAATAGTTG
Found at i:105051988 original size:18 final size:18
Alignment explanation
Indices: 105051931--105051989 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
105051921 AAAAGTGCTC
105051931 CAATACTTATTGATGTCA
1 CAATACTTATTGATGTCA
* **
105051949 CAATAGTTGAAAG-TGCTC-
1 CAATACTT-ATTGATG-TCA
105051967 CAATACTTATTGATGTCA
1 CAATACTTATTGATGTCA
105051985 CAATA
1 CAATA
105051990 GTACAAACTA
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
17 4 0.13
18 23 0.74
19 4 0.13
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.34
Consensus pattern (18 bp):
CAATACTTATTGATGTCA
Found at i:105052662 original size:40 final size:40
Alignment explanation
Indices: 105052607--105052688 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
105052597 ATGTGAAAAA
*
105052607 ATTGATATGCCTCTAGTGGATGTTATTACAACCTATTTGT
1 ATTGATATGCCTCTAGTGGATGTTATTACAACCTACTTGT
*
105052647 ATTGATATGCGTCTAGTGGATGTTATTACAACCTACTTGT
1 ATTGATATGCCTCTAGTGGATGTTATTACAACCTACTTGT
105052687 AT
1 AT
105052689 GGTACACTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (40 bp):
ATTGATATGCCTCTAGTGGATGTTATTACAACCTACTTGT
Found at i:105054465 original size:29 final size:25
Alignment explanation
Indices: 105054402--105054465 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 25
105054392 TATTTAAACC
*
105054402 ATATTA-ATAAAATAAAATAAAATT
1 ATATTATATAAAATAAAATAAAAAT
105054426 ATATT-TA-AAAATAAAAATAAAACAAT
1 ATATTATATAAAAT-AAAAT-AAA-AAT
105054452 ACTATTATATAAAA
1 A-TATTATATAAAA
105054466 ATAATGTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
23 5 0.16
24 11 0.34
25 3 0.09
26 3 0.09
27 4 0.12
28 2 0.06
29 4 0.12
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (25 bp):
ATATTATATAAAATAAAATAAAAAT
Found at i:105054900 original size:25 final size:25
Alignment explanation
Indices: 105054871--105054921 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
105054861 ACACTATAAT
105054871 TTATA-TAATATGAAATATAAAAATA
1 TTATATTAATAT-AAATATAAAAATA
105054896 TTATATTGTAATATAAATATAAAAAT
1 TTATA-T-TAATATAAATATAAAAAT
105054922 GCATTAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 5 0.22
27 12 0.52
28 6 0.26
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (25 bp):
TTATATTAATATAAATATAAAAATA
Found at i:105057088 original size:17 final size:18
Alignment explanation
Indices: 105057050--105057088 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
105057040 TTTTAATTTG
*
105057050 AAAATAGTTAATGGGACT
1 AAAATAGTTAATGGGACC
*
105057068 AAAATTGTTAAT-GGACC
1 AAAATAGTTAATGGGACC
105057085 AAAA
1 AAAA
105057089 ATTTAAGATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.49, C:0.08, G:0.18, T:0.26
Consensus pattern (18 bp):
AAAATAGTTAATGGGACC
Found at i:105057544 original size:21 final size:21
Alignment explanation
Indices: 105057504--105057553 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
105057494 TAGCAAAAAA
*
105057504 CTCTCAAATTTCTCCCTAAAG
1 CTCTCAAATTTCTCACTAAAG
* *
105057525 CTCTCAAATTTCTCATTAAAT
1 CTCTCAAATTTCTCACTAAAG
*
105057546 TTCTCAAA
1 CTCTCAAA
105057554 GCTCTCTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.32, C:0.28, G:0.02, T:0.38
Consensus pattern (21 bp):
CTCTCAAATTTCTCACTAAAG
Found at i:105058711 original size:7 final size:7
Alignment explanation
Indices: 105058696--105058727 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
105058686 AGTCGTTTCA
105058696 TATTTAG
1 TATTTAG
*
105058703 TACTTAG
1 TATTTAG
105058710 TATTTAG
1 TATTTAG
105058717 TATTTAG
1 TATTTAG
105058724 TATT
1 TATT
105058728 ATGTATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.28, C:0.03, G:0.12, T:0.56
