Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 184 of 198
Found at i:57226285 original size:43 final size:43
Alignment explanation
Indices: 57226174--57226467 Score: 226
Period size: 43 Copynumber: 6.8 Consensus size: 43
57226164 GGCAGTACAT
* * ** *
57226174 GATTTTGTATAAGACCACATCTGGGACGTTGGCATCAATTTGA
1 GATTTCGTGTAAGACCATGTCTGGGACGTTGGCATCGATTTGA
**
57226217 GATTTACGTGTAAGACCACATCTGGGACGTTGGCATCGATTTGA
1 GATTT-CGTGTAAGACCATGTCTGGGACGTTGGCATCGATTTGA
* **
57226261 GATTTTGTGTAAGACTTTGTCTGGGACAG-TGGCATCGATAGTT--
1 GATTTCGTGTAAGACCATGTCTGGGAC-GTTGGCATCGAT--TTGA
* * * *
57226304 GATTACGTGTAAGACCATGTCTGAGACATTGGCATCGCATAT--
1 GATTTCGTGTAAGACCATGTCTGGGACGTTGGCATCG-ATTTGA
* * *
57226346 GATTTCGTGTAAGACCACGTCTGGGACGTTGGAATCAATTTGA
1 GATTTCGTGTAAGACCATGTCTGGGACGTTGGCATCGATTTGA
* * * * *
57226389 GATTTACGTGTAATACCTTGTCTGGGATAG-TGGGATCGATATT-T
1 GATTT-CGTGTAAGACCATGTCTGGGA-CGTTGGCATCGAT-TTGA
* * *
57226433 GATTACATATAAGACC-TCGTCTGGGACGTTGGCAT
1 GATTTCGTGTAAGACCAT-GTCTGGGACGTTGGCAT
57226468 TGTACGAGCT
Statistics
Matches: 203, Mismatches: 35, Indels: 26
0.77 0.13 0.10
Matches are distributed among these distances:
41 3 0.01
42 34 0.17
43 88 0.43
44 73 0.36
45 5 0.02
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (43 bp):
GATTTCGTGTAAGACCATGTCTGGGACGTTGGCATCGATTTGA
Found at i:57226435 original size:129 final size:129
Alignment explanation
Indices: 57226217--57226467 Score: 353
Period size: 129 Copynumber: 1.9 Consensus size: 129
57226207 ATCAATTTGA
* * * *
57226217 GATTTACGTGTAAGACCACATCTGGGACGTTGGCATCGATTTGAGATTTTGTGTAAGACTTTGTC
1 GATTTACGTGTAAGACCACATCTGGGACGTTGGAATCAATTTGAGATTTCGTGTAAGACCTTGTC
* *
57226282 TGGGACAGTGGCATCGATAGTTGATTACGTGTAAGACCAT-GTCTGAGACATTGGCATCGCATAT
66 TGGGACAGTGGCATCGATAGTTGATTACATATAAGACC-TCGTCTGAGACATTGGCATCGCATAT
* *
57226346 GATTT-CGTGTAAGACCACGTCTGGGACGTTGGAATCAATTTGAGATTTACGTGTAATACCTTGT
1 GATTTACGTGTAAGACCACATCTGGGACGTTGGAATCAATTTGAGATTT-CGTGTAAGACCTTGT
* * * * *
57226410 CTGGGATAGTGGGATCGATATTTGATTACATATAAGACCTCGTCTGGGACGTTGGCAT
65 CTGGGACAGTGGCATCGATAGTTGATTACATATAAGACCTCGTCTGAGACATTGGCAT
57226468 TGTACGAGCT
Statistics
Matches: 107, Mismatches: 13, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
128 41 0.38
129 66 0.62
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (129 bp):
GATTTACGTGTAAGACCACATCTGGGACGTTGGAATCAATTTGAGATTTCGTGTAAGACCTTGTC
TGGGACAGTGGCATCGATAGTTGATTACATATAAGACCTCGTCTGAGACATTGGCATCGCATAT
Found at i:57228399 original size:22 final size:24
Alignment explanation
Indices: 57228360--57228409 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 24
57228350 TAAAGGGATC
57228360 TGGGGAAAAAAGAAAA-T-TGATT
1 TGGGGAAAAAAGAAAATTGTGATT
*
57228382 TGGGGAAAAAA-ATTAATTGTGATT
1 TGGGGAAAAAAGA-AAATTGTGATT
57228406 TGGG
1 TGGG
57228410 TTGGTTTGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 1 0.04
22 13 0.54
23 1 0.04
24 9 0.38
ACGTcount: A:0.42, C:0.00, G:0.30, T:0.28
Consensus pattern (24 bp):
TGGGGAAAAAAGAAAATTGTGATT
Found at i:57228687 original size:16 final size:16
Alignment explanation
Indices: 57228661--57228698 Score: 67
Period size: 16 Copynumber: 2.3 Consensus size: 16
57228651 GTTTTTTATT
57228661 TTTTGGATTTAGGGTTA
1 TTTT-GATTTAGGGTTA
57228678 TTTTGATTTAGGGTTA
1 TTTTGATTTAGGGTTA
57228694 TTTTG
1 TTTTG
57228699 GGTTATTTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.16, C:0.00, G:0.26, T:0.58
Consensus pattern (16 bp):
TTTTGATTTAGGGTTA
Found at i:57228736 original size:18 final size:18
Alignment explanation
Indices: 57228715--57228804 Score: 80
Period size: 18 Copynumber: 5.2 Consensus size: 18
57228705 TTCGATTCTG
57228715 ATTTTGATTTTGATTTTA
1 ATTTTGATTTTGATTTTA
* **
57228733 ATTTAG-GGTT-ATTTT-
1 ATTTTGATTTTGATTTTA
** *
57228748 AGGTT-ATTTCGATTTTA
1 ATTTTGATTTTGATTTTA
*
57228765 ATTTTGATTTTGATTTAA
1 ATTTTGATTTTGATTTTA
*
57228783 ATTTTGATTTTTATTTTA
1 ATTTTGATTTTGATTTTA
57228801 ATTT
1 ATTT
57228805 AGGGTTATTT
Statistics
Matches: 53, Mismatches: 15, Indels: 8
0.70 0.20 0.11
Matches are distributed among these distances:
15 3 0.06
16 10 0.19
17 5 0.09
18 35 0.66
ACGTcount: A:0.23, C:0.01, G:0.12, T:0.63
Consensus pattern (18 bp):
ATTTTGATTTTGATTTTA
Found at i:57228737 original size:50 final size:50
Alignment explanation
Indices: 57228677--57228786 Score: 175
Period size: 50 Copynumber: 2.2 Consensus size: 50
57228667 ATTTAGGGTT
* * *
57228677 ATTTTGATTTAGGGTTATTTTGGGTTATTTCGATTCTGATTTTGATTTTG
1 ATTTTAATTTAGGGTTATTTTAGGTTATTTCGATTCTAATTTTGATTTTG
*
57228727 ATTTTAATTTAGGGTTATTTTAGGTTATTTCGATTTTAATTTTGATTTTG
1 ATTTTAATTTAGGGTTATTTTAGGTTATTTCGATTCTAATTTTGATTTTG
*
57228777 ATTTAAATTT
1 ATTTTAATTT
57228787 TGATTTTTAT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 55 1.00
ACGTcount: A:0.21, C:0.03, G:0.17, T:0.59
Consensus pattern (50 bp):
ATTTTAATTTAGGGTTATTTTAGGTTATTTCGATTCTAATTTTGATTTTG
Found at i:57228773 original size:12 final size:12
Alignment explanation
Indices: 57228753--57228804 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
57228743 ATTTTAGGTT
*
57228753 ATTTCGATTTTA
1 ATTTTGATTTTA
*
57228765 ATTTTGATTTTG
1 ATTTTGATTTTA
** *
57228777 ATTTAAATTTTG
1 ATTTTGATTTTA
*
57228789 ATTTTTATTTTA
1 ATTTTGATTTTA
57228801 ATTT
1 ATTT
57228805 AGGGTTATTT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.25, C:0.02, G:0.08, T:0.65
Consensus pattern (12 bp):
ATTTTGATTTTA
Found at i:57229217 original size:62 final size:61
Alignment explanation
Indices: 57229116--57229247 Score: 194
Period size: 62 Copynumber: 2.1 Consensus size: 61
57229106 GTTAAAGTGT
* * *
57229116 TTGGTTATTGTTTGTCATGTGCATAACAGAAATGATTGTGTTTGTACTAAATTATTTTTGTA
1 TTGGTTATTGTATGCCATGCGCATAACAGAAATGATTGTGTTTGTACTAAATTA-TTTTGTA
* *
57229178 TTGGTTATTGTATGCCATGCGCATGACAGAAAT-AGTTGTGTTTGTATTAAATTATTTTGTA
1 TTGGTTATTGTATGCCATGCGCATAACAGAAATGA-TTGTGTTTGTACTAAATTATTTTGTA
57229239 TTGGTTATT
1 TTGGTTATT
57229248 ATTTGATAGA
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
61 17 0.27
62 47 0.73
ACGTcount: A:0.25, C:0.07, G:0.20, T:0.48
Consensus pattern (61 bp):
TTGGTTATTGTATGCCATGCGCATAACAGAAATGATTGTGTTTGTACTAAATTATTTTGTA
Found at i:57231183 original size:26 final size:27
Alignment explanation
Indices: 57231121--57231189 Score: 79
Period size: 26 Copynumber: 2.6 Consensus size: 27
57231111 TGTATGTGTA
* * *
57231121 TGACTGTTTTTTTAATATACATGCTGT
1 TGACTATTTTTTTAATATACATACAGT
*
57231148 TGACTA-TTTTTTAATATGCATACAG-
1 TGACTATTTTTTTAATATACATACAGT
*
57231173 TGAGTATTTTTTTAATA
1 TGACTATTTTTTTAATA
57231190 ATATGCATGC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
25 5 0.14
26 26 0.72
27 5 0.14
ACGTcount: A:0.28, C:0.09, G:0.13, T:0.51
Consensus pattern (27 bp):
TGACTATTTTTTTAATATACATACAGT
Found at i:57231240 original size:97 final size:97
Alignment explanation
Indices: 57231115--57231389 Score: 444
Period size: 97 Copynumber: 2.8 Consensus size: 97
57231105 GGTGTGTGTA
*
57231115 TGTGTATGACTGTTTTTTTAATATACATGCTGTTGACTATTTTTTAATATGCATACAGTGAGTAT
1 TGTGTATGACTGGTTTTTTAATATACATGCTGTTGACTATTTTTTAATATGCATACAGTGAGTAT
57231180 TTTTTTAATAATATGCATGCAGTGATTGTTGG
66 TTTTTTAATAATATGCATGCAGTGATTGTTGG
* *
57231212 TGTGTGTGATTGGTTTTTTAATATACATGCTGTTGACTATTTTTTAATATGCATACAGTGAGTAT
1 TGTGTATGACTGGTTTTTTAATATACATGCTGTTGACTATTTTTTAATATGCATACAGTGAGTAT
57231277 TTTTTTAATAATATGCATGCAGTGATTGTTGG
66 TTTTTTAATAATATGCATGCAGTGATTGTTGG
* * * * * ***
57231309 TGTGTATGACTGTTTTTTTAATATAAATGATATTGACTATTTTTTAATATGTATGTTGTGAGTA-
1 TGTGTATGACTGGTTTTTTAATATACATGCTGTTGACTATTTTTTAATATGCATACAGTGAGTAT
57231373 TTTTTTAATAATATGCA
66 TTTTTTAATAATATGCA
57231390 CGTAGTGACT
Statistics
Matches: 165, Mismatches: 13, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
96 17 0.10
97 148 0.90
ACGTcount: A:0.27, C:0.07, G:0.18, T:0.49
Consensus pattern (97 bp):
TGTGTATGACTGGTTTTTTAATATACATGCTGTTGACTATTTTTTAATATGCATACAGTGAGTAT
TTTTTTAATAATATGCATGCAGTGATTGTTGG
Found at i:57231277 original size:25 final size:27
Alignment explanation
Indices: 57231225--57231286 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 27
57231215 GTGTGATTGG
* *
57231225 TTTTTTAATATACATGCTGTTGACTA-
1 TTTTTTAATATACATACAGTTGACTAT
* *
57231251 TTTTTTAATATGCATACAG-TGAGTAT
1 TTTTTTAATATACATACAGTTGACTAT
57231277 TTTTTTAATA
1 TTTTTTAATA
57231287 ATATGCATGC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 5 0.16
26 26 0.84
ACGTcount: A:0.29, C:0.08, G:0.11, T:0.52
Consensus pattern (27 bp):
TTTTTTAATATACATACAGTTGACTAT
Found at i:57233302 original size:3 final size:3
Alignment explanation
Indices: 57233294--57233318 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
57233284 TCTATTTTTA
57233294 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
57233319 CTAACCCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:57241488 original size:22 final size:23
Alignment explanation
Indices: 57241446--57241490 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
57241436 GCTGCTGTTT
* *
57241446 TCATTGTTTTTGTTGTTGTTTTG
1 TCATTGTTTTTGGTGTCGTTTTG
57241469 TCATTG-TTTTGGTGTCGTTTTG
1 TCATTGTTTTTGGTGTCGTTTTG
57241491 CTATTATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.04, C:0.07, G:0.24, T:0.64
Consensus pattern (23 bp):
TCATTGTTTTTGGTGTCGTTTTG
Found at i:57244189 original size:9 final size:9
Alignment explanation
Indices: 57244175--57244205 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
57244165 AAATACCTTC
*
57244175 TAATCAACT
1 TAATCAACA
57244184 TAATCAACA
1 TAATCAACA
57244193 TAATCAACA
1 TAATCAACA
57244202 TAAT
1 TAAT
57244206 ATTAATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.29
Consensus pattern (9 bp):
TAATCAACA
Found at i:57245770 original size:9 final size:9
Alignment explanation
Indices: 57245744--57245782 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
57245734 TCTCTTTCTC
57245744 TGTTTCTCTT
1 TGTTTCT-TT
*
57245754 TCTGTTCTTT
1 TGT-TTCTTT
57245764 TGTTTCTTT
1 TGTTTCTTT
57245773 TGTTTCTTT
1 TGTTTCTTT
57245782 T
1 T
57245783 TATTTTACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
9 16 0.62
10 6 0.23
11 4 0.15
ACGTcount: A:0.00, C:0.15, G:0.10, T:0.74
Consensus pattern (9 bp):
TGTTTCTTT
Found at i:57247346 original size:14 final size:14
Alignment explanation
