Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A09
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: 77927517
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1491452 characters in sequence are not A, C, G, or T
File 178 of 250
Found at i:56538167 original size:19 final size:19
Alignment explanation
Indices: 56538143--56538179 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
56538133 TTGTAATTAA
56538143 ATATTATT-TAATTATAATT
1 ATATTATTAT-ATTATAATT
56538162 ATATTATTATATTATAAT
1 ATATTATTATATTATAAT
56538180 ATTGTCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATATTATTATATTATAATT
Found at i:56538378 original size:3 final size:3
Alignment explanation
Indices: 56538370--56538399 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
56538360 ATGACATTGG
56538370 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
56538400 AAATTAAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:56538802 original size:42 final size:42
Alignment explanation
Indices: 56538746--56538833 Score: 158
Period size: 42 Copynumber: 2.1 Consensus size: 42
56538736 GAAATTTTGA
*
56538746 AAGTTAGCAGATTATTAGATGTTGTTCATGTTAAATAAATTG
1 AAGTTAGCAAATTATTAGATGTTGTTCATGTTAAATAAATTG
*
56538788 AAGTTAGCAAATTATTAGATGTTGTTCATGTTGAATAAATTG
1 AAGTTAGCAAATTATTAGATGTTGTTCATGTTAAATAAATTG
56538830 AAGT
1 AAGT
56538834 AGTATTTATC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (42 bp):
AAGTTAGCAAATTATTAGATGTTGTTCATGTTAAATAAATTG
Found at i:56539183 original size:3 final size:3
Alignment explanation
Indices: 56539177--56539209 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
56539167 TTAATTTATT
56539177 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
56539210 CCAATGTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:56539421 original size:20 final size:20
Alignment explanation
Indices: 56539398--56539435 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
56539388 AAATGACAAT
56539398 ATTATAA-TATAATAATATAC
1 ATTATAATTA-AATAATATAC
56539418 ATTATAATTAAATAATAT
1 ATTATAATTAAATAATAT
56539436 TTAATTACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 15 0.88
21 2 0.12
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTATAATTAAATAATATAC
Found at i:56546076 original size:271 final size:271
Alignment explanation
Indices: 56545593--56546140 Score: 1024
Period size: 271 Copynumber: 2.0 Consensus size: 271
56545583 GTCGATCTAA
**
56545593 ATATTTTTGACTTTTAATCCAATCCCAGAACTTGCTCTACCATTTTTTCCCGTTCTACAAATTCT
1 ATATTTTCAACTTTTAATCCAATCCCAGAACTTGCTCTACCATTTTTTCCCGTTCTACAAATTCT
56545658 GTAATTCAGTGTGATACCAGTTGTACTCTGATTTCATCTCTTAAACCTTGTAGGAACTGCTTACA
66 GTAATTCAGTGTGATACCAGTTGTACTCTGATTTCATCTCTTAAACCTTGTAGGAACTGCTTACA
* *
56545723 ACTGTCGGGCTCTATCGGTATAAAATTTGAAGCATATCGGCTGAGTCTAGAAAATTCCCTTTCAT
131 ACTGTCGGCCTCTATCGGTATAAAATCTGAAGCATATCGGCTGAGTCTAGAAAATTCCCTTTCAT
*
56545788 AGTCTACCACTGATAGATCATAATGTTTTAACATCAGAAATTCTTGCTTTTTGTCTTCAATATAT
196 AGTCTACCACTGATAGATCATAATGTTTTAACATCAGAAATTCTTACTTTTTGTCTTCAATATAT
56545853 AATTACTTGAC
261 AATTACTTGAC
56545864 ATATTTTCAACTTTTAATCCAATCCCAGAACTTGCTCTACCATTTTTTCCCGTTCTACAAATTCT
1 ATATTTTCAACTTTTAATCCAATCCCAGAACTTGCTCTACCATTTTTTCCCGTTCTACAAATTCT
* *
56545929 GTGATTCGGTGTGATACCAGTTGTACTCTGATTTCATCTCTTAAACCTTGTAGGAACTGCTTACA
66 GTAATTCAGTGTGATACCAGTTGTACTCTGATTTCATCTCTTAAACCTTGTAGGAACTGCTTACA
*
56545994 ACTGTCGGCCTCTGTCGGTATAAAATCTGAAGCATATCGGCTGAGTCTAGAAAATTCCCTTTCAT
131 ACTGTCGGCCTCTATCGGTATAAAATCTGAAGCATATCGGCTGAGTCTAGAAAATTCCCTTTCAT
56546059 AGTCTACCACTGATAGATCATAATGTTTTAACATCAGAAATTCTTACTTTTTGTCTTCAATATAT
196 AGTCTACCACTGATAGATCATAATGTTTTAACATCAGAAATTCTTACTTTTTGTCTTCAATATAT
56546124 AATTACTTGAC
261 AATTACTTGAC
56546135 ATATTT
1 ATATTT
56546141 CTTCTGAAAT
Statistics
Matches: 269, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
271 269 1.00
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (271 bp):
ATATTTTCAACTTTTAATCCAATCCCAGAACTTGCTCTACCATTTTTTCCCGTTCTACAAATTCT
GTAATTCAGTGTGATACCAGTTGTACTCTGATTTCATCTCTTAAACCTTGTAGGAACTGCTTACA
ACTGTCGGCCTCTATCGGTATAAAATCTGAAGCATATCGGCTGAGTCTAGAAAATTCCCTTTCAT
AGTCTACCACTGATAGATCATAATGTTTTAACATCAGAAATTCTTACTTTTTGTCTTCAATATAT
AATTACTTGAC
Found at i:56547820 original size:20 final size:20
Alignment explanation
Indices: 56547795--56547833 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
56547785 GGCAAACACT
56547795 TATATTATT-TAATTATAATG
1 TATATTATTAT-ATTATAATG
56547815 TATATTATTATATTATAAT
1 TATATTATTATATTATAAT
56547834 ATTGTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (20 bp):
TATATTATTATATTATAATG
Found at i:56547880 original size:20 final size:18
Alignment explanation
Indices: 56547844--56547880 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 18
56547834 ATTGTAATTT
56547844 ATATTAATTATAAATAAG
1 ATATTAATTATAAATAAG
56547862 ATATTATATTATGAAATAA
1 ATATTA-ATTAT-AAATAA
56547881 ATAAATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 5 0.29
20 6 0.35
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (18 bp):
ATATTAATTATAAATAAG
Found at i:56548029 original size:3 final size:3
Alignment explanation
Indices: 56548021--56548052 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
56548011 ATGACATTGG
56548021 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
56548053 ATAAAGAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:56548231 original size:15 final size:15
Alignment explanation
Indices: 56548208--56548238 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
56548198 AAGGAAATGA
56548208 AAAAAAAAAAGAAAC
1 AAAAAAAAAAGAAAC
*
56548223 AAAACAAAAAGAAAC
1 AAAAAAAAAAGAAAC
56548238 A
1 A
56548239 GAGAGCAAAC
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:0.84, C:0.10, G:0.06, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAGAAAC
Found at i:56548456 original size:40 final size:40
Alignment explanation
Indices: 56548399--56548478 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
56548389 ACTTGATTTA
* *
56548399 TGTTGAAATTTTAAAAGTTAACATATTATTAGATGTTGTT
1 TGTTGAAATTTTAAAAGTTAACAGATTATTAGATATTGTT
* *
56548439 TGTTGAAATTTTGAAAGTTAGCAGATTATTAGATATTGTT
1 TGTTGAAATTTTAAAAGTTAACAGATTATTAGATATTGTT
56548479 CATGTTCATA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.34, C:0.03, G:0.17, T:0.46
Consensus pattern (40 bp):
TGTTGAAATTTTAAAAGTTAACAGATTATTAGATATTGTT
Found at i:56567563 original size:46 final size:46
Alignment explanation
Indices: 56567510--56567783 Score: 370
Period size: 46 Copynumber: 6.0 Consensus size: 46
56567500 GCTCTCTGAA
** *
56567510 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** * *
56567556 ATGAAATGTGTAAGACCATGGTTGAAAAATACCATGGCAACGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
56567602 ATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** * * *
56567648 GGGAAATGAATAAGACCATGGTTGAAAGGTACCATGGCAGCGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
56567694 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * * *
56567740 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATG
56567784 TTAAAGATAA
Statistics
Matches: 203, Mismatches: 24, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
45 1 0.00
46 202 1.00
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (46 bp):
ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:56571650 original size:40 final size:39
Alignment explanation
Indices: 56571606--56571834 Score: 137
Period size: 35 Copynumber: 6.1 Consensus size: 39
56571596 AAGTCGAATT
*
56571606 AACCAATGATATTGAATGTGAGCCCAGCTCTAGTTGGATA
1 AACCAACGATATT-AATGTGAGCCCAGCTCTAGTTGGATA
* * *
56571646 AACCAACGATATT--T-TCA-CCCA-ATGCTAGTTAGATA
1 AACCAACGATATTAATGTGAGCCCAGCT-CTAGTTGGATA
* * *
56571681 TACCAACAATAATAATTGTGAGCCCAGCTCTAGTTGGATA
1 AACCAACGATATTAA-TGTGAGCCCAGCTCTAGTTGGATA
* *
56571721 AACCAACGAT-TT--T-TGCA-CCCAG-TGCTAGTCGAATA
1 AACCAACGATATTAATGTG-AGCCCAGCT-CTAGTTGGATA
* ** * *
56571756 TACTGACGATAATAATTGTGAGCCCAGCTCTAGTTTGATA
1 AACCAACGATATTAA-TGTGAGCCCAGCTCTAGTTGGATA
* * * *
56571796 AACTAAC-A-A-TAAT-TGCGCGCAGCGCTAGTTGGATA
1 AACCAACGATATTAATGTGAGCCCAGCTCTAGTTGGATA
56571831 AACC
1 AACC
56571835 GACGGTTGTG
Statistics
Matches: 144, Mismatches: 29, Indels: 37
0.69 0.14 0.18
Matches are distributed among these distances:
34 2 0.01
35 68 0.47
36 6 0.04
37 4 0.03
38 2 0.01
39 6 0.04
40 54 0.38
41 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (39 bp):
AACCAACGATATTAATGTGAGCCCAGCTCTAGTTGGATA
Found at i:56571730 original size:75 final size:75
Alignment explanation
Indices: 56571622--56571798 Score: 268
Period size: 75 Copynumber: 2.4 Consensus size: 75
56571612 TGATATTGAA
56571622 TGTGAGCCCAGCTCTAGTTGGATAAACCAACGATATTTT-CACCCAATGCTAGTTAG-ATATACC
1 TGTGAGCCCAGCTCTAGTTGGATAAACCAACGAT-TTTTGCACCCAATGCTAG-TAGAATATACC
56571685 AACAATAATAAT
64 AACAATAATAAT
* * **
56571697 TGTGAGCCCAGCTCTAGTTGGATAAACCAACGATTTTTGCACCCAGTGCTAGTCGAATATACTGA
1 TGTGAGCCCAGCTCTAGTTGGATAAACCAACGATTTTTGCACCCAATGCTAGTAGAATATACCAA
*
56571762 CGATAATAAT
66 CAATAATAAT
*
56571772 TGTGAGCCCAGCTCTAGTTTGATAAAC
1 TGTGAGCCCAGCTCTAGTTGGATAAAC
56571799 TAACAATAAT
Statistics
Matches: 94, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
74 6 0.06
75 88 0.94
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.28
Consensus pattern (75 bp):
TGTGAGCCCAGCTCTAGTTGGATAAACCAACGATTTTTGCACCCAATGCTAGTAGAATATACCAA
CAATAATAAT
Found at i:56572711 original size:16 final size:16
Alignment explanation
Indices: 56572690--56572721 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