Consensus pattern (7 bp):
TATTTAG
Found at i:105059337 original size:18 final size:18
Alignment explanation
Indices: 105059314--105059351 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
105059304 TGTCAGGTGC
105059314 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
105059332 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
105059350 GT
1 GT
105059352 TTCATTTTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.26, G:0.08, T:0.39
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:105059769 original size:24 final size:23
Alignment explanation
Indices: 105059742--105059798 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 23
105059732 AATTTAATAA
*
105059742 AATAAAAGTTGTTTTTA-ATATTTT
1 AATAAAA-TTATTTTTATAT-TTTT
105059766 AATATTAAATTATTTTTATATTTTT
1 AATA--AAATTATTTTTATATTTTT
105059791 AATAAAAT
1 AATAAAAT
105059799 AGAAGTTCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 4 0.14
24 4 0.14
25 16 0.55
26 5 0.17
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (23 bp):
AATAAAATTATTTTTATATTTTT
Found at i:105063108 original size:125 final size:126
Alignment explanation
Indices: 105062819--105063190 Score: 545
Period size: 125 Copynumber: 3.0 Consensus size: 126
105062809 GGCCAAACAT
*
105062819 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGTTTTTTTCAGTAATTTTGTTGAC-ATGTATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAG-CTTTTTCAGTAATTTTGTTGACAATGTATC
* * * *
105062883 TTGCTTGAAGCATTTTTTACACTATTTATTCAGAAACGTGTTCTCAAAA--ATTTTTTTCAG
65 TTGCTTGAAGCATTTTTAACACTATTTGTTCAGAAATGTCTTCTCAAAATTATTTTTTTCAG
* * * *
105062943 GAACTACTGTAGAAAAATAGCATCCACGTGGGAGCATTTTTCAGTACTTTTGTTGACAATGCATC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGC-TTTTTCAGTAATTTTGTTGACAATGTATC
* *
105063008 TTGCTTAAAACATTTTTAACACTATTTGTTCAGAAATGTCTTCTCAAAATTATTTTTTT-AG
65 TTGCTTGAAGCATTTTTAACACTATTTGTTCAGAAATGTCTTCTCAAAATTATTTTTTTCAG
* * * *
105063069 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTCAGTAATTTTGCTGATAGTGTATCC
1 GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTCAGTAATTTTGTTGACAATGTATCT
* *
105063134 TGCTTGAAGCGTTTTTGACACTATTTGTTCAGAAATGTCTTCTCAAAATTATTTTTT
66 TGCTTGAAGCATTTTTAACACTATTTGTTCAGAAATGTCTTCTCAAAATTATTTTTT
105063191 AAGGTAAAAA
Statistics
Matches: 221, Mismatches: 23, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
124 52 0.24
125 126 0.57
126 35 0.16
127 8 0.04
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.39
Consensus pattern (126 bp):
GAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTCAGTAATTTTGTTGACAATGTATCT
TGCTTGAAGCATTTTTAACACTATTTGTTCAGAAATGTCTTCTCAAAATTATTTTTTTCAG
Found at i:105063291 original size:34 final size:34
Alignment explanation
Indices: 105063251--105063349 Score: 139
Period size: 34 Copynumber: 2.9 Consensus size: 34
105063241 ATTTTAACCC
105063251 TAAACCCTAATTTAATTAATTTATTTAAAACA-CA
1 TAAACCCTAATTTAATTAATTTATTTAAAA-ATCA
* * *
105063285 TAAACCCTAATGTACTTAATTTATTTAAAAATTA
1 TAAACCCTAATTTAATTAATTTATTTAAAAATCA
*
105063319 TAAACCCTAATTTAATTAATTT-TTAAAAAAT
1 TAAACCCTAATTTAATTAATTTATTTAAAAAT
105063350 AACTTTAAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
33 9 0.16
34 49 0.84
ACGTcount: A:0.46, C:0.12, G:0.01, T:0.40
Consensus pattern (34 bp):
TAAACCCTAATTTAATTAATTTATTTAAAAATCA
Found at i:105063468 original size:24 final size:24
Alignment explanation
Indices: 105063440--105063486 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
105063430 TTATTTTAGT
*
105063440 AAAA-CCTTAACCTAAAAAACCCTC
1 AAAACCCTAAACC-AAAAAACCCTC
105063464 AAAACCCTAAACCAAAAAACCCT
1 AAAACCCTAAACCAAAAAACCCT
