Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold501
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1397941
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31
Warning! 110142 characters in sequence are not A, C, G, or T
File 4 of 5
Found at i:796893 original size:22 final size:22
Alignment explanation
Indices: 796849--796923 Score: 123
Period size: 22 Copynumber: 3.4 Consensus size: 22
796839 AACGTACGTT
*
796849 ACATGATCTCTCAAACATAGGTC
1 ACATGATCTCT-AAACATTGGTC
796872 ACATGATCTCTAAACATTGGTC
1 ACATGATCTCTAAACATTGGTC
*
796894 ACATGATTTCTAAACATTGGTC
1 ACATGATCTCTAAACATTGGTC
796916 ACATGATC
1 ACATGATC
796924 ACAAATGTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
22 38 0.78
23 11 0.22
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (22 bp):
ACATGATCTCTAAACATTGGTC
Found at i:796998 original size:23 final size:23
Alignment explanation
Indices: 796953--797002 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
796943 ACATGATCCC
* *
796953 CCAAA-CATAGGTCACATGGTCT
1 CCAAATCATAGGTCACACGATCT
796975 CCAAATCATAGGTCACACGATCT
1 CCAAATCATAGGTCACACGATCT
796998 -CAAAT
1 CCAAAT
797003 ACTGTAGAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 10 0.40
23 15 0.60
ACGTcount: A:0.36, C:0.28, G:0.14, T:0.22
Consensus pattern (23 bp):
CCAAATCATAGGTCACACGATCT
Found at i:797916 original size:20 final size:20
Alignment explanation
Indices: 797886--797981 Score: 147
Period size: 20 Copynumber: 4.8 Consensus size: 20
797876 GGGATTCACA
*
797886 GTCATGTTTATCTCAGCACT
1 GTCAAGTTTATCTCAGCACT
*
797906 GCCAAGTTTATCTCAGCACT
1 GTCAAGTTTATCTCAGCACT
* *
797926 GTCAAGTGTATCTCGGCACT
1 GTCAAGTTTATCTCAGCACT
*
797946 GTCAAGTTTATCTGAGCACT
1 GTCAAGTTTATCTCAGCACT
797966 GTCAAGTTTATCTCAG
1 GTCAAGTTTATCTCAG
797982 TTTTGTAGAA
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 67 1.00
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (20 bp):
GTCAAGTTTATCTCAGCACT
Found at i:799700 original size:15 final size:15
Alignment explanation
Indices: 799680--799712 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
799670 GTCCGTTGTC
*
799680 TGTCGTCGTTGTCGT
1 TGTCGTCGTCGTCGT
799695 TGTCGTCGTCGTCGT
1 TGTCGTCGTCGTCGT
799710 TGT
1 TGT
799713 AAACTTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.21, G:0.33, T:0.45
Consensus pattern (15 bp):
TGTCGTCGTCGTCGT
Found at i:800163 original size:166 final size:166
Alignment explanation
Indices: 799877--800355 Score: 712
Period size: 166 Copynumber: 2.9 Consensus size: 166
799867 TTGTTGGTAT
* * * * * *** *
799877 TTTTCAAAAATCTTCTTCTCAAAAACTATTAGGCCGGTAAAGCTTAAACTT-GTGTGGAGGCATC
1 TTTTAAAAAAT-TTCTT-TCAAAAACTATCAGGCCAGAAAAGCTCAAA-TTAAAATGGAAGCATC
*
799941 ATCAGGTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATT
63 CTCAGGTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATT
800006 GGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATC
128 GGGGGATCAAGTTTTACATAGGAATATATAGAGAAAATC
* * *
800045 -TTTAAAAATTTTCTTCTCAAAAACTATCAGGCCAG-AAAGATTCAAATTAAAATGGGAGCATCC
1 TTTTAAAAAATTTCTT-TCAAAAACTATCAGGCCAGAAAAG-CTCAAATTAAAATGGAAGCATCC
*
800108 TCATGTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTG
64 TCAGGTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTG
800173 GGGGATCAAGTTTTACATAGGAATATATAGAGAAAATC
129 GGGGATCAAGTTTTACATAGGAATATATAGAGAAAATC
* **
800211 TTTTAAAAAATTTCTTTTAAAAACTATTTGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTC
1 TTTTAAAAAATTTCTTTCAAAAACTATCAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTC
* * *
800276 AGGAAGTGTTGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGAGGCCACAATTGGG
66 AGGTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGG
800341 GGATCAAGTTTTACA
131 GGATCAAGTTTTACA
800356 ATCCTTAAAA
Statistics
Matches: 284, Mismatches: 23, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
165 6 0.02
166 252 0.89
167 26 0.09
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (166 bp):
TTTTAAAAAATTTCTTTCAAAAACTATCAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTC
AGGTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAATTGGG
GGATCAAGTTTTACATAGGAATATATAGAGAAAATC
Found at i:802306 original size:10 final size:10
Alignment explanation
Indices: 802280--802309 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
802270 GATTACTTGT
*
802280 GATTACTTTA
1 GATTACATTA
802290 GATTACATTA
1 GATTACATTA
802300 GATTACATTA
1 GATTACATTA
802310 TCTGTTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (10 bp):
GATTACATTA
Found at i:803847 original size:46 final size:46
Alignment explanation
Indices: 803797--803885 Score: 151
Period size: 46 Copynumber: 1.9 Consensus size: 46
803787 GCCATATATC
*
803797 TATCAACAGTCACCTGGGCTGTAAGAGTAAGTGACGTATATATAAA
1 TATCAACAGTCACCTGGACTGTAAGAGTAAGTGACGTATATATAAA
* *
803843 TATCAACGGTCACCTGGACTGTAAGAGTAAGTGACTTATATAT
1 TATCAACAGTCACCTGGACTGTAAGAGTAAGTGACGTATATAT
803886 CTATCATCTA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (46 bp):
TATCAACAGTCACCTGGACTGTAAGAGTAAGTGACGTATATATAAA
Found at i:805488 original size:30 final size:30
Alignment explanation
Indices: 805452--805611 Score: 212
Period size: 30 Copynumber: 5.1 Consensus size: 30
805442 AAGTTGCGTG
805452 AGAAAAAAGGTAGGGAAAAATAGTCCCTGC
1 AGAAAAAAGGTAGGGAAAAATAGTCCCTGC
805482 AGAAAAAAGGTAGGGAAAAATAGTGACTGTCCCTGC
1 AGAAAAAAGGTAGGG-AAAA-A-T-A--GTCCCTGC
* *
805518 AGAAAAAAGGTAGGGAAAGATAGCCCCTGC
1 AGAAAAAAGGTAGGGAAAAATAGTCCCTGC
**
805548 AGAAAAAAGGTAGGGAAAAATAGTTACTGC
1 AGAAAAAAGGTAGGGAAAAATAGTCCCTGC
* *
805578 AGCAAAAAGGTAGGGAAAGATAGTCCCTGC
1 AGAAAAAAGGTAGGGAAAAATAGTCCCTGC
805608 AGAA
1 AGAA
805612 TTAGATTTAA
Statistics
Matches: 113, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
30 77 0.68
31 4 0.04
32 2 0.02
33 2 0.02
34 2 0.02
35 3 0.03
36 23 0.20
ACGTcount: A:0.45, C:0.13, G:0.28, T:0.14
Consensus pattern (30 bp):
AGAAAAAAGGTAGGGAAAAATAGTCCCTGC
Found at i:805558 original size:66 final size:60
Alignment explanation
Indices: 805452--805611 Score: 230
Period size: 66 Copynumber: 2.6 Consensus size: 60
805442 AAGTTGCGTG
* *
805452 AGAAAAAAGGTAGGGAAAAATAGTCCCTGCAGAAAAAAGGTAGGGAAAAATAGTGACTGTCCCTG
1 AGAAAAAAGGTAGGGAAAGATAGTCCCTGCAGAAAAAAGGTAGGGAAAAATA--G--T-T-ACTG
805517 C
60 C
*
805518 AGAAAAAAGGTAGGGAAAGATAGCCCCTGCAGAAAAAAGGTAGGGAAAAATAGTTACTGC
1 AGAAAAAAGGTAGGGAAAGATAGTCCCTGCAGAAAAAAGGTAGGGAAAAATAGTTACTGC
*
805578 AGCAAAAAGGTAGGGAAAGATAGTCCCTGCAGAA
1 AGAAAAAAGGTAGGGAAAGATAGTCCCTGCAGAA
805612 TTAGATTTAA
Statistics
Matches: 89, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
60 36 0.40
61 1 0.01
62 1 0.01
64 1 0.01
66 50 0.56
ACGTcount: A:0.45, C:0.13, G:0.28, T:0.14
Consensus pattern (60 bp):
AGAAAAAAGGTAGGGAAAGATAGTCCCTGCAGAAAAAAGGTAGGGAAAAATAGTTACTGC
Found at i:808956 original size:22 final size:22
Alignment explanation
Indices: 808931--808975 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
808921 TTAAGGGGTC
808931 CGGGTTCAAATCC-CAGTCTGGT
1 CGGGTTCAAA-CCTCAGTCTGGT
*
808953 CGGGTTCAAACCTTAGTCTGGT
1 CGGGTTCAAACCTCAGTCTGGT
808975 C
1 C
808976 CATCATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 2 0.10
22 19 0.90
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.29
Consensus pattern (22 bp):
CGGGTTCAAACCTCAGTCTGGT
Found at i:813942 original size:17 final size:20
Alignment explanation
Indices: 813907--813947 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
813897 TTGTAAAGGG
813907 GTTGTTGGTTTGTTGTTTTT
1 GTTGTTGGTTTGTTGTTTTT
* *
813927 GTTGTTGGTTTTTTTTTTTT
1 GTTGTTGGTTTGTTGTTTTT
813947 G
1 G
813948 GGTGGGTGTA
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:0.00, C:0.00, G:0.27, T:0.73
Consensus pattern (20 bp):
GTTGTTGGTTTGTTGTTTTT
Found at i:814222 original size:68 final size:68
Alignment explanation
Indices: 814113--814310 Score: 387
Period size: 68 Copynumber: 2.9 Consensus size: 68
814103 GTATAAATCG
814113 AGTAGACCACAGGAGAATTAGGCACAGAATATCCATTTTATAATTCTACAGCATTGTAAGAGTGT
1 AGTAGACCACAGGAGAATTAGGCACAGAATATCCATTTTATAATTCTACAGCATTGTAAGAGTGT
814178 ACA
66 ACA
814181 AGTAGACCACAGGAGAATTAGGCACAGAATATCCATTTTATAATTCTACAGCATTGTAAGAGTGT
1 AGTAGACCACAGGAGAATTAGGCACAGAATATCCATTTTATAATTCTACAGCATTGTAAGAGTGT
814246 ACA
66 ACA
*
814249 AGTAGACCACAGGAGAATTAGGCACAGAATATCCATTTTATAATTCTACAGCATTTTAAGAG
1 AGTAGACCACAGGAGAATTAGGCACAGAATATCCATTTTATAATTCTACAGCATTGTAAGAG
814311 CTAGTGTAAG
Statistics
Matches: 129, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 129 1.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (68 bp):
AGTAGACCACAGGAGAATTAGGCACAGAATATCCATTTTATAATTCTACAGCATTGTAAGAGTGT
ACA
Found at i:815439 original size:31 final size:31
Alignment explanation
Indices: 815399--815465 Score: 127
Period size: 31 Copynumber: 2.2 Consensus size: 31
815389 ACTATGCATA
815399 AGAA-GAATGGGCAAAGAGAGATAACTGCTG
1 AGAATGAATGGGCAAAGAGAGATAACTGCTG
815429 AGAATGAATGGGCAAAGAGAGATAACTGCTG
1 AGAATGAATGGGCAAAGAGAGATAACTGCTG
815460 AGAATG
1 AGAATG
815466 TTACCATTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 4 0.11
31 32 0.89
ACGTcount: A:0.43, C:0.09, G:0.33, T:0.15
Consensus pattern (31 bp):
AGAATGAATGGGCAAAGAGAGATAACTGCTG
Found at i:817170 original size:16 final size:18
