Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001736.1 Hibiscus syriacus cultivar Beakdansim tig00003507_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: 1778036
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 9
Found at i:805319 original size:42 final size:40
Alignment explanation
Indices: 805256--805376 Score: 125
Period size: 42 Copynumber: 2.9 Consensus size: 40
805246 ATATAAAATT
* *
805256 TGTCCCGAAGGACCACATATATGTCCCGAAGGACCACATAGA
1 TGTCCCG-AGGACTACGTATATGTCCC-AAGGACCACATAGA
* ** *
805298 TGTCCCAGAGGACTACGTATATGTCCCAGAGGACTATGTATA
1 TGTCCC-GAGGACTACGTATATGTCCCA-AGGACCACATAGA
*
805340 TATCCCCGAGGACTACGTATATGTCCCAAAGGACCAC
1 TGT-CCCGAGGACTACGTATATGTCCC-AAGGACCAC
805377 TCCTTAAGGA
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
41 1 0.02
42 60 0.91
43 5 0.08
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.21
Consensus pattern (40 bp):
TGTCCCGAGGACTACGTATATGTCCCAAGGACCACATAGA
Found at i:805619 original size:14 final size:14
Alignment explanation
Indices: 805600--805626 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
805590 GCTCATAGCT
805600 TCATATCACATATA
1 TCATATCACATATA
805614 TCATATCACATAT
1 TCATATCACATAT
805627 TCTTGTATTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.22, G:0.00, T:0.37
Consensus pattern (14 bp):
TCATATCACATATA
Found at i:806025 original size:29 final size:29
Alignment explanation
Indices: 805983--806067 Score: 170
Period size: 29 Copynumber: 2.9 Consensus size: 29
805973 TTTCTCTCTA
805983 GATAAATCTTATTTTGTCTACTTGTCGTC
1 GATAAATCTTATTTTGTCTACTTGTCGTC
806012 GATAAATCTTATTTTGTCTACTTGTCGTC
1 GATAAATCTTATTTTGTCTACTTGTCGTC
806041 GATAAATCTTATTTTGTCTACTTGTCG
1 GATAAATCTTATTTTGTCTACTTGTCG
806068 AGACTTTGCT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 56 1.00
ACGTcount: A:0.21, C:0.16, G:0.14, T:0.48
Consensus pattern (29 bp):
GATAAATCTTATTTTGTCTACTTGTCGTC
Found at i:808153 original size:23 final size:23
Alignment explanation
Indices: 808123--808171 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
808113 TGGTAGTTGG
*
808123 TTTAATGG-ATGTTTAAACTTTAT
1 TTTAATGGTATATTTAAAC-TTAT
*
808146 TTTAATGGTATATTTAAGCTTAT
1 TTTAATGGTATATTTAAACTTAT
808169 TTT
1 TTT
808172 GGTTTTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.29, C:0.04, G:0.12, T:0.55
Consensus pattern (23 bp):
TTTAATGGTATATTTAAACTTAT
Found at i:815097 original size:19 final size:20
Alignment explanation
Indices: 815058--815101 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
815048 TTAACTTTTT
*
815058 CTTTTCTCTTTCATCTTTAA
1 CTTTTCTATTTCATCTTTAA
815078 CTTTTCTATTTCAT-TTTAA
1 CTTTTCTATTTCATCTTTAA
815097 CTTTT
1 CTTTT
815102 ATTTTTCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.16, C:0.20, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTCTATTTCATCTTTAA
Found at i:815108 original size:19 final size:20
Alignment explanation
Indices: 815066--815108 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
815056 TTCTTTTCTC
*
815066 TTTCATCTTTAACTTTTCTA
1 TTTCATCTTTAACTTTTATA
*
815086 TTTCAT-TTTAACTTTTATT
1 TTTCATCTTTAACTTTTATA
815105 TTTC
1 TTTC
815109 TCTCTCATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.19, C:0.16, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTCATCTTTAACTTTTATA
Found at i:818381 original size:23 final size:23
Alignment explanation
Indices: 818351--818399 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
818341 TGGTGGTTAG
*
818351 TTTAATGG-ATGTTTAAACTTTAT
1 TTTAATGGTATATTT-AACTTTAT
*
818374 TTTAATGGTATATTTAATTTTAT
1 TTTAATGGTATATTTAACTTTAT
818397 TTT
1 TTT
818400 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.59
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:822066 original size:21 final size:21
Alignment explanation
Indices: 822020--822074 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
822010 TTTAAAAGGT
822020 AGTATCAATACTCAATCAAAG
1 AGTATCAATACTCAATCAAAG
* *
822041 TGTATCAATACTCGATGC-AAG
1 AGTATCAATACTCAAT-CAAAG
*
822062 AGTATCGATACTC
1 AGTATCAATACTC
822075 CCCGTAGAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (21 bp):
AGTATCAATACTCAATCAAAG
Found at i:822382 original size:11 final size:11
Alignment explanation
Indices: 822366--822391 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
822356 AATAATAATA
822366 AATATCTGAAT
1 AATATCTGAAT
822377 AATATCTGAAT
1 AATATCTGAAT
822388 AATA
1 AATA
822392 GAATAGTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.35
Consensus pattern (11 bp):
AATATCTGAAT
Found at i:823198 original size:20 final size:20
Alignment explanation
Indices: 823173--823216 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
823163 TGCTTGAACA
*
823173 GAGTCGAGTTATGCCTAGTC
1 GAGTCGAGTTATGCCTAGCC
* *
823193 GAGTCGAGTTGTGCTTAGCC
1 GAGTCGAGTTATGCCTAGCC
823213 GAGT
1 GAGT
823217 TGAATCATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.30
Consensus pattern (20 bp):
GAGTCGAGTTATGCCTAGCC
Found at i:825053 original size:29 final size:29
Alignment explanation
Indices: 825017--825167 Score: 123
Period size: 29 Copynumber: 5.3 Consensus size: 29
825007 CATTTTACAC
* **
825017 AAATAGCACCCTTTTTAAAATAATTACCA
1 AAATAGCACCCATTTCGAAATAATTACCA
* *
825046 AAATAGCACCCTTTTCGAACTAATT-CTCA
1 AAATAGCACCCATTTCGAAATAATTAC-CA
* * *
825075 AAATAGCACCAATTTCGAATTAATTCCCA
1 AAATAGCACCCATTTCGAAATAATTACCA
* * *
825104 GAATATCA--C-TTTTGAAA-AATTACCA
1 AAATAGCACCCATTTCGAAATAATTACCA
* * *
825129 AAATAGCACCCATTTGGAATTAATTCCCA
1 AAATAGCACCCATTTCGAAATAATTACCA
*
825158 TAATAGCACC
1 AAATAGCACC
825168 AAAACTGAAT
Statistics
Matches: 98, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
25 13 0.13
26 6 0.06
27 1 0.01
28 7 0.07
29 70 0.71
30 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.29
Consensus pattern (29 bp):
AAATAGCACCCATTTCGAAATAATTACCA
Found at i:825178 original size:83 final size:84
Alignment explanation
Indices: 825029--825191 Score: 222
Period size: 83 Copynumber: 2.0 Consensus size: 84
825019 ATAGCACCCT
* * **
825029 TTTTAAAATAATTACCAAAATAGCACCCTTTTCGAACTAATTCTCAAAATAGCACCAATTTCGAA
1 TTTTAAAATAATTACCAAAATAGCACCCATTTCGAACTAATTCCCAAAATAGCACCAAACTCGAA
825094 TTAATTCCCAGAATATCAC
66 TTAATTCCCAGAATATCAC
* * * *
825113 TTTTGAAA-AATTACCAAAATAGCACCCATTTGGAATTAATTCCCATAATAGCACCAAAACT-GA
1 TTTTAAAATAATTACCAAAATAGCACCCATTTCGAACTAATTCCCAAAATAGCACC-AAACTCGA
*
825176 ATTAATTCTCAGAATA
65 ATTAATTCCCAGAATA
825192 GCATCGGTCA
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
83 59 0.86
84 10 0.14
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.30
Consensus pattern (84 bp):
TTTTAAAATAATTACCAAAATAGCACCCATTTCGAACTAATTCCCAAAATAGCACCAAACTCGAA
TTAATTCCCAGAATATCAC
Found at i:825230 original size:18 final size:18
Alignment explanation
Indices: 825207--825248 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
825197 GGTCAACGAT
825207 CGGGTCGGGTCGGGTCAA
1 CGGGTCGGGTCGGGTCAA
825225 CGGGTCGGGTCGGGTCAA
1 CGGGTCGGGTCGGGTCAA
825243 CGGGTC
1 CGGGTC
825249 ATGACCGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.10, C:0.24, G:0.50, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCGGGTCAA
Found at i:825236 original size:23 final size:22
Alignment explanation
Indices: 825197--825240 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
825187 GAATAGCATC
825197 GGTCAACGATCGGGTCGGGTCG
1 GGTCAACGATCGGGTCGGGTCG
*
825219 GGTCAACGGGTCGGGTCGGGTC
1 GGTCAAC-GATCGGGTCGGGTC
825241 AACGGGTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.11, C:0.23, G:0.48, T:0.18
Consensus pattern (22 bp):
GGTCAACGATCGGGTCGGGTCG
Found at i:832471 original size:18 final size:18
Alignment explanation
Indices: 832439--832503 Score: 96
Period size: 18 Copynumber: 3.7 Consensus size: 18
832429 ACCGGTCAAC
*
832439 GGTCAAC-GATCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
832456 GGTTAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
832474 GGTCAACAGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
832492 GGTCAACGGGTC
1 GGTCAACGGGTC
832504 ATGACCCGTC
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
17 6 0.14
18 36 0.86
ACGTcount: A:0.15, C:0.22, G:0.45, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:832515 original size:36 final size:35
Alignment explanation
Indices: 832440--832515 Score: 80
Period size: 36 Copynumber: 2.1 Consensus size: 35
832430 CCGGTCAACG
* * * **
832440 GTCAACGATCGGGTCGGGTTAACGGGTCGGGTCGG
1 GTCAACGATCGGGTCGGGTCAACGGGTCAGGACCC
* *
832475 GTCAACAGGTCGGGTCGGGTCAACGGGTCATGACCC
1 GTCAAC-GATCGGGTCGGGTCAACGGGTCAGGACCC
832511 GTCAA
1 GTCAA
832516 ACCGATCAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
35 6 0.18
36 27 0.82
ACGTcount: A:0.18, C:0.24, G:0.39, T:0.18
Consensus pattern (35 bp):
GTCAACGATCGGGTCGGGTCAACGGGTCAGGACCC
Found at i:834096 original size:14 final size:13
Alignment explanation
Indices: 834059--834086 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
834049 TTTTAATTAT
834059 GAAATATAAATTG
1 GAAATATAAATTG
834072 GAAATATAAATTG
1 GAAATATAAATTG
834085 GA
1 GA
834087 TTAAATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.18, T:0.29
Consensus pattern (13 bp):
GAAATATAAATTG
Found at i:835631 original size:2 final size:2
Alignment explanation
Indices: 835624--835706 Score: 166
Period size: 2 Copynumber: 41.5 Consensus size: 2
835614 ATTAACTATG
835624 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
835666 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
835707 AAATTTTTTA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:841806 original size:40 final size:41
Alignment explanation
Indices: 841742--842095 Score: 276
Period size: 41 Copynumber: 8.7 Consensus size: 41
841732 TTTTAAGCAA
* * * *
841742 AAACGCCGTTAAATACTCTTACTTTAGTGGTGTTTTTATAC
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATAC
** * *
841783 AAACG-CGCTGTAGATTCGTACTTTAGTAGCG-TTTTATAC
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATAC
841822 AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATA-
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATAC
* * * * * * *
