Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 103 of 182
Found at i:30997756 original size:51 final size:53
Alignment explanation
Indices: 30997701--30997828 Score: 120
Period size: 53 Copynumber: 2.5 Consensus size: 53
30997691 AATAATAGTC
* * * *
30997701 ATTACATTATTGAAATTAATTAATAAAAATAT-ATAAAT-TATGAAAACAATA
1 ATTACATTATTGAAATTAATTAATAAAAAAATAAAAAATAAATAAAAACAATA
* * **
30997752 ATTACA-TATAT-AAATTATTTTAAAAAAAAAATAAAAAATAAATAAAAATTATA
1 ATTACATTAT-TGAAATTA-ATTAATAAAAAAATAAAAAATAAATAAAAACAATA
* *
30997805 ATTATATTTTTGAAATTAATTAAT
1 ATTACATTATTGAAATTAATTAAT
30997829 TCTCTAAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
50 9 0.15
51 18 0.31
52 5 0.08
53 19 0.32
54 8 0.14
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (53 bp):
ATTACATTATTGAAATTAATTAATAAAAAAATAAAAAATAAATAAAAACAATA
Found at i:30998988 original size:15 final size:15
Alignment explanation
Indices: 30998968--30999007 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
30998958 TGACTATTGT
30998968 TTTGGGCCTGGTTAG
1 TTTGGGCCTGGTTAG
*
30998983 TTTGGGCCTCTGTTTAG
1 TTTGGG-C-CTGGTTAG
30999000 TTTGGGCC
1 TTTGGGCC
30999008 ACATAGGCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 7 0.32
16 2 0.09
17 13 0.59
ACGTcount: A:0.05, C:0.17, G:0.35, T:0.42
Consensus pattern (15 bp):
TTTGGGCCTGGTTAG
Found at i:31002127 original size:22 final size:24
Alignment explanation
Indices: 31002084--31002127 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
31002074 TGATAATATG
31002084 TTTTGATATAACAAATTAAAGTGT
1 TTTTGATATAACAAATTAAAGTGT
*
31002108 TTTTGA-ATAA-AAGTTAAAGT
1 TTTTGATATAACAAATTAAAGT
31002128 TGAAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.43, C:0.02, G:0.14, T:0.41
Consensus pattern (24 bp):
TTTTGATATAACAAATTAAAGTGT
Found at i:31002252 original size:20 final size:20
Alignment explanation
Indices: 31002227--31002268 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
31002217 CCAACTTTAA
*
31002227 AATCAAGTTAAAATGATTTT
1 AATCAAGTAAAAATGATTTT
*
31002247 AATCAAGTAAAAATTATTTT
1 AATCAAGTAAAAATGATTTT
31002267 AA
1 AA
31002269 CTAGTCAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (20 bp):
AATCAAGTAAAAATGATTTT
Found at i:31004282 original size:22 final size:23
Alignment explanation
Indices: 31004252--31004296 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
31004242 ATTATTAAAG
31004252 TAGACTCATAT-TGAATTTATTC
1 TAGACTCATATATGAATTTATTC
* * *
31004274 TAGATTCATTTATGGATTTATTC
1 TAGACTCATATATGAATTTATTC
31004297 ACATGTGACA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (23 bp):
TAGACTCATATATGAATTTATTC
Found at i:31010128 original size:18 final size:19
Alignment explanation
Indices: 31010107--31010147 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
31010097 AGTTAACCTT
*
31010107 TATTATTTAA-AGAATTAA
1 TATTATTTAATAAAATTAA
31010125 TATTATTTAATAAAATTAA
1 TATTATTTAATAAAATTAA
31010144 TATT
1 TATT
31010148 TTGGACTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
TATTATTTAATAAAATTAA
Found at i:31014942 original size:18 final size:19
Alignment explanation
Indices: 31014921--31014961 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
31014911 AGTTAACCTT
*
31014921 TATTATTTAA-AGAATTAA
1 TATTATTTAATAAAATTAA
31014939 TATTATTTAATAAAATTAA
1 TATTATTTAATAAAATTAA
31014958 TATT
1 TATT
31014962 TTGGACTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
TATTATTTAATAAAATTAA
Found at i:31022495 original size:15 final size:15
Alignment explanation
Indices: 31022471--31022507 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
31022461 TGAATTTAGA
31022471 TTAA-TTCAAA-ATT
1 TTAATTTCAAATATT
31022484 TTGAATTTCAAATATT
1 TT-AATTTCAAATATT
31022500 TTAATTTC
1 TTAATTTC
31022508 CAAACAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 2 0.10
14 2 0.10
15 12 0.57
16 5 0.24
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (15 bp):
TTAATTTCAAATATT
Found at i:31027253 original size:50 final size:50
Alignment explanation
Indices: 31027198--31027321 Score: 142
Period size: 50 Copynumber: 2.5 Consensus size: 50
31027188 TATCCTAGAT
* * *
31027198 ATGGTCTTACATGGGA-GTCCTCATATCGGTGCCCATGCCATGTCCCAAAC
1 ATGGTCTTACATGGGACCT-CTCATATCGGTGCCAACGCCATGTCCCAAAC
** * * ** *
31027248 ATGGTCTTACGGGGGACCTCTCGTCTCGGTGCCAACGGGATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTCCCAAAC
31027298 ATGGTCTTACATGGGACCTCTCAT
1 ATGGTCTTACATGGGACCTCTCAT
31027322 GATCTCAAGG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
50 59 0.98
51 1 0.02
ACGTcount: A:0.19, C:0.29, G:0.26, T:0.26
Consensus pattern (50 bp):
ATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTCCCAAAC
Found at i:31033134 original size:13 final size:13
Alignment explanation
Indices: 31033116--31033140 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31033106 TTTCAGCAGA
31033116 AATCCACTATTAC
1 AATCCACTATTAC
31033129 AATCCACTATTA
1 AATCCACTATTA
31033141 TAATGGGGTT
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:0.40, C:0.28, G:0.00, T:0.32
Consensus pattern (13 bp):
AATCCACTATTAC
Found at i:31035008 original size:21 final size:21
Alignment explanation
Indices: 31034956--31035008 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
31034946 TAAGGTAGTA
* *
31034956 TTAAAGTTTCATTGAAAAATT
1 TTAACGTTTCGTTGAAAAATT
31034977 TTAACGTTTCGTTGAAAAATT
1 TTAACGTTTCGTTGAAAAATT
31034998 TTAACGTTTCG
1 TTAACGTTTCG
31035009 ATAGTTAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.34, C:0.09, G:0.13, T:0.43
Consensus pattern (21 bp):
TTAACGTTTCGTTGAAAAATT
Found at i:31044922 original size:13 final size:13
Alignment explanation
Indices: 31044885--31044948 Score: 85
Period size: 13 Copynumber: 4.9 Consensus size: 13
31044875 TTCTTCATTA
31044885 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
* *
31044898 CTGTGGAAAAGTG
1 CTTTTGAAAAGTG
*
31044911 CTTTTGAGAAGTG
1 CTTTTGAAAAGTG
31044924 CTTTT-AAGAAGTG
1 CTTTTGAA-AAGTG
31044937 CTTTTGAAAAGT
1 CTTTTGAAAAGT
31044949 TTGGTTTAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
12 1 0.02
13 40 0.93
14 2 0.05
ACGTcount: A:0.30, C:0.08, G:0.27, T:0.36
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:31055506 original size:15 final size:18
Alignment explanation
Indices: 31055468--31055508 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 18
31055458 AGCAAATACT
31055468 AATAATAAGAACAGTAAC
1 AATAATAAGAACAGTAAC
*
31055486 AGTAATAA-AA-A-TAAC
1 AATAATAAGAACAGTAAC
31055501 AATAATAA
1 AATAATAA
31055509 TACTAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 11 0.52
16 1 0.05
17 2 0.10
18 7 0.33
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.20
Consensus pattern (18 bp):
AATAATAAGAACAGTAAC
Found at i:31058052 original size:14 final size:14
Alignment explanation
Indices: 31058033--31058062 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
31058023 AGTGAGAGAG
*
31058033 GAGAGAAGAGTTGT
1 GAGAGAAGAGATGT
31058047 GAGAGAAGAGATGT
1 GAGAGAAGAGATGT
31058061 GA
1 GA
31058063 ATGAGGAATG
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:0.40, C:0.00, G:0.43, T:0.17
Consensus pattern (14 bp):
GAGAGAAGAGATGT
Found at i:31060906 original size:29 final size:28
Alignment explanation
Indices: 31060866--31060932 Score: 66
Period size: 29 Copynumber: 2.3 Consensus size: 28
31060856 TACCAGAAGC
31060866 AAAAA-AACAAAAA-ATTAGAATATAAAAAT
1 AAAAATAA-AAAAATATTA-AA-ATAAAAAT
* *
31060895 TAAATTAAAAAAATTATTAAAATAAAAAT
1 AAAAATAAAAAAA-TATTAAAATAAAAAT
31060924 AAAAATAAA
1 AAAAATAAA
31060933 TAATGACTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
29 23 0.74
30 4 0.13
31 4 0.13
ACGTcount: A:0.75, C:0.01, G:0.01, T:0.22
Consensus pattern (28 bp):
AAAAATAAAAAAATATTAAAATAAAAAT
Found at i:31061395 original size:54 final size:54
Alignment explanation
Indices: 31061313--31061421 Score: 200
Period size: 54 Copynumber: 2.0 Consensus size: 54
31061303 ATTTCTTCAC
* *
31061313 TTAGTATCTTGATCCGTAGAAATCCCTAAATTATGCTAATATCTCTTTCAAGAG
1 TTAGTATCCTGATCCGTAGAAATCCCTAAATTATGCTAATATATCTTTCAAGAG
31061367 TTAGTATCCTGATCCGTAGAAATCCCTAAATTATGCTAATATATCTTTCAAGAG
1 TTAGTATCCTGATCCGTAGAAATCCCTAAATTATGCTAATATATCTTTCAAGAG
31061421 T
1 T
31061422 AAGAGCAACT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (54 bp):
TTAGTATCCTGATCCGTAGAAATCCCTAAATTATGCTAATATATCTTTCAAGAG
Found at i:31063230 original size:12 final size:12
Alignment explanation
Indices: 31063213--31063259 Score: 62
Period size: 12 Copynumber: 4.0 Consensus size: 12
31063203 TTATTGCAAT
31063213 TGATTTTTTATA
1 TGATTTTTTATA
31063225 TGATTTTTTAT-
1 TGATTTTTTATA
*
31063236 TTATTTTTATATA
1 TGATTTTT-TATA
31063249 T-ATTTTTTATA
1 TGATTTTTTATA
31063260 ATTGTTGTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
11 11 0.34
12 20 0.62
13 1 0.03
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (12 bp):
TGATTTTTTATA
Found at i:31063253 original size:23 final size:23
Alignment explanation
Indices: 31063215--31063258 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
31063205 ATTGCAATTG
31063215 ATTTTTTATATGATTTTTTATTT
1 ATTTTTTATATGATTTTTTATTT
31063238 ATTTTTATATAT-ATTTTTTAT
1 ATTTTT-TATATGATTTTTTAT
31063259 AATTGTTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (23 bp):
ATTTTTTATATGATTTTTTATTT
Found at i:31063974 original size:39 final size:39
Alignment explanation
Indices: 31063846--31063976 Score: 113
Period size: 40 Copynumber: 3.3 Consensus size: 39
31063836 GGCGTTTGGA
* * * *
31063846 ACAAAAGCGCCACAAAAAAATCGAGCATTAGCGGCGATTT
1 ACAAAAGCGCCGC-TAAAAATAGAGAATTAGCGGCGATTT
* ** *
31063886 AGCCAAAGCGCCGCTAAAGGTAGAGAATCT-GCGACGATTT
1 A-CAAAAGCGCCGCTAAAAATAGAGAAT-TAGCGGCGATTT
*
31063926 CCAAGAAGCGCCGCTAAAAATAG-GAATTAGCGGCGATTT
1 ACAA-AAGCGCCGCTAAAAATAGAGAATTAGCGGCGATTT
*
31063965 ATATAAAGCGCC
1 ACA-AAAGCGCC
31063977 ACAAGAAACC
Statistics
Matches: 71, Mismatches: 15, Indels: 11
0.73 0.15 0.11
Matches are distributed among these distances:
38 1 0.01
39 23 0.32
40 36 0.51
41 11 0.15
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.17
Consensus pattern (39 bp):
ACAAAAGCGCCGCTAAAAATAGAGAATTAGCGGCGATTT
Found at i:31064079 original size:41 final size:41
Alignment explanation
