Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 80 of 198
Found at i:25278881 original size:19 final size:20
Alignment explanation
Indices: 25278849--25278886 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
25278839 CAAGCTGACT
25278849 TTAGCTCAATTTCAGCTCCC
1 TTAGCTCAATTTCAGCTCCC
25278869 TTAGCTC-ATTTCAGCTCC
1 TTAGCTCAATTTCAGCTCC
25278887 AATCAGCTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.18, C:0.34, G:0.11, T:0.37
Consensus pattern (20 bp):
TTAGCTCAATTTCAGCTCCC
Found at i:25278894 original size:20 final size:19
Alignment explanation
Indices: 25278851--25278896 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
25278841 AGCTGACTTT
* *
25278851 AGCTCAATTTCAGCTCCCTT
1 AGCTC-ATTTCAGCTCCATC
25278871 AGCTCATTTCAGCTCCAATC
1 AGCTCATTTCAGCTCC-ATC
25278891 AGCTCA
1 AGCTCA
25278897 CTTGAGCTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.24, C:0.35, G:0.11, T:0.30
Consensus pattern (19 bp):
AGCTCATTTCAGCTCCATC
Found at i:25280827 original size:11 final size:12
Alignment explanation
Indices: 25280797--25280830 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
25280787 GAAGTTTCGT
25280797 TTTTTTTTCAAA
1 TTTTTTTTCAAA
*
25280809 TTTTTTTT-GAA
1 TTTTTTTTCAAA
25280820 TTTTTTTTCAA
1 TTTTTTTTCAA
25280831 TACTTCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.21, C:0.06, G:0.03, T:0.71
Consensus pattern (12 bp):
TTTTTTTTCAAA
Found at i:25284802 original size:24 final size:23
Alignment explanation
Indices: 25284750--25284810 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 23
25284740 TATAATGTTT
25284750 TCCTTTAAATGATG--TAACAAC
1 TCCTTTAAATGATGTATAACAAC
* *
25284771 TCCATTAAATGATGTATAACACTC
1 TCCTTTAAATGATGTATAACA-AC
*
25284795 TCCTTTAATTGATGTA
1 TCCTTTAAATGATGTA
25284811 ACAGCCCCTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 13 0.39
23 5 0.15
24 15 0.45
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (23 bp):
TCCTTTAAATGATGTATAACAAC
Found at i:25284929 original size:11 final size:11
Alignment explanation
Indices: 25284913--25284944 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
25284903 ACATACAAAC
25284913 AAACACATTAA
1 AAACACATTAA
25284924 AAACACATT--
1 AAACACATTAA
25284933 AAACACATTAA
1 AAACACATTAA
25284944 A
1 A
25284945 CACATTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 9 0.47
11 10 0.53
ACGTcount: A:0.62, C:0.19, G:0.00, T:0.19
Consensus pattern (11 bp):
AAACACATTAA
Found at i:25284938 original size:9 final size:9
Alignment explanation
Indices: 25284913--25284950 Score: 58
Period size: 9 Copynumber: 4.0 Consensus size: 9
25284903 ACATACAAAC
25284913 AAACACATT
1 AAACACATT
25284922 AAAAACACATT
1 --AAACACATT
25284933 AAACACATT
1 AAACACATT
25284942 AAACACATT
1 AAACACATT
25284951 TTAACACATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 18 0.67
11 9 0.33
ACGTcount: A:0.58, C:0.21, G:0.00, T:0.21
Consensus pattern (9 bp):
AAACACATT
Found at i:25284954 original size:11 final size:10
Alignment explanation
Indices: 25284913--25284959 Score: 53
Period size: 9 Copynumber: 4.8 Consensus size: 10
25284903 ACATACAAAC
*
25284913 AAACACATTAA
1 AAACACATT-T
25284924 AAACACA-TT
1 AAACACATTT
25284933 AAACACA-TT
1 AAACACATTT
25284942 AAACACATTT
1 AAACACATTT
*
25284952 TAACACAT
1 AAACACAT
25284960 ATTATACTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
9 16 0.48
10 10 0.30
11 7 0.21
ACGTcount: A:0.55, C:0.21, G:0.00, T:0.23
Consensus pattern (10 bp):
AAACACATTT
Found at i:25285081 original size:19 final size:19
Alignment explanation
Indices: 25285054--25285090 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
25285044 TTATTCCAAC
25285054 AACTAAATTAACTAAGATA
1 AACTAAATTAACTAAGATA
*
25285073 AACTTAATTAACTAAGAT
1 AACTAAATTAACTAAGAT
25285091 GAGCAATTTA
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:0.54, C:0.11, G:0.05, T:0.30
Consensus pattern (19 bp):
AACTAAATTAACTAAGATA
Found at i:25285111 original size:54 final size:54
Alignment explanation
Indices: 25285044--25285170 Score: 191
Period size: 54 Copynumber: 2.4 Consensus size: 54
25285034 CAATAATAAA
* * *
25285044 TTATTCCAACAACTAAATTAACTAAGATAAACTTAATTAACTAAGATGAGCAAT
1 TTATTCCAGCAACTAAATTAACTAAGATAAACTCAATTAACTAAAATGAGCAAT
* * *
25285098 TTATTCCAGCAACTTAATTAACTAAGATGAACTCAATTAACTAAAATGAGTAAT
1 TTATTCCAGCAACTAAATTAACTAAGATAAACTCAATTAACTAAAATGAGCAAT
*
25285152 TTATTCTAGCAACTAAATT
1 TTATTCCAGCAACTAAATT
25285171 CCACCAAATT
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 65 1.00
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.32
Consensus pattern (54 bp):
TTATTCCAGCAACTAAATTAACTAAGATAAACTCAATTAACTAAAATGAGCAAT
Found at i:25285135 original size:19 final size:19
Alignment explanation
Indices: 25285108--25285146 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
25285098 TTATTCCAGC
* *
25285108 AACTTAATTAACTAAGATG
1 AACTCAATTAACTAAAATG
25285127 AACTCAATTAACTAAAATG
1 AACTCAATTAACTAAAATG
25285146 A
1 A
25285147 GTAATTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.51, C:0.13, G:0.08, T:0.28
Consensus pattern (19 bp):
AACTCAATTAACTAAAATG
Found at i:25296026 original size:35 final size:35
Alignment explanation
Indices: 25295977--25296058 Score: 121
Period size: 35 Copynumber: 2.3 Consensus size: 35
25295967 ATTCACTTAA
*
25295977 TTAAGCATGCCATTATTCTAATT-TAGACTTGTATG
1 TTAAGCATGCCATTATTCTAATTCTA-ACTTGCATG
* *
25296012 TTAAGCATGTCATTATTCTAATTCTAATTTGCATG
1 TTAAGCATGCCATTATTCTAATTCTAACTTGCATG
25296047 TTAAGCATGCCA
1 TTAAGCATGCCA
25296059 CTGTGTTAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
35 40 0.95
36 2 0.05
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.41
Consensus pattern (35 bp):
TTAAGCATGCCATTATTCTAATTCTAACTTGCATG
Found at i:25302624 original size:18 final size:17
Alignment explanation
Indices: 25302603--25302647 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
25302593 GAGTGACGAG
25302603 AGAAAAAGAAACTGAAAA
1 AGAAAAA-AAACTGAAAA
*
25302621 AGAAACAAAAATTGAAAA
1 AGAAA-AAAAACTGAAAA
25302639 AGAGAAAAA
1 AGA-AAAAA
25302648 GATTGGAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.73, C:0.04, G:0.16, T:0.07
Consensus pattern (17 bp):
AGAAAAAAAACTGAAAA
Found at i:25302652 original size:18 final size:18
Alignment explanation
Indices: 25302601--25302652 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
25302591 AAGAGTGACG
*
25302601 AGAGAAAAAGAAACTGAAAA
1 AGAGAAAAAG--ATTGAAAA
*
25302621 AGA-AACAAAAATTGAAAA
1 AGAGAA-AAAGATTGAAAA
25302639 AGAGAAAAAGATTG
1 AGAGAAAAAGATTG
25302653 GAGAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
18 17 0.63
19 4 0.15
20 6 0.22
ACGTcount: A:0.67, C:0.04, G:0.19, T:0.10
Consensus pattern (18 bp):
AGAGAAAAAGATTGAAAA
Found at i:25311243 original size:66 final size:66
Alignment explanation
Indices: 25311157--25311289 Score: 212
Period size: 66 Copynumber: 2.0 Consensus size: 66
25311147 CAGTAAATGG
* *
25311157 AAATAGTGTTCTAATCTTTCAAATTACCATTGTGCTGGTATCAATCAATATCGTTAAATTCCACA
1 AAATAGTGTTCCAATATTTCAAATTACCATTGTGCTGGTATCAATCAATATCGTTAAATTCCACA
25311222 T
66 T
* * * *
25311223 AAATAGTGTTCCAATATTTCAAATTACCATTGTTCTGGTATCCATGAATATCGTTAAATTTCACA
1 AAATAGTGTTCCAATATTTCAAATTACCATTGTGCTGGTATCAATCAATATCGTTAAATTCCACA
25311288 T
66 T
25311289 A
1 A
25311290 CTTTACGAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (66 bp):
AAATAGTGTTCCAATATTTCAAATTACCATTGTGCTGGTATCAATCAATATCGTTAAATTCCACA
T
Found at i:25312515 original size:21 final size:21
Alignment explanation
Indices: 25312489--25312528 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
25312479 AACATTACGA
25312489 TAATTAGGATAAAATCTTTTC
1 TAATTAGGATAAAATCTTTTC
*
25312510 TAATTAGGATACAATCTTT
1 TAATTAGGATAAAATCTTT
25312529 GATTCTAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (21 bp):
TAATTAGGATAAAATCTTTTC
Found at i:25314863 original size:39 final size:39
Alignment explanation
Indices: 25314807--25315151 Score: 503
Period size: 39 Copynumber: 8.8 Consensus size: 39
25314797 TTTACATGGG
* * * * *
25314807 AATCACATTAACTTTTAAGCATATATGACATTACAT-GTAT
1 AATCACA-TAACATTCAAGCATATATCACAATAC-TCATAT
* * *
25314847 AATCACATAACATTTAAGCATATACCACAATACACATAT
1 AATCACATAACATTCAAGCATATATCACAATACTCATAT
* * * *
25314886 AATCACATAACGTTTAAGCATATACCACAATACACATAT
1 AATCACATAACATTCAAGCATATATCACAATACTCATAT
*
25314925 AATCACATAACCTTCAAGCATATATCACAATACTCATAT
1 AATCACATAACATTCAAGCATATATCACAATACTCATAT
25314964 AATCACATAACATTCAAGCATATATCACAATACTCATAT
1 AATCACATAACATTCAAGCATATATCACAATACTCATAT
* * *
25315003 AATCACATATCATTCAAGCATATAACACAATACTAATAT
1 AATCACATAACATTCAAGCATATATCACAATACTCATAT
*
25315042 AATCACATAAGATTCAAGCATATATCACAATACTCATAT
1 AATCACATAACATTCAAGCATATATCACAATACTCATAT
25315081 AATCACATAACATTCAAGCATATATCACAATACTCATAT
1 AATCACATAACATTCAAGCATATATCACAATACTCATAT
*
25315120 AATCACATAACAATCAAGCATATATCACAATA
1 AATCACATAACATTCAAGCATATATCACAATA
25315152 ATCAAAAACA
Statistics
Matches: 283, Mismatches: 21, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
39 276 0.98
40 7 0.02
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (39 bp):
AATCACATAACATTCAAGCATATATCACAATACTCATAT
Found at i:25316930 original size:20 final size:20
Alignment explanation
Indices: 25316887--25316943 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
25316877 AATCTAATAA
* * *
25316887 TGAGCTCAAG-GAGTTGAAT
1 TGAGCTCGAGTGAGCTGACT
*
25316906 TGAGCTCGTGTGAGCTGACT
1 TGAGCTCGAGTGAGCTGACT
25316926 TGAGCTCGAGTGAGCTGA
1 TGAGCTCGAGTGAGCTGA
25316944 ACCGCATGGA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 8 0.25
20 24 0.75
ACGTcount: A:0.23, C:0.16, G:0.35, T:0.26
Consensus pattern (20 bp):
TGAGCTCGAGTGAGCTGACT
Found at i:25322230 original size:39 final size:39
Alignment explanation
Indices: 25322193--25322639 Score: 639
Period size: 39 Copynumber: 11.5 Consensus size: 39
25322183 CAATTTTAAT
* * *
25322193 CATATATCACATTACAT-GTATAAT-AGCATAACATTTAAG
1 CATATATCACAATAC-TCATATAATCA-CATAACATTCAAG
** * *
25322232 CATATATCACAATACAAATATAATCACATAATATTCAAA
1 CATATATCACAATACTCATATAATCACATAACATTCAAG
* *
25322271 CATATATCACTATACTAATATAATCACATAACATTCAAG
1 CATATATCACAATACTCATATAATCACATAACATTCAAG
* * *
25322310 CATATATCACAATACTCATATAATCACATAATATTAAAA
1 CATATATCACAATACTCATATAATCACATAACATTCAAG
*
25322349 CATATATCACAATACTCATATAATCACATAACCTTCAAG
1 CATATATCACAATACTCATATAATCACATAACATTCAAG
*
25322388 CATATATTACAATACTCATATAATCACATAACATTCAAG
1 CATATATCACAATACTCATATAATCACATAACATTCAAG
* *
25322427 CATATATCACAATACCCATATAATTACATAACATTCAAG
1 CATATATCACAATACTCATATAATCACATAACATTCAAG
* *
25322466 CATATATCACAATAATCATATAATCATATAACATTCAAG
1 CATATATCACAATACTCATATAATCACATAACATTCAAG
* *
25322505 CATATATCACAATACTCATATAATCACATAACCTTCGAG
1 CATATATCACAATACTCATATAATCACATAACATTCAAG
*
25322544 CATATATCACAATACTCATATAGTCACATAACATTCCAA-
1 CATATATCACAATACTCATATAATCACATAACATT-CAAG
* *
25322583 CATATATAACAATACTCATATAATCACATAACATTAAAG
1 CATATATCACAATACTCATATAATCACATAACATTCAAG
25322622 CATATATCACAATACTCA
1 CATATATCACAATACTCA
25322640 AAAATATGTT
Statistics
Matches: 365, Mismatches: 39, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
38 2 0.01
39 360 0.99
40 3 0.01
ACGTcount: A:0.47, C:0.21, G:0.03, T:0.30
Consensus pattern (39 bp):
CATATATCACAATACTCATATAATCACATAACATTCAAG
Found at i:25325100 original size:27 final size:27
Alignment explanation
Indices: 25325060--25325555 Score: 459
Period size: 27 Copynumber: 18.4 Consensus size: 27
25325050 TAATGGGCCC
* *
25325060 AAAATTACCAAAATACCTTCGAAGAGT
1 AAAATTACCGAAATACCTTCGAAGGGT
**
25325087 AAAATTACCGAAATACCCACGAAGGGT
1 AAAATTACCGAAATACCTTCGAAGGGT
25325114 AAAATTACCGAAATACCCTT-GAAGGGT
1 AAAATTACCGAAATA-CCTTCGAAGGGT
* ** *
25325141 AAAATGATTGAAATACCTTCAAAGGGT
1 AAAATTACCGAAATACCTTCGAAGGGT
* *
25325168 AAAATTATCGAAATA-CTCTCAAAGGGT
1 AAAATTACCGAAATACCT-TCGAAGGGT
* **
25325195 AAAATTACCAAAATACCCCCGAAGGGT
1 AAAATTACCGAAATACCTTCGAAGGGT
25325222 AAAATTACCGAAATACCCTT-GAAGGGT
1 AAAATTACCGAAATA-CCTTCGAAGGGT
*