56572680 AAAGATTAAG
56572690 CTTTTCTTTTTCTTTT
1 CTTTTCTTTTTCTTTT
56572706 CTTTTCTTTTTCTTTT
1 CTTTTCTTTTTCTTTT
56572722 ATTATTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (16 bp):
CTTTTCTTTTTCTTTT
Found at i:56576016 original size:32 final size:32
Alignment explanation
Indices: 56575922--56576017 Score: 174
Period size: 32 Copynumber: 3.0 Consensus size: 32
56575912 AACCATAAGA
* *
56575922 AAGCAACACACACAATGTGTTTGAGCATATAC
1 AAGCAATACACACAATGTGTTTGAGCATATGC
56575954 AAGCAATACACACAATGTGTTTGAGCATATGC
1 AAGCAATACACACAATGTGTTTGAGCATATGC
56575986 AAGCAATACACACAATGTGTTTGAGCATATGC
1 AAGCAATACACACAATGTGTTTGAGCATATGC
56576018 TCTCAAAAAG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 62 1.00
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.24
Consensus pattern (32 bp):
AAGCAATACACACAATGTGTTTGAGCATATGC
Found at i:56576892 original size:13 final size:14
Alignment explanation
Indices: 56576876--56576917 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
56576866 TTTCAATTTT
56576876 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
56576889 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
56576904 ATTTTAAATAATAT
1 ATTTT-AATAATAT
56576918 TATTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:56576902 original size:16 final size:16
Alignment explanation
Indices: 56576880--56576916 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
56576870 AATTTTATTT
56576880 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
56576897 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
56576912 TAATA
1 TAATA
56576917 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:56576969 original size:15 final size:15
Alignment explanation
Indices: 56576949--56577005 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
56576939 ATTCAATATT
56576949 AATATTTTAATAATA
1 AATATTTTAATAATA
*
56576964 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
56576983 AATATATTAATAATA
1 AATATTTTAATAATA
*
56576998 AATGTTTT
1 AATATTTT
56577006 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:56577490 original size:13 final size:14
Alignment explanation
Indices: 56577461--56577490 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
56577451 CCAGAAAAGT
56577461 AAATCATTTTTCAA
1 AAATCATTTTTCAA
*
56577475 AAATCATTTTTTAA
1 AAATCATTTTTCAA
56577489 AA
1 AA
56577491 GTAATTTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (14 bp):
AAATCATTTTTCAA
Found at i:56578235 original size:3 final size:3
Alignment explanation
Indices: 56578227--56578260 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
56578217 CGTGTTGCCC
56578227 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
56578261 CATTATTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:56578961 original size:38 final size:38
Alignment explanation
Indices: 56578913--56578988 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
56578903 AACTTATAAC
56578913 TATATACATATTCACAAGACATTCAAAATGCCAAATTA
1 TATATACATATTCACAAGACATTCAAAATGCCAAATTA
*
56578951 TATATACATATTCACAAGACATTCAAAATGCCATATTA
1 TATATACATATTCACAAGACATTCAAAATGCCAAATTA
56578989 GTCCAAGACA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.46, C:0.18, G:0.05, T:0.30
Consensus pattern (38 bp):
TATATACATATTCACAAGACATTCAAAATGCCAAATTA
Found at i:56584328 original size:28 final size:29
Alignment explanation
Indices: 56584282--56584349 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 29
56584272 CATTATTAAA
*
56584282 AAAAT-TAATACATAAT-AAACACAACAC
1 AAAATATAATACATAATAAAAAACAACAC
56584309 AAAATATAATA-ATAATTAAAAAAAACAACAC
1 AAAATATAATACATAA-T--AAAAAACAACAC
56584340 AAAATATAAT
1 AAAATATAAT
56584350 TTAAACATGA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
27 9 0.26
28 6 0.17
31 20 0.57
ACGTcount: A:0.68, C:0.12, G:0.00, T:0.21
Consensus pattern (29 bp):
AAAATATAATACATAATAAAAAACAACAC
Found at i:56586145 original size:19 final size:20
Alignment explanation
Indices: 56586118--56586155 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
56586108 TTATAAAGGT
*
56586118 TATATTTTA-ATATTTAAAA
1 TATAGTTTATATATTTAAAA
56586137 TATAGTTTATATATTTAAA
1 TATAGTTTATATATTTAAA
56586156 TTAACTCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
TATAGTTTATATATTTAAAA
Found at i:56588782 original size:16 final size:16
Alignment explanation
Indices: 56588761--56588812 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
56588751 TTTGGTTCGC
*
56588761 TGTATTGGATTAGAGG
1 TGTATTGGAATAGAGG
56588777 TGTATTGGAATAGAGG
1 TGTATTGGAATAGAGG
56588793 TGTATTGGAATAGAGG
1 TGTATTGGAATAGAGG
56588809 TGTA
1 TGTA
56588813 ATAGCAAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGAATAGAGG
Found at i:56589050 original size:16 final size:16
Alignment explanation
Indices: 56589013--56589054 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
56589003 TTAATCATAT
*
56589013 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
56589029 TT-AAATATATTATAA
1 TTAAAATATATTATAA
56589044 TTAAAATATAT
1 TTAAAATATAT
56589055 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:56589061 original size:14 final size:15
Alignment explanation
Indices: 56589022--56589063 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
56589012 TTTAAACATA
*
56589022 ATTATTATTAAATAT
1 ATTATAATTAAATAT
56589037 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
56589051 A-TATAATTTAATA
1 ATTATAATTAAATA
56589064 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:56589111 original size:54 final size:54
Alignment explanation
Indices: 56589053--56589285 Score: 236
Period size: 54 Copynumber: 4.1 Consensus size: 54
56589043 ATTAAAATAT
56589053 ATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATC
1 ATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATC
* * * * * * *
56589107 ATAATATATGATACTATAAAATATAAATTAA-CATAATTATTATTAAAT-ATATTATAATTAAAA
1 ATAAT-T-T-A-A-TA-AAATTCTTAA-TAATC--AA-TATTCTTATATGA-ATT-T-ACTCAAA
*
56589170 TAT
53 T-C
56589173 ATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATC
1 ATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATC
* *
56589227 ATAATTTAATAAAATTCTTAATAATTAATATTTTTATATGAATTTACTCAAATC
1 ATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATC
56589281 ATAAT
1 ATAAT
56589286 ATATGATACT
Statistics
Matches: 145, Mismatches: 18, Indels: 32
0.74 0.09 0.16
Matches are distributed among these distances:
54 62 0.43
55 7 0.05
56 2 0.01
57 13 0.09
58 4 0.03
59 5 0.03
60 16 0.11
61 5 0.03
62 4 0.03
63 13 0.09
64 2 0.01
65 7 0.05
66 5 0.03
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.43
Consensus pattern (54 bp):
ATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATC
Found at i:56589181 original size:14 final size:15
Alignment explanation
Indices: 56589132--56589183 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
56589122 ATAAAATATA
56589132 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
56589147 TATTAAATATATTAT
1 AATTAAATATATTAT
56589162 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
56589175 AATTTAATA
1 AATTAAATA
56589184 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:56589229 original size:120 final size:120
Alignment explanation
Indices: 56589016--56589231 Score: 432
Period size: 120 Copynumber: 1.8 Consensus size: 120
56589006 ATCATATTTA
56589016 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
56589081 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
56589136 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
56589201 TATTCTTATATGAATTTACTCAAATCATAAT
66 TATTCTTATATGAATTTACTCAAATCATAAT
56589232 TTAATAAAAT
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 96 1.00
ACGTcount: A:0.50, C:0.07, G:0.01, T:0.42
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
Found at i:56592929 original size:126 final size:126
Alignment explanation
Indices: 56592704--56592947 Score: 443
Period size: 126 Copynumber: 1.9 Consensus size: 126
56592694 GTTTTAGCCT
56592704 TAAGAGGATATTCGAATATTCAAAACAAACAAAGAAAGCAAAACCCAATACGTTAGGGCACGATT
1 TAAGAGGATATTCGAATATTCAAAACAAACAAAGAAAGCAAAACCCAATACGTTAGGGCACGATT
* *
56592769 CTTCGAATTCTTTAAATACCGAACATTGCCTTTATTTTGAAAATTTTTTAGAGTGAACTAG
66 CTTCGAATTCTTTAAATACCGAACATTGCCTTTATTTTGAAAAATTTTGAGAGTGAACTAG
* * *
56592830 TAAGAGGATATTCGAATATTCAAGACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATT
1 TAAGAGGATATTCGAATATTCAAAACAAACAAAGAAAGCAAAACCCAATACGTTAGGGCACGATT
56592895 CTTCGAATTCTTTAAATACCGAACATTGCCTTTATTTTGAAAAATTTTGAGAG
66 CTTCGAATTCTTTAAATACCGAACATTGCCTTTATTTTGAAAAATTTTGAGAG
56592948 AAGATCAATG
Statistics
Matches: 113, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
126 113 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (126 bp):
TAAGAGGATATTCGAATATTCAAAACAAACAAAGAAAGCAAAACCCAATACGTTAGGGCACGATT
CTTCGAATTCTTTAAATACCGAACATTGCCTTTATTTTGAAAAATTTTGAGAGTGAACTAG
Found at i:56593107 original size:18 final size:17
Alignment explanation
Indices: 56593084--56593130 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
56593074 AATTAATAGA
56593084 AATAATTAATAAAACAAC
1 AATAATTAATAAAA-AAC
*
56593102 AATAA-TAAT-AAATAC
1 AATAATTAATAAAAAAC
56593117 AATAATGTAATAAA
1 AATAAT-TAATAAA
56593131 CATTGTGCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
15 7 0.28
16 3 0.12
17 8 0.32
18 7 0.28
ACGTcount: A:0.66, C:0.06, G:0.02, T:0.26
Consensus pattern (17 bp):
AATAATTAATAAAAAAC
Found at i:56593832 original size:18 final size:18
Alignment explanation
Indices: 56593809--56593881 Score: 69
Period size: 18 Copynumber: 4.0 Consensus size: 18
