Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold35
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: 4812169
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 17994 characters in sequence are not A, C, G, or T
File 19 of 30
Found at i:2970717 original size:41 final size:42
Alignment explanation
Indices: 2970666--2970760 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 42
2970656 ACAATTCAAA
*
2970666 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAA-AT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
2970707 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
2970749 GTATCGATACAT
1 GTATCGATACAT
2970761 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 38 0.73
42 14 0.27
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (42 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
Found at i:2970817 original size:13 final size:13
Alignment explanation
Indices: 2970799--2970824 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2970789 TACAGCAAGT
2970799 ATGTATCGATACA
1 ATGTATCGATACA
2970812 ATGTATCGATACA
1 ATGTATCGATACA
2970825 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2975062 original size:22 final size:24
Alignment explanation
Indices: 2975036--2975082 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
2975026 TGATTAAAGA
2975036 AAATTGT-TTT-ATTAAGGGGGAG
1 AAATTGTATTTGATTAAGGGGGAG
*
2975058 AAATTTTATTTGATTAAGGGGGAG
1 AAATTGTATTTGATTAAGGGGGAG
2975082 A
1 A
2975083 GAAAAGGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 6 0.27
23 3 0.14
24 13 0.59
ACGTcount: A:0.34, C:0.00, G:0.30, T:0.36
Consensus pattern (24 bp):
AAATTGTATTTGATTAAGGGGGAG
Found at i:2975773 original size:15 final size:14
Alignment explanation
Indices: 2975753--2975785 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2975743 GTATCGATAC
2975753 ATACAAGATGTATCG
1 ATACAA-ATGTATCG
2975768 ATAC-AATGTATCG
1 ATACAAATGTATCG
2975781 ATACA
1 ATACA
2975786 TGACCAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 12 0.71
14 1 0.06
15 4 0.24
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (14 bp):
ATACAAATGTATCG
Found at i:2975778 original size:13 final size:13
Alignment explanation
Indices: 2975760--2975785 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2975750 TACATACAAG
2975760 ATGTATCGATACA
1 ATGTATCGATACA
2975773 ATGTATCGATACA
1 ATGTATCGATACA
2975786 TGACCAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2982068 original size:4 final size:4
Alignment explanation
Indices: 2982061--2982125 Score: 71
Period size: 4 Copynumber: 16.5 Consensus size: 4
2982051 GAGACGAAAA
* * *
2982061 AAAC AAAC AAAC AAAC AAAAC AAAC AAA- AAAC AAAA AAAC AAAA AAAA
1 AAAC AAAC AAAC AAAC -AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC
*
2982109 AAAC AAA- AAAA AAAC AA
1 AAAC AAAC AAAC AAAC AA
2982126 CAACAACAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
3 6 0.11
4 43 0.81
5 4 0.08
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:2982076 original size:12 final size:12
Alignment explanation
Indices: 2982057--2982125 Score: 88
Period size: 12 Copynumber: 5.8 Consensus size: 12
2982047 AAAAGAGACG
2982057 AAAAAAACAAAC
1 AAAAAAACAAAC
*
2982069 AAACAAACAAAAC
1 AAAAAAAC-AAAC
*
2982082 AAACAAA-AAAC
1 AAAAAAACAAAC
*
2982093 AAAAAAACAAAA
1 AAAAAAACAAAC
2982105 AAAAAAACAAA-
1 AAAAAAACAAAC
2982116 AAAAAAACAA
1 AAAAAAACAA
2982126 CAACAACAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
11 20 0.38
12 21 0.40
13 11 0.21
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAACAAAC
Found at i:2982080 original size:17 final size:16
Alignment explanation
Indices: 2982060--2982137 Score: 106
Period size: 16 Copynumber: 4.9 Consensus size: 16
2982050 AGAGACGAAA
2982060 AAAACAAACAAACAAAC
1 AAAACAAACAAA-AAAC
2982077 AAAACAAACAAAAAAC
1 AAAACAAACAAAAAAC
*
2982093 AAAA-AAACAAAAAAA
1 AAAACAAACAAAAAAC
*
2982108 AAAACAAAAAAAAAAC
1 AAAACAAACAAAAAAC
2982124 AACAAC-AACAAAAA
1 AA-AACAAACAAAAA
2982138 GGGTCCGGAT
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
15 14 0.25
16 26 0.47
17 15 0.27
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAACAAACAAAAAAC
Found at i:2982092 original size:20 final size:18
Alignment explanation
Indices: 2982057--2982137 Score: 90
Period size: 20 Copynumber: 4.1 Consensus size: 18
2982047 AAAAGAGACG
2982057 AAAAAAACAAACAAACAAA
1 AAAAAAACAAA-AAACAAA
2982076 CAAAACAAACAAAAAACAAAA
1 -AAAA-AAACAAAAAAC-AAA
*
2982097 AAACAAAAAAAAAAACAAA
1 AAA-AAAACAAAAAACAAA
2982116 AAAAAAACAACAACAACAAA
1 AAAAAAACAA-AA-AACAAA
2982136 AA
1 AA
2982138 GGGTCCGGAT
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
18 6 0.11
19 8 0.15
20 29 0.54
21 11 0.20
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (18 bp):
AAAAAAACAAAAAACAAA
Found at i:2982137 original size:1 final size:1
Alignment explanation
Indices: 2982057--2982122 Score: 51
Period size: 1 Copynumber: 66.0 Consensus size: 1
2982047 AAAAGAGACG
* * * * * * * * *
2982057 AAAAAAACAAACAAACAAACAAAACAAACAAAAAACAAAAAAACAAAAAAAAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2982122 A
1 A
2982123 CAACAACAAC
Statistics
Matches: 47, Mismatches: 18, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2983646 original size:57 final size:58
Alignment explanation
Indices: 2983569--2983973 Score: 416
Period size: 57 Copynumber: 7.0 Consensus size: 58
2983559 ATTCTTCACC
* *
2983569 CTTCAAAAACCC-CAAGTCAGTGGCATCTTTTTC-AAAGCCCACAAGTCAGTGGCAAC-
1 CTTCAAAAGCCCACAAGTCAGTGGCATC-TTTTCAAAAGCCCACAAGTCAGTGGCATCT
* *
2983625 CTTCAAAAGCCCACAAGTCAGTGGCATTTTTTTCAAAAGCCCACAGGTCAGTGGCATCTT
1 CTTCAAAAGCCCACAAGTCAGTGGCA-TCTTTTCAAAAGCCCACAAGTCAGTGGCATC-T
* * * * *
2983685 TTTCAAAAGCCCA-TAGATCAATGGCATCTCTTTC-AAAGTCCACAAGTTAGTGGCATCT
1 CTTCAAAAGCCCACAAG-TCAGTGGCATCT-TTTCAAAAGCCCACAAGTCAGTGGCATCT
* ** * * *
2983743 TTTTTAAAGCCCACAAGCCAGTGGCAAC-CTTCAAAAGCCCACAAGTCAGTGGCATCTT
1 CTTCAAAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACAAGTCAGTGGCATC-T
* * *
2983801 TTTCAAAAGCCCGCAAGTCAGTGGCATCTTTTTCAAAAGCCCACAGGTCAGTGGCATCT
1 CTTCAAAAGCCCACAAGTCAGTGGCATC-TTTTCAAAAGCCCACAAGTCAGTGGCATCT
* * * * *
2983860 CTTTC-AAAGCCCACAAGTCTGTGGCATC-CTTCAAAAGCCTACAGGTTAGTGGCATCT
1 C-TTCAAAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACAAGTCAGTGGCATCT
* * * *
2983917 CTTTC-AAAGCCCACAAGTTAGTGGCAAC-CTTCAAAAGCCCACAAGTCTGTGGCATCT
1 C-TTCAAAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACAAGTCAGTGGCATCT
2983974 TTTTCCTTCT
Statistics
Matches: 296, Mismatches: 40, Indels: 25
0.82 0.11 0.07
Matches are distributed among these distances:
56 14 0.05
57 115 0.39
58 66 0.22
59 48 0.16
60 53 0.18
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (58 bp):
CTTCAAAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACAAGTCAGTGGCATCT
Found at i:2983662 original size:30 final size:30
Alignment explanation
Indices: 2983570--2983978 Score: 461
Period size: 30 Copynumber: 14.1 Consensus size: 30
2983560 TTCTTCACCC
* *
2983570 TTCAAAAACCC-CAAGTCAGTGGCATCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCATCTCT
*
2983599 TTC-AAAGCCCACAAGTCAGTGGCAAC-C-
1 TTCAAAAGCCCACAAGTCAGTGGCATCTCT
* *
2983626 TTCAAAAGCCCACAAGTCAGTGGCATTTTT
1 TTCAAAAGCCCACAAGTCAGTGGCATCTCT
* *
2983656 TTCAAAAGCCCACAGGTCAGTGGCATCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCATCTCT
* *
2983686 TTCAAAAGCCCA-TAGATCAATGGCATCTCT
1 TTCAAAAGCCCACAAG-TCAGTGGCATCTCT
* *
2983716 TTC-AAAGTCCACAAGTTAGTGGCATCT-T
1 TTCAAAAGCCCACAAGTCAGTGGCATCTCT
** * *
2983744 TTTTAAAGCCCACAAGCCAGTGGCAAC-C-
1 TTCAAAAGCCCACAAGTCAGTGGCATCTCT
*
2983772 TTCAAAAGCCCACAAGTCAGTGGCATCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCATCTCT
* *
2983802 TTCAAAAGCCCGCAAGTCAGTGGCATCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCATCTCT
*
2983832 TTCAAAAGCCCACAGGTCAGTGGCATCTCT
1 TTCAAAAGCCCACAAGTCAGTGGCATCTCT
*
2983862 TTC-AAAGCCCACAAGTCTGTGGCATC-C-
1 TTCAAAAGCCCACAAGTCAGTGGCATCTCT
* * *
2983889 TTCAAAAGCCTACAGGTTAGTGGCATCTCT
1 TTCAAAAGCCCACAAGTCAGTGGCATCTCT
* *
2983919 TTC-AAAGCCCACAAGTTAGTGGCAAC-C-
1 TTCAAAAGCCCACAAGTCAGTGGCATCTCT
* *
2983946 TTCAAAAGCCCACAAGTCTGTGGCATCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCATCTCT
2983976 TTC
1 TTC
2983979 CTTCTAAGTC
Statistics
Matches: 321, Mismatches: 43, Indels: 31
0.81 0.11 0.08
Matches are distributed among these distances:
27 9 0.03
28 94 0.29
29 96 0.30
30 122 0.38
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.26
Consensus pattern (30 bp):
TTCAAAAGCCCACAAGTCAGTGGCATCTCT
Found at i:2983834 original size:146 final size:146
Alignment explanation
Indices: 2983581--2983978 Score: 545
Period size: 146 Copynumber: 2.7 Consensus size: 146
2983571 TCAAAAACCC
* *
2983581 CAAGTCAGTGGCATCTTTTTCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAG
1 CAAGTTAGTGGCATCTTTTTAAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAG
* * *
2983646 TGGCATTTTTTTCAAAAGCCCACAGGTCAGTGGCATCTTTTTCAAAAGCCCATAGATCAATGGCA
66 TGGCATCTTTTTCAAAAGCCCACAAGTCAGTGGCATCTTTTTCAAAAGCCCACAGATCAATGGCA
*
2983711 TCTCTTTCAAAGTCCA
131 TCTCTTTCAAAGCCCA
* *
2983727 CAAGTTAGTGGCATCTTTTTTAAAGCCCACAAGCCAGTGGCAACCTTCAAAAGCCCACAAGTCAG
1 CAAGTTAGTGGCATCTTTTTAAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAG
* * *
2983792 TGGCATCTTTTTCAAAAGCCCGCAAGTCAGTGGCATCTTTTTCAAAAGCCCACAGGTCAGTGGCA
66 TGGCATCTTTTTCAAAAGCCCACAAGTCAGTGGCATCTTTTTCAAAAGCCCACAGATCAATGGCA
2983857 TCTCTTTCAAAGCCCA
131 TCTCTTTCAAAGCCCA
* * * * * *
2983873 CAAGTCT-GTGGCATC-CTTCAAAAGCCTACAGGTTAGTGGCATCTCTTTC-AAAGCCCACAAGT
1 CAAGT-TAGTGGCATCTTTTTAAAAGCCCACAAGTCAGTGGCAAC-C-TTCAAAAGCCCACAAGT
* * * *
2983935 TAGTGGCAAC--CTTCAAAAGCCCACAAGTCTGTGGCATCTTTTTC
63 CAGTGGCATCTTTTTCAAAAGCCCACAAGTCAGTGGCATCTTTTTC
2983979 CTTCTAAGTC
Statistics
Matches: 226, Mismatches: 23, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
144 31 0.14
145 20 0.09
146 171 0.76
147 4 0.02
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (146 bp):
CAAGTTAGTGGCATCTTTTTAAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAG
TGGCATCTTTTTCAAAAGCCCACAAGTCAGTGGCATCTTTTTCAAAAGCCCACAGATCAATGGCA
TCTCTTTCAAAGCCCA
Found at i:2983992 original size:33 final size:33
Alignment explanation
Indices: 2983955--2984138 Score: 244
Period size: 33 Copynumber: 5.5 Consensus size: 33
2983945 CTTCAAAAGC
* * * * *
2983955 CCACAAGTCTGTGGCATCTTTTTCCTTCTAAGT
1 CCACAACTCCGTGGCACCTTTTTCTTTTTAAGT
* * *
2983988 CCACAACTTCATGGCACCTTTTTCTTTTTAAAGC
1 CCACAACTCCGTGGCACCTTTTTCTTTTT-AAGT
2984022 CCACAACTCCGTGGCACC-TTTTCTTTTTAAGT
1 CCACAACTCCGTGGCACCTTTTTCTTTTTAAGT
* *
2984054 CCACGACTCCGTGGCACCTTTTTCTTTTTAAAGC
1 CCACAACTCCGTGGCACCTTTTTCTTTTT-AAGT
2984088 CCACAACTCCGTGGCACCTTTTTCTTTTTAAGT
1 CCACAACTCCGTGGCACCTTTTTCTTTTTAAGT
*
2984121 CCACAACTCTGTGGCACC
1 CCACAACTCCGTGGCACC
2984139 CTTAAGCCCA
Statistics
Matches: 132, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
32 20 0.15
33 62 0.47
34 50 0.38
ACGTcount: A:0.20, C:0.32, G:0.13, T:0.36
Consensus pattern (33 bp):
CCACAACTCCGTGGCACCTTTTTCTTTTTAAGT
Found at i:2984072 original size:66 final size:66
Alignment explanation
Indices: 2983950--2984138 Score: 279
Period size: 66 Copynumber: 2.8 Consensus size: 66
2983940 GCAACCTTCA
* * * * * * *
2983950 AAAGCCCACAAGTCTGTGGCATCTTTTTCCTTCTAAGTCCACAACTTCATGGCACCTTTTTCTTT
1 AAAGCCCACAACTCCGTGGCA-CCTTTTCTTTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTT
2984015 TT
65 TT
*
2984017 AAAGCCCACAACTCCGTGGCACCTTTTCTTTTTAAGTCCACGACTCCGTGGCACCTTTTTCTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTCTTTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTT
2984082 T
66 T
*