25325249 AAAATTATCGAAATACCCTT-GAAGGGT
1 AAAATTACCGAAATA-CCTTCGAAGGGT
* * *
25325276 AAAATGACCGAAATACCCTT-AAATGGT
1 AAAATTACCGAAATA-CCTTCGAAGGGT
* * * *
25325303 -AAATTATCAAAATACCCTCGAAAGGT
1 AAAATTACCGAAATACCTTCGAAGGGT
* * * *
25325329 AAAATGACTGAAATACCATCAAAGGGT
1 AAAATTACCGAAATACCTTCGAAGGGT
** *
25325356 AAAATTATTGAAATACCCTT-TAAGGGT
1 AAAATTACCGAAATA-CCTTCGAAGGGT
* * * *
25325383 AAAATTATCAAAATACCCTCAAAGGGT
1 AAAATTACCGAAATACCTTCGAAGGGT
* *
25325410 AAAATTATCGAAATACCCTCGAAGGGT
1 AAAATTACCGAAATACCTTCGAAGGGT
*
25325437 AAAATTACTGAAATACCTTCGAAGGGT
1 AAAATTACCGAAATACCTTCGAAGGGT
*
25325464 AAAATTACCAAAATACCCTT-GAAGGGT
1 AAAATTACCGAAATA-CCTTCGAAGGGT
* * * *
25325491 AAAATTATCAAAATACCTTTGAAAGGT
1 AAAATTACCGAAATACCTTCGAAGGGT
* * **
25325518 AAAATGACTGAAATACCCCCGAAGGGGT
1 AAAATTACCGAAATACCTTCGAA-GGGT
*
25325546 AAAATGACCG
1 AAAATTACCG
25325556 TTATACCCTA
Statistics
Matches: 393, Mismatches: 64, Indels: 23
0.82 0.13 0.05
Matches are distributed among these distances:
25 3 0.01
26 29 0.07
27 337 0.86
28 24 0.06
ACGTcount: A:0.44, C:0.17, G:0.16, T:0.22
Consensus pattern (27 bp):
AAAATTACCGAAATACCTTCGAAGGGT
Found at i:25325143 original size:54 final size:54
Alignment explanation
Indices: 25325060--25325564 Score: 532
Period size: 54 Copynumber: 9.4 Consensus size: 54
25325050 TAATGGGCCC
* * * *
25325060 AAAATTACCAAAATA-CCTTCGAAGAGTAAAATTACCGAAATACCCACGAAGGGT
1 AAAATTACCGAAATACCCTT-GAAGGGTAAAATTATCGAAATACCCTCGAAGGGT
* * * *
25325114 AAAATTACCGAAATACCCTTGAAGGGTAAAATGATTGAAATACCTTCAAAGGGT
1 AAAATTACCGAAATACCCTTGAAGGGTAAAATTATCGAAATACCCTCGAAGGGT
* * ** * * *
25325168 AAAATTATCGAAATACTCTCAAAGGGTAAAATTACCAAAATACCCCCGAAGGGT
1 AAAATTACCGAAATACCCTTGAAGGGTAAAATTATCGAAATACCCTCGAAGGGT
*
25325222 AAAATTACCGAAATACCCTTGAAGGGTAAAATTATCGAAATACCCTTGAAGGGT
1 AAAATTACCGAAATACCCTTGAAGGGTAAAATTATCGAAATACCCTCGAAGGGT
* * * * *
25325276 AAAATGACCGAAATACCCTTAAATGGT-AAATTATCAAAATACCCTCGAAAGGT
1 AAAATTACCGAAATACCCTTGAAGGGTAAAATTATCGAAATACCCTCGAAGGGT
* * * ** * **
25325329 AAAATGACTGAAATACCATCAAAGGGTAAAATTATTGAAATACCCTTTAAGGGT
1 AAAATTACCGAAATACCCTTGAAGGGTAAAATTATCGAAATACCCTCGAAGGGT
* * **
25325383 AAAATTATCAAAATACCCTCAAAGGGTAAAATTATCGAAATACCCTCGAAGGGT
1 AAAATTACCGAAATACCCTTGAAGGGTAAAATTATCGAAATACCCTCGAAGGGT
* * * *
25325437 AAAATTACTGAAATA-CCTTCGAAGGGTAAAATTACCAAAATACCCTTGAAGGGT
1 AAAATTACCGAAATACCCTT-GAAGGGTAAAATTATCGAAATACCCTCGAAGGGT
* * * * * *
25325491 AAAATTATCAAAATACCTTTGAAAGGTAAAATGA-CTGAAATACCCCCGAAGGGGT
1 AAAATTACCGAAATACCCTTGAAGGGTAAAATTATC-GAAATACCCTCGAA-GGGT
* **
25325546 AAAATGACCGTTATACCCT
1 AAAATTACCGAAATACCCT
25325565 AGGAGATGAA
Statistics
Matches: 372, Mismatches: 73, Indels: 11
0.82 0.16 0.02
Matches are distributed among these distances:
53 50 0.13
54 298 0.80
55 24 0.06
ACGTcount: A:0.44, C:0.18, G:0.16, T:0.23
Consensus pattern (54 bp):
AAAATTACCGAAATACCCTTGAAGGGTAAAATTATCGAAATACCCTCGAAGGGT
Found at i:25325195 original size:81 final size:81
Alignment explanation
Indices: 25325060--25325550 Score: 519
Period size: 81 Copynumber: 6.1 Consensus size: 81
25325050 TAATGGGCCC
* * * * * *
25325060 AAAATTACCAAAATACCTTCGAAGAGTAAAATTACCGAAATACCCACGAAGGGTAAAATTACCGA
1 AAAATTATCAAAATACCTTCAAAGGGTAAAATTATCGAAATACCCTCAAAGGGTAAAATTACCGA
25325125 AATACCCTTGAAGGGT
66 AATACCCTTGAAGGGT
* ** * *
25325141 AAAATGATTGAAATACCTTCAAAGGGTAAAATTATCGAAATACTCTCAAAGGGTAAAATTACCAA
1 AAAATTATCAAAATACCTTCAAAGGGTAAAATTATCGAAATACCCTCAAAGGGTAAAATTACCGA
**
25325206 AATACCCCCGAAGGGT
66 AATACCCTTGAAGGGT
* * * ** *
25325222 AAAATTACCGAAATACCCTT-GAAGGGTAAAATTATCGAAATACCCTTGAAGGGTAAAATGACCG
1 AAAATTATCAAAATA-CCTTCAAAGGGTAAAATTATCGAAATACCCTCAAAGGGTAAAATTACCG
* *
25325286 AAATACCCTTAAATGGT
65 AAATACCCTTGAAGGGT
* * * **
25325303 -AAATTATCAAAATACCCTCGAAA-GGTAAAATGA-CTGAAATACCATCAAAGGGTAAAATTATT
1 AAAATTATCAAAATACCTTC-AAAGGGTAAAATTATC-GAAATACCCTCAAAGGGTAAAATTACC
*
25325365 GAAATACCCTTTAAGGGT
64 GAAATACCCTTGAAGGGT
* * *
25325383 AAAATTATCAAAATACCCTCAAAGGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATTACTGA
1 AAAATTATCAAAATACCTTCAAAGGGTAAAATTATCGAAATACCCTCAAAGGGTAAAATTACCGA
25325448 AATA-CCTTCGAAGGGT
66 AATACCCTT-GAAGGGT
* * * * * * *
25325464 AAAATTACCAAAATACCCTT-GAAGGGTAAAATTATCAAAATACCTTTGAAA-GGTAAAATGACT
1 AAAATTATCAAAATA-CCTTCAAAGGGTAAAATTATCGAAATACC-CTCAAAGGGTAAAATTACC
**
25325527 GAAATACCCCCGAAGGGGT
64 GAAATACCCTTGAA-GGGT
25325546 AAAAT
1 AAAAT
25325551 GACCGTTATA
Statistics
Matches: 344, Mismatches: 54, Indels: 23
0.82 0.13 0.05
Matches are distributed among these distances:
79 4 0.01
80 65 0.19
81 253 0.74
82 22 0.06
ACGTcount: A:0.44, C:0.17, G:0.16, T:0.23
Consensus pattern (81 bp):
AAAATTATCAAAATACCTTCAAAGGGTAAAATTATCGAAATACCCTCAAAGGGTAAAATTACCGA
AATACCCTTGAAGGGT
Found at i:25325889 original size:28 final size:28
Alignment explanation
Indices: 25325849--25325957 Score: 146
Period size: 28 Copynumber: 3.9 Consensus size: 28
25325839 TACTAATTAA
* *
25325849 TGTATTGTGCTAAGGCCCACATTGTTAC
1 TGTATTGGGCTAAGGCCCACACTGTTAC
*
25325877 TGTATTGGGCTAAGGCTCACACTGTTAC
1 TGTATTGGGCTAAGGCCCACACTGTTAC
*
25325905 TGTATTGGGCTAAGGCTCACACTGTTAC
1 TGTATTGGGCTAAGGCCCACACTGTTAC
* * * *
25325933 TGAAATCGGCGAAGGCCCACACTGT
1 TGTATTGGGCTAAGGCCCACACTGT
25325958 ATTGATAATG
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 73 1.00
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (28 bp):
TGTATTGGGCTAAGGCCCACACTGTTAC
Found at i:25347329 original size:23 final size:23
Alignment explanation
Indices: 25347303--25347352 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
25347293 TATAAATACG
25347303 ACAAAGGAAAACGTACCTATCGA
1 ACAAAGGAAAACGTACCTATCGA
25347326 ACAAAGGAAAACGTACCTATCGA
1 ACAAAGGAAAACGTACCTATCGA
25347349 ACAA
1 ACAA
25347353 TAGTATAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.50, C:0.22, G:0.16, T:0.12
Consensus pattern (23 bp):
ACAAAGGAAAACGTACCTATCGA
Found at i:25348114 original size:24 final size:24
Alignment explanation
Indices: 25348090--25348136 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
25348080 AAACTACTTC
25348090 TAAAAAAAACTCAAGAGAGAATTCT
1 TAAAAAAAACTCAA-AGAGAATTCT
** *
25348115 TGGAGAAAACTCAAAGAGAATT
1 TAAAAAAAACTCAAAGAGAATT
25348137 TTTCACTCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 8 0.42
25 11 0.58
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (24 bp):
TAAAAAAAACTCAAAGAGAATTCT
Found at i:25349303 original size:33 final size:34
Alignment explanation
Indices: 25349252--25349326 Score: 107
Period size: 33 Copynumber: 2.2 Consensus size: 34
25349242 AGATTTAAAC
* *
25349252 AAATTAATTACTAACACTTATTTAAGTTGAACTA
1 AAATTAATTACTAACACTTATTTAAGCTGAACCA
*
25349286 AAATTAATT-CTAACACTTATTTGAGCTGAACCA
1 AAATTAATTACTAACACTTATTTAAGCTGAACCA
*
25349319 AATTTAAT
1 AAATTAAT
25349327 AAACTTACTC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 28 0.76
34 9 0.24
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (34 bp):
AAATTAATTACTAACACTTATTTAAGCTGAACCA
Found at i:25351127 original size:18 final size:20
Alignment explanation
Indices: 25351081--25351130 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 20
25351071 TCACTCTCAA
25351081 TCTCTTTTTTCTCTTTTTCAT
1 TCTC-TTTTTCTCTTTTTCAT
*
25351102 TCTCTTTTTCT-TTTTTGAT
1 TCTCTTTTTCTCTTTTTCAT
*
25351121 T-TGTTTTTCT
1 TCTCTTTTTCT
25351131 GTCTTCCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 8 0.30
19 8 0.30
20 7 0.26
21 4 0.15
ACGTcount: A:0.04, C:0.18, G:0.04, T:0.74
Consensus pattern (20 bp):
TCTCTTTTTCTCTTTTTCAT
Found at i:25356237 original size:6 final size:6
Alignment explanation
Indices: 25356228--25356290 Score: 58
Period size: 6 Copynumber: 10.8 Consensus size: 6
25356218 GAAAGAGAAC
* ** * *
25356228 TAAAAA TAAAAA TAAACA TAAGCA T-AAAA TGAAAA T-AAAG TAAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
*
25356274 TAAAAA TAAAAC TAAAA
1 TAAAAA TAAAAA TAAAA
25356291 TGAAAACAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
5 7 0.15
6 41 0.85
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.17
Consensus pattern (6 bp):
TAAAAA
Found at i:25357984 original size:21 final size:22
Alignment explanation
Indices: 25357960--25358013 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
25357950 AAAAGCAAAA
25357960 GAATAAAATAAA-TAAACAT-AT
1 GAATAAAATAAATTAAA-ATAAT
25357981 GAAT-AAATAAATTAAAATAAT
1 GAATAAAATAAATTAAAATAAT
25358002 GAAATAAAATAA
1 G-AATAAAATAA
25358014 TAATAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
20 9 0.31
21 11 0.38
22 3 0.10
23 6 0.21
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.24
Consensus pattern (22 bp):
GAATAAAATAAATTAAAATAAT
Found at i:25358021 original size:14 final size:13
Alignment explanation
Indices: 25357934--25358032 Score: 76
Period size: 14 Copynumber: 7.2 Consensus size: 13
25357924 TAAATATCAT
25357934 AAATAAAATAA-A
1 AAATAAAATAATA
*
25357946 AAATAAAAGCAA-A
1 AAATAAAA-TAATA
25357959 AGAATAAAATAAATA
1 A-AATAAAAT-AATA
*
25357974 AACATATGAATAAATA
1 AA-ATA-AAAT-AATA
* *
25357990 AATTAAAATAATG
1 AAATAAAATAATA
25358003 AAATAAAATAATA
1 AAATAAAATAATA
*
25358016 ATAATAAACTAATA
1 A-AATAAAATAATA
25358030 AAA
1 AAA
25358033 ATAATAAGAA
Statistics
Matches: 71, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
12 8 0.11
13 21 0.30
14 25 0.35
15 7 0.10
16 10 0.14
ACGTcount: A:0.72, C:0.03, G:0.04, T:0.21
Consensus pattern (13 bp):
AAATAAAATAATA
Found at i:25361776 original size:18 final size:18
Alignment explanation
Indices: 25361753--25361787 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
25361743 ATTAGAAAGT
25361753 AAAAATTA-AACTAAAAAC
1 AAAAATTATAA-TAAAAAC
25361771 AAAAATTATAATAAAAA
1 AAAAATTATAATAAAAA
25361788 TAAATTGTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAAATTATAATAAAAAC
Found at i:25362492 original size:54 final size:53
Alignment explanation
Indices: 25362407--25362514 Score: 171
Period size: 54 Copynumber: 2.0 Consensus size: 53
25362397 AATTAAGCAC
*
25362407 ATTAAACATGAATTAATATCCTAGAAATATTAAAACAAGAAATAACACATACAT
1 ATTAAACATGAATTAATATCCGAGAAATATTAAAACAAGAAATAA-ACATACAT
* * *
25362461 ATTAAACGTGAATTAATATCCGAGAATTATTAAAACAAGAAATAAGCATACAT
1 ATTAAACATGAATTAATATCCGAGAAATATTAAAACAAGAAATAAACATACAT
25362514 A
1 A
25362515 ATTGAGAGCA
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
53 8 0.16
54 42 0.84
ACGTcount: A:0.54, C:0.12, G:0.08, T:0.26
Consensus pattern (53 bp):
ATTAAACATGAATTAATATCCGAGAAATATTAAAACAAGAAATAAACATACAT
Found at i:25381033 original size:10 final size:10
Alignment explanation
Indices: 25381018--25381068 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
25381008 TTGGGTTAAG
25381018 ATTGAGCTGA
1 ATTGAGCTGA
*
25381028 ATTGAGCTCA
1 ATTGAGCTGA
*
25381038 AATGAGCTGA
1 ATTGAGCTGA
*
25381048 CTTGAGCTCG-
1 ATTGAGCT-GA
*
25381058 AGTGAGCTGA
1 ATTGAGCTGA
25381068 A
1 A
25381069 CTAAGTTAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
9 1 0.03
10 30 0.94
11 1 0.03
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (10 bp):
ATTGAGCTGA
Found at i:25381043 original size:20 final size:20
Alignment explanation
Indices: 25381020--25381068 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
25381010 GGGTTAAGAT
25381020 TGAGCTGAATTGAGCTCAAA
1 TGAGCTGAATTGAGCTCAAA
* * *
25381040 TGAGCTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCAAA
25381060 TGAGCTGAA
1 TGAGCTGAA
25381069 CTAAGTTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.29, C:0.16, G:0.31, T:0.24
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAA
Found at i:25388100 original size:27 final size:25
Alignment explanation
Indices: 25388068--25388167 Score: 74
Period size: 25 Copynumber: 3.9 Consensus size: 25
25388058 CAAGCACTTA
* *
25388068 AACGGGAAGCTCTCTCTCGATCCATGT
1 AACGGGAAGCTC-ATCT-GAGCCATGT
* *
25388095 AACGGGAAACTCATGTGAGCCATGT
1 AACGGGAAGCTCATCTGAGCCATGT
* * * * * *
25388120 AACGGGAAGTTTATCCGGGCTATAT
1 AACGGGAAGCTCATCTGAGCCATGT
**
25388145 AACGGGAAGCTCATAAGAGCCAT
1 AACGGGAAGCTCATCTGAGCCAT
25388168 AATCAAGAAG
