Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A10
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: 110302803
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1825971 characters in sequence are not A, C, G, or T
File 268 of 343
Found at i:88773624 original size:40 final size:40
Alignment explanation
Indices: 88773452--88773617 Score: 271
Period size: 40 Copynumber: 4.2 Consensus size: 40
88773442 AACCCAAGTA
* *
88773452 CCTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
88773491 CCTTCGGGACTTAGCCCAGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
88773531 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
88773571 CCTTCGAGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
88773611 CCTTCGG
1 CCTTCGG
88773618 ATCTTAGTCC
Statistics
Matches: 118, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 13 0.11
40 105 0.89
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:88784951 original size:25 final size:25
Alignment explanation
Indices: 88784923--88784971 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
88784913 CCGGAGGACC
* *
88784923 AATCATATAACTCATGATAATGATT
1 AATCACATAACTCATCATAATGATT
* *
88784948 AATCACATAATTCTTCATAATGAT
1 AATCACATAACTCATCATAATGAT
88784972 AATAATAAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.43, C:0.14, G:0.06, T:0.37
Consensus pattern (25 bp):
AATCACATAACTCATCATAATGATT
Found at i:88791544 original size:56 final size:56
Alignment explanation
Indices: 88791477--88791587 Score: 204
Period size: 56 Copynumber: 2.0 Consensus size: 56
88791467 AATTTTTGAA
*
88791477 TTTATTCCATGTGTTTTTCTACTTTTATATATTGTATATTTTGAAACATTTTATAT
1 TTTATTACATGTGTTTTTCTACTTTTATATATTGTATATTTTGAAACATTTTATAT
*
88791533 TTTATTACATGTGTTTTTGTACTTTTATATATTGTATATTTTGAAACATTTTATA
1 TTTATTACATGTGTTTTTCTACTTTTATATATTGTATATTTTGAAACATTTTATA
88791588 GTTGTATGTC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.26, C:0.07, G:0.08, T:0.59
Consensus pattern (56 bp):
TTTATTACATGTGTTTTTCTACTTTTATATATTGTATATTTTGAAACATTTTATAT
Found at i:88801759 original size:20 final size:19
Alignment explanation
Indices: 88801736--88801778 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
88801726 AATTTAGCCT
* *
88801736 TTTTTATTTTTATTTTAATA
1 TTTTTATCTTTAATTTAA-A
*
88801756 TTTTTGTCTTTAATTTAAA
1 TTTTTATCTTTAATTTAAA
88801775 TTTT
1 TTTT
88801779 ACATTCTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (19 bp):
TTTTTATCTTTAATTTAAA
Found at i:88803952 original size:46 final size:46
Alignment explanation
Indices: 88803899--88804207 Score: 206
Period size: 46 Copynumber: 6.6 Consensus size: 46
88803889 TTTGTGTGCT
* * *
88803899 AGTGTAAGACATGTCCGGGACATGCTTCGGCCACGAGATTTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACGAGATGTAAGCC
* * **
88803945 AGTGTAAGACATGTCTAGGACATGAATCGGCCTTGAGATGTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACGAGATGTAAGCC
* * *
88803991 AGT-TGAAGACATGTCTGGGACATGCATCAGCTACGAGATGT--GTC
1 AGTGT-AAGACATGTCTGGGACATGCATCGGCCACGAGATGTAAGCC
* * **
88804035 AGTGTAAGACCATGTCTGGGACATGACATCAG-CAC-AGA--TATGTT
1 AGTGTAAGA-CATGTCTGGGACATG-CATCGGCCACGAGATGTAAGCC
* * *
88804079 AGTGTAAGACCATGTCTAGGACATGGCATCAG-CACG-GATAAGTGAGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACGAGAT--GT-A-AGCC
* * * * * *
88804129 AGTGTAAGACCATGTTTGGGACATGGCGTCGGCCTCGA-TTTTGATAGTC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACGAGATGT-A-AGCC
88804178 AGTGTAAGACCATGTCTGGGACATGGCATC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATC
88804208 AACTTGATGG
Statistics
Matches: 216, Mismatches: 31, Indels: 29
0.78 0.11 0.11
Matches are distributed among these distances:
42 1 0.00
44 48 0.22
45 20 0.09
46 78 0.36
48 1 0.00
49 34 0.16
50 30 0.14
51 4 0.02
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCACGAGATGTAAGCC
Found at i:88804198 original size:49 final size:47
Alignment explanation
Indices: 88803987--88804254 Score: 189
Period size: 44 Copynumber: 5.7 Consensus size: 47
88803977 TTGAGATGTA
*
88803987 AGCCAGT-TGAAGA-CATGTCTGGGACAT-GCATCAGCTACGA--GATG
1 AGCCAGTGT-AAGACCATGTCTGGGACATGGCATCAACT-CGATGGATG
* * * * *
88804031 TGTCAGTGTAAGACCATGTCTGGGACATGACATCAGCAC-A--GAT-
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCAACTCGATGGATG
** * * *
88804074 ATGTTAGTGTAAGACCATGTCTAGGACATGGCATCAGCACGGATAAGTGA-G
1 A-GCCAGTGTAAGACCATGTCTGGGACATGGCATCAACTC-GAT--G-GATG
* * * ** *
88804125 AGCTAGTGTAAGACCATGTTTGGGACATGGCGTCGGCCTCGATTTTGAT-
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATC-AACTCGA--TGGATG
* *
88804174 AGTCAGTGTAAGACCATGTCTGGGACATGGCATCAACTTGATGGATG
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCAACTCGATGGATG
*
88804221 AGCCAGTGGAAGACCATGTCTGGGACATGGCATC
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATC
88804255 GATATTATAC
Statistics
Matches: 181, Mismatches: 26, Indels: 31
0.76 0.11 0.13
Matches are distributed among these distances:
44 48 0.27
45 16 0.09
46 12 0.07
47 32 0.18
48 4 0.02
49 32 0.18
50 31 0.17
51 5 0.03
52 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (47 bp):
AGCCAGTGTAAGACCATGTCTGGGACATGGCATCAACTCGATGGATG
Found at i:88808868 original size:12 final size:12
Alignment explanation
Indices: 88808851--88808887 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
88808841 CAATTATTGA
88808851 TATCTAATTAGG
1 TATCTAATTAGG
88808863 TATCTAATTAGG
1 TATCTAATTAGG
88808875 TATCTAATTAGG
1 TATCTAATTAGG
88808887 T
1 T
88808888 GTGTTGGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.43
Consensus pattern (12 bp):
TATCTAATTAGG
Found at i:88812895 original size:22 final size:23
Alignment explanation
Indices: 88812853--88812895 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
88812843 TTAAAAAATT
88812853 ATTTATAATTGTTGGAAATAATG
1 ATTTATAATTGTTGGAAATAATG
*
88812876 ATTTGTAATTGTT-GAAATAA
1 ATTTATAATTGTTGGAAATAA
88812896 ATTTACATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (23 bp):
ATTTATAATTGTTGGAAATAATG
Found at i:88827966 original size:21 final size:22
Alignment explanation
Indices: 88827942--88827984 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
88827932 TCATCAGATC
*
88827942 TACACCTTGAGGCATC-GGGGG
1 TACACCTTGAGGAATCAGGGGG
**
88827963 TACAGGTTGAGGAATCAGGGGG
1 TACACCTTGAGGAATCAGGGGG
88827985 GTGGGGGAGG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.23, C:0.16, G:0.42, T:0.19
Consensus pattern (22 bp):
TACACCTTGAGGAATCAGGGGG
Found at i:88834907 original size:25 final size:24
Alignment explanation
Indices: 88834875--88834933 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
88834865 TATTTATCAT
*
88834875 ATTGACTGTTCGACTAAAATATTTC
1 ATTGACTGTT-GACTAAAATATATC
* * *
88834900 ATTGACTGATTGACTGAAATGTATG
1 ATTGACTG-TTGACTAAAATATATC
88834925 ATTGACTGT
1 ATTGACTGT
88834934 CCAACTAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 1 0.03
25 26 0.90
26 2 0.07
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.39
Consensus pattern (24 bp):
ATTGACTGTTGACTAAAATATATC
Found at i:88837867 original size:42 final size:42
Alignment explanation
Indices: 88837728--88837884 Score: 191
Period size: 40 Copynumber: 3.8 Consensus size: 42
88837718 ATGACAATTT
88837728 GACTATGTATGGCACTTA--GTGT-ACGATTCGAGATAGCTTC
1 GACTATGTATGGCACTTAGTGTGTGA-GATTCGAGATAGCTTC
* *
88837768 GGCTATGTATGGCACTTAGTGTGTG-G-TTCGAGATAGCTTT
1 GACTATGTATGGCACTTAGTGTGTGAGATTCGAGATAGCTTC
* * *
88837808 GGCTATGTATGCCACTTAGTGTGTGAGATT-GAAATAGCTTC
1 GACTATGTATGGCACTTAGTGTGTGAGATTCGAGATAGCTTC
*
88837849 AACTATGTATTGGCACTTAGTGTGTGAGAATTCGAG
1 GACTATGTA-TGGCACTTAGTGTGTGAG-ATTCGAG
88837885 TGTTCGACAT
Statistics
Matches: 100, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
40 54 0.54
41 18 0.18
42 23 0.23
43 3 0.03
44 2 0.02
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (42 bp):
GACTATGTATGGCACTTAGTGTGTGAGATTCGAGATAGCTTC
Found at i:88837872 original size:80 final size:79
Alignment explanation
Indices: 88837725--88837874 Score: 187
Period size: 82 Copynumber: 1.8 Consensus size: 79
88837715 TTGATGACAA
* * **
88837725 TTTGACTATGTATGGCACTTAGTGTACGATTCGAGATAGCTTCGGCTATGTATGGCACTTAGTGT
1 TTTGACTATGTATGCCACTTAGTGTACGATTCGAAATAGCTTCAACTATGTATGGCACTTAG-GT
88837790 GTGGTTCGAGATAGC
65 GTGGTTCGAGATAGC
*
88837805 TTTGGCTATGTATGCCACTTAGTGTGTGA-GATT-GAAATAGCTTCAACTATGTATTGGCACTTA
1 TTTGACTATGTATGCCACTTA--GTGT-ACGATTCGAAATAGCTTCAACTATGTA-TGGCACTTA
88837868 GTGTGTG
62 G-GTGTG
88837875 AGAATTCGAG
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
80 19 0.31
81 17 0.28
82 24 0.39
83 1 0.02
ACGTcount: A:0.22, C:0.14, G:0.27, T:0.37
Consensus pattern (79 bp):
TTTGACTATGTATGCCACTTAGTGTACGATTCGAAATAGCTTCAACTATGTATGGCACTTAGGTG
TGGTTCGAGATAGC
Found at i:88844885 original size:24 final size:24
Alignment explanation
Indices: 88844840--88844888 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
88844830 AGTTTGAGGA
88844840 TAGAATTTGAATAGTTATTGATAG
1 TAGAATTTGAATAGTTATTGATAG
88844864 TAGAATTTGAATAGTTATTGATAG
1 TAGAATTTGAATAGTTATTGATAG
88844888 T
1 T
88844889 TAAACAAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (24 bp):
TAGAATTTGAATAGTTATTGATAG
Found at i:88845425 original size:40 final size:40
Alignment explanation
Indices: 88845381--88845564 Score: 210
Period size: 40 Copynumber: 4.5 Consensus size: 40
88845371 CAATTCGACA
*
88845381 ATGTATGGCACTTAGTGTGCGATTCGAGATA-ACTTCGGCT
1 ATGTATGGCACTTAGTGTGCGATTCGAAATAGA-TTCGGCT
* *
88845421 ATGTATGGCACTCAGTGTGTGATTCGAAATAGATTCGGCT
1 ATGTATGGCACTTAGTGTGCGATTCGAAATAGATTCGGCT
* * * * * * * *
88845461 AGGTACGGCACTTAATGTGTGATTTGAGATAGCTTCAGCT
1 ATGTATGGCACTTAGTGTGCGATTCGAAATAGATTCGGCT
*
88845501 ATGTATGACACTTAGTGTGCGAGATT-GAAATAGATTCGGCT
1 ATGTATGGCACTTAGTGTGC--GATTCGAAATAGATTCGGCT
88845542 ATGTATTGGCACTTAGTGTGCGA
1 ATGTA-TGGCACTTAGTGTGCGA
88845565 GAATTTGAGT
Statistics
Matches: 120, Mismatches: 20, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
40 84 0.70
41 18 0.15
42 18 0.15
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.33
Consensus pattern (40 bp):
ATGTATGGCACTTAGTGTGCGATTCGAAATAGATTCGGCT
Found at i:88845506 original size:80 final size:81
Alignment explanation
Indices: 88845383--88845564 Score: 235
Period size: 80 Copynumber: 2.3 Consensus size: 81
88845373 ATTCGACAAT
* * *
88845383 GTAT-GGCACTTAGTGTGCGATTCGAGATAACTTCGGCTATGTATGGCACTCAGTGT-GTGATTC