841862 AGAACGTCG-TAATAGGACACATA-TATAATGGCATTTTTCA-AA
1 A-AACGCCGCTAA-A-GACTCGTACTTTAGTGGCGTTTTT-ATAC
* * ** * * **
841904 AAACACCG-TAAAAGATTCACACTGTAATGGCGTTTGCATAC
1 AAACGCCGCT-AAAGACTCGTACTTTAGTGGCGTTTTTATAC
* * *
841945 AAATGCCGCTAAAGACTTGTACTTTAGTGGTGTTTTTATAC
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATAC
* *
841986 AAACGCCGCTATAGACTCGTACTTTAGTGACGTTTTTATAC
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATAC
* * * * *
842027 AAAGGCC-CCATAA-ACTTGTATTTTAGTGGCATTTTTATAC
1 AAACGCCGCTA-AAGACTCGTACTTTAGTGGCGTTTTTATAC
* *
842067 AAACGCCACTAAATACTCGTACTTTAGTG
1 AAACGCCGCTAAAGACTCGTACTTTAGTG
842096 ACGTATATAT
Statistics
Matches: 244, Mismatches: 55, Indels: 28
0.75 0.17 0.09
Matches are distributed among these distances:
39 13 0.05
40 83 0.34
41 137 0.56
42 11 0.05
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.34
Consensus pattern (41 bp):
AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATAC
Found at i:844299 original size:2 final size:2
Alignment explanation
Indices: 844292--844316 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
844282 AAAATTTAAA
844292 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
844317 ATAATTAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:845793 original size:3 final size:3
Alignment explanation
Indices: 845774--845836 Score: 80
Period size: 3 Copynumber: 22.0 Consensus size: 3
845764 GGCCTATTTT
*
845774 TAA TAA TATA TAA -AA TAA TAA T-A TAA TTA TAA TAA TAA TAA TAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
845818 TAA TAA -AA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA
845837 ATAAATTAGT
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
2 8 0.15
3 42 0.79
4 3 0.06
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:845805 original size:26 final size:26
Alignment explanation
Indices: 845776--845836 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
845766 CCTATTTTTA
* *
845776 ATAATATATAA-AATAATAATATAATT
1 ATAATA-ATAATAATAATAATAAAATA
845802 ATAATAATAATAATAATAATAAAATA
1 ATAATAATAATAATAATAATAAAATA
845828 ATAA-AATAA
1 ATAATAATAA
845837 ATAAATTAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
25 9 0.28
26 23 0.72
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (26 bp):
ATAATAATAATAATAATAATAAAATA
Found at i:845808 original size:9 final size:9
Alignment explanation
Indices: 845774--845836 Score: 80
Period size: 8 Copynumber: 7.3 Consensus size: 9
845764 GGCCTATTTT
845774 TAATAATATA
1 TAATAATA-A
845784 TAA-AATAA
1 TAATAATAA
845792 TAAT-ATAA
1 TAATAATAA
*
845800 TTATAATAA
1 TAATAATAA
845809 TAATAATAA
1 TAATAATAA
845818 TAATAA-AA
1 TAATAATAA
845826 TAATAA-AA
1 TAATAATAA
845834 TAA
1 TAA
845837 ATAAATTAGT
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
8 24 0.49
9 22 0.45
10 3 0.06
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
TAATAATAA
Found at i:845819 original size:29 final size:29
Alignment explanation
Indices: 845774--845829 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
845764 GGCCTATTTT
*
845774 TAATAATATATAAAATAATAATATAATTA
1 TAATAATATATAAAATAATAAAATAATTA
845803 TAATAATA-ATAATAATAATAAAATAAT
1 TAATAATATATAA-AATAATAAAATAAT
845830 AAAATAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (29 bp):
TAATAATATATAAAATAATAAAATAATTA
Found at i:845840 original size:20 final size:19
Alignment explanation
Indices: 845775--845836 Score: 74
Period size: 20 Copynumber: 3.3 Consensus size: 19
845765 GCCTATTTTT
845775 AATAATATATAAAATAATAA
1 AATAATA-ATAAAATAATAA
* *
845795 TATAAT--TATAATAATAA
1 AATAATAATAAAATAATAA
845812 TAATAATAATAAAATAATAA
1 -AATAATAATAAAATAATAA
845832 AATAA
1 AATAA
845837 ATAAATTAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
17 10 0.29
18 5 0.14
19 5 0.14
20 15 0.43
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AATAATAATAAAATAATAA
Found at i:845840 original size:23 final size:22
Alignment explanation
Indices: 845774--845836 Score: 85
Period size: 23 Copynumber: 2.9 Consensus size: 22
845764 GGCCTATTTT
845774 TAATAATAT-ATAAAATAATAA
1 TAATAATATAATAAAATAATAA
845795 T-ATAATTATAATAATAATAATAA
1 TAATAA-TATAATAA-AATAATAA
*
845818 TAATAAAATAATAAAATAA
1 TAATAATATAATAAAATAA
845837 ATAAATTAGT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
20 4 0.11
21 4 0.11
22 9 0.24
23 16 0.43
24 4 0.11
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
TAATAATATAATAAAATAATAA
Found at i:846016 original size:45 final size:45
Alignment explanation
Indices: 845952--846653 Score: 1096
Period size: 45 Copynumber: 15.8 Consensus size: 45
845942 GATGGAAATG
* * *
845952 TTGAAAAGATCATGCACTGGAGGGCTTACAGATGACCC-ATTGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGA-AGGTT
* *
845997 TTGAAAACATCATGCACTGGAGGGCTTACAGATGACCCAAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
* * * **
846042 TTGAAAACATCATGCACTTAAGGGCTTGCAGATGACCTGAATATT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
846087 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
* *
846132 TTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGGAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
* * *
846177 TTGAAAACATCATGCACTGAAGGACTTACATATGACCCAAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
846222 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
* * *
846267 TTGAAAACATCATGCACTGAAGGACTTACAGATTACCCGATGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
* *
846312 TTGAAAACGTCATGCACTGAAGGACTTACAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
846357 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
846402 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
846447 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
* *
846492 TTGAAAACATCATGCATTGAAGGGCTTACAGATGACCTGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
*
846537 TTGAAAACATCATGCACTAAAGGGCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
* * * *
846582 TTG-----A--ATGCATTGAATGACTTACAGATGACCTGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
846620 TTGAAAACATCATGCACTGAAGGGCTTACAGATG
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATG
846654 TGGGAAGTAG
Statistics
Matches: 606, Mismatches: 43, Indels: 16
0.91 0.06 0.02
Matches are distributed among these distances:
38 32 0.05
40 1 0.00
43 1 0.00
45 571 0.94
46 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.24
Consensus pattern (45 bp):
TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
Found at i:846244 original size:25 final size:25
Alignment explanation
Indices: 846216--846289 Score: 61
Period size: 25 Copynumber: 3.2 Consensus size: 25
846206 ATATGACCCA
846216 AAGGTTTTGAAAACATCATGCACTG
1 AAGGTTTTGAAAACATCATGCACTG
** * *
846241 AAGGGCTT----ACA-GATG-ACCCG
1 AAGGTTTTGAAAACATCATGCA-CTG
846261 AAGGTTTTGAAAACATCATGCACTG
1 AAGGTTTTGAAAACATCATGCACTG
846286 AAGG
1 AAGG
846290 ACTTACAGAT
Statistics
Matches: 34, Mismatches: 8, Indels: 14
0.61 0.14 0.25
Matches are distributed among these distances:
19 1 0.03
20 11 0.32
21 3 0.09
24 3 0.09
25 15 0.44
26 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (25 bp):
AAGGTTTTGAAAACATCATGCACTG
Found at i:847794 original size:54 final size:54
Alignment explanation
Indices: 847724--847851 Score: 170
Period size: 54 Copynumber: 2.4 Consensus size: 54
847714 GTAAAACATG
* * * *
847724 TGACAATATATTCATCCTTTCTTGTGGCTTTTGCCCGGAT-TTTCGTAAAGCT-TT
1 TGACAACACATTCATCCTTTCTTGTGGCTTCTGCCCAGATGTTT-GTAAAG-TATT
* *
847778 TGATAACACATTCATCCTTTCTTGTGGCTTCTGGCCAGATGTTTGTAAAGTATT
1 TGACAACACATTCATCCTTTCTTGTGGCTTCTGCCCAGATGTTTGTAAAGTATT
847832 TGACAACACATTCATCCTTT
1 TGACAACACATTCATCCTTT
847852 TCTATGATTT
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
53 1 0.02
54 61 0.94
55 3 0.05
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (54 bp):
TGACAACACATTCATCCTTTCTTGTGGCTTCTGCCCAGATGTTTGTAAAGTATT
Found at i:857316 original size:2 final size:2
Alignment explanation
Indices: 857305--857350 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
857295 TAATTTTAAG
857305 TA TA TA -A TA TA 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
857346 TA TA T
1 TA TA T
857351 TCATTTTTAC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:861857 original size:23 final size:23
Alignment explanation
Indices: 861831--861890 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
861821 ATTAAATACA
*
861831 ATAACATATTAGGTA-CTGTTTAT
1 ATAACATAATAGGTAGC-GTTTAT
**
861854 ATAATGTAATAGGTAGCGTTTAT
1 ATAACATAATAGGTAGCGTTTAT
* *
861877 ATAATAAAATAGGT
1 ATAACATAATAGGT
861891 TAATTACTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 30 0.97
24 1 0.03
ACGTcount: A:0.40, C:0.05, G:0.17, T:0.38
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGTTTAT
Found at i:861960 original size:23 final size:23
Alignment explanation
Indices: 861934--862000 Score: 107
Period size: 23 Copynumber: 2.9 Consensus size: 23
861924 TATTTGGTAC
861934 CGCTTATATAATGTAATAGATAG
1 CGCTTATATAATGTAATAGATAG
*
861957 CGCTTATATAATGTAATAGGTAG
1 CGCTTATATAATGTAATAGATAG
**
861980 CGCTTATATAATAAAATAGAT
1 CGCTTATATAATGTAATAGAT
862001 TAATTACTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.34
Consensus pattern (23 bp):
CGCTTATATAATGTAATAGATAG
Found at i:862048 original size:110 final size:110
Alignment explanation
Indices: 861850--862076 Score: 357
Period size: 110 Copynumber: 2.1 Consensus size: 110
861840 TAGGTACTGT
* *
861850 TTATATAATGTAATAGGTAGCGTTTATATAATAAAATAGGTTAATTACTGAAAATATTATAAAGC
1 TTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGATTAATTACTGAAAATATTATAAAGC
* * *
861915 AGAATAACATATTTGGTACCGCTTATATAATGTAATAGATAGCGC
66 ACAATAACATATTAGGTACCGCTTATATAACGTAATAGATAGCGC
861960 TTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGATTAATTACTGAAAATATTATTAAA-
1 TTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGATTAATTACTGAAAATATTA-TAAAG
* * * *
862024 CACAATAACATATTAGGTAGCGCTTATATAACGTAATAGGTAGTGT
65 CACAATAACATATTAGGTACCGCTTATATAACGTAATAGATAGCGC
862070 TTATATA
1 TTATATA
862077 TTAAAATATG
Statistics
Matches: 107, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