Statistics
Matches: 55, Mismatches: 18, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
25 42 0.76
26 2 0.04
27 11 0.20
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (25 bp):
AACGGGAAGCTCATCTGAGCCATGT
Found at i:25388268 original size:26 final size:25
Alignment explanation
Indices: 25388232--25388290 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 25
25388222 AAAGCTCTGG
25388232 AGAGCCATTAATCAGGAAGCTCACAA
1 AGAGCCATTAATCAGGAAGCTC-CAA
* *
25388258 AGAGCCTTTAATCGGGAAGCTCCAA
1 AGAGCCATTAATCAGGAAGCTCCAA
25388283 AGAGCCAT
1 AGAGCCAT
25388291 ATAACGAGAC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 10 0.33
26 20 0.67
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (25 bp):
AGAGCCATTAATCAGGAAGCTCCAA
Found at i:25389363 original size:25 final size:26
Alignment explanation
Indices: 25389316--25389364 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
25389306 AAAGATGATA
**
25389316 TAAAATGATGATATTTCTTATTTAAT
1 TAAAATGATGATATTTCCAATTTAAT
*
25389342 TAAAAT-ATTATATTTCCAATTTA
1 TAAAATGATGATATTTCCAATTTA
25389365 GTCTTTTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (26 bp):
TAAAATGATGATATTTCCAATTTAAT
Found at i:25395083 original size:20 final size:19
Alignment explanation
Indices: 25395040--25395086 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
25395030 CATACTTGAA
25395040 TTCATTTCAATATTCACAT
1 TTCATTTCAATATTCACAT
* * *
25395059 CTCATTTCATTAATTCATAT
1 TTCATTTCAAT-ATTCACAT
25395079 TTCATTTC
1 TTCATTTC
25395087 GCATCCCATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.28, C:0.21, G:0.00, T:0.51
Consensus pattern (19 bp):
TTCATTTCAATATTCACAT
Found at i:25396107 original size:44 final size:43
Alignment explanation
Indices: 25396059--25396377 Score: 119
Period size: 44 Copynumber: 7.3 Consensus size: 43
25396049 GCTACTGCTT
*
25396059 AGGGAGACAAGATTTGCTATCTTCAACCTGCTCCACTACAACCG
1 AGGGAGGCAAGATTTGCTATCTTCAACCTGCTCCACT-CAACCG
** * * * ** *
25396103 AGGGAGGCAAGGCTTG-TGTCTTCGATCTGCTTCGTCGTCGA-CG
1 AGGGAGGCAAGATTTGCTATCTTCAACCTGC-TCCAC-TCAACCG
* *
25396146 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTGCAACCG
1 -AGGGAGGCAAGATTTGCTATCTTCAACCTGCTCCACT-CAACCG
* ** * ** * ** *
25396191 AGGAAGGCAAG-GCTGGTATCTTTGATCTGCTTCGCTGTC-ATCG
1 AGGGAGGCAAGATTTGCTATCTTCAACCTGC-TC-CACTCAACCG
* * * * *
25396234 CAGGAAGGCAAGATCTGCTATCTTTAACCTACTCCACTGCAACTG
1 -AGGGAGGCAAGATTTGCTATCTTCAACCTGCTCCACT-CAACCG
* ** * * * * * * *
25396279 AGCGAGGCAAG-GCTGGTGTCTTCGATCTGCTCCGCTGTCGA-TG
1 AGGGAGGCAAGATTTGCTATCTTCAACCTGCTCCAC--TCAACCG
* ** *
25396322 CAGGAAGGCAAGATCCGTTATCTTCAACCTGCTCCACTACAACCG
1 -AGGGAGGCAAGATTTGCTATCTTCAACCTGCTCCACT-CAACCG
25396367 AGGGAGGCAAG
1 AGGGAGGCAAG
25396378 GCTTGTGTCT
Statistics
Matches: 198, Mismatches: 59, Indels: 36
0.68 0.20 0.12
Matches are distributed among these distances:
43 52 0.26
44 95 0.48
45 51 0.26
ACGTcount: A:0.24, C:0.27, G:0.26, T:0.24
Consensus pattern (43 bp):
AGGGAGGCAAGATTTGCTATCTTCAACCTGCTCCACTCAACCG
Found at i:25396170 original size:88 final size:88
Alignment explanation
Indices: 25396066--25396787 Score: 1020
Period size: 88 Copynumber: 8.2 Consensus size: 88
25396056 CTTAGGGAGA
*
25396066 CAAGATTTGCTATCTTCAACCTGCTCCACTACAACCGAGGGAGGCAAGGCTTGTGTCTTCGATCT
1 CAAGATCTGCTATCTTCAACCTGCTCCACTACAACCGAGGGAGGCAAGGCTTGTGTCTTCGATCT
*
25396131 GCTTCG-TCGTCGACGCAGGAAGG
66 GCTTCGCT-GTCGATGCAGGAAGG
* * * * *
25396154 CAAGATCTGCTATCTTCAACCTGCTCCACTGCAACCGAGGAAGGCAAGGCTGGTATCTTTGATCT
1 CAAGATCTGCTATCTTCAACCTGCTCCACTACAACCGAGGGAGGCAAGGCTTGTGTCTTCGATCT
25396219 GCTTCGCTGTC-ATCGCAGGAAGG
66 GCTTCGCTGTCGAT-GCAGGAAGG
* * * * * *
25396242 CAAGATCTGCTATCTTTAACCTACTCCACTGCAACTGAGCGAGGCAAGGCTGGTGTCTTCGATCT
1 CAAGATCTGCTATCTTCAACCTGCTCCACTACAACCGAGGGAGGCAAGGCTTGTGTCTTCGATCT
*
25396307 GCTCCGCTGTCGATGCAGGAAGG
66 GCTTCGCTGTCGATGCAGGAAGG
* *
25396330 CAAGATCCGTTATCTTCAACCTGCTCCACTACAACCGAGGGAGGCAAGGCTTGTGTCTTCGATCT
1 CAAGATCTGCTATCTTCAACCTGCTCCACTACAACCGAGGGAGGCAAGGCTTGTGTCTTCGATCT
* *
25396395 GCTTTGCTATCGATGCAGGAAGG
66 GCTTCGCTGTCGATGCAGGAAGG
* * * *
25396418 CAAGATCCGCTATCTTCAACCTGCTCTACTACAACCGAGAGAGGCAAGGCTTGTGTCTTTGATCT
1 CAAGATCTGCTATCTTCAACCTGCTCCACTACAACCGAGGGAGGCAAGGCTTGTGTCTTCGATCT
** * *
25396483 GCTTTACTTTCGATGCAGGAAAG
66 GCTTCGCTGTCGATGCAGGAAGG
* *
25396506 CAAGATCTGCTATCTTCAACCTGCTCTACTACAACCGATGGAGGCAAGGCTTGTGTCTTCGATCT
1 CAAGATCTGCTATCTTCAACCTGCTCCACTACAACCGAGGGAGGCAAGGCTTGTGTCTTCGATCT
* *
25396571 GGTTTGCTGTCGATGCAGGAAGG
66 GCTTCGCTGTCGATGCAGGAAGG
* * * *
25396594 CAAGATCTACTATCTTCAACCTGCTCCACTACAACTGAGGGAGGTAAGGCTCGTGTCTTCGATCT
1 CAAGATCTGCTATCTTCAACCTGCTCCACTACAACCGAGGGAGGCAAGGCTTGTGTCTTCGATCT
*
25396659 GCTTTC-CTGTCGATACAGGAAGG
66 GC-TTCGCTGTCGATGCAGGAAGG
* * *
25396682 CAAGATCCT-CTATCTTCAACCTGTTCTACTACAACCGAGAGAGGCAAGGCTTGTGTCTTCGATC
1 CAAGAT-CTGCTATCTTCAACCTGCTCCACTACAACCGAGGGAGGCAAGGCTTGTGTCTTCGATC
* *
25396746 TGCTTTGTTGTCGATGCAGGAAGG
65 TGCTTCGCTGTCGATGCAGGAAGG
25396770 CAAGATCTGCTATCTTCA
1 CAAGATCTGCTATCTTCA
25396788 CTGATCTGTT
Statistics
Matches: 568, Mismatches: 59, Indels: 14
0.89 0.09 0.02
Matches are distributed among these distances:
87 5 0.01
88 556 0.98
89 7 0.01
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27
Consensus pattern (88 bp):
CAAGATCTGCTATCTTCAACCTGCTCCACTACAACCGAGGGAGGCAAGGCTTGTGTCTTCGATCT
GCTTCGCTGTCGATGCAGGAAGG
Found at i:25396545 original size:48 final size:48
Alignment explanation
Indices: 25396317--25396555 Score: 136
Period size: 44 Copynumber: 5.3 Consensus size: 48
25396307 GCTCCGCTGT
* * *
25396317 CGATGCAGGAAGGCAAGATCCGTTATCTTCAACCTGCTCCACTACAAC
1 CGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCTACTACAAC
* * * * * * *
25396365 CGA-G--GG-AGGCAAG-GCTTG-TGTCTTCGATCTGCT-T--TGCTAT
1 CGATGCAGGAAGGCAAGATC-TGCTATCTTCAACCTGCTCTACTACAAC
*
25396405 CGATGCAGGAAGGCAAGATCCGCTATCTTCAACCTGCTCTACTACAAC
1 CGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCTACTACAAC
* * ** * ***
25396453 CGA-G-A-G-AGGCAAG-GCTTG-TGTCTTTGATCTGCT-T--TACTTT
1 CGATGCAGGAAGGCAAGATC-TGCTATCTTCAACCTGCTCTACTACAAC
*
25396493 CGATGCAGGAAAGCAAGATCTGCTATCTTCAACCTGCTCTACTACAAC
1 CGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCTACTACAAC
*
25396541 CGATGGAGGCAAGGC
1 CGATGCAGG-AAGGC
25396556 TTGTGTCTTC
Statistics
Matches: 133, Mismatches: 37, Indels: 41
0.63 0.18 0.19
Matches are distributed among these distances:
40 12 0.09
41 2 0.02
42 2 0.02
43 28 0.21
44 32 0.24
45 28 0.21
46 3 0.02
47 2 0.02
48 20 0.15
49 4 0.03
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (48 bp):
CGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCTACTACAAC
Found at i:25398032 original size:7 final size:7
Alignment explanation
Indices: 25398019--25398065 Score: 67
Period size: 7 Copynumber: 6.6 Consensus size: 7
25398009 TTGGCCTTTC
25398019 CATTTTT
1 CATTTTT
*
25398026 AATTTTTT
1 CA-TTTTT
*
25398034 TATTTTT
1 CATTTTT
25398041 CATTTTT
1 CATTTTT
25398048 CATTTTT
1 CATTTTT
25398055 CATTTTT
1 CATTTTT
25398062 CATT
1 CATT
25398066 CTTTTTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
7 30 0.83
8 6 0.17
ACGTcount: A:0.17, C:0.11, G:0.00, T:0.72
Consensus pattern (7 bp):
CATTTTT
Found at i:25398074 original size:21 final size:19
Alignment explanation
Indices: 25398028--25398075 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
25398018 CCATTTTTAA
25398028 TTTTTTTATTTTTCATTTT
1 TTTTTTTATTTTTCATTTT
*
25398047 TCATTTTTCATTTTTCATTCTT
1 T--TTTTTTATTTTTCATT-TT
25398069 TTTTTTT
1 TTTTTTT
25398076 GACTCAAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 1 0.04
20 5 0.21
21 15 0.62
22 3 0.12
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTTTTATTTTTCATTTT
Found at i:25408017 original size:51 final size:50
Alignment explanation
Indices: 25407886--25408331 Score: 346
Period size: 51 Copynumber: 8.8 Consensus size: 50
25407876 AAAGTGATGG
* * * * *** * *
25407886 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAATGATGGG
1 TCACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGAAAACTTTGA
* * * * *
25407936 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGAATAGCTTTGA
1 TCACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGAA-AACTTTGA
* * * * *
25407987 TCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAA-TAATGG
1 TCACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGA-AAACT-TTGA
* * * *
25408038 TCACATGTGTAGTACTAAGTGAAGGCTACTATGTGTATCGAGAAGCTTTGA
1 TCACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGA-AAACTTTGA
* * * * * * * * *
25408089 GCACGTGTGTAGTATTGTGTGAATGCTACTACGTGTATCGGTAAACTATGG
1 TCACGTGTGTAGTACTATGTGAAGGCTACTATGTGTA-CCGAAAACTTTGA
* * * * * **
25408140 TTACATGTGTAGTACTAAGTGAAGGCTACAATGGGTACAAAAAAGCTTTCG-
1 TCACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGAAAA-CTTT-GA
* *
25408191 TCACGTATGTAGTACTATGTGAAGGCTACTATGTG-AGCCATAAAAC-TTGA
1 TCACGTGTGTAGTACTATGTGAAGGCTACTATGTGTA-CC-GAAAACTTTGA
* * *
25408241 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACTGTAAAAC--TGA
1 TCACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCG-AAAACTTTGA
* *
25408290 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAA
1 TCACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGAA
25408332 TGATAAAAAT
Statistics
Matches: 313, Mismatches: 71, Indels: 26
0.76 0.17 0.06
Matches are distributed among these distances:
48 2 0.01
49 41 0.13
50 83 0.27
51 179 0.57
52 8 0.03
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.30
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTGAAGGCTACTATGTGTACCGAAAACTTTGA
Found at i:25408094 original size:102 final size:101
Alignment explanation
Indices: 25407886--25408330 Score: 476
Period size: 102 Copynumber: 4.4 Consensus size: 101
25407876 AAAGTGATGG
* * * *
25407886 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCG--GAATGATGGGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATAAT-GGTCACATGTGTAGT
* * * *
25407949 ACTATGTGCAGGCTACTATGCGTACCGAATAGCTTTGA
65 ACTAAGTGAAGGCTACTATGTGTACAGAA-AGCTTTGA
*
25407987 TCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTA
25408052 CTAAGTGAAGGCTACTATGTGTATC-GAGAAGCTTTGA
66 CTAAGTGAAGGCTACTATGTGTA-CAGA-AAGCTTTGA
* * * * * *
25408089 GCACGTGTGTAGTATTGTGTGAATGCTACTACGTGTATCGGTAAACT-ATGGTTACATGTGTAGT
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAA-TAATGGTCACATGTGTAGT
* * *
25408153 ACTAAGTGAAGGCTACAATGGGTACAAAAAAGCTTTCG-
65 ACTAAGTGAAGGCTACTATGTGTAC-AGAAAGCTTT-GA
* * * * * * *
25408191 TCACGTATGTAGTACTATGTGAAGGCTACTATGTG-AGCCATAAA-ACTTGATCACGTGTGTAGT
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATA-ATGGTCACATGTGTAGT
* * * * *
25408254 ACTATGTGAAGGCTACTACGTGAACTGTAAAAC--TGA
65 ACTAAGTGAAGGCTACTATGTGTACAG-AAAGCTTTGA
25408290 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
1 TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
25408331 ATGATAAAAA
Statistics
Matches: 290, Mismatches: 41, Indels: 27
0.81 0.11 0.08
Matches are distributed among these distances:
98 1 0.00
99 34 0.12
100 3 0.01
101 82 0.28
102 160 0.55
103 10 0.03
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.31
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTA
CTAAGTGAAGGCTACTATGTGTACAGAAAGCTTTGA
Found at i:25414211 original size:27 final size:27
Alignment explanation
Indices: 25414174--25414225 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
25414164 AATGTGAAAG
25414174 GGGGTTGCTAAGTGCTGATTCCCCTGA
1 GGGGTTGCTAAGTGCTGATTCCCCTGA
* *
25414201 GGGGTTGCTAAGTGTTGATTTCCCT
1 GGGGTTGCTAAGTGCTGATTCCCCT
25414226 ATTCATTGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.13, C:0.19, G:0.33, T:0.35
Consensus pattern (27 bp):
GGGGTTGCTAAGTGCTGATTCCCCTGA
Found at i:25414233 original size:103 final size:103
Alignment explanation
Indices: 25414054--25414361 Score: 458
Period size: 103 Copynumber: 3.0 Consensus size: 103
25414044 GAATACATCA
25414054 TATTTTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTGTGTGCTGA-TT