Alignment explanation
Indices: 817146--817184 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
817136 GGACTATCCA
817146 TTTGACCTTG-GT-AAAG
1 TTTGACCTTGAGTCAAAG
*
817162 TTTGTCCTTGAGTCAAAG
1 TTTGACCTTGAGTCAAAG
817180 TTTGA
1 TTTGA
817185 TGTACTGCGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 9 0.47
17 2 0.11
18 8 0.42
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.41
Consensus pattern (18 bp):
TTTGACCTTGAGTCAAAG
Found at i:819974 original size:4 final size:4
Alignment explanation
Indices: 819965--820012 Score: 51
Period size: 4 Copynumber: 12.0 Consensus size: 4
819955 TCAATTTATG
* * * * *
819965 ATCA ATCA ATCG ATCG ATCG ATCG ATCG ATCA ATCA ATCA ATCA ATCA
1 ATCA ATCA ATCA ATCA ATCA ATCA ATCA ATCA ATCA ATCA ATCA ATCA
820013 GTTACTCAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (4 bp):
ATCA
Found at i:821789 original size:2 final size:2
Alignment explanation
Indices: 821782--821823 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
821772 ACAGTAAGTC
*
821782 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AC AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
821824 GTTGTATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:823604 original size:31 final size:31
Alignment explanation
Indices: 823561--823621 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
823551 TCTAGTTATT
823561 TAAGATAAAGTTGTACAATTTAACGTGAATA
1 TAAGATAAAGTTGTACAATTTAACGTGAATA
*
823592 TAAGATATAGTTGTACAATTTAACGTGAAT
1 TAAGATAAAGTTGTACAATTTAACGTGAAT
823622 CTAATTTTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.34
Consensus pattern (31 bp):
TAAGATAAAGTTGTACAATTTAACGTGAATA
Found at i:824926 original size:55 final size:54
Alignment explanation
Indices: 824829--825009 Score: 215
Period size: 54 Copynumber: 3.4 Consensus size: 54
824819 AACTGCTATA
* * *
824829 TATGTAGCAGGAATTTTTTTTAGATATTTTAGTTTTCAAATATCTATAAACTGG
1 TATGTAGCAGGAATTTTTTTTAAATATATTAGTTTTCAAATATCTATAAACTGC
*
824883 TATGTTGCAGGAATTTGTTTTTAAATATATTAGTTTTCAAATATCTATAAACTGC
1 TATGTAGCAGGAATTT-TTTTTAAATATATTAGTTTTCAAATATCTATAAACTGC
** * * ** *
824938 TATGTAGCAAGGAA-AATTTTCAGATAT-TTCAGCCTACAAATATCTATAAACTGC
1 TATGTAGC-AGGAATTTTTTTTAAATATATT-AGTTTTCAAATATCTATAAACTGC
824992 TATGTAGCAGG-ATTTTTT
1 TATGTAGCAGGAATTTTTT
825010 ATTATTTTTT
Statistics
Matches: 109, Mismatches: 14, Indels: 9
0.83 0.11 0.07
Matches are distributed among these distances:
52 1 0.01
53 8 0.07
54 53 0.49
55 42 0.39
56 5 0.05
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.42
Consensus pattern (54 bp):
TATGTAGCAGGAATTTTTTTTAAATATATTAGTTTTCAAATATCTATAAACTGC
Found at i:824991 original size:54 final size:54
Alignment explanation
Indices: 824785--825102 Score: 201
Period size: 54 Copynumber: 5.5 Consensus size: 54
824775 CTATAACGAA
* * *
824785 AATTTTCATACATTTCAGCTTACAAATATATATAAACTGCTATATATGTAGCAGGAAT
1 AATTTTCAGATATTTCAGCTTACAAATATCTATAAACTGC----TATGTAGCAGGAAT
** * * * * * *
824843 TTTTTTTAGATATTTTAGTTTTCAAATATCTATAAACTGGTATGTTGCAGGAATT
1 AATTTTCAGATATTTCAGCTTACAAATATCTATAAACTGCTATGTAGCAGGAA-T
** * * * *
824898 TGTTTTTAAATATATT-AGTTTTCAAATATCTATAAACTGCTATGTAGCAAGGAA-
1 AATTTTCAGATAT-TTCAGCTTACAAATATCTATAAACTGCTATGTAGC-AGGAAT
*
824952 AATTTTCAGATATTTCAGCCTACAAATATCTATAAACTGCTATGTAGCAGGATTTTTTATT
1 AATTTTCAGATATTTCAGCTTACAAATATCTATAAACTGCTATGTAGCAGGA------A-T
* * *
825013 ATTTTTTTTAGATATTTCAACTTACAAATTAAATATCTATAAACTGCTATGTAGCAAGGAA-
1 A--ATTTTCAGATATTTCAGCTTAC-----AAATATCTATAAACTGCTATGTAGC-AGGAAT
* * *
825074 AATTTTCCGATATTTCAGTTTTCAAATAT
1 AATTTTCAGATATTTCAGCTTACAAATAT
825103 TTAGTTGTTA
Statistics
Matches: 208, Mismatches: 32, Indels: 44
0.73 0.11 0.15
Matches are distributed among these distances:
53 6 0.03
54 56 0.27
55 42 0.20
56 7 0.03
58 30 0.14
59 17 0.08
61 2 0.01
63 19 0.09
68 25 0.12
69 4 0.02
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (54 bp):
AATTTTCAGATATTTCAGCTTACAAATATCTATAAACTGCTATGTAGCAGGAAT
Found at i:830698 original size:4 final size:4
Alignment explanation
Indices: 830689--830763 Score: 69
Period size: 4 Copynumber: 18.8 Consensus size: 4
830679 TTTCTGCTCT
* * * *
830689 GAGA GAGA GAGA GAGA GAGA GAGA CAGA GAGA CAAA GACA GAGA GAGA
1 GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA
* * * * *
830737 CAGA CAGA CAGA CAGA GACA GAGA GAG
1 GAGA GAGA GAGA GAGA GAGA GAGA GAG
830764 CTTGCTTTCA
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 60 1.00
ACGTcount: A:0.51, C:0.11, G:0.39, T:0.00
Consensus pattern (4 bp):
GAGA
Found at i:830708 original size:14 final size:14
Alignment explanation
Indices: 830689--830763 Score: 96
Period size: 14 Copynumber: 5.4 Consensus size: 14
830679 TTTCTGCTCT
*
830689 GAGAGAGAGAGAGA
1 GAGAGAGAGACAGA
830703 GAGAGAGAGACAGA
1 GAGAGAGAGACAGA
* *
830717 GAGACAAAGACAGA
1 GAGAGAGAGACAGA
*
830731 GAGAGACAGACAGA
1 GAGAGAGAGACAGA
* *
830745 CAGACAGAGACAGA
1 GAGAGAGAGACAGA
830759 GAGAG
1 GAGAG
830764 CTTGCTTTCA
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 51 1.00
ACGTcount: A:0.51, C:0.11, G:0.39, T:0.00
Consensus pattern (14 bp):
GAGAGAGAGACAGA
Found at i:830946 original size:16 final size:16
Alignment explanation
Indices: 830925--830955 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
830915 ATACAAACCT
830925 TTTAACAACCCGATAA
1 TTTAACAACCCGATAA
830941 TTTAACAACCCGATA
1 TTTAACAACCCGATA
830956 TAGCCACTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.42, C:0.26, G:0.06, T:0.26
Consensus pattern (16 bp):
TTTAACAACCCGATAA
Found at i:838605 original size:4 final size:4
Alignment explanation
Indices: 838598--838629 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
838588 CCTTTTTGTT
838598 TTTG TTTG TTTG TTTG TTTTG TTTG TTTG TTT
1 TTTG TTTG TTTG TTTG -TTTG TTTG TTTG TTT
838630 AAAAGTAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (4 bp):
TTTG
Found at i:838619 original size:17 final size:18
Alignment explanation
Indices: 838592--838629 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
838582 ACCCTCCCTT
838592 TTTGTTTTTGTTTGTTTG
1 TTTGTTTTTGTTTGTTTG
838610 TTTG-TTTTGTTTGTTTG
1 TTTGTTTTTGTTTGTTTG
838627 TTT
1 TTT
838630 AAAAGTAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (18 bp):
TTTGTTTTTGTTTGTTTG
Found at i:838620 original size:13 final size:13
Alignment explanation
Indices: 838592--838629 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
838582 ACCCTCCCTT
*
838592 TTTGTTTTTGTTTG
1 TTTGTTTGT-TTTG
838606 TTTGTTTGTTTTG
1 TTTGTTTGTTTTG
838619 TTTGTTTGTTT
1 TTTGTTTGTTT
838630 AAAAGTAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 15 0.65
14 8 0.35
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (13 bp):
TTTGTTTGTTTTG
Found at i:844035 original size:21 final size:22
Alignment explanation
Indices: 844011--844178 Score: 183
Period size: 21 Copynumber: 8.0 Consensus size: 22
844001 TGCGTCTTTT
844011 TACCCCAATGA-ACCCCAATGA
1 TACCCCAATGATACCCCAATGA
844032 TACCCCAATGA-ACCCCAATGA
1 TACCCCAATGATACCCCAATGA
844053 TACCCCAATGA-ACCCCAATGA
1 TACCCCAATGATACCCCAATGA
* * *
844074 TATCCCAATGA-ACCGCAATGT
1 TACCCCAATGATACCCCAATGA
844095 TACCCCAATGATA-CCCAA--A
1 TACCCCAATGATACCCCAATGA
* **
844114 TACACCGAATGATACCCTTATGA
1 TAC-CCCAATGATACCCCAATGA
* *
844137 TA-CCAAATGATATCCCAATGA
1 TACCCCAATGATACCCCAATGA
*
844158 -ACCCCAATGATACCCAAATGA
1 TACCCCAATGATACCCCAATGA
844179 ACTTTGAAAT
Statistics
Matches: 125, Mismatches: 16, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
19 3 0.02
20 10 0.08
21 108 0.86
22 1 0.01
23 3 0.02
ACGTcount: A:0.39, C:0.33, G:0.10, T:0.18
Consensus pattern (22 bp):
TACCCCAATGATACCCCAATGA
Found at i:844038 original size:11 final size:11
Alignment explanation
Indices: 844011--844178 Score: 183
Period size: 10 Copynumber: 16.0 Consensus size: 11
844001 TGCGTCTTTT
844011 TACCCCAATGA
1 TACCCCAATGA
844022 -ACCCCAATGA
1 TACCCCAATGA
844032 TACCCCAATGA
1 TACCCCAATGA
844043 -ACCCCAATGA
1 TACCCCAATGA
844053 TACCCCAATGA
1 TACCCCAATGA
844064 -ACCCCAATGA
1 TACCCCAATGA
*
844074 TATCCCAATGA
1 TACCCCAATGA
* *
844085 -ACCGCAATGT
1 TACCCCAATGA
844095 TACCCCAATGA
1 TACCCCAATGA
844106 TA-CCCAA--A
1 TACCCCAATGA
*
844114 TACACCGAATGA
1 TAC-CCCAATGA
**
844126 TACCCTTATGA
1 TACCCCAATGA
*
844137 TA-CCAAATGA
1 TACCCCAATGA
*
844147 TATCCCAATGA
1 TACCCCAATGA
844158 -ACCCCAATGA
1 TACCCCAATGA
*
844168 TACCCAAATGA
1 TACCCCAATGA
844179 ACTTTGAAAT
Statistics
Matches: 133, Mismatches: 14, Indels: 20
0.80 0.08 0.12
Matches are distributed among these distances:
8 3 0.02
10 63 0.47
11 63 0.47
12 4 0.03
ACGTcount: A:0.39, C:0.33, G:0.10, T:0.18
Consensus pattern (11 bp):
TACCCCAATGA
Found at i:845682 original size:11 final size:11
Alignment explanation
Indices: 845666--845729 Score: 114
Period size: 11 Copynumber: 6.0 Consensus size: 11
845656 ATTTAAAAGT
845666 TCATTGGGGTA
1 TCATTGGGGTA
845677 TCATTGGGGTA
1 TCATTGGGGTA
845688 TCATTGGGGT-
1 TCATTGGGGTA
845698 TCATTGGGGTA
1 TCATTGGGGTA
845709 TCATTGGGGT-
1 TCATTGGGGTA
845719 TCATTGGGGTA
1 TCATTGGGGTA
845730 AAAAGACGCA
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
10 20 0.39
11 31 0.61
ACGTcount: A:0.16, C:0.09, G:0.38, T:0.38
Consensus pattern (11 bp):