2984083 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAGTCCACAACTCTGTGGCACC
1 AAAGCCCACAACTCCGTGGCACC-TTTTCTTTTTAAGTCCACAACTCCGTGGCACC
2984139 CTTAAGCCCA
Statistics
Matches: 111, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
66 62 0.56
67 49 0.44
ACGTcount: A:0.21, C:0.31, G:0.13, T:0.35
Consensus pattern (66 bp):
AAAGCCCACAACTCCGTGGCACCTTTTCTTTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTT
T
Found at i:2988798 original size:19 final size:19
Alignment explanation
Indices: 2988774--2988826 Score: 106
Period size: 19 Copynumber: 2.8 Consensus size: 19
2988764 AGTAGCTTCA
2988774 TATGTATCGATACAACACT
1 TATGTATCGATACAACACT
2988793 TATGTATCGATACAACACT
1 TATGTATCGATACAACACT
2988812 TATGTATCGATACAA
1 TATGTATCGATACAA
2988827 ATCGTTGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (19 bp):
TATGTATCGATACAACACT
Found at i:2995928 original size:51 final size:51
Alignment explanation
Indices: 2995881--2996015 Score: 172
Period size: 51 Copynumber: 2.7 Consensus size: 51
2995871 TAGTATTCCC
*
2995881 TTGAAAAT-AAT-AGGGTTGGAGTATCCCTGATTAT-AGAAAATCGGTATT
1 TTGAAAATAAATCAGGGTTGGAGTATCCCCGATTATGAGAAAATCGGTATT
* * *
2995929 TTGAAAATAAAATCGGGGTTGGAGTATCCCCGATTATGAG-AAATCAGTGTT
1 TTGAAAAT-AAATCAGGGTTGGAGTATCCCCGATTATGAGAAAATCGGTATT
2995980 TTGAAAATAAAATC-GGAGTTGGAGTATCCCCGATTA
1 TTGAAAAT-AAATCAGG-GTTGGAGTATCCCCGATTA
2996016 CGGTAAATTG
Statistics
Matches: 78, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
48 8 0.10
50 5 0.06
51 63 0.81
52 2 0.03
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (51 bp):
TTGAAAATAAATCAGGGTTGGAGTATCCCCGATTATGAGAAAATCGGTATT
Found at i:2996075 original size:51 final size:52
Alignment explanation
Indices: 2995895--2996076 Score: 158
Period size: 51 Copynumber: 3.6 Consensus size: 52
2995885 AAATAATAGG
* * ** * **
2995895 GTTGGAGTATCCCTGATTATAG-AAAATCG-GTATTTTGAAAATAAAATCGGG
1 GTTGGAGTATCCCCGATTA-AGAAAAATTGAGTGCTTTGAAAAAAAAATCGAA
* * * * * *
2995946 GTTGGAGTATCCCCGATTATGAGAAA-TCAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTAAGAAAAATTGAGTGCTTTGAAAAAAAAATCGAA
* **
2995997 GTTGGAGTATCCCCGATTACGGTAAATTGA-TGCTTT-AAAAAAAATATCGAA
1 GTTGGAGTATCCCCGATTAAGAAAAATTGAGTGCTTTGAAAAAAAA-ATCGAA
*
2996048 GTTGGAGTATCCTCGATTAAGAAAAATTG
1 GTTGGAGTATCCCCGATTAAGAAAAATTG
2996077 TTGTTTTGGA
Statistics
Matches: 109, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
50 8 0.07
51 99 0.91
52 2 0.02
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.30
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTAAGAAAAATTGAGTGCTTTGAAAAAAAAATCGAA
Found at i:2998455 original size:20 final size:20
Alignment explanation
Indices: 2998429--2998484 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
2998419 ATGTATCAGT
2998429 ACAATGTATCGATACAATG-
1 ACAATGTATCGATACAATGC
*
2998448 AGCAATGTATCGATATAATGC
1 A-CAATGTATCGATACAATGC
*
2998469 AAAATGTATCGATACA
1 ACAATGTATCGATACA
2998485 TCTGGGTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (20 bp):
ACAATGTATCGATACAATGC
Found at i:2998547 original size:13 final size:13
Alignment explanation
Indices: 2998500--2998529 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2998490 GTAAACCCAG
*
2998500 AATGTATCGATGC
1 AATGTATCGATAC
2998513 AATGTATCGATAC
1 AATGTATCGATAC
2998526 AATG
1 AATG
2998530 AACAATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:2998893 original size:60 final size:60
Alignment explanation
Indices: 2998794--2998996 Score: 273
Period size: 60 Copynumber: 3.3 Consensus size: 60
2998784 GGTTTTGAGA
* * *
2998794 TTGGTGTGGGCTTTACAAAGAGAAAGCATCCTGCTCTTTGAAGACGAGAAAATGCCACCAAC
1 TTGG-GTGGGCTTT-GAAAGAGAAAGCATCCTGCTCTTTGAGGACAAGAAAATGCCACCAAC
*
2998856 TTGGGTGGGCTTTGAAAGAGAAAGCATCTTGCTCTTTGAGGACAAGAAAATGCCACCAAC
1 TTGGGTGGGCTTTGAAAGAGAAAGCATCCTGCTCTTTGAGGACAAGAAAATGCCACCAAC
* *
2998916 TTGGGTGGGCTTTGAAAG-GAAAAGGCGTCCTGCTCTTTGAGGACTTAGAAAAGTGCCACCAAC
1 TTGGGTGGGCTTTGAAAGAG-AAA-GCATCCTGCTCTTTGAGGAC-AAGAAAA-TGCCACCAAC
* *
2998979 TTGTGTGGGCTTTAAAAG
1 TTGGGTGGGCTTTGAAAG
2998997 GCGTCCTATT
Statistics
Matches: 128, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
59 1 0.01
60 64 0.50
61 27 0.21
62 10 0.08
63 26 0.20
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.25
Consensus pattern (60 bp):
TTGGGTGGGCTTTGAAAGAGAAAGCATCCTGCTCTTTGAGGACAAGAAAATGCCACCAAC
Found at i:2999010 original size:57 final size:57
Alignment explanation
Indices: 2998822--2999019 Score: 186
Period size: 60 Copynumber: 3.4 Consensus size: 57
2998812 AGAGAAAGCA
* * * * *
2998822 TCCTGCTCTTTGAAGAC-GAGAAAATGCCACCAACTTGGGTGGGCTTTGAAAGAGAAAGCA
1 TCCTACTCTTTGAGGACTAAGAAAATGCCACCAACTTGGGTGGGCTTT--AA-A-AAGGCG
* *
2998882 TCTTGCTCTTTGAGGAC-AAGAAAATGCCACCAACTTGGGTGGGCTTTGAAAGGAAAAGGCG
1 TCCTACTCTTTGAGGACTAAGAAAATGCCACCAACTTGGGTGGGCTTT---A--AAAAGGCG
* * *
2998943 TCCTGCTCTTTGAGGACTTAGAAAAGTGCCACCAACTTGTGTGGGCTTT-AAAAGGCG
1 TCCTACTCTTTGAGGACTAAGAAAA-TGCCACCAACTTGGGTGGGCTTTAAAAAGGCG
*
2999000 TCCTATTCTTTGAGGACTAA
1 TCCTACTCTTTGAGGACTAA
2999020 AGGGCGAAAG
Statistics
Matches: 121, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
57 25 0.21
60 44 0.36
61 22 0.18
62 7 0.06
63 23 0.19
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (57 bp):
TCCTACTCTTTGAGGACTAAGAAAATGCCACCAACTTGGGTGGGCTTTAAAAAGGCG
Found at i:2999098 original size:95 final size:96
Alignment explanation
Indices: 2998943--2999115 Score: 287
Period size: 95 Copynumber: 1.8 Consensus size: 96
2998933 GGAAAAGGCG
*
2998943 TCCTGCTCTTTGAGGACTTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTATTC
1 TCCTGCTCTTTGAGGACTTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTACTC
2999008 TTTGAGGACTAAAGGGCGAAAGGAGAGAGCA
66 TTTGAGGACTAAAGGGCGAAAGGAGAGAGCA
** *
2999039 TCCTGCTCTTTGAGGAC-T-GGGAAGTGCCACCAACATTGTGTGGGCTTTAAAAGGCGTCCTGCT
1 TCCTGCTCTTTGAGGACTTAGAAAAGTGCCACCAAC-TTGTGTGGGCTTTAAAAGGCGTCCTACT
2999102 CTTTGAGGACTAAA
65 CTTTGAGGACTAAA
2999116 AAAAATGCCA
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
94 14 0.19
95 41 0.57
96 17 0.24
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (96 bp):
TCCTGCTCTTTGAGGACTTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGCGTCCTACTC
TTTGAGGACTAAAGGGCGAAAGGAGAGAGCA
Found at i:2999183 original size:47 final size:47
Alignment explanation
Indices: 2999094--2999235 Score: 257
Period size: 47 Copynumber: 3.0 Consensus size: 47
2999084 TTTAAAAGGC
*
2999094 GTCCTGCTCTTTGAGGACTAAAAAAAATGCCACCAACTTGTGTGGGCTG
1 GTCCTGCTCTTTGAGGACT--AGAAAATGCCACCAACTTGTGTGGGCTG
2999143 GTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTG
1 GTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTG
2999190 GTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCT
1 GTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCT
2999236 TTGAAAGGAA
Statistics
Matches: 92, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
47 73 0.79
49 19 0.21
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.27
Consensus pattern (47 bp):
GTCCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTG
Found at i:2999383 original size:55 final size:56
Alignment explanation
Indices: 2999190--2999381 Score: 289
Period size: 55 Copynumber: 3.4 Consensus size: 56
2999180 GTGTGGGCTG
*
2999190 GTCCTGCTCTTTGAGGACTAGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGC
1 GTCCTGCTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGGCTTT-----G-AAAGGC
* *
2999251 ATCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGC
1 GTCCTGCTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGC
2999307 GTCCTGCTCTTTGAGGACTA-AAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGC
1 GTCCTGCTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGC
2999362 GTCCTGCTCTTTGAGGACTA
1 GTCCTGCTCTTTGAGGACTA
2999382 AAGGGTGAAA
Statistics
Matches: 126, Mismatches: 4, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
55 54 0.43
56 25 0.20
57 1 0.01
61 23 0.18
62 23 0.18
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (56 bp):
GTCCTGCTCTTTGAGGACTAGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGC
Found at i:2999457 original size:211 final size:211
Alignment explanation
Indices: 2999036--2999681 Score: 698
Period size: 200 Copynumber: 3.1 Consensus size: 211
2999026 AAAGGAGAGA
** *
2999036 GCATCCTGCTCTTTGAGGACT-GGGAAGTGCCACCAACATTGTGTGGGCTTTAAAAGGCGTCCTG
1 GCATCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAAC-TTGTGTGGGCTTTGAAAGGCGTCCTG
**
2999100 CTCTTTGAGGACTAAAAAAAATGCCACCAACTTGTGTGGGC--T-----G-GTCCTGCTCTTTGA
65 CTCTTTGAGGACT--AAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGA
** * * * * **
2999157 GGACTAGAA-AATGCCACCAACTTGTGTGGGCTGGTCCTGCTCTTTGAGGACTAGAAAATGCCAC
128 GGACTA-AAGGGTG--A--AA--GGAGAGAGC--GTCCTGCTCTTTGAGGACTAGAAGGTGCCAC
*
2999221 CAACTTGTGTGGGCTTTGAAAGGAAAAG
184 CAACTTGTGTGGGCTTTAAAAGGAAAAG
2999249 GCATCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGC
1 GCATCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGC
2999314 TCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGA
66 TCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGA
*
2999379 CTAAAGGGTGAAAGGAGAGAGCGTCCTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGG
131 CTAAAGGGTGAAAGGAGAGAGCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGG
*
2999444 GCTTTAAAAGGAAAAA
196 GCTTTAAAAGGAAAAG
* ** * *
2999460 GCGTCCTGCTCTTTGAGGACTA-AAGGGTG--A--AA--------GG---AGAGA-GCGTCCTGC
1 GCATCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGC
* *
2999508 TCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCCTGCTTTT
66 TCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-----G-AAAGGCGTCCTGCTCTT
*
2999573 TTAGGACTAAAGGGTGAAAGGAGAGAGCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTT
125 TGAGGACTAAAGGGTGAAAGGAGAGAGCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTT
*
2999638 GTGTGGGCTTTAAAAGGAATAG
190 GTGTGGGCTTTAAAAGGAAAAG
* *
2999660 GCGTCCTGCTCTTTGAAGACTA
1 GCATCCTGCTCTTTGAGGACTA
2999682 AAGGGTGAAA
Statistics
Matches: 389, Mismatches: 28, Indels: 45
0.84 0.06 0.10
Matches are distributed among these distances:
194 49 0.13
195 3 0.01
198 2 0.01
199 1 0.00
200 120 0.31
206 2 0.01
208 1 0.00
210 5 0.01
211 99 0.25
213 65 0.17
214 14 0.04
215 2 0.01
217 1 0.00
218 3 0.01
219 22 0.06
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.26
Consensus pattern (211 bp):
GCATCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGC
TCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGCGTCCTGCTCTTTGAGGA
CTAAAGGGTGAAAGGAGAGAGCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGG
GCTTTAAAAGGAAAAG
Found at i:2999504 original size:39 final size:40
Alignment explanation
Indices: 2999450--2999525 Score: 127
Period size: 39 Copynumber: 1.9 Consensus size: 40
2999440 GTGGGCTTTA
2999450 AAAGGAAAAAGCGTCCTGCTCTTTGAGGACTA-AAGGGTG
1 AAAGGAAAAAGCGTCCTGCTCTTTGAGGACTAGAAGGGTG
* *
2999489 AAAGGAGAGAGCGTCCTGCTCTTTGAGGACTAGAAGG
1 AAAGGAAAAAGCGTCCTGCTCTTTGAGGACTAGAAGG
2999526 TGCCACCAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 30 0.88
40 4 0.12
ACGTcount: A:0.32, C:0.16, G:0.33, T:0.20
Consensus pattern (40 bp):
AAAGGAAAAAGCGTCCTGCTCTTTGAGGACTAGAAGGGTG
Found at i:2999505 original size:100 final size:100
Alignment explanation
Indices: 2999305--2999789 Score: 811
Period size: 100 Copynumber: 4.9 Consensus size: 100
2999295 GCTTTGAAAG
*
2999305 GCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTT-----G-AAAGGCGT
1 GCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGT
2999364 CCTGCTCTTTGAGGACTAAAGGGTGAAAGGAGAGA
66 CCTGCTCTTTGAGGACTAAAGGGTGAAAGGAGAGA
* *
2999399 GCGTCCTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAAGCGT
1 GCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGT
2999464 CCTGCTCTTTGAGGACTAAAGGGTGAAAGGAGAGA
66 CCTGCTCTTTGAGGACTAAAGGGTGAAAGGAGAGA
2999499 GCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGT
1 GCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGT
* *
2999564 CCTGCTTTTTTAGGACTAAAGGGTGAAAGGAGAGA
66 CCTGCTCTTTGAGGACTAAAGGGTGAAAGGAGAGA
*
2999599 GCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAATAGGCGT
1 GCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGT
*
2999664 CCTGCTCTTTGAAGACTAAAGGGTGAAAGGAGAGA
66 CCTGCTCTTTGAGGACTAAAGGGTGAAAGGAGAGA
* * * *
2999699 GTGTGCTGCTCTTTGAGGACTAGAAGGTGCCATCAACTTGTGTGGGCTTTAAAAGAAAAAGGCGT
1 GCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGT
*
2999764 CCTGCTCTTTGAGGACTGAAAAGGTG
66 CCTGCTCTTTGAGGACT-AAAGGGTG
2999790 CCACCAACTT
Statistics
Matches: 366, Mismatches: 18, Indels: 7
0.94 0.05 0.02
Matches are distributed among these distances:
94 48 0.13
99 1 0.00
100 310 0.85
101 7 0.02
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.25
Consensus pattern (100 bp):
GCGTCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGT
CCTGCTCTTTGAGGACTAAAGGGTGAAAGGAGAGA
Found at i:2999878 original size:62 final size:62
Alignment explanation
Indices: 2999704--2999884 Score: 276
Period size: 62 Copynumber: 2.9 Consensus size: 62
2999694 AGAGAGTGTG
* * *
2999704 CTGCTCTTTGAGGACTAG-AAGGTGCCATCAACTTGTGTGGGCTTTAAAAGAAAAAGGCGTC
1 CTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTC
2999765 CTGCTCTTTGAGGACT-GAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTC
1 CTGCTCTTTGAGGACTAGAAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTC
* **
2999827 TTGCTCTTTGAGGACTAGAAAAGTGCCACCATTTTGTGTGGGCTTTAAAAGGGAAAAG
1 CTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAA-GGAAAAG
2999885 AAGGAAATGA
Statistics
Matches: 110, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
60 1 0.01
61 18 0.16
62 79 0.72
63 12 0.11
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.27
Consensus pattern (62 bp):
CTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTC
Found at i:3000038 original size:49 final size:51
Alignment explanation
Indices: 2999966--3000062 Score: 144
Period size: 49 Copynumber: 1.9 Consensus size: 51
2999956 AGGACTAGAA
* * *
2999966 GGTGCCACCAACTTGTGTGGGCTTT-GAAGG-AGAAGGCATCCTACTAAAG
1 GGTGCCACCAACTTATGTGGGCTTTAAAAGGAAAAAGGCATCCTACTAAAG
3000015 GGTGCCACCAACTTATGTGGGCTTTAAAAGGAAAAAAGGCATCCTACT
1 GGTGCCACCAACTTATGTGGGCTTTAAAAGG-AAAAAGGCATCCTACT
3000063 CTTTGAGGAC
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
49 24 0.57
50 4 0.10
52 14 0.33
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.23
Consensus pattern (51 bp):
GGTGCCACCAACTTATGTGGGCTTTAAAAGGAAAAAGGCATCCTACTAAAG
Found at i:3000111 original size:62 final size:62
Alignment explanation
Indices: 3000008--3000135 Score: 188
Period size: 61 Copynumber: 2.1 Consensus size: 62
2999998 AAGGCATCCT
*
3000008 ACTAAAGGGTGCCACCAACTTATGTGGGCTTTAAAAGGAAAAAAGGCATCCTACTCTTTGAGG
1 ACTAAAGGGTGCCACCAACTCATGTGGGCTTTAAAAGG-AAAAAGGCATCCTACTCTTTGAGG
* * *
3000071 ACTAAA-GGTGCCACCAACTCGTGTGGGCTTTGAAAA-GAAAAAGGCGTCCTACTTTTTGAGG
1 ACTAAAGGGTGCCACCAACTCATGTGGGCTTT-AAAAGGAAAAAGGCATCCTACTCTTTGAGG
3000132 ACTA
1 ACTA
3000136 GAAGCGCTAA
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
61 26 0.43
62 24 0.40
63 10 0.17
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (62 bp):
ACTAAAGGGTGCCACCAACTCATGTGGGCTTTAAAAGGAAAAAGGCATCCTACTCTTTGAGG
Found at i:3001435 original size:20 final size:20
Alignment explanation
Indices: 3001390--3001445 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
3001380 GGATCATTGT
*
3001390 GAAATGTATTGATACAATGA
1 GAAATGTATCGATACAATGA
*
3001410 GCAATGTATCGATACAATGCA
1 GAAATGTATCGATACAATG-A
3001431 -AAATGTATCGATACA
1 GAAATGTATCGATACA
3001446 TCTGGGTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (20 bp):
GAAATGTATCGATACAATGA
Found at i:3001474 original size:29 final size:30
Alignment explanation
Indices: 3001432--3001505 Score: 141
Period size: 29 Copynumber: 2.5 Consensus size: 30
3001422 TACAATGCAA
3001432 AATGTATCGATACATCTGGGTAAACCC-AG
1 AATGTATCGATACATCTGGGTAAACCCAAG
3001461 AATGTATCGATACATCTGGGTAAACCCAAG
1 AATGTATCGATACATCTGGGTAAACCCAAG
3001491 AATGTATCGATACAT
1 AATGTATCGATACAT
3001506 TGTATCGATA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 27 0.61
30 17 0.39
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (30 bp):
AATGTATCGATACATCTGGGTAAACCCAAG
Found at i:3001511 original size:13 final size:13
Alignment explanation
Indices: 3001493--3001518 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3001483 AACCCAAGAA
3001493 TGTATCGATACAT
1 TGTATCGATACAT
3001506 TGTATCGATACAT
1 TGTATCGATACAT
3001519 CTGGGTAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3001524 original size:43 final size:43
Alignment explanation
Indices: 3001463--3001560 Score: 196
Period size: 43 Copynumber: 2.3 Consensus size: 43
3001453 AAACCCAGAA
3001463 TGTATCGATACATCTGGGTAAACCCAAGAATGTATCGATACAT
1 TGTATCGATACATCTGGGTAAACCCAAGAATGTATCGATACAT
3001506 TGTATCGATACATCTGGGTAAACCCAAGAATGTATCGATACAT
1 TGTATCGATACATCTGGGTAAACCCAAGAATGTATCGATACAT
3001549 TGTATCGATACA
1 TGTATCGATACA
3001561 ATGAACAATG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 55 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (43 bp):
TGTATCGATACATCTGGGTAAACCCAAGAATGTATCGATACAT
Found at i:3001554 original size:13 final size:13
Alignment explanation
Indices: 3001536--3001560 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3001526 AACCCAAGAA
3001536 TGTATCGATACAT
1 TGTATCGATACAT
3001549 TGTATCGATACA
1 TGTATCGATACA
3001561 ATGAACAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3006449 original size:20 final size:21
Alignment explanation
Indices: 3006410--3006457 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
3006400 TATAATTTGT
*
3006410 ATCGATACAACAAGTTAATGA
1 ATCGATACAACAAGTGAATGA
* *
3006431 ATCGATAC-ATAAGTGAATGC
1 ATCGATACAACAAGTGAATGA
3006451 ATCGATA
1 ATCGATA
3006458 TTGGACCCTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.44, C:0.15, G:0.17, T:0.25
Consensus pattern (21 bp):
ATCGATACAACAAGTGAATGA
Found at i:3009128 original size:97 final size:98
Alignment explanation
Indices: 3008954--3009133 Score: 247
Period size: 97 Copynumber: 1.8 Consensus size: 98
3008944 ATTTTATTCA
* *
3008954 CGAGGATACACCAACCCTATTCTTCTGAGGGAATACTCCAACCCTCATTTTAAAACACATTAAGA
1 CGAGGATACACCAACCCCATTCTTCTAAGGGAATACTCCAACCCTCATTTTAAAACACATTAAGA
3009019 TTTAAATATTATTTTTGCTTAAATTTTCATCTT
66 TTTAAATATTATTTTTGCTTAAATTTTCATCTT
* * * * ***
3009052 CGAGGATACTCCAACCCCATTTTTTTAAAGGG-ATACTCCAA-CCTCATTTTTAAACTTGTTAAG
1 CGAGGATACACCAACCCCATTCTTCT-AAGGGAATACTCCAACCCTCATTTTAAAACACATTAAG
*
3009115 ATTTAAATCTTATTTTTGC
65 ATTTAAATATTATTTTTGC
3009134 CTCAGTTGTC
Statistics
Matches: 71, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
97 36 0.51
98 31 0.44
99 4 0.06
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (98 bp):
CGAGGATACACCAACCCCATTCTTCTAAGGGAATACTCCAACCCTCATTTTAAAACACATTAAGA
TTTAAATATTATTTTTGCTTAAATTTTCATCTT
Found at i:3009152 original size:97 final size:98
Alignment explanation
Indices: 3008954--3009168 Score: 240
Period size: 97 Copynumber: 2.2 Consensus size: 98
3008944 ATTTTATTCA
* * *
3008954 CGAGGATACACCAACCCTATTCTTCTGAGGGAATACTCCAACCCTCATTTTAAAACACATTAAGA
1 CGAGGATACTCCAACCCCATTCTTCTAAGGGAATACTCCAACCCTCATTTTAAAACACATTAAGA
* *
3009019 TTTAAATATTATTTTTGCTTAAATTTTCATCTT
66 TTTAAATATTATTTTTGCCTAAATTGTCATCTT
* * * ***
3009052 CGAGGATACTCCAACCCCATTTTTTTAAAGGG-ATACTCCAA-CCTCATTTTTAAACTTGTTAAG
1 CGAGGATACTCCAACCCCATTCTTCT-AAGGGAATACTCCAACCCTCATTTTAAAACACATTAAG
* * *
3009115 ATTTAAATCTTATTTTTGCCTCAGTTGTCA-CTAT
65 ATTTAAATATTATTTTTGCCTAAATTGTCATCT-T
* *
3009149 CGAGGACACT-CAACTCCATT
1 CGAGGATACTCCAACCCCATT
3009169 ACTCTGAAGA
Statistics
Matches: 99, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
96 11 0.11
97 53 0.54
98 31 0.31
99 4 0.04
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (98 bp):
CGAGGATACTCCAACCCCATTCTTCTAAGGGAATACTCCAACCCTCATTTTAAAACACATTAAGA
TTTAAATATTATTTTTGCCTAAATTGTCATCTT
Found at i:3013144 original size:41 final size:43
Alignment explanation
Indices: 3013039--3013144 Score: 132
Period size: 42 Copynumber: 2.5 Consensus size: 43
3013029 TAACTTCACT
*
3013039 TATCTTCTACCTAACTAGATGAAGCTGAAAATTGAATTTACCA
1 TATCTTCTACCTAACTAGATGAAGCTGAAAACTGAATTTACCA
*
3013082 -ATCTTCTACCTAACTAAATGAAGCT-AACAACTG-A-TT-CCA
1 TATCTTCTACCTAACTAGATGAAGCTGAA-AACTGAATTTACCA
*
3013121 CTATCGTCTACCTAACTAGATGAA
1 -TATCTTCTACCTAACTAGATGAA
3013145 ACAAATAATT
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
39 3 0.05
40 2 0.04
41 23 0.41
42 28 0.50
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.30
Consensus pattern (43 bp):
TATCTTCTACCTAACTAGATGAAGCTGAAAACTGAATTTACCA
Found at i:3013172 original size:304 final size:304
Alignment explanation
Indices: 3012609--3013217 Score: 1022
Period size: 304 Copynumber: 2.0 Consensus size: 304
3012599 TCCACTATTT
* *
3012609 TTTTGTCTAATCGAATGAAGTGGACAACTGACTTCACTGGTCTTTAGCGTAACCAAATGAAGCTA
1 TTTTGCCTAATCGAATGAAGTGGACAACTGACTTCACTGGTCTTTAGCCTAACCAAATGAAGCTA
*
3012674 ACAAAAGAAAAACTTCATCGATCTTGTACCTAATTGAATGAAATAGATGACTAACTTCACTTATC
66 ACAAAAGAAAAACTTCATCGATCTTATACCTAATTGAATGAAATAGATGACTAACTTCACTTATC
* * * * *
3012739 TTCTGCATAACTAGATGAAGCTGAAAATTGACTTTACTAGTCTTCCGCCTAACTAAATGAAGCAG
131 TTCTACATAACTAGATGAAGCTGAAAATTGAATTTACCAATCTTCCACCTAACTAAATGAAGCAG
* *
3012804 AGAACTGATTCCACTATTGTCTACCTAACTAGATGAAACAAATAATTAATTTCACTTGTTTTTTG
196 ACAACTGATTCCACTATCGTCTACCTAACTAGATGAAACAAATAATTAATTTCACTTGTTTTTTG
3012869 CCTCATTAAAAGAAGCGAATGATTACCTTTATCGGTATTCTGCC
261 CCTCATTAAAAGAAGCGAATGATTACCTTTATCGGTATTCTGCC
* * * **
3012913 TTTTGCCTAATTGGATGAAGTGGACAACTGACTTCATTGGTCTTTAGCCTAACTGAATGAAGCTA
1 TTTTGCCTAATCGAATGAAGTGGACAACTGACTTCACTGGTCTTTAGCCTAACCAAATGAAGCTA
3012978 ACAAAAGAAAAACTTCATCGATCTTATACCTAATTGAATGAAATAGATGACTAACTTCACTTATC
66 ACAAAAGAAAAACTTCATCGATCTTATACCTAATTGAATGAAATAGATGACTAACTTCACTTATC
* *
3013043 TTCTACCTAACTAGATGAAGCTGAAAATTGAATTTACCAATCTTCTACCTAACTAAATGAAGCTA
131 TTCTACATAACTAGATGAAGCTGAAAATTGAATTTACCAATCTTCCACCTAACTAAATGAAGC-A
3013108 -ACAACTGATTCCACTATCGTCTACCTAACTAGATGAAACAAATAATTAATTTCACTTGTTTTTT
195 GACAACTGATTCCACTATCGTCTACCTAACTAGATGAAACAAATAATTAATTTCACTTGTTTTTT
* * *
3013172 GCCTTATTAAAAGAAGCGAATGATTGCCTTTATCGTTATTCTGCC
260 GCCTCATTAAAAGAAGCGAATGATTACCTTTATCGGTATTCTGCC
3013217 T
1 T
3013218 AATTGAATAA
Statistics
Matches: 284, Mismatches: 20, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
304 283 1.00
305 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (304 bp):
TTTTGCCTAATCGAATGAAGTGGACAACTGACTTCACTGGTCTTTAGCCTAACCAAATGAAGCTA
ACAAAAGAAAAACTTCATCGATCTTATACCTAATTGAATGAAATAGATGACTAACTTCACTTATC
TTCTACATAACTAGATGAAGCTGAAAATTGAATTTACCAATCTTCCACCTAACTAAATGAAGCAG
ACAACTGATTCCACTATCGTCTACCTAACTAGATGAAACAAATAATTAATTTCACTTGTTTTTTG
CCTCATTAAAAGAAGCGAATGATTACCTTTATCGGTATTCTGCC
Found at i:3014130 original size:16 final size:17
Alignment explanation
Indices: 3014097--3014131 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3014087 TCACTAGTAT
3014097 TTTCACTTTTTTCGATA
1 TTTCACTTTTTTCGATA
*
3014114 TTTCATTTTTTTC-ATA
1 TTTCACTTTTTTCGATA
3014130 TT
1 TT
3014132 CGAATCGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.17, C:0.14, G:0.03, T:0.66
Consensus pattern (17 bp):
TTTCACTTTTTTCGATA
Found at i:3015252 original size:13 final size:13
Alignment explanation
Indices: 3015211--3015259 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
