Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 129432109
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: 129432109
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 196 of 425
Found at i:59653123 original size:14 final size:14
Alignment explanation
Indices: 59653106--59653136 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
59653096 AAAAAATCAC
59653106 TTAGTAAAAGTTGT
1 TTAGTAAAAGTTGT
59653120 TTAGTAAAAGTTGT
1 TTAGTAAAAGTTGT
59653134 TTA
1 TTA
59653137 TTACACTCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.45
Consensus pattern (14 bp):
TTAGTAAAAGTTGT
Found at i:59654594 original size:42 final size:41
Alignment explanation
Indices: 59654543--59654690 Score: 136
Period size: 42 Copynumber: 3.5 Consensus size: 41
59654533 TGAGTTTATT
* *
59654543 TGTAAGACCATACCTGGGATATGACATTATTATGAGATTTCG
1 TGTAAGACCATATCTGGGATATGACATTA-TATGAGATATCG
* * * *
59654585 TGTAGGACCATGTCTGGGACATGGCATTGATATGAGA-ATCG
1 TGTAAGACCATATCTGGGATATGACATT-ATATGAGATATCG
* * * * ** *
59654626 TGTAAGAACATAGCTGGGCTATTAGCATCTATATGAGATCCCA
1 TGTAAGACCATATCTGGGATATGA-CAT-TATATGAGATATCG
59654669 TGTAAGACCATATCTGGGATAT
1 TGTAAGACCATATCTGGGATAT
59654691 AAAATTGGTA
Statistics
Matches: 82, Mismatches: 20, Indels: 7
0.75 0.18 0.06
Matches are distributed among these distances:
41 19 0.23
42 41 0.50
43 22 0.27
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (41 bp):
TGTAAGACCATATCTGGGATATGACATTATATGAGATATCG
Found at i:59662796 original size:22 final size:22
Alignment explanation
Indices: 59662769--59662810 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
59662759 GCATGAAAAG
59662769 AGATGTTTCTAAATTTGTATCA
1 AGATGTTTCTAAATTTGTATCA
*
59662791 AGATGTTTCTGAATTTGTAT
1 AGATGTTTCTAAATTTGTAT
59662811 TGAAATGCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.48
Consensus pattern (22 bp):
AGATGTTTCTAAATTTGTATCA
Found at i:59667014 original size:29 final size:30
Alignment explanation
Indices: 59666981--59667040 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
59666971 TTCCCGAGCC
59666981 TAGGGGAAAAAGTGTAAATATG-CAAAGTT
1 TAGGGGAAAAAGTGTAAATATGCCAAAGTT
* * * *
59667010 TAGGGGCAAAATTGTAATTTTGCCAAAGTT
1 TAGGGGAAAAAGTGTAAATATGCCAAAGTT
59667040 T
1 T
59667041 GAGTTAAGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.38, C:0.07, G:0.25, T:0.30
Consensus pattern (30 bp):
TAGGGGAAAAAGTGTAAATATGCCAAAGTT
Found at i:59669052 original size:2 final size:2
Alignment explanation
Indices: 59669045--59669083 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
59669035 TCATGACATG
59669045 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 T
59669084 GACTAGTCTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:59674104 original size:71 final size:71
Alignment explanation
Indices: 59674022--59674160 Score: 233
Period size: 71 Copynumber: 2.0 Consensus size: 71
59674012 GCATCCGAAC
* * *
59674022 TCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGTTGAGTCCGAG
1 TCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGTTGACTCCGAG
59674087 TTCGTG
66 TTCGTG
* *
59674093 TCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACGCCCGAGCTCGTTGAGTTGACTCCGAG
1 TCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGTTGACTCCGAG
59674158 TTC
66 TTC
59674161 ACTTAGGGGC
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 63 1.00
ACGTcount: A:0.18, C:0.20, G:0.30, T:0.32
Consensus pattern (71 bp):
TCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGTTGACTCCGAG
TTCGTG
Found at i:59679094 original size:46 final size:46
Alignment explanation
Indices: 59679044--59679216 Score: 165
Period size: 46 Copynumber: 3.7 Consensus size: 46
59679034 TGGTTGAGCA
*
59679044 TCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
** * * * *
59679090 TCCGAACTCGTTGAGTTGAGTTTGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
59679135 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGGTGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
59679183 CCCGAGCTCGTTGAGTTGGGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
59679217 GGGGCGGGTT
Statistics
Matches: 102, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 59 0.58
47 27 0.26
48 3 0.03
50 2 0.02
51 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:59679210 original size:93 final size:93
Alignment explanation
Indices: 59679041--59679211 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
59679031 GGATGGTTGA
* * *
59679041 GCATCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
**
59679106 TGAGTTTGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* *
59679134 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGGTGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
*
59679199 TGGGTCCGAGTTC
66 TGAGTCCGAGTTC
59679212 ACTTAGGGGC
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:59684675 original size:40 final size:40
Alignment explanation
Indices: 59684607--59684691 Score: 100
Period size: 40 Copynumber: 2.1 Consensus size: 40
59684597 ATTGCACTTA
* * * *
59684607 CGTGCCCCTGTTTGTACTTCTGTACCCCTAAAT-GTACATT
1 CGTGCCCCTCTTTGCACCTCAGTACCCCT-AATCGTACATT
* *
59684647 TGTGCCCCTCTTTGCACCTCAGTGCCCCTAATCGTACATT
1 CGTGCCCCTCTTTGCACCTCAGTACCCCTAATCGTACATT
59684687 CGTGC
1 CGTGC
59684692 TCTTGATTGC
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
39 3 0.08
40 34 0.92
ACGTcount: A:0.15, C:0.34, G:0.16, T:0.34
Consensus pattern (40 bp):
CGTGCCCCTCTTTGCACCTCAGTACCCCTAATCGTACATT
Found at i:59688312 original size:49 final size:49
Alignment explanation
Indices: 59688195--59688369 Score: 147
Period size: 49 Copynumber: 3.6 Consensus size: 49
59688185 TACGATGTCG
* * * * * * *
59688195 ATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATCT-AAGTC-G
1 ATGCCATGTCCCAAACA-GGTCTTACACTAGCTCTCATATATCGAGGCTA
** * *
59688243 ATGCCATACCCCAGACAGGTCTTACACTAGCTTTCATATATCGAGGCTA
1 ATGCCATGTCCCAAACAGGTCTTACACTAGCTCTCATATATCGAGGCTA
* * * * * * * * *
59688292 ATGCCATGTCCTAGATAGGTCTTACACTGGCTCTCATCTATTGATGTTG
1 ATGCCATGTCCCAAACAGGTCTTACACTAGCTCTCATATATCGAGGCTA
59688341 ATGCCATGTCCCAAACAGGTCTTACACTA
1 ATGCCATGTCCCAAACAGGTCTTACACTA
59688370 ACACATGTCA
Statistics
Matches: 99, Mismatches: 26, Indels: 3
0.77 0.20 0.02
Matches are distributed among these distances:
47 20 0.20
48 16 0.16
49 63 0.64
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.30
Consensus pattern (49 bp):
ATGCCATGTCCCAAACAGGTCTTACACTAGCTCTCATATATCGAGGCTA
Found at i:59688407 original size:44 final size:44
Alignment explanation
Indices: 59688340--59688558 Score: 163
Period size: 46 Copynumber: 4.8 Consensus size: 44
59688330 TATTGATGTT
* * *
59688340 GATGCCATGTCCCAAACAGGTCTTACACTAACACATGTCAA-GTC
1 GATG-CATGTCCCAGACATGTCTTACACTAGCACATGTCAAGGTC
* * *
59688384 GATGCCATGTCCCAGACAAGTCTTACACTAGCTTGCATATCTCAAGGTC
1 GATG-CATGTCCCAGACATGTCTTACACTA----GCACATGTCAAGGTC
* * * * *
59688433 GATGCATGTCCCAGACATGTCTTACACTGGCTCTTGTCGCAATGCC
1 GATGCATGTCCCAGACATGTCTTACACTAGCACATGT--CAAGGTC
* * * * **
59688479 GATGCATGTCCCAGACATGTCTTACATTGGCTTTCATAAT-GTGGTC
1 GATGCATGTCCCAGACATGTCTTACACTAGC--ACAT-GTCAAGGTC
*
59688525 GATGCATGTCCCAGACATGTCTTACAATAGCACA
1 GATGCATGTCCCAGACATGTCTTACACTAGCACA
59688559 CATATCACCC
Statistics
Matches: 142, Mismatches: 23, Indels: 20
0.77 0.12 0.11
Matches are distributed among these distances:
44 34 0.24
46 66 0.46
48 34 0.24
49 8 0.06
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.27
Consensus pattern (44 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCACATGTCAAGGTC
Found at i:59688497 original size:46 final size:45
Alignment explanation
Indices: 59688381--59688550 Score: 173
Period size: 46 Copynumber: 3.6 Consensus size: 45
59688371 CACATGTCAA
* * * * *
59688381 GTCGATGCCATGTCCCAGACAAGTCTTACACTAGCTTGCATATCTCAAG
1 GTCGATG-CATGTCCCAGACATGTCTTACACTGGC-T-C-TTTCACAAT
*
59688430 GTCGATGCATGTCCCAGACATGTCTTACACTGGCTCTTGTCGCAAT
1 GTCGATGCATGTCCCAGACATGTCTTACACTGGCTCTT-TCACAAT
* * *
59688476 GCCGATGCATGTCCCAGACATGTCTTACATTGG--CTTTCATAATGT
1 GTCGATGCATGTCCCAGACATGTCTTACACTGGCTCTTTCACAA--T
59688521 GGTCGATGCATGTCCCAGACATGTCTTACA
1 -GTCGATGCATGTCCCAGACATGTCTTACA
59688551 ATAGCACACA
Statistics
Matches: 107, Mismatches: 10, Indels: 11
0.84 0.08 0.09
Matches are distributed among these distances:
43 4 0.04
44 3 0.03
45 2 0.02
46 65 0.61
47 1 0.01
48 25 0.23
49 7 0.07
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (45 bp):
GTCGATGCATGTCCCAGACATGTCTTACACTGGCTCTTTCACAAT
Found at i:59688781 original size:23 final size:23
Alignment explanation
Indices: 59688751--59688799 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
59688741 AGTGGAATAT
59688751 CATATTCCATCAAATTTCCAATG
1 CATATTCCATCAAATTTCCAATG
59688774 CATATTCCATCAAATTTCCAATG
1 CATATTCCATCAAATTTCCAATG
59688797 CAT
1 CAT
59688800 TCAATCATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.35
Consensus pattern (23 bp):
CATATTCCATCAAATTTCCAATG
Found at i:59690180 original size:28 final size:28
Alignment explanation
Indices: 59690134--59690202 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
59690124 TTTAAAACCC
*
59690134 TAGGGGT-ATATCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
59690161 TAGGGGTAATTTCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
59690189 TAGGGGTAATTTCG
1 TAGGGGTAATTTCG
59690203 TGATCTACGC
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 7 0.17
28 33 0.82
ACGTcount: A:0.19, C:0.10, G:0.28, T:0.43
Consensus pattern (28 bp):
TAGGGGTAATTTCGGTAATTTTGCTCTT
Found at i:59691854 original size:20 final size:20
Alignment explanation
Indices: 59691831--59691868 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
59691821 CACATCCAAA
*
59691831 TACAAAATTTTAAAAATCTT
1 TACAAAATATTAAAAATCTT
*
59691851 TACAAAATATTGAAAATC
1 TACAAAATATTAAAAATC
59691869 GCGAATAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (20 bp):
TACAAAATATTAAAAATCTT
Found at i:59698190 original size:28 final size:28
Alignment explanation
Indices: 59698144--59698212 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
59698134 TTTAAAACCC
*
59698144 TAGGGGT-ATATCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
59698171 TAGGGGTAATTTCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
59698199 TAGGGGTAATTTCG
1 TAGGGGTAATTTCG
59698213 TGATCTACGC
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 7 0.17
28 33 0.82
ACGTcount: A:0.19, C:0.10, G:0.28, T:0.43
Consensus pattern (28 bp):
TAGGGGTAATTTCGGTAATTTTGCTCTT
Found at i:59700177 original size:20 final size:18
