Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold53
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: 4419549
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 41486 characters in sequence are not A, C, G, or T
File 25 of 28
Found at i:3884063 original size:32 final size:31
Alignment explanation
Indices: 3883915--3884790 Score: 173
Period size: 28 Copynumber: 30.3 Consensus size: 31
3883905 ATTAGTGACA
3883915 TCTTTCTCAAAG-CC-CACAAGTCAGTGGC-A-
1 TCTTT-TCAAAGTCCACACAAGTC-GTGGCAAC
* * *
3883944 TCCTTTCAAAG-CC-CACATGTCAATGGC-A-
1 TCTTTTCAAAGTCCACACAAGTC-GTGGCAAC
* *
3883972 TCCTTTCAAAG-CC-CACAAGTTAGTGGC-AC
1 TCTTTTCAAAGTCCACACAAG-TCGTGGCAAC
* * * *
3884001 -CCTTTCAAAG-CC-CATAAGTCAATGGTAAC
1 TCTTTTCAAAGTCCACACAAGTC-GTGGCAAC
3884030 TCTTTTCAAAGTCCACACAAGTCGCTGGCAAC
1 TCTTTTCAAAGTCCACACAAGTCG-TGGCAAC
3884062 TCTTTTCAAAGTCCACACAAGTCAGTGGCAAC
1 TCTTTTCAAAGTCCACACAAGTC-GTGGCAAC
*
3884094 TCTTTTCAAAG-CCTACACAAATCGGTGGC-AC
1 TCTTTTCAAAGTCC-ACACAAGTC-GTGGCAAC
* * *
3884125 -CCTTCCAAAG-CC-CACAAGTTAGTGGC-AC
1 TCTTTTCAAAGTCCACACAAG-TCGTGGCAAC
* * *
3884153 -CCTTTGAAAG-CC-CACAAGTCAGTCGC-AC
1 TCTTTTCAAAGTCCACACAAGTC-GTGGCAAC
* *
3884181 -CCTTTCAAAG-CC-CACAAGTCGATCGC-AC
1 TCTTTTCAAAGTCCACACAAGTCG-TGGCAAC
* *
3884209 -CCTTTCAAAG-CC-CACAAGTCGGTCGC-AC
1 TCTTTTCAAAGTCCACACAAGTC-GTGGCAAC
* * *
3884237 -CCTTTCAAA--CCCCACAAGACAGTGGC-A-
1 TCTTTTCAAAGTCCACACAAGTC-GTGGCAAC
*
3884264 TCCTTTCAAAG-CC-CACAAGTCAGTGGC-A-
1 TCTTTTCAAAGTCCACACAAGTC-GTGGCAAC
* *
3884292 TCCTTTCAAAG-CC-CACAAGTTAGTGGC-AC
1 TCTTTTCAAAGTCCACACAAG-TCGTGGCAAC
* * * *
3884321 CCTTTTCAAAG-CC-CATAAGTTAGTGG-TA-
1 TCTTTTCAAAGTCCACACAAG-TCGTGGCAAC
* *
3884349 TCCTTTCAAAG-CC-CACAAGTCAATGGC-AC
1 TCTTTTCAAAGTCCACACAAGTC-GTGGCAAC
*
3884378 -CCTTTCAAAG--C-CACAAGTCAGTGG---C
1 TCTTTTCAAAGTCCACACAAGTC-GTGGCAAC
* * *
3884403 TTTTTTCAAAG-CC-CACAAGTTAGTGAC-A-
1 TCTTTTCAAAGTCCACACAAG-TCGTGGCAAC
* *
3884431 TCCTTTCAAAG-CC-CACAAGTTAGTGGC-AC
1 TCTTTTCAAAGTCCACACAAG-TCGTGGCAAC
*
3884460 T-TTTTTAAAG-CC-CACAAGTCAGTGG-AAC
1 TCTTTTCAAAGTCCACACAAGTC-GTGGCAAC
* *
3884488 -CCTTTCAAAG-CC-CACAAGTTAGTGGC-AC
1 TCTTTTCAAAGTCCACACAAG-TCGTGGCAAC
* * *
3884516 -CATTTCAAAG-CC-CATAAGTCAGTGAC-A-
1 TCTTTTCAAAGTCCACACAAGTC-GTGGCAAC
* * *
3884543 TCTTTTCAAAG--CTCATAAGTCAATGGC-AC
1 TCTTTTCAAAGTCCACACAAGTC-GTGGCAAC
* *
3884572 -CCTTTCAAAG-CC-CACAAGTTAGTGGC-A-
1 TCTTTTCAAAGTCCACACAAG-TCGTGGCAAC
* * *
3884599 TCCTTTCAAAG-CC-CACAAGTCAATAGC-AC
1 TCTTTTCAAAGTCCACACAAGTC-GTGGCAAC
* *
3884628 -CCTTTCAAAG-CC-CACAAGTCAGTGGCATC
1 TCTTTTCAAAGTCCACACAAGTC-GTGGCAAC
*
3884657 -CTTTTCAAAG-CC-CACAAGTCAGTGGTAAC
1 TCTTTTCAAAGTCCACACAAGTC-GTGGCAAC
* *
3884686 CCTTTT-AAAG-CCTACATAAGTCGGTGGCAAC
1 TCTTTTCAAAGTCC-ACACAAGTC-GTGGCAAC
* * * *
3884717 TTTTTTCAAAGCCCACACAAGTTAGTGGCACC
1 TCTTTTCAAAGTCCACACAAG-TCGTGGCAAC
* * * * *
3884749 TTTTTTTAAAGCCCGCGCAAGTCGGTGGCAAC
1 TCTTTTCAAAGTCCACACAAGTC-GTGGCAAC
*
3884781 CCTTTTCAAA
1 TCTTTTCAAA
3884791 TCACCACTTT
Statistics
Matches: 708, Mismatches: 88, Indels: 99
0.79 0.10 0.11
Matches are distributed among these distances:
25 1 0.00
26 8 0.01
27 33 0.05
28 424 0.60
29 73 0.10
30 24 0.03
31 25 0.04
32 116 0.16
33 4 0.01
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.24
Consensus pattern (31 bp):
TCTTTTCAAAGTCCACACAAGTCGTGGCAAC
Found at i:3885773 original size:51 final size:51
Alignment explanation
Indices: 3885688--3885885 Score: 324
Period size: 51 Copynumber: 3.9 Consensus size: 51
3885678 AAAAGTCACA
* * * *
3885688 TTTTTACCCAGATGTATCGATACATTTTTTAATGTATCGATACATTTTGTC
1 TTTTTACCCAGATGTATCGATACATGTATGAATGTATCGATACATTCTGTC
*
3885739 TTTTTACCCAGATGTATCGATACATGTATGAATGTATCGATACATTCTATC
1 TTTTTACCCAGATGTATCGATACATGTATGAATGTATCGATACATTCTGTC
3885790 TTTTTACCCAGATGTATCGATACATGTATGAATGTATCGATACATTCTGTC
1 TTTTTACCCAGATGTATCGATACATGTATGAATGTATCGATACATTCTGTC
* * *
3885841 TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACAT
1 TTTTTACCCAGATGTATCGATACATGTATGAATGTATCGATACAT
3885886 CTAGTTAAAA
Statistics
Matches: 138, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 138 1.00
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (51 bp):
TTTTTACCCAGATGTATCGATACATGTATGAATGTATCGATACATTCTGTC
Found at i:3886786 original size:20 final size:22
Alignment explanation
Indices: 3886746--3886786 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
3886736 TTGCCTTTGA
*
3886746 CCATGCATTTTTTTACTATGTT
1 CCATGCATTTTTTAACTATGTT
3886768 CCATGCA-TTTTTAAC-ATGT
1 CCATGCATTTTTTAACTATGT
3886787 ACAGCATCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 7 0.39
22 7 0.39
ACGTcount: A:0.22, C:0.20, G:0.10, T:0.49
Consensus pattern (22 bp):
CCATGCATTTTTTAACTATGTT
Found at i:3889851 original size:15 final size:15
Alignment explanation
Indices: 3889831--3889900 Score: 65
Period size: 15 Copynumber: 4.8 Consensus size: 15
3889821 TTTAACATAG
*
3889831 GTACTTTTGGCAGAA
1 GTACTTTTGGCAAAA
*
3889846 GTACTTTTGACAAAA
1 GTACTTTTGGCAAAA
3889861 GTAC-TTTGGCACAAA
1 GTACTTTTGGCA-AAA
* * *
3889876 -TAATTTTGGTAAAG
1 GTACTTTTGGCAAAA
3889890 GTAC-TTTGGCA
1 GTACTTTTGGCA
3889901 TAGCACTTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
14 16 0.36
15 28 0.64
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.34
Consensus pattern (15 bp):
GTACTTTTGGCAAAA
Found at i:3889868 original size:29 final size:29
Alignment explanation
Indices: 3889831--3889900 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 29
3889821 TTTAACATAG
* * *
3889831 GTACTTTTGGCAGAAGTACTTTTGACAAAA
1 GTAC-TTTGGCACAAATAATTTTGACAAAA
** *
3889861 GTACTTTGGCACAAATAATTTTGGTAAAG
1 GTACTTTGGCACAAATAATTTTGACAAAA
3889890 GTACTTTGGCA
1 GTACTTTGGCA
3889901 TAGCACTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 30 0.88
30 4 0.12
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.34
Consensus pattern (29 bp):
GTACTTTGGCACAAATAATTTTGACAAAA
Found at i:3896960 original size:25 final size:26
Alignment explanation
Indices: 3896930--3896978 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
3896920 ATTAATCATA
*
3896930 TATTTGA-ACTATTTAT-ATTTTTTAT
1 TATTTGATA-TATTAATCATTTTTTAT
3896955 TATTTGATATATTAATCATTTTTT
1 TATTTGATATATTAATCATTTTTT
3896979 TTTGCTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (26 bp):
TATTTGATATATTAATCATTTTTTAT
Found at i:3898915 original size:14 final size:14
Alignment explanation
Indices: 3898896--3898924 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3898886 TTAATTCAGG
3898896 TCCATTGAACAATA
1 TCCATTGAACAATA
3898910 TCCATTGAACAATA
1 TCCATTGAACAATA
3898924 T
1 T
3898925 AGGTTGGCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.31
Consensus pattern (14 bp):
TCCATTGAACAATA
Found at i:3899084 original size:15 final size:15
Alignment explanation
Indices: 3899064--3899094 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3899054 CTTTAATGTA
3899064 TATGCATATATAATT
1 TATGCATATATAATT
3899079 TATGCATATATAATT
1 TATGCATATATAATT
3899094 T
1 T
3899095 CCCTTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (15 bp):
TATGCATATATAATT
Found at i:3899402 original size:14 final size:14
Alignment explanation
Indices: 3899358--3899405 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
3899348 TTGACATATT
*
3899358 AAATATAATATAAA
1 AAATAAAATATAAA
* *
3899372 AAAT-AATTAAAATA
1 AAATAAAATATAA-A
3899386 AAATAAAATATAAA
1 AAATAAAATATAAA
3899400 AAATAA
1 AAATAA
3899406 TATGAACATG
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
13 5 0.19
14 16 0.59
15 6 0.22
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (14 bp):
AAATAAAATATAAA
Found at i:3903465 original size:24 final size:24
Alignment explanation
Indices: 3903438--3903483 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
3903428 GCTGCTACCG
3903438 TGTTCATGGATGCCGCTGCTGTCA
1 TGTTCATGGATGCCGCTGCTGTCA
* *
3903462 TGTTCGTGGATGCTGCTGCTGT
1 TGTTCATGGATGCCGCTGCTGT
3903484 GTTCGTGGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.09, C:0.22, G:0.33, T:0.37
Consensus pattern (24 bp):
TGTTCATGGATGCCGCTGCTGTCA
Found at i:3903478 original size:21 final size:21
Alignment explanation
Indices: 3903452--3903497 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3903442 CATGGATGCC
*
3903452 GCTGCTG-TCATGTTCGTGGAT
1 GCTGCTGCT-ATGTTCGTGGAA
*
3903473 GCTGCTGCTGTGTTCGTGGAA
1 GCTGCTGCTATGTTCGTGGAA
3903494 GCTG
1 GCTG
3903498 GAAAAGGCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.09, C:0.20, G:0.37, T:0.35
Consensus pattern (21 bp):
GCTGCTGCTATGTTCGTGGAA
Found at i:3903555 original size:31 final size:31
Alignment explanation
Indices: 3903486--3903580 Score: 104
Period size: 31 Copynumber: 3.0 Consensus size: 31
3903476 GCTGCTGTGT
* * *
3903486 TCGTGGAAGCTGGAAAAGGCTCGAGTTG-TTG
1 TCGTGGAAGCTGGAAGA-GCTCGAGCTGCTAG
*
3903517 TCATGGAAGCTGGAAGAGTCTCGAGCTGCTAG
1 TCGTGGAAGCTGGAAGAG-CTCGAGCTGCTAG
*
3903549 -CGTGGAAGCTAGAAGAAGCTCGAGCTGCTAG
1 TCGTGGAAGCTGGAAG-AGCTCGAGCTGCTAG
3903580 T
1 T
3903581 TTCGGGTGCT
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
30 1 0.02
31 49 0.91
32 4 0.07
ACGTcount: A:0.25, C:0.17, G:0.36, T:0.22
Consensus pattern (31 bp):
TCGTGGAAGCTGGAAGAGCTCGAGCTGCTAG
Found at i:3904165 original size:31 final size:31
Alignment explanation
Indices: 3904118--3904183 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
3904108 TTCTCTCCAT
*
3904118 TTGCTTGTGTCCCCCATGATTGCATGCTACA
1 TTGCATGTGTCCCCCATGATTGCATGCTACA
*
3904149 TTGCATGTGTCTCCCATGATTGCATGCTACA
1 TTGCATGTGTCCCCCATGATTGCATGCTACA
3904180 TTGC
1 TTGC
3904184 CTTGCATGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.17, C:0.27, G:0.20, T:0.36
Consensus pattern (31 bp):
TTGCATGTGTCCCCCATGATTGCATGCTACA
Found at i:3904940 original size:41 final size:42
Alignment explanation
Indices: 3904778--3906697 Score: 1081
Period size: 42 Copynumber: 45.9 Consensus size: 42
3904768 GGCAGTCTTT
* * * *
3904778 AGGGTCAAAGCCGACAGACAGACTGAA-GGTAGAAAAGTCTCT
1 AGGGTCAAAGCCGACAGGCAGACT-AAGGGAAGGAAAGTCTCC
*** * * * * *
3904820 AGGGTC-AAGATTAACAGGCAGGCTAAAGGTAGAAAAGTCTCA
1 AGGGTCAAAG-CCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
* * * * *
3904862 AGGGTCAAAGTCGACAGGCAGACTAAAGGTAGAAAAGTATCC
1 AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
* * * *
3904904 ATGGTC-AAGCCGACGGGCAGACTGAGGGAAAGAAAGTCTCC
1 AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
* * * *
3904945 AAGGTCAAAGTCGACAGGCAGACTAAGGGTAGGAAAGTCTCT
1 AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
* * *
3904987 AGGGTCAAAGCCGATAGGCAGACTAAGGGTAGGAAAGTCTCT
1 AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
*
3905029 A-GGTCAAAGTCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
1 AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
* * *
3905070 AGGGTCAAAGCTGACAGACAGACTAAGGGTAGGAAAGTCTCC
1 AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
* * *** * * * * *
3905112 AAGATCAAAATAGATAGGCAAACTATGGGAAGAAAACTCTCC
1 AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
* * *
3905154 AAGG-CTAAAGCCGACAGGAAGACTAAGGGAAGAAAAGTCTCC
1 AGGGTC-AAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
* * * *
3905196 AAGGTCAAAGCCGACAGGCAGACTAGGGGTAGAAAAGTCTCC
1 AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
* * * * *
3905238 AAGGTCAAAGCCAACAGGCAGACTAAGGAAAGAAAAGTCTCT
1 AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
* * * * * *
3905280 AAGGTCAAAGCCGGCAAGAAGACGAAGGGAAAGAAAGTCTCC
1 AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
* * * * * *
3905322 AGGGTCAAAGTCGACAAGTAGACTAAAGGTAGGAAAGTCTCT
1 AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
* *
3905364 AGGGTCAAAGCCGACAGGTAGACTAAGGGAAGGAAAGACTCC
1 AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
* * * ** * **
3905406 AAGGTCAAAGCCGACAAGTAGACTAAAAGAAAGAAAGTCTTT
1 AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
* * * * * *** *
3905448 AAGATCAAA-CTAAGGGA-AGGAAAGTCTCTAGAATCAAAGCCGACAAGTAGACT-A
1 AGGGTCAAAGC----CGACAGG-CAG--ACT--AAGGGAAG--GA-AAGT---CTCC
* * ** * * * *
3905502 AGGGTAAGAAAGTCTCCAGG--GTCAAAGCCGACAGGCAAA--CT-A
1 AGGGT--CAAAGCCGACAGGCAGACTAAG-GGA-AGG-AAAGTCTCC
*** * * * * * * *
3905544 AGAGAAAAAAAGTC-TCTAGG--GTCAAAGCCGACGGGCAAA--CT-A
1 AG-G-GTCAAAGCCGAC-AGGCAGACTAAG-GGA-AGG-AAAGTCTCC
** * * ** * *
3905586 AGGGAAAGAAAGTCTCCA-AGGTCAAAACT--GACAAGCAAA--CT-A
1 AGGG--TCAAAG-C-CGACAGG-C-AGACTAAGGGAAGGAAAGTCTCC
* * * ** * * *
3905628 AAGG--AAA---GAAAGTCTCA-TGAGGGTAGGAAAGTCTTC
1 AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
* * * * * * *
3905664 AAGGTCAAAGTCGACAGGCAAATTGAGGGTAGGAAAGTCTCT
1 AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
* ** * *
3905706 AGGGTCAAAACTAACAGGCAGACTGAGGGAAGAAAAGTCTCC
1 AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
* * *
3905748 AGGGTCAAAGCCGACAAGCAGACTGAGGGAAGAAAAGTCTCC
1 AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
* * **
3905790 AAGGTCAAAGCCGACAGGCAGACTAAGGGAAGAAAAGTCTGT
1 AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
* * *
3905832 AGGGTCAAAGCCGATAGGTAGACTAAGGGAAAGAAAGTCTCC
1 AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
* * ** * *
3905874 AAGGTCAAAGCCGATAGGCAGACTAAATGAAGGAAACTCTCA
