Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 76 of 103
Found at i:28502894 original size:10 final size:10
Alignment explanation
Indices: 28502879--28502944 Score: 96
Period size: 10 Copynumber: 6.6 Consensus size: 10
28502869 CCCCACTAGC
28502879 ATATATATAT
1 ATATATATAT
28502889 ATATATATAT
1 ATATATATAT
28502899 ATATATATAT
1 ATATATATAT
28502909 ATATATATAT
1 ATATATATAT
* *
28502919 ACATACATAT
1 ATATATATAT
* *
28502929 ACATATACAT
1 ATATATATAT
28502939 ATATAT
1 ATATAT
28502945 TATTTAAATT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 51 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (10 bp):
ATATATATAT
Found at i:28503560 original size:4 final size:4
Alignment explanation
Indices: 28503551--28503615 Score: 94
Period size: 4 Copynumber: 16.2 Consensus size: 4
28503541 ACCCCACTAG
* *
28503551 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA CATA CATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* *
28503599 TACA TATA CATA TATA T
1 TATA TATA TATA TATA T
28503616 TATTTAAATT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 55 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (4 bp):
TATA
Found at i:28503562 original size:6 final size:6
Alignment explanation
Indices: 28503551--28503615 Score: 94
Period size: 6 Copynumber: 10.8 Consensus size: 6
28503541 ACCCCACTAG
* *
28503551 TATATA TATATA TATATA TATATA TATATA TATATA TATACA TACATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* *
28503599 TACATA TACATA TATAT
1 TATATA TATATA TATAT
28503616 TATTTAAATT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 55 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (6 bp):
TATATA
Found at i:28503566 original size:10 final size:10
Alignment explanation
Indices: 28503551--28503615 Score: 94
Period size: 10 Copynumber: 6.5 Consensus size: 10
28503541 ACCCCACTAG
28503551 TATATATATA
1 TATATATATA
28503561 TATATATATA
1 TATATATATA
28503571 TATATATATA
1 TATATATATA
28503581 TATATATATA
1 TATATATATA
* *
28503591 CATACATATA
1 TATATATATA
* *
28503601 CATATACATA
1 TATATATATA
28503611 TATAT
1 TATAT
28503616 TATTTAAATT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 50 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (10 bp):
TATATATATA
Found at i:28520557 original size:24 final size:25
Alignment explanation
Indices: 28520530--28520576 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
28520520 AGTAATTATA
28520530 AATTGATTTT-AAAAAATT-GAATCG
1 AATT-ATTTTCAAAAAATTAGAATCG
*
28520554 AATTTTTTTCAAAAAATTAGAAT
1 AATTATTTTCAAAAAATTAGAAT
28520577 ATTTTGTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 12 0.60
25 4 0.20
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (25 bp):
AATTATTTTCAAAAAATTAGAATCG
Found at i:28527051 original size:22 final size:23
Alignment explanation
Indices: 28527009--28527053 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
28526999 GGACATGCAC
28527009 ATGACGTGAATGTATAACAATTT
1 ATGACGTGAATGTATAACAATTT
* *
28527032 ATGACGTG-CTGTGTAACAATTT
1 ATGACGTGAATGTATAACAATTT
28527054 TTTCATCATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (23 bp):
ATGACGTGAATGTATAACAATTT
Found at i:28527107 original size:28 final size:29
Alignment explanation
Indices: 28527049--28527108 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 29
28527039 GCTGTGTAAC
* * * * *
28527049 AATTTTTTCATCATGATGTGTAATAATTA
1 AATTTTTTAATCATAATGTATAACAACTA
28527078 AATTTTTTAAT-ATAATGTATAACAACTA
1 AATTTTTTAATCATAATGTATAACAACTA
28527106 AAT
1 AAT
28527109 CTTCGACATA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.45
Consensus pattern (29 bp):
AATTTTTTAATCATAATGTATAACAACTA
Found at i:28527138 original size:55 final size:55
Alignment explanation
Indices: 28527069--28527218 Score: 176
Period size: 55 Copynumber: 2.7 Consensus size: 55
28527059 TCATGATGTG
* * * *
28527069 TAATAATTAAATTTTTTAATATAATGTATAACAACTAAATCTTCGACATAGCGTA
1 TAATAATTAAATTTTTTAACATAATGTATAACAACTAAATCTTCAACATAACATA
* * * *
28527124 TAATAATTACATTTTTCAACAAAATGTGA-AACAACTAAATCTTCAACATAACATG
1 TAATAATTAAATTTTTTAACATAATGT-ATAACAACTAAATCTTCAACATAACATA
* * * *
28527179 TAATAATTATATTTTTTAACATGACGTATAACAATTAAAT
1 TAATAATTAAATTTTTTAACATAATGTATAACAACTAAAT
28527219 TTTTAACAGG
Statistics
Matches: 79, Mismatches: 14, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
54 1 0.01
55 77 0.97
56 1 0.01
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.37
Consensus pattern (55 bp):
TAATAATTAAATTTTTTAACATAATGTATAACAACTAAATCTTCAACATAACATA
Found at i:28527200 original size:28 final size:27
Alignment explanation
Indices: 28527073--28527226 Score: 69
Period size: 27 Copynumber: 5.6 Consensus size: 27
28527063 GATGTGTAAT
* **
28527073 AATTAAATTTTTTAATATAATGTATAAC
1 AATTAAA-TTTTTAACATAACATATAAC
* * ** * * *
28527101 AACTAAATCTTCGACATAGCGTATAAT
1 AATTAAATTTTTAACATAACATATAAC
* *
28527128 AATTACATTTTTCAACA-AA-ATGTGAAAC
1 AATTAAATTTTT-AACATAACATAT--AAC
* * * * *
28527156 AACTAAATCTTCAACATAACATGTAAT
1 AATTAAATTTTTAACATAACATATAAC
* * *
28527183 AATTATATTTTTTAACATGACGTATAAC
1 AATTA-AATTTTTAACATAACATATAAC
28527211 AATTAAATTTTTAACA
1 AATTAAATTTTTAACA
28527227 GGGTATATAA
Statistics
Matches: 89, Mismatches: 31, Indels: 13
0.67 0.23 0.10
Matches are distributed among these distances:
26 2 0.02
27 42 0.47
28 41 0.46
29 4 0.04
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.37
Consensus pattern (27 bp):
AATTAAATTTTTAACATAACATATAAC
Found at i:28527463 original size:25 final size:26
Alignment explanation
Indices: 28527421--28527496 Score: 65
Period size: 25 Copynumber: 3.1 Consensus size: 26
28527411 ACAAATGGAG
28527421 AAAAATTATTCAAATAA-TTAAAATA
1 AAAAATTATTCAAATAATTTAAAATA
*
28527446 AAAAATTATAT-AACTAATTT--AAT-
1 AAAAATTAT-TCAAATAATTTAAAATA
* *
28527469 ATAAATTATT-TAATAATTTAATAATA
1 AAAAATTATTCAAATAATTTAA-AATA
28527495 AA
1 AA
28527497 TTATTGATGT
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
22 8 0.20
23 8 0.20
24 3 0.08
25 17 0.43
26 4 0.10
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (26 bp):
AAAAATTATTCAAATAATTTAAAATA
Found at i:28527495 original size:23 final size:23
Alignment explanation
Indices: 28527423--28527501 Score: 88
Period size: 23 Copynumber: 3.3 Consensus size: 23
28527413 AAATGGAGAA
* * *
28527423 AAATTATTCAAATAATTAAAATAAA
1 AAATTATT-TAATAATT-TAATAAT
*
28527448 AAATTATATAACTAATTTAAT-AT
1 AAATTATTTAA-TAATTTAATAAT
28527471 AAATTATTTAATAATTTAATAAT
1 AAATTATTTAATAATTTAATAAT
28527494 AAATTATT
1 AAATTATT
28527502 GATGTGTAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
22 9 0.19
23 21 0.45
24 5 0.11
25 12 0.26
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (23 bp):
AAATTATTTAATAATTTAATAAT
Found at i:28527532 original size:136 final size:136
Alignment explanation
Indices: 28527355--28527636 Score: 460
Period size: 136 Copynumber: 2.1 Consensus size: 136
28527345 TTATATTGAT
* *
28527355 TAATAAATTATTGATGTTTATGAAAATAAAAATTAAAAGATTAA-AATATGAAAAATACAAATGG
1 TAATAAATTATTGATGTTAATGAAAATAAAAATTAAAAGATTAAGAA-ATGAAAAATACAAATAG
* * * *
28527419 AGAAAAATTATTCAAATAATTAAAATAAAAAATTATATAACTAATTTAAT-ATAAATTATTTAAT
65 AGAAAAATAATCCAAATAATTAAAATAAAAAATCATATAACTAATTTAATAATAAATTATTCAAT
28527483 AATTTAA
130 AATTTAA
*
28527490 TAATAAATTATTGATGTGTAATGAAAATAGAAATTAAAAGATTAAGAAATGAAAAATACAAATAG
1 TAATAAATTATTGATGT-TAATGAAAATAAAAATTAAAAGATTAAGAAATGAAAAATACAAATAG
*
28527555 AGAAAAATAATCCAAATAATTAAAATTAAAAATCATATAACTAATTTAATAATAAATTATTCAAT
65 AGAAAAATAATCCAAATAATTAAAATAAAAAATCATATAACTAATTTAATAATAAATTATTCAAT
28527620 AATTTAA
130 AATTTAA
28527627 TAATAAATTA
1 TAATAAATTA
28527637 AAATATATTA
Statistics
Matches: 136, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
135 17 0.12
136 87 0.64
137 32 0.24
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.33
Consensus pattern (136 bp):
TAATAAATTATTGATGTTAATGAAAATAAAAATTAAAAGATTAAGAAATGAAAAATACAAATAGA
GAAAAATAATCCAAATAATTAAAATAAAAAATCATATAACTAATTTAATAATAAATTATTCAATA
ATTTAA
Found at i:28527631 original size:11 final size:11
Alignment explanation
Indices: 28527591--28527674 Score: 52
Period size: 11 Copynumber: 7.6 Consensus size: 11
28527581 TAAAAATCAT
28527591 ATAACTAATTTA
1 ATAA-TAATTTA
*
28527603 ATAATAAATTA
1 ATAATAATTTA
*
28527614 TTCAATAATTTA
1 AT-AATAATTTA
*
28527626 ATAATAAATTA
1 ATAATAATTTA
28527637 A-AAT-ATATT-
1 ATAATAAT-TTA
28527646 A-AA-AATTTA
1 ATAATAATTTA
*
28527655 TATTAAAAATTTA
1 -A-TAATAATTTA
28527668 ATAATAA
1 ATAATAA
28527675 AATATTGATG
Statistics
Matches: 57, Mismatches: 7, Indels: 17
0.70 0.09 0.21
Matches are distributed among these distances:
8 2 0.04
9 6 0.11
10 6 0.11
11 21 0.37
12 16 0.28
13 6 0.11
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (11 bp):
ATAATAATTTA
Found at i:28527656 original size:13 final size:13
Alignment explanation
Indices: 28527640--28527667 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
28527630 TAAATTAAAA
28527640 TATATTAAAAATT
1 TATATTAAAAATT
28527653 TATATTAAAAATT
1 TATATTAAAAATT
28527666 TA
1 TA
28527668 ATAATAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TATATTAAAAATT
Found at i:28531946 original size:85 final size:87
Alignment explanation
Indices: 28531788--28531947 Score: 227
Period size: 85 Copynumber: 1.9 Consensus size: 87
28531778 CTCAAATTGC
28531788 GTTACATTAATAACCCTGGCCCTTAGAAGATGAATAGTAAAGAAGTTTCTATGAACCTGTTTCTG
1 GTTACATTAATAACCCTGGCCCTTAGAAGATGAATAGT-AAGAAGTTTCTATGAACCTGTTTCTG
28531853 TCATTCATCAATCATCGATGTTG
65 TCATTCATCAATCATCGATGTTG
** ** * *
28531876 GTTACATTAATAACTTTGGTCTTTTA-AAGATGAATAGT-A-AAGTTTTTATGAACTTGTTTCTG
1 GTTACATTAATAACCCTGG-CCCTTAGAAGATGAATAGTAAGAAGTTTCTATGAACCTGTTTCTG
28531938 TCATTCATCA
65 TCATTCATCA
28531948 GTGATGTTGA
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
85 31 0.48
86 1 0.02
88 29 0.45
89 4 0.06
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.39
Consensus pattern (87 bp):
GTTACATTAATAACCCTGGCCCTTAGAAGATGAATAGTAAGAAGTTTCTATGAACCTGTTTCTGT
CATTCATCAATCATCGATGTTG
Found at i:28532276 original size:95 final size:94
Alignment explanation
Indices: 28532100--28532282 Score: 228
Period size: 95 Copynumber: 1.9 Consensus size: 94
28532090 CAATTGTTAC
* * * * * * *
28532100 GTTTTATATTAATTTGTAAAATATTATTCATTTTAACTATTGAGTTTTATGATTTTGTTTTACAA
1 GTTTCATATCAATTTGTAAAATATTATTCATTTTAACTATTGAATATCATGATTTTATCTTACAA
*
28532165 AAAGTATTTAACAAATTAAAAATTATCAT
66 AAAATATTTAACAAATTAAAAATTATCAT
28532194 GTTTCATATCAATTTGTAAAATATTATTCATTTTGATA-TATTGAATATCACT-ATTTTATCTTA
1 GTTTCATATCAATTTGTAAAATATTATTCATTTT-A-ACTATTGAATATCA-TGATTTTATCTTA
*
28532257 CAAAAAATACTTT-ATAAATTAAAAAT
63 CAAAAAATA-TTTAACAAATTAAAAAT
28532283 AATGTGAACT
Statistics
Matches: 76, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
94 32 0.42
95 39 0.51
96 5 0.07
ACGTcount: A:0.40, C:0.07, G:0.06, T:0.47
Consensus pattern (94 bp):
GTTTCATATCAATTTGTAAAATATTATTCATTTTAACTATTGAATATCATGATTTTATCTTACAA
AAAATATTTAACAAATTAAAAATTATCAT
Found at i:28544147 original size:140 final size:140
Alignment explanation
Indices: 28543645--28544318 Score: 761
Period size: 140 Copynumber: 4.8 Consensus size: 140
28543635 TATATTCATT
* * * * * * * * *
28543645 TCTCACTTTAGGGGCCATTATCGGGCCCTTACTTAATTCCTTTTAATTTGAGATTTATGTCTATA
