Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 141 of 196
Found at i:41782209 original size:56 final size:57
Alignment explanation
Indices: 41782072--41782210 Score: 181
Period size: 56 Copynumber: 2.4 Consensus size: 57
41782062 TGCAGGATGT
*** *
41782072 GGAGAAGATAATCTTGGGATGTTAGTTTTTATCCTAGAAAAAAAAGAATTTAAAAAGA
1 GGAGAAGATAAAAATGGGATGTTGGTTTTTATCCTA-AAAAAAAAGAATTTAAAAAGA
***
41782130 GGAGAAGATAATTTTGGGATGTTGGTTTTTATCCT-AAAAAAAAGAATTTAAAAAGA
1 GGAGAAGATAAAAATGGGATGTTGGTTTTTATCCTAAAAAAAAAGAATTTAAAAAGA
* *
41782186 GTAGAAGATAAAAATGGGTTGTTGG
1 GGAGAAGATAAAAATGGGATGTTGG
41782211 ATTTACCCTA
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
56 41 0.55
58 33 0.45
ACGTcount: A:0.42, C:0.04, G:0.24, T:0.30
Consensus pattern (57 bp):
GGAGAAGATAAAAATGGGATGTTGGTTTTTATCCTAAAAAAAAAGAATTTAAAAAGA
Found at i:41787366 original size:5 final size:5
Alignment explanation
Indices: 41787356--41787383 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
41787346 GAATTTAACG
41787356 TCAAT TCAAT TCAAT TCAAT TCAAT TCA
1 TCAAT TCAAT TCAAT TCAAT TCAAT TCA
41787384 CATCTTTAAA
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:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (5 bp):
TCAAT
Found at i:41792209 original size:14 final size:14
Alignment explanation
Indices: 41792190--41792219 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
41792180 AATTCAACTC
*
41792190 GATTTGATTAATTT
1 GATTTGAATAATTT
41792204 GATTTGAATAATTT
1 GATTTGAATAATTT
41792218 GA
1 GA
41792220 AATTCAAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (14 bp):
GATTTGAATAATTT
Found at i:41796352 original size:23 final size:26
Alignment explanation
Indices: 41796312--41796358 Score: 64
Period size: 23 Copynumber: 1.9 Consensus size: 26
41796302 ATATTTATGT
*
41796312 TCAATATAGGAAGTAATT-CTAATAA
1 TCAATATAGGAAGAAATTACTAATAA
41796337 TCAAT-TA-GAAGAAATTACTAAT
1 TCAATATAGGAAGAAATTACTAAT
41796359 TTTAAAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 8 0.40
24 7 0.35
25 5 0.25
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.32
Consensus pattern (26 bp):
TCAATATAGGAAGAAATTACTAATAA
Found at i:41799445 original size:27 final size:28
Alignment explanation
Indices: 41799397--41799456 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 28
41799387 ATGATGATGT
**
41799397 AAGCAATGATGAAAGCGGCCA-TAACAC
1 AAGCAATGATGAAAGCAACCATTAACAC
*
41799424 AAGCAATGATGGAAA-CAACCATTAATAC
1 AAGCAATGAT-GAAAGCAACCATTAACAC
41799452 AAGCA
1 AAGCA
41799457 TACTATGTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 14 0.50
28 14 0.50
ACGTcount: A:0.48, C:0.20, G:0.18, T:0.13
Consensus pattern (28 bp):
AAGCAATGATGAAAGCAACCATTAACAC
Found at i:41807590 original size:210 final size:211
Alignment explanation
Indices: 41807227--41807650 Score: 674
Period size: 210 Copynumber: 2.0 Consensus size: 211
41807217 CAAGAAGTTT
* * *
41807227 ATAGTCTTGATTGCTGGTTCAGTTTCCTGATAATAGTTGGGGTCAAGAAATAACATTTTGAGAGA
1 ATAGTCTTGATTGCTGGTTCAGTTTCCTGATAATAGTAGGGCTCAAGAAATAACATTGTGAGAGA
* * *
41807292 TGAGGGTGGTGCATATGATTCTTAACAAACCAGCCAGTATACTGCACCAAATCAAGATGAAAATT
66 CGAGGGTGGTGCATATGATTCCTAACAAACCAACCAGTATACTGCACCAAATCAAGATGAAAATT
* ** * *
41807357 CGATATTGGAACTAACGAATTTTCATATGATGTCCTGGTTTACTAAATACAGAAGAGTAGGTTTA
131 CGATATTGGAACTAAAGAATTTTCATATGATACCCTAGTTTACTAAAGACAGAAGAGTAGGTTTA
41807422 ATATGGTTCAACTTCC
196 ATATGGTTCAACTTCC
* *
41807438 ATAGTCTTGATTGCTGGTTCAGTTTTCC-GATATTGGTAGGGCTCAAGAAATAACATTGT-AGAG
1 ATAGTCTTGATTGCTGGTTCAG-TTTCCTGATAATAGTAGGGCTCAAGAAATAACATTGTGAGAG
*
41807501 ACGAGGGTGGTGCATATGATTCCTAACAAACCAACCAGTATACTGCACCAAATCAAGGTGAAAAT
65 ACGAGGGTGGTGCATATGATTCCTAACAAACCAACCAGTATACTGCACCAAATCAAGATGAAAAT
*
41807566 TTGATATTGTG-ACTAAAGAATTTTCATATGATACCCTAGTTTACTAAAGACAGAAGAGTAGGTT
130 TCGATATTG-GAACTAAAGAATTTTCATATGATACCCTAGTTTACTAAAGACAGAAGAGTAGGTT
41807630 TAATATGGTTCAACTTCC
194 TAATATGGTTCAACTTCC
41807648 ATA
1 ATA
41807651 AAGAAGCCTG
Statistics
Matches: 196, Mismatches: 15, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
210 142 0.72
211 49 0.25
212 5 0.03
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (211 bp):
ATAGTCTTGATTGCTGGTTCAGTTTCCTGATAATAGTAGGGCTCAAGAAATAACATTGTGAGAGA
CGAGGGTGGTGCATATGATTCCTAACAAACCAACCAGTATACTGCACCAAATCAAGATGAAAATT
CGATATTGGAACTAAAGAATTTTCATATGATACCCTAGTTTACTAAAGACAGAAGAGTAGGTTTA
ATATGGTTCAACTTCC
Found at i:41809648 original size:6 final size:6
Alignment explanation
Indices: 41809639--41809671 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
41809629 ATAGTAGTAT
*
41809639 AGTACA AGTAGA AGTAGA AGTAGA AGTAGA AGT
1 AGTAGA AGTAGA AGTAGA AGTAGA AGTAGA AGT
41809672 TTATATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.48, C:0.03, G:0.30, T:0.18
Consensus pattern (6 bp):
AGTAGA
Found at i:41810929 original size:18 final size:18
Alignment explanation
Indices: 41810903--41810938 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
41810893 ATTGAATCGA
*
41810903 TTGTTATGTTGAAATATT
1 TTGTCATGTTGAAATATT
*
41810921 TTGTCATGTTGGAATATT
1 TTGTCATGTTGAAATATT
41810939 GCTTCTTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.03, G:0.19, T:0.53
Consensus pattern (18 bp):
TTGTCATGTTGAAATATT
Found at i:41811084 original size:55 final size:55
Alignment explanation
Indices: 41810940--41811257 Score: 295
Period size: 55 Copynumber: 5.8 Consensus size: 55
41810930 TGGAATATTG
* * * * *
41810940 CTTCTTTTGAATCGGTTGTTTATATGTTTAAAAT-AATTGTTAGGTAGGAATACTA
1 CTTCTTTTGAATAGATTGTTTATATGTTT-AAATCGATTGTTATGTAAGAATACTA
* * * * *
41810995 -TT-TTTTTAATTGACTGTTTACATGTGTAAATCGATTGTTATGTAAGAATACTA
1 CTTCTTTTGAATAGATTGTTTATATGTTTAAATCGATTGTTATGTAAGAATACTA
* * * * *
41811048 CTTCTTTTGAATCA-ATTGTTTATACGGTTAAATCGATTGTTCTGGTGAA-ATATTGCTT
1 CTTCTTTTGAAT-AGATTGTTTATATGTTTAAATCGATTGTTAT-GT-AAGA-A-TACTA
* **
41811106 CTTCTTTTGAATAGATTGTTTATATGTTTAAATCGATTATTATGTTGGAATACTA
1 CTTCTTTTGAATAGATTGTTTATATGTTTAAATCGATTGTTATGTAAGAATACTA
* ** * **
41811161 CTTCTTTTGAATAGATTGTTTATATATTTAAATTAATTGTTATATCGGAATACTA
1 CTTCTTTTGAATAGATTGTTTATATGTTTAAATCGATTGTTATGTAAGAATACTA
* * **
41811216 CTTCTTTTGAGTTGATTGTTTATATGTTTAAATTAATTGTTA
1 CTTCTTTTGAATAGATTGTTTATATGTTTAAATCGATTGTTA
41811258 AAAAGCACGT
Statistics
Matches: 217, Mismatches: 36, Indels: 20
0.79 0.13 0.07
Matches are distributed among these distances:
52 4 0.02
53 37 0.17
54 4 0.02
55 121 0.56
56 4 0.02
57 7 0.03
58 40 0.18
ACGTcount: A:0.28, C:0.08, G:0.15, T:0.49
Consensus pattern (55 bp):
CTTCTTTTGAATAGATTGTTTATATGTTTAAATCGATTGTTATGTAAGAATACTA
Found at i:41811220 original size:113 final size:110
Alignment explanation
Indices: 41810926--41811248 Score: 343
Period size: 113 Copynumber: 2.9 Consensus size: 110
41810916 ATATTTTGTC
* * * * * *
41810926 ATGTTGGAATATTGCTTCTTTTGAATCGGTTGTTTATATGTTTAAAATAATTGTTAGGTAGGAAT
1 ATGTTGGAATACTACTTCTTTTGAATAGATTGTTTATATGTTTAAATTAATTGTTATGT-GGAAT
* * * *
41810991 ACTAT-TT-TTTT-AATTGACTGTTTACATGTGTAAATCGATTGTT
65 ACTATCTTCTTTTGAATTGATTGTTTATATGTTTAAATCGATTATT
** * * ** * *
41811034 ATGTAAGAATACTACTTCTTTTGAATCA-ATTGTTTATACGGTTAAATCGATTGTTCTGGTGAAA
1 ATGTTGGAATACTACTTCTTTTGAAT-AGATTGTTTATATGTTTAAATTAATTGTTAT-GTGGAA
*
41811098 TATTGCT-TCTTCTTTTGAATAGATTGTTTATATGTTTAAATCGATTATT
64 TA---CTATCTTCTTTTGAATTGATTGTTTATATGTTTAAATCGATTATT
* *
41811147 ATGTTGGAATACTACTTCTTTTGAATAGATTGTTTATATATTTAAATTAATTGTTATATCGGAAT
1 ATGTTGGAATACTACTTCTTTTGAATAGATTGTTTATATGTTTAAATTAATTGTTATGT-GGAAT
*
41811212 ACTA-CTTCTTTTGAGTTGATTGTTTATATGTTTAAAT
65 ACTATCTTCTTTTGAATTGATTGTTTATATGTTTAAAT
41811249 TAATTGTTAA
Statistics
Matches: 173, Mismatches: 31, Indels: 20
0.77 0.14 0.09
Matches are distributed among these distances:
108 48 0.28
109 2 0.01
110 34 0.20
111 4 0.02
112 6 0.03
113 79 0.46
ACGTcount: A:0.28, C:0.08, G:0.16, T:0.48
Consensus pattern (110 bp):
ATGTTGGAATACTACTTCTTTTGAATAGATTGTTTATATGTTTAAATTAATTGTTATGTGGAATA
CTATCTTCTTTTGAATTGATTGTTTATATGTTTAAATCGATTATT
Found at i:41812554 original size:31 final size:29
Alignment explanation
Indices: 41812489--41812554 Score: 73
Period size: 28 Copynumber: 2.2 Consensus size: 29
41812479 GTTAGTGATT
41812489 TAATATAAATATATAATTATTATTTAACA
1 TAATATAAATATATAATTATTATTTAACA
* *
41812518 T-ATATAATTAATATAA-TATTTTTAATAACA
1 TAATATAAAT-ATATAATTATTATT--TAACA
41812548 TAATATA
1 TAATATA
41812555 TTCGGGCTCG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
28 13 0.42
29 7 0.23
30 6 0.19
31 5 0.16
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (29 bp):
TAATATAAATATATAATTATTATTTAACA
Found at i:41816712 original size:15 final size:14
Alignment explanation
Indices: 41816692--41816726 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
41816682 TAATCCTTAG
*
41816692 TAATTATCTTAATA
1 TAATTATCCTAATA
41816706 TTAATTATCCTAATA
1 -TAATTATCCTAATA
41816721 TAATTA
1 TAATTA
41816727 AAGTAGAGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (14 bp):
TAATTATCCTAATA
Found at i:41817634 original size:27 final size:26
Alignment explanation
Indices: 41817604--41817668 Score: 78
Period size: 25 Copynumber: 2.5 Consensus size: 26
41817594 GTACATAATT
*
41817604 GGGAAGCCTTCTCTCGAGCCATATAAC
1 GGGAAGCCTTATCT-GAGCCATATAAC
* *
41817631 GGGAAG-CTTATGTGAGCCATGTAAC
1 GGGAAGCCTTATCTGAGCCATATAAC
*
41817656 GGGAAGCTTTATC
1 GGGAAGCCTTATC
41817669 CAGGCTGTAG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
25 17 0.53
26 9 0.28
27 6 0.19
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (26 bp):
GGGAAGCCTTATCTGAGCCATATAAC
Found at i:41817883 original size:26 final size:26
Alignment explanation
Indices: 41817804--41817883 Score: 83
Period size: 26 Copynumber: 3.1 Consensus size: 26
41817794 AGCCATATTA
* * *
41817804 GGAAGCTC-CGGAGAGCTATTAATCA
1 GGAAGCTCACGAAGAGCCATTAATCG
** *
41817829 GGAAGCTCAAAAAGAGCCTTTAATCG
1 GGAAGCTCACGAAGAGCCATTAATCG
41817855 GGAAGCTCACGAAGAGCCATATAAT-G
1 GGAAGCTCACGAAGAGCCAT-TAATCG
41817881 GGA
1 GGA
41817884 CACTTATAAG
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
25 8 0.18
26 32 0.73
27 4 0.09
ACGTcount: A:0.36, C:0.19, G:0.28, T:0.17
Consensus pattern (26 bp):
GGAAGCTCACGAAGAGCCATTAATCG
Found at i:41818036 original size:24 final size:25
Alignment explanation
Indices: 41817976--41818038 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 25
41817966 ATTGCAAGAA
*
41817976 CCATATAACGGGAAGCTCAATAAGG
1 CCATATAACGGGATGCTCAATAAGG
*
41818001 CCATATACCGGGATGCTC-ATAAGAG
1 CCATATAACGGGATGCTCAATAAG-G
*
41818026 CTA-ATAACGGGAT
1 CCATATAACGGGAT
41818039 ACTCTTTCGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
