Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold123
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: 1422801
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 1358 characters in sequence are not A, C, G, or T
File 8 of 9
Found at i:1202157 original size:21 final size:21
Alignment explanation
Indices: 1202082--1202157 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
1202072 CTGCCAAGAA
* *
1202082 ATGTATCGATACAACTTTTTT
1 ATGTATCGATACATCTTTTTC
****
1202103 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1202123 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1202144 ATGTATCGATACAT
1 ATGTATCGATACAT
1202158 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1202842 original size:23 final size:23
Alignment explanation
Indices: 1202812--1202858 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1202802 ATCTCCCCCT
*
1202812 TAATCAAGTGATTCATATCAAAA
1 TAATCAAGTAATTCATATCAAAA
1202835 TAATCAAGTAATTCATATCAAAA
1 TAATCAAGTAATTCATATCAAAA
1202858 T
1 T
1202859 TTATTTGCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.32
Consensus pattern (23 bp):
TAATCAAGTAATTCATATCAAAA
Found at i:1204661 original size:13 final size:13
Alignment explanation
Indices: 1204643--1204681 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1204633 ATAATCACCC
*
1204643 TGTATCGATACAG
1 TGTATCGATACAA
1204656 TGTATCGATACAA
1 TGTATCGATACAA
1204669 TGTATCGATACAA
1 TGTATCGATACAA
1204682 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1204692 original size:20 final size:20
Alignment explanation
Indices: 1204667--1204745 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
1204657 GTATCGATAC
1204667 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
1204687 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
*
1204712 GATGTATCGATACACAA-AAA
1 AATGTATCGATACA-AAGAAA
*
1204732 CATGTATCGATACA
1 AATGTATCGATACA
1204746 TTTTGGACAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
20 32 0.65
25 16 0.33
26 1 0.02
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:1206779 original size:15 final size:15
Alignment explanation
Indices: 1206759--1206789 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1206749 ATTTCGTTTG
*
1206759 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1206774 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1206789 G
1 G
1206790 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1210833 original size:13 final size:13
Alignment explanation
Indices: 1210815--1210840 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1210805 CAATTTTTTG
1210815 TGTATCGATACAT
1 TGTATCGATACAT
1210828 TGTATCGATACAT
1 TGTATCGATACAT
1210841 ACTTACTGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1210925 original size:20 final size:20
Alignment explanation
Indices: 1210900--1210972 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1210890 CAACTTTTTT
1210900 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1210920 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1210941 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1210961 ATGTATCGATAC
1 ATGTATCGATAC
1210973 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1210938 original size:41 final size:41
Alignment explanation
Indices: 1210879--1210972 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
1210869 CTGCCAAGAA
*
1210879 ATGTATCGATACAACTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
*
1210920 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
1210961 ATGTATCGATAC
1 ATGTATCGATAC
1210973 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
Found at i:1210954 original size:21 final size:21
Alignment explanation
Indices: 1210879--1210954 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
1210869 CTGCCAAGAA
* *
1210879 ATGTATCGATACAACTTTTTT
1 ATGTATCGATACATCTTTTTC
****
1210900 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1210920 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1210941 ATGTATCGATACAT
1 ATGTATCGATACAT
1210955 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1211434 original size:42 final size:42
Alignment explanation
Indices: 1211268--1211508 Score: 151
Period size: 42 Copynumber: 5.7 Consensus size: 42
1211258 CTAACAAGAT
* ** * * ** * *
1211268 GATTGATAAAGAAGTCTCCCGGGTGTAAGCAGATGGGCAAAT
1 GATTGATGAAGAAGTCTCTTGGGTCTAAGCTGACAGGCAGAC
* * *** *
1211310 GATTGATGAAGAAGTCTCTTAGGTCTGAGCTGGTGGGCAGAT
1 GATTGATGAAGAAGTCTCTTGGGTCTAAGCTGACAGGCAGAC
* * * * *
1211352 GATGGATGAAAAAAGTCT-TTGCAGACTGAGCTGACAGGCAGAC
1 GATTGATG-AAGAAGTCTCTTG-GGTCTAAGCTGACAGGCAGAC
* * * *
1211395 GATAGAAGAAGAAGTCTCTTGGGTCTAAGTTGACGGGCAGAC
1 GATTGATGAAGAAGTCTCTTGGGTCTAAGCTGACAGGCAGAC
* * * ** * * * *
1211437 GATTGATCAATAAGTTTCCCGGGTCTGAGCCGACTGGTAGAC
1 GATTGATGAAGAAGTCTCTTGGGTCTAAGCTGACAGGCAGAC
*
1211479 GATTGATGAAGAAGTCTCTTAGGTCTAAGC
1 GATTGATGAAGAAGTCTCTTGGGTCTAAGC
1211509 AGATGGATAG
Statistics
Matches: 151, Mismatches: 45, Indels: 6
0.75 0.22 0.03
Matches are distributed among these distances:
42 119 0.79
43 32 0.21
ACGTcount: A:0.29, C:0.15, G:0.31, T:0.24
Consensus pattern (42 bp):
GATTGATGAAGAAGTCTCTTGGGTCTAAGCTGACAGGCAGAC
Found at i:1211520 original size:42 final size:41
Alignment explanation
Indices: 1211391--1211532 Score: 113
Period size: 42 Copynumber: 3.4 Consensus size: 41
1211381 GCTGACAGGC
* ** * *
1211391 AGACGATAGAAGAAGAAGTCTCTTGGGTCTAAGTTGACGGGC
1 AGACGATAGATGAAGAAGTCTCTTGGGTCTAAGCAGA-TGGT
* * * * ** * *
1211433 AGACGATTGATCAATAAGTTTCCCGGGTCTGAGCCGACTGGT
1 AGACGATAGATGAAGAAGTCTCTTGGGTCTAAGCAGA-TGGT
* *
1211475 AGACGATTGATGAAGAAGTCTCTTAGGTCTAAGCAGATGGAT
1 AGACGATAGATGAAGAAGTCTCTTGGGTCTAAGCAGATGG-T
*
1211517 AGACGAAAGATGAAGA
1 AGACGATAGATGAAGA
1211533 TTGGAATGAG
Statistics
Matches: 77, Mismatches: 22, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
41 3 0.04
42 74 0.96
ACGTcount: A:0.32, C:0.15, G:0.30, T:0.23
Consensus pattern (41 bp):
AGACGATAGATGAAGAAGTCTCTTGGGTCTAAGCAGATGGT
Found at i:1212159 original size:78 final size:78
Alignment explanation
Indices: 1212058--1212239 Score: 238
Period size: 78 Copynumber: 2.3 Consensus size: 78
1212048 CCATTTAGTG
* ** * * *
1212058 TTTGGGAAGGAGGGATACAATTGGGAATTTTTAGGAAATGTCCCCTTTGGACATGTGATGCACTA
1 TTTGGGAAGGAAGGATATGATTGGGAATGTGTAGGAAATGCCCCCTTTGGACATGTGATGCACTA
1212123 ATATCATCTGGTA
66 ATATCATCTGGTA
* * * * * *
1212136 TTTGGGAAGGAAGGATATGATTGGGAATGTGTGGGGAGTGCCCCCTTTGGCCTTGTGATTCACTA
1 TTTGGGAAGGAAGGATATGATTGGGAATGTGTAGGAAATGCCCCCTTTGGACATGTGATGCACTA
* *
1212201 GTATCATCTGGTG
66 ATATCATCTGGTA
1212214 TTTGGGAAGGAAGGATATGATTGGGA
1 TTTGGGAAGGAAGGATATGATTGGGA
1212240 GTGAGTGGTC
Statistics
Matches: 90, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
78 90 1.00
ACGTcount: A:0.25, C:0.12, G:0.32, T:0.31
Consensus pattern (78 bp):
TTTGGGAAGGAAGGATATGATTGGGAATGTGTAGGAAATGCCCCCTTTGGACATGTGATGCACTA
ATATCATCTGGTA
Found at i:1212655 original size:19 final size:20
Alignment explanation
Indices: 1212630--1212687 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 20
1212620 TTGAATCGAT
1212630 ACATTGTATCGATACATGA-
1 ACATTGTATCGATACATGAC
* *
1212649 TCATTGTGTCGATACAT-AC
1 ACATTGTATCGATACATGAC
*
1212668 ACAATTGTATCAATACATGA
1 AC-ATTGTATCGATACATGA
1212688 AACTGGCAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
18 1 0.03
19 16 0.52
20 13 0.42
21 1 0.03
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (20 bp):
ACATTGTATCGATACATGAC
Found at i:1215866 original size:30 final size:30
Alignment explanation
Indices: 1215827--1215933 Score: 103
Period size: 30 Copynumber: 3.6 Consensus size: 30
1215817 AGCTACTAGA
* * *
1215827 AGTTGCTGGATTGTTGGAGGCTATCGTGGG
1 AGTTACTGGACTGCTGGAGGCTATCGTGGG
* *
1215857 AGTTACTGGAGCTGCTGGA-GCTA-C-TAGA
1 AGTTACTGGA-CTGCTGGAGGCTATCGTGGG
* *
1215885 AGTTGCTAGACTGCTGGAGGCTATCGTGGG
1 AGTTACTGGACTGCTGGAGGCTATCGTGGG
*
1215915 AGCTACTGGAGCTGCTGGA
1 AGTTACTGGA-CTGCTGGA
1215934 AGTTTTCATG
Statistics
Matches: 60, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
27 8 0.13
28 14 0.23
29 2 0.03
30 22 0.37
31 14 0.23
ACGTcount: A:0.19, C:0.16, G:0.38, T:0.27
Consensus pattern (30 bp):
AGTTACTGGACTGCTGGAGGCTATCGTGGG
Found at i:1215873 original size:58 final size:58
Alignment explanation
Indices: 1215808--1215933 Score: 216
Period size: 58 Copynumber: 2.2 Consensus size: 58
1215798 TTGCCATGGA
* * * *
1215808 AGCTGCTGGAGCTACTAGAAGTTGCTGGATTGTTGGAGGCTATCGTGGGAGTTACTGG
1 AGCTGCTGGAGCTACTAGAAGTTGCTAGACTGCTGGAGGCTATCGTGGGAGCTACTGG
1215866 AGCTGCTGGAGCTACTAGAAGTTGCTAGACTGCTGGAGGCTATCGTGGGAGCTACTGG
1 AGCTGCTGGAGCTACTAGAAGTTGCTAGACTGCTGGAGGCTATCGTGGGAGCTACTGG
1215924 AGCTGCTGGA
1 AGCTGCTGGA
1215934 AGTTTTCATG
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 64 1.00
ACGTcount: A:0.20, C:0.17, G:0.37, T:0.26
Consensus pattern (58 bp):
AGCTGCTGGAGCTACTAGAAGTTGCTAGACTGCTGGAGGCTATCGTGGGAGCTACTGG
Found at i:1216220 original size:40 final size:40
Alignment explanation
Indices: 1216176--1216311 Score: 118
Period size: 40 Copynumber: 3.5 Consensus size: 40
1216166 CTATCGGTCA
1216176 CTACTGTTGGTGTTGGTTTGGGATGCTCGTCTGCTGGAAG
1 CTACTGTTGGTGTTGGTTTGGGATGCTCGTCTGCTGGAAG
*** *** *
1216216 CTACTGCCAGTGTTGGTTTCAAATGCTTGTCTGCTGGAAG
1 CTACTGTTGGTGTTGGTTTGGGATGCTCGTCTGCTGGAAG
* ** *
1216256 -T--TGTTGGTGTTGGTTTCGGG-TGCTCATGGGTTGGAAG
1 CTACTGTTGGTGTTGGTTT-GGGATGCTCGTCTGCTGGAAG
* *
1216293 CTGCTGTTCGTGTTGGTTT
1 CTACTGTTGGTGTTGGTTT
1216312 TTAGTTTTAG
Statistics
Matches: 73, Mismatches: 19, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
37 24 0.33
38 1 0.01
39 1 0.01
40 47 0.64
ACGTcount: A:0.10, C:0.15, G:0.35, T:0.40
Consensus pattern (40 bp):
CTACTGTTGGTGTTGGTTTGGGATGCTCGTCTGCTGGAAG
Found at i:1216812 original size:22 final size:22
Alignment explanation
Indices: 1216787--1216843 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
1216777 TTTTCTTTGG
1216787 ATTTTGATTTTTCATTGTTATT-
1 ATTTT-ATTTTTCATTGTTATTA
* *
1216809 ATTTTATTATTTGATTTTTATTA
1 ATTTTATT-TTTCATTGTTATTA
1216832 ATTTTTATTTTT
1 A-TTTTATTTTT
1216844 AAAAAATCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 3 0.10
22 16 0.53
23 4 0.13
24 7 0.23
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.72
Consensus pattern (22 bp):
ATTTTATTTTTCATTGTTATTA
Found at i:1217807 original size:43 final size:42
Alignment explanation
Indices: 1217760--1218246 Score: 130
Period size: 42 Copynumber: 11.6 Consensus size: 42
1217750 AAAGGTCCCC
1217760 GGGTCAAAGTCGATAGGTAGACTTAAGCGTTAAAAAGTCTCTA
1 GGGTCAAAGTCGATAGGTAGACTTAAG-GTTAAAAAGTCTCTA
** * * * *** *
1217803 GGGTCAAAACCGACAGGTAGACTCT-AGATGAGGCAGTCTCCA
1 GGGTCAAAGTCGATAGGTAGACT-TAAGGTTAAAAAGTCTCTA
* * * *
1217845 AGGTCAAAGTCGATAGGCAGAC-TAAGGATAGAAAAATCTCTA
1 GGGTCAAAGTCGATAGGTAGACTTAAGGTTA-AAAAGTCTCTA
* * * * * ** *
1217887 GGGTCAAAG-CAGACAAGAAGACTTTA-GATAAGGCAGTCTCGA
1 GGGTCAAAGTC-GATAGGTAGACTTAAGGTTAA-AAAGTCTCTA
* * * *
1217929 AGGTCAAAG-CTGATAGGTAGAC-TGAGGGTAGAAAAGTCTCCA
1 GGGTCAAAGTC-GATAGGTAGACTTAAGGTTA-AAAAGTCTCTA
** * ** * *
1217971 GCATTAAAGTCGATAGACAGACTTTA-G-AAAAAGTAGTCTCT-
1 GGGTCAAAGTCGATAGGTAGACTTAAGGTTAAAA--AGTCTCTA
* * * * * *
1218012 GAGGTCAAAG-CTGACAAGCAGAC-TAAGGGTAGGAAAGTCTCCA
1 G-GGTCAAAGTC-GATAGGTAGACTTAAGGTTA-AAAAGTCTCTA
** *
1218055 GGGTCAAAGTCGATAGACAGACTTTA-G--AAAAGGCAGTCTCTA