TCATTGGGGTA
Found at i:845703 original size:21 final size:21
Alignment explanation
Indices: 845666--845729 Score: 119
Period size: 21 Copynumber: 3.0 Consensus size: 21
845656 ATTTAAAAGT
845666 TCATTGGGGTATCATTGGGGTA
1 TCATTGGGGT-TCATTGGGGTA
845688 TCATTGGGGTTCATTGGGGTA
1 TCATTGGGGTTCATTGGGGTA
845709 TCATTGGGGTTCATTGGGGTA
1 TCATTGGGGTTCATTGGGGTA
845730 AAAAGACGCA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
21 32 0.76
22 10 0.24
ACGTcount: A:0.16, C:0.09, G:0.38, T:0.38
Consensus pattern (21 bp):
TCATTGGGGTTCATTGGGGTA
Found at i:845705 original size:32 final size:31
Alignment explanation
Indices: 845664--845728 Score: 121
Period size: 32 Copynumber: 2.1 Consensus size: 31
845654 GTATTTAAAA
845664 GTTCATTGGGGTATCATTGGGGTATCATTGGG
1 GTTCATTGGGGTATCATTGGGGT-TCATTGGG
845696 GTTCATTGGGGTATCATTGGGGTTCATTGGG
1 GTTCATTGGGGTATCATTGGGGTTCATTGGG
845727 GT
1 GT
845729 AAAAAGACGC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 10 0.30
32 23 0.70
ACGTcount: A:0.14, C:0.09, G:0.38, T:0.38
Consensus pattern (31 bp):
GTTCATTGGGGTATCATTGGGGTTCATTGGG
Found at i:849652 original size:18 final size:20
Alignment explanation
Indices: 849629--849665 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
849619 TAGGTAACTT
849629 TACAGAACT-T-GGATTATA
1 TACAGAACTATAGGATTATA
849647 TACAGAACTATAGGATTAT
1 TACAGAACTATAGGATTAT
849666 TTTTTTCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 1 0.06
20 7 0.41
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (20 bp):
TACAGAACTATAGGATTATA
Found at i:852149 original size:3 final size:3
Alignment explanation
Indices: 852134--852164 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
852124 ATTTGTTTTC
*
852134 GTT GTT GTG GTT GTT GTT GTT GTT GTT GTT G
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT GTT G
852165 ATGATGATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.39, T:0.61
Consensus pattern (3 bp):
GTT
Found at i:852169 original size:3 final size:3
Alignment explanation
Indices: 852163--852209 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
852153 TTGTTGTTGT
*
852163 TGA TGA TGA TGA TAA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
852210 TTTGTAATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (3 bp):
TGA
Found at i:854238 original size:58 final size:58
Alignment explanation
Indices: 854173--854286 Score: 192
Period size: 58 Copynumber: 2.0 Consensus size: 58
854163 AAGGTTTAAG
*
854173 TAAAAAATCAAAATGGAATCATTCGCAAGTTCTGTTAACAGTGAACTTATTCATTGTT
1 TAAAAAATCAAAATGAAATCATTCGCAAGTTCTGTTAACAGTGAACTTATTCATTGTT
* * *
854231 TAAAAAATGAAAATTAAATCATTCGCAAGTTCTGTTAACAGTGAACTTTTTCATTG
1 TAAAAAATCAAAATGAAATCATTCGCAAGTTCTGTTAACAGTGAACTTATTCATTG
854287 ACTCTGCTCT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (58 bp):
TAAAAAATCAAAATGAAATCATTCGCAAGTTCTGTTAACAGTGAACTTATTCATTGTT
Found at i:857041 original size:2 final size:2
Alignment explanation
Indices: 857034--857125 Score: 170
Period size: 2 Copynumber: 47.0 Consensus size: 2
857024 CTGCTTTGTT
857034 GA GA GA GA GA GA GA GA G- GA GA GA GA G- GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
857074 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
857116 GA GA GA GA GA
1 GA GA GA GA GA
857126 TTTTATGGAC
Statistics
Matches: 88, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
1 2 0.02
2 86 0.98
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:860033 original size:32 final size:32
Alignment explanation
Indices: 859992--860054 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
859982 AAGCCCGAGG
859992 CTTTATCCACACTTTATCCACTAAGTTACATA
1 CTTTATCCACACTTTATCCACTAAGTTACATA
860024 CTTTATCCACACTTTATCCACTAAGTTACAT
1 CTTTATCCACACTTTATCCACTAAGTTACAT
860055 CCACACTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.30, C:0.29, G:0.03, T:0.38
Consensus pattern (32 bp):
CTTTATCCACACTTTATCCACTAAGTTACATA
Found at i:860056 original size:25 final size:25
Alignment explanation
Indices: 860028--860079 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
860018 TACATACTTT
860028 ATCCACACTTTATCCACTAAGTTAC
1 ATCCACACTTTATCCACTAAGTTAC
860053 ATCCACACTTTATCCACTAAGTTAC
1 ATCCACACTTTATCCACTAAGTTAC
860078 AT
1 AT
860080 ACTTTATCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.33
Consensus pattern (25 bp):
ATCCACACTTTATCCACTAAGTTAC
Found at i:860085 original size:21 final size:22
Alignment explanation
Indices: 860033--860090 Score: 82
Period size: 25 Copynumber: 2.5 Consensus size: 22
860023 ACTTTATCCA
860033 CACTTTATCCACTAAGTTACAT
1 CACTTTATCCACTAAGTTACAT
860055 CCACACTTTATCCACTAAGTTACAT
1 ---CACTTTATCCACTAAGTTACAT
860080 -ACTTTATCCAC
1 CACTTTATCCAC
860091 ACTTTATCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
21 11 0.33
25 22 0.67
ACGTcount: A:0.31, C:0.31, G:0.03, T:0.34
Consensus pattern (22 bp):
CACTTTATCCACTAAGTTACAT
Found at i:860094 original size:32 final size:32
Alignment explanation
Indices: 860053--861126 Score: 1993
Period size: 32 Copynumber: 33.8 Consensus size: 32
860043 ACTAAGTTAC
*
860053 ATCCACACTTTATCCACTAAGTTACATACTTT
1 ATCCACACTTTATCCACTAAGTTACACACTTT
860085 ATCCACACTTTATCCACTAAGTTACACACTTT
1 ATCCACACTTTATCCACTAAGTTACACACTTT
*
860117 ATCCACACTTTATCCACTAAGTTACATACTTT
1 ATCCACACTTTATCCACTAAGTTACACACTTT
860149 ATCCACACTTTATCCACTAAGTTACACACTTT
1 ATCCACACTTTATCCACTAAGTTACACACTTT
860181 ATCCACACTTTATCCACTAAGTTACACACTTT
1 ATCCACACTTTATCCACTAAGTTACACACTTT
860213 ATCCACACTTTATCCACTAAGTTACACACTTT
1 ATCCACACTTTATCCACTAAGTTACACACTTT
860245 ATCCACACTTTATCCACTAAGTTACACACTTT
1 ATCCACACTTTATCCACTAAGTTACACACTTT
860277 ATCCACACTTTATCCACTAAGTTACACACTTT
1 ATCCACACTTTATCCACTAAGTTACACACTTT
860309 ATCCACACTTTATCCACTAAGTTACACACTTT
1 ATCCACACTTTATCCACTAAGTTACACACTTT
860341 ATCCACACTTTATCCACTAAGTTACACACTTT
1 ATCCACACTTTATCCACTAAGTTACACACTTT
860373 ATCCACACTTTATCCACTAAGTTACACACTTT
1 ATCCACACTTTATCCACTAAGTTACACACTTT
860405 ATCCACACTTTATCCACTAAGTTACACACTTT
1 ATCCACACTTTATCCACTAAGTTACACACTTT
860437 ATCCACACTTTATCCACTAAGTTACACACTTT
1 ATCCACACTTTATCCACTAAGTTACACACTTT
860469 ATCCACACTTTATCCACTAAGTTACACACTTT
1 ATCCACACTTTATCCACTAAGTTACACACTTT
860501 ATCCACACTTTATCCACTAAGTTACACACTTT
1 ATCCACACTTTATCCACTAAGTTACACACTTT
860533 ATCCACACTTTATCCACTAAGTTACACACTTT
1 ATCCACACTTTATCCACTAAGTTACACACTTT
860565 ATCCACACTTTATCCACTAAGTTACACACTTT
1 ATCCACACTTTATCCACTAAGTTACACACTTT
860597 ATCCACACTTTATCCACTAAGTTACACACTTT
1 ATCCACACTTTATCCACTAAGTTACACACTTT
860629 ATCCACACTTTATCCACTAAGTTACACACTTT
1 ATCCACACTTTATCCACTAAGTTACACACTTT
860661 ATCCACACTTTATCCACTAAGTTACACACTTT
1 ATCCACACTTTATCCACTAAGTTACACACTTT
860693 ATCCACACTTTATCCACTAAGTTACACACTTT
1 ATCCACACTTTATCCACTAAGTTACACACTTT
860725 ATCCACACTTTATCCACTAAGTTACACACTTT
1 ATCCACACTTTATCCACTAAGTTACACACTTT
860757 ATCCACACTTTATCCACTAAGTTACACACTTT
1 ATCCACACTTTATCCACTAAGTTACACACTTT
*
860789 ATCCACACTTTATCCACTAAGTTACATACTTT
1 ATCCACACTTTATCCACTAAGTTACACACTTT
*
860821 ATCCACACTTTATCCACTAAGTTAAACACTTT
1 ATCCACACTTTATCCACTAAGTTACACACTTT
*
860853 ATCCACACTTTATCCACTAAGTTACATACTTT
1 ATCCACACTTTATCCACTAAGTTACACACTTT
* **
860885 ATCCATAC--T-T----T-AGTTACATTCTTT
1 ATCCACACTTTATCCACTAAGTTACACACTTT
860909 ATCCACACTTTATCCACTAAGTTACACACTTT
1 ATCCACACTTTATCCACTAAGTTACACACTTT
860941 ATCCACACTTTATCCACTAAGTTACACACTTT
1 ATCCACACTTTATCCACTAAGTTACACACTTT
860973 ATCCACACTTTATCCACTAAGTTACACACTTT
1 ATCCACACTTTATCCACTAAGTTACACACTTT
861005 ATCCACACTTTATCCACTAAGTTACACACTTT
1 ATCCACACTTTATCCACTAAGTTACACACTTT
*
861037 ATCCACACTTTATCCACTAAGTTACATACTTT
1 ATCCACACTTTATCCACTAAGTTACACACTTT
*
861069 ATCCACACTTTATCCACTAAGTTACATACTTT
1 ATCCACACTTTATCCACTAAGTTACACACTTT
*
861101 ATCCACACTTTATCCACCAAGTTACA
1 ATCCACACTTTATCCACTAAGTTACA
861127 TACTGCCGTC
Statistics
Matches: 1019, Mismatches: 15, Indels: 16
0.97 0.01 0.02
Matches are distributed among these distances:
24 19 0.02
25 1 0.00
26 1 0.00
27 1 0.00
29 1 0.00
30 1 0.00
31 1 0.00
32 994 0.98
ACGTcount: A:0.31, C:0.30, G:0.03, T:0.35
Consensus pattern (32 bp):
ATCCACACTTTATCCACTAAGTTACACACTTT
Found at i:860883 original size:21 final size:22
Alignment explanation
Indices: 860859--860914 Score: 69
Period size: 24 Copynumber: 2.5 Consensus size: 22
860849 CTTTATCCAC
860859 ACTTTATCCAC-TAAGTTACAT
1 ACTTTATCCACTTAAGTTACAT
*
860880 ACTTTATCCATACTTTAGTTACAT
1 ACTTTATCC--ACTTAAGTTACAT
*
860904 TCTTTATCCAC
1 ACTTTATCCAC
860915 ACTTTATCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 9 0.30
22 2 0.07
23 2 0.07
24 17 0.57
ACGTcount: A:0.29, C:0.25, G:0.04, T:0.43
Consensus pattern (22 bp):
ACTTTATCCACTTAAGTTACAT
Found at i:860908 original size:24 final size:24
Alignment explanation
Indices: 860872--860920 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
860862 TTATCCACTA
*
860872 AGTTACATACTTTATCCATACTTT
1 AGTTACATACTTTATCCACACTTT
*
860896 AGTTACATTCTTTATCCACACTTT
1 AGTTACATACTTTATCCACACTTT
860920 A
1 A
860921 TCCACTAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.29, C:0.22, G:0.04, T:0.45
Consensus pattern (24 bp):
AGTTACATACTTTATCCACACTTT
Found at i:860938 original size:21 final size:22
Alignment explanation
Indices: 860907--861074 Score: 87
Period size: 21 Copynumber: 7.8 Consensus size: 22
