Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold365
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: 1826335
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 9 of 11
Found at i:1389679 original size:80 final size:78
Alignment explanation
Indices: 1389450--1389887 Score: 381
Period size: 79 Copynumber: 5.5 Consensus size: 78
1389440 GAAAATAAAA
* *
1389450 ATGGGGTTGGAGTATCCCCTGAGATTAAAAAAAATCGAA-GTTTAGGAAATAAAAATGGGGTTGG
1 ATGGGGTTGGAGTAT-CCCTGAGA-T--GAAAAATTGAATGTTTAGGAAATAAAAA-GGGGTTGG
1389514 AGTATCCCCTCAAAAAT-
61 AGTATCCCCTCAAAAATG
* * * * *
1389531 AGTGGGATTGGAGTATCCCTGAGATGAAAATTTTG-GTGTTTTA-GAAGTAAACACGGGGTTGGA
1 A-TGGGGTTGGAGTATCCCTGAGATGAAAA-ATTGAATG-TTTAGGAAATAAA-AAGGGGTTGGA
*
1389594 GTATCCCTTCAAAAATG
62 GTATCCCCTCAAAAATG
*
1389611 GTGGGGTTGGAGTATCGCCTGAGATGAAAAATTGAATGTTTAGGAAATAAAAAGGAGGTTGGAGT
1 ATGGGGTTGGAGTATC-CCTGAGATGAAAAATTGAATGTTTAGGAAATAAAAAGG-GGTTGGAGT
*
1389676 ATCCCCTCAGAAATG
64 ATCCCCTCAAAAATG
* * * * * * **
1389691 ATAGGGTTGGAATATCTCTGAGATAAAAAATTCAATGTTTGGGAAA-AAAAATGGGGTTACAGTA
1 ATGGGGTTGGAGTATCCCTGAGATGAAAAATTGAATGTTTAGGAAATAAAAA-GGGGTTGGAGTA
1389755 T-CCCT-ATGAAAATG
65 TCCCCTCA--AAAATG
** * * * * * *
1389769 ATGGGGTTAAAGTATCCCTAAGATGAAAAATTTG-GTGTTTGGGAATTAAAAATGAGGTTGGAGC
1 ATGGGGTTGGAGTATCCCTGAGATGAAAAA-TTGAATGTTTAGGAAATAAAAA-GGGGTTGGAGT
*
1389833 ATCCCCTCGAAAATG
64 ATCCCCTCAAAAATG
* ** *
1389848 ATGGTGTTGGAGTATCCCCAAGGTGAAAAATTCG-ATGTTT
1 ATGGGGTTGGAGTATCCCTGAGATGAAAAATT-GAATGTTT
1389888 TAGAAGTGAA
Statistics
Matches: 292, Mismatches: 47, Indels: 38
0.77 0.12 0.10
Matches are distributed among these distances:
76 1 0.00
77 4 0.01
78 58 0.20
79 140 0.48
80 67 0.23
81 9 0.03
82 13 0.04
ACGTcount: A:0.34, C:0.11, G:0.27, T:0.28
Consensus pattern (78 bp):
ATGGGGTTGGAGTATCCCTGAGATGAAAAATTGAATGTTTAGGAAATAAAAAGGGGTTGGAGTAT
CCCCTCAAAAATG
Found at i:1392767 original size:13 final size:13
Alignment explanation
Indices: 1392749--1392775 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1392739 ACATTATGGT
1392749 TTGTATCGATACA
1 TTGTATCGATACA
1392762 TTGTATCGATACA
1 TTGTATCGATACA
1392775 T
1 T
1392776 GTACAATTGT
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:1400838 original size:13 final size:13
Alignment explanation
Indices: 1400820--1400845 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1400810 ACATTATGCT
1400820 TTGTATCGATACA
1 TTGTATCGATACA
1400833 TTGTATCGATACA
1 TTGTATCGATACA
1400846 CGTTCATTGT
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):
TTGTATCGATACA
Found at i:1400876 original size:20 final size:19
Alignment explanation
Indices: 1400830--1400885 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
1400820 TTGTATCGAT
* *
1400830 ACATTGTATCGATACACGT
1 ACATTGTATCGATACATGC
*
1400849 TCATTGTATCGATACATGC
1 ACATTGTATCGATACATGC
1400868 ACAATTGTATCGATACAT
1 AC-ATTGTATCGATACAT
1400886 AAAACTGGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:1407700 original size:20 final size:20
Alignment explanation
Indices: 1407654--1407724 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
1407644 AACCATTATT
*
1407654 TGTATCGATACACA-TGAAAA
1 TGTATCGATACA-ATTCAAAA
*
1407674 T-TATCGATACAATTCAGAA
1 TGTATCGATACAATTCAAAA
*
1407693 TGTATCGATAC-ATCCATAAA
1 TGTATCGATACAATTCA-AAA
1407713 TGTATCGATACA
1 TGTATCGATACA
1407725 TTGAGTTTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
18 1 0.02
19 19 0.44
20 23 0.53
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.30
Consensus pattern (20 bp):
TGTATCGATACAATTCAAAA
Found at i:1410082 original size:70 final size:69
Alignment explanation
Indices: 1409979--1410118 Score: 226
Period size: 70 Copynumber: 2.0 Consensus size: 69
1409969 GGCTCTCAAA
* * * *
1409979 ATGTGTGCCTGTTGCTACTAATGATGACTTGTCTTGGTTATGGCATAGAATACTAGGACATGCTA
1 ATGTGTGCCTGCTACTAATAATGATGACTTGTCTTGGTTATGGCATAGAAGACTAGGACATGCTA
1410044 GTAT
66 GTAT
*
1410048 ATGTGTGCCTTGCTACTAATAATGATGACTTGTCTTGGTTTTGGCATAGAAGACTAGGACATGCT
1 ATGTGTGCC-TGCTACTAATAATGATGACTTGTCTTGGTTATGGCATAGAAGACTAGGACATGCT
1410113 AGTAT
65 AGTAT
1410118 A
1 A
1410119 AATGTTTTCT
Statistics
Matches: 65, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
69 9 0.14
70 56 0.86
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (69 bp):
ATGTGTGCCTGCTACTAATAATGATGACTTGTCTTGGTTATGGCATAGAAGACTAGGACATGCTA
GTAT
Found at i:1414840 original size:19 final size:19
Alignment explanation
Indices: 1414797--1414889 Score: 125
Period size: 19 Copynumber: 4.8 Consensus size: 19
1414787 CACACCCAAA
* * *
1414797 TGTATCGATACGTTATGCTT
1 TGTATCGATACATGAT-CAT
1414817 TGTATCGATACATGATCAT
1 TGTATCGATACATGATCAT
1414836 TGTATCGATACATGATCAT
1 TGTATCGATACATGATCAT
1414855 TGTATCGATACATGGA-CAAT
1 TGTATCGATACAT-GATC-AT
1414875 TGTATCGATACATGA
1 TGTATCGATACATGA
1414890 AACTGGCAGT
Statistics
Matches: 68, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
19 37 0.54
20 31 0.46
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (19 bp):
TGTATCGATACATGATCAT
Found at i:1414846 original size:39 final size:39
Alignment explanation
Indices: 1414797--1414889 Score: 127
Period size: 39 Copynumber: 2.4 Consensus size: 39
1414787 CACACCCAAA
* * *
1414797 TGTATCGATACGTTATGCTTTGTATCGATACAT-GATC-AT
1 TGTATCGATACATGAT-CATTGTATCGATACATGGA-CAAT
1414836 TGTATCGATACATGATCATTGTATCGATACATGGACAAT
1 TGTATCGATACATGATCATTGTATCGATACATGGACAAT
1414875 TGTATCGATACATGA
1 TGTATCGATACATGA
1414890 AACTGGCAGT
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
38 16 0.33
39 33 0.67
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (39 bp):
TGTATCGATACATGATCATTGTATCGATACATGGACAAT
Found at i:1414956 original size:13 final size:13
Alignment explanation
Indices: 1414934--1414963 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1414924 GATACATAGG
1414934 ACATTATATCGAT
1 ACATTATATCGAT
*
1414947 ACATTGTATCGAT
1 ACATTATATCGAT
1414960 ACAT
1 ACAT
1414964 GATGGACTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (13 bp):
ACATTATATCGAT
Found at i:1414959 original size:33 final size:33
Alignment explanation
Indices: 1414917--1414985 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
1414907 CTACCACTGT
1414917 TTGTATCGATACAT-A-GGACATTATATCGATACA
1 TTGTATCGATACATGATGGAC--TATATCGATACA
*
1414950 TTGTATCGATACATGATGGACTGTATCGATACA
1 TTGTATCGATACATGATGGACTATATCGATACA
1414983 TTG
1 TTG
1414986 CTTGTAACAG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
33 28 0.85
34 1 0.03
35 4 0.12
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (33 bp):
TTGTATCGATACATGATGGACTATATCGATACA
Found at i:1421105 original size:13 final size:13
Alignment explanation
Indices: 1421087--1421112 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1421077 AAAACCCAAA
1421087 TGTATCGATACAT
1 TGTATCGATACAT
1421100 TGTATCGATACAT
1 TGTATCGATACAT
1421113 GGATTACTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1423813 original size:13 final size:13
Alignment explanation
Indices: 1423795--1423824 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1423785 AATACATAAG
*
1423795 ACATTGTATCGGT
1 ACATTGTATCGAT
1423808 ACATTGTATCGAT
1 ACATTGTATCGAT
1423821 ACAT
1 ACAT
1423825 GATGGATTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.37
Consensus pattern (13 bp):
ACATTGTATCGAT
Found at i:1426768 original size:7 final size:7
Alignment explanation
Indices: 1426758--1426796 Score: 62
Period size: 7 Copynumber: 5.6 Consensus size: 7
1426748 AAGAACATAG
1426758 AAAAAAC
1 AAAAAAC
1426765 AAAATAAC
1 AAAA-AAC
1426773 AAAAAAC
1 AAAAAAC
1426780 AAAAAAC
1 AAAAAAC
1426787 -AAAAAC
1 AAAAAAC
1426793 AAAA
1 AAAA
1426797 GACTTGTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 6 0.20
7 17 0.57
8 7 0.23
ACGTcount: A:0.85, C:0.13, G:0.00, T:0.03
Consensus pattern (7 bp):
AAAAAAC
Found at i:1426776 original size:14 final size:14
Alignment explanation
Indices: 1426758--1426796 Score: 62
Period size: 15 Copynumber: 2.8 Consensus size: 14
1426748 AAGAACATAG
1426758 AAAAAACAAAATAAC
1 AAAAAACAAAA-AAC
1426773 AAAAAACAAAAAAC
1 AAAAAACAAAAAAC
1426787 -AAAAACAAAA
1 AAAAAACAAAA
1426797 GACTTGTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 10 0.42
14 3 0.12
15 11 0.46
ACGTcount: A:0.85, C:0.13, G:0.00, T:0.03
Consensus pattern (14 bp):
AAAAAACAAAAAAC
Found at i:1437575 original size:50 final size:50
Alignment explanation
Indices: 1437457--1437601 Score: 254
Period size: 50 Copynumber: 2.9 Consensus size: 50
1437447 TTTTAACTAG
1437457 ATGTATCGATACATTGAAGAATGTATCGATACATCTAGGTAACAAGACAGA
1 ATGTATCGATACATTGAAGAATGTATCGATACATCTAGGTAA-AAGACAGA
*
1437508 ATGTATCGATACATTGAAGAATGTATCGATGCATCTAGGTAAAAGACAGA
1 ATGTATCGATACATTGAAGAATGTATCGATACATCTAGGTAAAAGACAGA
* *
1437558 ATGTATCGATACATTGAAAAATGTATCAATACATCTAGGTAAAA
1 ATGTATCGATACATTGAAGAATGTATCGATACATCTAGGTAAAA
1437602 ATGTGACTTT
Statistics
Matches: 90, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
50 49 0.54
51 41 0.46
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (50 bp):
ATGTATCGATACATTGAAGAATGTATCGATACATCTAGGTAAAAGACAGA
Found at i:1439845 original size:28 final size:27
Alignment explanation
Indices: 1439804--1439883 Score: 108
Period size: 28 Copynumber: 2.9 Consensus size: 27
1439794 TTTTAGAGGT
*
1439804 AAAAAACAGTGTTGGAGTATCCCCTCA
1 AAAAAACAGGGTTGGAGTATCCCCTCA
1439831 AAAACAACAGGGTTGGAGTATCCCCTCA
1 AAAA-AACAGGGTTGGAGTATCCCCTCA
*
1439859 AAAATAAC-GAGGTTAGAGTATCCCC
1 AAAA-AACAG-GGTTGGAGTATCCCC
1439884 GATGGTGAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
27 5 0.10
28 43 0.90
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.20
Consensus pattern (27 bp):
AAAAAACAGGGTTGGAGTATCCCCTCA
Found at i:1439926 original size:78 final size:79
Alignment explanation
Indices: 1439842--1440015 Score: 253
Period size: 78 Copynumber: 2.2 Consensus size: 79
1439832 AAACAACAGG
*
1439842 GTTGGAGTATCCCCTCAAAAATAACGAGGTTAGAGTATCCCCGATGGT-GAAAATTGATA-TTTG
1 GTTGGAGTATCCCCTCAAAAATAACGAGGTTAGAGTATCCCCGATGGTAAAAAATTGATATTTTG
1439905 GAAATAAAAAACGGA
66 GAAAT-AAAAACGGA
* * *
1439920 GTTGGAGTATCCCCTCGAAAATGACGAGGTTGGAGTATCCCCGATGGTAAAAAATTGATATTTTG
1 GTTGGAGTATCCCCTCAAAAATAACGAGGTTAGAGTATCCCCGATGGTAAAAAATTGATATTTTG
* *
1439985 GGAATAAAAACGGG
66 GAAATAAAAACGGA
**
1439999 GTTAAAGTATCCCCTCA
1 GTTGGAGTATCCCCTCA
1440016 TAATTGATGG
Statistics
Matches: 85, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
78 45 0.53
79 32 0.38
80 8 0.09
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (79 bp):
GTTGGAGTATCCCCTCAAAAATAACGAGGTTAGAGTATCCCCGATGGTAAAAAATTGATATTTTG
GAAATAAAAACGGA
Found at i:1440013 original size:79 final size:77
Alignment explanation
Indices: 1439847--1440039 Score: 237
Period size: 78 Copynumber: 2.5 Consensus size: 77
1439837 ACAGGGTTGG
* * *
1439847 AGTATCCCCTCAAAAATAACGAGGTTAGAGTATCCCCGATGGTGAAAATTGATATTTGGAAATAA
1 AGTATCCCCTC-AAAATGACGAGGTTGGAGTATCCCCGATGGTAAAAATTGATATTTGGAAATAA
**
1439912 AAAACGGAGTTGG
65 AAAACGGAGTTAA
*
1439925 AGTATCCCCTCGAAAATGACGAGGTTGGAGTATCCCCGATGGTAAAAAATTGATATTTTGGGAAT
1 AGTATCCCCTC-AAAATGACGAGGTTGGAGTATCCCCGATGGT-AAAAATTGATA-TTTGGAAAT
*
1439990 -AAAAACGGGGTTAA
63 AAAAAACGGAGTTAA
* * *
1440004 AGTATCCCCTCATAATTGATGGGGTTGGA-TATCCCC
1 AGTATCCCCTCA-AAATGACGAGGTTGGAGTATCCCC
1440040 TCGGAAATAA
Statistics
Matches: 101, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
78 48 0.48
79 45 0.45
80 8 0.08
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (77 bp):
AGTATCCCCTCAAAATGACGAGGTTGGAGTATCCCCGATGGTAAAAATTGATATTTGGAAATAAA
AAACGGAGTTAA
Found at i:1440028 original size:28 final size:28
Alignment explanation
Indices: 1439996--1440064 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 28
1439986 GAATAAAAAC
* * * *
1439996 GGGGTTAAAGTATCCCCTCATAATTGAT
1 GGGGTTAGAGTATCCCCTCAGAAATAAT
* *
1440024 GGGGTTGGA-TATCCCCTCGGAAATAAT
1 GGGGTTAGAGTATCCCCTCAGAAATAAT
1440051 GGGGTTAGAGTATC
1 GGGGTTAGAGTATC
1440065 TTCGAAGGTG
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
27 22 0.67
28 11 0.33
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (28 bp):
GGGGTTAGAGTATCCCCTCAGAAATAAT
Found at i:1440148 original size:186 final size:185
Alignment explanation
Indices: 1439840--1440187 Score: 468
Period size: 186 Copynumber: 1.9 Consensus size: 185
1439830 AAAAACAACA
* * *
1439840 GGGTTGGAGTATCCCCTCAAAAATAACGAGGTTAGAGTATCCCCGATGGTGAAAATTGATATTTG
1 GGGTTGGAGTATCCCCTCAAAAATAACGAGGTTAGAGTATCCCCGAAGGTGAAAATCGATATTTA
** * *
1439905 GAAATAAAAAACGGAGTTGGAGTATCCCCTCGAAAATGACGAGGTTGGAGTATCCCCGATGGTAA
66 GAAATAAAAAACGGAGTTGGAGTATCCCCTCGAAAACAACGAAGTTAGAGTATCCCCGATGGTAA
1439970 AAAATTGATATTTTGGGAATAAAAACGGGGTTAAAGTATCCCCTCATAATTGATG
131 AAAATTGATATTTTGGGAATAAAAACGGGGTTAAAGTATCCCCTCATAATTGATG
** * * **
1440025 GGGTTGGA-TATCCCCTCGGAAATAATGGGGTTAGAGTATCTTCGAAGGTGAAAAATCGATATTT
1 GGGTTGGAGTATCCCCTCAAAAATAACGAGGTTAGAGTATCCCCGAAGGTG-AAAATCGATA-TT
* * * *
1440089 TAGAAATGGAAAAAA-GG-GTTGGAGTATCTCTTCGGAAACAATGAAGTTAGAGTATCCCCGATG
64 TAGAAAT--AAAAAACGGAGTTGGAGTATCCCCTCGAAAACAACGAAGTTAGAGTATCCCCGATG
* *
1440152 GTGAAAATTTGATATTTTGGGAATAAAAACGGGGTT
127 GTAAAAAATTGATATTTTGGGAATAAAAACGGGGTT
1440188 TATCCCCTAA
Statistics
Matches: 140, Mismatches: 19, Indels: 7
0.84 0.11 0.04
Matches are distributed among these distances:
184 35 0.25
185 17 0.12
186 80 0.57