3015201 CCGTTACAAG
3015211 CAATGTATCGATA
1 CAATGTATCGATA
*
3015224 CAAT-T-TC-CT-
1 CAATGTATCGATA
3015233 C-ATGTATCGATA
1 CAATGTATCGATA
3015245 CAATGTATCGATA
1 CAATGTATCGATA
3015258 CA
1 CA
3015260 TTGTCCCATG
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
8 2 0.07
9 2 0.07
10 3 0.10
11 3 0.10
12 2 0.07
13 17 0.59
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:3015252 original size:34 final size:33
Alignment explanation
Indices: 3015211--3015280 Score: 115
Period size: 33 Copynumber: 2.1 Consensus size: 33
3015201 CCGTTACAAG
3015211 CAATGTATCGATACAATT-TCCTCATGTATCGATA
1 CAATGTATCGATAC-ATTGTCC-CATGTATCGATA
3015245 CAATGTATCGATACATTGTCCCATGTATCGATA
1 CAATGTATCGATACATTGTCCCATGTATCGATA
3015278 CAA
1 CAA
3015281 ATAGTGATAG
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
33 18 0.51
34 17 0.49
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (33 bp):
CAATGTATCGATACATTGTCCCATGTATCGATA
Found at i:3015378 original size:32 final size:33
Alignment explanation
Indices: 3015310--3015387 Score: 97
Period size: 32 Copynumber: 2.4 Consensus size: 33
3015300 TGCCAGTTTC
* *
3015310 ATGTATCGATACAATTGTCTATGTATCGATAAA
1 ATGTATCGATACAATTGGCTATATATCGATAAA
*
3015343 ATGTATCGATACAA-TGAGC-ATATATCGATACA
1 ATGTATCGATACAATTG-GCTATATATCGATAAA
*
3015375 ATGTATTGATACA
1 ATGTATCGATACA
3015388 TCTGGGAGTG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
32 25 0.62
33 15 0.38
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.33
Consensus pattern (33 bp):
ATGTATCGATACAATTGGCTATATATCGATAAA
Found at i:3015957 original size:19 final size:18
Alignment explanation
Indices: 3015925--3015979 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 18
3015915 TCCCCCTTAA
3015925 TTAAAGAATTTCTCTCCTT
1 TTAAAGAATTTCTC-CCTT
3015944 TTAAA-AATTCTCTCCCTT
1 TTAAAGAATT-TCTCCCTT
*
3015962 AATCAAAGAATTTCTCCC
1 --TTAAAGAATTTCTCCC
3015980 CCTTTGTCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 8 0.26
19 9 0.29
20 10 0.32
21 4 0.13
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.40
Consensus pattern (18 bp):
TTAAAGAATTTCTCCCTT
Found at i:3015961 original size:18 final size:19
Alignment explanation
Indices: 3015925--3015977 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 19
3015915 TCCCCCTTAA
3015925 TTAAAGAATTTCTCTCCTT
1 TTAAAGAATTTCTCTCCTT
3015944 TTAAA-AA-TTCTCTCCCTT
1 TTAAAGAATTTCTCT-CCTT
*
3015962 AATCAAAGAATTTCTC
1 --TTAAAGAATTTCTC
3015978 CCCCTTTGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 6 0.21
18 6 0.21
19 5 0.18
20 4 0.14
21 2 0.07
22 5 0.18
ACGTcount: A:0.32, C:0.23, G:0.04, T:0.42
Consensus pattern (19 bp):
TTAAAGAATTTCTCTCCTT
Found at i:3015976 original size:22 final size:22
Alignment explanation
Indices: 3015918--3015983 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
3015908 GTTTTACTCC
3015918 CCCTTAATTAAAGAATTTCTCT
1 CCCTTAATTAAAGAATTTCTCT
3015940 -CCTT--TTAAA-AA-TTCTCT
1 CCCTTAATTAAAGAATTTCTCT
* *
3015957 CCCTTAATCAAAGAATTTCTCC
1 CCCTTAATTAAAGAATTTCTCT
3015979 CCCTT
1 CCCTT
3015984 TGTCAAATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
17 6 0.16
18 6 0.16
19 5 0.14
20 4 0.11
21 6 0.16
22 10 0.27
ACGTcount: A:0.29, C:0.29, G:0.03, T:0.39
Consensus pattern (22 bp):
CCCTTAATTAAAGAATTTCTCT
Found at i:3015989 original size:22 final size:21
Alignment explanation
Indices: 3015914--3015990 Score: 56
Period size: 22 Copynumber: 3.7 Consensus size: 21
3015904 TTTCGTTTTA
3015914 CTCCCCCTTAATT-AAAGAATTT
1 CTCCCCCTT--TTCAAAGAATTT
*
3015936 CT-CTCCTTTT-AAA-AA-TT
1 CTCCCCCTTTTCAAAGAATTT
* *
3015953 CTCTCCCTTAATCAAAGAATTT
1 CTCCCCCTT-TTCAAAGAATTT
3015975 CTCCCCCTTTGTCAAA
1 CTCCCCCTTT-TCAAA
3015991 TAAAAATTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
17 4 0.09
18 6 0.14
19 6 0.14
20 3 0.07
21 7 0.16
22 17 0.40
ACGTcount: A:0.29, C:0.30, G:0.04, T:0.38
Consensus pattern (21 bp):
CTCCCCCTTTTCAAAGAATTT
Found at i:3019099 original size:21 final size:21
Alignment explanation
Indices: 3019075--3019130 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
3019065 TTTTTGTCCA
3019075 AATGTATCGATACATTGTTAG
1 AATGTATCGATACATTGTTAG
3019096 AATGTATCGATACATTGTTAG
1 AATGTATCGATACATTGTTAG
3019117 AATGTATCGATACA
1 AATGTATCGATACA
3019131 AGGTCCCAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.36
Consensus pattern (21 bp):
AATGTATCGATACATTGTTAG
Found at i:3019206 original size:13 final size:13
Alignment explanation
Indices: 3019188--3019308 Score: 71
Period size: 13 Copynumber: 7.9 Consensus size: 13
3019178 TATAAAGTGT
3019188 TGTATCGATACAA
1 TGTATCGATACAA
3019201 TGTATCGATACATAA
1 TGTATCGATAC--AA
3019216 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
3019233 TGTATCGATACATAA
1 TGTATCGATAC--AA
*
3019248 GTGTTGTATCGATATAA
1 ----TGTATCGATACAA
3019265 TGTATCGATACATAA
1 TGTATCGATAC--AA
3019280 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
3019297 TGTATCGATACA
1 TGTATCGATACA
3019309 TAAGTTTTGT
Statistics
Matches: 88, Mismatches: 2, Indels: 36
0.70 0.02 0.29
Matches are distributed among these distances:
13 44 0.50
15 6 0.07
17 6 0.07
19 32 0.36
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3019223 original size:32 final size:32
Alignment explanation
Indices: 3019168--3019329 Score: 279
Period size: 32 Copynumber: 5.0 Consensus size: 32
3019158 TTCAACGATT
*
3019168 TGTATCGATATATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
3019201 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
3019233 TGTATCGATACATAAGTGTTGTATCGATATAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
3019265 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
* *
3019297 TGTATCGATACATAAGTTTTGTATCAATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
3019329 T
1 T
3019330 ATAAGCTACT
Statistics
Matches: 124, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
32 112 0.90
33 12 0.10
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:3019386 original size:13 final size:13
Alignment explanation
Indices: 3019368--3019392 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3019358 AAATTTCAAA
3019368 TGTATCGATACAT
1 TGTATCGATACAT
3019381 TGTATCGATACA
1 TGTATCGATACA
3019393 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3025583 original size:701 final size:701
Alignment explanation
Indices: 3024225--3025644 Score: 2770
Period size: 701 Copynumber: 2.0 Consensus size: 701
3024215 TGAAGAAGTA
*
3024225 GAAA-AGGCAGAAGGTCAAAAGTCTGCCATGATTGCGGAAGAAATGGATAAGCTTCAACTCCTAG
1 GAAAGAGGCAG-AGGCCAAAAGTCTGCCATGATTGCGGAAGAAATGGATAAGCTTCAACTCCTAG
*
3024289 AAAAACAACTCCAAGCTATCGAAGGGAGTGACAACTTCGGAGCTCTTGACGCAGAATCACTGTCT
65 AAAAACAACTCCAAGCTATCGAAGGGAGTGACAACTTCGGAGCTCTTGACACAGAATCACTGTCT
3024354 TTGGTATCCAACCTTGTCATTCCCCCTAAGTTCAAAGTCCCGGAGTTTGAAAAATTCAGTGGGAC
130 TTGGTATCCAACCTTGTCATTCCCCCTAAGTTCAAAGTCCCGGAGTTTGAAAAATTCAGTGGGAC
3024419 TACTGATCCTTCTGTCCACATCCGAATGTACCTACGCAAAATGGCCGGGTACGAGAAAGATGAGA
195 TACTGATCCTTCTGTCCACATCCGAATGTACCTACGCAAAATGGCCGGGTACGAGAAAGATGAGA
3024484 AACTCCTCATCCATTGCTTCCAACATAGCCTTACTAGGGCAGCTGCTCGATGGTATATCGAGTTG
260 AACTCCTCATCCATTGCTTCCAACATAGCCTTACTAGGGCAGCTGCTCGATGGTATATCGAGTTG
3024549 GATAATGCAAAAATCCAATCGTGGGCTGATTCAGCCAAAGCCTTCCTCATCCACTATCAGCATGT
325 GATAATGCAAAAATCCAATCGTGGGCTGATTCAGCCAAAGCCTTCCTCATCCACTATCAGCATGT
3024614 CTCGGATTGGGCCTCGGATCGTCTTTCTCTTATGAATCTGGAGAAAAAGTCCACCGAGAGCTTCA
390 CTCGGATTGGGCCTCGGATCGTCTTTCTCTTATGAATCTGGAGAAAAAGTCCACCGAGAGCTTCA
3024679 AACAATACGCACAAAGATGGCGAGAGGAGGCGGCCTTGGTTCAACCACCCCTCACAGAAAAAGAG
455 AACAATACGCACAAAGATGGCGAGAGGAGGCGGCCTTGGTTCAACCACCCCTCACAGAAAAAGAG
3024744 ATGACTGTCATATTCATTAACACCTTACGAGCTCCTTATTATGAGAAGCTTATCGGGAATGCCAC
520 ATGACTGTCATATTCATTAACACCTTACGAGCTCCTTATTATGAGAAGCTTATCGGGAATGCCAC
*
3024809 GAAAAAATTTGCCGATTTGGTCTTATCCGGTGAAATGATAGATGCCGCGATCAGGACTGGCAAAA
585 GAAAAAATTTGCCGATTTGGTCTTATCCGGTGAAATGATAAATGCCGCGATCAGGACTGGCAAAA
3024874 TGTCTATAGGAGAGTCATCTGAACCTAGCAAGAAACCTGCATTCGCCAGGAG
650 TGTCTATAGGAGAGTCATCTGAACCTAGCAAGAAACCTGCATTCGCCAGGAG
*
3024926 GAAAGAGGTAGAGGCCAAAAGTCTGCCATGATTGCGGAAGAAATGGATAAGCTTCAACTCCTAGA
1 GAAAGAGGCAGAGGCCAAAAGTCTGCCATGATTGCGGAAGAAATGGATAAGCTTCAACTCCTAGA
3024991 AAAACAACTCCAAGCTATCGAAGGGAGTGACAACTTCGGAGCTCTTGACACAGAATCACTGTCTT
66 AAAACAACTCCAAGCTATCGAAGGGAGTGACAACTTCGGAGCTCTTGACACAGAATCACTGTCTT
3025056 TGGTATCCAACCTTGTCATTCCCCCTAAGTTCAAAGTCCCGGAGTTTGAAAAATTCAGTGGGACT
131 TGGTATCCAACCTTGTCATTCCCCCTAAGTTCAAAGTCCCGGAGTTTGAAAAATTCAGTGGGACT
3025121 ACTGATCCTTCTGTCCACATCCGAATGTACCTACGCAAAATGGCCGGGTACGAGAAAGATGAGAA
196 ACTGATCCTTCTGTCCACATCCGAATGTACCTACGCAAAATGGCCGGGTACGAGAAAGATGAGAA
3025186 ACTCCTCATCCATTGCTTCCAACATAGCCTTACTAGGGCAGCTGCTCGATGGTATATCGAGTTGG
261 ACTCCTCATCCATTGCTTCCAACATAGCCTTACTAGGGCAGCTGCTCGATGGTATATCGAGTTGG
*
3025251 ATAATGCAAAAATCCAATTGTGGGCTGATTCAGCCAAAGCCTTCCTCATCCACTATCAGCATGTC
326 ATAATGCAAAAATCCAATCGTGGGCTGATTCAGCCAAAGCCTTCCTCATCCACTATCAGCATGTC
*
3025316 TCGGATTGGGCCTCGGATCGTCTTTCTCTTATGAATCTGGAGAAAAAGTCCACCGAGAGCTTCAG
391 TCGGATTGGGCCTCGGATCGTCTTTCTCTTATGAATCTGGAGAAAAAGTCCACCGAGAGCTTCAA
3025381 ACAATACGCACAAAGATGGCGAGAGGAGGCGGCCTTGGTTCAACCACCCCTCACAGAAAAAGAGA
456 ACAATACGCACAAAGATGGCGAGAGGAGGCGGCCTTGGTTCAACCACCCCTCACAGAAAAAGAGA
3025446 TGACTGTCATATTCATTAACACCTTACGAGCTCCTTATTATGAGAAGCTTATCGGGAATGCCACG
521 TGACTGTCATATTCATTAACACCTTACGAGCTCCTTATTATGAGAAGCTTATCGGGAATGCCACG
3025511 AAAAAATTTGCCGATTTGGTCTTATCCGGTGAAATGATAAATGCCGCGATCAGGACTGGCAAAAT
586 AAAAAATTTGCCGATTTGGTCTTATCCGGTGAAATGATAAATGCCGCGATCAGGACTGGCAAAAT
3025576 GTCTATAGGAGAGTCATCTGAACCTAGCAAGAAACCTGCATTCGCCAGGAG
651 GTCTATAGGAGAGTCATCTGAACCTAGCAAGAAACCTGCATTCGCCAGGAG
3025627 GAAAGAGGCAGAGGCCAA
1 GAAAGAGGCAGAGGCCAA
3025645 TGCCATTAGT
Statistics
Matches: 711, Mismatches: 7, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
701 706 0.99
702 5 0.01
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.23
Consensus pattern (701 bp):
GAAAGAGGCAGAGGCCAAAAGTCTGCCATGATTGCGGAAGAAATGGATAAGCTTCAACTCCTAGA
AAAACAACTCCAAGCTATCGAAGGGAGTGACAACTTCGGAGCTCTTGACACAGAATCACTGTCTT
TGGTATCCAACCTTGTCATTCCCCCTAAGTTCAAAGTCCCGGAGTTTGAAAAATTCAGTGGGACT
ACTGATCCTTCTGTCCACATCCGAATGTACCTACGCAAAATGGCCGGGTACGAGAAAGATGAGAA
ACTCCTCATCCATTGCTTCCAACATAGCCTTACTAGGGCAGCTGCTCGATGGTATATCGAGTTGG
ATAATGCAAAAATCCAATCGTGGGCTGATTCAGCCAAAGCCTTCCTCATCCACTATCAGCATGTC
TCGGATTGGGCCTCGGATCGTCTTTCTCTTATGAATCTGGAGAAAAAGTCCACCGAGAGCTTCAA
ACAATACGCACAAAGATGGCGAGAGGAGGCGGCCTTGGTTCAACCACCCCTCACAGAAAAAGAGA
TGACTGTCATATTCATTAACACCTTACGAGCTCCTTATTATGAGAAGCTTATCGGGAATGCCACG
AAAAAATTTGCCGATTTGGTCTTATCCGGTGAAATGATAAATGCCGCGATCAGGACTGGCAAAAT
GTCTATAGGAGAGTCATCTGAACCTAGCAAGAAACCTGCATTCGCCAGGAG
Found at i:3026975 original size:8 final size:8
Alignment explanation
Indices: 3026962--3026993 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
3026952 AAGTGATGAA
3026962 AAAAAAAC
1 AAAAAAAC
3026970 AAAAAAAAC
1 -AAAAAAAC
3026979 AAAAAAAC
1 AAAAAAAC
3026987 AAAAAAA
1 AAAAAAA
3026994 AAACATAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:3026975 original size:9 final size:9
Alignment explanation
Indices: 3026961--3026994 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
3026951 AAAGTGATGA
3026961 AAAAAAAAC
1 AAAAAAAAC
3026970 AAAAAAAAC
1 AAAAAAAAC
3026979 -AAAAAAAC
1 AAAAAAAAC
3026987 AAAAAAAA
1 AAAAAAAA
3026995 AACATAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:3026982 original size:17 final size:17
Alignment explanation
Indices: 3026962--3026994 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
3026952 AAGTGATGAA
3026962 AAAAAAACAAAAAAAAC
1 AAAAAAACAAAAAAAAC
3026979 AAAAAAACAAAAAAAA
1 AAAAAAACAAAAAAAA