1 AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
* * * * *
3905916 AGGGTCAAAGCCGATAGGTAGACTAAAGGAAGGAAACTCTCG
1 AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
* * *
3905958 AGGGTCAAAGCCAACAGGCAGACTAAAGGAAGGAAAGTCTCA
1 AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
* * * *
3906000 AGGGTTAAAGCCGACAGGCAGACTAAGGGTAGAAAAGTCTCA
1 AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
* * * **
3906042 AGGATCAAAGCCGATAGGCAGAGTAAGGGAAAAAAAGTCTCC
1 AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
* * * * * * *
3906084 AAGATCAAAGCCAACAAGAAGACAAAGGGAAGAAAAGTCTCC
1 AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
* * * * * *
3906126 AAGGTCAAAGTCGATAGGCAGACTAAGGAAAAGAAAGTCTGC
1 AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
*
3906168 AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCT
1 AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
* * * * ** * **
3906210 AAGGTCAAAGTCGACAAGTAGACTAAGGGTTGGAAAGTTTGT
1 AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
* * * *
3906252 AGGGTCAAAGCTGAGAGGTAAACTAAGGGAAGGAAAGTCTCC
1 AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
* * * * *
3906294 AAGGTCAAATCCGACAGGTAGACTAAGGGAA-AAAAGTCTTC
1 AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
* * * *
3906335 AGGGTCAAAGCCGATAAGTAGACTAAAGGAAGGAAAGTCTCC
1 AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
* * * * **
3906377 AGAGTCAAAGCCGATAGACAGACTGAA-GGTAGGAAAGTCTTT
1 AGGGTCAAAGCCGACAGGCAGACT-AAGGGAAGGAAAGTCTCC
* * *
3906419 AGGGTCAGAGTCGACAAGCAGACTAA-GGATAGGAAAGTCTCC
1 AGGGTCAAAGCCGACAGGCAGACTAAGGGA-AGGAAAGTCTCC
* * *
3906461 AAGGTCAAAGCCGACAGGCAGACTGAGGGAAGGAAAGTTTCC
1 AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
* * * *
3906503 AAGGTCAGAGCTGACAGGTAGACTAAGGGAAGGAAAGTCTCC
1 AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
*
3906545 TA-GGTCAAAGCCGACA-G--G-C-------A-GAAAGTCTCT
1 -AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
* * ** *
3906575 AGGGTCAAAGCTGACAGGAAGACTGTGGGAAAGAAAGTCTCC
1 AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
* ** **
3906617 AGGGTTAAAGTTGACAGGCAGACTAAGGGAAGGAAAGTCTTT
1 AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
** * * *
3906659 AATGTCAAAGCAGACAGGCCGACTAAGGGAAGAAAAGTC
1 AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTC
3906698 GACAGGCAGA
Statistics
Matches: 1496, Mismatches: 311, Indels: 142
0.77 0.16 0.07
Matches are distributed among these distances:
29 1 0.00
30 22 0.01
31 3 0.00
32 1 0.00
33 9 0.01
34 3 0.00
35 2 0.00
36 4 0.00
38 7 0.00
39 1 0.00
41 124 0.08
42 1258 0.84
43 15 0.01
44 4 0.00
45 5 0.00
47 8 0.01
48 3 0.00
49 8 0.01
51 3 0.00
52 4 0.00
54 6 0.00
55 2 0.00
56 3 0.00
ACGTcount: A:0.40, C:0.17, G:0.29, T:0.14
Consensus pattern (42 bp):
AGGGTCAAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCC
Found at i:3905501 original size:71 final size:71
Alignment explanation
Indices: 3905385--3905516 Score: 194
Period size: 71 Copynumber: 1.9 Consensus size: 71
3905375 CGACAGGTAG
*
3905385 ACTAAGGGAAGGAAAGACTCCAAGGTCAAAGCCGACAAGTAGACTAAAAGAAAGAAAGTCTTTAA
1 ACTAAGGGAAGGAAAGACTCCAAGATCAAAGCCGACAAGTAGACTAAAAGAAAGAAAGTCTTTAA
3905450 GATCAA
66 GATCAA
* * ** *
3905456 ACTAAGGGAAGGAAAGTCT-CTAGAATCAAAGCCGACAAGTAGACTAAGGGTAAGAAAGTCT
1 ACTAAGGGAAGGAAAGACTCCAAG-ATCAAAGCCGACAAGTAGACTAAAAGAAAGAAAGTCT
3905517 CCAGGGTCAA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
70 3 0.06
71 51 0.94
ACGTcount: A:0.45, C:0.15, G:0.24, T:0.15
Consensus pattern (71 bp):
ACTAAGGGAAGGAAAGACTCCAAGATCAAAGCCGACAAGTAGACTAAAAGAAAGAAAGTCTTTAA
GATCAA
Found at i:3905544 original size:113 final size:113
Alignment explanation
Indices: 3905343--3905558 Score: 308
Period size: 113 Copynumber: 1.9 Consensus size: 113
3905333 CGACAAGTAG
* ** *
3905343 ACTAAAGGTAGGAAAGTCTCTAGGGTCAAAGCCGACAGGTAGACTAAGGGAAGGAAAGACTCCAA
1 ACTAAAGGAAGGAAAGTCTCTAGAATCAAAGCCGACAAGTAGACTAAGGGAAGGAAAGACTCCAA
* * *
3905408 GGTCAAAGCCGACAAGTAGACTAAAAGAAAGAAAGTCTTTAAGATCAA
66 GGTCAAAGCCGACAAGCAAACTAAAAGAAAAAAAGTCTTTAAGATCAA
* *
3905456 ACTAAGGGAAGGAAAGTCTCTAGAATCAAAGCCGACAAGTAGACTAAGGGTAA-GAAAGTCTCCA
1 ACTAAAGGAAGGAAAGTCTCTAGAATCAAAGCCGACAAGTAGACTAAGGG-AAGGAAAGACTCCA
* * *
3905520 GGGTCAAAGCCGACAGGCAAACTAAGAGAAAAAAAGTCT
65 AGGTCAAAGCCGACAAGCAAACTAAAAGAAAAAAAGTCT
3905559 CTAGGGTCAA
Statistics
Matches: 90, Mismatches: 12, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
113 88 0.98
114 2 0.02
ACGTcount: A:0.44, C:0.17, G:0.25, T:0.14
Consensus pattern (113 bp):
ACTAAAGGAAGGAAAGTCTCTAGAATCAAAGCCGACAAGTAGACTAAGGGAAGGAAAGACTCCAA
GGTCAAAGCCGACAAGCAAACTAAAAGAAAAAAAGTCTTTAAGATCAA
Found at i:3905586 original size:155 final size:155
Alignment explanation
Indices: 3905304--3905600 Score: 396
Period size: 155 Copynumber: 1.9 Consensus size: 155
3905294 CAAGAAGACG
** * * *
3905304 AAGGGAAAGAAAGTCTCCAGGGTCAAAGTCGACAAGTAGACTAAAGGTAGGAAAGTCTCTAGGGT
1 AAGGGAAAGAAAGTCTCCAGAATCAAAGCCGACAAGTAGACTAAAGGTAAGAAAGTCTCCAGGGT
* * * ** * *
3905369 CAAAGCCGACAGGTAGACTAAGGGAAGGAAAGACTCCAAGGTCAAAGCCGACAAGTAGACTAAAA
66 CAAAGCCGACAGGCAAACTAAGAGAAAAAAAGACTCCAAGGTCAAAGCCGACAAGCAAACTAAAA
3905434 GAAAGAAAGTCTTTAAGATCAAACT
131 GAAAGAAAGTCTTTAAGATCAAACT
* * *
3905459 AAGGGAAGGAAAGTCTCTAGAATCAAAGCCGACAAGTAGACTAAGGGTAAGAAAGTCTCCAGGGT
1 AAGGGAAAGAAAGTCTCCAGAATCAAAGCCGACAAGTAGACTAAAGGTAAGAAAGTCTCCAGGGT
* * * ** **
3905524 CAAAGCCGACAGGCAAACTAAGAGAAAAAAAGTCTCTAGGGTCAAAGCCGACGGGCAAACTAAGG
66 CAAAGCCGACAGGCAAACTAAGAGAAAAAAAGACTCCAAGGTCAAAGCCGACAAGCAAACTAAAA
3905589 GAAAGAAAGTCT
131 GAAAGAAAGTCT
3905601 CCAAGGTCAA
Statistics
Matches: 120, Mismatches: 22, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
155 120 1.00
ACGTcount: A:0.42, C:0.17, G:0.27, T:0.14
Consensus pattern (155 bp):
AAGGGAAAGAAAGTCTCCAGAATCAAAGCCGACAAGTAGACTAAAGGTAAGAAAGTCTCCAGGGT
CAAAGCCGACAGGCAAACTAAGAGAAAAAAAGACTCCAAGGTCAAAGCCGACAAGCAAACTAAAA
GAAAGAAAGTCTTTAAGATCAAACT
Found at i:3905788 original size:145 final size:145
Alignment explanation
Indices: 3905502--3905767 Score: 345
Period size: 145 Copynumber: 1.8 Consensus size: 145
3905492 AAGTAGACTA
*
3905502 AGGGTAAGAAAGTCTCCAGGGTCAAAGCCGACAGGCAAACTAAGAGAAAAAAAGTCTCTAGGGTC
1 AGGGTAAGAAAGTCTCCAAGGTCAAAGCCGACAGGCAAACTAAGAGAAAAAAAGTCTCTAGGGTC
* * * *
3905567 AAAGCCGACGGGCAAACTAAGGGAAAGAAAGTCTCCAAGGTCAAAACTGACAAGCAAACTAAAGG
66 AAAACCAACAGGCAAACTAAGGGAAAGAAAGTCTCCAAGGTCAAAACCGACAAGCAAACTAAAGG
3905632 AAAGAAAGTCTCATG
131 AAAGAAAGTCTCATG
* * * * * * * **
3905647 AGGGTAGGAAAGTCTTCAAGGTCAAAGTCGACAGGCAAATTGAGGGTAGGAAAGTCTCTAGGGTC
1 AGGGTAAGAAAGTCTCCAAGGTCAAAGCCGACAGGCAAACTAAGAGAAAAAAAGTCTCTAGGGTC
* * * * *
3905712 AAAACTAACAGGCAGACTGAGGG-AAGAAAAGTCTCCAGGGTCAAAGCCGACAAGCA
66 AAAACCAACAGGCAAACTAAGGGAAAG-AAAGTCTCCAAGGTCAAAACCGACAAGCA
3905768 GACTGAGGGA
Statistics
Matches: 101, Mismatches: 19, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
144 3 0.03
145 98 0.97
ACGTcount: A:0.41, C:0.18, G:0.28, T:0.14
Consensus pattern (145 bp):
AGGGTAAGAAAGTCTCCAAGGTCAAAGCCGACAGGCAAACTAAGAGAAAAAAAGTCTCTAGGGTC
AAAACCAACAGGCAAACTAAGGGAAAGAAAGTCTCCAAGGTCAAAACCGACAAGCAAACTAAAGG
AAAGAAAGTCTCATG
Found at i:3906569 original size:30 final size:30
Alignment explanation
Indices: 3906535--3906592 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
3906525 CTAAGGGAAG
3906535 GAAAGTCTCCTA-GGTCAAAGCCGACAGGCA
1 GAAAGTCT-CTAGGGTCAAAGCCGACAGGCA
*
3906565 GAAAGTCTCTAGGGTCAAAGCTGACAGG
1 GAAAGTCTCTAGGGTCAAAGCCGACAGG
3906593 AAGACTGTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.33, C:0.22, G:0.29, T:0.16
Consensus pattern (30 bp):
GAAAGTCTCTAGGGTCAAAGCCGACAGGCA
Found at i:3906611 original size:72 final size:72
Alignment explanation
Indices: 3906505--3906638 Score: 180
Period size: 72 Copynumber: 1.9 Consensus size: 72
3906495 AAGTTTCCAA
* * *
3906505 GGTCAGAGCTGACAGGTAGACTAAGGGAAGGAAAGTCTCCTA-GGTCAAAGCCGACAGGCAGAAA
1 GGTCAAAGCTGACAGGAAGACTAAGGGAAAGAAAGTCTCC-AGGGTCAAAGCCGACAGGCAGAAA
3906569 GTCTCTAG
65 GTCTCTAG
** * **
3906577 GGTCAAAGCTGACAGGAAGACTGTGGGAAAGAAAGTCTCCAGGGTTAAAGTTGACAGGCAGA
1 GGTCAAAGCTGACAGGAAGACTAAGGGAAAGAAAGTCTCCAGGGTCAAAGCCGACAGGCAGA
3906639 CTAAGGGAAG
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
71 1 0.02
72 52 0.98
ACGTcount: A:0.34, C:0.17, G:0.33, T:0.16
Consensus pattern (72 bp):
GGTCAAAGCTGACAGGAAGACTAAGGGAAAGAAAGTCTCCAGGGTCAAAGCCGACAGGCAGAAAG
TCTCTAG
Found at i:3906651 original size:114 final size:114
Alignment explanation
Indices: 3906451--3907159 Score: 364
Period size: 126 Copynumber: 6.0 Consensus size: 114
3906441 CTAAGGATAG
* * * *
3906451 GAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTGAGGGAAGGAAAGTTTCCAAGGTCAGAGCTG
1 GAAAGTCTCCAAGGTCAAAGCCGACAGGAAGACTGAGGGAAAGAAAGTCTCCAAGGTCAAAGCTG
*
3906516 ACAGGTAGACTAAGGGAAGGAAAGTCTCCTAGGTCAAAGCCGACAGGCA
66 ACAGGCAGACTAAGGGAAGGAAAGTCTCCTAGGTCAAAGCCGACAGGCA
* * * * * * *
3906565 GAAAGTCTCTAGGGTCAAAGCTGACAGGAAGACTGTGGGAAAGAAAGTCTCCAGGGTTAAAGTTG
1 GAAAGTCTCCAAGGTCAAAGCCGACAGGAAGACTGAGGGAAAGAAAGTCTCCAAGGTCAAAGCTG
* * * *
3906630 ACAGGCAGACTAAGGGAAGGAAAGTCT-TTAATGTCAAAGCAGACAGGCC
66 ACAGGCAGACTAAGGGAAGGAAAGTCTCCT-AGGTCAAAGCCGACAGGCA
** * * * * * * * *
3906679 GACTAAG---GGAA-G-AAAAGTCGACAGGCAGACTAAAGGAATGAAAGTCTTCAGGGTCAAAG-
1 GA--AAGTCTCCAAGGTCAAAGCCGACAGGAAGACTGAGGGAAAGAAAGTCTCCAAGGTCAAAGC
* * * * * *
3906738 TCGACAAGTAGACTTAGGGAAAGAAAGT-TTCTAAGGTCAAAGCCAACAGGCAGACTAAAAGAA
64 T-GACAGGCAGACTAAGGGAAGGAAAGTCTCCT-AGGTCAAAGCCGACA-G--G-C-------A
* * *** * * *
3906801 GGAAAGTCTCCAAGGTCAAAGCCGACAAGCAGACTGAGGGTTGGAAAGTCTCTAGGGTCAAAGCC
1 -GAAAGTCTCCAAGGTCAAAGCCGACAGGAAGACTGAGGGAAAGAAAGTCTCCAAGGTCAAAGCT
* * * * * * * * *
3906866 AATAAGCAGACTGAGGGTAGGAAAGTCTCCAAGGTCAAAGCTGATAGGTAGATTGA
65 GACAGGCAGACTAAGGGAAGGAAAGTCTCCTAGGTCAAAGCCGACA-G--G---CA
* * * * * * *
3906922 GGGTAAAGAAGTCTCCAGGGTCAAAGCCGACAGGTAGACTGAGGGAAGGAAAATCTTCAGGGTCG
1 --G---A-AAGTCTCCAAGGTCAAAGCCGACAGGAAGACTGAGGGAAAGAAAGTCTCCAAGGTCA
* * *
3906987 AAGCTGATAAGCAAACTAAGGGTAA-GAAAGTCT-CTAGGGTCAAAGCCGACAGGCAA
60 AAGCTGACAGGCAGACTAAGGG-AAGGAAAGTCTCCTA-GGTCAAAGCCGACAGGC-A
** * * * * * *
3907043 GAAAAGTCTTTAAGGTCAAAGCCGACAGGCACACTAAGGGTAAA-AAAGTGTCTAGGGTCAAAGC
1 G-AAAGTCTCCAAGGTCAAAGCCGACAGGAAGACTGAGGG-AAAGAAAGTCTCCAAGGTCAAAGC
* * * *
3907107 CGATAGGTAGACTAAGGGAAAGG-AAGTCTCC-AGGGTCAAAGCCGACTGGCA
64 TGACAGGCAGACTAAGGG-AAGGAAAGTCTCCTA-GGTCAAAGCCGACAGGCA
3907158 GA
1 GA
3907160 TTAAGGGTAG
Statistics
Matches: 457, Mismatches: 101, Indels: 74
0.72 0.16 0.12
Matches are distributed among these distances:
110 2 0.00
111 73 0.16
112 2 0.00
113 2 0.00
114 100 0.22
115 3 0.01
116 89 0.19
117 6 0.01
119 1 0.00
121 5 0.01
122 2 0.00
123 3 0.01
124 2 0.00
125 5 0.01
126 159 0.35
127 3 0.01
ACGTcount: A:0.37, C:0.17, G:0.30, T:0.16
Consensus pattern (114 bp):
GAAAGTCTCCAAGGTCAAAGCCGACAGGAAGACTGAGGGAAAGAAAGTCTCCAAGGTCAAAGCTG
ACAGGCAGACTAAGGGAAGGAAAGTCTCCTAGGTCAAAGCCGACAGGCA
Found at i:3906738 original size:42 final size:42
Alignment explanation
Indices: 3906692--3907041 Score: 260
Period size: 42 Copynumber: 8.3 Consensus size: 42
3906682 TAAGGGAAGA
* * *
3906692 AAAGTCGACAGGCAGACTAAAGGAATGAAAGTCTTCAGGGTC
1 AAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTTCAGGGTC
* * * * * *
3906734 AAAGTCGACAAGTAGACTTAGGGAAAGAAAGT-TTCTAAGGTC
1 AAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTTC-AGGGTC
* ** * *
3906776 AAAGCCAACAGGCAGACTAAAAGAAGGAAAGTCTCCAAGGTC
1 AAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTTCAGGGTC
* * **
3906818 AAAGCCGACAAGCAGACTGAGGGTTGGAAAGTC-TCTAGGGTC
1 AAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTTC-AGGGTC
* * * * * * *
3906860 AAAGCCAATAAGCAGACTGAGGGTAGGAAAGTCTCCAAGGTC
1 AAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTTCAGGGTC
* * * * * * *
3906902 AAAGCTGATAGGTAGATTGAGGGTAAAG-AAGTCTCCAGGGTC
1 AAAGCCGACAGGCAGACTAAGGG-AAGGAAAGTCTTCAGGGTC
* * *
3906944 AAAGCCGACAGGTAGACTGAGGGAAGGAAAATCTTCAGGGTC
1 AAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTTCAGGGTC
* * * * *
3906986 GAAGCTGATAAGCAAACTAAGGGTAA-GAAAGTC-TCTAGGGTC
1 AAAGCCGACAGGCAGACTAAGGG-AAGGAAAGTCTTC-AGGGTC
3907028 AAAGCCGACAGGCA
1 AAAGCCGACAGGCA
3907042 AGAAAAGTCT
Statistics
Matches: 245, Mismatches: 55, Indels: 16
0.78 0.17 0.05
Matches are distributed among these distances:
41 9 0.04
42 229 0.93
43 7 0.03
ACGTcount: A:0.38, C:0.17, G:0.29, T:0.16
Consensus pattern (42 bp):
AAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTTCAGGGTC
Found at i:3906757 original size:69 final size:70
Alignment explanation
Indices: 3906623--3906763 Score: 169
Period size: 69 Copynumber: 2.0 Consensus size: 70
3906613 CTCCAGGGTT
* * * * * *
3906623 AAAGTTGACAGGCAGACTAAGGGAAGGAAAGTCTTTAATGTCAAAGCAGACAGGCCGACTAAGGG
1 AAAGTCGACAGGCAGACTAAAGGAAGGAAAGTCTTCAAGGTCAAAGCAGACAAGCAGACTAAGGG
3906688 -AAGA
66 AAAGA
* * * *
3906692 AAAGTCGACAGGCAGACTAAAGGAATGAAAGTCTTCAGGGTCAAAGTC-GACAAGTAGACTTAGG
1 AAAGTCGACAGGCAGACTAAAGGAAGGAAAGTCTTCAAGGTCAAAG-CAGACAAGCAGACTAAGG
3906756 GAAAGA
65 GAAAGA
3906762 AA
1 AA
3906764 GTTTCTAAGG
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
