Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D10
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: 65706892
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869813 characters in sequence are not A, C, G, or T
File 54 of 218
Found at i:16484361 original size:3 final size:3
Alignment explanation
Indices: 16484353--16484379 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
16484343 GTGTATTGCA
16484353 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
16484380 TGTAGTAGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:16489745 original size:13 final size:13
Alignment explanation
Indices: 16489727--16489805 Score: 52
Period size: 13 Copynumber: 6.0 Consensus size: 13
16489717 CATATATATC
16489727 CATATAAACATTT
1 CATATAAACATTT
* * *
16489740 CATATACATAATT
1 CATATAAACATTT
*
16489753 CACAT-AACTATTT
1 CATATAAAC-ATTT
* *
16489766 CCATATAACCAATT
1 -CATATAAACATTT
*
16489780 CATATAATCATTT
1 CATATAAACATTT
* *
16489793 TATATAATCATTT
1 CATATAAACATTT
16489806 TCCATATAAT
Statistics
Matches: 50, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
12 1 0.02
13 40 0.80
14 7 0.14
15 2 0.04
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.41
Consensus pattern (13 bp):
CATATAAACATTT
Found at i:16489792 original size:27 final size:25
Alignment explanation
Indices: 16489727--16489798 Score: 65
Period size: 27 Copynumber: 2.7 Consensus size: 25
16489717 CATATATATC
*
16489727 CATATAAACATTTCATATACATAATT
1 CATAT-AACATTTCATATACACAATT
*
16489753 CACATAACTATTTCCATATA-ACCAATT
1 CATATAAC-ATTT-CATATACA-CAATT
*
16489780 CATATAATCATTTTATATA
1 CATATAA-CATTTCATATA
16489799 ATCATTTTCC
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
25 3 0.08
26 14 0.37
27 20 0.53
28 1 0.03
ACGTcount: A:0.43, C:0.18, G:0.00, T:0.39
Consensus pattern (25 bp):
CATATAACATTTCATATACACAATT
Found at i:16489806 original size:13 final size:13
Alignment explanation
Indices: 16489781--16489847 Score: 73
Period size: 13 Copynumber: 5.0 Consensus size: 13
16489771 TAACCAATTC
16489781 ATATAATCATTTT
1 ATATAATCATTTT
16489794 ATATAATCATTTT
1 ATATAATCATTTT
* *
16489807 CCATATAATTGA-TTC
1 --ATATAA-TCATTTT
16489822 ATATAATCATTTT
1 ATATAATCATTTT
*
16489835 ATATATTCATTTT
1 ATATAATCATTTT
16489848 CCACTCGATT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
12 2 0.04
13 33 0.73
15 8 0.18
16 2 0.04
ACGTcount: A:0.36, C:0.10, G:0.01, T:0.52
Consensus pattern (13 bp):
ATATAATCATTTT
Found at i:16489813 original size:28 final size:27
Alignment explanation
Indices: 16489778--16489847 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 27
16489768 ATATAACCAA
16489778 TTCATATAATCATTTTATATAATCATT
1 TTCATATAATCATTTTATATAATCATT
* *
16489805 TTCCATATAATTGA-TTCATATAATCATT
1 TT-CATATAA-TCATTTTATATAATCATT
*
16489833 TT-ATATATTCATTTT
1 TTCATATAATCATTTT
16489848 CCACTCGATT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
25 2 0.06
26 7 0.20
27 2 0.06
28 22 0.63
29 2 0.06
ACGTcount: A:0.34, C:0.11, G:0.01, T:0.53
Consensus pattern (27 bp):
TTCATATAATCATTTTATATAATCATT
Found at i:16489813 original size:41 final size:41
Alignment explanation
Indices: 16489763--16489850 Score: 140
Period size: 41 Copynumber: 2.1 Consensus size: 41
16489753 CACATAACTA
16489763 TTTCCATATAACCAATTCATATAATCATTTTATATAATCAT
1 TTTCCATATAACCAATTCATATAATCATTTTATATAATCAT
*** *
16489804 TTTCCATATAATTGATTCATATAATCATTTTATATATTCAT
1 TTTCCATATAACCAATTCATATAATCATTTTATATAATCAT
16489845 TTTCCA
1 TTTCCA
16489851 CTCGATTAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.35, C:0.16, G:0.01, T:0.48
Consensus pattern (41 bp):
TTTCCATATAACCAATTCATATAATCATTTTATATAATCAT
Found at i:16497277 original size:39 final size:38
Alignment explanation
Indices: 16497148--16497284 Score: 114
Period size: 40 Copynumber: 3.5 Consensus size: 38
16497138 GCGTTTGGAT
* * *
16497148 AAAAAACGCAGCTAAAAATCAAGCATTAGCGGCGCTTTTA
1 AAAAAACGCCGCTAAAAAT-TAGCATTAGCGGC-TTTTTA
* * *
16497188 AAAAAACGCCACTAAAGATTGAGTATTAGCGACGCTTTTT-
1 AAAAAACGCCGCTAAAAATT-AGCATTAGCG--GCTTTTTA
** *
16497228 GGAAAACGCCGCTAAAAATTAGCATTAGCGGCATTTTTC
1 AAAAAACGCCGCTAAAAATTAGCATTAGCGGC-TTTTTA
* *
16497267 AAAAAGCGCCGCAAAAAA
1 AAAAAACGCCGCTAAAAA
16497285 CCTAAGCCCA
Statistics
Matches: 77, Mismatches: 15, Indels: 11
0.75 0.15 0.11
Matches are distributed among these distances:
37 2 0.03
38 5 0.06
39 23 0.30
40 41 0.53
41 4 0.05
42 2 0.03
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (38 bp):
AAAAAACGCCGCTAAAAATTAGCATTAGCGGCTTTTTA
Found at i:16499491 original size:23 final size:23
Alignment explanation
Indices: 16499459--16499506 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
16499449 GGTTGGTTTG
16499459 ATTATATGAGTTAAATTATGTGA
1 ATTATATGAGTTAAATTATGTGA
*
16499482 ATTATGTGAGTTAAATTATGTGA
1 ATTATATGAGTTAAATTATGTGA
16499505 AT
1 AT
16499507 GGTGTTTGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (23 bp):
ATTATATGAGTTAAATTATGTGA
Found at i:16501560 original size:43 final size:43
Alignment explanation
Indices: 16501497--16501670 Score: 240
Period size: 43 Copynumber: 4.0 Consensus size: 43
16501487 AAAGTCATGC
**
16501497 TTGTGAGAAAAGCGTTGCTAAAGGTCATGGTCTTTAGCGGCGT
1 TTGTGAGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGT
* *
16501540 TTGTGAGAAAAGCGCCGCTAAAGGTCATGGTTTTTAACGGCGT
1 TTGTGAGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGT
* * * *
16501583 TTGTGGGAAAAGTGCTGCTAAAGGTCTTGGTCTTTAGCGGCGT
1 TTGTGAGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGT
* * * *
16501626 TTGTGGGAAAAGCGCCACTAAAGGTCTTGTTCTTTAGCGGCGT
1 TTGTGAGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGT
16501669 TT
1 TT
16501671 ATTTCTAAAA
Statistics
Matches: 117, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 117 1.00
ACGTcount: A:0.22, C:0.16, G:0.32, T:0.31
Consensus pattern (43 bp):
TTGTGAGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGT
Found at i:16503651 original size:27 final size:25
Alignment explanation
Indices: 16503613--16503681 Score: 75
Period size: 27 Copynumber: 2.7 Consensus size: 25
16503603 CGTTCTGACC
*
16503613 CACAACTCGTGTGAGCAGGCCCATTTT
1 CACAGCTCGTGTGAGCAGGCCCA--TT
** *
16503640 CACAGCTCGTGTGAGCATTCTCATT
1 CACAGCTCGTGTGAGCAGGCCCATT
*
16503665 CACAGCTTGTGTGAGCA
1 CACAGCTCGTGTGAGCA
16503682 TACATGTGTA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 18 0.49
27 19 0.51
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.28
Consensus pattern (25 bp):
CACAGCTCGTGTGAGCAGGCCCATT
Found at i:16505485 original size:13 final size:13
Alignment explanation
Indices: 16505467--16505498 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
16505457 CGCACACGGG
16505467 CGTGTGGCTTGGC
1 CGTGTGGCTTGGC
16505480 CGTGTGGCTTGGC
1 CGTGTGGCTTGGC
*
16505493 TGTGTG
1 CGTGTG
16505499 ACCCCTACAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.00, C:0.19, G:0.47, T:0.34
Consensus pattern (13 bp):
CGTGTGGCTTGGC
Found at i:16511840 original size:30 final size:30
Alignment explanation
Indices: 16511806--16511881 Score: 125
Period size: 30 Copynumber: 2.5 Consensus size: 30
16511796 TGGTTAATAC
*
16511806 ATCCCTTTTCATAATTCGATAACTAAAGTT
1 ATCCCTTTTCATAATTCGATAACTAAAGCT
* *
16511836 ATCCCTTTTCATAGTTCGATAGCTAAAGCT
1 ATCCCTTTTCATAATTCGATAACTAAAGCT
16511866 ATCCCTTTTCATAATT
1 ATCCCTTTTCATAATT
16511882 TGATGGTCGT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.41
Consensus pattern (30 bp):
ATCCCTTTTCATAATTCGATAACTAAAGCT
Found at i:16511879 original size:60 final size:59
Alignment explanation
Indices: 16511805--16512147 Score: 236
Period size: 60 Copynumber: 5.7 Consensus size: 59
16511795 CTGGTTAATA
* * ** **
16511805 CATCCCTTTTCATAATTCGATAACTAAAGTTATCCCTTTTCATAGTTCGATAGCTAAAGC
1 CATCCCTTTTCATAATTTGATAGCCGAAGCCATCCCTTTTCATAGTTCGATAGCTAAA-C
* * * * * * *
16511865 TATCCCTTTTCATAATTTGATGGTCGTCA-CCATCCCTTTTCATTGTTCGATGGTCGT-CAC
1 CATCCCTTTTCATAATTTGATAGCCG-AAGCCATCCCTTTTCATAGTTCGATAG-C-TAAAC
* *
16511925 CATCCCTTTTCATAATTTGATAGCCGAAGCTATCCCTTTTCATAGATT-GATAGCCAAAAC
1 CATCCCTTTTCATAATTTGATAGCCGAAGCCATCCCTTTTCATAG-TTCGATAG-CTAAAC
* * *
16511985 CATCCCTTTTCATAGA-TTGATAGCCGAAGTCATCCCTTTTCATAAGTT-GATGGTCGT-CAC
1 CATCCCTTTTCATA-ATTTGATAGCCGAAGCCATCCCTTTTCAT-AGTTCGATAG-C-TAAAC
* * * * * * * *
16512045 CATCCCTTTTCATAATTTGATGGTCGTCA-CCATCCTTTTTCATAATTTGATGGTCGT-CAC
1 CATCCCTTTTCATAATTTGATAGCCG-AAGCCATCCCTTTTCATAGTTCGATAG-C-TAAAC
* * *
16512105 CATCCATTTTCATAATTTGATAGTC-AAACCTATCCCTTTTCAT
1 CATCCCTTTTCATAATTTGATAGCCGAAGCC-ATCCCTTTTCAT
16512148 TCGTCGATGA
Statistics
Matches: 230, Mismatches: 39, Indels: 28
0.77 0.13 0.09
Matches are distributed among these distances:
58 1 0.00
59 7 0.03
60 212 0.92
61 9 0.04
62 1 0.00
ACGTcount: A:0.24, C:0.25, G:0.12, T:0.38
Consensus pattern (59 bp):
CATCCCTTTTCATAATTTGATAGCCGAAGCCATCCCTTTTCATAGTTCGATAGCTAAAC
Found at i:16511900 original size:30 final size:30
Alignment explanation
Indices: 16511866--16512147 Score: 286
Period size: 30 Copynumber: 9.4 Consensus size: 30
16511856 AGCTAAAGCT
16511866 ATCCCTTTTCATAATTTGATGGTCGTCACC
1 ATCCCTTTTCATAATTTGATGGTCGTCACC
** *
16511896 ATCCCTTTTCATTGTTCGATGGTCGTCACC
1 ATCCCTTTTCATAATTTGATGGTCGTCACC
* * * *
16511926 ATCCCTTTTCATAATTTGATAGCCG-AAGCT
1 ATCCCTTTTCATAATTTGATGGTCGTCA-CC
* * ***
16511956 ATCCCTTTTCATAGA-TTGATAGCCAAAACC
1 ATCCCTTTTCATA-ATTTGATGGTCGTCACC
* * * *
16511986 ATCCCTTTTCATAGA-TTGATAGCCG-AAGTC
1 ATCCCTTTTCATA-ATTTGATGGTCGTCA-CC
*
16512016 ATCCCTTTTCATAAGTTGATGGTCGTCACC
1 ATCCCTTTTCATAATTTGATGGTCGTCACC
16512046 ATCCCTTTTCATAATTTGATGGTCGTCACC
1 ATCCCTTTTCATAATTTGATGGTCGTCACC
*
16512076 ATCCTTTTTCATAATTTGATGGTCGTCACC
1 ATCCCTTTTCATAATTTGATGGTCGTCACC
* * **
16512106 ATCCATTTTCATAATTTGATAGTC-AAACC
1 ATCCCTTTTCATAATTTGATGGTCGTCACC
16512135 TATCCCTTTTCAT
1 -ATCCCTTTTCAT
16512148 TCGTCGATGA
Statistics
Matches: 220, Mismatches: 25, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
29 7 0.03
30 209 0.95
31 4 0.02
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.38
Consensus pattern (30 bp):
ATCCCTTTTCATAATTTGATGGTCGTCACC
Found at i:16511958 original size:90 final size:89
Alignment explanation
Indices: 16511836--16512147 Score: 324
Period size: 90 Copynumber: 3.5 Consensus size: 89
16511826 AACTAAAGTT
* * *
16511836 ATCCCTTTTCATAGTTCGATAGCTAAAGCTATCCCTTTTCATAATTTGATGGTCGTCACCATCCC
1 ATCCCTTTTCATAATTTGATAGCCAAAGCTATCCCTTTTCATAATTTGATGGTCGTCACCATCCC
*
16511901 TTTTCATTGTTCGATGGTCGTCACC