56593799 ATAACAAGTA
*
56593809 GGGTGATGGAGTTAGTGG
1 GGGTGATGGAGGTAGTGG
56593827 GGGTGATGGAGGTAGTGG
1 GGGTGATGGAGGTAGTGG
* * *
56593845 ATGGT-TTAGTAGGGT-GTGG
1 -GGGTGAT-GGA-GGTAGTGG
56593864 GGGTGATGGAGGTAGTGG
1 GGGTGATGGAGGTAGTGG
56593882 ATGGTTTAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
17 3 0.07
18 27 0.63
19 10 0.23
20 3 0.07
ACGTcount: A:0.16, C:0.00, G:0.56, T:0.27
Consensus pattern (18 bp):
GGGTGATGGAGGTAGTGG
Found at i:56593860 original size:29 final size:29
Alignment explanation
Indices: 56593827--56593926 Score: 101
Period size: 29 Copynumber: 3.2 Consensus size: 29
56593817 GAGTTAGTGG
56593827 GGGTGATGGAGGTAGTGGATGGTTTAGTA
1 GGGTGATGGAGGTAGTGGATGGTTTAGTA
56593856 GGGTGTGGGGGTGATGGAGGTAGTGGATGGTTTAGTA
1 --------GGGTGATGGAGGTAGTGGATGGTTTAGTA
* * *
56593893 GGGTGATGGAGTTAGTGGTTGGTTTAGTG
1 GGGTGATGGAGGTAGTGGATGGTTTAGTA
56593922 GGGTG
1 GGGTG
56593927 TTTAATTTGG
Statistics
Matches: 60, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
29 31 0.52
37 29 0.48
ACGTcount: A:0.16, C:0.00, G:0.52, T:0.32
Consensus pattern (29 bp):
GGGTGATGGAGGTAGTGGATGGTTTAGTA
Found at i:56593873 original size:37 final size:37
Alignment explanation
Indices: 56593823--56593897 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
56593813 GATGGAGTTA
56593823 GTGGGGGTGATGGAGGTAGTGGATGGTTTAGTAGGGT
1 GTGGGGGTGATGGAGGTAGTGGATGGTTTAGTAGGGT
56593860 GTGGGGGTGATGGAGGTAGTGGATGGTTTAGTAGGGT
1 GTGGGGGTGATGGAGGTAGTGGATGGTTTAGTAGGGT
56593897 G
1 G
56593898 ATGGAGTTAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.16, C:0.00, G:0.55, T:0.29
Consensus pattern (37 bp):
GTGGGGGTGATGGAGGTAGTGGATGGTTTAGTAGGGT
Found at i:56602712 original size:23 final size:23
Alignment explanation
Indices: 56602686--56602731 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
56602676 GGTCACTCCG
56602686 AAAATGATAAAGTTTGATTCAAT
1 AAAATGATAAAGTTTGATTCAAT
56602709 AAAATGATAAAGTTTGATTCAAT
1 AAAATGATAAAGTTTGATTCAAT
56602732 CATTTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.13, T:0.35
Consensus pattern (23 bp):
AAAATGATAAAGTTTGATTCAAT
Found at i:56606705 original size:26 final size:27
Alignment explanation
Indices: 56606676--56606741 Score: 98
Period size: 30 Copynumber: 2.4 Consensus size: 27
56606666 GGATCTTTAG
56606676 ATGTATCCGGCA-GCTTCGTGCTGGAA
1 ATGTATCCGGCAGGCTTCGTGCTGGAA
56606702 ATGTATCCGGGCGCAGGCTTCGTGCTGGAA
1 ATGTATCC--G-GCAGGCTTCGTGCTGGAA
56606732 ATGTATCCGG
1 ATGTATCCGG
56606742 GCTAAAGTCC
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
26 8 0.22
27 1 0.03
28 2 0.06
29 3 0.08
30 22 0.61
ACGTcount: A:0.18, C:0.23, G:0.33, T:0.26
Consensus pattern (27 bp):
ATGTATCCGGCAGGCTTCGTGCTGGAA
Found at i:56606786 original size:25 final size:25
Alignment explanation
Indices: 56606752--56606802 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
56606742 GCTAAAGTCC
56606752 CGCAGGCTTCATGTTGGAAATGTAT
1 CGCAGGCTTCATGTTGGAAATGTAT
56606777 CGCAGGCTTCATGTTGGAAATGTAT
1 CGCAGGCTTCATGTTGGAAATGTAT
56606802 C
1 C
56606803 CGGGCTAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (25 bp):
CGCAGGCTTCATGTTGGAAATGTAT
Found at i:56606797 original size:64 final size:64
Alignment explanation
Indices: 56606713--56606841 Score: 204
Period size: 64 Copynumber: 2.0 Consensus size: 64
56606703 TGTATCCGGG
* * *
56606713 CGCAGGCTTCGTGCTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCATGTTGGAAATGTAT
1 CGCAGGCTTCATGCTGGAAATGTATCCGGGCTAAAGTCCAGCAGGCTTCATGCTGGAAATGTAT
* * *
56606777 CGCAGGCTTCATGTTGGAAATGTATCCGGGCTAAAGTCCAGTAGGCTTCGTGCTGGAAATGTAT
1 CGCAGGCTTCATGCTGGAAATGTATCCGGGCTAAAGTCCAGCAGGCTTCATGCTGGAAATGTAT
56606841 C
1 C
56606842 CGGGCTAAAG
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 59 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.27
Consensus pattern (64 bp):
CGCAGGCTTCATGCTGGAAATGTATCCGGGCTAAAGTCCAGCAGGCTTCATGCTGGAAATGTAT
Found at i:56606834 original size:39 final size:39
Alignment explanation
Indices: 56606777--56606910 Score: 214
Period size: 39 Copynumber: 3.4 Consensus size: 39
56606767 GGAAATGTAT
* *
56606777 CGCAGGCTTCATGTTGGAAATGTATCCGGGCTAAAGTCC
1 CGCAGGCTTCGTGCTGGAAATGTATCCGGGCTAAAGTCC
* *
56606816 AGTAGGCTTCGTGCTGGAAATGTATCCGGGCTAAAGTCC
1 CGCAGGCTTCGTGCTGGAAATGTATCCGGGCTAAAGTCC
*
56606855 CGCAGGCTTCGTGCTGGAAATGTATCCGAGCTAAAGTCC
1 CGCAGGCTTCGTGCTGGAAATGTATCCGGGCTAAAGTCC
*
56606894 CGCAGGCTTTGTGCTGG
1 CGCAGGCTTCGTGCTGG
56606911 TAATATAATT
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 87 1.00
ACGTcount: A:0.21, C:0.23, G:0.31, T:0.25
Consensus pattern (39 bp):
CGCAGGCTTCGTGCTGGAAATGTATCCGGGCTAAAGTCC
Found at i:56629392 original size:7 final size:8
Alignment explanation
Indices: 56629354--56629396 Score: 52
Period size: 9 Copynumber: 5.2 Consensus size: 8
56629344 TGAAAATATT
56629354 TATTTTAA
1 TATTTTAA
56629362 TATTTTTAA
1 TA-TTTTAA
*
56629371 TATATTATA
1 TATTTTA-A
56629380 TATTTTAA
1 TATTTTAA
56629388 T-TTTTAA
1 TATTTTAA
56629395 TA
1 TA
56629397 CGATCCGGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
7 7 0.23
8 8 0.27
9 15 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
TATTTTAA
Found at i:56635740 original size:14 final size:14
Alignment explanation
Indices: 56635721--56635842 Score: 59
Period size: 14 Copynumber: 7.6 Consensus size: 14
56635711 CTCCTCTGGT
56635721 CTTCTGCTTCGCTG
1 CTTCTGCTTCGCTG
* *
56635735 CTTCTGTTGTCTCCATTG
1 CTTCTGCT-TC-GC--TG
56635753 TCTTCTGCTTCGCTG
1 -CTTCTGCTTCGCTG
56635768 CTTCTGCGGTCTC-CATTG
1 CTTCTGC--T-TCGC--TG
56635786 TCTTCTGCTTCGCTG
1 -CTTCTGCTTCGCTG
56635801 CTTCTGCGGTCTC-CATTG
1 CTTCTGC--T-TCGC--TG
56635819 TCTTCTGCTTCGCTG
1 -CTTCTGCTTCGCTG
56635834 CTTCTGCTT
1 CTTCTGCTT
56635843 TCTCCTTCAT
Statistics
Matches: 85, Mismatches: 4, Indels: 38
0.67 0.03 0.30
Matches are distributed among these distances:
14 30 0.35
15 8 0.09
16 9 0.11
17 9 0.11
18 8 0.09
19 21 0.25
ACGTcount: A:0.02, C:0.33, G:0.20, T:0.45
Consensus pattern (14 bp):
CTTCTGCTTCGCTG
Found at i:56635792 original size:19 final size:19
Alignment explanation
Indices: 56635768--56635826 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
56635758 TGCTTCGCTG
56635768 CTTCTGCGGTCTCCATTGT
1 CTTCTGCGGTCTCCATTGT
56635787 CTTCTGC--T-TCGC--TG-
1 CTTCTGCGGTCTC-CATTGT
56635801 CTTCTGCGGTCTCCATTGT
1 CTTCTGCGGTCTCCATTGT
56635820 CTTCTGC
1 CTTCTGC
56635827 TTCGCTGCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 14
0.70 0.00 0.30
Matches are distributed among these distances:
14 7 0.21
15 2 0.06
16 4 0.12
17 4 0.12
18 2 0.06
19 14 0.42
ACGTcount: A:0.03, C:0.34, G:0.20, T:0.42
Consensus pattern (19 bp):
CTTCTGCGGTCTCCATTGT
Found at i:56635847 original size:33 final size:33
Alignment explanation
Indices: 56635719--56635840 Score: 226
Period size: 33 Copynumber: 3.7 Consensus size: 33
56635709 GGCTCCTCTG
**
56635719 GTCTTCTGCTTCGCTGCTTCTGTTGTCTCCATT
1 GTCTTCTGCTTCGCTGCTTCTGCGGTCTCCATT
56635752 GTCTTCTGCTTCGCTGCTTCTGCGGTCTCCATT
1 GTCTTCTGCTTCGCTGCTTCTGCGGTCTCCATT
56635785 GTCTTCTGCTTCGCTGCTTCTGCGGTCTCCATT
1 GTCTTCTGCTTCGCTGCTTCTGCGGTCTCCATT
56635818 GTCTTCTGCTTCGCTGCTTCTGC
1 GTCTTCTGCTTCGCTGCTTCTGC
56635841 TTTCTCCTTC
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 87 1.00
ACGTcount: A:0.02, C:0.33, G:0.20, T:0.44
Consensus pattern (33 bp):
GTCTTCTGCTTCGCTGCTTCTGCGGTCTCCATT
Found at i:56640139 original size:48 final size:48
Alignment explanation
Indices: 56640068--56640631 Score: 877
Period size: 48 Copynumber: 12.0 Consensus size: 48
56640058 AGATAAATAT
56640068 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* **
56640116 ATATGTATATGTAGTAAAGCCGAATGGCTAATGTGAAATACATATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* **
56640164 ATATGTATATGTGGTAAAGTCGAATGGCTAATGTGAAATACCTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
56640212 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
**
56640260 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATACATATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
56640308 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
56640356 ATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
** *
56640404 ATATGTATATGTGGTAAAGCCGAATATCT-A--TG--AGA--TAT--G
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
56640443 -TA--TA--TGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAT
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
56640486 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
56640534 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
* * * *
56640582 ATATGTATATGTGGTAAAGCTGAATGGCTAGTGTGAACTATGTAGGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
56640630 AT
1 AT
56640632 GTGAACTATA
Statistics
Matches: 475, Mismatches: 27, Indels: 28
0.90 0.05 0.05
Matches are distributed among these distances:
34 18 0.04
35 1 0.00
36 2 0.00
37 2 0.00
38 2 0.00
39 3 0.01
41 6 0.01
43 2 0.00
44 2 0.00
45 2 0.00
46 2 0.00
47 1 0.00
48 432 0.91
ACGTcount: A:0.36, C:0.07, G:0.26, T:0.31
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
Found at i:56640436 original size:34 final size:34
Alignment explanation
Indices: 56640392--56640462 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
56640382 GTTAATGTGA
*
56640392 AATATGTATGAGATATGTATATGTGGTAAAGCCG
1 AATATCTATGAGATATGTATATGTGGTAAAGCCG
56640426 AATATCTATGAGATATGTATATGTGGTAAAGCCG
1 AATATCTATGAGATATGTATATGTGGTAAAGCCG
56640460 AAT
1 AAT
56640463 GGCTAATGTG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.32