1 GTATCGGCACTTAGTGTGCGATTCGAGATAACTTCAGCTATGTATGACACTCAGTGTCGAGATT-
88845446 GAAATAGATTCGGCTAG
65 GAAATAGATTCGGCTAG
* * * * *
88845463 GTA-CGGCACTTAATGTGTGATTTGAGATAGCTTCAGCTATGTATGACACTTAGTGTGCGAGATT
1 GTATCGGCACTTAGTGTGCGATTCGAGATAACTTCAGCTATGTATGACACTCAGTGT-CGAGATT
*
88845527 GAAATAGATTCGGCTAT
65 GAAATAGATTCGGCTAG
*
88845544 GTATTGGCACTTAGTGTGCGA
1 GTATCGGCACTTAGTGTGCGA
88845565 GAATTTGAGT
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
80 48 0.56
81 19 0.22
82 19 0.22
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.32
Consensus pattern (81 bp):
GTATCGGCACTTAGTGTGCGATTCGAGATAACTTCAGCTATGTATGACACTCAGTGTCGAGATTG
AAATAGATTCGGCTAG
Found at i:88852131 original size:13 final size:13
Alignment explanation
Indices: 88852113--88852137 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
88852103 CTCGGCAGGG
88852113 ACACGCCCGTGTC
1 ACACGCCCGTGTC
88852126 ACACGCCCGTGT
1 ACACGCCCGTGT
88852138 GCGATTGCTT
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:0.16, C:0.44, G:0.24, T:0.16
Consensus pattern (13 bp):
ACACGCCCGTGTC
Found at i:88854729 original size:20 final size:20
Alignment explanation
Indices: 88854706--88854748 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
88854696 TAGCACACGA
88854706 CCTCTTCAGCCATCACACAG
1 CCTCTTCAGCCATCACACAG
* *
88854726 CCTCTTCGGCCATCACACGG
1 CCTCTTCAGCCATCACACAG
88854746 CCT
1 CCT
88854749 TGTCATGCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.19, C:0.47, G:0.14, T:0.21
Consensus pattern (20 bp):
CCTCTTCAGCCATCACACAG
Found at i:88855554 original size:43 final size:44
Alignment explanation
Indices: 88855470--88855555 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 44
88855460 TAGGCCAGCA
*
88855470 GGCCCATTTTGATATGGTTTTACAAATACTTAAATATAAGCGTT
1 GGCCCATTTTGATATGGTTTTAAAAATACTTAAATATAAGCGTT
*
88855514 GGCCCATTTTTATATGG-TTTAAAAATACTTAAATATAAGCGT
1 GGCCCATTTTGATATGGTTTTAAAAATACTTAAATATAAGCGT
88855556 ATTGAAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 24 0.60
44 16 0.40
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (44 bp):
GGCCCATTTTGATATGGTTTTAAAAATACTTAAATATAAGCGTT
Found at i:88857588 original size:49 final size:49
Alignment explanation
Indices: 88857526--88857653 Score: 141
Period size: 49 Copynumber: 2.6 Consensus size: 49
88857516 TGTTGTGTGT
* * * *
88857526 CAGTGTAAAACCTGTCTGGGGCATGGCAT-TGACACCGATAGATGAGAGC
1 CAGTGTAAGACCTGTCTGGGACATGGCATCGGAC-CCGATAGATGAAAGC
* * * * * * *
88857575 CAGTGTAAGACCTGTCTAGGACACGACATCGGGCTCGATATATGAAAGT
1 CAGTGTAAGACCTGTCTGGGACATGGCATCGGACCCGATAGATGAAAGC
88857624 CAGTGTAAGACCTGTCTGGGACATGGCATC
1 CAGTGTAAGACCTGTCTGGGACATGGCATC
88857654 CACTTTGATG
Statistics
Matches: 64, Mismatches: 14, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
49 62 0.97
50 2 0.03
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (49 bp):
CAGTGTAAGACCTGTCTGGGACATGGCATCGGACCCGATAGATGAAAGC
Found at i:88858457 original size:66 final size:66
Alignment explanation
Indices: 88858385--88858512 Score: 238
Period size: 66 Copynumber: 1.9 Consensus size: 66
88858375 ATGGGATAAA
88858385 ATTTATATAATTGGAATCCTTAATGAGTATATTTTCAAAATAAACAAACAGAAACATCATTCTAA
1 ATTTATATAATTGGAATCCTTAATGAGTATATTTTCAAAATAAACAAACAGAAACATCATTCTAA
88858450 T
66 T
* *
88858451 ATTTATATGATTGGAATCCTTAATGAGTATATTTTCAAAATAAACAAATAGAAACATCATTC
1 ATTTATATAATTGGAATCCTTAATGAGTATATTTTCAAAATAAACAAACAGAAACATCATTC
88858513 GAATCCCGTG
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.35
Consensus pattern (66 bp):
ATTTATATAATTGGAATCCTTAATGAGTATATTTTCAAAATAAACAAACAGAAACATCATTCTAA
T
Found at i:88864473 original size:49 final size:48
Alignment explanation
Indices: 88864410--88864512 Score: 136
Period size: 47 Copynumber: 2.1 Consensus size: 48
88864400 TTGTCTAGGG
* *
88864410 CATGACATCGACTTTGATAAATGAGAGCCAGTGTAAGACC-TGTTTGGGA
1 CATGGCATCCACTTTGAT--ATGAGAGCCAGTGTAAGACCATGTTTGGGA
* **
88864459 CATGGCATCCACTTTGATGTGCTAGCCAGTGTAAGACCATGTTTGGGA
1 CATGGCATCCACTTTGATATGAGAGCCAGTGTAAGACCATGTTTGGGA
88864507 CATGGC
1 CATGGC
88864513 GTCGGCATCT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
47 17 0.35
48 15 0.31
49 16 0.33
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.27
Consensus pattern (48 bp):
CATGGCATCCACTTTGATATGAGAGCCAGTGTAAGACCATGTTTGGGA
Found at i:88866169 original size:30 final size:30
Alignment explanation
Indices: 88866135--88866193 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
88866125 CATGTGAAAT
88866135 GGGATAGCTTCGGCTATCGAATGTAAAAAA
1 GGGATAGCTTCGGCTATCGAATGTAAAAAA
*
88866165 GGGATAGCTTCGGCTATCGAATGTGAAAA
1 GGGATAGCTTCGGCTATCGAATGTAAAAA
88866194 GGTTAGGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.34, C:0.14, G:0.29, T:0.24
Consensus pattern (30 bp):
GGGATAGCTTCGGCTATCGAATGTAAAAAA
Found at i:88866264 original size:32 final size:32
Alignment explanation
Indices: 88866188--88866313 Score: 164
Period size: 32 Copynumber: 3.9 Consensus size: 32
88866178 CTATCGAATG
* * *
88866188 TGAAAAGGTTAGGTATACTTTGTGTATACCACA
1 TGAAAAGGTTATGTATACTTTGTGTGTA-CACT
*
88866221 TGAAAATGTTATGTACT-CTTTGTGTGTACACT
1 TGAAAAGGTTATGTA-TACTTTGTGTGTACACT
*
88866253 TGAAAAGGTTATGTACACTTTGTGTGTACACT
1 TGAAAAGGTTATGTATACTTTGTGTGTACACT
**
88866285 TGAAAAGGAAATGTATACTTTGTGTGTAC
1 TGAAAAGGTTATGTATACTTTGTGTGTAC
88866314 CACTCAGAAA
Statistics
Matches: 82, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
32 58 0.71
33 23 0.28
34 1 0.01
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.37
Consensus pattern (32 bp):
TGAAAAGGTTATGTATACTTTGTGTGTACACT
Found at i:88885039 original size:44 final size:46
Alignment explanation
Indices: 88884935--88885054 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 46
88884925 GTTATTGTGA
88884935 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACGAGT
1 GCTAGTGTAAGACCATGTCTGGGACAT-GCATCGGCA-TGAGACGAGT
* * *
88884983 ACTAGTGTAAGA-CATGTATGAGACATGCATCGGC-T-ACGA-GATGT
1 GCTAGTGTAAGACCATGTCTGGGACATGCATCGGCATGA-GACGA-GT
88885027 GCTAGTGTAAGACCATGTCTGGGACATG
1 GCTAGTGTAAGACCATGTCTGGGACATG
88885055 GAATCAGCCT
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
43 3 0.05
44 16 0.25
45 13 0.21
46 8 0.13
47 12 0.19
48 11 0.17
ACGTcount: A:0.28, C:0.17, G:0.31, T:0.24
Consensus pattern (46 bp):
GCTAGTGTAAGACCATGTCTGGGACATGCATCGGCATGAGACGAGT
Found at i:88889430 original size:34 final size:34
Alignment explanation
Indices: 88889392--88889457 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
88889382 CAAATTTCTG
88889392 AGTGAATCTTTTAACAACTAGTTTTACCTTATTC
1 AGTGAATCTTTTAACAACTAGTTTTACCTTATTC
*
88889426 AGTGAATCTTTTAACAATTAGTTTTACCTTAT
1 AGTGAATCTTTTAACAACTAGTTTTACCTTAT
88889458 ACTTTTGAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.30, C:0.15, G:0.09, T:0.45
Consensus pattern (34 bp):
AGTGAATCTTTTAACAACTAGTTTTACCTTATTC
Found at i:88890777 original size:3 final size:3
Alignment explanation
Indices: 88890771--88890796 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
88890761 GTGGTGGTTG
88890771 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
88890797 AATGTAGTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:88893721 original size:27 final size:24
Alignment explanation
Indices: 88893693--88893748 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 24
88893683 AGTTAATAAA
88893693 TTTTCTTTGAGTTTTTCTTTTCAAGAAT
1 TTTTC-TTGAG-TTTTCTTTT--AGAAT
88893721 TTTTCTTGAGTTTTCTTTTAGAAT
1 TTTTCTTGAGTTTTCTTTTAGAAT
88893745 TTTT
1 TTTT
88893749 TTTTCTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
24 9 0.32
26 9 0.32
27 5 0.18
28 5 0.18
ACGTcount: A:0.16, C:0.09, G:0.11, T:0.64
Consensus pattern (24 bp):
TTTTCTTGAGTTTTCTTTTAGAAT
Found at i:88897447 original size:12 final size:12
Alignment explanation
Indices: 88897421--88897460 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
88897411 GAGTGGTCCA
* *
88897421 TTTGTTTTCTGT
1 TTTGTTTTTTTT
88897433 TTTGTTTTTTTT
1 TTTGTTTTTTTT
*
88897445 TTTATTTTTTTT
1 TTTGTTTTTTTT
88897457 TTTG
1 TTTG
88897461 AAGTAGTTGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.03, C:0.03, G:0.10, T:0.85
Consensus pattern (12 bp):
TTTGTTTTTTTT
Found at i:88901463 original size:20 final size:20
Alignment explanation
Indices: 88901438--88901487 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
88901428 TGGCTTAAAA
88901438 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
88901458 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
88901475 GTGGTAGTGGATT
1 TTGGTAGTGGATT
88901488 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:88906102 original size:20 final size:20
Alignment explanation
Indices: 88906077--88906126 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
88906067 TGGCTTAAAA
88906077 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
88906097 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
88906114 GTGGTAGTGGATT
1 TTGGTAGTGGATT
88906127 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:88907395 original size:18 final size:19
Alignment explanation
Indices: 88907372--88907408 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
88907362 TTGCTATTTT
88907372 TATA-TTACAAAATATCTA
1 TATATTTACAAAATATCTA
88907390 TATATTTTACAAAATATCT
1 TATA-TTTACAAAATATCT
88907409 GCTCTCACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
20 13 0.76
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (19 bp):
TATATTTACAAAATATCTA
Found at i:88921672 original size:15 final size:15
Alignment explanation
Indices: 88921649--88921687 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
88921639 ACGAAGTACG
*
88921649 TTAATTAATGCAACA
1 TTAAGTAATGCAACA
88921664 TTAAGTAATGCAACA
1 TTAAGTAATGCAACA
88921679 TTAAGTAAT
1 TTAAGTAAT
88921688 AATAGAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.33
Consensus pattern (15 bp):
TTAAGTAATGCAACA
Found at i:88922402 original size:31 final size:31
Alignment explanation
Indices: 88922367--88922426 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
88922357 TTGATGTCAT
*
88922367 TCCCTAATACGTATTTCTAGATCAAACATTG
1 TCCCTAATACATATTTCTAGATCAAACATTG
*
88922398 TCCCTAATACATATTTCTAGATCGAACAT
1 TCCCTAATACATATTTCTAGATCAAACAT
88922427 CGACCCACCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.33, C:0.23, G:0.08, T:0.35