1 GGGTCAAAGTCGATAGGTAGACTTAAGGTTAAAA---AGTCTCTA
* * * *
1218097 GGGTCAAAGCCGATAGGCAGAC-TAAGGGTAGGAAAGTCTCTA
1 GGGTCAAAGTCGATAGGTAGACTTAAGGTTA-AAAAGTCTCTA
* * * * * *
1218139 AGGTCAAAGCCAATAGGCAGACTTTA-G--AAAAGGTAGTCTCCA
1 GGGTCAAAGTCGATAGGTAGACTTAAGGTTAAAA---AGTCTCTA
* * * * *
1218181 AGGTCAAAGTCGATAGGCAGA-TTGAGGGTAAAAAAGTCTCCA
1 GGGTCAAAGTCGATAGGTAGACTT-AAGGTTAAAAAGTCTCTA
* * *
1218223 GGGTCAAAGCCGACAGGCAGACTT
1 GGGTCAAAGTCGATAGGTAGACTT
1218247 TAGAAAAGAC
Statistics
Matches: 326, Mismatches: 82, Indels: 72
0.68 0.17 0.15
Matches are distributed among these distances:
39 4 0.01
40 6 0.02
41 16 0.05
42 252 0.77
43 38 0.12
44 4 0.01
45 6 0.02
ACGTcount: A:0.36, C:0.17, G:0.28, T:0.19
Consensus pattern (42 bp):
GGGTCAAAGTCGATAGGTAGACTTAAGGTTAAAAAGTCTCTA
Found at i:1217867 original size:42 final size:41
Alignment explanation
Indices: 1217837--1218497 Score: 230
Period size: 42 Copynumber: 15.8 Consensus size: 41
1217827 TAGATGAGGC
* * * *
1217837 AGTCTCCAAGGTCAAAGTCGATAGGCAGACTAAGGATAGAAA
1 AGTCTCCAAGGTCAAAGTCGATAGGCAGACTTAGAAAAG-GA
* * * * * * * *
1217879 AATCTCTAGGGTCAAAG-CAGACAAGAAGACTTTAGATAAGGC
1 AGTCTCCAAGGTCAAAGTC-GATAGGCAGAC-TTAGAAAAGGA
* * * *** *
1217921 AGTCTCGAAGGTCAAAG-CTGATAGGTAGACTGAGGGTAGAAA
1 AGTCTCCAAGGTCAAAGTC-GATAGGCAGACTTAGAAAAG-GA
* * * * *
1217963 AGTCTCC-AGCATTAAAGTCGATAGACAGACTTTAGAAAAAGT
1 AGTCTCCAAG-GTCAAAGTCGATAGGCAGAC-TTAGAAAAGGA
** * * * ***
1218005 AGTCTCTGAGGTCAAAG-CTGACAAGCAGACTAAGGGTAGGAA
1 AGTCTCCAAGGTCAAAGTC-GATAGGCAGACTTAGAAAAGG-A
* * *
1218047 AGTCTCCAGGGTCAAAGTCGATAGACAGACTTTAGAAAAGGC
1 AGTCTCCAAGGTCAAAGTCGATAGGCAGAC-TTAGAAAAGGA
* * * * ***
1218089 AGTCTCTAGGGTCAAAGCCGATAGGCAGACTAAGGGTAGGAA
1 AGTCTCCAAGGTCAAAGTCGATAGGCAGACTTAGAAAAGG-A
* * * *
1218131 AGTCTCTAAGGTCAAAGCCAATAGGCAGACTTTAGAAAAGGT
1 AGTCTCCAAGGTCAAAGTCGATAGGCAGAC-TTAGAAAAGGA
1218173 AGTCTCCAAGGTCAAAGTCGATAGGCAGA-TTGAGGGTAAAA--A
1 AGTCTCCAAGGTCAAAGTCGATAGGCAGACTT-A--G-AAAAGGA
* * *
1218215 AGTCTCCAGGGTCAAAGCCGACAGGCAGACTTTAGAAAA-GA
1 AGTCTCCAAGGTCAAAGTCGATAGGCAGAC-TTAGAAAAGGA
* * * * ** *** *
1218256 CAATCTCTAGGGTCAAAG-CTGACAACCAGA-TTGAGGGTAGAAA
1 -AGTCTCCAAGGTCAAAGTC-GATAGGCAGACTT-AGAAAAG-GA
* * * * * * *
1218299 AGTCTCTAGGGTCAAAGCCAACATGCAGACTTTAGAAAAAGCA
1 AGTCTCCAAGGTCAAAGTCGATAGGCAGAC-TTAG-AAAAGGA
* * *
1218342 A-TCTCCAAGGTCAAAGCCGACAAGCAGACTTTAGAAAA-GA
1 AGTCTCCAAGGTCAAAGTCGATAGGCAGAC-TTAGAAAAGGA
* * * * ***
1218382 CAGTCTCTAGGGTCAAAGTCGACAGGCAGACTGAGGGTAGGAA
1 -AGTCTCCAAGGTCAAAGTCGATAGGCAGACTTAGAAAAGG-A
* * * *
1218425 AGTCTCCAAGGTCAAAGCCGACAGACAGACTTTAGAAAAGGT
1 AGTCTCCAAGGTCAAAGTCGATAGGCAGAC-TTAGAAAAGGA
* * * * *
1218467 AGTCTCTAGGGTCAAAGCCGACAGCCAGACT
1 AGTCTCCAAGGTCAAAGTCGATAGGCAGACT
1218498 GAGGGCAAAC
Statistics
Matches: 462, Mismatches: 123, Indels: 69
0.71 0.19 0.11
Matches are distributed among these distances:
40 9 0.02
41 37 0.08
42 366 0.79
43 40 0.09
44 10 0.02
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.18
Consensus pattern (41 bp):
AGTCTCCAAGGTCAAAGTCGATAGGCAGACTTAGAAAAGGA
Found at i:1218364 original size:84 final size:84
Alignment explanation
Indices: 1217761--1218497 Score: 627
Period size: 84 Copynumber: 8.8 Consensus size: 84
1217751 AAGGTCCCCG
* * * * *
1217761 GGTCAAAGTCGATAGGTAGACTTAAGCGTTA-AAAAGTCTCTAGGGTCAAAACCGACAGGTAGAC
1 GGTCAAAGCCGATAGGCAGAC-TAAG-GGTAGAAAAGTCTCTAGGGTCAAAGCCGACAGGCAGAC
* **
1217825 TCTAGATGAGGCAGTCTCCAA
64 TTTAGAAAAGGCAGTCTCCAA
* * * * * *
1217846 GGTCAAAGTCGATAGGCAGACTAAGGATAGAAAAATCTCTAGGGTCAAAGCAGACAAGAAGACTT
1 GGTCAAAGCCGATAGGCAGACTAAGGGTAGAAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTT
* *
1217911 TAGATAAGGCAGTCTCGAA
66 TAGAAAAGGCAGTCTCCAA
* * * * ** * * * *
1217930 GGTCAAAGCTGATAGGTAGACTGAGGGTAGAAAAGTCTCCAGCATTAAAGTCGATAGACAGACTT
1 GGTCAAAGCCGATAGGCAGACTAAGGGTAGAAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTT
* * **
1217995 TAGAAAAAGTAGTCTCTGA
66 TAGAAAAGGCAGTCTCCAA
* * * * * * * *
1218014 GGTCAAAGCTGACAAGCAGACTAAGGGTAGGAAAGTCTCCAGGGTCAAAGTCGATAGACAGACTT
1 GGTCAAAGCCGATAGGCAGACTAAGGGTAGAAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTT
* *
1218079 TAGAAAAGGCAGTCTCTAG
66 TAGAAAAGGCAGTCTCCAA
* * * *
1218098 GGTCAAAGCCGATAGGCAGACTAAGGGTAGGAAAGTCTCTAAGGTCAAAGCCAATAGGCAGACTT
1 GGTCAAAGCCGATAGGCAGACTAAGGGTAGAAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTT
*
1218163 TAGAAAAGGTAGTCTCCAA
66 TAGAAAAGGCAGTCTCCAA
* * * * *
1218182 GGTCAAAGTCGATAGGCAGATTGAGGGTAAAAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTT
1 GGTCAAAGCCGATAGGCAGACTAAGGGTAGAAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTT
* * * *
1218247 TAGAAAAGACAATCTCTAG
66 TAGAAAAGGCAGTCTCCAA
* * ** * * * *
1218266 GGTCAAAGCTGACAACCAGATTGAGGGTAGAAAAGTCTCTAGGGTCAAAGCCAACATGCAGACTT
1 GGTCAAAGCCGATAGGCAGACTAAGGGTAGAAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTT
* *
1218331 TAGAAAAAGCAATCTCCAA
66 TAGAAAAGGCAGTCTCCAA
* * * *** * *
1218350 GGTCAAAGCCGACAAGCAGACTTTAGAAAAG-ACAGTCTCTAGGGTCAAAGTCGACAGGCAGAC-
1 GGTCAAAGCCGATAGGCAGAC-TAAGGGTAGAAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACT
* *** *
1218413 TGAGGGTAGGAAAGTCTCCAA
65 TTAGAAAAGG-CAGTCTCCAA
* * * *** ** *
1218434 GGTCAAAGCCGACAGACAGACTTTAGAAAAG-GTAGTCTCTAGGGTCAAAGCCGACAGCCAGACT
1 GGTCAAAGCCGATAGGCAGAC-TAAGGGTAGAAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACT
1218498 GAGGGCAAAC
Statistics
Matches: 543, Mismatches: 105, Indels: 8
0.83 0.16 0.01
Matches are distributed among these distances:
83 8 0.01
84 510 0.94
85 25 0.05
ACGTcount: A:0.37, C:0.18, G:0.27, T:0.18
Consensus pattern (84 bp):
GGTCAAAGCCGATAGGCAGACTAAGGGTAGAAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTT
TAGAAAAGGCAGTCTCCAA
Found at i:1218790 original size:22 final size:22
Alignment explanation
Indices: 1218741--1218790 Score: 52
Period size: 21 Copynumber: 2.3 Consensus size: 22
1218731 TGTTCATGAT
1218741 TTGATTTGATTCTTTCTATGCC
1 TTGATTTGATTCTTTCTATGCC
*
1218763 TT-ATTTG-TTCATTT-TCATGGC
1 TTGATTTGATTC-TTTCT-ATGCC
1218784 TTGATTT
1 TTGATTT
1218791 ACTTCACCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
20 4 0.17
21 14 0.58
22 6 0.25
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.58
Consensus pattern (22 bp):
TTGATTTGATTCTTTCTATGCC
Found at i:1220371 original size:13 final size:13
Alignment explanation
Indices: 1220353--1220378 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1220343 CAATTTTTTG
1220353 TGTATCGATACAT
1 TGTATCGATACAT
1220366 TGTATCGATACAT
1 TGTATCGATACAT
1220379 ACTTGCTGTA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1220463 original size:20 final size:20
Alignment explanation
Indices: 1220438--1220510 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1220428 CATCCTTTTT
1220438 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1220458 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACA-TTGCAAC
1220479 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1220499 ATGTATCGATAC
1 ATGTATCGATAC
1220511 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1220483 original size:21 final size:21
Alignment explanation
Indices: 1220417--1220493 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
1220407 CTGCCAAGAA
*
1220417 ATGTATCGATACATCCTTTTT-
1 ATGTATCGATACAT-TTTTTTC
****
1220438 ATGTATCGATACA-TTGCAAC
1 ATGTATCGATACATTTTTTTC
1220458 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACATTTTTTTC
1220479 ATGTATCGATACATT
1 ATGTATCGATACATT
1220494 GCAACATGTA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
19 1 0.02
20 13 0.29
21 31 0.69
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.43
Consensus pattern (21 bp):
ATGTATCGATACATTTTTTTC
Found at i:1220483 original size:41 final size:41
Alignment explanation
Indices: 1220417--1220510 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
1220407 CTGCCAAGAA
1220417 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
*
1220458 ATGTATCGATACAT-TTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTT-ATGTATCGATACATTGCAAC
1220499 ATGTATCGATAC
1 ATGTATCGATAC
1220511 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 5 0.10
41 46 0.90
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
Found at i:1225557 original size:34 final size:35
Alignment explanation
Indices: 1225519--1225585 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1225509 CCTTACAACA
1225519 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
1225553 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
1225586 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:1226061 original size:13 final size:13
Alignment explanation
Indices: 1226043--1226068 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1226033 CAATTTTTTG
1226043 TGTATCGATACAT
1 TGTATCGATACAT
1226056 TGTATCGATACAT
1 TGTATCGATACAT
1226069 ACTTGCTATA
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:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1226153 original size:20 final size:20
Alignment explanation
Indices: 1226128--1226200 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1226118 CATCCTTTTT
1226128 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1226148 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACA-TTGCAAC
1226169 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1226189 ATGTATCGATAC
1 ATGTATCGATAC
1226201 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1226173 original size:21 final size:21
Alignment explanation
Indices: 1226107--1226183 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
1226097 CTGCCAAGAA
*
1226107 ATGTATCGATACATCCTTTTT-
1 ATGTATCGATACAT-TTTTTTC
****
1226128 ATGTATCGATACA-TTGCAAC
1 ATGTATCGATACATTTTTTTC
1226148 ATGTATCGATACATTTTTTTC
1 ATGTATCGATACATTTTTTTC
1226169 ATGTATCGATACATT
1 ATGTATCGATACATT
1226184 GCAACATGTA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
19 1 0.02
20 13 0.29
21 31 0.69
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.43
Consensus pattern (21 bp):
ATGTATCGATACATTTTTTTC
Found at i:1226173 original size:41 final size:41
Alignment explanation
Indices: 1226107--1226200 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
1226097 CTGCCAAGAA
1226107 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
*
1226148 ATGTATCGATACAT-TTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCCTTTTT-ATGTATCGATACATTGCAAC
1226189 ATGTATCGATAC
1 ATGTATCGATAC
1226201 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 5 0.10
41 46 0.90
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
ATGTATCGATACATCCTTTTTATGTATCGATACATTGCAAC
Found at i:1235521 original size:20 final size:20
Alignment explanation
Indices: 1235496--1235663 Score: 120
Period size: 20 Copynumber: 7.7 Consensus size: 20
1235486 TTTTACCCAG
1235496 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
1235516 ATGTATCGATACATTCTGTCATTTTACCTA
1 ATGTATCGATACA-----T--TTTT--C-A
*
1235546 GATGTATCGACACATTTTTCA
1 -ATGTATCGATACATTTTTCA
* * *
1235567 ATGTATCGATACATGTGTGA
1 ATGTATCGATACATTTTTCA
* *
1235587 ATGTATCAATACATTCTTCA
1 ATGTATCGATACATTTTTCA
* **
1235607 ATGAATCGATACATTCTACCCA
1 ATGTATCGATACATT-T-TTCA
*
1235629 GATGTATCGATACATTGTTCA
1 -ATGTATCGATACATTTTTCA
1235650 ATGTATCGATACAT
1 ATGTATCGATACAT
1235664 CTAGTTAAAA
Statistics
Matches: 115, Mismatches: 19, Indels: 28
0.71 0.12 0.17