1 TATTTTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTGTGTGCTGATTT
25414118 CCCTGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCG
66 CCCT-ATTCATTGGTGGTTGCTAAGTGCTGATTCCACCG
** ** *
25414157 TATTTTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCTGAGGGGTTGCTAAGTGTTGATTT
1 TATTTTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTGTGTGCTGATTT
*
25414222 CCCTATTCATTGGTGGTTGCTAAGTGCTGATTCCACTG
66 CCCTATTCATTGGTGGTTGCTAAGTGCTGATTCCACCG
* * * * * *
25414260 CATCTGAAATGTG-AAGGGGGTTACTAAGTGCTGATTCCCCCAAGGGATTGCTGTGTGCTGATTC
1 TATTTTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTGTGTGCTGATTT
* * *
25414324 CCCGATTCATTGGTGGTTGCTAAGTGCGGAATCCACCG
66 CCCTATTCATTGGTGGTTGCTAAGTGCTGATTCCACCG
25414362 ATAACGGTTA
Statistics
Matches: 183, Mismatches: 21, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
102 77 0.42
103 100 0.55
104 6 0.03
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.33
Consensus pattern (103 bp):
TATTTTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTGTGTGCTGATTT
CCCTATTCATTGGTGGTTGCTAAGTGCTGATTCCACCG
Found at i:25416000 original size:26 final size:25
Alignment explanation
Indices: 25415920--25416000 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 25
25415910 TTCGATCACG
25415920 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTA-GTGCAGGCTACTA
* *
25415946 CGTGTATCGGA-TAGTG-ATGG-TCAC-A
1 TGTGTA--GTACTAGTGCA-GGCT-ACTA
25415971 TGTGTAGTACTACGTGCAGGCTACTA
1 TGTGTAGTACTA-GTGCAGGCTACTA
25415997 TGTG
1 TGTG
25416001 AACCGAATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 18
0.66 0.06 0.28
Matches are distributed among these distances:
23 2 0.05
24 2 0.05
25 15 0.36
26 19 0.45
27 2 0.05
28 2 0.05
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (25 bp):
TGTGTAGTACTAGTGCAGGCTACTA
Found at i:25416248 original size:16 final size:16
Alignment explanation
Indices: 25416227--25416258 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
25416217 TGATTAAAAG
*
25416227 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
25416243 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
25416259 GCAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:25422501 original size:17 final size:17
Alignment explanation
Indices: 25422479--25422514 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
25422469 CTTTTTTATT
25422479 TTAAATACCCACAAGAG
1 TTAAATACCCACAAGAG
25422496 TTAAATACCCACAAGAG
1 TTAAATACCCACAAGAG
25422513 TT
1 TT
25422515 TCCTTGTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.22, G:0.11, T:0.22
Consensus pattern (17 bp):
TTAAATACCCACAAGAG
Found at i:25436033 original size:21 final size:20
Alignment explanation
Indices: 25436004--25436074 Score: 70
Period size: 21 Copynumber: 3.2 Consensus size: 20
25435994 TAGCTTTCCT
25436004 TTTGATCATATCCTCTAAAA
1 TTTGATCATATCCTCTAAAA
**
25436024 TTTGAATCATATCCAATAACACAA
1 TTTG-ATCATATCCTCT-A-A-AA
25436048 CTTTTGATCATATCCTCTAAAA
1 --TTTGATCATATCCTCTAAAA
25436070 TTTGA
1 TTTGA
25436075 ATCACTTTCT
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
20 9 0.22
21 10 0.24
22 3 0.07
23 2 0.05
24 3 0.07
25 10 0.24
26 4 0.10
ACGTcount: A:0.37, C:0.20, G:0.06, T:0.38
Consensus pattern (20 bp):
TTTGATCATATCCTCTAAAA
Found at i:25437704 original size:138 final size:138
Alignment explanation
Indices: 25437456--25437739 Score: 469
Period size: 138 Copynumber: 2.1 Consensus size: 138
25437446 AATAACATAG
*
25437456 ATATAATTAATATATGAATTTGGTTCATACAAAATATTAATTGTATATATTTTACCAAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATT
* * * *
25437521 AATATAAATAATTATATCAATTAATTTTGGTCAAAATATAAAAGACATGAAAGTTAATATTTTTT
66 AATATAAATAATTATATCAATTAATTTCGATCAAAATATAAAAGACATGAAAATTAATATTCTTT
**
25437586 TGGAAAGA
131 TAAAAAGA
*
25437594 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATT
* *
25437659 AATATAAATAGTTATATTAATTAATTTCGATCAAAATATAAAAGACATGAAAATTAATATTCTTT
66 AATATAAATAATTATATCAATTAATTTCGATCAAAATATAAAAGACATGAAAATTAATATTCTTT
*
25437724 TAAAAATA
131 TAAAAAGA
25437732 ATATAATT
1 ATATAATT
25437740 CATTTTTCTA
Statistics
Matches: 135, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
138 135 1.00
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (138 bp):
ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATT
AATATAAATAATTATATCAATTAATTTCGATCAAAATATAAAAGACATGAAAATTAATATTCTTT
TAAAAAGA
Found at i:25440293 original size:15 final size:15
Alignment explanation
Indices: 25440275--25440303 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
25440265 TCATTCTTTC
25440275 ATTTTTCATCCTTCT
1 ATTTTTCATCCTTCT
25440290 ATTTTTCATCCTTC
1 ATTTTTCATCCTTC
25440304 ATCTCCCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.28, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTTTTCATCCTTCT
Found at i:25446937 original size:17 final size:17
Alignment explanation
Indices: 25446896--25446942 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
25446886 ATATAGATAT
*
25446896 TAATAATATATAAATGTA
1 TAATAATAT-TAAATGGA
* *
25446914 AAATAATATTATATGGA
1 TAATAATATTAAATGGA
25446931 TAATAATATTAA
1 TAATAATATTAA
25446943 TACTTTTCAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.38
Consensus pattern (17 bp):
TAATAATATTAAATGGA
Found at i:25449160 original size:29 final size:29
Alignment explanation
Indices: 25449118--25449192 Score: 132
Period size: 29 Copynumber: 2.6 Consensus size: 29
25449108 ACATCAATAA
25449118 GACACACGGCCATGTGAGTAAGCCATGTG
1 GACACACGGCCATGTGAGTAAGCCATGTG
25449147 GACACACGGCCATGTGAGTAAGCCATGTG
1 GACACACGGCCATGTGAGTAAGCCATGTG
* *
25449176 GACACACAGCCGTGTGA
1 GACACACGGCCATGTGA
25449193 CAGCCCGTGT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.28, C:0.25, G:0.31, T:0.16
Consensus pattern (29 bp):
GACACACGGCCATGTGAGTAAGCCATGTG
Found at i:25459254 original size:50 final size:50
Alignment explanation
Indices: 25459117--25459303 Score: 167
Period size: 50 Copynumber: 3.6 Consensus size: 50
25459107 GAGATCCTAT
* **
25459117 GTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGGTTATGAGAGGTCCCAC
1 GTAAGACCATGTCTGGGATATGGCATTGGCACCA---A-G--ATGAGAGGTCCCAC
* * ** * *
25459173 GTAAAACCATGTCTGGGACATGGTGTTGGCACCGAGATGAGAGGTCCCCC
1 GTAAGACCATGTCTGGGATATGGCATTGGCACCAAGATGAGAGGTCCCAC
* * * ** *
25459223 GTAAGACCATGTCTGGGATATGGCATGGGCACCAATATAAGAACTCCCAT
1 GTAAGACCATGTCTGGGATATGGCATTGGCACCAAGATGAGAGGTCCCAC
* *
25459273 GTAAGACCATATCTAGGATATGGCATTGGCA
1 GTAAGACCATGTCTGGGATATGGCATTGGCA
25459304 GTATAGGAAA
Statistics
Matches: 109, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
50 79 0.72
52 1 0.01
53 1 0.01
56 28 0.26
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (50 bp):
GTAAGACCATGTCTGGGATATGGCATTGGCACCAAGATGAGAGGTCCCAC
Found at i:25459572 original size:12 final size:12
Alignment explanation
Indices: 25459555--25459593 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
25459545 ATGAGTTATT
25459555 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
25459567 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
25459579 TAAGAAAGTAAG
1 TAAGTAAGCAAG
25459591 TAA
1 TAA
25459594 AGAAGAAGCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.56, C:0.05, G:0.21, T:0.18
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:25459581 original size:20 final size:20
Alignment explanation
Indices: 25459556--25459604 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
25459546 TGAGTTATTT
25459556 AAGTAAGCAAGTAAGTAAAC
1 AAGTAAGCAAGTAAGTAAAC
* *
25459576 AAGTAAGAAAGTAAGTAAAG
1 AAGTAAGCAAGTAAGTAAAC
25459596 AAG-AAGCAA
1 AAGTAAGCAA
25459605 AGACCATGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.59, C:0.06, G:0.22, T:0.12
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:25462043 original size:81 final size:80
Alignment explanation
Indices: 25461939--25462129 Score: 202
Period size: 81 Copynumber: 2.4 Consensus size: 80
25461929 AGGCTACTCC
* * * * *
25461939 TTCATAATTCGCCTCAAAGGCTTTTCTTTCATGATTCGCCACAATGAATTTTCTTTCATACCTCA
1 TTCATATTTCACCACAAAGGCTTTTCTTTCATGATTCACCACAAAGAATTTTCTTTCATACCTCA
* **
25462004 CCATAATTGCTTTCCT
66 CCACAAAGGCTTT-CT
* * ** ** **
25462020 TTCATATTTCACCACAATGGCTTTCCTTTCATGATTCATTACAAAGGCTTTTCTTTCATATTTCA
1 TTCATATTTCACCACAAAGGCTTTTCTTTCATGATTCACCACAAAGAATTTTCTTTCATACCTCA
25462085 CCACAAAGGCTTTCT
66 CCACAAAGGCTTTCT
* *
25462100 TTACATATTTCACTACAAAGGCCTTTCTTT
1 TT-CATATTTCACCACAAAGGCTTTTCTTT
25462130 TTTACATGTT
Statistics
Matches: 89, Mismatches: 20, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
80 4 0.04
81 85 0.96
ACGTcount: A:0.25, C:0.26, G:0.08, T:0.41
Consensus pattern (80 bp):
TTCATATTTCACCACAAAGGCTTTTCTTTCATGATTCACCACAAAGAATTTTCTTTCATACCTCA
CCACAAAGGCTTTCT
Found at i:25462049 original size:54 final size:52
Alignment explanation
Indices: 25461953--25462129 Score: 158
Period size: 54 Copynumber: 3.3 Consensus size: 52
25461943 TAATTCGCCT
* **
25461953 CAAAGGCTTTTCTTTCATGA-TTCGCCACAATGAATTTTCTTTCATACCTCACCA
1 CAAAGGCTTTTCTTTCAT-ATTTCACCACAATG-GCTTTCTTTCATA-CTCACCA
* ** * * **
25462007 TAATTGCTTTCCTTTCATATTTCACCACAATGGCTTTCCTTTCATGATTCATTA
1 CAAAGGCTTTTCTTTCATATTTCACCACAATGGCTTT-CTTTCAT-ACTCACCA
* * *
25462061 CAAAGGCTTTTCTTTCATATTTCACCACAAAGGCTTTCTTTACATATTTCACTA
1 CAAAGGCTTTTCTTTCATATTTCACCACAATGGCTTTCTTT-CATA-CTCACCA
*
25462115 CAAAGGCCTTTCTTT
1 CAAAGGCTTTTCTTT
25462130 TTTACATGTT
Statistics
Matches: 101, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
53 9 0.09
54 91 0.90
55 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.08, T:0.41
Consensus pattern (52 bp):
CAAAGGCTTTTCTTTCATATTTCACCACAATGGCTTTCTTTCATACTCACCA
Found at i:25462107 original size:27 final size:26
Alignment explanation
Indices: 25461939--25462129 Score: 143
Period size: 27 Copynumber: 7.1 Consensus size: 26
25461929 AGGCTACTCC
* * *
25461939 TTCATAATTCGCCTCAAAGGCTTTTCT
1 TTCATATTTCACCACAAAGGC-TTTCT
* * **
25461966 TTCATGA-TTCGCCACAATGAATTTTCT
1 TTCAT-ATTTCACCACAAAG-GCTTTCT
** * **
25461993 TTCATACCTCACCATAATTGCTTTCCT
1 TTCATATTTCACCACAAAGGCTTT-CT
*
25462020 TTCATATTTCACCACAATGGCTTTCCT
1 TTCATATTTCACCACAAAGGCTTT-CT
**
25462047 TTCATGA-TTCATTACAAAGGCTTTTCT
1 TTCAT-ATTTCACCACAAAGGC-TTTCT
25462074 TTCATATTTCACCACAAAGGCTTTCT
1 TTCATATTTCACCACAAAGGCTTTCT
*
25462100 TTACATATTTCACTACAAAGGCCTTTCT
1 TT-CATATTTCACCACAAAGG-CTTTCT
25462128 TT
1 TT
25462130 TTTACATGTT
Statistics
Matches: 135, Mismatches: 20, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
26 12 0.09
27 110 0.81
28 13 0.10
ACGTcount: A:0.25, C:0.26, G:0.08, T:0.41
Consensus pattern (26 bp):
TTCATATTTCACCACAAAGGCTTTCT
Found at i:25473526 original size:25 final size:25
Alignment explanation
Indices: 25473482--25473552 Score: 97
Period size: 25 Copynumber: 2.8 Consensus size: 25
25473472 AATAAATCAG
* *
25473482 CATGCATGTTTCCTTGAATGCCATT
1 CATGCATGCTTCCTTTAATGCCATT
* * *
25473507 CATGCATGCTTCTTTTAATGTCGTT
1 CATGCATGCTTCCTTTAATGCCATT
25473532 CATGCATGCTTCCTTTAATGC
1 CATGCATGCTTCCTTTAATGC
25473553 TCTCCTTTGC
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.18, C:0.24, G:0.15, T:0.42
Consensus pattern (25 bp):
CATGCATGCTTCCTTTAATGCCATT
Found at i:25485023 original size:41 final size:40
Alignment explanation
Indices: 25484967--25485128 Score: 209
Period size: 41 Copynumber: 4.0 Consensus size: 40
25484957 AGAATATTGT
* *
25484967 TGAATTACACATACGTGCCTCTGTTTGTACTTCGGTACCC
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCC
* * *
25485007 TTAAATTGCAGATACGTGCCCCTGTTTGTACTTTGGTACCCC
1 -TGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTA-CCC
* * *
25485049 TGAATTGTACATATGTGCCCCTGTTTGTACTTCAGTAACCC
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTCGGT-ACCC
*
25485090 TGAATTGCACATATGTG-CCCTGTTTGTACTTCGGTACCC
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCC
25485129 CTAGATGTAC
Statistics
Matches: 106, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
39 4 0.04
40 17 0.16
41 81 0.76
42 4 0.04
ACGTcount: A:0.20, C:0.26, G:0.19, T:0.36
