Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 39 of 193
Found at i:12053202 original size:6 final size:6
Alignment explanation
Indices: 12053191--12053221 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
12053181 ATGATCGATG
*
12053191 GGTGAT GGTGAT GGTGAT GGTGAT TGTGAT G
1 GGTGAT GGTGAT GGTGAT GGTGAT GGTGAT G
12053222 TTAAGTTTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.16, C:0.00, G:0.48, T:0.35
Consensus pattern (6 bp):
GGTGAT
Found at i:12067278 original size:80 final size:80
Alignment explanation
Indices: 12067183--12067349 Score: 253
Period size: 80 Copynumber: 2.1 Consensus size: 80
12067173 AAACTTAAGA
* * * * * *
12067183 CAGTACAAGTTATTCTAAAATACTCTAAAAAAATAAACAGTTGAAGAGCTACCCACTTTCCAAGA
1 CAGTAGAAATTATTCTAAAATACTCTAAAAAAAGAAACAGATGAAAAGCCACCCACTTTCCAAGA
12067248 AAGATTGTTGATGGC
66 AAGATTGTTGATGGC
* * *
12067263 CAGTAGAAATTATTCTGAAATACTCTAAGAAAAGAAACAGATGAAAAGCCACCCACTTTTCAAGA
1 CAGTAGAAATTATTCTAAAATACTCTAAAAAAAGAAACAGATGAAAAGCCACCCACTTTCCAAGA
12067328 AAGATTGTTGATGGC
66 AAGATTGTTGATGGC
12067343 CAGTAGA
1 CAGTAGA
12067350 GTTTCAGCGA
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
80 78 1.00
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.25
Consensus pattern (80 bp):
CAGTAGAAATTATTCTAAAATACTCTAAAAAAAGAAACAGATGAAAAGCCACCCACTTTCCAAGA
AAGATTGTTGATGGC
Found at i:12070529 original size:3 final size:3
Alignment explanation
Indices: 12070521--12070551 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
12070511 TTCTTCCCAC
12070521 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
12070552 TAGTTTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:12106622 original size:27 final size:27
Alignment explanation
Indices: 12106588--12106656 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
12106578 TTTAACTCGA
12106588 ATAT-ATTATATTATAAAAAA-ATATTAT
1 ATATAATTATATT-TAAAAAATA-ATTAT
* *
12106615 AT-TAATTATGTGTTAAATAATAATTAT
1 ATATAATTATAT-TTAAAAAATAATTAT
12106642 ATATAATTATATTTA
1 ATATAATTATATTTA
12106657 TATTAAATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
26 1 0.03
27 24 0.69
28 10 0.29
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (27 bp):
ATATAATTATATTTAAAAAATAATTAT
Found at i:12106791 original size:25 final size:25
Alignment explanation
Indices: 12106763--12106812 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
12106753 AAAAATTATA
* *
12106763 TTTAATACAATAAAATATTTATTTT
1 TTTAACACAATAAAACATTTATTTT
*
12106788 TTTAACATAATAAAACATTTATTTT
1 TTTAACACAATAAAACATTTATTTT
12106813 ATACATGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (25 bp):
TTTAACACAATAAAACATTTATTTT
Found at i:12121599 original size:78 final size:80
Alignment explanation
Indices: 12121445--12121600 Score: 192
Period size: 80 Copynumber: 2.0 Consensus size: 80
12121435 ACAATCTAAG
* * * *
12121445 AAAAAAAAATTGTTTGCAATGTATTCTATTGTATTTCATATAAATAATATATATAATTATTTACA
1 AAAAAAAAATTGTTTACAATGTATTCTACTGTATTTCACATAAATAATATATACAATTATTTACA
**
12121510 ATCTATGAAAAAAAT
66 ATCTACCAAAAAAAT
* * *
12121525 AAAAAAAAATTGTTTATATTGTATTCTACTGTAATTT-ACATCAATAATATAT-CAA-TATTTAC
1 AAAAAAAAATTGTTTACAATGTATTCTACTGT-ATTTCACATAAATAATATATACAATTATTTAC
*
12121587 AATTTACCAAAAAA
65 AATCTACCAAAAAA
12121601 TAAGAAATGA
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
78 18 0.28
79 2 0.03
80 41 0.63
81 4 0.06
ACGTcount: A:0.47, C:0.08, G:0.05, T:0.39
Consensus pattern (80 bp):
AAAAAAAAATTGTTTACAATGTATTCTACTGTATTTCACATAAATAATATATACAATTATTTACA
ATCTACCAAAAAAAT
Found at i:12124537 original size:54 final size:54
Alignment explanation
Indices: 12124447--12124603 Score: 190
Period size: 54 Copynumber: 2.8 Consensus size: 54
12124437 TGAGAATTTG
* *
12124447 AAAAAAAAATTTGGTATTGGCCATTACATGGCCGACACCCCCTTTTTTATCTGAC
1 AAAAAAAAATTTTGTATT-GTCATTACATGGCCGACACCCCCTTTTTTATCTGAC
* * *
12124502 -AAAAAAAATTTTGTATTAGTCATTACACGGTCGACACTCCCTTTTTTATCTGAC
1 AAAAAAAAATTTTGTATT-GTCATTACATGGCCGACACCCCCTTTTTTATCTGAC
* * *
12124556 AGAAAAAAAATTTTGGTGTTGATCATTGCATGGGCGACACCCCCTTTT
1 A-AAAAAAAATTTT-GTATTG-TCATTACATGGCCGACACCCCCTTTT
12124604 AATTTGATAA
Statistics
Matches: 87, Mismatches: 11, Indels: 6
0.84 0.11 0.06
Matches are distributed among these distances:
54 48 0.55
56 13 0.15
57 26 0.30
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (54 bp):
AAAAAAAAATTTTGTATTGTCATTACATGGCCGACACCCCCTTTTTTATCTGAC
Found at i:12124653 original size:59 final size:58
Alignment explanation
Indices: 12124590--12124824 Score: 166
Period size: 60 Copynumber: 3.9 Consensus size: 58
12124580 ATTGCATGGG
* * * *
12124590 CGACACCCCCTTTTAATTTGATAAAAAATCAAACTTTTTGGTGTTGGTCATATAAT-GAC
1 CGACACCCCCTTTT-ATCTGATAAAAAATCAAATTTTTTGGTGTTGGCCATACAATAG-C
* * * * ** * * *
12124649 CGACATTCCCTTTTTGTCAGATAAAAAATTTAATTTTTTTGTGTTGGCCATGCCATAGC
1 CGACA-CCCCCTTTTATCTGATAAAAAATCAAATTTTTTGGTGTTGGCCATACAATAGC
* * * *
12124708 CGACACCCACTATTTATCTGATAAAAAAATCAAATTTTTTGGTGTTGGCCATGCAATGGT
1 CGACACCCCCT-TTTATCTGAT-AAAAAATCAAATTTTTTGGTGTTGGCCATACAATAGC
* ** * * * * * *
12124768 CAACACCCTTTATTTATCTAATAAAAAAATTAATTTTTTTTGTGTTGGTCATTCAAT
1 CGACACCCCCT-TTTATCTGAT-AAAAAATCAAATTTTTTGGTGTTGGCCATACAAT
12124825 GGCTGACATC
Statistics
Matches: 139, Mismatches: 33, Indels: 7
0.78 0.18 0.04
Matches are distributed among these distances:
58 3 0.02
59 49 0.35
60 87 0.63
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (58 bp):
CGACACCCCCTTTTATCTGATAAAAAATCAAATTTTTTGGTGTTGGCCATACAATAGC
Found at i:12124825 original size:60 final size:59
Alignment explanation
Indices: 12124669--12124827 Score: 192
Period size: 60 Copynumber: 2.7 Consensus size: 59
12124659 TTTTTGTCAG
* * * * *
12124669 ATAAAAAATTTAATTTTTTTGTGTTGGCCATGCCATAGCCGACACCCACTATTTATCTG
1 ATAAAAAAATTAATTTTTTTGTGTTGGCCATGCAATGGCCAACACCCACTATTTATCTA
* * * **
12124728 ATAAAAAAATCAAATTTTTTGGTGTTGGCCATGCAATGGTCAACACCCTTTATTTATCTA
1 ATAAAAAAAT-TAATTTTTTTGTGTTGGCCATGCAATGGCCAACACCCACTATTTATCTA
* *
12124788 ATAAAAAAATTAATTTTTTTTGTGTTGGTCATTCAATGGC
1 ATAAAAAAATTAA-TTTTTTTGTGTTGGCCATGCAATGGC
12124828 TGACATCAAC
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
59 11 0.13
60 72 0.87
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (59 bp):
ATAAAAAAATTAATTTTTTTGTGTTGGCCATGCAATGGCCAACACCCACTATTTATCTA
Found at i:12125644 original size:17 final size:16
Alignment explanation
Indices: 12125624--12125678 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 16
12125614 AAAAAATAAT
12125624 AATTAGAATATATAGGA
1 AATTAGAATATATA-GA
12125641 AATTAGAA-AT-TA-A
1 AATTAGAATATATAGA
* *
12125654 AATTAAAATATACAGAA
1 AATTAGAATATATAG-A
12125671 AATTAGAA
1 AATTAGAA
12125679 ATTAAATTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
13 8 0.26
14 2 0.06
15 3 0.10
16 2 0.06
17 16 0.52
ACGTcount: A:0.60, C:0.02, G:0.11, T:0.27
Consensus pattern (16 bp):
AATTAGAATATATAGA
Found at i:12125664 original size:30 final size:30
Alignment explanation
Indices: 12125624--12125727 Score: 118
Period size: 30 Copynumber: 3.5 Consensus size: 30
12125614 AAAAAATAAT
* * *
12125624 AATTAGAATATATAGGAAATTAGAAATTAA
1 AATTAAAATATAAAGAAAATTAGAAATTAA
*
12125654 AATTAAAATATACAGAAAATTAGAAATTAA
1 AATTAAAATATAAAGAAAATTAGAAATTAA
* * * *
12125684 ATTTAAAATAAAAACAAAATTACAAATTAA
1 AATTAAAATATAAAGAAAATTAGAAATTAA
* *
12125714 ATTTAAAAAATAAA
1 AATTAAAATATAAA
12125728 CGGAAAAAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 64 1.00
ACGTcount: A:0.63, C:0.03, G:0.06, T:0.28
Consensus pattern (30 bp):
AATTAAAATATAAAGAAAATTAGAAATTAA
Found at i:12126924 original size:21 final size:21
Alignment explanation
Indices: 12126898--12126940 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
12126888 TTTTAAAAAA
*
12126898 TTCGAAAATATAAAAAAATAT
1 TTCGAAAATAGAAAAAAATAT
12126919 TTCGAAAATAGAAAAAAATAT
1 TTCGAAAATAGAAAAAAATAT
12126940 T
1 T
12126941 ATAAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.60, C:0.05, G:0.07, T:0.28
Consensus pattern (21 bp):
TTCGAAAATAGAAAAAAATAT
Found at i:12126947 original size:21 final size:21
Alignment explanation
Indices: 12126902--12126949 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
12126892 AAAAAATTCG
* *
12126902 AAAATATAAAAAAATATTTCG
1 AAAATAGAAAAAAATATTTCA
*
12126923 AAAATAGAAAAAAATATTATAA
1 AAAATAGAAAAAAATATT-TCA
12126945 AAAAT
1 AAAAT
12126950 TTGAAAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (21 bp):
AAAATAGAAAAAAATATTTCA
Found at i:12128061 original size:134 final size:134
Alignment explanation
Indices: 12127821--12128088 Score: 500
Period size: 134 Copynumber: 2.0 Consensus size: 134
12127811 CCCACACGGT
*
12127821 GGTTGTCATGACTACAAAGAATGACATTCGGGTCCATAATGTGATGGACAGTACTCGGTCAATGG
1 GGTTGTCATGACTACAAAGAATGACATTCGGGTCCATAATGTGATGGACAGTACTCGGTCAACGG
* *
12127886 CGGACACAGTCGGTCAACGGTGGTCAATGATGGAATTGGGGTGTTGGTGAGCTTGAATTTCGATT
66 CGGACACAGTCGGTCAACGGCGGTCAATGATGGAATTGGGGTGTTGGTGAGCTGGAATTTCGATT
12127951 TTGG
131 TTGG
*
12127955 GGTTGTCATGACTACGAAGAATGACATTCGGGTCCATAATGTGATGGACAGTACTCGGTCAACGG
1 GGTTGTCATGACTACAAAGAATGACATTCGGGTCCATAATGTGATGGACAGTACTCGGTCAACGG
12128020 CGGACACAGTCGGTCAACGGCGGTCAATGATGGAATTGGGGTGTTGGTGAGCTGGAATTTCGATT
66 CGGACACAGTCGGTCAACGGCGGTCAATGATGGAATTGGGGTGTTGGTGAGCTGGAATTTCGATT
12128085 TTGG
131 TTGG
12128089 TAAGCTGAAA
Statistics
Matches: 130, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
134 130 1.00
ACGTcount: A:0.24, C:0.16, G:0.33, T:0.27
Consensus pattern (134 bp):
GGTTGTCATGACTACAAAGAATGACATTCGGGTCCATAATGTGATGGACAGTACTCGGTCAACGG
CGGACACAGTCGGTCAACGGCGGTCAATGATGGAATTGGGGTGTTGGTGAGCTGGAATTTCGATT
TTGG
Found at i:12128088 original size:22 final size:22
Alignment explanation
Indices: 12128063--12128123 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
12128053 AATTGGGGTG
12128063 TTGGTGAGCTGGAATTTCGATT
1 TTGGTGAGCTGGAATTTCGATT
* * *
12128085 TTGGTAAGCTGAAATTTCGGTT
1 TTGGTGAGCTGGAATTTCGATT
* *
12128107 TAGATGAGCTGGAATTT
1 TTGGTGAGCTGGAATTT
12128124 GGGTGGTCTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.23, C:0.08, G:0.30, T:0.39
Consensus pattern (22 bp):
TTGGTGAGCTGGAATTTCGATT
Found at i:12128319 original size:84 final size:84
Alignment explanation
Indices: 12128216--12128932 Score: 1200
Period size: 84 Copynumber: 8.5 Consensus size: 84
12128206 TAAATTTAAA
*
12128216 ATTTGATAAAAATTGTAATATAATAATAATTTTTAATTTAAATATTAAAATTTGGTAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTAAAATTTGGTAAATAATGT
*
12128281 ATTGTCAAACCAACACATT
66 ATTGTCAAATCAACACATT
* * * *
12128300 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATGTAAATATTAACATTTGATAAATAATAT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTAAAATTTGGTAAATAATGT
*
12128365 ATTGTCAAATCAACATATT
66 ATTGTCAAATCAACACATT
*
12128384 ATTTGATAAAAATTGTAATATAATAATAATTTTTTTATTTAAATATTAAAATTTGGTAAATAATA
1 ATTTGATAAAAATTGTAATATAATAATAA-TTTTTTATTTAAATATTAAAATTTGGTAAATAATG
*
12128449 TATTATCAAATCAACACATT
