Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold18
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: 4432388
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 63034 characters in sequence are not A, C, G, or T
File 9 of 27
Found at i:1249842 original size:13 final size:13
Alignment explanation
Indices: 1249824--1249850 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1249814 TTTCAACGAT
1249824 TTGTATCGATACA
1 TTGTATCGATACA
1249837 TTGTATCGATACA
1 TTGTATCGATACA
1249850 T
1 T
1249851 AAGTTTGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1249965 original size:52 final size:52
Alignment explanation
Indices: 1249909--1250037 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
1249899 CACTGATCTT
*
1249909 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
1249961 TGTATCGATACATGTAGGAAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1250013 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1250038 TCATATTTCG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1263865 original size:13 final size:13
Alignment explanation
Indices: 1263849--1263928 Score: 83
Period size: 13 Copynumber: 5.9 Consensus size: 13
1263839 ATAAAAAATA
* *
1263849 AAAAAAAACACAG
1 AAAAAAAACAAAC
1263862 AAAAAAAACAAAAC
1 AAAAAAAAC-AAAC
1263876 AAAAAAAACAAAC
1 AAAAAAAACAAAC
1263889 AAAAAAAAAGCAAA-
1 -AAAAAAAA-CAAAC
1263903 AAAAAAAA-AAAC
1 AAAAAAAACAAAC
1263915 AAAACAACAACAAA
1 AAAA-AA-AACAAA
1263929 AAGGGTCCAG
Statistics
Matches: 58, Mismatches: 2, Indels: 12
0.81 0.03 0.17
Matches are distributed among these distances:
11 3 0.05
12 4 0.07
13 23 0.40
14 21 0.36
15 7 0.12
ACGTcount: A:0.84, C:0.14, G:0.03, T:0.00
Consensus pattern (13 bp):
AAAAAAAACAAAC
Found at i:1263865 original size:14 final size:12
Alignment explanation
Indices: 1263824--1263930 Score: 81
Period size: 13 Copynumber: 8.2 Consensus size: 12
1263814 CATCCTCCGT
*
1263824 AAAAAAATAAAA
1 AAAAAAACAAAA
*
1263836 AAAATAAAAAATAA
1 AAAA-AAACAA-AA
*
1263850 AAAAAAACACAGA
1 AAAAAAACA-AAA
1263863 AAAAAAACAAAACA
1 AAAAAAAC-AAA-A
1263877 AAAAAAACAAACAA
1 AAAAAAAC-AA-AA
1263891 AAAAAAAGCAAAA
1 AAAAAAA-CAAAA
*
1263904 AAAAAAA-AAAC
1 AAAAAAACAAAA
*
1263915 AAAACAACAACAA
1 AAAAAAACAA-AA
1263928 AAA
1 AAA
1263931 GGGTCCAGAT
Statistics
Matches: 79, Mismatches: 7, Indels: 17
0.77 0.07 0.17
Matches are distributed among these distances:
11 9 0.11
12 6 0.08
13 32 0.41
14 30 0.38
15 2 0.03
ACGTcount: A:0.85, C:0.10, G:0.02, T:0.03
Consensus pattern (12 bp):
AAAAAAACAAAA
Found at i:1263896 original size:44 final size:43
Alignment explanation
Indices: 1263827--1263921 Score: 113
Period size: 44 Copynumber: 2.2 Consensus size: 43
1263817 CCTCCGTAAA
* * *
1263827 AAAATAAAAAAAATAAAAAATAAAAAA-AAACACAGAAAAAAAAC
1 AAAACAAAAAAAACAAAAAATAAAAAACAAA-A-AAAAAAAAAAC
1263871 AAAACAAAAAAAACAAACAAA-AAAAAAGCAAAAAAAAAAAAAAC
1 AAAACAAAAAAAACAAA-AAATAAAAAA-CAAAAAAAAAAAAAAC
1263915 AAAACAA
1 AAAACAA
1263922 CAACAAAAAG
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
44 38 0.84
45 4 0.09
46 3 0.07
ACGTcount: A:0.85, C:0.09, G:0.02, T:0.03
Consensus pattern (43 bp):
AAAACAAAAAAAACAAAAAATAAAAAACAAAAAAAAAAAAAAC
Found at i:1263924 original size:38 final size:40
Alignment explanation
Indices: 1263824--1263930 Score: 116
Period size: 38 Copynumber: 2.8 Consensus size: 40
1263814 CATCCTCCGT
* * *
1263824 AAAAAAATAAAAA-AAATAAA-AAATAAAAAAAAACACAG
1 AAAAAAAAAAAAACAAAAAAACAAACAAAAAAAAACACAG
* *
1263862 AAAAAAAACAAAACAAAAAAAACAAACAAAAAAAAA-GCA-
1 AAAAAAAAAAAAAC-AAAAAAACAAACAAAAAAAAACACAG
*
1263901 AAAAAAAAAAAAACAAAACAAC-AACAAAAA
1 AAAAAAAAAAAAACAAAAAAACAAACAAAAA
1263931 GGGTCCAGAT
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
37 8 0.14
38 18 0.31
39 13 0.22
40 8 0.14
41 12 0.20
ACGTcount: A:0.85, C:0.10, G:0.02, T:0.03
Consensus pattern (40 bp):
AAAAAAAAAAAAACAAAAAAACAAACAAAAAAAAACACAG
Found at i:1263926 original size:11 final size:10
Alignment explanation
Indices: 1263862--1263929 Score: 70
Period size: 10 Copynumber: 6.9 Consensus size: 10
1263852 AAAAACACAG
1263862 AAAA-AAAAC
1 AAAACAAAAC
1263871 AAAACAAAA-
1 AAAACAAAAC
1263880 AAAAC-AAAC
1 AAAACAAAAC
*
1263889 AAAAAAAAAGC
1 AAAACAAAA-C
* *
1263900 AAAAAAAAAA
1 AAAACAAAAC
1263910 AAAACAAAAC
1 AAAACAAAAC
1263920 AACAACAAAA
1 AA-AACAAAA
1263930 AGGGTCCAGA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
8 3 0.06
9 13 0.26
10 17 0.34
11 17 0.34
ACGTcount: A:0.85, C:0.13, G:0.01, T:0.00
Consensus pattern (10 bp):
AAAACAAAAC
Found at i:1263930 original size:1 final size:1
Alignment explanation
Indices: 1263824--1263918 Score: 73
Period size: 1 Copynumber: 95.0 Consensus size: 1
1263814 CATCCTCCGT
* * * * * * * * * *
1263824 AAAAAAATAAAAAAAATAAAAAATAAAAAAAAACACAGAAAAAAAACAAAACAAAAAAAACAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
** *
1263889 AAAAAAAAAGCAAAAAAAAAAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1263919 CAACAACAAA
Statistics
Matches: 69, Mismatches: 25, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 69 1.00
ACGTcount: A:0.86, C:0.08, G:0.02, T:0.03
Consensus pattern (1 bp):
A
Found at i:1265406 original size:29 final size:29
Alignment explanation
Indices: 1265367--1265686 Score: 173
Period size: 29 Copynumber: 10.7 Consensus size: 29
1265357 TCACCCTTCA
*
1265367 AAAGCCCACAAGTTAGTGGCATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* *
1265396 AAAGCCCACAAGTCAGGGGCATTTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
1265425 AAAGTCCACAAGTCAGTGGCAAC--CTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * * *
1265452 AAAGCTCACAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* ** *
1265482 GAAGCCCACAAGTTGGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
1265511 AAAGTCCACAACTCCGTGGCACTCTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* * * * * *
1265541 TTTTGTAAGCTCACAACTCTGTAGCACTTTTTTTCC
1 -----AAAGCCCACAAGTCAGTGGCA-TCTTTTT-C
* * * *
1265577 TTTTAAGCCCACAAGTTAGTGGCACCCTTTTC
1 ---AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
1265609 AAAAGCCCACAAGTCAGTGGCAAC-CTTTA
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * * *
1265638 AAAGACCATAAGTCAATGGCAATC--TTTA
1 AAAGCCCACAAGTCAGTGGC-ATCTTTTTC
1265666 AAAGCCCACAAGTCAGTGGCA
1 AAAGCCCACAAGTCAGTGGCA
1265687 ACCTTCAAAA
Statistics
Matches: 226, Mismatches: 54, Indels: 24
0.74 0.18 0.08
Matches are distributed among these distances:
27 22 0.10
28 39 0.17
29 73 0.32
30 45 0.20
32 1 0.00
33 4 0.02
34 18 0.08
35 23 0.10
36 1 0.00
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTTC
Found at i:1265461 original size:27 final size:27
Alignment explanation
Indices: 1265422--1265477 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
1265412 GGGCATTTTT
*
1265422 TTCAAAGTCCACAAGTCAGTGGCAACC
1 TTCAAAGTCCACAAATCAGTGGCAACC
*
1265449 TTCAAAG-CTCACAAATCAGTGGCACCC
1 TTCAAAGTC-CACAAATCAGTGGCAACC
1265476 TT
1 TT
1265478 TTCCGAAGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 25 0.96
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.21
Consensus pattern (27 bp):
TTCAAAGTCCACAAATCAGTGGCAACC
Found at i:1265514 original size:86 final size:86
Alignment explanation
Indices: 1265361--1265531 Score: 211
Period size: 86 Copynumber: 2.0 Consensus size: 86
1265351 CATTCCTCAC
* * * * * *
1265361 CCTTCAAAAGCCCACAAGTTAGTGGCATCTTTTTCAAAGCCCACAAGTCAGGGGCATTTTTTTCA
1 CCTTCAAAAGCCCACAAATCAGTGGCACCTTTTCCAAAGCCCACAAGTCAGGGGCATCTTTTCCA
*
1265426 AAGTCCACAAGTCAGTGGCAA
66 AAGTCCACAACTCAGTGGCAA
* * *
1265447 CCTTC-AAAGCTCACAAATCAGTGGCACCCTTTTCCGAAGCCCACAAGT-TGGTGGCATCTTTTC
1 CCTTCAAAAGCCCACAAATCAGTGGCA-CCTTTTCCAAAGCCCACAAGTCAGG-GGCATCTTTTC
*
1265510 CAAAGTCCACAACTCCGTGGCA
64 CAAAGTCCACAACTCAGTGGCA
1265532 CTCTTTTTCT
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
85 20 0.28
86 52 0.72
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (86 bp):
CCTTCAAAAGCCCACAAATCAGTGGCACCTTTTCCAAAGCCCACAAGTCAGGGGCATCTTTTCCA
AAGTCCACAACTCAGTGGCAA
Found at i:1265584 original size:34 final size:35
Alignment explanation
Indices: 1265516--1265590 Score: 98
Period size: 35 Copynumber: 2.2 Consensus size: 35
1265506 TTTCCAAAGT
* *
1265516 CCACAACTCCGTGGCACTCTTTTTCTTTTGTAAGC
1 CCACAACTCCGTAGCACTCTTTTTCCTTTGTAAGC
* * *
1265551 TCACAACTCTGTAGCACTTTTTTTCCTTT-TAAGC
1 CCACAACTCCGTAGCACTCTTTTTCCTTTGTAAGC
1265585 CCACAA
1 CCACAA
1265591 GTTAGTGGCA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
34 10 0.29
35 24 0.71
ACGTcount: A:0.21, C:0.31, G:0.11, T:0.37
Consensus pattern (35 bp):
CCACAACTCCGTAGCACTCTTTTTCCTTTGTAAGC
Found at i:1265650 original size:28 final size:28
Alignment explanation
Indices: 1265581--1265706 Score: 162
Period size: 28 Copynumber: 4.4 Consensus size: 28
1265571 TTTTCCTTTT
* *
1265581 AAGCCCACAAGTTAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTCAGTGGCAACC-TTT-AA
1265611 AAGCCCACAAGTCAGTGGCAACCTTTAA
1 AAGCCCACAAGTCAGTGGCAACCTTTAA
* * * *
1265639 AAGACCATAAGTCAATGGCAATCTTTAA
1 AAGCCCACAAGTCAGTGGCAACCTTTAA
*
1265667 AAGCCCACAAGTCAGTGGCAACCTTCAA
1 AAGCCCACAAGTCAGTGGCAACCTTTAA
*
1265695 AAGCACACAAGT
1 AAGCCCACAAGT
1265707 TGATGCAAAC
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
28 60 0.71
29 3 0.04
30 21 0.25
ACGTcount: A:0.37, C:0.27, G:0.17, T:0.19
Consensus pattern (28 bp):
AAGCCCACAAGTCAGTGGCAACCTTTAA
Found at i:1266013 original size:48 final size:49
Alignment explanation
Indices: 1265767--1266282 Score: 602
Period size: 48 Copynumber: 10.7 Consensus size: 49
1265757 GTCTGCTATC
* ** * **
1265767 GCTGGCCTTGAACCAGCATATTGGTGCCTTTATCTTTTAAACCCAATATA
1 GCTGGCCTTGAATCAGCATATTGGCACCTTCATC-TTTAAGTCCAATATA
* * * *
1265817 GTTGGCCTTGAATCAGCACATTGGTACCTTCATCTTTAAGTCCAATGTA
1 GCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATA
* *
1265866 GCCGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATA
1 GCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATA
* * *
1265909 GCTGGCCTTGAATTAGCATATTGGCACCTTCACCTTTAAGCCCAATATA
1 GCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATA
* *
1265958 GCTGGCCTTGAATCAGCATATTGGCACCTT-GTCTTTAAGTCCAATGTA
1 GCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATA
* * *
1266006 GCTGGCCTTGAATCAGCAAATTGG-AACTTCATCTTTAAGTCCAATATC
1 GCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATA
* * * * *
1266054 GCTGGCCTTGAATCAGCATATTGGCGTCTTTGGCACCTTTAAGTCTAATATC
1 GCTGGCCTTGAATCAGCATATTGGC-ACCTT--CATCTTTAAGTCCAATATA
*
1266106 GCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTA
1 GCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATA
* * * * *
1266155 GCTGGCCTTGAATCAGCACATTGGTACC-TCACCTTTAAGCCCAATATC
1 GCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATA
* * * *
1266203 GCTGGCCTTGAATCAGCATATTGGCACCTT-GTCTTTAAGACCAATGTC
1 GCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATA
*
1266251 GCTGGCCTTGAATCAGCATATTGTCACCTTCA
1 GCTGGCCTTGAATCAGCATATTGGCACCTTCA
1266283 AGTGTAACTG
Statistics
Matches: 401, Mismatches: 52, Indels: 27
0.84 0.11 0.06
Matches are distributed among these distances:
43 38 0.09
45 1 0.00
47 5 0.01
48 160 0.40
49 121 0.30
50 31 0.08
51 3 0.01
52 42 0.10
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (49 bp):
GCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATATA
Found at i:1266126 original size:197 final size:194
Alignment explanation
Indices: 1265767--1266273 Score: 659
Period size: 197 Copynumber: 2.6 Consensus size: 194
1265757 GTCTGCTATC
* * * *
1265767 GCTGGCCTTGAACCAGCATATTGGTGCCTTTATCTTTTAAACCCAATATAGTTGGCCTTGAATCA
1 GCTGGCCTTGAATCAGCATATTGGTACC-TTATC-TTTAAGCCCAATATAGCTGGCCTTGAATCA
* * * *
1265832 GCACATTGGTACCTTCATCTTTAAGTCCAATGTAGCCGGCCTTGAATCAGC--A---CATTGGCA
64 GCAAATTGGCACCTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGCATTGGCA
*
1265892 CCTTTAAGTCCAATATAGCTGGCCTTGAATTAGCATATTGGCACCTTCACCTTTAAGCCCAATAT
129 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCACCTTTAAGCCCAATAT
1265957 A
194 A
* * * *
1265958 GCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGC
1 GCTGGCCTTGAATCAGCATATTGGTACCTTATCTTTAAGCCCAATATAGCTGGCCTTGAATCAGC
* * *
1266023 AAATTGG-AACTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGTCTTTGG
66 AAATTGGCACCTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATT---G-CATTGG
* * * *
1266087 CACCTTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAAT
127 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCACCTTTAAGCCCAAT
*
1266152 GTA
192 ATA
* * * *
1266155 GCTGGCCTTGAATCAGCACATTGGTACCTCACCTTTAAGCCCAATATCGCTGGCCTTGAATCAGC
1 GCTGGCCTTGAATCAGCATATTGGTACCTTATCTTTAAGCCCAATATAGCTGGCCTTGAATCAGC
* * *
1266220 ATATTGGCACCTT-GTCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCATATTG
66 AAATTGGCACCTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTG
1266274 TCACCTTCAA
Statistics
Matches: 273, Mismatches: 33, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
188 37 0.14
189 34 0.12
190 5 0.02
191 25 0.09
194 1 0.00
197 167 0.61
198 4 0.01
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.32
Consensus pattern (194 bp):
GCTGGCCTTGAATCAGCATATTGGTACCTTATCTTTAAGCCCAATATAGCTGGCCTTGAATCAGC
AAATTGGCACCTTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGCATTGGCACC
TTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCACCTTTAAGCCCAATATA
Found at i:1267046 original size:20 final size:19
Alignment explanation
Indices: 1267023--1267074 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
1267013 TTTCAAAGAT
1267023 TTGTATCGATACATAAAGTG
1 TTGTATCGATACAT-AAGTG
*
1267043 TTGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTG
1267062 TTGTATCGATACA
1 TTGTATCGATACA
1267075 ATTTAAGCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:1267065 original size:19 final size:20
Alignment explanation
Indices: 1267017--1267074 Score: 91
Period size: 20 Copynumber: 3.0 Consensus size: 20
1267007 TTTGAATTTC
*
1267017 AAAGATTTGTATCGATACAT
1 AAAGTTTTGTATCGATACAT
*
1267037 AAAGTGTTGTATCGATACAT
1 AAAGTTTTGTATCGATACAT
1267057 -AAGTTTTGTATCGATACA
1 AAAGTTTTGTATCGATACA
1267075 ATTTAAGCTA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
19 17 0.49
20 18 0.51
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.36
Consensus pattern (20 bp):
AAAGTTTTGTATCGATACAT
Found at i:1268027 original size:20 final size:21
Alignment explanation
Indices: 1267985--1268027 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1267975 CAGCCCATAA
**
1267985 TTCATGCATTTTGAGCTATGT
1 TTCATGCATTTACAGCTATGT
1268006 TTCATGCATTTACAGC-ATGT
1 TTCATGCATTTACAGCTATGT
1268026 TT
1 TT
1268028 AGCACCTCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.21, C:0.16, G:0.16, T:0.47
Consensus pattern (21 bp):
TTCATGCATTTACAGCTATGT
Found at i:1273686 original size:24 final size:24
Alignment explanation
Indices: 1273639--1273686 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1273629 GGCATCCCAT
*
1273639 GTAAAAAAAATTAAAATAAAAAAA
1 GTAAAAAAAATTAAAACAAAAAAA
* * *
1273663 GTAAAAAAATTTCAAACAACAAAA
1 GTAAAAAAAATTAAAACAAAAAAA
1273687 CAAGAAAAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.73, C:0.06, G:0.04, T:0.17
Consensus pattern (24 bp):
GTAAAAAAAATTAAAACAAAAAAA
Found at i:1283248 original size:19 final size:20
Alignment explanation
Indices: 1283224--1283277 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 20
1283214 TTTTTACTAT
1283224 TTGTATCGATACATTATT-A
1 TTGTATCGATACATTATTCA
* *
1283243 TTGTATTGATACATTTTTCA
1 TTGTATCGATACATTATTCA
1283263 TTGTATCGATACATT
1 TTGTATCGATACATT
1283278 TTGGATTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.50
Consensus pattern (20 bp):
TTGTATCGATACATTATTCA
Found at i:1283267 original size:20 final size:19
Alignment explanation
Indices: 1283224--1283279 Score: 85
Period size: 20 Copynumber: 2.9 Consensus size: 19
1283214 TTTTTACTAT
*
1283224 TTGTATCGATACATTATTA
1 TTGTATCGATACATTTTTA
*
1283243 TTGTATTGATACATTTTTCA
1 TTGTATCGATACATTTTT-A
1283263 TTGTATCGATACATTTT
1 TTGTATCGATACATTTT
1283280 GGATTTTACC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.52
Consensus pattern (19 bp):
TTGTATCGATACATTTTTA
Found at i:1290662 original size:27 final size:27
Alignment explanation
Indices: 1290600--1290664 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
1290590 TCTACTCTTT
* *
1290600 GTGGCACCCTTTTAAGTCCACAACTCC
1 GTGGCACCTTTTTAAGTACACAACTCC
*
1290627 ATGGCACCTTTTTAAGTACACAACTCC
1 GTGGCACCTTTTTAAGTACACAACTCC
1290654 GTGGCACCTTT
1 GTGGCACCTTT
1290665 ACCCTTCTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.23, C:0.32, G:0.15, T:0.29
Consensus pattern (27 bp):
GTGGCACCTTTTTAAGTACACAACTCC
Found at i:1290726 original size:32 final size:31
Alignment explanation
Indices: 1290665--1290982 Score: 248
Period size: 32 Copynumber: 10.0 Consensus size: 31
1290655 TGGCACCTTT
* * * *
1290665 ACCCTTCTTAAAGCACATAGAAGTTGGTGGCG
1 ACCCTTC-TAAAGCCCACACAAGTCGGTGGCG
*
1290697 ACCCATTATAAAGCCCACACAAGTCGGTGGC-
1 ACCC-TTCTAAAGCCCACACAAGTCGGTGGCG
* *
1290728 AACCTTCTTTAAAGCCCACACAAGTTC-GTGGTG
1 ACCCTTC--TAAAGCCCACACAAG-TCGGTGGCG
** **
1290761 ACTTTTTCTAAAGCCCACTTAAGTCGGTGGC-
1 AC-CCTTCTAAAGCCCACACAAGTCGGTGGCG
* * * *
1290792 AACCTTCTTTAAAGCCCTCACAAGTTGGTGGTG
1 ACCCTTC--TAAAGCCCACACAAGTCGGTGGCG
* *
1290825 ACCCTTTTTAAAGCCCACACAAGTCGGTTGC-
1 ACCC-TTCTAAAGCCCACACAAGTCGGTGGCG
* * *
1290856 AACCTTTTCAAAGCCCACACAAGTTGGTGGCG
1 ACCCTTCT-AAAGCCCACACAAGTCGGTGGCG
* *
1290888 ACCCTTTCTAAGGCCCACACAAGTCGGTGGCA
1 ACCC-TTCTAAAGCCCACACAAGTCGGTGGCG
* * *
1290920 ACCTTTTCTAAAGCCCACACTAGTTGGTGGCG
1 ACC-CTTCTAAAGCCCACACAAGTCGGTGGCG
**
1290952 ACCCTTGCTAAAGCCTGCACAAGTCGGTGGC
1 ACCCTT-CTAAAGCCCACACAAGTCGGTGGC
1290983 AGCTCCAAAA
Statistics
Matches: 224, Mismatches: 46, Indels: 32
0.74 0.15 0.11
Matches are distributed among these distances:
30 9 0.04
31 31 0.14
32 168 0.75
33 11 0.05
34 5 0.02
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.25
Consensus pattern (31 bp):
ACCCTTCTAAAGCCCACACAAGTCGGTGGCG
Found at i:1290753 original size:64 final size:64
Alignment explanation
Indices: 1290667--1290983 Score: 415
Period size: 64 Copynumber: 5.0 Consensus size: 64
1290657 GCACCTTTAC
* * * * *
1290667 CCTTC-TTAAAGCACATAGAAGTTGGTGGCGACCCATTATAAAGCCCACACAAGTCGGTGGCAA
1 CCTTCTTTAAAGCCCACACAAGTTGGTGGCGACCCTTTCTAAAGCCCACACAAGTCGGTGGCAA
* * ** **
1290730 CCTTCTTTAAAGCCCACACAAGTTCGTGGTGACTTTTTCTAAAGCCCACTTAAGTCGGTGGCAA
1 CCTTCTTTAAAGCCCACACAAGTTGGTGGCGACCCTTTCTAAAGCCCACACAAGTCGGTGGCAA
* * * *
1290794 CCTTCTTTAAAGCCCTCACAAGTTGGTGGTGACCCTTTTTAAAGCCCACACAAGTCGGTTGCAA
1 CCTTCTTTAAAGCCCACACAAGTTGGTGGCGACCCTTTCTAAAGCCCACACAAGTCGGTGGCAA
* *
1290858 CCTT-TTCAAAGCCCACACAAGTTGGTGGCGACCCTTTCTAAGGCCCACACAAGTCGGTGGCAA
1 CCTTCTTTAAAGCCCACACAAGTTGGTGGCGACCCTTTCTAAAGCCCACACAAGTCGGTGGCAA
* * **
1290921 CCTT-TTCTAAAGCCCACACTAGTTGGTGGCGACCCTTGCTAAAGCCTGCACAAGTCGGTGGCA
1 CCTTCTT-TAAAGCCCACACAAGTTGGTGGCGACCCTTTCTAAAGCCCACACAAGTCGGTGGCA
1290984 GCTCCAAAAC
Statistics
Matches: 221, Mismatches: 31, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
63 64 0.29
64 157 0.71
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (64 bp):
CCTTCTTTAAAGCCCACACAAGTTGGTGGCGACCCTTTCTAAAGCCCACACAAGTCGGTGGCAA
Found at i:1290921 original size:127 final size:128
Alignment explanation
Indices: 1290685--1290983 Score: 413
Period size: 127 Copynumber: 2.3 Consensus size: 128
1290675 AAGCACATAG
* *
1290685 AAGTTGGTGGCGACCCATTATAAAGCCCACACAAGTCGGTGGCAACCTTCTTTAAAGCCCACACA
1 AAGTTGGTGGCGACCCTTTATAAAGCCCACACAAGTCGGTGGCAACCTTCTTCAAAGCCCACACA
* ** ** *
1290750 AGTTCGTGGTGACTTTTTCTAAAGCCCACTTAAGTCGGTGGCAACCTTCTT-TAAAGCCCTCAC
66 AGTTCGTGGCGACCCTTTCTAAAGCCCACACAAGTCGGTGGCAACCTT-TTCTAAAGCCCACAC
* * *
1290813 AAGTTGGTGGTGACCCTTTTTAAAGCCCACACAAGTCGGTTGCAACCTT-TTCAAAGCCCACACA
1 AAGTTGGTGGCGACCCTTTATAAAGCCCACACAAGTCGGTGGCAACCTTCTTCAAAGCCCACACA
* *
1290877 AGTTGGTGGCGACCCTTTCTAAGGCCCACACAAGTCGGTGGCAACCTTTTCTAAAGCCCACAC
66 AGTTCGTGGCGACCCTTTCTAAAGCCCACACAAGTCGGTGGCAACCTTTTCTAAAGCCCACAC
* ** **
1290940 TAGTTGGTGGCGACCCTTGCTAAAGCCTGCACAAGTCGGTGGCA
1 AAGTTGGTGGCGACCCTTTATAAAGCCCACACAAGTCGGTGGCA
1290984 GCTCCAAAAC
Statistics
Matches: 150, Mismatches: 20, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
126 2 0.01
127 103 0.69
128 45 0.30
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (128 bp):
AAGTTGGTGGCGACCCTTTATAAAGCCCACACAAGTCGGTGGCAACCTTCTTCAAAGCCCACACA
AGTTCGTGGCGACCCTTTCTAAAGCCCACACAAGTCGGTGGCAACCTTTTCTAAAGCCCACAC
Found at i:1292241 original size:20 final size:20
Alignment explanation
Indices: 1292218--1292290 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
1292208 ACAATTCAAA
1292218 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1292238 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
*
1292259 GTATCAATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1292279 GTATCGATACAT
1 GTATCGATACAT
1292291 AAAAAAGTTG
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1292262 original size:21 final size:21
Alignment explanation
Indices: 1292236--1292311 Score: 82
Period size: 21 Copynumber: 3.7 Consensus size: 21
1292226 ACATGTTGCA
1292236 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
* ****
1292257 ATGTATCAATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
1292277 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
*
1292298 TTGTATCGATACAT
1 ATGTATCGATACAT
1292312 TTCTTGGCAG
Statistics
Matches: 42, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 14 0.33
21 28 0.67
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:1292270 original size:41 final size:41
Alignment explanation
Indices: 1292218--1292311 Score: 161
Period size: 41 Copynumber: 2.3 Consensus size: 41
1292208 ACAATTCAAA
*
1292218 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
* *
1292259 GTATCAATACATGTTGCAATGTATCGATACATAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1292300 GTATCGATACAT
1 GTATCGATACAT
1292312 TTCTTGGCAG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:1292368 original size:13 final size:13
Alignment explanation
Indices: 1292350--1292375 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1292340 TACAGCAAGT
1292350 ATGTATCGATACA
1 ATGTATCGATACA
1292363 ATGTATCGATACA
1 ATGTATCGATACA
1292376 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:1294626 original size:21 final size:21
Alignment explanation
Indices: 1294593--1294637 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1294583 TTGCAAGTTG
*
1294593 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1294615 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1294635 AAA
1 AAA
1294638 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1296461 original size:15 final size:15
Alignment explanation
Indices: 1296441--1296471 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1296431 TAAAAATGTC
*
1296441 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1296456 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1296471 C
1 C
1296472 CAAACAAAAT
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1298427 original size:20 final size:20
Alignment explanation
Indices: 1298401--1298478 Score: 75
Period size: 20 Copynumber: 3.6 Consensus size: 20
1298391 AATGTCCAAA
1298401 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATGTTTCT
* *
1298421 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACA--T-G--TTTCT
*
1298446 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATGTTTCT
*
1298466 TTGTATCGATACA
1 ATGTATCGATACA