110 103 0.96
111 4 0.04
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (110 bp):
TTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGATTAATTACTGAAAATATTATAAAGC
ACAATAACATATTAGGTACCGCTTATATAACGTAATAGATAGCGC
Found at i:862063 original size:23 final size:23
Alignment explanation
Indices: 862028--862076 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
862018 ATTAAACACA
*
862028 ATAACATATTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
* * *
862051 ATAACGTAATAGGTAGTGTTTAT
1 ATAACATAATAGGTAGCGCTTAT
862074 ATA
1 ATA
862077 TTAAAATATG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:862107 original size:87 final size:88
Alignment explanation
Indices: 861954--862113 Score: 225
Period size: 87 Copynumber: 1.8 Consensus size: 88
861944 ATGTAATAGA
*
861954 TAGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGATTAATTACTGAAAATATTA
1 TAGCGCTTATATAACGTAATAGGTAGCGCTTATATAATAAAATAGATTAATTACTGAAAATATTA
862019 TTA-AACACAATAACATATTAGG
66 TTACAACACAATAACATATTAGG
* * * * ** *
862041 TAGCGCTTATATAACGTAATAGGTAGTGTTTATATATTAAAATATG-TTAATTACTTAATTTGTT
1 TAGCGCTTATATAACGTAATAGGTAGCGCTTATATAATAAAATA-GATTAATTACTGAAAATATT
862105 ATTACAACA
65 ATTACAACA
862114 TATTAGGTAA
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
87 58 0.92
88 5 0.08
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (88 bp):
TAGCGCTTATATAACGTAATAGGTAGCGCTTATATAATAAAATAGATTAATTACTGAAAATATTA
TTACAACACAATAACATATTAGG
Found at i:862778 original size:111 final size:111
Alignment explanation
Indices: 862470--862951 Score: 659
Period size: 111 Copynumber: 4.3 Consensus size: 111
862460 TAGCGCCTAT
* * * * *
862470 AAAGTATCAATAC-TTTATAAAAATGTATCGATATTTTACAATATAACAGGTAAAAATATGACAA
1 AAAGTATCGATCCTTTTATAAAAA-GGATAGATACTTTACAATATAACAGGTAAAAATATGACAA
* * * *
862534 AATCAATTTCATTATGAC-AAAACCAGTAAAATTTACTTGATATGTTG
65 AATCAGTTTCAATATGACAAAAACGA-TAAAATTTACCTGATATGTTG
* *
862581 AAAGTATCGATCCTTTTATAAATA-GATAGATACTTTACAATATAACATGTAAAAATATGACAAA
1 AAAGTATCGATCCTTTTATAAAAAGGATAGATACTTTACAATATAACAGGTAAAAATATGACAAA
* *
862645 ACCAGTTT-AATTATGACAAAAAACGATAAAATTTACCTGATAAGTTG
66 ATCAGTTTCAA-TATGAC-AAAAACGATAAAATTTACCTGATATGTTG
*
862692 AAAGTATCGATCCTTTTATAAAAAGGATAGATACTTTATAATATAACAGGTAAAAATATGACAAA
1 AAAGTATCGATCCTTTTATAAAAAGGATAGATACTTTACAATATAACAGGTAAAAATATGACAAA
*
862757 ATCAGTTTCAATATGACAAAAACGGTAAAATTTACCTGATATGTTG
66 ATCAGTTTCAATATGACAAAAACGATAAAATTTACCTGATATGTTG
* *
862803 AAAGTATCGATCATTTTATAAAAATGATAGATACTTTACAATATAACAGGTAAAAATATGACAAA
1 AAAGTATCGATCCTTTTATAAAAAGGATAGATACTTTACAATATAACAGGTAAAAATATGACAAA
* * *
862868 ATCAGTTTCATTATGA-AAAAACCGGTAAAATTTACCTTATATGTTG
66 ATCAGTTTCAATATGACAAAAA-CGATAAAATTTACCTGATATGTTG
* * * *
862914 AAAGTATAGATACTTTTTATAAAAAAGATCGATACTTT
1 AAAGTATCGAT-CCTTTTATAAAAAGGATAGATACTTT
862952 TTTTAAAGTT
Statistics
Matches: 335, Mismatches: 28, Indels: 15
0.89 0.07 0.04
Matches are distributed among these distances:
109 1 0.00
110 53 0.16
111 190 0.57
112 89 0.27
113 2 0.01
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (111 bp):
AAAGTATCGATCCTTTTATAAAAAGGATAGATACTTTACAATATAACAGGTAAAAATATGACAAA
ATCAGTTTCAATATGACAAAAACGATAAAATTTACCTGATATGTTG
Found at i:863603 original size:70 final size:70
Alignment explanation
Indices: 863514--863665 Score: 250
Period size: 70 Copynumber: 2.2 Consensus size: 70
863504 CCTTTTATGA
* *
863514 AAAGGATAAATACTTTACAATATAACAAGTAAAAATATGACAAAAACGGTAAAATTTACCTAATA
1 AAAGTATAGATACTTTACAATATAACAAGTAAAAATATGACAAAAACGGTAAAATTTACCTAATA
863579 TGTTG
66 TGTTG
* * * *
863584 AAAGTATCGATACTTTACAATATAACAGGTATAAATATGACAAAACCGGTAAAATTTACCTAATA
1 AAAGTATAGATACTTTACAATATAACAAGTAAAAATATGACAAAAACGGTAAAATTTACCTAATA
863649 TGTTG
66 TGTTG
863654 AAAGTATAGATA
1 AAAGTATAGATA
863666 TTTTTTATAA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
70 75 1.00
ACGTcount: A:0.49, C:0.11, G:0.12, T:0.28
Consensus pattern (70 bp):
AAAGTATAGATACTTTACAATATAACAAGTAAAAATATGACAAAAACGGTAAAATTTACCTAATA
TGTTG
Found at i:865590 original size:3 final size:3
Alignment explanation
Indices: 865582--865628 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
865572 CGAGACTATA
* *
865582 TAT TAT TAT TAT TAT TAT TA- TAT TAC AAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
865629 AAAATAAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:872089 original size:23 final size:22
Alignment explanation
Indices: 872057--872106 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
872047 AACTGTAAGC
872057 TATCAAAAGGCAGAGAAAAACG
1 TATCAAAAGGCAGAGAAAAACG
* * *
872079 TATCACAAAGGCATAGATAAATG
1 TATCA-AAAGGCAGAGAAAAACG
872102 TATCA
1 TATCA
872107 TAGAGACAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.50, C:0.14, G:0.18, T:0.18
Consensus pattern (22 bp):
TATCAAAAGGCAGAGAAAAACG
Found at i:877696 original size:184 final size:184
Alignment explanation
Indices: 877387--877757 Score: 742
Period size: 184 Copynumber: 2.0 Consensus size: 184
877377 CATAAGTTGT
877387 TGTCAAACTAATTCTGGAGATTCAAGGCATGGTTCGATGCCGAAGAAGGTGGTCGTGAGGTAGCT
1 TGTCAAACTAATTCTGGAGATTCAAGGCATGGTTCGATGCCGAAGAAGGTGGTCGTGAGGTAGCT
877452 TTGAATGTGAATAGTGAATAAAGATATAAATGGAGGGTGATTCAACAAAGTTCAAGTAAAAGTGT
66 TTGAATGTGAATAGTGAATAAAGATATAAATGGAGGGTGATTCAACAAAGTTCAAGTAAAAGTGT
877517 AAAGTGAAGTTAATCTACTAGATGACATTTTGAAATTTTCTTATATGTCCTCTA
131 AAAGTGAAGTTAATCTACTAGATGACATTTTGAAATTTTCTTATATGTCCTCTA
877571 TGTCAAACTAATTCTGGAGATTCAAGGCATGGTTCGATGCCGAAGAAGGTGGTCGTGAGGTAGCT
1 TGTCAAACTAATTCTGGAGATTCAAGGCATGGTTCGATGCCGAAGAAGGTGGTCGTGAGGTAGCT
877636 TTGAATGTGAATAGTGAATAAAGATATAAATGGAGGGTGATTCAACAAAGTTCAAGTAAAAGTGT
66 TTGAATGTGAATAGTGAATAAAGATATAAATGGAGGGTGATTCAACAAAGTTCAAGTAAAAGTGT
877701 AAAGTGAAGTTAATCTACTAGATGACATTTTGAAATTTTCTTATATGTCCTCTA
131 AAAGTGAAGTTAATCTACTAGATGACATTTTGAAATTTTCTTATATGTCCTCTA
877755 TGT
1 TGT
877758 TTTCCTCTTA
Statistics
Matches: 187, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
184 187 1.00
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.31
Consensus pattern (184 bp):
TGTCAAACTAATTCTGGAGATTCAAGGCATGGTTCGATGCCGAAGAAGGTGGTCGTGAGGTAGCT
TTGAATGTGAATAGTGAATAAAGATATAAATGGAGGGTGATTCAACAAAGTTCAAGTAAAAGTGT
AAAGTGAAGTTAATCTACTAGATGACATTTTGAAATTTTCTTATATGTCCTCTA
Found at i:880476 original size:17 final size:17
Alignment explanation
Indices: 880456--880488 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
880446 AATTTATTAT
880456 TAAATTAATATCCATTC
1 TAAATTAATATCCATTC
*
880473 TAAATTAATCTCCATT
1 TAAATTAATATCCATT
880489 TTAAGGTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATTAATATCCATTC
Found at i:883913 original size:16 final size:17
Alignment explanation
Indices: 883890--883923 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
883880 CTTTTATATA
883890 TATATATTATTTATTTTC
1 TATAT-TTATTTATTTTC
*
883908 TATATTTCTTTATTTT
1 TATATTTATTTATTTT
883924 TGGTTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (17 bp):
TATATTTATTTATTTTC
Found at i:883967 original size:3 final size:3
Alignment explanation
Indices: 883959--884022 Score: 71
Period size: 3 Copynumber: 21.7 Consensus size: 3
883949 ATTATACTAT
* *
883959 TTA TTA TTA TTA TTT TTG TCT- TTA TTA TTA TTA TTA TTA -TA TT-
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
884002 TTA TTA TTA TTA TTA TATA TT
1 TTA TTA TTA TTA TTA T-TA TT
884023 CTATACATTT
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
2 5 0.09
3 45 0.83
4 4 0.07
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:884007 original size:19 final size:19
Alignment explanation
Indices: 883983--884019 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
883973 TTTGTCTTTA
883983 TTATTATTATTATTATATT
1 TTATTATTATTATTATATT
884002 TTATTATTATTATTATAT
1 TTATTATTATTATTATAT
884020 ATTCTATACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATTATTATTATTATATT
Found at i:884022 original size:21 final size:21
Alignment explanation
Indices: 883943--884022 Score: 94
Period size: 21 Copynumber: 3.8 Consensus size: 21
883933 TATTTCTTAC
883943 TATTA-TATTATACTA-TTTAT
1 TATTATTATTATA-TATTTTAT
* *
883963 TATTATTATT-TTTGTCTTTAT
1 TATTATTATTATATAT-TTTAT
883984 TATTATTATTATTATATTTTAT
1 TATTATTATTA-TATATTTTAT
884006 TATTATTATTATATATT
1 TATTATTATTATATATT
884023 CTATACATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
19 1 0.02
20 6 0.12
21 25 0.49
22 16 0.31
23 3 0.06
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (21 bp):
TATTATTATTATATATTTTAT
Found at i:884117 original size:18 final size:19
Alignment explanation
Indices: 884096--884155 Score: 72
Period size: 18 Copynumber: 3.3 Consensus size: 19
884086 TTTATTTCCT
*
884096 TTTTCTTTA-TTTCATTTA
1 TTTTATTTACTTTCATTTA
*
884114 TTTTTTTTACTTTC-TTTA
1 TTTTATTTACTTTCATTTA
*
884132 TTTTATTTATTTTCATTT-
1 TTTTATTTACTTTCATTTA
884150 TTTTAT
1 TTTTAT
884156 CTAACACGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 30 0.81
19 7 0.19
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTATTTACTTTCATTTA
Found at i:884154 original size:23 final size:23
Alignment explanation
Indices: 884110--884155 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
884100 CTTTATTTCA
*
884110 TTTATTTTTTTTACTTTCTTTAT
1 TTTATTTTTTTCACTTTCTTTAT
*
884133 TTTATTTATTTTCA-TTTTTTTAT
1 TTTATTT-TTTTCACTTTCTTTAT
884156 CTAACACGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (23 bp):
TTTATTTTTTTCACTTTCTTTAT
Found at i:886187 original size:60 final size:60
Alignment explanation
Indices: 886113--886348 Score: 303
Period size: 60 Copynumber: 3.9 Consensus size: 60
886103 TCTTGTTCTG
* * * * * *
886113 ATCTTCTATATTGGACTCCTAGATCTTACTGGTCTATGGTAAGTCCTTATAGATGCCTAT
1 ATCTTCCATATTGGACTCCTAGATCTTAGTGGTCTACGGTAAGTCCTTATGGATGCATGT
* * * *
886173 ATCTTCCATATTGGATTTCTAGATCTTAGTGGTTTACAGTAAGTCCTTATGGATGCATGT
1 ATCTTCCATATTGGACTCCTAGATCTTAGTGGTCTACGGTAAGTCCTTATGGATGCATGT
* * * * *
886233 ATATTTCATATTGGACTCCTAGATCTTAGTGGCCTACGATAAGTTCTTATGGATGCATGT
1 ATCTTCCATATTGGACTCCTAGATCTTAGTGGTCTACGGTAAGTCCTTATGGATGCATGT
* *
886293 ATCTTCCATAATGGACTCCTTGATCTTAGTGGTCTA-GGTTAAGTCCTTATGGATGC