24 14 0.42
25 19 0.58
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.19
Consensus pattern (25 bp):
CCATATAACGGGATGCTCAATAAGG
Found at i:41820201 original size:3 final size:3
Alignment explanation
Indices: 41820193--41820240 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
41820183 ATTCCCACTC
* * * * *
41820193 ATA ATA ATA ATA ATA ATA CTA ATA ATT ATA TTA ATA CTA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
41820241 CTTACTTCAC
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (3 bp):
ATA
Found at i:41820242 original size:12 final size:12
Alignment explanation
Indices: 41820193--41820240 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
41820183 ATTCCCACTC
*
41820193 ATAATAATAATA
1 ATAATATTAATA
*
41820205 ATAATACTAATA
1 ATAATATTAATA
*
41820217 ATTATATTAATA
1 ATAATATTAATA
*
41820229 CTAATATTAATA
1 ATAATATTAATA
41820241 CTTACTTCAC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (12 bp):
ATAATATTAATA
Found at i:41821007 original size:19 final size:19
Alignment explanation
Indices: 41820962--41821001 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
41820952 TTTGTTTTGT
*
41820962 TTTTATTT-CTTTACTTTC
1 TTTTATTTACTTTACTTTA
41820980 TTTTATTTACTTTACTTTA
1 TTTTATTTACTTTACTTTA
41820999 TTT
1 TTT
41821002 CTTTTATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTATTTACTTTACTTTA
Found at i:41821183 original size:22 final size:22
Alignment explanation
Indices: 41821152--41821216 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
41821142 CTATTTAATT
*
41821152 TATATAATATAATACAATACAA
1 TATATAATATAATACAATAAAA
* * *
41821174 TATATTATATTATATAATAAAA
1 TATATAATATAATACAATAAAA
*
41821196 TAATATAA-ATAAAAC-ATAAAA
1 T-ATATAATATAATACAATAAAA
41821217 ATTTAAGATT
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
21 6 0.18
22 23 0.68
23 5 0.15
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.34
Consensus pattern (22 bp):
TATATAATATAATACAATAAAA
Found at i:41824978 original size:24 final size:24
Alignment explanation
Indices: 41824937--41825018 Score: 62
Period size: 24 Copynumber: 3.5 Consensus size: 24
41824927 AATTTATTTA
* *
41824937 AATA-TATATTTAATTTTAAATCT
1 AATATTATTTTTAAATTTAAATCT
** *
41824960 AATATTATTTTTATGTTT-AAGCTT
1 AATATTATTTTTAAATTTAAATC-T
* *
41824984 AATGTTATTTTTAAATTTATCATC-
1 AATATTATTTTTAAATTTA-AATCT
41825008 AATATTATTTT
1 AATATTATTTT
41825019 AAGTTTATCA
Statistics
Matches: 45, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
23 7 0.16
24 36 0.80
26 2 0.04
ACGTcount: A:0.35, C:0.05, G:0.04, T:0.56
Consensus pattern (24 bp):
AATATTATTTTTAAATTTAAATCT
Found at i:41825065 original size:24 final size:24
Alignment explanation
Indices: 41825010--41825066 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
41825000 TTATCATCAA
* *
41825010 TATTATTTTAAGTTTATCACGTAT
1 TATTATTTTAAGTTTATCAAGGAT
41825034 T-TTCATTTTGAA-TTTATCAAGGAT
1 TATT-ATTTT-AAGTTTATCAAGGAT
41825058 TATTATTTT
1 TATTATTTT
41825067 TTAACTTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
23 2 0.07
24 22 0.79
25 4 0.14
ACGTcount: A:0.28, C:0.07, G:0.09, T:0.56
Consensus pattern (24 bp):
TATTATTTTAAGTTTATCAAGGAT
Found at i:41825756 original size:18 final size:17
Alignment explanation
Indices: 41825729--41825763 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
41825719 GATTATTGCT
41825729 CTTATGTGTATTGTATTG
1 CTTATGTGTATT-TATTG
*
41825747 CTTATTTGTATTTATTG
1 CTTATGTGTATTTATTG
41825764 ATTTGTTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.17, C:0.06, G:0.17, T:0.60
Consensus pattern (17 bp):
CTTATGTGTATTTATTG
Found at i:41833832 original size:17 final size:16
Alignment explanation
Indices: 41833810--41833843 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
41833800 ATTTTTGAAT
41833810 TTTTATATTTTATATAA
1 TTTT-TATTTTATATAA
41833827 -TTTTATTTTATATAA
1 TTTTTATTTTATATAA
41833842 TT
1 TT
41833844 GATATATTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 3
0.84 0.00 0.16
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTTATTTTATATAA
Found at i:41833833 original size:15 final size:15
Alignment explanation
Indices: 41833815--41833843 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
41833805 TGAATTTTTA
41833815 TATTTTATATAATTT
1 TATTTTATATAATTT
41833830 TATTTTATATAATT
1 TATTTTATATAATT
41833844 GATATATTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TATTTTATATAATTT
Found at i:41835221 original size:43 final size:42
Alignment explanation
Indices: 41835031--41835279 Score: 308
Period size: 42 Copynumber: 5.9 Consensus size: 42
41835021 CTAAGAAAAT
*
41835031 AAACGCCGCTAAAGATCATGTTCTTTAGCAGCGCTTATGAAA
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTATGAAA
*
41835073 AAACGCAGCTAAAGATCATGTTCTTTAGCGGCGCTTATGAAA
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTATGAAA
* * *
41835115 AAACGCCGCTAAAGATCACGTTCTTTAGCGACGCTTAGGAAA
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTATGAAA
* *
41835157 AAACGCCGCTAAAGATCATGTTCTTTAACGGCGCTT-TGGGAGA
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAT--GAAA
* * * **
41835200 AAACGCCGCTAAA-ACTAATGTTCTATAGCGGCGCTTGTTTAA
1 AAACGCCGCTAAAGA-TCATGTTCTTTAGCGGCGCTTATGAAA
*
41835242 AAACGCCGCTAATAG-T-AGTGTTATTTAGCGGCGCTTAT
1 AAACGCCGCTAA-AGATCA-TGTTCTTTAGCGGCGCTTAT
41835280 TTCACAAACG
Statistics
Matches: 180, Mismatches: 20, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
41 1 0.01
42 143 0.79
43 35 0.19
44 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.27
Consensus pattern (42 bp):
AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTATGAAA
Found at i:41835741 original size:21 final size:21
Alignment explanation
Indices: 41835717--41835765 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
41835707 GCTTCTATCG
* * *
41835717 CTGCTTCTCTCGCTGTGGCTT
1 CTGCTTCTCTCACTGTAGCAT
41835738 CTGCTTCTCTCACTGTAGCAT
1 CTGCTTCTCTCACTGTAGCAT
41835759 CTGCTTC
1 CTGCTTC
41835766 CCTTGCTGCC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.06, C:0.35, G:0.18, T:0.41
Consensus pattern (21 bp):
CTGCTTCTCTCACTGTAGCAT
Found at i:41841270 original size:7 final size:7
Alignment explanation
Indices: 41841260--41841305 Score: 56
Period size: 7 Copynumber: 6.0 Consensus size: 7
41841250 TGATATATTT
41841260 TTATGTA
1 TTATGTA
41841267 TTATGTAA
1 TTATGT-A
41841275 GTTATGTAA
1 -TTATGT-A
41841284 GTTATGTA
1 -TTATGTA
41841292 TTATGTA
1 TTATGTA
41841299 TTATGTA
1 TTATGTA
41841306 AGTACTGTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
7 20 0.54
8 2 0.05
9 15 0.41
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.52
Consensus pattern (7 bp):
TTATGTA
Found at i:41841281 original size:9 final size:9
Alignment explanation
Indices: 41841267--41841407 Score: 113
Period size: 9 Copynumber: 16.4 Consensus size: 9
41841257 TTTTTATGTA
41841267 TTATGTAAG
1 TTATGTAAG
41841276 TTATGTAAG
1 TTATGTAAG
41841285 TTATGT-A-
1 TTATGTAAG
41841292 TTATGT-A-
1 TTATGTAAG
41841299 TTATGTAAG
1 TTATGTAAG
41841308 -TACTGTAAG
1 TTA-TGTAAG
*
41841317 TAATGTAAG
1 TTATGTAAG
41841326 TTATGTAAAG
1 TTATGT-AAG
*
41841336 TAATGT-A-
1 TTATGTAAG
*
41841343 TAATGTAAG
1 TTATGTAAG
*
41841352 TTAAG-AAGG
1 TTATGTAA-G
41841361 TTATGT-A-
1 TTATGTAAG
*
41841368 TAATGTAAG
1 TTATGTAAG
*
41841377 TCATGTAAG
1 TTATGTAAG
* *
41841386 TTATTTAAT
1 TTATGTAAG
41841395 TTATGTAAG
1 TTATGTAAG
41841404 TTAT
1 TTAT
41841408 TTATGTAAGT
Statistics
Matches: 108, Mismatches: 13, Indels: 22
0.76 0.09 0.15
Matches are distributed among these distances:
7 24 0.22
8 9 0.08
9 66 0.61
10 9 0.08
ACGTcount: A:0.36, C:0.01, G:0.19, T:0.43
Consensus pattern (9 bp):
TTATGTAAG
Found at i:41841296 original size:32 final size:33
Alignment explanation
Indices: 41841260--41841389 Score: 124
Period size: 32 Copynumber: 3.9 Consensus size: 33
41841250 TGATATATTT
41841260 TTATGTATTATGTAAGTTATGTAAGTTATGTA-
1 TTATGTATTATGTAAGTTATGTAAGTTATGTAG
*
41841292 TTATGTATTATGTAAG-TACTGTAAGTAATGTAAG
1 TTATGTATTATGTAAGTTA-TGTAAGTTATGT-AG
* * *
41841326 TTATGTA--AAGTAATGTATAATGTAAGTTAAGAAGG
1 TTATGTATTATGTAA-GT-T-ATGTAAGTTATGTA-G
* *
41841361 TTATGTATAATGTAAGTCATGTAAGTTAT
1 TTATGTATTATGTAAGTTATGTAAGTTAT
41841390 TTAATTTATG
Statistics
Matches: 80, Mismatches: 8, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
31 2 0.03
32 32 0.40
33 2 0.03
34 18 0.22
35 18 0.22
36 3 0.04
37 5 0.06
ACGTcount: A:0.36, C:0.02, G:0.20, T:0.42
Consensus pattern (33 bp):
TTATGTATTATGTAAGTTATGTAAGTTATGTAG
Found at i:41841411 original size:13 final size:13
Alignment explanation
Indices: 41841393--41841418 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41841383 AAGTTATTTA
41841393 ATTTATGTAAGTT
1 ATTTATGTAAGTT
41841406 ATTTATGTAAGTT
1 ATTTATGTAAGTT
41841419 GTCTTGGCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (13 bp):
ATTTATGTAAGTT
Found at i:41841547 original size:20 final size:20
Alignment explanation
Indices: 41841532--41841583 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
41841522 GTAAGTGTTG
41841532 TATTATGTAAGTAAGTTATT
1 TATTATGTAAGTAAGTTATT
41841552 TATTATGTAAGTAAGTTATT
1 TATTATGTAAGTAAGTTATT
41841572 TATTATGTAAGT
1 TATTATGTAAGT
41841584 TTTAAGTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (20 bp):
TATTATGTAAGTAAGTTATT
Found at i:41841613 original size:119 final size:121
Alignment explanation
Indices: 41841477--41841801 Score: 432
Period size: 119 Copynumber: 2.7 Consensus size: 121
41841467 ATGTAAGGCA
41841477 AATTAAGTTATGTAGGCTATGTATTATGCAAGTTATTTAAGTTGTGTAAGTGTTGTATTATGTAA
1 AATTAAGTTATGTAGGCTATGTATTATGCAAGTTATTTAAGTTGTGTAAGTGTTGTATTATGTAA
* ** *
41841542 GTAAGTTATTTATTATGTAAG-TAAGTTATTTAT-TATGTAAGT-TTTAAGTCAAA-T
66 GTAAGTTATTTATTATGTAAGTTAAGTCAAATATGTAAGT-AGTATTTAA-TCAAAGT
41841596 AATTAAGTTATGTAGGCTATGTATTATGCAAGTTATTTAAGTTGTGTAAGTGTTGTATTATGTAA
1 AATTAAGTTATGTAGGCTATGTATTATGCAAGTTATTTAAGTTGTGTAAGTGTTGTATTATGTAA
* * *
41841661 GTAAGTTATTTATTATGTAAGTTTTAAGTCAAATATGTAAGTTGTATTTTATGAAAGT
66 GTAAGTTATTTATTATGTAAG--TTAAGTCAAATATGTAAGTAGTATTTAATCAAAGT
* * * * *
41841719 TATATAAGTTATGTAGGCTATGTTTTATGCAAGTTATTTAATTTCTGTAAGTGCTGTATTA--T-
1 AAT-TAAGTTATGTAGGCTATGTATTATGCAAGTTATTTAAGTTGTGTAAGTGTTGTATTATGTA
*
41841781 A-TAAGTTATGTATTATGTAAG
65 AGTAAGTTATTTATTATGTAAG
41841802 ATATGTAAGT
Statistics
Matches: 186, Mismatches: 13, Indels: 13
0.88 0.06 0.06
Matches are distributed among these distances:
119 86 0.46
120 19 0.10
121 1 0.01
122 16 0.09
123 11 0.06
124 53 0.28
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.46
Consensus pattern (121 bp):
