Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 52 of 427
Found at i:12558462 original size:11 final size:11
Alignment explanation
Indices: 12558431--12558465 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
12558421 GTTTTTACAT
*
12558431 TTTTAAATATA
1 TTTTAAAAATA
12558442 TTTATAAAAATA
1 TTT-TAAAAATA
12558454 TTTTAAAAATA
1 TTTTAAAAATA
12558465 T
1 T
12558466 AAAAAGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
TTTTAAAAATA
Found at i:12563489 original size:80 final size:80
Alignment explanation
Indices: 12563393--12563547 Score: 283
Period size: 80 Copynumber: 1.9 Consensus size: 80
12563383 TGCACTTTGT
*
12563393 TGCTCGCACCAGGCTGAGCTTGCACCTTTGACAGGCTCACATTTTTTGCTTACTGTCTCTTAAGG
1 TGCTCGCACCAGGCTGAGCTTACACCTTTGACAGGCTCACATTTTTTGCTTACTGTCTCTTAAGG
12563458 TGTCTTCAACTCTGC
66 TGTCTTCAACTCTGC
* *
12563473 TGCTCGCACTAGGCTGAGCTTACACCTTTGACAGGCTCGCATTTTTTGCTTACTGTCTCTTAAGG
1 TGCTCGCACCAGGCTGAGCTTACACCTTTGACAGGCTCACATTTTTTGCTTACTGTCTCTTAAGG
12563538 TGTCTTCAAC
66 TGTCTTCAAC
12563548 AGGCTCGCAA
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 72 1.00
ACGTcount: A:0.17, C:0.28, G:0.20, T:0.35
Consensus pattern (80 bp):
TGCTCGCACCAGGCTGAGCTTACACCTTTGACAGGCTCACATTTTTTGCTTACTGTCTCTTAAGG
TGTCTTCAACTCTGC
Found at i:12563619 original size:25 final size:25
Alignment explanation
Indices: 12563591--12563674 Score: 91
Period size: 26 Copynumber: 3.3 Consensus size: 25
12563581 ATGAGCTCAT
*
12563591 AGCTTGCACTTCTCGCTAAGCTTGC
1 AGCTTGCACTTCTTGCTAAGCTTGC
12563616 AGCTTTG-A-TATCTTGCTAAGCTTGC
1 AGC-TTGCACT-TCTTGCTAAGCTTGC
* * *
12563641 AGCTTGCACATTTTTGTTGAGCTTGC
1 AGCTTGCAC-TTCTTGCTAAGCTTGC
12563667 AGCTTGCA
1 AGCTTGCA
12563675 TATTGGAAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
24 4 0.08
25 22 0.44
26 23 0.46
27 1 0.02
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.37
Consensus pattern (25 bp):
AGCTTGCACTTCTTGCTAAGCTTGC
Found at i:12571850 original size:83 final size:83
Alignment explanation
Indices: 12571752--12571918 Score: 309
Period size: 83 Copynumber: 2.0 Consensus size: 83
12571742 CTACGGTGAA
*
12571752 GGGGAAAAAATGGCAAACTGGATTCCCTTCAATCATTTG-ACATCAATGAAAATTTATTACCCCA
1 GGGGAAAAAATGGCAAACTGAATTCCCTTCAATCA-TTGCACATCAATGAAAATTTATTACCCCA
12571816 AGTAGTGCACTTAGTTATT
65 AGTAGTGCACTTAGTTATT
12571835 GGGGAAAAAATGGCAAACTGAATTCCCTTCAATCATTGCACATCAATGAAAATTTATTACCCCAA
1 GGGGAAAAAATGGCAAACTGAATTCCCTTCAATCATTGCACATCAATGAAAATTTATTACCCCAA
12571900 GTAGTGCACTTAGTTATT
66 GTAGTGCACTTAGTTATT
12571918 G
1 G
12571919 TGATCTATAA
Statistics
Matches: 82, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
82 3 0.04
83 79 0.96
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (83 bp):
GGGGAAAAAATGGCAAACTGAATTCCCTTCAATCATTGCACATCAATGAAAATTTATTACCCCAA
GTAGTGCACTTAGTTATT
Found at i:12573316 original size:22 final size:22
Alignment explanation
Indices: 12573291--12573332 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
12573281 ATATAAGTAC
*
12573291 AATAACAATAATGGTAATAAAA
1 AATAAAAATAATGGTAATAAAA
*
12573313 AATAAAAATAATTGTAATAA
1 AATAAAAATAATGGTAATAA
12573333 TAGCACGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.26
Consensus pattern (22 bp):
AATAAAAATAATGGTAATAAAA
Found at i:12573458 original size:35 final size:34
Alignment explanation
Indices: 12573392--12573459 Score: 91
Period size: 35 Copynumber: 2.0 Consensus size: 34
12573382 ACATCATAGT
* *
12573392 AAAATAATAATAGTAATAATGTTAATAAAGATAC
1 AAAATAATAATAGTAAAAATGTCAATAAAGATAC
* *
12573426 AAAATGATAATAAGTAAAAATGTCAATGAAGATA
1 AAAATAATAAT-AGTAAAAATGTCAATAAAGATA
12573460 ATAAAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 10 0.34
35 19 0.66
ACGTcount: A:0.59, C:0.03, G:0.12, T:0.26
Consensus pattern (34 bp):
AAAATAATAATAGTAAAAATGTCAATAAAGATAC
Found at i:12575032 original size:42 final size:40
Alignment explanation
Indices: 12574928--12575044 Score: 117
Period size: 42 Copynumber: 2.8 Consensus size: 40
12574918 TATTTGATTT
* * *
12574928 TCAACCTGTTACTCTACTGCTTAGAGGGTTAAGGCTTGTCA
1 TCAACCTGTTACTCTACTGCTTAG-GGGTTTAGACTTGTAA
* * * *
12574969 TCAGTGATCTGTTTCCCTACTGCTTAGGGGTTTAGATTTGTAAA
1 TCA---ACCTGTTACTCTACTGCTTAGGGGTTTAGACTTGT-AA
12575013 CTCAACCTGTTACTCTACTGCTTAGGGGTTTA
1 -TCAACCTGTTACTCTACTGCTTAGGGGTTTA
12575045 ATGTTTGAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 9
0.76 0.12 0.11
Matches are distributed among these distances:
41 3 0.05
42 25 0.41
43 11 0.18
44 19 0.31
45 3 0.05
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (40 bp):
TCAACCTGTTACTCTACTGCTTAGGGGTTTAGACTTGTAA
Found at i:12575081 original size:43 final size:45
Alignment explanation
Indices: 12574978--12575140 Score: 133
Period size: 43 Copynumber: 3.8 Consensus size: 45
12574968 ATCAGTGATC
* * * * *
12574978 TGTTTCCCTACTGCTTAGGGG-TTTA-GATTTG-TAAA-CTCAACC
1 TGTTACCCTACTGCTTAGGGGATTAATG-TTTGATAAATTTCAGCT
* * *
12575020 TGTTACTCTACTGCTTAGGGGTTTAATGTTTGA-AAATTT-GGCT
1 TGTTACCCTACTGCTTAGGGGATTAATGTTTGATAAATTTCAGCT
* * * * *
12575063 TGTTACCCTATTGCTTAGGGCAATAATATCT-ATAAATTTCAGCT
1 TGTTACCCTACTGCTTAGGGGATTAATGTTTGATAAATTTCAGCT
* *
12575107 TGTTACCCTACTGCTTAGGGGGTTAAAGTTTGAT
1 TGTTACCCTACTGCTTAGGGGATTAATGTTTGAT
12575141 GGTTTGAATC
Statistics
Matches: 92, Mismatches: 22, Indels: 11
0.74 0.18 0.09
Matches are distributed among these distances:
42 20 0.22
43 41 0.45
44 29 0.32
45 2 0.02
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (45 bp):
TGTTACCCTACTGCTTAGGGGATTAATGTTTGATAAATTTCAGCT
Found at i:12575584 original size:389 final size:389
Alignment explanation
Indices: 12574854--12575628 Score: 1300
Period size: 389 Copynumber: 2.0 Consensus size: 389
12574844 TCGATTAATC
*
12574854 CACTAAAACTTTAAGGAAATCTGTTGTGGCTTTTAGTTGCTCCAACGCCATTTCAGGGAGAAGAT
1 CACTAAAACTTCAAGGAAATCTGTTGTGGCTTTTAGTTGCTCCAACGCCATTTCAGGGAGAAGAT
12574919 ATTTGATTTTCAACCTGTTACTCTACTGCTTAGAGGGTTAAGGCTTGTCATCAGTGATCTGTTTC
66 ATTTGATTTTCAACCTGTTACTCTACTGCTTAGAGGGTTAAGGCTTGTCATCAGTGATCTGTTTC
* * *
12574984 CCTACTGCTTAGGGGTTTAGATTTGTAAACTCAACCTGTTACTCTACTGCTTAGGGGTTTAATGT
131 CCTACTGCTTAGGGGTTTAGATCTGTAAACTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGT
* *
12575049 TTGAAAATTTGGCTTGTTACCCTATTGCTTAGGGCAATAATATCTATAAATTTCAGCTTGTTACC
196 TTGAAAATTTGGCTTGTTACCCTATTACTTAGGGCAATAATATCTATAAACTTCAGCTTGTTACC
* *
12575114 CTACTGCTTAGGGGGTTAAAGTTTGATGGTTTGAATCTACTTCACTGCATTCGAGGAGGCAAAAT
261 CTACTGCTTAGGGGGTTAAAGCTTGATGGTTTGAATCTACTTCACTGCATTCGAAGAGGCAAAAT
* * *
12575179 TCGATGTATTTGATCTGCTCCACTGCACCTTCATGGAGATAAGACACGTGACTTCAATCAATTT
326 TCGATGTATCTGATCTGCTCCACTGCAACTTCATGGAGAAAAGACACGTGACTTCAATCAATTT
*
12575243 CACTGAAACTTCAAGGAAATCTGTTGTGGCTTTTAGTTGCTCCAACGCCATTTCAGGGAGAAGAT
1 CACTAAAACTTCAAGGAAATCTGTTGTGGCTTTTAGTTGCTCCAACGCCATTTCAGGGAGAAGAT
* * * * * *
12575308 ATTTGATTTTCAACTTGTT-TTCTTATTGTTTAGGGGGTTAAGGCTTGTCATCATTGATCTGTTT
66 ATTTGATTTTCAACCTGTTACTC-TACTGCTTAGAGGGTTAAGGCTTGTCATCAGTGATCTGTTT
* * *
12575372 TCCTATTGTTTAGGGGTTTAGATCTGTAAACTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGG
130 CCCTACTGCTTAGGGGTTTAGATCTGTAAACTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGG
*
12575437 TTTGAAAATTTGGCTTGTTACCCTATTACTTAGGGCAATAATATCTATAAACTTCAGTTTGTTAC
195 TTTGAAAATTTGGCTTGTTACCCTATTACTTAGGGCAATAATATCTATAAACTTCAGCTTGTTAC
* * * *
12575502 TCTACTGTTTAGGGGGTTAAAGCTTGGTGGTTTGAATCTGCTTCACTGCATTCGAAGAGGCAAAA
260 CCTACTGCTTAGGGGGTTAAAGCTTGATGGTTTGAATCTACTTCACTGCATTCGAAGAGGCAAAA
12575567 TTCGATGTATCTGATCTGCTCCACTGCAACTTCATGGAGAAAAGACACGTGACTTCAATCAA
325 TTCGATGTATCTGATCTGCTCCACTGCAACTTCATGGAGAAAAGACACGTGACTTCAATCAA
12575629 ATGCTCCTAA
Statistics
Matches: 359, Mismatches: 26, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
388 2 0.01
389 357 0.99
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (389 bp):
CACTAAAACTTCAAGGAAATCTGTTGTGGCTTTTAGTTGCTCCAACGCCATTTCAGGGAGAAGAT
ATTTGATTTTCAACCTGTTACTCTACTGCTTAGAGGGTTAAGGCTTGTCATCAGTGATCTGTTTC
CCTACTGCTTAGGGGTTTAGATCTGTAAACTCAACCTGTTACCCTACTGCTTAGGGGTTTAAGGT
TTGAAAATTTGGCTTGTTACCCTATTACTTAGGGCAATAATATCTATAAACTTCAGCTTGTTACC
CTACTGCTTAGGGGGTTAAAGCTTGATGGTTTGAATCTACTTCACTGCATTCGAAGAGGCAAAAT
TCGATGTATCTGATCTGCTCCACTGCAACTTCATGGAGAAAAGACACGTGACTTCAATCAATTT
Found at i:12576449 original size:86 final size:86
Alignment explanation
Indices: 12576265--12576467 Score: 232
Period size: 86 Copynumber: 2.3 Consensus size: 86
12576255 AAGCAGATTC
* * * *** *
12576265 AACCCCCTAAGTAGTAGGGTAACAAGTTGAAGTTTATAGATATTATTGCCCTAAACAATAGGGTA
1 AACCCCCTAAGCAGTAGGGTAACAGGTTG-AGTTTACAGATATTAAACCCCTAAACAATAGGGAA
**
12576330 ACAAGCCAAATTTTCAAACCTT
65 ACAAGCCAAATTGACAAACCTT
* *
12576352 AAACCCCTAAGCAGTAGGGTAACAGGTTGAGTTTACAGAT-TTAAACCCCTAAACAGTAGGGAAA
1 AACCCCCTAAGCAGTAGGGTAACAGGTTGAGTTTACAGATATTAAACCCCTAAACAATAGGGAAA
* *
12576416 C-AGATC-AATGATGACAAGCCTT
66 CAAG-CCAAAT--TGACAAACCTT
12576438 AACCCCCTAAGCAGTAGGGTAACAGGTTGA
1 AACCCCCTAAGCAGTAGGGTAACAGGTTGA
12576468 AAATCAAATA
Statistics
Matches: 99, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
84 5 0.05
85 21 0.21
86 47 0.47
87 26 0.26
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (86 bp):
AACCCCCTAAGCAGTAGGGTAACAGGTTGAGTTTACAGATATTAAACCCCTAAACAATAGGGAAA
CAAGCCAAATTGACAAACCTT
Found at i:12576981 original size:25 final size:25
Alignment explanation
Indices: 12576953--12577003 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
12576943 TCCTTGTTGG
*
12576953 CCACCAACCTTGGCCACCTACTCCA
1 CCACCAACCTTGGCCACCTACACCA
*
