Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2
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: 5794061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 68655 characters in sequence are not A, C, G, or T
File 35 of 38
Found at i:5370669 original size:24 final size:25
Alignment explanation
Indices: 5370642--5370696 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 25
5370632 AAATTTAAAT
5370642 AAAAATATT-AAATTAATAATTTTA
1 AAAAATATTAAAATTAATAATTTTA
**
5370666 AAAAA-ATTAAAATTAATTTTTTTA
1 AAAAATATTAAAATTAATAATTTTA
5370690 AAAAATA
1 AAAAATA
5370697 AAATTTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 3 0.11
24 23 0.85
25 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
AAAAATATTAAAATTAATAATTTTA
Found at i:5370705 original size:24 final size:23
Alignment explanation
Indices: 5370641--5370701 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
5370631 GAAATTTAAA
* *
5370641 TAAAAATATT-AAATTAATAATTT
1 TAAAAAAATTAAAATTAAT-TTTT
5370664 TAAAAAAATTAAAATTAATTTTT
1 TAAAAAAATTAAAATTAATTTTT
*
5370687 TTAAAAAA-TAAAATT
1 TAAAAAAATTAAAATT
5370702 TTAAATAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 7 0.21
23 19 0.56
24 8 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
TAAAAAAATTAAAATTAATTTTT
Found at i:5372097 original size:9 final size:9
Alignment explanation
Indices: 5372083--5372111 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
5372073 AATCAATTTA
5372083 TTTTTGATT
1 TTTTTGATT
5372092 TTTTTGATT
1 TTTTTGATT
5372101 TTTTT-ATT
1 TTTTTGATT
5372109 TTT
1 TTT
5372112 CACATAAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.30
9 14 0.70
ACGTcount: A:0.10, C:0.00, G:0.07, T:0.83
Consensus pattern (9 bp):
TTTTTGATT
Found at i:5372853 original size:23 final size:23
Alignment explanation
Indices: 5372781--5372866 Score: 102
Period size: 23 Copynumber: 3.7 Consensus size: 23
5372771 AGGAAAAAAC
* *
5372781 AGCAAAATGAAGAACACATAAAT
1 AGCAAAATGAAGAACACATGAGT
* *
5372804 AGTAAAATGAAGAACACACGAGT
1 AGCAAAATGAAGAACACATGAGT
* *
5372827 AGCAAAATGAATAACACATGAGG
1 AGCAAAATGAAGAACACATGAGT
5372850 AGC-AAATGAAGCAACAC
1 AGCAAAATGAAG-AACAC
5372867 GATAGCAGCT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
22 7 0.13
23 46 0.87
ACGTcount: A:0.55, C:0.15, G:0.19, T:0.12
Consensus pattern (23 bp):
AGCAAAATGAAGAACACATGAGT
Found at i:5373221 original size:19 final size:19
Alignment explanation
Indices: 5373199--5373247 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
5373189 CAACAGTAGT
5373199 AGCAAGAAACAAAACAATA
1 AGCAAGAAACAAAACAATA
*
5373218 AGCAAGAAA-ATAAACAGTA
1 AGCAAGAAACA-AAACAATA
*
5373237 AG-ACGAAACAA
1 AGCAAGAAACAA
5373248 TAAGTGAGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 7 0.27
19 19 0.73
ACGTcount: A:0.65, C:0.14, G:0.14, T:0.06
Consensus pattern (19 bp):
AGCAAGAAACAAAACAATA
Found at i:5373281 original size:22 final size:23
Alignment explanation
Indices: 5373256--5373312 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
5373246 AATAAGTGAG
*
5373256 GAAAGAAAAAAC-AGCAAGC-GAA
1 GAAAGAAAAAACGA-CAAGCAAAA
*
5373278 GAAAGAAGAAACGACAAGCAAAA
1 GAAAGAAAAAACGACAAGCAAAA
5373301 GCAAAGAAAAAA
1 G-AAAGAAAAAA
5373313 ACTTACAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 16 0.55
23 4 0.14
24 9 0.31
ACGTcount: A:0.67, C:0.12, G:0.21, T:0.00
Consensus pattern (23 bp):
GAAAGAAAAAACGACAAGCAAAA
Found at i:5375106 original size:156 final size:154
Alignment explanation
Indices: 5374454--5375125 Score: 762
Period size: 155 Copynumber: 4.3 Consensus size: 154
5374444 TTACTTATCA
* * *
5374454 TTTTTAAGTCCTTTAGGGGTA-CTAGAATACTTTCACGTCGAAGGTTTCCCTTAGGAGTATTTTC
1 TTTTTAAGTCCTTTAGGGGTATC-AGGATACTTTCACGTCGAAGGTATCCC-TAAGAGTATTTTC
* *
5374518 GTAATTTTTCTAGAA-CTAAGTCCTAGGTTGTCATCGGATCCGCTTTCATGCCAAAGGTGGATA-
64 GTAATTTTT-TAGAATC-AAGTCCTAGGTTGTCATCGGGTCCGCTTTCATGCCAAAAGTGGATAT
*
5374581 TGAGGATAGGTTCACCCCTTTTATAGTC
127 TTAGGATAGGTTCACCCCTTTTATAGTC
** *
5374609 CGTTTAAGTCCTTTAAGGGTATCAGGATACTTTCACGTCGAAGGTATCCTCTAAGAGTATTTTCG
1 TTTTTAAGTCCTTTAGGGGTATCAGGATACTTTCACGTCGAAGGTATCC-CTAAGAGTATTTTCG
* * * *
5374674 TAATTTTCTAGAACCAAATCCTAGGTTGTCACCGGGTCCGCTTTCATGCCAAAAGTGGATATTTA
65 TAATTTTTTAGAATCAAGTCCTAGGTTGTCATCGGGTCCGCTTTCATGCCAAAAGTGGATATTTA
5374739 GGATAGGTTCACCCCTTTTATAGTC
130 GGATAGGTTCACCCCTTTTATAGTC
* * * *
5374764 TTTTTAAGTCCTTTTGGGGTACCAGGATACTTTCACGTCGAAGGTATCCCCTAAGGGTATTTTCA
1 TTTTTAAGTCCTTTAGGGGTATCAGGATACTTTCACGTCGAAGGTAT-CCCTAAGAGTATTTTCG
* * * * * * *
5374829 TAATTTTTTAGAATTAAGTCTTAAGTTATCATCAGGTCCGTTTTTATGCCAAAAGT-GAGTATTT
65 TAATTTTTTAGAATCAAGTCCTAGGTTGTCATCGGGTCCGCTTTCATGCCAAAAGTGGA-TATTT
* * *
5374893 ATGATAGGCTCATCCCTTTTATAGTC
129 AGGATAGGTTCACCCCTTTTATAGTC
* * * * *
5374919 TTTTTAAGTCCTTTAGGGGTACCAAGATACTTTCACGTCGAAAGTAAAACCCT-AGAGGCATTTT
1 TTTTTAAGTCCTTTAGGGGTATCAGGATACTTTCACGTCGAAGGT--ATCCCTAAGA-GTATTTT
* * * * * * * * * *
5374983 TGTAATTTTTTAGAATCGAGTCTTAGGTTGTAATCGGGTCCACTTTTATGCCGAAGGTGGGTATC
63 CGTAATTTTTTAGAATCAAGTCCTAGGTTGTCATCGGGTCCGCTTTCATGCCAAAAGTGGATATT
* * * * *
5375048 TAGGGTAGGTTCATCCCATCTATAATCC
128 TAGGATAGGTTCACCCCTTTTATAGT-C
* *
5375076 TTTTTAAGTCCTTTAGGGGTATC-GGGTACTTTTACGTCGAAGGTATCCCT
1 TTTTTAAGTCCTTTAGGGGTATCAGGATACTTTCACGTCGAAGGTATCCCT
5375126 TAGGGGCATT
Statistics
Matches: 441, Mismatches: 65, Indels: 23
0.83 0.12 0.04
Matches are distributed among these distances:
154 54 0.12
155 262 0.59
156 100 0.23
157 25 0.06
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (154 bp):
TTTTTAAGTCCTTTAGGGGTATCAGGATACTTTCACGTCGAAGGTATCCCTAAGAGTATTTTCGT
AATTTTTTAGAATCAAGTCCTAGGTTGTCATCGGGTCCGCTTTCATGCCAAAAGTGGATATTTAG
GATAGGTTCACCCCTTTTATAGTC
Found at i:5378710 original size:25 final size:23
Alignment explanation
Indices: 5378656--5378710 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 23
5378646 AAAAAAGTGC
5378656 AAATGGAAAAAAAGAAAAATGAAA
1 AAAT-GAAAAAAAGAAAAATGAAA
5378680 ATAATGAAAAAAGATGAAGAAAT-AAA
1 A-AATGAAAAAA-A-GAA-AAATGAAA
5378706 AAATG
1 AAATG
5378711 TTGCATCCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
24 8 0.30
25 8 0.30
26 7 0.26
27 4 0.15
ACGTcount: A:0.71, C:0.00, G:0.16, T:0.13
Consensus pattern (23 bp):
AAATGAAAAAAAGAAAAATGAAA
Found at i:5378952 original size:17 final size:17
Alignment explanation
Indices: 5378916--5378968 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
5378906 AAGGGTTGTG
5378916 AAAG-AGAAAAAGATTGAA
1 AAAGAAGAAAAA-A-TGAA
5378934 AAAGAAGAAAAAATGAA
1 AAAGAAGAAAAAATGAA
*
5378951 AAATGAA-AAAAAAGGAA
1 AAA-GAAGAAAAAATGAA
5378968 A
1 A
5378969 GAATAAGGCT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
17 17 0.53
18 8 0.25
19 7 0.22
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.08
Consensus pattern (17 bp):
AAAGAAGAAAAAATGAA
Found at i:5379371 original size:81 final size:80
Alignment explanation
Indices: 5379230--5379430 Score: 230
Period size: 81 Copynumber: 2.5 Consensus size: 80
5379220 TTGGAAGGAT
* * *
5379230 ATCAAATTTGTTTGATTTTCAAAGAAATCTATATTTTGTACATCCTAATCCATTCATGCCTAAAT
1 ATCATATTTG-TTGATTTTCAAAGAAATCCATATTTTATACATCCTAATCCATTCATGCCTAAAT
*
5379295 TTTTGAGCCCCACAAC
65 TTTTGAGCCCAACAAC
* **
5379311 ATCATATTTGCTTGATTTTCAAAGAAATCCATATTTTATACACTCC-GATCCATTTGTGCCTAAA
1 ATCATATTTG-TTGATTTTCAAAGAAATCCATATTTTATACA-TCCTAATCCATTCATGCCTAAA
* *
5379375 TTTTTGAGCCTAACAGC
64 TTTTTGAGCCCAACAAC
* *
5379392 ATC-TAATTTGTCTAATTTTC-AA-AAATTCATATTTTATAC
1 ATCAT-ATTTGT-TGATTTTCAAAGAAATCCATATTTTATAC
5379431 GAGCCGATCT
Statistics
Matches: 105, Mismatches: 12, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
79 16 0.15
80 4 0.04
81 82 0.78
82 3 0.03
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.40
Consensus pattern (80 bp):
ATCATATTTGTTGATTTTCAAAGAAATCCATATTTTATACATCCTAATCCATTCATGCCTAAATT
TTTGAGCCCAACAAC
Found at i:5380751 original size:90 final size:89
Alignment explanation
Indices: 5380599--5380818 Score: 262
Period size: 90 Copynumber: 2.5 Consensus size: 89
5380589 ACTCCTAGGC
* * * *
5380599 GGTATTGATGCATCACAAAGTC-TAATTTCCATAGGGCAAGGTGCAGCCCACACACTCCCAATCG
1 GGTATTGATGCATCACAAA-TCTTGATTTCCTTAGGGCAAGGTGCAACCCACACACTCCCAATCA
* *
5380663 TATCCCCTTAATCCTACCACTACAT
65 CATCCCCTTAATCCAACCACTACAT
* * * *
5380688 GGTATTAATGCATCGCAAATCTTGATTTCCTTTGAGGCAAGGTGCAACCCACACATTCCCAATCA
1 GGTATTGATGCATCACAAATCTTGATTTCCTTAG-GGCAAGGTGCAACCCACACACTCCCAATCA
* * * *
5380753 CATCCTCTTCATCGAACCACTAGAT
65 CATCCCCTTAATCCAACCACTACAT
* * *
5380778 GGTATTGATGCATCACAAAGCTTGATATCCTTAGGGTAAGG
1 GGTATTGATGCATCACAAATCTTGATTTCCTTAGGGCAAGG
5380819 ATATCCCGCC
Statistics
Matches: 109, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
88 2 0.02
89 32 0.29
90 75 0.69
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (89 bp):
GGTATTGATGCATCACAAATCTTGATTTCCTTAGGGCAAGGTGCAACCCACACACTCCCAATCAC
ATCCCCTTAATCCAACCACTACAT
Found at i:5381132 original size:48 final size:48
Alignment explanation
Indices: 5381054--5381369 Score: 323
Period size: 48 Copynumber: 6.6 Consensus size: 48
5381044 ACTGTATCTG
* * *
5381054 GTCAAACTCTTTT-TCTCTCATCGTTTGACTATATTGGTATTAGGGCCTG
1 GTCAAACTCTTTTCT-TC-CCTCGTTTGACTATATTGGTGTTAGGGCCTA
* * *
5381103 GTCAAACTCTTTTCATCCCTCGTTTGACTATATTGGTGTTAAGGCTTA
1 GTCAAACTCTTTTCTTCCCTCGTTTGACTATATTGGTGTTAGGGCCTA
* ** * * *
5381151 GTTAAACT-TAAATCTTCCCTCGTTTGATTGTATTGGTGTTAGGGCCAA
1 GTCAAACTCT-TTTCTTCCCTCGTTTGACTATATTGGTGTTAGGGCCTA
*** * * *
5381199 GTCAAACTCAAGTCTTCCCTCGTTTAACTGTATTGGTGTTAGGGCCTG
1 GTCAAACTCTTTTCTTCCCTCGTTTGACTATATTGGTGTTAGGGCCTA
* * ** *
5381247 GTCAAACTCTTTTCATCCCTTGTTTGACTATATTAATGTCAGGGCCTA
1 GTCAAACTCTTTTCTTCCCTCGTTTGACTATATTGGTGTTAGGGCCTA
***
5381295 GTCAAACTCAAATCTTCCCTCGTTTGACTATATTGGTGTTAGGGCCTA
1 GTCAAACTCTTTTCTTCCCTCGTTTGACTATATTGGTGTTAGGGCCTA
* * *
5381343 GTTAAACTCTTATCTTTCCT-GTTTGAC
1 GTCAAACTCTTTTCTTCCCTCGTTTGAC
5381370 GTATGGTTAC
Statistics
Matches: 219, Mismatches: 45, Indels: 8
0.81 0.17 0.03
Matches are distributed among these distances:
47 8 0.04
48 196 0.89
49 15 0.07
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.40
Consensus pattern (48 bp):
GTCAAACTCTTTTCTTCCCTCGTTTGACTATATTGGTGTTAGGGCCTA
Found at i:5381334 original size:144 final size:144
Alignment explanation
Indices: 5381074--5381351 Score: 421
Period size: 144 Copynumber: 1.9 Consensus size: 144
5381064 TTTTCTCTCA
* **
5381074 TCGTTTGACTATATTGGTATTAGGGCCTGGTCAAACTCTTTTCATCCCTCGTTTGACTATATTGG
1 TCGTTTAACTATATTGGTATTAGGGCCTGGTCAAACTCTTTTCATCCCTCGTTTGACTATATTAA
* * * * * *
5381139 TGTTAAGGCTTAGTTAAACTTAAATCTTCCCTCGTTTGATTGTATTGGTGTTAGGGCCAAGTCAA
66 TGTCAAGGCCTAGTCAAACTCAAATCTTCCCTCGTTTGACTATATTGGTGTTAGGGCCAAGTCAA
5381204 ACTCAAGTCTTCCC
131 ACTCAAGTCTTCCC
* * *
5381218 TCGTTTAACTGTATTGGTGTTAGGGCCTGGTCAAACTCTTTTCATCCCTTGTTTGACTATATTAA
1 TCGTTTAACTATATTGGTATTAGGGCCTGGTCAAACTCTTTTCATCCCTCGTTTGACTATATTAA
* * *
5381283 TGTCAGGGCCTAGTCAAACTCAAATCTTCCCTCGTTTGACTATATTGGTGTTAGGGCCTAGTTAA
66 TGTCAAGGCCTAGTCAAACTCAAATCTTCCCTCGTTTGACTATATTGGTGTTAGGGCCAAGTCAA
5381348 ACTC
131 ACTC
5381352 TTATCTTTCC
Statistics
Matches: 119, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
144 119 1.00
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (144 bp):
TCGTTTAACTATATTGGTATTAGGGCCTGGTCAAACTCTTTTCATCCCTCGTTTGACTATATTAA
TGTCAAGGCCTAGTCAAACTCAAATCTTCCCTCGTTTGACTATATTGGTGTTAGGGCCAAGTCAA
ACTCAAGTCTTCCC
Found at i:5381684 original size:43 final size:42
Alignment explanation
Indices: 5381577--5381709 Score: 144