66 TTTTCATAGTT-GATGGTCGTCACC
* * * ***
16511926 ATCCCTTTTCATAATTTGATAGCCGAAGCTATCCCTTTTCATAGA-TTGATAGCCAAAACCATCC
1 ATCCCTTTTCATAATTTGATAGCCAAAGCTATCCCTTTTCATA-ATTTGATGGTCGTCACCATCC
* * * *
16511990 CTTTTCATAGATTGATAGCCG-AAGTC
65 CTTTTCATAG-TTGATGGTCGTCA-CC
* * *** *
16512016 ATCCCTTTTCATAAGTTGATGGTCGTCA-CCATCCCTTTTCATAATTTGATGGTCGTCACCATCC
1 ATCCCTTTTCATAATTTGATAG-CCAAAGCTATCCCTTTTCATAATTTGATGGTCGTCACCATCC
* *
16512080 TTTTTCATAATTTGATGGTCGTCACC
65 CTTTTCAT-AGTTGATGGTCGTCACC
* * *
16512106 ATCCATTTTCATAATTTGATAGTCAAACCTATCCCTTTTCAT
1 ATCCCTTTTCATAATTTGATAGCCAAAGCTATCCCTTTTCAT
16512148 TCGTCGATGA
Statistics
Matches: 175, Mismatches: 39, Indels: 16
0.76 0.17 0.07
Matches are distributed among these distances:
89 3 0.02
90 165 0.94
91 7 0.04
ACGTcount: A:0.24, C:0.25, G:0.13, T:0.38
Consensus pattern (89 bp):
ATCCCTTTTCATAATTTGATAGCCAAAGCTATCCCTTTTCATAATTTGATGGTCGTCACCATCCC
TTTTCATAGTTGATGGTCGTCACC
Found at i:16514784 original size:21 final size:21
Alignment explanation
Indices: 16514758--16514799 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
16514748 ACTTTTTCTT
16514758 TAATTAACTA-ACCAAAAATTA
1 TAATT-ACTAGACCAAAAATTA
16514779 TAATTACTAGACCAAAAATTA
1 TAATTACTAGACCAAAAATTA
16514800 ATTTGAAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.55, C:0.14, G:0.02, T:0.29
Consensus pattern (21 bp):
TAATTACTAGACCAAAAATTA
Found at i:16518799 original size:48 final size:48
Alignment explanation
Indices: 16518622--16518858 Score: 269
Period size: 48 Copynumber: 4.8 Consensus size: 48
16518612 TTATTATCAT
* * * *
16518622 TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAACTT
1 TCGATACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CCATCTA
* * *
16518671 TCCGGTTCACGTAGTAGCCTGCACATAGTACTACACACGTGACCAAAGCCT-
1 T-CGATACACGTAGTAGCCTGCACATAGTACTACACACGTGACC--A-TCTA
* * *
16518722 TCGGGTACACATAGTAGCCTGCACATAGTACTACACATGTGACCATCTA
1 TC-GATACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCTA
* * * *
16518771 TCGATACACGTTGTAACCTGCACTTAGTACTACACATGTGACCATCTA
1 TCGATACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCTA
* *
16518819 TTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTG
1 TCGATACACGTAGTAGCCTGCACATAGTACTACACACGTG
16518859 TTTATAGGCA
Statistics
Matches: 164, Mismatches: 18, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
48 79 0.48
49 5 0.03
50 38 0.23
51 40 0.24
52 2 0.01
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (48 bp):
TCGATACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCTA
Found at i:16524220 original size:41 final size:41
Alignment explanation
Indices: 16524129--16524222 Score: 125
Period size: 41 Copynumber: 2.3 Consensus size: 41
16524119 ACACAGACTT
* * * *
16524129 TAAGCCTGCTAGACTTATAGTCTGAATTGTTTCACCAGCAT
1 TAAGCCTGCTAGACGTAAAGTCTGAATGGTTTCACCAGCAA
* *
16524170 TTAGCCTGCTAGACGTAAAGTCTGAATGGTTTCACCGGCAA
1 TAAGCCTGCTAGACGTAAAGTCTGAATGGTTTCACCAGCAA
*
16524211 TAAGTCTGCTAG
1 TAAGCCTGCTAG
16524223 GCACTGAGCC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (41 bp):
TAAGCCTGCTAGACGTAAAGTCTGAATGGTTTCACCAGCAA
Found at i:16524848 original size:23 final size:23
Alignment explanation
Indices: 16524801--16524870 Score: 56
Period size: 23 Copynumber: 3.0 Consensus size: 23
16524791 TTTATACATT
*
16524801 ATACACATACATAT-TCGAAAT-TA
1 ATACACATATATATAT--AAATATA
16524824 ATACACATATATATATAAATATA
1 ATACACATATATATATAAATATA
* * *
16524847 AT-TACATATTTATACTCAATATA
1 ATACACATATATATA-TAAATATA
16524870 A
1 A
16524871 GTATTTATTC
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
22 14 0.35
23 25 0.62
24 1 0.03
ACGTcount: A:0.50, C:0.13, G:0.01, T:0.36
Consensus pattern (23 bp):
ATACACATATATATATAAATATA
Found at i:16537791 original size:13 final size:13
Alignment explanation
Indices: 16537773--16537799 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
16537763 TTTCTTGGAT
16537773 TATTATGTAATTG
1 TATTATGTAATTG
16537786 TATTATGTAATTG
1 TATTATGTAATTG
16537799 T
1 T
16537800 CACAACATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (13 bp):
TATTATGTAATTG
Found at i:16547371 original size:14 final size:14
Alignment explanation
Indices: 16547352--16547385 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
16547342 AATTTATTAG
16547352 TAAATTATTAAAAA
1 TAAATTATTAAAAA
*
16547366 TAAATTATTAAATA
1 TAAATTATTAAAAA
16547380 TAAATT
1 TAAATT
16547386 TATATTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAATTATTAAAAA
Found at i:16557476 original size:16 final size:16
Alignment explanation
Indices: 16557452--16557483 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
16557442 TCATATAATT
*
16557452 TACATGTACCAATTCA
1 TACAAGTACCAATTCA
16557468 TACAAGTACCAATTCA
1 TACAAGTACCAATTCA
16557484 CAACAATTCA
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:0.41, C:0.25, G:0.06, T:0.28
Consensus pattern (16 bp):
TACAAGTACCAATTCA
Found at i:16558164 original size:60 final size:60
Alignment explanation
Indices: 16558100--16558320 Score: 234
Period size: 60 Copynumber: 3.7 Consensus size: 60
16558090 AATCGAAGTT
* * *
16558100 ATCCCTTTTCATAATTCGACAGCCAAAGCTATCCCTTTTCATGATTTGGTGGTCGTCACC
1 ATCCCTTTTCATAATTCGATAGCCAAAGCCATCCCTTTTCATGATTTGATGGTCGTCACC
** * *** * *
16558160 ATCCCTTTTCATTGTTCGATGGTCGTCA-CCATCCCTTTTCATGATTTGATAGTCG-AAGCC
1 ATCCCTTTTCATAATTCGATAG-CCAAAGCCATCCCTTTTCATGATTTGATGGTCGTCA-CC
* * *
16558220 ATCCCTTTTCATAGA-TCAATAGCCAAAGCCATCCCTTTTCATAATTTGATGGTCGTCACA
1 ATCCCTTTTCATA-ATTCGATAGCCAAAGCCATCCCTTTTCATGATTTGATGGTCGTCACC
* * *
16558280 ATCCCTTTTCATAATT-GATAGTCGAAGCTATCCCTTTTCAT
1 ATCCCTTTTCATAATTCGATAGCCAAAGCCATCCCTTTTCAT
16558321 TCGTCGATGA
Statistics
Matches: 129, Mismatches: 26, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
59 25 0.19
60 101 0.78
61 3 0.02
ACGTcount: A:0.23, C:0.27, G:0.14, T:0.37
Consensus pattern (60 bp):
ATCCCTTTTCATAATTCGATAGCCAAAGCCATCCCTTTTCATGATTTGATGGTCGTCACC
Found at i:16558225 original size:90 final size:89
Alignment explanation
Indices: 16558158--16558320 Score: 263
Period size: 90 Copynumber: 1.8 Consensus size: 89
16558148 GTGGTCGTCA
** * *
16558158 CCATCCCTTTTCATTGTTCGATGGTCGTCACCATCCCTTTTCATGATTTGATAGTCGAAGCCATC
1 CCATCCCTTTTCATAATTCGATGGTCGTCACAATCCCTTTTCAT-ATTTGATAGTCGAAGCTATC
16558223 CCTTTTCATAGATCAATAGCCAAAG
65 CCTTTTCATAGATCAATAGCCAAAG
* *
16558248 CCATCCCTTTTCATAATTTGATGGTCGTCACAATCCCTTTTCATAATTGATAGTCGAAGCTATCC
1 CCATCCCTTTTCATAATTCGATGGTCGTCACAATCCCTTTTCATATTTGATAGTCGAAGCTATCC
16558313 CTTTTCAT
66 CTTTTCAT
16558321 TCGTCGATGA
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
89 27 0.40
90 40 0.60
ACGTcount: A:0.23, C:0.27, G:0.13, T:0.37
Consensus pattern (89 bp):
CCATCCCTTTTCATAATTCGATGGTCGTCACAATCCCTTTTCATATTTGATAGTCGAAGCTATCC
CTTTTCATAGATCAATAGCCAAAG
Found at i:16558292 original size:30 final size:31
Alignment explanation
Indices: 16558069--16558320 Score: 173
Period size: 30 Copynumber: 8.4 Consensus size: 31
16558059 ATGGTTGACA
* * * *
16558069 CATCCCTTTTCGTAATTAGATAATCG-AAGT
1 CATCCCTTTTCATAATTTGATAGTCGTAAGC
* * * **
16558099 TATCCCTTTTCATAATTCGACAG-CCAAAGC
1 CATCCCTTTTCATAATTTGATAGTCGTAAGC
* * * * *
16558129 TATCCCTTTTCATGATTTGGTGGTCGTCA-C
1 CATCCCTTTTCATAATTTGATAGTCGTAAGC
** * * *
16558159 CATCCCTTTTCATTGTTCGATGGTCGTCA-C
1 CATCCCTTTTCATAATTTGATAGTCGTAAGC
*
16558189 CATCCCTTTTCATGATTTGATAGTCG-AAGC
1 CATCCCTTTTCATAATTTGATAGTCGTAAGC
** **
16558219 CATCCCTTTTCATAGA-TCAATAG-CCAAAGC
1 CATCCCTTTTCATA-ATTTGATAGTCGTAAGC
* *
16558249 CATCCCTTTTCATAATTTGATGGTCGTCA-C
1 CATCCCTTTTCATAATTTGATAGTCGTAAGC
*
16558279 AATCCCTTTTCATAA-TTGATAGTCG-AAGC
1 CATCCCTTTTCATAATTTGATAGTCGTAAGC
*
16558308 TATCCCTTTTCAT
1 CATCCCTTTTCAT
16558321 TCGTCGATGA
Statistics
Matches: 175, Mismatches: 39, Indels: 17
0.76 0.17 0.07
Matches are distributed among these distances:
28 1 0.01
29 26 0.15
30 143 0.82
31 5 0.03
ACGTcount: A:0.24, C:0.26, G:0.13, T:0.37
Consensus pattern (31 bp):
CATCCCTTTTCATAATTTGATAGTCGTAAGC
Found at i:16558624 original size:23 final size:23
Alignment explanation
Indices: 16558590--16558640 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
16558580 ATTTTAGTAA
*
16558590 TGTAATATCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
16558613 TGTAATACCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
*
16558636 AGTAA
1 TGTAA
16558641 GAAAGTAGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (23 bp):
TGTAATACCCCGAAAATTACTAC
Found at i:16558833 original size:30 final size:31
Alignment explanation
Indices: 16558799--16558856 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
16558789 GTAAATTCTC
* **
16558799 AAAATTTGAGGGATTAA-AGTGTAAATACAA
1 AAAATTTGAAGGACCAATAGTGTAAATACAA
16558829 AAAATTTGAAGGACCAATAGTGTAAATA
1 AAAATTTGAAGGACCAATAGTGTAAATA
16558857 TTTTAAGGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 14 0.58
31 10 0.42
ACGTcount: A:0.50, C:0.05, G:0.19, T:0.26
Consensus pattern (31 bp):
AAAATTTGAAGGACCAATAGTGTAAATACAA
Found at i:16581068 original size:33 final size:33
Alignment explanation
Indices: 16580998--16581092 Score: 113
Period size: 33 Copynumber: 2.9 Consensus size: 33
16580988 ACTTGAGCCG
* * *
16580998 GGAGGAGTGGAGTACTACGGTGGATAC-GAGTCG
1 GGAGGAGTGGAGTACTGCGGTGGATACTG-GCCA
*
16581031 GGAGGAGTGGAGTAATGCGGTGGATACTGGCCA
1 GGAGGAGTGGAGTACTGCGGTGGATACTGGCCA
**
16581064 GGAGGAGTGTTGTACTGCGGTGG-TACTGG
1 GGAGGAGTGGAGTACTGCGGTGGATACTGG
16581093 AATGAAGATA
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
32 6 0.11
33 47 0.87
34 1 0.02
ACGTcount: A:0.21, C:0.12, G:0.46, T:0.21
Consensus pattern (33 bp):
GGAGGAGTGGAGTACTGCGGTGGATACTGGCCA
Found at i:16582687 original size:16 final size:16
Alignment explanation
Indices: 16582618--16582740 Score: 60
Period size: 16 Copynumber: 7.4 Consensus size: 16
16582608 ATAACATGCC
16582618 AAATAAATTACATAAAA
1 AAATAAATTACAT-AAA
16582635 AAATAAATCTA-ATAAA
1 AAATAAAT-TACATAAA
* * *
16582651 CCTAAA-ACA-TACATGAC
1 ---AAATAAATTACATAAA
16582668 AAATAAATTACATAAA
1 AAATAAATTACATAAA
16582684 AAATAAATCTA-ATAAA
1 AAATAAAT-TACATAAA
* * *
16582700 CCTAAA-ACA-CACATGACA
1 ---AAATAAATTACAT-AAA
16582718 AAATAAATTACATAAA
1 AAATAAATTACATAAA
16582734 AAATAAA
1 AAATAAA
16582741 ACATTCTTTC
Statistics
Matches: 79, Mismatches: 12, Indels: 31
0.65 0.10 0.25
Matches are distributed among these distances:
14 3 0.04
15 5 0.06
16 36 0.46
17 21 0.27
18 8 0.10
19 6 0.08
ACGTcount: A:0.64, C:0.13, G:0.02, T:0.21
Consensus pattern (16 bp):
