Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D01
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: 62811768
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 736185 characters in sequence are not A, C, G, or T
File 110 of 211
Found at i:30792609 original size:17 final size:18
Alignment explanation
Indices: 30792583--30792620 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
30792573 TTGATATTAT
*
30792583 CCACTTGGCCCACA-AGC
1 CCACTAGGCCCACACAGC
30792600 CCACTAGGCCCACACAGC
1 CCACTAGGCCCACACAGC
30792618 CCA
1 CCA
30792621 TTTCAGCCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.26, C:0.50, G:0.16, T:0.08
Consensus pattern (18 bp):
CCACTAGGCCCACACAGC
Found at i:30798950 original size:50 final size:53
Alignment explanation
Indices: 30798852--30799034 Score: 155
Period size: 50 Copynumber: 3.5 Consensus size: 53
30798842 GATCCCATGA
* *
30798852 AAGACCATGTCTGGGACATGGCATTGGCATTATTGAGGTTATGAGAGGTCTCACGT
1 AAGACCATGTCTGGGACATGGCATTGGC--TACTGAGG-TATGAGAGGTCCCACGT
* *
30798908 AAGACCATGTCTGGGACATGGTATTGGC-ACTGA-G-ATGAGAGGTCCCCCGT
1 AAGACCATGTCTGGGACATGGCATTGGCTACTGAGGTATGAGAGGTCCCACGT
* * ** * ** *
30798958 AAGACCATGAT-TGCGACATGACA-TGGGAACCGA--TATGAGAACTCCCATGT
1 AAGACCATG-TCTGGGACATGGCATTGGCTACTGAGGTATGAGAGGTCCCACGT
* *
30799008 AAGACCATATCTGGGATATGGCATTGG
1 AAGACCATGTCTGGGACATGGCATTGG
30799035 TAGTACAGGA
Statistics
Matches: 105, Mismatches: 17, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
49 4 0.04
50 65 0.62
51 4 0.04
52 1 0.01
53 4 0.04
56 27 0.26
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (53 bp):
AAGACCATGTCTGGGACATGGCATTGGCTACTGAGGTATGAGAGGTCCCACGT
Found at i:30807464 original size:40 final size:40
Alignment explanation
Indices: 30807411--30807602 Score: 253
Period size: 40 Copynumber: 4.8 Consensus size: 40
30807401 TATTACCACA
* * * * *
30807411 AGCACAATTGCCTTCGGGTCTTAACCCGG-GCATAGCAACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATCAAATC-ACT
* * *
30807451 CGCACGAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATCAAATC-ACT
*
30807491 CGCACAAATGCCTTCGGGTCTTAGCCCGGATCAAATCACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATCAAATCACT
*
30807531 AGCACAAATGCCTTCGGGACTTAGCCCGGATCAAATCACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATCAAATCACT
*
30807571 AGCACAAATGCCTTCGGGACTTAGCCCGGATC
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATC
30807603 TCATTCAAAT
Statistics
Matches: 140, Mismatches: 10, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
40 136 0.97
41 4 0.03
ACGTcount: A:0.26, C:0.31, G:0.22, T:0.22
Consensus pattern (40 bp):
AGCACAAATGCCTTCGGGTCTTAGCCCGGATCAAATCACT
Found at i:30823485 original size:40 final size:40
Alignment explanation
Indices: 30823432--30823623 Score: 253
Period size: 40 Copynumber: 4.8 Consensus size: 40
30823422 TATTACCACA
* * * * *
30823432 AGCACAATTGCCTTCGGGTCTTAACCCGG-GCATAGCAACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATCAAATC-ACT
* * *
30823472 CGCACGAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATCAAATC-ACT
*
30823512 CGCACAAATGCCTTCGGGTCTTAGCCCGGATCAAATCACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATCAAATCACT
*
30823552 AGCACAAATGCCTTCGGGACTTAGCCCGGATCAAATCACT
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATCAAATCACT
*
30823592 AGCACAAATGCCTTCGGGACTTAGCCCGGATC
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATC
30823624 TCATTCAAAT
Statistics
Matches: 140, Mismatches: 10, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
40 136 0.97
41 4 0.03
ACGTcount: A:0.26, C:0.31, G:0.22, T:0.22
Consensus pattern (40 bp):
AGCACAAATGCCTTCGGGTCTTAGCCCGGATCAAATCACT
Found at i:30830487 original size:30 final size:30
Alignment explanation
Indices: 30830451--30830725 Score: 209
Period size: 30 Copynumber: 9.2 Consensus size: 30
30830441 TTGTTTCCAC
* * *
30830451 CCCTTTTCATAGTTCGATAGCCGAAGCTAT
1 CCCTTTTCATAATTTGATAGCCGAAGCCAT
* *
30830481 CCCTTTTCATATTTTGATTGCCGAAGCCAT
1 CCCTTTTCATAATTTGATAGCCGAAGCCAT
* * * * *
30830511 CCCTTTTAATAATTAGATTGTC-ATCA-CTAT
1 CCCTTTTCATAATTTGATAGCCGA--AGCCAT
* * * * *
30830541 CCCTTTTCATTA-TTGATGGTCGTCA-TCAT
1 CCCTTTTCATAATTTGATAGCCG-AAGCCAT
* * **
30830570 CCCATTTCATAATTTGATAGCTGAAGATAT
1 CCCTTTTCATAATTTGATAGCCGAAGCCAT
* * *
30830600 CTCTTTTCATAATTCGGTAGCCGAAGCCAT
1 CCCTTTTCATAATTTGATAGCCGAAGCCAT
* *
30830630 CCCTTTTTATAATTTGATAGGCGAAGCCAT
1 CCCTTTTCATAATTTGATAGCCGAAGCCAT
* * *
30830660 CCCTTTTCATAATTTGATGGTCGTCA-CCAT
1 CCCTTTTCATAATTTGATAGCCG-AAGCCAT
* * *
30830690 CCCTTTTCATAATTCGATAACCGAAGCCTT
1 CCCTTTTCATAATTTGATAGCCGAAGCCAT
30830720 CCCTTT
1 CCCTTT
30830726 CCATTTGTCG
Statistics
Matches: 191, Mismatches: 46, Indels: 16
0.75 0.18 0.06
Matches are distributed among these distances:
29 23 0.12
30 166 0.87
31 2 0.01
ACGTcount: A:0.24, C:0.25, G:0.13, T:0.38
Consensus pattern (30 bp):
CCCTTTTCATAATTTGATAGCCGAAGCCAT
Found at i:30835479 original size:22 final size:22
Alignment explanation
Indices: 30835454--30835499 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
30835444 CACTAAGAAC
* * *
30835454 AAGAAGAAAGTAGAGTAATACA
1 AAGAAGAAAATAAAGTAAAACA
30835476 AAGAAGAAAATAAAGTAAAACA
1 AAGAAGAAAATAAAGTAAAACA
30835498 AA
1 AA
30835500 CTCTAAAACC
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:0.67, C:0.04, G:0.17, T:0.11
Consensus pattern (22 bp):
AAGAAGAAAATAAAGTAAAACA
Found at i:30841604 original size:31 final size:31
Alignment explanation
Indices: 30841554--30841613 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
30841544 TGTTTTAATT
30841554 TTTATTCATTATTATTTTATAATATACATACA
1 TTTATTCATTATTATTTTATAATA-ACATACA
*
30841586 TTTATT-ATTATT-TATTTATTATAACATA
1 TTTATTCATTATTAT-TTTATAATAACATA
30841614 TATATTACCC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 6 0.23
31 14 0.54
32 6 0.23
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (31 bp):
TTTATTCATTATTATTTTATAATAACATACA
Found at i:30850694 original size:12 final size:13
Alignment explanation
Indices: 30850677--30850706 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
30850667 CTCATACATG
30850677 AATAAATAAA-GC
1 AATAAATAAATGC
30850689 AATAAATAAATGC
1 AATAAATAAATGC
30850702 AATAA
1 AATAA
30850707 TTATAACCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.20
Consensus pattern (13 bp):
AATAAATAAATGC
Found at i:30852285 original size:15 final size:17
Alignment explanation
Indices: 30852263--30852299 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
30852253 GATTCGATAT
30852263 ATCCTTTTTATG-AATA
1 ATCCTTTTTATGCAATA
30852279 A-CC-TTTTATGCAATA
1 ATCCTTTTTATGCAATA
30852294 ATCCTT
1 ATCCTT
30852300 AAGTCCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 5
0.78 0.00 0.22
Matches are distributed among these distances:
14 7 0.39
15 7 0.39
16 3 0.17
17 1 0.06
ACGTcount: A:0.30, C:0.19, G:0.05, T:0.46
Consensus pattern (17 bp):
ATCCTTTTTATGCAATA
Found at i:30881254 original size:15 final size:15
Alignment explanation
Indices: 30881234--30881264 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
30881224 TTTTGAAGAG
30881234 CAATGGAATGTTTAT
1 CAATGGAATGTTTAT
30881249 CAATGGAATGTTTAT
1 CAATGGAATGTTTAT
30881264 C
1 C
30881265 CCGAGTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (15 bp):
CAATGGAATGTTTAT
Found at i:30887717 original size:32 final size:32
Alignment explanation
Indices: 30887666--30887865 Score: 258
Period size: 32 Copynumber: 6.3 Consensus size: 32
30887656 CAATGGATAC
* * *
30887666 AAGCCATAAGT-ACAGTAATATGATTGGCACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
* *
30887697 AAGTCATCAGTAGTAGTAATATGATCGGCACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
** *
30887729 CTGCCATCAGTAATAGTAGTATGATCGGCACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
* *
30887761 AAGCCATCAGTAGTAGTAATATGATTGGCACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
* * *
30887793 CACCCATCAGTAATGGTAATATGATCGGCACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
* *
30887825 CAGCCATCAGTAATGGTAATATGATCGGCACA
1 AAGCCATCAGTAATAGTAATATGATCGGCACA
30887857 AAGCCATCA
1 AAGCCATCA
30887866 ATAGCATCGC
Statistics
Matches: 146, Mismatches: 22, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
31 9 0.06
32 137 0.94
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.23
Consensus pattern (32 bp):
AAGCCATCAGTAATAGTAATATGATCGGCACA
Found at i:30887848 original size:96 final size:95
Alignment explanation
Indices: 30887666--30887865 Score: 301
Period size: 96 Copynumber: 2.1 Consensus size: 95
30887656 CAATGGATAC
* ** * *
30887666 AAGCCATAAGTACAGTAATATGATTGGCACAAAGTCATCAGTAGTAGTAATATGATCGGCACACT
1 AAGCCATCAGTACAGTAATATGATTGGCACAAACCCATCAGTAATAGTAATATGATCGGCACACA
*
30887731 GCCATCAGTAATAGTAGTATGATCGGCACA
66 GCCATCAGTAATAGTAATATGATCGGCACA
* * *
30887761 AAGCCATCAGTAGTAGTAATATGATTGGCACACACCCATCAGTAATGGTAATATGATCGGCACAC
1 AAGCCATCAGTA-CAGTAATATGATTGGCACAAACCCATCAGTAATAGTAATATGATCGGCACAC
*
30887826 AGCCATCAGTAATGGTAATATGATCGGCACA
65 AGCCATCAGTAATAGTAATATGATCGGCACA
30887857 AAGCCATCA
1 AAGCCATCA
30887866 ATAGCATCGC
Statistics
Matches: 94, Mismatches: 10, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
95 11 0.12
96 83 0.88
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.23
Consensus pattern (95 bp):
AAGCCATCAGTACAGTAATATGATTGGCACAAACCCATCAGTAATAGTAATATGATCGGCACACA
GCCATCAGTAATAGTAATATGATCGGCACA
Found at i:30887923 original size:26 final size:26
Alignment explanation
Indices: 30887859--30887924 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
30887849 TCGGCACAAA
* * *
30887859 GCCATCAATAGCATCGCAGCAAAGTT
1 GCCAACAATAGTATCGCAGCAAAGCT
* *
30887885 GCCAACAACAGTATCGCAGTAAAGCT
1 GCCAACAATAGTATCGCAGCAAAGCT
**
30887911 GCCAGTAATAGTAT
1 GCCAACAATAGTAT
30887925 ATGTGACCAA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (26 bp):
GCCAACAATAGTATCGCAGCAAAGCT
Found at i:30887942 original size:27 final size:27
Alignment explanation
Indices: 30887912--30887975 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
30887902 AGTAAAGCTG
* *
30887912 CCAGTAATAGT-ATATGTGACCAAGCCA
1 CCAGTAACAGTGAT-TGTGACAAAGCCA
*
30887939 CCAGTAACAGTGATTGTGGCAAAGCCA
1 CCAGTAACAGTGATTGTGACAAAGCCA
30887966 CCAGT-ACAGT
1 CCAGTAACAGT
30887976 ACTTCCTCCA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 5 0.15
27 26 0.79
28 2 0.06
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.20
Consensus pattern (27 bp):
CCAGTAACAGTGATTGTGACAAAGCCA
Found at i:30888071 original size:24 final size:24
Alignment explanation
Indices: 30888039--30888094 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
30888029 GCCATGCACG
*
30888039 AAATTAGTCATACAAATCACAAAC
1 AAATCAGTCATACAAATCACAAAC
** *
30888063 AAATCAGTCATTTAAATCACAGAC