12576978 CCACCCACCTTGGCCACCTACACCA
1 CCACCAACCTTGGCCACCTACACCA
12577003 C
1 C
12577004 TATGCCACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.55, G:0.08, T:0.14
Consensus pattern (25 bp):
CCACCAACCTTGGCCACCTACACCA
Found at i:12577700 original size:3 final size:3
Alignment explanation
Indices: 12577681--12577787 Score: 65
Period size: 3 Copynumber: 35.0 Consensus size: 3
12577671 TTCATATATA
* * * * *
12577681 TAT TA- TAT TGT TGT TAT TAT TAC TAT TAT TAAA TAT TCT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT
* * * * * *
12577726 TAC TAT TAT TTT TAT TCCT T-T TAT TAT TGTT TAT TAT CAA TATT TAT
1 TAT TAT TAT TAT TAT T-AT TAT TAT TAT T-AT TAT TAT TAT TA-T TAT
12577773 TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT
12577788 CTCTTAATTT
Statistics
Matches: 79, Mismatches: 19, Indels: 12
0.72 0.17 0.11
Matches are distributed among these distances:
2 4 0.05
3 67 0.85
4 8 0.10
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:12577843 original size:12 final size:12
Alignment explanation
Indices: 12577828--12577875 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
12577818 TATTTCTCTT
12577828 TTTATATTTATG
1 TTTATATTTATG
12577840 TTTATATTTTATG
1 TTTATA-TTTATG
** *
12577853 TATTATACCTATC
1 T-TTATATTTATG
12577866 TTTATATTTA
1 TTTATATTTA
12577876 CGCATGAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
12 13 0.45
13 11 0.38
14 5 0.17
ACGTcount: A:0.27, C:0.06, G:0.04, T:0.62
Consensus pattern (12 bp):
TTTATATTTATG
Found at i:12577954 original size:35 final size:34
Alignment explanation
Indices: 12577915--12577982 Score: 82
Period size: 35 Copynumber: 2.0 Consensus size: 34
12577905 ATTTTTTTAT
** *
12577915 TATCTTCATTGGCATTTTTACTTATTATCATTTTG
1 TATCTTCATTAACATTATTAC-TATTATCATTTTG
* *
12577950 TATCTTTATTAACATTATTACTATTATTATTTT
1 TATCTTCATTAACATTATTACTATTATCATTTT
12577983 ACTATCATGT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 11 0.39
35 17 0.61
ACGTcount: A:0.25, C:0.12, G:0.04, T:0.59
Consensus pattern (34 bp):
TATCTTCATTAACATTATTACTATTATCATTTTG
Found at i:12590655 original size:13 final size:13
Alignment explanation
Indices: 12590637--12590666 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
12590627 AATGTGAATG
*
12590637 AAAAAATTATATA
1 AAAAAATTATACA
12590650 AAAAAATTATACA
1 AAAAAATTATACA
12590663 AAAA
1 AAAA
12590667 TTAAAAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAAAATTATACA
Found at i:12591730 original size:7 final size:7
Alignment explanation
Indices: 12591718--12591749 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
12591708 ACTCGGACTC
12591718 TTTTTCT
1 TTTTTCT
12591725 TTTTTCT
1 TTTTTCT
12591732 TTTTTCT
1 TTTTTCT
12591739 TTTTT-T
1 TTTTTCT
12591745 TTTTT
1 TTTTT
12591750 AATTTTCACG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (7 bp):
TTTTTCT
Found at i:12591755 original size:20 final size:20
Alignment explanation
Indices: 12591716--12591755 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
12591706 TTACTCGGAC
**
12591716 TCTTTTTCTTTTTTCTTTTT
1 TCTTTTTCTTTTTTAATTTT
*
12591736 TCTTTTTTTTTTTTAATTTT
1 TCTTTTTCTTTTTTAATTTT
12591756 CACGTCTAAC
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:0.05, C:0.10, G:0.00, T:0.85
Consensus pattern (20 bp):
TCTTTTTCTTTTTTAATTTT
Found at i:12601462 original size:22 final size:22
Alignment explanation
Indices: 12601420--12601462 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
12601410 AATACCATTA
* *
12601420 AAATAGTAGCGACATAATAGTG
1 AAATAGTAGCAAAATAATAGTG
*
12601442 AAATAGTAGCAAAATAGTAGT
1 AAATAGTAGCAAAATAATAGT
12601463 TAAAAAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.49, C:0.07, G:0.21, T:0.23
Consensus pattern (22 bp):
AAATAGTAGCAAAATAATAGTG
Found at i:12602686 original size:31 final size:31
Alignment explanation
Indices: 12602628--12602686 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
12602618 CATACTGCTT
*
12602628 AACATTAATCATCAATAATGATGTAAAAAAA
1 AACATTAATCATCAATAATGATCTAAAAAAA
* * *
12602659 AACATTTATCATGAATAATGCTCTAAAA
1 AACATTAATCATCAATAATGATCTAAAA
12602687 TTCACGTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.53, C:0.12, G:0.07, T:0.29
Consensus pattern (31 bp):
AACATTAATCATCAATAATGATCTAAAAAAA
Found at i:12603538 original size:21 final size:22
Alignment explanation
Indices: 12603509--12603552 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
12603499 TAGTGAAATG
*
12603509 ATAGCAAAATAGTGAA-AAAAA
1 ATAGCAAAAAAGTGAAGAAAAA
* *
12603530 ATAGTAAAAAATTGAAGAAAAA
1 ATAGCAAAAAAGTGAAGAAAAA
12603552 A
1 A
12603553 ATGAAGTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.68, C:0.02, G:0.14, T:0.16
Consensus pattern (22 bp):
ATAGCAAAAAAGTGAAGAAAAA
Found at i:12604113 original size:31 final size:31
Alignment explanation
Indices: 12604053--12604113 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
12604043 CATGAATTTG
*
12604053 ACAATTGTTCCAATATTAGGATTTGAACTTA
1 ACAATTGTTCCAATATTAGGATTTAAACTTA
12604084 ACAATTGTT-CACATATTA-GATATTAAACTT
1 ACAATTGTTCCA-ATATTAGGAT-TTAAACTT
12604114 GATAATTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 5 0.19
31 22 0.81
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (31 bp):
ACAATTGTTCCAATATTAGGATTTAAACTTA
Found at i:12610119 original size:11 final size:12
Alignment explanation
Indices: 12610098--12610124 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
12610088 CCAAAACTCT
12610098 AAAATTAAAAAA
1 AAAATTAAAAAA
12610110 AAAATTAAAAAA
1 AAAATTAAAAAA
12610122 AAA
1 AAA
12610125 GTCAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAATTAAAAAA
Found at i:12619598 original size:18 final size:18
Alignment explanation
Indices: 12619575--12619649 Score: 123
Period size: 18 Copynumber: 4.2 Consensus size: 18
12619565 CCCAACTACT
*
12619575 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
12619593 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
12619611 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
* *
12619629 ATATATGTGAATAGTACC
1 GTATACGTGAATAGTACC
12619647 GTA
1 GTA
12619650 AACGATCGTA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 53 1.00
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:12631496 original size:21 final size:20
Alignment explanation
Indices: 12631459--12631497 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12631449 ATAGATTTAT
* *
12631459 AAAAAAACCCAGAAAAACTA
1 AAAAAAAACCAAAAAAACTA
12631479 AAAAAAAACCAAAGAAAAC
1 AAAAAAAACCAAA-AAAAC
12631498 AGAGAACAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.74, C:0.18, G:0.05, T:0.03
Consensus pattern (20 bp):
AAAAAAAACCAAAAAAACTA
Found at i:12632627 original size:18 final size:18
Alignment explanation
Indices: 12632601--12632638 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
12632591 CTTAATATAA
12632601 TTATATTAATAATAAATT
1 TTATATTAATAATAAATT
*
12632619 TTATTTTAATAATAAATT
1 TTATATTAATAATAAATT
12632637 TT
1 TT
12632639 GAAAATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTATATTAATAATAAATT
Found at i:12632647 original size:16 final size:14
Alignment explanation
Indices: 12632621--12632661 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
12632611 AATAAATTTT
12632621 ATTTT-AATAATAA
1 ATTTTAAATAATAA
12632634 ATTTTGAAAATAAT-A
1 ATTTT--AAATAATAA
12632649 ATTTTAAATAATA
1 ATTTTAAATAATA
12632662 TTATTAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
13 12 0.50
15 6 0.25
16 6 0.25
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (14 bp):
ATTTTAAATAATAA
Found at i:12633085 original size:40 final size:40
Alignment explanation
Indices: 12633011--12633086 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
12633001 CAGTACTAAT
* * *
12633011 TATGTGGTGTAATACTAGTAATGCGCTTGGACAATATTAA
1 TATGTGGTGTAATACTAATAATGCACTTGAACAATATTAA
*
12633051 TATGTGGTGTAGTACTAA-ATATGCACTTGAACAATA
1 TATGTGGTGTAATACTAATA-ATGCACTTGAACAATA
12633087 CTATTATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 1 0.03
40 30 0.97
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (40 bp):
TATGTGGTGTAATACTAATAATGCACTTGAACAATATTAA
Found at i:12635334 original size:28 final size:28
Alignment explanation
Indices: 12635293--12635349 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
12635283 AGAGTTTAGA
*
12635293 TGACTGTATTAATATGCTCTTTCAGGCG
1 TGACTGTATGAATATGCTCTTTCAGGCG
*
12635321 TGACTGTATGAATATTCTCTTTCAGGCG
1 TGACTGTATGAATATGCTCTTTCAGGCG
12635349 T
1 T
12635350 TGCAAAGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.40
Consensus pattern (28 bp):
TGACTGTATGAATATGCTCTTTCAGGCG
Found at i:12638543 original size:16 final size:16
Alignment explanation
Indices: 12638521--12638557 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
12638511 ATTATTATAT
12638521 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
12638538 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
12638553 TAATA
1 TAATA
12638558 TTCTTAACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:12638589 original size:14 final size:14
Alignment explanation
Indices: 12638506--12638602 Score: 60
Period size: 13 Copynumber: 7.1 Consensus size: 14
12638496 TAAATAAAAC
* *
12638506 TTAATATTATTATA
1 TTAATATTAATATT
*
12638520 TTAATAATAA-ATT
1 TTAATATTAATATT
* *
12638533 TTAAAAATAATAATT
1 TTAATATTAAT-ATT
12638548 TTAA-A-TAATATT
1 TTAATATTAATATT
* *
12638560 CTTAACA-AAATA-T
1 -TTAATATTAATATT
12638573 TTAATATTAATATT
1 TTAATATTAATATT
*
12638587 TTAATAATAAATATT
1 TTAAT-ATTAATATT
12638602 T
1 T
12638603 ATTACATTAA