1 TCTCACTTCAAGGGCCATTATCGGACTCTTGCTTAATTCCTTTCAATTTGGGACTTATATCTATA
* * * * * *
28543710 TATCCTTGACTCTTTCCCTAAAAAGCTAATCACATGATGTCCTCATCGCCATGGATCACCTTGCC
66 TATTCTTTACTCTCTCCCTAAAAAGCTAATCAAATGATGTCCTCGTCGCCATGGACCACCTTGCC
*
28543775 TGCCTCTTCC
131 TGCCTCCTCC
* * * * * * *
28543785 TCTTACTTC-AGGTGCCATTATC-AAGCTATTGCCTAATTCTTTTTAATTTAGGACTTATATCTA
1 TCTCACTTCAAGG-GCCATTATCGGA-CTCTTGCTTAATTCCTTTCAATTTGGGACTTATATCTA
* * * * *
28543848 TATATATCTTTTACTTTCTCCCTAAAAAGCTAATAAAATGATGTCCTCGTTGCCATGGACTACCG
64 TATAT-TC-TTTACTCTCTCCCTAAAAAGCTAATCAAATGATGTCCTCGTCGCCATGGACCACCT
* *
28543913 TGGCTGCCTCTTCC
127 TGCCTGCCTCCTCC
* * * * *
28543927 TCTTAC-TCAGGGGTCATTATCAGG-CTATTG-TCTAATT-CTTTCCAATTTGAGACTTATATCT
1 TCTCACTTCAAGGGCCATTATC-GGACTCTTGCT-TAATTCCTTT-CAATTTGGGACTTATATCT
* * * *
28543988 ATATATCCTTTACTCTCTCCCTAAAAAGCTAATCAAATGATATCCTCGTCACCGTGGACCACCTT
63 ATATATTCTTTACTCTCTCCCTAAAAAGCTAATCAAATGATGTCCTCGTCGCCATGGACCACCTT
*
28544053 GCTTGCCTCCTCC
128 GCCTGCCTCCTCC
*
28544066 TCTCACTTCAAGGGCCATTATTGGACTCTTGCTTAATTCCTTTCAATTTGGGACTTATATCTATA
1 TCTCACTTCAAGGGCCATTATCGGACTCTTGCTTAATTCCTTTCAATTTGGGACTTATATCTATA
* * *
28544131 TATTCTTTACTCTCTCCCTAAAAAACTAATCAAATGATGTCTTCGTCGCCATGGACCACCTTACC
66 TATTCTTTACTCTCTCCCTAAAAAGCTAATCAAATGATGTCCTCGTCGCCATGGACCACCTTGCC
*
28544196 TGCCTCCTCT
131 TGCCTCCTCC
* * *
28544206 TCTCACTTTAAGGGCCATTATCGGGCTCTTGCTTAATTTC-TTCTAATTTGGGACTTATATCTAT
1 TCTCACTTCAAGGGCCATTATCGGACTCTTGCTTAATTCCTTTC-AATTTGGGACTTATATCTAT
* *
28544270 ATA-TCTTTTACTCTCTTCCTAAAAAGCTAATCAAATGATGTTCTCGTCG
65 ATATTC-TTTACTCTCTCCCTAAAAAGCTAATCAAATGATGTCCTCGTCG
28544319 TCATAAACCA
Statistics
Matches: 450, Mismatches: 69, Indels: 30
0.82 0.13 0.05
Matches are distributed among these distances:
139 73 0.16
140 261 0.58
141 49 0.11
142 67 0.15
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.38
Consensus pattern (140 bp):
TCTCACTTCAAGGGCCATTATCGGACTCTTGCTTAATTCCTTTCAATTTGGGACTTATATCTATA
TATTCTTTACTCTCTCCCTAAAAAGCTAATCAAATGATGTCCTCGTCGCCATGGACCACCTTGCC
TGCCTCCTCC
Found at i:28547632 original size:24 final size:24
Alignment explanation
Indices: 28547597--28547985 Score: 152
Period size: 24 Copynumber: 16.8 Consensus size: 24
28547587 ATTTGAAGTT
*
28547597 TCACAGGTTTTTGTACATGACTTG
1 TCACAGGTTTTTGTACATGGCTTG
* * *
28547621 TCACAGGCTTTTGTATATGGCGTG
1 TCACAGGTTTTTGTACATGGCTTG
* * *
28547645 TCACACG---CT-AACCATGGCTTG
1 TCACAGGTTTTTGTA-CATGGCTTG
* * *
28547666 TCATAGGCTTTTGTACATGGCGTG
1 TCACAGGTTTTTGTACATGGCTTG
* *** **
28547690 TAACA--CACTAAT-CATGGCTTG
1 TCACAGGTTTTTGTACATGGCTTG
* *
28547711 TCATAGGCTTTTGTACATGGCTTG
1 TCACAGGTTTTTGTACATGGCTTG
** ** *
28547735 TCACA--TGCTAAT-CATGGTTTG
1 TCACAGGTTTTTGTACATGGCTTG
* *
28547756 TCACAGATTTTTGTACATGGCGTG
1 TCACAGGTTTTTGTACATGGCTTG
* * * * *
28547780 TCACACG---CT-AACTATGACTTA
1 TCACAGGTTTTTGTAC-ATGGCTTG
* *
28547801 TCACAGATTTTTGTACATGGCGTG
1 TCACAGGTTTTTGTACATGGCTTG
* ** * *
28547825 TCATATTTTTTTGTACATGACGTG
1 TCACAGGTTTTTGTACATGGCTTG
* * **
28547849 TCACACG--CTAAT-CATGGCTTG
1 TCACAGGTTTTTGTACATGGCTTG
* *
28547870 TCATAGGTTTTTGTACAT-GATGTG
1 TCACAGGTTTTTGTACATGGCT-TG
*
28547894 TCACAGATTTTTGTACATGG-TGTG
1 TCACAGGTTTTTGTACATGGCT-TG
* *
28547918 TCACAGATTTTTGTACAT-GATGTG
1 TCACAGGTTTTTGTACATGGCT-TG
* *
28547942 TCACAGATTTTTGTACATGGCGTG
1 TCACAGGTTTTTGTACATGGCTTG
*
28547966 TCACAGATTTTTGTACATGG
1 TCACAGGTTTTTGTACATGG
28547986 TCTGTAACAC
Statistics
Matches: 266, Mismatches: 76, Indels: 46
0.69 0.20 0.12
Matches are distributed among these distances:
20 3 0.01
21 60 0.23
22 7 0.03
23 11 0.04
24 180 0.68
25 5 0.02
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (24 bp):
TCACAGGTTTTTGTACATGGCTTG
Found at i:28547668 original size:45 final size:45
Alignment explanation
Indices: 28547612--28547827 Score: 270
Period size: 45 Copynumber: 4.8 Consensus size: 45
28547602 GGTTTTTGTA
* *
28547612 CATGACTTGTCACAGGCTTTTGTATATGGCGTGTCACACGCTAAC
1 CATGGCTTGTCACAGGCTTTTGTACATGGCGTGTCACACGCTAAC
* * * *
28547657 CATGGCTTGTCATAGGCTTTTGTACATGGCGTGTAACACACTAAT
1 CATGGCTTGTCACAGGCTTTTGTACATGGCGTGTCACACGCTAAC
* * * *
28547702 CATGGCTTGTCATAGGCTTTTGTACATGGCTTGTCACATGCTAAT
1 CATGGCTTGTCACAGGCTTTTGTACATGGCGTGTCACACGCTAAC
* **
28547747 CATGGTTTGTCACAGATTTTTGTACATGGCGTGTCACACGCTAAC
1 CATGGCTTGTCACAGGCTTTTGTACATGGCGTGTCACACGCTAAC
* * * **
28547792 TATGACTTATCACAGATTTTTGTACATGGCGTGTCA
1 CATGGCTTGTCACAGGCTTTTGTACATGGCGTGTCA
28547828 TATTTTTTTG
Statistics
Matches: 150, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 150 1.00
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.35
Consensus pattern (45 bp):
CATGGCTTGTCACAGGCTTTTGTACATGGCGTGTCACACGCTAAC
Found at i:28547827 original size:69 final size:69
Alignment explanation
Indices: 28547754--28548035 Score: 295
Period size: 69 Copynumber: 4.0 Consensus size: 69
28547744 AATCATGGTT
*
28547754 TGTCACAGATTTTTGTACATGGCGTGTCACACGCTAACTATGACTTATCACAGATTTTTGTACAT
1 TGTCACAGATTTTTGTACATGGCGTGTCACACGCTAACTATGACTTGTCACAGATTTTTGTACAT
28547819 GGCG
66 GGCG
* ** * * * *
28547823 TGTCATATTTTTTTGTACATGACGTGTCACACGCTAA-TCATGGCTTGTCATAGGTTTTTGTACA
1 TGTCACAGATTTTTGTACATGGCGTGTCACACGCTAACT-ATGACTTGTCACAGATTTTTGTACA
**
28547887 TGATG
65 TGGCG
* * *
28547892 TGTCACAGATTTTTGTACATGGTGTGTCACA-GATTTTTGTAC-ATGA-TGTGTCACAGATTTTT
1 TGTCACAGATTTTTGTACATGGCGTGTCACACG----CT-AACTATGACT-TGTCACAGATTTTT
28547954 GTACATGGCG
60 GTACATGGCG
* * * * *
28547964 TGTCACAGATTTTTGTACATGGTC-TGTAACACACTAACCATGACTTGTTATAGATTTTTGTACA
1 TGTCACAGATTTTTGTACATGG-CGTGTCACACGCTAACTATGACTTGTCACAGATTTTTGTACA
28548028 TGGCG
65 TGGCG
28548033 TGT
1 TGT
28548036 AACATCATAA
Statistics
Matches: 172, Mismatches: 29, Indels: 24
0.76 0.13 0.11
Matches are distributed among these distances:
68 4 0.02
69 113 0.66
70 1 0.01
71 1 0.01
72 52 0.30
73 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39
Consensus pattern (69 bp):
TGTCACAGATTTTTGTACATGGCGTGTCACACGCTAACTATGACTTGTCACAGATTTTTGTACAT
GGCG
Found at i:28547932 original size:48 final size:48
Alignment explanation
Indices: 28547801--28547984 Score: 232
Period size: 48 Copynumber: 3.9 Consensus size: 48
28547791 CTATGACTTA
* ** *
28547801 TCACAGATTTTTGTACATGGCGTGTCATATTTTTTTGTACATGACGTG
1 TCACAGATTTTTGTACATGGCGTGTCACAGATTTTTGTACATGATGTG
* ** * * *
28547849 TCACACG---CTAAT-CATGGCTTGTCATAGGTTTTTGTACATGATGTG
1 TCACA-GATTTTTGTACATGGCGTGTCACAGATTTTTGTACATGATGTG
*
28547894 TCACAGATTTTTGTACATGGTGTGTCACAGATTTTTGTACATGATGTG
1 TCACAGATTTTTGTACATGGCGTGTCACAGATTTTTGTACATGATGTG
28547942 TCACAGATTTTTGTACATGGCGTGTCACAGATTTTTGTACATG
1 TCACAGATTTTTGTACATGGCGTGTCACAGATTTTTGTACATG
28547985 GTCTGTAACA
Statistics
Matches: 116, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
44 1 0.01
45 34 0.29
46 2 0.02
47 2 0.02
48 76 0.66
49 1 0.01
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.41
Consensus pattern (48 bp):
TCACAGATTTTTGTACATGGCGTGTCACAGATTTTTGTACATGATGTG
Found at i:28549868 original size:23 final size:21
Alignment explanation
Indices: 28549817--28549869 Score: 52
Period size: 23 Copynumber: 2.4 Consensus size: 21
28549807 TTATATATAG
28549817 AAAAAAATAGTTGTTAAAAAT
1 AAAAAAATAGTTGTTAAAAAT
* ** *
28549838 CATTAAATATGTTGATTGAAAAT
1 AAAAAAATA-GTTG-TTAAAAAT
28549861 AAAAAAATA
1 AAAAAAATA
28549870 AAAAAAAATT
Statistics
Matches: 23, Mismatches: 7, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
21 6 0.26
22 4 0.17
23 13 0.57
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.30
Consensus pattern (21 bp):
AAAAAAATAGTTGTTAAAAAT
Found at i:28550080 original size:20 final size:20
Alignment explanation
Indices: 28550043--28550081 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
28550033 TTTAATTTTA
* *
28550043 TATATTTTAATATAATAAAT
1 TATATTATAAAATAATAAAT
*
28550063 TATATTATAAAATTATAAA
1 TATATTATAAAATAATAAA
28550082 GCCTATCTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TATATTATAAAATAATAAAT
Found at i:28552657 original size:2 final size:2
Alignment explanation
Indices: 28552650--28552683 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
28552640 TATTGAATAC
*
28552650 TA TA TA TA TA TA TA TA TA TA TC TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28552684 TTGTCCAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28553761 original size:11 final size:11
Alignment explanation
Indices: 28553741--28553777 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
28553731 ATTTCGTTAG
*
28553741 AAATCTGTTGA
1 AAATCCGTTGA
28553752 AAATCCGTTGA
1 AAATCCGTTGA
*
28553763 AAATCCATTGA
1 AAATCCGTTGA
28553774 AAAT
1 AAAT
28553778 TTGAAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.30
Consensus pattern (11 bp):
AAATCCGTTGA
Found at i:28554306 original size:35 final size:35
Alignment explanation
Indices: 28554235--28554315 Score: 94
Period size: 35 Copynumber: 2.3 Consensus size: 35
28554225 ATTTTCTTCC
* *
28554235 ACAAAAATATTAAAATTTAAATTTAAATAATAAAAA
1 ACAAAAATCTTAAAA-TTAAAATTAAATAATAAAAA
28554271 ACAAAAATCTTAAACA-TAAAATTAAATAACT-AAAA
1 ACAAAAATCTTAAA-ATTAAAATTAAATAA-TAAAAA
*
28554306 ACAAATATCT
1 ACAAAAATCT
28554316 GGGGAACCAG
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
35 25 0.62
36 14 0.35
37 1 0.03
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (35 bp):
ACAAAAATCTTAAAATTAAAATTAAATAATAAAAA
Found at i:28569183 original size:12 final size:13
Alignment explanation
Indices: 28569166--28569194 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
28569156 TTTTCCAACG
28569166 GAAAATTTCGTT-
1 GAAAATTTCGTTA
28569178 GAAAATTTCGTTA
1 GAAAATTTCGTTA
28569191 GAAA
1 GAAA
28569195 CTGTAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.34
Consensus pattern (13 bp):
GAAAATTTCGTTA
Found at i:28574862 original size:40 final size:40
Alignment explanation
Indices: 28574814--28574929 Score: 151
Period size: 40 Copynumber: 2.9 Consensus size: 40
28574804 AAAGATCTTA
* *
28574814 AACATAAACTTAAATAACTAAAAATAAATTTCCATACAAC
1 AACATAAACTTAAATAACTAAAAATAAATATCCAAACAAC
* * * * *
28574854 GATATAAACTTAAATAACTATACATAAATATCCAAATAAC
1 AACATAAACTTAAATAACTAAAAATAAATATCCAAACAAC
* *
28574894 AACATAAACTTAAATAACTAAACACAAATATCCAAA
1 AACATAAACTTAAATAACTAAAAATAAATATCCAAA
28574930 AAAAAATATA
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 65 1.00
ACGTcount: A:0.58, C:0.17, G:0.01, T:0.24
Consensus pattern (40 bp):
AACATAAACTTAAATAACTAAAAATAAATATCCAAACAAC
Found at i:28574891 original size:22 final size:21
Alignment explanation
Indices: 28574865--28574929 Score: 66
Period size: 20 Copynumber: 3.1 Consensus size: 21
28574855 ATATAAACTT
28574865 AAATAACTATACATAAATATCC
1 AAATAACTA-ACATAAATATCC
28574887 AAATAAC-AACATAAACT-T--
1 AAATAACTAACATAAA-TATCC
*
28574905 AAATAACTAAACACAAATATCC
1 AAATAACT-AACATAAATATCC
28574927 AAA
1 AAA
28574930 AAAAAATATA
Statistics
Matches: 36, Mismatches: 1, Indels: 12
0.73 0.02 0.24
Matches are distributed among these distances:
18 7 0.19
19 1 0.03
20 16 0.44
21 2 0.06
22 10 0.28
ACGTcount: A:0.60, C:0.18, G:0.00, T:0.22
Consensus pattern (21 bp):
AAATAACTAACATAAATATCC
Found at i:28574917 original size:20 final size:20
Alignment explanation
Indices: 28574812--28574917 Score: 78
Period size: 20 Copynumber: 5.3 Consensus size: 20