AAATAAATTACATAAA
Found at i:16582704 original size:49 final size:49
Alignment explanation
Indices: 16582611--16582740 Score: 224
Period size: 50 Copynumber: 2.6 Consensus size: 49
16582601 AATAATAATA
* *
16582611 ACATGCCAAATAAATTACATAAAAAAATAAATCTAATAAACCTAAAACAT
1 ACATGACAAATAAATTACAT-AAAAAATAAATCTAATAAACCTAAAACAC
16582661 ACATGACAAATAAATTACATAAAAAATAAATCTAATAAACCTAAAACAC
1 ACATGACAAATAAATTACATAAAAAATAAATCTAATAAACCTAAAACAC
16582710 ACATGACAAAATAAATTACATAAAAAATAAA
1 ACATGAC-AAATAAATTACATAAAAAATAAA
16582741 ACATTCTTTC
Statistics
Matches: 77, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
49 35 0.45
50 42 0.55
ACGTcount: A:0.62, C:0.15, G:0.02, T:0.21
Consensus pattern (49 bp):
ACATGACAAATAAATTACATAAAAAATAAATCTAATAAACCTAAAACAC
Found at i:16594946 original size:11 final size:11
Alignment explanation
Indices: 16594932--16594980 Score: 62
Period size: 11 Copynumber: 4.5 Consensus size: 11
16594922 ATATTTAAAC
16594932 AATAATAACAA
1 AATAATAACAA
*
16594943 AATAATAGCAA
1 AATAATAACAA
*
16594954 TATAATAACAA
1 AATAATAACAA
* *
16594965 AATGACAACAA
1 AATAATAACAA
16594976 AATAA
1 AATAA
16594981 CAGTTTTTTA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.67, C:0.10, G:0.04, T:0.18
Consensus pattern (11 bp):
AATAATAACAA
Found at i:16599901 original size:33 final size:33
Alignment explanation
Indices: 16599864--16599928 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
16599854 AATATAAGTC
16599864 TAGCCTACAATGGAATACAATCTAAACCATACA
1 TAGCCTACAATGGAATACAATCTAAACCATACA
*
16599897 TAGCCTACAATGGAATACAATCTGAACCATAC
1 TAGCCTACAATGGAATACAATCTAAACCATAC
16599929 CCCAATGATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.43, C:0.25, G:0.11, T:0.22
Consensus pattern (33 bp):
TAGCCTACAATGGAATACAATCTAAACCATACA
Found at i:16610613 original size:56 final size:51
Alignment explanation
Indices: 16610534--16610776 Score: 269
Period size: 50 Copynumber: 4.7 Consensus size: 51
16610524 GGGAATGAGA
* *
16610534 TCCCATGTAAGACCATGTTTGGGACATGGCATTGGCATCATTGAGATTTTGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAGA--TTGAGAGG
* *
16610590 TCACATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGA-TGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATTGAGAGG
* *
16610640 TCCCATGTAAGACCATGTCTTGGACATGGCGTTGGCACCGAGATT-AGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATTGAGAGG
** * **
16610690 TCCCCCGTAAGACCATGTCTGGGACATGGCA-TGGACACCGATA-TGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGG-CACCGAGATTGAGAGG
* * * *
16610740 TCCAATGTAAGACCATATCTGGGATATGGAATTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
16610777 GTTCAGGAAA
Statistics
Matches: 164, Mismatches: 19, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
49 4 0.02
50 117 0.71
51 4 0.02
53 4 0.02
55 1 0.01
56 34 0.21
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.24
Consensus pattern (51 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATTGAGAGG
Found at i:16632956 original size:41 final size:41
Alignment explanation
Indices: 16632896--16633144 Score: 264
Period size: 41 Copynumber: 6.1 Consensus size: 41
16632886 AGAAAAGTAT
* * * *
16632896 ATTTAGGGGTATCGTAGTACTAACAGGGGCACATATGTGCA
1 ATTTAGGGGTACCGAAGTACAAACAGGGGCACATAAGTGCA
*
16632937 ATTTAGGGGTACTGAAGTACAAACAGGGGCACATAAGTGCA
1 ATTTAGGGGTACCGAAGTACAAACAGGGGCACATAAGTGCA
* ** * *
16632978 ATTAAAAGGTACCGAAGTACAAAAAGGGGCACGTAAGTGCA
1 ATTTAGGGGTACCGAAGTACAAACAGGGGCACATAAGTGCA
* * *
16633019 ATTTAGGGGTACCAAAGTACAAATAGGGGCACATAAGTGTA
1 ATTTAGGGGTACCGAAGTACAAACAGGGGCACATAAGTGCA
* * * * * * ** *
16633060 ATTCAAGGGTATCAAAGTACAAACCGGGGTATGTAAGTGTA
1 ATTTAGGGGTACCGAAGTACAAACAGGGGCACATAAGTGCA
* * * *
16633101 ATTCAGGGGTATCGAAGTACAAACAAGGGCACGTAAGTGCA
1 ATTTAGGGGTACCGAAGTACAAACAGGGGCACATAAGTGCA
16633142 ATT
1 ATT
16633145 GATCAATTTT
Statistics
Matches: 175, Mismatches: 33, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 175 1.00
ACGTcount: A:0.37, C:0.14, G:0.28, T:0.21
Consensus pattern (41 bp):
ATTTAGGGGTACCGAAGTACAAACAGGGGCACATAAGTGCA
Found at i:16633026 original size:21 final size:21
Alignment explanation
Indices: 16633002--16633062 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 21
16632992 AAGTACAAAA
*
16633002 AGGGGCACGTAAGTGCAATTT
1 AGGGGCACATAAGTGCAATTT
* * *
16633023 AGGGGTACCA-AAGTACAA-AT
1 AGGGGCA-CATAAGTGCAATTT
*
16633043 AGGGGCACATAAGTGTAATT
1 AGGGGCACATAAGTGCAATT
16633063 CAAGGGTATC
Statistics
Matches: 29, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
19 2 0.07
20 13 0.45
21 13 0.45
22 1 0.03
ACGTcount: A:0.36, C:0.13, G:0.30, T:0.21
Consensus pattern (21 bp):
AGGGGCACATAAGTGCAATTT
Found at i:16633047 original size:20 final size:20
Alignment explanation
Indices: 16632985--16633047 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
16632975 GCAATTAAAA
* *
16632985 GGTACCGAAGTACAAAAAGG
1 GGTACCAAAGTACAAATAGG
* ** * *
16633005 GGCACGTAAGTGCAATTTAGG
1 GGTACCAAAGTACAA-ATAGG
16633026 GGTACCAAAGTACAAATAGG
1 GGTACCAAAGTACAAATAGG
16633046 GG
1 GG
16633048 CACATAAGTG
Statistics
Matches: 31, Mismatches: 11, Indels: 2
0.70 0.25 0.05
Matches are distributed among these distances:
20 17 0.55
21 14 0.45
ACGTcount: A:0.38, C:0.14, G:0.32, T:0.16
Consensus pattern (20 bp):
GGTACCAAAGTACAAATAGG
Found at i:16633056 original size:20 final size:20
Alignment explanation
Indices: 16632920--16633056 Score: 62
Period size: 21 Copynumber: 6.7 Consensus size: 20
16632910 TAGTACTAAC
* * *
16632920 AGGGGCACATATGTGCAATTT
1 AGGGGCACATAAGTACAA-AT
* *
16632941 AGGGGTAC-TGAAGTACAAAC
1 AGGGGCACAT-AAGTACAAAT
* *
16632961 AGGGGCACATAAGTGCAATT
1 AGGGGCACATAAGTACAAAT
** * ** *
16632981 AAAAGGTACCGAAGTACAAAA
1 -AGGGGCACATAAGTACAAAT
* * *
16633002 AGGGGCACGTAAGTGCAATTT
1 AGGGGCACATAAGTACAA-AT
*
16633023 AGGGGTACCA-AAGTACAAAT
1 AGGGGCA-CATAAGTACAAAT
16633043 AGGGGCACATAAGT
1 AGGGGCACATAAGT
16633057 GTAATTCAAG
Statistics
Matches: 80, Mismatches: 30, Indels: 13
0.65 0.24 0.11
Matches are distributed among these distances:
19 2 0.03
20 38 0.47
21 39 0.49
22 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.28, T:0.18
Consensus pattern (20 bp):
AGGGGCACATAAGTACAAAT
Found at i:16633078 original size:123 final size:123
Alignment explanation
Indices: 16632896--16633144 Score: 295
Period size: 123 Copynumber: 2.0 Consensus size: 123
16632886 AGAAAAGTAT
* ** * * * * *
16632896 ATTTAGGGGTATCGTAGTACTAACAGGGGCACATATGTGCAATTTAGGGGTACTGAAGTACAAAC
1 ATTTAGGGGTACCAAAGTACAAACAGGGGCACATAAGTGCAATTCAAGGGTACTAAAGTACAAAC
16632961 AGGGGCACATAAGTGCAATTAAAAGGTACCGAAGTACAAA-AAGGGGCACGTAAGTGCA
66 AGGGGCACATAAGTGCAATTAAAAGGTACCGAAGTACAAACAA-GGGCACGTAAGTGCA
* *
16633019 ATTTAGGGGTACCAAAGTACAAATAGGGGCACATAAGTGTAATTCAAGGGTA-TCAAAGTACAAA
1 ATTTAGGGGTACCAAAGTACAAACAGGGGCACATAAGTGCAATTCAAGGGTACT-AAAGTACAAA
* * ** * * ** *
16633083 CCGGGGTATGTAAGTGTAATTCAGGGGTATCGAAGTACAAACAAGGGCACGTAAGTGCA
65 CAGGGGCACATAAGTGCAATTAAAAGGTACCGAAGTACAAACAAGGGCACGTAAGTGCA
16633142 ATT
1 ATT
16633145 GATCAATTTT
Statistics
Matches: 105, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
122 1 0.01
123 102 0.97
124 2 0.02
ACGTcount: A:0.37, C:0.14, G:0.28, T:0.21
Consensus pattern (123 bp):
ATTTAGGGGTACCAAAGTACAAACAGGGGCACATAAGTGCAATTCAAGGGTACTAAAGTACAAAC
AGGGGCACATAAGTGCAATTAAAAGGTACCGAAGTACAAACAAGGGCACGTAAGTGCA
Found at i:16633118 original size:21 final size:21
Alignment explanation
Indices: 16633053--16633118 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
16633043 AGGGGCACAT
* *
16633053 AAGTGTAATTCAAGGGTATCA
1 AAGTGTAATTCAGGGGTATCG
** * *
16633074 AAGTACAA-ACCGGGGTAT-G
1 AAGTGTAATTCAGGGGTATCG
16633093 TAAGTGTAATTCAGGGGTATCG
1 -AAGTGTAATTCAGGGGTATCG
16633115 AAGT
1 AAGT
16633119 ACAAACAAGG
Statistics
Matches: 32, Mismatches: 10, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
20 13 0.41
21 18 0.56
22 1 0.03
ACGTcount: A:0.35, C:0.11, G:0.29, T:0.26
Consensus pattern (21 bp):
AAGTGTAATTCAGGGGTATCG
Found at i:16637452 original size:20 final size:20
Alignment explanation
Indices: 16637414--16637451 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
16637404 CCTTAAAGTA
16637414 AAAATGAATGTCAAATTTTG
1 AAAATGAATGTCAAATTTTG
*
16637434 AAAATGTATGTC-AATTTT
1 AAAATGAATGTCAAATTTT
16637452 TATTTTGGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.42, C:0.05, G:0.13, T:0.39
Consensus pattern (20 bp):
AAAATGAATGTCAAATTTTG
Found at i:16640259 original size:36 final size:35
Alignment explanation
Indices: 16640196--16640301 Score: 110
Period size: 36 Copynumber: 2.9 Consensus size: 35
16640186 CAATTCACAT
* *
16640196 ATCAATTCATATATA-ATATCATCATTTCATTTCATC
1 ATCAATTCATATATATATATCA-CATTTCATAT-AAC
16640232 ATCAATTCATATATATATATC-CAATTTCATATAAC
1 ATCAATTCATATATATATATCAC-ATTTCATATAAC
*
16640267 AT-AATTCATACTATATTCATATCACATATCATATA
1 ATCAATTCATA-TATA-T-ATATCACATTTCATATA
16640302 TCAATTATAT
Statistics
Matches: 61, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
34 8 0.13
35 9 0.15
36 24 0.39
37 19 0.31
38 1 0.02
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.42
Consensus pattern (35 bp):
ATCAATTCATATATATATATCACATTTCATATAAC
Found at i:16645239 original size:20 final size:20
Alignment explanation
Indices: 16645202--16645241 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
16645192 TTTTTACTTT
* *
16645202 AAAAAGAAGTCCATAAAATA
1 AAAAAGAAGTCAAAAAAATA
*
16645222 AAAAAGAATTCAAAAAAATA
1 AAAAAGAAGTCAAAAAAATA
16645242 TGTGAGATGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.70, C:0.07, G:0.07, T:0.15
Consensus pattern (20 bp):
AAAAAGAAGTCAAAAAAATA
Found at i:16647866 original size:3 final size:3
Alignment explanation
Indices: 16647860--16647990 Score: 235
Period size: 3 Copynumber: 43.7 Consensus size: 3
16647850 CAACAACTTT
* *
16647860 TTC TTC TTT TTC TTC TTC TTC TTT TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
16647908 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
16647956 TTC TTC TTC TTT TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
16647991 TTATTACCCA
Statistics
Matches: 122, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 122 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:16649351 original size:15 final size:14
Alignment explanation
Indices: 16649322--16649348 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
16649312 TAATCCCGAA
16649322 AATTTTTTTTGAAC
1 AATTTTTTTTGAAC
16649336 AATTTTTTTTGAA
1 AATTTTTTTTGAA