Statistics
Matches: 68, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
12 8 0.12
13 24 0.35
14 20 0.29
15 16 0.24
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (14 bp):
TTAATATTAATATT
Found at i:12638601 original size:15 final size:15
Alignment explanation
Indices: 12638520--12638636 Score: 58
Period size: 13 Copynumber: 8.1 Consensus size: 15
12638510 TATTATTATA
12638520 TTAATAAT-AA-ATT
1 TTAATAATAAATATT
*
12638533 TTAAAAAT-AATAATT
1 TTAATAATAAAT-ATT
12638548 TT-A-AAT-AATATT
1 TTAATAATAAATATT
*
12638560 CTTAA-CA-AAATA-T
1 -TTAATAATAAATATT
*
12638573 TTAAT-ATTAATATT
1 TTAATAATAAATATT
12638587 TTAATAATAAATATTT
1 TTAATAATAAATA-TT
*
12638603 ATTACATTAATAAATATA
1 -TTA-A-TAATAAATATT
*
12638621 TTGATAA-AAATATT
1 TTAATAATAAATATT
12638635 TT
1 TT
12638637 GTAGTATAAA
Statistics
Matches: 84, Mismatches: 7, Indels: 25
0.72 0.06 0.22
Matches are distributed among these distances:
12 8 0.10
13 22 0.26
14 21 0.25
15 14 0.17
16 3 0.04
17 5 0.06
18 2 0.02
19 9 0.11
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (15 bp):
TTAATAATAAATATT
Found at i:12638964 original size:19 final size:19
Alignment explanation
Indices: 12638923--12638964 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
12638913 ACAATATTAT
* *
12638923 TATGTGGTGAGCTATTAAT
1 TATGTGGTGAGCTACTAAA
12638942 TATGTGGTGTAG-TACTAAA
1 TATGTGGTG-AGCTACTAAA
12638961 TATG
1 TATG
12638965 CACCTGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.29, C:0.05, G:0.26, T:0.40
Consensus pattern (19 bp):
TATGTGGTGAGCTACTAAA
Found at i:12640596 original size:30 final size:30
Alignment explanation
Indices: 12640562--12640623 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
12640552 CTTAACAAGT
12640562 AAATGCCTCTAAAATAATAACAAAATTAAC
1 AAATGCCTCTAAAATAATAACAAAATTAAC
* *
12640592 AAATGCCTTTGAAATAATAACAAAATTAAC
1 AAATGCCTCTAAAATAATAACAAAATTAAC
12640622 AA
1 AA
12640624 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.56, C:0.15, G:0.05, T:0.24
Consensus pattern (30 bp):
AAATGCCTCTAAAATAATAACAAAATTAAC
Found at i:12640671 original size:14 final size:14
Alignment explanation
Indices: 12640648--12640684 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
12640638 TACAATATCC
*
12640648 AAATAATAACAATA
1 AAATAGTAACAATA
*
12640662 AAATGGTAACAATA
1 AAATAGTAACAATA
12640676 AAATAGTAA
1 AAATAGTAA
12640685 AAGGGTAGCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.65, C:0.05, G:0.08, T:0.22
Consensus pattern (14 bp):
AAATAGTAACAATA
Found at i:12643191 original size:11 final size:11
Alignment explanation
Indices: 12643175--12643215 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
12643165 CACAAATGAG
*
12643175 AAAAAAGGAAA
1 AAAAAAAGAAA
*
12643186 AAAAAAAAAAA
1 AAAAAAAGAAA
12643197 AAAAAAAGAAA
1 AAAAAAAGAAA
12643208 AGAAAAAA
1 A-AAAAAA
12643216 CAATTAGTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
11 20 0.77
12 6 0.23
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:12649241 original size:57 final size:58
Alignment explanation
Indices: 12649172--12649280 Score: 152
Period size: 58 Copynumber: 1.9 Consensus size: 58
12649162 TTTTGGGACT
* *
12649172 TGAATTTTACAATTA-TTTTAAATT-GAGGCTTGAACTTT-TTTATTTCAAGTTAGTCTC
1 TGAATTTAACAATTATTTTTAAATTAG-GGCTTGAACTTTATTT-GTTCAAGTTAGTCTC
*
12649229 TGAATTTAACAATTATTTTTACATTAGGGCTTGAACTTTATTTGTTCAAGTT
1 TGAATTTAACAATTATTTTTAAATTAGGGCTTGAACTTTATTTGTTCAAGTT
12649281 GTTCCTTAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
57 14 0.30
58 28 0.61
59 4 0.09
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.49
Consensus pattern (58 bp):
TGAATTTAACAATTATTTTTAAATTAGGGCTTGAACTTTATTTGTTCAAGTTAGTCTC
Found at i:12649661 original size:20 final size:20
Alignment explanation
Indices: 12649636--12649687 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
12649626 TGCATAGTAT
*
12649636 TTTAT-ATTGATTTGATTATA
1 TTTATAATT-ATTTGAATATA
12649656 TTTATAATTATTTGAATATA
1 TTTATAATTATTTGAATATA
*
12649676 TATTATGATTAT
1 T-TTATAATTAT
12649688 ATTTGTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (20 bp):
TTTATAATTATTTGAATATA
Found at i:12651586 original size:14 final size:14
Alignment explanation
Indices: 12651547--12651588 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
12651537 TATATATAGT
*
12651547 AAATAAAGAAAGAA
1 AAATAAAGAAACAA
*
12651561 AAAGAAAGGAAACAA
1 AAATAAA-GAAACAA
12651576 AAATAAAGAAACA
1 AAATAAAGAAACA
12651589 GAAACGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.76, C:0.05, G:0.14, T:0.05
Consensus pattern (14 bp):
AAATAAAGAAACAA
Found at i:12652291 original size:51 final size:51
Alignment explanation
Indices: 12652215--12652354 Score: 157
Period size: 45 Copynumber: 2.9 Consensus size: 51
12652205 TTACTGATTA
** * *
12652215 GGCACTTTGTGTGTCGTTTACTGTTACTGCTACTGTTACTGTTATCTATTC
1 GGCACTTTGTGTGTCGAATAATGTTACTGCTACTGTTACTGTTATCAATTC
* * *
12652266 GGCACTTTATGTGTCGAATATTGTTA---CTA---TTACTATTATCAATTC
1 GGCACTTTGTGTGTCGAATAATGTTACTGCTACTGTTACTGTTATCAATTC
* *
12652311 GGCACTTTGTGTGTCGAATAATGTTACTGTTACTGCTACTGTTA
1 GGCACTTTGTGTGTCGAATAATGTTACTGCTACTGTTACTGTTA
12652355 CTGATTATTG
Statistics
Matches: 72, Mismatches: 11, Indels: 12
0.76 0.12 0.13
Matches are distributed among these distances:
45 38 0.53
48 5 0.07
51 29 0.40
ACGTcount: A:0.20, C:0.17, G:0.19, T:0.44
Consensus pattern (51 bp):
GGCACTTTGTGTGTCGAATAATGTTACTGCTACTGTTACTGTTATCAATTC
Found at i:12652603 original size:29 final size:30
Alignment explanation
Indices: 12652558--12652625 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
12652548 GTGGCCAAGA
* * * *
12652558 GTAAATACTCAAAATTTGAGGGATTAA-GGT
1 GTAAATA-TAAAAATTTGAAGGAATAATAGT
12652588 GTAAATATAAAAATTTGAAGGAATAATAGT
1 GTAAATATAAAAATTTGAAGGAATAATAGT
12652618 GTAAATAT
1 GTAAATAT
12652626 TTTAAGGGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.47, C:0.03, G:0.19, T:0.31
Consensus pattern (30 bp):
GTAAATATAAAAATTTGAAGGAATAATAGT
Found at i:12660769 original size:14 final size:14
Alignment explanation
Indices: 12660750--12660779 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12660740 TATCTTATAA
12660750 ATATGCGTGAATCT
1 ATATGCGTGAATCT
*
12660764 ATATGCGTTAATCT
1 ATATGCGTGAATCT
12660778 AT
1 AT
12660780 CTTCAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (14 bp):
ATATGCGTGAATCT
Found at i:12668476 original size:18 final size:18
Alignment explanation
Indices: 12668453--12668548 Score: 120
Period size: 18 Copynumber: 5.3 Consensus size: 18
12668443 TAAATAAAGG
12668453 TACTGAATAAATGATTAT
1 TACTGAATAAATGATTAT
* * *
12668471 TACTGAATAATTGACTGT
1 TACTGAATAAATGATTAT
* *
12668489 TACTGAATAAATGACTGT
1 TACTGAATAAATGATTAT
*
12668507 TACTAAATAAATGATTAT
1 TACTGAATAAATGATTAT
* *
12668525 TACTGAATAACTGATTAA
1 TACTGAATAAATGATTAT
12668543 TACTGA
1 TACTGA
12668549 TGACTGACTG
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.36
Consensus pattern (18 bp):
TACTGAATAAATGATTAT
Found at i:12668493 original size:36 final size:36
Alignment explanation
Indices: 12668453--12668566 Score: 122
Period size: 36 Copynumber: 3.2 Consensus size: 36
12668443 TAAATAAAGG
*
12668453 TACTGAATAAATGATTATTACTGAATAATTGACTGT
1 TACTGAATAAATGATTATTACTGAATAAATGACTGT
* * * * *
12668489 TACTGAATAAATGACTGTTACTAAATAAATGATTAT
1 TACTGAATAAATGATTATTACTGAATAAATGACTGT
* * * * *
12668525 TACTGAATAACTGATTAATACTG-ATGACTGACTGA
1 TACTGAATAAATGATTATTACTGAATAAATGACTGT
12668560 TACTGAA
1 TACTGAA
12668567 CAATAAAGAT
Statistics
Matches: 62, Mismatches: 16, Indels: 1
0.78 0.20 0.01
Matches are distributed among these distances:
35 14 0.23
36 48 0.77
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (36 bp):
TACTGAATAAATGATTATTACTGAATAAATGACTGT
Found at i:12669316 original size:25 final size:25
Alignment explanation
Indices: 12669282--12669332 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
12669272 CCGTAATCCT
12669282 GTTCTAGGGATAGATAAGGGTTAGA
1 GTTCTAGGGATAGATAAGGGTTAGA
12669307 GTTCTAGGGATAGATAAGGGTTAGA
1 GTTCTAGGGATAGATAAGGGTTAGA
12669332 G
1 G
12669333 GTGTTACAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.04, G:0.37, T:0.27
Consensus pattern (25 bp):
GTTCTAGGGATAGATAAGGGTTAGA
Found at i:12676033 original size:14 final size:14
Alignment explanation
Indices: 12675999--12676044 Score: 58
Period size: 13 Copynumber: 3.1 Consensus size: 14
12675989 ATTACTTATG
12675999 AAAAATAATATTTCAAT
1 AAAAATAATATTT---T
12676016 AAAAATAA-ATTTT
1 AAAAATAATATTTT
12676029 AAAAATAATATTTT
1 AAAAATAATATTTT
12676043 AA
1 AA
12676045 TCTAAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
13 9 0.32
14 7 0.25
16 4 0.14
17 8 0.29
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (14 bp):
AAAAATAATATTTT
Found at i:12676513 original size:17 final size:18
Alignment explanation
Indices: 12676491--12676530 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
12676481 TAATTTTTCA
**
12676491 TTTATTATTTTATT-TAT
1 TTTATTATAATATTATAT
12676508 TTTATTATAATATTATAT
1 TTTATTATAATATTATAT
12676526 TTTAT
1 TTTAT
12676531 AGGTGATGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTATTATAATATTATAT
Found at i:12676814 original size:29 final size:30
Alignment explanation
Indices: 12676777--12676836 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
12676767 GTATATTTAC
* *
12676777 AATTTAATTTTTATATTTTT-ATTTTTAAA
1 AATTTAATTTCTATATTTTTAAATTTTAAA
*
12676806 AATTTAATTTCTCTATTTTTAAATTTTAAA
1 AATTTAATTTCTATATTTTTAAATTTTAAA
12676836 A
1 A