AATTAAGTTATGTAGGCTATGTATTATGCAAGTTATTTAAGTTGTGTAAGTGTTGTATTATGTAA
GTAAGTTATTTATTATGTAAGTTAAGTCAAATATGTAAGTAGTATTTAATCAAAGT
Found at i:41841792 original size:16 final size:16
Alignment explanation
Indices: 41841773--41841808 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
41841763 CTGTAAGTGC
*
41841773 TGTATTATATAAGTTA
1 TGTATTATATAAGATA
*
41841789 TGTATTATGTAAGATA
1 TGTATTATATAAGATA
41841805 TGTA
1 TGTA
41841809 AGTTGTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.17, T:0.47
Consensus pattern (16 bp):
TGTATTATATAAGATA
Found at i:41841810 original size:25 final size:25
Alignment explanation
Indices: 41841782--41841865 Score: 89
Period size: 25 Copynumber: 3.4 Consensus size: 25
41841772 CTGTATTATA
41841782 TAAGTTATGTATTATGTAAGATATG
1 TAAGTTATGTATTATGTAAGATATG
* * * *
41841807 TAAGTTGTATTTTATGTAAGTTATG
1 TAAGTTATGTATTATGTAAGATATG
* * *
41841832 TAAGTAACG-AGTTATGTAAGCTATG
1 TAAGTTATGTA-TTATGTAAGATATG
41841857 TAAGTTATG
1 TAAGTTATG
41841866 CAAGATTATA
Statistics
Matches: 46, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
25 46 1.00
ACGTcount: A:0.33, C:0.02, G:0.21, T:0.43
Consensus pattern (25 bp):
TAAGTTATGTATTATGTAAGATATG
Found at i:41841830 original size:9 final size:9
Alignment explanation
Indices: 41841709--41841865 Score: 82
Period size: 9 Copynumber: 18.6 Consensus size: 9
41841699 AAGTTGTATT
*
41841709 TTATGAAAG
1 TTATGTAAG
*
41841718 TTATATAAG
1 TTATGTAAG
*
41841727 TTATGTAGG
1 TTATGTAAG
* *
41841736 CTATGT--T
1 TTATGTAAG
*
41841743 TTATGCAAG
1 TTATGTAAG
* *
41841752 TTATTTAAT
1 TTATGTAAG
*
41841761 TTCTGTAAG
1 TTATGTAAG
**
41841770 TGCTGT-A-
1 TTATGTAAG
*
41841777 TTATATAAG
1 TTATGTAAG
41841786 TTATGT-A-
1 TTATGTAAG
41841793 TTATGTAAG
1 TTATGTAAG
*
41841802 ATATGTAAG
1 TTATGTAAG
**
41841811 -T-TGTATT
1 TTATGTAAG
41841818 TTATGTAAG
1 TTATGTAAG
41841827 TTATGTAAG
1 TTATGTAAG
* *
41841836 TAACG--AG
1 TTATGTAAG
41841843 TTATGTAAG
1 TTATGTAAG
*
41841852 CTATGTAAG
1 TTATGTAAG
41841861 TTATG
1 TTATG
41841866 CAAGATTATA
Statistics
Matches: 107, Mismatches: 31, Indels: 20
0.68 0.20 0.13
Matches are distributed among these distances:
7 22 0.21
8 6 0.06
9 79 0.74
ACGTcount: A:0.32, C:0.04, G:0.20, T:0.45
Consensus pattern (9 bp):
TTATGTAAG
Found at i:41841901 original size:8 final size:7
Alignment explanation
Indices: 41841883--41841928 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
41841873 ATAATATAAG
41841883 TTATGTA
1 TTATGTA
41841890 TTATGTTA
1 TTATG-TA
41841898 TTATGTA
1 TTATGTA
41841905 TTATGTA
1 TTATGTA
*
41841912 --ATTTA
1 TTATGTA
41841917 TTATGTTA
1 TTATG-TA
41841925 TTAT
1 TTAT
41841929 ATATAAGTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
5 4 0.12
7 16 0.48
8 13 0.39
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (7 bp):
TTATGTA
Found at i:41841901 original size:27 final size:26
Alignment explanation
Indices: 41841870--41841999 Score: 89
Period size: 27 Copynumber: 5.2 Consensus size: 26
41841860 GTTATGCAAG
41841870 ATTATAATATAAGTTATGTATTATGTT
1 ATTAT-ATATAAGTTATGTATTATGTT
* * * *
41841897 ATTATGTATTATGTAATTTATTATGTT
1 ATTATATA-TAAGTTATGTATTATGTT
* *
41841924 ATTATATATAAGTTA--TATGGAAGTT
1 ATTATATATAAGTTATGTAT-TATGTT
*
41841949 A-T-TATATAAGTTATGCA--A-GCTT
1 ATTATATATAAGTTATGTATTATG-TT
*
41841971 A-TA-AAATAAGTTATGTATTATGTT
1 ATTATATATAAGTTATGTATTATGTT
41841995 ATTAT
1 ATTAT
41842000 GTATTATGTA
Statistics
Matches: 80, Mismatches: 12, Indels: 23
0.70 0.10 0.20
Matches are distributed among these distances:
21 1 0.01
22 17 0.21
23 11 0.14
24 8 0.10
25 9 0.11
26 7 0.09
27 27 0.34
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (26 bp):
ATTATATATAAGTTATGTATTATGTT
Found at i:41841903 original size:15 final size:15
Alignment explanation
Indices: 41841883--41841928 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
41841873 ATAATATAAG
41841883 TTATGTATTATGTTA
1 TTATGTATTATGTTA
41841898 TTATGTATTATG-TA
1 TTATGTATTATGTTA
*
41841912 --ATTTATTATGTTA
1 TTATGTATTATGTTA
41841925 TTAT
1 TTAT
41841929 ATATAAGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 9 0.33
13 2 0.07
14 2 0.07
15 14 0.52
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (15 bp):
TTATGTATTATGTTA
Found at i:41842620 original size:33 final size:33
Alignment explanation
Indices: 41842582--41842685 Score: 104
Period size: 33 Copynumber: 3.2 Consensus size: 33
41842572 CTAGGGTTAA
41842582 TAAATTTAAAGTATATTAAATATAAGTTAATGG
1 TAAATTTAAAGTATATTAAATATAAGTTAATGG
* * ** * ** **
41842615 TAAA-TTCAATTATATT-TTTCTCTGCAACATGG
1 TAAATTTAAAGTATATTAAATATAAGTTA-ATGG
41842647 TAAATTTAAAGTATATTAAATATAAGTTAATGG
1 TAAATTTAAAGTATATTAAATATAAGTTAATGG
41842680 TAAATT
1 TAAATT
41842686 AAGGTCTGAT
Statistics
Matches: 50, Mismatches: 18, Indels: 6
0.68 0.24 0.08
Matches are distributed among these distances:
31 4 0.08
32 18 0.36
33 24 0.48
34 4 0.08
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (33 bp):
TAAATTTAAAGTATATTAAATATAAGTTAATGG
Found at i:41842630 original size:32 final size:32
Alignment explanation
Indices: 41842582--41842687 Score: 97
Period size: 32 Copynumber: 3.2 Consensus size: 32
41842572 CTAGGGTTAA
41842582 TAAATTTAAAGTATATTAAATATAAGTTAATGG
1 TAAA-TTAAAGTATATTAAATATAAGTTAATGG
* * ** * ** **
41842615 TAAATTCAATTATATT-TTTCTCTGCAACATGG
1 TAAATTAAAGTATATTAAATATAAGTTA-ATGG
41842647 TAAATTTAAAGTATATTAAATATAAGTTAATGG
1 TAAA-TTAAAGTATATTAAATATAAGTTAATGG
41842680 TAAATTAA
1 TAAATTAA
41842688 GGTCTGATTT
Statistics
Matches: 52, Mismatches: 18, Indels: 7
0.68 0.23 0.09
Matches are distributed among these distances:
31 4 0.08
32 22 0.42
33 22 0.42
34 4 0.08
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (32 bp):
TAAATTAAAGTATATTAAATATAAGTTAATGG
Found at i:41845068 original size:17 final size:17
Alignment explanation
Indices: 41845046--41845095 Score: 84
Period size: 17 Copynumber: 3.0 Consensus size: 17
41845036 TATCCTATTT
41845046 CCTACATTATATAATAA
1 CCTACATTATATAATAA
41845063 CCTACATTATATAATAA
1 CCTACATTATATAATAA
*
41845080 ACTACA-TATATAATAA
1 CCTACATTATATAATAA
41845096 TCTAGCAGCG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 10 0.31
17 22 0.69
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (17 bp):
CCTACATTATATAATAA
Found at i:41845274 original size:112 final size:108
Alignment explanation
Indices: 41845123--41845466 Score: 339
Period size: 114 Copynumber: 3.0 Consensus size: 108
41845113 CAACGCACCG
* * * *
41845123 CTAATAATATGTTTTAGCGGCGTTTTACCATAAGCGCCAC-AACTGCTAGTATACATCAAGACCA
1 CTAATACTATGCTTTAGCGGCGTTTTA-AATAAGCGCCACTAA-TGCTAATATACATCAAGACCA
*
41845187 ATGCGTTGCGTTTTGGTTAATATTTTGCGGACTTTACAATAAGCGCCT
64 A-GC-TTGCGTTTTGGTTAATATTTTGCGG-CTTTACAATAAGCGCCA
* * * *
41845235 CTAATACTATGCTTTAGTGGCGTTTTCAAATAAGCGCCACTAATCCTAATGTACCTCAAGACCAA
1 CTAATACTATGCTTTAGCGGCGTTTT-AAATAAGCGCCACTAATGCTAATATACATCAAGACCAA
* * * * * ** *
41845300 ACTCTGCGTTTTGGTTAAGAAATATTGCGGCGCTTTTCAGTACTCGCCG
65 GCT-TGCGTTTTGGTT-A-ATATTTTGC-G-GCTTTACAATAAGCGCCA
* * *
41845349 CTAATACTATTCTTTAGCGGCGTTTTAATATAAGCGCCACTAAGGCTACTATACATCAAGACCAA
1 CTAATACTATGCTTTAGCGGCGTTTTAA-ATAAGCGCCACTAATGCTAATATACATCAAGACC-A
* *
41845414 AGCACTGCGTTTTGGTTAATATTTTGCGGCGTTTTCCAATAAGCGCCA
64 AGC-TTGCGTTTTGGTTAATATTTTGCGGC--TTTACAATAAGCGCCA
41845462 CTAAT
1 CTAAT
41845467 CCTAATATAC
Statistics
Matches: 188, Mismatches: 32, Indels: 23
0.77 0.13 0.09
Matches are distributed among these distances:
110 1 0.01
111 15 0.08
112 54 0.29
113 35 0.19
114 67 0.36
115 16 0.09
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (108 bp):
CTAATACTATGCTTTAGCGGCGTTTTAAATAAGCGCCACTAATGCTAATATACATCAAGACCAAG
CTTGCGTTTTGGTTAATATTTTGCGGCTTTACAATAAGCGCCA
Found at i:41845487 original size:74 final size:73
Alignment explanation
Indices: 41845365--41845505 Score: 185
Period size: 74 Copynumber: 1.9 Consensus size: 73
41845355 CTATTCTTTA
* * *
41845365 GCGGCGTTTTAATATAAGCGCCACTAAGGCTACTATACATCAAGACCAAAGCACTGCGTTTTGGT
1 GCGGCGTTTTAATATAAGCGCCACTAAGCCTAATATACAGCAAGACCAAA-CACTGCGTTTTGGT
41845430 TAATATTTT
65 TAATATTTT
* * * * *
41845439 GCGGCGTTTTCCA-ATAAGCGCCACTAATCCTAATATACCGCAATACCAAACTCTGCGTTTTGGT
1 GCGGCGTTTT-AATATAAGCGCCACTAAGCCTAATATACAGCAAGACCAAACACTGCGTTTTGGT
41845503 TAA
65 TAA
41845506 GAAATATTGC
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
73 16 0.28
74 41 0.71
75 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (73 bp):
GCGGCGTTTTAATATAAGCGCCACTAAGCCTAATATACAGCAAGACCAAACACTGCGTTTTGGTT
AATATTTT
Found at i:41845570 original size:188 final size:188
Alignment explanation
Indices: 41845257--41845842 Score: 974
Period size: 188 Copynumber: 3.1 Consensus size: 188
41845247 TTTAGTGGCG
* * *
41845257 TTTTCAAATAAGCGCCACTAATCCTAATGTACCTCAAGACCAAACTCTGCGTTTTGGTTAAGAAA
1 TTTTCCAATAAGCGCCACTAATCCTAATATACCACAAGACCAAACTCTGCGTTTTGGTTAAGAAA
* *
41845322 TATTGCGGCGCTTTTCAGTACTCGCCGCTAATACTATTCTTTAGCGGCGTTTTAATATAAGCGCC
66 TATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATTCTTTAGCAGCGTTTTAATATAAGCGCC
** * * *
41845387 ACTAAGGCTACTATACATCAAGACCAAAGCACTGCGTTTTGGTTAATATTTTGCGGCG
131 ACTACTGCTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAATATTTTGCGGCA
* *
41845445 TTTTCCAATAAGCGCCACTAATCCTAATATACCGCAATACCAAACTCTGCGTTTTGGTTAAGAAA
1 TTTTCCAATAAGCGCCACTAATCCTAATATACCACAAGACCAAACTCTGCGTTTTGGTTAAGAAA
* * *
41845510 TATTGCGGTGCTTTTCACTACTTGCCGCTAATACTATTCTTTAGCAGCATTTTAATATAAGCGCC
66 TATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATTCTTTAGCAGCGTTTTAATATAAGCGCC
41845575 ACTACTGCTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAATATTTTGCGGCA
131 ACTACTGCTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAATATTTTGCGGCA
*
41845633 TTTTCCAATAAGCGCCACTAATCCTAATATACCACAAGACCGAACTCTGCGTTTTGGTTAAGAAA
1 TTTTCCAATAAGCGCCACTAATCCTAATATACCACAAGACCAAACTCTGCGTTTTGGTTAAGAAA
*
41845698 TCTTGCGGCGCTTTTCACTACTCGCCGCTAATACTATTCTTTAGCAGCGTTTTAATATAAGCGCC
66 TATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATTCTTTAGCAGCGTTTTAATATAAGCGCC
*
41845763 ACTACTGCTAGTATATATCAAGACCAAAGCGCTGCGTTTTGGTTAATATTTTGCGGCA
131 ACTACTGCTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAATATTTTGCGGCA
* * * *
41845821 CTTTACAATAAGCACCGCTAAT
1 TTTTCCAATAAGCGCCACTAAT
41845843 AATATGTTTT
Statistics
Matches: 372, Mismatches: 26, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
188 372 1.00
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (188 bp):
TTTTCCAATAAGCGCCACTAATCCTAATATACCACAAGACCAAACTCTGCGTTTTGGTTAAGAAA
TATTGCGGCGCTTTTCACTACTCGCCGCTAATACTATTCTTTAGCAGCGTTTTAATATAAGCGCC
ACTACTGCTAGTATACATCAAGACCAAAGCGCTGCGTTTTGGTTAATATTTTGCGGCA