Indices: 31064022--31064341 Score: 263
Period size: 41 Copynumber: 7.8 Consensus size: 41
31064012 ATTTTTAAAC
* * *
31064022 CTTTAGCGGCGTTTTTATTTGTGCGCCGCTAATGCTCGGAT
1 CTTTAGTGGCGTTTTTATCTGAGCGCCGCTAATGCTCGGAT
* * *
31064063 CTTTAGTGGCGTTTTTACCTTG-GCGCCGCTAATGCCCCGAT
1 CTTTAGTGGCGTTTTTATC-TGAGCGCCGCTAATGCTCGGAT
* * * * * *
31064104 CTTTAGCGGCATTTTTATATGAGCGCCACTAAAGCTCTGG-C
1 CTTTAGTGGCGTTTTTATCTGAGCGCCGCTAATGCTC-GGAT
* * * * *
31064145 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAAGGCTCGGAG
1 CTTTAGTGGCGTTTTTATCTGAGCGCCGCTAATGCTCGGAT
* * * * *
31064186 CTATAGTGGCGTTTTTATCTCAGCGCCACTAATCCTCTGG-C
1 CTTTAGTGGCGTTTTTATCTGAGCGCCGCTAATGCTC-GGAT
* * *
31064227 CTTTAGTGACGTTTTTGTCTAAGCGCCGCTAATGCTCGGAT
1 CTTTAGTGGCGTTTTTATCTGAGCGCCGCTAATGCTCGGAT
* * * * * *
31064268 CTTTAGTGACGTTTTTATCTGAGTGCCACTAATTCTCCTG-C
1 CTTTAGTGGCGTTTTTATCTGAGCGCCGCTAATGCT-CGGAT
* *
31064309 CTTTAGCGGCGTTTGTT-TCTAAGCGCCGCTAAT
1 CTTTAGTGGCGTTT-TTATCTGAGCGCCGCTAAT
31064342 AGTAACAAAA
Statistics
Matches: 223, Mismatches: 48, Indels: 16
0.78 0.17 0.06
Matches are distributed among these distances:
40 6 0.03
41 208 0.93
42 9 0.04
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (41 bp):
CTTTAGTGGCGTTTTTATCTGAGCGCCGCTAATGCTCGGAT
Found at i:31064159 original size:82 final size:82
Alignment explanation
Indices: 31064022--31064341 Score: 358
Period size: 82 Copynumber: 3.9 Consensus size: 82
31064012 ATTTTTAAAC
* * * * * ** **
31064022 CTTTAGCGGCGTTTTTATTTGTGCGCCGCTAATGCTC-GGATCTTTAGTGGCGTTTTTACCTTGG
1 CTTTAGCGGCGTTTTTATCTGAGCGCCACTAATGCTCTGG-CCTTTAGCGGCGTTTTTGTCTAAG
* *
31064086 CGCCGCTAATGCCCCGAT
65 CGCCGCTAATGCTCGGAT
* * *
31064104 CTTTAGCGGCATTTTTATATGAGCGCCACTAAAGCTCTGGCCTTTAGCGGCGTTTTTGTCTAAGC
1 CTTTAGCGGCGTTTTTATCTGAGCGCCACTAATGCTCTGGCCTTTAGCGGCGTTTTTGTCTAAGC
* *
31064169 GCCGCTAAGGCTCGGAG
66 GCCGCTAATGCTCGGAT
* * * * * *
31064186 CTATAGTGGCGTTTTTATCTCAGCGCCACTAATCCTCTGGCCTTTAGTGACGTTTTTGTCTAAGC
1 CTTTAGCGGCGTTTTTATCTGAGCGCCACTAATGCTCTGGCCTTTAGCGGCGTTTTTGTCTAAGC
31064251 GCCGCTAATGCTCGGAT
66 GCCGCTAATGCTCGGAT
* * * *
31064268 CTTTAGTGACGTTTTTATCTGAGTGCCACTAATTCTCCT-GCCTTTAGCGGCGTTTGTT-TCTAA
1 CTTTAGCGGCGTTTTTATCTGAGCGCCACTAATGCT-CTGGCCTTTAGCGGCGTTT-TTGTCTAA
31064331 GCGCCGCTAAT
64 GCGCCGCTAAT
31064342 AGTAACAAAA
Statistics
Matches: 202, Mismatches: 33, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
82 196 0.97
83 6 0.03
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (82 bp):
CTTTAGCGGCGTTTTTATCTGAGCGCCACTAATGCTCTGGCCTTTAGCGGCGTTTTTGTCTAAGC
GCCGCTAATGCTCGGAT
Found at i:31064833 original size:15 final size:15
Alignment explanation
Indices: 31064812--31064849 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
31064802 TTTAAGGTTA
31064812 ATTTAGGGGTTAGAG
1 ATTTAGGGGTTAGAG
* *
31064827 GTTTAGGGGTTTGAG
1 ATTTAGGGGTTAGAG
31064842 ATTTAGGG
1 ATTTAGGG
31064850 TTTCAACGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.42, T:0.37
Consensus pattern (15 bp):
ATTTAGGGGTTAGAG
Found at i:31064852 original size:14 final size:14
Alignment explanation
Indices: 31064785--31064852 Score: 52
Period size: 15 Copynumber: 4.9 Consensus size: 14
31064775 TACGGGGTAT
*
31064785 AGATTTAAGGTTTG
1 AGATTTAGGGTTTG
* *
31064799 GGATTTAAGG-TT-
1 AGATTTAGGGTTTG
*
31064811 A-ATTTAGGGGTTAG
1 AGATTTA-GGGTTTG
*
31064825 AGGTTTAGGGGTTTG
1 AGATTTA-GGGTTTG
31064840 AGATTTAGGGTTT
1 AGATTTAGGGTTT
31064853 CAACGGTCAT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
11 5 0.12
12 2 0.05
13 3 0.07
14 16 0.37
15 17 0.40
ACGTcount: A:0.24, C:0.00, G:0.35, T:0.41
Consensus pattern (14 bp):
AGATTTAGGGTTTG
Found at i:31075896 original size:42 final size:42
Alignment explanation
Indices: 31075837--31076328 Score: 585
Period size: 42 Copynumber: 11.8 Consensus size: 42
31075827 AAGGAAAACA
* * *
31075837 TTCATTGCATCTAGAGACACAGGTATGGAGGTCCATTCACTT
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTCACTT
*** * *
31075879 TTCATTGCATTTAGAGACCCAGGTGTTTTGATCCGTTCACTT
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTCACTT
*** * *
31075921 TTCATTGCATTTAGAGACCCAGGTGTTTTGATCCGTTCACTT
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTCACTT
*
31075963 TTCATTGCATTTAGAAACCCAGGTGTGGAGGTCCATTCACTT
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTCACTT
*
31076005 TTCATTGCATTTAGAGACCCAGGTGTGGGGGTCCATTCACTT
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTCACTT
*** * *
31076047 TTCATTGCATTTAGAGACCCAGGTGTTTTGATCCGTTCACTT
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTCACTT
*** * *
31076089 TTCATTGCATTTAGAGACCCAGGTGTTTTGATCCGTTCACTT
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTCACTT
* *
31076131 TTCATTGCATTTAGAAACCCAAGTGTGGAGGTCCATTCACTT
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTCACTT
* * * * *
31076173 TTCATTGCATTTAGAGACCTAGGTCTGGAGGTTCGTTCATTT
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTCACTT
* * *
31076215 TTAATTACATTTAGAGACCCAGGTGTGGAGGTTCATTCACTT
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTCACTT
* * * *
31076257 TTCATTGCATTTAGAGACCCAAGTGTGGAGGTACGTTTACTT
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTCACTT
* * *
31076299 TTC-TAG--TTTAGAGGCCCAGGTGTAGAGGTC
1 TTCATTGCATTTAGAGACCCAGGTGTGGAGGTC
31076329 TATTTACATT
Statistics
Matches: 398, Mismatches: 52, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
39 20 0.05
41 2 0.01
42 376 0.94
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (42 bp):
TTCATTGCATTTAGAGACCCAGGTGTGGAGGTCCATTCACTT
Found at i:31076327 original size:39 final size:38
Alignment explanation
Indices: 31076224--31076347 Score: 131
Period size: 39 Copynumber: 3.1 Consensus size: 38
31076214 TTTAATTACA
* *
31076224 TTTAGAGACCCAGGTGTGGAGGTTCATTCACTTTTCATTG
1 TTTAGAGACCCAGGTGTGGAGG-TCATTTACTTTTC-TAG
* *
31076264 CATTTAGAGACCCAAGTGTGGAGGTACGTTTACTTTTCTAG
1 --TTTAGAGACCCAGGTGTGGAGGT-CATTTACTTTTCTAG
* * *
31076305 TTTAGAGGCCCAGGTGTAGAGGTCTATTTACATTTCTAG
1 TTTAGAGACCCAGGTGTGGAGGTC-ATTTACTTTTCTAG
31076344 TTTA
1 TTTA
31076348 CTTTCCATTT
Statistics
Matches: 71, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
38 1 0.01
39 36 0.51
41 3 0.04
42 31 0.44
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.37
Consensus pattern (38 bp):
TTTAGAGACCCAGGTGTGGAGGTCATTTACTTTTCTAG
Found at i:31077361 original size:53 final size:49
Alignment explanation
Indices: 31077273--31077518 Score: 133
Period size: 52 Copynumber: 4.8 Consensus size: 49
31077263 AAAAAAAGGA
* ** *
31077273 GAAAGTTTAGATTTTGAAAAATAAAAATCTGTTTTTTTTAGTCATTTTAAAG
1 GAAAGTTTAAATTTT--AAAATAAAGTTTTGTTTTTTTTA-TCATTTTAAAG
* * *
31077325 GAAAGTTTAAAATTTTAAAATAAAGTTTTGATTTTTTTTCAACTATTTCAAAAT
1 GAAAGTTT-AAATTTTAAAATAAAGTTTTG-TTTTTTTT-ATC-ATTT-TAAAG
* * * * * * *
31077379 AAAAGCTTCAATCTTTAAGAAAAACAG-TGTGTTTTTTTTA--A--ATAAGG
1 GAAAGTTTAAAT-TTTAA-AATAA-AGTTTTGTTTTTTTTATCATTTTAAAG
* ** *
31077426 AGAAAGTTTAGATTTTGAAAAATAAAAATTTGTTTTTTTAAGTCATTTTAAAG
1 -GAAAGTTTAAATTTT--AAAATAAAGTTTTGTTTTTTTTA-TCATTTTAAAG
*
31077479 GAAAGTTTAAAATTTTAAAACAAAGTTTTGATTTTTTTTA
1 GAAAGTTT-AAATTTTAAAATAAAGTTTTG-TTTTTTTTA
31077519 ACTATTTAGA
Statistics
Matches: 144, Mismatches: 31, Indels: 38
0.68 0.15 0.18
Matches are distributed among these distances:
47 6 0.04
48 23 0.16
49 2 0.01
50 1 0.01
51 23 0.16
52 33 0.23
53 25 0.17
54 22 0.15
55 7 0.05
56 2 0.01
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.43
Consensus pattern (49 bp):
GAAAGTTTAAATTTTAAAATAAAGTTTTGTTTTTTTTATCATTTTAAAG
Found at i:31077473 original size:154 final size:155
Alignment explanation
Indices: 31077100--31077533 Score: 600
Period size: 154 Copynumber: 2.8 Consensus size: 155
31077090 AAAGTTTTGA
* * * *
31077100 TTTTT-TTTAAAAAAAAAGAGAAAGTTTAGATTTTCACAAAT---AATTT-TTTTTTTAGTTATT
1 TTTTTATTT-AAAAAAAGGAGAAAGTTTAGATTTTGAAAAATAAAAATTTGTTTTTTTAGTCATT
* * *
31077160 TTAAAGGAAA-TGTTAAATTTTTAAAACAAAGTTTTGATTTTTTTTTTCAACTACTTCAAAGTAA
65 TTAAAGGAAAGT-TTAAAATTTTAAAACAAAGTTTTGA--TTTTTTTTCAACTATTTCAAAATAA
* *
31077224 AAGCTTCAATCTTTAAGAAAAATAATATT
127 AAGCTTCAATCTTTAAGAAAAACAATATG
*
31077253 TTTTTATTTAAAAAAAAGGAGAAAGTTTAGATTTTGAAAAATAAAAATCTGTTTTTTTTAGTCAT
1 TTTTTATTT-AAAAAAAGGAGAAAGTTTAGATTTTGAAAAATAAAAATTTG-TTTTTTTAGTCAT
*
31077318 TTTAAAGGAAAGTTTAAAATTTTAAAATAAAGTTTTGATTTTTTTTCAACTATTTCAAAATAAAA
64 TTTAAAGGAAAGTTTAAAATTTTAAAACAAAGTTTTGATTTTTTTTCAACTATTTCAAAATAAAA
* *
31077383 GCTTCAATCTTTAAGAAAAACAGTGTG
129 GCTTCAATCTTTAAGAAAAACAATATG
*
31077410 TTTTT-TTT-AAATAAGGAGAAAGTTTAGATTTTGAAAAATAAAAATTTGTTTTTTTAAGTCATT
1 TTTTTATTTAAAAAAAGGAGAAAGTTTAGATTTTGAAAAATAAAAATTTGTTTTTTT-AGTCATT
31077473 TTAAAGGAAAGTTTAAAATTTTAAAACAAAGTTTTGATTTTTTTT-AACTATTT-AGAAATAA
65 TTAAAGGAAAGTTTAAAATTTTAAAACAAAGTTTTGATTTTTTTTCAACTATTTCA-AAATAA
31077534 GGTTTTGATT
Statistics
Matches: 256, Mismatches: 16, Indels: 18
0.88 0.06 0.06
Matches are distributed among these distances:
152 1 0.00
153 26 0.10
154 122 0.48
156 3 0.01
157 57 0.22
159 46 0.18
160 1 0.00
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.43
Consensus pattern (155 bp):
TTTTTATTTAAAAAAAGGAGAAAGTTTAGATTTTGAAAAATAAAAATTTGTTTTTTTAGTCATTT
TAAAGGAAAGTTTAAAATTTTAAAACAAAGTTTTGATTTTTTTTCAACTATTTCAAAATAAAAGC
TTCAATCTTTAAGAAAAACAATATG
Found at i:31078083 original size:25 final size:24
Alignment explanation
Indices: 31078055--31078101 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
31078045 TCACTTGCAT
31078055 TTATACA-TTATATATTTAATGTTAA
1 TTATACACTT-TAT-TTTAATGTTAA
*
31078080 TTATGCACTTTATTTTAATGTT
1 TTATACACTTTATTTTAATGTT
31078102 TTATATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 9 0.45
25 9 0.45
26 2 0.10
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.55
Consensus pattern (24 bp):
TTATACACTTTATTTTAATGTTAA
Found at i:31078132 original size:21 final size:21
Alignment explanation
Indices: 31078107--31078154 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
31078097 ATGTTTTATA
31078107 TTTATTCACACTTATATAATT
1 TTTATTCACACTTATATAATT
* **
31078128 TTTATTTATTCTTATATAATT
1 TTTATTCACACTTATATAATT
31078149 TTTATT
1 TTTATT
31078155 TATTTTCATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTATTCACACTTATATAATT
Found at i:31078155 original size:21 final size:21
Alignment explanation
Indices: 31078117--31078158 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
31078107 TTTATTCACA
31078117 CTTATATAATTTTTATTTATT
1 CTTATATAATTTTTATTTATT
31078138 CTTATATAATTTTTATTTATT
1 CTTATATAATTTTTATTTATT
31078159 TTCATGTCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (21 bp):
CTTATATAATTTTTATTTATT
Found at i:31094797 original size:23 final size:23
Alignment explanation
Indices: 31094767--31094811 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
31094757 ATCTAGACTA
*
31094767 ATCAGAGTTTGATTGAAGCAAAG
1 ATCAGAGTTTGATTGAAACAAAG
31094790 ATCAGAGTTTGATTGAAACAAA
1 ATCAGAGTTTGATTGAAACAAA
31094812 TAAATAGAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.42, C:0.09, G:0.22, T:0.27
Consensus pattern (23 bp):
ATCAGAGTTTGATTGAAACAAAG
Found at i:31101391 original size:30 final size:30
Alignment explanation
Indices: 31101335--31101391 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
31101325 TAAACCTTTT
*
31101335 CACTTTCCTCCCAAAATTTTTACTCCCTCA
1 CACTTTCCTCCCAAAACTTTTACTCCCTCA
* *
31101365 CACTTTCC-CCTCATAACTTTTGCTCCC
1 CACTTTCCTCC-CAAAACTTTTACTCCC
31101392 CTCCCATCCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 2 0.09
30 21 0.91
ACGTcount: A:0.19, C:0.42, G:0.02, T:0.37
Consensus pattern (30 bp):
CACTTTCCTCCCAAAACTTTTACTCCCTCA
Found at i:31101798 original size:38 final size:37
Alignment explanation
Indices: 31101744--31101823 Score: 92
Period size: 38 Copynumber: 2.2 Consensus size: 37
31101734 GGTATTAATT
*
31101744 TCACATTTTATCTTTAAGATAATTTTT-ATTAAAAAA
1 TCACATTTTATCTTTAAAATAATTTTTAATTAAAAAA
* * *
31101780 TCACATTTTTTACATTTAAAATATTTTTTAATTTAAAAA
1 TCACATTTTAT-C-TTTAAAATAATTTTTAATTAAAAAA
31101819 T-ACAT
1 TCACAT
31101824 AGTGACGAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
36 10 0.27
37 1 0.03
38 17 0.46
39 9 0.24
ACGTcount: A:0.41, C:0.09, G:0.01, T:0.49
Consensus pattern (37 bp):
TCACATTTTATCTTTAAAATAATTTTTAATTAAAAAA
Found at i:31101820 original size:18 final size:18
Alignment explanation
Indices: 31101784--31101817 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
31101774 AAAAAATCAC
31101784 ATTTTTTACATTTAAAAT
1 ATTTTTTACATTTAAAAT
31101802 ATTTTTTA-ATTTAAAA
1 ATTTTTTACATTTAAAA
31101818 ATACATAGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTTTTACATTTAAAAT
Found at i:31102455 original size:42 final size:42
Alignment explanation
Indices: 31102367--31102495 Score: 204
Period size: 43 Copynumber: 3.0 Consensus size: 42
31102357 ATGTCATTAT
*
31102367 AGAACATGACCTTTAGCGGCGCTTTCCCCACAAACGCCGCTCA
1 AGAACATGACCTTTAGCGGCGCTTT-CCCACAAACGCCGCTAA
* *
31102410 AGAACATGACCTTTAGCGACGCTTTCCCACAAACACCGCTAA
1 AGAACATGACCTTTAGCGGCGCTTTCCCACAAACGCCGCTAA
*
31102452 AGAACATGACCTTTAGCGGTGCTCTTCCCACAAACGCCGCTAA
1 AGAACATGACCTTTAGCGGCGCT-TTCCCACAAACGCCGCTAA
31102495 A
1 A
31102496 AAATATGGTC
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
42 36 0.46
43 43 0.54
ACGTcount: A:0.29, C:0.34, G:0.17, T:0.19
Consensus pattern (42 bp):
AGAACATGACCTTTAGCGGCGCTTTCCCACAAACGCCGCTAA
Found at i:31111793 original size:41 final size:41
Alignment explanation
Indices: 31111736--31112083 Score: 403
Period size: 41 Copynumber: 8.5 Consensus size: 41
31111726 CATATAGTGG
* *
31111736 CGTTTTTTAAGAAGCGCCGCTAATGCTCGGGCCGTTAGCGA
1 CGTTTTTGAAGAAGCGCCGCTAATGCTCGGGCCTTTAGCGA
**
31111777 CGTTTTTGAAGAAGCGCCGCTAATGCTCTAGCCTTTAGCGA
1 CGTTTTTGAAGAAGCGCCGCTAATGCTCGGGCCTTTAGCGA
* * * * *
31111818 CATTTTTTAA-ACAGTGTCGCTAATGCTCTGGCCTTTAGCGA
1 CGTTTTTGAAGA-AGCGCCGCTAATGCTCGGGCCTTTAGCGA
* * * * * * *
31111859 CGTTTCTTCAA-AAACACCGCTACTGCTGGGGTCTTTAGCGG
1 CGTTT-TTGAAGAAGCGCCGCTAATGCTCGGGCCTTTAGCGA
* * *
31111900 CGTTTTTGAAGCAGCACCGCTAATGCTCGGGCCTTTAGCGG
1 CGTTTTTGAAGAAGCGCCGCTAATGCTCGGGCCTTTAGCGA
* * * *
31111941 CATTTTTGAAGAAGCGCCGCTAATACTCGGGCCCTTAGCGG
1 CGTTTTTGAAGAAGCGCCGCTAATGCTCGGGCCTTTAGCGA
* * * *
31111982 TGTTTTTGAAGAAGCACCGCTAATGGTCGGGCCTTTAGCGG
1 CGTTTTTGAAGAAGCGCCGCTAATGCTCGGGCCTTTAGCGA
*
31112023 CGTTTTTGAGGAAGCGCCGCTAATGCTCGGGCCTTTAGCGA
1 CGTTTTTGAAGAAGCGCCGCTAATGCTCGGGCCTTTAGCGA
*
31112064 CGTTTTTGTAGAAGCGCCGC
1 CGTTTTTGAAGAAGCGCCGC
31112084 AAAAACATTT
Statistics
Matches: 260, Mismatches: 44, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
40 5 0.02
41 250 0.96
42 5 0.02
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.29
Consensus pattern (41 bp):
CGTTTTTGAAGAAGCGCCGCTAATGCTCGGGCCTTTAGCGA
Found at i:31112536 original size:7 final size:7
Alignment explanation
Indices: 31112526--31112634 Score: 65
Period size: 7 Copynumber: 15.1 Consensus size: 7
31112516 AAGGTTTATT
31112526 GGTTAGG
1 GGTTAGG
31112533 GGTTAGG
1 GGTTAGG
*
31112540 GGTTAGA
1 GGTTAGG
*
31112547 GGTTAGA
1 GGTTAGG
*
31112554 AGTTAGG
1 GGTTAGG
* *
31112561 AGTTTAAG
1 -GGTTAGG
* *
31112569 GTTTATTG
1 GGTTA-GG
*
31112577 GTTTAGG
1 GGTTAGG
*
31112584 GATTAGG
1 GGTTAGG
31112591 GGTTAGG
1 GGTTAGG
*
31112598 GGTTTGG
1 GGTTAGG
* *
31112605 GATTTAAG
1 G-GTTAGG
31112613 GGTTAGG
1 GGTTAGG
*
31112620 AGTTAGG
1 GGTTAGG
*
31112627 AGTTAGG
1 GGTTAGG
31112634 G
1 G
31112635 ATTTAGTGTT
Statistics
Matches: 81, Mismatches: 18, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
7 67 0.83
8 14 0.17
ACGTcount: A:0.22, C:0.00, G:0.44, T:0.34
Consensus pattern (7 bp):
GGTTAGG
Found at i:31112550 original size:21 final size:21
Alignment explanation
Indices: 31112526--31112632 Score: 56
Period size: 22 Copynumber: 5.0 Consensus size: 21
31112516 AAGGTTTATT
31112526 GGTTAGGGGTTAGGGGTTAGA
1 GGTTAGGGGTTAGGGGTTAGA
** *
31112547 GGTTAGAAGTTAGGAGTTTA-A
1 GGTTAGGGGTTAGG-GGTTAGA
* * * *
31112568 GGTTTATTGGTTTAGGGATTAGG
1 GG-TTA-GGGGTTAGGGGTTAGA
* *
31112591 GGTTAGGGGTTTGGGATTTA-A
1 GGTTAGGGGTTAGGG-GTTAGA
* *
31112612 GGGTTAGGAGTTAGGAGTTAG
1 -GGTTAGGGGTTAGGGGTTAG
31112633 GGATTTAGTG
Statistics
Matches: 61, Mismatches: 18, Indels: 13
0.66 0.20 0.14
Matches are distributed among these distances:
21 25 0.41
22 29 0.48
23 7 0.11
ACGTcount: A:0.22, C:0.00, G:0.43, T:0.35
Consensus pattern (21 bp):
GGTTAGGGGTTAGGGGTTAGA
Found at i:31112615 original size:22 final size:22
Alignment explanation
Indices: 31112576--31112619 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
31112566 AAGGTTTATT
*
31112576 GGTTTAGGGATTAGGGGTTAGG
1 GGTTTAGGGATTAAGGGTTAGG
31112598 GGTTT-GGGATTTAAGGGTTAGG
1 GGTTTAGGGA-TTAAGGGTTAGG
31112620 AGTTAGGAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.18, C:0.00, G:0.48, T:0.34
Consensus pattern (22 bp):
GGTTTAGGGATTAAGGGTTAGG
Found at i:31112624 original size:29 final size:30
Alignment explanation
Indices: 31112581--31112639 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
31112571 TTATTGGTTT
* * *
31112581 AGGGATTAGGGGTTAGGGGTTTGGGATTTA
1 AGGGATTAGGAGTTAGGAGTTAGGGATTTA
31112611 AGGG-TTAGGAGTTAGGAGTTAGGGATTTA
1 AGGGATTAGGAGTTAGGAGTTAGGGATTTA
31112640 GTGTTTTGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.24, C:0.00, G:0.44, T:0.32
Consensus pattern (30 bp):
AGGGATTAGGAGTTAGGAGTTAGGGATTTA
Found at i:31113330 original size:16 final size:16
Alignment explanation
Indices: 31113309--31113364 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
31113299 ACTTAGTAAT
31113309 TAAAAGATACAATTAA
1 TAAAAGATACAATTAA
*
31113325 TAAAAGATACTATTAA
1 TAAAAGATACAATTAA
* * *
31113341 GAAATAAATA-AATAAA
1 TAAA-AGATACAATTAA
31113357 TAAAAGAT
1 TAAAAGAT
31113365 GTGAGATTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
15 3 0.09
16 25 0.78
17 4 0.12
ACGTcount: A:0.64, C:0.04, G:0.07, T:0.25
Consensus pattern (16 bp):
TAAAAGATACAATTAA
Found at i:31113728 original size:24 final size:24
Alignment explanation
Indices: 31113680--31113725 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
31113670 CACTTAGCCG
31113680 AAATTCCCCCCAAATTTCTCCCCA
1 AAATTCCCCCCAAATTTCTCCCCA
* *
31113704 AAATTCCCCTCGAATTT-TCCCC
1 AAATTCCCCCCAAATTTCTCCCC
31113726 CAATTCTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.26, C:0.43, G:0.02, T:0.28
Consensus pattern (24 bp):
AAATTCCCCCCAAATTTCTCCCCA
Found at i:31115151 original size:22 final size:22
Alignment explanation
Indices: 31115126--31115167 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
31115116 CGCTGTTATT
31115126 ATATAATACATAACTTACATTA
1 ATATAATACATAACTTACATTA
*
31115148 ATATTATACATAACTTACAT
1 ATATAATACATAACTTACAT
31115168 AACTTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (22 bp):
ATATAATACATAACTTACATTA
Found at i:31115446 original size:25 final size:24
Alignment explanation
Indices: 31115411--31115461 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
31115401 TGAAATCCCA
31115411 TTTTTGAAAATTTAATTTAATATATT
1 TTTTTGAAAATTTAATTT-ATAT-TT
31115437 TTTTTG-AAATTTAATTTATATTT
1 TTTTTGAAAATTTAATTTATATTT
31115460 TT
1 TT
31115462 AATATAATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 4 0.16
24 4 0.16
25 11 0.44
26 6 0.24
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (24 bp):
TTTTTGAAAATTTAATTTATATTT
Found at i:31115494 original size:25 final size:25
Alignment explanation
Indices: 31115465--31115633 Score: 216
Period size: 25 Copynumber: 6.8 Consensus size: 25
31115455 TATTTTTAAT
*
31115465 ATAATACATAACTTACTTAATTTTC
1 ATAATACATAACTTACATAATTTTC
* * *
31115490 ATAATAAATAACTTACATAACTTAC
1 ATAATACATAACTTACATAATTTTC
* *
31115515 ATAATACATAACTTACATAACTTAC
1 ATAATACATAACTTACATAATTTTC
*
31115540 ATAATACACAACTTACATAATTTTC
1 ATAATACATAACTTACATAATTTTC
*
31115565 ATAATACATAACTTACATAATATTC
1 ATAATACATAACTTACATAATTTTC
* *
31115590 ATAATAAATAACTTACATAA--TAC
1 ATAATACATAACTTACATAATTTTC
31115613 ATAACTTACATAACTTACATA
1 ATAA--TACATAACTTACATA
31115634 GCTTAATTAT
Statistics
Matches: 129, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
23 6 0.05
25 123 0.95
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (25 bp):
ATAATACATAACTTACATAATTTTC
Found at i:31115509 original size:9 final size:9
Alignment explanation
Indices: 31115469--31115638 Score: 150
Period size: 9 Copynumber: 20.2 Consensus size: 9
31115459 TTTAATATAA
31115469 TACATAACT
1 TACATAACT
* *
31115478 TACTTAATT
1 TACATAACT
*
31115487 TTCATAA--
1 TACATAACT
*
