Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr12
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: 39383930
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.32
Warning! 780790 characters in sequence are not A, C, G, or T
File 8 of 126
Found at i:2120684 original size:144 final size:145
Alignment explanation
Indices: 2120531--2120820 Score: 564
Period size: 145 Copynumber: 2.0 Consensus size: 145
2120521 ACTTGTATCC
2120531 ATATTGTATTTGTGCTAGTGAAATTTTTAAAAATTTATAAAAAAATTTAAAATA-ATTATTTTTT
1 ATATTGTATTTGTGCTAGTGAAATTTTTAAAAATTTATAAAAAAATTTAAAATATATTATTTTTT
2120595 ATATTTTTATAAATATATTTAAATAAAAATACTTTTTTACTTGGGGGTTGTTTAATAAATTGAAA
66 ATATTTTTATAAATATATTTAAATAAAAATACTTTTTTACTTGGGGGTTGTTTAATAAATTGAAA
*
2120660 ATTTAACTCCTGAAG
131 ATTTAACTCCTAAAG
2120675 ATATTGTATTTGTGCTAGTGAAATTTTTAAAAATTTATAAAAAAATTTAAAATATATTATTTTTT
1 ATATTGTATTTGTGCTAGTGAAATTTTTAAAAATTTATAAAAAAATTTAAAATATATTATTTTTT
2120740 ATATTTTTATAAATATATTTAAATAAAAATACTTTTTTACTTGGGGGTTGTTTAATAAATTGAAA
66 ATATTTTTATAAATATATTTAAATAAAAATACTTTTTTACTTGGGGGTTGTTTAATAAATTGAAA
2120805 ATTTAACTCCTAAAG
131 ATTTAACTCCTAAAG
2120820 A
1 A
2120821 ATTAAGTATA
Statistics
Matches: 144, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
144 54 0.38
145 90 0.62
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (145 bp):
ATATTGTATTTGTGCTAGTGAAATTTTTAAAAATTTATAAAAAAATTTAAAATATATTATTTTTT
ATATTTTTATAAATATATTTAAATAAAAATACTTTTTTACTTGGGGGTTGTTTAATAAATTGAAA
ATTTAACTCCTAAAG
Found at i:2132746 original size:31 final size:31
Alignment explanation
Indices: 2132711--2132859 Score: 217
Period size: 31 Copynumber: 4.8 Consensus size: 31
2132701 CTTGTCACTT
*
2132711 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
2132742 GTAGCCGAAGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* ** * *
2132773 GTAGCTGAAGCTATTAATTTTCATTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
2132804 GTAGCCGAAGCTACCACTTTTCAGTAATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
2132835 GTAGCCGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
2132860 TGTCATTTGC
Statistics
Matches: 104, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 104 1.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.29
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:2132946 original size:50 final size:50
Alignment explanation
Indices: 2132835--2133010 Score: 262
Period size: 50 Copynumber: 3.5 Consensus size: 50
2132825 CAGTAATCAG
* * * *
2132835 GTAGCCGAAGCTACCACTTTTCACTTGTCATTTGCCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTT-TCACTTGTCCTTGATCAGATAAGT
2132886 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
* * *
2132936 GTAGCTGAAGCTATTACTTATCACTTTCACTTATCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
* *
2132986 GCAGCCAAAGCTATCACTTATCACT
1 GTAGCCGAAGCTATCACTTATCACT
2133011 GGTTGCCATG
Statistics
Matches: 114, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 90 0.79
51 24 0.21
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
Found at i:2138923 original size:16 final size:16
Alignment explanation
Indices: 2138902--2138956 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
2138892 GTTTGGTTCA
*
2138902 CTGTAATGGAATAGGG
1 CTGTAATGGAATAGAG
**
2138918 CTGTAATTAAATAGAG
1 CTGTAATGGAATAGAG
2138934 CTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
2138950 CTGTAAT
1 CTGTAAT
2138957 CAGTAATTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.36, C:0.07, G:0.27, T:0.29
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:2139031 original size:44 final size:46
Alignment explanation
Indices: 2138938--2139031 Score: 131
Period size: 44 Copynumber: 2.1 Consensus size: 46
2138928 ATAGAGCTGT
*
2138938 AATGGAATAGAGCTGTAATCAGTAATTCAGCTGTTTGGTTGAATGG
1 AATGGAATAGAACTGTAATCAGTAATTCAGCTGTTTGGTTGAATGG
* *
2138984 AATGGAATAGAACTGTAAT-AGT-ATTCTTG-TGTTTGGTTGGATGG
1 AATGGAATAGAACTGTAATCAGTAATTC-AGCTGTTTGGTTGAATGG
2139028 AATG
1 AATG
2139032 ATATTGTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
44 22 0.50
45 4 0.09
46 18 0.41
ACGTcount: A:0.30, C:0.06, G:0.29, T:0.35
Consensus pattern (46 bp):
AATGGAATAGAACTGTAATCAGTAATTCAGCTGTTTGGTTGAATGG
Found at i:2139198 original size:59 final size:61
Alignment explanation
Indices: 2139134--2139302 Score: 202
Period size: 63 Copynumber: 2.8 Consensus size: 61
2139124 TTATAATAGG
*
2139134 ATTATTATTAAATATAATTTAAT-AATA-AATAATAAATAATTTAAT-CATACTTTAATATA
1 ATTATTATTAAATATAATTTAATAAAGATAATAATAAATAATTTAATACATAC-TTAATATA
* *
2139193 ATTATTATTAAATATAATTTAATAAAGATAATAATATATAATTTAATAACATTCTTAATATA
1 ATTATTATTAAATATAATTTAATAAAGATAATAATAAATAATTTAAT-ACATACTTAATATA
* * * *
2139255 ATTATTATTAAAATATGAA-TGAATAAAAATCATAATATATAATATTAA
1 ATTATTATT-AAATAT-AATTTAATAAAGATAATAATAAATAAT-TTAA
2139303 AAAATAGTAT
Statistics
Matches: 97, Mismatches: 6, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
59 23 0.24
60 3 0.03
61 17 0.18
62 17 0.18
63 31 0.32
64 6 0.06
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (61 bp):
ATTATTATTAAATATAATTTAATAAAGATAATAATAAATAATTTAATACATACTTAATATA
Found at i:2145240 original size:30 final size:30
Alignment explanation
Indices: 2145200--2145285 Score: 118
Period size: 30 Copynumber: 2.9 Consensus size: 30
2145190 TAGGCACTTC
2145200 CACACGGGTAATCCACATGCCCGTGTTAGA
1 CACACGGGTAATCCACATGCCCGTGTTAGA
* * *
2145230 CACATGGGTAATCTACACGCCCGTGTTAGA
1 CACACGGGTAATCCACATGCCCGTGTTAGA
* **
2145260 CATACGGGTAGGCCACATGCCCGTGT
1 CACACGGGTAATCCACATGCCCGTGT
2145286 GTCATGGCCG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.24, C:0.29, G:0.26, T:0.21
Consensus pattern (30 bp):
CACACGGGTAATCCACATGCCCGTGTTAGA
Found at i:2149295 original size:30 final size:30
Alignment explanation
Indices: 2149261--2149321 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
2149251 TCCTTAATTC
2149261 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
2149291 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
2149321 A
1 A
2149322 GGCTCAGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:2156122 original size:36 final size:36
Alignment explanation
Indices: 2156082--2156152 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
2156072 GTACTGCTAT
2156082 GGTTGCACGAGTCACACAAGACGACTGTGGACCTAA
1 GGTTGCACGAGTCACACAAGACGACTGTGGACCTAA
* *
2156118 GGTTGCACGGGTCGCACAAGACGACTGTGGACCTA
1 GGTTGCACGAGTCACACAAGACGACTGTGGACCTA
2156153 CTGATGGCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.27, C:0.25, G:0.31, T:0.17
Consensus pattern (36 bp):
GGTTGCACGAGTCACACAAGACGACTGTGGACCTAA
Found at i:2156246 original size:20 final size:20
Alignment explanation
Indices: 2156218--2156336 Score: 141
Period size: 20 Copynumber: 6.0 Consensus size: 20
2156208 ATTGCTACGA
*
2156218 TATTTATGGCTTTGTGCCAC
1 TATTGATGGCTTTGTGCCAC
*
2156238 TATTCATGGCTTTGTGCCAC
1 TATTGATGGCTTTGTGCCAC
2156258 TATTGATGGCTTTGTGCCAC
1 TATTGATGGCTTTGTGCCAC
* *
2156278 TATTGATGGCTTTGTGTCGC
1 TATTGATGGCTTTGTGCCAC
* * * * *
2156298 TACTAATGGCTTCGAGCTAC
1 TATTGATGGCTTTGTGCCAC
2156318 TAGTT-ATGGCTTTGTGCCA
1 TA-TTGATGGCTTTGTGCCA
2156337 TATACTGATA
Statistics
Matches: 83, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
20 82 0.99
21 1 0.01
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.40
Consensus pattern (20 bp):
TATTGATGGCTTTGTGCCAC
Found at i:2156367 original size:25 final size:26
Alignment explanation
Indices: 2156339--2156388 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
2156329 TTGTGCCATA
2156339 TACTGATACTGGCAGC-TTGCTGTGT
1 TACTGATACTGGCAGCTTTGCTGTGT
*
2156364 TACTGTTACTGGCAGCTTTGCTGTG
1 TACTGATACTGGCAGCTTTGCTGTG
2156389 ATATTAGTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.14, C:0.20, G:0.28, T:0.38
Consensus pattern (26 bp):
TACTGATACTGGCAGCTTTGCTGTGT
Found at i:2159885 original size:20 final size:20
Alignment explanation
Indices: 2159842--2159919 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 20
2159832 ATTGCTACGA
* **
2159842 TATTTATGGCTTTGTGCTAC
1 TATTCATGGCTTTGTGCCGC
*
2159862 TATTCATGGCTTTGTGCCGG
1 TATTCATGGCTTTGTGCCGC
* * * *
2159882 TATTGATGGCTTCGAGTCGC
1 TATTCATGGCTTTGTGCCGC
*
2159902 TACTCATGGCTTTGTGCC
1 TATTCATGGCTTTGTGCC
2159920 ATATACTAAT
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.13, C:0.21, G:0.26, T:0.41
Consensus pattern (20 bp):
TATTCATGGCTTTGTGCCGC
Found at i:2163218 original size:23 final size:23
Alignment explanation
Indices: 2163145--2163239 Score: 113
Period size: 23 Copynumber: 4.1 Consensus size: 23
2163135 AAATAGTAAA
* *
2163145 CTCTATTGAGCTGAAAACGATAAG
1 CTCTATCGAGCTG-AATCGATAAG
*
2163169 CTCTATTGAGCTGAA-C-AGTAAG
1 CTCTATCGAGCTGAATCGA-TAAG
*
2163191 TTCTATCGAGCTGAATCGATAAG
1 CTCTATCGAGCTGAATCGATAAG
*
2163214 CTCTAACGAGCTGAATCGATAAG
1 CTCTATCGAGCTGAATCGATAAG
2163237 CTC
1 CTC
2163240 CAATGAGTTG
Statistics
Matches: 64, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
21 1 0.02
22 18 0.28
23 31 0.48
24 14 0.22
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (23 bp):
CTCTATCGAGCTGAATCGATAAG
Found at i:2163251 original size:23 final size:23
Alignment explanation
Indices: 2163197--2163295 Score: 87
Period size: 23 Copynumber: 4.3 Consensus size: 23
2163187 TAAGTTCTAT
*
2163197 CGAGCTGAATCGATAAGCTCTAA
1 CGAGCTGAATCGATAAGCTCCAA
2163220 CGAGCTGAATCGATAAGCTCCAA
1 CGAGCTGAATCGATAAGCTCCAA
* * * **
2163243 TGAGTTGAAAC-AGTAAGCTCTTA
1 CGAGCTGAATCGA-TAAGCTCCAA
*
2163266 CGAGCTTAATC-AGTAAGCT-CATA
1 CGAGCTGAATCGA-TAAGCTCCA-A
2163289 CGAGCTG
1 CGAGCTG
2163296 TGGTGAGTCT
Statistics
Matches: 61, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
22 1 0.02
23 60 0.98
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.23
Consensus pattern (23 bp):
CGAGCTGAATCGATAAGCTCCAA
Found at i:2163256 original size:69 final size:69
Alignment explanation
Indices: 2163152--2163295 Score: 170
Period size: 69 Copynumber: 2.1 Consensus size: 69
2163142 AAACTCTATT
* * *
2163152 GAGCTGAAAACGATAAGCTCTATTGAGCTGAACAGTAAGTTC-TATCGAGCTGAATC-GATAAGC
1 GAGCTGAAAACGATAAGCTCCAATGAGCTGAACAGTAAGCTCTTA-CGAGCTGAATCAG-TAAGC
2163215 TC-TAAC
64 TCAT-AC
* * *
2163221 GAGCTG-AATCGATAAGCTCCAATGAGTTGAAACAGTAAGCTCTTACGAGCTTAATCAGTAAGCT
1 GAGCTGAAAACGATAAGCTCCAATGAGCTG-AACAGTAAGCTCTTACGAGCTGAATCAGTAAGCT
2163285 CATAC
65 CATAC
2163290 GAGCTG
1 GAGCTG
2163296 TGGTGAGTCT
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
68 19 0.29
69 42 0.65
70 4 0.06
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.24
Consensus pattern (69 bp):