Consensus pattern (31 bp):
TCCCTAATACATATTTCTAGATCAAACATTG
Found at i:88923330 original size:126 final size:126
Alignment explanation
Indices: 88923029--88923550 Score: 692
Period size: 126 Copynumber: 4.2 Consensus size: 126
88923019 TAAGGCCAAA
* * * ** *
88923029 CAGGAACTACTGTAAAAAAAGAGCATACACATGGGAGCTTTTTTCAGTAATTTTGCT-ACAATGC
1 CAGGAACTACTGTAGAAAAAGAGCGTCCATGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGC
* * *
88923093 ATCCTGCTTGAAGCATTTTTGACACTATTTTTTTAGAACCGTCTTCTCAAAATTATTTTTT
66 ATCCTGCTTGAAGCATTTTTGACACTATTTTTTCAGAACCATCTTTTCAAAATTATTTTTT
* *
88923154 -AGGAATTACTGTAGAAAAAGAGCGTCCATGTGGGAGCTTTTTTCAATAATTTTGCTGACAGTGC
1 CAGGAACTACTGTAGAAAAAGAGCGTCCATGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGC
* *
88923218 ATCCTGCTTGAAGCATTTTTGACACTATTTTTTCATAATCATCTTTTCAAAATTATTTTTT
66 ATCCTGCTTGAAGCATTTTTGACACTATTTTTTCAGAACCATCTTTTCAAAATTATTTTTT
* * *
88923279 TAGGAACTACTGTAGAAAAAGAGCGTCCATGTGAGAGCTTTTTTCAGTAATTTTGCTAACAGTGC
1 CAGGAACTACTGTAGAAAAAGAGCGTCCATGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGC
* *
88923344 ATCTTGCTTGAAGCATTTTTGACACTATTTTTTCAGAACCGTCTTCTT-AAAATTATTTTTT
66 ATCCTGCTTGAAGCATTTTTGACACTATTTTTTCAGAACCATCTT-TTCAAAATTATTTTTT
* * * * * *
88923405 CAAGAACTACTGTAGAAAAAAAGTGTCCACGTGGGAGCTTTTTTCAGTACTTTTGCTGATAGTGC
1 CAGGAACTACTGTAGAAAAAGAGCGTCCATGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGC
* * * * * * **
88923470 ATCCTACTTGAACCGTTTTTGACATTATCTTTTCAGAACTAT-TTTCTCAAAATTAAATTTT
66 ATCCTGCTTGAAGCATTTTTGACACTATTTTTTCAGAACCATCTTT-TCAAAATTATTTTTT
* *
88923531 CAGAAACTACTGTAAAAAAA
1 CAGGAACTACTGTAGAAAAA
88923551 ATAAAAAATA
Statistics
Matches: 349, Mismatches: 43, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
124 50 0.14
125 65 0.19
126 232 0.66
127 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.38
Consensus pattern (126 bp):
CAGGAACTACTGTAGAAAAAGAGCGTCCATGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGC
ATCCTGCTTGAAGCATTTTTGACACTATTTTTTCAGAACCATCTTTTCAAAATTATTTTTT
Found at i:88923693 original size:33 final size:32
Alignment explanation
Indices: 88923640--88923705 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 32
88923630 AAACACAAAA
88923640 TTATTTTTTAAAAGACTAAACCCTAATTTAAT
1 TTATTTTTTAAAAGACTAAACCCTAATTTAAT
88923672 TTATTTTTTAAAA-ACTATAAACCCTAATTTAAT
1 TTATTTTTTAAAAGAC--TAAACCCTAATTTAAT
88923705 T
1 T
88923706 AATTAATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
31 2 0.06
32 13 0.41
33 17 0.53
ACGTcount: A:0.41, C:0.12, G:0.02, T:0.45
Consensus pattern (32 bp):
TTATTTTTTAAAAGACTAAACCCTAATTTAAT
Found at i:88929182 original size:11 final size:11
Alignment explanation
Indices: 88929166--88929190 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
88929156 AGCTTTCATG
88929166 ATTAATTAATT
1 ATTAATTAATT
88929177 ATTAATTAATT
1 ATTAATTAATT
88929188 ATT
1 ATT
88929191 TTAACATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATTAATTAATT
Found at i:88931623 original size:25 final size:24
Alignment explanation
Indices: 88931594--88931645 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
88931584 ATAATGGATA
* *
88931594 TTAATTAATAATTGTTTAAAAATAT
1 TTAATT-ATAAATGTTTAAAAAAAT
*
88931619 TTAATTTTAAATGTTTAAAAAAAT
1 TTAATTATAAATGTTTAAAAAAAT
88931643 TTA
1 TTA
88931646 GATGCAAAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
TTAATTATAAATGTTTAAAAAAAT
Found at i:88934702 original size:15 final size:15
Alignment explanation
Indices: 88934668--88934710 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
88934658 TTTAGTCATT
* *
88934668 TTTATTTTTATTGTAT
1 TTTATTTTT-TTATAG
88934684 TTTATTTTTTTATAG
1 TTTATTTTTTTATAG
*
88934699 TTTAATTTTTTA
1 TTTATTTTTTTA
88934711 GTTTTCTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (15 bp):
TTTATTTTTTTATAG
Found at i:88938650 original size:17 final size:17
Alignment explanation
Indices: 88938623--88938688 Score: 75
Period size: 17 Copynumber: 3.9 Consensus size: 17
88938613 TACCATTTGT
*
88938623 TTTATTTTATTATTGTTA
1 TTTAGTTTATTATT-TTA
88938641 TTTA-TTTATTATTCTTA
1 TTTAGTTTATTATT-TTA
88938658 -TTAGTTATATTATTTTA
1 TTTAGTT-TATTATTTTA
88938675 TTT-GTTTATTATTT
1 TTTAGTTTATTATTT
88938689 ATGGTTATTT
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
16 11 0.25
17 20 0.45
18 13 0.30
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.71
Consensus pattern (17 bp):
TTTAGTTTATTATTTTA
Found at i:88938711 original size:25 final size:22
Alignment explanation
Indices: 88938623--88938711 Score: 74
Period size: 25 Copynumber: 3.9 Consensus size: 22
88938613 TACCATTTGT
* *
88938623 TTTATTTTATTATTGTTATTTA
1 TTTATTTTATTTTTATTATTTA
* *
88938645 TTTA--TTATTCTTATTAGTTA
1 TTTATTTTATTTTTATTATTTA
88938665 TATTATTTTATTTGTTTATTATTTA
1 T-TTATTTTA-TT-TTTATTATTTA
88938690 TGGTTATTTTATTTTTAGTTAT
1 T--TTATTTTATTTTTA-TTAT
88938712 ATGTATACAT
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
20 14 0.26
21 3 0.06
22 4 0.07
23 3 0.06
24 6 0.11
25 16 0.30
26 8 0.15
ACGTcount: A:0.22, C:0.01, G:0.07, T:0.70
Consensus pattern (22 bp):
TTTATTTTATTTTTATTATTTA
Found at i:88944574 original size:32 final size:32
Alignment explanation
Indices: 88944538--88944601 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
88944528 CCCATCATAG
* * *
88944538 TATCAATTGGGCCTAGCCCATCTCATAATCAA
1 TATCAATTGGACCTAGCCCATATCAGAATCAA
88944570 TATCAATTGGACCTAGCCCATATCAGAATCAA
1 TATCAATTGGACCTAGCCCATATCAGAATCAA
88944602 ACCCATATGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.27
Consensus pattern (32 bp):
TATCAATTGGACCTAGCCCATATCAGAATCAA
Found at i:88944942 original size:27 final size:27
Alignment explanation
Indices: 88944906--88944985 Score: 108
Period size: 27 Copynumber: 3.0 Consensus size: 27
88944896 CGAGGGCAAA
* * *
88944906 CAGTCATTTTACCCTACAGGGGTATTT
1 CAGTAATTTTACACTACAAGGGTATTT
88944933 CAGTAATTTTACACTACAAGGGTATTT
1 CAGTAATTTTACACTACAAGGGTATTT
*
88944960 CAGTAATTTTACA-AACCAAGGGTATT
1 CAGTAATTTTACACTA-CAAGGGTATT
88944986 AACGACCTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
26 1 0.02
27 47 0.98
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35
Consensus pattern (27 bp):
CAGTAATTTTACACTACAAGGGTATTT
Found at i:88949193 original size:52 final size:52
Alignment explanation
Indices: 88949131--88949234 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
88949121 AGAGTATGGT
88949131 CACAAGCTGAAAGAAAAGGTTAGAATCGAGATTGAATTGAAGAAATCACCTA
1 CACAAGCTGAAAGAAAAGGTTAGAATCGAGATTGAATTGAAGAAATCACCTA
88949183 CACAAGCTGAAAGAAAAGGTTAGAATCGAGATTGAATTGAAGAAATCACCTA
1 CACAAGCTGAAAGAAAAGGTTAGAATCGAGATTGAATTGAAGAAATCACCTA
88949235 ACTAGAAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.46, C:0.13, G:0.21, T:0.19
Consensus pattern (52 bp):
CACAAGCTGAAAGAAAAGGTTAGAATCGAGATTGAATTGAAGAAATCACCTA
Found at i:88956765 original size:29 final size:27
Alignment explanation
Indices: 88956732--88956823 Score: 96
Period size: 29 Copynumber: 3.3 Consensus size: 27
88956722 TGTAAATAGT
88956732 GGCCATATGAATGTGATTTGGTCCTAATG
1 GGCCATATGAATGTGA-TTGGT-CTAATG
* * *
88956761 GGCCACATAAATGTGAATGGGTCTAATG
1 GGCCATATGAATGTG-ATTGGTCTAATG
* *
88956789 GGCCATATGGAA-GAGATTGGTCTAGTG
1 GGCCATAT-GAATGTGATTGGTCTAATG
88956816 GGCCATAT
1 GGCCATAT
88956824 ATATAGGTAT
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
27 18 0.34
28 15 0.28
29 19 0.36
30 1 0.02
ACGTcount: A:0.27, C:0.14, G:0.30, T:0.28
Consensus pattern (27 bp):
GGCCATATGAATGTGATTGGTCTAATG
Found at i:88965743 original size:34 final size:34
Alignment explanation
Indices: 88965705--88965778 Score: 148
Period size: 34 Copynumber: 2.2 Consensus size: 34
88965695 GGGCTAGTGA
88965705 GAAATGGTCTTTTTGGTAAGTTAGTTTTGTGGTT
1 GAAATGGTCTTTTTGGTAAGTTAGTTTTGTGGTT
88965739 GAAATGGTCTTTTTGGTAAGTTAGTTTTGTGGTT
1 GAAATGGTCTTTTTGGTAAGTTAGTTTTGTGGTT
88965773 GAAATG
1 GAAATG
88965779 TTTATAAATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.20, C:0.03, G:0.30, T:0.47
Consensus pattern (34 bp):
GAAATGGTCTTTTTGGTAAGTTAGTTTTGTGGTT
Found at i:88972648 original size:44 final size:44
Alignment explanation
Indices: 88972569--88972739 Score: 147
Period size: 43 Copynumber: 4.0 Consensus size: 44
88972559 ATAGGATTCT
* **
88972569 GATATTTGATTT-CATGTAAGACCACATCT-GAGACATTGGCATC
1 GATATTTGATTTACGTGTAAGACCATGTCTAG-GACATTGGCATC
* *
88972612 GAT-TTGAGATTTACGTGTAAGACCATGTCTAGGACATCGGCATC
1 GATATT-TGATTTACGTGTAAGACCATGTCTAGGACATTGGCATC
* * * * * *
88972656 -ATATTTGATTT-CGTGTAGGATCTTGTCTAGGATAGTGGTATC
1 GATATTTGATTTACGTGTAAGACCATGTCTAGGACATTGGCATC
* * * *
88972698 GATATTTGA-TTACATGTAAGACCATGTTTGGGACGTTGGCAT
1 GATATTTGATTTACGTGTAAGACCATGTCTAGGACATTGGCAT
88972740 TGTACGAGCT
Statistics
Matches: 99, Mismatches: 23, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
42 28 0.28
43 43 0.43
44 27 0.27
45 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (44 bp):
GATATTTGATTTACGTGTAAGACCATGTCTAGGACATTGGCATC
Found at i:88975652 original size:25 final size:25
Alignment explanation
Indices: 88975606--88975656 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
88975596 CCCTTATAAT
* *
88975606 GTGAAAATGACCTTTTTGCCCCTAG
1 GTGAAAATGACCTTTATACCCCTAG
88975631 GTGAAAATGA-CTATTATACCCCTAG
1 GTGAAAATGACCT-TTATACCCCTAG
88975656 G
1 G
88975657 GTTATGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 2 0.09
25 21 0.91
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (25 bp):
GTGAAAATGACCTTTATACCCCTAG
Found at i:88976081 original size:31 final size:31
Alignment explanation
Indices: 88976046--88976123 Score: 129
Period size: 31 Copynumber: 2.5 Consensus size: 31
88976036 GTTTATAGTG
*
88976046 AAGGCTTCAGCCCAGTGATATGAATAATGAA
1 AAGGCTTCGGCCCAGTGATATGAATAATGAA
* *
88976077 AAGGCTTCGGCCCAGTGGTATGAATAATGTA
1 AAGGCTTCGGCCCAGTGATATGAATAATGAA
88976108 AAGGCTTCGGCCCAGT
1 AAGGCTTCGGCCCAGT
88976124 ATGTGCTGAC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (31 bp):
AAGGCTTCGGCCCAGTGATATGAATAATGAA
Found at i:88979055 original size:48 final size:48
Alignment explanation
Indices: 88978919--88979058 Score: 140
Period size: 48 Copynumber: 2.9 Consensus size: 48
88978909 AAGGTGGAAG
** * * *
88978919 TATATGGCAGTTTATCTGCATTAATGTGACACTGTTCACGATTTTGAT
1 TATATGGCAGTTTATCTGTGTTACTATGACACTGTTCACAATTTTGAT
* * *** * *
88978967 TATATGGTAGTTTATCTGTG--ACTTTGGTGGCTTGTCCACAATTTTGTT