1 ATCTTCCATATTGGACTCCTAGATCTTAGTGGTCTACGG-TAAGTCCTTATGGATGC
886349 CTGTTTTGGG
Statistics
Matches: 149, Mismatches: 26, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
59 1 0.01
60 148 0.99
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.39
Consensus pattern (60 bp):
ATCTTCCATATTGGACTCCTAGATCTTAGTGGTCTACGGTAAGTCCTTATGGATGCATGT
Found at i:887529 original size:21 final size:21
Alignment explanation
Indices: 887489--887534 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 21
887479 AAAATTTTAA
*
887489 AAATAAATTTTAACTATTTT-
1 AAATAAATTTTAAATATTTTC
887509 AAAT-AATATTTAAATAGTTTTC
1 AAATAAAT-TTTAAATA-TTTTC
887531 AAAT
1 AAAT
887535 TTAGTAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 3 0.14
20 11 0.50
21 4 0.18
22 4 0.18
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (21 bp):
AAATAAATTTTAAATATTTTC
Found at i:892153 original size:2 final size:2
Alignment explanation
Indices: 892146--892175 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
892136 ACCCCTAGTT
892146 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
892176 ATAATCAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:893654 original size:26 final size:26
Alignment explanation
Indices: 893618--893673 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
893608 CCAACCACCA
* *
893618 CATTAGTTGATTTTCGGGCCATCATT
1 CATTAGTTGATGTTCCGGCCATCATT
893644 CATTAGTTGATGTTCCGGCCATCATT
1 CATTAGTTGATGTTCCGGCCATCATT
893670 CATT
1 CATT
893674 CTCTATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.20, C:0.21, G:0.18, T:0.41
Consensus pattern (26 bp):
CATTAGTTGATGTTCCGGCCATCATT
Found at i:895384 original size:31 final size:32
Alignment explanation
Indices: 895303--895385 Score: 107
Period size: 31 Copynumber: 2.7 Consensus size: 32
895293 AGCTCGCTAG
* * *
895303 TTTTCGAGTCGAGTCAAGCT-TCATTTCAGAG
1 TTTTCGAGTCGAGTCGAGCTCTCATTTCAAAA
*
895334 TTTTCAAGTCGAGTCGAGCTCT-ATTTCAAAA
1 TTTTCGAGTCGAGTCGAGCTCTCATTTCAAAA
*
895365 TTTTCGAGTCGAGTTGAGCTC
1 TTTTCGAGTCGAGTCGAGCTC
895386 AGCAATACTC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 44 0.98
32 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (32 bp):
TTTTCGAGTCGAGTCGAGCTCTCATTTCAAAA
Found at i:898896 original size:2 final size:2
Alignment explanation
Indices: 898889--898914 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
898879 TTGATTCGAC
898889 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
898915 TCTCATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:900025 original size:7 final size:7
Alignment explanation
Indices: 900013--900037 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
900003 ATTTAATTTT
900013 TTTTATA
1 TTTTATA
900020 TTTTATA
1 TTTTATA
900027 TTTTATA
1 TTTTATA
900034 TTTT
1 TTTT
900038 TTTGTGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTATA
Found at i:900059 original size:24 final size:24
Alignment explanation
Indices: 900010--900060 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
900000 AAAATTTAAT
*
900010 TTTTTTTATATTTTATATTTTATA
1 TTTTTTTATATTTTATATTATATA
* *
900034 TTTTTTTGTGTTTTATATTGAT-TA
1 TTTTTTTATATTTTATATT-ATATA
900058 TTT
1 TTT
900061 AATTTCGCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 22 0.96
25 1 0.04
ACGTcount: A:0.20, C:0.00, G:0.06, T:0.75
Consensus pattern (24 bp):
TTTTTTTATATTTTATATTATATA
Found at i:900289 original size:2 final size:2
Alignment explanation
Indices: 900282--900306 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
900272 GATTTGGTGC
900282 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
900307 ACGGCGGTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:902985 original size:10 final size:10
Alignment explanation
Indices: 902965--903000 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
902955 GTGGATGAAA
902965 ACCGG-TTTG
1 ACCGGTTTTG
902974 ACCGGTTTTG
1 ACCGGTTTTG
*
902984 ACCGGTTTCG
1 ACCGGTTTTG
902994 ACCGGTT
1 ACCGGTT
903001 CGAACCAGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 5 0.20
10 20 0.80
ACGTcount: A:0.11, C:0.25, G:0.31, T:0.33
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:903072 original size:17 final size:17
Alignment explanation
Indices: 903050--903087 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
903040 GACCCGACCC
*
903050 GACCCGACCCGTCCGTT
1 GACCCGACCCGACCGTT
903067 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
903084 GACC
1 GACC
903088 GTTGACCTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.16, C:0.47, G:0.24, T:0.13
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:910317 original size:19 final size:20
Alignment explanation
Indices: 910293--910349 Score: 68
Period size: 19 Copynumber: 3.0 Consensus size: 20
910283 AACCGGATTG
910293 ACCAGTTTGACCGGTTC-GA
1 ACCAGTTTGACCGGTTCTGA
*
910312 ACCAGTCTGACCGG-TCTGA
1 ACCAGTTTGACCGGTTCTGA
910331 ACC-GATTTGACCGG-TCTGA
1 ACCAG-TTTGACCGGTTCTGA
910350 CCCGACCCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.09
19 31 0.91
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.25
Consensus pattern (20 bp):
ACCAGTTTGACCGGTTCTGA
Found at i:910361 original size:19 final size:19
Alignment explanation
Indices: 910320--910384 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
910310 GAACCAGTCT
* ***
910320 GACCGGTCTGAACCGATTT
1 GACCGGTCTGACCCGACCC
910339 GACCGGTCTGACCCGACCC
1 GACCGGTCTGACCCGACCC
*
910358 GACCCGTCCGTTGACCCGACCC
1 GACCGGT-C--TGACCCGACCC
910380 GACCG
1 GACCG
910385 TTGACCGTTG
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
19 21 0.57
20 1 0.03
22 15 0.41
ACGTcount: A:0.17, C:0.42, G:0.26, T:0.15
Consensus pattern (19 bp):
GACCGGTCTGACCCGACCC
Found at i:910375 original size:17 final size:17
Alignment explanation
Indices: 910353--910390 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
910343 GGTCTGACCC
*
910353 GACCCGACCCGTCCGTT
1 GACCCGACCCGACCGTT
910370 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
910387 GACC
1 GACC
910391 GTTGACCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.16, C:0.47, G:0.24, T:0.13
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:919553 original size:21 final size:20
Alignment explanation
Indices: 919522--919613 Score: 55
Period size: 21 Copynumber: 4.3 Consensus size: 20
919512 AGACACTAGT
*
919522 TTTTTACATTTGGT-TTTTTA
1 TTTTTATATTT-GTATTTTTA
*
919542 TATTTTATATTTTTATTTTTA
1 T-TTTTATATTTGTATTTTTA
*
919563 TTTTTATTATTAT-TATTATTA
1 TTTTTA-TATT-TGTATTTTTA
*
919584 TTTATTATTATTAT-TATTATTA
1 TTT-TTA-TATT-TGTATTTTTA
919606 TTATTTAT
1 TT-TTTAT
919614 TATTAATTAC
Statistics
Matches: 63, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
20 7 0.11
21 31 0.49
22 24 0.38
23 1 0.02
ACGTcount: A:0.25, C:0.01, G:0.02, T:0.72
Consensus pattern (20 bp):
TTTTTATATTTGTATTTTTA
Found at i:919560 original size:6 final size:6
Alignment explanation
Indices: 919537--919614 Score: 75
Period size: 6 Copynumber: 12.3 Consensus size: 6
919527 ACATTTGGTT
* *
919537 TTTTATA TTTTATA TTTTTA TTTTTA TTTTTA TTATTA TTATTA TTATTTA
1 TTTT-TA TTTT-TA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TT-TTTA
* * *
919588 TTATTA TTATTA TTATTA TTATTTA TT
1 TTTTTA TTTTTA TTTTTA TT-TTTA TT
919615 ATTAATTACA
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
6 44 0.68
7 21 0.32
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (6 bp):
TTTTTA
Found at i:919574 original size:3 final size:3
Alignment explanation
Indices: 919549--919618 Score: 95
Period size: 3 Copynumber: 22.7 Consensus size: 3
919539 TTATATTTTA
* * *
919549 TAT TTT TAT TTT TAT TTT TAT TAT TAT TAT TAT TATT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
919595 TAT TAT TAT TAT TATT TAT TAT TA
1 TAT TAT TAT TAT TA-T TAT TAT TA
919619 ATTACAAGCC
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
3 53 0.90
4 6 0.10
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:919587 original size:25 final size:25
Alignment explanation
Indices: 919542--919618 Score: 94
Period size: 25 Copynumber: 3.3 Consensus size: 25
919532 TGGTTTTTTA
* *
919542 TATT-TTA-TATTTTTATTTTTATT
1 TATTATTATTATTATTATTATTATT
919565 T-TTATTA---TTATTATTATTATT
1 TATTATTATTATTATTATTATTATT
919586 TATTATTATTATTATTATTATTATT
1 TATTATTATTATTATTATTATTATT
919611 TATTATTA
1 TATTATTA
919619 ATTACAAGCC
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
21 13 0.28
22 8 0.17
23 4 0.09
25 22 0.47
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (25 bp):
TATTATTATTATTATTATTATTATT
Found at i:920845 original size:35 final size:34
Alignment explanation
Indices: 920805--920876 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 34
920795 ATTTAGTCAC
*
920805 TAATTTTAATTATAAGTTTTATTACTTTT-TATATT
1 TAATTTTAATTATAA-TTTT-TTAATTTTATATATT
* *
920840 TAATTTTAATTTTAATTTTTTAATTTTATATGTT
1 TAATTTTAATTATAATTTTTTAATTTTATATATT
920874 TAA
1 TAA
920877 ATTATTATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 7 0.21
34 12 0.36
35 14 0.42
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (34 bp):
TAATTTTAATTATAATTTTTTAATTTTATATATT
Found at i:921065 original size:31 final size:33
Alignment explanation
Indices: 921030--921092 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
921020 ATAATTAAAC
921030 ATTATAAAAATTAT-A-ATTTAGTTTTATTTAA
1 ATTATAAAAATTATAATATTTAGTTTTATTTAA
* * *
921061 ATTATTAAAATTTTAATATTTATTTTTATTTA
1 ATTATAAAAATTATAATATTTAGTTTTATTTA
921093 TTAATATCGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 12 0.44
32 1 0.04
33 14 0.52
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (33 bp):
ATTATAAAAATTATAATATTTAGTTTTATTTAA
Found at i:927597 original size:24 final size:25
Alignment explanation
Indices: 927523--927597 Score: 64
Period size: 24 Copynumber: 3.0 Consensus size: 25
927513 TTTATAAAAA
* * *
927523 TAATATATATATATATTAAATCATAT
1 TAATTTATATAT-TAATATATCATAT
* **
927549 TAATTTATAT-TTAAAATTAAAATAT
1 TAATTTATATATTAATA-TATCATAT
927574 T-ATTTATATATTAATATATCATAT
1 TAATTTATATATTAATATATCATAT
927598 AAAAATATTA
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
24 17 0.45
25 12 0.32
26 9 0.24