187 2 0.01
188 6 0.04
ACGTcount: A:0.34, C:0.13, G:0.26, T:0.27
Consensus pattern (185 bp):
GGGTTGGAGTATCCCCTCAAAAATAACGAGGTTAGAGTATCCCCGAAGGTGAAAATCGATATTTA
GAAATAAAAAACGGAGTTGGAGTATCCCCTCGAAAACAACGAAGTTAGAGTATCCCCGATGGTAA
AAAATTGATATTTTGGGAATAAAAACGGGGTTAAAGTATCCCCTCATAATTGATG
Found at i:1447204 original size:32 final size:33
Alignment explanation
Indices: 1447142--1447205 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
1447132 CACACCCAGA
*
1447142 TGTATCGATACATATTGCTTTGTATCGATACAT
1 TGTATCGATACATATTGCTTGGTATCGATACAT
*
1447175 TGTATTGATACATATT-CTTGGTATCGATACA
1 TGTATCGATACATATTGCTTGGTATCGATACA
1447206 CAGTGAATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATATTGCTTGGTATCGATACAT
Found at i:1448232 original size:15 final size:15
Alignment explanation
Indices: 1448208--1448249 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 15
1448198 TTAAAAAAAG
1448208 AATAATTAAAAATGTT
1 AATAA-TAAAAATGTT
1448224 AATAATAAAAAT-TT
1 AATAATAAAAATGTT
1448238 AAT--TAAAAATGT
1 AATAATAAAAATGT
1448250 ATATGTCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 7 0.28
13 1 0.04
14 5 0.20
15 7 0.28
16 5 0.20
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.36
Consensus pattern (15 bp):
AATAATAAAAATGTT
Found at i:1448239 original size:14 final size:16
Alignment explanation
Indices: 1448208--1448240 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1448198 TTAAAAAAAG
1448208 AATAATTAAAAATGTT
1 AATAATTAAAAATGTT
1448224 AATAA-TAAAAAT-TT
1 AATAATTAAAAATGTT
1448238 AAT
1 AAT
1448241 TAAAAATGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 7 0.41
16 5 0.29
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
AATAATTAAAAATGTT
Found at i:1450363 original size:43 final size:42
Alignment explanation
Indices: 1450315--1450547 Score: 152
Period size: 43 Copynumber: 5.5 Consensus size: 42
1450305 GATTGAACTA
* *
1450315 ACAAGTCAACAAAGGATAAAAGGATTTACTTGAGACTAAGCCG
1 ACAAGTAAACAAAGGATAAAAGGATTTAC-CGAGACTAAGCCG
* ** * *
1450358 ACAAGTAAATAAAGGATGGAA-GAGTTAACCGAGATTGAA-CCG
1 ACAAGTAAACAAAGGATAAAAGGA-TTTACCGAGACT-AAGCCG
* * * **
1450400 ACAGGTCAACAAAGAATAAAAGGATTTACCCGAGACCCAGCCG
1 ACAAGTAAACAAAGGATAAAAGGATTTA-CCGAGACTAAGCCG
* * * * **
1450443 ATAAGTAAATAAAGGATAAAAAGG-TTGACTG-GGTTGAA-CCG
1 ACAAGTAAACAAAGGAT-AAAAGGATTTACCGAGACT-AAGCCG
* * * * * *
1450484 AGAAGTCAATAAAGGATAAAAGGATTTACCCAAGGCTAAGCTG
1 ACAAGTAAACAAAGGATAAAAGGATTTA-CCGAGACTAAGCCG
1450527 ACAAGTAAACAAAGGATAAAA
1 ACAAGTAAACAAAGGATAAAA
1450548 AAGTTGACCG
Statistics
Matches: 141, Mismatches: 38, Indels: 22
0.70 0.19 0.11
Matches are distributed among these distances:
40 6 0.04
41 22 0.16
42 35 0.25
43 72 0.51
44 6 0.04
ACGTcount: A:0.46, C:0.15, G:0.23, T:0.17
Consensus pattern (42 bp):
ACAAGTAAACAAAGGATAAAAGGATTTACCGAGACTAAGCCG
Found at i:1450375 original size:85 final size:84
Alignment explanation
Indices: 1450262--1450552 Score: 289
Period size: 85 Copynumber: 3.4 Consensus size: 84
1450252 GGGTTACCTA
* * * * * **
1450262 AGACTAAACCGATAGGTAAACAAGGGATGAAAGAGTTAGCCAGGATTGAACTAACAAGTCAACAA
1 AGACTAAGCCGACAAGTAAACAAAGGATGAAAAAGTTAGCC-GGATTGAACCGACAAGTCAACAA
**
1450327 AGGATAAAAGGATTTACTTG
65 AGGATAAAAGGATTTACCCG
* * * * *
1450347 AGACTAAGCCGACAAGTAAATAAAGGATGGAAGAGTTAACCGAGATTGAACCGACAGGTCAACAA
1 AGACTAAGCCGACAAGTAAACAAAGGATGAAAAAGTTAGCCG-GATTGAACCGACAAGTCAACAA
*
1450412 AGAATAAAAGGATTTACCCG
65 AGGATAAAAGGATTTACCCG
** * * * * * *
1450432 AGACCCAGCCGATAAGTAAATAAAGGAT-AAAAAGGTT-GACTGGGTTGAACCGAGAAGTCAATA
1 AGACTAAGCCGACAAGTAAACAAAGGATGAAAAA-GTTAG-CCGGATTGAACCGACAAGTCAACA
*
1450495 AAGGATAAAAGGATTTACCCA
64 AAGGATAAAAGGATTTACCCG
* * *
1450516 AGGCTAAGCTGACAAGTAAACAAAGGATAAAAAAGTT
1 AGACTAAGCCGACAAGTAAACAAAGGATGAAAAAGTT
1450553 GACCGAGGCA
Statistics
Matches: 170, Mismatches: 32, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
84 65 0.38
85 105 0.62
ACGTcount: A:0.45, C:0.14, G:0.23, T:0.17
Consensus pattern (84 bp):
AGACTAAGCCGACAAGTAAACAAAGGATGAAAAAGTTAGCCGGATTGAACCGACAAGTCAACAAA
GGATAAAAGGATTTACCCG
Found at i:1450513 original size:84 final size:85
Alignment explanation
Indices: 1450305--1450559 Score: 298
Period size: 84 Copynumber: 3.0 Consensus size: 85
1450295 AGTTAGCCAG
** **
1450305 GATTGAACTAACAAGTCAACAAAGGATAAAAGGATTTACTTGAGACTAAGCCGACAAGTAAATAA
1 GATTGAACCGACAAGTCAACAAAGGATAAAAGGATTTACCCGAGACTAAGCCGACAAGTAAATAA
** *
1450370 AGGAT-GGAAGAGTTAACCGA
66 AGGATAAAAAG-GTTGACCGA
* * ** *
1450390 GATTGAACCGACAGGTCAACAAAGAATAAAAGGATTTACCCGAGACCCAGCCGATAAGTAAATAA
1 GATTGAACCGACAAGTCAACAAAGGATAAAAGGATTTACCCGAGACTAAGCCGACAAGTAAATAA
*
1450455 AGGATAAAAAGGTTGACTG-
66 AGGATAAAAAGGTTGACCGA
* * * * * * *
1450474 GGTTGAACCGAGAAGTCAATAAAGGATAAAAGGATTTACCCAAGGCTAAGCTGACAAGTAAACAA
1 GATTGAACCGACAAGTCAACAAAGGATAAAAGGATTTACCCGAGACTAAGCCGACAAGTAAATAA
*
1450539 AGGATAAAAAAGTTGACCGA
66 AGGATAAAAAGGTTGACCGA
1450559 G
1 G
1450560 GCAAAACTAA
Statistics
Matches: 141, Mismatches: 27, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
84 70 0.50
85 68 0.48
86 3 0.02
ACGTcount: A:0.45, C:0.15, G:0.23, T:0.17
Consensus pattern (85 bp):
GATTGAACCGACAAGTCAACAAAGGATAAAAGGATTTACCCGAGACTAAGCCGACAAGTAAATAA
AGGATAAAAAGGTTGACCGA
Found at i:1450607 original size:41 final size:41
Alignment explanation
Indices: 1450550--1450735 Score: 141
Period size: 41 Copynumber: 4.7 Consensus size: 41
1450540 GGATAAAAAA
* * *
1450550 GTTGACCGAGGCAAAACTAATAAAGCCAACGGGTTAGAAGG
1 GTTGACCAAGGCAAAACCAATAAAGCCAACGGGTTAGAAAG
* * *
1450591 GTTGACCAAAGCAAAACCGATAAAGTCAAC---TT-GAAAG
1 GTTGACCAAGGCAAAACCAATAAAGCCAACGGGTTAGAAAG
* * * *
1450628 GTTGGCCACGACAAAACCAATAAAACCAACGGGTTAGAAAG
1 GTTGACCAAGGCAAAACCAATAAAGCCAACGGGTTAGAAAG
* * ** * ***
1450669 GTTAACTAAGGCAAAATTAATAAAGTCAACTAATT-GAAAG
1 GTTGACCAAGGCAAAACCAATAAAGCCAACGGGTTAGAAAG
* *
1450709 GTT-AGCAAGGGCAAAACCGATAAAGCC
1 GTTGACCAA-GGCAAAACCAATAAAGCC
1450736 TATAGATTAG
Statistics
Matches: 109, Mismatches: 31, Indels: 11
0.72 0.21 0.07
Matches are distributed among these distances:
37 27 0.25
38 2 0.02
39 3 0.03
40 24 0.22
41 53 0.49
ACGTcount: A:0.44, C:0.18, G:0.22, T:0.16
Consensus pattern (41 bp):
GTTGACCAAGGCAAAACCAATAAAGCCAACGGGTTAGAAAG
Found at i:1450979 original size:40 final size:39
Alignment explanation
Indices: 1450933--1451083 Score: 117
Period size: 40 Copynumber: 3.8 Consensus size: 39
1450923 GTTGATCAGG
*
1450933 GTGAAACTAATAAAGTCAACCAATTGAAAGGTTGGCCAC
1 GTGAAACCAATAAAGTCAACCAATTGAAAGGTTGGCCAC
* * * * *
1450972 GTCGAAACCGAT-AAGTCAA-TAGTTTAGAAAGGTTGACCAAG
1 GT-GAAACCAATAAAGTCAACCA-ATT-GAAAGGTTGGCC-AC
* * * *
1451013 GTAAAACCAATAGAGTCAACCAATTGAAATGTTGGCCAGG
1 GTGAAACCAATAAAGTCAACCAATTGAAAGGTTGGCCA-C
* * * *
1451053 GTGAAACCGATAAAGCCAACGAATTAAAAGG
1 GTGAAACCAATAAAGTCAACCAATTGAAAGG
1451084 AGCTAGACCA
Statistics
Matches: 85, Mismatches: 20, Indels: 13
0.72 0.17 0.11
Matches are distributed among these distances:
38 1 0.01
39 12 0.14
40 60 0.71
41 11 0.13
42 1 0.01
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.19
Consensus pattern (39 bp):
GTGAAACCAATAAAGTCAACCAATTGAAAGGTTGGCCAC
Found at i:1451006 original size:129 final size:130
Alignment explanation
Indices: 1450686--1451041 Score: 358
Period size: 129 Copynumber: 2.8 Consensus size: 130
1450676 AAGGCAAAAT
* * *
1450686 TAATAAAGTCAACTAATTGAAAGGTTAG-CAAGGGCAAAACCGATAAAGCCTATAGATTAGAAGG
1 TAATAAAGTCAACCAATTGAAAGGTTGGCCAA-GGCAAAACCGATAAAGCCAATAG-TTAGAAGG
* * *
1450750 GTTGACTAGGGTGAAACTGATAAAGTC-A--AA-TGAAAATGAAAAGGGTTTGACCATGGTGGTA
64 GTTGACTAGGGTGAAACTGATAGAGTCAACCAATTGAAAATGAAAAGGGTTTGACCAGGGTGGAA
1450811 AC
129 AC
* * * *
1450813 TAATACAGTCAAACGA--GAAAGGTTGGCCAAGGCAAAACCGATAAAGCCAACAAGTT-GAAGGG
1 TAATAAAGTCAACCAATTGAAAGGTTGGCCAAGGCAAAACCGATAAAGCCAA-TAGTTAGAAGGG
* * * *
1450875 TTGACTAGGGTGAAACTGATAGAGCCAACCAATTGAAAGGTTAGAAA-GG-TTGATCAGGGT-GA
65 TTGACTAGGGTGAAACTGATAGAGTCAACCAATTGAAA-ATGA-AAAGGGTTTGACCAGGGTGGA
1450937 AAC
128 AAC
* * * * *
1450940 TAATAAAGTCAACCAATTGAAAGGTTGGCCACGTCGAAACCGAT-AAGTCAATAGTTTAGAAAGG
1 TAATAAAGTCAACCAATTGAAAGGTTGGCCAAGGCAAAACCGATAAAGCCAATAG-TTAGAAGGG
* * * **
1451004 TTGACCAAGGTAAAACCAATAGAGTCAACCAATTGAAA
65 TTGACTAGGGTGAAACTGATAGAGTCAACCAATTGAAA
1451042 TGTTGGCCAG
Statistics
Matches: 188, Mismatches: 29, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
124 30 0.16
125 31 0.16
126 5 0.03
127 33 0.18
128 22 0.12
129 64 0.34
130 3 0.02
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (130 bp):
TAATAAAGTCAACCAATTGAAAGGTTGGCCAAGGCAAAACCGATAAAGCCAATAGTTAGAAGGGT
TGACTAGGGTGAAACTGATAGAGTCAACCAATTGAAAATGAAAAGGGTTTGACCAGGGTGGAAAC
Found at i:1451048 original size:80 final size:80
Alignment explanation
Indices: 1450915--1451065 Score: 223
Period size: 80 Copynumber: 1.9 Consensus size: 80
1450905 AATTGAAAGG
* * * *
1450915 TTAGAAAGGTTGATCAGGGTGAAACTAATAAAGTCAACCAATTGAAAGGTTGGCCA-CGTCGAAA
1 TTAGAAAGGTTGACCAAGGTAAAACCAATAAAGTCAACCAATTGAAAGGTTGGCCAGCGT-GAAA
1450979 CCGATAAGTCAATAGT
65 CCGATAAGTCAATAGT
* * *
1450995 TTAGAAAGGTTGACCAAGGTAAAACCAATAGAGTCAACCAATTGAAATGTTGGCCAGGGTGAAAC
1 TTAGAAAGGTTGACCAAGGTAAAACCAATAAAGTCAACCAATTGAAAGGTTGGCCAGCGTGAAAC
1451060 CGATAA
66 CGATAA
1451066 AGCCAACGAA
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
80 61 0.97
81 2 0.03
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (80 bp):
TTAGAAAGGTTGACCAAGGTAAAACCAATAAAGTCAACCAATTGAAAGGTTGGCCAGCGTGAAAC
CGATAAGTCAATAGT
Found at i:1451083 original size:80 final size:80
Alignment explanation
Indices: 1450915--1451083 Score: 200
Period size: 80 Copynumber: 2.1 Consensus size: 80
1450905 AATTGAAAGG
* * * *
1450915 TTAGAAAGGTTGATCAGGGTGAAACTAATAAAGTCAACCAATTGAAAGGTTGGCCACGTCGAAAC
1 TTAGAAAGGTTGACCAAGGTAAAACCAATAAAGTCAACCAATTGAAAGGTTGGCCACGTCGAAAC
* * *
1450980 CGATAAGTCAATAGT
66 CGATAAGCCAAGAGA
* * *
1450995 TTAGAAAGGTTGACCAAGGTAAAACCAATAGAGTCAACCAATTGAAATGTTGGCCAGGGT-GAAA
1 TTAGAAAGGTTGACCAAGGTAAAACCAATAAAGTCAACCAATTGAAAGGTTGGCCA-CGTCGAAA
1451059 CCGATAAAGCCAACGA-A
65 CCGAT-AAGCCAA-GAGA
1451076 TTA-AAAGG
1 TTAGAAAGG
1451084 AGCTAGACCA
Statistics
Matches: 76, Mismatches: 10, Indels: 6
0.83 0.11 0.07
Matches are distributed among these distances:
80 64 0.84
81 11 0.14
82 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (80 bp):
TTAGAAAGGTTGACCAAGGTAAAACCAATAAAGTCAACCAATTGAAAGGTTGGCCACGTCGAAAC
CGATAAGCCAAGAGA
Found at i:1452635 original size:88 final size:85
Alignment explanation
Indices: 1452442--1452837 Score: 295
Period size: 88 Copynumber: 4.6 Consensus size: 85
1452432 TGATACGAAT
* * * *
1452442 GCAAGCATCAATAAAGAGGCAAATGCCTATGAAATGA--T--A--CTAATGTCATATAAAATGCA
1 GCAAGCATCAATAAATA-GCAAATGCATATGAAATGATGTAAATGCCAATGTCATCT-AAATGCA
* *
1452501 AATGTGCATGAAACAATGTAAAT-
64 AATGTGCATGAAA-GATG-CAATC
* ** * * * *
1452524 GCAAGCAACCGTAAAGTGGCAAATGCATAT-AAGATGATGTAAATGCCAATATTAACTAACATGC
1 GCAAGCATCAATAAA-TAGCAAATGCATATGAA-ATGATGTAAATGCCAATGTCATCTAA-ATGC
*
1452588 AGATGTGCATGAAATGATGCAATC
63 AAATGTGCATGAAA-GATGCAATC
* * * * * *
1452612 GCAAGCTTCAATCAAATAACAAATGCCTATTAAATGATGTATATGCTAATGTCATCTAAAGTGCA
1 GCAAGCATCAAT-AAATAGCAAATGCATATGAAATGATGTAAATGCCAATGTCATCTAAA-TGC-
* *
1452677 AAATGTGCATGAAAGAAGCAATG
63 AAATGTGCATGAAAGATGCAATC
* * *** * * *
1452700 GTAAGCATCCATAGAGGGGCAAATGCATATGCAATGATGAAAATGCCAATGTCATCTAAATACAA
1 GCAAGCATCAATA-AATAGCAAATGCATATGAAATGATGTAAATGCCAATGTCATCTAAATGCAA
** *
1452765 ATGTAAATGAAACGATGCAAAC
65 ATGTGCATGAAA-GATGCAATC
* *
1452787 GCAAGCATCACTAAAATAGCAAATGCATATGAAATGATGTAAATGCGAATG
1 GCAAGCATCAAT-AAATAGCAAATGCATATGAAATGATGTAAATGCCAATG
1452838 CGGTCTAATT
Statistics
Matches: 239, Mismatches: 58, Indels: 29
0.73 0.18 0.09
Matches are distributed among these distances:
81 2 0.01
82 27 0.11
84 1 0.00
86 13 0.05
87 55 0.23
88 123 0.51
89 18 0.08
ACGTcount: A:0.43, C:0.15, G:0.19, T:0.23
Consensus pattern (85 bp):
GCAAGCATCAATAAATAGCAAATGCATATGAAATGATGTAAATGCCAATGTCATCTAAATGCAAA
TGTGCATGAAAGATGCAATC
Found at i:1452766 original size:43 final size:45
Alignment explanation
Indices: 1452718--1452838 Score: 117
Period size: 43 Copynumber: 2.8 Consensus size: 45
1452708 CCATAGAGGG
*
1452718 GCAAATGCATATGCAATGATGAAAATGCCAATGTCAT-CT-AAATA
1 GCAAATGCATATGAAATGATGAAAATGCCAATG-CATACTAAAATA
* * * * *
1452762 -CAAATGTAAATGAAACGATGCAAACG-CAA-GCATCACTAAAATA
1 GCAAATGCATATGAAATGATGAAAATGCCAATGCAT-ACTAAAATA
* *
1452805 GCAAATGCATATGAAATGATGTAAATGCGAATGC
1 GCAAATGCATATGAAATGATGAAAATGCCAATGC
1452839 GGTCTAATTT
Statistics
Matches: 59, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
40 3 0.05
41 1 0.02
42 5 0.08
43 25 0.42
44 21 0.36
45 2 0.03
46 2 0.03
ACGTcount: A:0.45, C:0.16, G:0.17, T:0.21
Consensus pattern (45 bp):
GCAAATGCATATGAAATGATGAAAATGCCAATGCATACTAAAATA
Found at i:1453858 original size:19 final size:20
Alignment explanation
Indices: 1453832--1453883 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
1453822 CATTTCCTCG
* *
1453832 TCTTTTTTCCTT-TTTTTCT
1 TCTTTTTTTCTTATTCTTCT
1453851 T-TTTTTTTCTTATTCTTCT
1 TCTTTTTTTCTTATTCTTCT
1453870 TCTTTTTTTTCTTA
1 TC-TTTTTTTCTTA
1453884 CTATCTGCAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 9 0.32
19 8 0.29
21 11 0.39
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (20 bp):
TCTTTTTTTCTTATTCTTCT
Found at i:1453930 original size:13 final size:13