28574802 ACAAAGATCT
28574812 TAAACATAAACTTAAATAAC
1 TAAACATAAACTTAAATAAC
* * **
28574832 TAAAAATAAATTTCCAT-AC
1 TAAACATAAACTTAAATAAC
*
28574851 -AACGATATAAACTTAAATAAC
1 TAA--ACATAAACTTAAATAAC
*
28574872 TATACATAAA-TATCCAAATAAC
1 TAAACATAAACT-T--AAATAAC
28574894 --AACATAAACTTAAATAAC
1 TAAACATAAACTTAAATAAC
28574912 TAAACA
1 TAAACA
28574918 CAAATATCCA
Statistics
Matches: 65, Mismatches: 11, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
18 9 0.14
19 3 0.05
20 42 0.65
21 3 0.05
22 8 0.12
ACGTcount: A:0.58, C:0.16, G:0.01, T:0.25
Consensus pattern (20 bp):
TAAACATAAACTTAAATAAC
Found at i:28577662 original size:20 final size:20
Alignment explanation
Indices: 28577645--28577682 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
28577635 CCTCAAATCT
28577645 TACTCCAATAAGTCAAATTA
1 TACTCCAATAAGTCAAATTA
28577665 TACTCCAATAAGTCAAAT
1 TACTCCAATAAGTCAAAT
28577683 GGGGCCAAAA
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:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (20 bp):
TACTCCAATAAGTCAAATTA
Found at i:28581290 original size:29 final size:29
Alignment explanation
Indices: 28581230--28581293 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
28581220 GCAAATGTTT
** *
28581230 AAAAATTACACTTTTACCCCCGTAAAGTA
1 AAAAATTACACTTTTACCCCCAAAAACTA
* *
28581259 AAAAATTACATTTTTA-CCCCAAAAACTG
1 AAAAATTACACTTTTACCCCCAAAAACTA
28581287 AAAAATT
1 AAAAATT
28581294 GCCCATAGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 15 0.50
29 15 0.50
ACGTcount: A:0.47, C:0.20, G:0.05, T:0.28
Consensus pattern (29 bp):
AAAAATTACACTTTTACCCCCAAAAACTA
Found at i:28581891 original size:29 final size:28
Alignment explanation
Indices: 28581842--28582001 Score: 157
Period size: 29 Copynumber: 5.7 Consensus size: 28
28581832 TGACAGTTTT
*
28581842 AACATGTTTGTCTTATTTTAGACAAGAA
1 AACATGTTTGTCTTAATTTAGACAAGAA
* *
28581870 AACATGTTTGCTTTTAATTTAGACAAAAA
1 AACATGTTTG-TCTTAATTTAGACAAGAA
28581899 AACATGTTTGGTCTTAATTTAGACAAGAA
1 AACATGTTT-GTCTTAATTTAGACAAGAA
* *
28581928 AATATGTTTGTTTTAA--T-GACAAGAA
1 AACATGTTTGTCTTAATTTAGACAAGAA
* * * * *
28581953 AATATCTTTCATCTTAATCTAGACAAAAA
1 AACATGTTT-GTCTTAATTTAGACAAGAA
*
28581982 AACATAG-TTGTCTCAATTTA
1 AACAT-GTTTGTCTTAATTTA
28582002 AATAAGATAA
Statistics
Matches: 109, Mismatches: 16, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
25 16 0.15
26 6 0.06
28 25 0.23
29 61 0.56
30 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (28 bp):
AACATGTTTGTCTTAATTTAGACAAGAA
Found at i:28581953 original size:83 final size:83
Alignment explanation
Indices: 28581862--28582028 Score: 205
Period size: 83 Copynumber: 2.0 Consensus size: 83
28581852 TCTTATTTTA
* * * * *
28581862 GACAAGAAAACATGTTTGC-TTTTAATTTAGACAAAAAAACAT-GTTTGGTCTTAATTTAGACAA
1 GACAAGAAAACATCTTT-CATCTTAATCTAGACAAAAAAACATAG-TT-GTCTCAATTTAAACAA
28581925 G-AAAATATGTTTGTTTTAAT
63 GAAAAATATGTTTGTTTTAAT
* *
28581945 GACAAGAAAATATCTTTCATCTTAATCTAGACAAAAAAACATAGTTGTCTCAATTTAAATAAGAT
1 GACAAGAAAACATCTTTCATCTTAATCTAGACAAAAAAACATAGTTGTCTCAATTTAAACAAGA-
*
28582010 AAAATATTTTTGTTTTAAT
65 AAAATATGTTTGTTTTAAT
28582029 TAAAGATGAG
Statistics
Matches: 72, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
82 15 0.21
83 38 0.53
84 19 0.26
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.37
Consensus pattern (83 bp):
GACAAGAAAACATCTTTCATCTTAATCTAGACAAAAAAACATAGTTGTCTCAATTTAAACAAGAA
AAATATGTTTGTTTTAAT
Found at i:28581976 original size:54 final size:57
Alignment explanation
Indices: 28581860--28581986 Score: 152
Period size: 54 Copynumber: 2.3 Consensus size: 57
28581850 TGTCTTATTT
* ** *
28581860 TAGACAAGAAAACATGTTTGCTTTTAATTTAGACAAAAAAACATGTTTGGTCTTAATT
1 TAGACAAGAAAACATGTTTGCTTTTAA-TTAGACAAAAAAACATCTTTCATCTTAATC
* * *
28581918 TAGACAAGAAAATATGTTTG-TTTTAA-T-GACAAGAAAATATCTTTCATCTTAATC
1 TAGACAAGAAAACATGTTTGCTTTTAATTAGACAAAAAAACATCTTTCATCTTAATC
*
28581972 TAGACAAAAAAACAT
1 TAGACAAGAAAACAT
28581987 AGTTGTCTCA
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
54 34 0.57
55 1 0.02
57 6 0.10
58 19 0.32
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (57 bp):
TAGACAAGAAAACATGTTTGCTTTTAATTAGACAAAAAAACATCTTTCATCTTAATC
Found at i:28583524 original size:18 final size:17
Alignment explanation
Indices: 28583501--28583541 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
28583491 ATAATATAAA
*
28583501 GAAAAAAGAAAAAATGAT
1 GAAAAAAGAAAAAA-AAT
*
28583519 GAAAAAATAAAAAAAAT
1 GAAAAAAGAAAAAAAAT
28583536 GAAAAA
1 GAAAAA
28583542 GAGACACAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (17 bp):
GAAAAAAGAAAAAAAAT
Found at i:28584632 original size:43 final size:43
Alignment explanation
Indices: 28584586--28584891 Score: 291
Period size: 43 Copynumber: 7.1 Consensus size: 43
28584576 TGATATTTGT
* * * *
28584586 TTATTCAATTTAAAGTTATGTAGCCTCATTCCAAATG-AGAAGT
1 TTATTCATTTTAAAGTTATGTAGCCTCATTCTAGATGAAG-AGC
* * * * * *
28584629 TTATTCCTTTTAAAGTCACT-TAACTTCATTCCAGAT-AATAAGC
1 TTATTCATTTTAAAGTTA-TGTAGCCTCATTCTAGATGAA-GAGC
*
28584672 TTATTCATTTTAAAGTTATGTAGCTTCAATT-TAGATGAAGAGC
1 TTATTCATTTTAAAGTTATGTAGCCTC-ATTCTAGATGAAGAGC
* * *
28584715 TTATT-ACTTTTAAAGTTACGTAACTTCATTCTAGATGAAGAGC
1 TTATTCA-TTTTAAAGTTATGTAGCCTCATTCTAGATGAAGAGC
** *
28584758 TTATTCATTTTAAAGTTACATAGCCTCATTCTAGATGAGGAGC
1 TTATTCATTTTAAAGTTATGTAGCCTCATTCTAGATGAAGAGC
* **
28584801 TTATTCATTTAAAAGTTATGTAGCCTCATT-TCAGATGAATTGC
1 TTATTCATTTTAAAGTTATGTAGCCTCATTCT-AGATGAAGAGC
** * * *
28584844 TTATTCATTTTAAAGTTGCGTAACCTCATTCTAGATGAACAGT
1 TTATTCATTTTAAAGTTATGTAGCCTCATTCTAGATGAAGAGC
28584887 TTATT
1 TTATT
28584892 TCTTTTTTAA
Statistics
Matches: 220, Mismatches: 32, Indels: 22
0.80 0.12 0.08
Matches are distributed among these distances:
42 6 0.03
43 206 0.94
44 8 0.04
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (43 bp):
TTATTCATTTTAAAGTTATGTAGCCTCATTCTAGATGAAGAGC
Found at i:28584739 original size:86 final size:85
Alignment explanation
Indices: 28584586--28584897 Score: 333
Period size: 86 Copynumber: 3.6 Consensus size: 85
28584576 TGATATTTGT
* * * * * *
28584586 TTATTCAATTTAAAGTTATGTAGCCTCATTCCAAATG-AGAAGTTTATTCCTTTTAAAGTCACTT
1 TTATTCATTTTAAAGTTATGTAGCCTCATTCTAGATGAAG-AGCTTATT-CTTTTAAAGTTACGT
28584650 AACTTCATTCCAGAT-AATAAGC
64 AACTTCATTCCAGATGAAT-AGC
*
28584672 TTATTCATTTTAAAGTTATGTAGCTTCAATT-TAGATGAAGAGCTTATTACTTTTAAAGTTACGT
1 TTATTCATTTTAAAGTTATGTAGCCTC-ATTCTAGATGAAGAGCTTATT-CTTTTAAAGTTACGT
* *
28584736 AACTTCATTCTAGATGAAGAGC
64 AACTTCATTCCAGATGAATAGC
** * * *
28584758 TTATTCATTTTAAAGTTACATAGCCTCATTCTAGATGAGGAGCTTATTCATTTAAAAGTTATGTA
1 TTATTCATTTTAAAGTTATGTAGCCTCATTCTAGATGAAGAGCTTATTC-TTTTAAAGTTACGTA
* * * *
28584823 GCCTCATTTCAGATGAATTGC
65 ACTTCATTCCAGATGAATAGC
** * * *
28584844 TTATTCATTTTAAAGTTGCGTAACCTCATTCTAGATGAACAGTTTATTTCTTTT
1 TTATTCATTTTAAAGTTATGTAGCCTCATTCTAGATGAAGAGCTTA-TTCTTTT
28584898 TTAAGGTTAC
Statistics
Matches: 191, Mismatches: 29, Indels: 12
0.82 0.12 0.05
Matches are distributed among these distances:
85 4 0.02
86 177 0.93
87 10 0.05
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (85 bp):
TTATTCATTTTAAAGTTATGTAGCCTCATTCTAGATGAAGAGCTTATTCTTTTAAAGTTACGTAA
CTTCATTCCAGATGAATAGC
Found at i:28584802 original size:129 final size:131
Alignment explanation
Indices: 28584669--28584926 Score: 353
Period size: 129 Copynumber: 2.0 Consensus size: 131
28584659 CCAGATAATA
* *
28584669 AGCTTATTCATTTTAAAGTTATGTAGCTTCAATTT-AGATGAAGAGCTTATT-ACTTTTAAAGTT
1 AGCTTATTCATTTAAAAGTTATGTAGCCTC-ATTTCAGATGAAGAGCTTATTCA-TTTTAAAGTT
* * * *
28584732 ACGTAACTTCATTCTAGATGAAGAGCTTA-TTC-ATTTTAAAGTTACATAGCCTCATTCTAGATG
64 ACGTAACCTCATTCTAGATGAACAGCTTATTTCTATTTTAAAGTTACATAGCCTCATCCTAAATG
28584795 AGG
129 AGG
** *
28584798 AGCTTATTCATTTAAAAGTTATGTAGCCTCATTTCAGATGAATTGCTTATTCATTTTAAAGTTGC
1 AGCTTATTCATTTAAAAGTTATGTAGCCTCATTTCAGATGAAGAGCTTATTCATTTTAAAGTTAC
* * * *
28584863 GTAACCTCATTCTAGATGAACAGTTTATTTCTTTTTTAAGGTTACATAGCGTCATCCTAAATGA
66 GTAACCTCATTCTAGATGAACAGCTTATTTCTATTTTAAAGTTACATAGCCTCATCCTAAATGA
28584927 AAAGCTTTAT
Statistics
Matches: 112, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
128 4 0.04
129 77 0.69
130 4 0.04
131 27 0.24
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.40
Consensus pattern (131 bp):
AGCTTATTCATTTAAAAGTTATGTAGCCTCATTTCAGATGAAGAGCTTATTCATTTTAAAGTTAC
GTAACCTCATTCTAGATGAACAGCTTATTTCTATTTTAAAGTTACATAGCCTCATCCTAAATGAG
G
Found at i:28585324 original size:22 final size:22
Alignment explanation
Indices: 28585276--28585325 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
28585266 AGAGACAGAG
*
28585276 AAAAAATTAAGGAAAGAAAATG
1 AAAAAATTAAGGAAAGAAAATA
* *
28585298 GAAAAATTAGGGAAAGGAAAA-A
1 AAAAAATTAAGGAAA-GAAAATA
28585320 AAAAAA
1 AAAAAA
28585326 GAAAAGCAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.70, C:0.00, G:0.20, T:0.10
Consensus pattern (22 bp):
AAAAAATTAAGGAAAGAAAATA
Found at i:28587657 original size:24 final size:24
Alignment explanation
Indices: 28587622--28587689 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
28587612 TTTATTAAAA
28587622 ATAATATCTAATAATT-TTATATATT
1 ATAATAT-TAATAATTATTA-ATATT
*
28587647 TTAATATTAATAATTATTAATATT
1 ATAATATTAATAATTATTAATATT
* *
28587671 ATATTATTATATTATTATT
1 ATAATATTA-ATAATTATT
28587690 TACCATGTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
24 20 0.54
25 17 0.46
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (24 bp):
ATAATATTAATAATTATTAATATT
Found at i:28587668 original size:16 final size:15
Alignment explanation
Indices: 28587613--28587689 Score: 61
Period size: 16 Copynumber: 5.1 Consensus size: 15
28587603 AAATGTTTAT
* *
28587613 TTATTAAAAATAATA
1 TTATTAATATTAATA
* *
28587628 TCTAATAATTTTATATA
1 T-TATTAATATTA-ATA
28587645 TT-TTAATATTAATAA
1 TTATTAATATTAAT-A
28587660 TTATTAATATT-ATA
1 TTATTAATATTAATA
*
28587674 TTATT-ATATTATTA
1 TTATTAATATTAATA
28587688 TT
1 TT
28587690 TACCATGTTA
Statistics
Matches: 50, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
13 5 0.10
14 12 0.24
15 13 0.26
16 16 0.32
17 4 0.08
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (15 bp):
TTATTAATATTAATA
Found at i:28587680 original size:8 final size:8
Alignment explanation
Indices: 28587641--28587710 Score: 53
Period size: 8 Copynumber: 9.4 Consensus size: 8
28587631 AATAATTTTA
28587641 TATATT-T
1 TATATTAT
*
28587648 TAATATTAA
1 T-ATATTAT
28587657 TA-ATTAT
1 TATATTAT
28587664 TA-A-TAT
1 TATATTAT
28587670 TATATTAT
1 TATATTAT
28587678 TATATTAT
1 TATATTAT
*
28587686 TAT-TTAC
1 TATATTAT
* *
28587693 CATGTTAT
1 TATATTAT
28587701 TAT-TTAT
1 TATATTAT
28587708 TAT
1 TAT
28587711 TTTAAAGGAT
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
6 5 0.10
7 21 0.40
8 25 0.48
9 1 0.02
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (8 bp):
TATATTAT
Found at i:28596095 original size:15 final size:16
Alignment explanation
Indices: 28596074--28596112 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
28596064 TTTATTTATA
28596074 AAAATAAATAAAAAAC
1 AAAATAAATAAAAAAC
* *
28596090 -AAATAAATTAATAAC
1 AAAATAAATAAAAAAC
28596105 AAAATAAA
1 AAAATAAA
28596113 AATAGAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (16 bp):
AAAATAAATAAAAAAC
Found at i:28604806 original size:5 final size:5
