Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 40 of 190
Found at i:11164617 original size:8 final size:8
Alignment explanation
Indices: 11164587--11164665 Score: 59
Period size: 8 Copynumber: 9.0 Consensus size: 8
11164577 AAAATTTATT
*
11164587 TAAAAGTA
1 TAAAAATA
11164595 TAAAATATAA
1 TAAAA-AT-A
11164605 TAAAAATA
1 TAAAAATA
* *
11164613 GAAAATTA
1 TAAAAATA
11164621 TAAAAATA
1 TAAAAATA
11164629 TAAAAAGGTA
1 TAAAAA--TA
*
11164639 TTAAATATTA
1 -TAAA-AATA
11164649 TGAAAAATA
1 T-AAAAATA
11164658 TAAAAATA
1 TAAAAATA
11164666 ATATGAACAT
Statistics
Matches: 57, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
8 31 0.54
9 8 0.14
10 13 0.23
11 4 0.07
12 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (8 bp):
TAAAAATA
Found at i:11164684 original size:29 final size:28
Alignment explanation
Indices: 11164596--11164744 Score: 113
Period size: 29 Copynumber: 5.2 Consensus size: 28
11164586 TTAAAAGTAT
11164596 AAAATATAATAAAAATA-GAAA-ATTATA
1 AAAATATAA-AAAAATATGAAATATTATA
** *
11164623 AAAATATAAAAAGGTATTAAATATTATGA
1 AAAATATAAAAAAATATGAAATATTAT-A
11164652 AAAATATAAAAATAATATGAACATATTATA
1 AAAATATAAAAA-AATATGAA-ATATTATA
* * * ** * *
11164682 AAACTTTTAAAAGTTATAGAAATTTTTTA
1 AAAATATAAAAAAATAT-GAAATATTATA
* * *
11164711 AAAATATATAAAAATAATAAAATGTTATA
1 AAAATATAAAAAAAT-ATGAAATATTATA
11164740 AAAAT
1 AAAAT
11164745 TATTAAAATA
Statistics
Matches: 93, Mismatches: 22, Indels: 12
0.73 0.17 0.09
Matches are distributed among these distances:
26 5 0.05
27 12 0.13
28 5 0.05
29 44 0.47
30 20 0.22
31 7 0.08
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.32
Consensus pattern (28 bp):
AAAATATAAAAAAATATGAAATATTATA
Found at i:11164720 original size:21 final size:20
Alignment explanation
Indices: 11164686--11164725 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
11164676 ATTATAAAAC
* *
11164686 TTTTAAAAGTTATAGAAATT
1 TTTTAAAAATTATAAAAATT
11164706 TTTTAAAAATATATAAAAAT
1 TTTTAAAAAT-TATAAAAAT
11164726 AATAAAATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (20 bp):
TTTTAAAAATTATAAAAATT
Found at i:11164731 original size:19 final size:18
Alignment explanation
Indices: 11164711--11164759 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
11164701 AAATTTTTTA
11164711 AAAATATATAAAAATAAT
1 AAAATATATAAAAATAAT
* *
11164729 AAAATGTTATAAAAATTATT
1 AAAAT-ATATAAAAA-TAAT
11164749 AAAATA-ATAAA
1 AAAATATATAAA
11164760 TACAAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 10 0.38
19 8 0.31
20 8 0.31
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (18 bp):
AAAATATATAAAAATAAT
Found at i:11165061 original size:36 final size:35
Alignment explanation
Indices: 11165021--11165096 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 35
11165011 TTATAATATT
11165021 TTTATAGTTTTTCT-TTATTTCTAAAATTTTCTAAAA
1 TTTATAG-TTTTCTATTATTTCTAAAATTTTCT-AAA
* *
11165057 TTTATAGTTTTCTATTATTTTTACAATTTTCTAAA
1 TTTATAGTTTTCTATTATTTCTAAAATTTTCTAAA
11165092 TTTAT
1 TTTAT
11165097 TATAATATCA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
35 14 0.38
36 23 0.62
ACGTcount: A:0.29, C:0.08, G:0.03, T:0.61
Consensus pattern (35 bp):
TTTATAGTTTTCTATTATTTCTAAAATTTTCTAAA
Found at i:11167538 original size:7 final size:7
Alignment explanation
Indices: 11167526--11167560 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
11167516 TGACATTATT
11167526 TAATTTA
1 TAATTTA
11167533 TAATTTA
1 TAATTTA
11167540 TAATTTA
1 TAATTTA
11167547 TAATTTA
1 TAATTTA
11167554 TAATTTA
1 TAATTTA
11167561 ATATTTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TAATTTA
Found at i:11167566 original size:21 final size:21
Alignment explanation
Indices: 11167526--11167569 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
11167516 TGACATTATT
11167526 TAATTTATAATTTATAATTTA
1 TAATTTATAATTTATAATTTA
*
11167547 TAATTTATAATTTAATATTTTA
1 TAATTTATAATTT-ATAATTTA
11167569 T
1 T
11167570 TTGCCTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATTTATAATTTATAATTTA
Found at i:11174140 original size:50 final size:50
Alignment explanation
Indices: 11174068--11174254 Score: 187
Period size: 50 Copynumber: 3.6 Consensus size: 50
11174058 TCTGTACTGG
* * * *
11174068 CAATGTCATATCCCAGATATGGTCTTACATGAGAGCTCTCATATCGGTGC
1 CAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGGTGC
* * *
11174118 CCATGCCATGTCCCAGACATGGTCTTACAAGAGACCTCTCATCTCGGTGC
1 CAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGGTGC
* * * **
11174168 TAGCT-CCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATATTGC
1 CA-ATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCAT-A--TC---GGTGC
*
11174224 CAATGCCATGTCCCAAACATGGTCTTACATG
1 CAATGCCATGTCCCAGACATGGTCTTACATG
11174255 GAGTCTCATC
Statistics
Matches: 111, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
50 78 0.70
51 1 0.01
53 2 0.02
55 1 0.01
56 29 0.26
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (50 bp):
CAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGGTGC
Found at i:11176531 original size:43 final size:43
Alignment explanation
Indices: 11176470--11176553 Score: 150
Period size: 43 Copynumber: 2.0 Consensus size: 43
11176460 TGTTACACGA
* *
11176470 TTTGGCGACATGGCTATGTGACCTTATTTCGAATTGCACACAG
1 TTTGGCAACATGGCTATGTGACCTTATTTCGAATTACACACAG
11176513 TTTGGCAACATGGCTATGTGACCTTATTTCGAATTACACAC
1 TTTGGCAACATGGCTATGTGACCTTATTTCGAATTACACAC
11176554 GGTCTATGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.33
Consensus pattern (43 bp):
TTTGGCAACATGGCTATGTGACCTTATTTCGAATTACACACAG
Found at i:11178920 original size:2 final size:2
Alignment explanation
Indices: 11178915--11178944 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11178905 CTTCATACTA
11178915 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
11178945 TTGTTAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:11180323 original size:52 final size:52
Alignment explanation
Indices: 11180171--11180417 Score: 192
Period size: 52 Copynumber: 4.8 Consensus size: 52
11180161 TCACACAAAC
* ** * *
11180171 CAATACAATGATAGTTCGCATGCACATTACATTGCAAGACAATTCATGCATT
1 CAATGCAATGATAGTTCGCATAAACATTATATTGCAAGAAAATTCATGCATT
* * * *
11180223 TAATGCAATGATAGTTCGCATAAAAATTATATTACACA-AAAATACATGCATT
1 CAATGCAATGATAGTTCGCATAAACATTATATTGCA-AGAAAATTCATGCATT
* * * * * *
11180275 CAACGTAATGATAGTTTGCATAAACATTATATTGTAAGATAGTTCATGCATT
1 CAATGCAATGATAGTTCGCATAAACATTATATTGCAAGAAAATTCATGCATT
* * * * ** * * * *
11180327 CGATGCACTGATAATTTGCATAAACATTACCTTACAAGACAGTTCATACCA-T
1 CAATGCAATGATAGTTCGCATAAACATTATATTGCAAGAAAATTCAT-GCATT
* * * * *
11180379 CGATGCAATGACAATTCGTATAAAGATTATATTGCAAGA
1 CAATGCAATGATAGTTCGCATAAACATTATATTGCAAGA
11180418 CAGTTTATAT
Statistics
Matches: 154, Mismatches: 38, Indels: 6
0.78 0.19 0.03
Matches are distributed among these distances:
51 1 0.01
52 150 0.97
53 3 0.02
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (52 bp):
CAATGCAATGATAGTTCGCATAAACATTATATTGCAAGAAAATTCATGCATT
Found at i:11181855 original size:26 final size:26
Alignment explanation
Indices: 11181826--11181882 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
11181816 CAATGGGGGA
*
11181826 AAAATTGTCAAAATTTTACTA-GAGGT
1 AAAATCGTCAAAATTTTACTATG-GGT
*
11181852 AAAATCGTCAAAATTTTTCTATGGGT
1 AAAATCGTCAAAATTTTACTATGGGT
11181878 AAAAT
1 AAAAT
11181883 AGGGACAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 27 0.96
27 1 0.04
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (26 bp):
AAAATCGTCAAAATTTTACTATGGGT
Found at i:11185277 original size:21 final size:22
Alignment explanation
Indices: 11185235--11185276 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
11185225 CTCAAATGCA
*
11185235 TAAACCATAATCAACCAAAAAT
1 TAAACCATAATCAAACAAAAAT
11185257 TAAACCAT-ATCATAACAAAA
1 TAAACCATAATCA-AACAAAA
11185277 TCAACAAGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.60, C:0.21, G:0.00, T:0.19
Consensus pattern (22 bp):
TAAACCATAATCAAACAAAAAT
Found at i:11186037 original size:21 final size:19
Alignment explanation
Indices: 11186004--11186044 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
11185994 ATTTATTAAA
*
11186004 GATTAATTAAGCTAGTTAT
1 GATTAATTAAGCTAATTAT
11186023 GATTAATTATAAGCTAATTAT
1 GATTAA-T-TAAGCTAATTAT
11186044 G
1 G
11186045 GTATATAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 1 0.05
21 12 0.63
ACGTcount: A:0.39, C:0.05, G:0.15, T:0.41
Consensus pattern (19 bp):
GATTAATTAAGCTAATTAT
Found at i:11206812 original size:37 final size:39
Alignment explanation
Indices: 11206758--11206830 Score: 89
Period size: 37 Copynumber: 1.9 Consensus size: 39
11206748 GGATTAGTTT
*
11206758 TAAATAAAACAAAATCAT-TTTAT-TATAAA-AAAAGGA
1 TAAATAAAACAAAATCATATATATGTATAAAGAAAAGGA
* *
11206794 TAAATTAAAATAATATCATATATATGTATAAAGAAAA
1 TAAA-TAAAACAAAATCATATATATGTATAAAGAAAA
11206831 ATAACAATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
36 4 0.13
37 12 0.40
38 4 0.13
39 6 0.20
40 4 0.13
ACGTcount: A:0.60, C:0.04, G:0.05, T:0.30
Consensus pattern (39 bp):
TAAATAAAACAAAATCATATATATGTATAAAGAAAAGGA
Found at i:11213017 original size:20 final size:19
Alignment explanation
Indices: 11212985--11213025 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
11212975 TAGAGTTTGT
11212985 AAAAATAGAGTGAAATAGG
1 AAAAATAGAGTGAAATAGG
* *
11213004 AAAAATTAGTGTGATATAGG
1 AAAAA-TAGAGTGAAATAGG
11213024 AA
1 AA
11213026 CTATAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.54, C:0.00, G:0.24, T:0.22
Consensus pattern (19 bp):
AAAAATAGAGTGAAATAGG
Found at i:11226174 original size:29 final size:29
Alignment explanation
Indices: 11226053--11226293 Score: 164
Period size: 29 Copynumber: 8.3 Consensus size: 29
11226043 ATATAAGTGA
* * * *
11226053 GCCTTTGTGGTGATATCTATTATAAGGAA
1 GCCTTTGTGGCGATCTCTATTAAAAGGAT
* * * * * * *
11226082 GCCTCTATGGTGATCTTTGTTATAAGGAA
1 GCCTTTGTGGCGATCTCTATTAAAAGGAT
* * * * * *
11226111 GCCTTAGCGGCGATCTCTGTTATAAGAAA
1 GCCTTTGTGGCGATCTCTATTAAAAGGAT
*
11226140 GCCTTTATGGCGATCTCTATTAAAAGGAT
1 GCCTTTGTGGCGATCTCTATTAAAAGGAT
* * *
11226169 GCCTTTGTGGCTATCTC-AGTTAAATGAAT
1 GCCTTTGTGGCGATCTCTA-TTAAAAGGAT
* * **
11226198 GCCTTTGTGGCTATCTCTGTTAAAATAAT
1 GCCTTTGTGGCGATCTCTATTAAAAGGAT
* * **
11226227 GCCTTTGTGGCTATCTCTGTTAAAAATAT
1 GCCTTTGTGGCGATCTCTATTAAAAGGAT
* *
11226256 GCCTTTGTGGCCATCTCTATT-CAAGGAAT
1 GCCTTTGTGGCGATCTCTATTAAAAGG-AT
11226285 GCC-TTGTGG
1 GCCTTTGTGG
11226294 AAAACTCTGT
Statistics
Matches: 176, Mismatches: 33, Indels: 7
0.81 0.15 0.03
Matches are distributed among these distances:
28 9 0.05
29 167 0.95
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (29 bp):
GCCTTTGTGGCGATCTCTATTAAAAGGAT
Found at i:11226185 original size:58 final size:57
Alignment explanation
Indices: 11226053--11226307 Score: 194