Alignment explanation
Indices: 59700140--59700182 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
59700130 CTATATCAAC
59700140 TCACAATTT-CAATTATT
1 TCACAATTTACAATTATT
59700157 TCACACATTTACAACTTATT
1 TCACA-ATTTACAA-TTATT
*
59700177 TTACAA
1 TCACAA
59700183 ACTTTACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 5 0.23
18 4 0.18
19 4 0.18
20 9 0.41
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (18 bp):
TCACAATTTACAATTATT
Found at i:59702102 original size:15 final size:15
Alignment explanation
Indices: 59702069--59702135 Score: 62
Period size: 15 Copynumber: 4.5 Consensus size: 15
59702059 AGAGATGGTA
* * *
59702069 AGAAAACCAAGATAA
1 AGAAATCCAAAATAG
*
59702084 AGAAATCCAAAATGG
1 AGAAATCCAAAATAG
* * *
59702099 AGAAACCCATAATAA
1 AGAAATCCAAAATAG
*
59702114 AGAGATCCAAAATAG
1 AGAAATCCAAAATAG
59702129 AGAAATC
1 AGAAATC
59702136 TAAGATACGA
Statistics
Matches: 39, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.58, C:0.15, G:0.15, T:0.12
Consensus pattern (15 bp):
AGAAATCCAAAATAG
Found at i:59706129 original size:98 final size:95
Alignment explanation
Indices: 59705985--59706234 Score: 301
Period size: 98 Copynumber: 2.6 Consensus size: 95
59705975 CTCCAAACAT
* *
59705985 GGTCTTACACTGGCTCACATATCTAA-GTCGATGCCATGTCCCAGACAGGTCTTACACTAGATT-
1 GGTCTTACACTGGCTCTCATCTC-AATGTCGATGCCATGTCCCAGACAGGTCTTACACTAGATTG
*
59706048 TCATTTATCAAGGCCGATGCCATGGCCCAGACA
65 T-ATATATCAAGGCCGATG-CATGGCCCAGACA
* * * *
59706081 GGTTTTACACTGGCTCTCATCTATCAGTGTCGATGCCATGTCCTAGACAGGTCTTACACTAGCTT
1 GGTCTTACACTGGCTCTCATC--TCAATGTCGATGCCATGTCCCAGACAGGTCTTACACTAGATT
* * * *
59706146 GTATATCTCGAGGCCGATGGATGTCCCAGACA
64 GTATATATCAAGGCCGATGCATGGCCCAGACA
* *
59706178 TGTCTTACACTGGCTCTCATCTCAATG-CTGATG-CATGTCCCAGACATGTCTTACACT
1 GGTCTTACACTGGCTCTCATCTCAATGTC-GATGCCATGTCCCAGACAGGTCTTACACT
59706235 GGCTCTCATA
Statistics
Matches: 133, Mismatches: 16, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
94 23 0.17
95 9 0.07
96 18 0.14
97 31 0.23
98 51 0.38
99 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (95 bp):
GGTCTTACACTGGCTCTCATCTCAATGTCGATGCCATGTCCCAGACAGGTCTTACACTAGATTGT
ATATATCAAGGCCGATGCATGGCCCAGACA
Found at i:59706219 original size:46 final size:47
Alignment explanation
Indices: 59705959--59706280 Score: 230
Period size: 49 Copynumber: 6.7 Consensus size: 47
59705949 ATAGGGTATG
* * *
59705959 ATGCTGATGCCATGTTCTCCAAACATGGTCTTACACTGGCTCACATATCTA
1 ATGCTGATGCCATG-TC-CCAGACAT-GTCTTACACTGGCTCTCATCTC-A
* * * * *
59706010 A-G-TCGATGCCATGTCCCAGACAGGTCTTACACTAGATTTCATTTATCA
1 ATGCT-GATGCCATGTCCCAGACATGTCTTACACTGGCTCTCA--TCTCA
* * * * *
59706058 AGGCCGATGCCATGGCCCAGACAGGTTTTACACTGGCTCTCATCTATCA
1 ATGCTGATGCCATGTCCCAGACATGTCTTACACTGGCTCTCATC--TCA
* * * * * * *
59706107 GTG-TCGATGCCATGTCCTAGACAGGTCTTACACTAGCTTGTATATCTCG
1 ATGCT-GATGCCATGTCCCAGACATGTCTTACACTGGC-TCT-CATCTCA
* * *
59706156 AGGCCGATG-GATGTCCCAGACATGTCTTACACTGGCTCTCATCTCA
1 ATGCTGATGCCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCA
59706202 ATGCTGATG-CATGTCCCAGACATGTCTTACACTGGCTCTCA--T-A
1 ATGCTGATGCCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCA
*
59706245 ATGTGGCTGATG-CATGTCCCAAACATGTCTTACACT
1 A--T-GCTGATGCCATGTCCCAGACATGTCTTACACT
59706281 AGCACACATA
Statistics
Matches: 220, Mismatches: 37, Indels: 33
0.76 0.13 0.11
Matches are distributed among these distances:
43 2 0.01
44 1 0.00
45 1 0.00
46 73 0.33
47 17 0.08
48 31 0.14
49 79 0.36
50 12 0.05
51 4 0.02
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.30
Consensus pattern (47 bp):
ATGCTGATGCCATGTCCCAGACATGTCTTACACTGGCTCTCATCTCA
Found at i:59706940 original size:20 final size:18
Alignment explanation
Indices: 59706903--59706945 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
59706893 CTATAGAAAC
59706903 TCACAATTT-CAATTATT
1 TCACAATTTACAATTATT
59706920 TCACACATTTACAACTTATT
1 TCACA-ATTTACAA-TTATT
*
59706940 TTACAA
1 TCACAA
59706946 ACTTTACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 5 0.23
18 4 0.18
19 4 0.18
20 9 0.41
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (18 bp):
TCACAATTTACAATTATT
Found at i:59713227 original size:30 final size:30
Alignment explanation
Indices: 59713193--59713289 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
59713183 TAAACTAAAA
59713193 TGAGCTAAGCTTTAGCTCATGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCATGAGCTAAAGT
* * * * * *
59713223 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCATGAGCTAAAGT
* * *
59713253 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCATGAGCT-AAAGT
59713283 TGAGCTA
1 TGAGCTA
59713290 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCATGAGCTAAAGT
Found at i:59715472 original size:30 final size:30
Alignment explanation
Indices: 59715401--59715483 Score: 98
Period size: 30 Copynumber: 2.7 Consensus size: 30
59715391 CTTTTGTTTC
*
59715401 AATTTCTTTTTCATATTCTTTTTCACTCTCA
1 AATTTCTTTTTCAT-TTCTTTTTCAATCTCA
59715432 AATTTC-TTTTCATTCTCTTTTTCAATCTC-
1 AATTTCTTTTTCATT-TCTTTTTCAATCTCA
* *
59715461 ATTTTCTTTTTCTTTTTCTTTTT
1 AATTTCTTTTTC-ATTTCTTTTT
59715484 GCTTTTCAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
29 6 0.13
30 32 0.70
31 8 0.17
ACGTcount: A:0.14, C:0.20, G:0.00, T:0.65
Consensus pattern (30 bp):
AATTTCTTTTTCATTTCTTTTTCAATCTCA
Found at i:59715574 original size:6 final size:5
Alignment explanation
Indices: 59715552--59715604 Score: 54
Period size: 5 Copynumber: 10.0 Consensus size: 5
59715542 CACTTGCCTC
*
59715552 TCTTT TCTTT T-TATT TCATTT TCTTTT TTTTT TCTTTT TCTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TC-TTT TCTTT TC-TTT TCTTT TCTTT
59715600 TCTTT
1 TCTTT
59715605 GTTTTCTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
4 1 0.02
5 26 0.63
6 13 0.32
7 1 0.02
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (5 bp):
TCTTT
Found at i:59715575 original size:16 final size:16
Alignment explanation
Indices: 59715554--59715595 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
59715544 CTTGCCTCTC
59715554 TTTTCTTTTTATTTCA
1 TTTTCTTTTTATTTCA
* *
59715570 TTTTCTTTTTTTTTTCT
1 TTTTC-TTTTTATTTCA
59715587 TTTTCTTTT
1 TTTTCTTTT
59715596 CTTTTCTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTCTTTTTATTTCA
Found at i:59715584 original size:11 final size:11
Alignment explanation
Indices: 59715554--59715604 Score: 61
Period size: 11 Copynumber: 4.7 Consensus size: 11
59715544 CTTGCCTCTC
59715554 TTTTCTTTT-T
1 TTTTCTTTTCT
*
59715564 ATTTCATTTTCT
1 TTTTC-TTTTCT
*
59715576 TTTTTTTTTCT
1 TTTTCTTTTCT
59715587 TTTTCTTTTC-
1 TTTTCTTTTCT
59715597 TTTTCTTT
1 TTTTCTTT
59715605 GTTTTCTCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
10 12 0.34
11 19 0.54
12 4 0.11
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTCTTTTCT
Found at i:59715586 original size:27 final size:27
Alignment explanation
Indices: 59715554--59715615 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
59715544 CTTGCCTCTC
*
59715554 TTTTCTTTTT-ATTTCATTTTCTTTTTT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT
*
59715581 TTTTCTTTTTCTTTTCTTTTCTTTGTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTT
*
59715608 TTCTCTTT
1 TTTTCTTT
59715616 ACAAGAATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 27 0.87
28 4 0.13
ACGTcount: A:0.03, C:0.15, G:0.02, T:0.81
Consensus pattern (27 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTT
Found at i:59715600 original size:16 final size:15
Alignment explanation
Indices: 59715554--59715604 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 15
59715544 CTTGCCTCTC
59715554 TTTTCTTTTTATTTCAT
1 TTTTCTTTTT-TTTC-T
*
59715571 TTTCTTTTTTTTTTCT
1 TTT-TCTTTTTTTTCT
59715587 TTTTCTTTTCTTTTCT
1 TTTTCTTTT-TTTTCT
59715603 TT
1 TT
59715605 GTTTTCTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
15 5 0.17
16 12 0.40
17 7 0.23
18 6 0.20
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTCTTTTTTTTCT
Found at i:59717710 original size:17 final size:17
Alignment explanation
Indices: 59717668--59717710 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
59717658 TGCACTTAAG
*
59717668 CCATTCATGCATTTTAT
1 CCATTCATGCATTTGAT
*
59717685 -CATCCCATGCATTTGAT
1 CCAT-TCATGCATTTGAT
59717702 CCATTCATG
1 CCATTCATG
59717711 GACTAGCCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
16 3 0.14
17 15 0.71
18 3 0.14
ACGTcount: A:0.23, C:0.28, G:0.09, T:0.40
Consensus pattern (17 bp):
CCATTCATGCATTTGAT
Found at i:59722031 original size:24 final size:24
Alignment explanation
Indices: 59722004--59722211 Score: 380
Period size: 24 Copynumber: 8.7 Consensus size: 24
59721994 ATTATGTTCA
*
59722004 CACACATAGTGCCATAGTGAATCG
1 CACACATAGTGCCATAGTAAATCG
59722028 CACACATAGTGCCATAGTAAATCG
1 CACACATAGTGCCATAGTAAATCG
59722052 CACACATAGTGCCATAGTAAATCG
1 CACACATAGTGCCATAGTAAATCG
*
59722076 CACACATAGTGCCATAGTAAATAG
1 CACACATAGTGCCATAGTAAATCG
59722100 CACACATAGTGCCATAGTAAATCG
1 CACACATAGTGCCATAGTAAATCG
59722124 CACACATAGTGCCATAGTAAATCG
1 CACACATAGTGCCATAGTAAATCG
59722148 CACACATAGTGCCATAGTAAATCG
1 CACACATAGTGCCATAGTAAATCG
* *
59722172 CACACACAGTACCATAGTAAATCG
1 CACACATAGTGCCATAGTAAATCG
59722196 CACACATAGTGCCATA
1 CACACATAGTGCCATA
59722212 TATTTCCAGC
Statistics
Matches: 177, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 177 1.00
ACGTcount: A:0.38, C:0.25, G:0.16, T:0.20
Consensus pattern (24 bp):
CACACATAGTGCCATAGTAAATCG
Found at i:59731909 original size:49 final size:49
Alignment explanation
Indices: 59731842--59732247 Score: 686
Period size: 49 Copynumber: 8.1 Consensus size: 49
59731832 TTTACCACAT
* *
59731842 ATATATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
1 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
59731891 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
59731940 ATATATATACACTTTTACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATATATACA----T----TTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
59731997 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
* *
59732046 ATATGTATACATTTTCACATTCATCACCTCGGCCATTAGGCCTTATCAC
1 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
*
59732095 ATATGTATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
*
59732144 ATATATATACATTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
1 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
59732193 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
59732242 ATATAT
1 ATATAT
59732248 TATTATGTAC
Statistics
Matches: 341, Mismatches: 8, Indels: 16
0.93 0.02 0.04