Consensus pattern (34 bp):
AATATCTATGAGATATGTATATGTGGTAAAGCCG
Found at i:56640466 original size:178 final size:178
Alignment explanation
Indices: 56640248--56640606 Score: 664
Period size: 178 Copynumber: 2.0 Consensus size: 178
56640238 GCTAATGTGA
*
56640248 AATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATACATATGAGATATG
1 AATATCTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATACATATGAGATATG
56640313 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCG
66 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCG
*
56640378 AATGGTTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCG
131 AATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCG
** *
56640426 AATATCTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGATATATG
1 AATATCTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATACATATGAGATATG
56640491 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCG
66 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCG
*
56640556 AATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCTG
131 AATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCG
56640604 AAT
1 AAT
56640607 GGCTAGTGTG
Statistics
Matches: 175, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
178 175 1.00
ACGTcount: A:0.36, C:0.06, G:0.26, T:0.32
Consensus pattern (178 bp):
AATATCTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATACATATGAGATATG
TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCG
AATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCG
Found at i:56640599 original size:226 final size:226
Alignment explanation
Indices: 56640200--56640631 Score: 783
Period size: 226 Copynumber: 1.9 Consensus size: 226
56640190 GCTAATGTGA
56640200 AATACCTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
1 AATACCTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
56640265 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATACATATGAGATATGTATATGTGGTAAAGCCG
66 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATACATATGAGATATGTATATGTGGTAAAGCCG
*
56640330 AATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAAT
131 AATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
*
56640395 ATGTATGAGATATGTATATGTGGTAAAGCCG
196 ATGTAGGAGATATGTATATGTGGTAAAGCCG
* *
56640426 AATATCTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGATATATG
1 AATACCTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
**
56640491 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCG
66 TATATGTGGTAAAGCCGAATGGCTAATGTGAAATACATATGAGATATGTATATGTGGTAAAGCCG
* * *
56640556 AATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCTGAATGGCTAGTGTGAACT
131 AATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
56640621 ATGTAGGAGAT
196 ATGTAGGAGAT
56640632 GTGAACTATA
Statistics
Matches: 197, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
226 197 1.00
ACGTcount: A:0.35, C:0.07, G:0.26, T:0.31
Consensus pattern (226 bp):
AATACCTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATG
TATATGTGGTAAAGCCGAATGGCTAATGTGAAATACATATGAGATATGTATATGTGGTAAAGCCG
AATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
ATGTAGGAGATATGTATATGTGGTAAAGCCG
Found at i:56640665 original size:274 final size:273
Alignment explanation
Indices: 56640158--56640667 Score: 824
Period size: 274 Copynumber: 1.9 Consensus size: 273
56640148 GTGAAATACA
*
56640158 TATGAGATATGTATATGTGGTAAAGTCGAATGGCTAATGTGAAATACCTATGAGATATGTATATG
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATACCTATGAGATATGTATATG
56640223 TGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGC
66 TGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGC
*
56640288 TAATGTGAAATACATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTAT
131 TAATGTGAAATACATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTAG
* * ***
56640353 GAGATATGTATATGTGGTAAAGCCGAATGGTTAATGTGAAATATGTATGAGATATGTATATGTGG
196 GAGATATGAATATATGGT-AAGCCGAATGCCAAATGTGAAATATGTATGAGATATGTATATGTGG
56640418 TAAAGCCGAATATC
260 TAAAGCCGAATATC
** *
56640432 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGATATATGTATATG
1 TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATACCTATGAGATATGTATATG
56640497 TGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGC
66 TGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGC
** * * *
56640562 TAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCTGAATGGCTAGTGTGAACTATGTAG
131 TAATGTGAAATACATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTAG
* * *
56640627 GAGATGTGAACTATATTGT-GGCCGAATGACCAAATGTGAAA
196 GAGATATGAA-TATATGGTAAGCCGAATG-CCAAATGTGAAA
56640668 GGTGTGTATT
Statistics
Matches: 216, Mismatches: 18, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
273 8 0.04
274 202 0.94
275 6 0.03
ACGTcount: A:0.35, C:0.07, G:0.26, T:0.31
Consensus pattern (273 bp):
TATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATACCTATGAGATATGTATATG
TGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGC
TAATGTGAAATACATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTAG
GAGATATGAATATATGGTAAGCCGAATGCCAAATGTGAAATATGTATGAGATATGTATATGTGGT
AAAGCCGAATATC
Found at i:56642120 original size:14 final size:15
Alignment explanation
Indices: 56642084--56642120 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
56642074 AAGAAAATAG
56642084 ATGAATTAGGACCAA
1 ATGAATTAGGACCAA
56642099 ATTGAATTAGGACC-A
1 A-TGAATTAGGACCAA
56642114 ATGAATT
1 ATGAATT
56642121 CATTTCTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.29
15 3 0.14
16 12 0.57
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.27
Consensus pattern (15 bp):
ATGAATTAGGACCAA
Found at i:56644963 original size:31 final size:30
Alignment explanation
Indices: 56644907--56645023 Score: 164
Period size: 31 Copynumber: 3.8 Consensus size: 30
56644897 CTTGTCACTT
*
56644907 GTAGCCGAAGCTACCAC-ATTCACTGATCAG
1 GTAGCCG-AGCTACCACTTTTCACTGATCAG
*
56644937 GTAGCCAGAGCTACCATTTTTCACTGATCAG
1 GTAGCC-GAGCTACCACTTTTCACTGATCAG
*
56644968 GTAGTCGGAGCTACCACTTTTCACTGATCAG
1 GTAG-CCGAGCTACCACTTTTCACTGATCAG
56644999 GTAGCCGAAGCTACCACTTTTCACT
1 GTAGCCG-AGCTACCACTTTTCACT
56645024 TGTCATTTGT
Statistics
Matches: 78, Mismatches: 5, Indels: 7
0.87 0.06 0.08
Matches are distributed among these distances:
30 16 0.21
31 61 0.78
32 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (30 bp):
GTAGCCGAGCTACCACTTTTCACTGATCAG
Found at i:56645104 original size:50 final size:51
Alignment explanation
Indices: 56644999--56645127 Score: 215
Period size: 50 Copynumber: 2.5 Consensus size: 51
56644989 CACTGATCAG
* * * *
56644999 GTAGCCGAAGCTACCACTTTTCACTTGTCATTTGTCCTTTATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCACTTGTCCTTGATCAGATAAGT
56645050 GTAGCCGAAGCTATCACTTATCACTT-TCACTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCACTTGTCCTTGATCAGATAAGT
56645100 GTAGCCGAAGCTATCACTTATCACTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
56645128 TGCCGTGGTC
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
50 48 0.66
51 25 0.34
ACGTcount: A:0.25, C:0.24, G:0.16, T:0.35
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCACTTGTCCTTGATCAGATAAGT
Found at i:56650210 original size:31 final size:31
Alignment explanation
Indices: 56650172--56650233 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
56650162 GATTGATTGG
56650172 AGTGTCAACTCCAACGTCCTCATAGCTTACT
1 AGTGTCAACTCCAACGTCCTCATAGCTTACT
56650203 AGTGTCAACTCCAACGTCCTCATAGCTTACT
1 AGTGTCAACTCCAACGTCCTCATAGCTTACT
56650234 CTTCTTTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.26, C:0.32, G:0.13, T:0.29
Consensus pattern (31 bp):
AGTGTCAACTCCAACGTCCTCATAGCTTACT
Found at i:56651564 original size:23 final size:23
Alignment explanation
Indices: 56651534--56651583 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
56651524 CTCTTGGGAC
56651534 CTTTTGTATGTCCACTCCCCATT
1 CTTTTGTATGTCCACTCCCCATT
56651557 CTTTTGTATGTCCACTCCCCATT
1 CTTTTGTATGTCCACTCCCCATT
56651580 CTTT
1 CTTT
56651584 CTTACAAAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.12, C:0.34, G:0.08, T:0.46
Consensus pattern (23 bp):
CTTTTGTATGTCCACTCCCCATT
Found at i:56652688 original size:12 final size:12
Alignment explanation
Indices: 56652673--56652698 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
56652663 TAAAATTTAC
56652673 AAAAAAAAAGAA
1 AAAAAAAAAGAA
56652685 AAAAAAAAAGAA
1 AAAAAAAAAGAA
56652697 AA
1 AA
56652699 GAGAAAGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGAA
Found at i:56658525 original size:20 final size:20
Alignment explanation
Indices: 56658488--56658526 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
56658478 ATTAGTTTTT
*
56658488 TTTATATGATTTGGTTTTAG
1 TTTATATGATTTGATTTTAG
56658508 TTTATATGAATTT-ATTTTA
1 TTTATATG-ATTTGATTTTA
56658527 ATTCCTTCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.26, C:0.00, G:0.13, T:0.62
Consensus pattern (20 bp):
TTTATATGATTTGATTTTAG
Found at i:56667953 original size:16 final size:16
Alignment explanation
Indices: 56667932--56667964 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
56667922 CAAGTAAAGC
56667932 GGGTAATGAATTTAGA
1 GGGTAATGAATTTAGA
56667948 GGGTAATGAATTTAGA
1 GGGTAATGAATTTAGA
56667964 G
1 G
56667965 CCTGTTCTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.33, T:0.30
Consensus pattern (16 bp):
GGGTAATGAATTTAGA
Found at i:56669848 original size:8 final size:9
Alignment explanation
Indices: 56669801--56669884 Score: 50
Period size: 9 Copynumber: 9.1 Consensus size: 9
56669791 ATCCTTCTTG
*
56669801 AAAATGATA