Found at i:41845854 original size:113 final size:113
Alignment explanation
Indices: 41845640--41846165 Score: 574
Period size: 113 Copynumber: 4.6 Consensus size: 113
41845630 GCATTTTCCA
* * * * *
41845640 ATAAGCGCCACTAATCCTAATATACCA-CAAGACCGAA-CTCTGCGTTTTGGTTAAGAAATCTTG
1 ATAAGCGCCACTAATGCTAATATA-CATCAAGACCAAAGCGCTGCGTTTTGGTT-A-ATATTTTG
* * ** * *
41845703 CGGCGCTTTTCACTACTCGCCGCTAATACTATTCTTTAGCAGCGTTTTAAT
63 CGGCGCTTTACAATAAGCGCCGCTAATACTATGCTTTAGCGGCGTTTTAAT
* * *
41845754 ATAAGCGCCACTACTGCTAGTATATATCAAGACCAAAGCGCTGCGTTTTGGTTAATATTTTGCGG
1 ATAAGCGCCACTAATGCTAATATACATCAAGACCAAAGCGCTGCGTTTTGGTTAATATTTTGCGG
* * * * **
41845819 CACTTTACAATAAGCACCGCTAATAATATGTTTTAGCGGCGTTTTACC
66 CGCTTTACAATAAGCGCCGCTAATACTATGCTTTAGCGGCGTTTTAAT
* * * * *
41845867 ATAAGTGCCACAAATGCTAGTATACATCAAGACCAATGTGCTGCGTTTTGGTTAATATTTTGCGG
1 ATAAGCGCCACTAATGCTAATATACATCAAGACCAAAGCGCTGCGTTTTGGTTAATATTTTGCGG
41845932 CGCTTTACAATAAGCGCCGCTAATACTATGCTTTAGCGGCGTTTTCAA-
66 CGCTTTACAATAAGCGCCGCTAATACTATGCTTTAGCGGCGTTTT-AAT
* * * * ** * *
41845980 ATAAGCGCCACTAATCCTAATGTACCTCAAGATCAAA-CTATGCGTTTTGGTTAAGAAATATTGC
1 ATAAGCGCCACTAATGCTAATATACATCAAGACCAAAGCGCTGCGTTTTGGTT-A-ATATTTTGC
* * ** *
41846044 GGCGCTTTTCAGTACTCGCCGCTAATACTATACTTTAGCGGCGTTTTAAT
64 GGCGCTTTACAATAAGCGCCGCTAATACTATGCTTTAGCGGCGTTTTAAT
* * * *
41846094 ATAAGCACCACTAAGGCTAATATACATCAAGACCAAAGCACTGCGTTTTGGTTAAGAGCTTTTGC
1 ATAAGCGCCACTAATGCTAATATACATCAAGACCAAAGCGCTGCGTTTTGGTTAATA--TTTTGC
41846159 GGCGCTT
64 GGCGCTT
41846166 GGTAGTAAAT
Statistics
Matches: 344, Mismatches: 59, Indels: 17
0.82 0.14 0.04
Matches are distributed among these distances:
112 12 0.03
113 180 0.52
114 113 0.33
115 39 0.11
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.31
Consensus pattern (113 bp):
ATAAGCGCCACTAATGCTAATATACATCAAGACCAAAGCGCTGCGTTTTGGTTAATATTTTGCGG
CGCTTTACAATAAGCGCCGCTAATACTATGCTTTAGCGGCGTTTTAAT
Found at i:41846140 original size:227 final size:226
Alignment explanation
Indices: 41845640--41846165 Score: 574
Period size: 227 Copynumber: 2.3 Consensus size: 226
41845630 GCATTTTCCA
* * * *
41845640 ATAAGCGCCACTAATCCTAATATACCA-CAAGACCGAA-CTCTGCGTTTTGGTTAAGAAATCTTG
1 ATAAGCGCCACTAATGCTAATATA-CATCAAGACCAAAGCACTGCGTTTTGGTT-A-AAATTTTG
* * ** * *
41845703 CGGCGCTTTTCACTACTCGCCGCTAATACTATTCTTTAGCAGCGTTTTAATATAAGCGCCACTAC
63 CGGCGCTTTACAATAAGCGCCGCTAATACTATGCTTTAGCAGCGTTTTAATATAAGCGCCACTAA
* * * * * *
41845768 TGCTAGTATATATCAAGACCAAAGCGCTGCGTTTTGGTTAATATTTTGCGGCACTTTACAATAAG
128 TCCTAATATACATCAAGACCAAAGCGATGCGTTTTGGTTAAAATATTGCGGCACTTTACAATAAG
** *
41845833 CACCGCTAATAATATGTTTTAGCGGCGTTTTACC
193 CACCGCTAATAATATACTTTAGCGGCGTTTTAAC
* * * * ** *
41845867 ATAAGTGCCACAAATGCTAGTATACATCAAGACCAATGTGCTGCGTTTTGGTTAATATTTTGCGG
1 ATAAGCGCCACTAATGCTAATATACATCAAGACCAAAGCACTGCGTTTTGGTTAAAATTTTGCGG
*
41845932 CGCTTTACAATAAGCGCCGCTAATACTATGCTTTAGCGGCGTTTTCAA-ATAAGCGCCACTAATC
66 CGCTTTACAATAAGCGCCGCTAATACTATGCTTTAGCAGCGTTTT-AATATAAGCGCCACTAATC
* * * * * * * **
41845996 CTAATGTACCTCAAGATCAAA-CTATGCGTTTTGGTTAAGAAATATTGCGGCGCTTTTCAGTACT
130 CTAATATACATCAAGACCAAAGCGATGCGTTTTGGTT-A-AAATATTGCGGCACTTTACAATAAG
* * *
41846060 CGCCGCTAATACTATACTTTAGCGGCGTTTTAAT
193 CACCGCTAATAATATACTTTAGCGGCGTTTTAAC
* * *
41846094 ATAAGCACCACTAAGGCTAATATACATCAAGACCAAAGCACTGCGTTTTGGTTAAGAGCTTTTGC
1 ATAAGCGCCACTAATGCTAATATACATCAAGACCAAAGCACTGCGTTTTGGTTAA-A-ATTTTGC
41846159 GGCGCTT
64 GGCGCTT
41846166 GGTAGTAAAT
Statistics
Matches: 244, Mismatches: 48, Indels: 12
0.80 0.16 0.04
Matches are distributed among these distances:
225 13 0.05
226 81 0.33
227 124 0.51
228 13 0.05
229 13 0.05
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.31
Consensus pattern (226 bp):
ATAAGCGCCACTAATGCTAATATACATCAAGACCAAAGCACTGCGTTTTGGTTAAAATTTTGCGG
CGCTTTACAATAAGCGCCGCTAATACTATGCTTTAGCAGCGTTTTAATATAAGCGCCACTAATCC
TAATATACATCAAGACCAAAGCGATGCGTTTTGGTTAAAATATTGCGGCACTTTACAATAAGCAC
CGCTAATAATATACTTTAGCGGCGTTTTAAC
Found at i:41847857 original size:15 final size:16
Alignment explanation
Indices: 41847837--41847875 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
41847827 AGTTCAGTCC
41847837 AAAACCCAAA-TAAAT
1 AAAACCCAAACTAAAT
*
41847852 AAAACCCAAACTCAAT
1 AAAACCCAAACTAAAT
41847868 -AAACCCAA
1 AAAACCCAA
41847876 CAAACCCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.62, C:0.28, G:0.00, T:0.10
Consensus pattern (16 bp):
AAAACCCAAACTAAAT
Found at i:41849006 original size:3 final size:3
Alignment explanation
Indices: 41848998--41849040 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
41848988 GTTAATCTGT
*
41848998 TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
41849041 ATCCGTTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:41849173 original size:3 final size:3
Alignment explanation
Indices: 41849167--41849252 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
41849157 TCACATTTTA
* * * * * * *
41849167 TAT TAT TAT TGT TAT TAT TAT AAT AAT TAT TAT TGT TAC TAT CAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
41849215 TAT TAT TAT TAT TAT TAT TAG TAT TAG TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
41849253 ATATCAATTT
Statistics
Matches: 66, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
2 2 0.03
3 64 0.97
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:41857627 original size:16 final size:17
Alignment explanation
Indices: 41857597--41857629 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
41857587 TATACAAGAG
*
41857597 AAAATTATTACTTCAAA
1 AAAATTAATACTTCAAA
41857614 AAAATTAATA-TTCAAA
1 AAAATTAATACTTCAAA
41857630 TATGATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.58, C:0.09, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATTAATACTTCAAA
Found at i:41868509 original size:31 final size:31
Alignment explanation
Indices: 41868442--41868521 Score: 90
Period size: 31 Copynumber: 2.5 Consensus size: 31
41868432 AAGTTTAAAT
** * *
41868442 TTTAATATGAAAATAATTGTCAAGTTGATGA
1 TTTAATATGAAAATAATTAACAAATTGAGGA
41868473 TTTAATATGAAAATAATTAACAAATTGAAGGA
1 TTTAATATGAAAATAATTAACAAATTG-AGGA
41868505 -TTAATATGGATAAATAA
1 TTTAATAT-GA-AAATAA
41868522 AATTTAAGCC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
31 31 0.74
32 5 0.12
33 6 0.14
ACGTcount: A:0.49, C:0.03, G:0.14, T:0.35
Consensus pattern (31 bp):
TTTAATATGAAAATAATTAACAAATTGAGGA
Found at i:41883560 original size:15 final size:15
Alignment explanation
Indices: 41883535--41883569 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
41883525 GACTCTATTT
*
41883535 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
41883549 TAATTAATATTAAGA
1 TAATTAATATTAAGA
41883564 TAATTA
1 TAATTA
41883570 TTAAGGATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:41887488 original size:12 final size:12
Alignment explanation
Indices: 41887471--41887504 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
41887461 TTTTCTTTCT
41887471 TTACTTTATTTA
1 TTACTTTATTTA
41887483 TTACTTTATTTTA
1 TTACTTTA-TTTA
41887496 TTA-TTTATT
1 TTACTTTATT
41887505 ACTGATTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 2 0.10
12 12 0.57
13 7 0.33
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (12 bp):
TTACTTTATTTA
Found at i:41887506 original size:20 final size:20
Alignment explanation
Indices: 41887430--41887507 Score: 76
Period size: 20 Copynumber: 4.0 Consensus size: 20
41887420 AACACAATTA
41887430 TTATTATTATTATTTATTA-T
1 TTATT-TTATTATTTATTACT
*
41887450 TTATTAT-TTATTT-TT-CT
1 TTATTTTATTATTTATTACT
*
41887467 TT-CTTTACTTTATTTATTACT
1 TTATTTTA--TTATTTATTACT
41887488 TTATTTTATTATTTATTACT
1 TTATTTTATTATTTATTACT
41887508 GATTTGGATA
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
16 2 0.04
17 5 0.11
18 6 0.13
19 7 0.15
20 19 0.40
21 4 0.09
22 4 0.09
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (20 bp):
TTATTTTATTATTTATTACT
Found at i:41888402 original size:4 final size:4
Alignment explanation
Indices: 41888384--41888442 Score: 72
Period size: 4 Copynumber: 15.2 Consensus size: 4
41888374 TTCCTAAAGC
41888384 ATAA A-AA AT-A ATAA ATAA AT-A A-AA ATCAAA ATAA ATAA ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT--AA ATAA ATAA ATAA ATAA
41888430 ATAA ATAA ATAA A
1 ATAA ATAA ATAA A
41888443 AAGAAAAAGA
Statistics
Matches: 49, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
3 10 0.20
4 35 0.71
6 4 0.08
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (4 bp):
ATAA
Found at i:41893234 original size:23 final size:23
Alignment explanation
Indices: 41893186--41893240 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
41893176 ATTTTATGCA
* *
41893186 TGCAAGTGTTAGTGGCACTACGG
1 TGCAAGTGATAGTGGCACTACAG
**
41893209 TGCAAGTGATAGTGGCACTTTAG
1 TGCAAGTGATAGTGGCACTACAG
41893232 TGCAAGTGA
1 TGCAAGTGA
41893241 CAGAAGCACA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.25, C:0.15, G:0.33, T:0.27
Consensus pattern (23 bp):
TGCAAGTGATAGTGGCACTACAG
Found at i:41897084 original size:18 final size:18
Alignment explanation
Indices: 41897063--41897097 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
41897053 ATTCTGTAAT
41897063 TAGTTTAAATTTAATTTC
1 TAGTTTAAATTTAATTTC
*
41897081 TAGTTTAAATTTGATTT
1 TAGTTTAAATTTAATTT
41897098 TTAAAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.03, G:0.09, T:0.57
Consensus pattern (18 bp):
TAGTTTAAATTTAATTTC
Found at i:41899686 original size:28 final size:29
Alignment explanation
Indices: 41899625--41899682 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
41899615 AAATATTTTT
* * *
41899625 AATTAATAATTCCTTTATTTATATAAATA
1 AATTAATAATTCATATAATTATATAAATA
41899654 AATTAATAATT-ATATAATTATAT-AATA
1 AATTAATAATTCATATAATTATATAAATA
41899681 AA
1 AA
41899683 ATTATATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 6 0.23
28 9 0.35
29 11 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (29 bp):
AATTAATAATTCATATAATTATATAAATA
Found at i:41899687 original size:13 final size:14
Alignment explanation
Indices: 41899643--41899690 Score: 57
Period size: 13 Copynumber: 3.5 Consensus size: 14
41899633 ATTCCTTTAT
41899643 TTATATAA-ATAAA
1 TTATATAATATAAA
41899656 TTA-ATAATTATATAA
1 TTATATAA-TATA-AA
41899671 TTATATAATA-AAA
1 TTATATAATATAAA
41899684 TTATATA
1 TTATATA
41899691 TTTTTATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
12 4 0.13
13 12 0.39
14 4 0.13
15 7 0.23
16 4 0.13
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TTATATAATATAAA
Found at i:41910999 original size:17 final size:17
Alignment explanation
Indices: 41910977--41911009 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
