Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006936.1 Hibiscus syriacus cultivar Beakdansim tig00017808_pilon, whole genome shotgun sequence
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: 2176229
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 9
Found at i:5227 original size:3 final size:3
Alignment explanation
Indices: 5209--5258 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
5199 TAATTGTTAA
* * * *
5209 AAT AAT TAT CAT AAT AAT AAT AAT -AT AAT AGT AAT AAT TAT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5255 AAT A
1 AAT A
5259 TTTATAACCT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
2 4 0.11
3 34 0.89
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:5265 original size:20 final size:20
Alignment explanation
Indices: 5220--5258 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
5210 ATAATTATCA
5220 TAATAATAATAATATAATAG
1 TAATAATAATAATATAATAG
*
5240 TAATAATTATAATATAATA
1 TAATAATAATAATATAATA
5259 TTTATAACCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (20 bp):
TAATAATAATAATATAATAG
Found at i:5475 original size:53 final size:53
Alignment explanation
Indices: 5434--5903 Score: 577
Period size: 53 Copynumber: 8.9 Consensus size: 53
5424 CGACCAGCGA
* *
5434 GTTCGCTCCCTCTTATTTCAGGGAGTAGAACTCGAACAATCTTCTACCTACGG
1 GTTCGCTCCCTCTTGTTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACGG
* * * *
5487 GTTCGCTCCTTCTTGCTTT-AGGGAGTAGAACTCAAATAATCTTCTGCCTATGG
1 GTTCGCTCCCTCTTG-TTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACGG
* * *
5540 GTTCACTCCCTCTTGCTTT-AGGAAGTAGAACTCGAACAATCTCCTGCCTACGG
1 GTTCGCTCCCTCTTG-TTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACGG
* * *
5593 GTTTGATCCCTCTT-TCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACGT
1 GTTCGCTCCCTCTTGT-TTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACGG
* * * * * * * *
5646 GTTCACTCCCTTTTGCTTCAGAGATTAGAACTCGAATAATCTTCTACCTATGG
1 GTTCGCTCCCTCTTGTTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACGG
* * * * * *
5699 GTTTGCTCCCTCTTGCTTCAAGGAGAAGAACTGGAACAATCTTCTGCCTACGA
1 GTTCGCTCCCTCTTGTTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACGG
* * * * *
5752 TTTCGCTTCCTCTTGCTTGAGGGAGTAGAACTCGAACAATCTTCTACCTACGG
1 GTTCGCTCCCTCTTGTTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACGG
* * *
5805 GTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTTGAATAATCTTCTGCCTACGG
1 GTTCGCTCCCTCTTGTTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACGG
*
5858 GTTCGCTCCCTCTTGTTTCAAGGAGTAGAACTCGAACAATCTTCTG
1 GTTCGCTCCCTCTTGTTTCAGGGAGTAGAACTCGAACAATCTTCTG
5904 GTGTGATTCT
Statistics
Matches: 352, Mismatches: 61, Indels: 8
0.84 0.14 0.02
Matches are distributed among these distances:
51 1 0.00
52 2 0.01
53 346 0.98
54 3 0.01
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (53 bp):
GTTCGCTCCCTCTTGTTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACGG
Found at i:5900 original size:159 final size:159
Alignment explanation
Indices: 5414--5903 Score: 666
Period size: 159 Copynumber: 3.1 Consensus size: 159
5404 CCTTTTCTTT
* *
5414 GAACAATCTTC-GACC-AGCGAGTTCGCTCCCTCTTATTTCAGGGAGTAGAACTCGAACAATCTT
1 GAACAATCTTCTG-CCTA-CGATTTCGCTCCCTCTTACTTCAGGGAGTAGAACTCGAACAATCTT
* * *
5477 CTACCTACGGGTTCGCTCCTTCTTGCTTTAGGGAGTAGAACTCAAATAATCTTCTGCCTATGGGT
64 CTACCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAATAATCTTCTGCCTATGGGT
*
5542 TCACTCCCTCTTGCTTT--AGGAAGTAGAACTC
129 TCGCTCCCTCTTG-TTTCAAGG-AGTAGAACTC
* * * *
5573 GAACAATCTCCTGCCTACGGGTTT-GATCCCTCTTTCTTCAGGGAGTAGAACTCGAACAATCTTC
1 GAACAATCTTCTGCCTAC-GATTTCGCTCCCTCTTACTTCAGGGAGTAGAACTCGAACAATCTTC
* * * * * * *
5637 TGCCTACGTGTTCACTCCCTTTTGCTTCAGAGATTAGAACTCGAATAATCTTCTACCTATGGGTT
65 TACCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAATAATCTTCTGCCTATGGGTT
* * * *
5702 TGCTCCCTCTTGCTTCAAGGAGAAGAACTG
130 CGCTCCCTCTTGTTTCAAGGAGTAGAACTC
* * *
5732 GAACAATCTTCTGCCTACGATTTCGCTTCCTCTTGCTTGAGGGAGTAGAACTCGAACAATCTTCT
1 GAACAATCTTCTGCCTACGATTTCGCTCCCTCTTACTTCAGGGAGTAGAACTCGAACAATCTTCT
* *
5797 ACCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTTGAATAATCTTCTGCCTACGGGTTC
66 ACCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAATAATCTTCTGCCTATGGGTTC
5862 GCTCCCTCTTGTTTCAAGGAGTAGAACTC
131 GCTCCCTCTTGTTTCAAGGAGTAGAACTC
5891 GAACAATCTTCTG
1 GAACAATCTTCTG
5904 GTGTGATTCT
Statistics
Matches: 285, Mismatches: 40, Indels: 12
0.85 0.12 0.04
Matches are distributed among these distances:
158 6 0.02
159 271 0.95
160 8 0.03
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (159 bp):
GAACAATCTTCTGCCTACGATTTCGCTCCCTCTTACTTCAGGGAGTAGAACTCGAACAATCTTCT
ACCTACGGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAATAATCTTCTGCCTATGGGTTC
GCTCCCTCTTGTTTCAAGGAGTAGAACTC
Found at i:6497 original size:42 final size:41
Alignment explanation
Indices: 6422--6503 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 41
6412 ATATCTTATG
* * **
6422 AATGGCCCGAAGGACTTATCATTTTTCTCGAAAGACTTACA
1 AATGACCCGAAGGAATTATCATCATTCTCGAAAGACTTACA
*
6463 AATGACCCGAAGGAATTAATCATCATTCTTGAAAGACTTAC
1 AATGACCCGAAGGAATT-ATCATCATTCTCGAAAGACTTAC
6504 TGATGGATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
41 15 0.43
42 20 0.57
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (41 bp):
AATGACCCGAAGGAATTATCATCATTCTCGAAAGACTTACA
Found at i:6580 original size:42 final size:42
Alignment explanation
Indices: 6533--6626 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 42
6523 CTCTTCCGTG
* *
6533 AAGACTTA-TAAATTACTCGAAGGATTTAATCATCACGCTCGA
1 AAGACTTACT-AATGACCCGAAGGATTTAATCATCACGCTCGA
* * * *
6575 AAGACTTACTGATGGCCCGAAGGATTTCATCATCATGCTCGA
1 AAGACTTACTAATGACCCGAAGGATTTAATCATCACGCTCGA
*
6617 AAGCCTTACT
1 AAGACTTACT
6627 GATGGCACTT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 43 0.98
43 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (42 bp):
AAGACTTACTAATGACCCGAAGGATTTAATCATCACGCTCGA
Found at i:6627 original size:42 final size:42
Alignment explanation
Indices: 6550--6632 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
6540 ATAAATTACT
6550 CGAAGGATTTAATCATCACGCTCGAAAGACTTACTGATGGCC
1 CGAAGGATTTAATCATCACGCTCGAAAGACTTACTGATGGCC
* * *
6592 CGAAGGATTTCATCATCATGCTCGAAAGCCTTACTGATGGC
1 CGAAGGATTTAATCATCACGCTCGAAAGACTTACTGATGGC
6633 ACTTACTGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (42 bp):
CGAAGGATTTAATCATCACGCTCGAAAGACTTACTGATGGCC
Found at i:6692 original size:37 final size:37
Alignment explanation
Indices: 6640--6765 Score: 153
Period size: 37 Copynumber: 3.4 Consensus size: 37
6630 GGCACTTACT
*
6640 GATGGATTTATTTCACTACTCTTCAGTGAAGGCTTAA
1 GATGGATTTACTTCACTACTCTTCAGTGAAGGCTTAA
* * * *
6677 GATGGATTTGCTTCACTACACTTCAGTAAAGGCTTAG
1 GATGGATTTACTTCACTACTCTTCAGTGAAGGCTTAA
* * * *
6714 GAAGGATTTTCTCCACTACTCTTCGTGTGAAGGCTTAA
1 GATGGATTTACTTCACTACTCTTC-AGTGAAGGCTTAA
*
6752 GATGGATTCACTTC
1 GATGGATTTACTTC
6766 TTCATACATA
Statistics
Matches: 72, Mismatches: 16, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
37 52 0.72
38 20 0.28
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (37 bp):
GATGGATTTACTTCACTACTCTTCAGTGAAGGCTTAA
Found at i:9790 original size:22 final size:21
Alignment explanation
Indices: 9762--9809 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
9752 TTTTCCAGAA
9762 TGCTACAGGGGTA-TCGATACCC
1 TGCTACA-GGGTACT-GATACCC
*
9784 TGCTACAGTGTACTGATACCC
1 TGCTACAGGGTACTGATACCC
9805 TGCTA
1 TGCTA
9810 TAGTAATTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 16 0.67
22 8 0.33
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (21 bp):
TGCTACAGGGTACTGATACCC
Found at i:10527 original size:31 final size:31
Alignment explanation
Indices: 10492--10725 Score: 387
Period size: 31 Copynumber: 7.5 Consensus size: 31
10482 CATAGATTTT
* *
10492 GAAGAACCTAGGTAATCAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
*
10523 GAAGAACATAGGTAAACAATCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
* * *
10554 TAAGAACATAGGTAAACAGTCAATATATCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
*
10585 GAAGAACATAGGTAAATAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
10616 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
10647 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
*
10678 GAAGAACATAGGTAAACAGTCCATATTTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
*
10709 AAAGAACATAGGTAAAC
1 GAAGAACATAGGTAAAC
10726 CCTCGACCCT
Statistics
Matches: 189, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 189 1.00
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.21
Consensus pattern (31 bp):
GAAGAACATAGGTAAACAGTCCATATGTCCC
Found at i:17923 original size:3 final size:3
Alignment explanation
Indices: 17908--17954 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
17898 TAATTGTTAA
* * *
17908 AAT AAT TAT AAT AAT AAT AAT -AT AAT AGT AAT AAT TAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
17954 A
1 A
17955 TTTATAACCC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
2 4 0.11
3 32 0.89
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:17959 original size:14 final size:14
Alignment explanation
Indices: 17908--17961 Score: 74
Period size: 14 Copynumber: 3.8 Consensus size: 14
17898 TAATTGTTAA
17908 AATAATTATAATAAT
1 AATAATTATAAT-AT
17923 AATAA-TATAATAGT
1 AATAATTATAATA-T
17937 AATAATTATAATAT
1 AATAATTATAATAT
*
17951 AATATTTATAA
1 AATAATTATAA
17962 CCCGGAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
13 1 0.03
14 23 0.64
15 12 0.33
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (14 bp):
AATAATTATAATAT
Found at i:17961 original size:20 final size:20
Alignment explanation
Indices: 17916--17954 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
17906 AAAATAATTA
17916 TAATAATAATAATATAATAG
1 TAATAATAATAATATAATAG
*
17936 TAATAATTATAATATAATA
1 TAATAATAATAATATAATA
17955 TTTATAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (20 bp):
TAATAATAATAATATAATAG
Found at i:19784 original size:79 final size:79
Alignment explanation
Indices: 19642--19940 Score: 422
Period size: 79 Copynumber: 3.8 Consensus size: 79
19632 GAATGAATGA
* * * *