GAGCTGAAAACGATAAGCTCCAATGAGCTGAACAGTAAGCTCTTACGAGCTGAATCAGTAAGCTC
ATAC
Found at i:2164463 original size:29 final size:26
Alignment explanation
Indices: 2164401--2164458 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
2164391 ACAGTAAAAT
*
2164401 TTCTTTACGAAACTTTCACATAATAA
1 TTCTATACGAAACTTTCACATAATAA
2164427 TTCTATACGAAACTTTCACATAATAA
1 TTCTATACGAAACTTTCACATAATAA
2164453 TTCTAT
1 TTCTAT
2164459 CATACTGTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.38, C:0.19, G:0.03, T:0.40
Consensus pattern (26 bp):
TTCTATACGAAACTTTCACATAATAA
Found at i:2166336 original size:14 final size:16
Alignment explanation
Indices: 2166302--2166338 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2166292 TTTCATCATA
*
2166302 ACATTGATCCAATTAT
1 ACATTAATCCAATTAT
2166318 ACATTAATCC-ATT-T
1 ACATTAATCCAATTAT
2166332 ACATTAA
1 ACATTAA
2166339 AAATAACATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 8 0.40
15 3 0.15
16 9 0.45
ACGTcount: A:0.41, C:0.19, G:0.03, T:0.38
Consensus pattern (16 bp):
ACATTAATCCAATTAT
Found at i:2172689 original size:19 final size:17
Alignment explanation
Indices: 2172645--2172689 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
2172635 ATTATTCTAG
*
2172645 AATTTTTTTAATTTTTT
1 AATTTTTTTAATATTTT
*
2172662 AACTTTTTTATATAATTTT
1 AATTTTTTTA-AT-ATTTT
2172681 AATTTTTTT
1 AATTTTTTT
2172690 CCTGAAACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 9 0.39
18 2 0.09
19 12 0.52
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (17 bp):
AATTTTTTTAATATTTT
Found at i:2172727 original size:26 final size:28
Alignment explanation
Indices: 2172698--2172755 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 28
2172688 TTCCTGAAAC
*
2172698 TTTTAT-AATTTTTTTAAA-ACTATAAA
1 TTTTATGAATTTTTATAAATACTATAAA
* *
2172724 TTTT-TGAATTTTTATAAATATTTTAAA
1 TTTTATGAATTTTTATAAATACTATAAA
2172751 TTTTA
1 TTTTA
2172756 AAAATTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
25 1 0.04
26 15 0.58
27 10 0.38
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (28 bp):
TTTTATGAATTTTTATAAATACTATAAA
Found at i:2172739 original size:18 final size:19
Alignment explanation
Indices: 2172718--2172754 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2172708 TTTTTAAAAC
*
2172718 TATAAAT-TTTTGAATTTT
1 TATAAATATTTTAAATTTT
2172736 TATAAATATTTTAAATTTT
1 TATAAATATTTTAAATTTT
2172755 AAAAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
TATAAATATTTTAAATTTT
Found at i:2172747 original size:19 final size:19
Alignment explanation
Indices: 2172718--2172774 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 19
2172708 TTTTTAAAAC
2172718 TATAAAT-TTTTGAATTTT
1 TATAAATATTTTGAATTTT
*
2172736 TATAAATATTTT-AAATTT
1 TATAAATATTTTGAATTTT
* *
2172754 TAAAAATTATTTTGTATTTT
1 TATAAA-TATTTTGAATTTT
2172774 T
1 T
2172775 TTTGTTGAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 17 0.53
19 10 0.31
20 5 0.16
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:2173949 original size:25 final size:25
Alignment explanation
Indices: 2173892--2173940 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
2173882 TTTTTATTAT
2173892 ATTACTAA-ATTTATATTTAAAAATA
1 ATTA-TAATATTTATATTTAAAAATA
2173917 ATTATAATATTTA-ATTTAAAAATA
1 ATTATAATATTTATATTTAAAAATA
2173941 TTAATTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATTATAATATTTATATTTAAAAATA
Found at i:2182574 original size:29 final size:29
Alignment explanation
Indices: 2182542--2182598 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
2182532 TTTTAATCCT
* *
2182542 TTTTAAATTTTTTATATATAATTTATTTA
1 TTTTAAATATTTTAAATATAATTTATTTA
*
2182571 TTTTAAATATTTTAAATATTATTTATTT
1 TTTTAAATATTTTAAATATAATTTATTT
2182599 TTACTATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (29 bp):
TTTTAAATATTTTAAATATAATTTATTTA
Found at i:2182786 original size:20 final size:20
Alignment explanation
Indices: 2182748--2182787 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
2182738 TAATTTGTTG
*
2182748 ATTTATTTTCGTATTTTTTT
1 ATTTATTTTAGTATTTTTTT
*
2182768 ATTTA-TTTAGTATTGTTTT
1 ATTTATTTTAGTATTTTTTT
2182787 A
1 A
2182788 GTATGTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.20, C:0.03, G:0.07, T:0.70
Consensus pattern (20 bp):
ATTTATTTTAGTATTTTTTT
Found at i:2187181 original size:16 final size:16
Alignment explanation
Indices: 2187160--2187190 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2187150 TGGTAGAGGA
2187160 AATGATTGAGAACGCC
1 AATGATTGAGAACGCC
2187176 AATGATTGAGAACGC
1 AATGATTGAGAACGC
2187191 TAGAAGGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.16, G:0.26, T:0.19
Consensus pattern (16 bp):
AATGATTGAGAACGCC
Found at i:2194225 original size:45 final size:45
Alignment explanation
Indices: 2194174--2194508 Score: 230
Period size: 45 Copynumber: 7.5 Consensus size: 45
2194164 TTAGACGGGG
* *
2194174 AGCAGATCGAAGATAGCAGATCTGACATTTGTGTGTTTACATCGA
1 AGCAGATCGAAGATAGCAGATTTGACATTTCTGTGTTTACATCGA
* * * * * * * * *
2194219 AGCAGATCAAAGAT-GATAGATTTG--GTGTCTCTATATTAGATGGGG
1 AGCAGATCGAAGATAG-CAGATTTGACATTTCTGTGT-TTACAT-CGA
*
2194264 AGCAGATCGAAGATAGCAGATTTGACA-TTC-GTG--TATATCGA
1 AGCAGATCGAAGATAGCAGATTTGACATTTCTGTGTTTACATCGA
* * * * * *
2194305 AGCAGATCGAAGAT-GACAGATTTGGCGTCTCTGT-ATTAGA-CGGGG
1 AGCAGATCGAAGATAG-CAGATTTGACATTTCTGTGTTTACATC--GA
*
2194350 AGGAGATCGAAGATAGCAGATTTGACA-TTCATGTGTTTACATCGA
1 AGCAGATCGAAGATAGCAGATTTGACATTTC-TGTGTTTACATCGA
* * * * *
2194395 AGCAGATCGAAGAT-GACAGATTTGGCGTCTCTGTG-TTAGACCGA
1 AGCAGATCGAAGATAG-CAGATTTGACATTTCTGTGTTTACATCGA
*
2194439 GAGCAGATCGAAGATAGCAGATCTGACA-TTCATGTGTTTACATCGA
1 -AGCAGATCGAAGATAGCAGATTTGACATTTC-TGTGTTTACATCGA
* * *
2194485 AGAAGATCGATGATAGTAGATTTG
1 AGCAGATCGAAGATAGCAGATTTG
2194509 GCGTCTCTAT
Statistics
Matches: 219, Mismatches: 48, Indels: 46
0.70 0.15 0.15
Matches are distributed among these distances:
40 1 0.00
41 24 0.11
42 6 0.03
43 8 0.04
44 21 0.10
45 140 0.64
46 18 0.08
47 1 0.00
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.27
Consensus pattern (45 bp):
AGCAGATCGAAGATAGCAGATTTGACATTTCTGTGTTTACATCGA
Found at i:2194290 original size:90 final size:90
Alignment explanation
Indices: 2194145--2194533 Score: 563
Period size: 90 Copynumber: 4.4 Consensus size: 90
2194135 TCACTGTTAG
**
2194145 TAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTTGTGTGT
1 TAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCATGTGT
*
2194210 TTACATCGAAGCAGATCAAAGATGA
66 TTACATCGAAGCAGATCGAAGATGA
* * * *
2194235 TAGATTTGGTGTCTCTATATTAGATGGGGAGCAGATCGAAGATAGCAGATTTGACATTC--GTG-
1 TAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCATGTGT
*
2194297 -TATATCGAAGCAGATCGAAGATGA
66 TTACATCGAAGCAGATCGAAGATGA
* * *
2194321 CAGATTTGGCGTCTCTGTATTAGACGGGGAGGAGATCGAAGATAGCAGATTTGACATTCATGTGT
1 TAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCATGTGT
2194386 TTACATCGAAGCAGATCGAAGATGA
66 TTACATCGAAGCAGATCGAAGATGA
* * * *
2194411 CAGATTTGGCGTCTCTGTGTTAGACCGAGAGCAGATCGAAGATAGCAGATCTGACATTCATGTGT
1 TAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCATGTGT
* *
2194476 TTACATCGAAGAAGATCGATGAT-A
66 TTACATCGAAGCAGATCGAAGATGA
* *
2194500 GTAGATTTGGCGTCTCTATATTTGACGGGGAGCA
1 -TAGATTTGGCGTCTCTGTATTAGACGGGGAGCA
2194534 AATCAAGGAT
Statistics
Matches: 268, Mismatches: 26, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
86 76 0.28
88 6 0.02
89 1 0.00
90 185 0.69
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (90 bp):
TAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCATGTGT
TTACATCGAAGCAGATCGAAGATGA
Found at i:2194445 original size:176 final size:178
Alignment explanation
Indices: 2194146--2194533 Score: 557
Period size: 176 Copynumber: 2.2 Consensus size: 178
2194136 CACTGTTAGT
**
2194146 AGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTTGTGTGTT
1 AGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCATGTGTT
* * ** *
2194211 TACATCGAAGCAGATCAAAGATGATAGATTTGGTGTCTCTATATTAGATGGGGAGCAGATCGAAG
66 TACATCGAAGCAGATCAAAGATGACAGATTTGGCGTCTCTATATTAGACCGAGAGCAGATCGAAG
* * *
2194276 ATAGCAGATTTGACATTC-GTG-TATATCGAAGCAGATCGAAGAT-GAC
131 ATAGCAGATCTGACATTCAGTGTTACATCGAAGAAGATCGAAGATAG-C
* *
2194322 AGATTTGGCGTCTCTGTATTAGACGGGGAGGAGATCGAAGATAGCAGATTTGACATTCATGTGTT
1 AGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCATGTGTT
* * *
2194387 TACATCGAAGCAGATCGAAGATGACAGATTTGGCGTCTCTGTGTTAGACCGAGAGCAGATCGAAG
66 TACATCGAAGCAGATCAAAGATGACAGATTTGGCGTCTCTATATTAGACCGAGAGCAGATCGAAG
* *
2194452 ATAGCAGATCTGACATTCATGTGTTTACATCGAAGAAGATCGATGATAGT
131 ATAGCAGATCTGACATTCA-GTG-TTACATCGAAGAAGATCGAAGATAGC
* *
2194502 AGATTTGGCGTCTCTATATTTGACGGGGAGCA
1 AGATTTGGCGTCTCTGTATTAGACGGGGAGCA
2194534 AATCAAGGAT
Statistics
Matches: 187, Mismatches: 20, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
176 135 0.72
178 3 0.02
180 48 0.26
181 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (178 bp):
AGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATCGAAGATAGCAGATCTGACATTCATGTGTT
TACATCGAAGCAGATCAAAGATGACAGATTTGGCGTCTCTATATTAGACCGAGAGCAGATCGAAG
ATAGCAGATCTGACATTCAGTGTTACATCGAAGAAGATCGAAGATAGC
Found at i:2197276 original size:17 final size:16
Alignment explanation
Indices: 2197246--2197279 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2197236 AGAAATACAA
2197246 ATTAACAAAATTATAC
1 ATTAACAAAATTATAC
*
2197262 ATTATACAAACTTATAC
1 ATTA-ACAAAATTATAC
2197279 A
1 A
2197280 AACATAGCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTAACAAAATTATAC
Found at i:2197444 original size:27 final size:26
Alignment explanation
Indices: 2197402--2197457 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 26
2197392 TGGTCTTAAT
2197402 TAAGCGGTTCACACCTACAGAGAGGC
1 TAAGCGGTTCACACCTACAGAGAGGC
*
2197428 TAANGCGGTTCAGACCTACAGAGAGGC
1 TAA-GCGGTTCACACCTACAGAGAGGC
2197455 TAA
1 TAA
2197458 ATACAGTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 3 0.11
27 25 0.89
ACGTcount: A:0.32, C:0.23, G:0.27, T:0.16
Consensus pattern (26 bp):
TAAGCGGTTCACACCTACAGAGAGGC
Found at i:2198089 original size:25 final size:25
Alignment explanation
Indices: 2198061--2198151 Score: 121
Period size: 25 Copynumber: 3.4 Consensus size: 25
2198051 AACCATCAAC
2198061 TGAAAAAATAAA-ATCCAGAACAAAT
1 TGAAAAAA-AAATATCCAGAACAAAT
2198086 TGAAAAAAAAATATCCAGAACAAAT
1 TGAAAAAAAAATATCCAGAACAAAT
2198111 TGAAAAAAAACAAAATTATCCAGAACAAAT
1 TG---AAAAA-AAAA-TATCCAGAACAAAT
2198141 TGAAAAAAAAA
1 TGAAAAAAAAA
2198152 ACAAAATTAA
Statistics
Matches: 60, Mismatches: 0, Indels: 11