1298479 ATGTATCGAT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
20 28 0.60
22 1 0.02
23 2 0.04
25 16 0.34
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATGTTTCT
Found at i:1298485 original size:13 final size:13
Alignment explanation
Indices: 1298467--1298504 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1298457 CATTTTTCTT
1298467 TGTATCGATACAA
1 TGTATCGATACAA
*
1298480 TGTATCGATACAC
1 TGTATCGATACAA
1298493 TGTATCGATACA
1 TGTATCGATACA
1298505 GGGTGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1298649 original size:21 final size:21
Alignment explanation
Indices: 1298625--1298671 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1298615 AAATCTTTTG
1298625 CAAAAT-ACTT-GTTTTTCACTT
1 CAAAATAACTTCGTTTTTCA--T
1298646 C-AAATAACTTCGTTTTTCAT
1 CAAAATAACTTCGTTTTTCAT
1298666 CAAAAT
1 CAAAAT
1298672 CAGCATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (21 bp):
CAAAATAACTTCGTTTTTCAT
Found at i:1298668 original size:20 final size:19
Alignment explanation
Indices: 1298627--1298669 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
1298617 ATCTTTTGCA
1298627 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
1298647 AAATAACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
1298667 AAA
1 AAA
1298670 ATCAGCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:1301024 original size:20 final size:20
Alignment explanation
Indices: 1301001--1301073 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1300991 ACAATTCAAA
1301001 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1301021 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
1301042 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1301062 GTATCGATACAT
1 GTATCGATACAT
1301074 AAAAAAGTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1301045 original size:21 final size:21
Alignment explanation
Indices: 1301019--1301094 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
1301009 ACATGTTGCA
1301019 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
1301040 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
1301060 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
*
1301081 TTGTATCGATACAT
1 ATGTATCGATACAT
1301095 TTCTTGGCAG
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:1301052 original size:41 final size:41
Alignment explanation
Indices: 1301001--1301094 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
1300991 ACAATTCAAA
*
1301001 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
*
1301042 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1301083 GTATCGATACAT
1 GTATCGATACAT
1301095 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:1301151 original size:13 final size:13
Alignment explanation
Indices: 1301133--1301158 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1301123 TACAGCAAGT
1301133 ATGTATCGATACA
1 ATGTATCGATACA
1301146 ATGTATCGATACA
1 ATGTATCGATACA
1301159 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:1304118 original size:80 final size:81
Alignment explanation
Indices: 1304000--1304339 Score: 291
Period size: 80 Copynumber: 4.2 Consensus size: 81
1303990 TTTTTTGTGG
* * * * * *
1304000 AAATCAGGGTTGGAGTATCTCGTCAGAGATGGTAGGGTTAGAATATCCTTAGAGATGAAAAATTC
1 AAAT-AGGGTTGGAGTATCTCCTTATAGATGGTGGGGTTAGAGTATCCCTAGAGATGAAAAATTC
*
1304065 AATGTTTTGGAAGT-AA
65 AATGTTTTGAAAGTAAA
* *
1304081 AAATAGGATTGGAGTATCTCCTTATAGATAGTGGGGTTAGAGTATCCCTAGAGAT-AAAGAATTC
1 AAATAGGGTTGGAGTATCTCCTTATAGATGGTGGGGTTAGAGTATCCCTAGAGATGAAA-AATTC
*
1304145 GAT-TATTGTGAAAGTAAA
65 AATGT-TT-TGAAAGTAAA
** * * * *
1304163 AAATAGGGTTAAAGTATC-CCCT-TGGAT-GTGGGGGTTGGAGTATCCCTAGAGATAAAAAATTC
1 AAATAGGGTTGGAGTATCTCCTTATAGATGGT-GGGGTTAGAGTATCCCTAGAGATGAAAAATTC
**
1304225 AATGTTTCAAAAGTAAA
65 AATGTTTTGAAAGTAAA
** * * * * * * *
1304242 AACGA-GGTTGAAGTATCTTCTTGGT-GATGGTGGGGTTGGAGTATCACTAGAGATGAAGAATAC
1 AAATAGGGTTGGAGTATCTCCTT-ATAGATGGTGGGGTTAGAGTATCCCTAGAGATGAAAAATTC
* * * *
1304305 AGTATTGTGGAAGTAAA
65 AATGTTTTGAAAGTAAA
1304322 AAATAGGGTTGGAGTATC
1 AAATAGGGTTGGAGTATC
1304340 CCTCAGACAT
Statistics
Matches: 210, Mismatches: 37, Indels: 24
0.77 0.14 0.09
Matches are distributed among these distances:
78 11 0.05
79 19 0.09
80 132 0.63
81 31 0.15
82 17 0.08
ACGTcount: A:0.35, C:0.09, G:0.27, T:0.29
Consensus pattern (81 bp):
AAATAGGGTTGGAGTATCTCCTTATAGATGGTGGGGTTAGAGTATCCCTAGAGATGAAAAATTCA
ATGTTTTGAAAGTAAA
Found at i:1304337 original size:53 final size:53
Alignment explanation
Indices: 1304274--1304391 Score: 136
Period size: 53 Copynumber: 2.2 Consensus size: 53
1304264 GGTGATGGTG
* * *
1304274 GGGTTGGAGTATCACT-AGAGATGAAGAATAC-A-GTATTGTGGAAGTAAAAAATA
1 GGGTTGGAGTATCACTCAGACATGAAAAATACGATGT-TT-TGAAAGT-AAAAATA
* *
1304327 GGGTTGGAGTATCCCTCAGACATGAAAAATTCGATGTTTTGAAAGTAAAAATA
1 GGGTTGGAGTATCACTCAGACATGAAAAATACGATGTTTTGAAAGTAAAAATA
1304380 GGGTTGG-GTATC
1 GGGTTGGAGTATC
1304392 CTTTAGGAGA
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
52 5 0.09
53 29 0.51
54 18 0.32
55 3 0.05
56 2 0.04
ACGTcount: A:0.36, C:0.08, G:0.28, T:0.27
Consensus pattern (53 bp):
GGGTTGGAGTATCACTCAGACATGAAAAATACGATGTTTTGAAAGTAAAAATA
Found at i:1304443 original size:133 final size:136
Alignment explanation
Indices: 1304194--1304482 Score: 320
Period size: 133 Copynumber: 2.1 Consensus size: 136
1304184 TTGGATGTGG
* *
1304194 GGGTTGGAGTATCCCT-AGAGATAAAAAATTCAATGTTTCAAAAGTAAAAACGAGGTTGAAGTAT
1 GGGTTGGAGTATCCCTCAGACATAAAAAATTCAATGTTTCAAAAGTAAAAAAGAGGTTGAAGTAT
* * * *
1304258 CTTCTTGGTGATGGTGGGGTTGGAGTATCACTAGAGATGAAGAATACAGTATTGTGGAAGT-AAA
66 CTTCTAGGAGATGGTGGGGTTGGAGTATCACCAGAAATGAAGAATACAGTATTGTGGAAGTAAAA
1304322 -AAATA
131 GAAATA
* * ** *
1304327 GGGTTGGAGTATCCCTCAGACATGAAAAATTCGATGTTTTGAAAGTAAAAATAG-GGTTG-GGTA
1 GGGTTGGAGTATCCCTCAGACATAAAAAATTCAATGTTTCAAAAGTAAAAA-AGAGGTTGAAGTA
* * * *** ***
1304390 TCCTT-TAGGAGATGGTGGGGTTGGAGTATCCCCCGAAATGAAGAGTTTGGTATTGTGGGCTTAA
65 T-CTTCTAGGAGATGGTGGGGTTGGAGTATCACCAGAAATGAAGAATACAGTATTGTGGAAGTAA
*
1304454 AAGAAATG
129 AAGAAATA
1304462 GGGTTGGAGTATCCCCTCAGA
1 GGGTTGGAGTAT-CCCTCAGA
1304483 GATTGTGAGG
Statistics
Matches: 129, Mismatches: 21, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
133 64 0.50
134 40 0.31
135 17 0.13
136 8 0.06
ACGTcount: A:0.32, C:0.10, G:0.29, T:0.28
Consensus pattern (136 bp):
GGGTTGGAGTATCCCTCAGACATAAAAAATTCAATGTTTCAAAAGTAAAAAAGAGGTTGAAGTAT
CTTCTAGGAGATGGTGGGGTTGGAGTATCACCAGAAATGAAGAATACAGTATTGTGGAAGTAAAA
GAAATA
Found at i:1304495 original size:83 final size:82
Alignment explanation
Indices: 1304327--1304745 Score: 424
Period size: 79 Copynumber: 5.2 Consensus size: 82
1304317 GTAAAAAATA
* * * * * * * *
1304327 GGGTTGGAGTATCCCTCAGACATGAAAAATTCGATGTTTTGAAAGT--AAAAATAGGGTTGG-GT
1 GGGTTGGAGTATCCC-CAGAGATGAAAAGTTTGGTATTGTGGAAGTAAAAAAATGGGGTTGGAGT
* *
1304389 AT-CCTTTAGGAGATGGTG
65 ATCCCCTCA-GAGATGGTG
* * * ***
1304407 GGGTTGGAGTATCCCCCGAAATGAAGAGTTTGGTATTGTGGGCTTAAAAGAAATGGGGTTGGAGT
1 GGGTTGGAGTATCCCCAGAGATGAAAAGTTTGGTATTGTGGAAGTAAAA-AAATGGGGTTGGAGT
*
1304472 ATCCCCTCAGAGATTGTG
65 ATCCCCTCAGAGATGGTG
* * *
1304490 AGGTTGGAGTATCCCTAGAGATAAAAAGTTTGGTATTGTGGAAGTAAAAAAATGGGGTTGGAGTA
1 GGGTTGGAGTATCCCCAGAGATGAAAAGTTTGGTATTGTGGAAGTAAAAAAATGGGGTTGGAGTA
1304555 TCCCCTCAGAGATGGTG
66 TCCCCTCAGAGATGGTG
* * * * *
1304572 GGGTTGGAGTATCCCCAGAGATGAAAAATTTGATGTTTTGGAAGT---AAAATGGAGTTGGAGTA
1 GGGTTGGAGTATCCCCAGAGATGAAAAGTTTGGTATTGTGGAAGTAAAAAAATGGGGTTGGAGTA
*
1304634 TCCCCTCGGAGATGGTG
66 TCCCCTCAGAGATGGTG
* * * * * * *
1304651 GCGTTGGATTATCCCCAAAGATGAAAATTTTGATATTTTGGAAGT--AAAAATGGGGTTAGAGTA
1 GGGTTGGAGTATCCCCAGAGATGAAAAGTTTGGTATTGTGGAAGTAAAAAAATGGGGTTGGAGTA
* *
1304714 TCTCCTCAGAGATGGTC
66 TCCCCTCAGAGATGGTG
*
1304731 GGGTTGGAGTGTCCC
1 GGGTTGGAGTATCCC
1304746 AAAAAATGAA
Statistics
Matches: 285, Mismatches: 48, Indels: 12
0.83 0.14 0.03
Matches are distributed among these distances:
79 90 0.32
80 56 0.20
81 2 0.01
82 81 0.28
83 52 0.18
84 4 0.01
ACGTcount: A:0.28, C:0.12, G:0.31, T:0.29
Consensus pattern (82 bp):
GGGTTGGAGTATCCCCAGAGATGAAAAGTTTGGTATTGTGGAAGTAAAAAAATGGGGTTGGAGTA
TCCCCTCAGAGATGGTG
Found at i:1304573 original size:28 final size:26
Alignment explanation
Indices: 1304542--1304594 Score: 88
Period size: 28 Copynumber: 2.0 Consensus size: 26
1304532 AGTAAAAAAA
1304542 TGGGGTTGGAGTATCCCCTCAGAGATGG
1 TGGGGTTGGAGTAT-CCC-CAGAGATGG
1304570 TGGGGTTGGAGTATCCCCAGAGATG
1 TGGGGTTGGAGTATCCCCAGAGATG
1304595 AAAAATTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 8 0.32
27 3 0.12
28 14 0.56
ACGTcount: A:0.19, C:0.17, G:0.40, T:0.25
Consensus pattern (26 bp):
TGGGGTTGGAGTATCCCCAGAGATGG
Found at i:1304649 original size:79 final size:80
Alignment explanation
Indices: 1304327--1304798 Score: 452
Period size: 80 Copynumber: 5.9 Consensus size: 80
1304317 GTAAAAAATA
* * * * *
1304327 GGGTTGGAGTATCCCTCAGACATGAAAAATTCGATGTTTTGAAAGTAAAAATAGGGTTGG-GTAT
1 GGGTTGGAGTATCCC-CAGAGATGAAAAATTTGATATTTTGGAAGTAAAAATGGGGTTGGAGTAT
* *
1304391 -CCTTTAGGAGATGGTG
65 CCCCTCA-GAGATGGTG
* * * * * * ***
1304407 GGGTTGGAGTATCCCCCGAAATGAAGAGTTTGGTATTGTGGGCTTAAAAGAAATGGGGTTGGAGT
1 GGGTTGGAGTATCCCCAGAGATGAAAAATTTGATATTTTGGAAGT--AA-AAATGGGGTTGGAGT
*
1304472 ATCCCCTCAGAGATTGTG
63 ATCCCCTCAGAGATGGTG
* * * *
1304490 AGGTTGGAGTATCCCTAGAGAT-AAAAAGTTTGGTATTGTGGAAGTAAAAAAATGGGGTTGGAGT
1 GGGTTGGAGTATCCCCAGAGATGAAAAA-TTTGATATTTTGGAAGT--AAAAATGGGGTTGGAGT
1304554 ATCCCCTCAGAGATGGTG
63 ATCCCCTCAGAGATGGTG
* *
1304572 GGGTTGGAGTATCCCCAGAGATGAAAAATTTGATGTTTTGGAAGT-AAAATGGAGTTGGAGTATC
1 GGGTTGGAGTATCCCCAGAGATGAAAAATTTGATATTTTGGAAGTAAAAATGGGGTTGGAGTATC
*
1304636 CCCTCGGAGATGGTG
66 CCCTCAGAGATGGTG
* * * * *
1304651 GCGTTGGATTATCCCCAAAGATGAAAATTTTGATATTTTGGAAGTAAAAATGGGGTTAGAGTATC
1 GGGTTGGAGTATCCCCAGAGATGAAAAATTTGATATTTTGGAAGTAAAAATGGGGTTGGAGTATC
* *
1304716 TCCTCAGAGATGGTC
66 CCCTCAGAGATGGTG
* * * * * * * * * *
1304731 GGGTTGGAGTGTCCCAAAAAATGAAAACA-TCGATGTTTTAGAAGTAGAAACGGGGTTAGAGTA-
1 GGGTTGGAGTATCCCCAGAGATGAAAA-ATTTGATATTTTGGAAGTAAAAATGGGGTTGGAGTAT
1304794 CCCCT
65 CCCCT
1304799 TTTGATGTTT
Statistics
Matches: 328, Mismatches: 55, Indels: 19
0.82 0.14 0.05
Matches are distributed among these distances:
79 94 0.29
80 95 0.29
81 2 0.01
82 80 0.24
83 53 0.16
84 4 0.01
ACGTcount: A:0.30, C:0.12, G:0.30, T:0.28
Consensus pattern (80 bp):
GGGTTGGAGTATCCCCAGAGATGAAAAATTTGATATTTTGGAAGTAAAAATGGGGTTGGAGTATC
CCCTCAGAGATGGTG
Found at i:1306080 original size:17 final size:17
Alignment explanation
Indices: 1306058--1306093 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1306048 TTCATGGAAA
1306058 GAAAAGAAGAAAAAATG
1 GAAAAGAAGAAAAAATG
1306075 GAAAAGAAGAAAAAATG
1 GAAAAGAAGAAAAAATG
1306092 GA
1 GA
1306094 TGGTGATGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.06
Consensus pattern (17 bp):
GAAAAGAAGAAAAAATG
Found at i:1307500 original size:51 final size:50
Alignment explanation
Indices: 1307434--1307704 Score: 276
Period size: 51 Copynumber: 5.3 Consensus size: 50
1307424 CGAAAATAAT
* **
1307434 GGGGTTGGAGTATCCCCGATTGTGAAAATTTGATGCTTTAGAAATAAGGTC
1 GGGGTTGGAGTATCCCCGATTGTGAAAA-TTGGTGCTTTAGAAATAAAATC
* * * **** ** **
1307485 GCGGTTGTAGTATCCCCAATTGTGAGAAAACAATATTTTAGAAATAAAGCC
1 GGGGTTGGAGTATCCCCGATTGTGA-AAATTGGTGCTTTAGAAATAAAATC
* *
1307536 GGGGTTGGAGTATCCCCGATTATGAAAAATTGGTG-TTTTGAAAATAAAATC
1 GGGGTTGGAGTATCCCCGATTGTG-AAAATTGGTGCTTTAG-AAATAAAATC
* * *
1307587 GGAGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTTAGAGATAAAATC
1 GGGGTTGGAGTATCCCCGATTGT-GAAAATTGGTGCTTTAGAAATAAAATC
* * *
1307638 GGGGTTGGAGTATCCCC-ACTTATGAAAATTGGTGCTTTGGGAATAAAATC
1 GGGGTTGGAGTATCCCCGA-TTGTGAAAATTGGTGCTTTAGAAATAAAATC
1307688 GGGGTTGGAGTATCCCC
1 GGGGTTGGAGTATCCCC
1307705 TCAAAAATAA
Statistics
Matches: 182, Mismatches: 32, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