105063487 AAGGACTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.53, C:0.34, G:0.00, T:0.13
Consensus pattern (24 bp):
AAAACCCTAAACCAAAAAACCCTC
Found at i:105067378 original size:29 final size:29
Alignment explanation
Indices: 105067330--105067386 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
105067320 AGACGCATTT
105067330 TGCTAAAATCGGTCATTTTCGGTAAATAA
1 TGCTAAAATCGGTCATTTTCGGTAAATAA
*
105067359 TGCTAAAATCGGCTCA-TTTCTGTAAATA
1 TGCTAAAATCGG-TCATTTTCGGTAAATA
105067387 TACTTGGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 23 0.88
30 3 0.12
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (29 bp):
TGCTAAAATCGGTCATTTTCGGTAAATAA
Found at i:105076221 original size:16 final size:16
Alignment explanation
Indices: 105076202--105076233 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
105076192 AAATGACTAA
105076202 CATGTTTGATGAAATT
1 CATGTTTGATGAAATT
105076218 CATGTTTGATGAAATT
1 CATGTTTGATGAAATT
105076234 GTGTGTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.19, T:0.44
Consensus pattern (16 bp):
CATGTTTGATGAAATT
Found at i:105085515 original size:21 final size:21
Alignment explanation
Indices: 105085468--105085518 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
105085458 GAATTGAATG
*
105085468 AAAATATTATTTTATGTTTAT
1 AAAATATTATGTTATGTTTAT
* *
105085489 ATAATATTATAGTTAT-TTTTT
1 AAAATATTAT-GTTATGTTTAT
105085510 AAAATATTA
1 AAAATATTA
105085519 AAATAAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (21 bp):
AAAATATTATGTTATGTTTAT
Found at i:105087485 original size:14 final size:14
Alignment explanation
Indices: 105087449--105087485 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
105087439 ATATTGTATG
105087449 TTAAATA-TTTTAT
1 TTAAATATTTTTAT
105087462 TTGAAA-ATTTTTAT
1 TT-AAATATTTTTAT
105087476 TTAAATATTT
1 TTAAATATTT
105087486 AGTTAAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 6 0.29
14 15 0.71
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (14 bp):
TTAAATATTTTTAT
Found at i:105094802 original size:1 final size:1
Alignment explanation
Indices: 105094796--105094821 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
105094786 GTAATGATAA
105094796 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
105094822 GGTTTGGTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:105103529 original size:89 final size:89
Alignment explanation
Indices: 105103368--105103533 Score: 298
Period size: 88 Copynumber: 1.9 Consensus size: 89
105103358 CAGTACACTG
* *
105103368 GAGGTGATCAAATTCAGTTAAAAACTGGCAAATTTGCACTAATGACATTCCTCTGGAGTGAGGTT
1 GAGGTGATCAAATTCAGTTAAAAAATAGCAAATTTGCACTAATGACATTCCTCTGGAGTGAGGTT
105103433 GAGCAAGTCAACTTCAAAGACTCA
66 GAGCAAGTCAACTTCAAAGACTCA
105103457 GAGGTGAT-AAATTCAGTTAAAAAATAGCAAATTTGCACTAATGACATTCCTCTTGGAGTGAGGT
1 GAGGTGATCAAATTCAGTTAAAAAATAGCAAATTTGCACTAATGACATTCCTC-TGGAGTGAGGT
105103521 TGAGCAAGTCAAC
65 TGAGCAAGTCAAC
105103534 CATTCATTAC
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
88 42 0.57
89 32 0.43
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.27
Consensus pattern (89 bp):
GAGGTGATCAAATTCAGTTAAAAAATAGCAAATTTGCACTAATGACATTCCTCTGGAGTGAGGTT
GAGCAAGTCAACTTCAAAGACTCA
Found at i:105110467 original size:2 final size:2
Alignment explanation
Indices: 105110460--105110487 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
105110450 TTGAAAGGAA
105110460 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
105110488 TCTAAAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:105112517 original size:20 final size:20
Alignment explanation