0.85 0.00 0.15
Matches are distributed among these distances:
24 3 0.05
25 23 0.38
26 4 0.07
27 5 0.08
28 5 0.08
29 4 0.07
30 16 0.27
ACGTcount: A:0.66, C:0.11, G:0.08, T:0.15
Consensus pattern (25 bp):
TGAAAAAAAAATATCCAGAACAAAT
Found at i:2198154 original size:32 final size:30
Alignment explanation
Indices: 2198073--2198160 Score: 123
Period size: 30 Copynumber: 3.0 Consensus size: 30
2198063 AAAAAATAAA
2198073 ATCCAGAACAAATTG---AAAAA-AAAA-T
1 ATCCAGAACAAATTGAAAAAAAACAAAATT
2198098 ATCCAGAACAAATTGAAAAAAAACAAAATT
1 ATCCAGAACAAATTGAAAAAAAACAAAATT
2198128 ATCCAGAACAAATTGAAAAAAAAAACAAAATT
1 ATCCAGAACAAATTG--AAAAAAAACAAAATT
2198160 A
1 A
2198161 AGGAAAACAT
Statistics
Matches: 56, Mismatches: 0, Indels: 7
0.89 0.00 0.11
Matches are distributed among these distances:
25 15 0.27
28 5 0.09
29 4 0.07
30 16 0.29
32 16 0.29
ACGTcount: A:0.65, C:0.12, G:0.07, T:0.16
Consensus pattern (30 bp):
ATCCAGAACAAATTGAAAAAAAACAAAATT
Found at i:2199162 original size:16 final size:17
Alignment explanation
Indices: 2199141--2199181 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
2199131 TTACTTTTAG
2199141 ATAAAATCAAAATA-AA
1 ATAAAATCAAAATATAA
* *
2199157 ATAAAAACAAAATATAC
1 ATAAAATCAAAATATAA
2199174 ATAAAATC
1 ATAAAATC
2199182 CACTACTATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.20
Consensus pattern (17 bp):
ATAAAATCAAAATATAA
Found at i:2199259 original size:15 final size:15
Alignment explanation
Indices: 2199241--2199273 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2199231 TATCTTCTTT
*
2199241 TTTTTTTAAAAGAAA
1 TTTTTCTAAAAGAAA
2199256 TTTTTCTAAAAGAAA
1 TTTTTCTAAAAGAAA
2199271 TTT
1 TTT
2199274 GGAGGGTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.48
Consensus pattern (15 bp):
TTTTTCTAAAAGAAA
Found at i:2199393 original size:10 final size:10
Alignment explanation
Indices: 2199378--2199433 Score: 60
Period size: 10 Copynumber: 5.2 Consensus size: 10
2199368 TAATTAAAAT
2199378 AATTAATTAA
1 AATTAATTAA
2199388 AATTAATTAA
1 AATTAATTAA
2199398 AA-TAATTAA
1 AATTAATTAA
2199407 AATATATTATTTAAA
1 AAT-TA--A-TT-AA
2199422 AATTAATTAA
1 AATTAATTAA
2199432 AA
1 AA
2199434 ATCAGATACG
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
9 9 0.22
10 16 0.40
11 4 0.10
12 1 0.03
13 1 0.03
14 4 0.10
15 5 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
AATTAATTAA
Found at i:2199415 original size:23 final size:21
Alignment explanation
Indices: 2199368--2199434 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 21
2199358 TTATATTTAA
2199368 TAATTAAAATAATTAATTAAAAT
1 TAATTAAAATAATTAA--AAAAT
2199391 TAATTAAAATAATTAAAATATAT
1 TAATTAAAATAATTAAAA-A-AT
*
2199414 TATTTAAAAATTAATTAAAAA
1 TAATT-AAAA-TAATTAAAAA
2199435 TCAGATACGT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
21 2 0.05
22 1 0.03
23 22 0.56
24 5 0.13
25 9 0.23
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TAATTAAAATAATTAAAAAAT
Found at i:2206046 original size:20 final size:19
Alignment explanation
Indices: 2206008--2206049 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
2205998 TTTATTTTAC
2206008 TATAAATATTATGTATATA
1 TATAAATATTATGTATATA
2206027 TATAAATGATTTAT-TATATA
1 TATAAAT-A-TTATGTATATA
2206047 TAT
1 TAT
2206050 TATTTTTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.33
20 10 0.48
21 4 0.19
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (19 bp):
TATAAATATTATGTATATA
Found at i:2209577 original size:83 final size:83
Alignment explanation
Indices: 2209438--2209591 Score: 299
Period size: 83 Copynumber: 1.9 Consensus size: 83
2209428 ATTCTTGAAA
*
2209438 TTTTAGTTGAATTGTTGAGTATATGCACTATGCAGATTTAATAGTGCAAAATGCATAAACTTATA
1 TTTTAGTTGAATTGTTGAGTATATGCACTATGCAAATTTAATAGTGCAAAATGCATAAACTTATA
2209503 ATCTATTGAGCTTTAATT
66 ATCTATTGAGCTTTAATT
2209521 TTTTAGTTGAATTGTTGAGTATATGCACTATGCAAATTTAATAGTGCAAAATGCATAAACTTATA
1 TTTTAGTTGAATTGTTGAGTATATGCACTATGCAAATTTAATAGTGCAAAATGCATAAACTTATA
2209586 ATCTAT
66 ATCTAT
2209592 ATACATGAGC
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 70 1.00
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (83 bp):
TTTTAGTTGAATTGTTGAGTATATGCACTATGCAAATTTAATAGTGCAAAATGCATAAACTTATA
ATCTATTGAGCTTTAATT
Found at i:2210183 original size:17 final size:18
Alignment explanation
Indices: 2210163--2210213 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 18
2210153 TTGTGTATTG
*
2210163 TGTTATATT-GTGACCTA
1 TGTTATATTGGTGAACTA
*
2210180 TGTTA-ATTGGTGAATTA
1 TGTTATATTGGTGAACTA
2210197 TGTTAT-TATGGTGAACT
1 TGTTATAT-TGGTGAACT
2210214 GTATTAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 3 0.11
17 17 0.61
18 8 0.29
ACGTcount: A:0.25, C:0.06, G:0.22, T:0.47
Consensus pattern (18 bp):
TGTTATATTGGTGAACTA
Found at i:2215648 original size:44 final size:44
Alignment explanation
Indices: 2215591--2217645 Score: 2173
Period size: 44 Copynumber: 46.5 Consensus size: 44
2215581 TCACCAATAG
* * * *
2215591 CAGATTTGACGTCTCTGTATTGTCAGAGAACAGATCGAAAATAA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * *
2215635 CAAATTTGGCGTCTCTGTATTGACAAAGAGCAGATCGAAAATAA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * * * *
2215679 CAAATTTAGCGTCTTTGTATTGACAGAGAACAGATCGAAGTTAA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * *
2215723 CAAATTTGGCATCTCTGTATTGACAGAGAGCAGATCGAAGATGA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * *
2215767 CAGATTTGGCGTCTTTGTATTGATAGAGAGCAGATCGAAGATGA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * *
2215811 CAGATTTGGTGTCTCTGTATTGACAGGGAGTAGATCGAAGATGAA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGAT-AA
* * * *
2215856 -AAATTTGGCGTCTCTGTATTGTCAGAGAGTAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * * * * * *
2215899 CCGATTTGACATCTCTATATTGGCAAAGAGCAGATTGAAGATAA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * * *
2215943 CAGATTTGGCATTTCTGTATTGGCAGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * * * *
2215987 CAGATTTGACATTTCTGTATTGGCAAAGAGCAGATCGAAGATAA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * *
2216031 CAGATTTGGCGTTTCTGTATTGGCAGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * * * *
2216075 CAGATTTGACATTTCTGTATTGGCAAAGAGCAGATCGAAGATAA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * *
2216119 CAGATTTGGCGTTTCTGTATTGGCAGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * * * *
2216163 CAGATTTGACATTTCTGTATTGGCAAAGAGCAGATCGAAGATAA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * *
2216207 CAGATTTGGCGTTTCTGTATTGGCAGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * * * *
2216251 CAGATTTGACATTTCTGTATTGACAGAGAGCAGATCAAAGATAG
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* *
2216295 CAGATTTGGCGTCACTGTATTGGCAGAGAGCAGATC-AGAGATAA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGA-AGATAA
* * *
2216339 CAGATTTGGTGTCTCTGTATTGACAGGGAGTAGATCGAAGATGAA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGAT-AA
* * * *
2216384 -AAATTTGGCGTCTCTGTATTGTCAGAGAGTAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * * * * * *
2216427 CCGATTTGACATCTCTATATTGGCAAAGAGCAGATTGAAGATAA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * * * **
2216471 CAGATTTGGCATTTCTGTATTGGCAGATATTGACAGAGAGCAAATCGAATATGG
1 CAGATTTGG-----C-GT-CT--CTG-TATTGACAGAGAGCAGATCGAAGATAA
* * * * *
2216525 TAGATTTGGCATTTCTGTATTGACAGAGAGCGGATCGAAGATGA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * * * * *
2216569 TAGATTTAGTGTCTCTGTATTGTCAGAGAGCAGATCAAAGATAGC
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATA-A
* * ** * *
2216614 CA-ATTTGACATCTCTGTATTTTCAGAGAGCAGATCGAATATAG
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * *
2216657 TAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * * * *
2216701 TAGATTTGGCATTTCTGTATTGGCAGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * * * *
2216745 CAGATTTGACATTTCTGTATTGACAGAGAGCAGATCAAAGATAG
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* *
2216789 CAGATTTGGCGTCACTGTATTGGCAGAGAGCAGATC-AGAGATAA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGA-AGATAA
* *
2216833 CAGATTTGGTGTCTCTGTATTGACAGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
*
2216877 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * * **
2216921 CAGATTTGGCGTCTCTATATTGACAGAGAGCAAATCGAATATGG
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * * * *
2216965 TAGATTTGGCATTTCTGTATTGACAGAGAGCGGATCGAAGATGA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * * * * *
2217009 TAGATTTAGTGTCTCTGTATTGTCAGAGAGCAGATCAAAGATAGC
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATA-A
* * ** * *
2217054 CA-ATTTGACATCTCTGTATTTTCAGAGAGCAGATCGAATATAG
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * *
2217097 TAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * * * *
2217141 TAGATTTGGCATTTCTGTATTGGCAGAGAGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
*
2217185 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATGA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * * *
2217229 CAGATTTGGCGTCTCTATATTGTCAGAGGGCAGATCGAAGATAG
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * * *
2217273 CAGATTTGGCATTTCTGTATTGACAGAGAGCAGATCAAAGATAG
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * * *
2217317 CAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATTGGAGATAG
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * * *
2217361 CAGATTTGGTGTCTCTATATTGACAGAAAGTAGATCGAAGATAA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * * *
2217405 CAGATTTGTCATCTCTGTATTAACAAAGAGCAGATCGAAGATAA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* *
2217449 CAGATTTGTCGTCTC-GTTATTGACAAAGAGCAGATCGAAGATAA
1 CAGATTTGGCGTCTCTG-TATTGACAGAGAGCAGATCGAAGATAA
* * * * * *
2217493 TAGATTTGGCGTCTCTGTATTAATAGAGGGCAGATTGAAGATGA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * * *
2217537 TATATTTGGTGTCTCTGTATTGACAGAGAGAAGATCGAAGATAA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
* * *
2217581 CAGATTTGGTGTCTCTGTATTGACAAAG-GACAGATCGAAGATTA
1 CAGATTTGGCGTCTCTGTATTGACAGAGAG-CAGATCGAAGATAA
* * *
2217625 CAGATTCGGCTTCTCCGTATT
1 CAGATTTGGCGTCTCTGTATT
2217646 AGGCAAGGAG
Statistics
Matches: 1717, Mismatches: 269, Indels: 50
0.84 0.13 0.02
Matches are distributed among these distances:
43 8 0.00
44 1663 0.97
45 10 0.01
47 2 0.00
48 1 0.00
49 2 0.00
50 1 0.00
51 1 0.00
53 1 0.00
54 28 0.02
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (44 bp):
CAGATTTGGCGTCTCTGTATTGACAGAGAGCAGATCGAAGATAA