860897 GTTACATTCT
860907 TTATCCACACTTTATCCACTAAG
1 TTAT-CACACTTTATCCACTAAG
**
860930 TTA-CACACTTTATCCAC-ACT
1 TTATCACACTTTATCCACTAAG
860950 TTATC-CACTAAGTTA-CACACT---
1 TTATCACACT---TTATC-CACTAAG
860971 TTATCCACACTTTATCCACTAAG
1 TTAT-CACACTTTATCCACTAAG
**
860994 TTA-CACACTTTATCCAC-ACT
1 TTATCACACTTTATCCACTAAG
861014 TTATC-CACTAAGTTA-CACACT---
1 TTATCACACT---TTATC-CACTAAG
861035 TTATCCACACTTTATCCACTAAG
1 TTAT-CACACTTTATCCACTAAG
*
861058 TTA-CATACTTTATCCAC
1 TTATCACACTTTATCCAC
861075 ACTTTATCCA
Statistics
Matches: 116, Mismatches: 5, Indels: 50
0.68 0.03 0.29
Matches are distributed among these distances:
20 30 0.26
21 53 0.46
22 4 0.03
23 29 0.25
ACGTcount: A:0.31, C:0.31, G:0.03, T:0.35
Consensus pattern (22 bp):
TTATCACACTTTATCCACTAAG
Found at i:869113 original size:63 final size:63
Alignment explanation
Indices: 869009--869135 Score: 200
Period size: 63 Copynumber: 2.0 Consensus size: 63
868999 AGGGCGAAAT
* *
869009 TGGCAAAAATAAAACGAACAAGGGCGAATAGTTACTTGTATACAATAGTTTGTCCACGGTCAG
1 TGGCAAAAATAAAACGAACAAGGGCGAATAGTTACTAGTATACAATAGTTTGCCCACGGTCAG
* * * *
869072 TGGCGAAAATAAAACGAACGAGGGCGAATATTTTCTAGTATACAATAGTTTGCCCACGGTCAG
1 TGGCAAAAATAAAACGAACAAGGGCGAATAGTTACTAGTATACAATAGTTTGCCCACGGTCAG
869135 T
1 T
869136 ATTCATACAT
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (63 bp):
TGGCAAAAATAAAACGAACAAGGGCGAATAGTTACTAGTATACAATAGTTTGCCCACGGTCAG
Found at i:871891 original size:33 final size:33
Alignment explanation
Indices: 871849--871918 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
871839 GCAAAACGAC
871849 GCAGAAACAGGTGCGTCAAATCAGCATGATGGT
1 GCAGAAACAGGTGCGTCAAATCAGCATGATGGT
*
871882 GCAGAAACAGGTGCGTCCAATCAGCATGATGGT
1 GCAGAAACAGGTGCGTCAAATCAGCATGATGGT
871915 -CAGA
1 GCAGA
871919 GCGTTGAGCA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 4 0.11
33 32 0.89
ACGTcount: A:0.33, C:0.20, G:0.30, T:0.17
Consensus pattern (33 bp):
GCAGAAACAGGTGCGTCAAATCAGCATGATGGT
Found at i:877991 original size:8 final size:7
Alignment explanation
Indices: 877966--878095 Score: 90
Period size: 8 Copynumber: 17.7 Consensus size: 7
877956 GCCTTTAGGT
877966 CGAAGATG
1 CGAAG-TG
877974 CGAGAGTG
1 CGA-AGTG
877982 CGAAGTTG
1 CGAAG-TG
877990 CGAAG-G
1 CGAAGTG
877996 CGAAAGTG
1 CG-AAGTG
878004 CGAGAGTG
1 CGA-AGTG
*
878012 CGACG-G
1 CGAAGTG
*
878018 CGAAGGAG
1 CGAA-GTG
878026 CGAAAGTG
1 CG-AAGTG
878034 CGAAGATG
1 CGAAG-TG
*
878042 CGACG-G
1 CGAAGTG
*
878048 CGAAGCG
1 CGAAGTG
878055 CGAAGATG
1 CGAAG-TG
878063 CGAAG-G
1 CGAAGTG
878069 CGAAAGTG
1 CG-AAGTG
878077 CGAAGGTG
1 CGAA-GTG
878085 CGAAG-G
1 CGAAGTG
878091 CGAAG
1 CGAAG
878096 GAGCGATACT
Statistics
Matches: 102, Mismatches: 6, Indels: 30
0.74 0.04 0.22
Matches are distributed among these distances:
6 21 0.21
7 23 0.23
8 54 0.53
9 4 0.04
ACGTcount: A:0.32, C:0.16, G:0.44, T:0.08
Consensus pattern (7 bp):
CGAAGTG
Found at i:878005 original size:14 final size:14
Alignment explanation
Indices: 877966--878101 Score: 75
Period size: 14 Copynumber: 9.2 Consensus size: 14
877956 GCCTTTAGGT
*
877966 CGAAGATGCGAGAGTG
1 CGAAG-TGCGA-AGAG
877982 CGAAGTTGCGAAG-G
1 CGAAG-TGCGAAGAG
*
877996 CGAAAGTGCGAGAGTG
1 CG-AAGTGCGA-AGAG
*
878012 CGACG-GCGAAGGAG
1 CGAAGTGCGAA-GAG
878026 CGAAAGTGCGAAGATG
1 CG-AAGTGCGAAGA-G
* *
878042 CGACG-GCGAAGCG
1 CGAAGTGCGAAGAG
878055 CGAAGATGCGAAG-G
1 CGAAG-TGCGAAGAG
*
878069 CGAAAGTGCGAAGGTG
1 CG-AAGTGCGAA-GAG
878085 CGAAG-GCGAAGGAG
1 CGAAGTGCGAA-GAG
878099 CGA
1 CGA
878102 TACTACTATC
Statistics
Matches: 100, Mismatches: 8, Indels: 26
0.75 0.06 0.19
Matches are distributed among these distances:
13 6 0.06
14 42 0.42
15 28 0.28
16 24 0.24
ACGTcount: A:0.32, C:0.16, G:0.44, T:0.08
Consensus pattern (14 bp):
CGAAGTGCGAAGAG
Found at i:878008 original size:30 final size:30
Alignment explanation
Indices: 877972--878052 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 30
877962 AGGTCGAAGA
877972 TGCGAGAGTGCGAAGTTGCGAA-G-GCGAAAG
1 TGCGAGAGTGCGAAG--GCGAAGGAGCGAAAG
*
878002 TGCGAGAGTGCGACGGCGAAGGAGCGAAAG
1 TGCGAGAGTGCGAAGGCGAAGGAGCGAAAG
*
878032 TGCGA-AGATGCGACGGCGAAG
1 TGCGAGAG-TGCGAAGGCGAAG
878053 CGCGAAGATG
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
28 5 0.11
29 3 0.06
30 39 0.83
ACGTcount: A:0.30, C:0.16, G:0.44, T:0.10
Consensus pattern (30 bp):
TGCGAGAGTGCGAAGGCGAAGGAGCGAAAG
Found at i:878050 original size:22 final size:22
Alignment explanation
Indices: 877966--878094 Score: 108
Period size: 22 Copynumber: 5.8 Consensus size: 22
877956 GCCTTTAGGT
877966 CGAAGATGCGAGAGTGCG-AAGTTG
1 CGAAGATGCGA-AG-GCGAAAG-TG
*
877990 CGAAG--GCGAAAGTGCGAGAGTG
1 CGAAGATGCG-AAG-GCGAAAGTG
*
878012 CGACG--GCGAAGGAGCGAAAGTG
1 CGAAGATGCGAA-G-GCGAAAGTG
* *
878034 CGAAGATGCGACGGCG-AAGCG
1 CGAAGATGCGAAGGCGAAAGTG
878055 CGAAGATGCGAAGGCGAAAGTG
1 CGAAGATGCGAAGGCGAAAGTG
*
878077 CGAAGGTGCGAAGGCGAA
1 CGAAGATGCGAAGGCGAA
878095 GGAGCGATAC
Statistics
Matches: 89, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
21 21 0.24
22 55 0.62
23 4 0.04
24 9 0.10
ACGTcount: A:0.32, C:0.16, G:0.43, T:0.09
Consensus pattern (22 bp):
CGAAGATGCGAAGGCGAAAGTG
Found at i:878101 original size:22 final size:21
Alignment explanation
Indices: 878033--878101 Score: 84
Period size: 22 Copynumber: 3.2 Consensus size: 21
878023 GAGCGAAAGT
* *
878033 GCGAAGATGCGACGGCGAAGC
1 GCGAAGATGCGAAGGCGAAGA
*
878054 GCGAAGATGCGAAGGCGAAAGT
1 GCGAAGATGCGAAGGCG-AAGA
*
878076 GCGAAGGTGCGAAGGCGAAGGA
1 GCGAAGATGCGAAGGCGAA-GA
878098 GCGA
1 GCGA
878102 TACTACTATC
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
21 18 0.43
22 24 0.57
ACGTcount: A:0.32, C:0.17, G:0.45, T:0.06
Consensus pattern (21 bp):
GCGAAGATGCGAAGGCGAAGA
Found at i:878133 original size:14 final size:13
Alignment explanation
Indices: 878115--878174 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 13
878105 TACTATCGCT
878115 CCTTCGC-CTTCG
1 CCTTCGCACTTCG
878127 CAACTTCGCACTCTCG
1 C--CTTCGCACT-TCG
878143 CCTTCGCACCTTCG
1 CCTTCGCA-CTTCG
878157 CACTTTCGC-CTTCG
1 C-C-TTCGCACTTCG
878171 CCTT
1 CCTT
878175 TTTTGATAGC
Statistics
Matches: 41, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
12 3 0.07
13 1 0.02
14 23 0.56
15 5 0.12
16 9 0.22
ACGTcount: A:0.08, C:0.47, G:0.13, T:0.32
Consensus pattern (13 bp):
CCTTCGCACTTCG
Found at i:878143 original size:22 final size:22
Alignment explanation
Indices: 878118--878171 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
878108 TATCGCTCCT
878118 TCGCCTTCGCAACTTCGCACTC
1 TCGCCTTCGCAACTTCGCACTC
* *
878140 TCGCCTTCGCACCTTCGCACTT
1 TCGCCTTCGCAACTTCGCACTC
878162 TCGCCTTCGC
1 TCGCCTTCGC
878172 CTTTTTTGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.09, C:0.46, G:0.15, T:0.30
Consensus pattern (22 bp):
TCGCCTTCGCAACTTCGCACTC
Found at i:880042 original size:22 final size:22
Alignment explanation
Indices: 880014--880059 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
880004 TTATAAAAAG
880014 GCGAAGGCGAAAGTGCGAAGAT
1 GCGAAGGCGAAAGTGCGAAGAT
*
880036 GCGAAGGCGAGAGTGCGAAGAT
1 GCGAAGGCGAAAGTGCGAAGAT
880058 GC
1 GC
880060 CAATTATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.15, G:0.43, T:0.09
Consensus pattern (22 bp):
GCGAAGGCGAAAGTGCGAAGAT
Found at i:880203 original size:200 final size:200
Alignment explanation
Indices: 879860--880259 Score: 800
Period size: 200 Copynumber: 2.0 Consensus size: 200
879850 CCGACAAATA
879860 CAATTATTTATCCACCCCACCCCCTATAGAAAAAGTTATGGATCTGCGCAGGCTGTTGAAAATAA
1 CAATTATTTATCCACCCCACCCCCTATAGAAAAAGTTATGGATCTGCGCAGGCTGTTGAAAATAA
879925 ATTCTAAAAAGTTCATCGTCTGCCTCAGATGTCCTTTTATACAGCTAAAATTGTCTTTAAACGAT
66 ATTCTAAAAAGTTCATCGTCTGCCTCAGATGTCCTTTTATACAGCTAAAATTGTCTTTAAACGAT
879990 AGAGAGCTCCACAATTATAAAAAGGCGAAGGCGAAAGTGCGAAGATGCGAAGGCGAGAGTGCGAA
131 AGAGAGCTCCACAATTATAAAAAGGCGAAGGCGAAAGTGCGAAGATGCGAAGGCGAGAGTGCGAA
880055 GATGC
196 GATGC
880060 CAATTATTTATCCACCCCACCCCCTATAGAAAAAGTTATGGATCTGCGCAGGCTGTTGAAAATAA
1 CAATTATTTATCCACCCCACCCCCTATAGAAAAAGTTATGGATCTGCGCAGGCTGTTGAAAATAA
880125 ATTCTAAAAAGTTCATCGTCTGCCTCAGATGTCCTTTTATACAGCTAAAATTGTCTTTAAACGAT
66 ATTCTAAAAAGTTCATCGTCTGCCTCAGATGTCCTTTTATACAGCTAAAATTGTCTTTAAACGAT
880190 AGAGAGCTCCACAATTATAAAAAGGCGAAGGCGAAAGTGCGAAGATGCGAAGGCGAGAGTGCGAA
131 AGAGAGCTCCACAATTATAAAAAGGCGAAGGCGAAAGTGCGAAGATGCGAAGGCGAGAGTGCGAA
880255 GATGC
196 GATGC
880260 GAAGGCGAGA
Statistics
Matches: 200, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
200 200 1.00
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.24
Consensus pattern (200 bp):
CAATTATTTATCCACCCCACCCCCTATAGAAAAAGTTATGGATCTGCGCAGGCTGTTGAAAATAA
ATTCTAAAAAGTTCATCGTCTGCCTCAGATGTCCTTTTATACAGCTAAAATTGTCTTTAAACGAT
AGAGAGCTCCACAATTATAAAAAGGCGAAGGCGAAAGTGCGAAGATGCGAAGGCGAGAGTGCGAA
GATGC
Found at i:880233 original size:14 final size:15
Alignment explanation
Indices: 880210--880275 Score: 54
Period size: 14 Copynumber: 4.6 Consensus size: 15
880200 ACAATTATAA
880210 AAAG-GCGAAG-GCG
1 AAAGTGCGAAGTGCG
880223 AAAGTGCGAAGATGCG
1 AAAGTGCGAAG-TGCG
880239 -AAG-GCGAGAGTGCG
1 AAAGTGCGA-AGTGCG
880253 -AAGATGCGAAG-GCG
1 AAAG-TGCGAAGTGCG
*
880267 AGAGTGCGA
1 AAAGTGCGA
880276 TAGTAGTTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