1 TATATGGCAGTTTATCTGTGTTACTAT-GACAC-TGTTCACAATTTTGAT
88979015 TATATGGCAGTTTATCTGTGTTACTATGACACTGTTCACAATTT
1 TATATGGCAGTTTATCTGTGTTACTATGACACTGTTCACAATTT
88979059 GGTATGTTGG
Statistics
Matches: 71, Mismatches: 17, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
46 3 0.04
47 2 0.03
48 60 0.85
49 2 0.03
50 4 0.06
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.44
Consensus pattern (48 bp):
TATATGGCAGTTTATCTGTGTTACTATGACACTGTTCACAATTTTGAT
Found at i:88981084 original size:29 final size:29
Alignment explanation
Indices: 88980992--88981087 Score: 72
Period size: 29 Copynumber: 3.2 Consensus size: 29
88980982 GGGCTTTAAT
**
88980992 TAATAAAATTTAGAACGGTATATCAATTA
1 TAATAAAATTTAGAACAATATATCAATTA
** * *
88981021 TAATAAGTAAAATA-AA-AATTTAT-ATTTTGA
1 TAATAA--AATTTAGAACAATATATCA-ATT-A
88981051 TTAATAAAATTTAGAACAATATATCAATTA
1 -TAATAAAATTTAGAACAATATATCAATTA
88981081 TAATAAA
1 TAATAAA
88981088 CTAAGGGATT
Statistics
Matches: 49, Mismatches: 10, Indels: 16
0.65 0.13 0.21
Matches are distributed among these distances:
28 1 0.02
29 23 0.47
30 6 0.12
31 18 0.37
32 1 0.02
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.36
Consensus pattern (29 bp):
TAATAAAATTTAGAACAATATATCAATTA
Found at i:88982667 original size:9 final size:9
Alignment explanation
Indices: 88982646--88982693 Score: 55
Period size: 9 Copynumber: 5.6 Consensus size: 9
88982636 AAATAATTGA
*
88982646 ATTTTTTCG
1 ATTTATTCG
*
88982655 ATTTATTCA
1 ATTTATTCG
88982664 ATTT-TTCG
1 ATTTATTCG
*
88982672 GTTTATTCG
1 ATTTATTCG
88982681 ATTT-TTCG
1 ATTTATTCG
88982689 ATTTA
1 ATTTA
88982694 ATCTGTTTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
8 14 0.44
9 18 0.56
ACGTcount: A:0.19, C:0.10, G:0.10, T:0.60
Consensus pattern (9 bp):
ATTTATTCG
Found at i:88982670 original size:17 final size:17
Alignment explanation
Indices: 88982648--88982693 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
88982638 ATAATTGAAT
88982648 TTTTTCGATTTATTCAA
1 TTTTTCGATTTATTCAA
* *
88982665 TTTTTCGGTTTATTCGA
1 TTTTTCGATTTATTCAA
88982682 TTTTTCGATTTA
1 TTTTTCGATTTA
88982694 ATCTGTTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.17, C:0.11, G:0.11, T:0.61
Consensus pattern (17 bp):
TTTTTCGATTTATTCAA
Found at i:88982690 original size:8 final size:8
Alignment explanation
Indices: 88982648--88982692 Score: 54
Period size: 8 Copynumber: 5.4 Consensus size: 8
88982638 ATAATTGAAT
88982648 TTTTTCGA
1 TTTTTCGA
*
88982656 TTTATTCAA
1 TTT-TTCGA
*
88982665 TTTTTCGG
1 TTTTTCGA
88982673 TTTATTCGA
1 TTT-TTCGA
88982682 TTTTTCGA
1 TTTTTCGA
88982690 TTT
1 TTT
88982693 AATCTGTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
8 17 0.55
9 14 0.45
ACGTcount: A:0.16, C:0.11, G:0.11, T:0.62
Consensus pattern (8 bp):
TTTTTCGA
Found at i:88983422 original size:19 final size:19
Alignment explanation
Indices: 88983380--88983438 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 19
88983370 ATTTATGGAT
*
88983380 TTTTTATAATTTTT-AATGA
1 TTTTT-TAATTTTTAAATTA
* * *
88983399 ATTTTGATTTTTTAAA-TA
1 TTTTTTAATTTTTAAATTA
88983417 TTTTTTAATTTTTAAATTA
1 TTTTTTAATTTTTAAATTA
88983436 TTT
1 TTT
88983439 GATGATGTGA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
18 20 0.65
19 11 0.35
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (19 bp):
TTTTTTAATTTTTAAATTA
Found at i:88987534 original size:10 final size:10
Alignment explanation
Indices: 88987505--88987562 Score: 73
Period size: 10 Copynumber: 5.8 Consensus size: 10
88987495 AACATTCTAG
88987505 AAGATAAATA
1 AAGATAAATA
*
88987515 CAA-TTAAATA
1 -AAGATAAATA
*
88987525 AAGATGAATA
1 AAGATAAATA
*
88987535 AGGATAAATA
1 AAGATAAATA
88987545 AAGATAAATA
1 AAGATAAATA
88987555 AAGATAAA
1 AAGATAAA
88987563 AGCTAAAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
9 2 0.05
10 36 0.90
11 2 0.05
ACGTcount: A:0.66, C:0.02, G:0.12, T:0.21
Consensus pattern (10 bp):
AAGATAAATA
Found at i:88988227 original size:16 final size:15
Alignment explanation
Indices: 88988201--88988237 Score: 65
Period size: 16 Copynumber: 2.4 Consensus size: 15
88988191 ATCACTTTTT
88988201 TTTTTCTTTTTTCTA
1 TTTTTCTTTTTTCTA
88988216 TTTTTCTATTTTTCTA
1 TTTTTCT-TTTTTCTA
88988232 TTTTTC
1 TTTTTC
88988238 CCTTTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTCTTTTTTCTA
Found at i:88988243 original size:16 final size:16
Alignment explanation
Indices: 88988208--88988244 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
88988198 TTTTTTTTCT
*
88988208 TTTTTCTATTTTTCTA
1 TTTTTCTATTTTTCCA
*
88988224 TTTTTCTATTTTTCCC
1 TTTTTCTATTTTTCCA
88988240 TTTTT
1 TTTTT
88988245 TTTCTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTCTATTTTTCCA
Found at i:88988442 original size:99 final size:99
Alignment explanation
Indices: 88988270--88988453 Score: 296
Period size: 99 Copynumber: 1.9 Consensus size: 99
88988260 ATTATTATTG
* ** * *
88988270 CTTAAGAATATATTGAACCTTTTGACGCGAAGAGAGATGATAGCCAAGTACCCCACCCCAGTTAC
1 CTTAAGAACATAACGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCACCCCAGTTAC
*
88988335 TCAGTCCAACATACTCCTAATTTATTATATTTTT
66 TCAATCCAACATACTCCTAATTTATTATATTTTT
*
88988369 CTTAAGAACATAACGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCTACCCCAGTTAC
1 CTTAAGAACATAACGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCACCCCAGTTAC
*
88988434 TCAATCCAACATATTCCTAA
66 TCAATCCAACATACTCCTAA
88988454 AAAGAATTTA
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
99 77 1.00
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (99 bp):
CTTAAGAACATAACGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCACCCCAGTTAC
TCAATCCAACATACTCCTAATTTATTATATTTTT
Found at i:88991039 original size:29 final size:26
Alignment explanation
Indices: 88990999--88991091 Score: 84
Period size: 25 Copynumber: 3.5 Consensus size: 26
88990989 AATTTGTTAT
* * *
88990999 TTATTCATTTTAAATCTTTTTTCCTCATA
1 TTATTTATTTTAAAT-TTGTTTCAT--TA
88991028 TTATTTATTTTAAA-TTGTTTCATTA
1 TTATTTATTTTAAATTTGTTTCATTA
*
88991053 TTATTTATTTTAAA--TGTTTCACATA
1 TTATTTATTTTAAATTTGTTTCA-TTA
*
88991078 TTATGTATTTTAAA
1 TTATTTATTTTAAA
88991092 CTATTATCCA
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
24 7 0.12
25 31 0.53
27 7 0.12
29 13 0.22
ACGTcount: A:0.29, C:0.09, G:0.03, T:0.59
Consensus pattern (26 bp):
TTATTTATTTTAAATTTGTTTCATTA
Found at i:88991054 original size:25 final size:25
Alignment explanation
Indices: 88991024--88991091 Score: 102
Period size: 25 Copynumber: 2.7 Consensus size: 25
88991014 CTTTTTTCCT
88991024 CATATTATTTATTTTAAATTGTTTCA
1 CATATTATTTATTTTAAA-TGTTTCA
*
88991050 -TTATTATTTATTTTAAATGTTTCA
1 CATATTATTTATTTTAAATGTTTCA
*
88991074 CATATTATGTATTTTAAA
1 CATATTATTTATTTTAAA
88991092 CTATTATCCA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
24 7 0.18
25 31 0.82
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.57
Consensus pattern (25 bp):
CATATTATTTATTTTAAATGTTTCA
Found at i:88991154 original size:24 final size:24
Alignment explanation
Indices: 88991101--88991154 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
88991091 ACTATTATCC
* *
88991101 AATTA-TATATATTGTTTATTTTA
1 AATTATTATATATTATTTATTTCA
* *
88991124 AACTATTATATATTATTTATTTCG
1 AATTATTATATATTATTTATTTCA
88991148 AATTATT
1 AATTATT
88991155 TTTTTGTGTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (24 bp):
AATTATTATATATTATTTATTTCA
Found at i:88991267 original size:22 final size:22
Alignment explanation
Indices: 88991227--88991268 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
88991217 ACATATTATT
* *
88991227 TATTTTAAACTCTTTTATATGC
1 TATTTTAAACTATTATATATGC
*
88991249 TATTTTAAAGTATTATATAT
1 TATTTTAAACTATTATATAT
88991269 ATTATTTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (22 bp):
TATTTTAAACTATTATATATGC
Found at i:88991274 original size:22 final size:22
Alignment explanation
Indices: 88991226--88991275 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
88991216 TACATATTAT
* * *
88991226 TTATTTTAAACTCTTTTATATG
1 TTATTTTAAACTATTATATATA
* *
88991248 CTATTTTAAAGTATTATATATA
1 TTATTTTAAACTATTATATATA
88991270 TTATTT
1 TTATTT
88991276 ATTTTAAATT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.58
Consensus pattern (22 bp):
TTATTTTAAACTATTATATATA
Found at i:88991278 original size:26 final size:25
Alignment explanation
Indices: 88991106--88991377 Score: 126
Period size: 26 Copynumber: 10.5 Consensus size: 25
88991096 TATCCAATTA
* *
88991106 TATATATTGTTTATTTTAAACTA-T
1 TATATATTATTTATTTTAAATTATT
* *
88991130 TATATATTATTTATTTCGAATTATTTTTTT
1 TATATATTATTTATTT-TAA--A--TTATT
* * *
88991160 GTGTATATCT-TTTATTTTTAAGTTGTTT
1 -TATATAT-TATTTA-TTTTAAATT-ATT
* *
88991188 TGTATATTATTTATTTTAAATTTCTTTT
1 TATATATTATTTATTTTAAA--T-TATT
* * *
88991216 TACATATTATTTATTTTAAACTCTT
1 TATATATTATTTATTTTAAATTATT
** *
88991241 T-TATA-T-GCTATTTTAAAGTATT
1 TATATATTATTTATTTTAAATTATT
88991263 ATATATATTATTTATTTTAAATTACTT
1 -TATATATTATTTATTTTAAATTA-TT
* * *
88991290 TGTATATTATTTATTTTAATTTGTT
1 TATATATTATTTATTTTAAATTATT
*
88991315 T-TACGTATTATTTATCTTAAATTATT
1 TATA--TATTATTTATTTTAAATTATT
* * * * *
88991341 T-TATCTTATTTACTTCAATTTGCTT
1 TATATATTATTTATTTTAAATT-ATT
88991366 TATATATTATTT
1 TATATATTATTT
88991378 TGTTTCGTTT
Statistics
Matches: 192, Mismatches: 33, Indels: 44
0.71 0.12 0.16
Matches are distributed among these distances:
22 12 0.06
23 2 0.01
24 37 0.19
25 13 0.07
26 68 0.35
27 16 0.08
28 25 0.13
29 2 0.01
30 1 0.01
31 12 0.06
32 4 0.02
ACGTcount: A:0.28, C:0.06, G:0.05, T:0.62
Consensus pattern (25 bp):
TATATATTATTTATTTTAAATTATT
Found at i:88991374 original size:50 final size:52
Alignment explanation
Indices: 88991264--88991377 Score: 151
Period size: 50 Copynumber: 2.2 Consensus size: 52
88991254 TAAAGTATTA
* * * *
88991264 TATATATTATTTATTTTAAATTACTTTGTATATTATTTATTTTAATTTGTTT
1 TATATATTATTTATCTTAAATTACTTTGTATATTATTTACTTCAATTTGCTT
** *
88991316 TACGTATTATTTATCTTAAATTA-TTT-TATCTTATTTACTTCAATTTGCTT
1 TATATATTATTTATCTTAAATTACTTTGTATATTATTTACTTCAATTTGCTT
88991366 TATATATTATTT
1 TATATATTATTT
88991378 TGTTTCGTTT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
50 30 0.57
51 3 0.06
52 20 0.38
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (52 bp):
TATATATTATTTATCTTAAATTACTTTGTATATTATTTACTTCAATTTGCTT
Found at i:88993346 original size:93 final size:94