Matches are distributed among these distances:
20 71 0.62
21 3 0.03
22 3 0.03
23 14 0.12
24 4 0.03
25 1 0.01
26 1 0.01
27 4 0.03
29 1 0.01
30 1 0.01
31 12 0.10
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1243199 original size:40 final size:40
Alignment explanation
Indices: 1243155--1243245 Score: 119
Period size: 40 Copynumber: 2.3 Consensus size: 40
1243145 GCCACTGTTG
* *
1243155 CTGGTGTTGGTTTCGGATGCTCGTCTGCTGGAAGCTACTA
1 CTGGTGTTGGTTTCGGATGCTCGTCGGCTAGAAGCTACTA
* * * *
1243195 CTGGTGTTGGTTTCGGGTGCTCGTGGGCTAGAAGCTGCTG
1 CTGGTGTTGGTTTCGGATGCTCGTCGGCTAGAAGCTACTA
*
1243235 CTAGTGTTGGT
1 CTGGTGTTGGT
1243246 GTTTAGTTTC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.10, C:0.18, G:0.37, T:0.35
Consensus pattern (40 bp):
CTGGTGTTGGTTTCGGATGCTCGTCGGCTAGAAGCTACTA
Found at i:1243742 original size:22 final size:21
Alignment explanation
Indices: 1243717--1243771 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
1243707 TTTCTTTTGG
1243717 ATTTTGATTTTTCATTATTATT
1 ATTTT-ATTTTTCATTATTATT
* *
1243739 ATTTTATTATTTTATTTTTATT
1 ATTTTATT-TTTCATTATTATT
*
1243761 TTTTTATTTTT
1 ATTTTATTTTT
1243772 AAAAAAAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 6 0.21
22 23 0.79
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (21 bp):
ATTTTATTTTTCATTATTATT
Found at i:1243759 original size:19 final size:19
Alignment explanation
Indices: 1243731--1243770 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1243721 TGATTTTTCA
1243731 TTATTATTATTTTATTATT
1 TTATTATTATTTTATTATT
* *
1243750 TTATTTTTATTTTTTTATT
1 TTATTATTATTTTATTATT
1243769 TT
1 TT
1243771 TAAAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (19 bp):
TTATTATTATTTTATTATT
Found at i:1243771 original size:14 final size:14
Alignment explanation
Indices: 1243718--1243772 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
1243708 TTCTTTTGGA
*
1243718 TTTTGATTTTTCATT
1 TTTTTATTTTT-ATT
*
1243733 ATTATTA-TTTTATT
1 -TTTTTATTTTTATT
*
1243747 ATTTTATTTTTATT
1 TTTTTATTTTTATT
1243761 TTTTTATTTTTA
1 TTTTTATTTTTA
1243773 AAAAAAATCG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
13 4 0.12
14 21 0.64
15 4 0.12
16 4 0.12
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (14 bp):
TTTTTATTTTTATT
Found at i:1266705 original size:11 final size:11
Alignment explanation
Indices: 1266689--1266715 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1266679 CGTCAAGATT
1266689 AACATAAAAGA
1 AACATAAAAGA
1266700 AACATAAAAGA
1 AACATAAAAGA
1266711 AACAT
1 AACAT
1266716 GTTAATACGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.70, C:0.11, G:0.07, T:0.11
Consensus pattern (11 bp):
AACATAAAAGA
Found at i:1269216 original size:52 final size:52
Alignment explanation
Indices: 1269135--1269255 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
1269125 TGAAGAGTTA
*
1269135 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
1269187 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
1269239 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
1269256 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:1269268 original size:52 final size:51
Alignment explanation
Indices: 1269135--1269275 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
1269125 TGAAGAGTTA
1269135 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
1269187 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
1269239 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
1269276 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:1269282 original size:13 final size:13
Alignment explanation
Indices: 1269264--1269288 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1269254 CAAAGATCAG
1269264 TGTATCGATACAA
1 TGTATCGATACAA
1269277 TGTATCGATACA
1 TGTATCGATACA
1269289 TGTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1269372 original size:13 final size:13
Alignment explanation
Indices: 1269354--1269378 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1269344 CAAAAAAATA
1269354 TGTATCGATACAT
1 TGTATCGATACAT
1269367 TGTATCGATACA
1 TGTATCGATACA
1269379 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1269374 original size:33 final size:33
Alignment explanation
Indices: 1269332--1269398 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1269322 AGTAGCTTAA
1269332 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1269365 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1269398 A
1 A
1269399 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1270363 original size:171 final size:168
Alignment explanation
Indices: 1270168--1270552 Score: 611
Period size: 171 Copynumber: 2.3 Consensus size: 168
1270158 TTTTAGAGAT
1270168 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
1 GATGAA-GTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
1270233 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
65 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
* *
1270298 TGTCAACGTGCTGATTCAAGGCCAGC-TACATTGAACT-TAAA
130 TGTCAACGTGCTGATTCAAGGCCAGCTTA-A-AG-A-TGGAAA
* * *
1270339 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATGATGAGAAAA
1 GATGAAG-TGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
*
1270404 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGA
65 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
1270469 TGTCAACGTGCTGATTCAAGGCCAGCTTAAAGATGGAAA
130 TGTCAACGTGCTGATTCAAGGCCAGCTTAAAGATGGAAA
*
1270508 -AT---GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
1 GATGAAGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAG
1270553 GTGCCAATGT
Statistics
Matches: 203, Mismatches: 8, Indels: 13
0.91 0.04 0.06
Matches are distributed among these distances:
164 40 0.20
165 1 0.00
168 3 0.01
169 4 0.02
170 2 0.01
171 151 0.74
172 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.24
Consensus pattern (168 bp):
GATGAAGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAAG
TGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGAT
GTCAACGTGCTGATTCAAGGCCAGCTTAAAGATGGAAA
Found at i:1270385 original size:49 final size:49
Alignment explanation
Indices: 1270239--1270397 Score: 147
Period size: 49 Copynumber: 3.1 Consensus size: 49
1270229 AAAAGTGATA
* * * * *
1270239 AAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT--G
* ** * * *
1270290 AAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG
1 ---AA-GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
*
1270343 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
*
1270392 ATGATG
1 AAGATG
1270398 AGAAAAGTGA
Statistics
Matches: 85, Mismatches: 19, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
49 45 0.53
50 2 0.02
53 1 0.01
54 2 0.02
55 35 0.41
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.25
Consensus pattern (49 bp):
AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
Found at i:1270500 original size:45 final size:42
Alignment explanation
Indices: 1270448--1270580 Score: 126
Period size: 43 Copynumber: 3.1 Consensus size: 42
1270438 ACGATATTGG
* *
1270448 GCTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCA
1 GCTTAAAGATG-G-AAAAGG-TGCCAACATGCTGATTCAAGGCCA
* *
1270493 GCTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCA
1 GCTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCA
* * **
1270535 GC-TATA-TTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCA
1 GCTTAAAGATGGA---AAAGGTGCCAACATGCTGATTCAAGGCCA
1270578 GCT
1 GCT
1270581 ACATTGGACT
Statistics
Matches: 76, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
40 4 0.05
41 3 0.04
42 23 0.30
43 34 0.45
44 1 0.01
45 11 0.14
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (42 bp):
GCTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCA
Found at i:1270529 original size:42 final size:42
Alignment explanation
Indices: 1270477--1270672 Score: 148
Period size: 43 Copynumber: 4.5 Consensus size: 42
1270467 GATGTCAACG
*
1270477 TGCTGATTCAAGGCCAGCTTAAAGATGGA-AAATGTGCCAATA
1 TGCTGATTCAAGGCCAGCTTAAA-ATGGATAAAGGTGCCAATA
* * *
1270519 TGCTGATTCAAGGCCAGC-TATATTGGACTTAAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTTAAAATGGA--TAAAGGTGCCAATA
* *
1270562 TGCTGATTCAAGGCCAGC-TACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTTAAAATGGA--T-AA-A-G--G-TGCCAATA
* * * *
1270611 TGCTGATTCAAGGCCAGC-GATATTGGACTTAAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTTAAAATGGA--TAAAGGTGCCAATA
*
1270654 TGCTGAGTCAAGGCCAGCT
1 TGCTGATTCAAGGCCAGCT
1270673 ACATTGGACT
Statistics
Matches: 134, Mismatches: 10, Indels: 18
0.83 0.06 0.11
Matches are distributed among these distances:
40 4 0.03
41 3 0.02
42 18 0.13
43 64 0.48
44 3 0.02
45 1 0.01
46 2 0.01
47 1 0.01
48 3 0.02
49 35 0.26
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.25
Consensus pattern (42 bp):
TGCTGATTCAAGGCCAGCTTAAAATGGATAAAGGTGCCAATA
Found at i:1270609 original size:49 final size:49
Alignment explanation
Indices: 1270511--1271076 Score: 754
Period size: 49 Copynumber: 11.9 Consensus size: 49
1270501 ATGGAAAATG
*
1270511 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-G--G-
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
*
1270554 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* *
1270603 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-G--G-
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* *
1270646 TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* * * *
1270695 TGCCAATATGCTGATTCAAGTCCAGCGATATTGGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* *
1270744 TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* * *
1270793 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* * * *
1270842 TGCCAATGTGCTGAGTCAAGGCCAGCTACAGTGGACGTAAAGATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* *
1270891 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-G--G-
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* *
1270934 TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* * *
1270983 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* *
1271032 TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
1271077 GAAAAGGCCA
Statistics
Matches: 453, Mismatches: 52, Indels: 30
0.85 0.10 0.06
Matches are distributed among these distances:
43 104 0.23
44 8 0.02
45 3 0.01
46 5 0.01
47 2 0.00
48 7 0.02
49 324 0.72
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (49 bp):
TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
Found at i:1270771 original size:98 final size:92
Alignment explanation
Indices: 1270511--1271076 Score: 925
Period size: 98 Copynumber: 6.0 Consensus size: 92
1270501 ATGGAAAATG
* *
1270511 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGC
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGAGTCAAGGC
1270576 CAGCTACATTGGACTTAAAGATGAAGA
66 CAGCTACATTGGACTTAAAGATGAAGA
1270603 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGAGTCAAGGC
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGAGTCAAGGC
1270668 CAGCTACATTGGACTTAAAGATGAAGA
66 CAGCTACATTGGACTTAAAGATGAAGA
*
1270695 TGCCAATATGCTGATTCAAGTCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATGTGCTGAGT
1270760 CAAGGCCAGCTACATTGGACTTAAAGATGAAGA
60 CAAGGCCAGCTACATTGGACTTAAAGATGAAGA
1270793 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATGTGCTGAGT
* *
1270858 CAAGGCCAGCTACAGTGGACGTAAAGATGAAGA