50 45 0.25
51 128 0.70
52 9 0.05
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.30
Consensus pattern (50 bp):
GGGGTTGGAGTATCCCCGATTGTGAAAATTGGTGCTTTAGAAATAAAATC
Found at i:1307610 original size:102 final size:101
Alignment explanation
Indices: 1307434--1307704 Score: 307
Period size: 102 Copynumber: 2.7 Consensus size: 101
1307424 CGAAAATAAT
* * * ** *
1307434 GGGGTTGGAGTATCCCCGATTGTGAAAATTTGATGCTTT-AGAAATAAGGTCGCGGTTGTAGTAT
1 GGGGTTGGAGTATCCCCGATTATGAAAAATTGGTGCTTTGA-AAATAAAATCG-GGTTGGAGTAT
*
1307498 CCCCAATTGTGAGAAAA-CAATATTTTAGAAATAAAGCC
64 CCCCAATTGTG-GAAAATCAATATTTTAGAAATAAAACC
*
1307536 GGGGTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGAAAATAAAATCGGAGTTGGAGTATC
1 GGGGTTGGAGTATCCCCGATTATGAAAAATTGGTGCTTTGAAAATAAAATCGG-GTTGGAGTATC
* *** * * *
1307601 CCCGATTGTGGAAAATTGGTGTTTTAGAGATAAAATC
65 CCCAATTGTGGAAAATCAATATTTTAGAAATAAAACC
**
1307638 GGGGTTGGAGTATCCCC-ACTTATG-AAAATTGGTGCTTTGGGAATAAAATCGGGGTTGGAGTAT
1 GGGGTTGGAGTATCCCCGA-TTATGAAAAATTGGTGCTTTGAAAATAAAATC-GGGTTGGAGTAT
1307701 CCCC
64 CCCC
1307705 TCAAAAATAA
Statistics
Matches: 146, Mismatches: 18, Indels: 11
0.83 0.10 0.06
Matches are distributed among these distances:
101 44 0.30
102 101 0.69
103 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.30
Consensus pattern (101 bp):
GGGGTTGGAGTATCCCCGATTATGAAAAATTGGTGCTTTGAAAATAAAATCGGGTTGGAGTATCC
CCAATTGTGGAAAATCAATATTTTAGAAATAAAACC
Found at i:1307773 original size:79 final size:78
Alignment explanation
Indices: 1307637--1307783 Score: 215
Period size: 79 Copynumber: 1.9 Consensus size: 78
1307627 GAGATAAAAT
* * ** *
1307637 CGGGGTTGGAGTATCCCCACTTATGAAAATTGGTGCTTTGGGAATAAAATCGGGGTTGGAGTATC
1 CGGGATTGGAGTATCCCCACTTATGAAAATTGATGCTTTGAAAATAAAACCGGGGTTGGAGTATC
1307702 CCCTCAAAAATAA
66 CCCTCAAAAATAA
*
1307715 CGGGATTGGAGTATCCCCGA-TTATGAAAAATTGATGTTTTGAAAATAAAACCGGGGTTGGAGTA
1 CGGGATTGGAGTATCCCC-ACTTATG-AAAATTGATGCTTTGAAAATAAAACCGGGGTTGGAGTA
1307779 TCCCC
64 TCCCC
1307784 GAATGAAAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
78 22 0.36
79 39 0.64
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (78 bp):
CGGGATTGGAGTATCCCCACTTATGAAAATTGATGCTTTGAAAATAAAACCGGGGTTGGAGTATC
CCCTCAAAAATAA
Found at i:1310157 original size:33 final size:33
Alignment explanation
Indices: 1310099--1310197 Score: 153
Period size: 33 Copynumber: 3.0 Consensus size: 33
1310089 TACATTATAA
* * * *
1310099 AATGTATCGATATAATGAGCGATGTATCGATAC
1 AATGTATTGATACAGTGAGCAATGTATCGATAC
*
1310132 AATGTATTGATACAGTGAGTAATGTATCGATAC
1 AATGTATTGATACAGTGAGCAATGTATCGATAC
1310165 AATGTATTGATACAGTGAGCAATGTATCGATAC
1 AATGTATTGATACAGTGAGCAATGTATCGATAC
1310198 GATGCAAAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.31
Consensus pattern (33 bp):
AATGTATTGATACAGTGAGCAATGTATCGATAC
Found at i:1311499 original size:21 final size:20
Alignment explanation
Indices: 1311452--1311505 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
1311442 CATTACAAGC
* *
1311452 ATGTATCGATACATTCATTT
1 ATGTATCGATACATTAACTT
*
1311472 ATGTATCAATACATTAACTT
1 ATGTATCGATACATTAACTT
1311492 ATTGTATCGATACA
1 A-TGTATCGATACA
1311506 AATTGTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 18 0.62
21 11 0.38
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTAACTT
Found at i:1312580 original size:18 final size:19
Alignment explanation
Indices: 1312538--1312582 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
1312528 ATGTATCAAT
* *
1312538 ACAATTTTTCTAGAATGCA
1 ACAATTTTCCTAAAATGCA
1312557 ACAATTTTCCTAAAATGCA
1 ACAATTTTCCTAAAATGCA
1312576 A-AATTTT
1 ACAATTTT
1312583 GCCTCGACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 6 0.25
19 18 0.75
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.38
Consensus pattern (19 bp):
ACAATTTTCCTAAAATGCA
Found at i:1313433 original size:76 final size:76
Alignment explanation
Indices: 1313320--1313508 Score: 204
Period size: 76 Copynumber: 2.5 Consensus size: 76
1313310 TGGGCTTTGA
* * * * * *
1313320 AAAAAGAAAAAGCATCCTGCTCTTTGA-AGACTGAAAAGGCAAAGGGTGCTACCCA-CTTATGT-
1 AAAAAGGAAAAGCATCTTGCTCTTTGAGA-ACTAAAAAGGCAAAGAGTGCCA-CCAGCTTATATA
*
1313382 GGCCTTTGAAAAAG
64 AG-CTTTGAAAAAG
* * *
1313396 AAAAAGGAAAAGCATCTTGCGCTTTGAGAACTAAAAAGGTAAATAGTGCCACCAGCTTATATAAG
1 AAAAAGGAAAAGCATCTTGCTCTTTGAGAACTAAAAAGGCAAAGAGTGCCACCAGCTTATATAAG
*
1313461 CTTTGGAAAAG
66 CTTTGAAAAAG
* * *
1313472 AAAAAGGAAACGTATCTTGCTCTTTGAGGACTAAAAA
1 AAAAAGGAAAAGCATCTTGCTCTTTGAGAACTAAAAA
1313509 TAAAGGGTTT
Statistics
Matches: 95, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
75 3 0.03
76 90 0.95
77 2 0.02
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (76 bp):
AAAAAGGAAAAGCATCTTGCTCTTTGAGAACTAAAAAGGCAAAGAGTGCCACCAGCTTATATAAG
CTTTGAAAAAG
Found at i:1317285 original size:47 final size:47
Alignment explanation
Indices: 1317143--1317550 Score: 302
Period size: 47 Copynumber: 8.7 Consensus size: 47
1317133 GTGGTAATCG
* ** * * *
1317143 ATACAGTCAAATGAGAATGGAAAA-AGTTTAACTAGGTCCTAA-GTCCA
1 ATACAGTCAAACGAGGGT-GAAAAGAGTTTGACCAAGTCCTAACG-CCA
* * *
1317190 ATACAGTCAAACAAGGGTGAAAAAGGGTTTGACCAAGCCCTAACGCCA
1 ATACAGTCAAACGAGGGTG-AAAAGAGTTTGACCAAGTCCTAACGCCA
* * * * *
1317238 ATACAATCAAACGAGGGTGAAAAGAGTTTGTCCAGGTCTTAATGCCA
1 ATACAGTCAAACGAGGGTGAAAAGAGTTTGACCAAGTCCTAACGCCA
* ** * * * * *
1317285 ATATAGTCAAATAAGGATGGAAAGAGTTTGACTAAGTCTTAACGCTA
1 ATACAGTCAAACGAGGGTGAAAAGAGTTTGACCAAGTCCTAACGCCA
* * * * * *
1317332 CTATAGTCAAACTAAGGCGAAAAGAGTTTGACCAGGTCCTAACGCCA
1 ATACAGTCAAACGAGGGTGAAAAGAGTTTGACCAAGTCCTAACGCCA
* * * * * * *
1317379 ATACAGTCAAACGAGAGTGGAAAGAGTTTAACTAGGTCCTAACACTA
1 ATACAGTCAAACGAGGGTGAAAAGAGTTTGACCAAGTCCTAACGCCA
* * * * * * ***
1317426 ATATAATCAAATGA-GGTTATAAAGAGTTTGACTAATTCCTAATAACA
1 ATACAGTCAAACGAGGGTGA-AAAGAGTTTGACCAAGTCCTAACGCCA
* * *
1317473 ATACAGTCAAATGAGGGTGAAAAGAGTTTAACCAAGTCC-ACACACCA
1 ATACAGTCAAACGAGGGTGAAAAGAGTTTGACCAAGTCCTA-ACGCCA
**
1317520 ATACAGTCAAATAAGGGTGAAAAGAGTTTGA
1 ATACAGTCAAACGAGGGTGAAAAGAGTTTGA
1317551 TATCTAGGTC
Statistics
Matches: 283, Mismatches: 72, Indels: 12
0.77 0.20 0.03
Matches are distributed among these distances:
46 4 0.01
47 241 0.85
48 37 0.13
49 1 0.00
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (47 bp):
ATACAGTCAAACGAGGGTGAAAAGAGTTTGACCAAGTCCTAACGCCA
Found at i:1317373 original size:141 final size:141
Alignment explanation
Indices: 1317162--1317550 Score: 365
Period size: 141 Copynumber: 2.8 Consensus size: 141
1317152 AATGAGAATG
* * * * * * *
1317162 GAAAAAGTTTAACTAGGTCCTAAGT-CCAATACAGTCAAA-CAAGGGTGAAAAAGGGTTTGACCA
1 GAAAGAGTTTGACTAAGTCCTAA-TAACAATACAGTCAAATGAA-GGCG-AAAAGAGTTTGACCA
* * * * **
1317225 AGCCCTAACGCCAATACAATCAAACGAGGGTGAAAAGAGTTTGTCCAGGTCTTAATGCCAATATA
63 AGTCCTAACGCCAATACAGTCAAACGAGGGTGAAAAGAGTTTGACCAGGTCCTAACACCAATATA
* *
1317290 GTCAAATAAGGATG
128 ATCAAATAAGGATA
* ** * * *
1317304 GAAAGAGTTTGACTAAGTCTTAA-CGCTACTATAGTCAAACT-AAGGCGAAAAGAGTTTGACCAG
1 GAAAGAGTTTGACTAAGTCCTAATAAC-AATACAGTCAAA-TGAAGGCGAAAAGAGTTTGACCAA
* * * * *
1317367 GTCCTAACGCCAATACAGTCAAACGAGAGTGGAAAGAGTTTAACTAGGTCCTAACACTAATATAA
64 GTCCTAACGCCAATACAGTCAAACGAGGGTGAAAAGAGTTTGACCAGGTCCTAACACCAATATAA
* *
1317432 TCAAATGAGGTTA
129 TCAAATAAGGATA
* * * * *
1317445 TAAAGAGTTTGACTAATTCCTAATAACAATACAGTCAAATGAGGGTGAAAAGAGTTTAACCAAGT
1 GAAAGAGTTTGACTAAGTCCTAATAACAATACAGTCAAATGAAGGCGAAAAGAGTTTGACCAAGT
* **
1317510 CC-ACACACCAATACAGTCAAATAAGGGTGAAAAGAGTTTGA
66 CCTA-ACGCCAATACAGTCAAACGAGGGTGAAAAGAGTTTGA
1317551 TATCTAGGTC
Statistics
Matches: 198, Mismatches: 42, Indels: 15
0.78 0.16 0.06
Matches are distributed among these distances:
140 2 0.01
141 161 0.81
142 33 0.17
143 2 0.01
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.22
Consensus pattern (141 bp):
GAAAGAGTTTGACTAAGTCCTAATAACAATACAGTCAAATGAAGGCGAAAAGAGTTTGACCAAGT
CCTAACGCCAATACAGTCAAACGAGGGTGAAAAGAGTTTGACCAGGTCCTAACACCAATATAATC
AAATAAGGATA
Found at i:1318257 original size:87 final size:89
Alignment explanation
Indices: 1317975--1318316 Score: 388
Period size: 89 Copynumber: 3.8 Consensus size: 89
1317965 TTTGTGGTCA
* ** * * * *
1317975 TGTGATGCATCAATACCATCTAGTGGCTAAAAGAAAGGGATATGACTAGGAATGAGTGATCAGGA
1 TGTGATGCATCAATACCATCTAGTGGTTGGATGAAGGGGATATGACTAGGAAT--GTG-T-GGGC
* *
1318040 TAC-CCTTGCCCCAAGGAAATAAGGCTT
62 TGCACCTTGCCCCAAGGAAATTAGGCTT
* * * *
1318067 TGTGATGCATCAATACCATCTAGTGGTTGGGTGAAGGGGATATGATTAGGAATATGTGGGCTACA
1 TGTGATGCATCAATACCATCTAGTGGTTGGATGAAGGGGATATGACTAGGAATGTGTGGGCTGCA
1318132 CCTTGCCCCAAGGAAATTAGGCTT
66 CCTTGCCCCAAGGAAATTAGGCTT
* ** * * *
1318156 TGAGATGCATCAATACTGT-TCAGTTGTTGGATGAAGGGGATATGACT-GGAATGTAT-GGTTGC
1 TGTGATGCATCAATACCATCT-AGTGGTTGGATGAAGGGGATATGACTAGGAATGTGTGGGCTGC
*
1318218 ACCTTGCCCCAATGAAATTAGGCTT
65 ACCTTGCCCCAAGGAAATTAGGCTT
* * *
1318243 TGTGATACACCAATACCATCTAGTGGTTGGATAAAGGGGATATG-CTTAGGAATGTGTGGGCTGC
1 TGTGATGCATCAATACCATCTAGTGGTTGGATGAAGGGGATATGAC-TAGGAATGTGTGGGCTGC
1318307 ACCTTGCCCC
65 ACCTTGCCCC
1318317 TTTGTCAATA
Statistics
Matches: 213, Mismatches: 31, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
86 1 0.00
87 64 0.30
88 22 0.10
89 78 0.37
90 2 0.01
92 46 0.22
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.27
Consensus pattern (89 bp):
TGTGATGCATCAATACCATCTAGTGGTTGGATGAAGGGGATATGACTAGGAATGTGTGGGCTGCA
CCTTGCCCCAAGGAAATTAGGCTT
Found at i:1319409 original size:111 final size:112
Alignment explanation
Indices: 1319237--1319540 Score: 364
Period size: 111 Copynumber: 2.7 Consensus size: 112
1319227 ACTGATTGGG
*
1319237 TACATGCCCTATTTTCCTAGGCACCAATGGATTGGAATGTATAAAATATGAATTTCTCAAAAATT
1 TACATGCCCTATTTTCCTAGGCACCAATGGATTGCAATGTATAAAATATGAATTTCTCAAAAATT
1319302 AGACAAAATTTGATGTTGTT-GG-ACAAAAATATCAAAAATGATAAGA
66 AGAC-AAATTTGATGTTGTTAGGCACAAAAATATCAAAAATGATAAGA
* * * *
1319348 TACATGCCCTGTTTTCCTAGGCACTAATGGA-T-CAAGTTGTATAAAATATGAGTTTTTCAAAAA
1 TACATGCCCTATTTTCCTAGGCACCAATGGATTGCAA--TGTATAAAATATGAATTTCTCAAAAA
* * ** * *
1319411 TTAGACAAATTTGATGTTGTTAGGCTCAAAAATTTCAAAGTTTATAGGA
64 TTAGACAAATTTGATGTTGTTAGGCACAAAAATATCAAAAATGATAAGA
* * * * * * * *
1319460 TATATACCCCATTTTTCTAGGCACAAATGGATTGGAATGCATAAAGTATGAATTTCTTCAAAAAT
1 TACATGCCCTATTTTCCTAGGCACCAATGGATTGCAATGTATAAAATATGAATTTC-TCAAAAAT
*
1319525 CAGACAAATTTGATGT
65 TAGACAAATTTGATGT
1319541 CTTTCGAAGT
Statistics
Matches: 163, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
109 2 0.01
110 16 0.10
111 61 0.37
112 58 0.36
113 24 0.15
114 2 0.01
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (112 bp):
TACATGCCCTATTTTCCTAGGCACCAATGGATTGCAATGTATAAAATATGAATTTCTCAAAAATT
AGACAAATTTGATGTTGTTAGGCACAAAAATATCAAAAATGATAAGA
Found at i:1319828 original size:16 final size:15
Alignment explanation
Indices: 1319799--1319831 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1319789 TAGAGCTTCA
1319799 TTCTTTTCAATTTTT
1 TTCTTTTCAATTTTT
1319814 TTCTGTTTC-ATTTTT
1 TTCT-TTTCAATTTTT
1319829 TTC
1 TTC
1319832 ATCACGCTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.09, C:0.15, G:0.03, T:0.73
Consensus pattern (15 bp):
TTCTTTTCAATTTTT
Found at i:1321051 original size:20 final size:20
Alignment explanation
Indices: 1321026--1321078 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
1321016 CTACCACTGT
1321026 TTGTATCGATACATGGCA-CA
1 TTGTATCGATACATGG-ATCA
* * *
1321046 TTGTATCAATA-ATTGATTA
1 TTGTATCGATACATGGATCA
1321065 TTGTATCGATACAT
1 TTGTATCGATACAT
1321079 TGGTTCAAGC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
18 1 0.04
19 14 0.52
20 12 0.44
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (20 bp):
TTGTATCGATACATGGATCA
Found at i:1322663 original size:3 final size:3
Alignment explanation
Indices: 1322655--1322685 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1322645 CTTTCAAGAC
*