16649349 ACACATCAGA
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:0.30, C:0.04, G:0.07, T:0.59
Consensus pattern (14 bp):
AATTTTTTTTGAAC
Found at i:16652080 original size:35 final size:36
Alignment explanation
Indices: 16652028--16652100 Score: 130
Period size: 35 Copynumber: 2.1 Consensus size: 36
16652018 CATCCAAATC
16652028 AAATTTTATTCATACTAAATTCACCAATATTAAACT
1 AAATTTTATTCATACTAAATTCACCAATATTAAACT
*
16652064 AAATTTTA-TCATACTAAATTCGCCAATATTAAACT
1 AAATTTTATTCATACTAAATTCACCAATATTAAACT
16652099 AA
1 AA
16652101 CATGTAGCTA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 28 0.78
36 8 0.22
ACGTcount: A:0.45, C:0.16, G:0.01, T:0.37
Consensus pattern (36 bp):
AAATTTTATTCATACTAAATTCACCAATATTAAACT
Found at i:16652206 original size:6 final size:6
Alignment explanation
Indices: 16652195--16652267 Score: 146
Period size: 6 Copynumber: 12.2 Consensus size: 6
16652185 TCAACCGCAA
16652195 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
16652243 ACATAT ACATAT ACATAT ACATAT A
1 ACATAT ACATAT ACATAT ACATAT A
16652268 TGACCATCAT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 67 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (6 bp):
ACATAT
Found at i:16653452 original size:17 final size:17
Alignment explanation
Indices: 16653430--16653479 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
16653420 TAGTCATAAG
*
16653430 CTTTCTCTTTTTCTTTT
1 CTTTCTTTTTTTCTTTT
16653447 CTTTCTTTATTTTC-TTT
1 CTTTCTTT-TTTTCTTTT
16653464 CTTTCTTTTCTTTCTT
1 CTTTCTTTT-TTTCTT
16653480 AATGTTTGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 1 0.03
17 22 0.76
18 6 0.21
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (17 bp):
CTTTCTTTTTTTCTTTT
Found at i:16653459 original size:13 final size:13
Alignment explanation
Indices: 16653443--16653479 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
16653433 TCTCTTTTTC
16653443 TTTTCTTTCTTTA
1 TTTTCTTTCTTTA
*
16653456 TTTTCTTTCTTTC
1 TTTTCTTTCTTTA
16653469 TTTTCTTTCTT
1 TTTTCTTTCTT
16653480 AATGTTTGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTCTTTCTTTA
Found at i:16655008 original size:43 final size:43
Alignment explanation
Indices: 16654928--16655011 Score: 116
Period size: 43 Copynumber: 2.0 Consensus size: 43
16654918 AATCTAAGTG
* *
16654928 AATATACTAGCACACATAGTGCATCATCGGACGAACCAAAGCA
1 AATATACTAGCACACATAGTGCATCATCGAACAAACCAAAGCA
* *
16654971 AATATAC-AGGCACATATAGTGCATCATCTAACAAACCAAAG
1 AATATACTA-GCACACATAGTGCATCATCGAACAAACCAAAG
16655012 TATAAACTCG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
42 1 0.03
43 35 0.97
ACGTcount: A:0.44, C:0.24, G:0.14, T:0.18
Consensus pattern (43 bp):
AATATACTAGCACACATAGTGCATCATCGAACAAACCAAAGCA
Found at i:16661316 original size:21 final size:22
Alignment explanation
Indices: 16661285--16661339 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
16661275 GTTTCCCCCA
*
16661285 TTGCATGTGGCTATACAA-TTGT
1 TTGCA-GTGGCTATACAATTTAT
*
16661307 TTGCAGTGGCTATATAATTTAT
1 TTGCAGTGGCTATACAATTTAT
16661329 TTGCAGTGGCT
1 TTGCAGTGGCT
16661340 CCATCTGCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 11 0.37
22 19 0.63
ACGTcount: A:0.22, C:0.13, G:0.24, T:0.42
Consensus pattern (22 bp):
TTGCAGTGGCTATACAATTTAT
Found at i:16661599 original size:52 final size:50
Alignment explanation
Indices: 16661518--16661654 Score: 176
Period size: 52 Copynumber: 2.8 Consensus size: 50
16661508 CTTGGTGCTG
*
16661518 TTAATTTGTACTGTAATTTTGAATGCTTTGAAATGTTTGAAATGGTGTTA
1 TTAATTTGTACTGTAACTTTGAATGCTTTGAAATGTTTGAAATGGTGTTA
* *
16661568 TTAATTTGGTACTGTTAACTTTGAATGCTTTGAAATGTTTGAAATGGTGCTG
1 TTAATTT-GTACTG-TAACTTTGAATGCTTTGAAATGTTTGAAATGGTGTTA
*
16661620 TT-A---CTACT-TCAACTTTGAATGCTTTGAAATGTTTG
1 TTAATTTGTACTGT-AACTTTGAATGCTTTGAAATGTTTG
16661655 CTCACTGATA
Statistics
Matches: 80, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
45 1 0.01
46 25 0.31
47 4 0.05
50 7 0.09
51 7 0.09
52 36 0.45
ACGTcount: A:0.26, C:0.08, G:0.20, T:0.46
Consensus pattern (50 bp):
TTAATTTGTACTGTAACTTTGAATGCTTTGAAATGTTTGAAATGGTGTTA
Found at i:16661752 original size:116 final size:116
Alignment explanation
Indices: 16661548--16661845 Score: 569
Period size: 116 Copynumber: 2.6 Consensus size: 116
16661538 GAATGCTTTG
* *
16661548 AAATGTTTGAAATGGTGTTATTAATTTGGTACTGTTAACTTTGAATGCTTTGAAATGTTTGAAAT
1 AAATGTTTGAAATGGTGCTGTTAATTTGGTACTGTTAACTTTGAATGCTTTGAAATGTTTGAAAT
*
16661613 GGTGCTGTTACTACTTCAACTTTGAATGCTTTGAAATGTTTGCTCACTGAT
66 GGTGCTATTACTACTTCAACTTTGAATGCTTTGAAATGTTTGCTCACTGAT
16661664 AAATGTTTGAAATGGTGCTGTTAATTTGGTACTGTTAACTTTGAATGCTTTGAAATGTTTGAAAT
1 AAATGTTTGAAATGGTGCTGTTAATTTGGTACTGTTAACTTTGAATGCTTTGAAATGTTTGAAAT
16661729 GGTGCTATTACTACTTCAACTTTGAATGCTTTGAAATGTTTGCTCACTGAT
66 GGTGCTATTACTACTTCAACTTTGAATGCTTTGAAATGTTTGCTCACTGAT
16661780 AAATGTTTGAAATGGTGCTGTTAATTTGGTACTGTTAACTTTGAATGCTTTGAAATGTTTGAAAT
1 AAATGTTTGAAATGGTGCTGTTAATTTGGTACTGTTAACTTTGAATGCTTTGAAATGTTTGAAAT
16661845 G
66 G
16661846 AATTAACACC
Statistics
Matches: 179, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
116 179 1.00
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.43
Consensus pattern (116 bp):
AAATGTTTGAAATGGTGCTGTTAATTTGGTACTGTTAACTTTGAATGCTTTGAAATGTTTGAAAT
GGTGCTATTACTACTTCAACTTTGAATGCTTTGAAATGTTTGCTCACTGAT
Found at i:16662955 original size:24 final size:24
Alignment explanation
Indices: 16662928--16662983 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
16662918 ATCATTTTTG
16662928 ATTATTAATATTTTTAATTGAAAT
1 ATTATTAATATTTTTAATTGAAAT
16662952 ATTATTAATATTTTTAATTGAAAT
1 ATTATTAATATTTTTAATTGAAAT
16662976 ATTATTAA
1 ATTATTAA
16662984 AATCATTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (24 bp):
ATTATTAATATTTTTAATTGAAAT
Found at i:16666847 original size:122 final size:120
Alignment explanation
Indices: 16666703--16666998 Score: 463
Period size: 122 Copynumber: 2.4 Consensus size: 120
16666693 TAATTATTTT
* * *
16666703 AAATCTTATTAAATCATATATTTTAAATAAAATATATTTAATATTAATTAT-TTCAAATTT-TCA
1 AAAT-TTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT--AATTTAT-A
*
16666766 -TTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAAAG
62 TTTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATT--AAG
16666826 AAATTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AAATTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
16666891 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
16666946 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAAAAATTATGTT
1 AAATTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
16666999 TAAATATGAT
Statistics
Matches: 164, Mismatches: 6, Indels: 9
0.92 0.03 0.05
Matches are distributed among these distances:
120 54 0.33
121 6 0.04
122 98 0.60
123 6 0.04
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (120 bp):
AAATTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:16666963 original size:59 final size:59
Alignment explanation
Indices: 16666778--16666963 Score: 152
Period size: 56 Copynumber: 3.1 Consensus size: 59
16666768 TATAGTATCA
*
16666778 TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAAAGAAATTTATTAAAT
1 TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATT--AAGAATTTTATTAAAT
* * * ** * *
16666839 TATA-TAT--TTTAATTAAAAT-ATAT-TTAATAATAATTATGT--TAATTTATATTTTACAGTA
1 TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTAT-TAAGAATTT-TA--TTA-A--A
16666897 T
59 T
16666898 CATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
1 --TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
16666959 TATAT
1 TATAT
16666964 ATTTTAATTA
Statistics
Matches: 94, Mismatches: 15, Indels: 34
0.66 0.10 0.24
Matches are distributed among these distances:
53 4 0.04
54 2 0.02
56 14 0.15
57 6 0.06
58 9 0.10
59 7 0.07
60 3 0.03
61 10 0.11
62 3 0.03
63 1 0.01
64 12 0.13
65 5 0.05
66 13 0.14
67 5 0.05
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (59 bp):
TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
Found at i:16666975 original size:18 final size:17
Alignment explanation
Indices: 16666947--16666981 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
16666937 ATTATTAAGA
*
16666947 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
16666964 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
16666982 TTAATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:16666981 original size:16 final size:16
Alignment explanation
Indices: 16666947--16667001 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
16666937 ATTATTAAGA
16666947 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA--ATAT
16666964 ATTTTAATTAAAATAT
1 ATTTTAATTAAAATAT
*
16666980 A-TTTAATAAAAAT-T
1 ATTTTAATTAAAATAT
16666994 ATGTTTAA
1 AT-TTTAA
16667002 ATATGATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 2 0.06
15 11 0.32
16 10 0.29
17 5 0.15
18 6 0.18
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATTTTAATTAAAATAT
Found at i:16667226 original size:45 final size:44
Alignment explanation
Indices: 16667147--16667237 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 44
16667137 ACCTCTATTC
* * *
16667147 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTACTATTACACCTCTAATCCAATA
***
16667191 CATTCAACCAAACAGTTGATTTACTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGA-TTACTATTACACCTCTAATCCAATA
16667236 CA
1 CA
16667238 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 16 0.40
45 24 0.60
ACGTcount: A:0.37, C:0.29, G:0.04, T:0.30
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACACCTCTAATCCAATA
Found at i:16667239 original size:16 final size:16
Alignment explanation
Indices: 16667218--16667253 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
16667208 GATTTACTAT
16667218 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
16667234 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
16667250 TACA
1 TACA
16667254 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:16667881 original size:18 final size:18
Alignment explanation
Indices: 16667858--16667906 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
16667848 GTAGTGATTC
16667858 AATTCGATTAATTCGGGT
1 AATTCGATTAATTCGGGT
** * *
16667876 AATTCGGGTAATCCGGTT
1 AATTCGATTAATTCGGGT
16667894 AATTCGATTAATT
1 AATTCGATTAATT
16667907 TTTAACCAAA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (18 bp):
AATTCGATTAATTCGGGT
Found at i:16704501 original size:9 final size:9
Alignment explanation