31115494 TAAATAACT
1 TACATAACT
31115503 TACATAACT
1 TACATAACT
31115512 TACATAA--
1 TACATAACT
31115519 TACATAACT
1 TACATAACT
31115528 TACATAACT
1 TACATAACT
31115537 TACATAA--
1 TACATAACT
*
31115544 TACACAACT
1 TACATAACT
*
31115553 TACATAATT
1 TACATAACT
*
31115562 TTCATAA--
1 TACATAACT
31115569 TACATAACT
1 TACATAACT
31115578 TACATAA-T
1 TACATAACT
*
31115586 ATTCATAA--
1 -TACATAACT
*
31115594 TAAATAACT
1 TACATAACT
31115603 TACATAA--
1 TACATAACT
31115610 TACATAACT
1 TACATAACT
31115619 TACATAACT
1 TACATAACT
*
31115628 TACATAGCT
1 TACATAACT
31115637 TA
1 TA
31115639 ATTATACTTA
Statistics
Matches: 131, Mismatches: 17, Indels: 26
0.75 0.10 0.15
Matches are distributed among these distances:
7 36 0.27
8 1 0.01
9 94 0.72
ACGTcount: A:0.46, C:0.18, G:0.01, T:0.35
Consensus pattern (9 bp):
TACATAACT
Found at i:31115522 original size:16 final size:17
Alignment explanation
Indices: 31115469--31115638 Score: 133
Period size: 16 Copynumber: 10.1 Consensus size: 17
31115459 TTTAATATAA
* *
31115469 TACATAACTTACTTAATT
1 TACATAA-TTACATAACT
* *
31115487 TTCATAA-TAAATAACT
1 TACATAATTACATAACT
31115503 TACATAACTTACATAA--
1 TACATAA-TTACATAACT
31115519 TACATAACTTACATAACT
1 TACATAA-TTACATAACT
*
31115537 TACATAA-TACACAACT
1 TACATAATTACATAACT
*
31115553 TACATAATTTTCATAA--
1 TACATAA-TTACATAACT
31115569 TACATAACTTACATAA-T
1 TACATAA-TTACATAACT
* *
31115586 ATTCATAA-TAAATAACT
1 -TACATAATTACATAACT
31115603 TACATAA-TACATAACT
1 TACATAATTACATAACT
*
31115619 TACATAACTTACATAGCT
1 TACATAA-TTACATAACT
31115637 TA
1 TA
31115639 ATTATACTTA
Statistics
Matches: 125, Mismatches: 16, Indels: 22
0.77 0.10 0.13
Matches are distributed among these distances:
16 84 0.67
17 1 0.01
18 40 0.32
ACGTcount: A:0.46, C:0.18, G:0.01, T:0.35
Consensus pattern (17 bp):
TACATAATTACATAACT
Found at i:31121187 original size:19 final size:19
Alignment explanation
Indices: 31121163--31121199 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
31121153 GTAAATATTT
*
31121163 TTATCATTTTGACTTTTAA
1 TTATCATTTTAACTTTTAA
31121182 TTATCATTTTAACTTTTA
1 TTATCATTTTAACTTTTA
31121200 TCATTTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.11, G:0.03, T:0.59
Consensus pattern (19 bp):
TTATCATTTTAACTTTTAA
Found at i:31121514 original size:43 final size:41
Alignment explanation
Indices: 31121450--31121601 Score: 162
Period size: 43 Copynumber: 3.6 Consensus size: 41
31121440 GAAAAAATCA
*
31121450 CCGCTAAAGGTCAAGGTCTTTAGCGGCACTTGTGGAAAGAGTT
1 CCGCTAAAGGTCAGGGTCTTTAGCGGCA-TTGTGGAAA-AGTT
* *
31121493 CCGCTAAAGGTCAGGGCCTTTAGCGGCGATTGTAGGAAAAGCGT
1 CCGCTAAAGGTCAGGGTCTTTAGCGGC-ATTGT-GGAAAAG-TT
* * * *
31121537 -CGCTAAAGATCAGGGTCTTTAGCGGCGTTTGTCGAACAAGTG
1 CCGCTAAAGGTCAGGGTCTTTAGCGGC-ATTGTGGAA-AAGTT
*
31121579 CCGCTAAAGGTCATGGTCTTTAG
1 CCGCTAAAGGTCAGGGTCTTTAG
31121602 TGGCGCAATC
Statistics
Matches: 93, Mismatches: 11, Indels: 10
0.82 0.10 0.09
Matches are distributed among these distances:
42 3 0.03
43 83 0.89
44 7 0.08
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25
Consensus pattern (41 bp):
CCGCTAAAGGTCAGGGTCTTTAGCGGCATTGTGGAAAAGTT
Found at i:31124075 original size:142 final size:142
Alignment explanation
Indices: 31123904--31124171 Score: 527
Period size: 142 Copynumber: 1.9 Consensus size: 142
31123894 TTTTAAATTT
*
31123904 CATAATTTATAATCATTAAATTAATTTTTTTGTTAAATAGTATTTAGATAATGTTTTATAATTCT
1 CATAATTTATAATCATTAAATTAAATTTTTTGTTAAATAGTATTTAGATAATGTTTTATAATTCT
31123969 TAAAAGCATTGAATTTATAGCTGTTTTAATTATTGTTTCACTTATTGGTTTTAACAATATTAAAA
66 TAAAAGCATTGAATTTATAGCTGTTTTAATTATTGTTTCACTTATTGGTTTTAACAATATTAAAA
31124034 GTTTTAGAATAA
131 GTTTTAGAATAA
31124046 CATAATTTATAATCATTAAATTAAATTTTTTGTTAAATAGTATTTAGATAATGTTTTATAATTCT
1 CATAATTTATAATCATTAAATTAAATTTTTTGTTAAATAGTATTTAGATAATGTTTTATAATTCT
31124111 TAAAAGCATTGAATTTATAGCTGTTTTAATTATTGTTTCACTTATTGGTTTTAACAATATT
66 TAAAAGCATTGAATTTATAGCTGTTTTAATTATTGTTTCACTTATTGGTTTTAACAATATT
31124172 TTTTTGAATA
Statistics
Matches: 125, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
142 125 1.00
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.49
Consensus pattern (142 bp):
CATAATTTATAATCATTAAATTAAATTTTTTGTTAAATAGTATTTAGATAATGTTTTATAATTCT
TAAAAGCATTGAATTTATAGCTGTTTTAATTATTGTTTCACTTATTGGTTTTAACAATATTAAAA
GTTTTAGAATAA
Found at i:31126738 original size:21 final size:22
Alignment explanation
Indices: 31126690--31126740 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
31126680 GGTTTTTGAC
31126690 AGAAGAAAGAAAGAAGAAAAAA
1 AGAAGAAAGAAAGAAGAAAAAA
* * *
31126712 ATAAGAAAGGAA-AAGAAAAAG
1 AGAAGAAAGAAAGAAGAAAAAA
*
31126733 GGAAGAAA
1 AGAAGAAA
31126741 AGGAGGGAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (22 bp):
AGAAGAAAGAAAGAAGAAAAAA
Found at i:31130729 original size:18 final size:17
Alignment explanation
Indices: 31130695--31130744 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 17
31130685 TATTCTAGAA
31130695 AATTTTTAACTTTTTTTA-
1 AATTTTTAA--TTTTTTAG
31130713 ATATTCTTTAATTTTTTAG
1 A-ATT-TTTAATTTTTTAG
31130732 AATTTTTAATTTT
1 AATTTTTAATTTT
31130745 AAAAAATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 9 0.31
18 11 0.38
19 4 0.14
20 5 0.17
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (17 bp):
AATTTTTAATTTTTTAG
Found at i:31130782 original size:18 final size:19
Alignment explanation
Indices: 31130759--31130795 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
31130749 AATTTTAAAA
31130759 TATAAAT-TTTTGAATTTT
1 TATAAATATTTTGAATTTT
31130777 TATAAATATTTTGAATTTT
1 TATAAATATTTTGAATTTT
31130796 AAAAATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:31130796 original size:18 final size:18
Alignment explanation
Indices: 31130759--31130812 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 18
31130749 AATTTTAAAA
31130759 TATAAAT-TTTTGAATTTT
1 TATAAATATTTTGAA-TTT
31130777 TATAAATATTTTGAATTT
1 TATAAATATTTTGAATTT
* *
31130795 TAAAAATTATTTTAAATT
1 TATAAA-TATTTTGAATT
31130813 ATTTTGTAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
18 15 0.47
19 17 0.53
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.56
Consensus pattern (18 bp):
TATAAATATTTTGAATTT
Found at i:31130805 original size:19 final size:18
Alignment explanation
Indices: 31130733--31130812 Score: 60
Period size: 19 Copynumber: 4.6 Consensus size: 18
31130723 ATTTTTTAGA
*
31130733 ATTTTTAATTTTAAAAA-
1 ATTTTGAATTTTAAAAAT
** *
31130750 ATTTT-AA-AATATAAAT
1 ATTTTGAATTTTAAAAAT
*
31130766 -TTTTGAATTTTTATAAAT
1 ATTTTGAA-TTTTAAAAAT
31130784 ATTTTGAATTTTAAAAATT
1 ATTTTGAATTTTAAAAA-T
*
31130803 ATTTTAAATT
1 ATTTTGAATT
31130813 ATTTTGTAGT
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
15 9 0.18
16 4 0.08
17 5 0.10
18 15 0.30
19 17 0.34
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
ATTTTGAATTTTAAAAAT
Found at i:31130912 original size:18 final size:18
Alignment explanation
Indices: 31130889--31130927 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
31130879 ATACTAATTC
*
31130889 ATTATTTGAGTTATTCAA
1 ATTATTTGACTTATTCAA
*
31130907 ATTATTTGACTTATTCTA
1 ATTATTTGACTTATTCAA
31130925 ATT
1 ATT
31130928 GTAAAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (18 bp):
ATTATTTGACTTATTCAA
Found at i:31133921 original size:40 final size:40
Alignment explanation
Indices: 31133853--31134252 Score: 448
Period size: 40 Copynumber: 10.0 Consensus size: 40
31133843 TATTATATAT
* * *
31133853 TGAAATGTACGCGCTTTCAAGCCTTACCTACTGAATCTAC
1 TGAAATGTATGCGCTTTCGAGCCATACCTACTGAATCTAC
* * *
31133893 TGAAATGTATGTGTTTTCGAGCCATACCTATTGAATCTAC
1 TGAAATGTATGCGCTTTCGAGCCATACCTACTGAATCTAC
* * * * *
31133933 TAAAATGTATGTGCTTTCGAGCCATTCCTAATAAATCTAC
1 TGAAATGTATGCGCTTTCGAGCCATACCTACTGAATCTAC
* * * *
31133973 AGAAATGTACGCGCTTTTGAGCCATACCTATTGAATCTAC
1 TGAAATGTATGCGCTTTCGAGCCATACCTACTGAATCTAC
* * *
31134013 TGAAATGTATACGCTTTCTAGCCCTACCTACTGAATCTA-
1 TGAAATGTATGCGCTTTCGAGCCATACCTACTGAATCTAC
* * * *
31134052 TCGAAATATATGCACTTTCGAGCCATACGTATTGAATCTAC
1 T-GAAATGTATGCGCTTTCGAGCCATACCTACTGAATCTAC
* * *
31134093 CGAAATGTATGTGCTTTCGAGCCATACCTACTGAATATAC
1 TGAAATGTATGCGCTTTCGAGCCATACCTACTGAATCTAC
* *
31134133 TGAAAAGTATGTGCTTTCGAGCCATACCTACTGAATCTAC
1 TGAAATGTATGCGCTTTCGAGCCATACCTACTGAATCTAC
* * * *
31134173 TGAAATGTATGCACTTTTGAGCCATACCTA-TCGATTCTCC
1 TGAAATGTATGCGCTTTCGAGCCATACCTACT-GAATCTAC
* *
31134213 TGAAA-GTATGCCCTATT-GAGCCATACCTACTGATTCTAC
1 TGAAATGTATGCGCT-TTCGAGCCATACCTACTGAATCTAC
31134252 T
1 T
31134253 AAAAGCTGCT
Statistics
Matches: 304, Mismatches: 51, Indels: 11
0.83 0.14 0.03
Matches are distributed among these distances:
39 30 0.10
40 274 0.90
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (40 bp):
TGAAATGTATGCGCTTTCGAGCCATACCTACTGAATCTAC
Found at i:31152358 original size:27 final size:27
Alignment explanation
Indices: 31152327--31152504 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
31152317 TAAATTGTAC
31152327 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
31152354 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
31152380 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
31152408 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
31152436 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
31152463 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
31152490 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
31152505 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:31152441 original size:82 final size:81
Alignment explanation
Indices: 31152328--31152483 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
31152318 AAATTGTACA
* *
31152328 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
31152392 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
31152409 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
31152474 TGCGAGTTGA
65 TGCGAATTGA
31152484 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:31152495 original size:82 final size:81
Alignment explanation
Indices: 31152324--31152504 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
31152314 GATTAAATTG
* *
31152324 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
31152389 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