Matches are distributed among these distances:
49 291 0.85
53 2 0.01
57 48 0.14
ACGTcount: A:0.30, C:0.27, G:0.09, T:0.35
Consensus pattern (49 bp):
ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
Found at i:59734987 original size:40 final size:40
Alignment explanation
Indices: 59734943--59735333 Score: 622
Period size: 40 Copynumber: 9.8 Consensus size: 40
59734933 CCAGCATGAT
* * * *
59734943 TGCTCTTCGGGACCTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCATTAGCACGAA
* *
59734983 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACCAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCATTAGCACGAA
* * *
59735023 TGCTCTTCGGAATTTAGCCCGGATATATCATTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCATTAGCACGAA
* * * *
59735063 TGCTCTTCGGAATTTAGCCCAGATATATCATTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCATTAGCACGAA
59735103 TGCTCTTC-GAACTTAGTCCGGATACATCATTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCATTAGCACGAA
*
59735142 TGCTTTTCGGAACTTAGTCCGGATACATCATTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCATTAGCACGAA
59735182 TGCTCTTCGGAACTTAGTCCGGATACATCATTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCATTAGCACGAA
59735222 TGCTCTTCGGAACTTAGTCCGGATACATCATTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCATTAGCACGAA
* * *
59735262 TGCTCTTCGGAATTTAGCCCGGATATATCATTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCATTAGCACGAA
59735302 TGCTCTTCGGAACTTAGTCCGGATACATCATT
1 TGCTCTTCGGAACTTAGTCCGGATACATCATT
59735334 CTCAATTCTC
Statistics
Matches: 328, Mismatches: 22, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
39 34 0.10
40 294 0.90
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.28
Consensus pattern (40 bp):
TGCTCTTCGGAACTTAGTCCGGATACATCATTAGCACGAA
Found at i:59735301 original size:199 final size:200
Alignment explanation
Indices: 59734943--59735333 Score: 676
Period size: 199 Copynumber: 2.0 Consensus size: 200
59734933 CCAGCATGAT
*
59734943 TGCTCTTCGGGACCTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATA
1 TGCTCTTCGGAACCTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATA
* *
59735008 CATCACTAGCACCAATGCTCTTCGGAATTTAGCCCGGATATATCATTAGCACGAATGCTCTTCGG
66 CATCACTAGCACCAATGCTCTTCGGAACTTAGCCCGGATACATCATTAGCACGAATGCTCTTCGG
59735073 AATTTAGCCCAGATATATCATTAGCACGAATGCTCTTC-GAACTTAGTCCGGATACATCATTAGC
131 AATTTAGCCCAGATATATCATTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACATCATTAGC
59735137 ACGAA
196 ACGAA
* * * *
59735142 TGCTTTTCGGAACTTAGTCCGGATACATCATTAGCACGAATGCTCTTCGGAACTTAGTCCGGATA
1 TGCTCTTCGGAACCTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATA
* * *
59735207 CATCATTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACATCATTAGCACGAATGCTCTTCGG
66 CATCACTAGCACCAATGCTCTTCGGAACTTAGCCCGGATACATCATTAGCACGAATGCTCTTCGG
*
59735272 AATTTAGCCCGGATATATCATTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACATCATT
131 AATTTAGCCCAGATATATCATTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACATCATT
59735334 CTCAATTCTC
Statistics
Matches: 180, Mismatches: 11, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
199 157 0.87
200 23 0.13
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.28
Consensus pattern (200 bp):
TGCTCTTCGGAACCTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATA
CATCACTAGCACCAATGCTCTTCGGAACTTAGCCCGGATACATCATTAGCACGAATGCTCTTCGG
AATTTAGCCCAGATATATCATTAGCACGAATGCTCTTCGGAACTTAGTCCGGATACATCATTAGC
ACGAA
Found at i:59737260 original size:37 final size:36
Alignment explanation
Indices: 59737210--59737296 Score: 138
Period size: 37 Copynumber: 2.3 Consensus size: 36
59737200 TACGAAGTCT
59737210 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
1 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
*
59737246 GTACCCGGACATAATCTCCACACGTAGTCATTGGGTC
1 -TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
59737283 TCACCCGGAACATA
1 T-ACCCGG-ACATA
59737297 TTTCTAAGTT
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
36 1 0.02
37 41 0.87
38 5 0.11
ACGTcount: A:0.26, C:0.32, G:0.20, T:0.22
Consensus pattern (36 bp):
TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
Found at i:59737432 original size:49 final size:49
Alignment explanation
Indices: 59737365--59737770 Score: 677
Period size: 49 Copynumber: 8.1 Consensus size: 49
59737355 TTTACCACAT
*
59737365 ATATATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
1 ATATATATACATTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
*
59737414 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATATATACATTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
*
59737463 ATATATATACACTTTTACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATATATACA----T----TTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
*
59737520 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATATATACATTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
* *
59737569 ATATGTATACATTTTCACATTCATCACCTCGGCCATTAGGCCTTATCAC
1 ATATATATACATTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
*
59737618 ATATGTATACATTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
1 ATATATATACATTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
59737667 ATATATATACATTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
1 ATATATATACATTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
59737716 ATATATATACATTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
1 ATATATATACATTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
59737765 ATATAT
1 ATATAT
59737771 TATTATGTAC
Statistics
Matches: 343, Mismatches: 6, Indels: 16
0.94 0.02 0.04
Matches are distributed among these distances:
49 293 0.85
53 2 0.01
57 48 0.14
ACGTcount: A:0.29, C:0.27, G:0.09, T:0.35
Consensus pattern (49 bp):
ATATATATACATTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
Found at i:59741804 original size:28 final size:27
Alignment explanation
Indices: 59741749--59741843 Score: 124
Period size: 27 Copynumber: 3.6 Consensus size: 27
59741739 AACATGGCTG
* *
59741749 CCAGA-ACAGATAATGTGACAGAGTCA
1 CCAGATACAGATAATGTGGCAGAGCCA
*
59741775 CCAGATATAGATAATCGTGGCAGAGCCA
1 CCAGATACAGATAAT-GTGGCAGAGCCA
59741803 CCAGA-ACAGATATATGTGGCAGAGCCA
1 CCAGATACAGATA-ATGTGGCAGAGCCA
59741830 CCAGAT-CAGATAAT
1 CCAGATACAGATAAT
59741844 TTATGGCATA
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
26 7 0.11
27 37 0.61
28 17 0.28
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.17
Consensus pattern (27 bp):
CCAGATACAGATAATGTGGCAGAGCCA
Found at i:59741851 original size:55 final size:54
Alignment explanation
Indices: 59741749--59741858 Score: 141
Period size: 55 Copynumber: 2.0 Consensus size: 54
59741739 AACATGGCTG
* * *
59741749 CCAGAACAGATAATGTGACAGAGTCACCAGATATAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATAATGTGACAGAGCCACCAGATACAGATAATCATGGCAGAGCCA
* * *
59741803 CCAGAACAGATATATGTGGCAGAGCCACCAGAT-CAGATAATTTATGGCATAGCCA
1 CCAGAACAGATA-ATGTGACAGAGCCACCAGATACAGATAA-TCATGGCAGAGCCA
59741858 C
1 C
59741859 TAGGACGCTT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
54 18 0.38
55 30 0.62
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (54 bp):
CCAGAACAGATAATGTGACAGAGCCACCAGATACAGATAATCATGGCAGAGCCA
Found at i:59745499 original size:46 final size:46
Alignment explanation
Indices: 59745432--59745560 Score: 213
Period size: 46 Copynumber: 2.8 Consensus size: 46
59745422 TGTAACCCGC
* * * * *
59745432 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGTAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
59745478 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
59745524 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
59745561 TGCTCAACCA
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 78 1.00
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:59754303 original size:5 final size:5
Alignment explanation
Indices: 59754293--59754319 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
59754283 GTAATTTGGT
59754293 AATTA AATTA AATTA AATTA AATTA AA
1 AATTA AATTA AATTA AATTA AATTA AA
59754320 CCAAAATCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AATTA
Found at i:59757039 original size:7 final size:7
Alignment explanation
Indices: 59757021--59757052 Score: 50
Period size: 6 Copynumber: 4.9 Consensus size: 7
59757011 TTGCAATTCA
59757021 AATTTTT
1 AATTTTT
59757028 -ATTTTT
1 AATTTTT
59757034 -ATTTTT
1 AATTTTT
59757040 AATTTTT
1 AATTTTT
59757047 AATTTT
1 AATTTT
59757053 CTTTTCTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 12 0.50
7 12 0.50
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (7 bp):
AATTTTT
Found at i:59760190 original size:13 final size:13
Alignment explanation
Indices: 59760172--59760196 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59760162 AACGAAGCAA
59760172 GACACAGCTGTGC
1 GACACAGCTGTGC
59760185 GACACAGCTGTG
1 GACACAGCTGTG
59760197 TGCACCTACA
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:0.24, C:0.28, G:0.32, T:0.16
Consensus pattern (13 bp):
GACACAGCTGTGC
Found at i:59765378 original size:40 final size:40
Alignment explanation
Indices: 59765333--59765500 Score: 178
Period size: 40 Copynumber: 4.2 Consensus size: 40
59765323 CGGAATATAA
59765333 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
59765373 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
59765413 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
59765453 CCGGATATAATTTCCAGCATAATTGTCTTCGGGAT-TTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGG-TCTTAGC
59765493 CCGGATAT
1 CCGGATAT
59765501 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
39 1 0.01
40 105 0.98
41 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:59773341 original size:39 final size:40
Alignment explanation
Indices: 59773298--59773463 Score: 151
Period size: 39 Copynumber: 4.2 Consensus size: 40
59773288 CGGAATATAA
59773298 CCGGATATAATCACGT-GCACAAATGCCTTC-GGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
59773337 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* ** * *
59773377 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
59773417 CCGGAT-TAATTTCCAGCATAATTGTCTTCGGGAT-TTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGG-TCTTAGC
59773456 CCGGATAT
1 CCGGATAT
59773464 CATTCAATTT
Statistics
Matches: 103, Mismatches: 20, Indels: 7
0.79 0.15 0.05
Matches are distributed among these distances:
38 1 0.01
39 54 0.52
40 48 0.47
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:59773382 original size:40 final size:39