1 AAATCAGTCATACAAATCACAAAC
30888087 AAATCAGT
1 AAATCAGT
30888095 ATTTTACATC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.50, C:0.20, G:0.07, T:0.23
Consensus pattern (24 bp):
AAATCAGTCATACAAATCACAAAC
Found at i:30888100 original size:24 final size:24
Alignment explanation
Indices: 30888052--30888173 Score: 102
Period size: 24 Copynumber: 5.1 Consensus size: 24
30888042 TTAGTCATAC
30888052 AAATCACAAACAAATCAGTCATTT
1 AAATCACAAACAAATCAGTCATTT
*
30888076 AAATCACAGACAAATCAGT-ATTTT
1 AAATCACAAACAAATCAGTCA-TTT
* * * *
30888100 ACATCATAAAAAAATTAGTCATTT
1 AAATCACAAACAAATCAGTCATTT
* * ** *
30888124 ACATCTCGGACAAATCATTCATTT
1 AAATCACAAACAAATCAGTCATTT
* * * *
30888148 ACATCAGAAGCAAATCAATCATTT
1 AAATCACAAACAAATCAGTCATTT
30888172 AA
1 AA
30888174 CCCCGAGGGG
Statistics
Matches: 76, Mismatches: 20, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
23 1 0.01
24 74 0.97
25 1 0.01
ACGTcount: A:0.46, C:0.19, G:0.07, T:0.29
Consensus pattern (24 bp):
AAATCACAAACAAATCAGTCATTT
Found at i:30888139 original size:48 final size:48
Alignment explanation
Indices: 30888054--30888173 Score: 125
Period size: 48 Copynumber: 2.5 Consensus size: 48
30888044 AGTCATACAA
*
30888054 ATCACAAACAAATCAGTCATTTAAATCACAGACAAATCAGT-ATTTTAC
1 ATCACAAAAAAATCAGTCATTTAAATCACAGACAAATCAGTCA-TTTAC
* * * * * *
30888102 ATCATAAAAAAATTAGTCATTTACATCTCGGACAAATCATTCATTTAC
1 ATCACAAAAAAATCAGTCATTTAAATCACAGACAAATCAGTCATTTAC
* ** *
30888150 ATCAGAAGCAAATCAATCATTTAA
1 ATCACAAAAAAATCAGTCATTTAA
30888174 CCCCGAGGGG
Statistics
Matches: 58, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
48 57 0.98
49 1 0.02
ACGTcount: A:0.45, C:0.19, G:0.07, T:0.29
Consensus pattern (48 bp):
ATCACAAAAAAATCAGTCATTTAAATCACAGACAAATCAGTCATTTAC
Found at i:30888209 original size:27 final size:27
Alignment explanation
Indices: 30888179--30888264 Score: 64
Period size: 27 Copynumber: 3.2 Consensus size: 27
30888169 TTTAACCCCG
*
30888179 AGGGGAAAAATAGTCATTTTACCCTAT
1 AGGGGAAAAACAGTCATTTTACCCTAT
* ** * *
30888206 AGGGGCATTACGGTCATTTTACCTTAT
1 AGGGGAAAAACAGTCATTTTACCCTAT
* ** * * *
30888233 AGGGGCATTACGGTCATTTTATCCTAC
1 AGGGGAAAAACAGTCATTTTACCCTAT
30888260 AGGGG
1 AGGGG
30888265 CATTGCGGTT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.31
Consensus pattern (27 bp):
AGGGGAAAAACAGTCATTTTACCCTAT
Found at i:30888237 original size:54 final size:54
Alignment explanation
Indices: 30888179--30888291 Score: 127
Period size: 54 Copynumber: 2.1 Consensus size: 54
30888169 TTTAACCCCG
* * * *
30888179 AGGGGAAAAATAGTCATTTTACCCTATAGGGGCATTACGGTCATTTTACCTTAT
1 AGGGGAAAAACAGTCATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTAC
* ** * * * *
30888233 AGGGGCATTACGGTCATTTTATCCTACAGGGGCATTGCGGTTATTTTACCCTAC
1 AGGGGAAAAACAGTCATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTAC
30888287 AGGGG
1 AGGGG
30888292 CATTATAGTT
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (54 bp):
AGGGGAAAAACAGTCATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTAC
Found at i:30888265 original size:27 final size:27
Alignment explanation
Indices: 30888191--30888296 Score: 158
Period size: 27 Copynumber: 3.9 Consensus size: 27
30888181 GGGAAAAATA
*
30888191 GTCATTTTACCCTATAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
30888218 GTCATTTTACCTTATAGGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACG
* *
30888245 GTCATTTTATCCTACAGGGGCATTGCG
1 GTCATTTTACCCTACAGGGGCATTACG
*
30888272 GTTATTTTACCCTACAGGGGCATTA
1 GTCATTTTACCCTACAGGGGCATTA
30888297 TAGTTCTTCT
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 71 1.00
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGCATTACG
Found at i:30888309 original size:27 final size:27
Alignment explanation
Indices: 30888198--30888311 Score: 93
Period size: 27 Copynumber: 4.2 Consensus size: 27
30888188 ATAGTCATTT
* * * *
30888198 TACCCTATAGGGGCATTACGGTCATTT
1 TACCCTACAGGGGCATTACAGTTATTC
* * * * *
30888225 TACCTTATAGGGGCATTACGGTCATTT
1 TACCCTACAGGGGCATTACAGTTATTC
* * * *
30888252 TATCCTACAGGGGCATTGCGGTTATTT
1 TACCCTACAGGGGCATTACAGTTATTC
* *
30888279 TACCCTACAGGGGCATTATAGTTCTTC
1 TACCCTACAGGGGCATTACAGTTATTC
30888306 TACCCT
1 TACCCT
30888312 TCGAGAGTAT
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 75 1.00
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (27 bp):
TACCCTACAGGGGCATTACAGTTATTC
Found at i:30888360 original size:27 final size:28
Alignment explanation
Indices: 30888306--30888389 Score: 84
Period size: 27 Copynumber: 3.1 Consensus size: 28
30888296 ATAGTTCTTC
* *
30888306 TACCCTTCGAGAGTA-TTTCGATAATTT
1 TACCCTTCGAGGGTATTTTAGATAATTT
*
30888333 TACCCTTCGAGGGTATTTTAG-TAGTTT
1 TACCCTTCGAGGGTATTTTAGATAATTT
** **
30888360 TACCCTTTAAGGGTATTCCAG-TAATTT
1 TACCCTTCGAGGGTATTTTAGATAATTT
30888387 TAC
1 TAC
30888390 AACCTTTCCA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
27 44 0.92
28 4 0.08
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.42
Consensus pattern (28 bp):
TACCCTTCGAGGGTATTTTAGATAATTT
Found at i:30892338 original size:50 final size:50
Alignment explanation
Indices: 30892219--30892511 Score: 424
Period size: 50 Copynumber: 5.8 Consensus size: 50
30892209 GATAATAACA
* * * ** *
30892219 TGCCAAAGTCATGTCCCAAACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * * * *
30892270 TGCCCATGCCATGCCCCAGACATGGTCTTACATGGGACCTCTCATCTTGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
30892320 TGCCAGCGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
30892370 TGCCAACGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATCTCGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
30892420 TGCCAGCGTCATGTCCCAGACATGATCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
30892470 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
30892512 TTACCCAAAT
Statistics
Matches: 215, Mismatches: 27, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
50 183 0.85
51 32 0.15
ACGTcount: A:0.21, C:0.32, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:30923463 original size:27 final size:26
Alignment explanation
Indices: 30923400--30923544 Score: 132
Period size: 27 Copynumber: 5.4 Consensus size: 26
30923390 GGTATAACAA
* **
30923400 TCATTTTACCCTAT-GGGGTACTTCAG
1 TCATTTTACCCT-TCGGGGTATTTTGG
*
30923426 TCATTTTACCCTTTGGGGCTATTTTGG
1 TCATTTTACCCTTCGGGG-TATTTTGG
* * *
30923453 TTATTTTACCCTTCGACGGTATTTTGA
1 TCATTTTACCCTTCG-GGGTATTTTGG
* *
30923480 TCATTTTACCCTTCGGGGGTATTTCGA
1 TCATTTTACCCTTC-GGGGTATTTTGG
*
30923507 TTATTTTA-CCTTCCGGAGGTATTTTGG
1 TCATTTTACCCTT-CGG-GGTATTTTGG
30923534 TCATTTTACCC
1 TCATTTTACCC
30923545 ACGAATCGCA
Statistics
Matches: 98, Mismatches: 14, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
25 1 0.01
26 22 0.22
27 70 0.71
28 5 0.05
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.45
Consensus pattern (26 bp):
TCATTTTACCCTTCGGGGTATTTTGG
Found at i:30923489 original size:54 final size:54
Alignment explanation
Indices: 30923426--30923544 Score: 161
Period size: 54 Copynumber: 2.2 Consensus size: 54
30923416 GGTACTTCAG
* * *
30923426 TCATTTTACCCTTTGGGGCTATTTTGGTTATTTTACCCTT-C-GACGGTATTTTGA
1 TCATTTTACCCTTCGGGGCTATTTCGATTATTTTA-CCTTCCGGA-GGTATTTTGA
* *
30923480 TCATTTTACCCTTCGGGGGTATTTCGATTATTTTACCTTCCGGAGGTATTTTGG
1 TCATTTTACCCTTCGGGGCTATTTCGATTATTTTACCTTCCGGAGGTATTTTGA
30923534 TCATTTTACCC
1 TCATTTTACCC
30923545 ACGAATCGCA
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
53 4 0.07
54 52 0.90
55 2 0.03
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.46
Consensus pattern (54 bp):
TCATTTTACCCTTCGGGGCTATTTCGATTATTTTACCTTCCGGAGGTATTTTGA
Found at i:30930518 original size:28 final size:28
Alignment explanation
Indices: 30930486--30930595 Score: 157
Period size: 28 Copynumber: 3.9 Consensus size: 28
30930476 AATAGTACAG
*
30930486 TGTGGGCCTTAGCCCAAAACAGTAACAC
1 TGTGGGCCTTAGCCCAAAACAGTAACAA
*
30930514 TGTGGGCCTTAGCGCAAAACAGTAACAA
1 TGTGGGCCTTAGCCCAAAACAGTAACAA
* * *
30930542 TGTGGGCCTTAGCCCAATACAGTAATAG
1 TGTGGGCCTTAGCCCAAAACAGTAACAA
* *
30930570 TGTGGGTCTTAGCCCAATACAGTAAC
1 TGTGGGCCTTAGCCCAAAACAGTAAC
30930596 CAGTATAGTG
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 74 1.00
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.22
Consensus pattern (28 bp):
TGTGGGCCTTAGCCCAAAACAGTAACAA
Found at i:30930967 original size:26 final size:27
Alignment explanation
Indices: 30930938--30931018 Score: 112
Period size: 27 Copynumber: 3.0 Consensus size: 27
30930928 AGGGGTATAA
*
30930938 CAGTCATTTT-CCCTTTAGGGGTATTT
1 CAGTCATTTTACCCTTTAAGGGTATTT
*
30930964 CAGTCATTTTACCCTCTAAGGGTATTT
1 CAGTCATTTTACCCTTTAAGGGTATTT
*
30930991 C-GATCATTTTACCCTTCAAGGGTATTT
1 CAG-TCATTTTACCCTTTAAGGGTATTT
30931018 C
1 C
30931019 GGTTGTAGTG
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 11 0.22
27 38 0.78
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.42
Consensus pattern (27 bp):
CAGTCATTTTACCCTTTAAGGGTATTT
Found at i:30946451 original size:43 final size:42
Alignment explanation
Indices: 30946380--30946541 Score: 121
Period size: 43 Copynumber: 3.8 Consensus size: 42
30946370 CAAAAAGCTC
* * *
30946380 ATACAATGTCAATGTCTCAGAC-GTGGTCTTACATGTAATCAA
1 ATACGATGCCAATGTCCCAGACAG-GGTCTTACATGTAATCAA
* * * * * *
30946422 ATAACGATGTCACTGTCCCAGATAGGGTCTTACGTGAAATCAT
1 AT-ACGATGCCAATGTCCCAGACAGGGTCTTACATGTAATCAA
* * *
30946465 ATATGATGCCAATGTCCCAGACATGGTCTTACACGTAAATCTCAA
1 ATACGATGCCAATGTCCCAGACAGGGTCTTACATGT-AA--TCAA
* * * *
30946510 AT-CGATTCCAACGTCCCAAACATGGTCTTACA
1 ATACGATGCCAATGTCCCAGACAGGGTCTTACA
30946542 CGATATCACA
Statistics
Matches: 95, Mismatches: 20, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
42 28 0.29
43 35 0.37
44 27 0.28
45 5 0.05
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (42 bp):
ATACGATGCCAATGTCCCAGACAGGGTCTTACATGTAATCAA
Found at i:30953475 original size:43 final size:41
Alignment explanation
Indices: 30953383--30953531 Score: 140
Period size: 43 Copynumber: 3.6 Consensus size: 41
30953373 GTTACTCGGT
* ***
30953383 GGAATCAGCACTTAGCAACCACC-TTA-TATTTTGTGATACGG
1 GGAATCAGCACTTAGCAACC-CCTTTACAATCAAG-GATACGG
* *
30953424 GGAATCAGCACATAACAACCCCTTTCACAATCAAGGATACGG
1 GGAATCAGCACTTAGCAACCCCTTT-ACAATCAAGGATACGG
* ** *
30953466 TGGAATCAGCACTTAGCAACCACCTTTAGAATCAATAATTCGG
1 -GGAATCAGCACTTAGCAACC-CCTTTACAATCAAGGATACGG
*
30953509 GGAATCAACACTTAGCAACCCCT
1 GGAATCAGCACTTAGCAACCCCT
30953532 CAGGGAATCT
Statistics
Matches: 90, Mismatches: 13, Indels: 10
0.80 0.12 0.09
Matches are distributed among these distances:
40 2 0.02
41 23 0.26
42 27 0.30
43 33 0.37
44 5 0.06
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (41 bp):
GGAATCAGCACTTAGCAACCCCTTTACAATCAAGGATACGG
Found at i:30953537 original size:26 final size:26