3026995 AACATAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAAAACAAAAAAAAC
Found at i:3027007 original size:19 final size:19
Alignment explanation
Indices: 3026960--3026998 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
3026950 AAAAGTGATG
3026960 AAAAAAA-AACAAAAAAAAC
1 AAAAAAACAA-AAAAAAAAC
3026979 AAAAAAACAAAAAAAAAAC
1 AAAAAAACAAAAAAAAAAC
3026998 A
1 A
3026999 TAGAAACAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 17 0.89
20 2 0.11
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (19 bp):
AAAAAAACAAAAAAAAAAC
Found at i:3027278 original size:17 final size:17
Alignment explanation
Indices: 3027245--3027278 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3027235 TGTTCTTTTC
*
3027245 CAAAAAAAGAAACAAAA
1 CAAAAAAAGAAAAAAAA
*
3027262 CAAAAAAGGAAAAAAAA
1 CAAAAAAAGAAAAAAAA
3027279 AGAAACAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.82, C:0.09, G:0.09, T:0.00
Consensus pattern (17 bp):
CAAAAAAAGAAAAAAAA
Found at i:3027288 original size:13 final size:13
Alignment explanation
Indices: 3027246--3027295 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
3027236 GTTCTTTTCC
3027246 AAAAAAAGAAACA
1 AAAAAAAGAAACA
3027259 AAACAAAA-AAGGA-A
1 AAA-AAAAGAA--ACA
3027273 AAAAAAAGAAACA
1 AAAAAAAGAAACA
3027286 AAAAAAAGAA
1 AAAAAAAGAA
3027296 GAAGAAGGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
12 1 0.03
13 20 0.62
14 10 0.31
15 1 0.03
ACGTcount: A:0.84, C:0.06, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAAACA
Found at i:3028281 original size:31 final size:30
Alignment explanation
Indices: 3028243--3028519 Score: 304
Period size: 31 Copynumber: 8.9 Consensus size: 30
3028233 ATACCTTTTT
* *
3028243 AAAGTCCACGACTTAGTGGCAATCTCTTCTC
1 AAAGTCCACGACTCAGTGGC-ATCTTTTCTC
*
3028274 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
1 AAAGTCCACGACTCAGTGGC-ATCTTTTCTC
3028305 AAAGTCCACGACTCAGTGGCATCCTTTTCTTC
1 AAAGTCCACGACTCAGTGGCAT-CTTTTC-TC
* *
3028337 AAAGTCCACGACTCAGTGGCAATCTCTGCTC
1 AAAGTCCACGACTCAGTGGC-ATCTTTTCTC
*
3028368 GAAGTCCACGACTCAGTGGCATCCTTTTCTTC
1 AAAGTCCACGACTCAGTGGCAT-CTTTTC-TC
* *
3028400 AAAGTCCACAACTTAGTGGCAT-TTTGTCTC
1 AAAGTCCACGACTCAGTGGCATCTTT-TCTC
* *
3028430 AAAGTCCATGACTCAGTGGCATCCTTTTCTTT
1 AAAGTCCACGACTCAGTGGCAT-CTTTTC-TC
*
3028462 AAAGTCCACGACTCAGTGGCATTTTTTCTTC
1 AAAGTCCACGACTCAGTGGCATCTTTTC-TC
* ** * *
3028493 AAAGCCCATAACTCCGTGGCACCTTTT
1 AAAGTCCACGACTCAGTGGCATCTTTT
3028520 TCTTTTTAAA
Statistics
Matches: 214, Mismatches: 23, Indels: 18
0.84 0.09 0.07
Matches are distributed among these distances:
30 28 0.13
31 112 0.52
32 72 0.34
33 2 0.01
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.30
Consensus pattern (30 bp):
AAAGTCCACGACTCAGTGGCATCTTTTCTC
Found at i:3028354 original size:63 final size:63
Alignment explanation
Indices: 3028243--3028482 Score: 353
Period size: 63 Copynumber: 3.8 Consensus size: 63
3028233 ATACCTTTTT
* *
3028243 AAAGTCCACGACTTAGTGGCAAT-CTCTTC-TCAAAGTCCACGACTCAGTGGCAATCTCTTCTC
1 AAAGTCCACGACTCAGTGGC-ATCCTTTTCTTCAAAGTCCACGACTCAGTGGCAATCTCTTCTC
*
3028305 AAAGTCCACGACTCAGTGGCATCCTTTTCTTCAAAGTCCACGACTCAGTGGCAATCTCTGCTC
1 AAAGTCCACGACTCAGTGGCATCCTTTTCTTCAAAGTCCACGACTCAGTGGCAATCTCTTCTC
* * * *
3028368 GAAGTCCACGACTCAGTGGCATCCTTTTCTTCAAAGTCCACAACTTAGTGGC-AT-TTTGTCTC
1 AAAGTCCACGACTCAGTGGCATCCTTTTCTTCAAAGTCCACGACTCAGTGGCAATCTCT-TCTC
* *
3028430 AAAGTCCATGACTCAGTGGCATCCTTTTCTTTAAAGTCCACGACTCAGTGGCA
1 AAAGTCCACGACTCAGTGGCATCCTTTTCTTCAAAGTCCACGACTCAGTGGCA
3028483 TTTTTTCTTC
Statistics
Matches: 161, Mismatches: 13, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
61 4 0.02
62 76 0.47
63 81 0.50
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (63 bp):
AAAGTCCACGACTCAGTGGCATCCTTTTCTTCAAAGTCCACGACTCAGTGGCAATCTCTTCTC
Found at i:3028466 original size:125 final size:125
Alignment explanation
Indices: 3028244--3028482 Score: 367
Period size: 125 Copynumber: 1.9 Consensus size: 125
3028234 TACCTTTTTA
* *
3028244 AAGTCCACGACTTAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAG
1 AAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACAACTCAGTGGCAATCTCTTCTCAAAG
3028309 TCCACGACTCAGTGGCATCCTTTTCTTCAAAGTCCACGACTCAGTGGCAATCTCTGCTCG
66 TCCACGACTCAGTGGCATCCTTTTCTTCAAAGTCCACGACTCAGTGGCAATCTCTGCTCG
* * *
3028369 AAGTCCACGACTCAGTGGC-ATCCTTTTCTTCAAAGTCCACAACTTAGTGGC-AT-TTTGTCTCA
1 AAGTCCACGACTCAGTGGCAAT-CTCTTC-TCAAAGTCCACAACTCAGTGGCAATCTCT-TCTCA
* *
3028431 AAGTCCATGACTCAGTGGCATCCTTTTCTTTAAAGTCCACGACTCAGTGGCA
63 AAGTCCACGACTCAGTGGCATCCTTTTCTTCAAAGTCCACGACTCAGTGGCA
3028483 TTTTTTCTTC
Statistics
Matches: 104, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
124 4 0.04
125 80 0.77
126 20 0.19
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (125 bp):
AAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACAACTCAGTGGCAATCTCTTCTCAAAG
TCCACGACTCAGTGGCATCCTTTTCTTCAAAGTCCACGACTCAGTGGCAATCTCTGCTCG
Found at i:3028512 original size:125 final size:125
Alignment explanation
Indices: 3028272--3028547 Score: 333
Period size: 125 Copynumber: 2.2 Consensus size: 125
3028262 CAATCTCTTC
*
3028272 TCAAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGCATCCTTTTCTTC
1 TCAAAGTCCACAACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGCATCCTTTTCTTC
* * *
3028337 AAAGTCCACGACTCAGTGGCAATCTCTGCTCGAAGTCCACGACTCAGTGGCATCCTTTTCT
66 AAAGTCCACGACTCAGTGGCAATCTCTGCTCAAAGCCCACAACTCAGTGGCA-CCTTTTCT
* * *
3028398 TCAAAGTCCACAACTTAGTGGC-AT-TTTGTCTCAAAGTCCATGACTCAGTGGCATCCTTTTCTT
1 TCAAAGTCCACAACTCAGTGGCAATCTCT-TCTCAAAGTCCACGACTCAGTGGCATCCTTTTCTT
* * * * * *
3028461 TAAAGTCCACGACTCAGTGGC-ATTTTTTCTTCAAAGCCCATAACTCCGTGGCACCTTTTTCTTT
65 CAAAGTCCACGACTCAGTGGCAATCTCTGC-TCAAAGCCCACAACTCAGTGGCACC-TTTTC--T
* * *
3028525 TTAAAGCCCACAACTCCGTGGCA
1 TCAAAGTCCACAACTCAGTGGCA
3028548 CCTTTTCCTT
Statistics
Matches: 127, Mismatches: 17, Indels: 10
0.82 0.11 0.06
Matches are distributed among these distances:
124 9 0.07
125 79 0.62
126 20 0.16
127 19 0.15
ACGTcount: A:0.24, C:0.30, G:0.16, T:0.30
Consensus pattern (125 bp):
TCAAAGTCCACAACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGCATCCTTTTCTTC
AAAGTCCACGACTCAGTGGCAATCTCTGCTCAAAGCCCACAACTCAGTGGCACCTTTTCT
Found at i:3028534 original size:34 final size:34
Alignment explanation
Indices: 3028459--3029024 Score: 683
Period size: 34 Copynumber: 16.8 Consensus size: 34
3028449 CATCCTTTTC
* * * *
3028459 TTTAAAGTCCACGACTCAGTGGCA--TTTTT-TC
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
* *
3028490 TTCAAAGCCCATAACTCCGTGGCACCTTTTTCTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
*
3028524 TTTAAAGCCCACAACTCCGTGGCACCTTTTCCTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
*
3028558 TTTAAAGCCCACAACTCCGTGGCACC---TTCCT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
*
3028589 TTCAAAGCCCACAACTCCGTGGCACCTTTTTCTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
* *
3028623 TTTTAAGCCCATAACTCCGTGGCACCTTTTTCTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
3028657 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
*
3028691 TTCAAAGCCCACAACTCCGTGGCACTCTTTTT-TAT
1 TTTAAAGCCCACAACTCCGTGGCAC-CTTTTTCT-T
* * *
3028726 TCT-AAGTCCACAACTCCGTGGAACCTTTTTCTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
*
3028759 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCT
1 TTTAAAGCCCACAACTCCGTGGCAC-CTTTTTCTT
* * * *
3028794 TCT-AGGTCCACAACTCCGTGGCGCC---TTCTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
* *
3028824 TTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCT
1 TTTAAAGCCCACAACTCCGTGGCAC-CTTTTT-CTT
3028860 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
* * *
3028894 TTTAAAGCCCAAAACTCTGTGGCACTTTTTTCTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
* *
3028928 TTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCT
1 TTTAAAGCCCACAACTCCGTGGCAC-CTTTTT-CTT
* *
3028964 TTTAAAGTCCACAACCCCGTGGCA-CTTTATTCTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTT-TTCTT
* *
3028998 TTT-AAGTCCACGACTCCGTGGCACCTT
1 TTTAAAGCCCACAACTCCGTGGCACCTT
3029025 CCTCTCAAAG
Statistics
Matches: 460, Mismatches: 54, Indels: 39
0.83 0.10 0.07
Matches are distributed among these distances:
30 5 0.01
31 65 0.14
32 1 0.00
33 33 0.07
34 274 0.60
35 33 0.07
36 49 0.11
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.34
Consensus pattern (34 bp):
TTTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
Found at i:3028640 original size:133 final size:135
Alignment explanation
Indices: 3028493--3029024 Score: 693
Period size: 133 Copynumber: 3.9 Consensus size: 135
3028483 TTTTTTCTTC
3028493 AAAGCCCATAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTCCTT
1 AAAGCCCATAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTCCTT
*
3028558 TTTAAAGCCCACAACTCCGTGGCAC-C-TTCCTTTCAAAGCCCACAACTCCGTGGCACCTTTTTC
66 TTCAAAGCCCACAACTCCGTGGCACTCTTTCCTTTCAAAGCCCACAACTCCGTGGCACCTTTTTC
3028621 TTTTT
131 TTTTT
* *
3028626 TAAGCCCATAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCTT
1 AAAGCCCATAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTCCTT
** * * *
3028691 TTCAAAGCCCACAACTCCGTGGCACTCTTTTTTATTCTAAGTCCACAACTCCGTGGAACCTTTTT
66 TTCAAAGCCCACAACTCCGTGGCACTCTTTCCT-TTCAAAGCCCACAACTCCGTGGCACCTTTTT
3028756 CTTTTT
130 CTTTTT
* * * * * *
3028762 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT-AGGTCCACAACTCCGTGGCGCC--TT-CT
1 AAAGCCCATAACTCCGTGGCAC-CTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTCCT
*
3028823 TTTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAAGCCCACAACTCCGTGGCACCTT
65 TTTCAAAGCCCACAACTCCGTGGCACTC--TTT-CCTTTCAAAGCCCACAACTCCGTGGCACCTT
3028888 TTTCTTTTT
127 TTTCTTTTT
* * * *
3028897 AAAGCCCAAAACTCTGTGGCACTTTTTTCTTTTCAAAGCCCACAACTCCGTGGCACTCTTTTTCC
1 AAAGCCCATAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCAC-C-TTTT-C
* * * ** * *
3028962 CTTTT-AAAGTCCACAACCCCGTGGCACT-TTATTCTTTTTAAGTCCACGACTCCGTGGCACCTT
63 CTTTTCAAAGCCCACAACTCCGTGGCACTCTT-TCCTTTCAAAGCCCACAACTCCGTGGCACCTT
3029025 CCTCTCAAAG
Statistics
Matches: 348, Mismatches: 36, Indels: 26
0.85 0.09 0.06
Matches are distributed among these distances:
133 117 0.34
134 11 0.03
135 77 0.22
136 75 0.22
137 39 0.11
138 1 0.00
139 2 0.01
140 21 0.06
141 5 0.01
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.34
Consensus pattern (135 bp):
AAAGCCCATAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTCCTT
TTCAAAGCCCACAACTCCGTGGCACTCTTTCCTTTCAAAGCCCACAACTCCGTGGCACCTTTTTC
TTTTT
Found at i:3029138 original size:32 final size:32
Alignment explanation
Indices: 3029015--3029296 Score: 412
Period size: 33 Copynumber: 8.7 Consensus size: 32
3029005 CCACGACTCC
3029015 GTGGC-ACCTTCCTCTCAAAGCCCACACAAGTCG
1 GTGGCAACCTT-CTCT-AAAGCCCACACAAGTCG
**
3029048 GTGGCAACCCTTCTCTAAAGCCCATGCAAGTCG
1 GTGGCAA-CCTTCTCTAAAGCCCACACAAGTCG
3029081 GTGGCAACCTTCTTCTAAAGCCCACACAAGTCG
1 GTGGCAACCTTC-TCTAAAGCCCACACAAGTCG
3029114 GTGGCAACACTTCTC-AAAGCCCACACAAGTCG
1 GTGGCAAC-CTTCTCTAAAGCCCACACAAGTCG
3029146 GTGGCAACCTTCTTCTAAAGCCCACACAAGTCG
1 GTGGCAACCTTC-TCTAAAGCCCACACAAGTCG
3029179 GTGGCAACCCTTCTC-AAAGCCCACACAAGTCG
1 GTGGCAA-CCTTCTCTAAAGCCCACACAAGTCG
* *
3029211 GTGGCAACCCTCTCTAAAGCCCACACAAGTTG
1 GTGGCAACCTTCTCTAAAGCCCACACAAGTCG
*
3029243 GTGGCAACCATTCTCTAAAGCCCACAAAAGTCG
1 GTGGCAACC-TTCTCTAAAGCCCACACAAGTCG
3029276 GTGGCAACCTT-TCT-AAGCCCA
1 GTGGCAACCTTCTCTAAAGCCCA
3029297 ATATAGCTGG
Statistics
Matches: 231, Mismatches: 9, Indels: 21
0.89 0.03 0.08
Matches are distributed among these distances:
30 7 0.03
31 13 0.06
32 83 0.36
33 110 0.48
34 14 0.06
35 4 0.02
ACGTcount: A:0.28, C:0.34, G:0.19, T:0.19
Consensus pattern (32 bp):
GTGGCAACCTTCTCTAAAGCCCACACAAGTCG