Period size: 42 Copynumber: 3.1 Consensus size: 42
5381567 TTGCCCATCA
* * *
5381577 GCTTAGACCC-AGGAGACTTGTCTATCTTTTATCTACCCGTTG
1 GCTTAGACCCGA-GAGACTTCTCTATCTTTTGTCTACCCGTCG
*
5381619 GCTTAGACCCGAGAGACCTCTCTATCTTTTGTCTACCCGTCG
1 GCTTAGACCCGAGAGACTTCTCTATCTTTTGTCTACCCGTCG
* * * * *
5381661 CGTTTAGACTCG-GAAGACTTCTCTATCTTTTGTTTACTCGTCA
1 -GCTTAGACCCGAG-AGACTTCTCTATCTTTTGTCTACCCGTCG
5381704 GCTTAG
1 GCTTAG
5381710 GCTCGGGAGA
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
42 42 0.55
43 35 0.45
ACGTcount: A:0.18, C:0.27, G:0.19, T:0.36
Consensus pattern (42 bp):
GCTTAGACCCGAGAGACTTCTCTATCTTTTGTCTACCCGTCG
Found at i:5382606 original size:43 final size:42
Alignment explanation
Indices: 5381861--5382590 Score: 606
Period size: 43 Copynumber: 17.0 Consensus size: 42
5381851 TCATCTCAAA
* * * *
5381861 TCTGCCTGTCGGCTTTGA-CCTTGAAGACTTTCTT-ACCATCAG
1 TCTGCCTGTCGGCTTTGACCCTAG-AGAC-TTCTTCCCCTTAAG
* * * *
5381903 TCTCCCTGTCGACTTTGACCTTAGAGACTTCTTTCCCTTTAAG
1 TCTGCCTGTCGGCTTTGACCCTAGAGACTTC-TTCCCCTTAAG
* * * *
5381946 TCTGCCTGTCAGCTTTAATCCT-GAAGACTTCTTCGCCTTTAAG
1 TCTGCCTGTCGGCTTTGACCCTAG-AGACTTCTTC-CCCTTAAG
** ** * * * * * *
5381989 TCTGTTTGTCAACTTTGACCTTAGGGACTTTTTCTTCATTCAG
1 TCTGCCTGTCGGCTTTGACCCTAGAGACTTCTTC-CCCTTAAG
* * * *
5382032 TTTGCCTGTCGACTTTGACCCTGGAGACTTCTTCGTCCTTAAG
1 TCTGCCTGTCGGCTTTGACCCTAGAGACTTCTTC-CCCTTAAG
* * * * *
5382075 TTTGCTTGTCAGCTTTGACCCTAGAGATTTTTTCCCCCTTTAA-
1 TCTGCCTGTCGGCTTTGACCCTAGAGACTTCTT-CCCC-TTAAG
* * *
5382118 TCTGCTTGTCGGCTTTGACCCTAGAGACTTCCTCGCCTTTAAG
1 TCTGCCTGTCGGCTTTGACCCTAGAGACTTCTTC-CCCTTAAG
* * * * * *
5382161 ACTACCTGTCGACTTTGACCTTGGAGACTTCTTCGCCTTTAAG
1 TCTGCCTGTCGGCTTTGACCCTAGAGACTTCTTC-CCCTTAAG
* * * *
5382204 TCTACCTGTCGACTTTGACCCTAGAGATTTCTTCCCTCTTTAG
1 TCTGCCTGTCGGCTTTGACCCTAGAGACTTCTTCCC-CTTAAG
* * * *
5382247 TCTGCCTGTCAGTTTTGACCCTAGAGACTTTTTTCCTCTTAAG
1 TCTGCCTGTCGGCTTTGACCCTAGAGAC-TTCTTCCCCTTAAG
* * * *
5382290 TCTGCCTATCGGCTTTGACCTTGGAGACTTCTTCCCCCTAAAG
1 TCTGCCTGTCGGCTTTGACCCTAGAGACTTCTT-CCCCTTAAG
* * *
5382333 TCTGCCTATCAGCTTTGACCCTGGAGACTTCTTCGCCCTTAAG
1 TCTGCCTGTCGGCTTTGACCCTAGAGACTTCTTC-CCCTTAAG
* *
5382376 TCTGCCTGTCGACTTTGGCCTCTAGAGACTTCTTTCCCCTTAAG
1 TCTGCCTGTCGGCTTTGACC-CTAGAGACTTC-TTCCCCTTAAG
* *
5382420 TCTGCCTGTCGGCTTTGACCCTGGAGACTTCTTCTCCATTAAG
1 TCTGCCTGTCGGCTTTGACCCTAGAGACTTCTTC-CCCTTAAG
* * *
5382463 TCTGCCTGTCGGCTTTGATCCT-GAAAACTTCTTTCTCCTTAAG
1 TCTGCCTGTCGGCTTTGACCCTAG-AGACTTC-TTCCCCTTAAG
* * * *
5382506 TCTGCCTGTCAGCTTTGACCTTGGAGACTTTTTCACCCTTAAG
1 TCTGCCTGTCGGCTTTGACCCTAGAGACTTCTTC-CCCTTAAG
* * *
5382549 CCTGTCTGTCGGCTTTGACCTTAGAGACTTCTTCGCCCTTAA
1 TCTGCCTGTCGGCTTTGACCCTAGAGACTTCTTC-CCCTTAA
5382591 ATATGCCCGT
Statistics
Matches: 560, Mismatches: 107, Indels: 41
0.79 0.15 0.06
Matches are distributed among these distances:
41 3 0.01
42 45 0.08
43 457 0.82
44 52 0.09
45 3 0.01
ACGTcount: A:0.16, C:0.29, G:0.18, T:0.38
Consensus pattern (42 bp):
TCTGCCTGTCGGCTTTGACCCTAGAGACTTCTTCCCCTTAAG
Found at i:5382606 original size:129 final size:127
Alignment explanation
Indices: 5381861--5382590 Score: 702
Period size: 129 Copynumber: 5.7 Consensus size: 127
5381851 TCATCTCAAA
* * * * *
5381861 TCTGCCTGTCGGCTTTGACCTT-GAAGACTTTCTT-ACCATCAGTCTCCCTGTCGACTTTGACCT
1 TCTGCCTGTCAGCTTTGACCTTAG-AGACTTT-TTCCCCTTAAGTCTGCCTGTCGACTTTGACCT
* * * * *
5381924 TAGAGACTTCTTTC-CCTTTAAGTCTGCCTGTCAGCTTTAATCCTGAAGACTTCTTCGCCTTTAA
64 TGGAGACTTC-TTCGCCCTTAAGTCTGCCTGTCAGCTTTGACCCTGAAGACTTCTTC-CCCTTAA
5381988 G
127 G
** * * * * * * *
5381989 TCTGTTTGTCAACTTTGACCTTAGGGACTTTTTCTTCATTCAGTTTGCCTGTCGACTTTGACCCT
1 TCTGCCTGTCAGCTTTGACCTTAGAGACTTTTTC-CCCTTAAGTCTGCCTGTCGACTTTGACCTT
* * * * *
5382054 GGAGACTTCTTCGTCCTTAAGTTTGCTTGTCAGCTTTGACCCT-AGAGATTTTTTCCCCCTTTAA
65 GGAGACTTCTTCGCCCTTAAGTCTGCCTGTCAGCTTTGACCCTGA-AGACTTCTT-CCCC-TTAA
5382118 -
127 G
* * * ** * * *
5382118 TCTGCTTGTCGGCTTTGACCCTAGAGACTTCCTCGCCTTTAAGACTACCTGTCGACTTTGACCTT
1 TCTGCCTGTCAGCTTTGACCTTAGAGACTTTTTC-CCCTTAAGTCTGCCTGTCGACTTTGACCTT
* * * *
5382183 GGAGACTTCTTCGCCTTTAAGTCTACCTGTC-GACTTTGACCCT-AGAGATTTCTTCCCTCTTTA
65 GGAGACTTCTTCGCCCTTAAGTCTGCCTGTCAG-CTTTGACCCTGA-AGACTTCTTCCC-CTTAA
5382246 G
127 G
* * * * *
5382247 TCTGCCTGTCAGTTTTGACCCTAGAGACTTTTTTCCTCTTAAGTCTGCCTATCGGCTTTGACCTT
1 TCTGCCTGTCAGCTTTGACCTTAGAGAC-TTTTTCCCCTTAAGTCTGCCTGTCGACTTTGACCTT
* * * *
5382312 GGAGACTTCTTCCCCCTAAAGTCTGCCTATCAGCTTTGACCCTGGAGACTTCTTCGCCCTTAAG
65 GGAGACTTCTTCGCCCTTAAGTCTGCCTGTCAGCTTTGACCCTGAAGACTTCTTC-CCCTTAAG
* *
5382376 TCTGCCTGTC-GACTTTGGCCTCTAGAGACTTCTTTCCCCTTAAGTCTGCCTGTCGGCTTTGACC
1 TCTGCCTGTCAG-CTTTGACCT-TAGAGACTT-TTTCCCCTTAAGTCTGCCTGTCGACTTTGACC
* * * * * * *
5382440 CTGGAGACTTCTTCTCCATTAAGTCTGCCTGTCGGCTTTGATCCTGAAAACTTCTTTCTCCTTAA
63 TTGGAGACTTCTTCGCCCTTAAGTCTGCCTGTCAGCTTTGACCCTGAAGACTTC-TTCCCCTTAA
5382505 G
127 G
* * * *
5382506 TCTGCCTGTCAGCTTTGACCTTGGAGACTTTTTCACCCTTAAGCCTGTCTGTCGGCTTTGACCTT
1 TCTGCCTGTCAGCTTTGACCTTAGAGACTTTTTC-CCCTTAAGTCTGCCTGTCGACTTTGACCTT
*
5382571 AGAGACTTCTTCGCCCTTAA
65 GGAGACTTCTTCGCCCTTAA
5382591 ATATGCCCGT
Statistics
Matches: 497, Mismatches: 85, Indels: 39
0.80 0.14 0.06
Matches are distributed among these distances:
127 2 0.00
128 40 0.08
129 332 0.67
130 119 0.24
131 4 0.01
ACGTcount: A:0.16, C:0.29, G:0.18, T:0.38
Consensus pattern (127 bp):
TCTGCCTGTCAGCTTTGACCTTAGAGACTTTTTCCCCTTAAGTCTGCCTGTCGACTTTGACCTTG
GAGACTTCTTCGCCCTTAAGTCTGCCTGTCAGCTTTGACCCTGAAGACTTCTTCCCCTTAAG
Found at i:5382768 original size:42 final size:42
Alignment explanation
Indices: 5382722--5383016 Score: 202
Period size: 42 Copynumber: 7.0 Consensus size: 42
5382712 AACCATCATC
* *
5382722 TGCCCATCGACTCAGACTTGGGAGACTTCTTTATCAATCGTT
1 TGCCCGTCGACTCAGACTCGGGAGACTTCTTTATCAATCGTT
* * * ** * *
5382764 TGCCCGTCGGCTTAGACCCGTAAGACTT-TTTCATCCATCATT
1 TGCCCGTCGACTCAGACTCGGGAGACTTCTTT-ATCAATCGTT
** * * *
5382806 TGCTTGTCGACTCAAAC-CTAGGAGACTTCTTTATCAATAGTT
1 TGCCCGTCGACTCAGACTC-GGGAGACTTCTTTATCAATCGTT
* * * * * * *
5382848 TGCCCGTTGGCTTAGACTCGGGAGACTTCTTCATCCATTGTC
1 TGCCCGTCGACTCAGACTCGGGAGACTTCTTTATCAATCGTT
* * *
5382890 TACCCGTCGACTCTAGACTCGAGAGACTT-TTTCATCAATCATT
1 TGCCCGTCGACTC-AGACTCGGGAGACTTCTTT-ATCAATCGTT
* * * * * *
5382933 TGTCCGT-TAGCTCAGACCCAGGAGACTTCTTCATCAATCGTC
1 TGCCCGTCGA-CTCAGACTCGGGAGACTTCTTTATCAATCGTT
* * **
5382975 TGCCCGTCGTCTCAAACTTAGGAGACTTCTTTTATCAATCGT
1 TGCCCGTCGACTCAGACTCGGGAGACTTC-TTTATCAATCGT
5383017 CTGCTTGTCA
Statistics
Matches: 186, Mismatches: 57, Indels: 19
0.71 0.22 0.07
Matches are distributed among these distances:
41 4 0.02
42 137 0.74
43 45 0.24
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.33
Consensus pattern (42 bp):
TGCCCGTCGACTCAGACTCGGGAGACTTCTTTATCAATCGTT
Found at i:5382804 original size:84 final size:84
Alignment explanation
Indices: 5382691--5383016 Score: 332
Period size: 84 Copynumber: 3.9 Consensus size: 84
5382681 GCCCATCGGT
* * * *
5382691 TTAGACCCATGAGGCTTCTTCAACCATCATCTGCCCATCGACTCAGACTTGGGAGACTTCTTTAT
1 TTAGACCCGTGAGACTTCTTCATCCATCATCTGCCCGTCGACTCAGACTTGGGAGACTTCTTTAT
*
5382756 CAATCGTTTGCCCGTCGGC
66 CAATCGTTTGCCCGTTGGC
* * * ** * * *
5382775 TTAGACCCGTAAGACTTTTTCATCCATCATTTGCTTGTCGACTCAAACCTAGGAGACTTCTTTAT
1 TTAGACCCGTGAGACTTCTTCATCCATCATCTGCCCGTCGACTCAGACTTGGGAGACTTCTTTAT
*
5382840 CAATAGTTTGCCCGTTGGC
66 CAATCGTTTGCCCGTTGGC
* * ** * * *
5382859 TTAGACTCGGGAGACTTCTTCATCCATTGTCTACCCGTCGACTCTAGACTCGAGAGACTT-TTTC
1 TTAGACCCGTGAGACTTCTTCATCCATCATCTGCCCGTCGACTC-AGACTTGGGAGACTTCTTT-
* * *
5382923 ATCAATCATTTGTCCGTTAGC
64 ATCAATCGTTTGCCCGTTGGC
* * * * * *
5382944 TCAGACCCAG-GAGACTTCTTCATCAATCGTCTGCCCGTCGTCTCAAACTTAGGAGACTTCTTTT
1 TTAGACCC-GTGAGACTTCTTCATCCATCATCTGCCCGTCGACTCAGACTTGGGAGACTTC-TTT
5383008 ATCAATCGT
64 ATCAATCGT
5383017 CTGCTTGTCA
Statistics
Matches: 193, Mismatches: 44, Indels: 9
0.78 0.18 0.04
Matches are distributed among these distances:
84 118 0.61
85 71 0.37
86 4 0.02
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (84 bp):
TTAGACCCGTGAGACTTCTTCATCCATCATCTGCCCGTCGACTCAGACTTGGGAGACTTCTTTAT
CAATCGTTTGCCCGTTGGC
Found at i:5382957 original size:85 final size:85
Alignment explanation
Indices: 5382693--5383120 Score: 232
Period size: 85 Copynumber: 5.1 Consensus size: 85
5382683 CCATCGGTTT
* * * * * * * * *
5382693 AGACCCATGAGGCTTCTTCAACCATCATCTGCCCATCGACTC-AGACTTGGGAGACTTCTTTATC
1 AGACCCAGGAGACTTCTTCATCAATCGTCTACCCGTCGACTCTAGACTCGAGAGACTTCTTTATC
* ** *
5382757 AATCGTTTGCCCGTCGGCTT
66 AATAGTTTGCCCGTTAGCTC
* * * * * * ** * *
5382777 AGACCC-GTAAGACTTTTTCATCCATCATTTGCTTGTCGACTC-AAAC-CTAGGAGACTTCTTTA
1 AGACCCAG-GAGACTTCTTCATCAATCGTCTACCCGTCGACTCTAGACTCGA-GAGACTTCTTTA
* *
5382839 TCAATAGTTTGCCCGTTGGCTT
64 TCAATAGTTTGCCCGTTAGCTC
* * * *
5382861 AGACTCGGGAGACTTCTTCATCCATTGTCTACCCGTCGACTCTAGACTCGAGAGACTT-TTTCAT
1 AGACCCAGGAGACTTCTTCATCAATCGTCTACCCGTCGACTCTAGACTCGAGAGACTTCTTT-AT
*
5382925 CAATCA-TTTGTCCGTTAGCTC
65 CAAT-AGTTTGCCCGTTAGCTC
* * * *
5382946 AGACCCAGGAGACTTCTTCATCAATCGTCTGCCCGTCGTCTC-AAACT-TAGGAGACTTCTTTTA
1 AGACCCAGGAGACTTCTTCATCAATCGTCTACCCGTCGACTCTAGACTCGA-GAGACTTC-TTTA
* * ** *
5383009 TCAATCGTCTGCTTGTCAGCTC
64 TCAATAGTTTGCCCGTTAGCTC
* * * * * * * * *
5383031 A-AGCTCAGGAAACTTCTTCATCCATCATCTACTCGTTGACT-TAGTCTCGTA-AAACTTCCTTC
1 AGA-CCCAGGAGACTTCTTCATCAATCGTCTACCCGTCGACTCTAGACTCG-AGAGACTT-CTTT
* *
5383093 ATTAATAGTCTGCCCGTT-GACTC
63 ATCAATAGTTTGCCCGTTAG-CTC
5383116 AGACC
1 AGACC
5383121 TGGGAAACTC
Statistics
Matches: 264, Mismatches: 62, Indels: 35
0.73 0.17 0.10
Matches are distributed among these distances:
83 1 0.00
84 114 0.43
85 140 0.53
86 8 0.03
87 1 0.00
ACGTcount: A:0.22, C:0.29, G:0.17, T:0.32
Consensus pattern (85 bp):
AGACCCAGGAGACTTCTTCATCAATCGTCTACCCGTCGACTCTAGACTCGAGAGACTTCTTTATC
AATAGTTTGCCCGTTAGCTC
Found at i:5382960 original size:127 final size:126
Alignment explanation
Indices: 5382735--5383018 Score: 295
Period size: 127 Copynumber: 2.2 Consensus size: 126
5382725 CCATCGACTC
* * * * * *
5382735 AGACTTGGGAGACTTCTTTATCAATCGTTTGCCCGTCGGCTTAGACCCGTAAGACTTTTTCATCC
1 AGACTCGGGAGACTTCTTCATCAATCGTCTACCCGTCGACTTAGACCCGTAAGACTTTTTCATCA
* * * * *
5382800 ATCATTTGCTTGTCGACTCAAACCTAGGAGACTTCTTTATCAATAGTTTGCCCGTTGGCTT
66 ATCATTTGCGTGTAGACTCAAACCCAGGAGACTTCTTCATCAATAGTCTGCCCGTTGGCTT
* * *
5382861 AGACTCGGGAGACTTCTTCATCCATTGTCTACCCGTCGACTCTAGACTCG-AGAGACTTTTTCAT
1 AGACTCGGGAGACTTCTTCATCAATCGTCTACCCGTCGACT-TAGACCCGTA-AGACTTTTTCAT
* * * * *
5382925 CAATCATTTGTCCGT-TAG-CTCAGACCCAGGAGACTTCTTCATCAATCGTCTGCCCGTCGTCTC
64 CAATCATTTG--CGTGTAGACTCAAACCCAGGAGACTTCTTCATCAATAGTCTGCCCGTTGGCTT
* ** *
5382988 AAACTTAGGAGACTTCTTTTATCAATCGTCT
1 AGACTCGGGAGACTTC-TTCATCAATCGTCT
5383019 GCTTGTCAGC
Statistics
Matches: 128, Mismatches: 25, Indels: 8
0.80 0.16 0.05
Matches are distributed among these distances:
126 35 0.27
127 78 0.61
128 13 0.10
129 2 0.02
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.34
Consensus pattern (126 bp):
AGACTCGGGAGACTTCTTCATCAATCGTCTACCCGTCGACTTAGACCCGTAAGACTTTTTCATCA
ATCATTTGCGTGTAGACTCAAACCCAGGAGACTTCTTCATCAATAGTCTGCCCGTTGGCTT
Found at i:5383032 original size:43 final size:43
Alignment explanation
Indices: 5382742--5383052 Score: 160
Period size: 42 Copynumber: 7.4 Consensus size: 43
5382732 CTCAGACTTG
* * * * *
5382742 GGAGACTTCTTT-ATCAATCGTTTGCCCGTCGGCTTAGAC-CC
1 GGAGACTTCTTTCATCAATCGTCTGCCCGTCGTCTCAAACTCA
* * * * ** *
5382783 GTAAGACTT-TTTCATCCATCATTTGCTTGTCGACTCAAAC-CTA
1 G-GAGACTTCTTTCATCAATCGTCTGCCCGTCGTCTCAAACTC-A