Indices: 57247310--57247348 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
57247300 GCTTAATAAA
57247310 TTATGACATATGCT
1 TTATGACATATGCT
* * *
57247324 TAATAACATATGGT
1 TTATGACATATGCT
57247338 TTATGACATAT
1 TTATGACATAT
57247349 AAACTAATGA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (14 bp):
TTATGACATATGCT
Found at i:57247909 original size:16 final size:16
Alignment explanation
Indices: 57247888--57247957 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
57247878 TTCAATTACT
57247888 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
*
57247904 ATTACAGCTCTATTCT
1 ATTACAGCTCTATTCC
* * *
57247920 ATTACAACTCCATTCA
1 ATTACAGCTCTATTCC
57247936 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
57247952 ATTACA
1 ATTACA
57247958 ATGAACCAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.30, C:0.29, G:0.04, T:0.37
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:57248040 original size:38 final size:39
Alignment explanation
Indices: 57247986--57248059 Score: 132
Period size: 38 Copynumber: 1.9 Consensus size: 39
57247976 TAGAGTTAGG
*
57247986 CTTTAGTTTTATTTTTATTGGGTT-GGTAATTGGGTAGA
1 CTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGGTAGA
57248024 CTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGGT
1 CTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGGT
57248060 TGGGTTGAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
38 23 0.68
39 11 0.32
ACGTcount: A:0.16, C:0.03, G:0.28, T:0.53
Consensus pattern (39 bp):
CTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGGTAGA
Found at i:57248058 original size:13 final size:13
Alignment explanation
Indices: 57248040--57248064 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57248030 TTTTAGTTTT
57248040 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
57248053 ATTGGGTTGGGT
1 ATTGGGTTGGGT
57248065 TGAATAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:57257662 original size:12 final size:12
Alignment explanation
Indices: 57257645--57257670 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
57257635 AAAGGCGATC
57257645 CCAAGTCCAAGA
1 CCAAGTCCAAGA
57257657 CCAAGTCCAAGA
1 CCAAGTCCAAGA
57257669 CC
1 CC
57257671 GGCGGTTCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.38, G:0.15, T:0.08
Consensus pattern (12 bp):
CCAAGTCCAAGA
Found at i:57267261 original size:25 final size:25
Alignment explanation
Indices: 57267227--57267278 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
57267217 TGTACTATAT
57267227 ATTTATTTATATTTTATATGATCAA
1 ATTTATTTATATTTTATATGATCAA
*
57267252 ATTTATTTATATTTTATGTGATCAA
1 ATTTATTTATATTTTATATGATCAA
57267277 AT
1 AT
57267279 AATAAAGTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.56
Consensus pattern (25 bp):
ATTTATTTATATTTTATATGATCAA
Found at i:57271165 original size:22 final size:23
Alignment explanation
Indices: 57271140--57271184 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
57271130 GTAATTTGAA
57271140 ATTTTTTTGAATATTTT-AATAT
1 ATTTTTTTGAATATTTTGAATAT
**
57271162 ATTTTTTTTCATATTTTGAATAT
1 ATTTTTTTGAATATTTTGAATAT
57271185 TATATAGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.64
Consensus pattern (23 bp):
ATTTTTTTGAATATTTTGAATAT
Found at i:57284589 original size:12 final size:12
Alignment explanation
Indices: 57284552--57284589 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
57284542 ATGCTCACGA
57284552 ATAAGCTTGTTT
1 ATAAGCTTGTTT
*
57284564 AAAAGCTTGTTT
1 ATAAGCTTGTTT
*
57284576 ATAAGCTCGTTT
1 ATAAGCTTGTTT
57284588 AT
1 AT
57284590 TGACTCGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.45
Consensus pattern (12 bp):
ATAAGCTTGTTT
Found at i:57299048 original size:17 final size:17
Alignment explanation
Indices: 57299022--57299061 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
57299012 AATTCAAAGA
*
57299022 AATCCCTGAACTCTTCC
1 AATCCTTGAACTCTTCC
*
57299039 AATCCTTGAACTCTTCT
1 AATCCTTGAACTCTTCC
57299056 AATCCT
1 AATCCT
57299062 ATGTGTAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.25, C:0.35, G:0.05, T:0.35
Consensus pattern (17 bp):
AATCCTTGAACTCTTCC
Found at i:57299778 original size:22 final size:22
Alignment explanation
Indices: 57299753--57299855 Score: 91
Period size: 22 Copynumber: 4.4 Consensus size: 22
57299743 ACTAATGAAT
*
57299753 AGAGAGCACTGAAATGCTATAC
1 AGAGAGCACTGAAGTGCTATAC
* * *
57299775 AGAGAGCACAGATGTGCTAAAC
1 AGAGAGCACTGAAGTGCTATAC
*
57299797 AGAGAGCACTGACGTGCTAGTAATC
1 AGAGAGCACTGAAGTGCTA-T-A-C
57299822 AGAGAGCACT-AACGTGCTAATAATC
1 AGAGAGCACTGAA-GTGCT-AT-A-C
57299847 AGAGAGCAC
1 AGAGAGCAC
57299856 CAACGTGCTA
Statistics
Matches: 68, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
22 35 0.51
24 2 0.03
25 30 0.44
26 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.17
Consensus pattern (22 bp):
AGAGAGCACTGAAGTGCTATAC
Found at i:57299827 original size:25 final size:24
Alignment explanation
Indices: 57299753--57299878 Score: 134
Period size: 25 Copynumber: 5.3 Consensus size: 24
57299743 ACTAATGAAT
**
57299753 AGAGAGCACTGAAATGCTAT-A-C
1 AGAGAGCACTGACGTGCTATAATC
* *
57299775 AGAGAGCACAGATGTGCTA-AA-C
1 AGAGAGCACTGACGTGCTATAATC
57299797 AGAGAGCACTGACGTGCTAGTAATC
1 AGAGAGCACTGACGTGCTA-TAATC
*
57299822 AGAGAGCACTAACGTGCTAATAATC
1 AGAGAGCACTGACGTGCT-ATAATC
**
57299847 AGAGAGCACCAACGTGCTAATAATC
1 AGAGAGCACTGACGTGCT-ATAATC
57299872 AGAGAGC
1 AGAGAGC
57299879 GCGCTAAAGT
Statistics
Matches: 92, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
22 35 0.38
24 2 0.02
25 54 0.59
26 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.25, T:0.17
Consensus pattern (24 bp):
AGAGAGCACTGACGTGCTATAATC
Found at i:57300838 original size:5 final size:5
Alignment explanation
Indices: 57300828--57300865 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
57300818 TTATTTCTTT
57300828 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TAT
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TAT
57300866 TTATACTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TATAA
Found at i:57300922 original size:7 final size:7
Alignment explanation
Indices: 57300910--57300935 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
57300900 ATAATAATAT
57300910 ATTTTAG
1 ATTTTAG
57300917 ATTTTAG
1 ATTTTAG
57300924 ATTTTAG
1 ATTTTAG
57300931 ATTTT
1 ATTTT
57300936 TTTTTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.62
Consensus pattern (7 bp):
ATTTTAG
Found at i:57301772 original size:12 final size:12
Alignment explanation
Indices: 57301755--57301788 Score: 54
Period size: 10 Copynumber: 3.0 Consensus size: 12
57301745 CGTGGCTTCC
57301755 TTCTTTCTATTT
1 TTCTTTCTATTT
57301767 TTCTTTC--TTT
1 TTCTTTCTATTT
57301777 TTCTTTCTATTT
1 TTCTTTCTATTT
57301789 CGTTTAACCT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 10 0.50
12 10 0.50
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (12 bp):
TTCTTTCTATTT
Found at i:57301895 original size:8 final size:8
Alignment explanation
Indices: 57301838--57301905 Score: 52
Period size: 8 Copynumber: 8.4 Consensus size: 8
57301828 TATATTTACT
57301838 TATTATAA
1 TATTATAA
57301846 TA-TATAA
1 TATTATAA
*
57301853 TATAATATA
1 TATTATA-A
57301862 TATATACTTAA
1 TAT-TA--TAA
*
57301873 TAAT-TAA
1 TATTATAA
*
57301880 GA-TATAA
1 TATTATAA
57301887 TATTATAA
1 TATTATAA
57301895 TATTATAA
1 TATTATAA
57301903 TAT
1 TAT
57301906 ATATTTTTAA
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
6 1 0.02
7 15 0.31
8 21 0.44
9 4 0.08
10 2 0.04
11 3 0.06
12 2 0.04
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (8 bp):
TATTATAA
Found at i:57305495 original size:16 final size:15
Alignment explanation
Indices: 57305474--57305517 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 15
57305464 AAACGAAATG
57305474 AACAAACCAAATAATA
1 AACAAA-CAAATAATA
57305490 AACAAACAAATAAATA
1 AACAAACAAAT-AATA
*
57305506 AATAAACAAATA
1 AACAAACAAATA
57305518 CTAATGTAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 6 0.23
16 20 0.77
ACGTcount: A:0.73, C:0.14, G:0.00, T:0.14
Consensus pattern (15 bp):
AACAAACAAATAATA
Found at i:57305499 original size:20 final size:20
Alignment explanation
Indices: 57305474--57305515 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
57305464 AAACGAAATG
57305474 AACAAACCAAAT-AATAAACA
1 AACAAA-CAAATAAATAAACA
*
57305494 AACAAATAAATAAATAAACA
1 AACAAACAAATAAATAAACA
57305514 AA
1 AA
57305516 TACTAATGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.74, C:0.14, G:0.00, T:0.12
Consensus pattern (20 bp):
AACAAACAAATAAATAAACA
Found at i:57307136 original size:44 final size:44
Alignment explanation
Indices: 57307086--57307312 Score: 112
Period size: 44 Copynumber: 5.2 Consensus size: 44
57307076 TGCCTTGGGA
*
57307086 AGATAAGATTCACAGTCTTCGATCTGCTCCACTACTGCTTAGAG
1 AGATAAGATTCACAGTCTTCGATCTACTCCACTACTGCTTAGAG
* * * * *
57307130 AGATAAGA-TCTACAATCTTC-AACTTACTCTACTGCTGCTTAGGG
1 AGATAAGATTC-ACAGTCTTCGATC-TACTCCACTACTGCTTAGAG
* *** * *
57307174 AGATAGGATT-GGTGGCTT-GAATCTACTTCC-CTACTACCTT-GAG
1 AGATAAGATTCACAGTCTTCG-ATCTAC-TCCACTACT-GCTTAGAG
* * * *
57307217 AAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTACTTAG-G
1 -AGATAAGATTCACAGTCTTCGATCTACTCCACTACTGCTTAGAG
* * * * * *
57307261 AAGACATGATCTGCA-A-TCTTCAACCTACTCCACTACTACTTAGGG
1 -AGATAAGAT-T-CACAGTCTTCGATCTACTCCACTACTGCTTAGAG
57307306 AGATAAG
1 AGATAAG
57307313 GCTAGTGCCT
Statistics
Matches: 136, Mismatches: 32, Indels: 30
0.69 0.16 0.15
Matches are distributed among these distances:
43 16 0.12
44 99 0.73
45 19 0.14
46 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (44 bp):
AGATAAGATTCACAGTCTTCGATCTACTCCACTACTGCTTAGAG
Found at i:57307278 original size:132 final size:132
Alignment explanation
Indices: 57307040--57307310 Score: 377
Period size: 132 Copynumber: 2.1 Consensus size: 132
57307030 GCAACTTCAA
* * *
57307040 GGAGATAGAGTTTGTGGCTTATATCTACTTCCCTACTGCCTTGGGAAGATAAGATTCACAGTCTT
1 GGAGATAGAGTTGGTGGCTTATATCTACTTCCCTACTACCTTGAGAAGATAAGATTCACAGTCTT
* * * * * *
57307105 CGATCTGCTCCACTACTGCTTAGAGAGATAAGATCTACAATCTTCAACTTACTCTACTGCTGCTT
66 CGATCTGCTCCACTACTACTTAGAGAGACAAGATCTACAATCTTCAACCTACTCCACTACTACTT
57307170 AG
131 AG
* *
57307172 GGAGATAG-GATTGGTGGCTTGA-ATCTACTTCCCTACTACCTTGAGAAGATAAGATTCGCCGTC