1322655 GAT GAT GAT GAT GAT AAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1322686 GTCACTTAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:1325770 original size:22 final size:21
Alignment explanation
Indices: 1325732--1325772 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1325722 ATTAAATCTT
* *
1325732 CTTCAAATTTCTTATTTTTCA
1 CTTCAAAATACTTATTTTTCA
1325753 CTTCAAAATACTTCATTTTT
1 CTTCAAAATACTT-ATTTTT
1325773 TATCAAAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.27, C:0.20, G:0.00, T:0.54
Consensus pattern (21 bp):
CTTCAAAATACTTATTTTTCA
Found at i:1327525 original size:30 final size:30
Alignment explanation
Indices: 1327489--1327545 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1327479 AATAAATTTT
1327489 TTATCAA-GGGGAGAAAATCTTTTTAACCAA
1 TTATCAAGGGGGAG-AAATCTTTTTAACCAA
*
1327519 TTATCAAGGGGGAGAAATTTTTTTAAC
1 TTATCAAGGGGGAGAAATCTTTTTAAC
1327546 AAGAGCCTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 19 0.76
31 6 0.24
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (30 bp):
TTATCAAGGGGGAGAAATCTTTTTAACCAA
Found at i:1328181 original size:20 final size:19
Alignment explanation
Indices: 1328156--1328209 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 19
1328146 CTACCACTGT
1328156 TTGTATCGATACATG-GCACA
1 TTGTATCGATACATGAG-A-A
1328176 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGA-GAA
1328196 TTGTATCGATACAT
1 TTGTATCGATACAT
1328210 TGCTTCAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 30 0.94
21 1 0.03
22 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (19 bp):
TTGTATCGATACATGAGAA
Found at i:1332687 original size:139 final size:141
Alignment explanation
Indices: 1332392--1332732 Score: 395
Period size: 139 Copynumber: 2.4 Consensus size: 141
1332382 ACCAAAATGG
* * * * *
1332392 TACGAAAGGTTTTAAGAATTTTTATATCCCTACGGAAACCCATAGGAATAATAGAAATATTGGAA
1 TACGAAAAGTTTTAAG-ATTTCTATACCCCTACAGAAACCCATAGGAATATTAGAAATATTGGAA
* * * *
1332457 AAATAATAATATTATTTTTATTTAATTTTTTAATTTCCAAGAAAAATTCATTTTGTAACTTAATG
65 AAATAAGAATATAAATTTTATTTAA-TTTTTAATTTCC-AGAAAAATTCATTTCGTAACTTAATG
*
1332522 AAGAACTGAAAAGA
128 AAGAACCGAAAAGA
* * * *
1332536 TACGAAAAGTTTTGAAGATTTCAATACCCCTACAGAAAACCATAGGAATATTAAAAATCTT-GAA
1 TACGAAAAGTTTT-AAGATTTCTATACCCCTACAGAAACCCATAGGAATATTAGAAATATTGGAA
* *
1332600 AAATTAAGACA-ATAAATTTTATTTAA-TTTTAATTT-C-TAAAAATTCATTTCGTACCTTAATG
65 AAA-TAAGA-ATATAAATTTTATTTAATTTTTAATTTCCAGAAAAATTCATTTCGTAACTTAATG
**
1332661 GTGAACCGAAAAGA
128 AAGAACCGAAAAGA
* * *
1332675 TACGAAATGTTTTAAAGATTTCTATACCCCTACAGATACCCATGGGAATATTAGAAAT
1 TACGAAAAGTTTT-AAGATTTCTATACCCCTACAGAAACCCATAGGAATATTAGAAAT
1332733 TACAAAAAAT
Statistics
Matches: 169, Mismatches: 25, Indels: 11
0.82 0.12 0.05
Matches are distributed among these distances:
139 84 0.50
141 1 0.01
142 9 0.05
143 6 0.04
144 65 0.38
145 4 0.02
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.34
Consensus pattern (141 bp):
TACGAAAAGTTTTAAGATTTCTATACCCCTACAGAAACCCATAGGAATATTAGAAATATTGGAAA
AATAAGAATATAAATTTTATTTAATTTTTAATTTCCAGAAAAATTCATTTCGTAACTTAATGAAG
AACCGAAAAGA
Found at i:1333666 original size:10 final size:10
Alignment explanation
Indices: 1333642--1333709 Score: 66
Period size: 10 Copynumber: 6.6 Consensus size: 10
1333632 TCTTAACAAA
*
1333642 TTTTTCTATT
1 TTTTTCTCTT
*
1333652 ATTTTCTCTT
1 TTTTTCTCTT
*
1333662 TTTTTTTCTT
1 TTTTTCTCTT
1333672 TTTCTT-TCCTT
1 TTT-TTCT-CTT
1333683 TTTGTTCTCTT
1 TTT-TTCTCTT
*
1333694 TTTTTCCCTT
1 TTTTTCTCTT
1333704 TTTTTC
1 TTTTTC
1333710 CAAGCTTCTA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
10 32 0.65
11 16 0.33
12 1 0.02
ACGTcount: A:0.03, C:0.19, G:0.01, T:0.76
Consensus pattern (10 bp):
TTTTTCTCTT
Found at i:1333684 original size:20 final size:20
Alignment explanation
Indices: 1333642--1333709 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 20
1333632 TCTTAACAAA
* *
1333642 TTTTTCTATTATTTTCTCTTT
1 TTTTTCTCTTTTTTTC-CTTT
1333663 TTTTT-TCTTTTTCTTTCCTTT
1 TTTTTCTC-TTTT-TTTCCTTT
* *
1333684 TTGTTCTCTTTTTTTCCCTT
1 TTTTTCTCTTTTTTTCCTTT
1333704 TTTTTC
1 TTTTTC
1333710 CAAGCTTCTA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
20 13 0.33
21 20 0.51
22 6 0.15
ACGTcount: A:0.03, C:0.19, G:0.01, T:0.76
Consensus pattern (20 bp):
TTTTTCTCTTTTTTTCCTTT
Found at i:1333706 original size:11 final size:11
Alignment explanation
Indices: 1333653--1333708 Score: 64
Period size: 11 Copynumber: 5.3 Consensus size: 11
1333643 TTTTCTATTA
1333653 TTTTCTCTTTT
1 TTTTCTCTTTT
1333664 TTTT-TCTTTT
1 TTTTCTCTTTT
1333674 TCTTTC-CTTTT
1 T-TTTCTCTTTT
*
1333685 TGTTCTC-TTT
1 TTTTCTCTTTT
*
1333695 TTTTCCCTTTT
1 TTTTCTCTTTT
1333706 TTT
1 TTT
1333709 CCAAGCTTCT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
10 18 0.47
11 20 0.53
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (11 bp):
TTTTCTCTTTT
Found at i:1334871 original size:21 final size:22
Alignment explanation
Indices: 1334838--1334878 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1334828 TTTTCTATTA
*
1334838 TTTTCTTTCTTTTTCTTTCCCT
1 TTTTCCTTCTTTTTCTTTCCCT
*
1334860 TTTTCCTT-TTTTTTTTTCC
1 TTTTCCTTCTTTTTCTTTCC
1334879 AAGTTTCTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTTCCTTCTTTTTCTTTCCCT
Found at i:1336019 original size:19 final size:17
Alignment explanation
Indices: 1335995--1336051 Score: 53
Period size: 16 Copynumber: 3.3 Consensus size: 17
1335985 TCTTAACTAA
1335995 TTTTTCTATTATTTTCTCT
1 TTTTTCT-TTATTTT-TCT
*
1336014 TTTTTCTTTCTTTTTCT
1 TTTTTCTTTATTTTTCT
** *
1336031 TTCCT-TTTCTTTTTCT
1 TTTTTCTTTATTTTTCT
1336047 TTTTT
1 TTTTT
1336052 TTTTTTAGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
16 14 0.42
17 6 0.18
18 6 0.18
19 7 0.21
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTCTTTATTTTTCT
Found at i:1336025 original size:11 final size:11
Alignment explanation
Indices: 1336011--1336051 Score: 50
Period size: 10 Copynumber: 3.7 Consensus size: 11
1336001 TATTATTTTC
1336011 TCTTTTTTCTT
1 TCTTTTTTCTT
1336022 TC-TTTTTCTT
1 TCTTTTTTCTT
1336032 TCCTTTTCTT-TT
1 T-CTTTT-TTCTT
1336044 TCTTTTTT
1 TCTTTTTT
1336052 TTTTTTAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
10 11 0.41
11 8 0.30
12 6 0.22
13 2 0.07
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TCTTTTTTCTT
Found at i:1336027 original size:29 final size:26
Alignment explanation
Indices: 1335995--1336058 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 26
1335985 TCTTAACTAA
*
1335995 TTTTTCTATTATTTTCTCTTTTTTCTTTC
1 TTTTTCT-TTACTTT-TC-TTTTTCTTTC
*
1336024 TTTTTCTTTCCTTTTCTTTTTCTTT-
1 TTTTTCTTTACTTTTCTTTTTCTTTC
*
1336049 TTTTTTTTTA
1 TTTTTCTTTA
1336059 GTTTCTATTG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
25 8 0.26
26 9 0.29
27 2 0.06
28 5 0.16
29 7 0.23
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.80
Consensus pattern (26 bp):
TTTTTCTTTACTTTTCTTTTTCTTTC
Found at i:1336054 original size:11 final size:11
Alignment explanation
Indices: 1335995--1336055 Score: 59
Period size: 11 Copynumber: 5.5 Consensus size: 11
1335985 TCTTAACTAA
*
1335995 TTTTTCTATTAT
1 TTTTTCT-TTTT
*
1336007 TTTCTCTTTTT
1 TTTTTCTTTTT
*
1336018 TCTTTCTTTTT
1 TTTTTCTTTTT
* * *
1336029 CTTTCCTTTTC
1 TTTTTCTTTTT
1336040 TTTTTCTTTTT
1 TTTTTCTTTTT
1336051 TTTTT
1 TTTTT
1336056 TTAGTTTCTA
Statistics
Matches: 38, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
11 32 0.84
12 6 0.16
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:1337185 original size:20 final size:20
Alignment explanation
Indices: 1337160--1337209 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1337150 TCTTAACTAA
*
1337160 TTTTTTTAT-TTTTTCTCAC
1 TTTTTTTTTCTTTTTCTCAC
**
1337179 TTTTTTTTTCTTTTTCTTTC
1 TTTTTTTTTCTTTTTCTCAC
1337199 TTTTTTTTTCT
1 TTTTTTTTTCT
1337210 CTCTTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 8 0.30
20 19 0.70
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTTTTTTTCTTTTTCTCAC
Found at i:1337191 original size:10 final size:10
Alignment explanation
Indices: 1337178--1337219 Score: 57
Period size: 10 Copynumber: 4.0 Consensus size: 10
1337168 TTTTTTCTCA
1337178 CTTTTTTTTT
1 CTTTTTTTTT
*
1337188 CTTTTTCTTT
1 CTTTTTTTTT
1337198 CTTTTTTTTT
1 CTTTTTTTTT
1337208 CTCTCTTTTTTT
1 CT-T-TTTTTTT
1337220 TTCTAAGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 20 0.71
11 1 0.04
12 7 0.25
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:1337206 original size:14 final size:14
Alignment explanation
Indices: 1337184--1337223 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
1337174 CTCACTTTTT
*
1337184 TTTTCTTTTTCTTTC
1 TTTT-TTTTTCTCTC
1337199 TTTTTTTTTCTCTC
1 TTTTTTTTTCTCTC
1337213 TTTTTTTTTCT
1 TTTTTTTTTCT
1337224 AAGTTTCTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 20 0.83
15 4 0.17
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTTTTTTCTCTC
Found at i:1338063 original size:135 final size:135
Alignment explanation
Indices: 1337830--1338082 Score: 332
Period size: 135 Copynumber: 1.9 Consensus size: 135
1337820 AGAAAACTAG
* *
1337830 ATTTTTTGAAAACTAGAGAATTTCAAGAAAAAAATAGAAAACTCATGAAAATGAATAAATTTTTA
1 ATTTTTCGAAAACTAGAGAATTTCAAGAAAAAAATAGAAAACTCATAAAAATGAATAAATTTTTA
** * * *
1337895 AAAACTAATTTACTCTGATTTAAATGATGATATTTGAAGAATATTAAAAATTTTGAACAGAGAAA
66 AAAACTAATAAAATCTGATTTAAATAATAATATTTGAAGAATATTAAAAATTTTGAACAGAGAAA
1337960 AATCT
131 AATCT
* *
1337965 ATTTTTCGAAAAC-AGGAGAATTTTAAGAAAAAAAT-GAAAAACTCATAAAAATGAATGAATTTT
1 ATTTTTCGAAAACTA-GAGAATTTCAAGAAAAAAATAG-AAAACTCATAAAAATGAATAAATTTT
* * * * *
1338028 TTAAAACTGATAAAATGGTGA-TTAAATAATAATATTTGATGAATTTTAAAAATTT
64 TAAAAACTAATAAAAT-CTGATTTAAATAATAATATTTGAAGAATATTAAAAATTT
1338083 CAATCCGATG
Statistics
Matches: 101, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
134 2 0.02
135 96 0.95
136 3 0.03
ACGTcount: A:0.50, C:0.06, G:0.11, T:0.33
Consensus pattern (135 bp):
ATTTTTCGAAAACTAGAGAATTTCAAGAAAAAAATAGAAAACTCATAAAAATGAATAAATTTTTA
AAAACTAATAAAATCTGATTTAAATAATAATATTTGAAGAATATTAAAAATTTTGAACAGAGAAA
AATCT
Found at i:1342170 original size:13 final size:13
Alignment explanation
Indices: 1342152--1342176 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1342142 TTCACAATTT
1342152 GTATCGATACATC
1 GTATCGATACATC
1342165 GTATCGATACAT
1 GTATCGATACAT
1342177 TCTGGGTTTA
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:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
GTATCGATACATC
Found at i:1344607 original size:31 final size:28
Alignment explanation
Indices: 1344549--1344607 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
1344539 TTCATAATCG
* *
1344549 GGGATACTCCAATCCCGTTATTTCCAAA
1 GGGATACTCCAACCCCGTTATTCCCAAA
1344577 GGGATACTCCAACCCCGATTTTATTCCCAAA
1 GGGATACTCCAACCCCG---TTATTCCCAAA
1344608 ACAACAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 16 0.62
31 10 0.38
ACGTcount: A:0.29, C:0.31, G:0.14, T:0.27
Consensus pattern (28 bp):
GGGATACTCCAACCCCGTTATTCCCAAA
Found at i:1344799 original size:79 final size:79
Alignment explanation
Indices: 1344495--1344792 Score: 307
Period size: 79 Copynumber: 3.8 Consensus size: 79
1344485 ATTCTTCATG
* * * *
1344495 TCAGGGATACTCCAACCTCGGTTTTATTTCCAAAACATTAATTTTTCATAATCGGGGATACTCCA
1 TCAGGGATACTCCAACCCCGATTTTATTCCCAAAACATTAATTTTTCACAATCGGGGATACTCCA
*
1344560 ATCCCGTTATTTCCA
66 ACCCCGTTATTT-CA
* ** * *
1344575 -AAGGGATACTCCAACCCCGATTTTATTCCCAAAACAACAGTTTTTCACAATTGGGGATACTCCA
1 TCAGGGATACTCCAACCCCGATTTTATTCCCAAAACATTAATTTTTCACAATCGGGGATACTCCA
*
1344639 ACCCCGTCATTT--
66 ACCCCGTTATTTCA
* * * ** **
1344651 TCGAGGGGATATTCTAA-CCTGATTTTATTCCCAAAACACCAATTTTTCACAATCAAGGATACTC
1 TC-A-GGGATACTCCAACCCCGATTTTATTCCCAAAACATTAATTTTTCACAATCGGGGATACTC
1344715 CAACCCCGTTATTTCA
64 CAACCCCGTTATTTCA
* ** * * * * *