Alignment explanation
Indices: 28604796--28604821 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
28604786 AATCAACATG
28604796 ACAGC ACAGC ACAGC ACAGC ACAGC A
1 ACAGC ACAGC ACAGC ACAGC ACAGC A
28604822 ACCAGTGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.38, G:0.19, T:0.00
Consensus pattern (5 bp):
ACAGC
Found at i:28605230 original size:28 final size:29
Alignment explanation
Indices: 28605198--28605272 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
28605188 TTTTAAAAAA
28605198 ATTAAATAAATTTTTAT-TTTTTATTATG
1 ATTAAATAAATTTTTATATTTTTATTATG
* * * *
28605226 TTTAATTAAATTATTATATTTTTATTTTG
1 ATTAAATAAATTTTTATATTTTTATTATG
* *
28605255 ATCAAATAAGTTTTTATA
1 ATTAAATAAATTTTTATA
28605273 ATTGATAATT
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
28 14 0.38
29 23 0.62
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.59
Consensus pattern (29 bp):
ATTAAATAAATTTTTATATTTTTATTATG
Found at i:28605469 original size:88 final size:87
Alignment explanation
Indices: 28605377--28605552 Score: 343
Period size: 88 Copynumber: 2.0 Consensus size: 87
28605367 CTGATTAATT
28605377 AGCTGGTGCATGATCCCCTACTTAAATAATAAGATTTAAATCTCATTTCTCTTGATTATAATATA
1 AGCTGGTGCATGATCCCCTACTTAAATAATAAGATTTAAATCTCATTTCTCTTGATTATAATATA
28605442 TATATATATATATATAATATTG
66 TATATATATATATATAATATTG
28605464 NAGCTGGTGCATGATCCCCTACTTAAATAATAAGATTTAAATCTCATTTCTCTTGATTATAATAT
1 -AGCTGGTGCATGATCCCCTACTTAAATAATAAGATTTAAATCTCATTTCTCTTGATTATAATAT
28605529 ATATATATATATATATAATATTG
65 ATATATATATATATATAATATTG
28605552 A
1 A
28605553 TGTGAAAGAT
Statistics
Matches: 88, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
87 1 0.01
88 87 0.99
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.41
Consensus pattern (87 bp):
AGCTGGTGCATGATCCCCTACTTAAATAATAAGATTTAAATCTCATTTCTCTTGATTATAATATA
TATATATATATATATAATATTG
Found at i:28614651 original size:17 final size:16
Alignment explanation
Indices: 28614631--28614673 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 16
28614621 ATTTTTTATG
28614631 TTTTTTTCTTTTTCCC
1 TTTTTTTCTTTTTCCC
*
28614647 -TTTTTTCTTATTTTCC
1 TTTTTTTCTT-TTTCCC
28614663 TTTTTTTCTTT
1 TTTTTTTCTTT
28614674 AATAAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 9 0.38
16 6 0.25
17 9 0.38
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTTTCTTTTTCCC
Found at i:28624852 original size:26 final size:26
Alignment explanation
Indices: 28624823--28624906 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 26
28624813 TTTGAAAAAA
28624823 AAGATTTGTATTTATCTTACATAATC
1 AAGATTTGTATTTATCTTACATAATC
** * * ** * **
28624849 AAGAAATGTTTTGTTTCCTTTGAAAAAA
1 AAGATTTGTATT-TAT-CTTACATAATC
28624877 AAGATTTGTATTTATCTTACATAATC
1 AAGATTTGTATTTATCTTACATAATC
28624903 AAGA
1 AAGA
28624907 AATGTTAACG
Statistics
Matches: 38, Mismatches: 18, Indels: 4
0.63 0.30 0.07
Matches are distributed among these distances:
26 19 0.50
27 4 0.11
28 15 0.39
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.42
Consensus pattern (26 bp):
AAGATTTGTATTTATCTTACATAATC
Found at i:28624863 original size:54 final size:54
Alignment explanation
Indices: 28624805--28624912 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
28624795 CATGCTTAAA
28624805 TTGTTTCCTTTGAAAAAAAAGATTTGTATTTATCTTACATAATCAAGAAATGTT
1 TTGTTTCCTTTGAAAAAAAAGATTTGTATTTATCTTACATAATCAAGAAATGTT
28624859 TTGTTTCCTTTGAAAAAAAAGATTTGTATTTATCTTACATAATCAAGAAATGTT
1 TTGTTTCCTTTGAAAAAAAAGATTTGTATTTATCTTACATAATCAAGAAATGTT
28624913 AACGATTGTC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.43
Consensus pattern (54 bp):
TTGTTTCCTTTGAAAAAAAAGATTTGTATTTATCTTACATAATCAAGAAATGTT
Found at i:28626334 original size:2 final size:2
Alignment explanation
Indices: 28626327--28626356 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
28626317 CGAATTTTAA
28626327 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
28626357 TAAGCCTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28626649 original size:26 final size:26
Alignment explanation
Indices: 28626589--28626650 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
28626579 AATATAAAAA
* * *
28626589 AATTATTAATATTATATATCGTATTT
1 AATTATTTATATTATATATCATATAT
28626615 AATTATTTATATTATATAT-ATATAT
1 AATTATTTATATTATATATCATATAT
*
28626640 ATATTTTTTAT
1 A-ATTATTTAT
28626651 CTTTAACTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 5 0.16
26 26 0.84
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (26 bp):
AATTATTTATATTATATATCATATAT
Found at i:28628817 original size:20 final size:20
Alignment explanation
Indices: 28628792--28628833 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
28628782 ATCCAGCAAA
*
28628792 TTCTTCATCTTTTCTTC-TCT
1 TTCTTCA-CATTTCTTCTTCT
28628812 TTCTTCACATTTCTTCTTCT
1 TTCTTCACATTTCTTCTTCT
28628832 TT
1 TT
28628834 AATCCATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.07, C:0.29, G:0.00, T:0.64
Consensus pattern (20 bp):
TTCTTCACATTTCTTCTTCT
Found at i:28643925 original size:15 final size:15
Alignment explanation
Indices: 28643907--28643950 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
28643897 ATCATATACC
*
28643907 CAGTGATCACATTCT
1 CAGTAATCACATTCT
*
28643922 CAGTAATCACATTCC
1 CAGTAATCACATTCT
* *
28643937 CAATAATCTCATTC
1 CAGTAATCACATTC
28643951 CCAATAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.32, C:0.30, G:0.07, T:0.32
Consensus pattern (15 bp):
CAGTAATCACATTCT
Found at i:28643951 original size:15 final size:15
Alignment explanation
Indices: 28643912--28643957 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
28643902 ATACCCAGTG
* *
28643912 ATCACATTCTCAGTA
1 ATCACATTCCCAATA
28643927 ATCACATTCCCAATA
1 ATCACATTCCCAATA
*
28643942 ATCTCATTCCCAATA
1 ATCACATTCCCAATA
28643957 A
1 A
28643958 AATACCAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.37, C:0.30, G:0.02, T:0.30
Consensus pattern (15 bp):
ATCACATTCCCAATA
Found at i:28647441 original size:23 final size:23
Alignment explanation
Indices: 28647414--28647458 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
28647404 ATTGATGTGG
* *
28647414 CACATCATGATATTGACACATGA
1 CACATCAAGAGATTGACACATGA
*
28647437 CACATTAAGAGATTGACACATG
1 CACATCAAGAGATTGACACATG
28647459 GTACTATTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (23 bp):
CACATCAAGAGATTGACACATGA
Found at i:28647798 original size:18 final size:18
Alignment explanation
Indices: 28647775--28647813 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
28647765 ACACGATTAA
28647775 TAACACATTTAACACGAT
1 TAACACATTTAACACGAT
* * *
28647793 TAACACGTTTTACATGAT
1 TAACACATTTAACACGAT
28647811 TAA
1 TAA
28647814 ATAAAAATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (18 bp):
TAACACATTTAACACGAT
Found at i:28651991 original size:13 final size:13
Alignment explanation
Indices: 28651971--28652001 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
28651961 ATTTATAAAA
28651971 TTAAAAAAATTA-
1 TTAAAAAAATTAT
28651983 TTAAAAAAATTAT
1 TTAAAAAAATTAT
28651996 TTAAAA
1 TTAAAA
28652002 TTATTTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
TTAAAAAAATTAT
Found at i:28652317 original size:13 final size:13
Alignment explanation
Indices: 28652301--28652345 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
28652291 TTATTTTTTA
28652301 TTTCTTTTTTTCT
1 TTTCTTTTTTTCT
*
28652314 TTTCTCTTTTTCT
1 TTTCTTTTTTTCT
* *
28652327 TTTTTTTTCTTTCG
1 TTTCTTTT-TTTCT
28652341 TTTCT
1 TTTCT
28652346 CAAAACTACA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
13 18 0.69
14 8 0.31
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (13 bp):
TTTCTTTTTTTCT
Found at i:28652458 original size:14 final size:15
Alignment explanation
Indices: 28652439--28652471 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
28652429 TAGTTTTGAG
*
28652439 GAAAG-AAAGAAAAA
1 GAAAGAAAAAAAAAA
28652453 GAAAGAAAAAAAAAA
1 GAAAGAAAAAAAAAA
28652468 GAAA
1 GAAA
28652472 AGACAAGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (15 bp):
GAAAGAAAAAAAAAA
Found at i:28652468 original size:21 final size:23
Alignment explanation
Indices: 28652444--28652490 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 23
28652434 TTGAGGAAAG
28652444 AAAGAAAAAGA-AAGAA-AAA-AA
1 AAAG-AAAAGACAAGAAGAAATAA
28652465 AAAGAAAAGACAAGAAGAAATAA
1 AAAGAAAAGACAAGAAGAAATAA
28652488 AAA
1 AAA
28652491 ACAAGCAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 3 0.13
23 5 0.22
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.02
Consensus pattern (23 bp):
AAAGAAAAGACAAGAAGAAATAA
Found at i:28652468 original size:25 final size:28
Alignment explanation
Indices: 28652440--28652491 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
28652430 AGTTTTGAGG
28652440 AAAG-AAAGA-AA-AAGAAAGAAAAAAA
1 AAAGAAAAGACAAGAAGAAAGAAAAAAA
*
28652465 AAAGAAAAGACAAGAAGAAATAAAAAA
1 AAAGAAAAGACAAGAAGAAAGAAAAAA
28652492 CAAGCAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 4 0.17
26 5 0.22
27 2 0.09
28 12 0.52
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.02
Consensus pattern (28 bp):
AAAGAAAAGACAAGAAGAAAGAAAAAAA
Found at i:28658846 original size:3 final size:3
Alignment explanation
Indices: 28658838--28658863 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
28658828 TCCTTCATCC
28658838 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
28658864 GGTTGCAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:28665232 original size:58 final size:58
Alignment explanation
Indices: 28665140--28665281 Score: 162
Period size: 58 Copynumber: 2.5 Consensus size: 58
28665130 AGGAGCTAAT
* * * * * * * *
28665140 AAAGAA-AAACTGTATGTGAACAGG-AGTAAGAGAAGAAGTTGTACGTGAATAGGTACA
1 AAAGAAGAAACTGTACGTGAATAGGTA-CAAAAGAAGAAGCTGTACATGAACAAGTACA
*
28665197 AAAGAAGAAGCTGTACGTGAATAGGTACAAAAGAAGAAGCTGTACATGAACAAGTACA
1 AAAGAAGAAACTGTACGTGAATAGGTACAAAAGAAGAAGCTGTACATGAACAAGTACA
* *
28665255 AGAGAAGAAACTGTATGTGAATAGGTA
1 AAAGAAGAAACTGTACGTGAATAGGTA
28665282 TAAGAGAACA
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
57 6 0.08
58 64 0.90
59 1 0.01
ACGTcount: A:0.46, C:0.08, G:0.27, T:0.18
Consensus pattern (58 bp):
AAAGAAGAAACTGTACGTGAATAGGTACAAAAGAAGAAGCTGTACATGAACAAGTACA
Found at i:28665286 original size:29 final size:29
Alignment explanation
Indices: 28665167--28665289 Score: 165
Period size: 29 Copynumber: 4.2 Consensus size: 29
28665157 GAACAGGAGT
*
28665167 AAGAGAAGAAGTTGTACGTGAATAGGTAC
1 AAGAGAAGAAGCTGTACGTGAATAGGTAC
*
28665196 AAAAGAAGAAGCTGTACGTGAATAGGTAC
1 AAGAGAAGAAGCTGTACGTGAATAGGTAC
* * * *
28665225 AAAAGAAGAAGCTGTACATGAACAAGTAC
1 AAGAGAAGAAGCTGTACGTGAATAGGTAC
* * *
28665254 AAGAGAAGAAACTGTATGTGAATAGGTAT
1 AAGAGAAGAAGCTGTACGTGAATAGGTAC
28665283 AAGAGAA
1 AAGAGAA
28665290 CAAGATAAAA
Statistics
Matches: 82, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 82 1.00
ACGTcount: A:0.47, C:0.08, G:0.27, T:0.18
Consensus pattern (29 bp):
AAGAGAAGAAGCTGTACGTGAATAGGTAC
Found at i:28666966 original size:20 final size:20
Alignment explanation
Indices: 28666941--28666981 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
28666931 CTTTAATTAT
*
28666941 TTTTAATTATTATATATATA
1 TTTTAAATATTATATATATA
*
28666961 TTTTAAATATTGTATATATA
1 TTTTAAATATTATATATATA
28666981 T
1 T