Indices: 16704487--16704571 Score: 84
Period size: 9 Copynumber: 9.4 Consensus size: 9
16704477 TTTGGTTAAA
16704487 AATTAACCG
1 AATTAACCG
*
16704496 AATTAACCA
1 AATTAACCG
16704505 AATTAACCG
1 AATTAACCG
*
16704514 AATTACCCG
1 AATTAACCG
*
16704523 AATT-GCTCG
1 AATTAAC-CG
*
16704532 AATTACCCG
1 AATTAACCG
*
16704541 AATTAATCG
1 AATTAACCG
16704550 AATT-ACTCG
1 AATTAAC-CG
*
16704559 AATTAACCT
1 AATTAACCG
16704568 AATT
1 AATT
16704572 GAATCATACA
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
8 2 0.03
9 58 0.92
10 3 0.05
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:16704535 original size:27 final size:27
Alignment explanation
Indices: 16704487--16704571 Score: 100
Period size: 27 Copynumber: 3.1 Consensus size: 27
16704477 TTTGGTTAAA
*
16704487 AATTAACCGAATTAAC-CAAATTAACCG
1 AATTAACCGAATT-ACTCGAATTAACCG
* * *
16704514 AATTACCCGAATTGCTCGAATTACCCG
1 AATTAACCGAATTACTCGAATTAACCG
* *
16704541 AATTAATCGAATTACTCGAATTAACCT
1 AATTAACCGAATTACTCGAATTAACCG
16704568 AATT
1 AATT
16704572 GAATCATACA
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
26 1 0.02
27 47 0.98
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.28
Consensus pattern (27 bp):
AATTAACCGAATTACTCGAATTAACCG
Found at i:16704621 original size:6 final size:6
Alignment explanation
Indices: 16704610--16704638 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
16704600 ACTTTTATAC
16704610 TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
1 TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
16704639 AATTTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (6 bp):
TTTAGT
Found at i:16704662 original size:20 final size:20
Alignment explanation
Indices: 16704610--16704651 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
16704600 ACTTTTATAC
16704610 TTTAGTTTTAG--TTTTAGT
1 TTTAGTTTTAGAATTTTAGT
*
16704628 TTTAGTTTTAGAATTTTATT
1 TTTAGTTTTAGAATTTTAGT
16704648 TTTA
1 TTTA
16704652 TTTATTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.52
20 10 0.48
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.67
Consensus pattern (20 bp):
TTTAGTTTTAGAATTTTAGT
Found at i:16705787 original size:22 final size:21
Alignment explanation
Indices: 16705757--16705815 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
16705747 ATACAATCGT
*
16705757 AGATTTGATATGTAATCTTAGG
1 AGATTTGATTTGTAATCTTA-G
*
16705779 AGATATGATTTTGTAAATCTTAG
1 AGATTTGA-TTTGT-AATCTTAG
16705802 AGATTTGATTTGTA
1 AGATTTGATTTGTA
16705816 GATACCATTC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
21 1 0.03
22 12 0.38
23 12 0.38
24 7 0.22
ACGTcount: A:0.32, C:0.03, G:0.20, T:0.44
Consensus pattern (21 bp):
AGATTTGATTTGTAATCTTAG
Found at i:16710931 original size:22 final size:21
Alignment explanation
Indices: 16710901--16710959 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
16710891 ATACAATCGT
*
16710901 AGATTTGATATGTAATCTTAGG
1 AGATTTGATTTGTAATCTTA-G
*
16710923 AGATATGATTTTGTAAATCTTAG
1 AGATTTGA-TTTGT-AATCTTAG
16710946 AGATTTGATTTGTA
1 AGATTTGATTTGTA
16710960 GATACCATTC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
21 1 0.03
22 12 0.38
23 12 0.38
24 7 0.22
ACGTcount: A:0.32, C:0.03, G:0.20, T:0.44
Consensus pattern (21 bp):
AGATTTGATTTGTAATCTTAG
Found at i:16716084 original size:22 final size:22
Alignment explanation
Indices: 16716044--16716089 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
16716034 AAACATGACA
* *
16716044 AAAAAAATCAAGTATCAAATTG
1 AAAAAAATCAAGTACCAAAGTG
* *
16716066 AAAAAACTCATGTACCAAAGTG
1 AAAAAAATCAAGTACCAAAGTG
16716088 AA
1 AA
16716090 CATTGAGACC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.57, C:0.13, G:0.11, T:0.20
Consensus pattern (22 bp):
AAAAAAATCAAGTACCAAAGTG
Found at i:16716196 original size:82 final size:82
Alignment explanation
Indices: 16716109--16716264 Score: 249
Period size: 82 Copynumber: 1.9 Consensus size: 82
16716099 CAAACTTAGG
* *
16716109 TACCAAATTGGGAGAAAAAAAATGTAGGTACCAAATGACATCAACAATATACATAGTTGCTCAAG
1 TACCAAATTGGGACAAAAAAAACGTAGGTACCAAATGACATCAACAATATACATAGTTGCTCAAG
16716174 CATGATGCATTTCGAAA
66 CATGATGCATTTCGAAA
* * * * *
16716191 TACCAAATTGGGACAAAAATAGCGTAGGTACCAAATGACGTCAATAATATACATAGTTGTTCAAG
1 TACCAAATTGGGACAAAAAAAACGTAGGTACCAAATGACATCAACAATATACATAGTTGCTCAAG
16716256 CATGATGCA
66 CATGATGCA
16716265 GTCCAAAATA
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
82 67 1.00
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (82 bp):
TACCAAATTGGGACAAAAAAAACGTAGGTACCAAATGACATCAACAATATACATAGTTGCTCAAG
CATGATGCATTTCGAAA
Found at i:16718830 original size:50 final size:50
Alignment explanation
Indices: 16718755--16718855 Score: 175
Period size: 50 Copynumber: 2.0 Consensus size: 50
16718745 CAGACCAAGC
* *
16718755 TGCACAAGTAGAATCCGTATAGAACTACTCTTCTTTTATTTGACATTGAT
1 TGCACAAGTAGAATCCGTATAGAACTACTCTCCTTCTATTTGACATTGAT
*
16718805 TGCACAAGTAGAATCCGTATAGAACTACTCTCCTTCTATTTGGCATTGAT
1 TGCACAAGTAGAATCCGTATAGAACTACTCTCCTTCTATTTGACATTGAT
16718855 T
1 T
16718856 AGAATAATGT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.37
Consensus pattern (50 bp):
TGCACAAGTAGAATCCGTATAGAACTACTCTCCTTCTATTTGACATTGAT
Found at i:16726703 original size:18 final size:18
Alignment explanation
Indices: 16726676--16726729 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
16726666 CCTGCCATTC
16726676 TTTTCTTTTCTTTTTCTT
1 TTTTCTTTTCTTTTTCTT
* *
16726694 TTTTCCTTTCTTTTACCTT
1 TTTTCTTTTCTTTT-TCTT
*
16726713 TGTTCTTTTCTTTTTCT
1 TTTTCTTTTCTTTTTCT
16726730 GTTATCTTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 15 0.50
19 15 0.50
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (18 bp):
TTTTCTTTTCTTTTTCTT
Found at i:16726713 original size:19 final size:18
Alignment explanation
Indices: 16726676--16726726 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 18
16726666 CCTGCCATTC
*
16726676 TTTTCTTTTCTTTTTCTT
1 TTTTCTTTTCTTTTCCTT
*
16726694 TTTTCCTTTCTTTTACCTT
1 TTTTCTTTTCTTTT-CCTT
*
16726713 TGTTCTTTTCTTTT
1 TTTTCTTTTCTTTT
16726727 TCTGTTATCT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 13 0.46
19 15 0.54
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (18 bp):
TTTTCTTTTCTTTTCCTT
Found at i:16732717 original size:57 final size:57
Alignment explanation
Indices: 16732656--16732763 Score: 189
Period size: 57 Copynumber: 1.9 Consensus size: 57
16732646 GAATTAATTG
*
16732656 TTCAAGATATTGTTACACATTGAGTTTCGAAAACTCATATTCTATTTGACTGATATT
1 TTCAAGATATTGTTACACACTGAGTTTCGAAAACTCATATTCTATTTGACTGATATT
* *
16732713 TTCAAGTTATTGTTACACACTGAGTTTCGTAAACTCATATTCTATTTGACT
1 TTCAAGATATTGTTACACACTGAGTTTCGAAAACTCATATTCTATTTGACT
16732764 CAGTTACAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.43
Consensus pattern (57 bp):
TTCAAGATATTGTTACACACTGAGTTTCGAAAACTCATATTCTATTTGACTGATATT
Found at i:16733405 original size:189 final size:189
Alignment explanation
Indices: 16733084--16733653 Score: 1009
Period size: 189 Copynumber: 3.0 Consensus size: 189
16733074 ATGACATTTT
* * * *
16733084 TGAAAGGTTTTGAAAATTGAATTTACAACTGCTTTACGTAACATCTCCAGATTTGGACATAACGT
1 TGAAAGGTTTTGAAAACTGGATTTACAACTGCTTTACGTAACAACTCCAGATTTGGCCATAACGT
*
16733149 CTAGGTTGAGTTTGGGGTGTTACATATTGAATTGAAATGCTATGGTTGAAA-TGTAATA-TCGAG
66 CTAGGTTGAGTTTGGGGTGTTACATATTGACTTGAAATGCTATGGTTGAAATTG-AATATTC-AG
16733212 ATAGGGACAAAATTGAATAGAAATTTGTATGTCTTAGCTGATATAAGGAATTAGTATAAAA
129 ATAGGGACAAAATTGAATAGAAATTTGTATGTCTTAGCTGATATAAGGAATTAGTATAAAA
*
16733273 TGAAAGGTTTTGAAAACTGGATTTACAACTGCTTTACGAAACAACTCCAGATTTGGCCATAACGT
1 TGAAAGGTTTTGAAAACTGGATTTACAACTGCTTTACGTAACAACTCCAGATTTGGCCATAACGT
16733338 CTAGGTTGAGTTTGGGGTGTTACATATTGACTTGAAATGCTATGGTTGAAATTGAATATTCAGAT
66 CTAGGTTGAGTTTGGGGTGTTACATATTGACTTGAAATGCTATGGTTGAAATTGAATATTCAGAT
16733403 AGGGACAAAATTGAATAGAAATTTGTATGTCTTAGCTGATATAAGGAATTAGTATAAAA
131 AGGGACAAAATTGAATAGAAATTTGTATGTCTTAGCTGATATAAGGAATTAGTATAAAA
*
16733462 TGAAAGGTTTTGAAAACTGGATTTACAACTGCTTTACGTAACAACTCTAGATTTGGCCATAACGT
1 TGAAAGGTTTTGAAAACTGGATTTACAACTGCTTTACGTAACAACTCCAGATTTGGCCATAACGT
16733527 CTAGGTTGAGTTTGGGGTGTTACATATTGACTTGAAATGCTATGGTTGAAATTGAATATTCAGAT
66 CTAGGTTGAGTTTGGGGTGTTACATATTGACTTGAAATGCTATGGTTGAAATTGAATATTCAGAT
* * * *
16733592 AGGGACTAAATTGAATAAAAATTTGTATGTCTTAGCTAATATAAGAAATTAGTATAAAA
131 AGGGACAAAATTGAATAGAAATTTGTATGTCTTAGCTGATATAAGGAATTAGTATAAAA
16733651 TGA
1 TGA
16733654 GCTTATGTTA
Statistics
Matches: 367, Mismatches: 12, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
189 363 0.99
190 4 0.01
ACGTcount: A:0.35, C:0.10, G:0.21, T:0.34
Consensus pattern (189 bp):
TGAAAGGTTTTGAAAACTGGATTTACAACTGCTTTACGTAACAACTCCAGATTTGGCCATAACGT
CTAGGTTGAGTTTGGGGTGTTACATATTGACTTGAAATGCTATGGTTGAAATTGAATATTCAGAT
AGGGACAAAATTGAATAGAAATTTGTATGTCTTAGCTGATATAAGGAATTAGTATAAAA
Found at i:16743343 original size:50 final size:50
Alignment explanation
Indices: 16743243--16743343 Score: 132
Period size: 50 Copynumber: 2.0 Consensus size: 50
16743233 GGTCATACAC
* * ***
16743243 CTTATAATCCCCGTGTTTACTGTTTTGAATAACTCTATTAGTTTTTATAG
1 CTTATAATCCCCGTGTTTACTGTCTCGAATAACTCTATTAGTTGCCATAG
*
16743293 CTTATAATCCCTGTGTTTACTGTCTCG-ATAAACTCTATTAGTTGCCATAG
1 CTTATAATCCCCGTGTTTACTGTCTCGAAT-AACTCTATTAGTTGCCATAG
16743343 C
1 C
16743344 GGAGCTATGA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
49 2 0.05
50 42 0.95
ACGTcount: A:0.24, C:0.20, G:0.13, T:0.44
Consensus pattern (50 bp):
CTTATAATCCCCGTGTTTACTGTCTCGAATAACTCTATTAGTTGCCATAG
Found at i:16743404 original size:69 final size:69
Alignment explanation
Indices: 16743293--16743436 Score: 193
Period size: 69 Copynumber: 2.1 Consensus size: 69
16743283 GTTTTTATAG
* *
16743293 CTTATAATCCCTGTGTTTACTGTCTCGATAAACTCTATTAGTTGCCATAGCGGAGCTATGATCTT
1 CTTATAATCCCCGTGTTTACTATCTCGATAAACTCTATTAGTTGCCATAGCGGAGCTATGATCTT
16743358 A-CAC
66 ATC-C
* * * * *
16743362 CTTATAATCCCCGTGTTTACTATC-CTGATGAACTTTATTAGTTTCCATAGCTGAGCTATGGTCT
1 CTTATAATCCCCGTGTTTACTATCTC-GATAAACTCTATTAGTTGCCATAGCGGAGCTATGATCT
16743426 TATCC
65 TATCC
16743431 CTTATA
1 CTTATA
16743437 CCTCACTGGA
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
68 1 0.02
69 64 0.97
70 1 0.02
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.39
Consensus pattern (69 bp):
CTTATAATCCCCGTGTTTACTATCTCGATAAACTCTATTAGTTGCCATAGCGGAGCTATGATCTT
ATCC
Found at i:16745391 original size:23 final size:22
Alignment explanation
Indices: 16745347--16745406 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 22
16745337 AGGAAGTAAA
*
16745347 ATAAAA-ATA-AAAACATATGT