Alignment explanation
Indices: 59773314--59773422 Score: 123
Period size: 40 Copynumber: 2.7 Consensus size: 39
59773304 ATAATCACGT
* *
59773314 GCACAAATGCCTTC-GGTCTTAGCCCGGATAG-AATAACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GTAACAACTA
* *
59773353 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGTAACAACTA
*
59773393 GCACAATTGCCTTCGGGTCTTAACCCGGAT
1 GCACAA-TGCCTTCGGGTCTTAGCCCGGAT
59773423 TAATTTCCAG
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
39 16 0.26
40 45 0.74
ACGTcount: A:0.23, C:0.29, G:0.24, T:0.24
Consensus pattern (39 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGTAACAACTA
Found at i:59782760 original size:30 final size:30
Alignment explanation
Indices: 59782724--59782854 Score: 171
Period size: 30 Copynumber: 4.5 Consensus size: 30
59782714 GACAAGATTG
* * * * *
59782724 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
*
59782754 GCACTAAGTGTGCGAGTTTG---ATTATATA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATA
59782782 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
59782812 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
59782841 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
59782855 GATTCACTAT
Statistics
Matches: 92, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
27 2 0.02
28 22 0.24
29 20 0.22
30 46 0.50
31 2 0.02
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATA
Found at i:59782815 original size:58 final size:58
Alignment explanation
Indices: 59782724--59782854 Score: 174
Period size: 58 Copynumber: 2.2 Consensus size: 58
59782714 GACAAGATTG
* * * * * *
59782724 GCACTAAGTGTGCGGGTTTAAAATTGTACAGCACTAAGTGTGCGAGTTTG-ATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAG-CTGAAATATATA
*
59782782 GCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTG-AAATATATA
59782841 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
59782855 GATTCACTAT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
57 2 0.03
58 41 0.64
59 21 0.33
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (58 bp):
GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTGAAATATATA
Found at i:59790704 original size:30 final size:30
Alignment explanation
Indices: 59790668--59790798 Score: 171
Period size: 30 Copynumber: 4.5 Consensus size: 30
59790658 GACAAGATTG
* * * * *
59790668 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
*
59790698 GCACTAAGTGTGCGAGTTTG---ATTATATA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATA
59790726 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
59790756 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
59790785 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
59790799 GATTCACTAT
Statistics
Matches: 92, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
27 2 0.02
28 22 0.24
29 20 0.22
30 46 0.50
31 2 0.02
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATA
Found at i:59790759 original size:58 final size:58
Alignment explanation
Indices: 59790668--59790798 Score: 174
Period size: 58 Copynumber: 2.2 Consensus size: 58
59790658 GACAAGATTG
* * * * * *
59790668 GCACTAAGTGTGCGGGTTTAAAATTGTACAGCACTAAGTGTGCGAGTTTG-ATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAG-CTGAAATATATA
*
59790726 GCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTG-AAATATATA
59790785 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
59790799 GATTCACTAT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
57 2 0.03
58 41 0.64
59 21 0.33
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (58 bp):
GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTGAAATATATA
Found at i:59792399 original size:40 final size:40
Alignment explanation
Indices: 59792354--59792521 Score: 178
Period size: 40 Copynumber: 4.2 Consensus size: 40
59792344 CGGAATATAA
59792354 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
59792394 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
59792434 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
59792474 CCGGATATAATTTCCAGCATAATTGTCTTCGGGAT-TTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGG-TCTTAGC
59792514 CCGGATAT
1 CCGGATAT
59792522 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
39 1 0.01
40 105 0.98
41 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:59797263 original size:27 final size:28
Alignment explanation
Indices: 59797207--59797274 Score: 129
Period size: 27 Copynumber: 2.5 Consensus size: 28
59797197 AAATTTGTAC
59797207 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
59797235 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
59797262 AGCACTAAGTGTG
1 AGCACTAAGTGTG
59797275 TGGACTCACT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
27 23 0.57
28 17 0.43
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.32
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATAT
Found at i:59797287 original size:27 final size:27
Alignment explanation
Indices: 59797207--59797288 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 27
59797197 AAATTTGTAC
* * *
59797207 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
* * *
59797235 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGCTCACTATAT
*
59797262 AGCACTAAGTGTGTG-GACTCACTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
59797289 GTTTTTGAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 1 0.02
27 31 0.63
28 17 0.35
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGCTCACTATAT
Found at i:59805202 original size:27 final size:28
Alignment explanation
Indices: 59805146--59805215 Score: 133
Period size: 27 Copynumber: 2.5 Consensus size: 28
59805136 AAATTTGTAC
59805146 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
59805174 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATTATAT
59805201 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
59805216 GACTCACTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
27 25 0.60
28 17 0.40
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATTATAT
Found at i:59808317 original size:12 final size:12
Alignment explanation
Indices: 59808300--59808327 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
59808290 CCAGTCGTCC
59808300 TTCATGTTAGGG
1 TTCATGTTAGGG
59808312 TTCATGTTAGGG
1 TTCATGTTAGGG
59808324 TTCA
1 TTCA
59808328 GTCGTCTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.18, C:0.11, G:0.29, T:0.43
Consensus pattern (12 bp):
TTCATGTTAGGG
Found at i:59811041 original size:13 final size:13
Alignment explanation
Indices: 59811023--59811047 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59811013 TTAGTAAATT
59811023 AAAATAAAATTAA
1 AAAATAAAATTAA
59811036 AAAATAAAATTA
1 AAAATAAAATTA
59811048 GATTACAAGA
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAATAAAATTAA
Found at i:59821566 original size:67 final size:67
Alignment explanation
Indices: 59821458--59821589 Score: 210
Period size: 67 Copynumber: 2.0 Consensus size: 67
59821448 TTTGTCATTC
* ***
59821458 TAGGGGATTTAGCCTGGACTGGTAATCTTGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCT
1 TAGGGGATTTAGCCTGGACTAGTAATCCCACTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCT
59821523 CA
66 CA
* *
59821525 TAGGGGATTTAGCCTGGATTAGTAATCCCACTGTGAGAAATGAGGTTCGCGGGAGTGTGCTCTCT
1 TAGGGGATTTAGCCTGGACTAGTAATCCCACTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCT
59821590 GAAATGGAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
67 59 1.00
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.30
Consensus pattern (67 bp):
TAGGGGATTTAGCCTGGACTAGTAATCCCACTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCT
CA
Found at i:59822742 original size:2 final size:2
Alignment explanation
Indices: 59822735--59822764 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
59822725 TCTCTTGCAC
59822735 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
59822765 GTTTGCACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59834653 original size:28 final size:27
Alignment explanation
Indices: 59834593--59834653 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 27
59834583 CAGTAATGGA
*
59834593 TCAGTCTCAGTTAAGGCCTCAGCCCAC
1 TCAGTATCAGTTAAGGCCTCAGCCCAC
** *
59834620 TACAGTATCAGTTTGGGCCTGAGCCCATC
1 T-CAGTATCAGTTAAGGCCTCAGCCCA-C
59834649 TCAGT
1 TCAGT
59834654 GACAGTAACA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
27 1 0.04
28 25 0.89
29 2 0.07
ACGTcount: A:0.21, C:0.31, G:0.21, T:0.26
Consensus pattern (27 bp):
TCAGTATCAGTTAAGGCCTCAGCCCAC
Found at i:59834979 original size:26 final size:26
Alignment explanation
Indices: 59834950--59835004 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
59834940 CATCTCATAG
*
59834950 GGGCATAACAATCATTTTATCACTTA
1 GGGCATAACAATCATTTTATCAATTA
* *
59834976 GGGCATAATAGTCATTTTATCAATTA
1 GGGCATAACAATCATTTTATCAATTA
59835002 GGG
1 GGG
59835005 GTCTAGGTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.35
Consensus pattern (26 bp):
GGGCATAACAATCATTTTATCAATTA
Found at i:59835941 original size:48 final size:48
Alignment explanation
Indices: 59835856--59836137 Score: 374
Period size: 48 Copynumber: 5.9 Consensus size: 48
59835846 GGGAGGGGAG
* * *
59835856 AAGAACAAGAAGCAATCGGTC-AAGGGAAATCAATTGAGAAAGGGAAA
1 AAGAACTAGAAGCAATCGGTCAAAGGGAAACCGATTGAGAAAGGGAAA
* *
59835903 AATAACTAGAAGCAATCGGTCAAAGGGAAATCGATTGAGAAAGGG-AA
1 AAGAACTAGAAGCAATCGGTCAAAGGGAAACCGATTGAGAAAGGGAAA
* * * * *
59835950 AA-AACTAAAAGCAATCGATCAAAAGGAAACCGGTTGAGAAA-AGAAA
1 AAGAACTAGAAGCAATCGGTCAAAGGGAAACCGATTGAGAAAGGGAAA
* **
59835996 AACGAACTAGAAGCAATCGGTCAAATGGAAACTAATTGAGAAAGGGAAA
1 AA-GAACTAGAAGCAATCGGTCAAAGGGAAACCGATTGAGAAAGGGAAA
* * * *
59836045 AGGAACTAGAAGTAATCGATCAAAGGGAAACCGATTGGGAAAGGGAAA
1 AAGAACTAGAAGCAATCGGTCAAAGGGAAACCGATTGAGAAAGGGAAA
59836093 AAGAACTAGAAGCAATCGGTCAAAGGGAAACCGATTGAGAAAGGG
1 AAGAACTAGAAGCAATCGGTCAAAGGGAAACCGATTGAGAAAGGG
59836138 GAAGAATGAA
Statistics
Matches: 203, Mismatches: 27, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
45 1 0.00
46 38 0.19
47 23 0.11
48 136 0.67
49 5 0.02
ACGTcount: A:0.49, C:0.12, G:0.27, T:0.12
Consensus pattern (48 bp):
AAGAACTAGAAGCAATCGGTCAAAGGGAAACCGATTGAGAAAGGGAAA
Found at i:59838420 original size:41 final size:41
Alignment explanation
Indices: 59838358--59838443 Score: 163
Period size: 41 Copynumber: 2.1 Consensus size: 41
59838348 GTGTCACCTC
59838358 GGTTCCTATATTGCTAAGGTGGAAAGATGGATAGAAGGATA
1 GGTTCCTATATTGCTAAGGTGGAAAGATGGATAGAAGGATA
*
59838399 GGTTTCTATATTGCTAAGGTGGAAAGATGGATAGAAGGATA