41910967 TTCTGTAATT
41910977 AGTTTAAATTTAATTTC
1 AGTTTAAATTTAATTTC
*
41910994 AGTTTAAATTTGATTT
1 AGTTTAAATTTAATTT
41911010 TTAAAATTTT
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:0.33, C:0.03, G:0.09, T:0.55
Consensus pattern (17 bp):
AGTTTAAATTTAATTTC
Found at i:41913545 original size:18 final size:20
Alignment explanation
Indices: 41913522--41913564 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
41913512 ATTCCTTTAT
41913522 TTATATAAA-TA-ATAATAA
1 TTATATAAATTATATAATAA
41913540 TTATATAAATTATATAATAA
1 TTATATAAATTATATAATAA
*
41913560 ATATA
1 TTATA
41913565 ATTTTTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.41
19 2 0.09
20 11 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TTATATAAATTATATAATAA
Found at i:41913565 original size:18 final size:17
Alignment explanation
Indices: 41913523--41913565 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
41913513 TTCCTTTATT
41913523 TATATAAATAATAATAA
1 TATATAAATAATAATAA
41913540 TTATATAAATTATATAATAA
1 -TATATAAA-TA-ATAATAA
41913560 -ATATAA
1 TATATAA
41913566 TTTTTATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 14 0.61
19 2 0.09
20 7 0.30
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TATATAAATAATAATAA
Found at i:41937750 original size:44 final size:44
Alignment explanation
Indices: 41937695--41937789 Score: 147
Period size: 44 Copynumber: 2.2 Consensus size: 44
41937685 ATATCTCAAG
*
41937695 GTCCATATTTATAACATGGCAATTAA-AGAAGAATTGACAGAAAA
1 GTCCATGTTTATAACATGGCAATTAAGA-AAGAATTGACAGAAAA
*
41937739 GTCCATGTTTATAACATGGCAATTAAGAAAGAATTGACGGAAAA
1 GTCCATGTTTATAACATGGCAATTAAGAAAGAATTGACAGAAAA
*
41937783 GACCATG
1 GTCCATG
41937790 GTTGGACCAT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 46 0.98
45 1 0.02
ACGTcount: A:0.44, C:0.13, G:0.19, T:0.24
Consensus pattern (44 bp):
GTCCATGTTTATAACATGGCAATTAAGAAAGAATTGACAGAAAA
Found at i:41937801 original size:44 final size:44
Alignment explanation
Indices: 41937707--41937803 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 44
41937697 CCATATTTAT
* * *
41937707 AACATGGCAATTAAAGAAGAATTGACAGAAAAGTCCATGTTTAT
1 AACATGGCAATTAAAGAAGAATTGACAGAAAAGACCATGGTTAG
* *
41937751 AACATGGCAATT-AAGAAAGAATTGACGGAAAAGACCATGGTTGG
1 AACATGGCAATTAAAG-AAGAATTGACAGAAAAGACCATGGTTAG
*
41937795 ACCATGGCA
1 AACATGGCA
41937804 GTAAGTGTGC
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
43 3 0.07
44 43 0.93
ACGTcount: A:0.43, C:0.13, G:0.23, T:0.21
Consensus pattern (44 bp):
AACATGGCAATTAAAGAAGAATTGACAGAAAAGACCATGGTTAG
Found at i:41937869 original size:50 final size:50
Alignment explanation
Indices: 41937810--41938041 Score: 256
Period size: 50 Copynumber: 4.7 Consensus size: 50
41937800 GGCAGTAAGT
41937810 GTGCCAGTGTAAGACCATATCTGGGACATGGCATCGGCACAGACCGAGGA
1 GTGCCAGTGTAAGACCATATCTGGGACATGGCATCGGCACAGACCGAGGA
* * **
41937860 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATAGACCGTCGA
1 GTGCCAGTGTAAGACCATATCTGGGACATGGCATCGGCACAGACCGAGGA
* * * * *
41937910 GTGCTAGTGTAAGACCATATTTGGGACATGGCATCGGCACGGACAGAGAA
1 GTGCCAGTGTAAGACCATATCTGGGACATGGCATCGGCACAGACCGAGGA
* * * * * * *
41937960 GAGTCAGTGTAAGACCATGTATGGGACATGGCATCGACACCGA--TATGTGA
1 GTGCCAGTGTAAGACCATATCTGGGACATGGCATCGGCACAGACCGA-G-GA
* *
41938010 -TCCCA-TGTAAGACCATATCTGGGATATGGCAT
1 GTGCCAGTGTAAGACCATATCTGGGACATGGCAT
41938042 TGGCGTCCTA
Statistics
Matches: 152, Mismatches: 28, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
48 25 0.16
49 3 0.02
50 124 0.82
ACGTcount: A:0.28, C:0.21, G:0.30, T:0.21
Consensus pattern (50 bp):
GTGCCAGTGTAAGACCATATCTGGGACATGGCATCGGCACAGACCGAGGA
Found at i:41937968 original size:100 final size:100
Alignment explanation
Indices: 41937810--41937995 Score: 300
Period size: 100 Copynumber: 1.9 Consensus size: 100
41937800 GGCAGTAAGT
* * *
41937810 GTGCCAGTGTAAGACCATATCTGGGACATGGCATCGGCACAGACCGAGGAGTGCCAGTGTAAGAC
1 GTGCCAGTGTAAGACCATATCTGGGACATGGCATCGGCACAGACAGAGAAGAGCCAGTGTAAGAC
*
41937875 CATGTCTGGGACATGGCATCGGCATAGACCGTCGA
66 CATGTATGGGACATGGCATCGGCATAGACCGTCGA
* * * *
41937910 GTGCTAGTGTAAGACCATATTTGGGACATGGCATCGGCACGGACAGAGAAGAGTCAGTGTAAGAC
1 GTGCCAGTGTAAGACCATATCTGGGACATGGCATCGGCACAGACAGAGAAGAGCCAGTGTAAGAC
41937975 CATGTATGGGACATGGCATCG
66 CATGTATGGGACATGGCATCG
41937996 ACACCGATAT
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
100 78 1.00
ACGTcount: A:0.27, C:0.21, G:0.32, T:0.19
Consensus pattern (100 bp):
GTGCCAGTGTAAGACCATATCTGGGACATGGCATCGGCACAGACAGAGAAGAGCCAGTGTAAGAC
CATGTATGGGACATGGCATCGGCATAGACCGTCGA
Found at i:41939676 original size:16 final size:17
Alignment explanation
Indices: 41939655--41939705 Score: 63
Period size: 16 Copynumber: 3.1 Consensus size: 17
41939645 TTATTCTTAT
41939655 TTTTC-TCTTTTTTCCC
1 TTTTCATCTTTTTTCCC
*
41939671 TTTTCTTCTTCTTTT--C
1 TTTTCATCTT-TTTTCCC
41939687 TTTTCATCTTTTTTCCC
1 TTTTCATCTTTTTTCCC
41939704 TT
1 TT
41939706 CCAAACAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 4 0.13
16 15 0.50
17 7 0.23
18 4 0.13
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTCATCTTTTTTCCC
Found at i:41940929 original size:6 final size:6
Alignment explanation
Indices: 41940920--41940961 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
41940910 GATTTTCTCC
41940920 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG
41940962 GAGAAATAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (6 bp):
AAAATG
Found at i:41955357 original size:17 final size:16
Alignment explanation
Indices: 41955326--41955369 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
41955316 GATTTATTTA
41955326 ATAATATAATATCATT
1 ATAATATAATATCATT
*
41955342 ATAATTTAATTATCATT
1 ATAATATAA-TATCATT
*
41955359 AATTATATAAT
1 -ATAATATAAT
41955370 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 8 0.35
17 8 0.35
18 7 0.30
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (16 bp):
ATAATATAATATCATT
Found at i:41968033 original size:42 final size:42
Alignment explanation
Indices: 41967934--41968043 Score: 107
Period size: 42 Copynumber: 2.6 Consensus size: 42
41967924 TCTCATAAGC
* * * * * *
41967934 TTCAGTTAA-CTCATATGAGTTTCTGTTTAACCCTATTGGTT
1 TTCAGTTAAGCACTTATGAGCTTCTGTTCAACCCTATCGGGT
*
41967975 TTCAGTTAAGCTCTTATGAGCTTCTGTTCAACCCT-TACGGGT
1 TTCAGTTAAGCACTTATGAGCTTCTGTTCAACCCTAT-CGGGT
* * *
41968017 TTCCGTTTAGCACTTATGTGCTTCTGT
1 TTCAGTTAAGCACTTATGAGCTTCTGT
41968044 GTAGCCTTCG
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
41 10 0.17
42 48 0.83
ACGTcount: A:0.18, C:0.21, G:0.17, T:0.44
Consensus pattern (42 bp):
TTCAGTTAAGCACTTATGAGCTTCTGTTCAACCCTATCGGGT
Found at i:41968888 original size:108 final size:108
Alignment explanation
Indices: 41968699--41968914 Score: 423
Period size: 108 Copynumber: 2.0 Consensus size: 108
41968689 GAGATCTTGT
41968699 TATGGCCTATATGTATGAAATTTGAGGTGTGTAGGTTGAAGTCAAGAATGGGTGAGAAAAGAGGC
1 TATGGCCTATATGTATGAAATTTGAGGTGTGTAGGTTGAAGTCAAGAATGGGTGAGAAAAGAGGC
41968764 CATAAAATGACCTATTTTCGTCCATACGTGTAGACACACGGGC
66 CATAAAATGACCTATTTTCGTCCATACGTGTAGACACACGGGC
41968807 TATGGCCTATATGTATGAAATTTGAGGTGTGTAGGTTGAAGTCAAGAATGGGTGAGAAAAGAGGC
1 TATGGCCTATATGTATGAAATTTGAGGTGTGTAGGTTGAAGTCAAGAATGGGTGAGAAAAGAGGC
*
41968872 CATAAAATGACCTATTTTCGTCCATACGTGTAGAGACACGGGC
66 CATAAAATGACCTATTTTCGTCCATACGTGTAGACACACGGGC
41968915 GTGTGTCTCA
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
108 107 1.00
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.27
Consensus pattern (108 bp):
TATGGCCTATATGTATGAAATTTGAGGTGTGTAGGTTGAAGTCAAGAATGGGTGAGAAAAGAGGC
CATAAAATGACCTATTTTCGTCCATACGTGTAGACACACGGGC
Found at i:41979139 original size:30 final size:30
Alignment explanation
Indices: 41979105--41979190 Score: 93
Period size: 31 Copynumber: 2.8 Consensus size: 30
41979095 AATTTGGATT
41979105 AAATCAAAATTTCATGTATAAATTTACACA-
1 AAATCAAAATTT-ATGTATAAATTTACACAC
* * *
41979135 AAATCAAAGTTTATATATAAAATTACACATC
1 AAATCAAAATTTATGTATAAATTTACACA-C
* * *
41979166 AAACCAGAATTTATGTATAATTTTA
1 AAATCAAAATTTATGTATAAATTTA
41979191 AGATTTATCC
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
29 15 0.33
30 11 0.24
31 19 0.42
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.35
Consensus pattern (30 bp):
AAATCAAAATTTATGTATAAATTTACACAC
Found at i:41979163 original size:29 final size:30
Alignment explanation
Indices: 41979105--41979163 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
41979095 AATTTGGATT
* *
41979105 AAATCAAAATTTCATGTATAAATTTACACA
1 AAATCAAAATTTCATATATAAAATTACACA
*
41979135 AAATCAAAGTTT-ATATATAAAATTACACA
1 AAATCAAAATTTCATATATAAAATTACACA
41979164 TCAAACCAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.32
Consensus pattern (30 bp):
AAATCAAAATTTCATATATAAAATTACACA
Found at i:41979185 original size:31 final size:28
Alignment explanation
Indices: 41979111--41979185 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 28
41979101 GATTAAATCA
* *
41979111 AAATTTCATGTATAAATTTACACAAAATC
1 AAATTT-ATGTATAAAATTACACAAAACC
*
41979140 AAAGTTTATATATAAAATTACACATCAAACC
1 AAA-TTTATGTATAAAATTACACA--AAACC
41979171 AGAATTTATGTATAA
1 A-AATTTATGTATAA
41979186 TTTTAAGATT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
29 18 0.47
30 3 0.08
31 15 0.39
32 2 0.05
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.33
Consensus pattern (28 bp):
AAATTTATGTATAAAATTACACAAAACC
Found at i:41985175 original size:3 final size:3
Alignment explanation
Indices: 41985167--41985204 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
41985157 AAAATGCACA
*
41985167 AAT AAT AAT AAT AAT AAT AAT AAT TAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
41985205 AAGGAAAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:41988293 original size:27 final size:27
Alignment explanation
Indices: 41988236--41988299 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
41988226 GGTCTGTCAT
* * ** *
41988236 AGGCGGCACCAAAGGTGCCAGTGGCAG
1 AGGCGACACCAAAGGTGCCACTACCAC
*
41988263 AGGCGACACCAAAGGTGCCTCTACCAC
1 AGGCGACACCAAAGGTGCCACTACCAC
41988290 AGGCGACACC
1 AGGCGACACC
41988300 TGTGCCATGT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.28, C:0.33, G:0.31, T:0.08
Consensus pattern (27 bp):
AGGCGACACCAAAGGTGCCACTACCAC
Found at i:41988892 original size:76 final size:78
Alignment explanation
Indices: 41988687--41988918 Score: 238
Period size: 76 Copynumber: 2.9 Consensus size: 78
41988677 GTTTAGTTAT
* *
41988687 TAATAATTATTGTTACTTAGTATTATTGTTAGTAAAAAACTAATATTATTACTCTGGTTAGTTAT
1 TAATTATTATTGTTAGTTAGTATTATTGTTAGTAAAAAAC---TATTATTA-T-TGGTTAGTTAT
41988752 TAGGATTAGTAAAAACCC