28666982 ATATTTAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTTAAATATTATATATATA
Found at i:28667021 original size:20 final size:20
Alignment explanation
Indices: 28666946--28667021 Score: 56
Period size: 20 Copynumber: 3.9 Consensus size: 20
28666936 ATTATTTTTA
28666946 ATTATTATATATATATT-TT
1 ATTATTATATATATATTATT
* *
28666965 AAATATTGTATATATA-TA-T
1 -ATTATTATATATATATTATT
28666984 ATTTAGTT-T-TAT-TCATTATT
1 A-TTA-TTATATATAT-ATTATT
28667004 ATTATTATATATATATTA
1 ATTATTATATATATATTA
28667022 ATAAAAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 18
0.68 0.05 0.28
Matches are distributed among these distances:
17 1 0.02
18 7 0.16
19 11 0.25
20 24 0.55
21 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (20 bp):
ATTATTATATATATATTATT
Found at i:28682739 original size:25 final size:27
Alignment explanation
Indices: 28682686--28682740 Score: 69
Period size: 25 Copynumber: 2.1 Consensus size: 27
28682676 TAGGAAAGTG
* * *
28682686 TTAGGATAGTATTGAATTGTGATTTAA
1 TTAGGATAGTATTGAATTCTAATTAAA
28682713 TTAGGATAGT-TT-AATTCTAATTAAA
1 TTAGGATAGTATTGAATTCTAATTAAA
28682738 TTA
1 TTA
28682741 TATACCTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 13 0.52
26 2 0.08
27 10 0.40
ACGTcount: A:0.36, C:0.02, G:0.16, T:0.45
Consensus pattern (27 bp):
TTAGGATAGTATTGAATTCTAATTAAA
Found at i:28688518 original size:15 final size:15
Alignment explanation
Indices: 28688498--28688548 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 15
28688488 TATTGGGAAA
28688498 ATAAAATTAATATTT
1 ATAAAATTAATATTT
28688513 ATAAAA-TAATTATATT
1 ATAAAATTAA-TAT-TT
28688529 A-AAAATTCAATATTT
1 ATAAAATT-AATATTT
28688544 ATAAA
1 ATAAA
28688549 GATAAAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
14 3 0.10
15 16 0.52
16 10 0.32
17 2 0.06
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (15 bp):
ATAAAATTAATATTT
Found at i:28688562 original size:31 final size:30
Alignment explanation
Indices: 28688500--28688564 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 30
28688490 TTGGGAAAAT
*
28688500 AAAATTAATATTTATAAAATAATTATATTA
1 AAAATTAATATTTATAAAATAATAATATTA
*
28688530 AAAATTCAATATTTATAAAGATAA-AATTTTA
1 AAAATT-AATATTTATAAA-ATAATAATATTA
28688561 AAAA
1 AAAA
28688565 AATAAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 6 0.19
31 21 0.68
32 4 0.13
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (30 bp):
AAAATTAATATTTATAAAATAATAATATTA
Found at i:28693360 original size:4 final size:4
Alignment explanation
Indices: 28693353--28693381 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
28693343 TATATAGATA
28693353 TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG T
28693382 TACAGCTCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:28693655 original size:90 final size:89
Alignment explanation
Indices: 28693537--28693706 Score: 241
Period size: 89 Copynumber: 1.9 Consensus size: 89
28693527 ATTGACTATG
* * ** * * *
28693537 ATGATAAGGGAATAGAAAATCCTTGAAAGAATTTGTAAGGGATGCCAATTTTGTCTTAAAAAGTA
1 ATGATAAGGAAATAAAAAATCAATGAAAGAAATTGTAA-GAATGCCAATTATGTCTTAAAAAGTA
*
28693602 ATTGTTGGCTTGCTTTTTGTTTTTT
65 ATTGCTGGCTTGCTTTTTGTTTTTT
* *
28693627 ATGATAAGGAAATAAAAAATCAATGAAAGAAATTGTAAGAATGCTAATTATGTCTTTAAAAGTAA
1 ATGATAAGGAAATAAAAAATCAATGAAAGAAATTGTAAGAATGCCAATTATGTCTTAAAAAGTAA
28693692 TTGCTGGCTTGCTTT
66 TTGCTGGCTTGCTTT
28693707 GTTTTGTTTA
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
89 37 0.53
90 33 0.47
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.36
Consensus pattern (89 bp):
ATGATAAGGAAATAAAAAATCAATGAAAGAAATTGTAAGAATGCCAATTATGTCTTAAAAAGTAA
TTGCTGGCTTGCTTTTTGTTTTTT
Found at i:28699406 original size:33 final size:33
Alignment explanation
Indices: 28699369--28699433 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
28699359 ATATATTATG
*
28699369 TCATCAT-AAGTTATTATATATTAACATATCATA
1 TCATCATCAA-TTATGATATATTAACATATCATA
* *
28699402 TCATCATCAATTATGATATTTTAGCATATCAT
1 TCATCATCAATTATGATATATTAACATATCAT
28699434 GTTAGGTTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.43
Consensus pattern (33 bp):
TCATCATCAATTATGATATATTAACATATCATA
Found at i:28699573 original size:30 final size:30
Alignment explanation
Indices: 28699502--28699584 Score: 96
Period size: 30 Copynumber: 2.8 Consensus size: 30
28699492 ATAATGACTC
* * ** *
28699502 ATTTGATTCAAAATAAATATTTAAGCATTT
1 ATTTGATTCAAAATAAAAATATAAAAATTA
*
28699532 ATTT-AGCTCAAAATAAAAATATAAAAATTA
1 ATTTGA-TTCAAAATAAAAATATAAAAATTA
28699562 ATTTGATTCAAAATAAAAATATA
1 ATTTGATTCAAAATAAAAATATA
28699585 GAAACTTATT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
29 1 0.02
30 42 0.95
31 1 0.02
ACGTcount: A:0.53, C:0.06, G:0.05, T:0.36
Consensus pattern (30 bp):
ATTTGATTCAAAATAAAAATATAAAAATTA
Found at i:28700619 original size:27 final size:26
Alignment explanation
Indices: 28700525--28700616 Score: 84
Period size: 23 Copynumber: 3.6 Consensus size: 26
28700515 TATGATTATT
* *
28700525 TATTTTATTT-TATTTTTAAATATTAA
1 TATTTTATTTATA-ATTAAAATATTAA
* * *
28700551 TAATTTATAATGTAATTAAAATATTAA
1 TATTTTAT-TTATAATTAAAATATTAA
*
28700578 TA-ATT-TTTA-AATTAAAATATTAA
1 TATTTTATTTATAATTAAAATATTAA
28700601 TATTTTATTTATAATT
1 TATTTTATTTATAATT
28700617 TAATCATTAA
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
23 16 0.30
24 3 0.06
25 5 0.09
26 13 0.25
27 14 0.26
28 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (26 bp):
TATTTTATTTATAATTAAAATATTAA
Found at i:28700743 original size:22 final size:22
Alignment explanation
Indices: 28700718--28700865 Score: 97
Period size: 22 Copynumber: 6.5 Consensus size: 22
28700708 TAACTGAAAA
28700718 TTTAAATATTAATATTTTATTT
1 TTTAAATATTAATATTTTATTT
*
28700740 TTTAAATATTAATAATTGATCATTT
1 TTTAAATATTAAT-ATT--TTATTT
* **
28700765 ATTTAAAATATTAATATTTGATCA
1 -TTT-AAATATTAATATTTTATTT
* *
28700789 TTTAAATATTGATATTTTA-TG
1 TTTAAATATTAATATTTTATTT
* *
28700810 TAT-AAT-TTAATCA-TTAATATT
1 TTTAAATATTAAT-ATTTTAT-TT
* *
28700831 GTAAAATATTAATATTTTATTT
1 TTTAAATATTAATATTTTATTT
28700853 AATTTAAATATTA
1 --TTTAAATATTA
28700866 TGATGATCAA
Statistics
Matches: 95, Mismatches: 18, Indels: 24
0.69 0.13 0.18
Matches are distributed among these distances:
19 7 0.07
20 4 0.04
21 3 0.03
22 33 0.35
23 15 0.16
24 12 0.13
25 5 0.05
26 6 0.06
27 10 0.11
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.53
Consensus pattern (22 bp):
TTTAAATATTAATATTTTATTT
Found at i:28700780 original size:27 final size:26
Alignment explanation
Indices: 28700717--28700792 Score: 97
Period size: 27 Copynumber: 3.0 Consensus size: 26
28700707 ATAACTGAAA
*
28700717 ATTTAAATATTAAT-ATT--TTATTT
1 ATTTAAATATTAATAATTGATCATTT
28700740 -TTTAAATATTAATAATTGATCATTT
1 ATTTAAATATTAATAATTGATCATTT
*
28700765 ATTTAAAATATTAATATTTGATCATTT
1 ATTT-AAATATTAATAATTGATCATTT
28700792 A
1 A
28700793 AATATTGATA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
22 13 0.28
23 3 0.07
25 5 0.11
26 3 0.07
27 22 0.48
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (26 bp):
ATTTAAATATTAATAATTGATCATTT
Found at i:28700808 original size:42 final size:42
Alignment explanation
Indices: 28700754--28700854 Score: 102
Period size: 42 Copynumber: 2.4 Consensus size: 42
28700744 AATATTAATA
*
28700754 ATTGATCA-TTTATTTAAAATATTAAT-ATTTGATCATT-T-AAAT
1 ATTGAT-ATTTTATTTAAAAT-TTAATCA-TTAAT-ATTGTAAAAT
* *
28700796 ATTGATATTTTATGTATAATTTAATCATTAATATTGTAAAAT
1 ATTGATATTTTATTTAAAATTTAATCATTAATATTGTAAAAT
*
28700838 ATTAATATTTTATTTAA
1 ATTGATATTTTATTTAA
28700855 TTTAAATATT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
40 3 0.06
41 11 0.22
42 35 0.71
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (42 bp):
ATTGATATTTTATTTAAAATTTAATCATTAATATTGTAAAAT
Found at i:28700890 original size:200 final size:204
Alignment explanation
Indices: 28700530--28700958 Score: 541
Period size: 200 Copynumber: 2.1 Consensus size: 204
28700520 TTATTTATTT
* *
28700530 TATTTTA-TTTTTAAATATTAATAATTTATAATGTAATTAAAATATTAATAATTTTTAAATTAAA
1 TATTTTATTTTTTAAATATTAATAATTGATAATGTAATTAAAATATTAATAATTTATAAATTAAA
* * *
28700594 ATATTAATATTTTATTTATAATTTAATCATTAACATTTTTAAATATTAATGTTTATTTAATTTAA
66 ATATTAATATTTTATGTATAATTTAATCATTAACATTGTAAAATATTAATGTTTATTTAATTTAA
* ** * **
28700659 ATATTATTATGATTCCTTTTATATTTTTTATTTTATTTTTGCATATTAATAACTGA-AA-ATTTA
131 ATATTATGATGATTCCAATTATATTTTTTATTTTATTCTTAAATATTAATAACTGATAATATTTA
28700722 -AATATTAA
196 TAATATTAA
* * * * *
28700730 TATTTTATTTTTTAAATATTAATAATTGATCATTTATTTAAAATATTAAT-ATTTGAT-CATTTA
1 TATTTTATTTTTTAAATATTAATAATTGATAATGTAATTAAAATATTAATAATTT-ATAAATTAA
* * *
28700793 AATATTGATATTTTATGTATAATTTAATCATTAATATTGTAAAATATTAATATTTTATTTAATTT
65 AATATTAATATTTTATGTATAATTTAATCATTAACATTGTAAAATATTAAT-GTTTATTTAATTT
* *
28700858 AAATATTATGATGA-T-CAATTATTTTGTTTTATTTTATTCTTAAATATTAATAATTGATAATTT
129 AAATATTATGATGATTCCAATTATATT-TTTTATTTTATTCTTAAATATTAATAACTGATAA--T
28700921 ATTTATAATATTAA
191 ATTTATAATATTAA
* **
28700935 TAATTTATCATTTAAATATTAATA
1 TATTTTATTTTTTAAATATTAATA
28700959 TTTAACTTAT
Statistics
Matches: 196, Mismatches: 24, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
199 7 0.04
200 89 0.45
201 66 0.34
204 5 0.03
205 29 0.15
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (204 bp):
TATTTTATTTTTTAAATATTAATAATTGATAATGTAATTAAAATATTAATAATTTATAAATTAAA
ATATTAATATTTTATGTATAATTTAATCATTAACATTGTAAAATATTAATGTTTATTTAATTTAA
ATATTATGATGATTCCAATTATATTTTTTATTTTATTCTTAAATATTAATAACTGATAATATTTA
TAATATTAA
Found at i:28701003 original size:156 final size:147
Alignment explanation
Indices: 28700730--28701124 Score: 360
Period size: 156 Copynumber: 2.6 Consensus size: 147
28700720 TAAATATTAA
* *
28700730 TATTTTATTTTTTAAATATTAATAATTGATCATTTATTTAAAATATTAATATTTGATCATTTAAA
1 TATTTTA--TTTTAAATATTAATAATTGATAATTTATTTATAATATTAATATTT-ATCATTTAAA
* ** *
28700795 TATTGATATTTTATGTATAATTT-AATCATTAATATTGTAAAATATTAATATTTTATTTAATTTA
63 TATTAATATTTTAT-TATAATTTAAATGTTTAAAATTGTAAAATATT-ATA-TTTA--TAATTTA
* *
28700859 AAT-ATTATGATGATCAATTATTTTGTTT
123 AATGATAAT-ATGAT-AATT-TATT-TTT
28700887 TATTTTATTCTTAAATATTAATAATTGATAATTTATTTATAATATTAATAATTTATCATTTAAAT
1 TATTTTATT-TTAAATATTAATAATTGATAATTTATTTATAATATTAAT-ATTTATCATTTAAAT
* *
28700952 ATTAATATTTAACTTATAATTTAAATGTTTATAAAGTAT-TCAAAT-TT-TATTTATAATTTAAA
64 ATTAATATTTTA-TTATAATTTAAATGTTTA-AAA-T-TGTAAAATATTATATTTATAATTTAAA
* *
28701014 TGATAATATGGTTATTTATTTTT
125 TGATAATATGATAATTTATTTTT
* * * * * * *
28701037 TA--TT-TTTTAAATATTTACATTTTATAATTTATTTATAAT-TTAATCATTAAT-TTTTAAACA
1 TATTTTATTTTAAATATTAATAATTGATAATTTATTTATAATATTAAT-ATTTATCATTTAAATA
*
28701097 CTAATATTTTATTTATAATTTAAATGTT
65 TTAATATTTTA-TTATAATTTAAATGTT
28701125 ATTATGATTA
Statistics
Matches: 207, Mismatches: 23, Indels: 29
0.80 0.09 0.11
Matches are distributed among these distances:
144 32 0.15
145 10 0.05
146 29 0.14
147 2 0.01
148 2 0.01
150 5 0.02
151 3 0.01
152 3 0.01
153 14 0.07
154 4 0.02
155 6 0.03
156 68 0.33
157 18 0.09
158 4 0.02
159 6 0.03
160 1 0.00
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (147 bp):
TATTTTATTTTAAATATTAATAATTGATAATTTATTTATAATATTAATATTTATCATTTAAATAT
TAATATTTTATTATAATTTAAATGTTTAAAATTGTAAAATATTATATTTATAATTTAAATGATAA
TATGATAATTTATTTTT
Found at i:28701119 original size:260 final size:259
Alignment explanation