12676837 TTTCAAATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (30 bp):
AATTTAATTTCTATATTTTTAAATTTTAAA
Found at i:12676837 original size:29 final size:28
Alignment explanation
Indices: 12676772--12676839 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 28
12676762 TATTTGTATA
* * *
12676772 TTTACAATTTAATTTTTATATTTTTATT
1 TTTAAAATTTAATTTCTATATTTTTAAT
*
12676800 TTTAAAAATTTAATTTCTCTATTTTTAAAT
1 TTT-AAAATTTAATTTCTATATTTTT-AAT
12676830 TTTAAAATTT
1 TTTAAAATTT
12676840 CAAATCTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 3 0.09
29 26 0.76
30 5 0.15
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (28 bp):
TTTAAAATTTAATTTCTATATTTTTAAT
Found at i:12677948 original size:31 final size:31
Alignment explanation
Indices: 12677891--12677954 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
12677881 CGATTCAGAA
*
12677891 AATATAAAAATAAAATATTTGAAATATT-TT
1 AATATAAAAATAAAATATTAGAAATATTATT
*
12677921 AATATAAAAATAATCATATTA-AGAATATTATT
1 AATATAAAAATAA-AATATTAGA-AATATTATT
12677953 AA
1 AA
12677955 ATTATATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 14 0.48
31 11 0.38
32 4 0.14
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.38
Consensus pattern (31 bp):
AATATAAAAATAAAATATTAGAAATATTATT
Found at i:12677972 original size:38 final size:39
Alignment explanation
Indices: 12677929--12678022 Score: 129
Period size: 41 Copynumber: 2.4 Consensus size: 39
12677919 TTAATATAAA
12677929 AATAATCATATTAAGA-A-TATTATTAAATTATATTTAAT
1 AATAATCATATTAA-ATATTATTATTAAATTATATTTAAT
*
12677967 AATAATTATATTAAATTATTTATTATTAAATTATATTTAAT
1 AATAATCATATTAAA-TA-TTATTATTAAATTATATTTAAT
*
12678008 AATAATCCTATTAAA
1 AATAATCATATTAAA
12678023 ATTTAATAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
37 1 0.02
38 13 0.27
39 1 0.02
41 34 0.69
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (39 bp):
AATAATCATATTAAATATTATTATTAAATTATATTTAAT
Found at i:12681167 original size:20 final size:20
Alignment explanation
Indices: 12681129--12681195 Score: 66
Period size: 20 Copynumber: 3.3 Consensus size: 20
12681119 TTCTTTATAT
*
12681129 ATTTTTATATATATTTTTTGAA
1 ATTTTTATA-A-ATATTTTGAA
12681151 ATTTTTATAAATATTTTGAA
1 ATTTTTATAAATATTTTGAA
* *
12681171 AATTTGA-AAATTATTTTG-A
1 ATTTTTATAAA-TATTTTGAA
12681190 ATTTTT
1 ATTTTT
12681196 TTTTTTGTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
19 8 0.21
20 21 0.54
21 1 0.03
22 9 0.23
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (20 bp):
ATTTTTATAAATATTTTGAA
Found at i:12682298 original size:21 final size:21
Alignment explanation
Indices: 12682251--12682322 Score: 65
Period size: 21 Copynumber: 3.2 Consensus size: 21
12682241 TAAGATGATT
12682251 ATTAAATTGTATAAAAAATAAA
1 ATTAAATT-TATAAAAAATAAA
* *
12682273 TTTAAATTTAT-AAATATCAAA
1 ATTAAATTTATAAAAAAT-AAA
12682294 ATTAAATTTGACTTAAAATAATAAA
1 ATTAAATTT-A--TAAAA-AATAAA
12682319 ATTA
1 ATTA
12682323 TAATGCATTG
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
20 5 0.12
21 14 0.35
22 8 0.20
24 1 0.03
25 10 0.25
26 2 0.05
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (21 bp):
ATTAAATTTATAAAAAATAAA
Found at i:12685024 original size:12 final size:12
Alignment explanation
Indices: 12685007--12685031 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12684997 GCTGACTACT
12685007 GTTACTGTTACC
1 GTTACTGTTACC
12685019 GTTACTGTTACC
1 GTTACTGTTACC
12685031 G
1 G
12685032 ATTCGGCACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (12 bp):
GTTACTGTTACC
Found at i:12685386 original size:18 final size:18
Alignment explanation
Indices: 12685333--12685388 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
12685323 ATAACCGATC
* *
12685333 AATTGATTGATACTGAGT
1 AATTGATTGTTACTGAAT
* * *
12685351 AACTGATTATTATTGAAT
1 AATTGATTGTTACTGAAT
*
12685369 AATTGATTGTTACCGAAT
1 AATTGATTGTTACTGAAT
12685387 AA
1 AA
12685389 CTAACTGTTA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.39
Consensus pattern (18 bp):
AATTGATTGTTACTGAAT
Found at i:12686290 original size:69 final size:69
Alignment explanation
Indices: 12686180--12686847 Score: 495
Period size: 69 Copynumber: 9.7 Consensus size: 69
12686170 AATCAACTAA
* * * * * * * *
12686180 CCTTTATAATATAAGTTGAGAACGTAGGCCCGCGA-CTTGTTTTGGAGGTTACGGTATTAAACCG
1 CCTTTATAATATCAGCTGGGAACGTAGGTCCGCGAGC-TGTTTTGGAGGCTGCGATCTTAAACCG
*
12686244 TCTAG
65 TCGAG
* * * * * * * *
12686249 CTTTTATAATATCAGCTGGGAACATAGGTCTGCGAGCTGTTTTGGAGACTGTGATCTTAATCTGG
1 CCTTTATAATATCAGCTGGGAACGTAGGTCCGCGAGCTGTTTTGGAGGCTGCGATCTTAAACCGT
*
12686314 CAAG
66 CGAG
* * * * * * * * * * *
12686318 CCTTTACAATATTAGCTAGGAACATAGGTTCGTGAGTTGTTTTGAAGGCTACGATCTTAATTCGG
1 CCTTTATAATATCAGCTGGGAACGTAGGTCCGCGAGCTGTTTTGGAGGCTGCGATCTTAA-ACCG
12686383 T-GAG
65 TCGAG
* * * * * * ** * * *
12686387 CCTTTACAATATCAGCTGAGAGCATAGGTCCACAAGCTACTTAGGAGGCTGTGATCTTAAACTAG
1 CCTTTATAATATCAGCTGGGAACGTAGGTCCGCGAGCTGTTTTGGAGGCTGCGATCTTAAAC-CG
12686452 -CGAG
65 TCGAG
* * * * * *
12686456 CCTTTACAATATCAGCTGGGAACGTAGGTCCACGAGCTATTTTGGAGGCTGTGATCTTAAATCTT
1 CCTTTATAATATCAGCTGGGAACGTAGGTCCGCGAGCTGTTTTGGAGGCTGCGATCTTAAACCGT
12686521 CGA-
66 CGAG
* * ** ** * * * *
12686524 ACTGTTATAATATCAGTTGGGAATATAGGTTTGCGAGTTGTTTTGGAGGATGCGATCTTAGATCG
1 CCT-TTATAATATCAGCTGGGAACGTAGGTCCGCGAGCTGTTTTGGAGGCTGCGATCTTA-AACC
12686589 GT-GAG
64 GTCGAG
* * * *
12686594 CCTTTATAATATCAGCTAGGAGCGTAGGTCCGCGAGCTGTTTTGGAGGCTAC-AGTCTTAAACTA
1 CCTTTATAATATCAGCTGGGAACGTAGGTCCGCGAGCTGTTTTGGAGGCTGCGA-TCTTAAAC-C
12686658 G-CGAG
64 GTCGAG
* ** * * * * * *
12686663 CCTTTATAATATCAGCAGGGAACGTAGGTCCATGAGCTATTTTGGAGCCTGCAATATTAAATCGG
1 CCTTTATAATATCAGCTGGGAACGTAGGTCCGCGAGCTGTTTTGGAGGCTGCGATCTTAAACCGT
12686728 CGAG
66 CGAG
* * * * * * * *
12686732 CCTTTATAATATCAACTAGGAACTTAGGTCCGCGAGTTGTCTAGGAGGTTGCGATCTTAAACCGG
1 CCTTTATAATATCAGCTGGGAACGTAGGTCCGCGAGCTGTTTTGGAGGCTGCGATCTTAAACCGT
12686797 CGAG
66 CGAG
** * *
12686801 TTTTTATAATATCAACTGGGAACGTAGGTTCGCGAGCTGTTTTGGAG
1 CCTTTATAATATCAGCTGGGAACGTAGGTCCGCGAGCTGTTTTGGAG
12686848 TTGAAAACTT
Statistics
Matches: 465, Mismatches: 121, Indels: 26
0.76 0.20 0.04
Matches are distributed among these distances:
68 7 0.02
69 449 0.97
70 9 0.02
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (69 bp):
CCTTTATAATATCAGCTGGGAACGTAGGTCCGCGAGCTGTTTTGGAGGCTGCGATCTTAAACCGT
CGAG
Found at i:12686787 original size:207 final size:206
Alignment explanation
Indices: 12686180--12686847 Score: 675
Period size: 207 Copynumber: 3.2 Consensus size: 206
12686170 AATCAACTAA
* * * * * * *
12686180 CCTTTATAATATAAGTTGAGAACGTAGGCCCGCGA-CTTGTTTTGGAGGTTACGGTATTAAAC-C
1 CCTTTATAATATCAGCTGAGAACGTAGGTCCGCGAGC-TGTTTTGGAGGCTACAGTCTTAAACTA
* * * ** *
12686243 GTCTAGCTTTTATAATATCAGCTGGGAACATAGGTCTGCGAGCTGTTTTGGAGACTGTGATCTT-
65 G-CGAGCCTTTATAATATCAGCTGGGAACGTAGGTCCACGAGCTATTTTGGAGACTGTGATCTTA
* * * * * * * *
12686307 AATCTGGCAAGCCTTTACAATATTAGCTAGGAACATAGGTTCGTGAGTTGTTTTGAAGGCTACGA
129 AATC-GGCGAGCCTTTATAATATCAGCTAGGAACTTAGGTTCGCGAGTTGTTTTGGAGGATGCGA
12686372 TCTTAATTCGGTGAG
193 TCTTAA-TCGGTGAG
* * * * * ** * **
12686387 CCTTTACAATATCAGCTGAGAGCATAGGTCCACAAGCTACTTAGGAGGCT-GTGATCTTAAACTA
1 CCTTTATAATATCAGCTGAGAACGTAGGTCCGCGAGCTGTTTTGGAGGCTACAG-TCTTAAACTA
* *
12686451 GCGAGCCTTTACAATATCAGCTGGGAACGTAGGTCCACGAGCTATTTTGGAGGCTGTGATCTTAA
65 GCGAGCCTTTATAATATCAGCTGGGAACGTAGGTCCACGAGCTATTTTGGAGACTGTGATCTTAA
** * * * *
12686516 ATCTTCGA-ACTGTTATAATATCAGTTGGGAA-TATAGGTTTGCGAGTTGTTTTGGAGGATGCGA
130 ATCGGCGAGCCT-TTATAATATCAGCTAGGAACT-TAGGTTCGCGAGTTGTTTTGGAGGATGCGA
12686579 TCTTAGATCGGTGAG
193 TCTTA-ATCGGTGAG
*
12686594 CCTTTATAATATCAGCT-AGGAGCGTAGGTCCGCGAGCTGTTTTGGAGGCTACAGTCTTAAACTA
1 CCTTTATAATATCAGCTGA-GAACGTAGGTCCGCGAGCTGTTTTGGAGGCTACAGTCTTAAACTA
* * * ** *
12686658 GCGAGCCTTTATAATATCAGCAGGGAACGTAGGTCCATGAGCTATTTTGGAGCCTGCAATATTAA
65 GCGAGCCTTTATAATATCAGCTGGGAACGTAGGTCCACGAGCTATTTTGGAGACTGTGATCTTAA
* * * * *
12686723 ATCGGCGAGCCTTTATAATATCAACTAGGAACTTAGGTCCGCGAGTTGTCTAGGAGGTTGCGATC
130 ATCGGCGAGCCTTTATAATATCAGCTAGGAACTTAGGTTCGCGAGTTGTTTTGGAGGATGCGATC
* *
12686788 TTAAACCGGCGAG
195 TT-AATCGGTGAG
** * * *
12686801 TTTTTATAATATCAACTGGGAACGTAGGTTCGCGAGCTGTTTTGGAG
1 CCTTTATAATATCAGCTGAGAACGTAGGTCCGCGAGCTGTTTTGGAG
12686848 TTGAAAACTT
Statistics
Matches: 375, Mismatches: 73, Indels: 26
0.79 0.15 0.05
Matches are distributed among these distances:
206 4 0.01
207 359 0.96
208 12 0.03
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (206 bp):
CCTTTATAATATCAGCTGAGAACGTAGGTCCGCGAGCTGTTTTGGAGGCTACAGTCTTAAACTAG
CGAGCCTTTATAATATCAGCTGGGAACGTAGGTCCACGAGCTATTTTGGAGACTGTGATCTTAAA
TCGGCGAGCCTTTATAATATCAGCTAGGAACTTAGGTTCGCGAGTTGTTTTGGAGGATGCGATCT
TAATCGGTGAG
Found at i:12688140 original size:22 final size:21
Alignment explanation
Indices: 12688098--12688151 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
12688088 CACATTGAAA
*
12688098 ATATAAAAAATTGAAATAAAT
1 ATATAAAAAATTCAAATAAAT
12688119 ATATAAAAAAATTCAGAA-AAAT
1 ATAT-AAAAAATTCA-AATAAAT
* *
12688141 ATTTATAAAAT
1 ATATAAAAAAT
12688152 CTAAACATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 10 0.36
22 16 0.57
23 2 0.07
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (21 bp):
ATATAAAAAATTCAAATAAAT
Found at i:12705127 original size:26 final size:29
Alignment explanation
Indices: 12705053--12705129 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 29
12705043 AATCCAGAGA
12705053 AAAAAAATACCATACATAAAGAGTATGGTAT
1 AAAAAAATACCATACAT-AAGAG-ATGGTAT
** * *
12705084 AAATAAAATAGTAAACATAATA-AT-GT-T
1 AAA-AAAATACCATACATAAGAGATGGTAT