65 TATTGTCAAATCAACACATT
12128469 ATTTGATAAAAATTGTAATATAATAATAATTTTTTTATTTAAATATTAAAATTTGGTAAATAATG
1 ATTTGATAAAAATTGTAATATAATAATAA-TTTTTTATTTAAATATTAAAATTTGGTAAATAATG
*
12128534 TATTGTCAAATTAACACATT
65 TATTGTCAAATCAACACATT
* * *
12128554 ATTTGATAAAAATTATAATATAATAATATTTTTTTATTTAAATATTAAAATTTGATAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTAAAATTTGGTAAATAATGT
12128619 ATTGTCAAATCAACACATT
66 ATTGTCAAATCAACACATT
12128638 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTAAAATTTGGTAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTAAAATTTGGTAAATAATGT
*
12128703 ATTGTCAAATTAACACATT
66 ATTGTCAAATCAACACATT
* * *
12128722 ATTTGATAAAAATTATAATATAATAATATTTTTTTATTTAAATATTAAAATTTGATAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTAAAATTTGGTAAATAATGT
12128787 ATTGTCAAATCAACACATT
66 ATTGTCAAATCAACACATT
*
12128806 ATTTGATAAAAATTATAATATAATAATAATATTTTTTATTTAAATATTAAAATTTGGTAAATAAT
1 ATTTGATAAAAATTGTAATATAATAAT-A-ATTTTTTATTTAAATATTAAAATTTGGTAAATAAT
12128871 GTATTGTCAAATCAACACATT
64 GTATTGTCAAATCAACACATT
* *
12128892 ATTTGATATAAATTGAAATATAATAATAATCTTTTTTATTT
1 ATTTGATAAAAATTGTAATATAATAATAA--TTTTTTATTT
12128933 GATATAAATT
Statistics
Matches: 596, Mismatches: 32, Indels: 8
0.94 0.05 0.01
Matches are distributed among these distances:
84 347 0.58
85 161 0.27
86 88 0.15
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (84 bp):
ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTAAAATTTGGTAAATAATGT
ATTGTCAAATCAACACATT
Found at i:12128434 original size:40 final size:40
Alignment explanation
Indices: 12128390--12128532 Score: 105
Period size: 40 Copynumber: 3.5 Consensus size: 40
12128380 TATTATTTGA
12128390 TAAAAATT-GTAATATAATAATAATTTTTTTATTTAAATAT
1 TAAAAATTGGTAA-ATAATAATAATTTTTTTATTTAAATAT
* * *** **
12128430 TAAAATTTGGTAAATAAT-AT-ATTATCAAATCAACACATTATTT
1 TAAAAATTGGTAAATAATAATAATTTTTTTATTTA-A-A-TA--T
12128473 GATAAAAATT-GTAATATAATAATAATTTTTTTATTTAAATAT
1 --TAAAAATTGGTAA-ATAATAATAATTTTTTTATTTAAATAT
*
12128515 TAAAATTTGGTAAATAAT
1 TAAAAATTGGTAAATAAT
12128533 GTATTGTCAA
Statistics
Matches: 76, Mismatches: 15, Indels: 24
0.66 0.13 0.21
Matches are distributed among these distances:
38 7 0.09
39 3 0.04
40 25 0.33
41 10 0.13
42 1 0.01
43 1 0.01
44 6 0.08
45 13 0.17
46 3 0.04
47 7 0.09
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.45
Consensus pattern (40 bp):
TAAAAATTGGTAAATAATAATAATTTTTTTATTTAAATAT
Found at i:12128664 original size:254 final size:254
Alignment explanation
Indices: 12128216--12128932 Score: 1233
Period size: 254 Copynumber: 2.8 Consensus size: 254
12128206 TAAATTTAAA
*
12128216 ATTTGATAAAAATTGTAATATAATAATAA-TTTTTAATTTAAATATTAAAATTTGGTAAATAATG
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTTATTTAAATATTAAAATTTGGTAAATAATG
* * * *
12128280 TATTGTCAAACCAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTTATGTAAATAT
66 TATTGTCAAATCAACACATTATTTGATAAAAATTATAATATAATAATATTTTTTTATTTAAATAT
* * *
12128345 TAACATTTGATAAATAATATATTGTCAAATCAACATATTATTTGATAAAAATTGTAATATAATAA
131 TAAAATTTGATAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAA
12128410 TAATTTTTTTATTTAAATATTAAAATTTGGTAAATAATATATTATCAAATCAACACATT
196 TAATTTTTTTATTTAAATATTAAAATTTGGTAAATAATATATTATCAAATCAACACATT
12128469 ATTTGATAAAAATTGTAATATAATAATAATTTTTTTATTTAAATATTAAAATTTGGTAAATAATG
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTTATTTAAATATTAAAATTTGGTAAATAATG
*
12128534 TATTGTCAAATTAACACATTATTTGATAAAAATTATAATATAATAATATTTTTTTATTTAAATAT
66 TATTGTCAAATCAACACATTATTTGATAAAAATTATAATATAATAATATTTTTTTATTTAAATAT
12128599 TAAAATTTGATAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAA
131 TAAAATTTGATAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAA
* * *
12128664 TAA-TTTTTTATTTAAATATTAAAATTTGGTAAATAATGTATTGTCAAATTAACACATT
196 TAATTTTTTTATTTAAATATTAAAATTTGGTAAATAATATATTATCAAATCAACACATT
* *
12128722 ATTTGATAAAAATTATAATATAATAAT-ATTTTTTTATTTAAATATTAAAATTTGATAAATAATG
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTTATTTAAATATTAAAATTTGGTAAATAATG
12128786 TATTGTCAAATCAACACATTATTTGATAAAAATTATAATATAATAATAATATTTTTTATTTAAAT
66 TATTGTCAAATCAACACATTATTTGATAAAAATTATAATATAATAAT-AT-TTTTTTATTTAAAT
* * *
12128851 ATTAAAATTTGGTAAATAATGTATTGTCAAATCAACACATTATTTGATATAAATTGAAATATAAT
129 ATTAAAATTTGATAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAAT
12128916 AATAATCTTTTTTATTT
194 AATAAT-TTTTTTATTT
12128933 GATATAAATT
Statistics
Matches: 441, Mismatches: 18, Indels: 7
0.95 0.04 0.02
Matches are distributed among these distances:
252 82 0.19
253 109 0.25
254 240 0.54
256 10 0.02
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (254 bp):
ATTTGATAAAAATTGTAATATAATAATAATTTTTTTATTTAAATATTAAAATTTGGTAAATAATG
TATTGTCAAATCAACACATTATTTGATAAAAATTATAATATAATAATATTTTTTTATTTAAATAT
TAAAATTTGATAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAA
TAATTTTTTTATTTAAATATTAAAATTTGGTAAATAATATATTATCAAATCAACACATT
Found at i:12128843 original size:338 final size:338
Alignment explanation
Indices: 12128216--12128932 Score: 1222
Period size: 338 Copynumber: 2.1 Consensus size: 338
12128206 TAAATTTAAA
* * * *
12128216 ATTTGATAAAAATTGTAATATAATAATAATTTTTAATTTAAATATTAAAATTTGGTAAATAATGT
1 ATTTGATAAAAATTATAATATAATAATATTTTTTTATTTAAATATTAAAATTTGATAAATAATGT
12128281 ATTGTCAAACCAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTTATGTAAATATT
66 ATTGTCAAACCAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTTATGTAAATATT
* * *
12128346 AACATTTGATAAATAATATATTGTCAAATCAACATATTATTTGATAAAAATTGTAATATAATAAT
131 AAAATTTGATAAATAATATATTGTCAAATCAACACATTATTTGATAAAAATTATAATATAATAAT
*
12128411 AATTTTTTTATTTAAATATTAAAATTTGGTAAATAATATATTATCAAATCAACACATTATTTGAT
196 AATTTTTTTATTTAAATATTAAAATTTGATAAATAATATATTATCAAATCAACACATTATTTGAT
*
12128476 AAAAATTGTAATATAATAATAATTTTTTTATTTAAATATTAAAATTTGGTAAATAATGTATTGTC
261 AAAAATTATAATATAATAATAATTTTTTTATTTAAATATTAAAATTTGGTAAATAATGTATTGTC
*
12128541 AAATTAACACATT
326 AAATCAACACATT
12128554 ATTTGATAAAAATTATAATATAATAATATTTTTTTATTTAAATATTAAAATTTGATAAATAATGT
1 ATTTGATAAAAATTATAATATAATAATATTTTTTTATTTAAATATTAAAATTTGATAAATAATGT
* *
12128619 ATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATT
66 ATTGTCAAACCAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTTATGTAAATATT
* * *
12128684 AAAATTTGGTAAATAATGTATTGTCAAATTAACACATTATTTGATAAAAATTATAATATAATAAT
131 AAAATTTGATAAATAATATATTGTCAAATCAACACATTATTTGATAAAAATTATAATATAATAAT
* *
12128749 -ATTTTTTTATTTAAATATTAAAATTTGATAAATAATGTATTGTCAAATCAACACATTATTTGAT
196 AATTTTTTTATTTAAATATTAAAATTTGATAAATAATATATTATCAAATCAACACATTATTTGAT
12128813 AAAAATTATAATATAATAATAATATTTTTTATTTAAATATTAAAATTTGGTAAATAATGTATTGT
261 AAAAATTATAATATAATAATAAT-TTTTTTATTTAAATATTAAAATTTGGTAAATAATGTATTGT
12128878 CAAATCAACACATT
325 CAAATCAACACATT
*
12128892 ATTTGATATAAATTGA-AATATAATAATAATCTTTTTTATTT
1 ATTTGATAAAAATT-ATAATATAATAAT-AT-TTTTTTATTT
12128933 GATATAAATT
Statistics
Matches: 357, Mismatches: 18, Indels: 6
0.94 0.05 0.02
Matches are distributed among these distances:
337 83 0.23
338 261 0.73
339 3 0.01
340 10 0.03
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (338 bp):
ATTTGATAAAAATTATAATATAATAATATTTTTTTATTTAAATATTAAAATTTGATAAATAATGT
ATTGTCAAACCAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTTATGTAAATATT
AAAATTTGATAAATAATATATTGTCAAATCAACACATTATTTGATAAAAATTATAATATAATAAT
AATTTTTTTATTTAAATATTAAAATTTGATAAATAATATATTATCAAATCAACACATTATTTGAT
AAAAATTATAATATAATAATAATTTTTTTATTTAAATATTAAAATTTGGTAAATAATGTATTGTC
AAATCAACACATT
Found at i:12128931 original size:37 final size:37
Alignment explanation
Indices: 12128890--12128969 Score: 151
Period size: 37 Copynumber: 2.2 Consensus size: 37
12128880 AATCAACACA
*
12128890 TTATTTGATATAAATTGAAATATAATAATAATCTTTT
1 TTATTTGATATAAATTGAAATACAATAATAATCTTTT
12128927 TTATTTGATATAAATTGAAATACAATAATAATCTTTT
1 TTATTTGATATAAATTGAAATACAATAATAATCTTTT
12128964 TTATTT
1 TTATTT
12128970 AAATAATGTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (37 bp):
TTATTTGATATAAATTGAAATACAATAATAATCTTTT
Found at i:12129106 original size:12 final size:12
Alignment explanation
Indices: 12129089--12129138 Score: 55
Period size: 12 Copynumber: 3.8 Consensus size: 12
12129079 AACATGTACC
12129089 TTAATTTTTAAA
1 TTAATTTTTAAA
12129101 TTAATTTCAACTTAAA
1 TTAATTT----TTAAA
*
12129117 TTAATTTTCAAA
1 TTAATTTTTAAA
12129129 TTAATTTTTA
1 TTAATTTTTA
12129139 CACAAATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
12 20 0.62
16 12 0.38
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (12 bp):
TTAATTTTTAAA
Found at i:12129134 original size:16 final size:16
Alignment explanation
Indices: 12129096--12129132 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
12129086 ACCTTAATTT
*
12129096 TTAAATTAATTTCAAC
1 TTAAATTAATTTCAAA
12129112 TTAAATTAATTTTCAAA
1 TTAAATTAA-TTTCAAA
12129129 TTAA
1 TTAA
12129133 TTTTTACACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (16 bp):
TTAAATTAATTTCAAA
Found at i:12129145 original size:28 final size:28
Alignment explanation
Indices: 12129089--12129153 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 28
12129079 AACATGTACC
* **
12129089 TTAATTTTTAAATTAATTTCAACTTAAA
1 TTAATTTTCAAATTAATTTCAACACAAA
**
12129117 TTAATTTTCAAATTAATTTTTACACAAA
1 TTAATTTTCAAATTAATTTCAACACAAA
*
12129145 -TATTTTTCA
1 TTAATTTTCA
12129154 TGTATACTAG
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
27 8 0.26
28 23 0.74
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (28 bp):
TTAATTTTCAAATTAATTTCAACACAAA
Found at i:12131438 original size:18 final size:18
Alignment explanation
Indices: 12131415--12131451 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
12131405 ACAATTCATA
12131415 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
12131433 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
12131451 T
1 T
12131452 TGATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:12131782 original size:17 final size:18
Alignment explanation
Indices: 12131748--12131783 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
12131738 TGAATTTCTA
12131748 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
12131766 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
12131783 T
1 T
12131784 AACTCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:12135456 original size:24 final size:22
Alignment explanation
Indices: 12135412--12135464 Score: 52
Period size: 23 Copynumber: 2.3 Consensus size: 22
12135402 AGTTCGATTA
* *
12135412 ATTTTATGGTATATAAGTTTTTGT
1 ATTTT-TGGTATATAA-ATTTTAT
*
12135436 ATTTTTGGTAATTTAAATTTTAT
1 ATTTTTGGT-ATATAAATTTTAT
12135459 ATTTTT
1 ATTTTT
12135465 ATTTATAAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 15 0.60
24 10 0.40
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.62
Consensus pattern (22 bp):
ATTTTTGGTATATAAATTTTAT
Found at i:12135514 original size:14 final size:15
Alignment explanation