Alignment explanation
Indices: 30953508--30953557 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
30953498 CAATAATTCG
30953508 GGGAATCAACACTTAGCAACCCCTCA
1 GGGAATCAACACTTAGCAACCCCTCA
* *
30953534 GGGAATCTACATTTAGCAACCCCT
1 GGGAATCAACACTTAGCAACCCCT
30953558 TTTTTATCAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.20
Consensus pattern (26 bp):
GGGAATCAACACTTAGCAACCCCTCA
Found at i:30953579 original size:41 final size:41
Alignment explanation
Indices: 30953534--30953640 Score: 169
Period size: 41 Copynumber: 2.6 Consensus size: 41
30953524 CAACCCCTCA
* * *
30953534 GGGAATCTACATTTAGCAACCCCTTTTTTATCAGAGTTTCG
1 GGGAATCTGCACTTAGCAACCCCTTTTTGATCAGAGTTTCG
*
30953575 GGGAATCTGCACTTAGCAATCCCTTTTTGATCAGAGTTTCG
1 GGGAATCTGCACTTAGCAACCCCTTTTTGATCAGAGTTTCG
*
30953616 GGGAATCTGTACTTAGCAACCCCTT
1 GGGAATCTGCACTTAGCAACCCCTT
30953641 ACATTCAATG
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (41 bp):
GGGAATCTGCACTTAGCAACCCCTTTTTGATCAGAGTTTCG
Found at i:30953731 original size:19 final size:20
Alignment explanation
Indices: 30953682--30953732 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
30953672 TTCAATCGGG
* *
30953682 AACCTTATTTTACAACATTT
1 AACCATATTTTTCAACATTT
*
30953702 TACCA-ACTTTTTCAA-ATTT
1 AACCATA-TTTTTCAACATTT
30953721 AACCATATTTTT
1 AACCATATTTTT
30953733 GTAATCTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.47
Consensus pattern (20 bp):
AACCATATTTTTCAACATTT
Found at i:30959432 original size:12 final size:11
Alignment explanation
Indices: 30959406--30959458 Score: 54
Period size: 12 Copynumber: 4.6 Consensus size: 11
30959396 TGGCTAAGCC
*
30959406 AAAAATTTT-G
1 AAAATTTTTGG
30959416 AAAATTTTATGG
1 AAAATTTT-TGG
*
30959428 AAAATTTTCGG
1 AAAATTTTTGG
30959439 AAAAATTTTTGGG
1 -AAAATTTTT-GG
30959452 AAAATTT
1 AAAATTT
30959459 ACAAAACTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
10 7 0.19
11 3 0.08
12 24 0.67
13 2 0.06
ACGTcount: A:0.43, C:0.02, G:0.15, T:0.40
Consensus pattern (11 bp):
AAAATTTTTGG
Found at i:30964198 original size:16 final size:16
Alignment explanation
Indices: 30964177--30964208 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
30964167 ATTTTGTTGC
*
30964177 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
30964193 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
30964209 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:30976019 original size:16 final size:18
Alignment explanation
Indices: 30975998--30976034 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 18
30975988 TTTGAGTTAA
30975998 AAAACTAA-ATTG-AAAT
1 AAAACTAATATTGAAAAT
30976014 AAAACTAATATTGAAAAT
1 AAAACTAATATTGAAAAT
30976032 AAA
1 AAA
30976035 CTCCTAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.42
17 4 0.21
18 7 0.37
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.24
Consensus pattern (18 bp):
AAAACTAATATTGAAAAT
Found at i:30978201 original size:19 final size:18
Alignment explanation
Indices: 30978177--30978212 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
30978167 TCTAAAAAAA
*
30978177 TTTAATATTACAATTTTAT
1 TTTAATAATA-AATTTTAT
30978196 TTTAATAATAAATTTTA
1 TTTAATAATAAATTTTA
30978213 ACATTAAACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTAATAATAAATTTTAT
Found at i:30978286 original size:22 final size:21
Alignment explanation
Indices: 30978258--30978305 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
30978248 TAGTTAGTGC
*
30978258 TTTATAACATAAAATATGAAAT-
1 TTTATAAAATAAAA-A-GAAATA
30978280 TTTATAAAATAAAAAGAAATA
1 TTTATAAAATAAAAAGAAATA
30978301 TTTAT
1 TTTAT
30978306 TTAAATCTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 5 0.21
21 6 0.25
22 13 0.54
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (21 bp):
TTTATAAAATAAAAAGAAATA
Found at i:30984435 original size:27 final size:28
Alignment explanation
Indices: 30984405--30984460 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 28
30984395 ATGTAAATAC
30984405 TGATGT-ATCTTTGCTTTATAAT-ATATA
1 TGATGTAAT-TTTGCTTTATAATAATATA
*
30984432 TGATTTAATTTTGCTTTATAATAATATA
1 TGATGTAATTTTGCTTTATAATAATATA
30984460 T
1 T
30984461 ATGAGTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 18 0.69
28 8 0.31
ACGTcount: A:0.32, C:0.05, G:0.09, T:0.54
Consensus pattern (28 bp):
TGATGTAATTTTGCTTTATAATAATATA
Found at i:30985637 original size:16 final size:16
Alignment explanation
Indices: 30985597--30985638 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
30985587 TTTTTCATTT
*
30985597 TTTATTTTTTAAATTA
1 TTTATTTTTTAAATAA
*
30985613 TATATTTTTTAAA-AA
1 TTTATTTTTTAAATAA
30985628 TTTATGTTTTT
1 TTTAT-TTTTT
30985639 CATTTAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (16 bp):
TTTATTTTTTAAATAA
Found at i:30990339 original size:29 final size:29
Alignment explanation
Indices: 30990267--30990352 Score: 91
Period size: 29 Copynumber: 2.9 Consensus size: 29
30990257 CCACCACTGA
* * **
30990267 TACATAGTACCTGATAAATATAACACTGG
1 TACAAAGTACCTGATAACTATAACACCAG
* * * *
30990296 CACAGAGTGCTTGATAACTATAACACCAG
1 TACAAAGTACCTGATAACTATAACACCAG
30990325 TACAAAGTACCTGATAACTATAATCACC
1 TACAAAGTACCTGATAACTATAA-CACC
30990353 GGCACATAAT
Statistics
Matches: 45, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
29 41 0.91
30 4 0.09
ACGTcount: A:0.41, C:0.22, G:0.13, T:0.24
Consensus pattern (29 bp):
TACAAAGTACCTGATAACTATAACACCAG
Found at i:31009401 original size:21 final size:20
Alignment explanation
Indices: 31009354--31009413 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
31009344 AAGTCTAAGA
*
31009354 ACCATTCCATTTTCTTAGTT
1 ACCATTCCATTTACTTAGTT
*
31009374 ACCATTCCATTTACTTACTTT
1 ACCATTCCATTTACTTA-GTT
* *
31009395 TCCATTCCATTTATTTAGT
1 ACCATTCCATTTACTTAGT
31009414 ATAAACTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
20 17 0.50
21 17 0.50
ACGTcount: A:0.22, C:0.25, G:0.03, T:0.50
Consensus pattern (20 bp):
ACCATTCCATTTACTTAGTT
Found at i:31013109 original size:40 final size:39
Alignment explanation
Indices: 31013024--31013116 Score: 105
Period size: 40 Copynumber: 2.3 Consensus size: 39
31013014 ATATTTATTG
* * **
31013024 CCTGAATGGACATTCGTGCCCCTGTTTGTACTTCGGTAC
1 CCTGAATGCACATTCGTGCCCCTGTTAGTACTTCGACAC
* *
31013063 CACTGAATGCACATTCGTGCTCTTGTTAGTACTTCGACAC
1 C-CTGAATGCACATTCGTGCCCCTGTTAGTACTTCGACAC
*
31013103 TCCTGAAGGCACAT
1 -CCTGAATGCACAT
31013117 ACATGCTCCT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
39 1 0.02
40 43 0.96
41 1 0.02
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.31
Consensus pattern (39 bp):
CCTGAATGCACATTCGTGCCCCTGTTAGTACTTCGACAC
Found at i:31028619 original size:44 final size:44
Alignment explanation
Indices: 31028566--31028793 Score: 122
Period size: 44 Copynumber: 5.0 Consensus size: 44
31028556 ATCTTAATCC
*
31028566 GCTCCGCTGTAATCTCAGAGAGATAGGATTACTAGCTTCAATTT
1 GCTCCGCTGTAATCTCAGAGAGATAAGATTACTAGCTTCAATTT
* * * * *
31028610 GCTCTGCTGTGATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGAT
1 GCTCCGCTGTAATCTCAGAGAGATAAGATTACTAGCTTCAAT-T--T
* * * **
31028657 GCGATCTACTCTGCTGTAAAT-TCAGAGAGATAAGATCCT-TTA-TTTTAATCC
1 --G--CT-C-C-GCTGT-AATCTCAGAGAGATAAGAT--TACTAGCTTCAATTT
* * * * *
31028708 GCTCCACTATAATCTCAGGGAGATAGGATTACTAGCTTCAATCT
1 GCTCCGCTGTAATCTCAGAGAGATAAGATTACTAGCTTCAATTT
* * * *
31028752 GCTCCGCTATAATCTCA-AGGAAATAAGATTTCTGGCTTCAAT
1 GCTCCGCTGTAATCTCAGA-GAGATAAGATTACTAGCTTCAAT
31028794 CTAATGCGAC
Statistics
Matches: 138, Mismatches: 29, Indels: 34
0.69 0.14 0.17
Matches are distributed among these distances:
42 1 0.01
43 5 0.04
44 93 0.67
45 2 0.01
46 1 0.01
47 3 0.02
49 2 0.01
51 2 0.01
52 1 0.01
54 24 0.17
55 3 0.02
56 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (44 bp):
GCTCCGCTGTAATCTCAGAGAGATAAGATTACTAGCTTCAATTT
Found at i:31028767 original size:142 final size:142
Alignment explanation
Indices: 31028510--31028931 Score: 664
Period size: 142 Copynumber: 3.0 Consensus size: 142
31028500 GAGATAAGAC
* * * * *
31028510 CTGATGCGATCTACTCTACTGTAACTTCATAAAGATAAGATCCTTTATCTTAATCCGCTCCGCTG
1 CTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
* * * *
31028575 TAATCTCAGAGAGATAGGATTACTAGCTTCAATTTGCTCTGCTGTGATCTCAGGGAGATAAGATT
66 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCTGCTATAATCTCAGGGAGATAAGATT
31028640 TCTGGCTTCAAT
131 TCTGGCTTCAAT
* *
31028652 CTGATGCGATCTACTCTGCTGTAAATTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTA
1 CTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
* * *
31028717 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTATAATCTCAAGGAAATAAGATT
66 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCTGCTATAATCTCAGGGAGATAAGATT
31028782 TCTGGCTTCAAT
131 TCTGGCTTCAAT
* *
31028794 CTAATGCGACCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
* * * *
31028859 TAATCTTAGGGAGATAGGATTACTAGCTTCAATCTGCTTTACTATAATCTCAGGGAGATAAGAAT
66 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCTGCTATAATCTCAGGGAGATAAGATT
31028924 TCTGGCTT
131 TCTGGCTT
31028932 TGATCTGCTC
Statistics
Matches: 255, Mismatches: 25, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
142 255 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (142 bp):
CTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCTGCTATAATCTCAGGGAGATAAGATT
TCTGGCTTCAAT
Found at i:31028794 original size:44 final size:44
Alignment explanation
Indices: 31028703--31028795 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 44
31028693 CCTTTATTTT
* * * *
31028703 AATCCGCTCCACTATAATCTCAGGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTATAATCTCAAGGAAATAAGATTACTAGCTTC
* * *
31028747 AATCTGCTCCGCTATAATCTCAAGGAAATAAGATTTCTGGCTTC
1 AATCTGCTCCACTATAATCTCAAGGAAATAAGATTACTAGCTTC
31028791 AATCT
1 AATCT
31028796 AATGCGACCT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (44 bp):
AATCTGCTCCACTATAATCTCAAGGAAATAAGATTACTAGCTTC
Found at i:31030246 original size:15 final size:14
Alignment explanation
Indices: 31030219--31030251 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
31030209 CTCCATTTTT
31030219 ATTTTTTCATCATC
1 ATTTTTTCATCATC
31030233 ATTTTTTCAT--TC
1 ATTTTTTCATCATC
31030245 ATTTTTT
1 ATTTTTT
31030252 AGGAATCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.47
14 10 0.53
ACGTcount: A:0.18, C:0.15, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTTTTTCATCATC
Found at i:31060661 original size:31 final size:31
Alignment explanation
Indices: 31060623--31060686 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
31060613 AAGATAAAAA
*
31060623 ATTGGGTTAAGTGCGATTGGTGTTCCAAGCT
1 ATTGGGTTAAGTGCGATTGGTGTTCCAAACT
*
31060654 ATTGGGTTAAGTGTGATTGGTGTTCCAAACT
1 ATTGGGTTAAGTGCGATTGGTGTTCCAAACT
31060685 AT
1 AT
31060687 GTGATTCTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.22, C:0.11, G:0.30, T:0.38