1 AAAATTATA
*
56669810 AAAATTGATTT
1 AAAATT-A-TA
56669821 AAAATTATTTA
1 AAAATTA--TA
56669832 AAAATTATA
1 AAAATTATA
56669841 AAAA-TATA
1 AAAATTATA
56669849 AAATATT-T-
1 AAA-ATTATA
*
56669857 -AAATAATA
1 AAAATTATA
*
56669865 AAATTTCATA
1 AAAATT-ATA
56669875 AAAATTATA
1 AAAATTATA
56669884 A
1 A
56669885 TTTAATTTCA
Statistics
Matches: 59, Mismatches: 7, Indels: 18
0.70 0.08 0.21
Matches are distributed among these distances:
6 2 0.03
7 3 0.05
8 7 0.12
9 20 0.34
10 11 0.19
11 16 0.27
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (9 bp):
AAAATTATA
Found at i:56675065 original size:46 final size:46
Alignment explanation
Indices: 56674998--56675093 Score: 192
Period size: 46 Copynumber: 2.1 Consensus size: 46
56674988 GGACCAGAAC
56674998 AATTGGGGAATATTCAAGTCCCTAAAAAGGCCAGCTATATCAGAGT
1 AATTGGGGAATATTCAAGTCCCTAAAAAGGCCAGCTATATCAGAGT
56675044 AATTGGGGAATATTCAAGTCCCTAAAAAGGCCAGCTATATCAGAGT
1 AATTGGGGAATATTCAAGTCCCTAAAAAGGCCAGCTATATCAGAGT
56675090 AATT
1 AATT
56675094 ATGTTGGATT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.25
Consensus pattern (46 bp):
AATTGGGGAATATTCAAGTCCCTAAAAAGGCCAGCTATATCAGAGT
Found at i:56688201 original size:16 final size:16
Alignment explanation
Indices: 56688132--56688199 Score: 109
Period size: 16 Copynumber: 4.2 Consensus size: 16
56688122 TTTGGTTCGC
56688132 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
56688148 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
56688164 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* * *
56688180 TGTAATGGAATAGATG
1 TGTATTGGATTAGAGG
56688196 TGTA
1 TGTA
56688200 ATAGCAAATC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.28, C:0.00, G:0.35, T:0.37
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:56688231 original size:45 final size:44
Alignment explanation
Indices: 56688180--56688274 Score: 118
Period size: 45 Copynumber: 2.1 Consensus size: 44
56688170 GGATTAGAGG
* * * *
56688180 TGTAATGGAATAGATGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTCAA
* **
56688225 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTCAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTCAA
56688269 TGTAAT
1 TGTAAT
56688275 AGAGGTGTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
44 17 0.40
45 26 0.60
ACGTcount: A:0.35, C:0.06, G:0.25, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTCAA
Found at i:56688457 original size:18 final size:17
Alignment explanation
Indices: 56688436--56688470 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
56688426 TTATTATTTA
*
56688436 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
56688454 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
56688471 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:56688464 original size:28 final size:27
Alignment explanation
Indices: 56688394--56688466 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
56688384 TTTATTATCA
*
56688394 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
56688422 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
56688449 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
56688467 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:56688602 original size:18 final size:17
Alignment explanation
Indices: 56688580--56688614 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
56688570 TAATTATTAA
*
56688580 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
56688598 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
56688615 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:56688602 original size:144 final size:147
Alignment explanation
Indices: 56688355--56688626 Score: 478
Period size: 144 Copynumber: 1.9 Consensus size: 147
56688345 ATGATTATTG
*
56688355 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
56688420 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
66 ACATAATTATTA--TAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
56688485 AGAAATTTGTTTTGGTAAA
129 AGAAATTTGTTTTGGTAAA
* *
56688504 TTATT-TTATTTAAATTTTAATAAGATTA-TTAATATCAATAATAAATAATTTACTCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
56688567 ACATAATTATTA-AATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ACATAATTATTATAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
56688627 ATATTCTTAT
Statistics
Matches: 120, Mismatches: 3, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
144 48 0.40
147 44 0.37
148 23 0.19
149 5 0.04
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (147 bp):
TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
ACATAATTATTATAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAG
AAATTTGTTTTGGTAAA
Found at i:56688661 original size:59 final size:58
Alignment explanation
Indices: 56688598--56688780 Score: 153
Period size: 53 Copynumber: 3.1 Consensus size: 58
56688588 TAATTAAAAT
*
56688598 ATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATA
1 ATATAATTTAATAAAATTC-TAATAATTAATATTCTTATATGAATTTACTAAAATCATA
** ** * * *
56688657 ATATATGATACTGTAAAATATAAATTAAAATAA-TAATTATT-AAATAT-ATTTTAATTAAA--A
1 ATATA--AT--T-T--AATA-AAATTCTAATAATTAA-TATTCTTATATGAATTTACTAAAATCA
56688717 T-
57 TA
*
56688718 ATATAATTTAATAAAATTCTAATAATCAATATTCTTATATGAATTTACTAAAATCATA
1 ATATAATTTAATAAAATTCTAATAATTAATATTCTTATATGAATTTACTAAAATCATA
56688776 ATATA
1 ATATA
56688781 TGATACTATA
Statistics
Matches: 94, Mismatches: 15, Indels: 31
0.67 0.11 0.22
Matches are distributed among these distances:
53 14 0.15
54 10 0.11
55 9 0.10
56 1 0.01
57 3 0.03
58 5 0.05
59 7 0.07
61 7 0.07
62 2 0.02
63 1 0.01
64 10 0.11
65 7 0.07
66 13 0.14
67 5 0.05
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (58 bp):
ATATAATTTAATAAAATTCTAATAATTAATATTCTTATATGAATTTACTAAAATCATA
Found at i:56688722 original size:18 final size:17
Alignment explanation
Indices: 56688682--56688734 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
56688672 AAATATAAAT
56688682 TAAAATA-ATAA-TT-A
1 TAAAATATATAATTTAA
*
56688696 TTAAATATAT--TTTAA
1 TAAAATATATAATTTAA
56688711 TTAAAATATATAATTTAA
1 -TAAAATATATAATTTAA
56688729 TAAAAT
1 TAAAAT
56688735 TCTAATAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
14 8 0.26
15 3 0.10
16 9 0.29
17 6 0.19
18 5 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAAATATATAATTTAA
Found at i:56688787 original size:119 final size:120
Alignment explanation
Indices: 56688569--56688854 Score: 495
Period size: 119 Copynumber: 2.4 Consensus size: 120
56688559 ATATTTAAAC
*
56688569 ATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCT
1 ATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATATTCT
* *
56688634 TATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAAAATA
66 TATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAAATTAAAATA
56688689 ATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTC-TAATAATCAATATTCT
1 ATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATATTCT
* *
56688753 TATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAATTTGAAATA
66 TATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAAATTAAAATA
*
56688808 ATTAA-TATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 A-TAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
56688855 TAAAATAATT
Statistics
Matches: 159, Mismatches: 6, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
119 108 0.68
120 51 0.32
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.43
Consensus pattern (120 bp):
ATAATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATATTCT
TATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAAATTAAAATA
Found at i:56688792 original size:60 final size:59
Alignment explanation
Indices: 56688608--56688794 Score: 157
Period size: 60 Copynumber: 3.1 Consensus size: 59
56688598 ATATAATTTA
*
56688608 ATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 ATAAAATTC-TAATAA-TAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
* * ** * * * ** * * * *
56688669 GTAAAATAT-AAATTAA-AATAATAATTAT-TAAATATATTTTAATTAAAATATATAAT-TT
1 ATAAAAT-TCTAA-TAATAAT-ATTCTTATATGAATTTACTAAAATCATAATATATGATACT
56688727 AATAAAATTCTAATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
1 -ATAAAATTCTAATAAT-AATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
56688788 ATAAAAT
1 ATAAAAT
56688795 ATAATTTGAA
Statistics
Matches: 91, Mismatches: 26, Indels: 19
0.67 0.19 0.14
Matches are distributed among these distances:
58 5 0.05
59 37 0.41
60 38 0.42
61 10 0.11
62 1 0.01
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (59 bp):
ATAAAATTCTAATAATAATATTCTTATATGAATTTACTAAAATCATAATATATGATACT
Found at i:56688851 original size:59 final size:58
Alignment explanation
Indices: 56688574--56688853 Score: 162
Period size: 59 Copynumber: 4.7 Consensus size: 58
56688564 TAAACATAAT
* *
56688574 TATTAAATATATTTTAATTAAAATATATAATTTAATAAAAT-T--CTT-AATAATTAA
1 TATTAAATATATTTTAATTAAAATATATGATTTAATAAAATATAATTTAAATAATTAA
** * * * * *
56688628 TATTCTTATATGAATTTACTCAAATCATAATATATGATACT-GTAAAATATAAATTAAAATAA-T
1 TATT-AAATAT--ATTT--T--AATTAAAATATATGAT-TTAATAAAATAT-AATTTAAATAATT
56688691 AA
57 AA
* * * * **
56688693 TTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTAATAATCAAT-ATTCT
1 -TATTAAATATATTTTAATTAAAATATATGATTTAATAAAA-TATAAT-TTAAATAATTAA
* * * ** * * *
56688753 TATATGAATTTACTAAAATCATAATATATGATACT-ATAAAATATAATTTGAAATAATTAA
1 TAT-TAAATATATTTTAATTAAAATATATGAT-TTAATAAAATATAATTT-AAATAATTAA
56688813 TATTAAATATATTTTAATTAAAATATATGATTTAATAAAAT
1 TATTAAATATATTTTAATTAAAATATATGATTTAATAAAAT
56688854 TTAAAATAAT