1 GGAGATAGAG-TTGGTGGCTT-ATATCTACTTCCCTACTACCTTGAGAAGATAAGATTCACAGTC
* *
57307235 TTCGATCTGCTCCACTACTACTTAG-GAAGACATGATCTGCAATCTTCAACCTACTCCACTACTA
64 TTCGATCTGCTCCACTACTACTTAGAG-AGACAAGATCTACAATCTTCAACCTACTCCACTACTA
57307299 CTTAG
128 CTTAG
57307304 GGAGATA
1 GGAGATA
57307311 AGGCTAGTGC
Statistics
Matches: 123, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
131 2 0.02
132 120 0.98
133 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.31
Consensus pattern (132 bp):
GGAGATAGAGTTGGTGGCTTATATCTACTTCCCTACTACCTTGAGAAGATAAGATTCACAGTCTT
CGATCTGCTCCACTACTACTTAGAGAGACAAGATCTACAATCTTCAACCTACTCCACTACTACTT
AG
Found at i:57308000 original size:46 final size:45
Alignment explanation
Indices: 57307900--57308001 Score: 107
Period size: 45 Copynumber: 2.2 Consensus size: 45
57307890 GCAAAGCTCG
* * *
57307900 AAATGAATGAATCAATCAAGATAGCAAATTTTGCTAGAATACAAA
1 AAATGAATAAATCAATCAAGATAGCAAATTTTGCAAAAATACAAA
* * * **
57307945 ATGA-GAATAAATTAATCAAGATGGCGTATTTTGTCAAAAATACAAA
1 A-AATGAATAAATCAATCAAGATAGCAAATTTTG-CAAAAATACAAA
57307991 AAATGAATAAA
1 AAATGAATAAA
57308002 ATGGAAATAA
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
45 26 0.58
46 19 0.42
ACGTcount: A:0.52, C:0.09, G:0.14, T:0.25
Consensus pattern (45 bp):
AAATGAATAAATCAATCAAGATAGCAAATTTTGCAAAAATACAAA
Found at i:57328090 original size:39 final size:40
Alignment explanation
Indices: 57328041--57328127 Score: 133
Period size: 39 Copynumber: 2.2 Consensus size: 40
57328031 AAATTATATG
* *
57328041 TAATACAATAAAATATTTATTATATTTAT-TTA-TGCTTTT
1 TAATATAATAAAATATTTATTATATTTATGATAGTG-TTTT
57328080 TAATATAATAAAATATTTATTATATTTATGATAGTGTTTT
1 TAATATAATAAAATATTTATTATATTTATGATAGTGTTTT
57328120 TAATATAA
1 TAATATAA
57328128 ATATTTTTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
39 28 0.64
40 14 0.32
41 2 0.05
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (40 bp):
TAATATAATAAAATATTTATTATATTTATGATAGTGTTTT
Found at i:57330927 original size:16 final size:16
Alignment explanation
Indices: 57330908--57330944 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
57330898 CACAGTTTTC
57330908 TTAATACATACACTAA
1 TTAATACATACACTAA
*
57330924 TTAATACATACGCTAA
1 TTAATACATACACTAA
57330940 TTAAT
1 TTAAT
57330945 TAAAGCATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.46, C:0.16, G:0.03, T:0.35
Consensus pattern (16 bp):
TTAATACATACACTAA
Found at i:57333068 original size:18 final size:20
Alignment explanation
Indices: 57333032--57333068 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
57333022 AAAAGAAGCC
*
57333032 AAAAAGTAATATAAGAAGTA
1 AAAAAGTAATATAACAAGTA
57333052 AAAAAGTAA-A-AACAAGT
1 AAAAAGTAATATAACAAGT
57333069 TCAGGTGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 6 0.38
19 1 0.06
20 9 0.56
ACGTcount: A:0.68, C:0.03, G:0.14, T:0.16
Consensus pattern (20 bp):
AAAAAGTAATATAACAAGTA
Found at i:57340052 original size:21 final size:20
Alignment explanation
Indices: 57340027--57340065 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
57340017 TTTATTTATA
*
57340027 TAATTTTTATTATTCAATAAT
1 TAATTTTTAATATT-AATAAT
57340048 TAATTTTTAATATTAATA
1 TAATTTTTAATATTAATA
57340066 TTATCTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (20 bp):
TAATTTTTAATATTAATAAT
Found at i:57342873 original size:19 final size:19
Alignment explanation
Indices: 57342849--57342886 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
57342839 ATAAGTTAGA
57342849 CTTAATTCTTGTTTTTAAT
1 CTTAATTCTTGTTTTTAAT
57342868 CTTAATTCTTGTTTTTAAT
1 CTTAATTCTTGTTTTTAAT
57342887 AATAATATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.11, G:0.05, T:0.63
Consensus pattern (19 bp):
CTTAATTCTTGTTTTTAAT
Found at i:57342892 original size:19 final size:19
Alignment explanation
Indices: 57342851--57342892 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
57342841 AAGTTAGACT
**
57342851 TAATTCTTGTTTTTAATCT
1 TAATTCTTGTTTTTAATAA
57342870 TAATTCTTGTTTTTAATAA
1 TAATTCTTGTTTTTAATAA
57342889 TAAT
1 TAAT
57342893 ATTGAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.29, C:0.07, G:0.05, T:0.60
Consensus pattern (19 bp):
TAATTCTTGTTTTTAATAA
Found at i:57346211 original size:32 final size:32
Alignment explanation
Indices: 57346175--57346238 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
57346165 TAAAATAAAC
57346175 AAATAACTATTCATTT-AATAG-TATAACTATTT
1 AAATAA-TATT-ATTTAAATAGTTATAACTATTT
*
57346207 AAATAATATTATTTAAATAGTTATAATTATTT
1 AAATAATATTATTTAAATAGTTATAACTATTT
57346239 TTCAAAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 4 0.14
31 9 0.31
32 16 0.55
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (32 bp):
AAATAATATTATTTAAATAGTTATAACTATTT
Found at i:57348077 original size:26 final size:26
Alignment explanation
Indices: 57348039--57348096 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
57348029 CTTAATATAT
*
57348039 GGCTCTTCATGAGCTTTCC-GATTAAA
1 GGCTCTTCATGAG-TTTCCTAATTAAA
** *
57348065 GGCTCTTTGTGAGTTTCCTAATTAAT
1 GGCTCTTCATGAGTTTCCTAATTAAA
57348091 GGCTCT
1 GGCTCT
57348097 CCGGAGCTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 5 0.19
26 22 0.81
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.40
Consensus pattern (26 bp):
GGCTCTTCATGAGTTTCCTAATTAAA
Found at i:57348176 original size:25 final size:25
Alignment explanation
Indices: 57348037--57348218 Score: 76
Period size: 25 Copynumber: 7.4 Consensus size: 25
57348027 GTCTTAATAT
* *
57348037 ATGGCTCTTCATGAGCTTTCCGATTA
1 ATGGCTCTTC-GGAGCTTCCCGATTA
* * * **
57348063 AAGGCTCTTTGTGAGTTTCCTAATTA
1 ATGGCTCTTCG-GAGCTTCCCGATTA
* * *
57348089 ATGGCTCTCCGGAGCTT-CCTAAT-
1 ATGGCTCTTCGGAGCTTCCCGATTA
*
57348112 ATGGCTCGCTT--GAACTTCCCGA-TA
1 ATGGCT--CTTCGGAGCTTCCCGATTA
* *
57348136 TATGGCT-ATCTAGAGCTTCCCGATTA
1 -ATGGCTCTTC-GGAGCTTCCCGATTA
*
57348162 ATGGCTCTTCGGAGCTACCCG--TA
1 ATGGCTCTTCGGAGCTTCCCGATTA
* ** *
57348185 ATTGGCTCGTATGAGCTTCCTGATT-
1 A-TGGCTCTTCGGAGCTTCCCGATTA
57348210 ATGGCTCTT
1 ATGGCTCTT
57348219 ATAAGCTTCC
Statistics
Matches: 114, Mismatches: 28, Indels: 30
0.66 0.16 0.17
Matches are distributed among these distances:
22 1 0.01
23 15 0.13
24 28 0.25
25 39 0.34
26 31 0.27
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.35
Consensus pattern (25 bp):
ATGGCTCTTCGGAGCTTCCCGATTA
Found at i:57348226 original size:73 final size:73
Alignment explanation
Indices: 57348085--57348230 Score: 174
Period size: 73 Copynumber: 2.0 Consensus size: 73
57348075 GAGTTTCCTA
* *
57348085 ATTAATGGCTCTCCGGAGCTTCCTAATATGGCTCGCTTGAACTTCCCGATATATGGCTATCTAGA
1 ATTAATGGCTCTCCGGAGCTCCCTAATATGGCTCGCTTGAACTTCCCGATATATGGCTATCTAAA
57348150 GCTTCCCG
66 GCTTCCCG
* * * *
57348158 ATTAATGGCTCTTCGGAGCTACCCGTAAT-TGGCTCG-TATGAGCTTCCTGAT-TATGGCTCT-T
1 ATTAATGGCTCTCCGGAGCT-CCC-TAATATGGCTCGCT-TGAACTTCCCGATATATGGCTATCT
57348219 ATAAGCTTCCCG
63 A-AAGCTTCCCG
57348231 TTATACAGCC
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
72 2 0.03
73 37 0.59
74 20 0.32
75 4 0.06
ACGTcount: A:0.20, C:0.26, G:0.21, T:0.33
Consensus pattern (73 bp):
ATTAATGGCTCTCCGGAGCTCCCTAATATGGCTCGCTTGAACTTCCCGATATATGGCTATCTAAA
GCTTCCCG
Found at i:57348275 original size:25 final size:25
Alignment explanation
Indices: 57348110--57348292 Score: 106
Period size: 25 Copynumber: 7.4 Consensus size: 25
57348100 GAGCTTCCTA
* * *
57348110 ATATGGCTCGCTTGAACTTCCCGAT
1 ATATGGCTCGCATGAGCTTCCCGTT
**
57348135 ATATGGCTATC-TAGAGCTTCCCGATT
1 ATATGGCTCGCAT-GAGCTTCCCG-TT
* * * *
57348161 A-ATGGCTCTTC-GGAGCTACCCGTA
1 ATATGGCTC-GCATGAGCTTCCCGTT
* * *
57348185 AT-TGGCTCGTATGAGCTTCCTGAT
1 ATATGGCTCGCATGAGCTTCCCGTT
** *
57348209 -TATGGCTCTTATAAGCTTCCCGTT
1 ATATGGCTCGCATGAGCTTCCCGTT
** * * *
57348233 ATACAGCCCGGATAAGCTTCCCGTT
1 ATATGGCTCGCATGAGCTTCCCGTT
* *
57348258 ATATGGCTCACATGAGCTTCCTGTT
1 ATATGGCTCGCATGAGCTTCCCGTT
57348283 ATATGGCTCG
1 ATATGGCTCG
57348293 AGAGAAAGCT
Statistics
Matches: 119, Mismatches: 32, Indels: 14
0.72 0.19 0.08
Matches are distributed among these distances:
23 1 0.01
24 35 0.29
25 79 0.66
26 4 0.03
ACGTcount: A:0.20, C:0.26, G:0.21, T:0.33
Consensus pattern (25 bp):
ATATGGCTCGCATGAGCTTCCCGTT
Found at i:57348690 original size:23 final size:24
Alignment explanation
Indices: 57348632--57348695 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 24
57348622 TGATTAATAT
*
57348632 TATAAAAACATTAT-TTAATTAAAA
1 TATAAGAA-ATTATATTAATTAAAA
* *
57348656 TATTATAAATTATATTAATTAAAA
1 TATAAGAAATTATATTAATTAAAA
*
57348680 T-TAAGATATTATATTA
1 TATAAGAAATTATATTA
57348696 TAGGAAATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
23 17 0.50
24 17 0.50
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (24 bp):
TATAAGAAATTATATTAATTAAAA
Found at i:57349178 original size:16 final size:18
Alignment explanation
Indices: 57349145--57349178 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
57349135 TCGAAATTTT
57349145 GATTAGAATTGATAAAAG
1 GATTAGAATTGATAAAAG
57349163 GATTA-AATTG-TAAAAG
1 GATTAGAATTGATAAAAG
57349179 AAACTATAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 5 0.31
18 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (18 bp):
GATTAGAATTGATAAAAG
Found at i:57349590 original size:3 final size:3
Alignment explanation
Indices: 57349582--57349676 Score: 190
Period size: 3 Copynumber: 31.7 Consensus size: 3
57349572 GTGAGGTAAG
57349582 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
57349630 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
57349677 AGATGAGTGG
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 92 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:57350093 original size:37 final size:39
Alignment explanation
Indices: 57350034--57350129 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
57350024 CGGATAGATT
* * * *
57350034 CGATGAGGTACTGGGTACCAACT-TT-CTTC-AGCTTTAC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
57350071 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
57350110 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
57350130 TTTTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 23 0.48
40 4 0.08
ACGTcount: A:0.23, C:0.24, G:0.26, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:57354316 original size:21 final size:21