Alignment explanation
Indices: 88993137--88993454 Score: 342
Period size: 93 Copynumber: 3.4 Consensus size: 94
88993127 GTAAGGTGCC
* *
88993137 GATGCCATGTCCCAGACATGGTCTTACACTGGC-TATCA-TCTTCGAGGCCGATACTATGTCCCA
1 GATGCCATGTCCCAGACAT-GTCTTACACTGGCTTA-CATTC-TCGAGGCCGATGC-ATGTCCTA
* * * * *
88993200 GACATGGTCTTACATTAGCTCTCGTATATTC-GTGCC
62 GACAT-GTCTTACACTAGCACT--TAT-CTCAATGCT
*
88993236 GATGCCATGTCCTAGACATGTCTTACACTGGCTTACATTCT-GAGGCCGATGCATGTCCTAGACA
1 GATGCCATGTCCCAGACATGTCTTACACTGGCTTACATTCTCGAGGCCGATGCATGTCCTAGACA
*
88993300 TGCCTTACACTAGCACTTATCTCAATGCT
66 TGTCTTACACTAGCACTTATCTCAATGCT
* * * * * *
88993329 GATGCCATGTCCCAGACATGTCTTACACTAGCACT-CGTT-TCAATGCTGATGCATGTCCTAGAC
1 GATGCCATGTCCCAGACATGTCTTACACTGGC-TTACATTCTCGAGGCCGATGCATGTCCTAGAC
* * **
88993392 ATGTCTTATACTGGCACTCGTCTCAATGCT
65 ATGTCTTACACTAGCACTTATCTCAATGCT
88993422 GATGCCATGTCCCAGACATGTCTTACACTGGCT
1 GATGCCATGTCCCAGACATGTCTTACACTGGCT
88993455 CACACACAAA
Statistics
Matches: 191, Mismatches: 23, Indels: 17
0.83 0.10 0.07
Matches are distributed among these distances:
92 3 0.02
93 114 0.60
94 1 0.01
95 13 0.07
96 12 0.06
97 10 0.05
98 16 0.08
99 22 0.12
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.30
Consensus pattern (94 bp):
GATGCCATGTCCCAGACATGTCTTACACTGGCTTACATTCTCGAGGCCGATGCATGTCCTAGACA
TGTCTTACACTAGCACTTATCTCAATGCT
Found at i:88993347 original size:47 final size:46
Alignment explanation
Indices: 88993283--88993450 Score: 246
Period size: 47 Copynumber: 3.6 Consensus size: 46
88993273 TTCTGAGGCC
* * **
88993283 GATGCATGTCCTAGACATGCCTTACACTAGCACTTATCTCAATGCT
1 GATGCATGTCCCAGACATGTCTTACACTAGCACTCGTCTCAATGCT
*
88993329 GATGCCATGTCCCAGACATGTCTTACACTAGCACTCGTTTCAATGCT
1 GATG-CATGTCCCAGACATGTCTTACACTAGCACTCGTCTCAATGCT
* * *
88993376 GATGCATGTCCTAGACATGTCTTATACTGGCACTCGTCTCAATGCT
1 GATGCATGTCCCAGACATGTCTTACACTAGCACTCGTCTCAATGCT
88993422 GATGCCATGTCCCAGACATGTCTTACACT
1 GATG-CATGTCCCAGACATGTCTTACACT
88993451 GGCTCACACA
Statistics
Matches: 109, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
46 46 0.42
47 63 0.58
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.30
Consensus pattern (46 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCACTCGTCTCAATGCT
Found at i:88993452 original size:47 final size:47
Alignment explanation
Indices: 88993133--88993453 Score: 278
Period size: 46 Copynumber: 6.8 Consensus size: 47
88993123 TAGGGTAAGG
* *
88993133 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTA-TCATCTTCGA
1 TGCCGATGCCATGTCCCAGACAT-GTCTTACACTGGC-ACTCGTC-TCAA
* * * * * * * *
88993182 GGCCGATACTATGTCCCAGACATGGTCTTACATTAGCTCTCGTAT-ATTCG
1 TGCCGATGCCATGTCCCAGACAT-GTCTTACACTGGCACTCGTCTCA---A
* *
88993232 TGCCGATGCCATGTCCTAGACATGTCTTACACTGGCTTACAT--TCT-GA
1 TGCCGATGCCATGTCCCAGACATGTCTTACACTGGC--AC-TCGTCTCAA
* * * * **
88993279 GGCCGATG-CATGTCCTAGACATGCCTTACACTAGCACTTATCTCAA
1 TGCCGATGCCATGTCCCAGACATGTCTTACACTGGCACTCGTCTCAA
* * *
88993325 TGCTGATGCCATGTCCCAGACATGTCTTACACTAGCACTCGTTTCAA
1 TGCCGATGCCATGTCCCAGACATGTCTTACACTGGCACTCGTCTCAA
* * *
88993372 TGCTGATG-CATGTCCTAGACATGTCTTATACTGGCACTCGTCTCAA
1 TGCCGATGCCATGTCCCAGACATGTCTTACACTGGCACTCGTCTCAA
*
88993418 TGCTGATGCCATGTCCCAGACATGTCTTACACTGGC
1 TGCCGATGCCATGTCCCAGACATGTCTTACACTGGC
88993454 TCACACACAA
Statistics
Matches: 223, Mismatches: 37, Indels: 26
0.78 0.13 0.09
Matches are distributed among these distances:
43 1 0.00
44 2 0.01
45 3 0.01
46 74 0.33
47 73 0.33
48 1 0.00
49 46 0.21
50 21 0.09
51 1 0.00
52 1 0.00
ACGTcount: A:0.22, C:0.29, G:0.19, T:0.30
Consensus pattern (47 bp):
TGCCGATGCCATGTCCCAGACATGTCTTACACTGGCACTCGTCTCAA
Found at i:89002083 original size:55 final size:55
Alignment explanation
Indices: 89001986--89002091 Score: 131
Period size: 55 Copynumber: 1.9 Consensus size: 55
89001976 CTTCTCCCAC
* * * * *
89001986 GCCCGTGTTAATTTGACAGGTTCAACCACGGGTGTTAGACACGGGCGTGTCACAT
1 GCCCGTGCTAATTTAACAGGTTCAACCACGGGTCTTACACACGAGCGTGTCACAT
* * * *
89002041 GCCCGTGCTATTTTAACAGGTTCATCCACGGTTCTTCCACACGAGCGTGTC
1 GCCCGTGCTAATTTAACAGGTTCAACCACGGGTCTTACACACGAGCGTGTC
89002092 GCACACCCGT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
55 42 1.00
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.27
Consensus pattern (55 bp):
GCCCGTGCTAATTTAACAGGTTCAACCACGGGTCTTACACACGAGCGTGTCACAT
Found at i:89009178 original size:21 final size:21
Alignment explanation
Indices: 89009137--89009178 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
89009127 GTTTTCTCAA
*
89009137 ATTTTGTAAACCAAAATTGTT
1 ATTTTGTAAACCAAAAGTGTT
*
89009158 ATTTTAGTAAATC-AAAGTGTT
1 ATTTT-GTAAACCAAAAGTGTT
89009179 TTATTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.43
Consensus pattern (21 bp):
ATTTTGTAAACCAAAAGTGTT
Found at i:89010375 original size:19 final size:19
Alignment explanation
Indices: 89010351--89010395 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
89010341 TTTCTCTTTT
*
89010351 TGCATT-CATTTCATGCATC
1 TGCATTGCATTTCAT-CATA
89010370 TGCATTGCATTTCATCATA
1 TGCATTGCATTTCATCATA
89010389 TGCATTG
1 TGCATTG
89010396 AATGTCACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.42
Consensus pattern (19 bp):
TGCATTGCATTTCATCATA
Found at i:89015242 original size:44 final size:44
Alignment explanation
Indices: 89015179--89015394 Score: 153
Period size: 44 Copynumber: 4.7 Consensus size: 44
89015169 TAATGGCGAA
*
89015179 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACCAG
* * * *** **
89015223 TCTTATCTCCCTGAAGTTGCAGCGGAGCAAACTAAAAATAAAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACCAG
* * * * *
89015267 ATCTTATTTCCCTGACGTTGCAGTGGAACAGATTAAAGCTACAAATTATGGCGAA
1 -TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGC--C-----A---CCAG
* * * * * *
89015322 CCTTATCTCTCTAAAGTTACAGTGGAGCAGATTGAAGCTACCAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACCAG
89015366 TCTTATCTCCCTGAAGTTGCAGTGGAGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCA
89015395 AACTGAAGAT
Statistics
Matches: 125, Mismatches: 36, Indels: 22
0.68 0.20 0.12
Matches are distributed among these distances:
44 62 0.50
45 30 0.24
47 1 0.01
52 1 0.01
54 30 0.24
55 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACCAG
Found at i:89015434 original size:143 final size:142
Alignment explanation
Indices: 89015171--89015535 Score: 493
Period size: 143 Copynumber: 2.5 Consensus size: 142
89015161 TGAAGTTATA
*
89015171 ATGGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGTCTTATCTCCCTG
1 ATGGCGAATCTTATCT-CCTGAAGTTACAGTGGAGCAGATTGAAGCCACCAGTCTTATCTCCCTG
* * * *
89015236 AAGTTGCAGCGGAGCAAACTAAAAATAAAAGATCTTATTTCCCTGACGTTGCAGTGGAACAGATT
65 AAGTTGCAGTGGAGCAAACTAAAAATAAAAGATCTCATTTCCCTGAAGTTACAGTGGAACAGA-T
*
89015301 A-AAGCTACAAATT
129 AGAAGCTACAAATC
* * *
89015314 ATGGCGAACCTTATCTCTCTAAAGTTACAGTGGAGCAGATTGAAGCTACCAGTCTTATCTCCCTG
1 ATGGCGAATCTTATCTC-CTGAAGTTACAGTGGAGCAGATTGAAGCCACCAGTCTTATCTCCCTG
* * * * *
89015379 AAGTTGCAGTGGAGCAAACTGAAGATAGCAA-ATCTCATTTCCTTGAAGTTACAGTGGAATAGAT
65 AAGTTGCAGTGGAGCAAACTAAAAATA-AAAGATCTCATTTCCCTGAAGTTACAGTGGAACAGAT
89015443 AGAAGCTACAAATC
129 AGAAGCTACAAATC
* * * *
89015457 ATGGCGGATCTTATCTACCTGAAGTTACAGTGAAGCAGATTGAAGCCA-CAATCTTTATCTCTCT
1 ATGGCGAATCTTATCT-CCTGAAGTTACAGTGGAGCAGATTGAAGCCACCAGTC-TTATCTCCCT
89015521 GAAGTTGCAGTGGAG
64 GAAGTTGCAGTGGAG
89015536 TAGGTTGAAA
Statistics
Matches: 196, Mismatches: 21, Indels: 10
0.86 0.09 0.04
Matches are distributed among these distances:
142 7 0.04
143 186 0.95
144 3 0.02
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27
Consensus pattern (142 bp):
ATGGCGAATCTTATCTCCTGAAGTTACAGTGGAGCAGATTGAAGCCACCAGTCTTATCTCCCTGA
AGTTGCAGTGGAGCAAACTAAAAATAAAAGATCTCATTTCCCTGAAGTTACAGTGGAACAGATAG
AAGCTACAAATC
Found at i:89015565 original size:143 final size:139
Alignment explanation
Indices: 89015171--89015599 Score: 466
Period size: 143 Copynumber: 3.0 Consensus size: 139
89015161 TGAAGTTATA
*
89015171 ATGGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGTCTTATCTCCCTG
1 ATGGCGAATCTTATCT-CCTGAAGTTACAGTGGAGCAGATTGAAGCCACCAGTCTTATCTCCCTG
* * ** * * * *
89015236 AAGTTGCAGCGGAGCAAACTAAAAATAAAAGATCTTATTTCCCTGACGTTGCAGTGGAACAGATT
65 AAGTTGCAGTGGAG-AAAATTGAAATACAA-ATCTTATTTCCTTGAAGTT-CAGTGGAATAGA-T
*
89015301 A-AAGCTACAAATT
126 AGAAGCTACAAATC
* * *
89015314 ATGGCGAACCTTATCTCTCTAAAGTTACAGTGGAGCAGATTGAAGCTACCAGTCTTATCTCCCTG
1 ATGGCGAATCTTATCTC-CTGAAGTTACAGTGGAGCAGATTGAAGCCACCAGTCTTATCTCCCTG
* * *
89015379 AAGTTGCAGTGGAGCAAACTGAAGATAGCAAATCTCATTTCCTTGAAGTTACAGTGGAATAGATA
65 AAGTTGCAGTGGAGAAAATTGAA-ATA-CAAATCTTATTTCCTTGAAGTT-CAGTGGAATAGATA
89015444 GAAGCTACAAATC
127 GAAGCTACAAATC
* * * *
89015457 ATGGCGGATCTTATCTACCTGAAGTTACAGTGAAGCAGATTGAAGCCA-CAATCTTTATCTCTCT
1 ATGGCGAATCTTATCT-CCTGAAGTTACAGTGGAGCAGATTGAAGCCACCAGTC-TTATCTCCCT
* ** * * * *
89015521 GAAGTTGCAGTGGAGTAGGTTGAAATACACAATTCTTATCTCCTTTAAGTTCTAGCGGAGTAGAT
64 GAAGTTGCAGTGGAGAAAATTGAAATACA-AA-TCTTATTTCCTTGAAGTTC-AGTGGAATAGAT
*
89015586 CGAAGCTACAAATC
126 AGAAGCTACAAATC
89015600 TCTTCTCCTT
Statistics
Matches: 243, Mismatches: 34, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
141 2 0.01
142 17 0.07
143 221 0.91
144 3 0.01
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.28
Consensus pattern (139 bp):
ATGGCGAATCTTATCTCCTGAAGTTACAGTGGAGCAGATTGAAGCCACCAGTCTTATCTCCCTGA
AGTTGCAGTGGAGAAAATTGAAATACAAATCTTATTTCCTTGAAGTTCAGTGGAATAGATAGAAG
CTACAAATC
Found at i:89017146 original size:25 final size:25
Alignment explanation
Indices: 89017108--89017183 Score: 100
Period size: 25 Copynumber: 3.0 Consensus size: 25
89017098 TTTTAAACCT
*
89017108 TTTTTCCTCATATTATTTATTTTAAA
1 TTTTTCAT-ATATTATTTATTTTAAA
*
89017134 TTGTTTCAT-TATTATTTATTTTAAG
1 TT-TTTCATATATTATTTATTTTAAA
*
89017159 TTTTTCATATATTATGTATTTTAAA
1 TTTTTCATATATTATTTATTTTAAA
89017184 CTATTATCCA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
24 6 0.14
25 31 0.70
26 2 0.05
27 5 0.11
ACGTcount: A:0.28, C:0.07, G:0.04, T:0.62
Consensus pattern (25 bp):
TTTTTCATATATTATTTATTTTAAA
Found at i:89017267 original size:21 final size:21
Alignment explanation
Indices: 89017242--89017290 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
89017232 TTATTTCGAA
89017242 TTATTTT-TTTATGTATATCT-T
1 TTATTTTGTTT-TGTATAT-TAT
89017263 TTATTTTGTTTTGTATATTAT