* * * * * * *
5382826 GGAGACTTCTTT-ATCAATAGTTTGCCCGTTGGCTTAGACTCG
1 GGAGACTTCTTTCATCAATCGTCTGCCCGTCGTCTCAAACTCA
* * * * *
5382868 GGAGACTTC-TTCATCCATTGTCTACCCGTCGACTCTAGACTC-
1 GGAGACTTCTTTCATCAATCGTCTGCCCGTCGTCTC-AAACTCA
* * * * * *
5382910 GAGAGACTT-TTTCATCAATCATTTGTCCGTTAG-CTCAGACCCA
1 G-GAGACTTCTTTCATCAATCGTCTGCCCG-TCGTCTCAAACTCA
*
5382953 GGAGACTTC-TTCATCAATCGTCTGCCCGTCGTCTCAAACTTA
1 GGAGACTTCTTTCATCAATCGTCTGCCCGTCGTCTCAAACTCA
* ** *
5382995 GGAGACTTCTTTTATCAATCGTCTGCTTGTCAG-CTCAAGCTCA
1 GGAGACTTCTTTCATCAATCGTCTGCCCGTC-GTCTCAAACTCA
*
5383038 GGAAACTTC-TTCATC
1 GGAGACTTCTTTCATC
5383053 CATCATCTAC
Statistics
Matches: 206, Mismatches: 49, Indels: 29
0.73 0.17 0.10
Matches are distributed among these distances:
41 8 0.04
42 126 0.61
43 69 0.33
44 3 0.01
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.33
Consensus pattern (43 bp):
GGAGACTTCTTTCATCAATCGTCTGCCCGTCGTCTCAAACTCA
Found at i:5383391 original size:82 final size:83
Alignment explanation
Indices: 5383232--5383406 Score: 189
Period size: 82 Copynumber: 2.1 Consensus size: 83
5383222 TTTCAGATTG
* *
5383232 AGTCAACTTTTTATCCTTCATTTACCTGTCGGCTTAGTTCCAGGTAAATCTTTTATCCTCTATTG
1 AGTCAACTTTTTATCCTTCATTTACCTGTCAGCTTAGTTCCAAGTAAATCTTTTATCCTCTATTG
* * *
5383297 ACTTGTCGGTTCAAT-CC
66 ACTCGCCAGTTCAATCCC
* * * *
5383314 AGTCAACTTTTTATCCCTT-ATTT-CCTTGTCAGCTTAG-TCCTAAGTAAATTTTTTATCTTTTG
1 AGTCAACTTTTTAT-CCTTCATTTACC-TGTCAGCTTAGTTCC-AAGTAAATCTTTTATCCTCTA
5383376 TTGA-TACGCCAGTTCAATCCC
63 TTGACT-CGCCAGTTCAATCCC
*
5383397 AATCAACTTT
1 AGTCAACTTT
5383407 CCTTTCTCGA
Statistics
Matches: 78, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
81 6 0.08
82 57 0.73
83 15 0.19
ACGTcount: A:0.22, C:0.23, G:0.11, T:0.43
Consensus pattern (83 bp):
AGTCAACTTTTTATCCTTCATTTACCTGTCAGCTTAGTTCCAAGTAAATCTTTTATCCTCTATTG
ACTCGCCAGTTCAATCCC
Found at i:5384147 original size:10 final size:11
Alignment explanation
Indices: 5384124--5384150 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
5384114 AAATTTTTTA
5384124 TTTTTGAGATT
1 TTTTTGAGATT
5384135 TTTTTGAGATT
1 TTTTTGAGATT
5384146 TTTTT
1 TTTTT
5384151 AAAAATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.70
Consensus pattern (11 bp):
TTTTTGAGATT
Found at i:5384950 original size:19 final size:19
Alignment explanation
Indices: 5384928--5384964 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5384918 ACAAAAATCA
5384928 ATTTATTTTTGATTTTTTG
1 ATTTATTTTTGATTTTTTG
* *
5384947 ATTTTTTTTTTATTTTTT
1 ATTTATTTTTGATTTTTT
5384965 ACATATAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.05, T:0.81
Consensus pattern (19 bp):
ATTTATTTTTGATTTTTTG
Found at i:5386322 original size:157 final size:153
Alignment explanation
Indices: 5385821--5386519 Score: 599
Period size: 156 Copynumber: 4.5 Consensus size: 153
5385811 TTACTTATCA
* *
5385821 TTTTTAAGTCCTTTAGGGGTACCGA-GTTACTTTCACGTCGAAGGTATCCCCTAGGAGCTATTTT
1 TTTTTAAGTCCTTTAGGGGTACC-ATGATACTTTCACGTCGAAGGTATCCCCTAAG-GC-ATTTT
* * * ** * * *
5385885 CGTAATATTTCTAAAACCAAGTCTTAGGTTGCCACCGGGTCCACTTTCATG-CGAAAGGTGAATA
63 CGTAATTTTTC-AAAACCAAGTCATAAGTTATCACCGAGTTCGCTTTCATGCCG-AAGGTGAATA
*
5385949 TCTAGGATAGGTTCACCTCTTTTATAGT-
126 TCTAGGATAGGTTCACC-ATTTTATAGTC
* * * * *
5385977 TCTTTTAAGTCCTTTAGAGGTACCATAATACTTTTATGTCAAAGGTATCCCCTAAAGGCATTTTC
1 T-TTTTAAGTCCTTTAGGGGTACCATGATACTTTCACGTCGAAGGTATCCCCT-AAGGCATTTTC
*** * ** *
5386042 GTAA-TTTTCTAAGGTCAAGT-ACTAAGTTGTTGCCTGAGTTCGCTTTCATGCTGAAGGT-AGAT
64 GTAATTTTTC-AAAACCAAGTCA-TAAGTTATCACC-GAGTTCGCTTTCATGCCGAAGGTGA-AT
*
5386104 ATTTAGGATAGGTTCACTCATTTTATAGTC
125 ATCTAGGATAGGTTCAC-CATTTTATAGTC
* *
5386134 TTTTTAAGTCTTTTAGGGGTACCAAGATACTTTCACGTCGAAGGTATCCCTCTACAGGCATTTTC
1 TTTTTAAGTCCTTTAGGGGTACCATGATACTTTCACGTCGAAGGTATCCC-CTA-AGGCATTTTC
* * * * ** ** * *
5386199 GTAATTTTTCAGAACCAAGTCATAGGTTATCACCGGGTTCGCTTTTATGTTGAAGGTGGGTGTTT
64 GTAATTTTTCAAAACCAAGTCATAAGTTATCACCGAGTTCGCTTTCATGCCGAAGGTGAATATCT
*
5386264 AGGATAGGCTCATCCATTTTATAGTC
129 AGGATAGGTTCA-CCATTTTATAGTC
* *
5386290 ATTTTTAAGTCCTTTAGGGGTACCATGATACTTTCACGTCGAAGGTATCCCCTAAGGATATTTTT
1 -TTTTTAAGTCCTTTAGGGGTACCATGATACTTTCACGTCGAAGGTATCCCCTAAGG-CATTTTC
* * * * * * *
5386355 GTAATATTTT-AAAATCAAGTCTTAAGCTATAACCGAGTTCGCTTTTATGCCGAATGTGAGTATC
64 GTAAT-TTTTCAAAACCAAGTCATAAGTTATCACCGAGTTCGCTTTCATGCCGAAGGTGAATATC
* *
5386419 TAAGATAGGTTCATCCCA-TTTATAATCC
128 TAGGATAGGTTCA--CCATTTTATAGT-C
* * * * * * * * *
5386447 TTTTTAAGTCTTTTAGGGGTATC-GGGTAC-TTCTGCGTCGAAAGTATCCCCTAGGGGTATTTTT
1 TTTTTAAGTCCTTTAGGGGTACCATGATACTTTC-ACGTCGAAGGTATCCCCTA-AGGCATTTTC
5386510 GTAATTTTTC
64 GTAATTTTTC
5386520 CTGAACTCAA
Statistics
Matches: 448, Mismatches: 72, Indels: 47
0.79 0.13 0.08
Matches are distributed among these distances:
154 7 0.02
155 57 0.13
156 241 0.54
157 135 0.30
158 8 0.02
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.38
Consensus pattern (153 bp):
TTTTTAAGTCCTTTAGGGGTACCATGATACTTTCACGTCGAAGGTATCCCCTAAGGCATTTTCGT
AATTTTTCAAAACCAAGTCATAAGTTATCACCGAGTTCGCTTTCATGCCGAAGGTGAATATCTAG
GATAGGTTCACCATTTTATAGTC
Found at i:5386452 original size:313 final size:313
Alignment explanation
Indices: 5385821--5386467 Score: 751
Period size: 313 Copynumber: 2.1 Consensus size: 313
5385811 TTACTTATCA
* * * *
5385821 TTTTTAAGTCCTTTAGGGGTACCGAGTTACTTTCACGTCGAAGGTATCCCCTAGGAGCTATTTTC
1 TTTTTAAGTCTTTTAGGGGTACCAAGATACTTTCACGTCGAAGGTATCCCCTAAGAGCTATTTTC
* *
5385886 GTAATATTTCTAAAACCAAGTCTTAGGTTGCCACCGGGTCCACTTTCATGCGAAAGGTGAATATC
66 GTAATATTTCTAAAACCAAGTCATAGGTTACCACCGGGTCCACTTTCATGCGAAAGGTGAATATC
* * * *
5385951 TAGGATAGGTTCACCTCTTTTATAGTTCTTTTAAGTCCTTTAGAGGTACCATAATACTTTTATGT
131 TAGGATAGGCTCACCTATTTTATAGTTCTTTTAAGTCCTTTAGAGGTACCATAATACTTTCACGT
** * * **
5386016 CAAAGGTATCCCCTAAAGGCATTTTCGTAATTTTCTAAGGTCAAGTACTAAGTTGTTGCCTGAGT
196 CAAAGGTATCCCCTAAAGGCATTTTCGTAATTTTCTAAAATCAAGTACTAAGCTATAACCTGAGT
* * * * *
5386081 TCGCTTTCATGCTGAAGGTAGATATTTAGGATAGGTTCACTCATTTTATAGTC
261 TCGCTTTCATGCCGAAGGTAGATATCTAAGATAGGTTCACCCATTTTATAATC
5386134 TTTTTAAGTCTTTTAGGGGTACCAAGATACTTTCACGTCGAAGGTATCCCTCTACAG-GC-ATTT
1 TTTTTAAGTCTTTTAGGGGTACCAAGATACTTTCACGTCGAAGGTATCCC-CTA-AGAGCTATTT
* * * * * * * **
5386197 TCGTAATTTTTC-AGAACCAAGTCATAGGTTATCACCGGGTTCGCTTTTATGTTG-AAGGTGGGT
64 TCGTAATATTTCTAAAACCAAGTCATAGGTTACCACCGGGTCCACTTTCATG-CGAAAGGTGAAT
* * * *
5386260 GTTTAGGATAGGCTCATCC-ATTTTATAG-TCATTTTTAAGTCCTTTAGGGGTACCATGATACTT
128 ATCTAGGATAGGCTCA-CCTATTTTATAGTTC--TTTTAAGTCCTTTAGAGGTACCATAATACTT
* * *
5386323 TCACGTCGAAGGTATCCCCT-AAGGATATTTTTGTAATATTT-TAAAATCAAGT-CTTAAGCTAT
190 TCACGTCAAAGGTATCCCCTAAAGG-CATTTTCGTAAT-TTTCTAAAATCAAGTAC-TAAGCTAT
* *
5386385 AACC-GAGTTCGCTTTTATGCCGAATGT-GAGTATCTAAGATAGGTTCATCCCA-TTTATAATCC
252 AACCTGAGTTCGCTTTCATGCCGAAGGTAGA-TATCTAAGATAGGTTCA-CCCATTTTATAAT-C
5386447 TTTTTAAGTCTTTTAGGGGTA
1 TTTTTAAGTCTTTTAGGGGTA
5386468 TCGGGTACTT
Statistics
Matches: 283, Mismatches: 39, Indels: 24
0.82 0.11 0.07
Matches are distributed among these distances:
311 4 0.01
312 107 0.38
313 163 0.58
314 8 0.03
315 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.37
Consensus pattern (313 bp):
TTTTTAAGTCTTTTAGGGGTACCAAGATACTTTCACGTCGAAGGTATCCCCTAAGAGCTATTTTC
GTAATATTTCTAAAACCAAGTCATAGGTTACCACCGGGTCCACTTTCATGCGAAAGGTGAATATC
TAGGATAGGCTCACCTATTTTATAGTTCTTTTAAGTCCTTTAGAGGTACCATAATACTTTCACGT
CAAAGGTATCCCCTAAAGGCATTTTCGTAATTTTCTAAAATCAAGTACTAAGCTATAACCTGAGT
TCGCTTTCATGCCGAAGGTAGATATCTAAGATAGGTTCACCCATTTTATAATC
Found at i:5388568 original size:20 final size:21
Alignment explanation
Indices: 5388545--5388604 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
5388535 GAAATAAAGT
* *
5388545 AGAAAGGAAAAGAG-AGAGAA
1 AGAAAGGAAAAAAGAAAAGAA
5388565 AGAAA-GAAAAAAGAAAAGAA
1 AGAAAGGAAAAAAGAAAAGAA
*
5388585 AGAAAGATAAAAAAAGAAAA
1 AGAAAG--GAAAAAAGAAAA
5388605 AAATAGAGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
19 7 0.21
20 15 0.45
23 11 0.33
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (21 bp):
AGAAAGGAAAAAAGAAAAGAA
Found at i:5388588 original size:24 final size:24
Alignment explanation
Indices: 5388551--5388624 Score: 87
Period size: 24 Copynumber: 3.0 Consensus size: 24
5388541 AAGTAGAAAG
5388551 GAAAAGAGAGAGAAAGAAAGAAAAAA
1 GAAAAGA-AGAGAAAGAAA-AAAAAA
*
5388577 GAAAAGAA-AGAAAGATAAAAAAA
1 GAAAAGAAGAGAAAGAAAAAAAAA
* * *
5388600 GAAAAAAATAGAGAGAAAAAAAAA
1 GAAAAGAAGAGAAAGAAAAAAAAA
5388624 G
1 G
5388625 GGAAAATTTG
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
23 13 0.30
24 22 0.51
25 1 0.02
26 7 0.16
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.03
Consensus pattern (24 bp):
GAAAAGAAGAGAAAGAAAAAAAAA
Found at i:5388602 original size:14 final size:13
Alignment explanation
Indices: 5388552--5388622 Score: 56
Period size: 14 Copynumber: 5.3 Consensus size: 13
5388542 AGTAGAAAGG
*
5388552 AAAAGAGAGAGAAA
1 AAAAGAAAGA-AAA
* *
5388566 GAAAGAAA-AAAG
1 AAAAGAAAGAAAA
5388578 AAAAGAAAGAAAGA
1 AAAAGAAAGAAA-A
5388592 TAAAA-AAAGAAAA
1 -AAAAGAAAGAAAA
*
5388605 AAATAGAGAGAAAA
1 AAA-AGAAAGAAAA
5388619 AAAA
1 AAAA
5388623 AGGGAAAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
12 12 0.26
13 7 0.15
14 23 0.50
15 4 0.09
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (13 bp):
AAAAGAAAGAAAA
Found at i:5388618 original size:22 final size:23
Alignment explanation
Indices: 5388551--5388621 Score: 72
Period size: 22 Copynumber: 3.0 Consensus size: 23
5388541 AAGTAGAAAG
*
5388551 GAAAAGAGAGAGAAAGAAAGAAAAAA
1 GAAAAGA-A-AGAAAGAGA-AAAAAA
*
5388577 GAAAAGAAAGAAAGATAAAAAAA
1 GAAAAGAAAGAAAGAGAAAAAAA
* *
5388600 GAAAA-AAATAGAGAGAAAAAAA
1 GAAAAGAAAGAAAGAGAAAAAAA
5388622 AAGGGAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.34
23 11 0.27
24 8 0.20
25 1 0.02
26 7 0.17
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (23 bp):
GAAAAGAAAGAAAGAGAAAAAAA
Found at i:5389394 original size:124 final size:122
Alignment explanation
Indices: 5389247--5389472 Score: 278
Period size: 123 Copynumber: 1.8 Consensus size: 122
5389237 ATTTAGGAAA
* * * * *
5389247 AAAATTGTATGTTTGTATTATA-TTCGT-ATTGTATTTTAATTCACGACATATTTTGTATAATTT
1 AAAATTGTATGTTTATATCATATTTCGTCA-TG--TTTTAATTCACGACAGATTTTGTACAATTC
* *
5389310 GTTATAAT-ATTTAATTTAGAAAAAAATTTGTATATTTATATTTGCTCATGTCCATTAGAG
63 ATTATAATGATTTAATTTAG-AAAAAATTTATATATTTATATTTGCTCATGTCCATTAGAG
* * *
5389370 AAAATCTGTATGTTTATATCATATTTTGTCATGTTTTAGTTCATGACAGATTTTGTACAATTCAT
1 AAAAT-TGTATGTTTATATCATATTTCGTCATGTTTTAATTCACGACAGATTTTGTACAATTCAT
* *
5389435 TGTAATGATTTAATTTAGAAAAAATTTATATGTTTATA
65 TATAATGATTTAATTTAGAAAAAATTTATATATTTATA
5389473 CATGTTCATG
Statistics
Matches: 87, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
123 54 0.62
124 26 0.30
125 6 0.07
126 1 0.01
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.48
Consensus pattern (122 bp):
AAAATTGTATGTTTATATCATATTTCGTCATGTTTTAATTCACGACAGATTTTGTACAATTCATT
ATAATGATTTAATTTAGAAAAAATTTATATATTTATATTTGCTCATGTCCATTAGAG
Found at i:5390028 original size:19 final size:21
Alignment explanation
Indices: 5390004--5390042 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
5389994 ATTTTAAATA
*
5390004 TAAAAT-TATTAAAA-ATAAT
1 TAAAATATAATAAAATATAAT
5390023 TAAAATATAATAAAATATAA
1 TAAAATATAATAAAATATAA
5390043 AAATATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 7 0.41
21 4 0.24
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAAATATAATAAAATATAAT
Found at i:5390047 original size:8 final size:8
Alignment explanation