19642 ATAAAATAATAATGCATATGGGTGCATTATTGGCATGAAACGATGCTATAGCT-AAAGTGCATAT
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAACTGAAA-TGCATAT
19706 GGGTGTATTCTCGGC
65 GGGTGTATTCTCGGC
* ** * *
19721 ATAAAAGAATAATGCATACGGGTGCATTACAGGCATGAAAGGACGCCATAACTGAAATACATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAACTGAAATGCATATG
19786 GGT-TCATTCTCGGC
66 GGTGT-ATTCTCGGC
* *
19800 ATAAAAGAATAATGCATATGGGTGCATTATTGGAATGAAAGGATGCCATAGCTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAACTGAAATGCATATG
*
19865 GGTGCATTCTCGGC
66 GGTGTATTCTCGGC
* * * *
19879 ATAAAAGAATAATGCGTATGGGTGCATTATTGGCATAAAAGTATGCCATAACTAAAATGCAT
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAACTGAAATGCAT
19941 GAACGGATGC
Statistics
Matches: 194, Mismatches: 23, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
78 1 0.01
79 190 0.98
80 3 0.02
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (79 bp):
ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAACTGAAATGCATATG
GGTGTATTCTCGGC
Found at i:19818 original size:34 final size:34
Alignment explanation
Indices: 19780--19919 Score: 118
Period size: 34 Copynumber: 3.8 Consensus size: 34
19770 AACTGAAATA
* *
19780 CATATGGGTTCATTCTCGGCATAAAAGAATAATG
1 CATATGGGTGCATTATCGGCATAAAAGAATAATG
* *
19814 CATATGGGTGCATTATTGGAATGAAAGGATGCCATAGCTGAAATG
1 CATATGGGTGCATTATCGGCAT-AAA--A-G--A-A--T--AATG
*
19859 CATATGGGTGCATTCTCGGCATAAAAGAATAATG
1 CATATGGGTGCATTATCGGCATAAAAGAATAATG
* *
19893 CGTATGGGTGCATTATTGGCATAAAAG
1 CATATGGGTGCATTATCGGCATAAAAG
19920 TATGCCATAA
Statistics
Matches: 85, Mismatches: 10, Indels: 22
0.73 0.09 0.19
Matches are distributed among these distances:
34 46 0.54
35 3 0.04
36 1 0.01
37 1 0.01
38 2 0.02
39 1 0.01
40 1 0.01
41 2 0.02
42 1 0.01
43 1 0.01
44 3 0.04
45 23 0.27
ACGTcount: A:0.34, C:0.13, G:0.26, T:0.28
Consensus pattern (34 bp):
CATATGGGTGCATTATCGGCATAAAAGAATAATG
Found at i:20577 original size:68 final size:68
Alignment explanation
Indices: 20322--20536 Score: 358
Period size: 68 Copynumber: 3.2 Consensus size: 68
20312 ACAAGATTAA
* * *
20322 AGGCCTAACTGTGCATTTGAAAGAAAGGTGTCATTTATTCCAGTTAGATGAAAAGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
20387 TTG
66 TTG
* * *
20390 AGGCCTAATTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATAAAAGGCTAAGCGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
20455 TTG
66 TTG
* *
20458 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTATATGAAAGGCTAAGTTCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
20523 TTG
66 TTG
20526 AGGCCTAACTG
1 AGGCCTAACTG
20537 AGTAATTGGT
Statistics
Matches: 136, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 136 1.00
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.30
Consensus pattern (68 bp):
AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
TTG
Found at i:20595 original size:136 final size:136
Alignment explanation
Indices: 20322--20574 Score: 344
Period size: 136 Copynumber: 1.9 Consensus size: 136
20312 ACAAGATTAA
*
20322 AGGCCTAACTGTGCATTTGAAAGAAAGGTGTCATTTATTCCAGTTAGATGAAAAGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGAAAGAAAGGTGTCATTTATGCCAGTTAGATGAAAAGCTAAGTGCCT
* * * * * * * *
20387 TTGAGGCCTAATTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATAAAAGGCTAAGCG
66 TTGAGGCCTAACTGAGCAATTGACAGAAAGATGTCAATTATGCCAGTCAAATAAAAGGCTAAACG
*
20452 CCTTTG
131 ACTTTG
* * * *
20458 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTATATGAAAGGCTAAGTTCCT
1 AGGCCTAACTGTGCATTTGAAAGAAAGGTGTCATTTATGCCAGTTAGATGAAAAGCTAAGTGCCT
* ** *
20523 TTGAGGCCTAACTGAGTAATTGGTAGAAAGATGTCAATTATGTCAGTCAAAT
66 TTGAGGCCTAACTGAGCAATTGACAGAAAGATGTCAATTATGCCAGTCAAAT
20575 GAACGGTTAA
Statistics
Matches: 101, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
136 101 1.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (136 bp):
AGGCCTAACTGTGCATTTGAAAGAAAGGTGTCATTTATGCCAGTTAGATGAAAAGCTAAGTGCCT
TTGAGGCCTAACTGAGCAATTGACAGAAAGATGTCAATTATGCCAGTCAAATAAAAGGCTAAACG
ACTTTG
Found at i:20653 original size:29 final size:29
Alignment explanation
Indices: 20573--20719 Score: 222
Period size: 29 Copynumber: 5.0 Consensus size: 29
20563 TGTCAGTCAA
* * *
20573 ATGAACGGTTAAACACTATTGAGTAAAAG
1 ATGAAAGGTCAAACACTGTTGAGTAAAAG
20602 ATGAAAGGTTCAAACACTGTTGAGTAAAAG
1 ATGAAAGG-TCAAACACTGTTGAGTAAAAG
20632 ATGAAAGGTCAAACACTGTTGAGTAAAAG
1 ATGAAAGGTCAAACACTGTTGAGTAAAAG
20661 ATGAAAGGTCAAACACTGTTGAGTAAAAG
1 ATGAAAGGTCAAACACTGTTGAGTAAAAG
* * * *
20690 ATGAACGGTTAAACACTGTCGATTAAAAG
1 ATGAAAGGTCAAACACTGTTGAGTAAAAG
20719 A
1 A
20720 ATAATGGACT
Statistics
Matches: 110, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
29 83 0.75
30 27 0.25
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.22
Consensus pattern (29 bp):
ATGAAAGGTCAAACACTGTTGAGTAAAAG
Found at i:22735 original size:2 final size:2
Alignment explanation
Indices: 22728--22759 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
22718 ATTAGGTCGA
22728 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22760 TCTGGATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24659 original size:19 final size:18
Alignment explanation
Indices: 24613--24648 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
24603 ACCAGGCAAC
24613 ATCGA-ACCTAAAATGGGT
1 ATCGATACC-AAAATGGGT
24631 ATCGATACCAAAATGGGT
1 ATCGATACCAAAATGGGT
24649 TATCAGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (18 bp):
ATCGATACCAAAATGGGT
Found at i:25201 original size:45 final size:45
Alignment explanation
Indices: 25146--25233 Score: 158
Period size: 45 Copynumber: 2.0 Consensus size: 45
25136 ATGCATTATT
*
25146 GGCATGAAAGGATGCTATAGCTGAAATGTATATGGGTGCATTCAC
1 GGCATGAAAGGATGCTATAGCTGAAATGCATATGGGTGCATTCAC
*
25191 GGCATGAAAGGATGCTATAGCTGAAATGCATATGGGTTCATTC
1 GGCATGAAAGGATGCTATAGCTGAAATGCATATGGGTGCATTC
25234 TCGACATAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.31, C:0.14, G:0.28, T:0.27
Consensus pattern (45 bp):
GGCATGAAAGGATGCTATAGCTGAAATGCATATGGGTGCATTCAC
Found at i:25301 original size:79 final size:79
Alignment explanation
Indices: 25170--25424 Score: 352
Period size: 79 Copynumber: 3.2 Consensus size: 79
25160 CTATAGCTGA
* * * *
25170 AATGTATATGGGTGCATTCA-CGGCATGAAAGGATGCTATAGCTGAAATGCATATGGGTTCATTC
1 AATGCATATGGGTGCATT-ATTGGCATGAAAGGATGCCATAGCTAAAATGCATATGGGTTCATTC
25234 TCGACATAAAAGAAT
65 TCGACATAAAAGAAT
* *
25249 AATGTATATGGGAGCATTATTGGCATGAAAGGATGCCATAGCTAAAATGCATATGGGTTCATTCT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTAAAATGCATATGGGTTCATTCT
25314 CGACATAAAA-ATAT
66 CGACATAAAAGA-AT
* * * * * *
25328 AATACATATGAGTGCATTATTGGCCTGAAAGGATGCCATAGCTTAAATGCATATGGGTGCACTCT
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTAAAATGCATATGGGTTCATTCT
**
25393 CGGTATAAAAGAAT
66 CGACATAAAAGAAT
25407 AATGCATATGGGTGCATT
1 AATGCATATGGGTGCATT
25425 CTCTGCATAA
Statistics
Matches: 157, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
78 2 0.01
79 154 0.98
80 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.29
Consensus pattern (79 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTAAAATGCATATGGGTTCATTCT
CGACATAAAAGAAT
Found at i:25457 original size:34 final size:34
Alignment explanation
Indices: 25373--25458 Score: 145
Period size: 34 Copynumber: 2.5 Consensus size: 34
25363 CCATAGCTTA
* *
25373 AATGCATATGGGTGCACTCTCGGTATAAAAGAAT
1 AATGCATATGGGTGCATTCTCGGCATAAAAGAAT
*
25407 AATGCATATGGGTGCATTCTCTGCATAAAAGAAT
1 AATGCATATGGGTGCATTCTCGGCATAAAAGAAT
25441 AATGCATATGGGTGCATT
1 AATGCATATGGGTGCATT
25459 ATTGGCATGA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (34 bp):
AATGCATATGGGTGCATTCTCGGCATAAAAGAAT
Found at i:25955 original size:68 final size:68
Alignment explanation
Indices: 25846--26031 Score: 266
Period size: 68 Copynumber: 2.7 Consensus size: 68
25836 AAGATTAAAG
* *
25846 GCCTAACT-ATGCATTTAACATAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGGGCCTT
1 GCCTAACTGA-GCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGGGCCTT
25910 TGAA
65 TGAA
* *
25914 GCCTAACTGCGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCTTT
1 GCCTAACTGAGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGGGCCTTT
*
25979 GAG
66 GAA
* * * * *
25982 GCCTAACTGAGTAATTGGCAGAAAGGTGTCAATTATGCCAGTCAGATGAA
1 GCCTAACTGAGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAA
26032 CGGTTAAACA
Statistics
Matches: 106, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
68 106 1.00
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (68 bp):
GCCTAACTGAGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGGGCCTTT
GAA
Found at i:26074 original size:29 final size:29
Alignment explanation
Indices: 26025--26143 Score: 184
Period size: 29 Copynumber: 4.1 Consensus size: 29
26015 TATGCCAGTC
* *
26025 AGATGAACGGTTAAACACTGTTGAGTAAA
1 AGATGAAAGGTCAAACACTGTTGAGTAAA
* *
26054 AGATAAAAGGTCAAAAACTGTTGAGTAAA
1 AGATGAAAGGTCAAACACTGTTGAGTAAA
26083 AGATGAAAGGTCAAACACTGTTGAGTAAA
1 AGATGAAAGGTCAAACACTGTTGAGTAAA
* *
26112 AGATGAAAGGTCAAACACTATCGAGTAAA
1 AGATGAAAGGTCAAACACTGTTGAGTAAA
26141 AGA
1 AGA
26144 ATAATGGACT
Statistics
Matches: 82, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 82 1.00
ACGTcount: A:0.47, C:0.10, G:0.23, T:0.20
Consensus pattern (29 bp):
AGATGAAAGGTCAAACACTGTTGAGTAAA
Found at i:28134 original size:4 final size:4
Alignment explanation
Indices: 28127--28162 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
28117 TGTGTGTGTG
28127 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
28163 CATTTAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:28514 original size:18 final size:18
Alignment explanation
Indices: 28490--28536 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
28480 TTTAATTTCT
28490 TTATAATAATTTAAAGTTA
1 TTATAATAATTTAAA-TTA
*
28509 -TATAATGATTTTAAATTA
1 TTATAAT-AATTTAAATTA
28527 TTATAA-AATT
1 TTATAATAATT
28537 AGCATGTATC
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
17 3 0.12
18 9 0.38
19 12 0.50
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (18 bp):
TTATAATAATTTAAATTA
Found at i:32127 original size:45 final size:47
Alignment explanation
Indices: 32076--32164 Score: 155
Period size: 45 Copynumber: 1.9 Consensus size: 47