Alignment explanation
Indices: 1453912--1453966 Score: 53
Period size: 12 Copynumber: 4.5 Consensus size: 13
1453902 TCATTTCGTG
1453912 CTTTTTCTTTTTT
1 CTTTTTCTTTTTT
*
1453925 CTTTTTCATTTTT
1 CTTTTTCTTTTTT
* *
1453938 C-TTCTC-TCTTT
1 CTTTTTCTTTTTT
*
1453949 CTTTTT-TTGTTT
1 CTTTTTCTTTTTT
1453961 CTTTTT
1 CTTTTT
1453967 TTTAATTTAG
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
11 5 0.14
12 17 0.49
13 13 0.37
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.78
Consensus pattern (13 bp):
CTTTTTCTTTTTT
Found at i:1454597 original size:13 final size:13
Alignment explanation
Indices: 1454579--1454623 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
1454569 AATTAAAAAG
*
1454579 AAAATAATAATTA
1 AAAATATTAATTA
1454592 AAAATATTAATAGTA
1 AAAATATTAAT--TA
1454607 AAAA-ATTAATTA
1 AAAATATTAATTA
1454619 AAAAT
1 AAAAT
1454624 TTATATGTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
12 6 0.21
13 10 0.36
14 6 0.21
15 6 0.21
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (13 bp):
AAAATATTAATTA
Found at i:1458798 original size:67 final size:66
Alignment explanation
Indices: 1458678--1458810 Score: 162
Period size: 67 Copynumber: 2.0 Consensus size: 66
1458668 TGTGTCCTCT
* *
1458678 ATGCCACTTTTGTCACTTTCCCATATACAAGTTCTTCAAATGGAGAAGCCAACCATTATGGTCTC
1 ATGCCACTTTTGTCACTTTCCCATATACAAGTTCTT-AAATGAAAAAGCCAACCATTATGGTCTC
1458743 AA
65 AA
* * * *
1458745 ATGCCACTTTTTTCATTTTCCC-TAATACAAGTAGTCTT-AATGAAAAAGTCAACCATTGTGGTC
1 ATGCCACTTTTGTCACTTTCCCAT-ATACAAGT--TCTTAAATGAAAAAGCCAACCATTATGGTC
1458808 TCA
63 TCA
1458811 TTTCGCCATT
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
66 1 0.02
67 52 0.91
69 4 0.07
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (66 bp):
ATGCCACTTTTGTCACTTTCCCATATACAAGTTCTTAAATGAAAAAGCCAACCATTATGGTCTCA
A
Found at i:1459514 original size:43 final size:43
Alignment explanation
Indices: 1459465--1459560 Score: 131
Period size: 43 Copynumber: 2.2 Consensus size: 43
1459455 ACCATAATAC
* * *
1459465 CAAGTACTTTGGTATAGGTATTTTTGGCAC-AAGTAGTTTGCCA
1 CAAGTACTTTGGCATAAGTATTTTTGGCACTAA-TAATTTGCCA
* *
1459508 TAAGTACTTTGGCATAAGTATTTTTGGCACTAATAATTTGGCA
1 CAAGTACTTTGGCATAAGTATTTTTGGCACTAATAATTTGCCA
1459551 CAAGTACTTT
1 CAAGTACTTT
1459561 TTGGCACAGG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
43 44 0.96
44 2 0.04
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.39
Consensus pattern (43 bp):
CAAGTACTTTGGCATAAGTATTTTTGGCACTAATAATTTGCCA
Found at i:1459578 original size:30 final size:29
Alignment explanation
Indices: 1459487--1459578 Score: 91
Period size: 29 Copynumber: 3.2 Consensus size: 29
1459477 TATAGGTATT
* *
1459487 TTTGGCACAAGTA-GTTTGCCA-TAAGTAC
1 TTTGGCACAAGTATTTTTGGCACT-AGTAC
* * *
1459515 TTTGGCATAAGTATTTTTGGCACTAATAA
1 TTTGGCACAAGTATTTTTGGCACTAGTAC
1459544 TTTGGCACAAGTACTTTTTGGCAC-AGGTAC
1 TTTGGCACAAGTA-TTTTTGGCACTA-GTAC
1459574 TTTGG
1 TTTGG
1459579 TATAGGTACT
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
28 12 0.23
29 22 0.42
30 18 0.35
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (29 bp):
TTTGGCACAAGTATTTTTGGCACTAGTAC
Found at i:1459585 original size:14 final size:14
Alignment explanation
Indices: 1459468--1459621 Score: 85
Period size: 14 Copynumber: 10.6 Consensus size: 14
1459458 ATAATACCAA
*
1459468 GTACTTTGGTATAG
1 GTACTTTGGCATAG
* * *
1459482 GTATTTTTGGCACAA
1 GTA-CTTTGGCATAG
* * *
1459497 GTAGTTTGCCATAA
1 GTACTTTGGCATAG
*
1459511 GTACTTTGGCATAA
1 GTACTTTGGCATAG
*
1459525 GTATTTTTGGCACTA-
1 GTA-CTTTGGCA-TAG
* * * *
1459540 ATAATTTGGCACAA
1 GTACTTTGGCATAG
*
1459554 GTACTTTTTGGCACAG
1 GTAC--TTTGGCATAG
*
1459570 GTACTTTGGTATAG
1 GTACTTTGGCATAG
* *
1459584 GTACTTTAGCATAA
1 GTACTTTGGCATAG
1459598 GTACTTTTGGCATAG
1 GTAC-TTTGGCATAG
*
1459613 GAACTTTGG
1 GTACTTTGG
1459622 GCTAGCATAA
Statistics
Matches: 109, Mismatches: 24, Indels: 14
0.74 0.16 0.10
Matches are distributed among these distances:
13 1 0.01
14 63 0.58
15 30 0.28
16 15 0.14
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (14 bp):
GTACTTTGGCATAG
Found at i:1459588 original size:30 final size:30
Alignment explanation
Indices: 1459510--1459590 Score: 94
Period size: 30 Copynumber: 2.7 Consensus size: 30
1459500 GTTTGCCATA
1459510 AGTACTTTGGCATAAGTA-TTTTTGGCACT
1 AGTACTTTGGCATAAGTACTTTTTGGCACT
* * *
1459539 AATAATTTGGCACAAGTACTTTTTGGCAC-
1 AGTACTTTGGCATAAGTACTTTTTGGCACT
* *
1459568 AGGTACTTTGGTATAGGTACTTT
1 A-GTACTTTGGCATAAGTACTTT
1459591 AGCATAAGTA
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 16 0.38
30 26 0.62
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.40
Consensus pattern (30 bp):
AGTACTTTGGCATAAGTACTTTTTGGCACT
Found at i:1474466 original size:1 final size:1
Alignment explanation
Indices: 1474460--1474523 Score: 56
Period size: 1 Copynumber: 64.0 Consensus size: 1
1474450 CCTTCTCTTC
** * * * * * *
1474460 AAAAAAAAAAAGCAAAAAAAAAAAACAAAAAAAAAACAAAACAAAGAAAAAGAGAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1474524 TCTGCTTAAG
Statistics
Matches: 48, Mismatches: 15, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.88, C:0.06, G:0.06, T:0.00
Consensus pattern (1 bp):
A
Found at i:1474477 original size:13 final size:13
Alignment explanation
Indices: 1474459--1474523 Score: 71
Period size: 13 Copynumber: 4.9 Consensus size: 13
1474449 ACCTTCTCTT
*
1474459 CAAAAAAAAAAAG
1 CAAAAAAAAAAAA
1474472 CAAAAAAAAAAAA
1 CAAAAAAAAAAAA
1474485 C--AAAAAAAAAA
1 CAAAAAAAAAAAA
1474496 CAAAACAAAGAAAAA
1 CAAAA-AAA-AAAAA
*
1474511 GAGAAAAAAAAAA
1 CA-AAAAAAAAAA
1474524 TCTGCTTAAG
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
11 11 0.24
13 15 0.33
14 7 0.16
15 9 0.20
16 3 0.07
ACGTcount: A:0.86, C:0.08, G:0.06, T:0.00
Consensus pattern (13 bp):
CAAAAAAAAAAAA
Found at i:1474493 original size:29 final size:28
Alignment explanation
Indices: 1474460--1474523 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
1474450 CCTTCTCTTC
*
1474460 AAAAAAAA-AAAGCAAAAAAAAAAAACAA
1 AAAAAAAACAAAAC-AAAAAAAAAAACAA
* * *
1474488 AAAAAAAACAAAACAAAGAAAAAGAGAA
1 AAAAAAAACAAAACAAAAAAAAAAACAA
1474516 AAAAAAAA
1 AAAAAAAA
1474524 TCTGCTTAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 27 0.87
29 4 0.13
ACGTcount: A:0.88, C:0.06, G:0.06, T:0.00
Consensus pattern (28 bp):
AAAAAAAACAAAACAAAAAAAAAAACAA
Found at i:1475569 original size:55 final size:54
Alignment explanation
Indices: 1475486--1476241 Score: 947
Period size: 55 Copynumber: 13.4 Consensus size: 54
1475476 CTCCTTCCGC
*
1475486 TTTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1 TTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
1475540 TTTTCCAGTCCTCAAAGAGCAAGACACCTTTCAAAGCCCACATAAGTTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1475595 TTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
1475650 TTTTCCAATCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
1475705 TTTTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
1475766 CCTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACATAAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
1475821 TTTTCCAATCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
1475876 TTTTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCA
*
1475937 CCTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
1475992 TTTTCCAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
1476047 TTTTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
1476108 CCTTTCAGTCCCCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA
** * *
1476163 CCGTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* * * *
1476218 CTTTTTACTCCTCAATGAGAAGGA
1 -TTTTCAGTCCTCAAAGAGCAGGA
1476242 TACACTTTAT
Statistics
Matches: 622, Mismatches: 54, Indels: 51
0.86 0.07 0.07
Matches are distributed among these distances:
54 12 0.02
55 447 0.72
56 14 0.02
57 3 0.00
59 3 0.00
61 143 0.23
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (54 bp):
TTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:1475805 original size:171 final size:171
Alignment explanation
Indices: 1475497--1476242 Score: 1199
Period size: 171 Copynumber: 4.4 Consensus size: 171
1475487 TTTCAGTCCC
* * * *
1475497 CAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAA
1 CAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAG
* * * *
1475562 GA--C----ACCTTTCAAAGCCCACATAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGAC
66 GATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGAC
1475620 ACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCT
130 ACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCT
1475662 CAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAG
1 CAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAG
1475727 GATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACA
66 GATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACA
*
1475792 CCTTTCAAAGCCCACATAAGTTGGTGGCATTTTCCAATCCT
131 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCT
1475833 CAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAG
1 CAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAG
1475898 GATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACA
66 GATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACA
*
1475963 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCT
131 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCT
1476004 CAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAG
1 CAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAG
*
1476069 GATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACA
66 GATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACA
** *
1476134 CCTCTT-AAAGCCCACACAAGTTGGTGGCACCGTT-CAGTCCT
131 CCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAATCCT
* * * * *
1476175 CAAAGAGCAGGACGCCTTTCAAAGCCCACAC-GAGTTGGTGGCACTTTTT-ACTCCTCAATGAGA
1 CAAAGAGCAGGACACCTTTTAAAGCCCACACAG-GTTGGTGGCA-TTTTTCAGTCCTCAAAGAGC
1476238 AGGAT
64 AGGAT
1476243 ACACTTTATT
Statistics
Matches: 551, Mismatches: 19, Indels: 16
0.94 0.03 0.03
Matches are distributed among these distances:
165 63 0.11
167 1 0.00
170 1 0.00
171 474 0.86
172 12 0.02
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.24
Consensus pattern (171 bp):
CAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAG
GATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACA
CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCT
Found at i:1475971 original size:226 final size:220
Alignment explanation
Indices: 1475487--1476222 Score: 1033
Period size: 226 Copynumber: 3.3 Consensus size: 220
1475477 TCCTTCCGCT
*
1475487 TTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCT
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCT
*
1475552 CAAAGAGCAAGACACCTTTCAAAGCCCACATAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAG
66 CAAAGAGCAGGACACCTTTCAAAGCCCACATAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAG
* * *
1475617 GACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGCAGGACACCTTTT
131 GACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACACCTTTT
* **
1475682 AAAGCCCACACAGGTTGGTGGCATT
196 AAAGCCCACACAAGTTGGTGGCACC
* * *
1475707 TTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-
1 TTTCAGTCCTCAAAGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTC
*
1475771 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACATAAGTTGGTGGCATTTTCCAATCCTCAA
59 CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACATAAGTTGGTGGCATTTTCCAGTCCTCAA
*
1475836 AGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGAT
124 AGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGA-
**
1475901 GCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACC
188 -C---ACCTTTT-AAAGCCCACACAAGTTGGTGGCACC
1475939 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCT
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCT
* * * *
1476004 CAAAGAGCAGGACACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAG
66 CAAAGAGCAGGACACCTTTCAAAGCCCACATAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAG
** ** *
1476069 GATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACA
131 GA--C---ACCTTTT-AAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACA
*
1476134 CCTCTTAAAGCCCACACAAGTTGGTGGCACC
190 CCTTTTAAAGCCCACACAAGTTGGTGGCACC
* * *
1476165 GTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTT
1 TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTT
1476223 TACTCCTCAA
Statistics
Matches: 460, Mismatches: 35, Indels: 35
0.87 0.07 0.07
Matches are distributed among these distances:
220 21 0.05
222 1 0.00
225 3 0.01
226 323 0.70
227 11 0.02
228 2 0.00
230 2 0.00
231 10 0.02
232 87 0.19
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (220 bp):
TTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCT
CAAAGAGCAGGACACCTTTCAAAGCCCACATAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAG
GACACCTTTTAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGACACCTTTT
AAAGCCCACACAAGTTGGTGGCACC
Found at i:1480496 original size:79 final size:79
Alignment explanation
Indices: 1480211--1480496 Score: 319
Period size: 79 Copynumber: 3.6 Consensus size: 79
1480201 TCATTGATGT
* * * *
1480211 TTTTATTTCTAAAATATCGATTTTCCACCATCGGGGATACTCCAACCTCATTATTTTCGAAGGGA