1344731 TCAGGGATACTCTAACCCCGGCTTTATTTCCAAAATATTGATTTCTCACAATTGGGGATACT
1 TCAGGGATACTCCAACCCCGATTTTATTCCCAAAACATTAATTTTTCACAATCGGGGATACT
1344793 TTAACCCTGA
Statistics
Matches: 178, Mismatches: 34, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
78 66 0.37
79 110 0.62
80 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (79 bp):
TCAGGGATACTCCAACCCCGATTTTATTCCCAAAACATTAATTTTTCACAATCGGGGATACTCCA
ACCCCGTTATTTCA
Found at i:1344919 original size:130 final size:129
Alignment explanation
Indices: 1344690--1344931 Score: 317
Period size: 130 Copynumber: 1.9 Consensus size: 129
1344680 CCCAAAACAC
*
1344690 CAATTTTTCACAATCAAGGATACTCCAACCCCGTTATTTCATCAGGGATACTCTAACCCCGGCTT
1 CAATTTTTCACAATCAAGGATACTCCAACCCCGTTATTT-ATCAGGGATACTCTAACCCCGACTT
* ** **
1344755 TATTTCCAAAATATTGATTTCTCACAATTGGGGATACTTTAACCCTGACCTTATTTCTAAATCAT
65 TATTTCCAAAATATAGATTTCTCACAATCAGGGATACTCCAACCCTGACCTTATTTCTAAATCAT
* ** *
1344820 CAATTTTTCAGAATCGGGGATACTCCAACCCCGTTATTT-TCGAGGGAATACTCTAACCCCGATT
1 CAATTTTTCACAATCAAGGATACTCCAACCCCGTTATTTATC-AGGG-ATACTCTAACCCCGACT
** *
1344884 TTATTTTTAAAATATAGATTT-TCTATAATCAGGGATACTCCAACCCTG
64 TTATTTCCAAAATATAGATTTCTC-ACAATCAGGGATACTCCAACCCTG
1344932 TTATTTTTGA
Statistics
Matches: 96, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
128 2 0.02
129 6 0.06
130 88 0.92
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.34
Consensus pattern (129 bp):
CAATTTTTCACAATCAAGGATACTCCAACCCCGTTATTTATCAGGGATACTCTAACCCCGACTTT
ATTTCCAAAATATAGATTTCTCACAATCAGGGATACTCCAACCCTGACCTTATTTCTAAATCAT
Found at i:1344983 original size:78 final size:79
Alignment explanation
Indices: 1344822--1345009 Score: 243
Period size: 78 Copynumber: 2.4 Consensus size: 79
1344812 TAAATCATCA
* * *
1344822 ATTTTTCAGAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGAATACTCTAACCCCGATTTTA
1 ATTTTCCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGAATACTCCAACCCCGATTTTA
* * *
1344887 TTTTTAAAATATAG
66 TTTTCAAAACACAG
* * * * **
1344901 ATTTTCTATAATCAGGGATACTCCAACCCTGTTATTTTTGAGGG-ATACTCCAACCTTGATTTTA
1 ATTTTCCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGAATACTCCAACCCCGATTTTA
*
1344965 TTTTCAAAACACCG
66 TTTTCAAAACACAG
*
1344979 ATTTTCCATAATCGGGGATACTCCACCCCCG
1 ATTTTCCATAATCGGGGATACTCCAACCCCG
1345010 GTTTTATCTC
Statistics
Matches: 92, Mismatches: 17, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
78 54 0.59
79 38 0.41
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (79 bp):
ATTTTCCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGAATACTCCAACCCCGATTTTA
TTTTCAAAACACAG
Found at i:1344998 original size:208 final size:208
Alignment explanation
Indices: 1344615--1345000 Score: 465
Period size: 208 Copynumber: 1.9 Consensus size: 208
1344605 AAAACAACAG
* * * *
1344615 TTTTTCACAATTGGGGATACTCCAACCCCGTCATTTTCGAGGGGATATTCTAACCTGATTTTATT
1 TTTTTCACAATCGGGGATACTCCAACCCCGTCATTTTCGAGGGAATACTCTAACCCGATTTTATT
*
1344680 CCCAAAACACCAATTTTTCACAATCAAGGATACTCCAACCCCGTTATTTCATCAGGGATACTCTA
66 CCCAAAACACCAATTTTTCACAATCAAGGATACTCCAACCCCGTTATTTCATCAGGGATACTCCA
* * ** *
1344745 ACCCCGGCTTTATTTCCAAAATATTGATTTCTCACAATTGGGGATACTTTAACCCTGACCTTATT
131 ACCCCGACTTTATTTCCAAAACACCGATTTCTCACAATCGGGGATACTTTAACCCTGACCTTATT
1344810 TCTAAATCATCAA
196 TCTAAATCATCAA
* *
1344823 TTTTTCAGAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGAATACTCTAACCCCGATTTTAT
1 TTTTTCACAATCGGGGATACTCCAACCCCGTCATTTTCGAGGGAATACTCTAA-CCCGATTTTAT
*** * * * * * * *
1344888 TTTTAAAATA-TAGA-TTTTCTATAATCAGGGATACTCCAACCCTGTTATTT-TTGAGGGATACT
65 TCCCAAAACACCA-ATTTTTC-ACAATCAAGGATACTCCAACCCCGTTATTTCATCAGGGATACT
** * * *
1344950 CCAACCTTGATTTTATTTTCAAAACACCGATTT-TCCATAATCGGGGATACT
128 CCAACCCCGACTTTATTTCCAAAACACCGATTTCT-CACAATCGGGGATACT
1345001 CCACCCCCGG
Statistics
Matches: 147, Mismatches: 27, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
207 1 0.01
208 102 0.69
209 44 0.30
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.35
Consensus pattern (208 bp):
TTTTTCACAATCGGGGATACTCCAACCCCGTCATTTTCGAGGGAATACTCTAACCCGATTTTATT
CCCAAAACACCAATTTTTCACAATCAAGGATACTCCAACCCCGTTATTTCATCAGGGATACTCCA
ACCCCGACTTTATTTCCAAAACACCGATTTCTCACAATCGGGGATACTTTAACCCTGACCTTATT
TCTAAATCATCAA
Found at i:1346929 original size:51 final size:52
Alignment explanation
Indices: 1346874--1347006 Score: 180
Period size: 51 Copynumber: 2.6 Consensus size: 52
1346864 AATGGTCTAC
* * * *
1346874 ATGTATCGATACATTAAAGAATGTATTGATGCAGTTAGGTC-AAAACCCAGA
1 ATGTATCGATACAATAAAGAATGTATCGATACAGTTAGGTCAAAAACCCAAA
* * *
1346925 ATGTATCGATACAATGAATAATGTATCGATACATTTAGGTCAAAAACCCAAA
1 ATGTATCGATACAATAAAGAATGTATCGATACAGTTAGGTCAAAAACCCAAA
*
1346977 ATGTATCGATACAATAGA-AATGTATCGATA
1 ATGTATCGATACAATAAAGAATGTATCGATA
1347007 AATTTTCCTT
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
51 47 0.65
52 25 0.35
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.28
Consensus pattern (52 bp):
ATGTATCGATACAATAAAGAATGTATCGATACAGTTAGGTCAAAAACCCAAA
Found at i:1347092 original size:20 final size:20
Alignment explanation
Indices: 1347067--1347104 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1347057 CCATTTTAGA
1347067 CATGTATCGATACATTCACT
1 CATGTATCGATACATTCACT
1347087 CATGTATCGATACATTCA
1 CATGTATCGATACATTCA
1347105 TTTATTGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.34
Consensus pattern (20 bp):
CATGTATCGATACATTCACT
Found at i:1347762 original size:62 final size:62
Alignment explanation
Indices: 1347690--1347828 Score: 197
Period size: 62 Copynumber: 2.2 Consensus size: 62
1347680 ACAAAAGACA
* **
1347690 TAAAAAGTGCCATTAACTTGTGTCAACCTTAAAAAGAAAAAGGCATCCTACTCTTTGAGGAC
1 TAAAAGGTGCCACCAACTTGTGTCAACCTTAAAAAGAAAAAGGCATCCTACTCTTTGAGGAC
* *** * *
1347752 TAAAAGGTGCCACCAACTTGTTTGGGCTTTAGAAAGAAAAAGGCATCCTACTCTTTGAGGAC
1 TAAAAGGTGCCACCAACTTGTGTCAACCTTAAAAAGAAAAAGGCATCCTACTCTTTGAGGAC
1347814 TAAAAGGTGCCACCA
1 TAAAAGGTGCCACCA
1347829 GCTTATGTGG
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
62 68 1.00
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.24
Consensus pattern (62 bp):
TAAAAGGTGCCACCAACTTGTGTCAACCTTAAAAAGAAAAAGGCATCCTACTCTTTGAGGAC
Found at i:1347850 original size:62 final size:62
Alignment explanation
Indices: 1347718--1347856 Score: 233
Period size: 62 Copynumber: 2.2 Consensus size: 62
1347708 TGTGTCAACC
* *
1347718 TTAAAAAGAAAAAGGCATCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTTGTTTGGGCT
1 TTAAAAAGAAAAAGGCATCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTTATGTGGGCT
* * *
1347780 TTAGAAAGAAAAAGGCATCCTACTCTTTGAGGACTAAAAGGTGCCACCAGCTTATGTGGGTT
1 TTAAAAAGAAAAAGGCATCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTTATGTGGGCT
1347842 TTAAAAAGAAAAAGG
1 TTAAAAAGAAAAAGG
1347857 GAAAAGGTTG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 71 1.00
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (62 bp):
TTAAAAAGAAAAAGGCATCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTTATGTGGGCT
Found at i:1347882 original size:44 final size:43
Alignment explanation
Indices: 1347815--1347898 Score: 132
Period size: 44 Copynumber: 1.9 Consensus size: 43
1347805 TTTGAGGACT
*
1347815 AAAAGGTGCCACCAGCTTATGTGGGTTTTAAAAAGAAAAAGGG
1 AAAAGGTGCCACCAGCTTATGTGGGCTTTAAAAAGAAAAAGGG
* *
1347858 AAAAGGTTGCCACCAGCTTGTGTGGGCTTTGAAAAGAAAAA
1 AAAAGG-TGCCACCAGCTTATGTGGGCTTTAAAAAGAAAAA
1347899 AGTGTCTTGC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
43 6 0.16
44 31 0.84
ACGTcount: A:0.38, C:0.13, G:0.27, T:0.21
Consensus pattern (43 bp):
AAAAGGTGCCACCAGCTTATGTGGGCTTTAAAAAGAAAAAGGG
Found at i:1354590 original size:19 final size:19
Alignment explanation
Indices: 1354566--1354603 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1354556 CCACTTCAAA
1354566 GCGTATTGTCGAAAACTTT
1 GCGTATTGTCGAAAACTTT
1354585 GCGTATTGTCGAAAACTTT
1 GCGTATTGTCGAAAACTTT
1354604 CTTTTGCTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (19 bp):
GCGTATTGTCGAAAACTTT
Found at i:1361447 original size:80 final size:80
Alignment explanation
Indices: 1361312--1361560 Score: 232
Period size: 80 Copynumber: 3.1 Consensus size: 80
1361302 AACGAGTTTA
* * * * * ** *
1361312 GAGTATCCTCTTGGAAATGATAAGGTTGGAGTATCCTTGATGGTGAAAAAGTTGATGCTCTTGGA
1 GAGTATCCACTTGAAAAAGATAGGGTTGGAGTATCCCTGATGGTGAAAATTTTGAT-ATCTTGGA
*
1361377 AAT-ATAATAGGGTTG
65 AATAAAAATAGGGTTG
* * * * * *
1361392 GAGTATCC-CTTCGAAAAAGGTGGGGTTGGAATATCCCTCATGGTGAAAATTTTGATATTTTGTA
1 GAGTATCCACTT-GAAAAAGATAGGGTTGGAGTATCCCTGATGGTGAAAATTTTGATATCTTGGA
* *
1361456 AGTAAAAATGGGGTTG
65 AATAAAAATAGGGTTG
* ** * *
1361472 GAGTATCCACTTGAAAATGATAGGGTTGGAGTATCCCTGATTATAAAAATTTTGATATTTTGGAA
1 GAGTATCCACTTGAAAAAGATAGGGTTGGAGTATCCCTGATGGTGAAAATTTTGATATCTTGGAA
* *
1361537 TTAAAAAATGGGGTTG
66 AT-AAAAATAGGGTTG
*
1361553 AAGTATCC
1 GAGTATCC
1361561 CCGATGATAA
Statistics
Matches: 138, Mismatches: 27, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
79 10 0.07
80 105 0.76
81 23 0.17
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.33
Consensus pattern (80 bp):
GAGTATCCACTTGAAAAAGATAGGGTTGGAGTATCCCTGATGGTGAAAATTTTGATATCTTGGAA
ATAAAAATAGGGTTG
Found at i:1361598 original size:53 final size:53
Alignment explanation
Indices: 1361494--1361597 Score: 127
Period size: 53 Copynumber: 1.9 Consensus size: 53
1361484 GAAAATGATA
* * * * * *
1361494 GGGTTGGAGTATCCCTGATTATAAAAATTTTGATATTTTGGAATTAAAAAATG
1 GGGTTGAAGTATCCCCGATGATAAAAAATTCGATATTTTGGAATGAAAAAATG
* *
1361547 GGGTTGAAGTATCCCCGATGATAAAAAATTCGATGCTTTTGGAAGGAAAAA
1 GGGTTGAAGTATCCCCGATGATAAAAAATTCGAT-ATTTTGGAATGAAAAA
1361598 TTTTAAGTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
53 29 0.69
54 13 0.31
ACGTcount: A:0.37, C:0.09, G:0.23, T:0.32
Consensus pattern (53 bp):
GGGTTGAAGTATCCCCGATGATAAAAAATTCGATATTTTGGAATGAAAAAATG
Found at i:1363936 original size:11 final size:11
Alignment explanation
Indices: 1363920--1363980 Score: 63
Period size: 11 Copynumber: 5.5 Consensus size: 11
1363910 GAACTTAGCA
1363920 AAAAAAAAGAG
1 AAAAAAAAGAG
1363931 AAAAAAAAGA-
1 AAAAAAAAGAG
*
1363941 AAGAGAAAAGA-
1 AA-AAAAAAGAG
* *
1363952 AAGAAAACGAG
1 AAAAAAAAGAG
1363963 ACAAAAAAAGAG
1 A-AAAAAAAGAG
1363975 AAAAAA
1 AAAAAA
1363981 GAAAAACTAG
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
10 7 0.17
11 25 0.61
12 9 0.22
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAG
Found at i:1363943 original size:15 final size:15
Alignment explanation
Indices: 1363919--1363973 Score: 67
Period size: 15 Copynumber: 3.5 Consensus size: 15
1363909 GGAACTTAGC
1363919 AAAAAA-AAAGAGAA
1 AAAAAAGAAAGAGAA
1363933 AAAAAAGAAAGAGAA
1 AAAAAAGAAAGAGAA
*
1363948 AAGAAAGAAAACGAGACA
1 AAAAAAG-AAA-GAGA-A
1363966 AAAAAAGA
1 AAAAAAGA
1363974 GAAAAAAGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
14 6 0.17
15 14 0.40
16 3 0.09
17 5 0.14
18 7 0.20
ACGTcount: A:0.78, C:0.04, G:0.18, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAGAGAA
Found at i:1365277 original size:13 final size:13
Alignment explanation
Indices: 1365259--1365283 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1365249 AGATTGCACA
1365259 GTATCGATACATT
1 GTATCGATACATT
1365272 GTATCGATACAT
1 GTATCGATACAT
1365284 GACTAAATGT
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):
GTATCGATACATT
Found at i:1365296 original size:20 final size:20
Alignment explanation
Indices: 1365271--1365323 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1365261 ATCGATACAT
*
1365271 TGTATCGATACATGACTA-AA
1 TGTATCGATACATGA-AAGAA
*
1365291 TGTATCGATACTTGAAAGGAA
1 TGTATCGATACATGAAA-GAA
1365312 TGTATCGATACA
1 TGTATCGATACA
1365324 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.04
20 14 0.50
21 13 0.46
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (20 bp):
TGTATCGATACATGAAAGAA
Found at i:1365389 original size:20 final size:20