60 CAAGGCCAGCTACATTGGACTTAAAGATGAAGA
1270891 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGAGTCAAGGC
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGAGTCAAGGC
1270956 CAGCTACATTGGACTTAAAGATGAAGA
66 CAGCTACATTGGACTTAAAGATGAAGA
1270983 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATGTGCTGAGT
1271048 CAAGGCCAGCTACATTGGACTTAAAGATG
60 CAAGGCCAGCTACATTGGACTTAAAGATG
1271077 GAAAAGGCCA
Statistics
Matches: 454, Mismatches: 8, Indels: 18
0.95 0.02 0.04
Matches are distributed among these distances:
92 216 0.48
94 1 0.00
96 2 0.00
98 235 0.52
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (92 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGAGTCAAGGC
CAGCTACATTGGACTTAAAGATGAAGA
Found at i:1270777 original size:190 final size:186
Alignment explanation
Indices: 1270511--1271076 Score: 947
Period size: 190 Copynumber: 3.0 Consensus size: 186
1270501 ATGGAAAATG
* *
1270511 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGC
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGAGTCAAGGC
1270576 CAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
66 CAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1270641 -A-AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
131 AAGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
*
1270695 TGCCAATATGCTGATTCAAGTCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATGTGCTGAGT
1270760 CAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATT
60 CAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATT
* *
1270825 GGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACAGTGGACGTAAAGATGAAG
125 GGACTT--A-A-GAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAG
1270890 A
186 A
1270891 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGAGTCAAGGC
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGAGTCAAGGC
1270956 CAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
66 CAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1271021 AAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG
131 --A-A-GAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG
1271077 GAAAAGGCCA
Statistics
Matches: 362, Mismatches: 8, Indels: 18
0.93 0.02 0.05
Matches are distributed among these distances:
184 36 0.10
188 1 0.00
190 235 0.65
192 1 0.00
194 1 0.00
196 88 0.24
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (186 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGAGTCAAGGC
CAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
AAGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
Found at i:1271145 original size:33 final size:34
Alignment explanation
Indices: 1271106--1271170 Score: 123
Period size: 33 Copynumber: 1.9 Consensus size: 34
1271096 GGCTTAGAGG
1271106 GGTTGCCACCGACTTGTGTGGGCTTT-GGAAGAA
1 GGTTGCCACCGACTTGTGTGGGCTTTAGGAAGAA
1271139 GGTTGCCACCGACTTGTGTGGGCTTTAGGAAG
1 GGTTGCCACCGACTTGTGTGGGCTTTAGGAAG
1271171 GGAGAAAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 26 0.84
34 5 0.16
ACGTcount: A:0.17, C:0.18, G:0.37, T:0.28
Consensus pattern (34 bp):
GGTTGCCACCGACTTGTGTGGGCTTTAGGAAGAA
Found at i:1271286 original size:32 final size:32
Alignment explanation
Indices: 1271155--1271310 Score: 177
Period size: 34 Copynumber: 4.6 Consensus size: 32
1271145 CACCGACTTG
*
1271155 TGTGGGCTTTAGGAAGGGAGAAAGATGCCACGGAGT
1 TGTGGGCTTTA--AA-GGA-AAAGGTGCCACGGAGT
* *
1271191 TGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAAA-GG-AAAAG-GTGCCACGGAGT
*
1271226 TGTGGGCTTTAAAAAGAAGAAGGTGCCACGGAGT
1 TGTGGGCTTT-AAAGGAA-AAGGTGCCACGGAGT
1271260 TGTGGGCTTTAAAGGAAAAGGTGCCACGGAGT
1 TGTGGGCTTTAAAGGAAAAGGTGCCACGGAGT
* *
1271292 TGTGGGCTTTGAAGAAAAA
1 TGTGGGCTTTAAAGGAAAA
1271311 ATGCCATTGA
Statistics
Matches: 107, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
32 32 0.30
33 6 0.06
34 33 0.31
35 24 0.22
36 12 0.11
ACGTcount: A:0.32, C:0.11, G:0.37, T:0.21
Consensus pattern (32 bp):
TGTGGGCTTTAAAGGAAAAGGTGCCACGGAGT
Found at i:1271342 original size:30 final size:30
Alignment explanation
Indices: 1271281--1271425 Score: 157
Period size: 31 Copynumber: 4.7 Consensus size: 30
1271271 AAGGAAAAGG
* * * *
1271281 TGCCACGGAGTTGTGGGCTTTGAAGAAAAAA
1 TGCCACTGAGTCGTGGACTTTG-AGACAAAA
* *
1271312 TGCCATTGAGTCGTGGACCTTGAGACAAAA
1 TGCCACTGAGTCGTGGACTTTGAGACAAAA
* *
1271342 TGCCACTGAGTCGTGGACTTTAAAGAAAAAGA
1 TGCCACTGAGTCGTGGACTTT-GAGACAAA-A
*
1271374 TGCCACTGAGTCGTGGACTTTGAG-CAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGACA-A-AA
1271405 TGCCACTGAGTCGTGGACTTT
1 TGCCACTGAGTCGTGGACTTT
1271426 TTTTTTTTTT
Statistics
Matches: 97, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
30 27 0.28
31 47 0.48
32 23 0.24
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (30 bp):
TGCCACTGAGTCGTGGACTTTGAGACAAAA
Found at i:1271372 original size:93 final size:93
Alignment explanation
Indices: 1271249--1271422 Score: 224
Period size: 93 Copynumber: 1.9 Consensus size: 93
1271239 AAGAAGAAGG
* * * * * *
1271249 TGCCACGGAGTTGTGGGCTTTAAAGGAAAAGGTGCCACGGAGTTGTGGGCTTTGAAG-AAAAAAT
1 TGCCACGGAGTCGTGGACTTTAAAGAAAAAGATGCCACGGAGTCGTGGACTTTG-AGCAAAAAAT
*
1271313 GCCATTGAGTCGTGGACCTTGAGACAAAA
65 GCCACTGAGTCGTGGACCTTGAGACAAAA
* * * * *
1271342 TGCCACTGAGTCGTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACTTTGAGCAGAGATTG
1 TGCCACGGAGTCGTGGACTTTAAAGAAAAAGATGCCACGGAGTCGTGGACTTTGAGCAAAAAATG
1271407 CCACTGAGTCGTGGAC
66 CCACTGAGTCGTGGAC
1271423 TTTTTTTTTT
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
92 2 0.03
93 66 0.97
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (93 bp):
TGCCACGGAGTCGTGGACTTTAAAGAAAAAGATGCCACGGAGTCGTGGACTTTGAGCAAAAAATG
CCACTGAGTCGTGGACCTTGAGACAAAA
Found at i:1271382 original size:32 final size:32
Alignment explanation
Indices: 1271175--1271425 Score: 197
Period size: 32 Copynumber: 7.8 Consensus size: 32
1271165 AGGAAGGGAG
* *
1271175 AAAGATGCCACGGAGTTGTGGACTTAAAAGGGAA
1 AAAGATGCCACGGAGTCGTGGACTTTAAA--GAA
* *
1271209 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGA-TGCCACGGAGTCGTGGACTTT--AAAGAA
* * * * *
1271244 GAAGGTGCCACGGAGTTGTGGGCTTTAAAGGA
1 AAAGATGCCACGGAGTCGTGGACTTTAAAGAA
* * * *
1271276 AAAGGTGCCACGGAGTTGTGGGCTTTGAAGAA
1 AAAGATGCCACGGAGTCGTGGACTTTAAAGAA
** * * *
1271308 AAA-ATGCCATTGAGTCGTGGACCTT-GAGAC
1 AAAGATGCCACGGAGTCGTGGACTTTAAAGAA
*
1271338 AAA-ATGCCACTGAGTCGTGGACTTTAAAGAA
1 AAAGATGCCACGGAGTCGTGGACTTTAAAGAA
* * *
1271369 AAAGATGCCACTGAGTCGTGGACTTT-GAG-C
1 AAAGATGCCACGGAGTCGTGGACTTTAAAGAA
* *
1271399 AGAGATTGCCACTGAGTCGTGGACTTT
1 AAAGA-TGCCACGGAGTCGTGGACTTT
1271426 TTTTTTTTTT
Statistics
Matches: 188, Mismatches: 23, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
30 30 0.16
31 45 0.24
32 59 0.31
34 26 0.14
35 25 0.13
37 3 0.02
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.22
Consensus pattern (32 bp):
AAAGATGCCACGGAGTCGTGGACTTTAAAGAA
Found at i:1272478 original size:15 final size:15
Alignment explanation
Indices: 1272458--1272491 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1272448 CTTACCGAGA
*
1272458 TTTTCTGTTTTGTTT
1 TTTTCTGTTTTCTTT
*
1272473 TTTTCTTTTTTCTTT
1 TTTTCTGTTTTCTTT
1272488 TTTT
1 TTTT
1272492 TGTGTTTGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.85
Consensus pattern (15 bp):
TTTTCTGTTTTCTTT
Found at i:1276406 original size:21 final size:21
Alignment explanation
Indices: 1276382--1276424 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1276372 ATCAAAATGA
1276382 CATTCATTGCATGACGAGATG
1 CATTCATTGCATGACGAGATG
1276403 CATTCATTGCATGACGAGATG
1 CATTCATTGCATGACGAGATG
1276424 C
1 C
1276425 TCCTGACATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (21 bp):
CATTCATTGCATGACGAGATG
Found at i:1277249 original size:11 final size:11
Alignment explanation
Indices: 1277233--1277259 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1277223 CGTCAAGATT
1277233 AACATAAAAGA
1 AACATAAAAGA
1277244 AACATAAAAGA
1 AACATAAAAGA
1277255 AACAT
1 AACAT
1277260 GTTAATACGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.70, C:0.11, G:0.07, T:0.11
Consensus pattern (11 bp):
AACATAAAAGA
Found at i:1279759 original size:52 final size:52
Alignment explanation
Indices: 1279678--1279798 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
1279668 TGAAGAGTTA
*
1279678 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
1279730 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
1279782 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
1279799 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:1279811 original size:52 final size:51
Alignment explanation
Indices: 1279678--1279818 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
1279668 TGAAGAGTTA
1279678 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
1279730 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
1279782 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
1279819 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:1279825 original size:13 final size:13
Alignment explanation
Indices: 1279807--1279831 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1279797 CAAAGATCAG
1279807 TGTATCGATACAA
1 TGTATCGATACAA
1279820 TGTATCGATACA
1 TGTATCGATACA
1279832 TGTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1279915 original size:13 final size:13
Alignment explanation
Indices: 1279897--1279921 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1279887 CAAAAAAATA
1279897 TGTATCGATACAT
1 TGTATCGATACAT
1279910 TGTATCGATACA
1 TGTATCGATACA
1279922 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1279917 original size:33 final size:33
Alignment explanation
Indices: 1279875--1279941 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1279865 AGTAGCTTAA
1279875 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1279908 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1279941 A
1 A
1279942 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1280906 original size:171 final size:168
Alignment explanation
Indices: 1280711--1281095 Score: 611
Period size: 171 Copynumber: 2.3 Consensus size: 168
1280701 TTTTAGAGAT
1280711 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
1 GATGAA-GTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
1280776 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
65 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
* *
1280841 TGTCAACGTGCTGATTCAAGGCCAGC-TACATTGAACT-TAAA
130 TGTCAACGTGCTGATTCAAGGCCAGCTTA-A-AG-A-TGGAAA
* * *
1280882 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATGATGAGAAAA
1 GATGAAG-TGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
*
1280947 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGA
65 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
1281012 TGTCAACGTGCTGATTCAAGGCCAGCTTAAAGATGGAAA
130 TGTCAACGTGCTGATTCAAGGCCAGCTTAAAGATGGAAA
*
1281051 -AT---GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
1 GATGAAGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAG
1281096 GTGCCAATGT
Statistics
Matches: 203, Mismatches: 8, Indels: 13
0.91 0.04 0.06
Matches are distributed among these distances:
164 40 0.20
165 1 0.00
168 3 0.01
169 4 0.02
170 2 0.01
171 151 0.74
172 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.24
Consensus pattern (168 bp):
GATGAAGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAAG
TGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGAT
GTCAACGTGCTGATTCAAGGCCAGCTTAAAGATGGAAA
Found at i:1280928 original size:49 final size:49
Alignment explanation
Indices: 1280782--1280940 Score: 147
Period size: 49 Copynumber: 3.1 Consensus size: 49
1280772 AAAAGTGATA
* * * * *
1280782 AAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT--G
* ** * * *
1280833 AAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG
1 ---AA-GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
*
1280886 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
*
1280935 ATGATG
1 AAGATG
1280941 AGAAAAGTGA
Statistics
Matches: 85, Mismatches: 19, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
49 45 0.53
50 2 0.02
53 1 0.01
54 2 0.02
55 35 0.41
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.25
Consensus pattern (49 bp):
AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
Found at i:1281043 original size:45 final size:42
Alignment explanation
Indices: 1280991--1281123 Score: 126
Period size: 43 Copynumber: 3.1 Consensus size: 42
1280981 ACGATATTGG
* *
1280991 GCTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCA
1 GCTTAAAGATG-G-AAAAGG-TGCCAACATGCTGATTCAAGGCCA
* *
1281036 GCTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCA
1 GCTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCA
* * **
1281078 GC-TATA-TTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCA
1 GCTTAAAGATGGA---AAAGGTGCCAACATGCTGATTCAAGGCCA
1281121 GCT
1 GCT
1281124 ACATTGGACT
Statistics
Matches: 76, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
40 4 0.05
41 3 0.04
42 23 0.30
43 34 0.45
44 1 0.01
45 11 0.14
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (42 bp):
GCTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCA
Found at i:1281072 original size:42 final size:42
Alignment explanation
Indices: 1281020--1281215 Score: 148
Period size: 43 Copynumber: 4.5 Consensus size: 42
1281010 GATGTCAACG
*
1281020 TGCTGATTCAAGGCCAGCTTAAAGATGGA-AAATGTGCCAATA
1 TGCTGATTCAAGGCCAGCTTAAA-ATGGATAAAGGTGCCAATA
* * *
1281062 TGCTGATTCAAGGCCAGC-TATATTGGACTTAAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTTAAAATGGA--TAAAGGTGCCAATA
* *
1281105 TGCTGATTCAAGGCCAGC-TACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTTAAAATGGA--T-AA-A-G--G-TGCCAATA
* * * *
1281154 TGCTGATTCAAGGCCAGC-GATATTGGACTTAAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTTAAAATGGA--TAAAGGTGCCAATA
*
1281197 TGCTGAGTCAAGGCCAGCT
1 TGCTGATTCAAGGCCAGCT
1281216 ACATTGGACT
Statistics
Matches: 134, Mismatches: 10, Indels: 18
0.83 0.06 0.11
Matches are distributed among these distances:
40 4 0.03
41 3 0.02
42 18 0.13
43 64 0.48
44 3 0.02
45 1 0.01
46 2 0.01
47 1 0.01
48 3 0.02
49 35 0.26
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.25
Consensus pattern (42 bp):
TGCTGATTCAAGGCCAGCTTAAAATGGATAAAGGTGCCAATA
Found at i:1281152 original size:49 final size:49
Alignment explanation
Indices: 1281054--1281619 Score: 754
Period size: 49 Copynumber: 11.9 Consensus size: 49
1281044 ATGGAAAATG
*
1281054 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-G--G-
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
*
1281097 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* *
1281146 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-G--G-
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* *
1281189 TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* * * *
1281238 TGCCAATATGCTGATTCAAGTCCAGCGATATTGGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* *
1281287 TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* * *
1281336 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* * * *
1281385 TGCCAATGTGCTGAGTCAAGGCCAGCTACAGTGGACGTAAAGATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* *
1281434 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-G--G-
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* *
1281477 TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* * *
1281526 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* *
1281575 TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
1281620 GAAAAGGCCA
Statistics
Matches: 453, Mismatches: 52, Indels: 30
0.85 0.10 0.06
Matches are distributed among these distances:
43 104 0.23
44 8 0.02
45 3 0.01
46 5 0.01
47 2 0.00
48 7 0.02
49 324 0.72
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (49 bp):
TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
Found at i:1281314 original size:98 final size:92
Alignment explanation
Indices: 1281054--1281619 Score: 925
Period size: 98 Copynumber: 6.0 Consensus size: 92
1281044 ATGGAAAATG
* *
1281054 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGC
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGAGTCAAGGC
1281119 CAGCTACATTGGACTTAAAGATGAAGA
66 CAGCTACATTGGACTTAAAGATGAAGA
1281146 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGAGTCAAGGC
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGAGTCAAGGC
1281211 CAGCTACATTGGACTTAAAGATGAAGA
66 CAGCTACATTGGACTTAAAGATGAAGA
*
1281238 TGCCAATATGCTGATTCAAGTCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATGTGCTGAGT
1281303 CAAGGCCAGCTACATTGGACTTAAAGATGAAGA
60 CAAGGCCAGCTACATTGGACTTAAAGATGAAGA
1281336 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATGTGCTGAGT
* *
1281401 CAAGGCCAGCTACAGTGGACGTAAAGATGAAGA
60 CAAGGCCAGCTACATTGGACTTAAAGATGAAGA
1281434 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGAGTCAAGGC
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGAGTCAAGGC
1281499 CAGCTACATTGGACTTAAAGATGAAGA
66 CAGCTACATTGGACTTAAAGATGAAGA
1281526 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATGTGCTGAGT
1281591 CAAGGCCAGCTACATTGGACTTAAAGATG
60 CAAGGCCAGCTACATTGGACTTAAAGATG
1281620 GAAAAGGCCA
Statistics
Matches: 454, Mismatches: 8, Indels: 18
0.95 0.02 0.04
Matches are distributed among these distances:
92 216 0.48
94 1 0.00
96 2 0.00
98 235 0.52
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (92 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGAGTCAAGGC
CAGCTACATTGGACTTAAAGATGAAGA
Found at i:1281320 original size:190 final size:186
Alignment explanation
Indices: 1281054--1281619 Score: 947
Period size: 190 Copynumber: 3.0 Consensus size: 186
1281044 ATGGAAAATG
* *
1281054 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGC
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGAGTCAAGGC
1281119 CAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
66 CAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1281184 -A-AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
131 AAGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
*
1281238 TGCCAATATGCTGATTCAAGTCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATGTGCTGAGT
1281303 CAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATT
60 CAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATT
* *
1281368 GGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACAGTGGACGTAAAGATGAAG
125 GGACTT--A-A-GAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAG
1281433 A
186 A
1281434 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGAGTCAAGGC
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGAGTCAAGGC
1281499 CAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
66 CAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1281564 AAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG
131 --A-A-GAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG
1281620 GAAAAGGCCA
Statistics
Matches: 362, Mismatches: 8, Indels: 18
0.93 0.02 0.05
Matches are distributed among these distances:
184 36 0.10
188 1 0.00
190 235 0.65
192 1 0.00
194 1 0.00
196 88 0.24
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (186 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGAGTCAAGGC
CAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
AAGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
Found at i:1281688 original size:33 final size:34
Alignment explanation
Indices: 1281649--1281713 Score: 123
Period size: 33 Copynumber: 1.9 Consensus size: 34
1281639 GGCTTAGAGG
1281649 GGTTGCCACCGACTTGTGTGGGCTTT-GGAAGAA
1 GGTTGCCACCGACTTGTGTGGGCTTTAGGAAGAA
1281682 GGTTGCCACCGACTTGTGTGGGCTTTAGGAAG
1 GGTTGCCACCGACTTGTGTGGGCTTTAGGAAG
1281714 GGAGAAAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 26 0.84
34 5 0.16
ACGTcount: A:0.17, C:0.18, G:0.37, T:0.28
Consensus pattern (34 bp):
GGTTGCCACCGACTTGTGTGGGCTTTAGGAAGAA
Found at i:1281829 original size:32 final size:32
Alignment explanation
Indices: 1281698--1281853 Score: 177
Period size: 34 Copynumber: 4.6 Consensus size: 32
1281688 CACCGACTTG
*
1281698 TGTGGGCTTTAGGAAGGGAGAAAGATGCCACGGAGT
1 TGTGGGCTTTA--AA-GGA-AAAGGTGCCACGGAGT
* *
1281734 TGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAAA-GG-AAAAG-GTGCCACGGAGT
*
1281769 TGTGGGCTTTAAAAAGAAGAAGGTGCCACGGAGT
1 TGTGGGCTTT-AAAGGAA-AAGGTGCCACGGAGT
1281803 TGTGGGCTTTAAAGGAAAAGGTGCCACGGAGT
1 TGTGGGCTTTAAAGGAAAAGGTGCCACGGAGT
* *
1281835 TGTGGGCTTTGAAGAAAAA
1 TGTGGGCTTTAAAGGAAAA
1281854 ATGCCATTGA
Statistics
Matches: 107, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
32 32 0.30
33 6 0.06
34 33 0.31
35 24 0.22
36 12 0.11
ACGTcount: A:0.32, C:0.11, G:0.37, T:0.21
Consensus pattern (32 bp):
TGTGGGCTTTAAAGGAAAAGGTGCCACGGAGT
Found at i:1281885 original size:30 final size:30
Alignment explanation
Indices: 1281824--1281968 Score: 157
Period size: 31 Copynumber: 4.7 Consensus size: 30
1281814 AAGGAAAAGG
* * * *
1281824 TGCCACGGAGTTGTGGGCTTTGAAGAAAAAA
1 TGCCACTGAGTCGTGGACTTTG-AGACAAAA
* *
1281855 TGCCATTGAGTCGTGGACCTTGAGACAAAA
1 TGCCACTGAGTCGTGGACTTTGAGACAAAA
* *
1281885 TGCCACTGAGTCGTGGACTTTAAAGAAAAAGA
1 TGCCACTGAGTCGTGGACTTT-GAGACAAA-A
*
1281917 TGCCACTGAGTCGTGGACTTTGAG-CAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGACA-A-AA
1281948 TGCCACTGAGTCGTGGACTTT
1 TGCCACTGAGTCGTGGACTTT
1281969 TTTTTTTTTT
Statistics
Matches: 97, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
30 27 0.28
31 47 0.48
32 23 0.24
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (30 bp):
TGCCACTGAGTCGTGGACTTTGAGACAAAA
Found at i:1281915 original size:93 final size:93
Alignment explanation
Indices: 1281792--1281965 Score: 224
Period size: 93 Copynumber: 1.9 Consensus size: 93
1281782 AAGAAGAAGG
* * * * * *
1281792 TGCCACGGAGTTGTGGGCTTTAAAGGAAAAGGTGCCACGGAGTTGTGGGCTTTGAAG-AAAAAAT
1 TGCCACGGAGTCGTGGACTTTAAAGAAAAAGATGCCACGGAGTCGTGGACTTTG-AGCAAAAAAT
*
1281856 GCCATTGAGTCGTGGACCTTGAGACAAAA
65 GCCACTGAGTCGTGGACCTTGAGACAAAA
* * * * *
1281885 TGCCACTGAGTCGTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACTTTGAGCAGAGATTG
1 TGCCACGGAGTCGTGGACTTTAAAGAAAAAGATGCCACGGAGTCGTGGACTTTGAGCAAAAAATG
1281950 CCACTGAGTCGTGGAC
66 CCACTGAGTCGTGGAC
1281966 TTTTTTTTTT
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
92 2 0.03
93 66 0.97
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (93 bp):
TGCCACGGAGTCGTGGACTTTAAAGAAAAAGATGCCACGGAGTCGTGGACTTTGAGCAAAAAATG
CCACTGAGTCGTGGACCTTGAGACAAAA
Found at i:1281925 original size:32 final size:32
Alignment explanation
Indices: 1281718--1281968 Score: 197
Period size: 32 Copynumber: 7.8 Consensus size: 32
1281708 AGGAAGGGAG
* *