Consensus pattern (40 bp):
TGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCC
Found at i:25485050 original size:20 final size:19
Alignment explanation
Indices: 25485025--25485080 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 19
25485015 CAGATACGTG
25485025 CCCCTGTTTGTACTTTGGTA
1 CCCCTGTTTGTACTTT-GTA
* * *
25485045 CCCCTGAATTGTACATATGTG
1 CCCCTG-TTTGTAC-TTTGTA
25485066 CCCCTGTTTGTACTT
1 CCCCTGTTTGTACTT
25485081 CAGTAACCCT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
19 1 0.03
20 12 0.41
21 14 0.48
22 2 0.07
ACGTcount: A:0.14, C:0.27, G:0.18, T:0.41
Consensus pattern (19 bp):
CCCCTGTTTGTACTTTGTA
Found at i:25485069 original size:21 final size:21
Alignment explanation
Indices: 25485045--25485109 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
25485035 TACTTTGGTA
25485045 CCCCTGAATTGTACATATGTG
1 CCCCTGAATTGTACATATGTG
* * *
25485066 CCCCTG-TTTGTACTTCA-GTA
1 CCCCTGAATTGTACAT-ATGTG
* *
25485086 ACCCTGAATTGCACATATGTG
1 CCCCTGAATTGTACATATGTG
25485107 CCC
1 CCC
25485110 TGTTTGTACT
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.22, C:0.29, G:0.17, T:0.32
Consensus pattern (21 bp):
CCCCTGAATTGTACATATGTG
Found at i:25485600 original size:131 final size:131
Alignment explanation
Indices: 25485366--25485630 Score: 451
Period size: 131 Copynumber: 2.0 Consensus size: 131
25485356 GGTCAGTGTC
* *
25485366 ATGTATAAACATATTGAGTTGGATTTATGGTTGAAATGTGTTTAGAATGTTTAAAAGTGATGATT
1 ATGTATAAACATATTGAGTTGAATTTATGGTTGAAATGTATTTAGAATGTTTAAAAGTGATGATT
**
25485431 GATGAATATGTATAAAATAACTAAGTATGTTTGTGTTTTGGTAACATATGTGCATAATTGGCTAT
66 GATGAATATGTATAAAATAACTAAGTATGTTTGTGTTTTGGTAACATATGTGCATAACAGGCTAT
25485496 A
131 A
* *
25485497 ATGTATAAACATATAT-AGTTGAATTTATGGTTGAAATGTATTTAGAATGTTTGAAAGTGATGTT
1 ATGTATAAACATAT-TGAGTTGAATTTATGGTTGAAATGTATTTAGAATGTTTAAAAGTGATGAT
*
25485561 TGATGAATATGTATAAAATAACTAAGTGTGTTTGTGTTTTGGTAACATATGTGCATAACAGGCTA
65 TGATGAATATGTATAAAATAACTAAGTATGTTTGTGTTTTGGTAACATATGTGCATAACAGGCTA
25485626 TA
130 TA
25485628 ATG
1 ATG
25485631 CTTGTTGTAG
Statistics
Matches: 126, Mismatches: 7, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
131 125 0.99
132 1 0.01
ACGTcount: A:0.35, C:0.04, G:0.21, T:0.40
Consensus pattern (131 bp):
ATGTATAAACATATTGAGTTGAATTTATGGTTGAAATGTATTTAGAATGTTTAAAAGTGATGATT
GATGAATATGTATAAAATAACTAAGTATGTTTGTGTTTTGGTAACATATGTGCATAACAGGCTAT
A
Found at i:25491817 original size:21 final size:22
Alignment explanation
Indices: 25491791--25491851 Score: 56
Period size: 20 Copynumber: 2.9 Consensus size: 22
25491781 TTGTACTTCA
25491791 GTACCCCTGAATTGCACATAT-
1 GTACCCCTGAATTGCACATATG
* * ** *
25491812 GTACCCTTG-TTTATAC-TTTG
1 GTACCCCTGAATTGCACATATG
25491832 GTACCCCTGAATTGCACATA
1 GTACCCCTGAATTGCACATA
25491852 CGTGCGCTAT
Statistics
Matches: 27, Mismatches: 10, Indels: 5
0.64 0.24 0.12
Matches are distributed among these distances:
19 2 0.07
20 12 0.44
21 12 0.44
22 1 0.04
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (22 bp):
GTACCCCTGAATTGCACATATG
Found at i:25491823 original size:41 final size:40
Alignment explanation
Indices: 25491757--25491980 Score: 157
Period size: 41 Copynumber: 5.5 Consensus size: 40
25491747 AAAATATTGT
* * * *
25491757 TGAATTGCAAATATGT-GCCTCTGTTTGTACTTCAGTACCCC
1 TGAATTGCACATATGTACCCT-TATTTATACTTC-GTACCCC
* *
25491798 TGAATTGCACATATGTACCCTTGTTTATACTTTGGTACCCC
1 TGAATTGCACATATGTACCCTTATTTATAC-TTCGTACCCC
* * * * * *
25491839 TGAATTGCACATACGTGCGC-TATTTGTATTTCGGTACCCT
1 TGAATTGCACATATGTACCCTTATTTATACTTC-GTACCCC
* * * * *
25491879 TGTATTGCACATAGGTGCCCCTATTTATACTTCGATACCTC
1 TGAATTGCACATATGTACCCTTATTTATACTTCG-TACCCC
* * * *
25491920 TGAATTGCAGATACGTTCCCGTATTTATACTTCGATACCCC
1 TGAATTGCACATATGTACCCTTATTTATACTTCG-TACCCC
* * *
25491961 TGGA-TGTACTTATGTACCCT
1 TGAATTGCACATATGTACCCT
25491981 CTTTAGACTT
Statistics
Matches: 146, Mismatches: 32, Indels: 11
0.77 0.17 0.06
Matches are distributed among these distances:
39 2 0.01
40 40 0.27
41 99 0.68
42 5 0.03
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.37
Consensus pattern (40 bp):
TGAATTGCACATATGTACCCTTATTTATACTTCGTACCCC
Found at i:25491876 original size:81 final size:80
Alignment explanation
Indices: 25491757--25491995 Score: 228
Period size: 81 Copynumber: 3.0 Consensus size: 80
25491747 AAAATATTGT
* * * *
25491757 TGAATTGCAAATATGTGCCTCTGTTTGTACTTCAGTACCCCTGAATTGCACATATGTACCCTTGT
1 TGAATTGCAAATACGTGCC-CTATTTGTACTTCGGTACCCCTGAATTGCACATATGTACCC-TAT
25491822 TTATACTTTGGTACCCC
64 TTATACTTTGGTACCCC
* * * * * * *
25491839 TGAATTGCACATACGTGCGCTATTTGTATTTCGGTACCCTTGTATTGCACATAGGTGCCCCTATT
1 TGAATTGCAAATACGTGCCCTATTTGTACTTCGGTACCCCTGAATTGCACATATGT-ACCCTATT
* * *
25491904 TATACTTCGATACCTC
65 TATACTTTGGTACCCC
* * * * * * * *
25491920 TGAATTGCAGATACGTTCCCGTATTTATACTTCGATACCCCTGGA-TGTACTTATGTACCCTCTT
1 TGAATTGCAAATACGTGCCC-TATTTGTACTTCGGTACCCCTGAATTGCACATATGTACCCTATT
*
25491984 TAGACTTTGGTA
65 TATACTTTGGTA
25491996 ATTCTGAACT
Statistics
Matches: 125, Mismatches: 30, Indels: 6
0.78 0.19 0.04
Matches are distributed among these distances:
80 15 0.12
81 72 0.58
82 38 0.30
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.38
Consensus pattern (80 bp):
TGAATTGCAAATACGTGCCCTATTTGTACTTCGGTACCCCTGAATTGCACATATGTACCCTATTT
ATACTTTGGTACCCC
Found at i:25495954 original size:25 final size:25
Alignment explanation
Indices: 25495926--25496049 Score: 126
Period size: 25 Copynumber: 5.0 Consensus size: 25
25495916 TCATGTACAT
* *
25495926 GTATGCTCTTACGAGCTGTAAATCG
1 GTATGCTCTCACGAGCTATAAATCG
*
25495951 GTATGCTCATC-TGAGCTGA-AAATCG
1 GTATGCTC-TCACGAGCT-ATAAATCG
* * *
25495976 GTATGCTCTCCCAAGCTATGAATCG
1 GTATGCTCTCACGAGCTATAAATCG
* *
25496001 GTATGCTCTCATGAGCTATGAATCG
1 GTATGCTCTCACGAGCTATAAATCG
* *
25496026 GTACGCTCTCACAAGCTATAAATC
1 GTATGCTCTCACGAGCTATAAATC
25496050 AGTAACCCTA
Statistics
Matches: 82, Mismatches: 13, Indels: 8
0.80 0.13 0.08
Matches are distributed among these distances:
24 3 0.04
25 78 0.95
26 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (25 bp):
GTATGCTCTCACGAGCTATAAATCG
Found at i:25496001 original size:50 final size:50
Alignment explanation
Indices: 25495930--25496049 Score: 145
Period size: 50 Copynumber: 2.4 Consensus size: 50
25495920 GTACATGTAT
* * * *
25495930 GCTCTTACGAGCTGTAAATCGGTATGCTCATC-TGAGCTGA-AAATCGGTAT
1 GCTCTCACAAGCTATAAATCGGTATGCTC-TCATGAGCT-ATAAATCGGTAC
* * *
25495980 GCTCTCCCAAGCTATGAATCGGTATGCTCTCATGAGCTATGAATCGGTAC
1 GCTCTCACAAGCTATAAATCGGTATGCTCTCATGAGCTATAAATCGGTAC
25496030 GCTCTCACAAGCTATAAATC
1 GCTCTCACAAGCTATAAATC
25496050 AGTAACCCTA
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
49 3 0.05
50 56 0.95
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (50 bp):
GCTCTCACAAGCTATAAATCGGTATGCTCTCATGAGCTATAAATCGGTAC
Found at i:25512199 original size:3 final size:3
Alignment explanation
Indices: 25512193--25512228 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
25512183 TAAGTAGTAG
25512193 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
25512229 GATTAATGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:25513496 original size:13 final size:14
Alignment explanation
Indices: 25513478--25513507 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
25513468 GACTTATTTA
25513478 TTTATTTA-TTGGT
1 TTTATTTATTTGGT
25513491 TTTATTTATTTGGT
1 TTTATTTATTTGGT
25513505 TTT
1 TTT
25513508 GGGCCCGGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.13, C:0.00, G:0.13, T:0.73
Consensus pattern (14 bp):
TTTATTTATTTGGT
Found at i:25513771 original size:41 final size:42
Alignment explanation
Indices: 25513661--25513764 Score: 147
Period size: 43 Copynumber: 2.5 Consensus size: 42
25513651 TCCTCTGTGT
* * *
25513661 CTTGTTGCTTCGATGCACTCCACTGCACTTCAAAGAGATACGG
1 CTTGTAGCTTCAATACACTCCACTGCACTTCAAAGAGATA-GG
* *
25513704 CTTGTAGCTTCAATCCACTCCACTGCACTTCAACGAGAT-GG
1 CTTGTAGCTTCAATACACTCCACTGCACTTCAAAGAGATAGG
25513745 CTTGTAGCTTCAATACACTC
1 CTTGTAGCTTCAATACACTC
25513765 TGCTGCAACT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
41 21 0.38
43 35 0.62
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (42 bp):
CTTGTAGCTTCAATACACTCCACTGCACTTCAAAGAGATAGG
Found at i:25514003 original size:13 final size:14
Alignment explanation
Indices: 25513985--25514014 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
25513975 GACTTATTTA
25513985 TTTATTTA-TTGGT
1 TTTATTTATTTGGT
25513998 TTTATTTATTTGGT
1 TTTATTTATTTGGT
25514012 TTT
1 TTT
25514015 GGGCCCGGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.13, C:0.00, G:0.13, T:0.73
Consensus pattern (14 bp):
TTTATTTATTTGGT
Found at i:25514857 original size:22 final size:23
Alignment explanation
Indices: 25514804--25514859 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
25514794 CCCGTTTTTA
* * *
25514804 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
25514827 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
25514849 ATTAAAATTAA
1 ATTAAAATTAA
25514860 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:25514872 original size:16 final size:16
Alignment explanation
Indices: 25514835--25514874 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
25514825 TTAATAAAAT
* *
25514835 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
25514851 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
25514867 TAAAATTA
1 TAAAATTA
25514875 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:25514953 original size:59 final size:61
Alignment explanation
Indices: 25514884--25515063 Score: 265
Period size: 68 Copynumber: 2.9 Consensus size: 61
25514874 ATCAAATTAT
*
25514884 TAATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTA
1 TAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATC--A--A
25514949 TTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATC-A
1 -TAA-T-TATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAA
*
25515012 -AATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAA
1 TAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAA
25515064 ACAAACTTGA
Statistics
Matches: 110, Mismatches: 2, Indels: 11
0.89 0.02 0.09
Matches are distributed among these distances:
59 48 0.44
60 1 0.01
61 2 0.02
63 1 0.01
66 3 0.03
67 1 0.01
68 54 0.49
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (61 bp):
TAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAA
Found at i:25514980 original size:9 final size:9
Alignment explanation
Indices: 25514947--25514974 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
25514937 TTTATCAAAT
25514947 TATTAATTG
1 TATTAATTG
25514956 TATTAATTG
1 TATTAATTG
25514965 TATTAATTG
1 TATTAATTG
25514974 T
1 T
25514975 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:25514984 original size:68 final size:68
Alignment explanation
Indices: 25514863--25515033 Score: 319
Period size: 68 Copynumber: 2.5 Consensus size: 68
25514853 AAATTAATTG
*
25514863 TTAGTAAAATTATCAAATTATTAATTG--TTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
25514926 TGA
66 TGA
25514929 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
25514994 TGA
66 TGA
25514997 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGT
25515034 TGTAACAAAA
Statistics
Matches: 102, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
66 26 0.25
68 76 0.75
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (68 bp):
TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
TGA
Found at i:25515170 original size:22 final size:24
Alignment explanation
Indices: 25515130--25515173 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
25515120 AAATAAACTT
25515130 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
25515154 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAACTATTATATTT
25515174 AATATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:25518010 original size:50 final size:50
Alignment explanation
Indices: 25517942--25518134 Score: 224
Period size: 50 Copynumber: 3.7 Consensus size: 50