12705111 AAAAAAATACCATACATAA
1 AAAAAAATACCATACATAA
12705130 AGAGTATATA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
26 13 0.34
27 4 0.11
28 2 0.05
29 2 0.05
31 6 0.16
32 11 0.29
ACGTcount: A:0.60, C:0.09, G:0.08, T:0.23
Consensus pattern (29 bp):
AAAAAAATACCATACATAAGAGATGGTAT
Found at i:12705203 original size:3 final size:3
Alignment explanation
Indices: 12705195--12705284 Score: 73
Period size: 3 Copynumber: 30.0 Consensus size: 3
12705185 AATAGTAAAT
* *
12705195 ATA ATA ATA ATA ATA ATA A-A ATT A-A AT- ATA GT- ATAA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA
*
12705237 TATA CATA A-A AGTA ATA ATA ATA AGTA ACA ATA ATA ATA ATA ATA ATA
1 -ATA -ATA ATA A-TA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA
12705285 TAAAAATTCA
Statistics
Matches: 71, Mismatches: 7, Indels: 18
0.74 0.07 0.19
Matches are distributed among these distances:
2 8 0.11
3 50 0.70
4 13 0.18
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:12705401 original size:12 final size:13
Alignment explanation
Indices: 12705372--12705400 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
12705362 TATATATACC
12705372 TTTTAAATATTTT
1 TTTTAAATATTTT
12705385 TTTTAAATATTTT
1 TTTTAAATATTTT
12705398 TTT
1 TTT
12705401 ATATTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTAAATATTTT
Found at i:12710604 original size:56 final size:56
Alignment explanation
Indices: 12710537--12710648 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
12710527 TTCGGGGGAA
12710537 GACGTGATTTTTGACTCTGAAAACATAAAATATAGCATTAATCATCGAAGTCTTTT
1 GACGTGATTTTTGACTCTGAAAACATAAAATATAGCATTAATCATCGAAGTCTTTT
12710593 GACGTGATTTTTGACTCTGAAAACATAAAATATAGCATTAATCATCGAAGTCTTTT
1 GACGTGATTTTTGACTCTGAAAACATAAAATATAGCATTAATCATCGAAGTCTTTT
12710649 TTTACTTTAG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (56 bp):
GACGTGATTTTTGACTCTGAAAACATAAAATATAGCATTAATCATCGAAGTCTTTT
Found at i:12711100 original size:12 final size:12
Alignment explanation
Indices: 12711083--12711108 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12711073 TCTTATCTTT
12711083 AAAAAAACAAAA
1 AAAAAAACAAAA
12711095 AAAAAAACAAAA
1 AAAAAAACAAAA
12711107 AA
1 AA
12711109 GCACAAACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAACAAAA
Found at i:12715494 original size:15 final size:16
Alignment explanation
Indices: 12715474--12715525 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 16
12715464 TCTATTTACA
*
12715474 TATTTTATTCTTT-TT
1 TATTTTATTATTTATT
12715489 TATTTTATTATTTCATT
1 TATTTTATTATTT-ATT
** *
12715506 TATTTTCCTATTTATA
1 TATTTTATTATTTATT
12715522 TATT
1 TATT
12715526 GACCAATCAC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
15 12 0.39
16 6 0.19
17 13 0.42
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.71
Consensus pattern (16 bp):
TATTTTATTATTTATT
Found at i:12715983 original size:25 final size:26
Alignment explanation
Indices: 12715955--12716005 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
12715945 ATTTTTTTTT
*
12715955 TTTTTTATTTA-CATT-ATTATTATTA
1 TTTTTTA-TTACCATTAATTATCATTA
12715980 TTTTTTATTACCATTAATTATCATTA
1 TTTTTTATTACCATTAATTATCATTA
12716006 CTACTACTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 3 0.13
25 11 0.48
26 9 0.39
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (26 bp):
TTTTTTATTACCATTAATTATCATTA
Found at i:12716129 original size:3 final size:3
Alignment explanation
Indices: 12716121--12716232 Score: 95
Period size: 3 Copynumber: 37.7 Consensus size: 3
12716111 AGTATTTTCC
* * * * *
12716121 ATT ATT ATT ATT AAT ATC ACT ACT ATC ATT ATT ATT ATT ATT A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
** * * *
12716168 ACG A-T ACCTT TTT ATT ATT ATT ACT ATT -GT ATT ATT ATT ATT ATT
1 ATT ATT A--TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12716213 ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT AT
12716233 ATTTCCCTTT
Statistics
Matches: 87, Mismatches: 17, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
2 4 0.05
3 82 0.94
5 1 0.01
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:12716328 original size:20 final size:21
Alignment explanation
Indices: 12716303--12716365 Score: 56
Period size: 26 Copynumber: 2.8 Consensus size: 21
12716293 TATTTTAGCA
12716303 CATTTATTTTATTTATTT-AT
1 CATTTATTTTATTTATTTCAT
12716323 CATTTACTCTCATTATTATTATTTCAT
1 CATTTA-T-T--TTA-T-TTATTTCAT
*
12716350 CATCTATTTTATTTAT
1 CATTTATTTTATTTAT
12716366 AGTTTTTCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 13
0.71 0.02 0.27
Matches are distributed among these distances:
20 6 0.17
21 5 0.14
22 2 0.06
23 3 0.09
24 3 0.09
25 2 0.06
26 7 0.20
27 7 0.20
ACGTcount: A:0.25, C:0.13, G:0.00, T:0.62
Consensus pattern (21 bp):
CATTTATTTTATTTATTTCAT
Found at i:12718679 original size:20 final size:18
Alignment explanation
Indices: 12718656--12718699 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
12718646 AATTTTAAAA
12718656 ATATAAAAAATAATTTATTT
1 ATATAAAAAAT-ATTT-TTT
*
12718676 ATATATAAAATATTTTTT
1 ATATAAAAAATATTTTTT
*
12718694 AAATAA
1 ATATAA
12718700 TTTTAATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 7 0.33
19 4 0.19
20 10 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATATAAAAAATATTTTTT
Found at i:12718740 original size:29 final size:27
Alignment explanation
Indices: 12718686--12718752 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 27
12718676 ATATATAAAA
*
12718686 TATTTTTTAAATAATTTTAATTTTTTT
1 TATTTTTTAAATAATTTTAATATTTTT
12718713 TATTTTTTAAA-AATAGTTTATATATTTTT
1 TATTTTTTAAATAAT--TTTA-ATATTTTT
12718742 TAATTTTTTAA
1 T-ATTTTTTAA
12718753 GATTTAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
26 3 0.09
27 11 0.31
28 4 0.11
29 8 0.23
30 9 0.26
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (27 bp):
TATTTTTTAAATAATTTTAATATTTTT
Found at i:12718748 original size:30 final size:27
Alignment explanation
Indices: 12718687--12718752 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 27
12718677 TATATAAAAT
*
12718687 ATTTTTTAAATAATTTTAATTTTTTTT
1 ATTTTTTAAATAATTTTAATTTTTTTA
12718714 ATTTTTTAAA-AATAGTTTATATATTTTTTA
1 ATTTTTTAAATAAT--TTTA-AT-TTTTTTA
12718744 ATTTTTTAA
1 ATTTTTTAA
12718753 GATTTAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
26 3 0.09
27 10 0.29
28 4 0.12
29 2 0.06
30 15 0.44
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (27 bp):
ATTTTTTAAATAATTTTAATTTTTTTA
Found at i:12718880 original size:22 final size:23
Alignment explanation
Indices: 12718839--12718881 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
12718829 ATTTTACAAA
**
12718839 AAAAAAATACAAATTTAAATATT
1 AAAAAAATACAAATAAAAATATT
12718862 AAAAAAATA-AAATAAAAATA
1 AAAAAAATACAAATAAAAATA
12718882 AAAATATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (23 bp):
AAAAAAATACAAATAAAAATATT
Found at i:12718886 original size:28 final size:26
Alignment explanation
Indices: 12718836--12718892 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 26
12718826 ATTATTTTAC
* **
12718836 AAAAAAAAAATACAAATTTAAATATTA
1 AAAAAAAAAATAAAAATAAAAATA-TA
12718863 AAAAAATAAAATAAAAATAAAAATATA
1 AAAAAA-AAAATAAAAATAAAAATATA
12718890 AAA
1 AAA
12718893 TGATTCTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 11 0.42
28 15 0.58
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (26 bp):
AAAAAAAAAATAAAAATAAAAATATA
Found at i:12721797 original size:62 final size:62
Alignment explanation
Indices: 12721700--12721825 Score: 243
Period size: 62 Copynumber: 2.0 Consensus size: 62
12721690 AACTCAGTCC
12721700 CATCAACACAACAAAGACTTGTTTTTTTTCAATTCCCATATCTTTTTTCAATGAACCAAATT
1 CATCAACACAACAAAGACTTGTTTTTTTTCAATTCCCATATCTTTTTTCAATGAACCAAATT
*
12721762 CATCAACACAACAAAGACTTGTTTTTTTTCAATTCCCATATCTTTTTTCAATTAACCAAATT
1 CATCAACACAACAAAGACTTGTTTTTTTTCAATTCCCATATCTTTTTTCAATGAACCAAATT
12721824 CA
1 CA
12721826 ACTAAGTTCA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.34, C:0.23, G:0.04, T:0.39
Consensus pattern (62 bp):
CATCAACACAACAAAGACTTGTTTTTTTTCAATTCCCATATCTTTTTTCAATGAACCAAATT
Found at i:12722259 original size:24 final size:25
Alignment explanation
Indices: 12722221--12722270 Score: 93
Period size: 24 Copynumber: 2.0 Consensus size: 25
12722211 GGAGAAACGG
12722221 CCATGTTTTTTTTTTCTTCAATTCC
1 CCATGTTTTTTTTTTCTTCAATTCC
12722246 CCATG-TTTTTTTTTCTTCAATTCC
1 CCATGTTTTTTTTTTCTTCAATTCC
12722270 C
1 C
12722271 ATTATCAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 20 0.80
25 5 0.20
ACGTcount: A:0.12, C:0.26, G:0.04, T:0.58
Consensus pattern (25 bp):
CCATGTTTTTTTTTTCTTCAATTCC
Found at i:12723546 original size:18 final size:18
Alignment explanation
Indices: 12723509--12723551 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
12723499 TTTTGTGAAC
* *
12723509 TTTTTAAATTTTGTTGAT
1 TTTTTAAATATTATTGAT
*
12723527 TTTTTAAATATTATTTAT
1 TTTTTAAATATTATTGAT
12723545 TTATTTA
1 TT-TTTA
12723552 TTTTGAACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (18 bp):
TTTTTAAATATTATTGAT
Found at i:12725493 original size:18 final size:18
Alignment explanation
Indices: 12725470--12725507 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
12725460 ACAGCCTAAG
12725470 CATTATAAGTCTAAGATA
1 CATTATAAGTCTAAGATA
*
12725488 CATTATAAGTCTAATATA
1 CATTATAAGTCTAAGATA
12725506 CA
1 CA
12725508 AAATACATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.08, T:0.34
Consensus pattern (18 bp):
CATTATAAGTCTAAGATA
Found at i:12727590 original size:21 final size:20
Alignment explanation