Indices: 12135481--12135511 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
12135471 AAGGATTTAG
12135481 TTTATTATT-TAAAA
1 TTTATTATTATAAAA
12135495 TTTATTATTATAAAA
1 TTTATTATTATAAAA
12135510 TT
1 TT
12135512 ATTTTATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTATTATTATAAAA
Found at i:12137403 original size:171 final size:172
Alignment explanation
Indices: 12137100--12137457 Score: 533
Period size: 171 Copynumber: 2.1 Consensus size: 172
12137090 ACCGTGTGAA
* *
12137100 GCACACGGGCATGTGCCTAGAGCGTGTTTAAAAACAGTATAGATGCAGTTTTTACACGGGCAAAC
1 GCACACGGGCGTGTGCCCAGAGCGTGTTTAAAAACAGTATAGATGCAGTTTTTACACGGGCAAAC
* * * * *
12137165 ACACTGCCAGGGATATGGCTATGTGAAGGAACTTCGAATGTCACACGAGCTAACACATGACCTAC
66 ACACGGCCAGCGATATGACCATGTGAAGGAACTTCGAATGTCACACGAGCTAACACACGACCTAC
*
12137230 GACACGACCATGTGACCCAAATCAGAGAGTTACACGGTCCAT
131 GACACAACCATGTGACCCAAATCAGAGAGTTACACGGTCCAT
* *
12137272 GCACACGGG-GTGTGCCCAGAGCGTGTTTAAAAACAGTATAGGTGCAGTTTTTACATGGG-AAGA
1 GCACACGGGCGTGTGCCCAGAGCGTGTTTAAAAACAGTATAGATGCAGTTTTTACACGGGCAA-A
* * ** *
12137335 CACACGGCCAGCGATATGACCGTGTGAAGGAACTTCGAATGTCATAC-AGGCTAGGACACGGCCT
65 CACACGGCCAGCGATATGACCATGTGAAGGAACTTCGAATGTCACACGA-GCTAACACACGACCT
12137399 ACGACACAACCATGTGACCCAAATCAGAGAGTTACACGGTCCAT
129 ACGACACAACCATGTGACCCAAATCAGAGAGTTACACGGTCCAT
*
12137443 GCACACGGGTGTGTG
1 GCACACGGGCGTGTG
12137458 AGATTGCACA
Statistics
Matches: 168, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
170 3 0.02
171 151 0.90
172 14 0.08
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.20
Consensus pattern (172 bp):
GCACACGGGCGTGTGCCCAGAGCGTGTTTAAAAACAGTATAGATGCAGTTTTTACACGGGCAAAC
ACACGGCCAGCGATATGACCATGTGAAGGAACTTCGAATGTCACACGAGCTAACACACGACCTAC
GACACAACCATGTGACCCAAATCAGAGAGTTACACGGTCCAT
Found at i:12137902 original size:89 final size:87
Alignment explanation
Indices: 12137779--12137949 Score: 186
Period size: 87 Copynumber: 1.9 Consensus size: 87
12137769 AAAAAATTCA
* *
12137779 AACAAATAATAAGACGTAAATTTTTTTTCTATATACAAGAAAATATGAAAATTCTACAAAATT-A
1 AACAAATAATAAGACGTAAATTTATTTACTATATA-AA-AAAATATGAAAATTCTACAAAATTGA
* *
12137843 GTATACGAAAATATATAATTTGACC
64 -TATACAAAAATATAAAATTTGACC
* * * * * *
12137868 AACAAATAATACCGAC-TAAATTTGATTTAC-ATATATAATAATATGAATATTTTAGAAAATTGA
1 AACAAATAATA-AGACGTAAATTT-ATTTACTATATAAAAAAATATGAAAATTCTACAAAATTGA
12137931 TATACAAAAATATAAAATT
64 TATACAAAAATATAAAATT
12137950 CGAGCGGCAA
Statistics
Matches: 69, Mismatches: 10, Indels: 8
0.79 0.11 0.09
Matches are distributed among these distances:
87 37 0.54
88 2 0.03
89 23 0.33
90 7 0.10
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.33
Consensus pattern (87 bp):
AACAAATAATAAGACGTAAATTTATTTACTATATAAAAAAATATGAAAATTCTACAAAATTGATA
TACAAAAATATAAAATTTGACC
Found at i:12142128 original size:85 final size:85
Alignment explanation
Indices: 12141963--12142125 Score: 213
Period size: 85 Copynumber: 1.9 Consensus size: 85
12141953 TGAATTATAA
* * * *
12141963 ATTTTAAAAGAATCAAAGTATAATTTTATCACTGTATTAATTTATTATTTCAAATTTTTTAAAAG
1 ATTTTAAAAGAATCAAAATATAAATTTATCACTATATTAATTTATAATTTCAAATTTTTTAAAAG
*
12142028 AGATTAAACTAAAATTTATC
66 AGATTAAAATAAAATTTATC
* * * * *
12142048 ATTTTAAAAGTATCAAAATGTAAATTTATCATTATATTATTTTATAATTTTATAA-TTTTTAAAA
1 ATTTTAAAAGAATCAAAATATAAATTTATCACTATATTAATTTATAATTTCA-AATTTTTTAAAA
12142112 GA-ATTAAAATAAAA
65 GAGATTAAAATAAAA
12142126 ATTAAATATT
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
84 11 0.16
85 54 0.81
86 2 0.03
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (85 bp):
ATTTTAAAAGAATCAAAATATAAATTTATCACTATATTAATTTATAATTTCAAATTTTTTAAAAG
AGATTAAAATAAAATTTATC
Found at i:12142137 original size:85 final size:85
Alignment explanation
Indices: 12141955--12142137 Score: 203
Period size: 85 Copynumber: 2.2 Consensus size: 85
12141945 GGTCAAATTG
* * * *
12141955 AATTATAA-ATTTTAAAAGAATCAAAGTATAATTTTATCACTGTATTAATTTATTATTTCAAATT
1 AATTA-AATATTTTAAAAGAATCAAAATATAAATTTATCACTATATTAATTTATAATTTCAAATT
*
12142019 TTTTAAAAGAGATTAAACTAA
65 TTTTAAAAGAGATTAAAATAA
* * * * * *
12142040 AATT-TATCATTTTAAAAGTATCAAAATGTAAATTTATCATTATATTATTTTATAATTTTATAA-
1 AATTAAAT-ATTTTAAAAGAATCAAAATATAAATTTATCACTATATTAATTTATAATTTCA-AAT
12142103 TTTTTAAAAGA-ATTAAAATAAA
64 TTTTTAAAAGAGATTAAAAT-AA
12142125 AATTAAATATTTT
1 AATTAAATATTTT
12142138 TGGGAGGTCA
Statistics
Matches: 81, Mismatches: 12, Indels: 10
0.79 0.12 0.10
Matches are distributed among these distances:
83 1 0.01
84 7 0.09
85 69 0.85
86 4 0.05
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.45
Consensus pattern (85 bp):
AATTAAATATTTTAAAAGAATCAAAATATAAATTTATCACTATATTAATTTATAATTTCAAATTT
TTTAAAAGAGATTAAAATAA
Found at i:12143737 original size:2 final size:2
Alignment explanation
Indices: 12143730--12143773 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
12143720 CAATGTTAAA
*
12143730 AG AG AG AG AG AG AG AG AG AG AG AG TG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
12143772 AG
1 AG
12143774 TAAAAATGGG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.50, T:0.02
Consensus pattern (2 bp):
AG
Found at i:12146517 original size:12 final size:12
Alignment explanation
Indices: 12146502--12146527 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12146492 ATACACTTAA
12146502 AAATATTAAAAC
1 AAATATTAAAAC
12146514 AAATATTAAAAC
1 AAATATTAAAAC
12146526 AA
1 AA
12146528 CAAACAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
AAATATTAAAAC
Found at i:12151382 original size:21 final size:21
Alignment explanation
Indices: 12151348--12151402 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 21
12151338 AAAAAGAAAG
*
12151348 CGAGAAAAAAACTCTCCAAAC-
1 CGAGAGAAAAACTCT-CAAACA
*
12151369 CGAGAGAAACACTCTCAAACAA
1 CGAGAGAAAAACTCTCAAAC-A
12151391 CGAGAGAGAAAA
1 CGAGAGA-AAAA
12151403 AACCGTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 5 0.18
21 13 0.46
22 7 0.25
23 3 0.11
ACGTcount: A:0.53, C:0.24, G:0.16, T:0.07
Consensus pattern (21 bp):
CGAGAGAAAAACTCTCAAACA
Found at i:12163388 original size:21 final size:22
Alignment explanation
Indices: 12163362--12163406 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
12163352 CATTATCTCT
*
12163362 CAAGTATCGATCTGTTTC-GTA
1 CAAGTATCGATATGTTTCGGTA
*
12163383 CAAGTATTGATATGTTTCGGTA
1 CAAGTATCGATATGTTTCGGTA
12163405 CA
1 CA
12163407 CCAATGTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.38
Consensus pattern (22 bp):
CAAGTATCGATATGTTTCGGTA
Found at i:12175297 original size:18 final size:21
Alignment explanation
Indices: 12175274--12175312 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
12175264 ACTAAAGTTG
12175274 AAAAA-TAA-ATTG-TTAAAA
1 AAAAATTAAGATTGTTTAAAA
12175292 AAAAATTAAGATTGTTTAAAA
1 AAAAATTAAGATTGTTTAAAA
12175313 TGTAAGTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 3 0.17
20 4 0.22
21 6 0.33
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (21 bp):
AAAAATTAAGATTGTTTAAAA
Found at i:12178083 original size:15 final size:15
Alignment explanation
Indices: 12178063--12178096 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
12178053 TTAAATTATC
12178063 TTATTATTAACATTA
1 TTATTATTAACATTA
*
12178078 TTATTATTAATATTA
1 TTATTATTAACATTA
12178093 TTAT
1 TTAT
12178097 AACTTGTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (15 bp):
TTATTATTAACATTA
Found at i:12181471 original size:55 final size:57
Alignment explanation
Indices: 12181396--12181527 Score: 153
Period size: 55 Copynumber: 2.3 Consensus size: 57
12181386 CCAGATACCC
* *
12181396 AAAAAAATATTTTTTGGGTGTTTACCAAACCATAGTCGATA-CCCCTATT-TCAG-AT
1 AAAAAAATATTTTTTTGGTGTTTACCAAACCATAGTCGACACCCCCT-TTATCAGAAT
* *** *
12181451 AAAAAAATATTTTTTTGGTGTTTATCAAGTTATAGTTGACACCCCCTTTATCAGATAT
1 AAAAAAATATTTTTTTGGTGTTTACCAAACCATAGTCGACACCCCCTTTATCAGA-AT
12181509 AAAAAAATATATTTTTTGG
1 AAAAAAATAT-TTTTTTGG
12181528 GTGTCTGCCA
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
55 36 0.55
56 9 0.14
58 12 0.18
59 8 0.12
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.39
Consensus pattern (57 bp):
AAAAAAATATTTTTTTGGTGTTTACCAAACCATAGTCGACACCCCCTTTATCAGAAT
Found at i:12182098 original size:21 final size:21
Alignment explanation
Indices: 12182072--12182117 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
12182062 CTTGAGGGTA
12182072 GCCAAGAAATTT-ATGAAGTTG
1 GCCAAG-AATTTCATGAAGTTG
*
12182093 GCCAAGAATTTCTTGAAGTTG
1 GCCAAGAATTTCATGAAGTTG
12182114 GCCA
1 GCCA
12182118 GGTATTCAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (21 bp):
GCCAAGAATTTCATGAAGTTG
Found at i:12182634 original size:56 final size:57
Alignment explanation
Indices: 12182508--12182642 Score: 148
Period size: 56 Copynumber: 2.4 Consensus size: 57
12182498 GTCTACCAAG
* * *
12182508 CCATGACCGACACTCTCTTTTCCAGATACCCAAAAATATTTTTCGAGTGTTTACCAT
1 CCATGACCGAGACTCACTTTTCCAGATACCCAAAAATATTTATCGAGTGTTTACCAT
* * * * * * *
12182565 CCTATGGCTGAGACCCACTTTTGCAGGT-CCCAAAAATATTTAT-GGGTGTTTACTAT
1 CC-ATGACCGAGACTCACTTTTCCAGATACCCAAAAATATTTATCGAGTGTTTACCAT
12182621 CACATGACCGAGACTCACTTTT
1 C-CATGACCGAGACTCACTTTT
12182643 AACCCAGTAC
Statistics
Matches: 63, Mismatches: 13, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
56 28 0.44
57 17 0.27
58 18 0.29
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.33
Consensus pattern (57 bp):
CCATGACCGAGACTCACTTTTCCAGATACCCAAAAATATTTATCGAGTGTTTACCAT
Found at i:12185910 original size:15 final size:16
Alignment explanation
Indices: 12185877--12185914 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
12185867 ATGTAATAAT
*
12185877 ATAAATTTTAAAGCTA
1 ATAAAGTTTAAAGCTA
12185893 ATAAAGTTTAAA-CTA
1 ATAAAGTTTAAAGCTA
12185908 ATAAAGT
1 ATAAAGT
12185915 GTAATAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.53, C:0.05, G:0.08, T:0.34
Consensus pattern (16 bp):
ATAAAGTTTAAAGCTA
Found at i:12185962 original size:23 final size:23
Alignment explanation
Indices: 12185921--12185965 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
12185911 AAGTGTAATA
*
12185921 AAATTTAATTTTTAATTTAAATG
1 AAATTTAATTTTAAATTTAAATG
12185944 AAATTTAA-TTTAAACTTTAAAT
1 AAATTTAATTTTAAA-TTTAAAT
12185966 TAATAAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
AAATTTAATTTTAAATTTAAATG
Found at i:12185963 original size:60 final size:60
Alignment explanation
Indices: 12185894--12186021 Score: 152
Period size: 60 Copynumber: 2.1 Consensus size: 60
12185884 TTAAAGCTAA
* * * *
12185894 TAAAGTTTAAACTAATAAAGTGTAATAAAATTTAATTTTTAATTTAA-ATGAAATTTAA-TT
1 TAAACTTTAAACTAATAAAGTGTAA-AAAAATTAA-TTTAAAATTAAGATGAAATTTAAGTT
* * *
12185954 TAAACTTTAAATTAATAAAGTTTAAAAAAATTAATTTAAAATTAAGTATTAAATTTAAGTT
1 TAAACTTTAAACTAATAAAGTGTAAAAAAATTAATTTAAAATTAAG-ATGAAATTTAAGTT
12186015 TAAACTT
1 TAAACTT
12186022 ACAATTTATA
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
58 9 0.16
59 8 0.14
60 32 0.55
61 9 0.16
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.42