25517932 TTCCCTTTAC
* * * **
25517942 TGCCAATGCCATATCCCAGATATGGTTTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* ** *
25517992 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* *
25518042 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
*
25518098 TGCTAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
25518135 TTTCTTTACC
Statistics
Matches: 120, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
50 82 0.68
53 2 0.02
56 36 0.30
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:25522090 original size:30 final size:30
Alignment explanation
Indices: 25522032--25522090 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
25522022 TTTATAAGCC
* ***
25522032 TAGGGGCAAAATTATAATTTTTTGAAACTT
1 TAGGGGCAAAAATATAATTTTGCCAAACTT
*
25522062 TAGGGGCAAAAATGTAATTTTGCCAAACT
1 TAGGGGCAAAAATATAATTTTGCCAAACT
25522091 ATGATTTTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.34
Consensus pattern (30 bp):
TAGGGGCAAAAATATAATTTTGCCAAACTT
Found at i:25522451 original size:45 final size:45
Alignment explanation
Indices: 25522348--25522534 Score: 247
Period size: 45 Copynumber: 4.2 Consensus size: 45
25522338 TACTACGTGT
* * *
25522348 ACCGGGAACCATTGATTATAAAGGTGGTTGC-GGGTGCTGATTCC
1 ACCGGGTATCATTGATTATAAAGGTGGTTGCTGTGTGCTGATTCC
25522392 ACCGGGTATCATTGATTATAAAGGTGGTTGCTGTGTGCTGATTCC
1 ACCGGGTATCATTGATTATAAAGGTGGTTGCTGTGTGCTGATTCC
* *
25522437 ACCGGGTA-CAATTGATTATGAAGGTGGTTGCTATGTGCTGATTCC
1 ACCGGGTATC-ATTGATTATAAAGGTGGTTGCTGTGTGCTGATTCC
** * *
25522482 ACCTAGTATCATTGACTATAAGGGTGG-TGCTGTGTGCTGA-TCC
1 ACCGGGTATCATTGATTATAAAGGTGGTTGCTGTGTGCTGATTCC
*
25522525 ACCGTGTATC
1 ACCGGGTATC
25522535 TGTTATTATT
Statistics
Matches: 127, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
43 11 0.09
44 42 0.33
45 73 0.57
46 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (45 bp):
ACCGGGTATCATTGATTATAAAGGTGGTTGCTGTGTGCTGATTCC
Found at i:25522515 original size:89 final size:88
Alignment explanation
Indices: 25522348--25522528 Score: 256
Period size: 89 Copynumber: 2.0 Consensus size: 88
25522338 TACTACGTGT
* * * *
25522348 ACCGGGAACCATTGATTATAAAGGTGGTTGCGGGTGCTGATTCCACCGGGTATCATTGATTATAA
1 ACCGGGAACAATTGATTATAAAGGTGGTTGCAGGTGCTGATTCCACCGAGTATCATTGACTATAA
25522413 AGGTGGTTGCTGTGTGCTGATTCC
66 AGGTGGTTGCTGTGTGCTGA-TCC
* * * *
25522437 ACCGGGTACAATTGATTATGAAGGTGGTTGCTATGTGCTGATTCCACCTAGTATCATTGACTATA
1 ACCGGGAACAATTGATTATAAAGGTGGTTGC-AGGTGCTGATTCCACCGAGTATCATTGACTATA
*
25522502 AGGGTGG-TGCTGTGTGCTGATCC
65 AAGGTGGTTGCTGTGTGCTGATCC
25522525 ACCG
1 ACCG
25522529 TGTATCTGTT
Statistics
Matches: 82, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
88 7 0.09
89 41 0.50
90 34 0.41
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (88 bp):
ACCGGGAACAATTGATTATAAAGGTGGTTGCAGGTGCTGATTCCACCGAGTATCATTGACTATAA
AGGTGGTTGCTGTGTGCTGATCC
Found at i:25545252 original size:21 final size:21
Alignment explanation
Indices: 25545227--25545274 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
25545217 GTTGAGAAGG
* * *
25545227 AAGTTGTTGCTGTAGAAGAGA
1 AAGTTGTTGCTGAAGAAAAAA
25545248 AAGTTGTTGCTGAAGAAAAAA
1 AAGTTGTTGCTGAAGAAAAAA
25545269 AAGTTG
1 AAGTTG
25545275 AAGAAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.40, C:0.04, G:0.29, T:0.27
Consensus pattern (21 bp):
AAGTTGTTGCTGAAGAAAAAA
Found at i:25549236 original size:131 final size:130
Alignment explanation
Indices: 25549046--25549451 Score: 453
Period size: 131 Copynumber: 3.1 Consensus size: 130
25549036 CACAAGTGAG
* * *
25549046 ATTGTTCATGATCTTAAAATCAAATGAACTTAGATTGCGATATTAAATAAGCTAACCTTAATAAT
1 ATTGTTCATGATCAT-AAATCAAATGAACTTAGGTTGCGATCTTAAATAAGCTAACCTTAATAAT
* *
25549111 ATCATCTGGGATCTTAAATACGTGAGCTTTTTGTAGTTGTGATCTTAAATCAGCTAACTCCAATA
65 ATCATCTGGGATCTTAAATACGTGAG-TTTTTGCAGTTGTGATCTTAAATCAGCTAACTCAAATA
25549176 AA
129 AA
* * * ** *
25549178 ATTGTTCATGACCATAAATCAAATGAGCTTAGGTTGCGATCTTTAATAAATTAACCTTAATAACA
1 ATTGTTCATGATCATAAATCAAATGAACTTAGGTTGCGATCTTAAATAAGCTAACCTTAATAATA
* * * * * * * *
25549243 TAATTTGCGATCTTAAATTA-GCGAGTCGTTTGGAGTTGTAATCTTAAATAAGCTAACTCAAATA
66 TCATCTGGGATCTTAAA-TACGTGAGT-TTTTGCAGTTGTGATCTTAAATCAGCTAACTCAAATA
25549307 AA
129 AA
* * * *
25549309 ATTGTTCAAGATCATAAATCAAATGAACATAGGTTGCGATCTTCAATTAGCTAACCTTAATAATA
1 ATTGTTCATGATCATAAATCAAATGAACTTAGGTTGCGATCTTAAATAAGCTAACCTTAATAATA
* * *
25549374 TCATCTGGGAAT-TTAAAT-CAATGAGTTGTT-CAGATT-TGCAATCTTAAATCAACTAACTCAA
66 TCATCTGGG-ATCTTAAATAC-GTGAGTTTTTGCAG-TTGTG--ATCTTAAATCAGCTAACTCAA
25549435 ATAAA
126 ATAAA
*
25549440 ATTGTTAATGAT
1 ATTGTTCATGAT
25549452 TGTAACACCC
Statistics
Matches: 226, Mismatches: 40, Indels: 17
0.80 0.14 0.06
Matches are distributed among these distances:
129 3 0.01
130 6 0.03
131 200 0.88
132 17 0.08
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.35
Consensus pattern (130 bp):
ATTGTTCATGATCATAAATCAAATGAACTTAGGTTGCGATCTTAAATAAGCTAACCTTAATAATA
TCATCTGGGATCTTAAATACGTGAGTTTTTGCAGTTGTGATCTTAAATCAGCTAACTCAAATAAA
Found at i:25568162 original size:18 final size:18
Alignment explanation
Indices: 25568141--25568180 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
25568131 GATTGAGAGT
* * *
25568141 GAAAAGGAATGTGAAACA
1 GAAAAGAAAAGTGAAAAA
25568159 GAAAAGAAAAGTGAAAAA
1 GAAAAGAAAAGTGAAAAA
25568177 GAAA
1 GAAA
25568181 TTGAAGAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.65, C:0.03, G:0.25, T:0.07
Consensus pattern (18 bp):
GAAAAGAAAAGTGAAAAA
Found at i:25571165 original size:21 final size:19
Alignment explanation
Indices: 25571122--25571166 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
25571112 GAGCTCAAAT
* *
25571122 GAGCTGAAATGAGTTCATG
1 GAGCTGAAATGAGCTAATG
25571141 GAGCTGGAAATGAGCTAATTG
1 GAGCT-GAAATGAGCTAA-TG
25571162 GAGCT
1 GAGCT
25571167 CAATGAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 10 0.45
21 7 0.32
ACGTcount: A:0.31, C:0.11, G:0.33, T:0.24
Consensus pattern (19 bp):
GAGCTGAAATGAGCTAATG
Found at i:25577273 original size:18 final size:17
Alignment explanation
Indices: 25577252--25577294 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
25577242 GTTTGACACT
25577252 TATTGTTTGCAAAGCTCA
1 TATTGTTTGCAAAGCT-A
*
25577270 TATTGTGTGCAAAGCTA
1 TATTGTTTGCAAAGCTA
*
25577287 TGTTGTTT
1 TATTGTTT
25577295 TGAGAACATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.23, C:0.12, G:0.21, T:0.44
Consensus pattern (17 bp):
TATTGTTTGCAAAGCTA
Found at i:25594891 original size:36 final size:36
Alignment explanation
Indices: 25594844--25594918 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
25594834 TTAGAAAGTT
25594844 TTTGACTATATGACCTATTTTAATACTTAAAATATC
1 TTTGACTATATGACCTATTTTAATACTTAAAATATC
25594880 TTTGACTATATGACCTATTTTAATACTTAAAATATC
1 TTTGACTATATGACCTATTTTAATACTTAAAATATC
25594916 TTT
1 TTT
25594919 AAGTTTTCTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.35, C:0.13, G:0.05, T:0.47
Consensus pattern (36 bp):
TTTGACTATATGACCTATTTTAATACTTAAAATATC
Found at i:25596087 original size:14 final size:14
Alignment explanation
Indices: 25596068--25596094 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
25596058 TCATAATATA
25596068 ATTAATTAATTATT
1 ATTAATTAATTATT
25596082 ATTAATTAATTAT
1 ATTAATTAATTAT
25596095 GAAAAAGTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATTAATTAATTATT
Found at i:25600317 original size:32 final size:32
Alignment explanation
Indices: 25600276--25600339 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
25600266 AAACTTCAAG
*
25600276 AAAAACTCAAACTCATCAATGGCATTATGTAT
1 AAAAACTCAAAATCATCAATGGCATTATGTAT
25600308 AAAAACTCAAAATCATCAATGGCATTATGTAT
1 AAAAACTCAAAATCATCAATGGCATTATGTAT
25600340 GTTTTTTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.45, C:0.17, G:0.09, T:0.28
Consensus pattern (32 bp):
AAAAACTCAAAATCATCAATGGCATTATGTAT
Found at i:25609918 original size:50 final size:50
Alignment explanation
Indices: 25609793--25610040 Score: 223
Period size: 50 Copynumber: 4.9 Consensus size: 50
25609783 TAATAATAAC
* * * ** *
25609793 ATGCCAAAGACATGTCCCAGACATGGTCTTACAGGGGATGTTTC-T-T-G
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCG
* * * * **
25609840 TACTGCCAATGTCATATCCCAGATATGGTCTTAAATGGGAGTTCTCATATCG
1 -A-TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCG
* * ** *
25609892 GTGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCG
* *
25609942 ATGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATAACCTCAATG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---G
*
25609998 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
25610041 TTACCCAAAT
Statistics
Matches: 160, Mismatches: 30, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
48 1 0.01
49 34 0.21
50 80 0.50
51 1 0.01
52 1 0.01
53 2 0.01
56 41 0.26
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (50 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCG
Found at i:25609987 original size:100 final size:102
Alignment explanation
Indices: 25609793--25610038 Score: 250
Period size: 100 Copynumber: 2.4 Consensus size: 102
25609783 TAATAATAAC
* * * * * * *
25609793 ATGCCAAAGACATGTCCCAGACATGGTCTTACAGGGGATGTTTCTTGTACTGCCAATGTCATATC
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGATCTATCTCGTACTGCCAACGCCATATC
* **
25609858 CCAGATATGGTCTTAAATGGGAGTTCTCAT-A-TC-G
66 CCAGACATGGTCTTAAATGGGACCTCTCATAACTCAG
* * *
25609892 GTGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCG-A-TGCCAACGCCAT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA--TCT-ATCTCGTACTGCCAACGCCAT
* * *
25609955 GTCCTAGACATGGTCTTACATGGGACCTCTCATAACCTCAATG
63 ATCCCAGACATGGTCTTAAATGGGACCTCTCATAA-CTC-A-G
*
25609998 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGATCT
25610039 CTTTACCCAA
Statistics
Matches: 118, Mismatches: 20, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
99 33 0.28
100 37 0.31
101 4 0.03
102 4 0.03
103 2 0.02
104 3 0.03
106 35 0.30
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (102 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGATCTATCTCGTACTGCCAACGCCATATC
CCAGACATGGTCTTAAATGGGACCTCTCATAACTCAG
Found at i:25616868 original size:50 final size:50
Alignment explanation
Indices: 25616779--25616902 Score: 153
Period size: 50 Copynumber: 2.5 Consensus size: 50
25616769 TATCCCAAAT
* * *
25616779 ATGGTCTTACATGGGG--TTCTCATATCGGTGCCCATGCCATGTCCCAGAC
1 ATGGTCTTACA-GGGGACCTCTCATATCGGTGCCAACGCCATGTCCCAGAC
* * * *
25616828 ATGGTCTTACGGGGGACCTCTCATCTCGGTGCGAACGCCATGTCCTAGAC
1 ATGGTCTTACAGGGGACCTCTCATATCGGTGCCAACGCCATGTCCCAGAC
*
25616878 ATGGTCTTACATGGGACCTCTCATA
1 ATGGTCTTACAGGGGACCTCTCATA
25616903 ACCTCAATTA
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
48 4 0.06
49 10 0.16
50 49 0.78
ACGTcount: A:0.19, C:0.28, G:0.25, T:0.27
Consensus pattern (50 bp):
ATGGTCTTACAGGGGACCTCTCATATCGGTGCCAACGCCATGTCCCAGAC
Found at i:25620563 original size:37 final size:36
Alignment explanation
Indices: 25620512--25620657 Score: 159
Period size: 37 Copynumber: 4.0 Consensus size: 36
25620502 ACATAAGTAG
* *
25620512 TCCAACCGA-AACACGCCAAATGCTCATAAGAGCTAT
1 TCCAACTGATAACACGCCAAATGCTCA-AAGAGCTAA
* *
25620548 TCCAACTAATAACACGCCAAGTGCTCCAAAGAGCTAA
1 TCCAACTGATAACACGCCAAATGCT-CAAAGAGCTAA
* *
25620585 TCCAACTGATAACACACCAAATGCTCCGAAGAGCTAA
1 TCCAACTGATAACACGCCAAATGCT-CAAAGAGCTAA
* * * *
25620622 TCGAACCGATAACACGCCAAATACTTCGAAGAGCTA
1 TCCAACTGATAACACGCCAAATGC-TCAAAGAGCTA
25620658 TATATTTGCC
Statistics
Matches: 95, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
36 7 0.07
37 85 0.89
38 3 0.03
ACGTcount: A:0.40, C:0.29, G:0.14, T:0.16
Consensus pattern (36 bp):
TCCAACTGATAACACGCCAAATGCTCAAAGAGCTAA
Found at i:25620654 original size:74 final size:73
Alignment explanation
Indices: 25620512--25620657 Score: 175
Period size: 74 Copynumber: 2.0 Consensus size: 73
25620502 ACATAAGTAG
* * * * * *
25620512 TCCAACCGAAACACGCCAAATGCTCATAAGAGCTATTCCAACTAATAACACGCCAAGTGCTCCAA
1 TCCAACCGAAACACACCAAATGCTCAGAAGAGCTAATCCAACCAATAACACGCCAAATACTCCAA