Statistics
Matches: 159, Mismatches: 44, Indels: 41
0.65 0.18 0.17
Matches are distributed among these distances:
54 4 0.03
55 4 0.03
57 4 0.03
58 3 0.02
59 62 0.39
60 38 0.24
61 21 0.13
62 2 0.01
63 4 0.03
65 8 0.05
66 9 0.06
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (58 bp):
TATTAAATATATTTTAATTAAAATATATGATTTAATAAAATATAATTTAAATAATTAA
Found at i:56695064 original size:26 final size:26
Alignment explanation
Indices: 56695030--56695102 Score: 67
Period size: 25 Copynumber: 2.8 Consensus size: 26
56695020 TTTTTTTTAA
* *
56695030 TTTTCAAAATTAAATATAAAAATTAT
1 TTTTTAAAATTAAATATAAAAATAAT
* * *
56695056 TTTTTAAAAAT-AAGATACAAATAAT
1 TTTTTAAAATTAAATATAAAAATAAT
*
56695081 TTTAGTAAAATTTAAATATAAA
1 TTT-TTAAAA-TTAAATATAAA
56695103 TATGGGCGGA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
25 14 0.40
26 14 0.40
27 1 0.03
28 6 0.17
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (26 bp):
TTTTTAAAATTAAATATAAAAATAAT
Found at i:56697708 original size:23 final size:23
Alignment explanation
Indices: 56697682--56697734 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
56697672 TAATGCAATT
*
56697682 CATTCTGACA-CTTCGGTGTGATC
1 CATTCTGACATCTT-GGTGGGATC
* *
56697705 CATTCTGGCATCTTGGTGGGATT
1 CATTCTGACATCTTGGTGGGATC
56697728 CATTCTG
1 CATTCTG
56697735 TGGAGTGTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 23 0.88
24 3 0.12
ACGTcount: A:0.15, C:0.23, G:0.25, T:0.38
Consensus pattern (23 bp):
CATTCTGACATCTTGGTGGGATC
Found at i:56698465 original size:117 final size:117
Alignment explanation
Indices: 56698259--56698490 Score: 401
Period size: 117 Copynumber: 2.0 Consensus size: 117
56698249 ATGTGCTTAC
* *
56698259 CTTGATAGGTCATATACAACATGTATCTAGGTCATTAAGAAGTATTGTGGAGTTTTAGTGACGTT
1 CTTGATAGGTCATATACAACATGTATCTAGGTCATTAAGAAGTATTGTGGAGTCTTAATGACGTT
*
56698324 TTGAACATGGCTTAGATGTTTTGGATGATTTTAGTATTACATATCGTATGGT
66 TTGAACATGGCTTAGATGTTTTGGATGATTTTAGTAGTACATATCGTATGGT
*
56698376 CTTGATAGGTTATATACAACATGTATCTAGGTCATTAAGAAGTATTGTGGAGTCTTAATGACGTT
1 CTTGATAGGTCATATACAACATGTATCTAGGTCATTAAGAAGTATTGTGGAGTCTTAATGACGTT
* * *
56698441 TTGAACATGTCTTGGGTGTTTTGGATGATTTTAGTAGTACATATCGTATG
66 TTGAACATGGCTTAGATGTTTTGGATGATTTTAGTAGTACATATCGTATG
56698491 TTTAATGACT
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
117 108 1.00
ACGTcount: A:0.27, C:0.09, G:0.23, T:0.40
Consensus pattern (117 bp):
CTTGATAGGTCATATACAACATGTATCTAGGTCATTAAGAAGTATTGTGGAGTCTTAATGACGTT
TTGAACATGGCTTAGATGTTTTGGATGATTTTAGTAGTACATATCGTATGGT
Found at i:56698963 original size:6 final size:6
Alignment explanation
Indices: 56698952--56698983 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
56698942 TTAAAAAATA
56698952 TATATT TATATT TATATT TATATT TATATT TA
1 TATATT TATATT TATATT TATATT TATATT TA
56698984 ATAATTTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
TATATT
Found at i:56702213 original size:21 final size:21
Alignment explanation
Indices: 56702174--56702219 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
56702164 GCGGTGGTTG
* * *
56702174 TGAGATTAATTATTATAGCGA
1 TGAGATTAAATACTATAGCAA
*
56702195 TGAGATTAAATACTGTAGCAA
1 TGAGATTAAATACTATAGCAA
56702216 TGAG
1 TGAG
56702220 GTCAAAAACA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.33
Consensus pattern (21 bp):
TGAGATTAAATACTATAGCAA
Found at i:56703729 original size:31 final size:31
Alignment explanation
Indices: 56703694--56703756 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
56703684 TGGGTTTAAA
56703694 AAAATATT-AGTACTATAATGAAGGAATTGGG
1 AAAATATTGA-TACTATAATGAAGGAATTGGG
* * *
56703725 AAAATATTGATGCTATAGTGAAGGATTTGGG
1 AAAATATTGATACTATAATGAAGGAATTGGG
56703756 A
1 A
56703757 TTTGAATTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 27 0.96
32 1 0.04
ACGTcount: A:0.41, C:0.03, G:0.25, T:0.30
Consensus pattern (31 bp):
AAAATATTGATACTATAATGAAGGAATTGGG
Found at i:56704197 original size:12 final size:12
Alignment explanation
Indices: 56704180--56704205 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
56704170 GAAAAGGAAG
56704180 AAAACAAAAAGA
1 AAAACAAAAAGA
56704192 AAAACAAAAAGA
1 AAAACAAAAAGA
56704204 AA
1 AA
56704206 GATGTATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.85, C:0.08, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAACAAAAAGA
Found at i:56704356 original size:18 final size:18
Alignment explanation
Indices: 56704322--56704365 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
56704312 GAAGAGGAGG
* *
56704322 AAAAATAAAAAAGAAAAT
1 AAAAAGAAAAAAGAAAAA
56704340 AAAAAGAAAAACA-AAAAA
1 AAAAAGAAAAA-AGAAAAA
56704358 AAAAAGAA
1 AAAAAGAA
56704366 GTATAATAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 22 0.96
19 1 0.04
ACGTcount: A:0.86, C:0.02, G:0.07, T:0.05
Consensus pattern (18 bp):
AAAAAGAAAAAAGAAAAA
Found at i:56704362 original size:12 final size:12
Alignment explanation
Indices: 56704322--56704362 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
56704312 GAAGAGGAGG
56704322 AAAAATAAAAAA
1 AAAAATAAAAAA
* *
56704334 GAAAATAAAAAG
1 AAAAATAAAAAA
*
56704346 AAAAACAAAAAA
1 AAAAATAAAAAA
56704358 AAAAA
1 AAAAA
56704363 GAAGTATAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.88, C:0.02, G:0.05, T:0.05
Consensus pattern (12 bp):
AAAAATAAAAAA
Found at i:56704948 original size:24 final size:24
Alignment explanation
Indices: 56704903--56704949 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
56704893 TAAACTCAAT
* ** *
56704903 TTTTCTGAAAAATTAAATTAAAAG
1 TTTTATGAAAAACAAAAATAAAAG
56704927 TTTTATGAAAAACAAAAATAAAA
1 TTTTATGAAAAACAAAAATAAAA
56704950 TAAAGGATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.32
Consensus pattern (24 bp):
TTTTATGAAAAACAAAAATAAAAG
Found at i:56705300 original size:9 final size:9
Alignment explanation
Indices: 56705286--56705315 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
56705276 TTCATAACAA
56705286 TAAAAAAAT
1 TAAAAAAAT
56705295 TAAAAAAAAT
1 T-AAAAAAAT
56705305 TAAAAAAAT
1 TAAAAAAAT
56705314 TA
1 TA
56705316 TTAAACCCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
TAAAAAAAT
Found at i:56705320 original size:12 final size:10
Alignment explanation
Indices: 56705287--56705312 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
56705277 TCATAACAAT
56705287 AAAAAAATTA
1 AAAAAAATTA
56705297 AAAAAAATTA
1 AAAAAAATTA
56705307 AAAAAA
1 AAAAAA
56705313 TTATTAAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAAATTA
Found at i:56708242 original size:46 final size:45
Alignment explanation
Indices: 56708172--56708347 Score: 187
Period size: 46 Copynumber: 3.8 Consensus size: 45
56708162 TGTAACCCGC
* *
56708172 CCATAAGCGAACTTGGACTTAACTCAACGAGCTCAGGAGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTC-GGAGTTCGCAT
* *
56708218 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA-TGC-CTAGTT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGAGTTCGC-A--T
* * *
56708264 ACATCTTA-CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
1 CCA--TAAGCGAACTCGGACTCAACTCAACGAGCTCGGA-GTTCGCAT
* *
56708311 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA
56708348 TGCCCAAATA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 5 0.05
46 63 0.58
47 31 0.28
48 2 0.02
49 3 0.03
50 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.22
Consensus pattern (45 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGAGTTCGCAT
Found at i:56708293 original size:93 final size:93
Alignment explanation
Indices: 56708179--56708351 Score: 294
Period size: 93 Copynumber: 1.9 Consensus size: 93
56708169 CGCCCATAAG
* *
56708179 CGAACTTGGACTTAACTCAACGAGCTCAGGA-GTTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTC-GGACGTTCGCATCCATAAGTGAACTCGGACTCAACTC
56708243 AACGAGCTCGGATGCCTAGTTACATCTTA
65 AACGAGCTCGGATGCCTAGTTACATCTTA
*
56708272 CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
56708337 ACGAGTTCGGATGCC
66 ACGAGCTCGGATGCC
56708352 CAAATATCCT
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
92 3 0.04
93 72 0.96
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTTA
Found at i:56711833 original size:26 final size:26
Alignment explanation
Indices: 56711797--56711849 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
56711787 TACTTTTGAG
56711797 AACATTTACTTAAACACCTTGTATGC
1 AACATTTACTTAAACACCTTGTATGC
56711823 AACATTTACTTAAACACCTTGTATGC
1 AACATTTACTTAAACACCTTGTATGC
56711849 A
1 A
56711850 TGTTTTCTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.34
Consensus pattern (26 bp):
AACATTTACTTAAACACCTTGTATGC
Found at i:56714377 original size:21 final size:21
Alignment explanation
Indices: 56714350--56714414 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
56714340 AATCATCCTG
56714350 AAGGCCATTGCTTTCAATGTC
1 AAGGCCATTGCTTTCAATGTC
* * * *
56714371 GAGGCCATTTCCTTCTATGTC
1 AAGGCCATTGCTTTCAATGTC
* * *
56714392 AAGGCTATTGCTGTCAATATC
1 AAGGCCATTGCTTTCAATGTC
56714413 AA
1 AA
56714415 TGTCGTTCCC
Statistics
Matches: 33, Mismatches: 11, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (21 bp):
AAGGCCATTGCTTTCAATGTC
Found at i:56714734 original size:24 final size:24
Alignment explanation
Indices: 56714707--56714756 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
56714697 TTAGTCTTTA
56714707 TATACCATAAAAAGGACATGAAAC
1 TATACCATAAAAAGGACATGAAAC
56714731 TATACCATAAAAAGGACATGAAAC
1 TATACCATAAAAAGGACATGAAAC
56714755 TA
1 TA
56714757 CCTTAATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.54, C:0.16, G:0.12, T:0.18
Consensus pattern (24 bp):
TATACCATAAAAAGGACATGAAAC