Found at i:3029161 original size:65 final size:66
Alignment explanation
Indices: 3029015--3029286 Score: 435
Period size: 65 Copynumber: 4.2 Consensus size: 66
3029005 CCACGACTCC
* **
3029015 GTGGC-ACCTTCCTCTCAAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCATGCAAGT
1 GTGGCAACCTTCTTCT-AAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGT
3029079 CG
65 CG
*
3029081 GTGGCAACCTTCTTCTAAAGCCCACACAAGTCGGTGGCAACACTTCTC-AAAGCCCACACAAGTC
1 GTGGCAACCTTCTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTC
3029145 G
66 G
3029146 GTGGCAACCTTCTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTC-AAAGCCCACACAAGTC
1 GTGGCAACCTTCTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTC
3029210 G
66 G
* * * *
3029211 GTGGCAACCCTC-TCTAAAGCCCACACAAGTTGGTGGCAACCATTCTCTAAAGCCCACAAAAGTC
1 GTGGCAACCTTCTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTC
3029275 G
66 G
3029276 GTGGCAACCTT
1 GTGGCAACCTT
3029287 TCTAAGCCCA
Statistics
Matches: 194, Mismatches: 10, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
64 33 0.17
65 116 0.60
66 36 0.19
67 9 0.05
ACGTcount: A:0.28, C:0.34, G:0.19, T:0.19
Consensus pattern (66 bp):
GTGGCAACCTTCTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTC
G
Found at i:3029393 original size:43 final size:43
Alignment explanation
Indices: 3029332--3029608 Score: 311
Period size: 43 Copynumber: 6.1 Consensus size: 43
3029322 TTGGCACCTT
3029332 CATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG
1 CATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG
3029375 CATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG
1 CATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG
* * * * *
3029418 CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGTATATTGG
1 CATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG
3029461 CATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG
1 ------CATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG
* * * **
3029510 CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCGTATTGGCACCTTTTC
1 CATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGC--A----CA---TTGG
* *
3029562 CATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGA
1 CATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG
3029605 CATC
1 CATC
3029609 CTTTTTCTCA
Statistics
Matches: 198, Mismatches: 21, Indels: 30
0.80 0.08 0.12
Matches are distributed among these distances:
43 120 0.61
45 1 0.01
46 2 0.01
49 40 0.20
50 1 0.01
52 34 0.17
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.32
Consensus pattern (43 bp):
CATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG
Found at i:3029471 original size:92 final size:91
Alignment explanation
Indices: 3029335--3029612 Score: 404
Period size: 92 Copynumber: 3.0 Consensus size: 91
3029325 GCACCTTCAT
* * *
3029335 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG-----CATCTTTAAGTCCAATGTAG
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATTTCATCTTTAAGTCCAATGTAG
3029395 CTGGCCTTGAATCAGCACATTGGCAC
66 CTGGCCTTGAATCAGCACATTGGCAC
*
3029421 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGTATATTGGCATCTTCATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAT-TTCATCTTTAAGTCCAATGTA
3029486 GCTGGCCTTGAATCAGCACATTGGCAC
65 GCTGGCCTTGAATCAGCACATTGGCAC
* *
3029513 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCGTATTGGCACCTTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA---TTT-CATCTTTAAGTCCAAT
*
3029578 GTAGCTGGCCTTGAATCAGCACATTGACATC
62 GTAGCTGGCCTTGAATCAGCACATTGGCA-C
3029609 CTTT
1 CTTT
3029613 TTCTCATCTT
Statistics
Matches: 173, Mismatches: 8, Indels: 12
0.90 0.04 0.06
Matches are distributed among these distances:
86 36 0.21
92 86 0.50
94 2 0.01
95 44 0.25
96 5 0.03
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.32
Consensus pattern (91 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATTTCATCTTTAAGTCCAATGTAG
CTGGCCTTGAATCAGCACATTGGCAC
Found at i:3029536 original size:135 final size:135
Alignment explanation
Indices: 3029289--3029559 Score: 461
Period size: 135 Copynumber: 2.0 Consensus size: 135
3029279 GCAACCTTTC
3029289 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
1 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
* *
3029354 GGCCTTGAATCAGCACATTGGCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGC
66 GGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGC
3029419 ACCTT
131 ACCTT
* * * *
3029424 TAAGTCCAATATCGCTGGCCTTGAATCAGTATATTGGCATCTTCATCTTTAAGTCCAATGTAGCT
1 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
* **
3029489 GGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCGTATTGGC
66 GGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGC
3029554 ACCTT
131 ACCTT
3029559 T
1 T
3029560 TCCATCTTTA
Statistics
Matches: 127, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
135 127 1.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (135 bp):
TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCT
GGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGC
ACCTT
Found at i:3029591 original size:52 final size:55
Alignment explanation
Indices: 3029513--3029725 Score: 171
Period size: 67 Copynumber: 3.7 Consensus size: 55
3029503 ACATTGGCAC
* ** *
3029513 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCGTATTGGCA-CC-TTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
* *
3029565 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
* * * * * *
3029620 CTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTTATCACTTTTCTCATCTTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATT-G-A-C---ATC-C-TTT-T--TC-TC
3029685 AT
54 AT
* *
3029687 CTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTG
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTG
3029726 GCACCTTCAT
Statistics
Matches: 127, Mismatches: 19, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
52 36 0.28
53 2 0.02
54 5 0.04
55 33 0.26
56 1 0.01
57 1 0.01
58 1 0.01
61 3 0.02
62 1 0.01
63 3 0.02
64 1 0.01
66 3 0.02
67 37 0.29
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.37
Consensus pattern (55 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
Found at i:3029648 original size:55 final size:52
Alignment explanation
Indices: 3029513--3029650 Score: 168
Period size: 52 Copynumber: 2.6 Consensus size: 52
3029503 ACATTGGCAC
** *
3029513 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCGTATTGGCACCTTTTCCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGACACCTTTTCCAT
* * *
3029565 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGACA-CC-TTTTC-CAT
* * *
3029620 CTTTAAGCCCAATATCGTTGGCCGTGAATCA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCA
3029651 ACATATTGGC
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
52 36 0.51
53 2 0.03
54 5 0.07
55 28 0.39
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (52 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGACACCTTTTCCAT
Found at i:3029724 original size:67 final size:68
Alignment explanation
Indices: 3029616--3029742 Score: 184
Period size: 67 Copynumber: 1.9 Consensus size: 68
3029606 ATCCTTTTTC
* * *
3029616 TCATCTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTTATCA-CTTTTCTCA
1 TCATCTTTAAGCCCAATATCGCTGGCCGTGAATCAACATATTGGCACCTTCATCATCTTTTCTCA
3029680 TCT
66 TCT
* * * *
3029683 TCATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCATCTTT
1 TCATCTTTAAGCCCAATATCGCTGGCCGTGAATCAACATATTGGCACCTTCATCATCTTT
3029743 AAAACCCAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
67 48 0.92
68 4 0.08
ACGTcount: A:0.24, C:0.25, G:0.13, T:0.39
Consensus pattern (68 bp):
TCATCTTTAAGCCCAATATCGCTGGCCGTGAATCAACATATTGGCACCTTCATCATCTTTTCTCA
TCT
Found at i:3030557 original size:13 final size:13
Alignment explanation
Indices: 3030539--3030591 Score: 52
Period size: 13 Copynumber: 3.6 Consensus size: 13
3030529 CATAAAGTGT
3030539 TGTATCGATACAA
1 TGTATCGATACAA
3030552 TGTATCGATACATAAGTA
1 TGTATCGATAC---A--A
3030570 TTGTATCGATACAA
1 -TGTATCGATACAA
3030584 TGTATCGA
1 TGTATCGA
3030592 AACATAAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
13 19 0.56
14 1 0.03
16 2 0.06
18 1 0.03
19 11 0.32
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3030576 original size:19 final size:19
Alignment explanation
Indices: 3030518--3030614 Score: 74
Period size: 19 Copynumber: 5.7 Consensus size: 19
3030508 TTTCAACGAT
*
3030518 TTGTATCGATACATAAAGTG
1 TTGTATCGATACAT-AAGTA
3030538 TTGTATCGATAC---A--A
1 TTGTATCGATACATAAGTA
3030552 -TGTATCGATACATAAGTA
1 TTGTATCGATACATAAGTA
3030570 TTGTATCGATAC---A--A
1 TTGTATCGATACATAAGTA
* *
3030584 -TGTATCGAAACATAAGTT
1 TTGTATCGATACATAAGTA
3030602 TTGTATCGATACA
1 TTGTATCGATACA
3030615 ATATAAGCTA
Statistics
Matches: 61, Mismatches: 4, Indels: 25
0.68 0.04 0.28
Matches are distributed among these distances:
13 21 0.34
14 1 0.02
16 4 0.07
18 1 0.02
19 22 0.36
20 12 0.20
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.35
Consensus pattern (19 bp):
TTGTATCGATACATAAGTA
Found at i:3030579 original size:32 final size:32
Alignment explanation
Indices: 3030519--3030616 Score: 160
Period size: 32 Copynumber: 3.0 Consensus size: 32
3030509 TTCAACGATT
*
3030519 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTATTGTATCGATACAA
3030552 TGTATCGATACATAAGTATTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
* *
3030584 TGTATCGAAACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
3030616 T
1 T
3030617 ATAAGCTACT
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
32 49 0.79
33 13 0.21
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:3035259 original size:20 final size:21
Alignment explanation
Indices: 3035212--3035264 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
3035202 GCCAATGACC
**
3035212 TGTATCGATACATCTTTTTCA
1 TGTATCGATACATCTTGGTCA
*
3035233 AGTATCGATACAT-TTGGTCA
1 TGTATCGATACATCTTGGTCA
3035253 TGTATCGATACA
1 TGTATCGATACA
3035265 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATCTTGGTCA
Found at i:3035270 original size:13 final size:13
Alignment explanation
Indices: 3035252--3035276 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3035242 ACATTTGGTC
3035252 ATGTATCGATACA
1 ATGTATCGATACA
3035265 ATGTATCGATAC
1 ATGTATCGATAC
3035277 TGTGCAACAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3035930 original size:29 final size:29
Alignment explanation
Indices: 3035897--3035959 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 29
3035887 TTTAATCACA
*
3035897 TATTTCTTACTCCCCTTTAATAATAAATT
1 TATTTCTTACTCCCCCTTAATAATAAATT
*
3035926 TATTTCTTACTCCCCCTTAATCATAAATT
1 TATTTCTTACTCCCCCTTAATAATAAATT
3035955 TATTT
1 TATTT
3035960 GCAAAGATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.29, C:0.22, G:0.00, T:0.49
Consensus pattern (29 bp):
TATTTCTTACTCCCCCTTAATAATAAATT
Found at i:3035955 original size:25 final size:25
Alignment explanation
Indices: 3035888--3035955 Score: 64
Period size: 29 Copynumber: 2.6 Consensus size: 25
3035878 TAATAAATTT
* * *
3035888 TTAATCACATATTTCTTACTCCCCT
1 TTAATCATAAATTTCTTACTCCCCC
*
3035913 TTAATAATAAATTTATTTCTTACTCCCCC
1 TTAATCAT-AA---ATTTCTTACTCCCCC
3035942 TTAATCATAAATTT
1 TTAATCATAAATTT
3035956 ATTTGCAAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
25 10 0.29
26 1 0.03
28 2 0.06
29 21 0.62
ACGTcount: A:0.31, C:0.24, G:0.00, T:0.46
Consensus pattern (25 bp):
TTAATCATAAATTTCTTACTCCCCC
Found at i:3037771 original size:13 final size:13
Alignment explanation
Indices: 3037753--3037791 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
3037743 ATAATCCCCT
3037753 TGTATCGATACAG
1 TGTATCGATACAG