Consensus pattern (31 bp):
ATTGGGTTAAGTGCGATTGGTGTTCCAAACT
Found at i:31062694 original size:16 final size:15
Alignment explanation
Indices: 31062673--31062727 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 15
31062663 AAAAAAATGA
31062673 TATATTTTTATTAATT
1 TATATTTTT-TTAATT
31062689 TATATTTTTTTAAATT
1 TATATTTTTTT-AATT
* *
31062705 T-TTTTTATTTTTATT
1 TATATTT-TTTTAATT
31062720 TATATTTT
1 TATATTTT
31062728 CTTATCATGT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
15 11 0.33
16 22 0.67
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (15 bp):
TATATTTTTTTAATT
Found at i:31062721 original size:21 final size:21
Alignment explanation
Indices: 31062687--31062727 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
31062677 TTTTTATTAA
31062687 TTTATATTTTTTTAAATTTTT
1 TTTATATTTTTTTAAATTTTT
*
31062708 TTTAT-TTTTATTTATATTTT
1 TTTATATTTT-TTTAAATTTT
31062728 CTTATCATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTATATTTTTTTAAATTTTT
Found at i:31065665 original size:43 final size:43
Alignment explanation
Indices: 31065615--31065851 Score: 214
Period size: 43 Copynumber: 5.6 Consensus size: 43
31065605 AGTAATATGG
*
31065615 GGAATCAGCAAATAGCAACCCCTTTCACAATCAAAGATACAGT
1 GGAATCAGCACATAGCAACCCCTTTCACAATCAAAGATACAGT
* * * ** *
31065658 GGAATCAGCACTTAGCAACCACCTTT-ATATTCAGTGATAGAG-
1 GGAATCAGCACATAGCAACC-CCTTTCACAATCAAAGATACAGT
* * * * *
31065700 GGAATCAACACACAGCAACCCCTTTCATAATCAAATATACGGT
1 GGAATCAGCACATAGCAACCCCTTTCACAATCAAAGATACAGT
* * *
31065743 GGAATCAGCACATAGCAACCCCTTTCACAATAAAATATACGGT
1 GGAATCAGCACATAGCAACCCCTTTCACAATCAAAGATACAGT
* * * * * *
31065786 GGAATTAGCACTTAGCAACTACCTTT-AGAATCAATA-ATTC-GG
1 GGAATCAGCACATAGCAAC-CCCTTTCACAATCAA-AGATACAGT
*
31065828 GGAATCAGCACTTAGCAACCCCTT
1 GGAATCAGCACATAGCAACCCCTT
31065852 GGGGAATCTG
Statistics
Matches: 160, Mismatches: 29, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
41 9 0.06
42 46 0.29
43 94 0.59
44 11 0.07
ACGTcount: A:0.37, C:0.25, G:0.15, T:0.23
Consensus pattern (43 bp):
GGAATCAGCACATAGCAACCCCTTTCACAATCAAAGATACAGT
Found at i:31065732 original size:85 final size:85
Alignment explanation
Indices: 31065580--31065767 Score: 256
Period size: 85 Copynumber: 2.2 Consensus size: 85
31065570 CGGTGGATTT
* * *
31065580 AGCACTTAGCAACCACC-TTAAATTTAGTAATATGGGGAATCAGCAAATAGCAACCCCTTTCACA
1 AGCACTTAGCAACCACCTTTAAATTCAGTAATATGGGGAATCAACAAACAGCAACCCCTTTCACA
31065644 ATCAAAGATACAGTGGAATC
66 ATCAAAGATACAGTGGAATC
* * * *
31065664 AGCACTTAGCAACCACCTTTATATTCAGTGATA-GAGGGAATCAACACACAGCAACCCCTTTCAT
1 AGCACTTAGCAACCACCTTTAAATTCAGTAATATG-GGGAATCAACAAACAGCAACCCCTTTCAC
* *
31065728 AATCAAATATACGGTGGAATC
65 AATCAAAGATACAGTGGAATC
*
31065749 AGCACATAGCAACC-CCTTT
1 AGCACTTAGCAACCACCTTT
31065768 CACAATAAAA
Statistics
Matches: 92, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
84 23 0.25
85 69 0.75
ACGTcount: A:0.37, C:0.25, G:0.15, T:0.23
Consensus pattern (85 bp):
AGCACTTAGCAACCACCTTTAAATTCAGTAATATGGGGAATCAACAAACAGCAACCCCTTTCACA
ATCAAAGATACAGTGGAATC
Found at i:31065845 original size:128 final size:128
Alignment explanation
Indices: 31065615--31065851 Score: 332
Period size: 128 Copynumber: 1.9 Consensus size: 128
31065605 AGTAATATGG
*
31065615 GGAATCAGCAAATAGCAACCCCTTTCACAATCAAAGATACAGTGGAATCAGCACTTAGCAACCAC
1 GGAATCAGCAAATAGCAACCCCTTTCACAATAAAAGATACAGTGGAATCAGCACTTAGCAACCAC
* * * *
31065680 CTTTATATTCAGTGATAGAGGGAATCAACACACAGCAACCCCTTTCATAATCAAATATACGGT
66 CTTTAGAATCAATAATAGAGGGAATCAACACACAGCAACCCCTTTCATAATCAAATATACGGT
* * * * *
31065743 GGAATCAGCACATAGCAACCCCTTTCACAATAAAATATACGGTGGAATTAGCACTTAGCAACTAC
1 GGAATCAGCAAATAGCAACCCCTTTCACAATAAAAGATACAGTGGAATCAGCACTTAGCAACCAC
* * **
31065808 CTTTAGAATCAATAATTCG-GGGAATCAGCACTTAGCAACCCCTT
66 CTTTAGAATCAATAA-TAGAGGGAATCAACACACAGCAACCCCTT
31065852 GGGGAATCTG
Statistics
Matches: 94, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
128 92 0.98
129 2 0.02
ACGTcount: A:0.37, C:0.25, G:0.15, T:0.23
Consensus pattern (128 bp):
GGAATCAGCAAATAGCAACCCCTTTCACAATAAAAGATACAGTGGAATCAGCACTTAGCAACCAC
CTTTAGAATCAATAATAGAGGGAATCAACACACAGCAACCCCTTTCATAATCAAATATACGGT
Found at i:31066009 original size:19 final size:20
Alignment explanation
Indices: 31065960--31066010 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
31065950 TTCAATCGAG
* *
31065960 AACCTTATTTTACAACATTT
1 AACCATATTTTTCAACATTT
*
31065980 TACCA-ACTTTTTCAA-ATTT
1 AACCATA-TTTTTCAACATTT
31065999 AACCATATTTTT
1 AACCATATTTTT
31066011 GTAATCTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.47
Consensus pattern (20 bp):
AACCATATTTTTCAACATTT
Found at i:31071207 original size:11 final size:11
Alignment explanation
Indices: 31071191--31071215 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
31071181 GTTGGGCACC
31071191 AATAAGAAGAA
1 AATAAGAAGAA
31071202 AATAAGAAGAA
1 AATAAGAAGAA
31071213 AAT
1 AAT
31071216 GTATTTGCAG
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:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (11 bp):
AATAAGAAGAA
Found at i:31072439 original size:40 final size:39
Alignment explanation
Indices: 31072395--31072635 Score: 252
Period size: 40 Copynumber: 6.1 Consensus size: 39
31072385 ATTATTGTTG
* *
31072395 AATGCATATACGTGCCCCTGTTTGAACTTCGGTACCCCTA
1 AATGCACATACGTGCCCCTATTT-AACTTCGGTACCCCTA
* *
31072435 AATGCACATACGTGCCCCTATTTAAACATCGGTACCCCTG
1 AATGCACATACGTGCCCCTATTT-AACTTCGGTACCCCTA
* * * *
31072475 AATGCACATATGTGCCCCTATTTCTACTTCAGTACCCCTG
1 AATGCACATACGTGCCCCTATTT-AACTTCGGTACCCCTA
* * *
31072515 AATGCACATATGTGCCCCTATTTCTACTTCGGTACCCCTG
1 AATGCACATACGTGCCCCTATTT-AACTTCGGTACCCCTA
* *
31072555 AATGCACATACGTGCCCTTGTTTATACTTCGGTA-CCCTA
1 AATGCACATACGTGCCCCTATTTA-ACTTCGGTACCCCTA
* * * * *
31072594 AACGCACATACGTG-CCTTGTTTATACTTTGGTAACCCTA
1 AATGCACATACGTGCCCCTATTTA-ACTTCGGTACCCCTA
31072633 AAT
1 AAT
31072636 CAAATAGTAT
Statistics
Matches: 180, Mismatches: 19, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
38 18 0.10
39 24 0.13
40 138 0.77
ACGTcount: A:0.24, C:0.30, G:0.15, T:0.31
Consensus pattern (39 bp):
AATGCACATACGTGCCCCTATTTAACTTCGGTACCCCTA
Found at i:31072452 original size:20 final size:20
Alignment explanation
Indices: 31072429--31072494 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
31072419 AACTTCGGTA
31072429 CCCCTAAATGCACATACGTG
1 CCCCTAAATGCACATACGTG
** ** *
31072449 CCCCTATTTAAACAT-CGGTA
1 CCCCTAAATGCACATAC-GTG
* *
31072469 CCCCTGAATGCACATATGTG
1 CCCCTAAATGCACATACGTG
31072489 CCCCTA
1 CCCCTA
31072495 TTTCTACTTC
Statistics
Matches: 31, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.27, C:0.35, G:0.14, T:0.24
Consensus pattern (20 bp):
CCCCTAAATGCACATACGTG
Found at i:31072512 original size:20 final size:20
Alignment explanation
Indices: 31072489--31072553 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
31072479 CACATATGTG
31072489 CCCCTATTTCTACTTCAGTA
1 CCCCTATTTCTACTTCAGTA
* * * *
31072509 CCCCTGAATGC-ACAT-ATGTG
1 CCCCT-ATTTCTACTTCA-GTA
*
31072529 CCCCTATTTCTACTTCGGTA
1 CCCCTATTTCTACTTCAGTA
31072549 CCCCT
1 CCCCT
31072554 GAATGCACAT
Statistics
Matches: 32, Mismatches: 9, Indels: 8
0.65 0.18 0.16
Matches are distributed among these distances:
19 4 0.12
20 25 0.78
21 3 0.09
ACGTcount: A:0.18, C:0.37, G:0.11, T:0.34
Consensus pattern (20 bp):
CCCCTATTTCTACTTCAGTA
Found at i:31072530 original size:80 final size:80
Alignment explanation
Indices: 31072393--31072609 Score: 303
Period size: 80 Copynumber: 2.7 Consensus size: 80
31072383 TAATTATTGT
*
31072393 TGAATGCATATACGTGCCCCTGTTTGA-ACTTCGGTACCCCTAAATGCACATACGTGCCCCTATT
1 TGAATGCACATACGTGCCCCTGTTT-ATACTTCGGTACCCCTAAATGCACATACGTGCCCCTATT
31072457 TAAACATCGGTACCCC
65 TAAACATCGGTACCCC
* * * * * *
31072473 TGAATGCACATATGTGCCCCTATTTCTACTTCAGTACCCCTGAATGCACATATGTGCCCCTATTT
1 TGAATGCACATACGTGCCCCTGTTTATACTTCGGTACCCCTAAATGCACATACGTGCCCCTATTT
** *
31072538 CTACTTCGGTACCCC
66 AAACATCGGTACCCC
* *
31072553 TGAATGCACATACGTGCCCTTGTTTATACTTCGGTA-CCCTAAACGCACATACGTGCC
1 TGAATGCACATACGTGCCCCTGTTTATACTTCGGTACCCCTAAATGCACATACGTGCC
31072610 TTGTTTATAC
Statistics
Matches: 118, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
79 18 0.15
80 100 0.85
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.29
Consensus pattern (80 bp):
TGAATGCACATACGTGCCCCTGTTTATACTTCGGTACCCCTAAATGCACATACGTGCCCCTATTT
AAACATCGGTACCCC
Found at i:31078295 original size:43 final size:42
Alignment explanation
Indices: 31078203--31078341 Score: 158
Period size: 43 Copynumber: 3.3 Consensus size: 42
31078193 AGATTCCTCG
*
31078203 AGGGGTTGCTAAGTGCTGATTCC-CCGA-AT-TATTGATTTTAA
1 AGGGGTTGCTAAGTGCTGATTCCACC-ATATAT-TTGATTTGAA
* *
31078244 AGGTGGTTGCTAAGTGCTGATTTCACTATATATTTGATTGTGAA
1 AGG-GGTTGCTAAGTGCTGATTCCACCATATATTTGATT-TGAA
* * *
31078288 AGGGGTTGCTAAGTGCTTATTCCACCGTATATTTTATTTTGAA
1 AGGGGTTGCTAAGTGCTGATTCCACCATATATTTGA-TTTGAA
31078331 AGGGGTTGCTA
1 AGGGGTTGCTA
31078342 TATCACTGAA
Statistics
Matches: 84, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
41 3 0.04
42 20 0.24
43 52 0.62
44 9 0.11
ACGTcount: A:0.24, C:0.12, G:0.25, T:0.39
Consensus pattern (42 bp):
AGGGGTTGCTAAGTGCTGATTCCACCATATATTTGATTTGAA
Found at i:31078403 original size:43 final size:43
Alignment explanation
Indices: 31078342--31078511 Score: 157
Period size: 43 Copynumber: 4.0 Consensus size: 43
31078332 GGGGTTGCTA
*
31078342 TATCACTGAATATAAAGGTGGTTGCTAAATGCTGATTCCACCG
1 TATCACTAAATATAAAGGTGGTTGCTAAATGCTGATTCCACCG
* **
31078385 TATCACTAAATATAAAGGTGGTTGCTAAATACTGATTCCATTG
1 TATCACTAAATATAAAGGTGGTTGCTAAATGCTGATTCCACCG
** * * ** * *
31078428 TATCTTTAACTGTAAAAGG-GGTTGCTATGTGTTGATT-CATCG
1 TATCACTAAATAT-AAAGGTGGTTGCTAAATGCTGATTCCACCG
* * * * *
31078470 TATCACTGAAT-TTAAGGTGGTTACTAAGTGCTGAATCCACCG
1 TATCACTAAATATAAAGGTGGTTGCTAAATGCTGATTCCACCG
31078512 AGTAACGGAT
Statistics
Matches: 101, Mismatches: 23, Indels: 7
0.77 0.18 0.05
Matches are distributed among these distances:
40 4 0.04
41 15 0.15
42 15 0.15
43 62 0.61
44 5 0.05
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (43 bp):
TATCACTAAATATAAAGGTGGTTGCTAAATGCTGATTCCACCG
Found at i:31078408 original size:70 final size:68
Alignment explanation
Indices: 31078286--31078419 Score: 155
Period size: 70 Copynumber: 1.9 Consensus size: 68
31078276 TTTGATTGTG
* * * * * * *
31078286 AAAGGGGTTGCTAAGTGCTTATTCCACCGTATATTTTATTTTGAAAGGGGTTGCTATATCACTGA
1 AAAGGGGTTGCTAAATGCTGATTCCACCGTATATCTAAATATGAAAGGGGTTGCTAAAT-ACTGA
31078351 ATAT
65 ATAT
31078355 AAAGGTGGTTGCTAAATGCTGATTCCACCGTATCA-CTAAATAT-AAAGGTGGTTGCTAAATACT
1 AAAGG-GGTTGCTAAATGCTGATTCCACCGTAT-ATCTAAATATGAAAGG-GGTTGCTAAATACT
31078418 GA
63 GA
31078420 TTCCATTGTA
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