Indices: 12727562--12727600 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
12727552 CAAAACTTGT
12727562 ATAACTATCATCAAACATTC
1 ATAACTATCATCAAACATTC
*
12727582 ATAATCTATCATTAAACAT
1 ATAA-CTATCATCAAACAT
12727601 AAAAATACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAACTATCATCAAACATTC
Found at i:12730010 original size:19 final size:19
Alignment explanation
Indices: 12729983--12730028 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
12729973 TAAATTGATG
12729983 CCAATACCAGGTAGAGATA
1 CCAATACCAGGTAGAGATA
*
12730002 CCGATACCAGGTAGAGATA
1 CCAATACCAGGTAGAGATA
12730021 CCAATACC
1 CCAATACC
12730029 TTATATAGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.15
Consensus pattern (19 bp):
CCAATACCAGGTAGAGATA
Found at i:12735579 original size:37 final size:36
Alignment explanation
Indices: 12735510--12735588 Score: 104
Period size: 37 Copynumber: 2.2 Consensus size: 36
12735500 CGTATTATCA
* *
12735510 GTTGGATTAGCTCTCATGAGCAATTGGCGTGTTATTG
1 GTTGGATTAGCTCTCATGAGCAATTGGAGTGTT-TCG
* **
12735547 GTTGGATTAGCTCTTATGAGCTTTTGGAGTGTTTCG
1 GTTGGATTAGCTCTCATGAGCAATTGGAGTGTTTCG
12735583 GTTGGA
1 GTTGGA
12735589 CTACTTGTGT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 8 0.22
37 29 0.78
ACGTcount: A:0.16, C:0.11, G:0.32, T:0.41
Consensus pattern (36 bp):
GTTGGATTAGCTCTCATGAGCAATTGGAGTGTTTCG
Found at i:12749054 original size:3 final size:3
Alignment explanation
Indices: 12749046--12749083 Score: 58
Period size: 3 Copynumber: 12.0 Consensus size: 3
12749036 TATCGTTTAA
12749046 ATT ATT ATT ATT ATT ATT ATT ATT ATT ACTT ATAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT AT-T ATT
12749084 GGTACATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 27 0.82
4 6 0.18
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:12749222 original size:2 final size:2
Alignment explanation
Indices: 12749215--12749243 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12749205 TTAAATGTTC
12749215 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12749244 CTATCTGTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12749983 original size:2 final size:2
Alignment explanation
Indices: 12749976--12750003 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12749966 ATATTATAGC
12749976 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12750004 TCCTTGCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12750483 original size:131 final size:131
Alignment explanation
Indices: 12750306--12750655 Score: 373
Period size: 131 Copynumber: 2.7 Consensus size: 131
12750296 ATATTCAATA
* * ** * * * *
12750306 TTTGACAATTCGTGGAATCGTGCCCTAACGTATTGGGTTACAATTTCTCGTTTGCTCAAAGTAAT
1 TTTGACAATTCG-GGAATCATGCCCTATCGTGCTGGGTTGCAATTTCTCATTTGTTCAAAATAAT
* * * * * *** *
12750371 CGAAAGTCCCTTCAAAATTTCACCCATGTCTTCCAAAAATCCTTTAAAACGAACGCAATACTCGG
65 CGAAAGTCTCTTCGAAATTTCACCCACGTCTTCCAAAAACCCTTTAAAACAAAAAAAATACTCGA
12750436 TG
130 TG
** *
12750438 TTTGACAATTCGGGAATCATGCCCTATCGTGCTGGGTTGTGATTTCTCATTTGTTCAAAACAATC
1 TTTGACAATTCGGGAATCATGCCCTATCGTGCTGGGTTGCAATTTCTCATTTGTTCAAAATAATC
* * * * *
12750503 G--AGTATTCTTCGGAATTTCACTCACGTTTTCTAAAAACCCTTTAAAACAAAAAAAATACTCGA
66 GAAAGT-CTCTTCGAAATTTCACCCACGTCTTCCAAAAACCCTTTAAAACAAAAAAAATACTCGA
12750566 TG
130 TG
* * *
12750568 TTTGGCGATTCGGGGAAT-AGTGCCCTATCGTGCTGGGTTGCAATTTCCCATTTGTTCAAAATAA
1 TTTGACAATTC-GGGAATCA-TGCCCTATCGTGCTGGGTTGCAATTTCTCATTTGTTCAAAATAA
* *
12750632 TCGAATGTCTCTTCGTAATTTCAC
64 TCGAAAGTCTCTTCGAAATTTCAC
12750656 TCGTATTTTT
Statistics
Matches: 179, Mismatches: 34, Indels: 10
0.80 0.15 0.04
Matches are distributed among these distances:
129 3 0.02
130 56 0.31
131 92 0.51
132 26 0.15
133 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.33
Consensus pattern (131 bp):
TTTGACAATTCGGGAATCATGCCCTATCGTGCTGGGTTGCAATTTCTCATTTGTTCAAAATAATC
GAAAGTCTCTTCGAAATTTCACCCACGTCTTCCAAAAACCCTTTAAAACAAAAAAAATACTCGAT
G
Found at i:12753300 original size:31 final size:31
Alignment explanation
Indices: 12753265--12753326 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
12753255 ATGATCAATT
12753265 TTGCAGAAGGTCGAGAGAATATCAAGCATTG
1 TTGCAGAAGGTCGAGAGAATATCAAGCATTG
*
12753296 TTGCAGAAGGTCGAGGGAATATCAAGCATTG
1 TTGCAGAAGGTCGAGAGAATATCAAGCATTG
12753327 CCAGTATTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.34, C:0.13, G:0.31, T:0.23
Consensus pattern (31 bp):
TTGCAGAAGGTCGAGAGAATATCAAGCATTG
Found at i:12753811 original size:30 final size:32
Alignment explanation
Indices: 12753770--12753834 Score: 89
Period size: 30 Copynumber: 2.1 Consensus size: 32
12753760 ATGTCTAGCC
*
12753770 AAGTAAATTAATTG-ATTTTTTA-ATTAAATA
1 AAGTAAATTAATTGAATTTTATATATTAAATA
* *
12753800 AAGTTAATTAATTGAATTTTATATATTAATTA
1 AAGTAAATTAATTGAATTTTATATATTAAATA
12753832 AAG
1 AAG
12753835 GAAAATATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 13 0.43
31 7 0.23
32 10 0.33
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (32 bp):
AAGTAAATTAATTGAATTTTATATATTAAATA
Found at i:12756076 original size:22 final size:21
Alignment explanation
Indices: 12756034--12756079 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
12756024 TTTAAAGATA
12756034 TTTTATTTTAAATTTAGTCCTT
1 TTTTATTTTAAATTTA-TCCTT
12756056 TTTTATATTTAAATTGT-TCCTT
1 TTTTAT-TTTAAATT-TATCCTT
12756078 TT
1 TT
12756080 ATTTCTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 13 0.59
23 8 0.36
24 1 0.05
ACGTcount: A:0.22, C:0.09, G:0.04, T:0.65
Consensus pattern (21 bp):
TTTTATTTTAAATTTATCCTT
Found at i:12756142 original size:26 final size:25
Alignment explanation
Indices: 12756075--12756142 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 25
12756065 TAAATTGTTC
12756075 CTTTTATTT-CTTATTTTTCTTGTTTT
1 CTTTT-TTTCCTT-TTTTTCTTGTTTT
*
12756101 CTTCTTTTGCCATTTTTTT-TTGTTTT
1 CTT-TTTTTCC-TTTTTTTCTTGTTTT
12756127 CTTTTGTTTCCTTTTT
1 CTTTT-TTTCCTTTTT
12756143 GTGTTTTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
25 7 0.19
26 19 0.53
27 8 0.22
28 2 0.06
ACGTcount: A:0.04, C:0.15, G:0.06, T:0.75
Consensus pattern (25 bp):
CTTTTTTTCCTTTTTTTCTTGTTTT
Found at i:12756980 original size:20 final size:20
Alignment explanation
Indices: 12756955--12756996 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
12756945 GCCAAAGTCA
12756955 ATATTTTAATGAAATAAAAT
1 ATATTTTAATGAAATAAAAT
12756975 ATATTTTAATGAAATAAAAT
1 ATATTTTAATGAAATAAAAT
12756995 AT
1 AT
12756997 TTTATTATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (20 bp):
ATATTTTAATGAAATAAAAT
Found at i:12756998 original size:18 final size:19
Alignment explanation
Indices: 12756954--12757000 Score: 78
Period size: 20 Copynumber: 2.5 Consensus size: 19
12756944 TGCCAAAGTC
12756954 AATATTTTAATGAAATAAA
1 AATATTTTAATGAAATAAA
12756973 ATATATTTTAATGAAAT-AA
1 A-ATATTTTAATGAAATAAA
12756992 AATATTTTA
1 AATATTTTA
12757001 TTATGTGATC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.30
19 4 0.15
20 15 0.56
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (19 bp):
AATATTTTAATGAAATAAA
Found at i:12758077 original size:21 final size:21
Alignment explanation
Indices: 12758053--12758092 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12758043 CCACTAACTA
* *
12758053 CATCTCGTAATGAGCCAATGT
1 CATCTCGCAATGACCCAATGT
12758074 CATCTCGCAATGACCCAAT
1 CATCTCGCAATGACCCAAT
12758093 TGCGCTGAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.25
Consensus pattern (21 bp):
CATCTCGCAATGACCCAATGT
Found at i:12765065 original size:2 final size:2
Alignment explanation
Indices: 12765058--12765100 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
12765048 AATGCTAAAG
* *
12765058 TA TA TA TA CA TA -A TA -A TA TA TA TA TA TA TA TA TA TA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12765098 TA T
1 TA T
12765101 TAAAAAATGT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:12765074 original size:24 final size:25
Alignment explanation
Indices: 12765011--12765075 Score: 66
Period size: 24 Copynumber: 2.7 Consensus size: 25
12765001 AATATTTGAA
12765011 ATATATACATAA-AATAGTAAGAAT
1 ATATATACATAATAATAGTAAGAAT
* *
12765035 ATATATA-ATTAGTAAT-GCTAA-AGT
1 ATATATACA-TAATAATAG-TAAGAAT
12765059 ATATATACATAATAATA
1 ATATATACATAATAATA
12765076 TATATATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
23 1 0.03
24 25 0.76
25 7 0.21
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.34
Consensus pattern (25 bp):
ATATATACATAATAATAGTAAGAAT
Found at i:12765279 original size:14 final size:15
Alignment explanation
Indices: 12765239--12765279 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
12765229 AATAATATGG
12765239 TATTAAGAGTATACA
1 TATTAAGAGTATACA
* *
12765254 TATAAATA-TATA-A
1 TATTAAGAGTATACA
12765267 TATTAAGAGTATA
1 TATTAAGAGTATA
12765280 TATACATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
13 7 0.33
14 8 0.38
15 6 0.29
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.37
Consensus pattern (15 bp):
TATTAAGAGTATACA
Found at i:12765752 original size:3 final size:3
Alignment explanation
Indices: 12765744--12765852 Score: 78
Period size: 3 Copynumber: 35.3 Consensus size: 3
12765734 AATATTTATA
* * *
12765744 AAT AAT AAT AGT AA- ATAT AAT AAT AAT AAT AAT ATT AAT ATT AAT
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * *
12765789 TAT AGT -AT AAAT AAT ATGT ACAT AAC AGT AAT AAT AAT AAGT AAC AAT
1 AAT AAT AAT -AAT AAT A-AT A-AT AAT AAT AAT AAT AAT AA-T AAT AAT
12765837 AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT A
12765853 TAGAAATTCA