1 TTATTTTGTTTTGTATATTAT
89017284 TTATTTT
1 TTATTTT
89017291 AAATTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 1 0.04
21 22 0.85
22 3 0.12
ACGTcount: A:0.18, C:0.02, G:0.06, T:0.73
Consensus pattern (21 bp):
TTATTTTGTTTTGTATATTAT
Found at i:89017337 original size:22 final size:22
Alignment explanation
Indices: 89017312--89017361 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
89017302 TACATATTAT
* * *
89017312 TTATTTTAAACTCTTTTATATG
1 TTATTTTAAACTATTATATATA
*
89017334 TTATTTTAAAGTATTATATATA
1 TTATTTTAAACTATTATATATA
89017356 TTATTT
1 TTATTT
89017362 ATTTTAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (22 bp):
TTATTTTAAACTATTATATATA
Found at i:89017363 original size:26 final size:25
Alignment explanation
Indices: 89017195--89017462 Score: 163
Period size: 26 Copynumber: 10.5 Consensus size: 25
89017185 TATTATCCAA
*
89017195 TTATATATATAGTTTATTTTAAACTA-
1 TTATATAT-TA-TTTATTTTAAATTAT
**
89017221 TTATATATTATTTATTTCGAATTAT
1 TTATATATTATTTATTTTAAATTAT
* * * * ** *
89017246 TTTTTTATGTATATCTTTTATTTTGTT
1 TTATATAT-TATTTATTTTAAATT-AT
*
89017273 TTGTATATTATTTATTTTAAATTTATTT
1 TTATATATTATTTATTTTAAA-TTA--T
* * *
89017301 TTACATATTATTTATTTTAAACTCT
1 TTATATATTATTTATTTTAAATTAT
* *
89017326 TT-TATA-T-GTTATTTTAAAGTAT
1 TTATATATTATTTATTTTAAATTAT
89017348 TATATATATTATTTATTTTAAATTGCA-
1 T-TATATATTATTTATTTTAAATT--AT
* * *
89017375 TTGTATATTATTTATTTTAATTTTT
1 TTATATATTATTTATTTTAAATTAT
*
89017400 TTACT-TATTATTTATCTTAAATTAT
1 TTA-TATATTATTTATTTTAAATTAT
* * *
89017425 TT-TATCTTATTTACTTTAAATTGCT
1 TTATATATTATTTATTTTAAATT-AT
*
89017450 TTACATATTATTT
1 TTATATATTATTT
89017463 TGTTTCGTTT
Statistics
Matches: 183, Mismatches: 42, Indels: 34
0.71 0.16 0.13
Matches are distributed among these distances:
22 13 0.07
23 3 0.02
24 33 0.18
25 36 0.20
26 66 0.36
27 11 0.06
28 21 0.11
ACGTcount: A:0.29, C:0.05, G:0.04, T:0.62
Consensus pattern (25 bp):
TTATATATTATTTATTTTAAATTAT
Found at i:89019657 original size:21 final size:21
Alignment explanation
Indices: 89019621--89019695 Score: 82
Period size: 21 Copynumber: 3.5 Consensus size: 21
89019611 TCAATATCCA
*
89019621 AAAATAAATAATATAATAAAAT
1 AAAAT-AATAAAATAATAAAAT
89019643 AAAATAATAAAATAATAAAAT
1 AAAATAATAAAATAATAAAAT
*
89019664 AGTAA-AATAAAAT-ATAAAAT
1 A-AAATAATAAAATAATAAAAT
*
89019684 AAGAAAAATAAA
1 AA-AATAATAAA
89019696 TAAAAATAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
20 10 0.21
21 30 0.64
22 7 0.15
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.23
Consensus pattern (21 bp):
AAAATAATAAAATAATAAAAT
Found at i:89019672 original size:13 final size:13
Alignment explanation
Indices: 89019626--89019700 Score: 73
Period size: 13 Copynumber: 5.6 Consensus size: 13
89019616 ATCCAAAAAT
*
89019626 AAATAATATAATA
1 AAATAAAATAATA
89019639 AAATAAAATAATAAA
1 AAATAAAATAAT--A
*
89019654 ATAATAAAATAGTA
1 A-AATAAAATAATA
89019668 AAATAAAAT-ATA
1 AAATAAAATAATA
*
89019680 AAATAAGAAAAAT-
1 AAATAA-AATAATA
89019693 AAATAAAA
1 AAATAAAA
89019701 ATAAAGGTTG
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
12 10 0.19
13 27 0.51
14 4 0.08
15 2 0.04
16 10 0.19
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.23
Consensus pattern (13 bp):
AAATAAAATAATA
Found at i:89019690 original size:8 final size:8
Alignment explanation
Indices: 89019626--89019673 Score: 60
Period size: 8 Copynumber: 5.8 Consensus size: 8
89019616 ATCCAAAAAT
89019626 AAATAATA
1 AAATAATA
*
89019634 TAATAAAATA
1 -AA-ATAATA
89019644 AAATAATA
1 AAATAATA
89019652 AAATAATA
1 AAATAATA
*
89019660 AAATAGTA
1 AAATAATA
89019668 AAATAA
1 AAATAA
89019674 AATATAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
8 25 0.74
9 4 0.12
10 5 0.15
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (8 bp):
AAATAATA
Found at i:89019691 original size:29 final size:29
Alignment explanation
Indices: 89019621--89019693 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
89019611 TCAATATCCA
* *
89019621 AAAATAAATAATATAATAAAATAAAATAAT
1 AAAATAAA-AAAATAGTAAAATAAAATAAT
*
89019651 AAAATAATAAAATAGTAAAATAAAAT-AT
1 AAAATAAAAAAATAGTAAAATAAAATAAT
89019679 AAAATAAGAAAAATA
1 AAAATAA-AAAAATA
89019694 AATAAAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 9 0.24
29 22 0.58
30 7 0.18
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (29 bp):
AAAATAAAAAAATAGTAAAATAAAATAAT
Found at i:89029805 original size:19 final size:20
Alignment explanation
Indices: 89029781--89029818 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
89029771 GGTACCACCA
89029781 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
89029800 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
89029819 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:89030207 original size:93 final size:93
Alignment explanation
Indices: 89030048--89030218 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
89030038 GCCCCTAAGT
* * *
89030048 GAACTCGGACTCAACTTAACGAGCTCGGGCGTTCGCATCCATAAATGAACTCGAACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAATGAACTCGAACTCAACTCAA
89030113 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * *
89030141 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAATGAACTCGAACTCAACTCAA
89030206 CGAGTTCGGATGC
66 CGAGTTCGGATGC
89030219 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAATGAACTCGAACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:89030234 original size:46 final size:46
Alignment explanation
Indices: 89030043--89030220 Score: 200
Period size: 46 Copynumber: 3.8 Consensus size: 46
89030033 AACCCGCCCC
* * * *
89030043 TAAGTGAACTCGGACTCAACTTAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCA
* * * *
89030089 TAAATGAACTCGAACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CATCCA
* *
89030137 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCA
*
89030182 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTC
89030221 AACCATCCTA
Statistics
Matches: 109, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 66 0.61
47 31 0.28
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCA
Found at i:89031566 original size:10 final size:10
Alignment explanation
Indices: 89031534--89031592 Score: 57
Period size: 10 Copynumber: 5.9 Consensus size: 10
89031524 TTAAATTCTA
89031534 AAAGATAAAT
1 AAAGATAAAT
*
89031544 ACAA-TTAAAT
1 A-AAGATAAAT
*
89031554 AAAGATAATT
1 AAAGATAAAT
*
89031564 AAAGAAAAAT
1 AAAGATAAAT
*
89031574 AAGGATAAAT
1 AAAGATAAAT
*
89031584 AAATATAAA
1 AAAGATAAA
89031593 AACTAAAATT
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
9 2 0.05
10 34 0.89
11 2 0.05
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:89034857 original size:87 final size:87
Alignment explanation
Indices: 89034731--89034891 Score: 286
Period size: 87 Copynumber: 1.9 Consensus size: 87
89034721 TCATATTTCC
* **
89034731 TTTAAGCAAATATATATAGCAATATTTTGTACTAACATCAATGAAGGTAATAAAATATTTATTTT
1 TTTAAGCAAATATACATAGCAATATTTTGTACTAACATCAATGAAGGTAATAAAATATTTATTCC
89034796 CTCCTCTAGCTTCACCTTTGCT
66 CTCCTCTAGCTTCACCTTTGCT
*
89034818 TTTAAGCAAATATACATAGCAATATTTTGTACTATCATCAATGAAGGTAATAAAATATTTATTCC
1 TTTAAGCAAATATACATAGCAATATTTTGTACTAACATCAATGAAGGTAATAAAATATTTATTCC
89034883 CTCCTCTAG
66 CTCCTCTAG
89034892 TTTGAATAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 70 1.00
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (87 bp):
TTTAAGCAAATATACATAGCAATATTTTGTACTAACATCAATGAAGGTAATAAAATATTTATTCC
CTCCTCTAGCTTCACCTTTGCT
Found at i:89038288 original size:13 final size:14
Alignment explanation
Indices: 89038270--89038306 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
89038260 ATAATTTTTA
89038270 AATTT-AAATAAAT
1 AATTTAAAATAAAT
89038283 AATTTAAAATAAA-
1 AATTTAAAATAAAT
*
89038296 ATTTTAAAATA
1 AATTTAAAATA
89038307 TATAGACATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 15 0.68
14 7 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AATTTAAAATAAAT
Found at i:89042730 original size:9 final size:9
Alignment explanation
Indices: 89042578--89042743 Score: 65
Period size: 9 Copynumber: 17.6 Consensus size: 9
89042568 TGATATAAAT
89042578 TTAAAATTA
1 TTAAAATTA
89042587 -TAAAA-TA
1 TTAAAATTA
*
89042594 TAAAAATCTA
1 TTAAAAT-TA
*
89042604 AT-AAATTA
1 TTAAAATTA
*
89042612 TACAAGAATT-
1 T-TAA-AATTA
89042622 TATAAAATTA
1 T-TAAAATTA
*
89042632 ATAAAACTTA
1 TTAAAA-TTA
89042642 TTTAAAA-TA
1 -TTAAAATTA
89042651 TTTAAAATTA
1 -TTAAAATTA
**
89042661 GAAAAATGTA
1 TTAAAAT-TA
* *
89042671 TTATAATTC
1 TTAAAATTA
*
89042680 TTAAAAAATAA
1 TT--AAAATTA
*
89042691 TAATAAATTA
1 TTA-AAATTA
89042701 TTAAAATT-
1 TTAAAATTA
*
89042709 TATAAAGAATA
1 T-TAAA-ATTA
89042720 TTAAAATTA
1 TTAAAATTA
89042729 TTAAAATTA
1 TTAAAATTA
89042738 TATAAA
1 T-TAAA
89042744 CATATAAAAA
Statistics
Matches: 117, Mismatches: 22, Indels: 35
0.67 0.13 0.20
Matches are distributed among these distances:
7 2 0.02
8 12 0.10
9 53 0.45
10 35 0.30
11 15 0.13
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (9 bp):
TTAAAATTA
Found at i:89042748 original size:28 final size:28
Alignment explanation
Indices: 89042543--89042762 Score: 111
Period size: 28 Copynumber: 7.9 Consensus size: 28
89042533 AAAAAAACTT
* * *
89042543 TAAAAAATATAAAAAATATTAAAATTGA
1 TAAAGAATATAAAAATTATTAAAATTTA
* *
89042571 TATA-AAT-TTAAAATTA-TAAAA--TA
1 TAAAGAATATAAAAATTATTAAAATTTA
* *
89042594 TAAA-AATCTAATAAATTATACAAGAATTTA
1 TAAAGAATATAA-AAATTAT-TAA-AATTTA
* *
89042624 TAAA-ATTAATAAAACTTATTTAAAATATT-
1 TAAAGAAT-ATAAAAATTA-TTAAAAT-TTA
* * *
89042653 TAAA-ATTAGAAAAATGTATTATAATTCT-
1 TAAAGAATATAAAAAT-TATTAAAATT-TA
*
89042681 TAAAAAATAATAATAAATTATTAAAATTTA
1 TAAAGAAT-ATAA-AAATTATTAAAATTTA
*
89042711 TAAAGAATATTAAAATTATTAAAATTATA
1 TAAAGAATATAAAAATTATTAAAATT-TA
* * *
89042740 TAAA-CATATAAAAAGTATAAAAA
1 TAAAGAATATAAAAATTATTAAAA
89042763 AAACATAAAA
Statistics
Matches: 152, Mismatches: 23, Indels: 34
0.73 0.11 0.16
Matches are distributed among these distances:
23 7 0.05
24 2 0.01
25 11 0.07
26 7 0.05
27 6 0.04
28 51 0.34
29 24 0.16
30 36 0.24
31 8 0.05
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (28 bp):
TAAAGAATATAAAAATTATTAAAATTTA
Found at i:89043181 original size:8 final size:8
Alignment explanation
Indices: 89043168--89043239 Score: 51
Period size: 9 Copynumber: 8.5 Consensus size: 8