69 53 0.88
70 7 0.12
ACGTcount: A:0.42, C:0.14, G:0.29, T:0.15
Consensus pattern (70 bp):
AAAGTCGACAGGCAGACTAAAGGAAGGAAAGTCTTCAAGGTCAAAGCAGACAAGCAGACTAAGGG
AAAGA
Found at i:3906796 original size:84 final size:84
Alignment explanation
Indices: 3906692--3907041 Score: 315
Period size: 84 Copynumber: 4.2 Consensus size: 84
3906682 TAAGGGAAGA
* * * * * * *
3906692 AAAGTCGACAGGCAGACTAAAGGAATGAAAGTCTTCAGGGTCAAAGTCGACAAGTAGACTTAGGG
1 AAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTTCAGGGTCAAAGCCGACAGGCAGACTAAGGG
* *
3906757 AAAGAAAGTTTCTAAGGTC
66 AAAGAAAGTCTCTAGGGTC
* ** * * * *
3906776 AAAGCCAACAGGCAGACTAAAAGAAGGAAAGTCTCCAAGGTCAAAGCCGACAAGCAGACTGAGGG
1 AAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTTCAGGGTCAAAGCCGACAGGCAGACTAAGGG
***
3906841 TTGGAAAGTCTCTAGGGTC
66 AAAGAAAGTCTCTAGGGTC
* * * * * * * * * * * *
3906860 AAAGCCAATAAGCAGACTGAGGGTAGGAAAGTCTCCAAGGTCAAAGCTGATAGGTAGATTGAGGG
1 AAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTTCAGGGTCAAAGCCGACAGGCAGACTAAGGG
*
3906925 TAAAG-AAGTCTCCAGGGTC
66 -AAAGAAAGTCTCTAGGGTC
* * * * * * * *
3906944 AAAGCCGACAGGTAGACTGAGGGAAGGAAAATCTTCAGGGTCGAAGCTGATAAGCAAACTAAGGG
1 AAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTTCAGGGTCAAAGCCGACAGGCAGACTAAGGG
*
3907009 TAAGAAAGTCTCTAGGGTC
66 AAAGAAAGTCTCTAGGGTC
3907028 AAAGCCGACAGGCA
1 AAAGCCGACAGGCA
3907042 AGAAAAGTCT
Statistics
Matches: 218, Mismatches: 46, Indels: 4
0.81 0.17 0.01
Matches are distributed among these distances:
83 3 0.01
84 214 0.98
85 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.29, T:0.16
Consensus pattern (84 bp):
AAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTTCAGGGTCAAAGCCGACAGGCAGACTAAGGG
AAAGAAAGTCTCTAGGGTC
Found at i:3906807 original size:111 final size:111
Alignment explanation
Indices: 3906602--3906808 Score: 265
Period size: 111 Copynumber: 1.9 Consensus size: 111
3906592 GAAGACTGTG
* * * * *
3906602 GGAAAGAAAGTCTCCAGGGTTAAAGTTGACAGGCAGACTAAGGGAAGGAAAGTCTTTAATGTCAA
1 GGAAAGAAAGTCTCCAGGGTCAAAGTCGACAAGCAGACTAAGGGAAAGAAAGTCTTTAAGGTCAA
* **
3906667 AGCAGACAGGCCGACTAAGGGAAGAAAAGTCGACAGGCAGACTAAA
66 AGCAGACAGGCAGACTAAAAGAAGAAAAGTCGACAGGCAGACTAAA
* * * *
3906713 GGAATGAAAGTCTTCAGGGTCAAAGTCGACAAGTAGACTTAGGGAAAGAAAGT-TTCTAAGGTCA
1 GGAAAGAAAGTCTCCAGGGTCAAAGTCGACAAGCAGACTAAGGGAAAGAAAGTCTT-TAAGGTCA
*
3906777 AAGCCA-ACAGGCAGACTAAAAGAAGGAAAGTC
65 AAG-CAGACAGGCAGACTAAAAGAAGAAAAGTC
3906809 TCCAAGGTCA
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
110 2 0.02
111 77 0.95
112 2 0.02
ACGTcount: A:0.41, C:0.15, G:0.29, T:0.15
Consensus pattern (111 bp):
GGAAAGAAAGTCTCCAGGGTCAAAGTCGACAAGCAGACTAAGGGAAAGAAAGTCTTTAAGGTCAA
AGCAGACAGGCAGACTAAAAGAAGAAAAGTCGACAGGCAGACTAAA
Found at i:3906934 original size:126 final size:126
Alignment explanation
Indices: 3906692--3907390 Score: 563
Period size: 126 Copynumber: 5.6 Consensus size: 126
3906682 TAAGGGAAGA
* * * * * * *
3906692 AAAGTCGACAGGCAGACTAAAGGAATGAAAGTCT-TCAGGGTCAAAGTCGACAAGTAGACTTAGG
1 AAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCT-AGGGTCAAAGCCGATAAGCAGACTAAGG
* * * * * * * **
3906756 GAAAGAAAGTTTCTAAGGTCAAAGCCAACAGGCAGACTAAAAG-AAGGAAAGTCTCCAAGGTC
65 GAAGGAAAGTCTCCAAGGTCAAAGCCGATAGGTAGATTAAGGGTAA-GAAAGTCTCCAAGGTC
* * ** * *
3906818 AAAGCCGACAAGCAGACTGAGGGTTGGAAAGTCTCTAGGGTCAAAGCCAATAAGCAGACTGAGGG
1 AAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGATAAGCAGACTAAGGG
* * * *
3906883 TAGGAAAGTCTCCAAGGTCAAAGCTGATAGGTAGATTGAGGGTAA-AGAAGTCTCCAGGGTC
66 AAGGAAAGTCTCCAAGGTCAAAGCCGATAGGTAGATTAAGGGTAAGA-AAGTCTCCAAGGTC
* * * * * *
3906944 AAAGCCGACAGGTAGACTGAGGGAAGGAAAATCT-TCAGGGTCGAAGCTGATAAGCAAACTAAGG
1 AAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCT-AGGGTCAAAGCCGATAAGCAGACTAAGG
* * * * **
3907008 GTAA-GAAAGTCTCTAGGGTCAAAGCCGACA-G--G--CAA--G--A-AAAGTCTTTAAGGTC
65 G-AAGGAAAGTCTCCAAGGTCAAAGCCGATAGGTAGATTAAGGGTAAGAAAGTCTCCAAGGTC
* * * * *
3907060 AAAGCCGACAGGCACACTAAGGGTAA-AAAAGTGTCTAGGGTCAAAGCCGATAGGTAGACTAAGG
1 AAAGCCGACAGGCAGACTAAGGG-AAGGAAAGTCTCTAGGGTCAAAGCCGATAAGCAGACTAAGG
* * * * *
3907124 GAAAGG-AAGTCTCCAGGGTCAAAGCCGACT-GGCAGATTAAGGGTAGGAAAGTCT-CTAGCATC
65 G-AAGGAAAGTCTCCAAGGTCAAAGCCGA-TAGGTAGATTAAGGGTAAGAAAGTCTCCAAG-GTC
* * * * *
3907186 AAAGTCGACAGGCAGATTAAGGGAAGGAAAGTCTCTAGGGTCAAAGTCGATAGGAAGACTAAGGG
1 AAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGATAAGCAGACTAAGGG
* * * * * *
3907251 AAGAAAAGTCTCCAAGGTAAAAGCCGATAGGTAGACTAAGGGTAGGAAAGTCTCTAGGGTC
66 AAGGAAAGTCTCCAAGGTCAAAGCCGATAGGTAGATTAAGGGTAAGAAAGTCTCCAAGGTC
* * * * * * * *
3907312 AAAGCCGACAGGCAGACTAAAGGAAAGAAAGTCTTTAGGGTCAAAACTGATAGGTAAACTAAGGG
1 AAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGATAAGCAGACTAAGGG
* *
3907377 AAAGAAAGTTTCCA
66 AAGGAAAGTCTCCA
3907391 GAAGTTTAAT
Statistics
Matches: 456, Mismatches: 93, Indels: 48
0.76 0.16 0.08
Matches are distributed among these distances:
116 83 0.18
117 7 0.02
119 2 0.00
121 3 0.01
123 2 0.00
125 11 0.02
126 343 0.75
127 5 0.01
ACGTcount: A:0.38, C:0.16, G:0.29, T:0.16
Consensus pattern (126 bp):
AAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGATAAGCAGACTAAGGG
AAGGAAAGTCTCCAAGGTCAAAGCCGATAGGTAGATTAAGGGTAAGAAAGTCTCCAAGGTC
Found at i:3907050 original size:32 final size:32
Alignment explanation
Indices: 3907013--3907073 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
3907003 TAAGGGTAAG
*
3907013 AAAGTCTCTAGGGTCAAAGCCGACAGGCAAGA
1 AAAGTCTCTAAGGTCAAAGCCGACAGGCAAGA
*
3907045 AAAGTCTTTAAGGTCAAAGCCGACAGGCA
1 AAAGTCTCTAAGGTCAAAGCCGACAGGCA
3907074 CACTAAGGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.38, C:0.21, G:0.26, T:0.15
Consensus pattern (32 bp):
AAAGTCTCTAAGGTCAAAGCCGACAGGCAAGA
Found at i:3907103 original size:42 final size:41
Alignment explanation
Indices: 3907044--3907385 Score: 306
Period size: 42 Copynumber: 8.1 Consensus size: 41
3907034 GACAGGCAAG
* * *
3907044 AAAAGTCTTTAAGGTCAAAGCCGACAGGCACACTAAGGGTAA
1 AAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTAAGGG-AA
* * *
3907086 AAAAGTGTCTAGGGTCAAAGCCGATAGGTAGACTAAGGGAA
1 AAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTAAGGGAA
* * * * *
3907127 AGGAAGTCTCCAGGGTCAAAGCCGACTGGCAGATTAAGGGTAG
1 A-AAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTAAGGG-AA
* ** * *
3907170 GAAAGTCTCTAGCATCAAAGTCGACAGGCAGATTAAGGGAA
1 AAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTAAGGGAA
* * * *
3907211 GGAAAGTCTCTAGGGTCAAAGTCGATAGGAAGACTAAGGGAA
1 -AAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTAAGGGAA
* * * * * *
3907253 GAAAAGTCTCCAAGGTAAAAGCCGATAGGTAGACTAAGGGTAG
1 -AAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTAAGGG-AA
* *
3907296 GAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTAAAGGAA
1 AAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTAAGGGAA
* * * * * *
3907337 AGAAAGTCTTTAGGGTCAAAACTGATAGGTAAACTAAGGGAA
1 A-AAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTAAGGGAA
3907379 AGAAAGT
1 A-AAAGT
3907386 TTCCAGAAGT
Statistics
Matches: 245, Mismatches: 50, Indels: 10
0.80 0.16 0.03
Matches are distributed among these distances:
41 5 0.02
42 238 0.97
43 2 0.01
ACGTcount: A:0.39, C:0.15, G:0.30, T:0.17
Consensus pattern (41 bp):
AAAAGTCTCTAGGGTCAAAGCCGACAGGCAGACTAAGGGAA
Found at i:3907188 original size:84 final size:84
Alignment explanation
Indices: 3907056--3907391 Score: 368
Period size: 84 Copynumber: 4.0 Consensus size: 84
3907046 AAGTCTTTAA
* * *
3907056 GGTCAAAGCCGACAGGCACACTAAGGGTAAAAAAGTGTCTAGGGTCAAAGCCGATAGGTAGACTA
1 GGTCAAAGCCGACAGGCAGACTAAGGGAAAAAAAGTCTCTAGGGTCAAAGCCGATAGGTAGACTA
3907121 AGGGAAAGG-AAGTCTCCAG
66 AGGG-AAGGAAAGTCTCCAG
* * * ** ** * * * *
3907140 GGTCAAAGCCGACTGGCAGATTAAGGGTAGGAAAGTCTCTAGCATCAAAGTCGACAGGCAGATTA
1 GGTCAAAGCCGACAGGCAGACTAAGGGAAAAAAAGTCTCTAGGGTCAAAGCCGATAGGTAGACTA
*
3907205 AGGGAAGGAAAGTCTCTAG
66 AGGGAAGGAAAGTCTCCAG
* * * * * * *
3907224 GGTCAAAGTCGATAGGAAGACTAAGGGAAGAAAAGTCTCCAAGGTAAAAGCCGATAGGTAGACTA
1 GGTCAAAGCCGACAGGCAGACTAAGGGAAAAAAAGTCTCTAGGGTCAAAGCCGATAGGTAGACTA
* *
3907289 AGGGTAGGAAAGTCTCTAG
66 AGGGAAGGAAAGTCTCCAG
* * * * * *
3907308 GGTCAAAGCCGACAGGCAGACTAAAGGAAAGAAAGTCTTTAGGGTCAAAACTGATAGGTAAACTA
1 GGTCAAAGCCGACAGGCAGACTAAGGGAAAAAAAGTCTCTAGGGTCAAAGCCGATAGGTAGACTA
* *
3907373 AGGGAAAGAAAGTTTCCAG
66 AGGGAAGGAAAGTCTCCAG
3907392 AAGTTTAATG
Statistics
Matches: 204, Mismatches: 47, Indels: 2
0.81 0.19 0.01
Matches are distributed among these distances:
83 4 0.02
84 200 0.98
ACGTcount: A:0.38, C:0.15, G:0.30, T:0.16
Consensus pattern (84 bp):
GGTCAAAGCCGACAGGCAGACTAAGGGAAAAAAAGTCTCTAGGGTCAAAGCCGATAGGTAGACTA
AGGGAAGGAAAGTCTCCAG
Found at i:3920120 original size:13 final size:13
Alignment explanation
Indices: 3920098--3920145 Score: 64
Period size: 13 Copynumber: 3.7 Consensus size: 13
3920088 GATGAAAAGA
3920098 ATTTTTTTATTAT
1 ATTTTTTTATTAT
3920111 -TTTATTTTATTAT
1 ATTT-TTTTATTAT
3920124 CA-TTTTTTATTAT
1 -ATTTTTTTATTAT
3920137 ATTTTTTTA
1 ATTTTTTTA
3920146 AAATTTTACT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
12 4 0.13
13 25 0.81
14 2 0.06
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (13 bp):
ATTTTTTTATTAT
Found at i:3920151 original size:23 final size:24
Alignment explanation
Indices: 3920102--3920153 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
3920092 AAAAGAATTT
* **
3920102 TTTTATTATTTTATTTTATTATCA
1 TTTTATTATTATATTTTATTAAAA
*
3920126 TTTT-TTATTATATTTTTTTAAAA
1 TTTTATTATTATATTTTATTAAAA
3920149 TTTTA
1 TTTTA
3920154 CTTTCGTACC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (24 bp):
TTTTATTATTATATTTTATTAAAA
Found at i:3921082 original size:21 final size:21
Alignment explanation
Indices: 3921029--3921089 Score: 77
Period size: 24 Copynumber: 2.8 Consensus size: 21
3921019 GCTCGAGCTA
*
3921029 CTGCCGTGTTCGTGGATGCTG
1 CTGCTGTGTTCGTGGATGCTG
*
3921050 CTGTTGTCGTGTTCGTGGATGCTG
1 CTG--CT-GTGTTCGTGGATGCTG
3921074 CTGCTGTGTTCGTGGA
1 CTGCTGTGTTCGTGGA
3921090 AGCTAGAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
21 14 0.41
22 1 0.03
24 19 0.56
ACGTcount: A:0.05, C:0.20, G:0.38, T:0.38
Consensus pattern (21 bp):
CTGCTGTGTTCGTGGATGCTG
Found at i:3921121 original size:31 final size:31
Alignment explanation
Indices: 3921084--3921174 Score: 121
Period size: 31 Copynumber: 2.9 Consensus size: 31
3921074 CTGCTGTGTT
*
3921084 CGTGGAAGCTAGAAAAGGCTCGAGCTGCTGC
1 CGTGGAAGCTAGAAAAGGCTCGAGCTACTGC
* *
3921115 CGTGGAAGCTAGAATAGGCTCGAGCTACTGG
1 CGTGGAAGCTAGAAAAGGCTCGAGCTACTGC
* *
3921146 CATGGAAGCTGGAAGAA-GCTCGAGCTACT
1 CGTGGAAGCTAGAA-AAGGCTCGAGCTACT
3921175 AGTTTCAGGT
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
31 52 0.98
32 1 0.02
ACGTcount: A:0.27, C:0.21, G:0.34, T:0.18
Consensus pattern (31 bp):
CGTGGAAGCTAGAAAAGGCTCGAGCTACTGC
Found at i:3921769 original size:31 final size:31
Alignment explanation
Indices: 3921726--3921784 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
3921716 CATTTACTTG
3921726 TGTCCCCCATGATTGCATGCTACATTGCATA
1 TGTCCCCCATGATTGCATGCTACATTGCATA
*
3921757 TGTCTCCCATGATTGCATGCTACATTGC
1 TGTCCCCCATGATTGCATGCTACATTGC
3921785 CTTGCATGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.20, C:0.29, G:0.17, T:0.34
Consensus pattern (31 bp):
TGTCCCCCATGATTGCATGCTACATTGCATA
Found at i:3926091 original size:59 final size:66
Alignment explanation
Indices: 3926011--3926189 Score: 167
Period size: 67 Copynumber: 2.8 Consensus size: 66
3926001 GGCAATTTAA
* *
3926011 TGTCACTTACTTATACGTTGAGA-T-G-TTA-A-TTTTGAGATCATTTATTAT-A-GGTGACTAG
1 TGTCACTTACTTATACATTGAGAGTCGATTAGACCTTTGAGATCATTTATTATCATGGTGACTAG
3926069 G
66 G
** * *
3926070 TGTCACTTACTTATGTATTGAGATGTCGATTAGACCTTTGAGGTCATTTATTATCATGGTGACTT
1 TGTCACTTACTTATACATTGAGA-GTCGATTAGACCTTTGAGATCATTTATTATCATGGTGACTA
3926135 GG
65 GG
* * * * * *
3926137 TGTCAATTACTTAGACACTGAGATATC-AGTCAGACCTTTGAAATCATTTATTA
1 TGTCACTTACTTATACATTGAGA-GTCGA-TTAGACCTTTGAGATCATTTATTA
3926190 GACTAACTGA
Statistics
Matches: 96, Mismatches: 15, Indels: 10
0.79 0.12 0.08
Matches are distributed among these distances:
59 20 0.21
61 1 0.01
62 1 0.01
63 3 0.03
64 1 0.01
65 17 0.18
66 2 0.02
67 51 0.53
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.40
Consensus pattern (66 bp):
TGTCACTTACTTATACATTGAGAGTCGATTAGACCTTTGAGATCATTTATTATCATGGTGACTAG
G
Found at i:3926159 original size:67 final size:65
Alignment explanation
Indices: 3926041--3926189 Score: 176
Period size: 67 Copynumber: 2.3 Consensus size: 65
3926031 AGATGTTAAT
* * * * *
3926041 TTTGAGATCATTTATTATAGGTGACTAGGTGTCACTTACTTATGTATTGAGATGTC-GATTAGAC
1 TTTGAGATCATTTATTATAGGTGACTAGGTGTCAATTACTTATGCACTGAGATATCAG-TCAGAC
3926105 C
65 C
* *
3926106 TTTGAGGTCATTTATTATCATGGTGACTTGGTGTCAATTACTTA-GACACTGAGATATCAGTCAG
1 TTTGAGATCATTTATTAT-A-GGTGACTAGGTGTCAATTACTTATG-CACTGAGATATCAGTCAG
3926170 ACC
63 ACC
*
3926173 TTTGAAATCATTTATTA
1 TTTGAGATCATTTATTA
3926190 GACTAACTGA
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
65 17 0.24
66 2 0.03
67 51 0.72
68 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (65 bp):
TTTGAGATCATTTATTATAGGTGACTAGGTGTCAATTACTTATGCACTGAGATATCAGTCAGACC