61 TAGGATTAGTAAAAACCC
* *** * **
41988770 TAATTATTATT-TTAGTTAGTATGATTGTTAGTTTTTACACTA-TATTATT-GTTAGTTATTATT
1 TAATTATTATTGTTAGTTAGTATTATTGTTAG-TAAAAAACTATTATTATTGGTTAGTTATTAGG
*
41988832 TTTAGT-AAAACCC
65 ATTAGTAAAAACCC
* *
41988845 TAATTATTATTGTTAGTTAGTATTATTTTTAGTAAAAAACTATTATTATTATTTTGTTAGTTATT
1 TAATTATTATTGTTAGTTAGTATTATTGTTAGTAAAAAAC---TATTATTA-TTGGTTAGTTATT
41988910 AGGATTAGT
62 AGGATTAGT
41988919 GGTTAAATGT
Statistics
Matches: 122, Mismatches: 19, Indels: 18
0.77 0.12 0.11
Matches are distributed among these distances:
75 22 0.18
76 34 0.28
77 1 0.01
78 3 0.02
79 10 0.08
80 4 0.03
81 16 0.13
82 18 0.15
83 14 0.11
ACGTcount: A:0.33, C:0.06, G:0.12, T:0.50
Consensus pattern (78 bp):
TAATTATTATTGTTAGTTAGTATTATTGTTAGTAAAAAACTATTATTATTGGTTAGTTATTAGGA
TTAGTAAAAACCC
Found at i:41993999 original size:158 final size:159
Alignment explanation
Indices: 41993657--41994511 Score: 1314
Period size: 158 Copynumber: 5.4 Consensus size: 159
41993647 TTTTTTTATT
* * * * * *
41993657 TTCGGATTTATCTTATTTTCGAATTTTATTGCTTTCAAAAAATATATTATTTTTGTATTTTATTA
1 TTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTA
* * *
41993722 TTTTATATTATTTTAGTACATAA-AGTTTGAAATGTATTAATTTAGTGTATTTTTTTATATAAAT
66 TTTTATATTATTTTAGTACATAATA-TTTGAAATGTATTATTTTAGTGTGTTTTTATATATAAAT
*
41993786 TTAGTAAAAAACCCTTATTTTGACCATTTG
130 TTAGTAAAAAACCCTTATTTTGGCCATTTG
* * *
41993816 TTCGTATTTTTCTTATTTTCAGATTTTACTACTTTCAAAAAATATATTATTTTCGTATTTTATTA
1 TTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTA
41993881 TTTTATATTATTTTAGTACATAATATTTGAAATGTATTATTTTAGTGT-TTTTTATATATAAATT
66 TTTTATATTATTTTAGTACATAATATTTGAAATGTATTATTTTAGTGTGTTTTTATATATAAATT
*
41993945 TAGTAAAAAACTCTTATTTTGGTCC-TTTG
131 TAGTAAAAAACCCTTATTTTGG-CCATTTG
* *
41993974 TTCATATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATATTATTTTCGTATTTTATTA
1 TTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTA
* *
41994039 TTTTATATTATTTTAGTACATAA-AGTTTGAAATGTATTAATTTAGTGTGTGTTTTTTATATAAA
66 TTTTATATTATTTTAGTACATAATA-TTTGAAATGTATTATTTTAGTGTGT-TTTTATATATAAA
*
41994103 TTTAGTAAAAAAGCTCTTATTTTGGCCATTTG
129 TTTAGTAAAAAA-CCCTTATTTTGGCCATTTG
** *
41994135 TTCGTATTTTTCTTATTTTCAAATTTTATTACTTTCAAAAAATATACTATTTTTGTATTTTATTA
1 TTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTA
41994200 TTTTATATTATTTTAGTACATAATATTTGAAATGTATTATTTTAGTGTG-TTTT-TATATAAATT
66 TTTTATATTATTTTAGTACATAATATTTGAAATGTATTATTTTAGTGTGTTTTTATATATAAATT
*
41994263 TAGT-AAAAACCCCTATTTTGGCCATTTG
131 TAGTAAAAAACCCTTATTTTGGCCATTTG
*
41994291 TTCGTATTTTTCTTATTTTCGGATTTTATTACTTTTAAAAAATATACTATTTTCGTATTTTATTA
1 TTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTA
*
41994356 TTTTATATTATTTTAGTACATAATGTTTGAAATGTATTATTTTAGTGTGTTTTTATA-A-AAATT
66 TTTTATATTATTTTAGTACATAATATTTGAAATGTATTATTTTAGTGTGTTTTTATATATAAATT
* *
41994419 TAGTAAAAAACCATTATTTTGGCCCTTTG
131 TAGTAAAAAACCCTTATTTTGGCCATTTG
* ** * *
41994448 TTCGTATTTTTCTTATTTTTGGATTTTATTACTTTCAGTAAATATACTATTTTTGTTTTTTATT
1 TTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATT
41994512 TCTTTTCGTA
Statistics
Matches: 647, Mismatches: 38, Indels: 24
0.91 0.05 0.03
Matches are distributed among these distances:
156 135 0.21
157 90 0.14
158 162 0.25
159 110 0.17
160 27 0.04
161 122 0.19
162 1 0.00
ACGTcount: A:0.29, C:0.07, G:0.09, T:0.55
Consensus pattern (159 bp):
TTCGTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTA
TTTTATATTATTTTAGTACATAATATTTGAAATGTATTATTTTAGTGTGTTTTTATATATAAATT
TAGTAAAAAACCCTTATTTTGGCCATTTG
Found at i:41994282 original size:317 final size:317
Alignment explanation
Indices: 41993662--41994511 Score: 1381
Period size: 317 Copynumber: 2.7 Consensus size: 317
41993652 TTATTTTCGG
* * * *
41993662 ATTTATCTTATTTTCGAATTTTATTGCTTTCAAAAAATATATTATTTTTGTATTTTATTATTTTA
1 ATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATATTATTTTCGTATTTTATTATTTTA
*
41993727 TATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTAT-TTTTTTATATAAATTTAGT
66 TATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTGTGTTTTTTATATAAATTTAGT
* *
41993791 AAAAAACCCTTATTTTGACCATTTGTTCGTATTTTTCTTATTTTCAGATTTTACTACTTTCAAAA
131 AAAAAA-CCTTATTTTGGCCATTTGTTCGTATTTTTCTTATTTTCAGATTTTATTACTTTCAAAA
* *
41993856 AATATATTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAATATTTGAAATGTATTAT
195 AATATACTATTTTTGTATTTTATTATTTTATATTATTTTAGTACATAATATTTGAAATGTATTAT
* * *
41993921 TTTAGTGTTTTTTATATATAAATTTAGTAAAAAACTCTTATTTTGGTCC-TTTGTTCAT
260 TTTAGTGTGTTTTATATATAAATTTAGTAAAAAACCCCTATTTTGG-CCATTTGTTCAT
41993979 ATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATATTATTTTCGTATTTTATTATTTTA
1 ATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATATTATTTTCGTATTTTATTATTTTA
41994044 TATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTGTGTTTTTTATATAAATTTAGT
66 TATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTGTGTTTTTTATATAAATTTAGT
*
41994109 AAAAAAGCTCTTATTTTGGCCATTTGTTCGTATTTTTCTTATTTTCAAATTTTATTACTTTCAAA
131 AAAAAA-C-CTTATTTTGGCCATTTGTTCGTATTTTTCTTATTTTCAGATTTTATTACTTTCAAA
41994174 AAATATACTATTTTTGTATTTTATTATTTTATATTATTTTAGTACATAATATTTGAAATGTATTA
194 AAATATACTATTTTTGTATTTTATTATTTTATATTATTTTAGTACATAATATTTGAAATGTATTA
*
41994239 TTTTAGTGTGTTTT-TATATAAATTTAGT-AAAAACCCCTATTTTGGCCATTTGTTCGT
259 TTTTAGTGTGTTTTATATATAAATTTAGTAAAAAACCCCTATTTTGGCCATTTGTTCAT
* *
41994296 ATTTTTCTTATTTTCGGATTTTATTACTTTTAAAAAATATACTATTTTCGTATTTTATTATTTTA
1 ATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATATTATTTTCGTATTTTATTATTTTA
* * *
41994361 TATTATTTTAGTACATAATGTTTGAAATGTATTATTTTA--GTGTG-TTTTTATAAAAATTTAGT
66 TATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTGTGTTTTTTATATAAATTTAGT
* ** **
41994423 AAAAAACCATTATTTTGGCCCTTTGTTCGTATTTTTCTTATTTTTGGATTTTATTACTTTCAGTA
131 AAAAAACC-TTATTTTGGCCATTTGTTCGTATTTTTCTTATTTTCAGATTTTATTACTTTCAAAA
*
41994488 AATATACTATTTTTGTTTTTTATT
195 AATATACTATTTTTGTATTTTATT
41994512 TCTTTTCGTA
Statistics
Matches: 502, Mismatches: 27, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
312 1 0.00
313 74 0.15
314 23 0.05
315 5 0.01
316 2 0.00
317 228 0.45
318 40 0.08
319 129 0.26
ACGTcount: A:0.30, C:0.07, G:0.08, T:0.55
Consensus pattern (317 bp):
ATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATATTATTTTCGTATTTTATTATTTTA
TATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTGTGTTTTTTATATAAATTTAGT
AAAAAACCTTATTTTGGCCATTTGTTCGTATTTTTCTTATTTTCAGATTTTATTACTTTCAAAAA
ATATACTATTTTTGTATTTTATTATTTTATATTATTTTAGTACATAATATTTGAAATGTATTATT
TTAGTGTGTTTTATATATAAATTTAGTAAAAAACCCCTATTTTGGCCATTTGTTCAT
Found at i:41994708 original size:30 final size:30
Alignment explanation
Indices: 41994672--41994794 Score: 147
Period size: 30 Copynumber: 4.4 Consensus size: 30
41994662 AAATAAAATA
*
41994672 AAATAATAAAACATAGAATGTACATAACGT
1 AAATAATAAAACATAGAATGTACATAACAT
41994702 AAATAATAAAACATA-AA--TA-AT---A-
1 AAATAATAAAACATAGAATGTACATAACAT
* *
41994724 AAATAATAAGACATAGTATGTACATAACAT
1 AAATAATAAAACATAGAATGTACATAACAT
41994754 AAATAATAAAACATAGAATGTACATAACAT
1 AAATAATAAAACATAGAATGTACATAACAT
41994784 AAA-AATTAAAA
1 AAATAA-TAAAA
41994795 TTAAATTATG
Statistics
Matches: 79, Mismatches: 5, Indels: 18
0.77 0.05 0.18
Matches are distributed among these distances:
22 14 0.18
23 1 0.01
25 2 0.03
26 4 0.05
27 2 0.03
29 5 0.06
30 51 0.65
ACGTcount: A:0.62, C:0.08, G:0.07, T:0.24
Consensus pattern (30 bp):
AAATAATAAAACATAGAATGTACATAACAT
Found at i:41994720 original size:14 final size:14
Alignment explanation
Indices: 41994663--41994726 Score: 60
Period size: 14 Copynumber: 4.5 Consensus size: 14
41994653 AAATTAATTA
*
41994663 AATAAAATA-AAAT
1 AATAAAACATAAAT
41994676 AATAAAACATAGAAT
1 AATAAAACATA-AAT
* *
41994691 -GTACATAACGTAAAT
1 AATA-A-AACATAAAT
41994706 AATAAAACATAAAT
1 AATAAAACATAAAT
41994720 AATAAAA
1 AATAAAA
41994727 TAATAAGACA
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
13 8 0.20
14 18 0.44
15 8 0.20
16 7 0.17
ACGTcount: A:0.67, C:0.06, G:0.05, T:0.22
Consensus pattern (14 bp):
AATAAAACATAAAT
Found at i:41994726 original size:52 final size:52
Alignment explanation
Indices: 41994668--41994768 Score: 175
Period size: 52 Copynumber: 1.9 Consensus size: 52
41994658 AATTAAATAA
*
41994668 AATAAAATAATAAAACATAGAATGTACATAACGTAAATAATAAAACATAAAT
1 AATAAAATAATAAAACATAGAATGTACATAACATAAATAATAAAACATAAAT
* *
41994720 AATAAAATAATAAGACATAGTATGTACATAACATAAATAATAAAACATA
1 AATAAAATAATAAAACATAGAATGTACATAACATAAATAATAAAACATA
41994769 GAATGTACAT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.62, C:0.08, G:0.06, T:0.24
Consensus pattern (52 bp):
AATAAAATAATAAAACATAGAATGTACATAACATAAATAATAAAACATAAAT
Found at i:41994784 original size:16 final size:16
Alignment explanation
Indices: 41994734--41994784 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
41994724 AAATAATAAG
*
41994734 ACATAGTATGTACATA
1 ACATAGAATGTACATA
*
41994750 ACATA-AATAATA-A-A
1 ACATAGAAT-GTACATA
41994764 ACATAGAATGTACATA
1 ACATAGAATGTACATA
41994780 ACATA
1 ACATA
41994785 AAAATTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
14 8 0.29
15 7 0.25
16 13 0.46
ACGTcount: A:0.55, C:0.12, G:0.08, T:0.25
Consensus pattern (16 bp):
ACATAGAATGTACATA
Found at i:41994835 original size:82 final size:81
Alignment explanation
Indices: 41994664--41994836 Score: 183
Period size: 82 Copynumber: 2.1 Consensus size: 81
41994654 AATTAATTAA
*
41994664 ATAAA-ATAAAATAATAAAACATAGAATGTACATAACGTAAATAATAAAACATAAATAATAAAAT
1 ATAAACAT-AAATAATAAAACATAGAATGTACATAACATAAATAATAAAACATAAATAATAAAAT
* **
41994728 AATAAGACATAGTATGT
65 AATAAAACATAGTAAAT
* * * *
41994745 ACATAACATAAATAATAAAACATAGAATGTACATAACATAAA-AATTAAAA-TTAAATTAT-GAA
1 ATA-AACATAAATAATAAAACATAGAATGTACATAACATAAATAA-TAAAACATAAATAATAAAA
*
41994807 TGAATGAAAATATAGATAAAT
64 T-AAT-AAAACATAG-TAAAT
41994828 ATAAACATA
1 ATAAACATA
41994837 TATCTCTTTT
Statistics
Matches: 76, Mismatches: 10, Indels: 11
0.78 0.10 0.11
Matches are distributed among these distances:
80 3 0.04
81 14 0.18
82 52 0.68
83 7 0.09
ACGTcount: A:0.61, C:0.06, G:0.07, T:0.25
Consensus pattern (81 bp):
ATAAACATAAATAATAAAACATAGAATGTACATAACATAAATAATAAAACATAAATAATAAAATA
ATAAAACATAGTAAAT
Found at i:41995012 original size:3 final size:3
Alignment explanation
Indices: 41995004--41995119 Score: 55
Period size: 3 Copynumber: 39.3 Consensus size: 3
41994994 CTTCCCTCCC
* * * *
41995004 TCT TCT TCT TCT CCT TC- TCT TTT TCT TTT TCCT TTT TCT TCCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T-CT TCT TCT T-CT TCT
* * * * * * *
41995050 GCG CCT CCT TCC CCT TCT TCT TCT TC- TCT TC- TCT TC- TCT TTT TC-