Indices: 28700804--28701380 Score: 658
Period size: 260 Copynumber: 2.2 Consensus size: 259
28700794 ATATTGATAT
* *
28700804 TTTATGTATAATTTAATCATTAATATTGTAAAATATTAATATTTTA-TT-TAATTTAAATATTAT
1 TTTATTTATAATTTAATCATTAATATT-TTAAATATTAATATTTTATTTATAATTTAAATATTAT
* *
28700867 GATGATCAATTATTT-TGTTTTATTTTATTCTTAAATATTAATAAT-TG-ATAATTTATTTATAA
65 --T-AT-AATTATTTAT-TTTTATTTTATT-TT-AATATTAA-AATGTGAATAATTTATTAAAAA
** * *
28700929 TATTAATAATTTATCATTTAAATATTAATATTTAACTT-ATAATTTAA-ATGTTTATAAAGTATT
122 TATTAATAATAGATCATTTAAATATTAATATTTAA-TTAATAATTTAACAT-TTTATAAAATACT
* ***
28700992 CAA-ATTTTATTTATAATTTAAATGATAATATGGTTATTTA-T-T-TTTTATTTTTTAAATATTT
185 -AATATTTTATTTATAATTTAAATGATAATATGATTATTTATTATATTTTATTTTTTAAATAGCA
* *
28701053 ACATTTTATAA
249 ACAATATATAA
* * *
28701064 TTTATTTATAATTTAATCATTAAT-TTTTAAACACTAATATTTTATTTATAATTTAAATGTTATT
1 TTTATTTATAATTTAATCATTAATATTTTAAATATTAATATTTTATTTATAATTTAAATATTATT
* * * *
28701128 ATGATTATTTATTTTTATTTTATTTTATTGTTTAAATGTGAATAATTTATTAAAAATATTAATAA
66 ATAATTATTTATTTTTATTTTATTTTAATATTAAAATGTGAATAATTTATTAAAAATATTAATAA
*
28701193 TAGATCATTTAAATATTAATATTTTATTAATAATTTAATCATTTTATAAAATACTAATATTTTAT
131 TAGATCATTTAAATATTAATATTTAATTAATAATTTAA-CATTTTATAAAATACTAATATTTTAT
* * *
28701258 TTATAATTTAAATGTTAGTATGATTATTTATTTATATTTTATTTTTTAAATAGCAATAATATATA
195 TTATAATTTAAATGATAATATGATTATTTA-TTATATTTTATTTTTTAAATAGCAACAATATATA
28701323 A
259 A
* * * * *
28701324 TTTA-TTAAAATATTAATAAGTAATAATTTAAATATTAATATCTTATTTATAATTTAA
1 TTTATTTATAAT-TTAATCATTAATATTTTAAATATTAATATTTTATTTATAATTTAA
28701381 TCATTAATTT
Statistics
Matches: 270, Mismatches: 32, Indels: 29
0.82 0.10 0.09
Matches are distributed among these distances:
253 3 0.01
254 9 0.03
255 58 0.21
256 64 0.24
257 5 0.02
258 17 0.06
259 11 0.04
260 75 0.28
261 28 0.10
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.54
Consensus pattern (259 bp):
TTTATTTATAATTTAATCATTAATATTTTAAATATTAATATTTTATTTATAATTTAAATATTATT
ATAATTATTTATTTTTATTTTATTTTAATATTAAAATGTGAATAATTTATTAAAAATATTAATAA
TAGATCATTTAAATATTAATATTTAATTAATAATTTAACATTTTATAAAATACTAATATTTTATT
TATAATTTAAATGATAATATGATTATTTATTATATTTTATTTTTTAAATAGCAACAATATATAA
Found at i:28701144 original size:144 final size:146
Alignment explanation
Indices: 28700914--28701454 Score: 442
Period size: 149 Copynumber: 3.6 Consensus size: 146
28700904 TTAATAATTG
* * * * * *
28700914 ATAATTTATTTATAATATTAATAATTTATCATTTAAATATTAATATTTAACTTATAATTTAAATG
1 ATAATTTATTTATAAT-TTAATCATTAAT-TTTTAAATACTAATATTTTATTTATAATTTAAATG
* * * * * ***
28700979 -T-TTATAAAGTATTCAAATTTTATTTATAATTTAAATG-ATAATATGGTTATTTATT-TTTTAT
64 TTATTAT-GATTATT-TATTTTTATTTAT-ATTTAAATGAATAATATGGTAATTTATTAAAATAT
* *
28701040 TTTTTAAAT-ATTTACATTTT
126 TTATTAAATAATTTAAATTTT
*
28701060 ATAATTTATTTATAATTTAATCATTAATTTTTAAACACTAATATTTTATTTATAATTTAAATGTT
1 ATAATTTATTTATAATTTAATCATTAATTTTTAAATACTAATATTTTATTTATAATTTAAATGTT
* * **
28701125 ATTATGATTATTTATTTTTATTT-TATTTTATTGTTTAA-ATGTGAATAATTTATTAAAAATATT
66 ATTATGATTATTTATTTTTATTTATATTTAAATGAATAATATG-G--TAATTTATT-AAAATATT
* * * *
28701188 AATAATAGATCATTTAAATATTA
127 --TATTAAATAATTTAAAT-TTT
* * * *
28701211 ATATTTTATTAATAATTTAATCATT--TTATAAAATACTAATATTTTATTTATAATTTAAATGTT
1 ATAATTTATTTATAATTTAATCATTAATTTTTAAATACTAATATTTTATTTATAATTTAAATGTT
* * * *
28701274 AGTATGATTATTTATTTATATTTTATTTTTTAAATAGCAATAATAT-ATAATTTATTAAAATATT
66 ATTATGATTATTTATTTTTA-TTTA-TATTTAAAT-G-AATAATATGGTAATTTATTAAAATATT
* * *
28701338 AATAAGTAATAATTTAAATATT
127 TATTA--AATAATTTAAATTTT
*
28701360 A-ATATCTTATTTATAATTTAATCATTAATTTTTAAAATATTAATATTTTATTTATAATTTAAAT
1 ATA-AT-TTATTTATAATTTAATCATTAATTTTT-AAATACTAATATTTTATTTATAATTTAAAT
* *
28701424 ATTATTACT-ATTATTTACTTTTATTT-TATTT
63 GTTATTA-TGATTATTTATTTTTATTTATATTT
28701455 TTTCAAAAGT
Statistics
Matches: 316, Mismatches: 53, Indels: 48
0.76 0.13 0.12
Matches are distributed among these distances:
142 10 0.03
143 5 0.02
144 39 0.12
145 24 0.08
146 20 0.06
147 4 0.01
148 3 0.01
149 61 0.19
150 51 0.16
151 34 0.11
152 12 0.04
153 47 0.15
154 4 0.01
155 2 0.01
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (146 bp):
ATAATTTATTTATAATTTAATCATTAATTTTTAAATACTAATATTTTATTTATAATTTAAATGTT
ATTATGATTATTTATTTTTATTTATATTTAAATGAATAATATGGTAATTTATTAAAATATTTATT
AAATAATTTAAATTTT
Found at i:28701215 original size:111 final size:107
Alignment explanation
Indices: 28700995--28701230 Score: 260
Period size: 107 Copynumber: 2.2 Consensus size: 107
28700985 AAGTATTCAA
* * **
28700995 ATTTTATTTATAATTTAAATGATAATATGGTTATTTATTTTTTATTTTTTAAATATTTACATTTT
1 ATTTTATTTATAATTTAAATGATAATATGATTATTTATTTTTTATTTTTTAAATATTTAAATTGA
* * * *
28701060 ATAATTTATTTATAATTTAATCATTAATTTTTAAACACTAAT
66 ATAATTTATTAAAAATTTAATCAATAATATTTAAACACTAAT
* * * * *
28701102 ATTTTATTTATAATTTAAATGTTATTATGATTATTTA-TTTTTATTTTATTTTATTGTTTAAATG
1 ATTTTATTTATAATTTAAATGATAATATGATTATTTATTTTTTA-TTT-TTTAAATATTTAAAT-
* *
28701166 TGAATAATTTATTAAAAATATTAAT-AATAGATCATTTAAATATTAAT
63 TGAATAATTTATTAAAAAT-TTAATCAATA-AT-ATTTAAACACTAAT
*
28701213 ATTTTATTAATAATTTAA
1 ATTTTATTTATAATTTAA
28701231 TCATTTTATA
Statistics
Matches: 107, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
106 6 0.06
107 37 0.35
108 11 0.10
109 18 0.17
110 7 0.07
111 28 0.26
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (107 bp):
ATTTTATTTATAATTTAAATGATAATATGATTATTTATTTTTTATTTTTTAAATATTTAAATTGA
ATAATTTATTAAAAATTTAATCAATAATATTTAAACACTAAT
Found at i:28701380 original size:19 final size:19
Alignment explanation
Indices: 28701349--28701426 Score: 63
Period size: 20 Copynumber: 3.9 Consensus size: 19
28701339 ATAAGTAATA
28701349 ATTTA-AATATTAATATCTT
1 ATTTATAATATTAATAT-TT
28701368 ATTTATAAT-TTAATCATTAAT
1 ATTTATAATATTAAT-ATT--T
* *
28701389 TTTTAAAATATTAATATTTT
1 ATTTATAATATTAATA-TTT
28701409 ATTTATAAT-TTAAATATT
1 ATTTATAATATT-AATATT
28701427 ATTACTATTA
Statistics
Matches: 48, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
19 15 0.31
20 17 0.35
21 9 0.19
22 7 0.15
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTTATAATATTAATATTT
Found at i:28701409 original size:255 final size:253
Alignment explanation
Indices: 28700914--28701411 Score: 564
Period size: 255 Copynumber: 2.0 Consensus size: 253
28700904 TTAATAATTG
* * **
28700914 ATAATTTATTTATAATATTAATAATTTATCATTTAAATATTAATATTTAACTTATAATTTAAATG
1 ATAATTTATTAAAAATATTAATAATAGATCATTTAAATATTAATATTTAACTTATAATTTAAATG
* * *
28700979 TTTATAAAGTATTCAAATTTTATTTATAATTTAAATGATAATATGGTTATTTATTTTTTATTTTT
66 TTTATAAAATACTCAAATTTTATTTATAATTTAAATGATAATATGATTATTTATTTTTTATTTTT
*** * * * * * * *
28701044 TAAATATTTACATTTTATAATTTATTTATAATTTAATCATTAATTTTTAAACACTAATATTTTAT
131 TAAATAGCAACAATATATAATTTATTTAAAATTTAATAAGTAATATTTAAACACTAATATCTTAT
* *** *
28701109 TTATAATTTAAATGTTATTATGATTATTTATTTTTATTTTATTTTATTGTTTAAATGTGA
196 TTATAATTTAAA-GTCATTA-GATTATTTATAAATATTATATTTTATTGTTTAAATGTGA
*
28701169 ATAATTTATTAAAAATATTAATAATAGATCATTTAAATATTAATATTTTA-TTAATAATTTAATC
1 ATAATTTATTAAAAATATTAATAATAGATCATTTAAATATTAATATTTAACTT-ATAATTTAA--
* *
28701233 AT-TTTATAAAATACT-AATATTTTATTTATAATTTAAATGTTAGTATGATTATTTATTTATATT
63 ATGTTTATAAAATACTCAA-ATTTTATTTATAATTTAAATGATAATATGATTATTTA--T-T-TT
* * *
28701296 TTATTTTTTAAATAGCAATAATATATAATTTA-TTAAAATATTAATAAGTAATAATTTAAATATT
123 TTATTTTTTAAATAGCAACAATATATAATTTATTTAAAAT-TTAATAAGTAAT-ATTTAAACACT
28701360 AATATCTTATTTATAATTT-AA-TCATTA-ATT-TTTA-AAATATTAATATTTTATT
186 AATATCTTATTTATAATTTAAAGTCATTAGATTATTTATAAATATT-ATATTTTATT
28701412 TATAATTTAA
Statistics
Matches: 204, Mismatches: 28, Indels: 22
0.80 0.11 0.09
Matches are distributed among these distances:
254 6 0.03
255 69 0.34
256 48 0.24
257 2 0.01
258 6 0.03
259 7 0.03
260 40 0.20
261 26 0.13
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (253 bp):
ATAATTTATTAAAAATATTAATAATAGATCATTTAAATATTAATATTTAACTTATAATTTAAATG
TTTATAAAATACTCAAATTTTATTTATAATTTAAATGATAATATGATTATTTATTTTTTATTTTT
TAAATAGCAACAATATATAATTTATTTAAAATTTAATAAGTAATATTTAAACACTAATATCTTAT
TTATAATTTAAAGTCATTAGATTATTTATAAATATTATATTTTATTGTTTAAATGTGA
Found at i:28701453 original size:153 final size:148
Alignment explanation
Indices: 28701064--28701543 Score: 593
Period size: 149 Copynumber: 3.2 Consensus size: 148
28701054 CATTTTATAA
*
28701064 TTTATTTATAATTTAATCATTAATTTTT-AAACACTAATATTTTATTTATAATTTAAATGTTATT
1 TTTATTTATAATTTAATCATTAATTTTTAAAATACTAATATTTTATTTATAATTTAAATGTTATT
***
28701128 ATGATTATTTATTTTTATTTTATTTTATTGTTTA-AATGTGA-ATAATTTATTAAAAATATTAAT
66 ATGATTATTTA-TTTTATTTTATTTT-TTAAATAGAAT-T-ATATAATTTATT-AAAATATTAAT
*
28701191 AATAGATCATTTAAATATTAATAT
126 AATA-ATAATTTAAATATTAATAT
* * *
28701215 TTTATTAATAATTTAATCA-T--TTTATAAAATACTAATATTTTATTTATAATTTAAATGTTAGT
1 TTTATTTATAATTTAATCATTAATTTTTAAAATACTAATATTTTATTTATAATTTAAATGTTATT
28701277 ATGATTATTTATTTATATTTTATTTTTTAAATAGCAATAATATATAATTTATTAAAATATTAATA
66 ATGATTATTTATTT-TATTTTATTTTTTAAATAG-AAT--TATATAATTTATTAAAATATTAATA
28701342 AGTAATAATTTAAATATTAATAT
127 A-TAATAATTTAAATATTAATAT
* * *
28701365 CTTATTTATAATTTAATCATTAATTTTTAAAATATTAATATTTTATTTATAATTTAAATATTATT
1 TTTATTTATAATTTAATCATTAATTTTTAAAATACTAATATTTTATTTATAATTTAAATGTTATT
*
28701430 ACT-ATTATTTACTTTTATTTTATTTTTTCAAA-AG--TTTTATAATTTATTTAAAATATTAATA
66 A-TGATTATTTA-TTTTATTTTATTTTTT-AAATAGAATTATATAATTTA-TTAAAATATTAATA
* * *
28701491 ATTGATTAGTTAAATATTAATAT
127 A-TAATAATTTAAATATTAATAT
*
28701514 TTTATTTATAATTTAATTATTAATATTTTA
1 TTTATTTATAATTTAATCATTAAT-TTTTA
28701544 TTTACAAATA
Statistics
Matches: 292, Mismatches: 22, Indels: 31
0.85 0.06 0.09
Matches are distributed among these distances:
148 21 0.07
149 111 0.38
150 59 0.20
151 32 0.11
153 62 0.21
154 7 0.02
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (148 bp):
TTTATTTATAATTTAATCATTAATTTTTAAAATACTAATATTTTATTTATAATTTAAATGTTATT
ATGATTATTTATTTTATTTTATTTTTTAAATAGAATTATATAATTTATTAAAATATTAATAATAA
TAATTTAAATATTAATAT
Found at i:28705528 original size:7 final size:7
Alignment explanation
Indices: 28705516--28705541 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
28705506 CTAGGAAATG
28705516 TTTGAAC
1 TTTGAAC
28705523 TTTGAAC
1 TTTGAAC
28705530 TTTGAAC
1 TTTGAAC
28705537 TTTGA
1 TTTGA
28705542 TTAGTGAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (7 bp):
TTTGAAC
Found at i:28710034 original size:37 final size:37
Alignment explanation
Indices: 28709993--28710067 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
28709983 TATAGATTTT
28709993 TCCATTATTAAAATTCTTGAGCCTTTGGGAATTTAAA
1 TCCATTATTAAAATTCTTGAGCCTTTGGGAATTTAAA
*
28710030 TCCATTATTAAAGTTCTTGAGCCTTTGGGAATTTAAA
1 TCCATTATTAAAATTCTTGAGCCTTTGGGAATTTAAA
28710067 T
1 T
28710068 GTCTGTGTGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (37 bp):
TCCATTATTAAAATTCTTGAGCCTTTGGGAATTTAAA
Found at i:28722916 original size:2 final size:2
Alignment explanation
Indices: 28722909--28722983 Score: 125
Period size: 2 Copynumber: 38.0 Consensus size: 2
28722899 TTGTACATAA
28722909 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
28722950 AT AA AN 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
28722984 TAAAAAAGAG
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
1 1 0.01
2 68 0.99
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:28731888 original size:15 final size:15
Alignment explanation