32066 TCGAATAAAT
32076 GCATGCGAACTAGATATCATGCGGTTAGG-TTTATTTTT-TGAACAA
1 GCATGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAACAA
*
32121 GCATGCGAATTAGATATCATGCGGTTAGGATTTATTTTTGTGAA
1 GCATGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAA
32165 TGACAAAGCA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
45 28 0.68
46 9 0.22
47 4 0.10
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.37
Consensus pattern (47 bp):
GCATGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAACAA
Found at i:41814 original size:19 final size:18
Alignment explanation
Indices: 41790--41892 Score: 72
Period size: 19 Copynumber: 5.6 Consensus size: 18
41780 ATTTTGCTTG
41790 AAGAAGAAATAAAAGAGAA
1 AAGAAGAAA-AAAAGAGAA
*
41809 AAGAAGAAAAAATGAGAA
1 AAGAAGAAAAAAAGAGAA
*
41827 AA-AAGAAAAAATGATGGAA
1 AAGAAGAAAAAAAGA--GAA
*
41846 AA-AACGAAAAAGAA-AAAA
1 AAGAA-GAAAAA-AAGAGAA
*
41864 AAG-AGAAAAAATG-GAA
1 AAGAAGAAAAAAAGAGAA
41880 AATGGAAGAAAAA
1 AA--GAAGAAAAA
41893 GAGAAAAATG
Statistics
Matches: 70, Mismatches: 5, Indels: 18
0.75 0.05 0.19
Matches are distributed among these distances:
16 5 0.07
17 18 0.26
18 16 0.23
19 23 0.33
20 7 0.10
21 1 0.01
ACGTcount: A:0.73, C:0.01, G:0.20, T:0.06
Consensus pattern (18 bp):
AAGAAGAAAAAAAGAGAA
Found at i:41891 original size:44 final size:44
Alignment explanation
Indices: 41800--41900 Score: 109
Period size: 44 Copynumber: 2.2 Consensus size: 44
41790 AAGAAGAAAT
*
41800 AAAAGAGAAAAGAAGAAAAAATGAGAAAAAAGAAAAAATGATGGAA
1 AAAAGA-AAAAGAAGAAAAAATGAGAAAAAAGAAAAAATGA-AGAA
*
41846 AAAACGAAAAAGAA-AAAAAA-GAGAAAAAATG-GAAAATGGAAGAA
1 AAAA-GAAAAAGAAGAAAAAATGAGAAAAAA-GAAAAAAT-GAAGAA
41890 AAAGAGAAAAA
1 AAA-AGAAAAA
41901 TGGAAAAAGA
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
44 26 0.53
45 10 0.20
46 11 0.22
47 2 0.04
ACGTcount: A:0.73, C:0.01, G:0.21, T:0.05
Consensus pattern (44 bp):
AAAAGAAAAAGAAGAAAAAATGAGAAAAAAGAAAAAATGAAGAA
Found at i:41919 original size:19 final size:19
Alignment explanation
Indices: 41878--41919 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
41868 GAAAAAATGG
*
41878 AAAATGGAAGAAAAAGAGA
1 AAAATGGAAGAAAAAGAAA
*
41897 AAAATGGAA-AAAGAGAAA
1 AAAATGGAAGAAAAAGAAA
41915 TAAAA
1 -AAAA
41920 GTAGGGTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.07
Consensus pattern (19 bp):
AAAATGGAAGAAAAAGAAA
Found at i:41919 original size:27 final size:26
Alignment explanation
Indices: 41800--41920 Score: 115
Period size: 26 Copynumber: 4.6 Consensus size: 26
41790 AAGAAGAAAT
*
41800 AAAAGAGAAAAGAAGA-AAAAATGAGA
1 AAAAGAGAAAAAAAGAGAAAAATG-GA
* **
41826 AAAA-AGAAAAAATGATGGAAAAAACGA
1 AAAAGAGAAAAAAAGA--GAAAAATGGA
41853 AAAAGA-AAAAAAAGAGAAAAAATGGA
1 AAAAGAGAAAAAAAGAG-AAAAATGGA
*
41879 AAATG-GAAGAAAAAGAGAAAAATGGA
1 AAAAGAGAA-AAAAAGAGAAAAATGGA
41905 AAAAGAGAAATAAAAG
1 AAAAGAGAAA-AAAAG
41921 TAGGGTTCAG
Statistics
Matches: 77, Mismatches: 9, Indels: 17
0.75 0.09 0.17
Matches are distributed among these distances:
25 10 0.13
26 31 0.40
27 30 0.39
28 6 0.08
ACGTcount: A:0.72, C:0.01, G:0.21, T:0.06
Consensus pattern (26 bp):
AAAAGAGAAAAAAAGAGAAAAATGGA
Found at i:43269 original size:55 final size:54
Alignment explanation
Indices: 43114--43507 Score: 426
Period size: 55 Copynumber: 7.3 Consensus size: 54
43104 GAAGCAAATT
* *
43114 CGTTTGTTGAAGA--TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATTTTCGAGTCTTATACTCCCTGAAGGAATAGGGAGCGGACA
* * *
43165 AGTTTGTTGAAGA--TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATTTTCGAGTCTTATACTCCCTGAAGGAATAGGGAGCGGACA
* * * *
43216 AGTTTGTTGAAGATTGTTCGAGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACC
1 CGTTTGTTGAAGATT-TTCGAGTCT-TATACTCCCTGAAGGAATAGGGAGCGGACA
* *
43271 CGTTTGTTGAAGATTATTCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACA
1 CGTTTGTTGAAGATT-TTCGAGTCTTATACTCCCTGAAGGAATAGGGAGCGGACA
* *
43326 CGTTTGTTGAAGATTATTCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACA
1 CGTTTGTTGAAGATT-TTCGAGTCTTATACTCCCTGAAGGAATAGGGAGCGGACA
* * * *
43381 CGTTTGTTGAAGATTGTTTGAGTCTTATACTCCCTGAATGAATAGGGAACAGACA
1 CGTTTGTTGAAGATT-TTCGAGTCTTATACTCCCTGAAGGAATAGGGAGCGGACA
*** * * * * * * *
43436 CGTTTGCCAAAAATTGTTCGAGTCTTATACTCCTTGAAAGAAAAGGGAACAGACC
1 CGTTTGTTGAAGATT-TTCGAGTCTTATACTCCCTGAAGGAATAGGGAGCGGACA
43491 CGTTAT-TTGAAGATTTT
1 CGTT-TGTTGAAGATTTT
43508 TCAAGTATCA
Statistics
Matches: 308, Mismatches: 28, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
51 63 0.20
54 4 0.01
55 239 0.78
56 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (54 bp):
CGTTTGTTGAAGATTTTCGAGTCTTATACTCCCTGAAGGAATAGGGAGCGGACA
Found at i:53218 original size:30 final size:30
Alignment explanation
Indices: 53183--53517 Score: 286
Period size: 30 Copynumber: 11.2 Consensus size: 30
53173 GTGGTTGTTA
*
53183 TGAAAGTGGTGGTGTAGAAGTGGATAATGC
1 TGAAAGTGGTGGTGTAGAAATGGATAATGC
*
53213 TGAAAGTGGTGGTGTAGAAATAGATAATGC
1 TGAAAGTGGTGGTGTAGAAATGGATAATGC
* * *
53243 TGAAAGTGGTGGTGCATAAATGGATACTGC
1 TGAAAGTGGTGGTGTAGAAATGGATAATGC
** * *
53273 TGAAA-TGGGTCATGTAGAAACGGATAATGT
1 TGAAAGT-GGTGGTGTAGAAATGGATAATGC
* * * *
53303 TGAAA-TGGGTAGTGTTGAAAGGGAAAATGC
1 TGAAAGT-GGTGGTGTAGAAATGGATAATGC
* * * *
53333 TAAAAGTGGTGGTATAGAAATGAATAGTGC
1 TGAAAGTGGTGGTGTAGAAATGGATAATGC
*
53363 TGAAAGTGCTGGTGTAGAAATGGATAATGC
1 TGAAAGTGGTGGTGTAGAAATGGATAATGC
* * *
53393 TGAAA-TGGGTAGTGTAGAAAGGGACAATGC
1 TGAAAGT-GGTGGTGTAGAAATGGATAATGC
* *
53423 TGAAA-TGGGTAGTGTAGAAA-GGAACAATGC
1 TGAAAGT-GGTGGTGTAGAAATGG-ATAATGC
* * * * **
53453 TGAAA-TGGGTAGTGTTGAAAGGGACAATAT
1 TGAAAGT-GGTGGTGTAGAAATGGATAATGC
* * *
53483 TGAAAGTGTTGGAGTAGAAATGGATAATGT
1 TGAAAGTGGTGGTGTAGAAATGGATAATGC
53513 TGAAA
1 TGAAA
53518 TGAGTAATGT
Statistics
Matches: 253, Mismatches: 46, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
29 4 0.02
30 245 0.97
31 4 0.02
ACGTcount: A:0.36, C:0.05, G:0.34, T:0.25
Consensus pattern (30 bp):
TGAAAGTGGTGGTGTAGAAATGGATAATGC
Found at i:53396 original size:120 final size:120
Alignment explanation
Indices: 53208--53541 Score: 352
Period size: 120 Copynumber: 2.8 Consensus size: 120
53198 AGAAGTGGAT
* * * * *
53208 AATGCTGAAAGTGGTGGTGTAGAAATAGATAATGCTGAAAGTGGTGGTGCATAAATGGATACTGC
1 AATGCTAAAAGTGGTGGTATAGAAATAGATAATGCTGAAAGTGCTGGTGCAGAAATGGATAATGC
* * *
53273 TGAAATGGGTCA-TGTAGAAACGGATAATGTTGAAATGGGTAGTGTTGAAAGGGAA-
66 TGAAATGGGT-AGTGTAGAAACGGACAATGCTGAAATGGGTAGTGTAGAAA-GGAAC
* *
53328 AATGCTAAAAGTGGTGGTATAGAAAT-GAATAGTGCTGAAAGTGCTGGTGTAGAAATGGATAATG
1 AATGCTAAAAGTGGTGGTATAGAAATAG-ATAATGCTGAAAGTGCTGGTGCAGAAATGGATAATG
*
53392 CTGAAATGGGTAGTGTAGAAAGGGACAATGCTGAAATGGGTAGTGTAGAAAGGAAC
65 CTGAAATGGGTAGTGTAGAAACGGACAATGCTGAAATGGGTAGTGTAGAAAGGAAC
* * * * ** * ** * * *
53448 AATGCTGAAA-TGGGTAGTGTTGAAAGGGACAATATTGAAAGTGTTGGAGTAGAAATGGATAATG
1 AATGCTAAAAGT-GGTGGTATAGAAATAGATAATGCTGAAAGTGCTGGTGCAGAAATGGATAATG
* * * * *
53512 TTGAAATGAGTAATGTTGAAAGGGACAATG
65 CTGAAATGGGTAGTGTAGAAACGGACAATG
53542 AGAAAGACAA
Statistics
Matches: 183, Mismatches: 26, Indels: 10
0.84 0.12 0.05
Matches are distributed among these distances:
119 7 0.04
120 175 0.96
121 1 0.01
ACGTcount: A:0.37, C:0.05, G:0.33, T:0.25
Consensus pattern (120 bp):
AATGCTAAAAGTGGTGGTATAGAAATAGATAATGCTGAAAGTGCTGGTGCAGAAATGGATAATGC
TGAAATGGGTAGTGTAGAAACGGACAATGCTGAAATGGGTAGTGTAGAAAGGAAC
Found at i:53517 original size:15 final size:15
Alignment explanation
Indices: 53379--53532 Score: 64
Period size: 15 Copynumber: 10.3 Consensus size: 15
53369 TGCTGGTGTA
*
53379 GAAATGGATAATGCT
1 GAAATGGATAATGTT
* * *
53394 GAAATGGGTAGTGTA
1 GAAATGGATAATGTT
* * *
53409 GAAAGGGACAATGCT
1 GAAATGGATAATGTT
* * *
53424 GAAATGGGTAGTGTA
1 GAAATGGATAATGTT
* *
53439 GAAA-GGAACAATGCT
1 GAAATGG-ATAATGTT
* *
53454 GAAATGGGTAGTGTT
1 GAAATGGATAATGTT
* * *
53469 GAAAGGGACAATATT
1 GAAATGGATAATGTT
* * *
53484 GAAA-GTGTTGGA-GTA
1 GAAATG-GAT-AATGTT
53499 GAAATGGATAATGTT
1 GAAATGGATAATGTT
53514 GAAAT-GAGTAATGTT
1 GAAATGGA-TAATGTT
53529 GAAA
1 GAAA
53533 GGGACAATGA
Statistics
Matches: 94, Mismatches: 38, Indels: 14
0.64 0.26 0.10
Matches are distributed among these distances:
14 6 0.06
15 84 0.89
16 4 0.04
ACGTcount: A:0.39, C:0.04, G:0.32, T:0.25
Consensus pattern (15 bp):
GAAATGGATAATGTT
Found at i:55334 original size:10 final size:10
Alignment explanation
Indices: 55315--55394 Score: 61
Period size: 10 Copynumber: 7.5 Consensus size: 10
55305 TTAATATTTC
*
55315 GTTGAGATAT
1 GTTGAAATAT
*
55325 GTTGACATAT
1 GTTGAAATAT
*
55335 GCTATCAAATAT
1 G-T-TGAAATAT
*
55347 GTTAAGATATATT
1 GTT--GAAATA-T
*
55360 GCTGAAATAT
1 GTTGAAATAT
*
55370 GTTGAGATAT
1 GTTGAAATAT
55380 GTTGAAATAT
1 GTTGAAATAT
55390 GTTGA
1 GTTGA
55395 GACCATTTGA
Statistics
Matches: 55, Mismatches: 10, Indels: 10
0.73 0.13 0.13
Matches are distributed among these distances:
10 34 0.62
11 7 0.13
12 11 0.20
13 3 0.05
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.39
Consensus pattern (10 bp):
GTTGAAATAT
Found at i:56628 original size:22 final size:21
Alignment explanation
Indices: 56596--56636 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
56586 CTTGCAGTTC
56596 AATGCAAAATGAAGAAAAATTA
1 AATGCAAAATGAA-AAAAATTA
* *
56618 AATGCACAATGCAAAAAAT
1 AATGCAAAATGAAAAAAAT
56637 CAAAGTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.61, C:0.10, G:0.12, T:0.17
Consensus pattern (21 bp):
AATGCAAAATGAAAAAAATTA
Found at i:56735 original size:15 final size:15
Alignment explanation
Indices: 56715--56745 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
56705 AAACACATAC
*
56715 AAACTTCTATTACAA
1 AAACTTCCATTACAA
56730 AAACTTCCATTACAA
1 AAACTTCCATTACAA
56745 A
1 A
56746 GCTTTTAATC
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:0.48, C:0.23, G:0.00, T:0.29
Consensus pattern (15 bp):
AAACTTCCATTACAA
Found at i:58487 original size:18 final size:18
Alignment explanation
Indices: 58461--58504 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
58451 TAATGGAATG
*
58461 TAAGATTACCAGTGGGAA
1 TAAGATTACCAGTGGAAA
* *
58479 TAGGATTACCGGTGGAAA
1 TAAGATTACCAGTGGAAA
58497 TAAGATTA
1 TAAGATTA
58505 ATGAGAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.39, C:0.09, G:0.27, T:0.25