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
41995094 TCT T-T TCT TCT TCT CTCAT TCT TCT T
1 TCT TCT TCT TCT TCT -TC-T TCT TCT T
41995120 TCCTGCAGCT
Statistics
Matches: 84, Mismatches: 19, Indels: 20
0.68 0.15 0.16
Matches are distributed among these distances:
2 12 0.14
3 62 0.74
4 9 0.11
5 1 0.01
ACGTcount: A:0.01, C:0.36, G:0.02, T:0.61
Consensus pattern (3 bp):
TCT
Found at i:41995086 original size:13 final size:13
Alignment explanation
Indices: 41995063--41995109 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
41995053 CCTCCTTCCC
41995063 CTTCTTCTTCT-TCT
1 CTTC-TCTTCTCT-T
41995077 CTTCTCTTCTCTT
1 CTTCTCTTCTCTT
* *
41995090 TTTCTCTTTTCTT
1 CTTCTCTTCTCTT
41995103 CTTCTCT
1 CTTCTCT
41995110 CATTCTTCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
13 24 0.83
14 5 0.17
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (13 bp):
CTTCTCTTCTCTT
Found at i:41996225 original size:50 final size:49
Alignment explanation
Indices: 41996171--41996276 Score: 133
Period size: 50 Copynumber: 2.1 Consensus size: 49
41996161 TAATTTTAAT
*
41996171 TTTTAT-GTTATGGTTTACTATTTATGTTTTGTACATACTATGTCTTATTA
1 TTTTATAGTTAT-G-TTACTATTTATGTTATGTACATACTATGTCTTATTA
* * * *
41996221 TTTTATTATTTATGTTATTATTTATGTTATGTACATTCTATGTTTTATTA
1 TTTTA-TAGTTATGTTACTATTTATGTTATGTACATACTATGTCTTATTA
41996271 TTTTAT
1 TTTTAT
41996277 TTAATTAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
49 1 0.02
50 42 0.86
51 2 0.04
52 4 0.08
ACGTcount: A:0.23, C:0.06, G:0.09, T:0.62
Consensus pattern (49 bp):
TTTTATAGTTATGTTACTATTTATGTTATGTACATACTATGTCTTATTA
Found at i:41996238 original size:12 final size:12
Alignment explanation
Indices: 41996218--41996250 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
41996208 CTATGTCTTA
*
41996218 TTATTTTATTAT
1 TTATGTTATTAT
41996230 TTATGTTATTAT
1 TTATGTTATTAT
41996242 TTATGTTAT
1 TTATGTTAT
41996251 GTACATTCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (12 bp):
TTATGTTATTAT
Found at i:41996470 original size:51 final size:47
Alignment explanation
Indices: 41996377--41996498 Score: 136
Period size: 51 Copynumber: 2.5 Consensus size: 47
41996367 AAATAGTATT
* *
41996377 AAAAATAAAATACCGAAAAAATATGTTTATGAAAAAATAAAATACGAA
1 AAAAATAAAA-AACGAAAAAATATATTTATGAAAAAATAAAATACGAA
* * *
41996425 AAGAAATAAAAAACGAAAATAGTATATTTACTGAAAGTAATAAAATCCGAA
1 AA-AAATAAAAAACGAAAA-AATATATTTA-TGAAA-AAATAAAATACGAA
*
41996476 AAAAATAAAAATACGAACAAATA
1 AAAAATAAAAA-ACGAAAAAATA
41996499 GCCAAAATAA
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
48 9 0.15
49 16 0.26
50 17 0.27
51 20 0.32
ACGTcount: A:0.64, C:0.07, G:0.09, T:0.20
Consensus pattern (47 bp):
AAAAATAAAAAACGAAAAAATATATTTATGAAAAAATAAAATACGAA
Found at i:41996492 original size:17 final size:17
Alignment explanation
Indices: 41996408--41996492 Score: 59
Period size: 17 Copynumber: 5.1 Consensus size: 17
41996398 TATGTTTATG
41996408 AAAAAAT-AAAATACGA
1 AAAAAATAAAAATACGA
41996424 AAAGAAATAAAAA-ACGA
1 AAA-AAATAAAAATACGA
* * * **
41996441 AAATAGTATATTTACTGA
1 AAAAAATAAAAATAC-GA
** *
41996459 AAGTAAT-AAAATCCGA
1 AAAAAATAAAAATACGA
41996475 AAAAAATAAAAATACGA
1 AAAAAATAAAAATACGA
41996492 A
1 A
41996493 CAAATAGCCA
Statistics
Matches: 50, Mismatches: 14, Indels: 9
0.68 0.19 0.12
Matches are distributed among these distances:
16 14 0.28
17 25 0.50
18 11 0.22
ACGTcount: A:0.66, C:0.07, G:0.09, T:0.18
Consensus pattern (17 bp):
AAAAAATAAAAATACGA
Found at i:41996644 original size:158 final size:158
Alignment explanation
Indices: 41996429--41996963 Score: 831
Period size: 158 Copynumber: 3.4 Consensus size: 158
41996419 TACGAAAAGA
* ** * *
41996429 AATAAAAAACGAAAATAGTATATTTACTGAAAGTAATAAAATCCGAAAAAAATAAAAATACGAAC
1 AATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAATAAGAAAAATACGAAC
*
41996494 AAATAGCCAAAATAAGGGTTTTTTTACTAAATTTATAT-AAAAACACACTAAAATAATACATTTC
66 AAACAGCCAAAATAAGGG-TTTTTTACTAAATTTATATAAAAAACACACTAAAATAATACATTTC
* *
41996558 AAACATTATATACTAAAATAATATAAAGT
130 AAACATTATGTACTAAAATAATATAAAAT
*
41996587 AATAAAATATC-AAAATAGTATATTTTTTAAAAGTAATAAAATCCGAAAATAAGAAAAATACGAA
1 AATAAAATA-CGAAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAATAAGAAAAATACGAA
* * *
41996651 CAAACAGTCAAAATAAGGGCTTTTTACTAAATTTGTATAAAAAACACACTAAAATAATACATTTC
65 CAAACAGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAACACACTAAAATAATACATTTC
*
41996716 AAATATTATGTACTAAAATAATATAAAAT
130 AAACATTATGTACTAAAATAATATAAAAT
* * *
41996745 AATAAAATACGAAAATAGTATATTTTTTGAAAGTAAAAAAATTCGAAAATAAGAAAAATACAAAC
1 AATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAATAAGAAAAATACGAAC
** *
41996810 AAAGGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAACACACTAAATTAATACATTTCA
66 AAACAGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAACACACTAAAATAATACATTTCA
* *
41996875 AACTTTCTGTACTAAAATAATATAAAAT
131 AACATTATGTACTAAAATAATATAAAAT
* *
41996903 AATAAAATACGAAAATAATATATTTTTTGAAAGTAATAAAATCTGAAAATAAGAAAAATAC
1 AATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAATAAGAAAAATAC
41996964 ATTGAAATTA
Statistics
Matches: 344, Mismatches: 30, Indels: 6
0.91 0.08 0.02
Matches are distributed among these distances:
157 18 0.05
158 325 0.94
159 1 0.00
ACGTcount: A:0.55, C:0.09, G:0.07, T:0.28
Consensus pattern (158 bp):
AATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAATAAGAAAAATACGAAC
AAACAGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAACACACTAAAATAATACATTTCA
AACATTATGTACTAAAATAATATAAAAT
Found at i:42002219 original size:76 final size:76
Alignment explanation
Indices: 42002139--42002280 Score: 205
Period size: 76 Copynumber: 1.9 Consensus size: 76
42002129 ATAGTTTTTT
42002139 ACTAAAAATAATACTAACTAACAATAATAATTAAGG-TTTTACTAAAAATAATAACTAACAATAA
1 ACTAAAAATAATACTAACTAA-AATAATAATTAAGGTTTTTACTAAAAATAATAACTAACAATAA
42002203 TATAGTGTAAAA
65 TATAGTGTAAAA
* * * *** *
42002215 ACTAACAATCATACTAACTAAAATAATAATTAGGGTTTTTACTAATTCTAATAACTAACCATAAT
1 ACTAAAAATAATACTAACTAAAATAATAATTAAGGTTTTTACTAAAAATAATAACTAACAATAAT
42002280 A
66 A
42002281 ATATTAATTT
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
75 13 0.22
76 45 0.78
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.31
Consensus pattern (76 bp):
ACTAAAAATAATACTAACTAAAATAATAATTAAGGTTTTTACTAAAAATAATAACTAACAATAAT
ATAGTGTAAAA
Found at i:42002524 original size:13 final size:13
Alignment explanation
Indices: 42002510--42002550 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
42002500 CTATTTTTTT
*
42002510 TCTTCTCTTTCTT
1 TCTTCTCTTTCTC
42002523 TC-TC-CTTTCTC
1 TCTTCTCTTTCTC
*
42002534 TATTCTCTTTCTC
1 TCTTCTCTTTCTC
42002547 TCTT
1 TCTT
42002551 TTTCTTTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
11 7 0.30
12 4 0.17
13 12 0.52
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.63
Consensus pattern (13 bp):
TCTTCTCTTTCTC
Found at i:42006067 original size:32 final size:32
Alignment explanation
Indices: 42006031--42006096 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
42006021 TCATTCTATG
42006031 TTTATTGCCTTAGATTTTCTTGTTGAATGCTT
1 TTTATTGCCTTAGATTTTCTTGTTGAATGCTT
42006063 TTTATTGCCTTAGATTTTCTTGTTGAATGCTT
1 TTTATTGCCTTAGATTTTCTTGTTGAATGCTT
42006095 TT
1 TT
42006097 CATTTCATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.15, C:0.12, G:0.15, T:0.58
Consensus pattern (32 bp):
TTTATTGCCTTAGATTTTCTTGTTGAATGCTT
Found at i:42011143 original size:20 final size:20
Alignment explanation
Indices: 42011118--42011163 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
42011108 TAAATCGAGC
42011118 CTTTGAAGCCCTAAAAATAG
1 CTTTGAAGCCCTAAAAATAG
* *
42011138 CTTTGATGCCTTAAAAATAG
1 CTTTGAAGCCCTAAAAATAG
*
42011158 TTTTGA
1 CTTTGA
42011164 GGTAATTCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (20 bp):
CTTTGAAGCCCTAAAAATAG
Found at i:42014041 original size:16 final size:17
Alignment explanation
Indices: 42014020--42014051 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
42014010 TATAAAACAA
42014020 AAGAAAGAAA-AGAAAT
1 AAGAAAGAAACAGAAAT
42014036 AAGAAAGAAACAGAAA
1 AAGAAAGAAACAGAAA
42014052 GCTTAAAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.75, C:0.03, G:0.19, T:0.03
Consensus pattern (17 bp):
AAGAAAGAAACAGAAAT
Found at i:42015003 original size:25 final size:25
Alignment explanation
Indices: 42014952--42015007 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
42014942 ACTTTAGCGC
* ***
42014952 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCTGATTACTAGCACGACAGT
42014977 GCTCTCTGATTACTAGCACGACAGT
1 GCTCTCTGATTACTAGCACGACAGT
42015002 GCTCTC
1 GCTCTC
42015008 CGTTTAGCAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.18, C:0.27, G:0.21, T:0.34
Consensus pattern (25 bp):
GCTCTCTGATTACTAGCACGACAGT
Found at i:42035448 original size:9 final size:9
Alignment explanation
Indices: 42035434--42035477 Score: 79
Period size: 9 Copynumber: 4.9 Consensus size: 9
42035424 TTTGGTTAAA
42035434 AATTACCCG
1 AATTACCCG
42035443 AATTACCCG
1 AATTACCCG
*
42035452 AATTAACCG
1 AATTACCCG
42035461 AATTACCCG
1 AATTACCCG
42035470 AATTACCC
1 AATTACCC
42035478 AAAAATTACC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.36, C:0.32, G:0.09, T:0.23
Consensus pattern (9 bp):
AATTACCCG
Found at i:42036644 original size:3 final size:3
Alignment explanation
Indices: 42036636--42036669 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
42036626 GTATGTCAAT
42036636 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
42036670 CCTCTCCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:42045024 original size:22 final size:22
Alignment explanation
Indices: 42044998--42045043 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
42044988 ATATGTTTCG
42044998 ATATATGCTAT-ATTAGATTGAA
1 ATATATGC-ATGATTAGATTGAA
*
42045020 ATATATGCATGATTATATTGAA
1 ATATATGCATGATTAGATTGAA
42045042 AT
1 AT
42045044 TTTAGAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.41, C:0.04, G:0.13, T:0.41
Consensus pattern (22 bp):
ATATATGCATGATTAGATTGAA
Found at i:42047797 original size:23 final size:23
Alignment explanation
Indices: 42047771--42047832 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 23
42047761 ATATTCAATT
* *
42047771 ATTTTTTAAAAAATAAAGATCAA
1 ATTTATTAAAAAATAAAAATCAA
* *
42047794 ATTTAAT-AAAAATAAAAATTAA
1 ATTTATTAAAAAATAAAAATCAA
42047816 A-TTATTAAAAATATAAA
1 ATTTATTAAAAA-ATAAA
42047833 TGTTAAGAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
21 4 0.12
22 18 0.56
23 10 0.31
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.34
Consensus pattern (23 bp):
ATTTATTAAAAAATAAAAATCAA