1 GGTTCCTATATTGCTAAGGTGGAAAGATGGATAGAAGGATA
59838440 GGTT
1 GGTT
59838444 AACACCACAC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.33, C:0.06, G:0.33, T:0.29
Consensus pattern (41 bp):
GGTTCCTATATTGCTAAGGTGGAAAGATGGATAGAAGGATA
Found at i:59839475 original size:20 final size:21
Alignment explanation
Indices: 59839421--59839468 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
59839411 AAAAGGAATG
*
59839421 AGCTGAAACGAGCTAAAATCA
1 AGCTCAAACGAGCTAAAATCA
*
59839442 AGCTCAAACGAGCTAAAAT-G
1 AGCTCAAACGAGCTAAAATCA
59839462 AGCTCAA
1 AGCTCAA
59839469 GTGAGCTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.46, C:0.21, G:0.19, T:0.15
Consensus pattern (21 bp):
AGCTCAAACGAGCTAAAATCA
Found at i:59847993 original size:20 final size:19
Alignment explanation
Indices: 59847968--59848039 Score: 99
Period size: 20 Copynumber: 3.6 Consensus size: 19
59847958 TATCAACCAC
59847968 TCCATTTACTTACTCATCAT
1 TCCATTTACTTACT-ATCAT
59847988 TCCATTTACTTACTTATCAT
1 TCCATTTACTTAC-TATCAT
*
59848008 TCCATTTACTTACTTTCCAT
1 TCCATTTACTTACTAT-CAT
*
59848028 TTCATTTACTTA
1 TCCATTTACTTA
59848040 GCATAAGCTT
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.04
20 45 0.94
21 1 0.02
ACGTcount: A:0.24, C:0.26, G:0.00, T:0.50
Consensus pattern (19 bp):
TCCATTTACTTACTATCAT
Found at i:59848025 original size:15 final size:16
Alignment explanation
Indices: 59847997--59848029 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
59847987 TTCCATTTAC
59847997 TTACTTATCATTCCAT
1 TTACTTATCATTCCAT
*
59848013 TTACTTA-CTTTCCAT
1 TTACTTATCATTCCAT
59848028 TT
1 TT
59848030 CATTTACTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.21, C:0.24, G:0.00, T:0.55
Consensus pattern (16 bp):
TTACTTATCATTCCAT
Found at i:59850032 original size:33 final size:33
Alignment explanation
Indices: 59849995--59850142 Score: 197
Period size: 33 Copynumber: 4.4 Consensus size: 33
59849985 TACACTCTGT
*
59849995 TTGGTATGTTGGTTGGATTAGCTCTTATGAGCA
1 TTGGTGTGTTGGTTGGATTAGCTCTTATGAGCA
* *
59850028 TTGGTGTATTGGTTGGATTAGCTCTTATGAGAA
1 TTGGTGTGTTGGTTGGATTAGCTCTTATGAGCA
*
59850061 TTGGTGTGTTGGTTGGATTAGCTCTTATGAGTA
1 TTGGTGTGTTGGTTGGATTAGCTCTTATGAGCA
** * * *
59850094 TTGGTGTGTTGGAGGGATTGGCTCGTGTGAGCA
1 TTGGTGTGTTGGTTGGATTAGCTCTTATGAGCA
59850127 TTTGGTGTGTTTGGTT
1 -TTGGTGTG-TTGGTT
59850143 TGACTGACAA
Statistics
Matches: 100, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
33 88 0.88
34 8 0.08
35 4 0.04
ACGTcount: A:0.15, C:0.07, G:0.35, T:0.43
Consensus pattern (33 bp):
TTGGTGTGTTGGTTGGATTAGCTCTTATGAGCA
Found at i:59851267 original size:15 final size:16
Alignment explanation
Indices: 59851247--59851276 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
59851237 TGGTGCCTTC
59851247 TTGAT-ATGTGTTAAT
1 TTGATAATGTGTTAAT
59851262 TTGATAATGTGTTAA
1 TTGATAATGTGTTAA
59851277 AGCATGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTGATAATGTGTTAAT
Found at i:59852969 original size:18 final size:18
Alignment explanation
Indices: 59852946--59852983 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
59852936 AAAAATCACT
59852946 TAACAA-AATACTTATAAA
1 TAACAACAATACTT-TAAA
59852964 TAACAACTAATACTTTAAA
1 TAACAAC-AATACTTTAAA
59852983 T
1 T
59852984 TCATCACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 5 0.28
20 7 0.39
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (18 bp):
TAACAACAATACTTTAAA
Found at i:59863835 original size:47 final size:46
Alignment explanation
Indices: 59863770--59863937 Score: 193
Period size: 46 Copynumber: 3.6 Consensus size: 46
59863760 TGTGTGAGAT
59863770 AGTGTAAGACATGTTTGGGACATGCATCGGCCAAATT-ATGA-GAA-CC
1 AGTGTAAGACATGTTTGGGACATGCATCGGCC--ATTGA-GATGAAGCC
*
59863816 AGTGTAAGACCATGTTTGGGACATTGCATCGG-CATTGAGATGAATGCT
1 AGTGTAAGA-CATGTTTGGGACA-TGCATCGGCCATTGAGATGAA-GCC
* * *
59863864 AGTGTAAGACATGTTTGGGACATGCATCGGCC-TCGAAATGTAAGTC
1 AGTGTAAGACATGTTTGGGACATGCATCGGCCATTGAGATG-AAGCC
*
59863910 AGTGTAAGACATGTCTGGGACATGCATC
1 AGTGTAAGACATGTTTGGGACATGCATC
59863938 AGCTACGAGA
Statistics
Matches: 108, Mismatches: 6, Indels: 16
0.83 0.05 0.12
Matches are distributed among these distances:
45 5 0.05
46 55 0.51
47 30 0.28
48 18 0.17
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (46 bp):
AGTGTAAGACATGTTTGGGACATGCATCGGCCATTGAGATGAAGCC
Found at i:59867012 original size:40 final size:40
Alignment explanation
Indices: 59866957--59867099 Score: 216
Period size: 40 Copynumber: 3.6 Consensus size: 40
59866947 TATCTTGCAC
* * * **
59866957 AATGCCTTCGGGTCTTAGCCCGGATATAA-CAACTCGTACG
1 AATGCCTTCGGGACTTAGCCCGGATATAATC-ACTAGCATA
*
59866997 AATGCCTTCGGGTCTTAGCCCGGATATAATCACTAGCATA
1 AATGCCTTCGGGACTTAGCCCGGATATAATCACTAGCATA
59867037 AATGCCTTCGGGACTTAGCCCGGATATAATCACTAGCATA
1 AATGCCTTCGGGACTTAGCCCGGATATAATCACTAGCATA
59867077 AATGCCTTCGGGACTTAGCCCGG
1 AATGCCTTCGGGACTTAGCCCGG
59867100 GTATCATTCA
Statistics
Matches: 97, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
40 96 0.99
41 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAGCCCGGATATAATCACTAGCATA
Found at i:59875223 original size:28 final size:28
Alignment explanation
Indices: 59875158--59875258 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
59875148 ATAGTGAATC
*
59875158 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
59875187 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
59875215 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
59875245 CGCACACTTAGTGC
1 CGCACACTTAGTGC
59875259 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:59876746 original size:39 final size:39
Alignment explanation
Indices: 59876703--59876801 Score: 107
Period size: 39 Copynumber: 2.5 Consensus size: 39
59876693 TATAACCGGT
*
59876703 TAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC-AT-CGGGC
1 TAAGA-CCGAAGGCAATTGTGCGAGT--CATACTATCCGGGC
*
59876742 TAAGACCGAAGGC-ATTCGTGCGAGTCATTCTATCCGGGC
1 TAAGACCGAAGGCAATT-GTGCGAGTCATACTATCCGGGC
*
59876781 TAAGACCGAAGGCATTTGTGC
1 TAAGACCGAAGGCAATTGTGC
59876802 AAATCGTGAT
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
36 1 0.02
37 5 0.10
38 17 0.33
39 27 0.52
40 2 0.04
ACGTcount: A:0.25, C:0.23, G:0.29, T:0.22
Consensus pattern (39 bp):
TAAGACCGAAGGCAATTGTGCGAGTCATACTATCCGGGC
Found at i:59876815 original size:39 final size:39
Alignment explanation
Indices: 59876737--59876817 Score: 108
Period size: 39 Copynumber: 2.1 Consensus size: 39
59876727 GTGGCTACAT
* * **
59876737 CGGGCTAAGACCGAAGGCATTCGTGCGAGTCATTCTATC
1 CGGGCTAAGACCGAAGGCATTCGTGCAAATCATGATATC
* *
59876776 CGGGCTAAGACCGAAGGCATTTGTGCAAATCGTGATATC
1 CGGGCTAAGACCGAAGGCATTCGTGCAAATCATGATATC
59876815 CGG
1 CGG
59876818 TTAAGTCCGT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.25, C:0.23, G:0.30, T:0.22
Consensus pattern (39 bp):
CGGGCTAAGACCGAAGGCATTCGTGCAAATCATGATATC
Found at i:59884818 original size:13 final size:13
Alignment explanation
Indices: 59884800--59884829 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
59884790 ATGTATATTT
*
59884800 AAAAAAGAAAAAG
1 AAAAAAAAAAAAG
59884813 AAAAAAAAAAAAG
1 AAAAAAAAAAAAG
59884826 AAAA
1 AAAA
59884830 GCAAACATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAG
Found at i:59887831 original size:21 final size:21
Alignment explanation
Indices: 59887807--59887849 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
59887797 TCTGCTGCCA
**
59887807 TCGCGGCTGCCTCTGCCTCCC
1 TCGCGGCTGCAGCTGCCTCCC
*
59887828 TCGCTGCTGCAGCTGCCTCCC
1 TCGCGGCTGCAGCTGCCTCCC
59887849 T
1 T
59887850 TGTTGATGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.02, C:0.49, G:0.23, T:0.26
Consensus pattern (21 bp):
TCGCGGCTGCAGCTGCCTCCC
Found at i:59887859 original size:21 final size:21
Alignment explanation
Indices: 59887819--59887859 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
59887809 GCGGCTGCCT
*
59887819 CTGCCTCCCTCGCTGCTGCAG
1 CTGCCTCCCTCGCTGATGCAG
* *
59887840 CTGCCTCCCTTGTTGATGCA
1 CTGCCTCCCTCGCTGATGCA
59887860 TCCGCTCTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.07, C:0.41, G:0.22, T:0.29
Consensus pattern (21 bp):
CTGCCTCCCTCGCTGATGCAG
Found at i:59894080 original size:37 final size:36
Alignment explanation
Indices: 59894030--59894116 Score: 147
Period size: 37 Copynumber: 2.3 Consensus size: 36
59894020 TACGAAGTCT
59894030 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
1 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
59894066 GTACCCGGACATAATCTCCACACGTAGTCATCGGGTC
1 -TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
59894103 TCACCCGGAACATA
1 T-ACCCGG-ACATA
59894117 TTTCCAAGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
36 1 0.02
37 42 0.88
38 5 0.10
ACGTcount: A:0.26, C:0.33, G:0.20, T:0.21
Consensus pattern (36 bp):
TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
Found at i:59894314 original size:49 final size:49
Alignment explanation
Indices: 59894185--59894434 Score: 475
Period size: 49 Copynumber: 5.1 Consensus size: 49
59894175 TTTACCACAT
*
59894185 ATATATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
1 ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
59894234 ATATATAT-CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
59894282 ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
*
59894331 ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAT
1 ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
59894380 ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
59894429 ATATAT
1 ATATAT
59894435 TATTATGTAC
Statistics
Matches: 197, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
48 47 0.24
49 150 0.76
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.34
Consensus pattern (49 bp):
ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
Found at i:59897815 original size:40 final size:40
Alignment explanation
Indices: 59897771--59898082 Score: 498
Period size: 40 Copynumber: 7.8 Consensus size: 40
59897761 CCAGCATGAT
* * * *
59897771 TGCTCTTCGGGACCTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATATATCATTAGCACGAA
* * *
59897811 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATATATCATTAGCACGAA
*
59897851 TGCTCTTCGGAATTTAGCCCGGATATATCATTAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATATATCATTAGCACGAA
*
59897891 TGCTCTTCGGAATTTAGCCCGGATATATCATTAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATATATCATTAGCACGAA
*
59897931 TGCTCTTCGGAACTTAGTCCGGATATATCATTAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATATATCATTAGCACGAA
*