69 15 0.27
70 39 0.71
71 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.34
Consensus pattern (68 bp):
AAAGGGGTTGCTAAATGCTGATTCCACCGTATATCTAAATATGAAAGGGGTTGCTAAATACTGAA
TAT
Found at i:31087525 original size:25 final size:27
Alignment explanation
Indices: 31087497--31087557 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
31087487 AGGGGTAAAA
*
31087497 TGGTAATTTTA-CCATAG-GGGTATTT
1 TGGTCATTTTACCCATAGAGGGTATTT
* *
31087522 TGGTCATTTTACCCTTCGAGGGTATTT
1 TGGTCATTTTACCCATAGAGGGTATTT
31087549 TGGTCATTT
1 TGGTCATTT
31087558 AACAACCTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
25 10 0.32
26 4 0.13
27 17 0.55
ACGTcount: A:0.18, C:0.13, G:0.23, T:0.46
Consensus pattern (27 bp):
TGGTCATTTTACCCATAGAGGGTATTT
Found at i:31093454 original size:17 final size:18
Alignment explanation
Indices: 31093440--31093523 Score: 80
Period size: 19 Copynumber: 4.4 Consensus size: 18
31093430 ATAATCTTCG
31093440 AGGATATGCAATCTTAGA
1 AGGATATGCAATCTTAGA
*
31093458 TATGATATGCAATCTTAGA
1 -AGGATATGCAATCTTAGA
*
31093477 TATGATATATGCAATCTTAGA
1 -A-G-GATATGCAATCTTAGA
* *
31093498 TATGATATGTAATCTTAGA
1 -AGGATATGCAATCTTAGA
31093517 A-GATATG
1 AGGATATG
31093524 ATTTTGTAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
17 6 0.11
18 1 0.02
19 33 0.58
21 17 0.30
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.36
Consensus pattern (18 bp):
AGGATATGCAATCTTAGA
Found at i:31093466 original size:19 final size:19
Alignment explanation
Indices: 31093442--31093516 Score: 123
Period size: 19 Copynumber: 3.8 Consensus size: 19
31093432 AATCTTCGAG
31093442 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
31093461 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
31093480 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
31093501 GATATGTAATCTTAGA
1 GATATGCAATCTTAGA
31093517 AGATATGATT
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
19 34 0.64
21 19 0.36
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:31093488 original size:21 final size:21
Alignment explanation
Indices: 31093443--31093505 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
31093433 ATCTTCGAGG
31093443 ATATGCAATCTTAGATATG--
1 ATATGCAATCTTAGATATGAT
31093462 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
31093483 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
31093504 AT
1 AT
31093506 GTAATCTTAG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 19 0.45
21 23 0.55
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:31093535 original size:23 final size:22
Alignment explanation
Indices: 31093455--31093539 Score: 81
Period size: 21 Copynumber: 4.0 Consensus size: 22
31093445 ATGCAATCTT
*
31093455 AGATATGATATGCAATCTTAG-
1 AGATATGATATGTAATCTTAGA
* *
31093476 ATATGAT-ATATGCAATCTT---
1 AGAT-ATGATATGTAATCTTAGA
31093495 AGATATGATATGTAATCTTAGA
1 AGATATGATATGTAATCTTAGA
*
31093517 AGATATGATTTTGTAATCTTAGA
1 AGATATGA-TATGTAATCTTAGA
31093540 GATTTAATTT
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
18 2 0.04
19 14 0.26
21 15 0.28
22 10 0.19
23 13 0.24
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.39
Consensus pattern (22 bp):
AGATATGATATGTAATCTTAGA
Found at i:31093549 original size:22 final size:23
Alignment explanation
Indices: 31093505--31093549 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
31093495 AGATATGATA
*
31093505 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
31093528 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
31093550 GTAGATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:31094183 original size:27 final size:27
Alignment explanation
Indices: 31094136--31094214 Score: 72
Period size: 26 Copynumber: 2.9 Consensus size: 27
31094126 TCATATACGC
*
31094136 ATATTTATTT-TTTGTAGTATAATATAA
1 ATATTTATTTATTTATAGTAT-ATATAA
* *
31094163 ATATTTATTTATTTAT-TTATATGTAA
1 ATATTTATTTATTTATAGTATATATAA
* * *
31094189 TTATTTTTTTATCTATATGTATATAT
1 ATATTTATTTATTTATA-GTATATAT
31094215 TTATTTTAGT
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
26 18 0.44
27 13 0.32
28 10 0.24
ACGTcount: A:0.33, C:0.01, G:0.05, T:0.61
Consensus pattern (27 bp):
ATATTTATTTATTTATAGTATATATAA
Found at i:31094218 original size:26 final size:26
Alignment explanation
Indices: 31094136--31094221 Score: 74
Period size: 22 Copynumber: 3.4 Consensus size: 26
31094126 TCATATACGC
* * *
31094136 ATATTTATTTTTTGTA-GTATAATATAA
1 ATATTTATTTTTT-TATCTAT-ATGTAT
* *
31094163 ATATTTATTTATTTATTTATATG--T
1 ATATTTATTTTTTTATCTATATGTAT
31094187 A-A-TTATTTTTTTATCTATATGTAT
1 ATATTTATTTTTTTATCTATATGTAT
31094211 ATATTTATTTT
1 ATATTTATTTT
31094222 AGTATACATA
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
22 17 0.35
23 1 0.02
24 3 0.06
25 1 0.02
26 11 0.23
27 15 0.31
ACGTcount: A:0.31, C:0.01, G:0.05, T:0.63
Consensus pattern (26 bp):
ATATTTATTTTTTTATCTATATGTAT
Found at i:31098447 original size:6 final size:6
Alignment explanation
Indices: 31098438--31098482 Score: 83
Period size: 6 Copynumber: 7.7 Consensus size: 6
31098428 TAAAAGTGAT
31098438 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG -AAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
31098483 TGGAGAGGCC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 5 0.13
6 33 0.87
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:31100122 original size:176 final size:173
Alignment explanation
Indices: 31099686--31100150 Score: 547
Period size: 176 Copynumber: 2.6 Consensus size: 173
31099676 GCAGATCAGT
* * * *
31099686 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAG-ATGCAGATCTTGTCTT
1 GAAGAT-GCAGATCTTGTCTTCCTATATTGGT-GGAAGTAGATCGAAGAAAGCAGATCTTGTCTT
* * * * *
31099750 CCCATATTAGTGGC-GAAGTAGATCAAAGAAAGCAAATATTGTCTTCATTTATTGGCGTGAAGTA
64 --CATA-TATTGGCGGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTA
* * *
31099814 GATCGAAGATAGCAGGTCATGTCTTCCTATATTGGTAGGAAGTGGATC
126 GATCGAAAATAGCAGGTCATGTCTTCCTATATTAGTAGGAAGTAGATC
* * * * ***
31099862 GAAGATGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCAATCTTC
1 GAAGATGCAGATCTTGTCTTCCTATATTGGTG-GAAGTAGATCGAAGAAAGCAGATCTTGTCTTC
* *
31099927 CTATATTGGTAGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGA
65 ATATATTGG-CG-GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGA
* * *
31099992 TTGAAAATAGTAGGTCCTGTCTTCCTATATTAGTAGGAAGTAGATC
128 TCGAAAATAGCAGGTCATGTCTTCCTATATTAGTAGGAAGTAGATC
* *
31100038 GAAGATGCAGATCTTGTCTTCCCATAATGGTGGCAAAGTAGATCGAAGAAAGCAGATCTTGTCTT
1 GAAGATGCAGATCTTGTCTTCCTATATTGGTGG--AAGTAGATCGAAGAAAGCAGATCTTGTCTT
* * * *
31100103 CATGTATTGGCGTGAAGTAGATCGAAGATAGTAGATCTTGCCTTCATG
64 CATATATTGGCG-GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATG
31100151 CACCGACAGC
Statistics
Matches: 242, Mismatches: 40, Indels: 14
0.82 0.14 0.05
Matches are distributed among these distances:
173 5 0.02
174 4 0.02
175 34 0.14
176 165 0.68
177 34 0.14
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (173 bp):
GAAGATGCAGATCTTGTCTTCCTATATTGGTGGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCA
TATATTGGCGGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCG
AAAATAGCAGGTCATGTCTTCCTATATTAGTAGGAAGTAGATC
Found at i:31100150 original size:44 final size:44
Alignment explanation
Indices: 31099686--31100149 Score: 415
Period size: 44 Copynumber: 10.5 Consensus size: 44
31099676 GCAGATCAGT
* * * * *
31099686 GAAGATAGCAGGTCCTGTCTTCCTATATTGGTAG-GAAGTGGATC
1 GAAGATAGCAGATCTTGTCTTCATATATTGG-CGTGAAGTAGATC
*
31099730 GAAGAT-GCAGATCTTGTCTTCCCATATTAGTGGC--GAAGTAGATC
1 GAAGATAGCAGATCTTGTCTT--CATA-TATTGGCGTGAAGTAGATC
* * * * *
31099774 AAAGAAAGCAAATATTGTCTTCATTTATTGGCGTGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCATATATTGGCGTGAAGTAGATC
* * * * *
31099818 GAAGATAGCAGGTCATGTCTTCCTATATTGGTAG-GAAGTGGATC
1 GAAGATAGCAGATCTTGTCTTCATATATTGG-CGTGAAGTAGATC
*
31099862 GAAGAT-GCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCATATATTGGCGTGAAGTAGATC
*** * * *
31099905 GAAGATAGCAGATCCAATCTTCCTATATTGGTAGCGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCATATATTGG-CGTGAAGTAGATC
* * *
31099950 GAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATT
1 GAAGATAGCAGATCTTGTCTTCATATATTGGCGTGAAGTAGATC
* * * * * **
31099994 GAAAATAGTAGGTCCTGTCTTCCTATATTAGTAG-GAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCATATATT-GGCGTGAAGTAGATC
** * *
31100038 GAAGAT-GCAGATCTTGTCTTCCCATAATGGTG-GCAAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCATATATTGGCGTG--AAGTAGATC
* *
31100082 GAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATC
1 GAAGATAGCAGATCTTGTCTTCATATATTGGCGTGAAGTAGATC
* *
31100126 GAAGATAGTAGATCTTGCCTTCAT
1 GAAGATAGCAGATCTTGTCTTCAT
31100150 GCACCGACAG
Statistics
Matches: 334, Mismatches: 71, Indels: 30
0.77 0.16 0.07
Matches are distributed among these distances:
42 10 0.03
43 67 0.20
44 176 0.53
45 75 0.22
46 6 0.02
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (44 bp):
GAAGATAGCAGATCTTGTCTTCATATATTGGCGTGAAGTAGATC
Found at i:31100339 original size:44 final size:44
Alignment explanation
Indices: 31100271--31100476 Score: 206
Period size: 44 Copynumber: 4.7 Consensus size: 44
31100261 TGACCTCAGC
* *
31100271 CCTATCTCCCTGGTCAGCAATGGAATAGGTTAAAGATTGTGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* * *
31100315 CCTATCTCCCTGGTCAACAGTGGAATAGGGTGAAGATTGAGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* * * *
31100359 TCTATCTTCCTGGGT-AGTAGTGGAAT-GGATTGAAGATTGT-AGGT
1 CCTATCTCCCT-GGTCAGCAGTGGAATAGG-TTGAAGATTGTGA-AT
* *
31100403 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGTAA-ATCGTGAAC
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTG-AAGATTGTGAAT
* * *
31100447 CCTATCTCTCTGAGT-AGTAGTGGAGTAGGT
1 CCTATCTCCCTG-GTCAGCAGTGGAATAGGT
31100477 GGAAAATAGC
Statistics
Matches: 133, Mismatches: 21, Indels: 16
0.78 0.12 0.09
Matches are distributed among these distances:
43 6 0.05
44 117 0.88
45 10 0.08
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (44 bp):
CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
Found at i:31101341 original size:19 final size:19
Alignment explanation
Indices: 31101317--31101370 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
31101307 AATCTTCAAG
31101317 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
31101336 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
31101355 GATATGTAATCTTAGA
1 GATATGCAATCTTAGA
31101371 AGTTATGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:31102074 original size:26 final size:26
Alignment explanation
Indices: 31102009--31102077 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 26
31101999 TTTTTTGTAG
* *
31102009 TATA-ATATAAATATTTTTTTATTTA
1 TATATATATAATTATTTTTTTATCTA
* *