Found at i:2219148 original size:20 final size:19
Alignment explanation
Indices: 2219110--2219151 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
2219100 TTATTTTTAC
2219110 TATAAATATTATGTATATA
1 TATAAATATTATGTATATA
2219129 TATAAATGATTTAT-TATATA
1 TATAAAT-A-TTATGTATATA
2219149 TAT
1 TAT
2219152 TATTTTTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.33
20 10 0.48
21 4 0.19
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (19 bp):
TATAAATATTATGTATATA
Found at i:2219212 original size:13 final size:12
Alignment explanation
Indices: 2219180--2219224 Score: 56
Period size: 13 Copynumber: 3.8 Consensus size: 12
2219170 GTTTATCATA
*
2219180 TTATTAT-TAAT
1 TTATTATATATT
*
2219191 TCATTATATATT
1 TTATTATATATT
2219203 TTATTTATATATT
1 TTA-TTATATATT
2219216 TTATTATAT
1 TTATTATAT
2219225 TATATCATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
11 6 0.21
12 11 0.38
13 12 0.41
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (12 bp):
TTATTATATATT
Found at i:2219220 original size:18 final size:18
Alignment explanation
Indices: 2219203--2219261 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 18
2219193 ATTATATATT
2219203 TTAT-TTATAT-ATTTTA
1 TTATATTATATCATTTTA
2219219 TTATATTATATCATTTTA
1 TTATATTATATCATTTTA
* * *
2219237 CTATA-TATATTA-TTCA
1 TTATATTATATCATTTTA
2219253 TTATATTAT
1 TTATATTAT
2219262 TTTTATTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
16 11 0.31
17 15 0.42
18 10 0.28
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (18 bp):
TTATATTATATCATTTTA
Found at i:2219226 original size:5 final size:5
Alignment explanation
Indices: 2219197--2219273 Score: 52
Period size: 5 Copynumber: 15.2 Consensus size: 5
2219187 TAATTCATTA
* * * *
2219197 TATAT TTTAT T-TA- TATAT TTTAT TATAT TATAT CATTT TACTAT ATATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TA-TAT -TATAT
*
2219247 TATTCAT TATAT TAT-T TTTAT TATAT T
1 TA-T-AT TATAT TATAT TATAT TATAT T
2219274 TTATATTACT
Statistics
Matches: 56, Mismatches: 9, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
3 1 0.02
4 7 0.12
5 35 0.62
6 7 0.12
7 6 0.11
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (5 bp):
TATAT
Found at i:2219229 original size:30 final size:34
Alignment explanation
Indices: 2219177--2219261 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 34
2219167 ATTGTTTATC
* *
2219177 ATAT-TATTATTAATT-CATTATAT-ATTTTA-T
1 ATATATATTATTCATTATATTATATCATTTTACT
*
2219207 TTATATATT-TT-ATTATATTATATCATTTTACT
1 ATATATATTATTCATTATATTATATCATTTTACT
2219239 ATATATATTATTCATTATATTAT
1 ATATATATTATTCATTATATTAT
2219262 TTTTATTATA
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
29 3 0.07
30 12 0.26
31 10 0.22
32 9 0.20
33 2 0.04
34 10 0.22
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (34 bp):
ATATATATTATTCATTATATTATATCATTTTACT
Found at i:2219246 original size:34 final size:30
Alignment explanation
Indices: 2219193--2219261 Score: 77
Period size: 34 Copynumber: 2.2 Consensus size: 30
2219183 TTATTAATTC
*
2219193 ATTATATATTTTATTTATA-TATTTTATTAT
1 ATTATATATTTTATTTATATTA-TTCATTAT
2219223 ATTATATCATTTTACTATATATATTATTCATTAT
1 ATTATAT-ATTTTA-T-T-TATATTATTCATTAT
2219257 ATTAT
1 ATTAT
2219262 TTTTATTATA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
30 7 0.21
31 6 0.18
32 1 0.03
33 1 0.03
34 16 0.48
35 2 0.06
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (30 bp):
ATTATATATTTTATTTATATTATTCATTAT
Found at i:2219266 original size:30 final size:29
Alignment explanation
Indices: 2219184--2219272 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 29
2219174 ATCATATTAT
2219184 TATTAATTCATTATA-TATTTTATTTATATA
1 TATT-ATTCATTATATTATTTTA-TTATATA
* * * *
2219214 TTTTATTATATTATATCATTTTACTATATA
1 TATTATT-CATTATATTATTTTATTATATA
2219244 TATTATTCATTATATTATTTTTATTATAT
1 TATTATTCATTATATTA-TTTTATTATAT
2219273 TTTATATTAC
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
29 11 0.23
30 31 0.65
31 6 0.12
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (29 bp):
TATTATTCATTATATTATTTTATTATATA
Found at i:2219295 original size:33 final size:35
Alignment explanation
Indices: 2219242--2219311 Score: 92
Period size: 33 Copynumber: 2.1 Consensus size: 35
2219232 TTTTACTATA
* *
2219242 TATATTATTCATTATATTATTTTTAT-TAT-ATTT
1 TATATTATTCAATATATTATTATTATGTATAATTT
2219275 TATATTACTTCAATAT-TTATTATTATGTATAATTT
1 TATATTA-TTCAATATATTATTATTATGTATAATTT
2219310 TA
1 TA
2219312 AAAATTTGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
33 16 0.50
34 10 0.31
35 6 0.19
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.61
Consensus pattern (35 bp):
TATATTATTCAATATATTATTATTATGTATAATTT
Found at i:2219296 original size:48 final size:46
Alignment explanation
Indices: 2219195--2219311 Score: 111
Period size: 48 Copynumber: 2.5 Consensus size: 46
2219185 ATTAATTCAT
*
2219195 TATATATT-TT-ATTTATATATTTTATTATATTATATCATTTTACTA
1 TATATATTATTCA-TTATATATTTTATTATATTATATCATTTTACAA
*
2219240 TATATATTATTCATTATATTATTTTTATTATATTTTAT-ATTACTT-CAA
1 TATATATTATTCATTATA-TA-TTTTATTATATTATATCATT--TTACAA
*
2219288 TATTTATTATT-ATGTATA-ATTTTA
1 TATATATTATTCAT-TATATATTTTA
2219312 AAAATTTGCA
Statistics
Matches: 62, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
45 13 0.21
46 8 0.13
47 8 0.13
48 31 0.50
49 2 0.03
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (46 bp):
TATATATTATTCATTATATATTTTATTATATTATATCATTTTACAA
Found at i:2219548 original size:14 final size:14
Alignment explanation
Indices: 2219531--2219564 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2219521 CCCTCATTTA
2219531 TTTTTCAATTTGTT
1 TTTTTCAATTTGTT
*
2219545 TTTTTTAATTTGTT
1 TTTTTCAATTTGTT
2219559 TGTTTT
1 T-TTTT
2219565 TATCCTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.12, C:0.03, G:0.09, T:0.76
Consensus pattern (14 bp):
TTTTTCAATTTGTT
Found at i:2219549 original size:15 final size:15
Alignment explanation
Indices: 2219531--2219566 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
2219521 CCCTCATTTA
2219531 TTTTTCAATTTGTTT-
1 TTTTT-AATTTGTTTG
2219546 TTTTTAATTTGTTTG
1 TTTTTAATTTGTTTG
2219561 TTTTTA
1 TTTTTA
2219567 TCCTTTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.14, C:0.03, G:0.08, T:0.75
Consensus pattern (15 bp):
TTTTTAATTTGTTTG
Found at i:2224077 original size:17 final size:18
Alignment explanation
Indices: 2224057--2224107 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 18
2224047 TTGTGTATTG
*
2224057 TGTTATATT-GTGACCTA
1 TGTTATATTGGTGAACTA
*
2224074 TGTTA-ATTGGTGAATTA
1 TGTTATATTGGTGAACTA
2224091 TGTTAT-TATGGTGAACT
1 TGTTATAT-TGGTGAACT
2224108 GTATTAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 3 0.11
17 17 0.61
18 8 0.29
ACGTcount: A:0.25, C:0.06, G:0.22, T:0.47
Consensus pattern (18 bp):
TGTTATATTGGTGAACTA
Found at i:2228192 original size:14 final size:15
Alignment explanation
Indices: 2228173--2228202 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2228163 GTTTATTATA
2228173 TGTG-AAGTATCATG
1 TGTGAAAGTATCATG
2228187 TGTGAAAGTATCATG
1 TGTGAAAGTATCATG
2228202 T
1 T
2228203 CTTAATTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.37
Consensus pattern (15 bp):
TGTGAAAGTATCATG
Found at i:2234670 original size:74 final size:74
Alignment explanation
Indices: 2234592--2234736 Score: 193
Period size: 74 Copynumber: 2.0 Consensus size: 74
2234582 AATTTTCTCT
* * * * **
2234592 AAAACTTTTTTGCATCTCTTATATTTTCTTAACTTCTAAACACTCT-TAATTCCTTCAATTTTGT
1 AAAACATTTATGCATCTCTTATATTTTCTTAACATCCAAACACTCTCT-ATTCCTTCAATTTTAC
2234656 AAGAAAACAC
65 AAGAAAACAC
* * *
2234666 AAAACATTTATGCATCTTTTATATTTTCTTAGCATCCAAACACTCTCTATTCTTTCAATTTTACA
1 AAAACATTTATGCATCTCTTATATTTTCTTAACATCCAAACACTCTCTATTCCTTCAATTTTACA
2234731 AGAAAA
66 AGAAAA
2234737 TCACTCTTTC
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
74 60 0.98
75 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.04, T:0.42
Consensus pattern (74 bp):
AAAACATTTATGCATCTCTTATATTTTCTTAACATCCAAACACTCTCTATTCCTTCAATTTTACA
AGAAAACAC
Found at i:2234921 original size:19 final size:19
Alignment explanation
Indices: 2234897--2234934 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2234887 TCTAAGTAAG
2234897 AAAATTAACGATCCATGCT
1 AAAATTAACGATCCATGCT
2234916 AAAATTAACGATCCATGCT
1 AAAATTAACGATCCATGCT
2234935 TTTAAAGCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.21, G:0.11, T:0.26
Consensus pattern (19 bp):
AAAATTAACGATCCATGCT
Found at i:2235844 original size:28 final size:32
Alignment explanation
Indices: 2235789--2235867 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 32
2235779 TGTACGTGGG
* *
2235789 TGATTATATATATATTATATATGCATGG-CTT
1 TGATTATATATATAATATATATGAATGGACTT
* *
2235820 T-ATT-T-TATATAATATATATTAATGGATTT
1 TGATTATATATATAATATATATGAATGGACTT
2235849 TGATTATATATATAATATA
1 TGATTATATATATAATATA
2235868 ATGTATATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
28 17 0.43
29 4 0.10
30 6 0.15
31 2 0.05
32 11 0.28
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.51
Consensus pattern (32 bp):
TGATTATATATATAATATATATGAATGGACTT
Found at i:2237755 original size:45 final size:45
Alignment explanation
Indices: 2237703--2237789 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
2237693 TATGTAATCT
2237703 GAACTCATTGAGTTGTGATATGAGTTCATGATATATGTGACATCC
1 GAACTCATTGAGTTGTGATATGAGTTCATGATATATGTGACATCC
* * *
2237748 GAACTCATTGAGTTGTGGTCTGAGTTCGTGATATATGTGACA
1 GAACTCATTGAGTTGTGATATGAGTTCATGATATATGTGACA
2237790 CATGTTTTGG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.36
Consensus pattern (45 bp):
GAACTCATTGAGTTGTGATATGAGTTCATGATATATGTGACATCC
Found at i:2242029 original size:27 final size:27
Alignment explanation
Indices: 2241976--2242031 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
2241966 ATCTCATAGA
*
2241976 GGCATATCAGTCATTTTACTATGTAGG
1 GGCATATCAGTCATTTTACAATGTAGG
*
2242003 GGCATTTCAGTCATTTTATCAAT-TAGG
1 GGCATATCAGTCATTTTA-CAATGTAGG
2242030 GG
1 GG
2242032 GTCTAGGTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 23 0.88
28 3 0.12
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (27 bp):
GGCATATCAGTCATTTTACAATGTAGG
Found at i:2255301 original size:27 final size:28
Alignment explanation
Indices: 2255262--2255333 Score: 85
Period size: 27 Copynumber: 2.6 Consensus size: 28
2255252 GGGTCATGTG
* **
2255262 AAATTACCGAAATACCCTC-AATTTGTA
1 AAATTACCAAAATACCCTCTAATTTACA
2255289 AAATTACCAAAATACCC-CTAATTTACA
1 AAATTACCAAAATACCCTCTAATTTACA
**
2255316 AAATTATAAAAATACCCT