Period size: 58 Copynumber: 4.4 Consensus size: 57
11226043 ATATAAGTGA
* * * * * * * * *
11226053 GCCTTTGTGG-TGATATCTATTATAAGGAAGCCTCTATGGTGATCTTTGTTATAAGGAA
1 GCCTTTGTGGCT-ATCTCTGTTA-AAGAAAGCCTTTATGGCGATCTCTATTAAAAGGAT
* * *
11226111 GCCTTAGCGGCGATCTCTGTTATAAGAAAGCCTTTATGGCGATCTCTATTAAAAGGAT
1 GCCTTTGTGGCTATCTCTGTTA-AAGAAAGCCTTTATGGCGATCTCTATTAAAAGGAT
* * * * * **
11226169 GCCTTTGTGGCTATCTCAGTTAAATGAATGCCTTTGTGGCTATCTCTGTTAAAATAAT
1 GCCTTTGTGGCTATCTCTGTTAAA-GAAAGCCTTTATGGCGATCTCTATTAAAAGGAT
* * *
11226227 GCCTTTGTGGCTATCTCTGTTAAA-AATATGCCTTTGTGGCCATCTCTATT-CAAGGAAT
1 GCCTTTGTGGCTATCTCTGTTAAAGAA-A-GCCTTTATGGCGATCTCTATTAAAAGG-AT
** *
11226285 GCC-TTGTGGAAAACTCTGTTAAA
1 GCCTTTGTGGCTATCTCTGTTAAA
11226308 AAGGACACCT
Statistics
Matches: 160, Mismatches: 32, Indels: 11
0.79 0.16 0.05
Matches are distributed among these distances:
56 2 0.01
57 21 0.13
58 137 0.86
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.36
Consensus pattern (57 bp):
GCCTTTGTGGCTATCTCTGTTAAAGAAAGCCTTTATGGCGATCTCTATTAAAAGGAT
Found at i:11226214 original size:87 final size:86
Alignment explanation
Indices: 11226105--11226308 Score: 223
Period size: 87 Copynumber: 2.4 Consensus size: 86
11226095 TCTTTGTTAT
* * * *
11226105 AAGGAA-GCCTTAGCGGCGATCTCTGTTATAAGAAAGCCTTTATGGCGATCTCTATTAAAAGGAT
1 AAGGAATGCCTT-GTGGCTATCTCTGTTAAAAGAAAGCCTTTATGGCGATCTCTATTAAAAAGAT
*
11226169 GCCTTTGTGGCTATCTC-AGTTA
65 GCCTTTGTGGCCATCTCTA-TTA
* * * * * * *
11226191 AATGAATGCCTTTGTGGCTATCTCTGTTAAAATAATGCCTTTGTGGCTATCTCTGTTAAAAATAT
1 AAGGAATGCC-TTGTGGCTATCTCTGTTAAAAGAAAGCCTTTATGGCGATCTCTATTAAAAAGAT
*
11226256 GCCTTTGTGGCCATCTCTATTC
65 GCCTTTGTGGCCATCTCTATTA
** *
11226278 AAGGAATGCCTTGTGGAAAACTCTGTTAAAA
1 AAGGAATGCCTTGTGGCTATCTCTGTTAAAA
11226309 AGGACACCTA
Statistics
Matches: 98, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
86 23 0.23
87 72 0.73
88 3 0.03
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (86 bp):
AAGGAATGCCTTGTGGCTATCTCTGTTAAAAGAAAGCCTTTATGGCGATCTCTATTAAAAAGATG
CCTTTGTGGCCATCTCTATTA
Found at i:11228029 original size:19 final size:19
Alignment explanation
Indices: 11228005--11228051 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
11227995 AATTATTCAA
*
11228005 ATTTTTTATTTAT-TTAATT
1 ATTTTTT-TCTATCTTAATT
11228024 ATTTTTTTCTATCTTAATT
1 ATTTTTTTCTATCTTAATT
11228043 ATTTATTTT
1 ATTT-TTTT
11228052 AATTGATTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 4 0.16
19 17 0.68
20 4 0.16
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.72
Consensus pattern (19 bp):
ATTTTTTTCTATCTTAATT
Found at i:11235787 original size:6 final size:7
Alignment explanation
Indices: 11235769--11235795 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
11235759 ACATTTTCAC
11235769 ATTTTTT
1 ATTTTTT
11235776 ATTTTTT
1 ATTTTTT
11235783 ATTTTTT
1 ATTTTTT
11235790 ATTTTT
1 ATTTTT
11235796 CAACCTATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
ATTTTTT
Found at i:11243840 original size:3 final size:3
Alignment explanation
Indices: 11243828--11243863 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
11243818 TTGTGCAGCC
11243828 TCT T-T TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
11243864 TTTTCTTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:11246247 original size:17 final size:18
Alignment explanation
Indices: 11246206--11246249 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
11246196 TATAAAATTG
11246206 AATATTTTGTAATTATATT
1 AATATTTT-TAATTATATT
*
11246225 -ACATTTTTAATT-TATT
1 AATATTTTTAATTATATT
11246241 AATATTTTT
1 AATATTTTT
11246250 TGAAAAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 4 0.18
17 12 0.55
18 6 0.27
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (18 bp):
AATATTTTTAATTATATT
Found at i:11246248 original size:16 final size:17
Alignment explanation
Indices: 11246209--11246241 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
11246199 AAAATTGAAT
11246209 ATTTTGTAATTATATTAC
1 ATTTT-TAATTATATTAC
11246227 ATTTTTAATT-TATTA
1 ATTTTTAATTATATTA
11246242 ATATTTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (17 bp):
ATTTTTAATTATATTAC
Found at i:11257155 original size:37 final size:38
Alignment explanation
Indices: 11257089--11257174 Score: 111
Period size: 37 Copynumber: 2.2 Consensus size: 38
11257079 TTAAAAAAAT
*
11257089 CCTTCAATCTTTATCCAACCACGTTTTTTAAATCTTCAAC
1 CCTTCAATCTTTATCCAACCAC--ATTTTAAATCTTCAAC
* *
11257129 CCTTCAATCTTTATCCAACTA-ATTTTAAATCTTCAAT
1 CCTTCAATCTTTATCCAACCACATTTTAAATCTTCAAC
*
11257166 CTTTCAATC
1 CCTTCAATC
11257175 GAGCCCTCCT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
37 22 0.52
40 20 0.48
ACGTcount: A:0.29, C:0.28, G:0.01, T:0.42
Consensus pattern (38 bp):
CCTTCAATCTTTATCCAACCACATTTTAAATCTTCAAC
Found at i:11258936 original size:28 final size:28
Alignment explanation
Indices: 11258904--11258963 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
11258894 AATCTCGTAC
11258904 TTCACCACTTCGCAGTGTCATTTCGCAA
1 TTCACCACTTCGCAGTGTCATTTCGCAA
* * *
11258932 TTCACCACTTTGCGGTGTCATTTCGCAG
1 TTCACCACTTCGCAGTGTCATTTCGCAA
11258960 TTCA
1 TTCA
11258964 TCTTGCAACT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.18, C:0.30, G:0.17, T:0.35
Consensus pattern (28 bp):
TTCACCACTTCGCAGTGTCATTTCGCAA
Found at i:11262292 original size:4 final size:4
Alignment explanation
Indices: 11262283--11262312 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
11262273 AGATGTACTA
11262283 ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
11262313 GTATGTATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:11268724 original size:25 final size:24
Alignment explanation
Indices: 11268689--11268782 Score: 73
Period size: 25 Copynumber: 3.8 Consensus size: 24
11268679 CTGATTGCAG
11268689 CTCGTGAGAGCTTACCGATTCTCAA
1 CTCGT-AGAGCTTACCGATTCTCAA
* * * *
11268714 CTCGTATGAGCTCATCGATT-ACAG
1 CTCGTA-GAGCTTACCGATTCTCAA
* * *
11268738 CTTGTGAGAGCTTATCGATTCTCAT
1 CTCGT-AGAGCTTACCGATTCTCAA
*
11268763 CTCGCAAGAGCTTACCGATT
1 CTCG-TAGAGCTTACCGATT
11268783 TATAGCTAGC
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
24 19 0.35
25 35 0.65
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.31
Consensus pattern (24 bp):
CTCGTAGAGCTTACCGATTCTCAA
Found at i:11268774 original size:49 final size:49
Alignment explanation
Indices: 11268681--11268808 Score: 139
Period size: 49 Copynumber: 2.6 Consensus size: 49
11268671 AGGGATTACT
* * *
11268681 GATTGCAGCTCGTGAGAGCTTACCGATTCTCAACTCGTATGAGCTCATC
1 GATTACAGCTCGTGAGAGCTTACCGATTCTCAACTCGCAAGAGCTCATC
* * * * *
11268730 GATTACAGCTTGTGAGAGCTTATCGATTCTCATCTCGCAAGAGCTTACC
1 GATTACAGCTCGTGAGAGCTTACCGATTCTCAACTCGCAAGAGCTCATC
* * * *
11268779 GATTTATAGCTAGCGAGAGCATACCGATTC
1 GA-TTACAGCTCGTGAGAGCTTACCGATTC
11268809 ATAGCTCGTA
Statistics
Matches: 65, Mismatches: 13, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
49 43 0.66
50 22 0.34
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (49 bp):
GATTACAGCTCGTGAGAGCTTACCGATTCTCAACTCGCAAGAGCTCATC
Found at i:11268823 original size:25 final size:24
Alignment explanation
Indices: 11268769--11268827 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
11268759 TCATCTCGCA
* *
11268769 AGAGCTTACCGATTTATAGCTAGCG
1 AGAGCATACCGATTCATAGCTA-CG
11268794 AGAGCATACCGATTCATAGCT-CG
1 AGAGCATACCGATTCATAGCTACG
11268817 TATGAGCATAC
1 -A-GAGCATAC
11268828 ATGTACATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 2 0.07
24 1 0.03
25 27 0.90
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (24 bp):
AGAGCATACCGATTCATAGCTACG
Found at i:11291380 original size:20 final size:20
Alignment explanation
Indices: 11291332--11291394 Score: 81
Period size: 20 Copynumber: 3.0 Consensus size: 20
11291322 TTGAAATGCT
*
11291332 AACAGAGGCACCATAGTGCAA
1 AACAGAGGCACCAAAGTGC-A
*
11291353 ATACAGAGGCATCAAAGTGCA
1 A-ACAGAGGCACCAAAGTGCA
*
11291374 AACAGAGGCACCGAAGTGCA
1 AACAGAGGCACCAAAGTGCA
11291394 A
1 A
11291395 TCCCTTACAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 18 0.49
21 3 0.08
22 16 0.43
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (20 bp):
AACAGAGGCACCAAAGTGCA
Found at i:11294314 original size:3 final size:3
Alignment explanation
Indices: 11294306--11294353 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
11294296 ATAACCAAAT
** * *
11294306 ATA ATA ATA GCA ATA ATA ATA AGA GTA ATA ATA ATA ATTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA
11294352 AT
1 AT
11294354 TAATTAATTA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:11294324 original size:15 final size:15
Alignment explanation
Indices: 11294306--11294343 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
11294296 ATAACCAAAT
11294306 ATAATAATAGCAATA
1 ATAATAATAGCAATA
* *
11294321 ATAATAAGAGTAATA
1 ATAATAATAGCAATA
11294336 ATAATAAT
1 ATAATAAT
11294344 TAATAATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.29
Consensus pattern (15 bp):
ATAATAATAGCAATA
Found at i:11295930 original size:51 final size:49
Alignment explanation
Indices: 11295861--11296746 Score: 825
Period size: 51 Copynumber: 18.2 Consensus size: 49
11295851 CTTCAGGGAG
*
11295861 ATAAGATTCGCTGCCTTCAGCTCTAATCTGTTTCACTGCAACGCCAAGGAA
1 ATAAGATTCGCTGCCTTCAGCTTTAATC--TTTCACTGCAACGCCAAGGAA
** * * * *
11295912 ATAAGATTAACTGTCTTCAGCTTTAATC--T-ATTGCAACGCTAGGGAA
1 ATAAGATTCGCTGCCTTCAGCTTTAATCTTTCACTGCAACGCCAAGGAA
*
11295958 ACAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGCCAAGGAA
1 ATAAGATTCGCTGCCTTCAGCTTTAATCT-TT-CACTGCAACGCCAAGGAA
** * * * *
11296009 ATAAGATTCTTTACCTTCAGCTTTAATC--T-ATTGCAACGCTAGGGAA
1 ATAAGATTCGCTGCCTTCAGCTTTAATCTTTCACTGCAACGCCAAGGAA
* * * **
11296055 ATAAGATTTGCTGCCTTCATCTTTAATCTGTTCCACTACAACATCAAGGAA
1 ATAAGATTCGCTGCCTTCAGCTTTAATCT-TT-CACTGCAACGCCAAGGAA
* * *
11296106 ATAAGATTCGCTGCCTTCACCTTTAATCTGTTCCACTACAATGCCAAGGAA
1 ATAAGATTCGCTGCCTTCAGCTTTAATCT-TT-CACTGCAACGCCAAGGAA
* * *
11296157 ATAAGATTCGTTGCCTTCAACTTTAATC--T-ACTGCAACGCCAGGGAA
1 ATAAGATTCGCTGCCTTCAGCTTTAATCTTTCACTGCAACGCCAAGGAA
* * * **
11296203 ATAAGATTCGTTTCCTTCAGCTTTAATCTGTTCCATTGCAACGTTAAGGAA
1 ATAAGATTCGCTGCCTTCAGCTTTAATCT-TT-CACTGCAACGCCAAGGAA
* *
11296254 ATAAGATTCGCTGCCTTCAGCTTTAATC--T-ATTGCAAC-CTCAGGGAA
1 ATAAGATTCGCTGCCTTCAGCTTTAATCTTTCACTGCAACGC-CAAGGAA
* * * * *
11296300 ACAAGGTTCACTGCCTTCAGCTTTAATCTATTCCACTTCAACGTCAAGGAA
1 ATAAGATTCGCTGCCTTCAGCTTTAATCT-TT-CACTGCAACGCCAAGGAA
*
11296351 ATAAGATTCGCTGCCTTCAGCTTTAATCTATTCTACTGCAACGTCAAGGAA
1 ATAAGATTCGCTGCCTTCAGCTTTAATCT-TTC-ACTGCAACGCCAAGGAA
* * * * ** *
11296402 ATAAGATTCACTGCTTTCAACTTTAATC--T-ATTGCAATACCATGGAA
1 ATAAGATTCGCTGCCTTCAGCTTTAATCTTTCACTGCAACGCCAAGGAA
* * * *
11296448 ACAAGATTCGCTGCCTTCAGCTTTAATTTGTTCCACT-AAATGCCAAGGAA