31102034 TTTATATTTAATTATTTTTTTATCTA
1 TATATATATAATTATTTTTTTATCTA
* *
31102060 TATGTATATATTTATTTT
1 TATATATATAATTATTTT
31102078 AGTATACATA
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
25 3 0.09
26 32 0.91
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (26 bp):
TATATATATAATTATTTTTTTATCTA
Found at i:31125914 original size:28 final size:27
Alignment explanation
Indices: 31125883--31125936 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
31125873 AGCATAGTAT
* * *
31125883 CAGGTGAGCCTTAGCCCATTAATAGAAC
1 CAGGTGAACCTAAGCCCACT-ATAGAAC
31125911 CAGGTGAACCTAAGCCCACTATAGAA
1 CAGGTGAACCTAAGCCCACTATAGAA
31125937 TCAATATCAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (27 bp):
CAGGTGAACCTAAGCCCACTATAGAAC
Found at i:31128394 original size:45 final size:45
Alignment explanation
Indices: 31128345--31128430 Score: 163
Period size: 45 Copynumber: 1.9 Consensus size: 45
31128335 CCTAAGCAAG
31128345 AACAACCTCTCAAATTAGATAATCACCTAACTTAACAAATCGTCA
1 AACAACCTCTCAAATTAGATAATCACCTAACTTAACAAATCGTCA
*
31128390 AACAACCTCTCAAATTAGATAATCACGTAACTTAACAAATC
1 AACAACCTCTCAAATTAGATAATCACCTAACTTAACAAATC
31128431 ATCCTAAAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.45, C:0.26, G:0.05, T:0.24
Consensus pattern (45 bp):
AACAACCTCTCAAATTAGATAATCACCTAACTTAACAAATCGTCA
Found at i:31131078 original size:21 final size:21
Alignment explanation
Indices: 31131030--31131098 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
31131020 AACTGGTCCA
* *
31131030 TGTGGCTTTCCC-ACATGACCG
1 TGTGGC-TTCCCTACATGGCTG
*
31131051 TGAGGCTTCCCTACATGGCTG
1 TGTGGCTTCCCTACATGGCTG
* *
31131072 TGTGGCTTTCCTATAT-GCATG
1 TGTGGCTTCCCTACATGGC-TG
31131093 TGTGGC
1 TGTGGC
31131099 CAGACCGTGT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
20 7 0.17
21 33 0.82
ACGTcount: A:0.13, C:0.26, G:0.28, T:0.33
Consensus pattern (21 bp):
TGTGGCTTCCCTACATGGCTG
Found at i:31132008 original size:34 final size:34
Alignment explanation
Indices: 31131969--31132036 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
31131959 CCTATGAATA
31131969 GCCCATACATTTCTTTATTTCCCAACATTCTCAT
1 GCCCATACATTTCTTTATTTCCCAACATTCTCAT
31132003 GCCCATACATTTCTTTATTTCCCAACATTCTCAT
1 GCCCATACATTTCTTTATTTCCCAACATTCTCAT
31132037 AAACTTTTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.24, C:0.32, G:0.03, T:0.41
Consensus pattern (34 bp):
GCCCATACATTTCTTTATTTCCCAACATTCTCAT
Found at i:31132033 original size:17 final size:17
Alignment explanation
Indices: 31131979--31132033 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
31131969 GCCCATACAT
31131979 TTCTTTATTTCCCAACA
1 TTCTTTATTTCCCAACA
* *
31131996 TTC-TCA-TGCCCATACA
1 TTCTTTATTTCCCA-ACA
31132012 TTTCTTTATTTCCCAACA
1 -TTCTTTATTTCCCAACA
31132030 TTCT
1 TTCT
31132034 CATAAACTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
15 5 0.17
16 5 0.17
17 10 0.33
18 5 0.17
19 5 0.17
ACGTcount: A:0.22, C:0.31, G:0.02, T:0.45
Consensus pattern (17 bp):
TTCTTTATTTCCCAACA
Found at i:31133328 original size:43 final size:43
Alignment explanation
Indices: 31133289--31133410 Score: 165
Period size: 43 Copynumber: 2.9 Consensus size: 43
31133279 TATCACTTTT
* **
31133289 CCGTGTGTCACACATGGCTGAGACACACACCTGTGTCACTTGG
1 CCGTGTGTCACACATGGCTGAGACACACACCCGTGTCACTTAC
* * *
31133332 CTGTGTGTCACACATGACTGAGACACACACCCGTGTCTC-TAC
1 CCGTGTGTCACACATGGCTGAGACACACACCCGTGTCACTTAC
* *
31133374 CCGTGTGTCACACACGGCTGAGACACACACCCATGTC
1 CCGTGTGTCACACATGGCTGAGACACACACCCGTGTC
31133411 TCTGCTCGTG
Statistics
Matches: 69, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
42 34 0.49
43 35 0.51
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (43 bp):
CCGTGTGTCACACATGGCTGAGACACACACCCGTGTCACTTAC
Found at i:31133395 original size:42 final size:42
Alignment explanation
Indices: 31133289--31133422 Score: 178
Period size: 42 Copynumber: 3.2 Consensus size: 42
31133279 TATCACTTTT
* * *
31133289 CCGTGTGTCACACATGGCTGAGACACACACCTGTGTCACTTGG
1 CCGTGTGTCACACATGGCTGAGACACACACCCGTGTCTC-TGC
* * *
31133332 CTGTGTGTCACACATGACTGAGACACACACCCGTGTCTCTAC
1 CCGTGTGTCACACATGGCTGAGACACACACCCGTGTCTCTGC
* *
31133374 CCGTGTGTCACACACGGCTGAGACACACACCCATGTCTCTGC
1 CCGTGTGTCACACATGGCTGAGACACACACCCGTGTCTCTGC
*
31133416 TCGTGTG
1 CCGTGTG
31133423 GATGAAAATA
Statistics
Matches: 79, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
42 44 0.56
43 35 0.44
ACGTcount: A:0.21, C:0.33, G:0.23, T:0.23
Consensus pattern (42 bp):
CCGTGTGTCACACATGGCTGAGACACACACCCGTGTCTCTGC
Found at i:31142679 original size:26 final size:26
Alignment explanation
Indices: 31142629--31142679 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
31142619 CCAATATCGC
* *
31142629 AGCATAGCTGCCAATAGTAATAATGT
1 AGCAGAGCTGCCAATAGTAAGAATGT
* *
31142655 AGCAGAGCTGCCAGTAGTCAGAATG
1 AGCAGAGCTGCCAATAGTAAGAATG
31142680 GCTAAAAGCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (26 bp):
AGCAGAGCTGCCAATAGTAAGAATGT
Found at i:31142710 original size:22 final size:22
Alignment explanation
Indices: 31142673--31142737 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 22
31142663 TGCCAGTAGT
* * *
31142673 CAGAATGGCTAAAAGCCGTAAA
1 CAGAATAGCTATAAGCCATAAA
* *
31142695 CAGGATAGCTATAAGCTATAAA
1 CAGAATAGCTATAAGCCATAAA
*
31142717 CAGAATGGCTATAAGCCATAA
1 CAGAATAGCTATAAGCCATAA
31142738 GTACAGTAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.45, C:0.17, G:0.20, T:0.18
Consensus pattern (22 bp):
CAGAATAGCTATAAGCCATAAA
Found at i:31142784 original size:32 final size:32
Alignment explanation
Indices: 31142729--31142899 Score: 213
Period size: 32 Copynumber: 5.4 Consensus size: 32
31142719 GAATGGCTAT
* *
31142729 AAGCCATAAGT-ACAGTAATATGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* *
31142760 AAGCCATCAGTAGCAGTGATATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* *
31142792 CAA-CCATCAGTAACAGTAATATGATCAGCACC
1 -AAGCCATCAGTAACAGTAATATGATCGGCACA
* *
31142824 AAGCCATCAGTAAC-GATAATATGATTGACACA
1 AAGCCATCAGTAACAG-TAATATGATCGGCACA
* *
31142856 AAGCCATCAGTAACGGTAATATGATCGGCATA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
31142888 AAGCCATCAGTA
1 AAGCCATCAGTA
31142900 GTATCGCAGT
Statistics
Matches: 120, Mismatches: 15, Indels: 9
0.83 0.10 0.06
Matches are distributed among these distances:
31 13 0.11
32 104 0.87
33 3 0.03
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.20
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTAATATGATCGGCACA
Found at i:31142948 original size:27 final size:27
Alignment explanation
Indices: 31142918--31142973 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
31142908 GTAAAGCTGT
*
31142918 CAGTAATAGT-ATATGTGGCAAAGCAAC
1 CAGTAACAGTGAT-TGTGGCAAAGCAAC
* *
31142945 CAGTAACAGTGATTGTGGCAGAGCCAC
1 CAGTAACAGTGATTGTGGCAAAGCAAC
31142972 CA
1 CA
31142974 CTACAGTACT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 23 0.92
28 2 0.08
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.20
Consensus pattern (27 bp):
CAGTAACAGTGATTGTGGCAAAGCAAC
Found at i:31143145 original size:27 final size:27
Alignment explanation
Indices: 31143103--31143930 Score: 873
Period size: 27 Copynumber: 30.7 Consensus size: 27
31143093 TTACCCACTA
* *
31143103 GGGCATTACGATTATTTTACCCTATAG
1 GGGCATTACGATCATTTTACCCTACAG
* * *
31143130 GGGTATTACGATTATTTTACCCTATAG
1 GGGCATTACGATCATTTTACCCTACAG
* *
31143157 GGGCATTACAATCATTATACCCTACAG
1 GGGCATTACGATCATTTTACCCTACAG
* *
31143184 GGGTATTACGATCATTTTATCCTACAG
1 GGGCATTACGATCATTTTACCCTACAG
* * *
31143211 TGGCATTAC-AGTTATTTTACCCTATAG
1 GGGCATTACGA-TCATTTTACCCTACAG
* *
31143238 GGGCATTA-TAGTCATTTTACCCTACAA
1 GGGCATTACGA-TCATTTTACCCTACAG
* *
31143265 GGGTATTACGGTCATTTTACCCTACAG
1 GGGCATTACGATCATTTTACCCTACAG
31143292 GGGCATTAC-AGTCATTTTACCCTACAG
1 GGGCATTACGA-TCATTTTACCCTACAG
* *
31143319 GGGCATTACGACCATTTTACCCTACAA
1 GGGCATTACGATCATTTTACCCTACAG
* *
31143346 GAGTATTAC-AGTCATTTTACCCTACAG
1 GGGCATTACGA-TCATTTTACCCTACAG
* * *
31143373 GGGTATTAC-AGTTATTTTACCCTATAG
1 GGGCATTACGA-TCATTTTACCCTACAG
* * *
31143400 GGGCATTATGGTCATTTTACCGTACAG
1 GGGCATTACGATCATTTTACCCTACAG
* * * *
31143427 GGGCATTGCGGTCATTTTACCCAACAA
1 GGGCATTACGATCATTTTACCCTACAG
* *
31143454 GGGTATTA-TAGTCATTTTACCCTACAG
1 GGGCATTACGA-TCATTTTACCCTACAG
*
31143481 GGGCATTACGATCATTTTACCCTACAT
1 GGGCATTACGATCATTTTACCCTACAG
*
31143508 GGGCATTACGGTCATTTTACCCTACAG
1 GGGCATTACGATCATTTTACCCTACAG
* * * *
31143535 GGGTATTACGGTCATTTTATCCTACGG
1 GGGCATTACGATCATTTTACCCTACAG
* *
31143562 GGGTATTACGATCATTTTACCTTACAG
1 GGGCATTACGATCATTTTACCCTACAG
31143589 GGGCATTAC-AGTCATTTTACCCTACAG
1 GGGCATTACGA-TCATTTTACCCTACAG
* * *
31143616 GGGCATTACGGTCATTTTACCGTACAT
1 GGGCATTACGATCATTTTACCCTACAG
31143643 GGGCATTACGATCATTTTACCCTACAG
1 GGGCATTACGATCATTTTACCCTACAG
* * *
31143670 GGGTATTA-TAGTCATTTTACCCCACAG
1 GGGCATTACGA-TCATTTTACCCTACAG
*
31143697 GGGCATTACGATCATTTTACCCTACAT
1 GGGCATTACGATCATTTTACCCTACAG
* *
31143724 GGGCATTACGGTCATTTTACCCTACGG
1 GGGCATTACGATCATTTTACCCTACAG
* * *
31143751 GGGTATTACAATCATTTTACCCTATAG
1 GGGCATTACGATCATTTTACCCTACAG
* * *
31143778 GGGCATTACGGTCATTTTACCTTATAG
1 GGGCATTACGATCATTTTACCCTACAG
* *
31143805 GTGTATTACGATCATTTTACCCTACA-
1 GGGCATTACGATCATTTTACCCTACAG
* * * * *
31143831 AGGTATTACAATCATTTTACCTTACAA
1 GGGCATTACGATCATTTTACCCTACAG
* * *
31143858 GGGTATTACGGTCATTTTACCCTACAA
1 GGGCATTACGATCATTTTACCCTACAG
* * ** *
31143885 GGGTATTACGGTCATTTTACCCTGTAA
1 GGGCATTACGATCATTTTACCCTACAG
* *
31143912 GGGTATTACGGTCATTTTA
1 GGGCATTACGATCATTTTA
31143931 TAAATATTGG
Statistics
Matches: 682, Mismatches: 105, Indels: 28
0.84 0.13 0.03
Matches are distributed among these distances:
26 26 0.04
27 653 0.96
28 3 0.00
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (27 bp):
GGGCATTACGATCATTTTACCCTACAG
Found at i:31145949 original size:43 final size:43
Alignment explanation
Indices: 31145896--31146055 Score: 150
Period size: 43 Copynumber: 3.8 Consensus size: 43
31145886 TTCGAGGTGT
* * *
31145896 GATTTCGTGTAATACCATGTCTGGGACATTGGCATCGATATGA
1 GATTACGTGTAAGACCATATCTGGGACATTGGCATCGATATGA
* * *
31145939 GATTACGTGTAAGGCCATGTCTAGGACATTGGCAT-G-TAT-A
1 GATTACGTGTAAGACCATATCTGGGACATTGGCATCGATATGA
* * ** *
31145979 TGATT-TGTGTAAGACCCTATCTGGGACAGAGGCATCGATATGT
1 -GATTACGTGTAAGACCATATCTGGGACATTGGCATCGATATGA
* * *
31146022 GATAACATGTAAGACCATATCTGGGATA-TGGCAT
1 GATTACGTGTAAGACCATATCTGGGACATTGGCAT
31146056 TGTATGTGAT
Statistics
Matches: 94, Mismatches: 18, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
40 24 0.26
41 8 0.09
42 12 0.13
43 50 0.53
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (43 bp):
GATTACGTGTAAGACCATATCTGGGACATTGGCATCGATATGA
Found at i:31146060 original size:83 final size:84
Alignment explanation
Indices: 31145895--31146065 Score: 202