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (25 bp):
TAATTTATATATTAATATATCATAT
Found at i:927606 original size:32 final size:34
Alignment explanation
Indices: 927567--927648 Score: 98
Period size: 35 Copynumber: 2.4 Consensus size: 34
927557 ATTTAAAATT
**
927567 AAAATATTATTTAT-ATATT-A-ATATATCATATA
1 AAAATATTATAAATAATATTAACATATAT-ATATA
927599 AAAATATTATAAATAATATTAACATATATATATA
1 AAAATATTATAAATAATATTAACATATATATATA
*
927633 ATAAATAATATAAATA
1 A-AAATATTATAAATA
927649 GATAATGAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
32 12 0.28
33 5 0.12
34 7 0.16
35 19 0.44
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (34 bp):
AAAATATTATAAATAATATTAACATATATATATA
Found at i:928311 original size:107 final size:107
Alignment explanation
Indices: 928175--928704 Score: 969
Period size: 107 Copynumber: 5.0 Consensus size: 107
928165 GCCCTTGAAT
* * *
928175 GCTGATTTGTTGCTGTAGAGTTTTGAAAAAATTTATTTGTTGAAATAAGGTCTAACTGAAATTAT
1 GCTGATTTGCTGCTGTAGAGTTTTGAAAAAAATTATTTGTTGAAATAAGGTCTAACTAAAATTAT
**
928240 TTTCTGATCTAGTGTGAATGCTGTAGTACCTGTCGGAAGTCG
66 TTTCTGATCTAGTGTGAATGCTACAGTACCTGTCGGAAGTCG
928282 GCTGATTTGCTGCTGTAGAGTTTTGAAAAAAATTATTT-TTGAAATAAGGTCTAACTAAAATTAT
1 GCTGATTTGCTGCTGTAGAGTTTTGAAAAAAATTATTTGTTGAAATAAGGTCTAACTAAAATTAT
*
928346 TTTCTGATCTAGTGTGAATGCTACAGTACCTGTCAGAAGT--
66 TTTCTGATCTAGTGTGAATGCTACAGTACCTGTCGGAAGTCG
928386 -CTGATTTGCTGCTGTAGAGTTTTGAAAAAAATTATTTGTTGAAATAAGGTCTAACTAAAATTAT
1 GCTGATTTGCTGCTGTAGAGTTTTGAAAAAAATTATTTGTTGAAATAAGGTCTAACTAAAATTAT
928450 TTTCTGATCTAGTGTGAATGCTACAGTACCTGTCGGAAGTCG
66 TTTCTGATCTAGTGTGAATGCTACAGTACCTGTCGGAAGTCG
928492 GCTGATTTGCTGCTGTAGAGTTTTGAAAAAAATTATTTGTTGAAATAAGGTCTAACTAAAATTAT
1 GCTGATTTGCTGCTGTAGAGTTTTGAAAAAAATTATTTGTTGAAATAAGGTCTAACTAAAATTAT
928557 TTTCTGATCTAGTGTGAATGCTACAGTACCTGTCGGAAGTCG
66 TTTCTGATCTAGTGTGAATGCTACAGTACCTGTCGGAAGTCG
928599 GCTGATTTGCTGCTGTAGAGTTTTGAAAAAAATTATTTGTTGAAATAAGGTCTAACTAAAATTAT
1 GCTGATTTGCTGCTGTAGAGTTTTGAAAAAAATTATTTGTTGAAATAAGGTCTAACTAAAATTAT
*
928664 TTTCTGATCTAGTGTGAATGCTACAGTTCCTGTCGGAAGTC
66 TTTCTGATCTAGTGTGAATGCTACAGTACCTGTCGGAAGTC
928705 TTATGGACCA
Statistics
Matches: 411, Mismatches: 8, Indels: 8
0.96 0.02 0.02
Matches are distributed among these distances:
103 37 0.09
104 65 0.16
106 62 0.15
107 247 0.60
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.38
Consensus pattern (107 bp):
GCTGATTTGCTGCTGTAGAGTTTTGAAAAAAATTATTTGTTGAAATAAGGTCTAACTAAAATTAT
TTTCTGATCTAGTGTGAATGCTACAGTACCTGTCGGAAGTCG
Found at i:934033 original size:2 final size:2
Alignment explanation
Indices: 934026--934065 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
934016 TAATAAAGGA
934026 AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
934066 TAATGGAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:934045 original size:13 final size:13
Alignment explanation
Indices: 934027--934067 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
934017 AATAAAGGAA
934027 TATATATATATAT
1 TATATATATATAT
934040 TATATATATATA-
1 TATATATATATAT
934052 TATAATATATATAT
1 TAT-ATATATATAT
934066 TA
1 TA
934068 ATGGAAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 3 0.12
13 21 0.81
14 2 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TATATATATATAT
Found at i:934046 original size:15 final size:15
Alignment explanation
Indices: 934025--934065 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
934015 TTAATAAAGG
934025 AATATATATATATAT
1 AATATATATATATAT
*
934040 TATATATATATATAT
1 AATATATATATATAT
934055 AATATATATAT
1 AATATATATAT
934066 TAATGGAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AATATATATATATAT
Found at i:934048 original size:17 final size:17
Alignment explanation
Indices: 934026--934065 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
934016 TAATAAAGGA
*
934026 ATATATATATATATTAT
1 ATATATATATATAATAT
934043 ATATATATATATAATAT
1 ATATATATATATAATAT
934060 ATATAT
1 ATATAT
934066 TAATGGAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATATATATATAATAT
Found at i:936649 original size:37 final size:37
Alignment explanation
Indices: 936599--936672 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
936589 TCATATCTGA
**
936599 ATTTGCTTCACTACTCTTTTGTGAAGGCTTAAGATTG
1 ATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTG
*
936636 ATTTG-TTGCACTACTCTTCGGTGAAGGCTTTAGATTG
1 ATTTGCTT-CACTACTCTTCGGTGAAGGCTTAAGATTG
936673 CCCGTTGGAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
36 2 0.06
37 31 0.94
ACGTcount: A:0.20, C:0.16, G:0.22, T:0.42
Consensus pattern (37 bp):
ATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTG
Found at i:937124 original size:43 final size:43
Alignment explanation
Indices: 937069--937180 Score: 161
Period size: 43 Copynumber: 2.6 Consensus size: 43
937059 CGATTCCCTT
* *
937069 CGTCGTGAAGTTGAAATCGTGGATGGGTGGGCACGATATCCTC
1 CGTCGTGGAGTTGAAATCGTGGATGGATGGGCACGATATCCTC
** * *
937112 CGTCGTGGAGTTGAAATCGTGGATCCATTGGTACGATATCCTC
1 CGTCGTGGAGTTGAAATCGTGGATGGATGGGCACGATATCCTC
*
937155 CGTCATGGAGTTGAAATCGTGGATGG
1 CGTCGTGGAGTTGAAATCGTGGATGG
937181 CGCCTTCGTC
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.21, C:0.18, G:0.33, T:0.28
Consensus pattern (43 bp):
CGTCGTGGAGTTGAAATCGTGGATGGATGGGCACGATATCCTC
Found at i:937387 original size:335 final size:335
Alignment explanation
Indices: 936777--937696 Score: 1491
Period size: 335 Copynumber: 2.7 Consensus size: 335
936767 CTATTCCCTT
* * * * *
936777 CGTCGTGAAGTTAAAACCGTGGATCCGTGGGTACAATATCCTCCGTCGTGGAGTTGAAATCGTGG
1 CGTCGTGGAGTTGAAATCGTGGATCCGTTGGTACGATATCCTCCGTCGTGGAGTTGAAATCGTGG
* * * *
936842 ATGGTGCCTTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTGCGTCATGAAGTTAAAATCCAA
66 ATGGCGCCTTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAA
* * * * * * * *
936907 GCTTATGATGTTTCGGGTCCAATATCATTCGTCGTGAAGTTGATATTGACTCTGAAACTAGAAAA
131 GCTTGTGCTGTTTCGAGTCCAATATCCTTCGTCGTGAAGTTAAAATTGGCTCTGAAACTAGAAAG
* * * * * *
936972 TTTATTGACATACACTCATTGTTCGAGTTGGATATCCTTCATCGTGAAGTTGAAATCCAATCTAT
196 TTTATTGACAGACACTCCTTCTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAG
* *
937037 AGATGGATGTTGCTTGTGTGTACGATTCCCTTCGTCGTGAAGTTGAAATCGTGGATGGGTGGGCA
261 AGATGGATGTTGCTTGTGTATACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGGTGGGCA
937102 CGATATCCTC
326 CGATATCCTC
* *
937112 CGTCGTGGAGTTGAAATCGTGGATCCATTGGTACGATATCCTCCGTCATGGAGTTGAAATCGTGG
1 CGTCGTGGAGTTGAAATCGTGGATCCGTTGGTACGATATCCTCCGTCGTGGAGTTGAAATCGTGG
937177 ATGGCGCCTTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAA
66 ATGGCGCCTTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAA
* * * *
937242 GCTTGTGCTATTTCGAGTCCAATATCCTTCGCCGTGAAGTTAAAATTGGCTCTAAAACTGGAAAG
131 GCTTGTGCTGTTTCGAGTCCAATATCCTTCGTCGTGAAGTTAAAATTGGCTCTGAAACTAGAAAG
937307 TTTATTGACAGACACTCCTTCTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAG
196 TTTATTGACAGACACTCCTTCTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAG
**
937372 AGAT-GACTGTTGCTTGTGTATACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGTTTGGGC
261 AGATGGA-TGTTGCTTGTGTATACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGGTGGGC
937436 ACGATATCCTC
325 ACGATATCCTC
* *
937447 CATCGTGGAGTTGAAATCGTGGATCGGTTGGTACGATATCCTCCGTCGTGGAGTTGAAATCGTGG
1 CGTCGTGGAGTTGAAATCGTGGATCCGTTGGTACGATATCCTCCGTCGTGGAGTTGAAATCGTGG
* *
937512 ATGGCCCCTTCGTCGTGAAGTTGAGCTTTGACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAA
66 ATGGCGCCTTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAA
937577 GCTTGTGCTGTTTCGAGTCCAATATCCTTCGTCGTGAAGTTAAAATTGGCTCTGAAACTAGAAAG
131 GCTTGTGCTGTTTCGAGTCCAATATCCTTCGTCGTGAAGTTAAAATTGGCTCTGAAACTAGAAAG
937642 TTTATTGACAGACACTCCTTCTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAA
196 TTTATTGACAGACACTCCTTCTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAA
937697 CTGTGGATGT
Statistics
Matches: 541, Mismatches: 43, Indels: 2
0.92 0.07 0.00
Matches are distributed among these distances:
334 2 0.00
335 539 1.00
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (335 bp):
CGTCGTGGAGTTGAAATCGTGGATCCGTTGGTACGATATCCTCCGTCGTGGAGTTGAAATCGTGG
ATGGCGCCTTCGTCGTGAAGTTGAGCCTTGACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAA
GCTTGTGCTGTTTCGAGTCCAATATCCTTCGTCGTGAAGTTAAAATTGGCTCTGAAACTAGAAAG
TTTATTGACAGACACTCCTTCTTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAG
AGATGGATGTTGCTTGTGTATACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGGTGGGCA
CGATATCCTC
Found at i:937459 original size:43 final size:42
Alignment explanation
Indices: 937406--937515 Score: 157
Period size: 43 Copynumber: 2.6 Consensus size: 42
937396 ATTCCCTTCG
* * *
937406 TCGTGAAGTTGAAACCGTGGATGTTTGGGCACGATATCCTCCA
1 TCGTGGAGTTGAAATCGTGGATGGTT-GGCACGATATCCTCCA
* *
937449 TCGTGGAGTTGAAATCGTGGATCGGTTGGTACGATATCCTCCG
1 TCGTGGAGTTGAAATCGTGGAT-GGTTGGCACGATATCCTCCA
937492 TCGTGGAGTTGAAATCGTGGATGG
1 TCGTGGAGTTGAAATCGTGGATGG
937516 CCCCTTCGTC
Statistics
Matches: 61, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
42 2 0.03
43 56 0.92
44 3 0.05
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (42 bp):
TCGTGGAGTTGAAATCGTGGATGGTTGGCACGATATCCTCCA
Found at i:937736 original size:43 final size:43
Alignment explanation
Indices: 937672--937791 Score: 179
Period size: 43 Copynumber: 2.8 Consensus size: 43
937662 CTTTGAGTTG
* *
937672 GATATCCTTCGTCGTGAAGTTGAAA-CTGTGGATGTGTGGGCAC
1 GATATCCTCCGTCGTGGAGTTGAAATC-GTGGATGTGTGGGCAC
* * *
937715 GATATCCTCCGTCGTGGAGTTGAAATCGTGGATCTGTTGGTAC
1 GATATCCTCCGTCGTGGAGTTGAAATCGTGGATGTGTGGGCAC
937758 GATATCCTCCGTCGTGGAGTTGAAATCGTGGATG
1 GATATCCTCCGTCGTGGAGTTGAAATCGTGGATG
937792 GCCCATTCGT
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
43 69 0.99
44 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.32, T:0.31
Consensus pattern (43 bp):
GATATCCTCCGTCGTGGAGTTGAAATCGTGGATGTGTGGGCAC
Found at i:937742 original size:277 final size:277
Alignment explanation
Indices: 937400--937906 Score: 897
Period size: 277 Copynumber: 1.8 Consensus size: 277
937390 TATACGATTC
*
937400 CCTTCGTCGTGAAGTTGAAACCGTGGATGTTTGGGCACGATATCCTCCATCGTGGAGTTGAAATC