Statistics
Matches: 81, Mismatches: 19, Indels: 12
0.72 0.17 0.11
Matches are distributed among these distances:
2 2 0.02
3 69 0.85
4 10 0.12
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:12766623 original size:2 final size:2
Alignment explanation
Indices: 12766616--12766656 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
12766606 TTATTTTGTA
12766616 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12766657 CAGACTTGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12767637 original size:21 final size:21
Alignment explanation
Indices: 12767611--12767665 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
12767601 TCTGATATCC
* *
12767611 TCGATTAGTTCTACTGCAACT
1 TCGATTAGCTCCACTGCAACT
*
12767632 TCGATTAGCTCCACTGTAACT
1 TCGATTAGCTCCACTGCAACT
12767653 TCGATTAGCTCCA
1 TCGATTAGCTCCA
12767666 ATCTTTATTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.24, C:0.27, G:0.15, T:0.35
Consensus pattern (21 bp):
TCGATTAGCTCCACTGCAACT
Found at i:12767983 original size:87 final size:88
Alignment explanation
Indices: 12767749--12768281 Score: 602
Period size: 89 Copynumber: 6.0 Consensus size: 88
12767739 AATAGACATT
* * * **
12767749 AAAAACAGAAATTGAAAATAGCTTAGCACGTGAGCC-AAGGCTCAACTCATTTCTCGCAATATGA
1 AAAAACAGAAATTGAAAATACCTCAG--CGTGA-CCTGAGGCTCAACTCACCTCTCGCAATATGA
* * *
12767813 GTTGGTTCTTTG--AAACTTAATTTG-
63 GTTGATT-TTTGAAAAACATAAATTGA
* ** *
12767837 AAAAGCAGATTTTGAAAATACCTC-GACATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGA
1 AAAAACAGAAATTGAAAATACCTCAG-C--GTGACCTGAGGCTCAACTCACCTCTCGCAATATGA
* *
12767901 ATTGA-TTTTGAAAAATATAAATTGA
63 GTTGATTTTTGAAAAACATAAATTGA
* *
12767926 AAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGACTCAACTCACCTCTCGCAATATGAGTT
1 AAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
* *
12767991 GATTTTTGAAAAGCATAACTTG-
66 GATTTTTGAAAAACATAAATTGA
* * *
12768013 AAAAACGGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGTT
1 AAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
* * *
12768078 GATTTTTTTGAAAAGCAGAATTTG-
66 GA--TTTTTGAAAAACATAAATTGA
* * *
12768102 AAAAGCAGAAATTGAAAATACCTCAGCGTGACCTGCGGCTCAACTCACCTCTCGCAATATGAATT
1 AAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
* *
12768167 GATTTTTGAAAAATATAAATTAAA
66 GATTTTTGAAAAACATAAATT-GA
*
12768191 AAAAATAGAAATTGAAAATACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTCGCAATATGA
1 AAAAACAGAAATTGAAAATACCTCAGC--GTGA-CCTGAGGCTCAACTCACCTCTCGCAATATGA
12768255 GTTGATTTTTG--AAACATAAATTGA
63 GTTGATTTTTGAAAAACATAAATTGA
12768279 AAA
1 AAA
12768282 TACCTCAACG
Statistics
Matches: 384, Mismatches: 46, Indels: 30
0.83 0.10 0.07
Matches are distributed among these distances:
86 6 0.02
87 118 0.31
88 80 0.21
89 136 0.35
90 1 0.00
91 41 0.11
92 2 0.01
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.27
Consensus pattern (88 bp):
AAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
GATTTTTGAAAAACATAAATTGA
Found at i:12768103 original size:14 final size:14
Alignment explanation
Indices: 12768084--12768119 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
12768074 AGTTGATTTT
12768084 TTTGAAAAGCAGAA
1 TTTGAAAAGCAGAA
12768098 TTTGAAAAGCAGAA
1 TTTGAAAAGCAGAA
*
12768112 ATTGAAAA
1 TTTGAAAA
12768120 TACCTCAGCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.53, C:0.06, G:0.19, T:0.22
Consensus pattern (14 bp):
TTTGAAAAGCAGAA
Found at i:12768128 original size:176 final size:169
Alignment explanation
Indices: 12767750--12768368 Score: 633
Period size: 176 Copynumber: 3.6 Consensus size: 169
12767740 ATAGACATTA
* * * **
12767750 AAAACAGAAATTGAAAATAGCTTAGCACGTGAGCC-AAGGCTCAACTCATTTCTCGCAATATGAG
1 AAAACAGAAATTGAAAATACCTCAG--CGTGA-CCTGAGGCTCAACTCACCTCTCGCAATATGAG
* * * **
12767814 TTGGTTCTTTG-AAACTTAATTTGAAAAGCAGATTTTGAAAATACCTC-GACATGTGACCCGAGG
63 TTGATT-TTTGAAAACATAATTTGAAAAACAGAAATTGAAAATACCTCAG-CA-GTGA-CCGAGG
* *
12767877 CTCAACTCACCTCTCGCAATATGAATTGA-TTTTGAAAAATATAAATTG
124 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTG--AAA-ACAAATTG
* *
12767925 AAAAAACAGAAATTGAAAATACCTCAGCGTGCCCTGAGACTCAACTCACCTCTCGCAATATGAGT
1 --AAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGT
* * *
12767990 TGATTTTTGAAAAGCATAACTTGAAAAACGGAAATTGAAAATACCTCAGC-GTGTCCTGAGGCTC
64 TGATTTTTGAAAA-CATAATTTGAAAAACAGAAATTGAAAATACCTCAGCAGTGACC-GAGGCTC
*
12768054 AACTCACCTCTTGCAATATGAGTTGATTTTTTTGAAAAGCAGAATTTG
127 AACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAA-CA-AA-TTG
* *
12768102 AAAAGCAGAAATTGAAAATACCTCAGCGTGACCTGCGGCTCAACTCACCTCTCGCAATATGAATT
1 AAAA-CAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
* ** *
12768167 GATTTTTGAAAAATATAAATTAAAAAAAATAGAAATTGAAAATACCTCAGCATGTGAGCCGAGGC
65 GATTTTTG-AAAACAT-AATT-TGAAAAACAGAAATTGAAAATACCTCAGCA-GTGA-CCGAGGC
12768232 TCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAC--A-T-
125 TCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAAATTG
* * *
12768272 -------AAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
1 AAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
*
12768330 ATTTCTGAAAACATAAATTTGAAAAACAGAAATTGAAAA
66 ATTTTTGAAAACAT-AATTTGAAAAACAGAAATTGAAAA
12768369 AAAACAGAAA
Statistics
Matches: 384, Mismatches: 40, Indels: 53
0.81 0.08 0.11
Matches are distributed among these distances:
160 17 0.04
161 11 0.03
162 59 0.15
171 1 0.00
173 3 0.01
174 41 0.11
175 45 0.12
176 97 0.25
177 42 0.11
178 31 0.08
180 35 0.09
181 2 0.01
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.27
Consensus pattern (169 bp):
AAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
ATTTTTGAAAACATAATTTGAAAAACAGAAATTGAAAATACCTCAGCAGTGACCGAGGCTCAACT
CACCTCTCGCAATATGAGTTGATTTTTGAAAACAAATTG
Found at i:12768196 original size:16 final size:17
Alignment explanation
Indices: 12768175--12768208 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
12768165 TTGATTTTTG
*
12768175 AAAAATATAAATT-AAA
1 AAAAATAGAAATTGAAA
12768191 AAAAATAGAAATTGAAA
1 AAAAATAGAAATTGAAA
12768208 A
1 A
12768209 TACCTCAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (17 bp):
AAAAATAGAAATTGAAA
Found at i:12768357 original size:15 final size:14
Alignment explanation
Indices: 12768337--12768384 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 14
12768327 TTGATTTCTG
*
12768337 AAAACATAAATTTGA
1 AAAACAGAAA-TTGA
12768352 AAAACAGAAATTGAAAA
1 AAAACAGAAATTG---A
12768369 AAAACAGAAATTGA
1 AAAACAGAAATTGA
12768383 AA
1 AA
12768385 TTACCTCAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 6 0.21
15 9 0.31
17 14 0.48
ACGTcount: A:0.67, C:0.06, G:0.10, T:0.17
Consensus pattern (14 bp):
AAAACAGAAATTGA
Found at i:12768373 original size:17 final size:17
Alignment explanation
Indices: 12768351--12768384 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
12768341 CATAAATTTG
12768351 AAAAACAGAAATTGAAA
1 AAAAACAGAAATTGAAA
12768368 AAAAACAGAAATTGAAA
1 AAAAACAGAAATTGAAA
12768385 TTACCTCAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.71, C:0.06, G:0.12, T:0.12
Consensus pattern (17 bp):
AAAAACAGAAATTGAAA
Found at i:12769304 original size:43 final size:44
Alignment explanation
Indices: 12769257--12769340 Score: 152
Period size: 43 Copynumber: 1.9 Consensus size: 44
12769247 TTTTGTGTTA
12769257 ATCAAGACGCCCTTTTCGGGTTTTCACCTTGAT-CCTTTTTATT
1 ATCAAGACGCCCTTTTCGGGTTTTCACCTTGATCCCTTTTTATT
*
12769300 ATCAAGACGCTCTTTTCGGGTTTTCACCTTGATCCCTTTTT
1 ATCAAGACGCCCTTTTCGGGTTTTCACCTTGATCCCTTTTT
12769341 TTTAGGCATA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
43 32 0.82
44 7 0.18
ACGTcount: A:0.15, C:0.26, G:0.14, T:0.44
Consensus pattern (44 bp):
ATCAAGACGCCCTTTTCGGGTTTTCACCTTGATCCCTTTTTATT
Found at i:12780968 original size:26 final size:26
Alignment explanation
Indices: 12780939--12780994 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
12780929 TGATAAAAAT
*
12780939 TGATAATGGGTTAGGTAAATGTTCTA
1 TGATAATGGGTTAGGTAAATGTTCCA
12780965 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
12780991 TGAT
1 TGAT
12780995 GGGCATTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.30, C:0.05, G:0.27, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:12782516 original size:26 final size:26
Alignment explanation
Indices: 12782482--12782536 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
12782472 TTTATAGTTT
*
12782482 TACCTCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
12782508 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
12782534 TAC
1 TAC
12782537 ATGTTTAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:12784256 original size:3 final size:3
Alignment explanation
Indices: 12784248--12784353 Score: 83
Period size: 3 Copynumber: 34.3 Consensus size: 3
12784238 AATATTTATA
*
12784248 AAT AAT AAT AGT AA- ATAT AAT AAT AAT AAT AAT AAT AAT AAGT -AT
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AA-T AAT
* * * * *
12784293 AGT -AT AAAT AAT ATGT ACAT AAC AGT AAT AAT AAT AAGT AAC AAT AAT
1 AAT AAT -AAT AAT A-AT A-AT AAT AAT AAT AAT AAT AA-T AAT AAT AAT
12784341 AAT AAT AAT AAT A
1 AAT AAT AAT AAT A
12784354 TAGAAATTCA
Statistics
Matches: 82, Mismatches: 13, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
2 3 0.04
3 68 0.83
4 11 0.13
ACGTcount: A:0.60, C:0.03, G:0.06, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:12784459 original size:24 final size:23
Alignment explanation
Indices: 12784415--12784461 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
12784405 TTTTAAAAAA
*