Consensus pattern (60 bp):
TAAACTTTAAACTAATAAAGTGTAAAAAAATTAATTTAAAATTAAGATGAAATTTAAGTT
Found at i:12185968 original size:12 final size:11
Alignment explanation
Indices: 12185934--12186145 Score: 73
Period size: 12 Copynumber: 18.6 Consensus size: 11
12185924 TTTAATTTTT
*
12185934 AATTTAAATGA
1 AATTTAAATTA
*
12185945 AATTTAATTTA
1 AATTTAAATTA
12185956 AACTTTAAATT-
1 AA-TTTAAATTA
12185967 AA--TAAAGTTTA
1 AATTTAAA--TTA
*
12185978 AA--AAAATT-
1 AATTTAAATTA
12185986 AATTTAAAATTA
1 AATTT-AAATTA
*
12185998 AGTATTAAATTTA
1 AAT-TTAAA-TTA
*
12186011 AGTTTAAACTTA
1 AATTTAAA-TTA
12186023 CAATTTATAATTA
1 -AATTTA-AATTA
*
12186036 AATTGAAATTGA
1 AATTTAAATT-A
*
12186048 AA-TGAAATTGA
1 AATTTAAATT-A
*
12186059 AATTGAAATTGA
1 AATTTAAATT-A
*
12186071 AATTGAAATTGA
1 AATTTAAATT-A
* * *
12186083 AGTTGAAGTTGA
1 AATTTAAATT-A
* *
12186095 AATTTGAATGA
1 AATTTAAATTA
*
12186106 AATTAAAATTA
1 AATTTAAATTA
*
12186117 AA-TGAAATGT-
1 AATTTAAAT-TA
12186127 AATTTAAAATTA
1 AATTT-AAATTA
12186139 AATTTAA
1 AATTTAA
12186146 TAATTGCATA
Statistics
Matches: 162, Mismatches: 21, Indels: 36
0.74 0.10 0.16
Matches are distributed among these distances:
8 6 0.04
9 2 0.01
10 9 0.06
11 54 0.33
12 73 0.45
13 16 0.10
14 2 0.01
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.38
Consensus pattern (11 bp):
AATTTAAATTA
Found at i:12186005 original size:13 final size:12
Alignment explanation
Indices: 12185980--12186018 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
12185970 AAAGTTTAAA
12185980 AAAATTAA-TTT
1 AAAATTAAGTTT
12185991 AAAATTAAGTATT
1 AAAATTAAGT-TT
*
12186004 AAATTTAAGTTT
1 AAAATTAAGTTT
12186016 AAA
1 AAA
12186019 CTTACAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 8 0.32
12 6 0.24
13 11 0.44
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (12 bp):
AAAATTAAGTTT
Found at i:12186011 original size:6 final size:6
Alignment explanation
Indices: 12185986--12186145 Score: 53
Period size: 6 Copynumber: 27.2 Consensus size: 6
12185976 TAAAAAAATT
* * * *
12185986 AATTTA AAATTA AGTATTA AATTTA AGTTTA AACTTA CAATTTA TAA-TTA
1 AATTTA AATTTA AAT-TTA AATTTA AATTTA AATTTA -AATTTA -AATTTA
* * * * * * * *
12186036 AATTGA AATTGA AA-TGA AATTGA AATTGA AATTGA AATTGA AATTGA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
* * * * * * * * *
12186083 AGTTGA AGTTGA AATTTG AA-TGA AA-TTA AAATTA AA-TGA AATGT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
*
12186127 AATTTA AAATTA AATTTA A
1 AATTTA AATTTA AATTTA A
12186146 TAATTGCATA
Statistics
Matches: 124, Mismatches: 23, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
5 22 0.18
6 90 0.73
7 12 0.10
ACGTcount: A:0.50, C:0.01, G:0.11, T:0.38
Consensus pattern (6 bp):
AATTTA
Found at i:12186133 original size:16 final size:16
Alignment explanation
Indices: 12185934--12186134 Score: 75
Period size: 18 Copynumber: 11.5 Consensus size: 16
12185924 TTTAATTTTT
*
12185934 AATTTAAATGAAATTT
1 AATTTAAATGAAATTA
*
12185950 AATTTAAACTTTAAATTAATA
1 AATTTAAA--TGAAA-T--TA
*
12185971 AAGTTTAAA-AAAATT-
1 AA-TTTAAATGAAATTA
*
12185986 AATTTAAAATTAAGTATTA
1 AATTT-AAATGAA--ATTA
* *
12186005 AATTTAAGTTTAAACTTA
1 AATTTAA-ATGAAA-TTA
*
12186023 CAATTTATAATTAAATTGA
1 -AATTTA-AATGAAATT-A
*
12186042 AATTGAAATGAAATTGA
1 AATTTAAATGAAATT-A
*
12186059 AATTGAAATTGAAATTGA
1 AATTTAAA-TGAAATT-A
* * *
12186077 AATTGAAGTTGAAGTTGA
1 AATTTAA-ATGAAATT-A
*
12186095 AATTTGAATGAAATTA
1 AATTTAAATGAAATTA
*
12186111 AAATTAAATGAAATGT-
1 AATTTAAATGAAAT-TA
12186127 AATTTAAA
1 AATTTAAA
12186135 ATTAAATTTA
Statistics
Matches: 149, Mismatches: 17, Indels: 38
0.73 0.08 0.19
Matches are distributed among these distances:
14 3 0.02
15 5 0.03
16 31 0.21
17 26 0.17
18 49 0.33
19 25 0.17
20 1 0.01
21 3 0.02
22 6 0.04
ACGTcount: A:0.51, C:0.01, G:0.10, T:0.38
Consensus pattern (16 bp):
AATTTAAATGAAATTA
Found at i:12186465 original size:22 final size:21
Alignment explanation
Indices: 12186440--12186507 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 21
12186430 TAAATAAATA
12186440 AATAAATTTAAATAAAATAGTT
1 AATAAATTTAAATAAAAT-GTT
12186462 AAT-AATTT---TAAAATGTTT
1 AATAAATTTAAATAAAATG-TT
* *
12186480 AATAAAATTAAATAAAATCTTT
1 AATAAATTTAAATAAAAT-GTT
12186502 AATAAA
1 AATAAA
12186508 ATTAGTTACT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
17 1 0.03
18 11 0.29
19 4 0.11
21 5 0.13
22 17 0.45
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.38
Consensus pattern (21 bp):
AATAAATTTAAATAAAATGTT
Found at i:12186508 original size:22 final size:21
Alignment explanation
Indices: 12186470--12186546 Score: 82
Period size: 22 Copynumber: 3.5 Consensus size: 21
12186460 TTAATAATTT
12186470 TAAAATGTTTAATAAAATTAAA
1 TAAAAT-TTTAATAAAATTAAA
**
12186492 TAAAATCTTTAATAAAATTAGT
1 TAAAAT-TTTAATAAAATTAAA
* * *
12186514 TACTATTTTTAATAAACTTAAA
1 TA-AAATTTTAATAAAATTAAA
12186536 TAAAATTTTAA
1 TAAAATTTTAA
12186547 ATTATTAAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
21 7 0.16
22 35 0.80
23 2 0.05
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.42
Consensus pattern (21 bp):
TAAAATTTTAATAAAATTAAA
Found at i:12187659 original size:10 final size:10
Alignment explanation
Indices: 12187644--12187669 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
12187634 CATGGGCGGT
12187644 TGCTCCGATC
1 TGCTCCGATC
12187654 TGCTCCGATC
1 TGCTCCGATC
12187664 TGCTCC
1 TGCTCC
12187670 AATCATGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.08, C:0.42, G:0.19, T:0.31
Consensus pattern (10 bp):
TGCTCCGATC
Found at i:12191437 original size:41 final size:41
Alignment explanation
Indices: 12191356--12191582 Score: 213
Period size: 41 Copynumber: 5.5 Consensus size: 41
12191346 CCTTATGCTC
* * * * * *
12191356 TATCGAGTCATAAGTCTTACTTTAACCATATTCTTATTCTCA
1 TATCGAGACATGAGTCTT-CCTTAATCAAATTCTCATTCTCA
* *
12191398 TAACGAGACATGAGTCTTCCTTAATCAAAATCTCATTCTCA
1 TATCGAGACATGAGTCTTCCTTAATCAAATTCTCATTCTCA
* * * * *
12191439 TTTCGAGACATGAGTCTTCCTGATTCATAGTCTCATTCTCA
1 TATCGAGACATGAGTCTTCCTTAATCAAATTCTCATTCTCA
* * *
12191480 TCTCGAGACATGAGTCTTCCTTATTCATATTCTCATTCTCA
1 TATCGAGACATGAGTCTTCCTTAATCAAATTCTCATTCTCA
* * * * *
12191521 TCTCGAGACATGAGTTTTCCATTTATACAATTTCTCATGCTCA
1 TATCGAGACATGAGTCTTCC-TTAAT-CAAATTCTCATTCTCA
*
12191564 -ACCCGAGACATGAGTCTTC
1 TA-TCGAGACATGAGTCTTC
12191583 ATTATTATAC
Statistics
Matches: 156, Mismatches: 26, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
41 110 0.71
42 18 0.12
43 28 0.18
ACGTcount: A:0.26, C:0.25, G:0.11, T:0.37
Consensus pattern (41 bp):
TATCGAGACATGAGTCTTCCTTAATCAAATTCTCATTCTCA
Found at i:12191571 original size:43 final size:41
Alignment explanation
Indices: 12191382--12191587 Score: 227
Period size: 41 Copynumber: 5.0 Consensus size: 41
12191372 TTACTTTAAC
* **
12191382 CATATTCTTATTCTCATAACGAGACATGAGTCTTCCTTA-A
1 CATATTCTCATTCTCATCTCGAGACATGAGTCTTCCTTATA
* * * * *
12191422 TCAAAATCTCATTCTCATTTCGAGACATGAGTCTTCCTGATT
1 -CATATTCTCATTCTCATCTCGAGACATGAGTCTTCCTTATA
* *
12191464 CATAGTCTCATTCTCATCTCGAGACATGAGTCTTCCTTATT
1 CATATTCTCATTCTCATCTCGAGACATGAGTCTTCCTTATA
*
12191505 CATATTCTCATTCTCATCTCGAGACATGAGTTTTCCATTTATA
1 CATATTCTCATTCTCATCTCGAGACATGAGTCTTCC--TTATA
* * * *
12191548 CA-ATTTCTCATGCTCAACCCGAGACATGAGTCTTCATTAT
1 CATA-TTCTCATTCTCATCTCGAGACATGAGTCTTCCTTAT
12191588 TATACACCAA
Statistics
Matches: 142, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
41 108 0.76
42 1 0.01
43 33 0.23
ACGTcount: A:0.26, C:0.25, G:0.11, T:0.38
Consensus pattern (41 bp):
CATATTCTCATTCTCATCTCGAGACATGAGTCTTCCTTATA
Found at i:12192422 original size:22 final size:21
Alignment explanation
Indices: 12192375--12192422 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
12192365 GACTTTCATA
*
12192375 ATTAACTTAATTAATCATCTT
1 ATTAACTTAATTAATCATATT
* * *
12192396 TTTAACCTTAATTTATCCTATT
1 ATTAA-CTTAATTAATCATATT
12192418 ATTAA
1 ATTAA
12192423 TTAGTATTTG
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTAACTTAATTAATCATATT
Found at i:12198702 original size:41 final size:41
Alignment explanation
Indices: 12198544--12198702 Score: 203
Period size: 41 Copynumber: 3.9 Consensus size: 41
12198534 TTCCTTTAAC
* *
12198544 CATATTCTCATTCTCATCTCGAGACATGAGTCTTCTTTAATT
1 CATAGTCTCATTCTCATCTCGAGACATGAGTCTTC-CTAATT
* * * * * *
12198586 -AAAATCTCATTCTCATTTCGAGATATGATTCTTCCTTATT
1 CATAGTCTCATTCTCATCTCGAGACATGAGTCTTCCTAATT
* *
12198626 CATAGTCTCATTCTCATCTCAAGACATGAGTCTTCCTCATT
1 CATAGTCTCATTCTCATCTCGAGACATGAGTCTTCCTAATT
*
12198667 CATAGTCTCATTCTCATCTCGAGACATGAATCTTCC
1 CATAGTCTCATTCTCATCTCGAGACATGAGTCTTCC
12198703 ATTTATACAA
Statistics
Matches: 100, Mismatches: 16, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
40 4 0.04
41 96 0.96
ACGTcount: A:0.25, C:0.26, G:0.09, T:0.40
Consensus pattern (41 bp):
CATAGTCTCATTCTCATCTCGAGACATGAGTCTTCCTAATT
Found at i:12199466 original size:3 final size:3
Alignment explanation
Indices: 12199451--12199502 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
12199441 AGCCGTGTAG
*
12199451 AGA AGA CGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
12199499 AGA A
1 AGA A
12199503 AGAAAATGTG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.65, C:0.02, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:12199937 original size:11 final size:11
Alignment explanation
Indices: 12199923--12200038 Score: 53
Period size: 11 Copynumber: 10.6 Consensus size: 11
12199913 ATTTTCGAAT
12199923 TTTTTTAAATA
1 TTTTTTAAATA
**
12199934 TTTTTT-TCTA
1 TTTTTTAAATA
**
12199944 TTTTGGAAATA
1 TTTTTTAAATA
12199955 TTTTTT--ATA
1 TTTTTTAAATA
**
12199964 -TTTTCGAAT-
1 TTTTTTAAATA
12199973 TTTTTTAAAATTA
1 TTTTTT-AAA-TA
*
12199986 TATTTTCAAAATA
1 T-TTTT-TAAATA
*
12199999 TTTTTTACATA
1 TTTTTTAAATA
* *
12200010 TATTTTATATA
1 TTTTTTAAATA
**
12200021 TTTTCGAAATA
1 TTTTTTAAATA
12200032 TTTTTTA
1 TTTTTTA
12200039 GATTTTCGAA
Statistics
Matches: 74, Mismatches: 22, Indels: 18
0.65 0.19 0.16
Matches are distributed among these distances:
8 4 0.05
9 3 0.04
10 12 0.16
11 39 0.53
12 5 0.07
13 4 0.05
14 7 0.09
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.61
Consensus pattern (11 bp):
TTTTTTAAATA
Found at i:12199965 original size:20 final size:20
Alignment explanation
Indices: 12199929--12200056 Score: 76
Period size: 20 Copynumber: 6.6 Consensus size: 20
12199919 GAATTTTTTT
* *
12199929 AAATATTTTTTTCTATTTTGG
1 AAATA-TTTTTTATATTTTCG
12199950 AAATATTTTTTATATTTTCG
1 AAATATTTTTTATATTTTCG
* * *
12199970 AATTTTTTTAAAATTATATTTTCA
1 AAATATTTT----TTATATTTTCG
12199994 AAATA-TTTTT-TA----C-
1 AAATATTTTTTATATTTTCG
* *
12200007 ATATATTTTATATATTTTCG
1 AAATATTTTTTATATTTTCG
*
12200027 AAATATTTTTTAGATTTTCG
1 AAATATTTTTTATATTTTCG
12200047 -AAT-TTTTTTA
1 AAATATTTTTTA
12200057 AAAATATTTT
Statistics
Matches: 84, Mismatches: 12, Indels: 25
0.69 0.10 0.21
Matches are distributed among these distances:
13 4 0.05
14 5 0.06
15 2 0.02