1 CCTTCGTCGTGAAGTTGAAACCGTGGATGTGTGGGCACGATATCCTCCATCGTGGAGTTGAAATC
*
937465 GTGGATCGGTTGGTACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATGGCCCCTTCGTCGTGA
66 GTGGATCGGTTGGTACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATGGCCCATTCGTCGTGA
* *
937530 AGTTGAGCTTTGACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCTTGTGCTGTTTCGAGT
131 AGTTGAGCCTTGACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCTTGTGCTATTTCGAGT
* * *
937595 CCAATATCCTTCGTCGTGAAGTTAAAATTGGCTCTGAAACTAGAAAGTTTATTGACAGACACTCC
196 CCAATATCCTTCATCGTGAACTTAAAATTGACTCTGAAACTAGAAAGTTTATTGACAGACACTCC
937660 TTCTTTGAGTTGGATAT
261 TTCTTTGAGTTGGATAT
* *
937677 CCTTCGTCGTGAAGTTGAAACTGTGGATGTGTGGGCACGATATCCTCCGTCGTGGAGTTGAAATC
1 CCTTCGTCGTGAAGTTGAAACCGTGGATGTGTGGGCACGATATCCTCCATCGTGGAGTTGAAATC
*
937742 GTGGATCTGTTGGTACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATGGCCCATTCGTCGTGA
66 GTGGATCGGTTGGTACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATGGCCCATTCGTCGTGA
*
937807 AGTTGAGCCTTGACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCTTGTGCTATTTTGAGT
131 AGTTGAGCCTTGACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCTTGTGCTATTTCGAGT
* *
937872 CCAATATCCTTCATTGTGAACTTGAAATTGACTCT
196 CCAATATCCTTCATCGTGAACTTAAAATTGACTCT
937907 AAAAGCTGCA
Statistics
Matches: 217, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
277 217 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.33
Consensus pattern (277 bp):
CCTTCGTCGTGAAGTTGAAACCGTGGATGTGTGGGCACGATATCCTCCATCGTGGAGTTGAAATC
GTGGATCGGTTGGTACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATGGCCCATTCGTCGTGA
AGTTGAGCCTTGACTTGAATATCCTTCGTCGTGAAGTTGAAATCCAAGCTTGTGCTATTTCGAGT
CCAATATCCTTCATCGTGAACTTAAAATTGACTCTGAAACTAGAAAGTTTATTGACAGACACTCC
TTCTTTGAGTTGGATAT
Found at i:938136 original size:32 final size:32
Alignment explanation
Indices: 938067--938155 Score: 97
Period size: 32 Copynumber: 2.8 Consensus size: 32
938057 TTGCATCAGG
* * *
938067 ATGTTGAATCCCCAAATATGCCCCAATATTCA
1 ATGTTGAATCTCTAAATATGCCCCAACATTCA
**
938099 ATGTTGAATCTCTAAATATGCCCCAACATTTG
1 ATGTTGAATCTCTAAATATGCCCCAACATTCA
* * **
938131 TTGTTGAATCTTTAACGATGCCCCA
1 ATGTTGAATCTCTAAATATGCCCCA
938156 TTGTTCCTCA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (32 bp):
ATGTTGAATCTCTAAATATGCCCCAACATTCA
Found at i:939187 original size:9 final size:9
Alignment explanation
Indices: 939173--939229 Score: 51
Period size: 9 Copynumber: 6.1 Consensus size: 9
939163 TATCGTCCTT
939173 TTTTTTTTC
1 TTTTTTTTC
*
939182 TTTTTTTGC
1 TTTTTTTTC
*
939191 TTTTTGTTGC
1 TTTTT-TTTC
939201 TCTTTTTTTC
1 T-TTTTTTTC
* *
939211 TCTTTTCTC
1 TTTTTTTTC
*
939220 TTTTTGTTC
1 TTTTTTTTC
939229 T
1 T
939230 GATTGGATCT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
9 26 0.67
10 9 0.23
11 4 0.10
ACGTcount: A:0.00, C:0.16, G:0.07, T:0.77
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:944997 original size:2 final size:2
Alignment explanation
Indices: 944992--945030 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
944982 ATCTACTGAA
944992 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
945031 AAAGTAGTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:945154 original size:2 final size:2
Alignment explanation
Indices: 945147--945176 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
945137 TTTCATGATC
945147 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
945177 TAAATATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:945247 original size:2 final size:2
Alignment explanation
Indices: 945240--945269 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
945230 TTAATAAGGA
945240 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
945270 TAACATGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:947368 original size:3 final size:3
Alignment explanation
Indices: 947344--947394 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
947334 CTACAAAAGC
* * *
947344 AAT ATT AAT ATT AAT AAAT AAT AAT AAT AAT GAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
947390 AAT AA
1 AAT AA
947395 CGGGATGAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:962929 original size:105 final size:105
Alignment explanation
Indices: 962472--962932 Score: 708
Period size: 105 Copynumber: 4.4 Consensus size: 105
962462 TTCTTTTGTC
* * *
962472 GGATGAGTTCTTCTCATTATGAACTCTTCTGAAAATG-TGATTCACCTCCTTCTGGGGTGAATTT
1 GGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCCTTCTGCGGTGGATTT
* * * *
962536 GAAGGGAACATGCTCTTCTCATTACGATCCTTTTCCTTCA
66 GAAAGGAACATGCTCTTCTCATTACGAACCTTCTCCTTTA
* ** *
962576 AGACAAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTT
1 GGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCCTTCTGCGGTGGATTT
962641 GAAAGGAACATGCTCTTCTCATTACGAACCTTCTCCTTTA
66 GAAAGGAACATGCTCTTCTCATTACGAACCTTCTCCTTTA
* * * *
962681 GAACGAGTTATTCTCATTATGAACTCTTCTGGAAATATTGATTCACCTCCTTCTGCGGTGGATTT
1 GGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCCTTCTGCGGTGGATTT
*
962746 GAAAGGAACATGCTCTTCTCATTACGATCCTTCTCCTTTA
66 GAAAGGAACATGCTCTTCTCATTACGAACCTTCTCCTTTA
* *
962786 GGATGATTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCCTTCTGGGGTGGATTT
1 GGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCCTTCTGCGGTGGATTT
* *
962851 GAAAGGAACAAGTTCTTCTCATTACGAACCTTCTCCTTTA
66 GAAAGGAACATGCTCTTCTCATTACGAACCTTCTCCTTTA
* **
962891 GGATGAGTTCTTCTCATTATGAACTCTTATAAAAATGTTGAT
1 GGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGAT
962933 CGATTTATCC
Statistics
Matches: 325, Mismatches: 31, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
104 33 0.10
105 292 0.90
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (105 bp):
GGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCCTTCTGCGGTGGATTT
GAAAGGAACATGCTCTTCTCATTACGAACCTTCTCCTTTA
Found at i:963877 original size:42 final size:43
Alignment explanation
Indices: 963814--963914 Score: 125
Period size: 42 Copynumber: 2.4 Consensus size: 43
963804 CTTATCATCT
* * * *
963814 TGCTCGAAAAACTT-GTAGATGACATGAAGAATTTCAGCATAA
1 TGCTCGAAAGACTTACTAGATGACATGAAAAATTTAAGCATAA
* *
963856 TGCTCGAAAGACTTACT-GATGACCTGAAAAATTTAAGCATCA
1 TGCTCGAAAGACTTACTAGATGACATGAAAAATTTAAGCATAA
*
963898 TGATCGAAAGACTTACT
1 TGCTCGAAAGACTTACT
963915 TATCAAGAAC
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
42 50 0.98
43 1 0.02
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.27
Consensus pattern (43 bp):
TGCTCGAAAGACTTACTAGATGACATGAAAAATTTAAGCATAA
Found at i:964097 original size:52 final size:51
Alignment explanation
Indices: 963989--964142 Score: 121
Period size: 52 Copynumber: 2.9 Consensus size: 51
963979 TAGTTTCCTT
* * * * * *
963989 TTAAAAACTCATTGAAAATCATCATCAAGAAACCCTTGAAAATCATGCTTAGTTTC
1 TTAAAAACTCATTTAAAA--A-CATCAAAAAACCC-T-AAAATTAGGTTTAATTTC
* *
964045 -TAAAAACTCATTTGAAAATATCAAAAAATCCCTAAAAATTAGGTTTAATTTC
1 TTAAAAACTCATTTAAAAACATCAAAAAA-CCCT-AAAATTAGGTTTAATTTC
** * * *
964097 TTTGAAATTCATTTAAAAACATTAAGAAACCCTAAAATTAGGTTTA
1 TTAAAAACTCATTTAAAAACATCAAAAAACCCTAAAATTAGGTTTA
964143 GCTTCTTTCA
Statistics
Matches: 80, Mismatches: 16, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
51 13 0.16
52 27 0.34
53 25 0.31
55 15 0.19
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.32
Consensus pattern (51 bp):
TTAAAAACTCATTTAAAAACATCAAAAAACCCTAAAATTAGGTTTAATTTC
Found at i:964142 original size:51 final size:52
Alignment explanation
Indices: 964052--964179 Score: 150
Period size: 51 Copynumber: 2.5 Consensus size: 52
964042 TTCTAAAAAC
* * * * *
964052 TCATTTGAAAATATCAAAAAATCCCTAAAAATTAGGTTTAATTTCTTTGAAAT
1 TCATTTAAAAACATCAAGAAA-CCCTAAAAATTAGGTTTAACTTCTTTCAAAT
* * *
964105 TCATTTAAAAACATTAAGAAACCCT-AAAATTAGGTTTAGCTTCTTTCAAGT
1 TCATTTAAAAACATCAAGAAACCCTAAAAATTAGGTTTAACTTCTTTCAAAT
* *
964156 TCATTTGAAAACATCGAGAAACCC
1 TCATTTAAAAACATCAAGAAACCC
964180 CCGAAAATCA
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
51 43 0.67
52 4 0.06
53 17 0.27
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (52 bp):
TCATTTAAAAACATCAAGAAACCCTAAAAATTAGGTTTAACTTCTTTCAAAT
Found at i:964483 original size:34 final size:35
Alignment explanation
Indices: 964416--964566 Score: 120
Period size: 34 Copynumber: 4.4 Consensus size: 35
964406 GAAAAAAATG
* * *
964416 TCTCAAGTGAGACAAAGTTTGTTTTAAGGGAAACTA
1 TCTCAAGGGAGAC-AAGTTTGTTTCAAGAGAAACTA
* *
964452 TTTCAAGGGAGACAA-TTTGTTTCAAGAGAAACTG
1 TCTCAAGGGAGACAAGTTTGTTTCAAGAGAAACTA
* *
964486 TCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACATA
1 TCTCAAGGGAGAC--AAGTTTGTTTCAAGAGAAAC-TA
* * *
964524 T-TCAA---AG---ATTTTGTTTCAAGAGAAATTG
1 TCTCAAGGGAGACAAGTTTGTTTCAAGAGAAACTA
964552 TCTCAAGGGAGACAA
1 TCTCAAGGGAGACAA
964567 AATTTGTTCT
Statistics
Matches: 93, Mismatches: 11, Indels: 23
0.73 0.09 0.18
Matches are distributed among these distances:
28 2 0.02
29 21 0.23
32 2 0.02
34 30 0.32
35 3 0.03
36 13 0.14
37 20 0.22
38 2 0.02
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (35 bp):
TCTCAAGGGAGACAAGTTTGTTTCAAGAGAAACTA
Found at i:964554 original size:66 final size:68
Alignment explanation
Indices: 964414--964571 Score: 207
Period size: 66 Copynumber: 2.3 Consensus size: 68
964404 GAGAAAAAAA
* * *
964414 TGTCTCAAGTGAGAC-AAAGTTTGTTTTAAGGGAAACTATTTCAAGGGAGACAATTTGTTTCAAG
1 TGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATTTCAA--GAGA-AATTTGTTTCAAG
964478 AGAAAC
63 AGAAAC
*
964484 TGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAAC-ATATTCAA-AG-ATTTTGTTTCAAGAG
1 TGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTAT-TTCAAGAGAAATTTGTTTCAAGAG
*
964546 AAAT
65 AAAC
964550 TGTCTCAAGGGAGACAAAATTT
1 TGTCTCAAGGGAGACAAAATTT
964572 GTTCTTTGGA
Statistics
Matches: 81, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
66 39 0.48
68 2 0.02
70 16 0.20
71 24 0.30
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (68 bp):
TGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATTTCAAGAGAAATTTGTTTCAAGAGA
AAC
Found at i:964762 original size:37 final size:37
Alignment explanation
Indices: 964657--964762 Score: 176