31152405 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
31152469 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
31152487 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
31152505 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:31156076 original size:27 final size:27
Alignment explanation
Indices: 31156028--31156098 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
31156018 CTGTTTGGCA
31156028 AGCTGGGGTTCGCCTA-TCTGTTCGA-CG
1 AGCTGGGGTTCGCC-AGTCTGTT-GAGCG
* * *
31156055 AGCTGGGGTTCGCCAGTGTGTTTAGTG
1 AGCTGGGGTTCGCCAGTCTGTTGAGCG
*
31156082 AGCTGGGGTTTGCCAGT
1 AGCTGGGGTTCGCCAGT
31156099 TGAGTTGCGA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
26 2 0.05
27 36 0.95
ACGTcount: A:0.11, C:0.20, G:0.38, T:0.31
Consensus pattern (27 bp):
AGCTGGGGTTCGCCAGTCTGTTGAGCG
Found at i:31156118 original size:25 final size:25
Alignment explanation
Indices: 31156087--31156139 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
31156077 TAGTGAGCTG
31156087 GGGTTTGCCAGTTGAGTTGCGAACT
1 GGGTTTGCCAGTTGAGTTGCGAACT
31156112 GGGTTTGCCAGTTGAGTTGCGAACT
1 GGGTTTGCCAGTTGAGTTGCGAACT
31156137 GGG
1 GGG
31156140 GGTTCGCATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.15, C:0.15, G:0.40, T:0.30
Consensus pattern (25 bp):
GGGTTTGCCAGTTGAGTTGCGAACT
Found at i:31156277 original size:19 final size:18
Alignment explanation
Indices: 31156235--31156277 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
31156225 TTCTAAACTG
31156235 ACTAGGGTTCCTAAGTCT
1 ACTAGGGTTCCTAAGTCT
*
31156253 AGTAGGGTATCCTAAGATC-
1 ACTAGGGT-TCCTAAG-TCT
31156272 ACTAGG
1 ACTAGG
31156278 TCACTTAGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 7 0.33
19 12 0.57
20 2 0.10
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.28
Consensus pattern (18 bp):
ACTAGGGTTCCTAAGTCT
Found at i:31157054 original size:18 final size:18
Alignment explanation
Indices: 31157026--31157069 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
31157016 ATTTTTTGTG
*
31157026 ACCCTTGTATG-ATTGCGA
1 ACCCTTATATGCA-TGCGA
*
31157044 CCCCTTATATGCATGCGA
1 ACCCTTATATGCATGCGA
31157062 ACCCTTAT
1 ACCCTTAT
31157070 GAGCGATAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 21 0.95
19 1 0.05
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.32
Consensus pattern (18 bp):
ACCCTTATATGCATGCGA
Found at i:31157327 original size:68 final size:68
Alignment explanation
Indices: 31157217--31157444 Score: 289
Period size: 68 Copynumber: 3.4 Consensus size: 68
31157207 TCTTTTATTT
* * * * * *
31157217 TGCGAACTCATGTTTTTGTGTGAATTCATGCTTATTGCTGTTATGCGAACTCATGTGTTACTTCG
1 TGCGAACTTACGTTGTTGTGTGAATTCATTCTTATTGTTGTTATGCGAACTCATGTGTTACTTAG
31157282 ATA
66 ATA
* ** *
31157285 TGCGAACTTATGTTGTTGTGAAAATTCATTCTTATTGTTGTTATGTGAACTCATGTGTTACTTAG
1 TGCGAACTTACGTTGTTGTGTGAATTCATTCTTATTGTTGTTATGCGAACTCATGTGTTACTTAG
31157350 ATA
66 ATA
* * * *
31157353 TGCGGAGC-TACGTTGTTGTGTGAATTCATGT-TTATTGTTGTTATGCAAAATCATGTGATACTT
1 TGC-GAACTTACGTTGTTGTGTGAATTCAT-TCTTATTGTTGTTATGCGAACTCATGTGTTACTT
31157416 AGATA
64 AGATA
*
31157421 TGCGAACCTACGTTGTTGTGTGAA
1 TGCGAACTTACGTTGTTGTGTGAA
31157445 CCTTAATAAT
Statistics
Matches: 140, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
67 3 0.02
68 133 0.95
69 4 0.03
ACGTcount: A:0.23, C:0.13, G:0.22, T:0.42
Consensus pattern (68 bp):
TGCGAACTTACGTTGTTGTGTGAATTCATTCTTATTGTTGTTATGCGAACTCATGTGTTACTTAG
ATA
Found at i:31158230 original size:54 final size:54
Alignment explanation
Indices: 31158105--31158248 Score: 155
Period size: 54 Copynumber: 2.7 Consensus size: 54
31158095 CGGCCCTGTC
* * * * ** *
31158105 GCAGGCCGTGTGCCAGACTGTGTAACTCTCTGACTTGTGACACATGACCGTGTT
1 GCAGGCCATGTGCTAGGCCGTGTAACTCTCTGACTTGTGACACACAACCATGTT
** *
31158159 GCAGGCTGTGTGCTAGGCCGTGTAACTCTTTGACTTGTGACACACAACCATG-T
1 GCAGGCCATGTGCTAGGCCGTGTAACTCTCTGACTTGTGACACACAACCATGTT
* * *
31158212 GCTAGGCCATGTGTTAGGCCGTGTAACACACTGACTT
1 GC-AGGCCATGTGCTAGGCCGTGTAACTCTCTGACTT
31158249 AATACACACG
Statistics
Matches: 75, Mismatches: 14, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
53 3 0.04
54 72 0.96
ACGTcount: A:0.20, C:0.25, G:0.27, T:0.28
Consensus pattern (54 bp):
GCAGGCCATGTGCTAGGCCGTGTAACTCTCTGACTTGTGACACACAACCATGTT
Found at i:31159170 original size:37 final size:37
Alignment explanation
Indices: 31159128--31159233 Score: 131
Period size: 37 Copynumber: 2.9 Consensus size: 37
31159118 CGATCGCTTG
* * * *
31159128 TAAGAGCTAATCCAGCCTATAACATGTCAAATGCTCA
1 TAAGAGCTAATCCACCCAATAACACGCCAAATGCTCA
*
31159165 TAAGAGCTAATCCACCCAATAACACGCCAATTGCTCA
1 TAAGAGCTAATCCACCCAATAACACGCCAAATGCTCA
* * * *
31159202 TAAGAGCTAATCCAACCGACAACACACCAAAT
1 TAAGAGCTAATCCACCCAATAACACGCCAAAT
31159234 CAGGGAGTAT
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.41, C:0.29, G:0.11, T:0.19
Consensus pattern (37 bp):
TAAGAGCTAATCCACCCAATAACACGCCAAATGCTCA
Found at i:31159909 original size:22 final size:23
Alignment explanation
Indices: 31159857--31159912 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
31159847 TTAATCCTTT
*
31159857 AATAAAAAACTAACTAAAATCAC
1 AATACAAAACTAACTAAAATCAC
**
31159880 TTTACAAAAC-AACTAAAAATCAC
1 AATACAAAACTAACT-AAAATCAC
31159903 AAT-CAAAACT
1 AATACAAAACT
31159913 TCATACACAT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.61, C:0.20, G:0.00, T:0.20
Consensus pattern (23 bp):
AATACAAAACTAACTAAAATCAC
Found at i:31166853 original size:28 final size:28
Alignment explanation
Indices: 31166813--31166870 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
31166803 AGTGTGTGAC
31166813 TGTCACTAGTTCATTTGGGGATATTGTG
1 TGTCACTAGTTCATTTGGGGATATTGTG
31166841 TGTCACTAGTTCATTTGGGGATATTGTG
1 TGTCACTAGTTCATTTGGGGATATTGTG
31166869 TG
1 TG
31166871 GGGCATTAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.17, C:0.10, G:0.29, T:0.43
Consensus pattern (28 bp):
TGTCACTAGTTCATTTGGGGATATTGTG
Found at i:31169184 original size:36 final size:36
Alignment explanation
Indices: 31169127--31169201 Score: 123
Period size: 36 Copynumber: 2.1 Consensus size: 36
31169117 TGATTCATGC
*
31169127 TTATAATGTCTGTGCCTCAATCGATCATGTTTTCAA
1 TTATAATGTCTGTGCCTCAATCAATCATGTTTTCAA
* *
31169163 TTATTATGTTTGTGCCTCAATCAATCATGTTTTCAA
1 TTATAATGTCTGTGCCTCAATCAATCATGTTTTCAA
31169199 TTA
1 TTA
31169202 AAATCAAGTC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.45
Consensus pattern (36 bp):
TTATAATGTCTGTGCCTCAATCAATCATGTTTTCAA
Found at i:31170034 original size:6 final size:6
Alignment explanation
Indices: 31170009--31170052 Score: 70
Period size: 6 Copynumber: 7.2 Consensus size: 6
31169999 ACAGCACCTA
*
31170009 AACAGT AATCAGT AATAGT AACAGT AACAGT AACAGT AACAGT A
1 AACAGT AA-CAGT AACAGT AACAGT AACAGT AACAGT AACAGT A
31170053 TTCAACATAG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
6 29 0.83
7 6 0.17
ACGTcount: A:0.50, C:0.14, G:0.16, T:0.20
Consensus pattern (6 bp):
AACAGT
Found at i:31170130 original size:45 final size:45
Alignment explanation
Indices: 31170032--31170131 Score: 119
Period size: 45 Copynumber: 2.2 Consensus size: 45
31170022 AATAGTAACA
* * * * **
31170032 GTAACAGTAACAGTAACAGTATTCAACATAGACAGTGTTGAATTT
1 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGTCGAATCG
* * *
31170077 GTACCAGTAACGGTAACAGTATTTAACACACAAAGTGTCGAATCG
1 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGTCGAATCG
31170122 GTAACAGTAA
1 GTAACAGTAA
31170132 TAGTTGTCGG
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (45 bp):
GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGTCGAATCG
Found at i:31171377 original size:30 final size:29
Alignment explanation
Indices: 31171343--31171399 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
31171333 TTATCAAATA
31171343 AATAAA-ATCTTTTAATATAATAATTTAATT
1 AATAAATATCTTTTAAT-TAA-AATTTAATT
*
31171373 AATAAATATCTTTTACTTAAAATTTAA
1 AATAAATATCTTTTAATTAAAATTTAA
31171400 GAAAATACAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 7 0.28
30 9 0.36
31 9 0.36
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (29 bp):
AATAAATATCTTTTAATTAAAATTTAATT
Found at i:31171523 original size:17 final size:16
Alignment explanation
Indices: 31171492--31171535 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
31171482 GATTTATTTA
31171492 ATAATATAATATCATT
1 ATAATATAATATCATT
*
31171508 ATAATTTAATTATCATT
1 ATAATATAA-TATCATT
*
31171525 AATTATATAAT
1 -ATAATATAAT
31171536 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 8 0.35
17 8 0.35
18 7 0.30
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (16 bp):
ATAATATAATATCATT
Found at i:31190504 original size:52 final size:50
Alignment explanation
Indices: 31190389--31190506 Score: 148
Period size: 50 Copynumber: 2.3 Consensus size: 50
31190379 TAATAAAGTT
*
31190389 ATGCATTATGTAACTTCCATGCTAGTTAAGTATGCATCATAAATAATGAC
1 ATGCATTATGTAACTCCCATGCTAGTTAAGTATGCATCATAAATAATGAC
* * *
31190439 ATGCATTATGTAACTCCCATGTTAGTTTAAGTCTGCATCATTAAATTAA-GTC
1 ATGCATTATGTAACTCCCATGCTAG-TTAAGTATGCATCA-TAAA-TAATGAC
* *
31190491 TTGCATTAAGTAACTC
1 ATGCATTATGTAACTC
31190507 ATTTGTTCAT
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
50 23 0.39
51 13 0.22
52 20 0.34
53 3 0.05
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (50 bp):
ATGCATTATGTAACTCCCATGCTAGTTAAGTATGCATCATAAATAATGAC
Found at i:31191908 original size:11 final size:11
Alignment explanation
Indices: 31191892--31191929 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
31191882 GTAGGTTCGT
31191892 AAAAAAATTTG
1 AAAAAAATTTG
* *
31191903 AAAAAAAGTTC
1 AAAAAAATTTG
31191914 AAAAAAATTTG
1 AAAAAAATTTG
31191925 AAAAA
1 AAAAA
31191930 GAGGAGATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.68, C:0.03, G:0.08, T:0.21
Consensus pattern (11 bp):
AAAAAAATTTG
Found at i:31192855 original size:18 final size:18
Alignment explanation
Indices: 31192834--31192872 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
31192824 AAAAATAAAT
* *
31192834 AGAAAAATAAAGGGAAAA
1 AGAAAAAGAAAGCGAAAA
*
31192852 AGAAAAAGAAATCGAAAA
1 AGAAAAAGAAAGCGAAAA
31192870 AGA
1 AGA
31192873 GTGAGCCCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.72, C:0.03, G:0.21, T:0.05
Consensus pattern (18 bp):
AGAAAAAGAAAGCGAAAA