Indices: 105112492--105112542 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
105112482 TGGGATAAAG
*
105112492 GAAAAATTAAGTATCAAACT
1 GAAAAATTAAGTACCAAACT
105112512 GAAAAAATTTAAGTACCAAACT
1 G-AAAAA-TTAAGTACCAAACT
*
105112534 -AAACATTAA
1 GAAAAATTAA
105112543 AGTCAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 4 0.15
20 5 0.19
21 5 0.19
22 13 0.48
ACGTcount: A:0.57, C:0.12, G:0.08, T:0.24
Consensus pattern (20 bp):
GAAAAATTAAGTACCAAACT
Found at i:105112517 original size:21 final size:22
Alignment explanation
Indices: 105112493--105112533 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
105112483 GGGATAAAGG
*
105112493 AAAAA-TTAAGTATCAAACTGA
1 AAAAATTTAAGTACCAAACTGA
105112514 AAAAATTTAAGTACCAAACT
1 AAAAATTTAAGTACCAAACT
105112534 AAACATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.56, C:0.12, G:0.07, T:0.24
Consensus pattern (22 bp):
AAAAATTTAAGTACCAAACTGA
Found at i:105112605 original size:30 final size:29
Alignment explanation
Indices: 105112513--105112605 Score: 96
Period size: 30 Copynumber: 3.1 Consensus size: 29
105112503 TATCAAACTG
* *
105112513 AAAAAATTTAAGTACCAAACTAAACATTA
1 AAAAAATTTAGGTACCAAACTAAACTTTA
* * * *
105112542 AAGTCAAATTTAGATACCAAACTAAAATGTA
1 AA--AAAATTTAGGTACCAAACTAAACTTTA
*
105112573 AAAAGAATTTAGGTACCAAATTAAACTTTA
1 AAAA-AATTTAGGTACCAAACTAAACTTTA
105112603 AAA
1 AAA
105112606 CCCAACACAA
Statistics
Matches: 50, Mismatches: 11, Indels: 5
0.76 0.17 0.08
Matches are distributed among these distances:
29 3 0.06
30 24 0.48
31 23 0.46
ACGTcount: A:0.55, C:0.12, G:0.08, T:0.26
Consensus pattern (29 bp):
AAAAAATTTAGGTACCAAACTAAACTTTA
Found at i:105118484 original size:2 final size:2
Alignment explanation
Indices: 105118472--105118509 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
105118462 CTTTTTGTAA
105118472 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
105118510 TAGCTAATCA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:105122616 original size:18 final size:18
Alignment explanation
Indices: 105122580--105122613 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
105122570 AAATGTTTAC
105122580 AAATGTCAAATACTAAAT
1 AAATGTCAAATACTAAAT
*
105122598 AAATTTCAAATA-TAAA
1 AAATGTCAAATACTAAA
105122614 ATATCCATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (18 bp):
AAATGTCAAATACTAAAT
Found at i:105124112 original size:16 final size:16
Alignment explanation
Indices: 105124091--105124124 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
105124081 CCAATATCCA
* *
105124091 ATTATCATATTTGCAC
1 ATTATCACATTTACAC
105124107 ATTATCACATTTACAC
1 ATTATCACATTTACAC
105124123 AT
1 AT
105124125 GTATATTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.21, G:0.03, T:0.41
Consensus pattern (16 bp):
ATTATCACATTTACAC
Found at i:105129942 original size:10 final size:11
Alignment explanation
Indices: 105129921--105129949 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
105129911 TCAATATCAA
105129921 AATTCTGACTC
1 AATTCTGACTC
105129932 AATTC-GACTC
1 AATTCTGACTC
105129942 AATTCTGA
1 AATTCTGA
105129950 GCTCGATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.34
Consensus pattern (11 bp):
AATTCTGACTC
Found at i:105130779 original size:17 final size:18
Alignment explanation
Indices: 105130746--105130780 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
105130736 TTTCAATTCA
*
105130746 TTATATCACTTCCATTTC
1 TTATATCACTGCCATTTC
105130764 TTATATCA-TGCCATTTC
1 TTATATCACTGCCATTTC
105130781 AATATCAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.23, C:0.26, G:0.03, T:0.49
Consensus pattern (18 bp):
TTATATCACTGCCATTTC
Done.