1 AAATTACCAAAATACCCT
2255334 TGACTTTCTA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
26 1 0.03
27 37 0.97
ACGTcount: A:0.47, C:0.22, G:0.03, T:0.28
Consensus pattern (28 bp):
AAATTACCAAAATACCCTCTAATTTACA
Found at i:2256281 original size:16 final size:16
Alignment explanation
Indices: 2256260--2256290 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2256250 TCAAATATGG
*
2256260 CATGACATTTTGCATA
1 CATGACATGTTGCATA
2256276 CATGACATGTTGCAT
1 CATGACATGTTGCAT
2256291 GGGTTGGGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.35
Consensus pattern (16 bp):
CATGACATGTTGCATA
Found at i:2256403 original size:24 final size:25
Alignment explanation
Indices: 2256321--2256414 Score: 145
Period size: 25 Copynumber: 3.8 Consensus size: 25
2256311 AGGAAGTGCT
* *
2256321 AAAAGGGCTATGCCCCAGTTTATCG
1 AAAAGGGCTTTGCCCCAGTTTATCA
* *
2256346 AAAAGGGCTTTGCCCTAGTTTACCA
1 AAAAGGGCTTTGCCCCAGTTTATCA
2256371 AAAAGGGCTTTGCCCCAGTTTATC-
1 AAAAGGGCTTTGCCCCAGTTTATCA
2256395 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
2256415 ATTAAAAGAG
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
24 20 0.32
25 43 0.68
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATCA
Found at i:2256427 original size:24 final size:24
Alignment explanation
Indices: 2256321--2256427 Score: 144
Period size: 25 Copynumber: 4.4 Consensus size: 24
2256311 AGGAAGTGCT
*
2256321 AAAAGGGCTATGCCCCAGTTTATC
1 AAAAGGGCTTTGCCCCAGTTTATC
* *
2256345 GAAAAGGGCTTTGCCCTAGTTTACC
1 -AAAAGGGCTTTGCCCCAGTTTATC
2256370 AAAAAGGGCTTTGCCCCAGTTTATC
1 -AAAAGGGCTTTGCCCCAGTTTATC
*
2256395 AAAAGGGCTTTGCCCCAG-TTATT
1 AAAAGGGCTTTGCCCCAGTTTATC
2256418 AAAAGAGGCT
1 AAAAG-GGCT
2256428 AGGCCTCCAG
Statistics
Matches: 74, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.12
24 22 0.30
25 43 0.58
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTTATC
Found at i:2256671 original size:31 final size:31
Alignment explanation
Indices: 2256633--2256804 Score: 247
Period size: 31 Copynumber: 5.5 Consensus size: 31
2256623 CGTTTACAGT
2256633 AAAGGCTTCGGCCCAATGATATGATTTATGA
1 AAAGGCTTCGGCCCAATGATATGATTTATGA
* *
2256664 AAAGGCTTCGGCCTAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAATGATATGATTTATGA
2256695 AAAGGCTTCGGCCCAGA-GATATGATTTATGA
1 AAAGGCTTCGGCCCA-ATGATATGATTTATGA
* * * *
2256726 TAAGGCTTCGGCCCAGTGATATGTTTTGTGA
1 AAAGGCTTCGGCCCAATGATATGATTTATGA
* *
2256757 TAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAATGATATGATTTATGA
*
2256788 AAAGGCTTTGGCCCAAT
1 AAAGGCTTCGGCCCAAT
2256805 AACCGTTAAA
Statistics
Matches: 126, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
31 126 1.00
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAATGATATGATTTATGA
Found at i:2256793 original size:93 final size:93
Alignment explanation
Indices: 2256634--2256802 Score: 284
Period size: 93 Copynumber: 1.8 Consensus size: 93
2256624 GTTTACAGTA
*
2256634 AAGGCTTCGGCCCAATGATATGATTTATGAAAAGGCTTCGGCCTAGTGATATGATTTATGAAAAG
1 AAGGCTTCGGCCCAATGATATGATTTATGAAAAGGCTTCGGCCCAGTGATATGATTTATGAAAAG
2256699 GCTTCGGCCCAGAGATATGATTTATGAT
66 GCTTCGGCCCAGAGATATGATTTATGAT
* * * *
2256727 AAGGCTTCGGCCCAGTGATATGTTTTGTGATAAGGCTTCGGCCCAGTGATATGATTTATGAAAAG
1 AAGGCTTCGGCCCAATGATATGATTTATGAAAAGGCTTCGGCCCAGTGATATGATTTATGAAAAG
*
2256792 GCTTTGGCCCA
66 GCTTCGGCCCA
2256803 ATAACCGTTA
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (93 bp):
AAGGCTTCGGCCCAATGATATGATTTATGAAAAGGCTTCGGCCCAGTGATATGATTTATGAAAAG
GCTTCGGCCCAGAGATATGATTTATGAT
Found at i:2259867 original size:30 final size:31
Alignment explanation
Indices: 2259828--2259891 Score: 103
Period size: 30 Copynumber: 2.1 Consensus size: 31
2259818 GTATGACTTA
* *
2259828 GAGGTGGCCCCTCTCTTCTAGAAC-TTTCTG
1 GAGGCGGCCCCTCTCCTCTAGAACTTTTCTG
2259858 GAGGCGGCCCCTCTCCTCTAGAACTTTTCTG
1 GAGGCGGCCCCTCTCCTCTAGAACTTTTCTG
2259889 GAG
1 GAG
2259892 TACAAAACCA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 22 0.71
31 9 0.29
ACGTcount: A:0.14, C:0.31, G:0.25, T:0.30
Consensus pattern (31 bp):
GAGGCGGCCCCTCTCCTCTAGAACTTTTCTG
Found at i:2260615 original size:13 final size:13
Alignment explanation
Indices: 2260597--2260625 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
2260587 TCTAGTTTAA
2260597 TTAGTTAATTAGT
1 TTAGTTAATTAGT
2260610 TTAGTTAATTAGT
1 TTAGTTAATTAGT
2260623 TTA
1 TTA
2260626 ATAAACAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (13 bp):
TTAGTTAATTAGT
Found at i:2264008 original size:53 final size:53
Alignment explanation
Indices: 2263951--2264058 Score: 189
Period size: 53 Copynumber: 2.0 Consensus size: 53
2263941 CCCAATCTCT
2263951 TTCCCTTAGCATTTGTTTACTCTCTTCACTTCTATTTTACTTATTACAAATGC
1 TTCCCTTAGCATTTGTTTACTCTCTTCACTTCTATTTTACTTATTACAAATGC
* * *
2264004 TTCCCTTAGCATTTGTTTACTCTTTTCACTTCTATTTTACTTATTTCTAATGC
1 TTCCCTTAGCATTTGTTTACTCTCTTCACTTCTATTTTACTTATTACAAATGC
2264057 TT
1 TT
2264059 ATTATCAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.19, C:0.23, G:0.06, T:0.53
Consensus pattern (53 bp):
TTCCCTTAGCATTTGTTTACTCTCTTCACTTCTATTTTACTTATTACAAATGC
Found at i:2264219 original size:23 final size:23
Alignment explanation
Indices: 2264193--2264239 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2264183 CATTCTATTG
*
2264193 TCATACCCATGCCATTACTATGC
1 TCATACCCATGCCATTACCATGC
* * *
2264216 TCATTCTCATGCTATTACCATGC
1 TCATACCCATGCCATTACCATGC
2264239 T
1 T
2264240 AATGTCACAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.23, C:0.32, G:0.09, T:0.36
Consensus pattern (23 bp):
TCATACCCATGCCATTACCATGC
Found at i:2267213 original size:30 final size:30
Alignment explanation
Indices: 2267179--2267239 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
2267169 TCCTTAACTC
2267179 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
2267209 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
2267239 A
1 A
2267240 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:2268829 original size:6 final size:6
Alignment explanation
Indices: 2268820--2268893 Score: 89
Period size: 6 Copynumber: 12.7 Consensus size: 6
2268810 GATGATGATG
*
2268820 TTTAAT TTT-AT TTTATT TTTAAT TTTAAT TTTAAT TTTAAT TTT-AT
1 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT
* * * *
2268866 TTTTAT TTTCAT TTTCAT TTTTAT TTTA
1 TTTAAT TTTAAT TTTAAT TTTAAT TTTA
2268894 TGTTTTTATT
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
5 10 0.16
6 51 0.84
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (6 bp):
TTTAAT
Found at i:2268852 original size:18 final size:17
Alignment explanation
Indices: 2268820--2268893 Score: 96
Period size: 17 Copynumber: 4.2 Consensus size: 17
2268810 GATGATGATG
2268820 TTTAATTTTA-TTTTATT
1 TTTAATTTTATTTTTA-T
*
2268837 TTTAATTTTAATTTTAAT
1 TTTAATTTT-ATTTTTAT
2268855 TTTAATTTTATTTTTAT
1 TTTAATTTTATTTTTAT
*
2268872 TTTCATTTTCATTTTTAT
1 TTTAATTTT-ATTTTTAT
2268890 TTTA
1 TTTA
2268894 TGTTTTTATT
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
17 24 0.48
18 22 0.44
19 4 0.08
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTAATTTTATTTTTAT
Found at i:2269250 original size:11 final size:11
Alignment explanation
Indices: 2269234--2269261 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
2269224 ACCAAGAGTC
2269234 AAAAGGAGCCA
1 AAAAGGAGCCA
2269245 AAAAGGAGCCA
1 AAAAGGAGCCA
2269256 AAAAGG
1 AAAAGG
2269262 GACAAAATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.14, G:0.29, T:0.00
Consensus pattern (11 bp):
AAAAGGAGCCA
Found at i:2285158 original size:42 final size:43
Alignment explanation
Indices: 2285112--2285201 Score: 103
Period size: 44 Copynumber: 2.1 Consensus size: 43
2285102 CAAATAGGGA
* * **
2285112 CTTACA-CAAAAT-CAAATATGATGCCAATGTCCCAGATGTGGT
1 CTTACATCAAAATACAAAT-CGATGCCAACGTCCCAGACATGGT
*
2285154 CTTACATGAAAATAACAAATCGATGCCAACGTCCCAGACATGGT
1 CTTACATCAAAAT-ACAAATCGATGCCAACGTCCCAGACATGGT
2285198 CTTA
1 CTTA
2285202 ATTGATAACA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
42 6 0.15
43 5 0.12
44 24 0.60
45 5 0.12
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.24
Consensus pattern (43 bp):
CTTACATCAAAATACAAATCGATGCCAACGTCCCAGACATGGT
Found at i:2295788 original size:13 final size:14
Alignment explanation
Indices: 2295759--2295793 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
2295749 AAATAATTAT
2295759 AATATTTAATTTAAA
1 AATA-TTAATTTAAA
2295774 AATATTAATTTAAA
1 AATATTAATTTAAA
2295788 AA-ATTA
1 AATATTA
2295794 CATATAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 4 0.20
14 12 0.60
15 4 0.20
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATATTAATTTAAA
Found at i:2295836 original size:17 final size:17
Alignment explanation
Indices: 2295804--2295843 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2295794 CATATAATTT
*
2295804 TTTAATAATTATTATACA
1 TTTAATAATAATTATA-A
2295822 TTTAA-AATAATTATAA
1 TTTAATAATAATTATAA
2295838 TTTAAT
1 TTTAAT
2295844 TTAAATTGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 6 0.30
17 9 0.45
18 5 0.25
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTAATAATAATTATAA
Found at i:2295849 original size:20 final size:20
Alignment explanation
Indices: 2295749--2295849 Score: 51
Period size: 20 Copynumber: 5.2 Consensus size: 20
2295739 TCACATTTTA
2295749 AAATAATTATAATATTTAATTT
1 AAATAATTAT-A-ATTTAATTT
*
2295771 AAA-AA-TATTAATTTAA--A
1 AAATAATTA-TAATTTAATTT
2295788 AAATTACA-TATAATTT--TTT
1 AAA-TA-ATTATAATTTAATTT
*
2295807 -AATAATTAT--TATACATTT
1 AAATAATTATAATTTA-ATTT
2295825 AAAATAATTATAATTTAATTT
1 -AAATAATTATAATTTAATTT
2295846 AAAT
1 AAAT
2295850 TGTGATAGTA
Statistics
Matches: 61, Mismatches: 4, Indels: 30
0.64 0.04 0.32
Matches are distributed among these distances:
15 2 0.03
16 1 0.02
17 8 0.13
18 5 0.08
19 13 0.21
20 19 0.31
21 7 0.11
22 6 0.10
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATAATTATAATTTAATTT
Found at i:2312427 original size:25 final size:24
Alignment explanation
Indices: 2312398--2312453 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
2312388 ATTTTTATTA
* *
2312398 AATTTTAATATG-ATTATTATGAAT
1 AATTTTAATA-GAAATATTATAAAT
2312422 ATATTTTAATAGAAATATTATAAAT
1 A-ATTTTAATAGAAATATTATAAAT
2312447 AATTTTA
1 AATTTTA
2312454 TCATATTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 8 0.29
25 20 0.71
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.48
Consensus pattern (24 bp):
AATTTTAATAGAAATATTATAAAT
Found at i:2321969 original size:30 final size:30
Alignment explanation