59897971 TGCTCTTCGGAATTTAGCCCGGATATATCATTAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATATATCATTAGCACGAA
*
59898011 TGCTCTTCGGAACTTAGTCCGGATATATCATTAGCACGAA
1 TGCTCTTCGGAACTTAGCCCGGATATATCATTAGCACGAA
* *
59898051 TGCTCTTCGGAACTTAGTCCGGATACATCATT
1 TGCTCTTCGGAACTTAGCCCGGATATATCATT
59898083 CTCAATTCTC
Statistics
Matches: 258, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 258 1.00
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.29
Consensus pattern (40 bp):
TGCTCTTCGGAACTTAGCCCGGATATATCATTAGCACGAA
Found at i:59897984 original size:120 final size:120
Alignment explanation
Indices: 59897771--59898082 Score: 552
Period size: 120 Copynumber: 2.6 Consensus size: 120
59897761 CCAGCATGAT
* * * *
59897771 TGCTCTTCGGGACCTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGTCCGGATA
1 TGCTCTTCGGAACTTAGCCCGGATATATCATTAGCACGAATGCTCTTCGGAACTTAGTCCGGATA
*
59897836 CATCACTAGCACGAATGCTCTTCGGAATTTAGCCCGGATATATCATTAGCACGAA
66 CATCATTAGCACGAATGCTCTTCGGAATTTAGCCCGGATATATCATTAGCACGAA
*
59897891 TGCTCTTCGGAATTTAGCCCGGATATATCATTAGCACGAATGCTCTTCGGAACTTAGTCCGGATA
1 TGCTCTTCGGAACTTAGCCCGGATATATCATTAGCACGAATGCTCTTCGGAACTTAGTCCGGATA
*
59897956 TATCATTAGCACGAATGCTCTTCGGAATTTAGCCCGGATATATCATTAGCACGAA
66 CATCATTAGCACGAATGCTCTTCGGAATTTAGCCCGGATATATCATTAGCACGAA
*
59898011 TGCTCTTCGGAACTTAGTCCGGATATATCATTAGCACGAATGCTCTTCGGAACTTAGTCCGGATA
1 TGCTCTTCGGAACTTAGCCCGGATATATCATTAGCACGAATGCTCTTCGGAACTTAGTCCGGATA
59898076 CATCATT
66 CATCATT
59898083 CTCAATTCTC
Statistics
Matches: 182, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
120 182 1.00
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.29
Consensus pattern (120 bp):
TGCTCTTCGGAACTTAGCCCGGATATATCATTAGCACGAATGCTCTTCGGAACTTAGTCCGGATA
CATCATTAGCACGAATGCTCTTCGGAATTTAGCCCGGATATATCATTAGCACGAA
Found at i:59900009 original size:37 final size:36
Alignment explanation
Indices: 59899959--59900045 Score: 147
Period size: 37 Copynumber: 2.3 Consensus size: 36
59899949 TACAAAGTCT
59899959 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
1 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
59899995 GTACCCGGACATAATCTCCACACGTAGTCATCGGGTC
1 -TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
59900032 TCACCCGGAACATA
1 T-ACCCGG-ACATA
59900046 TTTCCAAGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
36 1 0.02
37 42 0.88
38 5 0.10
ACGTcount: A:0.26, C:0.33, G:0.20, T:0.21
Consensus pattern (36 bp):
TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
Found at i:59900181 original size:49 final size:49
Alignment explanation
Indices: 59900114--59900307 Score: 361
Period size: 49 Copynumber: 4.0 Consensus size: 49
59900104 TTTACCACAT
*
59900114 ATATATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTTATCAC
1 ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
*
59900163 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
59900212 ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
1 ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
*
59900261 ATATATATACATTTTCACATTCATCACATCGGCCATTAGGCCTTATC
1 ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC
59900308 TGTGACACCC
Statistics
Matches: 141, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 141 1.00
ACGTcount: A:0.30, C:0.27, G:0.09, T:0.34
Consensus pattern (49 bp):
ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC
Found at i:59901651 original size:23 final size:25
Alignment explanation
Indices: 59901615--59901661 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
59901605 TTAAGTGCTT
* *
59901615 AGTTAATGTGCATATAAGTAAGTGA
1 AGTTAATGTGCATAGAACTAAGTGA
59901640 AGTT-ATGT-CATAGAACTAAGTG
1 AGTTAATGTGCATAGAACTAAGTG
59901662 TGGCTAGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 4 0.20
25 4 0.20
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.32
Consensus pattern (25 bp):
AGTTAATGTGCATAGAACTAAGTGA
Found at i:59902790 original size:49 final size:49
Alignment explanation
Indices: 59902729--59902863 Score: 261
Period size: 49 Copynumber: 2.8 Consensus size: 49
59902719 GTATGAGATA
59902729 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
59902778 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
59902827 TGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 TATATATATGTGATAAGGCCTAATGGCCGATGTGATG
59902864 TATATATGTG
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
49 85 1.00
ACGTcount: A:0.31, C:0.09, G:0.29, T:0.31
Consensus pattern (49 bp):
TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
Found at i:59902873 original size:35 final size:35
Alignment explanation
Indices: 59902827--59902898 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
59902817 TGTGAAAGTG
59902827 TGTATATATGTGATAAGGCCTAATGGCCGATGTGA
1 TGTATATATGTGATAAGGCCTAATGGCCGATGTGA
59902862 TGTATATATGTGATAAGGCCTAATGGCCGATGTGA
1 TGTATATATGTGATAAGGCCTAATGGCCGATGTGA
59902897 TG
1 TG
59902899 AATGTGAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.28, C:0.11, G:0.29, T:0.32
Consensus pattern (35 bp):
TGTATATATGTGATAAGGCCTAATGGCCGATGTGA
Found at i:59902874 original size:84 final size:84
Alignment explanation
Indices: 59902780--59902945 Score: 323
Period size: 84 Copynumber: 2.0 Consensus size: 84
59902770 TGAAAGTGTA
*
59902780 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTGTATATATGTGATAAGG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGG
59902845 CCTAATGGCCGATGTGATG
66 CCTAATGGCCGATGTGATG
59902864 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGG
59902929 CCTAATGGCCGATGTGA
66 CCTAATGGCCGATGTGA
59902946 AGAATGTGAA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 81 1.00
ACGTcount: A:0.31, C:0.10, G:0.29, T:0.31
Consensus pattern (84 bp):
TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGG
CCTAATGGCCGATGTGATG
Found at i:59902877 original size:133 final size:139
Alignment explanation
Indices: 59902731--59903070 Score: 498
Period size: 133 Copynumber: 2.5 Consensus size: 139
59902721 ATGAGATATA
59902731 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGG
* ** *
59902796 CCTAATGGCCGATGTGATGAATGTGAAAGTGTGTATATATGTGATAAGGCCTAATGG-C-C-G-A
66 CCTAATGGCCGATGTGAAGAATGTGAAAGTGCATATATATGTGATAAGGCCGAATGGCCACGGAA
59902857 TGTG-A-TG
131 TGTGAAGTG
59902864 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGG
59902929 CCTAATGGCCGATGTGAAGAATGTGAAAGTGCATATATATGTGATAAGGCCGAATGGCCAACGTG
66 CCTAATGGCCGATGTGAAGAATGTGAAAGTGCATATATATGTGATAAGGCCGAATGGCC-AC--G
59902994 ATGAATGTGAAAGTG
128 --GAATGTG-AAGTG
* * * *
59903009 TATATATGTGATAGGGCCGAATGGCCAATGTGATGAATGTGAATGTGTATA-A-ATGTGATAAG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAG
59903071 TTCCGAAGGG
Statistics
Matches: 187, Mismatches: 8, Indels: 14
0.89 0.04 0.07
Matches are distributed among these distances:
133 118 0.63
134 1 0.01
136 1 0.01
141 1 0.01
142 5 0.03
143 10 0.05
144 2 0.01
145 49 0.26
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (139 bp):
TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGG
CCTAATGGCCGATGTGAAGAATGTGAAAGTGCATATATATGTGATAAGGCCGAATGGCCACGGAA
TGTGAAGTG
Found at i:59902921 original size:49 final size:49
Alignment explanation
Indices: 59902864--59903070 Score: 305
Period size: 49 Copynumber: 4.3 Consensus size: 49
59902854 CGATGTGATG
* *
59902864 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTA
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
* * * *
59902913 TATATATGTGATAAGGCCTAATGGCCGATGTGAAGAATGTGAAAGTGCA
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
*
59902962 TATATATGTGATAAGGCCGAATGGCCAACGTGATGAATGTGAAAGTG--
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
* *
59903009 TATATATGTGATAGGGCCGAATGGCCAATGTGATGAATGTGAATGTGTA
1 TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
59903058 TA-A-ATGTGATAAG
1 TATATATGTGATAAG
59903071 TTCCGAAGGG
Statistics
Matches: 146, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
47 53 0.36
48 1 0.01
49 92 0.63
ACGTcount: A:0.34, C:0.09, G:0.29, T:0.29
Consensus pattern (49 bp):
TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTA
Found at i:59909147 original size:40 final size:41
Alignment explanation
Indices: 59909092--59909255 Score: 158
Period size: 40 Copynumber: 4.1 Consensus size: 41
59909082 TGAATGATAC
* * * *
59909092 CCGGGCTAAGTCCCGAAGG-AATTTATTCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCAATTTGTGCAAGTGATTATAT
* *
59909132 CCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCAATTTGTGCAAG-TGATTATAT
* * * *
59909172 CCGGGTTAAGACCCGAAGGCAA-TTGTGCAAGTTACTAAAT
1 CCGGGCTAAGACCCGAAGGCAATTTGTGCAAGTGATTATAT
* ** *
59909212 CCGGGTTAAGACCCGAAGGCAA-TTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCAATTTGTGCAAGTGATTATAT
59909252 CCGG
1 CCGG
59909256 TTAAATCCCG
Statistics
Matches: 103, Mismatches: 17, Indels: 8
0.80 0.13 0.06
Matches are distributed among these distances:
39 1 0.01
40 99 0.96
41 3 0.03
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (41 bp):
CCGGGCTAAGACCCGAAGGCAATTTGTGCAAGTGATTATAT
Found at i:59911272 original size:9 final size:9
Alignment explanation
Indices: 59911255--59911550 Score: 214
Period size: 9 Copynumber: 33.6 Consensus size: 9
59911245 TATTTATGTA
59911255 TTATGTAAG
1 TTATGTAAG
*
59911264 TTTTGTAAG
1 TTATGTAAG
59911273 TTATGTAAG
1 TTATGTAAG
* *
59911282 ATATGATATG
1 TTATG-TAAG
* * *
59911292 ATATAT-AT
1 TTATGTAAG
59911300 TTATGTAAG
1 TTATGTAAG
* *
59911309 TTATAT-AT
1 TTATGTAAG
*
59911317 TTATCTAAG
1 TTATGTAAG
*
59911326 TTATATAAG
1 TTATGTAAG
59911335 TTATGTAAG
1 TTATGTAAG
*
59911344 TTATGATATG
1 TTATG-TAAG
* * *
59911354 ATATAT-AT
1 TTATGTAAG
59911362 TTATGT-A-
1 TTATGTAAG
59911369 TTATGTAAG
1 TTATGTAAG
* *
59911378 TAATGATATG
1 TTATG-TAAG
* * *
59911388 ATATAT-AT
1 TTATGTAAG
59911396 TTATGTAAG
1 TTATGTAAG
59911405 TTATGTAAG
1 TTATGTAAG
* *
59911414 TTATAT-AT
1 TTATGTAAG
*
59911422 TTATCTAAG
1 TTATGTAAG
*
59911431 TTATATAAG
1 TTATGTAAG
59911440 TTATGTAAG
1 TTATGTAAG
*
59911449 TTATGTAAA
1 TTATGTAAG
* *
59911458 TTATAT-AT
1 TTATGTAAG
*
59911466 TTATCTAAG
1 TTATGTAAG
59911475 TTATGTAAG
1 TTATGTAAG
59911484 TTATGTAAG
1 TTATGTAAG
59911493 TTATGTAAG
1 TTATGTAAG
* *
59911502 TTATAT-AT
1 TTATGTAAG
*
59911510 TTATCTAAG
1 TTATGTAAG
*
59911519 TTATATAAG
1 TTATGTAAG
*
59911528 TTATGTAAA
1 TTATGTAAG
59911537 TTATGTAAG
1 TTATGTAAG
59911546 TTATG
1 TTATG
59911551 ATATGATATA
Statistics
Matches: 223, Mismatches: 53, Indels: 22
0.75 0.18 0.07
Matches are distributed among these distances:
7 6 0.03
8 38 0.17
9 161 0.72
10 18 0.08