Found at i:3926327 original size:68 final size:68
Alignment explanation
Indices: 3926231--3926407 Score: 250
Period size: 68 Copynumber: 2.6 Consensus size: 68
3926221 ATTTATATGA
* * * *
3926231 ATGACTTAGTGTCACTTGCTTATATGTTGAGATGTCGATTAGA-CCTTTAAGGTCATTTATTAGT
1 ATGACTTGGTGTCACTTGCTTATATGTTGAGATGTCGATCAGATCCTTGAA-GTCATTTATTAGC
3926295 ATA-
65 ATAC
*
3926298 AGTGACTTGGTGTCACTTGCTTATATGTTGAGATGTAGATCAGATCCTTGAAGTCATTTATTAGC
1 A-TGACTTGGTGTCACTTGCTTATATGTTGAGATGTCGATCAGATCCTTGAAGTCATTTATTAGC
3926363 ATAC
65 ATAC
* * *
3926367 ATGACTTGGTGTCAATTGTTTATATGCTGAGATGTCGATCA
1 ATGACTTGGTGTCACTTGCTTATATGTTGAGATGTCGATCA
3926408 TATTGGCAAA
Statistics
Matches: 98, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
67 1 0.01
68 90 0.92
69 7 0.07
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.40
Consensus pattern (68 bp):
ATGACTTGGTGTCACTTGCTTATATGTTGAGATGTCGATCAGATCCTTGAAGTCATTTATTAGCA
TAC
Found at i:3932445 original size:63 final size:62
Alignment explanation
Indices: 3932332--3932460 Score: 222
Period size: 65 Copynumber: 2.0 Consensus size: 62
3932322 AAAAGATGGT
3932332 TGTGGTAGCTAAGAGCCTATGGCATTAAGGTTTGAGGTACACAGATATATATATATATATATA
1 TGTGGTAGCTAAGAGCCTATGGCATTAAGGTTTGAGGTACACAGA-ATATATATATATATATA
3932395 TGTGGTAGCTAAGAGCCTATTGGCATTAAGGTTTGAGGGTACACAGATATATATATATATATATA
1 TGTGGTAGCTAAGAGCCTA-TGGCATTAAGGTTTGA-GGTACACAGA-ATATATATATATATATA
3932460 T
1 T
3932461 ATATATATAT
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
63 19 0.30
64 16 0.25
65 29 0.45
ACGTcount: A:0.34, C:0.09, G:0.22, T:0.34
Consensus pattern (62 bp):
TGTGGTAGCTAAGAGCCTATGGCATTAAGGTTTGAGGTACACAGAATATATATATATATATA
Found at i:3932448 original size:2 final size:2
Alignment explanation
Indices: 3932441--3932474 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3932431 GGGTACACAG
3932441 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
3932475 GGATAGAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3933542 original size:2 final size:2
Alignment explanation
Indices: 3933495--3933525 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3933485 ACCAACAATT
3933495 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3933526 TAACAATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3934169 original size:14 final size:15
Alignment explanation
Indices: 3934150--3934178 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3934140 TTTTAATATT
3934150 ATATTA-AAATAAAA
1 ATATTATAAATAAAA
3934164 ATATTATAAATAAAA
1 ATATTATAAATAAAA
3934179 TCATGATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
ATATTATAAATAAAA
Found at i:3935733 original size:2 final size:2
Alignment explanation
Indices: 3935726--3935769 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3935716 GGATGTTGGG
3935726 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
3935768 AT
1 AT
3935770 GTTTGATGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3936043 original size:2 final size:2
Alignment explanation
Indices: 3936036--3936076 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3936026 TTTTCTTCAT
3936036 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3936077 GAATGGATCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3936736 original size:16 final size:16
Alignment explanation
Indices: 3936667--3936738 Score: 81
Period size: 16 Copynumber: 4.5 Consensus size: 16
3936657 TTTAGACTTA
*
3936667 TTCGGGTTCAAATTTT
1 TTCGGGTTCGAATTTT
**
3936683 TTTTGGTTCGAATTTT
1 TTCGGGTTCGAATTTT
* ** *
3936699 TTCGGATTCGAGCTTA
1 TTCGGGTTCGAATTTT
3936715 TTCGGGTTCGAATTTT
1 TTCGGGTTCGAATTTT
3936731 TTCGGGTT
1 TTCGGGTT
3936739 TGAGCTTTTT
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.14, C:0.12, G:0.24, T:0.50
Consensus pattern (16 bp):
TTCGGGTTCGAATTTT
Found at i:3936747 original size:16 final size:16
Alignment explanation
Indices: 3936696--3936749 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
3936686 TGGTTCGAAT
*
3936696 TTTTTCGGATTCGAGC
1 TTTTTCGGGTTCGAGC
* **
3936712 TTATTCGGGTTCGAAT
1 TTTTTCGGGTTCGAGC
*
3936728 TTTTTCGGGTTTGAGC
1 TTTTTCGGGTTCGAGC
3936744 TTTTTC
1 TTTTTC
3936750 AAGTTCGGGT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.11, C:0.15, G:0.24, T:0.50
Consensus pattern (16 bp):
TTTTTCGGGTTCGAGC
Found at i:3936756 original size:32 final size:32
Alignment explanation
Indices: 3936688--3936756 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 32
3936678 ATTTTTTTTG
**
3936688 GTTCGAATTTTTTCGGATTCGAGCTTATTCGG
1 GTTCGAATTTTTTCGGATTCGAGCTTATTCAA
* * *
3936720 GTTCGAATTTTTTCGGGTTTGAGCTTTTTCAA
1 GTTCGAATTTTTTCGGATTCGAGCTTATTCAA
3936752 GTTCG
1 GTTCG
3936757 GGTCAGTTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.14, C:0.14, G:0.25, T:0.46
Consensus pattern (32 bp):
GTTCGAATTTTTTCGGATTCGAGCTTATTCAA
Found at i:3937248 original size:14 final size:14
Alignment explanation
Indices: 3937229--3937255 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3937219 AACTCAATTA
3937229 AAATAAAAAAAATG
1 AAATAAAAAAAATG
3937243 AAATAAAAAAAAT
1 AAATAAAAAAAAT
3937256 CAAAATCTTC
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:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (14 bp):
AAATAAAAAAAATG
Found at i:3937261 original size:15 final size:14
Alignment explanation
Indices: 3937227--3937261 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
3937217 TAAACTCAAT
3937227 TAAAATAAAAAAAA
1 TAAAATAAAAAAAA
*
3937241 TGAAATAAAAAAAA
1 TAAAATAAAAAAAA
3937255 TCAAAAT
1 T-AAAAT
3937262 CTTCAGTATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.17
Consensus pattern (14 bp):
TAAAATAAAAAAAA
Found at i:3943094 original size:14 final size:15
Alignment explanation
Indices: 3943075--3943105 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
3943065 AAGACACAAC
3943075 AAATATAATCT-ACA
1 AAATATAATCTCACA
3943089 AAATATAATCTCACA
1 AAATATAATCTCACA
3943104 AA
1 AA
3943106 CATACAATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.26
Consensus pattern (15 bp):
AAATATAATCTCACA
Found at i:3945348 original size:28 final size:27
Alignment explanation
Indices: 3945281--3945349 Score: 66
Period size: 28 Copynumber: 2.5 Consensus size: 27
3945271 TTACTTTAAA
* **
3945281 TAAGATAGCCTTATCACATTGTCTTAT
1 TAAGATAACCTTATCACATTACCTTAT
* * *
3945308 TAAGACAAGCTTATCCATATTACCTTAT
1 TAAGATAACCTTAT-CACATTACCTTAT
*
3945336 TAAGATATCCTTAT
1 TAAGATAACCTTAT
3945350 TCGGATTTCT
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
27 11 0.34
28 21 0.66
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.39
Consensus pattern (27 bp):
TAAGATAACCTTATCACATTACCTTAT
Found at i:3951188 original size:13 final size:13
Alignment explanation
Indices: 3951170--3951195 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3951160 ACATAAGTTT
3951170 TGTATCGATACAA
1 TGTATCGATACAA
3951183 TGTATCGATACAA
1 TGTATCGATACAA
3951196 AACTACCCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3951244 original size:20 final size:20
Alignment explanation
Indices: 3951219--3951293 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 20
3951209 ACTGCCAAGG
3951219 AAATGTATCGATATGTTACT
1 AAATGTATCGATATGTTACT
*
3951239 AAATGTATCAATAAATGCTTAC-
1 AAATGTATCGAT--ATG-TTACT
* * *
3951261 AATTGTATCGATATATTTCT
1 AAATGTATCGATATGTTACT
* *
3951281 CATTGTATCGATA
1 AAATGTATCGATA
3951294 CATTATGGGT
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
19 3 0.07
20 25 0.56
22 13 0.29
23 4 0.09
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (20 bp):
AAATGTATCGATATGTTACT
Found at i:3953847 original size:26 final size:24
Alignment explanation
Indices: 3953803--3953852 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
3953793 GTATAGATTA
3953803 TTTCATACAACATTATTTCACTTGT
1 TTTCATACAACATTATTTC-CTTGT
3953828 TTTCATACTAACA-TATTTTCCTTGT
1 TTTCATAC-AACATTA-TTTCCTTGT
3953853 GATGATTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.26, C:0.20, G:0.04, T:0.50
Consensus pattern (24 bp):
TTTCATACAACATTATTTCCTTGT
Found at i:3961530 original size:31 final size:31
Alignment explanation
Indices: 3961480--3962380 Score: 470
Period size: 31 Copynumber: 28.0 Consensus size: 31
3961470 AACTTAACCC
* * * *
3961480 TTTCTATCTTTGTCATCAAAGAGTAGGACAT
1 TTTCTTTCTTTGTCCTCAAAGAGCAAGACAT
* * *
3961511 TTTCCTTCTTTATCTTCAAAGAGCAAGACAT
1 TTTCTTTCTTTGTCCTCAAAGAGCAAGACAT
* * * * * * *
3961542 TTTCTTCCTTTATCCACAAAAAACAGGACGT
1 TTTCTTTCTTTGTCCTCAAAGAGCAAGACAT
*
3961573 TTTCTTTC-TTGTCCTCAAAAAGCAAGACAT
1 TTTCTTTCTTTGTCCTCAAAGAGCAAGACAT
* * * *
3961603 TTTCTTCCTTTATCCTTAAAGAGCAAGATAT
1 TTTCTTTCTTTGTCCTCAAAGAGCAAGACAT
* * *
3961634 TTTC-ATCTTTGTCCTTAAA-A-AATAGAGCAT
1 TTTCTTTCTTTGTCCTCAAAGAGCA-AGA-CAT
*
3961664 TTTCTTTCTTTGTCCTCAAAGAGCAGGA-AGTT
1 TTTCTTTCTTTGTCCTCAAAGAGCAAGACA--T
* * * *
3961696 CTCTTCTTTTATTTATCTTCAAAGAGCAAGACGT
1 -T-TTC-TTTCTTTGTCCTCAAAGAGCAAGACAT
*
3961730 TTTCCTTTCTTTGTCCTTAAAGAGCAAGACAT
1 TTT-CTTTCTTTGTCCTCAAAGAGCAAGACAT
* * * *
3961762 TTTCTTTCTTTATCCTCAAAAAGCAGGGCAT
1 TTTCTTTCTTTGTCCTCAAAGAGCAAGACAT
* *
3961793 TTTCTTTCTTTGTCCTCAAAGAACATGACAT
1 TTTCTTTCTTTGTCCTCAAAGAGCAAGACAT
* * * *
3961824 TTTCTTTCTTTGTCCACAAAAAACAAGACGTTT
1 TTTCTTTCTTTGTCCTCAAAGAGCAAGAC--AT
*
3961857 TTTCTTTTCTTTGTCCTCAAAGAG-TAGAACAT
1 TTTC-TTTCTTTGTCCTCAAAGAGCAAG-ACAT
* * * *
3961889 TTTCTTTTTTTCTCCTTAAAGAGCATGACATTT
1 TTTCTTTCTTTGTCCTCAAAGAGCAAGACA--T
* * *
3961922 TCTTCCTTTCTTCGACCTCAAAGAGCAAGATATT
1 T-TT-CTTTCTTTGTCCTCAAAGAGCAAGACA-T
* * *
3961956 TTTTTTTCTTTATCCTCAAAGGGCAAGACATTAT
1 TTTCTTTCTTTGTCCTCAAAGAGCAAGAC---AT
* *
3961990 CTTTCTTTCTTCGTCCTCAAAGAGCAAGACGT
1 -TTTCTTTCTTTGTCCTCAAAGAGCAAGACAT
* * * **
3962022 TTT-TCTTATTTGTCCTCAAAGAGTAGGATGTTT
1 TTTCT-TTCTTTGTCCTCAAAGAGCAAGA--CAT
** * * * * **
3962055 TCTTCCTTTCTTTGTTATAAAAAAGTAGGATGTTT
1 T-TT-CTTTCTTTGTCCTCAAAGAGCAAGA--CAT
** **
3962090 TATTCTTTCTTCATCCTCAAAGAGCAAGATGT
1 T-TTCTTTCTTTGTCCTCAAAGAGCAAGACAT
* * * * *
3962122 TTTCTTTTTTTATCCTCAAAAAGCAGGATAT
1 TTTCTTTCTTTGTCCTCAAAGAGCAAGACAT
* * * *
3962153 TTTC-TTCATTTATCTTCAAAGAGCAGGATAT
1 TTTCTTTC-TTTGTCCTCAAAGAGCAAGACAT
* * *
3962184 TTTTTTTCTTTGCCCTCAAAAAGCAAGACATTT
1 TTTCTTTCTTTGTCCTCAAAGAGCAAGACA--T
* * *
3962217 TCTTCCTTTCTTTATCCTCAAAGGGCAGGACACTT
1 T-TT-CTTTCTTTGTCCTCAAAGAGCAAGACA--T
** * * * **
3962252 TCTTCCTTTCTTCATCCTCAAGGAACATGATGT
1 T-TT-CTTTCTTTGTCCTCAAAGAGCAAGACAT
* * * * *
3962285 TTACCTTT-TTTGTCTTTAAAGAGCATGACGT
1 TT-TCTTTCTTTGTCCTCAAAGAGCAAGACAT
* *
3962316 TTTCTATCTTCTTTTTTCTTCAAAGAGCAAGACAT
1 TTTC--T-TTC-TTTGTCCTCAAAGAGCAAGACAT
*
3962351 TTTCTTTCTTTGTCCTCAAAGAGTAAGACA
1 TTTCTTTCTTTGTCCTCAAAGAGCAAGACA
3962381 CCTCTTTTTT
Statistics
Matches: 674, Mismatches: 152, Indels: 88
0.74 0.17 0.10
Matches are distributed among these distances:
28 1 0.00
29 4 0.01
30 47 0.07
31 312 0.46
32 73 0.11
33 24 0.04
34 49 0.07
35 163 0.24
36 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.41
Consensus pattern (31 bp):
TTTCTTTCTTTGTCCTCAAAGAGCAAGACAT
Found at i:3961814 original size:62 final size:62
Alignment explanation
Indices: 3961480--3962380 Score: 479
Period size: 66 Copynumber: 14.0 Consensus size: 62
3961470 AACTTAACCC
* * * * * *
3961480 TTTCTATCTTTGTCATCAAAGAGTAGGACATTTTCCTTCTTTATCTTCAAAGAGCAAGACAT
1 TTTCTTTCTTTGTCCTCAAAGAGCAAGACATTTTCTTTCTTTATCCTCAAAGAGCAAGACAT
* * * * * * * * *
3961542 TTTCTTCCTTTATCCACAAAAAACAGGACGTTTTCTTTC-TTGTCCTCAAAAAGCAAGACAT
1 TTTCTTTCTTTGTCCTCAAAGAGCAAGACATTTTCTTTCTTTATCCTCAAAGAGCAAGACAT
* * * * * * * *
3961603 TTTCTTCCTTTATCCTTAAAGAGCAAGATATTTTC-ATCTTTGTCCTTAAA-A-AATAGAGCAT
1 TTTCTTTCTTTGTCCTCAAAGAGCAAGACATTTTCTTTCTTTATCCTCAAAGAGCA-AGA-CAT
* * *
3961664 TTTCTTTCTTTGTCCTCAAAGAGCAGGA-AGTTCTCTTCTTTTATTTATCTTCAAAGAGCAAGAC
1 TTTCTTTCTTTGTCCTCAAAGAGCAAGACA--T-T-TTC-TTTCTTTATCCTCAAAGAGCAAGAC
*
3961728 GT
61 AT
* * * *
3961730 TTTCCTTTCTTTGTCCTTAAAGAGCAAGACATTTTCTTTCTTTATCCTCAAAAAGCAGGGCAT
1 TTT-CTTTCTTTGTCCTCAAAGAGCAAGACATTTTCTTTCTTTATCCTCAAAGAGCAAGACAT
* * * * * * *
3961793 TTTCTTTCTTTGTCCTCAAAGAACATGACATTTTCTTTCTTTGTCCACAAAAAACAAGACGTTT
1 TTTCTTTCTTTGTCCTCAAAGAGCAAGACATTTTCTTTCTTTATCCTCAAAGAGCAAGAC--AT
* * * * *
3961857 TTTCTTTTCTTTGTCCTCAAAGAG-TAGAACATTTTCTTTTTTTCTCCTTAAAGAGCATGACATT
1 TTTC-TTTCTTTGTCCTCAAAGAGCAAG-ACATTTTCTTTCTTTATCCTCAAAGAGCAAGACA--
3961921 T
62 T
* * * * *
3961922 TCTTCCTTTCTTCGACCTCAAAGAGCAAGATATTTTTTTTTCTTTATCCTCAAAGGGCAAGACAT
1 T-TT-CTTTCTTTGTCCTCAAAGAGCAAGACA-TTTTCTTTCTTTATCCTCAAAGAGCAAGAC--
3961987 TAT
61 -AT
* * * * * * **
3961990 CTTTCTTTCTTCGTCCTCAAAGAGCAAGACGTTTT-TCTTATTTGTCCTCAAAGAGTAGGATGTT
1 -TTTCTTTCTTTGTCCTCAAAGAGCAAGACATTTTCT-TTCTTTATCCTCAAAGAGCAAGA--CA
3962054 T
62 T
** * * * * ** * *
3962055 TCTTCCTTTCTTTGTTATAAAAAAGTAGGATGTTTTATTCTTTCTTCATCCTCAAAGAGCAAGAT
1 T-TT-CTTTCTTTGTCCTCAAAGAGCAAGA--CATT-TTCTTTCTTTATCCTCAAAGAGCAAGAC
*
3962120 GT
61 AT
* * * * * * * *
3962122 TTTCTTTTTTTATCCTCAAAAAGCAGGATATTTTC-TTCATTTATCTTCAAAGAGCAGGATAT
1 TTTCTTTCTTTGTCCTCAAAGAGCAAGACATTTTCTTTC-TTTATCCTCAAAGAGCAAGACAT
* * * * *
3962184 TTTTTTTCTTTGCCCTCAAAAAGCAAGACATTTTCTTCCTTTCTTTATCCTCAAAGGGCAGGACA
1 TTTCTTTCTTTGTCCTCAAAGAGCAAGACA--TT-TT-CTTTCTTTATCCTCAAAGAGCAAGACA
3962249 CTT
62 --T