Period size: 83 Copynumber: 2.0 Consensus size: 84
31145885 TTTCGAGGTG
* * ** * * * *
31145895 TGATTTCGTGTAATACCATGTCTGGGACATTGGCATCGATATGAGATTACGTGTAAGGCCATGTC
1 TGATTTCGTGTAAGACCATATCTGGGACAGAGGCATCGATATGAGATAACATGTAAGACCATATC
31145960 TAGGACATTGGCATGTATA
66 TAGGACATTGGCATGTATA
* *
31145979 TGATTT-GTGTAAGACCCTATCTGGGACAGAGGCATCGATATGTGATAACATGTAAGACCATATC
1 TGATTTCGTGTAAGACCATATCTGGGACAGAGGCATCGATATGAGATAACATGTAAGACCATATC
* * *
31146043 TGGGATA-TGGCATTGTATG
66 TAGGACATTGGCA-TGTATA
31146062 TGAT
1 TGAT
31146066 ATATGTGTTT
Statistics
Matches: 73, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
82 5 0.07
83 62 0.85
84 6 0.08
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.32
Consensus pattern (84 bp):
TGATTTCGTGTAAGACCATATCTGGGACAGAGGCATCGATATGAGATAACATGTAAGACCATATC
TAGGACATTGGCATGTATA
Found at i:31149307 original size:47 final size:47
Alignment explanation
Indices: 31149220--31149387 Score: 250
Period size: 47 Copynumber: 3.6 Consensus size: 47
31149210 CCCTTCGGGA
* * * * * *
31149220 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31149267 TCTGT-T-ACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 -CT-TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31149314 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31149361 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
31149388 ACCAACCCTT
Statistics
Matches: 111, Mismatches: 6, Indels: 7
0.90 0.05 0.06
Matches are distributed among these distances:
45 1 0.01
46 3 0.03
47 103 0.93
48 3 0.03
49 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.08, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:31149683 original size:39 final size:40
Alignment explanation
Indices: 31149593--31149703 Score: 138
Period size: 39 Copynumber: 2.8 Consensus size: 40
31149583 CGGAATTTAA
**
31149593 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACATAGC
* *
31149633 CCGGTTATAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACATAGC
*
31149672 CCGGA-ATTAGTATCTCGCACAAATGCCTTCGG
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGG
31149704 ATCTTAGTCC
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
38 1 0.02
39 34 0.54
40 28 0.44
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACATAGC
Found at i:31167472 original size:24 final size:24
Alignment explanation
Indices: 31167445--31167492 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
31167435 CACGTGATTC
* *
31167445 TGTATGATGCCTTTATGGTGTATT
1 TGTATGACGCCTTTATGGAGTATT
*
31167469 TGTATGACGCCTTTGTGGAGTATT
1 TGTATGACGCCTTTATGGAGTATT
31167493 CCATAAGTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.17, C:0.10, G:0.27, T:0.46
Consensus pattern (24 bp):
TGTATGACGCCTTTATGGAGTATT
Found at i:31175900 original size:27 final size:27
Alignment explanation
Indices: 31175870--31176159 Score: 323
Period size: 27 Copynumber: 10.8 Consensus size: 27
31175860 CATCTTTTAG
*
31175870 GGGTATTTCGGGCATTTTACCCTATGA
1 GGGTATTTCGGTCATTTTACCCTATGA
* *
31175897 GGGTATTTCGATCATTTTATCCTATGA
1 GGGTATTTCGGTCATTTTACCCTATGA
31175924 GGGTATTTCGGTCATTTTACCCTAT-A
1 GGGTATTTCGGTCATTTTACCCTATGA
** *
31175950 GGTGTATTTCGGTCATTTTTTCCTATGG
1 GG-GTATTTCGGTCATTTTACCCTATGA
* ** *
31175978 GGGTCTTTTAGTCATTTTACCCTATAA
1 GGGTATTTCGGTCATTTTACCCTATGA
* *
31176005 GGGTATTTTGGTTATTTTACCCTATGA
1 GGGTATTTCGGTCATTTTACCCTATGA
* * *
31176032 GAGTATTTCGGTTATTTTACCTTATGA
1 GGGTATTTCGGTCATTTTACCCTATGA
* * ** *
31176059 GGGTATTTTGGTTATTTTTTCCTATAA
1 GGGTATTTCGGTCATTTTACCCTATGA
* *
31176086 GGGTATTTCAGTCATTTTATCCTATG-
1 GGGTATTTCGGTCATTTTACCCTATGA
* *
31176112 GGGTATTTCGGTCATTTTACCTTATGG
1 GGGTATTTCGGTCATTTTACCCTATGA
**
31176139 GGGTATTTTAGTCATTTTACC
1 GGGTATTTCGGTCATTTTACC
31176160 TATTTTGGGG
Statistics
Matches: 222, Mismatches: 38, Indels: 6
0.83 0.14 0.02
Matches are distributed among these distances:
26 26 0.12
27 194 0.87
28 2 0.01
ACGTcount: A:0.19, C:0.14, G:0.21, T:0.46
Consensus pattern (27 bp):
GGGTATTTCGGTCATTTTACCCTATGA
Found at i:31175993 original size:81 final size:80
Alignment explanation
Indices: 31175869--31176162 Score: 360
Period size: 81 Copynumber: 3.7 Consensus size: 80
31175859 TCATCTTTTA
* * * *
31175869 GGGGTATTTCGGGCATTTTACCCTATGAGGGTA-TTTCGATCATTTTATCCTATGAGGGTATTTC
1 GGGGTATTTCGGTCATTTTACCTTATGAGGGTATTTTAG-TCATTTTATCCTATAAGGGTATTTC
31175933 GGTCATTTTACCCTAT
65 GGTCATTTTACCCTAT
* * * * *
31175949 AGGTGTATTTCGGTCATTTTTTCC-TATGGGGGTCTTTTAGTCATTTTACCCTATAAGGGTATTT
1 -GGGGTATTTCGGTCA-TTTTACCTTATGAGGGTATTTTAGTCATTTTATCCTATAAGGGTATTT
* *
31176013 TGGTTATTTTACCCTAT
64 CGGTCATTTTACCCTAT
* * * * *
31176030 GAGAGTATTTCGGTTATTTTACCTTATGAGGGTATTTTGGTTATTTTTTCCTATAAGGGTATTTC
1 G-GGGTATTTCGGTCATTTTACCTTATGAGGGTATTTTAGTCATTTTATCCTATAAGGGTATTTC
* *
31176095 AGTCATTTTATCCTAT
65 GGTCATTTTACCCTAT
*
31176111 GGGGTATTTCGGTCATTTTACCTTATGGGGGTATTTTAGTCATTTTA-CCTAT
1 GGGGTATTTCGGTCATTTTACCTTATGAGGGTATTTTAGTCATTTTATCCTAT
31176163 TTTGGGGTCT
Statistics
Matches: 180, Mismatches: 29, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
79 5 0.03
80 47 0.26
81 118 0.66
82 10 0.06
ACGTcount: A:0.19, C:0.14, G:0.21, T:0.46
Consensus pattern (80 bp):
GGGGTATTTCGGTCATTTTACCTTATGAGGGTATTTTAGTCATTTTATCCTATAAGGGTATTTCG
GTCATTTTACCCTAT
Found at i:31185012 original size:16 final size:15
Alignment explanation
Indices: 31184985--31185018 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
31184975 ATAACTAGTA
*
31184985 TATAATTATATTTAT
1 TATAATTATATTAAT
31185000 TATAATATATATTAAT
1 TATAAT-TATATTAAT
31185016 TAT
1 TAT
31185019 TATCAACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATAATTATATTAAT
Found at i:31185714 original size:25 final size:24
Alignment explanation
Indices: 31185675--31185733 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 24
31185665 ACTTTTCTCC
*
31185675 TAAATTTTAATTTTATTTAATTATT
1 TAAATTTTAATTTTATTGAATTA-T
31185700 TAAATTTTCAA-TTTATTGAATTAT
1 TAAATTTT-AATTTTATTGAATTAT
31185724 TAATATTTTA
1 TAA-ATTTTA
31185734 TACTAACTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
24 5 0.16
25 24 0.77
26 2 0.06
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (24 bp):
TAAATTTTAATTTTATTGAATTAT
Found at i:31201422 original size:23 final size:24
Alignment explanation
Indices: 31201378--31201422 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
31201368 AAAATTCTAC
*
31201378 CCATCCAGCCTCTACACACCATCT
1 CCATCCAACCTCTACACACCATCT
*
31201402 CCATCCAACC-CTACACTCCAT
1 CCATCCAACCTCTACACACCAT
31201423 GTAGGGATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.27, C:0.51, G:0.02, T:0.20
Consensus pattern (24 bp):
CCATCCAACCTCTACACACCATCT
Found at i:31203422 original size:72 final size:72
Alignment explanation
Indices: 31203305--31203449 Score: 272
Period size: 72 Copynumber: 2.0 Consensus size: 72
31203295 TTCCCAAGTC
*
31203305 CTGGCTTGAACTTGGGACCTCCCAAACACTCCGAGAACACATAACCACTAAAGCTGACAAATATT
1 CTGGCTTGAACTTGGGACCTCCCAAACACTCCCAGAACACATAACCACTAAAGCTGACAAATATT
31203370 TATGTCA
66 TATGTCA
31203377 CTGGCTTGAACTTGGGACCTCCCAAACACTCCCAGAACACATAACCACTAAAGCTGACAAATATT
1 CTGGCTTGAACTTGGGACCTCCCAAACACTCCCAGAACACATAACCACTAAAGCTGACAAATATT
*
31203442 TGTGTCA
66 TATGTCA
31203449 C
1 C
31203450 ACATTCACAA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.34, C:0.29, G:0.15, T:0.22
Consensus pattern (72 bp):
CTGGCTTGAACTTGGGACCTCCCAAACACTCCCAGAACACATAACCACTAAAGCTGACAAATATT
TATGTCA
Found at i:31205612 original size:15 final size:15
Alignment explanation
Indices: 31205588--31205619 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
31205578 CATTCATCCA
*
31205588 CCATTGTTCTTCATT
1 CCATTATTCTTCATT
31205603 CCATTATTCTTCATT
1 CCATTATTCTTCATT
31205618 CC
1 CC
31205620 CTTGCCAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.31, G:0.03, T:0.50
Consensus pattern (15 bp):
CCATTATTCTTCATT
Found at i:31207058 original size:22 final size:19
Alignment explanation
Indices: 31207033--31207074 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
31207023 TGGTAATCAT
31207033 TAATATATAATTATATCTATTA
1 TAATATAT-ATTA-AT-TATTA
31207055 TAATATATATTAATTATTA
1 TAATATATATTAATTATTA
31207074 T
1 T
31207075 CAACTTTACC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 2 0.10
21 4 0.20
22 8 0.40
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
TAATATATATTAATTATTA
Found at i:31208676 original size:3 final size:3
Alignment explanation
Indices: 31208668--31208705 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
31208658 TGAGGATCTC
* *
31208668 GAA GAA GAA GAA AAA GAA GAA GAA GAC GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
31208706 TCCCACAGAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.66, C:0.03, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:31210680 original size:10 final size:10
Alignment explanation
Indices: 31210665--31210716 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
31210655 ATTAACATGT
31210665 TTAATTTTAA
1 TTAATTTTAA
31210675 TTAATTTTATA
1 TTAATTTTA-A
* *
31210686 TCAAATTTTGA
1 T-TAATTTTAA
*
31210697 TTAATTTTGA
1 TTAATTTTAA
*
31210707 TTATTTTTAA
1 TTAATTTTAA
31210717 CAGATATGCA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
10 25 0.71
11 4 0.11
12 6 0.17
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.60
Consensus pattern (10 bp):
TTAATTTTAA
Found at i:31217531 original size:27 final size:27
Alignment explanation
Indices: 31217501--31217832 Score: 357
Period size: 27 Copynumber: 12.3 Consensus size: 27
31217491 TCATCTCCTA
** *
31217501 GGGGTATAACAGTTATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* *
31217528 GGGGTATTTTAGTCATTTTATCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
** * *
31217555 GACGTATTTCGGTCATTTTACCTTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
** *
31217582 GGGGTATTTTGGTCAATTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* *
31217609 GGTGTATTT-AGGTCAATTTACCCTATG
1 GGGGTATTTCA-GTCATTTTACCCTATG
* *
31217636 AGGGTATTTC-GATCATTTTACCTTAT-
1 GGGGTATTTCAG-TCATTTTACCCTATG
* *
31217662 GGGGTATTTCAGTTATTTTACCCTATA
1 GGGGTATTTCAGTCATTTTACCCTATG
*
31217689 GGGGTATTTCAATCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* *
31217716 GGGGTATTTCGGTCATTTTACCCTATT
1 GGGGTATTTCAGTCATTTTACCCTATG
* *
31217743 GGGGTATTTCAATCATTTTACCCTATT
1 GGGGTATTTCAGTCATTTTACCCTATG
* *
31217770 GGGGTATTTCAATCATTTTACCCTATA
1 GGGGTATTTCAGTCATTTTACCCTATG
* *
31217797 GAGGTACTTC-GATCATTTTACCCTATG
1 GGGGTATTTCAG-TCATTTTACCCTATG
*
31217824 AGGGTATTT
1 GGGGTATTT
31217833 TGGTTATTTT
Statistics
Matches: 258, Mismatches: 41, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
26 22 0.09
27 236 0.91
ACGTcount: A:0.21, C:0.16, G:0.20, T:0.42
Consensus pattern (27 bp):
GGGGTATTTCAGTCATTTTACCCTATG