Indices: 2321935--2322009 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 30
2321925 CTTTATTGGA
2321935 AATTATTTTAAAATTATAATTTATAATTAT
1 AATTATTTTAAAATTATAATTTATAATTAT
* **
2321965 AATTATTCT-ATGTTATTAATTTATAATTAT
1 AATTATTTTAAAATTA-TAATTTATAATTAT
*
2321995 --TTGTTTTAAAATTAT
1 AATTATTTTAAAATTAT
2322010 TGATATATTA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
28 6 0.17
29 8 0.22
30 22 0.61
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (30 bp):
AATTATTTTAAAATTATAATTTATAATTAT
Found at i:2323096 original size:19 final size:19
Alignment explanation
Indices: 2323072--2323110 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
2323062 TTGATAAAAA
2323072 TTCATTTGTGAGATTTCTT
1 TTCATTTGTGAGATTTCTT
2323091 TTCATTTGTGAGATTTCTT
1 TTCATTTGTGAGATTTCTT
2323110 T
1 T
2323111 CTCTTCTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.10, G:0.15, T:0.59
Consensus pattern (19 bp):
TTCATTTGTGAGATTTCTT
Found at i:2324106 original size:46 final size:48
Alignment explanation
Indices: 2324039--2324135 Score: 135
Period size: 46 Copynumber: 2.1 Consensus size: 48
2324029 ACAGGACCGA
* * * *
2324039 AATGAGCCATGTAAGTCCATATCA-GT-TATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGCCCATATCATATATATATGGCATTGGAGACAAG
*
2324085 AATGAGCCATGTAAGCCCATATTATATATATATGGCATTGGAGACAAG
1 AATGAGCCATGTAAGCCCATATCATATATATATGGCATTGGAGACAAG
2324133 AAT
1 AAT
2324136 AATTCATGTA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
46 22 0.50
47 1 0.02
48 21 0.48
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (48 bp):
AATGAGCCATGTAAGCCCATATCATATATATATGGCATTGGAGACAAG
Found at i:2330534 original size:27 final size:26
Alignment explanation
Indices: 2330504--2330562 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
2330494 TATTCAGTAT
* *
2330504 CAGTACAGTCTGGGCCTTAGCCCTATA
1 CAGTACAGTCT-GGCCTAAGCCCAATA
* *
2330531 CAGTAATAGTGTGGCCTAAGCCCAATA
1 CAGT-ACAGTCTGGCCTAAGCCCAATA
2330558 CAGTA
1 CAGTA
2330563 TTAGTACAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 1 0.04
27 21 0.78
28 5 0.19
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (26 bp):
CAGTACAGTCTGGCCTAAGCCCAATA
Found at i:2330567 original size:27 final size:27
Alignment explanation
Indices: 2330516--2330567 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
2330506 GTACAGTCTG
* *
2330516 GGCCTTAGCCCTATACAGTAATAGTGT
1 GGCCTAAGCCCAATACAGTAATAGTGT
*
2330543 GGCCTAAGCCCAATACAGTATTAGT
1 GGCCTAAGCCCAATACAGTAATAGT
2330568 ACAGTGTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (27 bp):
GGCCTAAGCCCAATACAGTAATAGTGT
Found at i:2331118 original size:27 final size:27
Alignment explanation
Indices: 2330918--2331117 Score: 247
Period size: 27 Copynumber: 7.4 Consensus size: 27
2330908 GGGCATAATC
* *
2330918 GTCATTTTACCATACAGGGATATTACG
1 GTCATTTTACCCTACAGGGGTATTACG
* ** *
2330945 GTCATTTTATCCTACAGGGACATTACT
1 GTCATTTTACCCTACAGGGGTATTACG
2330972 GTCATTTTACCCTACAGGGGTATTACG
1 GTCATTTTACCCTACAGGGGTATTACG
* * * *
2330999 ATCATTTTATCCTACAGGGGCATTACA
1 GTCATTTTACCCTACAGGGGTATTACG
* *
2331026 GTCATTTTACCCTACAAGGGCATTACG
1 GTCATTTTACCCTACAGGGGTATTACG
*
2331053 GTCATTTTACCCTACAAGGGTATTACG
1 GTCATTTTACCCTACAGGGGTATTACG
* * *
2331080 GTCATTTTACCTTATAGGGGTATTATG
1 GTCATTTTACCCTACAGGGGTATTACG
*
2331107 GTTATTTTACC
1 GTCATTTTACC
2331118 TATTTTGGGG
Statistics
Matches: 151, Mismatches: 22, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 151 1.00
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGTATTACG
Found at i:2342955 original size:48 final size:48
Alignment explanation
Indices: 2342890--2343170 Score: 253
Period size: 48 Copynumber: 5.9 Consensus size: 48
2342880 TGAATTACCA
* * * * *
2342890 ATGCTATGTTCCAAACACGATCTTACACTGGCTCACATGTCGAGGCCG
1 ATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATATCGAGGCCG
* * * * * * *
2342938 ATGCCATGTCCCAAACACGGTCTTACACTAGCTCTCGTCTCAATGCCG
1 ATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATATCGAGGCCG
* * * ** * *
2342986 ATGCCATGTCCTAGACATGGTCTTACATTGGCTCTGATAAT-GTGGTCG
1 ATGCCATGTCCCAAACATGGTCTTACACTGGCTCACAT-ATCGAGGCCG
* * *
2343034 ATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATAAC-ATTGCCG
1 ATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATATCGA-GGCCG
* * * *
2343082 ATGCCATGTTCCAAACATGGTCTTACGCTGGCTCTA-ATATCGTGGCCA
1 ATGCCATGTCCCAAACATGGTCTTACACTGGCTC-ACATATCGAGGCCG
* * *
2343130 ATGCCATGTCCCAGACATGGTCTTACACTAGCGCACATATC
1 ATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATATC
2343171 ACCCAAATGT
Statistics
Matches: 186, Mismatches: 41, Indels: 12
0.78 0.17 0.05
Matches are distributed among these distances:
47 2 0.01
48 183 0.98
49 1 0.01
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (48 bp):
ATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATATCGAGGCCG
Found at i:2343081 original size:96 final size:96
Alignment explanation
Indices: 2342890--2343161 Score: 334
Period size: 96 Copynumber: 2.8 Consensus size: 96
2342880 TGAATTACCA
* * * * *
2342890 ATGCTATGTTCCAAACACGATCTTACACTGGCTC-ACATGTCGAGGCCGATGCCATGTCCCAAAC
1 ATGCCATGTTCCAAACATGGTCTTACACTGGCTCTA-ATATCGTGGCCGATGCCATGTCCCAAAC
* * **
2342954 ACGGTCTTACACTAGCTCTCGTCTCAATGCCG
65 ATGGTCTTACACTAGCTCTCATAACAATGCCG
* * * *
2342986 ATGCCATG-TCCTAGACATGGTCTTACATTGGCTCTGATAAT-GTGGTCGATGCCATGTCCCAAA
1 ATGCCATGTTCC-AAACATGGTCTTACACTGGCTCTAAT-ATCGTGGCCGATGCCATGTCCCAAA
* *
2343049 CATGGTCTTACACTGGCTCTCATAACATTGCCG
64 CATGGTCTTACACTAGCTCTCATAACAATGCCG
* * *
2343082 ATGCCATGTTCCAAACATGGTCTTACGCTGGCTCTAATATCGTGGCCAATGCCATGTCCCAGACA
1 ATGCCATGTTCCAAACATGGTCTTACACTGGCTCTAATATCGTGGCCGATGCCATGTCCCAAACA
2343147 TGGTCTTACACTAGC
66 TGGTCTTACACTAGC
2343162 GCACATATCA
Statistics
Matches: 148, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
95 5 0.03
96 139 0.94
97 4 0.03
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.28
Consensus pattern (96 bp):
ATGCCATGTTCCAAACATGGTCTTACACTGGCTCTAATATCGTGGCCGATGCCATGTCCCAAACA
TGGTCTTACACTAGCTCTCATAACAATGCCG
Found at i:2346232 original size:25 final size:24
Alignment explanation
Indices: 2346199--2346291 Score: 109
Period size: 25 Copynumber: 3.8 Consensus size: 24
2346189 GGCTCTTTGT
2346199 GAGCTTCCTGAATAATGGCTATCTG
1 GAGCTTCCTG-ATAATGGCTATCTG
*
2346224 GAGCTTCCTGAT-ATGGCTCA-CTT
1 GAGCTTCCTGATAATGGCT-ATCTG
* *
2346247 GAACTTCCTGATATATGGCTATCAG
1 GAGCTTCCTGATA-ATGGCTATCTG
2346272 GAGCTTCCTGATTAATGGCT
1 GAGCTTCCTGA-TAATGGCT
2346292 CTTCAGAGCT
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
23 19 0.33
24 4 0.07
25 33 0.57
26 2 0.03
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.33
Consensus pattern (24 bp):
GAGCTTCCTGATAATGGCTATCTG
Found at i:2346300 original size:25 final size:25
Alignment explanation
Indices: 2346156--2346306 Score: 75
Period size: 25 Copynumber: 6.0 Consensus size: 25
2346146 GAGTTTCTCC
* *
2346156 ATTATATGGCTCTTCGTGAGCTTCCCG
1 ATTA-ATGGCTCTTC-AGAGCTTCCTG
**
2346183 -TTAATTGGCTCTTTGTGAGCTTCCTG
1 ATTAA-TGGCTC-TTCAGAGCTTCCTG
* * *
2346209 AATAATGGCT-ATCTGGAGCTTCCTG
1 ATTAATGGCTCTTC-AGAGCTTCCTG
*
2346234 A-T-ATGGCTCACTT--GAACTTCCTG
1 ATTAATGGCT--CTTCAGAGCTTCCTG
*
2346257 A-TATATGGCT-ATCAGGAGCTTCCTG
1 ATTA-ATGGCTCTTCA-GAGCTTCCTG
*
2346282 ATTAATGGCTCTTCAGAGCTACCTG
1 ATTAATGGCTCTTCAGAGCTTCCTG
2346307 TTATAGGCTC
Statistics
Matches: 98, Mismatches: 12, Indels: 30
0.70 0.09 0.21
Matches are distributed among these distances:
22 1 0.01
23 17 0.17
24 2 0.02
25 43 0.44
26 30 0.31
27 5 0.05
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.36
Consensus pattern (25 bp):
ATTAATGGCTCTTCAGAGCTTCCTG
Found at i:2354373 original size:12 final size:14
Alignment explanation
Indices: 2354343--2354374 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2354333 AACAAAAGAA
2354343 AAAAATTAGAATAT
1 AAAAATTAGAATAT
2354357 AAAAATTA-AAT-T
1 AAAAATTAGAATAT
2354369 AAAAAT
1 AAAAAT
2354375 AAAAATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 3 0.17
14 8 0.44
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (14 bp):
AAAAATTAGAATAT
Found at i:2354385 original size:20 final size:18
Alignment explanation
Indices: 2354345--2354399 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 18
2354335 CAAAAGAAAA
*
2354345 AAATTAGAATATAAAAATT
1 AAATTA-AAAATAAAAATT
2354364 AAATTAAAAATAAAAATTTT
1 AAATTAAAAATAAAAA--TT
*
2354384 AAAATAAAAATAAAAA
1 AAATTAAAAATAAAAA
2354400 ATGGTTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
18 9 0.28
19 6 0.19
20 17 0.53
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (18 bp):
AAATTAAAAATAAAAATT
Found at i:2354409 original size:21 final size:19
Alignment explanation
Indices: 2354362--2354409 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 19
2354352 AATATAAAAA
*
2354362 TTAAATTAAAAATAAAAATT
1 TTAAA-TAAAAATAAAAATG
2354382 TTAAAATAAAAATAAAAAATGG
1 TT-AAATAAAAAT-AAAAAT-G
2354404 TTAAAT
1 TTAAAT
2354410 TAATAGAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 9 0.38
21 13 0.54
22 2 0.08
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (19 bp):
TTAAATAAAAATAAAAATG
Found at i:2354766 original size:31 final size:31
Alignment explanation
Indices: 2354728--2354790 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
2354718 CAGGAAAGAA
*
2354728 TTCACCTAGATTTCATCTGTCATTATCAATC
1 TTCACCTAGATTTCATCTATCATTATCAATC
*
2354759 TTCACCTAGATTTCATCTATTATTATCAATC
1 TTCACCTAGATTTCATCTATCATTATCAATC
2354790 T
1 T
2354791 AAATTATGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.27, C:0.24, G:0.05, T:0.44
Consensus pattern (31 bp):
TTCACCTAGATTTCATCTATCATTATCAATC
Found at i:2363582 original size:42 final size:42
Alignment explanation
Indices: 2363495--2363611 Score: 116
Period size: 42 Copynumber: 2.8 Consensus size: 42
2363485 AGCTCGTACA
*
2363495 ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCACATTCG
1 ATGCCAATGTCCCAGAAGTGGTCTTACATGTAATCACATTCG
* *
2363537 ATGCCACTGTCCCAGATAG-GGTCTTACATG-AACTCATATAT-G
1 ATGCCAATGTCCCAGA-AGTGGTCTTACATGTAA-TCACAT-TCG
** *
2363579 ATGCCAATGTCTGAGACA-TGGTCTTACACGTAA
1 ATGCCAATGTCCCAGA-AGTGGTCTTACATGTAA
2363612 ATCAAAAATC
Statistics
Matches: 62, Mismatches: 8, Indels: 9
0.78 0.10 0.11
Matches are distributed among these distances:
41 2 0.03
42 56 0.90
43 4 0.06
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (42 bp):
ATGCCAATGTCCCAGAAGTGGTCTTACATGTAATCACATTCG
Found at i:2364790 original size:13 final size:13
Alignment explanation
Indices: 2364772--2364796 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2364762 ACAAACGATA