89043158 GTTTTGTTAA
89043168 TTTTATAT
1 TTTTATAT
89043176 TTTTATAT
1 TTTTATAT
89043184 CAATTTTCAT-T
1 ---TTTT-ATAT
89043195 TTTTA-AT
1 TTTTATAT
89043202 TTTTAATAT
1 TTTT-ATAT
89043211 TTTT-TAT
1 TTTTATAT
*
89043218 TTTTCTAAT
1 TTTTAT-AT
89043227 TTTCTATAT
1 TTT-TATAT
89043236 TTTT
1 TTTT
89043240 TCTTATTTTT
Statistics
Matches: 53, Mismatches: 1, Indels: 20
0.72 0.01 0.27
Matches are distributed among these distances:
7 13 0.25
8 15 0.28
9 16 0.30
10 2 0.04
11 5 0.09
12 2 0.04
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (8 bp):
TTTTATAT
Found at i:89043204 original size:25 final size:24
Alignment explanation
Indices: 89043168--89043229 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 24
89043158 GTTTTGTTAA
89043168 TTTTATATTTTTATATCAATTTTCATT
1 TTTTA-ATTTTTA-AT-AATTTTCATT
* *
89043195 TTTTAATTTTTAATATTTTTTATT
1 TTTTAATTTTTAATAATTTTCATT
89043219 TTTCTAATTTT
1 TTT-TAATTTT
89043230 CTATATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 11 0.34
25 9 0.28
26 7 0.22
27 5 0.16
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (24 bp):
TTTTAATTTTTAATAATTTTCATT
Found at i:89043216 original size:10 final size:9
Alignment explanation
Indices: 89043192--89043259 Score: 61
Period size: 8 Copynumber: 7.7 Consensus size: 9
89043182 ATCAATTTTC
89043192 ATTTTTTA-
1 ATTTTTTAT
*
89043200 ATTTTTAAT
1 ATTTTTTAT
89043209 ATTTTTTAT
1 ATTTTTTAT
*
89043218 -TTTTCTA-
1 ATTTTTTAT
*
89043225 ATTTTCTAT
1 ATTTTTTAT
*
89043234 ATTTTTTCTT
1 ATTTTTT-AT
89043244 ATTTTTTAAT
1 ATTTTTT-AT
89043254 ATTTTT
1 ATTTTT
89043260 ATGGAAAAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
8 20 0.41
9 14 0.29
10 15 0.31
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (9 bp):
ATTTTTTAT
Found at i:89043235 original size:25 final size:24
Alignment explanation
Indices: 89043198--89043258 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 24
89043188 TTTCATTTTT
89043198 TAATTTTTAATATTTTTTATTTTT
1 TAATTTTTAATATTTTTTATTTTT
*
89043222 CTAATTTTCTATATTTTTTCTTATTTTT
1 -TAATTTT-TA-ATATTTT-TTATTTTT
89043250 TAATATTTT
1 TAAT-TTTT
89043259 TATGGAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
25 7 0.23
26 2 0.06
27 11 0.35
28 11 0.35
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (24 bp):
TAATTTTTAATATTTTTTATTTTT
Found at i:89043241 original size:19 final size:20
Alignment explanation
Indices: 89043217--89043259 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
89043207 ATATTTTTTA
89043217 TTTTTCTAATTTTCT-ATAT
1 TTTTTCTAATTTTCTAATAT
* *
89043236 TTTTTCTTATTTTTTAATAT
1 TTTTTCTAATTTTCTAATAT
89043256 TTTT
1 TTTT
89043260 ATGGAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTTCTAATTTTCTAATAT
Found at i:89043249 original size:20 final size:19
Alignment explanation
Indices: 89043217--89043259 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
89043207 ATATTTTTTA
89043217 TTTTTCTAATTTTCT-ATAT
1 TTTTTCTAATTTT-TAATAT
*
89043236 TTTTTCTTATTTTTTAATAT
1 TTTTTC-TAATTTTTAATAT
89043256 TTTT
1 TTTT
89043260 ATGGAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTTCTAATTTTTAATAT
Found at i:89048908 original size:24 final size:24
Alignment explanation
Indices: 89048876--89048926 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
89048866 AAGTCTGTCA
**
89048876 GGATAGGATTTAGGAGTTGATAAG
1 GGATAGGATTTAGGAGCAGATAAG
89048900 GGATAGGATTTAGGAGCAGATAAG
1 GGATAGGATTTAGGAGCAGATAAG
89048924 GGA
1 GGA
89048927 GGAAATCTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.02, G:0.39, T:0.24
Consensus pattern (24 bp):
GGATAGGATTTAGGAGCAGATAAG
Found at i:89050377 original size:27 final size:26
Alignment explanation
Indices: 89050337--89050448 Score: 125
Period size: 27 Copynumber: 4.2 Consensus size: 26
89050327 AGGAAGCGTC
* *
89050337 CTGGCGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
89050364 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
*
89050391 CTGGTGGTTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTG-AT
* * *
89050419 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGAT
89050445 CTGG
1 CTGG
89050449 CAGCCATGCT
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
26 7 0.10
27 50 0.68
28 16 0.22
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.37
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:89056710 original size:24 final size:24
Alignment explanation
Indices: 89056665--89056715 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
89056655 AAGTCTGTCA
***
89056665 GGATAGGATTTAGGAGTTGATAAG
1 GGATAGGATTTAGGAACAGATAAG
89056689 GGATAGGATTTAGGAACAGATAAG
1 GGATAGGATTTAGGAACAGATAAG
89056713 GGA
1 GGA
89056716 GGAAATCTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.02, G:0.37, T:0.24
Consensus pattern (24 bp):
GGATAGGATTTAGGAACAGATAAG
Found at i:89058174 original size:27 final size:26
Alignment explanation
Indices: 89058144--89058236 Score: 114
Period size: 27 Copynumber: 3.4 Consensus size: 26
89058134 GGCGACTATT
89058144 CCACAATTATCTGATCTGGTGGCTCTG
1 CCAC-ATTATCTGATCTGGTGGCTCTG
* *
89058171 CCACATATATCTGTTCTGGTGGTTCTG
1 CCACAT-TATCTGATCTGGTGGCTCTG
*
89058198 CCACGATTATCTGTATCTGGTGACTCTG
1 CCAC-ATTATCTG-ATCTGGTGGCTCTG
*
89058226 TCACATTATCT
1 CCACATTATCT
89058237 ATTCTGGCAG
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
26 2 0.04
27 39 0.68
28 16 0.28
ACGTcount: A:0.18, C:0.25, G:0.19, T:0.38
Consensus pattern (26 bp):
CCACATTATCTGATCTGGTGGCTCTG
Found at i:89064097 original size:24 final size:24
Alignment explanation
Indices: 89064052--89064098 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
89064042 TATATATACC
89064052 AATTCAATCAATATAAATTCAATA
1 AATTCAATCAATATAAATTCAATA
89064076 AATTC-ATCACATACTAAA-TCAAT
1 AATTCAATCA-ATA-TAAATTCAAT
89064099 CCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (24 bp):
AATTCAATCAATATAAATTCAATA
Found at i:89064792 original size:20 final size:20
Alignment explanation
Indices: 89064769--89064826 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
89064759 CTTCTTTCTC
89064769 CTTTTCTTTCCTTTTTCTTT
1 CTTTTCTTTCCTTTTTCTTT
* * * *
89064789 CTTTCCTTCCCTGTTTCATT
1 CTTTTCTTTCCTTTTTCTTT
*
89064809 C-TATCTTTCTCTTTTTCT
1 CTTTTCTTTC-CTTTTTCT
89064827 ATTTCCATTT
Statistics
Matches: 28, Mismatches: 9, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
19 5 0.18
20 23 0.82
ACGTcount: A:0.03, C:0.29, G:0.02, T:0.66
Consensus pattern (20 bp):
CTTTTCTTTCCTTTTTCTTT
Found at i:89064866 original size:5 final size:5
Alignment explanation
Indices: 89064856--89064897 Score: 84
Period size: 5 Copynumber: 8.4 Consensus size: 5
89064846 TTTGTATTAT
89064856 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TA
89064898 AATTTACTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:89068624 original size:18 final size:19
Alignment explanation
Indices: 89068598--89068654 Score: 62
Period size: 20 Copynumber: 3.0 Consensus size: 19
89068588 AGATGACTAG
89068598 GATGAGAAATGG-ATATGA
1 GATGAGAAATGGAATATGA
*
89068616 GATGGGAAATGGAATATGA
1 GATGAGAAATGGAATATGA
* * *
89068635 AATGATTAAATGGGATATGA
1 GATGA-GAAATGGAATATGA
89068655 ATATTGAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 11 0.34
19 9 0.28
20 12 0.38
ACGTcount: A:0.44, C:0.00, G:0.32, T:0.25
Consensus pattern (19 bp):
GATGAGAAATGGAATATGA
Found at i:89077845 original size:46 final size:46
Alignment explanation
Indices: 89077745--89077900 Score: 133
Period size: 46 Copynumber: 3.3 Consensus size: 46
89077735 GCCATGTCTG
* * * **
89077745 AGACAGGTCTTACACTAGCTCGT-AT-ATCTCGAGGCCGATGTATGTCTT
1 AGACATGTCTTACACTAGCTC-TCATAATCT---GGTCGATGCATGTCCC
*
89077793 AGACATGTCTTACACTAGCTCT-AGT-CTCAAT-GTCGATGCATGTCCC
1 AGACATGTCTTACACTAGCTCTCA-TAATC--TGGTCGATGCATGTCCC
* * *
89077839 GGACATGTCTTACACTGGCTCTCATAATCTGGTCGATGCATGTCCT
1 AGACATGTCTTACACTAGCTCTCATAATCTGGTCGATGCATGTCCC
89077885 AGACATGTCTTACACT
1 AGACATGTCTTACACT
89077901 GGTACACATA
Statistics
Matches: 91, Mismatches: 11, Indels: 14
0.78 0.09 0.12
Matches are distributed among these distances:
45 1 0.01
46 61 0.67
47 5 0.05
48 23 0.25
50 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.31
Consensus pattern (46 bp):
AGACATGTCTTACACTAGCTCTCATAATCTGGTCGATGCATGTCCC
Found at i:89077901 original size:46 final size:45
Alignment explanation
Indices: 89077780--89077902 Score: 142
Period size: 46 Copynumber: 2.7 Consensus size: 45
89077770 ATCTCGAGGC
* * * *
89077780 CGATGTATGTCTTAGACATGTCTTACACTAGCTCTAGTCTCAATGT
1 CGATGCATGTCCTAGACATGTCTTACACTGGCTCTAGTATC-ATGT
**
89077826 CGATGCATGTCCCGGACATGTCTTACACTGGCTCTCA-TAATC-TGGT
1 CGATGCATGTCCTAGACATGTCTTACACTGGCTCT-AGT-ATCAT-GT
89077872 CGATGCATGTCCTAGACATGTCTTACACTGG
1 CGATGCATGTCCTAGACATGTCTTACACTGG
89077903 TACACATACC
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
45 1 0.02
46 62 0.94
47 3 0.05
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (45 bp):
CGATGCATGTCCTAGACATGTCTTACACTGGCTCTAGTATCATGT
Found at i:89080763 original size:92 final size:93
Alignment explanation
Indices: 89080651--89080851 Score: 341
Period size: 92 Copynumber: 2.2 Consensus size: 93
89080641 TGAGACTTAC
* *
89080651 CCTGGACTGGTAATCCTAATTGACTGGATTTAGCTTGGACTGGTAATCCAGATATGACTCTATAG
1 CCTGGACTGGTAATCCTAATTGACTGGATTTAGCCTGGACTGGTAATCCAGATATGACGCTATAG
*
89080716 G-GATTCTTTGTCTTATAAAGGATTTAG
66 GTAATTCTTTGTCTTATAAAGGATTTAG
* *
89080743 CCTGGACTGGTAATCCTAATTGACTGGATTTAGCCTGGATTGGTAATCCATATATGACGCTATAG
1 CCTGGACTGGTAATCCTAATTGACTGGATTTAGCCTGGACTGGTAATCCAGATATGACGCTATAG
89080808 GTAATTCTTTGTCTTATAAAGGATTTAG
66 GTAATTCTTTGTCTTATAAAGGATTTAG
*
89080836 CCTGGACTAGTAATCC
1 CCTGGACTGGTAATCC
89080852 GACAAAGCTC
Statistics
Matches: 102, Mismatches: 6, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
92 62 0.61
93 40 0.39
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.35
Consensus pattern (93 bp):
CCTGGACTGGTAATCCTAATTGACTGGATTTAGCCTGGACTGGTAATCCAGATATGACGCTATAG
GTAATTCTTTGTCTTATAAAGGATTTAG
Found at i:89084318 original size:18 final size:19
Alignment explanation
Indices: 89084275--89084320 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
89084265 GGTTTTCTCC
*
89084275 AAAATGAAAATGACAATTGT
1 AAAATGAAAATGA-AATTGA
*
89084295 AAAATGAAAATG-ATTTGA
1 AAAATGAAAATGAAATTGA
89084313 AAAATGAA
1 AAAATGAA
89084321 TTTATGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 12 0.50