Indices: 5389999--5390051 Score: 52
Period size: 8 Copynumber: 6.1 Consensus size: 8
5389989 TAATAATTTT
5389999 AAATATAA
1 AAATATAA
*
5390007 AATTATTAA
1 AAATA-TAA
*
5390016 AAATAATTA
1 AAAT-ATAA
5390025 AAATATAATA
1 AAATAT-A-A
5390035 AAATATAA
1 AAATATAA
5390043 AAATATAA
1 AAATATAA
5390051 A
1 A
5390052 TACAATTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
8 16 0.43
9 13 0.35
10 8 0.22
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (8 bp):
AAATATAA
Found at i:5390053 original size:19 final size:19
Alignment explanation
Indices: 5389999--5390073 Score: 59
Period size: 19 Copynumber: 4.1 Consensus size: 19
5389989 TAATAATTTT
*
5389999 AAATATAAAATTATTAAA-A
1 AAATATAAAAATA-TAAATA
5390018 ATAAT-T-AAAATAT-AATA
1 A-AATATAAAAATATAAATA
5390035 AAATATAAAAATATAAATA
1 AAATATAAAAATATAAATA
* * * *
5390054 CAATTTAAATATATTAATA
1 AAATATAAAAATATAAATA
5390073 A
1 A
5390074 TCAATTTTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
16 5 0.11
17 4 0.09
18 12 0.27
19 21 0.47
20 3 0.07
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATATAAAAATATAAATA
Found at i:5390349 original size:5 final size:5
Alignment explanation
Indices: 5390306--5390388 Score: 56
Period size: 5 Copynumber: 17.2 Consensus size: 5
5390296 CCATAAGAAT
*
5390306 TATTA TA-TA T-TTA TATTA TGATCA TATTA -ATT- T-TTA TATTA TATTA
1 TATTA TATTA TATTA TATTA T-ATTA TATTA TATTA TATTA TATTA TATTA
5390352 TATTTTA TATT- T-TTA TATTA TATT- TATGTGA TATTA T
1 TA--TTA TATTA TATTA TATTA TATTA TAT-T-A TATTA T
5390389 TTAAATAAAT
Statistics
Matches: 63, Mismatches: 2, Indels: 26
0.69 0.02 0.29
Matches are distributed among these distances:
3 4 0.06
4 15 0.24
5 31 0.49
6 5 0.08
7 8 0.13
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (5 bp):
TATTA
Found at i:5390349 original size:17 final size:17
Alignment explanation
Indices: 5390311--5390370 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
5390301 AGAATTATTA
*
5390311 TATATT-TATATTATGAT
1 TATATTATATTTTAT-AT
*
5390328 CATATTA-ATTTTTATAT
1 TATATTATA-TTTTATAT
5390345 TATATTATATTTTATAT
1 TATATTATATTTTATAT
5390362 T-T-TTATATT
1 TATATTATATT
5390371 ATATTTATGT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
15 7 0.19
16 1 0.03
17 23 0.62
18 6 0.16
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (17 bp):
TATATTATATTTTATAT
Found at i:5390369 original size:25 final size:23
Alignment explanation
Indices: 5390306--5390375 Score: 88
Period size: 25 Copynumber: 3.0 Consensus size: 23
5390296 CCATAAGAAT
* *
5390306 TATTATATATTTATATTATGATCA
1 TATTATATTTTTATATTAT-ATTA
5390330 TATTA-ATTTTTATATTATATTA
1 TATTATATTTTTATATTATATTA
5390352 TATTTTATATTTTTATATTATATT
1 TA--TTATATTTTTATATTATATT
5390376 TATGTGATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
22 5 0.12
23 12 0.29
24 8 0.20
25 16 0.39
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (23 bp):
TATTATATTTTTATATTATATTA
Found at i:5390391 original size:25 final size:25
Alignment explanation
Indices: 5390310--5390391 Score: 82
Period size: 25 Copynumber: 3.4 Consensus size: 25
5390300 AAGAATTATT
* *
5390310 ATATATTTATATTATGATCATAT-T-
1 ATATTTTTATATTAT-ATTATATGTG
* *
5390334 A-ATTTTTATATTATATTATATTTT
1 ATATTTTTATATTATATTATATGTG
5390358 ATATTTTTATATTATATT-TATGTG
1 ATATTTTTATATTATATTATATGTG
5390382 ATATTATTTA
1 ATATT-TTTA
5390392 AATAAATTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
22 6 0.12
23 13 0.26
24 11 0.22
25 20 0.40
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (25 bp):
ATATTTTTATATTATATTATATGTG
Found at i:5393404 original size:44 final size:44
Alignment explanation
Indices: 5393354--5393487 Score: 207
Period size: 44 Copynumber: 3.0 Consensus size: 44
5393344 TCGTGCAGCG
5393354 GGCAAGGTAAGAATACTATCTATCTCTACTCTTCACTTGTCACT
1 GGCAAGGTAAGAATACTATCTATCTCTACTCTTCACTTGTCACT
* * *
5393398 GGCAAGGTAAGAATACTATCTATCTCTACCCTTTACTTGTCATT
1 GGCAAGGTAAGAATACTATCTATCTCTACTCTTCACTTGTCACT
* *
5393442 GGCAAGGTAAGAATTCTATCTATCTCTATTC-TCTACTTGTCACT
1 GGCAAGGTAAGAATACTATCTATCTCTACTCTTC-ACTTGTCACT
5393486 GG
1 GG
5393488 AATTTTGAGA
Statistics
Matches: 81, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
43 1 0.01
44 80 0.99
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (44 bp):
GGCAAGGTAAGAATACTATCTATCTCTACTCTTCACTTGTCACT
Found at i:5396612 original size:20 final size:20
Alignment explanation
Indices: 5396587--5396626 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
5396577 TAATCAAGAT
5396587 AGTTTGTTTAAGATAAAAAC
1 AGTTTGTTTAAGATAAAAAC
5396607 AGTTTGTTTAAGATAAAAAC
1 AGTTTGTTTAAGATAAAAAC
5396627 TTTTAGGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.15, T:0.35
Consensus pattern (20 bp):
AGTTTGTTTAAGATAAAAAC
Found at i:5397510 original size:36 final size:32
Alignment explanation
Indices: 5397426--5397513 Score: 92
Period size: 36 Copynumber: 2.7 Consensus size: 32
5397416 CCTTACAACA
5397426 CTATC-TTTC-AAGGCTAAGATAGAAACCTCC
1 CTATCTTTTCAAAGGCTAAGATAGAAACCTCC
* *
5397456 TTATCTTTTCATAA-GCTAAGATAGAATTTCTCTCC
1 CTATCTTTTCA-AAGGCTAAGATAGAA--AC-CTCC
5397491 CTATCTTTTTCAAAGGCTAAGAT
1 CTATC-TTTTCAAAGGCTAAGAT
5397514 GGAACATCTC
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
30 4 0.09
31 4 0.09
32 12 0.26
33 2 0.04
34 1 0.02
35 10 0.21
36 14 0.30
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (32 bp):
CTATCTTTTCAAAGGCTAAGATAGAAACCTCC
Found at i:5397975 original size:22 final size:22
Alignment explanation
Indices: 5397950--5397996 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
5397940 TACTATTGAC
* *
5397950 ATGTATTGATAAATAAACAGTG
1 ATGTATCGATAAATAAACAATG
* *
5397972 ATGTATCGATACATGAACAATG
1 ATGTATCGATAAATAAACAATG
5397994 ATG
1 ATG
5397997 AGCAGTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.09, G:0.19, T:0.30
Consensus pattern (22 bp):
ATGTATCGATAAATAAACAATG
Found at i:5398003 original size:32 final size:32
Alignment explanation
Indices: 5397967--5398027 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
5397957 GATAAATAAA
5397967 CAGTGATGTATCGATACATGAACAATGATGAG
1 CAGTGATGTATCGATACATGAACAATGATGAG
*
5397999 CAGTGATGTATCGATACATGAACAGTGAT
1 CAGTGATGTATCGATACATGAACAATGAT
5398028 TAATAGTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.26
Consensus pattern (32 bp):
CAGTGATGTATCGATACATGAACAATGATGAG
Found at i:5398040 original size:32 final size:32
Alignment explanation
Indices: 5397965--5398042 Score: 102
Period size: 32 Copynumber: 2.4 Consensus size: 32
5397955 TTGATAAATA
*
5397965 AACAGTGATGTATCGATACATGAACAATGATG
1 AACAGTAATGTATCGATACATGAACAATGATG
* * * *
5397997 AGCAGTGATGTATCGATACATGAACAGTGATT
1 AACAGTAATGTATCGATACATGAACAATGATG
*
5398029 AATAGTAATGTATC
1 AACAGTAATGTATC
5398043 AATTAAAAGT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (32 bp):
AACAGTAATGTATCGATACATGAACAATGATG
Found at i:5400082 original size:19 final size:21
Alignment explanation
Indices: 5400038--5400087 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
5400028 CGTAAGTAAA
**
5400038 TGTATCGATACAGTTACTGTT
1 TGTATCGATACAGTTACTCAT
5400059 TGTATCGATACA-TTAC-CAT
1 TGTATCGATACAGTTACTCAT
5400078 TGTATCGATA
1 TGTATCGATA
5400088 TATTCTGGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 11 0.41
20 4 0.15
21 12 0.44
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (21 bp):
TGTATCGATACAGTTACTCAT
Found at i:5401851 original size:13 final size:13
Alignment explanation
Indices: 5401833--5401859 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5401823 CATAAAATGT
5401833 TGTATCGATACAA
1 TGTATCGATACAA
5401846 TGTATCGATACAA
1 TGTATCGATACAA
5401859 T
1 T
5401860 TTAAGCTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5401918 original size:13 final size:12
Alignment explanation
Indices: 5401878--5401958 Score: 70
Period size: 13 Copynumber: 7.1 Consensus size: 12
5401868 CTGCCAAAAA
5401878 ATGTATCGATAC
1 ATGTATCGATAC
5401890 AT-TACTC-A-A-
1 ATGTA-TCGATAC
5401899 ATGTATCGATAC
1 ATGTATCGATAC
5401911 ATTGTATCGATAC
1 A-TGTATCGATAC
5401924 AT-TACTC-A-A-
1 ATGTA-TCGATAC
5401933 ATGTATCGATAC
1 ATGTATCGATAC
5401945 ATTGTATCGATAC
1 A-TGTATCGATAC
5401958 A
1 A
5401959 CTGATCTTTG
Statistics
Matches: 57, Mismatches: 0, Indels: 23
0.71 0.00 0.29
Matches are distributed among these distances:
9 8 0.14
10 8 0.14
11 8 0.14
12 9 0.16
13 24 0.42
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:5401922 original size:34 final size:34
Alignment explanation
Indices: 5401879--5401958 Score: 160
Period size: 34 Copynumber: 2.4 Consensus size: 34
5401869 TGCCAAAAAA
5401879 TGTATCGATACATTACTCAAATGTATCGATACAT
1 TGTATCGATACATTACTCAAATGTATCGATACAT
5401913 TGTATCGATACATTACTCAAATGTATCGATACAT
1 TGTATCGATACATTACTCAAATGTATCGATACAT
5401947 TGTATCGATACA
1 TGTATCGATACA
5401959 CTGATCTTTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (34 bp):
TGTATCGATACATTACTCAAATGTATCGATACAT
Found at i:5407168 original size:19 final size:19
Alignment explanation
Indices: 5407145--5407192 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
5407135 TCGGAACAGT
* *
5407145 AAAAAGTAAACACAAAAAA
1 AAAAAGAAAACAAAAAAAA
* *
5407164 CAAAACAAAACAAAAAAAA
1 AAAAAGAAAACAAAAAAAA
5407183 AAAAAGAAAA
1 AAAAAGAAAA
5407193 AGTGCAAAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.83, C:0.10, G:0.04, T:0.02
Consensus pattern (19 bp):
AAAAAGAAAACAAAAAAAA
Found at i:5408548 original size:30 final size:30
Alignment explanation
Indices: 5408494--5408708 Score: 211
Period size: 31 Copynumber: 6.9 Consensus size: 30
5408484 ATACCTTTTT
* *
5408494 AAAGTCCACGACTAAGTGGCAATCTCTTCTC
1 AAAGTCCACGACTCAGTGGC-ATCTTTTCTC
* *
5408525 AAAGTCCACGACTCAGT-GCAATCTCTGCTC
1 AAAGTCCACGACTCAGTGGC-ATCTTTTCTC
*
5408555 AAAGTCCACGAC-CTAGTGGCATCCTTTTCTTT
1 AAAGTCCACGACTC-AGTGGCAT-CTTTTC-TC
*
5408587 AAAGTCCACGACTCAGTGGCATCCTTTATCTTT
1 AAAGTCCACGACTCAGTGGCAT-CTTT-TC-TC
5408620 AAAGTCCACGACTCAGTGGCAT-TTTATCTC
1 AAAGTCCACGACTCAGTGGCATCTTT-TCTC
* *
5408650 AAAGTCCACGACTCAATGGCATTTTTTCTTC
1 AAAGTCCACGACTCAGTGGCATCTTTTC-TC
* * * *
5408681 AAAGCCCACAACTCCGTGGCACCTTTTC
1 AAAGTCCACGACTCAGTGGCATCTTTTC
5408709 CTTTAAAGCC
Statistics
Matches: 163, Mismatches: 13, Indels: 16
0.85 0.07 0.08
Matches are distributed among these distances:
29 1 0.01
30 53 0.33
31 55 0.34
32 26 0.16
33 28 0.17
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.29
Consensus pattern (30 bp):
AAAGTCCACGACTCAGTGGCATCTTTTCTC
Found at i:5408752 original size:34 final size:33
Alignment explanation
Indices: 5408570--5409774 Score: 1462
Period size: 34 Copynumber: 35.8 Consensus size: 33
5408560 CCACGACCTA
* * *
5408570 GTGGCATCC-TTTTC-TTTAAAGTCCACGACTCA
1 GTGGCA-CCTTTTTCTTTTAAAGCCCACAACTCC
* * * *
5408602 GTGGCATCCTTTATC-TTTAAAGTCCACGACTCA
1 GTGGCA-CCTTTTTCTTTTAAAGCCCACAACTCC
* * * *
5408635 GTGGCA--TTTTATC--TCAAAGTCCACGACTCA
1 GTGGCACCTTTT-TCTTTTAAAGCCCACAACTCC
* * *
5408665 ATGGCA-TTTTTTC-TTCAAAGCCCACAACTCC
1 GTGGCACCTTTTTCTTTTAAAGCCCACAACTCC
*
5408696 GTGGCACC-TTTTCCTTTAAAGCCCACAACTCC
1 GTGGCACCTTTTTCTTTTAAAGCCCACAACTCC
*
5408728 GTGGCACCTTCTTCTTTTCAAAGCCCACAACTCC
1 GTGGCACCTTTTTCTTTT-AAAGCCCACAACTCC
5408762 GTGGCACCTTTTTCTTTTCAAAGCCCACAACTCC
1 GTGGCACCTTTTTCTTTT-AAAGCCCACAACTCC
* *
5408796 GTGGCACTTTTTTCATCTTT-AAGTCCACAACTCC
1 GTGGCACCTTTTTC-T-TTTAAAGCCCACAACTCC
5408830 GTGGCACCTTTTTCTTTTTAAAGCCCACTAACTCC
1 GTGGCACCTTTTTC-TTTTAAAGCCCAC-AACTCC
5408865 GTGGCACCTTTTTCTGTTTAAAGCCCACAACTCC
1 GTGGCACCTTTTTCT-TTTAAAGCCCACAACTCC