Period size: 37 Copynumber: 2.9 Consensus size: 37
964647 GTGGCGATGC
* * *
964657 TTGTTTTGAGAGAAAAATATCTCAAGTGAAACAAAAT
1 TTGTTTTAAGAGAAAAATGTCTCAAGTGAGACAAAAT
*
964694 TTGTTTTAAGAGAAAAATGTCTCAAGCGAGACAAAAT
1 TTGTTTTAAGAGAAAAATGTCTCAAGTGAGACAAAAT
964731 TTGTTTTAAGAGAAAAATGTCTCAAGTGAGAC
1 TTGTTTTAAGAGAAAAATGTCTCAAGTGAGAC
964763 GACATTTTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 64 1.00
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.29
Consensus pattern (37 bp):
TTGTTTTAAGAGAAAAATGTCTCAAGTGAGACAAAAT
Found at i:968969 original size:3 final size:3
Alignment explanation
Indices: 968961--968985 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
968951 ACTTCAATCA
968961 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
968986 GCTACTTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:971224 original size:37 final size:36
Alignment explanation
Indices: 971182--971256 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 36
971172 TATACATATT
*
971182 TTCT-AAATATTATATTAAACATATAACAT-AATATTTA
1 TTCTAAAATA-TA-ATTAAA-ATATAAAATAAATATTTA
971219 TTCTAAAATATAATTAAAATATAAAATAAAATATTTA
1 TTCTAAAATATAATTAAAATATAAAAT-AAATATTTA
971256 T
1 T
971257 CATGCTATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
35 8 0.24
36 6 0.18
37 15 0.44
38 5 0.15
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.41
Consensus pattern (36 bp):
TTCTAAAATATAATTAAAATATAAAATAAATATTTA
Found at i:974444 original size:18 final size:18
Alignment explanation
Indices: 974423--974458 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
974413 TAACTTCTAA
974423 CTTAACTAGAACTCTTAT
1 CTTAACTAGAACTCTTAT
* *
974441 CTTAGCTAGAACTTTTAT
1 CTTAACTAGAACTCTTAT
974459 ATAAAAGATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.42
Consensus pattern (18 bp):
CTTAACTAGAACTCTTAT
Found at i:977502 original size:23 final size:23
Alignment explanation
Indices: 977472--977515 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
977462 AACATAGAAG
977472 ATCACCGTTTTCTTTATCTTCGT
1 ATCACCGTTTTCTTTATCTTCGT
*
977495 ATCACCGTTTTCTTTGTCTTC
1 ATCACCGTTTTCTTTATCTTC
977516 ATGGTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.11, C:0.27, G:0.09, T:0.52
Consensus pattern (23 bp):
ATCACCGTTTTCTTTATCTTCGT
Found at i:984489 original size:18 final size:18
Alignment explanation
Indices: 984466--984513 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
984456 AAATTGTCCT
* *
984466 TATTATATATTTGTATAA
1 TATTATATATTTATAAAA
*
984484 TATTATA-AATTATAAAA
1 TATTATATATTTATAAAA
984501 TATTTATATATTT
1 TA-TTATATATTT
984514 TCTTTAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 9 0.38
18 12 0.50
19 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
TATTATATATTTATAAAA
Found at i:993188 original size:2 final size:2
Alignment explanation
Indices: 993181--993231 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
993171 TGTTGTAATC
993181 TA TA TA TA TA TA 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
993223 TA TA TA TA T
1 TA TA TA TA T
993232 TTAAATTTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1001523 original size:21 final size:21
Alignment explanation
Indices: 1001471--1001517 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
1001461 GATCGATAAT
*
1001471 TCGCAACGCGAATTTCGACTA
1 TCGCAACGCGAACTTCGACTA
1001492 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
1001513 TCGCA
1 TCGCA
1001518 TTGCGATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.28, C:0.32, G:0.19, T:0.21
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGACTA
Found at i:1001629 original size:82 final size:81
Alignment explanation
Indices: 1001532--1002021 Score: 518
Period size: 82 Copynumber: 6.0 Consensus size: 81
1001522 GATTTACATA
*
1001532 TTCGCATTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCATTGCGATT-TTCCAAAT
1 TTCGCGTTGCGATAGTCCAAGTT--CGTTGCGATAGTCGAAGTTCGCATTGCGATTATTCCAAAT
*
1001596 TCGTTGCGGTAGTCTAAG
64 TCGTTGCGATAGTCTAAG
** * * *
1001614 TTCGCGTTGCGATAGTCCAAGTTCACGTTGCGATTTTTC-AAATT--CTTTGCGA-TAGT-CAAA
1 TTCGCGTTGCGATAGTCCAAGTT--CGTTGCGA-TAGTCGAAGTTCGCATTGCGATTATTCCAAA
*
1001674 GTTTGCGTTGCGATTTATTCTAAG
63 --TT-CGTTGCGA--TAGTCTAAG
* * *
1001698 TT--CGTTGCGATAGTCGAAGTTCGCGTTGCGATAGTCCAAGTTCGCGTTGCGATT-TTCCAAAT
1 TTCGCGTTGCGATAGTCCAAGTT--CGTTGCGATAGTCGAAGTTCGCATTGCGATTATTCCAAAT
*
1001760 TCGTTGCGATAGTCGAAG
64 TCGTTGCGATAGTCTAAG
* *
1001778 TTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCATTGCG-TTATTCCAAAT
1 TTCGCGTTGCGA--TAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCATTGCGATTATTCCAAAT
1001842 TCGTTGCGATAGT-TGAAG
64 TCGTTGCGATAGTCT-AAG
* *
1001860 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCG-AGTTGCAATTTATTCCAA
1 TTCGCGTTGCGA--TAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCA-TTGCGA-TTATTCCAA
*
1001924 ATTCGTTGCGATAGTCCAAG
62 ATTCGTTGCGATAGTCTAAG
** * * *
1001944 TTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
1 TTCGCGTTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCATTGCGA-TTATTCCAAATT
1002009 CGTTGCGATAGTC
65 CGTTGCGATAGTC
1002022 CAAAATCGCA
Statistics
Matches: 353, Mismatches: 32, Indels: 46
0.82 0.07 0.11
Matches are distributed among these distances:
79 5 0.01
80 17 0.05
81 8 0.02
82 248 0.70
83 5 0.01
84 65 0.18
85 5 0.01
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.36
Consensus pattern (81 bp):
TTCGCGTTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCGCATTGCGATTATTCCAAATTC
GTTGCGATAGTCTAAG
Found at i:1001718 original size:103 final size:103
Alignment explanation
Indices: 1001557--1002021 Score: 529
Period size: 103 Copynumber: 4.5 Consensus size: 103
1001547 TCCAAGTTCG
* * * *
1001557 CGTTGCGATAGTCGAAGTTCGCATTGCGA-TT-TTCCAAATTCGTTGCGGTAGTCTAAGTTCGCG
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCG
* *
1001620 TTGCGATAGTCCAAGTTCACGTTGCGATTTTTCAAATT
66 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATT
* * * * *
1001658 CTTTGCGATAGTCAAAGTTTGCGTTGCGATTTATTCTAAGTTCGTTGCGATAGTCGAAGTTCGCG
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCG
1001723 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATT
66 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATT
* *
1001761 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCA
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCG
* * * * * *
1001826 TTGCGTTATTCCAAATT--CGTTGCGATAGTT-GAAGTT
66 TTGCGATAGTCCAAGTTCGCGTTGCGAT-TTTCCAAATT
* * * * * * *
1001862 CGCGTTGCGATTTATTCCAAGTT--CGTTGCGA--TAGTCGAAGTTCGAGTTGCAATTTATTCCA
1 --CGTTGCGA--TAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTC--GTTGCGA--TAGTCGA
*
1001923 AATT--CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATT
58 AGTTCGCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATT
1001967 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTC
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTC
1002022 CAAAATCGCA
Statistics
Matches: 302, Mismatches: 44, Indels: 36
0.79 0.12 0.09
Matches are distributed among these distances:
101 61 0.20
102 4 0.01
103 196 0.65
104 2 0.01
105 39 0.13
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (103 bp):
CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCG
TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATT
Found at i:1001788 original size:124 final size:122
Alignment explanation
Indices: 1001532--1002021 Score: 507
Period size: 124 Copynumber: 4.0 Consensus size: 122
1001522 GATTTACATA
* * *
1001532 TTCGCATTGCGA-TAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCATTGCGATTTTCCAAAT
1 TTCGCGTTGCGATTAGTCCAAATT--CGTTGCGATAGTCGAAGTTCG-ATTGCGATATTCCAAAT
* * * * ** *
1001596 TCGTTGCGGTAGTCTAAGTTCGCGTTGCGA--TAGTCCAAGTTCACGTTGCGATTTTTC-AAA
63 TCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT--CGTTGCGA-TAGTCGAAG
* * * * *
1001656 TT--CTTTGCGA-TAGT-CAAAGTTTGCGTTGCGATTTATTCTAAGTTCG-TTGCGATAGTCGAA
1 TTCGCGTTGCGATTAGTCCAAA--TT-CGTTGCGA--TAGTCGAAGTTCGATTGCGATATTCCAA
*
1001716 GTTCGCGTTGCGATAGTCCAAGTTCGCGTTGCGA-TT-TTCCAAATTCGTTGCGATAGTCGAAG
61 ATT--CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAG
* *
1001778 TTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCATTGCGTTATTCCAAATT
1 TTCGCGTTGCGA-TTAGTCCAAATTCGTTGCGATAGTCGAAGTTCG-ATTGCGATATTCCAAATT
** *
1001843 CGTTGCGATAGTTGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
64 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAG
* * * * * *
1001902 TTCGAGTTGCAATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATT
1 TTCGCGTTGCGA-TTAGTCCAAATTCGTTGCGATAGTCGAAGTTCG-ATTGCGATATTCCAAATT
1001967 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTC
64 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTC
1002022 CAAAATCGCA
Statistics
Matches: 314, Mismatches: 35, Indels: 34
0.82 0.09 0.09
Matches are distributed among these distances:
121 6 0.02
122 83 0.26
123 4 0.01
124 211 0.67
125 3 0.01
126 3 0.01
127 4 0.01
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.36
Consensus pattern (122 bp):
TTCGCGTTGCGATTAGTCCAAATTCGTTGCGATAGTCGAAGTTCGATTGCGATATTCCAAATTCG
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAG
Found at i:1005833 original size:24 final size:23
Alignment explanation
Indices: 1005806--1005891 Score: 100
Period size: 24 Copynumber: 3.6 Consensus size: 23
1005796 TTCCGACTTA
* *
1005806 AATTCTGTTCTGATACATTACCTG
1 AATTCTGTTCTGATAC-TGATCTG
*
1005830 AATTCTGTTCTGATTTCTGATCTG
1 AATTCTGTTCTGA-TACTGATCTG
*
1005854 GATTCTGTTCTGATATCTGATCTG
1 AATTCTGTTCTGATA-CTGATCTG
*
1005878 AATTCTGTTTTGAT
1 AATTCTGTTCTGAT
1005892 TTCTGATATC
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
23 1 0.02
24 50 0.94
25 2 0.04
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.48
Consensus pattern (23 bp):
AATTCTGTTCTGATACTGATCTG
Found at i:1005842 original size:12 final size:12
Alignment explanation
Indices: 1005827--1005896 Score: 70
Period size: 12 Copynumber: 5.8 Consensus size: 12
1005817 GATACATTAC
1005827 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
1005839 CTGATTTCTGAT