2364772 AAATTTTCACACG
1 AAATTTTCACACG
2364785 AAATTTTCACAC
1 AAATTTTCACAC
2364797 ATATAAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:2373270 original size:6 final size:5
Alignment explanation
Indices: 2373242--2373334 Score: 75
Period size: 6 Copynumber: 17.6 Consensus size: 5
2373232 ATGTCTTTCG
* *
2373242 AAATA AAAT- -AATA AAATTG AAATGA AAATAA AAATCA AAAGAA AAATAA
1 AAATA AAATA AAATA AAA-TA AAAT-A AAAT-A AAAT-A AAA-TA AAAT-A
2373291 AAATA AAATA AAATA AAATA AAATAA AAATA AGAAT- AAATA AAA
1 AAATA AAATA AAATA AAATA AAAT-A AAATA A-AATA AAATA AAA
2373335 AAATAGGAGG
Statistics
Matches: 73, Mismatches: 6, Indels: 18
0.75 0.06 0.19
Matches are distributed among these distances:
3 3 0.04
4 3 0.04
5 33 0.45
6 34 0.47
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:2373335 original size:16 final size:15
Alignment explanation
Indices: 2373251--2373335 Score: 64
Period size: 16 Copynumber: 5.1 Consensus size: 15
2373241 GAAATAAAAT
*
2373251 AATAAAATTGAAATGAA
1 AATAAAA-T-AAATAAA
*
2373268 AATAAAAATCAAAAGAAA
1 AAT-AAAAT--AAATAAA
2373286 AATAAAAATAAA-ATAA
1 AAT-AAAATAAATA-AA
2373302 AATAAAATAAAATAAA
1 AATAAAAT-AAATAAA
2373318 AATAAGAATAAATAAA
1 AATAA-AATAAATAAA
2373334 AA
1 AA
2373336 AATAGGAGGA
Statistics
Matches: 59, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
15 6 0.10
16 27 0.46
17 8 0.14
18 18 0.31
ACGTcount: A:0.76, C:0.01, G:0.05, T:0.18
Consensus pattern (15 bp):
AATAAAATAAATAAA
Found at i:2378902 original size:55 final size:55
Alignment explanation
Indices: 2378826--2378935 Score: 184
Period size: 55 Copynumber: 2.0 Consensus size: 55
2378816 TGGTTTGAGG
2378826 AGTTCATACTCCTCATTCCTGCTGTCAATCTTAAAATAAGGTTTTAATTGAGTGT
1 AGTTCATACTCCTCATTCCTGCTGTCAATCTTAAAATAAGGTTTTAATTGAGTGT
* * * *
2378881 AGTTCATACTCCTCGTTCCTGCTGTTAATTTTAAAATCAGGTTTTAATTGAGTGT
1 AGTTCATACTCCTCATTCCTGCTGTCAATCTTAAAATAAGGTTTTAATTGAGTGT
2378936 TGTTTACCTT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.42
Consensus pattern (55 bp):
AGTTCATACTCCTCATTCCTGCTGTCAATCTTAAAATAAGGTTTTAATTGAGTGT
Found at i:2379388 original size:60 final size:61
Alignment explanation
Indices: 2379269--2379388 Score: 224
Period size: 60 Copynumber: 2.0 Consensus size: 61
2379259 AATCCCATGG
*
2379269 CAAGCAAAGAGCATTTATTTTGCTAACAGGGGGCGGCAAGAGTTGGTGTTGAATTTAAACA
1 CAAGCAAAGAGCATCTATTTTGCTAACAGGGGGCGGCAAGAGTTGGTGTTGAATTTAAACA
2379330 CAAGCAAAGAGCATCTATTTTGCTAACA-GGGGCGGCAAGAGTTGGTGTTGAATTTAAAC
1 CAAGCAAAGAGCATCTATTTTGCTAACAGGGGGCGGCAAGAGTTGGTGTTGAATTTAAAC
2379389 TCTAATGATG
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
60 31 0.53
61 27 0.47
ACGTcount: A:0.33, C:0.14, G:0.28, T:0.26
Consensus pattern (61 bp):
CAAGCAAAGAGCATCTATTTTGCTAACAGGGGGCGGCAAGAGTTGGTGTTGAATTTAAACA
Found at i:2379703 original size:46 final size:46
Alignment explanation
Indices: 2379647--2379737 Score: 173
Period size: 46 Copynumber: 2.0 Consensus size: 46
2379637 CGAAAGGGAC
2379647 CATGTAGTCCCAATGGGCCTACGGGCCCAATTGGATAAGTTGTTTT
1 CATGTAGTCCCAATGGGCCTACGGGCCCAATTGGATAAGTTGTTTT
*
2379693 CATGTGGTCCCAATGGGCCTACGGGCCCAATTGGATAAGTTGTTT
1 CATGTAGTCCCAATGGGCCTACGGGCCCAATTGGATAAGTTGTTT
2379738 GATTGTGTAG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.21, C:0.22, G:0.27, T:0.30
Consensus pattern (46 bp):
CATGTAGTCCCAATGGGCCTACGGGCCCAATTGGATAAGTTGTTTT
Found at i:2379925 original size:27 final size:27
Alignment explanation
Indices: 2379903--2380206 Score: 344
Period size: 27 Copynumber: 11.3 Consensus size: 27
2379893 CCAAATTATT
*
2379903 AAAATACCCCTGGTTTGTAAAATTACT
1 AAAATACCCCTGGTTTGTAAAATTACC
* *
2379930 AAAATACCCTTGGTTTATAAAATTACC
1 AAAATACCCCTGGTTTGTAAAATTACC
2379957 AAAATACCCCTGGTTTG-AATAATTACC
1 AAAATACCCCTGGTTTGTAA-AATTACC
*
2379984 AAAATACCCCTGGTTTGTAAAATTATC
1 AAAATACCCCTGGTTTGTAAAATTACC
*
2380011 AAAATACCCCTAGTTTGTAAAATTACC
1 AAAATACCCCTGGTTTGTAAAATTACC
*
2380038 AAAATACCCCTAGTTTGTAAAATTACC
1 AAAATACCCCTGGTTTGTAAAATTACC
*
2380065 AAAATACCCCTGATTTGTAAAATTACC
1 AAAATACCCCTGGTTTGTAAAATTACC
* * * * **
2380092 GAAATACCCCCGATTTGCAAAATTATT
1 AAAATACCCCTGGTTTGTAAAATTACC
* * *
2380119 GAAATACCTCC-GATTTGTAAAATTACT
1 AAAATACC-CCTGGTTTGTAAAATTACC
* ** *
2380146 GAAATACCCC-AATTTGTAAAATTACT
1 AAAATACCCCTGGTTTGTAAAATTACC
** **
2380172 AAAATACCTTTGACTTGTAAAATTACC
1 AAAATACCCCTGGTTTGTAAAATTACC
*
2380199 AAAGTACC
1 AAAATACC
2380207 ATCGATTTAC
Statistics
Matches: 248, Mismatches: 25, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
26 26 0.10
27 218 0.88
28 4 0.02
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.31
Consensus pattern (27 bp):
AAAATACCCCTGGTTTGTAAAATTACC
Found at i:2380220 original size:27 final size:27
Alignment explanation
Indices: 2380190--2380255 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
2380180 TTTGACTTGT
2380190 AAAATTACCAAAGTACCATCGATTTAC
1 AAAATTACCAAAGTACCATCGATTTAC
*** * *
2380217 AAAATTACCATTTTTCCCTCGATTTAC
1 AAAATTACCAAAGTACCATCGATTTAC
*
2380244 AAAATTATCAAA
1 AAAATTACCAAA
2380256 ACAACCCTGT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.42, C:0.21, G:0.05, T:0.32
Consensus pattern (27 bp):
AAAATTACCAAAGTACCATCGATTTAC
Found at i:2380240 original size:134 final size:135
Alignment explanation
Indices: 2379903--2380251 Score: 334
Period size: 135 Copynumber: 2.6 Consensus size: 135
2379893 CCAAATTATT
* * * * * * * *
2379903 AAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTGGTTTATAAAATTACCAAAATACCCCT
1 AAAATACCCCTAGCTTGTAAAATTACCAAAATACCCCTGATTTACAAAATTACCGAAATACCCCC
* * *** * *
2379968 GGTTTGA-ATAATTACCAAAATACC-CCTGGTTTGTAAAATTATCAAAATACCCCTAGTTTGTAA
66 GATTT-ACAAAATTATTGAAATACCTCC-GATTTGTAAAATTATCAAAATACCCCTAATTTGTAA
2380031 AATTACC
129 AATTACC
* **
2380038 AAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTGATTTGTAAAATTACCGAAATACCCCC
1 AAAATACCCCTAGCTTGTAAAATTACCAAAATACCCCTGATTTACAAAATTACCGAAATACCCCC
* *
2380103 GATTTGCAAAATTATTGAAATACCTCCGATTTGTAAAATTA-CTGAAATACCCC-AATTTGTAAA
66 GATTTACAAAATTATTGAAATACCTCCGATTTGTAAAATTATC-AAAATACCCCTAATTTGTAAA
*
2380166 ATTACT
130 ATTACC
* * * * ** *
2380172 AAAATA-CCTTTGACTTGTAAAATTACCAAAGTA-CCATCGATTTACAAAATTACC-ATTTTTCC
1 AAAATACCCCTAG-CTTGTAAAATTACCAAAATACCCCT-GATTTACAAAATTACCGA-AATACC
*
2380234 CTCGATTTACAAAATTAT
63 CCCGATTTACAAAATTAT
2380252 CAAAACAACC
Statistics
Matches: 179, Mismatches: 29, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
133 8 0.04
134 72 0.40
135 97 0.54
136 2 0.01
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (135 bp):
AAAATACCCCTAGCTTGTAAAATTACCAAAATACCCCTGATTTACAAAATTACCGAAATACCCCC
GATTTACAAAATTATTGAAATACCTCCGATTTGTAAAATTATCAAAATACCCCTAATTTGTAAAA
TTACC
Found at i:2380276 original size:27 final size:27
Alignment explanation
Indices: 2380246--2380504 Score: 260
Period size: 27 Copynumber: 9.7 Consensus size: 27
2380236 CGATTTACAA
* * *
2380246 AATTATCAAAACAACCCTGTAAGGTAG
1 AATTATCGAAATAACCCTGTAGGGTAG
* ** *
2380273 AATTACCGAAATAAAACTGTATGGTAG
1 AATTATCGAAATAACCCTGTAGGGTAG
*
2380300 AATTATTGAAAT-ACCTCTGTAGGGTAG
1 AATTATCGAAATAACC-CTGTAGGGTAG
* *
2380327 AATTATCGAAATACCCCTCTAGGGTAG
1 AATTATCGAAATAACCCTGTAGGGTAG
*
2380354 AATTA-CTGAAAT-ACCTCTGTAAGGTAG
1 AATTATC-GAAATAACC-CTGTAGGGTAG
*
2380381 AATTATCGAAATACCCCTGTAGGGTAG
1 AATTATCGAAATAACCCTGTAGGGTAG
* * *
2380408 AATTATCGAGATACCCCTCTAGGGTAG
1 AATTATCGAAATAACCCTGTAGGGTAG
* * *
2380435 AATTA-CTAAAATACCCCTGTAAGGTAG
1 AATTATC-GAAATAACCCTGTAGGGTAG
*
2380462 AATTATCGAAAT-ACCCTCTAGGGTAG
1 AATTATCGAAATAACCCTGTAGGGTAG
*
2380488 AATTATCGAGAT-ACCCT
1 AATTATCGAAATAACCCT
2380505 CTTGGGGTAA
Statistics
Matches: 194, Mismatches: 30, Indels: 17
0.80 0.12 0.07
Matches are distributed among these distances:
26 32 0.16
27 156 0.80
28 6 0.03
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.27
Consensus pattern (27 bp):
AATTATCGAAATAACCCTGTAGGGTAG
Found at i:2380320 original size:54 final size:54
Alignment explanation
Indices: 2380262--2380503 Score: 290
Period size: 54 Copynumber: 4.5 Consensus size: 54
2380252 CAAAACAACC
* *** * *
2380262 CTGTAAGGTAGAATTACCGAAATAAAACTGTATGGTAGAATTATTGAAATACCT
1 CTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTATCGAAATACCT
* *
2380316 CTGTAGGGTAGAATTATCGAAATACCCCTCTAGGGTAGAATTA-CTGAAATACCT
1 CTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTATC-GAAATACCT
* * * *
2380370 CTGTAAGGTAGAATTATCGAAATACCCCTGTAGGGTAGAATTATCGAGATACCC
1 CTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTATCGAAATACCT
* ** *
2380424 CTCTAGGGTAGAATTACTAAAATACCCCTGTAAGGTAGAATTATCGAAATACC-
1 CTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTATCGAAATACCT
* * *
2380477 CTCTAGGGTAGAATTATCGAGATACCC
1 CTGTAGGGTAGAATTACCGAAATACCC
2380504 TCTTGGGGTA
Statistics
Matches: 163, Mismatches: 23, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
53 23 0.14
54 139 0.85
55 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (54 bp):
CTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTATCGAAATACCT
Found at i:2380358 original size:81 final size:80
Alignment explanation
Indices: 2380268--2380521 Score: 366
Period size: 81 Copynumber: 3.1 Consensus size: 80
2380258 AACCCTGTAA
* ** * *
2380268 GGTAGAATTACCGAAATAAAACTGTATGGTAGAATTATTGAAATACCTCTGTAGGGTAGAATTAT
1 GGTAGAATTACTGAAATACCACTGTAAGGTAGAATTATCGAAATACC-CTGTAGGGTAGAATTAT
*
2380333 CGAAATACCCCTCTAG
65 CGAGATACCCCTCTAG
*
2380349 GGTAGAATTACTGAAATACCTCTGTAAGGTAGAATTATCGAAATACCCCTGTAGGGTAGAATTAT
1 GGTAGAATTACTGAAATACCACTGTAAGGTAGAATTATCGAAATA-CCCTGTAGGGTAGAATTAT
2380414 CGAGATACCCCTCTAG
65 CGAGATACCCCTCTAG
* * *
2380430 GGTAGAATTACTAAAATACCCCTGTAAGGTAGAATTATCGAAATACCCTCTAGGGTAGAATTATC
1 GGTAGAATTACTGAAATACCACTGTAAGGTAGAATTATCGAAATACCCTGTAGGGTAGAATTATC
*
2380495 GAGATA-CCCTCTTGG
66 GAGATACCCCTC-TAG
*
2380510 GGTAAAATTACT
1 GGTAGAATTACT
2380522 ATTTTGCTCC
Statistics
Matches: 159, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
79 5 0.03
80 38 0.24
81 114 0.72
82 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (80 bp):
GGTAGAATTACTGAAATACCACTGTAAGGTAGAATTATCGAAATACCCTGTAGGGTAGAATTATC
GAGATACCCCTCTAG
Found at i:2390742 original size:27 final size:26
Alignment explanation
Indices: 2390697--2390755 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 26
2390687 TTTGCTACAT
*
2390697 TATCTGTTCTGGTGGCTCTGTCACAA
1 TATCTGTTCTGGTGACTCTGTCACAA
2390723 TATCTGTATCTGGTGACTCTGTCACAA
1 TATCTGT-TCTGGTGACTCTGTCACAA
2390750 TATCTG
1 TATCTG
2390756 ATAACTGAGC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 7 0.23