5408899 GTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCC
1 GTGGCAC-CTTTTT--CTTTT-AAAGCCCACAACTCC
*
5408936 GTGGCACTTTTTTCTTTTAAAGCCCACAACTCC
1 GTGGCACCTTTTTCTTTTAAAGCCCACAACTCC
*
5408969 GTGGCACC-TTTTCCTTTAAAGCCCACAACTCC
1 GTGGCACCTTTTTCTTTTAAAGCCCACAACTCC
*
5409001 GTGGCACCTTCTTCTTTTCAAAGCCCACAACTCC
1 GTGGCACCTTTTTCTTTT-AAAGCCCACAACTCC
* * * *
5409035 GTGGCGCCTTCTTCTTTTCAAAGCCCACAATTTC
1 GTGGCACCTTTTTCTTTT-AAAGCCCACAACTCC
* * *
5409069 GTGGCACTTTTTTCATCTTT-AAGTCCACAACTCT
1 GTGGCACCTTTTTC-T-TTTAAAGCCCACAACTCC
5409103 GTGGCACCTTTTTCTTTTTAAAGCCCACAACTCC
1 GTGGCACCTTTTTC-TTTTAAAGCCCACAACTCC
5409137 GTGGCACCTTTTTCTGTTTAAAGCCCACAACTCC
1 GTGGCACCTTTTTCT-TTTAAAGCCCACAACTCC
5409171 GTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCC
1 GTGGCAC-CTTTTT--CTTTT-AAAGCCCACAACTCC
*
5409208 GTGGCACTTTTTTCTTTTAAAGCCCACAACTCC
1 GTGGCACCTTTTTCTTTTAAAGCCCACAACTCC
*
5409241 GTGGCACC-TTTTCCTTTAAAGCCCACAACTCC
1 GTGGCACCTTTTTCTTTTAAAGCCCACAACTCC
*
5409273 GTGGCACCTTCTTCTTTTCAAAGCCCACAACTCC
1 GTGGCACCTTTTTCTTTT-AAAGCCCACAACTCC
*
5409307 GTGGCACC---TTCTTTCAAAGCCCACAACTCC
1 GTGGCACCTTTTTCTTTTAAAGCCCACAACTCC
* *
5409337 GTGGCACTTTTTTCATCTTT-AAGTCCACAACTCC
1 GTGGCACCTTTTTC-T-TTTAAAGCCCACAACTCC
5409371 GTGGCACCTTTTTCTTTTTAAAGCCCACAACTCC
1 GTGGCACCTTTTTC-TTTTAAAGCCCACAACTCC
5409405 GTGGCACCTTTTTCTGTTTAAAGCCCACAACTCC
1 GTGGCACCTTTTTCT-TTTAAAGCCCACAACTCC
*
5409439 GTGGCACTCTTCTTCTTTTCAAAGCCCACAACTCC
1 GTGGCAC-CTTTTTCTTTT-AAAGCCCACAACTCC
*
5409474 GTGGCACTTTTTTCTTTTAAAGCCCACAACTCC
1 GTGGCACCTTTTTCTTTTAAAGCCCACAACTCC
*
5409507 GTGGCACC-TTTTCCTTTAAAGCCCACAACTCC
1 GTGGCACCTTTTTCTTTTAAAGCCCACAACTCC
*
5409539 GTGGCACCTTCTTCTTTTCAAAGCCCACAACTCC
1 GTGGCACCTTTTTCTTTT-AAAGCCCACAACTCC
*
5409573 GTGGCACCTTCTTCTTTTCAAAGCCCACAACTCC
1 GTGGCACCTTTTTCTTTT-AAAGCCCACAACTCC
* *
5409607 GTGGCACTTTTTTTCATCTTT-AAGTCCACAACTCC
1 GTGGCAC-CTTTTTC-T-TTTAAAGCCCACAACTCC
*
5409642 GTGGCACCTTCTTCTTTTCAAAGCCCACAACTCC
1 GTGGCACCTTTTTCTTTT-AAAGCCCACAACTCC
*
5409676 GTGGCACTTTTTTCTTTTAAAGCCCACAACTCC
1 GTGGCACCTTTTTCTTTTAAAGCCCACAACTCC
*
5409709 GTGGCACTCTTTTTCCCTTTT-AAGTCCACAACTCC
1 GTGGCAC-CTTTTT--CTTTTAAAGCCCACAACTCC
* *
5409744 GTGGCATCTTTCTCCCTTTCTAAAGCCCACA
1 GTGGCACCTTT-T-TCTTT-TAAAGCCCACA
5409775 CAAGTCGGTG
Statistics
Matches: 1052, Mismatches: 69, Indels: 100
0.86 0.06 0.08
Matches are distributed among these distances:
30 48 0.05
31 36 0.03
32 130 0.12
33 159 0.15
34 469 0.45
35 123 0.12
36 36 0.03
37 51 0.05
ACGTcount: A:0.21, C:0.34, G:0.12, T:0.33
Consensus pattern (33 bp):
GTGGCACCTTTTTCTTTTAAAGCCCACAACTCC
Found at i:5409793 original size:32 final size:32
Alignment explanation
Indices: 5409757--5409957 Score: 305
Period size: 33 Copynumber: 6.2 Consensus size: 32
5409747 GCATCTTTCT
5409757 CCCTTTCTAAAGCCCACACAAGTCGGTGGCAA
1 CCCTTTCTAAAGCCCACACAAGTCGGTGGCAA
5409789 CCCTTTCTAAAGCCCACACAAGTCGGTGGCAA
1 CCCTTTCTAAAGCCCACACAAGTCGGTGGCAA
5409821 CCCTTTCTAAAGCCCACACAAGTCGGTGGCAA
1 CCCTTTCTAAAGCCCACACAAGTCGGTGGCAA
5409853 CCTTCTTTC-AAAGCCCACACAAGTCGGTGGCAA
1 CC--CTTTCTAAAGCCCACACAAGTCGGTGGCAA
* * * *
5409886 CCTTCTTCCAAAGCCCACACAAGTTGGTGACAA
1 CCCT-TTCTAAAGCCCACACAAGTCGGTGGCAA
* *
5409919 CCATTCTCTAAAGCCCACACAAGTCGGTGGCGA
1 CCCTT-TCTAAAGCCCACACAAGTCGGTGGCAA
5409952 CCCTTT
1 CCCTTT
5409958 AAGTCCAATA
Statistics
Matches: 155, Mismatches: 9, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
31 1 0.01
32 71 0.46
33 78 0.50
34 5 0.03
ACGTcount: A:0.27, C:0.34, G:0.18, T:0.20
Consensus pattern (32 bp):
CCCTTTCTAAAGCCCACACAAGTCGGTGGCAA
Found at i:5410026 original size:49 final size:49
Alignment explanation
Indices: 5409954--5411183 Score: 1503
Period size: 49 Copynumber: 25.8 Consensus size: 49
5409944 GGTGGCGACC
* * *
5409954 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* *
5410003 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* *
5410052 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* *
5410101 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA----C--
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* *
5410144 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* *
5410193 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA----C--
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* *
5410236 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
*
5410285 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C-T
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * *
5410329 -TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACGTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
*
5410377 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C-T
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* *
5410421 -TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * *
5410469 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAACACATTGG------CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * *
5410512 CTTTAAGTCCAATATAGTTGGCCTTGAATCAGCATATTGGCACCTTTAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * * *
5410561 CTTTAAGACCAATGTAGCTGGCCTTGACTCAGCACATTGGCCCCTTCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * * *
5410610 CTTTAAGCCCGATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
*
5410659 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * * **
5410702 CTTTAAGCCCGATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * *
5410751 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA-CTTGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT-CAT
* * *
5410800 CATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * *
5410849 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * * *
5410898 CATTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * *
5410947 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA-CTTGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT-CAT
* * *
5410996 CATTAAGTCC-ATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* *
5411044 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* *
5411093 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CAT
* *
5411145 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTG
5411184 ACATCCTTTT
Statistics
Matches: 1005, Mismatches: 132, Indels: 85
0.82 0.11 0.07
Matches are distributed among these distances:
43 228 0.23
44 2 0.00
45 3 0.00
47 3 0.00
48 45 0.04
49 681 0.68
50 3 0.00
51 2 0.00
52 38 0.04
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.32
Consensus pattern (49 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
Found at i:5410123 original size:98 final size:97
Alignment explanation
Indices: 5409954--5411183 Score: 1838
Period size: 92 Copynumber: 12.9 Consensus size: 97
5409944 GGTGGCGACC
*
5409954 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
5410019 GCTGGCCTTGACTCAGCACATTGGCACCTTCAT
66 GCTGGCCTTGACTCAGCACATTGGCA-CTTCAT
5410052 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
5410117 GCTGGCCTTGACTCAGCACATTGGCA---C--
66 GCTGGCCTTGACTCAGCACATTGGCACTTCAT
5410144 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
5410209 GCTGGCCTTGACTCAGCACATTGGCA---C--
66 GCTGGCCTTGACTCAGCACATTGGCACTTCAT
* *
5410236 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
*
5410301 GCTGGCCTTGAATCAGCACATTGGCA---C-T
66 GCTGGCCTTGACTCAGCACATTGGCACTTCAT
* * *
5410329 -TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACGTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
*
5410393 GCTGGCCTTGAATCAGCACATTGGCA---C-T
66 GCTGGCCTTGACTCAGCACATTGGCACTTCAT
* *
5410421 -TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
*
5410485 GCTGGCCTTGACTCAACACATTGG-----CAT
66 GCTGGCCTTGACTCAGCACATTGGCACTTCAT
* *
5410512 CTTTAAGTCCAATATAGTTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
* *
5410577 GCTGGCCTTGACTCAGCACATTGGCCCCTTCAC
66 GCTGGCCTTGACTCAGCACATTGG-CACTTCAT
* * * * *
5410610 CTTTAAGCCCGATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
*
5410675 GCTGGCCTTGAATCAGCACATTGGCA---C--
66 GCTGGCCTTGACTCAGCACATTGGCACTTCAT
* * * *
5410702 CTTTAAGCCCGATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
*
5410767 GCTGGCCTTGACTCAGCACATTGGCACTTGCAC
66 GCTGGCCTTGACTCAGCACATTGGCACTT-CAT
*
5410800 CATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
*
5410865 GCTGGCCTTGACTCAGCACATTGGCACCTTCAC
66 GCTGGCCTTGACTCAGCACATTGGCA-CTTCAT
* * *
5410898 CATTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
*
5410963 GCTGGCCTTGACTCAGCACATTGGCACTTGCAC
66 GCTGGCCTTGACTCAGCACATTGGCACTT-CAT
*
5410996 CATTAAGTCC-ATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
5411060 GCTGGCCTTGACTCAGCACATTGGCACCTTCAT
66 GCTGGCCTTGACTCAGCACATTGGCA-CTTCAT
* *
5411093 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TTT--ATCTTTAAGTCCAAT
*
5411158 GTAGCTGGCCTTGAATCAGCACATTG
63 GTAGCTGGCCTTGACTCAGCACATTG
5411184 ACATCCTTTT
Statistics
Matches: 1069, Mismatches: 41, Indels: 41
0.93 0.04 0.04
Matches are distributed among these distances:
90 1 0.00
91 1 0.00
92 527 0.49
94 2 0.00
96 1 0.00
97 94 0.09
98 398 0.37
99 6 0.01
101 39 0.04
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.32
Consensus pattern (97 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
GCTGGCCTTGACTCAGCACATTGGCACTTCAT
Found at i:5411305 original size:67 final size:68
Alignment explanation
Indices: 5411197--5411323 Score: 184
Period size: 67 Copynumber: 1.9 Consensus size: 68
5411187 TCCTTTTTCA
* * *
5411197 TCATCTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCA-CTTTTCTCA
1 TCATCTTTAAGCCCAATATCGCTGGCCATGAATCAACATATTGGCACCTTCATCATCTTTTCTCA
5411261 TCT
66 TCT
* * * *
5411264 TCATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCATCTTT
1 TCATCTTTAAGCCCAATATCGCTGGCCATGAATCAACATATTGGCACCTTCATCATCTTT
5411324 AAAACCCAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
67 48 0.92
68 4 0.08
ACGTcount: A:0.24, C:0.25, G:0.12, T:0.39
Consensus pattern (68 bp):
TCATCTTTAAGCCCAATATCGCTGGCCATGAATCAACATATTGGCACCTTCATCATCTTTTCTCA
TCT
Found at i:5412123 original size:33 final size:33
Alignment explanation
Indices: 5412086--5412152 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
5412076 TTCAACGATT
5412086 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
5412119 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
5412152 T
1 T
5412153 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:5412124 original size:13 final size:13
Alignment explanation
Indices: 5412106--5412130 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5412096 CATAAAATGT
5412106 TGTATCGATACAA
1 TGTATCGATACAA
5412119 TGTATCGATACA
1 TGTATCGATACA
5412131 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5412211 original size:13 final size:13
Alignment explanation
Indices: 5412193--5412217 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5412183 ATTACTCAAA
5412193 TGTATCGATACAT
1 TGTATCGATACAT
5412206 TGTATCGATACA
1 TGTATCGATACA
5412218 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5412319 original size:52 final size:52
Alignment explanation
Indices: 5412226--5412353 Score: 224
Period size: 52 Copynumber: 2.5 Consensus size: 52
5412216 CACTGATCTT
*
5412226 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATT-AAA
5412277 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
5412329 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
5412354 TCATATTTCG
Statistics
Matches: 74, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
51 19 0.26