13 4 0.09
14 25 0.56
15 9 0.20
16 7 0.16
ACGTcount: A:0.35, C:0.14, G:0.44, T:0.08
Consensus pattern (15 bp):
AAAGTGCGAAGTGCG
Found at i:880242 original size:22 final size:22
Alignment explanation
Indices: 880214--880275 Score: 115
Period size: 22 Copynumber: 2.8 Consensus size: 22
880204 TTATAAAAAG
*
880214 GCGAAGGCGAAAGTGCGAAGAT
1 GCGAAGGCGAGAGTGCGAAGAT
880236 GCGAAGGCGAGAGTGCGAAGAT
1 GCGAAGGCGAGAGTGCGAAGAT
880258 GCGAAGGCGAGAGTGCGA
1 GCGAAGGCGAGAGTGCGA
880276 TAGTAGTTTC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.32, C:0.15, G:0.45, T:0.08
Consensus pattern (22 bp):
GCGAAGGCGAGAGTGCGAAGAT
Found at i:880275 original size:8 final size:7
Alignment explanation
Indices: 880214--880275 Score: 58
Period size: 8 Copynumber: 8.6 Consensus size: 7
880204 TTATAAAAAG
880214 GCGAAG-
1 GCGAAGT
880220 GCGAAAGT
1 GCG-AAGT
880228 GCGAAGAT
1 GCGAAG-T
880236 GCGAAG-
1 GCGAAGT
880242 GCGAGAGT
1 GCGA-AGT
880250 GCGAAGAT
1 GCGAAG-T
880258 GCGAAG-
1 GCGAAGT
880264 GCGAGAGT
1 GCGA-AGT
880272 GCGA
1 GCGA
880276 TAGTAGTTTC
Statistics
Matches: 48, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
6 11 0.23
7 12 0.25
8 25 0.52
ACGTcount: A:0.32, C:0.15, G:0.45, T:0.08
Consensus pattern (7 bp):
GCGAAGT
Found at i:880308 original size:14 final size:14
Alignment explanation
Indices: 880291--880394 Score: 65
Period size: 14 Copynumber: 7.1 Consensus size: 14
880281 GTTTCGCCCC
880291 TTCGCCTTCGCACT
1 TTCGCCTTCGCACT
880305 TTCGCCTTCGCA-T
1 TTCGCCTTCGCACT
880318 CTTCGCGCTTCGC-C-
1 -TTCGC-CTTCGCACT
*
880332 GTCGCATCTTCGCACT
1 TTCGC--CTTCGCACT
880348 TTCGCTCCTTCGC-C-
1 TTCG--CCTTCGCACT
*
880362 GTCGCACCTTCGCACT
1 TTCG--CCTTCGCACT
*
880378 TTCGCCGTCGCAACT
1 TTCGCCTTCGC-ACT
880393 TT
1 TT
880395 GCACTCTCGC
Statistics
Matches: 72, Mismatches: 7, Indels: 21
0.72 0.07 0.21
Matches are distributed among these distances:
13 5 0.07
14 40 0.56
15 14 0.19
16 12 0.17
18 1 0.01
ACGTcount: A:0.08, C:0.42, G:0.17, T:0.33
Consensus pattern (14 bp):
TTCGCCTTCGCACT
Found at i:880310 original size:22 final size:21
Alignment explanation
Indices: 880282--880394 Score: 79
Period size: 22 Copynumber: 5.1 Consensus size: 21
880272 GCGATAGTAG
880282 TTTCGCCCCTTCGCCTTCGCAC
1 TTTCG-CCCTTCGCCTTCGCAC
*
880304 TTTCG-CCTTCGCATCTTCGCGC
1 TTTCGCCCTTCGC--CTTCGCAC
*
880326 -TTCG-CCGTCGCATCTTCGCAC
1 TTTCGCCCTTCGC--CTTCGCAC
*
880347 TTTCGCTCCTTCGCCGTCGCAC
1 TTTCGC-CCTTCGCCTTCGCAC
* * *
880369 CTTCGCACTTTCGCCGTCGCAAC
1 TTTCGC-CCTTCGCCTTCGC-AC
880392 TTT
1 TTT
880395 GCACTCTCGC
Statistics
Matches: 76, Mismatches: 9, Indels: 11
0.79 0.09 0.11
Matches are distributed among these distances:
20 7 0.09
21 19 0.25
22 40 0.53
23 4 0.05
24 6 0.08
ACGTcount: A:0.07, C:0.43, G:0.17, T:0.33
Consensus pattern (21 bp):
TTTCGCCCTTCGCCTTCGCAC
Found at i:880331 original size:21 final size:21
Alignment explanation
Indices: 880305--880344 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
880295 CCTTCGCACT
*
880305 TTCGCCTTCGCATCTTCGCGC
1 TTCGCCGTCGCATCTTCGCGC
880326 TTCGCCGTCGCATCTTCGC
1 TTCGCCGTCGCATCTTCGC
880345 ACTTTCGCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.05, C:0.42, G:0.20, T:0.33
Consensus pattern (21 bp):
TTCGCCGTCGCATCTTCGCGC
Found at i:880361 original size:30 final size:30
Alignment explanation
Indices: 880325--880382 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
880315 CATCTTCGCG
*
880325 CTTCGCCGTCGCATCTTCGCACTTTCGCTC
1 CTTCGCCGTCGCACCTTCGCACTTTCGCTC
880355 CTTCGCCGTCGCACCTTCGCACTTTCGC
1 CTTCGCCGTCGCACCTTCGCACTTTCGC
880383 CGTCGCAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.07, C:0.45, G:0.17, T:0.31
Consensus pattern (30 bp):
CTTCGCCGTCGCACCTTCGCACTTTCGCTC
Found at i:880398 original size:22 final size:22
Alignment explanation
Indices: 880356--880404 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
880346 CTTTCGCTCC
*
880356 TTCGCCGTCGCACCTTCGCACT
1 TTCGCCGTCGCAACTTCGCACT
*
880378 TTCGCCGTCGCAACTTTGCACT
1 TTCGCCGTCGCAACTTCGCACT
*
880400 CTCGC
1 TTCGC
880405 ACCTCGACCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.10, C:0.43, G:0.18, T:0.29
Consensus pattern (22 bp):
TTCGCCGTCGCAACTTCGCACT
Found at i:882077 original size:2 final size:2
Alignment explanation
Indices: 882072--882117 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
882062 GTTTGTCTCT
882072 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
882114 GA GA
1 GA GA
882118 TGAACTAATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:887598 original size:19 final size:19
Alignment explanation
Indices: 887563--887600 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
887553 GCGGATCTAA
887563 GTTTTCTTTATTTTTATTT
1 GTTTTCTTTATTTTTATTT
*
887582 GTTTT-TTTTTTTCTTATTT
1 GTTTTCTTTATTT-TTATTT
887601 TTTAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.08, C:0.05, G:0.05, T:0.82
Consensus pattern (19 bp):
GTTTTCTTTATTTTTATTT
Found at i:887639 original size:22 final size:21
Alignment explanation
Indices: 887609--887655 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
887599 TTTTTAAATT
**
887609 ATATCTCTTAACCATTTTATG
1 ATATCTCTTAACCACGTTATG
*
887630 ATATCCTCTTGACCACGTTATG
1 ATAT-CTCTTAACCACGTTATG
887652 ATAT
1 ATAT
887656 ATTAGAAGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.43
Consensus pattern (21 bp):
ATATCTCTTAACCACGTTATG
Found at i:891140 original size:19 final size:19
Alignment explanation
Indices: 891118--891225 Score: 58
Period size: 19 Copynumber: 5.2 Consensus size: 19
891108 TGTTAAAACG
891118 AATTTAAATCGTTATAACA
1 AATTTAAATCGTTATAACA
* *
891137 AATTTTTGAATCCGTTATAACG
1 AA--TTTAAAT-CGTTATAACA
* *
891159 AA-TCAAATTGGTTATATAACA
1 AATTTAAA-TCG-T-TATAACA
*
891180 AATTTTAGGAATTCGTTATAACG
1 AA-TTTA--AA-TCGTTATAACA
891203 AATTT-AATCTGTTATAACA
1 AATTTAAATC-GTTATAACA
891222 AATT
1 AATT
891226 CGCTGAATTC
Statistics
Matches: 68, Mismatches: 10, Indels: 22
0.68 0.10 0.22
Matches are distributed among these distances:
18 2 0.03
19 20 0.29
20 2 0.03
21 14 0.21
22 14 0.21
23 10 0.15
24 1 0.01
25 5 0.07
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (19 bp):
AATTTAAATCGTTATAACA
Found at i:891217 original size:44 final size:41
Alignment explanation
Indices: 891104--891225 Score: 131
Period size: 44 Copynumber: 2.9 Consensus size: 41
891094 CGAATTCTTA
* * *
891104 AATTTGTTAAAACGAATTTAAATC-GTTATAACAAATTTTTG
1 AATTCGTTATAACGAATTT-AATCTGTTATAACAAATTTTGG
* **
891145 AATCCGTTATAACGAATCAAAT-TGGTTATATAACAAATTTTAGG
1 AATTCGTTATAACGAATTTAATCT-G-T-TATAACAAATTTT-GG
891189 AATTCGTTATAACGAATTTAATCTGTTATAACAAATT
1 AATTCGTTATAACGAATTTAATCTGTTATAACAAATT
891226 CGCTGAATTC
Statistics
Matches: 66, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
40 3 0.05
41 15 0.23
42 12 0.18
43 14 0.21
44 21 0.32
45 1 0.02
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.39
Consensus pattern (41 bp):
AATTCGTTATAACGAATTTAATCTGTTATAACAAATTTTGG
Found at i:898838 original size:78 final size:78
Alignment explanation
Indices: 898744--898899 Score: 303
Period size: 78 Copynumber: 2.0 Consensus size: 78
898734 ATATTCCTCT
*
898744 CGTACATATTCACCTCTCCCTCTAATTCGAGTTTTGGTGTTCAAAATTAGACATTGTTTTGAGTT
1 CGTACATATTCACCTCTCCCTCTAAATCGAGTTTTGGTGTTCAAAATTAGACATTGTTTTGAGTT
898809 TATAAAATCGACG
66 TATAAAATCGACG
898822 CGTACATATTCACCTCTCCCTCTAAATCGAGTTTTGGTGTTCAAAATTAGACATTGTTTTGAGTT
1 CGTACATATTCACCTCTCCCTCTAAATCGAGTTTTGGTGTTCAAAATTAGACATTGTTTTGAGTT
898887 TATAAAATCGACG
66 TATAAAATCGACG
898900 TTCGATTTTT
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (78 bp):
CGTACATATTCACCTCTCCCTCTAAATCGAGTTTTGGTGTTCAAAATTAGACATTGTTTTGAGTT
TATAAAATCGACG
Found at i:899920 original size:12 final size:12
Alignment explanation
Indices: 899900--899942 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
899890 CAGAGAATGG
*
899900 CGGACACACGGA
1 CGGATACACGGA
899912 CGGATACAC-GA
1 CGGATACACGGA
*
899923 GCGGATACATGGA
1 -CGGATACACGGA
899936 CGGATAC
1 CGGATAC
899943 GGCACTACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 2 0.07
12 23 0.85
13 2 0.07
ACGTcount: A:0.33, C:0.26, G:0.33, T:0.09
Consensus pattern (12 bp):
CGGATACACGGA
Found at i:901618 original size:25 final size:25
Alignment explanation
Indices: 901545--901612 Score: 136
Period size: 25 Copynumber: 2.7 Consensus size: 25
901535 ATAGATGATA
901545 AAGTATGGGGAGGTGTCCTATGTTT
1 AAGTATGGGGAGGTGTCCTATGTTT
901570 AAGTATGGGGAGGTGTCCTATGTTT
1 AAGTATGGGGAGGTGTCCTATGTTT
901595 AAGTATGGGGAGGTGTCC
1 AAGTATGGGGAGGTGTCC
901613 GTTGTTGGCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.21, C:0.09, G:0.38, T:0.32
Consensus pattern (25 bp):
AAGTATGGGGAGGTGTCCTATGTTT
Found at i:902596 original size:21 final size:21
Alignment explanation
Indices: 902570--902778 Score: 355
Period size: 21 Copynumber: 10.0 Consensus size: 21
902560 GTGGAAATCT
902570 ATTCACTAACTGTACGTTAAC
1 ATTCACTAACTGTACGTTAAC
*
902591 ATTCACTAAATGTACGTTAAC
1 ATTCACTAACTGTACGTTAAC
* *
902612 ATTCACTAACTGTACGTAAAT
1 ATTCACTAACTGTACGTTAAC
902633 ATTCACTAACTGTACGTTAAC
1 ATTCACTAACTGTACGTTAAC
902654 ATTCACTAACTGTACGTTAAC
1 ATTCACTAACTGTACGTTAAC
902675 ATTCACTAACTGTACGTTAAC
1 ATTCACTAACTGTACGTTAAC