1 TTTTATTTCTAAAATATCGATTTTCCACCATCGAGGATACTCCAACCCCGTTATTTTCGAGGGGA
*
1480276 TACTCCAACCCTGA
66 TACTCCAAACCTGA
* * * * * *
1480290 TTTTATTTTTAAAACAAT-GATTTTCCACCATC-AGAGATACACCAACCCTGTTATTTCCGAGAG
1 TTTTATTTCTAAAA-TATCGATTTTCCACCATCGAG-GATACTCCAACCCCGTTATTTTCGAGGG
*
1480353 GATACTCCAAACC-CA
64 GATACTCCAAACCTGA
* * * * *
1480368 GTTTTATTTCTAAAACACCGATTTTCCACCATTGGGGATACTCCAACCCCGTTATTTTTGAGGGG
1 -TTTTATTTCTAAAATATCGATTTTCCACCATCGAGGATACTCCAACCCCGTTATTTTCGAGGGG
* *
1480433 ATACCCCAAGCCTGA
65 ATACTCCAAACCTGA
* *
1480448 TTTTATTTCCAAAATATCGACTTTT-CACTATCGAGGATACTCCAACCCC
1 TTTTATTTCTAAAATATCGA-TTTTCCACCATCGAGGATACTCCAACCCC
1480497 ATTTTTATCT
Statistics
Matches: 169, Mismatches: 31, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
78 3 0.02
79 158 0.93
80 8 0.05
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.33
Consensus pattern (79 bp):
TTTTATTTCTAAAATATCGATTTTCCACCATCGAGGATACTCCAACCCCGTTATTTTCGAGGGGA
TACTCCAAACCTGA
Found at i:1483176 original size:67 final size:67
Alignment explanation
Indices: 1483094--1483288 Score: 182
Period size: 67 Copynumber: 2.9 Consensus size: 67
1483084 GTTCCCTTTG
* * *
1483094 CCACTTCTATTACTCTTTTTAATCCAAGTACTCTTAATGGAGAAGTCAACCATTATGGTCTCATG
1 CCACTTGTATCACTCTTTTTAATACAAGTACTCTTAATGGAGAAGTCAACCATTATGGTCTCATG
1483159 CA
66 CA
* * * ** * * * *
1483161 CCATTTTTGTCACTC-TCCTATATACAGGT--TCTTCCAGTGGAGAAATCGACCATTATGGTCTC
1 CCACTTGTATCACTCTTTTTA-ATACAAGTACTCTT--AATGGAGAAGTCAACCATTATGGTCTC
1483223 ATGCA
63 ATGCA
* * * *
1483228 TCACTTGTATCACT-TTCTTTAATGCATGTACTCTTAATAGAGAAGTCAACCATTATGGTCT
1 CCACTTGTATCACTCTT-TTTAATACAAGTACTCTTAATGGAGAAGTCAACCATTATGGTCT
1483289 TCCACGCCAC
Statistics
Matches: 98, Mismatches: 23, Indels: 14
0.73 0.17 0.10
Matches are distributed among these distances:
65 4 0.04
66 3 0.03
67 85 0.87
68 2 0.02
69 4 0.04
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (67 bp):
CCACTTGTATCACTCTTTTTAATACAAGTACTCTTAATGGAGAAGTCAACCATTATGGTCTCATG
CA
Found at i:1484066 original size:14 final size:14
Alignment explanation
Indices: 1484049--1484235 Score: 158
Period size: 14 Copynumber: 13.2 Consensus size: 14
1484039 CATATTACTA
* *
1484049 TTTGGCATAAATAC
1 TTTGGCACAAGTAC
* * *
1484063 TTTGGTATAGGTAC
1 TTTGGCACAAGTAC
* *
1484077 TTTTGGCACAAATGC
1 -TTTGGCACAAGTAC
* * *
1484092 TTTAGCATAGGTAC
1 TTTGGCACAAGTAC
*
1484106 TTTGGCACAAGTAA
1 TTTGGCACAAGTAC
* *
1484120 TTCGACACAAGTAC
1 TTTGGCACAAGTAC
* *
1484134 TTTGGCATAGGTAC
1 TTTGGCACAAGTAC
* *
1484148 TTTGTCACAAATAC
1 TTTGGCACAAGTAC
*
1484162 TTTTGGCACAAGTAA
1 -TTTGGCACAAGTAC
1484177 TTTGGCACAAGTAC
1 TTTGGCACAAGTAC
* *
1484191 TTTGGCATAGGTAC
1 TTTGGCACAAGTAC
* *
1484205 TTTGGCATAGGTAC
1 TTTGGCACAAGTAC
1484219 TTTGGCACAAGTAC
1 TTTGGCACAAGTAC
1484233 TTT
1 TTT
1484236 TGGTATAGGT
Statistics
Matches: 135, Mismatches: 36, Indels: 4
0.77 0.21 0.02
Matches are distributed among these distances:
14 115 0.85
15 20 0.15
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (14 bp):
TTTGGCACAAGTAC
Found at i:1484094 original size:29 final size:29
Alignment explanation
Indices: 1484044--1484281 Score: 110
Period size: 29 Copynumber: 8.3 Consensus size: 29
1484034 ATTGCCATAT
* * *
1484044 TACTATTTGGCATAAATACTTTGGTATAGG
1 TACT-TTTGGCACAAATACTTTAGCATAGG
*
1484074 TACTTTTGGCACAAATGCTTTAGCATAGG
1 TACTTTTGGCACAAATACTTTAGCATAGG
* * * * *
1484103 TAC-TTTGGCACAAGTA-ATTCGACACAAG
1 TACTTTTGGCACAAATACTTTAG-CATAGG
* ** * **
1484131 TAC-TTTGGCATAGGTACTTT-GTCACAAA
1 TACTTTTGGCACAAATACTTTAG-CATAGG
* * * * *
1484159 TACTTTTGGCACAAGTAATTTGGCACAAG
1 TACTTTTGGCACAAATACTTTAGCATAGG
* ** *
1484188 TAC-TTTGGCATAGGTACTTTGGCATAGG
1 TACTTTTGGCACAAATACTTTAGCATAGG
* * *
1484216 TAC-TTTGGCACAAGTACTTTTGGTATAGG
1 TACTTTTGGCACAAATAC-TTTAGCATAGG
* * * * *
1484245 TGCTTTTAGCACGAGTATTTTAGCATAGG
1 TACTTTTGGCACAAATACTTTAGCATAGG
1484274 TACTTTTG
1 TACTTTTG
1484282 ACGGAAGGGC
Statistics
Matches: 167, Mismatches: 35, Indels: 13
0.78 0.16 0.06
Matches are distributed among these distances:
27 3 0.02
28 73 0.44
29 75 0.45
30 16 0.10
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (29 bp):
TACTTTTGGCACAAATACTTTAGCATAGG
Found at i:1484237 original size:71 final size:71
Alignment explanation
Indices: 1484048--1484238 Score: 240
Period size: 71 Copynumber: 2.7 Consensus size: 71
1484038 CCATATTACT
* * * * * * *
1484048 ATTTGGCATAAATACTTTGGTATAGGTACTTTTGGCACAAATGC-TTTAGCATAGGTACTTTGGC
1 ATTTGGCATAAGTACTTTGGCATAGGTAC-TTTGGCACAAATACTTTTGGCACAAGTAATTTGGC
1484112 ACAAGTA
65 ACAAGTA
* * * *
1484119 ATTCGACACAAGTACTTTGGCATAGGTACTTTGTCACAAATACTTTTGGCACAAGTAATTTGGCA
1 ATTTGGCATAAGTACTTTGGCATAGGTACTTTGGCACAAATACTTTTGGCACAAGTAATTTGGCA
1484184 CAAGTA
66 CAAGTA
* * *
1484190 CTTTGGCATAGGTACTTTGGCATAGGTACTTTGGCACAAGTACTTTTGG
1 ATTTGGCATAAGTACTTTGGCATAGGTACTTTGGCACAAATACTTTTGG
1484239 TATAGGTGCT
Statistics
Matches: 101, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
70 12 0.12
71 89 0.88
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.34
Consensus pattern (71 bp):
ATTTGGCATAAGTACTTTGGCATAGGTACTTTGGCACAAATACTTTTGGCACAAGTAATTTGGCA
CAAGTA
Found at i:1488841 original size:52 final size:48
Alignment explanation
Indices: 1488722--1489095 Score: 231
Period size: 47 Copynumber: 7.8 Consensus size: 48
1488712 CGAAGAATGA
* * * * * *
1488722 CAATGTGCTGATTCATGGCCAGCGACATTAGACTTGAAG--AAGAATGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGTAAAG-GTGC
* ** *
1488769 CAATGTGCTGAGACAAGGCCAGCGACATTAGG-CTTAGGAATGTTAAAGATGC
1 CAATATGCTGATTCAAGGCCAGCGACATT-GGTCTTA--AA-G-TAAAGGTGC
* * * * * *
1488821 CAATATGCTGATTCATGGCCAACAATATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAG-TAAAGGTGC
* * *
1488870 CAATGTGCTGATTCAAGGCCAGCAACATTGGTCTTAAAGATGGTAAAGGCGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGTCTT-AA-A--GTAAAGGTGC
* *
1488922 CAATATACTGATTCAAGGCCAGGGACATTGGTCTTAAAG-ACAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGTA-AAGGTGC
* *
1488970 TAATATGCTGATTCAAGGCCAGCGATATTAGG-C-T----T--A--TGC
1 CAATATGCTGATTCAAGGCCAGCGACATT-GGTCTTAAAGTAAAGGTGC
* * * *
1489009 CAATGTGCTGATTCAAGGCCAGCGATATTAGTCTTAAAG--AAGAATGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGTAAAG-GTGC
* * * *
1489056 CAATGTGCTGATACAAGGCCAGCGATATTGGGCTTAAAGT
1 CAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGT
1489096 TGTCACGGGG
Statistics
Matches: 264, Mismatches: 37, Indels: 51
0.75 0.11 0.14
Matches are distributed among these distances:
38 1 0.00
39 31 0.12
40 1 0.00
41 1 0.00
44 1 0.00
47 70 0.27
48 34 0.13
49 42 0.16
50 6 0.02
51 5 0.02
52 68 0.26
53 4 0.02
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (48 bp):
CAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGTAAAGGTGC
Found at i:1488879 original size:49 final size:49
Alignment explanation
Indices: 1488722--1489094 Score: 249
Period size: 52 Copynumber: 7.8 Consensus size: 49
1488712 CGAAGAATGA
* * * * *
1488722 CAATGTGCTGATTCATGGCCAGCGACATTAGACTTGAAGAAGAA--TGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
* ** * * *
1488769 CAATGTGCTGAGACAAGGCCAGCGACATTAGG-CTTAGGAATGTTAAAGATGC
1 CAATATGCTGATTCAAGGCCAGCGACATT-GGACTTA--AA-GATGAAGGTGC
* * * *
1488821 CAATATGCTGATTCATGGCCAACAATATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
* * * *
1488870 CAATGTGCTGATTCAAGGCCAGCAACATTGGTCTTAAAGATGGTAAAGGCGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT-G--AAGGTGC
* * * *
1488922 CAATATACTGATTCAAGGCCAGGGACATTGGTCTTAAAGA-CAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
* *
1488970 TAATATGCTGATTCAAGGCCAGCGATATTAGG-C-T-----T--A--TGC
1 CAATATGCTGATTCAAGGCCAGCGACATT-GGACTTAAAGATGAAGGTGC
* * * * *
1489009 CAATGTGCTGATTCAAGGCCAGCGATATTAGTCTTAAAGAAGAA--TGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
* * * *
1489056 CAATGTGCTGATACAAGGCCAGCGATATTGGGCTTAAAG
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAG
1489095 TTGTCACGGG
Statistics
Matches: 264, Mismatches: 41, Indels: 42
0.76 0.12 0.12
Matches are distributed among these distances:
38 1 0.00
39 31 0.12
40 1 0.00
41 1 0.00
47 70 0.27
48 33 0.12
49 48 0.18
50 6 0.02
51 2 0.01
52 71 0.27
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.24
Consensus pattern (49 bp):
CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
Found at i:1488917 original size:101 final size:100
Alignment explanation
Indices: 1488722--1489005 Score: 306
Period size: 101 Copynumber: 2.8 Consensus size: 100
1488712 CGAAGAATGA
* * * **
1488722 CAATGTGCTGATTCATGGCCAGCGACATTAGACTTGAAGAAGAA--TGCCAATGTGCTGAGACAA
1 CAATATGCTGATTCATGGCCAGCGACATTGGACTTAAAG-AGAAGGTGCCAATGTGCTGATTCAA
* * * *
1488785 GGCCAGCGACATTAGGCTTAGGAATGTTAAAGATGC
65 GGCCAGCAACATTAGGCTTAAGAATGGTAAAGACGC
* * *
1488821 CAATATGCTGATTCATGGCCAACAATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAA
1 CAATATGCTGATTCATGGCCAGCGACATTGGACTTAAAGA-GAAGGTGCCAATGTGCTGATTCAA
*
1488886 GGCCAGCAACATT-GGTCTTAA-AGATGGTAAAGGCGC
65 GGCCAGCAACATTAGG-CTTAAGA-ATGGTAAAGACGC
* * * * * * *
1488922 CAATATACTGATTCAAGGCCAGGGACATTGGTCTTAAAGACAAGGTGCTAATATGCTGATTCAAG
1 CAATATGCTGATTCATGGCCAGCGACATTGGACTTAAAGAGAAGGTGCCAATGTGCTGATTCAAG
* *
1488987 GCCAGCGATATTAGGCTTA
66 GCCAGCAACATTAGGCTTA
1489006 TGCCAATGTG
Statistics
Matches: 154, Mismatches: 25, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
98 1 0.01
99 36 0.23
100 39 0.25
101 78 0.51
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.24
Consensus pattern (100 bp):
CAATATGCTGATTCATGGCCAGCGACATTGGACTTAAAGAGAAGGTGCCAATGTGCTGATTCAAG
GCCAGCAACATTAGGCTTAAGAATGGTAAAGACGC
Found at i:1489186 original size:34 final size:33
Alignment explanation
Indices: 1489099--1489278 Score: 175
Period size: 34 Copynumber: 5.4 Consensus size: 33
1489089 TTAAAGTTGT
* * *
1489099 CACGGGGTTGTGGACTT-ATAGGAAAAATGGATGC
1 CACGGAGTTGTGGACTTAAAAGG-AAAA-GGGTGC
* * * *
1489133 CACAGAGGTGTGGGCTTAAAAGGGAAAAGGGTGT
1 CACGGAGTTGTGGACTTAAAA-GGAAAAGGGTGC
* *
1489167 CACGGAGTCGTGGACTTAAAAAGAAAA-GGTGC
1 CACGGAGTTGTGGACTTAAAAGGAAAAGGGTGC
* *
1489199 CACGGAGTTGTGGGCTTTAAAAGGAAAAAGGTGC
1 CACGGAGTTGTGGAC-TTAAAAGGAAAAGGGTGC
* * *
1489233 CATGGAGTTGTGGACTTAAAAGGAAAAAGATGC
1 CACGGAGTTGTGGACTTAAAAGGAAAAGGGTGC
*
1489266 CACGGACTTGTGG
1 CACGGAGTTGTGG
1489279 GCTTTTGAAG
Statistics
Matches: 121, Mismatches: 21, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
32 17 0.14
33 44 0.36
34 52 0.43
35 6 0.05
36 2 0.02
ACGTcount: A:0.33, C:0.12, G:0.35, T:0.20
Consensus pattern (33 bp):
CACGGAGTTGTGGACTTAAAAGGAAAAGGGTGC
Found at i:1489225 original size:66 final size:68
Alignment explanation
Indices: 1489128--1489283 Score: 210
Period size: 66 Copynumber: 2.3 Consensus size: 68
1489118 AGGAAAAATG
* * * *
1489128 GATGCCACAGAGGTGTGGGC-TTAAAAGGGAAAAGGGTGTCACGGAGTCGTGGACTTAAAAAG-A
1 GATGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGGTGCCACGGAGTCGTGGACTTAAAAAGAA
1489191 AAA
66 AAA
* * * *
1489194 GGTGCCACGGAGTTGTGGGCTTTAAAA-GGAAAAAGGTGCCATGGAGTTGTGGACTTAAAAGGAA
1 GATGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGGTGCCACGGAGTCGTGGACTTAAAAAGAA
1489258 AAA
66 AAA
*
1489261 GATGCCACGGACTTGTGGGCTTT
1 GATGCCACGGAGTTGTGGGCTTT
1489284 TGAAGGTTGC
Statistics
Matches: 78, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
66 47 0.60
67 31 0.40
ACGTcount: A:0.32, C:0.13, G:0.35, T:0.21
Consensus pattern (68 bp):
GATGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGGTGCCACGGAGTCGTGGACTTAAAAAGAA
AAA
Found at i:1489338 original size:29 final size:28
Alignment explanation
Indices: 1489256--1489340 Score: 98
Period size: 28 Copynumber: 3.0 Consensus size: 28
1489246 ACTTAAAAGG
*
1489256 AAAAAGATGCCACGGACTTGTGGGCTTT
1 AAAAAGATGCCACTGACTTGTGGGCTTT
** * *
1489284 TGAAGGTTGCCACTGACTTGTGGGCTTT
1 AAAAAGATGCCACTGACTTGTGGGCTTT
* *
1489312 AAAAAAGATGCCACTGACCTGTAGGCTTT
1 -AAAAAGATGCCACTGACTTGTGGGCTTT
1489341 TGGAGGGTGA
Statistics
Matches: 45, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
28 23 0.51
29 22 0.49
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.28
Consensus pattern (28 bp):
AAAAAGATGCCACTGACTTGTGGGCTTT
Found at i:1490802 original size:20 final size:20
Alignment explanation
Indices: 1490777--1490814 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1490767 TCTGGACTCT
*
1490777 TTTTGTTTTTTTTTTGTTTG
1 TTTTGTTTTGTTTTTGTTTG
1490797 TTTTGTTTTGTTTTTGTT
1 TTTTGTTTTGTTTTTGTT
1490815 CTTGTTCGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (20 bp):
TTTTGTTTTGTTTTTGTTTG
Found at i:1490805 original size:26 final size:26
Alignment explanation
Indices: 1490777--1490826 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
1490767 TCTGGACTCT
* *
1490777 TTTTGTTTTT-TTTTTGTTTGTTTTG
1 TTTTGTTTTTGTTCTTGTTCGTTTTG
1490802 TTTTGTTTTTGTTCTTGTTCGTTTT
1 TTTTGTTTTTGTTCTTGTTCGTTTT
1490827 TGTTGTGGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.00, C:0.04, G:0.16, T:0.80
Consensus pattern (26 bp):
TTTTGTTTTTGTTCTTGTTCGTTTTG
Found at i:1490812 original size:16 final size:16
Alignment explanation
Indices: 1490776--1490830 Score: 62
Period size: 16 Copynumber: 3.5 Consensus size: 16
1490766 ATCTGGACTC
1490776 TTTTTGTTTT-TTTT-
1 TTTTTGTTTTGTTTTG
1490790 TTGTTTGTTTTGTTTTG
1 TT-TTTGTTTTGTTTTG
*
1490807 TTTTTGTTCTTG-TTCG
1 TTTTTGTT-TTGTTTTG
1490823 TTTTTGTT
1 TTTTTGTT