Alignment explanation
Indices: 57354274--57354312 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
57354264 TCGTAGAACC
*
57354274 TTTTAAATAATAACTAATTAA
1 TTTTAAATAATAAATAATTAA
*
57354295 TTTTATATAA-AAATAATT
1 TTTTAAATAATAAATAATT
57354313 TAATCAAGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (21 bp):
TTTTAAATAATAAATAATTAA
Found at i:57357488 original size:12 final size:11
Alignment explanation
Indices: 57357464--57357496 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
57357454 AATAGAATGG
57357464 AAAATAAAGAA
1 AAAATAAAGAA
57357475 AAAATAAAGAA
1 AAAATAAAGAA
57357486 AAAA-AAAGAA
1 AAAATAAAGAA
57357496 A
1 A
57357497 GTTAAAAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 7 0.32
11 15 0.68
ACGTcount: A:0.85, C:0.00, G:0.09, T:0.06
Consensus pattern (11 bp):
AAAATAAAGAA
Found at i:57363699 original size:39 final size:38
Alignment explanation
Indices: 57363635--57363762 Score: 156
Period size: 39 Copynumber: 3.3 Consensus size: 38
57363625 AAATTAAAAC
57363635 AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAAATTA
1 AAAAATT-AAAAAAGTATTTTAAAAATATTTTAAAATTA
57363674 CAAAAATT-AAAAAGTATTTTAAAAA-A-TTTAAAATTTA
1 -AAAAATTAAAAAAGTATTTTAAAAATATTTTAAAA-TTA
* *
57363711 AAAATTTAAAAAAAAGTATTTTAAAAGTATTTT-AAATTA
1 AAAAATT--AAAAAAGTATTTTAAAAATATTTTAAAATTA
*
57363750 AAAAATCAAAAAA
1 AAAAATTAAAAAA
57363763 TAATAAAAAT
Statistics
Matches: 78, Mismatches: 4, Indels: 15
0.80 0.04 0.15
Matches are distributed among these distances:
36 13 0.17
37 10 0.13
38 17 0.22
39 24 0.31
40 11 0.14
41 3 0.04
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.34
Consensus pattern (38 bp):
AAAAATTAAAAAAGTATTTTAAAAATATTTTAAAATTA
Found at i:57363736 original size:11 final size:11
Alignment explanation
Indices: 57363722--57363746 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
57363712 AAATTTAAAA
57363722 AAAAGTATTTT
1 AAAAGTATTTT
57363733 AAAAGTATTTT
1 AAAAGTATTTT
57363744 AAA
1 AAA
57363747 TTAAAAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:57367737 original size:3 final size:3
Alignment explanation
Indices: 57367731--57367764 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
57367721 AAGGAGGAGG
*
57367731 AGA AGA AAA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
57367765 AGGGATGGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:57369020 original size:21 final size:20
Alignment explanation
Indices: 57368995--57369044 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
57368985 AAAATATGTC
*
57368995 AATAATATTTTATTAAATAAA
1 AATAATATTTTAATAAA-AAA
*
57369016 AATAAT-CTTTAATAAAAAA
1 AATAATATTTTAATAAAAAA
*
57369035 AATTATATTT
1 AATAATATTT
57369045 GTAAATTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 8 0.33
20 10 0.42
21 6 0.25
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
AATAATATTTTAATAAAAAA
Found at i:57370464 original size:12 final size:12
Alignment explanation
Indices: 57370449--57370482 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
57370439 TAATGAGAAT
57370449 ATAAATAAGGAA
1 ATAAATAAGGAA
*
57370461 ATAAATAAAGAA
1 ATAAATAAGGAA
*
57370473 ATGAATAAGG
1 ATAAATAAGG
57370483 CTATAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.18, T:0.18
Consensus pattern (12 bp):
ATAAATAAGGAA
Found at i:57370698 original size:12 final size:12
Alignment explanation
Indices: 57370681--57370730 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
57370671 ACATGTTTTA
57370681 ATATATATAAAT
1 ATATATATAAAT
**
57370693 ATATATATGTAT
1 ATATATATAAAT
*
57370705 ATATATATGAAT
1 ATATATATAAAT
**
57370717 AGGTATATAAAT
1 ATATATATAAAT
57370729 AT
1 AT
57370731 TCGTGAAAGA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (12 bp):
ATATATATAAAT
Found at i:57370705 original size:18 final size:18
Alignment explanation
Indices: 57370684--57370730 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
57370674 TGTTTTAATA
*
57370684 TATATAAATAT-ATATATG
1 TATATAAATATGA-ATAGG
*
57370702 TATATATATATGAATAGG
1 TATATAAATATGAATAGG
57370720 TATATAAATAT
1 TATATAAATAT
57370731 TCGTGAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 24 0.96
19 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (18 bp):
TATATAAATATGAATAGG
Found at i:57370725 original size:2 final size:2
Alignment explanation
Indices: 57370612--57370712 Score: 66
Period size: 2 Copynumber: 52.0 Consensus size: 2
57370602 AATAATAATA
* * * *
57370612 AT AT AT AT AT AT AT AT A- AT AGT AC AC GT TT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
* * * * * *
57370653 AT AT AT AT AT AA AA AT AT AC AT GT -T TT A- AT AT AT AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
57370693 AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
57370713 GAATAGGTAT
Statistics
Matches: 79, Mismatches: 15, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
1 4 0.05
2 73 0.92
3 2 0.03
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:57370783 original size:18 final size:18
Alignment explanation
Indices: 57370756--57370872 Score: 54
Period size: 17 Copynumber: 6.9 Consensus size: 18
57370746 ATAAGAGAAA
* *
57370756 TAACAGTAATATTAATAC
1 TAACAATAATAGTAATAC
57370774 TAACAATAATAGT-A-A-
1 TAACAATAATAGTAATAC
* *
57370789 TAATAATAACCA-T-A-A-
1 TAACAATAA-TAGTAATAC
*
57370804 TAATAATAATAGTAA-AC
1 TAACAATAATAGTAATAC
* * *
57370821 TAATAATAATAATAATAA
1 TAACAATAATAGTAATAC
* *
57370839 T-ATAATAATAGTAATAA
1 TAACAATAATAGTAATAC
* *
57370856 TAATAATAATAATAATA
1 TAACAATAATAGTAATA
57370873 ATAAGAAAAG
Statistics
Matches: 84, Mismatches: 9, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
14 1 0.01
15 21 0.25
16 4 0.05
17 31 0.37
18 27 0.32
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.32
Consensus pattern (18 bp):
TAACAATAATAGTAATAC
Found at i:57370792 original size:3 final size:3
Alignment explanation
Indices: 57370762--57370876 Score: 135
Period size: 3 Copynumber: 39.0 Consensus size: 3
57370752 GAAATAACAG
* * * * **
57370762 TAA TAT TAA TAC TAA CAA TAA TAG TAA TAA TAA TAA CCA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
57370810 TAA TAG TAA -AC TAA TAA TAA TAA TAA TAA T-A TAA TAA TAG TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
57370856 TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
57370877 GAAAAGTTTG
Statistics
Matches: 92, Mismatches: 18, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
2 3 0.03
3 89 0.97
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:57371845 original size:5 final size:5
Alignment explanation
Indices: 57371835--57371870 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
57371825 AAACAAACAA
*
57371835 AAAAT AAAAT AAAAT AAAAT AGAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A
57371871 GCAATGTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:57372510 original size:48 final size:48
Alignment explanation
Indices: 57372443--57372712 Score: 193
Period size: 48 Copynumber: 5.5 Consensus size: 48
57372433 CGGGGAAATG
*
57372443 AGATTCGCTGTTGTAGCTTCAATCTTCTTCGCTGCATTGCCAGAAGTA
1 AGATTCGCCGTTGTAGCTTCAATCTTCTTCGCTGCATTGCCAGAAGTA
* * *** * ** *
57372491 AGATTCACCGTTGTGGCTTCAATCTT-TTAAATTGCAATGTCGGGGAAGTG
1 AGATTCGCCGTTGTAGCTTCAATCTTCTT-CGCTGCATTG-C-CAGAAGTA
* * *
57372541 AGATTCGCCGTTGTAGCTTCAATCTGCTCCGCTGCATCGCCAGAAGTA
1 AGATTCGCCGTTGTAGCTTCAATCTTCTTCGCTGCATTGCCAGAAGTA
* *** * ** *
57372589 AGATTCGCCGTTGTGGCTTCAATCTT-TTAAATTGCAATGTCGGGGAAGTG
1 AGATTCGCCGTTGTAGCTTCAATCTTCTT-CGCTGCATTG-C-CAGAAGTA
* * * ** * * *
57372639 AGATTCGCTGTTGTAGCTTCAATCTGCTCCGCTGCATCACTAGTAGTG
1 AGATTCGCCGTTGTAGCTTCAATCTTCTTCGCTGCATTGCCAGAAGTA
* *
57372687 AGATTCGCCGCTGTGGCTTCAATCTT
1 AGATTCGCCGTTGTAGCTTCAATCTT
57372713 TTTAAATGCA
Statistics
Matches: 164, Mismatches: 50, Indels: 16
0.71 0.22 0.07
Matches are distributed among these distances:
47 3 0.02
48 90 0.55
49 4 0.02
50 65 0.40
51 2 0.01
ACGTcount: A:0.21, C:0.22, G:0.24, T:0.33
Consensus pattern (48 bp):
AGATTCGCCGTTGTAGCTTCAATCTTCTTCGCTGCATTGCCAGAAGTA
Found at i:57372516 original size:98 final size:98
Alignment explanation
Indices: 57372359--57372747 Score: 521
Period size: 98 Copynumber: 4.0 Consensus size: 98
57372349 CACCGTTGAG
* * ** * *
57372359 GCTTCAATCTGTTCCGCTGCGTCGTCTGGAAGTAA-AATCTACCGTTGTGGCTTCGATCTTTTAA
1 GCTTCAATCTGCTCCGCTGCATCG-CCAGAAGTAAGATTC-ACCGTTGTGGCTTCAATCTTTTAA
* *
57372423 ATTCCAATATCGGGGAAATGAGATTCGCTGTTGTA
64 ATTGCAATGTCGGGGAAATGAGATTCGCTGTTGTA
* * *
57372458 GCTTCAATCTTCTTCGCTGCATTGCCAGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTAAAT
1 GCTTCAATCTGCTCCGCTGCATCGCCAGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTAAAT
* *
57372523 TGCAATGTCGGGGAAGTGAGATTCGCCGTTGTA
66 TGCAATGTCGGGGAAATGAGATTCGCTGTTGTA
*
57372556 GCTTCAATCTGCTCCGCTGCATCGCCAGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAAAT
1 GCTTCAATCTGCTCCGCTGCATCGCCAGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTAAAT
*
57372621 TGCAATGTCGGGGAAGTGAGATTCGCTGTTGTA
66 TGCAATGTCGGGGAAATGAGATTCGCTGTTGTA
* * * * * *
57372654 GCTTCAATCTGCTCCGCTGCATCACTAGTAGTGAGATTCGCCGCTGTGGCTTCAATCTTTTTAAA
1 GCTTCAATCTGCTCCGCTGCATCGCCAGAAGTAAGATTCACCGTTGTGGCTTCAATC-TTTTAAA
* * *
57372719 -TGCAATGTCAGGGAAATAAGATCCGCTGT
65 TTGCAATGTCGGGGAAATGAGATTCGCTGT
57372748 CAGTGCAGGA
Statistics
Matches: 261, Mismatches: 27, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
98 232 0.89
99 29 0.11
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (98 bp):
GCTTCAATCTGCTCCGCTGCATCGCCAGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTAAAT
TGCAATGTCGGGGAAATGAGATTCGCTGTTGTA
Found at i:57372552 original size:50 final size:50
Alignment explanation
Indices: 57372400--57372663 Score: 234
Period size: 50 Copynumber: 5.4 Consensus size: 50
57372390 GTAAAATCTA
* * * * *
57372400 CCGTTGTGGCTTCGATCTTTTAAATTCCAATATCGGGGAAATGAGATTCG
1 CCGTTGTAGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGTGAGATTCG
* *** * ** * *
57372450 CTGTTGTAGCTTCAATCTTCTT-CGCTGCATTG-C-CAGAAGTAAGATTCA
1 CCGTTGTAGCTTCAATCTT-TTAAATTGCAATGTCGGGGAAGTGAGATTCG
*
57372498 CCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGTGAGATTCG
1 CCGTTGTAGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGTGAGATTCG
** **** ** *
57372548 CCGTTGTAGCTTCAATCTGCTCCGCTGC-A--TCGCCAGAAGTAAGATTCG
1 CCGTTGTAGCTTCAATCTTTTAAATTGCAATGTCG-GGGAAGTGAGATTCG
*
57372596 CCGTTGTGGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGTGAGATTCG
1 CCGTTGTAGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGTGAGATTCG
*
57372646 CTGTTGTAGCTTCAATCT
1 CCGTTGTAGCTTCAATCT
57372664 GCTCCGCTGC
Statistics
Matches: 160, Mismatches: 46, Indels: 16
0.72 0.21 0.07
Matches are distributed among these distances:
47 5 0.03
48 66 0.41
49 4 0.03
50 80 0.50
51 5 0.03
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (50 bp):
CCGTTGTAGCTTCAATCTTTTAAATTGCAATGTCGGGGAAGTGAGATTCG
Found at i:57386446 original size:12 final size:12
Alignment explanation
Indices: 57386431--57386464 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
57386421 TAATGAGAAT
57386431 ATAAATAAGGAA
1 ATAAATAAGGAA
*
57386443 ATAAATAAAGAA
1 ATAAATAAGGAA
*
57386455 ATGAATAAGG
1 ATAAATAAGG
57386465 CTATAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.18, T:0.18
Consensus pattern (12 bp):
ATAAATAAGGAA
Found at i:57386721 original size:2 final size:2
Alignment explanation
Indices: 57386589--57386708 Score: 113
Period size: 2 Copynumber: 62.0 Consensus size: 2
57386579 AAAAAAAGAA
* * * * *
57386589 AT AT A- AT AT AT AT AT AT AT AT AA AT AT AC AC GT TT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
57386629 AT AT AT AT AT AT AT AT AT AT AT AA AA AT AT AC AT GT -T TT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
57386669 AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
57386709 GAATAGGTAT
Statistics
Matches: 99, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
1 4 0.04
2 95 0.96
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:57397609 original size:24 final size:24
Alignment explanation
Indices: 57397582--57397630 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
57397572 TAAAAAAATA
*
57397582 TATATTTTAATAAAATTTAAATTT
1 TATATTTCAATAAAATTTAAATTT
* *
57397606 TATATTTCATTAAAATTTAATTTT
1 TATATTTCAATAAAATTTAAATTT
57397630 T
1 T
57397631 TCTATTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
TATATTTCAATAAAATTTAAATTT
Found at i:57397774 original size:92 final size:92
Alignment explanation
Indices: 57397656--57397877 Score: 270
Period size: 92 Copynumber: 2.4 Consensus size: 92
57397646 AGAGTATGGC
* * * * *
57397656 CTTATTTG-TTTTTTTGAAAAATTTTGATGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACCCA
1 CTTAATTGCTTTTTTTGAAAAAGTTTGA-GGACTTTTTAATGCATTATGAAAGTTCAAGTACCCA
* *
57397720 ATTGAATGGAAA-AAAAAA-AAGGAGGAG
65 ATGGAATGCAAAGAAAAAAGAA-GAGGAG
* * * * *
57397747 TTTAATTGCTTTTTTTGAAGAAGTTTGAGAGACTTTTCAATGCATTATGAAAGTTCAAGTGCTCA
1 CTTAATTGCTTTTTTTGAAAAAGTTTGAG-GACTTTTTAATGCATTATGAAAGTTCAAGTACCCA
* *
57397812 ATGGAGTGCAAAGAAAAAAGAAGAGGGG
65 ATGGAATGCAAAGAAAAAAGAAGAGGAG
57397840 CTTAATTGCTTTTTTTGAAAAAGTTTGAGGACTTTTTA
1 CTTAATTGCTTTTTTTGAAAAAGTTTGAGGACTTTTTA
57397878 CACCCTTAAG
Statistics
Matches: 110, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
91 7 0.06
92 63 0.57
93 38 0.35
94 2 0.02
ACGTcount: A:0.34, C:0.08, G:0.21, T:0.37
Consensus pattern (92 bp):
CTTAATTGCTTTTTTTGAAAAAGTTTGAGGACTTTTTAATGCATTATGAAAGTTCAAGTACCCAA
TGGAATGCAAAGAAAAAAGAAGAGGAG
Found at i:57407458 original size:64 final size:64
Alignment explanation
Indices: 57407383--57407502 Score: 197
Period size: 64 Copynumber: 1.9 Consensus size: 64
57407373 GTTTAGTCGG
* * *
57407383 TTTGATTTCATGTTTCAATAGCAGTTTCAAGTGGTTCG-TTCAAAATTTAATTTAATTCAACCGA
1 TTTGATTTCATGTTTCAATAGCAATTTCAAGTGGTTCGCTT-AAAACTCAATTTAATTCAACCGA
57407447 TTTGATTTCATGTTTCAATAGCAATTTCAAGTGGTTCGCTTAAAACTCAATTTAAT
1 TTTGATTTCATGTTTCAATAGCAATTTCAAGTGGTTCGCTTAAAACTCAATTTAAT
57407503 GTCATTGCTC
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
64 50 0.96
65 2 0.04
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.42
Consensus pattern (64 bp):
TTTGATTTCATGTTTCAATAGCAATTTCAAGTGGTTCGCTTAAAACTCAATTTAATTCAACCGA
Found at i:57414113 original size:29 final size:30
Alignment explanation
Indices: 57414055--57414110 Score: 89
Period size: 28 Copynumber: 1.9 Consensus size: 30
57414045 ATTTGCATTT
57414055 TTAAAATAAAAAATAGAAGGATTAAATTCA
1 TTAAAATAAAAAATAGAAGGATTAAATTCA
*
57414085 TTAAAAT-AAAAGTAGAA-GATTAAATT
1 TTAAAATAAAAAATAGAAGGATTAAATT
57414111 TCAAATGTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 9 0.36
29 9 0.36
30 7 0.28
ACGTcount: A:0.59, C:0.02, G:0.11, T:0.29
Consensus pattern (30 bp):
TTAAAATAAAAAATAGAAGGATTAAATTCA
Found at i:57415721 original size:16 final size:17
Alignment explanation
Indices: 57415690--57415722 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
57415680 TTTTATTATG
57415690 GAAGCTTTGTTTTTTTA
1 GAAGCTTTGTTTTTTTA
57415707 GAAGCTTTGTTTTTTT
1 GAAGCTTTGTTTTTTT
57415723 GGGTGTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.06, G:0.18, T:0.61
Consensus pattern (17 bp):
GAAGCTTTGTTTTTTTA
Found at i:57422811 original size:44 final size:44
Alignment explanation
Indices: 57422748--57423467 Score: 437
Period size: 44 Copynumber: 15.6 Consensus size: 44
57422738 CATTATGGTG
*
57422748 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACA
* * *
57422792 AATCTTATCTCCCTAAAGTTGCGGTGGAGCAGATTGAAGCGACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACA
* * *
57422836 AATCCTATAC-CCCTGAAGTTGCAGTGG-G-ATGGATTGAAATCATCATGGCG
1 AATCTTAT-CTCCCTGAAGTTGCAGTGGAGCA--GATTG-AAGC--CA---CA
* * *
57422886 AATCTTATCCCCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACA
* **** *
57422930 AATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTGAATATGCG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACA
* ** * *
57422974 AATCTTATTTCCCTGAAGTTGCAGTGGAATAGAATAAAGCTACAGATCACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAG-AT--TG--A-AG-CCACA
* * * * * * * *
57423025 AATCCTA-CACCCCTAAAGTTGTAG-CGAG-ATGGGTTGAAGTCATTATGGCG
1 AATCTTATC-TCCCTGAAGTTGCAGTGGAGCA--GATTGAAG-C--CA---CA
* * * *
57423075 AATTTTATCTCCCTGAAGTGGCAGTGGAGTAGATTAAAGCCACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACA
* * * * *
57423119 AATCTTATCTCCCTGAAGTTACAGTAGAGCAAATTAAAGCTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACA
* * *
57423163 AATCTTATCTCCCTGAAGTTGCAGTGGAACAAATTAAAGCTACAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGC--C-----ACA
* * * * *
57423214 AGTCTTATCTCCTTGAAGTTGTAGTGGAGTAGATTGAAGCTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACA
* * * **
57423258 AATCTTATTTCCCTAAAGTTGCAGTGGAACAGATCAAAGCTACAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGC--C-----ACA
* * * *
57423309 AATATTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAGCTACT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACA
* * * * *
57423353 AATCTTATCTCCCTGAAGTTGAAGTAGAGTAGATTGAAGCTACT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACA
** * *
57423397 AATCTTATCTCCCCAAAGTTGCAGTGGAGCAGATTGAAGCGATA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACA
* *
57423441 ATTCTTAAAC-CCCTGAAGTTGCAGTGG
1 AATCTT-ATCTCCCTGAAGTTGCAGTGG
57423468 GTTAGAACGA
Statistics
Matches: 520, Mismatches: 111, Indels: 90
0.72 0.15 0.12
Matches are distributed among these distances:
42 1 0.00
43 1 0.00
44 338 0.65
45 10 0.02
46 1 0.00
47 6 0.01
48 1 0.00
49 7 0.01
50 56 0.11
51 97 0.19
52 2 0.00
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACA
Found at i:57422890 original size:94 final size:93
Alignment explanation
Indices: 57422792--57423143 Score: 290
Period size: 94 Copynumber: 3.7 Consensus size: 93
57422782 TGAAGCCACT
* * *
57422792 AATCTTATCTCCCTAAAGTTGCGGTGGAGCAGATTGAAGCGACAAATCCTATAC-CCCTGAAGTT
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCACAAATCCTAT-CTCCCTGAAGTT
57422856 GCAGTGGGATGGATTGAAATCATCATGGCG
65 GCAGTGGGATGGATTGAAATCAT-ATGGCG
* * * *
57422886 AATCTTATCCCCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACTAATCTTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCACAAATCCTATCTCCCTGAAGTTG
*
57422951 CAAT-GGA-GCAGATTG--A--ATAT-GCG
66 CAGTGGGATG--GATTGAAATCATATGGCG
* * ** * *
57422974 AATCTTATTTCCCTGAAGTTGCAGTGGAATAGAATAAAGCTACAGATCACAAATCCTA-CACCCC
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAG---C----CACAAATCCTATC-TCCC
* * * * * *
57423038 TAAAGTTGTAGCGAGATGGGTTGAAGTCATTATGGCG
58 TGAAGTTGCAGTGGGATGGATTGAAATCA-TATGGCG
* * * * * *
57423075 AATTTTATCTCCCTGAAGTGGCAGTGGAGTAGATTAAAGCCACAAATCTTATCTCCCTGAAGTTA
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCACAAATCCTATCTCCCTGAAGTTG
57423140 CAGT
66 CAGT
57423144 AGAGCAAATT
Statistics
Matches: 204, Mismatches: 34, Indels: 40
0.73 0.12 0.14
Matches are distributed among these distances:
88 35 0.17
89 2 0.01
90 2 0.01
91 1 0.00
92 2 0.01
93 4 0.02
94 88 0.43
95 25 0.12
96 2 0.01
97 1 0.00
98 1 0.00
99 1 0.00
100 3 0.01
101 37 0.18
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.27
Consensus pattern (93 bp):
AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCACAAATCCTATCTCCCTGAAGTTG
CAGTGGGATGGATTGAAATCATATGGCG
Found at i:57422988 original size:138 final size:138
Alignment explanation
Indices: 57422697--57423000 Score: 475
Period size: 138 Copynumber: 2.2 Consensus size: 138
57422687 GAGAAACCAT
* * *
57422697 AAATCTTATACCCCTGAAGTTGCAGTGGGATGGATTGAAATCATTATGGTGAATCTTATCTCCCT
1 AAATCTTATACCCCTGAAGTTGCAGTGGGATGGATTGAAATCATCATGGCGAATCTTATCCCCCT
* **
57422762 GAAGTTGCAGTGGAGCAGATTGAAGCCACTAATCTTATCTCCCTAAAGTTGCGGTGGAGCAGATT
66 AAAGTTGCAGTGGAGCAGATTGAAGCCACTAATCTTATCTCCCTAAAGTTGCAATGGAGCAGATT
*
57422827 GAAGCGAC
131 GAAACGAC
*
57422835 AAATCCTATACCCCTGAAGTTGCAGTGGGATGGATTGAAATCATCATGGCGAATCTTATCCCCCT
1 AAATCTTATACCCCTGAAGTTGCAGTGGGATGGATTGAAATCATCATGGCGAATCTTATCCCCCT
*
57422900 AAAGTTGCAGTGGAGCAGATTGAAGCCACTAATCTTATCTCCCTGAAGTTGCAATGGAGCAGATT
66 AAAGTTGCAGTGGAGCAGATTGAAGCCACTAATCTTATCTCCCTAAAGTTGCAATGGAGCAGATT
*
57422965 GAATATG-C
131 GAA-ACGAC
* **
57422973 GAATCTTATTTCCCTGAAGTTGCAGTGG
1 AAATCTTATACCCCTGAAGTTGCAGTGG
57423001 AATAGAATAA
Statistics
Matches: 151, Mismatches: 14, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
138 150 0.99
139 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (138 bp):
AAATCTTATACCCCTGAAGTTGCAGTGGGATGGATTGAAATCATCATGGCGAATCTTATCCCCCT