1 ATAAAATATATAAAACATACGT
16745367 ATAAAATATATATAAACATACGT
1 ATAAAATATATA-AAACATACGT
**
16745390 ATACTATATATAAAACA
1 ATAAAATATATAAAACA
16745407 ATATATATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.18
21 3 0.09
22 6 0.18
23 19 0.56
ACGTcount: A:0.60, C:0.08, G:0.03, T:0.28
Consensus pattern (22 bp):
ATAAAATATATAAAACATACGT
Found at i:16745415 original size:23 final size:23
Alignment explanation
Indices: 16745372--16745415 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
16745362 TATGTATAAA
*
16745372 ATATATATAAACATACGTATACT
1 ATATATATAAACATACATATACT
*
16745395 ATATATA-AAACAATATATATA
1 ATATATATAAAC-ATACATATA
16745416 TTACATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (23 bp):
ATATATATAAACATACATATACT
Found at i:16745717 original size:23 final size:23
Alignment explanation
Indices: 16745691--16745735 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
16745681 AAGAGATTTG
* *
16745691 AAATCAACAATATACAAATCAAT
1 AAATAAACAATACACAAATCAAT
**
16745714 AAATAAATTATACACAAATCAA
1 AAATAAACAATACACAAATCAA
16745736 CAAAATAAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.62, C:0.16, G:0.00, T:0.22
Consensus pattern (23 bp):
AAATAAACAATACACAAATCAAT
Found at i:16745972 original size:21 final size:21
Alignment explanation
Indices: 16745946--16746021 Score: 120
Period size: 21 Copynumber: 3.7 Consensus size: 21
16745936 AATCATATCT
16745946 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
16745967 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
16745988 TCTAAGATTGC--ATATCATA
1 TCTAAGATTGCATATATCATA
* *
16746007 GCTAAGATTACATAT
1 TCTAAGATTGCATAT
16746022 CCTTGAAGAT
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
19 17 0.33
21 34 0.67
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:16746020 original size:19 final size:19
Alignment explanation
Indices: 16745959--16746022 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
16745949 AAGATTGCAT
*
16745959 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATT--AC
*
16745980 ATATCATATCTAAGATTGC
1 ATATCATATCTAAGATTAC
*
16745999 ATATCATAGCTAAGATTAC
1 ATATCATATCTAAGATTAC
16746018 ATATC
1 ATATC
16746023 CTTGAAGATT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 22 0.56
21 17 0.44
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (19 bp):
ATATCATATCTAAGATTAC
Found at i:16746264 original size:36 final size:36
Alignment explanation
Indices: 16746224--16746294 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
16746214 TTTGTTTCTT
* *
16746224 CTCATATTCAACCATTCTTAAACATAAGCTCAAGAC
1 CTCATATTCAACCATCCATAAACATAAGCTCAAGAC
16746260 CTCATATTCAACCATCCATAAACATAAGCTCAAGA
1 CTCATATTCAACCATCCATAAACATAAGCTCAAGA
16746295 ACAAAACATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.41, C:0.28, G:0.06, T:0.25
Consensus pattern (36 bp):
CTCATATTCAACCATCCATAAACATAAGCTCAAGAC
Found at i:16749014 original size:51 final size:51
Alignment explanation
Indices: 16748900--16749189 Score: 465
Period size: 51 Copynumber: 5.6 Consensus size: 51
16748890 CGGATCACAT
*
16748900 TTATCACTTGTCACTTGTCCCTGATCAGATAAGTGTAGCTAAAGCTACCACC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCA-C
*
16748952 TATCACCTATCACTTGTTACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 --T----TATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
*
16749009 TTATCACTTGTTACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
16749060 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
*
16749111 TTATCACTTGTCACTTGT-ACTGATCAGATAAGTGTAGCTAAAGCTACTAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
*
16749161 TTGTCACTTGTCACTTGTCACTGATCAGA
1 TTATCACTTGTCACTTGTCACTGATCAGA
16749190 AGTACTCAAA
Statistics
Matches: 226, Mismatches: 5, Indels: 13
0.93 0.02 0.05
Matches are distributed among these distances:
50 48 0.21
51 128 0.57
54 1 0.00
55 1 0.00
57 1 0.00
58 47 0.21
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (51 bp):
TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
Found at i:16755528 original size:203 final size:203
Alignment explanation
Indices: 16755174--16755550 Score: 657
Period size: 203 Copynumber: 1.9 Consensus size: 203
16755164 TTGTCCTGAT
*
16755174 AGCTAAGCATGACAACCATTTATCGGTTAAACTAAAGGTGTTCAACCCTTAAAAACCTAGAATCC
1 AGCTAAGCATGACAACCATTTATCGGTTAAACTAAAGGTGTTCAACCCTTAAAAACCCAGAATCC
*
16755239 ATAATTATATAGAAGCTTTTAAGAGTTTTTACTCTACTTCTCTCTTCAATCCACAAGTACAGAGA
66 ATAATTATATAGAAGCTTTTAAGAGTTCTTACTCTACTTCTCTCTTCAATCCACAAGTACAGAGA
*
16755304 GGTAAGGAAGTTTACCAGTTCCTCAACTTATCTAATACTAGACTTCAGTTTTCATGATGGTTGCG
131 GGTAAGGAAGTTTACCAGTTCCTCAACTTATCTAATACCAGACTTCAGTTTTCATGATGGTTGCG
16755369 ACATGCAA
196 ACATGCAA
* *
16755377 AGCTAAGCATGACAACCATTTATTGGTTAAACTAAAGGTGTTCAACCCTTAAAAACCCATAATCC
1 AGCTAAGCATGACAACCATTTATCGGTTAAACTAAAGGTGTTCAACCCTTAAAAACCCAGAATCC
*
16755442 ATAATTATATAGAAGCTTTTAAGTA-TTCTTACTCTACTTCTCTCTTCAATCTACAAGTACAGAG
66 ATAATTATATAGAAGCTTTTAAG-AGTTCTTACTCTACTTCTCTCTTCAATCCACAAGTACAGAG
* * *
16755506 AGGTAAGGAAGTTTATCAGTTCCTCAACTTTTCTACTACCAGACT
130 AGGTAAGGAAGTTTACCAGTTCCTCAACTTATCTAATACCAGACT
16755551 ACAATTCTCA
Statistics
Matches: 164, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
203 163 0.99
204 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.32
Consensus pattern (203 bp):
AGCTAAGCATGACAACCATTTATCGGTTAAACTAAAGGTGTTCAACCCTTAAAAACCCAGAATCC
ATAATTATATAGAAGCTTTTAAGAGTTCTTACTCTACTTCTCTCTTCAATCCACAAGTACAGAGA
GGTAAGGAAGTTTACCAGTTCCTCAACTTATCTAATACCAGACTTCAGTTTTCATGATGGTTGCG
ACATGCAA
Found at i:16779392 original size:16 final size:14
Alignment explanation
Indices: 16779361--16779391 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
16779351 ATAAAAATAT
16779361 AATAAAATATTTAA
1 AATAAAATATTTAA
16779375 AATATAAATATTTAA
1 AATA-AAATATTTAA
16779390 AA
1 AA
16779392 AAAGAGATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AATAAAATATTTAA
Found at i:16781582 original size:18 final size:18
Alignment explanation
Indices: 16781548--16781583 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
16781538 TCACAAATTT
**
16781548 TAAATATAAACCGTAAAA
1 TAAATATAAACAATAAAA
16781566 TAAATATAAACAATAAAA
1 TAAATATAAACAATAAAA
16781584 AAAACTAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.67, C:0.08, G:0.03, T:0.22
Consensus pattern (18 bp):
TAAATATAAACAATAAAA
Found at i:16782137 original size:23 final size:25
Alignment explanation
Indices: 16782106--16782170 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 25
16782096 AGAGAGAATC
16782106 TTATATTAA-ATAACAATTTAAT-TT
1 TTATATTAATATAA-AATTTAATGTT
*
16782130 TTAT-TTAATATTAAATTTAATGTTT
1 TTATATTAATATAAAATTTAATG-TT
*
16782155 TTATATTACTA-AAAAT
1 TTATATTAATATAAAAT
16782171 GTGATGTGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
23 12 0.35
24 7 0.21
25 10 0.29
26 5 0.15
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (25 bp):
TTATATTAATATAAAATTTAATGTT
Found at i:16783317 original size:29 final size:31
Alignment explanation
Indices: 16783284--16783343 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 31
16783274 AAAAAATATA
* *
16783284 TTTAATA-AA-AAATATTTATTATATTTATT
1 TTTAATATAATAAACATTTATTACATTTATT
16783313 TTTAATATAATTAAACATTTATTACATTTAT
1 TTTAATATAA-TAAACATTTATTACATTTAT
16783344 GGTAGTGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 7 0.27
30 2 0.08
32 17 0.65
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (31 bp):
TTTAATATAATAAACATTTATTACATTTATT
Found at i:16785043 original size:93 final size:92
Alignment explanation
Indices: 16784795--16785077 Score: 338
Period size: 93 Copynumber: 3.0 Consensus size: 92
16784785 TGCTCCCTTA
* * *
16784795 AAAAGTTAATTTTAATCCTACATTGGCTAAAGAACACTCCCATGCTCGCACTTGCTTTATAAATA
1 AAAAGTTAATTTTAATCCTACATTGGCTAGAGAACACTCTCATGCTCGCACTTGCCTTATAAATA
* *
16784860 AGTGTTAGTTTTTTCACTATTTTCATT
66 AGTGTTAATTTCTTCACTATTTTCATT
* * * *
16784887 AAAAAGTTAATTTTAATCTTACATTGGCTAGAAAACACTCTCATGCTCGTACTTG-CTCAATAAA
1 -AAAAGTTAATTTTAATCCTACATTGGCTAGAGAACACTCTCATGCTCGCACTTGCCT-TATAAA
*
16784951 TAAGTGTTACTTTCTTCACTATTTTCATT
64 TAAGTGTTAATTTCTTCACTATTTTCATT
* * * * *
16784980 AAAAGTTAATTTTAATCCAATATTGACTAGAGAACACTCTCATATCTCACAC-TGACCTTATAAA
1 AAAAGTTAATTTTAATCCTACATTGGCTAGAGAACACTCTCAT-GCTCGCACTTG-CCTTATAAA
* *
16785044 TAAGT-TATAAATTTCTTTACTAATTTCATT
64 TAAGTGT-T-AATTTCTTCACTATTTTCATT
16785074 AAAA
1 AAAA
16785078 TTTTTATGTA
Statistics
Matches: 163, Mismatches: 21, Indels: 11
0.84 0.11 0.06
Matches are distributed among these distances:
92 42 0.26
93 97 0.60
94 24 0.15
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.39
Consensus pattern (92 bp):
AAAAGTTAATTTTAATCCTACATTGGCTAGAGAACACTCTCATGCTCGCACTTGCCTTATAAATA
AGTGTTAATTTCTTCACTATTTTCATT
Found at i:16794931 original size:36 final size:36
Alignment explanation
Indices: 16794880--16794950 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
16794870 GATTATGTAA
16794880 TCTTAGAGTTCTAATTATATACAGCTTCTAATTGTG
1 TCTTAGAGTTCTAATTATATACAGCTTCTAATTGTG
* * *
16794916 TCTTAGAGTTTTAATTGTATACAGCTTTTAATTGT
1 TCTTAGAGTTCTAATTATATACAGCTTCTAATTGT
16794951 AGCCCTTGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.48
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTATATACAGCTTCTAATTGTG
Found at i:16799991 original size:36 final size:36
Alignment explanation
Indices: 16799940--16800010 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
16799930 GATTATGTAA
16799940 TCTTAGAGTTCTAATTATATACAGCTTCTAATTGTG
1 TCTTAGAGTTCTAATTATATACAGCTTCTAATTGTG
* * *
16799976 TCTTAGAGTTTTAATTGTATACAGCTTTTAATTGT
1 TCTTAGAGTTCTAATTATATACAGCTTCTAATTGT
16800011 AGCCCTTGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.48
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTATATACAGCTTCTAATTGTG
Found at i:16801454 original size:14 final size:14
Alignment explanation
Indices: 16801435--16801465 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
16801425 AAGTGAGAGA
*
16801435 TGAGAGAAGAGTTG
1 TGAGAGAAGAGATG
16801449 TGAGAGAAGAGATG
1 TGAGAGAAGAGATG
16801463 TGA
1 TGA
16801466 ATGAGGGATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.42, T:0.19
Consensus pattern (14 bp):
TGAGAGAAGAGATG
Found at i:16802040 original size:20 final size:22
Alignment explanation
Indices: 16802015--16802062 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
16802005 CGAATCTGTC
16802015 AAAAATAA-T-CAAAATTCACT
1 AAAAATAATTGCAAAATTCACT
* *
16802035 AAAAATAATTGTAAAATTGACT