Found at i:31192957 original size:17 final size:18
Alignment explanation
Indices: 31192917--31192958 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
31192907 AAATGAAAAA
*
31192917 AGAAAAAAATAAATCGAG
1 AGAAAAAAAGAAATCGAG
**
31192935 TCAAAAAAAGAAAT-GAG
1 AGAAAAAAAGAAATCGAG
31192952 AGAAAAA
1 AGAAAAA
31192959 GAGGCAAGCT
Statistics
Matches: 19, Mismatches: 5, Indels: 1
0.76 0.20 0.04
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.69, C:0.05, G:0.17, T:0.10
Consensus pattern (18 bp):
AGAAAAAAAGAAATCGAG
Found at i:31195239 original size:22 final size:21
Alignment explanation
Indices: 31195213--31195255 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
31195203 GGGTAGAATT
*
31195213 GTAAATTAATAATAAAACTAAA
1 GTAAATTAATAAGAAAA-TAAA
31195235 GTAAATTAATAAGAAAATAAA
1 GTAAATTAATAAGAAAATAAA
31195256 CATTGTCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.26
Consensus pattern (21 bp):
GTAAATTAATAAGAAAATAAA
Found at i:31196269 original size:20 final size:20
Alignment explanation
Indices: 31196244--31196283 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
31196234 GCTTGTATAG
**
31196244 ATTTGCACTTTGGTGCCTCT
1 ATTTGCACTTCAGTGCCTCT
31196264 ATTTGCACTTCAGTGCCTCT
1 ATTTGCACTTCAGTGCCTCT
31196284 GATCGCACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.12, C:0.28, G:0.17, T:0.42
Consensus pattern (20 bp):
ATTTGCACTTCAGTGCCTCT
Found at i:31200669 original size:62 final size:62
Alignment explanation
Indices: 31200564--31200682 Score: 186
Period size: 62 Copynumber: 1.9 Consensus size: 62
31200554 AAATCAGTAA
*
31200564 TCGCTCTACGACTGAGACCATCGGCCACCACATTGGCCATACCAGGATGATACTCTACCGTG
1 TCGCTCTACGACTAAGACCATCGGCCACCACATTGGCCATACCAGGATGATACTCTACCGTG
* * *
31200626 TCGCTCTACGACTAAGAGCATCGGCCACTACATTAGG-CTTACCAGGATGATACTCTA
1 TCGCTCTACGACTAAGACCATCGGCCACCACATT-GGCCATACCAGGATGATACTCTA
31200683 TCATGTACTC
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
62 50 0.96
63 2 0.04
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (62 bp):
TCGCTCTACGACTAAGACCATCGGCCACCACATTGGCCATACCAGGATGATACTCTACCGTG
Found at i:31203162 original size:25 final size:25
Alignment explanation
Indices: 31203122--31203203 Score: 128
Period size: 25 Copynumber: 3.3 Consensus size: 25
31203112 GAGATTCATG
31203122 AACTCACGCCTACAAGCATCAACAT
1 AACTCACGCCTACAAGCATCAACAT
* * *
31203147 AGCTCGCGCCCACAAGCATCAACAT
1 AACTCACGCCTACAAGCATCAACAT
*
31203172 AACTCACACCTACAAGCATCAACAT
1 AACTCACGCCTACAAGCATCAACAT
31203197 AACTCAC
1 AACTCAC
31203204 ACCTTAGAAG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 50 1.00
ACGTcount: A:0.39, C:0.38, G:0.09, T:0.15
Consensus pattern (25 bp):
AACTCACGCCTACAAGCATCAACAT
Found at i:31218611 original size:29 final size:29
Alignment explanation
Indices: 31218563--31218649 Score: 93
Period size: 29 Copynumber: 3.0 Consensus size: 29
31218553 ACCAATACGT
* * *
31218563 AGTACTTGATAAATATAACACTAGCACAA
1 AGTACCTGATAAATGTAACACCAGCACAA
* * *
31218592 AGTGCCTGATAACTGTAACACCAGTACAA
1 AGTACCTGATAAATGTAACACCAGCACAA
* *
31218621 AGTACCAGATAATTGTAATCACCAGCACA
1 AGTACCTGATAAATGTAA-CACCAGCACA
31218650 TTGTGTCTGA
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 38 0.81
30 9 0.19
ACGTcount: A:0.43, C:0.22, G:0.14, T:0.22
Consensus pattern (29 bp):
AGTACCTGATAAATGTAACACCAGCACAA
Found at i:31225036 original size:8 final size:8
Alignment explanation
Indices: 31225001--31225028 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
31224991 TTTTAAATGA
31225001 TATTTTAT
1 TATTTTAT
31225009 TATTTTAT
1 TATTTTAT
31225017 TATTTTAT
1 TATTTTAT
31225025 TATT
1 TATT
31225029 AATTTATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
TATTTTAT
Found at i:31225114 original size:17 final size:17
Alignment explanation
Indices: 31225092--31225141 Score: 84
Period size: 17 Copynumber: 3.0 Consensus size: 17
31225082 TCATCTTCCA
31225092 TGCTTTCTTAACAATTT
1 TGCTTTCTTAACAATTT
31225109 TGCTTTCTTAACAA-TT
1 TGCTTTCTTAACAATTT
*
31225125 TGGTTTCTTAACAATTT
1 TGCTTTCTTAACAATTT
31225142 GGTCCTTCCT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 15 0.48
17 16 0.52
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (17 bp):
TGCTTTCTTAACAATTT
Found at i:31225131 original size:16 final size:16
Alignment explanation
Indices: 31225095--31225144 Score: 82
Period size: 16 Copynumber: 3.1 Consensus size: 16
31225085 TCTTCCATGC
*
31225095 TTTCTTAACAATTTTGC
1 TTTCTTAACAA-TTTGG
31225112 TTTCTTAACAATTTGG
1 TTTCTTAACAATTTGG
31225128 TTTCTTAACAATTTGG
1 TTTCTTAACAATTTGG
31225144 T
1 T
31225145 CCTTCCTCCA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 21 0.66
17 11 0.34
ACGTcount: A:0.24, C:0.14, G:0.10, T:0.52
Consensus pattern (16 bp):
TTTCTTAACAATTTGG
Found at i:31227690 original size:101 final size:101
Alignment explanation
Indices: 31227571--31227755 Score: 311
Period size: 101 Copynumber: 1.8 Consensus size: 101
31227561 ACAGTGATCG
*
31227571 TCACGTGTGTAGTACTATGTCCAGGCTACTACGTGTATCGGAAT-G-ATGGGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTCCAGGCTACTACGTGTATCGG-ATGGAAT-GGTCACATGTGTAGT
31227634 ACTATGTGCAGGCTACTATGCGTACCGAATGGCTTCGA
64 ACTATGTGCAGGCTACTATGCGTACCGAATGGCTTCGA
*
31227672 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGAAATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTCCAGGCTACTACGTGTATCGGATGG-AATGGTCACATGTGTAGTA
31227737 CTATGTGCAGGCTACTATG
65 CTATGTGCAGGCTACTATG
31227756 TGAATCGGGT
Statistics
Matches: 79, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
100 2 0.03
101 41 0.52
102 34 0.43
103 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTCCAGGCTACTACGTGTATCGGATGGAATGGTCACATGTGTAGTAC
TATGTGCAGGCTACTATGCGTACCGAATGGCTTCGA
Found at i:31227757 original size:26 final size:26
Alignment explanation
Indices: 31227677--31227757 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
31227667 TTCGATCACG
31227677 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
* * *
31227703 CGTGTA-T-CGGATG-GAAATGG-TCAC-A
1 TGTGTAGTAC-TATGTG-CA-GGCT-ACTA
31227728 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
31227754 TGTG
1 TGTG
31227758 AATCGGGTAC
Statistics
Matches: 40, Mismatches: 6, Indels: 18
0.62 0.09 0.28
Matches are distributed among these distances:
24 2 0.05
25 16 0.40
26 20 0.50
27 2 0.05
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.32
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:31227763 original size:51 final size:50
Alignment explanation
Indices: 31227566--31227763 Score: 222
Period size: 51 Copynumber: 3.9 Consensus size: 50
31227556 AAGTGACAGT
* *
31227566 GATC-GTCACGTGTGTAGTACTATGTCCAGGCTACTACGTGTATCGGAAT-
1 GATCGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGG-ATG
* * * * * *
31227615 GATGGGTCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGAATG
1 GATCGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATG
* * *
31227665 GCTTCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATG
1 G-ATCGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATG
* *
31227716 GAAAT-GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGAATCGG
1 G--ATCGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGG
31227764 GTACCATTGA
Statistics
Matches: 122, Mismatches: 23, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
49 5 0.04
50 36 0.30
51 80 0.66
52 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (50 bp):
GATCGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATG
Found at i:31232190 original size:27 final size:27
Alignment explanation
Indices: 31232145--31232214 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
31232135 ATGTGACACG
* *
31232145 AAGGCGTCCCTTTACATAGATCACCACA
1 AAGGCTTCCATTT-CATAGATCACCACA
**
31232173 AAGGCTTCCATTTCATAGATTGCCACA
1 AAGGCTTCCATTTCATAGATCACCACA
*
31232200 AAGGCTTTCATTTCA
1 AAGGCTTCCATTTCA
31232215 CCGATGTGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 26 0.70
28 11 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (27 bp):
AAGGCTTCCATTTCATAGATCACCACA
Found at i:31235186 original size:27 final size:27
Alignment explanation
Indices: 31235124--31235188 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
31235114 TTCTTTCAAT
* * *
31235124 GTTCACCATACGCACTATTTCTTCAGA
1 GTTCACCATATGCAATATTCCTTCAGA
** *
31235151 GTTTTCCATATGTAATATTCCTTCAGA
1 GTTCACCATATGCAATATTCCTTCAGA
31235178 GTTCACCATAT
1 GTTCACCATAT
31235189 CTATCATTCT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.26, C:0.25, G:0.11, T:0.38
Consensus pattern (27 bp):
GTTCACCATATGCAATATTCCTTCAGA
Found at i:31235312 original size:28 final size:27
Alignment explanation
Indices: 31235272--31235325 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
31235262 AATGCACCAA
*
31235272 AAAAGCGTTCATTTCCATAGATTTCCAT
1 AAAAGCGTTCATTT-CAAAGATTTCCAT
31235300 AAAAGC-TTCCATTTCAAAGATTTCCA
1 AAAAGCGTT-CATTTCAAAGATTTCCA
31235326 CAAAGAATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.33
Consensus pattern (27 bp):
AAAAGCGTTCATTTCAAAGATTTCCAT
Found at i:31235370 original size:27 final size:27
Alignment explanation
Indices: 31235281--31235370 Score: 90
Period size: 27 Copynumber: 3.3 Consensus size: 27
31235271 AAAAAGCGTT
* *
31235281 CATTTCCATAGATTTCCATAAAAGCTTC
1 CATTT-CATAGATTTCCACAAAGGCTTC
* **
31235309 CATTTCAAAGATTTCCACAAAGAATTC
1 CATTTCATAGATTTCCACAAAGGCTTC
* * * *
31235336 TATGTCATAGATTGCTACAAAGGCTTC
1 CATTTCATAGATTTCCACAAAGGCTTC
31235363 CATTTCAT
1 CATTTCAT
31235371 CGGCATGTTC
Statistics
Matches: 48, Mismatches: 14, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
27 43 0.90
28 5 0.10
ACGTcount: A:0.33, C:0.22, G:0.10, T:0.34
Consensus pattern (27 bp):
CATTTCATAGATTTCCACAAAGGCTTC
Found at i:31237782 original size:66 final size:66
Alignment explanation
Indices: 31237607--31237771 Score: 188
Period size: 66 Copynumber: 2.5 Consensus size: 66
31237597 CAGGAACTTA
* * * * *
31237607 AGAAGACCAAATATCTCATTCTGGAGCTTGGGAGGACTCAATATCTCATTCAAGATCTTAGGATT
1 AGAAGACCTAATATCTCATTCAGGAGCTTGGGAAGACTCGATATCGCATTCAAGATCTTAGGATT
31237672 G
66 G
* * * * * * * *
31237673 AGAAGACATGATATCTCGTTTAGGAGATTCGAAAGACTCGATATCGCATTCAAGAGT-TTGGGAT