* *
902696 ATTCACTAACTGTACGTAAAT
1 ATTCACTAACTGTACGTTAAC
902717 ATTCACTAACTGTACGTTAAC
1 ATTCACTAACTGTACGTTAAC
*
902738 ATTCACGAACTGTACGTTAAC
1 ATTCACTAACTGTACGTTAAC
*
902759 ATTCACGAACTGTACGTTAA
1 ATTCACTAACTGTACGTTAA
902779 ATTTGCATTG
Statistics
Matches: 177, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 177 1.00
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.33
Consensus pattern (21 bp):
ATTCACTAACTGTACGTTAAC
Found at i:908960 original size:1 final size:1
Alignment explanation
Indices: 908954--908987 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
908944 NNNNNNNNNN
908954 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
908988 TATACCTAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:929529 original size:21 final size:21
Alignment explanation
Indices: 929505--929544 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
929495 TTAAGTTCTC
929505 CTTAAAGATAGCTTAAAGATG
1 CTTAAAGATAGCTTAAAGATG
*
929526 CTTAAAGGTAGCTTAAAGA
1 CTTAAAGATAGCTTAAAGA
929545 CGATCTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.10, G:0.20, T:0.28
Consensus pattern (21 bp):
CTTAAAGATAGCTTAAAGATG
Found at i:929530 original size:10 final size:11
Alignment explanation
Indices: 929505--929544 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
929495 TTAAGTTCTC
929505 CTTAAAGATAG
1 CTTAAAGATAG
929516 CTTAAAGAT-G
1 CTTAAAGATAG
*
929526 CTTAAAGGTAG
1 CTTAAAGATAG
929537 CTTAAAGA
1 CTTAAAGA
929545 CGATCTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.42, C:0.10, G:0.20, T:0.28
Consensus pattern (11 bp):
CTTAAAGATAG
Found at i:929628 original size:22 final size:22
Alignment explanation
Indices: 929578--929630 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
929568 TATATGTGTT
929578 GCTTAAAGATGACTTAAAGAAA
1 GCTTAAAGATGACTTAAAGAAA
* * * **
929600 GCGTAAAGCTGGCTTAAAGGCA
1 GCTTAAAGATGACTTAAAGAAA
929622 GCTTAAAGA
1 GCTTAAAGA
929631 CTATCTTTAA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.42, C:0.13, G:0.25, T:0.21
Consensus pattern (22 bp):
GCTTAAAGATGACTTAAAGAAA
Found at i:929651 original size:11 final size:11
Alignment explanation
Indices: 929635--929662 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
929625 TAAAGACTAT
929635 CTTTAAGCCAC
1 CTTTAAGCCAC
929646 CTTTAAGCCAC
1 CTTTAAGCCAC
929657 CTTTAA
1 CTTTAA
929663 TGACAGCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.32, G:0.07, T:0.32
Consensus pattern (11 bp):
CTTTAAGCCAC
Found at i:929711 original size:11 final size:11
Alignment explanation
Indices: 929695--929737 Score: 77
Period size: 11 Copynumber: 3.9 Consensus size: 11
929685 GTCCAAACTT
929695 CTTTAAGCCAC
1 CTTTAAGCCAC
*
929706 CTTTAAGCTAC
1 CTTTAAGCCAC
929717 CTTTAAGCCAC
1 CTTTAAGCCAC
929728 CTTTAAGCCA
1 CTTTAAGCCA
929738 TTAAAAAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.28, C:0.33, G:0.09, T:0.30
Consensus pattern (11 bp):
CTTTAAGCCAC
Found at i:930894 original size:112 final size:112
Alignment explanation
Indices: 930752--930975 Score: 421
Period size: 112 Copynumber: 2.0 Consensus size: 112
930742 AACCCTGACT
*
930752 TGCACCTGGGCACACGACACACCTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTT
1 TGCACCTGGGCACACGACACAACTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTT
*
930817 TTCTTAAGTTGGACAAACAATAGACTCTAATTAGATATACACAAACG
66 TTCATAAGTTGGACAAACAATAGACTCTAATTAGATATACACAAACG
930864 TGCACCTGGGCACACGACACAACTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTT
1 TGCACCTGGGCACACGACACAACTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTT
*
930929 TTCATAAGTTGGACAAACAATAGGCTCTAATTAGATATACACAAACG
66 TTCATAAGTTGGACAAACAATAGACTCTAATTAGATATACACAAACG
930976 AACAAAACAT
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
112 109 1.00
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (112 bp):
TGCACCTGGGCACACGACACAACTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTT
TTCATAAGTTGGACAAACAATAGACTCTAATTAGATATACACAAACG
Found at i:931078 original size:2 final size:2
Alignment explanation
Indices: 931071--931124 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
931061 AGCTGATTTT
931071 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
931113 GA GA GA GA GA GA
1 GA GA GA GA GA GA
931125 TTATGCAGGT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:934299 original size:2 final size:2
Alignment explanation
Indices: 934292--934332 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
934282 GGATGAACTA
934292 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
934333 TAGATTTCAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:934746 original size:11 final size:10
Alignment explanation
Indices: 934723--934761 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
934713 GTAAATGCCA
934723 CTTAAAGATG
1 CTTAAAGATG
*
934733 CTTAAAGGTAG
1 CTTAAAGAT-G
934744 CTTAAAGATGG
1 CTTAAAGAT-G
934755 CTTAAAG
1 CTTAAAG
934762 GTGACTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
10 8 0.32
11 17 0.68
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.28
Consensus pattern (10 bp):
CTTAAAGATG
Found at i:934747 original size:21 final size:22
Alignment explanation
Indices: 934723--934763 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
934713 GTAAATGCCA
934723 CTTAAAGAT-GCTTAAAGGTAG
1 CTTAAAGATGGCTTAAAGGTAG
934744 CTTAAAGATGGCTTAAAGGT
1 CTTAAAGATGGCTTAAAGGT
934764 GACTTATAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.29
Consensus pattern (22 bp):
CTTAAAGATGGCTTAAAGGTAG
Found at i:934769 original size:22 final size:20
Alignment explanation
Indices: 934722--934769 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 20
934712 CGTAAATGCC
934722 ACTTAAAGATGCTTAAAGGT
1 ACTTAAAGATGCTTAAAGGT
934742 AGCTTAAAGATGGCTTAAAGGT
1 A-CTTAAAGAT-GCTTAAAGGT
934764 GACTTA
1 -ACTTA
934770 TAGAAGTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.04
21 9 0.36
22 14 0.56
23 1 0.04
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (20 bp):
ACTTAAAGATGCTTAAAGGT
Found at i:934865 original size:11 final size:11
Alignment explanation
Indices: 934845--934882 Score: 67
Period size: 11 Copynumber: 3.5 Consensus size: 11
934835 TGTATATTCG
934845 TTAAGCCACCT
1 TTAAGCCACCT
*
934856 TTACGCCACCT
1 TTAAGCCACCT
934867 TTAAGCCACCT
1 TTAAGCCACCT
934878 TTAAG
1 TTAAG
934883 GACTTGCTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.26, C:0.34, G:0.11, T:0.29
Consensus pattern (11 bp):
TTAAGCCACCT
Found at i:935621 original size:160 final size:159
Alignment explanation
Indices: 935358--935645 Score: 497
Period size: 160 Copynumber: 1.8 Consensus size: 159
935348 CAGTTTCCGT
* *
935358 TCATTTTTTTCGCAGAGGAAGACCGAATTGAAATGAAATTTGATATAAGGTTTATCATGATAATA
1 TCATTTTCTTCGCAGAGGAAGAACGAATTGAAATGAAATTTGATATAAGGTTTATCATGATAATA
935423 TCTAGGTCAAGTTCGATATTGGGTACGATCAAGCCATTTTCGACAGAGTTATGCCCCTTGGACGT
66 TCTAGGTCAAGTTCGATATTGGGTACGATCAAGCCATTTTCGACAGAGTTATGCCCCTTGGACGT
935488 AGTAAAATTCCAGTTATTTGCAGTCCCGC
131 AGTAAAATTCCAGTTATTTGCAGTCCCGC
* * *
935517 TCATTTTCTTCGCAGAGGATGAAC-ATATTGAAATGAAATTTGGTATTCAGGTTTATCATGATAA
1 TCATTTTCTTCGCAGAGGAAGAACGA-ATTGAAATGAAATTTGATA-TAAGGTTTATCATGATAA
*
935581 TATCTAGGTCAAGTTCGATATTGGGTACGATCGAGCCATTTTCGACAGAGTTATGCCCCTTGGAC
64 TATCTAGGTCAAGTTCGATATTGGGTACGATCAAGCCATTTTCGACAGAGTTATGCCCCTTGGAC
935646 CTTTATGTAA
Statistics
Matches: 121, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
158 1 0.01
159 39 0.32
160 81 0.67
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (159 bp):
TCATTTTCTTCGCAGAGGAAGAACGAATTGAAATGAAATTTGATATAAGGTTTATCATGATAATA
TCTAGGTCAAGTTCGATATTGGGTACGATCAAGCCATTTTCGACAGAGTTATGCCCCTTGGACGT
AGTAAAATTCCAGTTATTTGCAGTCCCGC
Found at i:938149 original size:2 final size:2
Alignment explanation
Indices: 938142--938217 Score: 118
Period size: 2 Copynumber: 38.0 Consensus size: 2
938132 AGACTGAATA
*
938142 TC TC TC TC TC TC TC GT- TC GC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC -TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
938184 TC TC TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
938218 AAGTGCTAGT
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.01
2 66 0.97
3 1 0.01
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (2 bp):
TC
Found at i:952832 original size:21 final size:21
Alignment explanation
Indices: 952806--952848 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
952796 TAAAATTTGA
952806 ACGAGCTCTCT-CATACGTTGC
1 ACGAGCTCT-TGCATACGTTGC
*
952827 ACGAGCTCTTGCATTCGTTGC
1 ACGAGCTCTTGCATACGTTGC
952848 A
1 A
952849 TGCATCAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.19, C:0.30, G:0.21, T:0.30
Consensus pattern (21 bp):
ACGAGCTCTTGCATACGTTGC
Found at i:953899 original size:4 final size:4
Alignment explanation
Indices: 953890--953941 Score: 104
Period size: 4 Copynumber: 13.0 Consensus size: 4
953880 CTGTTGCTCA
953890 ACGC ACGC ACGC ACGC ACGC ACGC ACGC ACGC ACGC ACGC ACGC ACGC
1 ACGC ACGC ACGC ACGC ACGC ACGC ACGC ACGC ACGC ACGC ACGC ACGC
953938 ACGC
1 ACGC
953942 NNNNNNNNNN
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 48 1.00
ACGTcount: A:0.25, C:0.50, G:0.25, T:0.00
Consensus pattern (4 bp):
ACGC