52 52 0.70
53 3 0.04
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:5416718 original size:19 final size:19
Alignment explanation
Indices: 5416690--5416748 Score: 75
Period size: 20 Copynumber: 3.1 Consensus size: 19
5416680 TTGTATCGAT
*
5416690 ACATTATATCGATACAT-A
1 ACATTGTATCGATACATGA
*
5416708 TTCATTGTATCGATACATGA
1 -ACATTGTATCGATACATGA
5416728 ACAATTGTATCGATACATGA
1 AC-ATTGTATCGATACATGA
5416748 A
1 A
5416749 ACTGGCAGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
19 16 0.46
20 19 0.54
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (19 bp):
ACATTGTATCGATACATGA
Found at i:5416736 original size:20 final size:20
Alignment explanation
Indices: 5416711--5416748 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
5416701 ATACATATTC
5416711 ATTGTATCGATACATGAACA
1 ATTGTATCGATACATGAACA
5416731 ATTGTATCGATACATGAA
1 ATTGTATCGATACATGAA
5416749 ACTGGCAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (20 bp):
ATTGTATCGATACATGAACA
Found at i:5416817 original size:20 final size:20
Alignment explanation
Indices: 5416775--5416827 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
5416765 CTACCATTGT
* *
5416775 TTGTATCGATACATGGTACA
1 TTGTATCGATACAAGATACA
5416795 TTGTATCGATACAAGATGA-A
1 TTGTATCGATACAAGAT-ACA
*
5416815 TTGTATCAATACA
1 TTGTATCGATACA
5416828 TTGCCTGTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (20 bp):
TTGTATCGATACAAGATACA
Found at i:5423024 original size:13 final size:13
Alignment explanation
Indices: 5423006--5423045 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
5422996 ACAACATTCC
5423006 TTGTATCGATACA
1 TTGTATCGATACA
5423019 TTGTATCGATACA
1 TTGTATCGATACA
*
5423032 TTGTATAGATACA
1 TTGTATCGATACA
5423045 T
1 T
5423046 GGGCTACTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:5425554 original size:13 final size:13
Alignment explanation
Indices: 5425536--5425562 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5425526 ACATTATGCT
5425536 TTGTATCGATACA
1 TTGTATCGATACA
5425549 TTGTATCGATACA
1 TTGTATCGATACA
5425562 T
1 T
5425563 ATTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:5425577 original size:32 final size:33
Alignment explanation
Indices: 5425517--5425581 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
5425507 CACACCCAGA
*
5425517 TGTATCAATACATTATGCTTTGTATCGATACAT
1 TGTATCAATACATTATGCATTGTATCGATACAT
* *
5425550 TGTATCGATACA-TATTCATTGTATCGATACAT
1 TGTATCAATACATTATGCATTGTATCGATACAT
5425582 GGACAATTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (33 bp):
TGTATCAATACATTATGCATTGTATCGATACAT
Found at i:5425592 original size:20 final size:19
Alignment explanation
Indices: 5425546--5425602 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
5425536 TTGTATCGAT
**
5425546 ACATTGTATCGATACATAT
1 ACATTGTATCGATACATGG
*
5425565 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
5425584 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
5425603 AAACTGGTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:5425656 original size:20 final size:20
Alignment explanation
Indices: 5425631--5425684 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
5425621 CTACCACTGT
* *
5425631 TTGTATTGATACATGGT-ACA
1 TTGTATCGATACATGATGA-A
5425651 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGATGAA
5425671 TTGTATCGATACAT
1 TTGTATCGATACAT
5425685 TGTCTATAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (20 bp):
TTGTATCGATACATGATGAA
Found at i:5435141 original size:46 final size:46
Alignment explanation
Indices: 5435085--5435176 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
5435075 GAGCAATTGG
*
5435085 TCCACATAAGTGAAGTCTATTCTAAGATGGATTCAGAAGATATCAT
1 TCCACATAAGTGAAGTCGATTCTAAGATGGATTCAGAAGATATCAT
* *
5435131 TCCACGTAAGTGAAGTCGATTCTGAGATGGATTCAGAAGATATCAT
1 TCCACATAAGTGAAGTCGATTCTAAGATGGATTCAGAAGATATCAT
5435177 CCCTCTTGAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (46 bp):
TCCACATAAGTGAAGTCGATTCTAAGATGGATTCAGAAGATATCAT
Found at i:5438529 original size:20 final size:20
Alignment explanation
Indices: 5438504--5438557 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
5438494 GTTACAAGCA
*
5438504 ATGTATCGATACAAT-TCATC
1 ATGTATCGATACAATGT-ACC
* *
5438524 ATGTATCAATATAATGTACC
1 ATGTATCGATACAATGTACC
5438544 ATGTATCGATACAA
1 ATGTATCGATACAA
5438558 ATAGTAGTAG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:5438630 original size:19 final size:19
Alignment explanation
Indices: 5438585--5438658 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
5438575 ACTGCCAGTT
5438585 TCATGTATCGATACAATTG-
1 TCATGTATCGATACAA-TGA
*
5438604 TCCATGTATCGATATAATGA
1 T-CATGTATCGATACAATGA
*
5438624 TCATGTATCGATACAAAGCA
1 TCATGTATCGATACAATG-A
*
5438644 TAATGTATCGATACA
1 TCATGTATCGATACA
5438659 TCTGGGTGTG
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
19 18 0.38
20 30 0.62
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.32
Consensus pattern (19 bp):
TCATGTATCGATACAATGA
Found at i:5438670 original size:20 final size:20
Alignment explanation
Indices: 5438647--5438698 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
5438637 CAAAGCATAA
5438647 TGTATCGATACATCTGGGTG
1 TGTATCGATACATCTGGGTG
5438667 TGTATCGATACATCTGGGTG
1 TGTATCGATACATCTGGGTG
5438687 TGTATCGATACA
1 TGTATCGATACA
5438699 CTCAAGGGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.15, G:0.27, T:0.35
Consensus pattern (20 bp):
TGTATCGATACATCTGGGTG
Found at i:5439625 original size:30 final size:29
Alignment explanation
Indices: 5439544--5439627 Score: 107
Period size: 29 Copynumber: 2.9 Consensus size: 29
5439534 ATACCAAAAG
* * *
5439544 TTTATGCAAGCTTTCCCCTTTAGTACAAGT
1 TTTATGCAAGCTCTCCCC-TTAATACAAAT
5439574 TTTAT-CAAGCTCTCCCCTTAATACAAAT
1 TTTATGCAAGCTCTCCCCTTAATACAAAT
*
5439602 TTTATGCAAACTCTCCACCTTAATAC
1 TTTATGCAAGCTCTCC-CCTTAATAC
5439628 GTTCTCACCC
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
28 14 0.29
29 20 0.42
30 14 0.29
ACGTcount: A:0.29, C:0.27, G:0.07, T:0.37
Consensus pattern (29 bp):
TTTATGCAAGCTCTCCCCTTAATACAAAT
Found at i:5439855 original size:30 final size:30
Alignment explanation
Indices: 5439821--5439905 Score: 111
Period size: 29 Copynumber: 2.9 Consensus size: 30
5439811 ATACCAAAAG
*
5439821 TTTATTCAAGCTCTCCCCTTTAGTACAAAT
1 TTTATTCAAGCTCTCCCCTTTAATACAAAT
*
5439851 TTTA-TCAAGCTCTCCCCCTTAATACAAAT
1 TTTATTCAAGCTCTCCCCTTTAATACAAAT
* *
5439880 TTTATGCAAACTCTCCACC-TTAATAC
1 TTTATTCAAGCTCTCC-CCTTTAATAC
5439906 GTTCTCCCCC
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
29 27 0.55
30 20 0.41
31 2 0.04
ACGTcount: A:0.29, C:0.29, G:0.05, T:0.36
Consensus pattern (30 bp):
TTTATTCAAGCTCTCCCCTTTAATACAAAT
Found at i:5441495 original size:23 final size:24
Alignment explanation
Indices: 5441450--5441496 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
5441440 CAAAGGATTG
*
5441450 AACACAAATTCAATTAAGCACAAA
1 AACACAAATTCAATTAAGAACAAA
5441474 AACACAAA-TCAATTGAA-AACAAA
1 AACACAAATTCAATT-AAGAACAAA
5441497 TTTTCAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.62, C:0.19, G:0.04, T:0.15
Consensus pattern (24 bp):
AACACAAATTCAATTAAGAACAAA
Found at i:5442407 original size:21 final size:21
Alignment explanation
Indices: 5442366--5442450 Score: 75
Period size: 21 Copynumber: 4.0 Consensus size: 21
5442356 TTTTAATTAG
*
5442366 CTAACTCA-TCATTTTCATTTT
1 CTAACTCATTTATTTTC-TTTT
*
5442387 GC-AACTCATTTCTTTTCTTTT
1 -CTAACTCATTTATTTTCTTTT
**
5442408 CTAACTCATTTATTTTCTCCT
1 CTAACTCATTTATTTTCTTTT
* * *
5442429 CTAATTCACTTAATTTCTTTT
1 CTAACTCATTTATTTTCTTTT
5442450 C
1 C
5442451 AAGAATATTA
Statistics
Matches: 51, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
20 1 0.02
21 43 0.84
22 7 0.14
ACGTcount: A:0.20, C:0.25, G:0.01, T:0.54
Consensus pattern (21 bp):
CTAACTCATTTATTTTCTTTT
Found at i:5444554 original size:13 final size:13
Alignment explanation
Indices: 5444536--5444562 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5444526 AAAATTGTCC
5444536 ATGTATCGATACA
1 ATGTATCGATACA
5444549 ATGTATCGATACA
1 ATGTATCGATACA
5444562 A
1 A
5444563 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:5446769 original size:40 final size:40
Alignment explanation
Indices: 5446714--5446789 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
5446704 GACACACTTT
* * *
5446714 TTTCCTTTTGTCCTCAAGGAGCAAGACTCATTTCATCTCC
1 TTTCCCTTTATCCTCAAGGAGCAAGACCCATTTCATCTCC
* *
5446754 TTTCCCTTTATCCTCAATGAGCAAGGCCCATTTCAT
1 TTTCCCTTTATCCTCAAGGAGCAAGACCCATTTCAT
5446790 TTTTTTTCCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.21, C:0.30, G:0.12, T:0.37
Consensus pattern (40 bp):
TTTCCCTTTATCCTCAAGGAGCAAGACCCATTTCATCTCC
Found at i:5446798 original size:40 final size:40
Alignment explanation
Indices: 5446710--5446798 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 40
5446700 GTAGGACACA
* * *
5446710 CTTTTTTCCTTTTGTCCTCAAGGAGCAAGACTCATTTCAT
1 CTTTTTTCCCTTTATCCTCAAGGAGCAAGACCCATTTCAT
** * *
5446750 CTCCTTTCCCTTTATCCTCAATGAGCAAGGCCCATTTCAT
1 CTTTTTTCCCTTTATCCTCAAGGAGCAAGACCCATTTCAT
*
5446790 TTTTTTTCC
1 CTTTTTTCC
5446799 TCATCCTTAA
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.18, C:0.29, G:0.10, T:0.43
Consensus pattern (40 bp):
CTTTTTTCCCTTTATCCTCAAGGAGCAAGACCCATTTCAT
Found at i:5446963 original size:31 final size:31
Alignment explanation
Indices: 5446928--5447108 Score: 159
Period size: 31 Copynumber: 5.8 Consensus size: 31
5446918 AACCCACACG
*
5446928 AGTTGGTGGCACTCTAGTCAAAGCCCATACA
1 AGTTGGTGGCACCCTAGTCAAAGCCCATACA
* * * * *
5446959 AGTTGGTGGTACCCGAGTCTAAGCCCACACG
1 AGTTGGTGGCACCCTAGTCAAAGCCCATACA
* *
5446990 AGTTTGTGGCACTCTAGTCAAAGCCCATACA
1 AGTTGGTGGCACCCTAGTCAAAGCCCATACA
* * *
5447021 AGTTGGTGGTACCCGAGTCTAAG-CC-TACA
1 AGTTGGTGGCACCCTAGTCAAAGCCCATACA
* * *
5447050 TGAGTTCGTGGCACCCTAATCAAAGCCCACACA
1 --AGTTGGTGGCACCCTAGTCAAAGCCCATACA
* * * * *
5447083 AGCTGGCGACACCCAAGTCTAAGCCC
1 AGTTGGTGGCACCCTAGTCAAAGCCC
5447109 GCACGAGTTG
Statistics
Matches: 115, Mismatches: 31, Indels: 8
0.75 0.20 0.05
Matches are distributed among these distances:
29 4 0.03
30 2 0.02
31 104 0.90
32 2 0.02
33 3 0.03
ACGTcount: A:0.27, C:0.29, G:0.23, T:0.20
Consensus pattern (31 bp):
AGTTGGTGGCACCCTAGTCAAAGCCCATACA
Found at i:5447017 original size:62 final size:62
Alignment explanation
Indices: 5446920--5447117 Score: 279
Period size: 62 Copynumber: 3.2 Consensus size: 62
5446910 CTTTTTTAAA
*
5446920 CCCACACGAGTTGGTGGCACTCTAGTCAAAGCCCATACAAGTTGGTGGTACCCGAGTCTAAG
1 CCCACACGAGTTCGTGGCACTCTAGTCAAAGCCCATACAAGTTGGTGGTACCCGAGTCTAAG
*
5446982 CCCACACGAGTTTGTGGCACTCTAGTCAAAGCCCATACAAGTTGGTGGTACCCGAGTCTAAG
1 CCCACACGAGTTCGTGGCACTCTAGTCAAAGCCCATACAAGTTGGTGGTACCCGAGTCTAAG
* * * * * * * ** *
5447044 CCTACATGAGTTCGTGGCACCCTAATCAAAGCCCACACAAGCTGGCGACACCCAAGTCTAAG
1 CCCACACGAGTTCGTGGCACTCTAGTCAAAGCCCATACAAGTTGGTGGTACCCGAGTCTAAG
*
5447106 CCCGCACGAGTT
1 CCCACACGAGTT
5447118 GACAACACCT
Statistics
Matches: 121, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 121 1.00
ACGTcount: A:0.27, C:0.30, G:0.23, T:0.20
Consensus pattern (62 bp):
CCCACACGAGTTCGTGGCACTCTAGTCAAAGCCCATACAAGTTGGTGGTACCCGAGTCTAAG
Found at i:5447147 original size:124 final size:124
Alignment explanation
Indices: 5446927--5447153 Score: 287
Period size: 124 Copynumber: 1.8 Consensus size: 124
5446917 AAACCCACAC
* * * * * * ** *
5446927 GAGTTGGTGGCACTCTAGTCAAAGCCCATACAAGTTGGTGGTACCCGAGTCTAAGCCCACACGAG