1 AGAAGACCTAATATCTCATTCAGGAGCTTGGGAAGACTCGATATCGCATTCAAGA-TCTTAGGAT
31237737 TG
65 TG
*
31237739 AGAAGACCTAATATCTCATTCAGGATCTTGGGA
1 AGAAGACCTAATATCTCATTCAGGAGCTTGGGA
31237772 CGATACGATA
Statistics
Matches: 77, Mismatches: 21, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
66 76 0.99
67 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.28
Consensus pattern (66 bp):
AGAAGACCTAATATCTCATTCAGGAGCTTGGGAAGACTCGATATCGCATTCAAGATCTTAGGATT
G
Found at i:31242688 original size:263 final size:263
Alignment explanation
Indices: 31242221--31242749 Score: 1058
Period size: 263 Copynumber: 2.0 Consensus size: 263
31242211 AAGGACTGGG
31242221 TGGCGGTGGCGGTGGTGCTGGAGGAGAAAGAGGAAACCTGACAGCAGTAGTAGAGGAGGCGGTGA
1 TGGCGGTGGCGGTGGTGCTGGAGGAGAAAGAGGAAACCTGACAGCAGTAGTAGAGGAGGCGGTGA
31242286 AGAGTTGTTTAACACCCGTGTTTAAGGAGTTGTTAGGTAGTTTAATTGGAGGAGGGGGAGGAGGG
66 AGAGTTGTTTAACACCCGTGTTTAAGGAGTTGTTAGGTAGTTTAATTGGAGGAGGGGGAGGAGGG
31242351 GGAAGAGGGATTAGTGGTATGGCTATGAATGCTATGCCATTGAGTTTTGGCGGAACTTTGAATTT
131 GGAAGAGGGATTAGTGGTATGGCTATGAATGCTATGCCATTGAGTTTTGGCGGAACTTTGAATTT
31242416 TGGTGGCGGTGTTGGAGGTAATGTGGAGTTCATGGATGAGAGGTGGAGGAAGCAGCAAATATTGG
196 TGGTGGCGGTGTTGGAGGTAATGTGGAGTTCATGGATGAGAGGTGGAGGAAGCAGCAAATATTGG
31242481 AGT
261 AGT
31242484 TGGCGGTGGCGGTGGTGCTGGAGGAGAAAGAGGAAACCTGACAGCAGTAGTAGAGGAGGCGGTGA
1 TGGCGGTGGCGGTGGTGCTGGAGGAGAAAGAGGAAACCTGACAGCAGTAGTAGAGGAGGCGGTGA
31242549 AGAGTTGTTTAACACCCGTGTTTAAGGAGTTGTTAGGTAGTTTAATTGGAGGAGGGGGAGGAGGG
66 AGAGTTGTTTAACACCCGTGTTTAAGGAGTTGTTAGGTAGTTTAATTGGAGGAGGGGGAGGAGGG
31242614 GGAAGAGGGATTAGTGGTATGGCTATGAATGCTATGCCATTGAGTTTTGGCGGAACTTTGAATTT
131 GGAAGAGGGATTAGTGGTATGGCTATGAATGCTATGCCATTGAGTTTTGGCGGAACTTTGAATTT
31242679 TGGTGGCGGTGTTGGAGGTAATGTGGAGTTCATGGATGAGAGGTGGAGGAAGCAGCAAATATTGG
196 TGGTGGCGGTGTTGGAGGTAATGTGGAGTTCATGGATGAGAGGTGGAGGAAGCAGCAAATATTGG
31242744 AGT
261 AGT
31242747 TGG
1 TGG
31242750 AAGTTTATTC
Statistics
Matches: 266, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
263 266 1.00
ACGTcount: A:0.25, C:0.08, G:0.41, T:0.26
Consensus pattern (263 bp):
TGGCGGTGGCGGTGGTGCTGGAGGAGAAAGAGGAAACCTGACAGCAGTAGTAGAGGAGGCGGTGA
AGAGTTGTTTAACACCCGTGTTTAAGGAGTTGTTAGGTAGTTTAATTGGAGGAGGGGGAGGAGGG
GGAAGAGGGATTAGTGGTATGGCTATGAATGCTATGCCATTGAGTTTTGGCGGAACTTTGAATTT
TGGTGGCGGTGTTGGAGGTAATGTGGAGTTCATGGATGAGAGGTGGAGGAAGCAGCAAATATTGG
AGT
Found at i:31245265 original size:15 final size:15
Alignment explanation
Indices: 31245225--31245265 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
31245215 AAAAATTAAT
31245225 TTTTA-ATTATTATA
1 TTTTATATTATTATA
*
31245239 TTCTAT-TATATTATA
1 TTTTATAT-TATTATA
31245254 TTTTATATTATT
1 TTTTATATTATT
31245266 TCTCTCTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
14 5 0.23
15 16 0.73
16 1 0.05
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTATATTATTATA
Found at i:31258513 original size:18 final size:19
Alignment explanation
Indices: 31258480--31258520 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
31258470 ATGTTCATAT
31258480 TTTTAAAATAATTTAATTA
1 TTTTAAAATAATTTAATTA
*
31258499 TTTTATAAT-ATTTAATTA
1 TTTTAAAATAATTTAATTA
31258517 TTTT
1 TTTT
31258521 TCGACAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTAAAATAATTTAATTA
Found at i:31258521 original size:19 final size:20
Alignment explanation
Indices: 31258477--31258535 Score: 68
Period size: 19 Copynumber: 3.0 Consensus size: 20
31258467 ATCATGTTCA
31258477 TATTTTTAAAATAATTTAAT
1 TATTTTTAAAATAATTTAAT
*
31258497 TA-TTTTATAAT-ATTTAAT
1 TATTTTTAAAATAATTTAAT
*
31258515 TATTTTTCGACAATAATTTAA
1 TATTTTT--AAAATAATTTAA
31258536 CCGAAATAGC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 9 0.27
19 12 0.36
20 2 0.06
21 4 0.12
22 6 0.18
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (20 bp):
TATTTTTAAAATAATTTAAT
Found at i:31260084 original size:57 final size:58
Alignment explanation
Indices: 31260004--31260134 Score: 178
Period size: 57 Copynumber: 2.3 Consensus size: 58
31259994 AGAAATGGTG
* *
31260004 AAATGAAGAATATGAAA-CATTTGGAAATGATTATGATTTTCTCCAAAATG-AAAATG-A
1 AAATGAA-AA-ATGAAATAATTTGGAAATGAATATGATTTTCTCCAAAATGAAAAATGAA
* *
31260061 AAATGCATAAATGAAATAATTTGGAAATGAATGTGATTTTCTCCAAAATGAAAAATGAA
1 AAATG-AAAAATGAAATAATTTGGAAATGAATATGATTTTCTCCAAAATGAAAAATGAA
31260120 AAATGAAAAATGAAA
1 AAATGAAAAATGAAA
31260135 AATGAAAAAT
Statistics
Matches: 65, Mismatches: 5, Indels: 7
0.84 0.06 0.09
Matches are distributed among these distances:
56 6 0.09
57 37 0.57
58 16 0.25
59 6 0.09
ACGTcount: A:0.51, C:0.06, G:0.15, T:0.27
Consensus pattern (58 bp):
AAATGAAAAATGAAATAATTTGGAAATGAATATGATTTTCTCCAAAATGAAAAATGAA
Found at i:31260200 original size:7 final size:7
Alignment explanation
Indices: 31260105--31260184 Score: 160
Period size: 7 Copynumber: 11.4 Consensus size: 7
31260095 GATTTTCTCC
31260105 AAAATGA
1 AAAATGA
31260112 AAAATGA
1 AAAATGA
31260119 AAAATGA
1 AAAATGA
31260126 AAAATGA
1 AAAATGA
31260133 AAAATGA
1 AAAATGA
31260140 AAAATGA
1 AAAATGA
31260147 AAAATGA
1 AAAATGA
31260154 AAAATGA
1 AAAATGA
31260161 AAAATGA
1 AAAATGA
31260168 AAAATGA
1 AAAATGA
31260175 AAAATGA
1 AAAATGA
31260182 AAA
1 AAA
31260185 TGACCTGAAA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 73 1.00
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (7 bp):
AAAATGA
Found at i:31265604 original size:44 final size:44
Alignment explanation
Indices: 31265554--31265953 Score: 581
Period size: 44 Copynumber: 9.1 Consensus size: 44
31265544 CTGTTTAGGA
31265554 AGATAGGA-TCTACAATCTTCAACCTATTCCACTGCTGGTCAAGG
1 AGATAGGACT-TACAATCTTCAACCTATTCCACTGCTGGTCAAGG
* * * *
31265598 AGATAGGACTTGCAATCTACAACCTATTCCAATGCTGGTCAGGG
1 AGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTCAAGG
* *
31265642 AGATAGGACTTACAATCTTCAACCTATTTCACTGCTGGTCAGGG
1 AGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTCAAGG
*
31265686 AGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTCAGGG
1 AGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTCAAGG
* *
31265730 AGATAGGACTTACAATCTTCCACCTATTCCACTGCTAG-CAAGGG
1 AGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTCAA-GG
* ** * *
31265774 AGATAGAACTTGTAATCTTCAACCTATTGCACTACTGGTC-AGAG
1 AGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTCAAG-G
*
31265818 AGATAGGACTTACAATCTTCAACCTATCCCACTGCTGGTCAAGG
1 AGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTCAAGG
*
31265862 AGATAGGACTTACAATCTTCAACCTATCCCACTGCTGGTCAAGG
1 AGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTCAAGG
* * *
31265906 AGATAGGACTTACAATCTTCAACCTATTCCACTGTTGGCCAGGG
1 AGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTCAAGG
31265950 AGAT
1 AGAT
31265954 GAGGCTTTGT
Statistics
Matches: 322, Mismatches: 29, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
43 3 0.01
44 315 0.98
45 4 0.01
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (44 bp):
AGATAGGACTTACAATCTTCAACCTATTCCACTGCTGGTCAAGG
Found at i:31268184 original size:6 final size:6
Alignment explanation
Indices: 31268175--31268210 Score: 54
Period size: 6 Copynumber: 5.7 Consensus size: 6
31268165 TGGCCTTTGC
31268175 TTTTCT TTTTCT TTTTCTT TTTTCTT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTC-T TTTTC-T TTTTCT TTTT
31268211 ATCATTTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 16 0.55
7 13 0.45
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTCT
Found at i:31268196 original size:7 final size:7
Alignment explanation
Indices: 31268175--31268210 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
31268165 TGGCCTTTGC
31268175 TTTTC-T
1 TTTTCTT
31268181 TTTTC-T
1 TTTTCTT
31268187 TTTTCTT
1 TTTTCTT
31268194 TTTTCTT
1 TTTTCTT
31268201 TTTTCTT
1 TTTTCTT
31268208 TTT
1 TTT
31268211 ATCATTTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 11 0.38
7 18 0.62
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTCTT
Found at i:31268198 original size:13 final size:12
Alignment explanation
Indices: 31268175--31268210 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 12
31268165 TGGCCTTTGC
31268175 TTTTCTTTTTCT
1 TTTTCTTTTTCT
31268187 TTTTCTTTTTTCTT
1 TTTTC-TTTTTC-T
31268201 TTTTCTTTTT
1 TTTTCTTTTT
31268211 ATCATTTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 5 0.23
13 11 0.50
14 6 0.27
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTCTTTTTCT
Found at i:31268244 original size:19 final size:18
Alignment explanation
Indices: 31268222--31268270 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 18
31268212 TCATTTTCAT
31268222 ATTTTTTATTTTGACTT-TG
1 ATTTTTT-TTTTG-CTTCTG
31268241 ATTTTTGGTTTTTGCTTCTG
1 ATTTTT--TTTTTGCTTCTG
31268261 ATTTTTTTTT
1 ATTTTTTTTT
31268271 CGTTTTTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 4 0.15
19 9 0.33
20 13 0.48
21 1 0.04
ACGTcount: A:0.10, C:0.06, G:0.12, T:0.71
Consensus pattern (18 bp):
ATTTTTTTTTTGCTTCTG
Found at i:31272764 original size:9 final size:9
Alignment explanation
Indices: 31272741--31272791 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
31272731 AATATTATCG
*
31272741 ATAATAGCA
1 ATAATAGTA
*
31272750 ACAATAGTA
1 ATAATAGTA
*
31272759 ATAATATTA
1 ATAATAGTA
*
31272768 ATAATAATA
1 ATAATAGTA
31272777 A-AAGTAGTA
1 ATAA-TAGTA
31272786 ATAATA
1 ATAATA
31272792 ATAGTGATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
8 2 0.06
9 30 0.88
10 2 0.06
ACGTcount: A:0.59, C:0.04, G:0.08, T:0.29
Consensus pattern (9 bp):
ATAATAGTA
Found at i:31272775 original size:30 final size:29
Alignment explanation
Indices: 31272728--31272809 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 29
31272718 TATATAAGCG
31272728 AATAATATT-ATCGATAATAGCAACAATAGT
1 AATAATATTAAT-GATAATA-CAACAATAGT
* *
31272758 AATAATATTAATAATAATA-AA-AGTAGT
1 AATAATATTAATGATAATACAACAATAGT
* *
31272785 AATAATAATAGTGATAATACCAACA
1 AATAATATTAATGATAATA-CAACA
31272810 CAATGATCCT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
27 21 0.49
28 2 0.05
29 2 0.05
30 16 0.37
31 2 0.05
ACGTcount: A:0.55, C:0.07, G:0.09, T:0.29
Consensus pattern (29 bp):
AATAATATTAATGATAATACAACAATAGT
Found at i:31272796 original size:12 final size:12
Alignment explanation
Indices: 31272752--31272803 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