1 ATAAGATTCGCTGCCTTCAGCTTTAATCT-TT-CACTGCAACGCCAAGGAA
* * * * *
11296498 ATAAGATTTGTTGCCTTCAGCTTTAAAC--T-ATTGCAACGCCAGGGAA
1 ATAAGATTCGCTGCCTTCAGCTTTAATCTTTCACTGCAACGCCAAGGAA
* * * *
11296544 ACAAGATTCGCTGCATTCAGCTTTAATCTGTTCCACTGAAACGTCAAGGAA
1 ATAAGATTCGCTGCCTTCAGCTTTAATCT-TT-CACTGCAACGCCAAGGAA
* *
11296595 ATAAGATTCGCTGCCTTCAGCTTTAATC--T-ATTGCAACGCCAGGGAA
1 ATAAGATTCGCTGCCTTCAGCTTTAATCTTTCACTGCAACGCCAAGGAA
* * *
11296641 ACAAGATTCGCTACCTTCAGCTTTAATCTGTTCAACTGCAACGTCAAGGAA
1 ATAAGATTCGCTGCCTTCAGCTTTAATCT-TTC-ACTGCAACGCCAAGGAA
*
11296692 ATAAGATTCGCTGCCTTCAGCTTTAATC--T-ACTGCAACGCCAGGGAA
1 ATAAGATTCGCTGCCTTCAGCTTTAATCTTTCACTGCAACGCCAAGGAA
11296738 ATAAGATTC
1 ATAAGATTC
11296747 TCTATCTTCA
Statistics
Matches: 682, Mismatches: 114, Indels: 83
0.78 0.13 0.09
Matches are distributed among these distances:
45 2 0.00
46 284 0.42
47 2 0.00
48 6 0.01
49 7 0.01
50 34 0.05
51 347 0.51
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (49 bp):
ATAAGATTCGCTGCCTTCAGCTTTAATCTTTCACTGCAACGCCAAGGAA
Found at i:11296028 original size:148 final size:139
Alignment explanation
Indices: 11295861--11296746 Score: 751
Period size: 148 Copynumber: 6.1 Consensus size: 139
11295851 CTTCAGGGAG
* ** *
11295861 ATAAGATTCGCTGCCTTCAGCTCTAATCTGTTTCACTGCAACGCCAAGGAAATAAGATTAACTGT
1 ATAAGATTCGCTGCCTTCAGCTTTAATC----T-ACTGCAACGCCAAGGAAATAAGATTCGCTGC
* *
11295926 CTTCAGCTTTAATCTATTGCAACGCT-AGGGAAACAAGATTCGCTGCCTTCAGCTTTAATCTGTT
61 CTTCAGCTTTAATCTATTGCAACGCTCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATC---T
11295990 CCACTGCAACGCCAAGGAA
123 --ACTGCAACGCCAAGGAA
** * * * * *
11296009 ATAAGATTCTTTACCTTCAGCTTTAATCTATTGCAACGCTAGGGAAATAAGATTTGCTGCCTTCA
1 ATAAGATTCGCTGCCTTCAGCTTTAATCTACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTCA
* * * * *
11296074 TCTTTAATCTGTTCCACTACAACATCAAGGAAATAAGATTCGCTGCCTTCACCTTTAATCTGTTC
66 GCTTTAATCTATTGCA--AC-GC-TCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATC---T-
* *
11296139 CACTACAATGCCAAGGAA
123 -ACTGCAACGCCAAGGAA
* * * * *
11296157 ATAAGATTCGTTGCCTTCAACTTTAATCTACTGCAACGCCAGGGAAATAAGATTCGTTTCCTTCA
1 ATAAGATTCGCTGCCTTCAGCTTTAATCTACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTCA
* *
11296222 GCTTTAATCTGTTCCATTGCAACG-TTAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTATT
66 GCTTTAATC---T--ATTGCAACGCTCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTACT
*
11296286 GCAAC-CTCAGGGAA
126 GCAACGC-CAAGGAA
* * * * *
11296300 ACAAGGTTCACTGCCTTCAGCTTTAATCTATTCCACTTCAACGTCAAGGAAATAAGATTCGCTGC
1 ATAAGATTCGCTGCCTTCAGCTTTAATC---T--ACTGCAACGCCAAGGAAATAAGATTCGCTGC
* * *
11296365 CTTCAGCTTTAATCTATTCTACTGCAACG-TCAAGGAAATAAGATTCACTGCTTTCAACTTTAAT
61 CTTCAGCTTTAATCTA---T--TGCAACGCTCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAAT
* ** *
11296429 CTATTGCAATACCATGGAA
121 CTACTGCAACGCCAAGGAA
* * * * * *
11296448 ACAAGATTCGCTGCCTTCAGCTTTAATTTGTTCCACT-AAATGCCAAGGAAATAAGATTTGTTGC
1 ATAAGATTCGCTGCCTTCAGCTTTAA-----TCTACTGCAACGCCAAGGAAATAAGATTCGCTGC
* * * *
11296512 CTTCAGCTTTAAACTATTGCAACGC-CAGGGAAACAAGATTCGCTGCATTCAGCTTTAATCTGTT
61 CTTCAGCTTTAATCTATTGCAACGCTCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATC---T
* *
11296576 CCACTGAAACGTCAAGGAA
123 --ACTGCAACGCCAAGGAA
* * * *
11296595 ATAAGATTCGCTGCCTTCAGCTTTAATCTATTGCAACGCCAGGGAAACAAGATTCGCTACCTTCA
1 ATAAGATTCGCTGCCTTCAGCTTTAATCTACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTCA
*
11296660 GCTTTAATCTGTT-CAACTGCAACGTCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTACT
66 GCTTTAATCTATTGCAAC-G---C-TCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTACT
*
11296724 GCAACGCCAGGGAA
126 GCAACGCCAAGGAA
11296738 ATAAGATTC
1 ATAAGATTC
11296747 TCTATCTTCA
Statistics
Matches: 607, Mismatches: 91, Indels: 85
0.78 0.12 0.11
Matches are distributed among these distances:
142 46 0.08
143 138 0.23
144 2 0.00
145 6 0.01
146 4 0.01
147 74 0.12
148 327 0.54
149 1 0.00
151 3 0.00
153 6 0.01
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (139 bp):
ATAAGATTCGCTGCCTTCAGCTTTAATCTACTGCAACGCCAAGGAAATAAGATTCGCTGCCTTCA
GCTTTAATCTATTGCAACGCTCAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTACTGCAAC
GCCAAGGAA
Found at i:11296756 original size:97 final size:97
Alignment explanation
Indices: 11295854--11296746 Score: 1007
Period size: 97 Copynumber: 9.2 Consensus size: 97
11295844 ACTGGAACTT
* * * *
11295854 CAGGGAGATAAGATTCGCTGCCTTCAGCTCTAATCTGTTTCACTGCAACGCCAAGGAAATAAGAT
1 CAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGTCAAGGAAATAAGAT
** *
11295919 TAACTGTCTTCAGCTTTAATCTATTGCAACGC
66 TCGCTGCCTTCAGCTTTAATCTATTGCAACGC
* * *
11295951 TAGGGAAACAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGCCAAGGAAATAAGAT
1 CAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGTCAAGGAAATAAGAT
** *
11296016 TCTTTACCTTCAGCTTTAATCTATTGCAACGC
66 TCGCTGCCTTCAGCTTTAATCTATTGCAACGC
* * * * *
11296048 TAGGGAAATAAGATTTGCTGCCTTCATCTTTAATCTGTTCCACTACAACATCAAGGAAATAAGAT
1 CAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGTCAAGGAAATAAGAT
* * *
11296113 TCGCTGCCTTCACCTTTAATCTGTTCCACTACAATGC
66 TCGCTGCCTTCAGCTTTAATCTATTGCA--AC---GC
* * * * *
11296150 CAAGGAAATAAGATTCGTTGCCTTCAACTTTAATC---T--ACTGCAACGCCAGGGAAATAAGAT
1 CAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGTCAAGGAAATAAGAT
* * *
11296210 TCGTTTCCTTCAGCTTTAATCTGTTCCATTGCAACGT
66 TCGCTGCCTTCAGCTTTAATC---T--ATTGCAACGC
* * * * * * *
11296247 TAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATC---T--ATTGCAACCTCAGGGAAACAAGGT
1 CAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGTCAAGGAAATAAGAT
* * *
11296307 TCACTGCCTTCAGCTTTAATCTATTCCACTTCAACGT
66 TCGCTGCCTTCAGCTTTAATCTA-T----TGCAACGC
* * *
11296344 CAAGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTATTCTACTGCAACGTCAAGGAAATAAGAT
1 CAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGTCAAGGAAATAAGAT
* * * **
11296409 TCACTGCTTTCAACTTTAATCTATTGCAATAC
66 TCGCTGCCTTCAGCTTTAATCTATTGCAACGC
* * * * * *
11296441 CATGGAAACAAGATTCGCTGCCTTCAGCTTTAATTTGTTCCACT-AAATGCCAAGGAAATAAGAT
1 CAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGTCAAGGAAATAAGAT
* * *
11296505 TTGTTGCCTTCAGCTTTAAACTATTGCAACGC
66 TCGCTGCCTTCAGCTTTAATCTATTGCAACGC
* * *
11296537 CAGGGAAACAAGATTCGCTGCATTCAGCTTTAATCTGTTCCACTGAAACGTCAAGGAAATAAGAT
1 CAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGTCAAGGAAATAAGAT
11296602 TCGCTGCCTTCAGCTTTAATCTATTGCAACGC
66 TCGCTGCCTTCAGCTTTAATCTATTGCAACGC
* * *
11296634 CAGGGAAACAAGATTCGCTACCTTCAGCTTTAATCTGTTCAACTGCAACGTCAAGGAAATAAGAT
1 CAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGTCAAGGAAATAAGAT
*
11296699 TCGCTGCCTTCAGCTTTAATCTACTGCAACGC
66 TCGCTGCCTTCAGCTTTAATCTATTGCAACGC
11296731 CAGGGAAATAAGATTC
1 CAGGGAAATAAGATTC
11296747 TCTATCTTCA
Statistics
Matches: 684, Mismatches: 91, Indels: 42
0.84 0.11 0.05
Matches are distributed among these distances:
92 1 0.00
93 1 0.00
94 1 0.00
96 82 0.12
97 515 0.75
99 3 0.00
100 4 0.01
101 1 0.00
102 76 0.11
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (97 bp):
CAGGGAAATAAGATTCGCTGCCTTCAGCTTTAATCTGTTCCACTGCAACGTCAAGGAAATAAGAT
TCGCTGCCTTCAGCTTTAATCTATTGCAACGC
Found at i:11296815 original size:44 final size:44
Alignment explanation
Indices: 11296752--11297376 Score: 332
Period size: 44 Copynumber: 13.9 Consensus size: 44
11296742 GATTCTCTAT
* *
11296752 CTTCAA-TCTACTCCACTGCAACTTCAGAGAGATAAGACTTGTAG
1 CTTCAATTCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGTAG
* * * *
11296796 CTTCAATTC-GCTCTACTGCAACTTCAGGGAGATAGGATTATTGG
1 CTTCAATTCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GTAG
* * * * * *
11296840 CTTTAAATCTACTCCACTGTAACTTCAGGGAGATTCAGGGAGATAAGATTCTCCAT
1 CTTCAATTCTGCTCCACTG------CA---A-CTTCAGGGAGATAAGATTGT--AG
* * *
11296896 CTTC-AGTCTACTCTACTGCAACTTCAGGGAGATAAGACTTGTAG
1 CTTCAATTCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGTAG
* * * * *
11296940 CTTCAA-TCCGCTCCACTACAACTTCAAGGAGATAGGATTATTAG
1 CTTCAATTCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GTAG
* * * *
11296984 CTTTAA-TATGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCAT
1 CTTCAATTCTGCTCCACTGCAACTTCAGGGAGATAAGATT-G-TAG
* * * * *
11297029 CTTC-AGTCTGCCCCACTGTAACTTCAGGGGGATAAGACTTGTAA
1 CTTCAATTCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGTAG
* *
11297073 CTTCAACT-TGCTCCACTGCAACTTCAGGGAGATAAGGTCTGCTAAG
1 CTTCAATTCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TG-T-AG
* * *
11297119 -TTCAA-TCTGCTCTACTACAACCTT-AGGGAGATAAGACTTGTGAC
1 CTTCAATTCTGCTCCACTGCAA-CTTCAGGGAGATAAGA-TTGT-AG
* *
11297163 CTT-AA-TCTGC-CCACTACAACTTCA-GGAGGATAAGATTGATAT
1 CTTCAATTCTGCTCCACTGCAACTTCAGGGA-GATAAGATTG-TAG
* * * * * *
11297205 CTTCAA-CCTACTCCACTACAACTTCAGGGAAATAAGGTCTGCTAA
1 CTTCAATTCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TG-TAG
* * * * * * *
11297250 CTTC-AGTCTACTCTACTACAACTTTAGGGAGATAAAACTTGTAA
1 CTTCAATTCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGTAG
* * * * * *
11297294 CTTTAATAC-GTTCCACTGCAACTTCAGGGAGATAGGATTATTGG
1 CTTCAATTCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GTAG
* *
11297338 CTTTAA-TCTGCTCCACTGCAACTTAAGGGAGATAAGATT
1 CTTCAATTCTGCTCCACTGCAACTTCAGGGAGATAAGATT
11297377 CGCCATAATA
Statistics
Matches: 453, Mismatches: 87, Indels: 82
0.73 0.14 0.13
Matches are distributed among these distances:
42 13 0.03
43 30 0.07
44 230 0.51
45 131 0.29
46 12 0.03
49 2 0.00
51 2 0.00
54 2 0.00
55 28 0.06
56 3 0.01
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (44 bp):
CTTCAATTCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTAG
Found at i:11297053 original size:89 final size:88
Alignment explanation
Indices: 11296910--11297374 Score: 233
Period size: 89 Copynumber: 5.3 Consensus size: 88
11296900 AGTCTACTCT
* * *
11296910 ACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAATCCGCTCCACTACAACTTCAAGGAGATAG
1 ACTGCAACTTCAGGGAGATAAGACTTGCAGCTTCAATCCGCCCCACTACAACTTCAAGGAGATAA
* * *
11296975 GA-TTATTAGCTTTAA-TATGCTCC
66 GACTT-GTAACTTCAACT-TGCTCC
* * * ** * *
11296998 ACTGCAACTTCAGGGAGATAAGA-TTCGCCATCTTCAGTCTGCCCCACTGTAACTTCAGGGGGAT
1 ACTGCAACTTCAGGGAGATAAGACTT-G-CAGCTTCAATCCGCCCCACTACAACTTCAAGGAGAT
11297062 AAGACTTGTAACTTCAACTTGCTCC
64 AAGACTTGTAACTTCAACTTGCTCC
* * * * *
11297087 ACTGCAACTTCAGGGAGATAAG-GTCTGCTAAG-TTCAATCTGCTCTACTACAACCTT-AGGGAG
1 ACTGCAACTTCAGGGAGATAAGACT-TGC--AGCTTCAATCCGCCCCACTACAA-CTTCAAGGAG
*
11297149 ATAAGACTTGTGACCTT-AA-TCTGC-CC
62 ATAAGACTTGT-AACTTCAACT-TGCTCC
* * * * * * *
11297175 ACTACAACTTCA-GGAGGATAAGA-TTGATATCTTCAA-CCTACTCCACTACAACTTCAGGGAAA
1 ACTGCAACTTCAGGGA-GATAAGACTTG-CAGCTTCAATCC-GCCCCACTACAACTTCAAGGAGA
* * * *
11297237 TAAG-GTCTGCTAACTTC-AGTCTACTCT
63 TAAGACT-TG-TAACTTCAACT-TGCTCC
* * * * * * * ** * * *