12784415 ATACTATGTAGATATAAATACAC
1 ATACTATGTAAATATAAATACAC
12784438 ATACGTATGTAAATA-AATATACAC
1 ATAC-TATGTAAATATAA-ATACAC
12784462 TAATATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.49, C:0.13, G:0.09, T:0.30
Consensus pattern (23 bp):
ATACTATGTAAATATAAATACAC
Found at i:12788595 original size:21 final size:21
Alignment explanation
Indices: 12788569--12788614 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
12788559 AACACCAACT
12788569 CACTAACACTCAGCTCACTAA
1 CACTAACACTCAGCTCACTAA
12788590 CACTAACACTCAGCTCACTAA
1 CACTAACACTCAGCTCACTAA
12788611 CACT
1 CACT
12788615 TATACACCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.37, C:0.39, G:0.04, T:0.20
Consensus pattern (21 bp):
CACTAACACTCAGCTCACTAA
Found at i:12790710 original size:16 final size:16
Alignment explanation
Indices: 12790689--12790720 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12790679 ACCAAAGAGA
*
12790689 AATTCATGCACGTAAG
1 AATTCATGCACATAAG
12790705 AATTCATGCACATAAG
1 AATTCATGCACATAAG
12790721 TCTTGCGGAT
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:0.19, G:0.16, T:0.25
Consensus pattern (16 bp):
AATTCATGCACATAAG
Found at i:12794999 original size:27 final size:27
Alignment explanation
Indices: 12794969--12795020 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
12794959 GTACCGATAC
12794969 CATGGAAAGGGTATTGATACTTGGGGT
1 CATGGAAAGGGTATTGATACTTGGGGT
12794996 CATGGAAAGGGTATTGATACTTGGG
1 CATGGAAAGGGTATTGATACTTGGG
12795021 TCAATGTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.27, C:0.08, G:0.37, T:0.29
Consensus pattern (27 bp):
CATGGAAAGGGTATTGATACTTGGGGT
Found at i:12796501 original size:25 final size:27
Alignment explanation
Indices: 12796464--12796516 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
12796454 TCAAACATGC
12796464 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
12796490 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
12796516 A
1 A
12796517 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:12798049 original size:26 final size:26
Alignment explanation
Indices: 12797991--12798150 Score: 243
Period size: 26 Copynumber: 6.2 Consensus size: 26
12797981 CATGAAATTC
* *
12797991 TTATCATGAAACATTTATCTAA-CCA
1 TTATCATGGAACATTTACCTAACCCA
* *
12798016 TTATCATGAAACATTTACATAACCCA
1 TTATCATGGAACATTTACCTAACCCA
*
12798042 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCCA
12798068 TTATCAT-GAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCCA
*
12798093 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCCA
*
12798119 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCCA
12798145 TTATCA
1 TTATCA
12798151 ATTTGTATCA
Statistics
Matches: 126, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
25 44 0.35
26 82 0.65
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.34
Consensus pattern (26 bp):
TTATCATGGAACATTTACCTAACCCA
Found at i:12798080 original size:51 final size:51
Alignment explanation
Indices: 12797991--12798150 Score: 259
Period size: 51 Copynumber: 3.1 Consensus size: 51
12797981 CATGAAATTC
* * *
12797991 TTATCATGAAACATTTATCTAACC-ATTATCATGAAACATTTACATAACCCA
1 TTATCATGGAACATTTACCTAACCTATTATCATG-AACATTTACCTAACCCA
12798042 TTATCATGGAACATTTACCTAACCTATTATCATGAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCTATTATCATGAACATTTACCTAACCCA
*
12798093 TTATCATGGAACATTTACCTAACCTATTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTATTATCAT-GAACATTTACCTAACCCA
12798145 TTATCA
1 TTATCA
12798151 ATTTGTATCA
Statistics
Matches: 103, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
51 71 0.69
52 32 0.31
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.34
Consensus pattern (51 bp):
TTATCATGGAACATTTACCTAACCTATTATCATGAACATTTACCTAACCCA
Found at i:12798122 original size:77 final size:77
Alignment explanation
Indices: 12797991--12798150 Score: 268
Period size: 77 Copynumber: 2.1 Consensus size: 77
12797981 CATGAAATTC
*
12797991 TTATCATGAAACATTTATCTAACCATTATCATGAAACATTTACATAACCCATTATCATGGAACAT
1 TTATCATGAAACATTTACCTAACCATTATCATGAAACATTTACATAACCCATTATCATGGAACAT
12798056 TTACCTAACCTA
66 TTACCTAACCTA
* * *
12798068 TTATCATG-AACATTTACCTAACCCATTATCATGGAACATTTACCTAACCTATTATCATGGAACA
1 TTATCATGAAACATTTACCTAA-CCATTATCATGAAACATTTACATAACCCATTATCATGGAACA
12798132 TTTACCTAACCTA
65 TTTACCTAACCTA
12798145 TTATCA
1 TTATCA
12798151 ATTTGTATCA
Statistics
Matches: 78, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
76 12 0.15
77 66 0.85
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.34
Consensus pattern (77 bp):
TTATCATGAAACATTTACCTAACCATTATCATGAAACATTTACATAACCCATTATCATGGAACAT
TTACCTAACCTA
Found at i:12799419 original size:32 final size:32
Alignment explanation
Indices: 12799383--12799447 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
12799373 CTAAAAAGTT
* *
12799383 AATATTGTTATCTTCAGGTGCCAAAATGTATA
1 AATATTGTTATCTTCAGATACCAAAATGTATA
* *
12799415 AATATTGTTATCTTTAGATATCAAAATGTATA
1 AATATTGTTATCTTCAGATACCAAAATGTATA
12799447 A
1 A
12799448 CTTTGTCAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.40
Consensus pattern (32 bp):
AATATTGTTATCTTCAGATACCAAAATGTATA
Found at i:12800847 original size:58 final size:58
Alignment explanation
Indices: 12800769--12800889 Score: 206
Period size: 58 Copynumber: 2.1 Consensus size: 58
12800759 GATATTTCAA
*
12800769 AATAATAAATTATTTCACGAGTCAGTTTGGACCCGTATTGCGTTGATTTTTATTTCTT
1 AATAATAAATTATTTCACGAGTCAGTTTGGACCCGTATTGCATTGATTTTTATTTCTT
* **
12800827 AATAATAAATTATTTCACGAGTCAGTTTGGACCTGTATTTTATTGATTTTTATTTCTT
1 AATAATAAATTATTTCACGAGTCAGTTTGGACCCGTATTGCATTGATTTTTATTTCTT
12800885 AATAA
1 AATAA
12800890 GTCTTCACTT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.46
Consensus pattern (58 bp):
AATAATAAATTATTTCACGAGTCAGTTTGGACCCGTATTGCATTGATTTTTATTTCTT
Found at i:12805372 original size:13 final size:15
Alignment explanation
Indices: 12805350--12805386 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
12805340 TTTAATCTCC
*
12805350 TTTTAAATTTTA-AT
1 TTTTATATTTTATAT
12805364 TTTT-TATTTTATAT
1 TTTTATATTTTATAT
12805378 TTTTATATT
1 TTTTATATT
12805387 ATTCTTAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 6 0.30
14 10 0.50
15 4 0.20
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTATATTTTATAT
Found at i:12820207 original size:3 final size:3
Alignment explanation
Indices: 12820169--12820293 Score: 51
Period size: 3 Copynumber: 41.7 Consensus size: 3
12820159 TAATACTAAG
* * * * * *
12820169 ATA ATG ATA ATA GTA ATA AAA ATA AAA ATG ATA ATA AT- ATA GTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * ** *
12820216 GTAA ATA A-A AGTA ATA GTA ATA GTA ATA ATG ACG GTA ATA ATAA ATA
1 AT-A ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA
* *
12820263 TTA ATA ATA ACA ATA ATA CA-A ATA A-A ATA AT
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA AT
12820294 CTAAAGTTTA
Statistics
Matches: 86, Mismatches: 28, Indels: 16
0.66 0.22 0.12
Matches are distributed among these distances:
2 7 0.08
3 71 0.83
4 8 0.09
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:12820222 original size:30 final size:30
Alignment explanation
Indices: 12820168--12820244 Score: 90
Period size: 29 Copynumber: 2.7 Consensus size: 30
12820158 TTAATACTAA
*
12820168 GATAATGATAATAGTAATAAAAATAAAAAT
1 GATAATAATAATAGTAATAAAAATAAAAAT
*
12820198 GATAATAAT-ATAGTAATAGTAAAT-AAAA-
1 GATAATAATAATAGTAATA-AAAATAAAAAT
*
12820226 G-TAATAGTAATAGTAATAA
1 GATAATAATAATAGTAATAA
12820245 TGACGGTAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
27 6 0.15
28 10 0.24
29 13 0.32
30 12 0.29
ACGTcount: A:0.60, C:0.00, G:0.12, T:0.29
Consensus pattern (30 bp):
GATAATAATAATAGTAATAAAAATAAAAAT
Found at i:12820462 original size:3 final size:3
Alignment explanation
Indices: 12820456--12820745 Score: 71
Period size: 3 Copynumber: 98.3 Consensus size: 3
12820446 AAATAAAATG
* * * *
12820456 TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA CAA AAA TAG TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * ** * * * ** *
12820504 T-G TAT TAAA TGG TAA -AA GAA TAA TAG TAA CAA TAA TTT TAA AAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * * *
12820548 AAA TGA TAA TAG TAA TAA -AA TAA -GA TTA TAT TAA TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * *
12820594 AAA TGAA -CA TAA -AA TAA -GA TAG TAA TAA TAG TAA TAA TAA TAG
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * * ***
12820637 T-A TAG TAA -AA GGAA TAA TAA TAG CAA TAA TAA GAG CGT TAA TAA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * *
12820681 TAG TAA TAA TAC GAA TAA TAA T-A TATA TGTA TGAA AAA TAA TAA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A T-AA T-AA TAA TAA TAA TAA
12820728 TAA -AA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA T
12820746 GGTATTAGAA
Statistics
Matches: 196, Mismatches: 75, Indels: 32
0.65 0.25 0.11
Matches are distributed among these distances:
2 17 0.09
3 167 0.85
4 12 0.06
ACGTcount: A:0.59, C:0.02, G:0.09, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:12823225 original size:20 final size:20
Alignment explanation
Indices: 12823182--12823227 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
12823172 AATACTAGGT
*
12823182 AAGGTATCGATACTTTTTTA
1 AAGGTATCGATACTTTTATA
*
12823202 AAGGTATCGATA-TTTTCATG
1 AAGGTATCGATACTTTT-ATA
12823222 AAGGTA
1 AAGGTA
12823228 CTGAATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.39
Consensus pattern (20 bp):
AAGGTATCGATACTTTTATA
Done.