31272742 TAATAGCAAC
31272752 AATAGTAATAAT
1 AATAGTAATAAT
* *
31272764 ATTAATAATAAT
1 AATAGTAATAAT
31272776 AAAAGTAGTAATAAT
1 --AA-TAGTAATAAT
*
31272791 AATAGTGATAAT
1 AATAGTAATAAT
31272803 A
1 A
31272804 CCAACACAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
12 20 0.62
13 2 0.06
14 1 0.03
15 9 0.28
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.33
Consensus pattern (12 bp):
AATAGTAATAAT
Found at i:31289359 original size:28 final size:28
Alignment explanation
Indices: 31289327--31289384 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
31289317 TCTTTAATGA
31289327 GAGTAAACTGAAACTGTAGGGAGACCTT
1 GAGTAAACTGAAACTGTAGGGAGACCTT
31289355 GAGTAAACTGAAACTGTAGGGAGACCTT
1 GAGTAAACTGAAACTGTAGGGAGACCTT
31289383 GA
1 GA
31289385 TTTGCGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.36, C:0.14, G:0.29, T:0.21
Consensus pattern (28 bp):
GAGTAAACTGAAACTGTAGGGAGACCTT
Found at i:31291504 original size:27 final size:27
Alignment explanation
Indices: 31291474--31291547 Score: 121
Period size: 27 Copynumber: 2.7 Consensus size: 27
31291464 AGGTCAATAT
*
31291474 ATGATCGAAATACCCCTATAGGGTAAA
1 ATGATCGAAATACCCCCATAGGGTAAA
*
31291501 ATGATCTAAATACCCCCATAGGGTAAA
1 ATGATCGAAATACCCCCATAGGGTAAA
*
31291528 ATGACCGAAATACCCCCATA
1 ATGATCGAAATACCCCCATA
31291548 TACCCTCATA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.41, C:0.24, G:0.15, T:0.20
Consensus pattern (27 bp):
ATGATCGAAATACCCCCATAGGGTAAA
Found at i:31291560 original size:37 final size:37
Alignment explanation
Indices: 31291510--31291584 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
31291500 AATGATCTAA
*
31291510 ATACCCCCATAGGGTAAAATGACCGAAATACCCCCAT
1 ATACCCCCATAGGGTAAAATGACCAAAATACCCCCAT
*
31291547 ATACCCTCATAGGGTAAAATGACCAAAATACCCCCAT
1 ATACCCCCATAGGGTAAAATGACCAAAATACCCCCAT
31291584 A
1 A
31291585 GGATAAAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.40, C:0.31, G:0.12, T:0.17
Consensus pattern (37 bp):
ATACCCCCATAGGGTAAAATGACCAAAATACCCCCAT
Found at i:31291577 original size:27 final size:27
Alignment explanation
Indices: 31291547--31291781 Score: 278
Period size: 27 Copynumber: 8.8 Consensus size: 27
31291537 ATACCCCCAT
* * *
31291547 ATACCCTCATAGGGTAAAATGACCAAA
1 ATACCCCCATAGGGTAAAATGATCGAA
* *
31291574 ATACCCCCATAGGATAAAATGATTGAA
1 ATACCCCCATAGGGTAAAATGATCGAA
* *
31291601 ATACCCTCATAGGGTAAAACGATCGAA
1 ATACCCCCATAGGGTAAAATGATCGAA
* * *
31291628 ATA-CCACATAAGGTAAAATGA-CTAAA
1 ATACCCCCATAGGGTAAAATGATC-GAA
*
31291654 ATACCCTCATAGGGTAAAATGATCGAA
1 ATACCCCCATAGGGTAAAATGATCGAA
* * *
31291681 ATA-CACCATAGGGTAAAATAACCGAA
1 ATACCCCCATAGGGTAAAATGATCGAA
31291707 ATACCCCCATAGGGTAAAATGATCGAA
1 ATACCCCCATAGGGTAAAATGATCGAA
* **
31291734 ATACCCCCATAGAGTAGTATGATCGAA
1 ATACCCCCATAGGGTAAAATGATCGAA
*
31291761 ATACCACCATAGGGTAAAATG
1 ATACCCCCATAGGGTAAAATG
31291782 GCTGTTATAC
Statistics
Matches: 174, Mismatches: 30, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
25 1 0.01
26 42 0.24
27 130 0.75
28 1 0.01
ACGTcount: A:0.44, C:0.20, G:0.17, T:0.20
Consensus pattern (27 bp):
ATACCCCCATAGGGTAAAATGATCGAA
Found at i:31291584 original size:64 final size:63
Alignment explanation
Indices: 31291487--31291611 Score: 187
Period size: 64 Copynumber: 2.0 Consensus size: 63
31291477 ATCGAAATAC
* * *
31291487 CCCTATAGGGTAAAATGATCTAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCATATA
1 CCCTATAGGGTAAAATGACCAAAATACCCCCATAGGATAAAATGACCGAAATACCCCCATATA
** *
31291550 CCCTCATAGGGTAAAATGACCAAAATACCCCCATAGGATAAAATGATTGAAATACCCTCATA
1 CCCT-ATAGGGTAAAATGACCAAAATACCCCCATAGGATAAAATGACCGAAATACCCCCATA
31291612 GGGTAAAACG
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
63 4 0.07
64 51 0.93
ACGTcount: A:0.41, C:0.25, G:0.14, T:0.21
Consensus pattern (63 bp):
CCCTATAGGGTAAAATGACCAAAATACCCCCATAGGATAAAATGACCGAAATACCCCCATATA
Found at i:31291668 original size:53 final size:53
Alignment explanation
Indices: 31291547--31291781 Score: 255
Period size: 53 Copynumber: 4.4 Consensus size: 53
31291537 ATACCCCCAT
* * * *
31291547 ATACCCTCATAGGGTAAAATGACCAAAATACCCCCAT-AGGATAAAATGATTGAA
1 ATACCCTCATAGGGTAAAATGATCGAAATA-CCACATAAGG-TAAAATGACTGAA
* *
31291601 ATACCCTCATAGGGTAAAACGATCGAAATACCACATAAGGTAAAATGACTAAA
1 ATACCCTCATAGGGTAAAATGATCGAAATACCACATAAGGTAAAATGACTGAA
* * *
31291654 ATACCCTCATAGGGTAAAATGATCGAAATA-CACCATAGGGTAAAATAACCGAA
1 ATACCCTCATAGGGTAAAATGATCGAAATACCA-CATAAGGTAAAATGACTGAA
* * **
31291707 ATACCCCCATAGGGTAAAATGATCGAAATACCCCCAT-AGAGTAGTATGA-TCGAA
1 ATACCCTCATAGGGTAAAATGATCGAAATA-CCACATAAG-GTAAAATGACT-GAA
31291761 ATACCAC-CATAGGGTAAAATG
1 ATACC-CTCATAGGGTAAAATG
31291782 GCTGTTATAC
Statistics
Matches: 156, Mismatches: 18, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
52 2 0.01
53 91 0.58
54 61 0.39
55 2 0.01
ACGTcount: A:0.44, C:0.20, G:0.17, T:0.20
Consensus pattern (53 bp):
ATACCCTCATAGGGTAAAATGATCGAAATACCACATAAGGTAAAATGACTGAA
Found at i:31291723 original size:80 final size:80
Alignment explanation
Indices: 31291547--31291780 Score: 292
Period size: 80 Copynumber: 2.9 Consensus size: 80
31291537 ATACCCCCAT
* * * * *
31291547 ATACCCTCATAGGGTAAAATGACCAAAATACCCCCATAGGATAAAATGATTGAAATACCCTCATA
1 ATACCCACATAGGGTAAAATGACTAAAATACCCCCATAGGGTAAAATGATCGAAATACAC-CATA
** *
31291612 GGGTAAAACGATCGAA
65 GGGTAAAATAACCGAA
* *
31291628 ATA-CCACATAAGGTAAAATGACTAAAATACCCTCATAGGGTAAAATGATCGAAATACACCATAG
1 ATACCCACATAGGGTAAAATGACTAAAATACCCCCATAGGGTAAAATGATCGAAATACACCATAG
31291692 GGTAAAATAACCGAA
66 GGTAAAATAACCGAA
* * * **
31291707 ATACCCCCATAGGGTAAAATGA-TCGAAATACCCCCATAGAGTAGTATGATCGAAATACCACCAT
1 ATACCCACATAGGGTAAAATGACT-AAAATACCCCCATAGGGTAAAATGATCGAAATA-CACCAT
31291771 AGGGTAAAAT
64 AGGGTAAAAT
31291781 GGCTGTTATA
Statistics
Matches: 133, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
79 21 0.16
80 93 0.70
81 19 0.14
ACGTcount: A:0.44, C:0.20, G:0.16, T:0.20
Consensus pattern (80 bp):
ATACCCACATAGGGTAAAATGACTAAAATACCCCCATAGGGTAAAATGATCGAAATACACCATAG
GGTAAAATAACCGAA
Found at i:31293438 original size:27 final size:27
Alignment explanation
Indices: 31293109--31293430 Score: 321
Period size: 27 Copynumber: 12.0 Consensus size: 27
31293099 GGGTATAACA
* * *
31293109 GTCATTTTACCCTAT-GGGGGCATTTTG
1 GTCATTTTACCC-ATCGAGGGTATTTCG
*
31293136 GTCATTTTACCCATC-AGGGGTATTTCA
1 GTCATTTTACCCATCGA-GGGTATTTCG
* * *
31293163 GTTATTTTACGCATCGGGGGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTTCG
* * *
31293190 ATAATTTTACCCATCGAGGGTATTTCT
1 GTCATTTTACCCATCGAGGGTATTTCG
*
31293217 ATCATTTTACCCATC-AGGGTATTTCG
1 GTCATTTTACCCATCGAGGGTATTTCG
* * *
31293243 GTCATTTTACCTATTGAGGGTATTTCA
1 GTCATTTTACCCATCGAGGGTATTTCG
*
31293270 GTCATTTTACCCATCGAGGGTATTTTG
1 GTCATTTTACCCATCGAGGGTATTTCG
* * *
31293297 GTCATTTTACCCATCAAAGGTATTTCA
1 GTCATTTTACCCATCGAGGGTATTTCG
* *
31293324 GCCATTTTACCCATCGAGGATATTTCG
1 GTCATTTTACCCATCGAGGGTATTTCG
* * *
31293351 ATCATTTTACCTATCG-GGGATATTTCA
1 GTCATTTTACCCATCGAGGG-TATTTCG
* *
31293378 GTTATTTTACCCATTG-GAGGTATTTCG
1 GTCATTTTACCCATCGAG-GGTATTTCG
* * *
31293405 GCCATTTTACCCATTGGGGGTATTTC
1 GTCATTTTACCCATCGAGGGTATTTC
31293431 AATCATTTGC
Statistics
Matches: 244, Mismatches: 44, Indels: 14
0.81 0.15 0.05
Matches are distributed among these distances:
26 26 0.11
27 215 0.88
28 3 0.01
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.40
Consensus pattern (27 bp):
GTCATTTTACCCATCGAGGGTATTTCG
Found at i:31294185 original size:29 final size:31
Alignment explanation
Indices: 31294127--31294186 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
31294117 GGAGAAAAGG
31294127 TTCGGCCAACAAGAAGAAAAGGGAAGAGAGA
1 TTCGGCCAACAAGAAGAAAAGGGAAGAGAGA
* *
31294158 TTCGGCCAA-AAGAA-AAAAGTGATGAGAGA
1 TTCGGCCAACAAGAAGAAAAGGGAAGAGAGA
31294187 AGAGAAACAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 13 0.48
30 5 0.19
31 9 0.33
ACGTcount: A:0.48, C:0.12, G:0.30, T:0.10
Consensus pattern (31 bp):
TTCGGCCAACAAGAAGAAAAGGGAAGAGAGA
Found at i:31302286 original size:28 final size:28
Alignment explanation
Indices: 31302247--31302300 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
31302237 TATCAGTACA
* *
31302247 GTGTAGGTCTTAGCCCATTACAGTAACT
1 GTGTAGGCCTTAGCCCAATACAGTAACT
31302275 GTGTAGGCCTTAGCCCAATACAGTAA
1 GTGTAGGCCTTAGCCCAATACAGTAA
31302301 TCAATGCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (28 bp):
GTGTAGGCCTTAGCCCAATACAGTAACT
Found at i:31302443 original size:26 final size:26
Alignment explanation
Indices: 31302413--31302482 Score: 131
Period size: 26 Copynumber: 2.7 Consensus size: 26
31302403 ACCAATATTA
31302413 CAGCAAAGCTGCCAGTAATAATGACG
1 CAGCAAAGCTGCCAGTAATAATGACG
*
31302439 TAGCAAAGCTGCCAGTAATAATGACG
1 CAGCAAAGCTGCCAGTAATAATGACG
31302465 CAGCAAAGCTGCCAGTAA
1 CAGCAAAGCTGCCAGTAA
31302483 CAGTATATGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.39, C:0.23, G:0.23, T:0.16
Consensus pattern (26 bp):
CAGCAAAGCTGCCAGTAATAATGACG
Found at i:31302694 original size:27 final size:27
Alignment explanation
Indices: 31302664--31302947 Score: 154
Period size: 27 Copynumber: 10.5 Consensus size: 27
31302654 GGGTATAACA
*
31302664 GTCATTTTACCTTAT-GGGGGTACTTTG
1 GTCATTTTACC-CATCGGGGGTACTTTG
*
31302691 GTCATTTTACCCATCGGGGGTATTTTG
1 GTCATTTTACCCATCGGGGGTACTTTG
* * * *
31302718 ATTATTTTACCCATCAGTGGTA-TTTCG
1 GTCATTTTACCCATCGGGGGTACTTT-G
* ** * *
31302745 GTCATTTTACACATCAAGAGTA-TTTCA
1 GTCATTTTACCCATCGGGGGTACTTT-G
* * * *
31302772 ATCATTTTACCCGTCGAGGGTATTTTG
1 GTCATTTTACCCATCGGGGGTACTTTG
* *
31302799 GTTATTTTACCCATCGAGGGTA-TTTCG
1 GTCATTTTACCCATCGGGGGTACTTT-G
* * **
31302826 ATCATTTTATCCATCGAAGGTA-TTTCG
1 GTCATTTTACCCATCGGGGGTACTTT-G
* * *
31302853 ATCATTTTACCCATCGAGGGTA-TTTCA
1 GTCATTTTACCCATCGGGGGTACTTT-G
* *
31302880 GTCATTTTATCCATCGGGGGGTA-TTTCA
1 GTCATTTTACCCATC-GGGGGTACTTT-G
* ** *
31302908 ATCATTTTACCCATCAAGGGTA-TTTCA
1 GTCATTTTACCCATCGGGGGTACTTT-G
31302935 GTCA-TTTACCCAT
1 GTCATTTTACCCAT
31302948 GAAATCCAGG
Statistics
Matches: 215, Mismatches: 37, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
26 17 0.08
27 171 0.80
28 27 0.13
ACGTcount: A:0.22, C:0.19, G:0.18, T:0.40
Consensus pattern (27 bp):
GTCATTTTACCCATCGGGGGTACTTTG
Done.