Alignment explanation
Indices: 1365346--1365397 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1365336 TAGCCAAATT
*
1365346 TGTATCGATACA-CACAATA
1 TGTATCGATACATCACAAAA
*
1365365 TGTATCGATACATCCCAAAA
1 TGTATCGATACATCACAAAA
1365385 TGTATCGATACAT
1 TGTATCGATACAT
1365398 TGACTTGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (20 bp):
TGTATCGATACATCACAAAA
Found at i:1375221 original size:32 final size:33
Alignment explanation
Indices: 1375160--1375222 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
1375150 CACCCAGATG
* *
1375160 TATCGATACATATTGTTTAGTATCGATACATTA
1 TATCGATACATATTGCTTAGTATCAATACATTA
* *
1375193 TATCGATACATGTT-CTTGGTATCAATACAT
1 TATCGATACATATTGCTTAGTATCAATACAT
1375223 CATGAATTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 13 0.50
33 13 0.50
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (33 bp):
TATCGATACATATTGCTTAGTATCAATACATTA
Found at i:1375335 original size:13 final size:13
Alignment explanation
Indices: 1375317--1375342 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1375307 CACTGTTCAC
1375317 GTATCGATACATT
1 GTATCGATACATT
1375330 GTATCGATACATT
1 GTATCGATACATT
1375343 AAGCCCAACG
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):
GTATCGATACATT
Found at i:1377225 original size:13 final size:13
Alignment explanation
Indices: 1377207--1377231 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1377197 CAATGAACAC
1377207 GTATCGATACAAT
1 GTATCGATACAAT
1377220 GTATCGATACAA
1 GTATCGATACAA
1377232 AGCAATATGT
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:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (13 bp):
GTATCGATACAAT
Found at i:1377227 original size:32 final size:33
Alignment explanation
Indices: 1377186--1377249 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1377176 TGCCAGTTTC
*
1377186 ATGTATCGATACAATG-AACACGTATCGATACA
1 ATGTATCGATACAAAGCAACACGTATCGATACA
* *
1377218 ATGTATCGATACAAAGCAATATGTATCGATAC
1 ATGTATCGATACAAAGCAACACGTATCGATAC
1377250 TTCTCGGCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.54
33 13 0.46
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.27
Consensus pattern (33 bp):
ATGTATCGATACAAAGCAACACGTATCGATACA
Found at i:1381199 original size:20 final size:20
Alignment explanation
Indices: 1381179--1381215 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
1381169 TATACATATA
*
1381179 AATAAAACAAAA-AAATGAT
1 AATAAAAAAAAACAAATGAT
1381198 AATAAAAAAAAACAAATG
1 AATAAAAAAAAACAAATG
1381216 CAAACATCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.14
Consensus pattern (20 bp):
AATAAAAAAAAACAAATGAT
Found at i:1381572 original size:17 final size:17
Alignment explanation
Indices: 1381550--1381605 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
1381540 ATTTCATATT
1381550 TTTTTCTTTTTTTTTTC
1 TTTTTCTTTTTTTTTTC
* *
1381567 TTTTTCTTTCTTTCTTC
1 TTTTTCTTTTTTTTTTC
** * *
1381584 TTCATCTTCTTTCTTTC
1 TTTTTCTTTTTTTTTTC
1381601 TTTTT
1 TTTTT
1381606 TACCTAACTT
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTCTTTTTTTTTTC
Found at i:1382919 original size:32 final size:32
Alignment explanation
Indices: 1382856--1383297 Score: 688
Period size: 32 Copynumber: 13.8 Consensus size: 32
1382846 AAAATGGTGA
* * * **
1382856 TTTGAAAAGGGGTGCCACTGACTTGCATGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
** *
1382888 TTTTTAATGGGTTACCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* **
1382920 TTTGAAAAGGGTCACCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
1382952 TTTGAAATGGGTTGCCACCGACTTATGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
1382984 TTTGGAATGGGTTGCCACCGACTTGCGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
1383016 TTTGAAATGGGTTGCCACCGAGTTGCGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1383048 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1383080 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
1383112 TTTGAAATGGGTTGCCACCGACTTTTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
1383144 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1383176 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1383208 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
1383240 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
1383272 TTTGAAATGGG-TGCCACAGAGTTGTG
1 TTTGAAATGGGTTGCCACCGACTTGTG
1383298 GATTTAAAAG
Statistics
Matches: 379, Mismatches: 31, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
31 13 0.03
32 366 0.97
ACGTcount: A:0.17, C:0.19, G:0.34, T:0.31
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:1383314 original size:27 final size:27
Alignment explanation
Indices: 1383280--1383989 Score: 1044
Period size: 27 Copynumber: 26.0 Consensus size: 27
1383270 GCTTTGAAAT
* *
1383280 GGGTGCCACAGAGTTGTGGATTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1383307 GGATGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1383334 GGGTGCCACGGAGTTGTGGACCTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1383361 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
1383388 GGGTGCCACAGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1383415 GGGTGCCACGGAGTTGTGGATTTTAAAA
1 GGGTGCCACGGAGTTGTGGA-CTTAAAA
*
1383443 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
1383470 GAGATGCCACGGAGTTATGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
*
1383498 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* * *
1383525 AGGTGCCACGGAGCTGTGGTCTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
1383552 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
1383579 GGGTGCCACAGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1383606 GGGTGCCACGGTGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
* *
1383634 GGGTGCCACAGAGTTGTGGAATTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
1383661 GAGATGCCACGGAGTTATGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
1383689 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1383716 GGGTGCCACGGAGTTGTGGTCTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1383743 GGAATGCCACGGAGTTGTGGACTTAAAA
1 GG-GTGCCACGGAGTTGTGGACTTAAAA
1383771 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1383798 GGGTGCCACGAAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
1383825 GGGTGCCACAGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
1383852 GGGTACCA-GGAGTTTTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
1383879 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
1383906 GGGTACCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
1383934 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
1383961 GGATGCCACAGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
1383989 G
1 G
1383990 AAAATGCCAC
Statistics
Matches: 614, Mismatches: 60, Indels: 17
0.89 0.09 0.02
Matches are distributed among these distances:
26 10 0.02
27 443 0.72
28 161 0.26
ACGTcount: A:0.29, C:0.14, G:0.34, T:0.23
Consensus pattern (27 bp):
GGGTGCCACGGAGTTGTGGACTTAAAA
Found at i:1383625 original size:191 final size:190
Alignment explanation
Indices: 1383283--1383982 Score: 1116
Period size: 191 Copynumber: 3.7 Consensus size: 190
1383273 TTGAAATGGG
* * * * *
1383283 TGCCACAGAGTTGTGGATTTAAAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
1 TGCCACGGAGTTATGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
*
1383348 TGTGGACCTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTAAA
66 TGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTAAA
1383413 AAGGGTGCCACGGAGTTGTGGATTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAGA
131 AAGGGTGCCACGGAGTTGTGGA-TTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAGA
* *
1383474 TGCCACGGAGTTATGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAAGGTGCCACGGAGC
1 TGCCACGGAGTTATGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
*
1383539 TGTGGTCTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTAAA
66 TGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTAAA
* *
1383604 AAGGGTGCCACGGTGTTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGAATTAAAAGAGA
131 AAGGGTGCCACGGAGTTGTGGA-TTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAGA
*
1383665 TGCCACGGAGTTATGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
1 TGCCACGGAGTTATGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
* * * *
1383730 TGTGGTCTTAAAAGGAATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTA
66 TGTGGACTTAAAAGG-GTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTAA
* * * *
1383795 AAAGGGTGCCACGAAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTAAAAAG-GG
130 AAAGGGTGCCACGGAGTTGTGGATTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAGA
* * *
1383855 TACCA-GGAGTTTTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTACCACGGAG
1 TGCCACGGAGTTATGGAC-TTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAG
* *
1383919 TTGTGGACTTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGATGCCACAGAGTTGTGGACT
65 TTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACT
1383983 TTAAAAGAAA
Statistics
Matches: 473, Mismatches: 33, Indels: 7
0.92 0.06 0.01
Matches are distributed among these distances:
189 11 0.02
190 99 0.21
191 296 0.63
192 67 0.14
ACGTcount: A:0.29, C:0.15, G:0.34, T:0.23
Consensus pattern (190 bp):
TGCCACGGAGTTATGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGTGCCACGGAGT
TGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTAAA
AAGGGTGCCACGGAGTTGTGGATTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAGA
Found at i:1391782 original size:17 final size:17
Alignment explanation
Indices: 1391760--1391815 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
1391750 ATTTCATATT
1391760 TTTTTCTTTTTTTTTTC
1 TTTTTCTTTTTTTTTTC
* *
1391777 TTTTTCTTTCTTTCTTC
1 TTTTTCTTTTTTTTTTC
** * *
1391794 TTCATCTTCTTTCTTTC
1 TTTTTCTTTTTTTTTTC
1391811 TTTTT
1 TTTTT
1391816 TACCTAACTT
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTCTTTTTTTTTTC
Found at i:1396488 original size:33 final size:33
Alignment explanation
Indices: 1396446--1396514 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
1396436 TTTTCACAAT
* *
1396446 TTGTATCGATACACTGTTCACTGTATCGATACA
1 TTGTATCGATACACTGCTCACTGTATCAATACA
* *
1396479 TTGTATCGATACATTGCTCATTGTATCAATACA
1 TTGTATCGATACACTGCTCACTGTATCAATACA
1396512 TTG
1 TTG
1396515 CTCATTGTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (33 bp):
TTGTATCGATACACTGCTCACTGTATCAATACA
Found at i:1396502 original size:20 final size:20
Alignment explanation
Indices: 1396477--1396574 Score: 117
Period size: 20 Copynumber: 4.8 Consensus size: 20
1396467 TGTATCGATA
1396477 CATTGTATCGATACATTGCT
1 CATTGTATCGATACATTGCT
*
1396497 CATTGTATCAATACATTGCT
1 CATTGTATCGATACATTGCT
* *
1396517 CATTGTATCGATACATTTCC
1 CATTGTATCGATACATTGCT
* *
1396537 CAGATGTATCGATACATT-TT
1 CA-TTGTATCGATACATTGCT
*
1396557 ACAATGTATCGATACATT
1 -CATTGTATCGATACATT
1396575 CAGGCAGTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
20 53 0.77
21 16 0.23
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (20 bp):
CATTGTATCGATACATTGCT
Found at i:1396513 original size:13 final size:13
Alignment explanation
Indices: 1396467--1396494 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1396457 CACTGTTCAC
1396467 TGTATCGATACAT
1 TGTATCGATACAT
1396480 TGTATCGATACAT
1 TGTATCGATACAT
1396493 TG
1 TG
1396495 CTCATTGTAT
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:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1396565 original size:41 final size:41
Alignment explanation
Indices: 1396475--1396574 Score: 123
Period size: 41 Copynumber: 2.5 Consensus size: 41
1396465 ACTGTATCGA
* *
1396475 TACATTGTATCGATACATTGCTCATTGTATCAATACATTGC