** * * * ** * * * * * *
3962252 TCTTCCTTTCTTCATCCTCAAGGAACATGATGTTTACCTTT-TTTGTCTTTAAAGAGCATGACGT
1 T-TT-CTTTCTTTGTCCTCAAAGAGCAAGACATTT-TCTTTCTTTATCCTCAAAGAGCAAGACAT
* * * *
3962316 TTTCTATCTTCTTTTTTCTTCAAAGAGCAAGACATTTTCTTTCTTTGTCCTCAAAGAGTAAGACA
1 TTTC--T-TTC-TTTGTCCTCAAAGAGCAAGACATTTTCTTTCTTTATCCTCAAAGAGCAAGACA
3962381 CCTCTTTTTT
Statistics
Matches: 639, Mismatches: 148, Indels: 100
0.72 0.17 0.11
Matches are distributed among these distances:
59 1 0.00
60 7 0.01
61 87 0.14
62 126 0.20
63 30 0.05
64 18 0.03
65 79 0.12
66 149 0.23
67 89 0.14
68 11 0.02
69 23 0.04
70 19 0.03
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.41
Consensus pattern (62 bp):
TTTCTTTCTTTGTCCTCAAAGAGCAAGACATTTTCTTTCTTTATCCTCAAAGAGCAAGACAT
Found at i:3961862 original size:159 final size:157
Alignment explanation
Indices: 3961568--3961930 Score: 428
Period size: 159 Copynumber: 2.3 Consensus size: 157
3961558 CAAAAAACAG
* * * * *
3961568 GACGTTTTCTTTC-TTGTCCTCAAAAAGCAAGACATTTTCTTCCTTTATCCTTAAAGAGCAAGAT
1 GACGTTTTCTTTCTTTGTCCTTAAAGAGCAAGACATTTTCTTCCTTTATCCTCAAAAAGCAAGAC
* * * * *
3961632 ATTTTCATCTTTGTCCTTAAAAAATAGAGCATTTTCTTTCTTTGTCCTCAAAGAGCAGGAAGTTC
66 ATTTTCATCTTTGTCCTCAAAAAATAGAGCATTTTCTTTCTTTGTCCACAAAAAACAAGAAGTTC
*
3961697 TCTTCTTTTATTTATCTTCAAAGAGCAA
131 TCTTCTTTTATTTATCCTCAAAGAG-AA
* * *
3961725 GACGTTTTCCTTTCTTTGTCCTTAAAGAGCAAGACATTTTCTTTCTTTATCCTCAAAAAGCAGGG
1 GACGTTTT-CTTTCTTTGTCCTTAAAGAGCAAGACATTTTCTTCCTTTATCCTCAAAAAGCAAGA
* *
3961790 CATTTTCTTTCTTTGTCCTCAAAGAACAT-GA-CATTTTCTTTCTTTGTCCACAAAAAACAAGAC
65 CATTTTC-ATCTTTGTCCTCAAA-AA-ATAGAGCATTTTCTTTCTTTGTCCACAAAAAACAAGAA
* * * *
3961853 GTT-TTTTCTTTTCTTTGTCCTCAAAGAGTA
127 GTTCTCTTCTTTTATTTATCCTCAAAGAGAA
* * * *
3961883 GAACATTTTCTTTTTTTCTCCTTAAAGAGCATGACATTTTCTTCCTTT
1 G-ACGTTTTCTTTCTTTGTCCTTAAAGAGCAAGACATTTTCTTCCTTT
3961931 CTTCGACCTC
Statistics
Matches: 175, Mismatches: 25, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
157 8 0.05
158 42 0.24
159 76 0.43
160 43 0.25
161 4 0.02
162 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.42
Consensus pattern (157 bp):
GACGTTTTCTTTCTTTGTCCTTAAAGAGCAAGACATTTTCTTCCTTTATCCTCAAAAAGCAAGAC
ATTTTCATCTTTGTCCTCAAAAAATAGAGCATTTTCTTTCTTTGTCCACAAAAAACAAGAAGTTC
TCTTCTTTTATTTATCCTCAAAGAGAA
Found at i:3961889 original size:65 final size:62
Alignment explanation
Indices: 3961480--3961895 Score: 259
Period size: 61 Copynumber: 6.6 Consensus size: 62
3961470 AACTTAACCC
* * * * * ** * * *
3961480 TTTCTATCTTTGTCATCAAAGAGTAGGACATTTTCCTTCTTTATCTTCAAAGAGCAAGACAT
1 TTTCTTTCTTTGTCCTCAAAGAGCAGAACATTTTCTTTCTTTATCCACAAAAAACAAGACGT
* * * * * * * * * * *
3961542 TTTCTTCCTTTATCCACAAAAAACAGGACGTTTTCTTTC-TTGTCCTCAAAAAGCAAGACAT
1 TTTCTTTCTTTGTCCTCAAAGAGCAGAACATTTTCTTTCTTTATCCACAAAAAACAAGACGT
* * * * * * ** * *
3961603 TTTCTTCCTTTATCCTTAAAGAGCA-AGATATTTTC-ATCTTTGTCCTTAAAAAA-TAGAGCAT
1 TTTCTTTCTTTGTCCTCAAAGAGCAGA-ACATTTTCTTTCTTTATCCACAAAAAACAAGA-CGT
** * ** * *
3961664 TTTCTTTCTTTGTCCTCAAAGAGCAGGAAGTTCTCTTCTTTTATTTATCTTCAAAGAGCAAGACG
1 TTTCTTTCTTTGTCCTCAAAGAGCA-GAACAT-T-TTC-TTTCTTTATCCACAAAAAACAAGACG
3961729 T
62 T
* * * * * *
3961730 TTTCCTTTCTTTGTCCTTAAAGAGCA-AGACATTTTCTTTCTTTATCCTCAAAAAGCAGGGCAT
1 TTT-CTTTCTTTGTCCTCAAAGAGCAGA-ACATTTTCTTTCTTTATCCACAAAAAACAAGACGT
* *
3961793 TTTCTTTCTTTGTCCTCAAAGAACATG-ACATTTTCTTTCTTTGTCCACAAAAAACAAGACGTTT
1 TTTCTTTCTTTGTCCTCAAAGAGCA-GAACATTTTCTTTCTTTATCCACAAAAAACAAGACG--T
*
3961857 TTTCTTTTCTTTGTCCTCAAAGAGTAGAACATTTTCTTT
1 TTTC-TTTCTTTGTCCTCAAAGAGCAGAACATTTTCTTT
3961896 TTTTCTCCTT
Statistics
Matches: 279, Mismatches: 57, Indels: 33
0.76 0.15 0.09
Matches are distributed among these distances:
60 5 0.02
61 83 0.30
62 79 0.28
63 26 0.09
64 12 0.04
65 32 0.11
66 18 0.06
67 24 0.09
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40
Consensus pattern (62 bp):
TTTCTTTCTTTGTCCTCAAAGAGCAGAACATTTTCTTTCTTTATCCACAAAAAACAAGACGT
Found at i:3961949 original size:225 final size:220
Alignment explanation
Indices: 3961495--3961997 Score: 557
Period size: 225 Copynumber: 2.3 Consensus size: 220
3961485 ATCTTTGTCA
* * *
3961495 TCAAAGAGTAGGACATTTTCC-TTCTTTAT-CTTCAAAGAGCAAGACATTTTCTTCCTTTATCCA
1 TCAAAGAGCAAGACATTTTCCTTTCTTTATCCTT-AAAGAGCAAGACATTTTCTTTCTTTATCCA
* **
3961558 CAAAAAACAGGACGTTTTCTTTCTTGTCCTCAAAAAGCAAGACATTTTCTTCCTTTATCCTTAAA
65 CAAAAAACAGGACATTTTCTTTCTTGTCCTCAAAAAGCAAGACATTTTCTTCCTTTATCCACAAA
* * * * *
3961623 GAGCAAGATATTTTCATCTTTGTCCTTAAAAAATAGAGCATTTTCTTTCTTTGTCCTCAAAGAGC
130 AAACAAGATATTTTCATCTTTGTCCTCAAAAAATAGAACATTTTCTTTCTTTCTCCTCAAAGAGC
* * *
3961688 AGGAAGTTCTCTTCTTTTATTTATCT
195 AGGAAGTTCTCTTCCTTTATTGATCC
* * *
3961714 TCAAAGAGCAAGACGTTTTCCTTTCTTTGTCCTTAAAGAGCAAGACATTTTCTTTCTTTATCCTC
1 TCAAAGAGCAAGACATTTTCCTTTCTTTATCCTTAAAGAGCAAGACATTTTCTTTCTTTATCCAC
* * * * *
3961779 AAAAAGCAGGGCATTTTCTTTCTTTGTCCTCAAAGAA-CATGACATTTTCTTTCTTTGTCCACAA
66 AAAAAACAGGACATTTTCTTTC-TTGTCCTCAAA-AAGCAAGACATTTTCTTCCTTTATCCACAA
* * * * * *
3961843 AAAACAAGACGTTTTTTCTTTTCTTTGTCCTCAAAGAGTAGAACATTTTCTTTTTTTCTCCTTAA
129 AAAACAAGA--TATTTTC--ATCTTTGTCCTCAAAAAATAGAACATTTTCTTTCTTTCTCCTCAA
* * *
3961908 AGAGCATGACA-TTTTCTTCCTTTCTTCGA-CC
190 AGAGCAGGA-AGTTCTCTTCCTTTATT-GATCC
* ** * * *
3961939 TCAAAGAGCAAGATATTTTTTTTTCTTTATCCTCAAAGGGCAAGACATTATCTTTCTTT
1 TCAAAGAGCAAGACATTTTCCTTTCTTTATCCTTAAAGAGCAAGACATTTTCTTTCTTT
3961998 CTTCGTCCTC
Statistics
Matches: 235, Mismatches: 39, Indels: 14
0.82 0.14 0.05
Matches are distributed among these distances:
219 18 0.08
220 55 0.23
221 43 0.18
222 2 0.01
223 6 0.03
225 109 0.46
226 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40
Consensus pattern (220 bp):
TCAAAGAGCAAGACATTTTCCTTTCTTTATCCTTAAAGAGCAAGACATTTTCTTTCTTTATCCAC
AAAAAACAGGACATTTTCTTTCTTGTCCTCAAAAAGCAAGACATTTTCTTCCTTTATCCACAAAA
AACAAGATATTTTCATCTTTGTCCTCAAAAAATAGAACATTTTCTTTCTTTCTCCTCAAAGAGCA
GGAAGTTCTCTTCCTTTATTGATCC
Found at i:3962957 original size:21 final size:20
Alignment explanation
Indices: 3962906--3962958 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
3962896 CATGAAGGCT
3962906 TGGTATCGATACCTAGGGTG
1 TGGTATCGATACCTAGGGTG
* *
3962926 TGGTGTCGATACCTAGTGTG
1 TGGTATCGATACCTAGGGTG
*
3962946 ATTGTATCGATAC
1 -TGGTATCGATAC
3962959 AAGCCTTGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 18 0.64
21 10 0.36
ACGTcount: A:0.21, C:0.15, G:0.30, T:0.34
Consensus pattern (20 bp):
TGGTATCGATACCTAGGGTG
Found at i:3967085 original size:15 final size:15
Alignment explanation
Indices: 3967065--3967095 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3967055 AAAAAATGAG
3967065 GGACGATCAAAGTGT
1 GGACGATCAAAGTGT
3967080 GGACGATCAAAGTGT
1 GGACGATCAAAGTGT
3967095 G
1 G
3967096 TCTCATGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.13, G:0.35, T:0.19
Consensus pattern (15 bp):
GGACGATCAAAGTGT
Found at i:3967458 original size:51 final size:51
Alignment explanation
Indices: 3967394--3967510 Score: 189
Period size: 51 Copynumber: 2.3 Consensus size: 51
3967384 AAAATAATGG
3967394 GGTTGAAGTATCCCCAATTATGAGAAATCAATATTTTAGAAATAAAGCCGA
1 GGTTGAAGTATCCCCAATTATGAGAAATCAATATTTTAGAAATAAAGCCGA
* * * *
3967445 GGTTGAAGTATCCCTAATTGTGAGAAATCAATATTTTGGAAATAAAGCCGG
1 GGTTGAAGTATCCCCAATTATGAGAAATCAATATTTTAGAAATAAAGCCGA
*
3967496 GGTTGGAGTATCCCC
1 GGTTGAAGTATCCCC
3967511 TCGAAAATAA
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (51 bp):
GGTTGAAGTATCCCCAATTATGAGAAATCAATATTTTAGAAATAAAGCCGA
Found at i:3967567 original size:28 final size:30
Alignment explanation
Indices: 3967493--3967569 Score: 108
Period size: 28 Copynumber: 2.7 Consensus size: 30
3967483 GAAATAAAGC
3967493 CGGGGTTGGAGTATCCCC--TCGAAAATAA
1 CGGGGTTGGAGTATCCCCGATCGAAAATAA
*
3967521 CGGGGTTAGAGTATCCCCGAT-G-AAATAA
1 CGGGGTTGGAGTATCCCCGATCGAAAATAA
*
3967549 CGGGGTTGGAGCATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
3967570 TGTGAAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
28 42 0.95
29 1 0.02
30 1 0.02
ACGTcount: A:0.26, C:0.22, G:0.31, T:0.21
Consensus pattern (30 bp):
CGGGGTTGGAGTATCCCCGATCGAAAATAA
Found at i:3967621 original size:51 final size:51
Alignment explanation
Indices: 3967561--3967668 Score: 121
Period size: 51 Copynumber: 2.1 Consensus size: 51
3967551 GGGTTGGAGC
* * *
3967561 ATCCCCGATTGTGAAAAATTAGTGT-TTTGAAAATAAAATCGGAGTTGGAA-T
1 ATCCCCGATTATGAAAAATTAGTGTCTTAG-AAATAAAACCGGAGTT-GAAGT
* * * *
3967612 ATCCTCGATTATGAAGAATTGGTGTCTTAGAAATAAAACCGGGGTTGAAGT
1 ATCCCCGATTATGAAAAATTAGTGTCTTAGAAATAAAACCGGAGTTGAAGT
3967663 ATCCCC
1 ATCCCC
3967669 TCGGAAGTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
50 3 0.06
51 41 0.87
52 3 0.06
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (51 bp):
ATCCCCGATTATGAAAAATTAGTGTCTTAGAAATAAAACCGGAGTTGAAGT
Found at i:3967988 original size:20 final size:20
Alignment explanation
Indices: 3967965--3968071 Score: 97
Period size: 20 Copynumber: 5.7 Consensus size: 20
3967955 AAAATACCTG
*
3967965 AATGTATCGATACATTGTAA
1 AATGTATCGATACAATGTAA
*
3967985 AATGTATCGATACAATG-AGC
1 AATGTATCGATACAATGTA-A
3968005 AATGTATCGAT---A--T--
1 AATGTATCGATACAATGTAA
* *
3968018 AATGTATCAATACAATG-AGC
1 AATGTATCGATACAATGTA-A
3968038 AATGTATCGATACAATGTAA
1 AATGTATCGATACAATGTAA
3968058 AATGTATCGATACA
1 AATGTATCGATACA
3968072 TCTGGGTAAA
Statistics
Matches: 71, Mismatches: 5, Indels: 22
0.72 0.05 0.22
Matches are distributed among these distances:
13 10 0.14
16 1 0.01
17 1 0.01
19 1 0.01
20 57 0.80
21 1 0.01
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (20 bp):
AATGTATCGATACAATGTAA
Found at i:3968031 original size:33 final size:33
Alignment explanation
Indices: 3967985--3968056 Score: 126
Period size: 33 Copynumber: 2.2 Consensus size: 33
3967975 TACATTGTAA
* *
3967985 AATGTATCGATACAATGAGCAATGTATCGATAT
1 AATGTATCAATACAATGAGCAATGTATCGATAC
3968018 AATGTATCAATACAATGAGCAATGTATCGATAC
1 AATGTATCAATACAATGAGCAATGTATCGATAC
3968051 AATGTA
1 AATGTA
3968057 AAATGTATCG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (33 bp):
AATGTATCAATACAATGAGCAATGTATCGATAC
Found at i:3969227 original size:111 final size:114
Alignment explanation
Indices: 3968998--3969246 Score: 312
Period size: 111 Copynumber: 2.2 Consensus size: 114
3968988 AAGAAAGGTG
** *
3968998 TCCTGCTCTTTGAGGACT--GGAAAATGCCACCAACTTGGGTGGGCTTTGAAAAAAAAAAGTGTC
1 TCCTGCTCTTTGAGGACTAAAAAAAATGCCACCAACTTGGGTGGGCTTTG-----AAAAAGCGTC
** * *
3969061 TGCTCTTTGAGGACTTAGACTAGTGCCACCAACTTGTATGGGCTTTAAAAGGCA
61 TGCTCTTTGAGGACTTAGAAAAATGCCACCAACTTGTACGGGCTTTAAAAGGCA
* *
3969115 TCCTGCTCTTTGAGGACTAAAAAAAATGCCACCAACTTGTGTGGGCTTTG-AAAGGCGTCCTGCT
1 TCCTGCTCTTTGAGGACTAAAAAAAATGCCACCAACTTGGGTGGGCTTTGAAAAAGCGT-CTGCT
*
3969179 CTTTGAGGAC-T-GAAAAATGCCACC-ACTTGTGCGGGCTTTAAAAGGCA
65 CTTTGAGGACTTAGAAAAATGCCACCAACTTGTACGGGCTTTAAAAGGCA
3969226 TCCTGCTCTTTGAGGACTAAA
1 TCCTGCTCTTTGAGGACTAAA
3969247 GGGTGAAAGG
Statistics
Matches: 119, Mismatches: 10, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
111 42 0.35
112 10 0.08
113 7 0.06
114 15 0.13
117 18 0.15
119 27 0.23
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.27
Consensus pattern (114 bp):
TCCTGCTCTTTGAGGACTAAAAAAAATGCCACCAACTTGGGTGGGCTTTGAAAAAGCGTCTGCTC
TTTGAGGACTTAGAAAAATGCCACCAACTTGTACGGGCTTTAAAAGGCA
Found at i:3969230 original size:54 final size:56
Alignment explanation
Indices: 3968937--3969244 Score: 293
Period size: 57 Copynumber: 5.3 Consensus size: 56
3968927 ATAAAGTGCG
* * **
3968937 TCCTGCTCTTTTAGGAC-A-AAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAAGAAAGGTG
1 TCCTGCTCTTTGAGGACTAGAAAAA-TGCCACCAACTTGTGTGGGCTTT-----A-AAAGGCA
* * ***
3968998 TCCTGCTCTTTGAGGACT-GGAAAATGCCACCAACTTGGGTGGGCTTTGAAAAAAAAAA
1 TCCTGCTCTTTGAGGACTAGAAAAATGCCACCAACTTGTGTGGGCTTT---AAAAGGCA
* ** * *
3969056 GTGTCTGCTCTTTGAGGACTTAGACTAGTGCCACCAACTTGTATGGGCTTTAAAAGGCA
1 -T-CCTGCTCTTTGAGGAC-TAGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCA
* * *
3969115 TCCTGCTCTTTGAGGACTAAAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACT-AGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCA
*
3969172 TCCTGCTCTTTGAGGACT-GAAAAATGCCACC-ACTTGTGCGGGCTTTAAAAGGCA
1 TCCTGCTCTTTGAGGACTAGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCA
3969226 TCCTGCTCTTTGAGGACTA
1 TCCTGCTCTTTGAGGACTA
3969245 AAGGGTGAAA
Statistics
Matches: 208, Mismatches: 31, Indels: 22
0.80 0.12 0.08
Matches are distributed among these distances:
54 38 0.18
55 12 0.06
56 1 0.00
57 64 0.31
58 4 0.02
59 9 0.04
60 15 0.07
61 38 0.18
62 27 0.13
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (56 bp):
TCCTGCTCTTTGAGGACTAGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGCA
Found at i:3969329 original size:94 final size:93
Alignment explanation
Indices: 3969169--3969340 Score: 281
Period size: 94 Copynumber: 1.8 Consensus size: 93
3969159 GCTTTGAAAG
*
3969169 GCGTCCTGCTCTTTGAGGACTGAAAAATGCCACCACTTGTGCGGGCTTTAAAAGGCATCCTGCTC
1 GCGTCCTGCTCTTTGAAGACTGAAAAATGCCACCACTTGTGCGGGCTTTAAAAGGCATCCTGCTC
*
3969234 TTTGAGGACTAAAGGGTGAAAGGAGAGA
66 TTTGAAGACTAAAGGGTGAAAGGAGAGA
** * *
3969262 GCGTCCTGCTCTTTGAAGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCT
1 GCGTCCTGCTCTTTGAAGACTGAAAAATGCCACC-ACTTGTGCGGGCTTTAAAAGGCATCCTGCT