11297264 ACTACAACTTTAGGGAGATAAAACTTGTAACTTTAATACGTTCCACTGCAACTTCAGGGAGATAG
1 ACTGCAACTTCAGGGAGATAAGACTTGCAGCTTCAATCCGCCCCACTACAACTTCAAGGAGATAA
* ** *
11297329 GA-TTATTGGCTTTAA-TCTGCTCC
66 GACTT-GTAACTTCAACT-TGCTCC
*
11297352 ACTGCAACTTAAGGGAGATAAGA
1 ACTGCAACTTCAGGGAGATAAGA
11297375 TTCGCCATAA
Statistics
Matches: 298, Mismatches: 51, Indels: 56
0.74 0.13 0.14
Matches are distributed among these distances:
86 6 0.02
87 39 0.13
88 82 0.28
89 152 0.51
90 19 0.06
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (88 bp):
ACTGCAACTTCAGGGAGATAAGACTTGCAGCTTCAATCCGCCCCACTACAACTTCAAGGAGATAA
GACTTGTAACTTCAACTTGCTCC
Found at i:11297211 original size:132 final size:132
Alignment explanation
Indices: 11297048--11297373 Score: 385
Period size: 132 Copynumber: 2.5 Consensus size: 132
11297038 GCCCCACTGT
*
11297048 AACTTCAGGGGGATAAGACTTG-TAACTTCAACTTGCTCCACTGCAACTTCAGGGAGATAAGGTC
1 AACTTCA-GGGGATAAGA-TTGATATCTTCAACTTGCTCCACTGCAACTTCAGGGAGATAAGGTC
* * * *
11297112 TGCTAAGTTCAATCTGCTCTACTACAACCTTAGGGAGATAAGACTTGTGACCTTAAT-C-TGCCC
64 TGCTAACTTCAATCTACTCTACTACAACCTTAGGGAGATAAAACTTGTAACCTTAATACGT-CCC
11297175 ACTAC
128 ACTAC
* * * *
11297180 AACTTCAGGAGGATAAGATTGATATCTTCAACCTACTCCACTACAACTTCAGGGAAATAAGGTCT
1 AACTTCAGG-GGATAAGATTGATATCTTCAACTTGCTCCACTGCAACTTCAGGGAGATAAGGTCT
* * * *
11297245 GCTAACTTCAGTCTACTCTACTACAACTTTAGGGAGATAAAACTTGTAACTTTAATACGTTCCAC
65 GCTAACTTCAATCTACTCTACTACAACCTTAGGGAGATAAAACTTGTAACCTTAATACGTCCCAC
*
11297310 TGC
130 TAC
* * *
11297313 AACTTCAGGGAGATAGGATT-AT-TGGCTTTAA-TCTGCTCCACTGCAACTTAAGGGAGATAAG
1 AACTTCAGGG-GATAAGATTGATAT--CTTCAACT-TGCTCCACTGCAACTTCAGGGAGATAAG
11297374 ATTCGCCATA
Statistics
Matches: 165, Mismatches: 21, Indels: 15
0.82 0.10 0.07
Matches are distributed among these distances:
131 6 0.04
132 105 0.64
133 53 0.32
134 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (132 bp):
AACTTCAGGGGATAAGATTGATATCTTCAACTTGCTCCACTGCAACTTCAGGGAGATAAGGTCTG
CTAACTTCAATCTACTCTACTACAACCTTAGGGAGATAAAACTTGTAACCTTAATACGTCCCACT
AC
Found at i:11297257 original size:221 final size:222
Alignment explanation
Indices: 11296897--11297327 Score: 516
Period size: 221 Copynumber: 1.9 Consensus size: 222
11296887 ATTCTCCATC
* * *
11296897 TTCAGTCTACTCTACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAATCCGCTCCACTACAAC
1 TTCAATCTACTCTACTACAACTTCAGGGAGATAAGACTTGTACCTTCAATCCGCTCCACTACAAC
* * * * * *
11296962 TTCAAGGAGATAGGATTATTAGCTTTAATATGCTCCACTGCAACTTCAGGGAGATAAGATTCGCC
66 TTCAAGGAGATAAGATTATTAGCTTCAACATACTCCACTACAACTTCAGGGAAATAAGATTCGCC
* * ** * * *
11297027 ATCTTCAGTCTGCCCCACTGTAACTTCAGGGGGATAAGACTTGTAACTTCAACT-TGCTCCACTG
131 AACTTCAGTCTACCCCACTACAACTTCAGGGAGATAAAACTTGTAACTTCAA-TACGCTCCACTG
11297091 CAACTTCAGGGAGATAAGGTCTGCTAAG
195 CAACTTCAGGGAGATAAGGTCTGCTAAG
* *
11297119 TTCAATCTGCTCTACTACAACCTT-AGGGAGATAAGACTTGTGACCTT-AATCTGC-CCACTACA
1 TTCAATCTACTCTACTACAA-CTTCAGGGAGATAAGACTTGT-ACCTTCAATCCGCTCCACTACA
* * *
11297181 ACTTC-AGGAGGATAAGATTGA-TATCTTCAACCTACTCCACTACAACTTCAGGGAAATAAG-GT
64 ACTTCAAGGA-GATAAGATT-ATTAGCTTCAACATACTCCACTACAACTTCAGGGAAATAAGATT
* * * * * *
11297243 CTGCTAACTTCAGTCTACTCTACTACAACTTTAGGGAGATAAAACTTGTAACTTTAATACGTTCC
127 C-GCCAACTTCAGTCTACCCCACTACAACTTCAGGGAGATAAAACTTGTAACTTCAATACGCTCC
11297308 ACTGCAACTTCAGGGAGATA
191 ACTGCAACTTCAGGGAGATA
11297328 GGATTATTGG
Statistics
Matches: 176, Mismatches: 27, Indels: 13
0.81 0.12 0.06
Matches are distributed among these distances:
220 7 0.04
221 121 0.69
222 41 0.23
223 7 0.04
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (222 bp):
TTCAATCTACTCTACTACAACTTCAGGGAGATAAGACTTGTACCTTCAATCCGCTCCACTACAAC
TTCAAGGAGATAAGATTATTAGCTTCAACATACTCCACTACAACTTCAGGGAAATAAGATTCGCC
AACTTCAGTCTACCCCACTACAACTTCAGGGAGATAAAACTTGTAACTTCAATACGCTCCACTGC
AACTTCAGGGAGATAAGGTCTGCTAAG
Found at i:11297760 original size:24 final size:24
Alignment explanation
Indices: 11297704--11297761 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
11297694 CAAATTGCCC
*
11297704 CCACTGTAATCTTCAAGGTTCAAT
1 CCACTGTACTCTTCAAGGTTCAAT
11297728 CCACTGTACTCTTCAAGGTTCAAT
1 CCACTGTACTCTTCAAGGTTCAAT
11297752 CCACTGTACT
1 CCACTGTACT
11297762 TTTTGGACAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.26, C:0.29, G:0.12, T:0.33
Consensus pattern (24 bp):
CCACTGTACTCTTCAAGGTTCAAT
Found at i:11298733 original size:43 final size:44
Alignment explanation
Indices: 11298664--11298789 Score: 164
Period size: 43 Copynumber: 2.9 Consensus size: 44
11298654 TGGCCTCTCC
* **
11298664 TTTTTTTTATGACTCAAAGCGCCCTTTTTGGGTTTTCACATTA-
1 TTTTTTTTAAGACTCAAAGCGCCCTTTGCGGGTTTTCACATTAG
* * *
11298707 TTTTTTTTAAGACTCAAGGCGTCCTTTGCGGGTTTTCACCTTAG
1 TTTTTTTTAAGACTCAAAGCGCCCTTTGCGGGTTTTCACATTAG
* * *
11298751 TCTTTTTTAGGACTCAAAGCGCCCTTTGCAGGTTTTCAC
1 TTTTTTTTAAGACTCAAAGCGCCCTTTGCGGGTTTTCAC
11298790 CTTGGTCCCT
Statistics
Matches: 71, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
43 37 0.52
44 34 0.48
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.44
Consensus pattern (44 bp):
TTTTTTTTAAGACTCAAAGCGCCCTTTGCGGGTTTTCACATTAG
Found at i:11298757 original size:44 final size:43
Alignment explanation
Indices: 11298666--11298792 Score: 164
Period size: 44 Copynumber: 2.9 Consensus size: 43
11298656 GCCTCTCCTT
* ** * *
11298666 TTTTTTATGACTCAAAGCGCCCTTTTTGGGTTTTCACATTATT
1 TTTTTTAAGACTCAAAGCGCCCTTTGCGGGTTTTCACCTTATC
* *
11298709 TTTTTTAAGACTCAAGGCGTCCTTTGCGGGTTTTCACCTTAGTC
1 TTTTTTAAGACTCAAAGCGCCCTTTGCGGGTTTTCACCTTA-TC
* *
11298753 TTTTTTAGGACTCAAAGCGCCCTTTGCAGGTTTTCACCTT
1 TTTTTTAAGACTCAAAGCGCCCTTTGCGGGTTTTCACCTT
11298793 GGTCCCTTCT
Statistics
Matches: 72, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
43 35 0.49
44 37 0.51
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.43
Consensus pattern (43 bp):
TTTTTTAAGACTCAAAGCGCCCTTTGCGGGTTTTCACCTTATC
Found at i:11300722 original size:16 final size:16
Alignment explanation
Indices: 11300701--11300732 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
11300691 ATTTTGTTGC
*
11300701 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
11300717 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
11300733 CTTTCAATCA
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:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:11301074 original size:50 final size:51
Alignment explanation
Indices: 11300950--11301086 Score: 161
Period size: 51 Copynumber: 2.7 Consensus size: 51
11300940 ATTAATGATA
* * * *
11300950 CTGGTTCACATAGTAGCCTGCAGATAGTATTACACATGTGAACATCACTAT
1 CTGGTACACATAGTAGCCTGCACATAGTACTACACATGCGAACATCACTAT
* * * * *
11301001 CCGATACACATAGTAGCCAGCACATAGTACTGCACATGCGACCTATCA-T-T
1 CTGGTACACATAGTAGCCTGCACATAGTACTACACATGCGAAC-ATCACTAT
*
11301051 CTGGTACACGTAGTAGCCTGCACATAGTACTACACA
1 CTGGTACACATAGTAGCCTGCACATAGTACTACACA
11301087 CGTGACCATC
Statistics
Matches: 71, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
50 32 0.45
51 35 0.49
52 4 0.06
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (51 bp):
CTGGTACACATAGTAGCCTGCACATAGTACTACACATGCGAACATCACTAT
Found at i:11304666 original size:3 final size:3
Alignment explanation
Indices: 11304658--11304707 Score: 57
Period size: 3 Copynumber: 16.3 Consensus size: 3
11304648 ATAACCAAAT
* *
11304658 ATA ATA AT- ATCA ATA ATA ATA AGA GTA ATA ATA ATA ATAA ATA ATA
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA
11304704 ATA A
1 ATA A
11304708 ATTAATTAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 2 0.05
3 33 0.82
4 5 0.12
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:11305936 original size:22 final size:20
Alignment explanation
Indices: 11305885--11305955 Score: 78
Period size: 19 Copynumber: 3.5 Consensus size: 20
11305875 CATACACAAT
11305885 AAATAAATATAT-AAAATAG
1 AAATAAATATATAAAAATAG
11305904 AAATAAATATATAAAAATTCAGG
1 AAATAAATATATAAAAA-T-A-G
11305927 AAA-AAATATATAAAATATA-
1 AAATAAATATATAAAA-ATAG
11305946 AAAT-AATATA
1 AAATAAATATA
11305956 AATTATAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
19 21 0.46
20 4 0.09
21 2 0.04
22 14 0.30
23 5 0.11
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.27
Consensus pattern (20 bp):
AAATAAATATATAAAAATAG
Found at i:11305954 original size:17 final size:16
Alignment explanation
Indices: 11305929--11305965 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
11305919 AATTCAGGAA
11305929 AAAATATATAAAATAT
1 AAAATATATAAAATAT
*
11305945 AAAATAATATAAATTAT
1 AAAAT-ATATAAAATAT
11305962 AAAA
1 AAAA
11305966 ATAAAATTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAATATATAAAATAT
Found at i:11306070 original size:32 final size:30
Alignment explanation
Indices: 11306027--11306097 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 30
11306017 ATATTTTTAC
*
11306027 AAAAAAA-TGTAAAAGAAATTGTAAAAATTAT
1 AAAAAAATTGTAAAA-AAAAT-TAAAAATTAT
*
11306058 AAAAAAATTGTAAAAAAAATTAAAAATTTT
1 AAAAAAATTGTAAAAAAAATTAAAAATTAT
11306088 AAAAATAATT
1 AAAAA-AATT
11306098 TTTTATCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
30 14 0.39
31 15 0.42
32 7 0.19
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (30 bp):
AAAAAAATTGTAAAAAAAATTAAAAATTAT
Found at i:11306078 original size:12 final size:11
Alignment explanation
Indices: 11306027--11306075 Score: 59
Period size: 11 Copynumber: 4.6 Consensus size: 11
11306017 ATATTTTTAC
11306027 AAAAAAA-TGT
1 AAAAAAATTGT
11306037 AAAAGAAATTGT
1 AAAA-AAATTGT
*
11306049 --AAAAATTAT
1 AAAAAAATTGT
11306058 AAAAAAATTGT
1 AAAAAAATTGT
11306069 AAAAAAA
1 AAAAAAA
11306076 ATTAAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
9 6 0.18
10 6 0.18
11 18 0.55
12 3 0.09
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.22
Consensus pattern (11 bp):
AAAAAAATTGT
Found at i:11306082 original size:20 final size:20
Alignment explanation
Indices: 11306027--11306097 Score: 63
Period size: 19 Copynumber: 3.5 Consensus size: 20
11306017 ATATTTTTAC
11306027 AAAAAAATGTAAAAGAAATTGTA
1 AAAAAAAT-T-AAA-AAATTGTA
** *
11306050 AAAATTATAAAAAAATTGTA
1 AAAAAAATTAAAAAATTGTA
*
11306070 AAAAAAATT-AAAAATTTTA
1 AAAAAAATTAAAAAATTGTA
*
11306089 AAAATAATT
1 AAAAAAATT
11306098 TTTTATCAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 17 0.43
20 14 0.35
21 3 0.08
23 6 0.15
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (20 bp):
AAAAAAATTAAAAAATTGTA
Found at i:11307783 original size:30 final size:27
Alignment explanation
Indices: 11307737--11307791 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 27
11307727 TATAGAGTTG
*
11307737 CCACAGAGGCTTTCCTTTGACAGAGATCA
1 CCACAAAGGCTTTCCTTT--CAGAGATCA
11307766 CCACAAAGGCGTTTCCTTTCAGAGAT
1 CCACAAAGGC-TTTCCTTTCAGAGAT
11307792 TTGCCATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 7 0.29