1 TACATTGTATCGATACATTGCCCAATGTATCAATACATTGC
* * *
1396516 T-CATTGTATCGATACATTTCCCAGATGTATCGATACATT-T
1 TACATTGTATCGATACATTGCCCA-ATGTATCAATACATTGC
*
1396556 TACAATGTATCGATACATT
1 TACATTGTATCGATACATT
1396575 CAGGCAGTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
40 21 0.41
41 30 0.59
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (41 bp):
TACATTGTATCGATACATTGCCCAATGTATCAATACATTGC
Found at i:1399014 original size:51 final size:51
Alignment explanation
Indices: 1398880--1399023 Score: 173
Period size: 51 Copynumber: 2.8 Consensus size: 51
1398870 TCACGGTTCC
* *
1398880 ATTTCCAAAACATCAATTTTTCTTAATCGGGGATACTCCAACT-CTAATTTT
1 ATTTCCAAAACATCAATTTTTCATAATCGGGGATACTCCAACTAC-GATTTT
* * * ** **
1398931 ATTTCTAAAGCATCGATTTACCGCAATCGGGGATACTCCAACTACGATTTT
1 ATTTCCAAAACATCAATTTTTCATAATCGGGGATACTCCAACTACGATTTT
* *
1398982 ATTTCCAAAACACCAATTTTTCATAATTGGGGATACTCCAAC
1 ATTTCCAAAACATCAATTTTTCATAATCGGGGATACTCCAAC
1399024 CCTGTTATTT
Statistics
Matches: 75, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
51 74 0.99
52 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.34
Consensus pattern (51 bp):
ATTTCCAAAACATCAATTTTTCATAATCGGGGATACTCCAACTACGATTTT
Found at i:1399035 original size:31 final size:28
Alignment explanation
Indices: 1399010--1399083 Score: 98
Period size: 28 Copynumber: 2.6 Consensus size: 28
1399000 TTTCATAATT
*
1399010 GGGGATACTCCAACCCTGTTATTTCATC
1 GGGGATACTCCAACCCCGTTATTTCATC
1399038 GGGGATACTCCAACCCCGTTATTT--TC
1 GGGGATACTCCAACCCCGTTATTTCATC
*
1399064 GAGGGGATACTTCAACCCCG
1 --GGGGATACTCCAACCCCG
1399084 GCTTTATGTC
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
26 2 0.05
28 40 0.95
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.27
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATTTCATC
Found at i:1399216 original size:108 final size:107
Alignment explanation
Indices: 1398959--1399238 Score: 380
Period size: 108 Copynumber: 2.6 Consensus size: 107
1398949 TACCGCAATC
** * *
1398959 GGGGATACTCCAACTACGATTTTATTTCCAAAACACCAATTTTTCATAATTGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCATAATTGGGGATACTCCAAC
* *
1399024 CCTGTTATTTCATCGGGGATACTCCAACCCCGTTATTTTCGA
66 CCCGTTATGTCATCGGGGATACTCCAACCCCGTTATTTTCGA
* ** * ** * * *
1399066 GGGGATACTTCAACCCCGGCTTTATGTCTAAAATATTGATTTTTTCATAATCGGGGATACTCCGA
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAATA-CCAATTTTTCATAATTGGGGATACTCCAA
*
1399131 CCCCGTTATGTCATCGGGGATACTCCAATCCCGTTATTTTCGA
65 CCCCGTTATGTCATCGGGGATACTCCAACCCCGTTATTTTCGA
* * *
1399174 GGGGATGCTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCACAATTAGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCATAATTGGGGATACTCCAAC
1399239 TTCGATTTTA
Statistics
Matches: 144, Mismatches: 28, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
107 50 0.35
108 94 0.65
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (107 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCATAATTGGGGATACTCCAAC
CCCGTTATGTCATCGGGGATACTCCAACCCCGTTATTTTCGA
Found at i:1399236 original size:51 final size:52
Alignment explanation
Indices: 1399175--1399294 Score: 156
Period size: 51 Copynumber: 2.3 Consensus size: 52
1399165 TATTTTCGAG
* *
1399175 GGGATGCTCCAACCCCGATTTTA-TTTCTAAAA-TACCAATTTT-TCACAATTA
1 GGGATACTCCAACCCCGATTTTATTTTC-AAAACT-CCAATTTTGTCACAATCA
** *
1399226 GGGATACTCCAACTTCGATTTTATTTTCAAAACTCCAATTTTGTCACAATCG
1 GGGATACTCCAACCCCGATTTTATTTTCAAAACTCCAATTTTGTCACAATCA
1399278 GGGATACTCCAACCCCG
1 GGGATACTCCAACCCCG
1399295 TTATTATCAT
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
51 32 0.54
52 27 0.46
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (52 bp):
GGGATACTCCAACCCCGATTTTATTTTCAAAACTCCAATTTTGTCACAATCA
Found at i:1399457 original size:78 final size:78
Alignment explanation
Indices: 1399226--1399528 Score: 346
Period size: 79 Copynumber: 3.8 Consensus size: 78
1399216 TTCACAATTA
* * * *
1399226 GGGATACTCCAACTTCGATTTTATTTTCAAAACTCCAATTTTGTCACAATCGGGGATACTCCAAC
1 GGGATACTCCAAC-CCGATTTTATTTTCAAAACACCGATTTT-CCACAATCGGGGATACTCCAAC
*
1399291 CCCGTTATTATC-ATG
64 CCCGTTATTTTCGA-G
* ** * **
1399306 AGGATACTCCAACCCCGACCTTA-TTTCTAAAGCATTGATTTTCCACAATCGGGGATACTCCAAC
1 GGGATACTCCAA-CCCGATTTTATTTTC-AAAACACCGATTTTCCACAATCGGGGATACTCCAAC
1399370 CCCGTTATTTTCGAG
64 CCCGTTATTTTCGAG
* *
1399385 GGGATACTCCAATCCCGATTTTATTTTC-AAACACCGATTTTCTATAATCAGGGG-TACTCCAAC
1 GGGATACTCCAA-CCCGATTTTATTTTCAAAACACCGATTTTCCACAATC-GGGGATACTCCAAC
* *
1399448 CCTGTTATTTCCGAG
64 CCCGTTATTTTCGAG
* *
1399463 GGGATACTCCAACCCTGATTTTATTTTCAAAACACCGATTTTCCATAATTGGGGATACTCC-ACC
1 GGGATACTCCAACCC-GATTTTATTTTCAAAACACCGATTTTCCACAATCGGGGATACTCCAACC
1399527 CC
65 CC
1399529 TATTGTTATC
Statistics
Matches: 190, Mismatches: 25, Indels: 18
0.82 0.11 0.08
Matches are distributed among these distances:
77 3 0.02
78 70 0.37
79 85 0.45
80 31 0.16
81 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.32
Consensus pattern (78 bp):
GGGATACTCCAACCCGATTTTATTTTCAAAACACCGATTTTCCACAATCGGGGATACTCCAACCC
CGTTATTTTCGAG
Found at i:1399517 original size:157 final size:158
Alignment explanation
Indices: 1399226--1399528 Score: 368
Period size: 157 Copynumber: 1.9 Consensus size: 158
1399216 TTCACAATTA
* * *
1399226 GGGATACTCCAACTTCGATTTTATTTTCAAAACTCCAATTTTGTCACAATCGGGGATACTCCAAC
1 GGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTCACAATCGGGGATACTCCAAC
* **
1399291 CCCGTTATTATCATGAGGATACTCCAACCCCGACCTTATTTCTAAAGCATTGATTTTCCACAATC
66 CCCGTTATTATCATGAGGATACTCCAACCCCGACCTTATTTCTAAAACACCGATTTTCCACAATC
1399356 GGGGATACTCCAACCCCGTTATTTTCGAG
131 GGGGATACTCC-ACCCCGTTATTTTCGAG
* *
1399385 GGGATACTCCAA-TCCCGATTTTATTTTC-AAACACCGATTTTCT-ATAATCAGGGG-TACTCCA
1 GGGATACTCCAACT-CCGATTTTATTTTCAAAACACCAATTTTCTCACAATC-GGGGATACTCCA
* * * **
1399446 ACCCTGTTATT-TCCGA-GGGGATACTCCAACCCTGATTTTATTT-TCAAAACACCGATTTTCCA
64 ACCCCGTTATTAT-C-ATGAGGATACTCCAACCCCGACCTTATTTCT-AAAACACCGATTTTCCA
* *
1399508 TAATTGGGGATACTCCACCCC
126 CAATCGGGGATACTCCACCCC
1399529 TATTGTTATC
Statistics
Matches: 124, Mismatches: 15, Indels: 13
0.82 0.10 0.09
Matches are distributed among these distances:
156 7 0.06
157 74 0.60
158 18 0.15
159 25 0.20
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.32
Consensus pattern (158 bp):
GGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTCACAATCGGGGATACTCCAAC
CCCGTTATTATCATGAGGATACTCCAACCCCGACCTTATTTCTAAAACACCGATTTTCCACAATC
GGGGATACTCCACCCCGTTATTTTCGAG
Found at i:1413374 original size:60 final size:60
Alignment explanation
Indices: 1413011--1413741 Score: 733
Period size: 61 Copynumber: 12.1 Consensus size: 60
1413001 AAGCAAGATG
* * *
1413011 CCTTTTAAAGGCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGTAGGACG------
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCTCAAAGAGCAGGACGCCTTCT
* ** *
1413066 CCTTTCAATGCCCACACAAGTTGGTGGCATTTTTTAGTCCTCAAAGAGCAGGACGCCTTCT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCA-CCTTCAGTCCTCAAAGAGCAGGACGCCTTCT
* * *
1413127 CCTTTTAAAGCCCACACGAGTTGGTGGCA-CTTCCCAGTCCTCAAAGAGCAGGACGCCTTCG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTT--CAGTCCTCAAAGAGCAGGACGCCTTCT
* * * * * * * *
1413188 CCTTTTAAAGCCCACACAAGTTGGTGGC-TCTTCCAATCCTCAAAAAAGTAAGATGCCTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTT-CAGTCCTC-AAAGAGCAGGACGCCTTCT
* ** * *
1413249 CCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAAAGCAGGACGCCTTCA
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTT-CAGTCCTCAAAGAGCAGGACGCCTTCT
* *
1413310 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCCTTCG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTCT
* *
1413370 CCTTTCAAAGCCCACACATGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGTCTTCGT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTC-T
* * *
1413431 -CTTTCAAAGCCCACACAAGCTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCCCTCT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTCT
* * * * * * *
1413490 CCTTTCAGAGCCCACAGAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGTAGGACACTTTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCAC-CTTC-AGTCCTCAAAGAGCAGGACGC-CTTCT
* * * * * *
1413553 CTTTTCAAAGCCCACACAAGTTGGTGGCACCTCTTAGTCTTCAAAGAGCAAGATGCCTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACCT-TCAGTCCTCAAAGAGCAGGACGCCTTCT
* * * * * * *
1413614 TCTTCTCAAAGTCCACACGAGTTGGTGGCACCTTTTAGTCCTTAAAAAGCAGGACGCCTTTT
1 CCTT-TCAAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCTCAAAGAGCAGGACGCCTTCT
* * * * * * * * *
1413676 CTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTAATCCTCGAAGAGTAGGATGCCTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCAC-CTTCAGTCCTCAAAGAGCAGGACGCCTTCT
1413737 CCTTT
1 CCTTT
1413742 TCTCCTTTAT
Statistics
Matches: 571, Mismatches: 84, Indels: 36
0.83 0.12 0.05
Matches are distributed among these distances:
55 47 0.08
59 3 0.01
60 167 0.29
61 227 0.40
62 96 0.17
63 31 0.05
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (60 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTCT
Found at i:1413839 original size:42 final size:43
Alignment explanation
Indices: 1413733--1413896 Score: 136
Period size: 42 Copynumber: 3.8 Consensus size: 43
1413723 GTAGGATGCC
* * * * **
1413733 TTTTCCTTTTCTCCTTTATCCTCAAAAAGCAAGACACATTTCA
1 TTTTCCTTTTTTCTTTTGTCCTCAAAAAGCAGGAGGCATTTCA
* * *
1413776 -TTTCCTTCATTTCCCTTTTGTCCTCAAAGAGCAGGGGGCACTTT-A
1 TTTTCCTT--TTT-TCTTTTGTCCTCAAAAAGCAGGAGGCA-TTTCA
* * *
1413821 TTTTCC-TTTTTCTTTTGTCTTCAAAAAGCAGGATGCATTTCG
1 TTTTCCTTTTTTCTTTTGTCCTCAAAAAGCAGGAGGCATTTCA
* * *
1413863 TTTTCCTTTTTTCCTTTGTCCTCGAAAAGTAGGA
1 TTTTCCTTTTTTCTTTTGTCCTCAAAAAGCAGGA
1413897 CGTACTCTTT
Statistics
Matches: 95, Mismatches: 19, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
41 3 0.03
42 35 0.37
43 26 0.27
44 2 0.02
45 21 0.22
46 8 0.08
ACGTcount: A:0.21, C:0.24, G:0.13, T:0.43
Consensus pattern (43 bp):
TTTTCCTTTTTTCTTTTGTCCTCAAAAAGCAGGAGGCATTTCA
Found at i:1413947 original size:41 final size:41
Alignment explanation
Indices: 1413901--1414003 Score: 120
Period size: 41 Copynumber: 2.5 Consensus size: 41
1413891 GTAGGACGTA
* *
1413901 CTCTTTTTCACTTTGTCCTCAAGAAACAGGACAC-TTTCCTT
1 CTCTTTTTC-CTTTGTCCTCAAGAAACAAGACACATTTCATT
* * * *
1413942 TTCTTTCTTCCTTTGTCCTCAAGGAGCAAGACCCATTTCATT
1 CTCTTT-TTCCTTTGTCCTCAAGAAACAAGACACATTTCATT
1413984 CTC-TTTTCCTTTGTCCTCAA
1 CTCTTTTTCCTTTGTCCTCAA
1414004 AAGTGGGACA
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
40 15 0.28
41 27 0.51
42 11 0.21
ACGTcount: A:0.18, C:0.30, G:0.10, T:0.42
Consensus pattern (41 bp):
CTCTTTTTCCTTTGTCCTCAAGAAACAAGACACATTTCATT
Found at i:1414662 original size:40 final size:40
Alignment explanation
Indices: 1414607--1414700 Score: 170
Period size: 40 Copynumber: 2.4 Consensus size: 40
1414597 TTTACCCTGA
1414607 TGTATCGATACATTTTGCATTATATCGATACATTGCTTAC
1 TGTATCGATACATTTTGCATTATATCGATACATTGCTTAC
*
1414647 TGTATCGATACATTTTGCATTGTATCGATACATTGCTTAC
1 TGTATCGATACATTTTGCATTATATCGATACATTGCTTAC
*
1414687 TGTATCAATACATT
1 TGTATCGATACATT
1414701 GTATCGATAC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.43
Consensus pattern (40 bp):
TGTATCGATACATTTTGCATTATATCGATACATTGCTTAC
Found at i:1414690 original size:20 final size:20
Alignment explanation
Indices: 1414629--1414701 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 20
1414619 TTTTGCATTA
1414629 TATCGATACATTGCTTACTG
1 TATCGATACATTGCTTACTG
*
1414649 TATCGATACATT--TTGCATTG
1 TATCGATACATTGCTT--ACTG
1414669 TATCGATACATTGCTTACTG
1 TATCGATACATTGCTTACTG
*
1414689 TATCAATACATTG
1 TATCGATACATTG
1414702 TATCGATACA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
18 2 0.04
20 42 0.91
22 2 0.04
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (20 bp):
TATCGATACATTGCTTACTG
Done.