18 9 0.11
19 6 0.07
20 37 0.44
21 5 0.06
23 3 0.04
24 13 0.15
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (20 bp):
AAATATTTTTTATATTTTCG
Found at i:12200122 original size:22 final size:22
Alignment explanation
Indices: 12200092--12200145 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
12200082 AAATTTTTCC
* *
12200092 ATATATTTTTTATATTTTCAAA
1 ATATTTTTTTTACATTTTCAAA
12200114 ATATTTTTTTTACATTTTCAAA
1 ATATTTTTTTTACATTTTCAAA
*
12200136 ATATTGTTTT
1 ATATTTTTTT
12200146 ACAAATGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (22 bp):
ATATTTTTTTTACATTTTCAAA
Found at i:12201126 original size:30 final size:30
Alignment explanation
Indices: 12201092--12201149 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
12201082 GATTTTTTTT
* *
12201092 GTTTATTTTTTAAATTTAATTTGTAATTTC
1 GTTTATATTTTAAATTTAATTTGAAATTTC
12201122 GTTTATATTTTAAATTTAATTTGAAATT
1 GTTTATATTTTAAATTTAATTTGAAATT
12201150 ATTATTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.60
Consensus pattern (30 bp):
GTTTATATTTTAAATTTAATTTGAAATTTC
Found at i:12202043 original size:58 final size:56
Alignment explanation
Indices: 12201981--12202172 Score: 194
Period size: 59 Copynumber: 3.4 Consensus size: 56
12201971 AGGTTTCGAC
*
12201981 CATGGCTTGGTC-GACACCCAAAAAATATATTTTTGTATCTGAAAAAGGGGGTGTCGTT
1 CATGGCTTGG-CAGACACCCAAAAAATATATTTTT-TATCT-AAAAAGGGGGTGTCGGT
* * * *
12202039 CATGGCTTGACAAACACCCAAAAAATATATTTTTTATATCTAATAAAGAGTGTGTCGGT
1 CATGGCTTGGCAGACACCCAAAAAATATA-TTTTT-TATCTAA-AAAGGGGGTGTCGGT
* * ***
12202098 CATGGTTTGGCAGACACCC--AAAA-ATATTTTTTATCTAAAAAATGGGGTGTCAAC
1 CATGGCTTGGCAGACACCCAAAAAATATATTTTTTATCT-AAAAAGGGGGTGTCGGT
*
12202152 CATGGCTTGGCAAACACCCAA
1 CATGGCTTGGCAGACACCCAA
12202173 GTTTTTTTTT
Statistics
Matches: 111, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
54 31 0.28
55 7 0.06
56 3 0.03
57 5 0.05
58 27 0.24
59 38 0.34
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (56 bp):
CATGGCTTGGCAGACACCCAAAAAATATATTTTTTATCTAAAAAGGGGGTGTCGGT
Found at i:12211984 original size:20 final size:20
Alignment explanation
Indices: 12211943--12211987 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
12211933 CATGATTTGT
**
12211943 ATTAAGATTAAATAGGCTTA
1 ATTAAGATTAAATAGGAATA
12211963 ATTAAGATTAAA-AGAGAATA
1 ATTAAGATTAAATAG-GAATA
12211983 ATTAA
1 ATTAA
12211988 ATCTTAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.53, C:0.02, G:0.13, T:0.31
Consensus pattern (20 bp):
ATTAAGATTAAATAGGAATA
Found at i:12217149 original size:41 final size:41
Alignment explanation
Indices: 12217095--12217308 Score: 266
Period size: 41 Copynumber: 5.2 Consensus size: 41
12217085 TTGTATAAAT
* *
12217095 GGAAGACTCATGTCTCGAGATGAGAATGAGACTATGAATAA
1 GGAAGACTCATGTCTCGAAATGAGAATGAGACTATGATTAA
* *
12217136 GGAAGACTCATGTCTCGAAATGAGAATGAGATTTTGATTAA
1 GGAAGACTCATGTCTCGAAATGAGAATGAGACTATGATTAA
* * * * * *
12217177 AGAAGATTCATGTCTTGAGATGACAATGAGACTATGAATAA
1 GGAAGACTCATGTCTCGAAATGAGAATGAGACTATGATTAA
* * * *
12217218 GGAAGACTCATGTCTCGAAATGAGAATAAGATTTTTATTAA
1 GGAAGACTCATGTCTCGAAATGAGAATGAGACTATGATTAA
* * *
12217259 GGAAGACTCATGTCTCGATATGAGAATGAGAATATGGTTAAA
1 GGAAGACTCATGTCTCGAAATGAGAATGAGACTATGATT-AA
12217301 GGAAGACT
1 GGAAGACT
12217309 TATGACTTGA
Statistics
Matches: 144, Mismatches: 28, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
41 134 0.93
42 10 0.07
ACGTcount: A:0.39, C:0.10, G:0.24, T:0.27
Consensus pattern (41 bp):
GGAAGACTCATGTCTCGAAATGAGAATGAGACTATGATTAA
Found at i:12217329 original size:82 final size:82
Alignment explanation
Indices: 12217095--12217308 Score: 329
Period size: 82 Copynumber: 2.6 Consensus size: 82
12217085 TTGTATAAAT
12217095 GGAAGACTCATGTCTCGAGATGAGAATGAGACTATGAATAAGGAAGACTCATGTCTCGAAATGAG
1 GGAAGACTCATGTCTCGAGATGAGAATGAGACTATGAATAAGGAAGACTCATGTCTCGAAATGAG
*
12217160 AATGAGATTTTGATTAA
66 AATAAGATTTTGATTAA
* * * *
12217177 AGAAGATTCATGTCTTGAGATGACAATGAGACTATGAATAAGGAAGACTCATGTCTCGAAATGAG
1 GGAAGACTCATGTCTCGAGATGAGAATGAGACTATGAATAAGGAAGACTCATGTCTCGAAATGAG
*
12217242 AATAAGATTTTTATTAA
66 AATAAGATTTTGATTAA
* * **
12217259 GGAAGACTCATGTCTCGATATGAGAATGAGAATATGGTTAAAGGAAGACT
1 GGAAGACTCATGTCTCGAGATGAGAATGAGACTATGAAT-AAGGAAGACT
12217309 TATGACTTGA
Statistics
Matches: 117, Mismatches: 14, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
82 107 0.91
83 10 0.09
ACGTcount: A:0.39, C:0.10, G:0.24, T:0.27
Consensus pattern (82 bp):
GGAAGACTCATGTCTCGAGATGAGAATGAGACTATGAATAAGGAAGACTCATGTCTCGAAATGAG
AATAAGATTTTGATTAA
Found at i:12223377 original size:22 final size:21
Alignment explanation
Indices: 12223319--12223377 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 21
12223309 TCCATTTTTT
*
12223319 ATTTTT-TATTATTCTCCTTTC
1 ATTTTTATTTTATT-TCCTTTC
12223340 ATTTTTATTTTAATTTCC-TTC
1 ATTTTTATTTT-ATTTCCTTTC
12223361 TATTTTTGATTTTATTT
1 -ATTTTT-ATTTTATTT
12223378 TTAAATATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
21 9 0.27
22 16 0.48
23 8 0.24
ACGTcount: A:0.17, C:0.12, G:0.02, T:0.69
Consensus pattern (21 bp):
ATTTTTATTTTATTTCCTTTC
Found at i:12225744 original size:136 final size:135
Alignment explanation
Indices: 12225584--12225920 Score: 457
Period size: 136 Copynumber: 2.5 Consensus size: 135
12225574 AGGGGTTAAA
* ** *
12225584 AATAAATATGATGATGGAATCATTTAATATGACGCCA-CTATTTTTGTCAAATCATTTATTATTT
1 AATAAATATGATGGTGGAGCCATTTAATATGAAGCCATC-A-TTTTGTCAAATCATTTATTATTT
* * *
12225648 TCAT-TTAAATTTTAAATGTTAAAAAA-TTATTATTTAAATATGTCAAATTTAGGGTTTCAAAAA
64 TCATCTTAAA-TTTAAA-ATTAAAAAACTTATTATTTAAATATGTCAAATTTAAGATTTCAAAAA
12225711 ATAATTATT
127 ATAATTATT
*
12225720 AATAAATATGATGGTGGAGCCATTTAATATGATA-CCATCACTTTGTCAAATCATTTATTACTTT
1 AATAAATATGATGGTGGAGCCATTTAATATGA-AGCCATCATTTTGTCAAATCATTTATTA-TTT
** * *
12225784 TTTTCTTAAATTTAAAATTAAAAAACTTATTATTTAAATATGTTAAGTTTAAGATTTCAAAAAAT
64 TCATCTTAAATTTAAAATTAAAAAACTTATTATTTAAATATGTCAAATTTAAGATTTCAAAAAAT
12225849 AATTATT
129 AATTATT
* *
12225856 AATAAATATGATGGTGAAGCCATTTAATATGAAGCCATCACTTTTGTCAAATCATTTATTTTTTT
1 AATAAATATGATGGTGGAGCCATTTAATATGAAGCCATCA-TTTTGTCAAATCATTTATTATTTT
12225921 AAAATTATCT
Statistics
Matches: 179, Mismatches: 15, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
135 28 0.16
136 127 0.71
137 24 0.13
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (135 bp):
AATAAATATGATGGTGGAGCCATTTAATATGAAGCCATCATTTTGTCAAATCATTTATTATTTTC
ATCTTAAATTTAAAATTAAAAAACTTATTATTTAAATATGTCAAATTTAAGATTTCAAAAAATAA
TTATT
Found at i:12228647 original size:21 final size:22
Alignment explanation
Indices: 12228614--12228658 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
12228604 CATCATCTCT
*
12228614 CAAGTACCGATCTATTTC-GTA
1 CAAGTACCAATCTATTTCGGTA
* *
12228635 CAAGTACTAATCTGTTTCGGTA
1 CAAGTACCAATCTATTTCGGTA
12228657 CA
1 CA
12228659 CCAATGTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (22 bp):
CAAGTACCAATCTATTTCGGTA
Found at i:12230311 original size:30 final size:30
Alignment explanation
Indices: 12230270--12230329 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
12230260 CCCACACGGT
* * * *
12230270 CCCCGTACTTTCCAAGGTTTTTGATTTGAG
1 CCCCATACTTTCCAAAGTTTCTAATTTGAG
12230300 CCCCATACTTTCCAAAGTTTCTAATTTGAG
1 CCCCATACTTTCCAAAGTTTCTAATTTGAG
12230330 TCTCGTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.22, C:0.25, G:0.15, T:0.38
Consensus pattern (30 bp):
CCCCATACTTTCCAAAGTTTCTAATTTGAG
Found at i:12230410 original size:16 final size:16
Alignment explanation
Indices: 12230389--12230424 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
12230379 CCCCTTCATC
*
12230389 TTTAATTCATTTTTAA
1 TTTAATCCATTTTTAA
12230405 TTTAATCCATTTTTAA
1 TTTAATCCATTTTTAA
12230421 TTTA
1 TTTA
12230425 TTTTATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTAATCCATTTTTAA
Found at i:12231114 original size:18 final size:18
Alignment explanation
Indices: 12231087--12231122 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
12231077 TACATTTAAG
*
12231087 AATCGCATTTTAAATTTT
1 AATCGAATTTTAAATTTT
*
12231105 AATCGAATTTTTAATTTT
1 AATCGAATTTTAAATTTT
12231123 TCAACAATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.08, G:0.06, T:0.53
Consensus pattern (18 bp):
AATCGAATTTTAAATTTT
Found at i:12231408 original size:26 final size:26
Alignment explanation
Indices: 12231371--12231420 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 26
12231361 GTTGCAACAT
12231371 TTTATTTAATTTGTTTGTTA-TTTATTA
1 TTTATTTAATTT-TTT-TTACTTTATTA
12231398 TTTA-TTAATTTTTTTTACTTTAT
1 TTTATTTAATTTTTTTTACTTTAT
12231421 CTTAGTGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 3 0.14
25 8 0.36
26 7 0.32
27 4 0.18
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.72
Consensus pattern (26 bp):
TTTATTTAATTTTTTTTACTTTATTA
Found at i:12238142 original size:19 final size:19
Alignment explanation
Indices: 12238118--12238154 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
12238108 TTCCAACAAC
12238118 TTTTTTTTCAAATGGCTAT
1 TTTTTTTTCAAATGGCTAT
*
12238137 TTTTTTTTCTAATGGCTA
1 TTTTTTTTCAAATGGCTA
12238155 GTTTATTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.11, T:0.59
Consensus pattern (19 bp):
TTTTTTTTCAAATGGCTAT
Found at i:12245877 original size:6 final size:6
Alignment explanation
Indices: 12245867--12245927 Score: 113
Period size: 6 Copynumber: 10.2 Consensus size: 6
12245857 ATAACCCCTT
*
12245867 AATTAT AATTAC AATTAC AATTAC AATTAC AATTAC AATTAC AATTAC
1 AATTAC AATTAC AATTAC AATTAC AATTAC AATTAC AATTAC AATTAC
12245915 AATTAC AATTAC A
1 AATTAC AATTAC A
12245928 TAACCATACT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 54 1.00
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (6 bp):
AATTAC
Found at i:12247261 original size:19 final size:18
Alignment explanation
Indices: 12247237--12247273 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
12247227 TATTATTAAT
12247237 ATATTTATAATTATAAAAA
1 ATATTTATAATTA-AAAAA
*
12247256 ATATTTATTATTAAAAAA
1 ATATTTATAATTAAAAAA
12247274 TTAATATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATTTATAATTAAAAAA
Found at i:12248165 original size:46 final size:44
Alignment explanation
Indices: 12248112--12248205 Score: 109
Period size: 44 Copynumber: 2.1 Consensus size: 44
12248102 GGTTCGCTGT
*
12248112 AATGGAATAGGGCTGTAATCAGTATTTCAAT-TGTTTGGTTGAATGG
1 AATGGAATAGAGCTGTAAT-AGTATTT--ATGTGTTTGGTTGAATGG
* * * *
12248158 AATGGAATATAGTTGTAATAGTATTTTTGTGTTTGGTTGATTGG
1 AATGGAATAGAGCTGTAATAGTATTTATGTGTTTGGTTGAATGG
12248202 AATG
1 AATG
12248206 ATACTGCAAC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
43 1 0.02
44 18 0.43
45 7 0.17
46 16 0.38
ACGTcount: A:0.28, C:0.03, G:0.28, T:0.41
Consensus pattern (44 bp):
AATGGAATAGAGCTGTAATAGTATTTATGTGTTTGGTTGAATGG
Found at i:12248330 original size:26 final size:26
Alignment explanation
Indices: 12248300--12248384 Score: 81
Period size: 26 Copynumber: 3.4 Consensus size: 26