Consensus pattern (18 bp):
TAAGATTACCAGTGGAAA
Found at i:60000 original size:22 final size:22
Alignment explanation
Indices: 59969--60032 Score: 96
Period size: 21 Copynumber: 3.0 Consensus size: 22
59959 TATATGAGAT
59969 TTGTCCCGAAGGACCTATGAA-
1 TTGTCCCGAAGGACCTATGAAG
*
59990 TATGTTCCGAAGGACCTAT-AAG
1 T-TGTCCCGAAGGACCTATGAAG
60012 TTGTCCCGAAGGACCTATGAA
1 TTGTCCCGAAGGACCTATGAA
60033 ACCCTCGAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
21 19 0.50
22 19 0.50
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (22 bp):
TTGTCCCGAAGGACCTATGAAG
Found at i:61640 original size:21 final size:21
Alignment explanation
Indices: 61604--61647 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 21
61594 TTAAATTTAA
61604 AAAATATATTCAAATTTT-TT
1 AAAATATATTCAAATTTTCTT
61624 AAAA-ATATTCACTAATTTTCTT
1 AAAATATATTCA--AATTTTCTT
61646 AA
1 AA
61648 GGAATTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 7 0.33
20 4 0.19
21 6 0.29
22 4 0.19
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (21 bp):
AAAATATATTCAAATTTTCTT
Found at i:62120 original size:18 final size:18
Alignment explanation
Indices: 62070--62109 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
62060 TAAATTTGTC
* *
62070 ATATAATTAATTA-TAAA
1 ATATTATTAAATATTAAA
62087 ATATTATTAAATATTAAA
1 ATATTATTAAATATTAAA
62105 ATATT
1 ATATT
62110 TATTCAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATATTATTAAATATTAAA
Found at i:65468 original size:21 final size:21
Alignment explanation
Indices: 65444--65483 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
65434 AAGAGTTTAT
65444 TTTCAAAA-TACAAAAATGATA
1 TTTCAAAATTA-AAAAATGATA
65465 TTTCAAAATTAAAAAATGA
1 TTTCAAAATTAAAAAATGA
65484 AAATAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.30
Consensus pattern (21 bp):
TTTCAAAATTAAAAAATGATA
Found at i:69331 original size:23 final size:23
Alignment explanation
Indices: 69288--69350 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
69278 TTTCTGGCAG
*
69288 GAGGAATCGATACCCCC-TTGAA
1 GAGGAATCGATTCCCCCTTTGAA
* *
69310 GGGGAACCGATTCCCCCTTTGAA
1 GAGGAATCGATTCCCCCTTTGAA
* *
69333 TAGGAATCAATTCCCCCT
1 GAGGAATCGATTCCCCCT
69351 GGAGGGAATC
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
22 14 0.42
23 19 0.58
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.22
Consensus pattern (23 bp):
GAGGAATCGATTCCCCCTTTGAA
Found at i:70991 original size:17 final size:17
Alignment explanation
Indices: 70969--71012 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
70959 CATTTATCAA
70969 CAACAAGAAACAACAAT
1 CAACAAGAAACAACAAT
70986 CAACAAGAAACAACAAT
1 CAACAAGAAACAACAAT
*
71003 TAACAA-AAAC
1 CAACAAGAAAC
71013 CAAGAGAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 4 0.15
17 22 0.85
ACGTcount: A:0.66, C:0.23, G:0.05, T:0.07
Consensus pattern (17 bp):
CAACAAGAAACAACAAT
Found at i:77700 original size:11 final size:11
Alignment explanation
Indices: 77684--77724 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
77674 TTTTTTAAAA
77684 TAAAATATTTT
1 TAAAATATTTT
77695 TAAAATATCATTT
1 TAAAATAT--TTT
*
77708 AAAAATATTTT
1 TAAAATATTTT
77719 TAAAAT
1 TAAAAT
77725 CTAAACGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 16 0.62
13 10 0.38
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (11 bp):
TAAAATATTTT
Found at i:79182 original size:36 final size:35
Alignment explanation
Indices: 79101--79239 Score: 233
Period size: 35 Copynumber: 3.9 Consensus size: 35
79091 AGATGAACAT
*
79101 TTGAATCGAAAGTGTTGATGCTTCCTTTCGTTCAC
1 TTGAATCGAAAGTGTCGATGCTTCCTTTCGTTCAC
* *
79136 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCTTC
1 TTGAATCGAAAGTGTCGATGCTTCCTTTCGTTC-AC
*
79172 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCAC
1 TTGAATCGAAAGTGTCGATGCTTCCTTTCGTTCAC
79207 TTGAATCGAAAGTGTCGATGCTTCCTTTCGTTC
1 TTGAATCGAAAGTGTCGATGCTTCCTTTCGTTC
79240 TTCTTATTCA
Statistics
Matches: 96, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
35 64 0.67
36 32 0.33
ACGTcount: A:0.19, C:0.23, G:0.20, T:0.38
Consensus pattern (35 bp):
TTGAATCGAAAGTGTCGATGCTTCCTTTCGTTCAC
Found at i:79217 original size:71 final size:71
Alignment explanation
Indices: 79101--79244 Score: 261
Period size: 71 Copynumber: 2.0 Consensus size: 71
79091 AGATGAACAT
* *
79101 TTGAATCGAAAGTGTTGATGCTTCCTTTCGTTCACTTGAATCGAAAGTGCCGATGCTTCCTTTCG
1 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCACTTGAATCGAAAGTGCCGATGCTTCCTTTCG
79166 TTCTTC
66 TTCTTC
*
79172 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCACTTGAATCGAAAGTGTCGATGCTTCCTTTCG
1 TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCACTTGAATCGAAAGTGCCGATGCTTCCTTTCG
79237 TTCTTC
66 TTCTTC
79243 TT
1 TT
79245 ATTCACCTTC
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
71 70 1.00
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.40
Consensus pattern (71 bp):
TTGAATCGAAAGTGTCGATGCTTCCTTCCGTTCACTTGAATCGAAAGTGCCGATGCTTCCTTTCG
TTCTTC
Found at i:80652 original size:22 final size:22
Alignment explanation
Indices: 80603--80644 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
80593 AACAAATTTT
80603 GAAAAAATATGTTCTATTTGAG
1 GAAAAAATATGTTCTATTTGAG
80625 GAAAAAATAT-TTCATATTTG
1 GAAAAAATATGTTC-TATTTG
80645 TGTTAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (22 bp):
GAAAAAATATGTTCTATTTGAG
Found at i:82430 original size:29 final size:29
Alignment explanation
Indices: 82327--82501 Score: 136
Period size: 30 Copynumber: 5.9 Consensus size: 29
82317 TTATAATTAC
* * *
82327 AAGGACTAACATGGTAAAAATA-ACAACTT
1 AAGGACTAAAATAGTAAAAACAGA-AACTT
** * * *
82356 AAAGGGTTAAAATAGTTAAAATAGAAAATT
1 -AAGGACTAAAATAGTAAAAACAGAAACTT
**
82386 AGAGGACTAAAATAGTAATTACAGAAACTT
1 A-AGGACTAAAATAGTAAAAACAGAAACTT
* * *
82416 AAGGACTAAATTAGTAAAAACATAAACCT
1 AAGGACTAAAATAGTAAAAACAGAAACTT
* * *
82445 AAGGAACTAAAATGGCAAAAATAGAAACTT
1 AAGG-ACTAAAATAGTAAAAACAGAAACTT
* * *
82475 AGGGACTAAAACAGTAAAAACAAAAAC
1 AAGGACTAAAATAGTAAAAACAGAAAC
82502 CTAGATTACT
Statistics
Matches: 112, Mismatches: 30, Indels: 7
0.75 0.20 0.05
Matches are distributed among these distances:
29 46 0.41
30 65 0.58
31 1 0.01
ACGTcount: A:0.55, C:0.10, G:0.15, T:0.19
Consensus pattern (29 bp):
AAGGACTAAAATAGTAAAAACAGAAACTT
Found at i:82456 original size:59 final size:59
Alignment explanation
Indices: 82391--82504 Score: 147
Period size: 59 Copynumber: 1.9 Consensus size: 59
82381 AAATTAGAGG
* ** ** *
82391 ACTAAAATAGTAATTACAGAAACTTAAGGACTAAATTAGTAAAAACATAAACCTAAGGA
1 ACTAAAATAGCAAAAACAGAAACTTAAGGACTAAAACAGTAAAAACAAAAACCTAAGGA
* * *
82450 ACTAAAATGGCAAAAATAGAAACTTAGGGACTAAAACAGTAAAAACAAAAACCTA
1 ACTAAAATAGCAAAAACAGAAACTTAAGGACTAAAACAGTAAAAACAAAAACCTA
82505 GATTACTAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 46 1.00
ACGTcount: A:0.56, C:0.13, G:0.12, T:0.18
Consensus pattern (59 bp):
ACTAAAATAGCAAAAACAGAAACTTAAGGACTAAAACAGTAAAAACAAAAACCTAAGGA
Found at i:82513 original size:59 final size:58
Alignment explanation
Indices: 82408--82533 Score: 150
Period size: 59 Copynumber: 2.2 Consensus size: 58
82398 TAGTAATTAC
** * **
82408 AGAAACTTAAGGACTAAATTAGTAAAAACATAAACCTAAGGAACTAAAATGGCAAAAAT
1 AGAAACTTAAGGACTAAAACAGTAAAAACAAAAACCTAAGGAACTAAAAT-AAAAAAAT
*
82467 AGAAACTTAGGGACTAAAACAGTAAAAACAAAAACCT-A-GATTACTAAAATAAAAAAAT
1 AGAAACTTAAGGACTAAAACAGTAAAAACAAAAACCTAAGGA--ACTAAAATAAAAAAAT
82525 AGAAA-TTAA
1 AGAAACTTAA
82534 AAGGGTTAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
57 5 0.09
58 12 0.21
59 41 0.71
ACGTcount: A:0.59, C:0.11, G:0.12, T:0.18
Consensus pattern (58 bp):
AGAAACTTAAGGACTAAAACAGTAAAAACAAAAACCTAAGGAACTAAAATAAAAAAAT
Found at i:84025 original size:13 final size:13
Alignment explanation
Indices: 84014--84055 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
84004 TAATATAATG
84014 TAATATATTAATAA
1 TAATA-ATTAATAA
84028 TAATAATTAATAA
1 TAATAATTAATAA
84041 -ACATAA-TAATAA
1 TA-ATAATTAATAA
84053 TAA
1 TAA
84056 AAAGAAATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 8 0.31
13 13 0.50
14 5 0.19
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (13 bp):
TAATAATTAATAA
Found at i:84707 original size:31 final size:29
Alignment explanation
Indices: 84614--84707 Score: 95
Period size: 28 Copynumber: 3.2 Consensus size: 29
84604 TAGAGATTTG
* * *
84614 GTTTCAAGAGAAACCAACTCAAATAT-TT
1 GTTTCAAGAAAAACAAACTCAAAGATATT
* *
84642 GTTTCAA-AAGAAGCAGACTCAAAGAT-TT
1 GTTTCAAGAA-AAACAAACTCAAAGATATT
84670 GTTTCAAGAAAAACAAACTCAAAGATGATGT
1 GTTTCAAGAAAAACAAACTCAAAGAT-AT-T
84701 GTTTCAA
1 GTTTCAA
84708 AAGCAACTAT
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
27 1 0.02
28 42 0.78
29 2 0.04
30 1 0.02
31 8 0.15
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.27
Consensus pattern (29 bp):
GTTTCAAGAAAAACAAACTCAAAGATATT
Found at i:84987 original size:66 final size:67
Alignment explanation
Indices: 84900--85052 Score: 181
Period size: 65 Copynumber: 2.3 Consensus size: 67
84890 GATGGTTTTA
* * *
84900 TTTCAAGAGAAACAGACTCAAATAAAAGTGCTT-TCAAAAGAAATTGTCTC-A-AGAGACAAAAC
1 TTTCCAGAGAAACAGACTCAAA-AAAA-TGCTTCTCAAAAGAAACTATCTCAAGAGAGACAAAAC
84962 TTTG
64 TTTG
* ** *
84966 TTTCCAGAGAAACAGACTC--AAAGATTTTTCTCAAAAGAAACTATCTCAAGAGAGACAAAATTT
1 TTTCCAGAGAAACAGACTCAAAAAAATGCTTCTCAAAAGAAACTATCTCAAGAGAGACAAAACTT
85029 TG
66 TG
*
85031 TTTCCAAAGAAACAGACTCAAA
1 TTTCCAGAGAAACAGACTCAAA
85053 GATGGGTTAC
Statistics
Matches: 74, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
62 3 0.04
63 18 0.24
64 2 0.03
65 32 0.43
66 18 0.24
67 1 0.01
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.24
Consensus pattern (67 bp):
TTTCCAGAGAAACAGACTCAAAAAAATGCTTCTCAAAAGAAACTATCTCAAGAGAGACAAAACTT
TG
Found at i:85001 original size:63 final size:65
Alignment explanation
Indices: 84933--85055 Score: 196
Period size: 65 Copynumber: 1.9 Consensus size: 65
84923 AAAAGTGCTT
* * *
84933 TCAAAAGAAATTGTCTC-A-AGAGACAAAACTTTGTTTCCAGAGAAACAGACTCAAAGATTTTTC
1 TCAAAAGAAACTATCTCAAGAGAGACAAAACTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTC
*
84996 TCAAAAGAAACTATCTCAAGAGAGACAAAATTTTGTTTCCAAAGAAACAGACTCAAAGAT
1 TCAAAAGAAACTATCTCAAGAGAGACAAAACTTTGTTTCCAAAGAAACAGACTCAAAGAT
85056 GGGTTACGTC