1 AAAAATAATTGCAAAATTCACT
16802057 AAAAAT
1 AAAAAT
16802063 TAACATGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.33
21 1 0.04
22 15 0.62
ACGTcount: A:0.60, C:0.08, G:0.04, T:0.27
Consensus pattern (22 bp):
AAAAATAATTGCAAAATTCACT
Found at i:16809861 original size:20 final size:19
Alignment explanation
Indices: 16809832--16809880 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
16809822 ATCAAATTGA
* *
16809832 ATTATCATTGAATGGATTT
1 ATTATAATTGAATGCATTT
*
16809851 GATTATAATTGGATGCATTT
1 -ATTATAATTGAATGCATTT
16809871 A-TATAATTGA
1 ATTATAATTGA
16809881 TGATAAAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 8 0.32
19 1 0.04
20 16 0.64
ACGTcount: A:0.35, C:0.04, G:0.16, T:0.45
Consensus pattern (19 bp):
ATTATAATTGAATGCATTT
Found at i:16812118 original size:17 final size:17
Alignment explanation
Indices: 16812096--16812145 Score: 91
Period size: 17 Copynumber: 2.9 Consensus size: 17
16812086 ATAGAAAGTC
16812096 AAAGATATGGGTATCAG
1 AAAGATATGGGTATCAG
*
16812113 AAAGATATTGGTATCAG
1 AAAGATATGGGTATCAG
16812130 AAAGATATGGGTATCA
1 AAAGATATGGGTATCA
16812146 AAATCTGAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.42, C:0.06, G:0.26, T:0.26
Consensus pattern (17 bp):
AAAGATATGGGTATCAG
Found at i:16814002 original size:200 final size:200
Alignment explanation
Indices: 16813659--16814061 Score: 788
Period size: 200 Copynumber: 2.0 Consensus size: 200
16813649 GACAATGGGA
16813659 GTAGGTACAATCCAATTGAAGAATCAGGACGGCTCAATTCAAGTCTTCACAGATGTTCGCTACAT
1 GTAGGTACAATCCAATTGAAGAATCAGGACGGCTCAATTCAAGTCTTCACAGATGTTCGCTACAT
*
16813724 ACCTAGCTTGAAGAAAAATCTCATCTCGTTAGGGGTCCTAGAATCTAAAGGGCTCACAATCACTT
66 ACCTAGCTTGAAGAAAAATCTCATCTCATTAGGGGTCCTAGAATCTAAAGGGCTCACAATCACTT
16813789 TGAGAGATGGATTACTAAAGGTAGTAGCTGGGGTATTGACAGTAATGAAAGACACAAGAAGGAAT
131 TGAGAGATGGATTACTAAAGGTAGTAGCTGGGGTATTGACAGTAATGAAAGACACAAGAAGGAAT
16813854 AACCT
196 AACCT
16813859 GTAGGTACAATCCAATTGAAGAATCAGGACGGCTCAATTCAAGTCTTCACAGATGTTCGCTACAT
1 GTAGGTACAATCCAATTGAAGAATCAGGACGGCTCAATTCAAGTCTTCACAGATGTTCGCTACAT
*
16813924 ACCTAGCTTGAAGAAAAATCTCATCTCATTAGGGGTCCTAGAATCTAAGGGGCTCACAATCACTT
66 ACCTAGCTTGAAGAAAAATCTCATCTCATTAGGGGTCCTAGAATCTAAAGGGCTCACAATCACTT
16813989 TGAGAGATGGATTACTAAAGGTAGTAGCTGGGGTATTGACAGTAATGAAAGACACAAGAAGGAAT
131 TGAGAGATGGATTACTAAAGGTAGTAGCTGGGGTATTGACAGTAATGAAAGACACAAGAAGGAAT
16814054 AACCT
196 AACCT
16814059 GTA
1 GTA
16814062 CTATTTAAAT
Statistics
Matches: 201, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
200 201 1.00
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.25
Consensus pattern (200 bp):
GTAGGTACAATCCAATTGAAGAATCAGGACGGCTCAATTCAAGTCTTCACAGATGTTCGCTACAT
ACCTAGCTTGAAGAAAAATCTCATCTCATTAGGGGTCCTAGAATCTAAAGGGCTCACAATCACTT
TGAGAGATGGATTACTAAAGGTAGTAGCTGGGGTATTGACAGTAATGAAAGACACAAGAAGGAAT
AACCT
Found at i:16815854 original size:17 final size:17
Alignment explanation
Indices: 16815832--16815864 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
16815822 ATAGAAATTC
16815832 AAAGATATGGGTATCAG
1 AAAGATATGGGTATCAG
16815849 AAAGATATGGGTATCA
1 AAAGATATGGGTATCA
16815865 AAATTTGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.27, T:0.24
Consensus pattern (17 bp):
AAAGATATGGGTATCAG
Found at i:16818608 original size:7 final size:7
Alignment explanation
Indices: 16818596--16818637 Score: 75
Period size: 7 Copynumber: 5.9 Consensus size: 7
16818586 TTTTATTTTC
16818596 AGTAGTT
1 AGTAGTT
16818603 AGTAGTT
1 AGTAGTT
16818610 AGTAGTT
1 AGTAGTT
16818617 AGTAGTT
1 AGTAGTT
16818624 AGTAGTT
1 AGTAGTT
16818631 AGGTAGT
1 A-GTAGT
16818638 AAAAGTCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 29 0.85
8 5 0.15
ACGTcount: A:0.29, C:0.00, G:0.31, T:0.40
Consensus pattern (7 bp):
AGTAGTT
Found at i:16825725 original size:29 final size:30
Alignment explanation
Indices: 16825693--16825750 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 30
16825683 ATATAATTTA
16825693 TTTTTTGTTTAATTTAT-AAAACCCAAAAT
1 TTTTTTGTTTAATTTATAAAAACCCAAAAT
16825722 TTTTTTGTTTAATTTATAAAAACCCAAAA
1 TTTTTTGTTTAATTTATAAAAACCCAAAA
16825751 ACCCAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (30 bp):
TTTTTTGTTTAATTTATAAAAACCCAAAAT
Found at i:16833201 original size:24 final size:24
Alignment explanation
Indices: 16833155--16833201 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
16833145 TCTCAATATT
* *
16833155 GGCTCGTATGAGCTTTCCAATTAC
1 GGCTCGTATAAGCTTCCCAATTAC
* *
16833179 GGCTCTTATAAGCTTCCCGATTA
1 GGCTCGTATAAGCTTCCCAATTA
16833202 ATGCCCTCAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (24 bp):
GGCTCGTATAAGCTTCCCAATTAC
Found at i:16833263 original size:49 final size:50
Alignment explanation
Indices: 16833154--16833280 Score: 124
Period size: 49 Copynumber: 2.6 Consensus size: 50
16833144 TTCTCAATAT
* *
16833154 TGGCTCGTATGAGCTTTC-CA-ATTACGGCTCTTATAAGCTTCCCGATTAA
1 TGGCTCGTATGAGCTTTCTGATATT-TGGCTCTTATAAGCTTCCCGATTAA
* *
16833203 T-GC-CCTCATGAGCTTTCTGATATTTGGCTCTCT-TAAGCTTCCCG-TTTA
1 TGGCTCGT-ATGAGCTTTCTGATATTTGGCTCT-TATAAGCTTCCCGATTAA
*
16833251 TGGCTCGTATGAGC-TTCTCGATAATTGGCT
1 TGGCTCGTATGAGCTTTCT-GATATTTGGCT
16833281 TGCAAGAGCT
Statistics
Matches: 65, Mismatches: 6, Indels: 14
0.76 0.07 0.16
Matches are distributed among these distances:
47 2 0.03
48 20 0.31
49 37 0.57
50 6 0.09
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.38
Consensus pattern (50 bp):
TGGCTCGTATGAGCTTTCTGATATTTGGCTCTTATAAGCTTCCCGATTAA
Found at i:16835263 original size:14 final size:14
Alignment explanation
Indices: 16835244--16835286 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
16835234 CATATAACAC
16835244 TTCATATAATTATT
1 TTCATATAATTATT
* *
16835258 TTCATATAATCA-A
1 TTCATATAATTATT
16835271 TTCATATAATTATT
1 TTCATATAATTATT
16835285 TT
1 TT
16835287 GTTCATCTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.53
Consensus pattern (14 bp):
TTCATATAATTATT
Found at i:16835280 original size:13 final size:13
Alignment explanation
Indices: 16835221--16835385 Score: 75
Period size: 13 Copynumber: 12.5 Consensus size: 13
16835211 CATATCTATC
*
16835221 CATATAAACATTT
1 CATATAATCATTT
*
16835234 CATATAA-CACTT
1 CATATAATCATTT
*
16835246 CATATAATTATTTT
1 CATATAATCA-TTT
*
16835260 CATATAATCAATT
1 CATATAATCATTT
*
16835273 CATATAATTATTT
1 CATATAATCATTT
** * *
16835286 TGT-TCATCTGTTT
1 CATATAATC-ATTT
*
16835299 CCATATAATTGA-TT
1 -CATATAA-TCATTT
* *
16835313 CATGTAAGCATTT
1 CATATAATCATTT
* * *
16835326 CGTATATTTATTT
1 CATATAATCATTT
* *
16835339 CTATATAACCAATT
1 C-ATATAATCATTT
*
16835353 CTTATAATCATTT
1 CATATAATCATTT
* * *
16835366 TACATAACCATTT
1 CATATAATCATTT
16835379 CATATAA
1 CATATAA
16835386 AAAATTCATA
Statistics
Matches: 105, Mismatches: 39, Indels: 16
0.66 0.24 0.10
Matches are distributed among these distances:
12 15 0.14
13 65 0.62
14 22 0.21
15 2 0.02
16 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.04, T:0.45
Consensus pattern (13 bp):
CATATAATCATTT
Found at i:16835280 original size:27 final size:26
Alignment explanation
Indices: 16835231--16835286 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 26
16835221 CATATAAACA
*
16835231 TTTCATATAACACTTCATATAATTAT
1 TTTCATATAACAATTCATATAATTAT
16835257 TTTCATATAATCAATTCATATAATTAT
1 TTTCATATAA-CAATTCATATAATTAT
16835284 TTT
1 TTT
16835287 GTTCATCTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 10 0.36
27 18 0.64
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (26 bp):
TTTCATATAACAATTCATATAATTAT
Found at i:16835410 original size:13 final size:13
Alignment explanation
Indices: 16835394--16835418 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16835384 AAAAAATTCA
16835394 TATAGCCATTTCG
1 TATAGCCATTTCG
16835407 TATAGCCATTTC
1 TATAGCCATTTC
16835419 AAAGTGTTAA
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:0.24, C:0.24, G:0.12, T:0.40
Consensus pattern (13 bp):
TATAGCCATTTCG
Found at i:16838455 original size:26 final size:26
Alignment explanation
Indices: 16838390--16838470 Score: 83
Period size: 26 Copynumber: 3.1 Consensus size: 26
16838380 AACACACTAA
16838390 TATCGCAGCAAAGCTGCCAGTAAT-AG
1 TATCGCAGCAAAGCTGCCAGT-ATCAG
* * **
16838416 TATTGTAGTGAAGCTGCCAGTATCAG
1 TATCGCAGCAAAGCTGCCAGTATCAG
* * *
16838442 TATCGCAGCAAAGCTACCAATAACAG
1 TATCGCAGCAAAGCTGCCAGTATCAG
16838468 TAT
1 TAT
16838471 ATGTGGCAAA
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
25 2 0.05
26 41 0.95
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (26 bp):
TATCGCAGCAAAGCTGCCAGTATCAG
Found at i:16842872 original size:31 final size:31
Alignment explanation
Indices: 16842787--16842881 Score: 93
Period size: 31 Copynumber: 3.0 Consensus size: 31
16842777 ATAAAAGAAA
** * *
16842787 TATTTAAACTTTTATTTTTAAAATTTAAAAG
1 TATTTAAAAATTTATTTCTAAAATTTAAAAT
*
16842818 TA-TTAGATATATATTATTTCTAAAATTTAAAAT
1 TATTTA-A-AAAT-TTATTTCTAAAATTTAAAAT
* *
16842851 TATTTAAAAATTTATTCCTAAAATTAAAAAT
1 TATTTAAAAATTTATTTCTAAAATTTAAAAT
16842882 AAAAATTAAG
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
30 3 0.06
31 21 0.40
32 5 0.09
33 21 0.40
34 3 0.06
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.47
Consensus pattern (31 bp):
TATTTAAAAATTTATTTCTAAAATTTAAAAT
Found at i:16846379 original size:6 final size:6
Alignment explanation
Indices: 16846368--16846393 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
16846358 ATCCTTTGGT
16846368 TGTTGC TGTTGC TGTTGC TGTTGC TG
1 TGTTGC TGTTGC TGTTGC TGTTGC TG
16846394 CGGCATTGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.35, T:0.50
Consensus pattern (6 bp):
TGTTGC
Found at i:16847558 original size:18 final size:18
Alignment explanation
Indices: 16847537--16847573 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
16847527 ATTAAAATGG
16847537 TACAAAAATTAAAAAAAA
1 TACAAAAATTAAAAAAAA
* *
16847555 TACAACAGTTAAAAAAAA
1 TACAAAAATTAAAAAAAA
16847573 T
1 T
16847574 GAAAAGATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.70, C:0.08, G:0.03, T:0.19
Consensus pattern (18 bp):
TACAAAAATTAAAAAAAA
Found at i:16847640 original size:27 final size:27
Alignment explanation
Indices: 16847606--16847669 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
16847596 CTGGTGGAGG
* * * *
16847606 GGCGGCACCAGAGGTGCCAGTGGCAGA
1 GGCGGCACCAAAGGTGCCACTGCCACA
*
16847633 GGCTGCACCAAAGGTGCCACTGCCACA
1 GGCGGCACCAAAGGTGCCACTGCCACA
16847660 GGCGGCACCA
1 GGCGGCACCA
16847670 CCCATTATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.23, C:0.33, G:0.36, T:0.08