1 CTGAATTCTGTT
*
1005851 CTGGATTCTGTT
1 CTGAATTCTGTT
*
1005863 CTG-ATATCTGAT
1 CTGAAT-TCTGTT
1005875 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
1005887 TTGATTTCTG
1 CTGAATTCTG
1005897 ATATCTCCGT
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
11 2 0.04
12 43 0.91
13 2 0.04
ACGTcount: A:0.16, C:0.16, G:0.19, T:0.50
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:1005846 original size:48 final size:48
Alignment explanation
Indices: 1005790--1005894 Score: 124
Period size: 48 Copynumber: 2.2 Consensus size: 48
1005780 AAATATTTTA
*
1005790 TCTGATTTCCGA-CTTAAATTCTGTTCTGATA-CATTACCTGAATTCTGT
1 TCTGATTTCCGATC-TAAATTCTGTTCTGATATC-TGACCTGAATTCTGT
* ** *
1005838 TCTGATTTCTGATCTGGATTCTGTTCTGATATCTGATCTGAATTCTGT
1 TCTGATTTCCGATCTAAATTCTGTTCTGATATCTGACCTGAATTCTGT
*
1005886 TTTGATTTC
1 TCTGATTTC
1005895 TGATATCTCC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
48 47 0.96
49 2 0.04
ACGTcount: A:0.19, C:0.18, G:0.15, T:0.48
Consensus pattern (48 bp):
TCTGATTTCCGATCTAAATTCTGTTCTGATATCTGACCTGAATTCTGT
Found at i:1005895 original size:48 final size:48
Alignment explanation
Indices: 1005807--1005898 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
1005797 TCCGACTTAA
*
1005807 ATTCTGTTCTGATACATTACCTGAATTCTGTTCTGATTTCTGATCTGG
1 ATTCTGTTCTGATACATGACCTGAATTCTGTTCTGATTTCTGATCTGG
* *
1005855 ATTCTGTTCTGATATC-TGATCTGAATTCTGTTTTGATTTCTGAT
1 ATTCTGTTCTGATA-CATGACCTGAATTCTGTTCTGATTTCTGAT
1005899 ATCTCCGTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
48 39 0.98
49 1 0.03
ACGTcount: A:0.18, C:0.16, G:0.16, T:0.49
Consensus pattern (48 bp):
ATTCTGTTCTGATACATGACCTGAATTCTGTTCTGATTTCTGATCTGG
Found at i:1005896 original size:24 final size:24
Alignment explanation
Indices: 1005827--1005898 Score: 117
Period size: 24 Copynumber: 3.0 Consensus size: 24
1005817 GATACATTAC
1005827 CTGAATTCTGTTCTGATTTCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
* *
1005851 CTGGATTCTGTTCTGATATCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
*
1005875 CTGAATTCTGTTTTGATTTCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
1005899 ATCTCCGTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.17, C:0.15, G:0.18, T:0.50
Consensus pattern (24 bp):
CTGAATTCTGTTCTGATTTCTGAT
Found at i:1010230 original size:12 final size:12
Alignment explanation
Indices: 1010215--1010284 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
1010205 GATACATTAC
1010215 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
1010227 CTGATTTCTGAT
1 CTGAATTCTGTT
* *
1010239 CTGGATTCTATT
1 CTGAATTCTGTT
*
1010251 CTG-ATATCTGAT
1 CTGAAT-TCTGTT
*
1010263 CTAAATTCTGTT
1 CTGAATTCTGTT
* *
1010275 TTGATTTCTG
1 CTGAATTCTG
1010285 ATATCTCCGT
Statistics
Matches: 43, Mismatches: 13, Indels: 4
0.72 0.22 0.07
Matches are distributed among these distances:
11 2 0.05
12 39 0.91
13 2 0.05
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.50
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:1010234 original size:48 final size:48
Alignment explanation
Indices: 1010178--1010282 Score: 115
Period size: 48 Copynumber: 2.2 Consensus size: 48
1010168 AAATATTTTA
* * *
1010178 TCTGATTTCGGA-CTTGAATTCTGTTCTGATA-CATTACCTGAATTCTGT
1 TCTGATTTCGGATC-TGAATTCTATTCTGATATC-TGACCTAAATTCTGT
* * *
1010226 TCTGATTTCTGATCTGGATTCTATTCTGATATCTGATCTAAATTCTGT
1 TCTGATTTCGGATCTGAATTCTATTCTGATATCTGACCTAAATTCTGT
*
1010274 TTTGATTTC
1 TCTGATTTC
1010283 TGATATCTCC
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
48 46 0.96
49 2 0.04
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.48
Consensus pattern (48 bp):
TCTGATTTCGGATCTGAATTCTATTCTGATATCTGACCTAAATTCTGT
Found at i:1010246 original size:24 final size:24
Alignment explanation
Indices: 1010218--1010286 Score: 93
Period size: 24 Copynumber: 2.9 Consensus size: 24
1010208 ACATTACCTG
*
1010218 AATTCTGTTCTGATTTCTGATCTG
1 AATTCTGTTCTGATTTCTGATCTA
* * *
1010242 GATTCTATTCTGATATCTGATCTA
1 AATTCTGTTCTGATTTCTGATCTA
*
1010266 AATTCTGTTTTGATTTCTGAT
1 AATTCTGTTCTGATTTCTGAT
1010287 ATCTCCGTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.20, C:0.14, G:0.14, T:0.51
Consensus pattern (24 bp):
AATTCTGTTCTGATTTCTGATCTA
Found at i:1020146 original size:20 final size:19
Alignment explanation
Indices: 1020109--1020156 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
1020099 TCTAAATCCT
*
1020109 TTTTCAAAATTTCATTTTG
1 TTTTCAAAATTCCATTTTG
1020128 ATTTTCAAAA-TCCATTTTTG
1 -TTTTCAAAATTCCA-TTTTG
*
1020148 CTTTCAAAA
1 TTTTCAAAA
1020157 GAAAATTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.31, C:0.15, G:0.04, T:0.50
Consensus pattern (19 bp):
TTTTCAAAATTCCATTTTG
Found at i:1029794 original size:29 final size:28
Alignment explanation
Indices: 1029762--1029957 Score: 243
Period size: 29 Copynumber: 6.8 Consensus size: 28
1029752 ACTAACACAC
1029762 TTTTAAAAATATTTAC-AGAAATAGCATCT
1 TTTTAAAAATATTTACGA-AAATAGCA-CT
*
1029791 TTTTAAAAATATTTATGAAAATAGCACAT
1 TTTTAAAAATATTTACGAAAATAGCAC-T
* *
1029820 TTTTAAAAATATTTACGAAAATATCACAC
1 TTTTAAAAATATTTACGAAAATAGCAC-T
1029849 TTTTAAAAATATTTACGAAAATAGCACCT
1 TTTTAAAAATATTTACGAAAATAGCA-CT
* *
1029878 TTTTAAAAATATTTACTAAAATATCACT
1 TTTTAAAAATATTTACGAAAATAGCACT
*
1029906 TCTTTAAAAATATTTACGAAAATATCACT
1 T-TTTAAAAATATTTACGAAAATAGCACT
* *
1029935 CTTTTAAAAA-AATTACAAAAATA
1 -TTTTAAAAATATTTACGAAAATA
1029958 TCACCCAGTT
Statistics
Matches: 151, Mismatches: 11, Indels: 11
0.87 0.06 0.06
Matches are distributed among these distances:
28 15 0.10
29 133 0.88
30 3 0.02
ACGTcount: A:0.48, C:0.11, G:0.04, T:0.37
Consensus pattern (28 bp):
TTTTAAAAATATTTACGAAAATAGCACT
Found at i:1029871 original size:87 final size:86
Alignment explanation
Indices: 1029745--1029954 Score: 309
Period size: 87 Copynumber: 2.4 Consensus size: 86
1029735 ACAGAATTAA
* * *
1029745 TTACGAAACTAACACACTTTTAAAAATATTTACAGAAATAGCATCTTTTTAAAAATATTTA-TGA
1 TTACGAAAATATCACACTTTTAAAAATATTTACA-AAATAGCACCTTTTTAAAAATATTTACT-A
1029809 AAATAGCACATT-TTTAAAAATAT
64 AAATAGCAC-TTCTTTAAAAATAT
1029832 TTACGAAAATATCACACTTTTAAAAATATTTACGAAAATAGCACCTTTTTAAAAATATTTACTAA
1 TTACGAAAATATCACACTTTTAAAAATATTTAC-AAAATAGCACCTTTTTAAAAATATTTACTAA
*
1029897 AATATCACTTCTTTAAAAATAT
65 AATAGCACTTCTTTAAAAATAT
* *
1029919 TTACGAAAATATCACTCTTTTAAAAA-AATTACAAAA
1 TTACGAAAATATCACACTTTTAAAAATATTTACAAAA
1029955 ATATCACCCA
Statistics
Matches: 114, Mismatches: 6, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
85 4 0.04
86 7 0.06
87 101 0.89
88 2 0.02
ACGTcount: A:0.48, C:0.13, G:0.04, T:0.35
Consensus pattern (86 bp):
TTACGAAAATATCACACTTTTAAAAATATTTACAAAATAGCACCTTTTTAAAAATATTTACTAAA
ATAGCACTTCTTTAAAAATAT
Found at i:1036832 original size:2 final size:2
Alignment explanation
Indices: 1036820--1036852 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1036810 CAGTGAAATA
*
1036820 TG TG CG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1036853 ATATATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.03, G:0.48, T:0.48
Consensus pattern (2 bp):
TG
Found at i:1037717 original size:58 final size:58
Alignment explanation
Indices: 1037566--1037719 Score: 199
Period size: 58 Copynumber: 2.7 Consensus size: 58
1037556 ACAGAATTAA
* *
1037566 TTACAAAACTATCA-C-TCTTAAAAATATTTAC-AGAAATAAAATCTTTTTAAAAATAT
1 TTACGAAACTATCACCTTTTTAAAAATATTTACGA-AAATAAAATCTTTTTAAAAATAT
* * * * *
1037622 TTACGAAAATAGCACTTTTTTAAAAATATTTACGAAAATAACA-CTTTTTTAAAAGTAT
1 TTACGAAACTATCACCTTTTTAAAAATATTTACGAAAATAAAATC-TTTTTAAAAATAT
1037680 TTACGAAACTATCACCTTTTTAAAAATATTTACGAAAATA
1 TTACGAAACTATCACCTTTTTAAAAATATTTACGAAAATA
1037720 TCACCCGGGT
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
56 11 0.13
57 1 0.01
58 71 0.85
59 1 0.01
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.36
Consensus pattern (58 bp):
TTACGAAACTATCACCTTTTTAAAAATATTTACGAAAATAAAATCTTTTTAAAAATAT
Found at i:1037721 original size:29 final size:29
Alignment explanation
Indices: 1037583--1037724 Score: 187
Period size: 29 Copynumber: 4.9 Consensus size: 29
1037573 ACTATCACTC
* *
1037583 TTAAAAATATTTAC-AGAAATAAAATCTTT
1 TTAAAAATATTTACGA-AAATAACACCTTT
* *
1037612 TTAAAAATATTTACGAAAATAGCACTTTT
1 TTAAAAATATTTACGAAAATAACACCTTT
*
1037641 TTAAAAATATTTACGAAAATAACACTTTT
1 TTAAAAATATTTACGAAAATAACACCTTT
* * *
1037670 TTAAAAGTATTTACGAAACTATCACCTTT
1 TTAAAAATATTTACGAAAATAACACCTTT
*
1037699 TTAAAAATATTTACGAAAATATCACC
1 TTAAAAATATTTACGAAAATAACACC
1037725 CGGGTCGGAC
Statistics
Matches: 101, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
29 100 0.99
30 1 0.01
ACGTcount: A:0.46, C:0.12, G:0.05, T:0.37
Consensus pattern (29 bp):
TTAAAAATATTTACGAAAATAACACCTTT
Found at i:1037744 original size:9 final size:9
Alignment explanation
Indices: 1037727--1037756 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1037717 ATATCACCCG
*
1037727 GGTCGGACC
1 GGTCAGACC
1037736 GGTCAGACC
1 GGTCAGACC
1037745 GGTCAGACC
1 GGTCAGACC
1037754 GGT
1 GGT
1037757 TCGCACCGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.17, C:0.30, G:0.40, T:0.13
Consensus pattern (9 bp):
GGTCAGACC
Found at i:1045129 original size:13 final size:13
Alignment explanation
Indices: 1045111--1045147 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
1045101 CCTCGGAGCA
1045111 AATTTTCACATCT
1 AATTTTCACATCT
1045124 AATTTTCAGCA--T
1 AATTTTCA-CATCT
1045136 AATTTTCACATC
1 AATTTTCACATC
1045148 ATTAAGCCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
11 2 0.10
12 9 0.43
13 8 0.38
14 2 0.10
ACGTcount: A:0.32, C:0.22, G:0.03, T:0.43
Consensus pattern (13 bp):
AATTTTCACATCT
Found at i:1046235 original size:18 final size:18
Alignment explanation
Indices: 1046212--1046264 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
1046202 ACTGAATATT
*
1046212 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
1046230 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
1046248 TGTCCTGAAGGACCACT
1 TGTCCCGAAGGACCACT
1046265 GATAATCCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.26, C:0.32, G:0.21, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Done.