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
63 15 0.28
64 1 0.02
65 38 0.70
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.24
Consensus pattern (65 bp):
TCAAAAGAAACTATCTCAAGAGAGACAAAACTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTC
Found at i:85238 original size:121 final size:118
Alignment explanation
Indices: 84951--85281 Score: 291
Period size: 120 Copynumber: 2.7 Consensus size: 118
84941 AATTGTCTCA
* * * *
84951 AGAGACAAAACTTTGTTTC-CAGAGAAACAGACTCAAAGATTTTTCTCAAAAGAAACTATCTCAA
1 AGAGACCAAA-TTTGTTTCAAAGA-AAACAGACTCAAAGATTTTTTTC-AAAGAAACTGTCTCAA
* * *
85015 GAGAGACAAAATTTTGTTTCCAAAGAAACAGACTCAAAGATGGGTTACGTCTTAAG
63 GAGAGACAAAACTTTGTTTTCAAAGAAACAGACTCAAAGATGGATTACGTCTTAAG
* * * *
85071 TGAGACGAAATTTGTTTCAAAGAAAACA-ATCTCAAAGGTTGGTTTTTCATTAGAAACTGTCTCA
1 AGAGACCAAATTTGTTTCAAAGAAAACAGA-CTCAAAGATT--TTTTTCA-AAGAAACTGTCTCA
* * * *
85135 AGAGAGACAAAA-TTTGTTTTTAAAGAAATATACTCAAAGAT-GATTTC-T-TTAAG
62 AGAGAGACAAAACTTTGTTTTCAAAGAAACAGACTCAAAGATGGATTACGTCTTAAG
* *
85188 AGAAACAGACTCAAAGGTTT-TTTCAAA-AGGAACAGACTCAAAGATTTTTTTTCCAAAGAAATT
1 AG----AGAC-CAAA--TTTGTTTCAAAGA-AAACAGACTCAAAGA-TTTTTTT-CAAAGAAACT
*
85251 GTCTCCAGAGAGACAAAACTTTGTTTTCAAA
56 GTCTCAAGAGAGACAAAACTTTGTTTTCAAA
85282 TTCTCAAAAT
Statistics
Matches: 173, Mismatches: 21, Indels: 31
0.77 0.09 0.14
Matches are distributed among these distances:
117 6 0.03
118 2 0.01
119 26 0.15
120 37 0.21
121 33 0.19
122 32 0.18
123 31 0.18
124 6 0.03
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (118 bp):
AGAGACCAAATTTGTTTCAAAGAAAACAGACTCAAAGATTTTTTTCAAAGAAACTGTCTCAAGAG
AGACAAAACTTTGTTTTCAAAGAAACAGACTCAAAGATGGATTACGTCTTAAG
Found at i:85680 original size:4 final size:4
Alignment explanation
Indices: 85636--85667 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
85626 TTATGTATCC
85636 TGTA TGTA TG-- TGTA TGTA TGTA TGTA TGTA TG
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TG
85668 AGTTGATGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
2 2 0.08
4 24 0.92
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:89553 original size:32 final size:32
Alignment explanation
Indices: 89517--89629 Score: 208
Period size: 32 Copynumber: 3.5 Consensus size: 32
89507 GTCATGATAT
89517 CTACCCGAACATGCTTTAATTAAATAACAATC
1 CTACCCGAACATGCTTTAATTAAATAACAATC
89549 CTACCCGAACATGCTTTAATTAAATAACAATC
1 CTACCCGAACATGCTTTAATTAAATAACAATC
*
89581 CTACCCGAACATGTTTTAATTAAATAACAATC
1 CTACCCGAACATGCTTTAATTAAATAACAATC
*
89613 CTACCTGAACATGCTTT
1 CTACCCGAACATGCTTT
89630 CTACCTATAA
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 78 1.00
ACGTcount: A:0.38, C:0.25, G:0.07, T:0.30
Consensus pattern (32 bp):
CTACCCGAACATGCTTTAATTAAATAACAATC
Found at i:91416 original size:30 final size:30
Alignment explanation
Indices: 91380--91534 Score: 99
Period size: 30 Copynumber: 5.2 Consensus size: 30
91370 CTTAAAGGGT
91380 TAAAATAGTAAAAATCGAAAATTAGAGGAC
1 TAAAATAGTAAAAATCGAAAATTAGAGGAC
** * *
91410 TAAAATAGTAATTATAGAAACTTA-AGGAC
1 TAAAATAGTAAAAATCGAAAATTAGAGGAC
* * *
91439 TAAATTAG-AAAAA-CCATAAACCTA-AGGAAC
1 TAAAATAGTAAAAATCGA-AAA-TTAGAGG-AC
* * *
91469 TAAAATGGGAAAAA-C-ATAAACTTAG-GGAA
1 TAAAATAGTAAAAATCGA-AAA-TTAGAGGAC
* **
91498 TAAAATAGTAAAAATAGAAACCTAGAGGAC
1 TAAAATAGTAAAAATCGAAAATTAGAGGAC
91528 TAAAATA
1 TAAAATA
91535 AAAAAATAGA
Statistics
Matches: 96, Mismatches: 21, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
27 1 0.01
28 5 0.05
29 33 0.34
30 50 0.52
31 7 0.07
ACGTcount: A:0.56, C:0.09, G:0.15, T:0.20
Consensus pattern (30 bp):
TAAAATAGTAAAAATCGAAAATTAGAGGAC
Found at i:91541 original size:29 final size:30
Alignment explanation
Indices: 91380--91546 Score: 126
Period size: 29 Copynumber: 5.7 Consensus size: 30
91370 CTTAAAGGGT
* * **
91380 TAAAATAGTAAAAATCGAAAATTAGAGGAC
1 TAAAATAGAAAAAATAGAAACCTAGAGGAC
* ** *
91410 TAAAATAGTAATTATAGAAACTTA-AGGAC
1 TAAAATAGAAAAAATAGAAACCTAGAGGAC
* ** *
91439 TAAATTAGAAAAACCATAAACCTA-AGGAAC
1 TAAAATAGAAAAAATAGAAACCTAGAGG-AC
* * * * * *
91469 TAAAATGGGAAAAACATAAACTTAG-GGAA
1 TAAAATAGAAAAAATAGAAACCTAGAGGAC
*
91498 TAAAATAGTAAAAATAGAAACCTAGAGGAC
1 TAAAATAGAAAAAATAGAAACCTAGAGGAC
91528 TAAAATA-AAAAAATAGAAA
1 TAAAATAGAAAAAATAGAAA
91547 TTAAAAGGGT
Statistics
Matches: 109, Mismatches: 25, Indels: 7
0.77 0.18 0.05
Matches are distributed among these distances:
29 56 0.51
30 53 0.49
ACGTcount: A:0.58, C:0.08, G:0.14, T:0.19
Consensus pattern (30 bp):
TAAAATAGAAAAAATAGAAACCTAGAGGAC
Found at i:92451 original size:19 final size:18
Alignment explanation
Indices: 92427--92464 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
92417 AATGTTTCAA
*
92427 TTGGGTTTTCTCATTTTTT
1 TTGGGTTATCTC-TTTTTT
92446 TTGGGTTATCTCTTTTTT
1 TTGGGTTATCTCTTTTTT
92464 T
1 T
92465 GTTTAGGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.05, C:0.11, G:0.16, T:0.68
Consensus pattern (18 bp):
TTGGGTTATCTCTTTTTT
Found at i:93054 original size:13 final size:13
Alignment explanation
Indices: 93043--93096 Score: 60
Period size: 13 Copynumber: 4.2 Consensus size: 13
93033 TAATATAATG
93043 TAATATATTAATAA
1 TAATA-ATTAATAA
93057 TAATAATTAATAA
1 TAATAATTAATAA
*
93070 AACATAA-TAATAA
1 TA-ATAATTAATAA
93083 TAA-AATTAA-AA
1 TAATAATTAATAA
93094 TAA
1 TAA
93097 ATAAAAAGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
11 7 0.19
12 4 0.11
13 16 0.44
14 9 0.25
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (13 bp):
TAATAATTAATAA
Found at i:93076 original size:17 final size:16
Alignment explanation
Indices: 93056--93087 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
93046 TATATTAATA
93056 ATAATAATTAATAAAAC
1 ATAATAA-TAATAAAAC
93073 ATAATAATAATAAAA
1 ATAATAATAATAAAA
93088 TTAAAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (16 bp):
ATAATAATAATAAAAC
Found at i:93096 original size:20 final size:19
Alignment explanation
Indices: 93052--93096 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
93042 GTAATATATT
*
93052 AATAATAATAATTAATAAA
1 AATAATAATAATAAATAAA
*
93071 ACATAATAATAATAAAATTAA
1 A-ATAATAATAAT-AAATAAA
93092 AATAA
1 AATAA
93097 ATAAAAAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 15 0.68
21 6 0.27
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (19 bp):
AATAATAATAATAAATAAA
Found at i:94451 original size:20 final size:20
Alignment explanation
Indices: 94426--94479 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
94416 GGTTCACGGG
*
94426 ATGTAAGATTACTAGT-GAGA
1 ATGTAAGATTACCAGTAG-GA
94446 ATGTAAGATTACCAGTAGGA
1 ATGTAAGATTACCAGTAGGA
94466 ATGTAAGATTACCA
1 ATGTAAGATTACCA
94480 AGGAATAAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (20 bp):
ATGTAAGATTACCAGTAGGA
Found at i:94490 original size:16 final size:18
Alignment explanation
Indices: 94428--94493 Score: 64
Period size: 20 Copynumber: 3.6 Consensus size: 18
94418 TTCACGGGAT
* *
94428 GTAAGATTACTAGTGAGAA
1 GTAAGATTACCAGAG-GAA
94447 TGTAAGATTACCAGTAGGAA
1 -GTAAGATTACCAG-AGGAA
94467 TGTAAGATTACCA-AGGAA
1 -GTAAGATTACCAGAGGAA
94485 -TAAGATTAC
1 GTAAGATTAC
94494 TGGGAATGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
16 9 0.21
18 5 0.12
20 28 0.65
21 1 0.02
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.26
Consensus pattern (18 bp):
GTAAGATTACCAGAGGAA
Found at i:94704 original size:35 final size:37
Alignment explanation
Indices: 94633--94705 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 37
94623 ATTGAAAAAT
* * *
94633 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATAATTTCTTTAAAAAATTAAAAATCATAAA
*
94670 ATTTATATAATTT-TTTACAAAATTAAAAAT-ATAAA
1 ATTTATATAATTTCTTTAAAAAATTAAAAATCATAAA
94705 A
1 A
94706 AGGTTTAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 6 0.19
36 14 0.44
37 12 0.38
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (37 bp):
ATTTATATAATTTCTTTAAAAAATTAAAAATCATAAA
Found at i:98502 original size:24 final size:24
Alignment explanation
Indices: 98468--98514 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
98458 TTCGGATCCA
* * *
98468 AATATTCAAAACTTCATATATCAG
1 AATATTAAAAAATTCAAATATCAG
98492 AATATTAAAAAATTCAAATATCA
1 AATATTAAAAAATTCAAATATCA
98515 AAATTTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.53, C:0.13, G:0.02, T:0.32
Consensus pattern (24 bp):
AATATTAAAAAATTCAAATATCAG
Found at i:98712 original size:16 final size:18
Alignment explanation
Indices: 98688--98722 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
98678 AAAAAAAAGA
98688 AAAATTATTTA-AAATTT
1 AAAATTATTTATAAATTT
98705 AAAA-TATTTATAAATTT
1 AAAATTATTTATAAATTT
98722 A
1 A
98723 TAAAATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AAAATTATTTATAAATTT
Found at i:98821 original size:18 final size:18
Alignment explanation
Indices: 98790--98828 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
98780 AAAACACTAT
*
98790 AAATATTATTAAAATTAA
1 AAATATTATTAAAAATAA
98808 AAATA-TATTAAAAAATAA
1 AAATATTATT-AAAAATAA
98826 AAA
1 AAA
98829 AAAACACTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AAATATTATTAAAAATAA
Found at i:99228 original size:16 final size:16
Alignment explanation
Indices: 99209--99242 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
99199 ACGTAACTTT
99209 TAAAAATTATATTTTC
1 TAAAAATTATATTTTC
99225 TAAAAATTATATTTTC
1 TAAAAATTATATTTTC
99241 TA
1 TA
99243 TTCTCCAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (16 bp):
TAAAAATTATATTTTC
Found at i:100107 original size:20 final size:20
Alignment explanation
Indices: 100082--100133 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
100072 GGTGACACAT
100082 TATTTGAAAATATCAGAAAA
1 TATTTGAAAATATCAGAAAA
100102 TATTTGAAAATATCAGAAAA
1 TATTTGAAAATATCAGAAAA
100122 TATTTGAAAATA
1 TATTTGAAAATA
100134 CGGTATTTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.54, C:0.04, G:0.10, T:0.33
Consensus pattern (20 bp):
TATTTGAAAATATCAGAAAA
Found at i:100130 original size:10 final size:10
Alignment explanation
Indices: 100082--100133 Score: 68
Period size: 10 Copynumber: 5.2 Consensus size: 10
100072 GGTGACACAT
100082 TATTTGAAAA
1 TATTTGAAAA
**
100092 TATCAGAAAA
1 TATTTGAAAA
100102 TATTTGAAAA
1 TATTTGAAAA
**
100112 TATCAGAAAA
1 TATTTGAAAA
100122 TATTTGAAAA