29 9 0.38
30 8 0.33
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (27 bp):
CCACAAAGGCTTTCCTTTCAGAGATCA
Found at i:11309440 original size:25 final size:25
Alignment explanation
Indices: 11309403--11309482 Score: 83
Period size: 25 Copynumber: 3.2 Consensus size: 25
11309393 TCCTGATATT
**
11309403 TGGCTCTCACGAGCTTCCCGTTATA
1 TGGCTCTTGCGAGCTTCCCGTTATA
*
11309428 TGGTTCTTGCGAGCTTCCCGATTA-A
1 TGGCTCTTGCGAGCTTCCCG-TTATA
***
11309453 TGGCTCTTTTAAGCTTCCCGTT-TA
1 TGGCTCTTGCGAGCTTCCCGTTATA
11309477 TGGCTC
1 TGGCTC
11309483 ATCGGAGCTT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
24 9 0.20
25 34 0.74
26 3 0.07
ACGTcount: A:0.14, C:0.28, G:0.21, T:0.38
Consensus pattern (25 bp):
TGGCTCTTGCGAGCTTCCCGTTATA
Found at i:11309555 original size:25 final size:23
Alignment explanation
Indices: 11309413--11309569 Score: 98
Period size: 25 Copynumber: 6.3 Consensus size: 23
11309403 TGGCTCTCAC
* *
11309413 GAGCTTCCCGTTATATGGTTCTTG
1 GAGCTTCTCGTTA-ATGGCTCTTG
* *
11309437 CGAGCTTCCCGATTAATGGCTCTTTT
1 -GAGCTTCTCG-TTAATGGCTC-TTG
* * * *
11309463 AAGCTTCCCGTTTATGGCTCATCG
1 GAGCTTCTCGTTAATGGCTC-TTG
* * *
11309487 GAGCTTTTCGATAATTGGATCTTAG
1 GAGCTTCTCGTTAA-TGGCTCTT-G
*
11309512 GAGCTTCTCGATAACTGGCTCTTG
1 GAGCTTCTCGTTAA-TGGCTCTTG
*
11309536 TGAGCTTCTCGGTTAATGGCTCTTCA
1 -GAGCTTCTC-GTTAATGGCTCTT-G
11309562 GAGCTTCT
1 GAGCTTCT
11309570 TGATATTGGC
Statistics
Matches: 106, Mismatches: 19, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
24 21 0.20
25 76 0.72
26 9 0.08
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.38
Consensus pattern (23 bp):
GAGCTTCTCGTTAATGGCTCTTG
Found at i:11309614 original size:48 final size:49
Alignment explanation
Indices: 11309562--11309666 Score: 126
Period size: 48 Copynumber: 2.2 Consensus size: 49
11309552 TGGCTCTTCA
* *
11309562 GAGCTTCTTG-ATATTGGCTCGCTTGAA-CTTCCTGATAT-TGGCTCGCAT
1 GAGCTTCCTGAAT-TTGGCTCGCTT-AAGCTTCCTGATATATGGCTCACAT
* * *
11309610 GAGCTTCCTGAATTTGGCTCTCTTAAGCTTCTTGTTATATGGCTCACAT
1 GAGCTTCCTGAATTTGGCTCGCTTAAGCTTCCTGATATATGGCTCACAT
11309659 GAGCTTCC
1 GAGCTTCC
11309667 CGTTATATGG
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
47 2 0.04
48 28 0.57
49 19 0.39
ACGTcount: A:0.17, C:0.24, G:0.21, T:0.38
Consensus pattern (49 bp):
GAGCTTCCTGAATTTGGCTCGCTTAAGCTTCCTGATATATGGCTCACAT
Found at i:11309638 original size:24 final size:24
Alignment explanation
Indices: 11309563--11309654 Score: 89
Period size: 24 Copynumber: 3.8 Consensus size: 24
11309553 GGCTCTTCAG
*
11309563 AGCTTCTTGATATTGGCTCGCTTGA
1 AGCTTCCTGATATTGGCTCGCTT-A
* *
11309588 A-CTTCCTGATATTGGCTCGCATG
1 AGCTTCCTGATATTGGCTCGCTTA
*
11309611 AGCTTCCTGA-ATTTGGCTCTCTTA
1 AGCTTCCTGATA-TTGGCTCGCTTA
* *
11309635 AGCTTCTTGTTATATGGCTC
1 AGCTTCCTGATAT-TGGCTC
11309655 ACATGAGCTT
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
23 2 0.04
24 45 0.82
25 8 0.15
ACGTcount: A:0.16, C:0.23, G:0.21, T:0.40
Consensus pattern (24 bp):
AGCTTCCTGATATTGGCTCGCTTA
Found at i:11309654 original size:25 final size:25
Alignment explanation
Indices: 11309624--11309679 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
11309614 TTCCTGAATT
* * **
11309624 TGGCTCTCTTAAGCTTCTTGTTATA
1 TGGCTCACATAAGCTTCCCGTTATA
*
11309649 TGGCTCACATGAGCTTCCCGTTATA
1 TGGCTCACATAAGCTTCCCGTTATA
11309674 TGGCTC
1 TGGCTC
11309680 GAAAGAGCTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.16, C:0.25, G:0.20, T:0.39
Consensus pattern (25 bp):
TGGCTCACATAAGCTTCCCGTTATA
Found at i:11309663 original size:49 final size:48
Alignment explanation
Indices: 11309562--11309680 Score: 125
Period size: 48 Copynumber: 2.4 Consensus size: 48
11309552 TGGCTCTTCA
* *
11309562 GAGCTTCTTGATATTGGCTCGCTTGAACTTCCTGATATTGGCTCGCAT
1 GAGCTTCCTGATATTGGCTCGCTTGAACTTCCTGATATTGGCTCACAT
* * *
11309610 GAGCTTCCTGA-ATTTGGCTCTCTT-AAGCTTCTTGTTATATGGCTCACAT
1 GAGCTTCCTGATA-TTGGCTCGCTTGAA-CTTCCTGATAT-TGGCTCACAT
* *
11309659 GAGCTTCCCGTTATATGGCTCG
1 GAGCTTCCTGATAT-TGGCTCG
11309681 AAAGAGCTTC
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
47 3 0.05
48 29 0.50
49 19 0.33
50 7 0.12
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.38
Consensus pattern (48 bp):
GAGCTTCCTGATATTGGCTCGCTTGAACTTCCTGATATTGGCTCACAT
Found at i:11309687 original size:25 final size:25
Alignment explanation
Indices: 11309643--11309697 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
11309633 TAAGCTTCTT
*
11309643 GTTATATGGCTCACATGAGCTTCCC
1 GTTATATGGCTCACAAGAGCTTCCC
*
11309668 GTTATATGGCTCGA-AAGAGCTTCTC
1 GTTATATGGCTC-ACAAGAGCTTCCC
11309693 GTTAT
1 GTTAT
11309698 GTGCTCGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 26 0.96
26 1 0.04
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (25 bp):
GTTATATGGCTCACAAGAGCTTCCC
Found at i:11317272 original size:9 final size:9
Alignment explanation
Indices: 11317258--11317288 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
11317248 GTTAAACGAA
11317258 TCGAGTTAT
1 TCGAGTTAT
*
11317267 TCGAGTTAA
1 TCGAGTTAT
11317276 TCGAGTTAT
1 TCGAGTTAT
11317285 TCGA
1 TCGA
11317289 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:11317781 original size:19 final size:20
Alignment explanation
Indices: 11317745--11317783 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
11317735 CAAATTTTTA
11317745 TTCCCCAAAACTTTTTATTT
1 TTCCCCAAAACTTTTTATTT
*
11317765 TTCCCCTAAAC-TTTTATTT
1 TTCCCCAAAACTTTTTATTT
11317784 CTCACCCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.23, C:0.26, G:0.00, T:0.51
Consensus pattern (20 bp):
TTCCCCAAAACTTTTTATTT
Found at i:11317791 original size:20 final size:20
Alignment explanation
Indices: 11317746--11317791 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
11317736 AAATTTTTAT
* *
11317746 TCCCCAAAACTTTTTATTTT
1 TCCCCTAAACTTTTTATTTC
11317766 TCCCCTAAAC-TTTTATTTC
1 TCCCCTAAACTTTTTATTTC
11317785 TCACCCT
1 TC-CCCT
11317792 TTACTCTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.22, C:0.33, G:0.00, T:0.46
Consensus pattern (20 bp):
TCCCCTAAACTTTTTATTTC
Found at i:11318405 original size:5 final size:5
Alignment explanation
Indices: 11318395--11318420 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
11318385 CTCGAAAATT
11318395 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
11318421 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:11323857 original size:27 final size:26
Alignment explanation
Indices: 11323787--11323912 Score: 92
Period size: 27 Copynumber: 4.7 Consensus size: 26
11323777 GGCGGACTGG
* * *
11323787 CTCGCGAACAGGAGACTGACGAACTGT
1 CTCGCGAACAGG-GACTGACGGATTGC
*
11323814 CTCGTGAACAGAGGACTGACGGATTGC
1 CTCGCGAACAG-GGACTGACGGATTGC
* *
11323841 CTCGCGAATAGGTGACTGATGGATTGC
1 CTCGCGAACAGG-GACTGACGGATTGC
* * *
11323868 CTTGCAAACAGGGGACT-AGCGGACTGC
1 CTCGCGAACA-GGGACTGA-CGGATTGC
* *
11323895 CTTGTGAACAGGGGACTG
1 CTCGCGAACA-GGGACTG
11323913 GTGGATTGTC
Statistics
Matches: 80, Mismatches: 14, Indels: 9
0.78 0.14 0.09
Matches are distributed among these distances:
26 2 0.03
27 75 0.94
28 3 0.04
ACGTcount: A:0.25, C:0.22, G:0.33, T:0.19
Consensus pattern (26 bp):
CTCGCGAACAGGGACTGACGGATTGC
Found at i:11326627 original size:26 final size:26
Alignment explanation
Indices: 11326597--11326647 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
11326587 CTTACTAACA
*
11326597 ACTTAACTACTGCAGTAGTTCATTCT
1 ACTTAACTACTGCAGCAGTTCATTCT
* *
11326623 ACTTAACTGCTGCTGCAGTTCATTC
1 ACTTAACTACTGCAGCAGTTCATTC
11326648 CTTAACATGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.24, C:0.25, G:0.14, T:0.37
Consensus pattern (26 bp):
ACTTAACTACTGCAGCAGTTCATTCT
Found at i:11331349 original size:22 final size:22
Alignment explanation
Indices: 11331323--11331367 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
11331313 AAGCAACTAG
11331323 CAGAAACATTGCCAATGCAGGT
1 CAGAAACATTGCCAATGCAGGT
11331345 CAGAAACATTGCCAATGCAGGT
1 CAGAAACATTGCCAATGCAGGT
11331367 C
1 C
11331368 GATAACTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.24, G:0.22, T:0.18
Consensus pattern (22 bp):
CAGAAACATTGCCAATGCAGGT
Found at i:11333604 original size:17 final size:17
Alignment explanation
Indices: 11333574--11333606 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
11333564 ATAGAAACAA
11333574 ACAAACAAACACCAAAC
1 ACAAACAAACACCAAAC
11333591 ACAAGACAAA-ACCAAA
1 ACAA-ACAAACACCAAA
11333607 ACTCTCTCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.67, C:0.30, G:0.03, T:0.00
Consensus pattern (17 bp):
ACAAACAAACACCAAAC
Found at i:11353463 original size:27 final size:27
Alignment explanation
Indices: 11353433--11353484 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
11353423 TAAAGTCTAT
* *
11353433 CTATAGTAGTCTCAGTATATACTATAC
1 CTATAGCAGTCTCAGGATATACTATAC
*
11353460 CTATAGCAGTTTCAGGATATACTAT
1 CTATAGCAGTCTCAGGATATACTAT
11353485 CAGAAACAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (27 bp):
CTATAGCAGTCTCAGGATATACTATAC
Found at i:11369635 original size:19 final size:20
Alignment explanation
Indices: 11369603--11369640 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
11369593 CGGCGCCGAT
11369603 TCTGTAAGTGTTTT-AAAAC
1 TCTGTAAGTGTTTTGAAAAC
11369622 TCTGATAAGT-TTTTGAAAA
1 TCTG-TAAGTGTTTTGAAAA
11369641 TATGAGTAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.34, C:0.08, G:0.16, T:0.42
Consensus pattern (20 bp):
TCTGTAAGTGTTTTGAAAAC
Found at i:11380764 original size:12 final size:12
Alignment explanation
Indices: 11380726--11380769 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
11380716 ACTGGTCATA
11380726 GAGAGAATTGAG
1 GAGAGAATTGAG
* *
11380738 GAGGGATATT-TG
1 GAGAGA-ATTGAG
11380750 GAGAGAATTGAG
1 GAGAGAATTGAG
11380762 GAGAGAAT
1 GAGAGAAT
11380770 ATTGAGATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 3 0.12
12 20 0.77
13 3 0.12
ACGTcount: A:0.39, C:0.00, G:0.41, T:0.20
Consensus pattern (12 bp):
GAGAGAATTGAG
Found at i:11380773 original size:14 final size:13
Alignment explanation
Indices: 11380726--11380775 Score: 52
Period size: 12 Copynumber: 4.0 Consensus size: 13
11380716 ACTGGTCATA
11380726 GAGAGA-ATTGAG
1 GAGAGATATTGAG
* *
11380738 GAGGGATATT-TG
1 GAGAGATATTGAG
11380750 GAGAGA-ATTGAG
1 GAGAGATATTGAG
11380762 GAGAGAATATTGAG
1 GAGAG-ATATTGAG
11380776 ATTTGGGGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
11 3 0.10
12 17 0.57
13 4 0.13
14 6 0.20
ACGTcount: A:0.38, C:0.00, G:0.40, T:0.22
Consensus pattern (13 bp):
GAGAGATATTGAG
Found at i:11381492 original size:27 final size:27
Alignment explanation
Indices: 11381441--11381533 Score: 93
Period size: 27 Copynumber: 3.5 Consensus size: 27
11381431 TCGATATCTA
11381441 GACCAAAATACCCTCGAAGGATAAAAT
1 GACCAAAATACCCTCGAAGGATAAAAT
* *
11381468 GACCAAAATACCCT-TAATGGGTAAAAT