Found at i:56716083 original size:15 final size:15
Alignment explanation
Indices: 56716043--56716086 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
56716033 AAATTTCAAT
*
56716043 AAATAAAAAATATCA
1 AAATAAAAAATATTA
* **
56716058 AATTATTAAATATTA
1 AAATAAAAAATATTA
56716073 AAATAAAAAATATT
1 AAATAAAAAATATT
56716087 TTATTCAAAA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATAAAAAATATTA
Found at i:56725399 original size:117 final size:118
Alignment explanation
Indices: 56725275--56725506 Score: 430
Period size: 118 Copynumber: 2.0 Consensus size: 118
56725265 TTTTGATGAG
56725275 AATGTTATATGTCG-AAAAAAATGTTGATTAAAATCTCGAGAAAGTTAAAAAAAATATGTTTGGT
1 AATGTTATATGTCGAAAAAAAATGTTGATTAAAATCTCGAGAAAGTTAAAAAAAATATGTTTGGT
*
56725339 ACACTCAACACTTTATTAAAATGATGCTTATTATAATGTCTTCCAAATTTGTT
66 ACACTCAACACTTTATTAAAATGATGCTTATTATAATATCTTCCAAATTTGTT
*
56725392 AATGTTATATGTCGAAAAAAAATGTTGATTAAAATTTCGAGAAAGTTAAAAAAAATATGTTTGGT
1 AATGTTATATGTCGAAAAAAAATGTTGATTAAAATCTCGAGAAAGTTAAAAAAAATATGTTTGGT
*
56725457 ACATTCAACACTTTATTAAAATGATGCTTATTATAATATCTTCCAAATTT
66 ACACTCAACACTTTATTAAAATGATGCTTATTATAATATCTTCCAAATTT
56725507 ATTTTTTTTA
Statistics
Matches: 111, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
117 14 0.13
118 97 0.87
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.37
Consensus pattern (118 bp):
AATGTTATATGTCGAAAAAAAATGTTGATTAAAATCTCGAGAAAGTTAAAAAAAATATGTTTGGT
ACACTCAACACTTTATTAAAATGATGCTTATTATAATATCTTCCAAATTTGTT
Found at i:56730375 original size:21 final size:21
Alignment explanation
Indices: 56730349--56730392 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
56730339 GTACTTGTGT
56730349 TAATTTTTATTTTAATTTTGG
1 TAATTTTTATTTTAATTTTGG
56730370 TAATTTTTATTTTAATTTTGG
1 TAATTTTTATTTTAATTTTGG
56730391 TA
1 TA
56730393 CTTAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66
Consensus pattern (21 bp):
TAATTTTTATTTTAATTTTGG
Found at i:56738043 original size:26 final size:26
Alignment explanation
Indices: 56738014--56738078 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
56738004 TTTAAAATAT
56738014 TTTTTATAATTTAAAT-TTTTATAGAA
1 TTTTTATAATTTAAATATTTTATA-AA
* *
56738040 TTTTTA-AATTATATATATTTTATATA
1 TTTTTATAATT-TAAATATTTTATAAA
56738066 TTTTTAATAATTT
1 TTTTT-ATAATTT
56738079 TAGAGTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
25 4 0.12
26 16 0.48
27 9 0.27
28 4 0.12
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (26 bp):
TTTTTATAATTTAAATATTTTATAAA
Found at i:56743809 original size:24 final size:24
Alignment explanation
Indices: 56743771--56743817 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
56743761 AGGTAAAATT
56743771 ATTTCTGCCTCTGCATTTTTTTTA
1 ATTTCTGCCTCTGCATTTTTTTTA
* *
56743795 ATTTCTTCCTTTGCATTTTTTTT
1 ATTTCTGCCTCTGCATTTTTTTT
56743818 CTTTTTTCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.11, C:0.19, G:0.06, T:0.64
Consensus pattern (24 bp):
ATTTCTGCCTCTGCATTTTTTTTA
Found at i:56749884 original size:35 final size:35
Alignment explanation
Indices: 56749842--56749913 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
56749832 ATATGCAAGA
56749842 TAATTAGAAAATGGTGACTAGTAGGATGATATGCC
1 TAATTAGAAAATGGTGACTAGTAGGATGATATGCC
56749877 TAATTAGAAAATGGTGACTAGTAGGATGATATGCC
1 TAATTAGAAAATGGTGACTAGTAGGATGATATGCC
56749912 TA
1 TA
56749914 CCAGTATGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.29
Consensus pattern (35 bp):
TAATTAGAAAATGGTGACTAGTAGGATGATATGCC
Found at i:56759210 original size:14 final size:14
Alignment explanation
Indices: 56759191--56759218 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
56759181 TAAAAACCTT
56759191 AAAAAAAAGAAAAA
1 AAAAAAAAGAAAAA
56759205 AAAAAAAAGAAAAA
1 AAAAAAAAGAAAAA
56759219 CTCTCCCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (14 bp):
AAAAAAAAGAAAAA
Found at i:56764335 original size:13 final size:13
Alignment explanation
Indices: 56764317--56764341 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56764307 AAATCTGTTT
56764317 TGAGTGCTGCTCA
1 TGAGTGCTGCTCA
56764330 TGAGTGCTGCTC
1 TGAGTGCTGCTC
56764342 TTGTTAAGGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.24, G:0.32, T:0.32
Consensus pattern (13 bp):
TGAGTGCTGCTCA
Found at i:56764799 original size:16 final size:16
Alignment explanation
Indices: 56764778--56764819 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
56764768 TTATTAAATT
*
56764778 ATATATTTTAATTATA
1 ATATATTTTAATAATA
56764794 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
56764809 AT-TATGTTTAA
1 ATATAT-TTTAA
56764820 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:56764804 original size:15 final size:15
Alignment explanation
Indices: 56764769--56764810 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
56764759 TTAAGAATTT
*
56764769 TATTAAATTAT-ATA
1 TATTTAATTATAATA
56764783 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
56764797 TATTTAATAATAAT
1 TATTTAATTATAAT
56764811 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:56764950 original size:18 final size:17
Alignment explanation
Indices: 56764922--56764956 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
56764912 ATTATTAAGA
*
56764922 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
56764939 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
56764957 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:56764955 original size:157 final size:157
Alignment explanation
Indices: 56764756--56765069 Score: 583
Period size: 157 Copynumber: 2.0 Consensus size: 157
56764746 AGAATATTAG
*
56764756 TTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAA
1 TTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAA
*
56764821 TATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAAATTAAATAACAATAACAATAA
66 TATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAAATTAAATAACAATAACAATAA
*
56764886 TAATTTACCAAAACAAATTTCTGCTAA
131 TAATTTACCAAAACAAATTTATGCTAA
56764913 TTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAA
1 TTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAA
*
56764978 TATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATAA
66 TATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAAATTAAATAACAATAACAATAA
*
56765043 TCATTTACCAAAACAAATTTATGCTAA
131 TAATTTACCAAAACAAATTTATGCTAA
56765070 GGGTATTCTA
Statistics
Matches: 152, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 152 1.00
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.44
Consensus pattern (157 bp):
TTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAA
TATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAAATTAAATAACAATAACAATAA
TAATTTACCAAAACAAATTTATGCTAA
Found at i:56765202 original size:45 final size:44
Alignment explanation
Indices: 56765121--56765211 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 44
56765111 ATCTCTATTC
* *
56765121 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTACTATTACACCTCTATTCCAATA
*** *
56765165 CATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCCAATA
1 CATTCAACCAAACACAAGA-TTACTATTACACCTCTATTCCAATA
56765210 CA
1 CA
56765212 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 16 0.40
45 24 0.60
ACGTcount: A:0.35, C:0.29, G:0.05, T:0.31
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACACCTCTATTCCAATA
Found at i:56765213 original size:16 final size:16
Alignment explanation
Indices: 56765192--56765259 Score: 109
Period size: 16 Copynumber: 4.2 Consensus size: 16
56765182 GATTTGCTAT
*
56765192 TACACCTCTATTCCAA
1 TACACCTCTAATCCAA
*
56765208 TACACCTCTAATCCAT
1 TACACCTCTAATCCAA
56765224 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
56765240 TACACCTTTAATCCAA
1 TACACCTCTAATCCAA
56765256 TACA
1 TACA
56765260 GCGAACCAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:56768432 original size:27 final size:23
Alignment explanation
Indices: 56768378--56768437 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
56768368 ATACACGGAT
56768378 TCCAACCAAACACATTGAAATAA
1 TCCAACCAAACACATTGAAATAA
56768401 TCCAACCAAACACATTGAAATAA
1 TCCAACCAAACACATTGAAATAA
*
56768424 TCCACCCAAACACA
1 TCCAACCAAACACA
56768438 CTAGAACGAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.50, C:0.32, G:0.03, T:0.15
Consensus pattern (23 bp):
TCCAACCAAACACATTGAAATAA
Found at i:56768641 original size:24 final size:23
Alignment explanation
Indices: 56768593--56768642 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
56768583 TATTCAATTT
56768593 TCATATTTCAATTCAATCACTTTC
1 TCATATTTCAATTCAATCAC-TTC
*
56768617 TCATATTTTCCATTCAAATCA-TTC
1 TCATA-TTTCAATTC-AATCACTTC
56768641 TC
1 TC
56768643 CATTTAATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 10 0.43
25 8 0.35
26 5 0.22
ACGTcount: A:0.28, C:0.26, G:0.00, T:0.46
Consensus pattern (23 bp):
TCATATTTCAATTCAATCACTTC
Found at i:56768667 original size:10 final size:10
Alignment explanation
Indices: 56768652--56768677 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
56768642 CCATTTAATC
56768652 ACAATTCAAT
1 ACAATTCAAT
56768662 ACAATTCAAT
1 ACAATTCAAT
56768672 ACAATT
1 ACAATT
56768678 TTCCACTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (10 bp):
ACAATTCAAT
Found at i:56769461 original size:16 final size:16
Alignment explanation
Indices: 56769442--56769474 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
56769432 GAATAGTCTC
56769442 TGTTTCTTTTCTTCTT
1 TGTTTCTTTTCTTCTT
*
56769458 TGTTTCTTTTGTTCTT
1 TGTTTCTTTTCTTCTT
56769474 T
1 T
56769475 TACTTTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.15, G:0.09, T:0.76