25620577 AGAGCTAA
66 AGAGCTAA
* * * * * *
25620585 TCCAACTGATAACACACCAAATGCTCCGAAGAGCTAATCGAACCGATAACACGCCAAATACTTCG
1 TCCAACCGA-AACACACCAAATGCTCAGAAGAGCTAATCCAACCAATAACACGCCAAATACTCCA
25620650 AAGAGCTA
65 AAGAGCTA
25620658 TATATTTGCC
Statistics
Matches: 60, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
73 8 0.13
74 52 0.87
ACGTcount: A:0.40, C:0.29, G:0.14, T:0.16
Consensus pattern (73 bp):
TCCAACCGAAACACACCAAATGCTCAGAAGAGCTAATCCAACCAATAACACGCCAAATACTCCAA
AGAGCTAA
Found at i:25632856 original size:20 final size:20
Alignment explanation
Indices: 25632832--25632885 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
25632822 TAATTTTTCT
25632832 TGTCTTAATTAAATTAAATGA
1 TGTCTTAATTAAATTAAAT-A
* **
25632853 -GTCTTGATTTTATTAAATA
1 TGTCTTAATTAAATTAAATA
25632872 TGTCTTAAATTAAA
1 TGTCTT-AATTAAA
25632886 ACATGAATTA
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
19 1 0.04
20 20 0.80
21 4 0.16
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.46
Consensus pattern (20 bp):
TGTCTTAATTAAATTAAATA
Found at i:25653159 original size:13 final size:13
Alignment explanation
Indices: 25653141--25653165 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25653131 TTAAAACTAA
25653141 AATTAACTAAATT
1 AATTAACTAAATT
25653154 AATTAACTAAAT
1 AATTAACTAAAT
25653166 AACACGACAA
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:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (13 bp):
AATTAACTAAATT
Found at i:25658748 original size:60 final size:59
Alignment explanation
Indices: 25658683--25658795 Score: 172
Period size: 59 Copynumber: 1.9 Consensus size: 59
25658673 AATAAATAGA
*
25658683 AAATTAAATCTATTTTAAAACATTTTTAAAATTGGGATTTAAATATTTTATATAAGTTTT
1 AAATT-AATCTAATTTAAAACATTTTTAAAATTGGGATTTAAATATTTTATATAAGTTTT
* * * *
25658743 AAATTAATTTAATTTAATATATTTTTAAAATTTGGATTTAAATATTTTATATA
1 AAATTAATCTAATTTAAAACATTTTTAAAATTGGGATTTAAATATTTTATATA
25658796 GATTTCAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
59 43 0.90
60 5 0.10
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.50
Consensus pattern (59 bp):
AAATTAATCTAATTTAAAACATTTTTAAAATTGGGATTTAAATATTTTATATAAGTTTT
Found at i:25659244 original size:71 final size:70
Alignment explanation
Indices: 25659110--25659293 Score: 192
Period size: 71 Copynumber: 2.6 Consensus size: 70
25659100 GGGTGTTACA
* * ** * *
25659110 AGGATATTAAATGAATGA-AGTATCAGTGTTGTGGCAGGATGTTAAATGAATAAGATGTTGGTGT
1 AGGATATTAAATGAATGAGA-TATCGGTGTTGTGGCGGGATGTTAAACAAATAAGATATCGGTGT
**
25659174 TGTGGCGG
65 T-AAG-GG
* * *
25659182 AGG-TATTAAATGAATGAGATATCGGTATTATGGCGGGATGTTAAACAAATGAGATATCGGTGTT
1 AGGATATTAAATGAATGAGATATCGGTGTTGTGGCGGGATGTTAAACAAATAAGATATCGGTGTT
*
25659246 AAGGT
66 AAGGG
* * *
25659251 AGGATGTTAAACGATTGAGATATCGGTGTTGTGGCGGGATGTT
1 AGGATATTAAATGAATGAGATATCGGTGTTGTGGCGGGATGTT
25659294 GAAGGTATTG
Statistics
Matches: 93, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
69 4 0.04
70 35 0.38
71 50 0.54
72 4 0.04
ACGTcount: A:0.30, C:0.05, G:0.33, T:0.32
Consensus pattern (70 bp):
AGGATATTAAATGAATGAGATATCGGTGTTGTGGCGGGATGTTAAACAAATAAGATATCGGTGTT
AAGGG
Found at i:25659291 original size:35 final size:35
Alignment explanation
Indices: 25659111--25659293 Score: 170
Period size: 35 Copynumber: 5.2 Consensus size: 35
25659101 GGTGTTACAA
* * * *
25659111 GGATATTAAATGAATGA-AGTATCAGTGTTGTGGCA
1 GGATGTTAAACGAATGAGA-TATCGGTGTTGTGGCG
* * * *
25659146 GGATGTTAAATGAATAAGATGTTGGTGTTGTGGCG
1 GGATGTTAAACGAATGAGATATCGGTGTTGTGGCG
* * * * *
25659181 GAGGTATTAAATGAATGAGATATCGGTATTATGGCG
1 G-GATGTTAAACGAATGAGATATCGGTGTTGTGGCG
* ** **
25659217 GGATGTTAAACAAATGAGATATCGGTGTTAAGGTA
1 GGATGTTAAACGAATGAGATATCGGTGTTGTGGCG
*
25659252 GGATGTTAAACGATTGAGATATCGGTGTTGTGGCG
1 GGATGTTAAACGAATGAGATATCGGTGTTGTGGCG
25659287 GGATGTT
1 GGATGTT
25659294 GAAGGTATTG
Statistics
Matches: 119, Mismatches: 27, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
35 90 0.76
36 29 0.24
ACGTcount: A:0.30, C:0.05, G:0.33, T:0.32
Consensus pattern (35 bp):
GGATGTTAAACGAATGAGATATCGGTGTTGTGGCG
Found at i:25677166 original size:22 final size:22
Alignment explanation
Indices: 25677141--25677184 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
25677131 ATAAAATAAA
* *
25677141 GAAAAATGTCATAAAGTGAATT
1 GAAAAATATCATAAAGTAAATT
*
25677163 GAAATATATCATAAAGTAAATT
1 GAAAAATATCATAAAGTAAATT
25677185 ATTTTTTGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.05, G:0.14, T:0.30
Consensus pattern (22 bp):
GAAAAATATCATAAAGTAAATT
Found at i:25697674 original size:272 final size:272
Alignment explanation
Indices: 25697188--25697734 Score: 824
Period size: 272 Copynumber: 2.0 Consensus size: 272
25697178 TCTTGGGTTC
*
25697188 GATCCTTGGAATACTCTAGTGTTCCATTGTAACACTACAAATATTACAACTGACATGTCACACTT
1 GATCCTTGGAATACTCCAGTGTTCCATTGTAACACTACAAATATTACAACTGACATGTCACACTT
* * * *
25697253 GCAGTAAAGCTGCGATATTTATATTCGTTTTAATCCCAGTGTTGATTCTTTTTCTCTCTTTGTTC
66 ACAGTAAAGCCGCGATATTTATACTCGTTTTAATCCCAGTGTTGATTCTTTTTCTCTCTTCGTTC
* * * **
25697318 AAGAGGACGGAGATAGGAGCGATCAGTAATAAACGAATATGTTCAATATTCTTTCACGGATAACA
131 AAGAGGACAGAGATAGGAGCGATCAGTAATAAACAAATATGTTCAATATTCTTTAACAAATAACA
* * *
25697383 AGCCACAGAGTTTGGCAGACCTCTATAAGAGGGCTCATAGGTTTGCGGAGGCAGAGGAGGTAAAG
196 AGCCACAGAGTTTGGCAGACCTCTATAAGAGGGCTCACAGGTTCGCGAAGGCAGAGGAGGTAAAG
25697448 AGGACAACTCAT
261 AGGACAACTCAT
* *
25697460 GATCCTTGGAATACTCCAGTGTTCCATTGTAACACTACAAATATTACAACTGACCTGTTACACTT
1 GATCCTTGGAATACTCCAGTGTTCCATTGTAACACTACAAATATTACAACTGACATGTCACACTT
* * *
25697525 ACAGTAAAGCCGTGATATTTATACTCGTTTTAATCCTAGTGTTGATTCTTTTTCTCTCTTCGTTT
66 ACAGTAAAGCCGCGATATTTATACTCGTTTTAATCCCAGTGTTGATTCTTTTTCTCTCTTCGTTC
* * * * * *
25697590 GAGAGGACAGAGATAGGAGTGGTCAGTAATAAACAAATATGTTCGATATTCTTTAACAAATGATA
131 AAGAGGACAGAGATAGGAGCGATCAGTAATAAACAAATATGTTCAATATTCTTTAACAAATAACA
* * * * * *
25697655 GGCCACAGAGTTTGGCAGACTTTTATGAGAGTGCTCACAGGTTCGCGAAGGTAGAGGAGGTAAAG
196 AGCCACAGAGTTTGGCAGACCTCTATAAGAGGGCTCACAGGTTCGCGAAGGCAGAGGAGGTAAAG
25697720 AGGACAACTCAT
261 AGGACAACTCAT
25697732 GAT
1 GAT
25697735 GTTTTGTATA
Statistics
Matches: 245, Mismatches: 30, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
272 245 1.00
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.31
Consensus pattern (272 bp):
GATCCTTGGAATACTCCAGTGTTCCATTGTAACACTACAAATATTACAACTGACATGTCACACTT
ACAGTAAAGCCGCGATATTTATACTCGTTTTAATCCCAGTGTTGATTCTTTTTCTCTCTTCGTTC
AAGAGGACAGAGATAGGAGCGATCAGTAATAAACAAATATGTTCAATATTCTTTAACAAATAACA
AGCCACAGAGTTTGGCAGACCTCTATAAGAGGGCTCACAGGTTCGCGAAGGCAGAGGAGGTAAAG
AGGACAACTCAT
Found at i:25701640 original size:12 final size:12
Alignment explanation
Indices: 25701623--25701647 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25701613 TTCTAAACTC
25701623 TCATTAAAAGTT
1 TCATTAAAAGTT
25701635 TCATTAAAAGTT
1 TCATTAAAAGTT
25701647 T
1 T
25701648 TCAAGGTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TCATTAAAAGTT
Found at i:25709249 original size:175 final size:174
Alignment explanation
Indices: 25708971--25709437 Score: 528
Period size: 175 Copynumber: 2.7 Consensus size: 174
25708961 ATTACAACAC
* * *
25708971 TCAAACTTTAAAGA-TATTCAAAATCTTAGAGCTAGCAATTTAAGATTGCGACTCTCCTTTAAGG
1 TCAAACTTCAAAGACT-TTCAAAATCTTAGAGCTAGC-GTTTAAGATCGCGACTC-CCTTTAAGG
*** * **
25709035 TTTTGCGATTTCAA-ATCGCAACCTTCAAACTTCAAAGATTTTCAGAATCTTAAAGCTAGTGATT
63 TTCACCGATTT-AAGATCGCAACCTTCAAACTTTAAAGATTTTCAGAATCTTAAAGCTAGCCATT
* * * *
25709099 TAAGATCGTGACATC-CTTTTAAGGTTTGT-TGATTTAAGATTGCAACCT
127 TAAGACCGTGAC-TCTCCTTTAAGGTTT-TCTAATTTAAGATCGCAACCT
* * *
25709147 TCAAACTTCAAATACTTTCATAATCTTAGAACTAGCGTTTAAGATCGCGACTCCCTTTTAAGGTT
1 TCAAACTTCAAAGACTTTCAAAATCTTAGAGCTAGCGTTTAAGATCGCGACTCCC-TTTAAGGTT
* * * *
25709212 CACCTATTTAAGATTGCAACCTTCAAACTTTAAAGATTTTAAGAATCTTAGAGCTAGCCATTTAA
65 CACCGATTTAAGATCGCAACCTTCAAACTTTAAAGATTTTCAGAATCTTAAAGCTAGCCATTTAA
* * *
25709277 GACCGTGGCTCTCCTTTATGGTTTTCTAATTTAATATCGCAACCT
130 GACCGTGACTCTCCTTTAAGGTTTTCTAATTTAAGATCGCAACCT
* * * * * ** *
25709322 TCAAACTTCAAAGATTTTCAAAACCATAGAGTTAGCGATTTAAGATGGTAACTCCCCTTTAAAGT
1 TCAAACTTCAAAGACTTTCAAAATCTTAGAGCTAGCG-TTTAAGATCGCGACT-CCCTTTAAGGT
* *
25709387 TCGCCGATTTAAGATCACAACCTTCAAACTTTAAAGATTTTCAGAATCTTA
64 TCACCGATTTAAGATCGCAACCTTCAAACTTTAAAGATTTTCAGAATCTTA
25709438 GTGTTAGTAA
Statistics
Matches: 245, Mismatches: 39, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
174 7 0.03
175 139 0.57
176 95 0.39
177 4 0.02
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (174 bp):
TCAAACTTCAAAGACTTTCAAAATCTTAGAGCTAGCGTTTAAGATCGCGACTCCCTTTAAGGTTC
ACCGATTTAAGATCGCAACCTTCAAACTTTAAAGATTTTCAGAATCTTAAAGCTAGCCATTTAAG
ACCGTGACTCTCCTTTAAGGTTTTCTAATTTAAGATCGCAACCT
Found at i:25709398 original size:263 final size:264
Alignment explanation
Indices: 25708902--25709438 Score: 672
Period size: 263 Copynumber: 2.0 Consensus size: 264
25708892 AAAAATTTTT
* * * *
25708902 AGAATCTTATAGCTAGCGATTTAAAATCGCGACTCCCCTTTAAGGTTCACCGATTTCATATTACA
1 AGAATCTTAGAACTAGCGATTTAAAATCGCGACTCCCCTTTAAGGTTCACCGATTTAAGATTACA
**
25708967 ACACTCAAACTTTAAAGATATTCAAAATCTTAGAGCTAGCAATTTAAGATTGCGACTCTCCTTTA
66 ACACTCAAACTTTAAAGATATTCAAAATCTTAGAGCTAGCAATTTAAGACCGCGACTCTCCTTTA
* * * * *
25709032 AGGTTTTGCGATTTCAAATCGCAACCTTCAAACTTCAAAGATTTTCAGAATCTTAAAGCTAGTGA
131 AGGTTTTGCAATTTCAAATCGCAACCTTCAAACTTCAAAGATTTTCAAAACCATAAAGCTAGCGA
* * * * ** ** *
25709097 TTTAAGATCGTGACATCCTTTTAAGGTTTGTTGATTTAAGATTGCAACCTTCAAACTTCAAATAC
196 TTTAAGATCGTAACATCCCTTTAAAGTTCGCCGATTTAAGATCACAACCTTCAAACTTCAAAGAC
25709162 TTTC
261 TTTC
* * * * *
25709166 ATAATCTTAGAACTAGCG-TTTAAGATCGCGACTCCCTTTTAAGGTTCACCTATTTAAGATTGCA
1 AGAATCTTAGAACTAGCGATTTAAAATCGCGACTCCCCTTTAAGGTTCACCGATTTAAGATTACA
* * * *
25709230 AC-CTTCAAACTTTAAAGAT-TTTAAGAATCTTAGAGCTAGCCATTTAAGACCGTGGCTCTCCTT
66 ACAC-TCAAACTTTAAAGATATTCAA-AATCTTAGAGCTAGCAATTTAAGACCGCGACTCTCCTT
* * *
25709293 TATGGTTTT-CTAATTT-AATATCGCAACCTTCAAACTTCAAAGATTTTCAAAACCATAGAGTTA
129 TAAGGTTTTGC-AATTTCAA-ATCGCAACCTTCAAACTTCAAAGATTTTCAAAACCATAAAGCTA
* *
25709356 GCGATTTAAGATGGTAAC-TCCCCTTTAAAGTTCGCCGATTTAAGATCACAACCTTCAAACTTTA
192 GCGATTTAAGATCGTAACAT-CCCTTTAAAGTTCGCCGATTTAAGATCACAACCTTCAAACTTCA
*
25709420 AAGATTTTC
256 AAGACTTTC
25709429 AGAATCTTAG
1 AGAATCTTAG
25709439 TGTTAGTAAT
Statistics
Matches: 232, Mismatches: 36, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
262 9 0.04
263 208 0.90
264 15 0.06
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.34
Consensus pattern (264 bp):
AGAATCTTAGAACTAGCGATTTAAAATCGCGACTCCCCTTTAAGGTTCACCGATTTAAGATTACA
ACACTCAAACTTTAAAGATATTCAAAATCTTAGAGCTAGCAATTTAAGACCGCGACTCTCCTTTA
AGGTTTTGCAATTTCAAATCGCAACCTTCAAACTTCAAAGATTTTCAAAACCATAAAGCTAGCGA
TTTAAGATCGTAACATCCCTTTAAAGTTCGCCGATTTAAGATCACAACCTTCAAACTTCAAAGAC
TTTC
Found at i:25709444 original size:88 final size:88
Alignment explanation
Indices: 25708889--25709438 Score: 534
Period size: 88 Copynumber: 6.3 Consensus size: 88
25708879 ACTTTCGAAT
* * * * *
25708889 TTCAAAAATTTTTAGAATCTTATAGCTAGCGATTTAAAATCGCGACTCCCCTTTAAGGTTCACCG
1 TTCAAAGATTTTCAGAATCTTAGAGCTAGCGATTTAAGATCGCGACTCCCCTTTAAGGTTCGCCG
* * **
25708954 ATTTCATATTACAACAC-TCAAAC
66 ATTTAAGATCGCAAC-CTTCAAAC
* * * * * * *
25708977 TTTAAAGATATTCAAAATCTTAGAGCTAGCAATTTAAGATTGCGACTCTCCTTTAAGGTTTTG-C
1 TTCAAAGATTTTCAGAATCTTAGAGCTAGCGATTTAAGATCGCGACTCCCCTTTAAGG-TTCGCC
25709041 GATTTCAA-ATCGCAACCTTCAAAC
65 GATTT-AAGATCGCAACCTTCAAAC
* * * * * **
25709065 TTCAAAGATTTTCAGAATCTTAAAGCTAGTGATTTAAGATCGTGACAT-CCTTTTAAGGTTTGTT
1 TTCAAAGATTTTCAGAATCTTAGAGCTAGCGATTTAAGATCGCGAC-TCCCCTTTAAGGTTCGCC
*
25709129 GATTTAAGATTGCAACCTTCAAAC
65 GATTTAAGATCGCAACCTTCAAAC
* * * * * * *
25709153 TTCAAATACTTTCATAATCTTAGAACTAGCG-TTTAAGATCGCGACTCCCTTTTAAGGTTCACCT
1 TTCAAAGATTTTCAGAATCTTAGAGCTAGCGATTTAAGATCGCGACTCCCCTTTAAGGTTCGCCG
*
25709217 ATTTAAGATTGCAACCTTCAAAC
66 ATTTAAGATCGCAACCTTCAAAC
* * * * * * * * ** **
25709240 TTTAAAGATTTTAAGAATCTTAGAGCTAGCCATTTAAGACCGTGGCTCTCCTTTATGGTTTTCTA
1 TTCAAAGATTTTCAGAATCTTAGAGCTAGCGATTTAAGATCGCGACTCCCCTTTAAGGTTCGCCG