1 TATTTGAAAA
100132 TA
1 TA
100134 CGGTATTTAG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
10 34 1.00
ACGTcount: A:0.54, C:0.04, G:0.10, T:0.33
Consensus pattern (10 bp):
TATTTGAAAA
Found at i:103367 original size:14 final size:14
Alignment explanation
Indices: 103347--103379 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
103337 TTTTAAAATT
103347 AAATTATTTTTATA
1 AAATTATTTTTATA
*
103361 TAATTATTTTTATA
1 AAATTATTTTTATA
103375 AAATT
1 AAATT
103380 TTAAATTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
AAATTATTTTTATA
Found at i:103462 original size:16 final size:17
Alignment explanation
Indices: 103441--103475 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
103431 TTAAAAATAA
103441 TTAT-AAATATATATTT
1 TTATAAAATATATATTT
103457 TTATAAAATATATATTT
1 TTATAAAATATATATTT
103474 TT
1 TT
103476 TCCTTTCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTATAAAATATATATTT
Found at i:103538 original size:79 final size:76
Alignment explanation
Indices: 103360--103541 Score: 231
Period size: 79 Copynumber: 2.3 Consensus size: 76
103350 TTATTTTTAT
*
103360 ATAATTATTTTTATAAAATTTTAAATTATATATATATATTCTTTCTTACAATGTTTTTATTCATT
1 ATAATTATTTTTA-AAAATTTTAAATAATATATATATATTCTTTCTTACAATGTTTTTATTCATT
103425 TATCATTTAAAA
65 TATCATTTAAAA
*** * * * *
103437 ATAATTATAAATATATATTTTTATAA-AATATATATTTTTTCCTTTCTTACAATGTTTGTTATTC
1 ATAATTATTTTTA-AAAATTTTA-AATAATATATATATATT-CTTTCTTACAATGTTT-TTATTC
103501 ATTTATCATTTAAAA
62 ATTTATCATTTAAAA
103516 ATAATTATTTTTAAACAATTTTAAAT
1 ATAATTATTTTTAAA-AATTTTAAAT
103542 TTTAAATTAT
Statistics
Matches: 87, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
77 29 0.33
78 21 0.24
79 37 0.43
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (76 bp):
ATAATTATTTTTAAAAATTTTAAATAATATATATATATTCTTTCTTACAATGTTTTTATTCATTT
ATCATTTAAAA
Found at i:104723 original size:18 final size:17
Alignment explanation
Indices: 104700--104734 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
104690 TAATTTTAGT
*
104700 TTATAATAATGAATAATA
1 TTATAAT-ATAAATAATA
104718 TTATAATATAAATAATA
1 TTATAATATAAATAATA
104735 AATAACATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (17 bp):
TTATAATATAAATAATA
Found at i:106894 original size:34 final size:34
Alignment explanation
Indices: 106851--106919 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
106841 GGAACTCCTA
106851 AATGATGTTGTTGTCTTGACCGAACCACAACACG
1 AATGATGTTGTTGTCTTGACCGAACCACAACACG
106885 AATGATGTTGTTGTCTTGACCGAACCACAACACG
1 AATGATGTTGTTGTCTTGACCGAACCACAACACG
106919 A
1 A
106920 TCTAACTACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.26
Consensus pattern (34 bp):
AATGATGTTGTTGTCTTGACCGAACCACAACACG
Found at i:108317 original size:14 final size:15
Alignment explanation
Indices: 108300--108329 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
108290 GTATATAGAA
108300 AAAACTTAAAA-TTT
1 AAAACTTAAAAGTTT
108314 AAAACTTAAAAGTTT
1 AAAACTTAAAAGTTT
108329 A
1 A
108330 TAATACATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (15 bp):
AAAACTTAAAAGTTT
Found at i:111096 original size:21 final size:19
Alignment explanation
Indices: 111058--111096 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
111048 AAAGTTATGG
*
111058 AATAATTGTTTAATTACTC
1 AATAATTGTGTAATTACTC
111077 AATAATTGATGTACATTACT
1 AATAATTG-TGTA-ATTACT
111097 TGAAATTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (19 bp):
AATAATTGTGTAATTACTC
Found at i:112207 original size:11 final size:11
Alignment explanation
Indices: 112177--112207 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
112167 GAAAAGCTTT
112177 AGGAAGTTTAA
1 AGGAAGTTTAA
112188 AGAGAAGTTTAA
1 AG-GAAGTTTAA
112200 AGGAAGTT
1 AGGAAGTT
112208 AATAAATGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.45, C:0.00, G:0.29, T:0.26
Consensus pattern (11 bp):
AGGAAGTTTAA
Found at i:115849 original size:116 final size:116
Alignment explanation
Indices: 115645--115873 Score: 440
Period size: 116 Copynumber: 2.0 Consensus size: 116
115635 TCCGAAGATC
115645 ATTGCAGATACTTTCCAGTTACTTGATAAATTAGTTTTGGTTTTGATATATCCAAGATCAACATA
1 ATTGCAGATACTTTCCAGTTACTTGATAAATTAGTTTTGGTTTTGATATATCCAAGATCAACATA
*
115710 TTTATATATTAGTAGTAATTGGTGAGAGAGTTTAAAGGATTCAATATGCCA
66 TTTATATAATAGTAGTAATTGGTGAGAGAGTTTAAAGGATTCAATATGCCA
*
115761 ATTGCAGATACTTTCCAGTTACTTGATAAATTAGTTTTGGTTTTGATATATCCGAGATCAACATA
1 ATTGCAGATACTTTCCAGTTACTTGATAAATTAGTTTTGGTTTTGATATATCCAAGATCAACATA
115826 TTTATATAATAGTAGTAATTGGTGAGAGAGTTTAAAGGATTCAATATG
66 TTTATATAATAGTAGTAATTGGTGAGAGAGTTTAAAGGATTCAATATG
115874 ACAAGGATCA
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
116 111 1.00
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.39
Consensus pattern (116 bp):
ATTGCAGATACTTTCCAGTTACTTGATAAATTAGTTTTGGTTTTGATATATCCAAGATCAACATA
TTTATATAATAGTAGTAATTGGTGAGAGAGTTTAAAGGATTCAATATGCCA
Found at i:119710 original size:18 final size:18
Alignment explanation
Indices: 119687--119732 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
119677 GGCAAAATTT
119687 TATCGATACCGAAGTGGG
1 TATCGATACCGAAGTGGG
119705 TATCGATACCGAAGTGGG
1 TATCGATACCGAAGTGGG
119723 TATCGATACC
1 TATCGATACC
119733 ATAGAAGGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (18 bp):
TATCGATACCGAAGTGGG
Found at i:120328 original size:22 final size:22
Alignment explanation
Indices: 120303--120368 Score: 53
Period size: 22 Copynumber: 3.0 Consensus size: 22
120293 AGTCAAGGGT
*
120303 TCTAAGCGG-TCATTCGGGATAA
1 TCTAAGCGGTTC-TTCGGGACAA
* *
120325 TCTATGTGGTTCTTCGGGACAA
1 TCTAAGCGGTTCTTCGGGACAA
* * * *
120347 TCTACGTGGTCCTTCGGAACAA
1 TCTAAGCGGTTCTTCGGGACAA
120369 ATTTCTACAC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
22 35 0.95
23 2 0.05
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (22 bp):
TCTAAGCGGTTCTTCGGGACAA
Found at i:124010 original size:44 final size:45
Alignment explanation
Indices: 123931--124018 Score: 142
Period size: 44 Copynumber: 2.0 Consensus size: 45
123921 ATTTTCTTAT
123931 CAATATACTTACCATTTTATCCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCA-TTTATCCCATAAGCTCGTAAGCTTATTTTAC
* *
123977 CAATATACTTGCCA-TTATTCCATAAGCTCGTAAGCTTATTTT
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTT
124019 CATGATTACC
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
44 27 0.68
46 13 0.32
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.40
Consensus pattern (45 bp):
CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
Found at i:124228 original size:60 final size:59
Alignment explanation
Indices: 124119--124232 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 59
124109 GTAGTGCTAA
*
124119 ACCTGCACTAAGCTCACGCCATAGTGCTAATCCGGATAATACACTTAAGGTCGTGCCACC
1 ACCTACACTAAGCTCACGCCATAGTGCTAATCCGGATAATACAC-TAAGGTCGTGCCACC
* * *
124179 ACCTACACTAAGCTTACGCTATAGTGCTAATCCGGACATGATACA-TAAGGTCGT
1 ACCTACACTAAGCTCACGCCATAGTGCTAATCCGG--ATAATACACTAAGGTCGT
124233 ATCCACCTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
60 41 0.85
62 7 0.15
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (59 bp):
ACCTACACTAAGCTCACGCCATAGTGCTAATCCGGATAATACACTAAGGTCGTGCCACC
Found at i:133694 original size:44 final size:45
Alignment explanation
Indices: 133615--133702 Score: 142
Period size: 44 Copynumber: 2.0 Consensus size: 45
133605 AATTTCTTAT
133615 CAATATACTTACCATTTTATCCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCA-TTTATCCCATAAGCTCGTAAGCTTATTTTAC
* *
133661 CAATATACTTGCCA-TTATTCCATAAGCTCGTAAGCTTATTTT
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTT
133703 CATTATTACC
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
44 27 0.68
46 13 0.32
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.40
Consensus pattern (45 bp):
CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTAC
Found at i:133924 original size:61 final size:61
Alignment explanation
Indices: 133808--133924 Score: 146
Period size: 61 Copynumber: 1.9 Consensus size: 61
133798 GCTAAACATG
* * * *
133808 CACTATGCTTACGCCATTGTGCTAATCTGGACAATACACATAAGGTCATCCCCACCACCTA
1 CACTAAGCTTACGCCATAGTGCTAATCCGGACAATACACATAAGGTCATACCCACCACCTA
* * * *
133869 CACTAAGCTTACGCTATAGTGCTAATCCGGAC-ATGATACATAAGGTCGTATCCACC
1 CACTAAGCTTACGCCATAGTGCTAATCCGGACAAT-ACACATAAGGTCATACCCACC
133925 TTCCCTGCAC
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
60 2 0.04
61 45 0.96
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.25
Consensus pattern (61 bp):
CACTAAGCTTACGCCATAGTGCTAATCCGGACAATACACATAAGGTCATACCCACCACCTA
Found at i:137879 original size:27 final size:28
Alignment explanation
Indices: 137827--137881 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
137817 AGTTGATATT
* *
137827 GAAGCTTTAAAAGGTAAAAAAGATTAAG
1 GAAGCTTAAAAACGTAAAAAAGATTAAG
137855 GAAGCTTAAAAACG-AAGAAAA-ATTAAG
1 GAAGCTTAAAAACGTAA-AAAAGATTAAG
137882 TTACTAATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.56, C:0.05, G:0.20, T:0.18
Consensus pattern (28 bp):
GAAGCTTAAAAACGTAAAAAAGATTAAG
Found at i:138247 original size:14 final size:14
Alignment explanation
Indices: 138224--138258 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
138214 AAAGGTATCG
*
138224 GTACCAAAAGAACA
1 GTACCGAAAGAACA
138238 GTACCGAAAGAACA
1 GTACCGAAAGAACA
*
138252 ATACCGA
1 GTACCGA
138259 TACTATAGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.51, C:0.23, G:0.17, T:0.09
Consensus pattern (14 bp):
GTACCGAAAGAACA
Found at i:139041 original size:22 final size:22
Alignment explanation
Indices: 139016--139058 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
139006 GCGGTCATTT
* *
139016 GGGACAATCTATGTGGTCCTTC
1 GGGACAATATAAGTGGTCCTTC
*
139038 GGGATAATATAAGTGGTCCTT
1 GGGACAATATAAGTGGTCCTT
139059 GATGACAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (22 bp):
GGGACAATATAAGTGGTCCTTC
Found at i:146159 original size:114 final size:114
Alignment explanation
Indices: 145958--146181 Score: 294
Period size: 114 Copynumber: 2.0 Consensus size: 114
145948 ACTGAATATT
*
145958 GGTATCTTCAATTACAATGCTGATAGCATCGTATTCATCGATGTCATTGGCCGATTCAGTATCCT
1 GGTATCTTCAATTACAATGCTGATAGCATCGTATTCATCGATGTCATTGCCCGATTCAGTATCCT
* * * *
146023 CAGTAGAAGGTATAGTAAAAGAAGAAGTGGGAGTAGATTAATTACCATA