27 24 0.77
ACGTcount: A:0.19, C:0.22, G:0.20, T:0.39
Consensus pattern (26 bp):
TATCTGTTCTGGTGACTCTGTCACAA
Found at i:2390955 original size:6 final size:6
Alignment explanation
Indices: 2390924--2391042 Score: 84
Period size: 6 Copynumber: 19.3 Consensus size: 6
2390914 CCTAATACTA
* * *
2390924 ATTCTG ATTTTG ATTCTG -TTACCTG ATACTG ATTCTG ATTTTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* * * *
2390973 -TTACCTG ATACTG ATTCTG ATTCTG ATTTTG -TCACCTA ATTCTG ATTCTG
1 ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG
2391023 ATTCTG ATTCT- AGTTCTG AT
1 ATTCTG ATTCTG A-TTCTG AT
2391043 AATGTTTCTT
Statistics
Matches: 88, Mismatches: 14, Indels: 22
0.71 0.11 0.18
Matches are distributed among these distances:
5 6 0.07
6 71 0.81
7 8 0.09
8 3 0.03
ACGTcount: A:0.19, C:0.17, G:0.15, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:2390956 original size:19 final size:19
Alignment explanation
Indices: 2390934--2390991 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
2390924 ATTCTGATTT
2390934 TGATTCTGTTACCTGATAC
1 TGATTCTGTTACCTGATAC
*
2390953 TGATTCTG--A--T--T-T
1 TGATTCTGTTACCTGATAC
2390965 TGATTCTGTTACCTGATAC
1 TGATTCTGTTACCTGATAC
2390984 TGATTCTG
1 TGATTCTG
2390992 ATTCTGATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
12 8 0.27
13 1 0.03
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 16 0.53
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.47
Consensus pattern (19 bp):
TGATTCTGTTACCTGATAC
Found at i:2390987 original size:37 final size:31
Alignment explanation
Indices: 2390900--2391033 Score: 196
Period size: 31 Copynumber: 4.3 Consensus size: 31
2390890 ACATTTTGAT
* *
2390900 TTTTGATTCTGTTACCTAATACTAATTCTGA
1 TTTTGATTCTGTTACCTGATACTGATTCTGA
2390931 TTTTGATTCTGTTACCTGATACTGATTCTGA
1 TTTTGATTCTGTTACCTGATACTGATTCTGA
2390962 TTTTGATTCTGTTACCTGATACTGATTCTGA
1 TTTTGATTCTGTTACCTGATACTGATTCTGA
* * * * *
2390993 TTCTGATTTTGTCACCTAATTCTGATTCTGA
1 TTTTGATTCTGTTACCTGATACTGATTCTGA
*
2391024 TTCTGATTCT
1 TTTTGATTCT
2391034 AGTTCTGATA
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 95 1.00
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.49
Consensus pattern (31 bp):
TTTTGATTCTGTTACCTGATACTGATTCTGA
Found at i:2395461 original size:10 final size:11
Alignment explanation
Indices: 2395435--2395460 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2395425 GTTTTGTCCC
2395435 TTTTTGGCTCA
1 TTTTTGGCTCA
2395446 TTTTTGGCTCA
1 TTTTTGGCTCA
2395457 TTTT
1 TTTT
2395461 GACTCCGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.15, T:0.62
Consensus pattern (11 bp):
TTTTTGGCTCA
Found at i:2397894 original size:22 final size:23
Alignment explanation
Indices: 2397869--2397911 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
2397859 TTGTCCCTGG
2397869 CACGCCCGTGGTTTTC-TATCCC
1 CACGCCCGTGGTTTTCGTATCCC
*
2397891 CACGCCCGTGTTTTTCGTATC
1 CACGCCCGTGGTTTTCGTATC
2397912 AAGTTCACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.09, C:0.37, G:0.19, T:0.35
Consensus pattern (23 bp):
CACGCCCGTGGTTTTCGTATCCC
Found at i:2400452 original size:28 final size:27
Alignment explanation
Indices: 2400408--2400516 Score: 94
Period size: 28 Copynumber: 3.9 Consensus size: 27
2400398 CTGCACAATC
* * *
2400408 GATGTCTT-GCACGCTAAGTGCTATACCG
1 GATGT-TTCGCACACTAAGTGCCAT-CCA
*
2400436 GATGTTTCGCACACTAAGTGCCATCCTC
1 GATGTTTCGCACACTAAGTGCCATCC-A
** *
2400464 GATACTTCGCACACTAAGTGCCATTTCA
1 GATGTTTCGCACACTAAGTGCCA-TCCA
* *
2400492 GATGTTTCACACACTAAGTGTCATC
1 GATGTTTCGCACACTAAGTGCCATC
2400517 ATCAATACTT
Statistics
Matches: 66, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
27 5 0.08
28 59 0.89
29 2 0.03
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (27 bp):
GATGTTTCGCACACTAAGTGCCATCCA
Found at i:2400496 original size:56 final size:55
Alignment explanation
Indices: 2400436--2400595 Score: 200
Period size: 54 Copynumber: 2.9 Consensus size: 55
2400426 TGCTATACCG
*
2400436 GATGTTTCGCACACTAAGTGCCATCCTCGATACTTCGCACACTAAGTGCCATTTC
1 GATGTTTCGCACACTAAGTGCCATCCTCAATACTTCGCACACTAAGTGCCATTTC
* * * ** *
2400491 AGATGTTTCACACACTAAGTGTCATCATCAATACTTCATACACT--GTGTCATTTC
1 -GATGTTTCGCACACTAAGTGCCATCCTCAATACTTCGCACACTAAGTGCCATTTC
*
2400545 GAATGTCTT-GCACACTAAGTGCCATCCTCAATACTTCGCAAACTAAGTGCC
1 G-ATGT-TTCGCACACTAAGTGCCATCCTCAATACTTCGCACACTAAGTGCC
2400596 GTTCGTTTGG
Statistics
Matches: 86, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
53 1 0.01
54 42 0.49
55 2 0.02
56 41 0.48
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (55 bp):
GATGTTTCGCACACTAAGTGCCATCCTCAATACTTCGCACACTAAGTGCCATTTC
Found at i:2400528 original size:28 final size:28
Alignment explanation
Indices: 2400441--2400595 Score: 131
Period size: 28 Copynumber: 5.6 Consensus size: 28
2400431 TACCGGATGT
*
2400441 TTCGCACACTAAGTGCCATCCTCGATAC
1 TTCGCACACTAAGTGCCATCCTCAATAC
* **
2400469 TTCGCACACTAAGTGCCAT-TTCAGATGT
1 TTCGCACACTAAGTGCCATCCTCA-ATAC
* * *
2400497 TTCACACACTAAGTGTCATCATCAATAC
1 TTCGCACACTAAGTGCCATCCTCAATAC
** * * *
2400525 TTCATACACT--GTGTCAT-TTCGAATGTC
1 TTCGCACACTAAGTGCCATCCTC-AAT-AC
2400552 TT-GCACACTAAGTGCCATCCTCAATAC
1 TTCGCACACTAAGTGCCATCCTCAATAC
*
2400579 TTCGCAAACTAAGTGCC
1 TTCGCACACTAAGTGCC
2400596 GTTCGTTTGG
Statistics
Matches: 101, Mismatches: 18, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
25 2 0.02
26 15 0.15
27 8 0.08
28 71 0.70
29 5 0.05
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.30
Consensus pattern (28 bp):
TTCGCACACTAAGTGCCATCCTCAATAC
Found at i:2409838 original size:40 final size:40
Alignment explanation
Indices: 2409783--2409862 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
2409773 TGAATGAGTA
* *
2409783 TGAGACTGTCGCCTTGACAAAGGAGTGCAGTGCATTCCTG
1 TGAGACTATCGCCTTGACAAAGGAATGCAGTGCATTCCTG
* *
2409823 TGAGACTATCGCCTTGACAAAGGAATGTAGTGCGTTCCTG
1 TGAGACTATCGCCTTGACAAAGGAATGCAGTGCATTCCTG
2409863 CAGAACAAGC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (40 bp):
TGAGACTATCGCCTTGACAAAGGAATGCAGTGCATTCCTG
Found at i:2411634 original size:28 final size:28
Alignment explanation
Indices: 2411594--2411651 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
2411584 TTGTTGTTAG
2411594 AGAAAGATGCAGAGTTCGATTTTAACAA
1 AGAAAGATGCAGAGTTCGATTTTAACAA
2411622 AGAAAGATGCAGAGTTCGATTTTAACAA
1 AGAAAGATGCAGAGTTCGATTTTAACAA
2411650 AG
1 AG
2411652 CATGTTTAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.43, C:0.10, G:0.22, T:0.24
Consensus pattern (28 bp):
AGAAAGATGCAGAGTTCGATTTTAACAA
Found at i:2421575 original size:18 final size:18
Alignment explanation
Indices: 2421552--2421588 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
2421542 TATGACACTA
2421552 ATTTTGTAAAAACTTTGT
1 ATTTTGTAAAAACTTTGT
*
2421570 ATTTTGTAAAAATTTTGT
1 ATTTTGTAAAAACTTTGT
2421588 A
1 A
2421589 AAAAGTGTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.03, G:0.11, T:0.51
Consensus pattern (18 bp):
ATTTTGTAAAAACTTTGT
Found at i:2423853 original size:27 final size:28
Alignment explanation
Indices: 2423822--2423876 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
2423812 GAATGTTTCC
*
2423822 ATTGATGA-ATATGTATGAAT-TTTGATG
1 ATTGATGATAGAT-TATGAATATTTGATG
2423849 ATTGATGATAGATTATGAATATTTGATG
1 ATTGATGATAGATTATGAATATTTGATG
2423877 TTAGTTAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 15 0.60
28 10 0.40
ACGTcount: A:0.35, C:0.00, G:0.22, T:0.44
Consensus pattern (28 bp):
ATTGATGATAGATTATGAATATTTGATG
Found at i:2424506 original size:28 final size:28
Alignment explanation
Indices: 2424461--2424593 Score: 160
Period size: 28 Copynumber: 4.8 Consensus size: 28
2424451 GGCTATGTAC
** * *
2424461 GGCACTTAGCATGTGAGACGTTGATTAT
1 GGCACTTAGTGTGCGAGACATTGATTAT
*
2424489 GGCACTTAGTGTGCGAGATATTGATTAT
1 GGCACTTAGTGTGCGAGACATTGATTAT
* * *
2424517 GGCACTTAGTGTGTGAGGCATTGATTGT
1 GGCACTTAGTGTGCGAGACATTGATTAT
2424545 GGCACTTAGTGTGCGATG-CATTGATTAT
1 GGCACTTAGTGTGCGA-GACATTGATTAT
* *
2424573 GGAACTTAGTGTACGAGACAT
1 GGCACTTAGTGTGCGAGACAT
2424594 CAAGTGTGCG
Statistics
Matches: 90, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
27 1 0.01
28 88 0.98
29 1 0.01
ACGTcount: A:0.24, C:0.13, G:0.30, T:0.33
Consensus pattern (28 bp):
GGCACTTAGTGTGCGAGACATTGATTAT
Found at i:2440534 original size:39 final size:39
Alignment explanation
Indices: 2440437--2440672 Score: 253
Period size: 40 Copynumber: 5.9 Consensus size: 39
2440427 AGCCCGGTTA
* * *
2440437 TAGTAACTCGCACAAATGCCTTTGGGACTTAACCCGGATT
1 TAGTAACTCGCACAAATGCCTTCGGG-CTTAGCCCGGAAT
* *
2440477 TAGTGACTCGCACCAATGCCTTCGGGCTTAGCCCGGAAT
1 TAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGAAT
* * *
2440516 TAGTAACTCACACAAATGCCTTCGGATCTTAGTCC-GAATT
1 TAGTAACTCGCACAAATGCCTTCGG-GCTTAGCCCGGAA-T
* *
2440556 TAGTGACTCGCACCAATGCCTTCGGGCTTAGCCCGGAAT
1 TAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGAAT
* * *
2440595 TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCAG-AT
1 TAGTAACTCGCACAAATGCCTTCGG-GCTTAGCCCGGAAT
* *
2440634 ATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 -TAGTAAC-TCGCACAAATGCCTTCGGG-CTTAGCCCGGA
2440673 CATCATTCGA
Statistics
Matches: 163, Mismatches: 25, Indels: 15
0.80 0.12 0.07
Matches are distributed among these distances:
39 69 0.42
40 86 0.53
41 8 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (39 bp):
TAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGAAT
Found at i:2440626 original size:79 final size:79
Alignment explanation
Indices: 2440437--2440672 Score: 334
Period size: 79 Copynumber: 3.0 Consensus size: 79
2440427 AGCCCGGTTA
* ** *
2440437 TAGTAACTCGCACAAATGCCTTTGGGA-CTTAACCCGGATTTAGTGACTCGCACCAATGCCTTCG
1 TAGTAACTCGCACAAATGCC-TTCGGATCTTAGTCCGAATTTAGTGACTCGCACCAATGCCTTCG
2440501 GGCTTAGCCCGGAAT
65 GGCTTAGCCCGGAAT
*
2440516 TAGTAACTCACACAAATGCCTTCGGATCTTAGTCCGAATTTAGTGACTCGCACCAATGCCTTCGG
1 TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGAATTTAGTGACTCGCACCAATGCCTTCGG
2440581 GCTTAGCCCGGAAT
66 GCTTAGCCCGGAAT
* * * *
2440595 TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCC-AGATATAGTCACTTAGCA-CAAAGCCTTC
1 TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGA-ATTTAGTGAC-TCGCACCAATGCCTTC
2440658 GGGACTTAGCCCGGA
64 GGG-CTTAGCCCGGA
2440673 CATCATTCGA
Statistics
Matches: 143, Mismatches: 10, Indels: 7
0.89 0.06 0.04
Matches are distributed among these distances:
78 6 0.04
79 122 0.85
80 15 0.10
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGAATTTAGTGACTCGCACCAATGCCTTCGG
GCTTAGCCCGGAAT
Done.