ACGTcount: A:0.36, C:0.01, G:0.15, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:59911330 original size:15 final size:17
Alignment explanation
Indices: 59911293--59911525 Score: 105
Period size: 17 Copynumber: 13.4 Consensus size: 17
59911283 TATGATATGA
*
59911293 TATATATTTATGTAAGT
1 TATATATTTATCTAAGT
59911310 TATATATTTATCTAAGT
1 TATATATTTATCTAAGT
* *
59911327 TATATAAGTTATGTAAGT
1 TATAT-ATTTATCTAAGT
* * *
59911345 TATGATA-TGATATATATT
1 TAT-ATATTTATCTA-AGT
* *
59911363 TATGTA-TTATGTAAGT
1 TATATATTTATCTAAGT
* * * *
59911379 AATGATA-TGATATATATT
1 TAT-ATATTTATCTA-AGT
* * *
59911397 TATGTAAGTTATGTAAGT
1 TATAT-ATTTATCTAAGT
59911415 TATATATTTATCTAAGT
1 TATATATTTATCTAAGT
* *
59911432 TATATAAGTTATGTAAGT
1 TATAT-ATTTATCTAAGT
* * * *
59911450 TATGTAAATTATAT-ATT
1 TATAT-ATTTATCTAAGT
* * *
59911467 TATCTAAGTTATGTAAGT
1 TATAT-ATTTATCTAAGT
* * *
59911485 TATGTAAGTTATGTAAGT
1 TATAT-ATTTATCTAAGT
59911503 TATATATTTATCTAAGT
1 TATATATTTATCTAAGT
59911520 TATATA
1 TATATA
59911526 AGTTATGTAA
Statistics
Matches: 170, Mismatches: 37, Indels: 18
0.76 0.16 0.08
Matches are distributed among these distances:
16 4 0.02
17 85 0.50
18 74 0.44
19 7 0.04
ACGTcount: A:0.37, C:0.02, G:0.13, T:0.48
Consensus pattern (17 bp):
TATATATTTATCTAAGT
Found at i:59911346 original size:35 final size:35
Alignment explanation
Indices: 59911300--59911566 Score: 204
Period size: 35 Copynumber: 7.6 Consensus size: 35
59911290 TGATATATAT
*
59911300 TTATGTAAGTTATATATTTATCTAAGTTATATAAG
1 TTATGTAAGTTATATATTTATATAAGTTATATAAG
* * *
59911335 TTATGTAAGTTATGATA-TGATATATATTTATGT-A-
1 TTATGTAAGTTAT-ATATTTATATA-AGTTATATAAG
* * * *
59911369 TTATGTAAGTAATGATA-TGATATATATTTATGTAAG
1 TTATGTAAGTTAT-ATATTTATATA-AGTTATATAAG
*
59911405 TTATGTAAGTTATATATTTATCTAAGTTATATAAG
1 TTATGTAAGTTATATATTTATATAAGTTATATAAG
* * * *
59911440 TTATGTAAGTTATGTAAATTATAT-ATTTATCTAAG
1 TTATGTAAGTTATAT-ATTTATATAAGTTATATAAG
* * * *
59911475 TTATGTAAGTTATGTAAGTTATGTAAGTTATAT-AT
1 TTATGTAAGTTATAT-ATTTATATAAGTTATATAAG
* * * * *
59911510 TTATCTAAGTTATATAAGTTATGTAAATTATGTAAG
1 TTATGTAAGTTATAT-ATTTATATAAGTTATATAAG
* *
59911546 TTATGATATGATATATATTTA
1 TTATG-TAAGTTATATATTTA
59911567 ACATTAAGAT
Statistics
Matches: 194, Mismatches: 29, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
34 32 0.16
35 107 0.55
36 47 0.24
37 8 0.04
ACGTcount: A:0.37, C:0.01, G:0.13, T:0.48
Consensus pattern (35 bp):
TTATGTAAGTTATATATTTATATAAGTTATATAAG
Found at i:59911353 original size:62 final size:63
Alignment explanation
Indices: 59911255--59911532 Score: 239
Period size: 62 Copynumber: 4.5 Consensus size: 63
59911245 TATTTATGTA
* * * *
59911255 TTATGTAAGTTTTGTAAGTTATGTAAGATATGATATGATATATATTTATGTAAGTTATAT-AT
1 TTATGTAAGTTATATAAGTTATGTAAGTTATGATATGATATATATTTATGTAAGTTATATAAG
* *
59911317 TTATCTAAGTTATATAAGTTATGTAAGTTATGATATGATATATATTTATGT-A-TTATGTAAG
1 TTATGTAAGTTATATAAGTTATGTAAGTTATGATATGATATATATTTATGTAAGTTATATAAG
* * * * * * *
59911378 TAATGATATGATATAT-ATTTATGTAAGTTATG-TAAGTTATATATTTATCTAAGTTATATAAG
1 TTATG-TAAGTTATATAAGTTATGTAAGTTATGATATGATATATATTTATGTAAGTTATATAAG
* * * * * * * * * *
59911440 TTATGTAAGTTATGTAAATTATAT-ATTTAT-CTAAGTTATGTAAGTTATGTAAGTTATGTAAG
1 TTATGTAAGTTATATAAGTTATGTAAGTTATGATATGATATAT-ATTTATGTAAGTTATATAAG
* * * *
59911502 TTATAT-ATTTATCTAAGTTATATAAGTTATG
1 TTATGTAAGTTATATAAGTTATGTAAGTTATG
59911533 TAAATTATGT
Statistics
Matches: 176, Mismatches: 31, Indels: 17
0.79 0.14 0.08
Matches are distributed among these distances:
60 20 0.11
61 56 0.32
62 100 0.57
ACGTcount: A:0.36, C:0.01, G:0.14, T:0.48
Consensus pattern (63 bp):
TTATGTAAGTTATATAAGTTATGTAAGTTATGATATGATATATATTTATGTAAGTTATATAAG
Found at i:59911399 original size:79 final size:74
Alignment explanation
Indices: 59911302--59911540 Score: 236
Period size: 79 Copynumber: 3.1 Consensus size: 74
59911292 ATATATATTT
* * *
59911302 ATGTAAGTTATATATTTATCTAAGTTATATAAGTTATGTAAGTTATGATATGATATATATTTATG
1 ATGTAAATTATATATTTATCTAAGTTATGTAAGTTATGTAAGTTATG-TAAG-TATATATTTATG
59911367 TATTATGTAAGTA
64 --TTATGTAAGTA
* * * * * *
59911380 ATG-ATATGATATATATTTATGTAAGTTATGTAAGTTATAT-ATTTATCTAAGT-TATA--TAAG
1 ATGTAAAT--TATATATTTATCTAAGTTATGTAAGTTATGTAAGTTATGTAAGTATATATTTATG
*
59911440 TTATGTAAGTT
64 TTATGTAAGTA
59911451 ATGTAAATTATATATTTATCTAAGTTATGTAAGTTATGTAAGTTATGTAAGTTATATATTTATCT
1 ATGTAAATTATATATTTATCTAAGTTATGTAAGTTATGTAAGTTATGTAAG-TATATATTTA--T
* *
59911516 AAGTTATATAAGTT
63 --GTTATGTAAGTA
59911530 ATGTAAATTAT
1 ATGTAAATTAT
59911541 GTAAGTTATG
Statistics
Matches: 132, Mismatches: 17, Indels: 23
0.77 0.10 0.13
Matches are distributed among these distances:
70 29 0.22
71 22 0.17
72 4 0.03
73 7 0.05
75 6 0.05
76 1 0.01
77 5 0.04
78 8 0.06
79 50 0.38
ACGTcount: A:0.37, C:0.02, G:0.13, T:0.48
Consensus pattern (74 bp):
ATGTAAATTATATATTTATCTAAGTTATGTAAGTTATGTAAGTTATGTAAGTATATATTTATGTT
ATGTAAGTA
Found at i:59911452 original size:44 final size:44
Alignment explanation
Indices: 59911396--59911554 Score: 282
Period size: 44 Copynumber: 3.6 Consensus size: 44
59911386 TGATATATAT
59911396 TTATGTAAGTTATGTAAGTTATATATTTATCTAAGTTATATAAG
1 TTATGTAAGTTATGTAAGTTATATATTTATCTAAGTTATATAAG
* *
59911440 TTATGTAAGTTATGTAAATTATATATTTATCTAAGTTATGTAAG
1 TTATGTAAGTTATGTAAGTTATATATTTATCTAAGTTATATAAG
59911484 TTATGTAAGTTATGTAAGTTATATATTTATCTAAGTTATATAAG
1 TTATGTAAGTTATGTAAGTTATATATTTATCTAAGTTATATAAG
*
59911528 TTATGTAAATTATGTAAGTTATGATAT
1 TTATGTAAGTTATGTAAGTTAT-ATAT
59911555 GATATATATT
Statistics
Matches: 109, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
44 105 0.96
45 4 0.04
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.48
Consensus pattern (44 bp):
TTATGTAAGTTATGTAAGTTATATATTTATCTAAGTTATATAAG
Found at i:59911952 original size:49 final size:49
Alignment explanation
Indices: 59911894--59911991 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
59911884 TAGTAATTTG
59911894 ATTTTTATAGTAAAATAAATTTAAATAATAAGATTCAGTAGTTAGTTGA
1 ATTTTTATAGTAAAATAAATTTAAATAATAAGATTCAGTAGTTAGTTGA
*
59911943 ATTTTTATAGTAAAATAAATTTAAATAATAAGATTGAGTAGTTAGTTGA
1 ATTTTTATAGTAAAATAAATTTAAATAATAAGATTCAGTAGTTAGTTGA
59911992 GATTATAGTA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.45, C:0.01, G:0.13, T:0.41
Consensus pattern (49 bp):
ATTTTTATAGTAAAATAAATTTAAATAATAAGATTCAGTAGTTAGTTGA
Found at i:59912330 original size:23 final size:23
Alignment explanation
Indices: 59912284--59912346 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
59912274 TTTTAAATAA
**
59912284 AAATAAATTTT-TTATTATTATC
1 AAATAAATTTTCTTAACATTATC
*
59912306 AAATGAATTTTCTTAACATTATC
1 AAATAAATTTTCTTAACATTATC
59912329 AAATAAATTTTCTTAACA
1 AAATAAATTTTCTTAACA
59912347 AAATACTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 10 0.28
23 26 0.72
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.46
Consensus pattern (23 bp):
AAATAAATTTTCTTAACATTATC
Found at i:59913279 original size:24 final size:24
Alignment explanation
Indices: 59913247--59913292 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
59913237 ACCCAAGATT
* *
59913247 TATGCATATTGGTATATGTATATA
1 TATGCATATTGATATATATATATA
59913271 TATGCATATTGATATATATATA
1 TATGCATATTGATATATATATA
59913293 CACATTACAA
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:0.37, C:0.04, G:0.13, T:0.46
Consensus pattern (24 bp):
TATGCATATTGATATATATATATA
Found at i:59915545 original size:28 final size:28
Alignment explanation
Indices: 59915511--59915565 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
59915501 CTTAAATCAT
*
59915511 TAAACTATATCCCC-ATAACCTTAAACTC
1 TAAACTATATCCCCTA-AACCCTAAACTC
59915539 TAAACTATATCCCCTAAACCCTAAACT
1 TAAACTATATCCCCTAAACCCTAAACT
59915566 ATATTCCCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 24 0.96
29 1 0.04
ACGTcount: A:0.40, C:0.33, G:0.00, T:0.27
Consensus pattern (28 bp):
TAAACTATATCCCCTAAACCCTAAACTC
Found at i:59915556 original size:21 final size:21
Alignment explanation
Indices: 59915532--59915585 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
59915522 CCCATAACCT
*
59915532 TAAACTCTAAACTATATCCCC
1 TAAACCCTAAACTATATCCCC
*
59915553 TAAACCCTAAACTATATTCCC
1 TAAACCCTAAACTATATCCCC
*
59915574 TAAACCATAAAC
1 TAAACCCTAAAC
59915586 CACAAAACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.43, C:0.31, G:0.00, T:0.26
Consensus pattern (21 bp):
TAAACCCTAAACTATATCCCC
Found at i:59915795 original size:14 final size:14
Alignment explanation
Indices: 59915739--59915826 Score: 61
Period size: 14 Copynumber: 6.1 Consensus size: 14
59915729 TATTAAAGTA
*
59915739 CCCTAAA-CTATATC
1 CCCTAAACCT-TAAC
59915753 CCCTAAACCTTAAAC
1 CCCTAAACCTT-AAC
* * **
59915768 CACAAAACAATAAC
1 CCCTAAACCTTAAC
*
59915782 CCCTAAGCCTTAAC
1 CCCTAAACCTTAAC
59915796 CCCTAAACCATTAAC
1 CCCTAAACC-TTAAC
* * *
59915811 CCATAACCCATAAC
1 CCCTAAACCTTAAC
59915825 CC
1 CC
59915827 ATAACCCATA
Statistics
Matches: 57, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
14 34 0.60
15 23 0.40
ACGTcount: A:0.41, C:0.40, G:0.01, T:0.18
Consensus pattern (14 bp):
CCCTAAACCTTAAC
Found at i:59915810 original size:29 final size:29
Alignment explanation
Indices: 59915739--59915851 Score: 88
Period size: 29 Copynumber: 4.0 Consensus size: 29
59915729 TATTAAAGTA
* * *
59915739 CCCTAAACTA-TATCCCCTAAACCTTAAAC
1 CCCTAAACCATTAACCCCTAACCCTT-AAC
* * * *
59915768 CAC-AAAACAATAACCCCTAAGCCTTAAC
1 CCCTAAACCATTAACCCCTAACCCTTAAC
* *
59915796 CCCTAAACCATTAACCCATAACCCATAAC
1 CCCTAAACCATTAACCCCTAACCCTTAAC
* * *
59915825 CCATAACCCATAAACCCC-AACCCTTAA
1 CCCTAAACCATTAACCCCTAACCCTTAA
59915852 ACCATAAGCC
Statistics
Matches: 66, Mismatches: 16, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
28 17 0.26
29 49 0.74
ACGTcount: A:0.42, C:0.40, G:0.01, T:0.18
Consensus pattern (29 bp):
CCCTAAACCATTAACCCCTAACCCTTAAC
Found at i:59915817 original size:7 final size:7
Alignment explanation
Indices: 59915777--59915865 Score: 72
Period size: 7 Copynumber: 12.6 Consensus size: 7
59915767 CCACAAAACA
59915777 ATAACCC
1 ATAACCC
* *
59915784 CTAAGCC
1 ATAACCC
*
59915791 TTAACCC
1 ATAACCC
* *
59915798 CTAAACC
1 ATAACCC
59915805 ATTAACCC
1 A-TAACCC
59915813 ATAACCC
1 ATAACCC
59915820 ATAACCC
1 ATAACCC
59915827 ATAACCC
1 ATAACCC
59915834 ATAAACCC
1 AT-AACCC
*
59915842 -CAACCC
1 ATAACCC
* *
59915848 TTAAACC
1 ATAACCC
*
59915855 ATAAGCC
1 ATAACCC
59915862 ATAA
1 ATAA
59915866 ACATAATATC
Statistics
Matches: 66, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
6 5 0.08
7 50 0.76
8 11 0.17
ACGTcount: A:0.42, C:0.39, G:0.02, T:0.17
Consensus pattern (7 bp):
ATAACCC