1490831 GTGGAGGATG
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
14 2 0.06
15 8 0.22
16 21 0.58
17 5 0.14
ACGTcount: A:0.00, C:0.04, G:0.16, T:0.80
Consensus pattern (16 bp):
TTTTTGTTTTGTTTTG
Found at i:1492595 original size:79 final size:79
Alignment explanation
Indices: 1492464--1492621 Score: 289
Period size: 79 Copynumber: 2.0 Consensus size: 79
1492454 TGTGCAGTCA
* * *
1492464 AAATTTAACCTTGTTGTGAATGGGTAATAACTCTCATTAGGTGATATCAGTATTGCCCCAATCCC
1 AAATTCAACCTTGCTGTGAATGGGTAATAACTCCCATTAGGTGATATCAGTATTGCCCCAATCCC
1492529 ATGACCTAAAGCAT
66 ATGACCTAAAGCAT
1492543 AAATTCAACCTTGCTGTGAATGGGTAATAACTCCCATTAGGTGATATCAGTATTGCCCCAATCCC
1 AAATTCAACCTTGCTGTGAATGGGTAATAACTCCCATTAGGTGATATCAGTATTGCCCCAATCCC
1492608 ATGACCTAAAGCAT
66 ATGACCTAAAGCAT
1492622 TTGATGCTCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 76 1.00
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (79 bp):
AAATTCAACCTTGCTGTGAATGGGTAATAACTCCCATTAGGTGATATCAGTATTGCCCCAATCCC
ATGACCTAAAGCAT
Found at i:1495376 original size:33 final size:32
Alignment explanation
Indices: 1495334--1495396 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
1495324 CACCTTCAGA
*
1495334 TGTATCGATACATAATCCACAGTGTCGATACAT
1 TGTATCGATACATAA-CCACAGTATCGATACAT
* *
1495367 TGTATCGATACATGACCACTGTATCGATAC
1 TGTATCGATACATAACCACAGTATCGATAC
1495397 TTGCAAAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (32 bp):
TGTATCGATACATAACCACAGTATCGATACAT
Found at i:1495492 original size:20 final size:20
Alignment explanation
Indices: 1495467--1495533 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 20
1495457 TATATACAAG
1495467 ATGTATCGATACATGACCAA
1 ATGTATCGATACATGACCAA
1495487 ATGTATCGATACAT------
1 ATGTATCGATACATGACCAA
1495501 -TGTATCGATACATGACCAA
1 ATGTATCGATACATGACCAA
1495520 ATGTATCGATACAT
1 ATGTATCGATACAT
1495534 TGGCTTGTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 13 0.32
20 27 0.68
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACATGACCAA
Found at i:1495505 original size:33 final size:33
Alignment explanation
Indices: 1495468--1495535 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
1495458 ATATACAAGA
1495468 TGTATCGATACATGACCAAATGTATCGATACAT
1 TGTATCGATACATGACCAAATGTATCGATACAT
1495501 TGTATCGATACATGACCAAATGTATCGATACAT
1 TGTATCGATACATGACCAAATGTATCGATACAT
1495534 TG
1 TG
1495536 GCTTGTAACG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (33 bp):
TGTATCGATACATGACCAAATGTATCGATACAT
Found at i:1495506 original size:13 final size:13
Alignment explanation
Indices: 1495488--1495513 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1495478 CATGACCAAA
1495488 TGTATCGATACAT
1 TGTATCGATACAT
1495501 TGTATCGATACAT
1 TGTATCGATACAT
1495514 GACCAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1501712 original size:13 final size:13
Alignment explanation
Indices: 1501694--1501731 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
1501684 CAGTATTTGC
*
1501694 TGTATCGATACAT
1 TGTATCGATACAG
*
1501707 TGTATCGATATAG
1 TGTATCGATACAG
1501720 TGTATCGATACA
1 TGTATCGATACA
1501732 AAGGGTTTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1504225 original size:13 final size:13
Alignment explanation
Indices: 1504207--1504231 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1504197 ATAATGCACA
1504207 GTATCGATACATT
1 GTATCGATACATT
1504220 GTATCGATACAT
1 GTATCGATACAT
1504232 GACCACTGTA
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:1504228 original size:33 final size:32
Alignment explanation
Indices: 1504186--1504248 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
1504176 CACCTTCAGA
*
1504186 TGTATCGATACATAATGCACAGTATCGATACAT
1 TGTATCGATACATAA-CCACAGTATCGATACAT
* *
1504219 TGTATCGATACATGACCACTGTATCGATAC
1 TGTATCGATACATAACCACAGTATCGATAC
1504249 TTGCAAAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (32 bp):
TGTATCGATACATAACCACAGTATCGATACAT
Found at i:1504318 original size:13 final size:13
Alignment explanation
Indices: 1504300--1504326 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1504290 CCTTAACTGT
1504300 TTGTATCGATACA
1 TTGTATCGATACA
1504313 TTGTATCGATACA
1 TTGTATCGATACA
1504326 T
1 T
1504327 GACCAAATGT
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:1504339 original size:20 final size:20
Alignment explanation
Indices: 1504314--1504366 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
1504304 ATCGATACAT
1504314 TGTATCGATACATGACCAAA
1 TGTATCGATACATGACCAAA
1504334 TGTATCGATACATGACCAAA
1 TGTATCGATACATGACCAAA
1504354 TGTATCGATACAT
1 TGTATCGATACAT
1504367 TGGCTTGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (20 bp):
TGTATCGATACATGACCAAA
Found at i:1505159 original size:13 final size:13
Alignment explanation
Indices: 1505141--1505165 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1505131 ATGTTGCACA
1505141 GTATCGATACATT
1 GTATCGATACATT
1505154 GTATCGATACAT
1 GTATCGATACAT
1505166 GTTGCATTGT
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:1505160 original size:33 final size:33
Alignment explanation
Indices: 1505118--1505183 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
1505108 TACACATTTA
1505118 ATTGTATCGATACATGTTGCACAGTATCGATAC
1 ATTGTATCGATACATGTTGCACAGTATCGATAC
**
1505151 ATTGTATCGATACATGTTGCATTGTATCGATAC
1 ATTGTATCGATACATGTTGCACAGTATCGATAC
1505184 TTGAAAAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (33 bp):
ATTGTATCGATACATGTTGCACAGTATCGATAC
Found at i:1505262 original size:19 final size:20
Alignment explanation
Indices: 1505238--1505288 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1505228 TAGCCAAACT
*
1505238 TGTATCGATACA-CA-AAGTA
1 TGTATCGATACACCATAA-AA
1505257 TGTATCGATACACCATAAAA
1 TGTATCGATACACCATAAAA
1505277 TGTATCGATACA
1 TGTATCGATACA
1505289 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 12 0.41
20 15 0.52
21 2 0.07
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (20 bp):
TGTATCGATACACCATAAAA
Found at i:1515309 original size:33 final size:33
Alignment explanation
Indices: 1515272--1515342 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
1515262 TTTAAAGATA
** *
1515272 ATTTGTATGTGTTTGATATATGTGTTTAAGTCC
1 ATTTGTACATGTTTAATATATGTGTTTAAGTCC
* * *
1515305 ATTTGTACATGTTTAATATGTTTGTTTAGGTCC
1 ATTTGTACATGTTTAATATATGTGTTTAAGTCC
1515338 ATTTG
1 ATTTG
1515343 GTTGTTGTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.21, C:0.07, G:0.20, T:0.52
Consensus pattern (33 bp):
ATTTGTACATGTTTAATATATGTGTTTAAGTCC
Found at i:1516376 original size:435 final size:435
Alignment explanation
Indices: 1515566--1516437 Score: 1735
Period size: 435 Copynumber: 2.0 Consensus size: 435
1515556 GACATTTAGA
1515566 TGTTTGAAAACTAGTTTGATAAAATTGCAATAAGTGTTTGGGCACACATGTTGTTCTTAATTCTT
1 TGTTTGAAAACTAGTTTGATAAAATTGCAATAAGTGTTTGGGCACACATGTTGTTCTTAATTCTT
1515631 AAGTCAATGTTGATTTCTAGCATAGTAGTTTTGTCAAAAAAAATATTTTTGTCTAGTTTCTCGTA
66 AAGTCAATGTTGATTTCTAGCATAGTAGTTTTGTCAAAAAAAATATTTTTGTCTAGTTTCTCGTA
1515696 GTATTAATTTTTTCAGTATTTTTAGCGTCATGACCAATGAGTTAACTTTGAAATGAGTTTCAAAA
131 GTATTAATTTTTTCAGTATTTTTAGCGTCATGACCAATGAGTTAACTTTGAAATGAGTTTCAAAA
1515761 GCTCGATTTCATGATAGGATGAGTCCAGAGGTAATTCCACAATAACAGCTATCTAGATTGCTTTG
196 GCTCGATTTCATGATAGGATGAGTCCAGAGGTAATTCCACAATAACAGCTATCTAGATTGCTTTG
1515826 TTAAAATGGTAATGTTATAAAACCAACCAAATTCAGTGCGATAAACCAGTTTTATTTTTCTTTTT
261 TTAAAATGGTAATGTTATAAAACCAACCAAATTCAGTGCGATAAACCAGTTTTATTTTTCTTTTT
1515891 TTGAATAAAAATATGTTAAATATGCTTTGCAACCATATATGGTACATCTGTAAGCGATCCAGACA
326 TTGAATAAAAATATGTTAAATATGCTTTGCAACCATATATGGTACATCTGTAAGCGATCCAGACA
1515956 AACTAAGAAATAAATTCACTAGGTAAGCTATTTAGATGTTCTGTG
391 AACTAAGAAATAAATTCACTAGGTAAGCTATTTAGATGTTCTGTG
1516001 TGTTTGAAAACTAGTTTGATAAAATTGCAATAAGTGTTTGGGCACACATGTTGTTCTTAATTCTT
1 TGTTTGAAAACTAGTTTGATAAAATTGCAATAAGTGTTTGGGCACACATGTTGTTCTTAATTCTT
1516066 AAGTCAATGTTGATTTCTAGCATAGTAGTTTTGTCAAAAAAAATATTTTTGTCTAGTTTCTCGTA
66 AAGTCAATGTTGATTTCTAGCATAGTAGTTTTGTCAAAAAAAATATTTTTGTCTAGTTTCTCGTA
1516131 GTATTAATTTTTTCAGTATTTTTAGCGTCATGACCAATGAGTTAACTTTGAAATGAGTTTCAAAA
131 GTATTAATTTTTTCAGTATTTTTAGCGTCATGACCAATGAGTTAACTTTGAAATGAGTTTCAAAA
*
1516196 GCTCGATTTCATGATAGGATGAGTCCTGAGGTAATTCCACAATAACAGCTATCTAGATTGCTTTG
196 GCTCGATTTCATGATAGGATGAGTCCAGAGGTAATTCCACAATAACAGCTATCTAGATTGCTTTG
1516261 TTAAAATGGTAATGTTATAAAACCAACCAAATTCAGTGCGATAAACCAGTTTTATTTTTCTTTTT
261 TTAAAATGGTAATGTTATAAAACCAACCAAATTCAGTGCGATAAACCAGTTTTATTTTTCTTTTT
1516326 TTGAATAAAAATATGTTAAATATGCTTTGCAACCATATATGGTACATCTGTAAGCGATCCAGACA
326 TTGAATAAAAATATGTTAAATATGCTTTGCAACCATATATGGTACATCTGTAAGCGATCCAGACA
1516391 AACTAAGAAATAAATTCACTAGGTAAGCTATTTAGATGTTCTGTG
391 AACTAAGAAATAAATTCACTAGGTAAGCTATTTAGATGTTCTGTG
1516436 TG
1 TG
1516438 ATGTAATAAT
Statistics
Matches: 436, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
435 436 1.00
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (435 bp):
TGTTTGAAAACTAGTTTGATAAAATTGCAATAAGTGTTTGGGCACACATGTTGTTCTTAATTCTT
AAGTCAATGTTGATTTCTAGCATAGTAGTTTTGTCAAAAAAAATATTTTTGTCTAGTTTCTCGTA
GTATTAATTTTTTCAGTATTTTTAGCGTCATGACCAATGAGTTAACTTTGAAATGAGTTTCAAAA
GCTCGATTTCATGATAGGATGAGTCCAGAGGTAATTCCACAATAACAGCTATCTAGATTGCTTTG
TTAAAATGGTAATGTTATAAAACCAACCAAATTCAGTGCGATAAACCAGTTTTATTTTTCTTTTT
TTGAATAAAAATATGTTAAATATGCTTTGCAACCATATATGGTACATCTGTAAGCGATCCAGACA
AACTAAGAAATAAATTCACTAGGTAAGCTATTTAGATGTTCTGTG
Found at i:1520550 original size:20 final size:19
Alignment explanation
Indices: 1520472--1520551 Score: 72
Period size: 20 Copynumber: 4.0 Consensus size: 19
1520462 TCAAAAACCC
* *
1520472 AGAATGTATCGATACAATG
1 AGAATGTATCGATACATTT
*
1520491 AGAAATATATCGATACAATTGT
1 AG-AATGTATCGATAC-ATT-T
*
1520513 AAGCATGTATCG-TACATTT
1 -AGAATGTATCGATACATTT
1520532 AGTAATGTATCGATACATTT
1 AG-AATGTATCGATACATTT
1520552 CCTTGGCAGT
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
18 2 0.04
19 11 0.22
20 22 0.45
21 5 0.10
22 7 0.14
23 2 0.04
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (19 bp):
AGAATGTATCGATACATTT
Found at i:1521409 original size:61 final size:61
Alignment explanation
Indices: 1521265--1521457 Score: 198
Period size: 61 Copynumber: 3.2 Consensus size: 61
1521255 CAACACTGGA
* * * * *
1521265 CTTAAAGATGATAAGAAT-A-AGAAGAATGCCAATGTGCTGATTCAAGGCTAGCGACT-TAGA-
1 CTTAAAGATGAGAAGAATGATA-AAG-ATGCCAATATGCTGATTCAAGGCCAGC-AATATCGAG
* * * *
1521325 CTTAAGGATGCA-AAGAATGATAAAGGTGCCAATATGCTGATTCACGGCCAGTAATATCGAG
1 CTTAAAGATG-AGAAGAATGATAAAGATGCCAATATGCTGATTCAAGGCCAGCAATATCGAG
* * * *
1521386 CTTAAAGATGAGAAGAATGATAAAGATGCCAATATGCTGATTTAAGGCCAGCGATATTGGG
1 CTTAAAGATGAGAAGAATGATAAAGATGCCAATATGCTGATTCAAGGCCAGCAATATCGAG
1521447 CTTAAAGATGA
1 CTTAAAGATGA
1521458 CAAAGGTGCC
Statistics
Matches: 111, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
59 2 0.02
60 41 0.37
61 67 0.60
62 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.24
Consensus pattern (61 bp):
CTTAAAGATGAGAAGAATGATAAAGATGCCAATATGCTGATTCAAGGCCAGCAATATCGAG
Found at i:1521505 original size:113 final size:111
Alignment explanation
Indices: 1521385--1521728 Score: 292
Period size: 113 Copynumber: 3.1 Consensus size: 111
1521375 GTAATATCGA
* *
1521385 GCTTAAAGATGAGAAGAATGATAAAGATGCCAATATGCTGATTTAAGGCCAGCGATATTGGGCTT
1 GCTTAAAGATGA-AAGAATGATAAAGAT-CCAATATGCTGATTCAAGGCCAGCGATATTAGGCTT
* * * * * *
1521450 AAAGATGACAAAGGTGCCAAGGTGTTGATTCAAGGCTAGCGATATTGG
64 AAAAATGACAAAGCTGCCAAGGTGCTGATTCAAGGCTAGCGACACTAG
* ** *
1521498 GCTTAAAGATGACA-AA-G-----GCA-CCAATATGCTGATTCAAGGCCAATGATATTAGACTTA
1 GCTTAAAGATGAAAGAATGATAAAG-ATCCAATATGCTGATTCAAGGCCAGCGATATTAGGCTTA
* * * * *
1521555 AAAAAGAAAAAGCTGCTAATGTGCTGATTCAAGGTTAGCGACACTAG
65 AAAATGACAAAGCTGCCAAGGTGCTGATTCAAGGCTAGCGACACTAG
* * * * *
1521602 ACTTAAAGATAAAAGGAATGATAAAGGTACCAATATGCTGATTCAAGACCAGCAATATTAGGCTT
1 GCTTAAAGATGAAA-GAATGATAAAGAT-CCAATATGCTGATTCAAGGCCAGCGATATTAGGCTT
** * * * * * *
1521667 AAAAATGACAAATATGCTAATGTGCTGATTTAAGGCCTA-TGACATTAC
64 AAAAATGACAAAGCTGCCAAGGTGCTGATTCAAGG-CTAGCGACACTAG
*
1521715 ACTTAAAGATGAAA
1 GCTTAAAGATGAAA
1521729 AAAGCGCCAA
Statistics
Matches: 183, Mismatches: 36, Indels: 24
0.75 0.15 0.10
Matches are distributed among these distances:
104 79 0.43
105 1 0.01
106 3 0.02
107 1 0.01
110 1 0.01
111 2 0.01
112 2 0.01
113 92 0.50
114 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (111 bp):
GCTTAAAGATGAAAGAATGATAAAGATCCAATATGCTGATTCAAGGCCAGCGATATTAGGCTTAA
AAATGACAAAGCTGCCAAGGTGCTGATTCAAGGCTAGCGACACTAG
Found at i:1521555 original size:52 final size:52
Alignment explanation
Indices: 1521402--1521992 Score: 252
Period size: 52 Copynumber: 11.0 Consensus size: 52
1521392 GATGAGAAGA
* * * * *
1521402 ATGATAAAGATGCCAATATGCTGATTTAAGGCCAGCGATATTGGGCTTAAAG
1 ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGACTTAAAG
** * * * *
1521454 ATGACAAAGGTGCCAAGGTGTTGATTCAAGGCTAGCGATATTGGGCTTAAAG
1 ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGACTTAAAG
** ** *
1521506 ATGACAAAGGCACCAATATGCTGATTCAAGGCCAATGATATTAGACTTAAAA
1 ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGACTTAAAG
* * * * * ** * *
1521558 AAGAAAAAGCTGCTAATGTGCTGATTCAAGGTTAGCGACACTAGACTTAAAGATAAAAGG
1 ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGAC-T-----T-AAA-G
* * * * * *
1521618 AATGATAAAGGTACCAATATGCTGATTCAAGACCAGCAATATTAGGCTTAAAA
1 -ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGACTTAAAG
** * * * * * *
1521671 ATGACAAATATGCTAATGTGCTGATTTAAGGCCTA-TGACATTACACTTAAAG
1 ATGACAAAGGTGCCAATATGCTGATTCAAGGCC-AGCGATATTAGACTTAAAG
* * * * * *** *
1521723 ATGAAAAAAGCGCCAATATGTTAATTCAAGGCCAATAATATTGGACTT-AAG
1 ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGACTTAAAG
* * * ** * *
1521774 AAAGAAAAAGGTGCCAATGTGCTGATTCAAATCCAGTGATATTAGACTTAAAA
1 -ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGACTTAAAG
* * * * * * * * *
1521827 ATGA-GAAGAATGCTAATGTACTGATTCAAGGCCAGTGACATTGGGCTTAAAAATG
1 ATGACAAAG-GTGCCAATATGCTGATTCAAGGCCAGCGATATTAGACTT--AAA-G
* * ** * * * * * *
1521882 ATAAGGATGAGAAGAATGCCGCTGTGCTGATTCAAAGCCAACGACATTAGGCTTAAAA
1 AT---GA-CA-AAG-GTGCCAATATGCTGATTCAAGGCCAGCGATATTAGACTTAAAG
* ** * * *
1521940 AGGTTAAAGGTGCCAATATACTGATTCAAAGCCAGCGATATCAGACTTAAAG
1 ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGACTTAAAG
1521992 A
1 A
1521993 AAGAAGATTT
Statistics
Matches: 397, Mismatches: 119, Indels: 46
0.71 0.21 0.08
Matches are distributed among these distances:
51 7 0.02
52 293 0.74
53 7 0.02
54 7 0.02
55 4 0.01
58 4 0.01
59 6 0.02
60 1 0.00
61 68 0.17
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.25
Consensus pattern (52 bp):
ATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTAGACTTAAAG
Found at i:1521822 original size:217 final size:216
Alignment explanation
Indices: 1521337--1521838 Score: 551
Period size: 217 Copynumber: 2.3 Consensus size: 216
1521327 TAAGGATGCA
* * * * * * * *
1521337 AAGAATGATAAAGGTGCCAATATGCTGATTCACGGCCAGTAATATCGAGCTTAAAGATGAGAAGA
1 AAGAAAGAAAAAGGTGCCAATGTGCTGATTCAAGTCCAGTGATATAGA-CTTAAAGATGAAAAGA
* * * * * * *
1521402 ATGATAAAGATGCCAATATGCTGATTTAAGGCCAGCGATATTGGGCTTAAAGATGACAAAGGTGC
65 ATGATAAAGATACCAATATGCTGATTCAAGACCAGCAATATTAGGCTTAAAAATGACAAAGATGC
* * *** * * *
1521467 CAAGGTGTTGATTCAAGGCTAGCGATATTGGGCTTAAAGATGACAAAGGCACCAATATGCTGATT
130 CAAGGTGCTGATTCAAGGCTAGCGACATTACACTTAAAGATGAAAAAAGCACCAATATGCTAATT
*
1521532 CAAGGCCAATGATATTAGACTT
195 CAAGGCCAATAATATTAGACTT
* * * * * *
1521554 AAAAAAGAAAAAGCTGCTAATGTGCTGATTCAAGGT-TAGCGACACTAGACTTAAAGAT-AAAAG
1 AAGAAAGAAAAAGGTGCCAATGTGCTGATTCAA-GTCCAGTGATA-TAGACTTAAAGATGAAAA-
* *
1521617 GAATGATAAAGGTACCAATATGCTGATTCAAGACCAGCAATATTAGGCTTAAAAATGACAAATAT
63 GAATGATAAAGATACCAATATGCTGATTCAAGACCAGCAATATTAGGCTTAAAAATGACAAAGAT
* * * * * *
1521682 GCTAATGTGCTGATTTAAGGCCTA-TGACATTACACTTAAAGATGAAAAAAGCGCCAATATGTTA
128 GCCAAGGTGCTGATTCAAGG-CTAGCGACATTACACTTAAAGATGAAAAAAGCACCAATATGCTA
*
1521746 ATTCAAGGCCAATAATATTGGACTT
192 ATTCAAGGCCAATAATATTAGACTT
* * *
1521771 AAGAAAGAAAAAGGTGCCAATGTGCTGATTCAAATCCAGTGATATTAGACTTAAAAATGAGAAGA
1 AAGAAAGAAAAAGGTGCCAATGTGCTGATTCAAGTCCAGTGATA-TAGACTTAAAGATGAAAAGA
1521836 ATG
65 ATG
1521839 CTAATGTACT
Statistics
Matches: 230, Mismatches: 49, Indels: 12
0.79 0.17 0.04
Matches are distributed among these distances:
216 4 0.02
217 216 0.94
218 10 0.04
ACGTcount: A:0.40, C:0.14, G:0.22, T:0.25
Consensus pattern (216 bp):
AAGAAAGAAAAAGGTGCCAATGTGCTGATTCAAGTCCAGTGATATAGACTTAAAGATGAAAAGAA
TGATAAAGATACCAATATGCTGATTCAAGACCAGCAATATTAGGCTTAAAAATGACAAAGATGCC
AAGGTGCTGATTCAAGGCTAGCGACATTACACTTAAAGATGAAAAAAGCACCAATATGCTAATTC
AAGGCCAATAATATTAGACTT
Found at i:1521823 original size:104 final size:103
Alignment explanation
Indices: 1521413--1521879 Score: 312
Period size: 104 Copynumber: 4.4 Consensus size: 103
1521403 TGATAAAGAT
* *** * * * * *
1521413 GCCAATATGCTGATTTAAGGCCAGCGATATTGGGCTTAAAGATGACAAAGGTGCCAAGGTGTTGA
1 GCCAATATGCTGATTCAAGGCCAATAATATTGGACTTAAA-AAGAAAAAGGTGCCAATGTGCTGA
* * * * * *
1521478 TTCAAGGCTAGCGATATTGGGCTTAAAGATGACAAAGGC
65 TTCAAGGCCAGCGACATTAGACTTAAAGATGAAAAAAGC
* * * * *
1521517 ACCAATATGCTGATTCAAGGCCAATGATATTAGACTTAAAAAAGAAAAAGCTGCTAATGTGCTGA
1 GCCAATATGCTGATTCAAGGCCAATAATATTGGACTT-AAAAAGAAAAAGGTGCCAATGTGCTGA
** *
1521582 TTCAAGGTTAGCGACACTAGACTTAAAGATAAAAGGAATGATAAAG-
65 TTCAAGGCCAGCGACATTAGACTTAAAGAT-----GAA--A-AAAGC
* ** * ** *
1521628 GTACCAATATGCTGATTCAAGACCAGCAATATTAGG-CTTAAAAATGACAAATATGCTAATGTGC
1 G--CCAATATGCTGATTCAAGGCCAATAATATT-GGACTTAAAAA-GAAAAAGGTGCCAATGTGC
* * *
1521692 TGATTTAAGGCCTA-TGACATTACACTTAAAGATGAAAAAAGC
62 TGATTCAAGGCC-AGCGACATTAGACTTAAAGATGAAAAAAGC
* *
1521734 GCCAATATGTTAATTCAAGGCCAATAATATTGGACTTAAGAAAGAAAAAGGTGCCAATGTGCTGA
1 GCCAATATGCTGATTCAAGGCCAATAATATTGGACTTAA-AAAGAAAAAGGTGCCAATGTGCTGA
** * * * * *
1521799 TTCAAATCCAGTGATATTAGACTTAAAAATGAGAAGAA-T
65 TTCAAGGCCAGCGACATTAGACTTAAAGATGA-AAAAAGC
* * * * * * *
1521838 GCTAATGTACTGATTCAAGGCCAGTGACATTGGGCTTAAAAA
1 GCCAATATGCTGATTCAAGGCCAATAATATTGGACTTAAAAA
1521880 TGATAAGGAT
Statistics
Matches: 284, Mismatches: 60, Indels: 39
0.74 0.16 0.10
Matches are distributed among these distances:
103 6 0.02
104 176 0.62
105 14 0.05
106 2 0.01
108 3 0.01
109 2 0.01
111 1 0.00
112 8 0.03
113 70 0.25
114 2 0.01
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (103 bp):
GCCAATATGCTGATTCAAGGCCAATAATATTGGACTTAAAAAGAAAAAGGTGCCAATGTGCTGAT
TCAAGGCCAGCGACATTAGACTTAAAGATGAAAAAAGC
Found at i:1522088 original size:31 final size:31
Alignment explanation
Indices: 1522050--1522396 Score: 371
Period size: 31 Copynumber: 11.0 Consensus size: 31
1522040 TGGGCTTAGG
1522050 GGTTGCCACCAACTTGTGTGGGCTTTAGAAA
1 GGTTGCCACCAACTTGTGTGGGCTTTAGAAA
*
1522081 GGTTGCCACCGACTTGTGTGGGCTTTAGAAGA
1 GGTTGCCACCAACTTGTGTGGGCTTTAGAA-A
** * * *
1522113 GGGTTGCCACTGACTTGTCTGAGCTTTAGAAGGG
1 -GGTTGCCACCAACTTGTGTGGGCTTTAGAA--A
* *
1522147 GGTTGCCACCAAATTGTGTGGGCTTTAAAAGA
1 GGTTGCCACCAACTTGTGTGGGCTTTAGAA-A
1522179 GGTTGCCACCAACTTGTGTGGGCTTTAGAAA
1 GGTTGCCACCAACTTGTGTGGGCTTTAGAAA
* *
1522210 GGTTGTCACCAGCTTGTGTGGGCTTTA-AGAA
1 GGTTGCCACCAACTTGTGTGGGCTTTAGA-AA
* *
1522241 GGTTACCACCAACTTGTGTGGGCTTTAAAAA
1 GGTTGCCACCAACTTGTGTGGGCTTTAGAAA
* * *
1522272 GGTTGTCACCAGCTTGTGTGGGCTTTA-AGAG
1 GGTTGCCACCAACTTGTGTGGGCTTTAGA-AA
* * *
1522303 GGTTGCGACCAGCTTGTGTGGGCTTTA-AGAG
1 GGTTGCCACCAACTTGTGTGGGCTTTAGA-AA
* *
1522334 GGTTGCCACCGACTTGTATGGGCTTT-GAAAA
1 GGTTGCCACCAACTTGTGTGGGCTTTAG-AAA
* *
1522365 GGGGTGCCACCGACTTGTGTGGGCTTTA-AAA
1 -GGTTGCCACCAACTTGTGTGGGCTTTAGAAA
1522396 G
1 G
1522397 AAAAAAGTGC
Statistics
Matches: 274, Mismatches: 32, Indels: 21
0.84 0.10 0.06
Matches are distributed among these distances:
30 3 0.01
31 163 0.59
32 56 0.20
33 51 0.19
34 1 0.00
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (31 bp):
GGTTGCCACCAACTTGTGTGGGCTTTAGAAA
Found at i:1522296 original size:93 final size:91
Alignment explanation
Indices: 1522050--1522396 Score: 412
Period size: 93 Copynumber: 3.7 Consensus size: 91
1522040 TGGGCTTAGG
*
1522050 GGTTGCCACCAACTTGTGTGGGCTTTAGAAAGGTTGCCACCGACTTGTGTGGGCTTTAGAAGAGG
1 GGTTGCCACCAACTTGTGTGGGCTTTAAAAAGGTTGCCACCGACTTGTGTGGGCTTTA-AA-A-G
* * *
1522115 GTTGC-CACTGACTTGTCTGAGCTTT-AGAA
63 GTTGCAC-CAG-CTTGTGTGGGCTTTAAGAA
* *
1522144 GGGGGTTGCCACCAAATTGTGTGGGCTTTAAAAGAGGTTGCCACCAACTTGTGTGGGCTTTAGAA
1 ---GGTTGCCACCAACTTGTGTGGGCTTTAAAA-AGGTTGCCACCGACTTGTGTGGGCTTTA-AA
1522209 AGGTTGTCACCAGCTTGTGTGGGCTTTAAGAA
61 AGGTTG-CACCAGCTTGTGTGGGCTTTAAGAA
* * *
1522241 GGTTACCACCAACTTGTGTGGGCTTTAAAAAGGTTGTCACC-AGCTTGTGTGGGCTTTAAGAGGG
1 GGTTGCCACCAACTTGTGTGGGCTTTAAAAAGGTTGCCACCGA-CTTGTGTGGGCTTTAA-AAGG
*
1522305 TTGCGACCAGCTTGTGTGGGCTTTAAGAG
64 TTGC-ACCAGCTTGTGTGGGCTTTAAGAA
* * * *
1522334 GGTTGCCACCGACTTGTATGGGCTTTGAAAAGGGGTGCCACCGACTTGTGTGGGCTTTAAAAG
1 GGTTGCCACCAACTTGTGTGGGCTTT-AAAAAGGTTGCCACCGACTTGTGTGGGCTTTAAAAG
1522397 AAAAAAGTGC
Statistics
Matches: 223, Mismatches: 18, Indels: 22
0.85 0.07 0.08
Matches are distributed among these distances:
92 3 0.01
93 79 0.35
94 56 0.25
95 1 0.00
96 17 0.08
97 36 0.16
98 31 0.14
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (91 bp):
GGTTGCCACCAACTTGTGTGGGCTTTAAAAAGGTTGCCACCGACTTGTGTGGGCTTTAAAAGGTT
GCACCAGCTTGTGTGGGCTTTAAGAA
Found at i:1523798 original size:20 final size:20
Alignment explanation
Indices: 1523773--1523843 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 20
1523763 TGCCTTTGCA
1523773 CATTTTTTTGTTTTTCTTTT
1 CATTTTTTTGTTTTTCTTTT
* *
1523793 CATTTTTGTGCTTTTGCTTTT
1 CATTTTTTTG-TTTTTCTTTT
* * * *
1523814 AACTTTTTTTCTTTTTATTGGT
1 CA-TTTTTTTGTTTTTCTT-TT
1523836 CATTTTTT
1 CATTTTTT
1523844 AAGGGAACTT
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
20 9 0.23
21 22 0.56
22 8 0.21
ACGTcount: A:0.08, C:0.11, G:0.08, T:0.72
Consensus pattern (20 bp):
CATTTTTTTGTTTTTCTTTT
Found at i:1527862 original size:20 final size:20
Alignment explanation
Indices: 1527837--1527913 Score: 66
Period size: 20 Copynumber: 3.8 Consensus size: 20
1527827 CAAAAACCCA
1527837 AAATGTATCGATACAATAAG
1 AAATGTATCGATACAATAAG
*
1527857 AAATGTATCGACACAATTGTAAG
1 AAATGTATCGATACAA---TAAG
* * *
1527880 -CATGTATCGATACATTTAG
1 AAATGTATCGATACAATAAG
* *
1527899 TAATGTATGGATACA
1 AAATGTATCGATACA
1527914 TTTCCTTGCC
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
19 3 0.07
20 27 0.59
22 12 0.26
23 4 0.09
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.30
Consensus pattern (20 bp):
AAATGTATCGATACAATAAG
Found at i:1527965 original size:19 final size:20
Alignment explanation
Indices: 1527941--1527994 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
1527931 AGGGTGGTTT
1527941 TGTATCGATACAAAACT-TA
1 TGTATCGATACAAAACTATA
** *
1527960 TGTATCGATACATTTACTATT
1 TGTATCGATACA-AAACTATA
1527981 TGTATCGATACAAA
1 TGTATCGATACAAA
1527995 TTGTAGAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 12 0.43
20 3 0.11
21 13 0.46
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (20 bp):
TGTATCGATACAAAACTATA
Found at i:1527986 original size:21 final size:19
Alignment explanation
Indices: 1527938--1527994 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
1527928 TGTAGGGTGG
1527938 TTTTGTATCGATACAAAAC
1 TTTTGTATCGATACAAAAC
* **
1527957 TTATGTATCGATACATTTAC
1 TTTTGTATCGATACA-AAAC
1527977 TATTTGTATCGATACAAA
1 T-TTTGTATCGATACAAA
1527995 TTGTAGAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
19 14 0.47
20 3 0.10
21 13 0.43
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (19 bp):
TTTTGTATCGATACAAAAC
Found at i:1531585 original size:12 final size:12
Alignment explanation
Indices: 1531568--1531592 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1531558 ACCTCATATT
1531568 TGTAGTTGCCAA
1 TGTAGTTGCCAA
1531580 TGTAGTTGCCAA
1 TGTAGTTGCCAA
1531592 T
1 T
1531593 AGAGAATACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (12 bp):
TGTAGTTGCCAA
Found at i:1532767 original size:120 final size:120
Alignment explanation
Indices: 1532609--1532848 Score: 455
Period size: 120 Copynumber: 2.0 Consensus size: 120
1532599 TCAAATTAAG
1532609 GCTACTGCAAATGGTAAAGAATAATAAAAAAAAGAAAAGAAATATAGCAAATCAAACACGCATGG
1 GCTACTGCAAATGGTAAAGAATAATAAAAAAAAGAAAAGAAATATAGCAAATCAAACACGCATGG
1532674 CAGCATCAAGTGGGCAACATGAGTGTAGATACCAAATTTTGTTC-GGCCATTTTTA
66 CAGCATCAAGTGGGCAACATGAGTGTAGATACCAAATTTT-TTCGGGCCATTTTTA
1532729 GCTACTGCAAATGGTAAAGAATAATAAAAAAAAGAAAAGAAATATAGCAAATCAAACACGCATGG
1 GCTACTGCAAATGGTAAAGAATAATAAAAAAAAGAAAAGAAATATAGCAAATCAAACACGCATGG
*
1532794 CAGCATCAAGTGGGCAGCATGAGTGTAGATACCAAATTTTTTCGGGCCATTTTTA
66 CAGCATCAAGTGGGCAACATGAGTGTAGATACCAAATTTTTTCGGGCCATTTTTA
1532849 AGACACTCAT
Statistics
Matches: 118, Mismatches: 1, Indels: 2
0.98 0.01 0.02
Matches are distributed among these distances:
119 3 0.03
120 115 0.97
ACGTcount: A:0.43, C:0.15, G:0.20, T:0.23
Consensus pattern (120 bp):
GCTACTGCAAATGGTAAAGAATAATAAAAAAAAGAAAAGAAATATAGCAAATCAAACACGCATGG
CAGCATCAAGTGGGCAACATGAGTGTAGATACCAAATTTTTTCGGGCCATTTTTA
Found at i:1533729 original size:17 final size:16
Alignment explanation
Indices: 1533696--1533741 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
1533686 ATAAGTAAGA
**
1533696 AAGAAAGAAGATGAAG
1 AAGAAAGAAGAAAAAG
1533712 AAGAAAGGAAGAAAAAG
1 AAGAAA-GAAGAAAAAG
1533729 AA-AAA-AAGAAAAA
1 AAGAAAGAAGAAAAA
1533742 AACATATGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 8 0.30
16 9 0.33
17 10 0.37
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (16 bp):
AAGAAAGAAGAAAAAG
Found at i:1536245 original size:31 final size:31
Alignment explanation
Indices: 1536199--1536267 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
1536189 TTCCTATTTG
*
1536199 ACTGTATTCGATCAAATCTTATCCCTTCTTC
1 ACTGTATACGATCAAATCTTATCCCTTCTTC
* * *
1536230 ACTGTATACGGTCAAATTTTATCCTTTCTTC
1 ACTGTATACGATCAAATCTTATCCCTTCTTC
1536261 ACTGTAT
1 ACTGTAT
1536268 TCAGTCAAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.23, C:0.25, G:0.09, T:0.43
Consensus pattern (31 bp):
ACTGTATACGATCAAATCTTATCCCTTCTTC
Found at i:1536275 original size:31 final size:30
Alignment explanation
Indices: 1536199--1536275 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 30
1536189 TTCCTATTTG
1536199 ACTGTATTCGATCAAATCTTATCCCTTCTTC
1 ACTGTATTCG-TCAAATCTTATCCCTTCTTC
* * *
1536230 ACTGTATACGGTCAAATTTTATCCTTTCTTC
1 ACTGTATTC-GTCAAATCTTATCCCTTCTTC
1536261 ACTGTATTCAGTCAA
1 ACTGTATTC-GTCAA
1536276 GACCTTCCTT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 39 0.98
32 1 0.03
ACGTcount: A:0.25, C:0.25, G:0.09, T:0.42
Consensus pattern (30 bp):
ACTGTATTCGTCAAATCTTATCCCTTCTTC
Found at i:1536399 original size:123 final size:125
Alignment explanation
Indices: 1536238--1536503 Score: 310