1 GAGTTCGTGGCACCCTAATCAAAGCCCACACAAGCTGGCGACACCCAAGTCTAAGCCCACACGAG
*** *
5446992 TTTGTGGCACTCTAGTCAAAGCCCATACAAGTTGGTGGTACCCGAGTCTAAGCCTACAT
66 TTTGCAACACTCTAGTCAAAGCCCACACAAGTTGGTGGTACCCGAGTCTAAGCCTACAT
*
5447051 GAGTTCGTGGCACCCTAATCAAAGCCCACACAAGCTGGCGACACCCAAGTCTAAGCCCGCACGAG
1 GAGTTCGTGGCACCCTAATCAAAGCCCACACAAGCTGGCGACACCCAAGTCTAAGCCCACACGAG
*
5447116 -TTGACAACAC-CTAAGTCAAAGTCCACACAAGTTGGTGG
66 TTTG-CAACACTCT-AGTCAAAGCCCACACAAGTTGGTGG
5447154 CACGTAAGTC
Statistics
Matches: 86, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
123 5 0.06
124 81 0.94
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.20
Consensus pattern (124 bp):
GAGTTCGTGGCACCCTAATCAAAGCCCACACAAGCTGGCGACACCCAAGTCTAAGCCCACACGAG
TTTGCAACACTCTAGTCAAAGCCCACACAAGTTGGTGGTACCCGAGTCTAAGCCTACAT
Found at i:5447149 original size:31 final size:31
Alignment explanation
Indices: 5447064--5447149 Score: 93
Period size: 31 Copynumber: 2.8 Consensus size: 31
5447054 TTCGTGGCAC
* * *
5447064 CCTAA-TCAAAGCCCACACAAGCTGGCGACA
1 CCTAAGTCAAAGCCCACACAAGTTGACAACA
* * * *
5447094 CCCAAGTCTAAGCCCGCACGAGTTGACAACA
1 CCTAAGTCAAAGCCCACACAAGTTGACAACA
*
5447125 CCTAAGTCAAAGTCCACACAAGTTG
1 CCTAAGTCAAAGCCCACACAAGTTG
5447150 GTGGCACGTA
Statistics
Matches: 43, Mismatches: 12, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
30 4 0.09
31 39 0.91
ACGTcount: A:0.35, C:0.34, G:0.17, T:0.14
Consensus pattern (31 bp):
CCTAAGTCAAAGCCCACACAAGTTGACAACA
Found at i:5447911 original size:20 final size:21
Alignment explanation
Indices: 5447867--5447940 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
5447857 TTTTACAATT
* *
5447867 TGTATCGATATAAACAGTAAA
1 TGTATCGATACATACAGTAAA
*
5447888 TGTATCGATACATA-AGTGAA
1 TGTATCGATACATACAGTAAA
* * *
5447908 TGTATAGATACATGC-CTAAAA
1 TGTATCGATACATACAGT-AAA
5447929 TGTATCGATACA
1 TGTATCGATACA
5447941 AAATCACCTC
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
20 18 0.42
21 25 0.58
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATACAGTAAA
Found at i:5453188 original size:20 final size:20
Alignment explanation
Indices: 5453132--5453192 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
5453122 TCAAATTAAA
5453132 AACAATTTTCCACAAAACATC
1 AACAA-TTTCCACAAAACATC
** *
5453153 AACAATTAACATCAAAA-GTC
1 AACAATTTCCA-CAAAACATC
5453173 AACAATGTTCCACAAAACAT
1 AACAAT-TTCCACAAAACAT
5453193 AGGATCAATG
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
20 17 0.55
21 14 0.45
ACGTcount: A:0.51, C:0.25, G:0.03, T:0.21
Consensus pattern (20 bp):
AACAATTTCCACAAAACATC
Found at i:5459083 original size:21 final size:21
Alignment explanation
Indices: 5459034--5459089 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
5459024 ACTGTTGGGC
*
5459034 TAAATGTATCAATACAATTCT
1 TAAATGTATCGATACAATTCT
*
5459055 T-GATGTATCGATACAA-TCT
1 TAAATGTATCGATACAATTCT
5459074 TAAAATGTATCGATAC
1 T-AAATGTATCGATAC
5459090 GATTTCAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 4 0.13
20 13 0.43
21 13 0.43
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (21 bp):
TAAATGTATCGATACAATTCT
Found at i:5459107 original size:22 final size:21
Alignment explanation
Indices: 5459058--5459133 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
5459048 CAATTCTTGA
* *
5459058 TGTATCGATACAATCTT-AAAA
1 TGTATCGATACAAT-TTCATAG
*
5459079 TGTATCGATACGATTTCA-AGG
1 TGTATCGATACAATTTCATA-G
*
5459100 TTGTATCGATATAATTTCATAG
1 -TGTATCGATACAATTTCATAG
5459122 TGTATCGATACA
1 TGTATCGATACA
5459134 TAGCAATTTG
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
20 3 0.07
21 25 0.54
22 17 0.37
23 1 0.02
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (21 bp):
TGTATCGATACAATTTCATAG
Found at i:5459147 original size:20 final size:19
Alignment explanation
Indices: 5459122--5459188 Score: 63
Period size: 20 Copynumber: 3.7 Consensus size: 19
5459112 AATTTCATAG
5459122 TGTATCGATACATAGCAATT
1 TGTATCGATACATAGCAA-T
5459142 TGTATCGAT--AT---AAT
1 TGTATCGATACATAGCAAT
* *
5459156 TATATCGATACTTAGCAACT
1 TGTATCGATACATAGCAA-T
5459176 TGTATCGATACAT
1 TGTATCGATACAT
5459189 CTGCATGAGT
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
14 9 0.24
15 2 0.05
16 1 0.03
18 2 0.05
19 2 0.05
20 21 0.57
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.37
Consensus pattern (19 bp):
TGTATCGATACATAGCAAT
Found at i:5464792 original size:44 final size:44
Alignment explanation
Indices: 5464739--5464827 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 44
5464729 TAAAGTCATA
* * *
5464739 ATAATGAAATAAATTATTTTGTGATAATAAAATAAAATTAAAAT
1 ATAATGAAATAAATTATTCTATGAGAATAAAATAAAATTAAAAT
** * *
5464783 ATAATGAAATATGTTATTCTATGAGAATTAAATAAAGTTAAAAT
1 ATAATGAAATAAATTATTCTATGAGAATAAAATAAAATTAAAAT
5464827 A
1 A
5464828 AAATAGAATA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.54, C:0.01, G:0.09, T:0.36
Consensus pattern (44 bp):
ATAATGAAATAAATTATTCTATGAGAATAAAATAAAATTAAAAT
Found at i:5465369 original size:29 final size:29
Alignment explanation
Indices: 5465336--5465394 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
5465326 GAAACGGCCA
5465336 GCATTAGGATTATATAATTATTAATTTAG
1 GCATTAGGATTATATAATTATTAATTTAG
*
5465365 GCATTAGGATTATATAATTATTATTTTAG
1 GCATTAGGATTATATAATTATTAATTTAG
5465394 G
1 G
5465395 ATACAGATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.36, C:0.03, G:0.15, T:0.46
Consensus pattern (29 bp):
GCATTAGGATTATATAATTATTAATTTAG
Found at i:5466965 original size:19 final size:20
Alignment explanation
Indices: 5466931--5466970 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
5466921 TACTAATATT
5466931 TTTTTTCTTCTCTTTCACAC
1 TTTTTTCTTCTCTTTCACAC
5466951 TTTTTTCTTCT-TTTCACAC
1 TTTTTTCTTCTCTTTCACAC
5466970 T
1 T
5466971 GATCGCTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.10, C:0.28, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTTTCTTCTCTTTCACAC
Found at i:5467704 original size:26 final size:26
Alignment explanation
Indices: 5467668--5467752 Score: 109
Period size: 26 Copynumber: 3.3 Consensus size: 26
5467658 TTTATAGAGA
*
5467668 TAGGATTGATAAAATTCAATTTTATC
1 TAGGATTGATAAAATTCAACTTTATC
*
5467694 TAGGATTGATAAAATTCAACTTTATT
1 TAGGATTGATAAAATTCAACTTTATC
* * *
5467720 TTGGATT-ACTAAAGTTAAACTTTATC
1 TAGGATTGA-TAAAATTCAACTTTATC
5467746 TAGGATT
1 TAGGATT
5467753 CTAGTTAAGT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
25 1 0.02
26 50 0.98
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.42
Consensus pattern (26 bp):
TAGGATTGATAAAATTCAACTTTATC
Found at i:5470133 original size:20 final size:20
Alignment explanation
Indices: 5470108--5470164 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
5470098 TTTTCACAAT
5470108 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
*
5470128 TTGTATCGATACAGTGTTCA
1 TTGTATCGATACATTGTTCA
*
5470148 TTGTATTGATACATTGT
1 TTGTATCGATACATTGT
5470165 ATCGATACAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.25, C:0.12, G:0.18, T:0.46
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:5470164 original size:13 final size:13
Alignment explanation
Indices: 5470146--5470175 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5470136 ATACAGTGTT
*
5470146 CATTGTATTGATA
1 CATTGTATCGATA
5470159 CATTGTATCGATA
1 CATTGTATCGATA
5470172 CATT
1 CATT
5470176 CTGGGTTTAC
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:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:5470216 original size:18 final size:19
Alignment explanation
Indices: 5470191--5470263 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 19
5470181 TTTACCCAGA
5470191 TGTATCGATACATTTTGCA-
1 TGTATCGATACATTTT-CAT
*
5470210 T-TATCGATACATTGCTCAT
1 TGTATCGATACATT-TTCAT
5470229 TGTATCGATACATTTT-AT
1 TGTATCGATACATTTTCAT
*
5470247 AATGTATCGATATATTT
1 --TGTATCGATACATTT
5470264 AGGCATTTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
18 16 0.35
19 4 0.09
20 26 0.57
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (19 bp):
TGTATCGATACATTTTCAT
Found at i:5470236 original size:20 final size:19
Alignment explanation
Indices: 5470190--5470242 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
5470180 GTTTACCCAG
*
5470190 ATGTATCGATACATTTTGC
1 ATGTATCGATACATTCTGC
5470209 AT-TATCGATACATTGCT-C
1 ATGTATCGATACATT-CTGC
5470227 ATTGTATCGATACATT
1 A-TGTATCGATACATT
5470243 TTATAATGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 14 0.47
19 4 0.13
20 12 0.40
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (19 bp):
ATGTATCGATACATTCTGC
Found at i:5472708 original size:28 final size:28
Alignment explanation
Indices: 5472646--5472717 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
5472636 TTTCATAATC
5472646 AGGGG-TACTCCAACCCCGTTATGTCAT
1 AGGGGATACTCCAACCCCGTTATGTCAT
* * * *
5472673 CGGCGATACTCCAATCCCGTTATTTC-T
1 AGGGGATACTCCAACCCCGTTATGTCAT
5472700 GAGGGGATACTCCAACCC
1 -AGGGGATACTCCAACCC
5472718 TGATTTTATT
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
27 4 0.11
28 32 0.89
ACGTcount: A:0.22, C:0.32, G:0.21, T:0.25
Consensus pattern (28 bp):
AGGGGATACTCCAACCCCGTTATGTCAT
Found at i:5472748 original size:107 final size:107
Alignment explanation
Indices: 5472562--5472766 Score: 274
Period size: 107 Copynumber: 1.9 Consensus size: 107
5472552 TTTAGATTTT
*
5472562 TCATCAGGGATACTCCAACCCTGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATATTTAAA
1 TCATCAGGGATACTCCAACCCTGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATATTTAAA
***
5472627 ATATTGATTTTTCATAATCAGGGG-TACTCCAACCCCGTTATG
66 ATACCAATTTTTCATAATC-GGGGATACTCCAACCCCGTTATG
* * *
5472669 TCATC-GGCGATACTCCAATCCC-GTTATTTCTGAGGGGATACTCCAACCCTGATTTTAT-TTCT
1 TCATCAGG-GATACTCCAA-CCCTGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATATT-T
*
5472731 TAAATACCAATTTTTCATAATCGGGGATACTCCAAC
63 AAAATACCAATTTTTCATAATCGGGGATACTCCAAC
5472767 TTCGATTTTA
Statistics
Matches: 86, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
106 8 0.09
107 75 0.87
108 3 0.03
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (107 bp):
TCATCAGGGATACTCCAACCCTGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATATTTAAA
ATACCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATG
Found at i:5472763 original size:51 final size:51
Alignment explanation
Indices: 5472702--5472821 Score: 156
Period size: 51 Copynumber: 2.4 Consensus size: 51
5472692 TTATTTCTGA
* *
5472702 GGGGATACTCCAACCCTGATTTTA-TTTCTTAAATACCAATTTT-TCATAATC
1 GGGGATACTCCAACCCTGATTTTATTTTC-AAAACACCAATTTTCT-ATAATC
*
5472753 GGGGATACTCCAA-CTTCGATTTTATTTTCAAAACACCAATTTTCTATAATC
1 GGGGATACTCCAACCCT-GATTTTATTTTCAAAACACCAATTTTCTATAATC
*
5472804 AGGGATACTCCAACCCTG
1 GGGGATACTCCAACCCTG
5472822 TTATTTCGAG
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
50 2 0.03
51 51 0.85
52 7 0.12
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (51 bp):
GGGGATACTCCAACCCTGATTTTATTTTCAAAACACCAATTTTCTATAATC
Found at i:5472842 original size:78 final size:79
Alignment explanation
Indices: 5472753--5472972 Score: 291
Period size: 78 Copynumber: 2.8 Consensus size: 79
5472743 TTTCATAATC
* * *
5472753 GGGGATACTCCAACTTCGATTTTATTTTCAAAACACCAATTTTCTATAATCAGGGATACTCCAAC
1 GGGGATACTCCAACTCCGATTTTACTTTCAAAACACCGATTTTCTATAATCAGGGATACTCCAAC
5472818 CCTGTTATTT-CGA
66 CCTGTTATTTCCGA
* * * ** * *
5472831 GGGGATACTCCAACCCCGATTTTAGTTTCAAAATATTGATTTTCAATAATCAGGGATATTCCAAC
1 GGGGATACTCCAACTCCGATTTTACTTTCAAAACACCGATTTTCTATAATCAGGGATACTCCAAC
5472896 CCTGTTATTTCCGA
66 CCTGTTATTTCCGA
* * * *