12248290 GTTATTAAAT
12248300 TTTAATAAGATTATTATTAAATATAA
1 TTTAATAAGATTATTATTAAATATAA
* *
12248326 TTTAATAA-A-TA--ATTTAATCAT-T
1 TTTAATAAGATTATTATTAAAT-ATAA
* * *
12248348 TTTAACATGATTATTATTAAATACAA
1 TTTAATAAGATTATTATTAAATATAA
12248374 TTTAATAAGAT
1 TTTAATAAGAT
12248385 AGTATATAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 12
0.68 0.14 0.18
Matches are distributed among these distances:
22 12 0.27
23 3 0.07
24 4 0.09
25 2 0.05
26 23 0.52
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46
Consensus pattern (26 bp):
TTTAATAAGATTATTATTAAATATAA
Found at i:12249887 original size:40 final size:40
Alignment explanation
Indices: 12249841--12249921 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
12249831 CATTATAAAT
* *
12249841 TTAACATACTGTACTGTTATAGATTTATGGAACATTAACA
1 TTAACATACTGTACTGTTACAGACTTATGGAACATTAACA
* *
12249881 TTAACATATTGTACTGTTACATACTTATGGAACATTAACA
1 TTAACATACTGTACTGTTACAGACTTATGGAACATTAACA
12249921 T
1 T
12249922 AGCTTGAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (40 bp):
TTAACATACTGTACTGTTACAGACTTATGGAACATTAACA
Found at i:12255413 original size:17 final size:18
Alignment explanation
Indices: 12255383--12255417 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
12255373 GAAGCTATAG
12255383 TAATTATAAATTTAATAA
1 TAATTATAAATTTAATAA
12255401 TAATTAT-AATTTAATAA
1 TAATTATAAATTTAATAA
12255418 AAAATGTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATTATAAATTTAATAA
Found at i:12256062 original size:22 final size:21
Alignment explanation
Indices: 12256037--12256079 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
12256027 TAGATGAAGT
*
12256037 ACAATATTATTTAACTACATAA
1 ACAATATAATTTAACTA-ATAA
*
12256059 ACAATATAATTTACCTAATAA
1 ACAATATAATTTAACTAATAA
12256080 TTACATGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (21 bp):
ACAATATAATTTAACTAATAA
Found at i:12259678 original size:20 final size:22
Alignment explanation
Indices: 12259638--12259683 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
12259628 CATGACTAAG
12259638 CCTATCTTCGATTTTACTTG-A
1 CCTATCTTCGATTTTACTTGAA
12259659 CCTAT-TTC-ATTTTCACTTGAA
1 CCTATCTTCGATTTT-ACTTGAA
12259680 CCTA
1 CCTA
12259684 AAGCTCTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.22
20 8 0.35
21 10 0.43
ACGTcount: A:0.22, C:0.26, G:0.07, T:0.46
Consensus pattern (22 bp):
CCTATCTTCGATTTTACTTGAA
Found at i:12262470 original size:20 final size:21
Alignment explanation
Indices: 12262428--12262472 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 21
12262418 TCAATAAAAT
12262428 TTAATTTACAATTATTTTTTTCC
1 TTAATTTACAATTA--TTTTTCC
12262451 TTAATTTACAATTA-TTTTCC
1 TTAATTTACAATTATTTTTCC
12262471 TT
1 TT
12262473 CAAACATGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.36
23 14 0.64
ACGTcount: A:0.27, C:0.13, G:0.00, T:0.60
Consensus pattern (21 bp):
TTAATTTACAATTATTTTTCC
Found at i:12262880 original size:24 final size:24
Alignment explanation
Indices: 12262845--12262917 Score: 110
Period size: 24 Copynumber: 3.0 Consensus size: 24
12262835 TGAGAAATAA
*
12262845 TATTTCAGTTAAACTCTGTTTATT
1 TATTTCAATTAAACTCTGTTTATT
* *
12262869 TCTTTCAATTAAACTTTGTTTATT
1 TATTTCAATTAAACTCTGTTTATT
*
12262893 TATTTTAATTAAACTCTGTTTATT
1 TATTTCAATTAAACTCTGTTTATT
12262917 T
1 T
12262918 GTTTGAGTCA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.26, C:0.11, G:0.05, T:0.58
Consensus pattern (24 bp):
TATTTCAATTAAACTCTGTTTATT
Found at i:12264846 original size:24 final size:24
Alignment explanation
Indices: 12264819--12264880 Score: 81
Period size: 23 Copynumber: 2.6 Consensus size: 24
12264809 AAAAATAATC
12264819 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTATTTG
* *
12264843 TTTCAATTAAA-TTTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTATTTG
* *
12264866 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
12264881 TATTAGTCTA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
23 19 0.61
24 12 0.39
ACGTcount: A:0.24, C:0.11, G:0.11, T:0.53
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTATTTG
Found at i:12278887 original size:24 final size:23
Alignment explanation
Indices: 12278851--12278897 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
12278841 TGTGGGTATT
*
12278851 GAGGAAGAGAAAGAAGAAGAGAAA
1 GAGGAAGAAAAAGAAGAAG-GAAA
* *
12278875 GAGGAGGAAAAAGAGGAAGGAAA
1 GAGGAAGAAAAAGAAGAAGGAAA
12278898 AGAATGAGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (23 bp):
GAGGAAGAAAAAGAAGAAGGAAA
Found at i:12283321 original size:52 final size:52
Alignment explanation
Indices: 12283254--12283543 Score: 354
Period size: 52 Copynumber: 5.6 Consensus size: 52
12283244 TAAATGAAAA
*
12283254 AGGTTCGATGACTATGTATCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTATCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * *
12283306 AGGTCCGATGGCTATGTGTCATCATGAGTATATGAATCCTTTATGGATTATG
1 AGGTCCGATGACTATGTATCATCGTGAGTATATGAATCCTTTACGGATTATG
* * *
12283358 AGGTCTGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTATGTATCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * * * * *
12283410 AGATCCGATGGCTATGTGTTATTGTGAGTATATGAACCCTTTACGGATTAAG
1 AGGTCCGATGACTATGTATCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
12283462 AGGTTCGATGACTATGTATCATCGTGAGCGTATA-G-ATCCTTTTACGGATT-TA
1 AGGTCCGATGACTATGTATCATCGTGA--GTATATGAATCC-TTTACGGATTATG
*
12283514 AGGTCCGATGACTTTGTATCA-CAGTGAGTA
1 AGGTCCGATGACTATGTATCATC-GTGAGTA
12283544 ATAAATAGGA
Statistics
Matches: 209, Mismatches: 25, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
50 3 0.01
51 1 0.00
52 189 0.90
53 11 0.05
54 5 0.02
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.36
Consensus pattern (52 bp):
AGGTCCGATGACTATGTATCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:12288843 original size:52 final size:52
Alignment explanation
Indices: 12288697--12288928 Score: 265
Period size: 52 Copynumber: 4.5 Consensus size: 52
12288687 AAAAAGGTTT
* * *
12288697 GATGATTATGTGTCATCGTGAGTATATGAATCCTGTACGGATTATAAGGTCC
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATAAGGTCC
* * * * *
12288749 GATTA-TATGCGTCATCGTGAGTATTTGAATCCTTTACGGATTATGAGGTCC
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATAAGGTCC
* * * *
12288800 GGTGGCTATGTGTCATCGTGAGTATATGAATCATTTATAGATTA-AGAGGTCC
1 GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATA-AGGTCC
* * *
12288852 GATGACTATGTGTCATCGTGAGCATATAGATTCTTTTACAGATT-TAAGGTCC
1 GATGACTATGTGTCATCGTGAGTATAT-GAATCCTTTACAGATTATAAGGTCC
*
12288904 GATGACT-TCGTGTCATCATGAGTAT
1 GATGACTAT-GTGTCATCGTGAGTAT
12288929 TAAATGGGAA
Statistics
Matches: 153, Mismatches: 22, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
51 45 0.29
52 94 0.61
53 14 0.09
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (52 bp):
GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATAAGGTCC
Found at i:12296410 original size:20 final size:20
Alignment explanation
Indices: 12296372--12296410 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12296362 AAATATATTA
* **
12296372 AAATTTTTATTTTGGTATCT
1 AAATTTTTAATTTAATATCT
12296392 AAATTTTTAATTTAATATC
1 AAATTTTTAATTTAATATC
12296411 AGTTAAAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.56
Consensus pattern (20 bp):
AAATTTTTAATTTAATATCT
Found at i:12317410 original size:51 final size:52
Alignment explanation
Indices: 12317254--12317442 Score: 195
Period size: 51 Copynumber: 3.6 Consensus size: 52
12317244 TTTCATTTAA
** ** * *
12317254 TACTCACGATGACATATAGTCATCGGA-CCTCTTGTTCCGTATAGGAATTCATA
1 TACTCACGATGACACCTAGTCATCGGATCCT-TTAATCCGTAAAGG-ATTCATT
* * * *** * *
12317307 TACTCATGATAAC-CCTGAGTCATCGGATCATTTAATCCACCATGAATTCATT
1 TACTCACGATGACACCT-AGTCATCGGATCCTTTAATCCGTAAAGGATTCATT
12317359 TACTCACGATGACACCTAGTCATCGGA-CCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACCTAGTCATCGGATCCTTTAATCCGTAAAGGATTCATT
*
12317410 TACTCACGATGACACTTAGTCATCGGATCCTTT
1 TACTCACGATGACACCTAGTCATCGGATCCTTT
12317443 CGTTTATAAC
Statistics
Matches: 109, Mismatches: 23, Indels: 9
0.77 0.16 0.06
Matches are distributed among these distances:
51 44 0.40
52 33 0.30
53 30 0.28
54 2 0.02
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.32
Consensus pattern (52 bp):
TACTCACGATGACACCTAGTCATCGGATCCTTTAATCCGTAAAGGATTCATT
Found at i:12324092 original size:13 final size:14
Alignment explanation
Indices: 12324052--12324094 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
12324042 ATTTATTATA
12324052 ATATCATTTTTAATT
1 ATAT-ATTTTTAATT
*
12324067 ATATAGTTATTAATT
1 ATATA-TTTTTAATT
12324082 ATAT-TTTTTAATT
1 ATATATTTTTAATT
12324095 TTAAAATGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 8 0.32
14 1 0.04
15 16 0.64
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (14 bp):
ATATATTTTTAATT
Found at i:12324201 original size:23 final size:25
Alignment explanation
Indices: 12324170--12324225 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
12324160 CTATAATTTA
*
12324170 AAAAGTAAAAAG-AC-TAAATTCTTG
1 AAAA-TAAAAAGTACATAAATTATTG
12324194 AAAAT-AAAAGTACATAAATTATTG
1 AAAATAAAAAGTACATAAATTATTG
12324218 AAAA-AAAA
1 AAAATAAAA
12324226 CTGTTGGTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
22 5 0.18
23 3 0.11
24 20 0.71
ACGTcount: A:0.62, C:0.05, G:0.09, T:0.23
Consensus pattern (25 bp):
AAAATAAAAAGTACATAAATTATTG
Found at i:12327763 original size:11 final size:10
Alignment explanation
Indices: 12327737--12327843 Score: 63
Period size: 10 Copynumber: 11.6 Consensus size: 10
12327727 TATTTTTCTA
*
12327737 ATAAAAAATC
1 ATAAAAAATT
12327747 ATAAAAAATT
1 ATAAAAAATT
12327757 AT-AAAAA-T
1 ATAAAAAATT
*
12327765 ATTAACAAA--
1 A-TAAAAAATT
*
12327774 ATAAAAATTT
1 ATAAAAAATT
12327784 AT-AAAAA-T
1 ATAAAAAATT
*
12327792 ATTAAAAA-T
1 ATAAAAAATT
* *
12327801 ATATAAACTT
1 ATAAAAAATT
12327811 AT-AAAAATT
1 ATAAAAAATT
* *
12327820 CTAAAATATT
1 ATAAAAAATT
12327830 AT--AAAATT
1 ATAAAAAATT
12327838 ATAAAA
1 ATAAAA
12327844 TACATATAAA
Statistics
Matches: 74, Mismatches: 14, Indels: 18
0.70 0.13 0.17
Matches are distributed among these distances:
8 17 0.23
9 28 0.38
10 29 0.39
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (10 bp):
ATAAAAAATT
Found at i:12327764 original size:19 final size:18
Alignment explanation
Indices: 12327740--12327843 Score: 79
Period size: 19 Copynumber: 5.7 Consensus size: 18
12327730 TTTTCTAATA
12327740 AAAAATCATAAAAAATTAT
1 AAAAAT-ATAAAAAATTAT
*
12327759 AAAAATATTAACAAA--AT
1 AAAAATA-TAAAAAATTAT
*
12327776 AAAAATTTATAAAAA-TATT
1 AAAAATATA-AAAAATTA-T
* *
12327795 AAAAATATATAAACTTAT
1 AAAAATATAAAAAATTAT
* *
12327813 AAAAATTCTAAAATATTAT
1 AAAAA-TATAAAAAATTAT
*
12327832 AAAATTATAAAA
1 AAAAATATAAAA
12327844 TACATATAAA
Statistics
Matches: 67, Mismatches: 12, Indels: 13
0.73 0.13 0.14
Matches are distributed among these distances:
16 2 0.03
17 12 0.18
18 17 0.25
19 36 0.54