*
25709305 ATTTAATATCGCAACCTTCAAAC
66 ATTTAAGATCGCAACCTTCAAAC
* * * * * ** *
25709328 TTCAAAGATTTTCAAAACCATAGAGTTAGCGATTTAAGATGGTAACTCCCCTTTAAAGTTCGCCG
1 TTCAAAGATTTTCAGAATCTTAGAGCTAGCGATTTAAGATCGCGACTCCCCTTTAAGGTTCGCCG
*
25709393 ATTTAAGATCACAACCTTCAAAC
66 ATTTAAGATCGCAACCTTCAAAC
*
25709416 TTTAAAGATTTTCAGAATCTTAG
1 TTCAAAGATTTTCAGAATCTTAG
25709439 TGTTAGTAAT
Statistics
Matches: 372, Mismatches: 82, Indels: 16
0.79 0.17 0.03
Matches are distributed among these distances:
86 1 0.00
87 79 0.21
88 288 0.77
89 4 0.01
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.35
Consensus pattern (88 bp):
TTCAAAGATTTTCAGAATCTTAGAGCTAGCGATTTAAGATCGCGACTCCCCTTTAAGGTTCGCCG
ATTTAAGATCGCAACCTTCAAAC
Found at i:25712124 original size:93 final size:93
Alignment explanation
Indices: 25711809--25712407 Score: 671
Period size: 93 Copynumber: 6.4 Consensus size: 93
25711799 CCTTAAAAGA
* ** * * * *
25711809 GGTTACATGTGTAAGACCATAGTTTGAATATTGCAACATGGGGAGTCCG-CCAGGATAGTAAACA
1 GGTTACATGTGTAAGACCATAGCTTGGCTATGGCAACATGGGGAGTCTGTCGA-GATCGTAAACA
** *
25711873 TGGGGTAGTCTACCAGAACATTAAACATG
65 TGGGGTAGTCCGCCAGGACATTAAACATG
* * * * *** * *
25711902 GTGTTACATGTGTATGACCATAGCTCGGCAATGGCAACATGAGGAGTCCACCGGGATAGTAAACA
1 G-GTTACATGTGTAAGACCATAGCTTGGCTATGGCAACATGGGGAGTCTGTCGAGATCGTAAACA
* * * *
25711967 AGAGTTAGTCCGCCAGGCCA-TAAACATG
65 TGGGGTAGTCCGCCAGGACATTAAACATG
* * *
25711995 GGTTACATGTGTAAGACCATAGCTTGACTATGGCAACATGAGGAGTCTGTCAAGATCGTAAACAT
1 GGTTACATGTGTAAGACCATAGCTTGGCTATGGCAACATGGGGAGTCTGTCGAGATCGTAAACAT
*
25712060 GGGTTAGTCCGCCAGGACATTAAACATG
66 GGGGTAGTCCGCCAGGACATTAAACATG
* * * * *
25712088 GGTTATATGTGTAAGACCATAGCTTAGCTGTGGCAACATGGGGAGTCTGTTGAGATTGTAAACAT
1 GGTTACATGTGTAAGACCATAGCTTGGCTATGGCAACATGGGGAGTCTGTCGAGATCGTAAACAT
* * * *
25712153 GGGGTAGTTCGTCAGGATATTAAATATG
66 GGGGTAGTCCGCCAGGACATTAAACATG
* *
25712181 GGTTACATCTGTAAGACCATAGCTTGGCTATGGCAACATGGGGAGTCTGTCGAGACCGTAAACAT
1 GGTTACATGTGTAAGACCATAGCTTGGCTATGGCAACATGGGGAGTCTGTCGAGATCGTAAACAT
* *
25712246 GGGGTAGTCCACCAGGACATTAAACGTG
66 GGGGTAGTCCGCCAGGACATTAAACATG
* *
25712274 GGTTACATGTGTAAGACCATAGCTTGGCTATGGAAACATGGGGAGTCTGTCGAGACCGTAAACAT
1 GGTTACATGTGTAAGACCATAGCTTGGCTATGGCAACATGGGGAGTCTGTCGAGATCGTAAACAT
* * * * * *
25712339 GGGGTAGTCCTCTATGAAAATAAACATAC
66 GGGGTAGTCCGCCAGGACATTAAACAT-G
* * * * * *
25712368 AGTTACATGTGGAAGACTATAGCTCGACTATGGCAGCATG
1 GGTTACATGTGTAAGACCATAGCTTGGCTATGGCAACATG
25712408 TGAAGTCTAC
Statistics
Matches: 429, Mismatches: 73, Indels: 7
0.84 0.14 0.01
Matches are distributed among these distances:
92 70 0.16
93 262 0.61
94 96 0.22
95 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.27, T:0.25
Consensus pattern (93 bp):
GGTTACATGTGTAAGACCATAGCTTGGCTATGGCAACATGGGGAGTCTGTCGAGATCGTAAACAT
GGGGTAGTCCGCCAGGACATTAAACATG
Found at i:25716126 original size:21 final size:21
Alignment explanation
Indices: 25716084--25716128 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
25716074 AGAACATACA
*
25716084 AATATGTGGACAAGCCACCAG
1 AATATGTGGACAAGCCAACAG
*
25716105 AATATGTGGATATA-CCAACAG
1 AATATGTGGACA-AGCCAACAG
25716126 AAT
1 AAT
25716129 GTGTCGATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.42, C:0.18, G:0.20, T:0.20
Consensus pattern (21 bp):
AATATGTGGACAAGCCAACAG
Found at i:25717658 original size:32 final size:32
Alignment explanation
Indices: 25717611--25717677 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
25717601 AGCTCAGCTC
*
25717611 AGCTCGCCACACCACTCAGCTCACCACCGTCT
1 AGCTCGACACACCACTCAGCTCACCACCGTCT
* * *
25717643 AGCTCGACACTCCACTCAGGTCACCACTGTCT
1 AGCTCGACACACCACTCAGCTCACCACCGTCT
25717675 AGC
1 AGC
25717678 CTGCCCACTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.22, C:0.45, G:0.15, T:0.18
Consensus pattern (32 bp):
AGCTCGACACACCACTCAGCTCACCACCGTCT
Found at i:25723433 original size:24 final size:24
Alignment explanation
Indices: 25723406--25723451 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
25723396 AGAACAGTCC
* *
25723406 CAAAAGGAAATGCAGGAGCAGCTT
1 CAAAAGCAAATGAAGGAGCAGCTT
*
25723430 CAAAAGCAAATGAATGAGCAGC
1 CAAAAGCAAATGAAGGAGCAGC
25723452 AAAAAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (24 bp):
CAAAAGCAAATGAAGGAGCAGCTT
Found at i:25727807 original size:44 final size:43
Alignment explanation
Indices: 25727748--25727958 Score: 239
Period size: 45 Copynumber: 4.8 Consensus size: 43
25727738 GATCGCATTT
* * *
25727748 AGTCTTATCCCCCTGAAGTTGCAATGGAGTAGACTAAGCAAGCA
1 AGTCTTATCCTCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCA
*
25727792 AGTCTTGTCCTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATAGCA
1 AGTCTTATCCTCCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AGCA
*
25727837 AATCTTAT-CTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
1 AGTCTTATCCT-CCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCA
* * *
25727881 AGTCTTATCTTCCTGAAGTTGCAGTGAAGCAGATTGAAGATAGCA
1 AGTCTTATCCTCCTGAAGTTGCAGTGGAGCAGACT-AAGA-AGCA
*
25727926 AATCTTAT-CTACCTGAAGTTGCAGTGGAGCAGA
1 AGTCTTATCCT-CCTGAAGTTGCAGTGGAGCAGA
25727959 TTAGAGCCGA
Statistics
Matches: 144, Mismatches: 13, Indels: 19
0.82 0.07 0.11
Matches are distributed among these distances:
43 2 0.01
44 69 0.48
45 71 0.49
46 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (43 bp):
AGTCTTATCCTCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
Found at i:25727854 original size:45 final size:44
Alignment explanation
Indices: 25727750--25727999 Score: 253
Period size: 44 Copynumber: 5.6 Consensus size: 44
25727740 TCGCATTTAG
* * * *
25727750 TCTTATCCCCCTGAAGTTGCAATGGAGTAGACTAAGCA-AGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-ATAGCAAA
*
25727794 TCTTGTC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATAGCAAA
1 TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGATAGCAAA
*
25727839 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-TAAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAT-AGCAAA
* * *
25727883 TCTTATCTTCCTGAAGTTGCAGTGAAGCAGATTGAAGATAGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGATAGCAAA
* *
25727928 TCTTATCTACCTGAAGTTGCAGTGGAGCAGA-TTAG--AGCCGATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGATAG-C-A-AA
* *
25727972 TCCTATCTCCCTGAAGTTGCAGGGGAGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGC
25728000 GGATTAAAAC
Statistics
Matches: 178, Mismatches: 16, Indels: 24
0.82 0.07 0.11
Matches are distributed among these distances:
41 2 0.01
42 1 0.01
43 7 0.04
44 92 0.52
45 72 0.40
46 4 0.02
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGATAGCAAA
Found at i:25727857 original size:89 final size:89
Alignment explanation
Indices: 25727750--25727958 Score: 337
Period size: 89 Copynumber: 2.3 Consensus size: 89
25727740 TCGCATTTAG
* * * *
25727750 TCTTATCCCCCTGAAGTTGCAATGGAGTAGACTAAGCAAGCAAGTCTTGTCCTCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAGCAAGTCTTATCCTCCTGAAGTTGCA
*
25727815 GTGAGGCAGACTGAAGATAGCAAA
66 GTGAAGCAGACTGAAGATAGCAAA
* *
25727839 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCTTCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAGCAAGTCTTATCCTCCTGAAGTTGCA
*
25727904 GTGAAGCAGATTGAAGATAGCAAA
66 GTGAAGCAGACTGAAGATAGCAAA
*
25727928 TCTTATCTACCTGAAGTTGCAGTGGAGCAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
25727959 TTAGAGCCGA
Statistics
Matches: 111, Mismatches: 9, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
89 111 1.00
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (89 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGCAAGCAAGTCTTATCCTCCTGAAGTTGCA
GTGAAGCAGACTGAAGATAGCAAA
Found at i:25727979 original size:89 final size:88
Alignment explanation
Indices: 25727750--25727993 Score: 294
Period size: 89 Copynumber: 2.7 Consensus size: 88
25727740 TCGCATTTAG
** * * * * * *
25727750 TCTTATCCCCCTGAAGTTGCAATGGAGTAGACTAAGCAAGCAAGTCTTGTCCTCCTGAAGTTGCA
1 TCTTATCTACCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAATCCTATCTTCCTGAAGTTGCA
*
25727815 GTGAGGCAGACTGAAGATAGCAAA
65 GTGAAGCAGACTGAAGATAGCAAA
* * *
25727839 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCTTCCTGAAGTTGCA
1 TCTTATCTACCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAATCCTATCTTCCTGAAGTTGCA
*
25727904 GTGAAGCAGATTGAAGATAGCAAA
65 GTGAAGCAGACTGAAGATAGCAAA
* *
25727928 TCTTATCTACCTGAAGTTGCAGTGGAGCAGA-TTAG-AGCCGATAATCCTATCTCCCTGAAGTTG
1 TCTTATCTACCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A-AATCCTATCTTCCTGAAGTTG
25727991 CAG
63 CAG
25727994 GGGAGCGGAT
Statistics
Matches: 139, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
86 2 0.01
87 1 0.01
88 4 0.03
89 132 0.95
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (88 bp):
TCTTATCTACCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAATCCTATCTTCCTGAAGTTGCAG
TGAAGCAGACTGAAGATAGCAAA
Found at i:25727999 original size:44 final size:42
Alignment explanation
Indices: 25727664--25728086 Score: 241
Period size: 44 Copynumber: 9.8 Consensus size: 42
25727654 GGTAGCCAAT
* ** * * *
25727664 AATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATAAAAATCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAAGCA
* * * ***
25727706 AGGATCTTATCTCTCTGAAGTTGCAGAT--AGCAGA-TCGCATTT
1 A--ATCTTATCTCCCTGAAGTTGCAG-TGGAGCAGATTAGAAGCA
* * * * *
25727748 AGTCTTATCCCCCTGAAGTTGCAATGGAGTAGACTAAGCAAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAG-AAGCA
* * *
25727792 AGTCTTGTC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATAGCA
1 AATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-T-TAGA-AGCA
*
25727837 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAG-AAGCA
* * *
25727881 AGTCTTATCTTCCTGAAGTTGCAGTGAAGCAGATTGAAGATAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT--AGA-AGCA
*
25727926 AATCTTATCTACCTGAAGTTGCAGTGGAGCAGATTAG-AGCCGA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAAG-C-A
* * * * *
25727969 TAATCCTATCTCCCTGAAGTTGCAGGGGAGCGGATTAAAACCTTA
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAAGC--A
* * * * * * * *
25728014 GATCTTATCTCTCTGAAGTTGCAG-AGAGCATA-TCGCATCT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAAGCA
* * *
25728054 AGTCTTATCTCCTTCAAGTTGCAGTGGAGCAGA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
25728087 CTAATGGAGT
Statistics
Matches: 299, Mismatches: 58, Indels: 49
0.74 0.14 0.12
Matches are distributed among these distances:
39 1 0.00
40 38 0.13
41 13 0.04
42 8 0.03
43 17 0.06
44 142 0.47
45 77 0.26
46 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.27
Consensus pattern (42 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAGAAGCA
Found at i:25734317 original size:21 final size:22
Alignment explanation
Indices: 25734291--25734336 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 22
25734281 AATCTATATA
25734291 TATACATGT-ATATTTATTTTT
1 TATACATGTAATATTTATTTTT
25734312 TATACATGTACATATTTATTTTT
1 TATACATGTA-ATATTTATTTTT
25734335 TA
1 TA
25734337 ACTAATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 9 0.39
23 14 0.61
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (22 bp):
TATACATGTAATATTTATTTTT
Found at i:25734671 original size:16 final size:16
Alignment explanation
Indices: 25734650--25734682 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
25734640 TTACGCACTC
25734650 TCTTTTCTTTT-TTTTT
1 TCTTTT-TTTTATTTTT
25734666 TCTTTTTTTTATTTTT
1 TCTTTTTTTTATTTTT
25734682 T
1 T
25734683 TGTTGATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.88
Consensus pattern (16 bp):
TCTTTTTTTTATTTTT
Found at i:25734812 original size:19 final size:20
Alignment explanation
Indices: 25734771--25734812 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
25734761 ATTTCTCTGC
* *
25734771 CATTGTAATATTTATTATTG
1 CATTGTAATATTTAATATAG
*
25734791 CATTGT-ATATTTAATGTAG
1 CATTGTAATATTTAATATAG
25734810 CAT
1 CAT
25734813 CACATCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (20 bp):
CATTGTAATATTTAATATAG
Done.