*
3037766 TGTATCGATACAA
1 TGTATCGATACAG
3037779 TGTATCGATACAG
1 TGTATCGATACAG
3037792 AGAATGCTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:3037804 original size:20 final size:20
Alignment explanation
Indices: 3037779--3037830 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
3037769 ATCGATACAA
3037779 TGTATCGATACAGAGAATGC
1 TGTATCGATACAGAGAATGC
3037799 TGTATCGATACAGAGAATGC
1 TGTATCGATACAGAGAATGC
3037819 TGTATCGATACA
1 TGTATCGATACA
3037831 TCTGCATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (20 bp):
TGTATCGATACAGAGAATGC
Found at i:3042367 original size:9 final size:9
Alignment explanation
Indices: 3042353--3042383 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
3042343 TCTGAGTCAC
*
3042353 CATCATCAT
1 CATCATCTT
3042362 CATCATCTT
1 CATCATCTT
3042371 CATCATCTT
1 CATCATCTT
3042380 CATC
1 CATC
3042384 GTCCTTGGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.26, C:0.35, G:0.00, T:0.39
Consensus pattern (9 bp):
CATCATCTT
Found at i:3044011 original size:13 final size:13
Alignment explanation
Indices: 3043993--3044017 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3043983 CATTTTATGG
3043993 TGTATCGATACAA
1 TGTATCGATACAA
3044006 TGTATCGATACA
1 TGTATCGATACA
3044018 TACTATGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3044033 original size:32 final size:33
Alignment explanation
Indices: 3043971--3044037 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
3043961 GTTACAAGCT
**
3043971 AATGTATCGATACATTTTATGGTGTATCGATAC
1 AATGTATCGATACATACTATGGTGTATCGATAC
3044004 AATGTATCGATACATACTAT-GTGTATCGATAC
1 AATGTATCGATACATACTATGGTGTATCGATAC
3044036 AA
1 AA
3044038 GTTTGGCTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.36
Consensus pattern (33 bp):
AATGTATCGATACATACTATGGTGTATCGATAC
Found at i:3044116 original size:20 final size:21
Alignment explanation
Indices: 3044069--3044121 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
3044059 GCCAATGACC
**
3044069 TGTATCGATACATCTTTTTCA
1 TGTATCGATACATCTTGGTCA
*
3044090 AGTATCGATACAT-TTGGTCA
1 TGTATCGATACATCTTGGTCA
3044110 TGTATCGATACA
1 TGTATCGATACA
3044122 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (21 bp):
TGTATCGATACATCTTGGTCA
Found at i:3044127 original size:13 final size:13
Alignment explanation
Indices: 3044109--3044133 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3044099 ACATTTGGTC
3044109 ATGTATCGATACA
1 ATGTATCGATACA
3044122 ATGTATCGATAC
1 ATGTATCGATAC
3044134 TGTGCAACAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3049062 original size:33 final size:34
Alignment explanation
Indices: 3048998--3049067 Score: 106
Period size: 33 Copynumber: 2.1 Consensus size: 34
3048988 CCGTTACAAG
* * *
3048998 CAATGTATCGATACAATTTTCTCATGTATCGATA
1 CAATGAATCGATACAATTGTCCCATGTATCGATA
3049032 CAATGAATCGATAC-ATTGTCCCATGTATCGATA
1 CAATGAATCGATACAATTGTCCCATGTATCGATA
3049065 CAA
1 CAA
3049068 ATAGTGATAG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 20 0.61
34 13 0.39
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (34 bp):
CAATGAATCGATACAATTGTCCCATGTATCGATA
Found at i:3049141 original size:19 final size:18
Alignment explanation
Indices: 3049096--3049151 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 18
3049086 CTACCAGTTT
*
3049096 CATGTATCGATACAATTGT
1 CATGTATCGATACAA-TGG
3049115 CTATGTATCGATACAATGAG
1 C-ATGTATCGATACAATG-G
*
3049135 CATGTATCGACACAATG
1 CATGTATCGATACAATG
3049152 TACCGATACA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (18 bp):
CATGTATCGATACAATGG
Found at i:3061018 original size:21 final size:22
Alignment explanation
Indices: 3060994--3061043 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
3060984 ATTAAATCTT
* *
3060994 CTTCAAATTTCTT-ATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
3061015 CTTCAAAATACTTCATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
3061037 --TCAAAAT
1 CTTCAAAAT
3061044 CATCAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 7 0.27
21 11 0.42
22 8 0.31
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (22 bp):
CTTCAAAATACTTCATTTTTCA
Found at i:3063709 original size:21 final size:21
Alignment explanation
Indices: 3063668--3063711 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3063658 CTCCCCTTTA
* *
3063668 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
3063689 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
3063710 TC
1 TC
3063712 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:3065532 original size:13 final size:13
Alignment explanation
Indices: 3065514--3065552 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
3065504 ATAATCACCC
3065514 TGTATCGATACAA
1 TGTATCGATACAA
*
3065527 TGTATCGATACAT
1 TGTATCGATACAA
3065540 TGTATCGATACAA
1 TGTATCGATACAA
3065553 AGAAAAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3067651 original size:15 final size:15
Alignment explanation
Indices: 3067631--3067661 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3067621 ATTTCGTTTG
*
3067631 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
3067646 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
3067661 G
1 G
3067662 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:3069490 original size:21 final size:21
Alignment explanation
Indices: 3069461--3069505 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3069451 AAGTTTTCAT
*
3069461 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
3069481 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
3069503 TTT
1 TTT
3069506 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:3073439 original size:33 final size:32
Alignment explanation
Indices: 3073402--3073493 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 32
3073392 CACTGTTTAT
3073402 ATCGATACATG-GCACATTGTATCGATACAATGC
1 ATCGATACATGAG-A-ATTGTATCGATACAATGC
3073435 ATCGATACATGATGAATTGTATCGATACAATGC
1 ATCGATACATGA-GAATTGTATCGATACAATGC
3073468 ATCGATACATGATGAATTGTATCGAT
1 ATCGATACATGA-GAATTGTATCGAT
3073494 GCATTGCTTC
Statistics
Matches: 57, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
33 55 0.96
34 1 0.02
35 1 0.02
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.30
Consensus pattern (32 bp):
ATCGATACATGAGAATTGTATCGATACAATGC
Found at i:3073440 original size:13 final size:13
Alignment explanation
Indices: 3073422--3073476 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 13
3073412 GGCACATTGT
3073422 ATCGATACAATGC
1 ATCGATACAATGC
3073435 ATCGATAC-ATG-
1 ATCGATACAATGC
* *
3073446 AT-G--A-ATTGT
1 ATCGATACAATGC
3073455 ATCGATACAATGC
1 ATCGATACAATGC
3073468 ATCGATACA
1 ATCGATACA
3073477 TGATGAATTG
Statistics
Matches: 33, Mismatches: 3, Indels: 12
0.69 0.06 0.25
Matches are distributed among these distances:
8 3 0.09
9 2 0.06
10 2 0.06
11 2 0.06
12 4 0.12
13 20 0.61
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.27
Consensus pattern (13 bp):
ATCGATACAATGC
Found at i:3073460 original size:20 final size:20
Alignment explanation
Indices: 3073435--3073493 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 20
3073425 GATACAATGC
3073435 ATCGATACATGATGAATTGT
1 ATCGATACATGATGAATTGT
*
3073455 ATCGATAC------AA-TGC
1 ATCGATACATGATGAATTGT
3073468 ATCGATACATGATGAATTGT
1 ATCGATACATGATGAATTGT
3073488 ATCGAT
1 ATCGAT
3073494 GCATTGCTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
13 10 0.33
14 2 0.07
19 2 0.07
20 16 0.53
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
ATCGATACATGATGAATTGT
Found at i:3075465 original size:20 final size:21
Alignment explanation
Indices: 3075442--3075481 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
3075432 GAGAGGTTGG
*
3075442 ACATGTTATAA-ATGCATGAA
1 ACATGGTATAACATGCATGAA
3075462 ACATGGTATAACATGCATGA
1 ACATGGTATAACATGCATGA
3075482 TCAATGGCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.28
Consensus pattern (21 bp):
ACATGGTATAACATGCATGAA
Found at i:3076468 original size:22 final size:22
Alignment explanation
Indices: 3076443--3076624 Score: 73
Period size: 22 Copynumber: 7.6 Consensus size: 22
3076433 CTGATCATCC
3076443 TTTGCTTGCTCTTTTCTCGTAT
1 TTTGCTTGCTCTTTTCTCGTAT
* *
3076465 TTTGCTTTCTC-TTCCTACTGCTCACCT
1 TTTGCTTGCTCTTTTCT-C-G-T-A--T
*
3076492 TTTGCTTGCTCTTTTCTCGTCT
1 TTTGCTTGCTCTTTTCTCGTAT
* *
3076514 TTTGCTTTCTC-TTCCTACTGCTCACCT
1 TTTGCTTGCTCTTTTCT-C-G-T-A--T
* *
3076541 TTTGCTTGCTCTTTTCTCATCT
1 TTTGCTTGCTCTTTTCTCGTAT
* *
3076563 TTTGCTTTCTC-TTCCTACTGCTCACCT
1 TTTGCTTGCTCTTTTCT-C-G-T-A--T
*
3076590 TTTGCTTGCTCTTTTCTCATAT
1 TTTGCTTGCTCTTTTCTCGTAT
* *
3076612 TTTTCTTTCTCTT
1 TTTGCTTGCTCTT
3076625 CGTATTGCTC
Statistics
Matches: 118, Mismatches: 21, Indels: 42
0.65 0.12 0.23
Matches are distributed among these distances:
21 12 0.10
22 47 0.40
23 2 0.02
24 4 0.03
25 4 0.03
26 1 0.01
27 36 0.31
28 12 0.10
ACGTcount: A:0.05, C:0.30, G:0.09, T:0.55
Consensus pattern (22 bp):
TTTGCTTGCTCTTTTCTCGTAT
Found at i:3076494 original size:27 final size:27
Alignment explanation
Indices: 3076464--3076602 Score: 154
Period size: 27 Copynumber: 5.5 Consensus size: 27
3076454 TTTTCTCGTA
*
3076464 TTTTGCTTTCTCTTCCTACTGCTCACC
1 TTTTGCTTGCTCTTCCTACTGCTCACC
**
3076491 TTTTGCTTGCTCTT--T--T-CTCGTC
1 TTTTGCTTGCTCTTCCTACTGCTCACC
*
3076513 TTTTGCTTTCTCTTCCTACTGCTCACC
1 TTTTGCTTGCTCTTCCTACTGCTCACC
*
3076540 TTTTGCTTGCTCTT--T--T-CTCATC
1 TTTTGCTTGCTCTTCCTACTGCTCACC
*
3076562 TTTTGCTTTCTCTTCCTACTGCTCACC
1 TTTTGCTTGCTCTTCCTACTGCTCACC
3076589 TTTTGCTTGCTCTT
1 TTTTGCTTGCTCTT
3076603 TTCTCATATT
Statistics
Matches: 91, Mismatches: 11, Indels: 20
0.75 0.09 0.16
Matches are distributed among these distances:
22 35 0.38
23 2 0.02
24 2 0.02
25 2 0.02
26 2 0.02
27 48 0.53
ACGTcount: A:0.05, C:0.32, G:0.09, T:0.53
Consensus pattern (27 bp):
TTTTGCTTGCTCTTCCTACTGCTCACC
Found at i:3076497 original size:49 final size:49
Alignment explanation
Indices: 3076443--3076635 Score: 323
Period size: 49 Copynumber: 3.9 Consensus size: 49
3076433 CTGATCATCC
*
3076443 TTTGCTTGCTCTTTTCTCGTATTTTGCTTTCTCTTCCTACTGCTCACCT
1 TTTGCTTGCTCTTTTCTCATATTTTGCTTTCTCTTCCTACTGCTCACCT
* *
3076492 TTTGCTTGCTCTTTTCTCGTCTTTTGCTTTCTCTTCCTACTGCTCACCT
1 TTTGCTTGCTCTTTTCTCATATTTTGCTTTCTCTTCCTACTGCTCACCT
*
3076541 TTTGCTTGCTCTTTTCTCATCTTTTGCTTTCTCTTCCTACTGCTCACCT
1 TTTGCTTGCTCTTTTCTCATATTTTGCTTTCTCTTCCTACTGCTCACCT
* * *
3076590 TTTGCTTGCTCTTTTCTCATATTTTTCTTTCTCTTCGTATTGCTCA
1 TTTGCTTGCTCTTTTCTCATATTTTGCTTTCTCTTCCTACTGCTCA
3076636 TTCCTCGTTT
Statistics
Matches: 138, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 138 1.00
ACGTcount: A:0.06, C:0.30, G:0.09, T:0.54
Consensus pattern (49 bp):
TTTGCTTGCTCTTTTCTCATATTTTGCTTTCTCTTCCTACTGCTCACCT
Found at i:3077130 original size:17 final size:16
Alignment explanation
Indices: 3077108--3077139 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
3077098 GATGCTACTT
3077108 CACGTTGCTTTGCTTTA
1 CACGTTGCTTT-CTTTA
3077125 CACGTTGCTTTCTTT
1 CACGTTGCTTTCTTT
3077140 GCTGGCAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.09, C:0.25, G:0.16, T:0.50
Consensus pattern (16 bp):
CACGTTGCTTTCTTTA
Found at i:3077277 original size:20 final size:20
Alignment explanation
Indices: 3077252--3077291 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3077242 CACATTCCAT
*
3077252 TTGCTTTTGTTTCCCATTGC
1 TTGCTTTTGTCTCCCATTGC
3077272 TTGCTTTTGTCTCCCATTGC
1 TTGCTTTTGTCTCCCATTGC
3077292 ATGCATGTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.05, C:0.28, G:0.15, T:0.53
Consensus pattern (20 bp):
TTGCTTTTGTCTCCCATTGC
Found at i:3077368 original size:16 final size:15
Alignment explanation
Indices: 3077342--3077392 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