20 12 0.50
ACGTcount: A:0.59, C:0.02, G:0.15, T:0.24
Consensus pattern (19 bp):
AAAATGAAAATGAAATTGA
Found at i:89085018 original size:272 final size:272
Alignment explanation
Indices: 89084526--89085077 Score: 809
Period size: 272 Copynumber: 2.0 Consensus size: 272
89084516 ATAGAAAAAT
*
89084526 AAATATTGGGTTGGATCAAATTATAAAGTATTGGATTAAAAGCCAAAGAATTACTTGTAATCAGA
1 AAATATTGGGTTGGATCAAATTATAAAGTATTGGATTAAAAGCCAAAGAAGTACTTGTAATCAGA
* *
89084591 CCCGATAGGGAAGAAGCCTAAAAGTCCATTATGTTATAAGGTGGGATAACAAATCATAGTATCAT
66 CCCGATAGGGAAGAAGCCTAAAAGCCCATTATGTTATAAGGTGGGACAACAAATCATAGTATCAT
* ** *
89084656 TAACTAAAGTTGTTGCCGCCTACATCCTAGTTGAACTAAGGTTTCACTATTCTAGTTAAAATGAA
131 TAACTAAAGTTGTCGCCGCCTACATCCTAGTTGAACTAACATTTCACTATTCTAGTTAAAATAAA
89084721 CTCCTATAATTAAACAAAAGTTCTACATTCTCTCATTAAAAATAGATGGCACCAGAAAGGCTATT
196 CTCCTATAATTAAACAAAAGTTCTACATTCTCTCATTAAAAATAGATGGCACCAGAAAGGCTATT
89084786 TACACAACTTTA
261 TACACAACTTTA
* ** *
89084798 AAATATTGGGTTGGATCAAATTATAAAGTATTGGATTGAAAGCCCGAGAAGTACTTGTAATTAGA
1 AAATATTGGGTTGGATCAAATTATAAAGTATTGGATTAAAAGCCAAAGAAGTACTTGTAATCAGA
** * *
89084863 CTTGATAGGGAATAAGCCTAAAAGCCCCTTATGTTATAAGGTGGGACAACAAATCATAGTATCAT
66 CCCGATAGGGAAGAAGCCTAAAAGCCCATTATGTTATAAGGTGGGACAACAAATCATAGTATCAT
* * *** *
89084928 TAACTAAGGTTGTCG-CTCCTACATCCTAGTTGAACTAACATTTTGTTTTTCTAGTTAAAATAAA
131 TAACTAAAGTTGTCGCCGCCTACATCCTAGTTGAACTAACATTTCACTATTCTAGTTAAAATAAA
** * * ** * * * *
89084992 CTTTTTATGATTAAATAAGGGTTCTACATTCTCTCCTTATAAATAGATGGCACCAGTAGGGCTAT
196 C-TCCTATAATTAAACAAAAGTTCTACATTCTCTCATTAAAAATAGATGGCACCAGAAAGGCTAT
89085057 TTACACAACTTTA
260 TTACACAACTTTA
89085070 AAATATTG
1 AAATATTG
89085078 TTACTCTGCT
Statistics
Matches: 248, Mismatches: 31, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
271 42 0.17
272 206 0.83
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (272 bp):
AAATATTGGGTTGGATCAAATTATAAAGTATTGGATTAAAAGCCAAAGAAGTACTTGTAATCAGA
CCCGATAGGGAAGAAGCCTAAAAGCCCATTATGTTATAAGGTGGGACAACAAATCATAGTATCAT
TAACTAAAGTTGTCGCCGCCTACATCCTAGTTGAACTAACATTTCACTATTCTAGTTAAAATAAA
CTCCTATAATTAAACAAAAGTTCTACATTCTCTCATTAAAAATAGATGGCACCAGAAAGGCTATT
TACACAACTTTA
Found at i:89094728 original size:49 final size:49
Alignment explanation
Indices: 89094656--89094871 Score: 227
Period size: 49 Copynumber: 4.5 Consensus size: 49
89094646 TGAGGTCACG
*
89094656 TGTGTAGTACTAAGTGTAGGCTACTACGTGTACCGGATAATCGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATCGGTCGCA
* * * * *
89094705 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCTGATAACTTCGATCACA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA--TCGGTCGCA
* * *
89094756 TGTATAGTACTAAGTGCAGGCTACTACGTGTATC--A-AAT-GGT--TA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATCGGTCGCA
* *
89094799 -G-GTCACGT-GT-AGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
1 TGTGT-A-GTACTAAGTGCAGGCTACTACGTGTACCGGATAATCGGTCGCA
89094846 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
89094872 TGCGTACTAG
Statistics
Matches: 136, Mismatches: 17, Indels: 28
0.75 0.09 0.15
Matches are distributed among these distances:
41 22 0.16
42 3 0.02
43 4 0.03
44 3 0.02
45 5 0.04
46 1 0.01
47 3 0.02
48 5 0.04
49 53 0.39
51 37 0.27
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATCGGTCGCA
Found at i:89096415 original size:40 final size:40
Alignment explanation
Indices: 89096337--89096560 Score: 283
Period size: 40 Copynumber: 5.5 Consensus size: 40
89096327 ACCCAAGTAT
* * *
89096337 CTTCGGGATTTAG-CCGGATATA-ACAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* **
89096376 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
89096416 CTTTGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
89096456 CTTTGGGACTTAGCCCGGGTATAG-CAACTACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTA---GCACAAATGC
* *
89096499 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
89096539 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
89096561 CATCCGAATA
Statistics
Matches: 163, Mismatches: 15, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
39 12 0.07
40 115 0.71
41 1 0.01
43 35 0.21
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:89096522 original size:83 final size:80
Alignment explanation
Indices: 89096337--89096560 Score: 283
Period size: 83 Copynumber: 2.8 Consensus size: 80
89096327 ACCCAAGTAT
* * * *
89096337 CTTCGGGATTTAG-CCGGATATA-ACAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAG
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
**
89096400 TCACTAGCATGAATGC
65 TCACTAGCACAAATGC
* * *
89096416 CTTTGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTTGGGACTTAGCCCGGGTATAG-
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
89096480 CAACTACTCGCACAAATGC
66 C-ACTA---GCACAAATGC
* *
89096499 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
89096561 CATCCGAATA
Statistics
Matches: 125, Mismatches: 14, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
79 12 0.10
80 47 0.38
81 1 0.01
83 65 0.52
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
CACTAGCACAAATGC
Found at i:89110054 original size:36 final size:36
Alignment explanation
Indices: 89110012--89110080 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
89110002 TTTGCCATAG
*
89110012 TTCGATCAGGATCCATTACTATAAGAAAACATAATA
1 TTCGATCAGGATCCATTACTACAAGAAAACATAATA
89110048 TTCGATCAGGATCCATTACTACAAGAAAACATA
1 TTCGATCAGGATCCATTACTACAAGAAAACATA
89110081 GTAATAAGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.43, C:0.19, G:0.12, T:0.26
Consensus pattern (36 bp):
TTCGATCAGGATCCATTACTACAAGAAAACATAATA
Found at i:89116038 original size:25 final size:24
Alignment explanation
Indices: 89115984--89116038 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
89115974 TTTTTTTAAG
*
89115984 CAAAATTTTATAACATTATTTTAT
1 CAAAATTTTATAACATTATCTTAT
* *
89116008 CTAAATTTTATAACAATTCTCTTAT
1 CAAAATTTTATAAC-ATTATCTTAT
*
89116033 GAAAAT
1 CAAAAT
89116039 AAACCAAGCT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 13 0.52
25 12 0.48
ACGTcount: A:0.42, C:0.11, G:0.02, T:0.45
Consensus pattern (24 bp):
CAAAATTTTATAACATTATCTTAT
Found at i:89119743 original size:37 final size:36
Alignment explanation
Indices: 89119692--89119766 Score: 91
Period size: 37 Copynumber: 2.1 Consensus size: 36
89119682 TATTTTAAAA
*
89119692 AATATTATTTTAATAGT-TTAATATTAAATTTAAT-TT
1 AATATTATCTTAATAGTATT-ATATT-AATTTAATATT
*
89119728 AATATTTATCTTAATAGTATTTTATTAATTTAATATT
1 AATA-TTATCTTAATAGTATTATATTAATTTAATATT
89119765 AA
1 AA
89119767 AATGATTAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
36 12 0.35
37 20 0.59
38 2 0.06
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (36 bp):
AATATTATCTTAATAGTATTATATTAATTTAATATT
Found at i:89123863 original size:37 final size:36
Alignment explanation
Indices: 89123817--89123924 Score: 116
Period size: 37 Copynumber: 2.9 Consensus size: 36
89123807 ATTCCAAAAA
89123817 TAATATTATTTTAATAGTTTAATATTACATTTAAT-T
1 TAATATTATTTTAATAGTTTAATATTA-ATTTAATAT
*
89123853 TAATACTTATTTTAATAGTATT-TTATTAATTTAATAT
1 TAATA-TTATTTTAATAGT-TTAATATTAATTTAATAT
*
89123890 TAAAGTGATTATCTTAATA-TTTAAT-TTAATTTAAT
1 T-AA-T-ATTATTTTAATAGTTTAATATTAATTTAAT
89123925 GTTTATCTTG
Statistics
Matches: 62, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
36 12 0.19
37 32 0.52
38 6 0.10
39 11 0.18
40 1 0.02
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.55
Consensus pattern (36 bp):
TAATATTATTTTAATAGTTTAATATTAATTTAATAT
Found at i:89123890 original size:11 final size:11
Alignment explanation
Indices: 89123817--89123892 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
89123807 ATTCCAAAAA
*
89123817 TAATATTATTT
1 TAATATTAATT
89123828 TAATAGTTTAATAT
1 TAATA--TTAAT-T
89123842 TACAT-TTAATT
1 TA-ATATTAATT
*
89123853 TAATACTTATTT
1 TAATA-TTAATT
*
89123865 TAATAGT-ATT
1 TAATATTAATT
89123875 T--TATTAATT
1 TAATATTAATT
89123884 TAATATTAA
1 TAATATTAA
89123893 AGTGATTATC
Statistics
Matches: 51, Mismatches: 5, Indels: 18
0.69 0.07 0.24
Matches are distributed among these distances:
8 3 0.06
9 4 0.08
10 5 0.10
11 15 0.29
12 15 0.29
13 4 0.08
14 3 0.06
15 2 0.04
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (11 bp):
TAATATTAATT
Found at i:89125996 original size:74 final size:74
Alignment explanation
Indices: 89125909--89126127 Score: 338
Period size: 74 Copynumber: 3.0 Consensus size: 74
89125899 AAAGTAATAC
* * *
89125909 TGAGATGCCTTTATTGGTCCTTTGTCATAAAGTTGTGTAACAATTATTATTATTTAAATCATCTT
1 TGAGATGCCTTTATTGGTCCTTTATCATATAGTTGTGTTACAATTATTATTATTTAAATCATCTT
89125974 GTCTTGTCT
66 GTCTTGTCT
* * * *
89125983 TGAGATGTCTTTATTGGTCCTTTATCATGTAGTTGTGTTACAGTTATTATAATTTAAATCATCTT
1 TGAGATGCCTTTATTGGTCCTTTATCATATAGTTGTGTTACAATTATTATTATTTAAATCATCTT
89126048 GTCTTGTCT
66 GTCTTGTCT
*
89126057 TGAGATGCCTTTATTGGTCCTTTATCACATAGTTGTGTTAC-A--ATTATTATTTAAATCATCTT
1 TGAGATGCCTTTATTGGTCCTTTATCATATAGTTGTGTTACAATTATTATTATTTAAATCATCTT
89126119 GTCTT-TCT
66 GTCTTGTCT
89126127 T
1 T
89126128 AAGGCTAAGA
Statistics
Matches: 133, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
70 4 0.03
71 24 0.18
74 105 0.79
ACGTcount: A:0.23, C:0.14, G:0.15, T:0.49
Consensus pattern (74 bp):
TGAGATGCCTTTATTGGTCCTTTATCATATAGTTGTGTTACAATTATTATTATTTAAATCATCTT
GTCTTGTCT
Found at i:89127688 original size:26 final size:26
Alignment explanation
Indices: 89127658--89127709 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
89127648 AAATTAGTTT
89127658 TTATAACTTTAATGTAATCATACTTC
1 TTATAACTTTAATGTAATCATACTTC
89127684 TTATAACTTTAATGTAATCATACTTC
1 TTATAACTTTAATGTAATCATACTTC
89127710 CGAATTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.15, G:0.04, T:0.46
Consensus pattern (26 bp):
TTATAACTTTAATGTAATCATACTTC
Found at i:89129947 original size:26 final size:27
Alignment explanation
Indices: 89129910--89129963 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
89129900 GTTACTCAAG
*
89129910 CTGTTGTTGATTGCCTTCTAGAG-CTT
1 CTGTTGTCGATTGCCTTCTAGAGTCTT
*
89129936 CTGTTGTCGATTGTCTTCTAGAGTCTT
1 CTGTTGTCGATTGCCTTCTAGAGTCTT
89129963 C
1 C
89129964 AATTGAAGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 21 0.84
27 4 0.16
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.46
Consensus pattern (27 bp):
CTGTTGTCGATTGCCTTCTAGAGTCTT
Done.