AAAGTTGCAGTGGAGCAGATTGAAGCCACTAATCTTATCTCCCTAAAGTTGCAATGGAGCAGATT
GAAACGAC
Found at i:57423134 original size:189 final size:186
Alignment explanation
Indices: 57422748--57423373 Score: 558
Period size: 189 Copynumber: 3.3 Consensus size: 186
57422738 CATTATGGTG
* * *
57422748 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACTAATCTTATCTCCCTAAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATCTCCCTGAAGTTG
* * * * * * * *
57422813 CGGTGGAGCAGATTGAAG---C-GACAAATCCTATACCCCTGAAGTTGCAGTGGGATGGATTGAA
66 CAGTGGAACAGAATAAAGCTACAGACAAATCCTACACCCCTAAAGTTGCAGCGAGATGGATTGAA
* * *
57422874 ATCATCATGGCGAATCTTATCCCCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACT
131 ATCATCATGGCGAATCTTATCCCCCTAAAGTGGCAGTGGAGCAGATTAAAGCCACA
* ** * * *
57422930 AATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTGAATATGCGAATCTTATTTCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATCTCCCTGAAGTTG
* * *
57422995 CAGTGGAATAGAATAAAGCTACAGATCACAAATCCTACACCCCTAAAGTTGTAGCGAGATGGGTT
66 CAGTGGAACAGAATAAAGCTACAG---ACAAATCCTACACCCCTAAAGTTGCAGCGAGATGGATT
* * * * * *
57423060 GAAGTCATTATGGCGAATTTTATCTCCCTGAAGTGGCAGTGGAGTAGATTAAAGCCACA
128 GAAATCATCATGGCGAATCTTATCCCCCTAAAGTGGCAGTGGAGCAGATTAAAGCCACA
* * * *
57423119 AATCTTATCTCCCTGAAGTTACAGTAGAGCAAATTAAAGCTACAAATCTTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATCTCCCTGAAGTTG
* * * * * * * *
57423184 CAGTGGAACA-AATTAAAGCTACAAGTTACAAGTCTTATC-TCCTTGAAGTTGTAGTG-GAGTAG
66 CAGTGGAACAGAA-TAAAGCTAC-AG--ACAAATCCTA-CACCCCTAAAGTTGCAGCGAGA-TGG
* * ** * * *
57423246 ATTG-AAGC-T-A---CAAATCTTATTTCCCTAAAGTTGCAGTGGAACAGATCAAAGCTACAAGT
125 ATTGAAATCATCATGGCGAATCTTATCCCCCTAAAGTGGCAGTGGAGCAGATTAAAGC--C----
57423305 TACA
184 -ACA
* * *
57423309 AATATTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAGCTACTAATCTTATCTCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATCTCCCTGAAGTTG
57423374 AAGTAGAGTA
Statistics
Matches: 361, Mismatches: 65, Indels: 28
0.80 0.14 0.06
Matches are distributed among these distances:
182 70 0.19
183 34 0.09
185 2 0.01
186 2 0.01
187 1 0.00
188 6 0.02
189 182 0.50
190 64 0.18
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.28
Consensus pattern (186 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATCTCCCTGAAGTTG
CAGTGGAACAGAATAAAGCTACAGACAAATCCTACACCCCTAAAGTTGCAGCGAGATGGATTGAA
ATCATCATGGCGAATCTTATCCCCCTAAAGTGGCAGTGGAGCAGATTAAAGCCACA
Found at i:57423240 original size:51 final size:51
Alignment explanation
Indices: 57423159--57423351 Score: 211
Period size: 51 Copynumber: 3.9 Consensus size: 51
57423149 AAATTAAAGC
*
57423159 TACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAAATTAAAGCTACAAGT
1 TACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAGT
* * * ** *
57423210 TACAAGTCTTATCTCCTTGAAGTTGTAGTGGAGTAGATT---G----AAGC
1 TACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAGT
* * *
57423254 TACAAATCTTATTTCCCTAAAGTTGCAGTGGAACAGATCAAAGCTACAAGT
1 TACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAGT
* * * *
57423305 TACAAATATTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAGCTAC
1 TACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTAC
57423352 TAATCTTATC
Statistics
Matches: 112, Mismatches: 23, Indels: 14
0.75 0.15 0.09
Matches are distributed among these distances:
44 34 0.30
47 1 0.01
48 1 0.01
51 76 0.68
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.30
Consensus pattern (51 bp):
TACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAGT
Found at i:57423261 original size:139 final size:132
Alignment explanation
Indices: 57423079--57423467 Score: 393
Period size: 139 Copynumber: 2.8 Consensus size: 132
57423069 ATGGCGAATT
* * * * * *
57423079 TTATCTCCCTGAAGTGGCAGTGGAGTAGATTAAAGCCACAAATCTTATCTCCCTGAAGTTACAGT
1 TTATCTCCCTGAAGTTGAAGTGGAGTAGATTGAAGCTACAAATCTTATCTCCCTAAAGTTGCAGT
57423144 AGAGCAAATTAAAGCTACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAAATTAAAGCTACAAG
66 AGAGCAAATTAAAGCTACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAAATTAAAGCTAC---
57423209 TTACAAGTC
128 -T--AA-TC
* * *
57423218 TTATCTCCTTGAAGTTGTAGTGGAGTAGATTGAAGCTACAAATCTTATTTCCCTAAAGTTGCAGT
1 TTATCTCCCTGAAGTTGAAGTGGAGTAGATTGAAGCTACAAATCTTATCTCCCTAAAGTTGCAGT
* * * * * * * *
57423283 GGAACAGATCAAAGCTACAAGTTACAAATATTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAG
66 -----AGAGCAAA-TTA-AAGCTACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAAATTAAAG
57423348 CTACTAATC
124 CTACTAATC
* * *
57423357 TTATCTCCCTGAAGTTGAAGTAGAGTAGATTGAAGCTACTAATCTTATCTCCCCAAAGTTGCAGT
1 TTATCTCCCTGAAGTTGAAGTGGAGTAGATTGAAGCTACAAATCTTATCTCCCTAAAGTTGCAGT
* * * * * * *
57423422 GGAGCAGATTGAAGCGATAATTCTTAAAC-CCCTGAAGTTGCAGTGG
66 AGAGCAAATTAAAGCTACAAATCTT-ATCTCCCTGAAGTTGCAGTGG
57423468 GTTAGAACGA
Statistics
Matches: 208, Mismatches: 34, Indels: 23
0.78 0.13 0.09
Matches are distributed among these distances:
132 25 0.12
133 3 0.01
134 5 0.02
139 118 0.57
140 2 0.01
142 1 0.00
144 7 0.03
145 2 0.01
146 45 0.22
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.29
Consensus pattern (132 bp):
TTATCTCCCTGAAGTTGAAGTGGAGTAGATTGAAGCTACAAATCTTATCTCCCTAAAGTTGCAGT
AGAGCAAATTAAAGCTACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAAATTAAAGCTACTAA
TC
Found at i:57423393 original size:95 final size:94
Alignment explanation
Indices: 57422748--57423467 Score: 428
Period size: 95 Copynumber: 7.7 Consensus size: 94
57422738 CATTATGGTG
* * *
57422748 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACTAATCTTATCTCCCTAAAGTTG
1 AATCTTATCT-CCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATCTCCCTGAAGTTG
* * *
57422813 CGGTGGAGCAGATTGAAG---C--G--ACA
65 CAGTGGAACAGATTAAAGCTACAAGTTACA
* * * * *
57422836 AATCCTATACCCCTGAAGTTGCAGTGG-G-ATGGATTGAAATCATCATGGCGAATCTTATCCCCC
1 AATCTTAT-CTCCTGAAGTTGCAGTGGAGCA--GATTG-AAGC-T-A---CAAATCTTATCTCCC
* * * *
57422899 TAAAGTTGCAGTGGAGCAGATTGAAGC--C-----ACT
57 TGAAGTTGCAGTGGAACAGATTAAAGCTACAAGTTACA
* ** * * *
57422930 AATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTGAATATGCGAATCTTATTTCCCTGAAGTTG
1 AATCTTATCT-CCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATCTCCCTGAAGTTG
* * *
57422995 CAGTGGAATAGAATAAAGCTAC-AGATCACA
65 CAGTGGAACAGATTAAAGCTACAAG-TTACA
* * * * * * * * *
57423025 AATCCTACACCCCTAAAGTTGTAG-CGAG-ATGGGTTGAAGTCATTATGGCGAATTTTATCTCCC
1 AATCTTA-TCTCCTGAAGTTGCAGTGGAGCA--GATTGAAG-C--TA---CAAATCTTATCTCCC
* **
57423088 TGAAGTGGCAGTGGAGTAGATTAAAGC--C-----ACA
57 TGAAGTTGCAGTGGAACAGATTAAAGCTACAAGTTACA
* * * *
57423119 AATCTTATCTCCCTGAAGTTACAGTAGAGCAAATTAAAGCTACAAATCTTATCTCCCTGAAGTTG
1 AATCTTATCT-CCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATCTCCCTGAAGTTG
*
57423184 CAGTGGAACAAATTAAAGCTACAAGTTACA
65 CAGTGGAACAGATTAAAGCTACAAGTTACA
* * * * *
57423214 AGTCTTATCTCCTTGAAGTTGTAGTGGAGTAGATTGAAGCTACAAATCTTATTTCCCTAAAGTTG
1 AATCTTATCTCC-TGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATCTCCCTGAAGTTG
*
57423279 CAGTGGAACAGATCAAAGCTACAAGTTACA
65 CAGTGGAACAGATTAAAGCTACAAGTTACA
* *
57423309 AATATTATCTCTCTGAAGTTGCAGTGGAGCAGATTGAAGCTACTAATCTTATCTCCCTGAAGTTG
1 AATCTTATCTC-CTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATCTCCCTGAAGTTG
* * ** *
57423374 AAGTAGAGTAGATTGAAGCTAC----T---
65 CAGTGGAACAGATTAAAGCTACAAGTTACA
** * * * *
57423397 AATCTTATCTCCCCAAAGTTGCAGTGGAGCAGATTGAAGCGATAATTCTTAAAC-CCCTGAAGTT
1 AATCTTATCT-CCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTT-ATCTCCCTGAAGTT
57423461 GCAGTGG
64 GCAGTGG
57423468 GTTAGAACGA
Statistics
Matches: 502, Mismatches: 87, Indels: 86
0.74 0.13 0.13
Matches are distributed among these distances:
86 1 0.00
87 1 0.00
88 155 0.31
89 7 0.01
90 2 0.00
91 4 0.01
92 1 0.00
93 7 0.01
94 96 0.19
95 185 0.37
96 4 0.01
98 1 0.00
99 1 0.00
101 37 0.07
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (94 bp):
AATCTTATCTCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAATCTTATCTCCCTGAAGTTGC
AGTGGAACAGATTAAAGCTACAAGTTACA
Found at i:57429939 original size:25 final size:25
Alignment explanation
Indices: 57429901--57429949 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 25
57429891 ATTAATTTTG
57429901 TATATTTTAATTAAAAACATAAAAATT
1 TATATTTT-ATT-AAAACATAAAAATT
*
57429928 TATATTTT-TTAAAAGATAAAAA
1 TATATTTTATTAAAACATAAAAA
57429950 AATTATGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 11 0.52
25 2 0.10
27 8 0.38
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (25 bp):
TATATTTTATTAAAACATAAAAATT
Found at i:57434597 original size:17 final size:17
Alignment explanation
Indices: 57434570--57434615 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 17
57434560 AAAGTTTAGG
57434570 GGGGAAATAAAAAGTTTT
1 GGGGAAAT-AAAAGTTTT
57434588 GGGG-AATAAAAG-TTT
1 GGGGAAATAAAAGTTTT
57434603 GAGGGAAAGTAAA
1 G-GGGAAA-TAAA
57434616 TAGGGGGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 4 0.16
16 8 0.32
17 5 0.20
18 8 0.32
ACGTcount: A:0.46, C:0.00, G:0.33, T:0.22
Consensus pattern (17 bp):
GGGGAAATAAAAGTTTT
Found at i:57434733 original size:30 final size:31
Alignment explanation
Indices: 57434694--57434753 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
57434684 AGAGGTGGGA
*
57434694 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
57434725 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
57434754 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:57435069 original size:9 final size:9
Alignment explanation
Indices: 57435055--57435094 Score: 80
Period size: 9 Copynumber: 4.4 Consensus size: 9
57435045 TCGAGTTGAT
57435055 TCGAATAAC
1 TCGAATAAC
57435064 TCGAATAAC
1 TCGAATAAC
57435073 TCGAATAAC
1 TCGAATAAC
57435082 TCGAATAAC
1 TCGAATAAC
57435091 TCGA
1 TCGA
57435095 TTTGTTTAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.42, C:0.23, G:0.12, T:0.23
Consensus pattern (9 bp):
TCGAATAAC
Found at i:57435874 original size:20 final size:18
Alignment explanation
Indices: 57435826--57435880 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
57435816 ATAAAAATTT
57435826 AAAAA-AAA-AATAT-TG
1 AAAAATAAAGAATATATG
*
57435841 AAAAATAAATAATATAGTG
1 AAAAATAAAGAATATA-TG
57435860 AAAAATATAAGAATATATG
1 AAAAATA-AAGAATATATG
57435879 AA
1 AA
57435881 TATTGTAGTC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