Indices: 28731878--28731907 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
28731868 ATATAAAGTT
28731878 TAAAAAAATAAAAAA
1 TAAAAAAATAAAAAA
28731893 TAAAAAAATAAAAAA
1 TAAAAAAATAAAAAA
28731908 GCCTAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (15 bp):
TAAAAAAATAAAAAA
Found at i:28731889 original size:8 final size:8
Alignment explanation
Indices: 28731878--28731907 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
28731868 ATATAAAGTT
28731878 TAAAAAAA
1 TAAAAAAA
28731886 T-AAAAAA
1 TAAAAAAA
28731893 TAAAAAAA
1 TAAAAAAA
28731901 TAAAAAA
1 TAAAAAA
28731908 GCCTAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (8 bp):
TAAAAAAA
Found at i:28737835 original size:30 final size:30
Alignment explanation
Indices: 28737799--28737911 Score: 142
Period size: 29 Copynumber: 3.8 Consensus size: 30
28737789 GTATAACAAA
*
28737799 ATTTTTTTAAATATGACATGTAACAATAAT
1 ATTTTTTTAAATATGACGTGTAACAATAAT
*
28737829 A-TTTTTTCAATATGACGTGTAACAATAAT
1 ATTTTTTTAAATATGACGTGTAACAATAAT
* *
28737858 ATTTTTTTCAACATGACGTGTAACAACT--T
1 ATTTTTTTAAATATGACGTGTAACAA-TAAT
* *
28737887 TTTTTTTTAACTATGACGTGTAACA
1 ATTTTTTTAAATATGACGTGTAACA
28737912 TGTTTTTATA
Statistics
Matches: 74, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
29 49 0.66
30 24 0.32
31 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (30 bp):
ATTTTTTTAAATATGACGTGTAACAATAAT
Found at i:28737840 original size:29 final size:29
Alignment explanation
Indices: 28737792--28738043 Score: 141
Period size: 29 Copynumber: 9.2 Consensus size: 29
28737782 CATTAAAGTA
* *
28737792 TAACAA-AAT-TTTTTTAAATATGACATG
1 TAACAATAATATTTTTTCAATATGACGTG
28737819 TAACAATAATATTTTTTCAATATGACGTG
1 TAACAATAATATTTTTTCAATATGACGTG
*
28737848 TAACAATAATATTTTTTTCAACATGACGTG
1 TAACAATAATA-TTTTTTCAATATGACGTG
* *
28737878 TAACAACT--TTTTTTTTTAACTATGACGTG
1 TAACAA-TAATATTTTTTCAA-TATGACGTG
* *
28737907 TAAC-AT-GT-TTTTAT-ACATA-G-CGTG
1 TAACAATAATATTTTTTCA-ATATGACGTG
* * *
28737931 TAAAAATAATATTCTTTT-AACATGATGTG
1 TAACAATAATATT-TTTTCAATATGACGTG
* * *
28737960 TAAC-A-ACT-TTTGTT-AATTATGATGTG
1 TAACAATAATATTTTTTCAA-TATGACGTG
* *
28737986 T---AAT-AT-GTTTTT-ATACATGACGTG
1 TAACAATAATATTTTTTCA-ATATGACGTG
* *
28738010 TAACAATAATTTTTTTTCAACATGACGTG
1 TAACAATAATATTTTTTCAATATGACGTG
28738039 TAACA
1 TAACA
28738044 TCATATGCAC
Statistics
Matches: 180, Mismatches: 22, Indels: 44
0.73 0.09 0.18
Matches are distributed among these distances:
24 22 0.12
25 9 0.05
26 15 0.08
27 22 0.12
28 21 0.12
29 66 0.37
30 24 0.13
31 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.42
Consensus pattern (29 bp):
TAACAATAATATTTTTTCAATATGACGTG
Found at i:28737880 original size:59 final size:59
Alignment explanation
Indices: 28737799--28737911 Score: 149
Period size: 59 Copynumber: 1.9 Consensus size: 59
28737789 GTATAACAAA
*
28737799 ATTTTTTTAAATATGACATGTAACAA-TAATATTTTTTCAA-TATGACGTGTAACAATAAT
1 ATTTTTTTAAACATGACATGTAACAACT--TATTTTTTCAACTATGACGTGTAACAATAAT
* * * *
28737858 ATTTTTTTCAACATGACGTGTAACAACTTTTTTTTTTAACTATGACGTGTAACA
1 ATTTTTTTAAACATGACATGTAACAACTTATTTTTTCAACTATGACGTGTAACA
28737912 TGTTTTTATA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
58 9 0.19
59 37 0.79
60 1 0.02
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (59 bp):
ATTTTTTTAAACATGACATGTAACAACTTATTTTTTCAACTATGACGTGTAACAATAAT
Found at i:28737999 original size:79 final size:81
Alignment explanation
Indices: 28737840--28738043 Score: 290
Period size: 79 Copynumber: 2.5 Consensus size: 81
28737830 TTTTTTCAAT
*
28737840 ATGACGTGTAACAATAATATTTTTTTCAACATGACGTGTAACAACTTTTTTTTTTAACTATGACG
1 ATGACGTGTAACAATAATATTTTTTTCAACATGACGTGTAACAAC--TTTTTGTTAACTATGACG
28737905 TGTAACATGTTTTTATAC
64 TGTAACATGTTTTTATAC
* * * * *
28737923 AT-AGCGTGTAAAAATAATATTCTTTT-AACATGATGTGTAACAAC-TTTTGTTAATTATGATGT
1 ATGA-CGTGTAACAATAATATTTTTTTCAACATGACGTGTAACAACTTTTTGTTAACTATGACGT
*
28737985 GTAATATGTTTTTATAC
65 GTAACATGTTTTTATAC
28738002 ATGACGTGTAACAATAAT-TTTTTTTCAACATGACGTGTAACA
1 ATGACGTGTAACAATAATATTTTTTTCAACATGACGTGTAACA
28738044 TCATATGCAC
Statistics
Matches: 108, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
78 6 0.06
79 61 0.56
80 1 0.01
82 18 0.17
83 22 0.20
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.42
Consensus pattern (81 bp):
ATGACGTGTAACAATAATATTTTTTTCAACATGACGTGTAACAACTTTTTGTTAACTATGACGTG
TAACATGTTTTTATAC
Found at i:28741184 original size:30 final size:30
Alignment explanation
Indices: 28741148--28741208 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 30
28741138 ATATTTACGG
28741148 TGTCCAGCTTGTAATGGCAAAACT-CAGGAA
1 TGTCCAGCTTGTAATGGCAAAA-TGCAGGAA
28741178 TGTCCAGCTTGTAATGGCAAAATGCAGGAA
1 TGTCCAGCTTGTAATGGCAAAATGCAGGAA
28741208 T
1 T
28741209 TATAATTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 1 0.03
30 29 0.97
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.25
Consensus pattern (30 bp):
TGTCCAGCTTGTAATGGCAAAATGCAGGAA
Found at i:28748599 original size:14 final size:16
Alignment explanation
Indices: 28748573--28748605 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
28748563 TAGACACCTA
28748573 AAAATATATATAT-AT
1 AAAATATATATATAAT
28748588 AAAATA-ATATATAAT
1 AAAATATATATATAAT
28748603 AAA
1 AAA
28748606 TAAATAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAATATATATATAAT
Found at i:28748610 original size:18 final size:17
Alignment explanation
Indices: 28748571--28748612 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
28748561 TGTAGACACC
*
28748571 TAAA-AATATATATATA
1 TAAATAATATATATAAA
28748587 TAAAATAATATATAATAAA
1 T-AAATAATATAT-ATAAA
28748606 TAAATAA
1 TAAATAA
28748613 ATAATTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 1 0.05
17 3 0.14
18 13 0.59
19 5 0.23
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAATAATATATATAAA
Found at i:28749694 original size:16 final size:16
Alignment explanation
Indices: 28749666--28749707 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
28749656 TTTTTAAAAA
28749666 AATAAAATAAATAAAT
1 AATAAAATAAATAAAT
28749682 AATAATAAT-AATAAAAT
1 AATAA-AATAAAT-AAAT
*
28749699 AAAAAAATA
1 AATAAAATA
28749708 TAAATGGAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AATAAAATAAATAAAT
Found at i:28749698 original size:17 final size:16
Alignment explanation
Indices: 28749660--28749711 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
28749650 ACTATTTTTT
*
28749660 TAAAAAAATAAAATAA
1 TAAAATAATAAAATAA
28749676 -ATAAATAATAATAATAA
1 TA-AAATAATAA-AATAA
*
28749693 TAAAATAAAAAAAT-A
1 TAAAATAATAAAATAA
28749708 TAAA
1 TAAA
28749712 TGGAACAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 6 0.19
16 11 0.35
17 13 0.42
18 1 0.03
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
TAAAATAATAAAATAA
Found at i:28749898 original size:13 final size:13
Alignment explanation
Indices: 28749880--28749912 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
28749870 TAAAAAAATA
*
28749880 ATAAATAATAATG
1 ATAAATAATAACG
28749893 ATAAATAATAACG
1 ATAAATAATAACG
28749906 ATAAATA
1 ATAAATA
28749913 TATGAATAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.64, C:0.03, G:0.06, T:0.27
Consensus pattern (13 bp):
ATAAATAATAACG
Found at i:28753411 original size:228 final size:227
Alignment explanation
Indices: 28753014--28753468 Score: 865
Period size: 228 Copynumber: 2.0 Consensus size: 227
28753004 ACGACCTATC
* *
28753014 AACAGGAATATGAATGCCTCAAGCAACAGAGCACCAGAATTCAAGAGTAGGGTGAATCTTACAGA
1 AACAGGAATATGAACGCCTCAAGCAACAGAGCACCAGAATTCAAGAATAGGGTGAATCTTACAGA
28753079 CAAGCTTATACAGAGAAACAAGACCAGATGGATTACTTGGTTTGGCAAATGAAGGAGGTGGCTTA
66 CAAGCTTATACAGAGAAACAAGACCAGATGGATTACTTGGTTTGGCAAATGAAGGAGGTGGCTTA
28753144 CAAGGCGAGAAGCATGGCTTGGAAGACGGACATATTAAGAAGCCAGATCTTTCCAATTGGAAAAC
131 CAAGGCGAGAAGCATGGCTTGGAAGACGGACATATTAAGAAGCCAGATCTTTCCAATTGGAAAAC
28753209 AAGAGCAATAGTTGATCAAGTATTTAGATGAA
196 AAGAGCAATAGTTGATCAAGTATTTAGATGAA
* *
28753241 NAACAGGAATATGAACGCCTCAAGTAACAGAGCACCAGAATTCAAGAATGGGGTGAATCTTACAG
1 -AACAGGAATATGAACGCCTCAAGCAACAGAGCACCAGAATTCAAGAATAGGGTGAATCTTACAG
28753306 ACAAGCTTATACAGAGAAACAAGACCAGATGGATTACTTGGTTTGGCAAATGAAGGAGGTGGCTT
65 ACAAGCTTATACAGAGAAACAAGACCAGATGGATTACTTGGTTTGGCAAATGAAGGAGGTGGCTT
28753371 ACAAGGCGAGAAGCATGGCTTGGAAGACGGACATATTAAGAAGCCAGATCTTTCCAATTGGAAAA
130 ACAAGGCGAGAAGCATGGCTTGGAAGACGGACATATTAAGAAGCCAGATCTTTCCAATTGGAAAA
28753436 CAAGAGCAATAGTTGATCAAGTATTTAGATGAA
195 CAAGAGCAATAGTTGATCAAGTATTTAGATGAA
28753469 GTGTATAGCC
Statistics
Matches: 223, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
228 223 1.00
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.21
Consensus pattern (227 bp):
AACAGGAATATGAACGCCTCAAGCAACAGAGCACCAGAATTCAAGAATAGGGTGAATCTTACAGA
CAAGCTTATACAGAGAAACAAGACCAGATGGATTACTTGGTTTGGCAAATGAAGGAGGTGGCTTA
CAAGGCGAGAAGCATGGCTTGGAAGACGGACATATTAAGAAGCCAGATCTTTCCAATTGGAAAAC
AAGAGCAATAGTTGATCAAGTATTTAGATGAA
Found at i:28760749 original size:59 final size:59
Alignment explanation
Indices: 28760522--28761067 Score: 675
Period size: 59 Copynumber: 9.1 Consensus size: 59
28760512 GCATTAAGGA
* *
28760522 AATTTTTAAATCGAACCTGTTCTAATG-TAGGTCGAGCCTAGATTAAGTCTAGGAATTTT
1 AATTTTTAAATCGAACCTGTTGTGA-GATAGGTCGAGCCTAGATTAAGTCTAGGAATTTT
* * * * * *
28760581 AGTTTTGTTTAAATCGAACCTGTTATGAGATAGGTCGAACCT-GAATTAAGTTTAGAAATTTC
1 A--ATT-TTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAG-ATTAAGTCTAGGAATTTT
* *
28760643 AATTTTTTCAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTT
1 AA-TTTTT-AAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTT
* * * * *
28760704 AATTTTTAAATCGAACCTGTTTTGATATAGATCGAGACTAGATTAAGCCTAGGAATTTT
1 AATTTTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTT
* *
28760763 AATTTTGTTTAAATTGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTC
1 AA--TT-TTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTT
* * *
28760825 AATTTTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTC
1 AATTTTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTT
* * *
28760884 AATTTTTAAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTC
1 AATTTTT-AAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTT
* **
28760944 AATTTTTAAATCGAACTTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAAAAATTTT
1 AATTTTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTT
* * *
28761003 AATTTTGTTTAAATCAAACCTGTTGTGAGAT-GAGTCGAGCCAAGATTAGGTCTAGGAATTTT
1 AA--TT-TTTAAATCGAACCTGTTGTGAGATAG-GTCGAGCCTAGATTAAGTCTAGGAATTTT
28761065 AAT
1 AAT
28761068 CGAATTTGTT
Statistics
Matches: 429, Mismatches: 42, Indels: 31
0.85 0.08 0.06
Matches are distributed among these distances:
59 155 0.36
60 70 0.16
61 59 0.14
62 145 0.34
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.37
Consensus pattern (59 bp):
AATTTTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTT
Found at i:28760812 original size:121 final size:120
Alignment explanation
Indices: 28760524--28761067 Score: 693
Period size: 121 Copynumber: 4.5 Consensus size: 120
28760514 ATTAAGGAAA
* * *
28760524 TTTTTAAATCGAACCTGTTCTAATG-TAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAGTTTTG
1 TTTTTAAATCGAACCTGTTGTGA-GATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTA--ATT-
* *