1281718 AAAGATGCCACGGAGTTGTGGACTTAAAAGGGAA
1 AAAGATGCCACGGAGTCGTGGACTTTAAA--GAA
* *
1281752 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGA-TGCCACGGAGTCGTGGACTTT--AAAGAA
* * * * *
1281787 GAAGGTGCCACGGAGTTGTGGGCTTTAAAGGA
1 AAAGATGCCACGGAGTCGTGGACTTTAAAGAA
* * * *
1281819 AAAGGTGCCACGGAGTTGTGGGCTTTGAAGAA
1 AAAGATGCCACGGAGTCGTGGACTTTAAAGAA
** * * *
1281851 AAA-ATGCCATTGAGTCGTGGACCTT-GAGAC
1 AAAGATGCCACGGAGTCGTGGACTTTAAAGAA
*
1281881 AAA-ATGCCACTGAGTCGTGGACTTTAAAGAA
1 AAAGATGCCACGGAGTCGTGGACTTTAAAGAA
* * *
1281912 AAAGATGCCACTGAGTCGTGGACTTT-GAG-C
1 AAAGATGCCACGGAGTCGTGGACTTTAAAGAA
* *
1281942 AGAGATTGCCACTGAGTCGTGGACTTT
1 AAAGA-TGCCACGGAGTCGTGGACTTT
1281969 TTTTTTTTTT
Statistics
Matches: 188, Mismatches: 23, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
30 30 0.16
31 45 0.24
32 59 0.31
34 26 0.14
35 25 0.13
37 3 0.02
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.22
Consensus pattern (32 bp):
AAAGATGCCACGGAGTCGTGGACTTTAAAGAA
Found at i:1283018 original size:15 final size:15
Alignment explanation
Indices: 1282998--1283031 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1282988 CTCACCGAGA
*
1282998 TTTTCTGTTTTGTTT
1 TTTTCTGTTTTCTTT
*
1283013 TTTTCTTTTTTCTTT
1 TTTTCTGTTTTCTTT
1283028 TTTT
1 TTTT
1283032 TGTGTTTGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.85
Consensus pattern (15 bp):
TTTTCTGTTTTCTTT
Found at i:1286946 original size:21 final size:21
Alignment explanation
Indices: 1286922--1286964 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1286912 ATCAAAATGA
1286922 CATTCATTGCATGACGAGATG
1 CATTCATTGCATGACGAGATG
1286943 CATTCATTGCATGACGAGATG
1 CATTCATTGCATGACGAGATG
1286964 C
1 C
1286965 TCCTGACATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (21 bp):
CATTCATTGCATGACGAGATG
Found at i:1287789 original size:11 final size:11
Alignment explanation
Indices: 1287773--1287799 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1287763 CGTCAAGATT
1287773 AACATAAAAGA
1 AACATAAAAGA
1287784 AACATAAAAGA
1 AACATAAAAGA
1287795 AACAT
1 AACAT
1287800 GTTAATACGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.70, C:0.11, G:0.07, T:0.11
Consensus pattern (11 bp):
AACATAAAAGA
Found at i:1290299 original size:52 final size:52
Alignment explanation
Indices: 1290218--1290338 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
1290208 TGAAGAGTTA
*
1290218 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
1290270 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
1290322 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
1290339 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:1290351 original size:52 final size:51
Alignment explanation
Indices: 1290218--1290358 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
1290208 TGAAGAGTTA
1290218 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
1290270 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
1290322 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
1290359 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:1290365 original size:13 final size:13
Alignment explanation
Indices: 1290347--1290371 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1290337 CAAAGATCAG
1290347 TGTATCGATACAA
1 TGTATCGATACAA
1290360 TGTATCGATACA
1 TGTATCGATACA
1290372 TGTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1290455 original size:13 final size:13
Alignment explanation
Indices: 1290437--1290461 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1290427 CAAAAAAATA
1290437 TGTATCGATACAT
1 TGTATCGATACAT
1290450 TGTATCGATACA
1 TGTATCGATACA
1290462 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1290457 original size:33 final size:33
Alignment explanation
Indices: 1290415--1290481 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1290405 AGTAGCTTAA
1290415 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1290448 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1290481 A
1 A
1290482 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1291030 original size:31 final size:30
Alignment explanation
Indices: 1290903--1291063 Score: 90
Period size: 31 Copynumber: 5.2 Consensus size: 30
1290893 CATTCCTTTT
*
1290903 GCAGCACCCTAGTCAGAGCCCGCACGAGCTG
1 GCAGCA-CCTAGTCAAAGCCCGCACGAGCTG
* * * * * *
1290934 ACGGCACCTAAGTCTAAGCACACACGAGTTG
1 GCAGCACCT-AGTCAAAGCCCGCACGAGCTG
** * * *
1290965 GTGGTACCCTAGTCAAAGCCTGCAC-ATGCGG
1 GCAGCA-CCTAGTCAAAGCCCGCACGA-GCTG
* *
1290996 GCAGCACCTGAGTCTAAGCCCGCACGAGTTG
1 GCAGCACCT-AGTCAAAGCCCGCACGAGCTG
* * * *
1291027 GCAGCACTTGAGTCAAAGCTCACACAAGCTG
1 GCAGCACCT-AGTCAAAGCCCGCACGAGCTG
*
1291058 GTAGCA
1 GCAGCA
1291064 AGTAAGTTCG
Statistics
Matches: 95, Mismatches: 30, Indels: 10
0.70 0.22 0.07
Matches are distributed among these distances:
30 7 0.07
31 84 0.88
32 4 0.04
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.16
Consensus pattern (30 bp):
GCAGCACCTAGTCAAAGCCCGCACGAGCTG
Found at i:1291197 original size:86 final size:86
Alignment explanation
Indices: 1291041--1291210 Score: 218
Period size: 86 Copynumber: 2.0 Consensus size: 86
1291031 CACTTGAGTC
* * * * *
1291041 AAAGCTCACACAAGCTGGTAGCAAGTAAGTTCGAGTCAGGTCCACATTAGTTGGCACCTATCTGA
1 AAAGCCCACACAAGCTGGTAGCAACTAAGTCCGAGTCAAGTCCACATTAGTTGGCA-CTATCTAA
1291106 GGAGGTCAAACCTTAAAATGTT
65 GGAGGTCAAACCTTAAAATGTT
* *
1291128 AAAGCCCACA-AAGCTGGTGGCACCTAAGTCCGAGTCAAGTCCACATTAGTTGGCA-TATGGCTA
1 AAAGCCCACACAAGCTGGTAGCAACTAAGTCCGAGTCAAGTCCACATTAGTTGGCACTAT--CTA
* *
1291191 AGGAGGTTAAGCCTTAAAAT
64 AGGAGGTCAAACCTTAAAAT
1291211 ACCAAAACCC
Statistics
Matches: 72, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
84 3 0.04
86 60 0.83
87 9 0.12
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.23
Consensus pattern (86 bp):
AAAGCCCACACAAGCTGGTAGCAACTAAGTCCGAGTCAAGTCCACATTAGTTGGCACTATCTAAG
GAGGTCAAACCTTAAAATGTT
Found at i:1291739 original size:13 final size:13
Alignment explanation
Indices: 1291721--1291746 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1291711 CGAACAGTAC
1291721 ATGTATCGATACA
1 ATGTATCGATACA
1291734 ATGTATCGATACA
1 ATGTATCGATACA
1291747 TGCCTAAAAT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1292912 original size:19 final size:19
Alignment explanation
Indices: 1292867--1292922 Score: 94
Period size: 20 Copynumber: 2.9 Consensus size: 19
1292857 ACTGCCAATC
*
1292867 TCATGTATCGATACAATTG
1 TCATGTATCGATACAATTA
1292886 TCCATGTATCGATACAATTA
1 T-CATGTATCGATACAATTA
1292906 TCATGTATCGATACAAT
1 TCATGTATCGATACAAT
1292923 GTATTGATAC
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
19 17 0.49
20 18 0.51
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.36
Consensus pattern (19 bp):
TCATGTATCGATACAATTA
Found at i:1293429 original size:12 final size:12
Alignment explanation
Indices: 1293412--1293451 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
1293402 GAGGATCCCC
*
1293412 TTTTCAATCACA
1 TTTTCAACCACA
1293424 TTTTCAACCACA
1 TTTTCAACCACA
* *
1293436 TTATCAGCCACA
1 TTTTCAACCACA
1293448 TTTT
1 TTTT
1293452 AGCCAAACAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.30, C:0.28, G:0.03, T:0.40
Consensus pattern (12 bp):
TTTTCAACCACA
Found at i:1293936 original size:19 final size:19
Alignment explanation
Indices: 1293912--1293949 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1293902 TTTATGCATT
1293912 TTTTGCTATGTTTC-AAGCA
1 TTTTGC-ATGTTTCTAAGCA
*
1293931 TTTTGCATTTTTCTAAGCA
1 TTTTGCATGTTTCTAAGCA
1293950 CAACTTGCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.21, C:0.16, G:0.13, T:0.50
Consensus pattern (19 bp):
TTTTGCATGTTTCTAAGCA
Found at i:1305283 original size:52 final size:52
Alignment explanation
Indices: 1305198--1305322 Score: 216
Period size: 52 Copynumber: 2.4 Consensus size: 52
1305188 ATATGAAAAG
* *
1305198 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
1305250 TTGCCTGCATGTATCGATACATTATAA-AATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATT-TAATAATGTATCGATACATCTGGGCAAAT
1305302 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
1305323 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
52 67 0.96
53 3 0.04
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:1305335 original size:52 final size:50
Alignment explanation
Indices: 1305198--1305342 Score: 193
Period size: 52 Copynumber: 2.8 Consensus size: 50
1305188 ATATGAAAAG
* *
1305198 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA--AAATAGTGTATCGATACATCTGGGCAAAT
*
1305250 TTGCCTGCATGTATCGATACATTATAA-AATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA--A-AATAGTGTATCGATACATCTGGGCAAAT
1305302 TTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACAAA-AT-AGTGTATCGATACA
1305343 ATGTATCAAT
Statistics
Matches: 85, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
49 1 0.01
50 2 0.02
52 80 0.94
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (50 bp):
TTGCCTGCATGTATCGATACAAAATAGTGTATCGATACATCTGGGCAAAT
Found at i:1305427 original size:20 final size:19
Alignment explanation
Indices: 1305398--1305466 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 19
1305388 GCAGTAGCTT
1305398 AAATTGTATCGATACAAAA
1 AAATTGTATCGATACAAAA
1305417 AAATATGTATCGATAC----
1 AAAT-TGTATCGATACAAAA
1305433 --ATTGTATCGATACAAAA
1 AAATTGTATCGATACAAAA
1305450 AAATATGTATCGATACA
1 AAAT-TGTATCGATACA
1305467 TTGTATCGAT
Statistics
Matches: 42, Mismatches: 0, Indels: 15
0.74 0.00 0.26
Matches are distributed among these distances:
13 11 0.26
14 2 0.05
19 6 0.14
20 23 0.55
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.29
Consensus pattern (19 bp):
AAATTGTATCGATACAAAA
Found at i:1305440 original size:13 final size:13
Alignment explanation
Indices: 1305422--1305479 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 13
1305412 CAAAAAAATA
1305422 TGTATCGATACAT
1 TGTATCGATACAT
1305435 TGTATCGATACAAAAAAAT
1 TGTATCGATAC------AT
1305454 ATGTATCGATACAT
1 -TGTATCGATACAT
1305468 TGTATCGATACA
1 TGTATCGATACA
1305480 ACATTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 23 0.61
14 2 0.05
19 2 0.05
20 11 0.29
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1305442 original size:33 final size:33
Alignment explanation
Indices: 1305400--1305499 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
1305390 AGTAGCTTAA
1305400 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1305433 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1305466 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1305499 A
1 A
1305500 AATCGTTGAA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 63 1.00
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1306547 original size:171 final size:171
Alignment explanation
Indices: 1306258--1306822 Score: 1022
Period size: 171 Copynumber: 3.3 Consensus size: 171
1306248 TTTTAGAGAT
* * * * *
1306258 GATGAAGGTGCCAATATGCTGATTCAAGACCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
1 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATGATGAGAAAA
* *
1306323 GTGATAAAGATGTCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
66 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGA
1306388 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
131 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
1306429 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATGATGAGAAAA
1 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATGATGAGAAAA
1306494 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGA
66 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGA
1306559 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
131 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
1306600 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATGATGAGAAAA
1 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATGATGAGAAAA
1306665 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGA
66 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGA
1306730 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
131 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
* *
1306771 GATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
1 GAT-GAAGA--TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
1306823 GGTGCCAATG
Statistics
Matches: 382, Mismatches: 9, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
171 338 0.88
172 4 0.01
174 40 0.10
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.25
Consensus pattern (171 bp):
GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATGATGAGAAAA
GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGA
TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
Found at i:1306646 original size:49 final size:49
Alignment explanation
Indices: 1306500--1306658 Score: 156
Period size: 49 Copynumber: 3.1 Consensus size: 49
1306490 AAAAGTGATA
* * * *
1306500 AAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT--G
* ** * * *
1306551 AAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG
1 ---AA-GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
*
1306604 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
*
1306653 ATGATG
1 AAGATG
1306659 AGAAAAGTGA
Statistics
Matches: 86, Mismatches: 18, Indels: 7
0.77 0.16 0.06
Matches are distributed among these distances:
49 45 0.52
50 2 0.02
53 1 0.01
54 2 0.02
55 36 0.42
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (49 bp):
AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
Found at i:1306880 original size:49 final size:49
Alignment explanation
Indices: 1306738--1307206 Score: 575
Period size: 49 Copynumber: 9.6 Consensus size: 49
1306728 GATGTCAACG
* *
1306738 TGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-GAAGA--TGCCAATA
* *
1306790 TGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-G--G-TGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1306833 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* * *
1306882 TGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-G--G-TGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
*
1306925 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* * * *
1306974 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* * *
1307023 TGCTGAGTCAAGGCCAGCTACATTAGACTTAAAGATGGAAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGATGCCAATA
* * *
1307075 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
* *
1307124 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGATGCCAATA
* *
1307176 TGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTA
1307207 GAGGGGTTGC
Statistics
Matches: 366, Mismatches: 33, Indels: 36
0.84 0.08 0.08
Matches are distributed among these distances:
43 70 0.19
44 5 0.01
45 2 0.01
46 3 0.01
47 1 0.00
48 5 0.01
49 163 0.45
50 3 0.01
51 3 0.01
52 111 0.30
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (49 bp):
TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
Found at i:1307115 original size:101 final size:101
Alignment explanation
Indices: 1306670--1307206 Score: 734
Period size: 101 Copynumber: 5.4 Consensus size: 101
1306660 GAAAAGTGAT
* * * * *
1306670 AAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCA
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT--G---AAGG-TGCCA
* * *
1306735 ACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
60 ATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
*
1306777 AAATG-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGCCAATGTG
1 AAA-GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTG
*
1306835 CTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G-
65 CTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
1306870 -AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATGTGC
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGC
1306928 TGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G-
66 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
1306962 -AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGC
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGC
*
1307026 TGAGTCAAGGCCAGCTACATTAGACTTAAAGATGGA
66 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
* *
1307062 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGC
1307127 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
66 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
* * *
1307163 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 AAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA
1307207 GAGGGGTTGC
Statistics
Matches: 404, Mismatches: 15, Indels: 28
0.90 0.03 0.06
Matches are distributed among these distances:
91 1 0.00
92 130 0.32
94 1 0.00
95 41 0.10
96 5 0.01
98 47 0.12
99 1 0.00
101 140 0.35
103 1 0.00
107 36 0.09
108 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (101 bp):
AAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGC
TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGA
Found at i:1307307 original size:32 final size:33
Alignment explanation
Indices: 1307211--1307303 Score: 154
Period size: 33 Copynumber: 2.8 Consensus size: 33
1307201 GGCTTAGAGG
1307211 GGTTGCCACCGACTTGTGTGGGCTTTGGAAGAA
1 GGTTGCCACCGACTTGTGTGGGCTTTGGAAGAA
*
1307244 GGTTGCCACCAACTTGTGTGGGCTTTAGGAAG-A
1 GGTTGCCACCGACTTGTGTGGGCTTT-GGAAGAA
1307277 -GTTGCCACCGACTTGTGTGGGCTTTGG
1 GGTTGCCACCGACTTGTGTGGGCTTTGG
1307304 GAAGGAAAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
31 2 0.04
32 24 0.42
33 26 0.46
34 5 0.09
ACGTcount: A:0.16, C:0.19, G:0.35, T:0.29
Consensus pattern (33 bp):
GGTTGCCACCGACTTGTGTGGGCTTTGGAAGAA
Found at i:1307381 original size:34 final size:35
Alignment explanation
Indices: 1307377--1307498 Score: 176
Period size: 37 Copynumber: 3.4 Consensus size: 35
1307367 GGCTTTAAAA
1307377 GAAAAA-AGTGCCACGGAGTTGTGGGCTTTGAAAAGG
1 GAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAA-G
*
1307413 GAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACG
1 GAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
1307448 GAAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGG
1 GAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAA-G
*
1307484 GAAAGAGAGTGCCAC
1 GAAAAAGAGTGCCAC
1307499 AAAGTCGTCG
Statistics
Matches: 79, Mismatches: 3, Indels: 7
0.89 0.03 0.08
Matches are distributed among these distances:
34 22 0.28
35 11 0.14
36 16 0.20
37 30 0.38
ACGTcount: A:0.34, C:0.13, G:0.35, T:0.18
Consensus pattern (35 bp):
GAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
Found at i:1307383 original size:70 final size:69
Alignment explanation
Indices: 1307308--1307912 Score: 392
Period size: 71 Copynumber: 8.4 Consensus size: 69
1307298 CTTTGGGAAG
*
1307308 GAAAAAAGATGCCACGGAGTTGTGGAC-TTAAAAGTGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1 GAAAAAAGATGCCACGGAGTTGTGGGCTTTAAAAG-GAAAAAGAGTGCCACGGAGTTGTGGGCTT
1307372 TAAAA
65 TAAAA
1307377 GAAAAAAG-TGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCT
1 GAAAAAAGATGCCACGGAGTTGTGGGCTTT-AAAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCT
*
1307441 TTAAAC
64 TTAAAA
* * * ** *
1307447 GGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAGAGAGTGCCACAAAGTCGTCGGTG
1 GAAAAAAGATGCCACGGAGTTGTGGGCTTT-AAAA-GGAAAAAGAGTGCCACGGAGTTGT-GG-G
****
1307512 CCACAGAGTTGTGGGC
62 ---C----TT-TAAAA
*** ** * * **** **** * * **
1307528 TTTAAAAGA--AAAAGGTGCCACGGAG-TTGTGGGCTTTGAAAAGGAAAAAAGTGTGCCACAAAG
1 GAAAAAAGATGCCACGGAGTTGTGG-GCTT-T---AAAAGGAAA------AAGAGTGCCACGGAG
1307590 TTGTGGGCTTTAAAA
55 TTGTGGGCTTTAAAA
* * * * *
1307605 G-AAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAA-GAAGAAG-GTTGCCACCGACTTGTGTGGG
1 GAAAAAAGATGCCACGGAGTTGTGGGCTTT-AAAAGGAAAAAGAG-TGCCACGGA-GT-TGTGGG
*
1307667 CTTTAGGAAG
62 CTTTA--AAA
* * *
1307677 GGAGAAAGATGCCACGGAGTTGTGGAC-TTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1 GAAAAAAGATGCCACGGAGTTGTGGGCTTTAAAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1307741 TAAAA
65 TAAAA
1307746 GAAAAAAG-TGCCACGGAGTTGTGGGCTTTAAAA-GAAAAA-AGTGCCACGGAGTTGTGGGCTTT
1 GAAAAAAGATGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
1307808 GAAAA
66 -AAAA
* *
1307813 GGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACGGAAAAAG-GTGCCACGGAGTTGTGGGCT
1 -GAAAAAAGA-TGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCT
1307877 TTGAAAA
64 TT-AAAA
*
1307884 G-AAAAAGGTGCCACGGAGTTGTGGGCTTT
1 GAAAAAAGATGCCACGGAGTTGTGGGCTTT
1307913 GAAGAAAAGG
Statistics
Matches: 421, Mismatches: 72, Indels: 87
0.73 0.12 0.15
Matches are distributed among these distances:
66 23 0.05
67 11 0.03
68 72 0.17
69 31 0.07
70 80 0.19
71 95 0.23
72 8 0.02
73 36 0.09
74 3 0.01
75 1 0.00
76 5 0.01
77 3 0.01
78 10 0.02
79 8 0.02
80 4 0.01
81 11 0.03
82 1 0.00
85 1 0.00
86 2 0.00
87 16 0.04
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.20
Consensus pattern (69 bp):
GAAAAAAGATGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
AAAA
Found at i:1307569 original size:87 final size:88
Alignment explanation
Indices: 1307421--1307590 Score: 279
Period size: 87 Copynumber: 1.9 Consensus size: 88
1307411 GGGAAAAAGA
* * *
1307421 GTGCCACGGAGTTGTGGGCTTTAAACGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGA
1 GTGCCACAGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGAA
*
1307486 AAGAGAGTGCCACAAAGTCGTCG
66 AAAAGAGTGCCACAAAGTCGTCG
*
1307509 GTGCCACAGAGTTGTGGGCTTTAAA-AGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAA
1 GTGCCACAGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGAA
*
1307573 AAAAGTGTGCCACAAAGT
66 AAAAGAGTGCCACAAAGT
1307591 TGTGGGCTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
87 52 0.68
88 24 0.32
ACGTcount: A:0.32, C:0.15, G:0.34, T:0.20
Consensus pattern (88 bp):
GTGCCACAGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGAA
AAAAGAGTGCCACAAAGTCGTCG
Found at i:1307644 original size:34 final size:33
Alignment explanation
Indices: 1307508--1307929 Score: 499
Period size: 33 Copynumber: 12.2 Consensus size: 33
1307498 CAAAGTCGTC
*
1307508 GGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAA
1 GGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAA
1307541 GGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAA
1 GGTGCCACGGAGTTGTGGGCTTT-AAAA-G-AAAAA
** *
1307577 GTGTGCCACAAAGTTGTGGGCTTTAAAAGAAGAA
1 G-GTGCCACGGAGTTGTGGGCTTTAAAAGAAAAA
*
1307611 GGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAA
1 GGTGCCACGGAGTTGTGGGCTTT-AAAAGAAAAA
* * * *
1307645 GGTTGCCACCGACTTGTGTGGGCTTTAGGAAGGGAGAAA
1 GG-TGCCACGGA-GT-TGTGGGCTTTA--AA-AGAAAAA
* *
1307684 GATGCCACGGAGTTGTGGAC-TTAAAAGGGAAAAA
1 GGTGCCACGGAGTTGTGGGCTTTAAAA--GAAAAA
1307718 GAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAA
1 G-GTGCCACGGAGTTGTGGGCTTTAAAAGAAAAA
*
1307752 AGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAA
1 GGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAA
*
1307785 AGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAA
1 GGTGCCACGGAGTTGTGGGCTTT-AAAA--GAAAAA
*
1307821 GAGTGCCACGGAGTTGTGGGCTTTAAACGGAAAAA
1 G-GTGCCACGGAGTTGTGGGCTTTAAA-AGAAAAA
1307856 GGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAA
1 GGTGCCACGGAGTTGTGGGCTTT-AAAAGAAAAA
*
1307890 GGTGCCACGGAGTTGTGGGCTTT-GAAG-AAAA
1 GGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAA
1307921 GGATGCCAC
1 GG-TGCCAC
1307930 TAAGTCGTGG
Statistics
Matches: 343, Mismatches: 24, Indels: 45
0.83 0.06 0.11
Matches are distributed among these distances:
31 6 0.02
32 9 0.03
33 99 0.29
34 88 0.26
35 40 0.12
36 33 0.10
37 53 0.15
38 10 0.03
39 5 0.01
ACGTcount: A:0.32, C:0.13, G:0.34, T:0.21
Consensus pattern (33 bp):
GGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAA
Found at i:1307945 original size:32 final size:30
Alignment explanation
Indices: 1307886--1308064 Score: 207
Period size: 31 Copynumber: 5.8 Consensus size: 30
1307876 TTTGAAAAGA
* * * *
1307886 AAAAGGTGCCACGGAGTTGTGGGCTTTGAAG
1 AAAAGATGCCACTGAGTCGTGGACTTTG-AG
*
1307917 AAAAGGATGCCACTAAGTCGTGGACTTTGAG
1 AAAA-GATGCCACTGAGTCGTGGACTTTGAG
1307948 ACAAA-ATGCCACTGAGTCGTGGACTTTGAAG
1 A-AAAGATGCCACTGAGTCGTGGACTTTG-AG
*
1307979 AAAAGGATGCCACTGCGTCGTGGACTTTGAG
1 AAAA-GATGCCACTGAGTCGTGGACTTTGAG
* *
1308010 CAGAGATTGCCACTGAGTCGTGGACTTTGAG
1 AAAAGA-TGCCACTGAGTCGTGGACTTTGAG
*
1308041 AAGAGATTGCCACTGAGTCGTGGA
1 AAAAGA-TGCCACTGAGTCGTGGA
1308065 TTTTTTTTTA
Statistics
Matches: 131, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
30 27 0.21
31 60 0.46
32 44 0.34
ACGTcount: A:0.28, C:0.17, G:0.32, T:0.23
Consensus pattern (30 bp):
AAAAGATGCCACTGAGTCGTGGACTTTGAG
Found at i:1307946 original size:137 final size:136
Alignment explanation
Indices: 1307588--1307929 Score: 225
Period size: 138 Copynumber: 2.5 Consensus size: 136
1307578 TGTGCCACAA
* * *
1307588 AGTTGTGGGCTTTAAAA--GAAGAAG-GTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTTG
1 AGTTGTGGAC-TTAAAACGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAGAAAAAGG-TG
* * * *
1307650 CCACCGACTTGTGTGGGCTTTAGGAAGGGAGAAA-GATGCCACGGAGTTGTGGAC-TT-A-AAAG
63 CCACGGA-GT-TGTGGGCTTT--GAA--GA-AAAGGATGCCACGAAG-TGTGGGCTTTGAGAAAG
1307711 GGAAAAAGAGTGCCACGG
120 GGAAAAAGA-TGCCACGG
* *
1307729 AGTTGTGGGCTTTAAAA--GAAAAA-AGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCC
1 AGTTGTGGAC-TTAAAACGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGGTGCC
* * *
1307791 ACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT---AAACGGAA
65 ACGGAGTTGTGGGCTTTG--AA--GAAAAGGA-TGCCACGAAG-TGTGGGCTTTGAGAAAGGGAA
*
1307853 AAAGGTGCCACGG
124 AAAGATGCCACGG
* *
1307866 AGTTGTGGGCTTTGAAAA--GAAAAAG-GTGCCACGGAGTTGTGGGCTTT-GAAG-AAAAGGATG
1 AGTTGTGGAC-TT-AAAACGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGG-TG
1307926 CCAC
63 CCAC
1307930 TAAGTCGTGG
Statistics
Matches: 182, Mismatches: 10, Indels: 22
0.85 0.05 0.10
Matches are distributed among these distances:
135 1 0.01
136 8 0.04
137 48 0.26
138 61 0.34
139 10 0.05
140 10 0.05
141 44 0.24
ACGTcount: A:0.32, C:0.13, G:0.35, T:0.21
Consensus pattern (136 bp):
AGTTGTGGACTTAAAACGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCA
CGGAGTTGTGGGCTTTGAAGAAAAGGATGCCACGAAGTGTGGGCTTTGAGAAAGGGAAAAAGATG
CCACGG
Found at i:1307981 original size:62 final size:63
Alignment explanation
Indices: 1307892--1308064 Score: 237
Period size: 62 Copynumber: 2.8 Consensus size: 63
1307882 AAGAAAAAGG
* * * *
1307892 TGCCACGGAGTTGTGGGCTTTGAAGAAAAGGATGCCACTAAGTCGTGGACTTTGAGACA-A-AA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAGGATGCCACTGAGTCGTGGACTTTGAG-CAGAGAA
* *
1307954 TGCCACTGAGTCGTGGACTTTGAAGAAAAGGATGCCACTGCGTCGTGGACTTTGAGCAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAGGATGCCACTGAGTCGTGGACTTTGAGCAGAGAA
*
1308017 TGCCACTGAGTCGTGGACTTTG-AGAAGA-GATTGCCACTGAGTCGTGGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAGGA-TGCCACTGAGTCGTGGA
1308065 TTTTTTTTTA
Statistics
Matches: 100, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
61 4 0.04
62 73 0.73
63 23 0.23
ACGTcount: A:0.27, C:0.18, G:0.32, T:0.24
Consensus pattern (63 bp):
TGCCACTGAGTCGTGGACTTTGAAGAAAAGGATGCCACTGAGTCGTGGACTTTGAGCAGAGAA
Found at i:1309305 original size:14 final size:13
Alignment explanation
Indices: 1309286--1309377 Score: 78
Period size: 14 Copynumber: 6.7 Consensus size: 13
1309276 ACCTTTGCAC
1309286 TTTTTTTTTGTGT
1 TTTTTTTTTGTGT
*
1309299 TTGTTTTTTTTTGT
1 TT-TTTTTTTGTGT
*
1309313 TTTTTGTTTTTTGT
1 TTTTT-TTTTGTGT
*
1309327 GTTTTTTGTTGT-T
1 -TTTTTTTTTGTGT
*
1309340 TTTTTTTGGTGTGT
1 TTTTTTT-TTGTGT
*
1309354 TTTTTTTTGTTTGT
1 TTTTTTTT-TGTGT
1309368 TTGTTTTTTT
1 TT-TTTTTTT
1309378 TTCATCACTT
Statistics
Matches: 65, Mismatches: 7, Indels: 13
0.76 0.08 0.15
Matches are distributed among these distances:
12 6 0.09
13 9 0.14
14 39 0.60
15 11 0.17
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (13 bp):
TTTTTTTTTGTGT
Found at i:1309305 original size:16 final size:16
Alignment explanation
Indices: 1309286--1309379 Score: 91
Period size: 18 Copynumber: 5.6 Consensus size: 16
1309276 ACCTTTGCAC
1309286 TTTTTTTTTGTGTTTG
1 TTTTTTTTTGTGTTTG
*
1309302 TTTTTTTTTGTTTTTTG
1 TTTTTTTTTG-TGTTTG
* *
1309319 TTTTTTGTGTTTTTTGTTG
1 TTTTTT-T-TTGTGT-TTG
*
1309338 TTTTTTTTTG-GTGTG
1 TTTTTTTTTGTGTTTG
1309353 TTTTTTTTTGTTTGTTTG
1 TTTTTTTTTG--TGTTTG
1309371 TTTTTTTTT
1 TTTTTTTTT
1309380 CATCACTTCT
Statistics
Matches: 65, Mismatches: 6, Indels: 12
0.78 0.07 0.14
Matches are distributed among these distances:
15 12 0.18
16 11 0.17
17 13 0.20
18 18 0.28
19 11 0.17
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (16 bp):
TTTTTTTTTGTGTTTG
Found at i:1316527 original size:21 final size:21
Alignment explanation
Indices: 1316494--1316534 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1316484 CTAAGTAAAA
1316494 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
1316515 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
1316535 CAAGGTTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:1316617 original size:20 final size:20
Alignment explanation
Indices: 1316594--1316667 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
1316584 ACAATTCAAA
1316594 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1316614 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
1316635 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1316655 GTATCGATACATG
1 GTATCGATACATG
1316668 AAAAAGATGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1316638 original size:21 final size:21
Alignment explanation
Indices: 1316612--1316687 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
1316602 ACATGTTGCA
1316612 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
1316633 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
1316653 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
1316674 ATGTATCGATACAT
1 ATGTATCGATACAT
1316688 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:1316645 original size:41 final size:41
Alignment explanation
Indices: 1316594--1316687 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
1316584 ACAATTCAAA
1316594 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1316635 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1316676 GTATCGATACAT
1 GTATCGATACAT
1316688 TTCTTGGCAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
Found at i:1316744 original size:13 final size:13
Alignment explanation
Indices: 1316726--1316751 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1316716 TACAGCAAGT
1316726 ATGTATCGATACA
1 ATGTATCGATACA
1316739 ATGTATCGATACA
1 ATGTATCGATACA
1316752 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1317273 original size:34 final size:35
Alignment explanation
Indices: 1317210--1317276 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1317200 CTAAGTAATT
1317210 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
1317246 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
1317277 TCTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:1320471 original size:13 final size:13
Alignment explanation
Indices: 1320453--1320477 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1320443 TTTTCCAAAT
1320453 TGTATCGATACAA
1 TGTATCGATACAA
1320466 TGTATCGATACA
1 TGTATCGATACA
1320478 TTGCTTCAGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1320734 original size:1 final size:1
Alignment explanation
Indices: 1320728--1320756 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
1320718 TAAAATTCTC
1320728 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1320757 CCATTTTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1321361 original size:21 final size:21
Alignment explanation
Indices: 1321336--1321387 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
1321326 TTGTATAAAT
1321336 TTTGTATTAAAGGGAAGAACA
1 TTTGTATTAAAGGGAAGAACA
*
1321357 TTTGTATTAAAGGGAAGAACG
1 TTTGTATTAAAGGGAAGAACA
1321378 TTTGTATTAA
1 TTTGTATTAA
1321388 GGGGGAGAGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.35
Consensus pattern (21 bp):
TTTGTATTAAAGGGAAGAACA
Found at i:1322179 original size:21 final size:21
Alignment explanation
Indices: 1322146--1322186 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1322136 CTAAGTAAAA
1322146 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
1322167 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
1322187 CAAGGTTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:1322269 original size:20 final size:20
Alignment explanation
Indices: 1322246--1322319 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
1322236 ACAATTCAAA
1322246 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1322266 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
1322287 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1322307 GTATCGATACATG
1 GTATCGATACATG
1322320 AAAAAGATGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1322290 original size:21 final size:21
Alignment explanation
Indices: 1322264--1322339 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
1322254 ACATGTTGCA
1322264 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
1322285 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
1322305 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
1322326 ATGTATCGATACAT
1 ATGTATCGATACAT
1322340 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:1322297 original size:41 final size:41
Alignment explanation
Indices: 1322246--1322339 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
1322236 ACAATTCAAA
1322246 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1322287 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1322328 GTATCGATACAT
1 GTATCGATACAT
1322340 TTCTTGGCAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
Found at i:1322396 original size:13 final size:13
Alignment explanation
Indices: 1322378--1322403 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1322368 TACAGCAAGT
1322378 ATGTATCGATACA
1 ATGTATCGATACA
1322391 ATGTATCGATACA
1 ATGTATCGATACA
1322404 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Done.