15 5 0.15
16 3 0.09
17 5 0.15
19 13 0.38
20 8 0.24
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (18 bp):
AAAAATAAAGAATATATG
Found at i:57436409 original size:22 final size:22
Alignment explanation
Indices: 57436384--57436435 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
57436374 GCGCTTCAAC
*
57436384 GCTTACTGCTTCGCACTTCGGT
1 GCTTACTGATTCGCACTTCGGT
* * *
57436406 GCTTAGTGATTTGCACTTTGGT
1 GCTTACTGATTCGCACTTCGGT
*
57436428 GCATACTG
1 GCTTACTG
57436436 TTGAATTAGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.13, C:0.23, G:0.25, T:0.38
Consensus pattern (22 bp):
GCTTACTGATTCGCACTTCGGT
Found at i:57436712 original size:21 final size:21
Alignment explanation
Indices: 57436666--57436712 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
57436656 TGTAAAGATT
57436666 AATT-GTGAATGAAATGATAA
1 AATTAGTGAATGAAATGATAA
*
57436686 AGATTAGTG-ATGAAATTATGAA
1 A-ATTAGTGAATGAAATGAT-AA
57436708 AATTA
1 AATTA
57436713 CATGTATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 16 0.70
22 6 0.26
ACGTcount: A:0.49, C:0.00, G:0.19, T:0.32
Consensus pattern (21 bp):
AATTAGTGAATGAAATGATAA
Found at i:57455298 original size:2 final size:2
Alignment explanation
Indices: 57455291--57455330 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
57455281 GCTCTATTTA
57455291 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
57455331 TAGCTTGGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57457657 original size:29 final size:31
Alignment explanation
Indices: 57457589--57457646 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
57457579 TAATGATTAG
*
57457589 AACTAAATT-TTGAAATATAAAAAGTAGATT
1 AACTAAATTCTTGAAATATAAAAAGTACATT
57457619 AACTAAATTCTTGAAA-ATAAAAAG-ACAT
1 AACTAAATTCTTGAAATATAAAAAGTACAT
57457647 GTGCTAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 3 0.12
30 17 0.65
31 6 0.23
ACGTcount: A:0.55, C:0.07, G:0.09, T:0.29
Consensus pattern (31 bp):
AACTAAATTCTTGAAATATAAAAAGTACATT
Found at i:57459863 original size:12 final size:12
Alignment explanation
Indices: 57459846--57459870 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
57459836 AAATAAATTG
57459846 AAAAAGAAACAA
1 AAAAAGAAACAA
57459858 AAAAAGAAACAA
1 AAAAAGAAACAA
57459870 A
1 A
57459871 TTGAAACGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.08, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAGAAACAA
Found at i:57459902 original size:21 final size:21
Alignment explanation
Indices: 57459873--57459920 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
57459863 GAAACAAATT
*
57459873 GAAACGAAAACAGAGAAG-GAAA
1 GAAA-GAAAACA-AAAAGAGAAA
*
57459895 GAAAGAAAAGAAAAAGAGAAA
1 GAAAGAAAACAAAAAGAGAAA
57459916 GAAAG
1 GAAAG
57459921 GAGAAAAAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 4 0.17
21 15 0.65
22 4 0.17
ACGTcount: A:0.69, C:0.04, G:0.27, T:0.00
Consensus pattern (21 bp):
GAAAGAAAACAAAAAGAGAAA
Found at i:57459906 original size:17 final size:17
Alignment explanation
Indices: 57459894--57459929 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 17
57459884 AGAGAAGGAA
57459894 AGAAAGAAAAGAAAAAG
1 AGAAAGAAAAGAAAAAG
57459911 AGAAAGAAAGGAGAAAAAG
1 AGAAAGAAA--AGAAAAAG
57459930 CTAGGGTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
19 8 0.47
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (17 bp):
AGAAAGAAAAGAAAAAG
Found at i:57459929 original size:25 final size:26
Alignment explanation
Indices: 57459847--57459920 Score: 71
Period size: 28 Copynumber: 2.8 Consensus size: 26
57459837 AATAAATTGA
* * *
57459847 AAAAG-AAACAAAAAAAGAAACAAATTG
1 AAAAGAAAACAGAGAAAGAAAGAAA--G
* *
57459874 AAACGAAAACAGAGAAGGAAAGAAAG
1 AAAAGAAAACAGAGAAAGAAAGAAAG
57459900 AAAAGAAAA-AGAGAAAGAAAG
1 AAAAGAAAACAGAGAAAGAAAG
57459921 GAGAAAAAGC
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
25 11 0.28
26 9 0.23
27 4 0.10
28 15 0.38
ACGTcount: A:0.72, C:0.05, G:0.20, T:0.03
Consensus pattern (26 bp):
AAAAGAAAACAGAGAAAGAAAGAAAG
Found at i:57460641 original size:21 final size:20
Alignment explanation
Indices: 57460608--57460646 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
57460598 TGAGGAATTT
*
57460608 ATTGAATTTATATTGATTGA
1 ATTGAATATATATTGATTGA
57460628 ATTGATATATATATTGATT
1 ATTGA-ATATATATTGATT
57460647 ATTTGATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (20 bp):
ATTGAATATATATTGATTGA
Found at i:57465340 original size:17 final size:18
Alignment explanation
Indices: 57465320--57465355 Score: 56
Period size: 17 Copynumber: 2.0 Consensus size: 18
57465310 AAGGAAAGAA
57465320 AGAAAGAAA-AGAAAAAG
1 AGAAAGAAAGAGAAAAAG
57465337 AGAAAGAAATGAGAAAAAG
1 AGAAAGAAA-GAGAAAAAG
57465356 CTAGGGTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
19 8 0.47
ACGTcount: A:0.72, C:0.00, G:0.25, T:0.03
Consensus pattern (18 bp):
AGAAAGAAAGAGAAAAAG
Found at i:57470175 original size:29 final size:28
Alignment explanation
Indices: 57470136--57470205 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
57470126 ACTACAATTT
*
57470136 AAACTTATTTAATTT-TTTAATAATATAA
1 AAACTAATTTAATTTATTTAATAATA-AA
*
57470164 AAATTAAATTT-ATTTATTTAATAATAAA
1 AAACT-AATTTAATTTATTTAATAATAAA
*
57470192 TAACTAATTTAATT
1 AAACTAATTTAATT
57470206 CATTCCCAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
27 5 0.14
28 16 0.46
29 14 0.40
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (28 bp):
AAACTAATTTAATTTATTTAATAATAAA
Found at i:57475901 original size:25 final size:25
Alignment explanation
Indices: 57475867--57475917 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
57475857 TCGGTGGTTG
*
57475867 ATGTAATTTTTTGAATTTGAGTCTA
1 ATGTAATTTTCTGAATTTGAGTCTA
57475892 ATGTAATTTTCTGAATTTGAGTCTA
1 ATGTAATTTTCTGAATTTGAGTCTA
57475917 A
1 A
57475918 CGTCTAAGCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.06, G:0.16, T:0.49
Consensus pattern (25 bp):
ATGTAATTTTCTGAATTTGAGTCTA
Found at i:57476357 original size:58 final size:58
Alignment explanation
Indices: 57476293--57476481 Score: 161
Period size: 58 Copynumber: 3.2 Consensus size: 58
57476283 AAACATTTAA
* *
57476293 CAAGTACCAAATCGAACAAAAAAAG-TTAGGTACCAAATTAGGAAAAAAGTGTCAAACT
1 CAAGTACCAAATAGAACAAAAAAAGATTAGGTACCAAATTAAG-AAAAAGTGTCAAACT
* * * **
57476351 CAAGTACCAAATTGAACCCCCAAAAAAGATTAAGTACCAAATTAAGAAAAAGTGTCAAGTT
1 CAAGTACCAAATAGAA---CAAAAAAAGATTAGGTACCAAATTAAGAAAAAGTGTCAAACT
*** * * * *
57476412 TGGGTACCAAATTAGAA-AAAAAAAGGTTTAGGTACCAAATTAA-AAAAATTATCAAATT
1 CAAGTACCAAA-TAGAACAAAAAAA-GATTAGGTACCAAATTAAGAAAAAGTGTCAAACT
57476470 C-AGATACCAAAT
1 CAAG-TACCAAAT
57476482 GTTATATTAA
Statistics
Matches: 106, Mismatches: 18, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
57 2 0.02
58 40 0.38
59 16 0.15
61 29 0.27
62 19 0.18
ACGTcount: A:0.51, C:0.15, G:0.14, T:0.21
Consensus pattern (58 bp):
CAAGTACCAAATAGAACAAAAAAAGATTAGGTACCAAATTAAGAAAAAGTGTCAAACT
Found at i:57482648 original size:2 final size:2
Alignment explanation
Indices: 57482643--57482668 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
57482633 CACACACACG
57482643 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
57482669 CATAACAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:57486167 original size:34 final size:35
Alignment explanation
Indices: 57486100--57486169 Score: 97
Period size: 34 Copynumber: 2.0 Consensus size: 35
57486090 TTATTTTCTT
* *
57486100 AATAAATTTCGAAAGAAAAAAATCTTTTTTTAATA
1 AATAAATTTCAAAAGAAAAAAATCTTTTCTTAATA
* *
57486135 AATAAATTTTAAAAG-AAAATATCTTTTCTTAATA
1 AATAAATTTCAAAAGAAAAAAATCTTTTCTTAATA
57486169 A
1 A
57486170 TTTTGTTTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 18 0.58
35 13 0.42
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (35 bp):
AATAAATTTCAAAAGAAAAAAATCTTTTCTTAATA
Found at i:57492137 original size:14 final size:13
Alignment explanation
Indices: 57492120--57492155 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
57492110 GTTTAAGGTT
57492120 TTTAGGGTTTATAG
1 TTTAGGGTTTA-AG
57492134 TTTAGGGTTTAAG
1 TTTAGGGTTTAAG
*
57492147 GTTAGGGTT
1 TTTAGGGTT
57492156 AGGGTTAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.19, C:0.00, G:0.33, T:0.47
Consensus pattern (13 bp):
TTTAGGGTTTAAG
Found at i:57492163 original size:12 final size:13
Alignment explanation
Indices: 57492121--57492164 Score: 54
Period size: 12 Copynumber: 3.4 Consensus size: 13
57492111 TTTAAGGTTT
*
57492121 TTAGGGTTTATAGT
1 TTAGGGTTTA-AGG
57492135 TTAGGGTTTAAGG
1 TTAGGGTTTAAGG
*
57492148 TTAGGG-TTAGGG
1 TTAGGGTTTAAGG
57492160 TTAGG
1 TTAGG
57492165 ATTTTGTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 10 0.36
13 8 0.29
14 10 0.36
ACGTcount: A:0.20, C:0.00, G:0.39, T:0.41
Consensus pattern (13 bp):
TTAGGGTTTAAGG
Found at i:57492256 original size:35 final size:35
Alignment explanation
Indices: 57492218--57492328 Score: 127
Period size: 34 Copynumber: 3.2 Consensus size: 35
57492208 ATGGTTTTAA
57492218 GGTTTAAAGGTTTTTTTAA-AAAATTAATTAAATTAG
1 GGTTTAAAGG--TTTTTAAGAAAATTAATTAAATTAG
* ** * *
57492254 GTTTTATGGGTTTTAAATAAAATTAATTAAATTAG
1 GGTTTAAAGGTTTTTAAGAAAATTAATTAAATTAG
* *
57492289 GGTTTAGA-GTTTTTAAGAAAATTAATTAAATTAT
1 GGTTTAAAGGTTTTTAAGAAAATTAATTAAATTAG
57492323 GGTTTA
1 GGTTTA
57492329 GTTTTTAAAT
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
34 35 0.55
35 22 0.34
36 7 0.11
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (35 bp):
GGTTTAAAGGTTTTTAAGAAAATTAATTAAATTAG
Found at i:57492310 original size:34 final size:33
Alignment explanation
Indices: 57492230--57492342 Score: 140
Period size: 34 Copynumber: 3.4 Consensus size: 33
57492220 TTTAAAGGTT
* *
57492230 TTTTTAAAAAATTAATTAAATTAGGTTTTATGGG
1 TTTTTAAAAAATTAATTAAATTAGGGTTTA-GAG
*
57492264 TTTTAAATAAAATTAATTAAATTAGGGTTTAGAG
1 TTTTTAA-AAAATTAATTAAATTAGGGTTTAGAG
*
57492298 TTTTTAAGAAAATTAATTAAATTATGGTTT--AG
1 TTTTTAA-AAAATTAATTAAATTAGGGTTTAGAG
*
57492330 TTTTTAAATAATT
1 TTTTTAAAAAATT
57492343 TTGTGTTTAG
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
31 5 0.07
32 9 0.13
34 35 0.49
35 22 0.31
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (33 bp):
TTTTTAAAAAATTAATTAAATTAGGGTTTAGAG
Found at i:57494293 original size:56 final size:54
Alignment explanation
Indices: 57494202--57494391 Score: 227