1 GACCAAAATACCCTCGAA-GGATAAAAT
* * *
11381495 GACCGAAATACTCTCGTAGG-TAAGAAT
1 GACCAAAATACCCTCGAAGGATAA-AAT
*
11381522 -ACCGAAATACCC
1 GACCAAAATACCC
11381534 CCATAAGTTA
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
26 16 0.29
27 39 0.70
28 1 0.02
ACGTcount: A:0.43, C:0.23, G:0.16, T:0.18
Consensus pattern (27 bp):
GACCAAAATACCCTCGAAGGATAAAAT
Found at i:11381572 original size:27 final size:27
Alignment explanation
Indices: 11381462--11381739 Score: 260
Period size: 27 Copynumber: 10.4 Consensus size: 27
11381452 CCTCGAAGGA
** *
11381462 TAAAATGACCAAAATACCCTTA-ATGGG
1 TAAAATGACCGTAATACCCCTATA-GGG
* * *
11381489 TAAAATGACCGAAATA-CTCTCGTA-GG
1 TAAAATGACCGTAATACCCCT-ATAGGG
* * * *
11381515 TAAGAAT-ACCGAAATACCCCCATAAGT
1 TAA-AATGACCGTAATACCCCTATAGGG
* ** *
11381542 TAAAATGATCGTAATATTCCTGTAGGG
1 TAAAATGACCGTAATACCCCTATAGGG
* * * *
11381569 TAAAATAACTGTAATGCCCCTGTAGGG
1 TAAAATGACCGTAATACCCCTATAGGG
11381596 TAAAATGACCGTAATACCCCTATAGGG
1 TAAAATGACCGTAATACCCCTATAGGG
11381623 TAAAATGACCGTAATACCCCTATAGGG
1 TAAAATGACCGTAATACCCCTATAGGG
* * * *
11381650 TAAAATGATCGTAAT-GCCCTGTAGGA
1 TAAAATGACCGTAATACCCCTATAGGG
*
11381676 TAAAATGACCGTAATGCCCCTATAGGG
1 TAAAATGACCGTAATACCCCTATAGGG
* * *
11381703 TAAAATGATCGTAATGCCCCTATAGGT
1 TAAAATGACCGTAATACCCCTATAGGG
11381730 TAAAATGACC
1 TAAAATGACC
11381740 ACAATGCCCT
Statistics
Matches: 207, Mismatches: 37, Indels: 14
0.80 0.14 0.05
Matches are distributed among these distances:
26 43 0.21
27 163 0.79
28 1 0.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.24
Consensus pattern (27 bp):
TAAAATGACCGTAATACCCCTATAGGG
Found at i:11381671 original size:107 final size:108
Alignment explanation
Indices: 11381486--11381739 Score: 318
Period size: 107 Copynumber: 2.4 Consensus size: 108
11381476 TACCCTTAAT
* * * *
11381486 GGGTAAAATGACCGAAATA-CTCTCGTA-GGTAAGAAT-ACCGAAATACCCCCATAAGTTAAAAT
1 GGGTAAAATGACCGTAATACCCCT-ATAGGGTAA-AATGACCGAAATACCCCCATAAGGTAAAAT
** * * *
11381548 GATCGTAATATTCCTGTAGGGTAAAATAACTGTAATGCCCCTGTA
64 GATCGTAATAGCCCTGTAGGATAAAATAACCGTAATGCCCCTATA
* * *
11381593 GGGTAAAATGACCGTAATACCCCTATAGGGTAAAATGACCGTAATACCCCTATAGGGTAAAATGA
1 GGGTAAAATGACCGTAATACCCCTATAGGGTAAAATGACCGAAATACCCCCATAAGGTAAAATGA
*
11381658 TCGTAAT-GCCCTGTAGGATAAAATGACCGTAATGCCCCTATA
66 TCGTAATAGCCCTGTAGGATAAAATAACCGTAATGCCCCTATA
* * *
11381700 GGGTAAAATGATCGTAATGCCCCTATAGGTTAAAATGACC
1 GGGTAAAATGACCGTAATACCCCTATAGGGTAAAATGACC
11381740 ACAATGCCCT
Statistics
Matches: 128, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
107 89 0.70
108 39 0.30
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.24
Consensus pattern (108 bp):
GGGTAAAATGACCGTAATACCCCTATAGGGTAAAATGACCGAAATACCCCCATAAGGTAAAATGA
TCGTAATAGCCCTGTAGGATAAAATAACCGTAATGCCCCTATA
Found at i:11381723 original size:80 final size:82
Alignment explanation
Indices: 11381510--11381737 Score: 295
Period size: 80 Copynumber: 2.8 Consensus size: 82
11381500 AAATACTCTC
* * * * ** *
11381510 GTAGG-TAAGAAT-ACCGAAATACCCCCATAAGTTAAAATGATCGTAATATTCCTGTAGGGTAAA
1 GTAGGATAA-AATGACCGTAATACCCCTATAGGGTAAAATGATCGTAATACCCCTATAGGGTAAA
11381573 AT-AACTGTAATGCCCCT
65 ATGAACTGTAATGCCCCT
* *
11381590 GTAGGGTAAAATGACCGTAATACCCCTATAGGGTAAAATGACCGTAATACCCCTATAGGGTAAAA
1 GTAGGATAAAATGACCGTAATACCCCTATAGGGTAAAATGATCGTAATACCCCTATAGGGTAAAA
*
11381655 TGATC-GTAATG-CCCT
66 TGAACTGTAATGCCCCT
* * *
11381670 GTAGGATAAAATGACCGTAATGCCCCTATAGGGTAAAATGATCGTAATGCCCCTATAGGTTAAAA
1 GTAGGATAAAATGACCGTAATACCCCTATAGGGTAAAATGATCGTAATACCCCTATAGGGTAAAA
11381735 TGA
66 TGA
11381738 CCACAATGCC
Statistics
Matches: 131, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
80 75 0.57
81 54 0.41
82 2 0.02
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.25
Consensus pattern (82 bp):
GTAGGATAAAATGACCGTAATACCCCTATAGGGTAAAATGATCGTAATACCCCTATAGGGTAAAA
TGAACTGTAATGCCCCT
Found at i:11381760 original size:80 final size:80
Alignment explanation
Indices: 11381462--11381760 Score: 284
Period size: 80 Copynumber: 3.7 Consensus size: 80
11381452 CCTCGAAGGA
** * * *
11381462 TAAAATGACCAAAATACCCTTA-ATGGGTAAAATGACCGA-AATACTCTCGTA-GGTAAGAAT-A
1 TAAAATGACCGTAATACCCCTATA-GGGTAAAATGACC-ACAATGCCCT-GTAGGGTAA-AATGA
* * * *
11381523 CCGAAATACCCCCATAAGT
62 CCGTAATACCCCTATAGGG
* ** * * ***
11381542 TAAAATGATCGTAATATTCCTGTAGGGTAAAATAACTGTAATGCCCCTGTAGGGTAAAATGACCG
1 TAAAATGACCGTAATACCCCTATAGGGTAAAATGACCACAATG-CCCTGTAGGGTAAAATGACCG
11381607 TAATACCCCTATAGGG
65 TAATACCCCTATAGGG
* ** *
11381623 TAAAATGACCGTAATACCCCTATAGGGTAAAATGATCGTAATGCCCTGTAGGATAAAATGACCGT
1 TAAAATGACCGTAATACCCCTATAGGGTAAAATGACCACAATGCCCTGTAGGGTAAAATGACCGT
*
11381688 AATGCCCCTATAGGG
66 AATACCCCTATAGGG
* * *
11381703 TAAAATGATCGTAATGCCCCTATAGGTTAAAATGACCACAATGCCCTGGT-GGGTAAAA
1 TAAAATGACCGTAATACCCCTATAGGGTAAAATGACCACAATGCCCT-GTAGGGTAAAA
11381761 GACTATTTTT
Statistics
Matches: 181, Mismatches: 32, Indels: 12
0.80 0.14 0.05
Matches are distributed among these distances:
80 118 0.65
81 63 0.35
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.24
Consensus pattern (80 bp):
TAAAATGACCGTAATACCCCTATAGGGTAAAATGACCACAATGCCCTGTAGGGTAAAATGACCGT
AATACCCCTATAGGG
Found at i:11381811 original size:23 final size:23
Alignment explanation
Indices: 11381784--11381850 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
11381774 CATCGAGGTC
*
11381784 AAATGATTGTTTTGTCTGTGGTT
1 AAATGATTGATTTGTCTGTGGTT
*
11381807 AAATGATTGATTTGTCTGTGTTT
1 AAATGATTGATTTGTCTGTGGTT
* *
11381830 AGTATGACTGATTTGTCTGTG
1 A-AATGATTGATTTGTCTGTG
11381851 ATTTGAATGA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
23 22 0.56
24 17 0.44
ACGTcount: A:0.19, C:0.06, G:0.25, T:0.49
Consensus pattern (23 bp):
AAATGATTGATTTGTCTGTGGTT
Found at i:11381841 original size:24 final size:24
Alignment explanation
Indices: 11381785--11381866 Score: 96
Period size: 24 Copynumber: 3.5 Consensus size: 24
11381775 ATCGAGGTCA
* * *
11381785 AATGATTGTTTTGTCTGTGGTTA-
1 AATGACTGATTTGTCTGTGTTTAG
*
11381808 AATGATTGATTTGTCTGTGTTTAG
1 AATGACTGATTTGTCTGTGTTTAG
*
11381832 TATGACTGATTTGTCTGTGATTT-G
1 AATGACTGATTTGTCTGTG-TTTAG
11381856 AATGACTGATT
1 AATGACTGATT
11381867 CTGAGCATGG
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
23 21 0.40
24 28 0.54
25 3 0.06
ACGTcount: A:0.21, C:0.06, G:0.24, T:0.49
Consensus pattern (24 bp):
AATGACTGATTTGTCTGTGTTTAG
Found at i:11381991 original size:27 final size:26
Alignment explanation
Indices: 11381930--11381992 Score: 65
Period size: 27 Copynumber: 2.4 Consensus size: 26
11381920 ATCGAGGAAG
*
11381930 TACTA-TACTGGTGGCTCTACCACAA
1 TACTATTACTAGTGGCTCTACCACAA
* * *
11381955 TCACTGTTACTAGTGGCTTTGCCACATA
1 T-ACTATTACTAGTGGCTCTACCACA-A
11381983 TACTATTACT
1 TACTATTACT
11381993 GGCAGCTTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
25 1 0.03
26 3 0.10
27 24 0.80
28 2 0.07
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.35
Consensus pattern (26 bp):
TACTATTACTAGTGGCTCTACCACAA
Found at i:11382047 original size:26 final size:26
Alignment explanation
Indices: 11381992--11382047 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
11381982 ATACTATTAC
* *
11381992 TGGCAGCTTTACTGCGATACTATTGC
1 TGGCAGCTTTACTGCGATACTACTGA
* *
11382018 TGGCAGCTTTGCTTG-GATGCTACTGA
1 TGGCAGCTTTAC-TGCGATACTACTGA
11382044 TGGC
1 TGGC
11382048 TTTGTGCCGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 23 0.92
27 2 0.08
ACGTcount: A:0.16, C:0.21, G:0.29, T:0.34
Consensus pattern (26 bp):
TGGCAGCTTTACTGCGATACTACTGA
Found at i:11382082 original size:32 final size:32
Alignment explanation
Indices: 11382038--11382125 Score: 124
Period size: 32 Copynumber: 2.8 Consensus size: 32
11382028 GCTTGGATGC
*
11382038 TACTGATGGCTTTGTGCCGATCATAGTACCGT
1 TACTGATGGCTTTGTGCCGATCATAGTACCAT
* *
11382070 TACTGATAGCTTTGTGCCGATCATATTACCAT
1 TACTGATGGCTTTGTGCCGATCATAGTACCAT
*
11382102 TACT-AGTGGCTATGTGCCGATCAT
1 TACTGA-TGGCTTTGTGCCGATCAT
11382126 TTCATTGTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
31 1 0.02
32 49 0.98
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATAGTACCAT
Found at i:11382157 original size:32 final size:32
Alignment explanation
Indices: 11382035--11382208 Score: 104
Period size: 32 Copynumber: 5.5 Consensus size: 32
11382025 TTTGCTTGGA
* *
11382035 TGCTACTGATGGCTTTGTGCCGATCATAGT-AC
1 TGCTACTGATGGCTTTGTGACAATCATA-TCAC
* * * * * *
11382067 CGTTACTGATAGCTTTGTGCCGATCATATTAC
1 TGCTACTGATGGCTTTGTGACAATCATATCAC
*** * * * * *
11382099 CATTACT-AGTGGCTATGTGCCGATCATTTCAT
1 TGCTACTGA-TGGCTTTGTGACAATCATATCAC
*
11382131 TGTTACTGATGG-TTGTGTGACAATCATATCAC
1 TGCTACTGATGGCTT-TGTGACAATCATATCAC
* * *
11382163 TGCTACTGATGGCTTTGTGCCAATCACATTAC
1 TGCTACTGATGGCTTTGTGACAATCATATCAC
*
11382195 TG-TACTTATGGCTT
1 TGCTACTGATGGCTT
11382209 GTAGTCATTC
Statistics
Matches: 116, Mismatches: 21, Indels: 11
0.78 0.14 0.07
Matches are distributed among these distances:
31 14 0.12
32 99 0.85
33 3 0.03
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (32 bp):
TGCTACTGATGGCTTTGTGACAATCATATCAC
Found at i:11382287 original size:26 final size:26
Alignment explanation
Indices: 11382258--11382310 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
11382248 GGCTCTTAGC
* *
11382258 CATTCTGACTACTGGCAGCTCTGCTG
1 CATTATGACTACTGGCAGCTATGCTG
*
11382284 CATTATTACTACTGGCAGCTATGCTG
1 CATTATGACTACTGGCAGCTATGCTG
11382310 C
1 C
11382311 GATATTGGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.19, C:0.28, G:0.21, T:0.32
Consensus pattern (26 bp):
CATTATGACTACTGGCAGCTATGCTG
Found at i:11388829 original size:21 final size:21
Alignment explanation
Indices: 11388796--11388844 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
11388786 ATCATGTTAT
*
11388796 TTAT-TTTTATTTGATTTTG-
1 TTATGTTTTATTTGAATTTGA
11388815 TTATGTTTATATTTGAATTTGAA
1 TTATGTTT-TATTTGAATTTG-A
11388838 TTATGTT
1 TTATGTT
11388845 AGCACCACTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 4 0.16
20 3 0.12
21 11 0.44
23 7 0.28
ACGTcount: A:0.22, C:0.00, G:0.12, T:0.65
Consensus pattern (21 bp):
TTATGTTTTATTTGAATTTGA
Found at i:11389822 original size:23 final size:23
Alignment explanation
Indices: 11389796--11389841 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
11389786 GAGTGTATAA
*
11389796 ATGTATGCATATGAAT-TATTTTG
1 ATGTATGAAT-TGAATGTATTTTG
*
11389819 ATGTTTGAATTGAATGTATTTTG
1 ATGTATGAATTGAATGTATTTTG
11389842 TTATAATAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.28, C:0.02, G:0.20, T:0.50
Consensus pattern (23 bp):
ATGTATGAATTGAATGTATTTTG
Found at i:11390963 original size:14 final size:14
Alignment explanation
Indices: 11390944--11390979 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
11390934 ATTTTCTTCA
11390944 CTTGAACCCTGCAC
1 CTTGAACCCTGCAC