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAAATATAAAAAATTAT
Found at i:12327785 original size:27 final size:27
Alignment explanation
Indices: 12327740--12327843 Score: 115
Period size: 27 Copynumber: 3.8 Consensus size: 27
12327730 TTTTCTAATA
12327740 AAAAATCATAAAAAATTATAAAAATATT
1 AAAAAT-ATAAAAAATTATAAAAATATT
*
12327768 AACAAA-ATAAAAATTTATAAAAATATT
1 AA-AAATATAAAAAATTATAAAAATATT
* *
12327795 AAAAATATATAAACTTATAAAAAT-TCT
1 AAAAATATAAAAAATTATAAAAATAT-T
*
12327822 -AAAATATTATAAAATTATAAAA
1 AAAAATA-TAAAAAATTATAAAA
12327844 TACATATAAA
Statistics
Matches: 68, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
26 10 0.15
27 53 0.78
28 2 0.03
29 3 0.04
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (27 bp):
AAAAATATAAAAAATTATAAAAATATT
Found at i:12327789 original size:10 final size:9
Alignment explanation
Indices: 12327740--12327843 Score: 76
Period size: 9 Copynumber: 11.4 Consensus size: 9
12327730 TTTTCTAATA
*
12327740 AAAAATCAT
1 AAAAATTAT
12327749 AAAAAATTAT
1 -AAAAATTAT
12327759 AAAAA-TATT
1 AAAAATTA-T
12327768 AACAAA--AT
1 AA-AAATTAT
12327776 AAAAATTTAT
1 AAAAA-TTAT
12327786 AAAAA-TATT
1 AAAAATTA-T
12327795 AAAAA-TAT
1 AAAAATTAT
*
12327803 ATAAACTTAT
1 A-AAAATTAT
*
12327813 AAAAATTCT
1 AAAAATTAT
12327822 AAAATATTAT
1 AAAA-ATTAT
12327832 -AAAATTAT
1 AAAAATTAT
12327840 AAAA
1 AAAA
12327844 TACATATAAA
Statistics
Matches: 79, Mismatches: 5, Indels: 21
0.75 0.05 0.20
Matches are distributed among these distances:
7 3 0.04
8 14 0.18
9 36 0.46
10 26 0.33
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:12327854 original size:18 final size:18
Alignment explanation
Indices: 12327735--12327857 Score: 69
Period size: 18 Copynumber: 6.8 Consensus size: 18
12327725 TTTATTTTTC
* *
12327735 TAATAAAAAATCATAAAA
1 TAATATAAAATTATAAAA
*
12327753 -AATTATAAAAATATTAACAA
1 TAA-TATAAAATTA-TAA-AA
12327773 -AATA-AAAATTTATAAAAA
1 TAATATAAAA-TTAT-AAAA
* *
12327791 TATTA-AAAATATATAAAC
1 TAATATAAAAT-TATAAAA
* *
12327809 TTATA-AAAATTCTAAAA
1 TAATATAAAATTATAAAA
*
12327826 TATTATAAAATTATAAAA
1 TAATATAAAATTATAAAA
12327844 TACATAT-AAATTAT
1 TA-ATATAAAATTAT
12327858 CATTTATTGT
Statistics
Matches: 82, Mismatches: 14, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
17 10 0.12
18 46 0.56
19 22 0.27
20 4 0.05
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (18 bp):
TAATATAAAATTATAAAA
Found at i:12328935 original size:16 final size:16
Alignment explanation
Indices: 12328886--12328940 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
12328876 TTTTTAATTA
*
12328886 TTTGAAATTGAATAAT
1 TTTGAATTTGAATAAT
* * * *
12328902 TTAGGATTTGATTTAT
1 TTTGAATTTGAATAAT
12328918 TTTGAATTTGAATAAT
1 TTTGAATTTGAATAAT
*
12328934 TTCGAAT
1 TTTGAAT
12328941 CCCGGTTACT
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.49
Consensus pattern (16 bp):
TTTGAATTTGAATAAT
Found at i:12329466 original size:24 final size:24
Alignment explanation
Indices: 12329439--12329485 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
12329429 AAGCCTAATT
*
12329439 CTAATCAATGCAAAATATATTATG
1 CTAATAAATGCAAAATATATTATG
*
12329463 CTAATAAATGCTAAATATATTAT
1 CTAATAAATGCAAAATATATTAT
12329486 AATACTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.36
Consensus pattern (24 bp):
CTAATAAATGCAAAATATATTATG
Found at i:12329494 original size:24 final size:24
Alignment explanation
Indices: 12329440--12329495 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
12329430 AGCCTAATTC
* **
12329440 TAATCAATGCAAAATATATTATGC
1 TAATAAATGCAAAATATATTATAA
*
12329464 TAATAAATGCTAAATATATTATAA
1 TAATAAATGCAAAATATATTATAA
*
12329488 TACTAAAT
1 TAATAAAT
12329496 CTTCTAGAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.50, C:0.09, G:0.05, T:0.36
Consensus pattern (24 bp):
TAATAAATGCAAAATATATTATAA
Found at i:12331542 original size:26 final size:26
Alignment explanation
Indices: 12331513--12331598 Score: 70
Period size: 26 Copynumber: 3.3 Consensus size: 26
12331503 ATTCAAATCC
12331513 AACTTAATTTAATCATAAAAATCAAG
1 AACTTAATTTAATCATAAAAATCAAG
* * * * *
12331539 AACTCAAATCTAAAATTATTCAAATTC---
1 AACT-TAAT-T-TAATCA-TAAAAATCAAG
12331566 AACTTAATTTAATCATAAAAATCAAG
1 AACTTAATTTAATCATAAAAATCAAG
12331592 AACTTAA
1 AACTTAA
12331599 ATCTAAATTT
Statistics
Matches: 43, Mismatches: 10, Indels: 14
0.64 0.15 0.21
Matches are distributed among these distances:
23 6 0.14
24 4 0.09
25 1 0.02
26 14 0.33
27 7 0.16
28 1 0.02
29 4 0.09
30 6 0.14
ACGTcount: A:0.52, C:0.14, G:0.02, T:0.31
Consensus pattern (26 bp):
AACTTAATTTAATCATAAAAATCAAG
Found at i:12331583 original size:53 final size:53
Alignment explanation
Indices: 12331503--12331620 Score: 200
Period size: 53 Copynumber: 2.2 Consensus size: 53
12331493 AATTAAACTC
*
12331503 ATTCAAATCCAACTTAATTTAATCATAAAAATCAAGAACTCAAATCTAAAATT
1 ATTCAAATTCAACTTAATTTAATCATAAAAATCAAGAACTCAAATCTAAAATT
* *
12331556 ATTCAAATTCAACTTAATTTAATCATAAAAATCAAGAACTTAAATCTAAATTT
1 ATTCAAATTCAACTTAATTTAATCATAAAAATCAAGAACTCAAATCTAAAATT
*
12331609 ATTCAAACTCAA
1 ATTCAAATTCAA
12331621 AACAATTTAA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 61 1.00
ACGTcount: A:0.50, C:0.16, G:0.02, T:0.32
Consensus pattern (53 bp):
ATTCAAATTCAACTTAATTTAATCATAAAAATCAAGAACTCAAATCTAAAATT
Found at i:12331628 original size:53 final size:53
Alignment explanation
Indices: 12331518--12331635 Score: 173
Period size: 53 Copynumber: 2.2 Consensus size: 53
12331508 AATCCAACTT
* ***
12331518 AATTTAATCATAAAAATCAAGAACTCAAATCTAAAATTATTCAAATTCAACTT
1 AATTTAATCATAAAAATCAAGAACTCAAATCTAAAATTATTCAAACTCAAAAC
* *
12331571 AATTTAATCATAAAAATCAAGAACTTAAATCTAAATTTATTCAAACTCAAAAC
1 AATTTAATCATAAAAATCAAGAACTCAAATCTAAAATTATTCAAACTCAAAAC
12331624 AATTTAAATCAT
1 AATTT-AATCAT
12331636 CCTCACTTTA
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
53 52 0.90
54 6 0.10
ACGTcount: A:0.52, C:0.14, G:0.02, T:0.32
Consensus pattern (53 bp):
AATTTAATCATAAAAATCAAGAACTCAAATCTAAAATTATTCAAACTCAAAAC
Found at i:12338022 original size:24 final size:24
Alignment explanation
Indices: 12337981--12338043 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
12337971 GAGTAATAAG
* * * *
12337981 AGTTTGACTCAAACAAATAAATAA
1 AGTTTAACTGAAAGAAATAAACAA
* *
12338005 AGTTTAATTGAAAGAAATAAACAG
1 AGTTTAACTGAAAGAAATAAACAA
12338029 AGTTTAACTGAAAGA
1 AGTTTAACTGAAAGA
12338044 TTATTTTTCA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.52, C:0.08, G:0.14, T:0.25
Consensus pattern (24 bp):
AGTTTAACTGAAAGAAATAAACAA
Found at i:12339692 original size:17 final size:17
Alignment explanation
Indices: 12339649--12339707 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 17
12339639 TAAAAAATAC
12339649 TAAATATTATTAAAATATT
1 TAAATATTA-TAAAAT-TT
*
12339668 GTATATATTATAAAATTT
1 -TAAATATTATAAAATTT
*
12339686 TAAATATGTAAAAAATTAT
1 TAAATAT-TATAAAATT-T
12339705 TAA
1 TAA
12339708 TAATTTATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
17 6 0.18
18 10 0.29
19 10 0.29
20 8 0.24
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
TAAATATTATAAAATTT
Found at i:12340063 original size:9 final size:9
Alignment explanation
Indices: 12340051--12340109 Score: 57
Period size: 9 Copynumber: 6.3 Consensus size: 9
12340041 ACAATTATTC
12340051 TTTTTATAA
1 TTTTTATAA
12340060 -TTTTATAA
1 TTTTTATAA
*
12340068 TATTTATAAA
1 TTTTTAT-AA
12340078 TATCTTTATAA
1 T-T-TTTATAA
**
12340089 TTTTTATTT
1 TTTTTATAA
12340098 TTTTTATAA
1 TTTTTATAA
12340107 TTT
1 TTT
12340110 GACACTCATC
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
8 8 0.20
9 20 0.50
10 4 0.10
11 3 0.08
12 5 0.12
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (9 bp):
TTTTTATAA
Found at i:12340450 original size:81 final size:81
Alignment explanation
Indices: 12340358--12340513 Score: 260
Period size: 81 Copynumber: 1.9 Consensus size: 81
12340348 ACTTTACCCT
* * **
12340358 CTAAAATTGATAAAATTTTGATTTAATCCTTTAAAAATTACT-TTTTTACTATCATAAAAATTTT
1 CTAAAAATGATAAAATTTTGATCTAATCCTTTAAAAATTA-TATTTTTACTATCATAAAAATTAC
12340422 AATTTAACTTCGGCCCC
65 AATTTAACTTCGGCCCC
12340439 CTAAAAATGATAAAATTTTGATCTAATCCTTTAAAAATTATATTTTTACTATCATAAAAATTACA
1 CTAAAAATGATAAAATTTTGATCTAATCCTTTAAAAATTATATTTTTACTATCATAAAAATTACA
12340504 ATTTAACTTC
66 ATTTAACTTC
12340514 AACCTCTTAA
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
80 1 0.01
81 69 0.99
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.42
Consensus pattern (81 bp):
CTAAAAATGATAAAATTTTGATCTAATCCTTTAAAAATTATATTTTTACTATCATAAAAATTACA
ATTTAACTTCGGCCCC
Found at i:12340864 original size:45 final size:45
Alignment explanation
Indices: 12340813--12340905 Score: 123
Period size: 45 Copynumber: 2.1 Consensus size: 45
12340803 ATCAATGTTT
* *
12340813 GCAGCATCAATGCTCGCAACATTCATGTTCGCACAAGTCATGCTC
1 GCAGCATCAATGCTCACAACATTCATGTTCACACAAGTCATGCTC
* * * * *
12340858 GCAGCATTAGTGCTCACCATATTCATGTTCACACTAGTCATGCTC
1 GCAGCATCAATGCTCACAACATTCATGTTCACACAAGTCATGCTC
12340903 GCA
1 GCA
12340906 TCATATAGCT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27
Consensus pattern (45 bp):
GCAGCATCAATGCTCACAACATTCATGTTCACACAAGTCATGCTC
Found at i:12341336 original size:80 final size:80
Alignment explanation
Indices: 12341202--12341373 Score: 281
Period size: 80 Copynumber: 2.1 Consensus size: 80
12341192 GAAGCCAGAA
* * ** * *
12341202 AATTTTTAGGGGGCGAAGTTAAATTGTAATTTTTATTATAGTAAAAATGTAATTTTTAAAGGATT
1 AATTTTTAGGGGACAAAGTTAAATTGTAATTTTTAGGACAGTAAAAATGCAATTTTTAAAGGATT
12341267 AAATCAAAATTTTAT
66 AAATCAAAATTTTAT
*
12341282 CATTTTTAGGGGACAAAGTTAAATTGTAATTTTTAGGACAGTAAAAATGCAATTTTTAAAGGATT
1 AATTTTTAGGGGACAAAGTTAAATTGTAATTTTTAGGACAGTAAAAATGCAATTTTTAAAGGATT
12341347 AAATCAAAATTTTAT
66 AAATCAAAATTTTAT
12341362 AATTTTTAGGGG
1 AATTTTTAGGGG
12341374 GTCAAGTGCA
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
80 84 1.00
ACGTcount: A:0.40, C:0.04, G:0.16, T:0.40
Consensus pattern (80 bp):
AATTTTTAGGGGACAAAGTTAAATTGTAATTTTTAGGACAGTAAAAATGCAATTTTTAAAGGATT
AAATCAAAATTTTAT
Found at i:12359165 original size:38 final size:38
Alignment explanation
Indices: 12359107--12359186 Score: 119
Period size: 38 Copynumber: 2.1 Consensus size: 38
12359097 TGAAGTTGTT
12359107 TTAATATATTTTAAATTTTTTTGTGA-ATTTTATAATTC
1 TTAATATATTTTAAATTTTTTT-TGATATTTTATAATTC
*
12359145 TTAATAT-TTTTAAATATTTTTTTGATATTTTATAATTT
1 TTAATATATTTTAAAT-TTTTTTTGATATTTTATAATTC
12359183 TTAA
1 TTAA
12359187 AACTAACAAC
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
37 11 0.28
38 28 0.72
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.62
Consensus pattern (38 bp):
TTAATATATTTTAAATTTTTTTTGATATTTTATAATTC
Found at i:12361889 original size:6 final size:7
Alignment explanation
Indices: 12361870--12361896 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
12361860 TTCGTCCCCC
12361870 ACGGGGG
1 ACGGGGG
12361877 ACGGGGG
1 ACGGGGG
12361884 ACGGGGG
1 ACGGGGG
12361891 ACGGGG
1 ACGGGG