5472910 GGGGATACTCCAAATCCGATTTTACTTCCAAAACACCGATTTT-TCATAGTCGGGGATACTCCA
1 GGGGATACTCCAACTCCGATTTTACTTTCAAAACACCGATTTTCT-ATAATCAGGGATACTCCA
5472973 GCCTCGTTAT
Statistics
Matches: 120, Mismatches: 20, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
78 66 0.55
79 54 0.45
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (79 bp):
GGGGATACTCCAACTCCGATTTTACTTTCAAAACACCGATTTTCTATAATCAGGGATACTCCAAC
CCTGTTATTTCCGA
Found at i:5474881 original size:20 final size:20
Alignment explanation
Indices: 5474844--5474897 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
5474834 TTCTATAATT
* *
5474844 TGTATCGATACAATAAGTTAA
1 TGTATCAATAC-ATAAGTGAA
*
5474865 TGTTTCAATACATAAGTGAA
1 TGTATCAATACATAAGTGAA
*
5474885 TGTATCGATACAT
1 TGTATCAATACAT
5474898 GCTTAAAATG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 19 0.68
21 9 0.32
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (20 bp):
TGTATCAATACATAAGTGAA
Found at i:5475000 original size:21 final size:21
Alignment explanation
Indices: 5474974--5475032 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
5474964 TACGTAAGTA
5474974 AATGTATCGATACATTCTCAT
1 AATGTATCGATACATTCTCAT
* * *
5474995 AATGTAACTATACATTTTTCAT
1 AATGTATCGATACA-TTCTCAT
5475017 --TGTATCGATACATTCT
1 AATGTATCGATACATTCT
5475033 TGGTTTCTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
19 3 0.10
20 10 0.32
21 12 0.39
22 6 0.19
ACGTcount: A:0.32, C:0.17, G:0.08, T:0.42
Consensus pattern (21 bp):
AATGTATCGATACATTCTCAT
Found at i:5475027 original size:20 final size:21
Alignment explanation
Indices: 5474975--5475030 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
5474965 ACGTAAGTAA
5474975 ATGTATCGATACA-TTCTCAT
1 ATGTATCGATACATTTCTCAT
* * *
5474995 AATGTAACTATACATTTTTCAT
1 -ATGTATCGATACATTTCTCAT
5475017 -TGTATCGATACATT
1 ATGTATCGATACATT
5475031 CTTGGTTTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 12 0.41
21 11 0.38
22 6 0.21
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.43
Consensus pattern (21 bp):
ATGTATCGATACATTTCTCAT
Found at i:5478224 original size:27 final size:28
Alignment explanation
Indices: 5478182--5478241 Score: 95
Period size: 27 Copynumber: 2.2 Consensus size: 28
5478172 CAGGATCGAT
*
5478182 GTTTCGAGTTTAGTAAC-CCAAACATAG
1 GTTTCGAGTTTAGTAACTCAAAACATAG
*
5478209 GTTTCGAGTTTTGTAACTCAAAACATAG
1 GTTTCGAGTTTAGTAACTCAAAACATAG
5478237 GTTTC
1 GTTTC
5478242 AATAGGTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 16 0.53
28 14 0.47
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (28 bp):
GTTTCGAGTTTAGTAACTCAAAACATAG
Found at i:5478649 original size:105 final size:105
Alignment explanation
Indices: 5478482--5478678 Score: 349
Period size: 105 Copynumber: 1.9 Consensus size: 105
5478472 TGCTTATACA
5478482 TTAGTTGTTACAGAGAGCATTATTTCTAATGAACCAAGGTCATATAAAGAGATAGTACAGAGTAA
1 TTAGTTGTTACAGAGAGCATTATTTCTAATGAACCAAGGTCATATAAAGAGATAGTACAGAGTAA
*
5478547 AGAAGCATCAGAATGGTTGATTGCCATTACTACTTATGCG
66 AGAAGCATCAAAATGGTTGATTGCCATTACTACTTATGCG
* * *
5478587 TTAGTTGTTGCAGAGAGCATTATTTCTAATGAACCAAGGTCATATAAAGAGGTAGTATAGAGTAA
1 TTAGTTGTTACAGAGAGCATTATTTCTAATGAACCAAGGTCATATAAAGAGATAGTACAGAGTAA
*
5478652 AGAAGCATCAAAATGGTTGATTTCCAT
66 AGAAGCATCAAAATGGTTGATTGCCAT
5478679 GAATGAAGAG
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
105 87 1.00
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (105 bp):
TTAGTTGTTACAGAGAGCATTATTTCTAATGAACCAAGGTCATATAAAGAGATAGTACAGAGTAA
AGAAGCATCAAAATGGTTGATTGCCATTACTACTTATGCG
Found at i:5480404 original size:23 final size:23
Alignment explanation
Indices: 5480378--5480425 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
5480368 AGAACTCTAA
* *
5480378 TAAAGTTAAACTTTATTTGGGAT
1 TAAAGTTAAACTTTATCTGAGAT
*
5480401 TAAAGTTTAACTTTATCTGAGAT
1 TAAAGTTAAACTTTATCTGAGAT
5480424 TA
1 TA
5480426 CTAAAGTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (23 bp):
TAAAGTTAAACTTTATCTGAGAT
Found at i:5488285 original size:2 final size:2
Alignment explanation
Indices: 5488278--5488309 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5488268 GACACAGGTA
5488278 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
5488310 ATATATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:5488798 original size:2 final size:2
Alignment explanation
Indices: 5488791--5488826 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5488781 TAATTAAGAG
5488791 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5488827 GACTTGAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5490131 original size:14 final size:14
Alignment explanation
Indices: 5490112--5490170 Score: 52
Period size: 13 Copynumber: 4.2 Consensus size: 14
5490102 ATATATTAAA
5490112 ATATAAATTATAAT
1 ATATAAATTATAAT
*
5490126 ATATAAAATATTTAAT
1 ATAT-AAAT-TATAAT
5490142 A-ATAAA-TAGTAA-
1 ATATAAATTA-TAAT
*
5490154 ATATAAATAATAAT
1 ATATAAATTATAAT
5490168 ATA
1 ATA
5490171 ATAGTTAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 12
0.71 0.06 0.24
Matches are distributed among these distances:
12 2 0.06
13 11 0.31
14 11 0.31
15 6 0.17
16 6 0.17
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (14 bp):
ATATAAATTATAAT
Found at i:5491815 original size:22 final size:21
Alignment explanation
Indices: 5491764--5491815 Score: 50
Period size: 22 Copynumber: 2.4 Consensus size: 21
5491754 CATAAAGGTC
* *
5491764 TTTTTTGTTTCTCTTTCTTCA
1 TTTTTTTTTTCTCCTTCTTCA
**
5491785 TTACCTTTTTTCTCCTTCTTCA
1 TT-TTTTTTTTCTCCTTCTTCA
*
5491807 ATTTTTTTT
1 TTTTTTTTT
5491816 ATTTTTACTA
Statistics
Matches: 23, Mismatches: 7, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.08, C:0.21, G:0.02, T:0.69
Consensus pattern (21 bp):
TTTTTTTTTTCTCCTTCTTCA
Found at i:5496397 original size:18 final size:18
Alignment explanation
Indices: 5496374--5496417 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
5496364 TTTTCTCGAG
5496374 TTTAATTTTAGTCAT-AAT
1 TTTAATTTTAGT-ATCAAT
*
5496392 TTTAATTTTAGTTTCAAT
1 TTTAATTTTAGTATCAAT
5496410 TTTAATTT
1 TTTAATTT
5496418 CAGAGAATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 1 0.04
18 23 0.96
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.61
Consensus pattern (18 bp):
TTTAATTTTAGTATCAAT
Found at i:5497106 original size:3 final size:3
Alignment explanation
Indices: 5497100--5497129 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
5497090 ATTGATGATT
5497100 TTA TTA TTA TTAA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TT
5497130 GTTTTGCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5500915 original size:15 final size:15
Alignment explanation
Indices: 5500897--5500925 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5500887 TTATTTAACT
5500897 TTAATTTTTTTATTC
1 TTAATTTTTTTATTC
5500912 TTAATTTTTTTATT
1 TTAATTTTTTTATT
5500926 TAGTTACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (15 bp):
TTAATTTTTTTATTC
Found at i:5504564 original size:2 final size:2
Alignment explanation
Indices: 5504553--5504582 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5504543 GTGTGTAAAA
*
5504553 AT AT AA 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
5504583 GATGAGATGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5504964 original size:11 final size:11
Alignment explanation
Indices: 5504948--5505049 Score: 50
Period size: 11 Copynumber: 9.0 Consensus size: 11
5504938 TATAATTATG
5504948 TAATA-TAATA
1 TAATATTAATA
*
5504958 TTAATATTTATA
1 -TAATATTAATA
*
5504970 TAATATATAAAA
1 TAATAT-TAATA
*
5504982 TAAT-TAAAATA
1 TAATAT-TAATA
5504993 TAATATATAA-A
1 TAATAT-TAATA
* *
5505004 TAAAATAAATA
1 TAATATTAATA
*
5505015 TAATATTTATA
1 TAATATTAATA
*
5505026 T-TTATATAATA
1 TAATAT-TAATA
5505037 TAAATTATTAATA
1 T-AA-TATTAATA
5505050 CATTAAAATT
Statistics
Matches: 69, Mismatches: 14, Indels: 14
0.71 0.14 0.14
Matches are distributed among these distances:
10 5 0.07
11 41 0.59
12 15 0.22
13 5 0.07
14 3 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TAATATTAATA
Found at i:5504973 original size:22 final size:22
Alignment explanation
Indices: 5504943--5505049 Score: 82
Period size: 22 Copynumber: 5.0 Consensus size: 22
5504933 TATACTATAA
*
5504943 TTATGTAATATAATATTAATAT
1 TTATATAATATAATATTAATAT
* *
5504965 TTATATAATAT-ATA-AAATAA
1 TTATATAATATAATATTAATAT
5504985 TTA-A-AATATAATATATAA-A-
1 TTATATAATATAATAT-TAATAT
* * *
5505004 TAAAATAAATATAATATTTATAT
1 TTATAT-AATATAATATTAATAT
5505027 TTATATAATATAAATTATTAATA
1 TTATATAATAT-AA-TATTAATA
5505050 CATTAAAATT
Statistics
Matches: 66, Mismatches: 9, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
18 5 0.08
19 6 0.09
20 9 0.14
21 7 0.11
22 26 0.39
23 6 0.09
24 7 0.11
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (22 bp):
TTATATAATATAATATTAATAT
Found at i:5504993 original size:23 final size:22
Alignment explanation
Indices: 5504967--5505020 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 22
5504957 ATTAATATTT
*
5504967 ATATAATATATAAA-ATAATTAAA
1 ATATAATATATAAATA-AAAT-AA
5504990 ATATAATATATAAATAAAATAA
1 ATATAATATATAAATAAAATAA
5505012 ATATAATAT
1 ATATAATAT
5505021 TTATATTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 11 0.38
23 17 0.59
24 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
ATATAATATATAAATAAAATAA
Found at i:5504995 original size:16 final size:18
Alignment explanation
Indices: 5504949--5505016 Score: 61
Period size: 18 Copynumber: 3.9 Consensus size: 18
5504939 ATAATTATGT
* *
5504949 AATATAATATTAATATTTA
1 AATAAAATA-TAATATATA
* *
5504968 TATAATATATAA-A-ATA
1 AATAAAATATAATATATA
*
5504984 ATTAAAATATAATATATA
1 AATAAAATATAATATATA
5505002 AATAAAATA-AATATA
1 AATAAAATATAATATA
5505017 ATATTTATAT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
16 11 0.28
17 8 0.21
18 14 0.36
19 6 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AATAAAATATAATATATA
Found at i:5505060 original size:17 final size:15
Alignment explanation
Indices: 5505038--5505071 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
5505028 TATATAATAT
5505038 AAATTATTAATACATTA
1 AAATTATT-ATA-ATTA
5505055 AAATTATTATAATTA
1 AAATTATTATAATTA
5505070 AA
1 AA
5505072 TAATATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 3 0.18
17 8 0.47
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
AAATTATTATAATTA
Found at i:5505077 original size:62 final size:60
Alignment explanation
Indices: 5504938--5505077 Score: 151
Period size: 62 Copynumber: 2.3 Consensus size: 60
5504928 TTGAATATAC
**
5504938 TATAATTATGTAATATAATATTAATATTTATATAATATATAAAATAATTAAAATATAATA
1 TATAATTAAATAATATAATATTAATATTTATATAATATATAAAATAATTAAAATATAATA
* * *
5504998 TATAAATAAAATAAATATAATATTTATATTTATATAATATAAATTATTAATACATTAAAAT-T-A
1 TAT-AATTAAAT-AATATAATATTAATATTTATATAATAT--A-TA-AAATA-ATTAAAATATAA
5505061 T-
59 TA
5505062 TATAATTAAATAATAT
1 TATAATTAAATAATAT
5505078 TTTAAATATA
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
60 3 0.04
61 5 0.07
62 31 0.46
63 7 0.10
64 4 0.06
65 4 0.06
66 5 0.07
67 8 0.12
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.44
Consensus pattern (60 bp):
TATAATTAAATAATATAATATTAATATTTATATAATATATAAAATAATTAAAATATAATA
Found at i:5506206 original size:13 final size:13
Alignment explanation
Indices: 5506190--5506216 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5506180 AAAAAAAATA
5506190 TTTAATATATATT
1 TTTAATATATATT
5506203 TTTAATATATATT
1 TTTAATATATATT
5506216 T
1 T
5506217 AAATATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTAATATATATT
Done.