Found at i:954006 original size:2 final size:2
Alignment explanation
Indices: 953999--954105 Score: 214
Period size: 2 Copynumber: 53.5 Consensus size: 2
953989 NNNNNNNNNN
953999 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
954041 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
954083 CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA C
954106 CAAAATATGA
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 105 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:963471 original size:16 final size:16
Alignment explanation
Indices: 963450--963481 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
963440 CAAGTGTAGA
963450 AGGGCGAAAATAACAC
1 AGGGCGAAAATAACAC
*
963466 AGGGCGGAAATAACAC
1 AGGGCGAAAATAACAC
963482 TGTATACAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.19, G:0.28, T:0.06
Consensus pattern (16 bp):
AGGGCGAAAATAACAC
Found at i:970449 original size:2 final size:2
Alignment explanation
Indices: 970432--970473 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
970422 ATGAAACACT
* *
970432 TC TC TC CC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
970474 ATCGACTTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:970558 original size:2 final size:2
Alignment explanation
Indices: 970545--970594 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
970535 ATTTTGATAT
*
970545 TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
970587 TC TC TC TC
1 TC TC TC TC
970595 ATACTTATTA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:972673 original size:25 final size:25
Alignment explanation
Indices: 972639--972690 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
972629 ATACTTAGTT
972639 TCCTACGAAAGCCCAGAAGGCTCAA
1 TCCTACGAAAGCCCAGAAGGCTCAA
972664 TCCTACGAAAGCCCAGAAGGCTCAA
1 TCCTACGAAAGCCCAGAAGGCTCAA
972689 TC
1 TC
972691 GAGATTCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.35, C:0.33, G:0.19, T:0.13
Consensus pattern (25 bp):
TCCTACGAAAGCCCAGAAGGCTCAA
Found at i:972709 original size:14 final size:14
Alignment explanation
Indices: 972690--972727 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
972680 AAGGCTCAAT
972690 CGAGATTCAAAATA
1 CGAGATTCAAAATA
*
972704 CGAGATTCGAAATA
1 CGAGATTCAAAATA
972718 CGAGATTCAA
1 CGAGATTCAA
972728 GATTCGGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.45, C:0.16, G:0.18, T:0.21
Consensus pattern (14 bp):
CGAGATTCAAAATA
Found at i:972730 original size:21 final size:21
Alignment explanation
Indices: 972706--972748 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
972696 TCAAAATACG
*
972706 AGATTCGAAATACGAGATTCA
1 AGATTCGAAATACGAAATTCA
* *
972727 AGATTCGGAATTCGAAATTCA
1 AGATTCGAAATACGAAATTCA
972748 A
1 A
972749 CATCAAGTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.26
Consensus pattern (21 bp):
AGATTCGAAATACGAAATTCA
Found at i:972739 original size:28 final size:28
Alignment explanation
Indices: 972690--972744 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
972680 AAGGCTCAAT
972690 CGAGATTCAAAATACGAGATTCGAAATA
1 CGAGATTCAAAATACGAGATTCGAAATA
* *
972718 CGAGATTCAAGATTCG-GAATTCGAAAT
1 CGAGATTCAAAATACGAG-ATTCGAAAT
972745 TCAACATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 1 0.04
28 23 0.96
ACGTcount: A:0.42, C:0.15, G:0.20, T:0.24
Consensus pattern (28 bp):
CGAGATTCAAAATACGAGATTCGAAATA
Found at i:972746 original size:14 final size:14
Alignment explanation
Indices: 972689--972746 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
972679 GAAGGCTCAA
*
972689 TCGAGATTCAAAAT
1 TCGAGATTCGAAAT
*
972703 ACGAGATTCGAAAT
1 TCGAGATTCGAAAT
*
972717 ACGAGATTC-AAGAT
1 TCGAGATTCGAA-AT
972731 TCG-GAATTCGAAAT
1 TCGAG-ATTCGAAAT
972745 TC
1 TC
972747 AACATCAAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
13 3 0.08
14 33 0.87
15 2 0.05
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.26
Consensus pattern (14 bp):
TCGAGATTCGAAAT
Found at i:988083 original size:2 final size:2
Alignment explanation
Indices: 988076--988130 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
988066 GGCAATAAAC
*
988076 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
988118 CT CT CT CT CT CT C
1 CT CT CT CT CT CT C
988131 AATACTGATT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:988884 original size:16 final size:16
Alignment explanation
Indices: 988860--989054 Score: 92
Period size: 16 Copynumber: 11.8 Consensus size: 16
988850 ACTGTTTCCT
* *
988860 TTTATCACCCTATATC
1 TTTACCACCCTTTATC
*
988876 TTTACCACCCTTTCTC
1 TTTACCACCCTTTATC
* * *
988892 TCTAGCACCC-TTACTTG
1 TTTACCACCCTTTA--TC
* *
988909 TTTA-CACCCTTTCTA
1 TTTACCACCCTTTATC
*
988924 TTTACCA-CCTTATGTC
1 TTTACCACCCTT-TATC
* * *
988940 TTTTCCACCCTTTGTA
1 TTTACCACCCTTTATC
*
988956 TTTACCACTCTTTATC
1 TTTACCACCCTTTATC
*
988972 TTCACCACCCTTTCACCCTTCTC
1 TTTACCACCCTTT-A------TC
* *
988995 TTTACCACCTTTTACC
1 TTTACCACCCTTTATC
* *
989011 TTTA-CAGCCTTTCTC
1 TTTACCACCCTTTATC
* *
989026 TTTACCAACCTTTGTC
1 TTTACCACCCTTTATC
989042 TTTACCACCCTTT
1 TTTACCACCCTTT
989055 CACCCTATCT
Statistics
Matches: 135, Mismatches: 30, Indels: 28
0.70 0.16 0.15
Matches are distributed among these distances:
15 22 0.16
16 88 0.65
17 11 0.08
22 1 0.01
23 13 0.10
ACGTcount: A:0.17, C:0.36, G:0.03, T:0.44
Consensus pattern (16 bp):
TTTACCACCCTTTATC
Found at i:988901 original size:32 final size:32
Alignment explanation
Indices: 988860--988985 Score: 112
Period size: 32 Copynumber: 3.9 Consensus size: 32
988850 ACTGTTTCCT
* *
988860 TTTATCACCCTATATCTTTACCACCCTTTCTC
1 TTTACCACCCTATATCTTTACCACCCTTTCTA
* * *
988892 TCTAGCACCCT-TACTTGTTTA-CACCCTTTCTA
1 TTTACCACCCTATA--TCTTTACCACCCTTTCTA
* * * *
988924 TTTACCACCTTATGTCTTTTCCACCCTTTGTA
1 TTTACCACCCTATATCTTTACCACCCTTTCTA
* * *
988956 TTTACCACTCTTTATCTTCACCACCCTTTC
1 TTTACCACCCTATATCTTTACCACCCTTTC
988986 ACCCTTCTCT
Statistics
Matches: 72, Mismatches: 18, Indels: 8
0.73 0.18 0.08
Matches are distributed among these distances:
31 6 0.08
32 60 0.83
33 6 0.08
ACGTcount: A:0.17, C:0.36, G:0.03, T:0.44
Consensus pattern (32 bp):
TTTACCACCCTATATCTTTACCACCCTTTCTA
Found at i:989045 original size:31 final size:31
Alignment explanation
Indices: 988985--989055 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
988975 ACCACCCTTT
988985 CACCC-TTCTCTTTACCACCTTTTACCTTTA-
1 CACCCTTTCTCTTTACCACCTTTTA-CTTTAC
*
989015 CAGCCTTTCTCTTTACCAACCTTTGT-CTTTAC
1 CACCCTTTCTCTTTACC-ACCTTT-TACTTTAC
989047 CACCCTTTC
1 CACCCTTTC
989056 ACCCTATCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
30 4 0.11
31 16 0.46
32 14 0.40
33 1 0.03
ACGTcount: A:0.15, C:0.39, G:0.03, T:0.42
Consensus pattern (31 bp):
CACCCTTTCTCTTTACCACCTTTTACTTTAC
Found at i:989084 original size:40 final size:38
Alignment explanation
Indices: 989018--989176 Score: 120
Period size: 40 Copynumber: 3.9 Consensus size: 38
989008 ACCTTTACAG
* *
989018 CCTTTCTCTTTACCAACCTTTGTCTTTACCACCCTTTCAC
1 CCTTTCT-TTTTCC-ACCTTTCTCTTTACCACCCTTTCAC
* *
989058 CCTATCTTTTTCTCATCCTTTCTCTTTACAACCCTTTCATC
1 CCTTTCTTTTTC-CA-CCTTTCTCTTTACCACCCTTTCA-C
* * * * * *
989099 CTTTTCTCTTTACCAGCCTTTTTCTTTACTAACCTTTCAT
1 CCTTTCT-TTTTCCA-CCTTTCTCTTTACCACCCTTTCAC
* * *
989139 CCTTTCTCTTTCCCACTTTTTCTCTTTACCGCCCTTTC
1 CCTTTCT-TTTTCCAC-CTTTCTCTTTACCACCCTTTC
989177 TGTTTAACAC
Statistics
Matches: 95, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
39 6 0.06
40 57 0.60
41 28 0.29
42 4 0.04
ACGTcount: A:0.13, C:0.37, G:0.02, T:0.48
Consensus pattern (38 bp):
CCTTTCTTTTTCCACCTTTCTCTTTACCACCCTTTCAC
Found at i:989134 original size:16 final size:17
Alignment explanation
Indices: 989098--989135 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
989088 ACCCTTTCAT
*
989098 CCTTTTCTCTTTACCAG
1 CCTTTTCTCTTTACCAA
*
989115 CCTTTT-TCTTTACTAA
1 CCTTTTCTCTTTACCAA
989131 CCTTT
1 CCTTT
989136 CATCCTTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.13, C:0.32, G:0.03, T:0.53
Consensus pattern (17 bp):
CCTTTTCTCTTTACCAA
Found at i:989161 original size:81 final size:81
Alignment explanation
Indices: 989020--989176 Score: 199
Period size: 81 Copynumber: 1.9 Consensus size: 81
989010 CTTTACAGCC
* * *
989020 TTTCTCTTTACCAACCTTTGTCTTTACCACCCTTTCACCCTATCTTTTTCTCATCCTTTCTCTTT
1 TTTCTCTTTACCAACCTTTGTCTTTACCAACCTTTCACCCTATCTCTTTCCCATCCTTTCTCTTT
989085 ACAACCCTTTCATCCT
66 ACAACCCTTTCATCCT
* * * * * *
989101 TTTCTCTTTACCAGCCTTTTTCTTTACTAACCTTTCATCCTTTCTCTTTCCCA-CTTTTTCTCTT
1 TTTCTCTTTACCAACCTTTGTCTTTACCAACCTTTCACCCTATCTCTTTCCCATC-CTTTCTCTT
**
989165 TACCGCCCTTTC
65 TACAACCCTTTC
989177 TGTTTAACAC
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
80 1 0.02
81 63 0.98
ACGTcount: A:0.13, C:0.36, G:0.02, T:0.49
Consensus pattern (81 bp):
TTTCTCTTTACCAACCTTTGTCTTTACCAACCTTTCACCCTATCTCTTTCCCATCCTTTCTCTTT
ACAACCCTTTCATCCT
Found at i:989192 original size:16 final size:16
Alignment explanation
Indices: 989173--989208 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
989163 TTTACCGCCC
*
989173 TTTCTGTTTAACACCT
1 TTTCTGGTTAACACCT
*
989189 TTTCTGGTTAACATCT
1 TTTCTGGTTAACACCT
989205 TTTC
1 TTTC
989209 CCATTACCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.17, C:0.22, G:0.08, T:0.53