* *
11390958 CTTGAATCCTGCGC
1 CTTGAACCCTGCAC
11390972 CTTGAACC
1 CTTGAACC
11390980 TTAAATCCTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.19, C:0.39, G:0.17, T:0.25
Consensus pattern (14 bp):
CTTGAACCCTGCAC
Found at i:11391080 original size:28 final size:27
Alignment explanation
Indices: 11391036--11391088 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
11391026 GGGTCTTGGA
* * *
11391036 CAAGTTCAGGGTTCAAAGTCTAAGATT
1 CAAGTTCACGGTCCAAAGTATAAGATT
11391063 CAAGATTCACGGTCCAAAGTATAAGA
1 CAAG-TTCACGGTCCAAAGTATAAGA
11391089 CCTAGGAGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 4 0.18
28 18 0.82
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.25
Consensus pattern (27 bp):
CAAGTTCACGGTCCAAAGTATAAGATT
Found at i:11394693 original size:3 final size:3
Alignment explanation
Indices: 11394685--11394731 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
11394675 ACAACCTTGA
11394685 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
11394732 AACAAAGCAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:11398665 original size:43 final size:43
Alignment explanation
Indices: 11398569--11398880 Score: 193
Period size: 43 Copynumber: 7.3 Consensus size: 43
11398559 GCATTATCAA
* * * * *
11398569 ATAAACCGGAAG-AAATACACTAGCACACACAGTGCATCGTTGG
1 ATAAACC-GAAGTAATTATACTGGCACACATAGTGCATCATTGG
* * * *
11398612 ACAGGA-CGAAGTAATTATACTGGTACACATAGTACATCATTGG
1 ATA-AACCGAAGTAATTATACTGGCACACATAGTGCATCATTGG
* ** **
11398655 ATAAACCGAAGCAATTATGTTGGCACGTA-AGTGCATCATTGG
1 ATAAACCGAAGTAATTATACTGGCACACATAGTGCATCATTGG
** * * * * ** *
11398697 ATGTACTGAAGAAAATATA-TCG-ACATGTAAGTGCATCATAGG
1 ATAAACCGAAGTAATTATACTGGCACACAT-AGTGCATCATTGG
* * * * * *
11398739 ATATACCAAAGCAATTATACTGACACACATAGTGCATTATCGG
1 ATAAACCGAAGTAATTATACTGGCACACATAGTGCATCATTGG
* ** * * * *
11398782 ACAAGTCAAATTAATTATACTAGCACACACAGTGCATCATTGG
1 ATAAACCGAAGTAATTATACTGGCACACATAGTGCATCATTGG
* ***
11398825 ACAAGGTGAAGTAATTATACTGGCACACATAGTGCATCATTGG
1 ATAAACCGAAGTAATTATACTGGCACACATAGTGCATCATTGG
*
11398868 ATAAATCGAAGTA
1 ATAAACCGAAGTA
11398881 TAAATTATAC
Statistics
Matches: 202, Mismatches: 60, Indels: 14
0.73 0.22 0.05
Matches are distributed among these distances:
40 3 0.01
41 2 0.01
42 56 0.28
43 136 0.67
44 5 0.02
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (43 bp):
ATAAACCGAAGTAATTATACTGGCACACATAGTGCATCATTGG
Found at i:11398698 original size:42 final size:42
Alignment explanation
Indices: 11398646--11398757 Score: 125
Period size: 42 Copynumber: 2.7 Consensus size: 42
11398636 ACACATAGTA
* * * *
11398646 CATCATTGGATAAACCGAAGCAATTATGTTGGCACGTAAGTG
1 CATCATTGGATATACCGAAGCAATTATATCGACACGTAAGTG
* * * * *
11398688 CATCATTGGATGTACTGAAGAAAATATATCGACATGTAAGTG
1 CATCATTGGATATACCGAAGCAATTATATCGACACGTAAGTG
* *
11398730 CATCATAGGATATACCAAAGCAATTATA
1 CATCATTGGATATACCGAAGCAATTATA
11398758 CTGACACACA
Statistics
Matches: 55, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (42 bp):
CATCATTGGATATACCGAAGCAATTATATCGACACGTAAGTG
Found at i:11405428 original size:14 final size:14
Alignment explanation
Indices: 11405409--11405435 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11405399 AAAAATTAAA
11405409 AAAATATTAGAATT
1 AAAATATTAGAATT
11405423 AAAATATTAGAAT
1 AAAATATTAGAAT
11405436 CACAATAAAA
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:0.59, C:0.00, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAATATTAGAATT
Found at i:11405442 original size:14 final size:14
Alignment explanation
Indices: 11405409--11405442 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
11405399 AAAAATTAAA
*
11405409 AAAATATTAGAATT
1 AAAATATTAGAATC
11405423 AAAATATTAGAATC
1 AAAATATTAGAATC
*
11405437 ACAATA
1 AAAATA
11405443 AAACAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.29
Consensus pattern (14 bp):
AAAATATTAGAATC
Found at i:11408615 original size:28 final size:30
Alignment explanation
Indices: 11408583--11408646 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 30
11408573 ATCCTAGATT
*
11408583 TTAAAATTTAAAAA-GTAG-GACTAAATTC
1 TTAAAATTTAAAAATATAGAGACTAAATTC
* *
11408611 TTAAAA-ATAAAAATATAGAGACTCAATTC
1 TTAAAATTTAAAAATATAGAGACTAAATTC
11408640 -TAAAATT
1 TTAAAATT
11408647 ACGAAGACTA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
27 6 0.21
28 14 0.48
29 9 0.31
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.31
Consensus pattern (30 bp):
TTAAAATTTAAAAATATAGAGACTAAATTC
Found at i:11409601 original size:14 final size:14
Alignment explanation
Indices: 11409590--11409619 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
11409580 TCAAAATGTT
11409590 TTTC-GGAAAATGA
1 TTTCTGGAAAATGA
11409603 TTTCTGGAAAATGA
1 TTTCTGGAAAATGA
11409617 TTT
1 TTT
11409620 ACTTTTCTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (14 bp):
TTTCTGGAAAATGA
Found at i:11409628 original size:20 final size:20
Alignment explanation
Indices: 11409603--11409642 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
11409593 CGGAAAATGA
*
11409603 TTTCTGGAAAATGATTTACT
1 TTTCTGGAAAATGACTTACT
11409623 TTTCTGGAAAATGACTTACT
1 TTTCTGGAAAATGACTTACT
11409643 GAAAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.12, G:0.15, T:0.42
Consensus pattern (20 bp):
TTTCTGGAAAATGACTTACT
Found at i:11409632 original size:34 final size:32
Alignment explanation
Indices: 11409589--11409652 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 32
11409579 ATCAAAATGT
*
11409589 TTTTCGGAAAATGA-TTTCTGGAAAATGATTTAC
1 TTTTCGGAAAATGACTTACT-GAAAAT-ATTTAC
11409622 TTTTCTGGAAAATGACTTACTGAAAATATTT
1 TTTTC-GGAAAATGACTTACTGAAAATATTT
11409653 TCTGGTGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 9 0.32
34 15 0.54
35 4 0.14
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (32 bp):
TTTTCGGAAAATGACTTACTGAAAATATTTAC
Found at i:11409763 original size:20 final size:20
Alignment explanation
Indices: 11409740--11409778 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
11409730 ATTTTTACAT
11409740 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
11409760 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
11409779 TTTTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:11411079 original size:32 final size:32
Alignment explanation
Indices: 11411033--11411097 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
11411023 TGTCAATCAT
11411033 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCCAACAAGCTTAAAACATAATAAA
*
11411065 TTCAATATCTAACAAGCTTAAAACATAATAAA
1 TTCAATATCCAACAAGCTTAAAACATAATAAA
11411097 T
1 T
11411098 ATCTAACATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.52, C:0.17, G:0.03, T:0.28
Consensus pattern (32 bp):
TTCAATATCCAACAAGCTTAAAACATAATAAA
Found at i:11411100 original size:27 final size:29
Alignment explanation
Indices: 11411036--11411105 Score: 90
Period size: 32 Copynumber: 2.4 Consensus size: 29
11411026 CAATCATTTC
*
11411036 AATATCCAACAAGCTTAAAACATAATAAATT
1 AATATCTAACAAGCTTAAAACATAAT-AA-T
11411067 CAATATCTAACAAGCTTAAAACATAAT-A-
1 -AATATCTAACAAGCTTAAAACATAATAAT
11411095 AATATCTAACA
1 AATATCTAACA
11411106 TTCAAGACAT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
27 11 0.30
30 1 0.03
32 25 0.68
ACGTcount: A:0.54, C:0.17, G:0.03, T:0.26
Consensus pattern (29 bp):
AATATCTAACAAGCTTAAAACATAATAAT
Found at i:11413351 original size:2 final size:2
Alignment explanation
Indices: 11413344--11413377 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
11413334 GCTCGTTGTA
* *
11413344 AT AT AT AT TT AT AT AT AT AT AT AC AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11413378 CCAAGAATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11420121 original size:19 final size:18
Alignment explanation
Indices: 11420097--11420132 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
11420087 CATGCTTTCT
11420097 ATTCACATTTTCATATTCA
1 ATTCACATTTT-ATATTCA
11420116 ATTCACATTTTATATTC
1 ATTCACATTTTATATTC
11420133 CACAATCACG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTCACATTTTATATTCA
Found at i:11421099 original size:29 final size:29
Alignment explanation
Indices: 11421051--11421108 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
11421041 TTAAGCAATT
11421051 CTAATCAATAATTCTATCAA-ATAAACCC
1 CTAATCAATAATTCTATCAACATAAACCC
* *
11421079 CTAATTCAATCATT-TATTCAACATGAACCC
1 CTAA-TCAATAATTCTA-TCAACATAAACCC
11421109 TACTAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
28 6 0.24
29 12 0.48
30 7 0.28
ACGTcount: A:0.41, C:0.26, G:0.02, T:0.31
Consensus pattern (29 bp):
CTAATCAATAATTCTATCAACATAAACCC
Found at i:11421351 original size:22 final size:21
Alignment explanation
Indices: 11421326--11421366 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
11421316 TCTTTTTCTA
11421326 TTTGTTTTATCTATTTATTTGT
1 TTTGTTTTATCT-TTTATTTGT
11421348 TTTGTTTTATCTTTTATTT
1 TTTGTTTTATCTTTTATTT
11421367 TACTTTACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.12, C:0.05, G:0.07, T:0.76
Consensus pattern (21 bp):
TTTGTTTTATCTTTTATTTGT
Found at i:11421540 original size:31 final size:30
Alignment explanation
Indices: 11421505--11421574 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
11421495 TATTTATCAT
11421505 ATAAAAATAT-TTTACTAATTAATAATAAATA
1 ATAAAAATATGTTTACTAATT-AT-ATAAATA
* *
11421536 ATAAAATATTTGTTTACTAATTATATATATA
1 ATAAAA-ATATGTTTACTAATTATATAAATA
*
11421567 ATACAAAT
1 ATAAAAAT
11421575 GTACTCATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
30 2 0.06
31 17 0.50
32 5 0.15
33 10 0.29
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.41
Consensus pattern (30 bp):
ATAAAAATATGTTTACTAATTATATAAATA
Found at i:11421675 original size:29 final size:29
Alignment explanation
Indices: 11421633--11421689 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
11421623 ATCTTTTCTT
*
11421633 AATTTATTTCATAATATAATAATATAATC
1 AATTTATTTCATAATATAATAAAATAATC
*
11421662 AATTTAATTT-ATAATATATTAAAATAAT
1 AATTT-ATTTCATAATATAATAAAATAAT
11421690 AACAATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (29 bp):
AATTTATTTCATAATATAATAAAATAATC
Found at i:11426943 original size:25 final size:25
Alignment explanation
Indices: 11426915--11426962 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
11426905 TCATATAAAT
11426915 ATTTTTTTTATAACTAATTGACTTC
1 ATTTTTTTTATAACTAATTGACTTC
*
11426940 ATTTTTTTTATTACTAATTGACT
1 ATTTTTTTTATAACTAATTGACT
11426963 CAATATAACC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.27, C:0.10, G:0.04, T:0.58
Consensus pattern (25 bp):
ATTTTTTTTATAACTAATTGACTTC
Found at i:11427654 original size:19 final size:18
Alignment explanation
Indices: 11427630--11427665 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
11427620 CATGCTTTCT
11427630 ATTCACATTTTCATATTCA