3969327 CTTTGAAGACTAAA
65 CTTTGAAGACTAAA
3969341 AAAAATGCCA
Statistics
Matches: 72, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
93 30 0.42
94 42 0.58
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (93 bp):
GCGTCCTGCTCTTTGAAGACTGAAAAATGCCACCACTTGTGCGGGCTTTAAAAGGCATCCTGCTC
TTTGAAGACTAAAGGGTGAAAGGAGAGA
Found at i:3969447 original size:61 final size:59
Alignment explanation
Indices: 3969262--3969817 Score: 592
Period size: 55 Copynumber: 9.5 Consensus size: 59
3969252 AAAGGAGAGA
* *
3969262 GCGTCCTGCTCTTTGAAGACTGGGAA-GTGCCACCAACTTGTGTGGGCTTT----AAAAG
1 GCGTCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAGAAAAG
* * * **
3969317 GCATCCTGCTCTTTGAAGACTAAAAAAAATGCCACCAACTTGTGTGGGCTTT---G-AAAG
1 GCGTCCTGCTCTTTGAGGACT--GAAAGGTGCCACCAACTTGTGTGGGCTTTAAAGAAAAG
* * **
3969374 GCGTCTTACTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAG
1 GCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAA-GAAAAG
*
3969435 GCGTCCTGCTCTTTGAGGACT-AAAGGTGCTACCAACTTGTGTGGGCTTTAAAAAGAAAAAG
1 GCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT--AAAG-AAAAG
* * * * *
3969496 GCATCCTGCTCTTTGAGGACTGGAGGGTGCCACCAACTCGTGTGGGCTTCAAAGGAAAAAAG
1 GCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAA-G--AAAAG
* * *
3969558 GTGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTTGGCTTT----AAAAG
1 GCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAGAAAAG
*
3969613 GCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGAGCTTT---G-AAAG
1 GCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAGAAAAG
* *
3969668 GCGTCCTGCTCTTTGAAGACTGAAAGGTGCCACCAACTTGTGTGAGCTTTAAAAAGAAAAG
1 GCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT--AAAGAAAAG
* *
3969729 GCATCTTGCTCTTTGAGGACT-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAAG
1 GCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAA-G-AAAAG
*
3969790 GCATCCTGCTCTTTGAGGACTGGAAAGG
1 GCGTCCTGCTCTTTGAGGACT-GAAAGG
3969818 CTAAAAGAGG
Statistics
Matches: 436, Mismatches: 40, Indels: 42
0.84 0.08 0.08
Matches are distributed among these distances:
55 152 0.35
56 2 0.00
57 44 0.10
59 4 0.01
60 59 0.14
61 99 0.23
62 71 0.16
63 5 0.01
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (59 bp):
GCGTCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAGAAAAG
Found at i:3969668 original size:29 final size:29
Alignment explanation
Indices: 3969633--3969717 Score: 72
Period size: 29 Copynumber: 3.0 Consensus size: 29
3969623 CTTTGAGGAC
3969633 TGAAAGGTGCCACCAACTTGTGTGAGCTT
1 TGAAAGGTGCCACCAACTTGTGTGAGCTT
* ** * *
3969662 TGAAAGGCGTCCTGC-TCTT-TG-AAGAC--
1 TGAAAGGTG-CCACCAACTTGTGTGAG-CTT
3969688 TGAAAGGTGCCACCAACTTGTGTGAGCTT
1 TGAAAGGTGCCACCAACTTGTGTGAGCTT
3969717 T
1 T
3969718 AAAAAGAAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 14
0.62 0.16 0.22
Matches are distributed among these distances:
25 3 0.08
26 11 0.28
27 5 0.13
28 5 0.13
29 12 0.31
30 3 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (29 bp):
TGAAAGGTGCCACCAACTTGTGTGAGCTT
Found at i:3969795 original size:294 final size:295
Alignment explanation
Indices: 3969264--3969813 Score: 870
Period size: 294 Copynumber: 1.9 Consensus size: 295
3969254 AGGAGAGAGC
**
3969264 GTCCTGCTCTTTGAAGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTCT
1 GTCCTGCTCTTTGAAGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTCT
* * *
3969329 TTGAAGACTAAAAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCTTACTCTTTGAGGAC
66 TTGAAGACT-AAAAAAATGCCACCAACTTGTGTGAGCTTTGAAAGGCGTCCTACTCTTTGAAGAC
* * * *
3969394 TGAAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCGTCCTGCTCTTTGAGGACTAAA
130 TGAAAAATGCCACCAACTTGTGTGAGCTTTAAAAAGAAAAGGCATCCTGCTCTTTGAGGACTAAA
*
3969459 GGTGCTACCAACTTGTGTGGGCTTTAAAAAGAAAAAGGCATCCTGCTCTTTGAGGACTGGAGGGT
195 GGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGGCATCCTGCTCTTTGAGGACTGGAGGGT
3969524 GCCACCAACTCGTGTGGGCTTCAAAGGAAAAAAGGT
260 GCCACCAACTCGTGTGGGCTTCAAAGGAAAAAAGGT
* * *
3969560 GTCCTGCTCTTTGAGGACT-AAAAGGTGCCACCAACTTGTGTTGGCTTTAAAAGGCGTCCTGCTC
1 GTCCTGCTCTTTGAAGACTGAAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTC
* * ** *
3969624 TTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGAGCTTTGAAAGGCGTCCTGCTCTTTGAAGAC
65 TTTGAAGACTAAAAAAATGCCACCAACTTGTGTGAGCTTTGAAAGGCGTCCTACTCTTTGAAGAC
** *
3969688 TGAAAGGTGCCACCAACTTGTGTGAGCTTTAAAAAGAAAAGGCATCTTGCTCTTTGAGGACTAAA
130 TGAAAAATGCCACCAACTTGTGTGAGCTTTAAAAAGAAAAGGCATCCTGCTCTTTGAGGACTAAA
*
3969753 GGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAAGGCATCCTGCTCTTTGAGGACTGGA
195 GGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGGCATCCTGCTCTTTGAGGACTGGA
3969814 AAGGCTAAAA
Statistics
Matches: 231, Mismatches: 22, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
294 164 0.71
295 2 0.01
296 65 0.28
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (295 bp):
GTCCTGCTCTTTGAAGACTGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCATCCTGCTCT
TTGAAGACTAAAAAAATGCCACCAACTTGTGTGAGCTTTGAAAGGCGTCCTACTCTTTGAAGACT
GAAAAATGCCACCAACTTGTGTGAGCTTTAAAAAGAAAAGGCATCCTGCTCTTTGAGGACTAAAG
GTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGGCATCCTGCTCTTTGAGGACTGGAGGGTG
CCACCAACTCGTGTGGGCTTCAAAGGAAAAAAGGT
Found at i:3976122 original size:51 final size:51
Alignment explanation
Indices: 3976056--3976174 Score: 193
Period size: 51 Copynumber: 2.3 Consensus size: 51
3976046 CGAAAATAAT
*
3976056 GGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTAGAAATAAGGCC
1 GGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTAGAAATAAAGCC
* ** *
3976107 GGGGTTGAAGTATCCCTGATTATGAGAAATCAATATTTTGGAAATAAAGCC
1 GGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTAGAAATAAAGCC
3976158 GGGGTTGGAGTATCCCC
1 GGGGTTGGAGTATCCCC
3976175 TCGGAAATAA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 61 1.00
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (51 bp):
GGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTAGAAATAAAGCC
Found at i:3976194 original size:28 final size:28
Alignment explanation
Indices: 3976159--3976230 Score: 117
Period size: 28 Copynumber: 2.6 Consensus size: 28
3976149 AATAAAGCCG
**
3976159 GGGTTGGAGTATCCCCTCGGAAATAACA
1 GGGTTGGAGTATCCCCGAGGAAATAACA
*
3976187 GGGTTGGAGTATCCCCGATGAAATAACA
1 GGGTTGGAGTATCCCCGAGGAAATAACA
3976215 GGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
3976231 AATTGTGAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.22
Consensus pattern (28 bp):
GGGTTGGAGTATCCCCGAGGAAATAACA
Found at i:3976287 original size:51 final size:51
Alignment explanation
Indices: 3976218--3976446 Score: 237
Period size: 51 Copynumber: 4.5 Consensus size: 51
3976208 AATAACAGGG
* * * * *
3976218 TTGGAGTATCCCCAATTGTGAAAAATT-AGTGTTTTGGAAATAAAATCGGAA
1 TTGGAGTATCCCCGATTATGAAAAATTGA-TGTTTTAGAAATAAAACCGGGA
* * * * * *
3976269 TTGGAATATCCCCGATTGTGGAGAATTGGTGTTTTAGAAATAAAACCGGGG
1 TTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGA
* *
3976320 TTGCAGTATCACCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGA
1 TTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGA
* * * ** *
3976371 TTGGAGTATCCCCGATTAAGAAAAATTGACGTTTTGGAAATGGAACTGGGA
1 TTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGA
* * *
3976422 ATGAAGTATCCCCGA-GATGAAAAAT
1 TTGGAGTATCCCCGATTATGAAAAAT
3976447 CTAGAAATTT
Statistics
Matches: 148, Mismatches: 29, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
50 8 0.05
51 140 0.95
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (51 bp):
TTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGA
Found at i:3978779 original size:20 final size:19
Alignment explanation
Indices: 3978756--3978860 Score: 114
Period size: 20 Copynumber: 5.6 Consensus size: 19
3978746 TCCATTGTAA
3978756 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGA-C
3978776 AATGTATCG-----AT-AC
1 AATGTATCGATACAATGAC
3978789 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGA-C
*
3978809 AATGTATCGATACAATGCAA
1 AATGTATCGATACAATG-AC
*
3978829 AATGTATCGATACAATGAAT
1 AATGTATCGATACAATG-AC
3978849 AATGTATCGATA
1 AATGTATCGATA
3978861 AAAATTGCAA
Statistics
Matches: 74, Mismatches: 3, Indels: 16
0.80 0.03 0.17
Matches are distributed among these distances:
13 10 0.14
14 1 0.01
15 2 0.03
18 2 0.03
19 1 0.01
20 57 0.77
21 1 0.01
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (19 bp):
AATGTATCGATACAATGAC
Found at i:3978798 original size:33 final size:33
Alignment explanation
Indices: 3978756--3978825 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
3978746 TCCATTGTAA
3978756 AATGTATCGATACAATGAGCAATGTATCGATAC
1 AATGTATCGATACAATGAGCAATGTATCGATAC
3978789 AATGTATCGATACAATGAGCAATGTATCGATAC
1 AATGTATCGATACAATGAGCAATGTATCGATAC
3978822 AATG
1 AATG
3978826 CAAAATGTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (33 bp):
AATGTATCGATACAATGAGCAATGTATCGATAC
Found at i:3978824 original size:13 final size:13
Alignment explanation
Indices: 3978775--3978805 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
3978765 ATACAATGAG
3978775 CAATGTATCGATA
1 CAATGTATCGATA
3978788 CAATGTATCGATA
1 CAATGTATCGATA
3978801 CAATG
1 CAATG
3978806 AGCAATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:3983766 original size:27 final size:25
Alignment explanation
Indices: 3983726--3983776 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
3983716 ATTTGGATCA
3983726 TTATTTATTTAATTA-AATAATATTT
1 TTATTTATTTAATTATAA-AATATTT
3983751 TTATTTAATTTTAATTATAAAATATT
1 TTATTT-A-TTTAATTATAAAATATT
3983777 AATATAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 6 0.26
26 1 0.04
27 14 0.61
28 2 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
TTATTTATTTAATTATAAAATATTT
Found at i:3983778 original size:14 final size:14
Alignment explanation
Indices: 3983761--3983802 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
3983751 TTATTTAATT
3983761 TTAATTATAAAATA
1 TTAATTATAAAATA
3983775 TTAA-TATAAAA-A
1 TTAATTATAAAATA
* *
3983787 TTATTTTTAAAATA
1 TTAATTATAAAATA
3983801 TT
1 TT
3983803 TTATTATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 4 0.17
13 13 0.54
14 7 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TTAATTATAAAATA
Found at i:3994533 original size:13 final size:14
Alignment explanation
Indices: 3994494--3994536 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 14
3994484 TAAATTCATT
*
3994494 TAAAAATATAATAA
1 TAAAAATATTATAA
*
3994508 TAAAATATTTTATAA
1 TAAAA-ATATTATAA
3994523 TAAAAA-ATTATAA
1 TAAAAATATTATAA
3994536 T
1 T
3994537 TATTTTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 7 0.28
14 6 0.24
15 12 0.48
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TAAAAATATTATAA
Found at i:3999488 original size:26 final size:26
Alignment explanation
Indices: 3999449--3999545 Score: 78
Period size: 26 Copynumber: 3.8 Consensus size: 26
3999439 ACAACGATCC
*
3999449 ATTTAATTACTTAAATAAAATTAATAT
1 ATTTTATTA-TTAAATAAAATTAATAT
* *
3999476 ATTTTATT-TT---TAATATTTATAT
1 ATTTTATTATTAAATAAAATTAATAT
* * *
3999498 ATTTTATAATTAAATTTAAA-TAAAAT
1 ATTTTATTATTAAA-TAAAATTAATAT
3999524 ATTTTATTATTAAATAATAATT
1 ATTTTATTATTAAATAA-AATT
3999546 TAAATTAAAT
Statistics
Matches: 53, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
22 17 0.32
23 2 0.04
25 4 0.08
26 19 0.36
27 11 0.21
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (26 bp):
ATTTTATTATTAAATAAAATTAATAT
Found at i:3999510 original size:22 final size:21
Alignment explanation
Indices: 3999466--3999515 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
3999456 TACTTAAATA
* **
3999466 AAATTAATATATTTTATTTTT
1 AAATTTATATATTTTATAATT
3999487 AATATTTATATATTTTATAATT
1 AA-ATTTATATATTTTATAATT
3999509 AAATTTA
1 AAATTTA
3999516 AATAAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
AAATTTATATATTTTATAATT
Found at i:3999527 original size:48 final size:42
Alignment explanation
Indices: 3999459--3999573 Score: 115
Period size: 48 Copynumber: 2.6 Consensus size: 42
3999449 ATTTAATTAC
* * * *
3999459 TTAAATAAAATTAATATATTTTATTTTTAATATTTATATATTTTATAA
1 TTAAATTAAA-TAAAATATTTTATTATTAA-A--TA-ATAATTTA-AA
3999507 TTAAATTTAAATAAAATATTTTATTATTAAATAATAATTTAAA
1 TTAAA-TTAAATAAAATATTTTATTATTAAATAATAATTTAAA
*
3999550 TTAAATTAATTAAAAT-TTTTATTA
1 TTAAATTAAATAAAATATTTTATTA
3999574 AAAATTAATT
Statistics
Matches: 61, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
41 8 0.13
42 10 0.16
43 7 0.11
44 7 0.11
45 2 0.03
47 1 0.02
48 22 0.36
49 4 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (42 bp):
TTAAATTAAATAAAATATTTTATTATTAAATAATAATTTAAA
Found at i:3999593 original size:41 final size:42
Alignment explanation
Indices: 3999501--3999596 Score: 117
Period size: 41 Copynumber: 2.3 Consensus size: 42
3999491 TTTATATATT
*
3999501 TTATAATTAAATTTAAATAAAATATTTTATTATTAAATAATAA
1 TTATAATTAAA-TTAAATAAAATATTTTATTATAAAATAATAA
* *
3999544 TT-TAAATTAAATTAATTAAAAT-TTTTATTA-AAAATTAATTA
1 TTAT-AATTAAATTAAATAAAATATTTTATTATAAAA-TAATAA
3999585 TTATAATTAAAT
1 TTATAATTAAAT
3999597 ATATCAAACT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
40 3 0.06
41 23 0.49
42 12 0.26
43 9 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (42 bp):