66 CAGTAGAAAGTAGAGTAAAAGAAGAAGTGGAAGTAGATGAATTACCATA
*
146072 GGTATCTT-ATATTACAATG-TTACTAGCATCGTATTCATCGATGTCATTGCCCGATTCAGTGTA
1 GGTATCTTCA-ATTACAATGCTGA-TAGCATCGTATTCATCGATGTCATTGCCCGATTCA--GTA
* * * *
146135 T-GT-GGTAGAAAGTGGAGTAGAAGAAGAAGTGGAAGTAGATGAATTAC
62 TCCTCAGTAGAAAGTAGAGTAAAAGAAGAAGTGGAAGTAGATGAATTAC
146182 ATTACTAAGT
Statistics
Matches: 96, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
113 3 0.03
114 88 0.92
115 1 0.01
116 4 0.04
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (114 bp):
GGTATCTTCAATTACAATGCTGATAGCATCGTATTCATCGATGTCATTGCCCGATTCAGTATCCT
CAGTAGAAAGTAGAGTAAAAGAAGAAGTGGAAGTAGATGAATTACCATA
Found at i:152959 original size:22 final size:22
Alignment explanation
Indices: 152914--152960 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
152904 TGTTTATTTG
* *
152914 TTTTGGAATTATTAATTTCTAT
1 TTTTGGAATTAATAATTTCAAT
152936 TTTTGGAAATTAATAATTT-AAT
1 TTTTGG-AATTAATAATTTCAAT
152958 TTT
1 TTT
152961 AATTGGTGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (22 bp):
TTTTGGAATTAATAATTTCAAT
Found at i:156687 original size:24 final size:24
Alignment explanation
Indices: 156641--156688 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
156631 TGATGTTATG
*
156641 ACTGAGGTGATAATTGATGCCCTT
1 ACTGAGGTGATAATTGATACCCTT
*
156665 ACTGAGGTGATAATTGGTACCCTT
1 ACTGAGGTGATAATTGATACCCTT
156689 CACTAAGTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (24 bp):
ACTGAGGTGATAATTGATACCCTT
Found at i:162038 original size:17 final size:17
Alignment explanation
Indices: 162016--162060 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
162006 ACTAGATAAC
162016 TAATTAAACTAATTCAT
1 TAATTAAACTAATTCAT
* *
162033 TCATTAAATTAATTCAT
1 TAATTAAACTAATTCAT
162050 TAATTAAACTA
1 TAATTAAACTA
162061 GCTTCTTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (17 bp):
TAATTAAACTAATTCAT
Found at i:163007 original size:821 final size:818
Alignment explanation
Indices: 161505--163030 Score: 2263
Period size: 821 Copynumber: 1.9 Consensus size: 818
161495 TATTAAATCA
** *
161505 GATTTTGGTTGCTACTGATTTGGATGGGTTAAGTGGTGACTAGGAGTTAATTTTAGTTGTTATTG
1 GATTTTGGTTGCTACTGATTTGGACAGGTTAAGTGGTGACTAGGAGTTAATCTTAGTTGTTATTG
* * *
161570 ATTAGCTTTAGGTGAGGCATTTGTGTGTGAGAATTTAATTGAGGTAAGTTGTTTACATCCGAGAA
66 ATTAGCTTTAGGTGAGGAATTTGTGTGTGAAAATTTAATTGAGGCAAGTTGTTTACATCCGAGAA
* * * * *
161635 GCTTTAAGAAGCTTATTCGAGCTTAATCTCAGAATTTCAAACAAGGTTCAGATTTTTGGAAGCCT
131 GATTAAAGAAACTTATTCGAGCTTAATCTCACAATTTCAAACAAGGTTCAGATTTTTGGAAGACT
* * * * *
161700 TTTGCAATCCAAAATAATAATCTCCACCATCATATTGAAGGCTGGGATGTCAAAAATGAACAACC
196 TTTGCAATCCAAAAGAATAACCTCCACCATCATACTGAAGGCTGGGACGTCAAAAAGGAACAACC
* ** *
161765 AAGTTAAAGGGAGGACTTCTATCTTTTACCTGTGCAAGAATTTACTTTAATAAATTTTCATGATT
261 AAGTTAAAGGGAGGACTTATATCTTAGACCTGTGCAAGAATTTACTTTAATAAATTTGCATGATT
** * *
161830 ATACTTGTGCACGAGATTAAATGAACATTTCTTAGTTTGAATGTTTAATTATGCATATTAGTTGA
326 ATACTTGTGCAAAAGATTAAATGAACATTACTTAGTTTGAATGTTTAATTATGCATATCAGTTGA
* * * *
161895 TTCAATTCACTATAATTAATTTGCATGGAAATTCATTAAAGCACAAGTTTATTAAAGCAATAGAA
391 TTCAATTCACTAGAATAAATTTCCATGGAAATTCATTAAAGCACAAGTTCATTAAAGCAATAGAA
* * *
161960 TTTTTATGAAGCTATTTTGTTTAAGTATGCTACTTTATTCAATAAAACTAGATAACTAATTAAAC
456 TTTTTATGAAGCTACTCTGCTTAAGTATGCTACTTTATTCAATAAAACTAGATAACTAATTAAAC
* * * * *
162025 TAATTCATTCATTAAATTAATTCATTAATTAAACTAGCTTCTTTAAATGTTTGCTTGACATGTTT
521 TAATTCATTCATTAAATTAATTCAATAATTAAACTAGATCCATTAAATGTTTGCATGACATGTTT
* * *
162090 GTTTTTAATTTGTTTTAAAGCATGAATGTGTACTCTTTTTTGTCTATGTGCATGAGGGAAGTTGA
586 GTTTTTAATTTGTTTTAAACCATGAATGTGTACTCTTTTGTGTCTATGTGCATAAGGGAAGTTGA
* * ** * *
162155 ATGGTCATAAGAAATGCAAGAATATCAGTAAGAATTTATTCTA-TTTTTGGATGCGATACAAAGT
651 ATAGTCATAACAAATAAAAGAATATCAGTAAGAATGTATTCCATTTTTTGGATGCGATACAAAGT
162219 GTTTGCTCTTTTACGTTAAATCATATTTTTCATTTGATTATGGTTTGGATATCAATTTCACGTAA
716 GTTTGCTCTTTTACGTTAAATCATATTTTTCATTTGATTATGGTTTGGATATCAATTTCACGTAA
162284 ACAAGTGTGCTTTTGGCGTTTTAGGTAATCCAATAATT
781 ACAAGTGTGCTTTTGGCGTTTTAGGTAATCCAATAATT
*
162322 GATTTTGGTTGCTACTGATTTGGACAGTTTAAGTGGTGACTAGGAGTTAATCTTAGTTGTTCA-T
1 GATTTTGGTTGCTACTGATTTGGACAGGTTAAGTGGTGACTAGGAGTTAATCTTAGTTGTT-ATT
* *
162386 GATTAGCTTTAGGTGAGGAATTTGTGTGTGAAAATTTGATTGAGGCAAGTTGTTTACATCTGAGA
65 GATTAGCTTTAGGTGAGGAATTTGTGTGTGAAAATTTAATTGAGGCAAGTTGTTTACATCCGAGA
* *
162451 AGATTAAATAAACTTATTCGAGCTTAATCTCACAATTTTAAATC-AGGTTCAGATTTTTGGAAGA
130 AGATTAAAGAAACTTATTCGAGCTTAATCTCACAATTTCAAA-CAAGGTTCAGATTTTTGGAAGA
* * *
162515 CTTTT-CAATCCAAAAGAATAACCTCCACCATCATACTGAAGGTTGGGACGTGAAGAAGGAACAA
194 CTTTTGCAATCCAAAAGAATAACCTCCACCATCATACTGAAGGCTGGGACGTCAAAAAGGAACAA
*
162579 CCAAGTTAAAGGGAGGACTTATATCTTAGACTTGTGCAAGAATTTACATGAGTGTTAATAAATTT
259 CCAAGTTAAAGGGAGGACTTATATCTTAGACCTGTGCAAGAATTTAC-----T-TTAATAAATTT
* ** *
162644 GCATGATTATACTTGTGGAAAAGATTGTATGAACATTACTTAGTTTGCATGTTTAATTATGCATA
318 GCATGATTATACTTGTGCAAAAGATTAAATGAACATTACTTAGTTTGAATGTTTAATTATGCATA
* * * * *
162709 TCAGTTTATTTAATTCACTAGAATAAATTTCCATGGCAGTTCATTAAA-CACCAGTTCATTAAAG
383 TCAGTTGATTCAATTCACTAGAATAAATTTCCATGGAAATTCATTAAAGCACAAGTTCATTAAAG
* * *
162773 TAATAGATTTTTTATGAATCTACTCTGCTTAAGTATGCTACTTTATTCAATAAAGA-TAGATAAC
448 CAATAGAATTTTTATGAAGCTACTCTGCTTAAGTATGCTACTTTATTCAATAAA-ACTAGATAAC
* * *
162837 TAATTAAACTAATTCATTCATTAAATTAGTTCAATAATTAATCTAGATCCATTAAATGTTTTCAT
512 TAATTAAACTAATTCATTCATTAAATTAATTCAATAATTAAACTAGATCCATTAAATGTTTGCAT
* * *
162902 GCCATGTTTGTTTTTAATTTGTTTTAAACCATGAATGTGTACTCTTTTGTGTGTATGTGTATAAG
577 GACATGTTTGTTTTTAATTTGTTTTAAACCATGAATGTGTACTCTTTTGTGTCTATGTGCATAAG
* *
162967 GGAATTTGAATAGTCATAACAAATAAAAGAATATCAGTAAGAATGTCTTCCATTTTTTGGATGC
642 GGAAGTTGAATAGTCATAACAAATAAAAGAATATCAGTAAGAATGTATTCCATTTTTTGGATGC
163031 AATAAACAAT
Statistics
Matches: 625, Mismatches: 74, Indels: 15
0.88 0.10 0.02
Matches are distributed among these distances:
816 94 0.15
817 178 0.28
818 2 0.00
821 231 0.37
822 120 0.19
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (818 bp):
GATTTTGGTTGCTACTGATTTGGACAGGTTAAGTGGTGACTAGGAGTTAATCTTAGTTGTTATTG
ATTAGCTTTAGGTGAGGAATTTGTGTGTGAAAATTTAATTGAGGCAAGTTGTTTACATCCGAGAA
GATTAAAGAAACTTATTCGAGCTTAATCTCACAATTTCAAACAAGGTTCAGATTTTTGGAAGACT
TTTGCAATCCAAAAGAATAACCTCCACCATCATACTGAAGGCTGGGACGTCAAAAAGGAACAACC
AAGTTAAAGGGAGGACTTATATCTTAGACCTGTGCAAGAATTTACTTTAATAAATTTGCATGATT
ATACTTGTGCAAAAGATTAAATGAACATTACTTAGTTTGAATGTTTAATTATGCATATCAGTTGA
TTCAATTCACTAGAATAAATTTCCATGGAAATTCATTAAAGCACAAGTTCATTAAAGCAATAGAA
TTTTTATGAAGCTACTCTGCTTAAGTATGCTACTTTATTCAATAAAACTAGATAACTAATTAAAC
TAATTCATTCATTAAATTAATTCAATAATTAAACTAGATCCATTAAATGTTTGCATGACATGTTT
GTTTTTAATTTGTTTTAAACCATGAATGTGTACTCTTTTGTGTCTATGTGCATAAGGGAAGTTGA
ATAGTCATAACAAATAAAAGAATATCAGTAAGAATGTATTCCATTTTTTGGATGCGATACAAAGT
GTTTGCTCTTTTACGTTAAATCATATTTTTCATTTGATTATGGTTTGGATATCAATTTCACGTAA
ACAAGTGTGCTTTTGGCGTTTTAGGTAATCCAATAATT
Found at i:171968 original size:45 final size:45
Alignment explanation
Indices: 171869--172402 Score: 545
Period size: 45 Copynumber: 11.8 Consensus size: 45
171859 CATTGATGAT
* ** ** *
171869 ATCCGTTCATGCTTATAATGCACCATTATGCATTTTCATTTACGGC
1 ATCCTTTCATGCCGATAATGCACTGTTATGCA-TTTCATTTATGGC
* * *
171915 ATCATTTCATGCCGATAATGCACTGTTATTCATTTCATTTATGGG
1 ATCCTTTCATGCCGATAATGCACTGTTATGCATTTCATTTATGGC
* *
171960 ATCCTTTCATGCCAATAATGCACCT-TTATGAATTTCATTTATGGC
1 ATCCTTTCATGCCGATAATGCA-CTGTTATGCATTTCATTTATGGC
* * * *
172005 ATTCTTTCATTCTGATAATGCACCGTTATGCATTTCATTTATGGC
1 ATCCTTTCATGCCGATAATGCACTGTTATGCATTTCATTTATGGC
** * * * *
172050 ATTTTTTCATTCTGATAATGCACCGTTATGCATTTCATTTA-GAGT
1 ATCCTTTCATGCCGATAATGCACTGTTATGCATTTCATTTATG-GC
*
172095 ATCATTTCATGCCGATAATGCACTGTTATGCATTTCATTTATGGC
1 ATCCTTTCATGCCGATAATGCACTGTTATGCATTTCATTTATGGC
* * * * *
172140 ATCCTTTCATGCCGATAATGTACCGTTATACATTTTATTTATGGT
1 ATCCTTTCATGCCGATAATGCACTGTTATGCATTTCATTTATGGC
* * * * * *
172185 ATACTTTCATGTCGAAAATGCA-TCGTTATGCATTTTATTTGTGGT
1 ATCCTTTCATGCCGATAATGCACT-GTTATGCATTTCATTTATGGC
* * ** *
172230 TTCCTTTCATGCCAATAATGCACCATTATGCATTTCATTTATTGC
1 ATCCTTTCATGCCGATAATGCACTGTTATGCATTTCATTTATGGC
** * * * *
172275 ATTATTTCATGCCAATAATACA-TCGTTATGTATTTCATTTATGAC
1 ATCCTTTCATGCCGATAATGCACT-GTTATGCATTTCATTTATGGC
* * **
172320 ATCATTTCATGCCGATAACGCACAATTATGCATTTCATTTATGGC
1 ATCCTTTCATGCCGATAATGCACTGTTATGCATTTCATTTATGGC
* *
172365 ATCCTTTCATGCCAATAATGCATTGTTATGCATTTCAT
1 ATCCTTTCATGCCGATAATGCACTGTTATGCATTTCAT
172403 GTATTCATTT
Statistics
Matches: 405, Mismatches: 75, Indels: 17
0.81 0.15 0.03
Matches are distributed among these distances:
44 2 0.00
45 375 0.93
46 28 0.07
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.42
Consensus pattern (45 bp):
ATCCTTTCATGCCGATAATGCACTGTTATGCATTTCATTTATGGC
Found at i:172069 original size:135 final size:135
Alignment explanation
Indices: 171874--172402 Score: 618
Period size: 135 Copynumber: 3.9 Consensus size: 135
171864 ATGATATCCG
** * *
171874 TTCATGCTTATAATGCACCATTATGCATTTTCATTTACGGCATCATTTCATGCCGATAATGCACT
1 TTCATGCCGATAATGCACCGTTATGCA-TTTCATTTATGGCATCATTTCATGCCGATAATGCACT
* * *
171939 GTTATTCATTTCATTTATGGGATCCTTTCATGCCAATAATGCACCTTTATGAATTTCATTTATGG
65 GTTATGCATTTCATTTATGGTATCCTTTCATGCCAATAATGCACCTTTATGCATTTCATTTATGG
172004 CATTCT
130 CATTCT
* * ** * * *
172010 TTCATTCTGATAATGCACCGTTATGCATTTCATTTATGGCATTTTTTCATTCTGATAATGCACCG
1 TTCATGCCGATAATGCACCGTTATGCATTTCATTTATGGCATCATTTCATGCCGATAATGCACTG
* *
172075 TTATGCATTTCATTTA-GAGTATCATTTCATGCCGATAATGCA-CTGTTATGCATTTCATTTATG
66 TTATGCATTTCATTTATG-GTATCCTTTCATGCCAATAATGCACCT-TTATGCATTTCATTTATG
*
172138 GCATCCT
129 GCATTCT
* * * * * *
172145 TTCATGCCGATAATGTACCGTTATACATTTTATTTATGGTAT-ACTTTCATGTCGAAAATGCA-T
1 TTCATGCCGATAATGCACCGTTATGCATTTCATTTATGGCATCA-TTTCATGCCGATAATGCACT
* * * * *
172208 CGTTATGCATTTTATTTGTGGTTTCCTTTCATGCCAATAATGCACCATTATGCATTTCATTTATT
65 -GTTATGCATTTCATTTATGGTATCCTTTCATGCCAATAATGCACCTTTATGCATTTCATTTATG
*
172273 GCATTAT
129 GCATTCT
* * * * * * **
172280 TTCATGCCAATAATACATCGTTATGTATTTCATTTATGACATCATTTCATGCCGATAACGCACAA
1 TTCATGCCGATAATGCACCGTTATGCATTTCATTTATGGCATCATTTCATGCCGATAATGCACTG
* *
172345 TTATGCATTTCATTTATGGCATCCTTTCATGCCAATAATGCA-TTGTTATGCATTTCAT
66 TTATGCATTTCATTTATGGTATCCTTTCATGCCAATAATGCACCT-TTATGCATTTCAT