3077332 TATTGTAATT
3077342 TTTTA-ATTTTTTGA
1 TTTTAGATTTTTTGA
3077356 TTACTT-GATTTTTTTGA
1 TT--TTAGA-TTTTTTGA
3077373 TTTTAGATTTTTTGA
1 TTTTAGATTTTTTGA
3077388 CTTTT
1 -TTTT
3077393 TTATTATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
14 2 0.06
15 10 0.32
16 9 0.29
17 10 0.32
ACGTcount: A:0.18, C:0.04, G:0.10, T:0.69
Consensus pattern (15 bp):
TTTTAGATTTTTTGA
Found at i:3077376 original size:8 final size:8
Alignment explanation
Indices: 3077339--3077394 Score: 51
Period size: 8 Copynumber: 6.9 Consensus size: 8
3077329 TTTTATTGTA
*
3077339 ATTTTTTA
1 ATTTTTTG
3077347 ATTTTTTG
1 ATTTTTTG
**
3077355 ATTACTTG
1 ATTTTTTG
3077363 ATTTTTTTG
1 A-TTTTTTG
*
3077372 A-TTTTAG
1 ATTTTTTG
3077379 ATTTTTTG
1 ATTTTTTG
3077387 ACTTTTTT
1 A-TTTTTT
3077395 ATTATTATTT
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
7 6 0.16
8 20 0.53
9 12 0.32
ACGTcount: A:0.18, C:0.04, G:0.09, T:0.70
Consensus pattern (8 bp):
ATTTTTTG
Found at i:3077424 original size:16 final size:16
Alignment explanation
Indices: 3077392--3077421 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3077382 TTTTGACTTT
3077392 TTTATTATTATTTTTA
1 TTTATTATTATTTTTA
3077408 TTTATT-TTATTTTT
1 TTTATTATTATTTTT
3077422 TATCAAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTATTATTATTTTTA
Found at i:3083864 original size:11 final size:11
Alignment explanation
Indices: 3083848--3083917 Score: 74
Period size: 11 Copynumber: 6.2 Consensus size: 11
3083838 TTTGTTGTTG
3083848 TTGTTTTTTTT
1 TTGTTTTTTTT
3083859 TTGTTTGTTCTATT
1 TTGTTT-TT-T-TT
3083873 TTGTTTTTTTT
1 TTGTTTTTTTT
3083884 TTG---TTTTT
1 TTGTTTTTTTT
3083892 TTGTTTTTTTT
1 TTGTTTTTTTT
3083903 TTGTCTCTTTTTT
1 TTGT-T-TTTTTT
3083916 TT
1 TT
3083918 TACGGAGGAC
Statistics
Matches: 51, Mismatches: 0, Indels: 14
0.78 0.00 0.22
Matches are distributed among these distances:
8 8 0.16
11 20 0.39
12 4 0.08
13 11 0.22
14 8 0.16
ACGTcount: A:0.01, C:0.04, G:0.10, T:0.84
Consensus pattern (11 bp):
TTGTTTTTTTT
Found at i:3083874 original size:19 final size:19
Alignment explanation
Indices: 3083845--3083918 Score: 80
Period size: 19 Copynumber: 3.8 Consensus size: 19
3083835 CTTTTTGTTG
* *
3083845 TTGTTGTTTT-TTTTTTGT
1 TTGTTCTTTTGTTTTTTTT
3083863 TTGTTCTATTTTGTTTTTTTT
1 TTGTTC--TTTTGTTTTTTTT
*
3083884 TTGTTTTTTTGTTTTTTTT
1 TTGTTCTTTTGTTTTTTTT
3083903 TTGTCTCTTTT-TTTTT
1 TTGT-TCTTTTGTTTTT
3083919 ACGGAGGACG
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
18 5 0.10
19 22 0.46
20 9 0.19
21 12 0.25
ACGTcount: A:0.01, C:0.04, G:0.11, T:0.84
Consensus pattern (19 bp):
TTGTTCTTTTGTTTTTTTT
Found at i:3101515 original size:20 final size:20
Alignment explanation
Indices: 3101470--3101543 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 20
3101460 AAAAAACAAG
**
3101470 AATGTATCGATACA-AAGCA
1 AATGTATCGATACATTTGCA
*
3101489 AATTGTATCGATACATTTGGA
1 AA-TGTATCGATACATTTGCA
* * *
3101510 AATGTATCAATACATTTACT
1 AATGTATCGATACATTTGCA
*
3101530 TATGTATCGATACA
1 AATGTATCGATACA
3101544 ATTTTTCATC
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
19 2 0.05
20 38 0.86
21 4 0.09
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.34
Consensus pattern (20 bp):
AATGTATCGATACATTTGCA
Found at i:3101620 original size:20 final size:21
Alignment explanation
Indices: 3101595--3101647 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 21
3101585 TTGAGACATG
**
3101595 TGTATCGATACATTCA-CTTT
1 TGTATCGATACATTCACCAAT
3101615 TGTATCGATACATTCACCAAT
1 TGTATCGATACATTCACCAAT
3101636 TGTATCGATACA
1 TGTATCGATACA
3101648 AATTGTAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCACCAAT
Found at i:3102431 original size:31 final size:31
Alignment explanation
Indices: 3102395--3102516 Score: 104
Period size: 31 Copynumber: 3.9 Consensus size: 31
3102385 ACTGAAACTT
*
3102395 AGGTGCCACCAACTTGTGTGGGCTTTGACTC
1 AGGTGCCACCAACTTGTGCGGGCTTTGACTC
** *
3102426 AGGTGCTGCCAACTTATGCGGG-TTTAGACTC
1 AGGTGCCACCAACTTGTGCGGGCTTT-GACTC
* ** * *
3102457 AAGTGCTGCCAGCTTGTGCGGGCTTTAACT-
1 AGGTGCCACCAACTTGTGCGGGCTTTGACTC
* * *
3102487 AGGGTGCCACCAGCTCGTGTGGGCTTTGAC
1 A-GGTGCCACCAACTTGTGCGGGCTTTGAC
3102517 ATTCTAAGGC
Statistics
Matches: 74, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
30 4 0.05
31 67 0.91
32 3 0.04
ACGTcount: A:0.16, C:0.25, G:0.31, T:0.28
Consensus pattern (31 bp):
AGGTGCCACCAACTTGTGCGGGCTTTGACTC
Found at i:3102492 original size:180 final size:180
Alignment explanation
Indices: 3102159--3102738 Score: 774
Period size: 180 Copynumber: 3.2 Consensus size: 180
3102149 GGTTTTAGTT
*
3102159 TTCTAA-GCTTGACCTCTTTAGACAAGTGCCAACAAATTTGGACTTAACTCAAACTTAGGTGCCA
1 TTCTAAGGCTTGACCTCTTTAGACAAGTGCCAACTAATTTGGACTTAACTCAAACTTAGGTGCCA
* * * *
3102223 CCAGCTTGTCTGGGCTTTGACTTAGGTGCTGCCAACTCATGCTA-GCTTAGACTCGAGTGCTGTC
66 CCAGCTTGTGTGGGCTTTGACTCAGGTGCTGCCAACTCATGC-AGGTTTAGACTCGAGTGCTGCC
* * *
3102287 AACTTGTGCAGGCTTTGATTAGGGTGCCACCAACTCGTGTGGGCTTTGACA
130 AGCTTGTGCGGGCTTTGACTAGGGTGCCACCAACTCGTGTGGGCTTTGACA
* *
3102338 TTCTAAGGCTTCACCT-TCTTAGACAAGTGCCAACTAATTTGGACTTAACTGAAACTTAGGTGCC
1 TTCTAAGGCTTGACCTCT-TTAGACAAGTGCCAACTAATTTGGACTTAACTCAAACTTAGGTGCC
* * * *
3102402 ACCAACTTGTGTGGGCTTTGACTCAGGTGCTGCCAACTTATGCGGGTTTAGACTCAAGTGCTGCC
65 ACCAGCTTGTGTGGGCTTTGACTCAGGTGCTGCCAACTCATGCAGGTTTAGACTCGAGTGCTGCC
* *
3102467 AGCTTGTGCGGGCTTTAACTAGGGTGCCACCAGCTCGTGTGGGCTTTGACA
130 AGCTTGTGCGGGCTTTGACTAGGGTGCCACCAACTCGTGTGGGCTTTGACA
* * * *
3102518 TTCTAAGGCTTGACCTCTTTAGATAGGTGCCAACTAATTTAGACTTGACTCAAACTTAGGTGCCA
1 TTCTAAGGCTTGACCTCTTTAGACAAGTGCCAACTAATTTGGACTTAACTCAAACTTAGGTGCCA
* * * * * * *
3102583 CGAGCTTGTGTGGGCTTTGACTCAGGTACCGTCAACTCGT-CTAGGTTTAAACTCGGGTGCTGCC
66 CCAGCTTGTGTGGGCTTTGACTCAGGTGCTGCCAACTCATGC-AGGTTTAGACTCGAGTGCTGCC
* * ** *
3102647 AGCTTGTGCGGGCTTTGACTAGGGTGCCACCAACTTGTCTGAACTTTAACA
130 AGCTTGTGCGGGCTTTGACTAGGGTGCCACCAACTCGTGTGGGCTTTGACA
* * *
3102698 TTCTAAGGCTTGACCT-TCTTAAATAGGTGCCAACTAATTTG
1 TTCTAAGGCTTGACCTCT-TTAGACAAGTGCCAACTAATTTG
3102739 TTTTGACTCA
Statistics
Matches: 353, Mismatches: 42, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
179 9 0.03
180 343 0.97
181 1 0.00
ACGTcount: A:0.22, C:0.23, G:0.24, T:0.31
Consensus pattern (180 bp):
TTCTAAGGCTTGACCTCTTTAGACAAGTGCCAACTAATTTGGACTTAACTCAAACTTAGGTGCCA
CCAGCTTGTGTGGGCTTTGACTCAGGTGCTGCCAACTCATGCAGGTTTAGACTCGAGTGCTGCCA
GCTTGTGCGGGCTTTGACTAGGGTGCCACCAACTCGTGTGGGCTTTGACA
Found at i:3102828 original size:319 final size:321
Alignment explanation
Indices: 3102465--3103152 Score: 834
Period size: 319 Copynumber: 2.1 Consensus size: 321
3102455 TCAAGTGCTG
* *
3102465 CCAGCTTGTGCGGGCTTTAACTAGGGTGCCACCAGCTCGTGTGGGCTTTGA-CATTCTAAGGCTT
1 CCAGCTTGTGCGGGCTTTGACTAGGGTGCCACCAACTCGTGTGGGCTTT-ATCATTCTAAGGCTT
* * *
3102529 GACCTCTTTAGATAGGTGCCAACTAATTTAGACTTGACTCAAACTTAGGTGCCACGAGCTTGTGT
65 GACCTCCTTAGATAGGTGCCAACTAATTTAGACCTGACTCAAACTTAGGTGCCACCAGCTTGTGT
* * * * * ** *
3102594 GGGCTTTGACTC-AGGTACCGTCAACTCGT-CTAGGTTTAAACTCGGGTGCTGCCAGCTTGTGCG
130 GGGCTTTGACTCTA-GTACCGCCAACTCATGCGA-GCTTAAACTCGGGTACCACCAGCTTGTGCA
* * ** * *
3102657 GGCTTTGACTAGGGTGCCACCAACTTGTCTGAACTTTAACATTCTAAGGCTTGACCTTCTTAAAT
193 AGCTTTGAATAGGGTGCCACCAACTCATCTGAACTTTAA-ATTCTAAGGCTTGACCATCTTAAAC
* * * *
3102722 AGGTGCCAACTAATTTGTTTTGACTCA-GT-C-GCCAACTCGTGT-GA-GCTTAGACTCAGGTAC
257 AGGTGCCAACTAATTTGCTTTAACTCAGGTGCAACCAACT--TGTACAGGCTTAGACTCAGGTAC
*
3102782 CG
320 CA
* * *
3102784 CTAGGTTGTCCGGGCTTTGACTAGGGTGCCACCAACTCGTGTGGGCTTTATCATTCTAAGGCTTG
1 CCAGCTTGTGCGGGCTTTGACTAGGGTGCCACCAACTCGTGTGGGCTTTATCATTCTAAGGCTTG
* * * *
3102849 AGCTCCTTAGATAGGTGCCAACTAATTTGGACCTGAGTCGAACTTAGGTGCCACCAGCTTGTGTG
66 ACCTCCTTAGATAGGTGCCAACTAATTTAGACCTGACTCAAACTTAGGTGCCACCAGCTTGTGTG
* * * *
3102914 GGCTTTGACTCTAGTGCCGCCAACTCATGCGAGCTTAGACTCGGGTACCACTAGTTTGTGCAAGC
131 GGCTTTGACTCTAGTACCGCCAACTCATGCGAGCTTAAACTCGGGTACCACCAGCTTGTGCAAGC
** * ** * * *
3102979 TTTGAATAGGGTGTTACCAACTCATGTGGGCTTTCAATTTTAAGGCTTGACCATCTTAGACAGGT
196 TTTGAATAGGGTGCCACCAACTCATCTGAACTTTAAATTCTAAGGCTTGACCATCTTAAACAGGT
* *
3103044 GCCAACTAATTTGCTTTAACTTAGGTGCAACCAACTTGTACAGGCTTAGACTCGGGTACCA
261 GCCAACTAATTTGCTTTAACTCAGGTGCAACCAACTTGTACAGGCTTAGACTCAGGTACCA
* * *
3103105 CCAGCTTGTGCGAGCTTTGACTAGGGTGCCACCAATTCATGTGGGCTT
1 CCAGCTTGTGCGGGCTTTGACTAGGGTGCCACCAACTCGTGTGGGCTT
3103153 ATAAAAGAGG
Statistics
Matches: 310, Mismatches: 51, Indels: 14
0.83 0.14 0.04
Matches are distributed among these distances:
318 46 0.15
319 195 0.63
320 5 0.02
321 64 0.21
ACGTcount: A:0.21, C:0.24, G:0.25, T:0.30
Consensus pattern (321 bp):
CCAGCTTGTGCGGGCTTTGACTAGGGTGCCACCAACTCGTGTGGGCTTTATCATTCTAAGGCTTG
ACCTCCTTAGATAGGTGCCAACTAATTTAGACCTGACTCAAACTTAGGTGCCACCAGCTTGTGTG
GGCTTTGACTCTAGTACCGCCAACTCATGCGAGCTTAAACTCGGGTACCACCAGCTTGTGCAAGC
TTTGAATAGGGTGCCACCAACTCATCTGAACTTTAAATTCTAAGGCTTGACCATCTTAAACAGGT
GCCAACTAATTTGCTTTAACTCAGGTGCAACCAACTTGTACAGGCTTAGACTCAGGTACCA
Found at i:3104026 original size:13 final size:13
Alignment explanation
Indices: 3104008--3104035 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3103998 ATACAAAGAT
3104008 CAATGTATCGATA
1 CAATGTATCGATA
3104021 CAATGTATCGATA
1 CAATGTATCGATA
3104034 CA
1 CA
3104036 TTGAATATGT
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:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:3104953 original size:7 final size:6
Alignment explanation
Indices: 3104913--3104952 Score: 64
Period size: 6 Copynumber: 6.7 Consensus size: 6
3104903 TTTTTTTTCC
3104913 TTTT-T TTTTGTT TTTTGT TTTTGT TTTTGT TTTTGT TTTT
1 TTTTGT TTTTG-T TTTTGT TTTTGT TTTTGT TTTTGT TTTT
3104953 TTAGCCATAG
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 4 0.12
6 23 0.70
7 6 0.18
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (6 bp):
TTTTGT
Found at i:3107877 original size:20 final size:19
Alignment explanation
Indices: 3107854--3107922 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 19
3107844 CACATCCAGA
*
3107854 TGTATCGATACAT-TATGCTT
1 TGTATCGATACATGT-T-CAT
*
3107874 TGTATCGATATATGTTCAT
1 TGTATCGATACATGTTCAT
**
3107893 TGTATCGATACACATTCAAT
1 TGTATCGATACATGTTC-AT
3107913 TGTATCGATA
1 TGTATCGATA
3107923 TATGAAACTG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 16 0.38
20 25 0.60
21 1 0.02
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.42
Consensus pattern (19 bp):
TGTATCGATACATGTTCAT
Found at i:3107897 original size:19 final size:20
Alignment explanation
Indices: 3107873--3107926 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
3107863 ACATTATGCT
3107873 TTGTATCGATATATGTTC-A
1 TTGTATCGATATATGTTCAA
* **
3107892 TTGTATCGATACACATTCAA
1 TTGTATCGATATATGTTCAA
3107912 TTGTATCGATATATG
1 TTGTATCGATATATG
3107927 AAACTGGCAG
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.43
Consensus pattern (20 bp):
TTGTATCGATATATGTTCAA
Found at i:3109585 original size:3 final size:3
Alignment explanation
Indices: 3109577--3109608 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
3109567 AACCATCAAA
*
3109577 GAT GAT GAT GAT GAT GAT GAT GAT AAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
3109609 AGTTGACTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:3114219 original size:21 final size:22
Alignment explanation
Indices: 3114186--3114237 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
3114176 TTAATCAAAC
3114186 TCAAAT-TTCTTCAATTTCAC-T
1 TCAAATCTTCTTC-ATTTCACTT
*
3114207 TCAAATCTT-TTCATTTTACTT
1 TCAAATCTTCTTCATTTCACTT
*
3114228 TAAAATCTTC
1 TCAAATCTTC
3114238 ATCAAAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 6 0.23
21 18 0.69
22 2 0.08
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (22 bp):
TCAAATCTTCTTCATTTCACTT
Done.