TTATAATTAAATTAAATAAAATATTTTATTATAAAATAATAA
Found at i:3999719 original size:24 final size:24
Alignment explanation
Indices: 3999688--3999739 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
3999678 TAATTGTTGT
* * *
3999688 ATATAATTTTTTAATTCATTGTAA
1 ATATAATTTTGTAATTAAGTGTAA
3999712 ATATAATTTTGTAATTAAGTGTAA
1 ATATAATTTTGTAATTAAGTGTAA
3999736 ATAT
1 ATAT
3999740 GATACGAAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.50
Consensus pattern (24 bp):
ATATAATTTTGTAATTAAGTGTAA
Found at i:4000290 original size:22 final size:23
Alignment explanation
Indices: 4000241--4000291 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
4000231 TTTTTATTGG
* *
4000241 TTTTTTTTATTATTATAATAATA
1 TTTTTTTAATTATTAAAATAATA
* *
4000264 ATTTTTTAATTCTTAAAAT-ATA
1 TTTTTTTAATTATTAAAATAATA
4000286 TTTTTT
1 TTTTTT
4000292 GATGAATATT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTTTTTAATTATTAAAATAATA
Found at i:4001096 original size:74 final size:73
Alignment explanation
Indices: 4000908--4001125 Score: 191
Period size: 74 Copynumber: 3.0 Consensus size: 73
4000898 TTAATTTGAC
* * * * *
4000908 TAAAGGTATTATTTATTTCT-ATTTATAG-AAGTTTAA-AT-TTTTTTA--TCTAATTATGCAGG
1 TAAA-GTATAATTTATTT-TGATTTATAGAAAGTTTAATGTATTTTTTAGGTATAATTATACAAG
4000967 TTTAAATTTT
64 TTTAAATTTT
* **
4000977 TAAAGTATAATTTATTTTGATTTATAGAAATTTTAATGTATTTTTTAGGTATAATTATATGAGTT
1 TAAAGTATAATTTATTTTGATTTATAGAAAGTTTAATGTATTTTTTAGGTATAATTATACAAGTT
4001042 TAAATTTT
66 TAAATTTT
* * * * * * * *
4001050 TTATGATGTAATTTATTTTTATTTATAG-AAGTTTAGGATTTGTTTTTT-GGTTTGATTATACAA
1 TAAAG-TATAATTTATTTTGATTTATAGAAAGTTTA--ATGTATTTTTTAGGTATAATTATACAA
4001113 GTTTAAATTTT
63 GTTTAAATTTT
4001124 TA
1 TA
4001126 GTCACAATGG
Statistics
Matches: 120, Mismatches: 20, Indels: 13
0.78 0.13 0.08
Matches are distributed among these distances:
67 1 0.01
68 20 0.17
69 11 0.09
70 1 0.01
71 7 0.06
73 28 0.23
74 43 0.36
75 9 0.08
ACGTcount: A:0.32, C:0.02, G:0.12, T:0.55
Consensus pattern (73 bp):
TAAAGTATAATTTATTTTGATTTATAGAAAGTTTAATGTATTTTTTAGGTATAATTATACAAGTT
TAAATTTT
Found at i:4001181 original size:9 final size:8
Alignment explanation
Indices: 4001167--4001245 Score: 74
Period size: 8 Copynumber: 9.9 Consensus size: 8
4001157 CTTTAGAGAA
4001167 AAAAAAAGG
1 AAAAAAA-G
4001176 AAAAAAAG
1 AAAAAAAG
4001184 -AAAAAAG
1 AAAAAAAG
4001191 AAAAAAAG
1 AAAAAAAG
*
4001199 AAGAAAGAG
1 AA-AAAAAG
*
4001208 AAAGAGAAG
1 AAA-AAAAG
4001217 -AAAAAAG
1 AAAAAAAG
*
4001224 AAAACAA-
1 AAAAAAAG
*
4001231 AAAAAATG
1 AAAAAAAG
4001239 AAAAAAA
1 AAAAAAA
4001246 AATGGGTGGC
Statistics
Matches: 57, Mismatches: 8, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
7 16 0.28
8 24 0.42
9 17 0.30
ACGTcount: A:0.81, C:0.01, G:0.16, T:0.01
Consensus pattern (8 bp):
AAAAAAAG
Found at i:4001187 original size:7 final size:7
Alignment explanation
Indices: 4001177--4001244 Score: 66
Period size: 7 Copynumber: 8.9 Consensus size: 7
4001167 AAAAAAAGGA
4001177 AAAAAAG
1 AAAAAAG
4001184 AAAAAAG
1 AAAAAAG
4001191 AAAAAAAG
1 -AAAAAAG
4001199 AAGAAAGAG
1 AA-AAA-AG
4001208 AAAGAGAAG
1 AAA-A-AAG
4001217 AAAAAAG
1 AAAAAAG
4001224 AAAACAA-
1 AAAA-AAG
4001231 AAAAAATG
1 AAAAAA-G
4001239 AAAAAA
1 AAAAAA
4001245 AAATGGGTGG
Statistics
Matches: 53, Mismatches: 0, Indels: 15
0.78 0.00 0.22
Matches are distributed among these distances:
6 2 0.04
7 20 0.38
8 20 0.38
9 10 0.19
10 1 0.02
ACGTcount: A:0.81, C:0.01, G:0.16, T:0.01
Consensus pattern (7 bp):
AAAAAAG
Found at i:4001193 original size:15 final size:15
Alignment explanation
Indices: 4001168--4001245 Score: 86
Period size: 15 Copynumber: 4.9 Consensus size: 15
4001158 TTTAGAGAAA
4001168 AAAAAAGGAAAAAAAG
1 AAAAAA-GAAAAAAAG
4001184 AAAAAAGAAAAAAAG
1 AAAAAAGAAAAAAAG
*
4001199 AAGAAAGAGAAAGAGAAG
1 AA-AAA-AGAAA-AAAAG
4001217 AAAAAAGAAAACAAA-
1 AAAAAAGAAAA-AAAG
*
4001232 AAAAATGAAAAAAA
1 AAAAAAGAAAAAAA
4001246 AATGGGTGGC
Statistics
Matches: 55, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
14 3 0.05
15 22 0.40
16 16 0.29
17 8 0.15
18 6 0.11
ACGTcount: A:0.81, C:0.01, G:0.17, T:0.01
Consensus pattern (15 bp):
AAAAAAGAAAAAAAG
Found at i:4001727 original size:147 final size:141
Alignment explanation
Indices: 4001452--4001879 Score: 501
Period size: 139 Copynumber: 3.0 Consensus size: 141
4001442 AATTGAATAA
*
4001452 AAAAAATAAAAAGACTTAGTTTTACATGGTTTTGGGTTATATTTTTTGTTTAATATGAAATGCTC
1 AAAAAATAAAAAGACTTAGTTTAACATGGTTTTGGGTT-TATTTTTTGTTTAATATGAAATGCTC
* * * * * *
4001517 ATTTAAATACCTTTTAATATTATTTGAGATTTCTAATATTATTAATTTTTTATGGCATGCTTGTT
65 ATTTAAATA-CTTTTTATGTTGTTTAAGATTTCTGATATTATTAATTTTTTATAGCATGCTTGTT
4001582 TAATATGTCAAAT
129 TAATATGTCAAAT
* *
4001595 ATGTCAAAAATAAAAAG-CTTTAGCTTAACGTGGTTTTGGGTTTATTTTTTGTTTAATATGAAAT
1 A----AAAAATAAAAAGAC-TTAGTTTAACATGGTTTTGGGTTTATTTTTTGTTTAATATGAAAT
* * * *
4001659 GCTCGTTTAGATACTTTTTATGTTGTTTAAGATTTCTGATATTATTAATTTTTTAAATTGCTTGC
61 GCTCATTTAAATACTTTTTATGTTGTTTAAGATTTCTGATATTATTAATTTTTT--ATAGCATGC
4001724 TTGTTTAATATG-----T
124 TTGTTTAATATGTCAAAT
* * *
4001737 AAAAAATAAAAAGACTTAGTTTGACATGGTTTTGGGTAATATTTTTTGTTTAATATAAAATGCTC
1 AAAAAATAAAAAGACTTAGTTTAACATGGTTTTGGGT-TTATTTTTTGTTTAATATGAAATGCTC
* * * * *
4001802 ATTTAAATA-TTTGTTGATGTTGCTTAAAATTTTTGATATTATTAATTTTTTTATAGCATACTTA
65 ATTTAAATACTTT-TT-ATGTTGTTTAAGATTTCTGATATTATTAA-TTTTTTATAGCATGCTTG
4001866 TTTAATATGTCAAA
127 TTTAATATGTCAAA
4001880 ATATATTTAA
Statistics
Matches: 242, Mismatches: 26, Indels: 33
0.80 0.09 0.11
Matches are distributed among these distances:
138 34 0.14
139 52 0.21
140 26 0.11
141 6 0.02
142 2 0.01
143 1 0.00
145 36 0.15
146 34 0.14
147 51 0.21
ACGTcount: A:0.32, C:0.07, G:0.13, T:0.48
Consensus pattern (141 bp):
AAAAAATAAAAAGACTTAGTTTAACATGGTTTTGGGTTTATTTTTTGTTTAATATGAAATGCTCA
TTTAAATACTTTTTATGTTGTTTAAGATTTCTGATATTATTAATTTTTTATAGCATGCTTGTTTA
ATATGTCAAAT
Found at i:4002289 original size:29 final size:30
Alignment explanation
Indices: 4002257--4002323 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
4002247 AGTTCCGCCT
* *
4002257 AAGCCATTTC-TTGATTTTTGGTTTTGTCC
1 AAGCCATTTCTTTGAATCTTGGTTTTGTCC
*
4002286 AAGCTATTTCTTTGAATCTTGGTTTTGTCC
1 AAGCCATTTCTTTGAATCTTGGTTTTGTCC
*
4002316 AAGTCATT
1 AAGCCATT
4002324 ATTTAGGTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 9 0.28
30 23 0.72
ACGTcount: A:0.18, C:0.16, G:0.16, T:0.49
Consensus pattern (30 bp):
AAGCCATTTCTTTGAATCTTGGTTTTGTCC
Found at i:4002355 original size:60 final size:60
Alignment explanation
Indices: 4002282--4002399 Score: 148
Period size: 60 Copynumber: 2.0 Consensus size: 60
4002272 TTTTGGTTTT
* * * *
4002282 GTCCAAGCTATTTCTTTGAA-TCTTGGTTTTGTCCAAGTCATTATTTAGGTTTCCAATTTC
1 GTCCAAGCCATTTCATT-AAGTCTTGGTTTCGCCCAAGTCATTATTTAGGTTTCCAATTTC
** * *
4002342 GTCCAAGCCATTTCATTAAGTCTTGGTTTCGCCCTTGTCATTGTTTAGGTTTCTAATT
1 GTCCAAGCCATTTCATTAAGTCTTGGTTTCGCCCAAGTCATTATTTAGGTTTCCAATT
4002400 CCATCTAAGC
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 2 0.04
60 47 0.96
ACGTcount: A:0.19, C:0.19, G:0.16, T:0.46
Consensus pattern (60 bp):
GTCCAAGCCATTTCATTAAGTCTTGGTTTCGCCCAAGTCATTATTTAGGTTTCCAATTTC
Found at i:4003383 original size:21 final size:21
Alignment explanation
Indices: 4003338--4003393 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 21
4003328 GTTGGGCTCA
4003338 ATGTATCGATACAA-TAGACT
1 ATGTATCGATACAATTAGACT
*
4003358 ATGTATCGATACAATTCA-AGT
1 ATGTATCGATACAATT-AGACT
4003379 ATGTATCGATACAAT
1 ATGTATCGATACAAT
4003394 ATATCGATAC
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 14 0.42
21 18 0.55
22 1 0.03
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (21 bp):
ATGTATCGATACAATTAGACT
Found at i:4003494 original size:32 final size:33
Alignment explanation
Indices: 4003453--4003516 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
4003443 CTTTTCAAGG
*
4003453 TGTATCGATACTATG-AACATATATCGATACAA
1 TGTATCGATACTAAGCAACATATATCGATACAA
* *
4003485 TGTATCGATACTAAGCAATATGTATCGATACA
1 TGTATCGATACTAAGCAACATATATCGATACA
4003517 TCTGGGTGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (33 bp):
TGTATCGATACTAAGCAACATATATCGATACAA
Found at i:4003645 original size:21 final size:22
Alignment explanation
Indices: 4003616--4003658 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
4003606 ACTTTAAATT
*
4003616 ATTTTTACTTG-AAAACATTTG
1 ATTTATACTTGAAAAACATTTG
4003637 ATTTATACTTGAAAAACATTTG
1 ATTTATACTTGAAAAACATTTG
4003659 TACTTAACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.44
Consensus pattern (22 bp):
ATTTATACTTGAAAAACATTTG
Found at i:4003673 original size:22 final size:22
Alignment explanation
Indices: 4003621--4003664 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
4003611 AAATTATTTT
*
4003621 TACTTG-AAAACATTTGATTTA
1 TACTTGAAAAACATTTGACTTA
4003642 TACTTGAAAAACATTTGTACTTA
1 TACTTGAAAAACATTTG-ACTTA
4003665 ACTCTAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 6 0.30
22 10 0.50
23 4 0.20
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (22 bp):
TACTTGAAAAACATTTGACTTA
Found at i:4004362 original size:20 final size:21
Alignment explanation
Indices: 4004337--4004375 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4004327 CCCCTTTTTG
4004337 TTAT-CCCCTTTACAAAACTA
1 TTATCCCCCTTTACAAAACTA
*
4004357 TTATCCCCCTTTATAAAAC
1 TTATCCCCCTTTACAAAAC
4004376 AAATTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.31, G:0.00, T:0.36
Consensus pattern (21 bp):
TTATCCCCCTTTACAAAACTA
Found at i:4004648 original size:18 final size:18
Alignment explanation
Indices: 4004622--4004656 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4004612 TATAAAAATA
*
4004622 AAAACGACTACTCCTATC
1 AAAACGACTAATCCTATC
*
4004640 AAAATGACTAATCCTAT
1 AAAACGACTAATCCTAT
4004657 GACTAATCGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.26, G:0.06, T:0.26
Consensus pattern (18 bp):
AAAACGACTAATCCTATC
Found at i:4010179 original size:52 final size:52
Alignment explanation
Indices: 4010101--4010229 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
4010091 CGAAAGATGA
*
4010101 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTACCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
* * *
4010153 AAATTTTCCTGCATCTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTACCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
*
4010205 AAATTTGCCTGCATGTATCGATACA
1 AAATTTACCTGCATGTATCGATACA
4010230 AAGATCAGTG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.36
Consensus pattern (52 bp):
AAATTTACCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
Found at i:4010242 original size:52 final size:51
Alignment explanation
Indices: 4010101--4010249 Score: 201
Period size: 52 Copynumber: 2.9 Consensus size: 51
4010091 CGAAAGATGA
4010101 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTACCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
* * * *
4010153 AAATTTTCCTGCATCTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTACCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
* *
4010205 AAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTACCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
4010250 ATGTATCGAT
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.98
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (51 bp):
AAATTTACCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGC
Found at i:4010256 original size:13 final size:13
Alignment explanation
Indices: 4010238--4010262 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4010228 CAAAGATCAG
4010238 TGTATCGATACAA
1 TGTATCGATACAA
4010251 TGTATCGATACA
1 TGTATCGATACA
4010263 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4010350 original size:33 final size:33
Alignment explanation
Indices: 4010305--4010371 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
4010295 AGTAGCTTAA
4010305 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* * ***
4010338 ATTGTATTGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
4010371 A
1 A
4010372 AATCGTTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:4014288 original size:3 final size:3
Alignment explanation
Indices: 4014280--4014322 Score: 70
Period size: 3 Copynumber: 14.3 Consensus size: 3
4014270 CAAGCCAACT
4014280 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC- TCCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T-CA TCA TCA T
4014323 TGATGGTTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 1 0.03
3 36 0.95
4 1 0.03
ACGTcount: A:0.30, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:4016966 original size:64 final size:64
Alignment explanation
Indices: 4016895--4017025 Score: 163
Period size: 64 Copynumber: 2.0 Consensus size: 64
4016885 TATTGAAGGC
** * * *
4016895 TTCGCCTTGGTCATTTTTTTGACTAATAGCTTTCACCCCAATAATCTTTTTTGATTATCATGGT
1 TTCGCCTTAATCATCTTTTTGACTAATAGCTTTCACCCCAATAATCTTCTTTGACTATCATGGT
* ** * **
4016959 TTCGCCTTAATCATCTTTTTGACTAATAGGTTTTGCCCTAATCGTCTTCTTTGACTATCATGGT
1 TTCGCCTTAATCATCTTTTTGACTAATAGCTTTCACCCCAATAATCTTCTTTGACTATCATGGT
4017023 TTC
1 TTC
4017026 ACCCTGGTGA
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
64 56 1.00