12361897 TATAACGACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.70, T:0.00
Consensus pattern (7 bp):
ACGGGGG
Found at i:12371014 original size:21 final size:21
Alignment explanation
Indices: 12370973--12371016 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
12370963 TTCTTGAAAC
*
12370973 GGTGAGTAGCCTCGAGCAGTA
1 GGTGAGTAGCCTCAAGCAGTA
*
12370994 GGTGAGTTCGCCTCAAG-AGTA
1 GGTGAG-TAGCCTCAAGCAGTA
12371015 GG
1 GG
12371017 CGATGAAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.23, C:0.18, G:0.39, T:0.20
Consensus pattern (21 bp):
GGTGAGTAGCCTCAAGCAGTA
Found at i:12376433 original size:30 final size:30
Alignment explanation
Indices: 12376379--12376455 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 30
12376369 AGAACTTAAA
* * * *
12376379 GATACTGCTCCCACTGTCCCTCCACCTGAG
1 GATACTCCTCCTACTATCTCTCCACCTGAG
* *
12376409 GATGCTCCTCCTACTATCTCTCCACCTTAG
1 GATACTCCTCCTACTATCTCTCCACCTGAG
*
12376439 GATACTCCTCTTACTAT
1 GATACTCCTCCTACTAT
12376456 TCCTCTAGTC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.18, C:0.39, G:0.12, T:0.31
Consensus pattern (30 bp):
GATACTCCTCCTACTATCTCTCCACCTGAG
Found at i:12380546 original size:30 final size:31
Alignment explanation
Indices: 12380495--12380596 Score: 129
Period size: 30 Copynumber: 3.4 Consensus size: 31
12380485 CAAGAACTTG
*
12380495 AGGATACTGCTCTC-ACTATCCCTCCACCTA
1 AGGATACTCCTCTCTACTATCCCTCCACCTA
* * * *
12380525 AGGACACTCCTCT-TGCTATCCCTCTACCTG
1 AGGATACTCCTCTCTACTATCCCTCCACCTA
*
12380555 AGGATACTCCT-TCTACTATCCCTCCACCAA
1 AGGATACTCCTCTCTACTATCCCTCCACCTA
12380585 AGGATACTCCTC
1 AGGATACTCCTC
12380597 CCACTGGTCC
Statistics
Matches: 59, Mismatches: 10, Indels: 5
0.80 0.14 0.07
Matches are distributed among these distances:
29 1 0.02
30 58 0.98
ACGTcount: A:0.23, C:0.39, G:0.11, T:0.27
Consensus pattern (31 bp):
AGGATACTCCTCTCTACTATCCCTCCACCTA
Found at i:12384912 original size:30 final size:30
Alignment explanation
Indices: 12384876--12384934 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
12384866 TTCAAGAACT
* *
12384876 TGAGGATACTACTTCTACTATCCCTCCACC
1 TGAGGATACTACTCCTACTATCCCCCCACC
* *
12384906 TGAGGATATTTCTCCTACTATCCCCCCAC
1 TGAGGATACTACTCCTACTATCCCCCCAC
12384935 TAGAGGACAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.22, C:0.37, G:0.10, T:0.31
Consensus pattern (30 bp):
TGAGGATACTACTCCTACTATCCCCCCACC
Found at i:12386105 original size:15 final size:16
Alignment explanation
Indices: 12386085--12386115 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
12386075 AAAATGGGGG
12386085 TTAGGTTACC-AGAGC
1 TTAGGTTACCGAGAGC
12386100 TTAGGTTACCGAGAGC
1 TTAGGTTACCGAGAGC
12386116 GCAAGTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (16 bp):
TTAGGTTACCGAGAGC
Found at i:12393258 original size:82 final size:79
Alignment explanation
Indices: 12393157--12393336 Score: 279
Period size: 80 Copynumber: 2.2 Consensus size: 79
12393147 GTAAAATTGC
* * *
12393157 ACTTGGCCCCCTAAAAATGATAAAATTTTTATTTAATCCTTTAAAAAATTGCATTTTTACTATCA
1 ACTTCGCCCCCTAAAAATGATAAAATTTTGATTTAATCCTTT--AAAACTGCATTTTTACTATCA
12393222 TAAAAATTACAATTTA
64 TAAAAATTACAATTTA
*
12393238 ACTTCGCCCTCCTAAGAATGATAAAATTTTGATTTAATCCTTTAAAACTGCATTTTTACTATCAT
1 ACTTCGCCC-CCTAAAAATGATAAAATTTTGATTTAATCCTTTAAAACTGCATTTTTACTATCAT
12393303 AAAAATTACAATTTA
65 AAAAATTACAATTTA
12393318 ACTTCGACCCCCCTAAAAA
1 ACTTCG--CCCCCTAAAAA
12393337 AATTTTTGAC
Statistics
Matches: 91, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
80 42 0.46
81 15 0.16
82 34 0.37
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.37
Consensus pattern (79 bp):
ACTTCGCCCCCTAAAAATGATAAAATTTTGATTTAATCCTTTAAAACTGCATTTTTACTATCATA
AAAATTACAATTTA
Found at i:12394449 original size:26 final size:24
Alignment explanation
Indices: 12394420--12394477 Score: 57
Period size: 23 Copynumber: 2.4 Consensus size: 24
12394410 TTTACATATT
*
12394420 TATTTTTTAAAAATTGTTAAATAATA
1 TATTTATTAAAAATT-TTAAA-AATA
* *
12394446 TA-TTCTT-ATAATTTTAAAAATA
1 TATTTATTAAAAATTTTAAAAATA
12394468 TATTTATTAA
1 TATTTATTAA
12394478 TTAAAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
22 6 0.22
23 9 0.33
24 6 0.22
25 4 0.15
26 2 0.07
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (24 bp):
TATTTATTAAAAATTTTAAAAATA
Found at i:12398727 original size:28 final size:28
Alignment explanation
Indices: 12398686--12398963 Score: 129
Period size: 28 Copynumber: 9.6 Consensus size: 28
12398676 TTCGAGGTCG
*
12398686 AAAATGTGACTTTTAGAAATTTGAGGGT-
1 AAAATGT-AATTTTAGAAATTTGAGGGTA
* * *
12398714 AAAATGGTAATTTTTG-AATGTTCAGGG-C
1 AAAAT-GTAATTTTAGAAAT-TTGAGGGTA
* *
12398742 AAAATGGTAATTTTTAGAAAAGTTCGA-GGTC
1 AAAAT-GTAA-TTTTAG-AAA-TTTGAGGGTA
* *
12398773 AAAATGTAATTTTTGAAAGTTTGGGGGTA
1 AAAATGTAATTTTAGAAA-TTTGAGGGTA
* * * **
12398802 AAAATGTGATTTTGGAAGTTTG-GGGGC
1 AAAATGTAATTTTAGAAATTTGAGGGTA
* * * *
12398829 AAAATGTGATTTTTGGAAGTTCGAGGGGTA
1 AAAATGT-AATTTTAGAAATTTGA-GGGTA
* * *
12398859 AAAATGTGATTTTTGGAAGTTTGAGGGT-
1 AAAATGT-AATTTTAGAAATTTGAGGGTA
* * *
12398887 AAAGTGTAATTTTGGAGAAATTTAAGAGTA
1 AAAATGTAATTTT--AGAAATTTGAGGGTA
* *
12398917 AAAATGTAATTTTTGAGAAGTTCGA-GGTA
1 AAAATGTAA-TTTT-AGAAATTTGAGGGTA
* *
12398946 AAAATATAATTTTGGAAA
1 AAAATGTAATTTTAGAAA
12398964 GTTCAGAGGT
Statistics
Matches: 199, Mismatches: 35, Indels: 33
0.75 0.13 0.12
Matches are distributed among these distances:
27 21 0.11
28 60 0.30
29 55 0.28
30 48 0.24
31 14 0.07
32 1 0.01
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.35
Consensus pattern (28 bp):
AAAATGTAATTTTAGAAATTTGAGGGTA
Found at i:12398871 original size:86 final size:86
Alignment explanation
Indices: 12398666--12398966 Score: 251
Period size: 87 Copynumber: 3.5 Consensus size: 86
12398656 AAAATCGAAC
* * * *
12398666 TTTTGGAAAA-TTCGAGGTCGAAAATGTGACTTTTAGAAA-TTTGAGGGTAAAATGGTAATTTTT
1 TTTTAGAAAAGTTCGAGGT-AAAAATGTGA-TTTTTGAAAGTTTGAGGGTAAAAT-GTAATTTTG
12398729 GAATGTTCAGGGCAAAATGGTAAT
63 GAATGTTCAGGGCAAAATGGTAAT
* * * *
12398753 TTTTAGAAAAGTTCGAGGTCAAAATGTAATTTTTGAAAGTTTGGGGGTAAAAATGTGATTTTGGA
1 TTTTAGAAAAGTTCGAGGTAAAAATGTGATTTTTGAAAGTTTGAGGGT-AAAATGTAATTTTGGA
** *
12398818 A-GTTTGGGGGCAAAAT-GTGAT
65 ATG-TTCAGGGCAAAATGGTAAT
* * *
12398839 TTTT-G-GAAGTTCGAGGGGTAAAAATGTGATTTTTGGAAGTTTGAGGGTAAAGTGTAATTTTGG
1 TTTTAGAAAAGTTCGA--GGTAAAAATGTGATTTTTGAAAGTTTGAGGGTAAAATGTAATTTT-G
* **
12398902 AGAAAT-TTAAGAGTAAAAAT-GTAAT
63 -G-AATGTTCAG-GGCAAAATGGTAAT
* * * *
12398927 TTTT-GAGAAGTTCGAGGTAAAAATATAATTTTGGAAAGTT
1 TTTTAGAAAAGTTCGAGGTAAAAATGTGATTTTTGAAAGTT
12398967 CAGAGGTCAA
Statistics
Matches: 176, Mismatches: 26, Indels: 24
0.78 0.12 0.11
Matches are distributed among these distances:
84 8 0.05
85 12 0.07
86 46 0.26
87 71 0.40
88 30 0.17
89 9 0.05
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (86 bp):
TTTTAGAAAAGTTCGAGGTAAAAATGTGATTTTTGAAAGTTTGAGGGTAAAATGTAATTTTGGAA
TGTTCAGGGCAAAATGGTAAT
Found at i:12398956 original size:29 final size:29
Alignment explanation
Indices: 12398714--12398990 Score: 185
Period size: 29 Copynumber: 9.6 Consensus size: 29
12398704 ATTTGAGGGT
* **
12398714 AAAATGGTAATTTTTGA-ATGTTC-AGGGC
1 AAAAT-GTAATTTTTGAGAAGTTCGAGGTA
* *
12398742 AAAATGGTAATTTTTAGAAAAGTTCGAGGTC
1 AAAAT-GTAATTTTT-GAGAAGTTCGAGGTA
* *
12398773 AAAATGTAATTTTTGA-AAGTTTGGGGGTA
1 AAAATGTAATTTTTGAGAAG-TTCGAGGTA
* * * **
12398802 AAAATGTGA-TTTTG-GAAGTTTGGGGGC
1 AAAATGTAATTTTTGAGAAGTTCGAGGTA
*
12398829 AAAATGTGATTTTTG-GAAGTTCGAGGGGTA
1 AAAATGTAATTTTTGAGAAGTTCGA--GGTA
* *
12398859 AAAATGTGATTTTTG-GAAGTTTGAGGGT-
1 AAAATGTAATTTTTGAGAAGTTCGA-GGTA
* * * **
12398887 AAAGTGTAATTTTGGAGAAATTTAAGAGTA
1 AAAATGTAATTTTTGAGAAGTTCGAG-GTA
12398917 AAAATGTAATTTTTGAGAAGTTCGAGGTA
1 AAAATGTAATTTTTGAGAAGTTCGAGGTA
* * *
12398946 AAAATATAATTTTGGA-AAGTTCAGAGGTC
1 AAAATGTAATTTTTGAGAAGTTC-GAGGTA
* *
12398975 AAAACGTGATTTTTGA
1 AAAATGTAATTTTTGA
12398991 AAAATTTAGG
Statistics
Matches: 206, Mismatches: 31, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
27 15 0.07
28 57 0.28
29 65 0.32
30 60 0.29
31 9 0.04
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.35
Consensus pattern (29 bp):
AAAATGTAATTTTTGAGAAGTTCGAGGTA
Found at i:12398965 original size:28 final size:28
Alignment explanation
Indices: 12398666--12398992 Score: 164
Period size: 29 Copynumber: 11.3 Consensus size: 28
12398656 AAAATCGAAC
* * *
12398666 TTTTGGAAAATTCGAGGTCGAAAATGTGAC
1 TTTTGGAAAGTTCGAGGT-AAAAATGT-AA
* *
12398696 TTTTAGAAA-TTTGAGGGT-AAAATGGTAA
1 TTTTGGAAAGTTCGA-GGTAAAAAT-GTAA
* * **
12398724 TTTTTGAATGTTC-AGGGCAAAATGGTAA
1 TTTTGGAAAGTTCGAGGTAAAAAT-GTAA
* *
12398752 TTTTTAGAAAAGTTCGAGGTCAAAATGTAA
1 -TTTT-GGAAAGTTCGAGGTAAAAATGTAA
* * * *
12398782 TTTTTGAAAGTTTGGGGGTAAAAATGTGA
1 TTTTGGAAAG-TTCGAGGTAAAAATGTAA
* * ** *
12398811 TTTTGG-AAGTTTGGGGGCAAAATGTGAT
1 TTTTGGAAAGTTCGAGGTAAAAATGT-AA
*
12398839 TTTTGG-AAGTTCGAGGGGTAAAAATGTGAT
1 TTTTGGAAAGTTCGA--GGTAAAAATGT-AA
* *
12398869 TTTTGG-AAGTTTGAGGGT-AAAGTGTAA
1 TTTTGGAAAGTTCGA-GGTAAAAATGTAA
* **
12398896 TTTTGGAGAAATTTAAGAGTAAAAATGTAA
1 TTTTGGA-AAGTTCGAG-GTAAAAATGTAA
* *
12398926 TTTTTGAGAAGTTCGAGGTAAAAATATAA
1 TTTTGGA-AAGTTCGAGGTAAAAATGTAA
* * *
12398955 TTTTGGAAAGTTCAGAGGTCAAAACGTGA
1 TTTTGGAAAGTTC-GAGGTAAAAATGTAA
*
12398984 TTTTTGAAA
1 TTTTGGAAA
12398993 AATTTAGGGA
Statistics
Matches: 237, Mismatches: 44, Indels: 33
0.75 0.14 0.11
Matches are distributed among these distances:
27 22 0.09
28 56 0.24
29 83 0.35
30 67 0.28
31 9 0.04
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.35
Consensus pattern (28 bp):
TTTTGGAAAGTTCGAGGTAAAAATGTAA
Found at i:12398987 original size:58 final size:57
Alignment explanation
Indices: 12398666--12398990 Score: 236
Period size: 58 Copynumber: 5.6 Consensus size: 57
12398656 AAAATCGAAC
* * * *
12398666 TTTTGGAAAATTC-GAGGTCGAAAATGTGACTTTT-AGAAATTTGAGGGTAAAATGGTAA
1 TTTTGGAAAGTTCAGAGGT-AAAAATGTGATTTTTGAGAAGTTTGA-GGTAAAAT-GTAA
* * * * * *
12398724 TTTTTGAATGTTCAG-GG-CAAAATGGTAATTTTTAGAAAAGTTCGAGGTCAAAATGTAA
1 TTTTGGAAAGTTCAGAGGTAAAAAT-GTGATTTTT-GAGAAGTTTGAGGT-AAAATGTAA
* ** * * * *
12398782 TTTTTGAAAGTTTGGGGGTAAAAATGTGA-TTTTG-GAAGTTTGGGGGCAAAATGTGAT
1 TTTTGGAAAGTTCAGAGGTAAAAATGTGATTTTTGAGAAGTTT-GAGGTAAAATGT-AA
* *
12398839 TTTTGG-AAGTTCGAGGGGTAAAAATGTGATTTTTG-GAAGTTTGAGGGTAAAGTGTAA
1 TTTTGGAAAGTTC-AGAGGTAAAAATGTGATTTTTGAGAAGTTTGA-GGTAAAATGTAA
* * * * *
12398896 TTTTGGAGAAATTTA-AGAGTAAAAATGTAATTTTTGAGAAGTTCGAGGTAAAAATATAA
1 TTTTGGA-AAGTTCAGAG-GTAAAAATGTGATTTTTGAGAAGTTTGAGGT-AAAATGTAA
* *
12398955 TTTTGGAAAGTTCAGAGGTCAAAACGTGATTTTTGA
1 TTTTGGAAAGTTCAGAGGTAAAAATGTGATTTTTGA
12398991 AAAATTTAGG
Statistics
Matches: 211, Mismatches: 38, Indels: 36
0.74 0.13 0.13
Matches are distributed among these distances:
56 22 0.10
57 41 0.19
58 97 0.46
59 46 0.22
60 5 0.02
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.35
Consensus pattern (57 bp):
TTTTGGAAAGTTCAGAGGTAAAAATGTGATTTTTGAGAAGTTTGAGGTAAAATGTAA
Done.