Consensus pattern (16 bp):
TGTTTCTTTTCTTCTT
Found at i:56777058 original size:27 final size:27
Alignment explanation
Indices: 56777029--56777081 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
56777019 TTTTTAGATT
56777029 TTTTTA-AAAAAATATAAATTTTAAAA
1 TTTTTATAAAAAATATAAATTTTAAAA
* * *
56777055 TTTTTATAAATATTTTAAATTTTAAAA
1 TTTTTATAAAAAATATAAATTTTAAAA
56777082 ATCATTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
TTTTTATAAAAAATATAAATTTTAAAA
Found at i:56777076 original size:19 final size:19
Alignment explanation
Indices: 56777041--56777097 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 19
56777031 TTTAAAAAAA
*
56777041 TATAAAT-TTTAAAATTTT
1 TATAAATATTTTAAATTTT
56777059 TATAAATATTTTAAA-TTT
1 TATAAATATTTTAAATTTT
* *
56777077 TAAAAATCATTTTGAATTTT
1 TATAAAT-ATTTTAAATTTT
56777097 T
1 T
56777098 GAAAATTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 16 0.48
19 13 0.39
20 4 0.12
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (19 bp):
TATAAATATTTTAAATTTT
Found at i:56777078 original size:18 final size:18
Alignment explanation
Indices: 56777041--56777096 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 18
56777031 TTTAAAAAAA
*
56777041 TATAAAT-TTTAAAATTTT
1 TATAAATATTTTAAA-TTT
56777059 TATAAATATTTTAAATTT
1 TATAAATATTTTAAATTT
* *
56777077 TAAAAATCATTTTGAATTT
1 TATAAAT-ATTTTAAATTT
56777096 T
1 T
56777097 TGAAAATTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 16 0.48
19 17 0.52
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (18 bp):
TATAAATATTTTAAATTT
Found at i:56777102 original size:20 final size:18
Alignment explanation
Indices: 56777053--56777114 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 18
56777043 TAAATTTTAA
*
56777053 AATTTTTATAAATATTTTA
1 AATTTTTA-AAATATTTTG
*
56777072 AATTTTAAAAATCATTTTG
1 AATTTTTAAAAT-ATTTTG
56777091 AATTTTTGAAAATTATTTTG
1 AATTTTT-AAAA-TATTTTG
56777111 AATT
1 AATT
56777115 ATTTTGTAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
18 4 0.11
19 18 0.49
20 14 0.38
21 1 0.03
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (18 bp):
AATTTTTAAAATATTTTG
Found at i:56780933 original size:25 final size:25
Alignment explanation
Indices: 56780885--56780936 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
56780875 TAAAAAGATG
* *
56780885 GAACAGAGCAGAGCAATACTGAACA
1 GAACAGAACAGAGCAATACAGAACA
56780910 GAACAGAACAGAGCAA-AGCAGAACA
1 GAACAGAACAGAGCAATA-CAGAACA
56780935 GA
1 GA
56780937 GCATGTATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 1 0.04
25 23 0.96
ACGTcount: A:0.52, C:0.19, G:0.25, T:0.04
Consensus pattern (25 bp):
GAACAGAACAGAGCAATACAGAACA
Found at i:56783744 original size:29 final size:29
Alignment explanation
Indices: 56783663--56783781 Score: 93
Period size: 29 Copynumber: 4.2 Consensus size: 29
56783653 TACATACATG
*
56783663 CATATGGCCCACTAGGCCCAA-T-ATTATT
1 CATATAGCCCACTAGGCCCAATTCA-TATT
* * * *
56783691 CAAATTGCTCATCT-GGCCCAGTTCATATT
1 CATATAGCCCA-CTAGGCCCAATTCATATT
* * * *
56783720 CTTATGGCCCACTAGGCTCAATTCACATT
1 CATATAGCCCACTAGGCCCAATTCATATT
* *
56783749 CATATAGCCCATTAGGCCCAAATCATATT
1 CATATAGCCCACTAGGCCCAATTCATATT
56783778 -ATAT
1 CATAT
56783782 TCATGCTCAC
Statistics
Matches: 70, Mismatches: 17, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
28 20 0.29
29 49 0.70
30 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.13, T:0.31
Consensus pattern (29 bp):
CATATAGCCCACTAGGCCCAATTCATATT
Found at i:56788053 original size:89 final size:89
Alignment explanation
Indices: 56787908--56788072 Score: 258
Period size: 89 Copynumber: 1.9 Consensus size: 89
56787898 TATTGACAAT
*
56787908 TTAATAATCTACAACACTAGTGGTTCATCCACAAATTACTGGCAACTTTTAGCTGCAAATATGTT
1 TTAATAATCTACAACACTAGTGGTTCATCCACAAATTACTGACAACTTTTAGCTGCAAATATGTT
56787973 GTGCATCCACAGCCTGTTGACAGC
66 GTGCATCCACAGCCTGTTGACAGC
* * * * * * *
56787997 TTAATAATTTGCAACATTGGTGGTTCATCCATAAATTACTGACAGCTTTTATCTGCAAATATGTT
1 TTAATAATCTACAACACTAGTGGTTCATCCACAAATTACTGACAACTTTTAGCTGCAAATATGTT
56788062 GTGCATCCACA
66 GTGCATCCACA
56788073 ACAAGTGGTA
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
89 68 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.33
Consensus pattern (89 bp):
TTAATAATCTACAACACTAGTGGTTCATCCACAAATTACTGACAACTTTTAGCTGCAAATATGTT
GTGCATCCACAGCCTGTTGACAGC
Found at i:56788185 original size:100 final size:100
Alignment explanation
Indices: 56788012--56788191 Score: 301
Period size: 100 Copynumber: 1.8 Consensus size: 100
56788002 AATTTGCAAC
56788012 ATTGGTGGTTCATCCATAAATTACTGACAGCTTTTATCTGCAAATATGTTGTGCATCCACAACAA
1 ATTGGTGGTTCATCCATAAATTACTGACAGCTTTTATCTGCAAATATGTTGTGCATCCACAACAA
56788077 GTGGTAGCTTGTCTGTGAACTATTTTTTTTTAAAT
66 GTGGTAGCTTGTCTGTGAACTATTTTTTTTTAAAT
** *
56788112 ATTGGTGGTTCATCCATAAATTACT-AGTTGCTTTTATCTGCAAATATGTTGTGCA-CCTACAAT
1 ATTGGTGGTTCATCCATAAATTACTGA-CAGCTTTTATCTGCAAATATGTTGTGCATCC-ACAAC
56788175 AAGTGGTAGCTTGTCTG
64 AAGTGGTAGCTTGTCTG
56788192 CAAACTGTTT
Statistics
Matches: 75, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
99 3 0.04
100 72 0.96
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.39
Consensus pattern (100 bp):
ATTGGTGGTTCATCCATAAATTACTGACAGCTTTTATCTGCAAATATGTTGTGCATCCACAACAA
GTGGTAGCTTGTCTGTGAACTATTTTTTTTTAAAT
Found at i:56788257 original size:100 final size:99
Alignment explanation
Indices: 56788016--56788227 Score: 236
Period size: 100 Copynumber: 2.2 Consensus size: 99
56788006 TGCAACATTG
**
56788016 GTGGTTCATCCATAAATTACT-G-ACAGCTTTTATCTGCAAATATGTTGTGCATCCACAACAAGT
1 GTGGTTCATCCATAAATTACTAGTTGAG--TTTATCTGCAAATATGTTGTGCATCCACAACAAGT
* * * * * *
56788079 GGTAGCTTGTCTGTGAACTATTTTTTTTTAAATATTG
64 GGTAGCTTGTCTGTCAAC-ACTGTTTTTAAAATACTA
** *
56788116 GTGGTTCATCCATAAATTACTAGTTGCTTTTATCTGCAAATATGTTGTGCA-CCTACAATAAGTG
1 GTGGTTCATCCATAAATTACTAGTTGAGTTTATCTGCAAATATGTTGTGCATCC-ACAACAAGTG
56788180 GTAGCTTGTCTG-CAA-ACTGTTTTTAAAATACTA
65 GTAGCTTGTCTGTCAACACTGTTTTTAAAATACTA
* *
56788213 GTTGTTTATCCATAA
1 GTGGTTCATCCATAA
56788228 TTTTTACTGT
Statistics
Matches: 96, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
97 26 0.27
99 4 0.04
100 65 0.68
101 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.40
Consensus pattern (99 bp):
GTGGTTCATCCATAAATTACTAGTTGAGTTTATCTGCAAATATGTTGTGCATCCACAACAAGTGG
TAGCTTGTCTGTCAACACTGTTTTTAAAATACTA
Found at i:56789552 original size:25 final size:27
Alignment explanation
Indices: 56789509--56789559 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
56789499 CATAATAAAC
*
56789509 AAAATAAAAATCACGAAAAATATGGAT
1 AAAATAAAAACCACGAAAAATATGGAT
*
56789536 AAAAT-AAAACCAC-AAAATTATGGA
1 AAAATAAAAACCACGAAAAATATGGA
56789560 CAGAAACATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 10 0.45
26 7 0.32
27 5 0.23
ACGTcount: A:0.63, C:0.10, G:0.10, T:0.18
Consensus pattern (27 bp):
AAAATAAAAACCACGAAAAATATGGAT
Found at i:56790305 original size:23 final size:21
Alignment explanation
Indices: 56790262--56790307 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
56790252 TACAAATAAT
**
56790262 ATTTTTTAAAATTTAGGTTTA
1 ATTTTTTAAAATTTAACTTTA
56790283 ATTTTTTAAATATTTTAACTTTA
1 ATTTTTTAAA-A-TTTAACTTTA
56790306 AT
1 AT
56790308 AATAAATAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 10 0.48
22 1 0.05
23 10 0.48
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (21 bp):
ATTTTTTAAAATTTAACTTTA
Found at i:56792941 original size:27 final size:25
Alignment explanation
Indices: 56792910--56792962 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
56792900 TATTTATTTC
*
56792910 TTTAAATATCTATGATTAAATTAAAAT
1 TTTAAATATCCAT--TTAAATTAAAAT
* *
56792937 TTTAAGTATCCATTTAAATTATAAT
1 TTTAAATATCCATTTAAATTAAAAT
56792962 T
1 T
56792963 AAAATTTCGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 12 0.52
27 11 0.48
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (25 bp):
TTTAAATATCCATTTAAATTAAAAT
Found at i:56793009 original size:29 final size:28
Alignment explanation
Indices: 56792924--56793013 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 28
56792914 AATATCTATG
* *
56792924 ATTAAATTAAAATTTTA-AGTATCCATTTAA
1 ATTAAATTAAAATTTTATA-TAT--AATTAC
** *
56792954 ATTATAATTAAAATTTCGTATGTAATTAC
1 ATTA-AATTAAAATTTTATATATAATTAC
56792983 ATTAAATTAAAATTTATATATATAATTAC
1 ATTAAATTAAAATTT-TATATATAATTAC
56793012 AT
1 AT
56793014 ATTTTAAAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
28 11 0.22
29 20 0.41
30 4 0.08
31 13 0.27
32 1 0.02
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (28 bp):
ATTAAATTAAAATTTTATATATAATTAC
Found at i:56795061 original size:22 final size:23
Alignment explanation
Indices: 56795025--56795076 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
56795015 GTGTTATTGC
* *
56795025 CACTTGTACCGTAGTGCCAC-AA
1 CACTTGCACCATAGTGCCACTAA
*
56795047 CACTTGCACCATAGTGCCACTAT
1 CACTTGCACCATAGTGCCACTAA
56795070 CACTTGC
1 CACTTGC
56795077 GCGTATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.25, C:0.35, G:0.15, T:0.25
Consensus pattern (23 bp):
CACTTGCACCATAGTGCCACTAA
Found at i:56797984 original size:15 final size:16
Alignment explanation
Indices: 56797964--56797999 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 16
56797954 TATACGTTTG
56797964 TTTATTGAATT-TTTT
1 TTTATTGAATTATTTT
56797979 TTTATTGAATTAATTTT
1 TTTATTGAATT-ATTTT
56797996 TTTA
1 TTTA
56798000 GATAATTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 11 0.58
17 8 0.42
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (16 bp):
TTTATTGAATTATTTT
Done.