28760588 TTTAAATCGAACCTGTTATGAGATAGGTCGA-ACCT-GAATTAAGTTTAGAAATTTCAATT
62 TTTAAATCGAACCTGTTGTGAGATAGGTCGAGA-CTAG-ATTAAGTCTAGAAATTTCAATT
* * *
28760647 TTTTCAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTTAATTTTTA
1 TTTTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTTTTA
* * * * * *
28760712 AATCGAACCTGTTTTGATATAGATCGAGACTAGATTAAGCCTAGGAATTTTAATT
66 AATCGAACCTGTTGTGAGATAGGTCGAGACTAGATTAAGTCTAGAAATTTCAATT
* *
28760767 TTGTTTAAATTGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTTTT
1 TT-TTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTTTT
* * * *
28760832 AAATCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTCAA-T
65 AAATCGAACCTGTTGTGAGATAGGTCGAGACTAGATTAAGTCTAGAAATTTCAATT
* * * *
28760887 TTTTAAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTCAATTTTTA
1 TTTTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTTTTA
* * * *
28760952 AATCGAACTTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAAAAATTTTAATT
66 AATCGAACCTGTTGTGAGATAGGTCGAGACTAGATTAAGTCTAGAAATTTCAATT
* * *
28761007 TTGTTTAAATCAAACCTGTTGTGAGAT-GAGTCGAGCCAAGATTAGGTCTAGGAATTTTAAT
1 TT-TTTAAATCGAACCTGTTGTGAGATAG-GTCGAGCCTAGATTAAGTCTAGGAATTTTAAT
28761068 CGAATTTGTT
Statistics
Matches: 371, Mismatches: 43, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
119 106 0.29
120 57 0.15
121 156 0.42
122 1 0.00
123 51 0.14
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.37
Consensus pattern (120 bp):
TTTTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAATTTTTA
AATCGAACCTGTTGTGAGATAGGTCGAGACTAGATTAAGTCTAGAAATTTCAATT
Found at i:28760953 original size:240 final size:243
Alignment explanation
Indices: 28760526--28761063 Score: 816
Period size: 240 Copynumber: 2.2 Consensus size: 243
28760516 TAAGGAAATT
* * * *
28760526 TTTAAATCGAACCTGTTCTAATG-TAGGTCGAGCCTAGATTAAGTCTAGGAATTTTAGTTTTGTT
1 TTTAAATCGAACCTGTTGTGA-GATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAG-ATTGTT
* *
28760590 TAAATCGAACCTGTTATGAGATAGGTCGAACCTGAATTAAGTTTAGAAATTTCAATTTTTTCAAA
64 TAAATCGAACCTGTTATGAGATAGGTCGAACCTAAATTAAGTTTAGAAATTTCAATTTTTTAAAA
*
28760655 TCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTTAATTTTTAAATCGAAC
129 TCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTCAATTTTTAAATCGAAC
* * **
28760720 CTGTTTTGATATAGATCGAGACTAGATTAAGCCTAGGAATTTTAATTTTG
194 CTGTTGTGAGATAGATCGAGACTAGATTAAGCCTAAAAATTTTAATTTTG
*
28760770 TTTAAATTGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCA-ATT-TTTA
1 TTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAGATTGTTTA
* * *
28760833 AATCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTCAA-TTTTTAAAATC
66 AATCGAACCTGTTATGAGATAGGTCGAACCTAAATTAAGTTTAGAAATTTCAATTTTTTAAAATC
*
28760897 GAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTCAATTTTTAAATCGAACTT
131 GAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTCAATTTTTAAATCGAACCT
* * *
28760962 GTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAAAAATTTTAATTTTG
196 GTTGTGAGATAGATCGAGACTAGATTAAGCCTAAAAATTTTAATTTTG
* * *
28761010 TTTAAATCAAACCTGTTGTGAGAT-GAGTCGAGCCAAGATTAGGTCTAGGAATTT
1 TTTAAATCGAACCTGTTGTGAGATAG-GTCGAGCCTAGATTAAGTCTAGGAATTT
28761064 TAATCGAATT
Statistics
Matches: 269, Mismatches: 23, Indels: 8
0.90 0.08 0.03
Matches are distributed among these distances:
239 1 0.00
240 162 0.60
241 53 0.20
242 2 0.01
243 1 0.00
244 50 0.19
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (243 bp):
TTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAGATTGTTTA
AATCGAACCTGTTATGAGATAGGTCGAACCTAAATTAAGTTTAGAAATTTCAATTTTTTAAAATC
GAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTTTAGGAATTTCAATTTTTAAATCGAACCT
GTTGTGAGATAGATCGAGACTAGATTAAGCCTAAAAATTTTAATTTTG
Found at i:28762305 original size:22 final size:21
Alignment explanation
Indices: 28762272--28762314 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
28762262 ACCCTTTTTG
* *
28762272 TAAAAAATATATATATATAAT
1 TAAAAAACATATATAAATAAT
28762293 TAAAAATACATATATAAATAAT
1 TAAAAA-ACATATATAAATAAT
28762315 AACAATAACG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAAAAACATATATAAATAAT
Found at i:28762394 original size:3 final size:3
Alignment explanation
Indices: 28762382--28762416 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
28762372 CTTGCAAACG
*
28762382 ATA A-A ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
28762417 CTTCATGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:28764478 original size:20 final size:20
Alignment explanation
Indices: 28764455--28764492 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
28764445 TCTTTTCGGG
28764455 TTTTTTTAGTTTTTTTGTGA
1 TTTTTTTAGTTTTTTTGTGA
*
28764475 TTTTTTTATTTTTTTTGT
1 TTTTTTTAGTTTTTTTGT
28764493 TTTTCTGGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.08, C:0.00, G:0.11, T:0.82
Consensus pattern (20 bp):
TTTTTTTAGTTTTTTTGTGA
Found at i:28765369 original size:27 final size:28
Alignment explanation
Indices: 28765317--28765369 Score: 74
Period size: 26 Copynumber: 1.9 Consensus size: 28
28765307 TTAAAATTTT
28765317 TAAAATAGTAATCATTATTTAGCTAAAA
1 TAAAATAGTAATCATTATTTAGCTAAAA
*
28765345 TAAAATA-TAAT-ATTTTTTAGACTAA
1 TAAAATAGTAATCATTATTTAG-CTAA
28765370 TATGTATCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 8 0.35
27 8 0.35
28 7 0.30
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (28 bp):
TAAAATAGTAATCATTATTTAGCTAAAA
Found at i:28765709 original size:59 final size:60
Alignment explanation
Indices: 28765641--28765758 Score: 166
Period size: 59 Copynumber: 2.0 Consensus size: 60
28765631 GAGAATAAAA
* * *
28765641 GAAAGAGTTTTTCTAATTTGATGAATGATAACTGTTTGATTGATTGACA-AAAAAAAAGT
1 GAAAGAGTTTTTCTAATTTGATAAATGATAACTATTTGATTGATTCACACAAAAAAAAGT
* * * *
28765700 GAAAGAGTTTTTTTAATTTGCTAAATGATAATTATTTGATTGGTTCACACAAAAAAAAG
1 GAAAGAGTTTTTCTAATTTGATAAATGATAACTATTTGATTGATTCACACAAAAAAAAG
28765759 AAAATGAGAG
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
59 42 0.82
60 9 0.18
ACGTcount: A:0.41, C:0.06, G:0.17, T:0.36
Consensus pattern (60 bp):
GAAAGAGTTTTTCTAATTTGATAAATGATAACTATTTGATTGATTCACACAAAAAAAAGT
Found at i:28765832 original size:2 final size:2
Alignment explanation
Indices: 28765813--28765854 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
28765803 CTAAAAGATT
28765813 TA TA -A TA TA T- TA TA -A TA TA TA TA TA TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28765851 TA TA
1 TA TA
28765855 AAATANNNNN
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
1 4 0.11
2 32 0.89
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:28765841 original size:15 final size:15
Alignment explanation
Indices: 28765817--28765859 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
28765807 AAGATTTATA
28765817 ATATAT-TATAATAT
1 ATATATATATAATAT
28765831 ATATATATATAATAT
1 ATATATATATAATAT
*
28765846 ATATATATAAAATA
1 ATATATATATAATA
28765860 NNNNNNNNNN
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
14 6 0.22
15 21 0.78
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATATATATATAATAT
Found at i:28765845 original size:13 final size:13
Alignment explanation
Indices: 28765813--28765855 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
28765803 CTAAAAGATT
28765813 TATAATATAT-TA
1 TATAATATATATA
28765825 TA-ATATATATATA
1 TATA-ATATATATA
28765838 TATAATATATATA
1 TATAATATATATA
28765851 TATAA
1 TATAA
28765856 AATANNNNNN
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 1 0.04
12 8 0.29
13 18 0.64
14 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TATAATATATATA
Found at i:28767794 original size:16 final size:15
Alignment explanation
Indices: 28767766--28767808 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 15
28767756 AATTAATTAT
28767766 ATTAAAAATATATAAAA
1 ATTAAAAA-ATAT-AAA
28767783 ATTAAAAAATATAAA
1 ATTAAAAAATATAAA
*
28767798 AGTAAAAAATA
1 ATTAAAAAATA
28767809 ATTAATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 13 0.52
16 4 0.16
17 8 0.32
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (15 bp):
ATTAAAAAATATAAA
Found at i:28768993 original size:2 final size:2
Alignment explanation
Indices: 28768986--28769016 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
28768976 CACCTATAAA
*
28768986 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28769017 ATAAAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:28779646 original size:62 final size:62
Alignment explanation
Indices: 28779433--28779733 Score: 475
Period size: 62 Copynumber: 4.9 Consensus size: 62
28779423 CATTAAAGAA
* *
28779433 TTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAAATTAAGTTTAAGAATTTTAA-TTT-
1 TTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAAGAATTTTAATTTTG
28779493 TTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCT-AGAAATTTTAAATTTTG
1 TTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAAG-AATTTT-AATTTTG
28779556 TTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAAGAATTTTAATTTTG
1 TTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAAGAATTTTAATTTTG
* * * *
28779618 TTTAAATCAAACCTGTTGCGAGATAGGTCGAGCCTAGATTAAGT-TTAGAAATTTTAATTTGG
1 TTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAAG-AATTTTAATTTTG
* *
28779680 TTTAAATCGAACCTGCTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTT
1 TTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAAGAATTT
28779734 NNNNNNNNNN
Statistics
Matches: 223, Mismatches: 11, Indels: 12
0.91 0.04 0.05
Matches are distributed among these distances:
59 2 0.01
60 50 0.22
61 5 0.02
62 110 0.49
63 54 0.24
64 2 0.01
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.36
Consensus pattern (62 bp):
TTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAAGAATTTTAATTTTG
Found at i:28781145 original size:7 final size:7
Alignment explanation
Indices: 28781135--28781173 Score: 69
Period size: 7 Copynumber: 5.4 Consensus size: 7
28781125 AGTATATAGT
28781135 AATAATA
1 AATAATA
28781142 AATAATA
1 AATAATA
28781149 AATAATA
1 AATAATA
28781156 AATAATA
1 AATAATA
28781163 AATAATCA
1 AATAAT-A
28781171 AAT
1 AAT
28781174 TTTTTTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 27 0.87
8 4 0.13
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (7 bp):
AATAATA
Found at i:28789511 original size:2 final size:2
Alignment explanation
Indices: 28789500--28789531 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
28789490 TAGTGATAGT
28789500 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28789532 TTAACCTCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28791586 original size:11 final size:11
Alignment explanation
Indices: 28791549--28791584 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
28791539 CATTACTCTT
28791549 CTCCCCTTCTC
1 CTCCCCTTCTC
28791560 CTCCCCTT-TC
1 CTCCCCTTCTC
*
28791570 CTCCTCTTCTC
1 CTCCCCTTCTC
28791581 CTCC
1 CTCC
28791585 TCCTCCTTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (11 bp):
CTCCCCTTCTC
Found at i:28806619 original size:2 final size:2
Alignment explanation
Indices: 28806612--28806643 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
28806602 ATAGCATTGA
28806612 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
28806644 TAATGCGAAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.