Found at i:42047824 original size:21 final size:22
Alignment explanation
Indices: 42047779--42047833 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
42047769 TTATTTTTTA
*
42047779 AAAAATAAAGATCAAATTTAAT
1 AAAAATAAAAATCAAATTTAAT
* *
42047801 AAAAATAAAAATTAAA-TTATT
1 AAAAATAAAAATCAAATTTAAT
*
42047822 AAAAATATAAAT
1 AAAAATAAAAAT
42047834 GTTAAGAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 15 0.52
22 14 0.48
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (22 bp):
AAAAATAAAAATCAAATTTAAT
Found at i:42047852 original size:14 final size:14
Alignment explanation
Indices: 42047806--42047853 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
42047796 TTAATAAAAA
42047806 TAAAAATTAAATTAT
1 TAAAAATTAAATT-T
*
42047821 TAAAAATATAAATGT
1 TAAAAAT-TAAATTT
*
42047836 TAAGAATTAAATTT
1 TAAAAATTAAATTT
42047850 TAAA
1 TAAA
42047854 TTATACCATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 9 0.32
15 14 0.50
16 5 0.18
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (14 bp):
TAAAAATTAAATTT
Found at i:42053696 original size:95 final size:95
Alignment explanation
Indices: 42053576--42053766 Score: 364
Period size: 95 Copynumber: 2.0 Consensus size: 95
42053566 AATCTCCTTA
42053576 GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATATTGTTATATTTACTTTTACATTA
1 GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATATTGTTATATTTACTTTTACATTA
42053641 TCTCATGATGGCTTGCACCCCAATTGTTTT
66 TCTCATGATGGCTTGCACCCCAATTGTTTT
* *
42053671 GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATCTTGTTATATTTACTTTTGCATTA
1 GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATATTGTTATATTTACTTTTACATTA
42053736 TCTCATGATGGCTTGCACCCCAATTGTTTT
66 TCTCATGATGGCTTGCACCCCAATTGTTTT
42053766 G
1 G
42053767 CTATTCCTTT
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
95 94 1.00
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (95 bp):
GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATATTGTTATATTTACTTTTACATTA
TCTCATGATGGCTTGCACCCCAATTGTTTT
Found at i:42069504 original size:95 final size:94
Alignment explanation
Indices: 42069341--42069530 Score: 353
Period size: 95 Copynumber: 2.0 Consensus size: 94
42069331 AATCTCCTTA
42069341 GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATATTGTTATATTTACTTTTACATTA
1 GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATATTGTTATATTTACTTTTACATTA
42069406 TCTCATGATGGCTTGCACCCCAATTGTTTT
66 TCTCATGATGGCTTGCA-CCCAATTGTTTT
* *
42069436 GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATCTTGTTATATTTACTTTTGCATTA
1 GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATATTGTTATATTTACTTTTACATTA
42069501 TCTCATGATGGCTTGCACCCAATTGTTTT
66 TCTCATGATGGCTTGCACCCAATTGTTTT
42069530 G
1 G
42069531 CTATTCCTTT
Statistics
Matches: 93, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
94 13 0.14
95 80 0.86
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (94 bp):
GTCGAACTGACAACTAAATAATGCTATTTAGCCATTTTGATATTGTTATATTTACTTTTACATTA
TCTCATGATGGCTTGCACCCAATTGTTTT
Found at i:42078925 original size:19 final size:20
Alignment explanation
Indices: 42078882--42078925 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
42078872 CTTGGTACAA
42078882 ATACACATAAAATTGTGTGAAG
1 ATACACATAAAA-T-TGTGAAG
*
42078904 ATACACATAAAA-TGTGACG
1 ATACACATAAAATTGTGAAG
42078923 ATA
1 ATA
42078926 GACGAAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 9 0.43
22 12 0.57
ACGTcount: A:0.48, C:0.11, G:0.16, T:0.25
Consensus pattern (20 bp):
ATACACATAAAATTGTGAAG
Found at i:42085323 original size:31 final size:29
Alignment explanation
Indices: 42085253--42085324 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
42085243 GGCTCAGGTT
* *
42085253 ACATTTTAGTCACTTATGTTTGAAATGTT
1 ACATTTTAGTCACTTATGTTTCAAATGTA
* **
42085282 ACGTTTTAGTCACTTATGTTATCACGTTGTA
1 ACATTTTAGTCACTTATGTT-TCA-AATGTA
42085313 ACATTTTAGTCA
1 ACATTTTAGTCA
42085325 TTGAGCCATT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 19 0.54
30 2 0.06
31 14 0.40
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.46
Consensus pattern (29 bp):
ACATTTTAGTCACTTATGTTTCAAATGTA
Found at i:42085951 original size:31 final size:29
Alignment explanation
Indices: 42085887--42085955 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
42085877 ATGATAACGT
* *
42085887 AAGTGACTAAAACGTAACATTTCAAACAT
1 AAGTGACTAAAACGTAACATGTCAAACAA
* *
42085916 AAGTGACTAAAATGTAACCTGAGTCAAACAA
1 AAGTGACTAAAACGTAACAT--GTCAAACAA
42085947 AAGTGACTA
1 AAGTGACTA
42085956 TTTTGATAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 18 0.53
31 16 0.47
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.22
Consensus pattern (29 bp):
AAGTGACTAAAACGTAACATGTCAAACAA
Found at i:42087703 original size:12 final size:13
Alignment explanation
Indices: 42087674--42087706 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
42087664 TTTTTAACTA
*
42087674 ATAATTGTAAATT
1 ATAATTATAAATT
42087687 ATAATTATAAA-T
1 ATAATTATAAATT
42087699 ATAATTAT
1 ATAATTAT
42087707 CACAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (13 bp):
ATAATTATAAATT
Found at i:42088111 original size:19 final size:22
Alignment explanation
Indices: 42088083--42088128 Score: 64
Period size: 19 Copynumber: 2.3 Consensus size: 22
42088073 AGATCATACC
42088083 TTTT-AAATAAT-TTT-TAAT-
1 TTTTAAAATAATCTTTATAATA
42088101 TTTTAAAATAATCTTTATAATA
1 TTTTAAAATAATCTTTATAATA
42088123 TTTTAA
1 TTTTAA
42088129 TTTTAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.17
19 7 0.29
20 3 0.12
21 4 0.17
22 6 0.25
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTAAAATAATCTTTATAATA
Found at i:42098757 original size:19 final size:20
Alignment explanation
Indices: 42098716--42098754 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
42098706 TTATTTTTAT
*
42098716 ATTTTTATACTTTTTAAATA
1 ATTTTTATACTTTTTAAAAA
42098736 ATTTTTA-A-TTTTTAAAAA
1 ATTTTTATACTTTTTAAAAA
42098754 A
1 A
42098755 ATTAATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
19 1 0.06
20 7 0.39
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTTTATACTTTTTAAAAA
Found at i:42108616 original size:21 final size:21
Alignment explanation
Indices: 42108590--42108630 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
42108580 ATCTGCTCAA
* *
42108590 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
42108611 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
42108631 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:42118961 original size:10 final size:10
Alignment explanation
Indices: 42118946--42118975 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
42118936 GTAAGACATA
42118946 TTATAAATAT
1 TTATAAATAT
42118956 TTATAAATA-
1 TTATAAATAT
42118965 TTATAAATAT
1 TTATAAATAT
42118975 T
1 T
42118976 AAGCAATGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
TTATAAATAT
Found at i:42118968 original size:9 final size:9
Alignment explanation
Indices: 42118943--42118976 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
42118933 TTGGTAAGAC
42118943 ATATTATAA
1 ATATTATAA
42118952 ATATTTATAA
1 ATA-TTATAA
42118962 ATATTATAA
1 ATATTATAA
42118971 ATATTA
1 ATATTA
42118977 AGCAATGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 15 0.62
10 9 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
ATATTATAA
Found at i:42125968 original size:29 final size:30
Alignment explanation
Indices: 42125901--42125969 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 30
42125891 ATTTGATCTT
* *
42125901 ATTTAATTCTTTTTAATAATACAATGACTA
1 ATTTAATTCTATTTAATAATACAAGGACTA
* * *
42125931 AATTGATTC-ATTTAATAATA-GAGGAACTA
1 ATTTAATTCTATTTAATAATACAAGG-ACTA
42125960 ATTTAATTCT
1 ATTTAATTCT
42125970 GTTCCTATAA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
28 2 0.07
29 21 0.70
30 7 0.23
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (30 bp):
ATTTAATTCTATTTAATAATACAAGGACTA
Found at i:42127517 original size:14 final size:14
Alignment explanation
Indices: 42127498--42127529 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
42127488 TCCAATCACC
42127498 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
42127512 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
42127526 GGGC
1 GGGC
42127530 TAAATGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.16, G:0.47, T:0.31
Consensus pattern (14 bp):
GGGCCAGTTTGGTT
Found at i:42132638 original size:14 final size:14
Alignment explanation
Indices: 42132619--42132650 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
42132609 TCCAATCACC
42132619 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
42132633 GGGCCAGTTTGGTT
1 GGGCCAGTTTGGTT
42132647 GGGC
1 GGGC
42132651 TAAATGACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.16, G:0.47, T:0.31
Consensus pattern (14 bp):
GGGCCAGTTTGGTT
Found at i:42134464 original size:20 final size:20
Alignment explanation
Indices: 42134439--42134487 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
42134429 TTTTCTTTAA
42134439 ATTATTTTATTTATA-AGACT
1 ATTATTTTATTTATAGA-ACT
*
42134459 ATTATTTTATTTATAGAATT
1 ATTATTTTATTTATAGAACT
42134479 ATTATTTTA
1 ATTATTTTA
42134488 ATAAATAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 26 0.96
21 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (20 bp):
ATTATTTTATTTATAGAACT
Found at i:42141183 original size:38 final size:36
Alignment explanation
Indices: 42141104--42141236 Score: 153
Period size: 37 Copynumber: 3.6 Consensus size: 36
42141094 TACCGTATGC
* * *
42141104 AATTTTGAAAATATA-TTAAAAAATATGAA-TAGATA
1 AATTTTGAAAAAAGATTTAAAAAATACGAACT-GATA
42141139 AATTTTGAAAAAAGATTTTAAAAGAATACGAACTGATA
1 AATTTTGAAAAAAGA-TTTAAAA-AATACGAACTGATA
* *
42141177 AATTTTGAAAAAATATTTAAGAAAATACGATCTGATA
1 AATTTTGAAAAAAGATTTAA-AAAATACGAACTGATA
* *
42141214 AATTTTGAAAAAAAAATTAAAAA
1 AATTTTGAAAAAAGATTTAAAAA
42141237 TAAAATGCAA
Statistics
Matches: 86, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
35 13 0.15
36 3 0.03
37 42 0.49
38 27 0.31
39 1 0.01
ACGTcount: A:0.56, C:0.03, G:0.10, T:0.31
Consensus pattern (36 bp):
AATTTTGAAAAAAGATTTAAAAAATACGAACTGATA
Found at i:42141287 original size:22 final size:23
Alignment explanation
Indices: 42141248--42141292 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
42141238 AAAATGCAAA
*
42141248 ATTGATAAATTTATGGAACGTGG
1 ATTGATAAATATATGGAACGTGG
42141271 ATTGATAAA-ATATGGAACGTGG
1 ATTGATAAATATATGGAACGTGG
42141293 CCATGGGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.38, C:0.04, G:0.27, T:0.31
Consensus pattern (23 bp):
ATTGATAAATATATGGAACGTGG
Done.