ACGTcount: A:0.19, C:0.21, G:0.13, T:0.47
Consensus pattern (64 bp):
TTCGCCTTAATCATCTTTTTGACTAATAGCTTTCACCCCAATAATCTTCTTTGACTATCATGGT
Found at i:4016978 original size:32 final size:32
Alignment explanation
Indices: 4016942--4017030 Score: 101
Period size: 31 Copynumber: 2.8 Consensus size: 32
4016932 CCAATAATCT
* *
4016942 TTTTTGATTATCATGGTTTCGCCTTAATCATC
1 TTTTTGACTATCATGGTTTCGCCCTAATCATC
* *
4016974 TTTTTGACTA--ATAGGTTTTGCCCTAATCGTC
1 TTTTTGACTATCAT-GGTTTCGCCCTAATCATC
*
4017005 TTCTTTGACTATCATGGTTTCACCCT
1 TT-TTTGACTATCATGGTTTCGCCCT
4017031 GGTGAATTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
30 2 0.04
31 17 0.36
32 17 0.36
33 9 0.19
34 2 0.04
ACGTcount: A:0.18, C:0.21, G:0.13, T:0.47
Consensus pattern (32 bp):
TTTTTGACTATCATGGTTTCGCCCTAATCATC
Found at i:4017001 original size:31 final size:31
Alignment explanation
Indices: 4016905--4017180 Score: 98
Period size: 31 Copynumber: 8.7 Consensus size: 31
4016895 TTCGCCTTGG
* * * *
4016905 TCATTTTTTTGACTAATAGCTTTCACCCCAA
1 TCATCTTTTTGACTAATAGGTTTCGCCCTAA
* * *
4016936 TAATCTTTTTTGA-TTATCATGGTTTCGCCTTAA
1 TCATC-TTTTTGACTAAT-A-GGTTTCGCCCTAA
*
4016969 TCATCTTTTTGACTAATAGGTTTTGCCCTAA
1 TCATCTTTTTGACTAATAGGTTTCGCCCTAA
* * **
4017000 TCGTCTTCTTTGACT-ATCATGGTTTCACCCTGG
1 TCATCTT-TTTGACTAAT-A-GGTTTCGCCCTAA
* * * * **
4017033 TGAAT-TTTTTCGATTGA-AGGTTTC-ACCTTG
1 T-CATCTTTTT-GACTAATAGGTTTCGCCCTAA
* ** * * *
4017063 TCATCTTTTTTACTAATAAATTTCACCTTAG
1 TCATCTTTTTGACTAATAGGTTTCGCCCTAA
* * * ** * *
4017094 TCATCTTTTTTTACT-ATCGTGGTTCTACTTGGA
1 TCATC-TTTTTGACTAATAG-GTTTCGCCCT-AA
* *
4017127 TCAATCTTTTCGACCAA-AGGTTTCGCCCTAA
1 TC-ATCTTTTTGACTAATAGGTTTCGCCCTAA
4017158 TCATCTTTTTGACTAATAGGTTT
1 TCATCTTTTTGACTAATAGGTTT
4017181 TACCGTTATC
Statistics
Matches: 177, Mismatches: 49, Indels: 38
0.67 0.19 0.14
Matches are distributed among these distances:
29 5 0.03
30 27 0.15
31 50 0.28
32 49 0.28
33 40 0.23
34 6 0.03
ACGTcount: A:0.21, C:0.20, G:0.13, T:0.46
Consensus pattern (31 bp):
TCATCTTTTTGACTAATAGGTTTCGCCCTAA
Found at i:4017016 original size:159 final size:158
Alignment explanation
Indices: 4016831--4017172 Score: 377
Period size: 159 Copynumber: 2.2 Consensus size: 158
4016821 TTTGTAGAGG
* ** * *
4016831 TTTGCCCTAATTGTCTTCTTTGACTATCATGGTTTTGCCTTAGTCAATCTTTCCTATTGAAGGCT
1 TTTGCCCTAATCGTCTTCTTTGACTATCATGGTTTCACCCTAGTCAATCTTTCCGATTGAAGGCT
* ** *
4016896 TCGCCTTGGTCAT-TTTTTTGACTAATAGCTTTCACCCCAATAATCTTTTTTGATTATCATGGTT
66 TCACCTT-GTCATCTTTTTT-ACTAATAAATTTCACCCCAATAATCTTTTTTGACTATCATGG-T
* * *
4016960 TCGCCTT-AATC-ATCTTTTTGACTAATAGGT
128 TCGACTTGAATCAATCTTTTCGACCAA-AGGT
* * * * *
4016990 TTTGCCCTAATCGTCTTCTTTGACTATCATGGTTTCACCCTGGTGAATTTTTTCGATTGAAGGTT
1 TTTGCCCTAATCGTCTTCTTTGACTATCATGGTTTCACCCTAGTCAATCTTTCCGATTGAAGGCT
** * * * * *
4017055 TCACCTTGTCATCTTTTTTACTAATAAATTTCACCTTAGTCATCTTTTTTTACTATCGTGGTTCT
66 TCACCTTGTCATCTTTTTTACTAATAAATTTCACCCCAATAATCTTTTTTGACTATCATGGTTCG
*
4017120 ACTTGGATCAATCTTTTCGACCAAAGGT
131 ACTTGAATCAATCTTTTCGACCAAAGGT
* *
4017148 TTCGCCCTAATCATCTT-TTTGACTA
1 TTTGCCCTAATCGTCTTCTTTGACTA
4017173 ATAGGTTTTA
Statistics
Matches: 153, Mismatches: 27, Indels: 8
0.81 0.14 0.04
Matches are distributed among these distances:
157 14 0.09
158 60 0.39
159 79 0.52
ACGTcount: A:0.20, C:0.21, G:0.13, T:0.45
Consensus pattern (158 bp):
TTTGCCCTAATCGTCTTCTTTGACTATCATGGTTTCACCCTAGTCAATCTTTCCGATTGAAGGCT
TCACCTTGTCATCTTTTTTACTAATAAATTTCACCCCAATAATCTTTTTTGACTATCATGGTTCG
ACTTGAATCAATCTTTTCGACCAAAGGT
Found at i:4017079 original size:94 final size:94
Alignment explanation
Indices: 4016969--4017417 Score: 327
Period size: 94 Copynumber: 4.8 Consensus size: 94
4016959 TTCGCCTTAA
** * *
4016969 TCATCTTTTTGACTAATAGGTTTTGCCCTAATCGTCTTCTTTGACTATCATGGTTTCACCCTGGT
1 TCATCTTTTTGACTAATAGGTTTCACCTTAATCGTCTTCTTTGACTATCATGGTTTCACCTTGGT
* * *
4017034 GAATTTTTTCGATTGAAGGTTTCACCTTG
66 CAATCTTTTCGACTGAAGGTTTCACCTTG
* ** * * * * *
4017063 TCATCTTTTTTACTAATAAATTTCACCTTAGTCATCTTTTTTTACTATCGTGG-TTCTA-CTTGG
1 TCATCTTTTTGACTAATAGGTTTCACCTTAATCGTCTTCTTTGACTATCATGGTTTC-ACCTTGG
** * **
4017126 ATCAATCTTTTCGACCAAAGGTTTCGCCCTAA
65 -TCAATCTTTTCGACTGAAGGTTTC-ACCTTG
* * * * ***
4017158 TCATCTTTTTGACTAATAGGTTTTACCGTT-ATCGTCTTCTATGACTATTAT-ATTTTGTCTTGG
1 TCATCTTTTTGACTAATAGGTTTCACC-TTAATCGTCTTCTTTGACTATCATGGTTTCACCTTGG
* * **
4017221 TCAATCTTTCCAACTGAAGGTTTTGCCTTAG
65 TCAATCTTTTCGACTGAAGGTTTCACCTT-G
* * * * *
4017252 TCATCTCTTTGACTAGTAGGTTTCACCTTAGTCGTTTTCTTTGACTATCATGGTTTCACCTTAGT
1 TCATCTTTTTGACTAATAGGTTTCACCTTAATCGTCTTCTTTGACTATCATGGTTTCACCTTGGT
* * * * * *
4017317 TAATC-TTTCTAACTAAAGATTTCGCCTTAA
66 CAATCTTTTC-GACTGAAGGTTTCACCTT-G
* ** ** * * *
4017347 TCATCTTTTCGACTAATAGGTTTCGTC-TGGTCATCTTTTTTGACTATCATGGTTTCATCC-TAG
1 TCATCTTTTTGACTAATAGGTTTCACCTTAATCGTCTTCTTTGACTATCATGGTTTCA-CCTTGG
4017410 TCAATCTT
65 TCAATCTT
4017418 CTCAATTTAT
Statistics
Matches: 273, Mismatches: 70, Indels: 23
0.75 0.19 0.06
Matches are distributed among these distances:
93 12 0.04
94 159 0.58
95 100 0.37
96 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.45
Consensus pattern (94 bp):
TCATCTTTTTGACTAATAGGTTTCACCTTAATCGTCTTCTTTGACTATCATGGTTTCACCTTGGT
CAATCTTTTCGACTGAAGGTTTCACCTTG
Found at i:4017171 original size:189 final size:190
Alignment explanation
Indices: 4016956--4017417 Score: 479
Period size: 189 Copynumber: 2.4 Consensus size: 190
4016946 TGATTATCAT
4016956 GGTTTCGCCTTAATCATCTTTTTGACTAATAGGTTTTGCCCTAATCGTCTTCTTTGACTATCATG
1 GGTTTCGCCTTAATCATCTTTTTGACTAATAGGTTTTGCCCTAATCGTCTTCTTTGACTATCATG
* * * * * * *
4017021 GTTTCACCCTGGTGAATTTTTTCGATTGAAGGTTTCACCTT-GTCATCTTTTTTACTAATAAATT
66 GTTTCACCCTGGTCAATCTTTCCAACTGAAGGTTTCACCTTAGTCATCTCTTTGACTAATAAATT
* * * *
4017085 TCACCTTAGTCATCTTT-TTTTACTATCGTGG-TTCTA-CTTGGATCAATCTTT-TCGACCAAA
131 TCACCTTAGTCAT-TTTCTTTGACTATCATGGTTTC-ACCTTAG-TCAATCTTTCT-AACCAAA
* * * * * *
4017145 GGTTTCGCCCTAATCATCTTTTTGACTAATAGGTTTTACCGTTATCGTCTTCTATGACTATTAT-
1 GGTTTCGCCTTAATCATCTTTTTGACTAATAGGTTTTGCCCTAATCGTCTTCTTTGACTATCATG
* *** * ** * **
4017209 ATTTTGTCTTGGTCAATCTTTCCAACTGAAGGTTTTGCCTTAGTCATCTCTTTGACTAGTAGGTT
66 GTTTCACCCTGGTCAATCTTTCCAACTGAAGGTTTCACCTTAGTCATCTCTTTGACTAATAAATT
* * *
4017274 TCACCTTAGTCGTTTTCTTTGACTATCATGGTTTCACCTTAGTTAATCTTTCTAACTAAA
131 TCACCTTAGTCATTTTCTTTGACTATCATGGTTTCACCTTAGTCAATCTTTCTAACCAAA
* * * * ** * *
4017334 GATTTCGCCTTAATCATCTTTTCGACTAATAGGTTTCG-TCTGGTCATCTTTTTTGACTATCATG
1 GGTTTCGCCTTAATCATCTTTTTGACTAATAGGTTTTGCCCTAATCGTCTTCTTTGACTATCATG
* *
4017398 GTTTCATCCTAGTCAATCTT
66 GTTTCACCCTGGTCAATCTT
4017418 CTCAATTTAT
Statistics
Matches: 219, Mismatches: 48, Indels: 12
0.78 0.17 0.04
Matches are distributed among these distances:
188 49 0.22
189 162 0.74
190 8 0.04
ACGTcount: A:0.20, C:0.21, G:0.14, T:0.45
Consensus pattern (190 bp):
GGTTTCGCCTTAATCATCTTTTTGACTAATAGGTTTTGCCCTAATCGTCTTCTTTGACTATCATG
GTTTCACCCTGGTCAATCTTTCCAACTGAAGGTTTCACCTTAGTCATCTCTTTGACTAATAAATT
TCACCTTAGTCATTTTCTTTGACTATCATGGTTTCACCTTAGTCAATCTTTCTAACCAAA
Found at i:4017273 original size:31 final size:32
Alignment explanation
Indices: 4017246--4017316 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 32
4017236 GAAGGTTTTG
4017246 CCTTAGTC-ATCTCTTTGACTAGTAGGTTTCA
1 CCTTAGTCGATCTCTTTGACTAGTAGGTTTCA
* *
4017277 CCTTAGTCGTTTTCTTTGACTA-TCATGGTTTCA
1 CCTTAGTCGATCTCTTTGACTAGT-A-GGTTTCA
4017310 CCTTAGT
1 CCTTAGT
4017317 TAATCTTTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 9 0.26
32 12 0.34
33 14 0.40
ACGTcount: A:0.17, C:0.23, G:0.15, T:0.45
Consensus pattern (32 bp):
CCTTAGTCGATCTCTTTGACTAGTAGGTTTCA
Found at i:4017371 original size:31 final size:31
Alignment explanation
Indices: 4017130--4017371 Score: 77
Period size: 31 Copynumber: 7.7 Consensus size: 31
4017120 ACTTGGATCA
* *
4017130 ATCTTTTCGACCAA-AGGTTTCGCCCTAATC
1 ATCTTTTCGACTAATAGGTTTCGCCTTAATC
* **
4017160 ATCTTTTTGACTAATAGGTTTTACCGTT-ATC
1 ATCTTTTCGACTAATAGGTTTCGCC-TTAATC
* * ** * * **
4017191 GTCTTCTAT-GACTATTATATTTTGTCTTGGTC
1 ATCTT-T-TCGACTAATAGGTTTCGCCTTAATC
* * * * *
4017223 AATCTTTCCAACTGA-AGGTTTTGCCTTAGTC
1 -ATCTTTTCGACTAATAGGTTTCGCCTTAATC
* * *
4017254 ATCTCTTT-GACTAGTAGGTTTCACCTTAGTC
1 ATCT-TTTCGACTAATAGGTTTCGCCTTAATC
* * * * * *
4017285 GTTTTCTTTGACT-ATCATGGTTTCACCTTAGTTA
1 ATCTT-TTCGACTAAT-A-GGTTTCGCCTTA-ATC
* *
4017319 ATC-TTTCTAACTAA-AGATTTCGCCTTAATC
1 ATCTTTTC-GACTAATAGGTTTCGCCTTAATC
4017349 ATCTTTTCGACTAATAGGTTTCG
1 ATCTTTTCGACTAATAGGTTTCG
4017372 TCTGGTCATC
Statistics
Matches: 152, Mismatches: 42, Indels: 35
0.66 0.18 0.15
Matches are distributed among these distances:
30 29 0.19
31 71 0.47
32 28 0.18
33 21 0.14
34 3 0.02
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.44
Consensus pattern (31 bp):
ATCTTTTCGACTAATAGGTTTCGCCTTAATC
Found at i:4018876 original size:28 final size:28
Alignment explanation
Indices: 4018821--4018886 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 28
4018811 TTCTTATGGT
*
4018821 ATTTTAATTAGAATTTTACATGATT-AA
1 ATTTTAATTAGAATTTTACATCATTAAA
4018848 ATTTCTAATT-GAATTTTATCA-CATATAAA
1 ATTT-TAATTAGAATTTTA-CATCAT-TAAA
4018877 ATTTTAATTA
1 ATTTTAATTA
4018887 ACCCCTTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
27 14 0.42
28 13 0.39
29 6 0.18
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.48
Consensus pattern (28 bp):
ATTTTAATTAGAATTTTACATCATTAAA
Found at i:4022842 original size:46 final size:46
Alignment explanation
Indices: 4022789--4022877 Score: 151
Period size: 46 Copynumber: 1.9 Consensus size: 46
4022779 TGGAACCATA
*
4022789 ATTCATGTGCTGCCTGGAGCATCACTTCCAGCAGGTGGCTTGCATG
1 ATTCATGTGCTGCCCGGAGCATCACTTCCAGCAGGTGGCTTGCATG
* *
4022835 ATTCATGTGCTTCCCGGAGCATCACTTCCAGGAGGTGGCTTGC
1 ATTCATGTGCTGCCCGGAGCATCACTTCCAGCAGGTGGCTTGC
4022878 GATTCAGATA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.17, C:0.27, G:0.28, T:0.28
Consensus pattern (46 bp):
ATTCATGTGCTGCCCGGAGCATCACTTCCAGCAGGTGGCTTGCATG
Found at i:4025905 original size:28 final size:28
Alignment explanation
Indices: 4025868--4025945 Score: 81
Period size: 28 Copynumber: 2.8 Consensus size: 28
4025858 TATTTAATAT
* *
4025868 ATTTTTATTTATAATT-TTATCAAATTTA
1 ATTTATATTTAT-ATTATTATAAAATTTA
4025896 ATTTATATTTATATTATTATAAAATTTA
1 ATTTATATTTATATTATTATAAAATTTA
* *
4025924 TTATTAAATTTA-A-TATTATAAA
1 AT-TTATATTTATATTATTATAAA
4025946 TTAGGTAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
27 12 0.27
28 24 0.55
29 8 0.18
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (28 bp):
ATTTATATTTATATTATTATAAAATTTA
Found at i:4026503 original size:17 final size:17
Alignment explanation
Indices: 4026470--4026519 Score: 75
Period size: 16 Copynumber: 2.9 Consensus size: 17
4026460 GTATATTTTT
4026470 TATTAAATATTTA-TTA
1 TATTAAATATTTATTTA
*
4026486 TATTTAATATTTATTTA
1 TATTAAATATTTATTTA
4026503 TATTAAATTATTTATTT
1 TATTAAA-TATTTATTT
4026520 TTTTAATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 12 0.40
17 9 0.30
18 9 0.30
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTAAATATTTATTTA
Found at i:4026518 original size:22 final size:22
Alignment explanation
Indices: 4026493--4026540 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
4026483 TTATATTTAA
4026493 TATTTATTT-ATATTAAATTATT
1 TATTTATTTAAT-TTAAATTATT
* *
4026515 TATTTTTTTAATTTAATTTATT
1 TATTTATTTAATTTAAATTATT
4026537 TATT
1 TATT
4026541 CAATTAATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 21 0.91
23 2 0.09
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (22 bp):
TATTTATTTAATTTAAATTATT
Found at i:4026525 original size:17 final size:16
Alignment explanation
Indices: 4026466--4026525 Score: 59
Period size: 16 Copynumber: 3.6 Consensus size: 16
4026456 AAATGTATAT
4026466 TTTTTATTAAATATTTA
1 TTTTT-TTAAATATTTA
*
4026483 TTATATTT-AATATTTA
1 TT-TTTTTAAATATTTA
*
4026499 TTTATATTAAATTATTTA
1 TTT-TTTTAAA-TATTTA
4026517 TTTTTTTAA
1 TTTTTTTAA
4026526 TTTAATTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 1 0.03
16 12 0.34
17 11 0.31
18 11 0.31
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTTTTAAATATTTA
Found at i:4026533 original size:18 final size:18
Alignment explanation
Indices: 4026453--4026539 Score: 78
Period size: 18 Copynumber: 5.0 Consensus size: 18
4026443 TTATTATTCA
4026453 ATTAAATGTATATT-TTT-T
1 ATTAAAT-TAT-TTATTTAT
4026471 ATTAAA-TATTTA-TTAT
1 ATTAAATTATTTATTTAT
*
4026487 ATTTAA-TATTTATTTAT
1 ATTAAATTATTTATTTAT
4026504 ATTAAATTATTTATTT-T
1 ATTAAATTATTTATTTAT
* *
4026521 TTTAATTTAATTTATTTAT
1 ATTAAATT-ATTTATTTAT
4026540 TCAATTAATC
Statistics
Matches: 59, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
15 4 0.07
16 15 0.25
17 16 0.27
18 23 0.39
19 1 0.02
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (18 bp):
ATTAAATTATTTATTTAT
Found at i:4026994 original size:19 final size:19
Alignment explanation
Indices: 4026950--4026995 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
4026940 ATAAAATAAA
4026950 AATTTAA-ATAATGATTAT
1 AATTTAATATAATGATTAT
* *
4026968 AATATAATATTATGATTAT
1 AATTTAATATAATGATTAT
*
4026987 TATTTAATA
1 AATTTAATA
4026996 ATTTTAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (19 bp):
AATTTAATATAATGATTAT
Done.