Period size: 123 Copynumber: 2.1 Consensus size: 125
1536228 TCACTGTATA
* *
1536238 CGGTCAAATTTTATCCTTTCTTCACTGTATTCAGTCAAGACCTTCCTTATTCGGCTGTACTCAGT
1 CGGTCAAATCTT-TCCTTTCTTCACTGTATTCAGTCAAGACCTTCCTTATTCAGCTGTACTCAGT
** * *
1536303 TGACTAGAATTTCC-TCC-TACTTAACTATATTCAGTTGAGCCTTTT-C-ATTTGACTATACT
65 CAAATAGAA--TCCACCCTTACTTAACTATATTCAGTTGAGCCTTTTCCTATTTGACTATACT
* * * * *
1536362 CGGTCAAATCTTTCCTTTTTTGATTGTATTC-GATCAAGACCTTCCTTATTCAGCTGTATTCGGT
1 CGGTCAAATCTTTCCTTTCTTCACTGTATTCAG-TCAAGACCTTCCTTATTCAGCTGTACTCAGT
* * *
1536426 CAAATAGAATCCACCCTTACTTAACTGTATTCGGTTGAGCCTTTTCCTATTTGACTATATT
65 CAAATAGAATCCACCCTTACTTAACTATATTCAGTTGAGCCTTTTCCTATTTGACTATACT
*
1536487 CGATCAAGATC-TTCCTT
1 CGGTCAA-ATCTTTCCTT
1536504 AGTCAACTAT
Statistics
Matches: 121, Mismatches: 15, Indels: 11
0.82 0.10 0.07
Matches are distributed among these distances:
121 3 0.02
122 3 0.02
123 76 0.63
124 12 0.10
125 24 0.20
126 3 0.02
ACGTcount: A:0.23, C:0.24, G:0.13, T:0.41
Consensus pattern (125 bp):
CGGTCAAATCTTTCCTTTCTTCACTGTATTCAGTCAAGACCTTCCTTATTCAGCTGTACTCAGTC
AAATAGAATCCACCCTTACTTAACTATATTCAGTTGAGCCTTTTCCTATTTGACTATACT
Found at i:1536633 original size:30 final size:30
Alignment explanation
Indices: 1536566--1536667 Score: 82
Period size: 30 Copynumber: 3.4 Consensus size: 30
1536556 CTTTCCCTAT
* * * *
1536566 TTAACTGTACTCGATCAAATCATACCT-GTC
1 TTAACTGTATTCGGTCAAATCTTTCCTCG-C
* *
1536596 TTGACTGTATTCGGTCAGGATCTTT-CTCGC
1 TTAACTGTATTCGGTCA-AATCTTTCCTCGC
* * *
1536626 TTAACTGTACTCGGTTAAATCTTTCCTTGC
1 TTAACTGTATTCGGTCAAATCTTTCCTCGC
*
1536656 TTAATTGTATTC
1 TTAACTGTATTC
1536668 ATTTAAGCCT
Statistics
Matches: 56, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
29 6 0.11
30 45 0.80
31 5 0.09
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.41
Consensus pattern (30 bp):
TTAACTGTATTCGGTCAAATCTTTCCTCGC
Found at i:1536884 original size:47 final size:47
Alignment explanation
Indices: 1536768--1536894 Score: 148
Period size: 47 Copynumber: 2.7 Consensus size: 47
1536758 CCCCTATCTA
* * * *
1536768 ACTGTATTGGCGTTAAGACCTAGTTAAACTCTT-TTTCACACTTATTTG
1 ACTGTATTGGCATTAAGACCT-GTTCAAC-CTTCTTACACACTCATTTG
* * *
1536816 ACTGTATTGGCATTAGGACCTGGTCAACCTTCTTACACACTCGTTTG
1 ACTGTATTGGCATTAAGACCTGTTCAACCTTCTTACACACTCATTTG
* *
1536863 ACTGTATTGGCATTAAAACCTGTTCAAACTTC
1 ACTGTATTGGCATTAAGACCTGTTCAACCTTC
1536895 AATTCCCTTA
Statistics
Matches: 67, Mismatches: 11, Indels: 3
0.83 0.14 0.04
Matches are distributed among these distances:
46 3 0.04
47 45 0.67
48 19 0.28
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (47 bp):
ACTGTATTGGCATTAAGACCTGTTCAACCTTCTTACACACTCATTTG
Found at i:1537253 original size:42 final size:42
Alignment explanation
Indices: 1537206--1537343 Score: 129
Period size: 42 Copynumber: 3.3 Consensus size: 42
1537196 CTTTCCCATA
*
1537206 AGTCTGCCTATCAATTTTGACCTTAGAGACTTTCTTACCTTC
1 AGTCTGCCTATCAATTTTAACCTTAGAGACTTTCTTACCTTC
* ** * * *
1537248 AGTCTGCCTGTCAGCTTTAACCTTGGAGA-TTGCTT-CATCTC
1 AGTCTGCCTATCAATTTTAACCTTAGAGACTTTCTTACCT-TC
* * *
1537289 AAGTCTGCTTGTCAATTTTAACCTTAGAGAC-TTCATTATCCTTA
1 -AGTCTGCCTATCAATTTTAACCTTAGAGACTTTC-TTA-CCTTC
1537333 AGTCTGCCTAT
1 AGTCTGCCTAT
1537344 TAGCCTTGAC
Statistics
Matches: 74, Mismatches: 16, Indels: 11
0.73 0.16 0.11
Matches are distributed among these distances:
40 2 0.03
41 7 0.09
42 51 0.69
43 11 0.15
44 1 0.01
45 2 0.03
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.39
Consensus pattern (42 bp):
AGTCTGCCTATCAATTTTAACCTTAGAGACTTTCTTACCTTC
Found at i:1537484 original size:44 final size:44
Alignment explanation
Indices: 1537372--1537512 Score: 158
Period size: 44 Copynumber: 3.2 Consensus size: 44
1537362 CTTCCTCACC
* ** * * * * *
1537372 CCTTAAGTCTGCTTACCGGCTTTGATCTTGGACACTT-CATTAC
1 CCTTAAGTCTACTTGTCGGCCTTGACCTTGGAAACTTCCTTTAT
* * *
1537415 CCTTAAGTCTACTTGTCGGCTTTGACTTTGGAAACTTTCTTTAT
1 CCTTAAGTCTACTTGTCGGCCTTGACCTTGGAAACTTCCTTTAT
* *
1537459 CCTTAAGTCTACTTGTTGGCCTTGACCTTGGAGACTTCCTTTAT
1 CCTTAAGTCTACTTGTCGGCCTTGACCTTGGAAACTTCCTTTAT
1537503 CCTTAAGTCT
1 CCTTAAGTCT
1537513 GTCTGTCAAC
Statistics
Matches: 84, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
43 31 0.37
44 53 0.63
ACGTcount: A:0.18, C:0.25, G:0.16, T:0.41
Consensus pattern (44 bp):
CCTTAAGTCTACTTGTCGGCCTTGACCTTGGAAACTTCCTTTAT
Found at i:1537528 original size:44 final size:43
Alignment explanation
Indices: 1536900--1537632 Score: 427
Period size: 43 Copynumber: 17.0 Consensus size: 43
1536890 ACTTCAATTC
* *
1536900 CCTTAAGTCTGCCTGTTAGCTTTGACCCTAGAGACTTCCTT-T
1 CCTTAAGTCTGCCTGTCAGCTTTGACCTTAGAGACTTCCTTAT
* * * **
1536942 CTCTTAAGTCTGTCTATCGGCTTTGACCTCGGAGACTTCCTTA-
1 C-CTTAAGTCTGCCTGTCAGCTTTGACCTTAGAGACTTCCTTAT
* * * *
1536985 CGTTTAAGTCTGCCTGTC-GACTTTGACCCTAAAGACTTTCTT-T
1 C-CTTAAGTCTGCCTGTCAG-CTTTGACCTTAGAGACTTCCTTAT
* * * * * *
1537028 ACCTTTAAATCTGTCTATTAGCTTTGACCTTAGAAACTTCCTCAT
1 -CC-TTAAGTCTGCCTGTCAGCTTTGACCTTAGAGACTTCCTTAT
* * * *
1537073 -TTTAAGTCTGCCTGTTAGCTTTGACCCTAAAGACTTCCTTAT
1 CCTTAAGTCTGCCTGTCAGCTTTGACCTTAGAGACTTCCTTAT
* * * * * *
1537115 CCTTGAGTTTGCCTAT-TGACTTTAACCCTAGAGACTTCCTTA-
1 CCTTAAGTCTGCCTGTCAG-CTTTGACCTTAGAGACTTCCTTAT
* *
1537157 CCTTTAAGTTTGCCTGT-TGACTTTGACCTT-GAAGACTTCCTT-T
1 CC-TTAAGTCTGCCTGTCAG-CTTTGACCTTAG-AGACTTCCTTAT
* * ** *
1537200 CCCATAAGTCTGCCTATCAATTTTGACCTTAGAGACTTTCTTA-
1 -CCTTAAGTCTGCCTGTCAGCTTTGACCTTAGAGACTTCCTTAT
* * * *
1537243 CCTTCAGTCTGCCTGTCAGCTTTAACCTTGGAGA-TTGCTTCAT
1 CCTTAAGTCTGCCTGTCAGCTTTGACCTTAGAGACTTCCTT-AT
* * ** * *
1537286 -CTCAAGTCTGCTTGTCAATTTTAACCTTAGAGACTTCATTAT
1 CCTTAAGTCTGCCTGTCAGCTTTGACCTTAGAGACTTCCTTAT
* * * * * *
1537328 CCTTAAGTCTGCCTATTAGCCTTGACCCTAGAGACTTCCTCACC
1 CCTTAAGTCTGCCTGTCAGCTTTGACCTTAGAGACTTCCTTA-T
* ** * * * * * *
1537372 CCTTAAGTCTGCTTACCGGCTTTGATCTTGGACACTTCATTAC
1 CCTTAAGTCTGCCTGTCAGCTTTGACCTTAGAGACTTCCTTAT
* * * * * * *
1537415 CCTTAAGTCTACTTGTCGGCTTTGACTTTGGAAACTTTCTTTAT
1 CCTTAAGTCTGCCTGTCAGCTTTGACCTTAGAGAC-TTCCTTAT
* * ** * *
1537459 CCTTAAGTCTACTTGTTGGCCTTGACCTTGGAGACTTCCTTTAT
1 CCTTAAGTCTGCCTGTCAGCTTTGACCTTAGAGACTTCC-TTAT
* * * *
1537503 CCTTAAGTCTGTCTGTCAACTTTGACCCTAGAGACTTCATTA-
1 CCTTAAGTCTGCCTGTCAGCTTTGACCTTAGAGACTTCCTTAT
* * * * * *
1537545 CCTATAAGTCTACCT-ACTGGCTTTGACCTTAAAGACTTCATTAC
1 CCT-TAAGTCTGCCTGTC-AGCTTTGACCTTAGAGACTTCCTTAT
* ** *
1537589 CCTTAAGTCTGCCTGTC-GACTTAGACCCGAGAGACTTCTTTAT
1 CCTTAAGTCTGCCTGTCAG-CTTTGACCTTAGAGACTTCCTTAT
1537632 C
1 C
1537633 TTTCGTCTAC
Statistics
Matches: 533, Mismatches: 129, Indels: 57
0.74 0.18 0.08
Matches are distributed among these distances:
41 5 0.01
42 102 0.19
43 287 0.54
44 137 0.26
45 2 0.00
ACGTcount: A:0.21, C:0.26, G:0.15, T:0.38
Consensus pattern (43 bp):
CCTTAAGTCTGCCTGTCAGCTTTGACCTTAGAGACTTCCTTAT
Found at i:1537701 original size:42 final size:42
Alignment explanation
Indices: 1537611--1537869 Score: 173
Period size: 42 Copynumber: 6.2 Consensus size: 42
1537601 CTGTCGACTT
* * *
1537611 AGACCCGAGAGACTTCTTT-ATCTTTCGTCTACCGATCGGCTT
1 AGACCCGAGAGACTT-TTTCATCTTTCGTCTGCCCATCGGCTC
* * *
1537653 AGACCCGACAGACTTTTTCATCTTTCGTTTGCCCATCAGCTC
1 AGACCCGAGAGACTTTTTCATCTTTCGTCTGCCCATCGGCTC
* * * ** **
1537695 AAACCCGGGAGACCTCGTCATCTTTCGTCTGCCTGTCGGCTC
1 AGACCCGAGAGACTTTTTCATCTTTCGTCTGCCCATCGGCTC
* * ** * * ** *
1537737 AAACCCGAAAGAC-TTTTCATCAATCGTCTGCTCGTCAACTT
1 AGACCCGAGAGACTTTTTCATCTTTCGTCTGCCCATCGGCTC
* * * * * * * *
1537778 AGACTCGGGAGACCTCTTCATCTTTCATTTGCCCATTGGCTT
1 AGACCCGAGAGACTTTTTCATCTTTCGTCTGCCCATCGGCTC
* * * *
1537820 AGACCCGAAAGACTCTTTT-ATCATTCATTTGCCCATCGGCTC
1 AGACCCGAGAGACT-TTTTCATCTTTCGTCTGCCCATCGGCTC
1537862 AGACCCGA
1 AGACCCGA
1537870 AAAACTTCCT
Statistics
Matches: 165, Mismatches: 49, Indels: 6
0.75 0.22 0.03
Matches are distributed among these distances:
41 31 0.19
42 131 0.79
43 3 0.02
ACGTcount: A:0.21, C:0.31, G:0.17, T:0.31
Consensus pattern (42 bp):
AGACCCGAGAGACTTTTTCATCTTTCGTCTGCCCATCGGCTC
Found at i:1537826 original size:83 final size:83
Alignment explanation
Indices: 1537607--1537856 Score: 239
Period size: 83 Copynumber: 3.0 Consensus size: 83
1537597 CTGCCTGTCG
* * * * * *
1537607 ACTTAGACCCGAGAGACTTCTTTATCTTTCGTCTACCGATCGGCTTAGACCCGACAGACTTTTTC
1 ACTTAGACCCGGGAGACCTCTTCATCTTTCGTCTGCCCATCGGCTTAGACCCGAAAGAC-TTTTC
** *
1537672 ATCTTTCGTTTGCCCATCA
65 ATCAATCGTCTGCCCATCA
* * * * ** * *
1537691 GCTCAAACCCGGGAGACCTCGTCATCTTTCGTCTGCCTGTCGGCTCAAACCCGAAAGACTTTTCA
1 ACTTAGACCCGGGAGACCTCTTCATCTTTCGTCTGCCCATCGGCTTAGACCCGAAAGACTTTTCA
* *
1537756 TCAATCGTCTGCTCGTCA
66 TCAATCGTCTGCCCATCA
* * * * *
1537774 ACTTAGACTCGGGAGACCTCTTCATCTTTCATTTGCCCATTGGCTTAGACCCGAAAGACTCTTTT
1 ACTTAGACCCGGGAGACCTCTTCATCTTTCGTCTGCCCATCGGCTTAGACCCGAAAGACT-TTTC
* * *
1537839 ATCATTCATTTGCCCATC
65 ATCAATCGTCTGCCCATC
1537857 GGCTCAGACC
Statistics
Matches: 129, Mismatches: 36, Indels: 2
0.77 0.22 0.01
Matches are distributed among these distances:
83 67 0.52
84 62 0.48
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.32
Consensus pattern (83 bp):
ACTTAGACCCGGGAGACCTCTTCATCTTTCGTCTGCCCATCGGCTTAGACCCGAAAGACTTTTCA
TCAATCGTCTGCCCATCA
Found at i:1537870 original size:42 final size:43
Alignment explanation
Indices: 1537801--1537885 Score: 127
Period size: 42 Copynumber: 2.0 Consensus size: 43
1537791 CTCTTCATCT
* * * *
1537801 TTCATTTGCCCATTGGCTTAGACCCGAAAGAC-TCTTTTATCA
1 TTCATTTGCCCATCGGCTCAGACCCGAAAAACTTCCTTTATCA
1537843 TTCATTTGCCCATCGGCTCAGACCCGAAAAACTTCCTTTATCA
1 TTCATTTGCCCATCGGCTCAGACCCGAAAAACTTCCTTTATCA
1537886 ATTATCTACC
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
42 29 0.76
43 9 0.24
ACGTcount: A:0.25, C:0.29, G:0.13, T:0.33
Consensus pattern (43 bp):
TTCATTTGCCCATCGGCTCAGACCCGAAAAACTTCCTTTATCA
Found at i:1538289 original size:40 final size:41
Alignment explanation
Indices: 1538234--1538316 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 41
1538224 TTGTTATCTT
**
1538234 TCGTCTGCCCGTCAGCT-CTAGTAGGGAGATTTCTCATCAA
1 TCGTCTGCCCGTCAGCTAAGAGTAGGGAGATTTCTCATCAA
1538274 TCGTCTGCCCGTCAGCTAAGAGTAGGGAGATTTCTCATCAA
1 TCGTCTGCCCGTCAGCTAAGAGTAGGGAGATTTCTCATCAA
1538315 TC
1 TC
1538317 AGCTTAGACC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
40 17 0.43
41 23 0.57
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.29
Consensus pattern (41 bp):
TCGTCTGCCCGTCAGCTAAGAGTAGGGAGATTTCTCATCAA
Found at i:1538468 original size:42 final size:42
Alignment explanation
Indices: 1538318--1538914 Score: 311
Period size: 42 Copynumber: 14.2 Consensus size: 42
1538308 TCATCAATCA
** * * * *
1538318 GCTTAGACCCAAGAGACCTCTTCATCTTTCGTCTGCCTAAT-G
1 GCTTAGACCCGGGAGACTTCTTCATCTTTTGTCTACC-CATCG
* * * * *
1538360 GCTTAGACCCGGGAGAGTTGTTTATCATTCGTCTACCCATCG
1 GCTTAGACCCGGGAGACTTCTTCATCTTTTGTCTACCCATCG
* * * ** * * * * *
1538402 CCTCAAACTTGGGAGATTTTTTCATATTTTGTCTACTCATTG
1 GCTTAGACCCGGGAGACTTCTTCATCTTTTGTCTACCCATCG
* * ** * * * *
1538444 GCTTAGACCGGGGAGACTCCTTCATCCATCGTTTGCCCGTCG
1 GCTTAGACCCGGGAGACTTCTTCATCTTTTGTCTACCCATCG
* * *
1538486 GCTTAGACCCGGGAGACTTCTTTATCTTTTGTCTGCCCGTCG
1 GCTTAGACCCGGGAGACTTCTTCATCTTTTGTCTACCCATCG
*
1538528 GCTTAGACCCGGGAGACTTTTTCATCTTTTGTCTACCCATCG
1 GCTTAGACCCGGGAGACTTCTTCATCTTTTGTCTACCCATCG
* ** * ** * * * * *
1538570 GCTCAGACCTAGAAGAC-TCTTTCATCCATCGTTTGCTCGTCG
1 GCTTAGACCCGGGAGACTTC-TTCATCTTTTGTCTACCCATCG
** * * * *
1538612 GCTTAGACTTGGGAGACTTTTTTATCTTTTGTCTACCCGTAG
1 GCTTAGACCCGGGAGACTTCTTCATCTTTTGTCTACCCATCG
* ** * * * **
1538654 GCTAAGACCTAGGAGACTTTTTCATCTTTCGTCTGCCTGTCG
1 GCTTAGACCCGGGAGACTTCTTCATCTTTTGTCTACCCATCG
* * * ** ** * *
1538696 ACTTAGACCTGGGAGACTTTTTCATCCATCATCTGCCCGTCG
1 GCTTAGACCCGGGAGACTTCTTCATCTTTTGTCTACCCATCG
* * * * *
1538738 ACTTAGACCCGAGAGACTTCTTTATCTTTCGTCTGCCCATCG
1 GCTTAGACCCGGGAGACTTCTTCATCTTTTGTCTACCCATCG
** * * * *
1538780 GCTTAGACCTAGGAGACTTTTTCAT-TTTTCGTTTTCCCGTCG
1 GCTTAGACCCGGGAGACTTCTTCATCTTTT-GTCTACCCATCG
* ** * *
1538822 GCTTAGACCTGGGAGACTTC-TCATCAATTATCTACCCGTCG
1 GCTTAGACCCGGGAGACTTCTTCATCTTTTGTCTACCCATCG
* * * * * * * *
1538863 GTTTAGATCTGGGAGACCTCTTCATCTTTCGTTTGCTCAATCG
1 GCTTAGACCCGGGAGACTTCTTCATCTTTTGTCTAC-CCATCG
1538906 GCTTAGACC
1 GCTTAGACC
1538915 TAGATAACTA
Statistics
Matches: 420, Mismatches: 128, Indels: 13
0.75 0.23 0.02
Matches are distributed among these distances:
41 36 0.09
42 372 0.89
43 12 0.03
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.35
Consensus pattern (42 bp):
GCTTAGACCCGGGAGACTTCTTCATCTTTTGTCTACCCATCG
Found at i:1538543 original size:126 final size:125
Alignment explanation
Indices: 1538359--1538917 Score: 530
Period size: 126 Copynumber: 4.4 Consensus size: 125
1538349 TCTGCCTAAT
* * * * * * * * *
1538359 GGCTTAGACCCGGGAGAGTTGTTTATCATTCGTCTACCCATCGCCTCAAACTTGGGAGATTTTTT
1 GGCTTAGACCCGGGAGACTTCTTTATCTTTCGTCTACCCATCGGCTTAGACCTAGGAGACTTTTT
* * *
1538424 CATATTTTGTCTACTCATTGGCTTAGACCGGGGAGACTCCTTCATCCATCGTTTGCCCGTC
66 CATCTTTTGTCTAC-CATTGGCTTAGACCTGGGAGACTCTTTCATCCATCGTTTGCCCGTC
* * * **
1538485 GGCTTAGACCCGGGAGACTTCTTTATCTTTTGTCTGCCCGTCGGCTTAGACCCGGGAGACTTTTT
1 GGCTTAGACCCGGGAGACTTCTTTATCTTTCGTCTACCCATCGGCTTAGACCTAGGAGACTTTTT
* * * * *
1538550 CATCTTTTGTCTACCCATCGGCTCAGACCTAGAAGACTCTTTCATCCATCGTTTGCTCGTC
66 CATCTTTTGTCTA-CCATTGGCTTAGACCTGGGAGACTCTTTCATCCATCGTTTGCCCGTC
** * * * * *
1538611 GGCTTAGACTTGGGAGACTTTTTTATCTTTTGTCTACCCGTAGGCTAAGACCTAGGAGACTTTTT