Consensus pattern (27 bp):
GGCGGCACCAAAGGTGCCACTGCCACA
Found at i:16847724 original size:20 final size:20
Alignment explanation
Indices: 16847699--16847741 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
16847689 GATTCGACTG
* *
16847699 AAGGAGAAGATAGAAAAGGA
1 AAGGAGAAGAAAGAAAAAGA
16847719 AAGGAGAAGAAAGAAAAAGA
1 AAGGAGAAGAAAGAAAAAGA
16847739 AAG
1 AAG
16847742 AAAAGAAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (20 bp):
AAGGAGAAGAAAGAAAAAGA
Found at i:16847731 original size:15 final size:15
Alignment explanation
Indices: 16847713--16847772 Score: 70
Period size: 15 Copynumber: 4.0 Consensus size: 15
16847703 AGAAGATAGA
*
16847713 AAAGGAAAGGAGAAG
1 AAAGAAAAGGAGAAG
*
16847728 AAAGAAAAAGA-AAG
1 AAAGAAAAGGAGAAG
16847742 AAAAGAAAAGGAGAAG
1 -AAAGAAAAGGAGAAG
16847758 -AAGAAAAAGGAGAAG
1 AAAG-AAAAGGAGAAG
16847773 GAGGCGCAGG
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
14 6 0.15
15 30 0.77
16 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGGAGAAG
Found at i:16847744 original size:30 final size:29
Alignment explanation
Indices: 16847705--16847766 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 29
16847695 ACTGAAGGAG
* *
16847705 AAGATAGAAAAGGAAAGGAGAAGAAAGAAA
1 AAGAAAGAAAAGAAAAGGAGAAG-AAGAAA
16847735 AAGAAAGAAAAGAAAAGGAGAAGAAGAAA
1 AAGAAAGAAAAGAAAAGGAGAAGAAGAAA
16847764 AAG
1 AAG
16847767 GAGAAGGAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 9 0.30
30 21 0.70
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (29 bp):
AAGAAAGAAAAGAAAAGGAGAAGAAGAAA
Found at i:16847751 original size:20 final size:19
Alignment explanation
Indices: 16847705--16847749 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
16847695 ACTGAAGGAG
* * *
16847705 AAGATAGAAAAGGAAAGGAG
1 AAGAAAGAAAAAGAAA-GAA
16847725 AAGAAAGAAAAAGAAAGAA
1 AAGAAAGAAAAAGAAAGAA
16847744 AAGAAA
1 AAGAAA
16847750 AGGAGAAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (19 bp):
AAGAAAGAAAAAGAAAGAA
Found at i:16847758 original size:20 final size:21
Alignment explanation
Indices: 16847735--16847775 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
16847725 AAGAAAGAAA
16847735 AAGAAAG-AAAAGAAAAGGAG
1 AAGAAAGAAAAAGAAAAGGAG
*
16847755 AAG-AAGAAAAAGGAGAAGGAG
1 AAGAAAGAAAAA-GAAAAGGAG
16847776 GCGCAGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
19 3 0.17
20 7 0.39
21 8 0.44
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (21 bp):
AAGAAAGAAAAAGAAAAGGAG
Found at i:16847849 original size:48 final size:49
Alignment explanation
Indices: 16847699--16847849 Score: 121
Period size: 48 Copynumber: 3.1 Consensus size: 49
16847689 GATTCGACTG
* ** *
16847699 AAGGAGAAGATAG-AAAAGGA-AAGGAGAAGAAAGAAAAAGAAAGAAAAGAA
1 AAGGAGAAGA-AGAAAAAGAAGAAGGAGGCGAAGGAAAAAGAAA-AAAA-AA
* * * * *
16847749 AAGGAGAAGAAGAAAAAGGAGAAGGAGGCGCAGGAAAAAG-AGAAAGAG
1 AAGGAGAAGAAGAAAAAGAAGAAGGAGGCGAAGGAAAAAGAAAAAAAAA
* * * * *
16847797 AAGGAGGAGAAGAAGAAGAAGATGTAGG-GAAGGAAAAAGAAAAAAAAT
1 AAGGAGAAGAAGAAAAAGAAGAAGGAGGCGAAGGAAAAAGAAAAAAAAA
16847845 AAGGA
1 AAGGA
16847850 AAGGTATTTT
Statistics
Matches: 82, Mismatches: 16, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
47 10 0.12
48 34 0.41
49 5 0.06
50 18 0.22
51 15 0.18
ACGTcount: A:0.62, C:0.01, G:0.34, T:0.03
Consensus pattern (49 bp):
AAGGAGAAGAAGAAAAAGAAGAAGGAGGCGAAGGAAAAAGAAAAAAAAA
Found at i:16847884 original size:20 final size:20
Alignment explanation
Indices: 16847855--16847892 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
16847845 AAGGAAAGGT
16847855 ATTTTCTTTGTATTATTTTA
1 ATTTTCTTTGTATTATTTTA
*
16847875 ATTTTTTTTGTATTATTT
1 ATTTTCTTTGTATTATTT
16847893 GTGTAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.03, G:0.05, T:0.74
Consensus pattern (20 bp):
ATTTTCTTTGTATTATTTTA
Found at i:16848461 original size:161 final size:158
Alignment explanation
Indices: 16848126--16848994 Score: 1133
Period size: 161 Copynumber: 5.6 Consensus size: 158
16848116 ACGAAAAGAA
** * *
16848126 ACGAAAATAGTATATTTACTGAAAGTAATAAAATC-CGAAAATAAGAAAAATACGAACAAATGGC
1 ACGAAAATAGTATATTTTTTGAAAGTAATAAAATCGGGAAAA-AAGAAAAATACGAACAAAGGGC
* * * * * * *
16848190 CAAAATAAGGGTTTTTTATTAAATTTATTTAAAAAATATACTAAAATAATACATTTCAAACATAA
65 CAAAATAAGAGTTTTTTACTAAATTTATATAAAAAACACACTAAATTAATACATTTCAAACATTA
*
16848255 TGCACTAAAATAATATAAAATAATAAAAT
130 TGTACTAAAATAATATAAAATAATAAAAT
*
16848284 ACGAAAATAGTATATTTTTTGAAAGTAATAAAATTCGGGAAAAAAGAAAAATACGAATAAAGGGC
1 ACGAAAATAGTATATTTTTTGAAAGTAATAAAA-TCGGGAAAAAAGAAAAATACGAACAAAGGGC
*
16848349 CAAAATAAGATTTTTTTACTAAATTTATATAAAAAAAACACACTAAATTAATACATTTCAAACAT
65 CAAAATAAGAGTTTTTTACTAAATTTATAT--AAAAAACACACTAAATTAATACATTTCAAACAT
16848414 TATGTACTAAAATAATATAAAATAATAAAAT
128 TATGTACTAAAATAATATAAAATAATAAAAT
* * * *
16848445 ACAAAAATAATATATTTTTTGAAAGTAATAAAATCTGAGAAAAAAGAAAAATACGAATAAAGGGC
1 ACGAAAATAGTATATTTTTTGAAAGTAATAAAATC-GGGAAAAAAGAAAAATACGAACAAAGGGC
* * * *
16848510 TAAAATAAGTGTTTTTTACTAAATTTATATAAAAAACACATTAAATTAATACACTT----CA--A
65 CAAAATAAGAGTTTTTTACTAAATTTATATAAAAAACACACTAAATTAATACATTTCAAACATTA
*
16848569 ---AC----AT-A-AT---GTAATAAAAT
130 TGTACTAAAATAATATAAAATAATAAAAT
*
16848586 ACGAAAATAGTATATTTTTTGAAAGTAATAAAATCTGGAAAAAAAAGAAAGAAAAATAC-AAGCA
1 ACGAAAATAGTATATTTTTTGAAAGTAATAAAATC-GG----GAAA-AAAGAAAAATACGAA-CA
*
16848650 AATGGCCAAAATAAGAGTTTTTTACTAAATTTATAT-AAAAACACACTAAATTAATACATTTCAA
59 AAGGGCCAAAATAAGAGTTTTTTACTAAATTTATATAAAAAACACACTAAATTAATACATTTCAA
16848714 ACATTATGTACTAAAATAATATAAAATAATAAAAT
124 ACATTATGTACTAAAATAATATAAAATAATAAAAT
* * * * *
16848749 ACGAAAATAGCATATTTTTTTAAAGTAATAAAATC--CAGAAAA-AAAAATACGAACAAATGGCC
1 ACGAAAATAGTATATTTTTTGAAAGTAATAAAATCGGGAAAAAAGAAAAATACGAACAAAGGGCC
*
16848811 AAAATAAG-GGTTTTTACTAAATTTATATAAAAAACACACTAAATTAATACATTTCAAACATTAT
66 AAAATAAGAGTTTTTTACTAAATTTATATAAAAAACACACTAAATTAATACATTTCAAACATTAT
16848875 GTACTAAAATAATATAAAAT-ATGAAAAT
131 GTACTAAAATAATATAAAATAAT-AAAAT
*
16848903 ATGAAAATAGTATATTTTTTGAAAGTAATAAAATCTGGGAAAAAAGAAAAATACGAACAAAGGGC
1 ACGAAAATAGTATATTTTTTGAAAGTAATAAAATC-GGGAAAAAAGAAAAATACGAACAAAGGGC
16848968 CAAAATAAGAGTTTTTTTACTAAATTT
65 CAAAATAAGAG-TTTTTTACTAAATTT
16848995 GTTTTGAAGT
Statistics
Matches: 627, Mismatches: 46, Indels: 74
0.84 0.06 0.10
Matches are distributed among these distances:
141 44 0.07
144 2 0.00
145 29 0.05
146 48 0.08
149 2 0.00
150 2 0.00
151 1 0.00
153 22 0.04
154 119 0.19
155 7 0.01
156 2 0.00
157 5 0.01
158 60 0.10
159 74 0.12
160 23 0.04
161 145 0.23
163 42 0.07
ACGTcount: A:0.54, C:0.09, G:0.09, T:0.29
Consensus pattern (158 bp):
ACGAAAATAGTATATTTTTTGAAAGTAATAAAATCGGGAAAAAAGAAAAATACGAACAAAGGGCC
AAAATAAGAGTTTTTTACTAAATTTATATAAAAAACACACTAAATTAATACATTTCAAACATTAT
GTACTAAAATAATATAAAATAATAAAAT
Found at i:16848593 original size:141 final size:143
Alignment explanation
Indices: 16848436--16848731 Score: 429
Period size: 145 Copynumber: 2.1 Consensus size: 143
16848426 TAATATAAAA
*
16848436 TAATAAAATACAAAAATAATATATTTTTTGAAAGTAATAAAATCT-G-AGAAA-AAAGAAAAATA
1 TAATAAAATACAAAAATAATATATTTTTTGAAAGTAATAAAATCTGGAAAAAAGAAAGAAAAATA
* * * *
16848498 CGAA-TAAAGGGCTAAAATAAGTGTTTTTTACTAAATTTATATAAAAAACACATTAAATTAATAC
66 C-AAGCAAAGGGCCAAAATAAGAGTTTTTTACTAAATTTATAT-AAAAACACACTAAATTAATAC
16848562 ACTTCAAACATAATG
129 ACTTCAAACATAATG
* *
16848577 TAATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAATCTGGAAAAAAAAGAAAGAAAAA
1 TAATAAAATACAAAAATAATATATTTTTTGAAAGTAATAAAATCTGG--AAAAAAGAAAGAAAAA
*
16848642 TACAAGCAAATGGCCAAAATAAGAGTTTTTTACTAAATTTATATAAAAACACACTAAATTAATAC
64 TACAAGCAAAGGGCCAAAATAAGAGTTTTTTACTAAATTTATATAAAAACACACTAAATTAATAC
* *
16848707 ATTTCAAACATTATG
129 ACTTCAAACATAATG
*
16848722 TACTAAAATA
1 TAATAAAATA
16848732 ATATAAAATA
Statistics
Matches: 138, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
141 43 0.31
142 1 0.01
145 48 0.35
146 46 0.33
ACGTcount: A:0.54, C:0.08, G:0.09, T:0.29
Consensus pattern (143 bp):
TAATAAAATACAAAAATAATATATTTTTTGAAAGTAATAAAATCTGGAAAAAAGAAAGAAAAATA
CAAGCAAAGGGCCAAAATAAGAGTTTTTTACTAAATTTATATAAAAACACACTAAATTAATACAC
TTCAAACATAATG
Found at i:16848685 original size:146 final size:140
Alignment explanation
Indices: 16848436--16848885 Score: 446
Period size: 154 Copynumber: 3.1 Consensus size: 140
16848426 TAATATAAAA
*
16848436 TAATAAAATACAAAAATAATATATTTTTTGAAAGTAATAAAATCTGAGAAAAAAGAAAAATACGA
1 TAATAAAATACAAAAATAATATATTTTTTGAAAGTAATAAAATCTGAAAAAAAAGAAAAATACGA
* * * *
16848501 ATAAAGGGCTAAAATAAGTGTTTTTTACTAAATTTATATAAAAAACACATTAAATTAATACACTT
66 ACAAAGGGCCAAAATAAGAGTTTTTTACTAAATTTATAT-AAAAACACACTAAATTAATACACTT
16848566 CAAACATAATG
130 CAAACATAATG
* *
16848577 TAATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAATCTGGAAAAAAAAGAAAGAAAAA
1 TAATAAAATACAAAAATAATATATTTTTTGAAAGTAATAAAATCT-G---AAAAA-AAAGAAAAA
*
16848642 TAC-AAGCAAATGGCCAAAATAAGAGTTTTTTACTAAATTTATATAAAAACACACTAAATTAATA
61 TACGAA-CAAAGGGCCAAAATAAGAGTTTTTTACTAAATTTATATAAAAACACACTAAATTAATA
* *
16848706 CATTTCAAACATTATGTACTAAAA
125 CACTTCAAACA-TA---A-T---G
* * *
16848730 TAATATAAAATA-ATAAAATACGAAAATAGCATATTTTTTTAAAGTAATAAAATC---CAGAAAA
1 T-A-ATAAAATACA-AAAAT-----AAT---ATATTTTTTGAAAGTAATAAAATCTGAAAAAAAA
* *
16848791 -AAAAATACGAACAAATGGCCAAAATAAG-GGTTTTTACTAAATTTATATAAAAAACACACTAAA
55 GAAAAATACGAACAAAGGGCCAAAATAAGAGTTTTTTACTAAATTTATAT-AAAAACACACTAAA
* *
16848854 TTAATACATTTCAAACATTATG
119 TTAATACACTTCAAACATAATG
*
16848876 TACTAAAATA
1 TAATAAAATA
16848886 ATATAAAATA
Statistics
Matches: 263, Mismatches: 19, Indels: 51
0.79 0.06 0.15
Matches are distributed among these distances:
141 43 0.16
142 1 0.00
144 7 0.03
145 36 0.14
146 49 0.19
149 2 0.01
150 2 0.01
153 21 0.08
154 57 0.22
155 18 0.07
156 2 0.01
160 2 0.01
163 23 0.09
ACGTcount: A:0.54, C:0.09, G:0.08, T:0.29
Consensus pattern (140 bp):
TAATAAAATACAAAAATAATATATTTTTTGAAAGTAATAAAATCTGAAAAAAAAGAAAAATACGA
ACAAAGGGCCAAAATAAGAGTTTTTTACTAAATTTATATAAAAACACACTAAATTAATACACTTC
AAACATAATG
Found at i:16851322 original size:8 final size:8
Alignment explanation
Indices: 16851309--16851354 Score: 60
Period size: 8 Copynumber: 5.9 Consensus size: 8
16851299 GGGTGTTACA
16851309 ACAACATT
1 ACAACATT
16851317 ACAACATT
1 ACAACATT
16851325 ACAACATT
1 ACAACATT
*
16851333 AC-ACATA
1 ACAACATT
16851340 ACAAC-TT
1 ACAACATT
16851347 CACAACAT
1 -ACAACAT
16851355 AAGCTTAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
7 7 0.21
8 25 0.76
9 1 0.03
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (8 bp):
ACAACATT
Done.