1 ATTCACATTTT-ATATTCA
11427649 ATTCACATTTTATATTC
1 ATTCACATTTTATATTC
11427666 CACAATCACG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTCACATTTTATATTCA
Found at i:11428637 original size:29 final size:29
Alignment explanation
Indices: 11428589--11428646 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
11428579 TTAAGCAATT
11428589 CTAATCAATAATTCTATCAA-ATAAACCC
1 CTAATCAATAATTCTATCAACATAAACCC
* *
11428617 CTAATTCAATCATT-TATTCAACATGAACCC
1 CTAA-TCAATAATTCTA-TCAACATAAACCC
11428647 TACTAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
28 6 0.24
29 12 0.48
30 7 0.28
ACGTcount: A:0.41, C:0.26, G:0.02, T:0.31
Consensus pattern (29 bp):
CTAATCAATAATTCTATCAACATAAACCC
Found at i:11428950 original size:18 final size:17
Alignment explanation
Indices: 11428925--11428963 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
11428915 TTACTTTATT
* *
11428925 ATATTATTTTATAATAA
1 ATATTATTTAATAACAA
11428942 ATATCTATTTAATAACAA
1 ATAT-TATTTAATAACAA
11428960 ATAT
1 ATAT
11428964 AAATATTACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATTATTTAATAACAA
Found at i:11429097 original size:33 final size:31
Alignment explanation
Indices: 11429049--11429111 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 31
11429039 TATTTATCAT
11429049 ATAAAAATCTTTTACTAATTA-ATAATAATAA
1 ATAAAAATCTTTTACTAATTATAT-ATAATAA
11429080 ATAAAATATCTTTTTACTAATTATATATAATA
1 ATAAAA-ATC-TTTTACTAATTATATATAATA
11429112 CAAATGTACT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
31 6 0.21
32 3 0.10
33 18 0.62
34 2 0.07
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (31 bp):
ATAAAAATCTTTTACTAATTATATATAATAA
Found at i:11433901 original size:24 final size:24
Alignment explanation
Indices: 11433867--11433918 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
11433857 TTTCAAGAAG
* **
11433867 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAACATAATAT
*
11433891 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATGAACATAATAT
11433915 ATTT
1 ATTT
11433919 GACTTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAACATAATAT
Found at i:11436240 original size:51 final size:52
Alignment explanation
Indices: 11436180--11436398 Score: 223
Period size: 51 Copynumber: 4.3 Consensus size: 52
11436170 CGGTGGTTTG
* * *
11436180 CACATAGTACCACCCATGTGACCATTGTC-ATCTGATACACGTAGTAGCCTA
1 CACATAGTACTACACATGTGACCATTGTCTATCCGATACACGTAGTAGCCTA
* * * * * *
11436231 CACATAGTACTACACATGTGATCA-AG-CTTTCCGGTTCACGTACTAGCCTA
1 CACATAGTACTACACATGTGACCATTGTCTATCCGATACACGTAGTAGCCTA
* * * * * *
11436281 CACATAGTACTACACACGTGACCA-AGGCCATCCGATACACATAGTAGCCTG
1 CACATAGTACTACACATGTGACCATTGTCTATCCGATACACGTAGTAGCCTA
* * *
11436332 CACATAGTACTACACATGTGACCATTATCTAT-AGATACACGTAGTAGCCTG
1 CACATAGTACTACACATGTGACCATTGTCTATCCGATACACGTAGTAGCCTA
* *
11436383 CACTTATTACTACACA
1 CACATAGTACTACACA
11436399 CGTGTTCATA
Statistics
Matches: 138, Mismatches: 27, Indels: 6
0.81 0.16 0.04
Matches are distributed among these distances:
49 1 0.01
50 42 0.30
51 92 0.67
52 3 0.02
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (52 bp):
CACATAGTACTACACATGTGACCATTGTCTATCCGATACACGTAGTAGCCTA
Found at i:11444608 original size:31 final size:31
Alignment explanation
Indices: 11444570--11444664 Score: 181
Period size: 31 Copynumber: 3.1 Consensus size: 31
11444560 TTACCAGTCC
*
11444570 AGGCTAAATCCCCTGAAATATAAACTCATAG
1 AGGCTAAATCCCCTGTAATATAAACTCATAG
11444601 AGGCTAAATCCCCTGTAATATAAACTCATAG
1 AGGCTAAATCCCCTGTAATATAAACTCATAG
11444632 AGGCTAAATCCCCTGTAATATAAACTCATAG
1 AGGCTAAATCCCCTGTAATATAAACTCATAG
11444663 AG
1 AG
11444665 TATTGTCAGG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.40, C:0.22, G:0.14, T:0.24
Consensus pattern (31 bp):
AGGCTAAATCCCCTGTAATATAAACTCATAG
Found at i:11447029 original size:50 final size:49
Alignment explanation
Indices: 11446957--11447144 Score: 223
Period size: 51 Copynumber: 3.7 Consensus size: 49
11446947 TGTCATCTGA
* * *
11446957 TACAAGTAGTAGCCTACACATAGTACTACACACGTGATCAAGCTTTCAGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAGCTTTC-GG
* *
11447007 TGCACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAGGCATTCCGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAA-GC-TTTCGG
* * * * *
11447058 TACACATAGGAGCCTGCACATAGTACTACACATGTGACCATTATCTATCGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA--AGCTTTCGG
* *
11447109 TACACGTAGTAGGCTGCACTTAGTACTACACACGTG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTG
11447145 TTCATAAGTA
Statistics
Matches: 117, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
50 37 0.32
51 75 0.64
52 4 0.03
53 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.23
Consensus pattern (49 bp):
TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAGCTTTCGG
Found at i:11449816 original size:46 final size:46
Alignment explanation
Indices: 11449741--11449828 Score: 117
Period size: 46 Copynumber: 1.9 Consensus size: 46
11449731 ATATGTGCAG
*
11449741 TGTGGGCCTTAGCCAATTACAGTATCAGAATCAGAAATAGAATACA
1 TGTGGGCCTAAGCCAATTACAGTATCAGAATCAGAAATAGAATACA
* *
11449787 TGTGGGCCTAAGCCCAA-TATAGTGA-CAGAATCAGTAATAGAA
1 TGTGGGCCTAAG-CCAATTACAGT-ATCAGAATCAGAAATAGAA
11449829 ATGCAACAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
46 32 0.86
47 5 0.14
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.23
Consensus pattern (46 bp):
TGTGGGCCTAAGCCAATTACAGTATCAGAATCAGAAATAGAATACA
Found at i:11450105 original size:32 final size:32
Alignment explanation
Indices: 11450056--11450185 Score: 156
Period size: 32 Copynumber: 4.1 Consensus size: 32
11450046 GCCATAAATA
* * *
11450056 CAGTAATATGATTGGCACAAAACCATCAGTAG
1 CAGTAATATGATCGACACAAAGCCATCAGTAG
* * * *
11450088 CAGTGATATGATCGGCACATAGCCATCAGTAA
1 CAGTAATATGATCGACACAAAGCCATCAGTAG
*
11450120 CGGTAATATGATCGACACAAAGCCATCAGTA-
1 CAGTAATATGATCGACACAAAGCCATCAGTAG
11450151 -ATGATAATATGATCGACACAAAGCCATCAGTAG
1 CA-G-TAATATGATCGACACAAAGCCATCAGTAG
11450184 CA
1 CA
11450186 TCGTAGCAAA
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
31 1 0.01
32 82 0.98
34 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (32 bp):
CAGTAATATGATCGACACAAAGCCATCAGTAG
Found at i:11450379 original size:11 final size:11
Alignment explanation
Indices: 11450363--11450405 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
11450353 AATCAGTCAT
11450363 ACAAATCACAG
1 ACAAATCACAG
*
11450374 ACAAATCAGTCAT
1 ACAAATCA--CAG
*
11450387 ACCAATCACAG
1 ACAAATCACAG
11450398 ACAAATCA
1 ACAAATCA
11450406 GTAAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 17 0.65
13 9 0.35
ACGTcount: A:0.51, C:0.28, G:0.07, T:0.14
Consensus pattern (11 bp):
ACAAATCACAG
Found at i:11450380 original size:24 final size:24
Alignment explanation
Indices: 11450353--11450431 Score: 101
Period size: 24 Copynumber: 3.4 Consensus size: 24
11450343 CCATGCTCAG
11450353 AATCAGTCATACAAATCACAGACA
1 AATCAGTCATACAAATCACAGACA
*
11450377 AATCAGTCATACCAATCACAGACA
1 AATCAGTCATACAAATCACAGACA
* *
11450401 AATCAGT-A-A-ATATCACCGACA
1 AATCAGTCATACAAATCACAGACA
*
11450422 AATCAATCAT
1 AATCAGTCAT
11450432 TTACACTCGA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
21 15 0.31
22 2 0.04
23 1 0.02
24 30 0.62
ACGTcount: A:0.48, C:0.25, G:0.08, T:0.19
Consensus pattern (24 bp):
AATCAGTCATACAAATCACAGACA
Found at i:11450528 original size:27 final size:27
Alignment explanation
Indices: 11450495--11450862 Score: 415
Period size: 27 Copynumber: 13.7 Consensus size: 27
11450485 TTACCTGAAA
*
11450495 AGGGTATTTCAGTCATTTTACCCAAT-G
1 AGGGTATTTCGGTCATTTTACCC-ATCG
* * *
11450522 AGCGTATTACGGTCATTTTA-CCTTAC-
1 AGGGTATTTCGGTCATTTTACCCAT-CG
* * *
11450548 AGGGGCATTACGATCATTTTACCC-TACG
1 A-GGGTATTTCGGTCATTTTACCCAT-CG
*
11450576 AGGGTATTTCGGTTATTTTACCCATCG
1 AGGGTATTTCGGTCATTTTACCCATCG
* **
11450603 AGGGTATTTCGATCATTTTATTCATCG
1 AGGGTATTTCGGTCATTTTACCCATCG
** *
11450630 AGGGTATTTCAATAATTTTACCCATCG
1 AGGGTATTTCGGTCATTTTACCCATCG
*
11450657 AGGGTATTTCGATCATTTTACCCATCG
1 AGGGTATTTCGGTCATTTTACCCATCG
11450684 AGGGTATTTCGGTCATTTTACCCATCG
1 AGGGTATTTCGGTCATTTTACCCATCG
**
11450711 AGGGTATTTCAATCATTTTACCCATC-
1 AGGGTATTTCGGTCATTTTACCCATCG
*
11450737 AGGGTATTTCGATCATTTTACCCATC-
1 AGGGTATTTCGGTCATTTTACCCATCG
* *
11450763 AGGGGCATTTTGGTCATTTTACCCATCG
1 A-GGGTATTTCGGTCATTTTACCCATCG
* *
11450791 AGGGTATTTCAGTAATTTTACCCATCG
1 AGGGTATTTCGGTCATTTTACCCATCG
*
11450818 AGAGTATTTCGGTCATTTTACCCATCG
1 AGGGTATTTCGGTCATTTTACCCATCG
* * *
11450845 AGAGTTTTTCGATCATTT
1 AGGGTATTTCGGTCATTT
11450863 AACAAATATT
Statistics
Matches: 296, Mismatches: 37, Indels: 16
0.85 0.11 0.05
Matches are distributed among these distances:
25 1 0.00
26 29 0.10
27 261 0.88
28 5 0.02
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.38
Consensus pattern (27 bp):
AGGGTATTTCGGTCATTTTACCCATCG
Found at i:11453255 original size:264 final size:263
Alignment explanation
Indices: 11452776--11453294 Score: 876
Period size: 264 Copynumber: 2.0 Consensus size: 263
11452766 AATTTTTTCA
* *
11452776 AAAGCCCAGGTTTGAACCCAGGACTTTTCCAGCTCCTATCAGGACCCTTAACCACTAAAGCAGAC
1 AAAGCCCAGGTTTGAACCCAGGACTTTTCCAACTCCTATCAGGACCCTTAACCACTAAAGCAAAC
* *
11452841 ATACTTTTGTACATAGTTTCCTAACCGTTCCCTTGCTCAAGGCTCAATACTTCTAGCCCCAAATT
66 ATACTTTTGTACACAGTTTCCTAACCGTTCCCTTGCTCAAGGCCCAATACTTCTAGCCCCAAATT
11452906 TCAGGGCGTTACATTATTTAAATGCCAAAGTTTTAAATTATTTTGTAATGCCCGTAACTCTAATC
131 TCAGGGCGTTACATTATTTAAATGCCAAAGTTTTAAATTATTTTGTAATGCCCGTAACTCTAATC
* *
11452971 TGGTGACGGAGACAGGTTTAGGGTGTTACAATACGGATAGAGAAGTATCATACTTACTTAGATTT
196 TGGCGACCGAGACAGGTTTAGGGTGTTACAATACGGATAGAGAAGTATCATACTTACTTAGATTT
11453036 GCT
261 GCT
* * * *
11453039 AAAGCCCAGGTTTGAACCCAGGACTTTTCCAACTCCTCTCAGGGCCCTTTTACCGCTAAAGCAAA
1 AAAGCCCAGGTTTGAACCCAGGACTTTTCCAACTCCTATCAGGACCC-TTAACCACTAAAGCAAA
* *
11453104 CATACTTTTGTACACAGTTTCCTAACTGTTCCCTTGCTCAAGGCCCAATACTTCTAGGCCCAAAT
65 CATACTTTTGTACACAGTTTCCTAACCGTTCCCTTGCTCAAGGCCCAATACTTCTAGCCCCAAAT
* * *
11453169 TTCGGGGCGTTACATTATTTGAATGCCAAAGTTTTGAATTATTTTGTAATGCCCGTAACTCTAAT
130 TTCAGGGCGTTACATTATTTAAATGCCAAAGTTTTAAATTATTTTGTAATGCCCGTAACTCTAAT
* *
11453234 CTGGCGACCGAGACGGGTTTAGGGTGTTACAATACGGATAGAGAAGTATCATACTTGCTTA
195 CTGGCGACCGAGACAGGTTTAGGGTGTTACAATACGGATAGAGAAGTATCATACTTACTTA
11453295 AGTGACCTCT
Statistics
Matches: 238, Mismatches: 17, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
263 44 0.18
264 194 0.82
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (263 bp):
AAAGCCCAGGTTTGAACCCAGGACTTTTCCAACTCCTATCAGGACCCTTAACCACTAAAGCAAAC
ATACTTTTGTACACAGTTTCCTAACCGTTCCCTTGCTCAAGGCCCAATACTTCTAGCCCCAAATT
TCAGGGCGTTACATTATTTAAATGCCAAAGTTTTAAATTATTTTGTAATGCCCGTAACTCTAATC
TGGCGACCGAGACAGGTTTAGGGTGTTACAATACGGATAGAGAAGTATCATACTTACTTAGATTT
GCT
Done.