1 GGCTTAGACCCGGGAGACTTCTTTATCTTTCGTCTACCCATCGGCTTAGACCTAGGAGACTTTTT
* * * * * *
1538676 CATCTTTCGTCTGCC-TGTCGACTTAGACCTGGGAGACTTTTTCATCCATCATCTGCCCGTC
66 CATCTTTTGTCTACCAT-T-GGCTTAGACCTGGGAGACTCTTTCATCCATCGTTTGCCCGTC
* * *
1538737 GACTTAGACCCGAGAGACTTCTTTATCTTTCGTCTGCCCATCGGCTTAGACCTAGGAGACTTTTT
1 GGCTTAGACCCGGGAGACTTCTTTATCTTTCGTCTACCCATCGGCTTAGACCTAGGAGACTTTTT
* * * * * * ** * *
1538802 CAT-TTTTCGTTTTCCCGTCGGCTTAGACCTGGGAGACT-TCTCATCAATTATCTACCCGTC
66 CATCTTTT-G-TCTACCATTGGCTTAGACCTGGGAGACTCTTTCATCCATCGTTTGCCCGTC
* * * * * * * *
1538862 GGTTTAGATCTGGGAGACCTCTTCATCTTTCGTTTGCTCAATCGGCTTAGACCTAG
1 GGCTTAGACCCGGGAGACTTCTTTATCTTTCGTCTAC-CCATCGGCTTAGACCTAG
1538918 ATAACTACTT
Statistics
Matches: 359, Mismatches: 67, Indels: 14
0.82 0.15 0.03
Matches are distributed among these distances:
124 1 0.00
125 52 0.14
126 300 0.84
127 5 0.01
128 1 0.00
ACGTcount: A:0.18, C:0.27, G:0.21, T:0.35
Consensus pattern (125 bp):
GGCTTAGACCCGGGAGACTTCTTTATCTTTCGTCTACCCATCGGCTTAGACCTAGGAGACTTTTT
CATCTTTTGTCTACCATTGGCTTAGACCTGGGAGACTCTTTCATCCATCGTTTGCCCGTC
Found at i:1538553 original size:84 final size:84
Alignment explanation
Indices: 1538443--1538915 Score: 432
Period size: 84 Copynumber: 5.6 Consensus size: 84
1538433 TCTACTCATT
* ** ** * *
1538443 GGCTTAGACCGGGGAGACTCCTTCATCCATCGTTTGCCCGTCGGCTTAGACCCGGGAGACTTCTT
1 GGCTTAGACCTGGGAGACTTTTTCATCTTTCGTCTGCCCGTCGGCTTAGACCTGGGAGACTTCTT
*
1538508 TATCTTTTGTCTGCCCGTC
66 TATCTTTCGTCTGCCCGTC
* * * * * * *
1538527 GGCTTAGACCCGGGAGACTTTTTCATCTTTTGTCTACCCATCGGCTCAGACCTAGAAGAC-TCTT
1 GGCTTAGACCTGGGAGACTTTTTCATCTTTCGTCTGCCCGTCGGCTTAGACCTGGGAGACTTCTT
** * *
1538591 TCATCCATCGTTTGCTCGTC
66 T-ATCTTTCGTCTGCCCGTC
* * * * * * *
1538611 GGCTTAGACTTGGGAGACTTTTTTATCTTTTGTCTACCCGTAGGCTAAGACCTAGGAGACTT-TT
1 GGCTTAGACCTGGGAGACTTTTTCATCTTTCGTCTGCCCGTCGGCTTAGACCTGGGAGACTTCTT
*
1538675 TCATCTTTCGTCTGCCTGTC
66 T-ATCTTTCGTCTGCCCGTC
* ** * * * *
1538695 GACTTAGACCTGGGAGACTTTTTCATCCATCATCTGCCCGTCGACTTAGACCCGAGAGACTTCTT
1 GGCTTAGACCTGGGAGACTTTTTCATCTTTCGTCTGCCCGTCGGCTTAGACCTGGGAGACTTCTT
*
1538760 TATCTTTCGTCTGCCCATC
66 TATCTTTCGTCTGCCCGTC
* * * *
1538779 GGCTTAGACCTAGGAGACTTTTTCATTTTTCGTTTTCCCGTCGGCTTAGACCTGGGAGACTTC-T
1 GGCTTAGACCTGGGAGACTTTTTCATCTTTCGTCTGCCCGTCGGCTTAGACCTGGGAGACTTCTT
* * * *
1538843 CATCAATT-ATCTACCCGTC
66 TATC-TTTCGTCTGCCCGTC
* * * * * **
1538862 GGTTTAGATCTGGGAGACCTCTTCATCTTTCGTTTGCTCAATCGGCTTAGACCT
1 GGCTTAGACCTGGGAGACTTTTTCATCTTTCGTCTGC-CCGTCGGCTTAGACCT
1538916 AGATAACTAC
Statistics
Matches: 313, Mismatches: 71, Indels: 10
0.79 0.18 0.03
Matches are distributed among these distances:
83 47 0.15
84 262 0.84
85 4 0.01
ACGTcount: A:0.17, C:0.28, G:0.21, T:0.35
Consensus pattern (84 bp):
GGCTTAGACCTGGGAGACTTTTTCATCTTTCGTCTGCCCGTCGGCTTAGACCTGGGAGACTTCTT
TATCTTTCGTCTGCCCGTC
Found at i:1540417 original size:40 final size:41
Alignment explanation
Indices: 1540320--1540433 Score: 149
Period size: 40 Copynumber: 2.8 Consensus size: 41
1540310 AAAAAAGAAA
* * * *
1540320 AAACTAGCAAGTAACGAAAAGATAACCAAGCTGCAACAAAGC
1 AAAC-AGCAAGCAATGAAGAGAGAACCAAGCTGCAACAAAGC
* *
1540362 AAACAGCAAGCAATGAAGAGGGAACCAAGCTGCAGC-AAGC
1 AAACAGCAAGCAATGAAGAGAGAACCAAGCTGCAACAAAGC
*
1540402 AAACAGCAAGGAATGAAGAGAGAACCAAGCTG
1 AAACAGCAAGCAATGAAGAGAGAACCAAGCTG
1540434 TAATCAACAA
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
40 34 0.53
41 26 0.41
42 4 0.06
ACGTcount: A:0.49, C:0.20, G:0.24, T:0.07
Consensus pattern (41 bp):
AAACAGCAAGCAATGAAGAGAGAACCAAGCTGCAACAAAGC
Found at i:1544849 original size:28 final size:28
Alignment explanation
Indices: 1544791--1544872 Score: 78
Period size: 28 Copynumber: 3.0 Consensus size: 28
1544781 ATTGAAAAAT
* **
1544791 AAGAAAGATCAAA-GAAGTGAAATCAAC
1 AAGAAATATCAAAGGAAACGAAATCAAC
*
1544818 AAGAAATATGAAAGGAAACGAAAT-AAGC
1 AAGAAATATCAAAGGAAACGAAATCAA-C
* **
1544846 AAGAAATTTCAAAGGAAAATAAATCAA
1 AAGAAATATCAAAGGAAACGAAATCAA
1544873 TAAAGAATTC
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
27 13 0.30
28 29 0.66
29 2 0.05
ACGTcount: A:0.61, C:0.09, G:0.17, T:0.13
Consensus pattern (28 bp):
AAGAAATATCAAAGGAAACGAAATCAAC
Found at i:1545039 original size:28 final size:28
Alignment explanation
Indices: 1544999--1545052 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
1544989 ATAGCTAAAG
1544999 GTTAGAATTCTAGAACACTTTTTTTTTT
1 GTTAGAATTCTAGAACACTTTTTTTTTT
1545027 GTTAGAATTCTAGAACACTTTTTTTT
1 GTTAGAATTCTAGAACACTTTTTTTT
1545053 CTTTTGTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.52
Consensus pattern (28 bp):
GTTAGAATTCTAGAACACTTTTTTTTTT
Found at i:1554159 original size:407 final size:407
Alignment explanation
Indices: 1553404--1554219 Score: 1623
Period size: 407 Copynumber: 2.0 Consensus size: 407
1553394 CTACTTAGAG
1553404 GCATTTCGAGTTTGTAAAATCTCTTTGTATTGTAAAAGGTTGTATTCAACCTTGGGGTACAATCT
1 GCATTTCGAGTTTGTAAAATCTCTTTGTATTGTAAAAGGTTGTATTCAACCTTGGGGTACAATCT
1553469 CTCAAGGATTTGGGGTATAATTCTTGGAGAGATTGAGAGGTTCTTATCTTAGCCTTCAAAAGATA
66 CTCAAGGATTTGGGGTATAATTCTTGGAGAGATTGAGAGGTTCTTATCTTAGCCTTCAAAAGATA
1553534 AGTGTTGTAAGGTTATACCTTTGCCTTAAAGGTAAACAATTCTAGTAGTGAATTATGATATACAC
131 AGTGTTGTAAGGTTATACCTTTGCCTTAAAGGTAAACAATTCTAGTAGTGAATTATGATATACAC
1553599 TTGACAAGGAAGTGTCGAGGAGAGAGGACGTAGATGCCGTGTTTGGACCGAACCTCTATAAACAC
196 TTGACAAGGAAGTGTCGAGGAGAGAGGACGTAGATGCCGTGTTTGGACCGAACCTCTATAAACAC
1553664 TTATATCAAGCTTTCTCTTTTCCTAATTCTTTTTATCTTCGATTTGTTTTTGCATCAATTCTTTC
261 TTATATCAAGCTTTCTCTTTTCCTAATTCTTTTTATCTTCGATTTGTTTTTGCATCAATTCTTTC
1553729 AAAACTTTCATTTTTTGATAAGAACCAATTCACCCCCCATCTTGGTTCATTCTCTATATTTGAGC
326 AAAACTTTCATTTTTTGATAAGAACCAATTCACCCCCCATCTTGGTTCATTCTCTATATTTGAGC
1553794 TTACAATTAGTATAAGA
391 TTACAATTAGTATAAGA
1553811 GCATTTCGAGTTTGTAAAATCTCTTTGTATTGTAAAAGGTTGTATTCAACCTTGGGGTACAATCT
1 GCATTTCGAGTTTGTAAAATCTCTTTGTATTGTAAAAGGTTGTATTCAACCTTGGGGTACAATCT
*
1553876 CTCAAGGATTTGGGGTATAATTTTTGGAGAGATTGAGAGGTTCTTATCTTAGCCTTCAAAAGATA
66 CTCAAGGATTTGGGGTATAATTCTTGGAGAGATTGAGAGGTTCTTATCTTAGCCTTCAAAAGATA
1553941 AGTGTTGTAAGGTTATACCTTTGCCTTAAAGGTAAACAATTCTAGTAGTGAATTATGATATACAC
131 AGTGTTGTAAGGTTATACCTTTGCCTTAAAGGTAAACAATTCTAGTAGTGAATTATGATATACAC
1554006 TTGACAAGGAAGTGTCGAGGAGAGAGGACGTAGATGCCGTGTTTGGACCGAACCTCTATAAACAC
196 TTGACAAGGAAGTGTCGAGGAGAGAGGACGTAGATGCCGTGTTTGGACCGAACCTCTATAAACAC
1554071 TTATATCAAGCTTTCTCTTTTCCTAATTCTTTTTATCTTCGATTTGTTTTTGCATCAATTCTTTC
261 TTATATCAAGCTTTCTCTTTTCCTAATTCTTTTTATCTTCGATTTGTTTTTGCATCAATTCTTTC
1554136 AAAACTTTCATTTTTTGATAAGAACCAATTCACCCCCCATCTTGGTTCATTCTCTATATTTGAGC
326 AAAACTTTCATTTTTTGATAAGAACCAATTCACCCCCCATCTTGGTTCATTCTCTATATTTGAGC
1554201 TTACAATTAGTATAAGA
391 TTACAATTAGTATAAGA
1554218 GC
1 GC
1554220 CTAATCTCTT
Statistics
Matches: 408, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
407 408 1.00
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.37
Consensus pattern (407 bp):
GCATTTCGAGTTTGTAAAATCTCTTTGTATTGTAAAAGGTTGTATTCAACCTTGGGGTACAATCT
CTCAAGGATTTGGGGTATAATTCTTGGAGAGATTGAGAGGTTCTTATCTTAGCCTTCAAAAGATA
AGTGTTGTAAGGTTATACCTTTGCCTTAAAGGTAAACAATTCTAGTAGTGAATTATGATATACAC
TTGACAAGGAAGTGTCGAGGAGAGAGGACGTAGATGCCGTGTTTGGACCGAACCTCTATAAACAC
TTATATCAAGCTTTCTCTTTTCCTAATTCTTTTTATCTTCGATTTGTTTTTGCATCAATTCTTTC
AAAACTTTCATTTTTTGATAAGAACCAATTCACCCCCCATCTTGGTTCATTCTCTATATTTGAGC
TTACAATTAGTATAAGA
Found at i:1556286 original size:20 final size:19
Alignment explanation
Indices: 1556232--1556287 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
1556222 AAAACCCTTA
*
1556232 AAAGTATCGATACACAGTTC
1 AAAGTATCGATACA-TGTTC
1556252 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATGTT-C
*
1556272 AATGTATCGATACATG
1 AAAGTATCGATACATG
1556288 AAAAAGTTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 3 0.09
20 30 0.91
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:1556381 original size:20 final size:20
Alignment explanation
Indices: 1556338--1556389 Score: 88
Period size: 19 Copynumber: 2.6 Consensus size: 20
1556328 GTAGCCAAAC
*
1556338 TTGTATCGATACACAAAATA
1 TTGTATCGATACACAAAAAA
1556358 -TGTATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
1556377 TTGTATCGATACA
1 TTGTATCGATACA
1556390 TTAGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:1559688 original size:52 final size:52
Alignment explanation
Indices: 1559631--1559759 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
1559621 CACTGATCTT
1559631 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
* *
1559683 TGTATCGATACATACAGGCAAATTTGCCTAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1559735 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1559760 TCATATTTCG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:1566672 original size:14 final size:12
Alignment explanation
Indices: 1566661--1566700 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
1566651 AATCAAAAGT
1566661 AAACACAAAAAA
1 AAACACAAAAAA
1566673 CAAA-ACAAAAAA
1 -AAACACAAAAAA
1566685 AAACACACAAAAA
1 AAACACA-AAAAA
1566698 AAA
1 AAA
1566701 AGTGTAAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.12
12 11 0.44
13 11 0.44
ACGTcount: A:0.82, C:0.17, G:0.00, T:0.00
Consensus pattern (12 bp):
AAACACAAAAAA
Found at i:1566687 original size:15 final size:14
Alignment explanation
Indices: 1566667--1566701 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
1566657 AAGTAAACAC
1566667 AAAAAACAAAACAAA
1 AAAAAAC-AAACAAA
*
1566682 AAAAAACACACAAA
1 AAAAAACAAACAAA
1566696 AAAAAA
1 AAAAAA
1566702 GTGTAAAGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAACAAACAAA
Found at i:1566701 original size:14 final size:13
Alignment explanation
Indices: 1566661--1566701 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
1566651 AATCAAAAGT
1566661 AAACACAAAAAACA
1 AAACACAAAAAA-A
1566675 AAACA-AAAAAAA
1 AAACACAAAAAAA
*
1566687 ACACACAAAAAAA
1 AAACACAAAAAAA
1566700 AA
1 AA
1566702 GTGTAAAGGC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 5 0.21
13 14 0.58
14 5 0.21
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (13 bp):
AAACACAAAAAAA
Found at i:1567276 original size:31 final size:29
Alignment explanation
Indices: 1567224--1567282 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 29
1567214 TTGTTAGAAA
1567224 CAAACCATTATCTTTCTTGTCAAACAAAT
1 CAAACCATTATCTTTCTTGTCAAACAAAT
*
1567253 CAAACCATATCATCTTTAC-TGTCAAGCAAA
1 CAAACCAT-T-ATCTTT-CTTGTCAAACAAA
1567283 CCTTTTGTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 8 0.31
30 1 0.04
31 16 0.62
32 1 0.04
ACGTcount: A:0.39, C:0.25, G:0.05, T:0.31
Consensus pattern (29 bp):
CAAACCATTATCTTTCTTGTCAAACAAAT
Found at i:1568043 original size:32 final size:31
Alignment explanation
Indices: 1567931--1568090 Score: 198
Period size: 32 Copynumber: 5.1 Consensus size: 31
1567921 TTCAAATACC
* *
1567931 TTCTTAAAGTCCACGACTTAGTGGCAATC-TT
1 TTCTCAAAGTCCACGACTCAGTGGC-ATCTTT
*
1567962 TTCTCAAAGCCCACGACTCAGTGGCAT-TTT
1 TTCTCAAAGTCCACGACTCAGTGGCATCTTT
*
1567992 GTCTCAAAGTCCACGACTCAGTGGCATCCTTT
1 TTCTCAAAGTCCACGACTCAGTGGCAT-CTTT
* * *
1568024 TTTTCAAAGTTCACAACTCAGTGGCATCTTT
1 TTCTCAAAGTCCACGACTCAGTGGCATCTTT
* *
1568055 TGTCTCAAAGTCCACGACTTAGTGGCATCCTT
1 T-TCTCAAAGTCCACGACTCAGTGGCATCTTT
1568087 TTCT
1 TTCT
1568091 GTAAAGCCCA
Statistics
Matches: 111, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
30 29 0.26
31 30 0.27
32 52 0.47
ACGTcount: A:0.23, C:0.27, G:0.16, T:0.34
Consensus pattern (31 bp):
TTCTCAAAGTCCACGACTCAGTGGCATCTTT
Found at i:1568067 original size:64 final size:62
Alignment explanation
Indices: 1567936--1568106 Score: 231
Period size: 64 Copynumber: 2.7 Consensus size: 62
1567926 ATACCTTCTT
*
1567936 AAAGTCCACGACTTAGTGGCAAT-C-TTTTCTCAAAGCCCACGACTCAGTGGCATTTTGTCTC
1 AAAGTCCACGACTTAGTGGC-ATCCTTTTTCTCAAAGCCCACAACTCAGTGGCATTTTGTCTC
* * **
1567997 AAAGTCCACGACTCAGTGGCATCCTTTTTTTCAAAGTTCACAACTCAGTGGCATCTTTTGTCTC
1 AAAGTCCACGACTTAGTGGCATCCTTTTTCTCAAAGCCCACAACTCAGTGGCA--TTTTGTCTC
*
1568061 AAAGTCCACGACTTAGTGGCATCC-TTTTCTGTAAAGCCCACAACTC
1 AAAGTCCACGACTTAGTGGCATCCTTTTTCT-CAAAGCCCACAACTC
1568107 TGTGACACTT
Statistics
Matches: 95, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
60 2 0.02
61 20 0.21
62 24 0.25
63 5 0.05
64 44 0.46
ACGTcount: A:0.25, C:0.28, G:0.16, T:0.30
Consensus pattern (62 bp):
AAAGTCCACGACTTAGTGGCATCCTTTTTCTCAAAGCCCACAACTCAGTGGCATTTTGTCTC
Found at i:1568118 original size:94 final size:92
Alignment explanation
Indices: 1567936--1568122 Score: 209
Period size: 94 Copynumber: 2.0 Consensus size: 92
1567926 ATACCTTCTT
* *
1567936 AAAGTCCACGACTTAGTGGCAATCTTTTCTCAAAGCCCACGACTCAGTGGCATTTTGTCTCAAAG
1 AAAGTCCACAACTCAGTGGCAATCTTTTCTCAAAGCCCACGACTCAGTGGCATTTTGTCTCAAAG
* * *
1568001 TCCACGACTCAGTGGCATCCTTTTTTTC
66 CCCACAACTCAGTGACA-CCTTTTTTTC
* * *
1568029 AAAGTTCACAACTCAGTGGC-ATCTTTTGTCTCAAAGTCCACGACTTAGTGGCATCCTTT-TCTG
1 AAAGTCCACAACTCAGTGGCAATC-TTT-TCTCAAAGCCCACGACTCAGTGGCAT--TTTGTCT-
* *
1568092 TAAAGCCCACAACTCTGTGACA-CTTTTTTTC
61 CAAAGCCCACAACTCAGTGACACCTTTTTTTC
1568123 CTTTTAAGTC
Statistics
Matches: 79, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
92 3 0.04
93 20 0.25
94 33 0.42
95 3 0.04
96 20 0.25
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (92 bp):
AAAGTCCACAACTCAGTGGCAATCTTTTCTCAAAGCCCACGACTCAGTGGCATTTTGTCTCAAAG
CCCACAACTCAGTGACACCTTTTTTTC
Done.