172403 GTATTCATTT
Statistics
Matches: 328, Mismatches: 56, Indels: 19
0.81 0.14 0.05
Matches are distributed among these distances:
134 3 0.01
135 298 0.91
136 27 0.08
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (135 bp):
TTCATGCCGATAATGCACCGTTATGCATTTCATTTATGGCATCATTTCATGCCGATAATGCACTG
TTATGCATTTCATTTATGGTATCCTTTCATGCCAATAATGCACCTTTATGCATTTCATTTATGGC
ATTCT
Found at i:172953 original size:21 final size:21
Alignment explanation
Indices: 172927--172977 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
172917 CTTTCTCTTG
172927 GTATCGATACTAATTGCATCA
1 GTATCGATACTAATTGCATCA
172948 GTATCGATACTAATTGCATCA
1 GTATCGATACTAATTGCATCA
172969 GTATCGATA
1 GTATCGATA
172978 TTGTTCATCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (21 bp):
GTATCGATACTAATTGCATCA
Found at i:174895 original size:11 final size:11
Alignment explanation
Indices: 174876--174908 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
174866 AGAACTATTA
*
174876 TTTTCAAATTC
1 TTTTAAAATTC
174887 TTTTAAAATTC
1 TTTTAAAATTC
174898 TTTTAAAATTC
1 TTTTAAAATTC
174909 ATCTCAACCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.55
Consensus pattern (11 bp):
TTTTAAAATTC
Found at i:186248 original size:11 final size:11
Alignment explanation
Indices: 186232--186270 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
186222 TTTTTCAAAA
186232 AAAAAAAAAGC
1 AAAAAAAAAGC
*
186243 AAAAAAAAAAC
1 AAAAAAAAAGC
186254 -AAAAAAAAGC
1 AAAAAAAAAGC
*
186264 TAAAAAA
1 AAAAAAA
186271 TCCAAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.85, C:0.08, G:0.05, T:0.03
Consensus pattern (11 bp):
AAAAAAAAAGC
Found at i:186248 original size:12 final size:11
Alignment explanation
Indices: 186231--186261 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
186221 TTTTTTCAAA
186231 AAAAAAAAAAGC
1 AAAAAAAAAA-C
186243 AAAAAAAAAAC
1 AAAAAAAAAAC
186254 AAAAAAAA
1 AAAAAAAA
186262 GCTAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.90, C:0.06, G:0.03, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:186257 original size:21 final size:20
Alignment explanation
Indices: 186228--186270 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 20
186218 TATTTTTTTC
186228 AAAAAAAAAAAAAGCAAAAA
1 AAAAAAAAAAAAAGCAAAAA
186248 AAAAACAAAAAAAAGCTAAAAA
1 AAAAA-AAAAAAAAGC-AAAAA
186270 A
1 A
186271 TCCAAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 5 0.24
21 10 0.48
22 6 0.29
ACGTcount: A:0.86, C:0.07, G:0.05, T:0.02
Consensus pattern (20 bp):
AAAAAAAAAAAAAGCAAAAA
Found at i:198958 original size:18 final size:18
Alignment explanation
Indices: 198935--198973 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
198925 TTCTAAGCCC
*
198935 ACCTCGAAGACCCGTCCA
1 ACCTCGAAGACCCATCCA
198953 ACCTCGAAGACCCATCCA
1 ACCTCGAAGACCCATCCA
198971 ACC
1 ACC
198974 ACACGGTGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.31, C:0.46, G:0.13, T:0.10
Consensus pattern (18 bp):
ACCTCGAAGACCCATCCA
Found at i:205711 original size:2 final size:2
Alignment explanation
Indices: 205694--205729 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
205684 TCATAATAAC
*
205694 TA TA GA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
205730 GTATGTGTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:208616 original size:30 final size:30
Alignment explanation
Indices: 208573--208630 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
208563 TGGCTTTGCT
208573 TTCTTTTTGAATTTATTCT-TTTTCTTTTC
1 TTCTTTTTGAATTTATTCTCTTTTCTTTTC
* *
208602 TTCTTTTCTGAATTTTTTGTCTTTTCTTT
1 TTCTTTT-TGAATTTATTCTCTTTTCTTT
208631 ATTTTTGTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 7 0.28
30 10 0.40
31 8 0.32
ACGTcount: A:0.09, C:0.14, G:0.05, T:0.72
Consensus pattern (30 bp):
TTCTTTTTGAATTTATTCTCTTTTCTTTTC
Found at i:209970 original size:2 final size:2
Alignment explanation
Indices: 209953--210002 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
209943 TCAAAATAAC
*
209953 TA TA GA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
209994 TA TA TA TA T
1 TA TA TA TA T
210003 GAAAATAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:217147 original size:22 final size:22
Alignment explanation
Indices: 217122--217177 Score: 76
Period size: 25 Copynumber: 2.4 Consensus size: 22
217112 ACTTCCGTAC
217122 CAGTGCTAAATCATTTTAGTAT
1 CAGTGCTAAATCATTTTAGTAT
217144 CAGTGGTGCTAAATCATTTTAGTAT
1 CA---GTGCTAAATCATTTTAGTAT
*
217169 CAATGCTAA
1 CAGTGCTAA
217178 GACACTTCTG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 8 0.27
25 22 0.73
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (22 bp):
CAGTGCTAAATCATTTTAGTAT
Found at i:218640 original size:19 final size:19
Alignment explanation
Indices: 218618--218663 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
218608 AATTGATGAG
218618 TTTTATTTTATAGCTCAAA
1 TTTTATTTTATAGCTCAAA
218637 TTTTATTTTATAGCTCAAA
1 TTTTATTTTATAGCTCAAA
218656 TTTTATTT
1 TTTTATTT
218664 GAATTTTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.28, C:0.09, G:0.04, T:0.59
Consensus pattern (19 bp):
TTTTATTTTATAGCTCAAA
Found at i:224492 original size:2 final size:2
Alignment explanation
Indices: 224485--224513 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
224475 TAGTCACTAC
224485 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
224514 TAAGGTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:225977 original size:22 final size:22
Alignment explanation
Indices: 225952--226002 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
225942 AGGGGTACCA
*
225952 ATTCCCCCCCTAGGGGGAACAG
1 ATTCCCCCCCAAGGGGGAACAG
* *
225974 ATT-CCCCCCAAGGGGGTACTG
1 ATTCCCCCCCAAGGGGGAACAG
225995 ATTCCCCC
1 ATTCCCCC
226003 TGTCTAACGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.20, C:0.39, G:0.24, T:0.18
Consensus pattern (22 bp):
ATTCCCCCCCAAGGGGGAACAG
Found at i:227309 original size:19 final size:19
Alignment explanation
Indices: 227276--227322 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
227266 AATGTTTTTC
*
227276 TTTTGAAAACAAAAT-AGA
1 TTTTGAAAACAAAATGAAA
*
227294 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAA-ACAAAATGAAA
227314 TTTTGAAAA
1 TTTTGAAAA
227323 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 8 0.33
19 6 0.25
20 10 0.42
ACGTcount: A:0.51, C:0.06, G:0.13, T:0.30
Consensus pattern (19 bp):
TTTTGAAAACAAAATGAAA
Found at i:228505 original size:23 final size:23
Alignment explanation
Indices: 228471--228522 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
228461 TAGATTTTCA
* *
228471 TTTC-AAAGATGATGGATTCTCT
1 TTTCAAAAGATGATAGATTCTAT
228493 TTTCAAAAGATGATAGATTCTAT
1 TTTCAAAAGATGATAGATTCTAT
228516 TTTCAAA
1 TTTCAAA
228523 GGTGGAAGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 4 0.15
23 23 0.85
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (23 bp):
TTTCAAAAGATGATAGATTCTAT
Found at i:228839 original size:20 final size:21
Alignment explanation
Indices: 228794--228840 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
228784 ACGAAGATTA
228794 ATACATTCATGCATTCATAAG
1 ATACATTCATGCATTCATAAG
*
228815 A-ACATT-ATGCATTTCAT-TG
1 ATACATTCATGCA-TTCATAAG
228834 ATACATT
1 ATACATT
228841 TGATTGCATT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 7 0.30
20 15 0.65
21 1 0.04
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (21 bp):
ATACATTCATGCATTCATAAG
Found at i:229311 original size:96 final size:97
Alignment explanation
Indices: 229142--229332 Score: 271
Period size: 96 Copynumber: 2.0 Consensus size: 97
229132 AAGCTTACGG
* * * *
229142 AAGACTAGTGAAGCAGAAAGCAAGAACTAGAATAAAATTTAGTTTCCACGGAAGAGTAGTGGAAC
1 AAGACTAGTGAAGCAGAAAACAAGAACAAGAATAAAATTCAGTTTCCACGGAAGAGTAATGGAAC
*
229207 AGATTTTTCAGTAAAGTATCA-AACTTCACAA
66 AGATTTTTCAGCAAAGTATCAGAACTTCACAA
* *
229238 AAGAGTAGTGAAGCAGAAAACAAGAACCAAG-ATAAAATTCAGTTTTCACGGAAGAGTAATGGAA
1 AAGACTAGTGAAGCAGAAAACAAGAA-CAAGAATAAAATTCAGTTTCCACGGAAGAGTAATGGAA
*
229302 C-GTATTTTTCAGCAAAGTATGAGAACTTCAC
65 CAG-ATTTTTCAGCAAAGTATCAGAACTTCAC
229333 GGAAGAGCAG
Statistics
Matches: 84, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
95 1 0.01
96 72 0.86
97 11 0.13
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.23
Consensus pattern (97 bp):
AAGACTAGTGAAGCAGAAAACAAGAACAAGAATAAAATTCAGTTTCCACGGAAGAGTAATGGAAC
AGATTTTTCAGCAAAGTATCAGAACTTCACAA
Found at i:229758 original size:14 final size:14
Alignment explanation
Indices: 229705--229760 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
229695 TAACGTTTTA
* *
229705 TAATATTATTATAAA
1 TAATA-TATTATTAT
*
229720 TAATATATAATCTAT
1 TAATATATTAT-TAT
*
229735 AAAT-TATTATTAT
1 TAATATATTATTAT
229748 TAATATATTATTA
1 TAATATATTATTA
229761 CAAAACCAGA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
13 6 0.18
14 18 0.55
15 9 0.27
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (14 bp):
TAATATATTATTAT
Found at i:230843 original size:22 final size:22
Alignment explanation
Indices: 230815--230867 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
230805 TCGAAATCAG
230815 GTTTTTAGTATATTTTAAT-TTT
1 GTTTTTAGTAT-TTTTAATATTT
230837 GTTTTTA-TATTTTTAATATTT
1 GTTTTTAGTATTTTTAATATTT
*
230858 ATATTTTAGT
1 GT-TTTTAGT
230868 CACTACTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 7 0.26
21 7 0.26
22 12 0.44
23 1 0.04
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.68
Consensus pattern (22 bp):
GTTTTTAGTATTTTTAATATTT
Found at i:232875 original size:29 final size:29
Alignment explanation
Indices: 232772--232885 Score: 99
Period size: 30 Copynumber: 3.8 Consensus size: 29
232762 CAAAAATGGA
*
232772 AAAAACAAAAACTTAAATGGCTAAAACAAT
1 AAAAACAAAAACTTAAA-GGCTAAAAAAAT
* *
232802 AAAAACAAAAACTTAAGGGCCT--AAATAT
1 AAAAACAAAAACTTAAAGG-CTAAAAAAAT
* * *
232830 CAAATACAAACATTTAAAGGACTAAAAAAAT
1 -AAAAACAAAAACTTAAAGG-CTAAAAAAAT
232861 AAAAACAAAAA-TTAAAAGGGCTAAA
1 AAAAACAAAAACTT-AAA-GGCTAAA
232886 CAGTAATTAC
Statistics
Matches: 67, Mismatches: 11, Indels: 12
0.74 0.12 0.13
Matches are distributed among these distances:
28 4 0.06
29 21 0.31
30 35 0.52
31 7 0.10
ACGTcount: A:0.62, C:0.12, G:0.09, T:0.17
Consensus pattern (29 bp):
AAAAACAAAAACTTAAAGGCTAAAAAAAT
Done.