Period size: 56 Copynumber: 3.6 Consensus size: 54
57494192 GGTGATGACA
*
57494202 TCCCATGTAAGACCATGTCTGGGACATGGAATTGGCATCATTGAGATTATGAGAAG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATC--TGAGATTATGAGAAG
*
57494258 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CTGAGATTA-GAG--G
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCTGAGATTATGAGAAG
* * *
57494308 TCCC-CGTAAGACCATGTCTGGGACATGGCATGGGCATC---GA-TATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCTGAGATTATGAGAAG
* * *
57494357 TCCCATGTAAGACCCTATCTGGGATATGGCATTGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGG
57494392 TAGTACAAGA
Statistics
Matches: 118, Mismatches: 11, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
46 2 0.02
47 5 0.04
49 33 0.28
50 31 0.26
52 3 0.03
53 8 0.07
55 1 0.01
56 35 0.30
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (54 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCTGAGATTATGAGAAG
Found at i:57494386 original size:50 final size:50
Alignment explanation
Indices: 57494202--57494428 Score: 192
Period size: 49 Copynumber: 4.5 Consensus size: 50
57494192 GGTGATGACA
* *
57494202 TCCCATGTAAGACCATGTCTGGGACATGGAATTGGCATCATTGAGATTATGAGAAG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-C--T--GA-TATGAGAAG
* * * * *
57494258 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGAGATTAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACTGATATGAGAAG
* *
57494308 TCCC-CGTAAGACCATGTCTGGGACATGGCATGGGCA-TCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACT-GATATGAGAAG
* * * * * * * * *
57494357 TCCCATGTAAGACCCTATCTGGGATATGGCATTGGTAGT-ACAAGA-AACA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACTGATATGAGAA-G
57494406 TCCCATGTAAGACCATGTCTGGG
1 TCCCATGTAAGACCATGTCTGGG
57494429 TTATTATCAG
Statistics
Matches: 144, Mismatches: 23, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
48 3 0.02
49 65 0.45
50 36 0.25
51 3 0.02
53 1 0.01
55 1 0.01
56 35 0.24
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACTGATATGAGAAG
Found at i:57494416 original size:99 final size:102
Alignment explanation
Indices: 57494199--57494428 Score: 252
Period size: 99 Copynumber: 2.3 Consensus size: 102
57494189 TTGGGTGATG
* *
57494199 ACATCCCATGTAAGACCATGTCTGGGACATGGAATTGGCATCATTGAGATTATGAGAAGTCCCAT
1 ACATCCCATGTAAGACCATGTCTGGGACATGGAATGGGCATC----AGATTATGAGAACTCCCAT
* * * ** *
57494264 GTAAGACCATGTCTGGGACATGGCGTTGGCACTGAGATTAG
62 GTAAGACCATATCTGGGACATGGCATTGGCACTGACAAGAA
** * *
57494305 AGGTCCC-CGTAAGACCATGTCTGGGACATGGCATGGGCATC-GA-TATGAGAACTCCCATGTAA
1 ACATCCCATGTAAGACCATGTCTGGGACATGGAATGGGCATCAGATTATGAGAACTCCCATGTAA
* * * *
57494367 GACCCTATCTGGGATATGGCATTGGTAGT-ACAAGAA
66 GACCATATCTGGGACATGGCATTGGCACTGACAAGAA
57494403 ACATCCCATGTAAGACCATGTCTGGG
1 ACATCCCATGTAAGACCATGTCTGGG
57494429 TTATTATCAG
Statistics
Matches: 104, Mismatches: 19, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
98 8 0.08
99 58 0.56
100 2 0.02
105 31 0.30
106 5 0.05
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (102 bp):
ACATCCCATGTAAGACCATGTCTGGGACATGGAATGGGCATCAGATTATGAGAACTCCCATGTAA
GACCATATCTGGGACATGGCATTGGCACTGACAAGAA
Found at i:57500915 original size:18 final size:17
Alignment explanation
Indices: 57500882--57500920 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
57500872 TTGTATAAAT
57500882 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
57500900 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
57500917 TGTG
1 TGTG
57500921 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:57501038 original size:8 final size:8
Alignment explanation
Indices: 57501025--57501053 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
57501015 CACTAGAGAC
57501025 CAGTGTTA
1 CAGTGTTA
57501033 CAGTGTTA
1 CAGTGTTA
57501041 CAGTGTTA
1 CAGTGTTA
57501049 CAGTG
1 CAGTG
57501054 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:57501167 original size:23 final size:23
Alignment explanation
Indices: 57501140--57501215 Score: 134
Period size: 23 Copynumber: 3.3 Consensus size: 23
57501130 AGTGTTATTG
57501140 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
57501163 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
57501186 ATCAGTGGTATCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
57501209 ATCAGTG
1 ATCAGTG
57501216 TGGCACTTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:57503234 original size:20 final size:17
Alignment explanation
Indices: 57503198--57503236 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 17
57503188 TAAATTTTTC
57503198 TTTAAAAAAACAAAAAT
1 TTTAAAAAAACAAAAAT
57503215 TTTAAAATAAACCTAAAAAT
1 TTTAAAA-AAA-C-AAAAAT
57503235 TT
1 TT
57503237 GAGATTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 3 0.16
19 1 0.05
20 8 0.42
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (17 bp):
TTTAAAAAAACAAAAAT
Found at i:57505150 original size:11 final size:11
Alignment explanation
Indices: 57505134--57505173 Score: 71
Period size: 11 Copynumber: 3.6 Consensus size: 11
57505124 TTCAAAAATT
57505134 CTCTTAAGTTC
1 CTCTTAAGTTC
57505145 CTCTTAAGTTC
1 CTCTTAAGTTC
*
57505156 CTCTTAAGTTT
1 CTCTTAAGTTC
57505167 CTCTTAA
1 CTCTTAA
57505174 CTCCCTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.20, C:0.25, G:0.07, T:0.47
Consensus pattern (11 bp):
CTCTTAAGTTC
Found at i:57507403 original size:123 final size:124
Alignment explanation
Indices: 57507178--57507552 Score: 576
Period size: 124 Copynumber: 3.0 Consensus size: 124
57507168 CCCAAACATG
57507178 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTCACAAATTCTTCTCAAATAGCATCCTG
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTT-ACAAATTCTTCTCAAATAGCATCCTG
*
57507243 CTAGAAGCGATTTTATACTATTTGCTCAGAAAAGTC-AAAAAAAATATTTCTTCCATGA-
65 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATATTTCTTCCATGAC
* *
57507301 CTGACTGTAGCAAAAGCGCATCCACGAGGGCGCGATTTTACAAATTCTTCTCAAACAGCATCCTG
1 CT-ACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCCTG
* *
57507366 TTAGAAGCGATTTTATACTATTTGCTTAGAAACGTCAAAAAAAAATATTTCTTCCATGAC
65 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATATTTCTTCCATGAC
* * *
57507426 CTACTATAGCAAAAGCGCGTCCACGAGGGCGCAATTTCACAAATT-TTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCCTGC
* *** * *
57507490 TAGAAGCGATTTTATACTATTTGATCAGAAACGTCGACTCAAAATTATTTCTTCCAAGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTC-AAAAAAAAATATTTCTTCCATGAC
57507550 CTA
1 CTA
57507553 AAAACCCTGA
Statistics
Matches: 230, Mismatches: 18, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
123 110 0.48
124 118 0.51
125 2 0.01
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATATTTCTTCCATGAC
Found at i:57516261 original size:31 final size:31
Alignment explanation
Indices: 57516202--57516261 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
57516192 GTTTGAACAA
* *
57516202 AAATATTATATCTGAATAATTAATTTAGGAC
1 AAATATTATATCTGAAAAATTAACTTAGGAC
*
57516233 AAATATTATATCTGAAAAATTAGCTTAGG
1 AAATATTATATCTGAAAAATTAACTTAGG
57516262 TAAAAAATGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.37
Consensus pattern (31 bp):
AAATATTATATCTGAAAAATTAACTTAGGAC
Found at i:57517716 original size:12 final size:12
Alignment explanation
Indices: 57517699--57517744 Score: 58
Period size: 12 Copynumber: 3.7 Consensus size: 12
57517689 AATATAATAG
57517699 TTAATTTTAGTT
1 TTAATTTTAGTT
57517711 TTAATTTTAAGTTT
1 TTAATTTT-AG-TT
57517725 TTAATTTTTAGTT
1 TTAA-TTTTAGTT
57517738 TT-ATTTT
1 TTAATTTT
57517745 TCACTTTCCC
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
11 4 0.13
12 9 0.29
13 6 0.19
14 8 0.26
15 4 0.13
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.70
Consensus pattern (12 bp):
TTAATTTTAGTT
Found at i:57517728 original size:14 final size:13
Alignment explanation
Indices: 57517699--57517739 Score: 57
Period size: 14 Copynumber: 3.1 Consensus size: 13
57517689 AATATAATAG
57517699 TTAATTTTAG-TT
1 TTAATTTTAGTTT
57517711 TTAATTTTAAGTTT
1 TTAATTTT-AGTTT
57517725 TTAATTTTTAGTTT
1 TTAA-TTTTAGTTT
57517739 T
1 T
57517740 ATTTTTCACT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 8 0.31
13 2 0.08
14 12 0.46
15 4 0.15
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.68
Consensus pattern (13 bp):
TTAATTTTAGTTT
Found at i:57521894 original size:29 final size:27
Alignment explanation
Indices: 57521836--57521919 Score: 62
Period size: 29 Copynumber: 2.9 Consensus size: 27
57521826 CGAATCTGCC
* *
57521836 CCATTTTTTTCGTTTTTAATTCAATCTAGT
1 CCATTTTTTT-GTTTTTTATT--ATTTAGT
57521866 CCATTTTTTTAGTTATTTTATTATTTAGT
1 CCATTTTTTT-GTT-TTTTATTATTTAGT
*
57521895 -TATTTTTGTTGTTGTTATTATTATT
1 CCATTTTT-TTGTT-TT-TTATTATT
57521920 ATATTGATAC
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
28 11 0.24
29 16 0.35
30 13 0.28
31 6 0.13
ACGTcount: A:0.19, C:0.08, G:0.08, T:0.64
Consensus pattern (27 bp):
CCATTTTTTTGTTTTTTATTATTTAGT
Found at i:57521943 original size:22 final size:21
Alignment explanation
Indices: 57521926--57521971 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
57521916 TATTATATTG
57521926 ATACACGCATTTTTTTATAAT
1 ATACACGCATTTTTTTATAAT
* *
57521947 ATATATGCATTTTTTATATAAT
1 ATACACGCATTTTTT-TATAAT
57521969 ATA
1 ATA
57521972 TATTTTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.37, C:0.09, G:0.04, T:0.50
Consensus pattern (21 bp):
ATACACGCATTTTTTTATAAT
Found at i:57521972 original size:22 final size:21
Alignment explanation
Indices: 57521932--57521974 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 21
57521922 ATTGATACAC
57521932 GCATTTTTTTATAATATATAT
1 GCATTTTTTTATAATATATAT
57521953 GCATTTTTTATATAATATATAT
1 GCATTTTTT-TATAATATATAT
57521975 TTTTTAACTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.56
Consensus pattern (21 bp):
GCATTTTTTTATAATATATAT
Found at i:57522093 original size:18 final size:19
Alignment explanation
Indices: 57522059--57522096 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
57522049 TATACTTTAT
*
57522059 ATTTTATATATACATATAC
1 ATTTTATATACACATATAC
57522078 ATTTTATA-ACACATATAC
1 ATTTTATATACACATATAC
57522096 A
1 A
57522097 CTTTCCACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (19 bp):
ATTTTATATACACATATAC
Done.