Found at i:31224007 original size:30 final size:30
Alignment explanation
Indices: 31223885--31224010 Score: 128
Period size: 30 Copynumber: 4.2 Consensus size: 30
31223875 TTATTACCAC
* *
31223885 CCCTTTTCATAGTTCGATAGCCGAAGCTAT
1 CCCTTTTCATAATTCGATAGCCGAAGCCAT
* * * * *
31223915 CCATTTCCATATTTTGATAGCCGAATCCAT
1 CCCTTTTCATAATTCGATAGCCGAAGCCAT
* * * *
31223945 CCCTTTTCATAATTCAATGGTCGTCA-CCAT
1 CCCTTTTCATAATTCGATAGCCG-AAGCCAT
*
31223975 CCCTTTTCATAATTCGATAGCCGAAGCTAT
1 CCCTTTTCATAATTCGATAGCCGAAGCCAT
31224005 CCCTTT
1 CCCTTT
31224011 CCATTGGTCG
Statistics
Matches: 75, Mismatches: 19, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
29 1 0.01
30 73 0.97
31 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.36
Consensus pattern (30 bp):
CCCTTTTCATAATTCGATAGCCGAAGCCAT
Found at i:31228493 original size:79 final size:81
Alignment explanation
Indices: 31228357--31228541 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
31228347 TTGAATGATG
* *
31228357 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
31228421 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
31228436 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
31228498 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
31228516 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
31228542 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:31228555 original size:40 final size:40
Alignment explanation
Indices: 31228358--31228541 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
31228348 TGAATGATGT
* * * *
31228358 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
31228398 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
31228438 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
31228476 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
31228517 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
31228542 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:31228563 original size:79 final size:79
Alignment explanation
Indices: 31228410--31228574 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
31228400 GGACTAAGAT
* * **
31228410 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
31228475 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
31228489 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
31228552 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
31228568 CCGAAGG
1 CCGAAGG
31228575 TACGTGATTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:31234835 original size:79 final size:79
Alignment explanation
Indices: 31234752--31234908 Score: 185
Period size: 79 Copynumber: 2.0 Consensus size: 79
31234742 CTGAAGGCAT
* * **
31234752 TTGTGCGAGATACTA-ATTCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTA-CTAAATCCGGG
1 TTGTGCGAGATACTATA-ACCGGGCTAAGTCCCAAAGGCATTTGAACGAG-TAGCTAAATCC-GG
*
31234814 TTAAGTCCCGAAGGTAA
63 TTAAATCCCGAAGGTAA
* * *
31234831 TTGTGCGAGTTACTATAACCGGGCTATGTCCCAAAGGCATTTGAACGAGTAGCTATATCCGGTTA
1 TTGTGCGAGATACTATAACCGGGCTAAGTCCCAAAGGCATTTGAACGAGTAGCTAAATCCGGTTA
*
31234896 AATTCCGAAGGTA
66 AATCCCGAAGGTA
31234909 CGTGATTTGG
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
79 41 0.62
80 25 0.38
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (79 bp):
TTGTGCGAGATACTATAACCGGGCTAAGTCCCAAAGGCATTTGAACGAGTAGCTAAATCCGGTTA
AATCCCGAAGGTAA
Found at i:31234880 original size:40 final size:40
Alignment explanation
Indices: 31234689--31234873 Score: 189
Period size: 40 Copynumber: 4.7 Consensus size: 40
31234679 TTGAATGATG
* * * *
31234689 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * * *
31234729 TCCAGACTAAGAT-CTGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
31234769 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
31234808 TCCGGGTTAAGTCCCGAAGGTAATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
31234849 -CCGGGCTATGTCCCAAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
31234874 AACGAGTAGC
Statistics
Matches: 118, Mismatches: 22, Indels: 10
0.79 0.15 0.07
Matches are distributed among these distances:
39 34 0.29
40 74 0.63
41 10 0.08
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:31236324 original size:6 final size:6
Alignment explanation
Indices: 31236313--31236340 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
31236303 AGGATTGCAA
31236313 ATTTCC ATTTCC ATTTCC ATTTCC ATTT
1 ATTTCC ATTTCC ATTTCC ATTTCC ATTT
31236341 TTGGAAACCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.29, G:0.00, T:0.54
Consensus pattern (6 bp):
ATTTCC
Found at i:31242349 original size:18 final size:18
Alignment explanation
Indices: 31242326--31242368 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
31242316 ACTCAATCCA
**
31242326 AACCCAAGTATTCAACCC
1 AACCCAAGTACCCAACCC
*
31242344 AACCCAATTACCCAACCC
1 AACCCAAGTACCCAACCC
31242362 AACCCAA
1 AACCCAA
31242369 TCATAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.44, G:0.02, T:0.12
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:31242484 original size:9 final size:9
Alignment explanation
Indices: 31242466--31242514 Score: 62
Period size: 9 Copynumber: 5.4 Consensus size: 9
31242456 GTAGTGATTC
31242466 AATTCGGTT
1 AATTCGGTT
*
31242475 AATTCAGTT
1 AATTCGGTT
*
31242484 AATTCGGGT
1 AATTCGGTT
*
31242493 AATCCGGTT
1 AATTCGGTT
*
31242502 AATTCAGTT
1 AATTCGGTT
31242511 AATT
1 AATT
31242515 TTTAACCAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (9 bp):
AATTCGGTT
Found at i:31247909 original size:26 final size:26
Alignment explanation
Indices: 31247871--31248043 Score: 181
Period size: 26 Copynumber: 6.7 Consensus size: 26
31247861 AAAATTATTA
31247871 AAATTACTGAAATACCCTTAATGGGT
1 AAATTACTGAAATACCCTTAATGGGT
* * *
31247897 AAATTACTAAAATACCCCTAATGAGT
1 AAATTACTGAAATACCCTTAATGGGT
* *
31247923 AAATTA-TCAAAATACCCTTGATGGGT
1 AAATTACT-GAAATACCCTTAATGGGT
** *
31247949 AAATTACTGAAATACCCTCGATGCGT
1 AAATTACTGAAATACCCTTAATGGGT
* *
31247975 AAATTACCGAAATA-CCTCTAATGTGT
1 AAATTACTGAAATACCCT-TAATGGGT
** *
31248001 AAATTACTGAAATACCCTCGATGGAT
1 AAATTACTGAAATACCCTTAATGGGT
31248027 AAATTA-TCGAAATACCC
1 AAATTACT-GAAATACCC
31248044 CCAAAGGGTC
Statistics
Matches: 124, Mismatches: 18, Indels: 10
0.82 0.12 0.07
Matches are distributed among these distances:
25 5 0.04
26 115 0.93
27 4 0.03
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (26 bp):
AAATTACTGAAATACCCTTAATGGGT
Found at i:31247936 original size:52 final size:51
Alignment explanation
Indices: 31247871--31248043 Score: 217
Period size: 52 Copynumber: 3.3 Consensus size: 51
31247861 AAAATTATTA
* *
31247871 AAATTA-CTGAAATACCCTTAATGGGTAAATTACTAAAATACCC-CTAATGAGT
1 AAATTATC-GAAATACCCTTAATGGGTAAATTACTGAAATACCCTC-GATG-GT
* *
31247923 AAATTATCAAAATACCCTTGATGGGTAAATTACTGAAATACCCTCGATGCGT
1 AAATTATCGAAATACCCTTAATGGGTAAATTACTGAAATACCCTCGATG-GT
* *
31247975 AAATTACCGAAATA-CCTCTAATGTGTAAATTACTGAAATACCCTCGATGGAT
1 AAATTATCGAAATACCCT-TAATGGGTAAATTACTGAAATACCCTCGATGG-T
31248027 AAATTATCGAAATACCC
1 AAATTATCGAAATACCC
31248044 CCAAAGGGTC
Statistics
Matches: 106, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
51 4 0.04
52 98 0.92
53 4 0.04
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (51 bp):
AAATTATCGAAATACCCTTAATGGGTAAATTACTGAAATACCCTCGATGGT
Found at i:31248003 original size:78 final size:78
Alignment explanation
Indices: 31247871--31248043 Score: 224
Period size: 78 Copynumber: 2.2 Consensus size: 78
31247861 AAAATTATTA
* * *
31247871 AAATTACTGAAATACCCTTAATGGGTAAATTACTAAAATACCCCTAATGAGTAAATTA-TCAAAA
1 AAATTACTGAAATACCCTCAATGCGTAAATTACCAAAATACCCCTAATGAGTAAATTACT-AAAA
* *
31247935 TACCCTTGATGGGT
65 TACCCTCGATGGAT
* * * * *
31247949 AAATTACTGAAATACCCTCGATGCGTAAATTACCGAAATACCTCTAATGTGTAAATTACTGAAAT
1 AAATTACTGAAATACCCTCAATGCGTAAATTACCAAAATACCCCTAATGAGTAAATTACTAAAAT
31248014 ACCCTCGATGGAT
66 ACCCTCGATGGAT
31248027 AAATTA-TCGAAATACCC
1 AAATTACT-GAAATACCC
31248044 CCAAAGGGTC
Statistics
Matches: 83, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
77 1 0.01
78 81 0.98
79 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (78 bp):
AAATTACTGAAATACCCTCAATGCGTAAATTACCAAAATACCCCTAATGAGTAAATTACTAAAAT
ACCCTCGATGGAT
Found at i:31270215 original size:31 final size:30
Alignment explanation
Indices: 31270175--31270235 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
31270165 TCAAGTTTCC
*
31270175 ATATACATGTAACATCCATAT-CATGTATTT
1 ATATACATGTAAAAT-CATATCCATGTATTT
*
31270205 ATATATCATGTAAAATCATTTCCATGTATTT
1 ATATA-CATGTAAAATCATATCCATGTATTT
31270236 CATGTAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 9 0.33
31 18 0.67
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.43
Consensus pattern (30 bp):
ATATACATGTAAAATCATATCCATGTATTT
Found at i:31270408 original size:25 final size:25
Alignment explanation
Indices: 31270379--31270428 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
31270369 ATCCTGTACA
31270379 GGTATGCT-TATACGAGCTGTAAATC
1 GGTATGCTCTAT-CGAGCTGTAAATC
*
31270404 GGTATGCTCTCTCGAGCTGTAAATC
1 GGTATGCTCTATCGAGCTGTAAATC
31270429 AGTAAGCGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 21 0.91
26 2 0.09
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (25 bp):
GGTATGCTCTATCGAGCTGTAAATC
Found at i:31270892 original size:21 final size:23
Alignment explanation
Indices: 31270851--31270892 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
31270841 CTAGATCTAT
31270851 ACATATAAATTTAACTCAATTCA
1 ACATATAAATTTAACTCAATTCA
31270874 ACATAT-AATTTAA-TCAATT
1 ACATATAAATTTAACTCAATT
31270893 TAATCCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 6 0.32
22 7 0.37
23 6 0.32
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (23 bp):
ACATATAAATTTAACTCAATTCA
Found at i:31285072 original size:21 final size:23
Alignment explanation
Indices: 31285047--31285094 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
31285037 ATCATATTTA
* *
31285047 AAAAATTCTAATTTTC-AA-AAT
1 AAAAATTATAATATTCTAATAAT
31285068 AAAAATTATAATATTCTAATAAT
1 AAAAATTATAATATTCTAATAAT
31285091 AAAA
1 AAAA
31285095 TTCATTAGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 14 0.61
22 2 0.09
23 7 0.30
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (23 bp):
AAAAATTATAATATTCTAATAAT
Found at i:31285169 original size:20 final size:21
Alignment explanation
Indices: 31285132--31285181 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
31285122 TTGATAAATT
31285132 TTACAAATATAATTTTATTTA
1 TTACAAATATAATTTTATTTA
*
31285153 TTACAAA-ATATTTTTATTTA
1 TTACAAATATAATTTTATTTA
*
31285173 ATA-AAATAT
1 TTACAAATAT
31285182 GAATAATAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 3 0.12
20 16 0.62
21 7 0.27
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (21 bp):
TTACAAATATAATTTTATTTA
Done.