Consensus pattern (16 bp):
TTTCTGGTTAACACCT
Found at i:989233 original size:16 final size:16
Alignment explanation
Indices: 989212--989261 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
989202 TCTTTTCCCA
989212 TTACCACCCATTCTCT
1 TTACCACCCATTCTCT
989228 TTACCA-CCATCTCTCT
1 TTACCACCCAT-TCTCT
* *
989244 CTACCACCCTTTCT-T
1 TTACCACCCATTCTCT
989259 TTA
1 TTA
989262 AACACCCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 7 0.24
16 19 0.66
17 3 0.10
ACGTcount: A:0.18, C:0.42, G:0.00, T:0.40
Consensus pattern (16 bp):
TTACCACCCATTCTCT
Found at i:989368 original size:40 final size:40
Alignment explanation
Indices: 989308--989420 Score: 106
Period size: 40 Copynumber: 2.8 Consensus size: 40
989298 TCTTTAACAT
* * *
989308 CCTTTCTCTTTC-CCATCCTTTGTCTTTACCACTTTACCAC
1 CCTTTCTC-TTCACCACCCTTTATCTTTACCACTTTACAAC
* *
989348 CCTTTCTCTTCACCACCCTTTCACCTTTTA--TCTTTACAAC
1 CCTTTCTCTTCACCACCCTTT-ATC-TTTACCACTTTACAAC
* * *
989388 CATTTGTCTTTACCACCCTTTATCTTTACCACT
1 CCTTTCTCTTCACCACCCTTTATCTTTACCACT
989421 CTTTCTCTTT
Statistics
Matches: 58, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
38 4 0.07
39 5 0.09
40 44 0.76
41 1 0.02
42 4 0.07
ACGTcount: A:0.16, C:0.38, G:0.02, T:0.44
Consensus pattern (40 bp):
CCTTTCTCTTCACCACCCTTTATCTTTACCACTTTACAAC
Found at i:989399 original size:16 final size:16
Alignment explanation
Indices: 989378--989463 Score: 86
Period size: 16 Copynumber: 5.4 Consensus size: 16
989368 TCACCTTTTA
989378 TCTTTACAACCATTTG
1 TCTTTACAACCATTTG
* * *
989394 TCTTTACCACCCTTTA
1 TCTTTACAACCATTTG
* *
989410 TCTTTACCACTC-TTTC
1 TCTTTACAAC-CATTTG
*
989426 TCTTTACCACCCA-TTG
1 TCTTTA-CAACCATTTG
989442 TCTTTACAACCATTTG
1 TCTTTACAACCATTTG
989458 TCTTTA
1 TCTTTA
989464 TCATCCTTTC
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
15 5 0.09
16 50 0.86
17 3 0.05
ACGTcount: A:0.20, C:0.31, G:0.03, T:0.45
Consensus pattern (16 bp):
TCTTTACAACCATTTG
Found at i:989413 original size:32 final size:31
Alignment explanation
Indices: 989369--989472 Score: 118
Period size: 32 Copynumber: 3.3 Consensus size: 31
989359 ACCACCCTTT
*
989369 CACCTTTTATCTTTACAACCATTTGTCTTTAC
1 CACCCTTTATCTTTACAACC-TTTGTCTTTAC
* *
989401 CACCCTTTATCTTTACCACTCTTTCTCTTTAC
1 CACCCTTTATCTTTACAAC-CTTTGTCTTTAC
* * *
989433 CACCCATTGTCTTTACAACCATTTGTCTTTAT
1 CACCCTTTATCTTTACAACC-TTTGTCTTTAC
*
989465 CATCCTTT
1 CACCCTTT
989473 CACCTTTCCT
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
31 1 0.02
32 58 0.97
33 1 0.02
ACGTcount: A:0.19, C:0.32, G:0.03, T:0.46
Consensus pattern (31 bp):
CACCCTTTATCTTTACAACCTTTGTCTTTAC
Found at i:989500 original size:16 final size:16
Alignment explanation
Indices: 989475--989560 Score: 95
Period size: 16 Copynumber: 5.4 Consensus size: 16
989465 CATCCTTTCA
989475 CCTTTCCTCTTTACCAC
1 CCTTT-CTCTTTACCAC
*
989492 CCTATCTC-TTACCAC
1 CCTTTCTCTTTACCAC
* * *
989507 CTTTTATCTTTA-CAA
1 CCTTTCTCTTTACCAC
*
989522 CCTTTCGTCTTCACCAC
1 CCTTTC-TCTTTACCAC
989539 CCTTTCTCTTTACCAC
1 CCTTTCTCTTTACCAC
989555 CCTTTC
1 CCTTTC
989561 AACTTTTGTC
Statistics
Matches: 56, Mismatches: 10, Indels: 7
0.77 0.14 0.10
Matches are distributed among these distances:
15 18 0.32
16 26 0.46
17 12 0.21
ACGTcount: A:0.15, C:0.42, G:0.01, T:0.42
Consensus pattern (16 bp):
CCTTTCTCTTTACCAC
Found at i:989532 original size:87 final size:87
Alignment explanation
Indices: 989394--989632 Score: 200
Period size: 87 Copynumber: 2.7 Consensus size: 87
989384 CAACCATTTG
* * * *
989394 TCTTTACCACCCTTTATCTTTACCACTCTTTCTCTTTACCACCCATTGTCTTTACAACCATTTGT
1 TCTTTACCACCC-TTATCTTTACCACTCTTTATCTTTACCAACCATTGTCTTCACAACCATTTCT
* * *
989459 CTTTATCATCCTTTCACCTTTCC
65 CTTTACCACCCTTTCAACTTTCC
* * *
989482 TCTTTACCACCC-TATCTCTTACCAC-CTTTTATCTTTA-CAACCTTTCGTCTTCACCACCCTTT
1 TCTTTACCACCCTTATCT-TTACCACTC-TTTATCTTTACCAACCATT-GTCTTCACAACCATTT
**
989544 CTCTTTACCACCCTTTCAACTTTTG
63 CTCTTTACCACCCTTTCAACTTTCC
* * * * * ** * *
989569 TCCTT-CCAGCCTGT-TCTTTAACCACCCTTTCTTTTTACCGCCCATTGTCTTTACAACCCTTTC
1 TCTTTACCACCCT-TATCTTT-ACCACTCTTTATCTTTACCAACCATTGTCTTCACAACCATTTC
989632 T
64 T
989633 ATTAGACTTT
Statistics
Matches: 122, Mismatches: 21, Indels: 17
0.76 0.13 0.11
Matches are distributed among these distances:
86 19 0.16
87 84 0.69
88 19 0.16
ACGTcount: A:0.16, C:0.37, G:0.03, T:0.44
Consensus pattern (87 bp):
TCTTTACCACCCTTATCTTTACCACTCTTTATCTTTACCAACCATTGTCTTCACAACCATTTCTC
TTTACCACCCTTTCAACTTTCC
Found at i:989543 original size:71 final size:72
Alignment explanation
Indices: 989410--989544 Score: 175
Period size: 71 Copynumber: 1.9 Consensus size: 72
989400 CCACCCTTTA
* * * * * *
989410 TCTTTACCACTCTTTCTCTTTACCACCCATTGTCTTTACAACCATTTGTCTTTATCATCCTTTCA
1 TCTTTACCACCCTATCTCTTTACCACCCATTATCTTTACAACCATTTGTCTTCACCACCCTTTCA
989475 CCTTTCC
66 CCTTTCC
**
989482 TCTTTACCACCCTATCTC-TTACCACCTTTTATCTTTACAACC-TTTCGTCTTCACCACCCTTTC
1 TCTTTACCACCCTATCTCTTTACCACCCATTATCTTTACAACCATTT-GTCTTCACCACCCTTTC
989545 TCTTTACCAC
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
70 3 0.06
71 35 0.65
72 16 0.30
ACGTcount: A:0.17, C:0.37, G:0.02, T:0.44
Consensus pattern (72 bp):
TCTTTACCACCCTATCTCTTTACCACCCATTATCTTTACAACCATTTGTCTTCACCACCCTTTCA
CCTTTCC
Found at i:993714 original size:2 final size:2
Alignment explanation
Indices: 993695--993790 Score: 76
Period size: 2 Copynumber: 48.5 Consensus size: 2
993685 AGTAAACGTC
* * *
993695 CT CT -T CT CT CT AT GT CT CT CT C- CAT CT CT GT CT CT C- CAT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT C-T CT CT CT CT CT CT C-T CT
*
993736 CT AT CT CT CAT -T CT CAT -T CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT C-T CT CT C-T CT CT CT CT CT CT CT CT CT CT CT CT CT
*
993778 TT CT CT CT CT CT C
1 CT CT CT CT CT CT C
993791 GTGGGCGGAT
Statistics
Matches: 76, Mismatches: 9, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
1 5 0.07
2 67 0.88
3 4 0.05
ACGTcount: A:0.06, C:0.43, G:0.02, T:0.49
Consensus pattern (2 bp):
CT
Found at i:994821 original size:20 final size:20
Alignment explanation
Indices: 994796--994834 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
994786 ATCCTTATAT
994796 AAATGCGGGTTACTTGAAAA
1 AAATGCGGGTTACTTGAAAA
994816 AAATGCGGGTTACTTGAAA
1 AAATGCGGGTTACTTGAAA
994835 CATACTTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.26
Consensus pattern (20 bp):
AAATGCGGGTTACTTGAAAA
Found at i:999123 original size:2 final size:2
Alignment explanation
Indices: 999118--999159 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
999108 TTGTCTACTC
* *
999118 AT AT AT AT AT AT AC AT AT AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
999160 TGATTGATTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:999165 original size:4 final size:4
Alignment explanation
Indices: 999158--999183 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
999148 ATATATATAT
999158 ATTG ATTG ATTG ATTG ATTG ATTG AT
1 ATTG ATTG ATTG ATTG ATTG ATTG AT
999184 GACATGCTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
ATTG
Found at i:1004131 original size:28 final size:27
Alignment explanation
Indices: 1004091--1004145 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 27
1004081 TTCTTCAGGA
1004091 CAACAAAATAAAAACTACATAAGAAAG
1 CAACAAAATAAAAACTACATAAGAAAG
*
1004118 NCAACAAAATAAAAACTACATATGAAAG
1 -CAACAAAATAAAAACTACATAAGAAAG
1004146 AAGAAAAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.64, C:0.15, G:0.07, T:0.13
Consensus pattern (27 bp):
CAACAAAATAAAAACTACATAAGAAAG
Found at i:1018264 original size:2 final size:2
Alignment explanation
Indices: 1018257--1018302 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
1018247 CATCTTGCTT
*
1018257 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1018299 TC TC
1 TC TC
1018303 ATAATGACAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1018634 original size:9 final size:9
Alignment explanation
Indices: 1018617--1018665 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
1018607 ACGCCTGTTG
*
1018617 TTTTCTTGT
1 TTTTATTGT
1018626 TTTTATTGT
1 TTTTATTGT
*
1018635 TTTTATTAT
1 TTTTATTGT
*
1018644 TTTTAATTTT
1 TTTT-ATTGT
*
1018654 TTTTATCGT
1 TTTTATTGT
1018663 TTT
1 TTT
1018666 GATATTGCTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
9 26 0.76
10 8 0.24
ACGTcount: A:0.12, C:0.04, G:0.06, T:0.78
Consensus pattern (9 bp):
TTTTATTGT
Found at i:1020406 original size:4 final size:4
Alignment explanation
Indices: 1020397--1020452 Score: 89
Period size: 4 Copynumber: 14.5 Consensus size: 4
1020387 TTAAAAGTTA
*
1020397 ATCT ATCT ATCT A-C- ATGT ATCT ATCT ATCT ATCT ATCT ATCT ATCT
1 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT
1020443 ATCT ATCT AT
1 ATCT ATCT AT
1020453 ATATGAAAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 1 0.02
3 1 0.02
4 46 0.96
ACGTcount: A:0.27, C:0.23, G:0.02, T:0.48
Consensus pattern (4 bp):
ATCT
Found at i:1021368 original size:4 final size:4
Alignment explanation
Indices: 1021359--1021402 Score: 88
Period size: 4 Copynumber: 11.0 Consensus size: 4
1021349 AGGTAAGTAT
1021359 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1021403 GTGTGTGTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
ATAG
Done.