Found at i:59916534 original size:40 final size:39
Alignment explanation
Indices: 59916466--59916543 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 39
59916456 TTAATCTTAA
* *
59916466 ACATATTTGCGGCGTTTTAGTGAAAAACGCCGCTAATGAC
1 ACATATTTGCGGCGTTTTAG-CAAAAACGCCACTAATGAC
59916506 ACATATATTGCGGCGTTTTA-CAACAAACGCCACTAATG
1 ACATAT-TTGCGGCGTTTTAGCAA-AAACGCCACTAATG
59916544 CCAGTATAGC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 2 0.06
40 19 0.56
41 13 0.38
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (39 bp):
ACATATTTGCGGCGTTTTAGCAAAAACGCCACTAATGAC
Found at i:59920436 original size:2 final size:2
Alignment explanation
Indices: 59920429--59920462 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
59920419 GGTTAAATTA
59920429 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
59920463 GAATTTGATT
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:59923488 original size:20 final size:20
Alignment explanation
Indices: 59923465--59923536 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
59923455 TACTGGTATT
*
59923465 TTGTCTGCAATACTAGTGGC
1 TTGTCTACAATACTAGTGGC
** *
59923485 TTGTCTACAATACT-GACAGT
1 TTGTCTACAATACTAG-TGGC
*
59923505 TTATCTACAATACTAGTGGC
1 TTGTCTACAATACTAGTGGC
*
59923525 TTGTCCACAATA
1 TTGTCTACAATA
59923537 TTGACAGTTT
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
19 1 0.03
20 38 0.95
21 1 0.03
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.35
Consensus pattern (20 bp):
TTGTCTACAATACTAGTGGC
Found at i:59923516 original size:40 final size:40
Alignment explanation
Indices: 59923472--59923578 Score: 162
Period size: 40 Copynumber: 2.7 Consensus size: 40
59923462 ATTTTGTCTG
*
59923472 CAATACTAGTGGCTTGTCTACAATACTGACAGTTTATCTA
1 CAATACTAGTGGCTTGTCCACAATACTGACAGTTTATCTA
* *
59923512 CAATACTAGTGGCTTGTCCACAATATTGACAGTTTATCTC
1 CAATACTAGTGGCTTGTCCACAATACTGACAGTTTATCTA
* *
59923552 CAATACTGGTGGCTTATCCACAA-ACTG
1 CAATACTAGTGGCTTGTCCACAATACTG
59923579 GTGTTATTAG
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 3 0.05
40 58 0.95
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (40 bp):
CAATACTAGTGGCTTGTCCACAATACTGACAGTTTATCTA
Found at i:59927682 original size:42 final size:42
Alignment explanation
Indices: 59927574--59927735 Score: 168
Period size: 42 Copynumber: 3.9 Consensus size: 42
59927564 AAAGATACCA
* * ** *
59927574 ATGCCATATCCCAGATATGGTCTTACATGGGATCACATATCA
1 ATGCCATATCCCAGACATGGTCTTACACGAAATCACATATCG
* * * **
59927616 ATACGATA-GCCAG-CTATGGTCTTACACGATGTCTA-ATATCG
1 ATGCCATATCCCAGAC-ATGGTCTTACACGAAATC-ACATATCG
59927657 ATGCCATATCCCAGACATGGTCTTACACGAAATCACATATCG
1 ATGCCATATCCCAGACATGGTCTTACACGAAATCACATATCG
* * *
59927699 ATGCCATATCCCAGATATGATCTTACATGAAATCACA
1 ATGCCATATCCCAGACATGGTCTTACACGAAATCACA
59927736 CATAACCCTA
Statistics
Matches: 98, Mismatches: 17, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
41 30 0.31
42 67 0.68
43 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (42 bp):
ATGCCATATCCCAGACATGGTCTTACACGAAATCACATATCG
Found at i:59931899 original size:19 final size:18
Alignment explanation
Indices: 59931854--59931892 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
59931844 TATTGTTGTG
59931854 TTTT-GTTTTTTGTGGTT
1 TTTTAGTTTTTTGTGGTT
59931871 TTTTAGTTTTCTTGT-GTT
1 TTTTAGTTTT-TTGTGGTT
59931889 TTTT
1 TTTT
59931893 CATTTTTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.20
18 12 0.60
19 4 0.20
ACGTcount: A:0.03, C:0.03, G:0.18, T:0.77
Consensus pattern (18 bp):
TTTTAGTTTTTTGTGGTT
Found at i:59932089 original size:22 final size:22
Alignment explanation
Indices: 59932063--59932108 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
59932053 CTGATGACAT
59932063 AAATGCAATGCTCAAAAGATTG
1 AAATGCAATGCTCAAAAGATTG
*
59932085 AAATGCGATGCTCAAAAGATTG
1 AAATGCAATGCTCAAAAGATTG
59932107 AA
1 AA
59932109 GTTTTTAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.46, C:0.13, G:0.20, T:0.22
Consensus pattern (22 bp):
AAATGCAATGCTCAAAAGATTG
Found at i:59937823 original size:43 final size:43
Alignment explanation
Indices: 59937752--59937835 Score: 123
Period size: 43 Copynumber: 2.0 Consensus size: 43
59937742 TACATGAATC
* *
59937752 GCATCCACCATGAACTCATACCTCTCAACGAGCTCGGATGCTT
1 GCATCCACAATGAACTCAGACCTCTCAACGAGCTCGGATGCTT
* * *
59937795 GCATCCATAATGAACTCGGACCTTTCAACGAGCTCGGATGC
1 GCATCCACAATGAACTCAGACCTCTCAACGAGCTCGGATGC
59937836 CACATATCTC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.23
Consensus pattern (43 bp):
GCATCCACAATGAACTCAGACCTCTCAACGAGCTCGGATGCTT
Found at i:59938092 original size:22 final size:22
Alignment explanation
Indices: 59938047--59938092 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
59938037 AAAATTCATA
**
59938047 ATTATAATAAAGCATTTATCAC
1 ATTATAATAAAGCATTTAAAAC
*
59938069 ATTATATTAAAGCATTTAAAAC
1 ATTATAATAAAGCATTTAAAAC
59938091 AT
1 AT
59938093 ACTACCATAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.48, C:0.11, G:0.04, T:0.37
Consensus pattern (22 bp):
ATTATAATAAAGCATTTAAAAC
Found at i:59942383 original size:17 final size:17
Alignment explanation
Indices: 59942361--59942394 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
59942351 GATAAAAATA
*
59942361 TATTGTCATTGCATTTT
1 TATTGTCATTACATTTT
59942378 TATTGTCATTACATTTT
1 TATTGTCATTACATTTT
59942395 CATGTTAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.59
Consensus pattern (17 bp):
TATTGTCATTACATTTT
Found at i:59946309 original size:28 final size:27
Alignment explanation
Indices: 59946246--59946315 Score: 131
Period size: 27 Copynumber: 2.6 Consensus size: 27
59946236 ATAGTGAGTC
59946246 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
59946273 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
59946301 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
59946316 GTACAAATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
27 23 0.55
28 19 0.45
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:59949559 original size:26 final size:26
Alignment explanation
Indices: 59949523--59949632 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
59949513 CATGAAATTC
59949523 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
59949549 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
59949575 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
* *
59949601 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
59949627 TTATCA
1 TTATCA
59949633 ATTTGTATCA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:59951771 original size:26 final size:26
Alignment explanation
Indices: 59951735--59951818 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
59951725 CATGAAATTC
*
59951735 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCTA
59951761 TTATCATGAAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
*
59951787 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCTA
59951813 TTATCA
1 TTATCA
59951819 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCTA
Found at i:59956325 original size:10 final size:10
Alignment explanation
Indices: 59956305--59956338 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
59956295 CACTTAACAA
*
59956305 ATATGTATAT
1 ATATTTATAT
*
59956315 ATGTTTATAT
1 ATATTTATAT
59956325 ATATTTATAT
1 ATATTTATAT
59956335 ATAT
1 ATAT
59956339 AGCCACATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (10 bp):
ATATTTATAT
Found at i:59957859 original size:18 final size:19
Alignment explanation
Indices: 59957822--59957862 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
59957812 ATTTAGAATC
59957822 AAAACTAAAATAAATAATA
1 AAAACTAAAATAAATAATA
* *
59957841 AAAACTAGATTAAAT-ATA
1 AAAACTAAAATAAATAATA
59957859 AAAA
1 AAAA
59957863 TATCAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.22
Consensus pattern (19 bp):
AAAACTAAAATAAATAATA
Found at i:59957864 original size:31 final size:31
Alignment explanation
Indices: 59957788--59957861 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 31
59957778 TCAAATTATC
*
59957788 TTAAATATTAAAATAAAAATAAAAATTTAGAA
1 TTAAATA-TAAAATAAAAATAAAAATCTAGAA
*
59957820 TCAAA-ACTAAAATAAATAATAAAAA-CTAG-A
1 TTAAATA-TAAAATAAA-AATAAAAATCTAGAA
59957850 TTAAATATAAAA
1 TTAAATATAAAA
59957862 ATATCAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
30 10 0.28
31 14 0.39
32 12 0.33
ACGTcount: A:0.66, C:0.04, G:0.03, T:0.27
Consensus pattern (31 bp):
TTAAATATAAAATAAAAATAAAAATCTAGAA
Found at i:59963985 original size:7 final size:7
Alignment explanation
Indices: 59963973--59964065 Score: 51
Period size: 7 Copynumber: 12.7 Consensus size: 7
59963963 AGTTAACTCG
59963973 TAAACCT
1 TAAACCT
*
59963980 TAAACCC
1 TAAACCT
*
59963987 TAAACCA
1 TAAACCT
* *
59963994 TATATCT
1 TAAACCT
59964001 TAAACCAT
1 TAAACC-T
* *
59964009 AGTTAACTCA
1 --TAAAC-CT
59964019 TAAACCT
1 TAAACCT
*
59964026 TAAACCC
1 TAAACCT
*
59964033 TAAACCA
1 TAAACCT
* *
59964040 TATATCT
1 TAAACCT
*
59964047 TAAACCA
1 TAAACCT
59964054 TAAACCT
1 TAAACCT
59964061 TAAAC
1 TAAAC
59964066 TATAATGATA
Statistics
Matches: 62, Mismatches: 20, Indels: 8
0.69 0.22 0.09
Matches are distributed among these distances:
7 52 0.84
8 5 0.08
10 4 0.06
11 1 0.02
ACGTcount: A:0.45, C:0.27, G:0.01, T:0.27
Consensus pattern (7 bp):
TAAACCT
Found at i:59964004 original size:21 final size:21
Alignment explanation
Indices: 59963978--59964059 Score: 92
Period size: 21 Copynumber: 3.7 Consensus size: 21
59963968 ACTCGTAAAC
*
59963978 CTTAAACCCTAAACCATATAT
1 CTTAAACCATAAACCATATAT
* *
59963999 CTTAAACCATAGTTAACTCATAAAC
1 CTTAAACCATA---AAC-CATATAT
*
59964024 CTTAAACCCTAAACCATATAT
1 CTTAAACCATAAACCATATAT
59964045 CTTAAACCATAAACC
1 CTTAAACCATAAACC
59964060 TTAAACTATA
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
21 29 0.58
22 3 0.06
24 3 0.06
25 15 0.30
ACGTcount: A:0.44, C:0.28, G:0.01, T:0.27
Consensus pattern (21 bp):
CTTAAACCATAAACCATATAT
Found at i:59964013 original size:46 final size:46
Alignment explanation
Indices: 59963962--59964055 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 46
59963952 CTTCAAATAC
*
59963962 TAGTTAACTCGTAAACCTTAAACCCTAAACCATATATCTTAAACCA
1 TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAACCA
59964008 TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAACCA
1 TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAACCA
59964054 TA
1 TA
59964056 AACCTTAAAC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.43, C:0.26, G:0.03, T:0.29
Consensus pattern (46 bp):
TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAACCA
Done.